Amoeboid - Thierry Karsenti

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Amoeboid 

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Amoeboid 

Scientific classification 

Classes and subclasses 

Class Lobose pseudopods 

Amoebozoa 

Percolozoa 

Class Filose pseudopods 

Cercozoa 

Vampyrellids 

Nucleariids 

Class Reticulose pseudopods 

Foraminifera 

Gymnophryids 

Class Actinopods 

Radiolaria 

Heliozoa 

Foraminiferan (Ammonia tepida)

Heliozoan (Actinophrys sol) 

Amoeboids are unicellular lifeforms that mainly consist of contractile vacuoles, a 

nucleus, and cytoplasm as their basic structure. They move and feed by means of 

temporary cytoplasmic projections, called pseudopods (false feet). They have 

appeared in a number of different groups. Some cells in multicellular animals may be 

amoeboid, for instance human white blood cells, which consume pathogens. Many 

protists also exist as individual amoeboid cells, or take such a form at some point in 

their life-cycle. The most famous such organism is Amoeba proteus; the name amoeba 

is variously used to describe its close relatives, other organisms similar to it, or the 

amoeboids in general. 

[edit] Morphological categories 

Amoeboids may be divided into several morphological categories based on the form 

and structure of the pseudopods. Those where the pseudopods are supported by 

regular arrays of microtubules are called actinopods, and forms where they are not are 

called rhizopods, further divided into lobose, filose, and reticulose amoebae. There is 

also a strange group of giant marine amoeboids, the xenophyophores, that do not fall 

into any of these categories. 

• Lobose pseudopods are blunt, and there may be one or several on a cell, 

which is usually divided into a layer of clear ectoplasm surrounding more 

granular endoplasm. Most, including Amoeba itself, move by the body mass 

flowing into an anterior pseudopod. The vast majority form a monophyletic 

group called the Amoebozoa, which also includes most slime moulds. A 

second group, the Percolozoa, includes protists that can transform between 

amoeboid and flagellate forms. 

• Filose pseudopods are narrow and tapering. The vast majority of filose 

amoebae, including all those that produce shells, are placed within the 

Cercozoa together with various flagellates that tend to have amoeboid forms. 

The naked filose amoebae comprise two other groups, the vampyrellids and 

nucleariids. The latter appear to be close relatives of animals and fungi. 

• Reticulose pseudopods are cytoplasmic strands that branch and merge to 

form a net. They are found most notably among the Foraminifera, a large

group of marine protists that generally produce multi-chambered shells. There 

are only a few sorts of naked reticulose amoeboids, notably the gymnophryids, 

and their relationships are not certain. 

• Actinopods are divided into the radiolaria and heliozoa. The radiolaria are 

mostly marine protists with complex internal skeletons, including central 

capsules that divide the cells into granular endoplasm and frothy ectoplasm 

that keeps them buoyant. The heliozoa include both freshwater and marine 

forms that use their axopods to capture small prey, and only have simple 

scales or spines for skeletal elements. Both groups appear to be polyphyletic. 

. However, amoeboids have appeared separately in many other groups, including 

various different lines of algae not listed above. 

Δů==Subphylum Sarcodina== Sarcodina is a subphylum of the phylum 

Sarcomastigophora, of unicellular life forms that move by cytoplasmic flow. Some 

species use cytoplasmic extensions called pseudopodia for locomotion or feeding. The 

subphylum includes such protozoa as the common amoeba and the Foraminifera and 

Radiolaria. Most members of the subphylum reproduce asexually through fission, 

although some reproduce sexually. Sarcodina is sometimes subdůivided into two 

classes - Rhizopoda and Actinopoda.ÒΜκŁΔβΑhi mom. 

[edit] External links 

• The Amoebae website brings together information from published sources. 

• Amoebas are more than just blobs 

• sun animacules and amoebas 

• Molecular Expressions Digital Video Gallery: Pond Life - Amoeba (Protozoa) 

Some good, informative Amoeba videos. 

• Joseph Leidy's Amoeba Plates 

Retrieved from "http://en.wikipedia.org/wiki/Amoeboid" 

Categories: Protista | Cell biology | Amoeboids | Motile cells 

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http://en.wikipedia.org/wiki/Sporozoans 

Apicomplexa 


(Redirected from Sporozoans) 


Apicomplexa 


Domain: Eukaryota 

Kingdom: Chromalveolata 

Superphylum: Alveolata 

Phylum: Apicomplexa 

Aconoidasida 

Classes & Subclasses 

• Haemosporasina 

• Piroplasmasina 

Blastocystea

Conoidasida 

• Coccidiasina 

• Gregarinasina 

The Apicomplexa are a large group of protists, characterized by the presence of a 

unique organelle called an apical complex (see also apicoplast). They are unicellular, 

spore-forming, and exclusively parasites of animals. Motile structures such as flagella 

or pseudopods are absent except in certain gamete stages. This is a diverse group 

including organisms such as coccidia, gregarines, piroplasms, haemogregarines, and 

malarias; some diseases caused by apicomplexan organisms include: 

• Babesiosis (Babesia) 

• Malaria (Plasmodium) 

• Cryptosporidiosis (Cryptosporidium) 

• Coccidian diseases including: 

o Cryptosporidiosis (Cryptosporidium parvum) 

o Cyclosporiasis (Cyclospora cayetanensis) 

o Toxoplasmosis (Toxoplasma gondii) 

Most members have a complex life-cycle, involving both asexual and sexual 

reproduction. Typically, a host is infected by ingesting cysts, which divide to produce 

sporozoites that enter its cells. Eventually, the cells burst, releasing merozoites which 

infect new cells. This may occur several times, until gamonts are produced, forming 

gametes that fuse to create new cysts. There are many variations on this basic pattern, 

however, and many Apicomplexa have more than one host. 

Generic life cycle of an apicomplexa: 1-zygote (cyst), 2-sporozoites, 3-merozoites, 4gametocytes.

Apicomplexan structure: 1-polar ring, 2-conoid, 3-micronemes, 4-rhoptries, 5nucleus, 

6-nucleolus, 7-mitochondria, 8-posterior ring, 9-alveoli, 10-golgi apparatus, 

11-micropore. 

The apical complex includes vesicles called rhoptries and micronemes, which open at 

the anterior of the cell. These secrete enzymes that allow the parasite to enter other 

cells. The tip is surrounded by a band of microtubules, called the polar ring, and 

among the Conoidasida there is also a funnel of rods called the conoid.. [1] Over the 

rest of the cell, except for a diminished mouth called the micropore, the membrane is 

supported by vesicles called alveoli, forming a semi-rigid pellicle. 

The presence of alveoli and other traits place the Apicomplexa among a group called 

the alveolates. Several related flagellates, such as Perkinsus and Colpodella have 

structures similar to the polar ring and were formerly included here, but most appear 

to be closer relatives of the dinoflagellates. They are probably similar to the common 

ancestor of the two groups. 

Another similarity is that apicomplexan cells contain a single plastid, called the 

apicoplast, surrounded by either 3 or four membranes. Its functions are thought to 

include tasks such as lipid synthesis, it appears to be necessary for survival. They are 

generally considered to share a common origin with the chloroplasts of 

dinoflagellates, although some studies suggest they are ultimately derived from green 

rather than red algae. 

The Apicomplexa comprise the bulk of what used to be called the Sporozoa, a group 

for parasitic protozoans without flagella, pseudopods, or cilia. Most of the 

Apicomplexa are motile however. The other main lines were the Ascetosporea, the 

Myxozoa (now known to be derived from animals), and the Microsporidia (now 

known to be derived from fungi). Sometimes the name Sporozoa is taken as a 

synonym for the Apicomplexa, or occasionally as a subset. 

Contents 

[hide] 

• 1 Blood borne genera 

• 2 Disease Genomics 

• 3 References 

• 4 External links 

[edit] Blood borne genera 

Within the Apicomplexa there are three groups of blood borne parasites. These 

species lie within in three suborders. 

• suborder Adeleorina - 8 genera 

• suborder Haemosporina - all genera in this suborder

• suborder Eimeriorina - 2 genera (Lankesterella and Schellackia) 

Blood parasites belonging to the suborder Adeleorina are collectively known as 

haemogregarines. Currently their sister group is thought to be the piroplasms. 

Suborder Adeleorina has ~400 species and has been organised into four large and 4 

small genera. 

The larger genera are: 

genera: 

• family Haemogregarinidae - taxon created by Neveu-Lemaire in 1901 

• Haemogregarina - taxon created by Danilewsky in 1885 

• Cyrilia - taxon created by Lainson in 1981 

genera: 

genera: 

• family Karyolysidae - taxon created by Wenyon in 1926 

• Karyolysus - taxon created by Labbe in 1894 

• family Hepatozoidae - taxon created by Wenyon in 1926 

• Hepatozoon - taxon created by Miller in 1908 

The smaller genera are : 

• Hemolivia - taxon created by Petit et al in 1990 

• Desseria - taxon created by Siddall in 1995 

genera: 

• family Dactylosomatidae 

• Dactylosoma 

• Babesiosoma

Notes: 

Species of the genus Desseria infect fish and lack erythrocytic merogony. 

The species of the genera Dactylosoma and Babesiosoma infect fish and reptiles. 

Leeches are the only known vectors for these species and their vertebrate hosts are 

aquatic. 

[edit] Disease Genomics 

As noted above, many of the apicomplexan parasites are important pathogens of 

human and domestic animals. In contrast to bacterial pathogens, these apicomplexan 

parasites are eukaryotes and share many metabolic pathways with their animal hosts. 

This fact makes therapeutic target development extremely difficult – a drug that 

harms an apicomplexan parasite is also likely to harm its human host. Currently there 

are no effective vaccines or treatments available for most diseases caused by these 

parasites. Biomedical research on these parasites is challenging because it is often 

difficult, if not impossible, to maintain live parasite cultures in the laboratory and to 

genetically manipulate these organisms. In the recent years, several of the 

apicomplexan species have been selected for genome sequencing. The availability of 

genome sequences provides a new opportunity for scientists to learn more about the 

evolution and biochemical capacity of these parasite. A NIH-funded database, 

ApiDB.org, provides public access to currently available genomic data sets. 

[edit] References 

1. ^ Duszynski1, Donald W.; Steve J. Upton and Lee Couch (2004-02-21). The 

Coccidia of the World (Online database). Department of Biology, University of New 

Mexico, and Division of Biology, Kansas State University. 


• The Taxonomicon & Systema Naturae (Website database). Taxon: Genus 

Cryptosporidium. Universal Taxonomic Services, Amsterdam, The 

Netherlands (2000). 

Retrieved from "http://en.wikipedia.org/wiki/Apicomplexa" 

Categories: Parasitic protists | Apicomplexa 

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http://en.wikipedia.org/wiki/Bacterial_growth 

Bacterial growth 



Growth is shown as L = log(numbers) where numbers is the number of colony 

forming units per ml, versus T (time.) 

Bacterial growth is the division of one bacterium into two idential daughter cells 

during a process called binary fission. Hence, local doubling of the bacterial 

population occurs. Both daughter cells from the division do not necessarily survive. 

However, if the number surviving exceeds unity on average, the bacterial population 

undergoes exponential growth. The measurement of an exponential bacterial growth 

curve in batch culture was traditionally a part of the training of all microbiologists; the 

basic means requires bacterial enumeration (cell counting) by direct and individual 

(microscopic, flow cytometry [1] ), direct and bulk (biomass), indirect and individual 

(colony counting), or indirect and bulk (most probable number, turbidity, nutrient 

uptake) methods. Models reconcile theory with the measurements [2] . 

In autecological studies, bacterial growth in batch culture can be modeled with four 

different phases: lag phase (A), exponential or log phase (B), stationary phase (C), 

and death phase (D). 

1. During lag phase, bacteria adapt themselves to growth conditions. It is the 

period where the individual bacteria are maturing and not yet able to divide. 

During the lag phase of the bacterial growth cycle, synthesis of RNA, enzymes 

and other molecules occurs.

2. During the exponential phase (sometimes called the log phase), the number of 

new bacteria appearing per unit time is proportional to the present population. 

This gives rise to the classic exponential growth curve, in which the logarithm 

of the population density rises linearly with time (see figure). The actual rate 

of this growth (i.e. the slope of the line in the figure) depends upon the growth 

conditions, which affect the frequency of cell division events and the 

probability of both daughter cells surviving. Exponential growth cannot 

continue indefinitely, however, because the medium is soon depleted of 

nutrients and enriched with wastes. 

3. During stationary phase, the growth rate slows as a result of nutrient depletion 

and accumulation of toxic products. This phase is reached as the bacteria 

begin to exhaust the resources that are available to them. 

4. At death phase, bacteria run out of nutrients and die. 

This basic batch culture growth model draws out and emphasizes aspects of bacterial 

growth which may differ from the growth of macrofauna. It emphasizes clonality, 

asexual binary division, the short development time relative to replication itself, the 

seemingly low death rate, the need to move from a dormant state to a reproductive 

state or to condition the media, and finally, the tendency of lab adapted strains to 

exhaust their nutrients. 

In reality, even in batch culture, the four phases are not well defined. The cells do not 

reproduce in synchrony without explicit and continual prompting (as in experiments 

with stalked bacteria [3] ) and their logarithmic phase growth is often not ever a 

constant rate, but instead a slowly decaying rate, a constant stochastic response to 

pressures both to reproduce and to go dormant in the face of declining nutrient 

concentrations and increasing waste concentrations. 

Batch culture is the most common laboratory growth environment in which bacterial 

growth is studied, but it is only one of many. It is ideally spatially unstructured and 

temporally structured. The bacterial culture is incubated in a closed vessel with a 

single batch of medium. In some experimental regimes, some of the bacterial culture 

is periodically removed to a fresh sterile media is added. In the extreme case, this 

leads to the continual renewal of the nutrients. This is a chemostat also known as 

continuous culture. It is ideally spatially unstructured and temporally unstructured, in 

an equilibrium state defined by the nutrient supply rate and the reaction of the 

bacteria. In comparison to batch culture, bacteria are maintained in expodential 

growth phase and the grow growth rate of the bacteria is known. Related devices 

include turbidostats and auxostats. 

Bacterial growth can be suppressed with bacteriostats, without necessarily 

killing the bacteria. In a synecological, a true-to-nature situation, where more than 

one bacterial species is present, the growth of microbes is more dynamic and 

continual. 

Liquid is not the only laboratory environment for bacterial growth. Spatially 

structured environments such as biofilms or agar surfaces present additional complex 

growth models.


1. ^ Skarstad K, Steen HB, Boye E (1983). "Cell cycle parameters of slowly growing 

Escherichia coli B/r studied by flow cytometry". J. Bacteriol. 154 (2): 656–62. PMID 

6341358. 

2. ^ Zwietering M H, Jongenburger I, Rombouts F M, van 'T Riet K (1990). "Modeling 

of the Bacterial Growth Curve". Applied and Environmental Microbiology 56 (6): 

1875-1881. 

3. ^ Novick A (1955). "Growth of Bacteria". Annual Review of Microbiology 9: 97- 

110. 


• An examination of the exponential growth of bacterial populations 

• Science aid: Microbial Populations 

• Microbial Growth, BioMineWiki 

This article includes material from an article posted on 26 April 2003 on Nupedia; 

written by Nagina Parmar; reviewed and approved by the Biology group; editor, 

Gaytha Langlois; lead reviewer, Gaytha Langlois ; lead copyeditors, Ruth Ifcher. and 

Jan Hogle. 

Retrieved from "http://en.wikipedia.org/wiki/Bacterial_growth" 

Categories: Bacteriology | Population 

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Bacteria 

http://en.wikipedia.org/wiki/Bacteria 

From Wikipedia, the free encyclopedia


For other uses, see Bacteria (disambiguation). 

Bacteria 

Fossil range: Archean or earlier - 

Recent 

Escherichia coli cells magnified 

25,000 times 


Domain: Bacteria 

Phyla 

Acidobacteria 

Actinobacteria 

Aquificae 

Bacteroidetes 

Chlamydiae 

Chlorobi 

Chloroflexi 

Chrysiogenetes 

Cyanobacteria 

Deferribacteres 

Deinococcus-Thermus 

Dictyoglomi 

Fibrobacteres 

Firmicutes 

Fusobacteria 

Gemmatimonadetes 

Nitrospirae 

Planctomycetes 

Proteobacteria 

Spirochaetes 

Thermodesulfobacteria 

Thermomicrobia 

Thermotogae 

Verrucomicrobia 

Bacteria (singular: bacterium) are unicellular microorganisms. Typically a few 

micrometres in length, bacteria have a wide range of shapes, ranging from spheres to

ods to spirals. Bacteria are ubiquitous in every habitat on Earth, growing in soil, 

acidic hot springs, radioactive waste, [1] seawater, and deep in the Earth's crust. There 

are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in 

a millilitre of fresh water; in all, there are approximately five nonillion (5×10 30 ) 

bacteria on Earth, [2] forming much of the world's biomass. [3] Bacteria are vital in 

recycling nutrients, and many important steps in nutrient cycles depend on bacteria, 

such as the fixation of nitrogen from the atmosphere. However, most of these bacteria 

have not been characterized, and only about half of the phyla of bacteria have species 

that can be cultured in the laboratory. [4] The study of bacteria is known as 

bacteriology, a branch of microbiology. 

There are approximately ten times as many bacterial cells as human cells in the 

human body, with large numbers of bacteria on the skin and in the digestive tract. [5] 

Although the vast majority of these bacteria are rendered harmless or beneficial by the 

protective effects of the immune system, a few are pathogenic bacteria and cause 

infectious diseases, including cholera, syphilis, anthrax, leprosy and bubonic plague. 

The most common fatal bacterial diseases are respiratory infections, with tuberculosis 

alone killing about 2 million people a year, mostly in sub-Saharan Africa. [6] In 

developed countries, antibiotics are used to treat bacterial infections and in various 

agricultural processes, so antibiotic resistance is becoming common. In industry, 

bacteria are important in processes such as sewage treatment, the production of cheese 

and yoghurt, and the manufacture of antibiotics and other chemicals. [7] 

Bacteria are prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells 

do not contain a nucleus and rarely harbour membrane-bound organelles. Although 

the term bacteria traditionally included all prokaryotes, the scientific classification 

changed after the discovery in the 1990s that prokaryotic life consists of two very 

different groups of organisms that evolved independently from an ancient common 

ancestor. These evolutionary domains are called Bacteria and Archaea. [8] 

Contents 

[hide] 

• 1 History of bacteriology 

• 2 Origin and early evolution 

• 3 Morphology 

• 4 Cellular structure 

o 4.1 Intracellular structures 

o 4.2 Extracellular structures 

o 4.3 Endospores 

• 5 Metabolism 

• 6 Growth and reproduction 

• 7 Genetics 

• 8 Movement 

• 9 Classification and identification 

• 10 Interactions with other organisms 

o 10.1 Mutualists 

o 10.2 Pathogens

• 11 Significance in technology and industry 

• 12 See also 


• 14 Further reading 


History of bacteriology 

Further information: Microbiology 

Antonie van Leeuwenhoek, the first microbiologist and the first person to observe 

bacteria using a microscope. 

Bacteria were first observed by Antonie van Leeuwenhoek in 1676, using a singlelens 

microscope of his own design. [9] He called them "animalcules" and published his 

observations in a series of letters to the Royal Society. [10][11][12] The name bacterium 

was introduced much later, by Christian Gottfried Ehrenberg in 1828, and is derived 

from the Greek word βακτήριον -α , bacterion -a , meaning "small staff". [13] 

Louis Pasteur demonstrated in 1859 that the fermentation process is caused by the 

growth of microorganisms, and that this growth is not due to spontaneous generation. 

(Yeasts and molds, commonly associated with fermentation, are not bacteria, but 

rather fungi.) Along with his contemporary, Robert Koch, Pasteur was an early 

advocate of the germ theory of disease. [14] Robert Koch was a pioneer in medical 

microbiology and worked on cholera, anthrax and tuberculosis. In his research into 

tuberculosis, Koch finally proved the germ theory, for which he was awarded a Nobel 

Prize in 1905. [15] In Koch's postulates, he set out criteria to test if an organism is the 

cause of a disease; these postulates are still used today. [16] 

Though it was known in the nineteenth century that bacteria are the cause of many 

diseases, no effective antibacterial treatments were available. [17] In 1910, Paul Ehrlich 

developed the first antibiotic, by changing dyes that selectively stained Treponema 

pallidum—the spirochaete that causes syphilis—into compounds that selectively

killed the pathogen. [18] Ehrlich had been awarded a 1908 Nobel Prize for his work on 

immunology, and pioneered the use of stains to detect and identify bacteria, with his 

work being the basis of the Gram stain and the Ziehl-Neelsen stain. [19] 

A major step forward in the study of bacteria was the recognition in 1977 by Carl 

Woese that archaea have a separate line of evolutionary descent from bacteria. [20] This 

new phylogenetic taxonomy was based on the sequencing of 16S ribosomal RNA, and 

divided prokaryotes into two evolutionary domains, as part of the three-domain 

system. [21] 

Origin and early evolution 

Further information: Timeline of evolution 

The ancestors of modern bacteria were single-celled microorganisms that were the 

first forms of life to develop on earth, about 4 billion years ago. For about 3 billion 

years, all organisms were microscopic, and bacteria and archaea were the dominant 

forms of life. [22][23] Although bacterial fossils exist, such as stromatolites, their lack of 

distinctive morphology prevents them from being used to examine the past history of 

bacterial evolution, or to date the time of origin of a particular bacterial species. 

However, gene sequences can be used to reconstruct the bacterial phylogeny, and 

these studies indicate that bacteria diverged first from the archaeal/eukaryotic 

lineage. [24] The most recent common ancestor of bacteria and archaea was probably a 

hyperthermophile that lived about 2.5 billion–3.2 billion years ago. [25][26] 

Bacteria were also involved in the second great evolutionary divergence, that of the 

archaea and eukaryotes. Here, eukaryotes resulted from ancient bacteria entering into 

endosymbiotic associations with the ancestors of eukaryotic cells, which were 

themselves possibly related to the Archaea. [27][28] This involved the engulfment by 

proto-eukaryotic cells of alpha-proteobacterial symbionts to form either mitochondria 

or hydrogenosomes, which are still being found in all known Eukarya (sometimes in 

highly reduced form, e.g. in ancient "amitochondrial" protozoa). Later on, an 

independent second engulfment by some mitochondria-containing eukaryotes of 

cyanobacterial-like organisms led to the formation of chloroplasts in algae and plants. 

There are even some algal groups known that clearly originated from subsequent 

events of endosymbiosis by heterotrophic eukaryotic hosts engulfing a eukaryotic 

algae that developed into "second-generation" plastids. [29][30] 

Morphology

Bacteria display a large diversity of cell morphologies and arrangements 

Bacteria display a wide diversity of shapes and sizes, called morphologies. Bacterial 

cells are about 10 times smaller than eukaryotic cells and are typically 0.5– 

5.0 micrometres in length. However, a few species–for example Thiomargarita 

namibiensis and Epulopiscium fishelsoni–are up to half a millimetre long and are 

visible to the unaided eye. [31] Among the smallest bacteria are members of the genus 

Mycoplasma, which measure only 0.3 micrometres, as small as the largest viruses. [32] 

Most bacterial species are either spherical, called cocci (sing. coccus, from Greek 

kókkos, grain, seed) or rod-shaped, called bacilli (sing. bacillus, from Latin baculus, 

stick). Some rod-shaped bacteria, called vibrio, are slightly curved or comma-shaped; 

others, can be spiral-shaped, called spirilla, or tightly coiled, called spirochaetes. A 

small number of species even have tetrahedral or cuboidal shapes. [33] This wide 

variety of shapes is determined by the bacterial cell wall and cytoskeleton, and is 

important because it can influence the ability of bacteria to acquire nutrients, attach to 

surfaces, swim through liquids and escape predators. [34][35] 

Many bacterial species exist simply as single cells, others associate in characteristic 

patterns: Neisseria form diploids (pairs), Streptococcus form chains, and 

Staphylococcus group together in "bunch of grapes" clusters. Bacteria can also be 

elongated to form filaments, for example the Actinobacteria. Filamentous bacteria are 

often surrounded by a sheath that contains many individual cells; certain types, such 

as species of the genus Nocardia, even form complex, branched filaments, similar in 

appearance to fungal mycelia. [36]

The range of sizes shown by prokaryotes, relative to those of other organisms and 

biomolecules 

Bacteria often attach to surfaces and form dense aggregations called biofilms or 

bacterial mats. These films can range from a few micrometers in thickness to up to 

half a meter in depth, and may contain multiple species of bacteria, protists and 

archaea. Bacteria living in biofilms display a complex arrangement of cells and 

extracellular components, forming secondary structures such as microcolonies, 

through which there are networks of channels to enable better diffusion of 

nutrients. [37][38] In natural environments, such as soil or the surfaces of plants, the 

majority of bacteria are bound to surfaces in biofilms. [39] Biofilms are also important 

for chronic bacterial infections and infections of implanted medical devices, as 

bacteria protected within these structures are much harder to kill than individual 

bacteria. [40] 

Even more complex morphological changes are sometimes possible. For example, 

when starved of amino acids, Myxobacteria detect surrounding cells in a process 

known as quorum sensing, migrate towards each other, and aggregate to form fruiting 

bodies up to 500 micrometres long and containing approximately 100,000 bacterial 

cells. [41] In these fruiting bodies, the bacteria perform separate tasks; this type of 

cooperation is a simple type of multicellular organisation. For example, about one in 

10 cells migrate to the top of these fruiting bodies and differentiate into a specialised 

dormant state called myxospores, which are more resistant to desiccation and other 

adverse environmental conditions than are ordinary cells. [42] 

Cellular structure 

Further information: Bacterial cell structure

Diagram of the cellular structure of a typical bacterial cell 

Intracellular structures 

The bacterial cell is surrounded by a lipid membrane, or cell membrane, which 

encompasses the contents of the cell and acts as a barrier to hold nutrients, proteins 

and other essential components of the cytoplasm within the cell. As they are 

prokaryotes, bacteria do not tend to have membrane-bound organelles in their 

cytoplasm and thus contain few intracellular structures. They consequently lack a 

nucleus, mitochondria, chloroplasts and the other organelles present in eukaryotic 

cells, such as the Golgi apparatus and endoplasmic reticulum. [43] However, recent 

research is identifying increasing amounts of structural complexity in bacteria, such as 

the discovery of the prokaryotic cytoskeleton. [44][45] 

Many important biochemical reactions, such as energy generation, occur due to 

concentration gradients across membranes, creating a potential difference analogous 

to a battery. The absence of internal membranes in bacteria means these reactions, 

such as electron transport, occur across the cell membrane, between the cytoplasm 

and the periplasmic space. [46] Additionally, while some transporter proteins consume 

chemical energy, others harness concentration gradients to import nutrients across the 

cell membrane or to expel undesired molecules from the cytoplasm. 

Bacteria do not have a membrane-bound nucleus, and their genetic material is 

typically a single circular chromosome located in the cytoplasm in an irregularly 

shaped body called the nucleoid. [47] The nucleoid contains the chromosome with 

associated proteins and RNA. Like all living organisms, bacteria contain ribosomes 

for the production of proteins, but the structure of the bacterial ribosome is different 

from those of eukaryotes and Archaea. [48] The order Planctomycetes are an exception 

to the general absence of internal membranes in bacteria, because they have a 

membrane around their nucleoid and contain other membrane-bound cellular 

structures. [49] 

Some bacteria produce intracellular nutrient storage granules, such as glycogen, [50] 

polyphosphate, [51] sulfur [52] or polyhydroxyalkanoates. [53] These granules enable 

bacteria to store compounds for later use. Certain bacterial species, such as the

photosynthetic Cyanobacteria, produce internal gas vesicles, which they use to 

regulate their buoyancy - allowing them to move up or down into water layers with 

different light intensities and nutrient levels. [54] 

Extracellular structures 

Further information: Cell envelope 

Around the outside of the cell membrane is the bacterial cell wall. Bacterial cell walls 

are made of peptidoglycan (called murein in older sources), which is made from 

polysaccharide chains cross-linked by unusual peptides containing D-amino acids. [55] 

Bacterial cell walls are different from the cell walls of plants and fungi, which are 

made of cellulose and chitin, respectively. [56] The cell wall of bacteria is also distinct 

from that of Archaea, which do not contain peptidoglycan. The cell wall is essential to 

the survival of many bacteria, and the antibiotic penicillin is able to kill bacteria by 

inhibiting a step in the synthesis of peptidoglycan. [56] 

There are broadly speaking two different types of cell wall in bacteria, called Grampositive 

and Gram-negative. The names originate from the reaction of cells to the 

Gram stain, a test long-employed for the classification of bacterial species. [57] 

Gram-positive bacteria possess a thick cell wall containing many layers of 

peptidoglycan and teichoic acids. In contrast, Gram-negative bacteria have a relatively 

thin cell wall consisting of a few layers of peptidoglycan surrounded by a second lipid 

membrane containing lipopolysaccharides and lipoproteins. Most bacteria have the 

Gram-negative cell wall, and only the Firmicutes and Actinobacteria (previously 

known as the low G+C and high G+C Gram-positive bacteria, respectively) have the 

alternative Gram-positive arrangement. [58] These differences in structure can produce 

differences in antibiotic susceptibility; for instance, vancomycin can kill only Grampositive 

bacteria and is ineffective against Gram-negative pathogens, such as 

Haemophilus influenzae or Pseudomonas aeruginosa. [59] 

In many bacteria an S-layer of rigidly arrayed protein molecules covers the outside of 

the cell. [60] This layer provides chemical and physical protection for the cell surface 

and can act as a macromolecular diffusion barrier. S-layers have diverse but mostly 

poorly understood functions, but are known to act as virulence factors in 

Campylobacter and contain surface enzymes in Bacillus stearothermophilus. [61] 

Helicobacter pylori electron micrograph, showing multiple flagella on the cell surface

Flagella are rigid protein structures, about 20 nanometres in diameter and up to 

20 micrometres in length, that are used for motility. Flagella are driven by the energy 

released by the transfer of ions down an electrochemical gradient across the cell 

membrane. [62] 

Fimbriae are fine filaments of protein, just 2–10 nanometres in diameter and up to 

several micrometers in length. They are distributed over the surface of the cell, and 

resemble fine hairs when seen under the electron microscope. Fimbriae are believed 

to be involved in attachment to solid surfaces or to other cells and are essential for the 

virulence of some bacterial pathogens. [63] Pili (sing. pilus) are cellular appendages, 

slightly larger than fimbriae, that can transfer genetic material between bacterial cells 

in a process called conjugation (see bacterial genetics, below). [64] 

Capsules or slime layers are produced by many bacteria to surround their cells, and 

vary in structural complexity: ranging from a disorganised slime layer of extracellular 

polymer, to a highly structured capsule or glycocalyx. These structures can 

protect cells from engulfment by eukaryotic cells, such as macrophages. [65] They can 

also act as antigens and be involved in cell recognition, as well as aiding attachment 

to surfaces and the formation of biofilms. [66] 

The assembly of these extracellular structures is dependent on bacterial secretion 

systems. These transfer proteins from the cytoplasm into the periplasm or into the 

environment around the cell. Many types of secretion systems are known and these 

structures are often essential for the virulence of pathogens, so are intensively 

studied. [67] 

Endospores 

Further information: Endospores 

Bacillus anthracis (stained purple) growing in cerebrospinal fluid 

Certain genera of Gram-positive bacteria, such as Bacillus, Clostridium, 

Sporohalobacter, Anaerobacter and Heliobacterium, can form highly resistant, 

dormant structures called endospores. [68] In almost all cases, one endospore is formed 

and this is not a reproductive process, although Anaerobacter can make up to seven 

endospores in a single cell. [69] Endospores have a central core of cytoplasm containing 

DNA and ribosomes surrounded by a cortex layer and protected by an impermeable 

and rigid coat.

Endospores show no detectable metabolism and can survive extreme physical and 

chemical stresses, such as high levels of UV light, gamma radiation, detergents, 

disinfectants, heat, pressure and desiccation. [70] In this dormant state, these organisms 

may remain viable for millions of years, [71][72] and endospores even allow bacteria to 

survive exposure to the vacuum and radiation in space. [73] Endospore-forming bacteria 

can also cause disease: for example, anthrax can be contracted by the inhalation of 

Bacillus anthracis endospores, and contamination of deep puncture wounds with 

Clostridium tetani endospores causes tetanus. [74] 

Metabolism 

Further information: Microbial metabolism 

Filaments of photosynthetic cyanobacteria 

In contrast to higher organisms, bacteria exhibit an extremely wide variety of 

metabolic types. [75] The distribution of metabolic traits within a group of bacteria has 

traditionally been used to define their taxonomy, but these traits often do not 

correspond with modern genetic classifications. [76] Bacterial metabolism is classified 

on the basis of three major criteria: the kind of energy used for growth, the source of 

carbon, and the electron donors used for growth. An additional criterion of respiratory 

microorganisms are the electron acceptors used for aerobic or anaerobic 

respiration. [77] 

Carbon metabolism in bacteria is either heterotrophic, where organic carbon 

compounds are used as carbon sources, or autotrophic, meaning that cellular carbon is 

obtained by fixing carbon dioxide. Typical autotrophic bacteria are phototrophic 

cyanobacteria, green sulfur-bacteria and some purple bacteria, but also many 

chemolithotrophic species, such as nitrifying or sulfur-oxidising bacteria. [78] Energy 

metabolism of bacteria is either based on phototrophy, the use of light through 

photosynthesis, or on chemotrophy, the use of chemical substances for energy, which 

are mostly oxidised at the expense of oxygen or alternative electron acceptors 

(aerobic/anaerobic respiration). 

Finally, bacteria are further divided into lithotrophs that use inorganic electron donors 

and organotrophs that use organic compounds as electron donors. Chemotrophic 

organisms use the respective electron donors for energy conservation (by 

aerobic/anaerobic respiration or fermentation) and biosynthetic reactions (e.g. carbon 

dioxide fixation), whereas phototrophic organisms use them only for biosynthetic 

purposes. Respiratory organisms use chemical compounds as a source of energy by 

taking electrons from the reduced substrate and transferring them to a terminal

electron acceptor in a redox reaction. This reaction releases energy that can be used to 

synthesise ATP and drive metabolism. In aerobic organisms, oxygen is used as the 

electron acceptor. In anaerobic organisms other inorganic compounds, such as nitrate, 

sulfate or carbon dioxide are used as electron acceptors. This leads to the ecologically 

important processes of denitrification, sulfate reduction and acetogenesis, 

respectively. 

Another way of life of chemotrophs in the absence of possible electron acceptors is 

fermentation, where the electrons taken from the reduced substrates are transferred to 

oxidised intermediates to generate reduced fermentation products (e.g. lactate, 

ethanol, hydrogen, butyric acid). Fermentation is possible, because the energy content 

of the substrates is higher than that of the products, which allows the organisms to 

synthesise ATP and drive their metabolism. [79][80] 

These processes are also important in biological responses to pollution; for example, 

sulfate-reducing bacteria are largely responsible for the production of the highly toxic 

forms of mercury (methyl- and dimethylmercury) in the environment. [81] Nonrespiratory 

anaerobes use fermentation to generate energy and reducing power, 

secreting metabolic by-products (such as ethanol in brewing) as waste. Facultative 

anaerobes can switch between fermentation and different terminal electron acceptors 

depending on the environmental conditions in which they find themselves. 

Lithotrophic bacteria can use inorganic compounds as a source of energy. Common 

inorganic electron donors are hydrogen, carbon monoxide, ammonia (leading to 

nitrification), ferrous iron and other reduced metal ions, and several reduced sulfur 

compounds. Unusually, the gas methane can be used by methanotrophic bacteria as 

both a source of electrons and a substrate for carbon anabolism. [82] In both aerobic 

phototrophy and chemolithotrophy, oxygen is used as a terminal electron acceptor, 

while under anaerobic conditions inorganic compounds are used instead. Most 

lithotrophic organisms are autotrophic, whereas organotrophic organisms are 

heterotrophic. 

In addition to fixing carbon dioxide in photosynthesis, some bacteria also fix nitrogen 

gas (nitrogen fixation) using the enzyme nitrogenase. This environmentally important 

trait can be found in bacteria of nearly all the metabolic types listed above, but is not 

universal. [83] 

Growth and reproduction 

Further information: Bacterial growth 

Unlike multicellular organisms, increases in the size of bacteria (cell growth) and 

their reproduction by cell division are tightly linked in unicellular organisms. Bacteria 

grow to a fixed size and then reproduce through binary fission, a form of asexual 

reproduction. [84] Under optimal conditions, bacteria can grow and divide extremely 

rapidly, and bacterial populations can double as quickly as every 9.8 minutes. [85] In 

cell division, two identical clone daughter cells are produced. Some bacteria, while 

still reproducing asexually, form more complex reproductive structures that help 

disperse the newly-formed daughter cells. Examples include fruiting body formation

y Myxobacteria and arial hyphae formation by Streptomyces, or budding. Budding 

involves a cell forming a protrusion that breaks away and produces a daughter cell. 

A growing colony of Escherichia coli cells [86] 

In the laboratory, bacteria are usually grown using solid or liquid media. Solid growth 

media such as agar plates are used to isolate pure cultures of a bacterial strain. 

However, liquid growth media are used when measurement of growth or large 

volumes of cells are required. Growth in stirred liquid media occurs as an even cell 

suspension, making the cultures easy to divide and transfer, although isolating single 

bacteria from liquid media is difficult. The use of selective media (media with specific 

nutrients added or deficient, or with antibiotics added) can help identify specific 

organisms. [87] 

Most laboratory techniques for growing bacteria use high levels of nutrients to 

produce large amounts of cells cheaply and quickly. However, in natural 

environments nutrients are limited, meaning that bacteria cannot continue to 

reproduce indefinitely. This nutrient limitation has led the evolution of different 

growth strategies (see r/K selection theory). Some organisms can grow extremely 

rapidly when nutrients become available, such as the formation of algal (and 

cyanobacterial) blooms that often occur in lakes during the summer. [88] Other 

organisms have adaptations to harsh environments, such as the production of multiple 

antibiotics by Streptomyces that inhibit the growth of competing microorganisms. [89] 

In nature, many organisms live in communities (e.g. biofilms) which may allow for 

increased supply of nutrients and protection from environmental stresses. [39] These 

relationships can be essential for growth of a particular organism or group of 

organisms (syntrophy). [90] 

Bacterial growth follows three phases. When a population of bacteria first enter a 

high-nutrient environment that allows growth, the cells need to adapt to their new 

environment. The first phase of growth is the lag phase, a period of slow growth when 

the cells are adapting to the high-nutrient environment and preparing for fast growth. 

The lag phase has high biosynthesis rates, as proteins necessary for rapid growth are 

produced. [91] The second phase of growth is the logarithmic phase (log phase), also

known as the exponential phase. The log phase is marked by rapid exponential 

growth. The rate at which cells grow during this phase is known as the growth rate 

(k), and the time it takes the cells to double is known as the generation time (g). 

During log phase, nutrients are metabolised at maximum speed until one of the 

nutrients is depleted and starts limiting growth. The final phase of growth is the 

stationary phase and is caused by depleted nutrients. The cells reduce their metabolic 

activity and consume non-essential cellular proteins. The stationary phase is a 

transition from rapid growth to a stress response state and there is increased 

expression of genes involved in DNA repair, antioxidant metabolism and nutrient 

transport. [92] 

Genetics 

Further information: Plasmid, Genome 

Most bacteria have a single circular chromosome that can range in size from only 

160,000 base pairs in the endosymbiotic bacteria Candidatus Carsonella ruddii, [93] to 

12,200,000 base pairs in the soil-dwelling bacteria Sorangium cellulosum. [94] 

Spirochaetes of the genus Borrelia are a notable exception to this arrangement, with 

bacteria such as Borrelia burgdorferi, the cause of Lyme disease, containing a single 

linear chromosome. [95] The genes in bacterial genomes are usually a single continuous 

stretch of DNA and although several different types of introns do exist in bacteria, 

these are much more rare than in eukaryotes. [96] 

Bacteria may also contain plasmids, which are small extra-chromosomal DNAs that 

may contain genes for antibiotic resistance or virulence factors. Another type of 

bacterial DNA are integrated viruses (bacteriophages). Many types of bacteriophage 

exist, some simply infect and lyse their host bacteria, while others insert into the 

bacterial chromosome. A bacteriophage can contain genes that contribute to its host's 

phenotype: for example, in the evolution of Escherichia coli O157:H7 and 

Clostridium botulinum, the toxin genes in an integrated phage converted a harmless 

ancestral bacteria into a lethal pathogen. [97] 

Bacteria, as asexual organisms, inherit identical copies of their parent's genes (i.e., 

they are clonal). However, all bacteria can evolve by selection on changes to their 

genetic material DNA caused by genetic recombination or mutations. Mutations come 

from errors made during the replication of DNA or from exposure to mutagens. 

Mutation rates vary widely among different species of bacteria and even among 

different clones of a single species of bacteria. [98] Genetic changes in bacterial 

genomes come from either random mutation during replication or "stress-directed 

mutation", where genes involved in a particular growth-limiting process have an 

increased mutation rate. [99] 

Some bacteria also transfer genetic material between cells. This can occur in three 

main ways. Firstly, bacteria can take up exogenous DNA from their environment, in a 

process called transformation. Genes can also be transferred by the process of 

transduction, when the integration of a bacteriophage introduces foreign DNA into the 

chromosome. The third method of gene transfer is bacterial conjugation, where DNA 

is transferred through direct cell contact. This gene acquisition from other bacteria or

the environment is called horizontal gene transfer and may be common under natural 

conditions. [100] Gene transfer is particularly important in antibiotic resistance as it 

allows the rapid transfer of resistance genes between different pathogens. [101] 

Movement 

Further information: Chemotaxis, Flagella, Pilus 

The different arrangements of bacterial flagella: A-Monotrichous; B-Lophotrichous; 

C-Amphitrichous and D-Peritrichous 

Motile bacteria can move using flagella, bacterial gliding, twitching motility or 

changes of buoyancy. [102] In twitching motility, bacterial use their type IV pili as a 

grappling hook, repeatedly extending it, anchoring it and then retracting it with 

remarkable force (>80 pN). [103] 

Bacterial species differ in the number and arrangement of flagella on their surface; 

some have a single flagellum (monotrichous), a flagellum at each end 

(amphitrichous), clusters of flagella at the poles of the cell (lophotrichous), while 

others have flagella distributed over the entire surface of the cell (peritrichous). The 

bacterial flagella is the best-understood motility structure in any organism and is made 

of about 20 proteins, with approximately another 30 proteins required for its 

regulation and assembly. [102] The flagellum is a rotating structure driven by a motor at 

the base that uses the electrochemical gradient across the membrane for power. This 

motor drives the motion of the filament, which acts as a propeller. Many bacteria 

(such as E. coli) have two distinct modes of movement: forward movement 

(swimming) and tumbling. The tumbling allows them to reorient and makes their 

movement a three-dimensional random walk. [104] (See external links below for link to 

videos.) The flagella of a unique group of bacteria, the spirochaetes, are found 

between two membranes in the periplasmic space. They have a distinctive helical 

body that twists about as it moves. [102] 

Motile bacteria are attracted or repelled by certain stimuli in behaviors called taxes: 

these include chemotaxis, phototaxis and magnetotaxis. [105][106] In one peculiar group,

the myxobacteria, individual bacteria move together to form waves of cells that then 

differentiate to form fruiting bodies containing spores. [107] The myxobacteria move 

only when on solid surfaces, unlike E. coli which is motile in liquid or solid media. 

Several Listeria and Shigella species move inside host cells by usurping the 

cytoskeleton, which is normally used to move organelles inside the cell. By promoting 

actin polymerization at one pole of their cells, they can form a kind of tail that pushes 

them through the host cell's cytoplasm. [108] 

Classification and identification 

Streptococcus mutans visualized with a Gram stain 

Further information: Scientific classification, Systematics and Clinical 

pathology 

Classification seeks to describe the diversity of bacterial species by naming and 

grouping organisms based on similarities. Bacteria can be classified on the basis of 

cell structure, cellular metabolism or on differences in cell components such as DNA, 

fatty acids, pigments, antigens and quinones. [87] While these schemes allowed the 

identification and classification of bacterial strains, it was unclear whether these 

differences represented variation between distinct species or between strains of the 

same species. This uncertainty was due to the lack of distinctive structures in most 

bacteria, as well as lateral gene transfer between unrelated species. [109] Due to lateral 

gene transfer, some closely related bacteria can have very different morphologies and 

metabolisms. To overcome this uncertainty, modern bacterial classification 

emphasizes molecular systematics, using genetic techniques such as guanine cytosine 

ratio determination, genome-genome hybridization, as well as sequencing genes that 

have not undergone extensive lateral gene transfer, such as the rRNA gene. [110] 

Classification of bacteria is determined by publication in the International Journal of 

Systematic Bacteriology, [111] and Bergey's Manual of Systematic Bacteriology. [112] 

The term "bacteria" was traditionally applied to all microscopic, single-celled 

prokaryotes. However, molecular systematics showed prokaryotic life to consist of 

two separate domains, originally called Eubacteria and Archaebacteria, but now 

called Bacteria and Archaea that evolved independently from an ancient common 

ancestor. [113] The archaea and eukaryotes are more closely-related to each other than 

either is to the bacteria. These two domains, along with Eukarya, are the basis of the 

three-domain system, which is currently the most widely used classification system in 

microbiolology. [114] However, due to the relatively recent introduction of molecular 

systematics and a rapid increase in the number of genome sequences that are

available, bacterial classification remains a changing and expanding field. [4][115] For 

example, a few biologists argue that the Archaea and Eukaryotes evolved from Grampositive 

bacteria. [116] 

Identification of bacteria in the laboratory is particularly relevant in medicine, where 

the correct treatment is determined by the bacterial species causing an infection. 

Consequently, the need to identify human pathogens was a major impetus for the 

development of techniques to identify bacteria. 

Phylogenetic tree showing the diversity of bacteria, compared to other organisms. [117] 

Eukaryotes are colored red, archaea green and bacteria blue. 

The Gram stain, developed in 1884 by Hans Christian Gram, characterises bacteria 

based on the structural characteristics of their cell walls. [57] The thick layers of 

peptidoglycan in the "Gram-positive" cell wall stain purple, while the thin "Gramnegative" 

cell wall appears pink. By combining morphology and Gram-staining, most 

bacteria can be classified as belonging to one of four groups (Gram-positive cocci, 

Gram-positive bacilli, Gram-negative cocci and Gram-negative bacilli). Some 

organisms are best identified by stains other than the Gram stain, particularly 

mycobacteria or Nocardia, which show acid-fastness on Ziehl–Neelsen or similar 

stains. [118] Other organisms may need to be identified by their growth in special 

media, or by other techniques, such as serology. 

Culture techniques are designed to promote the growth and identify particular 

bacteria, while restricting the growth of the other bacteria in the sample. Often these 

techniques are designed for specific specimens; for example, a sputum sample will be 

treated to identify organisms that cause pneumonia, while stool specimens are 

cultured on selective media to identify organisms that cause diarrhoea, while 

preventing growth of non-pathogenic bacteria. Specimens that are normally sterile, 

such as blood, urine or spinal fluid, are cultured under conditions designed to grow all 

possible organisms. [119][87] Once a pathogenic organism has been isolated, it can be 

further characterised by its morphology, growth patterns such as (aerobic or anaerobic 

growth, patterns of hemolysis) and staining.

As with bacterial classification, identification of bacteria is increasingly using 

molecular methods. Diagnostics using such DNA-based tools, such as polymerase 

chain reaction, are increasingly popular due to their specificity and speed, compared 

to culture-based methods. [120] These methods also allow the detection and 

identification of "viable but nonculturable" cells that are metabolically active but nondividing. 

[121] However, even using these improved methods, the total number of 

bacterial species is not known and cannot even be estimated with any certainty. 

Attempts to quantify bacterial diversity have ranged from 10 7 to 10 9 total species, but 

even these diverse estimates may be out by many orders of magnitude. [122][123] 

Interactions with other organisms 

Despite their apparent simplicity, bacteria can form complex associations with other 

organisms. These symbiotic associations can be divided into parasitism, mutualism 

and commensalism. Due to their small size, commensal bacteria are ubiquitous and 

grow on animals and plants exactly as they will grow on any other surface. However, 

their growth can be increased by warmth and sweat, and large populations of these 

organisms in humans are the cause of body odor. 

Mutualists 

Certain bacteria form close spatial associations that are essential for their survival. 

One such mutualistic association, called interspecies hydrogen transfer, occurs 

between clusters of anaerobic bacteria that consume organic acids such as butyric acid 

or propionic acid and produce hydrogen, and methanogenic Archaea that consume 

hydrogen. [124] The bacteria in this association are unable to consume the organic acids 

as this reaction produces hydrogen that accumulates in their surroundings. Only the 

intimate association with the hydrogen-consuming Archaea keeps the hydrogen 

concentration low enough to allow the bacteria to grow. 

In soil, microorganisms which reside in the rhizosphere (a zone that includes the root 

surface and the soil that adheres to the root after gentle shaking) carry out nitrogen 

fixation, converting nitrogen gas to nitrogenous compounds. [125] This serves to 

provide an easily absorbable form of nitrogen for many plants, which cannot fix 

nitrogen themselves. Many other bacteria are found as symbionts in humans and other 

organisms. For example, the presence of over 1,000 bacterial species in the normal 

human gut flora of the intestines can contribute to gut immunity, synthesise vitamins 

such as folic acid, vitamin K and biotin, convert milk protein to lactic acid (see 

Lactobacillus), as well as fermenting complex undigestible carbohydrates. [126][127][128] 

The presence of this gut flora also inhibits the growth of potentially pathogenic 

bacteria (usually through competitive exclusion) and these beneficial bacteria are 

consequently sold as probiotic dietary supplements. [129] 

Pathogens 

Main article: Pathogenic bacteria

Color-enhanced scanning electron micrograph showing Salmonella typhimurium (red) 

invading cultured human cells 

If bacteria form a parasitic association with other organisms, they are classed as 

pathogens. Pathogenic bacteria are a major cause of human death and disease and 

cause infections such as tetanus, typhoid fever, diphtheria, syphilis, cholera, 

foodborne illness, leprosy and tuberculosis. A pathogenic cause for a known medical 

disease may only be discovered many years after, as was the case with Helicobacter 

pylori and peptic ulcer disease. Bacterial diseases are also important in agriculture, 

with bacteria causing leaf spot, fire blight and wilts in plants, as well as Johne's 

disease, mastitis, salmonella and anthrax in farm animals. 

Each species of pathogen has a characteristic spectrum of interactions with its human 

hosts. Some organisms, such as Staphylococcus or Streptococcus, can cause skin 

infections, pneumonia, meningitis and even overwhelming sepsis, a systemic 

inflammatory response producing shock, massive vasodilation and death. [130] Yet 

these organisms are also part of the normal human flora and usually exist on the skin 

or in the nose without causing any disease at all. Other organisms invariably cause 

disease in humans, such as the Rickettsia, which are obligate intracellular parasites 

able to grow and reproduce only within the cells of other organisms. One species of 

Rickettsia causes typhus, while another causes Rocky Mountain spotted fever. 

Chlamydia, another phylum of obligate intracellular parasites, contains species that 

can cause pneumonia, or urinary tract infection and may be involved in coronary heart 

disease. [131] Finally, some species such as Pseudomonas aeruginosa, Burkholderia 

cenocepacia, and Mycobacterium avium are opportunistic pathogens and cause 

disease mainly in people suffering from immunosuppression or cystic fibrosis. [132][133] 

Bacterial infections may be treated with antibiotics, which are classified as 

bacteriocidal if they kill bacteria, or bacteriostatic if they just prevent bacterial 

growth. There are many types of antibiotics and each class inhibits a process that is 

different in the pathogen from that found in the host. An example of how antibiotics 

produce selective toxicity are chloramphenicol and puromycin, which inhibit the 

bacterial ribosome, but not the structurally different eukaryotic ribosome. [134] 

Antibiotics are used both in treating human disease and in intensive farming to 

promote animal growth, where they may be contributing to the rapid development of 

antibiotic resistance in bacterial populations. [135] Infections can be prevented by 

antiseptic measures such as sterilizating the skin prior to piercing it with the needle of 

a syringe, and by proper care of indwelling catheters. Surgical and dental instruments

are also sterilized to prevent contamination and infection by bacteria. Disinfectants 

such as bleach are used to kill bacteria or other pathogens on surfaces to prevent 

contamination and further reduce the risk of infection. 

Significance in technology and industry 

Further information: Economic importance of bacteria 

Bacteria, often Lactobacillus in combination with yeasts and molds, have been used 

for thousands of years in the preparation of fermented foods such as cheese, pickles, 

soy sauce, sauerkraut, vinegar, wine and yoghurt. [136][137] 

The ability of bacteria to degrade a variety of organic compounds is remarkable and 

has been used in waste processing and bioremediation. Bacteria capable of digesting 

the hydrocarbons in petroleum are often used to clean up oil spills. [138] Fertilizer was 

added to some of the beaches in Prince William Sound in an attempt to promote the 

growth of these naturally occurring bacteria after the infamous 1989 Exxon Valdez oil 

spill. These efforts were effective on beaches that were not too thickly covered in oil. 

Bacteria are also used for the bioremediation of industrial toxic wastes. [139] In the 

chemical industry, bacteria are most important in the production of enantiomerically 

pure chemicals for use as pharmaceuticals or agrichemicals. [140] 

Bacteria can also be used in the place of pesticides in the biological pest control. This 

commonly involves Bacillus thuringiensis (also called BT), a Gram-positive, soil 

dwelling bacterium. Subspecies of this bacteria are used as a Lepidopteran-specific 

insecticides under trade names such as Dipel and Thuricide. [141] Because of their 

specificity, these pesticides are regarded as environmentally friendly, with little or no 

effect on humans, wildlife, pollinators and most other beneficial insects. [142][143] 

Because of their ability to quickly grow and the relative ease with which they can be 

manipulated, bacteria are the workhorses for the fields of molecular biology, genetics 

and biochemistry. By making mutations in bacterial DNA and examining the resulting 

phenotypes, scientists can determine the function of genes, enzymes and metabolic 

pathways in bacteria, then apply this knowledge to more complex organisms. [144] This 

aim of understanding the biochemistry of a cell reaches its most complex expression 

in the synthesis of huge amounts of enzyme kinetic and gene expression data into 

mathematical models of entire organisms. This is achievable in some well-studied 

bacteria, with models of Escherichia coli metabolism now being produced and 

tested. [145][146] This understanding of bacterial metabolism and genetics allows the use 

of biotechnology to bioengineer bacteria for the production of therapeutic proteins, 

such as insulin, growth factors, or antibodies. [147][148] 

See also 

• Human flora 

• Bioaerosol 

• Biotechnology 

• Contamination control 

• Denitrification

• Desulforudis audaxviator 

• Extremophiles 

• Transgenic bacteria 

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• Alcamo IE (2001). Fundamentals of microbiology. Boston: Jones and Bartlett. 

ISBN 0-7637-1067-9. 

• Atlas RM (1995). Principles of microbiology. St. Louis: Mosby. ISBN 0- 

8016-7790-4. 

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• Holt JC, Bergey DH (1994). Bergey's manual of determinative bacteriology, 

9th ed., Baltimore: Williams & Wilkins. ISBN 0-683-00603-7.

• Hugenholtz P, Goebel BM, Pace NR (1998). "Impact of culture-independent 

studies on the emerging phylogenetic view of bacterial diversity". J Bacteriol 

180 (18): 4765–74. PMID 9733676. 

• Funke BR, Tortora GJ, Case CL (2004). Microbiology: an introduction, 8th 

ed,, San Francisco: Benjamin Cummings. ISBN 0-8053-7614-3. 

External links 

Find more about Bacteria on 

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• Bacterial Nomenclature Up-To-Date from DSMZ 

• The largest bacteria 

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• Videos of bacteria swimming and tumbling, use of optical tweezers and other 

videos. 

• Planet of the Bacteria by Stephen Jay Gould 

• On-line text book on bacteriology 

• Animated guide to bacterial cell structure. 

Chemotaxis 

http://en.wikipedia.org/wiki/Chemotaxis 


Jump to: navigation, search

Chemotaxis, a kind of taxis, is the phenomenon in which bodily cells, bacteria, and 

other single-cell or multicellular organisms direct their movements according to 

certain chemicals in their environment. This is important for bacteria to find food (for 

example, glucose) by swimming towards the highest concentration of food molecules, 

or to flee from poisons (for example, phenol). In multicellular organisms, chemotaxis 

is critical to early (e.g. movement of sperm towards the egg during fertilization) and 

subsequent phases of development (e.g. migration of neurons or lymphocytes) as well 

as in normal function. In addition, it has been recognized that mechanisms that allow 

chemotaxis in animals can be subverted during cancer metastasis. 

Chemotaxis is called positive if movement is in the direction of a higher concentration 

of the chemical in question, and negative if the direction is opposite. 

Contents 

[hide] 

• 1 History of chemotaxis research 

• 2 Phylogeny and chemotactic signalling 

• 3 Bacterial chemotaxis 

o 3.1 Behavior 

o 3.2 Signal transduction 

3.2.1 Flagellum regulation 

3.2.2 Receptor regulation 

• 4 Eukaryotic chemotaxis 

o 4.1 Motility 

4.1.1 Chemotaxis related migratory responses 

o 4.2 Receptors 

4.2.1 Chemotactic selection 

o 4.3 Chemotactic ligands 

4.3.1 Chemotactic range fitting (CRF) 

• 5 Clinical significance 

• 6 In the mirror of publications 

• 7 Measurement of chemotaxis 



[edit] History of chemotaxis research

Milestones of chemotaxis research 

Although migration of cells was detected from the early days of the development of 

microscopy (Leeuwenhoek), erudite description of chemotaxis was first made by T.W. 

Engelmann (1881) and W.F. Pfeffer (1884) in bacteria and H.S. Jennings (1906) in 

ciliates. The Nobel Prize Laureate E. Metchnikoff also contributed to the study of the 

field with investigations of the process as an initial step of phagocytosis. The 

significance of chemotaxis in biology and clinical pathology was widely accepted in 

the 1930s. The most fundamental definitions belonging to the phenomenon were also 

drafted by this time. The most important aspects in quality control of chemotaxis 

assays were described by H. Harris in the 1950s. In the 1960s and 1970s, the 

revolution of modern cell biology and biochemistry provided a series of novel 

techniques which became available to investigate the migratory responder cells and 

subcellular fractions responsible for chemotactic activity. The pioneering works of J. 

Adler represented a significant turning point in understanding the whole process of 

intracellular signal transduction of bacteria. [1] 

On November 3, 2006, Dr. Dennis Bray of University of Cambridge was awarded the 

Microsoft European Science Award for his work on chemotaxis on E. coli. [2][3] 

[edit] Phylogeny and chemotactic signalling 

Chemotaxis is one of the most basic cell physiological responses. Development of 

receptor systems for the detection of harmful and favorable substances in the 

environment was most essential to unicellular organisms from the very early stages of 

phylogeny. Comprehensive analysis of chemotactic activity of the eukaryotic 

protozoon Tetrahymena pyriformis and consensus sequences of appearance of amino 

acids in the primordial soup suggest that there was a good correlation between the 

chemotactic character of these relative simple organic molecules and their 

development on the Earth. In this way the earliest molecules are suggested to be

highly chemoattractant (e.g. Gly, Glu, Pro), while latter ones are thought to be 

strongly chemorepellent (e.g. Tyr, Trp, Phe) amino acids. [4] 

[edit] Bacterial chemotaxis 

Some bacteria, such as E. coli, have several flagella per cell (4–10 typically). These 

can rotate in two ways : 

1. Counter-clockwise rotation aligns the flagella into a single rotating bundle, 

causing the bacterium to swim in a straight line. 

2. Clockwise rotation breaks the flagella bundle apart such that each flagellum 

points in a different direction, causing the bacterium to tumble in place. 

The directions of rotation are given for an observer outside the cell looking down the 

flagella toward the cell. 

[edit] Behavior 

The overall movement of a bacterium is the result of alternating tumble and swim 

phases. If one watches a bacterium swimming in a uniform environment, its 

movement will look like a random walk with relatively straight swims interrupted by 

random tumbles that reorient the bacterium. Bacteria such as E. coli are unable to 

choose the direction in which they swim, and are unable to swim in a straight line for 

more than a few seconds due to rotational diffusion. In other words, bacteria "forget" 

the direction in which they are going. Given these limitations, it is remarkable that 

bacteria can direct their motion to find favorable locations with high concentrations of 

attractants (usually food) and avoid repellents (usually poisons). 

In the presence of a chemical gradient bacteria will chemotax, or direct their overall 

motion based on the gradient. If the bacterium senses that it is moving in the correct 

direction (toward attractant/away from repellent), it will keep swimming in a straight 

line for a longer time before tumbling. If it is moving in the wrong direction, it will 

tumble sooner and try a new direction at random. In other words, bacteria like E. coli 

use temporal sensing to decide whether life is getting better or worse. In this way, it

finds the location with the highest concentration of attractant (usually the source) 

quite well. Even under very high concentrations, it can still distinguish very small 

differences in concentration. Fleeing from a repellent works with the same efficiency. 

It seems remarkable that this purposeful random walk is a result of simply choosing 

between two methods of random movement; namely tumbling and straight swimming. 

In fact, chemotactic responses such as forgetting direction and choosing movements 

resemble the decision-making abilities of higher lifeforms with brains that process 

sensory data. 

The helical nature of the individual flagellar filament is critical for this movement to 

occur. As such, the protein that makes up the flagellar filament, flagellin, is quite 

similar among all flagellated bacteria. Vertebrates seem to have taken advantage of 

this fact by possessing an immune receptor (TLR5) designed to recognize this 

conserved protein. 

As in many instances in biology, there are bacteria that do not follow this rule. Many 

bacteria, such as Vibrio, are monoflagellated and have a single flagellum at one pole 

of the cell. Their method of chemotaxis is different. Others possess a single flagellum 

that is kept inside the cell wall. These bacteria move by spinning the whole cell, 

which is shaped like a corkscrew. [5] 

[edit] Signal transduction 

Chemical gradients are sensed through multiple transmembrane receptors, called 

methyl accepting chemotaxis proteins (MCPs), which vary in the molecules that they 

detect. These receptors may bind attractants or repellents directly or indirectly through 

interaction with proteins of periplasmatic space. The signals from these receptors are 

transmitted across the plasma membrane into the cytosol, where Che proteins are 

activated. The Che proteins alter the tumbling frequency, and alter the receptors. 

[edit] Flagellum regulation 

The proteins CheW and CheA bind to the receptor. The activation of the receptor by 

an external stimulus causes autophosphorylation in the histidine kinase, CheA, at a

single highly conserved histidine residue. CheA in turn transfers phosphoryl groups to 

conserved aspartate residues in the response regulators CheB and CheY [ note: CheA 

is a histidine kinase and it does not actively transfer the phosphoryl group. The 

response regulator CheB takes the phosphoryl group from CheA]. This mechanism of 

signal transduction is called a 'Two Component System' and is a common form of 

signal transduction in bacteria. CheY induces tumbling by interacting with the 

flagellar switch protein FliM, inducing a change from counter-clockwise to clockwise 

rotation of the flagellum. Change in the rotation state of a single flagellum can disrupt 

the entire flagella bundle and cause a tumble. 

[edit] Receptor regulation 

CheB, when activated by CheA, acts as a methylesterase, removing methyl groups 

from glutamate residues on the cytosolic side of the receptor. It works antagonistically 

with CheR, a methyltransferase, which adds methyl residues to the same glutamate 

residues. The more methyl residues are attached to the receptor, the more sensitive the 

receptor. As the signal from the receptor induces demethylation of the receptor in a 

feedback loop, the system is continuously adjusted to environmental chemical levels, 

remaining sensitive for small changes even under extreme chemical concentrations. 

This regulation allows the bacterium to 'remember' chemical concentrations from the 

recent past and compare them to those it is currently experiencing, thus 'know' 

whether it is traveling up or down a gradient. However, the methylation system alone 

cannot account for the wide range of sensitivity that bacteria have to chemical 

gradients. Additional regulatory mechanisms such as receptor clustering and receptorreceptor 

interactions also modulate the signalling pathway. 

http://en.wikipedia.org/wiki/Coccidia 

Coccidia 



Coccidia 

Coccidia oocysts 


Kingdom: Protista

Phylum: Apicomplexa 

Class: Conoidasida 

Subclass: Coccidiasina 

Order: Eucoccidiorida 

Suborder, Family, Genera & Species 

Adeleorina 

• Adeleidae 

• Dactylosomatidae 

• Haemogregarinidae 

• Hepatozoidae 

o Hepatozoon 

• Karyolysidae 

• Klossiellidae 

• Legerellidae 

Eimeriorina 

• Aggregatidae 

o Aggregata 

o Merocystis 

o Selysina 

• Calyptosporiidae 

o Calyptospora 

• Cryptosporidiidae 

o Cryptosporidium 

• Eimeriidae 

o Atoxoplasma 

o Barrouxia 

o Caryospora 

o Caryotropha 

o Cyclospora 

o Diaspora 

o Dorisa 

o Dorisiella 

o Eimeria 

o Grasseella 

o Isospora 

o Mantonella 

o Ovivora 

o Pfeifferinella 

o Pseudoklossia 

o Tyzzeria 

o Wenyonella 

• Elleipsisomatidae 

o Elleipsisoma 

• Lankesterellidae

o Lankesterella 

o Schellackia 

• Sarcocystidae 

o Sarcocystinae 

Frenkelia 

Sarcocystis 

o Toxoplasmatinae 

Besnoitia 

Hammondia 

Neospora 

Toxoplasma 

• Selenococcidiidae 

o Selenococcidium 

• Spirocystidae 

o Spirocystis 

Coccidia are microscopic, spore-forming, single-celled parasites belonging to the 

apicomplexan class Conoidasida. [1] Coccidian parasites infect the intestinal tracts of 

animals [2] , and are the largest group of apicomplexan protozoa. 

Coccidia are obligate, intracellular parasites, which means that they must live and 

reproduce within an animal cell. 

Contents 

[hide] 

• 1 Coccidiosis 

o 1.1 Coccidia in dogs 

• 2 Genera and species that cause coccidiosis 




[edit] Coccidiosis 

Coccidiosis is the disease caused by coccidian infection. Coccidiosis is a parasitic 

disease of the intestinal tract of animals, caused by coccidian protozoa. The disease 

spreads from one animal to another by contact with infected feces, or ingestion of 

infected tissue. Diarrhea, which may become bloody in severe cases, is the primary 

symptom. Most animals infected with coccidia are asymptomatic; however, young or 

immuno-compromised animals may suffer severe symptoms, including death. 

While coccidian organisms can infect a wide variety of animals, including humans, 

birds, and livestock, they are usually species-specific. One well-known exception is 

toxoplasmosis, caused by Toxoplasma gondii.

[edit] Coccidia in dogs 

People often first encounter coccidia when they acquire a young puppy who is 

infected. The infectious organisms are canine-specific and are not contagious to 

humans (compare to zoonotic diseases). 

Young puppies are frequently infected with coccidia and often develop active 

Coccidiosis -- even puppies obtained from diligent professional breeders. Infected 

puppies almost always have received the parasite from their mother's feces. Typically, 

healthy adult animals shedding the parasite's oocysts in their feces will be 

asymptomatic because of their developed immune systems. However, undeveloped 

immune systems make puppies more susceptible. Further, stressors such as new 

owners, travel, weather changes, and unsanitary conditions are believed to activate 

infections in susceptible animals. 

Symptoms in young dogs are universal: at some point around 2-3 months of age, an 

infected dog develops persistently loose stools. This diarrhea proceeds to stool 

containing liquid, thick mucus, and light colored fecal matter. As the infection 

progresses, spots of blood may become apparent in the stool, and sudden bowel 

movements may surprise both dog and owner alike. Coccidia infection is so common 

that any pup under 4 months old with these symptoms can almost surely be assumed 

to have coccidiosis. 

Fortunately, the treatment is inexpensive, extremely effective, and routine. A 

veterinarian can easily diagnose the disease through low-powered microscopic 

examination of an affected dog's feces, which usually will be replete with oocysts. 

One of many easily administered and inexpensive drugs will be prescribed, and, in the 

course of just a few days, an infection will be eliminated or perhaps reduced to such a 

level that the dog's immune system can make its own progress against the infection. 

Even when an infection has progressed sufficiently that blood is present in feces, 

permanent damage to the gastrointestinal system is rare, and the dog will most likely 

make a complete recovery without long-lasting negative effects. 

If one dog of a litter has coccidiosis, then most certainly all dogs at a breeder's 

kennels have active coccidia infections. Breeders should be notified if a newlyacquired 

pup is discovered to be infected with coccidia. Breeders can take steps to 

eradicate the organism from their kennels, including applying medications in bulk to 

an entire facility. 

[edit] Genera and species that cause coccidiosis 

• Genus Isospora is the most common cause of intestinal coccidiosis in dogs 

and cats and is usually what is meant by coccidiosis. Species of Isospora are 

species specific, meaning they only infects one type of species. Species that 

infect dogs include I. canis, I. ohioensis, I. burrowsi, and I. neorivolta. Species 

that infect cats include I. felis and I. rivolta. The most common symptom is 

diarrhea. Sulfonamides are the most common treatment. [3] 

• Genus Cryptosporidium contains two species known to cause 

cryptosporidiosis, C. parvum and C. muris. Cattle are most commonly affected

y Cryptosporidium, and their feces are often assumed to be a source of 

infection for other mammals including humans. Recent genetic analyses of 

Cryptosporidium in humans have identified Cryptosporidium hominis as a 

new species specific for humans. Infection occurs most commonly in 

individuals that are immunocompromised, e.g. dogs with canine distemper, 

cats with feline leukemia virus infection, and humans with AIDS. Very young 

puppies and kittens can also become infected with Cryptosporidium, but the 

infection is usually eliminated without treatment. [3] 

• Genus Hammondia is transmitted by ingestion of cysts found in the tissue of 

grazing animals and rodents. Dogs and cats are the definitive hosts, with the 

species H. heydorni infecting dogs and the species H. hammondi and H. 

pardalis infecting cats. Hammondia usually does not cause disease. [3] 

• Genus Besnoitia infect cats that ingest cysts found in the tissue of rodents and 

opossum, but usually does not cause disease. [3] 

• Genus Sarcocystis infect carnivores that ingest cysts from various intermediate 

hosts. It is possible for Sarcocystis to cause disease in dogs and cats. [3] 

• Genus Toxoplasma has one important species, Toxoplasma gondii. Cats are 

the definitive host, but all mammals and some fish, reptiles, and amphibians 

can be intermediate hosts. Therefore, only cat feces will hold infective 

oocysts, but infection through ingestion of cysts can occur with the tissue of 

any intermediate host. Toxoplasmosis occurs in humans usually as low-grade 

fever or muscle pain for a few days. A normal immune system will suppress 

the infection but the tissue cysts will persist in that animal or human for years 

or the rest of its life. In immunocompromised individuals, those dormant cysts 

can be reactivated and cause many lesions in the brain, heart, lungs, eyes, etc. 

Without a competent immune system, the animal or human will most likely 

die from the infection. For pregnant women, the fetus is at risk if the pregnant 

woman becomes infected for the first time during pregnancy. If the woman 

had been infected during childhood or adolescence, she will have an immunity 

that will protect her developing fetus during pregnancy. The most important 

misconception about the transmission of toxoplasmosis comes from statements 

like 'ingestion of raw or undercooked meat, or cat feces.' Kitchen hygiene is 

much more important because people do tend to taste marinades or sauces 

before being cooked, or chop meat then vegetables without properly cleaning 

the knife and cutting board. Many physicians mistakenly put panic in their 

pregnant clients and advise them to get rid of their cat without really warning 

them of the likely sources of infection. Adult cats are very unlikely to shed 

infective oocysts. Symptoms in cats include fever, weight loss, diarrhea, 

vomiting, uveitis, and central nervous system signs. Disease in dogs includes a 

rapidly progressive form seen in dogs also infected with distemper, and a 

neurological form causing paralysis, tremors, and seizures. Dogs and cats are 

usually treated with clindamycin. [3] 

• Genus Neospora has one important species, Neospora caninum, that affects 

dogs in a manner similar to toxoplasmosis. Neosporosis is difficult to treat. [3] 

• Genus Hepatozoon contains one species that causes hepatozoonosis in dogs 

and cats, Hepatozoon canis. Animals become infected by ingesting an infected 

Rhipicephalus sanguineus, also known as the brown dog tick. Symptoms 

include fever, weight loss, and pain of the spine and limbs.

The most common medications used to treat coccidian infections are in the 

sulphonamide family. Although unusual, sulphonamides can damage the tear glands 

in some dogs, causing keratoconjunctivitis sicca, or "dry eye", which may have a lifelong 

impact. Some veterinarians recommend measuring tear production prior to 

sulphonamide administration, and at various intervals after administration. Other 

veterinarians will simply avoid using sulphonamides, instead choosing another 

product effective against coccidia. 

Left untreated, the infection may clear of its own accord, or in some cases may 

continue to ravage an animal and cause permanent damage or, occasionally, death. 


1. ^ The Taxonomicon & Systema Naturae (Website database). Taxon: Genus 

Cryptosporidium. Universal Taxonomic Services, Amsterdam, The 

Netherlands (2000). 

2. ^ Biodiversity explorer: Apicomplexa (apicomplexans, sporozoans). Iziko 

Museums of Cape Town. 

3. ^ a b c d e f g Ettinger, Stephen J.; Feldman, Edward C. (1995). Textbook of 

Veterinary Internal Medicine, 4th ed., W.B. Saunders Company. ISBN 0- 

7216-6795-3. 

[edit] See also 

• cryptosporidiosis 

• Zoalene is a fodder additive for poultry, used to prevent infections from 

coccidia. 


• Mar Vista Animal Medical Center. 

• The Coccidia of the World, Donald W. Duszynski, Steve J. Upton, Lee Couch, 

Feb. 21, 2004. 

• Life Cycle EIMERIA, Andreas Weck-Heimann, 1996-2005 

• FarmingUK, Information about Coccidiosis 

• Lillehoj, Hyun S. (October 1996). "Two Strategies for Protecting Poultry 

From Coccidia". Agricultural Research magazine (October 1996). United 

States Department of Agriculture: Agrigultural Research Service. Describes 

using live-parasite vaccine versus a monoclonal antibody to block the 

sporozoite from invading a host's cell. 

Retrieved from "http://en.wikipedia.org/wiki/Coccidia" 

Categories: Apicomplexa | Dog diseases | Cat diseases | Animal diseases | Veterinary 

protozoology

http://en.wikipedia.org/wiki/Deer_Island_Waste_Water_Treatment_Plant 

http://ludb.clui.org/ex/i/MA3134/ 

Deer Island Waste Water Treatment 

Plant 



The Deer Island Waste Water Treatment Plant (also known as Deer Island Sewage 

Treatment Plant) run and operated by The Massachusetts Water Resources Authority 

is located on Deer Island, one of the Boston Harbor Islands in Boston Harbor. 

[1] [2] [3] 

It is the second largest sewage treatment plant in the United States. 

It is a key part of the program to protect Boston Harbor against pollution from sewer 

systems in eastern Massachusetts. 

The plant removes human, household, business and industrial pollutants from 

wastewater that originates in homes and businesses in forty three greater Boston 

communities. It complies with all federal and state environmental standards and 

subject to the discharge permit issued for it by EPA and DEP. Its treated wastewater 

can safely be released into the marine environment. 

It has an array of 150 foot tall egg-like sludge digesters and these are major harbor 

landmarks. [4][5] 

[edit] Notes 

1. ^ Deer Island Sewage Treatment Plant. The Center for Land Use 

Interpretation. 

2. ^ Jardine Water Purification Plant article 

3. ^ 1867 "The First Tunnel Under the Lake". Chicago Public Library. 

4. ^ Islands You Can Visit - Deer Island. Boston Harbor Islands Partnership. 

Retrieved on August 21, 2006. 

5. ^ Deer Island Factsheet. Boston Harbor Islands Partnership. Retrieved on 

August 21, 2006. 

[edit] Bibliography 

• Baldwin, Sandy, "Boston Harbor Pipe Dreams Come True!": USGS Visits the 

Deer Island Sewage Treatment Plant and a Cleaner Harbor, USGS Sound 

Waves, April 2006.


• MWRA article on The Deer Island Sewage Treatment Plant 

• A History of the sewer system in Boston 

Retrieved from 

"http://en.wikipedia.org/wiki/Deer_Island_Waste_Water_Treatment_Plant" 

Categories: Buildings and structures in Boston, Massachusetts | Sewage treatment 

plants 

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• This page was last modified on 19 October 2007, at 15:11. 








http://en.wikipedia.org/wiki/Flagellate 

Flagellate 



"Flagellata" from Ernst Haeckel's Artforms of Nature, 1904

Parasitic excavate (Giardia lamblia) 

Green alga (Chlamydomonas) 

Flagellates are cells with one or more whip-like organelles called flagella. Some cells 

in animals may be flagellate, for instance the spermatozoa of most phyla. Higher 

plants and fungi do not produce flagellate cells, but the closely related green algae and 

chytrids do. Many protists take the form of single-celled flagellates. 

[edit] Form and behavior 

Flagellates r protozoans (animal-like protists). Eukaryotic flagella are supported by 

microtubules in a characteristic arrangement, with nine fused pairs surrounding two 

central singlets. These arise from a basal body or kinetosome, with microtubule roots 

that are an important part of the cell's brain. In some, for instance, they support a 

cytostome or mouth, where food is ingested. The flagella often support hairs, called 

mastigonemes, or contain rods. Their ultrastructure plays an important role in 

classifying eukaryotes. 

In protists and microscopic animals, flagella are generally used for propulsion. They 

may also be used to create a current that brings in food. In most things, one or more 

flagella are located at or near the anterior of the cell eg Euglena. Often there is one 

directed forwards and one trailing behind. Among animals, fungi, and Choanozoa, 

which make up a group called the opisthokonts, there is a single posterior flagellum. 

They are from the phylum Mastigophora. They can cause diseases and they can make 

their own food. For example, Trypanosome which causes the African sleeping 

sickness. 

[edit] Groups of flagellates 

Originally the flagellated protozoa were treated as a single class of phylum, the 

Mastigophora. This was divided into the Phytomastigina or phytoflagellates, which 

have chloroplasts or are closely related to such forms, and the Zoomastigina or 

zooflagellates, which do not. Most phytoflagellates were given a separate 

classification by botanists, treating them in several divisions of algae. 

This scheme has generally been abandoned or is retained only for convenience. 

However, the relationships among the flagellates are still mostly unknown, and their

higher classification is confused. Some argue that the Linnaean ranks are not 

appropriate for such a diverse set of organisms. 

Phytoflagellates are found in most groups of algae. Both the green algae and 

heterokonts include a variety of flagellates in addition to non-motile and multicellular 

forms. The dinoflagellates, cryptomonads, haptophytes, and euglenids are almost 

entirely single-celled flagellates. 

Many of the other flagellates make up what are called the excavate taxa. These 

include the euglenids and a number of important parasites, such as trypanosomes and 

Giardia. The excavates generally show similarities in the structure of their flagella 

and typically have a cytostome. However, they may be a paraphyletic group, and in 

particular may have been ancestral to most or all other eukaryotes. Aprils fools day 

yaeaahhhhh 

Other notable groups including flagellates are the Cercozoa, alveolates (including 

dinoflagellates), ebriids, and Apusozoa. 


• MeSH Flagellata 

Retrieved from "http://en.wikipedia.org/wiki/Flagellate" 

http://en.wikipedia.org/wiki/Fungus#With_plants 

accessed 03/04/08 

Fungus 



For the fictional character, see Fungus the Bogeyman. For the music genre, see 

Fungi (music). 

Fungi 

Fossil range: Early Silurian - Recent

Clockwise from top left: Amanita muscaria, a 

basidiomycete; Sarcoscypha coccinea, an 

ascomycete; black bread mold, a zygomycete; a 

chytrid; a Penicillium conidiophore. 


Domain: Eukarya 

(unranked) Opisthokonta 

Kingdom: Fungi 

(L., 1753) R.T. Moore, 1980 [1] 

Subkingdoms/Phyla 

Chytridiomycota 

Blastocladiomycota 

Neocallimastigomycota 

Glomeromycota 

Zygomycota 

Dikarya (inc. Deuteromycota) 

Ascomycota 

Basidiomycota 

A fungus (pronounced / f ŋgәs/) is any eukaryotic organism that is a member of the 

kingdom Fungi (pronounced / f nd a /). [2] The fungi are heterotrophic organisms 

characterized by a chitinous cell wall, and in the majority of species, filamentous 

growth as multicellular hyphae forming a mycelium; some fungal species also grow 

as single cells. Sexual and asexual reproduction is commonly via spores, often 

produced on specialized structures or in fruiting bodies. Some fungal species have lost 

the ability to form specialized reproductive structures, and propagate solely by 

vegetative growth. Yeasts, molds, and mushrooms are examples of fungi. The fungi 

are a monophyletic group that is phylogenetically clearly distinct from the 

morphologically similar slime molds (myxomycetes) and water molds (oomycetes). 

The fungi are more closely related to animals than plants, yet the discipline of biology 

devoted to the study of fungi, known as mycology, often falls under a branch of 

botany.

Occurring worldwide, most fungi are largely invisible to the naked eye, living for the 

most part in soil, dead matter and as symbionts of plants, animals, or other fungi. 

They perform an essential role in all ecosystems in decomposing matter and are 

indispensable in nutrient cycling and exchange. Some fungi become noticeable when 

fruiting, either as mushrooms or molds. Many fungal species have long been used as a 

direct source of food, such as mushrooms and truffles and in fermentation of various 

food products, such as wine, beer, and soy sauce. More recently, fungi are being used 

as sources for antibiotics and various enzymes, such as cellulases, pectinases, and 

proteases, important for industrial use or as active ingredients of detergents. Many 

fungi produce bioactive compounds, such as alkaloids and polyketides that are toxic 

to animals including humans and are, therefore, called mycotoxins. Some fungi are 

used recreationally or in traditional ceremonies as a source of psychotropic 

compounds. Several species of the fungi are significant pathogens of humans and 

other animals, and losses due to diseases of crops (e.g., rice blast disease) or food 

spoilage caused by fungi can have a large impact on human food supply and local 

economies. 

Contents 

[hide] 

• 1 Etymology and definition 

• 2 Diversity 

• 3 Importance for human use 

o 3.1 Cultured foods 

o 3.2 Other human uses 

o 3.3 Mycotoxins 

o 3.4 Edible and poisonous fungi 

o 3.5 Fungi in the biological control of pests 

• 4 Ecology 

o 4.1 Symbiosis 

4.1.1 With plants 

4.1.2 With insects 

4.1.3 As pathogens and parasites 

o 4.2 Nutrition and possible autotrophy 

• 5 Morphology 

o 5.1 Microscopic structures 

o 5.2 Macroscopic structures 

o 5.3 Morphological and physiological features for substrate penetration 

• 6 Reproduction 

o 6.1 Asexual reproduction 

o 6.2 Sexual reproduction 

o 6.3 Spore dispersal 

o 6.4 Other sexual processes 

• 7 Phylogeny and classification 

o 7.1 Physiological and morphological traits 

o 7.2 Evolutionary history 

7.2.1 Cladogram 

o 7.3 The taxonomic groups of fungi

o 7.4 Phylogenetic relationships with other fungus-like organisms 


• 9 Notes and references 

• 10 Further reading 


Etymology and definition 

The English word fungus is directly adopted from the Latin fungus, meaning 

"mushroom", used in Horace and Pliny. [3] This in turn is derived from the Greek word 

sphongos/σφογγος ("sponge"), referring to the macroscopic structures and 

morphology of some mushrooms and molds and also used in other languages (e.g., the 

German Schwamm ("sponge") or Schwammerl for some types of mushroom). 

Diversity 

Fungi have a worldwide distribution, and grow in a wide range of habitats, including 

deserts. Most fungi grow in terrestrial environments, but several species occur only in 

aquatic habitats. Fungi along with bacteria are the primary decomposers of organic 

matter in most if not all terrestrial ecosystems worldwide. Based on observations of 

the ratio of the number of fungal species to the number of plant species in some 

environments, the fungal kingdom has been estimated to contain about 1.5 million 

species. [4] Around 70,000 fungal species have been formally described by 

taxonomists, but the true dimension of fungal diversity is still unknown. [5] Most fungi 

grow as thread-like filaments called hyphae, which form a mycelium, while others 

grow as single cells. [6][7] Until recently many fungal species were described based 

mainly on morphological characteristics, such as the size and shape of spores or 

fruiting structures, and biological species concepts; the application of molecular tools, 

such as DNA sequencing, to study fungal diversity has greatly enhanced the 

resolution and added robustness to estimates of diversity within various taxonomic 

groups. [8] 

Importance for human use 

Sacharomyces cerevisiae cells in DIC microscopy. 

Human use of fungi for food preparation or preservation and other purposes is 

extensive and has a long history: yeasts are required for fermentation of beer, wine [9]

and bread, some other fungal species are used in the production of soy sauce and 

tempeh. Mushroom farming and mushroom gathering are large industries in many 

countries. Many fungi are producers of antibiotics, including β-lactam antibiotics such 

as penicillin and cephalosporin. [10] Widespread use of these antibiotics for the 

treatment of bacterial diseases, such as tuberculosis, syphilis, leprosy, and many 

others began in the early 20th century and continues to play a major part in antibacterial 

chemotherapy. The study of the historical uses and sociological impact of 

fungi is known as ethnomycology. 

Cultured foods 

Baker's yeast or Saccharomyces cerevisiae, a single-cell fungus, is used in the baking 

of bread and other wheat-based products, such as pizza and dumplings. [11] Several 

yeast species of the genus Saccharomyces are also used in the production of alcoholic 

beverages through fermentation. [12] Mycelial fungi, such as the shoyu koji mold 

(Aspergillus oryzae), are used in the brewing of Shoyu (soy sauce) and preparation of 

tempeh. [13] Quorn is a high-protein product made from the mold, Fusarium 

venenatum, and is used in vegetarian cooking. 

Other human uses 

Fungi are also used extensively to produce industrial chemicals like lactic acid, 

antibiotics and even to make stonewashed jeans. [14] Several fungal species are 

ingested for their psychedelic properties, both recreationally and religiously (see main 

article, Psilocybin mushrooms). 

Mycotoxins 

Main article: Mycotoxins 

Many fungi produce compounds with biological activity. Several of these compounds 

are toxic and are therefore called mycotoxins, referring to their fungal origin and toxic 

activity. Of particular relevance to humans are those mycotoxins that are produced by 

moulds causing food spoilage and poisonous mushrooms (see below). Particularly 

infamous are the aflatoxins, which are insidious liver toxins and highly carcinogenic 

metabolites produced by Aspergillus species often growing in or on grains and nuts 

consumed by humans, and the lethal amatoxins produced by mushrooms of the genus 

Amanita. Other notable mycotoxins include ochratoxins, patulin, ergot alkaloids, and 

trichothecenes and fumonisins, all of which have significant impact on human food 

supplies or animal livestock. [15] 

Mycotoxins belong to the group of secondary metabolites (or natural products). 

Originally, this group of compounds had been thought to be mere byproducts of 

primary metabolism, hence the name "secondary" metabolites. However, recent 

research has shown the existence of biochemical pathways solely for the purpose of 

producing mycotoxins and other natural products in fungi. [16] Mycotoxins provide a 

number of fitness benefits to the fungi that produce them in terms of physiological 

adaptation, competition with other microbes and fungi, and protection from 

fungivory. [17][18] These fitness benefits and the existence of dedicated biosynthetic

pathways for mycotoxin production suggest that the mycotoxins are important for 

fungal persistence and survival. 

Edible and poisonous fungi 

Asian mushrooms, clockwise from left, enokitake, buna-shimeji, bunapi-shimeji, king 

oyster mushroom and shiitake. 

Black Périgord Truffle (Tuber melanosporum), cut in half. 

Stilton cheese veined with Penicillium roqueforti. 

Some of the best known types of fungi are the edible and the poisonous mushrooms. 

Many species are commercially raised, but others must be harvested from the wild. 

Agaricus bisporus, sold as button mushrooms when small or Portobello mushrooms 

when larger, are the most commonly eaten species, used in salads, soups, and many 

other dishes. Many Asian fungi are commercially grown and have gained in 

popularity in the West. They are often available fresh in grocery stores and markets, 

including straw mushrooms (Volvariella volvacea), oyster mushrooms (Pleurotus 

ostreatus), shiitakes (Lentinula edodes), and enokitake (Flammulina spp.). 

There are many more mushroom species that are harvested from the wild for personal 

consumption or commercial sale. Milk mushrooms, morels, chanterelles, truffles, 

black trumpets, and porcini mushrooms (Boletus edulis) (also known as king boletes) 

all demand a high price on the market. They are often used in gourmet dishes.

For certain types of cheeses, it is also a common practice to inoculate milk curds with 

fungal spores to foment the growth of specific species of mold that impart a unique 

flavor and texture to the cheese. This accounts for the blue colour in cheeses such as 

Stilton or Roquefort which is created using Penicillium roqueforti spores. [19] Molds 

used in cheese production are usually non-toxic and are thus safe for human 

consumption; however, mycotoxins (e.g., aflatoxins, roquefortine C, patulin, or 

others) may accumulate due to fungal spoilage during cheese ripening or storage. [20] 

Many mushroom species are toxic to humans, with toxicities ranging from slight 

digestive problems or allergic reactions as well as hallucinations to severe organ 

failures and death. Some of the most deadly mushrooms belong to the genera Inocybe, 

Cortinarius, and most infamously, Amanita, which includes the destroying angel (A. 

virosa) and the death cap (A. phalloides), the most common cause of deadly 

mushroom poisoning. [21] The false morel (Gyromitra esculenta) is considered a 

delicacy by some when cooked yet can be deadly when raw. Tricholoma equestre is 

one which was considered edible for centuries yet recently responsible for a series of 

serious poisonings in France. 

Fly agaric mushrooms (A. muscaria) also cause occasional poisonings, mostly as a 

result of ingestion for use as a recreational drug for its hallucinogenic properties. 

Historically Fly agaric was used by Celtic Druids in Northern Europe and the Koryak 

people of north-eastern Siberia for religious or shamanic purposes. [22] It is difficult to 

identify a safe mushroom without proper training and knowledge, thus it is often 

advised to assume that a mushroom in the wild is poisonous and not to consume it. 

Fungi in the biological control of pests 

In agricultural settings, fungi that actively compete for nutrients and space with, and 

eventually prevail over, pathogenic microorganisms, such as bacteria or other fungi, 

via the competitive exclusion principle, [23] or are parasites of these pathogens, may be 

beneficial agents for human use. For example, some fungi may be used to suppress 

growth or eliminate harmful plant pathogens, such as insects, mites, weeds, 

nematodes and other fungi that cause diseases of important crop plants. [24] This has 

generated strong interest in the use and practical application of these fungi for the 

biological control of these agricultural pests. Entomopathogenic fungi can be used as 

biopesticides, as they actively kill insects. [25] Examples of fungi that have been used 

as bioinsecticides are Beauveria bassiana, Metarhizium anisopliae, Hirsutella spp, 

Paecilomyces fumosoroseus, and Verticillium lecanii. [26] [27] Endophytic fungi of 

grasses of the genus Neotyphodium, such as N. coenophialum produce alkaloids that 

are toxic to a range of invertebrate and vertebrate herbivores. These alkaloids protect 

the infected grass plants from herbivory, but some endophyte alkaloids can cause 

poisoning of grazing animals, such as cattle and sheep. [28] Infection of grass cultivars 

of turf or forage grasses with isolates of the grass endophytes that produce only 

specific alkaloids to improve grass hardiness and resistance to herbivores such as 

insects, while being non-toxic to livestock, is being used in grass breeding 

programs. [29] 

Ecology

Polypores growing on a tree in Borneo 

Although often inconspicuous, fungi occur in every environment on Earth and play 

very important roles in most ecosystems. Along with bacteria, fungi are the major 

decomposers in most terrestrial (and some aquatic) ecosystems, and therefore play a 

critical role in biogeochemical cycles and in many food webs. As decomposers, they 

play an indispensable role in nutrient cycling, especially as saprotrophs and 

symbionts, degrading organic matter to inorganic molecules, which can then re-enter 

anabolic metabolic pathways in plants or other organisms. [30][31] 

Symbiosis 

Many fungi have important symbiotic relationships with organisms from most if not 

all Kingdoms. [32][33][34] These interactions can be mutualistic or antagonistic in nature, 

or in case of commensal fungi are of no apparent benefit or detriment to the host. 

[35][36][37] 

With plants 

Mycorrhizal symbiosis between plants and fungi is one of the most well-known plantfungus 

associations and is of significant importance for plant growth and persistence 

in many ecosystems; over 90% of all plant species engage in some kind of 

mycorrhizal relationship with fungi and are dependent upon this relationship for 

survival. [38][39][40] The mycorrhizal symbiosis is ancient, dating to at least 400 million 

years ago. [41] It often increases the plant's uptake of inorganic compounds, such as 

nitrate and phosphate from soils having low concentrations of these key plant 

nutrients. [30] In some mycorrhizal associations, the fungal partners may mediate plantto-plant 

transfer of carbohydrates and other nutrients. Such mycorrhizal communities 

are called "common mycorrhizal networks". [42] 

Lichens are formed by a symbiotic relationship between algae or cyanobacteria 

(referred to in lichens as "photobionts") and fungi (mostly various species of 

ascomycetes and a few basidiomycetes), in which individual photobiont cells are 

embedded in a tissue formed by the fungus. [43] As in mycorrhizas, the photobiont 

provides sugars and other carbohydrates, while the fungus provides minerals and 

water. The functions of both symbiotic organisms are so closely intertwined that they 

function almost as a single organism.

With insects 

Many insects also engage in mutualistic relationships with various types of fungi. 

Several groups of ants cultivate fungi in the order Agaricales as their primary food 

source, while ambrosia beetles cultivate various species of fungi in the bark of trees 

that they infest. [44] Termites on the African Savannah are also known to cultivate 

fungi. [45] 

As pathogens and parasites 

However, many fungi are parasites on plants, animals (including humans), and other 

fungi. Serious fungal pathogens of many cultivated plants causing extensive damage 

and losses to agriculture and forestry include the rice blast fungus Magnaporthe 

oryzae, [46] tree pathogens such as Ophiostoma ulmi and Ophiostoma novo-ulmi 

causing Dutch elm disease, [47] and Cryphonectria parasitica responsible for chestnut 

blight, [48] and plant-pathogenic fungi in the genera Fusarium, Ustilago, Alternaria, 

and Cochliobolus; [36] fungi with the potential to cause serious human diseases, 

especially in persons with immuno-deficiencies, are in the genera Aspergillus, 

Candida, Cryptoccocus, [49][37][50] Histoplasma, [51] and Pneumocystis. [52] Several 

pathogenic fungi are also responsible for relatively minor human diseases, such as 

athlete’s foot and ringworm. Some fungi are predators of nematodes, which they 

capture using an array of specialized structures, such as constricting rings or adhesive 

nets. [53] 

Nutrition and possible autotrophy 

Growth of fungi as hyphae on or in solid substrates or single cells in aquatic 

environments is adapted to efficient extraction of nutrients from these environments, 

because these growth forms have high surface area to volume ratios. These 

adaptations in morphology are complemented by hydrolytic enzymes secreted into the 

environment for digestion of large organic molecules, such as polysaccharides, 

proteins, lipids, and other organic substrates into smaller molecules. [54][55][56] These 

molecules are then absorbed as nutrients into the fungal cells. 

Traditionally, the fungi are considered heterotrophs, organisms that rely solely on 

carbon fixed by other organisms for metabolism. Fungi have evolved a remarkable 

metabolic versatility that allows many of them to use a large variety of organic 

substrates for growth, including simple compounds as nitrate, ammonia, acetate, or 

ethanol. [57] [58] Recent research raises the possibility that some fungi utilize the 

pigment melanin to extract energy from ionizing radiation, such as gamma radiation 

for "radiotrophic" growth. [59] It has been proposed that this process might bear some 

similarity to photosynthesis in plants, [59] but detailed biochemical data supporting the 

existence of this hypothetical pathway are presently lacking. 

Morphology 

Microscopic structures

Mold covering a decaying peach over a period of six days. The frames were taken 

approximately 12 hours apart. 

Though fungi are part of the opisthokont clade, all phyla except for the chytrids have 

lost their posterior flagella. [60] Fungi are unusual among the eukaryotes in having a 

cell wall that, besides glucans (e.g., β-1,3-glucan) and other typical components, 

contains the biopolymer chitin. [61] 

Many fungi grow as thread-like filamentous microscopic structures called hyphae, 

and an assemblage of intertwined and interconnected hyphae is called a mycelium. [6] 

Hyphae can be septate, i.e., divided into hyphal compartments separated by a septum, 

each compartment containing one or more nuclei or can be coenocytic, i.e., lacking 

hyphal compartmentalization. However, septa have pores, such as the doliporus in the 

basidiomycetes that allow cytoplasm, organelles, and sometimes nuclei to pass 

through. [6] Coenocytic hyphae are essentially multinucleate supercells. [62] In some 

cases, fungi have developed specialized structures for nutrient uptake from living 

hosts; examples include haustoria in plant-parasitic fungi of nearly all divisions, and 

arbuscules of several mycorrhizal fungi, [63] which penetrate into the host cells for 

nutrient uptake by the fungus. 

Macroscopic structures 

Fungal mycelia can become visible macroscopically, for example, as concentric rings 

on various surfaces, such as damp walls, and on other substrates, such as spoilt food 

(see figure), and are commonly and generically called mould (American spelling, 

mold); fungal mycelia grown on solid agar media in laboratory petri dishes are usually 

referred to as colonies, with many species exhibiting characteristic macroscopic 

growth morphologies and colours, due to spores or pigmentation. 

Specialized fungal structures important in sexual reproduction are the apothecia, 

perithecia, and cleistothecia in the ascomycetes, and the fruiting bodies of the 

basidiomycetes, and a few ascomycetes. These reproductive structures can sometimes 

grow very large, and are well known as mushrooms. 

Morphological and physiological features for substrate penetration 

Fungal hyphae are specifically adapted to growth on solid surfaces and within 

substrates, and can exert astoundingly large penetrative mechanical forces. The plant 

pathogen, Magnaporthe grisea, forms a structure called an appressorium specifically

designed for penetration of plant tissues, and the pressure generated by the 

appressorium, which is directed against the plant epidermis can exceed 8 MPa (80 

bars). [64] The generation of these mechanical pressures is the result of an interplay 

between physiological processes to increase intracellular turgor by production of 

osmolytes such as glycerol, and the morphology of the appressorium. [65] 

Reproduction 

Fungi on a fence post near Orosí, Costa Rica. 

Reproduction of fungi is complex, reflecting the heterogeneity in lifestyles and 

genetic make up within this group of organisms. [6] Many fungi reproduce both 

sexually or asexually, depending on conditions in the environment. These conditions 

trigger genetically determined developmental programs leading to the expression of 

specialized structures for sexual or asexual reproduction. These structures aid both 

reproduction and efficient dissemination of spores or spore-containing propagules. 

Asexual reproduction 

Asexual reproduction via vegetative spores or through mycelial fragmentation is 

common in many fungal species and allows more rapid dispersal than sexual 

reproduction. In the case of the "Fungi imperfecti" or Deuteromycota, which lack a 

sexual cycle, it is the only means of propagation. Asexual spores, upon germination, 

may found a population that is clonal to the population from which the spore 

originated, and thus colonize new environments. 

Sexual reproduction 

Sexual reproduction with meiosis exists in all fungal phyla, except the 

Deuteromycota. It differs in many aspects from sexual reproduction in animals or 

plants. Many differences also exist between fungal groups and have been used to 

discriminate fungal clades and species based on morphological differences in sexual 

structures and reproductive strategies. Experimental crosses between fungal isolates 

can also be used to identify species based on biological species concepts. The major 

fungal clades have initially been delineated based on the morphology of their sexual 

structures and spores; for example, the spore-containing structures, asci and basidia, 

can be used in the identification of ascomycetes and basidiomycetes, respectively. 

Many fungal species have elaborate vegetative incompatibility systems that allow 

mating only between individuals of opposite mating type, while others can mate and

sexually reproduce with any other individual or itself. Species of the former mating 

system are called heterothallic, and of the latter homothallic. [66] 

Most fungi have both a haploid and diploid stage in their life cycles. In all sexually 

reproducing fungi, compatible individuals combine by cell fusion of vegetative 

hyphae by anastomosis, required for the initiation of the sexual cycle. Ascomycetes 

and basidiomycetes go through a dikaryotic stage, in which the nuclei inherited from 

the two parents do not fuse immediately after cell fusion, but remain separate in the 

hyphal cells (see heterokaryosis). 

In ascomycetes, dikaryotic hyphae of the hymenium form a characteristic hook at the 

hyphal septum. During cell division formation of the hook ensures proper distribution 

of the newly divided nuclei into the apical and basal hyphal compartments. An ascus 

(plural asci) is then formed, in which karyogamy (nuclear fusion) occurs. These asci 

are embedded in an ascocarp, or fruiting body, of the fungus. Karyogamy in the asci is 

followed immediately by meiosis and the production of ascospores. The ascospores 

are disseminated and germinate and may form a new haploid mycelium. [67] 

Sexual reproduction in basidiomycetes is similar to that of the ascomycetes. 

Compatible haploid hyphae fuse to produce a dikaryotic mycelium. However, the 

dikaryotic phase is more extensive in the basidiomycetes, in many cases also present 

in the vegetatively growing mycelium. A specialized anatomical structure, called a 

clamp connection, is formed at each hyphal septum. As with the structurally similar 

hook in the ascomycetes, formation of the clamp connection in the basidiomycetes is 

required for controlled transfer of nuclei during cell division, to maintain the 

dikaryotic stage with two genetically different nuclei in each hyphal compartment. [67] 

A basidiocarp is formed in which club-like structures known as basidia generate 

haploid basidiospores after karyogamy and meiosis. [68] The most commonly known 

basidiocarps are mushrooms, but they may also take many other forms (see 

Morphology section). 

In zygomycetes, haploid hyphae of two individuals fuse, forming a zygote, which 

develops into a zygospore. When the zygospore germinates, it quickly undergoes 

meiosis, generating new haploid hyphae, which in turn may form asexual 

sporangiospores. These sporangiospores are means of rapid dispersal of the fungus 

and germinate into new genetically identical haploid fungal colonies, able to mate and 

undergo another sexual cycle followed by the generation of new zygospores, thus 

completing the lifecycle. 

Spore dispersal 

Both asexual and sexual spores or sporangiospores of many fungal species are 

actively dispersed by forcible ejection from their reproductive structures. This 

ejection ensures exit of the spores from the reproductive structures as well as 

travelling through the air over long distances. Many fungi thereby possess specialized 

mechanical and physiological mechanisms as well as spore-surface structures, such as 

hydrophobins, for spore ejection. These mechanisms include, for example, forcible 

discharge of ascospores enabled by the structure of the ascus and accumulation of 

osmolytes in the fluids of the ascus that lead to explosive discharge of the ascospores 

into the air. [69] The forcible discharge of single spores termed ballistospores involves

formation of a small drop of water (Buller's drop), which upon contact with the spore 

leads to its projectile release with an initial acceleration of more than 10,000 g. [70] 

Other fungi rely on alternative mechanisms for spore release, such as external 

mechanical forces, exemplified by puffballs. Attracting insects, such as flies, to 

fruiting structures, by virtue of their having lively colours and a putrid odour, for 

dispersal of fungal spores is yet another strategy, most prominently used by the 

stinkhorns. 

Other sexual processes 

Besides regular sexual reproduction with meiosis, some fungal species may exchange 

genetic material via parasexual processes, initiated by anastomosis between hyphae 

and plasmogamy of fungal cells. The frequency and relative importance of parasexual 

events is unclear and may be lower than other sexual processes. However, it is known 

to play a role in intraspecific hybridization [71] and is also likely required for 

hybridization between fungal species, which has been associated with major events in 

fungal evolution. [72] 

Phylogeny and classification 

The mushroom Oudemansiella nocturnum eats wood 

For a long time taxonomists considered fungi to be members of the Plant Kingdom. 

This early classification was based mainly on similarities in lifestyle: both fungi and 

plant are mainly sessile, have similarities in general morphology and growth habitat 

(like plants, fungi often grow in soil, in the case of mushrooms forming conspicuous 

fruiting bodies, which sometimes bear resemblance to plants such as mosses). 

Moreover, both groups possess a cell wall, which is absent in the Animal Kingdom. 

However, the fungi are now considered a separate kingdom, distinct from both plants 

and animals, from which they appear to have diverged approximately one billion 

years ago. [73] Many studies have identified several distinct morphological, 

biochemical, and genetic features in the Fungi, clearly delineating this group from the 

other kingdoms. For these reasons, the fungi are placed in their own kingdom. 

Physiological and morphological traits 

Similar to animals and unlike most plants, fungi lack the capacity to synthesize 

organic carbon by chlorophyll-based photosynthesis; whereas plants store the reduced 

carbon as starch, fungi, like animals and some bacteria, use glycogen [74] for storage 

of carbohydrates. A major component of the cell wall in many fungal species is the 

nitrogen-containing carbohydrate, chitin, [75] also present in some animals, such as the 

insects and crustaceans, while the plant cell wall consists chiefly of the carbohydrate 

cellulose. The defining and unique characteristics of fungal cells include growth as

hyphae, which are microscopic filaments of between 2-10 microns in diameter and up 

to several centimetres in length, and which combined form the fungal mycelium. 

Some fungi, such as yeasts, grow as single ovoid cells, similar to unicellular algae and 

the protists. 

Unlike many plants, most fungi lack an efficient vascular system, such as xylem or 

phloem for long-distance transport of water and nutrients; as an example for 

convergent evolution, some fungi, such as Armillaria, form rhizomorphs or mycelial 

cords, [76] resembling and functionally related to, but morphologically distinct from, 

plant roots. 

Some characteristics shared between plants and fungi include the presence of 

vacuoles in the cell, [77] and a similar pathway in the biosynthesis of terpenes using 

mevalonic acid and pyrophosphate as biochemical precursors; plants however use an 

additional terpene biosynthesis pathway in the chloroplasts that is apparently absent in 

fungi. [78] Ancestral traits shared among members of the fungi include chitinous cell 

walls and heterotrophy by absorption. [67] A further characteristic of the fungi that is 

absent from other eukaryotes, and shared only with some bacteria, is the biosynthesis 

of the amino acid, L-lysine, via the α-aminoadipate pathway. [79] 

Similar to plants, fungi produce a plethora of secondary metabolites functioning as 

defensive compounds or for niche adaptation; however, biochemical pathways for the 

synthesis of similar or even identical compounds often differ markedly between fungi 

and plants. [80][81] 

Evolutionary history 

Even though traditionally included in many botany curricula and textbooks, fungi are 

now thought to be more closely related to animals than to plants, and are placed with 

the animals in the monophyletic group of opisthokonts. [67] For much of the Paleozoic 

Era, the fungi appear to have been aquatic, and consisted of organisms similar to the 

extant Chytrids in having flagellum-bearing spores. [82] The first land fungi probably 

appeared in the Silurian, right after the first land plants appeared, even though their 

fossils are fragmentary. For some time after the Permian-Triassic extinction event, a 

fungal spike, detected as an extraordinary abundance of fungal spores in sediments 

formed shortly after this event, indicates that they were the dominant life form during 

this period—nearly 100% of the fossil record available from this period. [83] 

Analyses using molecular phylogenetics support a monophyletic origin of the 

Fungi. [8] The taxonomy of the Fungi is in a state of constant flux, especially due to 

recent research based on DNA comparisons. These current phylogenetic analyses 

often overturn classifications based on older and sometimes less discriminative 

methods based on morphological features and biological species concepts obtained 

from experimental matings. [84][85] 

There is no unique generally accepted system at the higher taxonomic levels and there 

are constant name changes at every level, from species upwards. However, efforts 

among fungal researchers are now underway to establish and encourage usage of a 

unified and more consistent nomenclature. [8] Fungal species can also have multiple 

scientific names depending on its life cycle and mode (sexual or asexual) of

eproduction. Web sites such as Index Fungorum and ITIS define preferred up-to-date 

names (with cross-references to older synonyms), but do not always agree with each 

other. 

Cladogram 

Unikonta 

Opisthokonta 

The taxonomic groups of fungi 

Amoebozoa 

Fungi 

Animalia 

Choanozoa 

Dikarya 

Chytridiomycota 

Blastocladiomycota 

Neocallimastigomycota 

Zygomycota 

Glomeromycota 

Ascomycota 

Basidiomycota 

The major divisions (phyla) of fungi have been classified based mainly on their sexual 

reproductive structures. Currently, seven fungal divisions are proposed: [8] 

Arbuscular mycorrhiza seen under microscope. Flax root cortical cells containing 

paired arbuscules.

Conidiophores of molds of the genus Aspergillus, an ascomycete, seen under 

microscope. 

• The Chytridiomycota are commonly known as chytrids. These fungi are 

ubiquitous with a worldwide distribution; chytrids produce zoospores that are 

capable of active movement through aqueous phases with a single flagellum. 

Consequently, some taxonomists had earlier classified them as protists on the 

basis of the flagellum. Molecular phylogenies, inferred from the rRNA-operon 

sequences representing the 18S, 28S, and 5.8S ribosomal subunits, suggest 

that the Chytrids are a basal fungal group divergent from the other fungal 

divisions, consisting of four major clades with some evidence for paraphyly or 

possibly polyphyly. [82] 

• The Blastocladiomycota were previously considered a taxonomic clade within 

the Chytridiomycota. Recent molecular data and ultrastructural characteristics, 

however, place the Blastocladiomycota as a sister clade to the Zygomycota, 

Glomeromycota, and Dikarya (Ascomycota and Basiomycota). The 

blastocladiomycetes are fungi that are saprotrophs and parasites of all 

eukaryotic groups and undergo sporic meiosis unlike their close relatives, the 

chytrids, which mostly exhibit zygotic meiosis. [82] 

• The Neocallimastigomycota were earlier placed in the phylum 

Chytridomycota. Members of this small phylum are anaerobic organisms, 

living in the digestive system of larger herbivorous mammals and possibly in 

other terrestrial and aquatic environments. They lack mitochondria but contain 

hydrogenosomes of mitochondrial origin. As the related chrytrids, 

neocallimastigomycetes form zoospores that are posteriorly uniflagellate or 

polyflagellate. [8] 

• The Zygomycota contain the taxa, Zygomycetes and Trichomycetes, and 

reproduce sexually with meiospores called zygospores and asexually with 

sporangiospores. Black bread mold (Rhizopus stolonifer) is a common species 

that belongs to this group; another is Pilobolus, which is capable of ejecting 

spores several meters through the air. Medically relevant genera include 

Mucor, Rhizomucor, and Rhizopus. Molecular phylogenetic investigation has 

shown the Zygomycota to be a polyphyletic phylum with evidence of 

paraphyly within this taxonomic group. [86] 

• Members of the Glomeromycota are fungi forming arbuscular mycorrhizae 

with higher plants. Only one species has been observed forming zygospores; 

all other species solely reproduce asexually. The symbiotic association 

between the Glomeromycota and plants is ancient, with evidence dating to 400 

million years ago. [41]

Diagram of an apothecium (the typical cup-like reproductive structure of 

Ascomycetes) showing sterile tissues as well as developing and mature asci. 

• The Ascomycota, commonly known as sac fungi or ascomycetes, constitute 

the largest taxonomic group within the Eumycota. These fungi form meiotic 

spores called ascospores, which are enclosed in a special sac-like structure 

called an ascus. This division includes morels, a few mushrooms and truffles, 

single-celled yeasts (e.g., of the genera Saccharomyces, Kluyveromyces, 

Pichia, and Candida), and many filamentous fungi living as saprotrophs, 

parasites, and mutualistic symbionts. Prominent and important genera of 

filamentous ascomycetes include Aspergillus, Penicillium, Fusarium, and 

Claviceps. Many ascomycetes species have only been observed undergoing 

asexual reproduction (called anamorphic species), but molecular data has often 

been able to identify their closest teleomorphs in the Ascomycota. Because the 

products of meiosis are retained within the sac-like ascus, several ascomyctes 

have been used for elucidating principles of genetics and heredity (e.g. 

Neurospora crassa). 

• Members of the Basidiomycota, commonly known as the club fungi or 

basidiomycetes, produce meiospores called basidiospores on club-like stalks 

called basidia. Most common mushrooms belong to this group, as well as rust 

(fungus) and smut fungi, which are major pathogens of grains. Other 

important Basidiomyces include the maize pathogen,Ustilago maydis, human 

commensal species of the genus Malassezia, and the opportunistic human 

pathogen, Cryptococcus neoformans. 

Phylogenetic relationships with other fungus-like organisms 

Because of some similarities in morphology and lifestyle, the slime molds 

(myxomycetes) and water molds (oomycetes) were formerly classified in the kingdom 

Fungi. Unlike true fungi, however, the cell walls of these organisms contain cellulose 

and lack chitin. Slime molds are unikonts like fungi, but are grouped in the 

Amoebozoa. Water molds are diploid bikonts, grouped in the Chromalveolate 

kingdom. Neither water molds nor slime molds are closely related to the true fungi, 

and, therefore, taxonomists no longer group them in the kingdom Fungi. Nonetheless, 

studies of the oomycetes and myxomycetes are still often included in mycology 

textbooks and primary research literature. 

It has been suggested that the nucleariids, currently grouped in the Choanozoa, may 

be a sister group to the oomycete clade, and as such could be included in an expanded 

fungal kingdom. [87]

See also 

• Bioaerosol 

• Carnivorous fungus 

• Fusicoccin 

• List of fungal orders 

• MycoBank 

• Mycotoxin 

• Plant pathology 

• Wood-decay fungus 

• Quorn 

• Pathogenic fungi 

Notes and references 

1. ^ (1980) "Taxonomic proposals for the classification of marine yeasts and other 

yeast-like fungi including the smuts". Bot. Mar. 23: 371. 

2. ^ These are the pronunciations listed first in most dictionaries. See, for example, the 

Merriam-Webster Online entry Alternative pronunciations for fungi include 

/ f ŋga /, / f nd i/, and / f ŋgi/. Funguses (/ f ŋgәsәz/) is an alternative 

plural form. 

3. ^ Simpson, D.P. (1979). Cassell's Latin Dictionary, 5, London: Cassell Ltd., 883. 

ISBN 0-304-52257-0. 

4. ^ Hawksworth DL (2006). "The fungal dimension of biodiversity: magnitude, 

significance, and conservation". Mycol. Res. 95: 641–655. 

5. ^ Mueller GM, Schmit JP (2006). "Fungal biodiversity: what do we know? What can 

we predict?". Biodivers Conserv 16: 1–5. 

6. ^ a b c d Alexopoulos CJ, Mims CW, Blackwell M (1996). Introductory Mycology. 

John Wiley and Sons. ISBN 0471522295. 

7. ^ Meredith Blackwell; Rytas Vilgalys, and John W. Taylor (2005-02-14). Eumycota: 

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six-gene phylogeny.". Nature 443: 818-822. PMID 17051209. 

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and recovery across the Permian-Triassic boundary. Geology, 23, 967-970. 

84. ^ See Palaeos: Fungi for an introduction to fungal taxonomy, including recent 

controversies. 

85. ^ “A Higher-Level Phylogenetic Classification of the Fungi” by David S. Hibbett, 

(.pdf file) Retrieved on 8 March 2007 

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"Phylogeny of the Zygomycota based on nuclear ribosomal sequence data.". 

Mycologia 98: 872-884. PMID 17486964. 

87. ^ Esser, Karl; Paul A. Lemke (1994). The Mycota: A Comprehensive Treatise on 

Fungi as Experimental Systems for Basic and Applied Research. Springer. ISBN 

3540580085. 

Further reading 

• Alexopoulos, C.J., Charles W. Mims, M. Blackwell et al., Introductory 

Mycology, 4 th ed. (John Wiley and Sons, Hoboken NJ, 2004) ISBN 0-471- 

52229-5 

• Arora, David. (1986). "Mushrooms Demystified: A Comprehensive Guide to 

the Fleshy Fungi". 2nd ed. Ten Speed Press. ISBN 0898151694 

• Deacon JW. (2005). "Fungal Biology" (4th ed). Malden, MA: Blackwell 

Publishers. ISBN 1-4051-3066-0. 

• Kaminstein D. (2002). Mushroom poisoning. 

External links 

Wikimedia Commons has media related to: 

Fungi 

Look up fungi in 

Wiktionary, the free dictionary. 

Wikispecies has information related to: 

fungi 

• The WWW Virtual Library: Mycology 

• MykoWeb 

• Illinois Mycological Association Mycological Glossary

v • d • e 

• Tree of Life web project: Fungi 

• Fungal Biology, University of Sydney, School of Biological Sciences, June, 

2004. – Online textbook 

• The Fifth Kingdom – Online textbook 

• CABI Bioscience Databases - Includes Index Fungorum genus and species 

names and top-down hierarchy 

• Comparative Analysis of Fungal Genomes (at DOE's IMG system) 

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An Agar Plate -- an example of a bacterial growth medium. Specifically, it is a streak 

plate; the orange lines and dots are formed by bacterial colonies. 

A growth medium or culture medium is a liquid or gel designed to support the 

growth of microorganisms or cells. [1] There are different types of media for growing 

different types of cells. [2] 

There are two major types of growth media: those used for cell culture, which use 

specific cell types derived from plants or animals, and microbiological culture, which 

are used for growing microorganisms, such as bacteria or yeast. The most common 

growth media for microorganisms are nutrient broths and agar plates; specialized 

media are sometimes required for microorganism and cell culture growth. [1] Some 

organisms, termed fastidious organisms, require specialized environments due to 

complex nutritional requirements. Viruses, for example, are obligatory intracellular 

parasites and require a growth medium composed of living cells. 

Contents 

[hide] 

• 1 Types of growth mediums 

o 1.1 Nutrient media 

o 1.2 Minimal media 

o 1.3 Selective media 

o 1.4 Differential media 

• 2 Transport media 

• 3 Enriched media 




[edit] Types of growth mediums 

This article needs additional citations for verification. 

Please help improve this article by adding reliable references. Unsourced material may be 

challenged and removed. (August 2007)

The most common growth mediums for microorganisms are nutrient broths (liquid 

nutrient medium) or Luria Bertani medium (LB medium or Lysogeny Broth). Liquid 

mediums are often mixed with agar and poured into petri dishes to solidify. These 

agar plates provide a solid medium on which microbes may be cultured. Bacteria 

grown in liquid cultures often form colloidal suspensions. 

The differences between growth mediums used for cell culture and those used for 

microbiological culture are due to the fact that cells derived from whole organisms 

and grown in culture often cannot grow without the addition of, for instance, 

hormones or growth factors which usually occur in vivo. [3] In the case of animal cells, 

this difficulty is often addressed by the addition of blood serum to the medium. In the 

case of microorganisms, there are no such limitations, as they are often unicellular 

organisms. One other major difference is that animal cells in culture are often grown 

on a flat surface to which they attach, and the medium is provided in a liquid form, 

which covers the cells. In contrast, bacteria such as Escherichia coli may be grown on 

solid media or in liquid media. 

An important distinction between growth media types is that of defined versus 

undefined media. [1] A defined medium will have known quantities of all ingredients. 

For microorganisms, they consist of providing trace elements and vitamins required 

by the microbe and especially a defined carbon source and nitrogen source. Glucose 

or glycerol are often used as carbon sources, and ammonium salts or nitrates as 

inorganic nitrogen sources). An undefined medium has some complex ingredients, 

such as yeast extract or casein hydrolysate, which consist of a mixture of many, many 

chemical species in unknown proportions. Undefined media are sometimes chosen 

based on price and sometimes by necessity - some microorganisms have never been 

cultured on defined media. 

A good example of a growth medium is the wort used to make beer. The wort 

contains all the nutrients required for yeast growth, and under anaerobic conditions, 

alcohol is produced. When the fermentation process is complete, the combination of 

medium and dormant microbes, now beer, is ready for consumption. 

[edit] Nutrient media 

Undefined media (also known as basal or complex media) is an undefined media that 

contains: 

• a carbon source such as glucose for bacterial growth 

• water 

• various salts need for bacterial growth 

• a source of amino acids and nitrogen (e.g., beef, yeast extract) 

This is an undefined medium because the amino acid source contains a variety of 

compounds with the exact composition unknown. Nutrient media contain all the 

elements that most bacteria need for growth and are non-selective, so they are used 

for the general cultivation and maintenance of bacteria kept in laboratory culture 

collections. 

Defined media (also known as chemical defined media)

• all the chemicals used are known and 

• does not contain any animal, yeast, plant tissue. 

Differential medium 

• some sort of indicator, typically a dye, is added, that allows for the 

differentiation of particular chemical reactions occurring during growth. 

[edit] Minimal media 

Minimal media are those that contain the minimum nutrients possible for colony 

growth, generally without the presence of amino acids, and are often used by 

microbiologists and geneticists to grow "wild type" microorganisms. Minimal media 

can also be used to select for or against recombinants or exconjugants. 

Minimal medium typically contains: 

• a carbon source for bacterial growth, which may be a sugar such as glucose, or 

a less energy-rich source like succinate 

• various salts, which may vary among bacteria species and growing conditions; 

these generally provide essential elements such as magnesium, nitrogen, 

phosphorus, and sulfur to allow the bacteria to synthesize protein and nucleic 

acid 

• water 

Supplementary minimal media are a type of minimal media that also contains a single 

selected agent, usually an amino acid or a sugar. This supplementation allows for the 

culturing of specific lines of auxotrophic recombinants. 

[edit] Selective media 

Blood-free, charcoal-based selective medium agar (CSM) for isolation of 

Campylobacter.

Blood agar plates are often used to diagnose infection. On the right is a positive 

Streptococcus culture; on the left a positive Staphylococcus culture. 

Selective mediums are used for the growth of only select microorganisms. For 

example, if a microorganism is resistant to a certain antibiotic, such as ampicillin or 

tetracycline, then that antibiotic can be added to the medium in order to prevent other 

cells, which do not possess the resistance, from growing. Media lacking an amino acid 

such as proline in conjunction with E. coli unable to synthesize it were commonly 

used by geneticists before the emergence of genomics to map bacterial chromosomes. 

Selective growth media are also used in cell culture to ensure the survival or 

proliferation of cells with certain properties, such as antibiotic resistance or the ability 

to synthesize a certain metabolite. Normally, the presence of a specific gene or an 

allele of a gene confers upon the cell the ability to grow in the selective medium. In 

such cases, the gene is termed a marker. 

Selective growth media for eukaryotic cells commonly contain neomycin to select 

cells that have been successfully transfected with a plasmid carrying the neomycin 

resistance gene as a marker. Gancyclovir is an exception to the rule as it is used to 

specifically kill cells that carry its respective marker, the Herpes simplex virus 

thymidine kinase (HSV TK). 

Four types of agar plates demonstrating differential growth depending on bacterial 

metabolism.

Some examples of selective media include: 

• eosin-methylen blue agar (EMB) that contains methylene blue – toxic to 

Gram-positive bacteria, allowing only the growth of Gram negative bacteria 

• YM (yeast and mold) which has a low pH, deterring bacterial growth 

• blood agar (used in strep tests), which contains beef heart blood that becomes 

transparent in the presence of hemolytic Streptococcus 

• MacConkey agar for Gram-negative bacteria 

• Hektoen Enteric (HE) which is selective for Gram-negative bacteria 

• Mannitol Salt Agar (MSA) which is selective for Gram-positive bacteria and 

differential for mannitol 

• xylose lysine desoxyscholate (XLD), which is selective for Gram-negative 

bacteria 

• Buffered charcoal yeast extract agar, which is selective for certain gramnegative 

bacteria, especially Legionella pneumophila 

[edit] Differential media 

Differential media or indicator media distinguish one microorganism type from 

another growing on the same media. [4] This type of media uses the biochemical 

characteristics of a microorganism growing in the presence of specific nutrients or 

indicators (such as neutral red, phenol red, eosin y, or methylene blue) added to the 

medium to visibly indicate the defining characteristics of a microorganism. This type 

of media is used for the detection of microorganisms and by molecular biologists to 

detect recombinant strains of bacteria. 

Examples of differential media include: 

• Eosin methylene blue (EMB), which is differential for lactose and sucrose 

fermentation 

• MacConkey (MCK), which is differential for lactose fermentation 

• Mannitol Salt Agar (MSA), which is differential for mannitol fermentation 

• X-gal plates, which are differential for lac operon mutants 

[edit] Transport media 

These are used for the temporary storage of specimens being transported to the 

laboratory for cultivation. Such media ideally maintain the viability of all organisms 

in the specimen without altering their concentration. Transport media typically 

contain only buffers and salt. The lack of carbon, nitrogen, and organic growth factors 

prevents microbial multiplication. Transport media used in the isolation of anaerobes 

must be free of molecular oxygen. 

[edit] Enriched media 

Enriched media contain the nutrients required to support the growth of a wide variety 

of organisms, including some of the more fastidious ones. They are commonly used to 

harvest as many different types of microbes as are present in the specimen. Blood 

agar is an enriched medium in which nutritionally rich whole blood supplements the

asic nutrients. Chocolate agar is enriched with heat-treated blood (40-45°C), which 

turns brown and gives the medium the color for which it is named. 


• R2a agar 

• MRS agar 

• Cell biology 


1. ^ a b c Madigan M, Martinko J (editors). (2005). Brock Biology of Microorganisms, 

11th ed., Prentice Hall. ISBN 0131443291. 

2. ^ Ryan KJ, Ray CG (editors) (2004). Sherris Medical Microbiology, 4th ed., 

McGraw Hill. ISBN 0838585299. 

3. ^ Cooper GM (2000). "Tools of Cell Biology", The cell: a molecular approach. 

Washington, D.C: ASM Press. ISBN 0-87893-106-6. 

4. ^ Washington JA (1996). "Principles of Diagnosis", Baron's Medical Microbiology 

(Baron S et al, eds.), 4th ed., Univ of Texas Medical Branch. ISBN 0-9631172-1-1. 

INTESTINAL PROTOZOA 

http://www.tulane.edu/~wiser/protozoology/notes/inte 

s.html 

Lumen-Dwelling Protozoa 

Flagellates: 

Giardia lamblia 

Dientamoeba fragilis 

Chilomastix mesnili 

Enteromonas hominis 

Retortamonas intestinalis 

Trichomonas hominis 

Trichomonas tenax (oral) 

Trichomonas vaginalis 

(urogenital) 

Ameba: 

Entamoeba histolytica 

Entamoeba dispar 

Entamoeba coli 

Entamoeba hartmanni 

Entamoeba polecki 

Entamoeba gingivalis (oral) 

Endolimax nana 

Iodamoeba bütschlii

Apicomplexa: 

Cryptosporidium parvum 

Cryptosporidium hominis 

Cyclospora cayetanensis 

Isospora belli 

Microsporidia: 

Enterocytozoon bieneusi 

Encephalitozoon intestinalis 

Other: 

Blastocystis hominis 

Balantidium coli 

Numerous protozoa inhabit the gastrointestinal 

tract of humans (see Box). 

This list includes representatives from 

many diverse protozoan groups. The 

majority of these protozoa are nonpathogenic 

commensals, or only result 

in mild disease. Some of these 

organisms can cause severe disease 

under certain circumstances. For 

example, Giardia lamblia can cause 

severe acute diarrhea which may lead 

to a chronic diarrhea and nutritional 

disorders; Entamoeba histolytica can become a highly virulent and 

invasive organism that causes a potentially lethal systemic disease. 

Apicomplexa and microsporidia species (discussed elsewhere), 

which normally do not evoke severe disease, can cause severe and 

life-threatening diarrhea in AIDS patients and other 

immunocompromised individuals. Trichomonas vaginalis does not 

reside within the gastro-intestinal tract, but is often discussed with 

the intestinal flagellates. It infects the urogenital tract and and 

causes a sexually-transmitted disease. 

Intestinal protozoa are transmitted by the fecal-oral route and tend 

to exhibit similar life cycles consisting of a cyst stage and a 

trophozoite stage (Figure). Fecal-oral transmission involves the 

ingestion of food or water contaminated with cysts. After ingestion 

by an appropriate host, the cysts transform into trophozoites which 

exhibit an active metabolism and are usually motile. The parasite 

takes up nutrients and undergoes asexual replication during the 

trophic phase. Some of the trophozoites will develop into cysts 

instead of undergoing replication. Cysts are characterized by a 

resistant wall and are excreted with the feces. The cyst wall 

functions to protect the organism from desiccation in the external 

environment as the parasite undergoes a relatively dormant period

waiting to be ingested by the next host. Factors which increase the 

likelyhood of ingesting material contaminated with fecal material 

play a role in the transmission of this intestinal protozoa (see Box). 

In general, situations involving close human-human contact and 

unhygenic conditions promote 

transmission. 

TOPICS: 

• Giardiasis 

o Life Cycle and 

Morphology 

Trophozoite 

Cyst 

o The Adhesive Disk 

o Symptoms and 

Pathogenesis 

o Diagnosis 

o Treatment and Control 

• Trichomoniasis 

• Balantidosis 

• Amebiasis 

• Non-Pathogenic Commensals 

GIARDIASIS 

Giardia lamblia (also known as G. 

duodenalis, see comments on 

taxonomy) is a protozoan parasite 

that colonizes the upper portions of 

the small intestine. It has a 

worldwide distribution and is the 

most common protozoan isolated 

from human stools. The incidence is 

estimated at 200 million clinical 

cases per year. In fact, it was 

probably the first symbiotic 

Fecal-Oral Transmission Factors 

poor personal hygiene 

• children (eg, day-care 

centers) 

• institutions (eg, prisons, 

mental hospitals, orphanages) 

• food handlers 

developing countries 

• poor sanitation 

• lack of indoor plumbing 

• endemic 

• travelers' diarrhea 

water-borne epidemics 

• water treatment failures 

male homosexuality 

• oral-anal contact 

zoonosis? 

• Entamoeba = no 

• Cryptosporidium = yes 

• Giardia = controversial 

protozoan ever observed. It is quite likely that Van Leeuwenhoek, 

the inventor of the microscope, first described Giardia in 1681in his 

own stools based upon his description of its characteristic 

movement. However, van Leeuwenhoek never submitted drawings 

of the organisms and Lambl is usually given credit for the 

identification of Giardia in the stools of pediatric patients in Praque 

in 1859. 

Typically Giardia is non-invasive and often results in asymptomatic 

infections. Symptomatic giardiasis is characterized by acute or 

chronic diarrhea and/or other gastro-intestinal manifestations.

LIFE CYCLE AND MORPHOLOGY 

Giardia exhibits a typical fecal-oral transmission 

cycle (see above). The infection is acquired 

through the ingestion of cysts. Factors leading to 

contamination of food or water with fecal 

material are correlated with transmission (Box). 

For example, giardiasis is especially prevalent in 

children and particularly those children in 

institutions or day-care centers. In developing 

countries, poor sanitation contributes to the 

higher levels of giardiasis, and water-borne 

outbreaks due to inadequate water treatment 

have also been documented. Backpackers in areas of no human 

habitation are believed to acquire from drinking from streams and 

some data suggest that beavers are the reservoir. However, the 

zoonotic transmission of Giardia is controversial and has not been 

unambiguously demonstrated. It is not clear whether Giardia 

lamblia represents a single species capable of infecting a wide range 

of animals, or whether each host has their own 'pet' Giardia. 

Evidence indicating that Giardia transmission between dogs and 

humans is quite rare favors the latter. Molecular evidence suggests 

that some isolates exhibit narrow host ranges whereas others 

exhibit wide host ranges (see notes on taxonomy). Regardless of 

whether zoonotic transmission is possible, person-to-person 

transmission is the most prevalent mode of transmission and the 

risk factors are close human contact combined with unhygienic 

conditions. 

The ingested cyst passes through the stomach and excystation 

takes place in the duodenum. Excystation can be induced in vitro by 

a brief exposure of the cysts to acidic pH (~2) or other sources of 

hydrogen ions. This exposure to the acidic pH mimics the conditions 

of the stomach and probably functions as an environmental cue for 

the parasite. Flagellar activity begins within 5-10 minutes following 

the acid treatment and the trophozoite emerges through a break in 

the cyst wall. The breakdown of the cyst wall is believed to be 

mediated by proteases. The trophozoite will undergo cytokinesis 

(cell division without nuclear replication) within 30 minutes after 

emerging from the cyst resulting in two binucleated trophozoites. 

The Giardia trophozoite exhibits a characteristic pear, or tear-drop, 

shape with bilateral symmetry when viewed from the top (Figure). 

It is typically 12-15 µm long, 5-10 µm wide, and 2-4 µm thick. 

Characteristic features of the stained trophozoite include: two nuclei 

(Nu) with central karyosomes (k), fibrils running the length of the 

parasite, and median bodies (MB). The large karyosome and lack of

peripheral chromatin gives the nuclei a halo 

appearance. The fibrils are called axonemes (Ax) and 

are formed from the proximal regions of the flagella 

(Fg) within the body of the trophozoite. The median 

bodies are a pair of curved rod-shaped structures 

which lie posterior to the nuclei. At the ultrastructural 

level the median bodies contain an array of 

microtubules. The function of the median bodies is not 

known, but most believe they are somehow involved 

with the adhesive disk and its formation. An adhesive disk (AD), not 

always visible by light microscopy, occupies the ventral side of the 

anterior end. 

Giardia trophozoites possess four pairs of flagella and are motile. 

Three pairs of flagella emerge from the dorsal surface (anterior, 

posterior-lateral, caudal) and one pair emerges from the ventral 

surface. Trophozoites exhibit a distinctive erratic twisting motion, 

sometimes compared to that of a falling leaf. However, the 

trophozoites are predominantly found attached to epithelial cells of 

the small intestine (especially the duodenum and jejunum) and are 

rarely found in stools, except in the cases of severe diarrhea. This 

attachment to the intestinal epithelium is mediated by an organelle 

on the ventral side of the parasite referred to as the adhesive disk 

(see below). The trophozoite absorbs nutrients from the intestinal 

lumen via pinocytosis and no specialized feeding organelles have 

been described. 

The trophic stage is also characterized by an asexual replication. 

Both nuclei divide at about the same time and cytokinesis restores 

the binucleated state. Each daughter cell receives one copy of each 

nuclei. Both nuclei appear equal in regards to gene expression and 

other properties. 

As an alternative to replication the trophozoite can encyst. During 

encystment the parasite rounds up, detaches from the intestinal 

epithelium, and secretes a cyst wall. Encystation can also be carried 

out in vitro. Optimal induction of encystment is obtained by 

depriving the trophozoites of bile at pH 7 followed by an exposure 

to high concentrations of bile at pH 7.8. The lack of bile at neutral 

pH mimics the conditions under the mucus blanket adjacent to the 

intestinal epithelial cells, whereas exposure to high concentrations 

of bile at more alkaline pH is analogous to the intestinal lumen. 

These studies highlight the extent to which Giardia has adapted to 

life within the gastrointestinal tract. 

Molecular and ultrastructural studies reveal the synthesis of cyst 

wall proteins and the appearance of large secretory vesicles in the 

parasite cytoplasm follow the induction of encystment. After cyst

wall formation the parasite undergoes one round of nuclear division 

without cytokinesis resulting in four nuclei. These four nuclei (Nu) 

are usually located at the anterior end of the cyst (Figure). The 

flagella and adhesive disk are lost as the cyst matures, but the 

axonemes (Ax) and median bodies (MB) persist. The distinctive 

fibrils (ie, axonemes), which extend across the length of the cyst, 

result in Giardia being relatively easy to unambiguously identify. 

The cysts are oval shaped and typical measure 11-14 µm in length 

and 6-10 µm wide. Other characteristics of Giardia cysts include a 

well-defined wall (CW) which is often set apart from the cytoplasm 

of the parasite. The cysts are passed in the feces and can survive 

for up to three months under appropriate temperature and moisture 

conditions. Mature cysts are infective to the next host that happens 

to ingest them, thus completing the life cycle. 

THE ADHESIVE DISK 

A unique ultrastructural feature of Giardia is the adhesive disk (also 

called ventral disk, sucking disk, sucker, or striated disk). The 

adhesive disk is a concave structure which occupies approximately 

two-thirds of the anterior end of the ventral surface (Figure, left 

panel). As the names imply, this structure plays a role in the 

attachment of the trophozoite to the intestinal epithelium and 

ultrastructural studies reveal close associations between the 

adhesive disk and the intestinal brush border (Figure, upper right 

panel). (Click here for larger image.) 

The adhesive disk appears to be 

a relatively rigid structure and 

striations are evident by 

transmission electron 

microscopy. These striations are 

the result of microtubules (mT) 

and a unique cytoskeletal 

element called microribbons 

(mR). Microribbons are long 

flattened structures and each 

microribbon is associated with a 

microtubule (Figure, middle 

right panel). The combined microtubule-microribbon structure are 

arranged in concentric rows that form a flatten spiral with minimal 

overlap. The outer rim of the adhesive disk, called the lateral crest, 

contains components of the actin-myosin cytoskeleton. 

A major component of microribbons are proteins called giardins 

(aka beta-giardins). These giardins play primarily a structural role in 

the formation of the microribbons. Interestingly, the giardins show

a limited homology to a protein called 'striated fibre assemblin' from 

Chlamydomonas (a free-living, bi-flagellated unicellular algae). In 

Chlamydomonas this protein forms filamentous structures at the 

base of the flagella. The giardins have evolved to play a different 

functional role in Giardia, but are still associated with microtubule 

based cytoskeletal elements. 

This association of proteins involved in the generation of contractile 

force and other cytoskeletal elements in the adhesive disk suggests 

that attachment is mediated by mechanical forces generated by the 

parasite. The observation that imprints and circular dome-shaped 

lesions remain in the intestinal brush border (ie, microvilli) following 

detachment of trophozoites (Figure, lower right panel) is consistent 

with contractile forces playing a role in attachment. Other proposed 

mechanisms for the attachment of Giardia to the intestinal 

epithelium include hydrodynamic forces generated by the ventral 

flagella and receptor-mediated binding via lectins on the trophozoite 

surface. However, flagellar movement is poorly correlated with 

attachment and the surface lectins cover the entire trophozoite and 

are not specifically localized to the adhesive disk. 

SYMPTOMS AND PATHOGENESIS 

The clinical features associated with Giardia infection range from 

total latency (ie, asymptomatic), to acute self-resolving diarrhea, to 

chronic syndromes associated with nutritional disorders, weight loss 

and failure to thrive. Children exhibit clinical symptoms more 

frequently that adults and subsequent infections tend to be less 

severe than initial infections. The incubation period is generally 1-2 

weeks, but ranges of 1-75 days have been reported. 

The first signs of acute giardiasis include nausea, loss of appetite 

and an upper gastro-intestinal uneasiness. These signs are often 

followed or accompanied by a sudden onset of explosive, watery, 

foul-smelling diarrhea. Stools associated with Giardia infection are 

generally described as loose, bulky, frothy and/or greasy with the 

absence of blood or mucus, which may help distinguish giardiasis 

from other acute diarrheas. Other gastro-intestinal disturbances 

associated with giardiasis include: flatulence, bloating, anorexia, 

cramps, and foul sulfuric belching (sometimes called 'purple burbs'). 

The acute stage usually resolves spontaneously in 3-4 days and is 

often not recognized as being giardiasis. Occasionally, though, an 

acute infection will persist and lead to malabsorption, steatorrhea 

(excessive loss of fat in the feces), debility (loss of strength) and 

weight loss. Some of the individuals who resolve the acute 

symptoms do not clear the infection, but become asymptomatic cyst

passers without clinical manifestations, whereas others may have a 

few sporadic recurrences of the acute symptoms. 

Acute infections can also develop into long-standing subacute or 

chronic infections which in rare cases last for years. The typical 

chronic stage patient presents with recurrent brief episodes of loose 

foul stools which may be yellowish, frothy and float, accompanied 

by intestinal gurgling, abdominal distention and flatulence. Between 

episodes the stools are usually mushy, but normal stools or 

constipation can also occur. Cramps are uncommon during chronic 

infections, but sulfuric belching is frequent. Anorexia, nausea, and 

epigastric uneasiness are additional frequent complaints during 

chronic infections. In the majority of chronic cases the parasites and 

symptoms spontaneously 

disappear. 

The specific mechanisms of Giardia 

pathogenesis leading to diarrhea 

and intestinal malabsorption are not 

completely understood and no 

Click for larger image 

specific virulence factors have been 

identified. Attachment of trophozoites to the brush border could 

produce a mechanical irritation or mucosal injury. In addition, 

normal villus structure is affected in some patients. For example, 

villus blunting (atrophy) and crypt cell hypertrophy and an increase 

in crypt depth have been observed to varying degrees. The increase 

in crypt cells will lead to a repopulation of the intestinal epithelium 

by relatively immature enterocytes with reduced absorptive 

capacities. An increased inflammatory cell infiltration in the lamina 

propria has also been observed and this inflammation may be 

associated with the pathology. Giardia infection can also lead to 

lactase deficiency (see lactose intolerance below) as well as other 

enzyme deficiencies in the microvilli. This reduced digestion and 

absorption of solutes may lead to an osmotic diarrhea and could 

also explain the malabsorption syndromes. Thus far, no single 

virulence factor or unifying mechanism explains the pathogenesis of 

giardiasis. [See also Pathophysiology of Diarrhea for a general 

discussion of diarrhea.] 

Post-Giardia Lactose Intolerance. Some patients may present 

with a lactose intolerence during active Giardia infections which can 

persist after parasite clearance. This clinical manifestation is due to 

the parasite-induced lactase deficiency and is most common in 

ethnic groups with a predisposition for lactase deficiency. Lactase is 

an enzyme that breaks down lactose, a sugar found in milk, to 

monosaccharides which can be absorbed. This lactose intolerence 

syndrome should be considered in persons who still present mushy

stools and excessive gas following treatment, but have no 

detectable parasites. 

DIAGNOSIS 

Parasite Detection 

Stool Examination 

• 3 non-consecutive days 

• wet mount or stained 

• IFA, copro-antigens 

Duodenal Aspirate or Biopsy 

• Enterotest® 

Diagnosis is confirmed by finding cysts 

or trophozoites in feces or in 

duodenojejunal aspirates or biopsies. 

Detection of the parasites can be difficult 

since Giardia does not appear 

consistently in the stools of all patients. 

Some patients will express high levels of 

cysts in nearly all the stools, whereas 

others will only exhibit low parasite 

counts in some of the stools. A mixed 

pattern, in which periods of high cyst 

excretion alternate with periods of low 

excretion, has also been observed. In 

addition, parasites are easier to find during acute infections than 

chronic infections. Aspiration and biopsy may also fail to confirm the 

infection due to patchy loci of infection, and some question the 

usefulness of these invasive procedures. 

Stool examination is the preferred method for Giardia diagnosis. 

Three stools taken at intervals of at least two days should be 

examined. Watery or loose stools may contain motile trophozoites 

which are detectable by the immediate examination of wet smears. 

Otherwise the specimen should be preserved and stained due to 

trophozoite lability. The hardier cysts are relatively easy to 

recognize in either direct or stained smears (see cyst morphology). 

In addition, diagnostic kits based on immunofluorescence or the 

detection of copro-antigens are also available. 

Diagnosis can also be made by examining duodenal fluid for 

trophozoites. Duodenal fluid is obtained by either intubation or the 

Enterotest® (also called 'string test'). The Enterotest® consists of a 

gelatin capsule containing a nylon string of the appropriate length. 

The free end of the string is taped to the patient's face and the 

capsule is swallowed. After four hours to overnight the string is 

retrieved and the bile-stained mucus on the distal portion of the 

string is scraped off and examined by both wet mount and 

permanent staining. A small intestinal biopsy, preferably from 

multiple duodenal and jejunal sites, may also reveal trophozoites 

attached to the intestinal epithelium. [The small intestine is divided 

into 3 sections: the duodenum (first or proximal portion after the 

stomach); the jejunum (the middle portion); and the ileum (the 

distal or last portion before the large intestine).]

TREATMENT AND CONTROL 

Infected individuals should be treated since Giardia can persist and 

lead to severe malabsorption syndromes and weight loss. Treatment 

is effective at reducing morbidity and there are no sequelae. 

Metronidazole (Flagyl®), although not licensed in the United States 

for giardiasis, effectively clears the parasite (cure rates 

approximately 85%) and is the drug of choice. The recommended 

dosage is 750 mg three times per day for five days (or at least >3 

days). For children 15 mg/kg/d in three doses is recommended. 

Other effective drugs include: quinacrine (Atabrine®), tinidazole 

(Fasigyn®), furazolidone (Furoxone®), and paramomycin 

(Humatin®). Tinidazole is effective as a single two gram dose; 

paramomycin is not absorbed and may be useful during pregnancy. 

The widespread distribution of Giardia and the infectivity of the 

cysts make it unlikely that human infection will be completely 

eliminated. Control measures to prevent or reduce Giardia infection 

will depend on the specific circumstances of transmission, but in 

general involve measures which prevent the ingestion of substances 

contaminated with fecal material (see fecal-oral transmission 

factors). Health promotion and education aimed at improving 

personal hygiene, and emphasizing hand washing, sanitation and 

food handling, are effective control activities for the reduction of 

person-to-person transmission. Special attention to personal 

hygiene in high-risk situations such as day-care centers and other 

institutions is needed. Treatment of asymptomatic household 

members prevents reinfection in non-endemic areas. However, the 

value of treating asymptomatic carriers in hyperendemic 

communities is questionable since reinfection rates are high. The 

socio-economic situation in many developing countries makes it 

difficult to prevent infection. Public health measures to protect 

water supplies from contamination are required to prevent 

epidemics and to reduce endemicity. Tourists should not drink tap 

water without additional treatment in places where purity is 

questionable. Boiling or iodine treatment kills Giardia cysts, but 

standard chlorination does not. There are no safe or effective 

chemoprophylatic drugs for giardiasis. 

TRICHOMONIASIS 

• Tricomonad Morphology and Species 

• Transmission and Life Cycle 

• Symptoms and Pathogenesis 

• Diagnosis, Treatment and Control

The trichomonads are a group of flagellated protozoa. Most of the 

members of this group are parasitic and only a few free-living 

species have been identified. Generally the trichomonads are nonpathogenic 

commensals and only a few species are of importance in 

animals and humans. Four species of trichomonads infect humans 

(Table). Among these only Trichomonas vaginalis is clearly 

pathogenic and it is usually of low virulence. The others exhibit a 

questionable pathogenicity. 

Trichomonads of Humans The trichomonads of humans 

inhabit different anatomical 

Species Location locations. T. vaginalis is a 

Trichomonas vaginalis uro-genital tract common sexually transmitted 

Trichomonas tenax oral cavity disease found in the urogenital 

tract. T. tenax, also 

Pentatrichomonas hominis intestine 

called T. buccalis, is a 

Dientamoeba fragilis intestine 

commensal of the human oral 

cavity, found particularly in 

patients with poor oral hygiene and advanced periodontal disease. 

T. tenax, or an organism with similar morphology is also 

occasionally found in the lungs. Such cases have reported mainly in 

patients with underlying cancers or other lung diseases or following 

surgery. Pentatrichomonas hominis, formerly known as 

Trichomonas hominis, is a non-pathogenic commensal of the large 

intestine (see non-pathogenic intestinal flagellates). Some authors 

divide the trichomonads into three genera based on the number of 

free flagella. Species with three flagella are called Tritrichomonas, 

those with four are called Trichomonas, and Pentatrichomonas 

refers to trichomonads with five free anterior flagella. Dientamoeba 

fragilis was originally believed to be an ameba (see non-pathogenic 

intestinal ameba). Now it is know to be a flagellate—however 

without flagella—related to the trichomonads. 

A distinctive feature of the trichomonads is an axostyle (ax) which 

runs the length of the organism and appears to protrude from the 

posterior end (Figure). The axostyle is a cytoskeletal element 

composed of concentric rows of microtubules and is believed to 

function in the attachment of the parasite to epithelial cells. 

Trichomonads are also characterized by 4-6 flagella (fg) emerging 

from the anterior end. One of the flagella is attached to the body of 

the organism and forms a posteriorly-directed undulating 

membrane (um), whereas the remaining flagella are free. The 

combined basal bodies (bb) and the base of the undulating 

membrane, called the costa (cs), are often seen is stained 

preparations. Less frequently seen is the cytostomal groove (cy). A 

single nucleus (nu) is found at the anterior end of the parasite.

Schematic representation of major structural features of trichmonads (left). Giemsa-stained trophoz 

vaginalis from in vitro culture (middle). Electron micrograph of axostyle cross-section showing conce 

of microtubules (right). 

The trichomonads, like many other intestinal protozoa, exhibit an 

anerobic metabolism and lack mitochondria. Part of energy 

metabolism of trichomonads involves a unique organelle called the 

hydrogenosome. The hydrogenosome has a double membrane and 

is distantly related to the mitochondrion. However, it lacks DNA, 

cytochromes and many typical mitochnondrial functions such as 

enzymes of the tricarboxylic acid cycle and oxidative 

phosphorylation. The primary function of the hydrogenosome is the 

metabolism of pyruvate, produced during glycolysis within the 

cytosol, to acetate and carbon dioxide with the concomitant 

production of ATP. The electrons release from the oxidation of 

pyruvate are transferred to hydrogen ions to produce molecular 

hydrogen, hence the name hydrogenosome. 

TRICHOMONAS VAGINALIS 

Trichomonas vaginalis was first described from purulent vaginal 

discharges in 1836 and by the early part of the twentieth century 

was recognized as an etiological agent of vaginitis. Trichomoniasis is 

a common sexually transmitted disease with a worldwide 

distribution and an estimated 167 million people becoming infected 

per year worldwide and 5 million new infections per year in the 

United States. Trichomoniasis is believed to be the most common 

non-viral sexually transmitted disease. Despite the frequency of

trichomoniasis it has in the past been considered more of a 

nuisance parasite rather than a major pathogen. However it is now 

recognized a factor in promoting HIV infection (see Box), causing 

low-weight and premature births, and predisposing women to 

substantial discomfort and stress. 

Trichomonas and HIV 

The pathology caused by Trichomonas may enhance the efficiency of HIV transmission 

(1). T. vaginalis infection typically elicits a local cellular immune response with 

inflammation of the vaginal epithelium and cervix in women and the urethra of men. This 

inflammatory response includes the infiltration of potential HIV target cells such as CD4+ 

bearing lymphocytes and macrophages. In addition, T. vaginalis can cause punctate 

hemorrhages on the vaginal walls and cervix. This leukocyte infiltration and the genital 

lesions may increase the number of target cells for the virus and allowing direct viral 

access to the bloodstream through open lesions. In addition, the hemorrhages and 

inflammation can increase the level of virus in body fluids and the numbers of HIVinfected 

lymphocytes and macrophages present in the genital area in persons already 

infected with HIV. This increase of free virus and virus-infected leukocytes can increase 

the probability of HIV exposure and transmission to an uninfected partner. Increased 

cervical shedding of HIV has been shown to be associated with cervical inflammation, and 

substantially increased viral loads in semen have been documented in men with 

trichomoniasis. Moreover, since many patients with Trichomonas infection are 

asymptomatic, or only mildly symptomatic, they are likely to remain sexually active in 

spite of infection. 

1. Sorvillo F, Smith L, Kerndt P, Ash L. (2001) Trichomonas vaginalis, HIV, and 

African-Americans. Emerg Infect Dis. 7:927-32. 

T. vaginalis, despite its name, infects both men and women. In 

females the organism primarily inhabits the vagina, and in males it 

is usually found in the urethra, prostate or epididymis. The life cycle 

consists only of a trophozoite stage which is transmitted by direct 

contact during sexual intercourse. Non-venereal transmission is 

rare, but possible since the trophozoites can survive 1-2 days in 

urine and 2-3 hours on a wet sponge. In addition, neonatals have 

been infected during the birth process. The trophozoites live closely 

associated or attached to the epithelium of the urogenital tract, 

where they replicate by binary fission.

SYMPTOMS AND PATHOGENESIS 

Clinical Manifestations 

Females Males 

• asymptomatic 

(15-20%*) 

• vaginal discharge 

(50-75%*) 

• dyspareunia 

(50%*) 

• pruritus (25- 

50%*) 

*% of infected; **% of symptomatic 

• asymptomatic 

(50-90%*) 

• urethral discharge 

(50-60%**) 

• dysuria (12- 

25%**) 

• urethral pruritus 

(25%**) 

T. vaginalis causes 

different clinical 

manifestations in men 

and women and women 

(Table) are more likely 

to exhibit symptoms 

which tend to persist 

longer. The incubation 

period typically ranges 

from 4-28 days. In 

females the infection 

can present as a mild 

vaginitis, an acute or 

chronic vulvovaginitis, 

or urethritis. The onset 

or exacerbation of symptoms commonly occurs during or 

immediately after menstration. The most common complaint 

associated with T. vaginalis infection is a persistent mild vaginitis 

associated with a copious, foul-smelling discharge that is often 

accompanied by burning or itching. This discharge is most often 

gray, but can be yellow or green and is occasionally frothy or blood 

tinged. The discharge diminishes as the infection becomes more 

chronic. Many women also experience painful or difficult coitus. 

Urethral involvement occurs in a large number of cases and is 

characterized by dysuria (painful urination) and frequent urination. 

The vaginal epithelium is the primary site of infection. Thus the 

vaginal walls are usually erythematous (i.e., red) and may show 

petechial (a small non-raised spot) hemorrhages. Punctate 

hemorrhages of the cervix, called strawberry cervix, are observed in 

approximately 2% of the cases. This strawberry cervix is a 

distinctive pathological observation associated with trichomonasis 

not seen with other sexually transmitted diseases. 

Males are likely to be asymptomatic (50-90%) and the infection 

tends to be self-limiting. The urethra and prostate are the most 

common sites of infection. Common symptoms include: urethral 

discharge (ranging from scant to purulent), dysuria, and urethral 

pruritus (itching). Some men experience burning immediately after 

coitus. 

Little is known about the pathophysiology associated with T. 

vaginalis infection, but is presumably due to interactions between 

the parasite and host epithelial cells. In vitro studies indicate that T. 

vaginalis can destroy cells in a contact dependent manner. 

Therefore adhesion of the trophozoites to the epithelium is believed

to be a major factor in the pathogenesis. Several adhesion proteins 

have been identified on the surface of the trophozoites. In addition, 

secreted proteases that could play a role in pathogenesis have also 

been identified. 

DIAGNOSIS, TREATMENT AND CONTROL 

In general, the clinical manifestations are not reliable as sole means 

of diagnosis since the clinical presentation is similar to other STDs 

and many patients have mild or no symptoms. Diagnosis is 

confirmed by the demonstration of trophozoites in vaginal, urethral, 

prostatic secretions, or urine sediment (following prostate 

massage). Microscopic examination of wet mounts of fresh vaginal 

discharge, preferably collected with a speculum on a cotton-tipped 

applicator, is the most practical method of diagnosis. Specimens 

should be diluted in saline and examined immediately. T. vaginalis 

is recognized by its characteristic morphological features (see 

above) and its rapid jerky motility. Specimens can also be fixed and 

stained with Giemsa or fluorescent dyes. However, the organism 

may be difficult to recognize on stained slides. 

The sensitivity of direct observation ranges from 40-80%. 

Therefore, in vitro culture is considered the gold standard for 

diagnosis despite some limitations. For example, access to facilities 

is needed and organisms require 2-7 days of growth before they are 

detected. The accessibility issue is partly resolved by the 

InPouchTV culture system (Biomed Diagnostics). This is a 

commercially available self-contained system for the detection of T. 

vaginalis in clinical specimens. Antibody and DNA-based tests with 

high sensitivity and specificity are being developed. 

Metronidazole (Flagyl®) and other nitroimidazoles, such as 

tinidazole, are highly effective against trichomoniasis. The 

metronidazole is activated by the hydrogensome to a nitro radical 

ion intermediate. Either a single two gram dose (85-92% cure rate) 

or 250 mg three time daily for 7-10 days (>95% cure rate) can be 

used. Sexual partners should be treated at the same time to 

prevent reinfection. Some drug resistance has been reported, but 

this is not a wide-spread problem. Treatment failures are generally 

due to noncompliance or reinfection. 

Trichomoniasis as an STD 

• 5% females attending 

family planning clinics 

• 7-32% females attending 

venereal disease clinics 

• 50-75% prostitutes

The epidemiology of trichomonasis 

exhibits features similar to other 

sexually transmitted diseases (Box) 

and incidence correlates with the 

number of sexual partners. In 

addition, co-infection with other STDs 

is common. It is estimated that up to 25% of sexually active women 

will become infected at some point during their lives and the 

disease will be transmitted to 30-70% of their male partners. 

Measures used in the control of other STD, such as limiting number 

of sexual partners and use of condoms, are also effective in 

preventing trichomoniasis. 

Reviews on Trichomoniasis: 

• Lehker, M.W. and Alderete, J.F. (2000) Biology of 

trichomonosis. Current Opinion in Infectious Diseases 13, 37- 

45. 

• Petrin, D., Delgaty, K., Bhatt, R., Garber, G. (1998) Clinical 

and microbiological aspects of Trichomonas vaginalis. Clin. 

Microbiol. Rev. 11: 300-317. 

• Schwebke, J.R. and Burgess, D. (2004) Trichomoniasis. 

Clinical Microbiology Reviews 17, 794-803. 

DIENTAMOEBA FRAGILIS 

• 4% males attending 

venereal disease clinics 

• 5-15% males with nongonococcal 

urethritis 

Dientamoeba fragilis was originally described as an ameba based 

upon its morphology. However, later it was recognized to exhibit a 

morphology more similar to the turkey parasite Histomonas 

meleagridis, except for the lack of flagella. Ultrastructural studies 

also suggest similarities to the trichomonads, including the 

possession of hydrogenosomes and molecular studies have 

confirmed a close phylogenetic relationship between Dientamoeba 

and Histomonas and a possible more distal relationship to 

Trichomonas. 

As with other trichomonads, Dientamoeba only exhibits a 

trophozoite stage (Figure). This raises some questions about the 

mode of transmission in that a cyst stage is usually involved in fecal 

oral transmission. In addition, the trophozoites of Dientamoeba 

survive outside of the body for a very short time. H. meleagridis 

also lacks a cyst stage and has been demonstrated to be 

transmitted via the eggs of a nematode. Due to the close 

relationship between Histomonas and Dientamoeba, it is proposed 

that Dientamoeba is also transmitted via helminth eggs. 

Epidemiological and experimental evidence tends to incriminate the 

pinworm Enterobius vermicularis as the carrier for Dientamoeba.

Morphology of Dientamoeba fragilis from a stool sample. Trophozoites exhibit an amebalike 

morphology and are often bi-nucleated. 

Historically Dientamoeba has been considered as a non-pathogenic 

commensal. However, clinical symptoms often correlate with the 

presence of large numbers of trophozoites and treatment of the 

infection resolves the symptoms. The incidence of symptoms is 

estimated at 15-30% of infected individuals. Clinical symptoms 

associated with Dientamoeba include intermittent diarrhea, 

abdominal pain, flatulence, nausea and fatigue. Little is known 

about the pathogenesis and Dientamoeba probably acts as a lowgrade 

irritant of intestinal mucosal surfaces that may lead to some 

inflammation. Iodoquinol is generally the drug of choice for the 

treatment of Dientamoeba. Tetracycline, paromomycin, and 

metronidazole are also effective. 

For a comprehensive review of Dientamoeba see: Johnson et al, 

Clin. Microbiol. Rev. 17:553, 2004.

BALANTIDOSIS 

Balantidium coli is the only ciliate which infects 

humans. It is found world wide, but like many other 

fecal-oral transmitted diseases, it is more prevalent 

in the tropics. However, prevalence rates rarely 

exceed 1%. B. coli also infects a wide variety of 

mammals and is especially common in monkeys and 

pigs. Prevalence in pigs ranges from 20–100% and 

human balantidiosis usually exhibits an increased 

prevalence in communities that live in close 

association with pigs. For example, in Papua New 

Guinea, where pigs are the principal domestic 

animals, the prevalence among swine herders and 

slaughterhouse workers has been reported to be as 

high as 28%. Human-to-human transmission has also been 

documented and this mode of transmission is likely to occur in 

environments with crowding and poor personal hygiene such as 

mental hospitals and prisons. (Skip general ciliate biology) 

GENERAL CILIATE BIOLOGY 

Ciliates are a large and diverse group of protozoa. Most ciliates are 

free-living and are found in a variety of habitats. Well-known 

ciliates include Paramecium species, which are found in ponds 

throughout the world, and Ichthyophthirius multifiliis, an 

ectoparasite of fish that causes white spot disease (also called 'ick'). 

As the name implies, ciliates possess cilia at some point during their 

life cycles. The cilia are generally arranged in longitudinal rows and 

typically cover the surface of the organism. Ciliates are also 

characterized by nuclear dimorphism in that they have two distinct 

nuclei. The large kidney-shaped macronucleus is involved in the 

'housekeeping' or somatic functions of the cell, whereas the smaller 

spherical micronucleus contains the complete genome. The 

macronucleus contains thousands of copies of transcriptionally 

active 'minichromosomes' representing 10-20,000 different DNA 

molecules. This large number of telomeres (chromosome ends) 

resulted in ciliates being an early model system for the study of 

telomeres and telomerase (the enzyme that synthesizes telomeres).

Ciliates undergo both an asexual reproduction (ie, binary fission) 

and a sexual reproduction involving conjugation (Figure above). 

During conjugation, two ciliates of opposite mating types pair and 

exchange genetic material. Conjugal contact triggers meiosis in the 

micronuclei resulting in 4 haploid micronuclei. Concurrently, the 

macronucleus breaks down and disappears. Three of the micronuclei 

disintegrate and the remaining micronucleus divides again. Each of 

the conjugating organisms donates a micronucleus (gametic or 

male) to its mate via a cytoplasmic bridge that connects them. The 

gametic micronucleus fuses with the stationary (or female) 

micronucleus forming the diploid zygotic micronucleus. The 

conjucating pair separates and the zygotic nucluei undergo another 

round of division. One of these micronuclei develops into the the 

macronucleus, thus completing the cycle. Formation of the 

macronucleus involves fragmentation of the chromosomes and loss 

of some DNA sequences. The remaining minichromosomes are then 

amplified. (See diagram of DNA processing during macronucleus 

formation.) 

BALANTIDOSIS 

B. coli usually lives as a non-pathogenic commensal in the large 

intestine and produces no symptoms. Superficial inflammation of 

the colonic mucosa may occur which can result in diarrhea and 

colicky pain. Mild or chronic infections are characterized by 

intermittent diarrhea and constipation, weight loss, and abdominal 

pain. On rare occasions the trophozoites will invade the intestinal 

epithelium and produce ulceration. Clinically this results in an acute

diarrhea with mucus and blood (ie, dysentery). This balantidial 

dysentery is similar to the dysentery produced by Entameoba 

histolytica (see below). Rare extra-intestinal infections involving 

lungs, vagina, ureter and urinary bladder and intestinal perforations 

leading to peritonitis have been reported. 

Laboratory diagnosis is made by identifying the organism in feces. 

Balantidium exhibits a typical fecal-oral life cycle consisting of 

trophozoite and cyst stages. The large size and unique 

morphological features of Balantidium (Figure) precludes its 

confusion with any other protozoa found in human feces. The 

trophozoite is ovoid and has an average size of 70 x 45 µm, but can 

range upwards to 150-200 µm. The cyst has a distinctive cyst wall 

(CW) and is more spherical with an average diameter of 55 µm. In 

stained specimens the most obvious internal structure is the large 

macronucleus (maN). The micronucleus (miN) may not always be 

apparent because of its close association with the macronucleus. 

Contractile vacuoles (CV), which function in osmotic regulation, are 

often visible and occasionally the cytostome (Cy) is detectable. 

Similar to many other ciliates, Balantidium is covered by rows of 

cilia. The cilia give the parasite surface a fuzzy appearance and are 

less pronounced in the cyst stage. 

The treatment of choice is tetracycline given at 500 mg four times 

per day for 10 days. Iodoquinol is the recommended alternate drug. 

Metronidazole has not produced consistent results. Preventive 

measures are the same as other diseases transmitted by the fecaloral 

route (see fecal-oral transmission factors or discussion of 

Giardia prevention). In addition, pig sewerage should be kept away 

from supplies of drinking water and food. 

AMEBIASIS 

Several members of the genus Entamoeba infect humans (see 

below). Among these only E. histolytica is considered pathogenic 

and the disease it causes is called amebiasis or amebic dysentery. 

E. dispar is morphologically identical to E. histolytica and the two 

were previously considered to be the same species. However, 

genetic and biochemical data indicate that the non-pathogenic E. 

histolytica is a distinct species (see discussion of criteria). The two 

species are found throughout the world, but like many other 

intestinal protozoa, they are more common in tropical countries or 

other areas with poor sanitary conditions. It is estimated that up to 

10% of the world's population may be infected with either E. 

histolytica or E. dispar and in many tropical countries the 

prevalence may approach 50%. There are an estimated 50 million 

cases of amebiasis per year and up to 100,000 deaths.

• Life Cycle and Morphology 

• Pathogenesis 

• Possible Mechanisms of Pathogenisis 

o Schematic Figure of Trophozoite 

Invasion 

• Clinical Presentation 

• Diagnosis, Treatment and 

Control 

LIFE CYCLE AND MORPHOLOGY 

E. histolytica exhibits a typical fecal-oral life cycle consisting of 

infectious cysts passed in the feces and trophozoites which replicate 

within the large intestine. The infection is acquired through the 

ingestion of cysts and the risk factors are similar to other diseases 

transmitted by the fecal-oral route (see Table). Contaminated food 

and water are probably the primary sources of infection. The higher 

prevalence in areas of lower socioeconomic status is likely due to 

poor sanitation and a lack of indoor plumbing. However, E. 

histolytica is rarely the cause of travelers' diarrhea and is usually 

associated with a long-term (>1 month) stay in an endemic area. A 

higher prevalence of E. histolytica infection is also observed in 

institutions, such as mental hospitals, orphanages and prisons, 

where crowding and problems with fecal contamination are 

contributing factors. A high prevalence among male homosexuals 

has also been noted. Humans are the only host of E. histolytica and 

there are no animal reservoirs. 

Upon ingestion the cysts pass through the stomach and excyst in 

the lower portion of the small intestine. Excystation involves a 

disruption of the cyst wall and the quadranucleated ameba emerges 

through the opening. The ameba undergoes another round of 

nuclear division followed by three successive rounds of cytokinesis 

(ie, cell division) to produce eight small uninucleated trophozoites, 

sometimes called amebulae. These immature trophozoites colonize 

the large intestine, especially the cecal and sigmoidorectal regions, 

where they feed on bacteria and cellular debris and undergo 

repeated rounds of binary fission. 

E. histolytica trophozoites have an amorphous shape and are 

generally 15-30 µm in diameter. The trophozoites move by 

extending a finger-like pseudopodium (psd) and pulling the rest of 

the body forward (called ameboid movement). The pseudopodia, 

and sometimes the outer edge of the trophozoite, have a clear 

refractile appearance and is referred to as the ectoplasm (ecto). The 

rest of the cytoplasm has a granular appearance and is called the 

endoplasm (endo). Occasionally a glycogen vacuole (vac) is evident.

Nuclear (Nu) morphology in stained specimens 

is characterized by a finely granular ring of 

peripheral chromatin and a centrally located 

karyosome (ka). 

As an alternative to asexual replication 

trophozoites can also encyst. The factors 

responsible for the induction of encystation 

are not known. Encystation begins with the 

trophozoites become more spherical and the 

appearance of chromatoid bodies in the 

cytoplasm. Chromatoid bodies (cb) are stained 

elongated structures with round ends and 

represent the aggregation of ribosomes. The cyst wall is composed 

of chitin and has a smooth refractile appearance. Cyst maturation 

involves two rounds of nuclear replication without cell division and 

cysts with 1-4 nuclei (Nu) are found in feces. The nuclear 

morphology of the cyst is similar to that of the trophozoite except 

that the nuclei become progressively smaller following each 

division. Sometimes the young cysts (ie, 1-2 nuclei) will have a 

glycogen vacuole (vac) which will appear as a clear area in stained 

specimens. This vacuole will sometimes displace and alter the 

morphology of the nuclei. The chromatoid bodies tend to disappear 

as the cyst matures. The cysts are generally 12-15 µm in diameter. 

Cysts are immediately infective upon excretion with the feces and 

will be viable for weeks-to-months depending on environmental 

conditions. 

PATHOGENESIS 

non-invasive 

Amebiasis Progression 

• ameba colony on mucosa surface 

o asymptomatic cyst passer 

o non-dysenteric diarrhea 

invasive 

• necrosis of mucosa → ulcer 

o dysentery 

o hematophagous trophozoites 

• ulcer enlargement → peritonitis 

o occasional ameboma 

• metastasis → extraintestinal 

amebiasis 

o via blood-stream or direct

E. histolytica frequently lives as 

a commensal within the large 

intestine with no overt clinical 

manifestations. However, 

trophozoites can invade the 

colonic epithelium and produce 

ulcers and dysentery (see Box). 

extension 

o primarily liver → amebic 

abscess 

o other sites infrequent 

o ameba-free stools common 

This invasive disease can become progressively worse and lead to a 

more serious disease. The amebas can also metastasize to other 

organs and produce anextraintestinal amebiasis. In other words, E. 

histolytica is a facultative pathogen that exhibits a wide range of 

virulence. 

The non-invasive disease is often asymptomatic, but can cause 

diarrhea or other gastro-intestinal symptoms such as abdominal 

pain or cramps. This non-invasive infection can persist or progress 

to an invasive disease in which trophozoites penetrate the intestinal 

mucosa and kill the epithelial cells. The early lesion is a small area 

of necrosis, or ulcer, characterized by raised edges and virtually no 

inflammation between lesions (Figure). The ameba will spread 

laterally and downward in the submucosa (beneath the epithelium) 

and kill host cells as they progress. This results in the classic 'flaskshaped' 

ulcer with a small opening and a wide base. Trophozoites 

are most numerous at the boundary between the healthy tissue and 

the necrotic tissue. These invasive ameba are ingesting host cells 

and trophozoites with ingested erythrocytes are often evident. 

These hematophagous trophozoites are sometimes found in the 

dysenteric feces. Cyst production decreases during the invasive 

stage of the infection and cysts are never found in the tissue 

lesions. 

Left: The lumenal side of the colon from fulminating amebiasis case showing several ulcers. Note 

raised edges (arrow). Middle: Histological preparation showing cross-section of ulcer. Note the 

high degree of necrosis in center of ulcer. The amebas are advancing laterally under the intact 

mucosa as indicated by the microvilli. Right: Higher magnification of ulcer showing several 

hematophagous trophozoites. The nucleus (arrow) is evident in one of the amebas. Pictures from

Peters and Gilles (1989), A Colour Atlas of Tropical Medicine and Parasitology (3rd edition). 

E. histolytica is found primarily in 

the colon where it can live as a 

non-pathogenic commensal or 

invade the intestinal mucosa 

(green). The ameba can 

metastasize to other organs via a 

hematogenous route (purple); 

primarily involving the portal vein 

and liver. The ameba can also 

spread via a direct expansion 

(blue) causing a pulmonary 

infection, cutaneous lesions or 

perianal ulcers. 

The ulcerative process may continue 

to expand laterally or downward. If 

large numbers of ulcers are present, 

they may coalesce which could lead 

to a localized sloughing off of the 

intestinal wall. Ulcer expansion can 

also penetrate the serous layer and 

lead to perforation of the intestinal 

wall. This perforation can lead to 

local abscesses or a generalized 

peritonitis. (See also schematic 

representation of tissue invasion.) 

Amebic ulcers can also become 

secondarily infected with bacteria 

which may confuse the clinical 

picture. In addition, E. histolytica 

infection can occasionally lead to the 

formation of an amebic granuloma, 

also called an ameboma. The 

ameboma is an inflammatory 

thickening of the intestinal wall 

around the ulcer which can be 

confused with a tumor. 

Amebiasis can also progress to a 

systemic, or extraintestinal infection. 

Dissemination from the primary 

intestinal lesion is predominantly via 

the blood stream, but can also occur 

by direct extension of the lesion. The 

liver is the most commonly affected 

organ and this is probably due to the 

direct transport of trophozoites from 

the large intestine to the liver via the 

hepatic portal vein (Figure). Initially 

the lesions are small foci of necrosis 

which tend to coalesce into a single 

abscess as they expand. This hepatic 

abscess will continue to enlarge as the trophozoites progressively 

destroy and ingest host cells. The center of the abscess, consisting 

of lysed hepatocytes, erythrocytes, bile and fat, may liquefy and 

this necrotic material (sometimes incorrectly called pus) will range 

in color from yellowish to reddish brown. Secondary bacterial 

infections in the liver abscess are not common (~2%).

Hematogenous spread of trophozoites to other sites, such as the 

lungs or brain, is rare, but does occur. The second most common 

extraintestinal site after the liver is the lungs. Pulmonary infections 

generally result from a direct extension of the hepatic lesion across 

the diaphragm and into the pleura and lungs. Cutaneous lesions 

formed as a result of hepatic or intestinal fistula can also occur, 

although extremely rare. Other cutaneous lesions include perianal 

ulcers and involvement of the genitalia, including the penis of 

homosexuals. These later manifestations are likely due to the skin 

or mucous membranes coming in contact with invasive 

trophozoites. 

POSSIBLE MECHANISMS OF 

PATHOGENESIS 

As discussed above, E. histolytica is 

pathogen that exhibits a wide 

spectrum of virulence, ranging from 

an avirulent commensal to a highly 

invasive and destructive organism 

(see discussion of pathogenicity vs. 

virulence). Some of this difference in 

virulence is explained by the 

existence of the morphologically 

identical, but avirulent, E. dispar. E. 

dispar has never been associated with 

a symptomatic invasive disease and 

infection does not elicit serum 

Entamoeba Prevalences 

• E. dispar ~10-fold > E. 

histolytica 

• discrete endemic pockets of 

E. histolytica observed 

• ~25% seropositive for E. 

histolytica in endemic areas 

• ~10% infected with E. 

histolytica will develop 

invasive amebiasis 

antibodies. In contrast, anti-ameba humoral responses are 

observed in both asymptomatic and symptomatic E. histolytica 

infections. This suggests that even in asymptomatic cases there is a 

limited amount of invasion. However, infection with E. histolytica 

does not always lead to invasive disease, though, in that only about 

10% of the infected individuals will develop symptomatic invasive 

amebiasis. The factors responsible for the pathogenesis of E. 

histolytica are not well understood. One approach to understanding 

the pathogenesis is to compare possible virulence factors between 

these two closely related species. 

Possible Virulence Factors 

host factors 

• ineffective innate immunity 

• inflammatory response

parasite factors 

• resistance to host response 

(eg, complement resistance) 

• adherence properties (eg, 

'Eh-lectin') 

• cytolytic properties (eg, 

adherence + 'amebapore') 

• ability to breakdown tissues 

(eg, secreted proteases) 

Pathology results from host-parasite 

interactions, and therefore, host 

factors, parasite factors or a 

combination of both may contribute 

to the disease state. For example, the 

development of invasive disease 

could be due to quantitative or 

qualitative aspects of the host 

immune response. Recruitment of 

neutrophils and intense inflammation 

are noted in the early phases of 

amebic invasion. However, 

inflammation surrounding established ulcers and abscesses if often 

minimal given the degree of tissue damage. 

The nature of protective immune responses is not clear. Innate or 

nonspecific immunity, as well as acquired immunity, are probably 

both important for the prevention of invasive disease. The mucous 

layer covering the epitheilial cells can prevent contact between 

trophozoite and host cells. In addition, mucosal IgA responses do 

occur as a result of infection and fecal IgA against a trophozoite 

surface lectin (see Eh-lectin) are associated with a lower incidence 

of new E. histolytica infections. High titers of serum antibodies also 

develop in patients with liver abscesses. However, since the 

invasive disease is often progressive and unremitting, the role of 

these anti-ameba antibodies is in question. Cell-mediated responses 

appear to play a role in limiting the extent of invasive amebiasis 

and protecting the host from recurrence following successful 

treatment. 

Resistance to the host immune response is another possible 

virulence factor which could contribute to the development and 

exacerbation of invasive disease. For example, one phenotypic 

difference between E. dispar and E. histolytica is the resistance of 

the latter to complement mediated lysis (see E. dispar). In addition, 

E. histolytica rapidly degrades secretory IgA and possibly 

suppresses T-cell responses to E. histolytica antigens. E. histolytica 

is also able to kill cells, including neutrophils and other immune 

effector cells, in a contact dependent manner. Lysis of neutrophils 

could also release toxic products which contribute to the destruction 

of host tissue. However, the role of these various phenomena in 

pathogenesis is not known. 

Invasion of intestinal mucosa by E. histolytica is an active process 

mediated by the parasite and distinct steps can be recognized 

(Figure, click here for larger image and detailed legend). 

Trophozoites adhere to the mucus layer (step 1). This adherence

per se probably does not contribute to pathogenesis and is simply a 

mechanism for the ameba to crawl along the substratum. Depletion 

of the mucus barrier allows for the trophozoite to come in contact 

with epithelial cells. Epithelial cells are killed in a contact dependent 

manner leading to a disruption of the intestinal mucosa (step 2). 

The trophozoites will continue to kill host cells in the submucosa 

and further disrupt the tissue as they advance (step 3). Disruption 

of the intestinal wall (step 4) or metastasis via the circulatory 

system (step 5) is also possible. Adherence, cytotoxicity, and 

disruption of the tissues are important factors in the pathogenesis 

of E. histolytica. Parasite proteins which could play a role in these 

processes include: the Eh-lectin, amebapore, and proteases. 

(Skip detailed discussions of Eh-lectin, amebapore, and proteases and go to 

clinical symptoms.) 

Eh-lectin. E. histolytica can kill cells within minutes of adhering to 

them in the presence of extracellular calcium. Adherence of E. 

histolytica trophozoites to host cells and colonic mucins is mediated 

by a lectin-activity expressed on the ameba's surface. This lectin 

binds galactose or N-acetyl-D-galactosamine (GalNAc) with a high 

affinity and is also called the galactose-inhibitable adherence 

protein (GIAP) or the Gal/GalNAc lectin. The contact-dependent 

killing of target cells is almost completely inhibited by galactose or 

GalNAc and target cells lacking terminal galactose residues on their 

surface glycoproteins are resistant to trophozoite adherence and 

cytotoxicity. This suggests that the Gal/GalNAc lectin is an 

important virulence factor. In addition, the Eh-lectin is involved in 

resistance to complement mediated lysis. Because of its potential 

role in adherence and virulence and since fecal IgA against it 

protect against amebic colitis, the Gal/GalNAc is a vaccine candidate 

(Petri et al, 2006, Arch. Med. Res. 37:288).

The Eh-lectin is a heterodimer consisting of a 170 kDa heavy chain 

and a 31-35 kDa light chain joined by disulfide bonds. An 

intermediate subunit of 150 kDa is noncovalently associated with 

the heterodimer. The heavy chain has a transmembrane domain 

and a carbohydrate binding domain. All of subunits are encoded by 

multigene families. There are five members of the heavy chain 

family, 6-7 members of the light chain family and 30 members of 

the intermediate chain family. The members of the heavy chain 

gene family exhibit 89-95% sequence identity at the amino acid 

level whereas the light chain family members are less conserved 

sharing only 79-85% sequence identity. 

E. dispar also expresses Gal/GalNAc lectin on its surface. Both E. 

dispar and E. histolytica need to adhere to the mucous layer which 

is medicated by the Gal/GalNAc lectin. Mucus is composed of 

glycoproteins called mucins. The predominant mucin found on the 

intestinal mucosa is Muc2 which is extensively glycosylated with Olinked 

GalNAc residues. The sequence of the light and heavy chain 

genes from E. dispar are homologous, but not identical, to those of 

E. histolytica. Antigenic differences between the GIAP of E. dispar 

and E. histolytica have also been described in that only two epitopes 

out of six are shared between the two species (see E. dispar). It is 

not known whether these sequence differences can account for the 

differences in virulence between E. dispar and E. histolytica. 

Adherence is obviously important for both species, but it is possible 

that the adherence is qualitatively or quantitatively different 

between the two species. 

[Review on the Eh-lectin: Petri et al (2002) Annu. Rev. Microbiol. 

56:39.] 

Amebapore. A family of pore-forming polypeptides has been 

identified in E. histolytica and E. dispar. The three family members 

are designated as amebapore A, B and C with amebapore A being 

predominant expressed. The mature polypeptide is 77 amino acids 

long and forms dimers at low pH (4-6). Three of these dimers then 

assemble into a hollow ring-shaped structure. This hexamer then 

can intercalate into membranes and introduce 2 nm pores (i.e., 

holes) which results in cell death. The pore-forming activity is 

dependent on this assembly process beginning with the 

dimerization. Amebabpore A is 95% identical (i.e., four residues are 

different) between E. histolytica and E. dispar. In addition, the E. 

dispar amebapore has approximately half of the pore-forming 

activity as the E. histolytica amebapore. This difference in poreforming 

activity has been attributed to a glutamate residue at 

position 2 in the E. histolytica amebapore, as compared to a proline 

residue in the E. dispar amebapore. This particular amino acid

esidue is important for the formation of the dimers and it is 

believed that the dimers of E. dispar amebapore are less stable. 

Amebapore is localized to vacuolar compartments (eg, food 

vacuoles) within the trophozoite and is most active at acidic pH 

suggesting that the major function of amebapore is to lyse ingested 

bacteria. Nonetheless, amebapore is implicated as a virulence factor 

in that genetic manipulation of E. histolytica resulting in decreased 

expression of amebapore leads to a reduction in pathogenicity 

(ability to form liver abscesses) as well as a reduction in 

bacteriocidal activity (Bracha et al Mol. Microbiol. 34:363, 1999). 

Similarly, modified E. histolytica completely devoid of amebapore 

production are unable to form liver abscesses in model systems 

(Zhang et al, Inf. Imm. 72:678, 2004). However, these amebas are 

able to cause inflammation and tissue damage in models for amebic 

colitis. 

[Review on amebapore: Leippe et al, Tr. Parasitol. 21:5, 2005.] 

Proteases. Proteases are enzymes that degrade other proteins and 

could contribute to the pathogenesis cause by E. histolytica. In this 

regard, E. histolytica expresses and secretes higher levels of 

cysteine proteases, a particular class of protease, than E. dispar. 

Cysteine proteases have been shown to disrupt the polymerization 

of MUC2, the major component of colonic mucus. This degraded 

mucus is less efficient at blocking adherence of trophozoites to 

epithelial cells. Destruction of the extracellular matrix (ECM) by 

proteases may also facilitate trophozoite invasion. Inhibitors of 

cysteine proteases can decrease liver abscess size in experimental 

models. 

Twenty different cysteine 

protease genes have been 

identified in E. histolytica. 

Orthologs of two of the E. 

histolytica cysteine protease 

genes are not found in E. 

dispar. One of these, 

designated CP5, is expressed at 

high levels on the trophozoite 

surface. Mutants expressing 

lower levels of CP5 had a 

reduced ability to generate liver 

abscesses in a hamster 

amebiasis model. However, 

these mutants also had a 

reduced growth rate and lower 

erythrophagocytic activity, thus 

Figure from Horstmann et al (1992) Trop. Med. 

Parasitol. 43, 213. 

Factor histolytica vs dispar 

Eh-lectin 

sequence and epitope 

differences 

amebapore Ed has less activity (Pro/Glu) 

proteases 

Eh has unique genes and 

expresses more activity 

Figure from Horstmann et al (1992) Trop. Med. 

Parasitol. 43, 213.

it is not clear whether CP5 directly participates in the invasiveness 

of E. histolytica. Furthermore inhibition of 90% of CP5 activity did 

not affect the ability of E. histolytica trophozoites to destroy cell 

monolayers in vitro. CP1, CP2, and CP5 are the most abundantly 

expressed cysteine proteases in E. histolytica, whereas CP3 is the 

most abundant in E. dispar. Interestingly, over expression of CP2 in 

E. dispar increased the ability of trophozoites to destroy cell 

monolayers in vitro. However, the over expression of CP2 did not 

lead to the ability of E. dispar to form liver abscesses in gerbils. 

Therefore, it is not clear the precise roles proteases may play in 

pathogenesis. 

In summary, the pathogenesis associated with E. histolytica 

infection is primarily due to its ability to invade tissues and kill host 

cells. Several potential virulence factors have been identified (see 

Table). However, it is not clear the exact role these various 

virulence factors play in the development of invasive disease. One 

approach to understanding the pathogenesis is to compare these 

factors from E. histolytica and E. dispar. These two species are 

closely related and the potential virulence factors are found in both 

species. Adherence, cytolytic activity and proteolytic activity are 

inherent biological features of both species and these activities do 

not necessarily lead to pathology. However, there are qualitative 

and quantitative differences between E. histolytica and E. dispar 

which may account for the differences in virulence. These genetic 

differences between E. histolytica and E. dispar indicate that 

pathogenesis is in part an inherent feature of the parasite. 

However, pathogenesis is probably due to the combined effects of 

several host and parasite factors, and the virulence may represent 

the degree to which the host can control trophozoite invasion and 

replication. 

[See Huston, 2004, Tr. Parasitol. 20:23 for review of 

pathogenesis.] 

CLINICAL PRESENTATION 

Amebiasis presents a wide range of clinical syndromes (Table) 

which reflects the potential for E. histolytica to become invasive and 

cause a progressive disease. The incubation period can range from 

a few days to months or years with 2-4 weeks being the most 

common. Transitions from one type of intestinal syndrome to 

another can occur and intestinal infections can give rise to 

extraintestinal infections. 

Clinical Syndromes

Clinical Syndromes 

Associated with Amebiasis 

Intestinal Disease 

• asymptomatic cyst passer 

• symptomatic nondysenteric 

infection 

• amebic dysentery (acute) 

• fulminant colitis 

o + perforation 

(peritonitis) 

• ameboma (amebic 

granuloma) 

• perianal ulceration 

Extraintestinal Disease 

• liver abscess 

• pleuropulmonary amebiasis 

• brain and other organs 

• cutaneous and genital 

diseases 

The majority of individuals diagnosed 

with E. histolytica (or E. dispar) 

exhibit no symptoms or have vague 

and nonspecific abdominal 

symptoms. This state can persist or 

progress to a symptomatic infection. 

Symptomatic nondysenteric 

infections exhibit variable symptoms 

ranging from mild and transient to 

intense and long lasting. Typical 

symptoms include: diarrhea, cramps, 

flatulence, nausea, and anorexia. The 

diarrhea frequently alternates with 

periods of constipation or soft stools. 

Stools sometimes contain mucus, but 

there is no visible blood. 

Amebic dysentery usually starts 

slowly over several days with 

abdominal cramps, tenesmus, and 

occassional loose stools, but 

progresses to diarrhea with blood 

and mucus. Blood, mucus and pieces of necrotic tissue become 

more evident as the number of stools increases (10-20 or more per 

day) and stools will often contain little fecal material. A few patients 

may develop fever, vomiting, abdominal tenderness, or dehydration 

(especially children) as the severity of the disease increases. 

Fulminant, or grangrenous, colitus is a rare but extremely severe 

form of intestinal amebiasis. Patients present with severe bloody 

diarrhea, fever, and diffuse abdominal tenderness. Most of the 

mucosa is involved and mortality exceeds 50%. A chronic 

amebiasis, characterized by recurrent attacks of dysentery with 

intervening periods of mild or moderate gastrointestinal symptoms, 

can also occur. 

Amebomas present as painful abdominal masses which occur most 

frequently in the cecum and ascending colon. Obstructive symptoms 

or hemorrhages may also be associated with an ameboma. 

Amebomas are infrequent and can be confused with carcinomas or 

tumors. Perianal ulcers are a form of cutaneous amebiasis that 

result from the direct spread of the intestinal infection. 

Amebic liver abscesses are the most common form of extraintestinal 

amebiasis. The onset of hepatic symptoms can be rapid or gradual. 

Hepatic infections are characterized by hepatomegaly, liver 

tenderness, pain in the upper right quadrant, fever and anorexia. 

Fever sometimes occurs on a daily basis in the afternoon or

evening. Liver function tests are usually normal or slightly abnormal 

and jaundice is unusual. Liver abscesses will occasionally rupture 

into the peritoneum resulting in peritonitis. 

Pulmonary amebiasis is generally results from the direct extension 

of the liver abscess through the diaphragm. Clinical symptoms most 

often include cough, chest pain, dyspnea (difficult breathing), and 

fever. The sputum may be purulent or blood-stained and contain 

trophozoites. A profuse expectoration (ie, vomica) of purulent 

material can also occur. Primary metastasis to the lungs is rare, but 

does occur. Similarly, infection of other organs (eg., brain, spleen, 

pericardium) is also rare. Clinical symptoms are related to the 

affected organ. 

Cutaneous amebiasis is the result of skin or mucus membranes 

being bathed in fluids containing trophozoites. This contact can be 

the result of fistula (intestinal, hepatic, perineal) or an invasion of 

the genitalia. Cutaneous lesions have a wet, granular, necrotic 

surface with prominent borders and can be highly destructive. 

Clinical diagnosis is difficult and is usually considered with 

epidemiological risk factors (eg., endemic areas, male 

homosexuality, etc.).

DIAGNOSIS, TREATMENT AND CONTROL 

Intestinal Disease 

Diagnosis 

• stool examination 

o cysts and/or 

trophozoites 

• sigmoidoscopy 

o lesions, aspirate, 

biopsy 

• antigen detection 

o histolytica/dispar 

Extraintestinal (hepatic) Disease 

• serology 

o current or past? 

• imaging 

o CT, MRI, ultrasound 

• abscess aspiration 

o only select cases 

o reddish brown liquid 

o trophozoites at 

abscess wall 

Definitive diagnosis of amebiasis 

requires the demonstration of E. 

histolytica cysts or trophozoites in 

feces or tissues. Stool specimens 

should be preserved and stained and 

microscopically examined. Cysts will 

tend to predominate in formed stools 

and trophozoites in diarrheic stools 

(see morphology). Fresh stools can 

also be immediately examined for 

motile trophozoites which exhibit a 

progressive motility. Sigmoidoscopy 

may reveal the characteristic ulcers, 

especially in more severe disease. 

Aspirates or biopsies should also be 

examined microscopically for 

trophozoites. 

E. histolytica and E. dispar cannot be 

distinguished on morphological 

criteria. Antigen detection kits are 

available for the positive 

identification of these species. 

Serology is especially useful for the diagnosis of extraintestinal 

amebiasis. Greater than 90% of patients with invasive colitis and 

liver abscesses exhibit serum antibodies against E. histolytica. 

However, the antibodies can persist for years and distinguishing 

past and current infections may pose problems in endemic areas. 

Non-invasive imaging techniques (eg., ultrasound, CT, MRI) can be 

used to detect hepatic abscesses. It is also possible to aspirate 

hepatic abscesses. However, this is rarely done and only indicated 

in selected cases (eg., serology and imaging not available, 

therapeutic purposes). The aspirate is usually a thick reddish brown 

liquid that rarely contains trophozoites. Trophozoites are most likely 

to be found at the abscess wall and not in the necrotic debris at the 

abscess center. 

Several drugs are available for the treatment of amebiasis and the 

choice of drug(s) depends on the clinical stage of the infection 

(Table). The prognosis following treatment is generally good in 

uncomplicated cases. In cases where E. histolytica is confirmed or 

the species (ie, dispar or histolytica) is unknown, asymptomatic cyst 

passers should be treated to prevent the progression to severe 

disease and to control the spread of the disease. However, in many 

endemic areas, where the rates of reinfection are high and

treatment is expensive, the standard practice is to only treat 

symptomatic cases. Metronidazole or tinidazole (if available) is 

recommended for all symptomatic infections. This treatment should 

be followed by or combined with lumenal antiamebic drugs as 

described for asymptomatic patients. 

Drugs Uses 

Iodoquinol, Paromomycin, or 

Diloxanide furoate 

Metronidazole or Tinidazole 

Dehydroemetine or Emetine 

Amebiasis Treatment 

Luminal agents to treat asymptomatic cases and as a follow up 

treatment after a nitroimidazole. 

Treatment of nondysenteric colitis, dysentery, and extraintestinal 

infections. 

Treatment of severe disease such as necrotic colitis, perforation 

of intestinal wall, rupture of liver abscess. 

In the cases of fulminant amemic colitis or perforation of the 

intestinal wall a broad spectrum antibiotic can also be used to treat 

intestinal bacteria in the peritoneum. Necrotic colitis requires urgent 

hospitalization to restore fluid and electrolyte balance. In addition, 

emetine or dehydroemetine are sometimes co-administered with 

the nitroimidazole. This is only done in the most severe cases due 

to the toxicity of these drugs. Surgery may also be needed to close 

perforations or a partial colostomy. Abscess drainage of hepatic 

lesions (ie, needle aspiration or surgical drainage) is now rarely 

performed for therapeutic purposes and is only indicated in cases of 

large abscesses with a high probability of rupture. 

Prevention and control measures are similar to other diseases 

transmitted by the fecal-oral route (see Risk Factors or discussion of 

Giardia control). The major difference is that humans are the only 

host for E. histolytica and there is no possibility of zoonotic 

transmission. Control is based on avoiding the contamination of 

food or water with fecal material. Health education in regards to 

improving personal hygiene, sanitary disposal of feces, and hand 

washing are particularly effective. Protecting water supplies will 

lower endemicity and epidemics. Like Giardia, Entamoeba cysts are 

resistant to standard chlorine treatment, but are killed by iodine or 

boiling. Sedimentation and filtration processes are quite effective at 

removing Entamoeba cysts. Chemoprophylaxis is not 

recommended. 

Recent review on amebiasis: 

• Haque, R. et al (2003) Amebiasis. N. Engl. J. Med. 348:1565. 

• Stanley, S.L. (2003) Amoebiasis. The Lancet 361:1025.

NON-PATHOGENIC COMMENSALS 

Numerous protozoa can inhabit the gastro-intestinal tract of 

humans. Most of these exhibit little or no overt pathology. Infection 

with these protozoa is evidence of fecal contamination and indicates 

a risk for more serious infections such as Giardia or E. histolytica. 

These non-pathogenic species can also be confused with the 

potentially pathogenic Giardia or E. histolytica and result in 

unnecessary drug treatment. In addition, such a misdiagnosis is 

also problematic in that the true cause of the symptoms may be 

missed and the appropriate treatment will be 

delayed. 

• Other Entamoeba 

• Other Intestinal Amebae 

• Other Intestinal Flagellates 

• Blastocystis 

Entamoeba Species Infecting 

Humans 

Several Entamoeba species infect humans (box). E. histolytica can 

cause a severe intestinal disease characterized by dysentery as well 

as an invasive disease affecting primarily the liver (see Amebiasis). 

E. dispar is morphologically identical to E. histolytica, but does not 

produce an invasive disease (see further discussion on E. dispar). A 

distinguishing feature of the Entamoeba is their nuclear morphology 

which is described as having peripheral chromatin and a small 

karyosome. E. histolytica/dispar, E.coli, and E. hartmanni can be 

distinguished by size and minor morphological differences (see 

Table). 

Intestinal Entamoeba Species 

E. dispar* E. coli E. hartmanni 

Trophozoites Trophozoites Trophozoites 

• 15-20 µm** 

• extend pseudopodia 

• progressive movement 

• 20-25 µm 

• broad blunt pseudopodia 

• sluggish, non-directional 

movement 

Cysts Cysts Cysts 

• 12-15 µm 

• 4 nuclei 

• blunt chromatoid bodies 

• 15-25 µm 

• 8 nuclei 

• pointed chromatoid 

bodies 

• E. histolytica 

• E. dispar 

• E. coli 

• E. hartmanni 

• E. polecki 

• E. gingivalis 

• 8-10 µm 

• less progressive than E. 

dispar 

• 6-8 µm 

• 4 nuclei 


• CB persist in mature 

cysts

• blunt chromatoid bodies • pointed chromatoid 

bodies 

*=E. histolytica; **invasive E. histolytica can be >20 mm 


• CB persist in mature 

cysts 

E. coli is the largest and is best distinguished by 8 nuclei in the 

mature cyst. The trophozoites of E. coli can be difficult to 

distinguish from E. histolytica/dispar since there is some overlap in 

the size ranges. E. hartmanni is quite similar to E. histolytica and 

was previously considered a 'small race' of E. histolytica. Generally 

10 µm is chosen as the boundary between E. histolytica and E. 

hartmanni. 

E. polecki is usually associated with pigs and monkeys, but human 

cases have been occasionally documented. It appears to be 

geographically restricted to particular areas such a Papua, New 

Guinea. The trophozoites are similar to E. coli, except a little 

smaller, and the cysts are similar to E. histolytica except that the 

mature cyst has a single nucleus. 

E. gingivalis can be recovered from the soft tartar between teeth 

and exhibits a similar morphology to E. histolytica except that it has 

no cyst stage. E. gingivalis can also multiply in bronchial mucus, 

and thus can appear in the sputum. In this case it could be 

confused with E. histolytica from a pulmonary abscess. E. gingivalis 

trophozoites will often contain ingested leukocytes which can be 

used to differentiate it from E. histolytica. The trophozoites are 

most often recovered from patients with periodontal disease, but an 

etiology between the organism and disease has not been 

established and E. gingivalis is considered to be non-pathogenic. 

Other Intestinal Amebae 

Other non-pathogenic amebae include Endolimax nana and 

Iodoamoeba bütschlii. Historically, Dientamoeba fragilis has been 

grouped with the ameba, but electron microscopy and molecular 

phylogenetics suggests that it is actually a flagellate and may be 

closely related to the trichomonads (see above). All three of these 

organisms exhibit similar morphologies and have nuclei which do 

not have peripheral chromatin and a large karyosome. Minor 

morphological differences allow these organims to be distinguished 

(Table). 

Other Intestinal Amebae

Endolimax nana Iodoamoeba bütschlii Dientamoeba fragilis* 

Trophozoites Trophozoites Trophozoites 

• 8-10 µm • 12-15 µm • 8-10 µm 

• often bi-nucleated 

• fragmented karyosome 

Cysts Cysts Cysts 

• 6-8 µm 

• 4 nuclei 

• 10-12 µm 

• 1 nuclei 

• glycogen vacuole 

*A flagellate possibly related to the trichomonads. 

Other Intestinal Flagellates 

• no cysts 

Four additional non-pathogenic flagellates recovered from human 

stools are: Trichomonas hominis, Chilomastix mesnili, Enteromonas 

hominis, and Retortamonas intestinalis. Among these T. hominis, 

also called Pentatrichomonas hominis, is the most common and is 

often recovered from diarrheic stools. These flagellates exhibit 

similar morphologies (Table) and can be difficult to distinguish. The 

trophozoites from all of these flagellates are somewhat teardrop 

shaped and contain a single nucleus and the cyst tend to be slightly 

elongated or oval. 

Other Intestinal Flagellates 

trophozoites cysts 

Size Flagella Size Nuclei 

Trichomonas hominis 6-14 µm 4 anterior, 1 posterior No cyst stage 

Chilomastix mesnili 10-15 µm 3 anterior, 1 in cytostome 7-9 µm 1 

Enteromonas hominis 6-8 µm 3 anterior, 1 posterior 4-8 µm 1-4 

Retortamonas intestinalis 4-10 µm 1 anterior, 1 posterior 4-7 µm 1 

Blastocystis hominis 

Blastocystis hominis is a common organism found in human stools. 

Since its initial description approximately 100 years ago, it has been 

variously classified as an ameba, a yeast, a sporozoan, and the cyst 

stage of a flagellate. Analysis of the small subunit rRNA sequence 

indicates that Blastocystis is most closely related to the

stramenopiles, a complex assemblage of unicellular and muticellular 

protists. Other stramenopiles include diatoms, brown algae, and 

water molds. Many of the characteristics of Blastocystis are 

unknown or controversial. The mode of transmission, mechanism of 

cell replication, and other features of the life cycle have not 

conclusively demonstrated. 

Similarly, the status of 

Blastocystis as a pathogen, 

commensal, or opportunistic 

organism is unknown. 

Blastocystis is polymorphic in 

that a variety of 

morphological forms are found 

in feces and in vitro culture. 

The most widely recognized 

form is spherical 10-15 µm in 

diameter with a large central 

vacuole (Figure). This large 

vacuole pushes the nuclei and 

other organelles to the 

periphery of the cell. The vacuole is sometimes filled with a granular 

material. Small resistant cyst-like forms have been identified from 

in vitro cultures and occasionally observed in feces. These 

presumed cysts are approximately 5 µm and surround by a 

multilayered wall. Furthermore, the cysts do not lyse when placed in 

water suggesting that they are resistant to environmental 

conditions. Presumably Blastocystis is transmitted via a fecal-oral 

route. However, this has not been conclusively demonstrated. 

There have been several reports suggesting Blastocystis causes 

disease, as well as many reports suggesting the opposite. Diarrhea, 

cramps, nausea, vomiting and abdominal pain have been associated 

with large numbers of organisms in the stool. In addition, some 

studies have shown that treatment alleviates the symptoms and 

clears the organisms. However, the drugs used against Blastocystis 

(eg., metronidazole) also work against many other intestinal 

protozoa and bacteria. The inability to rule out other organisms as 

the source of symptoms and the observation that many infected 

persons exhibit no symptoms makes it difficult to draw any 

definitive conclusions about the pathogenesis of Blastocystis. 

Furthermore, it could be that Blastocystis is primarily a commensal, 

but can exhibit virulence under specific host conditions like 

concomitant infections, poor nutrition, or immunosuppression. 

Blastocystis is also found in a wide range of animals, including 

mammals, birds, reptiles, amphibians and even insects, and exhibits

a wide range of molecular diversity. The genetic distance between 

Blastocystis isolates is greater than the genetic distance between E. 

histolytica and E. dispar (see discussion on E. dispar). This 

complicates the designation of species and historically human 

isolates have been designated as B. hominis and isolates for other 

hosts as Blastocytis sp.. However, phylogenetic analysis reveals 

that there are no exclusively human clades and human isolates are 

found in all of the clades. This raises the possibility that Blastocystis 

is not host specific and can be transmitted zoonotically. In addition, 

the wide range of genetic diversity might explain the controversy 

concerning the pathogenecity of Blastocystis in that some 

genotypes may be more virulent than others. However, studies 

addressing this issue suggest that this is not the case. Resolution of 

the confusion about the taxonomy, transmission and virulence of 

Blastocystis will require additional studies. 

Recent reviews on Blastocystis: 

• Stenzel, D.J. and Boreham, P.F.L. (1996) Blastocystis hominis 

revisited. Clinical Microbiology Reviews 9, 563-584. 

• Tan, K.S.W. (2004) Blastocystis in humans and animals: new 

insights using modern methodologies. Veterinary Parasitology 

126, 121-144. 

• Yoshikawa, H. Morimoto, K., Wu, Z., Singh, M. and 

Hashimoto, T. (2004) Problems in speciation in the genus 

Blastocystis. Trends in Parasitology 20, 251-255. 

LINKS 

• Top 

• Contents 

• Giardiasis 

• Trichomoniasis 

• Balantidosis 

• Amebiasis 

• Non-pathogenic Commensals 

• Protozoology Home 

o Study Guides 

o Syllabus 

• Other Courses and Lectures 

• Wiser Home 

• Other Internet Sites 

o Parasites, Division of Parasitic Diseases, CDC 

o The Medical Letter (treatment recommendations) 

http://en.wikipedia.org/wiki/Category:Laboratory_techniques

Category:Laboratory techniques 



Laboratory techniques, as used in Biology, Biochemistry, Chemistry, Molecular 

biology, etc. 

Subcategories 

This category has the following 8 subcategories, out of 8 total. 

B 

C 

• [+] Biochemistry 

methods 

• [+] 

Chromatography 

D 

E 

M 

• [+] Distillation 

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techniques 

M cont. 

P 

• [+] Microscopy 

Pages in category "Laboratory techniques" 

The following 132 pages are in this category, out of 132 total. 

A 

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• Acid-base extraction 

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oligonucleotide 

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F cont. 

G 

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spectrometry 

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chromatography 

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reaction 

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P cont. 

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culture 

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chain reaction 

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freshness 

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Misfolding 

Cyclic 

Amplification 

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electrophoresis 

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C 

D 

E 

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nitrogen 

decompression 

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(disambiguation) 

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equation 

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fragment 

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polymerase 


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polymerase 


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landmark 

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scanning 

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transcription 

polymerase 


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hybridization 

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group 

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microextraction 

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hybridization 

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synthesis 

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http://www.who.int/mediacentre/factsheets/fs094/en/ 

WHO > Programmes and projects > Media centre > Fact sheets 

Main content 

printable version 

Fact sheet N°94 

May 2007 

Malaria 

- Malaria is both preventable and curable. 

- A child dies of malaria every 30 seconds. 

- More than one million people die of malaria every year, mostly infants, young 

children and pregnant women and most of them in Africa. 

INFECTION AND TRANSMISSION 

Malaria is a disease which can be transmitted to people of all ages. It is caused by 

parasites of the species Plasmodium that are spread from person to person through the 

bites of infected mosquitoes. The common first symptoms – fever, headache, chills, and 

vomiting – appear 10 to 15 days after a person is infected. If not treated promptly with 

effective medicines, malaria can cause severe illness that is often fatal. 

There are four types of human malaria – Plasmodium falciparum, P.vivax, P.malariae, and 

P.ovale. P.falciparum and P.vivax are the most common. P.falciparum is by far the most 

deadly type of malaria infection. 

Malaria transmission differs in intensity and regularity depending on local factors such as 

rainfall patterns, proximity of mosquito breeding sites and mosquito species. Some regions 

have a fairly constant number of cases throughout the year – these are malaria endemic – 

whereas in other areas there are “malaria” seasons, usually coinciding with the rainy 

season.

Malaria transmission differs in intensity and regularity depending on local factors such as 

rainfall patterns, proximity of mosquito breeding sites and mosquito species. Some regions 

have a fairly constant number of cases throughout the year – these are malaria endemic – 

whereas in other areas there are “malaria” seasons, usually coinciding with the rainy 

season. 

Large and devastating epidemics can occur in areas where people have had little contact 

with the malaria parasite, and therefore have little or no immunity. These epidemics can be 

triggered by weather conditions and further aggravated by complex emergencies or natural 

disasters. 

GLOBAL AND REGIONAL RISK 

Approximately, 40% of the world’s population, mostly 

those living in the world’s poorest countries, are at risk of 

malaria. Every year, more than 500 million people become 

severely ill with malaria. Most cases and deaths are in sub- 

Saharan Africa. However, Asia, Latin America, the Middle 

East and parts of Europe are also affected. Travellers from 

malaria-free regions going to areas where there is malaria 

transmission are highly vulnerable – they have little or no 

immunity and are often exposed to delayed or wrong 

malaria diagnosis when returning to their home country. 

TREATMENT 

Early diagnosis and prompt treatment are the basic 

elements of malaria control. Early and effective treatment of malaria disease will shorten 

its duration and prevent the development of complications and the great majority of deaths 

from malaria. Access to disease management should be seen not only as a component of 

malaria control but a fundamental right of all populations at risk. Malaria control must be 

an essential part of health care development. In contemporary control, treatment is 

provided to cure patients rather than to reduce parasite reservoirs. 

Antimalarial treatment policies will vary between countries depending on the 

epidemiology of the disease, transmission, patterns of drug resistance and political and 

economic contexts. 

DRUG RESISTANCE 

Related links 

:: Global Malaria 

Programme 

:: Roll Back Malaria 

Partnership 

:: Malaria (Special 

Programme for Research 

and Training in Tropical 

Diseases, TDR) 

The rapid spread of antimalarial drug resistance over the past few decades has required 

more intensive monitoring of drug resistance to ensure proper management of clinical 

cases and early detection of changing patterns of resistance so that national malaria 

treatment policies can be revised where necessary. Surveillance of therapeutic efficacy 

over time is an essential component of malaria control. Recent efforts to scale-up malaria 

control in endemic countries throughout the world including increased support for 

commodities and health systems, as well as the proposed price subsidy on artemisininbased 

combination therapies (ACTs) is resulting in greater access to and a vastly increased 

use of antimalarial medicines, in particular ACTs. This is leading to a much higher degree

of drug pressure on the parasite which will almost certainly increase the likelihood of 

selecting for resistant parasite genotypes. There are currently no effective alternatives to 

artemisinins for the treatment of P. falciparum malaria either on the market or towards the 

end of the development pipeline. 

The parasite's resistance to medicines continues to undermine malaria control efforts. 

WHO has therefore called for continuous monitoring of the efficacy of recently 

implemented ACTs, and countries are being assisted in strengthening their drug resistance 

surveillance systems. In order to preserve the efficacy of artemisinins as an essential 

component of life-saving ACTs, WHO has called for a ban on the use of oral artemisinin 

monotherapies, at various levels, including manufacturers, international drug suppliers, 

national health authorities and international aid and funding agencies involved in the 

funding of essential antimalarial medicines. 

PREVENTION: VECTOR CONTROL AND INTERMITTENT 

PREVENTIVE THERAPY IN PREGNANT WOMEN 

The main objective of malaria vector control is to significantly reduce both the number 

and rate of parasite infection and clinical malaria by controlling the malaria-bearing 

mosquito and thereby reducing and/or interrupting transmission. There are two main 

operational interventions for malaria vector control currently available: Indoor Residual 

Spraying of long-acting insecticide (IRS) and Long-Lasting Insecticidal Nets (LLINs). 

These core interventions can be locally complemented by other methods (e.g. larval 

control or environmental management) in the context of Integrated Vector Management 

(IVM). Effective and sustained implementation of malaria vector control interventions 

(IRS or LLINs) requires clear political commitment and engagement from national 

authorities as well as long-term support from funding partners. 

Pregnant women are at high risk of malaria. Non-immune pregnant women risk both acute 

and severe clinical disease, resulting in up to 60% fetal loss and over 10% maternal deaths, 

including 50% mortality for severe disease. Semi-immune pregnant women with malaria 

infection risk severe anaemia and impaired fetal growth, even if they show no signs of 

acute clinical disease. An estimated 10 000 of these women and 200 000 of their infants 

die annually as a result of malaria infection during pregnancy. HIV-infected pregnant 

women are at increased risk. WHO recommends that all endemic countries provide a 

package of interventions for prevention and management of malaria in pregnancy, 

consisting of (1) diagnosis and treatment for all episodes of clinical disease and anaemia 

and (2) insecticide-treated nets for night-time prevention of mosquito bites and infection. 

In highly endemic falciparum malaria areas, this should be complemented by (3) 

intermittent preventive treatment with sulfadoxine–pyrimethamine (IPT/SP) to clear the 

placenta periodically of parasites. 

INSECTICIDE RESISTANCE 

In spite of increased national and international efforts to scale up cost-effective malaria 

vector control interventions and maximize the protection of populations at risk, significant 

challenges continue to threaten these objectives and the sustainability of achievements. 

Challenges include increasing resistance of vector mosquitoes to insecticides, the 

behaviour and ecology of local malaria vectors – which often change as a result of vector

control interventions -- and the diminishing number of available insecticides that can be 

used against malaria vectors (adulticides). 

There are currently no alternatives to DDT and pyrethroids and the development of new 

insecticides will be an expensive long-term endeavour. Therefore, immediate sound vector 

resistance management practices are required to assure the continued utility of the 

currently available insecticides. At present there is only limited evidence of the impact of 

various resistance mechanisms on the efficacy of vector control interventions, whether 

they are implemented singly or in combination. 

Recent evidence from Africa indicates that pyrethroid and DDT resistance is more 

widespread than anticipated. It is believed that the same level of resistance will have a 

more detrimental impact on the efficacy of IRS than on that of LLINs, but evidence for 

this is very limited. Networks for vector resistance monitoring still need greater 

strengthening in order to make resistance detection a routine operational feature of 

national programmes, particularly in countries in Africa and the Eastern Mediterranean 

region. Regional level databases feeding into a global database accessible by governments, 

scientists and policy-makers would greatly assist in the rational use and deployment of 

vector control interventions. 

SOCIOECONOMIC IMPACT 

Malaria causes an average loss of 1.3% annual economic growth in countries with intense 

transmission. When compounded over the years, this loss has lead to substantial 

differences in GDP between countries with and without malaria. Malaria traps families 

and communities in a downward spiral of poverty, disproportionately affecting 

marginalized populations and poor people who cannot afford treatment or who have 

limited access to health care. Malaria’s direct costs include a combination of personal and 

public expenditures on both prevention and treatment of disease. In some countries with a 

very heavy malaria burden, the disease may account for as much as 40% of public health 

expenditure, 30-50% of inpatient admissions and up to 60% of outpatient visits. Malaria 

has lifelong effects through increased poverty, impaired learning and decreases attendance 

in schools and the workplace. 

For more information contact: 

WHO Media centre 

Telephone: +41 22 791 2222 

E-mail: mediainquiries@who.int 

http://pathmicro.med.sc.edu/mycology/mycology-1.htm 

MYCOLOGY - CHAPTER ONE 

INTRODUCTION TO MYCOLOGY

Figure 1. 

Chaetomium globosum 

spores. Chaetomium is an 

ascomycete, and in most 

species the spores are lemonshaped, 

with a single germ 

pore 

© Dennis Kunkel Microscopy, Inc. Used 

with permission 

Figure 2. 

Bracket fungus basidiocarp 

(fruiting body) lower surface 

showing generative hyphae 

(gill, spore producing). 

Reproductive spores are 

dispersed through pores in 

the surface of the brackets. 

© Dennis Kunkel Microscopy, Inc. Used 

with permission 

Figure 3. 

Mucor spp. fruiting structure 

with spores. The fruiting 

structure (condiophore) has 

matured and its outer 

membrane is disintegrating 

allowing the spores (conidia) 

to be released. Mucor is a 

common fungus found in 

many environments. It is a 

Zygomycetes fungus which 

may be allergenic and is often 

found as saprobes in soils, 

dead plant material (such as 

hay), horse dung, and fruits. It 

is an opportunistic pathogen 

and may cause mucorosis in 

immuno-compromised 

individuals. The sites of 

infections are the lung, nasal 

sinus, brain, eye, and skin. 

Few species have been 

isolated from cases of 

zygomycosis, but the term 

mucormycosis has often been 

used. Zygomycosis includes 

mucocutaneous and 

rhinocerebral infections, as 

well as renal infections, 

gastritis, and pulmonary 

INTRODUCTION 

A. CLASSIFICATION 

Fungi are eukaryotic organisms that do not contain chlorophyll, but have cell walls, 

filamentous structures, and produce spores. These organisms grow as 

saprophytes and decompose dead organic matter. There are between 100,000 to 

200,000 species depending on how they are classified. About 300 species are 

presently known to be pathogenic for man. 

There are five kingdoms of living things. The fungi are in the Kingdom Fungi. 

KINGDOM CHARACTERISTIC EXAMPLE 

Monera Prokaryocyte Bacteria 

Actinomycetes 

Protista Eukaryocyte Protozoa 

Fungi Eukaryocyte * Fungi 

Plantae Eukaryocyte Plants, Moss 

Animalia Eukaryocyte * Arthropods 

Mammals 

Man 

*This common characteristic is responsible for the therapeutic dilemma in antimycotic 

therapy. 

The taxonomy of the Kingdom Fungi is evolving and is controversial. Formerly 

based on gross and light microscopic morphology, studies of ultra structure, 

biochemistry and molecular biology provide new evidence on which to base 

taxonomic positions. Medically important fungi are in four phyla: 

1. Ascomycota - Sexual reproduction in a sack called an ascus with the production 

of ascopspores (figure 1). 

2. Basidiomycota -Sexual reproduction in a sack called a basidium with the 

production of basidiospores (figure 2). 

3. Zygomycota - sexual reproduction by gametes and asexual reproduction with 

the formation of zygospores (figure 3). 

4. Mitosporic Fungi (Fungi Imperfecti) - no recognizable form of sexual 

reproduction. Includes most pathogenic fungi.

Figure 4. 

Candida albicans - yeast and 

hyphae stages. A yeast-like 

fungus commonly occuring on 

human skin, in the upper 

respiratory, alimentary & 

female genital tracts. This 

fungus has a dimorphic life 

cycle with yeast and hyphal 

stages. The yeast produces 

hyphae (strands) and 

pseudohyphae. The 

pseudohyphae can give rise 

to yeast cells by apical or 

lateral budding. Causes 

candidiasis which includes 

thrush (an infection of the 

mouth & vagina) and vulvovaginitis. 

© Dennis Kunkel 

Microscopy, Inc. Used with permission 

VIDEO 

Growth and Division of 

Budding Yeast 

(Saccharomyces cerevisiae) 

High Resolution 

Low resolution 

© Philip Meaden 

Heriot-Watt University 

Edinburgh, Scotland and The 

MicrobeLibrary 

B. MORPHOLOGY 

Pathogenic fungi can exist as yeasts or as hyphae (figure 4). A mass of hyphae is 

called mycelia. Yeasts are unicellular organisms and mycelia are multicellular 

filamentous structures, constituted by tubular cells with cell walls. The yeasts 

reproduce by budding. The mycelial forms branch and the pattern of branching is 

an aid to the morphological identification. If the mycelia do not have SEPTA, they 

are called coenocytic (nonseptate). The terms "hypha" and "mycelium" are 

frequently used interchangeably. Some fungi occur in both the yeast and mycelial 

forms. These are called dimorphic fungi. 

Dimorphic fungi 

The dimorphic fungi have two forms (figure 5): 

1. YEAST - (parasitic or pathogenic form). This is the form usually seen in tissue, 

in exudates, or if cultured in an incubator at 37 degrees C. 

2. MYCELIUM - (saprophytic form). The form observed in nature or when cultured 

at 25 degrees C. Conversion to the yeast form appears to be essential for 

pathogenicity. In the dimorphic fungi. Fungi are identified by several morphological 

or biochemical characteristics, including the appearance of their fruiting bodies. 

The asexual spores may be large (macroconidia, chlamydospores) or small 

(microconidia, blastospores, arthroconidia). 

There are four types of mycotic diseases: 

1. Hypersensitivity - an allergic reaction to molds and spores. 

2. Mycotoxicoses - poisoning of man and animals by feeds and food products 

contaminated by fungi which produce toxins from the grain substrate. 

3. Mycetismus - the ingestion of toxin (mushroom poisoning). 

4. Infection 

We shall be concerned only with the last type: pathogenic fungi that cause 

infections. Most common pathogenic fungi do not produce toxins but they do show 

physiologic modifications during a parasitic infection (e.g., increased metabolic 

rate, modified metabolic pathways and modified cell wall structure). The 

mechanisms that cause these modifications as well as their significance as a 

pathogenic mechanism are just being described. Most pathogenic fungi are also 

thermotolerant, and can resist the effects of the active oxygen radicals released 

during the respiratory burst of phagocytes. Thus, fungi are able to withstand many 

host defenses. Fungi are ubiquitous in nature and most people are exposed to 

them. The establishment of a mycotic infection usually depends on the size of the 

inoculum and on the resistance of the host. The severity of the infection seems to 

depend mostly on the immunologic status of the host. Thus, the demonstration of 

fungi, for example, in blood drawn from an intravenous catheter can correspond to

A 

Candida albicans is a 

dimorphic fungus in that it 

grows as a unicellular yeast 

under some environmental 

conditions and as a 

filamentous fungus under 

other conditions. 

Budding yeast cells. C. 

albicans was grown at 37°C 

with aeration for 3 h in yeastpeptone-dextrose 

(YPD) 

medium. In this image, 

unstained cells are magnified 

x400. The image was taken 

with phase- contrast 

microscopy. 

colonization of the catheter, to transient fungemia (i.e., dissemination of fungi 

through the blood stream), or to a true infection. The physician must decide which 

is the clinical status of the patient based on clinical parameters, general status of 

the patient, laboratory results, etc. The decision is not trivial, since treatment of 

systemic fungal infections requires the aggressive use of drugs with considerable 

toxicity. Most mycotic agents are soil saprophytes and mycotic diseases are 

generally not communicable from person-to-person (occasional exceptions: 

Candida and some dermatophytes). Outbreaks of disease may occur, but these 

are due to a common environmental exposure, not communicability. Most of the 

fungi which cause systemic infections have a peculiar, characteristic ecologic 

niche in nature. This habitat is specific for several fungi which will be discussed 

later. In this environment, the normally saprophytic organisms proliferate and 

develop. This habitat is also the source of fungal elements and/or spores, where 

man and animals, incidental hosts, are exposed to the infectious particles. It is 

important to be aware of these associations to diagnose mycotic diseases. The 

physician must be able to elicit a complete history from the patient including 

occupation, avocation and travel history. This information is frequently required to 

raise, or confirm, your differential diagnosis. The incidence of mycotic infections is 

currently increasing dramatically, due to an increased population of susceptibles. 

Examples are patients with AIDS, patients on immunosuppressive therapy, and 

the use of more invasive diagnostic and surgical procedures (prosthetic implants). 

Fungal diseases are non-contagious and non-reportable diseases in the national 

public health statistics. However, in South Carolina most of the important mycotic 

(fungal) diseases were notifiable to the public health authorities until 1994. 

B 

Budding yeast with septum. The septum has formed between the daughter bud and the mother 

cell, but separation of the two has not occurred. This image is from a culture of cells grown at 37° 

C for 3 h in YPD medium. The unstained cell is magnified x1,000 using phase- contrast 

microscopy. 

C 

Candida albicans mother and daughter cells. Cells were grown under conditions that induced 

hypha formation for 30 min. The daughter cell is on the right; the mother cell is on the left. The 

daughter cell has not reached a threshold volume and therefore has not yet formed a hypha. The 

mother cell has passed the threshold volume and has started forming a germ tube which will 

become a hypha. The germ tube seen here is 6 min old. A septum between the germ tube and the

Figure 5 A-E 

© Phillip Stafford 

Dartmouth Medical School 

Hanover, New Hampshire and 

The MicrobeLibrary 

mother cell has not yet formed. The unstained cells are magnified x1,000 using phase-contrast 

microscopy. 

D 

C. albicans cell at 3 h. Three hours after the appearance of the germ tube, the hypha has septa. A 

new germ tube at the distal pole of the 

cell is also evident at this time. The unstained cells are magnified x1,000 using phase-contrast 

microscopy. 

E 

C. albicans hyphal cells at 5 h. After 5 h in hypha-inducing medium, many hyphae are evident. 

Clumping of the hyphae is 

also apparent, and hyphae are beginning to form hypha blastospores, which are new budding 

cells.

Figure 6 

A Sabouraud’s dextrose agar 

plate culture growing a 

Mexican isolate of T. rubrum 

var. rodhaini. Dermatophytic 

members of the genus 

Trichophyton are some of the 

leading causes of hair, skin, 

and nail infections in humans, 

known as dermatophytoses. 

The genus includes 

anthropophilic, zoophilic, and 

geophilic species 

CDC/Dr. Libero Ajello 

MOLECULAR 

STRUCTURE 

Amphotericin B 

Ketoconazole 

Griseofulvin 

5-fluorocytosine 

C. DIAGNOSIS 

1. Skin scrapings suspected to contain dermatophytes or pus from a lesion can be 

mounted in KOH on a slide and examined directly under the microscope. 

2. Skin testing (dermal hypersensitivity) used to be popular as a diagnostic tool, 

but this use is now discouraged because the skin test may interfere with 

serological studies, by causing false positive results. It may still be used to 

evaluate the patient's immunity, as well as a population exposure index in 

epidemiological studies. 

3. Serology may be helpful when it is applied to a specific fungal disease; there 

are no screening antigens for 'fungi' in general. Because fungi are poor antigens, 

the efficacy of serology varies with different fungal infections. The serologic tests 

will be discussed under each mycosis. The most common serological tests for 

fungi are based on latex agglutination, double immunodiffusion, complement 

fixation and enzyme immunoassays. While latex agglutination may favor the 

detection of IgM antibodies, double immunodiffusion and complement fixation 

usually detect IgG antibodies. Some EIA tests are being developed to detect both 

IgG and IgM antibodies. There are some tests which can detect specific fungal 

antigens, but they are just coming into general use. 

4. Direct fluorescent microscopy may be used for identification, even on nonviable 

cultures or on fixed tissue sections. The reagents for this test are difficult to 

obtain. 

5. Biopsy and histopathology. A biopsy may be very useful for the identification 

and as a source of the of tissue-invading fungi. Usually the Gomori methenamine 

silver (GMS) stain is used to reveal the organisms which stain black against a 

green background. The H&E stain does not always tint the organism, but it will 

stain the inflammatory cells. 

6. Culture. A definitive diagnosis requires a culture and identification. Pathogenic 

fungi are usually grown on Sabouraud dextrose agar (figure 6). It has a slightly 

acidic pH (~5.6); cyclohexamide, penicillin, streptomycin or other inhibitory 

antibiotics are often added to prevent bacterial contamination and overgrowth. 

Two cultures are inoculated and incubated separately at 25 degrees C and 37 

degrees C to reveal dimorphism. The cultures are examined macroscopically and 

microscopically. They are not considered negative for growth until after 4 weeks of 

incubation. 

D. TREATMENT 

Mammalian cells do not contain the enzymes which will degrade the cell wall 

polysaccharides of fungi. Therefore, these pathogens are difficult to eradicate by 

the animal host defense mechanisms. Because mammals and fungi are both

eukaryotic, the cellular milieu is biochemically similar in both. The cell membranes 

of all eukaryotic cells contain sterols; ergosterol in the fungal cell membrane and 

cholesterol in the mammalian cell membrane. Thus, most substances which may 

impair the invading fungus will usually have serious side effects on the host. 

Although one of the first chemotherapeutic agents (oral iodides) was an antimycotic 

used in 1903, the further development of such agents has been left far 

behind the development of anti-bacterial agents. The selective toxicity necessary 

to inhibit the invading organism with minimal damage to the host has been difficult 

to establish within eukaryotic cells. 

The primary antifungal agents are: 

Amphotericin B 

A polyene antimycotic. It is usually the drug of choice for most systemic fungal 

infections. It has a greater affinity for ergosterol in the cell membranes of fungi 

than for the cholesterol in the host's cells; once bound to ergosterol, it causes 

disruption of the cell membrane and death of the fungal cell. Amphotericin B is 

usually administered intravenously (patient usually needs to be hospitalized), often 

for 2-3 months. The drug is rather toxic; thrombo-phlebitis, nephrotoxicity, fever, 

chills and anemia frequently occur during administration. 

Azoles 

The azoles (imidazoles and triazoles), including ketoconazole, fluconazole, and 

itraconozole, are being used for muco-cutaneous candidiasis, dermatophytosis, 

and for some systemic fungal infections. Fluconazole is presently essential for the 

maintenance of AIDS patients with cryptococcosis. The general mechanism of 

action of the azoles is the inhibition of ergosterol synthesis. Oral administration 

and reduced toxicity are distinct advantages. 

Griseofulvin 

Griseofulvin is a very slow-acting drug which is used for severe skin and nail 

infections. Its effect depends on its accumulation in the stratum corneum where it 

is incorporated into the tissue and forms a barrier which stops further fungal 

penetration and growth. It is administered orally. The exact mechanism of action is 

unknown. 

5-fluorocytosine 

5-fluorocytosine (Flucytosine or 5-FC) inhibits RNA synthesis and has found its 

main application in cryptococcosis (to be discussed later). It is administered orally. 

E. CLINICAL CLASSIFICATION OF THE MYCOSES 

Fungal diseases may be discussed in a variety of ways. The most practical 

method for medical students is the clinical taxonomy which divides the fungi into: 

a. Superficial mycoses 

b. Subcutaneous mycoses 

c. Systemic mycoses

MOLECULAR 

STRUCTURE 

Ergosterol 

Figure 7. 

Ringworm on the skin of the 

neck due to Trichophyton 

rubrum. 

CDC/Lucille K. Georg 

Return to the Mycology Section of Microbiology and Immunology On-line 

This page copyright 2007, The Board of Trustees of the University of South Carolina 

This page last changed on 

Page maintained by Richard Hunt 

Please report any problems to rhunt@med.sc.edu 

http://en.wikipedia.org/wiki/Microbial_metabolism 

Microbial metabolism 



Microbial metabolism is the means by which a microbe obtains the energy and 

nutrients (e.g. carbon) it needs to live and reproduce. Microbes use many different 

types of metabolic strategies and species can often be differentiated from each other 

based on metabolic characteristics. The specific metabolic properties of a microbe are 

the major factors in determining that microbe’s ecological niche, and often allow for 

that microbe to be useful in industrial processes or responsible for biogeochemical 

cycles. 

Contents

[hide] 

• 1 Types of microbial metabolism 

• 2 Heterotrophic microbial metabolism 

• 3 Fermentation 

• 4 Special metabolic properties 

o 4.1 Methylotrophy 

o 4.2 Syntrophy 

• 5 Anaerobic respiration 

o 5.1 Denitrification 

o 5.2 Sulfate reduction 

o 5.3 Acetogenesis 

o 5.4 Inorganic electron acceptors 

o 5.5 Organic terminal electron acceptors 

• 6 Chemolithotrophy 

o 6.1 Hydrogen oxidation 

o 6.2 Sulfur oxidation 

o 6.3 Ferrous iron (Fe 2+ ) oxidation 

o 6.4 Nitrification 

o 6.5 Anammox 

• 7 Phototrophy 

• 8 Nitrogen fixation 



Types of microbial metabolism 

Flow chart to determine the metabolic characteristics of microorganisms 

Main article: Primary nutritional groups 

All microbial metabolism can be arranged according to three principles:

1. How the organism obtains carbon for synthesising cell mass: 

• autotrophic – carbon is obtained from carbon dioxide (CO2) 

• heterotrophic – carbon is obtained from organic compounds 

• mixotrophic – carbon is obtained from both organic compounds and by fixing 

carbon dioxide 

2. How the organism obtains reducing equivalents used either in energy conservation 

or in biosynthetic reactions: 

• lithotrophic – reducing equivalents are obtained from inorganic compounds 

• organotrophic – reducing equivalents are obtained from organic compounds 

3. How the organism obtains energy for living and growing: 

• chemotrophic – energy is obtained from external chemical compounds 

• phototrophic – energy is obtained from light 

In practice, these terms are almost freely combined. Typical examples are as follows: 

• chemolithoautotrophs obtain energy from the oxidation of inorganic 

compounds and carbon from the fixation of carbon dioxide. Examples: 

Nitrifying bacteria, Sulfur-oxidising bacteria, Iron-oxidising bacteria, 

Knallgas-bacteria 

• photolithoautotrophs obtain energy from light and carbon from the fixation 

of carbon dioxide, using reducing equivalents from inorganic compounds. 

Examples: Cyanobacteria (water as reducing equivalent donor), 

Chlorobiaceae, Chromaticaceae (hydrogen sulfide as reducing equivalent 

donor), Chloroflexus (hydrogen as reducing equivalent donor) 

• chemolithoheterotrophs obtain energy from the oxidation of inorganic 

compounds, but can not fix carbon dioxide. Examples: some Nitrobacter spp., 

Wolinella (with H2 as reducing equivalent donor), some Knallgas-bacteria 

• chemoorganoheterotrophs obtain energy, carbon and reducing equivalents 

for biosynthetic reactions from organic compounds. Examples: most bacteria, 

e. g. Escherichia coli, Bacillus spp., Actinobacteria 

• photoorganoheterotrophs obtain energy from light, carbon and reducing 

equivalents for biosynthetic reactions from organic compounds. Some species 

are strictly heterotrophic, many others can also fix carbon dioxide and are 

mixotrophic. Examples: Rhodobacter, Rhodopseudomonas, Rhodospirillum, 

Rhodomicrobium, Rhodocyclus, Heliobacterium, Chloroflexus (alternatively to 

photolithoautotrophy with hydrogen) 

[edit] Heterotrophic microbial metabolism 

Most microbes are heterotrophic (more precisely chemoorganoheterotrophic), using 

organic compounds as both carbon and energy sources. Heterotrophic microbes live 

off of nutrients that they scavenge from living hosts (as commensals or parasites) or 

find in dead organic matter of all kind (saprophages). Microbial metabolism is the 

main contribution for the bodily decay of all organisms after death. Many eukaryotic

microorganisms are heterotrophic by predation or parasitism, properties also found in 

some bacteria such as Bdellovibrio (an intracellular parasite of other bacteria, causing 

death of its victims) and Myxobacteria such as Myxococcus (predators of other 

bacteria which are killed and lysed by cooperating swarms of many single cells of 

Myxobacteria). Most pathogenic bacteria can be viewed as heterotrophic parasites of 

humans or whatever other eukaryotic species they affect. Heterotrophic microbes are 

extremely abundant in nature and are responsible for the breakdown of large organic 

polymers such as cellulose, chitin or lignin which are generally indigestible to larger 

animals. Generally, the breakdown of large polymers to carbon dioxide 

(mineralization) requires several different organisms, with one breaking down the 

polymer into its constituent monomers, one able to use the monomers and excreting 

simpler waste compounds as by-products and one able to use the excreted wastes. 

There are many variations on this theme, as different organisms are able to degrade 

different polymers and secrete different waste products. Some organisms are even 

able to degrade more recalcitrant compounds such as petroleum compounds or 

pesticides, making them useful in bioremediation. 

Biochemically, prokaryotic heterotrophic metabolism is much more versatile than that 

of eukaryotic organisms, although many prokaryotes share the most basic metabolic 

models with eukaryotes, e. g. using glycolysis (also called EMP pathway) for sugar 

metabolism and the citric acid cycle to degrade acetate, producing energy in the form 

of ATP and reducing power in the form of NADH or quinols. These basic pathways 

are well conserved because they are also involved in biosynthesis of many conserved 

building blocks needed for cell growth (sometimes in reverse direction). However, 

many bacteria and archaea utilise alternative metabolic pathways other than glycolysis 

and the citric acid cycle. A well studied example is sugar metabolism via the ketodeoxy-phosphogluconate 

pathway (also called ED pathway) in Pseudomonas] instead 

of the glycolytic pathway. Moreover, there is even a third alternative sugar-catabolic 

pathway used by some bacteria, the pentose-phosphate pathway. This metabolic 

diversity and ability of prokaryotes to use a huge variety of organic compounds arises 

from the much deeper evolutionary history and diversity of prokaryotes, as compared 

to eukaryotes. It is also noteworthy that the mitochondrion, the small membranebound 

intracellular organelle that is the site of eukaryotic energy metabolism, arose 

from the endosymbiosis of a bacterium related to obligate intracellular Rickettsia, and 

also to plant-associated Rhizobium or Agrobacterium. Therefore it is not surprising 

that all mitrochondriate eukaryotes share metabolic properties with these 

Proteobacteria. Most microbes respire (use an electron transport chain), although 

oxygen is not the only terminal electron acceptor that may be used. As discussed 

below, the use of terminal electron acceptors other than oxygen has important 

biogeochemical consequences. 

[edit] Fermentation 

Main article: Fermentation (biochemistry) 

Fermentation is a specific type of heterotrophic metabolism that uses organic carbon 

instead of oxygen as a terminal electron acceptor. This means that these organisms do 

not use an electron transport chain to oxidize NADH to NAD + and therefore must 

have an alternative method of using this reducing power and maintaining a supply of 

NAD + for the proper functioning of normal metabolic pathways (e.g. glycolysis). As

oxygen is not required, fermentative organisms are anaerobic. Many organisms can 

use fermentation under anaerobic conditions and respiration when oxygen is not 

present. These organisms are facultative anaerobes. To avoid the overproduction of 

NADH obligately fermentative organisms usually do not have a complete citric acid 

cycle. Instead of using an ATPase as in respiration, ATP in fermentative organisms is 

produced by substrate-level phosphorylation where a phosphate group is transferred 

from a high-energy organic compound to ADP to form ATP. As a result of the need to 

produce high energy phosphate-containing organic compounds (generally in the form 

of CoA-esters) fermentative organisms use NADH and other cofactors to produce 

many different reduced metabolic by-products, often including hydrogen gas (H2). 

These reduced organic compounds are generally small organic acids and alcohols 

derived from pyruvate, the end product of glycolysis. Examples include ethanol, 

acetate, lactate and butyrate. Fermentative organisms are very important industrially 

and are used to make many different types of food products. The different metabolic 

end products produced by each specific bacterial species are responsible for the 

different tastes and properties of each food. 

Not all fermentative organisms use substrate-level phosphorylation. Instead, some 

organisms are able to couple the oxidation of low-energy organic compounds directly 

to the formation of a proton (or sodium) motive force and therefore ATP synthesis. 

Examples of these unusual forms of fermentation include succinate fermentation by 

Propionigenium modestum and oxalate fermentation by Oxalobacter formigenes. 

These reactions are extremely low energy-yielding. Humans and other higher animals 

also use fermentation to use excess NADH to produce lactate, although this is not the 

major form of metabolism as it is in fermentative microorganisms. 

[edit] Special metabolic properties 

[edit] Methylotrophy 

Methylotrophy refers to the ability of an organism to use C1-compounds as energy 

sources. These compounds include methanol, methyl amines, formaldehyde and 

formate. Several other, less common substrates may also be used for metabolism, all 

of which lack carbon-carbon bonds. Examples of methylotrophs include the bacteria 

Methylomonas and Methylobacter. Methanotrophs are a specific type of methylotroph 

that are also able to use methane (CH4) as a carbon source by oxidizing it sequentially 

to methanol (CH3OH), formaldehyde (CH2O), formate (HCOO - ) and finally carbon 

dioxide CO2 initially using the important enzyme methane monooxygenase. As 

oxygen is required for this process, all (conventional) methanotrophs are obligate 

aerobes. Reducing power in the form of quinones and NADH is produced during 

these oxidations to produce a proton motive force and therefore ATP generation. 

Methylotrophs and methanotrophs are not considered as autotrophic, because they are 

able to incorporate some of the oxidized methane (or other metabolites) into cellular 

carbon before it is completely oxidised to CO2 (at the level of formaldehyde), using 

either the serine pathway (Methylosinus, Methylocystis) or the ribulose 

monophosphate pathway (Methylococcus), depending on the species of methylotroph. 

In addition to aerobic methylotrophy, methane can also be oxidized anaerobically. 

This occurs by a consortium of sulfate-reducing bacteria and relatives of

methanogenic Archaea working syntrophically (see below). Little is currently known 

about the biochemistry and ecology of this process. 

Methanogenesis is the biological production of methane. It is carried out by 

methanogens, strictly anaerobic archaea such as Methanococcus, 

Methanocaldococcus, Methanobacterium, Methanothermus, Methanosarcina, 

Methanosaeta and Methanopyrus. The biochemistry of methanogenesis is unique in 

nature in its use of a number of unusual cofactors to sequentially reduce 

methanogenic substrates to methane. These cofactors are responsible (among other 

things) for the establishment of a proton gradient across the outer membrane thereby 

driving ATP synthesis. Several different types of methanogenesis occurs, which differ 

in the starting compounds oxidized. Some methanogens reduce carbon dioxide (CO2) 

to methane (CH4) using electrons (most often) from hydrogen gas (H2) 

chemolithoautotrophically. These methanogens can often be found in environments 

containing fermentative organisms. The tight association of methanogens and 

fermentative bacteria can be considered to be syntrophic (see below) because the 

methanogens, which rely on the fermentors for hydrogen, relieve feedback inhibition 

of the fermentors by the build-up of excess hydrogen that would otherwise inhibit 

their growth. This type of syntrophic relationship is specifically known as interspecies 

hydrogen transfer. A second group of methanogens use methanol (CH3OH) as a 

substrate for methanogenesis. These are chemoorganotrophic, but still autotrophic in 

using CO2 as only carbon source. The biochemistry of this process is quite different 

from that of the carbon dioxide reducing methanogens. Lastly, a third group of 

methanogens produce both methane and carbon dioxide from acetate (CH3COO - ) with 

the acetate being literally split between the two carbons. These acetate-cleaving 

organisms are the only chemoorganoheterotrophic methanogens. All 

autotrophicmethanogens use a variation of the acetyl-CoA pathway to fix CO2 and 

obtain cellular carbon. 

[edit] Syntrophy 

Syntrophy, in the context of microbial metabolism, refers to the pairing of multiple 

species to achieve a chemical reaction that, on its own, would be energetically 

unfavorable. The best studied example of this process is the oxidation of fermentative 

end products (such as acetate, ethanol and butyrate) by organisms such as 

Syntrophomonas. Alone, the oxidation of butyrate to acetate and hydrogen gas is 

energetically unfavorable. However, when a hydrogenotrophic (hydrogen using) 

methanogen is present the use of the hydrogen gas will significantly lower the 

concentration of hydrogen (down to 10 -5 atm) and thereby shift the equilibrium of the 

butyrate oxidation reaction under standard conditions (ΔGº’) to non-standard 

conditions (ΔG’). Because the concentration of one product is lowered, the reaction is 

"pulled" towards the products and shifted towards net energetically favorable 

conditions (for butyrate oxidation: ΔGº’= +48.2 kJ/mol, but ΔG' = -8.9 kJ/mol at 10 -5 

atm hydrogen and even lower if also the initially produced acetate is further 

metabolised by methanogens). Conversely, the available free energy from 

methanogenesis is lowered from ΔGº’= -131 kJ/mol under standard conditions to ΔG' 

= -17 kJ/mol at 10 -5 atm hydrogen. This is an example of intraspecies hydrogen 

transfer. In this way, low energy-yielding carbon sources can be used by a consortium 

of organisms to achieve further degradation and eventual mineralization of these 

compounds. These reactions help prevent the excess sequestration of carbon over

geologic time scales, releasing it back to the biosphere in usable forms such as 

methane and CO2. 

[edit] Anaerobic respiration 

In aerobic organisms, oxygen is used as a terminal electron acceptor during 

respiration. This is largely because oxygen has a very low reduction potential 

allowing for aerobic organisms to utilize their electron transport systems most 

efficiently. In anaerobic organisms, terminal electron acceptors other than oxygen are 

used. These inorganic compounds have a higher reduction potential compared to 

oxygen, meaning that respiration is less efficient in these organisms generally leading 

to slower growth rates compared to aerobes. Many facultative anaerobes can use 

either oxygen or alternative terminal electron acceptors for respiration depending on 

the environmental conditions. Most respiring anaerobes are heterotrophs, although 

some do live autotrophically. All of the processes described below are dissimilative, 

meaning that they are used during energy production and not to provide nutrients for 

the cell (assimilative). Assimilative pathways for many forms of anaerobic respiration 

are also known. 

[edit] Denitrification 

Main article: Denitrification 

Denitrification is the utilization of nitrate (NO3 - ) as a terminal electron acceptor. It is a 

widespread process that is used by many members of the Proteobacteria. Many 

facultative anaerobes use denitrification because nitrate, like oxygen, has a low 

reduction potential. Many denitrifying bacteria can also use ferric iron (Fe 3+ ) and 

some organic electron acceptors. Denitrification involves the stepwise reduction of 

nitrate to nitrite (NO2 - ), nitric oxide (NO), nitrous oxide (N2O) and dinitrogen (N2) by 

the enzymes nitrate reductase, nitrite reductase, nitric oxide reductase and nitrous 

oxide reductase, respectively. Protons are transported across the membrane by the 

initial NADH reductase, quinones and nitrous oxide reductase to produce the 

electrochemical gradient critical for respiration. Some organisms (e.g. E. coli) only 

produce nitrate reductase and therefore can accomplish only the first reduction 

leading to the accumulation of nitrite. Others (e.g. Paracoccus denitrificans or 

Pseudomonas stutzeri) reduce nitrate completely. Complete denitrification is an 

environmentally significant process because some intermediates of denitrification 

(nitric oxide and nitrous oxide) are important greenhouse gases that react with 

sunlight and ozone to produce nitric acid, a component of acid rain. Denitrification is 

also important in biological wastewater treatment where it is used to reduce the 

amount of nitrogen released into the environment thereby reducing eutrophication. 

[edit] Sulfate reduction 

Sulfate reduction is a relatively energetically poor process used by many Gram 

negative bacteria found within the δ-Proteobacteria, Gram positive organisms relating 

to Desulfotomaculum or the archaeon Archaeoglobus. Hydrogen sulfide (H2S) is 

produced as a metabolic end product. Many sulfate reducers are heterotrophic, using 

carbon compounds such as lactate and pyruvate (among many others) as electron

donors while others are autotrophic, using hydrogen gas (H2) as an electron donor. 

Some unusual autotrophic sulfate reducing-bacteria can use phosphite (HPO3 - ) as an 

electron donor (e.g. Desulfotignum phosphitoxidans) or are capable of sulfur 

disproportionation (splitting one compound into two different compounds, in this case 

an electron donor and an electron acceptor) using thiosulfate (S2O3 2- e.g. 

Desulfovibrio sulfodismutans). All sulfate reducing-organisms are strict anaerobes. 

Because sulfate is energetically stable before it can be metabolized it must first be 

activated by adenylation to form APS (adenosine 5’-phosphosulfate) thereby 

consuming ATP. The APS is then reduced by the enzyme APS reductase to form 

sulfite (SO3 2- and AMP. In organisms that use carbon compounds as electron donors, 

the ATP consumed is accounted for by fermentation of the carbon substrate. The 

hydrogen produced during fermentation is actually what drives respiration during 

sulfate reduction. Electrons are passed from the hydrogenase enzyme eventually to the 

APS reductase, which along with sulfite reductase completes the reduction of sulfate 

to hydrogen sulfide. A proton motive force is established due to a fact that the 

hydrogenase, which converts H2 to 2H + is located in the periplasm (or extracellularly 

in Gram positive bacteria). 

[edit] Acetogenesis 

Main article: Acetogenesis 

Acetogenesis is a type of microbial metabolism that uses hydrogen (H2) as an electron 

donor and carbon dioxide (CO2) as an electron acceptor to produce acetate. This is 

similar to methanogenesis (see above) in having the same electron donors and 

acceptors. Bacteria that can autotrophically synthesize acetate are called 

homoacetogens. Carbon dioxide reduction in all homoacetogens occurs by the acetyl- 

CoA pathway. This pathway is also used for carbon fixation by autotrophic sulfatereducing 

bacteria and hydrogenotrophic methanogens. Often homoacetogens can also 

be fermentative, using the hydrogen and carbon dioxide produced as a result of 

fermentation to produce acetate, which is secreted as an end product. 

[edit] Inorganic electron acceptors 

Ferric iron (Fe 3+ ) is a widespread anaerobic terminal electron acceptor both for 

autotrophic and heterotrophic organisms. Electron flow in these organisms is similar 

to those in electron transport ending in oxygen or nitrate except that in ferric ironreducing 

organisms the final enzyme in this system is a ferric iron reductase. Model 

organisms include Shewanella putrifaciens and Geobacter metallireducens. Since 

some ferric iron-reducing bacteria (e.g. G. metallireducens) can use toxic 

hydrocarbons such as toluene as a carbon source there is significant interest in using 

these organisms as bioremediation agents in ferric iron-rich contaminated aquifers. 

Although Ferric iron is the most prevalent inorganic electron acceptor, a number of 

organisms (including the iron-reducing bacteria mentioned above) can use other 

inorganic ions in anaerobic respiration. While these processes may often be less 

significant ecologically, they are of considerable interest for bioremediation, 

especially when heavy metals or radionuclides are used as electron acceptors. 

Examples include:

• Manganic ion (Mn 4+ ) reduction to manganous ion (Mn 2+ ) 

• Selenate (SeO4 2- ) reduction to selenite (SeO3 2- ) and selenite reduction to 

inorganic selenium (Se 0 ) 

• Arsenate (AsO4 3- ) reduction to arsenite (AsO3 3- ) 

• Uranyl ion ion (UO2 2+ ) reduction to uranium dioxide (UO2) 

[edit] Organic terminal electron acceptors 

An number of organisms, instead of using inorganic compounds as terminal electron 

acceptors are able to use organic compounds to accept electrons from respiration. 

Examples include: 

• Fumarate reduction to succinate 

• Trimethylamine N-oxide (TMAO) reduction to trimethylamine (TMA) 

• Dimethyl sulfoxide (DMSO) reduction to Dimethyl sulfide (DMS) 

• Reductive dechlorination 

TMAO is a chemical commonly produced by fish, and when reduced to TMA 

produces a strong odor. DMSO is a common marine and freshwater chemical which is 

also odiferous when reduced to DMS. Reductive dechlorination is the process by 

which chlorinated organic compounds are reduced to form their non-chlorinated 

endproducts. As chlorinated organic compounds are often important (and difficult to 

degrade) environmental polutants, reductive dechlorination is an important process in 

bioremediation. 

[edit] Chemolithotrophy 

Chemolithotrophy is a type of metabolism where energy is obtained from the 

oxidation of inorganic compounds. Most chemolithotrophic organisms are also 

autotrophic. There are two major objectives to chemolithotrophy: the generation of 

energy (ATP) and the generation of reducing power (NADH). 

[edit] Hydrogen oxidation 

Many organisms are capable of using hydrogen (H2) as a source of energy. While 

several mechanisms of anaerobic hydrogen oxidation have been mentioned previously 

(e.g. sulfate reducing- and acetogenic bacteria) hydrogen can also be used as an 

energy source aerobically. In these organisms hydrogen is oxidized by a membranebound 

hydrogenase causing proton pumping via electron transfer to various quinones 

and cytochromes. In many organisms, a second cytoplasmic hydrogenase is used to 

generate reducing power in the form of NADH, which is subsequently used to fix 

carbon dioxide via the Calvin cycle. Hydrogen oxidizing organisms, such as 

Cupriavidus necator (formerly Ralstonia eutropha)--Louegger (talk) 16:11, 3 

February 2008 (UTC), often inhabit oxic-anoxic interfaces in nature to take advantage 

of the hydrogen produced by anaerobic fermentative organisms while still maintaining 

a supply of oxygen. 

[edit] Sulfur oxidation

Sulfur oxidation involves the oxidation of reduced sulfur compounds (such as sulfide 

(H2S), inorganic sulfur (S 0 ) and thiosulfate (S2O2 2- ) ) to form sulfuric acid (H2SO4). A 

classic example of a sulfur oxidizing bacterium is Beggiatoa, a microbe originally 

described by Sergei Winogradsky, one of the founders of microbiology. Generally, 

the oxidation of sulfide occurs in stages, with inorganic sulfur being stored either 

inside or outside of the cell until needed. This two step process occurs because 

energetically sulfide is a better electron donor than inorganic sulfur or thiosulfate, 

allowing for a greater number of protons to be translocated across the membrane. 

Sulfur oxidizing organisms generate reducing power for carbon dioxide fixation via 

the Calvin cycle using reverse electron flow, an energy-requiring process that pushes 

the electrons against their thermodynamic gradient to produce NADH. Biochemically, 

reduced sulfur compounds are converted to sulfite (SO3 2- ) and subsequently converted 

to sulfate by the enzyme sulfite oxidase. Some organisms, however, accomplish the 

same oxidation using a reversal of the APS reductase system used by sulfate-reducing 

bacteria (see above). In all cases the energy liberated is transferred to the electron 

transport chain for ATP and NADH production. In addition to aerobic sulfur 

oxidation, some organisms (e.g. Thiobacillus denitrificans) use nitrate (NO3 2- ) as a 

terminal electron acceptor and therefore grow anaerobically. 

[edit] Ferrous iron (Fe 2+ ) oxidation 

Ferrous iron is a soluble form of iron that is stable at extremely low pHs or under 

anaerobic conditions. Under aerobic, moderate pH conditions ferrous iron is oxidized 

spontaneously to the ferric (Fe 3+ ) form and is hydrolyzed abiotically to insoluble 

ferric hydroxide (Fe(OH)3). There exists, therefore, three distinct types of ferrous 

iron-oxidizing microbes. The first are acidophiles, such as the bacteria 

Acidithiobacillus ferooxidans and Leptospirrillum ferrooxidans, as well as the 

archaeon Ferroplasma. These microbes oxidize iron in environments that have a very 

low pH and are important in acid mine drainage. The second type of microbes oxidize 

ferrous iron at neutral pH along oxic-anoxic interfaces. Both these bacteria, such as 

Gallionella ferruginea and Sphaerotilus natans, and the acidophilic iron oxidizingbacteria 

are aerobes. The third type of iron-oxidizing microbes are anaerobic 

photosynthetic bacteria such as Chlorobium, which use ferrous iron to produce 

NADH for autotrophic carbon dioxide fixation. Biochemically, aerobic iron reduction 

is a very energetically poor process which therefore requires large amounts of iron to 

be oxidized by the enzyme rusticyanin to facilitate the formation of proton motive 

force. Like during sulfur oxidation reverse electron flow must be used to form the 

NADH used for carbon dioxide fixation via the Calvin cycle. 

[edit] Nitrification 

Nitrification is the process by which ammonia (NH3) is converted to nitrate (NO3 - ). 

Nitrification is actually the net result of two distinct processes: oxidation of ammonia 

to nitrite (NO2 - ) by nitrosifying bacteria (e.g. Nitrosomonas) and oxidation of nitrite to 

nitrate by the nitrite-oxidizing bacteria (e.g. Nitrobacter). Both of these processes are 

extremely poor energetically leading to very slow growth rates for both types of 

organisms. Biochemically, ammonia oxidation occurs by the stepwise oxidation of 

ammonia to hydroxylamine (NH2OH) by the enzyme ammonia monooxygenase in the 

cytoplasm followed by the oxidation of hydroxylamine to nitrite by the enzyme 

hydroxylamine oxidoreductase in the periplasm.

Electron and proton cycling are very complex but as a net result only one proton is 

translocated across the membrane per molecule of ammonia oxidized. Nitrite 

reduction is much simpler, with nitrite being oxidized by the enzyme nitrite 

oxidoreductase coupled to proton translocation by a very short electron transport 

chain, again leading to very low growth rates for these organisms. In both ammonia- 

and nitrite-oxidation oxygen is required, meaning that both nitrosifying and nitriteoxidizing 

bacteria are aerobes. As in sulfur and iron oxidation, NADH for carbon 

dioxide fixation using the Calvin cycle is generated by reverse electron flow, thereby 

placing a further metabolic burden on an already energy-poor process. 

[edit] Anammox 

Anammox stands for anaerobic ammonia oxidation and is a relatively recently (late 

1990’s) discovered process. It occurs in members of the Planctomycetes (e.g. 

Candidatus Brocadia anammoxidans) and involves the coupling of ammonia 

oxidation to nitrite reduction. As oxygen is not required for this process these 

organisms are strict anaerobes. Amazingly, hydrazine (N2H4-rocket fuel) is produced 

as an intermediate during anammox metabolism. To deal with the high toxicity of 

hydrazine, anammox bacteria contain an hydrazine-containing intracellular organelle 

called the anammoxasome surrounded by highly compact (and unusual) ladderane 

lipid membrane. These lipids are unique in nature, as is the use of hydrazine as a 

metabolic intermediate. Anammox organisms are autotrophs although the mechanism 

for carbon dioxide fixation is unclear. Because of this property, these organisms have 

been applied industrially to remove nitrogen in wastewater treatment processes. 

Anammox has also been shown have widespread occurrence in anaerobic aquatic 

systems and has been speculated to account for approximately 50% of nitrogen gas 

production in some marine environments. 

[edit] Phototrophy 

Many microbes are capable of using light as a source of energy (phototrophy). Of 

these, algae are particularly significant because they are oxygenic, using water as an 

electron donor for electron transfer during photosynthesis. [citation needed] Phototrophic 

bacteria are found in the phyla Cyanobacteria, Chlorobi, Proteobacteria, Chloroflexi 

and Firmicutes. [1] Along with plants these microbes are responsible for all biological 

generation of diatomic oxygen on Earth. Because chloroplasts were derived from a 

lineage of the Cyanobacteria, the general principles of metabolism in these 

endosymbionts can also be applied to chloroplasts. In addition to oxygenic 

photosynthesis, many bacteria can also photosynthesize anaerobically, typically using 

sulfide (H2S) as an electron donor to produce sulfate. Inorganic sulfur (S 0 ), thiosulfate 

(S2O3 2- ) and ferrous iron (Fe 2+ ) can also be used by some organisms. 

Phylogenetically, all oxygenic photosynthetic bacteria are Cyanobacteria, while 

anoxygenic photosynthetic bacteria belong to the purple bacteria (Proteobacteria), 

Green sulfur bacteria (e.g. Chlorobium), Green non-sulfur bacteria (e.g. Chloroflexus) 

or the heliobacteria (Low %G+C Gram positives). In addition to these organisms, 

some microbes (e.g. the archaeon Halobacterium or the bacterium Roseobacter, 

among others) can utilize light to produce energy using the enzyme 

bacteriorhodopsin, a light-driven proton pump. This type of metabolism is not

considered to be photosynthesis but rather photophosphorylation, since it generates 

energy, but does not directly fix carbon. 

As befits the large diversity of photosynthetic bacteria, there exist many different 

mechanisms by which light is converted into energy for metabolism. All 

photosynthetic organisms locate their photosynthetic reaction centers within a 

membrane, which may be invaginations of the cytoplasmic membrane (purple 

bacteria), thylakoid membranes (Cyanobacteria), specialized antenna structures called 

chlorosomes (Green sulfur and non-sulfur bacteria) or the cytoplasmic membrane 

itself (heliobacteria). Different photosynthetic bacteria also contain different 

photosynthetic pigments such as chlorophylls and carotenoids allowing them to take 

advantage of different portions of the electromagnetic spectrum and thereby inhabit 

different niches. Some groups of organisms contain more specialized light-harvesting 

structures e.g. phycobilisomes in Cyanobacteria and chlorosomes in Green sulfur and 

non-sulfur bacteria, allowing for increased light utilization efficiency. 

Biochemically, anoxygenic photosynthesis is very different from oxygenic 

photosynthesis. Cyanobacteria (and by extension chloroplasts) use the Z scheme of 

electron flow in which electrons eventually are used to form NADH. Two different 

reaction centers (photosystems) are used and proton motive force is generated both by 

using cyclic electron flow and the quinone pool. In anoxygenic photosynthetic 

bacteria electron flow is cyclic, with all electrons used in photosynthesis eventually 

being transferred back to the single reaction center. A proton motive force is 

generated using only the quinone pool. In heliobacteria, Green sulfur and non-sulfur 

bacteria NADH is formed using the protein ferredoxin, an energetically favorable 

reaction. In purple bacteria NADH is formed by reverse electron flow due to the 

lower chemical potential of this reaction centre. In all cases, however, a proton motive 

force is generated and used to drive ATP production via an ATPase. 

Most photosynthetic microbes are autotrophic, fixing carbon dioxide via the Calvin 

cycle. Some photosynthetic bacteria (e.g. Chloroflexus) are photoheterotrophs, 

meaning that they use organic carbon compounds as a carbon source for growth. 

Some photosynthetic organisms also fix nitrogen (see below). 

[edit] Nitrogen fixation 

Main article: Nitrogen fixation 

Nitrogen is an element required for growth by all biological systems. While extremely 

common (80% by volume) in the atmosphere, dinitrogen gas (N2) is generally 

biologically inaccessible due to its high activation energy. Throughout all of nature, 

only specialized bacteria are capable of nitrogen fixation, converting dinitrogen gas 

into ammonia (NH3), which is easily assimilated by all organisms. These bacteria, 

therefore are very important ecologically and are often essential for the survival entire 

ecosystems. This is especially true in the ocean, where nitrogen-fixing cyanobacteria 

are often the only sources or fixed nitrogen and in soils where specialized symbioses 

exist between legumes and their nitrogen-fixing partners to provide the nitrogen 

needed by these plants for growth.

Nitrogen fixation can be found distributed throughout nearly all bacterial lineages and 

physiological classes but is not a universal property. Because the enzyme nitrogenase, 

responsible for nitrogen fixation, is very sensitive to oxygen which will inhibit it 

irreversibly, all nitrogen-fixing organisms must possess some mechanism to keep the 

concentration of oxygen low. Examples include: 

• heterocyst formation (cyanobacteria e.g. Anabaena) where one cell does not 

photosynthesize but instead fixed nitrogen for its neighbors which in turn 

provide it with energy 

• root nodule symbioses (e.g. Rhizobium) with plants that supply oxygen to the 

bacteria bound to molecules of leghaemoglobin 

• anaerobic lifestyle (e.g. Clostridium pasteurianum) 

• very fast metabolism (e.g. Azotobacter vinelandii) 

The production and activity of nitrogenases is very highly regulated, both because 

nitrogen fixation is an extremely energetically expensive process (16-24 ATP are used 

per N2 fixed) and due to the extreme sensitivity of the nitrogenase to oxygen. 


• lipophilic bacteria, a minority of bacteria with lipid metabolism 


1. ^ D.A. Bryant & N.-U. Frigaard (Nov 2006). "Prokaryotic photosynthesis and 

phototrophy illuminated". Trends Microbiol. 14 (11): 488. 

doi:doi:10.1016/j.tim.2006.09.001. 

• Madigan, M. T., Martinko, J. M. "Brock Biology of Microorganisms, 11th 

Ed." (2005) Pearson 

http://en.wikipedia.org/wiki/Category:Microbiology_techniques 

Category:Microbiology techniques 



Pages in category "Microbiology techniques" 

There are 19 pages in this section of this category. 

A 

• Antibiogram 

C 

• Clonogenic assay 

M cont. 

• Microscopy

B 

• Aseptic technique 

• Auraminerhodamine 

stain 

• Axenic 

• Bacterial water 

analysis 

• Blood culture 

G 

I 

K 

M 

• Cryogenic grinding 

• Guthrie test 

• Indole test 

• Industrial fermentation 

• Kirby-Bauer antibiotic 

testing 

• Microbiological 

culture 

O 

R 

S 

Z 

• Miles and Misra 

method 

• Oxidase test 

• Replica plating 

• Streaking 

(microbiology) 

• Ziehl-Neelsen 

stain 

Retrieved from "http://en.wikipedia.org/wiki/Category:Microbiology_techniques" 

Categories: Microbiology | Laboratory techniques 

Microscopy mi·cros·co·py (Pronunciation[mahy-kros-kuh-pee, mahy-kruh-skoh-pee]) 

is the technical field of using microscopes to view samples or objects. There are three 

well-known branches of microscopy, optical, electron and scanning probe 

microscopy. 

Optical and electron microscopy involve the diffraction, reflection, or refraction of 

electromagnetic radiation incident upon the subject of study, and the subsequent 

collection of this scattered radiation in order to build up an image. This process may 

be carried out by wide field irradiation of the sample (for example standard light 

microscopy and transmission electron microscopy) or by scanning of a fine beam over 

the sample (for example confocal microscopy and scanning electron microscopy). 

Scanning probe microscopy involves the interaction of a scanning probe with the 

surface or object of interest. The development of microscopy revolutionized biology 

and remains an essential tool in that science, along with many others.

Scanning electron microscope image of pollen. 

Contents 

[hide] 

• 1 Optical microscopy 

o 1.1 Limitations of optical microscopy 

o 1.2 Optical microscopy techniques 

1.2.1 Bright field optical microscopy and what it means 

1.2.2 Oblique illumination and what it means 

1.2.3 Dark field optical microscopy and what it means 

1.2.4 Phase contrast optical microscopy 

1.2.5 Differential interference contrast microscopy 

1.2.6 Fluorescence microscopy 

1.2.7 Confocal laser scanning microscopy 

1.2.8 Deconvolution microscopy 

o 1.3 Sub-diffraction optical microscopy techniques 

1.3.1 NSOM 

1.3.2 Local enhancement / ANSOM / bowties 

1.3.3 STED 

1.3.4 Fitting the PSF 

1.3.5 PALM & STORM 

1.3.6 Structured illumination 

o 1.4 Extensions of the optical microscope 

o 1.5 Other optical microscope enhancements 

o 1.6 X-ray microscopy 

o 1.7 Electron Microscopy 

o 1.8 Atomic de Broglie microscope 

• 2 Scanning probe microscopy 

o 2.1 Ultrasonic force microscopy 

• 3 Infrared microscopy 

• 4 Amateur Microscopy



o 6.1 Further reading 


o 7.1 Organizations 

[edit] Optical microscopy 

See also: Optical microscope 

Optical or light microscopy involves passing visible light transmitted through or 

reflected from the sample through a single or multiple lenses to allow a magnified 

view of the sample. [1] The resulting image can be detected directly by the eye, imaged 

on a photographic plate or captured digitally. The single lens with its attachments, or 

the system of lenses and imaging equipment, along with the appropriate lighting 

equipment, sample stage and support, makes up the basic light microscope. 

[edit] Limitations of optical microscopy 

See also: Microscopy#Super-Resolution Optical Microscopy Techniques 

Limitations of standard optical microscopy (bright field microscopy) lie in three 

areas; 

• The technique can only image dark or strongly refracting objects effectively. 

• Diffraction limits resolution to approximately 0.2 micrometre (see: 

microscope). 

• Out of focus light from points outside the focal plane reduces image clarity. 

Live cells in particular generally lack sufficient contrast to be studied successfully, 

internal structures of the cell are colourless and transparent. The most common way to 

increase contrast is to stain the different structures with selective dyes, but this 

involves killing and fixing the sample. Staining may also introduce artifacts, apparent 

structural details that are caused by the processing of the specimen and are thus not a 

legitimate feature of the specimen. 

These limitations have, to some extent, all been overcome by specific microscopy 

techniques which can non-invasively increase the contrast of the image. In general, 

these techniques make use of differences in the refractive index of cell structures. It is 

comparable to looking through a glass window: you (bright field microscopy) don't 

see the glass but merely the dirt on the glass. There is however a difference as glass is 

a more dense material, and this creates a difference in phase of the light passing 

through. The human eye is not sensitive to this difference in phase but clever optical 

solutions have been thought out to change this difference in phase into a difference in 

amplitude (light intensity). 

[edit] Optical microscopy techniques

[edit] Bright field optical microscopy and what it means 

Main article: Bright field microscopy 

Bright field microscopy is the simplest of all the light microscopy techniques. Sample 

illumination is via transmitted white light, i.e. illuminated from below and observed 

from above. Limitations include low contrast of most biological samples and low 

apparent resolution due to the blur of out of focus material. The simplicity of the 

technique and the minimal sample preparation required are significant advantages. 

[edit] Oblique illumination and what it means 

The use of oblique (from the side) illumination gives the image a 3-dimensional 

appearance and can highlight otherwise invisible features. A more recent technique 

based on this method is Hoffmann's modulation contrast, a system found on inverted 

microscopes for use in cell culture. Oblique illumination suffers from the same 

limitations as bright field microscopy (low contrast of many biological samples; low 

apparent resolution due to out of focus objects), but may highlight otherwise invisible 

structures. 

[edit] Dark field optical microscopy and what it means 

Main article: Dark field microscopy 

Dark field microscopy is a technique for improving the contrast of unstained, 

transparent specimens. [2] Darkfield illumination uses a carefully aligned light source 

to minimise the quantity of directly-transmitted (un-scattered) light entering the image 

plane, collecting only the light scattered by the sample. Darkfield can dramatically 

improve image contrast—especially of transparent objects—while requiring little 

equipment setup or sample preparation. However, the technique does suffer from low 

light intensity in final image of many biological samples, and continues to be affected 

by low apparent resolution. 

Rheinberg illumination is a special variant of dark field illumination in which 

transparent, colored filters are inserted just before the condenser so that light rays at 

high aperture are differently colored than those at low aperture (i.e. the background to 

the specimen may be blue while the object appears self-luminous yellow). Other color 

combinations are possible but their effectiveness is quite variable. [3] 

[edit] Phase contrast optical microscopy 

Main articles: Phase contrast microscope and Phase contrast microscopy 

In electron microscopy: Phase-contrast imaging 

More sophisticated techniques will show differences in optical density in proportion. 

Phase contrast is a widely used technique that shows differences in refractive index 

as difference in contrast. It was developed by the Dutch physicist Frits Zernike in the 

1930s (for which he was awarded the Nobel Prize in 1953). The nucleus in a cell for 

example will show up darkly against the surrounding cytoplasm. Contrast is excellent; 

however it is not for use with thick objects. Frequently, a halo is formed even around 

small objects, which obscures detail. The system consists of a circular annulus in the 

condenser which produces a cone of light. This cone is superimposed on a similar

sized ring within the phase-objective. Every objective has a different size ring, so for 

every objective another condenser setting has to be chosen. The ring in the objective 

has special optical properties: it first of all reduces the direct light in intensity, but 

more importantly, it creates an artificial phase difference of about a quarter 

wavelength. As the physical properties of this direct light have changed, interference 

with the diffracted light occurs, resulting in the phase contrast image. 

[edit] Differential interference contrast microscopy 

Main article: Differential interference contrast microscopy 

Superior and much more expensive is the use of interference contrast. Differences in 

optical density will show up as differences in relief. A nucleus within a cell will 

actually show up as a globule in the most often used differential interference 

contrast system according to Georges Nomarski. However, it has to be kept in mind 

that this is an optical effect, and the relief does not necessarily resemble the true 

shape! Contrast is very good and the condenser aperture can be used fully open, 

thereby reducing the depth of field and maximizing resolution. 

The system consists of a special prism (Nomarski prism, Wollaston prism) in the 

condenser that splits light in an ordinary and an extraordinary beam. The spatial 

difference between the two beams is minimal (less than the maximum resolution of 

the objective). After passage through the specimen, the beams are reunited by a 

similar prism in the objective. 

In a homogeneous specimen, there is no difference between the two beams, and no 

contrast is being generated. However, near a refractive boundary (say a nucleus within 

the cytoplasm), the difference between the ordinary and the extraordinary beam will 

generate a relief in the image. Differential interference contrast requires a polarized 

light source to function; two polarizing filters have to be fitted in the light path, one 

below the condenser (the polarizer), and the other above the objective (the analyzer). 

Note: In cases where the optical design of a microscope produces an appreciable 

lateral separation of the two beams we have the case of classical interference 

microscopy, which does not result in relief images, but can nevertheless be used for 

the quantitative determination of mass-thicknesses of microscopic objects. 

[edit] Fluorescence microscopy 

Main article: Fluorescence microscopy 

When certain compounds are illuminated with high energy light, they then emit light 

of a different, lower frequency. This effect is known as fluorescence. Often specimens 

show their own characteristic autofluorescence image, based on their chemical 

makeup. 

This method is of critical importance in the modern life sciences, as it can be 

extremely sensitive, allowing the detection of single molecules. Many different 

fluorescent dyes can be used to stain different structures or chemical compounds. One 

particularly powerful method is the combination of antibodies coupled to a 

fluorochrome as in immunostaining. Examples of commonly used fluorochromes are

fluorescein or rhodamine. The antibodies can be made tailored specifically for a 

chemical compound. For example, one strategy often in use is the artificial production 

of proteins, based on the genetic code (DNA). These proteins can then be used to 

immunize rabbits, which then form antibodies which bind to the protein. The 

antibodies are then coupled chemically to a fluorochrome and then used to trace the 

proteins in the cells under study. 

Highly-efficient fluorescent proteins such as the green fluorescent protein (GFP) have 

been developed using the molecular biology technique of gene fusion, a process 

which links the expression of the fluorescent compound to that of the target 

protein.Piston DW, Patterson GH, Lippincott-Schwartz J, Claxton NS, Davidson MW 

(2007). Nikon MicroscopyU: Introduction to Fluorescent Proteins. Nikon 

MicroscopyU. Retrieved on 2007-08-22. This combined fluorescent protein is 

generally non-toxic to the organism and rarely interferes with the function of the 

protein under study. Genetically modified cells or organisms directly express the 

fluorescently-tagged proteins, which enables the study of the function of the original 

protein in vivo. 

Since fluorescence emission differs in wavelength (color) from the excitation light, a 

fluorescent image ideally only shows the structure of interest that was labelled with 

the fluorescent dye. This high specificity led to the widespread use of fluorescence 

light microscopy in biomedical research. Different fluorescent dyes can be used to 

stain different biological structures, which can then be detected simultaneously, while 

still being specific due to the individual color of the dye. 

To block the excitation light from reaching the observer or the detector, filter sets of 

high quality are needed. These typically consist of an excitation filter selecting the 

range of excitation wavelengths, a dichroic mirror, and an emission filter blocking the 

excitation light. Most fluorescence microscopes are operated in the Epi-illumination 

mode (illumination and detection from one side of the sample) to further decrease the 

amount of excitation light entering the detector. 

See also total internal reflection fluorescence microscope. 

[edit] Confocal laser scanning microscopy 

Main article: Confocal laser scanning microscopy 

Generates the image by a completely different way than the normal visual bright field 

microscope. It gives slightly higher resolution, but most importantly it provides 

optical sectioning without disturbing out-of-focus light degrading the image. 

Therefore it provides sharper images of 3D objects. This is often used in conjunction 

with fluorescence microscopy. 

[edit] Deconvolution microscopy 

Fluorescence microscopy is extremely powerful due to its ability to show specifically 

labelled structures within a complex environment but also because of its inherent 

ability to provide three dimensional information of biological structures. 

Unfortunately this information is blurred by the fact, that upon illumination all

fluorescently labeled structures emit light no matter if they are in focus or not. This 

means, that an image of a certain structure is always blurred by the contribution of 

light from structures which are out of focus. This phenomenon becomes apparent as a 

loss of contrast especially when using objectives with a high resolving power, 

typically oil immersion objectives with a high numerical aperture. 

Fortunately though, this phenomenon is not caused by random processes such as light 

scattering but can be relatively well defined by the optical properties of the image 

formation in the microscope imaging system. If one considers a small fluorescent 

light source (essentially a bright spot), light coming from this spot spreads out the 

further out of focus one is. Under ideal conditions this produces a sort of "hourglass" 

shape of this point source in the third (axial) dimension. This shape is called the point 

spread function (PSF) of the microscope imaging system. Since any fluorescence 

image is made up of a large number of such small fluorescent light sources the image 

is said to be "convolved by the point spread function". 

Knowing this point spread function means, that it is possible to reverse this process to 

a certain extent by computer based methods commonly known as deconvolution 

microscopy. [4] There are various algorithms available for 2D or 3D Deconvolution. 

They can be roughly classified in non restorative and restorative methods. While the 

non restorative methods can improve contrast by removing out of focus light from 

focal planes, only the restorative methods can actually reassign light to it proper place 

of origin. This can be an advantage over other types of 3D microscopy such as 

confocal microscopy, because light is not thrown away but reused. For 3D 

deconvolution one typically provides a series of images derived from different focal 

planes (called a Z-stack) plus the knowledge of the PSF which can be either derived 

experimentally or theoretically from knowing all contributing parameters of the 

microscope. 

[edit] Sub-diffraction optical microscopy techniques 

It is well known that there is a spatial limit to which light can focus: approximately 

half of the wavelength of the light you are using. But this is not a true barrier, because 

this diffraction limit is only true in the far-field and localization precision can be 

increased with many photons and careful analysis (although two objects still cannot 

be resolved); and like the sound barrier, the diffraction barrier is breakable. This 

section explores some approaches to imaging objects smaller than ~250 nm. Most of 

the following information was gathered (with permission) from a chemistry blog's 

review of sub-diffraction microscopy techniques Part I and Part II. For a review, see 

also reference [5] . 

[edit] NSOM 

Probably the most conceptual way to break the diffraction barrier is to use a light 

source and/or a detector that is itself nanometer in scale. Diffraction as we know it is 

truly a far-field effect: the light from an aperture is the Fourier transform of the 

aperture in the far-field. [6] But in the near-field, all of this is not necessarily the case. 

Near-field scanning optical microscopy (NSOM) forces light through the tiny tip of a 

pulled fiber—and the aperture can be on the order of tens of nanometers. [7] When the 

tip is brought to nanometers away from a molecule, the resolution is not limited by

diffraction but by the size of the tip aperture (because only that one molecule will see 

the light coming out of the tip). An image can be built by a raster scan of the tip over 

the surface to create an image. 

The main down-side to NSOM is the limited number of photons you can force out a 

tiny tip, and the minuscule collection efficiency (if you are trying to collect 

fluorescence in the near-field). Other techniques such as ANSOM (see below) try to 

avoid this drawback. 

[edit] Local enhancement / ANSOM / bowties 

Instead of forcing photons down a tiny tip, some techniques create a local bright spot 

in an otherwise diffraction-limited spot. ANSOM is apertureless NSOM: it uses a tip 

very close to a fluorophore to enhance the local electric field the fluorophore sees. [8] 

Basically, the ANSOM tip is like a lightning rod which creates a hot spot of light. 

Bowtie nanoantennas have been used to greatly and reproducibly enhance the electric 

field in the nanometer gap between the tips two gold triangles. Again, the point is to 

enhance a very small region of a diffraction-limited spot, thus improving the 

mismatch between light and nanoscale objects—and breaking the diffraction barrier. [9] 

[edit] STED 

A recent favorite is STED—stimulated emission depletion. Stefan Hell at the Max 

Planck Institute developed this method, which uses two laser pulses. The first pulse is 

a diffraction-limited spot that is tuned to the absorption wavelength, so excites any 

fluorophores in that region; an immediate second pulse is red-shifted to the emission 

wavelength and stimulates emission back to the ground state before, thus depleting 

the excited state of any fluorophores in this depletion pulse. The trick is that the 

depletion pulse goes through a phase modulator that makes the pulse illuminate the 

sample in the shape of a donut, so the outer part of the diffraction limited spot is 

depleted and the small center can still fluoresce. By saturating the depletion pulse, the 

center of the donut gets smaller and smaller until they can get resolution of tens of 

nanometers. [10] 

This technique also requires a raster scan like NSOM and standard confocal laser 

scanning microscopy. 

[edit] Fitting the PSF 

The methods above (and below) use experimental techniques to circumvent the 

diffraction barrier, but one can also use crafty analysis to increase the ability to know 

where a nanoscale object is located. The image of a point source on a charge-coupled 

device camera is called a point-spread function (PSF), which is limited by diffraction 

to be no less than approximately half the wavelength of the light. But it is possible to 

simply fit that PSF with a Gaussian to locate the center of the PSF—and thus the 

location of the fluorophore. The precision by which this technique can locate the 

center depends on the number of photons collected (as well as the CCD pixel size and 

other factors). [11] Regardless, groups like the Selvin lab and many others have

employed this analysis to localize single fluorophores to a few nanometers. This, of 

course, requires careful measurements and collecting many photons. 

[edit] PALM & STORM 

What fitting a PSF is to localization, photo-activated localization microscopy (PALM) 

is to "resolution"—this term is here used loosely to mean measuring the distance 

between objects, not true optical resolution. Eric Betzig and colleagues developed 

PALM; [12] Xiaowei Zhuang at Harvard used a similar techniques and calls it STORM: 

stochastic optical reconstruction microscopy. [13] The basic premise of both techniques 

is to fill the imaging area with many dark fluorophores that can be photoactivated into 

a fluorescing state by a flash of light. Because photoactivation is stochastic, only a 

few, well separated molecules "turn on." Then Gaussians are fit to their PSFs to high 

precision (see section above). After the few bright dots photobleach, another flash of 

the photoactivating light activates random fluorophores again and the PSFs are fit of 

these different well spaced objects. This process is repeated many times, building up 

an image molecule-by-molecule; and because the molecules were localized at 

different times, the "resolution" of the final image can be much higher than that 

limited by diffraction. 

The major problem with these techniques is that to get these beautiful pictures, it 

takes on the order of hours to collect the data. This is certainly not the technique to 

study dynamics (fitting the PSF is better for that). 

[edit] Structured illumination 

There is also the wide-field structured-illumination (SI) approach to breaking the 

diffraction limit of light. [14][15] SI—or patterned illumination—relies on both specific 

microscopy protocols and extensive software analysis post-exposure. But, because SI 

is a wide-field technique, it is usually able to capture images at a higher rate than 

confocal-based schemes like STED. (This is only a generalization, because SI isn't 

actually super fast. I'm sure someone could make STED fast and SI slow!) The main 

concept of SI is to illuminate a sample with patterned light and increase the resolution 

by measuring the fringes in the Moiré pattern (from the interference of the 

illumination pattern and the sample). "Otherwise-unobservable sample information 

can be deduced from the fringes and computationally restored." [16] 

SI enhances spatial resolution by collecting information from frequency space outside 

the observable region. This process is done in reciprocal space: the Fourier transform 

(FT) of an SI image contains superimposed additional information from different 

areas of reciprocal space; with several frames with the illumination shifted by some 

phase, it is possible to computationally separate and reconstruct the FT image, which 

has much more resolution information. The reverse FT returns the reconstructed 

image to a super-resolution image. 

But this only enhances the resolution by a factor of 2 (because the SI pattern cannot 

be focused to anything smaller than half the wavelength of the excitation light). To 

further increase the resolution, you can introduce nonlinearities, which show up as 

higher-order harmonics in the FT. In reference [16] , Gustafsson uses saturation of the 

fluorescent sample as the nonlinear effect. A sinusoidal saturating excitation beam

produces the distorted fluorescence intensity pattern in the emission. This 

nonpolynomial nonlinearity yields a series of higher-order harmonics in the FT. 

Each higher-order harmonic in the FT allows another set of images that can be used to 

reconstruct a larger area in reciprocal space, and thus a higher resolution. In this case, 

Gustafsson achieves less than 50-nm resolving power, more than five times that of the 

microscope in its normal configuration. 

The main problems with SI are that, in this incarnation, saturating excitation powers 

cause more photodamage and lower fluorophore photostability, and sample drift must 

be kept to below the resolving distance. The former limitation might be solved by 

using a different nonlinearity (such as stimulated emission depletion or reversible 

photoactivation, both of which are used in other sub-diffraction imaging schemes); the 

latter limits live-cell imaging and may require faster frame rates or the use of some 

fiducial markers for drift subtraction. Nevertheless, SI is certainly a strong contender 

for further application in the field of super-resolution microscopy. 

[edit] Extensions of the optical microscope 

Most modern instruments provide simple solutions for micro-photography and image 

recording electronically. However such capabilities are not always present and the 

more experienced microscopist will, in many cases, still prefer a hand drawn image 

rather than a photograph. This is because a microscopist with knowledge of the 

subject can accurately convert a three dimensional image into a precise two 

dimensional drawing . In a photograph or other image capture system however, only 

one thin plane is ever in good focus. 

The creation of careful and accurate micrographs requires a microscopical technique 

using a monocular eyepiece. It is essential that both eyes are open and that the eye 

that is not observing down the microscope is instead concentrated on a sheet of paper 

on the bench besides the microscope. With practice, and without moving the head or 

eyes, it is possible to accurately record the observed details by tracing round the 

observed shapes by simultaneously "seeing" the pencil point in the microscopical 

image. 

Practising this technique also establishes good general microscopical technique. It is 

always less tiring to observe with the microscope focussed so that the image is seen at 

infinity and with both eyes open at all times. 

[edit] Other optical microscope enhancements 

stereomicroscope 

[edit] X-ray microscopy 

Main article: X-ray microscopy 

As resolution depends on the wavelength of the light. Electron microscopy has been 

developed since the 1930s that use electron beams instead of light. Because of the 

much lower wavelength of the electron beam, resolution is far higher.

Though less common, X-ray microscopy has also been developed since the late 

1940s. The resolution of X-ray microscopy lies between that of light microscopy and 

the electron microscopy. 

[edit] Electron Microscopy 

For light microscopy the wavelength of the light limits the resolution to around 0.2 

micrometers. In order to gain higher resolution, the use of an electron beam with a far 

smaller wavelength is used in electron microscopes. 

• Transmission electron microscopy (TEM) is principally quite similar to the 

compound light microscope, by sending an electron beam through a very thin 

slice of the specimen. The resolution limit nowadays (2005) is around 0.05 

nanometer. 

• Scanning electron microscopy (SEM) visualizes details on the surfaces of cells 

and particles and gives a very nice 3D view. It gives results much like the 

stereo light microscope and akin to that its most useful magnification is in the 

lower range than that of the transmission electron microscope. 

[edit] Atomic de Broglie microscope 

Main article: Atomic de Broglie microscope 

The atomic de Broglie microscope is an imaging system which is expected to provide 

resolution at the nanometer scale using neutral He atoms as probe particles. [17][18] . 

Such a device could provide the resolution at nanometer scale and be absolutely nondestructive, 

but it is not developed so well as optical microscope or an electron 

microscope. 

[edit] Scanning probe microscopy 

This is a sub-diffraction technique. Examples of scanning probe microscopes are the 

atomic force microscope (AFM), the Scanning tunneling microscope and the photonic 

force microscope. All such methods imply a solid probe tip in the vicinity (near field) 

of an object, which is supposed to be almost flat. For more detail, see Scanning probe 

microscopy. 

[edit] Ultrasonic force microscopy 

Ultrasonic Force Microscopy (UFM) has been developed in order to improve the 

details and image contrast on "flat" areas of interest where the AFM images are 

limited in contrast. The combination of AFM-UFM allows a near field acoustic 

microscopic image to be generated. The AFM tip is used to detect the ultrasonic 

waves and overcomes the limitation of wavelength that occurs in acoustic 

microscopy. By using the elastic changes under the AFM tip, an image of much 

greater detail than the AFM topography can be generated. 

Ultrasonic force microscopy allows the local mapping of elasticity in atomic force 

microscopy by the application of ultrasonic vibration to the cantilever or sample. In an

attempt to analyse the results of ultrasonic force microscopy in a quantitative fashion, 

a force-distance curve measurement is done with ultrasonic vibration applied to the 

cantilever base, and the results are compared with a model of the cantilever dynamics 

and tip-sample interaction based on the finite-difference technique. 

[edit] Infrared microscopy 

The term infrared microscope covers two main types of diffraction-limited 

microscopy. The first provides optical visualisation plus IR spectroscopic data 

collection. The second (more recent and more advanced) technique employs focal 

plane array detection for infrared chemical imaging, where the image contrast is 

determined by the response of individual sample regions to particular IR wavelengths 

selected by the user. 

IR versions of sub-diffraction microscopy (see above) exist also. These include IR 

NSOM [19] and photothermal microspectroscopy. 

[edit] Amateur Microscopy 

Amateur Microscopy is the investigation and observation of biological and nonbiological 

specimens for recreational purposes using an optical microscope (light 

microscopes). Collectors of minerals, insects, seashells and plants may use 

microscopes as tools to uncover features that help them classify their collected items. 

Other amateurs may be interested in observing the life found in pond water and of 

other samples. Microscopes may also prove useful for the water quality assessment 

for people that keep a home aquarium. Photographic documentation and drawing of 

the microscopic images are additional tasks that augment the spectrum of tasks of the 

amateur. There are even competitions for photomicrograph art. Participants of this 

pastime may either use commercially prepared microscopic slides or may engage in 

the task of specimen preparation. 

While microscopy is a central tool in the documentation of biological specimens, it is 

rarely sufficient to justify the discovery of a new species based on microscopic 

investigations alone. Often genetic and biochemical tests are necessary to confirm the 

discovery of a new species. A fully equipped laboratory may be necessary, something 

often not available to amateurs. For this reason it may be unlikely that amateur 

microscopists are capable of substantiating their find to the extent to yield a scientific 

publication. 

In the late 1800's amateur microscopy became a popular hobby in the United States 

and Europe. Professor John Phin published "Practical Hints on the Selection and Use 

of the Microscope (Second Edition, 1878)," and was also the editor of the “American 

Journal of Microscopy.” 


• Köhler illumination 

• Two-photon excitation microscopy


1. ^ Abramowitz M, Davidson MW (2007). Introduction to Microscopy. Molecular 

Expressions. Retrieved on 2007-08-22. 

2. ^ Abramowitz M, Davidson MW (2007). Darkfield Illumination. Retrieved on 2007- 

08-22. 

3. ^ Abramowitz M, Davidson MW (2007). Rheinberg Illumination. Retrieved on 2007- 

08-22. 

4. ^ Wallace W, Schaefer LH, Swedlow JR (2001). "A workingperson's guide to 

deconvolution in light microscopy". BioTechniques 31 (5): 1076-8, 1080, 1082 

passim. PMID 11730015. 

5. ^ WEM News and Views 

6. ^ Fresnel Diffraction Applet (Java applet). Retrieved on 2007-08-22. 

7. ^ Cummings JR, Fellers TJ, Davidson MW (2007). Specialized Microscopy 

Techniques - Near-Field Scanning Optical Microscopy. Olympus Microscopy 

Resource Center. Retrieved on 2007-08-22. 

8. ^ Sánchez EJ, Novotny L, Xie XS (1999). "Near-Field Fluorescence Microscopy 

Based on Two-Photon Excitation with Metal Tips". Phys Rev Lett 82: 4014-7. 

doi:10.1103/PhysRevLett.82.4014. 

9. ^ Schuck PJ, Fromm DP, Sundaramurthy A, Kino GS, Moerner WE (2005). 

"Improving the Mismatch between Light and Nanoscale Objects with Gold Bowtie 

Nanoantennas". Phys Rev Lett 94: 017402. doi:10.1103/PhysRevLett.94.017402. 

10. ^ STED 

11. ^ Webb paper 

12. ^ PALM 

13. ^ STORM 

14. ^ Bailey, B.; Farkas, D. L.; Taylor, D. L.; Lanni, F. Enhancement of axial resolution 

in fluorescence microscopy by standing-wave excitation. Nature 1993, 366, 44–48. 

15. ^ Gustafsson, M. G. L. Surpassing the lateral resolution limit by a factor of two using 

structured illumination microscopy. J. of Microsc. 2000, 198(2), 82–87. 

16. ^ a b Gustafsson, M. G. L. http://dx.doi.org/10.1073/pnas.0406877102 Nonlinear 

structured-illumination microscopy: Wide-field fluorescence imaging with 

theoretically unlimited resolution. PNAS 2005, 102(37), 13081–13086. 

17. ^ D.Kouznetsov; H. Oberst, K. Shimizu, A. Neumann, Y. Kuznetsova, J.-F. Bisson, 

K. Ueda, S. R. J. Brueck (2006). "Ridged atomic mirrors and atomic nanoscope". 

JOPB 39: 1605-1623. 

18. ^ Atom Optics and Helium Atom Microscopy. Cambridge University, http://wwwsp.phy.cam.ac.uk/research/mirror.php3 

19. ^ H M Pollock and D A Smith, The use of near-field probes for vibrational 

spectroscopy and photothermal imaging, in Handbook of vibrational spectroscopy, 

J.M. Chalmers and P.R. Griffiths (eds), John Wiley & Sons Ltd, Vol. 2, pp. 1472 - 

1492 (2002) 

[edit] Further reading 

• Advanced Light Microscopy vol. 1 Principles and Basic Properties by Maksymilian 

Pluta, Elsevier (1988) 

• Advanced Light Microscopy vol. 2 Specialised Methods by Maksymilian Pluta, 

Elsevier (1989) 

• Introduction to Light Microscopy by S. Bradbury, B. Bracegirdle, BIOS Scientific 

Publishers (1998) 

• Video Microscopy by Shinya Inoue, Plenum Press (1986)

• A review of sub-diffraction microscopy techniques Part I and Part II - a blog post 

with helpful information, some of which appears in this article 


• Microscopy Techniques Various Techniques Used In Microscopy 

• Carl Zeiss "Microscopy from the very beginning", a step by step tutorial into 

the basics of microscopy. 

• Interactive Fluorescence Dye and Filter Database Carl Zeiss Interactive 

Fluorescence Dye and Filter Database. 

• Nikon MicroscopyU - The source for microscopy education 

• Olympus Microscopy Resource Center 

• Microscopy in Detail - A resource with many illustrations elaborating the most 

common microscopy techniques 

• Images formed by simple microscopes - examples of observations with singlelens 

microscopes. 

• Portraits of life, one molecule at a time, a feature article on sub-diffraction 

microscopy from the March 1, 2007 issue of Analytical Chemistry 

[edit] Organizations 

v • d • e 

• Royal Microscopical Society (RMS) 

• Microscopy Society of America (MSA) 

• European Microscopy Society (EMS) 

Instrumentation 

Techniques 

Sampling 

Prominent 

publications 

[hide] 

Analytical chemistry 

Atomic absorption spectrometer · Flame emmission spectrometer · 

Gas chromatograph · High performance liquid chromatograph · 

Infrared Spectrometer · Mass spectrometer · Melting point apparatus · 

Microscope · Spectrometer · Spectrophotometer 

Calorimetry · Chemometrics · Chromatography · Electrochemistry · 

Gravimetric analysis 

Coning and quartering · Dilution · Dissolution · Filtration · Masking · 

Pulverization · Sample preparation · Separation process · Subsampling 

Analytical chemistry 

http://mycology.cornell.edu/fteach.html 

Fungi Perfecti (Olympia, Washington, USA) supplies a plethora of mushroomgrowing 

equipment, spawn and kits, books, and dried edible and medicinal 

mushrooms. Their online catalog and information about Paul Stamets' mushroom

cultivation seminars and consultation services can be found here. This elegant web 

site includes many impressive images of mushrooms and other products, including 

scanning electron micrographs of mushroom ultrastructure. 

George Barron's website 

This website includes some lovely images of fungi, including Entomophthora, 

Spinellus, and some nematode parasites. It also includes information on Barron's book 

"Mushrooms of Northeast North America" (in Canada entitled "Mushrooms of 

Ontario and Eastern Canada"). 

Glossary of Technical Terms in Plant Pathology 

This useful Glossary of technical terms in Plant Pathology was created by Phil 

Arneson of Cornell University. It includes definitions, illustrations, and sound files by 

Richard Korf to aid pronunciation. 

Irish Potato Famine 

A compilation of information on the Irish Potato Famine of the 1840s, during which 

time over 3 million Irish died, and many others (including some of my own ancestors) 

emigrated to other parts of the world. The Famine resulted from an outbreak of late 

blight, caused by Phytophthora infestans. 

John C. Tacoma Mushroom Slide Collection 

Many, many scanned images of mushrooms and allies, from photographs taken by 

John C. Tacoma, 1968-1978. Maintained by the Library of Indiana University-Purdue 

University Indianapolis. 

LichenLand 

Lichenland provides a fine introduction to lichens for both professionals and 

amateurs. Synoptic keys to taxa and to terms lead to many fine images of lichens, a 

compilation of their characteristics, and pertinent literature. 

Meredith Blackwell's Lab 

Meredith Blackwell's lab at Louisiana State University provides information on 

current research on insect-fungus associations, history of mycology, the genealogy of 

American mycologists, teaching resources, the LSU herbarium, and other tidbits. 

Microfungal home page 

Color images of many microfungi taken under the microscope. Over 100 genera of 

molds are represented.

Moulds: their isolation, cultivation and identification 

An online version of David Malloch's excellent guide to moulds (University of 

Toronto Press, 1981), complete with keys, media recipes, and illustrations of common 

genera. This book makes a great introduction to hyphomycetes for those with access 

to a microscope. 

Mushroom Toxins 

This discussion of mushroom toxins and the symptoms they produce forms a chapter 

of the "Bad Bug Book" by the US Food and Drug Administration. Other mycotoxins 

(aflatoxin and ilk) are discussed in a subsequent chapter. 

Mushrooms and Magic 

The Mycotheology Home Page provides an interesting discussion of the role of fungi 

in magic, folklore, and religion. 

Mushrooms of North Carolina 

Mycology students at Duke University (NC, USA) have prepared this site 

documenting the mushrooms of North Carolina. Their excellent photographs are 

available here. 

Mycologue Publications 

Mycologue is a publishing company founded by W. Bryce Kendrick. It provides 

books, teaching materials, and computerized keys to fungi (Canada). The site also 

includes information and many illustrations of fungi that complement Dr. Kendrick's 

textbook, The Fifth Kingdom (q.v.). 

Mycology class at Arizona State University 

Home page of the General Mycology class at Arizona State University, USA. 

Mycology class at Oregon State University 

Home page of the mycology class at Oregon State University, USA. 

Mycology class at Towson University 

The home page of the Mycology class at Towson University, in Maryland, USA. 

Mycology classes at Humboldt University 

Home page of Mycology classes at Humboldt University, California, USA.

Mycology Course at the University of Illinois at Urbana/Champaign 

This web site for Dr. Carol Shearer's Mycology class includes a syllabus, lab 

exercises, and many excellent lecture illustrations. 

Mycology Online 

Mycology Online is a guide to fungal pathogens of humans, the diseases they cause, 

and selected case studies. This Australian site is searchable, nicely illustrated (not for 

the squeamish!), and replete with information. 

Mycorrhiza information exchange 

The Mycorrhiza Information Exchange covers everything you need: literature 

databases, job ads, teaching tips, images, inoculum sources, links, etc. Participation is 

invited. 

Mycorrhizae and Plant Phylogeny 

A website devoted to mycorrhizae and plant systematics, and the evolution of 

mycorrhizal symbiosis. 

Mycorrhizas webpage 

This guide to mycorrhizal associations (adapted and excerpted from a larger book) is 

provided by Mark Brundett at CSIRO (Australia). It details the structure and 

development of mycorrhizae, with handsome images and good textual explanation. It 

makes a wonderful teaching tool. 

Mycorrhizospheres of boreal forest trees 

This site from the Biocenter at the University of Helsinki (Finland) includes scientific 

publications documenting the diversity, interactions and functions of forest tree 

mycorrhizae. 

Mycotoxin homepage 

A unit of the US Dept. of Agriculture, Agricultural Research Service that focuses on 

mycotoxin research. 3-dimensional molecular structures of a few mycotoxins 

produced by molds are available here. 

MyxoWeb 

This web site devoted to myxomycetes provides information on the plasmodial slime 

molds, including some impressively gooey images.

Natural Perspective's introduction to fungi 

Natural Perspective's nicely illustrated introduction to the fungal kingdom. 

North American Lichen Project 

The North American Lichen Project includes essays on lichen biology and the uses of 

lichens by people and animals, as well as excerpts and lovely photographs from the 

forthcoming book Lichens of North America, by I.M. Brodo, S.D. Sharnoff, and S. 

Sharnoff (Yale University Press). 

North American Mycological Association 

NAMA is a great group for amateur mycologists. It provides a national mushroom 

poisoning registry, sponsors an annual foray, and publishes a fine annual journal, 

McIlvainea, and a bimonthly newsletter, The Mycophile. Also available through 

NAMA are suggestions for teaching K-12 students about fungi, and other tidbits. 

Penn State Mushroom Spawn Lab 

Pennsylvania State University's strong program in mushroom cultivation presents fact 

sheets and other information about commercial mushroom production on these pages. 

PSU's mushroom growers' information pages are part of this site. 

Plant Pathogenic Fungi 

The University of Kentucky's course in plant pathogenic fungi has web pages that 

include the syllabus and other information. 

Plant Pathology 

The Plant Pathology courses at the University of Nebraska-Lincoln (USA). Most 

materials are for registered students only; a distance learning course is offered. 

Plant Pathology Internet Guidebook 

The Plant Pathology Internet Guidebook is a comprehensive source for Plant 

Pathology resources online. It is available through the Institute of Plant Diseases and 

Plant Protection in Hannover, Germany. 

Plant Pathology Simulations 

Computer simulations for teaching aspects of plant pathology and epidemiology.

Plasmodiophorid Home Page 

These are pages devoted to the Plasmodiophorales that include information about life 

histories, cytology, and biology of this interesting group of fungus-like protists. The 

site is no longer being updated. 

Pythium insidiosum 

Pythiosis is a disease of humans and animals that can be caused by the subject of this 

web page, Pythium insidiosum. The site includes graphic images and information on 

biology, epidemiology, diagnosis, and treatment. 

Spongospora Homepage 

Spongospora subterranea is a plasmodiophorid pathogen of potatoes (and other plants) 

and an emerging pathogen in some regions. This workshop site introduces the biology 

and control of S. subterranea and related species, and includes images and a 

discussion board. 

The Fifth Kingdom 

W.B. Kendrick's delightful introductory mycology textbook, The Fifth Kingdom, is 

partly available online. This site includes over 800 lavish, colorful illustrations as a 

supplement to the text, which is available from Mycologue Publications (q.v.). The 

text of sample chapters is available, too. Dr. Kendrick's website also includes other 

publications for sale. 

The Rhynie Chert and its Flora 

The Rhynie Chert is a fossilized Devonian lake shore in Scotland that includes some 

of the oldest fossils of plants and their associated fungi. This nice site introduces the 

botanical and mycological finds of the Rhynie Chert, and provides photos of the 

oldest known lichen and early arbuscular mycorrhizal fungi. 

This is Not Just Plant Pathogenic Fungi! 

Students at Texas A M University have prepared a guide to plant pathogenic (and 

other) fungi. 

Tom Volk's web pages 

One stop shopping for mycology. These pages feature a "fungus of the month" 

column, with entertaining text and nice photos, in addition to a plethora of other 

information about fungi. Tom is a professor at the University of Wisconsin-La Crosse, 

USA.

Tree of Life 

This phylogenetic navigator provides a tree that shows the evolutionary relationships 

of living organisms, including fungi. It also supplies descriptive pages on selected 

terminal taxa. Like biological systematics itself, it's a work in progress. 

UC Berkeley's Introduction to Fungi 

The Museum of Paleontology at the University of California, Berkeley provides a 

well-prepared introduction to the kingdom Fungi, and also to two groups that have 

historically been studied by mycologists, the Oomycota and slime molds. Similar 

introductions are available for all other taxa. This link makes a valuable addition to 

any teaching program. 

University of Tennessee Mycology Labs 

Drs. Ron Petersen and Karen Hughes maintain a nice set of web pages that include a 

primer on Botanical Nomenclature, a synopsis of molecular phylogenetic techniques. 

These pages also provide an important resources on color standards used by 

mycologists: a synopsis of Fries' color terminology, and a concordance of colors in 

the Ridgway and Methuen color handbooks. Lots of information is also provided on 

the projects of staff and students. 

Views of the Famine 

An illustrated history of news coverage of the Irish Potato Famine that occurred in the 

1840s due to Phytophthora infestans, causal agent of late blight of potato. 

Wayne's Word on the fungal kingdom 

A delightful introduction to selected members of the kingdom Fungi from the e-zine, 

Wayne's Word. 

Western Montana Mycological Association (USA): Fungal Jungal 

The Western Montana Mycological Association maintains this nice site. It includes 

photos of Montana mushrooms, recipes, an oyster mushroom cultivation project, a 

mushroom "trunk" for teachers, a morel information site, and information on the 

WMMA's current activities. 

World-Wide Web Virtual Library 

You're there now! This is a distributed library of resources maintained at many 

different sites all over the world. Unlike some of the big search engines, VL site 

maintainers personally select and evaluate the links they recommend, with the result 

that VL sites generally have a high signal to noise ratio. The WWW VL is a good 

place to start when looking for electronic information on all kinds of different topics.

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Robert Koch 



Robert Koch 

Born 

Died 

Robert Koch 

December 11, 1843 

Clausthal, Hanover 

May 27, 1910 (aged 66) 

Baden-Baden, Germany 

Field Microbiology 

Institutions Imperial Health Office, Berlin, University of Berlin 

Alma mater University of Göttingen 

Academic advisor Friedrich Gustav Jakob Henle 

Known for 

Co-founder of bacteriology, 

Koch's postulates of germ theory, 

Isolator of anthrax, tuberculosis and cholera 

Notable awards Nobel Prize in Medicine, 1905 

For the American lobbyist, see Bobby Koch. 

Robert Koch (December 11, 1843 – May 27, 1910) was a German physician. He 

became famous for isolating Bacillus anthracis (1877), the tuberculosis bacillus 

(1882) and the cholera vibrio (1883) and for his development of Koch's postulates.

He was awarded the Nobel Prize in Physiology or Medicine for his tuberculosis 

findings in 1905. He is considered one of the founders of microbiology - he inspired 

such major figures as Paul Ehrlich and Gerhard Domagk. 

Contents 

[hide] 

• 1 Biography 


• 3 Consult 



[edit] Biography 

Robert Koch was born in Clausthal, Germany as the son of a mining official. He 

studied medicine under Friedrich Gustav Jakob Henle at the University of Göttingen 

and graduated in 1866. He then served in the Franco-Prussian War and later became 

district medical officer in Wollstein (now Wolsztyn, Poland). Working with very 

limited resources, he became one of the founders of bacteriology, the other major 

figure being Louis Pasteur. 

After Casimir Davaine showed the direct transmission of the anthrax bacillus between 

cows, Koch studied anthrax more closely. He invented methods to purify the bacillus 

from blood samples and grow pure cultures. He found that, while it could not survive 

outside a host for long, anthrax built persisting endospores that could last a long time. 

These endospores, embedded in soil, were the cause of unexplained "spontaneous" 

outbreaks of anthrax. Koch published his findings in 1876, and was rewarded with a 

job at the Imperial Health Office in Berlin in 1880. In 1881, he urged the sterilization 

of surgical instruments using heat. 

In Berlin, he improved the methods he used in Wollstein, including staining and 

purification techniques, and bacterial growth media, including agar plates (thanks to 

the advice of Angelina and Walther Hesse) and the Petri dish, named after its 

inventor, his assistant Julius Richard Petri. These devices are still used today. With 

these techniques, he was able to discover the bacterium causing tuberculosis 

(Mycobacterium tuberculosis) in 1882 (he announced the discovery on March 24). 

Tuberculosis was the cause of one in seven deaths in the mid-19th century. 

In 1883, Koch worked with a French research team in Alexandria, Egypt, studying 

cholera. Koch identified the vibrio bacterium that caused cholera, though he never 

managed to prove it in experiments. The bacterium had been previously isolated by 

Italian anatomist Filippo Pacini in 1854, but his work had been ignored due to the 

predominance of the miasma theory of disease. Koch was unaware of Pacini's work 

and made an independent discovery, and his greater preeminence allowed the

discovery to be widely spread for the benefit of others. In 1965, however, the 

bacterium was formally renamed Vibrio cholera Pacini 1854. 

In 1885, he became professor of hygiene at the University of Berlin, and later, in 

1891, director of the newly formed Institute of Infectious Diseases, a position which 

he resigned from in 1904. He started traveling around the world, studying diseases in 

South Africa, India, and Java. 

Probably as important as his work on tuberculosis, for which he was awarded a Nobel 

Prize (1905), are Koch's postulates, which say that to establish that an organism is the 

cause of a disease, it must be: 

• found in all cases of the disease examined 

• prepared and maintained in a pure culture 

• capable of producing the original infection, even after several generations in 

culture 

• be retrievable from an inoculated animal and cultured again. 

After Koch's success the quality of his own research declined (especially with the 

fiasco over his ineffective TB cure "tuberculin"), although his pupils found the 

organisms responsible for diphtheria, typhoid, pneumonia, gonorrhoea, cerebrospinal 

meningitis, leprosy, bubonic plague, tetanus, and syphilis, among others, by using his 

methods. 

He died on 27 May 1910 of a heart-attack in Baden-Baden, aged 66. [1] 

Koch crater on the Moon was named after him. The Robert Koch Prize and Medal 

were created to honour Microbiologists who make groundbreaking discoveries or who 

contribute to global health in a unique way. The first non-German to be awarded the 

medal was Professor Bill Hutchison of Strathclyde University in Glasgow. [2] 


1. ^ Robert Koch Institute 

2. ^ Parasitology in Scotland 

[edit] Consult 

• Thomas Brock, Robert Koch: A Life in Medicine and Bacteriology, 

Washington D.C. (1999) 


• History of medicine 

• Microbiology 

• Timeline of medicine and medical technology 

[edit] External links

v • d • e 

• Biography at the Nobel Foundation website 

• Biography and bibliography in the Virtual Laboratory of the Max Planck 

Institute for the History of Science 

[hide] 

Nobel Laureates in Physiology or Medicine 

Emil Behring (1901) · Ronald Ross (1902) · Niels Finsen (1903) · Ivan Pavlov (1904) · 

Robert Koch (1905) · Camillo Golgi / Santiago Ramón y Cajal (1906) · Alphonse 

Laveran (1907) · Ilya Mechnikov / Paul Ehrlich (1908) · Emil Kocher (1909) · Albrecht 

Kossel (1910) · Allvar Gullstrand (1911) · Alexis Carrel (1912) · Charles Robert Richet 

(1913) · Robert Bárány (1914) · Jules Bordet (1919) · August Krogh (1920) · Archibald 

Hill / Otto Meyerhof (1922) · Frederick Banting / John Macleod (1923) · Willem 

Einthoven (1924) 

Complete roster · 1901–1925 · 1926–1950 · 1951–1975 · 1976–2000 · 2001–present 

Retrieved from "http://en.wikipedia.org/wiki/Robert_Koch" 

Categories: 1843 births | 1910 deaths | German biologists | German physicians | 

German inventors | German microbiologists | Tuberculosis | Nobel laureates in 

Physiology or Medicine | German Nobel laureates | German military personnel of the 

Franco-Prussian War | University of Göttingen alumni | Deaths by myocardial 

infarction | People from the Kingdom of Hanover 

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Kenneth Todar has taught microbiology to undergraduate students at The University of Texas, 

University of Alaska and University of Wisconsin since 1969. He received a PhD in Microbiology 

in 1972 from The University of Texas-Austin. His main teaching interests are in general 

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"The Microbial World". He resides in Madison, Wisconsin and Silvergate, Montana. 

WEB TEXT REVIEW (SCIENCE Magazine Vol 304: 1421) 

"The Good, the Bad, and the Deadly" 

The pearly droplets in this photo are colonies of Bacillus 

anthracis, the bacterium that causes anthrax. The bugs exude a 

goopy coating that repels immune system assaults and allows 

them to establish a foothold in the body. Learn more about the 

tricks bacteria use to prosper almost everywhere on Earth in 

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University of Wisconsin, Madison. High school and college 

students can absorb the basics of bacterial structure, physiology, 

classification, and ecology.The book emphasizes medical 

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host, how the body tries to corral invading microbes, and how 

the bugs elude these defenses. For example, the cholera 

bacterium releases a toxin that induces intestinal cells to spill 

ions and water, producing potentially lethal diarrhea.

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