Fungal Diversity

15
CONTENTS
Fungal Diversity
A. M. C. Tang, B. D. Shenoy and K. D. Hyde
Centre for Research in Fungal Diversity, Department of Ecology and Biodiversity, The University of Hong Kong, P. R. China
15.1 Introduction to the Fungi .................................................................................................. 15.1.1 General Characteristics........................................................................................ 15.1.2 Ascomycota ......................................................................................................... 15.1.3 Basidiomycota ..................................................................................................... 15.1.4 Chytridiomycota .................................................................................................. 15.1.5 Zygomycota ......................................................................................................... 15.2 Problems in Estimating Fungal Diversity ......................................................................... 15.2.1 Fungal Species Concepts and Nomenclature...................................................... 15.2.2 Use of Biodiversity Measures ............................................................................. 15.2.3 Knowledge of Fungal Diversity .......................................................................... 15.3 Global Fungal Diversity Estimate: Described and Undescribed...................................... 15.4 Examples of Fungal Diversity from Selected Hosts ........................................................ 15.4.1 Fungi on Poaceae, Cyperaceae and Juncaceae ................................................... 15.4.2 Leaf Litter Fungi ................................................................................................. 15.4.3 Fungi on Invertebrates ......................................................................................... 15.5 Species Rich Genera of Fungi .......................................................................................... 15.5.1 Colletotrichum ..................................................................................................... 15.5.2 Pestalotiopsis ....................................................................................................... 15.5.3 Mycosphaerella.................................................................................................... 15.6 An Era of Genomics and Molecular Biology................................................................... 15.6.1 Applications of Molecular Biology in Mycological Systematics ...................... 15.6.2 Molecular Study on Fungal Diversity in Soil..................................................... 15.6.3 Unravelling Species Rich Genera Using Molecular Techniques........................ 15.6.4 Fungal Endophytes: Underestimated?................................................................. 15.7 Concluding Remarks ......................................................................................................... References ....................................................................................................................................
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ABSTRACT
Fungi are ubiquitous, benecial, harmful and mutualistic. They perform some of the most important basic roles in life and have some of the greatest potential for biotechnology, yet as few as 7% of the total estimated fungal species on Earth are described. There are thought to be 1.5 million fungal species, but there are huge problems in obtaining estimates of fungal diversity. These include: species recognition, as there are usually few useful characters to distinguish species; separate taxonomic binomials for asexual and sexual states of the same species; lack of specialist mycologists;
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2007 by Taylor & Francis Group, LLC
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Reconstructing the Tree of Life
and the unfortunate downward trend for mycological biodiversity funding. Estimates of fungal diversity are discussed for selected plant groups, insects and species rich genera with more than 1,000 species. We conclude that it is important to identify habitats and substrates where a greater fungal diversity may occur in order to offer maximum protection to fungal resources. The large variation in estimates of fungal diversity means that considerable data are required before we can produce a reliable estimate of the number of species of fungi.
15.1 INTRODUCTION TO THE FUNGI 15.1.1 GENERAL CHARACTERISTICS

Fungi are extremely important organisms, as they have benecial, harmful, mutualistic and basic roles in life. They cause diseases of animals, including humans, and particularly of plants and can have deleterious effects on crop yields. They also provide food in the form of mushrooms and are used in numerous biotechnological applications, including wine and bread production and as avourings. Their role in biodegradation is basic to life through nutrient cycling, but this ability itself causes problems, such as in wood decay and food moulds. The motivation for a better understanding of fungal diversity results from the need for knowledge on their ecological functioning, evolutionary relationships, physiological and biochemical properties, and biotechnological and pharmaceutical potential. The decline in fungal diversity following habitat destruction in tropical forests has prompted mycologists to stress the need to accelerate exploration and characterisation of fungal resources in order to use them sustainably and protect them from destruction1,2. Fungal resources have been extensively screened for novel compounds, and bioexploitation has been undertaken by numerous biotechnological and pharmaceutical companies3. Six of the top 20 best-selling drugs are of fungal origin, and it has been estimated that the overall value of the fungal bioprospecting market may range between US$100 and 200 million46. In order to offer maximum protection to fungal resources and optimise the potential for biologically active novel compound discovery, it is important to identify habitats and substrates where a greater fungal diversity may occur3. Fungi are eukaryotic organisms that lack chlorophyll and are saprobic on dead organic matter. They are generally microscopic, and their cell walls are composed primarily of chitin and glucans7. These organisms encompass a huge range of forms from microscopic single celled yeasts to large macrofungi such as trufes and puffballs. Moulds are composed of long laments of cells, termed hyphae, joined together. When moulds grow, the hyphae intertwine to form the mycelium. Fungi are primarily responsible for the recycling of mineral nutrients in forest ecosystems8,9. During the decomposition process, nutrients that are immobilised in the detritus are mineralised and released into the soil in a form suitable for plant uptake10. The role of fungi is crucial in the decomposition process, since they can degrade the lignocellulose matrix in forest litter, whilst other organisms cannot11,12. Fungi also form mutualistic relationships with other organisms, such as lichens, mycorrhizae and endophytes. Lichens are formed from the symbiosis of algae or cyanobacteria with certain fungi, mostly ascomycetes. It is estimated that about one fth of all known extant fungal species form these obligate symbiotic relationships, and major Ascomycota lineages today were once derived from lichenforming ancestors13. Fungi exist as benecial symbionts with plants, occurring within their roots systems and aerial parts. Mycorrhizal symbiosis within the root systems are ubiquitous, ancient and essential for plants to survive in natural ecosystems, and molecular evidence suggests that successful colonisation of land by plants probably was facilitated by mycorrhizal symbiosis14. Endophytic symbiosis within plants is also ubiquitous, and endophytes have been isolated from all plants that have been examined, and every individual plant is probably host to at least two to four endophytes6,15,16. Fungi are well known for causing diseases of plants, animals and other fungi. Notable phytopathological examples include chestnut blight caused by Cryphonectria parasitica, Dutch elm disease by Ceratocystis ulmi, ergot of sorghum by Claviceps africana and the devastating late blight of potato
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by Phytophthora infestans, which was responsible for the epidemics that contributed to the Irish famine in 184517. Contrary to fungal diseases in plants, fungal diseases in animals are more specic, and probably every species of animal has some specic fungal parasites; Beauveria and Metarhizium are examples of well studied insect parasites. Fungi have been tested and formulated for application in insect pest management systems as important biocontrol agents18. For example, Cordyceps is a pathogenic fungus which produces fruiting bodies from caterpillars after killing the host. It is well known for its ability to produce numerous bioactive metabolites, including cyclosporins and efrapeptins that have been used in medicine for the immunosuppressive capabilities19,20. Fungi form one of the six kingdoms of life (Animalia, Bacteria, Chromista, Fungi, Plantae and Protozoa; but see Hodkinson and Parnell, Chapter 1 for a more recent phylogenetic interpretation of the major groups of life)21. Surprisingly, fungi are a group more closely related to animals than plants according to ribosomal DNA and protein coding gene sequences, but this theory is still controversial2224. Fungi are subdivided into four phyla, namely Ascomycota, Basidiomycota, Chytridiomycota and Zygomycota25. Molecular data suggest that some phyla that were once considered as fungi, such as the plasmodial and cellular slime moulds (Myxomycota and Dictyosteliomycota) and the water moulds (Oomycota), should now be excluded from the kingdom23. The following is a summary of the characteristic features of the four phyla within the Fungi.
15.1.2 ASCOMYCOTA
The phylum Ascomycota, or sac fungi (Greek (hereafter Gr.) ascus, sac; mycetos, fungi) is a group in which the sexual process involves the production of eight (or multiples of eight) haploid ascospores through the meiosis of a diploid nucleus in an ascus (Figure 15.1ad)26. It is the largest phylum of fungi, with approximately 45,000 described species, and it represents 65% of the known species of fungi27. It includes many notable members such as Claviceps purpurea, the natural hallucinogen producer which grows on the grains of grasses, Penicillium notatum and P. chryosogenum used in the production of antibiotic penicillin, Saccharomyces cerevisiae responsible for fermentation in the production of alcohol, and Neurospora, the model organism for genetic studies, as well as morels (Morchella esculenta) and trufes, such as Tuber melanosporum, used in Western cuisines. As well as reproducing sexually, Ascomycetes also sporulate asexually, with the formation of conidia (spores) on conidiophores (Hyphomycetes) or inside a conidiomata (Coelomycetes). The sexual stage of an ascomycete is termed the teleomorph, and the asexual stage is the anamorph. Three subphyla are designated in Ascomycota according to our recent classication28. They are the subphylum Pezizomycotina (Euascomycetes), Saccharomycotina (Hemiascomycetes) and Taphrinomycotina (Archiascomycetes). Pezizomycotina (Euascomycetes) are a group comprising more than 90% of Ascomycota, and 98% are lichenised. Members of Pezizomycotina are designated into two groups: ascohymenial and ascolocular. Ascohymenial relates to an ascocarp that forms after nuclear pairing. The ascohymenial type ascomata may be closed (cleistothecium) (Figure 15.1a), provided with an opening (perithecium) (Figure 15.1b), or open as a cup (apothecium) (Figure 15.1c). Ascolocular relates to a mode of ascocarp growth in which a perithecium (ask-shaped fruiting body) develops within a cushioning hollow of cells (stroma) in a depression of the hymenium (locule). Notable examples of ascohymenial ascomycetes include Aspergillus and Penicillium (class Eurotiomycetes), Ascobolus and Morchella (Pezizomycetes), and Claviceps, Cordyceps and Neurospora (Sordariomycetes). Examples of ascolocular ascomycetes include Pleospora, Pyrenophora and Venturia (Dothideomycetes). Saccharomycotina (Hemiascomycetes) are a small subphylum but of tremendous importance. They are characterised by the absence of ascoma so that the asci are naked. They include the true yeast Saccharomyces cerevisiae (Figure 15.1d), which is important in the processing of bread and alcoholic beverages. Saccharomyces was also the rst eukaryote to have its genome completely sequenced29,30. Taphrinomycotina (Archiascomycetes) are a diverse group including saprobic and parasitic forms that have been grouped primarily on the basis of rDNA sequence analysis31,32. In some
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FIGURE 15.1 Fungi representing different fungal classes. (a) Cleistothecium fruiting body (ascomycete); (b) Perithecium fruiting body (ascomycete); (c) Apothecium fruiting body (ascomycete); (d) Saccharomyces cerevisiae (ascomycete); (e) Amanita species (basidiomycete); (f) Zoosporangium stage of Chytriomyces species (chytridiomycete); (g) Zoospore stage of Chytriomyces species (chytridiomycete); (h) Sporangium (asexual) stage of Rhizopus stolonifer (zygomycete); (i) Zygosporangium (sexual) stage of Rhizopus stolonifer (zygomycete). (Drawings by Alvin M.C. Tang.)
species, such as Schizosaccharomyces pombe, the ssion yeast was surprisingly separated from Saccharomyces cerevisiae (budding yeast, subphylum Saccharomycotina) based on molecular data33. Pneumocystis carinii, an extracellular biotroph of alveoli in infected lungs of mammals, was once thought to be a protozoan, but is now classied to this subphylum based on DNA sequences34.
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15.1.3 BASIDIOMYCOTA
The phylum Basidiomycota (Gr. basidion, small base or pestal; mykes, fungi) is a group in which the sexual process involves the production of haploid basidiospores borne on a basidium in which a diploid nucleus undergoes meiosis (Figure 15.1e; Figure 15.2)26. It contains approximately 30,000 described species, which accounts for about 35% of the known species of fungi27. Molecular analyses have dened three lineages from Basidiomycota, two without fruiting bodies, Urediniomycetes and Ustilaginomycetes, and one with fruiting bodies, Hymenomycetes35. Urediniomycetes contain approximately 7,400 (34%) of the described species of Basidiomycota27,36. It includes the plant pathogenic fungi, the rusts (Uredinales) and the yeasts (Sporidiales), which are saprotrophs and pathogens of plants, animals and fungi. Ustilaginomycetes contain approximately
FIGURE 15.2 (A colour version of this gure follows page 240) Basidiomycete fungi. (a) Dacryopinax spathularia, (b) Pseudocoprinus disseminatus. (Photos reproduced with permission from Edward Grand, Chiang Mai, Thailand.)
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1,300 (6%) of the described species of Basidiomycota27,37. It includes the smut fungi (Ustilaginales), which form black and dusty masses of teliospores in diseased plants. Smuts are notorious as they cause millions of dollars of damage to important food crops and ornamentals. Hymenomycetes consists of about 13,500 (60%) of the described species of Basidiomycota27,35. There are two basal evolutionary branches (sister groups to the rest of Hymenomycetes), one leading to Tremellales (jelly fungi) and the other to Dacrymycetales, Auriculariales (tree ear fungi), Agaricales (mushrooms) and Aphyllophorales (shelf fungi). Agaricales contains many names that have been known since humans started to collect mushrooms. Amanita (Figure 15.1e) is a genus commonly associated with mushroom poisoning, whilst Agaricus bitorquis (button mushroom), Flammulina velutipes (Enokitake), Lentinula edodes (shiitake), and Pleurotus ostreatus (oyster mushroom) are widely known as food.
15.1.4 CHYTRIDIOMYCOTA
The Chytridiomycota is the only fungal phylum that produces motile zoospores and requires water for dispersal (Figure 15.1fg). They have been classied in the Protista and Protoctista38,39, but based on SSU rDNA sequence they were recently included in the kingdom Fungi40. Chytridiomycota are probably a very ancient group, with extant forms possibly having changed little since the early periods of eukaryotic evolution41. They are commonly found in lakes, streams, ponds, roadside ditches and coastal marine environments, as well as in soil. As members of terrestrial and aquatic microbial communities, chytrids play an important ecological role in decomposition of chitin, cellulose, keratin and hemicellulose42. Notable plant pathogenic species include Synchytrium endobioticum (potato black wart), Physoderma maydis (corn brown spot) and Urophlytis alfalfae (alfalfa crown wart). As a representative of lower fungi, Allomyces macrogynus has become fashionable in molecular biology for the comparative study of the primitive genetic features with other higher fungi4345.
15.1.5 ZYGOMYCOTA
The phylum Zygomycota (Gr. zygos, yoke of marriage; mykes, fungi) is principally characterised by the presence of nonseptate (coenocytic) mycelium and the production of dark, thick-walled, ornamented sexual spores, called zygospores (Figure 15.1hi). Members of the phylum are generally morphologically and ecologically diverse, with some species not possessing zygospores46. Zygomycota has been subdivided into two classes: Trichomycetes and Zygomycetes47,48. Trichomycetes are symbionts in the gut of arthropods, while Zygomycetes are saprobic, haustorial or nonhaustorial parasites of animals, plants or fungi48. The position of Trichomycetes within the kingdom Fungi remains controversial, since members of Amoebidiales in this class have recently grouped with protists by molecular data, and phylogenetic relationships of Eccrinales and Asellariales are still unresolved49,50. Members of Mucorales in the class Zygomycetes, on the other hand, are the most well known group. Rhizopus and Mucor are the most notable fungi, because they cause fruit rots and bread moulds. Clinically, members of this order, such as Cokeromyces, Cunninghamella, Rhizomucor, Rhizopus and Saksenaea, are potential human or animal pathogens, especially in immunosuppressed patients during organ transplants and patients with immunological disorders48,51. Members of Glomales in Zygomycetes are the most important order ecologically, as they form mycorrhizae with the majority of plants worldwide.
15.2 PROBLEMS IN ESTIMATING FUNGAL DIVERSITY 15.2.1 FUNGAL SPECIES CONCEPTS

AND
NOMENCLATURE
The concepts of species recognition in fungi have often been problematic. Attempts to derive a universally applicable concept have been difcult, with several concepts currently in use5254. Species denitions have been based on phenotypic similarity, ecological parameters, reproductive isolation or
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cohesion and evolutionary principles. In practice, fungal species concepts are always the combinations of morphological, biological and phylogenetic species concepts5558. There are often very few useful characters to separate fungal species, and therefore visual observation may not always be denitive. Cultures are usually required to ascertain species status using morphological and biological species concepts, and yet only 16% of the approximately 100,000 known fungal species are in culture collections worldwide59. This makes progress of species determination difcult. Further complications are caused by the presence of asexual forms (anamorphs) of Ascomycota and Basidiomycota. A single fungal genome always has separate taxonomic binomials for the teleomorph (sexual stage), multiple anamorphs (asexual stage), the chlamydospores, the sclerotia and even the vegetative mycelium60. Some Ascomycota may have two or more anamorphs, whilst others seem to be strictly asexual, as sexual reproduction has not clearly been observed60. Article 59 of the International Code of Botanical Nomenclature was specically written for fungi to allow dual or multiple names for a single fungal genome. Whether a single name or multiple names should be used has been controversial; however, it remains an unavoidable complication for many fungal groups, due to the rarity with which multiple morphs are encountered and technical difculties in linking stages of life cycles60,61.
15.2.2 USE
OF
BIODIVERSITY MEASURES
Biodiversity measures are quantitative expressions of community structure. The species richness (number of species of a given taxon) and evenness (how similar species are in their abundances) are important measures of diversity62. There are many indices available for estimating these measures, and each index emphasises different components of diversity so that no unied diversity index is available62,63. For example, Menhinicks index and Margalefs diversity index64 are measures of species richness. The use of species richness indices to interpret biodiversity may cause variations in results due to factors such as sampling size, scope and duration65. For example, the most frequently used Shannon index has problems of confounding species richness and evenness; changes of either richness or evenness can result in changes in the index62. The Brillouin index is a more appropriate choice when the randomness of the sample cannot be guaranteed, or if the community is completely censused6669. However, the Brillouin index has been less popular than the Shannon index, since it is more time consuming to produce and is dependent on sample size62.
15.2.3 KNOWLEDGE
OF
FUNGAL DIVERSITY
The signicance of microorganisms as a component of biological diversity had not been fully acknowledged until the recent growth in bioprospecting research (the search for novel compounds or organisms that might have potential economic uses)7075. The major problem in obtaining reliable estimates of fungal diversity is the lack of specialist mycologists, especially in most developing countries where there are few careers available and no training is offered. The other problem is the lack of funds. A recent trend is the diversion of resources from basic inventories and monographic works to molecular systematic studies76. The huge sums supplied by the National Science Foundation (NSF) to support ATOL (Assembling the Tree of Life) (US$8 million in 2002; US$12 million in 2003) or the Deep Hypha Project for fungi for molecular work have inevitably de-emphasised the theoretical basis for taxonomy and undermined the intellectual contents of species identication76. Taxonomy, an already weakened component of science due to decades of negligence, is now suffering from the loss of positions and funding77. The rate of description of new fungal species has been declining since the 1960s, from about 1,4001,500 species per year to 1,097 species per year in 1990s78,79. New species being catalogued in Index of Fungi (http://www.cabi.org) are documented at the rate of about 800 each year. So far, we know as little as 7% of the estimated 1.5 million world fungal diversity. If we calculate according to recent cataloguing rates, we will probably need about 800 more years before we can know 50% of all the fungal species. The unfortunate fact is that our knowledge is already 70100 years behind that of vascular plants59,73.
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15.3 GLOBAL FUNGAL DIVERSITY ESTIMATE: DESCRIBED AND UNDESCRIBED

Fungal names have been catalogued in a variety of printed records, such as: Index of Fungi (1940present, published twice yearly by CAB International), Sylloge Fungorum (18821931, 1972 by P.A. Saccardo) and Petraks List (19201939 by F. Petrak). Searching for early records of fungal names is a daunting task and is effectively restricted to the several institutions where a range of publications are available. Since the mid-1980s, efforts have been made in the International Mycological Institute (IMI; now incorporated into CABI Bioscience) to convert all the printed records into an open and accessible computerised database80, and it is now available both in the fungal database Index Fungorum (http://www.indexfungorum.org/Names/Names.asp) and the world species database Species 2000 (http://www.sp2000.org/). In June 2005, there were 382,808 records in Index Fungorum, which probably include less than 10% of duplicates that could not be easily or unambiguously identied by automatic means, and also perhaps >50% synonyms. Hawksworth59 and Kirk80 tried to estimate the actual number of known fungal species by using a synonym percentage of 65%, derived from 15 fungal monographs81, and concluded that about 105,000 species of fungi may already be known. This gure was a little lower than the estimation of 120,000 from the same data set when only directly ascribed synonyms and no excluded taxa were considered79. Nevertheless, these gures are higher than the 72,065 in the eighth edition of Ainsworth and Bibsys Dictionary of the Fungi and 80,060 of the ninth edition in which about 510% of the duplicated names have not been adjusted27,81,82. The question of how many fungal species there are in the world has challenged mycologists for nearly half a century. Information has been analysed through different attempts, such as plantto-fungus ratios, insect-to-fungus ratios, inferences from intensive sampling and extrapolation from numbers of new species being found in a group73,84,85. The 1.5 million species estimate of Hawksworth was the rst in-depth analysis of the magnitude of fungal diversity73. It was based on extrapolations from three independent data sets: ratios of the numbers of fungi in all habitats to plants in the British Isles, number of species on native plants, and the number of species in an alpine community study. Nonetheless, the gure was considered a conservative estimate due to the modest 270,000 gure used for the world number of vascular plants, the fact that no separate allowances were made for fungi on insect species and on unstudied plants, and the fact that no special account was taken of potentially hyperdiverse tropical and polar regions73,79. Since Hawksworths estimation73, keen discussion and arguments have produced gures ranging from 0.5 to 9.9 million (Table 15.1). Amongst the 15 estimates under review, only one author accepted Hawksworths gure as moderately accurate86, three proposed estimates lower than 1.5 million2,87,88, and eleven proposed higher estimates70,74,84,8895. Those that proposed higher estimates tend to draw particular attention to species richness in tropical forests74,94,96. Empirical evidence appears to substantiate the view that tropical fungi are hyperdiverse and that newly visited sites and substrates should yield a high percentage of species new to science74,92,95,97. For example, during surveys of palm fungi, Hyde et al.98 discovered as many as 75% of the fungal species were new to science, and Frhlich and Hyde yielded a very high plant to fungus ratio of 1:33 for palm fungi in the tropics84. Particular groups, such as endophytes, insect fungi and macromycetes are considered to be hyperdiverse and may comprise 11.5 million species each9193,95. For example, Cifuentes Blanco et al.93 found that there were 1,300 species of macromycetes associated with 450 plants in Mexico; such a macromycete to plant ratio of about 3.5:1 yields a total of 1 million macromycete species worldwide. May88, who adopted a 0.5 million gure for fungi, however, stressed the problems of scaling up from local to global totals and considered that his gure was more likely for fungal species, as they tend to have a wider geographic distribution than plant species. Rossman produced an overall gure of about 1 million by using information from the US National Fungus Collection Database, literature, discussions with other mycologists and personal experience of Rossman2.
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TABLE 15.1 Published Fungal Diversity Estimates Since 1990

Author Pascoe89 May74 Hawksworth73 Hammond87 Smith and Waller90 Hywel-Jones91 Dreyfuss and Chapela92 Rossman2 Hammond83 Aptroot100 Cannon70 Cifuentes Blanco et al.93 Shivas and Hyde94 Frhlich and Hyde84 Arnold et al.95 May88 Year 1990 1991 1991 1992 1992 1993 1994 1994 1995 1997 1997 1997 1997 1999 2000 2000 Estimated Species (Millions) 2.7 1.5+ 1.5 1 1 (on tropical plants alone) 1.5 (insect fungi alone) 1.3 (endophytes only) 1 1.5 0.040.07 (ascomycetes alone) 9.9 1 (macromycetes alone) 0.27 (plant pathogens alone) 1.5+ 1.5+ 0.5
Source: Modied from Hawksworth79.
With such large variations in estimates of fungal diversity, it is important that work is carried out in selected research topics to provide data for poorly understood diversity questions. To achieve that, we need more detailed information on particular sites, fungus to plant and fungus to insect ratios and sustained increased attention on the fungi associated with particular plants or groups of insects, especially in the tropics79. Several researchers have been carrying out such research, and their data provide more insights into fungal diversity, and some of these data are discussed below. Selected groups and hosts have also been proposed for rapid biodiversity assessments, such as macromycetes, Xylariaceae, lichen-forming fungi, endophytes, palms, bamboos, Pandanus species, freshwater fungi and pathogens99.
15.4 EXAMPLES OF FUNGAL DIVERSITY FROM SELECTED HOSTS 15.4.1 FUNGI

ON
POACEAE, CYPERACEAE
AND JUNCACEAE
We select grasses, as they are the worlds most important agricultural plants and because fungal diversity on grasses has rarely been reviewed101. Poaceae (Gramineae) includes cereals, sugar cane, forage grasses for farm animals, ornamental grasses and bamboos and comprises about 10,000 species in 650 genera101,102 (see Hilu, Chapter 11; Hodkinson et al., Chapter 17). Grasses (especially cereal grasses) provide favourable substrates for fungal colonisation, as evident from fungal records on various grasses available from the fungal databases of the Systematic Botany and Mycology Laboratory (SBML), Agricultural Research Service, United States Department of Agriculture (http://nt.ars-grin.gov/fungaldatabases/index.cfm)103. As many as 14 well studied grass genera support more than 800 fungal taxa, and these are listed in Table 15.2. There are at least 30,000 records of fungi in the SBML database. These records cover terrestrial habitats104109, freshwater habitats107, estuarine regions110112 and marine regions113,114. However, they are not exhaustive. Previous studies were biased towards economically important plants, and estimates used small sample sizes and a limited number of sampling sites. Increased sampling,
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TABLE 15.2 Fungal Records on Selected Grass Genera

Genus Zea Triticum Panicum Sorghum Saccharum Paspalum Setaria No. of Fungal Records 4,788 3,731 3,328 2,985 1,894 1,894 1,771 Genus Oryza Bambusa Pennisetum Digitaria Cynodon Phragmites Sporobolus No. of Fungal Records 1,719 1,333 1,303 1,232 1,170 898 928
Source: Data from Farr et al.103.
longer study periods, new habitats and unexplored sites tend to yield new data. For example, the number of different saprobic fungi on one well studied cosmopolitan reed, Phragmites australis, based on seven studies, can be more than 300107,109,112,115,116 . Intensive survey of smut fungi (microscopic Basidiomycota) also yielded surprising results. More than 350 species of smut fungi were isolated from nine grasses (including Bothriochloa, Capillipedium, Chrysopogon, Cynodon, Dichanthium, Hyparrhenia, Muhlenbergia, Saccharum and Sorghum) in New Zealand117135. If we accept 10% of the fungi associated with the P. australis above to be host specic, a high ratio of 30:1 results. This fungi to host ratio will increase when endophytes, mycorrhizal fungi, pathogens, rusts and smut fungi are included in the estimation, as these groups are more host specic136. Our knowledge of bamboo fungi is still at the cataloguing stage, and new species are often described after eld sampling137143. Eriksson and Yue144 provided an annotated checklist of bambusicolous fungi, and Hyde et al.143 provided a review of bambusicolous fungi recorded worldwide. There have been some taxonomic or ecological studies on bamboo fungi, but these are limited to France145, Hong Kong137139,143,146 and Japan147155. In June 2005, there were in total 3,222 records of fungi associated with 11 of the most common bamboo genera (Arundinaria, Bambusa, Chusquea, Dendrocalamus, Gigantochloa, Guadua, Phyllostachys, Pleioblastus, Pseudosasa, Schizostachyum and Sinobambusa) in the SBML database103. After correction (allowing about 3040% for duplicated names and multiple records of single species), there are at least 1,933 fungal species known for bamboo. This gure is much higher than the 1,100 species reviewed by Hyde and coworkers in 2002143. It is obvious that this gure will continue to increase as more eld studies are conducted. Fungal diversity on sedges has not been well studied in comparison with fungi reported on grass hosts. The obvious reason may be that sedges have less economic value156,157. There are 9,585 records of fungi associated with Cyperaceae in the SBML database103. Most of the records were contributed from studies with the genera Carex and Cyperus (Table 15.3), while the records on
TABLE 15.3 Fungal Records on Selected Sedge Genera

Genus Carex Cyperus Scirpus Rhynchospora Eleocharis No. of Fungal Records 5,836 1,075 634 563 318 Genus Fimbristylis Eriophorum Kyllinga Uncinia Schoenoplectus No. of Fungal Records 304 110 91 86 83
Source: Data from Farr et al.103.
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other genera are below 800. This disparity between Poaceae and Cyperaceae may also be attributed to the more diverse morphology and anatomy of the former family than the latter156. Juncaceae (rushes) are the sister group of Cyperaceae and are a family of eight genera and about 400 species. They are distributed mainly in temperate climates or the montane regions of the tropics. Juncus is one of the dominant genera in estuarine marshes of the American East coast. This genus has received fairly intensive studies in relation to fungi. One endemic species, Juncus roemerianus (needle rush)158,159, was reported to harbour 117 fungal species160. If we adopt 10% of host specic fungi, the fungi to host ratio will be 11:1, which is much higher than an estimated average of 5.7 to 8.573. The 117 species (66 Ascomycota, one Basidiomycota and 50 anamorphic taxa) include 48 novel species, 14 novel genera and one novel family160.
15.4.2 LEAF LITTER FUNGI

Degradation of leaves in an aquatic ecosystem involves a diverse assemblage of bacteria, fungi and invertebrates161,162. Among aquatic fungi, aquatic hyphomycetes, especially Ingoldian fungi, play an important role in the decomposition of submerged leaf in streams163. In 1942, Ingold described 16 species of Ingoldian fungi; in 1981 Webster and Descals described 150 species163,164. However, about 300 species of Ingoldian fungi have now been described, mostly from temperate regions165. Chan et al.166 reviewed the Ingoldian fungi from Hong Kong and listed 51 species in 37 genera. There has been some research on fungi occurring on leaves in tropical forests in different parts of the world. Bills et al.167 and Polishook et al.168 have isolated large numbers of rare species and a few common species from leaf litter in Costa Rica and Puerto Rico. Parungao et al.169 studied the fungi degrading leaf litter of 13 tree species in Australia and identied two to three unique fungi from leaves of each species, with overlap in only 40% of species. Paulus et al.170 studied diversity of microfungi on decaying leaves of Ficus pleurocarpa, and 104 species were identified. Promputtha et al.171 who have been studying fungal communities on leaves of Magnolia liliifera, also recently reported some new species from the host172,173. Photita et al.174 examined the large decaying leaves of Musa sp. (banana) in Hong Kong and found 27 taxa at two sites.
15.4.3 FUNGI
ON INVERTEBRATES
Few studies have addressed fungal numbers on invertebrates. In fact, since the important paper of Weir and Hammond175 there have been relatively little data on biodiversity of invertebrate fungi. If invertebrate fungi were host specic and occurred in most insects this would have extreme implications for fungal numbers. Weir and Hammond suggest that between 5 and 7% of beetle species may act as hosts for Laboulbeniales (ascomycetous obligate ectoparasites of Arthropoda) and speculated that at least 20,000 and possibly 50,000 species of Laboulbeniales await description175. Trichomycetes (symbiotic gut fungi) numbers were also shown to be dependent on host diversity, and host specicity was shown to be a crucial factor in trichomycete diversity176. Much work is still needed to address fungal numbers in this area.
15.5 SPECIES RICH GENERA OF FUNGI

One of the largest problems in estimating fungal diversity is the genera containing more than 1,000 species. Are these genera really so diverse, or considering the paucity of characters that can be used to separate species, have their species numbers been exaggerated? Plant pathogenic genera such as Colletotrichum, Pestalotiopsis and Mycosphaerella comprise numerous species, but generally, these species have been described based on the host on which they were found, with little reference to their own characteristics. Whether these genera are megadiverse requires investigation, and molecular techniques are now available to help address this question.
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15.5.1 COLLETOTRICHUM
The species rich genus Colletotrichum causes various plant diseases often known as anthracnose and is worldwide in distribution177. Colletotrichum species cause major damage to crops in tropical, subtropical and temperate regions. Cereal, vegetables, legumes, ornamentals and fruit trees may be seriously affected by this pathogen178. Colletotrichum species are also commonly isolated as endophytes, and latent and quiescent infections by these species on several hosts have been reported16. Their ability to cause latent infection, that is, infection without visible symptoms, makes them one of the most successful pathogens causing postharvest disease in a wide range of crop species177. Colletotrichum is the anamorphic stage of several species of Glomerella and has a taxonomic history of about 200 years179. There are 17 acknowledged generic synonyms for Colletotrichum, and two further names are tentatively included, and there are about 900 species names assigned to this genus177,180. The identication and characterisation of Colletotrichum species are mainly based on morphological and cultural criteria or a combination of both. It has become apparent that the classication system presently used has limited scope, since some species names assigned to collections and isolates lack the precision required by users. The numbers of morphological characters derived from growth in culture are limited, and growth conditions have rarely been standardised. Moreover, the inherent phenotypic plasticity of individual isolates creates confusion in identication. There are group species or species complexes such as C. dematium, C. gloeosporioides and C. lindemuthianum, which are known to be represented by at least nine distinct subtaxa177. At least nine different Colletotrichum species (C. capsici, C. coccodes, C. crassipes, C. dematium, C. destructivum, C. gloeosporioides, C. lindemuthianum, C. trifolii and C. truncatum) have been reported on economically important legumes in tropical and temperate regions181. All of these species are reported to infect at least two hosts, and C. capsici, C. gloeosporioides and C. lindemuthianum are reported to have the widest host ranges amongst these nine. C. gloeosporioides is a particularly large complex comprising taxa that cause diseases of a wide range of crops. The taxa have been isolated as pathogens, endophytes and saprobes, and it is not clear whether these different lifestyles are associated with specic lineages or have evolved many times. It is therefore particularly important that we gain an understanding of the diversity of organisms within this complex. Under these circumstances the species name has limited practical signicance to the plant pathologist involved in disease management and quarantine and the breeder involved in resistance breeding. The development of different systems for identication of species over time has largely been the result of subtle changes in species concept involving different aspects of morphology combined with ideas about host range and hostpathogen relationships for particular taxa. Despite these amendments the current species concept used in Colletotrichum systematics is still very broad, unreliable and unpredictable, being based on the combination of classical criteria such as conidial shape and size, presence, absence and morphology of setae, presence of sclerotia and appressoria and symptom expression on host. Moreover, the current classication system for Colletotrichum in general is unsatisfactory because the constituent species are inadequately dened61. With further research we may expect to uncover signicant levels of synonymy but also discover new species in complexes such as C. gloeosporioides.
15.5.2 PESTALOTIOPSIS
Pestalotiopsis species commonly cause diseases on a variety of plants and are commonly isolated as endophytes or occur as saprobes182. The genus contains about 205 named species with many named after their hosts in much the same way as Colletotrichum. The understanding of species relationships within this weakly parasitic genus is complicated by the lack of morphological
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characters to differentiate species, and in many cases host association has provided a convenient means to separate species. Jeewon et al.182 used DNA data from a number of Pestalotiopsis isolates to test whether isolates from the same host are phylogenetically related. They also investigated the validity of naming species based on host association. Their results indicated that there was a close phylogenetic relationship between isolates possessing similar morphological characteristics, but isolates from the same host were not necessarily closely related. They advised that, when describing new Pestalotiopsis species, morphological characteristics should be taken into account rather than host association. They considered that the high numbers of Pestalotiopsis species named in the literature was an overestimate given that naming species based on host is not valid.
15.5.3 MYCOSPHAERELLA
Species of Mycosphaerella (and their anamorphs) are commonly associated with leaf spots or stem cankers183. As in the previous two genera, many species have been described based on host association. However, unlike those genera, as well as being host specic, most of these taxa are also highly tissue specic, to the degree that some cercosporoids will sporulate on either the upper or lower leaf surface. Since 1993, Crous and coworkers have described nearly 40 new species of Mycosphaerella and associated anamorphs from Eucalyptus183 which appear to be highly specic to this host. An exception to the rule is the Mycosphaerella tassiana complex, as well as other species with Cladosporium anamorphs.
15.6 AN ERA OF GENOMICS AND MOLECULAR BIOLOGY 15.6.1 APPLICATIONS

OF
MOLECULAR BIOLOGY
IN
MYCOLOGICAL SYSTEMATICS
Classication of fungi in the past 250 years has been largely based on morphological characters. Our current knowledge of phylogenetics and classication mainly stems from morphological studies184. However, the dependence of morphological characters to infer the evolutionary history has a number of limitations, the major one of which is the difculty of recognising homology185. Morphology is generally more susceptible to directional selection pressures and often exhibits high levels of homoplasy186. In the case of Ascomycota, problems are particularly bad due to the relatively small number of morphological characters that appear to be phylogenetically informative and with the complication of the anamorphic stage185,187. As a result, conicting classication schemes have been proposed for many fungal classes28,46,188191. With the availability of molecular techniques, studies of mycology have entered a new era in the last two decades. These techniques can be applied in many disciplines, and some of these are summarised in Table 15.4. In studies of fungal diversity, DNA-based techniques can provide a comprehensive measure of diversity and composition of fungal communities, as they review both the culturable and often predominant nonculturable members of a community192,193. Results from DNA sequencing of genes of different species can be compared and analysed with the sequences from the other studies downloaded from the world DNA sequence database such as GenBank (http://www.ncbi.nlm.nih.gov) or the Assembling Fungal Tree Of Life Project (AFTOL) (http://aftol.org/data.php). Large-scale comparisons are now possible with other distant organisms such as plants and animals to elucidate patterns of organism diversications and relationships22,23,194,195. For instance, the exclusion of the morphologically similar phyla Myxomycota and Dictyosteliomycota from kingdom Fungi was made after molecular data were available. On the other hand, application of specic statistical testing and mathematical models in DNA analyses on different genetic levels can elucidate differences in rates and modes of evolution and estimate the time for diversication in ecological characters and will result in a deeper understanding of biological diversity196,197.
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TABLE 15.4 Synopsis of Potential Applications of Molecular Biology

Areas of Study Fungal systematics and evolutionary studies Fungal biotechnology Application of Molecular Techniques Provide semi-quantitative measures of relationships Elucidate evolutionary pathways Dene particular systematic groupings Predict protein structures and determine gene function Identify genes with particular properties Modify the genes in target fungi Develop diagnostic tests for human fungal infections Understand the pathogenicity of fungal diseases Characterise and identify plant pathogens Develop and genetically modify biocontrol fungi Trace and detect spoilage fungi Measure the fungal diversity Analyse the composition of fungal communities
Medical mycology Agriculture Food Environmental studies
Source: Modied from Bridge196.
15.6.2 MOLECULAR STUDY
ON
FUNGAL DIVERSITY
IN
SOIL
Microorganisms in soil are critical to the maintenance of soil function and quality because of their involvement in soil structuring, decomposition of organic matters, recycling of nutrients and promoting plant growth198,199. Traditionally, cultivation and isolation were used to analyse the soil microbial communities. Unfortunately, the number and range of fungal species present in the soil are not accurately represented by those methods, as some of the fungi are either nonculturable or suppressed by other fungi in the cultivation based system199,200. It is increasingly common to use molecular approaches to study fungal communities in soil. These molecular techniques are generally based on PCR or RT-PCR of specic or generic targets in the soil DNA or RNA. The use of specic PCR primers further enables specic groups of fungi, such as Ascomycota and Basidiomycota, to be amplied in the presence of other groups of organisms, such as algae or bacteria201. PCR products amplied using specic fungal primers yield a mixture of DNA fragments representing a number of PCR-accessible species present in the soil199. These mixed PCR products can be used for preparing the clone libraries and a range of ngerprinting techniques such as denaturing or temperature gradient gel electrophoresis (DGGE/TGGC)202204, amplied rDNA restriction analysis (ARDRA), terminal restriction fragment length polymorphism (T-RFLP)205, and ribosomal intergenic spacer length polymorphism (RISA)206.
15.6.3 UNRAVELLING SPECIES RICH GENERA USING MOLECULAR TECHNIQUES

Various DNA-based systems have been used to study phylogeny, systematics, genetic diversity and population structure of species rich fungi. The molecular markers include restriction fragment length polymorphisms (RFLP), random amplied polymorphic DNA (RAPD), amplied fragment length polymorphisms (AFLP), rDNA internal transcribed spacer (ITS-1 to ITS-2) and small subunit ribosomal RNA (18S rDNA sequences). They have been utilised successfully in differentiating populations of different Colletotrichum species and to reliably assign correct names to morphologically different but genetically similar species. For instance, C. orbiculare from cucumber, C. trifolii from alfalfa, C. malvarum from prickly sida and C. lindermuthianum from bean were found to be closely related207209. Sheriff et al.210 further proposed that C. lindermuthianum, C. malvarum, C. orbiculare and C. trifolii should be considered as a single species based
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on rDNA sequence analysis. In a study of Colletotrichum from almond, avocado and strawberry, Freeman et al.211 found that, although morphological criteria indicated that the Israeli isolates of almond are unique, the population was grouped within the C. acutatum species according to molecular analyses. It is obvious that further studies of other species rich genera at the molecular level are necessary before we can obtain a conclusion of the effects of these genera on fungal numbers.
15.6.4 FUNGAL ENDOPHYTES: UNDERESTIMATED?

The term endophyte refers to the symptomless, mutualistic fungi which grow within aerial parts of plants27. Almost all vascular plant species examined have been found to harbour endophytic fungi, and each species of vascular plant harbours at least two to four endophyte species unique to that plant species16,95,206. Some taxa, especially coelomycetous anamorphic taxa, such as Collectotrichum, Coniothyrium, Cylindrosporium, Hendersonia, Phoma, Phomopsis, Phyllosticta, Septoria and Stagonospora, have been found to occur on nearly all vascular plants examined16. Traditional isolation techniques involve plating healthy, surface-sterilised plant tissues on agar media and observing the outgrowth of fungi, or incubation of washed plant tissues under humid conditions and subsequent collection and plating of discharged spores, as summarised in Kirk et al.27. In most of the studies on the diversity of fungal endophytic communities in the tropics211220, as well as in temperate regions212,218,221223, a large number of fungi did not sporulate in culture. The nonsporulating fungi, commonly categorised as mycelia sterilia, are grouped into morphological species on the basis of similarity in colony surface textures, hyphal pigments, exudates, margin shapes and growth rate16. This concept of morphospecies has provided a practical means to estimate endophytic fungal diversity by incorporating the nonsporulating fungal isolates. Lacap et al.224 summarised the proportions of mycelia sterilia found in some of the earlier studies of fungal communities. For a given host, mycelia sterilia can comprise an average of 20% of the population of fungal endophytes and may be as high as 54%222,224. Lacap et al.224 also conducted a study to verify the concept of morphospecies based on DNA sequence data on mycelia sterilia isolated from Polygonum multiforum and to identify the valid taxonomic groups. With the aid of phylogenetic analyses, those morphospecies can also be grouped into their respective orders and families, or even assigned to genera or species. Guo et al.225 performed a phylogenetic analysis of 5.8S DNA gene sequences on the morphospecies isolated from palm Livistona chinensis and found that the morphospecies were mostly ascomycetes, belonging to the Loculoascomycetes and Sordariomycetes. The culture-based methods above, however, have their limitations in that they do not reveal nonculturable endophytic fungi. In a litter decomposition study, Nikolcheva et al.226 investigated the early stages of colonisation of ve leaf species and birch wood by aquatic hyphomycetous taxa using both the traditional methods and DGGE. They extracted the total DNA from senescent leaves, and DNA fragments were amplied using PCR with specic fungal primers. The mixture of PCR products of 18S rDNA was then separated by DGGE, based on differences in the ease of denaturation arising from sequence variability, and the separated bands sequenced and identied. In a modern endophytic fungal community study, a multipronged approach will often be used. This includes the use of traditional microscope-based methods after plating of sterilised plant tissues on agar medium215, DNA sequence analysis to identify fungi on nonsporulating culture plates after designation to morphospecies, and DGGE to reveal the nonculturable endophytic fungi225,226. This combined approach provides a comprehensive measure of endophytic fungal diversity and reliably reveals the diversity of endophytic fungal communities.
15.7 CONCLUDING REMARKS

In order to gain a better understanding of fungal diversity, we should continue to concentrate on studying the fungal communities in selected habitats and substrates, especially those that appear to support high diversity and also explore understudied or unstudied habitats and substrates.
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For example, palms have been shown to be hyperdiverse substrates for fungi84,98,214,227229, and recent studies in palm swamps in Thailand have yielded numerous new taxa230,231. Palms and other unstudied substrates in other areas should be investigated to establish if new species discovery will continue unabated. To advance our knowledge, we must prioritise funding for inventory and monographic studies simultaneously with funding for molecular biology. This will provide an invaluable legacy of data for conservation evaluation and biotechnological and pharmaceutical utilisation.
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15

Reconstructing the Tree of Life

15.1 INTRODUCTION TO THE FUNGI 15.1.1 GENERAL CHARACTERISTICS

Reconstructing the Tree of Life

Reconstructing the Tree of Life

15.2 PROBLEMS IN ESTIMATING FUNGAL DIVERSITY 15.2.1 FUNGAL SPECIES CONCEPTS

Reconstructing the Tree of Life

15.3 GLOBAL FUNGAL DIVERSITY ESTIMATE: DESCRIBED AND UNDESCRIBED

TABLE 15.1 Published Fungal Diversity Estimates Since 1990

Source: Modied from Hawksworth79.

15.4 EXAMPLES OF FUNGAL DIVERSITY FROM SELECTED HOSTS 15.4.1 FUNGI

Reconstructing the Tree of Life

TABLE 15.2 Fungal Records on Selected Grass Genera

Source: Data from Farr et al.103.

TABLE 15.3 Fungal Records on Selected Sedge Genera

Source: Data from Farr et al.103.

2007 by Taylor & Francis Group, LLC

15.4.2 LEAF LITTER FUNGI

15.5 SPECIES RICH GENERA OF FUNGI

Reconstructing the Tree of Life

2007 by Taylor & Francis Group, LLC

15.6 AN ERA OF GENOMICS AND MOLECULAR BIOLOGY 15.6.1 APPLICATIONS

Reconstructing the Tree of Life

TABLE 15.4 Synopsis of Potential Applications of Molecular Biology

Medical mycology Agriculture Food Environmental studies

Source: Modied from Bridge196.

15.6.2 MOLECULAR STUDY

15.6.3 UNRAVELLING SPECIES RICH GENERA USING MOLECULAR TECHNIQUES

15.6.4 FUNGAL ENDOPHYTES: UNDERESTIMATED?

15.7 CONCLUDING REMARKS

Reconstructing the Tree of Life

Reconstructing the Tree of Life

Reconstructing the Tree of Life

Reconstructing the Tree of Life

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