Skip to main content
SpringerLink
Log in

Microbial Transformation of Nutrients in Soil: An Overview

  • Chapter
  • First Online:
Rhizosphere Microbes

Part of the book series: Microorganisms for Sustainability ((MICRO,volume 23))

Abstract

The indiscriminate as well as imbalanced application of inorganic fertilizers and climate change associated land degradation negatively affected the soil’s physical, chemical, and microbiological characteristics, thereby affecting global food production. In soils, various microbial communities are involved in nutrient transformations, thereby determining the mobilization, and fixation capacity of nutrients impacting crop growth and development. Some bacterial and fungal genera are involved in a number of mechanisms such as organic acid production, proton extrusion, critical enzyme production that enables the transformation of unavailable forms of nutrients into available forms. Furthermore, the definitive role of different soil abiotic and biotic components also determines the fate of the nutrient transformation and its availability to the plants by affecting the microbial community structure as well as diversity. Taking sustainability into consideration, the exploitation of microbial inoculants to increase the availability of essential plant nutrients could be a viable alternative option for increasing food productivity without compromising soil quality. In this chapter, we discussed the role of diverse microbial communities in nutrients transformation of major (nitrogen, phosphorus, potassium, sulfur) and minor elements (iron, manganese, and copper), their mechanism, and their key roles in plant and soil health, and the conditions favouring the availability of nutrients are elucidated in detail.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 199.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Ahmad M, Pataczek L, Hilger TH, Zahir ZA, Hussain A, Rasche F, Solberg SØ (2018) Perspectives of microbial inoculation for sustainable development and environmental management. Front Microbiol 9:2992

    Article  PubMed  PubMed Central  Google Scholar 

  • Ahmed M, Rauf M, Akhtar M, Mukhtar Z, Saeed NA (2020) Hazards of nitrogen fertilizers and ways to reduce nitrate accumulation in crop plants. Environ Sci Pollut Res 27:1–10

    Article  Google Scholar 

  • Aleixo S, Gama-Rodrigues AC, Gama-Rodrigues EF, Campello EFC, Silva EC, Schripsema J (2020) Can soil phosphorus availability in tropical forest systems be increased by nitrogen-fixing leguminous trees? Sci Total Environ 712:136405

    Article  CAS  PubMed  Google Scholar 

  • Alloway BJ (2008a) Micronutrients and crop production: an introduction. In: Micronutrient deficiencies in global crop production. Springer, Dordrecht, pp 1–39

    Chapter  Google Scholar 

  • Alloway BJ (2008b) Zinc in soils and crop nutrition. IZA and IFA, Brussels

    Google Scholar 

  • Alori ET, Glick BR, Babalola OO (2017) Microbial phosphorus solubilization and its potential for use in sustainable agriculture. Front Microbiol 8:971

    Article  PubMed  PubMed Central  Google Scholar 

  • Anandham R, Gandhi PI, SenthilKumar M, Sridar R, Nalayini P, Sa TM (2011) Sulfur-oxidizing bacteria: a novel bioinoculant for sulfur nutrition and crop production. In: Bacteria in agrobiology: plant nutrient management. Springer, Berlin, pp 81–107

    Chapter  Google Scholar 

  • Anantharaman K, Hausmann B, Jungbluth SP, Kantor RS, Lavy A, Warren LA, Banfield JF (2018) Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. ISME J 12(7):1715–1728

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Angus JF, Bolger TP, Kirkegaard JA, Peoples MB (2006) Nitrogen mineralisation in relation to previous crops and pastures. Soil Res 44(4):355–365

    Article  CAS  Google Scholar 

  • Anjanadevi IP, John NS, John KS, Jeeva ML, Misra RS (2016) Rock inhabiting potassium solubilizing bacteria from Kerala, India: characterization and possibility in chemical K fertilizer substitution. J Basic Microbiol 56(1):67–77

    Article  CAS  PubMed  Google Scholar 

  • Antheunisse J (1972) Decomposition of nucleic acids and some of their degradation products by microorganisms. Antonie Van Leeuwenhoek 38(1):311–327

    Article  CAS  PubMed  Google Scholar 

  • Babalola OO, Igiehon NO (2017) Biofertilizers and sustainable agriculture: exploring arbuscular mycorrhizal fungi. Appl Microbiol Biotechnol 101(12):4871–4881

    Article  PubMed  CAS  Google Scholar 

  • Bagyaraj DJ, Rangaswami G (2007) Agricultural microbiology. PHI Learning Pvt. Ltd., New Delhi

    Google Scholar 

  • Bakri MM (2019) Tri-calcium and zinc phosphates solubilization by Aspergillus niger and its relation to organic acids production. BioNanoScience 9(2):238–244

    Article  Google Scholar 

  • Bao S, Wang Q, Bao X, Li M, Wang Z (2016) Biological treatment of saline-alkali soil by sulfur-oxidizing bacteria. Bioengineered 7(5):372–375

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Beeckman F, Motte H, Beeckman T (2018) Nitrification in agricultural soils: impact, actors and mitigation. Curr Opin Biotechnol 50:166–173

    Article  CAS  PubMed  Google Scholar 

  • Bender SF, Conen F, Van der Heijden MG (2015) Mycorrhizal effects on nutrient cycling, nutrient leaching and N2O production in experimental grassland. Soil Biol Biochem, 80:283-292

    Google Scholar 

  • Bhagyalakshmi B, Ponmurugan P, Marimuthu S (2012) Influence of potassium solubilizing bacteria on crop productivity and quality of tea (Camellia sinensis). Afr J Agric Res 7(30):4250–4259

    Google Scholar 

  • Bhatt K, Maheshwari DK (2020) Zinc solubilizing bacteria (Bacillus megaterium) with multifarious plant growth promoting activities alleviates growth in Capsicum annuum L. 3 Biotech 10(2):36

    Article  PubMed  PubMed Central  Google Scholar 

  • Bhattacharya S, Bachani P, Jain D, Patidar SK, Mishra S (2016) Extraction of potassium from K-feldspar through potassium solubilization in the halophilic Acinetobacter soli (MTCC 5918) isolated from the experimental salt farm. Int J Miner Process 152:53–57

    Article  CAS  Google Scholar 

  • Billings SA, Ziegler SE (2005) Linking microbial activity and soil organic matter transformations in forest soils under elevated CO2. Glob Chang Biol 11(2):203–212

    Article  Google Scholar 

  • Bitew Y, Alemayehu M (2017) Impact of crop production inputs on soil health: a review. Asian J Plant Sci 16(3):109–131

    Article  CAS  Google Scholar 

  • Bolan NS, Currie LD, Baskaran S (1996) Assessment of the influence of phosphate fertilizers on the microbial activity of pasture soils. Biol Fertil Soils 21(4):284–292

    Article  Google Scholar 

  • Bolten CJ, Schroder H, Dickschat J, Wittmann C (2010) Towards methionine overproduction in Corynebacterium glutamicum—methanethiol and dimethyldisulfide as reduced sulfur sources. J Microbiol Biotechnol 20(8):1196–1203

    Article  CAS  PubMed  Google Scholar 

  • Booth MS, Stark JM, Rastetter E (2005) Controls on nitrogen cycling in terrestrial ecosystems: a synthetic analysis of literature data. Ecol Monogr 75(2):139–157

    Article  Google Scholar 

  • Bowles MW, Mogollón JM, Kasten S, Zabel M, Hinrichs KU (2014) Global rates of marine sulfate reduction and implications for sub–sea-floor metabolic activities. Science 344(6186):889–891

    Article  CAS  PubMed  Google Scholar 

  • Bowles TM, Jackson LE, Cavagnaro TR (2018) Mycorrhizal fungi enhance plant nutrient acquisition and modulate nitrogen loss with variable water regimes. Glob Chang Biol 24(1):e171–e182

    Article  PubMed  Google Scholar 

  • Cáceres R, Malińska K, Marfà O (2018) Nitrification within composting: a review. Waste Manag 72:119–137

    Article  PubMed  CAS  Google Scholar 

  • Cai J, Jiang JX, Zheng P (2010) Isolation and identification of bacteria responsible for simultaneous anaerobic ammonium and sulphate removal. Sci China Chem 53:645–665

    Article  CAS  Google Scholar 

  • Calle-Castañeda SM, Márquez-Godoy MA, Hernández-Ortiz JP (2018) Solubilization of phosphorus from phosphate rocks with Acidithiobacillus thiooxidans following a growing-then-recovery process. World J Microbiol Biotechnol 34(1):17

    Article  CAS  Google Scholar 

  • Castellano SD, Dick RP (1991) Cropping and sulfur fertilization influence on sulfur transformations in soil. Soil Sci Soc Am J 55(1):114–121

    Article  CAS  Google Scholar 

  • Chen P, Song C, Liu XM, Zhou L, Yang H, Zhang X, Wang XC (2019) Yield advantage and nitrogen fate in an additive maize-soybean relay intercropping system. Sci Total Environ 657:987–999

    Article  CAS  PubMed  Google Scholar 

  • Cheng Y, Wang J, Chang SX, Cai Z, Müller C, Zhang J (2019) Nitrogen deposition affects both net and gross soil nitrogen transformations in forest ecosystems: a review. Environ Pollut 244:608–616

    Article  CAS  PubMed  Google Scholar 

  • Colman DR, Poundel S, Hamilton TL, Havig JR, Selensky MJ, Shock EL, Boyd ES (2018) Geobiological feed backs and the evolution of thermoacidophiles. ISMS J 12:225–236. Commun. Soil Sci. Plant Anal. 15:1257–1268

    Article  CAS  Google Scholar 

  • Coskun D, Britto DT, Shi W, Kronzucker HJ (2017) Nitrogen transformations in modern agriculture and the role of biological nitrification inhibition. Nat Plants 3(6):1–10

    Article  CAS  Google Scholar 

  • Coyne MS, Coyne MS (1999) Soil microbiology: an exploratory approach. Delmar, New York

    Google Scholar 

  • Crews TE, Peoples MB (2005) Can the synchrony of nitrogen supply and crop demand be improved in legume and fertilizer-based agroecosystems? A review. Nutr Cycl Agroecosyst 72(2):101–120

    Article  CAS  Google Scholar 

  • Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, Kirkegaard RH (2015) Complete nitrification by Nitrospira bacteria. Nature 528(7583):504

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dan X, Chen Z, Dai S, He X, Cai Z, Zhang J, Müller C (2019) Effects of changing temperature on gross N transformation rates in acidic subtropical Forest soils. Forests 10(10):894

    Article  Google Scholar 

  • Daye M, Klepac-Ceraj V, Pajusalu M, Rowland S, Farrell-Sherman A, Beukes N, Bosak T (2019) Light-driven anaerobic microbial oxidation of manganese. Nature 576(7786):311–314

    Article  PubMed  CAS  Google Scholar 

  • De Boer W, Kowalchuk GA (2001) Nitrification in acid soils: micro-organisms and mechanisms. Soil Biol Biochem 33(7–8):853–866

    Article  Google Scholar 

  • Dhiman S, Dubey RC, Maheshwari DK, Kumar S (2019) Sulfur-oxidizing buffalo dung bacteria enhance growth and yield of Foeniculum vulgare mill. Can J Microbiol 65(5):377–386

    Article  CAS  PubMed  Google Scholar 

  • Ding H, Zheng X, Zhang J, Zhang Y, Yu J, Chen D (2019) Influence of chlorothalonil and carbendazim fungicides on the transformation processes of urea nitrogen and related microbial populations in soil. Environ Sci Pollut Res 26(30):31133–31141

    Article  CAS  Google Scholar 

  • Dong X, Lv L, Wang W, Liu Y, Yin C, Xu Q, Liu X (2019) Differences in distribution of potassium-solubilizing bacteria in forest and plantation soils in Myanmar. Int J Environ Res Public Health 16(5):700

    Article  CAS  PubMed Central  Google Scholar 

  • Drehe I, Simonetti E, Ruiz JA (2018) Contribution of the siderophores pyoverdine and enantio-pyochelin to fitness in soil of Pseudomonas protegens Pf-5. Curr Microbiol 75(12):1560–1565

    Article  CAS  PubMed  Google Scholar 

  • Eshaghi E, Nosrati R, Owlia P, Malboobi MA, Ghaseminejad P, Ganjali MR (2019) Zinc solubilization characteristics of efficient siderophore-producing soil bacteria. Iran J Microbiol 11(5):419

    PubMed  PubMed Central  Google Scholar 

  • Etesami H, Emami S, Alikhani HA (2017) Potassium solubilizing bacteria (KSB):: mechanisms, promotion of plant growth, and future prospects a review. J Soil Sci Plant Nutr 17(4):897–911

    Article  CAS  Google Scholar 

  • Fdz-Polanco F, Fdz-Polanco M, Fernandez N, Urueña MA, Garcia PA, Villaverde S (2001a) New process for simultaneous removal of nitrogen and Sulphur under anaerobic conditions. Water Res 35(4):1111–1114

    Article  CAS  PubMed  Google Scholar 

  • Fdz-Polanco F, Fdz-Polanco M, Fernandez N, Uruena MA, Gracia PA, Villaverda S (2001b) Combining the biological nitrogen and sulphur cycles in anaerobic conditions. Water Sci Technol 44:77–84

    Article  CAS  PubMed  Google Scholar 

  • Feng K, Cai Z, Ding T, Yan H, Liu X, Zhang Z (2019) Effects of potassium-solubulizing and photosynthetic bacteria on tolerance to salt stress in maize. J Appl Microbiol 126(5):1530–1540

    Article  CAS  PubMed  Google Scholar 

  • Ferrol N, Azcón-Aguilar C, Pérez-Tienda J (2019) Arbuscular mycorrhizas as key players in sustainable plant phosphorus acquisition: an overview on the mechanisms involved. Plant Sci 280:441–447

    Article  CAS  PubMed  Google Scholar 

  • Friedrich CG, Bardischewsky F, Rother D, Quentmeier A, Fischer J (2005) Prokaryotic sulphur oxidation. Curr Opin Microbiol 8(3):253–259

    Article  CAS  PubMed  Google Scholar 

  • Fuentes-Lara LO, Medrano-Macías J, Pérez-Labrada F, Rivas-Martínez EN, García-Enciso EL, González-Morales S, Benavides-Mendoza A (2019) From elemental sulfur to hydrogen sulfide in agricultural soils and plants. Molecules 24(12):2282

    Article  CAS  PubMed Central  Google Scholar 

  • Germida JJ, Jansen HH (1993) Factors affecting the oxidation of elemental Sulphur in soils. Fertil Res 35:101–114

    Article  CAS  Google Scholar 

  • Ghani A, McLaren RG, Swift RS (1992) Sulphur mineralisation and transformations in soils as influenced by additions of carbon, nitrogen and sulphur. Soil Biol Biochem 24(4):331–341

    Article  CAS  Google Scholar 

  • Ghiorse WC (1988) The biology of manganese transforming microorganisms in soil. In: Manganese in soils and plants. Springer, Dordrecht, pp 75–85

    Chapter  Google Scholar 

  • Ghosh W, Dam B (2009) Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaea. FEMS Microbiol Rev 33(6):999–1043

    Article  CAS  PubMed  Google Scholar 

  • Ghosh W, George A, Agarwal A, Raj P, Alam M, Pyne P, Gupta SKD (2011) Whole-genome shotgun sequencing of the sulfur-oxidizing chemoautotroph Tetrathiobacter kashmirensis. J Bacteriol 193(19):5553–5554

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gonzalez-Chavez MC, Carrillo-Gonzalez R, Wright SF, Nichols KA (2004) The role of glomalin, a protein produced by arbuscular mycorrhizal fungi, in sequestering potentially toxic elements. Environ Pollut 130(3):317–323

    Article  CAS  PubMed  Google Scholar 

  • González-Guerrero M, Azcón-Aguilar C, Mooney M, Valderas A, MacDiarmid CW, Eide DJ, Ferrol N (2005) Characterization of a Glomus intraradices gene encoding a putative Zn transporter of the cation diffusion facilitator family. Fungal Genet Biol 42(2):130–140

    Article  PubMed  CAS  Google Scholar 

  • Goteti PK, Emmanuel LDA, Desai S, Shaik MHA (2013) Prospective zinc solubilising bacteria for enhanced nutrient uptake and growth promotion in maize (Zea mays L.). Int J Microbiol 2013

    Google Scholar 

  • Gounot AM (1994) Microbial oxidation and reduction of manganese: consequences in groundwater and applications. FEMS Microbiol Rev 14(4):339–349

    Article  CAS  PubMed  Google Scholar 

  • Greenwood DJ, Lees H (1956) Studies on the decomposition of amino acids in soils. Plant Soil 7(3):253–268

    Article  CAS  Google Scholar 

  • Grein F, Ramos AR, Venceslau SS, Pereira IA (2013) Unifying concepts in anaerobic respiration: insights from dissimilatory sulfur metabolism. Biochim Biophys Acta Bioenergetics 1827(2):145–160

    Article  CAS  Google Scholar 

  • Haro R, Benito B (2019) The role of soil fungi in K+ plant nutrition. Int J Mol Sci 20(13):3169

    Article  CAS  PubMed Central  Google Scholar 

  • Hayatsu M, Tago K, Saito M (2008) Various players in the nitrogen cycle: diversity and functions of the microorganisms involved in nitrification and denitrification. Soil Sci Plant Nutr 54(1):33–45

    Article  CAS  Google Scholar 

  • Hensen D, Sperling D, Trüper HG, Brune DC, Dahl C (2006) Thiosulphate oxidation in the phototrophic sulphur bacterium Allochromatium vinosum. Mol Microbiol 62(3):794–810

    Article  CAS  PubMed  Google Scholar 

  • Hirsch AM, Fujishige NA (2012) Molecular signals and receptors: communication between nitrogen-fixing bacteria and their plant hosts. In: Biocommunication of plants. Springer, Berlin, pp 255–280

    Chapter  Google Scholar 

  • Hochstein LI, Tomlinson GA (1988) The enzymes associated with denitrification. Ann Rev Microbiol 42(1):231–261

    Article  CAS  Google Scholar 

  • Howard MB, Ekborg NA, Weiner RM, Hutcheson SW (2003) Detection and characterization of chitinases and other chitin-modifying enzymes. J Ind Microbiol Biotechnol 30(11):627–635

    Article  CAS  PubMed  Google Scholar 

  • Hu Y, Ribbe MW (2013) Nitrogenase assembly. Biochim Biophys Acta Bioenergetics 1827(8–9):1112–1122

    Article  CAS  Google Scholar 

  • Hu Y, Zheng Q, Zhang S, Noll L, Wanek W (2018) Significant release and microbial utilization of amino sugars and D-amino acid enantiomers from microbial cell wall decomposition in soils. Soil Biol Biochem 123:115–125

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hussain A, Zahir ZA, Asghar HN, Ahmad M, Jamil M, Naveed M, Akhtar MFUZ (2018) Zinc solubilizing bacteria for zinc biofortification in cereals: a step toward sustainable nutritional security. In: Role of rhizospheric microbes in soil. Springer, Singapore, pp 203–227

    Chapter  Google Scholar 

  • Igarashi RY, Seefeldt LC (2003) Nitrogen fixation: the mechanism of the Mo-dependent nitrogenase. Crit Rev Biochem Mol Biol 38(4):351–384

    Article  CAS  PubMed  Google Scholar 

  • Ingle KP, Padole DA (2017) Phosphate solubilizing microbes: an overview. Int J Curr Microbiol App Sci 6(1):844–852

    Article  CAS  Google Scholar 

  • Jaivel N, Sivakumar U, Marimuthu P (2017) Characterization of zinc solubilization and organic acid detection in Pseudomonas sp. RZ1 from rice phyllosphere. Int J Chem 5(6):272–277

    CAS  Google Scholar 

  • Jamal A, Ayub N, Usman M, Khan AG (2002) Arbuscular mycorrhizal fungi enhance zinc and nickel uptake from contaminated soil by soya bean and lentil. Int J Phytorem 4:205–221

    Article  CAS  Google Scholar 

  • Janusz G, Pawlik A, Sulej J, Świderska-Burek U, Jarosz-Wilkołazka A, Paszczyński A (2017) Lignin degradation: microorganisms, enzymes involved, genomes analysis and evolution. FEMS Microbiol Rev 41(6):941–962

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jetten MS, Niftrik LV, Strous M, Kartal B, Keltjens JT, Op den Camp HJ (2009) Biochemistry and molecular biology of anammox bacteria. Crit Rev Biochem Mol Biol 44(2–3):65–84

    Article  CAS  PubMed  Google Scholar 

  • Kai H, Ahmad Z, Harada T (1973) Factors affecting immobilization and release of nitrogen in soil and chemical characteristics of the nitrogen newly immobilized III. Transformation of the nitrogen immobilized in soil and its chemical characteristics. Soil Sci Plant Nutr 19(4):275–286

    Article  CAS  Google Scholar 

  • Kalayu G (2019) Phosphate solubilizing microorganisms: promising approach as biofertilizers. Int J Agronomy 2019:1–7

    Article  CAS  Google Scholar 

  • Karandashov V, Bucher M (2005) Symbiotic phosphate transport in arbuscular mycorrhizas. Trends Plant Sci 10(1):22–29

    Article  CAS  PubMed  Google Scholar 

  • Kaur G, Reddy MS (2014) Role of phosphate-solubilizing bacteria in improving the soil fertility and crop productivity in organic farming. Arch Agron Soil Sci 60(4):549–564

    Article  CAS  Google Scholar 

  • Kertesz MA, Mirleau P (2004) The role of soil microbes in plant sulphur nutrition. J Exp Botany 55(404):1939–1945

    Article  CAS  Google Scholar 

  • Keshavarz Zarjani J, Aliasgharzad N, Oustan S, Emadi M, Ahmadi A (2013) Isolation and characterization of potassium solubilizing bacteria in some Iranian soils. Arch Agron Soil Sci 59(12):1713–1723

    Article  CAS  Google Scholar 

  • Khande R, Sharma SK, Ramesh A, Sharma MP (2017) Zinc solubilizing Bacillus strains that modulate growth, yield and zinc biofortification of soybean and wheat. Rhizosphere 4:126–138

    Article  Google Scholar 

  • Killham K (1994) Soil ecology. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Kour R, Jain D, Bhojiya AA, Sukhwal A, Sanadhya S, Saheewala H, Mohanty SR (2019) Zinc biosorption, biochemical and molecular characterization of plant growth-promoting zinc-tolerant bacteria. 3 Biotech 9(11):421

    Article  PubMed  PubMed Central  Google Scholar 

  • Krishnaraj PU, Dahale S (2014) Mineral phosphate solubilization: concepts and prospects in sustainable agriculture. Proc Indian Natl Sci Acad 80(2):389–405

    Article  Google Scholar 

  • Kumar A, Dewangan S, Lawate P, Bahadur I, Prajapati S (2019) Zinc-solubilizing bacteria: a boon for sustainable agriculture. In: Plant growth promoting rhizobacteria for sustainable stress management. Springer, Singapore, pp 139–155

    Chapter  Google Scholar 

  • Kumawat N, Kumar R, Kumar S, Meena VS (2017) Nutrient solubilizing microbes (NSMs): its role in sustainable crop production. In: Agriculturally important microbes for sustainable agriculture. Springer, Singapore, pp 25–61

    Chapter  Google Scholar 

  • Kuypers MM, Marchant HK, Kartal B (2018) The microbial nitrogen-cycling network. Nat Rev Microbiol 16(5):263

    Article  CAS  PubMed  Google Scholar 

  • Lee CC, Ribbe MW, Hu Y (2019) Purification of nitrogenase proteins. In: Metalloproteins. Humana Press, New York, pp 111–124

    Chapter  Google Scholar 

  • Lehmann A, Rillig MC (2015) Arbuscular mycorrhizal contribution to copper, manganese and iron nutrient concentrations in crops–a meta-analysis. Soil Biol Biochem 81:147–158

    Article  CAS  Google Scholar 

  • Lehmann A, Veresoglou SD, Leifheit EF, Rillig MC (2014) Arbuscular mycorrhizal influence on zinc nutrition in crop plants–a meta-analysis. Soil Biol Biochem 69:123–131

    Article  CAS  Google Scholar 

  • Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Schleper C (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442(7104):806

    Article  CAS  PubMed  Google Scholar 

  • Li D, Liu J, Chen H, Zheng L, Wang K (2018) Soil gross nitrogen transformations in responses to land use conversion in a subtropical karst region. J Environ Manag 212:1–7

    Article  CAS  Google Scholar 

  • Li C, Li Q, Wang Z, Ji G, Zhao H, Gao F, Li H (2019) Environmental fungi and bacteria facilitate lecithin decomposition and the transformation of phosphorus to apatite. Sci Rep 9(1):1–8

    Article  CAS  Google Scholar 

  • Likens GE, Bormann FH, Johnson NM (1981) Interactions between major biogeochemical cycles in terrestrial ecosystems. In: Some perspectives of the major biogeochemical cycles, vol 17. Wiley, New York, pp 93–112

    Google Scholar 

  • Lin X, Hou L, Liu M, Li X, Zheng Y, Yin G, Jiang X (2016) Nitrogen mineralization and immobilization in sediments of the East China Sea: spatiotemporal variations and environmental implications. J Geophys Res Biogeo 121(11):2842–2855

    Article  CAS  Google Scholar 

  • Lindahl B, Olsson S, Stenlid J, Finlay RD (2001) Effects of resource availability on mycelia interactions and 32P transfer between a saprotrophic and an ectomycorrhizal fungus in soil microcosms. FEMS Microbiol Ecol 38:43–52

    Article  CAS  Google Scholar 

  • Lindahl BD, Ihrmark K, Boberg J, Trumbore SE, Hogberg P, Stenlid J, Finlay RD (2007) Spatial separation of litter decomposition and mycorrhizal nitrogen uptake in a boreal forest. New Phytol 173:611–620

    Article  CAS  PubMed  Google Scholar 

  • Liu A, Hamel C, Elmi A, Costa C, Ma B, Smith DL (2002) Concentrations of K, Ca and Mg in maize colonized by arbuscular mycorrhizal fungi under field conditions. Can J Soil Sci 82(3):272–278

    Article  Google Scholar 

  • Liu ST, Yang FL, Gong Z, Meng FG, Chen HH, Xue Y, Furukawa K (2008) Application of anaerobic ammonium oxidizing consortium to achieve completely autotrophic ammonium and sulphate removal. Bioresour Technol 99:6817–6825

    Article  CAS  PubMed  Google Scholar 

  • Liu D, Lian B, Dong H (2012) Isolation of Paenibacillus sp. and assessment of its potential for enhancing mineral weathering. Geomicrobiol J 29(5):413–421

    Article  CAS  Google Scholar 

  • Liu D, Yang Q, Ge K, Hu X, Qi G, Du B, Ding Y (2017a) Promotion of iron nutrition and growth on peanut by Paenibacillus illinoisensis and Bacillus sp. strains in calcareous soil. Braz J Microbiol 48(4):656–670

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu W, Huo R, Xu J, Liang S, Li J, Zhao T, Wang S (2017b) Effects of biochar on nitrogen transformation and heavy metals in sludge composting. Bioresour Technol 235:43–49

    Article  CAS  PubMed  Google Scholar 

  • Liu Z, Wang H, Xu W, Wang Z (2020) Isolation and evaluation of the plant growth promoting rhizobacterium Bacillus methylotrophicus (DD-1) for growth enhancement of rice seedling. Arch Microbiol 1–11

    Google Scholar 

  • López-Mondéjar R, Zühlke D, Becher D, Riedel K, Baldrian P (2016) Cellulose and hemicellulose decomposition by forest soil bacteria proceeds by the action of structurally variable enzymatic systems. Sci Rep 6:25279

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Mandal A, Sarkar B, Mandal S, Vithanage M, Patra AK, Manna MC (2020) Impact of agrochemicals on soil health. In: Agrochemicals detection, treatment and remediation. Butterworth-Heinemann, Oxford, pp 161–187

    Chapter  Google Scholar 

  • Mardad I, Serrano A, Soukri A (2013) Solubilization of inorganic phosphate and production of organic acids by bacteria isolated from a Moroccan mineral phosphate deposit. Afr J Microbiol Res 7(8):626–635

    CAS  Google Scholar 

  • Masuda Y, Itoh H, Shiratori Y, Isobe K, Otsuka S, Senoo K (2017) Predominant but previously-overlooked prokaryotic drivers of reductive nitrogen transformation in paddy soils, revealed by metatranscriptomics. Microbes Environ 32(2):180–183

    Article  PubMed  PubMed Central  Google Scholar 

  • Matos AD, Gomes IC, Nietsche S, Xavier AA, Gomes WS, Dos Santos Neto JA, Pereira MC (2017) Phosphate solubilization by endophytic bacteria isolated from banana trees. Anais da Academia Brasileira de Ciencias 89(4):2945–2954

    Article  CAS  PubMed  Google Scholar 

  • Meena VS, Maurya BR, Bahadur I (2014a) Potassium solubilization by bacterial strain in waste mica. Bangladesh J Botany 43(2):235–237

    Article  Google Scholar 

  • Meena VS, Maurya BR, Verma JP (2014b) Does a rhizospheric microorganism enhance K+ availability in agricultural soils? Microbiol Res 169(5–6):337–347

    Article  CAS  PubMed  Google Scholar 

  • Meena VS, Maurya BR, Verma JP, Aeron A, Kumar A, Kim K, Bajpai VK (2015) Potassium solubilizing rhizobacteria (KSR): isolation, identification, and K-release dynamics from waste mica. Ecol Eng 81:340–347

    Article  Google Scholar 

  • Meena VS, Maurya BR, Verma JP, Meena RS (eds) (2016) Potassium solubilizing microorganisms for sustainable agriculture. Springer, New Delhi

    Google Scholar 

  • Mo Q, Zhu W, Zou B, Li Y, Yu S, Ding Y, Wang F (2016) Reforestation in southern China: revisiting soil N mineralization and nitrification after 8 years restoration. Sci Rep 6:19770

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mohammadi K (2012) Phosphorus solubilizing bacteria: occurrence, mechanisms and their role in crop production. Resour Environ 2(1):80–85

    Google Scholar 

  • Mori F, Umezawa Y, Kondo R, Wada M (2018) Dynamics of sulfate-reducing bacteria community structure in surface sediment of a seasonally hypoxic enclosed bay. Microbes Environ:ME18092

    Google Scholar 

  • Mumtaz MZ, Ahmad M, Jamil M, Hussain T (2017) Zinc solubilizing Bacillus spp. potential candidates for biofortification in maize. Microbiol Res 202:51–60

    Article  CAS  PubMed  Google Scholar 

  • Mus F, Crook MB, Garcia K, Costas AG, Geddes BA, Kouri ED, Udvardi MK (2016) Symbiotic nitrogen fixation and the challenges to its extension to nonlegumes. Appl Environ Microbiol 82(13):3698–3710

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nakamura Y, Fukuhara H, Sano K (2000) Secreted phytase activities of yeasts. Biosci Biotechnol Biochem 64(4):841–844

    Article  CAS  PubMed  Google Scholar 

  • Nall V (2010) Role of mycorrhizae in rhizosphere processes and phosphorus dynamics. Doctoral dissertation. Lincoln University, Lincoln

    Google Scholar 

  • Näsholm T, Kielland K, Ganeteg U (2009) Uptake of organic nitrogen by plants. New Phytol 182(1):31–48

    Article  PubMed  CAS  Google Scholar 

  • Nealson KH (2006) The manganese-oxidizing bacteria. PRO 5:222–231

    Google Scholar 

  • Nealson KH, Myers CR (1992) Microbial reduction of manganese and iron: new approaches to carbon cycling. Appl Environ Microbiol 58(2):439

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nealson KH, Tebo BM, Rosson RA (1988) Occurrence and mechanisms of microbial oxidation of manganese. In: Advances in applied microbiology, vol 33. Academic Press, Cambridge, pp 279–318

    Google Scholar 

  • Neilands JB (1981) Microbial iron compounds. Annu Rev Biochem 50(1):715–731

    Article  CAS  PubMed  Google Scholar 

  • Neptune AML, Tabatabai MA, Hanway JJ (1975) Sulfur fractions and carbon-nitrogen-phosphorus-sulfur relationships in some Brazilian and Iowa soils. Soil Sci Soc Am J 39(1):51–55

    Article  CAS  Google Scholar 

  • Nobile CM, Bravin MN, Becquer T, Paillat JM (2020) Phosphorus sorption and availability in an andosol after a decade of organic or mineral fertilizer applications: importance of pH and organic carbon modifications in soil as compared to phosphorus accumulation. Chemosphere 239:124709

    Article  CAS  PubMed  Google Scholar 

  • Noll L, Zhang S, Zheng Q, Hu Y, Wanek W (2019) Wide-spread limitation of soil organic nitrogen transformations by substrate availability and not by extracellular enzyme content. Soil Biol Biochem 133:37–49

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Oldroyd GE, Murray JD, Poole PS, Downie JA (2011) The rules of engagement in the legume-rhizobial symbiosis. Annu Rev Genet 45:119–144

    Article  CAS  PubMed  Google Scholar 

  • Ollivier J, Töwe S, Bannert A, Hai B, Kastl EM, Meyer A, Schloter M (2011) Nitrogen turnover in soil and global change. FEMS Microbiol Ecol 78(1):3–16

    Article  CAS  PubMed  Google Scholar 

  • Oshiki M, Araki M, Hirakata Y, Hatamoto M, Yamaguchi T, Araki N (2018) Ureolytic prokaryotes in soil: community abundance and diversity. Microbes Environ 33(2):230–233

    Article  PubMed  PubMed Central  Google Scholar 

  • Ouyang Y, Norton JM (2020) Short-term nitrogen fertilization affects microbial community composition and nitrogen mineralization functions in an agricultural soil. Appl Environ Microbiol 86(5):e02278-19

    Article  PubMed  PubMed Central  Google Scholar 

  • Parihar M, Meena VS, Mishra PK, Rakshit A, Choudhary M, Yadav RP, Bisht JK (2019) Arbuscular mycorrhiza: a viable strategy for soil nutrient loss reduction. Arch Microbiol 201(6):723–735

    Article  CAS  PubMed  Google Scholar 

  • Parniske M (2008) Arbuscular mycorrhiza: the mother of plant root endosymbioses. Nat Rev Microbiol 6(10):763

    Article  CAS  PubMed  Google Scholar 

  • Peng Q, Yi L, Peng Q, Peng Y (2017) Draft genome sequence of the potassium feldspar-solubilizing bacterium Ensifer adhaerens L18. Genome Announc 5(17):e00199-17

    Article  PubMed  PubMed Central  Google Scholar 

  • Pester M, Knorr KH, Friedrich MW, Wagner M, Loy A (2012) Sulfate reducing microorganisms in wetlands-fameless actors in carbon cycling and climate change. Front Microbiol 3:72

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Phillips LA, Schefe CR, Fridman M, O’Halloran N, Armstrong RD, Mele PM (2015) Organic nitrogen cycling microbial communities are abundant in a dry Australian agricultural soil. Soil Biol Biochem 86:201–211

    Article  CAS  Google Scholar 

  • Pierzynski GM, McDowell RW, Thomas Sims J (2005) Chemistry, cycling, and potential movement of inorganic phosphorus in soils. Phosphorus Agric Environ 46:51–86

    Google Scholar 

  • Pramanik P, Goswami AJ, Ghosh S, Kalita C (2019) An indigenous strain of potassium-solubilizing bacteria Bacillus pseudomycoides enhanced potassium uptake in tea plants by increasing potassium availability in the mica waste-treated soil of north-East India. J Appl Microbiol 126(1):215–222

    Article  CAS  PubMed  Google Scholar 

  • Prashar P, Shah S (2016) Impact of fertilizers and pesticides on soil microflora in agriculture. In: Sustainable agriculture reviews. Springer, Cham, pp 331–361

    Chapter  Google Scholar 

  • Purkhold U, Pommerening-Röser A, Juretschko S, Schmid MC, Koops HP, Wagner M (2000) Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys. Appl Environ Microbiol 66(12):5368–5382

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rabus R, Venceslau SS, Woehlbrand L, Voordouw G, Wall JD, Pereira IA (2015) A post-genomic view of the ecophysiology, catabolism and biotechnological relevance of sulphate-reducing prokaryotes. In: Advances in microbial physiology, vol 66. Academic Press, Cambridge, pp 55–321

    Google Scholar 

  • Radzki W, Mañero FG, Algar E, García JL, García-Villaraco A, Solano BR (2013) Bacterial siderophores efficiently provide iron to iron-starved tomato plants in hydroponics culture. Antonie Van Leeuwenhoek 104(3):321–330

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rafi MM, Krishnaveni MS, Charyulu PBBN (2019) Phosphate-solubilizing microorganisms and their emerging role in sustainable agriculture. In: Recent developments in applied microbiology and biochemistry. Academic Press, Cambridge, pp 223–233

    Chapter  Google Scholar 

  • Rajawat MVS, Singh R, Singh D, Saxena AK (2019) Psychrotrophs of the genus Janthinobacterium with potential to weather potassium aluminosilicate mineral. 3 Biotech 9(4):142

    Article  PubMed  PubMed Central  Google Scholar 

  • Ramesh A, Sharma SK, Sharma MP, Yadav N, Joshi OP (2014) Inoculation of zinc solubilizing Bacillus aryabhattai strains for improved growth, mobilization and biofortification of zinc in soybean and wheat cultivated in Vertisols of Central India. Appl Soil Ecol 73:87–96

    Article  Google Scholar 

  • Rasul M, Yasmin S, Suleman M, Zaheer A, Reitz T, Tarkka MT, Mirza MS (2019) Glucose dehydrogenase gene containing phosphobacteria for biofortification of phosphorus with growth promotion of rice. Microbiol Res 223:1–12

    Article  PubMed  CAS  Google Scholar 

  • Robertson GP, Groffman PM (2007) Nitrogen transformations. In: Soil microbiology, ecology and biochemistry. Academic Press, Cambridge, pp 341–364

    Chapter  Google Scholar 

  • Rösch C, Mergel A, Bothe H (2002) Biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil. Appl Environ Microbiol 68(8):3818–3829

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Rousk J, Brookes PC, Bååth E (2009) Contrasting soil pH effects on fungal and bacterial growth suggest functional redundancy in carbon mineralization. Appl Environ Microbiol 75(6):1589–1596

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Saeid A, Prochownik E, Dobrowolska-Iwanek J (2018) Phosphorus solubilization by bacillus species. Molecules 23(11):2897

    Article  PubMed Central  CAS  Google Scholar 

  • Sah S, Singh N, Singh R (2017) Iron acquisition in maize (Zea mays L.) using Pseudomonas siderophore. 3 Biotech 7(2):1–7

    Article  CAS  Google Scholar 

  • Saha B, Saha S, Roy PD, Padhan D, Pati S, Hazra GC (2018) Microbial transformation of sulphur: an approach to combat the sulphur deficiencies in agricultural soils. In: Role of rhizospheric microbes in soil. Springer, Singapore, pp 77–97

    Chapter  Google Scholar 

  • Sahu N, Vasu D, Sahu A, Lal N, Singh SK (2017) Strength of microbes in nutrient cycling: a key to soil health. In: Agriculturally important microbes for sustainable agriculture. Springer, Singapore, pp 69–86

    Chapter  Google Scholar 

  • Sahu A, Bhattacharjya S, Mandal A, Thakur JK, Atoliya N, Sahu N, Patra AK (2018) Microbes: a sustainable approach for enhancing nutrient availability in agricultural soils. In: Role of rhizospheric microbes in soil. Springer, Singapore, pp 47–75

    Chapter  Google Scholar 

  • Sammauria R, Kumawat S, Kumawat P, Singh J, Jatwa TK (2020) Microbial inoculants: potential tool for sustainability of agricultural production systems. Arch Microbiol 202:1–17

    Article  CAS  Google Scholar 

  • Sanchez Gomez C, Minamisawa K (2019) Nitrogen cycling in soybean rhizosphere: sources and sinks of nitrous oxide (N2O). Front Microbiol 10:1943

    Article  Google Scholar 

  • Santana MM, Gonzalez JM, Clara MI (2016) Inferring pathways leading to organic-sulfur mineralization in the Bacillales. Crit Rev Microbiol 42(1):31–45

    Article  CAS  PubMed  Google Scholar 

  • Saravanan VS, Madhaiyan M, Thangaraju M (2007) Solubilization of zinc compounds by the diazotrophic, plant growth promoting bacterium Gluconacetobacter diazotrophicus. Chemosphere 66(9):1794–1798

    Article  CAS  PubMed  Google Scholar 

  • Sathiyadash K, Rajendran K, Karthikeyan V, Muthukumar T (2017) Modulation of plant micronutrient uptake by arbuscular mycorrhizal fungi. In: Probiotics and plant health. Springer, Singapore, pp 337–352

    Chapter  Google Scholar 

  • Sattar A, Naveed M, Ali M, Zahir ZA, Nadeem SM, Yaseen M, Meena HN (2018) Perspectives of potassium solubilizing microbes in sustainable food production system: a review. Appl Soil Ecol 133:146–159

    Article  Google Scholar 

  • Savci S (2012) Investigation of effect of chemical fertilizers on environment. Apcbee Procedia 1:287–292

    Article  CAS  Google Scholar 

  • Selvakumar G, Panneerselvam P, Ganeshamurthy AN (2013) Legume root nodule associated bacteria. In: Plant microbe symbiosis: fundamentals and advances. Springer, New Delhi, pp 215–232

    Chapter  Google Scholar 

  • Setiawati TC, Mutmainnah L (2016) Solubilization of potassium containing mineral by microorganisms from sugarcane rhizosphere. Agric Agric Sci Procedia 9:108–117

    Google Scholar 

  • Shah F, Rineau F, Canbäck B, Johansson T, Tunlid A (2013) The molecular components of the extracellular protein-degradation pathways of the ectomycorrhizal fungus Paxillus involutus. New Phytol 200(3):875–887

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sharma N, Singhvi R (2017) Effects of chemical fertilizers and pesticides on human health and environment: a review. Int J Agric Environ Biotechnol 10(6):675–679

    Article  Google Scholar 

  • Shaw LJ, Nicol GW, Smith Z, Fear J, Prosser JI, Baggs EM (2006) Nitrosospira spp. can produce nitrous oxide via a nitrifier denitrification pathway. Environ Microbiol 8(2):214–222

    Article  CAS  PubMed  Google Scholar 

  • Shen H, He X, Liu Y, Chen Y, Tang J, Guo T (2016) A complex inoculant of N2-fixing, P-and K-solubilizing bacteria from a purple soil improves the growth of kiwifruit (Actinidia chinensis) plantlets. Front Microbiol 7:841

    PubMed  PubMed Central  Google Scholar 

  • Singh PK (2012) Role of glomalin related soil protein produced by arbuscular mycorrhizal fungi: a review. Agric Sci Res J 2(3):119–125

    Google Scholar 

  • Singh B, Natesan SKA, Singh BK, Usha K (2005) Improving zinc efficiency of cereals under zinc deficiency. Curr Sci 88:36–44

    Google Scholar 

  • Singh RS, Tripathi N, Singh SK (2007) Impact of degradation on nitrogen transformation in a forest ecosystem of India. Environ Monit Assess 125(1–3):165–173

    Article  CAS  PubMed  Google Scholar 

  • Singh VK, Singh AL, Singh R, Kumar A (2018) Iron oxidizing bacteria: insights on diversity, mechanism of iron oxidation and role in management of metal pollution. Environ Sustain 1(3):221–231

    Article  Google Scholar 

  • Smith SE, Andrew Smith F (2011) Roles of arbuscular mycorrhizas in plant nutrition and growth: new paradigms from cellular to ecosystem scales. Annu Rev Plant Biol 62(1):227–250

    Article  CAS  PubMed  Google Scholar 

  • Sparrow LA, Uren NC (2014) Manganese oxidation and reduction in soils: effects of temperature, water potential, pH and their interactions. Soil Res 52(5):483–494

    Article  CAS  Google Scholar 

  • Strickland TC, Fitzgerald JW, Ash JT, Swank WT (1987) Organic sulfur transformations and sulfur pool sizes in soil and litter from a southern Appalachian hardwood forest. Soil Sci 143(6):453–458

    Article  CAS  Google Scholar 

  • Sun K, Cao W, Hu LY, Fu WQ, Gong JH, Kang N, Dai CC (2019) Symbiotic fungal endophyte Phomopsis liquidambari-rice system promotes nitrogen transformation by influencing below-ground straw decomposition in paddy soil. J Appl Microbiol 126(1):191–203

    Article  CAS  PubMed  Google Scholar 

  • Sunithakumari K, Padma Devi SN, Vasandha S (2016) Zinc solubilizing bacterial isolates from the agricultural fields of Coimbatore, Tamil Nadu, India. Curr Sci 110(2):196

    Article  CAS  Google Scholar 

  • Sylvia DM, Fuhrmann JJ, Hartel PG, Zuberer DA (2005) Principles and applications of soil microbiology (No. QR111 S674 2005). Pearson, London

    Google Scholar 

  • Tandon A, Fatima T, Shukla D, Tripathi P, Srivastava S, Singh PC (2019) Phosphate solubilization by Trichoderma koningiopsis (NBRI-PR5) under abiotic stress conditions. J King Saud Univ Sci 32(1):791–798

    Article  Google Scholar 

  • Tao R, Li J, Guan Y, Liang Y, Hu B, Lv J, Chu G (2018) Effects of urease and nitrification inhibitors on the soil mineral nitrogen dynamics and nitrous oxide (N 2 O) emissions on calcareous soil. Environ Sci Pollut Res 25(9):9155–9164

    Article  CAS  Google Scholar 

  • Tatsumi C, Taniguchi T, Du S, Yamanaka N, Tateno R (2019) The steps in the soil nitrogen transformation process vary along an aridity gradient via changes in the microbial community. Biogeochemistry 144(1):15–29

    Article  CAS  Google Scholar 

  • Tebo BM, Johnson HA, McCarthy JK, Templeton AS (2005) Geomicrobiology of manganese (II) oxidation. Trends Microbiol 13(9):421–428

    Article  CAS  PubMed  Google Scholar 

  • Thangarajan R, Bolan NS, Naidu R, Surapaneni A (2015) Effects of temperature and amendments on nitrogen mineralization in selected Australian soils. Environ Sci Pollut Res 22(12):8843–8854

    Article  CAS  Google Scholar 

  • Thirukkumaran CM, Parkinson D (2002) Microbial activity, nutrient dynamics and litter decomposition in a Canadian Rocky Mountain pine forest as affected by N and P fertilizers. For Ecol Manag 159(3):187–201

    Article  Google Scholar 

  • Thorup C, Schramm A, Findlay AJ, Finster KW, Schreiber L (2017) Disguised as a sulfate reducer: growth of the deltaproteobacterium Desulfurivibrio alkaliphilus by sulfide oxidation with nitrate. MBio 8(4):e00671-17

    Google Scholar 

  • Uren NC (2013) Cobalt and manganese. In: Heavy metals in soils. Springer, Dordrecht, pp 335–366

    Chapter  Google Scholar 

  • Vaid SK, Kumar B, Sharma A, Shukla AK, Srivastava PC (2014) Effect of Zn solubilizing bacteria on growth promotion and Zn nutrition of rice. J Soil Sci Plant Nutr 14(4):889–910

    Google Scholar 

  • Van Nguyen T, Pawlowski K (2017) Frankia and actinorhizal plants: symbiotic nitrogen fixation. In: Rhizotrophs: plant growth promotion to bioremediation. Springer, Singapore, pp 237–261

    Chapter  Google Scholar 

  • van Niftrik L, Jetten MS (2012) Anaerobic ammonium-oxidizing bacteria: unique microorganisms with exceptional properties. Microbiol Mol Biol Rev 76(3):585–596

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Van Spanning RJM, Delgado MJ, Richardson DJ (2005) The nitrogen cycle: denitrification and its relationship to N 2 fixation. In: Nitrogen fixation in agriculture, forestry, ecology, and the environment. Springer, Dordrecht, pp 277–342

    Chapter  Google Scholar 

  • Venceslau SS, Stockdreher Y, Dahl C, Pereira IAC (2014) The “bacterial heterodisulfide” DsrC is a key protein in dissimilatory sulfur metabolism. Biochim Biophys Acta Bioenergetics 1837(7):1148–1164

    Article  CAS  Google Scholar 

  • Verma P, Yadav AN, Khannam KS, Panjiar N, Kumar S, Saxena AK, Suman A (2015) Assessment of genetic diversity and plant growth promoting attributes of psychrotolerant bacteria allied with wheat (Triticum aestivum) from the northern hills zone of India. Ann Microbiol 65(4):1885–1899

    Article  CAS  Google Scholar 

  • Vidyalakshmi R, Paranthaman R, Bhakyaraj R (2009) Sulphur oxidizing bacteria and pulse nutrition- a review. World J Agric Sci 5(3):270–278

    CAS  Google Scholar 

  • Volpe V, Giovannetti M, Sun XG, Fiorilli V, Bonfante P (2016) The phosphate transporters LjPT4 and MtPT4 mediate early root responses to phosphate status in non-mycorrhizal roots. Plant Cell Environ 39(3):660–671

    Article  CAS  PubMed  Google Scholar 

  • Vranova V, Rejsek K, Formanek P (2013) Proteolytic activity in soil: a review. Appl Soil Ecol 70:23–32

    Article  Google Scholar 

  • Wang F, Li J, Wang X, Zhang W, Zou B, Neher DA, Li Z (2014) Nitrogen and phosphorus addition impact soil N 2 O emission in a secondary tropical forest of South China. Sci Rep 4:5615

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang W, Shi J, Xie Q, Jiang Y, Yu N, Wang E (2017a) Nutrient exchange and regulation in arbuscular mycorrhizal symbiosis. Mol Plant 10(9):1147–1158

    Article  CAS  PubMed  Google Scholar 

  • Wang Z, Wang J, Liu J, Chen H, Li M, Li L (2017b) Mechanistic insights into manganese oxidation of a soil-borne Mn (II)-oxidizing Escherichia coli strain by global proteomic and genetic analyses. Sci Rep 7(1):1–13

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wang R, Lin JQ, Liu XM, Pang X, Zhang CJ, Yang CL, Lin JQ (2019) Sulfur oxidation in the acidophilic autotrophic Acidithiobacillus spp. Front Microbiol 9:3290

    Article  PubMed  PubMed Central  Google Scholar 

  • Wani FS, Ahmad L, Ali T, Mushtaq A (2015) Role of microorganisms in nutrient mobilization and soil health—a review. J Pure Appl Microbiol 9:1401–1410

    Google Scholar 

  • Weber DF, Gainey PL (1962) Relative sensitivity of nitrifying organisms to hydrogen ions in soils and in solutions. Soil Sci 94(3):138–145

    Article  CAS  Google Scholar 

  • Wei H, Xu J, Quan G, Zhang J, Qin Z (2017) Effects of Praxelis clematidea invasion on soil nitrogen fractions and transformation rates in a tropical savanna. Environ Sci Pollut Res 24(4):3654–3663

    Article  CAS  Google Scholar 

  • Wei Y, Zhao Y, Shi M, Cao Z, Lu Q, Yang T, Fan Y, Wei Z (2018) Effect of organic acids production and bacterial community on the possible mechanism of phosphorus solubilization during composting with enriched phosphate-solubilizing bacteria inoculation. Bioresour Technol 247:190–199

    Article  CAS  PubMed  Google Scholar 

  • Welch SA, Vandevivere P (1994) Effect of microbial and other naturally occurring polymers on mineral dissolution. Geomicrobiol J 12(4):227–238

    Article  CAS  Google Scholar 

  • Wen X, Hu C, Sun X, Zhao X, Tan Q (2019) Research on the nitrogen transformation in rhizosphere of winter wheat (Triticum aestivum) under molybdenum addition. Environ Sci Pollut Res 26(3):2363–2374

    Article  CAS  Google Scholar 

  • Xin J, Liu Y, Chen F, Duan Y, Wei G, Zheng X, Li M (2019) The missing nitrogen pieces: a critical review on the distribution, transformation, and budget of nitrogen in the vadose zone-groundwater system. Water Res 165:114977

    Article  CAS  PubMed  Google Scholar 

  • Xu Y, Xu Z (2015) Effects of land use change on soil gross nitrogen transformation rates in subtropical acid soils of Southwest China. Environ Sci Pollut Res 22(14):10850–10860

    Article  CAS  Google Scholar 

  • Xue S, Jiang X, Wu C, Hartley W, Qian Z, Luo X, Li W (2020) Microbial driven iron reduction affects arsenic transformation and transportation in soil-rice system. Environ Pollut 260:114010

    Article  CAS  PubMed  Google Scholar 

  • Yadav AN, Sharma D, Gulati S, Singh S, Dey R, Pal KK, Saxena AK (2015) Haloarchaea endowed with phosphorus solubilization attribute implicated in phosphorus cycle. Sci Rep 5(1):1–10

    CAS  Google Scholar 

  • Yang XC, Han ZZ, Ruan XY, Chai J, Jiang SW, Zheng R (2019) Composting swine carcasses with nitrogen transformation microbial strains: succession of microbial community and nitrogen functional genes. Sci Total Environ 688:555–566

    Article  CAS  PubMed  Google Scholar 

  • Yuan C, Liu T, Li F, Liu C, Yu H, Sun W, Huang W (2018) Microbial iron reduction as a method for immobilization of a low concentration of dissolved cadmium. J Environ Manag 217:747–753

    Article  CAS  Google Scholar 

  • Zaheer A, Malik A, Sher A, Qaisrani MM, Mehmood A, Khan SU, Rasool M (2019) Isolation, characterization, and effect of phosphate-zinc-solubilizing bacterial strains on chickpea (Cicer arietinum L.) growth. Saudi J Biol Sci 26(5):1061–1067

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang M, Xu Z, Teng Y, Christie P, Wang J, Ren W, Li Z (2016) Non-target effects of repeated chlorothalonil application on soil nitrogen cycling: the key functional gene study. Sci Total Environ 543:636–643

    Article  CAS  PubMed  Google Scholar 

  • Zhang X, Baars O, Morel FM (2019) Genetic, structural, and functional diversity of low and high-affinity siderophores in strains of nitrogen fixing Azotobacter chroococcum. Metallomics 11(1):201–212

    Article  PubMed  Google Scholar 

  • Zhang H, Shi L, Lu H, Shao Y, Liu S, Fu S (2020) Drought promotes soil phosphorus transformation and reduces phosphorus bioavailability in a temperate forest. Sci Total Environ 139295

    Google Scholar 

  • Zhao C, Degryse F, Gupta V, McLaughlin MJ (2015) Elemental sulphur oxidation in Australian cropping soils. Soil Sci Soc Am J 79:89–96

    Article  CAS  Google Scholar 

  • Zhi-Hui YANG, Stöven K, Haneklaus S, Singh BR, Schnug E (2010) Elemental sulfur oxidation by Thiobacillus spp. and aerobic heterotrophic sulfur-oxidizing bacteria. Pedosphere 20(1):71–79

    Article  Google Scholar 

  • Zhou H, Zhao Y, Yang H, Zhu L, Cai B, Luo S, Wei Z (2018) Transformation of organic nitrogen fractions with different molecular weights during different organic wastes composting. Bioresour Technol 262:221–228

    Article  CAS  PubMed  Google Scholar 

  • Zhu G, Song X, Ju X, Zhang J, Müller C, Sylvester-Bradley R, Rees RM (2019a) Gross N transformation rates and related N2O emissions in Chinese and UK agricultural soils. Sci Total Environ 666:176–186

    Article  CAS  PubMed  Google Scholar 

  • Zhu L, Zhao Y, Zhang W, Zhou H, Chen X, Li Y, Wei Z (2019b) Roles of bacterial community in the transformation of organic nitrogen toward enhanced bioavailability during composting with different wastes. Bioresour Technol 285:121326

    Article  CAS  PubMed  Google Scholar 

  • Zumft WG (1997) Cell biology and molecular basis of denitrification. Microbiol Mol Biol Rev 61(4):533–616

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

The authors are grateful to the editorial team for giving critical comments for substantial improvement in the quality of this chapter.

Author information

Authors and Affiliations

  1. ICAR-Indian Institute of Maize Research, Ludhiana, Punjab, India

    Deep Mohan Mahala

  2. Ecophysiology of Plants, Faculty of Science and Engineering, GELIFES-Groningen Institute for Evolutionary Life Sciences, Groningen, The Netherlands

    Hemant S. Maheshwari

  3. ICAR-Indian Institute of Soybean Research, Indore, Madhya Pradesh, India

    Hemant S. Maheshwari, Abhishek Bharti & Aketi Ramesh

  4. Agriculture University, Kota, Rajasthan, India

    Rajendra Kumar Yadav

  5. Agricultural College and Research Institute, Killikulam, Tamil Nadu Agricultural University, Vallanadu, Tamil Nadu, India

    B. Jeberlin Prabina

  6. ICAR- Directorate of Groundnut Research, Junagarh, Gujarat, India

    Kiran K. Reddy

  7. SKN Agriculture University, Jobner, Rajasthan, India

    Chiranjeev Kumawat

Authors
  1. Deep Mohan Mahala
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hemant S. Maheshwari
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Rajendra Kumar Yadav
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. B. Jeberlin Prabina
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Abhishek Bharti
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Kiran K. Reddy
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Chiranjeev Kumawat
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Aketi Ramesh
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hemant S. Maheshwari .

Editor information

Editors and Affiliations

  1. NAIMCC, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, Uttar Pradesh, India

    Sushil Kumar Sharma

  2. Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, Uttar Pradesh, India

    Udai B. Singh

  3. Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, Uttar Pradesh, India

    Pramod Kumar Sahu

  4. Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, Uttar Pradesh, India

    Harsh Vardhan Singh

  5. Plant Pathology, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, Uttar Pradesh, India

    Pawan Kumar Sharma

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Mahala, D.M. et al. (2020). Microbial Transformation of Nutrients in Soil: An Overview. In: Sharma, S.K., Singh, U.B., Sahu, P.K., Singh, H.V., Sharma, P.K. (eds) Rhizosphere Microbes. Microorganisms for Sustainability, vol 23. Springer, Singapore. https://doi.org/10.1007/978-981-15-9154-9_7

Download citation

Publish with us

Policies and ethics

Search

Navigation