Skip to main content

Soil Microbial Diversity: An Ecophysiological Study and Role in Plant Productivity

  • Chapter
  • First Online:
Advances in Soil Microbiology: Recent Trends and Future Prospects

Abstract

Soil is considered as one of the most competent ecosystems for subsistence of microorganisms. Soil microbial community structure and activity depend largely on structure and status of the soil habitat. Diverse heterotrophic microbial communities in soil along with their complex web of interaction facilitate the cycling of micro- and macro-nutrients in soil ecosystem. The demand of sustained plant productivity is achieved through managing soil fertility. The dynamic relationships between different components, living or nonliving, of agroecosystem control the richness of plants or crops. In turn, soil organic matter is influenced by the inputs from plants and also their chemistry makes each ecosystem somewhat unique in its microbial community. Though the role of soil microbiome is widely known, we still have a limited understanding of its complexity. Thus, understanding the microbial diversity will enhance our ability of increasing agricultural production.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
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

  • Agamy R, Hashem M, Alamri S (2013) Effect of soil amendment with yeasts as bio-fertilizers on the growth and productivity of sugar beet. Afr J Agri Res 8(1):46–56. https://doi.org/10.5897/AJAR12.1989

    Google Scholar 

  • Ahemad M, Kibret M (2014) Mechanisms and applications of plant growth promoting rhizobacteria: current perspective. J King Saud Univ Sci 26:1–20. https://doi.org/10.1016/j.jksus.2013.05.001

    Article  Google Scholar 

  • Aislabie J, Deslippe JR (2013) Soil microbes and their contribution to soil services. Soil Microbial Diversity

    Google Scholar 

  • Al-Falih AM, Wainwright M (1995) Nitrification, S oxidation and P-solubilization by the soil yeast Williopsis californica and by Saccharomyces cerevisiae. Mycol Res 99:200–204. https://doi.org/10.1016/S0953-7562(09)80886-1

    Article  Google Scholar 

  • Angel R, Claus P, Conrad R (2012) Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions. ISME J 6:847–862. https://doi.org/10.1038/ismej.2011.141

    Article  CAS  PubMed  Google Scholar 

  • Badri DV, Vivanco JM (2009) Regulation and function of root exudates. Plant Cell Environ 32:666–681

    Article  CAS  PubMed  Google Scholar 

  • Balser TC, Wixon D, Moritz LK, Lipps L (2010) The microbiology of natural soils. In: Dixon GR, Tilston EL (eds) Soil microbiology and sustainable crop production. Springer, Berlin, pp 27–57

    Chapter  Google Scholar 

  • Bano SA, Iqbal SM (2016) Biological nitrogen fixation to improve plant growth and productivity. Int J Ag Innov Res 4(4):2319–1473

    Google Scholar 

  • Bargett RD, Shine A (1999) Linkages between plant litter diversity, soil microbial biomass and ecosystem function in temperate grasslands. Soil Biol Biochem 31:317–321. https://doi.org/10.1016/S0038-0717(98)00121-7

    Article  Google Scholar 

  • Bhattacharyya PN, Jha DK (2012) Plant growth-promoting rhizo-bacteria (PGPR): emergence in agriculture. World J Microbiol Biotechnol 28:1327–1350. https://doi.org/10.1007/s11274-011-0979-9

    Article  CAS  PubMed  Google Scholar 

  • Brady NC, Weil RR (2002) The nature and properties of soils, 13th edn. Prentice Hall, Upper Saddle River

    Google Scholar 

  • Carson JK, Rooney D, Gleeson DB, Clipson N (2007) Altering the mineral composition of soil causes a shift in microbial community structure. FEMS Microbiol Ecol 61:414–423. https://doi.org/10.1111/j.1574-6941.2007.00361.x

    Article  CAS  PubMed  Google Scholar 

  • Carson JK, Campbell L, Rooney D, Clipson N, Gleeson DB (2009) Minerals in soil select distinct bacterial communities in their microhabitats. FEMS Microbiol Ecol 67:381–388. https://doi.org/10.1111/j.1574-6941.2008.00645

    Article  CAS  PubMed  Google Scholar 

  • Carson JK, Gonzalez-Quinones V, Murphy DV, Hinz C, Shaw JA, Gleeson DB (2010) Low pore connectivity increases bacterial diversity in soil. Appl Environ Microbiol 76(12):3936–3942. https://doi.org/10.1128/AEM.03085-09

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Castro-Sowinski S, Herschkovitz Y, Okon Y, Jurkevitch E (2007) Effects of inoculation with plant growth-promoting rhizobacteria on resident rhizosphere microorganisms. FEMS Microbiol Lett 276:1–11. https://doi.org/10.1111/j.1574-6968.2007.00878.x

    Article  CAS  PubMed  Google Scholar 

  • Certini G, Campbell CD, Edwards AC (2004) Rock fragments in soil support a different microbial community from the fine earth. Soil Biol Biochem 36:1119–1128. https://doi.org/10.1016/j.soilbio.2004.02.022

    Article  CAS  Google Scholar 

  • Cho DH, Chae HJ, Kim EY (2001) Synthesis and characterization of a novel extracellular polysaccharide by Rhodotorula glutinis. Appl Biochem Biotech 95:183–193

    Article  CAS  Google Scholar 

  • Di H, Cameron KC, Shen JP, Winefield CS, O’Callaghan M, Bowatte S et al (2010) Ammonia-oxidizing bacteria and archaea grow under contrasting soil nitrogen conditions. FEMS Microbiol Ecol 72:386–394. https://doi.org/10.1111/j.1574-6941.2010.00861.x

    Article  CAS  PubMed  Google Scholar 

  • El-Ayouty YMF, Ghazal M, El-Etr WT, EL-Abdeen HAZ (2012) Effect of Cyanobacteria Inoculation associated with different nitrogen levels on some Sandy and Calcareous soils properties and wheat productivity. Nat Sci 10(12):233–240

    Google Scholar 

  • Ellouze W, Taheri AE, Bainard LD, Yang C, Bazghaleh N, Navarro-Borrell A, Hanson K, Hamel C (2014) Soil fungal resources in annual cropping systems and their potential for management. BioMed Res Int. https://doi.org/10.1155/2014/531824

  • Eman AAA, Saleh MMS, Mostaza EAM (2008) Minimizing the quantity of mineral nitrogen fertilizers on grapevine by using humic acid, organic and bio-fertilizers. Res J Agric Biol Sci 4:46–50

    Google Scholar 

  • Fierer N, Bradford MA, Jackson RB (2007) Toward an ecological classification of soil bacteria. Ecology 88(6):1354–1364. https://doi.org/10.1890/05-1839

    Article  PubMed  Google Scholar 

  • Franco-Correa M and Chavarro-Anzola V (2014) Chapter 10: Actinobacteria as plant growth-promoting. Actinobacteria – basics and biotechnological applications. https://doi.org/10.5772/61291

  • Garrett SD (1951) Ecological groups of soil fungi: a survey of substrate relationships. New Phytol 50:149–166

    Article  Google Scholar 

  • Gaur AC (1990) Phosphate solubilizing microorganisms as biofertilizers. Omega Scientific Publication, New Delhi

    Google Scholar 

  • Giordano W, Hirsch AM (2004) The expression of MaEXP1, a Melilotus alba expansin gene, is upregulated during the sweet clover-Sinorhizobium meliloti interaction. Mol Plant Microbe Interact 17(6):613–622. https://doi.org/10.1094/MPMI.2004.17.6.613

    Article  CAS  PubMed  Google Scholar 

  • Glick BR, Patten CL, Holguin G, Penrose GM (1999) Biochemical and genetic mechanisms used by plant growth promoting bacteria. Imperial College Press, London

    Book  Google Scholar 

  • Grundmann GL, Normand P (2000) Microscale diversity of the genus Nitrobacter in soil on the basis of analysis of genes encoding rRNA. Appl Environ Microb 66(10):4543–4546

    Article  CAS  Google Scholar 

  • Harris RF, Chesters G, Allen ON (1966) Dynamics of soil aggregation. Advances in agronomy 18:107–169

    Article  CAS  Google Scholar 

  • Hattori T, Hattori R (1976) The physical environment in soil microbiology: an attempt to extend principles of microbiology to soil microorganisms. Crit Rev Microbiol 4:423–460. https://doi.org/10.3109/10408417609102305

    Article  CAS  Google Scholar 

  • Insam H (2001) Developments in soil microbiology since the mid 1960s. Geoderma 100:389–402. https://doi.org/10.1007/s00374-010-0442-3

    Article  CAS  Google Scholar 

  • Jobbágy EG, Jackson RB (2000) The vertical distribution of soil organic carbon and its relation to climate and vegetation. Ecol Appl 10(2):423–436. https://doi.org/10.1890/1051-0761(2000)010[0423:TVDOSO]2.0.CO;2

    Article  Google Scholar 

  • Klironomos JN, McCune J, Hart M, Neville J (2000) The influence of arbuscular mycorrhizae on the relationship between plant diversity and productivity. Ecol Lett 3:137–141. https://doi.org/10.1046/j.1461-0248.2000.00131.x

    Article  Google Scholar 

  • Koide RT (1991) Nutrient supply, nutrient demand and plant response to mycorrhizal infection. New Phytol 117:365–386. https://doi.org/10.1111/j.1469-8137.1991.tb00001.x

    Article  CAS  Google Scholar 

  • Kuramae EE, Yergeau E, Wong LC, Pijl AS, van Veen JA, Kowalchuk GA (2012) Soil characteristics more strongly influence soil bacterial communities than land-use type. FEMS Microbiol Ecol 79:12–24

    Article  CAS  PubMed  Google Scholar 

  • Lipson DA (2007) Relationship between temperature responses and bacterial community structure along seasonal and altitudinal gradients. FEMS Microb Ecol 59:418–427. https://doi.org/10.1111/j.1574-6941.2006.00240.x

    Article  CAS  Google Scholar 

  • Lovelock CH, Patterson PG, Walker RH (2004) Services marketing: an Asia pacific perspective, 3rd edn. Prentice Hall, Sydney

    Google Scholar 

  • Mauchline TH, Kerry BR, Hirsch PR (2002) Quantification in soil and the rhizosphere of the nematophagous fungus Verticillium chlamydosporium by competitive PCR and comparison with selective plating. Appl Environ Microbiol 68:1846–1853. https://doi.org/10.1128/AEM.68.4.1846-1853.2002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mitchell CE (2003) Trophic control of grassland production and biomass by pathogens. Ecol Lett 6:147–155. https://doi.org/10.1046/j.1461-0248.2003.00408.x

    Article  Google Scholar 

  • Murali M, Amruthesh KN, Sudisha J, Niranjana SR, Shetty HS (2012) Screening for plant growth promoting fungi and their ability for growth promotion and induction of resistance in pearl millet against downy mildew disease. J Phyto 4(5):30–36

    Google Scholar 

  • Nakayan P, Shen FT, Hung MH, Young CC (2009) Effectiveness of Pichia sp. CC1 in decreasing chemical fertilization requirements of garden lettuce in pot experiments. As. J Food Ag-Ind Special:S66–S68

    Google Scholar 

  • Pankhurst CE (1997) Biodiversity of soil organisms as an indicator of soil health. In: Pankhurst C, Doube BM, Gupta VVSR (eds) Biological indicators of soil health. CAB International, Oxfordshire, pp 297–324

    Google Scholar 

  • Pradhan A, Baisakh B, Mishra BB (2014) Plant growth characteristics of bacteria isolated from rhizosphere region of Santalum album. J Pure Appl Microbio 8(6):4775–4781

    Google Scholar 

  • Rudakov KI (1951) Mikroorganizmy i struktura pochvy (Microorganisms and soil structure). SeFkhozgiz, Moscow. (in Russian)

    Google Scholar 

  • Singh A, Vishwakarma P, Adhya TK, Inubushi K, Dubey SK (2017) Molecular ecological perspective of methanogenic archaeal community in rice agroecosystem. Sci Total Environ 596–597:136–146

    Google Scholar 

  • Smith JL, Paul EA (1990) The significance of soil microbial biomass estimations. In: Bollag J, Stotsky G (eds) Soil biochemistry. Marcel Dekker, New York, pp 357–396

    Google Scholar 

  • Spiller H, Stallings W, Woods T, Gunasekaran M (1993) Requirement for direct association of ammonia-excreting Anabaena variabilis mutant (SA-1) with roots for maximal growth and yield of wheat. Appl Microbiol Biotechnol 40:557–566. https://doi.org/10.1007/BF00175748

    Article  CAS  Google Scholar 

  • Starkey RL (1931) Some influences of the development of higher plants upon the microorganisms in the soil: iv. Influence of proximity to roots on abundance and activity of microorganisms. Soil Sci 32(5):367–394

    Article  CAS  Google Scholar 

  • Stephan A, Meyer AH, Schmid B (2000) Plant diversity affects culturable soil bacteria in experimental grassland communities. J Ecol 88:988–999

    Article  Google Scholar 

  • Sylvia DM, Fuhrmann JJ, Hartel PG, Zuberer DA (2005) Principles and applications of soil microbiology, 2nd edn. Prentice Hall, Upper Saddle River

    Google Scholar 

  • Tilman D (1982) Resource competition and community structure. Princeton University Press, Princeton

    Google Scholar 

  • Tilman D (1987) Secondary succession and the pattern of plant dominance along experimental nitrogen gradients. Ecol Monogr 57:189–214

    Article  Google Scholar 

  • van der Heijden MGA, Bardgett RD, van Straalen NM (2008) The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett 11:296–301. https://doi.org/10.1111/j.1461-0248.2007.01139.x

    Article  PubMed  Google Scholar 

  • Veldkamp E, Becker A, Schwendenmann L, Clark DA, Schulte-Bisping H (2003) Substantial labile carbon stocks and microbial activity in deeply weathered soils below a tropical wet forest. Glob Change Biol 9(8):1171–1184. https://doi.org/10.1046/j.1365-2486.2003.00656.x

    Article  Google Scholar 

  • Vishniac HS (1995) Simulated in situ competitive ability and survival of a representative soil yeasts, Cryptococcus albidus. Microbial Ecol 30:309–320. https://doi.org/10.1007/BF00171937

    Article  CAS  Google Scholar 

  • Wardle DA, Bonner KI, Barker GM, Yeates GW, Nicholson KS, Bardgett RD, Watson RN, Ghani A (1999) Plant removals in perennial grassland: vegetation dynamics, decomposers, soil biodiversity, and ecosystem properties. Ecol Monogr 69:535–568. https://doi.org/10.1890/0012-9615(1999)069[0535:PRIPGV]2.0.CO;2

    Article  Google Scholar 

  • Wertz JT, Kim E, Breznak JA, Schmidt TM, Rodrigues JLM (2012) Genomic and physiological characterization of the Verrucomicrobia isolate Diplosphaera colitermitum gen. nov., sp. nov., reveals microaerophily and nitrogen fixation genes. Am Soc Microbiol 78(5):1544–1555. https://doi.org/10.1128/AEM.06466-11

    CAS  Google Scholar 

  • Whipps JM (2001) Microbial interactions and biocontrol in the rhizosphere. J Exp Bot 52:487–511

    Article  CAS  PubMed  Google Scholar 

  • Wixon DL, Balser TC (2009) Investigating biological control over soil carbon temperature sensitivity. Glob Chang Biol 15(12):2803–3065. https://doi.org/10.1111/j.1365-2486.2009.01946.x

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Suraja Kumar Nayak .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Baliyarsingh, B., Nayak, S.K., Mishra, B.B. (2017). Soil Microbial Diversity: An Ecophysiological Study and Role in Plant Productivity. In: Adhya, T., Mishra, B., Annapurna, K., Verma, D., Kumar, U. (eds) Advances in Soil Microbiology: Recent Trends and Future Prospects. Microorganisms for Sustainability, vol 4. Springer, Singapore. https://doi.org/10.1007/978-981-10-7380-9_1

Download citation

Publish with us

Policies and ethics