Soil Microbiology Research in the Coming Decades: Translational Research Opportunities

  • Tapan Kumar Adhya
  • K. Annapurna
Part of the Microorganisms for Sustainability book series (MICRO, volume 3)


Soil microbiology deals with the diverse group of living organisms that resides in the soil. The microflora and fauna function to maintain the soil process and other ecosystem services to keep the soil healthy and functional, and thereby support plant growth. Agriculture and land-use changes including rapid urbanization irrevocably alter the soil microflora – both structurally and functionally. While plant supports microbes in their root region by transferring part of the photosynthate, microbes dwelling in the rhizosphere form the second genome for the plant and provide physiological and ecological fitness to the plant. For meeting the demand for the burgeoning population of the earth, microorganisms provide a green alternative to grow plants, especially crop plants, in a sustainable manner.


Soil microbiology Microbial diversity Plant microbiome Rhizosphere Sustainable agriculture 


  1. Abrol YP, Adhya TK (2017) Technical summary. In: Abrol YP, Adhya TK, Aneja VP, Raghuram N, Pathak H, Kulshrestha U, Sharma C, Singh B (eds) The Indian nitrogen assessment. Elsevier, ColomboGoogle Scholar
  2. Adesemoye AO, Torbert HA, Kloepper JW (2009) Plant growth-promoting rhizobacteria allow reduced application rates of chemical fertilizers. Microb Ecol 2009(58):921–929CrossRefGoogle Scholar
  3. Ahkami AH, White RA III, Handakumburaa PP, Jansson C (2017) Rhizosphere engineering: enhancing sustainable plant ecosystem productivity. Rhizosphere 3(2017):233–243CrossRefGoogle Scholar
  4. Bardgett RD, van der Putten WH (2014) Belowground biodiversity and ecosystem functioning. Nature 515:505–511CrossRefPubMedGoogle Scholar
  5. Bardgett RD, Usher MB, Hopkins DW (2005) Biological diversity and function in soils. Cambridge University Press, CambridgeCrossRefGoogle Scholar
  6. Biswas R, Sarkar A (2017) “Omics” tools in soil microbiology: the state of the art. In: Adhya TK, Lal B, Mahapatra B, Paul D, Das S (eds) Advances in soil microbiology: recent trends and future prospects: Vol. 1: Soil-microbe interaction. Springer, New Delhi, pp 35–64Google Scholar
  7. Bulgarelli D et al (2013) Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol 64:807–838CrossRefPubMedGoogle Scholar
  8. Carey J (2016) Crucial role of belowground biodiversity. PNAS 113:7682–7685CrossRefPubMedPubMedCentralGoogle Scholar
  9. Chaparro JM, Badri DV, Vivanco JM (2014) Rhizosphere microbiome assemblage is affected by plant development. ISME J 8:790–803CrossRefPubMedGoogle Scholar
  10. de Vries W, Leip A, Reinds GJ, Kros J, Lesschen JP, Bouwman AF (2011) Comparison of land nitrogen budgets for European agriculture by various modeling approaches. Environ Pollut 159:3254–3268CrossRefPubMedGoogle Scholar
  11. Edwards J, Johnson C, Santos-Medellín C, Lurie E, Podishetty NK, Bhatnagar S, Eisen JA, Sundaresan V (2015) Structure, variation, and assembly of the root-associated microbiomes of rice. PNAS 112:E911–E920CrossRefPubMedPubMedCentralGoogle Scholar
  12. Guerrero R, Margulis L, Berlanga M (2013) Symbiogenesis: the holobiont as a unit of evolution. Int Microbiol 16:133–143PubMedGoogle Scholar
  13. Hutchison CA, Chuang RY, Noskov VN, Assad-Garcia N, Deerinck TJ, Ellisman MH et al (2016) Design and synthesis of a minimal bacterial genome. Science 351.
  14. Kashyap PL, Rai P, Srivastava AK, Kumar S (2017) Trichoderma for climate resilient agriculture. World J Microbiol Biotechnol 33:155. CrossRefPubMedGoogle Scholar
  15. Knief C (2014) Analysis of plant microbe interactions in the era of next generation sequencing technologies. Front Plant Sci 5:Article 216. CrossRefPubMedGoogle Scholar
  16. Lagos ML, Maruyama F, Nannipieri P, Mora ML, Ogram A, Jorquera MA (2015) Current overview on the study of bacteria in the rhizosphere by modern molecular techniques: a mini–review. J Soil Sci Plant Nutr 15(2):504–523Google Scholar
  17. Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, del Rio TG, Edgar RC, Eickhorst T, Ley RE, Hugenholtz P, Tringe SG, Dang JL (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488:86–90CrossRefPubMedPubMedCentralGoogle Scholar
  18. Mendes R, Kruijt M, de Bruijn I, Dekkers E, van der Voort M, Schneider JHM, Piceno YM, DeSantis TZ, Andersen GL, Bakker PAHM, Raaijmakers JM (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332:1097–1100CrossRefPubMedGoogle Scholar
  19. Mendes R, Garbeva P, Raaijmakers JM (2013) The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev 37:634–663CrossRefPubMedGoogle Scholar
  20. Nannipieri P, Ascher J, Ceccherini M, Landi L, Pietramellara G, Renella G (2002) Microbial diversity and soil. Eur J Soil Sci 54:655–670CrossRefGoogle Scholar
  21. Newman MM, Lorenz N, Hoilett N, Lee NR, Dick RP, Liles MR, Ramsier C, Kloepper JW (2016) Changes in rhizosphere bacterial gene expression following glyphosate treatment. Sci Total Environ 553:32–41CrossRefPubMedGoogle Scholar
  22. Nogales A, Valadas V, Ragonezi C, Polidoros A, Arnholdt-schmitt B (2015) Can functional hologenomics aid tackling current challenges in plant breeding? Brief Funct Genomics:1–10.
  23. Pieterse CMJ et al (2016) The soil-borne supremacy. Trends Plant Sci 21:171–173CrossRefPubMedGoogle Scholar
  24. Pineda A, Kaplan I, Bezemer T (2017) Steering soil microbiomes to suppress aboveground insect pests. Trends Plant Sci 22:770–778CrossRefPubMedGoogle Scholar
  25. Sahoo RK, Bhardwaj D, Tuteja N (2013) Biofertilizers: a sustainable eco-friendly agricultural approach to crop improvement. In: Tuteja N, Gill SS (eds) Plant acclimation to environmental stress. Springer, New York, pp 403–432CrossRefGoogle Scholar
  26. Sessitsch A, Hardoim P, Döring J, Weilharter A, Krause A, Woyke T, Mitter B, Hauberg-Lotte L, Friedrich F, Rahalkar M, Hurek T, Sarkar A, Bodrossy L, van Overbeek L, Brar D, van Elsas JD, Reinhold-Hurek B (2012) Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis. Mol Plant-Microbe Interact 25:28–36CrossRefPubMedGoogle Scholar
  27. Singh JS, Pandey VC, Singh DP (2011) Efficient soil microorganisms: a new dimension for sustainable agriculture and environmental development. Agric Ecosyst Environ 140:339–353CrossRefGoogle Scholar
  28. Smil V (1997) Global population and the nitrogen cycle. Sci Am 277:76–81CrossRefGoogle Scholar
  29. SSSA [Soil Science Society of America] (2008) Glossary of soil science terms. ASA-CSSA-SSSA, MadisonGoogle Scholar
  30. Sutton MA, Howard CM, Erisman JW, Billen G, Bleeker A, Greenfelt P et al (eds) (2011) The European nitrogen assessment. Cambridge University Press, CambridgeGoogle Scholar
  31. Tilman D, Cassman KG, Matson PA, Naylor R, Polasky S (2002) Agricultural sustainability and intensive production practices. Nature 418:671–677CrossRefPubMedGoogle Scholar
  32. Valverde A, De Maayer P, Oberholster T, Henschel J, Louw MK, Cowan D (2016) Specific microbial communities associate with the rhizosphere of Welwitschia mirabilis, a living fossil. PLoS One 11:e0153353CrossRefPubMedPubMedCentralGoogle Scholar
  33. Vandenkoornhuyse P, Quaiser A, Duhamel M, Le Van A, Dufresne A (2015) The importance of the microbiome of the plant holobiont. New Phytol 206:1196–1206CrossRefPubMedGoogle Scholar
  34. Velthof G, Barot S, Bloem J, Butterbach-Bahl K, de Vries W, Kros J, Lavelle P, Olesen EJ, Oenema O (2011) Nitrogen as a threat to European soil quality. In: Sutton MA, Howard CM, Erisman JW, Billen G, Bleeker A, Grennfelt P, van Grinsven H, Grizzetti B (eds) The European nitrogen assessment. Cambridge University Press, Cambridge, pp 495–510CrossRefGoogle Scholar
  35. Wallenstein MD (2017) Managing and manipulating the rhizosphere microbiome for plant health: a systems approach. Rhizosphere 3:230–232CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  1. 1.KIIT School of BiotechnologyBhubaneswarIndia
  2. 2.Division of MicrobiologyICAR-Indian Agricultural Research InstituteNew DelhiIndia

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