Microbial Diversity and Soil Health in Tropical Agroecosystems

  • Dipanti Chourasiya
  • Mahaveer P. Sharma
  • Hemant S. Maheshwari
  • Aketi Ramesh
  • Sushil K. Sharma
  • Tapan Kumar AdhyaEmail author
Part of the Microorganisms for Sustainability book series (MICRO, volume 4)


Microbial diversity is one important factor which controls agroecosystem productivity and quality. Microbial diversity is critical to ecosystem functioning due to its specificity in processes for which microbes are responsible. The presence of diverse soil microbes, bacteria, fungi, and archaea plays a critical role in cycling of major elements (C, N, P) which helps to maintain good soil health. These microbes help in maintaining soil structure, reduce susceptibility to pests and diseases, and eliminate hazardous substances from soil. In this review we addressed two significant questions concerning soil health: (1) how microbial diversity and community structure most effectively describe soil health and can be used as indicators and (2) how can soil health assessed by such indicators be improved or maintained? A summary of available techniques to characterize microbial community structure and diversity is provided, and information pertaining to strategies that can improve microbial diversity in relation to soil health by adopting suitable agricultural practices to sustain soil and crop productivity is furnished. These techniques include those for structural profiling, functional profiling, and other tools being used to assess microbial community diversity and their management through agricultural practices for improving the quality of soil and enhancing the crop productivity. Healthy soil supports high microbial diversity, activity, fertility, nutrient cycling, and disease-suppressive abilities. There is a considerable interest in understanding the nutrient cycles that regulates C, N, and P (carbon, nitrogen, phosphorus) exchange between the soil and atmosphere and how this exchange responds into tropical agroecosystem functioning under diverse edapho-climatic conditions.


Soil health Tropical agroecosystem Microbial diversity Structural community profiling Soil health indicators 


  1. Adhya TK, Kumar N, Reddy G, Podile AR, Bee H, Samantaray B (2015) Microbial mobilization of soil phosphorus and sustainable P management in agricultural soils. Curr Sci 108:1280–1287Google Scholar
  2. Altieri MA (1999) The ecological role of biodiversity in agroecosystems. Agric Ecosyst Environ 74:19–31CrossRefGoogle Scholar
  3. Anderson JPE, Domsch KH (1973) Quantification of bacterial and fungal contributions to soil respiration. Arch Mikrobiol 93:113–127CrossRefGoogle Scholar
  4. Aparna K, Rao D, Manna M (2014) Microbial inoculation of chickpea (Cicer arietinum L.) enhances rhizosphere effects on soil biological quality. Agrochimica 58:114–125Google Scholar
  5. Arias ME, González-Pérez JA, González-Vila FJ, Ball AS (2005) Soil health—a new challenge for microbiologists and chemists. Int Microbiol 8:13–21PubMedGoogle Scholar
  6. Avidano L, Gamalero E, Cossa GP, Carraro E (2005) Characterization of soil health in an Italian polluted site by using microorganisms as bioindicators. Appl Soil Ecol 30:21–33CrossRefGoogle Scholar
  7. Bagyaraj DJ, Thilagar G, Ravisha C, Kushalappa CG, Krishnamurthy KN, Vaast P (2015) Below ground microbial diversity as influenced by coffee agroforestry systems in the Western Ghats, India. Agric Ecosyst Environ 202:198–202CrossRefGoogle Scholar
  8. Bainard LD, Koch AM, Gordon AM, Klironomos JN (2012) Temporal and compositional differences of arbuscular mycorrhizal fungal communities in conventional monocropping and tree-based intercropping systems. Soil Biol Biochem 45:172–180CrossRefGoogle Scholar
  9. Balota EL, Kanashiro M, Filho AC, Andrade DS, Dick RP (2004) Soil enzyme activities under long-term tillage and crop rotation systems in subtropical agro-ecosystems. Braz J Microbiol 35:300–306CrossRefGoogle Scholar
  10. Bonebrake TC, Mastrandrea MD (2010) Tolerance adaptation and precipitation changes complicate latitudinal patterns of climate change impacts. Proc Natl Acad Sci U S A 107:12581–12586CrossRefPubMedPubMedCentralGoogle Scholar
  11. Brevik EC (2009) Soil health and productivity. In: Verheye W (ed) Plant growth and crop production. EOLSS Publishers, OxfordGoogle Scholar
  12. Butler E, Whelana MJ, Ritza K, Sakrabania R, Egmond R (2012) The effect of Triclosan on microbial community structure in three soils. Chemosphere 89:1CrossRefPubMedGoogle Scholar
  13. Buyer JS, Sasser M (2012) High throughput phospholipid fatty acid analysis of soils. Appl Soil Ecol 61:127–130CrossRefGoogle Scholar
  14. Buyer JS, Teasdale JR, Roberts DP, Zasada IA, Maul JE (2010) Factors affecting soil microbial community structure in tomato cropping systems. Soil Biol Biochem 42:831–841CrossRefGoogle Scholar
  15. Campbell CA, Zentner RP, Liang BC, Roloff G, Gregorich EC, Blomert B (2000) Organic C accumulation in soil over 30 years in semiarid southwestern Saskatchewan – effect of crop rotations and fertilizers. Can J Soil Sci 80:179–192CrossRefGoogle Scholar
  16. Campbell PM, De Q, Robin GC, Court LN, Dorrian SJ, Russell RJ, Oakeshott JG (2003) Developmental expression and gene/enzyme identifications in the alpha esterase gene cluster of Drosophila melanogaster. Insect Mol Biol 12:459–471CrossRefPubMedGoogle Scholar
  17. Capelle VC, Schrader S, Brunotte J (2012) Tillage-induced changes in the functional diversity of soil biota – a review with a focus on German data. Eur J Soil Biol 50:165–181CrossRefGoogle Scholar
  18. Castillo C, Rubio R, Rouanet J, Borie F (2006) Early effects of tillage and crop rotation on arbuscular mycorrhizal fungal propagules in an Ultisol. Biol Fertil Soils 43:83–92CrossRefGoogle Scholar
  19. Chaudhary DR, Saxena J, Lorenz N, Dick LK, Dick PR (2012) Microbial profiles of rhizosphere and bulk soil microbial communities of biofuel crops switchgrass (Panicum virgatum L.) and Jatropha (Jatropha curcas L.) Appl Environ Soil Sci 2012:906864-6CrossRefGoogle Scholar
  20. Degens BP, Harris JA (1997) Development of a physiological approach to measuring the metabolic diversity of soil microbial communities. Soil Biol Biochem 29:1309–1320CrossRefGoogle Scholar
  21. Doran JW, Zeiss MR (2000) Soil health and sustainability: managing the biotic component of soil quality. Appl Soil Ecol 15:3–11CrossRefGoogle Scholar
  22. Doran JW, Sarrantonio M, Liebig M (1996) Soil health and sustainability. In: Sparks DL (ed) Adv Agron 56:1–54Google Scholar
  23. Douds DD, Galvez L, Janke RR, Wagoner P (1995) Effect of tillage and farming system upon populations and distribution of vesicular-arbuscular mycorrhizal fungi. Agric Ecosyst Environ 52:111–118CrossRefGoogle Scholar
  24. Elliott LF, Lynch JM (1994) Biodiversity and soil resilience. In: Greenland DJ, Szabolcs I (eds) Soil resilience and sustainable land use. CAB International, Wallingford, pp 353–364Google Scholar
  25. Enriqueta-Arias M, Gonzalez-Perez JA, Gonzalez-Vila FJ, Ball AS (2005) Soil health a new challenge for microbiologists and chemists. Int Microbiol 8:13–21Google Scholar
  26. Feng Y, Motta AC, Reeves DW, Burmester CH, Van SE, Osborne JA (2003) Soil microbial communities under conventional-till and no-till continuous cotton systems. Soil Biol Biochem 35:1693–1703CrossRefGoogle Scholar
  27. Frostegard A, Baath E (1996) The use of phospholipid fatty acid analysis to estimate bacterial and fungal biomass. Biol Fertil Soils 22:59–65CrossRefGoogle Scholar
  28. Garland JL, Mills AL (1991) Classification and characterization of heterothrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization. Appl Environ Microbiol 57:2351–2359PubMedPubMedCentralGoogle Scholar
  29. Gibson L, Lee TM, Kohl P, Brook BW, Gardner TA, Barlow J, Peres CA, Bradshaw CJA, Laurance WF, Lovejoy TE, Sodhi NS (2011) Primary forests are irreplaceable for sustaining tropical biodiversity. Nature 478:378–381CrossRefPubMedGoogle Scholar
  30. Giller KE, Beare MH, Lavelle P, Izac AMN, Swift MJ (1997) Agricultural intensification, soil biodiversity and agroecosystem function. Appl Soil Ecol 6:3–16CrossRefGoogle Scholar
  31. Glick BR, Cheng Z, Czarny J, Duan J (2007) Promotion of plant growth by ACC deaminase-producing soil bacteria. Plant Pathol 119:329–339CrossRefGoogle Scholar
  32. Harrison NG, Allan JD, Colwell RK, Futuyma DJ, Howell J, Lubin MD, Mathias J, Vandermeer JJ (1968) The relationship between species diversity and stability: an experimental approach with protozoa and bacteria. Ecology 49:1091–1101CrossRefGoogle Scholar
  33. Hill MO (1973) Diversity and evenness: a unifying notation and its consequences. Ecology 54:427–432CrossRefGoogle Scholar
  34. Hillel D (1982) Introduction to soil physics. Academic Press, San Diego, CAGoogle Scholar
  35. Huber DM, Watson RD (1970) Effect of organic amendments on soil borne plant pathogens. Phytopathology 60:22–26CrossRefGoogle Scholar
  36. Ibekwe AM, Kennedy AC (1998) Phospholipid fatty acid profiles and carbon utilization patterns for analysis of microbial community structure under field and greenhouse conditions. FEMS Microbiol Ecol 26:151–163CrossRefGoogle Scholar
  37. Jat HS, Singh G, Singh R, Sharma DK (2015) Management influence on maize–wheat system performance, water productivity and soil biology. Soil Use Manag 31:534–543CrossRefGoogle Scholar
  38. Jesus EC, Liang C, Quensen JF, Susilawati E, Jackson RD, Balser TC, Tiedje JM (2016) Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper midwest of the United States. Glob Change Boil Bioenergy 8:481–494CrossRefGoogle Scholar
  39. Jost L (2006) Entropy and diversity. Oikos 113:363–375CrossRefGoogle Scholar
  40. Kabir Z (2005) Tillage or no-tillage: impact on mycorrhizae. Can J Plant Sci 85:23–29CrossRefGoogle Scholar
  41. Karlen DL, Andrews SS, Doran JW (2001) Soil quality: current concepts and applications. Adv Agron 74:1–40CrossRefGoogle Scholar
  42. Karlen DL, Andrews SS, Weinhold BJ, Doran JW (2003) Soil quality: humankind’s foundation for survival. J Soil Water Conserv 58:171–179Google Scholar
  43. Kaur A, Chaudhary A, Kaur A, Choudhary R, Kaushik R (2005) Phospholipid fatty acid – a bioindicator of environment monitoring and assessment in soil ecosystem. Curr Sci 89:1103–1112Google Scholar
  44. Kennedy AC, Smith KL (1995) Soil microbial diversity and the sustainability of agricultural soils. Plant Soil 170:75–86CrossRefGoogle Scholar
  45. Kurle JE, Grau CR, Oplinger ES, Mengistu A (2001) Tillage, crop sequence and cultivar effects on Sclerotinia stem rot incidence and yield in soybean. Agron J 93:973–982CrossRefGoogle Scholar
  46. Lal R (1997) Residue management conservation tillage and soil restoration for mitigating greenhouse effect by CO2- enrichment. Soil Tillage Res 43:81–107CrossRefGoogle Scholar
  47. Lal R (2004) Carbon sequestration in dryland ecosystems. Environ Manag 33:528–544CrossRefGoogle Scholar
  48. Larson WE, Pierce FJ (1994) The dynamics of soil quality as a measure of sustainable management. In: Doran JW et al (eds) Defining soil quality for a sustainable environment, vol 35. SSSA Special Publication, Madison, pp 37–52Google Scholar
  49. Li X, Sun M, Zhang H, Xu N, Sun G (2016) Use of mulberry-soybean intercropping in salt-alkali soil impacts the diversity of the soil bacterial community. Microb Biotechnol 9:293–304CrossRefPubMedPubMedCentralGoogle Scholar
  50. Lovelock CE, Wright SF, Nichols KA (2004) Using glomalin as an indicator for arbuscular mycorrhizal hyphae growth: an example from a tropical rain forest soil. Soil Biol Biochem 36:1009–1012CrossRefGoogle Scholar
  51. Mandic-Mulec I, Stefanic P, Van Elsas JD (2015) Ecology of Bacillaceae. Microbiol Spectr 3(2):TBS-0017–2013. doi:10.1128/microbiolspecGoogle Scholar
  52. Mathimaran N, Ruh R, Jama B, Verchot L, Frossard E, Jansa J (2007) Impact of agricultural management on arbuscular mycorrhizal fungal communities in Kenyan ferralsol. Agric Ecosyst Environ 119:22–32CrossRefGoogle Scholar
  53. Nakamoto T, Wakahara S (2004) Development of substrate induced respiration (SIR) method combined with selective inhibition for estimating fungal and bacterial biomass in humic andosols. Plant Prod Sci 7:70–76CrossRefGoogle Scholar
  54. Nielsen MN, Winding A (2002) Microorganisms as indicators of soil health. National Environmental Research Institute (NERI), Technical Report no. 388Google Scholar
  55. Oehl F, Sieverding E, Ineichen K, Paul Ma d, Boller T, Wiemken A (2003) The impact of land use intensity on the species diversity of arbuscular mycorrhizal fungi in agroecosystems of central Europe. Appl Environ Microbiol 69:2816–2824CrossRefPubMedPubMedCentralGoogle Scholar
  56. Olsson PA (1999) Signature fatty acids provide tools for determination of the distribution and interactions of mycorrhizal fungi in soil. FEMS Microb Ecol 29:303–310CrossRefGoogle Scholar
  57. Olsson PA, Johansen A (2000) Lipid and fatty acid composition of hyphae and spores of arbuscular mycorrhizal fungi at different growth stages. Mycol Res 104:429–434CrossRefGoogle Scholar
  58. Ovreas L (2000) Population and community level approaches for analyzing microbial diversity in natural environments. Ecol Lett 3:236–251CrossRefGoogle Scholar
  59. Petersen SO, Klug MJ (1994) Effect of sieving, storage, and incubation temperature on the phospholipid fatty acid profile of a soil microbial community. Appl Environ Microbiol 60:2421–2430PubMedPubMedCentralGoogle Scholar
  60. Purcaro G, Tranchida PQ, Dugo P, La Camera E, Bisignano G, Conte L, Mondello L (2010) Characterization of bacterial lipid profiles by using rapid sample preparation and fast comprehensive two-dimensional gas chromatography in combination with mass spectrometry. J Sep Sci 33:2334–2340CrossRefPubMedGoogle Scholar
  61. Ringelberg DB, Stair JO, Almeida J, Norby RJ, O’Neill EG, White DC (1997) Consequences of rising atmospheric carbon dioxide levels for the belowground microbiota associated with white oak. J Environ Qual 26:495–503CrossRefGoogle Scholar
  62. Sandhya V, Ali SKZ, Grover M, Reddy G, Venkatswarlu B (2010) Effect of plant growth promoting Pseudomonas sp. on compatible solutes, antioxidant status and plant growth of maize under drought stress. Plant Growth Regul 62:21–30CrossRefGoogle Scholar
  63. Schalamuk S, Velazquez S, Chidichimo H, Cabello M (2006) Fungal spore diversity of arbuscular mycorrhizal fungi associated with spring wheat: effects of tillage. Mycol Soc Am 98:16–22CrossRefGoogle Scholar
  64. Shannon CE, Weaver W (1963) The mathematical theory of communication. University of Illinois Press, UrbanaGoogle Scholar
  65. Sharma MP, Buyer JS (2015) Comparison of biochemical and microscopic methods for quantification of mycorrhizal fungi in soil and roots. Appl Soil Ecol 95:86–89CrossRefGoogle Scholar
  66. Sharma SK, Ramesh A, Sharma MP, Joshi OP, Govaerts B, Steenwerth KL, Karlen DL (2010) Microbial community structure and diversity as indicators for evaluating soil quality. In: Lichtfouse E (ed) Biodiversity, biofuels, agroforestry and conservation agriculture. Springer, Dordrecht, pp 317–358CrossRefGoogle Scholar
  67. Sharma MP, Gupta S, Sharma SK, Vyas AK (2012) Effect of tillage and crop sequences on arbuscular mycorrhizal symbiosis and soil enzyme activities in soybean (Glycine max L. Merril) rhizosphere. Indian J Agric Sci 82:25–30Google Scholar
  68. Simpson EH (1949) Measurement of diversity. Nature 163:688CrossRefGoogle Scholar
  69. Sparling G, Parfitt RL, Hewitt AE, Schipper LA (2003) Three approaches to define desired soil organic matter contents. J Environ Qual 32:760–766CrossRefPubMedGoogle Scholar
  70. Teygeler R., De Bruin G, Wassink BW, Van Z (2001) Preservation of archives in tropical climates: an annotated bibliography comma. Int J Pharm Biol Sci Arch 3/4: 233–257Google Scholar
  71. Tivy J (1987) Nutrient cycling in agro-ecosystems. Appl Geoger 7:93–113CrossRefGoogle Scholar
  72. Van Elsas JD, Duarte GF, Keijzer-Wolters A, Smit E (2000) Analysis of the dynamics of fungal communities in soil via fungal-specific PCR of soil DNA followed by denaturing gradient gel electrophoresis. J Microbiol Methods 43:133–151CrossRefPubMedGoogle Scholar
  73. Visser S, Parkinson D (1992) Soil biological criteria as indicators of soil quality: soil microorganisms. Am J Altern Agric 7:33–37CrossRefGoogle Scholar
  74. Wani PA, Khan MS, Zaidi A (2007) Synergistic effects of the inoculation with nitrogen-fixing and phosphate-solubilizing rhizobacteria on the performance of field-grown chickpea. J Plant Nutr Soil Sci 170:283–287CrossRefGoogle Scholar
  75. West AW, Sparling GP (1986) Modifications to the substrate-induced respiration method to permit measurement of microbial biomass in soils of differing water contents. J Microbiol Methods 5:177–189CrossRefGoogle Scholar
  76. Woignier T, Etcheverria P, Borie F, Quiquampoix H, Staunton S (2014) Role of allophanes in the accumulation of glomalin-related soil protein in tropical soils (Martinique, French West Indies). Eur J Soil Sci 65:531–538CrossRefGoogle Scholar
  77. Zabaloy MC, Gómez MA (2005) Diversity of rhizobia isolated from an agricultural soil in Argentina based on carbon utilization and effects of herbicides on growth. Biol Fertil Soils 42:83–88CrossRefGoogle Scholar
  78. Zelles L (1999) Fatty acid patterns of phospholipids and lipopolysaccharides in the characterisation of microbial communities in soil: a review. Biol Fertil Soils 29:111–129CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2017

Authors and Affiliations

  • Dipanti Chourasiya
    • 1
  • Mahaveer P. Sharma
    • 1
  • Hemant S. Maheshwari
    • 1
  • Aketi Ramesh
    • 1
  • Sushil K. Sharma
    • 2
  • Tapan Kumar Adhya
    • 3
    Email author
  1. 1.ICAR-Indian Institute of Soybean ResearchIndoreIndia
  2. 2.ICAR-National Bureau of Agriculturally Important MicroorganismsMau Nath BhanjanIndia
  3. 3.KIIT School of BiotechnologyBhubaneswarIndia

Personalised recommendations