Abstract
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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
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 108:1280–1287
Altieri MA (1999) The ecological role of biodiversity in agroecosystems. Agric Ecosyst Environ 74:19–31
Anderson JPE, Domsch KH (1973) Quantification of bacterial and fungal contributions to soil respiration. Arch Mikrobiol 93:113–127
Aparna K, Rao D, Manna M (2014) Microbial inoculation of chickpea (Cicer arietinum L.) enhances rhizosphere effects on soil biological quality. Agrochimica 58:114–125
Arias ME, González-Pérez JA, González-Vila FJ, Ball AS (2005) Soil health—a new challenge for microbiologists and chemists. Int Microbiol 8:13–21
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 30:21–33
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 202:198–202
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 45:172–180
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 35:300–306
Bonebrake TC, Mastrandrea MD (2010) Tolerance adaptation and precipitation changes complicate latitudinal patterns of climate change impacts. Proc Natl Acad Sci U S A 107:12581–12586
Brevik EC (2009) Soil health and productivity. In: Verheye W (ed) Plant growth and crop production. EOLSS Publishers, Oxford
Butler E, Whelana MJ, Ritza K, Sakrabania R, Egmond R (2012) The effect of Triclosan on microbial community structure in three soils. Chemosphere 89:1
Buyer JS, Sasser M (2012) High throughput phospholipid fatty acid analysis of soils. Appl Soil Ecol 61:127–130
Buyer JS, Teasdale JR, Roberts DP, Zasada IA, Maul JE (2010) Factors affecting soil microbial community structure in tomato cropping systems. Soil Biol Biochem 42:831–841
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 80:179–192
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 12:459–471
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 50:165–181
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 43:83–92
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 2012:906864-6
Degens BP, Harris JA (1997) Development of a physiological approach to measuring the metabolic diversity of soil microbial communities. Soil Biol Biochem 29:1309–1320
Doran JW, Zeiss MR (2000) Soil health and sustainability: managing the biotic component of soil quality. Appl Soil Ecol 15:3–11
Doran JW, Sarrantonio M, Liebig M (1996) Soil health and sustainability. In: Sparks DL (ed) Adv Agron 56:1–54
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 52:111–118
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 353–364
Enriqueta-Arias M, Gonzalez-Perez JA, Gonzalez-Vila FJ, Ball AS (2005) Soil health a new challenge for microbiologists and chemists. Int Microbiol 8:13–21
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 35:1693–1703
Frostegard A, Baath E (1996) The use of phospholipid fatty acid analysis to estimate bacterial and fungal biomass. Biol Fertil Soils 22:59–65
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 57:2351–2359
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 478:378–381
Giller KE, Beare MH, Lavelle P, Izac AMN, Swift MJ (1997) Agricultural intensification, soil biodiversity and agroecosystem function. Appl Soil Ecol 6:3–16
Glick BR, Cheng Z, Czarny J, Duan J (2007) Promotion of plant growth by ACC deaminase-producing soil bacteria. Plant Pathol 119:329–339
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 49:1091–1101
Hill MO (1973) Diversity and evenness: a unifying notation and its consequences. Ecology 54:427–432
Hillel D (1982) Introduction to soil physics. Academic Press, San Diego, CA
Huber DM, Watson RD (1970) Effect of organic amendments on soil borne plant pathogens. Phytopathology 60:22–26
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 26:151–163
Jat HS, Singh G, Singh R, Sharma DK (2015) Management influence on maize–wheat system performance, water productivity and soil biology. Soil Use Manag 31:534–543
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 8:481–494
Jost L (2006) Entropy and diversity. Oikos 113:363–375
Kabir Z (2005) Tillage or no-tillage: impact on mycorrhizae. Can J Plant Sci 85:23–29
Karlen DL, Andrews SS, Doran JW (2001) Soil quality: current concepts and applications. Adv Agron 74:1–40
Karlen DL, Andrews SS, Weinhold BJ, Doran JW (2003) Soil quality: humankind’s foundation for survival. J Soil Water Conserv 58:171–179
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 89:1103–1112
Kennedy AC, Smith KL (1995) Soil microbial diversity and the sustainability of agricultural soils. Plant Soil 170:75–86
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 93:973–982
Lal R (1997) Residue management conservation tillage and soil restoration for mitigating greenhouse effect by CO2- enrichment. Soil Tillage Res 43:81–107
Lal R (2004) Carbon sequestration in dryland ecosystems. Environ Manag 33:528–544
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 37–52
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 9:293–304
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 36:1009–1012
Mandic-Mulec I, Stefanic P, Van Elsas JD (2015) Ecology of Bacillaceae. Microbiol Spectr 3(2):TBS-0017–2013. doi:10.1128/microbiolspec
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 119:22–32
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 7:70–76
Nielsen MN, Winding A (2002) Microorganisms as indicators of soil health. National Environmental Research Institute (NERI), Technical Report no. 388
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 69:2816–2824
Olsson PA (1999) Signature fatty acids provide tools for determination of the distribution and interactions of mycorrhizal fungi in soil. FEMS Microb Ecol 29:303–310
Olsson PA, Johansen A (2000) Lipid and fatty acid composition of hyphae and spores of arbuscular mycorrhizal fungi at different growth stages. Mycol Res 104:429–434
Ovreas L (2000) Population and community level approaches for analyzing microbial diversity in natural environments. Ecol Lett 3:236–251
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 60:2421–2430
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 33:2334–2340
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 26:495–503
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 62:21–30
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 98:16–22
Shannon CE, Weaver W (1963) The mathematical theory of communication. University of Illinois Press, Urbana
Sharma MP, Buyer JS (2015) Comparison of biochemical and microscopic methods for quantification of mycorrhizal fungi in soil and roots. Appl Soil Ecol 95:86–89
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 317–358
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 82:25–30
Simpson EH (1949) Measurement of diversity. Nature 163:688
Sparling G, Parfitt RL, Hewitt AE, Schipper LA (2003) Three approaches to define desired soil organic matter contents. J Environ Qual 32:760–766
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: 233–257
Tivy J (1987) Nutrient cycling in agro-ecosystems. Appl Geoger 7:93–113
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 43:133–151
Visser S, Parkinson D (1992) Soil biological criteria as indicators of soil quality: soil microorganisms. Am J Altern Agric 7:33–37
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 170:283–287
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 5:177–189
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 65:531–538
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 42:83–88
Zelles L (1999) Fatty acid patterns of phospholipids and lipopolysaccharides in the characterisation of microbial communities in soil: a review. Biol Fertil Soils 29:111–129
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Chourasiya, D., Sharma, M.P., Maheshwari, H.S., Ramesh, A., Sharma, S.K., Adhya, T.K. (2017). Microbial Diversity and Soil Health in Tropical Agroecosystems. 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_2
Download citation
DOI: https://doi.org/10.1007/978-981-10-7380-9_2
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-10-7379-3
Online ISBN: 978-981-10-7380-9
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)