Skip to main content

Advertisement

Log in

Changes in Bacterial Community Structure of Agricultural Land Due to Long-Term Organic and Chemical Amendments

  • Soil Microbiology
  • Published:
Microbial Ecology Aims and scope Submit manuscript

Abstract

Community level physiological profiling and pyrosequencing-based analysis of the V1-V2 16S rRNA gene region were used to characterize and compare microbial community structure, diversity, and bacterial phylogeny from soils of chemically cultivated land (CCL), organically cultivated land (OCL), and fallow grass land (FGL) for 16 years and were under three different land use types. The entire dataset comprised of 16,608 good-quality sequences (CCL, 6,379; OCL, 4,835; FGL, 5,394); among them 12,606 sequences could be classified in 15 known phylum. The most abundant phylum were Proteobacteria (29.8%), Acidobacteria (22.6%), Actinobacteria (11.1%), and Bacteroidetes (4.7%), while 24.3% of the sequences were from bacterial domain but could not be further classified to any known phylum. Proteobacteria, Bacteroidetes, and Gemmatimonadetes were found to be significantly abundant in OCL soil. On the contrary, Actinobacteria and Acidobacteria were significantly abundant in CCL and FGL, respectively. Our findings supported the view that organic compost amendment (OCL) activates diverse group of microorganisms as compared with conventionally used synthetic chemical fertilizers. Functional diversity and evenness based on carbon source utilization pattern was significantly higher in OCL as compared to CCL and FGL, suggesting an improvement in soil quality. This abundance of microbes possibly leads to the enhanced level of soil organic carbon, soil organic nitrogen, and microbial biomass in OCL and FGL soils as collated with CCL. This work increases our current understanding on the effect of long-term organic and chemical amendment applications on abundance, diversity, and composition of bacterial community inhabiting the soil for the prospects of agricultural yield and quantity of soil.

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

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6

Similar content being viewed by others

References

  1. Aira M, Brandón MG, Lazcano C, Bååth E, Domínguez J (2010) Plant genotype strongly modifies the structure and growth of maize rhizosphere microbial communities. Soil Biol Biochem 42:2276

    Article  CAS  Google Scholar 

  2. Bastida F, Kandeler E, Moreno JL, Ros M, García C, Hernández T (2008) Application of fresh and composted organic wastes modifies structure, size and activity of soil microbial community under semiarid climate. Appl Soil Ecol 40:318

    Article  Google Scholar 

  3. Bremner JM, Mulvaney CS (1982) Nitrogen-total. In: Page AL (ed) Methods of soil analysis. Part 2. Chemical and microbiological properties. Book series no. 9 SSSA, Madison, p 595

    Google Scholar 

  4. Chu H, Fujii T, Morimoto S, Lin X, Yagi K, Hu J, Zhang J (2007) Soil microbial biomass, dehydrogenase activity, bacterial community structure in response to long-term fertilizer management. Soil Biol Biochem 39:2971

    Article  CAS  Google Scholar 

  5. Dunfield KE, Germida JJ (2004) Impact of genetically modified crops on soil and plant-associated microbial communities. J Environ Qual 33:806

    Article  PubMed  CAS  Google Scholar 

  6. Elshahed MS, Youssef NH, Spain AM, Sheik C, Najar FZ, Sukharnikov LO, Roe BA, Davis JP, Schloss PD, Bailey VL, Krumholz LR (2008) Novelty and uniqueness patterns of rare members of the soil biosphere. Appl Environ Microbiol 74:5422

    Article  PubMed  CAS  Google Scholar 

  7. Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci U S A 103:626

    Article  PubMed  CAS  Google Scholar 

  8. Fierer N, Hamadyc M, Lauberb CL, Knightd R (2008) The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci U S A 18:17994

    Article  Google Scholar 

  9. Fulthorpe RR, Roesch LFW, Riva A, Triplett EW (2008) Distantly sampled soils carry few species in common. ISME J 2:901

    Article  PubMed  CAS  Google Scholar 

  10. Gans J, Wolinsky M, Dunbar J (2005) Computational improvements reveals great bacterial diversity and high metal toxicity in soil. Science 309:1387

    Article  PubMed  CAS  Google Scholar 

  11. Garland JL, Mills AL (1991) Classification and characterization of heterotrophic microbial communities on the basis of patterns of community level sole carbon source utilization. Appl Environ Microbiol 57:2351

    PubMed  CAS  Google Scholar 

  12. Garland JL (1996) Analytical approaches to the characterization of samples of microbial communities using patterns of potential C source utilization. Soil Biol Biochem 28:213

    Article  CAS  Google Scholar 

  13. Giongo A, Crabb DB, Davis-Richardson AG, Chauliac D, Mobberley JM, Gano KA, Mukherjee N, Casella G, Roesch LF, Walts B, Riva A, King G, Triplett EW (2010) PANGEA: pipeline for analysis of next generation amplicons. ISME J 4:852

    Article  PubMed  CAS  Google Scholar 

  14. Gomez E, Ferreras L, Toresani S (2006) Soil bacterial functional diversity as influenced by organic amendment application. Biores Technol 97:1484

    Article  CAS  Google Scholar 

  15. Goyal S, Mishra MM, Hooda IS, Singh R (1992) Organic matter–microbial biomass relationships in field experiments under tropical conditions: effects of inorganic fertilization and organic amendments. Soil Biol Biochem 24:1081

    Article  Google Scholar 

  16. Hallmann J, Rodríguez-Kábana R, Kloepper JW (1999) Chitin-mediated changes in bacterial communities of the soil, rhizosphere and within roots of cotton in relation to nematode control. Soil Biol Biochem 31:551

    Article  CAS  Google Scholar 

  17. Heilmann B, Lebuhn M, Beese F (1995) Methods for the investigation of metabolic activities and shifts in the microbial community in a soil treated with a fungicide. Biol Fertil Soils 19:186

    Article  CAS  Google Scholar 

  18. Huse SM, Dethlefsen L, Huber JA, Mark Welch D, Welch DM, Relman DA, Sogin ML (2008) Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet 4:e1000255

    Article  PubMed  Google Scholar 

  19. Islam MR, Trivedi P, Palaniappan P, Reddy MS, Sa T (2009) Evaluating the effect of fertilizer application on soil microbial community structure in rice based cropping system using fatty acid methyl esters (FAME) analysis. World J Microbiol Biotechnol 25:1115

    Article  CAS  Google Scholar 

  20. Islam MR, Trivedi P, Madhaiyan M, Seshadri S, Lee G, Yang J, Kim Y, Kim M, Han GH, Chauhan PS, Sa T (2010) Isolation, enumeration, and characterization of diazotrophic bacteria from paddy soil sample under long-term fertilizer management experiment. Biol Fertil Soils 46:261

    Article  CAS  Google Scholar 

  21. Janssen PH (2006) Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 72:1719

    Article  PubMed  CAS  Google Scholar 

  22. Jenkinson DS, Powlson DS (1976) The effects of biocidal treatment on metabolism in soil. I. Fumigation with chloroform. Soil Biol Biochem 8:167

    Article  CAS  Google Scholar 

  23. Jones RT, Robeson MS, Lauber CL, Hamady M, Knight R, Fierer N (2009) A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J 3:442e453

    Article  Google Scholar 

  24. Kinyua D, McGeoch LE, Georgiadis N, Young TP (2010) Short-term and long-term effects of soil ripping, seeding, and fertilization on the restoration of a tropical Rangeland. Rest Ecol 18:226–233

    Article  Google Scholar 

  25. Lagomarsino A, Moscatelli MC, Di Tizio A, Mancinelli R, Grego S, Marinari S (2009) Soil biochemical indicators as a tool to assess the short-term impact of agricultural management on changes in organic C in a Mediterranean environment. Ecol Indic 9:518

    Article  CAS  Google Scholar 

  26. Lauber CL, Hamady M, Knight R, Fierer N (2009) Pyrosequencing-based assessment of soil ph as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75:5111

    Article  PubMed  CAS  Google Scholar 

  27. Lesaulnier C, Papamichail D, McCorkle S, Ollivier B, Skiena S, Taghavi S, Zak D, van der Lelie D (2008) Elevated atmospheric CO2 affects soil microbial diversity associated with trembling aspen. Environ Microbiol 10:926

    Article  PubMed  CAS  Google Scholar 

  28. Maeder P, Fliessbach A, Dubois D, Gunst L, Fried P, Niggli U (2002) Soil fertility and biodiversity in organic farming. Science 296:1694

    Article  Google Scholar 

  29. Marinari S, Mancinelli R, Campiglia E, Grego S (2006) Chemical and biological indicators of soil quality in organic and conventional farming systems in Central Italy. Ecol Indic 6:701

    Article  Google Scholar 

  30. Nacke H, Thürmer A, Wollherr A, Will C, Hodac L, Herold N, Schöning I, Schrumpf M, Daniel R (2011) Pyrosequencing based assessment of bacterial community structure along different management types in German forest and grassland soils. PLoS One 6:e17000

    Article  PubMed  CAS  Google Scholar 

  31. Nannipieri P, Ascher J, Ceccherini MT, Landi L, Pietramellara G, Renella G, Valori F (2008) Effects of root exudates in microbial diversity and activity in rhizosphere soils. In: Nautiyal CS, Dion P (eds) Molecular mechanisms of plant and microbe coexistence. Soil Biology Series, vol 15. Springer, Berlin, p 339

    Chapter  Google Scholar 

  32. Nautiyal CS, Chauhan PS, Bhatia CR (2010) Changes in soil physico-chemical properties and microbial functional diversity due to 14 years of conversion of grassland to organic agriculture in semi-arid agroecosystem. Soil Till Res 109:55–60

    Article  Google Scholar 

  33. Nelson DW, Sommers LE (1982) Total carbon, organic carbon, and organic matter. In: PageMiller AL, Keeney RH (eds) Methods of soil analysis. Part 2, 2nd edn. American Society of Agronomy–Soil Science Society of America, Madison, p 539

    Google Scholar 

  34. Nene YL (2006) Indian pulses through the millennia. Asian Agri Hist 10:179–202

    Google Scholar 

  35. Page AL, Miller RH, Keeney DR (1982) Methods of soil analysis. Part 2, Chemical and microbiological properties, 2nd ed., Agronomy vol. 9. ASA, SSSA, Madison, p 1159

    Google Scholar 

  36. Peacock A, Mullen M, Ringelberg D, Tyler D, Hedrick D, Gale P, White DC (2001) Soil microbial community responses to dairy manure or ammonium nitrate applications. Soil Biol Biochem 33:1011

    Article  CAS  Google Scholar 

  37. Sala MM, Terrado R, Lovejoy C, Unrein F, Pedrós-Alió C (2008) Metabolic diversity of heterotrophic bacterioplankton over winter and spring in the coastal Arctic Ocean. Environ Microbiol 10:942

    Article  PubMed  CAS  Google Scholar 

  38. Schloss PD, Larget BR, Handelsman J (2004) Integration of microbial ecology and statistics: a test to compare gene libraries. Appl Environ Microbiol 70:5485–5492

    Article  PubMed  CAS  Google Scholar 

  39. Schloss PD, Handelsman J (2004) Status of the microbial census. Microbiol Mol Biol Rev 68:686

    Article  PubMed  Google Scholar 

  40. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing MOTHUR: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537

    Article  PubMed  CAS  Google Scholar 

  41. Schönfeld J, Gelsomino A, Overbeek LS, Gorissen A, Smalla K, Elsas JD (2003) Effects of compost addition and simulated solarisation on the fate of Ralstonia solanacearum biovar 2 and indigenous bacteria in soil. FEMS Microbiol Ecol 43:63

    Article  PubMed  Google Scholar 

  42. Shannon D, Sen AM, Johnson DB (2002) A comparative study of the microbiology of soils managed under organic and conventional regimes. Soil Use Manag 18:274

    Article  Google Scholar 

  43. Sheik CS, Beasley WH, Elshahed MS, Zhou X, Luo Y, Krumholz LR (2011) Effect of warming and drought on grassland microbial communities. ISME J 5:1692

    Article  PubMed  CAS  Google Scholar 

  44. Shi W, Dell E, Bowman D, Iyyemperumal K (2006) Soil enzyme activities and organic matter composition in a turfgrass chronosequence. Plant Soil 288:285

    Article  CAS  Google Scholar 

  45. Shinjiro K, Susumu A, Yasuo T (1988) Effect of fertilizer and manure application on microbial numbers, biomass, and enzyme activities in volcanic ash soils: I. Microbial numbers and biomass carbon. Soil Sci Plant Nutr 34:429

    Article  Google Scholar 

  46. Staddon WJ, Duchesne LC, Trevors JT (1997) Microbial diversity and community structure of post-disturbance forest soils as determined by sole-carbon-source utilization patterns. Microb Ecol 34:125

    Article  PubMed  CAS  Google Scholar 

  47. Swain MR, Ray RC (2009) Biocontrol and other beneficial activities of Bacillus subtilis isolated from cow dung microflora. Microbiol Res 164:12

    Article  Google Scholar 

  48. Torsvik V, Øvreås L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5:240

    Article  PubMed  CAS  Google Scholar 

  49. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261

    Article  PubMed  CAS  Google Scholar 

  50. Wu M, Qin H, Chen Z, Wu J, Wei W (2011) Effect of long-term fertilization on bacterial composition in rice paddy soil. Biol Fertil Soils 47:397

    Article  Google Scholar 

  51. Wu T, Chellemi DO, Graham JH, Martin KJ, Rosskopf EN (2008) Comparison of soil bacterial communities under diverse agricultural land management and crop production practices. Microb Ecol 55:293

    Article  PubMed  Google Scholar 

  52. Zak DR, Holmes WE, White DC, Peacock AD, Tilman D (2003) Plant diversity, soil microbial communities, and ecosystem function: are there any links? Ecology 84:2042

    Article  Google Scholar 

  53. Zhong WH, Cai ZC (2007) Long-term effects of inorganic fertilizers on microbial biomass and community functional diversity in a paddy soil derived from quaternary red clay. Appl Soil Ecol 36:84

    Article  Google Scholar 

Download references

Acknowledgments

We are indebted to Dr. D.V. Amla, Chief Scientist, CSIR-National Botanical Research Institute, Lucknow, India for his valuable suggestions and critical editing of the manuscript. The study was partially supported by TATA Innovation Fellowship, Department of Biotechnology, Government of India, New Delhi and Task Force grant NWP-006 from Council of Scientific and Industrial Research (CSIR), New Delhi and awarded to CSN. VC would like to thank CSIR for providing her Senior Research Fellowship.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Chandra Shekhar Nautiyal.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Chaudhry, V., Rehman, A., Mishra, A. et al. Changes in Bacterial Community Structure of Agricultural Land Due to Long-Term Organic and Chemical Amendments. Microb Ecol 64, 450–460 (2012). https://doi.org/10.1007/s00248-012-0025-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00248-012-0025-y

Keywords

Navigation