Skip to main content

Advertisement

SpringerLink
Log in

Systemic analysis of soil microbiome deciphers anthropogenic influence on soil ecology and ecosystem functioning

  • Original Paper
  • Published:
International Journal of Environmental Science and Technology Aims and scope Submit manuscript

Abstract

Soil is a complex ecosystem with defined microbial community signatures, modulated by the interaction between biotic and abiotic factors. Amidst biotic factors, land usage have significant impact onto the soil microbial structure and ecosystem functioning. In the current study, metagenomic approach was used to decipher effect of hospital settings on soil microbiome structure and physiological functions. Physico-chemical properties analysis revealed that key elements for maintenance of soil microflora, such as organic carbon, nitrogen, phosphorus and sulfur were relatively diminished within hospital soil, compared to garden soil. Comparative microbial diversity analysis with 97,315 SSU rRNA gene sequences generated from both the soil samples highlight relatively low microbial diversity, with an enrichment for Acidobacteria and Bacteroidetes and decreased Proteobacteria/Acidobacteria ratio. Comparative shotgun metagenome sequence analysis further revealed a shift in the physiological role of soil microbiomes with change in soil usage. Genes for carbohydrate, sulfur, potassium and nitrogen metabolism were significantly (q value <0.05) higher in the garden soil; while the genes for phage, plasmid DNA, transposon and aromatic compound metabolism were significantly enriched within hospital soil. Thus, the current study highlights a correlation between soil biochemistry and microbial ecology based on land usage.

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

Access this article

Log in via an institution

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

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Acosta-Martínez V, Dowd S, Sun Y, Allen V (2008) Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biol Biochem 40:2762–2770

    Article  Google Scholar 

  • Ademoroti CMA (1996) Standard methods for water and effluent analysis. Foludex Press Ltd., Ibadan, Nigeria. pp 27–30, 44–71, 103–112

  • Alzubaidy H, Essack M, Malas TB et al (2016) Rhizosphere microbiome metagenomics of gray mangroves (Avicennia marina) in the Red Sea. Gene 576:626–636

    Article  CAS  Google Scholar 

  • Arnebrant K, Söderström B (1990) The influence of nitrogen fertilization on ectomycorrhizal mycelial colonization and infection. Agric Ecosyst Environ 28:21–25

    Article  Google Scholar 

  • Aziz RK, Bartels D, Best AA et al (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genom 9:75

    Article  Google Scholar 

  • Baath E, Anderson T (2003) Comparison of soil fungal/bacterial ratios in a pH gradient using physiological and PLFA-based techniques. Soil Biol Biochem 35:955–963

    Article  CAS  Google Scholar 

  • Baath E, Frostegard A, Pennanen T, Fritz H (1995) Microbial community structure and pH response in relation to soil organic matter quality in wood-ash fertilized, clear-cut or burned coniferous forest soils. Soil Biol Biochem 27:229–240

    Article  Google Scholar 

  • Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Stat Methodol 57:289–300

    Google Scholar 

  • Blagodatskaya E, Anderson T (1998) Interactive effects of pH and substrate quality on the fungal-to-bacterial ratio and qCO2 of microbial communities in forest soils. Soil Biol Biochem 30:1269–1274

    Article  CAS  Google Scholar 

  • Bowers R, McLetchie S, Knight R, Fierer N (2010) Spatial variability in airborne bacterial communities across land-use types and their relationship to the bacterial communities of potential source environments. ISME J 5:601–612

    Article  Google Scholar 

  • Buckley D, Schmidt T (2003) Diversity and dynamics of microbial communities in soils from agro-ecosystems. Environ Microbiol 5:441–452

    Article  Google Scholar 

  • Caporaso JG, Kuczynski J, Stombaugh J et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336

    Article  CAS  Google Scholar 

  • Carbonetto B, Rascovan N, Alvarez R et al (2014) Structure, composition and metagenomic profile of soil microbiomes associated to agricultural land use and tillage systems in Argentine Pampas. PLoS ONE 9:e99949

    Article  Google Scholar 

  • Carvalho F, Souza R, Barcellos F et al (2010) Genomic and evolutionary comparisons of diazotrophic and pathogenic bacteria of the order Rhizobiales. BMC Microbiol 10:37

    Article  Google Scholar 

  • Ceja-Navarro J, Rivera-Orduna F, Patino-Zuniga L et al (2010) Phylogenetic and multivariate analyses to determine the effects of different tillage and residue management practices on soil bacterial communities. Appl Environ Microbiol 76:3685–3691

    Article  CAS  Google Scholar 

  • Chauhan N, Ranjan R, Purohit HJ et al (2009) Identification of genes conferring arsenic resistance to Escherichia coli from an effluent treatment plant sludge metagenomic library. FEMS Microbiol Ecol 67:130–139

    Article  CAS  Google Scholar 

  • Cookson W, Osman M, Marschner P et al (2007) Controls on soil nitrogen cycling and microbial community composition across land use and incubation temperature. Soil Biol Biochem 39:744–756

    Article  CAS  Google Scholar 

  • da C Jesus E, Marsh T, Tiedje J et al (2009) Changes in land use alter the structure of bacterial communities in Western Amazon soils. ISME J 3:1004–1011

    Article  CAS  Google Scholar 

  • Davies J, Davies D (2010) Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev 74:417–433

    Article  CAS  Google Scholar 

  • Dedysh S, Pankratov T, Belova S (2006) Phylogenetic analysis and in situ identification of bacteria community composition in an acidic Sphagnum peat bog. Appl Environ Microbiol 72:2110–2117

    Article  CAS  Google Scholar 

  • Delmont TO, Prestat E, Keegan KP et al (2012) Structure, fluctuation and magnitude of a natural grassland soil metagenome. ISME J 6:1677–1687

    Article  CAS  Google Scholar 

  • Eilers K, Debenport S, Anderson S, Fierer N (2012) Digging deeper to find unique microbial communities: the strong effect of depth on the structure of bacterial and archaeal communities in soil. Soil Biol Biochem 50:58–65

    Article  CAS  Google Scholar 

  • Fierer N, Bradford M, Jackson R (2007) Toward an ecological classification of soil bacteria. Ecology 88:1354–1364

    Article  Google Scholar 

  • Fierer N, Lauber C, Ramirez K (2011) Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J 6:1007–1017

    Article  Google Scholar 

  • Fierer N, Leff JW, Adams BJ et al (2012) Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci USA 109:21390–21395

    Article  CAS  Google Scholar 

  • Frisli T, Haverkamp T, Jakobsen K et al (2012) Estimation of metagenome size and structure in an experimental soil microbiota from low coverage next-generation sequence data. J Appl Microbiol 114:141–151

    Article  Google Scholar 

  • Gerdes S, El Yacoubi B, Bailly M et al (2011) Synergistic use of plant-prokaryote comparative genomics for functional annotations. BMC Genom 12:S2

    Article  Google Scholar 

  • Glass E, Wilkening J, Wilke A et al (2010) Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes. Cold Spring Harb Protoc 2010:5368

    Article  Google Scholar 

  • Guan X, Wang J, Zhao H et al (2013) Soil bacterial communities shaped by geochemical factors and land use in a less-explored area, Tibetan Plateau. BMC Genomics 14:820

    Article  Google Scholar 

  • Hallin S, Jones C, Schloter M et al (2009) Relationship between N-cycling communities and ecosystem functioning in a 50-year-old fertilization experiment. ISME J 3:597–605

    Article  CAS  Google Scholar 

  • Hao X, Chen T (2012) OTU analysis using metagenomic shotgun sequencing data. PLoS ONE 7:e49785

    Article  CAS  Google Scholar 

  • Kato H, Mori H, Maruyama F et al (2015) Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance. DNA Res 22:413–424

    Article  CAS  Google Scholar 

  • Lauber C, 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 75:5111–5120

    Article  CAS  Google Scholar 

  • Li D, Sharp J, Saikaly PE et al (2012) Dissolved organic carbon influences microbial community composition and diversity in managed aquifer recharge systems. Appl Environ Microbiol 78:6819–6828

    Article  CAS  Google Scholar 

  • Margesin R, Miteva V (2011) Diversity and ecology of psychrophilic microorganisms. Res Microbiol 162:346–361

    Article  Google Scholar 

  • McGrath K, Mondav R, Sintrajaya R et al (2010) Development of an environmental functional gene microarray for soil microbial communities. Appl Environ Microbiol 76:7161–7170

    Article  CAS  Google Scholar 

  • McMichael P (2009) Banking on agriculture: a review of the world development report 2008. J Agrar Change 9:235–246

    Article  Google Scholar 

  • Mendes L, Kuramae E, Navarrete A et al (2014) Taxonomical and functional microbial community selection in soybean rhizosphere. ISME J 8:1577–1587

    Article  CAS  Google Scholar 

  • Morales S, Mouser P, Ward N et al (2006) Comparison of bacterial communities in New England Sphagnum bogs using terminal restriction fragment length polymorphism (T-RFLP). Microb Ecol 52:34–44

    Article  CAS  Google Scholar 

  • Morowitz MJ, Denef VJ, Costello EK et al (2011) Strain-resolved community genomic analysis of gut microbial colonization in a premature infant. Proc Natl Acad Sci USA 108:1128–1133

    Article  CAS  Google Scholar 

  • Navarrete A, Tsai S, Mendes L et al (2015) Soil microbiome responses to the short-term effects of Amazonian deforestation. Mol Ecol 24:2433–2448

    Article  CAS  Google Scholar 

  • Newcombe R (1998) Two-sided confidence intervals for the single proportion: comparison of seven methods. Stat Med 17:857–872

    Article  CAS  Google Scholar 

  • Pankratov T, Ivanova A, Dedysh S (2011) Bacterial populations and environmental factors controlling cellulose degradation in an acidic Sphagnum peat. Environ Microbiol 13:1800–1814

    Article  CAS  Google Scholar 

  • Parks D, Beiko R (2010) Identifying biologically relevant differences between metagenomic communities. Bioinformatics 26:715–721

    Article  CAS  Google Scholar 

  • Pearce D, Newsham K, Thorne M et al (2012) Metagenomic analysis of a southern maritime antarctic soil. Front Microbiol 3:403

    Article  Google Scholar 

  • Philippot L, Andersson S, Battin T et al (2010) The ecological coherence of high bacterial taxonomic ranks. Nat Rev Microbiol 8:523–529

    Article  CAS  Google Scholar 

  • Ranjan R, Grover A, Kapardar R, Sharma R (2005) Isolation of novel lipolytic genes from uncultured bacteria of pond water. Biochem Biophys Res Commun 335:57–65

    Article  CAS  Google Scholar 

  • Reith F, Brugger J, Zammit CM et al (2012) Influence of geogenic factors on microbial communities in metallogenic Australian soils. ISME J 6:2107–2118

    Article  CAS  Google Scholar 

  • Ringner M (2008) What is principal component analysis? Nat Biotechnol 26:303–304

    Article  CAS  Google Scholar 

  • Smit E, Leeflang P, Gommans S et al (2001) Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Appl Environ Microbiol 67:2284–2291

    Article  CAS  Google Scholar 

  • Stenuit B, Agathos SN (2015) Deciphering microbial community robustness through synthetic ecology and molecular systems synecology. Curr Opin Biotechnol 33:305–317

    Article  CAS  Google Scholar 

  • Tian B, Cao Y, Zhang K (2015) Metagenomic insights into communities, functions of endophytes, and their associates with infection by root-knot nematode, Meloidogyne incognita, in tomato roots. Sci Rep 5:7087

    Google Scholar 

  • Van Horn D, Okie J, Buelow HN et al (2014) Soil microbial responses to increased moisture and organic resources along a salinity gradient in a polar desert. Appl Environ Microbiol 80:3034–3043

    Article  Google Scholar 

  • Viles H, Naylor LA, Carter NEA, Chaput D (2008) Biogeomorphological disturbance regimes: progress in linking ecological and geomorphological systems. Earth Surf Process Landf 33:1419–1435

    Article  Google Scholar 

  • Vogel T, Simonet P, Jansson J et al (2009) TerraGenome: a consortium for the sequencing of a soil metagenome. Nat Rev Microbiol 7:252

    Article  CAS  Google Scholar 

  • Wakelin S, Macdonald L, Rogers S, Gregga AL (2008) Habitat selective factors influencing the structural composition and functional capacity of microbial communities in agricultural soils. Soil Biol Biochem 40:803–813

    Article  CAS  Google Scholar 

  • Whitman W, Coleman D, Wiebe W (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95:6578–6583

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by Counsil of Scientific and Industrial Research sponsored research Scheme [60(0099)/11/EMRII] and University Grants Commission[41-1256/2012 SR]. Dr Manu Bhambi and Dr Manoj Kumar thanks Department of Biotechnology (DBT, Govt. of India) and Department of Science and Technology (DST,Govt. of India), for their fellowships.

Author information

Authors and Affiliations

  1. Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, 124001, India

    S. Gupta, M. Kumar, J. Kumar, V. Ahmad & N. S. Chauhan

  2. Ayurgenomics Unit-TRISUTRA, Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, 110020, India

    R. Pandey

Authors
  1. S. Gupta
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. M. Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. J. Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. V. Ahmad
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. R. Pandey
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. N. S. Chauhan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to N. S. Chauhan.

Ethics declarations

Conflict of interest

No conflict of interest exists.

Additional information

Editorial responsibility: Necip Atar.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 610 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Gupta, S., Kumar, M., Kumar, J. et al. Systemic analysis of soil microbiome deciphers anthropogenic influence on soil ecology and ecosystem functioning. Int. J. Environ. Sci. Technol. 14, 2229–2238 (2017). https://doi.org/10.1007/s13762-017-1301-7

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13762-017-1301-7

Keywords

Search

Navigation