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Advances in Soil Microbiology: Recent Trends and Future Prospects pp 35–64Cite as

‘Omics’ Tools in Soil Microbiology: The State of the Art

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Part of the book series: Microorganisms for Sustainability ((MICRO,volume 3))

Abstract

The soil being the most heterogeneous substance hosts the dynamic environments for diverse microorganisms. Traditional techniques are limited to explore only few portion of massive unknown soil microbial world due to their well-known biasness in detecting microbial genetics and functional diversity. With this respect, omics targets the powerful genomics, metagenomics, transcriptomics, proteomics and metabolomic tools to explore the vast microbial community, new biomolecules and novel pathways. It helps to better understand the toxicity mechanisms, predicts the risks associated with environmental toxicity and aids in bioprospecting of value-added products. These new approaches will be useful to establish the linkage between structure and function of soil microbial community and help to get better insight of the ecological processes in the environment with special emphasis on plant-microbe ecosystems. The present chapter will give an overview of the application of the advanced molecular tools as well as their potentials and limitations in studying the soil microbial ecology.

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References

  • Allison SD (2012) A trait-based approach for modelling microbial litter decomposition. Ecol Lett 15:1058–1070

    Article  CAS  PubMed  Google Scholar 

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  CAS  PubMed  Google Scholar 

  • Amellal N, Burtin G, Bartoli F, Heulin T (1998) Colonization of wheat roots by an exopolysaccharide-producing Pantoea agglomerans strain and its effect on rhizosphere soil aggregation. Appl Environ Microbiol 64:3740–3747

    CAS  PubMed  PubMed Central  Google Scholar 

  • Andreote FD, Jimenez DJ, Chaves D, Dias ACF, Luvizotto DM, Andreote FD, Fasanella CC, Lopez MV, Baena S, Taketani RG, Melo ISD (2012) The microbiome of Brazilian mangrove sediments as revealed by metagenomics. PLoS One 7(6):e38600. https://doi.org/10.1371/journal.pone.0038600.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ankley GT, Daston GP, Degitz SJ, Denslow ND, Hoke RA, Kennedy SW, Miracle AL, Perkins EJ, Snape J, Tillitt DE, Tyler CR, Versteeg D (2006) Toxi-cogenomics in regulatory ecotoxicology. Environ Sci Technol 40:4055–4065

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bailly J, Tachet LF, Verner MC, Debaud JC, Lemaire M, Louvel MW, Marmeisse R (2007) Soil eukaryotic functional diversity, a metatranscriptomic approach. ISME J 1:632–642

    Article  CAS  PubMed  Google Scholar 

  • Banfield DJF, Verberkmoes NC, Hettich RL, Thelen MP (2005) Proteogenomic approaches for the molecular characterization of natural microbial communities. OMICS 9:301–333

    Article  CAS  PubMed  Google Scholar 

  • Bastida F, Moreno JL, Nicolas C, Hernandez T, Garcia C (2009) Soil metaproteomics: a review of an emerging environmental science. Significance, methodology and perspectives. Eur J Soil Sci 60:845–885

    Article  CAS  Google Scholar 

  • Bastida F, Nicolas C, Moreno JL, Hernandez T, Garcia C (2010) Tracing changes in the microbial community of a hydrocarbon-polluted soil by culture-dependent proteomics. Pedosphere 20:479–485

    Article  CAS  Google Scholar 

  • Bastida F, Hernández T, García C (2014) Metaproteomics of soils from semiarid environment: functional and phylogenetic information obtained with different protein extraction methods. J Proteome 101:31–42

    Article  CAS  Google Scholar 

  • Benndorf D, Balcke GU, Harms H, Bergen MV (2007) Functional metaproteome analysis of protein extracts from contaminated soil and groundwater. ISME J 1:224–234

    Article  CAS  PubMed  Google Scholar 

  • Blazewicz SJ, Barnard RL, Daly RA, Firestone MK (2013) Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses. ISME J 7(11):2061–2068. https://doi.org/10.1038/ismej.2013.102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen LS, Figueredo A, Pedrosa FO, Hungria M (2000) Genetic characterization of soybean rhizobia in Paraguay. Appl Environ Microbiol 66:5099–5103

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Choi YH, Kim HK, Linthorst HJM, Hollander JG, Lefeber AWM, Erkelens C, Nuzillard JM, Verpoorte R (2006) NMR Metabolomics to revisit the tobacco mosaic virus infection in Nicotiana tabacum leaves. J Nat Prod 69:742–748

    Article  CAS  PubMed  Google Scholar 

  • Chourey K, Jansson J, VerBerkmoes N, Shah M, Chavarria KL, Tom LM, Brodie EL, Hettich RL (2010) Direct cellular lysis/protein extraction protocol for soil metaproteomics. Proteome Res 9:6615–6622

    Article  CAS  Google Scholar 

  • Chung EJ, Lim HK, Kim JC, Choi GJ, Park EJ, Lee MH, Chung YR, Lee SW (2008) Forest soil metagenome gene cluster involved in antifungal activity expression in Escherichia coli. Appl Environ Microbiol 74:723–730

    Article  CAS  PubMed  Google Scholar 

  • Cieśliński H, Białkowskaa A, Tkaczuk K, Długołecka A, Kur J, Turkiewicz M (2009) Identification and molecular modeling of a novel lipase from an Antarctic soil metagenomic library. Pol J Microbiol 58:199–204

    PubMed  Google Scholar 

  • Croucher NJ, Thomson NR (2010) Studying bacterial transcriptomes using RNA-seq. Curr Opin Microbiol 13:619–624

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dam NM, Bouwmeester HJ (2016) Metabolomics in the Rhizosphere: tapping into belowground chemical communication. Trends Plant Sci 21:256–265

    Article  PubMed  CAS  Google Scholar 

  • Damon C, Lehembre F, Desfeux CO, Luis P, Ranger J, Tachet LF, Marmeisse R (2012) Metatranscriptomics reveals the diversity of genes expressed by eukaryotes in forest soils. PLoS One 7(1):e28967. https://doi.org/10.1371/journal.pone.0028967

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Delmont TO, Robe P, Cecillon S, Clark IM, Constancias F, Simonet P, Hirsch PR, Vogel TM (2011) Accessing the soil metagenome for studies of microbial diversity. Appl Environ Microbiol 77:1315–1324

    Article  CAS  PubMed  Google Scholar 

  • Delmotte N, Knief C, Chaffron S, Innerebner G, Roschitzki B, Schlapbach R, Mering CV, Vorholt JA (2009) Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc Natl Acad Sci U S A 106:16428–16433

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Draghi WO, Papa MFD, Barsch A, Albicoro FJ, Lozano MJ, Pühler A, Niehaus K, Lagares A (2017) A metabolomic approach to characterize the acid-tolerance response in Sinorhizobium meliloti. Metabolomics 24:13–71

    Google Scholar 

  • Fan TWM, Bird JA, Brodie EL, Lane AN (2009) 13C Isotoper – based metabolomics of microbial groups isolated from two forest soils. Metabolomics 5:108–122

    Article  CAS  Google Scholar 

  • Fan B, Carvalhais LC, Becker A, Fedoseyenko D, Wirén NV, Borriss R (2012) Transcriptomic profiling of Bacillus amyloliquefaciens FZB42 in response to maize root exudates. BMC Microbiol. https://doi.org/10.1186/1471-2180-12-116

  • Fedurco M, Romieu A, Williams S, Lawrence I, Turcatti G (2006) BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies. Nucleic Acids Res 34(3):e22. https://doi.org/10.1093/nar/qnj023

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Feng YY (2013) Omics breakthroughs for environmental microbiology. Omics Environ Microbiol 40:18–33

    Google Scholar 

  • Fierer N, Jackson JA, Vilgalys R, Jackson RB (2005) Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Appl Environ Microbiol 71:4117–4120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fierer N, Breitbart M, Nulton J, Salamon P, Lozupone C, Jones R, Robeson M, Edwards RA, Felts B, Rayhawk S, Knight R, Rohwer F, Jackson RB (2007) Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol 73:7059–7066

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Garbeva P, Veen JAV, Elsas JDV (2004) Microbial diversity in soil: selection microbial populations by plant and soil type and implications for disease suppressiveness. Annu Rev Phytopathol 42:243–270

    Article  CAS  PubMed  Google Scholar 

  • Gerry Q, Ed D, Stefan D, Peter M, Ingrid H, Richard W, Rhys A, Tom D, Lewis F, Andrea GS, Geertje VK (2016) The metaproteome of “Park Grass” soil – a reference for EU soil science. Copernicus 82:15981–15982

    Google Scholar 

  • Ghebremedhin B, Layer F, König W, König B (2008) Genetic classification and distinguishing of Staphylococcus species based on different partial gap, 16 rRNA, hsp60, rpoB, sodA, and tuf gene sequences. J Clin Microbiol 46:1019–1025

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Giagnoni L, Magherini F, Landi L, Taghavi S, Lelie DVD, Puglia M, Bianchi L, Bini L, Nannipieri P, Renella G, Modesti A (2012) Soil solid phases effects on the proteomic analysis of Cupriavidus metallidurans CH34. Biol Fertil Soils 48:425–433

    Article  CAS  Google Scholar 

  • Gieger C, Geistlinger L, Altmaier E, Angelis MHD, Kronenberg F, Meitinger T, Mewes HW, Wichmann HE, Weinberger KM, Adamski J, Illig T, Suhre K (2008) Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum. PLoS Genet 4(11):e1000282. https://doi.org/10.1371/journal.pgen.1000282

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gigliucci F, Brambilla G, Tozzoli R, Michelacci V, Morabito S (2017) Comparative analysis of metagenomes of Italian top soil improvers. Environ Res 155:108–115

    Article  CAS  PubMed  Google Scholar 

  • Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P, Joint I (2008) Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS One 3(8):E3042. https://doi.org/10.1371/journal.pone.0003042

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Goufo P, Pereira JMM, Jorge TF, Correia CM, Oliveira MR, Rosa EAS, Antonio C, Trindade H (2017) Cowpea (Vigna unguiculata L. Walp.) Metabolomics: osmoprotection as a physiological strategy for drought stress resistance and improved yield. Front Plant Sci. https://doi.org/10.3389/fpls.2017.00586

  • Gresa MPL, Maltese F, Bellés JM, Conejero V, Kim HK, Choi YH, Verpoorte R (2010) Metabolic response of tomato leaves upon different plant–pathogen interactions. Phytochem Anal 21:89–94

    Article  CAS  Google Scholar 

  • Hassink J, Bouwman LA, Zwart KB, Bloem J, Brussaard L (1993) Relationships between soil texture, physical protection of organic matter, soil biota, and C and N mineralization in grassland soils. Geoderma 57:105–128

    Article  CAS  Google Scholar 

  • Hédiji H, Diebali W, Cabasson C, Maucourt M, Baldet P, Bertrand A, Zoghlami LB, Deborde C, Moing A, Brouquisse R, Chaibi W, Gallusci P (2010) Effects of long-term cadmium exposure on growth and metabolomic profile of tomato plants. Ecotoxicol Environ Saf 73:1965–1974

    Article  PubMed  CAS  Google Scholar 

  • Holmes DE, Shrestha PM, Walker DJF, Dang Y, Nevin KP, Woodard TL, Lovley DR (2017) Metatranscriptomic evidence for direct interspecies electron transfer between Geobacter and Methanothrix species in methanogenic rice paddy soils. Appl Environ Microbiol 83:9–17

    Article  Google Scholar 

  • Howe AC, Jansson JK, Malfatti SA, Tringe SG, Tiedje JM, Brown CT (2014) Tackling soil diversity with the assembly of large, complex metagenomes. PNAS 111:4904–4909

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hugenholtz P (2002) Exploring prokaryotic diversity in the genomic era. Genome Biol 3(2). https://doi.org/10.1186/gb-2002-3-2-reviews0003

  • Insam H (2001) Developments in soil microbiology since the mid 1960s. Geoderma 100:389–482

    Article  CAS  Google Scholar 

  • Ivanova AA, Wegner CE, Kim Y, Liesack W, Dedysh SN (2016) Identification of microbial populations driving biopolymer degradation in acidic peatlands by metatranscriptomic analysis. Mol Ecol 25:4818–4835

    Article  CAS  PubMed  Google Scholar 

  • Jahangir M, Farid IBA, Choi YH, Verpoorte R (2008a) Metal ion-inducing metabolite accumulation in Brassica rapa. J Plant Physiol 165:1429–1437

    Article  CAS  PubMed  Google Scholar 

  • Jahangir M, Kim HK, Choi YH, Verpoorte R (2008b) Metabolomic response of Brassica rapa submitted to pre-harvest bacterial contamination. Food Chem 107:362–368

    Article  CAS  Google Scholar 

  • Jones OAH, Sdepanian S, Lofts S, Svendsen C, Spurgeon DJ, Maguire ML, Griffin JL (2013) Metabolomic analysis of soil communities can be used for pollution assessment. Environ Toxicol Chem 33:61–64

    Article  PubMed  CAS  Google Scholar 

  • Jones OAH, Sdepanian S, Lofts S, Svendsen C, Spurgeon DJ, Maguire ML, Griffin JL (2014) Metabolomic analysis of soil communities can be used for pollution assessment. Environ Toxicol Chem 33:61–64

    Article  CAS  PubMed  Google Scholar 

  • Júnior GVL, Noronha MF, Sousa STP, Cabral L, Domingos DF, Saber ML, Melo IS, Oliveira VM, Baldrian P (2017) Potential of semiarid soil from Caatinga biome as a novel source for mining lignocellulose-degrading enzymes. FEMS Microbiology 93:62–68

    Google Scholar 

  • Keiblinger KM, Fuchs S, Boltenstern SZ, Riedel K (2016) Soil and leaf litter metaproteomics – a brief guideline from sampling to understanding. FEMS Microbiol Ecol 92:66–74

    Article  CAS  Google Scholar 

  • Keller M, Hettich R (2009) Environmental proteomics: a paradigm shifts in characterizing microbial activities at the molecular level. Microbiol Mol Biol Rev 73:62–70

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim JS, Lim HK, Lee MH, Park JH, Hwang EC, Moon BJ, Lee SW (2009) Production of porphyrin intermediates in Escherichia coli carrying soil metagenomic genes. FEMS Microbiol Lett 295:42–49

    Article  CAS  PubMed  Google Scholar 

  • Kleiner M, Thorson E, Sharp CE, Dong X, Liu D, Li C, Strous M (2017) Assessing species biomass contributions in microbial communities via metaproteomics. bior Xiv. https://doi.org/10.1101/130575

  • Konstantinidis KT, Ramette A, Tiedje JM (2006) The bacterial species definition in the genomic era. Philos Trans R Soc B 361:1929–1940

    Article  Google Scholar 

  • Liang YS, Choi YH, Kim HK, Linthorst HJM, Verpoorte R (2006) Metabolomic analysis of methyl jasmonate treated Brassica rapa leaves by 2-dimensional NMR spectroscopy. Phytochemistry 67:2503–2511

    Article  CAS  PubMed  Google Scholar 

  • Lim HK, Chung EJ, Kim JC, Choi GJ, Jang KS, Chung YR, Cho KY, Lee SW (2005) Characterization of a forest soil metagenome clone that confers indirubin and Indigo production on Escherichia coli. Appl Environ Microbiol 71:7768–7777

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lin W, WuL LS, Zhang A, Zhou M, Lin R, Wang H, Chen J, Zhang Z, Lin R (2013) Metaproteomic analysis of ratoon sugarcane rhizospheric soil. BMC Microbiol. https://doi.org/10.1186/1471-2180-13-135

  • Mark GL, Dow JM, Kiely PD, Higgins H, Haynes J, Baysse C, Abbas A, Foley T, Franks A, Morrissey J, Gara F (2005) Transcriptome profiling of bacterial responses to root exudates identifies genes involved in microbe-plant interactions. G. Louise Mark 102:17454–17459

    CAS  Google Scholar 

  • Masuda Y, Itoh H, Shiratori Y, Isobe K, Otsuka S, Senoo K (2017) Predominant but previously looked prokaryotic drivers of reductive nitrogen transformation in paddy soils, revealed by metatranscriptomics. Microbes Environ 62:1347–4405

    Google Scholar 

  • Mattarozzi M, Manfredi M, Montanini B, Gosetti F, Sanangelantoni AM, Marengo E, Careri M, Visioli G (2017) A metaproteomic approach dissecting major bacterial functions in the rhizosphere of plants living in serpentine soil. Anal Bioanal Chem 409:2237–2339

    Google Scholar 

  • Miller MG (2007) Environmental metabolomics: SWOT analysis (strengths, weaknesses opportunities and threats). J Proteome Res 6:540–545

    Article  CAS  PubMed  Google Scholar 

  • Mocalli S, Benedetti A (2010) Exploring research frontiers in microbiology: the challenge of metagenomics in soil microbiology. Res Microbiol 161:497–505

    Article  Google Scholar 

  • Molina LG, Fonseca GCD, Morais GLD, Oliveira LFVD, Carvalho JBD, Kulcheski FR, Margis R (2012) Metatranscriptomic analysis of small RNAs present in soybean deep sequencing libraries. Genet Mol Biol 35:292–303

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Moran MA (2009) Metatranscriptomics: eavesdropping on complex microbial communities. Microbe 4:329–335

    Google Scholar 

  • Myrold DD, Zeglin LH, Jansson JK (2013) The potential of metagenomic approaches for understanding soil microbial processes. SSSAJ 78:3–10

    Article  CAS  Google Scholar 

  • Nacke H, Will C, Herzog S, Nowka B, Engelhaupt M, Daniel R (2011) Identification of novel lipolytic genes and gene families by screening of metagenomic libraries derived from soil samples of the German Biodiversity Exploratories. FEMS Microbiol Ecol 78:188–201

    Article  CAS  PubMed  Google Scholar 

  • Nannipieri P (2006) Roles of stabilised enzyme in microbial ecology and enzyme extraction from soil and potential applications in soil proteomics. Soil Biol 8:75–94

    Article  CAS  Google Scholar 

  • Peng J, Wegner CE, Liesack W (2017) Short-term exposure of paddy soil microbial communities to salt stress triggers different transcriptional responses of key taxonomic groups. Front Microbiol 8:400–482

    PubMed  PubMed Central  Google Scholar 

  • Quaiser A, Ochsenreiter T, Klenk HP, Kletzin A, Treusch AH, Meurer G, Eck J, Sensen CW, Schleper C (2002) First insight into the genome of an uncultivated crenarchaeote from soil. Environ Microbiol 4:603–611

    Article  CAS  PubMed  Google Scholar 

  • Quaiser A, Ochsenreiter T, Lanz C, Schuster SC, Treusch AH, Eck J, Schleper C (2003) Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Mol Microbiol 50:563–575

    Article  CAS  PubMed  Google Scholar 

  • Riesenfeld CS, Schloss PD, Handelsman J (2004) Metagenomics: genomic analysis of microbial communities. Annu Rev Genet 38:525–552

    Article  CAS  PubMed  Google Scholar 

  • Rochfort S (2005) Metabolomics reviewed: a new “omics” platform technology for systems biology and implications for natural products research. J Nat Prod 68:1813–1820

    Article  CAS  PubMed  Google Scholar 

  • Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, MacNei IA, Minor C, Tiong CL, Gilman M, Osburne MS, Clardy J, Handelsman J, Goodman RM (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66:2541–2547

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schenk PM, Carvalhais LC, Kazan K (2012) Unraveling plant–microbe interactions: can multi-species transcriptomics help? Trends Biotechnol 30:177–184

    Article  CAS  PubMed  Google Scholar 

  • Schleper C, Jurgens G, Jonuscheit M (2005) Genomic studies of uncultivated archaea. Nat Rev Microbiol 3:479–488

    Article  CAS  PubMed  Google Scholar 

  • Schulze WX, Gleixner G, Kaiser K, Guggenberger G, Mann M, Schulze ED (2005) A proteomic fingerprint of dissolved organic carbon and of soil particles. Oecologia 142:335–343

    Article  PubMed  Google Scholar 

  • Sessitsch A, Weilharter A, Gerzabek MH, Kirchmann H, Kandeler E (2001) Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment. Appl Environ Microbiol 67:4215–4224

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Siggins A, Gunnigle E, Abram F (2012) Exploring mixed microbial community functioning: recent advances in metaproteomics. FEMS Microbiol Ecol 80:265–280

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Singh BK, Campbell CD, Sorenson SJ, Zhou J (2009) Soil genomics. Nat Rev Microbiol 7:756. https://doi.org/10.1038/nrmicro2119-c1

    Article  CAS  PubMed  Google Scholar 

  • Stewart FJ, Sharma AK, Bryant JA, Eppley JM, De Long EF (2011) Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities. Genome Biol 12(3):R26. https://doi.org/10.1186/gb-2011-12-3-r26

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Su JQ, Xia Y, Yao HY, Li YY, An XL, Singh BK, Zhang T, Zhu YG (2017) Metagenomic assembly unravel microbial response to redox fluctuation in acid sulfate soil. Soil Biol Biochem 105:244–252

    Article  CAS  Google Scholar 

  • Sukul P, Schäkermann S, Bandow JE, Kusnezowa A, Nowrousian M, Leicher LI (2017) Simple discovery of bacterial biocatalysts from environmental samples through functional metaproteomics. Microbiome 64:5–28

    Google Scholar 

  • Sun X, Zhang J, Zhang H, Ni Y, Zhang Q, Chen J, Guan Y (2010) The responses of Arabidopsis thaliana to cadmium exposure explored via metabolite profiling. Chemosphere 78:840–845

    Article  CAS  PubMed  Google Scholar 

  • Taylor EB, Williams MA (2010) Microbial protein in soil: influence of extraction method and C amendment on extraction and recovery. Microb Ecol 59:390–399

    Google Scholar 

  • Toplin JA, Norris TB, Lehr CR, McDermott TR, Castenholz RW (2008) Biogeographic and phylogenetic diversity of Thermoacidophilic Cyanidiales in Yellowstone National Park, Japan, and New Zealand. Appl Environ Microbiol 74:2822–2833

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Topp E, Zhu H, Nour SM, Houot S, Lewis M, Cuppels D (2000) Characterization of an Atrazine-degrading Pseudaminobacter sp. Isolated from Canadian and French Agricultural Soils. Appl Environ Microbiol 66:2773–2782

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Torvisk V, Ovreas L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5:240–245

    Article  Google Scholar 

  • Treusch AH, Kletzin A, Raddatz G, Ochsenreiter T, Quaiser A, Meurer G, Schuster SC, Schleper C (2004) Characterization of large-insert DNA libraries from soil for environmental genomic studies of Archaea. Environ Microbiol 6:970–980

    Article  CAS  PubMed  Google Scholar 

  • Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM (2005) Comparative metagenomics of microbial communities. Science 308:554–557

    Google Scholar 

  • Uga Y (2017) Genomic based ideotype breeding for root system architecture to enhance rice production. Plant Anim Genome 86:12–17

    Google Scholar 

  • Urich T, Schleper C (2011) The “double-RNA” approach to simultaneously assess the structure and function of a soil microbial community. https://doi.org/10.1002/9781118010518.ch64

  • Urich T, Lanzen A, Qu J, Huson DH, Schleper C, Schuster SC (2008) Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS One 3(6):e2527. https://doi.org/10.1371/journal.pone.0002527

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Utturkar SM, Bollmann A, Brzoska RM, Klingeman DM, Epstein SE, Palumbo AV, Brown SD (2013) Draft genome sequence for Caulobacter sp. strain OR37, a Bacterium tolerant to heavy metals. Genome Announc 1(3):e00322–e00313. https://doi.org/10.1128/genomeA.00322-13

    PubMed  PubMed Central  Google Scholar 

  • Utturkar SM, Cude WN, Robeson Jr MS, Yang ZK, Klingeman DM, Land ML, Allman SL, Lu TYS, Brown SD, Schadt CW, Podar M, Doktycz MJ, Pelletier DA (2016) Enrichment of root endophytic bacteria from Populus deltoides and single cell genomic analysis. Appl Environ Microbiol 82:5698–5708

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Viant MR (2009) Applications of metabolomics to the environmental sciences. Metabolomics 5:1–2

    Article  CAS  Google Scholar 

  • Vinaixa M, Schymanski EL, Neumann S, Navarro M, Salek RM, Yanes O (2016) Mass spectral databases for LC/MS- and GC/MS-based metabolomics: state of the field and future prospects. TrAC Trends Anal Chem 78:23–35

    Article  CAS  Google Scholar 

  • Wang DZ, Kong LF, Li YY, Xie ZX (2016) Environmental microbial community proteomics: status, challenges and perspectives. Int J Mol Sci 17:1275–1278

    Article  PubMed Central  Google Scholar 

  • Warnecke F, Hess M (2009) A perspective: metatranscriptomics as a tool for the discovery of novel biocatalysts. J Biotechnol 142(1):91–95

    Article  CAS  PubMed  Google Scholar 

  • Wellington EMH, Berry A, Krsek M (2003) Resolving functional diversity in relation to microbial community structure in soil: exploiting genomics and stable isotope probing. Curr Opin Microbiol 6:295–301

    Article  CAS  PubMed  Google Scholar 

  • Willers C, Rensburg PJJ, Claassens S (2016) Can a metabolomics-based approach be used as alternative to analyse fatty acid methyl esters from soil microbial communities? Soil Biol Biochem 103:417–428

    Article  CAS  Google Scholar 

  • Williams MA, Taylor EB, Mula HP (2010) Metaproteomic characterization of a soil microbial community following carbon amendment. Soil Biol Biochem 42:1148–1156

    Article  CAS  Google Scholar 

  • Wilmes P, Bond PL (2006) Metaproteomics: studying functional gene expression in microbial ecosystems. Trends Microbiol 14:92–97

    Article  CAS  PubMed  Google Scholar 

  • Winding A, Santos SS, Browne PD, Hansen LH, Johansen A, Krogh PH (2016) Metagenomics of bacteria, fungi and protists affected by biochar and earthworms in soil. Environ Microbiol 86:54–58

    Google Scholar 

  • Wu L, Wang H, Zhang Z, Lin R, Zhang Z, Lin W (2011) Comparative metaproteomic analysis on consecutively Rehmannia glutinosa-monocultured rhizosphere soil. PLoS One 6:e20611. https://doi.org/10.1371/journal.pone.0020611

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xie S, Wu H, Chen L, Zang H, Xie Y, Gao X (2015) Transcriptome profiling of Bacillus subtilis OKB105 in response to rice seedlings. BMC Microbiol 15:21. https://doi.org/10.1186/s12866-015-0353-4

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Yadav RK, Bragalini C, Tachet LF, Marmeisse R, Luis P (2016) Metatranscriptomics of soil eukaryotic communities. Microb Environ Genomics 1399:273–287

    Article  CAS  Google Scholar 

  • Yergeau E, Sanschagrin S, Beaumier D, Greer CW (2012) Metagenomic analysis of the bioremediation of diesel-contaminated Canadian high Arctic soils. PLoS One 7(1):e30058. https://doi.org/10.1371/journal.pone.0030058

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang J, Sun X, Zhang Z, Ni Y, Zhang Q, Liang X, Xio H, Chen J, Tokuhisa JG (2011) Metabolite profiling of Arabidopsis seedlings in response to exogenous sinalbin and sulfur deficiency. Phytochemistry 72:1767–1778

    Article  CAS  PubMed  Google Scholar 

  • Zhou J, Deng Y, Luo F, He Z, Yang Y (2011) Phylogenetic molecular ecological network of soil microbial communities in response to elevated CO2. MBio 2(4):e00122–e00111. https://doi.org/10.1128/mBio.00122-11

    Article  PubMed  PubMed Central  Google Scholar 

  • Zyśko A, Sanguin H, Hayes A, Wardleworth L, Zeef LAH, Sim A, Paterson E, Singh BK, Kertes MA (2012) Transcriptional response of Pseudomonas aeruginosa to a phosphate-deficient Lolium perenne rhizosphere. Plant Soil 359:25–44

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela, Odisha, India

    Rimi Biswas & Angana Sarkar

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  1. Rimi Biswas
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  2. Angana Sarkar
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Correspondence to Angana Sarkar .

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Editors and Affiliations

  1. KIIT School of Biotechnology, Bhubaneswar, Odisha, India

    Tapan Kumar Adhya

  2. Environmental & Industrial Biotechnology, The Energy & Resources Institute (TERI), New Delhi, India

    Banwari Lal

  3. Environmental Microbiology Laboratory, Indian Institute of Technology, Kharagpur, West Bengal, India

    Balaram Mohapatra

  4. Microbial Ecology Laboratory, National Centre for Cell Science, Pune, Maharashtra, India

    Dhiraj Paul

  5. Environmental & Industrial Biotechnology, The Energy & Resources Institute (TERI), New Delhi, Delhi, India

    Subhasis Das

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Biswas, R., Sarkar, A. (2018). ‘Omics’ Tools in Soil Microbiology: The State of the Art. In: Adhya, T., Lal, B., Mohapatra, B., Paul, D., Das, S. (eds) Advances in Soil Microbiology: Recent Trends and Future Prospects. Microorganisms for Sustainability, vol 3. Springer, Singapore. https://doi.org/10.1007/978-981-10-6178-3_3

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