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

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


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.


Omics Soil Bacteria Microbiology Ecology 


  1. Allison SD (2012) A trait-based approach for modelling microbial litter decomposition. Ecol Lett 15:1058–1070PubMedCrossRefGoogle Scholar
  2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410PubMedCrossRefGoogle Scholar
  3. 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 64:3740–3747PubMedPubMedCentralGoogle Scholar
  4. 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. PubMedPubMedCentralCrossRefGoogle Scholar
  5. 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 40:4055–4065PubMedPubMedCentralCrossRefGoogle Scholar
  6. Bailly J, Tachet LF, Verner MC, Debaud JC, Lemaire M, Louvel MW, Marmeisse R (2007) Soil eukaryotic functional diversity, a metatranscriptomic approach. ISME J 1:632–642PubMedCrossRefGoogle Scholar
  7. Banfield DJF, Verberkmoes NC, Hettich RL, Thelen MP (2005) Proteogenomic approaches for the molecular characterization of natural microbial communities. OMICS 9:301–333PubMedCrossRefGoogle Scholar
  8. 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 60:845–885CrossRefGoogle Scholar
  9. 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 20:479–485CrossRefGoogle Scholar
  10. 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 101:31–42CrossRefGoogle Scholar
  11. Benndorf D, Balcke GU, Harms H, Bergen MV (2007) Functional metaproteome analysis of protein extracts from contaminated soil and groundwater. ISME J 1:224–234PubMedCrossRefGoogle Scholar
  12. 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 PubMedPubMedCentralCrossRefGoogle Scholar
  13. Chen LS, Figueredo A, Pedrosa FO, Hungria M (2000) Genetic characterization of soybean rhizobia in Paraguay. Appl Environ Microbiol 66:5099–5103PubMedPubMedCentralCrossRefGoogle Scholar
  14. 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 69:742–748PubMedCrossRefGoogle Scholar
  15. 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 9:6615–6622CrossRefGoogle Scholar
  16. 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 74:723–730PubMedCrossRefGoogle Scholar
  17. 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 58:199–204PubMedGoogle Scholar
  18. Croucher NJ, Thomson NR (2010) Studying bacterial transcriptomes using RNA-seq. Curr Opin Microbiol 13:619–624PubMedPubMedCentralCrossRefGoogle Scholar
  19. Dam NM, Bouwmeester HJ (2016) Metabolomics in the Rhizosphere: tapping into belowground chemical communication. Trends Plant Sci 21:256–265PubMedCrossRefGoogle Scholar
  20. 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 PubMedPubMedCentralCrossRefGoogle Scholar
  21. 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 77:1315–1324PubMedCrossRefGoogle Scholar
  22. 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 106:16428–16433PubMedPubMedCentralCrossRefGoogle Scholar
  23. 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 24:13–71Google Scholar
  24. Fan TWM, Bird JA, Brodie EL, Lane AN (2009) 13C Isotoper – based metabolomics of microbial groups isolated from two forest soils. Metabolomics 5:108–122CrossRefGoogle Scholar
  25. 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
  26. 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 PubMedPubMedCentralCrossRefGoogle Scholar
  27. Feng YY (2013) Omics breakthroughs for environmental microbiology. Omics Environ Microbiol 40:18–33Google Scholar
  28. 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 71:4117–4120PubMedPubMedCentralCrossRefGoogle Scholar
  29. 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 73:7059–7066PubMedPubMedCentralCrossRefGoogle Scholar
  30. 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 42:243–270PubMedCrossRefGoogle Scholar
  31. 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 82:15981–15982Google Scholar
  32. 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 46:1019–1025PubMedPubMedCentralCrossRefGoogle Scholar
  33. 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 48:425–433CrossRefGoogle Scholar
  34. 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 PubMedPubMedCentralCrossRefGoogle Scholar
  35. Gigliucci F, Brambilla G, Tozzoli R, Michelacci V, Morabito S (2017) Comparative analysis of metagenomes of Italian top soil improvers. Environ Res 155:108–115PubMedCrossRefGoogle Scholar
  36. 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 PubMedPubMedCentralCrossRefGoogle Scholar
  37. 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
  38. 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 21:89–94CrossRefGoogle Scholar
  39. 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 57:105–128CrossRefGoogle Scholar
  40. 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 73:1965–1974PubMedCrossRefGoogle Scholar
  41. 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 83:9–17CrossRefGoogle Scholar
  42. Howe AC, Jansson JK, Malfatti SA, Tringe SG, Tiedje JM, Brown CT (2014) Tackling soil diversity with the assembly of large, complex metagenomes. PNAS 111:4904–4909PubMedPubMedCentralCrossRefGoogle Scholar
  43. Hugenholtz P (2002) Exploring prokaryotic diversity in the genomic era. Genome Biol 3(2). https://doi.org/10.1186/gb-2002-3-2-reviews0003
  44. Insam H (2001) Developments in soil microbiology since the mid 1960s. Geoderma 100:389–482CrossRefGoogle Scholar
  45. 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 25:4818–4835PubMedCrossRefGoogle Scholar
  46. Jahangir M, Farid IBA, Choi YH, Verpoorte R (2008a) Metal ion-inducing metabolite accumulation in Brassica rapa. J Plant Physiol 165:1429–1437PubMedCrossRefGoogle Scholar
  47. Jahangir M, Kim HK, Choi YH, Verpoorte R (2008b) Metabolomic response of Brassica rapa submitted to pre-harvest bacterial contamination. Food Chem 107:362–368CrossRefGoogle Scholar
  48. 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 33:61–64PubMedCrossRefGoogle Scholar
  49. 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 33:61–64PubMedCrossRefGoogle Scholar
  50. 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 93:62–68Google Scholar
  51. Keiblinger KM, Fuchs S, Boltenstern SZ, Riedel K (2016) Soil and leaf litter metaproteomics – a brief guideline from sampling to understanding. FEMS Microbiol Ecol 92:66–74CrossRefGoogle Scholar
  52. Keller M, Hettich R (2009) Environmental proteomics: a paradigm shifts in characterizing microbial activities at the molecular level. Microbiol Mol Biol Rev 73:62–70PubMedPubMedCentralCrossRefGoogle Scholar
  53. 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 295:42–49PubMedCrossRefGoogle Scholar
  54. 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
  55. Konstantinidis KT, Ramette A, Tiedje JM (2006) The bacterial species definition in the genomic era. Philos Trans R Soc B 361:1929–1940CrossRefGoogle Scholar
  56. 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 67:2503–2511PubMedCrossRefGoogle Scholar
  57. 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 71:7768–7777PubMedPubMedCentralCrossRefGoogle Scholar
  58. 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
  59. 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 102:17454–17459Google Scholar
  60. 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 62:1347–4405Google Scholar
  61. 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 409:2237–2339Google Scholar
  62. Miller MG (2007) Environmental metabolomics: SWOT analysis (strengths, weaknesses opportunities and threats). J Proteome Res 6:540–545PubMedCrossRefGoogle Scholar
  63. Mocalli S, Benedetti A (2010) Exploring research frontiers in microbiology: the challenge of metagenomics in soil microbiology. Res Microbiol 161:497–505CrossRefGoogle Scholar
  64. 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 35:292–303PubMedPubMedCentralCrossRefGoogle Scholar
  65. Moran MA (2009) Metatranscriptomics: eavesdropping on complex microbial communities. Microbe 4:329–335Google Scholar
  66. Myrold DD, Zeglin LH, Jansson JK (2013) The potential of metagenomic approaches for understanding soil microbial processes. SSSAJ 78:3–10CrossRefGoogle Scholar
  67. 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 78:188–201PubMedCrossRefGoogle Scholar
  68. Nannipieri P (2006) Roles of stabilised enzyme in microbial ecology and enzyme extraction from soil and potential applications in soil proteomics. Soil Biol 8:75–94CrossRefGoogle Scholar
  69. 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 8:400–482PubMedPubMedCentralGoogle Scholar
  70. 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 4:603–611PubMedCrossRefGoogle Scholar
  71. 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 50:563–575PubMedCrossRefGoogle Scholar
  72. Riesenfeld CS, Schloss PD, Handelsman J (2004) Metagenomics: genomic analysis of microbial communities. Annu Rev Genet 38:525–552PubMedCrossRefGoogle Scholar
  73. Rochfort S (2005) Metabolomics reviewed: a new “omics” platform technology for systems biology and implications for natural products research. J Nat Prod 68:1813–1820PubMedCrossRefGoogle Scholar
  74. 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 66:2541–2547PubMedPubMedCentralCrossRefGoogle Scholar
  75. Schenk PM, Carvalhais LC, Kazan K (2012) Unraveling plant–microbe interactions: can multi-species transcriptomics help? Trends Biotechnol 30:177–184PubMedCrossRefGoogle Scholar
  76. Schleper C, Jurgens G, Jonuscheit M (2005) Genomic studies of uncultivated archaea. Nat Rev Microbiol 3:479–488PubMedCrossRefGoogle Scholar
  77. 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 142:335–343PubMedCrossRefGoogle Scholar
  78. 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 67:4215–4224PubMedPubMedCentralCrossRefGoogle Scholar
  79. Siggins A, Gunnigle E, Abram F (2012) Exploring mixed microbial community functioning: recent advances in metaproteomics. FEMS Microbiol Ecol 80:265–280PubMedPubMedCentralCrossRefGoogle Scholar
  80. Singh BK, Campbell CD, Sorenson SJ, Zhou J (2009) Soil genomics. Nat Rev Microbiol 7:756. https://doi.org/10.1038/nrmicro2119-c1 PubMedCrossRefGoogle Scholar
  81. 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 PubMedPubMedCentralCrossRefGoogle Scholar
  82. 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 105:244–252CrossRefGoogle Scholar
  83. 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 64:5–28Google Scholar
  84. 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 78:840–845PubMedCrossRefGoogle Scholar
  85. Taylor EB, Williams MA (2010) Microbial protein in soil: influence of extraction method and C amendment on extraction and recovery. Microb Ecol 59:390–399Google Scholar
  86. 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 74:2822–2833PubMedPubMedCentralCrossRefGoogle Scholar
  87. 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 66:2773–2782PubMedPubMedCentralCrossRefGoogle Scholar
  88. Torvisk V, Ovreas L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5:240–245CrossRefGoogle Scholar
  89. 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 6:970–980PubMedCrossRefGoogle Scholar
  90. 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 308:554–557Google Scholar
  91. Uga Y (2017) Genomic based ideotype breeding for root system architecture to enhance rice production. Plant Anim Genome 86:12–17Google Scholar
  92. 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
  93. 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 PubMedPubMedCentralCrossRefGoogle Scholar
  94. 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 PubMedPubMedCentralGoogle Scholar
  95. 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 82:5698–5708PubMedPubMedCentralCrossRefGoogle Scholar
  96. Viant MR (2009) Applications of metabolomics to the environmental sciences. Metabolomics 5:1–2CrossRefGoogle Scholar
  97. 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 78:23–35CrossRefGoogle Scholar
  98. Wang DZ, Kong LF, Li YY, Xie ZX (2016) Environmental microbial community proteomics: status, challenges and perspectives. Int J Mol Sci 17:1275–1278PubMedCentralCrossRefGoogle Scholar
  99. Warnecke F, Hess M (2009) A perspective: metatranscriptomics as a tool for the discovery of novel biocatalysts. J Biotechnol 142(1):91–95PubMedCrossRefGoogle Scholar
  100. 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 6:295–301PubMedCrossRefGoogle Scholar
  101. 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 103:417–428CrossRefGoogle Scholar
  102. Williams MA, Taylor EB, Mula HP (2010) Metaproteomic characterization of a soil microbial community following carbon amendment. Soil Biol Biochem 42:1148–1156CrossRefGoogle Scholar
  103. Wilmes P, Bond PL (2006) Metaproteomics: studying functional gene expression in microbial ecosystems. Trends Microbiol 14:92–97PubMedCrossRefGoogle Scholar
  104. 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 86:54–58Google Scholar
  105. 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 PubMedPubMedCentralCrossRefGoogle Scholar
  106. 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 PubMedPubMedCentralCrossRefGoogle Scholar
  107. Yadav RK, Bragalini C, Tachet LF, Marmeisse R, Luis P (2016) Metatranscriptomics of soil eukaryotic communities. Microb Environ Genomics 1399:273–287CrossRefGoogle Scholar
  108. 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 PubMedPubMedCentralCrossRefGoogle Scholar
  109. 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 72:1767–1778PubMedCrossRefGoogle Scholar
  110. 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 PubMedPubMedCentralCrossRefGoogle Scholar
  111. 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 359:25–44CrossRefGoogle Scholar

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© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  1. 1.Department of Biotechnology and Medical EngineeringNational Institute of Technology RourkelaRourkelaIndia

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