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Advances in Soil Microbiology: Recent Trends and Future Prospects pp 9–33Cite as

Molecular Genomic Techniques for Identification of Soil Microbial Community Structure and Dynamics

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

Abstract

Soil microorganisms play a crucial role in maintaining major biogeochemical/nutrient cycle, soil quality, and productivity. Hence, the understanding of soil microbial community structure, distribution, and their metabolic function is essential for getting a deeper insight into soil ecosystem and its health. A number of molecular methods for extracting metagenome, total RNA, protein, and metabolites from the diverse environmental samples, sequencing technology, etc. are present which help to know about microbial structure, composition, and their metabolic function in the specific environmental ecosystem. Genetic fingerprinting like ARDRA, RFLP, DGGE, and T-RFLP and omics approaches like metagenomics, metatranscriptomics, and metabolomics are essential techniques for identifying and depicting the total microbial community structure and their interactions with environmental and biotic factors. So for these molecular techniques, it is possible to identify and functionally characterize soil microbes that are not culturable in a laboratory environment. This chapter describes old and modern novel state of the art molecular techniques which proved insights into the phylogenetic and functional activities of microbial assemblages in a terrestrial ecosystem.

Keywords

  • Microbial ecology
  • Stable isotope probing
  • Autoradiography
  • Fluorescence in situ hybridisation
  • DGGE
  • Next generation sequencing

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References

  • Adamczyk J, Hesselsoe M, Iversen N, Horn M, Lehner A, Nielsen PH et al (2003) The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function. Appl Environ Microbiol 69(11):6875–6887

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Adzitey F, Rusul G, Huda N, Cogan T, Corry J (2012) Prevalence, antibiotic resistance and RAPD typing of Campylobacter species isolated from ducks, their rearing and processing environments in Penang, Malaysia. Int J Food Microbiol 154(3):197–205

    CAS  PubMed  CrossRef  Google Scholar 

  • Antony CP, Kumaresan D, Ferrando L, Boden R, Moussard H, Scavino AF, Shouche YS, Murrell JC (2010) Active methylotrophs in the sediments of Lonar Lake, a saline and alkaline ecosystem formed by meteor impact. ISME J 4(11):1470–1480

    CAS  PubMed  CrossRef  Google Scholar 

  • Asuming-Brempong S (2012) Microarray technology and its applicability in soil science–a short review. Open J Soil Sci 2(3):333

    CrossRef  CAS  Google Scholar 

  • Barakat MA (2011) New trends in removing heavy metals from industrial wastewater. Arab J Chem 4:361–377

    CAS  CrossRef  Google Scholar 

  • Beaver CL, Williams AE, Atekwana EA, Mewafy FM, Abdel Aal G, Slater LD, Rossbach S (2016) Microbial communities associated with zones of elevated magnetic susceptibility in hydrocarbon-contaminated sediments. Geomicrobiol J 33(5):441–452

    CAS  CrossRef  Google Scholar 

  • Bentley DR (2006) Whole-genome re-sequencing. Curr Opin Genet Dev 16(6):545–552

    CAS  PubMed  CrossRef  Google Scholar 

  • Błaszczyk D, Bednarek I, Machnik G, Sypniewski D, Sołtysik D, Loch T, Gałka S (2011) Amplified ribosomal dna restriction analysis (ARDRA) as a screening method for normal and bulking activated sludge sample differentiation. Pol J Environ Stud 20:29–36

    Google Scholar 

  • Bossio DA, Scow KM, Gunapala N, Graham KJ (1998) Determinants of soil microbial communities: effects of agricultural management, season, and soil type on phospholipid fatty acid profiles. Microb Ecol 36:1–12

    CAS  PubMed  CrossRef  Google Scholar 

  • Bustin SA, Benes V, Nolan T, Pfaffl MW (2005) Quantitative real-time RT-PCR – a perspective. J Mol Endocrinol 34:597–601

    CAS  PubMed  CrossRef  Google Scholar 

  • Ciesielski S, Bułkowska K, Dabrowska D, Kaczmarczyk D, Kowal P, Możejko J (2013) Ribosomal intergenic spacer analysis as a tool for monitoring methanogenic archaea changes in an anaerobic digester. Curr Microbiol 67(2):240–248

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Cleary DF, Smalla K, Mendonça-Hagler LC, Gomes NC (2012) Assessment of variation in bacterial composition among microhabitats in a mangrove environment using DGGE fingerprints and barcoded pyrosequencing. PLoS One 7(1):e29380

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Cummings DE, Snoeyenbos-West OL, Newby DT, Niggemyer AM, Lovley DR, Achenbach LA, Rosenzweig RF (2003) Diversity of Geobacteraceae species inhabiting metal-polluted freshwater lake sediments ascertained by 16S rDNA analyses. Microb Ecol 46(2):257–269

    CAS  PubMed  CrossRef  Google Scholar 

  • DeRito CM, Pumphrey GM, Madsen EL (2005) Use of field-based stable isotope probing to identify adapted populations and track carbon flow through a phenol-degrading soil microbial community. Appl Environ Microbiol 71(12):7858–7865

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Dodd JC, Boddington CL, Rodriguez A, Gonzalez-Chavez C, Mansur I (2000) Mycelium of arbuscular mycorrhizal fungi (AMF) from different genera: form, function and detection. Plant Soil 226(2):131–151

    CAS  CrossRef  Google Scholar 

  • Dorn-In S, Hölzel CS, Janke T, Schwaiger K, Balsliemke J, Bauer J (2013) PCR-SSCP-based reconstruction of the original fungal flora of heat-processed meat products. Int J Food Microbiol 162(1):71–81

    CAS  PubMed  CrossRef  Google Scholar 

  • Dunbar J, Barns SM, Ticknor LO, Kuske CR (2002) Empirical and theoretical bacterial diversity in four Arizona soils. Appl Environ Microbiol 68(6):3035–3045

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Dunford EA, Neufeld JD (2010) DNA stable-isotope probing (DNA-SIP). JoVE (J Vis Exp) 42:e2027–e2027

    Google Scholar 

  • Feligini M, Panelli S, Sacchi R, Ghitti M, Capelli E (2015) Tracing the origin of raw milk from farm by using Automated Ribosomal Intergenic Spacer Analysis (ARISA) fingerprinting of microbiota. Food Control 50:51–56

    CAS  CrossRef  Google Scholar 

  • Felske A, Akkermans AD, De Vos WM (1998) In situ detection of an uncultured predominant Bacillus in Dutch grassland soils. Appl Environ Microbiol 64(11):4588–4590

    CAS  PubMed  PubMed Central  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

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Filion M, St-Arnaud M, Fortin JA (1999) Direct interaction between the arbuscular mycorrhizal fungus Glomus intraradices and different rhizosphere microorganisms. New Phytol 141(3):525–533

    CrossRef  Google Scholar 

  • Fischer SG, Lerman LS (1980) Separation of random fragments of DNA according to properties of their sequences. Proc Natl Acad Sci 77(8):4420–4424

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Fisher MM, Triplett EW (1999) Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 65(10):4630–4636

    CAS  PubMed  PubMed Central  Google Scholar 

  • Foti M, Sorokin DY, Lomans B, Mussman M, Zacharova EE, Pimenov NV, Kuenen JG, Muyzer G (2007) Diversity, activity, and abundance of sulfate-reducing bacteria in saline and hypersaline soda lakes. Appl Environ Microbiol 73:2093–3000

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Franklin RB, Taylor DR, Mills AL (1999) Characterization of microbial communities using randomly amplified polymorphic DNA (RAPD). J Microbiol Methods 35(3):225–235

    CAS  PubMed  CrossRef  Google Scholar 

  • Frostegard A, Tunlid A, Baath E (1993) Phospholipid fatty acid composition, biomass and activity of microbial communities from two soil types experimentally exposed to different heavy metals. Appl Environ Microbiol 59:3605–3617

    CAS  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  CrossRef  Google Scholar 

  • George E, Marschner H, Jakobsen I (1995) Role of arbuscular mycorrhizal fungi in uptake of phosphorus and nitrogen from soil. Crit Rev Biotechnol 15(3–4):257–270

    CrossRef  Google Scholar 

  • Goszczynski DE (2007) Single-strand conformation polymorphism (SSCP), cloning and sequencing reveal a close association between related molecular variants of Grapevine virus A (GVA) and Shiraz disease in South Africa. Plant Pathol 56(5):755–762

    Google Scholar 

  • Goszczynski DE, Jooste AEC (2015) The application of single-strand conformation polymorphism (SSCP) technique for the analysis of molecular heterogeneity of grapevine virus A. VITIS-J Grapevine Res 41(2):77

    Google Scholar 

  • Goupil K, Nkongolo KK, Nasserulla S (2015) Characterization of fungal communities in limed and unlimed lands contaminated with metals: phospholipid fatty acid (PLFA) analysis and soil respiration. Am J Biochem Biotechnol 11(2):45

    CrossRef  Google Scholar 

  • Gulitz A, Stadie J, Ehrmann MA, Ludwig W, Vogel RF (2013) Comparative phylobiomic analysis of the bacterial community of water kefir by 16S rRNA gene amplicon sequencing and ARDRA analysis. J Appl Microbiol 114(4):1082–1091

    CAS  PubMed  CrossRef  Google Scholar 

  • Hesselsoe M, Füreder S, Schloter M, Bodrossy L, Iversen N, Roslev P et al (2009) Isotope array analysis of Rhodocyclales uncovers functional redundancy and versatility in an activated sludge. ISME J 3(12):1349–1364

    CAS  PubMed  CrossRef  Google Scholar 

  • Heyndrickx M, Vauterin L, Vandamme P, Kersters K, De Vos P (1996) Applicability of combined amplified ribosomal DNA restriction analysis (ARDRA) patterns in bacterial phylogeny and taxonomy. J Microbiol Methods 26(3):247–259

    CAS  CrossRef  Google Scholar 

  • Hill GT, Mitkowski NA, Aldrich-Wolfe L, Emele LR, Jurkonie DD, Ficke A et al (2000) Methods for assessing the composition and diversity of soil microbial communities. Appl Soil Ecol 15(1):25–36

    CrossRef  Google Scholar 

  • Hugenholtz P (2002) Exploring prokaryotic diversity in the genomic era. Genome Biol 3:1. reviews0003-1

    CrossRef  Google Scholar 

  • Ivone VM, Conceição E (2013) Bacterial diversity from the source to the tap: a comparative study based on 16S rRNA gene-DGGE and culture-dependent methods. FEMS Microbiol Ecol 83(2):361–374

    CrossRef  CAS  Google Scholar 

  • Jehmlich N, Schmidt F, Hartwich M, von Bergen M, Richnow HH, Vogt C (2008) Incorporation of carbon and nitrogen atoms into proteins measured by protein-based stable isotope probing (Protein-SIP). Rapid Commun Mass Spectrom 22:2889–2897

    CAS  PubMed  CrossRef  Google Scholar 

  • Jehmlich N, Kopinke FD, Lenhard S, Herbst FA, Seifert J, Lissner U, Vo¨lker U, Schmidt F, von Bergen M (2012) Sulphur-36S stable isotope labeling of amino acids for quantification (SULAQ). Proteomics 12:37–42

    CAS  PubMed  CrossRef  Google Scholar 

  • Karbin S, Guillet C, Kammann CI, Niklaus PA (2015) Effects of long-term CO2 enrichment on soil-atmosphere CH 4 fluxes and the spatial micro-distribution of methanotrophic bacteria. PLoS One 10(7):e0131665

    PubMed  PubMed Central  CrossRef  CAS  Google Scholar 

  • Keinänen MM, Martikainen PJ, Kontro MH (2004) Microbial community structure and biomass in developing drinking water biofilms. Can J Microbiol 50(3):183–191

    PubMed  CrossRef  Google Scholar 

  • Key KC, Sublette KL, Duncan K, Mackay DM, Scow KM, Ogles D (2013) Using DNA-Stable isotope probing to identify MTBE- and TBA-degrading microorganisms in contaminated groundwater. Ground Water Monit Remediat 33:57–68

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kindaichi T, Awata T, Mugimoto Y, Rathnayake RM, Kasahara S, Satoh H (2016) Effects of organic matter in livestock manure digester liquid on microbial community structure and in situ activity of anammox granules. Chemosphere 159:300–307

    CAS  PubMed  CrossRef  Google Scholar 

  • Kolb S, Knief C, Stubner S, Conrad R (2003) Quantitative detection of methanotrophs in soil by novel pmoA-targeted real-time PCR assays. Appl Environ Microbiol 69:2423–2429

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD (2013) Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol 79(17):5112–5120

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Letowski J, Brousseau R, Masson L (2003) DNA microarray applications in environmental microbiology. Anal Lett 36(15):3165–3184

    CAS  CrossRef  Google Scholar 

  • Liou JS-C, DeRito CM, Madsen EL (2008) Field-based and laboratory stable isotope probing surveys of the identities of both aerobic and anaerobic benzene-metabolizing microorganisms in freshwater sediment. Environ Microbiol 10:1964–1977

    CAS  PubMed  CrossRef  Google Scholar 

  • Liu WT, Marsh TL, Cheng H, Forney LJ (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63(11):4516–4522

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lu Y, Conrad R (2005) In situ stable isotope probing of methanogenic archaea in the rice rhizosphere. Science 309(5737):1088–1090

    CAS  PubMed  CrossRef  Google Scholar 

  • Lueders T, Wagner B, Claus P, Friedrich MW (2004) Stable isotope probing of rRNA and DNA reveals a dynamic methylotroph community and trophic interactions with fungi and protozoa in oxic rice field soil. Environ Microbiol 6:60–72

    CAS  PubMed  CrossRef  Google Scholar 

  • MacNaughton SJ, Stephen JR, Venosa AD, Davis GA, Chang YJ, White DC (1999) Microbial population changes during bioremediation of an experimental oil spill. Appl Environ Microbiol 65(8):3566–3574

    CAS  PubMed  PubMed Central  Google Scholar 

  • Malik S, Beer M, Megharaj M, Naidu R (2008) The use of molecular techniques to characterize the microbial communities in contaminated soil and water. Environ Int 34(2):265–276

    CAS  PubMed  CrossRef  Google Scholar 

  • Manefield M, Whiteley AS, Griffiths RI, Bailey MJ (2002) RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol 68(11):5367–e5373

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387–402

    CAS  PubMed  CrossRef  Google Scholar 

  • Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437(7057):376–380

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • McGarry JW, Ortiz PL, Hodgkinson JE, Goreish I, Williams DJ (2013). PCR-based differentiation of Fasciola species (Trematoda: Fasciolidae), using primers based on RAPD-derived sequences. Ann Trop Med Parasitol

    Google Scholar 

  • Metzker ML (2010) Sequencing technologies-the next generation. Nat Rev Genet 11(1):31–46

    CAS  PubMed  CrossRef  Google Scholar 

  • Molin J, Molin S (1997) CASE: complex adaptive systems ecology. In: Advances in microbial ecology. Springer US, Boston, pp 27–79

    CrossRef  Google Scholar 

  • Müller H, Bosch J, Griebler C, Damgaard LR, Nielsen LP, Lueders T, Meckenstock RU (2016) Long-distance electron transfer by cable bacteria in aquifer sediments. ISME J 10:2010

    PubMed  PubMed Central  CrossRef  CAS  Google Scholar 

  • Muyzer G, De Waal EC, Uitterlinden AG (1993) Profiling of complex microbial population by DGGE analysis of polymerase chain reaction amplified genes encoding for 16S rRNA. Appl Environ Microbiol 62:2676–2680

    Google Scholar 

  • Neufeld JD, Vohra J, Dumont MG, Lueders T, Manefield M, Friedrich MW, Murrell JC (2007) DNA stable-isotope probing. Nat Protoc 2(4):860–866

    CAS  PubMed  CrossRef  Google Scholar 

  • Neufeld JD, Chen Y, Dumont MG, Murrell JC (2008) Marine methylotrophs revealed by stable-isotope probing, multiple displacement amplification and metagenomics. Environ Microbiol 10:1526–1535

    CAS  PubMed  CrossRef  Google Scholar 

  • O’Donnell GA et al (2007) Visualization, modelling and prediction in soil microbiology. Nat Rev Microbiol 5:9689–9699

    Google Scholar 

  • Orita M, Suzuki Y, Sekiya T, Hayashi K (1989) Rapid and sensitive detection of point mutations and DNA polymorphisms using the polymerase chain reaction. Genomics 5(4):874–879

    CAS  PubMed  CrossRef  Google Scholar 

  • Osborn AM, Moore ER, Timmis KN (2000) An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. Environ Microbiol 2(1):39–50

    CAS  PubMed  CrossRef  Google Scholar 

  • Ouverney CC, Fuhrman JA (1999) Combined microautoradiography-16S rRNA probe technique for determination of radioisotope uptake by specific microbial cell types in situ. Appl Environ Microbiol 65(4):1746–1752

    CAS  PubMed  PubMed Central  Google Scholar 

  • Paes F, Liu X, Mattes TE, Cupples AM (2015) Elucidating carbon uptake from vinyl chloride using stable isotope probing and Illumina sequencing. Appl Microbiol Biotechnol 99:7735–7743

    CAS  PubMed  CrossRef  Google Scholar 

  • Pascual J, Blanco S, García-López M, García-Salamanca A, Bursakov SA, Genilloud O et al (2016) Assessing bacterial diversity in the rhizosphere of thymus zygis growing in the Sierra Nevada National Park (Spain) through culture-dependent and independent approaches. PLoS One 1(1):e0146558

    CrossRef  Google Scholar 

  • Petersen SO, Debosz K, Schjonning P, Christensen BT, Elmholt S (1998) Phospholipid fatty acid profiles and C availability in wet-stable macro-aggregates from conventionally and organically farmed soils. Geoderma 78:181–196

    CrossRef  Google Scholar 

  • Radajewski S, Ineson P, Parekh NR, Murrell JC (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403:646–649

    CAS  PubMed  CrossRef  Google Scholar 

  • Radajewski S, Webster G, Reay DS, Morris SA, Ineson P, Nedwell DB, Prosser JI, Murrell JC (2002) Identification of active methylotroph populations in an acidic forest soil by stable-isotope probing. Microbiology 148:2331–2342

    CAS  PubMed  CrossRef  Google Scholar 

  • Ralebitso TK, Röling WF, Braster M, Senior E, van Verseveld HW (2000) 16S rDNA-based characterization of BTX-catabolizing microbial associations isolated from a South African sandy soil. Biodegradation 11(6):351–357

    CAS  PubMed  CrossRef  Google Scholar 

  • Rangel-Castro JI, Killham K, Ostle N, Nicol GW, Anderson IC, Scrimgeour CM, Ineson P, Meharg AA, Prosser JI (2005) Stable isotope probing analysis of the influence of liming on root exudate utilization by soil microorganisms. Environ Microbiol 7:828–838

    CAS  PubMed  CrossRef  Google Scholar 

  • Reichardt W, Mascarina G, Padre B, Doll J (1997) Microbial communities of continuously cropped, irrigated rice fields. Appl Environ Microbiol 63:233–238

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rickwood D (1992) Centrifugal methods for characterizing macromolecules and their interactions. In: Rickwood D (ed) Preparative centrifugation: a practical approach. Oxford University Press, Oxford, pp 143–186

    Google Scholar 

  • Rogers SW, Thomas BM, Say KO (2007) Fluorescent in situ hybridization and micro-autoradiography applied to ecophysiology in soil. Soil SciSoc Am J 71(2):620–631

    CAS  CrossRef  Google Scholar 

  • Schloss PD, Handelsman J (2004) Status of the microbial census. Microbiol Mol Biol Rev 68:686–691

    PubMed  PubMed Central  CrossRef  Google Scholar 

  • Schwieger F, Tebbe CC (1998) A new approach to utilize PCR–single-strand-conformation polymorphism for 16S rRNA gene-based microbial community analysis. Appl Environ Microbiol 64(12):4870–4876

    CAS  PubMed  PubMed Central  Google Scholar 

  • Seifert J, Taubert M, Jehmlich N, Schmidt F, Völker U, Vogt C et al (2012) Protein-based stable isotope probing (protein-SIP) in functional metaproteomics. Mass Spectrom Rev 31(6):683–697

    CAS  PubMed  CrossRef  Google Scholar 

  • Sheffield VC, Beck JS, Kwitek AE, Sandstrom DW, Stone EM (1993) The sensitivity of single-strand conformation polymorphism analysis for the detection of single base substitutions. Genomics 16(2):325–332

    CAS  PubMed  CrossRef  Google Scholar 

  • Shehata AI (2012) Molecular identification of probiotics Lactobacillus strain isolates by: amplified ribosomal DNA restriction analysis (ARDRA). Sci J Microbiol 6:3034

    CAS  Google Scholar 

  • Singh BK, Campbell CD, Sorenson SJ, Zhou J (2009) Soil genomics. Nat Rev Microbiol 7(10):756–756

    CAS  PubMed  CrossRef  Google Scholar 

  • Small J, Call DR, Brockman FJ, Straub TM, Chandler DP (2001) Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays. Appl Environ Microbiol 67:4708–4716

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Smith KP, Goodman RM (1999) Host variation for interactions with beneficial plant-associated microbes. Annu Rev Phytopathol 37(1):473–491

    CAS  PubMed  CrossRef  Google Scholar 

  • Smith CJ, Osborn AM (2009) Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology. FEMS Microbiol Ecol 67:6–20

    CAS  PubMed  CrossRef  Google Scholar 

  • Srivastava J, Lambert J, Vietmeyer N (1996) Medicinal plants: An expanding role in development, vol Vol. 320. World Bank Publications, Washington, DC

    CrossRef  Google Scholar 

  • Taubert M, Baumann S, von Bergen M, Seifert J (2011) Exploring the limits of robust detection of incorporation of13C by mass spectrometry in protein-based stable isotope probing (protein-SIP). Anal Bioanal Chem 401:1975–1982

    CAS  PubMed  CrossRef  Google Scholar 

  • Tiedje JM, Asuming-Brempong S, Nüsslein K, Marsh TL, Flynn SJ (1999) Opening the black box of soil microbial diversity. Appl Soil Ecol 13(2):109–122

    CrossRef  Google Scholar 

  • Timonen S, Finlay RD, Olsson S, Söderström B (1996) Dynamics of phosphorus translocation in intact ectomycorrhizal systems: non-destructive monitoring using a β-scanner. FEMS Microbiol Ecol 19(3):171–180

    CAS  Google Scholar 

  • Uhlik O, Leewis MC, Strejcek M, Musilova L, Mackova M, Leigh MB, Macek T (2013) Stable isotope probing in the metagenomics era: a bridge towards improved bioremediation. Biotechnol Adv 31(2):154–165

    CAS  PubMed  CrossRef  Google Scholar 

  • Vaneechoutte M, De Beenhouwer H, Claeys G, Verschraegen GERDA, De Rouck A, Paepe N et al (1993) Identification of Mycobacterium species by using amplified ribosomal DNA restriction analysis. J Clin Microbiol 31(8):2061–2065

    CAS  PubMed  PubMed Central  Google Scholar 

  • Vaneechoutte M, Riegel P, De Briel D, Monteil H, Verschraegen GERDA, De Rouck A, Claeys G (1995) Evaluation of the applicability of amplified rDNA-restriction analysis (ARDRA) to identification of species of the genus Corynebacterium. Res Microbiol 146(8):633–641

    CAS  PubMed  CrossRef  Google Scholar 

  • Varró T, Gelencser J, Somogyi G (1986) Study of transport processes in soils and plants by microautoradiographic and radioabsorption methods. Acta Biochim Biophys Hung 22(1):31–43

    Google Scholar 

  • Vogt C, Lueders T, Richnow HH, Krüger M, von Bergen M, Seifert J (2016) Stable isotope probing approaches to study anaerobic hydrocarbon degradation and degraders. J Mol Microbiol Biotechnol 26(1–3):195–210

    CAS  PubMed  CrossRef  Google Scholar 

  • Wald J, Hroudova M, Jansa J, Vrchotova B, Macek T, Uhlik O (2015) Pseudomonads rule degradation of polyaromatic hydrocarbons in aerated sediment. Front Microbiol 6:1268

    PubMed  PubMed Central  CrossRef  Google Scholar 

  • Wall DH, Virginia RA (1999) Controls on soil biodiversity: insights from extreme environments. Appl Soil Ecol 13(2):137–150

    CrossRef  Google Scholar 

  • Watanabe K, Kodama Y, Harayama S (2001) Design and evaluation of PCR primers to amplify bacterial 16S ribosomal DNA fragments used for community fingerprinting. J Microbiol Methods 44(3):253–262

    CAS  PubMed  CrossRef  Google Scholar 

  • White DC, Gouffon JS, Peacock AD, Geyer R, Biernacki A, Davis GA, Pryor M, Tabacco MB, Sublette KL (2003) Forensic analysis by comprehensive rapid detection of pathogens and contamination concentrated in biofilms in drinking water systems for water resource protection and management. Environ Forensic 4:63–74

    CAS  CrossRef  Google Scholar 

  • Whiteley AS et al (2007) RNA stable-isotope probing. Nat Protoc 2(4):838–844

    CAS  PubMed  CrossRef  Google Scholar 

  • Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad 95(12):6578–6583

    CAS  CrossRef  Google Scholar 

  • Williams JG, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18(22):6531–6535

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Wright SF, Upadhyaya A (1998) A survey of soils for aggregate stability and glomalin, a glycoprotein produced by hyphae of arbuscular mycorrhizal fungi. Plant Soil 198(1):97–107

    CAS  CrossRef  Google Scholar 

  • Yao H, He ZL, Wilson M, Campbell CD (2000) Microbial biomass and community structure in a sequence of soils with increasing fertility and changing land use. Microb Ecol 40(3):223–237

    CAS  PubMed  Google Scholar 

  • Yao Z, Xing J, Gu H, Wang H, Wu J, Xu J, Brookes PC (2016) Development of microbial community structure in vegetable-growing soils from open-field to plastic-greenhouse cultivation based on the PLFA analysis. J Soils Sediments:16, 1–19

    Google Scholar 

  • Zarda B, Hahn D, Chatzinotas A, Schonhuber W, Neef A, Amann RI, Zeyer J (1997) Analysis of bacterial community structure in bulk soil by in situ hybridization. Arch Microbiol 168:185–192

    CAS  CrossRef  Google Scholar 

  • Zelles L, Rackwitz R, Bai QY, Beck T, Beese F (1995) Discrimination of microbial diversity by fatty acid profiles of phospholipids and lipopolysaccharides in differently cultivated soils. Plant Soil 170:115–122

    CAS  CrossRef  Google Scholar 

  • Zhang Y, Deng W, Xie X, Jiao N (2016) Differential Incorporation of Carbon Substrates among Microbial Populations Identified by Field-Based, DNA Stable-Isotope Probing in South China Sea. PLoS One 11(6):e0157178

    PubMed  PubMed Central  CrossRef  CAS  Google Scholar 

  • Zhou J, Thompson DK (2002) Challenges in applying microarrays to environmental studies. Curr Opin Biotechnol 13:204–207

    CAS  PubMed  CrossRef  Google Scholar 

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Authors and Affiliations

  1. Microbial Culture Collection, National Centre for Cell Science, Savitribai Phule University of Pune Campus, Ganeshkhind, Pune, Maharashtra, India

    Dhiraj Paul, Satish Kumar, Mrinal Mishra, Sushant Parab, Sunil Banskar & Yogesh S. Shouche

  2. ICAR-National Institute of Abiotic Stress Management, Baramati Pune, Maharashtra, India

    Satish Kumar

Authors
  1. Dhiraj Paul
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  2. Satish Kumar
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  3. Mrinal Mishra
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  4. Sushant Parab
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  5. Sunil Banskar
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  6. Yogesh S. Shouche
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Corresponding authors

Correspondence to Dhiraj Paul or Yogesh S. Shouche .

Editor information

Editors and Affiliations

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

    Dr. Tapan Kumar Adhya

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

    Dr. 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

    Dr. Dhiraj Paul

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

    Dr. Subhasis Das

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Paul, D., Kumar, S., Mishra, M., Parab, S., Banskar, S., Shouche, Y.S. (2018). Molecular Genomic Techniques for Identification of Soil Microbial Community Structure and Dynamics. 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_2

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