Skip to main content
SpringerLink
Log in

Culture Independent Diversity Analysis of Soil Microbial Community and their Significance

  • Chapter
  • First Online:
Bacterial Diversity in Sustainable Agriculture

Part of the book series: Sustainable Development and Biodiversity ((SDEB,volume 1))

Abstract

Soil is considered as one of the richest source of microbes on the earth. Understanding microbial diversity of soil is a daunting and challenging task. The culture-independent techniques have revealed that the soil microbial diversity is much larger than was understood through culture-dependent techniques. Various DNA- and RNA-based techniques have revolutionized our understanding of soil microbial diversity. This chapter deals with the major culture-independent methods used for the study of soil microbial diversity, their advantages and limitations and advent of metagenomics in microbial diversity studies. Significance of culture-independent techniques in conservation of microbes has also been discussed.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Abe T, Sugawara H, Kinouchi M, Kanaya S, Ikemura T (2005) Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples. DNA Res 12:281−190

    Google Scholar 

  • Acinas SG, Marcelino LA, Klepac-Ceraj V, Polz MF (2004) Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol 186:2629–2635

    CAS  PubMed Central  PubMed  Google Scholar 

  • Acinas S, Sarma-Rupavtarm R, Klepac-Ceraj V, Polz M (2005) PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl Environ Microbiol 71:8966–8969

    CAS  PubMed Central  PubMed  Google Scholar 

  • Allen HK, Moe LA, Rodbumrer J, Gaarder A, Handelsman J (2009) Functional metagenomics reveals diverse beta-lactamases in a remote Alaskan soil. ISME J 3(2):243–251

    CAS  PubMed Central  PubMed  Google Scholar 

  • Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169

    CAS  PubMed Central  PubMed  Google Scholar 

  • Arora DK, Saikia R, Dwievdi R, Smith D (2005) Current status, strategy and future prospects of microbial resource collections. Curr Sci 89(3):488–495

    Google Scholar 

  • Avis PG, Dickie IA, Mueller GM (2006) A ‘dirty’ business: testing the limitations of 13 terminal restriction fragment length polymorphism (TRFLP) analysis of soil fungi. Mol Ecol 15:873–882

    CAS  PubMed  Google Scholar 

  • Bae JW, Rhee SK, Park JR, Chung WH, Nam YD, Lee I, Kim H, Park YH (2005) Development and evaluation of genome-probing microarrays for monitoring lactic acid bacteria. Appl Environ Microbiol 71:8825–8835

    CAS  PubMed Central  PubMed  Google Scholar 

  • Barns SM, Takala SL, Kuske CR (1999) Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment. Appl Environ Microbiol 65(4):1731–1737

    CAS  PubMed Central  PubMed  Google Scholar 

  • Behrens S, Lösekann T, Pett-Ridge J, Weber PK, Ng WO, Stevenson BS, Hutcheon ID, Relman DA, Spormann AM (2008) Linking microbial phylogeny to metabolic activity at the single-cell level by using enhanced element labeling-catalyzed reporter deposition fluorescence in situ hybridization (EL-FISH) and NanoSIMS. Appl Environ Microbiol 74:3143–3150

    CAS  PubMed Central  PubMed  Google Scholar 

  • Berlemont R, Pipers D, Delsaute M, Angiono F, Feller G, Galleni M, Power P (2011) Exploring the Antarctic soil metagenome as a source of novel cold-adapted enzymes and genetic mobile elements. Revista Argentina de Microbiología 43:94–103

    CAS  PubMed  Google Scholar 

  • Berry AE, Chiocchini C, Selby T, Sosio M, Wellington EM (2003) Isolation of higher molecular weight DNA from soil for cloning into BAC vectors. FEMS Microbiol Lett 223:15–20

    CAS  PubMed  Google Scholar 

  • Bhattacharyya PN, Tanti B, Barman P, Jha DK (2013) Culture-independent metagenomic approach to characterize the surface and subsurface soil bacterial community in the Brahmaputra valley, Assam, North-East India, an Indo-Burma mega-biodiversity hotspot. World J Microbiol Biotechnol 30:519–528

    PubMed  Google Scholar 

  • Bing-Ru L, Guo-Mei J, Jian C, Gang W (2006) A review of methods for studying microbial diversity in soils. Pedosphere 16(1):18–24

    Google Scholar 

  • Bodrossy L, Sessitsch A (2004) Oligonucleotide microarrays in microbial diagnostics. Curr Opin Microbiol 7:245–254

    CAS  PubMed  Google Scholar 

  • Brady SF, Clardy J (2000) Long- chain N-Acyl amino acid antibiotics isolated from heterologously expressed environmental DNA. J Am Chem Soc 122:12903–12904

    CAS  Google Scholar 

  • Brazelton WJ, Baross JA (2009) Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm. ISME J 3(12):1420–1424

    CAS  PubMed  Google Scholar 

  • Brehm-Stecher BF, Johnson EA (2004) Single-cell microbiology: tools, technologies, and applications. Microbiol Mol Biol Rev 68:538–539

    CAS  PubMed Central  PubMed  Google Scholar 

  • Brodie E, Edwards S, Clipson N (2003) Soil fungal community structure in a temperate upland grassland soil. FEMS Microbiol Ecol 45:105–114

    CAS  PubMed  Google Scholar 

  • Broughton LC, Gross KL (2000) Patterns of diversity in plant and soil microbial communities along a productivity gradient in a Michigan old-field. Oecologia 125:420–427

    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  Google Scholar 

  • Callon C, Delbès C, Duthoit F, Montel M (2006) Application of SSCP-PCR 16 fingerprinting to profile the yeast community in raw milk salers cheeses. Syst Appl Microbiol 29:172–180

    CAS  PubMed  Google Scholar 

  • Campbell CD, Grayston SJ, Hirst DJ (1997) Use of rhizosphere carbon sources in sole carbon source tests to discriminate soil microbial communities. J Microbiol Methods 30:33–41

    Google Scholar 

  • Caracciolo AB, Bottoni P, Grenni P (2010) Fluorescence in situ hybridization in soil and water ecosystems: a useful method for studying the effect of xenobiotics on bacterial community structure. Toxicol Environ Chem 92:567–579

    CAS  Google Scholar 

  • Clarke KR, Ainsworth M (1993) A method of linking multivariate community structure to environmental variables. Mar Ecol Prog Ser 92:205–219

    Google Scholar 

  • Clarke L, Carbon J (1976) A colony bank containing synthetic Col El hybrid plasmids representative of the entire E. coli genome. Cell 9(1):91–99

    CAS  PubMed  Google Scholar 

  • Cockell CS, Jones HL (2009) Advancing the case for microbial conservation. Oryx 43(4):520–526

    Google Scholar 

  • Cohan FM, Perry EB (2007) A systematics for discovering the fundamental units of bacterial diversity. Curr Biol 17(10):R373–R386

    CAS  PubMed  Google Scholar 

  • Craig JW, Chang FY, Kim JH (2010) Expanding small molecule functional metagenomics through parallel screening of broad-host-range cosmid environmental DNA libraries in diverse proteobacteria. Appl Environ Microbiol 76:1633–1641

    CAS  PubMed Central  PubMed  Google Scholar 

  • Das A, Krishnaswamy J, Bawa KS, Kiran MC, Srinivas V, Kumar NS, Karanth KU (2006) Prioritisation of conservation areas in the Western Ghats, India. Biol Conserv 133(1):16–31

    Google Scholar 

  • Daubin V, Moran NA, Ochman H (2003) Phylogenetics and the cohesion of bacterial genomes. Science 301:829–832

    CAS  PubMed  Google Scholar 

  • Dekas AE, Orphan VJ (2011) Identification of diazotrophic microorganisms in marine sediment via fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS). Methods Enzymol 486:281–305

    CAS  PubMed  Google Scholar 

  • Dethlefsen L, Huse S, Sogin ML, Relman DA (2008) The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 6(11):e280

    PubMed Central  PubMed  Google Scholar 

  • Delbès C, Ali-Mandjee L, Montel MC (2007) Monitoring bacterial communities in raw milk and cheese by culture-dependent and -independent 16S rRNA gene-based analyses. Appl Environ Microbiol 73:1882–1891

    PubMed Central  PubMed  Google Scholar 

  • Delmont TO, Robe P, Clark I, Simonet P, Vogel TM (2011) Metagenomic comparison of direct and indirect soil DNA extraction approaches. J Microbiol Methods 86(3):397–400

    CAS  PubMed  Google Scholar 

  • DeLong EF, Pace NR (2001) Environmental diversity of bacteria and archaea. Syst Biol 50:470–478

    CAS  PubMed  Google Scholar 

  • Dickie IA, Xu B, Koide RT (2002) Vertical niche differentiation of ectomycorrhizal hyphae in soil as shown by T-RFLP analysis. New Phytol 156:527–535

    CAS  Google Scholar 

  • Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM (1999) Expression profiling using cDNA microarrays. Nat Genet 21:10–14

    CAS  PubMed  Google Scholar 

  • El-Baradei G, Delacroix-Buchet A, Ogier JC (2007) Biodiversity of bacterial ecosystems in traditional Egyptian Domiati cheese. Appl Environ Microbiol 73:1248–1255

    CAS  PubMed Central  PubMed  Google Scholar 

  • Entcheva P, Liebl W, Johann A, Hartsch T, Streit W (2001) Direct cloning from enrichment cultures. A reliable strategy for isolation of complete operons and genes from microbial consortia. Appl Environ Microbiol 67:89–99

    CAS  PubMed Central  PubMed  Google Scholar 

  • Ercolini D, Moschetti G, Blaiotta G, Coppola S (2001) The potential of a polyphasic PCR-DGGE approach in evaluating microbial diversity of natural whey cultures for water-buffalo mozzarella cheese production: bias of culture-dependent and culture-independent analyses. Syst Appl Microbiol 24:610–617

    CAS  PubMed  Google Scholar 

  • Farrelly V, Rainey FA, Stackebrandt E (1995) Effect of genomic size and rRNA gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl Environ Microbiol 61:2798–2801

    CAS  PubMed Central  PubMed  Google Scholar 

  • Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci U S A 103:626–631

    CAS  PubMed Central  PubMed  Google Scholar 

  • Feurer C, Vallaeys T, Corrieu G, Irlinger F (2004a) Does smearing inoculum reflect the bacterial composition of the smear at the end of the ripening of a French soft, red-smear cheese? J Dairy Sci 87:3189–3197

    CAS  Google Scholar 

  • Feurer C, Irlinger F, Spinnler HE, Glaser P, Vallaeys T (2004b) Assessment of the rind microbial diversity in a farmhouse-produced vs a pasteurized industrially produced soft red-smear cheese using both cultivation and rDNA-1 based methods. J Appl Microbiol 97:546–556

    CAS  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 65:4630–4636

    CAS  PubMed Central  PubMed  Google Scholar 

  • Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269(5223):496–512

    CAS  PubMed  Google Scholar 

  • Florez AB, Mayo B (2006) Microbial diversity and succession during the manufacture and ripening of traditional, Spanish, blue-veined Cabrales cheese, as determined by PCR-DGGE. Int J Food Microbiol 110:165–171

    CAS  PubMed  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 73:2093–2100

    CAS  PubMed Central  PubMed  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  Google Scholar 

  • Frerichs J, Oppermann BI, Gwosdz S, Möller I, Herrmann M, Krüger M (2013) Microbial community changes at a terrestrial volcanic CO2 vent induced by soil acidification and anaerobic microhabitats within the soil column. FEMS Microbial Ecol 84(1):60–74

    CAS  Google Scholar 

  • Gans J, Wolinsky M, Dunbar J (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309:1387–1390

    CAS  PubMed  Google Scholar 

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

    CAS  Google Scholar 

  • Gerhardson B, Wright S (2002) Bacterial associations with plants: beneficial, non-fixing interactions. In: Sivasithamparam K, Dixon KW, Barrett RL (eds) Microorganisms in plant conservation and biodiversity, Kluwer, Netherlands, pp 79–103

    Google Scholar 

  • Gihring TM, Green SJ, Schadt CW (2012) Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes. Environ Microbiol 14:285–290

    CAS  PubMed  Google Scholar 

  • Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60–63

    CAS  PubMed  Google Scholar 

  • Green JL, Holmes AJ, Westoby M, Oliver L, Briscoe D, Dangerfield M, Gillings M, Beattie AJ (2004) Spatial scaling of microbial eukaryote diversity. Nature 432:747–750

    CAS  PubMed  Google Scholar 

  • Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, NISC Comparative Sequencing Program, Bouffard GG, Blakesely RW, Murray PR, Green ED, Turner ML, Segre JA (2009) Topographical and temporal diversity of the human skin microbiome. Science 324(5931):1190–1192

    CAS  PubMed Central  PubMed  Google Scholar 

  • Guerrero R (2001) Bergey’s manuals and the classification of prokaryotes. Int Microbiol 4:103–109

    CAS  PubMed  Google Scholar 

  • Gugliandolo C, Lentini V, Maugeri TL (2010) Distribution and diversity of bacteria in a saline meromictic lake as determined by PCR DGGE of 16S rRNA gene fragments. Curr Microbiol 62:159–166

    PubMed  Google Scholar 

  • Guschin DY, Mobarry BK, Proudnikov D, Stahl DA, Rittmann BE, Mirzabekov AD (1997) Oligonucleotide microchips as genosensors for determinative and 20 environmental studies in microbiology. Appl Environ Microbiol 63:2397–2402

    CAS  PubMed Central  PubMed  Google Scholar 

  • Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methe B, DeSantis TZ, The Human Microbiome Consortium, Petrosino JF, Knight R, Birren BW (2011) Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21:494–504

    CAS  PubMed Central  PubMed  Google Scholar 

  • Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669–685

    CAS  PubMed Central  PubMed  Google Scholar 

  • Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5:R245–R249

    CAS  PubMed  Google Scholar 

  • Henne A, Schmitz RA, Bömeke M, Gottaschalk G, Daniel R (2000) Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli. Appl Environ Microbiol 66:3113–3116

    CAS  PubMed Central  PubMed  Google Scholar 

  • Hoefel D, Paul T, Warwick M, Grooby L, Andrews S, Saint CP (2005) Culture-independent techniques for rapid detection of bacteria associated with loss of chloramine residual in a drinking water system. Appl Environ Microbiol 71(11):6479–6488

    CAS  PubMed Central  PubMed  Google Scholar 

  • Holland PM, Abramson RD, Watson R, Gelfand DH (1991) Detection of specific polymerase chain reaction product by utilizing the 5′ to 3′ exonuclease activity of Thermus aquaticus DNA polymerase. Proc Natl Acad Sci U S A 88:7276–7280

    CAS  PubMed Central  PubMed  Google Scholar 

  • Hong S, Bunge J, Leslin C, Jeon S, Epstein SS (2009) Polymerase chain reaction primers miss half of rRNA microbial diversity. ISME J 3:1365–1373

    CAS  PubMed  Google Scholar 

  • Huang WE, Griffiths RI, Thompson IP, Bailey MJ, Whiteley AS (2004) Raman microscopic analysis of single microbial cells. Anal Chem 76:4452–4458

    CAS  PubMed  Google Scholar 

  • Huang WE, Ferguson A, Singer A, Lawson K, Thompson IP, Kalin RM, Larkin MJ, Bailey MJ, Whiteley AS (2009) Resolving genetic functions within microbial populations: in situ analyses using rRNA and mRNA stable isotope probing coupled with single-cell Raman-fluorescence in situ hybridization. Appl Environ Microbiol 75:234–241

    CAS  PubMed Central  PubMed  Google Scholar 

  • Huang WE, Li M, Jarvis RM, Goodacre R, Banwart SA (2010) Shining light on the microbial world the application of Raman microspectroscopy. Adv Appl Microbiol 70:153–186

    CAS  PubMed  Google Scholar 

  • Huber JA, Welch DB, Morrison HG, Huse SM, Neal PR, Butterfield DA, Sogin ML (2007) Microbial population structures in the deep marine biosphere. Science 318:97–100

    CAS  PubMed  Google Scholar 

  • Huse SM, Welch DM, Morrison HG, Sogin ML (2010) Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol 12:1889–1898

    CAS  PubMed Central  PubMed  Google Scholar 

  • Jany J, Barbier G (2008) Culture-independent methods for 1 identifying microbial 2 communities in cheese. Food Microbiol 25(7):839–848

    CAS  PubMed  Google Scholar 

  • Knietsch A, Waschkowitz T, Bowien S, Henne A, Daniel R (2003) Metagenomes of complex microbial consortia derived from different soils as sources of novel genes conferring formation of carbonyls from short-chain polyols on Escherichia coli. J Mol Microbiol Biotechnol 5:46–56

    CAS  PubMed  Google Scholar 

  • Kirk JL, Beaudette LA, Hart M, Moutoglis P, Klironomos JN, Lee H, Trevors JT (2004) Methods of studying soil microbial diversity. J Microbiol Methods 58:169–188

    Google Scholar 

  • Klappenbach JA, Saxman PR, Cole JR, Schmidt TM (2001) rrndb: the ribosomal RNA operon copy number database. Nucleic Acid Res 29:181–184

    CAS  PubMed Central  PubMed  Google Scholar 

  • Kuypers MMM, Jorgensen BB (2007) The future of single-cell environmental microbiology. Environ Microbiol 9:6–7

    PubMed  Google Scholar 

  • Lafarge V, Ogier JC, Girard V, Maladen V, Leveau J, Delacroix-Buchet A (2004) Le potentiel de la TTGE pour l’étude bactérienne de quelques laits crus. Le Lait 84:169–178

    CAS  Google Scholar 

  • Lauber CL, Hamady M, Knight R, Fierer N (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75:5111–5120

    CAS  PubMed Central  PubMed  Google Scholar 

  • Liu W, 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 Central  PubMed  Google Scholar 

  • Lo I, Denef VJ, Verberkmoes NC, Shah MB, Goltsman D, Dibartolo G, Tyson GW, Allen EE, Ram RJ, Detter C, Richardson P, Thelen MP, Hettich RL, Banfield JF (2007) Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 446(7135):537–541

    CAS  PubMed  Google Scholar 

  • Martín-Cuadrado AB, López-García P, Alba JC et al. (2007) Metagenomics of the deep Mediterranean, a warm bathypelagic habitat. PLoS One. 2(9):e914

    CAS  PubMed  Google Scholar 

  • Mills DK, Entry JA, Gillevet PM (2007) Assessing microbial community diversity using amplicon length heterogeneity polymerase chain reaction. Soil Sci Soc Am J 71:572–578

    CAS  Google Scholar 

  • Myers RM, Maniatis T, Lerman LS (1987) Detection and localization of single base changes by denaturing gradient gel electrophoresis. Methods Enzymol 155:501–527.

    CAS  PubMed  Google Scholar 

  • Nakamura S, Maeda N, Miron IM, Yoh M, Izutsu K, Kataoka C, Honda T, Yasunaga T, Nakaya T, Kawai Jun, Hayashizaki Y, Toshihiro H, Lida T (2008) Metagenomic diagnosis of bacterial infections. Emerg Infect Dis 14(11):1784–1786

    PubMed Central  PubMed  Google Scholar 

  • Nakatsua CH, Torsvik V, Ovreas L (2000) Soil community analysis using DGGE of 16S rDNA polymerase chain reaction products. Soil Sci Soc Am J 64:1382–1388

    Google Scholar 

  • Noonan JP, Coop G, Kudaravalli S, Smith D, Krause J, Alessi J, Chen F, Platt D, Paabo S, Pritchard JK, Rubin EM (2006) Sequencing and analysis of Neanderthal genomic DNA. Science 314(5802):1113–1118

    CAS  PubMed Central  PubMed  Google Scholar 

  • Nüsslein K, Tiedje JM (1999) Soil bacterial community shift correlated with change from forest to pasture vegetation in a tropical soil. Appl Environ Microbiol 65:3622–3626.

    PubMed Central  PubMed  Google Scholar 

  • Oehler DZ, Robert F, Walter MR, Sugitani K, Meibom A, Mostefaoui S, Gibson EK (2010) Diversity in the Archean biosphere: new insights from NanoSIMS. Astrobiology 10:413–424

    CAS  PubMed  Google Scholar 

  • Ogier JC, Son O, Gruss A, Tailliez P, Delacroix-Buchet A (2002) Identification of the bacterial microflora in dairy products by temporal temperature gradient gel electrophoresis. Appl Environ Microbiol 68:3691–3701

    CAS  PubMed Central  PubMed  Google Scholar 

  • Olsen GJ, Woese CR (1993) Ribosomal RNA: a key to phylogeny. FASEB J 7:113–123

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Pace NR (1997) A molecular view of microbial diversity and the biosphere. Science 276: 734–740

    CAS  PubMed  Google Scholar 

  • Pace NR (2009) Mapping the tree of life: progress and prospects. Microbiol Mol Biol Rev 73:565–576

    CAS  PubMed Central  PubMed  Google Scholar 

  • Pace NR, Stahl DJ, Lane DJ, Olsen GJ (1985) Analyzing natural microbial populations by rRNA sequences. ASM News 51:4–12

    Google Scholar 

  • Pernthaler A, Pernthaler J, Amann R (2002) Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl Environ Microbiol 68:3094–3101

    CAS  PubMed Central  PubMed  Google Scholar 

  • Prakash T, Taylor TD (2012) Functional assignment of metagenomic data: challenges and applications. Brief Bioinform 13(6):711–727

    PubMed Central  PubMed  Google Scholar 

  • Qu A, Brulc JM, Wilson MK, Law BF, Theoret JR, Joens LA, Konkel ME, Angly F, Dinsdale EA, Edwards RA, Nelson KE, White BA (2008) Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome. PLoS ONE 3(8):e2945

    PubMed Central  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

    CAS  PubMed  Google Scholar 

  • Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011) Removing noise from pyrosequenced amplicons. BMC Bioinform 12:38

    Google Scholar 

  • Ranjard L, Poly F, Lata JC, Mougel C, Thioulouse J, Nazaret S (2001) Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability. Appl Environ Microbiol 67:4479−4487

    Google Scholar 

  • Ravnik-Glavac M, Glavac D, Dean M (1994) Sensitivity of single-strand conformation polymorphism and heteroduplex method for mutation detection on the cystic fibrosis gene. Hum Mol Genet 3:801–807

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Rincon-Florez VA, Carvalhais LC, Schenck PM (2013) Culture-independent molecular tools for soil and rhizosphere microbiology. Diversity 5:581–612

    Google Scholar 

  • Ritchie NJ, Schutter ME, Dick RP, Myrold DD (2000) Use of length heterogeneity PCR and fatty acid methyl ester profiles to characterize microbial communities in soil. Appl Environ Microbiol 66:1668–1675

    CAS  PubMed Central  PubMed  Google Scholar 

  • Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, MacNeil 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

    CAS  PubMed Central  PubMed  Google Scholar 

  • Schloss PD, Gevers D, Westcott SL (2011) Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE 6:e27310

    CAS  PubMed Central  PubMed  Google Scholar 

  • Schmeisser C, Steele H, Streit WR (2007) Metagenomics, biotechnology with non-culturable microbes. Appl Microbiol Biotechnol 75:955–962

    CAS  PubMed  Google Scholar 

  • Schmidt TM, DeLong EF, Pace NR (1991) Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J Bacteriol 173:4371–4378

    CAS  PubMed Central  PubMed  Google Scholar 

  • Schweiger 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 64:4870–4876

    Google Scholar 

  • Shizuya H, Birren B, Kim UJ, Mancino V, Slepak T, Tachiiri Y, Simon M (1992) Cloning and stable maintenance of 300-kilobase -pair fragments of human DNA in Escherichia coli using an F-factor-based vector. PNAS 89:8794–8797

    CAS  PubMed Central  PubMed  Google Scholar 

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

    CAS  Google Scholar 

  • Staley JT, Konopka A (1985) Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Ann Rev Microbiol 39:321–346

    CAS  Google Scholar 

  • Stierle DB, Stierle AA, Patacini B (2007) The berkeleyacetals, three meroterpenes from a deep water acid mine waste Penicillium. J Nat Prod 70:1820–1823

    CAS  PubMed Central  PubMed  Google Scholar 

  • Streit WR, Daniel R, Jaeger KE (2004) Prospecting for biocatalysts and drugs in the genomes of non-cultured microorganisms. Curr Opin Biotechnol 15:285–290

    CAS  PubMed  Google Scholar 

  • Supardiyono EK, Smith D (1997) Microbial diversity: ex situ conservation of Indonesian microorganisms. World J Microbiol Biotechnol 13:359–361

    Google Scholar 

  • Swift MJ, Andre´ n O, Brussaard L, Briones M, Couteaux M, Ekschmitt K, Kjoller A, Loiseau P, Smith P (1998) Global change, soil biodiversity, and nitrogen cycling in terrestrial ecosystems: three case studies, Global Change Biol 4:729–743

    Google Scholar 

  • Tabacchioni S, Chiaini L, Bevivino A, Cantale C, Dalmastri C (2000) Bias caused by using different isolation media for assessing the genetic diversity of a natural microbial population. Microb Ecol 40:169–176

    CAS  PubMed  Google Scholar 

  • Thomas T, Gilbert J, Meyer F (2012) Metagenomics- a guide from sampling to data analysis. Microb Inform Exp 2:3

    PubMed Central  PubMed  Google Scholar 

  • Theron J, Cloete TE (2000) Molecular techniques for determining microbial diversity and community structure in natural environments. Critic Rev Microbiol 26:37–57

    CAS  Google Scholar 

  • Thurnheer T, Gmur R, Guggenheim B (2004) Multiplex FISH analysis of a six-species bacterial biofilm. J Microbiol Methods 56:37–47

    CAS  PubMed  Google Scholar 

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

    Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Torsvik V, Goksoyr J, Daae FL (1990) High diversity in DNA of soil bacteria. Appl Environ Microbiol 56:782–787

    Google Scholar 

  • Torsvik V, Daae FL, Sandaa RA, Overeas L (1998) Novel techniques for analyzing microbial diversity in natural and perturbed environments. J Biotechnol 64:53–62

    CAS  PubMed  Google Scholar 

  • Tringe SG, Hugenholtz P (2008) A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol 11:442–446

    CAS  PubMed  Google Scholar 

  • Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Mircea P, Short JM, Mathur JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM (2005) Comparative metagenomics of microbial communities. Science 308(5721):554–557

    CAS  PubMed  Google Scholar 

  • Tringe SG, Zhang T, Liu X, Yu Y, Lee WH, Yap J, Yao F, Suan ST, Ing SK, Haynes M, Rohwer F, Wei CL, Tan P, Bristow J, Rubin EM, Ruan Y (2008) The airborne metagenome in an indoor urban environment. PLoS ONE 3(4):e1862

    PubMed Central  PubMed  Google Scholar 

  • Valinsky L, Della Vedova G, Scupham AJ, Alvey S, Figueroa A, Yin B, Hartin RJ, Chrobak M, Crowley DE, Jiang T, Borneman J (2002) Analysis of bacterial community composition by oligonucleotide fingerprinting of rRNA genes. Appl Environ Microbiol 68:3243–3250

    CAS  PubMed Central  PubMed  Google Scholar 

  • van Elsas JD, Trevors JT (1997) Modern soil microbiology (Marcel Dekker). CRC Press, New York

    Google Scholar 

  • van Elsas JD, Frois-Duarte G, Keijzer-Wolters A, Smit E (2000) Analysis of the dynamics of fungal communities in soil via fungal-specific PCR of soil DNA followed by denaturing gradient gel electrophoresis. J Microbiol Methods 43: 133–151

    CAS  PubMed  Google Scholar 

  • Vartoukian SR, Palmer RM, Wade WG (2010) Strategies for culture of ‘unculturable’ bacteria. FEMS Microbiol Lett 309:1–7

    CAS  PubMed  Google Scholar 

  • VÄ›trovský T, Baldrian P (2013) The Variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS ONE 8(2):57923

    Google Scholar 

  • Vogel TM, Simonet P, Jansson JK, Hirsch PR, Tiedje JM, Van Elsas JD, Bailey MJ, Nalin R, Philippot L (2009) TerraGenome: a consortium for the sequencing of a soil metagenome. Nat Rev Microbiol 7:252

    CAS  Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acid Res 23:4407–4414

    CAS  PubMed Central  PubMed  Google Scholar 

  • Wagner M, Smidt H, Loy A, Zhou J (2007) Unravelling microbial communities with 24 DNA-microarrays: challenges and future directions. Microbial Ecol 53:498–506

    CAS  Google Scholar 

  • Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acid Res 18:7213–7218

    CAS  PubMed Central  PubMed  Google Scholar 

  • Werner JJ, Koren O, Hugenholtz P, DeSantis TZ, Walters WA, Caporaso JG, Angenent LT, Knight R, Ley RE (2012) Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. ISME J 6:94–103

    CAS  PubMed Central  PubMed  Google Scholar 

  • White JR, Nagarajan N, Pop M (2009) Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5(4):1000352

    Google Scholar 

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

    CAS  PubMed Central  PubMed  Google Scholar 

  • Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271

    CAS  PubMed Central  PubMed  Google Scholar 

  • Xie CG, Li YQ (2002) Raman spectra and optical trapping of highly refractive and nontransparent particles. Appl Phys Lett 81:951–953

    CAS  Google Scholar 

  • Xie C, Mace J, Dinno MA, Li YQ, Tang W, Newton RJ, Gemperline PJ (2005) Identification of single bacterial cells in aqueous solution using conflocal laser tweezers Raman spectroscopy. Anal Chem 77:4390–4397

    CAS  PubMed  Google Scholar 

  • Yang B, Peng Y, Leung H, Yiu SM, Chen JC, Chin F (2009) Unsupervised binning of environmental genomic fragments based on an error robust selection of lmers. In: DTMBIO ’09: Proceeding of the third international workshop on data and text mining in bioinformatics, ACM, Hong Kong, China, pp 3–10

    Google Scholar 

  • Yoshino K, Nishigaki K, Husimi Y (1991) Temperature sweep gel electrophoresis: a simple method to detect point mutations. Nucleic Acid Res 19:3153–3153

    CAS  PubMed Central  PubMed  Google Scholar 

  • Zelles L (1999) Fatty acid patterns of phospholipids and lipopolysaccharides in the characterisation of microbial communities in soil: a review. Biol Fertility Soils 29:111–129

    CAS  Google Scholar 

  • Zhou X, Wu F (2012) p-Coumaric acid influenced cucumber rhizosphere soil microbial communities and the growth of Fusarium oxysporum f. sp. Cucumerinum owen. PLoS ONE 7:e48288

    CAS  PubMed Central  PubMed  Google Scholar 

  • Zhou J, Xia B, Huang H, Treves DS, Hauser LJ, Mural RJ, Palumbo AV, Tiedje JM (2003) Bacterial phylogenetic diversity and a novel candidate division of two humid region, sandy surface soils. Soil Biol Biochem 35:915–924

    CAS  Google Scholar 

  • Zinder SH, Salyers AA (2001) Microbial ecology-new directions, new importance. In: Boone DR, Castenholz RW (eds) Bergey’s manual of systematic bacteriology, vol 1: the Archaea and the deeply branching and phototrophic Bacteria. Springer-Verlag, New York, pp 101–109

    Google Scholar 

  • Zwolinski MD (2007) DNA sequencing: strategies for soil microbiology. Soil Sci Soc Am J 71:592–600

    CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Microbial Ecology Laboratory, Department of Botany, Gauhati University, 781014, Guwahati, Assam, India

    Bidisha Sharma, Diganta Narzary & Dhruva Kumar Jha

Authors
  1. Bidisha Sharma
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Diganta Narzary
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Dhruva Kumar Jha
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Dhruva Kumar Jha .

Editor information

Editors and Affiliations

  1. Dept. of Botany and Microbiology, Gurukul Kangri University, Haridwar (Uttarakhand), India

    Dinesh K. Maheshwari

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer International Publishing Switzerland

About this chapter

Cite this chapter

Sharma, B., Narzary, D., Jha, D. (2014). Culture Independent Diversity Analysis of Soil Microbial Community and their Significance. In: Maheshwari, D. (eds) Bacterial Diversity in Sustainable Agriculture. Sustainable Development and Biodiversity, vol 1. Springer, Cham. https://doi.org/10.1007/978-3-319-05936-5_12

Download citation

Publish with us

Policies and ethics

Search

Navigation