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Molecular Identification, Systematics, and Population Structure of Prokaryotes pp 219–259Cite as

Assessment of Microbial Phylogenetic Diversity Based on Environmental Nucleic Acids

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Abstract

“It is a Golden Age for the discovery of new organisms and for achieving a better understanding of the global ecosystem, which is, after all, based upon the microbial world” (Hugenholtz and Pace 1996). These sentiments reflect renewed confidence in microbial ecology, as the last decades of the twentieth century witnessed the circumvention of culture-based approaches by the advent of molecular methodology. Molecular methods have enabled novel insight into microbial community composition and expanded the range of ecological questions that may now be addressed. Despite tremendous advances, a major consideration remains the enormous and largely unexplored diversity of most microbial communities on Earth.

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References

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

    PubMed  CAS  Google Scholar 

  • Avaniss-Aghajani E, Jones K, Chapman D, Brunk C (1994) A molecular technique for identification of bacteria using small subunit ribosomal RNA sequences. Biotechniques 17:144–146

    PubMed  CAS  Google Scholar 

  • Bano N, Hollibaugh JT (2000) Diversity and distribution of DNA sequences with affinity to ammonia-oxidizing bacteria of the β subdivision of the class Proteobacteria in the Arctic Ocean. Appl Environ Microbiol 66:1960–1969

    Article  PubMed  CAS  Google Scholar 

  • Becker S, Boger P, Oehlmann R, Ernst A (2000) PCR bias in ecological analysis: a case study for quantitative Taq nuclease assays in analyses of microbial communities. Appl Environ Microbiol 66:4945–4953

    Article  PubMed  CAS  Google Scholar 

  • Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL (2000) GenBank. Nucleic Acids Res 28:15–18

    Article  PubMed  CAS  Google Scholar 

  • Besemer K, Moeseneder MM, Arrieta JM, Herndl GJ, Peduzzi P (2005) Complexity of bacterial communities in a river-floodplain system (Danube, Austria). Appl Environ Microbiol 71:609–620

    Article  PubMed  CAS  Google Scholar 

  • Blackall LL, Burrell PC, Gwilliam H, Bradford D, Bond PL, Hugenholtz P (1998) The use of 16S rDNA clone libraries to describe the microbial diversity of activated sludge communities. Water Sci Technol 37:451–454

    CAS  Google Scholar 

  • Blank CE, Cady SL, Pace NR (2002) Microbial composition of near-boiling silica-depositing thermal springs throughout Yellowstone national park. Appl Environ Microbiol 68:5123–5135

    Article  PubMed  CAS  Google Scholar 

  • Bodrossy L, Stralis-Pavese N, Murrell JC, Radajewski S, Weilharter A, Sessitsch A (2003) Development and validation of a diagnostic microbial microarray for methanotrophs. Environ Microbiol 5:566–582

    Article  PubMed  CAS  Google Scholar 

  • Bohannan B, Hughes J (2003) New approaches to analyzing microbial biodiversity data. Curr Opin Microbiol 6:282–287

    Article  PubMed  CAS  Google Scholar 

  • Borneman J, Triplett EW (1997) Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl Environ Microbiol 63:2647–2653

    PubMed  CAS  Google Scholar 

  • Borneman J, Skroch PW, O’Sullivan KM, Palus JA, Rumjanek NG, Jansen JL, Nienhuis J, Triplett EW (1996) Molecular microbial diversity of an agricultural soil in Wisconsin. Appl Environ Microbiol 62:1935–1943

    PubMed  CAS  Google Scholar 

  • Casamayor EO, Schäfer H, Bañeras L, Pedrós-Alió C, Muyzer G (2000) Identification of and spatio-temporal differences between microbial assemblages from two neighboring sulfurous lakes: Comparison by microscopy and denaturing gradient gel electrophoresis. Appl Environ Microbiol 66:499–508

    Article  PubMed  CAS  Google Scholar 

  • Castiglioni B, Rizzi E, Frosini A, Sivonen K, Rajaniemi P, Rantala A, Mugnai MA, Ventura S, Wilmotte A, Boutte C, Grubisic S, Balthasart P, Consolandi C, Bordoni R, Mezzelani A, Battaglia C, De Bellis G (2004) Development of a universal microarray based on the ligation detection reaction and 16S rRNA gene polymorphism to target diversity of cyanobacteria. Appl Environ Microbiol 70:7161–7172

    Article  PubMed  CAS  Google Scholar 

  • Chao A (1984) Non-parametric estimation of the number of classes in a population. Scand J Stat 11:265–270

    Google Scholar 

  • Chao A, Lee S-M (1992) Estimating the number of classes via sample coverage. J Am Stat Assoc 87:210–217

    Article  Google Scholar 

  • Chase JM, Leibold MA (2002) Spatial scale dictates the productivity-biodiversity relationship. Nature 416:427–430

    Article  PubMed  CAS  Google Scholar 

  • Chow ML, Radomski CC, McDermott JM, Davies J, Axelrood PE (2002) Molecular characterization of bacterial diversity in Lodgepole pine (Pinus contorta) rhizosphere soils from British Columbia forest soils differing in disturbance and geographic source. FEMS Microbiol Ecol 42:347–357

    Article  PubMed  CAS  Google Scholar 

  • Coeyne T, Vandamme P (2003) Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced bacterial genomes. FEMS Microbiol Lett 228:45–49

    Article  CAS  Google Scholar 

  • Cole JR, Chai B, Marsh TL, Farris RJ, Wang Q, Kulam SA, Chandra S, McGarrell DM, Schmidt TM, Garrity GM, Tiedje JM (2003) The ribosomal database project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31:442–443

    Article  PubMed  CAS  Google Scholar 

  • Colwell RK, Coddington JA (1994) Estimating terrestrial biodiversity through extrapolation. Phil Trans R Soc Lond B 345:101–118

    Article  CAS  Google Scholar 

  • Connon SA, Giovannoni SJ (2002) High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl Environ Microbiol 68:3878–3885

    Article  PubMed  CAS  Google Scholar 

  • Cook KL, Sayler GS (2003) Environmental application of array technology: promise, problems and practicalities. Curr Opin Biotechnol 14:311–318

    Article  PubMed  CAS  Google Scholar 

  • Curtis TP, Sloan WT (2004) Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology. Curr Opin Microbiol 7:221–226

    Article  PubMed  Google Scholar 

  • Curtis TP, Sloan WT, Scannell JW (2002) Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci USA 99:10494–10499

    Article  PubMed  CAS  Google Scholar 

  • Dahllöf I, Baillie H, Kjelleberg S (2000) rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity. Appl Environ Microbiol 66:3376–3380

    Article  PubMed  Google Scholar 

  • Delbes C, Moletta R, Godon JJ (2000) Monitoring of activity dynamics of an anaerobic digester bacterial community using 16S rRNA polymerase chain reaction-single-strand conformation polymorphism analysis. Environ Microbiol 2:506–515

    Article  PubMed  CAS  Google Scholar 

  • Dennis P, Edwards EA, Liss SN, Fulthorpe R (2003) Monitoring gene expression in mixed microbial communities by using DNA microarrays. Appl Environ Microbiol 69:769–778

    Article  PubMed  CAS  Google Scholar 

  • Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284:2124–2128

    Article  PubMed  CAS  Google Scholar 

  • Dunbar J, Takala S, Barns SM, Davis JA, Kuske CR (1999) Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl Environ Microbiol 65:1662–1669

    PubMed  CAS  Google Scholar 

  • Dunbar J, Ticknor LO, Kuske CR (2000) Assessment of microbial diversity in four south-western United States soils by 16S rRNA gene terminal restriction fragment analysis. Appl Environ Microbiol 66:2943–2950

    Article  PubMed  CAS  Google Scholar 

  • Dunbar J, Ticknor LO, Kuske CR (2001) Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities. Appl Environ Microbiol 67:190–197

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Dykhuizen DE (1998) Santa Rosalia revisited: why are there so many species of bacteria? Antonie van Leeuwenhoek 73:25–33

    Article  PubMed  CAS  Google Scholar 

  • Egert M, Friedrich MW (2003) Formation of pseudo-terminal restriction fragments, a PCR-related bias affecting terminal restriction fragment length polymorphism analysis of microbial community structure. Appl Environ Microbiol 69:2555–2562

    Article  PubMed  CAS  Google Scholar 

  • El Fantroussi S, Urakawa H, Bernhard AE, Kelly JJ, Noble PA, Smidt H, Yershov GM, Stahl DA (2003) Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarrays. Appl Environ Microbiol 69:2377–2382

    Article  PubMed  CAS  Google Scholar 

  • Farnleitner AH, Kreuzinger N, Kavka GG, Grillenberger S, Rath J, Mach RL (2000) Comparative analysis of denaturing gradient gel electrophoresis and temporal temperature gradient gel electrophoresis in separating Escherichia coli uidA amplicons differing in single base substitutions. Lett Appl Microbiol 30:427–431

    Article  PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Felske A, Wolterink A, van Lis R, Akkermans AD (1998) Phylogeny of the main bacterial 16S rRNA sequences in Drentse A grassland soils (The Netherlands). Appl Environ Microbiol 64:871–879

    PubMed  CAS  Google Scholar 

  • Ferrari VC, Hollibaugh JT (1999) Distribution of microbial assemblages in the Central Arctic Ocean basin studied by PCR/DGGE: analysis of a large data set. Hydrobiologia 401:55–68

    Article  CAS  Google Scholar 

  • Finlay BJ (2002) Global dispersal of free-living microbial eukaryote species. Science 296:1061–1063

    Article  PubMed  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

    PubMed  CAS  Google Scholar 

  • Fitz-Gibbon ST, House CH (1999) Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res 27:4218–4222

    Article  PubMed  CAS  Google Scholar 

  • Fox GE, Stackebrandt E, Hespell RB, Gibson J, Maniloff J, Dyer TA, Wolfe RS, Balch WE, Tanner R, Magrum L, Zablen LB, Blakemore R, Gupta R, Bonen L, Lewis BJ, Stahl DA, Luehrsen KR, Chen KN, Woese CR (1980) The phylogeny of prokaryotes. Science 209:457–463

    Article  PubMed  CAS  Google Scholar 

  • Fox GE, Wisotzkey J, Jurtshuk P Jr (1992) How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 42:166–170

    Article  PubMed  CAS  Google Scholar 

  • Fromin N, Hamelin J, Tarnawski S, Roesti D, Jourdain-Miserez K, Forestier N, Teyssier-Cuvelle S, Gillet F, Aragno M, Rossi P (2002) Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns. Environ Microbiol 4:634–643

    Article  PubMed  CAS  Google Scholar 

  • Giovannoni SJ, DeLong EF, Olsen GJ, Pace NR (1988) Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial cells. J Bacteriol 170:720–726

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Girvan MS, Bullimore J, Pretty JN, Osborn AM, Ball AS (2003) Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl Environ Microbiol 69:1800–1809

    Article  PubMed  CAS  Google Scholar 

  • Girvan MS, Campbell CD, Killham K, Prosser JI, Glover LA (2005) Bacterial diversity pro-motes community stability and functional resilience after perturbation. Environ Microbiol 7:301–313

    Article  PubMed  CAS  Google Scholar 

  • Gonzalez N, Romero J, Espejo RT (2003) Comprehensive detection of bacterial populations by PCR amplification of the 16S-23S rRNA spacer region. J Microbiol Methods 55:91–97

    Article  PubMed  CAS  Google Scholar 

  • Graham DE, Overbeek R, Olsen GJ, Woese CR (2000) An archaeal genomic signature. Proc Natl Acad Sci USA 97:3304–3308

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Griffiths BS, Kuan HL, Ritz K, Glover LA, McCaig AE, Fenwick C (2004) The relationship between microbial community structure and functional stability, tested experimentally in an upland pasture soil. Microb Ecol 47:104–113

    Article  PubMed  CAS  Google Scholar 

  • Griffiths RI, Whiteley AS, O’Donnell AG, Bailey MJ (2003) Influence of depth and sampling time on bacterial community structure in an upland grassland soil. FEMS Microbiol Ecol 43:35–43

    Article  PubMed  CAS  Google Scholar 

  • Grundmann GL (2004) Spatial scales of soil bacterial diversity — the size of a clone. FEMS Microbiol Ecol 48:119–127

    Article  PubMed  CAS  Google Scholar 

  • Gutell RR, Larsen N, Woese CR (1994) Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol Rev 58:10–26

    PubMed  CAS  Google Scholar 

  • Hackl E, Zechmeister-Boltenstern S, Bodrossy L, Sessitsch A (2004) Comparison of diver-sities and compositions of bacterial populations inhabiting natural forest soils. Appl Environ Microbiol 70:5057–5065

    Article  PubMed  CAS  Google Scholar 

  • Hagstrom A, Pommier T, Rohwer F, Simu K, Stolte W, Svensson D, Zweifel UL (2002) Use of 16S ribosomal DNA for delineation of marine bacterioplankton species. Appl Environ Microbiol 68:3628–3633

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Hill JE, Seipp RP, Betts M, Hawkins L, van Kessel AG, Crosby WL, Hemmingsen SM (2002) Extensive profiling of a complex microbial community by high-throughput sequencing. Appl Environ Microbiol 68:3055–3066

    Article  PubMed  CAS  Google Scholar 

  • Hill JE, Penny SL, Crowell KG, Goh SH, Hemmingsen SM (2004) cpnDB: a chaperonin sequence database. Genome Res 14:1669–1675

    Article  PubMed  CAS  Google Scholar 

  • Hill TCJ, Walsh KA, Harris JA, Moffett BF (2003) Using ecological diversity measures with bacterial communities. FEMS Microbiol Ecol 43:1–11

    Article  PubMed  CAS  Google Scholar 

  • Höfle MG, Flavier S, Christen R, Bötel J, Labrenz M, Brettar I (2005) Retrieval of nearly complete 16S rRNA gene sequences from environmental DNA following 16S rRNA-based community fingerprinting. Environ Microbiol 7:670–675

    Article  PubMed  Google Scholar 

  • Holben WE, Feris KP, Kettunen A, Apajalahti JHA (2004) GC fractionation enhances microbial community diversity assessment and detection of minority populations of bacteria by denaturing gradient gel electrophoresis. Appl Environ Microbiol 70:2263–2270

    Article  PubMed  CAS  Google Scholar 

  • Holben WE, Harris D (1995) DNA-based monitoring of total bacterial community structure in environmental samples. Mol Ecol 4:627–631

    Article  PubMed  CAS  Google Scholar 

  • Horner-Devine MC, Leibold MA, Smith VH, Bohannan BJM (2003) Bacterial diversity patterns along a gradient of primary productivity. Ecol Lett 6:613–622

    Article  Google Scholar 

  • Horner-Devine MC, Carney KM, Bohannan BJM (2004a) An ecological perspective on bacterial biodiversity. Proc R Soc Lond Ser B Biol Sci 271:113–122

    Article  Google Scholar 

  • Horner-Devine MC, Lage M, Hughes JB, Bohannan BJM (2004b) A taxa-area relationship for bacteria. Nature 432:750–753

    Article  PubMed  CAS  Google Scholar 

  • Hugenholtz P, Huber T (2003) Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. Int J Syst Evol Microbiol 53:289–293

    Article  CAS  Google Scholar 

  • Hugenholtz P, Pace NR (1996) Identifying microbial diversity in the natural environment: a molecular phylogenetic approach. Trends Biotechnol 14:190–197

    Article  PubMed  CAS  Google Scholar 

  • Hugenholtz P, Pitulle C, Hershberger KL, Pace NR (1998) Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 180:366–376

    PubMed  CAS  Google Scholar 

  • Hughes AR, Stachowicz JJ (2004) Genetic diversity enhances the resistance of a seagrass ecosystem to disturbance. Proc Natl Acad Sci USA 101:8998–9002

    Article  PubMed  CAS  Google Scholar 

  • Hughes JB, Bohannan BJM (2004) Application of ecological diversity statistics in microbial ecology. In: Kowalchuk GA, de Bruijn FJ, Head IM, Akkermans AD, van Elsas JD (eds) Molecular microbial ecology manual, 2nd edn. Kluwer, London, pp 1321–1344

    Google Scholar 

  • Hughes JB, Hellmann JJ, Ricketts TH, Bohannan BJM (2001) Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol 67:4399–4406

    Article  PubMed  CAS  Google Scholar 

  • Jain R, Rivera MC, Lake JA (1999) Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA 96:3801–3806

    Article  PubMed  CAS  Google Scholar 

  • Janse I, Bok J, Zwart G (2004) A simple remedy against artifactual double bands in denaturing gradient gel electrophoresis. J Microbiol Methods 57:279–281

    Article  PubMed  CAS  Google Scholar 

  • Janssen PH, Yates PS, Grinton BE, Taylor PM, Sait M (2002) Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl Environ Microbiol 68:2391–2396

    Article  PubMed  CAS  Google Scholar 

  • Jaspers E, Overmann J (2004) Ecological significance of microdiversity: identical 16S rRNA gene sequences can be found in bacteria with highly divergent genomes and ecophysiologies. Appl Environ Microbiol 70:4831–4839

    Article  PubMed  CAS  Google Scholar 

  • Jensen MA, Webster JA, Straus N (1993) Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms. Appl Environ Microbiol 59:945–952

    PubMed  CAS  Google Scholar 

  • Joseph SJ, Hugenholtz P, Sangwan P, Osborne CA, Janssen PH (2003) Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl Environ Microbiol 69:7210–7215

    Article  PubMed  CAS  Google Scholar 

  • Kelly JJ (2003) Molecular techniques for the analysis of soil microbial processes: functional gene analysis and the utility of DNA microarrays. Soil Sci 168:597–605

    Article  CAS  Google Scholar 

  • Kemp PF, Aller JY (2004) Bacterial diversity in aquatic and other environments: what 16S rDNA libraries can tell us. FEMS Microbiol Ecol 47:161–177

    Article  PubMed  CAS  Google Scholar 

  • Kent AD, Smith DJ, Benson BJ, Triplett EW (2003) Web-based phylogenetic assignment tool for analysis of terminal restriction fragment length polymorphism profiles of microbial communities. Appl Environ Microbiol 69:6768–6776

    Article  PubMed  CAS  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

    Article  PubMed  CAS  Google Scholar 

  • Klappenbach JA, Dunbar JM, Schmidt TM (2000) rRNA operon copy number reflects eco-logical strategies of bacteria. Appl Environ Microbiol 66:1328–1333

    Article  PubMed  CAS  Google Scholar 

  • Kopczynski ED, Bateson MM, Ward DM (1994) Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms. Appl Environ Microbiol 60:746–748

    PubMed  CAS  Google Scholar 

  • Kroes I, Lepp PW, Relman DA (1999) Bacterial diversity within the human subgingival crevice. Proc Natl Acad Sci USA 96:14547–14552

    Article  PubMed  CAS  Google Scholar 

  • Kropf S, Heuer H, Gruning M, Smalla K (2004) Significance test for comparing complex microbial community fingerprints using pairwise similarity measures. J Microbiol Meth-ods 57:187–195

    Article  CAS  Google Scholar 

  • Kuske CR, Ticknor LO, Miller ME, Dunbar JM, Davis JA, Barns SM, Belnap J (2002) Comparison of soil bacterial communities in rhizospheres of three plant species and the interspaces in an arid grassland. Appl Environ Microbiol 68:1854–1863

    Article  PubMed  CAS  Google Scholar 

  • Kysela DT, Palacios C, Sogin ML (2005) Serial analysis of V6 ribosomal sequence tags (SARST-V6). Environ Microbiol 7:356–364

    Article  PubMed  CAS  Google Scholar 

  • Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci USA 82:6955–6959

    Article  PubMed  CAS  Google Scholar 

  • Lawrence JG, Ochman H (1998) Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci USA 95:9413–9417

    Article  PubMed  CAS  Google Scholar 

  • Leckie SE, Prescott CE, Grayston SJ, Neufeld JD, Mohn WW (2004) Characterization of humus microbial communities in adjacent forest types that differ in nitrogen availability. Microb Ecol 48:29–40

    Article  PubMed  CAS  Google Scholar 

  • Leclerc M, Delgenes JP, Godon JJ (2004) Diversity of the archaeal community in 44 anaerobic digesters as determined by single strand conformation polymorphism analysis and 16S rDNA sequencing. Environ Microbiol 6:809–819

    Article  PubMed  CAS  Google Scholar 

  • Lee D, Zo Y, Kim S (1996) Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation polymorphism. Appl Environ Microbiol 62:3112–3120

    PubMed  CAS  Google Scholar 

  • Leveau JHJ, Gerards S, de Boer W, van Veen JA (2004) Phylogeny-function analysis of (meta)genomic libraries: screening for expression of ribosomal RNA genes by large-insert library fluorescent in situ hybridization (LIL-FISH). Environ Microbiol 6:990–998

    Article  PubMed  CAS  Google Scholar 

  • Liesack W, Stackebrandt E (1992) Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J Bacteriol 174:5072–5078

    PubMed  CAS  Google Scholar 

  • Liles MR, Manske BF, Bintrim SB, Handelsman J, Goodman RM (2003) A census of rRNA genes and linked genomic sequences within a soil metagenomic library. Appl Environ Microbiol 69:2684–2691

    Article  PubMed  CAS  Google Scholar 

  • Lipson DA, Schmidt SK (2004) Seasonal changes in an alpine soil bacterial community in the Colorado rocky mountains. Appl Environ Microbiol 70:2867–2879

    Article  PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Lloyd-Jones G, Lau PCK (1998) A molecular view of microbial diversity in a dynamic landfill in Québec. FEMS Microbiol Lett 162:219–226

    PubMed  CAS  Google Scholar 

  • Loy A, Lehner A, Lee N, Adamczyk J, Meier H, Ernst J, Schleifer KH, Wagner M (2002) Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl Environ Microbiol 68:5064–5081

    Article  PubMed  CAS  Google Scholar 

  • Lunn M, Sloan WT, Curtis TP (2004) Estimating bacterial diversity from clone libraries with flat rank abundance distributions. Environ Microbiol 6:1081–1085

    Article  PubMed  CAS  Google Scholar 

  • Marsh TL, Saxman P, Cole J, Tiedje J (2000) Terminal restriction fragment length polymorphism analysis program, a web-based research tool for microbial community analysis. Appl Environ Microbiol 66:3616–3620

    Article  PubMed  CAS  Google Scholar 

  • Martin AP (2002) Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl Environ Microbiol 68:3673–3682

    Article  PubMed  CAS  Google Scholar 

  • Martinez-Murcia A, Benlloch S, Collins M (1992) Phylogenetic interrelationships of members of the genera Aeromonas and Plesiomonas as determined by 16S ribosomal DNA sequencing: lack of congruence with results of DNA-DNA hybridizations. Int J Syst Bacteriol 42:412–421

    Article  PubMed  CAS  Google Scholar 

  • McCaig AE, Glover LA, Prosser JI (1999) Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. Appl Environ Microbiol 65:1721–1730

    PubMed  CAS  Google Scholar 

  • McCann KS (2000) The diversity-stability debate. Nature 405:228–233

    Article  PubMed  CAS  Google Scholar 

  • Moeseneder MM, Arrieta JM, Muyzer G, Winter C, Herndl GJ (1999) Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacte-rioplankton communities and comparison with denaturing gradient gel electrophoresis. Appl Environ Microbiol 65:3518–3525

    PubMed  CAS  Google Scholar 

  • Morris CE, Bardin M, Berge O, Frey-Klett P, Fromin N, Girardin H, Guinebretière M-H, Lebaron P, Thiéry JM, Troussellier M (2002) Microbial biodiversity: approaches to experimental design and hypothesis testing in primary scientific literature from 1975 to 1999. Microbiol Mol Biol Rev 66:592–616

    Article  PubMed  Google Scholar 

  • Mulder CP, Uliassi DD, Doak DF (2001) Physical stress and diversity-productivity relation-ships: the role of positive interactions. Proc Natl Acad Sci USA 98:6704–6708

    Article  PubMed  CAS  Google Scholar 

  • Muyzer G (1999) DGGE/TGGE a method for identifying genes from natural ecosystems. Curr Opin Microbiol 2:317–322

    Article  PubMed  CAS  Google Scholar 

  • Muyzer G, Smalla K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek 73:127–141

    Article  PubMed  CAS  Google Scholar 

  • Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700

    PubMed  CAS  Google Scholar 

  • Muyzer G, Brinkhoff T, Nübel U, Santegoeds C, Schäfer H, Wawer C (2004) Denaturing gradient gel electrophoresis (DGGE) in microbial ecology. In: Kowalchuk GA, de Bruijn FJ, Head IM, Akkermans AD, van Elsas JD (eds) Molecular microbial ecology manual, 2nd edn. Kluwer, London

    Google Scholar 

  • Myers R, Fischer S, Lerman L, Maniatis T (1985) Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis. Nucleic Acids Res 13:3131–3145

    Article  PubMed  CAS  Google Scholar 

  • Nazaret S, Brothier E, Ranjard L (2003) Shifts in diversity and microscale distribution of the adapted bacterial phenotypes due to Hg(II) spiking in soil. Microb Ecol 45:259–269

    Article  PubMed  CAS  Google Scholar 

  • Nee S (2003) Unveiling prokaryotic diversity. Trends Ecol Evol 18:62–63

    Article  Google Scholar 

  • Neufeld JD, Mohn WW (2005a) Fluorophore-labeled primers improve the sensitivity, versatility and normalization of denaturing gradient gel electrophoresis (DGGE). Appl Environ Microbiol 71:4893–4896

    Article  PubMed  CAS  Google Scholar 

  • Neufeld JD, Mohn WW (2005b) Unexpectedly high bacterial diversity in arctic tundra relative to boreal forest soils revealed with serial analysis of ribosomal sequence tags (SARST). Appl Environ Microbiol 71:5710–5718

    Article  PubMed  CAS  Google Scholar 

  • Neufeld JD, Driscoll BT, Knowles R, Archibald FS (2001) Quantifying functional gene populations: comparing gene abundance and corresponding enzymatic activity using deni-trification and nitrogen fixation in pulp and paper mill effluent treatment systems. Can J Microbiol 47:925–934

    Article  PubMed  CAS  Google Scholar 

  • Neufeld JD, Yu Z, Lam W, Mohn WW (2004a) SARST, serial analysis of ribosomal sequence tags. In: Kowalchuk GA, de Bruijn FJ, Head IM, Akkermans AD, van Elsas JD (eds) Molecular microbial ecology manual, 2nd edn. Kluwer, London, pp 543–568

    Google Scholar 

  • Neufeld JD, Yu Z, Lam W, Mohn WW (2004b) Serial analysis of ribosomal sequence tags (SARST): a high-throughput method for profiling complex microbial communities. Environ Microbiol 6:131–144

    Article  PubMed  CAS  Google Scholar 

  • Neufeld JD, Mohn WW, de Lorenzo V (2005) Composition of microbial communities in hexachlorocyclohexane (HCH) contaminated soils from Spain revealed with a habitat-specific microarray. Environ Microbiol (in press)

    Google Scholar 

  • Noll M, Matthies D, Frenzel P, Derakshani M, Liesack W (2005) Succession of bacterial community structure and diversity in a paddy soil oxygen gradient. Environ Microbiol 7:382–395

    Article  PubMed  CAS  Google Scholar 

  • Nübel U, Engelen B, Felske A, Snaidr J, Wieshuber A, Amann R, Ludwig W, Backhaus H (1996) Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J Bacteriol 178:5636–5643

    PubMed  Google Scholar 

  • Nübel U, Garcia-Pichel F, Kühl M, Muyzer G (1999a) Quantifying microbial diversity: morphotyoes, 16S rRNA genes, and carotenoids of oxygenic phototrophs in microbial mats. Appl Environ Microbiol 65:422–430

    PubMed  Google Scholar 

  • Nübel U, Garcia-Pichel F, Kühl M, Muyzer G (1999b) Spatial scale and the diversity of benthic cyanobacteria and diatoms in a salina. Hydrobiologia 401:199–206

    Article  Google Scholar 

  • Ogier J-C, 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

    Article  PubMed  CAS  Google Scholar 

  • Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR, Stahl DA (1986) Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol 40:337–365

    Article  PubMed  CAS  Google Scholar 

  • Orita M, Iwahana H, Kanazawa H, Hayashi K, Sekiya T (1989) Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc Natl Acad Sci USA 86:2766–2770

    Article  PubMed  CAS  Google Scholar 

  • Osborn AM, Moore ERB, 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 2:39–50

    Article  PubMed  CAS  Google Scholar 

  • Palleroni NJ (1997) Prokaryotic diversity and the importance of culturing. Antonie van Leeuwenhoek 72:3–19

    Article  PubMed  CAS  Google Scholar 

  • Palys T, Nakamura LK, Cohan FM (1997) Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data. Int J Syst Bacteriol 47:1145–1156

    Article  PubMed  CAS  Google Scholar 

  • Peixoto RS, da Costa Coutinho HL, Rumjanek NG, Macrae A, Rosado AS (2002) Use of rpoB and 16S rRNA genes to analyse bacterial diversity of a tropical soil using PCR and DGGE. Lett Appl Microbiol 35:316–320

    Article  PubMed  CAS  Google Scholar 

  • Peplies J, Glockner FO, Amann R (2003) Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes. Appl Environ Microbiol 69:1397–1407

    Article  PubMed  CAS  Google Scholar 

  • Peplies J, Lau SC, Pernthaler J, Amann R, Glockner FO (2004) Application and validation of DNA microarrays for the 16S rRNA-based analysis of marine bacterioplankton. Environ Microbiol 6:638–645

    Article  PubMed  CAS  Google Scholar 

  • Peters S, Koschinsky S, Schwieger F, Tebbe CC (2000) Succession of microbial communities during hot composting as detected by PCR-single-strand-conformation polymorphism-based genetic profiles of small-subunit rRNA genes. Appl Environ Microbiol 66:930–936

    Article  PubMed  CAS  Google Scholar 

  • Petersen DG, Dahllöf I (2005) Improvements for comparative analysis of changes in diversity of microbial communities using internal standards in PCR-DGGE. FEMS Microbiol Ecol 53:339–348

    Article  PubMed  CAS  Google Scholar 

  • Polz MF, Cavanaugh CM (1998) Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol 64:3724–3730

    PubMed  CAS  Google Scholar 

  • Porteous LA, Seidler RJ, Watrud LS (1997) An improved method for purifying DNA from soil for polymerase chain reaction amplification and molecular ecology applications. Mol Ecol 6:787–791

    Article  CAS  Google Scholar 

  • Powell SM, Bowman JP, Snape I, Stark JS (2003) Microbial community variation in pristine and polluted nearshore Antarctic sediments. FEMS Microbiol Ecol 45:135–145

    Article  PubMed  CAS  Google Scholar 

  • Qiu X, Wu L, Huang H, McDonel PE, Palumbo AV, Tiedje JM, Zhou J (2001) Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning. Appl Environ Microbiol 67:880–887

    Article  PubMed  CAS  Google Scholar 

  • Ragan MA (2001) Detection of lateral gene transfer among microbial genomes. Curr Opin Genet Dev 11:620–626

    Article  PubMed  CAS  Google Scholar 

  • Rainey FA, Ward N, Sly LI, Stackebrandt E (1994) Dependence on the taxon composition of clone libraries for PCR amplified, naturally occuring 16S rRNA, on the primer pair and the cloning system. Experientia 50:796–797

    Article  Google Scholar 

  • Ranjard L, Nazaret S, Gourbière F, Thioulouse J, Linet P, Richaume A (2000a) A soil mi-croscale study to reveal the heterogeneity of Hg(II) impact on indigenous bacteria by quantification of adapted phenotypes and analysis of community DNA fingerprints. FEMS Microbiol Ecol 31:107–115

    Article  PubMed  CAS  Google Scholar 

  • Ranjard L, Poly F, Nazaret S (2000b) Monitoring complex bacterial communities using culture-independent molecular techniques: application to soil environment. Res Microbiol 151:167–177

    Article  PubMed  CAS  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

    Article  PubMed  CAS  Google Scholar 

  • Ranjard L, Lejon DP, Mougel C, Schehrer L, Merdinoglu D, Chaussod R (2003) Sampling strategy in molecular microbial ecology: influence of soil sample size on DNA finger-printing analysis of fungal and bacterial communities. Environ Microbiol 5:1111–1120

    Article  PubMed  CAS  Google Scholar 

  • Rappé MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369–394

    Article  PubMed  CAS  Google Scholar 

  • Ravenschlag K, Sahm K, Pernthaler J, Amann R (1999) High bacterial diversity in perma-nently cold marine sediments. Appl Environ Microbiol 65:3982–3989

    PubMed  CAS  Google Scholar 

  • Reysenbach A-L, Giver LJ, Wickham GS, Pace NR (1992) Differential amplification of rRNA genes by polymerase chain reaction. Appl Environ Microbiol 58:3417–3418

    PubMed  CAS  Google Scholar 

  • Rhee SK, Liu X, Wu L, Chong SC, Wan X, Zhou J (2004) Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl Environ Microbiol 70:4303–4317

    Article  PubMed  CAS  Google Scholar 

  • Rochelle PA, Cragg BA, Fry JC, Parkes RJ, Weightman AJ (1994) Effect of sample handling on estimation of bacterial diversity in marine sediments by 16S rRNA gene sequence analysis. FEMS Microbiol Ecol 15:215–226

    Article  CAS  Google Scholar 

  • Rosenbaum V, Riesner D (1987) Temperature-gradient gel electrophoresis. Thermodynamic analysis of nucleic acids and proteins in purified form and in cellular extracts. Biophys Chem 26:235–246

    Article  PubMed  CAS  Google Scholar 

  • Rosenzweig M (1995) Species diversity in space and time. Cambridge University, Cambridge

    Book  Google Scholar 

  • Rossello-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67

    Article  PubMed  CAS  Google Scholar 

  • Rosswall T, Kvillner E (1978) Principal-components and factor analysis for the description of microbial populations. Adv Microb Ecol 2:1–48

    Google Scholar 

  • Ruijter JM, van Kampen AH, Baas F (2002) Statistical evaluation of SAGE libraries: consequences for experimental design. Physiol Genomics 11:37–44

    PubMed  CAS  Google Scholar 

  • Saiki RK, Scharf S, Faloona F, Mullis KB, Horn GT, Erlich HA, Amheim N (1985) Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230:1350–1354

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  Google Scholar 

  • Schloss PD, Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxanomic units and estimating species richness. Appl Environ Microbiol 71:1501–1506

    Article  PubMed  CAS  Google Scholar 

  • Schloss PD, Larget BR, Handelsman J (2004) Integration of microbial ecology and statistics: a test to compare gene libraries. Appl Environ Microbiol 70:5485–5492

    Article  PubMed  CAS  Google Scholar 

  • Schmalenberger A, Schwieger F, Tebbe CC (2001) Effect of primers hybridizing to different evolutionarily conserved regions of the small-subunit rRNA gene in PCR-based microbial community analyses and genetic profiling. Appl Environ Microbiol 67:3557–3563

    Article  PubMed  CAS  Google Scholar 

  • Schmidt TM (1997) Multiplicity of ribosomal RNA operons in prokaryotes. In: De Bruijn JF, Lupiski JR, Weinstock G (eds) Bacterial genomes: physical structure and analysis. Chapman and Hall, London, pp 221–229

    Google Scholar 

  • Schramm A, Fuchs BM, Nielsen JL, Tonolla M, Stahl DA (2002) Fluorescence in situ hybridization of 16S rRNA gene clones (clone-FISH) for probe validation and screening of clone libraries. Environ Microbiol 4:713–720

    Article  PubMed  CAS  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 64:4870–4876

    PubMed  CAS  Google Scholar 

  • Sebat JL, Colwell FS, Crawford RL (2003) Metagenomic profiling: microarray analysis of an environmental genomic library. Appl Environ Microbiol 69:4927–4934

    Article  PubMed  CAS  Google Scholar 

  • Seguritan V, Rohwer F (2001) FastGroup: a program to dereplicate libraries of 16S rDNA sequences. BMC Bioinform 2:9

    Article  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Shendure J, Mitra RD, Varma C, Church GM (2004) Advanced sequencing technologies: methods and goals. Nat Rev Genet 5:335–344

    Article  PubMed  CAS  Google Scholar 

  • Short SM, Suttle CA (1999) Use of the polymerase chain reaction and denaturing gradient gel electrophoresis to study diversity in natural virus communities. Hydrobiologia 401:19–33

    Article  CAS  Google Scholar 

  • Short SM, Suttle CA (2000) Denaturing gradient gel electrophoresis resolves virus sequences amplified with degenerate primers. Biotechniques 28:20–26

    PubMed  CAS  Google Scholar 

  • Sigler WV, Zeyer J (2002) Microbial diversity and activity along the forefields of two receding glaciers. Microb Ecol 43:397–407

    Article  PubMed  CAS  Google Scholar 

  • Sigler WV, Miniaci C, Zeyer J (2004) Electrophoresis time impacts the denaturing gradient gel electrophoresis-based assessment of bacterial community structure. J Microbiol Methods 57:17–22

    Article  PubMed  CAS  Google Scholar 

  • Singleton DR, Furlong MA, Rathbun SL, Whitman WB (2001) Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl Environ Microbiol 67:4374–4376

    Article  PubMed  CAS  Google Scholar 

  • Skirnisdottir S, Hreggvidsson GO, Hjorleifsdottir S, Marteinsson VT, Petursdottir SK, Hoist O, Kristjansson JK (2000) Influence of sulfide and temperature on species composition and community structure of hot spring microbial mats. Appl Environ Microbiol 66:2835–2841

    Article  PubMed  CAS  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

    Article  PubMed  CAS  Google Scholar 

  • Smith NR, Yu Z, Mohn WW (2003) Stability of the bacterial community in a pulp mill effluent treatment system during normal operation and a system shutdown. Water Res 37:4873–4884

    Article  PubMed  CAS  Google Scholar 

  • Snaidr J, Amann R, Huber I, Ludwig W, Schleifer K-H (1997) Phylogenetic analysis and in situ identification of bacteria in activated sludge. Appl Environ Microbiol 63:2884–2896

    PubMed  CAS  Google Scholar 

  • Snel B, Bork P, Huynen MA (1999) Genome phylogeny based on gene content. Nat Genet 21:108–110

    Article  PubMed  CAS  Google Scholar 

  • Stackebrandt E, Goebel B (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849

    Article  CAS  Google Scholar 

  • Stackebrandt E, Liesack W, Goebel BM (1993) Bacterial diversity in a soil sample from a subtropical Australian environment as determined by 16S rDNA analysis. FASEB J 7:232–236

    PubMed  CAS  Google Scholar 

  • Stackebrandt E, Frederiksen W, Garrity GM, Grimont P, Kampfer P, Maiden M, Nesme X, Rossello-Mora R, Swings J, Truper HG, Vauterin L, Ward AC, Whitman WB (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043–1047

    Article  PubMed  CAS  Google Scholar 

  • Stahl DA, Lane DJ, Olsen GJ, Pace NR (1985) Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences. Appl Environ Microbiol 49:1379–1384

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Stralis-Pavese N, Sessitsch A, Weilharter A, Reichenauer T, Riesing J, Csontos J, Murrell JC, Bodrossy L (2004) Optimization of diagnostic microarray for application in analyzing landfill methanotroph communities under different plant covers. Environ Microbiol 6:347–363

    Article  PubMed  CAS  Google Scholar 

  • Taroncher-Oldenburg G, Griner EM, Francis CA, Ward BB (2003) Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl Environ Microbiol 69:1159–1171

    Article  PubMed  CAS  Google Scholar 

  • Tekaia F, Lazcano A, Dujon B (1999) The genomic tree as revealed from whole proteome comparisons. Genome Res 9:550–557

    PubMed  CAS  Google Scholar 

  • Thompson JR, Marcelino LA, Polz MF (2002) Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by ‘reconditioning PCR’. Nucleic Acids Res 30:2083–2088

    Article  PubMed  CAS  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 13:109–122

    Article  Google Scholar 

  • Tilman D, Knops J, Wedin D, Reich P, Ritchie M, Siemann E (1997) The influence of functional diversity and composition on ecosystem processes. Science 277:1300–1302

    Article  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37–43

    Article  PubMed  CAS  Google Scholar 

  • Valinsky L, Delia Vedova G, Jiang T, Borneman J (2002a) Oligonucleotide fingerprinting of rRNA genes for analysis of fungal community composition. Appl Environ Microbiol 68:5999–6004

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Valinsky L, Scupham AJ, Vedova GD, Liu Z, Figueroa A, Jampachaisri K, Yin B, Bent E, Mancini-Jones R, Press J, Jiang T, Borneman J (2004) Oligonucleotide fingerprinting of ribosomal RNA genes (OFRG). In: Kowalchuk GA, de Bruijn FJ, Head IM, Akkermans AD, van Elsas JD (eds) Molecular microbial ecology manual, 2nd edn. Kluwer, London, pp 569–585

    Google Scholar 

  • Velculescu VE, Zhang L, Vogelstein B, Kinzler KW (1995) Serial analysis of gene expression. Science 270:484–487

    Article  PubMed  CAS  Google Scholar 

  • Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers Y-H, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso sea. Science 304:66–74

    Article  PubMed  CAS  Google Scholar 

  • Vergin KL, Urbach E, Stein JL, DeLong EF, Lanoil BD, Giovannoni SJ (1998) Screening of a fosmid library of marine environmental genomic DNA fragments reveals four clones related to members of the order Planctomycetales. Appl Environ Microbiol 64:3075–3078

    PubMed  CAS  Google Scholar 

  • von Wintzingerode F, Göbel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213–229

    Article  Google Scholar 

  • Wang G, Wang Y (1996) The frequency of chimeric molecules as a consequence of PCR co-amplification of 16S rRNA genes from different bacterial species. Microbiology 142:1107–1114

    Article  PubMed  CAS  Google Scholar 

  • Wang G, Wang Y (1997) Frequency of formation of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes. Appl Environ Microbiol 63:4645–4650

    PubMed  CAS  Google Scholar 

  • Wang M, Ahrne S, Antonsson M, Molin G (2004) T-RFLP combined with principal compo-nent analysis and 16S rRNA gene sequencing: an effective strategy for comparison of fecal microbiota in infants of different ages. J Microbiol Methods 59:53–69

    Article  PubMed  CAS  Google Scholar 

  • Wang Y, Zhang Z, Ramanan N (1997) The actinomycete Thermobispora bispora contains two distinct types of transcriptionally active 16S rRNA genes. J Bacteriol 179:3270–3276

    PubMed  CAS  Google Scholar 

  • Ward DM, Ferris MJ, Nold SC, Bateson MM (1998) A natural view of microbial biodiversity within hot spring cyanobacterial mat communities. Microbiol Mol Biol Rev 62:1353–1370

    PubMed  CAS  Google Scholar 

  • Watanabe K, Yamamoto S, Hino S, Harayama S (1998) Population dynamics of phenol-degrading bacteria in activated sludge determined by gyrB-targeted quantitative PCR. Appl Environ Microbiol 64:1203–1209

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Wilson KH, Wilson WJ, Radosevich JL, DeSantis TZ, Viswanathan VS, Kuczmarski TA, Andersen GL (2002) High-density microarray of small-subunit ribosomal DNA probes. Appl Environ Microbiol 68:2535–2541

    Article  PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Woese CR (2000) Interpreting the universal phylogenetic tree. Proc Natl Acad Sci USA 97:8392–8396

    Article  PubMed  CAS  Google Scholar 

  • Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74:5088–5090

    Article  PubMed  CAS  Google Scholar 

  • Woese CR, Stackebrandt E, Macke TJ, Fox GE (1985) A phylogenetic definition of the major eubacterial taxa. Syst Appl Microbiol 6:143–151

    PubMed  CAS  Google Scholar 

  • Woese CR, Kandler O, Wheeler ML (1990) Towards a natural system of organsims: Proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87:4576–4579

    Article  PubMed  CAS  Google Scholar 

  • Wu L, Thompson DK, Li G, Hurt RA, Tiedje JM, Zhou J (2001) Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl Environ Microbiol 67:5780–5790

    Article  PubMed  CAS  Google Scholar 

  • Xia X, Bollinger J, Ogram A (1995) Molecular genetic analysis of the response of three soil microbial communities to the application of 2,4-D. Mol Ecol 4:17–28

    Article  PubMed  CAS  Google Scholar 

  • Yannarell AC, Kent AD, Lauster GH, Kratz TK, Triplett EW (2003) Temporal patterns in bacterial communities in three temperate lakes of different trophic status. Microbial Ecol 46:391–405

    Article  CAS  Google Scholar 

  • Yap WH, Zhang Z, Wang Y (1999) Distinct types of rRNA operons exist in the genome of the actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon. J Bacteriol 181:5201–5209

    PubMed  CAS  Google Scholar 

  • Yin B, Valinsky L, Gao X, Becker JO, Borneman J (2003a) Bacterial rRNA genes associated with soil suppressiveness against the plant-parasitic nematode Heterodera schachtii. Appl Environ Microbiol 69:1573–1580

    Article  PubMed  CAS  Google Scholar 

  • Yin B, Valinsky L, Gao X, Becker JO, Borneman J (2003b) Identification of fungal rDNA associated with soil suppressiveness against Heterodera schachtii using oligonucleotide fingerprinting of ribosomal RNA genes. Phytopathology 93:1006–1013

    Article  PubMed  CAS  Google Scholar 

  • Yu Z, Mohn WW (2001) Bacterial diversity and community structure in an aerated lagoon revealed by ribosomal intergenic spacer analyses and 16S ribosomal DNA sequencing. Appl Environ Microbiol 67:1565–1574

    Article  PubMed  CAS  Google Scholar 

  • Yu Z, Morrison M (2004) Comparisons of different hypervariable regions of rrs genes for use in fingerprinting of microbial communities by PCR-denaturing gradient gel electrophoresis. Appl Environ Microbiol 70:4800–4806

    Article  PubMed  CAS  Google Scholar 

  • Yu Z, Yu M, Morrison M (2005) Improved serial analysis of V1 ribosomal sequence tags (SARST-V1) provides a rapid, comprehensive, sequence-based characterisation of bacterial diversity and community composition. Environ Microbiol (in press)

    Google Scholar 

  • Zhang X, Yan X, Gao P, Wang L, Zhou Z, Zhao L (2005) Optimized sequence retrieval from single bands of temperature gradient gel electrophoresis profiles of the amplified 16S rDNA fragments from an activated sludge system. J Microbiol Methods 60:1–11

    Article  PubMed  CAS  Google Scholar 

  • Zheng D, Alm EW, Stahl DA, Raskin L (1996) Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies. Appl Environ Microbiol 62:4504–4513

    PubMed  CAS  Google Scholar 

  • Zhou J, Davey ME, Figueras JB, Rivkina E, Gilichinsky D, Tiedje JM (1997) Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA. Microbiology 143:3913–3919

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Zhou J, Xia B, Treves DS, Wu LY, Marsh TL, O’Neill RV, Palumbo AV, Tiedje JM (2002) Spatial and resource factors influencing high microbial diversity in soil. Appl Environ Microbiol 68:326–334

    Article  PubMed  CAS  Google Scholar 

  • Zuckerkandl E, Pauling L (1965) Molecules as documents of evolutionary history. J Theor Biol 8:357–366

    Article  PubMed  CAS  Google Scholar 

  • Zumstein E, Moletta R, Godon JJ (2000) Examination of two years of community dynamics in an anaerobic bioreactor using fluorescence polymerase chain reaction (PCR) single-strand conformation polymorphism analysis. Environ Microbiol 2:69–78

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Biological Sciences, University of Warwick, Coventry, CV4 7AL, UK

    Josh D. Neufeld

  2. Department of Microbiology and Immunology, University of British Columbia, 300-6174

    William W. Mohn

  3. University Boulevard, Vancouver, British Columbia, V6T 1Z3, Canada

    William W. Mohn

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  1. DSMZ GmbH, Macheroder Weg 1b, 38124, Braunschweig, Germany

    Erko Stackebrandt

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Neufeld, J.D., Mohn, W.W. (2006). Assessment of Microbial Phylogenetic Diversity Based on Environmental Nucleic Acids. In: Stackebrandt, E. (eds) Molecular Identification, Systematics, and Population Structure of Prokaryotes. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-31292-5_7

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