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The Microbial Soil Flora: Novel Approaches for Accessing the Phylogenetic and Physiological Diversity of Prokaryotes

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Intestinal Microorganisms of Termites and Other Invertebrates

Part of the book series: Soil Biology ((SOILBIOL,volume 6))

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References

  • Adamczyk J, Hesselsoe M, Iversen N, Horn M, Lehner A, Nielsen PH, Schloter M, Roslev P, Wagner M (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: 6875–6887

    Article  PubMed  CAS  Google Scholar 

  • Amann RI, Lin C, Key R, Montgomery L, Stahl DA (1992) Diversity among fibrobacter isolates: towards a phylogenetic classification. Syst Appl Microbiol 15: 23–31

    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, 148–149

    PubMed  CAS  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: 1731–1737

    PubMed  CAS  Google Scholar 

  • Beja O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP, Jovanovich SB, Gates CM, Feldman RA, Spudich JL, Spudich EN, DeLong EF (2000) Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289: 1902–1906

    Article  PubMed  CAS  Google Scholar 

  • Beja O, Spudich EN, Spudich JL, Leclerc M, DeLong EF (2001) Proteorhodopsin phototrophy in the ocean. Nature 411: 786–789

    PubMed  CAS  Google Scholar 

  • Bintrim SB, Donohue TJ, Handelsman J, Roberts GP, Goodman RM (1997) Molecular phylogeny of Archaea from soil. Proc Natl Acad Sci U S A 94: 277–282

    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 

  • Burgmann H, Widmer F, Sigler WV, Zeyer J (2003) mRNA extraction and reverse transcription-PCR protocol for detection of nifH gene expression by Azotobacter vinelandii in soil. Appl Environ Microbiol 69: 1928–1935

    Article  PubMed  CAS  Google Scholar 

  • Chakravarti A (1999) Population genetics-making sense out of sequence. Nat Genet 21: 56–60

    Article  PubMed  CAS  Google Scholar 

  • Chin KJ, Hahn D, Hengstmann U, Liesack W, Janssen PH (1999) Characterization and identification of numerically abundant culturable bacteria from the anoxic bulk soil of rice paddy microcosms. Appl Environ Microbiol 65: 5042–5049

    PubMed  CAS  Google Scholar 

  • Cho JC, Tiedje JM (2001) Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays. Appl Environ Microbiol 67: 3677–3682

    Article  PubMed  CAS  Google Scholar 

  • Courtois S, Cappellano CM, Ball M, Francou FX, Normand P, Helynck G, Martinez A, Kolvek SJ, Hopke J, Osburne MS, August PR, Nalin R, Guerineau M, Jeannin P, Simonet P, Pernodet JL (2003) Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products. Appl Environ Microbiol 69: 49–55

    Article  PubMed  CAS  Google Scholar 

  • DeLong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci U S A 89: 5685–5689

    PubMed  CAS  Google Scholar 

  • DSMZ (2004) Bacterial Nomenclature Up-to-date [http://www.dsmz.de/bactnom/bactname.htm].

    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 

  • Eilers H, Pernthaler J, Amann R (2000) Succession of pelagic marine bacteria during enrichment: a close look at cultivation-induced shifts. Appl Environ Microbiol 66: 4634–4640

    PubMed  CAS  Google Scholar 

  • Ferguson RL, Buckley EN, Palumbo AV (1984) Response of marine bacterioplankton to differential filtration and confinement. Appl Environ Microbiol 47: 49–55

    PubMed  CAS  Google Scholar 

  • Fischer SG, Lerman LS (1983) DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: correspondence with melting theory. Proc Natl Acad Sci U S A 80: 1579–1583

    PubMed  CAS  Google Scholar 

  • Fogel GB, Collins CR, Li J, Brunk CF (1999) Prokaryotic Genome Size and SSU rDNA Copy Number: Estimation of Microbial Relative Abundance from a Mixed Population. Microb Ecol 38: 93–113

    Article  PubMed  CAS  Google Scholar 

  • Garcia-Martinez J, Acinas SG, Anton AI, Rodriguez-Valera F (1999) Use of the 16S–23S ribosomal genes spacer region in studies of prokaryotic diversity. J Microbiol Methods 36: 55–64

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Heuer H, Krsek M, Baker P, Smalla K, Wellington EM (1997) Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl Environ Microbiol 63: 3233–3241

    PubMed  CAS  Google Scholar 

  • Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO (2002) A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417: 63–67

    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 

  • 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 

  • Kaeberlein T, Lewis K, Epstein SS (2002) Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science 296: 1127–1129

    Article  PubMed  CAS  Google Scholar 

  • Krsek M, Wellington EM (1999) Comparison of different methods for the isolation and purification of total community DNA from soil. J Microbiol Methods 39: 1–16

    Article  PubMed  CAS  Google Scholar 

  • Lee KY, Wahl, R., and Barbu, E. (1956) Contenu en bases purique et pyrimidiques des acides deoxyribonucleiques des bacteries. Ann Inst Pasteur 91: 212–224

    CAS  Google Scholar 

  • Liesack W, Schnell S, Revsbech NP (2000) Microbiology of flooded rice paddies. FEMS Microbiol Rev 24: 625–645

    Article  PubMed  CAS  Google Scholar 

  • Ludwig W (1999) http://www.mikrobiologie.tu-muenchen.de/pub/ARB, Department of Microbiology, TU-München, Munich.

    Google Scholar 

  • Ludwig W, Strunk O, Klugbauer S, Klugbauer N, Weizenegger M, Neumaier J, Bachleitner M, Schleifer KH (1998) Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19: 554–568

    Article  PubMed  CAS  Google Scholar 

  • Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar Buchner A, Lai T, Steppi S, Jobb G, Forster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, König, A, Liss T, Lussmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A and Schleifer KH (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363–71

    Article  PubMed  CAS  Google Scholar 

  • Man D, Wang W, Sabehi G, Aravind L, Post AF, Massana R, Spudich EN, Spudich JL, Beja O (2003) Diversification and spectral tuning in marine proteorhodopsins. Embo J 22: 1725–1731

    Article  PubMed  CAS  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: 5367–5373

    Article  PubMed  CAS  Google Scholar 

  • Miller DN, Bryant JE, Madsen EL, Ghiorse WC (1999) Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl Environ Microbiol 65: 4715–4724

    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 

  • Mylvaganam S, Dennis PP (1992) Sequence heterogeneity between the two genes encoding 16S rRNA from the halophilic archaebacterium Haloarcula marismortui. Genetics 130: 399–410

    PubMed  CAS  Google Scholar 

  • Nubel U, Engelen B, Felske A, Snaidr J, Wieshuber A, Amann RI, 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  CAS  Google Scholar 

  • Ochsenreiter T, Selezi D, Quaiser A, Bonch-Osmolovskaya L, Schleper C (2003) Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR. Environ Microbiol 5: 787–797

    Article  PubMed  CAS  Google Scholar 

  • Okano Y, Hristova KR, Leutenegger CM, Jackson LE, Denison RF, Gebreyesus B, Lebauer D, Scow KM (2004) Application of real-time PCR to study effects of ammonium on population size of ammonia-oxidizing bacteria in soil. Appl Environ Microbiol 70: 1008–1016

    Article  PubMed  CAS  Google Scholar 

  • Ovreas L, Torsvik VV (1998) Microbial diversity and community structure in two different agricultural soil communities. Microb Ecol 36: 303–315

    PubMed  CAS  Google Scholar 

  • Perez Luz S, Rodriguez-Valera F, Lan R, Reeves PR (1998) Variation of the ribosomal operon 16S–23S gene spacer region in representatives of Salmonella enterica subspecies. J Bacteriol 180: 2144–2151

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  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

    Article  PubMed  CAS  Google Scholar 

  • Rösch C, Mergel A, Bothe H (2002) Biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil. Appl Environ Microbiol 68: 3818–3829

    PubMed  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Sait M, Hugenholtz P, Janssen PH (2002) Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ Microbiol 4: 654–666

    Article  PubMed  CAS  Google Scholar 

  • Salama N, Guillemin K, McDaniel TK, Sherlock G, Tompkins L, Falkow S (2000) A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc Natl Acad Sci U S A 97: 14668–14673

    Article  PubMed  CAS  Google Scholar 

  • Schleper C, Jurgens G, Jonuscheit M (2005) Genomic Studies of uncultivated archaea. Nat Rev Microbiol: 3(6): 479–88

    Article  PubMed  CAS  Google Scholar 

  • Schleper C, DeLong EF, Preston CM, Feldman RA, Wu KY, Swanson RV (1998) Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosum. J Bacteriol 180: 5003–5009

    PubMed  CAS  Google Scholar 

  • Schleper C, Holben W, Klenk HP (1997) Recovery of crenarchaeotal ribosomal DNA sequences from freshwater-lake sediments. Appl Environ Microbiol 63: 321–323

    PubMed  CAS  Google Scholar 

  • Smit E, Leeflang P, Gommans S, van den Broek J, van Mil S, Wernars K (2001) Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Appl Environ Microbiol 67: 2284–2291

    Article  PubMed  CAS  Google Scholar 

  • Stackebrandt E, and Goebel, B.M. (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

    CAS  Google Scholar 

  • Stein JL, Marsh TL, Wu KY, Shizuya H, DeLong EF (1996) Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J Bacteriol 178: 591–599

    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 

  • Tebbe CC, Vahjen W (1993) Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast. Appl Environ Microbiol 59: 2657–2665

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Torsvik V, Salte K, Sorheim R, Goksoyr J (1990b) Comparison of phenotypic diversity and DNA heterogeneity in a population of soil bacteria. Appl Environ Microbiol 56: 776–781

    PubMed  CAS  Google Scholar 

  • Torsvik V, Sorheim R, Goksoyr J (1996) Total bacterial diversity in soil and sediment communities-a review. J Ind Microbiol 17: 170–178

    CAS  Google Scholar 

  • Treusch AH, Leininger S, Kletzin A, Schuster S, Klenk HP, Schleper C (2005) Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenardaeota in nitrogen cycling. Environ Microbiol: in press

    Google Scholar 

  • Treusch AH, Kletzin A, Raddatz G, Ochsenreiter T, Quaiser A, Meurer G, Schuster SC, Schleper C (2004) Characterization of Large-Insert DNA Libraries from Soil for Environmental Genomic Studies of Archaea. Environ Microbiol. 6(9): 970–80

    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 

  • 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 YH, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66–74

    Article  PubMed  CAS  Google Scholar 

  • Wayne LG e.a. (1987) Report of the Ad Hoc Committee on reconciliation of approaches to Bacterial Systematics. Int J Syst Bacteriol 37: 463–464

    Article  Google Scholar 

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

    PubMed  CAS  Google Scholar 

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

    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

    PubMed  CAS  Google Scholar 

  • Zengler K, Toledo G, Rappe M, Elkins J, Mathur EJ, Short JM, Keller M (2002) Cultivating the uncultured. Proc Natl Acad Sci U S A 99: 15681–15686

    Article  PubMed  CAS  Google Scholar 

  • Zhou J, Bruns MA, Tiedje JM (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62: 316–322

    PubMed  CAS  Google Scholar 

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Author notes

  1. Christa Schleper

    Present address: Departement of Biology, University of Bergen, Jalmebakken 5, N-5020, Bergen, Norway

Authors and Affiliations

  1. Institut für Mikrobiologie und Genetik, Darmstadt University of Technology, Schnittspahnstr. 10, 64287, Darmstadt, Germany

    Alexander H. Treusch & Christa Schleper

Authors
  1. Alexander H. Treusch
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  2. Christa Schleper
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Editors and Affiliations

  1. Institute of Microbiology and Wine Research, Johannes Gutenberg University, 55099, Mainz, Germany

    Helmut König

  2. Amity School of Herbal and Microbial Studies Sector 125, New Super Express Highway, Noida, 201303, UP, India

    Ajit Varma (Director) (Director)

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Treusch, A.H., Schleper, C. (2006). The Microbial Soil Flora: Novel Approaches for Accessing the Phylogenetic and Physiological Diversity of Prokaryotes. In: König, H., Varma, A. (eds) Intestinal Microorganisms of Termites and Other Invertebrates. Soil Biology, vol 6. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-28185-1_17

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