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Extraction and Amplification of 16S rRNA Genes from Deep Marine Sediments and Seawater to Assess Bacterial Community Diversity

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Nucleic Acids in the Environment

Part of the book series: Springer Lab Manuals ((SLM))

Abstract

Deep marine sediments remain poorly studied with respect to bacterial communities inhabiting them. Sediments up to 500 m below the sea floor (mbsf) in the Japan Sea have been laid down over the last 3 million years and therefore represent the early stages of sediment diagenesis. These sediments contain substantial bacterial populations (1.1 × 107 to 1.4 × 109 bacteria/g wet weight) with surprisingly high activity (Cragg et al. 1992; Getliff et al. 1992). Better knowledge of the types and diversity of bacteria which are dominant in these sediments, particularly those predominantly involved in important biogeochemical and biochemical processes, will lead to increased understanding of the diagenesis and evolution of organic matter. This unique habitat might also contain bacteria not found elsewhere in the biosphere.

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References

  • Ash C, Farrow JAE, Wallbanks S, Collins MD (1991) Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small subunit ribosomal RNA sequences. Lett Appl Microbiol 13: 202–206

    Article  Google Scholar 

  • Bakken LR, Olsen RA (1989) DNA content of soil bacteria of different cell size. Soil Biol Biochem 21: 789–793

    Article  Google Scholar 

  • Benson D, Lipman DJ, Ostell J (1993) GenBank. Nucleic Acids Res 21: 2963–2965

    Article  Google Scholar 

  • Birnboim HC, Doly J (1979) A rapid alkaline extraction procedure for screening recombinant Plasmid DNA. Nucleic Acids Res 7: 1513–1523

    Article  Google Scholar 

  • Britschgi TB, Giovannoni SJ (1991) Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing. Appl Environ Microbiol 57: 1707–1713

    Google Scholar 

  • Cragg BA, Harvey FM, Fry JC, Herbert RA, Parkes RJ (1992) Bacterial biomass and activity in deep sediment layers of the Japan Sea. In: Pisciotto K (ed) Proc Ocean Drilling Prog Scientific Results, vol 128. US Government Printing Office, Washington, USA

    Google Scholar 

  • Dunning AM, TalmundP, Humphries, S (1988) Errors in the polymerase chain reaction. Nucleic Acids Res 16: 10393

    Google Scholar 

  • Fitch WM, Margoliash E (1967) Construction of phylogenetic trees. Science 155: 279–284

    Article  Google Scholar 

  • Fry JC (1990) Direct methods and biomass estimation. In: Grigorova R, Norris JR (eds) Methods Microbiol 22: pp 41–85

    Google Scholar 

  • Fuhrman JA, McCallum K, Davis AA (1992) Novel major archaebacterial group from marine plankton. Nature 356: 148–149

    Article  Google Scholar 

  • Fuhrman JA, McCallum K, Davis AA (1993) Phylogenetic diversity of subsurface marine microbial communities of the Atlantic and Pacific Oceans. Appl Environ Microbiol 59: 1294–1302

    Google Scholar 

  • Furrer B, Candrian U, Wieland P, Luthy J (1990) Improving PCR efficiency. Nature 346: 324

    Article  Google Scholar 

  • Getliff JM, Fry JC, Cragg BA, Parkes RJ (1992) The potential for growth in deep sediment layers of the Japan Sea, Hole 798B-Leg 128. In: Pisciotto K (ed) Proc Ocean Drilling Prog Scientific Results, vol 128. US Government Printing Office, Washington, USA

    Google Scholar 

  • Giovannoni SJ (1991) The polymerase chain reaction. In: Stackebrandt, E. and Goodfellow, M. (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp. 177–203

    Google Scholar 

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

    Google Scholar 

  • Hagelberg E, Sykes B, Hedges R (1989) Ancient bone DNA amplified. Nature 342: 485

    Article  Google Scholar 

  • Holben WE, Jansson JK, Chelm BK, Tiedje JM (1988) DNA probe method for the detection of specific microorganisms in the soil bacterial community. Appl Environ Microbiol 54: 703–711

    Google Scholar 

  • Ingraham JL, Maaloe O, Neidhardt FC (1983) Growth of the bacterial cell. Sinauer Associates, Sunderland, USA

    Google Scholar 

  • Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism, Academic, New York, pp 21–132

    Google Scholar 

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

    Google Scholar 

  • Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics, Wiley, Chichester, pp 115–175

    Google Scholar 

  • Liesack W, Weyland H, Stackebrandt E (1991) Potential risks of gene amplification by PCR as determined by 16S analysis of a mixed-culture of strict barophilic bacteria. Microb Ecol 21: 191–198

    Article  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

    Google Scholar 

  • Mead DA, Pey NK, Hermstadt C, Marcil RA, Smith LM (1991) A universal method for the direct cloning of PCR amplified nucleic acid. Biotechnology 9: 657–663

    Article  Google Scholar 

  • Meier A, Persing DH, Finken M, Bottger EC (1993) Elimination of contaminating DNA within Polymerase Chain Reaction reagents: implications for a general approach to detection of uncultured pathogens. J Clin Microbiol 31: 646–652

    Google Scholar 

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

    Google Scholar 

  • Ogram A, Sayler GS, Barkay T (1987) The extraction and purification of microbial DNA from sediments. J Microbiol Method 7: 57–66

    Article  Google Scholar 

  • Pace NR, Stahl DA, Lane DJ, Olsen GJ (1986) The analysis of natural microbial populations by ribosomal RNA sequences. Adv Microb Ecol 9: 1–55

    Google Scholar 

  • Parkes RJ, Cragg BA, Fry JC, Herbert RA, Wimpenny JWT (1990) Bacterial biomass and activity in deep sediment layers from the Peru margin. Phil Trans R Soc Lond 133: 139–153

    Article  Google Scholar 

  • Rochelle PA, Fry JC, Parkes RJ, Weightman AJ (1992a) DNA extraction for 16S rRNA gene analysis to determine genetic diversity in deep sediment communities. FEMS Microb Lett 100: 59 - 66

    Google Scholar 

  • Rochelle PA, Weightman AJ, Fry JC (1992b) DNasel treatment of Taq DNA polymerase for complete PCR decontamination. Biotechniques 13: 520

    Google Scholar 

  • Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239: 487–491

    Article  Google Scholar 

  • Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning. Cold Spring Harbor Laboratory, Cold Spring Harbor, USA

    Google Scholar 

  • Sarkar G, Sommer SS (1990) Shedding light on PCR contamination. Nature 343: 27

    Article  Google Scholar 

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

    Google Scholar 

  • Schmidt TM, Pace B, Pace NR (1991b) Detection of DNA contamination in Taq polymerase. Biotechniques 11: 176–177

    Google Scholar 

  • Selenska S, Klingmüller W (1991) DNA recovery and direct detection of Tn5 sequences in soil. Lett Appl Microb 13: 21–24

    Article  Google Scholar 

  • Smalla K, Cresswell N, Mendonca-Hagler LC, Wolters A, van Elsas JD (1993) Rapid DNA extraction protocol from soil for polymerase chain reaction mediated amplification. J Appl Bacteriol 74: 78–85

    Article  Google Scholar 

  • Steffan RJ, Goksoyr J, Bej AK, Atlas RM (1988) Recovery of DNA from soils and sediments. Appl Environ Microbiol 54: 2908–2915

    Google Scholar 

  • Steffan RJ, Atlas RJ (1991) Polymerase chain reaction: applications in environmental microbiology. Annu Rev Microbiol 45: 137–161

    Article  Google Scholar 

  • Trevors JT (1992) DNA extraction from soil. Microbial Releases 1: 3–9

    Google Scholar 

  • Tsai YL, Olson BH (1991) Rapid method for direct extraction of DNA from soil and sediments. Appl Environ Microbiol 57: 1070–1074

    Google Scholar 

  • Tsai YL, Olson BH (1992) Rapid method for separation of bacterial DNA for humie substances in sediments for polymerase chain reaction. Appl Environ Microbiol 58: 2292–2295

    Google Scholar 

  • Weller R, Ward DM (1989) Selective recovery of 16S rRNA sequences from natural microbial communities in the form of cDNA. Appl Environ Microbiol 55: 1818–1822

    Google Scholar 

  • Weller R, Bateson MM, Heimbuch BK, Kopezynski ED, Ward DM (1992) Uncultivated cyanobacteria, ehloroflexus-like inhabitants, and spirochete-like inhabitants of a hot spring microbial mat. Appl Environ Microbiol 58: 3964–3969

    Google Scholar 

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

    Google Scholar 

  • Young CC, Burghoff RL, Keim LG, Minak-Bernero V, Lute JR, Hinton SM (1993) Polyvinyl pyrrolidone-agarose gel electrophoresis purification of polymerase chain reaction-amplifiable DNA from soils. Appl Environ Microbiol 59: 1972–1974

    Google Scholar 

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Authors
  1. P. A. Rochelle
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  2. J. A. K. Will
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  3. J. C. Fry
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  4. G. J. S. Jenkins
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  5. R. J. Parkes
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  6. C. M. Turley
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  7. A. J. Weightman
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Editor information

Editors and Affiliations

  1. Department of Environmental Biology, University of Guelph Lab. Microbial Techniques, N1G 2W1, Guelph, Ontario, Canada

    Jack T. Trevors

  2. DLO-Institute for Soil Fertility Research c/o IPO-DLO, Binnenhaven 12, P.O. Box 9060, 6700 GW, Wageningen, The Netherlands

    J. Dick van Elsas

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© 1995 Springer-Verlag Berlin Heidelberg

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Rochelle, P.A. et al. (1995). Extraction and Amplification of 16S rRNA Genes from Deep Marine Sediments and Seawater to Assess Bacterial Community Diversity. In: Trevors, J.T., van Elsas, J.D. (eds) Nucleic Acids in the Environment. Springer Lab Manuals. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-79050-8_11

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  • DOI: https://doi.org/10.1007/978-3-642-79050-8_11

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-58069-0

  • Online ISBN: 978-3-642-79050-8

  • eBook Packages: Springer Book Archive

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