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Appl Environ Microbiol. Sep 1997; 63(9): 3367–3373.
PMCID: PMC168642

Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA.

Abstract

The community structure of bacterioplankton in meromictic Lake Saelenvannet was examined by PCR amplification of the V3 region of 16S rRNA from microbial communities recovered from various depths in the water column. Two different primer sets were used, one for amplification of DNA from the domain Bacteria and another specific for DNA from the domain Archaea. Amplified DNA fragments were resolved by denaturing gradient gel electrophoresis (DGGE), and the resulting profiles were reproducible and specific for the communities from different depths. Bacterial diversity estimated from the number and intensity of specific fragments in DGGE profiles decreased with depth. The reverse was true for the Archaea, with the diversity increasing with depth. Hybridization of DGGE profiles with oligonucleotide probes specific for phylogenetic groups of microorganisms showed the presence of both sulfate-reducing bacteria and methanogens throughout the water column, but they appeared to be most abundant below the chemocline. Several dominant fragments in the DGGE profiles were excised and sequenced. Among the dominant populations were representatives related to Chlorobium phaeovibrioides, chloroplasts from eukaryotic algae, and unidentified Archaea.

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Selected References

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  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. [PubMed]
  • Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol. 1990 Jun;56(6):1919–1925. [PMC free article] [PubMed]
  • Amann RI, Stromley J, Devereux R, Key R, Stahl DA. Molecular and microscopic identification of sulfate-reducing bacteria in multispecies biofilms. Appl Environ Microbiol. 1992 Feb;58(2):614–623. [PMC free article] [PubMed]
  • DeLong EF. Archaea in coastal marine environments. Proc Natl Acad Sci U S A. 1992 Jun 15;89(12):5685–5689. [PMC free article] [PubMed]
  • DeLong EF, Wickham GS, Pace NR. Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science. 1989 Mar 10;243(4896):1360–1363. [PubMed]
  • DeLong EF, Wu KY, Prézelin BB, Jovine RV. High abundance of Archaea in Antarctic marine picoplankton. Nature. 1994 Oct 20;371(6499):695–697. [PubMed]
  • Ferris MJ, Muyzer G, Ward DM. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl Environ Microbiol. 1996 Feb;62(2):340–346. [PMC free article] [PubMed]
  • Fuhrman JA, McCallum K, Davis AA. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Appl Environ Microbiol. 1993 May;59(5):1294–1302. [PMC free article] [PubMed]
  • Giovannoni SJ, Britschgi TB, Moyer CL, Field KG. Genetic diversity in Sargasso Sea bacterioplankton. Nature. 1990 May 3;345(6270):60–63. [PubMed]
  • Ludwig W, Dorn S, Springer N, Kirchhof G, Schleifer KH. PCR-based preparation of 23S rRNA-targeted group-specific polynucleotide probes. Appl Environ Microbiol. 1994 Sep;60(9):3236–3244. [PMC free article] [PubMed]
  • Murray AE, Hollibaugh JT, Orrego C. Phylogenetic compositions of bacterioplankton from two California estuaries compared by denaturing gradient gel electrophoresis of 16S rDNA fragments. Appl Environ Microbiol. 1996 Jul;62(7):2676–2680. [PMC free article] [PubMed]
  • Muyzer G, de Waal EC, Uitterlinden AG. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol. 1993 Mar;59(3):695–700. [PMC free article] [PubMed]
  • Myers RM, Maniatis T, Lerman LS. Detection and localization of single base changes by denaturing gradient gel electrophoresis. Methods Enzymol. 1987;155:501–527. [PubMed]
  • Ramsing NB, Fossing H, Ferdelman TG, Andersen F, Thamdrup B. Distribution of bacterial populations in a stratified fjord (Mariager Fjord, Denmark) quantified by in situ hybridization and related to chemical gradients in the water column. Appl Environ Microbiol. 1996 Apr;62(4):1391–1404. [PMC free article] [PubMed]
  • Reysenbach AL, Giver LJ, Wickham GS, Pace NR. Differential amplification of rRNA genes by polymerase chain reaction. Appl Environ Microbiol. 1992 Oct;58(10):3417–3418. [PMC free article] [PubMed]
  • Rölleke S, Muyzer G, Wawer C, Wanner G, Lubitz W. Identification of bacteria in a biodegraded wall painting by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microbiol. 1996 Jun;62(6):2059–2065. [PMC free article] [PubMed]
  • Suzuki MT, Giovannoni SJ. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol. 1996 Feb;62(2):625–630. [PMC free article] [PubMed]
  • Teske A, Wawer C, Muyzer G, Ramsing NB. Distribution of sulfate-reducing bacteria in a stratified fjord (Mariager Fjord, Denmark) as evaluated by most-probable-number counts and denaturing gradient gel electrophoresis of PCR-amplified ribosomal DNA fragments. Appl Environ Microbiol. 1996 Apr;62(4):1405–1415. [PMC free article] [PubMed]
  • Tuomi P, Torsvik T, Heldal M, Bratbak G. Bacterial population dynamics in a meromictic lake. Appl Environ Microbiol. 1997 Jun;63(6):2181–2188. [PMC free article] [PubMed]
  • Ward DM, Weller R, Bateson MM. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature. 1990 May 3;345(6270):63–65. [PubMed]
  • Wawer C, Rüggeberg H, Meyer G, Muyzer G. A simple and rapid electrophoresis method to detect sequence variation in PCR-amplified DNA fragments. Nucleic Acids Res. 1995 Dec 11;23(23):4928–4929. [PMC free article] [PubMed]
  • Weidner S, Arnold W, Puhler A. Diversity of uncultured microorganisms associated with the seagrass Halophila stipulacea estimated by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes. Appl Environ Microbiol. 1996 Mar;62(3):766–771. [PMC free article] [PubMed]

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