Journal ArticleDOI
Genetic diversity in Sargasso Sea bacterioplankton.
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TLDR
The phylogenetically analysed clone libraries of eubacterial 16S ribosomal RNA genes amplified from natural populations of Sargasso Sea picoplankton indicate the presence of a novel microbial group, the SAR 11 cluster, which appears to be a significant component of this oligotrophic bacterioplankton community.Abstract:
BACTERIOPLANKTON are recognized as important agents of biogeochemical change in marine ecosystems, yet relatively little is known about the species that make up these communities. Uncertainties about the genetic structure and diversity of natural bacterioplankton populations stem from the traditional difficulties associated with microbial cultivation techniques. Discrepancies between direct counts and plate counts are typically several orders of magnitude, raising doubts as to whether cultivated marine bacteria are actually representative of dominant planktonic species1–3. We have phylogenetically analysed clone libraries of eubacterial 16S ribosomal RNA genes amplified from natural populations of Sargasso Sea picoplankton by the polymerase chain reaction4. The analysis indicates the presence of a novel microbial group, the SAR 11 cluster, which appears to be a significant component of this oligotrophic bacterioplankton community. A second cluster of lineages related to the oxygenic phototrophs—cyanobacteria, prochlorophytes and chloroplasts—was also observed. However, none of the genes matched the small subunit rRNA sequences of cultivated marine cyanobacteria from similar habitats. The diversity of 16S rRNA genes observed within the clusters suggests that these bacterioplankton may be consortia of independent lineages sharing surprisingly distant common ancestors.read more
Citations
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Journal ArticleDOI
High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences
Kevin L. Vergin,Bank Beszteri,Adam Monier,J. Cameron Thrash,Ben Temperton,Alexander H. Treusch,Alexander H. Treusch,Fabian Kilpert,Alexandra Z. Worden,Stephen J. Giovannoni +9 more
TL;DR: The high-resolution phylogenetic analyses performed herein highlight significant, previously unknown, patterns of evolutionary diversification, within perhaps the most widely distributed heterotrophic marine bacterial clade, and strongly links to ecosystem regimes.
Journal ArticleDOI
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
TL;DR: It was brought to the attention of the authors that a more extensive treatment of the hydrodynamics of Mariager Fjord and the vertical distribution of bacteria and protozoa therein was published in a recent article by Fenchel et al., but the existence of this work was realized only after publication of this article.
Journal ArticleDOI
Polyphasic Analyses of Methanogenic Archaeal Communities in Agricultural Biogas Plants
Edith Nettmann,Edith Nettmann,Ingo Bergmann,Ingo Bergmann,S. Pramschüfer,S. Pramschüfer,Kerstin Mundt,V. Plogsties,Christiane Herrmann,Christiane Herrmann,Michael Klocke +10 more
TL;DR: Results point to hydrogenotrophic methanogenesis as a predominant pathway for methane synthesis in five of the six analyzed biogas plants.
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Geomicrobiology of Pyrite (FeS2) Dissolution: Case Study at Iron Mountain, California
Katrina J. Edwards,Brett M. Goebel,Teresa M. Rodgers,Matthew O. Schrenk,Thomas M. Gihring,Margarita M. Cardona,Molly M. McGuire,Robert J. Hamers,Norman R. Pace,Jillian F. Banfield +9 more
TL;DR: Geomicrobiology of pyrite weathering at Iron Mountain, CA, was investigated by molecular biological, surface chemical, surface structural, and solution chemical methods in both laboratory and field-based studies.
Journal ArticleDOI
Microbial diversity in marine sediments from Sagami Bay and Tokyo Bay, Japan, as determined by 16S rRNA gene analysis
TL;DR: Although the depths of SB and TK were very different, the community diversity inferred from ARDRA and the taxonomic position of the dominant clones were similar, indicating that the microbial diversity of SA was higher than at the other two stations.
References
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Journal ArticleDOI
DNA sequencing with chain-terminating inhibitors
TL;DR: A new method for determining nucleotide sequences in DNA is described, which makes use of the 2',3'-dideoxy and arabinon nucleoside analogues of the normal deoxynucleoside triphosphates, which act as specific chain-terminating inhibitors of DNA polymerase.
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Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase
Randall Keichi Saiki,David H. Gelfand,Susanne Stoffel,Stephen J. Scharf,Russell Higuchi,Glenn Thomas Horn,Kary B. Mullis,Henry A. Erlich +7 more
TL;DR: A thermostable DNA polymerase was used in an in vitro DNA amplification procedure, the polymerase chain reaction, which significantly improves the specificity, yield, sensitivity, and length of products that can be amplified.
Journal ArticleDOI
Site-directed mutagenesis by overlap extension using the polymerase chain reaction.
TL;DR: In this paper, complementary oligodeoxyribonucleotide (oligo) primers and the polymerase chain reaction are used to generate two DNA fragments having overlapping ends, and these fragments are combined in a subsequent 'fusion' reaction in which the overlapping ends anneal, allowing the 3' overlap of each strand to serve as a primer for the three' extension of the complementary strand.
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