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
Prokaryotic and viral diversity patterns in marine plankton
TL;DR: Recent advances in bacterial and virus diversity studies are summarized, examples of measurements from polar, tropical, and temperate marine waters are presented, and some distinct differences with depth are presented.
Journal ArticleDOI
Shifts in archaeal communities associated with lithological and geochemical variations in subsurface Cretaceous rock
Ken Takai,Melanie R. Mormile,James P. McKinley,Fred J. Brockman,William E. Holben,William P. Kovacik,James K. Fredrickson +6 more
TL;DR: Results indicated that active, phylogenetically diversearchaeal communities were present in the subsurface Cretaceous rock environment at this site and that major archaeal clades shifted dramatically over scales of tens of centimetres, corresponding to changes in the lithology and geochemical gradients.
Book ChapterDOI
Microbial disease causation in marine invertebrates: problems, practices, and future prospects
TL;DR: A set of nucleic acid sequence-based approaches for establishing microbial disease causation in marine invertebrates is outlined that can be used in collaboration with traditional culture-based and histopathological methods to build a compelling case for microbial disease correlation.
Journal ArticleDOI
Sequence analysis of 16S rRNA gene of cyanobacteria associated with the marine sponge Mycale (Carmia) hentscheli
TL;DR: The phylogenetic analysis indicated the presence of four closely related clones which have a high sequence divergence from known cyanobacteria, Cyanobacterium stanieri being the closest, followed by Prochloron sp.
Book ChapterDOI
Use of the polymerase chain reaction and denaturing gradient gel electrophoresis to study diversity in natural virus communities
Steven M. Short,Curtis A. Suttle +1 more
TL;DR: An overview of how PCR and DGGE can be used to examine diversity in natural viral communities drawing on viruses that infect phytoplankton as an example is provided.
References
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DNA sequencing with chain-terminating inhibitors
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Journal ArticleDOI
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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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