Journal ArticleDOI
Genetic diversity in Sargasso Sea bacterioplankton.
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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Book ChapterDOI
Molecular Approaches to Microbial Biomass Estimation in the Sea
David M. Karl,Fred C. Dobbs +1 more
TL;DR: The marine environment is composed of several distinct ecosystems including high-latitude (polar) zones, midlatitude open-ocean gyres, equatorial upwelling systems and a diverse assemblage of coastal habitats (e.g. continental shelves, bays, coral reefs, mudflats and estuaries).
Journal ArticleDOI
Viral and bacterial assemblage covariance in oligotrophic waters of the West Florida Shelf (Gulf of Mexico)
TL;DR: These cultivation-independent observations demonstrate relationships between viral and bacterial assemblages, which are dynamic in patches of open ocean water, and support the idea that viruses may influence the species composition of hostassemblages.
Journal ArticleDOI
Linking bacterial community structure to carbon fluxes in marine environments
Taichi Yokokawa,Toshi Nagata +1 more
TL;DR: A survey of approaches used to assess variation in and factors controlling bacterial communities in marine environments, emphasizing the importance of quantitative studies that examine growth and grazing parameters of bacterial subgroups as mentioned in this paper.
Journal ArticleDOI
Utilization of iron/organic ligand complexes by marine bacterioplankton
TL;DR: Fe uptake by cultures of gamma and alpha marine proteobacteria grown under Fe-replete and Fe-limited conditions, and by natural bacterio- plankton communities from the Sargasso Sea and California upwelling region, observed variable degrees of Fe availability relative to ligand structure in natural communities.
Journal ArticleDOI
Fingerprinting of mixed bacterial strains and BIOLOG gram-negative (GN) substrate communities by enterobacterial repetitive intergenic consensus sequence-PCR (ERIC-PCR).
TL;DR: It is suggested that ERIC-PCR represents a rapid and highly discriminating method for fingerprinting DNA of mixed Gram-negative bacterial strains and BIOLOG GN substrate communities.
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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