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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Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
TL;DR: Analysis of the genomic DNA from a bacterial biofilm grown under aerobic conditions suggests that sulfate-reducing bacteria, despite their anaerobicity, were present in this environment.
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Phylogenetic identification and in situ detection of individual microbial cells without cultivation.
TL;DR: Phylogenetic analysis of the retrieved rRNA sequence of an uncultured microorganism reveals its closest culturable relatives and may, together with information on the physicochemical conditions of its natural habitat, facilitate more directed cultivation attempts.
Journal ArticleDOI
Microbial diversity in the deep sea and the underexplored “rare biosphere”
Mitchell L. Sogin,Hilary G. Morrison,Julie A. Huber,David B. Mark Welch,Susan M. Huse,Phillip R. Neal,Jesús M. Arrieta,Gerhard J. Herndl +7 more
TL;DR: It is shown that bacterial communities of deep water masses of the North Atlantic and diffuse flow hydrothermal vents are one to two orders of magnitude more complex than previously reported for any microbial environment.
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Gut Microbiota in Health and Disease
TL;DR: The advances in modeling and analysis of gut microbiota will further the authors' knowledge of their role in health and disease, allowing customization of existing and future therapeutic and prophylactic modalities.
Journal ArticleDOI
Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA.
TL;DR: Computer-simulated analysis of terminal restriction fragment length polymorphisms (T-RFLP) for 1,002 eubacterial sequences showed that with proper selection of PCR primers and restriction enzymes, 686 sequences could be PCR amplified and classified into 233 unique terminal restriction fragments lengths or "ribotypes."
References
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Journal ArticleDOI
Bacterial Populations in Sea Water as Determined by Different Methods of Enumeration1
Journal ArticleDOI
On the stochastic model for estimation of mutational distance between homologous proteins
Motoo Kimura,Tomoko Ohta +1 more
TL;DR: A set of simple equations is derived which gives the relationship between the observed amino acid differences per 100 codons and the evolutionary distance per 100codons using Holmquist's stochastic model of molecular evolution.
Journal ArticleDOI
The annual cycle of primary production in the Sargasso Sea off Bermuda
David W. Menzel,John H. Ryther +1 more
TL;DR: Gross and net primary production have been measured at bi-weekly intervals for 18 months in the Northwestern Sargasso Sea 15 miles SE of Bermuda in 1500 fm of water.
Journal ArticleDOI
Contribution of bacteria to standing crop of coastal plankton1
TL;DR: Water samples were collected from coastal waters near Cape Lookout, N.C., during March 1975 for direct count of bacteria and for adenosine triphosphate (ATP) analysis as mentioned in this paper.
Book ChapterDOI
Phylogenetic analysis using ribosomal RNA.
TL;DR: The discussion that follows is directed toward analyses based on rRNA sequences, but nearly all of the concepts, and many of the details, are equally applicable to the other DNA, RNA, or protein sequences.
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