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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Raman-activated cell sorting and metagenomic sequencing revealing carbon-fixing bacteria in the ocean.
Xiaoyan Jing,Honglei Gou,Yanhai Gong,Xiaolu Su,La Xu,Yuetong Ji,Yizhi Song,Ian P. Thompson,Jian Xu,Wei E. Huang +9 more
TL;DR: It is shown that mini-metagenomic sequences from RACE can be used as a reference to reconstruct nearly complete genomes of key functional bacteria by binning shotgun metagenomic sequencing data and genetic analysis of the reconstructed genomes suggests that both Synechococcus and Pelagibacter spp.
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Detection and characterization of cyanobacterial nifH genes.
TL;DR: The DNA sequence of a 359-bp fragment of nifH was determined for the heterocystous strains Anabaena sp.
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Spatially differing bacterial communities in water columns of the northern Baltic Sea
TL;DR: The diversity and community structure of the northern Baltic Sea bacterial communities in the water column were thoroughly studied by 454 sequencing, finding that the spring and autumn bacterial communities were one order of magnitude less diverse than those in recently studied oceanic habitats.
Journal ArticleDOI
Depth variation of bacterial extracellular enzyme activity and population diversity in the northeastern North Atlantic Ocean
Katherine E Davey,Katherine E Davey,Richard R. Kirby,Carol Turley,Andrew J. Weightman,John C. Fry +5 more
TL;DR: Observations indicate clear stratification of bacterial associated extracellular enzyme activity, with the maximum activity in surface waters, consistent with some environmental changes in the water column, especially algal biomass and nitrate concentration.
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Stable Isotope Probing:Linking Functional Activity to Specific Members of Microbial Communities
TL;DR: An overview of the lipid and nucleic acid approaches is provided, discusses their strengths and weaknesses, gives examples of applications in various settings, and looks at prospects for the future of SIP technology.
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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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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