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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Evaluation of Nearest-Neighbor Methods for Detection of Chimeric Small-Subunit rRNA Sequences
TL;DR: A naive statistical test based on CHECK_CHIMERA output is developed and it suggests that chimeras might be formed by retrieving SSU rRNAs as cDNA, and the amount of uncertainty associated with nearest-neighbor analyses indicates that such tests alone are insufficient and that better methods are needed.
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Ribosomal DNA sequence analysis of mucosa-associated bacteria in Crohn's disease
TL;DR: These findings suggest that CD is not caused by invasive pathogens associated specifically with the sites of lesions but that dysbiosis exists in this condition.
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Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter
William D. Orsi,Jason M. Smith,Heather M. Wilcox,Jarred E. Swalwell,Paul Carini,Alexandra Z. Worden,Alyson E. Santoro +6 more
TL;DR: The hypothesis that a widely distributed and uncultivated microbial group—the marine group II euryarchaea (MGII)—interacts with living and detrital particulate organic matter (POM) in the euphotic zone of the central California Current System is investigated, implying that marine archaea have a role in elemental cycling through interactions with particles.
Journal ArticleDOI
Phylogenetic diversity, composition and distribution of bacterioplankton community in the Dongjiang River, China
TL;DR: In this paper, the Dongjiang River was characterized using denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone library construction, and the results showed that the bacterial species distribution strongly correlated with environmental variables, such as nitrate and ammonia, suggesting that nitrogen nutrients may shape the microbial community structure and composition.
References
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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.
Journal ArticleDOI
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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