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
Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity.
TL;DR: The results of this study suggest that caution should be used when interpreting rrn-based community analysis techniques, as techniques may underestimate diversity by grouping similar ribotypes or overestimate diversity by allowing multiple signals for one organism.
Book ChapterDOI
Molecular Evolution and Taxonomy of the Cyanobacteria
TL;DR: In the cyanobacteria, the use of molecular methods to study the genotypic relationships is underway, and initial results are promising and may be used to evaluate and revise existing classifications.
Journal ArticleDOI
Characterization of 16S rRNA Genes from Oil Field Microbial Communities Indicates the Presence of a Variety of Sulfate- Reducing, Fermentative, and Sulfide-Oxidizing Bacteria
TL;DR: A newly discovered sulfide oxidizer may provide a vital link in the oil field sulfur cycle by reoxidizing sulfide formed by microbial sulfate or sulfur reduction.
Journal ArticleDOI
Intraspecific Variation in Small-Subunit rRNA Sequences in GenBank: Why Single Sequences May Not Adequately Represent Prokaryotic Taxa
TL;DR: Unexpected high levels of intraspecific variation (within and between strains) of prokaryote SSU rRNA sequences deposited in GenBank are reported, and phylogenetic studies and biodiversity estimates obtained by using proKaryoticSSU r RNA sequences cannot proceed under the assumption that rRNA sequence of single operons from single isolates adequately represent their taxa.
Journal ArticleDOI
Analysis of bacterial communities in heavy metal-contaminated soils at different levels of resolution
TL;DR: DNA reassociation analysis indicated a dramatic decrease in bacterial diversity in soil bacterial communities studied in soils amended for many years with sewage sludge contaminated with heavy metals to varying extents, and shifts in populations of larger phylogenetic groups of bacteria were largely confirmed.
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.
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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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