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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DNA Sequencing as a Tool to Monitor Marine Ecological Status
Kelly D. Goodwin,Luke R. Thompson,Luke R. Thompson,Bernardo Duarte,Tim Kahlke,Andrew R. Thompson,João Carlos Marques,Isabel Caçador +7 more
TL;DR: DNA sequencing of bioindicators promises to improve assessment of marine biological quality by increasing the breadth, depth, and throughput of information and by reducing costs and reliance on specialized taxonomic expertise.
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Prevalence and microdiversity of Alteromonas macleodii-like microorganisms in different oceanic regions.
TL;DR: Analysis of the ribosomal ITS (16S-23S internal transcribed spacers) revealed that A. macleodii-like microorganisms are present in high proportions in North Atlantic and, especially, Mediterranean waters, being higher at deep samples and particle-associated fractions, in agreement with previous findings.
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Evidence for Circumpolar Distribution of Planktonic Archaea in the Southern Ocean
TL;DR: The hypothesis that planktonic archaea are a common, widespread and likely ecologically important component of Antarctic picoplankton assemblages is supported.
The most conserved genome segments for life detection on Earth and other planets (Supplemental material)
Gary Ruvkun,Maria T. Zuber,Walter Gilbert,George M. Church,Michael Finney,Sarah Stewart Johnson,Christopher E. Carr,Thomas A. Isenbarger +7 more
TL;DR: In this paper, the 16S and 23S ribosomal RNA genes as well as other universally conserved nucleotide sequences in genes encoding particular classes of transfer RNAs and within the nucleotide binding domains of ABC transporters are identified as the most conserved DNA sequence segments across phylogeny.
Book ChapterDOI
Microbial Diversity in Oceanic Systems: rRNA Approaches to the Study of Unculturable Microbes
TL;DR: A standard method for enumerating marine bacteria from a water sample is to grow them on nutrient plates and count colonies, but in low nutrient aquatic habitats the number of bacterial colonies that can be grown using standard plating methods is frequently from one to four orders of magnitude fewer than the number observed by direct microscopic count.
References
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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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