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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How Many Species?: Discussion
Robert M. May,R. J. H. Beverton +1 more
TL;DR: In this paper, a survey of the patterns in discovering and recording species of animals and plants, from Linnaeus' time to the present, is presented, along with various approaches to estimating what the total number of species on Earth might be: these approaches include extrapolation of past trends; direct assessments based on the overall fraction previously recorded among newly studied groups of tropical insects; indirect assessment derived from recent studies of arthropods in the canopies of tropical trees.
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Selective detection, enumeration and identification of potentially probiotic Lactobacillus and Bifidobacterium species in mixed bacterial populations.
TL;DR: The combined use of differential plating and molecular strain typing methodologies provides food and medical microbiologists with a powerful and targeted approach to the detection, enumeration and identification of these bacterial groups and their members in a wide range of food and biological materials.
Journal ArticleDOI
Estimation of the Abundance of an Uncultured Soil Bacterial Strain by a Competitive Quantitative PCR Method
TL;DR: The number of EA25 16S rRNA genes was estimated to be 2.17 x 10(8) copies per g of soil, suggesting that strains similar to EA25 and the similar Australian strain could be widely distributed and present in significant numbers in soils from temperate regions.
Journal ArticleDOI
Contribution of SAR11 bacteria to dissolved dimethylsulfoniopropionate and amino acid uptake in the North Atlantic ocean.
TL;DR: The contribution of SAR11 bacteria to amino acid assimilation was greater than would be expected based on their overall abundance, implying that SAR11acteria outcompete other prokaryotes for these labile compounds.
Structural rna homology search and alignment using covariance models
Sean R. Eddy,Eric P. Nawrocki +1 more
TL;DR: Improvements are made to Covariance models by making them faster and more sensitive to remote homology, and introducing a query-dependent banding technique that makes scoring sequences more efficient by restricting the possible lengths of structural elements based on their probability given the model.
References
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DNA sequencing with chain-terminating inhibitors
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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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