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
Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton
TL;DR: ITS sequences confirmed the close intragroup relationships among members of the SAR11, SAR116 and SAR86 clades that were predicted by SSU and LSU rDNA sequence analyses and found strong support for homologous recombination between the ITS regions of operons from the SAR 11 clade.
Journal ArticleDOI
Novel bacterial lineages at the (sub)division level as detected by signature nucleotide-targeted recovery of 16S rRNA genes from bulk soil and rice roots of flooded rice microcosms.
TL;DR: The results indicate the presence of bacterial diversity at a subdivision and/or division level that has not been detected previously by the so-called universal 16S rDNA PCR assays.
Journal ArticleDOI
Molecular phylogenetic analysis of a soil microbial community in a soybean field
T Ueda,Y. Suga,T. Matsuguchi +2 more
TL;DR: The phylogenetic characterization of small subunit rRNA gene sequences obtained by polymerase chain reaction (PCR) amplification of mixed population DNA extracted directly from soil in a soybean field without culturing the organisms suggests a global distribution of this archaeal group.
Journal ArticleDOI
Microdiversity of uncultured marine prokaryotes: the SAR11 cluster and the marine Archaea of Group I.
TL;DR: The results show that although depth‐related factors seem to be predominant in the final associations of the clones, geography also plays a significant role and a major group of surface‐associated sequences was found in both SAR11 and marine Archaea.
Journal ArticleDOI
Loss of Bacterial Diversity during Antibiotic Treatment of Intubated Patients Colonized with Pseudomonas aeruginosa
Judith Flanagan,Eoin L. Brodie,L. Weng,Susan V. Lynch,Oscar Garcia,Ronald T. Brown,Philip Hugenholtz,Todd Z. DeSantis,Gary L. Andersen,Jeanine P. Wiener-Kronish,James Bristow +10 more
TL;DR: In this article, the authors analyzed bacterial diversity in endotracheal aspirates obtained from intubated patients colonized by Pseudomonas aeruginosa by using 16S rRNA clone libraries and microarrays (PhyloChip) to determine changes in bacterial community compositions during antibiotic treatment.
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.
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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