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Genome Streamlining in a Cosmopolitan Oceanic Bacterium
P. ubique, the first cultured member of the SAR11 clade, has the smallest genome and encodes the smallest number of predicted open reading frames known for a free-living microorganism.
SAR11 clade dominates ocean surface bacterioplankton communities
Quantitative measurements of the cellular abundance of the SAR11 clade in northwestern Sargasso Sea waters to 3,000 m and in Oregon coastal surface waters support the conclusion that this microbial group is among the most successful organisms on Earth.
Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR
Three rRNA gene standards were prepared by PCR, mixed in known proportions, and amplified a second time by using primer pairs in which one primer was labeled with a fluorescent nucleotide derivative to fit a kinetic model in which the reannealing of genes progressively inhibits the formation of template-primer hybrids.
Genetic diversity in Sargasso Sea bacterioplankton
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.
The uncultured microbial majority.
Genome sequence information that would allow ribosomal RNA gene trees to be related to broader patterns in microbial genome evolution is scant, and therefore microbial diversity remains largely unexplored territory.
Cultivation of the ubiquitous SAR11 marine bacterioplankton clade
The isolation of representatives of the SAR11 clade is reported, which indicates that diverse uncultivated microbial taxa dominate most natural ecosystems, which has prompted widespread efforts to elucidate the geochemical activities of these organisms without the benefit of cultures for study.
Kinetic Bias in Estimates of Coastal Picoplankton Community Structure Obtained by Measurements of Small-Subunit rRNA Gene PCR Amplicon Length Heterogeneity
- Marcelino T. Suzuki, M. Rappé, S. Giovannoni
- BiologyApplied and Environmental Microbiology
- 1 November 1998
The analysis revealed that the relative frequencies of genes amplified from natural communities are highly reproducible for replicate sets of PCRs but that a bias possibly caused by the reannealing kinetics of product molecules can skew gene frequencies when PCR product concentrations exceed threshold values.
Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial cells
Examination of collections of 16S rRNA sequences revealed sequence domains that were unique to (and invariant within) the three primary lines of cellular descent: the archaebacteria, the eubacteria,…
Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals
Profiles of the phospholipid ester-linked fatty acids indicated that both the anaerobic desaturase and the branched pathways for fatty acid biosynthesis were operative, and the 16S rRNA sequence indicated that this organism belongs in the delta proteobacteria.
Implications of streamlining theory for microbial ecology
Streamlining theory is belied by the observation that many successful bacteria are large cells with complex genomes, which means that to fully appreciate streamlining, the authors must look to the life histories and adaptive strategies of cells, which impose minimum requirements for complexity that vary with niche.