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Search: WFRF:(Pommier Thomas) > (2005-2009)

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  • Pommier, Thomas, et al. (author)
  • Global patterns of diversity and community structure in marine bacterioplankton
  • 2007
  • In: Molecular Ecology. - : Blackwell Publishing Ltd. - 0962-1083 .- 1365-294X. ; 16:4, s. 867-880
  • Journal article (peer-reviewed)abstract
    • Because of their small size, great abundance and easy dispersal, it is often assumed that marine planktonic microorganisms have a ubiquitous distribution that prevents any structured assembly into local communities. To challenge this view, marine bacterioplankton communities from coastal waters at nine locations distributed world-wide were examined through the use of comprehensive clone libraries of 16S ribosomal RNA genes, used as operational taxonomic units (OTU). Our survey and analyses show that there were marked differences in the composition and richness of OTUs between locations. Remarkably, the global marine bacterioplankton community showed a high degree of endemism, and conversely included few cosmopolitan OTUs. Our data were consistent with a latitudinal gradient of OTU richness. We observed a positive relationship between the relative OTU abundances and their range of occupation, i.e. cosmopolitans had the largest population sizes. Although OTU richness differed among locations, the distributions of the major taxonomic groups represented in the communities were analogous, and all local communities were similarly structured and dominated by a few OTUs showing variable taxonomic affiliations. The observed patterns of OTU richness indicate that similar evolutionary and ecological processes structured the communities. We conclude that marine bacterioplankton share many of the biogeographical and macroecological features of macroscopic organisms. The general processes behind those patterns are likely to be comparable across taxa and major global biomes.
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3.
  • Pommier, Thomas, et al. (author)
  • RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities
  • 2009
  • In: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1460-2059. ; 25:6, s. 736-742
  • Journal article (peer-reviewed)abstract
    • Motivation: The most common approach to estimate microbial diversity is based on the analysis of DNA sequences of specific target genes including ribosomal genes. Commonly, the sequences are grouped into operational taxonomic units based on genetic distance (sequence similarity) instead of genetic change (patristic distance). This method may fail to adequately identify clusters of evolutionary related sequences and it provides no information on the phylogenetic structure of the community. An ease-of-use web application for this purpose has been missing. Results: We have developed RAMI, which clusters related nodes in a phylogenetic tree based on the patristic distance. RAMI also produces indices of cluster properties and other indices used in population and community studies on-the-fly.
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