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| Gobet, Angelique; Boeer, Simone I.; Huse, Susan M.; Van Beusekom, Justus E. E.; Quince, Christopher; Sogin, Mitchell L.; Boetius, Antje; Ramette, Alban. |
| Coastal sands filter and accumulate organic and inorganic materials from the terrestrial and marine environment, and thus provide a high diversity of microbial niches. Sands of temperate climate zones represent a temporally and spatially highly dynamic marine environment characterized by strong physical mixing and seasonal variation. Yet little is known about the temporal fluctuations of resident and rare members of bacterial communities in this environment. By combining community fingerprinting via pyrosequencing of ribosomal genes with the characterization of multiple environmental parameters, we disentangled the effects of seasonality, environmental heterogeneity, sediment depth and biogeochemical gradients on the fluctuations of bacterial communities... |
| Tipo: Text |
Palavras-chave: 454 pyrosequencing; Coastal seas; Bacterial diversity; Multivariate analysis; Rare biosphere. |
| Ano: 2012 |
URL: https://archimer.ifremer.fr/doc/00488/59947/63192.pdf |
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| Gobet, Angelique; Boetius, Antje; Ramette, Alban. |
| Changes in richness and bacterial community structure obtained via 454 Massively Parallel Tag Sequencing (MPTS) and Automated Ribosomal Intergenic Analysis (ARISA) were systematically compared to determine whether and how the ecological knowledge obtained from both molecular techniques could be combined. We evaluated community changes over time and depth in marine coastal sands at different levels of taxonomic resolutions, sequence corrections and sequence abundances. Although richness over depth layers or sampling dates greatly varied [approximate to 30% and 70-80% new operational taxonomic units (OTU) between two samples with ARISA and MPTS respectively], overall patterns of community variations were similar with both approaches. Alpha-diversity... |
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| Ano: 2014 |
URL: https://archimer.ifremer.fr/doc/00488/59943/63180.pdf |
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| Gobet, Angelique; Quince, Christopher; Ramette, Alban. |
| High-throughput sequencing techniques are becoming attractive to molecular biologists and ecologists as they provide a time- and cost-effective way to explore diversity patterns in environmental samples at an unprecedented resolution. An issue common to many studies is the definition of what fractions of a data set should be considered as rare or dominant. Yet this question has neither been satisfactorily addressed, nor is the impact of such definition on data set structure and interpretation been fully evaluated. Here we propose a strategy, MultiCoLA (Multivariate Cutoff Level Analysis), to systematically assess the impact of various abundance or rarity cutoff levels on the resulting data set structure and on the consistency of the further ecological... |
| Tipo: Text |
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| Ano: 2010 |
URL: https://archimer.ifremer.fr/doc/00488/59949/63199.pdf |
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