Marine DNA/RNA samples from Western English Channel site L4

Sampling

Marine DNA/RNA samples from Western English Channel site L4. The seasonal structure of microbial communities in the Western English Channel - 2007 Here we present a multi-omic study of the Bacterial and Archaeal diversity found at the L4 long-term marine observatory. We have previously generated a six year time series from L4 that showed that the bacterial community shows strong seasonal structuring and diversity peaks every year on the winter solstice. Here we further confirm this pattern by extending this study to include genes and transcripts generated for eight additional time points in 2008. This data includes further 16S datasets as well as eight metagenomes (1.2GB) and eight metatranscriptomes (157MB). These time points cover three seasons (Jan, April and August) and include day and night (diel) samples. In addition, the August samples (4) include 4 consecutive samplings within 24 hours at six hour intervals. Using these data we test whether Archaea also show the same observed seasonal patterns and whether these patterns hold true at the gene (functional) level. Analysis of this combined data set allows five main conclusions to be drawn. First, Archaea show evidence of following the same seasonal patterns as Bacteria, but have ~6% the richness. Second, for both Bacteria and Archaea, we confirm that higher 16S diversity reflects higher diversity at the gene-level (including expressed genes) and this diversity also peaks at the winter solstice. Third, interestingly, detectable diversity appears to be higher at night, and this is of special potential relevance as there is more diversity in winter when nights are longer. Fourth, despite the diversity of these communities, night and day samples taken using Lagrangian (drift) sampling were successful in isolating the same community suggesting communities are more structured than is commonly believed. Finally, this data, as expected, contains a large proportion of orphan genes without known homologues. When compared to the housekeeping genes identified through SEED subsystem classification, these unknown genes appear to be driving the differences between samples across seasons. This underscores the importance of determining the functions of more of these sequences in the future. In summary, this study further confirms the strong seasonal patterns characterizing both the bacterial and archaeal communities at this important marine site. The finding that, despite the huge diversity of these communities, there are evident signs of predictable patterns and detectable stability over time provides compelling evidence that renewed efforts should

Method steps

1. Pipeline used: https://www.ebi.ac.uk/metagenomics/pipelines/4.1