Dataset Information

Metagenomes and metatranscriptomes from the L4 long-term coastal monitoring station in the Western English Channel.

ABSTRACT: Both metagenomic data and metatranscriptomic data were collected from surface water (0-2m) of the L4 sampling station (50.2518 N, 4.2089 W), which is part of the Western Channel Observatory long-term coastal-marine monitoring station. We previously generated from this area a six-year time series of 16S rRNA V6 data, which demonstrated robust seasonal structure for the bacterial community, with diversity correlated with day length. Here we describe the features of these metagenomes and metatranscriptomes. We generated 8 metagenomes (4.5 million sequences, 1.9 Gbp, average read-length 350 bp) and 7 metatranscriptomes (392,632 putative mRNA-derived sequences, 159 Mbp, average read-length 272 bp) for eight time-points sampled in 2008. These time points represent three seasons (winter, spring, and summer) and include both day and night samples. These data demonstrate the major differences between genetic potential and actuality, whereby genomes follow general seasonal trends yet with surprisingly little change in the functional potential over time; transcripts tended to be far more structured by changes occurring between day and night.

SUBMITTER: Gilbert JA

PROVIDER: S-EPMC3035373 | biostudies-literature | 2010 Oct

REPOSITORIES: biostudies-literature

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Metagenomes and metatranscriptomes from the L4 long-term coastal monitoring station in the Western English Channel.

Gilbert Jack A JA Meyer Folker F Schriml Lynn L Joint Ian R IR Mühling Martin M Field Dawn D

Standards in genomic sciences 20101027 2

Both metagenomic data and metatranscriptomic data were collected from surface water (0-2m) of the L4 sampling station (50.2518 N, 4.2089 W), which is part of the Western Channel Observatory long-term coastal-marine monitoring station. We previously generated from this area a six-year time series of 16S rRNA V6 data, which demonstrated robust seasonal structure for the bacterial community, with diversity correlated with day length. Here we describe the features of these metagenomes and metatransc ...[more]

PMID: 21304748

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Project description:The abundance of bacterial (AOB) and archaeal (AOA) ammonia oxidisers, assessed using quantitative PCR measurements of their respective a-subunit of the ammonia monooxygenase (amoA) genes, and ammonia oxidation rates were measured in four contrasting coastal sediments in the Western English Channel. Sediment was sampled bimonthly from July 2008 to May 2011, and measurements of ammonia oxidiser abundance and activity compared to a range of environmental variables including salinity, temperature, water column nutrients and sediment carbon and nitrogen content. Despite a higher abundance of AOA amoA genes within all sediments, and at all time-points, rates of ammonia oxidation correlated with AOB and not AOA amoA gene abundance. Other than ammonia oxidation rate, sediment particle size was the only variable that correlated with the spatial and temporal patterns of AOB amoA gene abundance, implying a preference of the AOB for larger sediment particles. This is possibly due to deeper oxygen penetration into the sandier sediments, increasing the area available for ammonia oxidation to occur, higher concentrations of inhibitory sulphide with pore waters of muddier sediments or a combination of both oxygen and sulphide concentrations. Similar to many other temporal studies of nitrification within estuarine and coastal sediments, decreases in AOB amoA gene abundance were evident during summer and autumn, with maximum abundance and ammonia oxidation rates occurring in winter and early spring. The lack of correlation between AOA amoA gene abundance and ammonium oxidation rate suggests an alternative role for amoAÂ-carrying AOA within these sediments. Two color array (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype). Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array. Signal is the ratio of Cy3 to Cy5. Three replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.

Dataset Information

Metagenomes and metatranscriptomes from the L4 long-term coastal monitoring station in the Western English Channel.

Publications

Metagenomes and metatranscriptomes from the L4 long-term coastal monitoring station in the Western English Channel.

Similar Datasets

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