MdRNA-Seq analysis of marine microbial communities from the northern Red Sea.
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ABSTRACT:
SUBMITTER: Hou S
PROVIDER: S-EPMC5069720 | biostudies-literature | 2016 Oct
REPOSITORIES: biostudies-literature
Publications
mdRNA-Seq analysis of marine microbial communities from the northern Red Sea.
Hou Shengwei S Pfreundt Ulrike U Miller Dan D Berman-Frank Ilana I Hess Wolfgang R WR
Scientific reports 20161019
Metatranscriptomic differential RNA-Seq (mdRNA-Seq) identifies the suite of active transcriptional start sites at single-nucleotide resolution through enrichment of primary transcript 5' ends. Here we analyzed the microbial community at 45 m depth at Station A in the northern Gulf of Aqaba, Red Sea, during 500 m deep mixing in February 2012 using mdRNA-Seq and a parallel classical RNA-Seq approach. We identified promoters active in situ for five different pico-planktonic genera (the SAR11 clade ...[more]
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Project description:Microarrays are useful tools for detecting and quantifying specific functional and phylogenetic genes in natural microbial communities. In order to track uncultivated microbial genotypes and their close relatives in an environmental context, we designed and implemented a âgenome proxyâ microarray that targets microbial genome fragments recovered directly from the environment. Fragments consisted of sequenced clones from large-insert genomic libraries from microbial communities in Monterey Bay, the Hawaii Ocean Time-series station ALOHA, and Antarctic coastal waters. In a prototype array, we designed probe sets to thirteen of the sequenced genome fragments and to genomic regions of the cultivated cyanobacterium Prochlorococcus MED4. Each probe set consisted of multiple 70-mers, each targeting an individual ORF, and distributed along each ~40-160kbp contiguous genomic region. 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