title: mdRNA-Seq analysis of marine microbial communities from the northern Red Sea.
abstract: 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 of Alphaproteobacteria, Synechococcus of Cyanobacteria, Euryarchaeota, Thaumarchaeota, and Micromonas as an example for picoeukaryotic algae), showing the applicability of this approach to highly diverse microbial communities. 16S rDNA quantification revealed that 24% of the analyzed community were group II marine Euryarchaeota in which we identified a highly abundant non-coding RNA, Tan1, and detected very high expression of genes encoding intrinsically disordered proteins, as well as enzymes for the synthesis of specific B vitamins, extracellular peptidases, carbohydrate-active enzymes, and transport systems. These results highlight previously unknown functions of Euryarchaeota with community-wide relevance. The complementation of metatranscriptomic studies with mdRNA-Seq provides substantial additional information regarding transcriptional start sites, promoter activities, and the identification of non-coding RNAs.
authors.affiliation: Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.
authors.forename: Shengwei
authors.initials: S
authors.lastname: Hou
authors.affiliation: Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Pfreundt
authors.affiliation: Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel.
authors.forename: Dan
authors.initials: D
authors.lastname: Miller
authors.affiliation: Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel.
authors.forename: Ilana
authors.initials: I
authors.lastname: Berman-Frank
authors.affiliation: Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.
authors.forename: Wolfgang R
authors.initials: WR
authors.lastname: Hess
mesh_terms: D059001:Aquatic Organisms; D044822:Biodiversity; D004777:Environment; D005786:Gene Expression Regulation; D059014:High-Throughput Nucleotide Sequencing; D054892:Metagenome; D056186:Metagenomics / Q000379:methods; D064307:Microbiota; D009690:Nucleic Acid Conformation; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D058928:Riboswitch / Q000235:genetics; D012623:Seawater / Q000382:microbiology*; D059467:Transcriptome; D014871:Water Microbiology
chemical_list: D012336:RNA, Ribosomal, 16S; D058928:Riboswitch