MdRNA-Seq analysis of marine microbial communities from the northern Red Sea

Shengwei Hou, Ulrike Pfreundt, Dan Miller, Ilana Berman-Frank, Wolfgang R. Hess

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Article number35470
JournalScientific Reports
Volume6
DOIs
StatePublished - 19 Oct 2016
Externally publishedYes

Bibliographical note

Funding Information:
This work was supported by the Association of European Marine Biological Laboratories Infrastructure Access Call 5 to the Interuniversity Institute for Marine Sciences, Eilat, Israel, by a BMBF and the Israel Ministry of Science and Technology Joint German-Israeli Research 03F0640A/GR2378 to WRH and IBF and by the EU project MaCuMBA (grant no. 311975) to WRH. The financial support to SWH by China Scholarship Council is gratefully acknowledged. For help at sea we thank Noga Stambler, Bar-Ilan University, Martin Hagemann, University of Rostock, and especially the captain and crew of the R/V "Sam Rothberg" and the IUI logistics team.

Publisher Copyright:
© The Author(s) 2016.

ASJC Scopus subject areas

  • General

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