Depth dependent metatranscriptomes of the marine pico-/nanoplanktonic communities in the Gulf of Aqaba/Eilat during seasonal deep mixing

Ulrike Pfreundt, Dan Miller, Lakshmi Adusumilli, Noga Stambler, Ilana Berman-Frank, Wolfgang R. Hess

Research output: Contribution to journalArticlepeer-review


Metatranscriptomics is a widely used approach to study the gene expression within a whole microbial community. Spatial or temporal differences observed between datasets point to transcriptional responses to changes or alterations in the community's environment. No transcriptomic data has yet been published from the oligotrophic Gulf of Aqaba/Eilat, northern Red Sea. The primary objective of this study was to create a depth-specific snapshot of community gene expression ranging from the surface waters to the bottom of the mixed-layer depth during winter when thermal destratification occurs. Our secondary objective was to compare two different methods for transcriptome analysis. While random RNA sequencing (RNA-seq) is routinely used, differential RNA sequencing (dRNA-seq, enriched in primary transcripts) has never been used for metatranscriptomics. In this dataset, we used dRNA-seq for samples that were collected from three depths while applying RNA-seq for one of the samples to obtain direct comparison between the methods. We de-novo assembled the reads into contigs and show a high percentage of reads mapping back to the contigs, supporting the validity of the assembly.

Original languageEnglish
Pages (from-to)93-95
Number of pages3
JournalMarine Genomics
Issue numberPB
StatePublished - 1 Dec 2014
Externally publishedYes

Bibliographical note

Funding Information:
This work was supported by the Assemble (Association of European Marine Biological Laboratories) Infrastructure Access Call 5 to the Interuniversity Institute for Marine Sciences, Eilat, (IUI) Israel, by a BMBF-MOST JOINT GERMAN-ISRAELI RESEARCH PROJECT, project number GR2378/03F0640A to WRH and IBF and by the EU project MaCuMBA (Marine Microorganisms: Cultivation Methods for Improving their Biotechnological Applications; grant agreement no: 311975 ) to WRH. For support during the sampling we thank Martin Hagemann, University of Rostock, and especially the captain of the research ship “Sam Rothberg”, Sefi Baruch, Assaf Rivlin and the IUI logistic support teams.

Publisher Copyright:
© 2014 Elsevier B.V.


  • Gene expression
  • Metatranscriptomics
  • Microbial community
  • RNA-Seq
  • Transcriptome

ASJC Scopus subject areas

  • Aquatic Science
  • Genetics


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