Adaptation of an abundant Roseobacter RCA organism to pelagic systems revealed by genomic and transcriptomic analyses

ISME J. 2015 Feb;9(2):371-84. doi: 10.1038/ismej.2014.134. Epub 2014 Aug 1.


The RCA (Roseobacter clade affiliated) cluster, with an internal 16S rRNA gene sequence similarity of >98%, is the largest cluster of the marine Roseobacter clade and most abundant in temperate to (sub)polar oceans, constituting up to 35% of total bacterioplankton. The genome analysis of the first described species of the RCA cluster, Planktomarina temperata RCA23, revealed that this phylogenetic lineage is deeply branching within the Roseobacter clade. It shares not >65.7% of homologous genes with any other organism of this clade. The genome is the smallest of all closed genomes of the Roseobacter clade, exhibits various features of genome streamlining and encompasses genes for aerobic anoxygenic photosynthesis (AAP) and CO oxidation. In order to assess the biogeochemical significance of the RCA cluster we investigated a phytoplankton spring bloom in the North Sea. This cluster constituted 5.1% of the total, but 10-31% (mean 18.5%) of the active bacterioplankton. A metatranscriptomic analysis showed that the genome of P. temperata RCA23 was transcribed to 94% in the bloom with some variations during day and night. The genome of P. temperata RCA23 was also retrieved to 84% from metagenomic data sets from a Norwegian fjord and to 82% from stations of the Global Ocean Sampling expedition in the northwestern Atlantic. In this region, up to 6.5% of the total reads mapped on the genome of P. temperata RCA23. This abundant taxon appears to be a major player in ocean biogeochemistry.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acclimatization
  • Gene Expression Profiling
  • Genome, Bacterial
  • Metagenomics
  • Molecular Sequence Data
  • North Sea
  • Oceans and Seas
  • Phylogeny
  • Phytoplankton / genetics
  • Phytoplankton / isolation & purification
  • Rhodobacteraceae / classification*
  • Rhodobacteraceae / genetics*
  • Rhodobacteraceae / isolation & purification
  • Roseobacter / classification
  • Seawater / microbiology*

Associated data

  • GENBANK/CP003984