The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea

ISME J. 2010 Jan;4(1):61-77. doi: 10.1038/ismej.2009.94. Epub 2009 Sep 10.


Dinoroseobacter shibae DFL12(T), a member of the globally important marine Roseobacter clade, comprises symbionts of cosmopolitan marine microalgae, including toxic dinoflagellates. Its annotated 4 417 868 bp genome sequence revealed a possible advantage of this symbiosis for the algal host. D. shibae DFL12(T) is able to synthesize the vitamins B(1) and B(12) for which its host is auxotrophic. Two pathways for the de novo synthesis of vitamin B(12) are present, one requiring oxygen and the other an oxygen-independent pathway. The de novo synthesis of vitamin B(12) was confirmed to be functional, and D. shibae DFL12(T) was shown to provide the growth-limiting vitamins B(1) and B(12) to its dinoflagellate host. The Roseobacter clade has been considered to comprise obligate aerobic bacteria. However, D. shibae DFL12(T) is able to grow anaerobically using the alternative electron acceptors nitrate and dimethylsulfoxide; it has the arginine deiminase survival fermentation pathway and a complex oxygen-dependent Fnr (fumarate and nitrate reduction) regulon. Many of these traits are shared with other members of the Roseobacter clade. D. shibae DFL12(T) has five plasmids, showing examples for vertical recruitment of chromosomal genes (thiC) and horizontal gene transfer (cox genes, gene cluster of 47 kb) possibly by conjugation (vir gene cluster). The long-range (80%) synteny between two sister plasmids provides insights into the emergence of novel plasmids. D. shibae DFL12(T) shows the most complex viral defense system of all Rhodobacterales sequenced to date.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Aerobiosis
  • Anaerobiosis
  • Biosynthetic Pathways / genetics
  • DNA, Bacterial / chemistry*
  • DNA, Bacterial / genetics*
  • Dimethyl Sulfoxide / metabolism
  • Eukaryota / growth & development
  • Eukaryota / microbiology
  • Genome, Bacterial*
  • Molecular Sequence Data
  • Nitrates / metabolism
  • Plasmids
  • Rhodobacteraceae / genetics*
  • Rhodobacteraceae / isolation & purification
  • Rhodobacteraceae / physiology
  • Sequence Analysis, DNA*
  • Sequence Homology
  • Symbiosis*
  • Synteny
  • Thiamine / biosynthesis
  • Vitamin B 12 / biosynthesis


  • DNA, Bacterial
  • Nitrates
  • Vitamin B 12
  • Thiamine
  • Dimethyl Sulfoxide

Associated data

  • RefSeq/NC_009952
  • RefSeq/NC_009955
  • RefSeq/NC_009956
  • RefSeq/NC_009957
  • RefSeq/NC_009958
  • RefSeq/NC_009959