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

• Published in: The ISME Journal Vol. 4; no. 1; pp. 61 - 77
• Main Authors: Wagner-Döbler, Irene, Ballhausen, Britta, Berger, Martine, Brinkhoff, Thorsten, Buchholz, Ina, Bunk, Boyke, Cypionka, Heribert, Daniel, Rolf, Drepper, Thomas, Gerdts, Gunnar, Hahnke, Sarah, Han, Cliff, Jahn, Dieter, Kalhoefer, Daniela, Kiss, Hajnalka, Klenk, Hans-Peter, Kyrpides, Nikos, Liebl, Wolfgang, Liesegang, Heiko, Meincke, Linda, Pati, Amrita, Petersen, Jörn, Piekarski, Tanja, Pommerenke, Claudia, Pradella, Silke, Pukall, Rüdiger, Rabus, Ralf, Stackebrandt, Erko, Thole, Sebastian, Thompson, Linda, Tielen, Petra, Tomasch, Jürgen, von Jan, Mathias, Wanphrut, Nittaya, Wichels, Antje, Zech, Hajo, Simon, Meinhard
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.01.2010; Oxford University Press
• Subjects: Aerobic bacteria; Aerobiosis; Anaerobiosis; Biomedical and Life Sciences; Biosynthetic Pathways - genetics; Dimethyl Sulfoxide - metabolism; DNA, Bacterial - chemistry; DNA, Bacterial - genetics; Ecology; Eukaryota - growth & development; Eukaryota - microbiology; Evolutionary Biology; Fermentation; Genome, Bacterial; Life Sciences; Microalgae; Microbial Ecology; Microbial Genetics and Genomics; Microbiology; Molecular Sequence Data; Nitrate reduction; Nitrates - metabolism; original-article; Oxygen; Plasmids; Rhodobacteraceae - genetics; Rhodobacteraceae - isolation & purification; Rhodobacteraceae - physiology; Sequence Analysis, DNA; Sequence Homology; Symbiosis; Synteny; Thiamine - biosynthesis; Vitamin B 12 - biosynthesis; Vitamins; thiamine; cobalamin; dinoflagellate; symbiosis; vitamin
• ISSN: 1751-7362; 1751-7370; 1751-7370
• DOI: 10.1038/ismej.2009.94

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.