The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea.
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.
Wagner-Döbler
Irene
I
Helmholtz-Centre for Infection Research, Braunschweig, Germany. iwd@helmholtz-hzi.de
Ballhausen
Britta
B
Berger
Martine
M
Brinkhoff
Thorsten
T
Buchholz
Ina
I
Bunk
Boyke
B
Cypionka
Heribert
H
Daniel
Rolf
R
Drepper
Thomas
T
Gerdts
Gunnar
G
Hahnke
Sarah
S
Han
Cliff
C
Jahn
Dieter
D
Kalhoefer
Daniela
D
Kiss
Hajnalka
H
Klenk
Hans-Peter
HP
Kyrpides
Nikos
N
Liebl
Wolfgang
W
Liesegang
Heiko
H
Meincke
Linda
L
Pati
Amrita
A
Petersen
Jörn
J
Piekarski
Tanja
T
Pommerenke
Claudia
C
Pradella
Silke
S
Pukall
Rüdiger
R
Rabus
Ralf
R
Stackebrandt
Erko
E
Thole
Sebastian
S
Thompson
Linda
L
Tielen
Petra
P
Tomasch
Jürgen
J
von Jan
Mathias
M
Wanphrut
Nittaya
N
Wichels
Antje
A
Zech
Hajo
H
Simon
Meinhard
M
D000332:Aerobiosis; D000693:Anaerobiosis; D053898:Biosynthetic Pathways / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics*; D004121:Dimethyl Sulfoxide / Q000378:metabolism; D056890:Eukaryota / Q000254:growth & development / Q000382:microbiology; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D009566:Nitrates / Q000378:metabolism; D010957:Plasmids; D041902:Rhodobacteraceae / Q000235:genetics* / Q000302:isolation & purification / Q000502:physiology; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D013559:Symbiosis; D026801:Synteny; D013831:Thiamine / Q000096:biosynthesis; D014805:Vitamin B 12 / Q000096:biosynthesis
D004269:DNA, Bacterial; D009566:Nitrates; D014805:Vitamin B 12; D013831:Thiamine; D004121:Dimethyl Sulfoxide