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. shib...
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| Published in | The ISME Journal Vol. 4; no. 1; pp. 61 - 77 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
Nature Publishing Group UK
01.01.2010
Oxford University Press |
| Subjects | |
| Online Access | Get full text |
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| Abstract | 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. |
|---|---|
| AbstractList | 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.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. 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. 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. Dinoroseobacter shibae DFL12T, 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 DFL12T is able to synthesize the vitamins B1 and B12 for which its host is auxotrophic. Two pathways for the de novo synthesis of vitamin B12 are present, one requiring oxygen and the other an oxygen-independent pathway. The de novo synthesis of vitamin B12 was confirmed to be functional, and D. shibae DFL12T was shown to provide the growth-limiting vitamins B1 and B12 to its dinoflagellate host. The Roseobacter clade has been considered to comprise obligate aerobic bacteria. However, D. shibae DFL12T 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 DFL12T 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 DFL12T shows the most complex viral defense system of all Rhodobacterales sequenced to date. |
| Author | Klenk, Hans-Peter Buchholz, Ina Pommerenke, Claudia Liebl, Wolfgang Thole, Sebastian Wanphrut, Nittaya Liesegang, Heiko Tomasch, Jürgen Drepper, Thomas Simon, Meinhard Kalhoefer, Daniela von Jan, Mathias Gerdts, Gunnar Han, Cliff Kyrpides, Nikos Rabus, Ralf Wagner-Döbler, Irene Meincke, Linda Wichels, Antje Hahnke, Sarah Petersen, Jörn Tielen, Petra Daniel, Rolf Jahn, Dieter Zech, Hajo Bunk, Boyke Cypionka, Heribert Kiss, Hajnalka Pradella, Silke Piekarski, Tanja Pukall, Rüdiger Ballhausen, Britta Berger, Martine Brinkhoff, Thorsten Stackebrandt, Erko Pati, Amrita Thompson, Linda |
| Author_xml | – sequence: 1 givenname: Irene surname: Wagner-Döbler fullname: Wagner-Döbler, Irene email: iwd@helmholtz-hzi.de organization: Helmholtz-Centre for Infection Research – sequence: 2 givenname: Britta surname: Ballhausen fullname: Ballhausen, Britta organization: Helmholtz-Centre for Infection Research – sequence: 3 givenname: Martine surname: Berger fullname: Berger, Martine organization: Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg – sequence: 4 givenname: Thorsten surname: Brinkhoff fullname: Brinkhoff, Thorsten organization: Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg – sequence: 5 givenname: Ina surname: Buchholz fullname: Buchholz, Ina organization: Helmholtz-Centre for Infection Research – sequence: 6 givenname: Boyke surname: Bunk fullname: Bunk, Boyke organization: Institute of Microbiology, Technical University of Braunschweig – sequence: 7 givenname: Heribert surname: Cypionka fullname: Cypionka, Heribert organization: Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg – sequence: 8 givenname: Rolf surname: Daniel fullname: Daniel, Rolf organization: Institute for Microbiology and Genetics, University of Göttingen – sequence: 9 givenname: Thomas surname: Drepper fullname: Drepper, Thomas organization: Forschungszentrum Jülich – sequence: 10 givenname: Gunnar surname: Gerdts fullname: Gerdts, Gunnar organization: Biologische Anstalt Helgoland, Alfred-Wegener Institute for Polar and Marine Research – sequence: 11 givenname: Sarah surname: Hahnke fullname: Hahnke, Sarah organization: Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg – sequence: 12 givenname: Cliff surname: Han fullname: Han, Cliff organization: Joint Genome Institute – sequence: 13 givenname: Dieter surname: Jahn fullname: Jahn, Dieter organization: Institute of Microbiology, Technical University of Braunschweig – sequence: 14 givenname: Daniela surname: Kalhoefer fullname: Kalhoefer, Daniela organization: Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg – sequence: 15 givenname: Hajnalka surname: Kiss fullname: Kiss, Hajnalka organization: Joint Genome Institute – sequence: 16 givenname: Hans-Peter surname: Klenk fullname: Klenk, Hans-Peter organization: German Collection for Microorganisms and Cell Cultures – sequence: 17 givenname: Nikos surname: Kyrpides fullname: Kyrpides, Nikos organization: Joint Genome Institute – sequence: 18 givenname: Wolfgang surname: Liebl fullname: Liebl, Wolfgang organization: Technical University of München – sequence: 19 givenname: Heiko surname: Liesegang fullname: Liesegang, Heiko organization: Institute for Microbiology and Genetics, University of Göttingen – sequence: 20 givenname: Linda surname: Meincke fullname: Meincke, Linda organization: Joint Genome Institute – sequence: 21 givenname: Amrita surname: Pati fullname: Pati, Amrita organization: Joint Genome Institute – sequence: 22 givenname: Jörn surname: Petersen fullname: Petersen, Jörn organization: German Collection for Microorganisms and Cell Cultures – sequence: 23 givenname: Tanja surname: Piekarski fullname: Piekarski, Tanja organization: Institute of Microbiology, Technical University of Braunschweig – sequence: 24 givenname: Claudia surname: Pommerenke fullname: Pommerenke, Claudia organization: Helmholtz-Centre for Infection Research – sequence: 25 givenname: Silke surname: Pradella fullname: Pradella, Silke organization: German Collection for Microorganisms and Cell Cultures – sequence: 26 givenname: Rüdiger surname: Pukall fullname: Pukall, Rüdiger organization: German Collection for Microorganisms and Cell Cultures – sequence: 27 givenname: Ralf surname: Rabus fullname: Rabus, Ralf organization: Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg – sequence: 28 givenname: Erko surname: Stackebrandt fullname: Stackebrandt, Erko organization: German Collection for Microorganisms and Cell Cultures – sequence: 29 givenname: Sebastian surname: Thole fullname: Thole, Sebastian organization: Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg – sequence: 30 givenname: Linda surname: Thompson fullname: Thompson, Linda organization: Joint Genome Institute – sequence: 31 givenname: Petra surname: Tielen fullname: Tielen, Petra organization: Institute of Microbiology, Technical University of Braunschweig – sequence: 32 givenname: Jürgen surname: Tomasch fullname: Tomasch, Jürgen organization: Helmholtz-Centre for Infection Research – sequence: 33 givenname: Mathias surname: von Jan fullname: von Jan, Mathias organization: German Collection for Microorganisms and Cell Cultures – sequence: 34 givenname: Nittaya surname: Wanphrut fullname: Wanphrut, Nittaya organization: Institute of Microbiology, Technical University of Braunschweig – sequence: 35 givenname: Antje surname: Wichels fullname: Wichels, Antje organization: Biologische Anstalt Helgoland, Alfred-Wegener Institute for Polar and Marine Research – sequence: 36 givenname: Hajo surname: Zech fullname: Zech, Hajo organization: Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg – sequence: 37 givenname: Meinhard surname: Simon fullname: Simon, Meinhard organization: Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/19741735$$D View this record in MEDLINE/PubMed https://www.osti.gov/biblio/1153571$$D View this record in Osti.gov |
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| Keywords | thiamine cobalamin dinoflagellate symbiosis vitamin |
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| Snippet | Dinoroseobacter shibae
DFL12
T
, a member of the globally important marine
Roseobacter
clade, comprises symbionts of cosmopolitan marine microalgae, including... Dinoroseobacter shibae DFL12T, a member of the globally important marine Roseobacter clade, comprises symbionts of cosmopolitan marine microalgae, including... Dinoroseobacter shibae DFL12(T), a member of the globally important marine Roseobacter clade, comprises symbionts of cosmopolitan marine microalgae, including... |
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| SubjectTerms | 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 |
| Title | The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea |
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