The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea
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.
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In co-culture, the thiamine producer Pseudoalteromonas sp. allows growth of the marine thiamine auxotroph Ostreococcus lucimarinus, and Dinoroseobacter shibae provides vitamins B1 and B12 to its dinoflagellate host.
“in co-culture, the thiamine producer Pseudoalteromonas sp. allows the growth of the marine thiamine auxotroph microalgae Ostreococcus lucimarinus [48], and the marine bacterium Dinoroseobacter shibae, isolated from the benthic dinoflagellate Prorocentrum lima, provides vitamins B1 and B12 to its dinoflagellate host [49].”
From Toward the Enhancement of Microalgal Metabolite Production through Microalgae–Bacteria Consortia (2021) · cites this paper as [49]
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- Authors
- Wagner-Döbler, I., Ballhausen, B., Berger, M., Brinkhoff, T., Buchholz, I., Bunk, B., Cypionka, H., Daniel, R., Drepper, T., Gerdts, G., Hahnke, S., Han, C., Jahn, D., Kalhoefer, D., Kiss, H., Klenk, H.-P., Kyrpides, N., Liebl, W., Liesegang, H., Meincke, L., Pati, A., Petersen, J., Piekarski, T., Pommerenke, C., Pradella, S., Pukall, R., Rabus, R., Stackebrandt, E., Thole, S., Thompson, L., Tielen, P., Tomasch, J., von Jan, M., Wanphrut, N., Wichels, A., Zech, H., & Simon, M.
- Affiliations
- Helmholtz-Centre for Infection Research , Braunschweig , Germany
- Helmholtz Centre for Infection Research (DE)
- Carl von Ossietzky Universität Oldenburg (DE)
- Technische Universität Braunschweig (DE)
- University of Göttingen (DE)
- Forschungszentrum Jülich (DE)
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung (DE)
- Joint Genome Institute (US)
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg , Oldenburg , Germany
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures (DE)
- Technical University of Munich (DE)
- German Collection for Microorganisms and Cell Cultures , Braunschweig , Germany
- ORCID
- Brinkhoff, Thorsten
- Bunk, Boyke
- Cypionka, Heribert
- Daniel, Rolf
- Drepper, Thomas
- Gerdts, Gunnar
- Hahnke, Sarah
- Han, Cliff
- Jahn, Dieter
- Klenk, Hans-Peter
- Kyrpides, Nikos
- Liebl, Wolfgang
- Liesegang, Heiko
- Petersen, Jörn
- Pommerenke, Claudia
- Pradella, Silke
- Pukall, Rüdiger
- Rabus, Ralf
- Stackebrandt, Erko
- Tomasch, Jürgen
- Wichels, Antje
- Simon, Meinhard
- Venue
- The ISME Journal
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-09-10
- Volume
- 4
- Issue
- 1
- Pages
- 61-77
- ISSN
- 1751-7362 (ISSN-L)
- 1751-7370
- OpenAlex
- W2077685605
- Cited by
- 271
- References
- 105
- Citations by year
- 2026: 6 · 2025: 15 · 2024: 15 · 2023: 13 · 2022: 21 · 2021: 20 · 2020: 12 · 2019: 13 · 2018: 17 · 2017: 23 · 2016: 18 · 2015: 25 · 2014: 26 · 2013: 17 · 2012: 9
- FWCI
- 8.77
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- The ISME Journal (publishedVersion)
- PubMed (publishedVersion)
- Helmholtz-Zentrum für Polar-und Meeresforschung (Alfred-Wegener-Institut) (submittedVersion)
- GRO (submittedVersion)
- Funders
- U.S. Department of Energy (DE-AC03-?, AC03-76SF00098, W-7405, DEAC03-76SF00098, -7405-ENG-48, W-7405-ENG-36)
- Gordon and Betty Moore Foundation
- Volkswagen Foundation
- Office of Science (DEAC03-76SF00098)
- Biological and Environmental Research
- Lawrence Livermore National Laboratory (W-7405-ENG 48, -7405-Eng-48, DE-AC03-76SF00098, W-7405-ENG-36)
- Lawrence Berkeley National Laboratory (DE AC03 76SF00098)
- Los Alamos National Laboratory (W‐7405‐ENG‐36)
- Topics
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protist diversity and phylogeny
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- Dinoroseobacter shibae, Roseobacter clade, vitamin B12 biosynthesis, anaerobic growth, nitrate respiration, plasmids, horizontal gene transfer, conjugation, Rhodobacterales, genome annotation
- MeSH terms
- Aerobiosis, Anaerobiosis, Dimethyl Sulfoxide, DNA, Bacterial, Molecular Sequence Data, Nitrates, Plasmids, Symbiosis, Thiamine, Vitamin B 12, Genome, Bacterial, Sequence Homology, Sequence Analysis, DNA, Synteny, Rhodobacteraceae, Biosynthetic Pathways, Eukaryota
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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