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Wagner-Dobler I.,Helmholtz Center for Infection Research | Ballhausen B.,Helmholtz Center for Infection Research | Berger M.,University of Oldenburg | Brinkhoff T.,University of Oldenburg | And 33 more authors.
ISME Journal | Year: 2010

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 B 12 was confirmed to be functional, and D. shibae DFL12T was shown to provide the growth-limiting vitamins B1 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 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. © 2010 International Society for Microbial Ecology All rights reserved.

Eppinger M.,University of Maryland Baltimore County | Bunk B.,German Collection for Microorganisms and Cell Cultures | Johns M.A.,Northern Illinois University | Edirisinghe J.N.,Northern Illinois University | And 22 more authors.
Journal of Bacteriology | Year: 2011

Bacillus megaterium is deep-rooted in the Bacillus phylogeny, making it an evolutionarily key species and of particular importance in understanding genome evolution, dynamics, and plasticity in the bacilli. B. megaterium is a commercially available, nonpathogenic host for the biotechnological production of several substances, including vitamin B 12, penicillin acylase, and amylases. Here, we report the analysis of the first complete genome sequences of two important B. megaterium strains, the plasmidless strain DSM319 and QM B1551, which harbors seven indigenous plasmids. The 5.1-Mbp chromosome carries approximately 5,300 genes, while QM B1551 plasmids represent a combined 417 kb and 523 genes, one of the largest plasmid arrays sequenced in a single bacterial strain. We have documented extensive gene transfer between the plasmids and the chromosome. Each strain carries roughly 300 strain-specific chromosomal genes that account for differences in their experimentally confirmed phenotypes. B. megaterium is able to synthesize vitamin B 12 through an oxygen-independent adenosylcobalamin pathway, which together with other key energetic and metabolic pathways has now been fully reconstructed. Other novel genes include a second ftsZ gene, which may be responsible for the large cell size of members of this species, as well as genes for gas vesicles, a second β-galactosidase gene, and most but not all of the genes needed for genetic competence. Comprehensive analyses of the global Bacillus gene pool showed that only an asymmetric region around the origin of replication was syntenic across the genus. This appears to be a characteristic feature of the Bacillus spp. genome architecture and may be key to their sporulating lifestyle. © 2011, American Society for Microbiology.

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