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

Abstract

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 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 DFL12T 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.

You are what you talk: quorum sensing induces individual morphologies and cell division modes in Dinoroseobacter shibae

“…The vir gene clusters of D. shibae encode a T4SS, which is highly conserved among Roseobacter strains (Wagner-Dö bler et al, 2010). Its physiological function has not yet been unraveled.…”

Ribonucleotide reductases reveal novel viral diversity and predict biological and ecological features of unknown marine viruses

“…Class II (B 12 -dependent) RNRs are rarely observed in eukaryotes but have been identified in several microalgal species and are the result of horizontal gene transfer from bacteria (10). Many microalgal species, including V. carteri, are B 12 -dependent auxotrophs and rely upon bacteria for this essential cofactor (16), and several algal-associated bacteria are capable of de novo B 12 synthesis and supporting growth of auxotrophic algal cultures in minimal media (17,18). The presence of two CRISPR (clustered regularly interspaced short palindromic repeats) arrays in the B 12 -producing, dinoflagellate-associated bacterium Dinoroseobacter shibae DFL12 T indicates that phage infections occur in these bacteria (17).…”

“…Many microalgal species, including V. carteri, are B 12 -dependent auxotrophs and rely upon bacteria for this essential cofactor (16), and several algal-associated bacteria are capable of de novo B 12 synthesis and supporting growth of auxotrophic algal cultures in minimal media (17,18). The presence of two CRISPR (clustered regularly interspaced short palindromic repeats) arrays in the B 12 -producing, dinoflagellate-associated bacterium Dinoroseobacter shibae DFL12 T indicates that phage infections occur in these bacteria (17). Based on this information, we hypothesize that these class II RTPR sequences are from podoviruses whose hosts are B 12 -producing heterotrophic bacteria associated with microalgal species.…”

Trimethylamine and trimethylamine N-oxide are supplementary energy sources for a marine heterotrophic bacterium: implications for marine carbon and nitrogen cycling

“…Here we demonstrate a 'proof of concept', whereby the turnover of TMA resulted in the release of remineralised N in the form of ammonia, which was subsequently taken up by another bacterium and used to support growth. As a number of MRC species are frequently associated with phytoplankton blooms (González et al, 2000;Buchan et al, 2005;Wagner-Dobler et al, 2009;Hahnke et al, 2013;Nelson et al, 2014), we predict that this N remineralisation process may take place with several different 'nitrogen-rich' compounds, for example, glycine betaine, choline and carnintine. This process has strong implications for the 'microbial loop', which ultimately controls the level of both primary and secondary production in the world's oceans (Azam et al, 1983).…”