Global occurrence and heterogeneity of the Roseobacter-clade species Ruegeria mobilis

Abstract

Tropodithietic acid (TDA)-producing Ruegeria mobilis strains of the Roseobacter clade have primarily been isolated from marine aquaculture and have probiotic potential due to inhibition of fish pathogens. We hypothesized that TDA producers with additional novel features are present in the oceanic environment. We isolated 42 TDA-producing R. mobilis strains during a global marine research cruise. While highly similar on the 16S ribosomal RNA gene level (99-100% identity), the strains separated into four sub-clusters in a multilocus sequence analysis. They were further differentiated to the strain level by average nucleotide identity using pairwise genome comparison. The four sub-clusters could not be associated with a specific environmental niche, however, correlated with the pattern of sub-typing using co-isolated phages, the number of prophages in the genomes and the distribution in ocean provinces. Major genomic differences within the sub-clusters include prophages and toxin-antitoxin systems. In general, the genome of R. mobilis revealed adaptation to a particle-associated life style and querying TARA ocean data confirmed that R. mobilis is more abundant in the particle-associated fraction than in the free-living fraction occurring in 40% and 6% of the samples, respectively. Our data and the TARA data, although lacking sufficient data from the polar regions, demonstrate that R. mobilis is a globally distributed marine bacterial species found primarily in the upper open oceans. It has preserved key phenotypic behaviors such as the production of TDA, but contains diverse sub-clusters, which could provide new capabilities for utilization in aquaculture.

Stumbling across the Same Phage: Comparative Genomics of Widespread Temperate Phages Infecting the Fish Pathogen Vibrio anguillarum

“…Further, the high levels of identity with spacers of the CRISPR systems detected in both V. anguillarum and in other Vibrio bacteria, indicated long term interactions between Vibrios and H20- like phages. This is in line with recent observations of susceptibility to specific phages in 36 isolates of the cosmopolitan Roseobacter-clade species, Rugeria mobilis obtained across the world’s oceans covering large ranges in temperature, oxygen concentration and habitat (free-living, particle attached, sediment) [25]. These results suggest the co-existence of specific phages and bacteria on a global scale in groups of ubiquitous marine bacteria such as Roseobacter and Vibrio .…”

Phaeobacter inhibens as probiotic bacteria in non-axenic Artemia and algae cultures

“…Marine Roseobacter clade bacteria can antagonize fish pathogenic bacteria in axenic systems of live larval feed and they can also, in controlled model systems, improve the survival of infected fish larvae (D'Alvise et al, 2012(D'Alvise et al, , 2013Grotkjaer et al, 2016). The roseobacters are marine alphaProteobacteria that are widely distributed across climate zones (Buchan et al, 2005;Segev et al, 2015;Sonnenshein et al, 2016). Especially the genera Phaeobacter and Ruegeria have repeatedly been isolated from aquaculture units (Grotkjaer et al, 2016;Hjelm et al, 2004b;Porsby et al, 2008) and recently, Phaeobacter inhibens was repeatedly isolated from biofilms in Danish habour areas (Gram et al, 2015).…”

Phylogenetic distribution of roseobacticides in the Roseobacter group and their effect on microalgae

“…). The roseobacticide producer 8‐1 was collected in the same location and year as 27‐4 underlining the high diversity among genetically similar Roseobacter ‐group strains (Table ) (Freese et al ., ; Sonnenschein et al ., ,b; Simon et al ., ). Strains from the closely related genera Pseudophaeobacter and Leisingera as well as TDA‐producers from the genera Ruegeria and Pseudovibrio did not produce roseobacticides under the tested conditions.…”

“…This scenario was proposed for the interaction between Emiliania huxleyi , a globally important, bloom‐forming haptophyte (Read et al ., ) and the alphaproteobacterium Phaeobacter inhibens (Seyedsayamdost et al ., ; Segev et al ., ; Wang et al ., ; Wang and Seyedsayamdost, ). The bacterium belongs to the Roseobacter group, one of the most common and widespread marine bacterial groups and a group often co‐appearing with microalgae (Sapp et al ., ; Luo and Moran, ; Tan et al ., ; Sonnenschein et al ., ,b). Roseobacter ‐group bacteria can be involved in the degradation of the algae‐produced dimethylsulfoniopropionate into dimethylsulfide, which is released into the atmosphere and serves as cloud nuclei (Miller and Belas, ; Dickschat et al ., ).…”