title: 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.
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Eva C
authors.identifier: 0000-0001-6959-5100
authors.initials: EC
authors.lastname: Sonnenschein
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Kristian F
authors.identifier: 0000-0002-5848-0911
authors.initials: KF
authors.lastname: Nielsen
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Paul
authors.initials: P
authors.lastname: D'Alvise
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark.|Biogen Manufacturing, Biogen Idec Allé 1, Hillerød, Denmark.
authors.forename: Cisse H
authors.initials: CH
authors.lastname: Porsby
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Jette
authors.initials: J
authors.lastname: Melchiorsen
authors.affiliation: Technical University of Denmark, National Institute for Aquatic Resources, Charlottenlund, Denmark.
authors.forename: Jens
authors.initials: J
authors.lastname: Heilmann
authors.affiliation: Hellenic Centre for Marine Research, Institute of Aquaculture, Heraklion, Greece.|Section for Marine Biology, University of Copenhagen, Helsingør, Denmark.
authors.forename: Panos G
authors.initials: PG
authors.lastname: Kalatzis
authors.affiliation: División de Microbiología, Evolutionary Genomics Group, Universidad Miguel Hernández, San Juan, Alicante, Spain.
authors.forename: Mario
authors.initials: M
authors.lastname: López-Pérez
authors.affiliation: Helmholtz Centre for Infection Research, Braunschweig, Germany.
authors.forename: Boyke
authors.initials: B
authors.lastname: Bunk
authors.affiliation: Helmholtz Centre for Infection Research, Braunschweig, Germany.
authors.forename: Cathrin
authors.initials: C
authors.lastname: Spröer
authors.affiliation: Section for Marine Biology, University of Copenhagen, Helsingør, Denmark.
authors.forename: Mathias
authors.identifier: 0000-0002-9587-9171
authors.initials: M
authors.lastname: Middelboe
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Lone
authors.initials: L
authors.lastname: Gram
mesh_terms: D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D014644:Genetic Variation; D016680:Genome, Bacterial / Q000235:genetics*; D005843:Geography; D058885:Multilocus Sequence Typing; D009792:Oceans and Seas; D010802:Phylogeny; D041902:Rhodobacteraceae / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D041904:Roseobacter / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D017422:Sequence Analysis, DNA; D014334:Tropolone / Q000031:analogs & derivatives / Q000378:metabolism
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; C527336:tropodithietic acid; D014334:Tropolone