Roseobacter fucihabitans sp. nov., isolated from the brown alga Fucus spiralis.

A Gram-negative, aerobic, pink-pigmented, and bacteriochlorophyll a-containing bacterial strain, designated B14T, was isolated from the macroalga Fucus spiralis sampled from the southern North Sea, Germany. Based on 16S rRNA gene sequences, species of the genera Roseobacter and Sulfitobacter were most closely related to strain B14T with sequence identities ranging from 98.15 % (Roseobacter denitrificans Och 114T) to 99.11 % (Roseobacter litoralis Och 149T), whereas Sulfitobacter mediterraneus CH-B427T exhibited 98.52 % sequence identity. Digital DNA-DNA hybridization and average nucleotide identity values between the genome of the novel strain and that of closely related Roseobacter and Sulfitobacter type strains were <20 % and <77 %, respectively. The novel strain contained ubiquinone-10 as the only respiratory quinone and C18 : 1 ω7c, C16 : 0, C18 : 0, C12 : 1 ω7c, C18 : 2 ω7,13c, and C10 : 0 3-OH as the major cellular fatty acids. The predominant polar lipids of strain B14T were phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol. The genome of strain B14T comprises a chromosome with a size of 4.5 Mbp, one chromid, and four plasmids. The genome contains the complete gene cluster for aerobic anoxygenic photosynthesis required for a photoheterotrophic lifestyle. The results of this study indicate that strain B14T (=DSM 116946T=LMG 33352T) represents a novel species of the genus Roseobacter for which the name Roseobacter fucihabitans sp. nov. is proposed.

Muriiphilus fusiformis gen. nov., sp. nov., a novel non-marine bacterium belonging to the Roseobacter group, and reclassification of Maritimibacter lacisalsi (Zhong et al. 2015) as Muriicola lacisalsi gen. nov., comb. nov.

An aerobic, Gram-stain-negative, non-sporulating, flagellated and spindle-like bacterium, designated HY14T, was isolated from a pickle-processing factory wastewater sample. The isolate chemoheterotrophically grew at 4-42 °C (optimum, 35 °C) and pH 5.5-9.0 (optimum, pH 6.0-6.5). Salt was required for growth (0.5-12 % NaCl, w/v). A deep brown and water-soluble uncharacterized pigment was produced when grown in certain media. The predominant fatty acids (>5 %) included C16 : 0, C18 : 1 ω7c, 11-methyl C18 : 1 ω7c and C19 : 0 cyclo ω8c. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids, two unidentified phospholipids, two unidentified glycolipids and five unknown lipids. The major isoprenoid quinone was ubiquinone-10. Pairwise alignment based on 16S rRNA gene sequences indicated that strain HY14T had the highest sequence similarity to genera Maritimibacter (95.61-96.05 %) and Boseongicola (95.82 %). Phylogenetic analysis based on core genome illustrated that strain HY14T formed a monophyletic lineage with members of the genus Maritimibacter in the clade of the Roseobacter group in the family Rhodobacteraeceae. The core-gene average amino acid identity used to define bacterial genera by a threshold of 60-80 % was calculated to be 68.56-76.5 % between HY14T and closely related taxa. Several genomic characteristics, such as carrying two RuBisCO-mediated pathways and different osmoprotectant transport pathways, exhibited the genotypic discrepancies of strain HY14T. Based on the polyphasic taxonomic characterization, strain HY14T is considered to represent a novel species of a novel genus belonging to the family Rhodobacteraeceae, for which the name Muriiphilus fusiformis gen. nov., sp. nov. is proposed. The type strain is HY14T (=CGMCC 1.15973T=KCTC 52499T). Maritimibacter lacisalsi (Zhong et al. 2015) is considered to diverge from Maritimibacter alkaliphilus at the genus level, and should be reassigned as a novel genus, for which the name Muriicola lacisalsi gen. nov., comb. nov. is proposed.

Roseobacter cerasinus sp. nov., isolated from a fish farm.

An obligate aerobic and bacteriochlorophyll a-containing bacterium, designated strain AI77T, was isolated from a fish farm in Uwa Sea, Japan. Cells were Gram-stain-negative, coccoid- to oval-shaped, and showed no motility. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain AI77T is a member of the genus Roseobacter and closely related to Roseobacter ponti MM-7T (97.8 %), Roseobacter denitrificans OCh 114T (97.3 %) and Roseobacter litoralis OCh 149T (97.3 %). The G+C content of strain AI77T was 61.0 mol%. The average amino acid identity values of the genome in strain AI77T with those in R. denitrificans OCh 114T and R. litoralis OCh 149T were 73.26 % (SD 16.46) and 72.63 % (SD 16.76), respectively. The digital DNA-DNA hybridization values of strain AI77T with the type strains R. denitrificans OCh 114T and R. litoralis OCh 149T were 18.70 and 18.50 %, respectively. The dominant fatty acids (>10 % of total fatty acids) of AI77T were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and saturated fatty acid C16 : 0. The sole respiratory quinone was ubiquinone-10. The predominant polar lipids were phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol. Based on the genetic and phenotypic data obtained herein, we conclude that strain AI77T represents a new species of the genus Roseobacter, for which we propose the name Roseobacter cerasinus sp. nov.; the type strain is AI77T (=DSM 110091T=NBRC 114115T).

Description of Palleronia rufa sp. nov., a biofilm-forming and AHL-producing Rhodobacteraceae, reclassification of Hwanghaeicola aestuarii as Palleronia aestuarii comb. nov., Maribius pontilimi as Palleronia pontilimi comb. nov., Maribius salinus as Palleronia salina comb. nov., Maribius pelagius as Palleronia pelagia comb. nov. and emended description of the genus Palleronia.

Strain MOLA 401T was isolated from marine waters in the southwest lagoon of New Caledonia and was shown previously to produce an unusual diversity of quorum sensing signaling molecules. This strain was Gram-negative, formed non-motile cocci and colonies were caramel. Optimum growth conditions were 30°C, pH 8 and 3% NaCl (w/v). Based on 16S rRNA gene sequence analysis, this strain was found to be closely related to Pseudomaribius aestuariivivens NBRC 113039T (96.9% of similarity), Maribius pontilimi DSM 104950T (96.4% of similarity) and Palleronia marisminoris LMG 22959T (96.3% of similarity), belonging to the Roseobacter group within the family Rhodobacteraceae. As its closest relatives, strain MOLA 401T is able to form a biofilm on polystyrene, supporting the view of Roseobacter group strains as prolific surface colonizers. An in-depth genomic study allowed us to affiliate strain MOLA 401T as a new species of genus Palleronia and to reaffiliate some of its closest relatives in this genus. Consequently, we describe strain MOLA 401T (DSM 106827T=CIP 111607T=BBCC 401T) for which we propose the name Palleronia rufa sp. nov. We also propose to emend the description of the genus Palleronia and to reclassify Maribius and Hwanghaeicola species as Palleronia species.

A marine plasmid hitchhiking vast phylogenetic and geographic distances.

Horizontal gene transfer (HGT) plays an important role in bacterial evolution and serves as a driving force for bacterial diversity and versatility. HGT events often involve mobile genetic elements like plasmids, which can promote their own dissemination by associating with adaptive traits in the gene pool of the so-called mobilome. Novel traits that evolve through HGT can therefore lead to the exploitation of new ecological niches, prompting an adaptive radiation of bacterial species. In this study, we present phylogenetic, biogeographic, and functional analyses of a previously unrecognized RepL-type plasmid found in diverse members of the marine Roseobacter group across the globe. Noteworthy, 100% identical plasmids were detected in phylogenetically and geographically distant bacteria, revealing a so-far overlooked, but environmentally highly relevant vector for HGT. The genomic and functional characterization of this plasmid showed a completely conserved backbone dedicated to replication, stability, and mobilization as well as an interchangeable gene cassette with highly diverse, but recurring motifs. The majority of the latter appear to be involved in mechanisms coping with toxins and/or pollutants in the marine environment. Furthermore, we provide experimental evidence that the plasmid has the potential to be transmitted across bacterial orders, thereby increasing our understanding of evolution and microbial niche adaptation in the environment.

Microbial communities across nearshore to offshore coastal transects are primarily shaped by distance and temperature.

Recent studies have focused on linking marine microbial communities with environmental factors, yet, relatively little is known about the drivers of microbial community patterns across the complex gradients from the nearshore to open ocean. Here, we examine microbial dynamics in 15 five-station transects beginning at the estuarine Piver's Island Coastal Observatory (PICO) time-series site and continuing 87 km across the continental shelf to the oligotrophic waters of the Sargasso Sea. 16S rRNA gene libraries reveal strong clustering by sampling site with distinct nearshore, continental shelf and offshore oceanic communities. Water temperature and distance from shore (which serves as a proxy for gradients in factors such as productivity, terrestrial input and nutrients) both most influence community composition. However, at the phylotype level, modelling shows the distribution of some taxa is linked to temperature, others to distance from shore and some by both factors, highlighting that taxa with distinct environmental preferences underlie apparent clustering by station. Thus, continental margins contain microbial communities that are distinct from those of either the nearshore or the offshore environments and contain mixtures of phylotypes with nearshore or offshore preferences rather than those unique to the shelf environment.

Diversity of Dimethylsulfoniopropionate Degradation Genes Reveals the Significance of Marine Roseobacter Clade in Sulfur Metabolism in Coastal Areas of Antarctic Maxwell Bay.

Dimethylsulfoniopropionate (DMSP) is an organic sulfur compound that occurs in large amounts in oceans around the world, and it plays an important role in the global sulfur cycle. DMSP released into seawater can be rapidly catabolized by bacteria via two pathways, namely, demethylation or cleavage pathway. Members of the Roseobacter clade frequently possess enzymes involved in the DMSP demethylation or cleavage pathway. We tried to measure the diversity of genes encoding DMSP demethylase (dmdA) and DMSP lyases (dddD, dddL, and dddP) in bacteria in the surface seawater of Ardley Cove and Great Wall Cove in Antarctic Maxwell Bay using DMSP degradation gene clone library analysis. Although we did not detect sequences related to the dddD or dddL gene, both bacterial dmdA and dddP genes found in the two coves were completely confined to the Roseobacter clade, which indicated that this clade plays a significant role in DMSP catabolism in the coastal seawaters of Maxwell Bay. In addition, compared with bacterial DMSP degradation genes in Arctic coastal seawater, our results suggest that both bipolar and endemic bacterial DMSP degradation genes exist in polar marine environments. The findings of this study improve our knowledge of the distribution of DMSP degradation genes in polar marine ecosystems.

Phosphate-limited ocean regions select for bacterial populations enriched in the carbon-phosphorus lyase pathway for phosphonate degradation.

In tropical and subtropical oceanic surface waters phosphate scarcity can limit microbial productivity. However, these environments also have bioavailable forms of phosphorus incorporated into dissolved organic matter (DOM) that microbes with the necessary transport and hydrolysis metabolic pathways can access to supplement their phosphorus requirements. In this study we evaluated how the environment shapes the abundance and taxonomic distribution of the bacterial carbon-phosphorus (C-P) lyase pathway, an enzyme complex evolved to extract phosphate from phosphonates. Phosphonates are organophosphorus compounds characterized by a highly stable C-P bond and are enriched in marine DOM. Similar to other known bacterial adaptions to low phosphate environments, C-P lyase was found to become more prevalent as phosphate concentrations decreased. C-P lyase was particularly enriched in the Mediterranean Sea and North Atlantic Ocean, two regions that feature sustained periods of phosphate depletion. In these regions, C-P lyase was prevalent in several lineages of Alphaproteobacteria (Pelagibacter, SAR116, Roseobacter and Rhodospirillales), Gammaproteobacteria, and Actinobacteria. The global scope of this analysis supports previous studies that infer phosphonate catabolism via C-P lyase is an important adaptive strategy implemented by bacteria to alleviate phosphate limitation and expands the known geographic extent and taxonomic affiliation of this metabolic pathway in the ocean.

Profundibacter amoris gen. nov., sp. nov., a new member of the Roseobacter clade isolated from Loki's Castle Vent Field on the Arctic Mid-Ocean Ridge.

A bacterial strain, designated BAR1T, was isolated from a microbial mat growing on the surface of a barite chimney at the Loki's Castle Vent Field, at a depth of 2216 m. Cells of strain BAR1T were rod-shaped, Gram-reaction-negative and grew on marine broth 2216 at 10-37 °C (optimum 27-35 °C), pH 5.5-8.0 (optimum pH 6.5-7.5) and 0.5-5.0 % NaCl (optimum 2 %). The DNA G+C content was 57.38 mol%. The membrane-associated major ubiquinone was Q-10, the fatty acid profile was dominated by C18 : 1ω7c (91 %), and the polar lipids detected were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid, one unidentified lipid and one unidentified phospholipid. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain BAR1T clustered together with Rhodobacterales bacterium PRT1, as well as the genera Halocynthiibacter and Pseudohalocynthiibacter in a polyphyletic clade within the Roseobacter clade. Several characteristics differentiate strain BAR1T from the aforementioned genera, including its motility, its piezophilic behaviour and its ability to grow at 35 °C and under anaerobic conditions. Accordingly, strain BAR1T is considered to represent a novel genus and species within the Roseobacter clade, for which the name Profundibacter amoris gen. nov., sp. nov. is proposed. The type strain is Profundibacter amoris BAR1T (=JCM 31874T=DSM 104147T).

Genomic reconstructions and potential metabolic strategies of generalist and specialist heterotrophic bacteria associated with an estuary Synechococcus culture.

Interactions between photoautotrophs and heterotrophs are central to marine microbial ecosystems. Synechococcus are dominant marine phototrophs, and they are frequently associated with heterotrophic bacteria. These co-cultures provide a useful research system to investigate photoautotroph-heterotroph interactions in marine systems. Bacteria within the Roseobacter clade and Flavobacteria are two of the main bacterial lineages that exhibit intimate associations with Synechococcus populations. We conducted metagenomic analyses of a Synechococcus culture, followed by genomic binning of metagenomic contigs, and recovered five nearly complete genomes, including members of the Roseobacter clade (i.e. Marivita sp. XM-24) and Flavobacteria (i.e. Fluviicola sp. XM-24). Marivita sp. XM-24 is an ecological generalist of the Roseobacter clade and displays diverse metabolic capacities for the acquisition of nutrients and energy sources. Specifically, the genome contained numerous gene complements involved in the uptake and metabolism of nitrogen- and phosphorus-containing inorganic and organic compounds, in addition to the potential for aerobic anoxygenic photosynthesis, oxidation of carbon monoxide, inorganic sulfur oxidation, DMSP demethylation and PHA metabolism. The genome of the Flavobacteria representative, Fluviicola sp. XM-24, contained numerous peptidases, glycoside hydrolases, adhesion-related proteins and genes involved in gliding motility. Fluviicola sp. XM-24 likely specialize in the degradation of high molecular weight compound exudates from Synechococcus cells, including polysaccharides and polypeptides via attachment to particles, surfaces or cells. The distinct metabolic strategies identified within several heterotrophic bacteria that are associated with Syneochococcus cells provide insights into their lifestyles and nutrient utilization patterns, in addition to their interactions with photoautotrophs. Biological interactions, including mutualism, competition and antagonism, shape the microbial community structure of marine environments and are critical for understanding biogeochemical cycling in the ocean. These results provide valuable insights into the nature of interactions between dominant marine photoautotrophs and associated bacterial heterotrophs.

Bacteriophages that infect marine roseobacters: genomics and ecology.

Viruses are the most abundant biological entities in seawater. They influence microbial population dynamics, genetic heterogeneity and biogeochemical cycles in marine ecosystems. The isolation and characterization of viruses that infect specific hosts have greatly advanced our knowledge of the biological and ecological interactions between viruses and their hosts. Marine Roseobacter are abundant, ubiquitous and diverse in the ocean and play active roles in global biogeochemical cycling, especially the sulfur cycle. Currently, 32 bacteriophages that infect multiple lineages of roseobacters have been isolated and sequenced. These roseophages exhibit diverse morphologies, nucleic acid types and genomic features. Here, we provide the most up-to-date overview of roseophages. Most roseophages are host specific and have a wide range of genome sizes and open reading frames. Based on a genome-wide comparison, at least eight distinctly different types of roseophages were identified, indicating their diversity. Lysogenic-related and gene transfer agent-related genes are commonly found in roseophage genomes, implying the importance of genetic transfer within roseobacters. This feature could provide the versatility for roseobacters to quickly adapt to the changing environments. A wide distribution range of roseophages in the global ocean, especially in coastal environments, has been observed, reflecting the cosmopolitan nature of the Roseobacter lineage.

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

The Roseobacter-group species Phaeobacter inhibens produces the antibacterial tropodithietic acid (TDA) and the algaecidal roseobacticides with both compound classes sharing part of the same biosynthetic pathway. The purpose of this study was to investigate the production of roseobacticides more broadly in TDA-producing roseobacters and to compare the effect of producers and non-producers on microalgae. Of 33 roseobacters analyzed, roseobacticide production was a unique feature of TDA-producing P. inhibens, P. gallaeciensis and P. piscinae strains. One TDA-producing Phaeobacter, 27-4, did not produce roseobacticides, possibly due to a transposable element. TDA-producing Ruegeria and Pseudovibrio did not produce roseobacticides. Addition of roseobacticide-containing bacterial extracts affected the growth of the microalgae Rhodomonas salina, Thalassiosira pseudonana and Emiliania huxleyi, while growth of Tetraselmis suecica was unaffected. During co-cultivation, growth of E. huxleyi was initially stimulated by the roseobacticide producer DSM 17395, while the subsequent decline in algal cell numbers during senescence was enhanced. Strain 27-4 that does not produce roseobacticides had no effect on algal growth. Both bacterial strains, DSM 17395 and 27-4, grew during co-cultivation presumably utilizing algal exudates. Furthermore, TDA-producing roseobacters have potential as probiotics in marine larviculture and it is promising that the live feed Tetraselmis was unaffected by roseobacticides-containing extracts.

A member of the Roseobacter clade, Octadecabacter sp., is the dominant symbiont in the brittle star Amphipholis squamata.

Symbiotic associations with subcuticular bacteria (SCB) have been identified and studied in many echinoderms, including the SCB of the brooding brittle star, Amphipholis squamata. Previous studies on the SCB of A. squamata placed the isolated bacterium, designated as AS1, in the genus Vibrio (Gammaproteobacteria), but subsequent studies suggested that the SCB of echinoderms belong to the Alphaproteobacteria. This study examines the taxonomic composition of SCB associated with A. squamata from the Northwest Atlantic using the 16S rRNA gene and next generation sequencing. Results show the presence of a single dominant bacterial type, within the Roseobacter clade, family Rhodobacteraceae, which composes 70%-80% of the A. squamata microbiome. These Rhodobacteraceae sequences were identified as members of the genus Octadecabacter. Additionally, the original isolate, AS1, from the brittle star A. squamata also belongs in the genus Octadecabacter based on Sanger sequencing of cloned 16S rRNA gene sequences. By comparison, adjacent seawater and sediment porewater communities were significantly more diverse, hosting bacteria in the phyla Proteobacteria, Bacteroidetes, Cyanobacteria, Verrucomicrobia and Actinobacteria. Thus, a distinct SCB community is present in A. squamata that is dominated by a member of the genus Octadecabacter and is identical to the original isolate, AS1, from this brittle star.

Aestuarium zhoushanense gen. nov., sp. nov., Isolated from the Tidal Flat.

A gram-stain-negative, aerobic, ovoid or short rod-shaped, and non-motile strain, designed G7T was isolated from a tidal flat sample collected from the coast of East Sea in Zhoushan, China. Strain G7T grew at 4-40 °C and pH 6.0-9.0 (optimum, 28 °C and pH 7.5) and with 0-7% (w/v) NaCl (optimum, 1%). The predominant respiratory quinone was Q-10 and the major fatty acids (>10%) identified were C18:1 ω7c, C16:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The polar lipids of strain G7T consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, and four unidentified lipids. The genomic DNA G+C content was 56.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain G7T formed a distinct lineage belonging to the Roseobacter clade of the family Rhodobacteraceae. On the basis of morphological, physiological, and chemotaxonomic characteristics, together with the results of phylogenetic analysis, strain G7T is described as a novel species in a new genus, for which the name Aestuarium zhoushanense gen. nov., sp. nov. (type strain G7T = MCCC 1K03229T = KCTC 52584T) is proposed.

Roseobacter ponti sp. nov., isolated from seawater.

A Gram-stain-negative, coccoid to oval-shaped and non-motile bacterial strain, designated MM-7T, was isolated from seawater of the Yellow Sea, South Korea, and was subjected to a polyphasic taxonomic study. Strain MM-7T grew optimally at pH 7.0-8.0, at 25 °C and in the presence of 2-3 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain MM-7T joins the branch comprising the species of the genus Roseobacter, clustering with the type strains of Roseobacter litoralis and Roseobacter denitrificans, with which it exhibited 97.9 and 96.8 % sequence similarity values, respectively. The DNA G+C content of strain MM-7T was determined to be 60.8 mol%, and its mean DNA-DNA relatedness values with Rsb. litoralis JCM 21268T was 10.3±0.4 %. Strain MM-7T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as the major fatty acid. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and an unidentified lipid. Differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain MM-7T is distinguishable from other species of the genus Roseobacter. On the basis of the data presented, strain MM-7T is considered to represent a novel species of the genus Roseobacter, for which the name Roseobacter ponti sp. nov. is proposed. The type strain is MM-7T (=KCTC 52469T=NBRC 112431T).

Bacterial diversity across a highly stratified ecosystem: A salt-wedge Mediterranean estuary.

Highly stratified Mediterranean estuaries are unique environments where the tidal range is low and the tidal currents are almost negligible. The main characteristics of these environments are strong salinity gradients and other environmental parameters. In this study, 454 pyrosequencing of the 16S rRNA gene in combination with catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) was used to estimate the bacterial diversity across the Krka estuary in February and July 2013. The comparison of the data derived from these two techniques resulted in a significant but weak positive correlation (R=0.28) indicating a substantial difference in the bacterial community structure, depending on the applied method. The phytoplankton bloom observed in February was identified as one of the main factors shaping the bacterial community structure between the two environmentally contrasting sampling months. Roseobacter, Bacteroidetes and Gammaproteobacteria differed substantially between February and July. Typical freshwater bacterial classes (Actinobacteria and Betaproteobacteria) showed strong vertical distribution patterns depending on the salinity gradient. Cyanobacteria decreased in abundance in February due to competition with phytoplankton, while the SAR11 clade increased its abundance in July as a result of a better adaptation toward more oligotrophic conditions. The results provided the first detailed insight into the bacterial diversity in a highly stratified Mediterranean karstic estuary.

Biogeography and environmental genomics of the Roseobacter-affiliated pelagic CHAB-I-5 lineage.

The identification and functional characterization of microbial communities remains a prevailing topic in microbial oceanography as information on environmentally relevant pelagic prokaryotes is still limited. The Roseobacter group, an abundant lineage of marine Alphaproteobacteria, can constitute large proportions of the bacterioplankton. Roseobacters also occur associated with eukaryotic organisms and possess streamlined as well as larger genomes from 2.2 to >5 Mpb. Here, we show that one pelagic cluster of this group, CHAB-I-5, occurs globally from tropical to polar regions and accounts for up to 22% of the active North Sea bacterioplankton in the summer. The first sequenced genome of a CHAB-I-5 organism comprises 3.6 Mbp and exhibits features of an oligotrophic lifestyle. In a metatranscriptome of North Sea surface waters, 98% of the encoded genes were present, and genes encoding various ABC transporters, glutamate synthase and CO oxidation were particularly upregulated. Phylogenetic gene content analyses of 41 genomes of the Roseobacter group revealed a unique cluster of pelagic organisms distinct from other lineages of this group, highlighting the adaptation to life in nutrient-depleted environments.

Multiple opportunistic pathogens can cause a bleaching disease in the red seaweed Delisea pulchra.

While macroalgae (or seaweeds) are increasingly recognized to suffer from disease, in most cases the causative agents are unknown. The model macroalga Delisea pulchra is susceptible to a bleaching disease and previous work has identified two epiphytic bacteria, belonging to the Roseobacter clade, that cause bleaching under laboratory conditions. However, recent environmental surveys have shown that these in vitro pathogens are not abundant in naturally bleached D. pulchra, suggesting the presence of other pathogens capable of causing this algal disease. To test this hypothesis, we cultured bacteria that were abundant on bleached tissue across multiple disease events and assessed their ability to cause bleaching disease. We identified the new pathogens Alteromonas sp. BL110, Aquimarina sp. AD1 and BL5 and Agarivorans sp BL7 that are phylogenetically diverse, distinct from the previous two pathogens and can also be found in low abundance in healthy individuals. Moreover, we found that bacterial communities of diseased individuals that were infected with these pathogens were less diverse and more divergent from each other than those of healthy algae. This study demonstrates that multiple and opportunistic pathogens can cause the same disease outcome for D. pulchra and we postulate that such pathogens are more common in marine systems than previously anticipated.

Biofilm plasmids with a rhamnose operon are widely distributed determinants of the 'swim-or-stick' lifestyle in roseobacters.

Alphaproteobacteria of the metabolically versatile Roseobacter group (Rhodobacteraceae) are abundant in marine ecosystems and represent dominant primary colonizers of submerged surfaces. Motility and attachment are the prerequisite for the characteristic 'swim-or-stick' lifestyle of many representatives such as Phaeobacter inhibens DSM 17395. It has recently been shown that plasmid curing of its 65-kb RepA-I-type replicon with >20 genes for exopolysaccharide biosynthesis including a rhamnose operon results in nearly complete loss of motility and biofilm formation. The current study is based on the assumption that homologous biofilm plasmids are widely distributed. We analyzed 33 roseobacters that represent the phylogenetic diversity of this lineage and documented attachment as well as swimming motility for 60% of the strains. All strong biofilm formers were also motile, which is in agreement with the proposed mechanism of surface attachment. We established transposon mutants for the four genes of the rhamnose operon from P. inhibens and proved its crucial role in biofilm formation. In the Roseobacter group, two-thirds of the predicted biofilm plasmids represent the RepA-I type and their physiological role was experimentally validated via plasmid curing for four additional strains. Horizontal transfer of these replicons was documented by a comparison of the RepA-I phylogeny with the species tree. A gene content analysis of 35 RepA-I plasmids revealed a core set of genes, including the rhamnose operon and a specific ABC transporter for polysaccharide export. Taken together, our data show that RepA-I-type biofilm plasmids are essential for the sessile mode of life in the majority of cultivated roseobacters.

Isolation of TDA-producing Phaeobacter strains from sea bass larval rearing units and their probiotic effect against pathogenic Vibrio spp. in Artemia cultures.

Fish-pathogenic Vibrio can cause large-scale crashes in marine larval rearing units and, since the use of antibiotics can result in bacterial antibiotic resistance, new strategies for disease prevention are needed. Roseobacter-clade bacteria from turbot larval rearing facilities can antagonize Vibrio anguillarum and reduce mortality in V. anguillarum-infected cod and turbot larvae. In this study, it was demonstrated that antagonistic Roseobacter-clade bacteria could be isolated from sea bass larval rearing units. In addition, it was shown that they not only antagonized V. anguillarum but also V. harveyi, which is the major bacterial pathogen in crustaceans and Mediterranean sea bass larvae cultures. Concomitantly, they significantly improved survival of V. harveyi-infected brine shrimp. 16S rRNA gene sequence homology identified the antagonists as Phaeobacter sp., and in silico DNA-DNA hybridization indicated that they could belong to a new species. The genomes contained genes involved in synthesis of the antibacterial compound tropodithietic acid (TDA), and its production was confirmed by UHPLC-TOFMS. The new Phaeobacter colonized live feed (Artemia) cultures and reduced Vibrio counts significantly, since they reached only 10(4)CFUmL(-1), as opposed to 10(8)CFUmL(-1) in non-Phaeobacter treated controls. Survival of V. anguillarum-challenged Artemia nauplii was enhanced by the presence of wild type Phaeobacter compared to challenged control cultures (89±1.0% vs 8±3.2%). In conclusion, TDA-producing Phaeobacter isolated from Mediterranean marine larviculture are promising probiotic bacteria against pathogenic Vibrio in crustacean live-feed cultures for marine fish larvae.