Reclassification of Roseobacter gallaeciensis Ruiz-Ponte et al. 1998 as Phaeobacter gallaeciensis gen. nov., comb. nov., description of Phaeobacter inhibens sp. nov., reclassification of Ruegeria algicola (Lafay et al. 1995) Uchino et al. 1999 as Marinovum algicola gen. nov., comb. nov., and emended descriptions of the genera Roseobacter, Ruegeria and Leisingera

Phaeobacter aquaemixtae sp. nov., isolated from the junction between the ocean and a freshwater spring

A Gram-reaction-negative, aerobic, non-spore-forming, non-motile and rod-shaped or ovoid bacterial strain, designated SSK6-1(T), was isolated from the zone where the ocean and a freshwater spring meet at Jeju island, South Korea. Strain SSK6-1(T) grew optimally at 30 °C, at pH 7.0-7.5 and in the presence of 2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain SSK6-1(T) clustered with Phaeobacter daeponensis TF-218(T) and Phaeobacter caeruleus LMG 24369(T), exhibiting sequence similarities of 98.6 and 98.3 %, respectively. The novel strain exhibited sequence similarities of 94.6-97.8 % to the type strains of other recognized species of the genera Phaeobacter and Leisingera. Strain SSK6-1(T) contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and 11-methyl C18 : 1ω7c as the major fatty acids. The major polar lipids of strain SSK6-1(T) were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain SSK6-1(T) was 64.6 mol% and its DNA-DNA relatedness values with P. daeponensis TF-218(T) and P. caeruleus were 21 and 25 %, respectively. The differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain SSK6-1(T) is separate from recognized Phaeobacter species. On the basis of the data presented, strain SSK6-1(T) is considered to represent a novel species of the genus Phaeobacter, for which the name Phaeobacter aquaemixtae sp. nov. is proposed. The type strain is SSK6-1(T) ( = KCTC 32538(T) = CECT 8399(T)).

Genome sequence of Phaeobacter inhibens type strain (T5(T)), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens

Strain T5(T) is the type strain of the species Phaeobacter inhibens Martens et al. 2006, a secondary metabolite producing bacterium affiliated to the Roseobacter clade. Strain T5(T) was isolated from a water sample taken at the German Wadden Sea, southern North Sea. Here we describe the complete genome sequence and annotation of this bacterium with a special focus on the secondary metabolism and compare it with the genomes of the Phaeobacter inhibens strains DSM 17395 and DSM 24588 (2.10), selected because of the close phylogenetic relationship based on the 16S rRNA gene sequences of these three strains. The genome of strain T5(T) comprises 4,130,897 bp with 3.923 protein-coding genes and shows high similarities in genetic and genomic characteristics compared to P. inhibens DSM 17395 and DSM 24588 (2.10). Besides the chromosome, strain T5(T) possesses four plasmids, three of which show a high similarity to the plasmids of the strains DSM 17395 and DSM 24588 (2.10). Analysis of the fourth plasmid suggested horizontal gene transfer. Most of the genes on this plasmid are not present in the strains DSM 17395 and DSM 24588 (2.10) including a nitrous oxide reductase, which allows strain T5(T) a facultative anaerobic lifestyle. The G+C content was calculated from the genome sequence and differs significantly from the previously published value, thus warranting an emendation of the species description.

Planktomarina temperata gen. nov., sp. nov., belonging to the globally distributed RCA cluster of the marine Roseobacter clade, isolated from the German Wadden Sea

Four heterotrophic bacterial strains belonging to the globally distributed marine RCA (Roseobacter clade-affiliated) cluster (family Rhodobacteraceae , class Alphaproteobacteria ) were obtained from coastal seawater samples. Strain RCA23T was isolated from a 10−7 dilution culture inoculated with seawater from the German Wadden Sea (southern North Sea), reflecting the high abundance of RCA bacteria in this habitat. Strains IMCC1909, IMCC1923 and IMCC1933 were isolated from diluted seawater (10−3) of the Yellow Sea, South Korea. Based on 16S rRNA gene sequence comparison, Octadecabacter antarcticus 307T is the closest described relative of the RCA strains, with 95.4–95.5 % sequence similarity. Cells of RCA23T, IMCC1909, IMCC1923 and IMCC1933 are small motile rods requiring sodium ions. Optimal growth of RCA23T occurs at 25 °C and within a very narrow pH range (pH 7–8, optimum pH 7.5). The DNA G+C base content of RCA23T is 53.67 mol%. The major respiratory lipoquinone is ubiquinone-10 (Q-10) and the dominant fatty acids (>1 %) are 12 : 1 3-OH, 16 : 1ω7c, 16 : 0, 18 : 1ω7c, 18 : 0 and 11-methyl 18 : 1ω7c. The polar lipid pattern indicated the presence of phosphatidylglycerol, two unidentified aminolipids and two unidentified phospholipids. On marine agar, RCA23T forms non-pigmented, transparent to light beige, small (<1 mm), circular, convex colonies. Strain RCA23T harbours all genes for the production of bacteriochlorophyll a (BChl a). Genes encoding the light-harvesting reaction centre of BChl a (pufM) were identified in all RCA strains. No visible pigmentation was observed for any of the strains under laboratory conditions, but spectrophotometric analysis revealed weak production of BChl a by RCA23T. Morphological, physiological and genotypic features of strain RCA23T suggest that it represents a novel species of a new genus within the Rhodobacteraceae , for which we propose the name Planktomarina temperata gen. nov., sp. nov., described previously by Giebel et al. [ISME J 5 (2011), 8–19] as ‘Candidatus Planktomarina temperata’. The type strain of Planktomarina temperata is RCA23T ( = DSM 22400T = JCM 18269T).

Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336(T)), a representative of the Roseobacter clade

Leisingera methylohalidivorans Schaefer et al. 2002 emend. Vandecandelaere et al. 2008 is the type species of the genus Leisingera. The genus belongs to the Roseobacter clade (Rhodobacteraceae, Alphaproteobacteria), a widely distributed lineage in marine environments. Leisingera and particularly L. methylohalidivorans strain MB2(T) is of special interest due to its methylotrophy. Here we describe the complete genome sequence and annotation of this bacterium together with previously unreported aspects of its phenotype. The 4,650,996 bp long genome with its 4,515 protein-coding and 81 RNA genes consists of three replicons, a single chromosome and two extrachromosomal elements with sizes of 221 kb and 285 kb.

Genome sequence of Phaeobacter daeponensis type strain (DSM 23529(T)), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis

TF-218^T is the type strain of the species Phaeobacter daeponensis Yoon et al. 2007, a facultatively anaerobic Phaeobacter species isolated from tidal flats. Here we describe the draft genome sequence and annotation of this bacterium together with previously unreported aspects of its phenotype. We analyzed the genome for genes involved in secondary metabolite production and its anaerobic lifestyle, which have also been described for its closest relative Phaeobacter caeruleus. The 4,642,596 bp long genome of strain TF-218^T contains 4,310 protein-coding genes and 78 RNA genes including four rRNA operons and consists of five replicons: one chromosome and four extrachromosomal elements with sizes of 276 kb, 174 kb, 117 kb and 90 kb. Genome analysis showed that TF-218^T possesses all of the genes for indigoidine biosynthesis, and on specific media the strain showed a blue pigmentation. We also found genes for dissimilatory nitrate reduction, gene-transfer agents, NRPS/ PKS genes and signaling systems homologous to the LuxR/I system.

Roseovarius lutimaris sp. nov., isolated from a marine tidal flat

A novel Gram-staining-negative, moderately halophilic and strictly aerobic bacterium, designated strain 112T, was isolated from a tidal flat at Taean, Korea. Cells were catalase- and oxidase-positive ovoids to rods and did not produce bacteriochlorophyll a. Optimum growth of strain 112T was observed at 30 °C, at pH 6.5–7.5 and in the presence of 2–4 % (w/v) NaCl. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0 and Q-10 was detected as the predominant ubiquinone. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid and three unidentified lipids. The genomic DNA G+C content of strain 112T was 58.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 112T formed a phyletic lineage within the genus Roseovarius of the class Alphaproteobacteria . Strain 112T was most closely related to Roseovarius mucosus DFL-24T, with 96.52 % similarity. On the basis of phenotypic, chemotaxonomic and molecular properties, strain 112T represents a novel species of the genus Roseovarius , for which the name Roseovarius lutimaris sp. nov. is proposed. The type strain is 112T ( = KACC 16185T = JCM 17743T).

Genome sequence of Phaeobacter caeruleus type strain (DSM 24564(T)), a surface-associated member of the marine Roseobacter clade

In 2009 Phaeobacter caeruleus was described as a novel species affiliated with the marine Roseobacter clade, which, in turn, belongs to the class Alphaproteobacteria. The genus Phaeobacter is well known for members that produce various secondary metabolites. Here we report of putative quorum sensing systems, based on the finding of six N-acyl-homoserine lactone synthetases, and show that the blue color of P. caeruleus is probably due to the production of the secondary metabolite indigoidine. Therefore, P. caeruleus might have inhibitory effects on other bacteria. In this study the genome of the type strain DSM 24564^T was sequenced, annotated and characterized. The 5,344,419 bp long genome with its seven plasmids contains 5,227 protein-coding genes (3,904 with a predicted function) and 108 RNA genes.

Genome sequence of the phage-gene rich marine Phaeobacter arcticus type strain DSM 23566(T.)

Phaeobacter arcticus Zhang et al. 2008 belongs to the marine Roseobacter clade whose members are phylogenetically and physiologically diverse. In contrast to the type species of this genus, Phaeobacter gallaeciensis, which is well characterized, relatively little is known about the characteristics of P. arcticus. Here, we describe the features of this organism including the annotated high-quality draft genome sequence and highlight some particular traits. The 5,049,232 bp long genome with its 4,828 protein-coding and 81 RNA genes consists of one chromosome and five extrachromosomal elements. Prophage sequences identified via PHAST constitute nearly 5% of the bacterial chromosome and included a potential Mu-like phage as well as a gene-transfer agent (GTA). In addition, the genome of strain DSM 23566(T) encodes all of the genes necessary for assimilatory nitrate reduction. Phylogenetic analysis and intergenomic distances indicate that the classification of the species might need to be reconsidered.

Genome sequence of the Leisingera aquimarina type strain (DSM 24565(T)), a member of the marine Roseobacter clade rich in extrachromosomal elements

Leisingera aquimarina Vandecandelaere et al. 2008 is a member of the genomically well characterized Roseobacter clade within the family Rhodobacteraceae. Representatives of the marine Roseobacter clade are metabolically versatile and involved in carbon fixation and biogeochemical processes. They form a physiologically heterogeneous group, found predominantly in coastal or polar waters, especially in symbiosis with algae, in microbial mats, in sediments or associated with invertebrates. Here we describe the features of L. aquimarina DSM 24565(T) together with the permanent-draft genome sequence and annotation. The 5,344,253 bp long genome consists of one chromosome and an unusually high number of seven extrachromosomal elements and contains 5,129 protein-coding and 89 RNA genes. It was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2010 and of the activities of the Transregional Collaborative Research Centre 51 funded by the German Research Foundation (DFG).

Dynamics of amino acid utilization in Phaeobacter inhibens DSM 17395

Time-resolved utilization of multiple amino acids by Phaeobacter inhibens DSM 17395 was studied during growth with casamino acids. The 15 detected amino acids could be grouped according to depletion rate into four different categories, i.e. from rapid (category I) to nondepletion (category IV). Upon entry into stationary growth phase, amino acids of category I (e.g. glutamate) were (almost) completely depleted, while those of categories II (e.g. leucine) and III (e.g. serine) were further consumed at varying rates and to different extents. Thus, cultures entered stationary growth phase despite the ample presence of organic nutrients, i.e. under nonlimiting conditions. Integrated proteomic and metabolomic analysis identified 1747 proteins and 94 intracellular metabolites. Of these, 180 proteins and 86 metabolites displayed altered abundance levels during growth. Most strikingly, abundance and activity profiles of alanine dehydrogenase concomitantly increased with the onset of enhanced alanine utilization during transition into stationary growth phase. Most enzymes of amino acid and central metabolism, however, displayed unaltered abundances across exponential and stationary growth phases. In contrast, metabolites of the Entner-Doudoroff pathway and gluconeogenesis as well as cellular fatty acids increased markedly in abundance in early stationary growth phase.

Adaptation of Phaeobacter inhibens DSM 17395 to growth with complex nutrients

Phaeobacter inhibens DSM 17395, a member of the Roseobacter clade, was studied for its adaptive strategies to complex and excess nutrient supply, here mimicked by cultivation with Marine Broth (MB). During growth in process-controlled fermenters, P. inhibens DSM 17395 grew faster (3.6-fold higher μmax ) and reached higher optical densities (2.2-fold) with MB medium, as compared to the reference condition of glucose-containing mineral medium. Apparently, in the presence of MB medium, metabolism was tuned to maximize growth rate at the expense of efficiency. Comprehensive proteomic analysis of cells harvested at ½ ODmax identified 1783 (2D DIGE, membrane and extracellular protein-enriched fractions, shotgun) different proteins (50.5% coverage), 315 (based on 2D DIGE) of which displayed differential abundance profiles. Moreover, 145 different metabolites (intra- and extracellular combined) were identified, almost all of which (140) showed abundance changes. During growth with MB medium, P. inhibens DSM 17395 specifically formed the various proteins required for utilization of phospholipids and several amino acids, as well as for gluconeogenesis. Metabolic tuning on amino acid utilization is also reflected by massive discharge of urea to dispose the cell of excess ammonia. Apparently, P. inhibens DSM 17395 modulated its metabolism to simultaneously utilize diverse substrates from the complex nutrient supply.

Ruegeria intermedia sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring

A cream-coloured, Gram-negative, aerobic, non-motile moderately thermophilic, rod-to-irregular-shaped bacterium, CC-GIMAT-2T, was isolated from a coastal hot spring of Green Island (Lutao), located off Taituang, Taiwan, on marine agar 2216. The 16S rRNA gene sequence analysis and subsequent comparisons showed that it was placed into the genus Ruegeria with 97.4 % similarity to Ruegeria lacuscaerulensis ITI-1157T, and a lower sequence similarity to all other species of the genus Ruegeria . Reconstruction of phylogenetic trees indicated that strain CC-GIMAT-2T clustered within the genus Ruegeria . Robust tree topology for the genus Ruegeria including the new strain was only obtained by including all Rhodobacteraceae type strains but not if the analysis was limited to few selected taxa. The quinone system contained exclusively ubiquinone Q-10 and the fatty acid profile consisted mainly of C18 : 1ω7c, 11-methyl C18 : 1ω7c and C12 : 0 3-OH. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified aminolipid. Other lipids were detected in moderate to minor amounts. The characteristic feature of the polyamine pattern was the predominant triamine spermidine. On the basis of the 16S rRNA gene sequence analysis and of the chemotaxonomic and physiological data, strain CC-GIMAT-2T represents a novel species of the genus Ruegeria , for which the name Ruegeria intermedia sp. nov. is proposed. The type strain is CC-GIMAT-2T ( = CCUG 59209T = LMG 25539T = CCM 7758T).

Sagittula marina sp. nov., isolated from seawater and emended description of the genus Sagittula

A novel bacterium, designated strain F028-2T, was isolated from seawater at Damupo beach in Pohang, Korea, and investigated in a taxonomic study using a polyphasic approach. This novel strain was strictly aerobic, non-motile, Gram-stain-negative and rod-shaped, and occasionally formed aggregates. The temperature, pH and NaCl ranges for growth were 4–30 °C, pH 6.5–9.0 and 1–7 % (w/v), respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain F028-2T formed a lineage within the family Rhodobacteraceae of the class Alphaproteobacteria , and was closely related to members of the genera Sagittula and Antarctobacter with 96.3–96.4 % sequence similarities. The polar lipid profile of strain F028-2T comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, one unidentified phospholipid and six unidentified lipids. The predominant cellular fatty acids were C18 : 1ω7c and C12 : 1 3-OH. The genomic DNA G+C content of strain F028-2T was 61.6 mol% and the major respiratory quinone was Q-10. Based on phenotypic, phylogenetic and genotypic data, strain F028-2T is considered to represent a novel species in the genus Sagittula , for which the name Sagittula marina sp. nov. is proposed. The type strain is F028-2T ( = KCTC 23543T = JCM 17627T). An emended description of the genus Sagittula is also proposed.

Phaeobacter leonis sp. nov., an alphaproteobacterium from Mediterranean Sea sediments

A novel Gram-stain-negative, strictly aerobic, heterotrophic bacterium, designated 306(T), was isolated from near-surface (109 cm below the sea floor) sediments of the Gulf of Lions, in the Mediterranean Sea. Strain 306(T) grew at temperatures between 4 and 32 °C (optimum 17-22 °C), from pH 6.5 to 9.0 (optimum 8.0-9.0) and between 0.5 and 6.0% (w/v) NaCl (optimum 2.0%). Its DNA G+C content was 58.8 mol%. On the basis of 16S rRNA gene sequence similarity, the novel isolate belongs to the class Alphaproteobacteria and is related to the genus Phaeobacter. It shares 98.7% 16S rRNA sequence identity with Phaeobacter arcticus, its closest phylogenetic relative. It contained Q-10 as the only respiratory quinone, C(18:1)ω7c and C(16:0) as major fatty acids (>5%) and phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, two unidentified lipids and an aminolipid as polar lipids. The chemotaxonomic data are consistent with the affiliation of strain 306(T) to the genus Phaeobacter. Results of physiological experiments, biochemical tests and DNA-DNA hybridizations (with P. arcticus) indicate that strain 306(T) is genetically and phenotypically distinct from the five species of the genus Phaeobacter with validly published names. Strain 306(T) therefore represents a novel species, for which the name Phaeobacter leonis sp. nov. is proposed. The type strain is 306(T) ( =DSM 25627(T) =CIP 110369(T) =UBOCC 3187(T)).

Extrachromosomal, extraordinary and essential--the plasmids of the Roseobacter clade

The alphaproteobacterial Roseobacter clade (Rhodobacterales) is one of the most important global players in carbon and sulfur cycles of marine ecosystems. The remarkable metabolic versatility of this bacterial lineage provides access to diverse habitats and correlates with a multitude of extrachromosomal elements. Four non-homologous replication systems and additional subsets of individual compatibility groups ensure the stable maintenance of up to a dozen replicons representing up to one third of the bacterial genome. This complexity presents the challenge of successful partitioning of all low copy number replicons. Based on the phenomenon of plasmid incompatibility, we developed molecular tools for target-oriented plasmid curing and could generate customized mutants lacking hundreds of genes. This approach allows one to analyze the relevance of specific replicons including so-called chromids that are known as lifestyle determinants of bacteria. Chromids are extrachromosomal elements with a chromosome-like genetic imprint (codon usage, GC content) that are essential for competitive survival in the natural habitat, whereas classical dispensable plasmids exhibit a deviating codon usage and typically contain type IV secretion systems for conjugation. The impact of horizontal plasmid transfer is exemplified by the scattered occurrence of the characteristic aerobic anoxygenic photosynthesis among the Roseobacter clade and the recently reported transfer of the 45-kb photosynthesis gene cluster to extrachromosomal elements. Conjugative transmission may be the crucial driving force for rapid adaptations and hence the ecological prosperousness of this lineage of pink bacteria.

Ruegeria conchae sp. nov., isolated from the ark clam Scapharca broughtonii

A slightly halophilic, Gram-negative, strictly aerobic, non-motile rod, designated TW15T, was isolated from an ark clam in South Korea. Growth occurred at 10–37 °C, with 1–5 % (w/v) NaCl and at pH 7.0–10.0. Optimal growth occurred at 25–30 °C, with 2 % (w/v) NaCl and at pH 8.0. Strain TW15T exhibited both oxidase and catalase activities. The major fatty acids of strain TW15T were summed feature 8 (consisting of C18 : 1ω7c and/or C18 : 1ω6c) and 11-methyl C18 : 1ω7c. The predominant isoprenoid quinone was ubiquinone-10 (Q-10). The polar lipids of strain TW15T comprised phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid and five unidentified lipids. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain TW15T was most closely related to Ruegeria lacuscaerulensis DSM 11314T (98.0 % 16S rRNA gene sequence similarity). DNA–DNA relatedness with closely related strains was <52±3 %. The DNA G+C content was 55.7 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain TW15T represents a novel species of the genus Ruegeria , for which the name Ruegeria conchae sp. nov. is proposed. The type strain is TW15T ( = KACC 15115T  = JCM 17315T).

Phaeobacter gallaeciensis reduces Vibrio anguillarum in cultures of microalgae and rotifers, and prevents vibriosis in cod larvae

Phaeobacter gallaeciensis can antagonize fish-pathogenic bacteria in vitro, and the purpose of this study was to evaluate the organism as a probiont for marine fish larvae and their feed cultures. An in vivo mechanism of action of the antagonistic probiotic bacterium is suggested using a non-antagonistic mutant. P. gallaeciensis was readily established in axenic cultures of the two microalgae Tetraselmis suecica and Nannochloropsis oculata, and of the rotifer Brachionus plicatilis. P. gallaeciensis reached densities of 10(7) cfu/ml and did not adversely affect growth of algae or rotifers. Vibrio anguillarum was significantly reduced by wild-type P. gallaeciensis, when introduced into these cultures. A P. gallaeciensis mutant that did not produce the antibacterial compound tropodithietic acid (TDA) did not reduce V. anguillarum numbers, suggesting that production of the antibacterial compound is important for the antagonistic properties of P. gallaeciensis. The ability of P. gallaeciensis to protect fish larvae from vibriosis was determined in a bath challenge experiment using a multidish system with 1 larva per well. Unchallenged larvae reached 40% accumulated mortality which increased to 100% when infected with V. anguillarum. P. gallaeciensis reduced the mortality of challenged cod larvae (Gadus morhua) to 10%, significantly below the levels of both the challenged and the unchallenged larvae. The TDA mutant reduced mortality of the cod larvae in some of the replicates, although to a much lesser extent than the wild type. It is concluded that P. gallaeciensis is a promising probiont in marine larviculture and that TDA production likely contributes to its probiotic effect.

Planktotalea frisia gen. nov., sp. nov., isolated from the southern North Sea

A heterotrophic, aerobic bacterium, designated strain SH6-1T, was obtained from a seawater sample collected from the open North Sea during a phytoplankton bloom. Strain SH6-1T was isolated from a 10−6 dilution culture, which indicated a high abundance of this organism in the environmental sample. 16S rRNA gene sequence comparison revealed that strain SH6-1T belonged to the marine Roseobacter clade (order Rhodobacterales ) within the class Alphaproteobacteria . Pelagicola litoralis CL-ES2T was the closest phylogenetic neighbour (96.4 % 16S rRNA gene sequence similarity). Cells of strain SH6-1T were small or elongated irregular rods. Optimal growth occurred between 20 and 25 °C and between pH 7.5 and 9.0 with peptone and yeast extract. On marine agar, the isolate formed non-pigmented, small, circular, convex colonies. For growth, cells required sodium ions and the vitamins pantothenic acid and nicotinic acid amide. The DNA G+C content was 53.8 mol%. The fatty acids (>1 %) were C10 : 0 3-OH, C16 : 0, C12 : 1, C12 : 1 3-OH, C18 : 0, C18 : 1ω7c, C18 : 2 and 11-methyl C18 : 1ω7c. The polar lipid pattern indicated the presence of phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and one unidentified phospholipid. The major respiratory lipoquinone was ubiquinone Q-10. Strain SH6-1T contained the genes pufLM, which code for the bacterial photosynthesis reaction centre; however, no bacteriochlorophyll a could be detected. Physiological, genotypic and phenotypic differences from P. litoralis support the description of a novel genus and species, for which we suggest the name Planktotalea frisia gen. nov., sp. nov; the type strain of the type species is SH6-1T ( = DSM 23709T = LMG 25294T).

Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life

Phaeobacter gallaeciensis, a member of the abundant marine Roseobacter clade, is known to be an effective colonizer of biotic and abiotic marine surfaces. Production of the antibiotic tropodithietic acid (TDA) makes P. gallaeciensis a strong antagonist of many bacteria, including fish and mollusc pathogens. In addition to TDA, several other secondary metabolites are produced, allowing the mutualistic bacterium to also act as an opportunistic pathogen. Here we provide the manually annotated genome sequences of the P. gallaeciensis strains DSM 17395 and 2.10, isolated at the Atlantic coast of north western Spain and near Sydney, Australia, respectively. Despite their isolation sites from the two different hemispheres, the genome comparison demonstrated a surprisingly high level of synteny (only 3% nucleotide dissimilarity and 88% and 93% shared genes). Minor differences in the genomes result from horizontal gene transfer and phage infection. Comparison of the P. gallaeciensis genomes with those of other roseobacters revealed unique genomic traits, including the production of iron-scavenging siderophores. Experiments supported the predicted capacity of both strains to grow on various algal osmolytes. Transposon mutagenesis was used to expand the current knowledge on the TDA biosynthesis pathway in strain DSM 17395. This first comparative genomic analysis of finished genomes of two closely related strains belonging to one species of the Roseobacter clade revealed features that provide competitive advantages and facilitate surface attachment and interaction with eukaryotic hosts.

Pelagimonas varians gen. nov., sp. nov., isolated from the southern North Sea

A heterotrophic, Gram-stain-negative, aerobic bacterium, designated strain SH4-1(T), was obtained from a seawater sample collected from the southern North Sea during a phytoplankton bloom. The 16S rRNA gene sequence comparison revealed affiliation to the Roseobacter clade (class Alphaproteobacteria) with Sulfitobacter marinus SW-265(T) as the most closely related characterized strain, showing 97.2 % 16S rRNA gene sequence similarity. Calculation of phylogenetic trees based on 16S rRNA gene sequences indicated, however, that members of the genus Roseobacter, Roseobacter denitrificans Och 114(T) and Roseobacter litoralis Och 149(T) (95 % and 96 % sequence similarity, respectively) fall between strain SH4-1(T) and the Sulfitobacter cluster including Oceanibulbus indolifex HEL-45(T) (≥95.4 % sequence similarity). Cells of strain SH4-1(T) are irregular rods with at least one flagellum. Optimal growth occurred between 28 and 32 °C and at a pH between 7.0 and 8.5. Cells require the vitamin nicotinic acid amide as well as sodium ions for growth. The DNA G+C content was 55.1 mol%. The fatty acids (>1 %) comprised C10 : 0 3-OH, C12 : 1, C14 : 1 3-OH, C16 : 0, C18 : 0, C18 : 2, C18 : 1ω7c and 11-methyl C18 : 1ω7c. The polar lipid pattern indicated the presence of phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylmonomethylethanolamine, an unidentified aminolipid, one unidentified phospholipid and one other unidentified lipid. On the basis of phenotypic, chemotaxonomic and phylogenetic differences, strain SH4-1(T) represents a novel species in a new genus within the family Rhodobacteraceae, for which we propose the name Pelagimonas varians gen. nov., sp. nov. The type strain of the type species is SH4-1(T) ( = DSM 23678(T) = LMG 26343(T) = CIP 110297(T)).

Ruegeria halocynthiae sp. nov., isolated from the sea squirt Halocynthia roretzi

A Gram-negative, non-motile, rod-shaped bacterial strain, designated MA1-6T, was isolated from a sea squirt (Halocynthia roretzi) collected from the South Sea, Korea, and was characterized to determine its taxonomic position. Strain MA1-6T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2–3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MA1-6T fell within the clade comprising Ruegeria species and exhibited 95.3–96.5 % similarity to the type strains of recognized Ruegeria species. Strain MA1-6T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid, which is consistent with data for Ruegeria species. The major polar lipids detected in strain MA1-6T and Ruegeria atlantica KCTC 12424T were phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and an unidentified lipid. The DNA G+C content of strain MA1-6T was 58.6 mol%. Differential phenotypic properties, together with phylogenetic distinctiveness, demonstrated that strain MA1-6T can be distinguished from recognized Ruegeria species. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain MA1-6T is considered to represent a novel species of the genus Ruegeria , for which the name Ruegeria halocynthiae sp. nov. is proposed; the type strain is MA1-6T ( = KCTC 23463T = CCUG 60744T).

Algimonas porphyrae gen. nov., sp. nov., a member of the family Hyphomonadaceae, isolated from the red alga Porphyra yezoensis

Three Gram-negative, stalked, motile bacteria, designated 0C-2-2(T), 0C-17 and LNM-3, were isolated from the red alga Porphyra yezoensis. 16S rRNA gene sequence analysis revealed that the three novel strains belonged to the family Hyphomonadaceae, and were closely related to Litorimonas taeanensis G5(T) (96.5 % 16S rRNA gene sequence similarity) and Hellea balneolensis 26III/A02/215(T) (94.3 %). The DNA G+C contents of the novel isolates (58.5-60.2 mol%) were clearly distinguished from those of L. taeanensis G5(T) (47.1 mol%) and H. balneolensis DSM 19091(T) (47.9 mol%). The G+C content of L. taeanensis G5(T) obtained in this study was quite different from a previous report (63.6 mol%). DNA-DNA hybridization experiments showed that the novel strains constituted a single species. Eleven phenotypic features of the three isolates differed from those of both related genera. The predominant respiratory quinone was ubiquinone-10 and the major fatty acid was C(18 : 1)ω7c. On the basis of this polyphasic taxonomic analysis, the novel strains represent a novel genus and species, for which the name Algimonas porphyrae gen. nov., sp. nov. is proposed. The type strain of Algimonas porphyrae is 0C-2-2(T) (= LMG 26424(T) = NBRC 108216(T)).

Genetic analysis of the upper phenylacetate catabolic pathway in the production of tropodithietic acid by Phaeobacter gallaeciensis

Production of the antibiotic tropodithietic acid (TDA) depends on the central phenylacetate catabolic pathway, specifically on the oxygenase PaaABCDE, which catalyzes epoxidation of phenylacetyl-coenzyme A (CoA). Our study was focused on genes of the upper part of this pathway leading to phenylacetyl-CoA as precursor for TDA. Phaeobacter gallaeciensis DSM 17395 encodes two genes with homology to phenylacetyl-CoA ligases (paaK1 and paaK2), which were shown to be essential for phenylacetate catabolism but not for TDA biosynthesis and phenylalanine degradation. Thus, in P. gallaeciensis another enzyme must produce phenylacetyl-CoA from phenylalanine. Using random transposon insertion mutagenesis of a paaK1-paaK2 double mutant we identified a gene (ior1) with similarity to iorA and iorB in archaea, encoding an indolepyruvate:ferredoxin oxidoreductase (IOR). The ior1 mutant was unable to grow on phenylalanine, and production of TDA was significantly reduced compared to the wild-type level (60%). Nuclear magnetic resonance (NMR) spectroscopic investigations using (13)C-labeled phenylalanine isotopomers demonstrated that phenylalanine is transformed into phenylacetyl-CoA by Ior1. Using quantitative real-time PCR, we could show that expression of ior1 depends on the adjacent regulator IorR. Growth on phenylalanine promotes production of TDA, induces expression of ior1 (27-fold) and paaK1 (61-fold), and regulates the production of TDA. Phylogenetic analysis showed that the aerobic type of IOR as found in many roseobacters is common within a number of different phylogenetic groups of aerobic bacteria such as Burkholderia, Cupriavidis, and Rhizobia, where it may also contribute to the degradation of phenylalanine.

Tropicimonas aquimaris sp. nov., isolated from seawater, and emended description of the genus Tropicimonas Harwati et al. 2009

A Gram-staining-negative, aerobic, non-motile and rod-shaped bacterial strain, designated DPG-21T, was isolated from seawater from the South Sea in Korea, and investigated using a polyphasic taxonomic approach. Strain DPG-21T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. In a neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain DPG-21T clustered with Tropicimonas isoalkanivorans B51T (with a sequence similarity of 97.1 %); the novel strain showed lower 16S rRNA gene sequence similarities (<95.4 %) with the other species included in the tree. The mean DNA–DNA relatedness value between strain DPG-21T and T. isoalkanivorans DSM 19548T was 12 %. The predominant ubiquinones of strain DPG-21T were Q-10 and Q-9 while C18 : 1ω7c was the strain’s major fatty acid. The polar lipid profile of strain DPG-21T was similar to that of T. isoalkanivorans DSM 19548T. The genomic DNA G+C content of the novel strain was 69.6 mol%. Some phenotypic properties and the phylogenetic and genetic data indicated that strain DPG-21T was distinct from T. isoalkanivorans and represents a novel species of the genus Tropicimonas, for which the name Tropicimonas aquimaris sp. nov. is proposed. The type strain is DPG-21T ( = KCTC 23424T = CCUG 60524T).

Spatio-temporal diversity of free-living and particle-attached prokaryotes in the tropical lagoon of Ahe atoll (Tuamotu Archipelago) and its surrounding oceanic waters

Spatio-temporal variability of prokaryotic water column communities inside and outside a Polynesian tropical lagoon subjected to pearl oysters farming was assessed in terms of abundance by quantitative PCR and diversity by DGGE. Communities and operational taxonomic units (OTUs) were analysed according to dry/rainy seasons and free-living/particle-attached state. Bacterial density was higher in the lagoon compared to ocean and a seasonal trend was observed. No influence of the localisation within lagoon or of the planktonic/attached states was noticed on bacterial abundance and diversity. The OTUs belonged to Cyanobacteria, to heterotrophic groups in Proteobacteria and Flavobacteria. Archaeal abundance showed seasonal tendency and particle-prevalence, but no effect of lagoon or oceanic location was observed. Lagoon and oceanic archaeal diversity were different and Euryarchaeota (MG-II, MBG, and Halobacteria) were detected. During the dry season, planktonic and particle-associated community differed, whereas at rainy season, both communities were similar and included members usually associated with coral.

An overview of 2D DIGE analysis of marine (environmental) bacteria

Microbes are the "unseen majority" of living organisms on Earth and main drivers of the biogeochemical cycles in marine and most other environments. Their significance for an intact biosphere is bringing environmental bacteria increasingly into the focus of genome-based science. Proteomics is playing a prominent role for providing a molecular understanding of how these microbes work and for identifying the key biocatalysts involved in the major biogeochemical processes. This overview describes the major insights obtained from two-dimensional difference gel electrophoresis (2D DIGE) analyses of specific degradation pathways, complex metabolic networks, cellular processes, and regulatory patterns in the marine aerobic heterotrophs Rhodopirellula baltica SH1 (Planctomycetes) and Phaeobacter gallaeciensis DSM 17395 (Roseobacter clade) and the anaerobic aromatic compound degrader Aromatoleum aromaticum EbN1 (Betaproteobacteria).

Genomes and virulence factors of novel bacterial pathogens causing bleaching disease in the marine red alga Delisea pulchra

Nautella sp. R11, a member of the marine Roseobacter clade, causes a bleaching disease in the temperate-marine red macroalga, Delisea pulchra. To begin to elucidate the molecular mechanisms underpinning the ability of Nautella sp. R11 to colonize, invade and induce bleaching of D. pulchra, we sequenced and analyzed its genome. The genome encodes several factors such as adhesion mechanisms, systems for the transport of algal metabolites, enzymes that confer resistance to oxidative stress, cytolysins, and global regulatory mechanisms that may allow for the switch of Nautella sp. R11 to a pathogenic lifestyle. Many virulence effectors common in phytopathogenic bacteria are also found in the R11 genome, such as the plant hormone indole acetic acid, cellulose fibrils, succinoglycan and nodulation protein L. Comparative genomics with non-pathogenic Roseobacter strains and a newly identified pathogen, Phaeobacter sp. LSS9, revealed a patchy distribution of putative virulence factors in all genomes, but also led to the identification of a quorum sensing (QS) dependent transcriptional regulator that was unique to pathogenic Roseobacter strains. This observation supports the model that a combination of virulence factors and QS-dependent regulatory mechanisms enables indigenous members of the host alga's epiphytic microbial community to switch to a pathogenic lifestyle, especially under environmental conditions when innate host defence mechanisms are compromised.

Roseobacticides: small molecule modulators of an algal-bacterial symbiosis

Marine bacteria and microalgae engage in dynamic symbioses mediated by small molecules. A recent study of Phaeobacter gallaeciensis, a member of the large roseobacter clade of α-proteobacteria, and Emiliania huxleyi, a prominent member of the microphytoplankton found in large algal blooms, revealed that an algal senescence signal produced by E. huxleyi elicits the production of novel algaecides, the roseobacticides, from the bacterial symbiont. In this report, the generality of these findings are examined by expanding the number of potential elicitors. This expansion led to the identification of nine new members of the roseobacticide family, rare bacterial troponoids, which provide insights into both their biological roles and their biosynthesis. The qualitative and quantitative changes in the levels of roseobacticides induced by the additional elicitors and the elicitors’ varied efficiencies support the concept of host-targeted roseobacticide production. Structures of the new family members arise from variable substituents at the C3 and C7 positions of the roseobacticide core as the diversifying elements and suggest that the roseobacticides result from modifications and combinations of aromatic amino acids. Together these studies support a model in which algal senescence converts a mutualistic bacterial symbiont into an opportunistic parasite of its hosts.

Identification of the antibacterial compound produced by the marine epiphytic bacterium Pseudovibrio sp. D323 and related sponge-associated bacteria

Surface-associated marine bacteria often produce secondary metabolites with antagonistic activities. In this study, tropodithietic acid (TDA) was identified to be responsible for the antibacterial activity of the marine epiphytic bacterium Pseudovibrio sp. D323 and related strains. Phenol was also produced by these bacteria but was not directly related to the antibacterial activity. TDA was shown to effectively inhibit a range of marine bacteria from various phylogenetic groups. However TDA-producers themselves were resistant and are likely to possess resistance mechanism preventing autoinhibition. We propose that TDA in isolate D323 and related eukaryote-associated bacteria plays a role in defending the host organism against unwanted microbial colonisation and, possibly, bacterial pathogens.

Primorskyibacter sedentarius gen. nov., sp. nov., a novel member of the class Alphaproteobacteria from shallow marine sediments

Two Gram-negative, aerobic, non-pigmented, non-motile, rod-shaped bacteria, strains KMM 9015 and KMM 9018T, were isolated from a sample of shallow sediment collected from the Sea of Japan. An analysis of the nearly complete 16S rRNA gene sequences showed that the isolates were very close to each other phylogenetically (99.9 % sequence similarity) and their close relatives were Marinovum algicola FF3T (95.8 and 95.9 %, respectively) and members of the genera Leisingera (95.7–95.1 and 95.8–95.2 %), Phaeobacter (95.0–94.2 and 95.1–94.2 %) and Thalassobius (96.3–94.8 and 96.2–94.7 %) of the class Alphaproteobacteria. In phylogenetic trees based on 16S rRNA gene sequences, strains KMM 9015 and KMM 9018T were positioned as a distinct phylogenetic line adjacent to Marinovum algicola. The major isoprenoid quinone was Q-10, the polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown lipid and the major fatty acid was C18 : 1ω7c, followed by 11-methyl C18 : 1ω7c, in both strains. The DNA G+C contents of strains KMM 9015 and KMM 9018T were 60.2 and 61.9 mol%, respectively. Based on distinctive phenotypic characteristics and phylogenetic analysis, strains KMM 9015 and KMM 9018T represent a novel species in a novel genus, for which the name Primorskyibacter sedentarius gen. nov., sp. nov. is proposed. The type strain of Primorskyibacter sedentarius is strain KMM 9018T ( = NRIC 0784T  = JCM 16874T).

Lentibacter algarum gen. nov., sp. nov., isolated from coastal water during a massive green algae bloom

Two novel Gram-stain-negative, aerobic strains (ZXM100(T) and ZXM098) were isolated from seawater in the coastal region of Qingdao (36.027° N 120.184° E), China, during a massive green algae bloom. Cells were ovoid to irregular short rods and lacked flagella. Poly-β-hydroxybutyrate was accumulated. Cells did not contain bacteriochlorophyll a. The isolates grew at NaCl concentrations of 3-9 % and 22-28 °C. C(18 : 1)ω7c, C(18 : 0) and C(16 : 0) were the major fatty acid components. The polar lipids of ZXM100(T) were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, a single lipid and an unidentified aminolipid. The predominant isoprenoid quinone of ZXM100(T) was Q-10. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains belonged to the family Rhodobacteraceae. Based on the results obtained in this study, strain ZXM100(T) was considered to represent a novel species in a new genus, for which the name Lentibacter algarum gen. nov., sp. nov. is proposed. The type strain is ZXM100(T) ( = LMG 24861(T) = CGMCC 1.10234(T)); the DNA G+C content of the type strain is 54.6 mol%.

Pacificibacter maritimus gen. nov., sp. nov., isolated from shallow marine sediment

An aerobic, Gram-stain-negative, non-pigmented, non-motile bacterium, strain KMM 9031T, was isolated from a sandy sediment sample collected from the shore of the Sea of Japan and subjected to phenotypic and phylogenetic analysis. Based on comparative 16S rRNA gene sequence analysis, strain KMM 9031T constituted a separate phylogenetic line within the Roseobacter clade of the class Alphaproteobacteria, sharing highest sequence similarities with members of the genera Roseovarius (92.7–95.3 %), Pseudoruegeria (94.5 %), Sulfitobacter (92.7–94.4 %) and Thalassobacter (94.2–94.3 %). The predominant fatty acid of strain KMM 9031T was C18 : 1ω7c, with C16 : 0, C10 : 0 3-OH and C12 : 1 3-OH present in lesser amounts. The DNA G+C content of the isolate was 52.6 mol%. The major isoprenoid quinone was Q-10 and polar lipids comprised phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol and two unknown lipids. On the basis of phylogenetic analysis and physiological and biochemical characterization, strain KMM 9031T represents a novel species in a new genus, for which the name Pacificibacter maritimus gen. nov., sp. nov. is proposed; the type strain is KMM 9031T ( = NRIC 0785T  = JCM 17096T).

Maritalea porphyrae sp. nov., isolated from a red alga (Porphyra yezoensis), and transfer of Zhangella mobilis to Maritalea mobilis comb. nov

Three Gram-negative, motile, aerobic bacteria were isolated from cultures of the marine red alga Porphyra yezoensis. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the novel strains were closely related to Maritalea myrionectae CL-SK30(T) (97.9% 16S rRNA gene sequence similarity) and Zhangella mobilis E6(T) (96.2 %). 16S rRNA gene sequence similarity between Z. mobilis E6(T) and M. myrionectae CL-SK30(T) was 97.9%. The DNA G+C contents of the isolates (49.4-50.0 mol%) were similar to those of M. myrionectae DSM 19524(T) (52.3 mol%) and Z. mobilis JCM 15144(T) (50.3 mol%). From these results, it was difficult to differentiate the genus Zhangella from the genus Maritalea. DNA-DNA hybridization demonstrated that the isolates belonged to a single species. The isolates could also be distinguished from M. myrionectae and Z. mobilis on the basis of chemotaxonomic and phenotypic features, including fatty acid composition (particularly C(16:1)ω7c), growth with 6-9% (w/v) NaCl, carbon utilization, oxidation patterns and so on. A novel species of the genus Maritalea is proposed to accommodate the three isolates, with the name Maritalea porphyrae sp. nov. The type strain is LCM-3(T) (=LMG 25872(T)=NBRC 107169(T)). Furthermore, it is proposed that Zhangella mobilis should be transferred from the genus Zhangella to the genus Maritalea, with the name Maritalea mobilis comb. nov. (type strain E6(T)=CGMCC 1.7002(T)=JCM 15144(T)).

Litoreibacter albidus gen. nov., sp. nov. and Litoreibacter janthinus sp. nov., members of the class Alphaproteobacteria isolated from the seashore

Two Gram-negative, strictly aerobic, non-motile bacteria designated strains KMM 3851T and KMM 3842T were respectively isolated from a marine snail specimen (Umbonium costatum) and from surrounding sediments collected simultaneously from the shore of the Sea of Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains KMM 3851T and KMM 3842T were affiliated with the Roseobacter lineage of the class Alphaproteobacteria as a separate phylogenetic line adjacent to the members of the genus Thalassobacter. These novel isolates shared 98.5 % 16S rRNA gene sequence similarity and 15 % DNA–DNA relatedness. The major isoprenoid quinone of both strains was Q-10 and polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and aminophospholipids. In addition, strain KMM 3851T contained two unknown lipids, whereas strain KMM 3842T contained diphosphatidylglycerol. Fatty acid analysis revealed C18 : 1 ω7c and C16 : 0 as major components and small amounts of C18 : 2. The DNA G+C contents were 60.4 mol% (KMM 3851T) and 58.5 mol% (KMM 3842T). Based on distinctive phenotypic characteristics, DNA–DNA hybridization data and phylogenetic distance, strains KMM 3851T and KMM 3842T should be classified as representatives of two novel species in a new genus, Litoreibacter gen. nov., with the type species Litoreibacter albidus sp. nov. (type strain KMM 3851T =NRIC 0773T =JCM 16493T) and a second species Litoreibacter janthinus sp. nov. (type strain KMM 3842T =NRIC 0772T =JCM 16492T).

Quorum quenching in cultivable bacteria from dense marine coastal microbial communities

Acylhomoserine lactone (AHLs)-mediated quorum-sensing (QS) processes seem to be common in the marine environment and among marine pathogenic bacteria, but no data are available on the prevalence of bacteria capable of interfering with QS in the sea, a process that has been generally termed 'quorum quenching' (QQ). One hundred and sixty-six strains isolated from different marine dense microbial communities were screened for their ability to interfere with AHL activity. Twenty-four strains (14.4%) were able to eliminate or significantly reduce N-hexanoyl-l-homoserine lactone activity as detected by the biosensor strain Chromobacterium violaceum CV026, a much higher percentage than that reported for soil isolates, which reinforces the ecological role of QS and QQ in the marine environment. Among these, 15 strains were also able to inhibit N-decanoyl-l-homoserine lactone activity and all of them were confirmed to enzymatically inactivate the AHL signals by HPLC-MS. Active isolates belonged to nine different genera of prevalently or exclusively marine origin, including members of the Alpha- and Gammaproteobacteria (8), Actinobacteria (2), Firmicutes (4) and Bacteroidetes (1). Whether the high frequency and diversity of cultivable bacteria with QQ activity found in near-shore marine isolates reflects their prevalence among pelagic marine bacterial communities deserves further investigation in order to understand the ecological importance of AHL-mediated QS and QQ processes in the marine environment.

Origin and evolution of a novel DnaA-like plasmid replication type in Rhodobacterales

Large extrachromosomal elements are widespread among Alphaproteobacteria, but it is unclear how up to a dozen low-copy plasmids can stably coexist within the same cell. We systematically analyzed the distribution of different replicons in about 40 completely sequenced genomes of the Roseobacter clade (Rhodobacterales) and surprisingly identified a novel plasmid replicon type. The conserved replication module comprises the characteristic partitioning operon (parAB) and a hitherto unknown replicase. The latter shows a weak homology to the chromosomal replication initiator DnaA and was accordingly named "DnaA-like." Phylogenetic analyses of the adjacent parAB genes document a common ancestry with repA- and repB-type plasmids and moreover indicate the presence of two dnaA-like compatibility groups. This conclusion is supported by conserved palindrome sequences within the replication module that probably represent crucial centromeric anchors for plasmid partitioning. The functionality of dnaA-like replicons was proven by transformation experiments in Phaeobacter gallaeciensis BS107 (DSM 17395). This Roseobacter strain furthermore allows the phenotypical monitoring of plasmid incompatibility, based on a 262-kb dnaA-like replicon required for the brown pigmentation of the bacterium. Uptake of an incompatible construct induces its loss, hence resulting in white colonies. Accordingly, we could substantiate the in silico predictions about stable maintenance of dnaA-like plasmids and thereby functionally validate our approach of plasmid classification based on phylogenetic analyses.

Litorimicrobium taeanense gen. nov., sp. nov., isolated from a sandy beach

A Gram-reaction-negative, strictly aerobic, non-motile bacterium, designated strain G4(T), was isolated from a sandy beach of Taean in South Korea. Cells were ovoid rods and were catalase- and oxidase-positive. Growth of strain G4(T) was determined at 15-35 °C (optimum 25-30 °C) and pH 6-8 (optimum pH 6.5-7.5). Strain G4(T) contained Q-10 as the predominant isoprenoid quinone and C(18 : 1)ω7c (59.0 %), C(18 : 1)ω7c 11-methyl (11.3 %) and C(12 : 1) 3-OH (9.8 %) as the major fatty acids. The major cellular polar lipids were identified as phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unidentified amino lipid, an unidentified phospholipid and an unidentified lipid. The DNA G+C content was 62.4 mol%. Phylogenetic and comparative analysis based on 16S rRNA gene sequences indicated that strain G4(T) fell within the family Rhodobacteraceae of Alphaproteobacteria and was most closely related to members of the genera Marinovum, Leisingera and Phaeobacter with 95.5-96.4 % sequence similarities. On the basis of phenotypic, chemotaxonomic and molecular properties, strain G4(T) represents a novel species of a novel genus within the family Rhodobacteraceae, for which the name Litorimicrobium taeanense gen. nov., sp. nov. is proposed. The type strain is G4(T) ( = KACC 13706(T)  = DSM 22007(T)).

Celeribacter neptunius gen. nov., sp. nov., a new member of the class Alphaproteobacteria

A whitish Gram-negative, motile, aerobic bacterium, designated strain H 14T, was isolated from seawater collected at St Kilda beach in Port Phillip Bay, Melbourne, Australia. Analysis of 16S rRNA gene sequences revealed that the organism belonged to the Roseobacter lineage of the class Alphaproteobacteria, forming a distinct evolutionary lineage at the genus level. Strain H 14T was distantly related to the genera Nautella, Ruegeria and Pseudoruegeria (family Rhodobacteraceae). Strain H 14T was unable to degrade gelatin, casein, chitin, agar and starch, did not produce any carotenoids, did not possess bacteriochlorophyll a and had a limited ability to utilize carbon sources. Strain H 14T grew with concentrations of 1–8 % (w/v) NaCl and over a temperature range of 5–35 °C. Phosphatidylglycerol was the major phospholipid (90 %); phosphatidylcholine (7.9 %) and phosphatidylethanolamine (2.0 %) were present in minor quantities. The predominant fatty acids were C18 : 1 ω7c (82.4 %), C18 : 1 ω9c (5.1 %) and C18 : 0 (3.8 %). The DNA G+C composition for strain H 14T was 59.1 mol%. Based on the results of physiological, biochemical, chemotaxonomic and phylogenetic investigations, a new genus, Celeribacter gen. nov., with the type species Celeribacter neptunius sp. nov. is proposed. The type strain of the type species is H 14T (=KMM 6012T=CIP 109922T).

Ruegeria faecimaris sp. nov., isolated from a tidal flat sediment

A Gram-negative-staining, non-motile and rod-shaped bacterial strain, HD-28(T), was isolated from a tidal flat of the Yellow Sea, Korea. Strain HD-28(T) grew optimally at pH 7.0-8.0 and 30 °C in the presence of 2-3 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain HD-28(T) was most closely related to species of the genus Ruegeria and exhibited 95.5-96.9 % 16S rRNA gene sequence similarity to the type strains of Ruegeria species. A neighbour-joining phylogenetic tree based on gyrB gene sequences also showed that strain HD-28(T) fell within the cluster comprising recognized species of the genus Ruegeria, showing 77.5-83.9 % sequence similarity. Strain HD-28(T) contained Q-10 as the predominant ubiquinone and C(18 : 1)ω7c as the major fatty acid. The major polar lipids detected in strain HD-28(T) were phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and two unidentified lipids. The DNA G+C content was 57.9 mol%. Differential phenotypic properties, together with phylogenetic distinctiveness, demonstrated that strain HD-28(T) could be distinguished from recognized species of the genus Ruegeria. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain HD-28(T) is considered to represent a novel species of the genus Ruegeria, for which the name Ruegeria faecimaris sp. nov. is proposed. The type strain is HD-28(T) ( = KCTC 23044(T) = CCUG 58878(T)).

Microfabrication of patterns of adherent marine bacterium Phaeobacter inhibens using soft lithography and scanning probe lithography

Two lithographic approaches have been explored for the microfabrication of cellular patterns based on the attachment of marine bacterium Phaeobacter inhibens strain T5. Strain T5 produces a new antibiotic that makes this bacterium potentially interesting for the pharmaceutical market and as a probiotic organism in aquacultures and in controlling biofouling. The microcontact printing (microCP) method is based on the micropatterning of self-assembled monolayers (SAMs) terminated with adhesive end groups such as CH(3) and COOH and nonadhesive groups (e.g., short oligomers of ethylene glycol (OEG)) to form micropatterned substrates for the adhesion of strain T5. The scanning probe lithographic method is based on the surface modification of OEG SAM by using a microelectrode, the probe of a scanning electrochemical microscope (SECM). Oxidizing agents (e.g., Br(2)) were electrogenerated in situ at the microelectrodes from Br(-) in aqueous solution to remove OEG SAMs locally, which allows the subsequent adsorption of bacteria. Various micropatterns of bacteria could be formed in situ on the substrate without a prefabricated template. The fabricated cellular patterns may be applied to a variety of marine biological studies that require the analysis of biofilm formation, cell-cell and cell-surface interactions, and cell-based biosensors and bioelectronics.

Ruegeria marina sp. nov., isolated from marine sediment

A Gram-negative, neutrophilic and rod-shaped bacterium, strain ZH17(T), was isolated from a marine sediment of the East China Sea and subjected to a polyphasic taxonomic characterization. The isolate grew in the presence of 0-7.5 % (w/v) NaCl and at pH 6.5-9.0; optimum growth was observed with 0.5-3.0 % (w/v) NaCl and at pH 7.5. Chemotaxonomic analysis showed ubiquinone-10 as predominant respiratory quinone and C(18 : 1)ω7c, 11-methyl C(18 : 1)ω7c, C(16 : 0), C(12 : 0) 3-OH and C(16 : 0) 2-OH as major fatty acids. The genomic DNA G+C content was 63.5 mol%. Comparative 16S rRNA gene sequence analysis revealed that the isolate belongs to the genus Ruegeria. Strain ZH17(T) exhibited the closest phylogenetic affinity to the type strain of Ruegeria pomeroyi, with 97.2 % sequence similarity, and less than 97 % sequence similarity with respect to other described species of the genus Ruegeria. The DNA-DNA reassociation value between strain ZH17(T) and R. pomeroyi DSM 15171(T) was 50.7 %. On the basis of phenotypic and genotypic data, strain ZH17(T) represents a novel species of the genus Ruegeria, for which the name Ruegeria marina sp. nov. (type strain ZH17(T) =CGMCC 1.9108(T) =JCM 16262(T)) is proposed.