Octadecabacter algicola sp. nov. and Octadecabacter dasysiphoniae sp. nov., isolated from a marine red alga and emended description of the genus Octadecabacter

Two Gram-stain-negative, strictly aerobic, catalase- and oxidase-positive and non-motile rod-shaped bacteria, strains D2-3^T and G9-8^T, were isolated from a marine red alga. Both strains contained ubiquinone-10 as the sole isoprenoid quinone. As the major cellular fatty acids (>5.0 %), D2-3^T contained C_16 : 0, 11-methyl-C_18 : 1ω7c, summed feature 3 (C_16 : 1ω7c and/or C_16 : 1ω6c), and summed feature 8 (C_18 : 1ω7c and/or C_18 : 1ω6c), whereas G9-8^T contained C_16 : 0, 11-methyl-C_18 : 1ω7c, C_12 : 1 3-OH, and summed feature 8. The DNA G+C contents of D2-3^T and G9-8^T were 54.4 % and 56.0 %, respectively. As the major polar lipids, phosphatidylglycerol, diphosphatidylglycerol and unidentified phospholipid, aminolipid and lipid were identified from both strains, and phosphatidylcholine was additionally detected from G9-8^T only. The 16S rRNA gene sequence similarity of D2-3^T and G9-8^T was 98.5 % and their digital DNA-DNA hybridization (DDH) value was 19.1 %. Phylogenetic analyses based on 16S rRNA gene and genome sequences revealed that D2-3^T and G9-8^T formed respectively distinct phylogenetic lineages within the genus Octadecabacter. D2-3^T and G9-8^T were most closely related to Octadecabacter ascidiaceicola RA1-3^T and Octadecabacter antarcticus 307^T, with 98.9 % and 98.5 % 16S rRNA gene sequence similarities, respectively, and digital DDH values between D2-3^T and O. ascidiaceicola and between G9-8^T and O. antarcticus were 18.3 % and 19.5 %, respectively. Phenotypic, chemotaxonomic and molecular features support the hypothesis that D2-3^T and G9-8^T represent two novel species of the genus Octadecabacter, for which the names Octadecabacter algicola sp. nov. and Octadecabacter dasysiphoniae sp. nov. are proposed. The type strains of O. algicola and O. dasysiphoniae are D2-3^T (=KACC 22493^T =JCM 34969^T) and G9-8^T (=KACC 22488^T =JCM 34973^T), respectively.

TCA cycle enhancement and uptake of monomeric substrates support growth of marine Roseobacter at low temperature

Members of the marine Roseobacter group are ubiquitous in global oceans, but their cold-adaptive strategies have barely been studied. Here, as represented by Loktanella salsilacus strains enriched in polar regions, we firstly characterized the metabolic features of a cold-adapted Roseobacter by multi-omics, enzyme activities, and carbon utilization procedures. Unlike in most cold-adapted microorganisms, the TCA cycle is enhanced by accumulating more enzyme molecules, whereas genes for thiosulfate oxidation, sulfate reduction, nitrate reduction, and urea metabolism are all expressed at lower abundance when L. salsilacus was growing at 5 °C in comparison with higher temperatures. Moreover, a carbon-source competition experiment has evidenced the preferential use of glucose rather than sucrose at low temperature. This selective utilization is likely to be controlled by the carbon source uptake and transformation steps, which also reflects an economic calculation balancing energy production and functional plasticity. These findings provide a mechanistic understanding of how a Roseobacter member and possibly others as well counteract polar constraints.

The metabolic adaptation of Loktanella salsilacus strains to cold involves an increase of enzymes involved in the TCA cycle and preferential use of glucose rather than sucrose at low temperature, providing insights into how Roseobacter adapts in polar regions.

Gymnodinialimonas ceratoperidinii gen. nov., sp. nov., isolated from rare marine dinoflagellate Ceratoperidinium margalefii

A bacterial strain, designated J12C1-MA-4^T, was isolated from liquid culture of the dinoflagellate Ceratoperidinium margalefii. The bacterium was Gram-negative, aerobic, and rod-shaped. Oxidase and catalase were positive. Optimal growth was observed at 30 °C, pH 7.0, in the presence of 1% (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene and a 92 core gene set suggested that the strain J12C1-MA-4^T belongs to the family Rhodobacteraceae in the class Alphaproteobacteria and represents a taxon separated from other genera. 16S rRNA gene sequence of the strain J12C1-MA-4^T showed high similarities to Loktanella ponticola KCTC 42133^T (95.7%), Pseudooctadecabacter jejudonensis KCTC 32525^T (95.5%) and Jannaschia helgolandensis KCTC 12191^T (95.3%). The genome length of strain J12C1-MA-4^T was 3,621,968 bp with a DNA G + C content of 64.48 mol%. The major cellular fatty acids of strain J12C1-MA-4^T were summed feature 8 (comprising C_18:1ω7c and/or C_18:1ω6c) (> 10%). Phosphatidylglycerol (PG), phosphatidylcholine (PC), phospholipids (PL), lipids 1 (L1) and aminolipid (AL) were shown to be the major polar lipids. The sole predominant isoprenoid quinone was Q-10. Based on phylogenetic, phenotypic, chemotaxonomic and genomic features, we propose that strain J12C1-MA-4^T represent a novel species in the novel genus of the family Rhodobacteraceae, with the proposed name Gymnodinialimonas ceratoperidinii gen. nov., sp. nov.. The type strain is J12C1-MA-4^T (=KCTC 82770^T =GDMCC 1.2729^T).

Roseitranquillus sediminis gen. nov., sp. nov. a novel genus and species of the family Rhodobacteraceae, isolated from sediment of an Arctic fjord

A Gram-negative, aerobic, non-motile, oxidase-positive, catalase-positive, rod-shaped bacterium, designated strain MCCB 386^T was isolated from sediment samples collected from Kongsfjorden, an Arctic fjord. The strain MCCB 386^T showed growth at 4-37 °C (optimum 27°C) in the presence of 1-8% NaCl (w/v, optimum 3.5%) and at pH 6.0-8.0 (optimum pH 7.0). The major fatty acids were C_18:1ω7c (54.0%) and 11-methyl C_18:1ω7c (22.6%). The dominant respiratory quinone was Q-10. The major polar lipids comprised of phosphatidylcholine (PC), diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphoglycolipid (PGL), one unidentified aminolipid, two glycolipids and two unidentified lipids. The genomic G+C content of the strain MCCB 386^T was 68.1 mol%. The 16 S rRNA gene sequences based phylogenetic analysis of MCCB 386^T showed that Psychromarinibacter halotolerans YBW34^T (95.88%) is the most closely related species. In addition, overall genome relatedness indices (OGRI) of MCCB 386^T with closely related strains were lower than threshold level for species and genus delineation. The analysis of Biosynthetic Gene clusters (BGCs) revealed the potential of this strain for production of novel bioactive secondary metabolites. As per polyphasic taxonomic characterisation, strain MCCB 386^T represents a novel species of a novel genus for which the name Roseitranquillus sediminis gen. nov., sp. nov. is suggested. The type strain of the species is MCCB 386^T (= JCM 33,538^T= KACC 21,531^T).

Patterns in Benthic Microbial Community Structure Across Environmental Gradients in the Beaufort Sea Shelf and Slope

The paradigm of tight pelagic-benthic coupling in the Arctic suggests that current and future fluctuations in sea ice, primary production, and riverine input resulting from global climate change will have major impacts on benthic ecosystems. To understand how these changes will affect benthic ecosystem function, we must characterize diversity, spatial distribution, and community composition for all faunal components. Bacteria and archaea link the biotic and abiotic realms, playing important roles in organic matter (OM) decomposition, biogeochemical cycling, and contaminant degradation, yet sediment microbial communities have rarely been examined in the North American Arctic. Shifts in microbial community structure and composition occur with shifts in OM inputs and contaminant exposure, with implications for shifts in ecological function. Furthermore, the characterization of benthic microbial communities provides a foundation from which to build focused experimental research. We assessed diversity and community structure of benthic prokaryotes in the upper 1 cm of sediments in the southern Beaufort Sea (United States and Canada), and investigated environmental correlates of prokaryotic community structure over a broad spatial scale (spanning 1,229 km) at depths ranging from 17 to 1,200 m. Based on hierarchical clustering, we identified four prokaryotic assemblages from the 85 samples analyzed. Two were largely delineated by the markedly different environmental conditions in shallow shelf vs. upper continental slope sediments. A third assemblage was mainly comprised of operational taxonomic units (OTUs) shared between the shallow shelf and upper slope assemblages. The fourth assemblage corresponded to sediments receiving heavier OM loading, likely resulting in a shallower anoxic layer. These sites may also harbor microbial mats and/or methane seeps. Substructure within these assemblages generally reflected turnover along a longitudinal gradient, which may be related to the quantity and composition of OM deposited to the seafloor; bathymetry and the Mackenzie River were the two major factors influencing prokaryote distribution on this scale. In a broader geographical context, differences in prokaryotic community structure between the Beaufort Sea and Norwegian Arctic suggest that benthic microbes may reflect regional differences in the hydrography, biogeochemistry, and bathymetry of Arctic shelf systems.

Pseudooceanicola algae sp. nov., isolated from the marine macroalga Fucus spiralis, shows genomic and physiological adaptations for an algae-associated lifestyle

The genus Pseudooceanicola from the alphaproteobacterial Roseobacter group currently includes ten validated species. We herein describe strain Lw-13eT, the first Pseudooceanicola species from marine macroalgae, isolated from the brown alga Fucus spiralis abundant at European and North American coasts. Physiological and pangenome analyses of Lw-13eT showed corresponding adaptive features. Adaptations to the tidal environment include a broad salinity tolerance, degradation of macroalgae-derived substrates (mannitol, mannose, proline), and resistance to several antibiotics and heavy metals. Notably, Lw-13eT can degrade oligomeric alginate via PL15 alginate lyase encoded in a polysaccharide utilization locus (PUL), rarely described for roseobacters to date. Plasmid localization of the PUL strengthens the importance of mobile genetic elements for evolutionary adaptations within the Roseobacter group. PL15 homologs were primarily detected in marine plant-associated metagenomes from coastal environments but not in the open ocean, corroborating its adaptive role in algae-rich habitats. Exceptional is the tolerance of Lw-13eT against the broad-spectrum antibiotic tropodithietic acid, produced by Phaeobacter spp. co-occurring in coastal habitats. Furthermore, Lw-13eT exhibits features resembling terrestrial plant-bacteria associations, i.e. biosynthesis of siderophores, terpenes and volatiles, which may contribute to mutual bacteria-algae interactions. Closest described relative of Lw-13eT is Pseudopuniceibacterium sediminis CY03T with 98.4% 16S rRNA gene sequence similarity. However, protein sequence-based core genome phylogeny and average nucleotide identity indicate affiliation of Lw-13eT with the genus Pseudooceanicola. Based on phylogenetic, physiological and (chemo)taxonomic distinctions, we propose strain Lw-13eT (=DSM 29013T=LMG 30557T) as a novel species with the name Pseudooceanicola algae.

Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.

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.

Taxonomic profiles in metagenomic analyses of free-living microbial communities in the Ofunato Bay

The Ofunato Bay in Iwate Prefecture, Japan is a deep coastal bay located at the center of the Sanriku Rias Coast and considered an economically and environmentally important asset. Here, we describe the first whole genome sequencing (WGS) study on the microbial community of the bay, where surface water samples were collected from three stations along its length to cover the entire bay; we preliminarily sequenced a 0.2 μm filter fraction among sequentially size-fractionated samples of 20.0, 5.0, 0.8 and 0.2 μm filters, targeting the free-living fraction only. From the 0.27-0.34 Gb WGS library, 0.9 × 10⁶-1.2 × 10⁶ reads from three sampling stations revealed 29 bacterial phyla (~80% of assigned reads), 3 archaeal phyla (~4%) and 59 eukaryotic phyla (~15%). Microbial diversity obtained from the WGS approach was compared with 16S rRNA gene results by mining WGS metagenomes, and we found similar estimates. The most frequently recovered bacterial sequences were Proteobacteria, predominantly comprised of 18.0-19.6% Planktomarina (Family Rhodobacteraceae) and 13.7-17.5% Candidatus Pelagibacter (Family Pelagibacterales). Other dominant bacterial genera, including Polaribacter (3.5-6.1%), Flavobacterium (1.8-2.6%), Sphingobacterium (1.4-1.6%) and Cellulophaga (1.4-2.0%), were members of Bacteroidetes and likely associated with the degradation and turnover of organic matter. The Marine Group I Archaea Nitrosopumilus was also detected. Remarkably, eukaryotic green alga Bathycoccus, Ostreococcus and Micromonas accounted for 8.8-15.2%, 3.6-4.9% and 2.1-3.1% of total read counts, respectively, highlighting their potential roles in the phytoplankton bloom after winter mixing.

Aestuariibius insulae gen. nov., sp. nov., isolated from a tidal flat sediment

A Gram-stain-negative, non-motile and ovoid or rod-shaped bacterial strain, DBTF-13^T, which was isolated from a tidal flat sediment of the Yellow Sea in South Korea, was characterized taxonomically. Strain DBTF-13^T grew optimally at 25-30 °C and pH 7.0-8.0, and in the presence of 2.0 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences revealed that strain DBTF-13^T formed an evolutionary lineage independent of other genera, including the genera Pseudooctadecabacter and Octadecabacter. Strain DBTF-13^T exhibited 16S rRNA gene sequence similarity values of 96.9 % to the type strain of Pseudooctadecabacter jejudonensis, and of 95.8-96.5 % to the type strains of Octadecabacter species. Strain DBTF-13^T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and C16 : 0 as the major fatty acids. The major polar lipids of strain DBTF-13^T were phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain DBTF-13^T was 61.6 mol%. The chemotaxonomic data and other differential phenotypic properties made it reasonable to differentiate strain DBTF-13^T from the genera Pseudooctadecabacter and Octadecabacter. On the basis of the data presented, strain DBTF-13^T constitutes a new genus and species within the class Alphaproteobacteria, for which the name Aestuariibius insulae gen. nov., sp. nov. is proposed. The type strain is DBTF-13^T (=KACC 19432^T=NBRC 113038^T).

Psychromarinibacter halotolerans gen. nov., sp. nov., isolated from seawater of the Yellow Sea

A Gram-stain-negative, strictly aerobic, motile, non-gliding, oxidase-positive, catalase-positive, rod-shaped bacterium, designated strain YBW34T, was isolated from seawater from the bottom of the Yellow Sea at station H12 (-73m in depth). Growth occurred at 10-45 °C (optimum 28 °C), in the presence of 1-12 % NaCl (w/v, optimum 4 %) and at pH 6.0-8.0 (optimum pH 7.0). The major fatty acids (>10 %) were C18 : 1 ω7c and C16 : 0. The major polar lipids comprised phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and three unidentified aminolipids. The major respiratory quinone was ubiquinone-10 (Q-10). The DNA G+C content of strain YBW34T was 64.2 mol%. The most closely related species was Tropicimonas isoalkanivorans JCM 14837T with 95.8 % sequence similarity in Alphaproteobacteria. It showed 16S rRNA gene sequence similarities of 93.03-95.49, 93.03-95.49 and 95.31-95.32 % to species of genera Rhodovulum, Lutimaribacter and Oceanicola, respectively. Nevertheless, strain YBW34T formed a distinct lineage in the trees which did not join the genera mentioned above in the phylogenetic dendrogram based on 16S rRNA gene sequences. The phenotypic, chemotaxonomic and phylogenetic data indicated that strain YBW34T represents a novel genus and species, for which the name Psychromarinibacter halotolerans gen. nov., sp. nov. is proposed. The type strain is YBW34T (=JCM 31462T=KCTC 52366T=MCCC 1K03203T).

Octadecabacterponticola sp. nov., isolated from seawater

A Gram-stain-negative, non-spore-forming, non-flagellated and coccoid, ovoid or rod-shaped bacterial strain, HDSW-34T, was isolated from seawater of Hwang-do on the Yellow Sea, South Korea, and subjected to a taxonomic study using a polyphasic approach. Strain HDSW-34T grew optimally at 30 °C, at pH 7.0-8.0 and in the presence of 1.0-2.0 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain HDSW-34Tclustered with the type strains of four species of the genus Octadecabacter, showing 96.7-97.6 % sequence similarity. Strain HDSW-34T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids detected in strain HDSW-34T were phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain HDSW-34T was 62.0 mol% and its DNA-DNA relatedness values with Octadecabacterantarcticus CIP 106731T and Octadecabacterarcticus DSM 13978T were 11-18 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain HDSW-34T is separated from other recognized species of the genus Octadecabacter. On the basis of the data presented, strain HDSW-34T is considered to represent a novel species of the genus Octadecabacter, for which the name Octadecabacterponticola sp. nov. is proposed. The type strain is HDSW-34T (= KCTC 52250T=NBRC 112296T).

Closed Genome Sequence of Octadecabacter temperatus SB1, the First Mesophilic Species of the Genus Octadecabacter

The Gram-negative alphaproteobacterium Octadecabacter temperatus SB1 (DSM 26878) belongs to the marine Roseobacter clade. The genome of this strain is the smallest closed genome of the Roseobacter clade. O. temperatus SB1 is the first described nonpolar mesophilic isolate of the genus Octadecabacter and the type strain of the species.