Pelagivirga sediminicola gen. nov., sp. nov. isolated from the Bohai Sea

Oceanospirillum sediminis sp. nov., Isolated From Coastal Sediment in the Yellow Sea

A novel Gram-negative, motile, aerobic, spiral-shaped bacterium designated D5^T, was isolated from a coastal sediment collected in the Yellow Sea. Optimal growth occurred at 30 °C, pH 7.0-8.0 and in the presence of 1-3% (w/v) NaCl. Strain D5^T contained ubiquinone 8 (Q-8) as the predominant respiratory quinone. The major fatty acids (> 10%) were C_16:0, C_16:1 ω7c/C_16:1 ω6c and C_18:1w7c/C_18:1w6c. The main polar lipids were phosphatidylglycerol and phosphatidylethanolamine. The draft genome is 5.6 Mb in length, and DNA G + C content is 47.2 mol%. 16S rRNA gene sequences showed that strain D5^T is most closely related to Oceanospirillum beijerinckii NBRC 15445^T (97.8%, sequence similarity). However, the digital DNA-DNA hybridization (dDDH) value and average nucleotide identity (ANI) between strain D5^T and O. beijerinckii is only 27.8% and 77.1%. Phylogenetic trees based on 16S rRNA gene sequences and whole genomes all indicated that strain D5^T formed a separate branch in the genus Oceanospirillum. Combined results of the polyphasic analyses suggested that strain D5^T represents a novel species in the genus Oceanospirillum, for which the name Oceanospirillum sediminis sp. nov. is proposed. The type strain is D5^T (= MCCC 1K06061^T = KCTC 62987^T).

Roseobacters in a Sea of Poly- and Paraphyly: Whole Genome-Based Taxonomy of the Family Rhodobacteraceae and the Proposal for the Split of the "Roseobacter Clade" Into a Novel Family, Roseobacteraceae fam. nov

The family Rhodobacteraceae consists of alphaproteobacteria that are metabolically, phenotypically, and ecologically diverse. It includes the roseobacter clade, an informal designation, representing one of the most abundant groups of marine bacteria. The rapid pace of discovery of novel roseobacters in the last three decades meant that the best practice for taxonomic classification, a polyphasic approach utilizing phenotypic, genotypic, and phylogenetic characteristics, was not always followed. Early efforts for classification relied heavily on 16S rRNA gene sequence similarity and resulted in numerous taxonomic inconsistencies, with several poly- and paraphyletic genera within this family. Next-generation sequencing technologies have allowed whole-genome sequences to be obtained for most type strains, making a revision of their taxonomy possible. In this study, we performed whole-genome phylogenetic and genotypic analyses combined with a meta-analysis of phenotypic data to review taxonomic classifications of 331 type strains (under 119 genera) within the Rhodobacteraceae family. Representatives of the roseobacter clade not only have different environmental adaptions from other Rhodobacteraceae isolates but were also found to be distinct based on genomic, phylogenetic, and in silico-predicted phenotypic data. As such, we propose to move this group of bacteria into a new family, Roseobacteraceae fam. nov. In total, reclassifications resulted to 327 species and 128 genera, suggesting that misidentification is more problematic at the genus than species level. By resolving taxonomic inconsistencies of type strains within this family, we have established a set of coherent criteria based on whole-genome-based analyses that will help guide future taxonomic efforts and prevent the propagation of errors.

Vibrio marinisediminis sp. nov., Isolated from Marine Sediment

A novel Gram-stain-negative, facultative anaerobic, motile bacterium, designated as 404^T, was isolated from a marine sediment sample in the Bohai Gulf, China. Growth was observed at 10-35 °C (optimum, 20-25 °C) and in the presence of 1.0-6.0% (w/v) NaCl (optimum, 1.0-3.0%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain 404^T belonged to the genus Vibrio, showing the highest sequence similarity to Vibrio renipiscarius KCTC 42287^T (97.6%). The draft genome is 4.5 Mb in length, containing 4278 protein-coding genes, 60 tRNA genes and 9 rRNA genes, and DNA G+C content is 44.1 mol%. Strain 404^T contains phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, and phospholipid as the main polar lipids, and the predominant quinone is ubiquinone Q-8. The major cellular fatty acids (>8.0%) are C_16 : 1ω6c and/or C_16 : 1ω7c, C_16 : 0, C_18 : 1ω6c and/or C_18 : 1ω7c. Strain 404^T shows some typical characteristics among the members of genus Vibrio, while it can be clearly distinguished from the closely related type strains through genome analysis (average nucleotide identity and digital DNA-DNA hybridization values), fatty acid composition and a series of physiological and biochemical characteristics. On the basis of the polyphasic analysis, strain 404^T is considered to represent a novel species of the genus Vibrio, for which the name Vibrio marinisediminis sp. nov., is proposed. The type strain is 404^T (= MCCC 1H00367^T = KCTC 62958^T).

Halomonas marinisediminis sp. nov., A Moderately Halophilic Bacterium Isolated from the Bohai Gulf

A novel Gram-stain-negative, moderately halophilic bacterium, designated strain 204^T, was isolated from a marine sediment sample in the Bohai Gulf, Yellow Sea, China. Cells of strain 204^T are aerobic, motile, cocci or short rods with two lateral flagella. Growth was observed at 15-40 °C (optimum, 30 °C), pH 6.0-9.0 (optimum, 7.0-7.5) and in the presence of 1.0-18.0% (w/v) NaCl (optimum, 3.0-8.0%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 204^T belonged to the genus Halomonas, showing highest sequence similarity to Halomonas alimentaria YKJ-16^T (98.08%), followed by Halomonas sediminicola (97.47%), Halomonas fontilapidosi (97.14%), Halomonas halodenitrificans (96.98%), Halomonas ventosae (96.92%), and Halomonas shengliensis (96.85%). The draft genome is 3.8 Mb in length, containing 3673 protein-coding genes, 62 tRNA genes and 10 rRNA genes, and DNA G+C content is 62.7 mol%. Strain 204^T contains phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol as the main polar lipids, and the predominant respiratory quinone was ubiquinone Q-9. The major cellular fatty acids (> 5%) are C_18:1ω7c, C_16:1ω7c and/or C_16:1ω6c, C_16:0 and C_12:03-OH. Strain 204^T was clearly distinguished from the closely related type strains through phylogenetic analysis, dDNA-DNA hybridization, fatty acid composition data and a range of physiological and biochemical characteristics comparisons. On the basis of the polyphasic analysis, strain 204^T is considered to represent a novel species of the genus Halomonas, for which the name Halomonas marinisediminis sp. nov. is proposed. The type strain is 204^T (= MCCC 1H00366^T = KCTC 62957^T).

Pukyongiella litopenaei gen. nov., sp. nov., a novel bacterium isolated from the gut content of a whiteleg shrimp Litopenaeus vannamei

A Gram-negative, aerobic bacterium, designated as SH-1^T, was isolated from the gut content of a whiteleg shrimp, Litopenaeus vannamei collected in a shrimp farm in South Korea. The bacterial cells were ovoid rod-shaped, non-motile, oxidase-positive and catalase-negative. Growth was observed at 20-35 °C (optimum, 30 °C), pH 5.0-9.5 (pH 8.5) and in the presence of 0-6 % (w/v) NaCl (2-3 %). The major polar lipids were phosphatidylglycerol, phosphatidylinositolmannoside, unidentified aminolipid and two unidentified lipids. The G+C content was 66.1 mol% and the predominant respiratory quinone was Q-10. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain SH-1^T was placed in a distinct clade with Primorskyibacter marinus PX7^T (96.97 % sequence similarity), Pontibaca methylaminivorans DSM 21219^T (96.03 %) and Pelagivirga sediminicola BH-SD19^T (95.02 %) in the family Rhodobacteraceae and distantly related with them to be a new genus. The digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI) and average amino acid identity (AAI) values calculated from whole-genome-sequence comparison between the SH-1^T and the close species were in the ranges of 19.0-19.8, 73.8-74.9 and 64.1-65.9 %, respectively. Based on the polyphasic analysis presented in this study, we suggest that strain SH-1^T represents a novel genus and species in the family Rhodobacteraceae, for which the name Pukyongiella litopenaei gen. nov., sp. nov. is proposed. The type strain of Pukyongiella litopenaei is SH-1^T (=KCTC 62276^T=MCCC 1K04072^T).

Roseovarius spongiae sp. nov., a bacterium isolated from marine sponge

A taxonomic study was carried out on strain HN-E21^T, which was isolated from sponge collected from Yangpu Bay, Hainan, PR China. Cells of strain HN-E21^T were Gram-stain-negative, non-spore-forming, tumbling-motile, ovoid- to rod-shaped and pale-yellow-pigmented that could grow at 15-42 °C (optimum, 37 °C), at pH 6-11 (pH 7) and in 0-14 % (w/v) NaCl (2-3 %). This isolate was positive for oxidase and catalase, but negative for hydrolysis of aesculin and gelatin. The phylogenetic tree based on 16S rRNA gene sequences showed that strain HN-E21^T formed a clade with Pelagivirga sediminicola BH-SD19^T, Pontibaca methylaminivorans GRP21^T, Roseovarius antarcticus M-S13-148^T, Roseovarius aquimarinus CAU1059^T and Roseovarius nanhaiticus NH52J^T within the family Rhodobacteraceae. Strain HN-E21^T shared the highest similarity to Pelagivirga sediminicola BH-SD19^T (95.5 %), followed by Roseovarius lutimaris 112^T (95.3 %), Pelagicola litorisediminis D1-W8^T (95.2 %), Roseovarius gaetbuli YM-20^T (95.0 %) and Roseovarius marisflavi H50^T (95.0 %). The dominant fatty acids were summed feature 8 (C_18 : 1ω7c and/or C_18 : 1ω6c) and C_16:0. The major polar lipids comprised phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, three unidentified lipids and one unidentified phospholipid. The respiratory quinone was identified as Q-10. The G+C content of the genomic DNA was 66.4 mol%. Based on the phenotypic and phylogenetic data, strain HN-E21^T represents a novel species of the genus Roseovarius, for which the name Roseovarius spongiae sp. nov. is proposed, with the type strain HN-E21^T (=MCCC 1K03333^T=LMG 30456^T).

Polyphasic taxonomic analysis of Parasedimentitalea marina gen. nov., sp. nov., a psychrotolerant bacterium isolated from deep sea water of the New Britain Trench

A novel Rhodobacteraceae bacterium, strain W43T, was isolated from a deep-sea water sample from the New Britain Trench. Strain W43T exhibited the highest 16S rRNA gene sequence similarity of 96.5% to Sedimentitalea nanhaiensis DSM 24252T, Phaeobacter gallaeciensis DSM 26640T, Phaeobacter inhibens DSM 16374T, and Phaeobacter porticola P97T. Phylogenetic analysis of the 16S rRNA gene and phylogenomic analysis of the genome showed that strain W43T formed an independent monophyletic branch within the family Rhodobacteraceae. Strain W43T was Gram-stain-negative, rod-shaped, and grew optimally at 16-20°C, pH 6.5-7.0 and 2% (w/v) NaCl. The principal fatty acids were C18:1ω7c/C18:1ω6c, major respiratory quinone was ubiquinone-10 and predominant polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The 5 080 916 bp long genome, comprising a circular chromosome and four plasmids, exhibits a G + C content of 55.9 mol%. The combined phenotypic, chemotaxonomic and molecular data show that strain W43T represents a novel species of a novel genus, for which the name Parasedimentitalea marina gen. nov. sp. nov. is proposed (type strain W43T = MCCC 1K03532T = KCTC 62635T).

Pelagivirga dicentrarchi sp. nov., a member of the family Rhodobacteraceae isolated from the gut microflora of sea bass (Dicentrarchus labrax L.)

A Gram-stain negative, aerobic, non-flagellated, non-gliding, rod-shaped bacterium, designated strain YLY04^T, was isolated from the gut microflora of a sea bass (Dicentrarchus labrax L.) collected from the coast of Yuanyao Wharf, Weihai, China. Growth was found to occur at pH 6.0-9.0 (optimum, 7.0-8.0), 4-37 °C (optimum, 28-30 °C) in the presence of 0-11.0% (w/v) NaCl (optimum, 3.0-4.0%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YLY04^T is closely related to Pelagivirga sediminicola BH-SD19^T and Roseovarius antarcticus M-S13-148^T. Strain YLY04^T contains ubiquinone-10 as the sole respiratory quinone and summed feature 8 (C_18:1ω7c and/or C_18:1ω6c), cyclo-C_19:0ω8c, C_16:0 and 11-methyl-C_18:1ω7c as the major fatty acids. The polar lipids of strain YLY04^T were found to consist of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid, an unidentified phospholipid and three unidentified lipids. The DNA G+C content was determined to be 62.7 mol%. The phenotypic, chemotaxonomic and phylogenetic properties, and genome analysis, indicated that strain YLY04^T represents a novel species within the genus Pelagivirga, for which the name Pelagivirga dicentrarchi sp. nov. is proposed. The type strain is YLY04^T (= MCCC 1H00334^T = KCTC 62452^T).