Polaribacter uvawellassae sp. nov., a Member of the Family Flavobacteriaceae Isolated from Mud Crab (Scylla serrata)

A Gram-stain-negative, strictly aerobic, rod-shaped, and no flagella, designated SLMDC-22 T, was isolated from the intestine of a mud crab (Scylla serrata). The molecular phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SLMDC-22 T belonged to the genus Polaribacter and exhibited 96.9% similarity to P. huanghezhanensis, 96.5% to P. pacificus, 95.8% to P. lacunae, and 94.1% to P. marinivivus. The G + C content of the DNA of strain SLMDC-22 T was 30.3%. Growth occurred at 4-34 °C (optimum, 23 °C), at pH 5-9 (optimum, pH 7.0), and with 0.5-2.0% (w/v) NaCl (optimum, 2%). The major fatty acid was iso-C15:0. Major polar lipids include phospholipid, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, amino lipid, glycolipid, amino phospholipid, and an unknown polar lipid. The major respiratory quinone is MK-6. Based on whole-genome analysis, the orthologous average nucleotide identity (ANI) with the two closest relatives, Polaribacter huanghezhanensis and Polaribacter pacificus, were 87.3% and 75.7%, respectively. Furthermore, the digital DNA-DNA hybridization (dDDH) values against Polaribacter huanghezhanensis and Polaribacter pacificus were 75.8% and 19.6%, respectively. Notably, 25 genes of SLMDC-22 T were associated with nitrogen metabolism, including denitrification, nitrate ammonification, ammonium assimilation, and nitrosative stress. The phenotypic, genotypic, phylogenetic, and chemotaxonomic data revealed that strain SLMDC-22 T represents a novel species of the genus Polaribacter, for which the name Polaribacter uvawellassae sp. nov. is proposed. The type strain is SLMDC-22 T (= KCTC 102289 T = MCCC 1K09222T).

Polaribacter ponticola sp. nov., isolated from seawater, reclassification of Polaribacter undariae as a later heterotypic synonym of Polaribacter sejongensis, and emended description of Polaribacter sejongensis Kim et al. 2013

A Gram-stain-negative, yellow-pigmented, and strictly aerobic bacterium, designated as strain MSW5T, was isolated from seawater of the Yellow Sea in South Korea. The cells were non-motile rods exhibiting oxidase- and catalase-positive activities. Growth was observed at 15-25 °C (optimum, 25 °C) and pH 5.0-9.0 (optimum, pH 7.0-8.0) and in the presence of 1.0-5.0% (w/v) NaCl (optimum, 2.0%). Menaquinone-6 was the sole respiratory quinone, and iso-C15 : 0, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c), iso-C15 : 0 3-OH, and C15 : 1  ω6c were the major cellular fatty acids. Major polar lipids included phosphatidylethanolamine, two unidentified aminolipids, and three unidentified lipids. Phylogenetic analyses based on 16S rRNA gene sequences and 92 concatenated core protein sequences revealed that strain MSW5T formed a distinct lineage within the genus Polaribacter. The genome of strain MSW5T was 3582 kb in size with a 29.1 mol% G+C content. Strain MSW5T exhibited the highest similarity to Polaribacter atrinae WP25T, with a 97.9% 16S rRNA gene sequence similarity. However, the average nucleotide identity and digital DNA-DNA hybridization values were 79.4 and 23.3%, respectively, indicating that strain MSW5T represents a novel species. Based on its phenotypic, chemotaxonomic, and phylogenetic characteristics, strain MSW5T is proposed to represent a novel species, with the name Polaribacter ponticola sp. nov. The type strain is MSW5T (=KACC 22340T=NBRC 116025T). In addition, whole genome sequence comparisons and phenotypic features suggested that Polaribacter sejongensis and Polaribacter undariae belong to the same species, with P. undariae proposed as a later heterotypic synonym of P. sejongensis. An emended description of Polaribacter sejongensis is also proposed.

Colwellia maritima sp. nov. and Polaribacter marinus sp. nov., isolated from seawater

Two Gram-stain-negative, catalase- and oxidase-positive, and aerobic bacteria, strains MSW7^T and MSW13^T, were isolated from seawater. Cells of strains MSW7^T and MSW13^T are motile and non-motile rods, respectively. Strain MSW7^T optimally grew at 25 °C and pH 7.0 and in the presence of 3 % (w/v) NaCl, whereas strain MSW13^T optimally grew at 25 °C and pH 6.0-7.0 and in the presence of 2 % NaCl. As the sole respiratory quinone and the major fatty acids and polar lipids, strain MSW7^T contained ubiquinone-8, C_16 : 0, C_15 : 1  ω8c, C_17 : 1  ω8c and summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c), and phosphatidylethanolamine and phosphatidylglycerol, respectively, whereas strain MSW13^T contained menaquinone-6, C_15 : 1  ω6c, iso-C_15 : 0, anteiso-C_15 : 0, and iso-C_15 : 0 3-OH, and phosphatidylethanolamine, respectively. The DNA G+C contents of strains MSW7^T and MSW13^T were 37.3 and 29.9 %, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains MSW7^T and MSW13^T were most closely related to Colwellia echini A3^T and Polaribacter atrinae WP25^T with 98.8 and 98.1 % sequence similarities, respectively. The average nucleotide identity and digital DNA-DNA hybridization values between strain MSW7^T and C. echini A3^T and between strain MSW13^T and P. atrinae KACC 17473^T were 73.6 and 22.6 % and 80.4 and 23.8 %, respectively. Based on phenotypic, chemotaxonomic and phylogenetic data, strains MSW7^T and MSW13^T represent novel species of the genera Colwellia and Polaribacter, respectively, for which the names Colwellia maritima sp. nov. and Polaribacter marinus sp. nov. are proposed, respectively. The type strains of C. maritima sp. nov. and P. marinus sp. nov. are MSW7^T (=KACC 22339^T=JCM 35001^T) and MSW13^T (=KACC 22341^T=JCM 35021^T), respectively.

Quantifying dominant bacterial genera detected in metagenomic data from fish eggs and larvae using genus-specific primers

The goal of this study was to design genus-specific primers for rapid evaluation of the most abundant bacterial genera identified using amplicon-based sequencing of the 16S rRNA gene in fish-related samples and surrounding water. Efficient genus-specific primers were designed for 11 bacterial genera including Alkalimarinus, Colwellia, Enterovibrio, Marinomonas, Massilia, Oleispira, Phaeobacter, Photobacterium, Polarbacerium, Pseudomonas, and Psychrobium. The specificity of the primers was confirmed by the phylogeny of the sequenced polymerase chain reaction (PCR) amplicons that indicated primers were genus-specific except in the case of Colwellia and Phaeobacter. Copy number of the 16S rRNA gene obtained by quantitative PCR using genus-specific primers and the relative abundance obtained by 16S rRNA gene sequencing using universal primers were well correlated for the five analyzed abundant bacterial genera. Low correlations between quantitative PCR and 16S rRNA gene sequencing for Pseudomonas were explained by the higher coverage of known Pseudomonas species by the designed genus-specific primers than the universal primers used in 16S rRNA gene sequencing. The designed genus-specific primers are proposed as rapid and cost-effective tools to evaluate the most abundant bacterial genera in fish-related or potentially other metagenomics samples.

Description of Polaribacter aestuariivivens sp. nov., isolated from a tidal flat

A bacterial strain, DBTF-3T, was isolated from a tidal flat of Republic of Korea. Phylogenetic trees of 16S rRNA gene sequences showed that strain DBTF-3T belonged to the genus Polaribacter. Strain DBTF-3T exhibited 16S rRNA gene sequence similarities of 97.1-98.1% to type strains of P. dokdonensis, P. haliotis, P. marinaquae, P. insulae, P. vadi, P. glomeratus, P. irgensii and P. reichenbachii, and 94.0-96.9% to those of the other Polaribacter species. DNA-DNA relatedness values of strain DBTF-3T with type strains of P. marinaquae and P. insulae were 14-19%. Average nucleotide identity and digital DNA-DNA hybridization values between strain DBTF-3T and type strains of six other Polaribacter species were 76.5-83.5% and 20.9-27.1%, respectively. Strain DBTF-3T contained MK-6 as the predominant menaquinone, and iso-C15:0, summed feature 3, iso-C15:1 G and iso-C15:0 3-OH as the major fatty acids. The major polar lipids were phosphatidylethanolamine and one unidentified lipid. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain DBTF-3T is separated from Polaribacter species. On the basis of the data presented, strain DBTF-3T (= KACC 19612T = NBRC 113191T) represents a novel species of the genus Polaribacter, for which the name Polaribacter aestuariivivens sp. nov. is proposed.

Polaribacter insulae sp. nov., isolated from a tidal flat

A Gram-stain-negative, aerobic, non-motile and ovoid or rod-shaped bacterial strain, designated OITF-22^T, was isolated from a tidal flat of Oido, an island of South Korea, and subjected to a polyphasic taxonomic study. Strain OITF-22^T grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of 2.0-3.0 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences showed that strain OITF-22^T fell within the clade comprising the type strains of Polaribacter species. Strain OITF-22^T exhibited 16S rRNA gene sequence similarity values of 97.2-99.4 % to the type strains of Polaribacter vadi, P. haliotis, P. atrinae, P. dokdonensis, P. litorisediminis,P. reichenbachii, P. irgensii and P. marinaquae, and of 93.0-96.9 % to the type strains of the other Polaribacter species. Strain OITF-22^T contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C15 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain OITF-22^T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain OITF-22^T was 32.3 mol% and its DNA-DNA relatedness values with the type strains of the eight phylogenetically most closely related Polaribacter species were 9-32 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain OITF-22^T is separated from recognized species of the genus Polaribacter. On the basis of the data presented, strain OITF-22^T is considered to represent a novel species of the genus Polaribacter, for which the name Polaribacter insulae sp. nov. is proposed. The type strain is OITF-22^T (=KCTC 52658^T=NBRC 112706^T).

Polaribacter pacificus sp. nov., isolated from a deep-sea polymetallic nodule from the Eastern Pacific Ocean

A Gram-staining-negative, yellow-colony-forming, rod-shaped, non-flagellated and facultatively aerobic strain, designed HRA130-1T, was isolated from a deep-sea polymetallic nodule from the Pacific Clarion-Clipperton Fracture Zone (CCFZ). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HRA130-1T belonged to the genus Polaribacter (96.3-93.2 % 16S rRNA gene sequence similarity), and exhibited 94 % 16S rRNA gene sequence similarity to Polaribacter filamentus KCTC 23135T (type species) and the highest sequence similarity to Polaribacter huanghezhanensis KCTC 32516T (96.3 %). Optimal growth occurred in the presence of 4 % (w/v) NaCl, at pH 7.0 and 16 °C. The DNA G+C content of strain HRA130-1T was 35.9 mol%. The major fatty acid was iso-C15 : 0. The predominant respiratory quinone was menaquinone-6 (MK-6). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, one unidentified phospholipid and an unidentified aminolipid. On the basis of data from the present taxonomic study using a polyphasic approach, strain HRA130-1T represents a novel species of the genus Polaribacter, for which the name Polaribacter pacificus sp. nov. is proposed. The type strain is HRA130-1T (=KCTC 52370T=MCCC 1K03199T=JCM 31460T=CGMCC 1.15763T).

Polaribacter litorisediminis sp. nov., isolated from a tidal flat

A Gram-stain-negative, aerobic, non-motile and ovoid or rod-shaped bacterial strain, designated OITF-11T, was isolated from a tidal flat in Oido, an island of South Korea, and subjected to a polyphasic taxonomic study. Strain OITF-11T grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of 2.0 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences showed that strain OITF-11T belonged to the genus Polaribacter. Strain OITF-11T exhibited 16S rRNA gene sequence similarity values of 97.4-98.1 % to Polaribacter haliotis RA4-7T, Polaribacter atrinae KACC 17473T, Polaribacter dokdonensis DSW-5T and Polaribacter marinaquae KCTC 42664T, and of 94.1-96.9 % to the type strains of the other Polaribacter species. Strain OITF-11T contained menaquinone MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 1 G, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH and C15 : 1ω6c as the major fatty acids. The major polar lipids detected in strain OITF-11T were phosphatidylethanolamine, phosphatidylmonomethylethanolamine and one unidentified lipid. The DNA G+C content of strain OITF-11T was 32.2 mol% and its DNA-DNA relatedness values with the type strains of P. haliotis, P. atrinae, P. dokdonensis and P. marinaquae were 14-33 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain OITF-11T is separated from recognized species of the genus Polaribacter. On the basis of the data presented, strain OITF-11T is considered to represent a novel species of the genus Polaribacter, for which the name Polaribacter litorisediminis sp. nov. is proposed. The type strain is OITF-11T (=KCTC 52500T=NBRC 112457T).

Microbial communities of aquatic environments on Heard Island characterized by pyrotag sequencing and environmental data

Heard Island in the Southern Ocean is a biological hotspot that is suffering the effects of climate change. Significant glacier retreat has generated proglacial lagoons, some of which are open to the ocean. We used pyrotag sequencing of SSU rRNA genes and environmental data to characterize microorganisms from two pools adjacent to animal breeding areas, two glacial lagoons and Atlas Cove (marine site). The more abundant taxa included Actinobacteria, Bacteroidetes and Proteobacteria, ciliates and picoflagellates (e.g. Micromonas), and relatively few Archaea. Seal Pool, which is rich in organic matter, was characterized by a heterotrophic degradative community, while the less eutrophic Atlas Pool had more eucaryotic primary producers. Brown Lagoon, with the lowest nutrient levels, had Eucarya and Bacteria predicted to be oligotrophs, possess small cell sizes, and have the ability to metabolize organic matter. The marine influence on Winston Lagoon was evident by its salinity and the abundance of marine-like Gammaproteobacteria, while also lacking typical marine eucaryotes indicating the system was still functioning as a distinct niche. This is the first microbiology study of Heard Island and revealed that communities are distinct at each location and heavily influenced by local environmental factors.

Spongiiferula fulva gen. nov., sp. nov., a Bacterium of the Family Flavobacteriaceae Isolated from a Marine Sponge

A Gram stain-negative, strictly aerobic, brown-pigmented, non-motile, rod-shaped, chemoheterotrophic bacterial strain-designated A6F-119(T) was isolated from a marine sponge (Rhabdastrella sp.). Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the new strain represented a member of the family Flavobacteriaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (93 %) to Tenacibaculum maritimum NBRC 15946(T). The strain could be differentiated phenotypically from the recognized members of the family Flavobacteriaceae. The DNA G + C content of strain A6F-119(T) was determined to be 30.8 mol%; MK-6 was identified as the major menaquinone; and the presence of iso-C15:0, iso-C17:0 3-OH, and C16:1 ω7c and/or C16:1 ω6c as the major (>10 %) cellular fatty acids. A polar lipid profile was present consisting of phosphatidylethanolamine, an unidentified aminolipid, and three unidentified lipids. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus for which the name Spongiiferula fulva gen. nov., sp. nov. is proposed. The type strain of S. fulva is A6F-119(T) (= KCTC 42752(T) = NBRC 111402(T)).

Proteus cibarius sp. nov., a swarming bacterium from Jeotgal, a traditional Korean fermented seafood, and emended description of the genus Proteus

A novel Proteus-like, Gram-stain-negative, facultatively anaerobic, rod-shaped bacterium, designated strain JS9T, was isolated from Korean fermented seafood, Jeotgal. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain JS9T belonged to the genus Proteus in the family Enterobacteriaceae. The highest 16S rRNA gene sequence similarity of strain JS9T was to Proteus vulgaris KCTC 2579T (98.98 %) and the genomic DNA G+C content is 39.0 mol%. DNA-DNA hybridization values were measured and strain JS9T showed <20.8 % genomic relatedness with closely-related members of the genus Proteus. The isolate showed bacterial motility and swarming activity similar to those of pathogenic Proteus mirabilis but distinct from those of other species of the genus Proteus. The isolate grows optimally at 30 °C, at pH 7, and in the presence of 2 % (w/v) NaCl. The main respiratory quinones are ubiquinone Q-8 and Q-10, and the major cellular fatty acids are C16 : 0, summed feature 3 and summed feature 8. The polar lipids comprise phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, an unidentified amino lipid, two unidentified amino-phospholipids, and three unidentified lipids. Based on phylogenetic, phenotypic, chemotaxonomic and genotypic analyses, strain JS9T represents a novel species of the genus Proteus, for which the name Proteus cibarius sp. nov. is proposed. The type strain is JS9T (=KACC 18404T=JCM 30699T). An emended description of the genus Proteus is also provided.

Simplicispira piscis sp. nov., isolated from the gut of a Korean rockfish, Sebastes schlegelii

A novel Gram-stain-negative, aerobic, motile and rod-shaped bacterium, designated strain RSG39T, was isolated from the gut of a Korean rockfish, Sebastes schlegelii. The 16S rRNA gene sequence analysis revealed that strain RSG39T belonged to the genus Simplicispira in the class Betaproteobacteria and its highest sequence similarity was shared with S. psychrophila (98.4 %). The isolate grew optimally at 20 °C, at pH 7 and with 0 % (w/v) NaCl. The main respiratory quinone of the isolate was ubiquinone Q-8. The major cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The polar lipids of the isolate were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and six unidentified lipids. The DNA–DNA hybridization values showed < 7.4 % genomic relatedness with closely related strains. The genomic DNA G+C content was 65.2 mol %. Based on phylogenetic, phenotypic, chemotaxonomic and genotypic analyses, strain RSG39T represents a novel species of the genus Simplicispira, for which the name Simplocospira piscis sp. nov. is proposed. The type strain is RSG39T ( = KACC 17539T = JCM 19291T).

Polaribacter undariae sp. nov., isolated from a brown alga reservoir

A Gram-stain-negative, non-flagellated, non-gliding, aerobic and rod-shaped or ovoid bacterial strain, designated W-BA7(T), was isolated from a brown alga reservoir on the South Sea in South Korea. This strain grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of approximately 2.0% (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain W-BA7(T) belonged to the genus Polaribacter, clustering coherently with the type strain of Polaribacter sejongensis, showing 99.3% sequence similarity. Strain W-BA7(T) exhibited 16S rRNA gene sequence similarity of 93.4-98.6% to the type strains of the other species of the genus Polaribacter. Strain W-BA7(T) contained MK-6 as the predominant menaquinone and iso-C15 : 0 3-OH and anteiso-C15 : 0 as the major fatty acids. The major polar lipids of strain W-BA7(T) were phosphatidylethanolamine, three unidentified lipids, one unidentified glycolipid, one unidentified aminolipid and one unidentified aminophospholipid. The DNA G+C content of strain W-BA7(T) was 31.9 mol%, and the mean DNA-DNA relatedness with the type strains of four phylogenetically related species of the genus Polaribacter was 12-27%. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain W-BA7(T) is separated from recognized species of the genus Polaribacter. On the basis of the data presented, strain W-BA7(T) is considered to represent a novel species of the genus Polaribacter, for which the name Polaribacter undariae sp. nov. is proposed. The type strain is W-BA7(T) ( =KCTC 42175(T) =CECT 8670(T)).

Niches of two polysaccharide-degrading Polaribacter isolates from the North Sea during a spring diatom bloom

Members of the flavobacterial genus Polaribacter thrive in response to North Sea spring phytoplankton blooms. We analyzed two respective Polaribacter species by whole genome sequencing, comparative genomics, substrate tests and proteomics. Both can degrade algal polysaccharides but occupy distinct niches. The liquid culture isolate Polaribacter sp. strain Hel1_33_49 has a 3.0-Mbp genome with an overall peptidase:CAZyme ratio of 1.37, four putative polysaccharide utilization loci (PULs) and features proteorhodopsin, whereas the agar plate isolate Polaribacter sp. strain Hel1_85 has a 3.9-Mbp genome with an even peptidase:CAZyme ratio, eight PULs, a mannitol dehydrogenase for decomposing algal mannitol-capped polysaccharides but no proteorhodopsin. Unlike other sequenced Polaribacter species, both isolates have larger sulfatase-rich PULs, supporting earlier assumptions that Polaribacter take part in the decomposition of sulfated polysaccharides. Both strains grow on algal laminarin and the sulfated polysaccharide chondroitin sulfate. For strain Hel1_33_49, we identified by proteomics (i) a laminarin-induced PUL, (ii) chondroitin sulfate-induced CAZymes and (iii) a chondroitin-induced operon that likely enables chondroitin sulfate recognition. These and other data suggest that strain Hel1_33_49 is a planktonic flavobacterium feeding on proteins and a small subset of algal polysaccharides, while the more versatile strain Hel1_85 can decompose a broader spectrum of polysaccharides and likely associates with algae.

Endozoicomonas atrinae sp. nov., isolated from the intestine of a comb pen shell Atrina pectinata

A novel bacterium, designated strain WP70(T), was isolated from the gut of a comb pen shell (Atrina pectinata) collected from the southern sea of Yeosu in Korea. The isolate was Gram-stain-negative, aerobic, non-motile and rod-shaped. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain WP70(T) belonged to the genus Endozoicomonas. The highest level of sequence similarity (98.4%) was shared with Endozoicomonas elysicola MKT110(T). Optimal growth occurred in 2% (w/v) NaCl at 30 °C and at pH 7. The major cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The main respiratory quinone was Q-9. The polar lipids comprised phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, three unidentified phospholipids, an unidentified aminolipid, an unidentified aminophospholipid and an unidentified lipid. The genomic DNA G+C content was 50.5 mol% and DNA-DNA hybridization values indicated <11% genomic relatedness to the closest species. Physiological, biochemical, chemotaxonomic and genotypic analyses indicated that strain WP70(T) represents a novel species of the genus Endozoicomonas, for which the name Endozoicomonas atrinae sp. nov. is proposed. The type strain is WP70(T) ( = KACC 17474(T)  = JCM 19190(T)).