Tropicibacter oceani sp. nov., a novel sulfur-metabolizing bacteria isolated from the intertidal zone sediment of Chinese Yellow Sea.

In this study, we reported a Gram-stain-negative, rod-shaped, atrichous, and aerobic bacterial strain named YMD87T, which was isolated from the intertidal zone sediment of Chinese Yellow Sea. Growth of strain YMD87T occurred at 10.0-40.0 °C (optimum, 25-30 °C), pH 4.0-12.0 (optimum, 8.0) and with 0-6.0% (w/v) NaCl (optimum, 0.0-2.0%). Phylogenetic tree analysis based on 16S rRNA gene sequence indicated that strain YMD87T belonged to the genus Tropicibacter and was closely related to Tropicibacter alexandrii LMIT003T (97.2% sequence similarity). Genomic analysis indicated that strain YMD87T contains a circular chromosome of 3,932,460 bp with G + C content of 63.8% and three circular plasmids of 116,492 bp, 49,209 bp and 49,673 bp, with G + C content of 64.3%. Genomic functional analysis revealed that strain YMD87T is potential a novel sulfur-metabolizing bacteria. The predominant respiratory quinone of YMD87T was ubiquinone-10 (Q-10). The major polar lipids of YMD87T contained phosphatidylglycerol, phosphatidylethanolamine, five unidentified lipids, five unidentified phospholipids, phosphatidylcholine, unidentified glycolipid and five unidentified aminolipids. The major fatty acids of strain YMD87T contained C12:1 3-OH, C16:0, and summed feature 8 (C18:1 ω7c or/and C18:1 ω6c). Phylogenetic, physiological, biochemical and morphological analyses suggested that strain YMD87T represents a novel species of the genus Tropicibacter, and the name Tropicibacter oceani sp. nov is proposed. The type strain is YMD87T (= MCCC 1K08473T = KCTC 92856 T).

Ruegeria spongiae sp. nov., isolated from Callyspongia elongata.

A Gram-stain-negative, rod-shaped, polar flagellated, aerobic, light-yellow bacterium, designated as 2012CJ41-6T, was isolated from a sponge sample of Callyspongia elongata from Chuja-myeon, Jeju-si, Jeju-do, Republic of Korea. On the basis of 16S rRNA gene sequencing, strain 2012CJ41-6T clustered with species of the genus Ruegeria and appeared closely related to R. halocynthiae DSM 27839T (96.46 % similarity), R. denitrificans CECT 4357T (96.32 %), R. profundi ZGT108T (96.32 %), R. litorea CECT 7639T (96.32 %) and R. atlantica CECT 4292T (96.16 %). The average nucleotide identity and digital DNA-DNA hybridization between strain 2012CJ41-6T and the most closely related strain was 75.3 % and 19.6 %, indicating that 2012CJ41-6T represents a novel species of the genus Ruegeria. Growth occurred at 15-37 °C on marine medium in the presence of 0.5-10 % (w/v) NaCl and at pH 5.5-8.5. The DNA G+C content of the genomic DNA was 60.80 mol%, and ubiquinone-10 (Q-10) was the major respiratory quinone. The major cellular fatty acids (>5 %) were C18 : 1 ω7c and/or C18:1 ω6c (summed feature 8). The polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, one unidentified phospholipid, one unidentified aminolipid, one unidentified aminophospholipid and five unidentified lipids. Physiological and biochemical characteristics indicated that strain 2012CJ41-6T represents a novel species of the genus Ruegeria, for which the name Ruegeria spongiae sp. nov. is proposed. The type strain is 2012CJ41-6T (=KACC 22645T=LMG 32585T).

Roseovarius pelagicus sp. nov., a facultatively anaerobic bacterium with potential for degrading polypropylene, isolated from Arctic seawater.

A Gram-stain-negative, facultatively anaerobic, non-motile, rod-shaped bacterial strain, designated HL-MP18T, was isolated from Arctic seawater after a prolonged incubation employing polypropylene as the sole carbon source. Phylogenetic analyses of the 16S rRNA gene sequence revealed that strain HL-MP18T was affiliated to the genus Roseovarius with close relatives Roseovarius carneus LXJ103T (96.8 %) and Roseovarius litorisediminis KCTC 32327T (96.5 %). The complete genome sequence of strain HL-MP18T comprised a circular chromosome of 3.86 Mbp and two circular plasmids of 0.17 and 0.24 Mbp. Genomic comparisons based on average nucleotide identity and digital DNA-DNA hybridization showed that strain HL-MP18T was consistently discriminated from its closely related taxa in the genus Roseovarius. Strain HL-MP18T showed optimal growth at 25 °C, pH 7.0 and 2.5 % (w/v) sea salts. The major cellular fatty acids were C18 : 1 ω6c and/or C18 : 1 ω7c (49.6 %), C19 : 0 cyclo ω8c (13.5 %), and C16 : 0 (12.8 %). The major respiratory quinone was ubiquinone-10. The polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and three unidentified lipids. The genomic DNA G+C content of the strain was 59.2 mol%. The phylogenetic, genomic, phenotypic and chemotaxonomic results indicate that strain HL-MP18T is distinguishable from the recognized species of the genus Roseovarius. Therefore, we propose that strain HL-MP18T represents a novel species belonging to the genus Roseovarius, for which the name Roseovarius pelagicus sp. nov. is proposed. The type strain is HL-MP18T (=KCCM 90405T=JCM 35639T).

Genomic basis for the unique phenotype of the alkaliphilic purple nonsulfur bacterium Rhodobaca bogoriensis.

Although several species of purple sulfur bacteria inhabit soda lakes, Rhodobaca bogoriensis is the first purple nonsulfur bacterium cultured from such highly alkaline environments. Rhodobaca bogoriensis strain LBB1T was isolated from Lake Bogoria, a soda lake in the African Rift Valley. The phenotype of Rhodobaca bogoriensis is unique among purple bacteria; the organism is alkaliphilic but not halophilic, produces carotenoids absent from other purple nonsulfur bacteria, and is unable to grow autotrophically or fix molecular nitrogen. Here we analyze the draft genome sequence of Rhodobaca bogoriensis to gain further insight into the biology of this extremophilic purple bacterium. The strain LBB1T genome consists of 3.91 Mbp with no plasmids. The genome sequence supports the defining characteristics of strain LBB1T, including its (1) production of a light-harvesting 1-reaction center (LH1-RC) complex but lack of a peripheral (LH2) complex, (2) ability to synthesize unusual carotenoids, (3) capacity for both phototrophic (anoxic/light) and chemotrophic (oxic/dark) energy metabolisms, (4) utilization of a wide variety of organic compounds (including acetate in the absence of a glyoxylate cycle), (5) ability to oxidize both sulfide and thiosulfate despite lacking the capacity for autotrophic growth, and (6) absence of a functional nitrogen-fixation system for diazotrophic growth. The assortment of properties in Rhodobaca bogoriensis has no precedent among phototrophic purple bacteria, and the results are discussed in relation to the organism's soda lake habitat and evolutionary history.

Limimaricola litoreus sp. nov., isolated from intertidal sand of the Yellow Sea.

A novel species of the genus Limimaricola, designated ASW11-118T, was isolated from an intertidal sand sample of the Yellow Sea, PR China. Growth of strain ASW11-118T occurred at 10-40 °C (optimum, 28 °C), pH 5.5-8.5 (optimum, pH 7.5) and with 0.5-8.0 % (w/v) NaCl (optimum, 1.5%). Strain ASW11-118T has the highest 16S rRNA gene sequence similarity to Limimaricola cinnabarinus LL-001T (98.8%) and 98.6 % to Limimaricola hongkongensis DSM 17492T. Phylogenetic analysis based on genomic sequences indicated that strain ASW11-118T belongs to the genus Limimaricola. The genome size of strain ASW11-118T was 3.8 Mb and DNA G+C content was 67.8 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain ASW11-118T and other members of the genus Limimaricola were below 86.6 and 31.3 %, respectively. The predominant respiratory quinone was ubiquinone-10. The predominant cellular fatty acid was C18 : 1 ω7c. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and one unknown aminolipid. On the basis of the data presented, strain ASW11-118T is considered to represent a novel species of the genus Limimaricola, for which the name Limimaricola litoreus sp. nov. is proposed. The type strain is ASW11-118T (=MCCC 1K05581T=KCTC 82494T).

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 D2-3T and G9-8T, 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 %), D2-3T contained C16 : 0, 11-methyl-C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), whereas G9-8T contained C16 : 0, 11-methyl-C18 : 1ω7c, C12 : 1 3-OH, and summed feature 8. The DNA G+C contents of D2-3T and G9-8T 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 G9-8T only. The 16S rRNA gene sequence similarity of D2-3T and G9-8T 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 D2-3T and G9-8T formed respectively distinct phylogenetic lineages within the genus Octadecabacter. D2-3T and G9-8T were most closely related to Octadecabacter ascidiaceicola RA1-3T and Octadecabacter antarcticus 307T, with 98.9 % and 98.5 % 16S rRNA gene sequence similarities, respectively, and digital DDH values between D2-3T and O. ascidiaceicola and between G9-8T and O. antarcticus were 18.3 % and 19.5 %, respectively. Phenotypic, chemotaxonomic and molecular features support the hypothesis that D2-3T and G9-8T 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 D2-3T (=KACC 22493T =JCM 34969T) and G9-8T (=KACC 22488T =JCM 34973T), respectively.

Szabonella alba gen. nov., sp. nov., a motile alkaliphilic bacterium of the family Rhodobacteraceae isolated from a soda lake.

A Gram-stain-negative, oxidase- and catalase-positive, rod-shaped, creamy white coloured bacterial strain, DMG-N-6T, was isolated from a water sample of Lake Ferto/Neusiedler See (Hungary). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain forms a distinct linage within the family Rhodobacteraceae. Its closest relatives are Tabrizicola alkalilacus DJCT (96.76% similarity) and Tabrizicola piscis K13M18T (96.76%), followed by Tabrizicola sediminis DRYC-M-16T (96.69 %), Rhodobacter sediminicola JA983T (96.62 %), Tabrizicola aquatica RCRI19T (96.47 %) and Cereibacter johrii JA192T (96.18 %). The novel bacterial strain favours an alkaline environment (pH 8.0-12.0) and grows optimally at 18-28°C in the presence of 2-4 % (w/v) NaCl. Cells of DMG-N-6T were motile by a single subpolar flagellum. Bacteriochlorophyll a was not detected. The predominant respiratory quinone was ubiquinone Q-10. The major cellular fatty acid was C18:1 ω7c. The polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, phosphatidylcholine, an unidentified phospholipid and five unidentified lipids. The assembled draft genome of strain DMG-N-6T had 52 contigs with a total length of 4 219 778 bp and a G+C content of 64.3 mol%. Overall genome-related indices (ANI <77.8 %, AAI <69.0 %, dDDH <19.6 %) with respect to close relatives were all significantly below the corresponding threshold to demarcate bacterial genus and species. Strain DMG-N-6T (=DSM 108208T=NCAIM B.02645T) is strongly different from its closest relatives and is suggested as the type strain of a novel species of a new genus in the family Rhodobacteraceae, for which the name Szabonella alba gen. nov., sp. nov. is proposed.

Methylphosphonate Degradation and Salt-Tolerance Genes of Two Novel Halophilic Marivita Metagenome-Assembled Genomes from Unrestored Solar Salterns.

Aerobic bacteria that degrade methylphosphonates and produce methane as a byproduct have emerged as key players in marine carbon and phosphorus cycles. Here, we present two new draft genome sequences of the genus Marivita that were assembled from metagenomes from hypersaline former industrial salterns and compare them to five other Marivita reference genomes. Phylogenetic analyses suggest that both of these metagenome-assembled genomes (MAGs) represent new species in the genus. Average nucleotide identities to the closest taxon were <85%. The MAGs were assembled with SPAdes, binned with MetaBAT, and curated with scaffold extension and reassembly. Both genomes contained the phnCDEGHIJLMP suite of genes encoding the full C-P lyase pathway of methylphosphonate degradation and were significantly more abundant in two former industrial salterns than in nearby reference and restored wetlands, which have lower salinity levels and lower methane emissions than the salterns. These organisms contain a variety of compatible solute biosynthesis and transporter genes to cope with high salinity levels but harbor only slightly acidic proteomes (mean isoelectric point of 6.48).

Paenihalocynthiibacter styelae gen. nov., sp. nov., isolated from stalked sea squirt Styela clava.

A Gram-stain-negative, strictly aerobic, non-motile and rod-shaped bacterial strain, MYP1-1T, was isolated from the intestine of a stalked sea squirt (Styela clava) of the South Sea in the Republic of Korea. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain MYP1-1T clustered with the type strains of Halocynthiibacter species and Pseudohalocynthiibacter aestuariivivens. Strain MYP1-1T exhibited 16S rRNA gene sequence similarity values of 97.0-97.6 % to the type strains of Halocynthiibacter namhaensis, Halocynthiibacter arcticus and P. aestuariivivens. The phylogenetic tree based on genomic sequences showed that strain MYP1-1T formed a distinct branch separating it from the type strains of two Halocynthiibacter species and P. aestuariivivens and other taxa. The DNA G+C content of strain MYP1-1T from its genomic sequence was 55.0 mol%. Strain MYP1-1T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The major polar lipids of strain MYP1-1T were phosphatidylcholine, phosphatidylglycerol, one unidentified lipid and one unidentified aminolipid. The differences in fatty acid and polar lipid profiles and other differential phenotypic properties made it reasonable to distinguish strain MYP1-1T from the genera Halocynthiibacter and Pseudohalocynthiibacter. On the basis of the polyphasic taxonomic investigations, we conclude that strain MYP1-1T constitutes a new genus and species within the class Alphaproteobacteria, for which the name Paenihalocynthiibacter styelae gen. nov., sp. nov. is proposed. The type strain is MYP1-1T (=KCTC 82143T=NBRC 114355T).

Cochlodiniinecator piscidefendens gen. nov., sp. nov., an algicidal bacterium against the ichthyotoxic dinoflagellate Cochlodinium polykrikoides.

Harmful algal blooms caused by Cochlodinium polykrikoides result in enormous economic damage to the aquaculture industry. Biological control methods have attracted wide attention due to their environmental-friendliness. In this study, a novel algicidal bacterium, designated strain M26A2MT, was determined for its taxonomic position and was evaluated for its potential to mitigate C. polykrikoides blooms. Strain M26A2MT exhibited the highest 16S rRNA gene sequence similarity to the type strains of Planktotalea lamellibrachiae (97.3%), Halocynthiibacter namhaensis (97.2%), Pseudohalocynthiibacter aestuariivivens (96.8%) and Halocynthiibacter arcticus (96.4%) in the family Rhodobacteraceae. The predominant fatty acids were C10 : 0 3-OH and summed feature 8 (comprising C18 : 1 ω7c and/or C18 : 1 ω6c). The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and three unidentified lipids. Q-10 was the respiratory quinone. Strain M26A2MT exerted significant algicidal activity against C. polykrikoides cells by destroying the membrane integrity and the photosynthetic system. Our findings suggest that strain M26A2MT shows a high potential to control outbreaks of C. polykrikoides. Based on the polyphasic characterization, strain M26A2MT is considered to represent a novel species within a novel genus of the family Rhodobacteraceae, for which the name Cochlodiniinecator piscidefendens gen. nov., sp. nov. is proposed. The type strain is M26A2MT (=KCTC 82083T=JCM 34119T).

Pseudooceanicola endophyticus sp. nov., a novel endophytic bacterium isolated from bark Aegiceras corniculatum.

A Gram-stain-negative, aerobic, short-rod-shaped bacterium, designated strain CBS1P-1T, was isolated from a surface-sterilized bark of Aegiceras corniculatum. Growth of strain CBS1P-1T was observed with between 0 and 12.0 % (w/v) NaCl (optimally with 5.0 %) and at between pH 6.0-9.0. It grew at temperatures between 25-37 °C (optimum, 30 °C). Chemotaxonomic analysis showed that ubiquinone-10 was the respiratory quinone. The lipids comprised diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid, an unidentified phospholipid and an unidentified aminolipid. The major fatty acids of strain CBS1P-1T were C18 : 1 ω7c, C16 : 0 and C19 : 0 cyclo ω8c. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CBS1P-1T was most related to Pseudooceanicola antarcticus CGMCC 1.12662T with a sequence similarity of 96.5 %. The average nucleotide identity and digital DNA-DNA hybridization values between strain CBS1P-1T and P. antarcticus 1.12662T were 77.5 and 21.1 %, respectively. The G+C content of the genomic DNA was 67.3 mol%. Based on phylogenetic, chemotaxonomic and phenotypic data, strain CBS1P-1T is considered to represent a novel species of the genus Pseudooceanicola, for which the name Pseudooceanicola endophyticus is proposed. The type strain is CBS1P-1T (=KCTC 62836T=CGMCC 1.13743T).

Mangrovicoccus algicola sp. nov., an alginate lyase - producing marine bacterium.

A Gram-stain-negative, non-motile, ellipsoid bacterium, designated HB182678T, was isolated from brown alga collected from Hainan province, PR China. Growth was observed at 10-50 °C (optimum 37-40 °C), at pH 6-10 (optimum pH 8) and in the presence of 0.5-13% (w/v) NaCl (optimum, 2-4%). The predominant isoprenoid quinone was Q-10 and the major fatty acids were C18 : 1 ω7c, C16 : 0, C18 : 0 and C19 : 0 cyclo ω8c. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, an unidentified phospholipid, two unidentified glycolipids and three unidentified aminophospholipids. The size of the draft genome was 4.40 Mbp with G+C content 68.8 mol%. Phylogenetic analysis of 16S rRNA gene sequence indicated that strain HB182678T belonged to the genus Mangrovicoccus, and the closest phylogenetically related species was Mangrovicoccus ximenensis T1lg56T (with the similarity of 96.3%). Whole genome average nucleotide identity (ANI) value between them was 84.3% and in silico DNA-DNA hybridization value was 27.2%. The combined phylogenetic relatedness, phenotypic and genotypic features supported the conclusion that strain HB182678T represents a novel species of the genus Mangrovicoccus, for which the name Mangrovicoccus algicola sp. nov. is proposed. The type strain is HB182678T (=MCCC 1K04624T=KCTC 82318T).

Pontivivens ytuae sp. nov., isolated from deep sea sediment of the Mariana Trench.

A Gram-stain-negative, light pink-coloured, rod-shaped, flagellated and facultative anaerobic bacterial strain, designated MT2928T, was isolated from deep-sea sediment collected from the Mariana Trench. Growth of strain MT2928T occurred optimally at 28 °C, pH 8.0-9.0 and in the presence of 1.0-2.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MT2928T belongs to the genus Pontivivens and has the highest sequence similarity to Pontivivens insulae GYSW-23T (96.6 %). Genomic analysis indicated that strain MT2928T contains a circular chromosome of 4 199 362 bp with G+C content of 67.2 mol%. The strain did not produce bacteriochlorophyll a, but produced carotenoid. The predominant respiratory quinone of MT2928T was ubiquinone-10. The polar lipids of MT2928T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified lipids and two unidentified phospholipids. The major fatty acids of strain MT2928T contained summed feature 8 (C18 : 1 ω7c or/and C18 : 1 ω6c), C18 : 0 and summed feature 2 (iso-C16 : 1 I and/or C14 : 0 3-OH). On the basis of phylogenetic, physiological, biochemical and other phenotypic properties, strain MT2928T represents a novel species of the genus Pontivivens, and the name Pontivivens ytuae sp. nov. is proposed with the type species MT2928T (=MCCC 1K05575T=JCM 34320T).

Palleronia sediminis sp. nov. and Flavivirga algicola sp. nov., two marine bacteria isolated from offshore areas near Weihai.

Two bacterial strains, designated SS33T and Y03T, were isolated from marine sediment and marine red alga collected on the coast of Weihai, PR China. Based on the results of 16S rRNA gene sequence analysis, strain SS33T was found to be closely related to Primorskyibacter marinus PX7T, Pelagivirga dicentrarchi YLY04T, Palleronia marisminoris DSM 26347T and Maribius pontilimi GH1-23T with 94.8, 94.6, 94.5 and 94.5 % sequence similarity; strain Y03T was found to be closest to Flavivirga aquimarina EC2D5T, Flavivirga eckloniae ECD14T and Flavivirga amylovorans JC2681T with 96.4, 96.1 and 96.0 % sequence similarity. Strain SS33T grew at 4-37 °C (optimum, 33 °C), at pH 6.0-9.5 (optimum, pH 7.5-8.0) and in the presence of 0-10 % (w/v) NaCl (optimum, 3.0 %). Chemotaxonomic analysis of strain SS33T showed that the predominant respiratory quinone was ubiquinone-10. The major fatty acids (>10.0 %) included C18 : 1 ω7c and C16 : 0. The major polar lipids included phosphatidylglycerol, phosphatidylcholine, one unidentified phospholipid, one unidentified glycolipid, one unidentified polar lipid and two unidentified aminolipids. Strain Y03T grew at 15-40 °C (optimum, 28 °C), at pH 6.5-8.0 (optimum, pH 7.0) and in the presence of 0.5-9.0 % (w/v) NaCl (optimum, 2.0%). Chemotaxonomic analysis showed that the predominant respiratory quinone was menaquinone-6. The major fatty acids (>10.0 %) included iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The major polar lipids included phosphatidylethanolamine, one unidentified phospholipid, one unidentified aminolipid and four unidentified polar lipids. Based on the polyphasic data, strain SS33T is considered to represent a novel species of the genus Palleronia, for which the name Palleronia sediminis sp. nov. is proposed, with the type strain SS33T (=KCTC 62986T=MCCC 1H00387T). Strain Y03T is considered to represent a novel species of the genus Flavivirga, for which the name Flavivirga algicola sp. nov. is proposed, with the type strain Y03T (=KCTC 72001T=MCCC 1H00386T).

Chachezhania sediminis sp. nov., isolated from marine sediment.

A Gram-stain-negative, aerobic, non-motile, rod-shaped bacterial strain (CAU 1508T) was isolated from marine sediment collected in the Republic of Korea. Growth was observed at 10-45 °C (optimum, 30 °C), pH 4.0-11.0 (optimum, pH 6.0-8.0) and with 0-8.0 % (w/v) NaCl (optimum, 2-4 %). The isolate formed a monophyletic clade in the phylogenetic analyses using 16S rRNA gene and whole-genome sequences, exhibiting the highest similarity to Chachezhania antarctica SM1703T (96.5 %), and representing a distinct branch within the genus Chachezhania (family Rhodobacteraceae). Its whole genome sequence was 5.59 Mb long, with a G+C content of 65.7 mol% and 2183 predicted genes belonging to six functional categories. The average nucleotide identity and digital DNA-DNA hybridization values between CAU 1508T and C. antarctica SM1703T were 79.1 and 22.2 %, respectively. The predominant cellular fatty acids were C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, two unidentified phospholipids and one unidentified aminophospholipid. The sole isoprenoid quinone was ubiquinone 10. Phenotypic phylogenetic properties supported the classification of CAU 1508T as representing a novel species of the genus Chachezhania, with the proposed name Chachezhania sediminis sp. nov. The type strain is CAU 1508T (=KCTC 62999T=NBRC 113697T).

Specific Detection of Coral-Associated Ruegeria, a Potential Probiotic Bacterium, in Corals and Subtropical Seawater.

Coral microbial flora has been attracting attention because of their potential to protect corals from environmental stresses or pathogens. Although coral-associated bacteria are considered to be acquired from seawater, little is known about the relationships between microbial composition in corals and its surrounding seawater. Here, we tested several methods to identify coral-associated bacteria in coral and its surrounding seawater to detect specific types of Ruegeria species, some of which exhibit growth inhibition activities against the coral pathogen Vibrio coralliilyticus. We first isolated coral-associated bacteria from the reef-building coral Galaxea fascicularis collected at Sesoko Island, Okinawa, Japan, via random colony picking, which showed the existence of varieties of bacteria including Ruegeria species. Using newly constructed primers for colony PCR, several Ruegeria species were successfully isolated from G. fascicularis and seawater. We further investigated the seawater microbiome in association with the distance from coral reefs. By seasonal sampling, it was suggested that the seawater microbiome is more affected by seasonality than the distance from coral reefs. These methods and results may contribute to investigating and understanding the relationships between the presence of corals and microbial diversity in seawater, in addition to the efficient isolation of specific bacterial species from coral or its surrounding seawater.

Sulfitobacter aestuariivivens sp. nov., isolated from a tidal flat.

A Gram-stain-negative, aerobic, non-flagellated, coccoid, ovoid or rod-shaped bacterial strain, TSTF-M16T, was isolated from a tidal flat on the Yellow Sea, Republic of Korea. The neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain TSTF-M16T fell within a clade comprising the type strains of Sulfitobacter species. Strain TSTF-M16T exhibited 16S rRNA gene sequence similarities of 98.5 and 98.1 % to the type strains of Sulfitobacter mediterraneus and Sulfitobacter sabulilitoris, respectively, and 96.2-97.8 % to the type strains of the other Sulfitobacter species. The average nucleotide identity and digital DNA-DNA hybridization values between the genomic sequences of strain TSTF-M16T and the type strains of 16 Sulfitobacter species were 70.6-74.2 and 17.9-19.0 %, respectively. The DNA G+C content of strain TSTF-M16T from genomic sequence data was 59.26 mol%. Strain TSTF-M16T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The major polar lipids of strain TSTF-M16T were phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. Distinguished phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain TSTF-M16T is separated from recognized Sulfitobacter species. On the basis of the data presented here, strain TSTF-M16T is considered to represent a novel species of the genus Sulfitobacter, for which the name Sulfitobacter aestuariivivens sp. nov. is proposed. The type strain is TSTF-M16T (=KACC 21645T=NBRC 114501T).

Stappia albiluteola sp. nov., isolated from marine sediment.

A Gram-stain negative, rod-shaped, facultatively aerobic, pale-beige-coloured bacterial strain, designated F7233T, was isolated from coastal sediment sampled at Jingzi Bay, Weihai, PR China. Cells of strain F7233T were 0.3-0.4 µm wide, 1.2-1.4 µm wide long, non-spore-forming and motile with one flagellum. Optimum growth occurred at 30 °C, with 1.0 % (w/v) NaCl and at pH 6.5-7.0. Positive for nitrate reduction, hydrolysis of Tweens and oxidase activity. The sole respiratory quinone of strain F7233T was ubiquinone-10 and the predominant cellular fatty acid was summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and one unidentified aminophospholipid. The G+C content of the chromosomal DNA was 63.3 mol%. Phylogenetic analysis of the 16S rRNA gene sequence revealed that the newly isolate belonged to the genus Stappia, with 96.8 % sequence similarity to Stappia indica MCCC 1A01226T, 96.1 % similarity to Stappia stellulata JCM 20692T and 95.5% similarity to Stappia taiwanensis CC-SPIO-10-1T. On the basis of phylogenetic, phenotypic and chemotaxonomic data, it is considered that strain F7233T should represent a novel species within the genus Stappia, for which the name Stappia albiluteola sp. nov. is proposed. The type strain is F7233T (=MCCC 1H00419T=KCTC 72859T).

Isolation of Thalassobius mangrovi sp. nov., a novel bacterium in the family Rhodobacteraceae, from marine mangrove sediment.

A Gram-stain-negative, strictly aerobic and oval-shaped bacterial strain with a flagellum, designated GS-10T, was isolated from mangrove wetland sediment. GS-10T grew at 20-40 °C (optimum, 37 °C), in the pH range of 5.0-11.0 (optimum, 6.0-8.0) and under various NaCl concentrations from 1 to 11 % (w/v) (optimum, 5-6 %). The respiratory quinone was ubiquinone-10, and the predominant polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids (>10 % of the total fatty acids) were summed feature 4 (C17 : 1iso I/anteiso B) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The G+C content of the genomic DNA was 63.71 %. On the basis of the results from comparative analysis of the 16S rRNA gene sequence, GS-10T represents a member of the family Rhodobacteraceae and had the highest sequence similarity to Thalassobius gelatinovorus CECT 4357T (97.47 %), followed by Lutimaribacter pacificus W11-2BT (97.03 %), Marivita cryptomonadis CL-SK44T (96.83 %), Thalassobius autumnalis CECT 5118T (96.75 %) and Thalassobius mediterraneus CECT 5383T (96.68 %). Phylogenetic trees based on 16S rRNA gene sequences, multilocus sequence analysis (MLSA) and whole genome sequences revealed that GS-10T clustered with species within the genus Thalassobius. The average nucleotide identity (ANI) and the average amino acid identity (AAI) values were calculated from complete genome sequences and indicated that GS-10T represented a novel species of the genus Thalassobius, and the name Thalassobius mangrovi sp. nov. is proposed for this species. The type strain of Thalassobius mangrovi is GS-10T (=MCCC 1K03624T=KCTC 82131T).

Shimia sediminis sp. nov., a bacterium isolated from marine sediment in the East China Sea.

A Gram-stain-negative, ovoid-shaped, motile and strictly aerobic bacterium, designated ZQ172T, was isolated from marine sediment sampled on Zhoushan Island located in the East China Sea. Strain ZQ172T grew optimally at temperatures of 25-30 °C, at NaCl concentration of 2.0 % (w/v) and at pH 7.0-8.5. Catalase and oxidase activities, urease, and nitrate reduction were positive. Indole production, methyl red reaction, H2S production and hydrolysis of gelatin, starch, casein and Tweens 20, 40, 60 and 80 were negative. The major cellular fatty acid was summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The only respiratory quinone was ubiquinone-10. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine. Comparative analysis of the 16S rRNA gene sequence showed highest similarities to Shimia aestuarii JC2049T (97.5 %), Shimia abyssi JAMH 043T (97.5 %) and Shimia thalassica CECT 7735T (97.3 %). Phylogenetic analyses indicated that strain ZQ172T clustered with the genus Shimia and was closely related to Shimia thalassica CECT 7735T. The average nucleotide identity and digital DNA-DNA hybridization values between strain ZQ172T and related species of the genus Shimia were well below the threshold limit for prokaryotic species delineation. The DNA G+C content was 59.6 mol%. Based on its phenotypic, chemotaxonomic and genotypic data, strain ZQ172T is considered to be a representative of a novel species in the genus Shimia, for which the name Shimia sediminis sp. nov. is proposed. The type strain is ZQ172T (=KCTC 62578T=MCCC 1K03531T).