Chun-Sheng Wang

Pelagibacterium halotolerans gen. nov., sp. nov. and Pelagibacterium luteolum sp. nov., novel members of the family Hyphomicrobiaceae

Two Gram-negative, motile, aerobic bacterial strains, designated B2(T) and 1_C16_27(T), were respectively isolated from a seawater sample collected from the East China Sea and a semi-coke sample from north-eastern Estonia. Their genetic, phenotypic and chemotaxonomic properties were studied. The isolates were short rods with polar flagella and were positive for catalase and oxidase activities. Q-10 was the predominant respiratory ubiquinone. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and two unidentified glycolipids. The major fatty acids were nonadecanoic (C(19 : 0) cyclo), octadecanoic (C(18 : 0) and C(18 : 0) 3-OH), octadecenoic (C(18 : 1)) and hexadecanoic (C(16 : 0)) acids. The G+C content of the genomic DNA was 58.1-59.3 mol%. 16S rRNA gene sequence analysis revealed that the two isolates represent a distinct lineage within the family Hyphomicrobiaceae. The phylogenetically closest relatives were Cucumibacter (92.7-93.7 % 16S rRNA gene sequence similarity), Devosia (92.9-94.4 %) and Zhangella (91.7-92.1 %). Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strains B2(T) and 1_C16_27(T) could be differentiated from each other and from members of the genera Cucumibacter, Devosia and Zhangella. Therefore, it is proposed that strains B2(T) and 1_C16_27(T) represent two novel species in a new genus, for which the names Pelagibacterium halotolerans gen. nov., sp. nov. (the type species; type strain B2(T)  = CGMCC 1.7692(T)  = JCM 15775(T)) and Pelagibacterium luteolum sp. nov. (type strain 1_C16_27(T)  = CGMCC 1.10267(T)  = JCM 16552(T)  = CELMS EEUT 1C1627(T)) are proposed.

Marinobacter pelagius sp. nov., a moderately halophilic bacterium

A Gram-negative, aerobic, neutrophilic, moderately halophilic bacterial strain, HS225(T), was isolated from seawater samples around the Zhoushan Archipelago, Zhejiang Province, China. The isolate grew optimally in media with 5.0 % NaCl, at pH 7.0-8.0 and at 25-30 degrees C. The predominant fatty acids were C(16 : 0)omega9c, C(16 : 0), C(12 : 0) 3-OH and C(18 : 1)omega9c. The genomic DNA G+C content was 59.0 mol%. Based on 16S rRNA gene sequence analysis, the isolate was found to be affiliated to the genus Marinobacter. Strain HS225(T) exhibited closest phylogenetic affinity to Marinobacter koreensis DD-M3(T) (98.1 % 16S rRNA gene sequence similarity). DNA-DNA relatedness data and DNA G+C contents as well as physiological and biochemical test results allowed the genotypic and phenotypic differentiation of strain HS225(T) from closely related species. Therefore, it is proposed that strain HS225(T) represents a novel species of the genus Marinobacter, for which the name Marinobacter pelagius sp. nov. is proposed. The type strain is HS225(T) (=CGMCC 1.6775(T) =JCM 14804(T)).

Altererythrobacter atlanticus sp. nov., isolated from deep-sea sediment.

A Gram-stain-negative, short rod-shaped bacterium, designated 26DY36(T), was isolated from a deep-sea sediment sample collected from the North Atlantic Rise. The isolate required NaCl and grew best with 2 % (w/v) sea salts at a temperature of 30-35 °C and at pH 7.0. It formed yellow colonies, produced carotenoid-like pigments and did not produce bacteriochlorophyll a. Strain 26DY36(T) was positive for hydrolysis of aesculin, gelatin, tyrosine and Tweens 20, 40, 60 and 80, but negative for hydrolysis of casein, DNA and starch. The major respiratory quinone was ubiquinone-10. The major polar lipid profile consisted of sphingoglycolipid, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and two unidentified glycolipids. The principal fatty acids (>5 %) were C18 : 1ω7c, C17 : 1ω6c, C15 : 0 2-OH and C16 : 0. The genomic DNA G+C content was 59.4 mol%. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain 26DY36(T) should be assigned to the genus Altererythrobacter. 16S rRNA gene sequence similarities between the isolate and the type strains of species of the genus Altererythrobacter were in the range 92.7-96.5 %. On the basis of phenotypic and genotypic data, strain 26DY36(T) represents a novel species of the genus Altererythrobacter, for which the name Altererythrobacter atlanticus sp. nov. (type strain, 26DY36(T) = CGMCC 1.12411(T) = JCM 18865(T)) is proposed.

Microbial diversity in deep‐sea sediment from the cobalt‐rich crust deposit region in the Pacific Ocean

Cobalt-rich crusts are important metallic mineral resources with great economic potential, usually distributed on seamounts located in the Pacific Ocean. Microorganisms are believed to play a role in the formation of crusts as well as in metal cycling. To explore the microbial diversity related to cobalt-rich crusts, 16S ribosomal RNA gene clone libraries were constructed from three consecutive sediment layers. In total, 417 bacterial clones were obtained from three bacterial clone libraries, representing 17 distinct phylogenetic groups. Proteobacteria dominated in the bacterial communities, followed by Acidobacteria and Planctomycetes. Compared with high bacterial diversity, archaea showed a remarkably low diversity, with all 137 clones belonging to marine archaeal group I except one novel euryarchaeotal clone. The microbial communities were potentially involved in sulfur, nitrogen and metal cycling in the area of cobalt-rich crusts. Sulfur oxidation and metal oxidation were potentially major sources of energy for this ecosystem. This is the first reported investigation of microbial diversity in sediments associated with cobalt-rich crusts, and it casts fresh light on the microbial ecology of these important ecosystems.

Ruegeria marina sp. nov., isolated from Marine Sediment

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

Kordiimonas lacus sp. nov., isolated from a ballast water tank, and emended description of the genus Kordiimonas.

A Gram-negative, motile, rod-shaped bacterial strain, designated S3-22(T), was isolated from a sediment sample collected from a ballast water tank of a commercial ship and subjected to a polyphasic taxonomic characterization. The isolate formed small, light-yellow, semi-translucent and circular colonies on solid complex media. The strain was oxidase- and catalase-positive and metabolized a large number of carbon sources. Chemotaxonomic analysis showed ubiquinone Q-10 as predominant respiratory quinone, phosphatidylglycerol and an unidentified glycolipid as major polar lipids and iso-C(17 : 1)ω9c, iso-C(15 : 0), C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH, C(16 : 0), iso-C(17 : 0) and C(18 : 1)ω7c as major fatty acids and the hydroxy fatty acids iso-C(17 : 0) 3-OH and C(16 : 0) 3-OH. The genomic DNA G+C content was 54.9 mol%. 16S rRNA gene sequence analysis revealed that the isolate has 96.1 % similarity to the type strain of Kordiimonas gwangyangensis, the sole described species within the order Kordiimonadales, and less than 91.0 % similarity to other recognized species. On the basis of phenotypic and genotypic data, strain S3-22(T) represents a novel species of the genus Kordiimonas, for which the name Kordiimonas lacus sp. nov. is proposed, with the type strain S3-22(T) (=CGMCC 1.9109(T) =JCM 16261(T)). An emended description of the genus Kordiimonas is also presented.

Pseudoalteromonas lipolytica sp. nov., isolated from the Yangtze River estuary

A strictly aerobic, Gram-negative, non-pigmented bacterial strain, designated LMEB 39(T), was isolated from a seawater sample collected from the Yangtze River estuary near the East China Sea and was examined physiologically, chemotaxonomically and phylogenetically. The novel isolate was motile by a single polar flagellum and positive for nitrate reduction and decomposition of casein, gelatin, Tween 20 and Tween 80, but negative for indole production. Chemotaxonomic analysis revealed ubiquinone-8 as the predominant respiratory quinone and phosphatidylethanolamine and phosphatidylglycerol as major polar lipids. The major fatty acids were C(16 : 1) ω 7c/iso-C(15 : 0) 2-OH, C(16 : 0), C(18 : 1) ω 7c, C(12 : 0) 3-OH, C(17 : 1)ω 8c and C(17 : 0). The genomic DNA G+C content was 42.3 mol%. Comparative 16S rRNA gene sequence analysis revealed that the isolate belongs to the genus Pseudoalteromonas. Strain LMEB 39(T) exhibited the closest phylogenetic affinity to Pseudoalteromonas byunsanensis JCM 12483(T) (97.4 % sequence similarity). The DNA-DNA reassociation values between strain LMEB 39(T) and P. byunsanensis JCM 12483(T) and Pseudoalteromonas undina DSM 6065(T) (97.2 % sequence similarity) were 31.7 and 30.3 %, respectively. On the basis of phenotypic and genotypic data, strain LMEB 39(T) represents a novel species of the genus Pseudoalteromonas, for which the name Pseudoalteromonas lipolytica sp. nov. is proposed; the type strain is LMEB 39(T) (=CGMCC 1.8499(T)=JCM 15903(T)).

Croceicoccus marinus gen. nov., sp. nov., a yellow-pigmented bacterium from deep-sea sediment, and emended description of the family Erythrobacteraceae.

A Gram-negative, aerobic, neutrophilic, coccoid bacterium, strain E4A9T, was isolated from a deep-sea sediment sample collected from the East Pacific polymetallic nodule region. 16S rRNA gene sequence analysis showed that the isolate was related to the type strain of Altererythrobacter epoxidivorans (96.0% sequence similarity). Lower 16S rRNA gene sequence similarities were observed with other members of the genera Altererythrobacter (94.7%), Erythrobacter (94.0-95.4%), Erythromicrobium (94.8%) and Porphyrobacter (94.6-95.1%) of the family Erythrobacteraceae. Phylogenetic analysis including all described species of the family Erythrobacteraceae and several members of the family Sphingomonadaceae revealed that the isolate formed a distinct phylogenetic lineage with the family Erythrobacteraceae. Chemotaxonomic analysis revealed ubiquinone-10 as the predominant respiratory quinone, anteiso-C15:0, iso-C14:0 and iso-C15:0 as major fatty acids, and phosphatidylglycerol as the major polar lipid. The DNA G+C content was 71.5 mol%. The isolate contained carotenoids, but no bacteriochlorophyll a. On the basis of phenotypic and genotypic data presented in this study, strain E4A9T represents a novel species in a new genus in the family Erythrobacteraceae for which the name Croceicoccus marinus gen. nov., sp. nov. is proposed; the type strain is E4A9T (=CGMCC 1.6776T=JCM 14846T).

Bacterial and archaeal communities in the surface sediment from the northern slope of the South China Sea.

Microbial diversity of sediments from the northern slope of the South China Sea was studied by constructing bacterial and archaeal 16S rRNA gene clone libraries. Fourteen bacterial phylogenetic groups were detected, including Gammaproteobacteria, Deltaproteobacteria, Planctomycetes, Alphaproteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Chloroflexi, Acidobacteria, Betaproteobacteria, Nitrospirae, candidate divisions OP8 and OP11, and an unknown group. Gammaproteobacteria was the predominant group in bacterial libraries with the percentage ranging from 31.8% to 63.2%. However, archaeal libraries had relatively lower diversity, with most clones belonging to marine archaeal group I uncultured Crenarchaeota. In addition, two novel euryarchaeal clones were detected not to match any culture-dependent or -independent isolates. Compared with other gas hydrate-rich ecosystems and different areas of the South China Sea, a distinct microbial community was revealed in this study.

Brevirhabdus pacifica gen. nov., sp. nov., isolated from deep-sea sediment in a hydrothermal vent field

A Gram-stain-negative, motile, aerobic bacterial strain, designated 22DY15T, was isolated from a deep-sea sediment sample collected from a hydrothermal vent field located in the East Pacific Rise. The isolate was a short rod with a single flagellum and was positive for catalase and oxidase activities. Q-10 was the predominant respiratory quinone. The major polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphoglycolipid, one aminolipid and three unidentified phospholipids. The principal fatty acid (>70 %) was C18 : 1ω7c. The genomic DNA G+C content was 64.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 22DY15T represents a distinct lineage within the family Rhodobacteraceae. The closest relatives were species of the genera Aliiroseovarius (93.3–96.0 % 16S rRNA gene sequence similarity), Sulfitobacter (94.0–96.0 %) and Loktanella (92.0–95.9 %). Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain 22DY15T could be differentiated from its most closely related genera. Therefore, it is proposed that strain 22DY15T represents a novel species in a new genus of the family Rhodobacteraceae, for which the name Brevirhabdus pacifica gen. nov., sp. nov. is proposed. The type strain of the type species is 22DY15T ( = JCM 19489T = DSM 27767T = CGMCC 1.12416T = MCCC 1K00276T).