Xu-Fen Zhu

Brassicibacter mesophilus gen. nov., sp. nov., a strictly anaerobic bacterium isolated from food industry wastewater.

A novel mesophilic, strictly anaerobic bacterium, strain BM(T), was isolated from food industry wastewater. The cells were motile, non-spore-forming rods and stained Gram-negative. Growth of strain BM(T) was observed at 16-44 °C (optimum 37 °C) and pH 6.0-9.0 (optimum pH 7.5). The NaCl concentration range for growth was 0-8% (optimum 1.5%, w/v). Strain BM(T) was chemo-organotrophic, using a few sugars and amino acids as sole carbon and energy sources. The fermentation products from peptone-yeast extract broth were propionate, formate, acetate, ethanol and isovalerate. Indole, NH(3) and H(2)S were produced from peptone. No respiratory quinones could be detected. The major fatty acids were iso-C(15:0) (39.3%), iso-C(15:0) dimethyl acetal (10.1%), anteiso-C(15:0) (7.6%), C(14:0) (6.1%) and C(16:0) (5.6%). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol and a number of unidentified aminoglycolipids, glycolipids and phospholipids. The DNA G+C content was 28.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain BM(T) was related to various genera of the family Clostridiaceae, and its closest relatives were Sporosalibacterium faouarense SOL3f37(T) (94.3% 16S rRNA gene sequence similarity), Proteiniborus ethanoligenes GW(T) (92.1%) and Clostridiisalibacter paucivorans 37HS60(T) (92.0%). In recognition of its distinct phenotypic and genotypic characteristics, isolate BM(T) is proposed to represent a novel species of a new genus, Brassicibacter mesophilus gen. nov., sp. nov. The type strain of Brassicibacter mesophilus is BM(T) ( = JCM 16868(T)  = DSM 24659(T)).

Parabacteroides chartae sp. nov., an obligately anaerobic species from wastewater of a paper mill

A bacterial strain, designated NS31-3(T), was isolated from the wastewater of a paper mill. Cells of the isolate were obligately anaerobic, non-pigmented, non-motile, Gram-negative, short rods (0.7-1.0 × 1.4-2.5 µm). The isolate was able to grow on media containing 20% bile salts. API 20A tests showed that acid was produced from glucose, lactose, sucrose, maltose, D-xylose, L-arabinose, cellobiose, D-mannose, D-melezitose, D-raffinose, D-trehalose, D-mannitol, salicin and D-sorbitol. The main fermentation products from PYG broth were lactic acid, propionic acid, formic acid and acetic acid. Chemotaxonomic analysis showed that the major fatty acids were anteiso-C(15:0), C(15:0) and iso-C(17:0) 3-OH and the predominant respiratory quinones were MK-9 and MK-10. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NS31-3(T) was related to members of genus Parabacteroides (91.2-93.2% sequence similarity); the isolate had the closest affinity with Parabacteroides merdae JCM 9497(T). The G+C content of the genomic DNA was 37.2 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic analysis, strain NS31-3(T) represents a novel species of the genus Parabacteroides, for which the name Parabacteroides chartae sp. nov. is proposed. The type strain is NS31-3(T) (=JCM 17797(T) =DSM 24967(T)).

Amphibacillus jilinensis sp. nov., a facultatively anaerobic, alkaliphilic bacillus from a soda lake

A facultatively anaerobic, alkaliphilic, spore-forming, Gram-positive-staining rod, designated Y1(T), was isolated under strictly anaerobic conditions from sediment of a soda lake in Jilin province, China. The strain was not dependent on Na(+) but was highly halotolerant and grew optimally in medium JY with 0.5 M Na(+) (0.06 M NaHCO(3) and 0.44 M NaCl). The optimum pH for growth was 9.0, with a range of pH 7.5-10.5. No growth occurred at pH 7.0 or 11.0. The strain was mesophilic, with a temperature range of 15-45 °C and optimum growth at 32 °C. Strain Y1(T) was able to use certain mono- and oligosaccharides. Soluble starch and casein were hydrolysed. The methyl red test, Voges-Proskauer test and tests for catalase and oxidase activities were negative. The predominant fatty acids were anteiso-C(15 : 0) and iso-C(15 : 0). Comparative 16S rRNA gene sequence analysis revealed 93.4-96.8 % sequence similarity to members of the genus Amphibacillus. The DNA G+C content was 37.7 mol% (T(m) method). The DNA-DNA relatedness of strain Y1(T) with respect to Amphibacillus tropicus DSM 13870(T) and Amphibacillus sediminis DSM 21624(T) was 48 and 37 %, respectively. On the basis of its phylogenetic position and the DNA-DNA relatedness data as well as its physiological and biochemical properties, strain Y1(T) represents a novel species of the genus Amphibacillus, for which the name Amphibacillus jilinensis sp. nov. is proposed. The type strain is Y1(T) (=CGMCC 1.5123(T) =JCM 16149(T)).

Thermus arciformis sp. nov., a thermophilic species from a geothermal area

Two aerobic, Gram-negative, non-motile, non-sporulating, yellow-pigmented bacteria, strains TH92(T) and TH91, were isolated from a hot spring located in Laibin, Guangxi, in the south-eastern geothermal area of China. The isolates grew at 40-77 degrees C (optimally at 70 degrees C) and at pH 6.0-9.5 (optimally at pH 7.5-8.0). Phylogenetic analysis of 16S rRNA gene sequences and levels of DNA-DNA relatedness together indicated that the new isolates represented a novel species of the genus Thermus with closest affinity to Thermus aquaticus, Thermus igniterrae and Thermus thermophilus. Compared with their closest relatives, strains TH92( T) and TH91 were able to assimilate a wider range of carbohydrates, amino acids and organic acids as sole carbon sources for growth, such as lactose and melibiose. The new isolates had lower combined levels of C(16 : 0 ) and iso-C(16 : 0) compared with their closest relatives. On the basis of polyphasic taxonomic characterization, strains TH92(T) and TH91 are considered to represent a single novel species of the genus Thermus, for which the name Thermus arciformis sp. nov. is proposed. The type strain is TH92(T) (=CGMCC 1.6992(T) =JCM 15153(T)).

Cloning, Expression, and Characterization of a New β-Agarase from Vibrio sp. Strain CN41

ABSTRACT A new agarase, AgaACN41, cloned from Vibrio sp. strain CN41, consists of 990 amino acids, with only 49% amino acid sequence identity with known β-agarases. AgaACN41 belongs to the GH50 (glycoside hydrolase 50) family but yields neoagarotetraose as the end product. AgaACN41 was expressed and characterized.

Paracoccus sediminis sp. nov., isolated from Pacific Ocean marine sediment.

Strain CMB17(T) was a short rod-shaped bacterium isolated from marine sediment of the Pacific Ocean. Cells were Gram-stain-negative and non-motile. Optimal growth occurred at 25-30 °C, pH 6.5-7 and 0.5-1% (w/v) NaCl. The major fatty acid was C(18 : 1)ω7c (87.59%), and ubiquinone-10 was detected as the only isoprenoid quinone. The DNA G+C content of the genomic DNA was 62.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CMB17(T) is most closely related to Paracoccus stylophorae KTW-16(T) (96.7%), P. solventivorans DSM 6637(T) (96.4%) and P. saliphilus YIM 90738(T) (96.4%). Based on phenotypic, genotypic and phylogenetic characteristics, strain CMB17(T) is proposed to represent a novel species, denominated Paracoccus sediminis sp. nov. (type strain CMB17(T) = JCM 18467(T) = DSM 26170(T) = CGMCC 1.12681(T)).

Halolamina salifodinae sp. nov. and Halolamina salina sp. nov., two extremely halophilic archaea isolated from a salt mine.

Two strictly aerobic, extremely halophilic archaea, strains WSY15-H1(T) and WSY15-H3(T), were isolated from a salt mine in Wensu county, Xinjiang province, China. Cells of the two strains were Gram-stain-negative, non-motile and pleomorphic. Colonies were pink- and red-pigmented, respectively. Strain WSY15-H1(T) grew at 20-45 °C (optimum 37-42 °C), 1.6-5.4 M NaCl (optimum 3.4-3.9 M), 0-2.0 M MgCl2 (optimum 0.1-0.5 M) and pH 6.0-9.0 (optimum 7.0), whereas strain WSY15-H3(T) grew at 20-50 °C (optimum 37 °C), 1.9-5.4 M NaCl (optimum 3.4 M), 0.02-2.5 M MgCl2 (optimum 0.5-1.0 M) and pH 6.0-7.5 (optimum 6.5). The minimal NaCl concentrations to prevent cell lysis were 9 % (w/v) for strain WSY15-H1(T) and 8 % (w/v) for strain WSY15-H3(T). The major polar lipids of the two isolates were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate, as well as nine glycolipids for strain WSY15-H1(T) and seven glycolipids for strain WSY15-H3(T); two of these glycolipids (GL1 and GL3) were chromatographically identical to bis-sulfated diglycosyl diether (S2-DGD-1) and sulfated diglycosyl diether (S-DGD-1), respectively. The genomic DNA G+C contents of strains WSY15-H1(T) and WSY15-H3(T) were 65.4 and 66.2 mol%. On the basis of 16S rRNA gene sequence analysis, strains WSY15-H1(T) and WSY15-H3(T) shared 97.0% similarity with each other and showed respectively 98.4 and 97.6% sequence similarity to Halolamina pelagica TBN21(T), which was the only type strain that had higher than 91% sequence similarity with the two isolates. Analysis of phylogenetic relationships and DNA-DNA relatedness indicated that strains WSY15-H1(T) and WSY15-H3(T) represent two novel lineages with closest affinity to H. pelagica TBN21(T). Based on phenotypic, chemotaxonomic and genotypic characteristics, two novel species of the genus Halolamina are proposed, Halolamina salifodinae sp. nov. (type strain WSY15-H1(T) = JCM 18548(T) = GCMCC 1.12371(T)) and Halolamina salina sp. nov. (type strain WSY15-H3(T) = JCM 18549(T) = GCMCC 1.12285(T)).

Maribacter thermophilus sp. nov., isolated from an algal bloom in an intertidal zone, and emended description of the genus Maribacter.

A novel facultatively anaerobic, Gram-stain-negative bacterium, designated strain HT7-2(T), was isolated from Ulva prolifera collected from the intertidal zone of Qingdao sea area, China, during its bloom. Cells were rod-shaped (1.9-3.5×0.4-0.6 µm), non-sporulating and motile by gliding. Strain HT7-2(T) was able to grow at 4-50 °C (optimum 40-42 °C), pH 5.5-8.5 (optimum pH 7.0), 0-8 % (w/v) NaCl (optimum 2-3 %) and 0.5-10 % (w/v) sea salts (optimum 2.5 %). The genomic DNA G+C content was 38.8 mol%. The phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HT7-2(T) belonged to the genus Maribacter with sequence similarity values of 94.5-96.6 %, and was most closely related to Maribacter aestuarii GY20(T) (96.6%). Chemotaxonomic analysis showed that the main isoprenoid quinone was MK-6 and the major fatty acids were iso-C15:0 and unknown equivalent chain-length 13.565. The polar lipids of strain HT7-2(T) consisted of one phosphatidylethanolamine, four unidentified lipids and one unidentified aminolipid. On the basis of the phenotypic, phylogenetic and chemotaxonomic characteristics, strain HT7-2(T) ( =CGMCC 1.12207(T) =JCM 18466(T)) is concluded to represent a novel species of the genus Maribacter, for which the name Maribacter thermophilus sp. nov. is proposed. An emended description of the genus Maribacter is also proposed.

Complete Genome Sequence of Pelagibacterium halotolerans B2T

Pelagibacterium halotolerans B2(T) is a marine halotolerant bacterium that was isolated from a seawater sample collected from the East China Sea. Here, we present the complete genome sequence of the type strain P. halotolerans B2(T), which consists of one chromosome (3,944,837 bp; 61.4% G+C content) and one plasmid (4,050 bp; 56.1% G+C content). This is the first complete genome of a member of the Pelagibacterium genus.

Marinobacterium nitratireducens sp. nov. and Marinobacterium sediminicola sp. nov., isolated from marine sediment

Two strains, CN44(T) and CN47(T), isolated from marine sediment of the East China Sea, were characterized by using a polyphasic approach. The isolates were Gram-negative, strictly aerobic, non-spore-forming rods. The chemotaxonomic characteristics of these isolates included the presence of C(18 : 1)omega7c, C(16 : 0), iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c and C(10 : 0) 3-OH as the major cellular fatty acids and Q-8 as the predominant ubiquinone. The DNA G+C contents of strains CN44(T) and CN47(T) were 62.5 and 56.3 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain CN44(T) was related to members of the genus Marinobacterium. The most closely related described organism was the type strain of Marinobacterium rhizophilum (95.3 % sequence similarity). Strain CN47(T) showed the highest sequence similarity to the type strain of Marinobacterium stanieri (97.8 %) and <97 % similarity to other type strains of described Marinobacterium species. The level of DNA-DNA relatedness between strain CN47(T) and M. stanieri DSM 7027(T) was 46 %. On the basis of phenotypic and genotypic properties, strains CN44(T) and CN47(T) represent two novel species within the genus Marinobacterium, for which the names Marinobacterium nitratireducens sp. nov. (type strain, CN44(T) =CGMCC 1.7286(T) =JCM 15523(T)) and Marinobacterium sediminicola sp. nov. (type strain, CN47(T) =CGMCC 1.7287(T) =JCM 15524(T)) are proposed.