Xin-Qi Zhang

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)).

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.

Isolation and Complete Genome Sequence of Algibacter alginolytica sp. nov., a Novel Seaweed-Degrading Bacteroidetes Bacterium with Diverse Putative Polysaccharide Utilization Loci

ABSTRACT The members of the phylum Bacteroidetes are recognized as some of the most important specialists for the degradation of polysaccharides. However, in contrast to research on Bacteroidetes in the human gut, research on polysaccharide degradation by marine Bacteroidetes is still rare. The genus Algibacter belongs to the Flavobacteriaceae family of the Bacteroidetes, and most species in this genus are isolated from or near the habitat of algae, indicating a preference for the complex polysaccharides of algae. In this work, a novel brown-seaweed-degrading strain designated HZ22 was isolated from the surface of a brown seaweed (Laminaria japonica). On the basis of its physiological, chemotaxonomic, and genotypic characteristics, it is proposed that strain HZ22 represents a novel species in the genus Algibacter with the proposed name Algibacter alginolytica sp. nov. The genome of strain HZ22, the type strain of this species, harbors 3,371 coding sequences (CDSs) and 255 carbohydrate-active enzymes (CAZymes), including 104 glycoside hydrolases (GHs) and 18 polysaccharide lyases (PLs); this appears to be the highest proportion of CAZymes (∼7.5%) among the reported strains in the class Flavobacteria. Seventeen polysaccharide utilization loci (PUL) are predicted to be specific for marine polysaccharides, especially algal polysaccharides from red, green, and brown seaweeds. In particular, PUL N is predicted to be specific for alginate. Taking these findings together with the results of assays of crude alginate lyases, we prove that strain HZ22T can completely degrade alginate. This work reveals that strain HZ22T has good potential for the degradation of algal polysaccharides and that the structure and related mechanism of PUL in strain HZ22T are worth further research.

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)).

Thalassomonas eurytherma sp. nov., a marine proteobacterium.

Two Gram-staining-negative, aerobic, rod-shaped bacterial strains, designated Za6a-12(T) and Za6a-17, were isolated from seawater of the East China Sea. Cells of Za6a-12(T) and Za6a-17 were approximately 1.5-2.0 µm×0.5-0.7 µm and motile by a single polar flagellum. Strains grew optimally at pH 7.5-8.0, 28 °C, and in the presence of 2.5-3.0% (w/v) NaCl. Chemotaxonomic analysis showed that the predominant respiratory quinone of strains Za6a-12(T) and Za6a-17 was ubiquinone-8 (>97%), and the major fatty acids were C(14 : 0), C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH, C(16 : 0) and C(17 : 1)ω8c. Their DNA G+C contents were 42.7 mol% and 42.8 mol%, respectively. 16S rRNA gene sequence analysis revealed that the isolates belonged to the genus Thalassomonas and showed the highest sequence similarity to Thalassomonas loyana CBMAI 722(T) (95.9%). Strains Za6a-12(T) and Za6a-17 could be differentiated from T. loyana CBMAI 722(T) according to their phenotypic and chemotaxonomic features, DNA G+C contents and fatty acid composition. On the basis of these features, we propose strains Za6a-12(T) and Za6a-17 to be representatives of a novel species of the genus Thalassomonas with the name Thalassomonas eurytherma sp. nov. suggested. Strain Za6a-12(T) ( = CGMCC 1.12115(T) = JCM 18482(T)) is the type strain of this novel species.

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.