Yi-Guang Chen

Virgibacillus sediminis sp. nov., a moderately halophilic bacterium isolated from a salt lake in China

A Gram-positive, moderately halophilic, alkalitolerant, strictly aerobic, oxidase- and catalase-positive, rod-shaped bacterium, strain YIM kkny3T, was isolated from a sediment sample collected from a salt lake in the Qaidam Basin of north-west China. Cells were motile by means of peritrichous flagella and formed ellipsoidal endospores lying in subterminal swollen sporangia. Growth occurred with 1-20% (w/v) total salts (optimum, 5-10%) and at pH 6.0-10.5 (optimum, pH 7.5-8.0) and 10-55 degrees C (optimum, 35-40 degrees C). It was unable to grow with NaCl as the only salt. meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The strain contained menaquinone 7 (MK-7) as the predominant respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as polar lipids. The major cellular fatty acids were anteiso-C15:0 and anteiso-C17:0. The DNA G+C content was 40.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM kkny3T belonged to the genus Virgibacillus, and was most closely related to the type strains of Virgibacillus olivae (97.1% similarity), Virgibacillus marismortui (97.0%) and Virgibacillus kekensis (96.8%). Levels of DNA-DNA relatedness between strain YIM kkny3T and the type strains of V. olivae, V. marismortui and V. kekensis were 12.4, 10.6 and 15.7%, respectively. The combination of phylogenetic analysis, genotypic data, phenotypic characteristics and chemotaxonomic differences indicated that strain YIM kkny3T represents a novel species of the genus Virgibacillus, for which the name Virgibacillus sediminis sp. nov. is proposed. The type strain is YIM kkny3T (=CCTCC AA 207023T=DSM 19797T=KCTC 13193T).

Nocardiopsis quinghaiensis sp. nov., isolated from saline soil in China.

A previously unknown Gram-positive, obligately aerobic actinomycete, YIM 28A4(T), was isolated from a sample of saline soil collected from the Qaidam Basin in Qinghai Province, north-west China, and was investigated using a polyphasic taxonomic approach. The strain grew well on most of the media tested, producing white to pale-yellow substrate mycelium, white aerial mycelium and straight to flexuous hyphae. The substrate mycelium was well developed and fragmented with age; the aerial mycelium produced long, straight spore chains. The spore chains were composed of non-motile, smooth-surfaced, rod-shaped spores. No diffusible pigments were produced on any of the media tested. The strain grew in the presence of 0-10 % (w/v) NaCl and at pH 6.0-8.0, with optimum growth occurring at 3 % (w/v) NaCl and pH 7.0. It grew at 10-37 degrees C, the optimum growth temperature being 28 degrees C. Whole-cell hydrolysates of strain YIM 28A4(T) contained meso-diaminopimelic acid and no diagnostic sugars. The predominant phospholipids were phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol. The predominant menaquinones were MK-10, MK-10(H(2)), MK-11 and MK-11(H(2)). The major cellular fatty acids were iso-C(16 : 0), anteiso-C(15 : 0) and anteiso-C(17 : 0). The DNA G+C content was 67.1 mol%. The morphological and chemotaxonomic characteristics of the isolate matched those described for Nocardiopsis species. A phylogenetic analysis based on 16S rRNA gene sequence comparisons confirmed that strain YIM 28A4(T) was a member of the genus Nocardiopsis and most closely related to the type strains Nocardiopsis aegyptia DSM 44442(T) and Nocardiopsis halotolerans DSM 44410(T), showing 98.1 and 97.8 % 16S rRNA gene sequence similarity, respectively. Strain YIM 28A4(T) can be differentiated from these type strains by using phenotypic, phylogenetic and DNA-DNA hybridization data. On the basis of the polyphasic evidence, strain YIM 28A4(T) represents a novel species of the genus Nocardiopsis, for which the name Nocardiopsis quinghaiensis sp. nov. is proposed. The type strain is YIM 28A4(T) (=DSM 44739(T) =CGMCC 4.3494(T)).

Gracilibacillus halophilus sp. nov., a moderately halophilic bacterium isolated from saline soil.

A Gram-positive, moderately halophilic, moderately thermophilic, endospore-forming, catalase- and oxidase-positive, obligately aerobic bacterium, strain YIM-C55.5(T), was isolated from saline soil in the Qaidam Basin, north-west China. Cells were slender rods, motile by means of peritrichous flagella. Filamentous forms were present throughout the growth cycle. Strain YIM-C55.5(T) was able to grow in the presence of 7-30 % (w/v) NaCl and at pH 6.0-9.0, with optimum growth at 15 % (w/v) NaCl and pH 7.0. It was able to grow at 28-60 degrees C, with optimum growth at 45-50 degrees C. meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The major cellular fatty acids were iso-C(15 : 0), C(16 : 0), anteiso-C(15 : 0), anteiso-C(17 : 0) and C(18 : 0). Strain YIM-C55.5(T) possessed menaquinone 7 (MK-7) as the predominant respiratory quinone and diphosphatidylglycerol and phosphatidylglycerol as polar lipids. The genomic DNA G+C content was 42.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM-C55.5(T) belonged to the family Bacillaceae and was related most closely to members of the genus Gracilibacillus, but with low levels of similarity to the type strains of recognized species of the genus (Gracilibacillus orientalis XH-63(T), 95.1 %; Gracilibacillus boraciitolerans T-16X(T), 94.0 %; Gracilibacillus dipsosauri DD1(T), 93.7 %; Gracilibacillus halotolerans NN(T), 93.5 %). Together with phenotypic data, these results suggest that strain YIM-C55.5(T) represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus halophilus sp. nov. is proposed. The type strain is YIM-C55.5(T) (=DSM 17856(T) =CGMCC 1.6303(T)).

Paraliobacillus quinghaiensis sp. nov., isolated from salt-lake sediment in China

A Gram-positive, moderately halophilic, endospore-forming, catalase- and oxidase-positive, obligately aerobic bacterium, designated strain YIM-C158T, was isolated from sediment of a salt lake in the Qaidam Basin, north-west China. Cells were motile with peritrichous flagella and rod-shaped, with meso-diaminopimelic acid in the cell-wall peptidoglycan. Strain YIM-C158T grew in the presence of 1-20 % (w/v) NaCl and pH 6.0-10.0, with optimum growth at 5 % (w/v) NaCl and pH 8.0. The strain grew at 4-50 degrees C, with optimum growth at 37 degrees C. The major cellular fatty acids were anteiso-C(15 : 0), iso-C(14 : 0), C(16 : 0), anteiso-C(17 : 0), iso-C(16 : 0), C(16 : 1)omega7c alcohol and C(16 : 1)omega11c. Strain YIM-C158T contained menaquinone MK-7 as the sole respiratory quinone and phosphatidylmethylethanolamine and phosphatidylcholine as the polar lipids. The genomic DNA G+C content was 39.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM-C158T was most closely related to Paraliobacillus ryukyuensis DSM 15140T (96.8 % similarity), and the two strains formed a distinct branch in the phylogenetic tree. The level of DNA-DNA relatedness between the two strains was 15.6 %. The combination of phylogenetic analysis, phenotypic characteristics, chemotaxonomic differences and DNA-DNA hybridization data supported the view that strain YIM-C158T represents a novel species of the genus Paraliobacillus, for which the name Paraliobacillus quinghaiensis sp. nov. is proposed. The type strain is YIM-C158T (=DSM 17857T=CGMCC 1.6333T).

Salinimicrobium terrae sp. nov., isolated from saline soil, and emended description of the genus Salinimicrobium

A novel yellow-pigmented, Gram-negative, slightly halophilic, catalase-positive, oxidase-negative, obligately aerobic bacterium, designated strain YIM-C338(T), was isolated from saline soil from the Qaidam Basin in north-west China. Cells were non-sporulating, non-motile, short rods, predominantly occurring singly. Coccoid bodies and slightly curved rod-shaped cells of varying length developed in older cultures. Growth occurred with 0.5-8 % (w/v) NaCl (optimally with 1-3 %, w/v), at pH 6.0-9.0 (optimally at pH 7.0) and at 4-37 degrees C (optimally at 28 degrees C). The major cellular fatty acids were C(16 : 0), C(18 : 0), C(16 : 1)omega7c, C(18 : 1)omega7c, iso-C(13 : 0) 3-OH and iso-C(15 : 1). MK-6 was the only respiratory quinone. Non-diffusible carotenoid pigments were produced. Flexirubin-type pigments were absent. The genomic DNA G+C content was 42.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM-C338(T) was a member of the genus Salinimicrobium, having sequence similarities of 97.3 and 94.0 % with respect to Salinimicrobium xinjiangense BH206(T) and Salinimicrobium catena HY1(T). The combination of the phylogenetic data, phenotypic characteristics and chemotaxonomic differences supported the view that strain YIM-C338(T) represents a novel species of the genus Salinimicrobium, for which the name Salinimicrobium terrae sp. nov. is proposed. The type strain is YIM-C338(T) (=DSM 17865(T) =CGMCC 1.6308(T)). An emended description of the genus Salinimicrobium is also provided.

Fodinicurvata sediminis gen. nov., sp. nov. and Fodinicurvata fenggangensis sp. nov., poly-β-hydroxybutyrate-producing bacteria in the family Rhodospirillaceae

Two Gram-negatively stained, facultatively anaerobic, non-motile, vibrioid and rod-shaped, chemoheterotrophic bacterial strains, designated YIM D82(T) and YIM D812(T), were isolated from a salt mine in Yunnan, south-west China. DNA-DNA hybridization, genomic DNA G+C content and phylogenetic analyses based on 16S rRNA gene sequences divided the two isolates into two distinct genospecies that were also clearly differentiated by fatty acid profiles, carbon source utilization patterns, antibiotic susceptibility and biochemical characteristics. The two isolates grew in the presence of 1.5-20 % NaCl, and optimally at 28 degrees C and pH 7.5. The genomic DNA G+C contents of strains YIM D82(T) and YIM D812(T) were 61.5 and 62.3 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains YIM D82(T) and YIM D812(T) were members of the family Rhodospirillaceae and showed 90.5-90.6 % and 90.1-90.2 % similarities with their closest relatives, Rhodovibrio sodomensis and Rhodovibrio salinarum, respectively. Differential phenotypic and genotypic characteristics of the two isolates from recognized genera showed that the two strains should be classified as representing a new genus and two novel species for which the names Fodinicurvata sediminis gen. nov., sp. nov. (type strain YIM D82(T)=DSM 21159(T)=KCTC 22351(T)) and Fodinicurvata fenggangensis sp. nov. (type strain YIM D812(T)=CCTCC AA 208037(T)=DSM 21160(T)) are proposed.

Salinarimonas rosea gen. nov., sp. nov., a new member of the α-2 subgroup of the Proteobacteria

A Gram-negative, rod-shaped, facultatively anaerobic, halotolerant bacterial strain, designated YIM YD3(T), was isolated from a salt mine in Yunnan, south-west China. The taxonomy of strain YIM YD3(T) was investigated by a polyphasic approach. Strain YIM YD3(T) was motile, formed pink colonies and was positive for catalase and oxidase activities. Q-10 was the predominant respiratory ubiquinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine and two unknown phospholipids. The major fatty acids (>10 % of total fatty acids) were C(18 : 1)omega7c, C(18 : 1)omega9c, C(16 : 0) and C(19 : 0) cyclo omega8c. The DNA G+C content was 71.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the isolate formed a distinct line within a clade containing the genera Balneimonas, Bosea, Chelatococcus and Microvirga in the order Rhizobiales, with highest levels of 16S RNA gene sequence similarity to the type strain of Balneimonas flocculans (93.5 %). On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain YIM YD3(T) represents a novel species in a new genus, for which the name Salinarimonas rosea gen. nov., sp. nov. is proposed, with strain YIM YD3(T) (=KCTC 22346(T)=CCTCC AA208038(T)) as the type strain.

Salinicoccus albus sp. nov., a halophilic bacterium from a salt mine

A novel Gram-positive-staining, catalase- and oxidase-positive, non-motile, non-spore-forming coccus, designated YIM-Y21(T), was isolated from a salt mine in Yunnan, south-west China. The strain was moderately halophilic, facultatively alkaliphilic and obligately aerobic. Colonies were white. Growth occurred with 1.0-30.0 % NaCl (optimum, 10.0 % NaCl), at pH 6.0-10.0 (optimum, pH 8.5) and at 5-40 degrees C (optimum, 25 degrees C). The major amino acid constituents of the cell wall were glycine and lysine. The major cellular fatty acids were anteiso-C(15 : 0), anteiso-C(17 : 0) and iso-C(15 : 0). MK-6 was the predominant respiratory quinone, with MK-7 present in minor amounts. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and an unidentified phospholipid. The DNA G+C content was 46.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain YIM-Y21(T) was most closely related to the type strains of the nine recognized species of the genus Salinicoccus. The sequence similarities between the isolate and the type strains of members of this genus were in the range of 90.6-93.8 %, which indicated that strain YIM-Y21(T) is a representative of a novel species within the genus Salinicoccus. Together with the phenotypic characteristics and chemotaxonomic differences, these results support the proposal of a novel species of the genus Salinicoccus, Salinicoccus albus sp. nov., with YIM-Y21(T) (=CCTCC AA 207024(T) =DSM 19776(T) =KCTC 13192(T)) as the type strain.

Fodinibacter luteus gen. nov., sp. nov., an actinobacterium isolated from a salt mine.

A Gram-positive-staining, aerobic, catalase- and oxidase-positive, irregular short rod-shaped actinobacterium, designated strain YIM C003T, was isolated from a salt mine in Yunnan, PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM C003T was most closely related to strains of the genera Knoellia (94.2-96.0% similarity), Oryzihumus (95.6%), Terrabacter (94.9-95.4%), Janibacter (94.9-95.4%), Kribbia (95.0%), Lapillicoccus (95.0%) and Phycicoccus (94.2-95.0%) of the family Intrasporangiaceae and that it formed an independent monophyletic lineage with three strains of Oryzihumus leptocrescens. The DNA G+C content of strain YIM C003T was 72.0 mol%. The diagnostic cell-wall diamino acid was meso-diaminopimelic acid. The predominant menaquinone was MK-8(H4). Mycolic acids were not detected. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and two unknown phospholipids. The major cellular fatty acids were C18:1omega9c and C16:0. These chemotaxonomic properties, together with data from phylogenetic analysis, enabled the novel isolate to be differentiated from all other members of the family. A novel species in a new genus, Fodinibacter luteus gen. nov., sp. nov., is proposed, with strain YIM C003T (=DSM 21208T=CCTCC AA 208036T) as the type strain of Fodinibacter luteus.

Psychroflexus sediminis sp nov., a mesophilic bacterium isolated from salt lake sediment in China

A novel Gram-negative, mesophilic, slightly halophilic, catalase- and oxidase-positive, obligately aerobic bacterium, designated strain YIM-C238(T), was isolated from a sediment sample from a salt lake in the Qaidam Basin, north-west China. Cells were non-sporulating, non-motile, straight to slightly curved rods. Coccoid bodies and filaments of varying length developed in older cultures. Growth occurred with 0.5-6 % (w/v) NaCl [optimum, 2-3 % (w/v) NaCl], at pH 6.0-10.0 (optimum, pH 7.0-8.0) and at 10-40 degrees C (optimum, 25-30 degrees C). The major cellular fatty acids were anteiso-C(15 : 0), 3-OH iso-C(16 : 0) and anteiso-C(15 : 1)omega10c, and menaquinone 6 was the sole respiratory quinone. Non-diffusible carotenoid pigments were produced. Flexirubin pigments were absent. The genomic DNA G+C content was 35.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM-C238(T) should be assigned to the genus Psychroflexus. The sequence similarities between the isolate and the type strains of members of the genus Psychroflexus were in the range 95.5-97.0 %. The combination of phylogenetic analysis, DNA-DNA hybridization data, phenotypic characteristics and chemotaxonomic differences supported the view that strain YIM-C238(T) represents a novel species of the genus Psychroflexus, for which the name Psychroflexus sediminis sp. nov. is proposed. The type strain is YIM-C238(T) (=CCTCC AA 207030(T)=KCTC 22166(T)).