Chengxiang Fang

Knockout of crtB or crtI gene blocks the carotenoid biosynthetic pathway in Deinococcus radiodurans R1 and influences its resistance to oxidative DNA-damaging agents due to change of free radicals scavenging ability

Deinococcus radiodurans R1, a red-pigmented strain of the extremely radioresistant genus Deinococcus, contains a major carotenoid namely deinoxanthin. The high resistance of this organism against the lethal actions of DNA-damaging agents including ionizing radiation and ultraviolet light (UV) has been widely reported. However, the possible antioxidant role of carotenoids in this strain has not been completely elucidated. In this study, we constructed two colorless mutants by knockout of crtB and crtI genes, respectively. Comparative analysis of the two colorless mutants and the wild type showed that the two colorless mutants were more sensitive to ionizing radiation, UV, and hydrogen peroxide, but not to mitomycin-C (MMC). With electron spin resonance (ESR) and spin trapping techniques, we observed that hydroxyl radical signals occurred in the suspensions of UV irradiated Deinococcus radiodurans cells and the intensity of signals was influenced by carotenoids levels. We further showed that the carotenoid extract from the wild type could obviously scavenge superoxide anions generated by the irradiated riboflavin/EDTA system. These results suggest that carotenoids in D. radiodurans R1 function as free radical scavengers to protect this organism against the deleterious effects of oxidative DNA-damaging agents.

Pedobacter arcticus sp. nov., a facultative psychrophile isolated from Arctic soil, and emended descriptions of the genus Pedobacter, Pedobacter heparinus, Pedobacter daechungensis, Pedobacter terricola, Pedobacter glucosidilyticus and Pedobacter lentus

A Gram-stain-negative, short rod-shaped, motile (by gliding) bacterial strain, designated A12(T), was isolated from tundra soil collected from Ny-Ålesund, in the Arctic region of Norway. The temperature, NaCl and pH ranges for growth were 4-25 °C (optimum, 18 °C), 0-2% (optimum, 0%) and pH 6-9 (optimum, pH 7). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the Arctic isolate belonged to the genus Pedobacter and showed highest sequence similarity (94.4%) to Pedobacter daechungensis KCTC 12637(T). The DNA G+C content (38.3 mol%), polar lipid profile, presence of sphingolipid, MK-7 as the only respiratory quinone, and summed feature 3 (comprising C(16:1)ω7c and/or C(16:1)ω6c), iso-C(15:0) and iso-C(17:0) 3-OH as major fatty acids supported the allocation of strain A12(T) to the genus Pedobacter as a representative of a novel species, for which the name Pedobacter arcticus sp. nov. is proposed. The type strain is A12(T) ( = CCTCC AB 2010223(T) = NRRL B-59457(T)). Emended descriptions of the genus Pedobacter and of Pedobacter heparinus, Pedobacter daechungensis, Pedobacter terricola, Pedobacter glucosidilyticus and Pedobacter lentus are also given.

Kocuria flava sp. nov. and Kocuria turfanensis sp. nov., airborne actinobacteria isolated from Xinjiang, China

Two coloured bacteria were isolated from the same plate for detecting cultivable bacteria from the air of Xinjiang in China. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the isolates were members of the genus Kocuria, in which they represented two novel lineages. Although the two strains presented high 16S rRNA gene sequence similarity (above 97 %), their DNA G+C contents were very different (6 mol%). The G+C contents of strains HO-9041(T) and HO-9042(T) are 71 and 65 mol%, respectively. DNA relatedness analysis and other taxonomic evidence supports the placement of the two isolates in the genus Kocuria. The diagnostic diamino acid of the cell-wall peptidoglycan is l-lysine and both strains contain MK-8(H(2)) and MK-9(H(2)) as major menaquinones. In addition, they share similar fatty acid patterns containing straight-chain saturated and iso- and anteiso-branched acids, with a major component being anteiso-C(15:O). Genotypic, morphological and physiological characteristics are used to describe two novel species of Kocuria, for which the names Kocuria flava sp. nov. (type strain HO-9041(T) =CCTCC AB 206,106(T) =KCTC 19,306(T)) and Kocuria turfanensis sp. nov. (type strain HO-9,042(T) =CCTCC AB 206,107(T) =KCTC 19,307(T)) are proposed.

Pontibacter korlensis sp. nov., isolated from the desert of Xinjiang, China.

Two Gram-negative, rod-shaped, gliding and pink-pigmented bacterial strains, X14-1T and X19-1, were isolated from a mixture of sand samples collected from the desert of Xinjiang, China, and characterized by using a polyphasic taxonomic approach. Strains X14-1T and X19-1 contained MK-7 as the predominant menaquinone. The major cellular fatty acids included iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 and summed feature 4. The DNA G+C contents of strains X14-1T and X19-1 were 48.2 and 48.9 mol%, respectively. 16S rRNA gene sequence analysis showed that the isolates were highly related to each other (99.2 %) and confirmed their placement in the genus Pontibacter. Strains X14-1T and X19-1 exhibited 16S rRNA gene similarity levels of 95.0-97.2 % to the type strains of the two Pontibacter species with validly published names. DNA-DNA hybridization experiments revealed a high level of relatedness between the two new isolates (82 %), but low levels of relatedness between strain X14-1T and the phylogenetically most closely related species Pontibacter actiniarum KMM 6156T (51 %). On the basis of genotypic and phenotypic evidence, strains X14-1T and X19-1 are considered to represent a novel species of the genus Pontibacter, for which the name Pontibacter korlensis sp. nov. is proposed. The type strain is X14-1T (=CCTCC AB 206081T=NRRL B-51097T).

Hymenobacter tibetensis sp. nov., a UV-resistant bacterium isolated from Qinghai–Tibet plateau

A brick-red-pigmented strain (XTM003(T)) isolated from the Qinghai-Tibet plateau was investigated using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequence indicated that the organism belonged to the genus Hymenobacter. The predominant menaquinone was MK7. The major fatty acids included iso-15:0, 16:1w5c and summed feature 3 (C(16: 1)omega7c and/or C(16: 1)omega6c). The G+C content of the DNA was 55.8%. In addition, DNA-DNA hybridization studies demonstrated that strain XTM003(T) had a relatedness value of 50.7% with the phylogenetically most closely related species Hymenobacter norwichensis DSM 15439(T). Based on the results of phenotypic characteristics and DNA-DNA hybridization studies, strain XTM003(T) is considered to represent a novel species, for which the name Hymenobacter tibetensis sp. nov. is proposed. The type strain is XTM003(T) (=CCTCC AB 207089(T)=NRRL B-51271(T)).

Altererythrobacter xinjiangensis sp. nov., isolated from desert sand, and emended description of the genus Altererythrobacter

A Gram-negative, rod-shaped, non-motile, strictly aerobic bacterium, strain S3-63(T), was isolated from desert sand of Xinjiang, China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S3-63(T) had highest similarity to type strains of the genus Altererythrobacter, i.e. Altererythrobacter marinus H32(T) (97.2% similarity), Altererythrobacter marensis MSW-14(T) (95.9%), Altererythrobacter aestuarii KCTC 22735(T) (95.5%), Altererythrobacter epoxidivorans JCS350(T) (95.1%), Altererythrobacter namhicola KCTC 22736(T) (95.1%), Altererythrobacter luteolus SW-109(T) (95.0%) and Altererythrobacter indicus LMG 23789(T) (93.5%). Growth occurred at 20-37 °C (optimum 30 °C), at pH 7.0-9.0 (optimum pH 8.0) and in 0-3% (w/v) NaCl (optimum 1%). The major respiratory quinone was ubiquinone-10 and the predominant cellular fatty acids were C(18:1)ω7c (50.8%), summed feature 3 (C(16:1)ω7c and/or C(16:1)ω6c; 12.6%), C(16:0) (12.3%), C(14:0) 2-OH (7.3%) and C(17:1)ω6c (4.5%). The DNA G+C content was 64.6 mol%. Therefore, the phylogenetic, physiological and chemotaxonomic data demonstrated that strain S3-63(T) represents a novel species of the genus Altererythrobacter, for which the name Altererythrobacter xinjiangensis sp. nov. is proposed; the type strain is S3-63(T) (=CCTCC AB 207166(T)=CIP 110125(T)). An emended description of the genus Altererythrobacter is provided.

Bacillus korlensis sp. nov., a moderately halotolerant bacterium isolated from a sand soil sample in China.

A Gram-positive-staining, rod-shaped, motile, spore-forming and moderately halotolerant bacterium, designated ZLC-26(T), was isolated from a sand soil sample collected from Xinjiang Province, China, and was characterized by using a polyphasic taxonomic approach. This isolate grew optimally at 30-37 degrees C and pH 7-8. It grew with 0-8% NaCl (optimum, 0-2 %). Comparative 16S rRNA gene sequence analysis showed that strain ZLC-26(T) was closely related to members of the genus Bacillus, exhibiting the highest 16S rRNA gene sequence similarities to Bacillus nealsonii DSM 15077(T) (97.1 %), B. shackletonii LMG 18435(T) (97.0 %), B. siralis 171544(T) (97.0 %), B. circulans IAM 12462(T) (96.7 %) and B. pocheonensis Gsoil 420(T) (96.7 %). Strain ZLC-26(T) contained MK-7 as the predominant menaquinone. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major cellular fatty acids were iso-C(15 : 0), C(16 : 1)omega11c and anteiso-C(15 : 0). The DNA G+C content was 38.2 mol%. These chemotaxonomic results supported the affiliation of strain ZLC-26(T) to the genus Bacillus. However, low DNA-DNA relatedness values and distinguishing phenotypic characteristics allowed genotypic and phenotypic differentiation of strain ZLC-26(T) from recognized Bacillus species. On the basis of the evidence presented, strain ZLC-26(T) is considered to represent a novel species of the genus Bacillus, for which the name Bacillus korlensis sp. nov. is proposed. The type strain is ZLC-26(T) (=CCTCC AB 207172(T)=NRRL B-51302(T)).

Hymenobacter deserti sp. nov., isolated from the desert of Xinjiang, China

A Gram-negative, rod-shaped, non-motile and pink-pigmented bacterium, designated strain ZLB-3T, was isolated from a desert soil sample collected from Xinjiang Province, China, and characterized by using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the phylum Bacteroidetes and is related to the genus Hymenobacter. 16S rRNA gene sequence similarities between strain ZLB-3T and the type strains of Hymenobacter species with validly published names ranged from 90.0 to 94.6 %. No other taxa in the phylum Bacteroidetes showed more than 90 % sequence similarity to the isolate. The strain contained MK-7 as the predominant menaquinone. The major fatty acids were iso-C(15 : 0) (27.8 %), anteiso-C(17 : 1) B/iso-C(17 : 1) I (25.2 %), iso-C(17 : 0) 3-OH (9.6 %) and C(16 : 1)omega7c/iso-C(15 : 0) 2-OH (8.5 %). Phosphatidylethanolamine, two unknown aminophospholipids, an unknown aminolipid, an unknown glycolipid and six unknown polar lipids were detected in the polar lipid profile. The DNA G+C content was 58.6 mol%. These chemotaxonomic data supported the affiliation of strain ZLB-3T to the genus Hymenobacter. However, the results of physiological and biochemical tests allowed phenotypic differentiation of the isolate from recognized Hymenobacter species. On the basis of the evidence presented, it is proposed that strain ZLB-3T represents a novel species, Hymenobacter deserti sp. nov. The type strain is ZLB-3T (=CCTCC AB 207171T =NRRL B-51267T).

Mucilaginibacter soli sp. nov., isolated from Arctic tundra soil

A novel pale-pink-coloured strain, designated R9-65(T), was isolated from a tundra soil near Ny-Ålesund, Svalbard Archipelago, Norway (78° N). The cells were facultatively anaerobic, Gram-staining-negative, non-motile and rod-shaped. Growth occurred at 4-32 °C (optimum, 25-28 °C), at pH 5.0-9.0 (optimum, pH 6.0-7.0) and with 0-1.0% (w/v) NaCl (optimum, no NaCl). Flexirubin-type pigments were absent. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R9-65(T) belonged to the genus Mucilaginibacter in the family Sphingobacteriaceae. The 16S rRNA gene sequence similarity between strain R9-65(T) and type strains of related species ranged from 93.4 to 96.6%. Strain R9-65(T) contained summed feature 3 (C(16:1)ω7c and/or C(16:1)ω6c, 34.3%) and iso-C(15:0) (20.3%) as major cellular fatty acids, MK-7 as the major respiratory quinone, and phosphatidylethanolamine as the main polar lipid. The DNA G+C content of strain R9-65(T) was 47.2 mol%. On the basis of phylogenetic, physiological and chemotaxonomic data, strain R9-65(T) is considered to represent a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter soli sp. nov. is proposed. The type strain is R9-65(T) (=CCTCC AB 2010331(T)=NRRL B-59458(T)).

Spirosoma arcticum sp. nov., isolated from high Arctic glacial till.

A novel orange-pigmented strain, designated R2-35(T), was isolated from a glacier till near Ny-Alesund, Svalbard Archipelago, Norway. The cells were aerobic, Gram-negative, rod-shaped and sometimes filamentous. Growth occurred at 4-28 °C (optimum, 20 °C), at pH 7.0-9.0 (optimum, pH 8.0) and with 0-1% NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R2-35(T) belonged to the genus Spirosoma with sequence similarity to related species ranging from 91.65 to 95.19%. Strain R2-35(T) contained C16 : 0 (10.7%), C18 : 0 (9.2%), C16 : 1ω5c (16.5%) and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) (24.6%) as the major cellular fatty acids, MK-7 as the major respiratory quinone, and phosphatidylethanolamine as the main polar lipid. The DNA G+C content of strain R2-35(T) was 54.9 mol%. On the basis of phylogenetic, physiological and chemotaxonomic data, strain R2-35(T) is considered to represent a novel species of the genus Spirosoma, for which the name Spirosoma arcticum sp. nov., is proposed, The type strain is R2-35(T) ( = CCTCC AB 2012849(T) = LMG 28141(T)).