- Volume 59, Issue 6, 2009
Volume 59, Issue 6, 2009
- Notification List
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Notification that new names and new combinations have appeared in volume 59, part 3, of the IJSEM
This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles). Taxonomic opinions included in this List (i.e. the creation of synonyms or the emendation of circumscriptions) cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission.
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- New Taxa
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- Actinobacteria
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Haloglycomyces albus gen. nov., sp. nov., a halophilic, filamentous actinomycete of the family Glycomycetaceae
More LessA novel halophilic actinobacterium, designated YIM 92370T, was isolated from a hypersaline habitat in Xinjiang Province, north-west China. The strain was aerobic, Gram-positive-staining and halophilic, with an optimum NaCl concentration for growth of 8–12 % (w/v). The whole-cell sugar pattern consisted of ribose, xylose and glucose. The predominant menaquinone was MK-9(H4) and the major fatty acids were iso-C16 : 0, iso-C17 : 0 and anteiso-C17 : 0. The phospholipid pattern consisted of phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, two unknown phosphoglycolipids and one unknown phospholipid. The G+C content of the genomic DNA was 60.8 mol%. Phylogenetic analysis showed that strain YIM 92370T can be distinguished from representatives of Glycomyces and Stackebrandtia, the two existing genera in the family Glycomycetaceae, by low 16S rRNA gene sequence similarities (<93.7 %). Strain YIM 92370T therefore represents a novel genus and species of the family Glycomycetaceae, for which the name Haloglycomyces albus gen. nov., sp. nov. is proposed. The type strain of Haloglycomyces albus is YIM 92370T (=DSM 45210T =KCTC 19481T).
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Streptomyces polyantibioticus sp. nov., isolated from the banks of a river
More LessAs part of an antibiotic-screening programme, an actinomycete, designated strain SPRT, was isolated from soil collected from the banks of the Umgeni River, KwaZulu-Natal Province, South Africa. The isolate produced branching vegetative mycelia with sporangiophores bearing sporangia developing at a late stage of growth. The sporangia contained smooth, almond-shaped, non-motile spores. Strain SPRT exhibited antibiosis against various Gram-positive and Gram-negative bacteria, including Enterococcus faecium VanA (a vancomycin-resistant strain), Mycobacterium aurum A+ and Escherichia coli ATCC 25922. The chemotaxonomic characteristics of the strain, with the exception of the phospholipid pattern, corresponded with those of the members of the family Streptomycetaceae Waksman and Henrici 1943. Furthermore, phylogenetic analysis based on 16S rRNA genes showed that the strain was closely related to members of the genus Streptomyces, which supports its classification in the family Streptomycetaceae. Thus strain SPRT represents a novel species of the genus Streptomyces, for which the name Streptomyces polyantibioticus sp. nov. is proposed. The type strain is SPRT (=DSM 44925T=NRRL B-24448T).
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Kocuria halotolerans sp. nov., an actinobacterium isolated from a saline soil in China
A Gram-positive actinobacterium, designated strain YIM 90716T, was isolated from a saline soil sample collected from Ganjiahu Suosuo Forest National Nature Reserve in Xinjiang Province, north-west China. The new isolate contained lysine, glutamic acid and alanine with peptidoglycan type Lys–Ala3 (variation A3α). The major phospholipids were phosphatidylglycerol and diphosphatidylglycerol. The predominant menaqinone was MK-7(H2). The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The DNA G+C content of strain YIM 90716T was 68.0 mol%. Chemotaxonomic properties supported the affiliation of strain YIM 90716T to the genus Kocuria. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism was related most closely to Kocuria kristinae DSM 20032T (96.8 % similarity) and showed lower levels of 16S rRNA gene similarity (<96.5 %) with the type strains of other species of the genus Kocuria. The results of fatty acid analysis and physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain YIM 90716T from its closest relatives. On the basis of data from the present polyphasic study, strain YIM 90716T is considered to represent a novel species of the genus Kocuria, for which the name Kocuria halotolerans sp. nov. is proposed. The type strain is YIM 90716T (=DSM 18442T=KCTC 19172T=CCTCC AB 206069T).
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Streptomyces plumbiresistens sp. nov., a lead-resistant actinomycete isolated from lead-polluted soil in north-west China
More LessThe taxonomic position of an actinomycete isolated from a lead-polluted soil in Gansu province, north-west China, was determined by using a polyphasic approach. Chemical and morphological properties of the isolate, designated strain CCNWHX 13-160T, were similar to those of streptomycetes. Analysis of the almost complete 16S rRNA gene sequence placed strain CCNWHX 13-160T in the genus Streptomyces where it formed a distinct phyletic line with recognized Streptomyces species. The strain was most similar to Streptomyces pseudovenezuelae NBRC 12904T (98.9 %) and Streptomyces resistomycificus NBRC 12814T (98.8 %). Furthermore, DNA–DNA hybridization studies between the novel isolate and these two strains showed relatedness values of 49.7±0.8 and 43.2±1.1 %, respectively. It is proposed that strain CCNWHX 13-160T (=ACCC 41207T=HAMBI 2991T) be classified as the type strain of a novel species in the genus Streptomyces, Streptomyces plumbiresistens sp. nov. The MIC of Pb2+ for growth of strain CCNWHX 13-160T was 4.0 mM.
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Mycobacterium kyorinense sp. nov., a novel, slow-growing species, related to Mycobacterium celatum, isolated from human clinical specimens
Mitsuhiro Okazaki, Kiyofumi Ohkusu, Hiroyuki Hata, Hiroaki Ohnishi, Keiko Sugahara, Chizuko Kawamura, Nagatoshi Fujiwara, Sohkichi Matsumoto, Yukiko Nishiuchi, Kouichi Toyoda, Hajime Saito, Shota Yonetani, Yoko Fukugawa, Masayuki Yamamoto, Hiroo Wada, Akiko Sejimo, Akio Ebina, Hajime Goto, Takayuki Ezaki and Takashi WatanabeA novel, non-pigmented, slow-growing mycobacterium was identified on the basis of biochemical and nucleic acid analyses, as well as growth characteristics. Three isolates were cultured from clinical samples (two from sputum and one from pus in lymph nodes) obtained from three immunocompetent patients with infections. Bacterial growth occurred at 28–42 °C on Middlebrook 7H11-OADC agar. The isolates showed negative results for Tween hydrolysis, nitrate reductase, semiquantitative catalase, urease activity, 3 day arylsulfatase activity, pyrazinamidase, tellurite reduction and niacin accumulation tests, but positive results for 14 day arylsulfatase activity and heat-stable catalase tests. The isolates contained α-, keto-, and dicarboxymycolates in their cell walls. Sequence analysis revealed that all isolates had identical, unique 16S rRNA sequences. Phylogenetic analysis of the 16S rRNA, rpoB, hsp65 and sodA gene sequences confirmed that these isolates are unique but closely related to Mycobacterium celatum. DNA–DNA hybridization of the isolates demonstrated less than 50 % reassociation with M. celatum and Mycobacterium branderi. On the basis of these findings, a novel species designated Mycobacterium kyorinense sp. nov. is proposed. The type strain is KUM 060204T (=JCM 15038T=DSM 45166T).
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Description of Leifsonia kafniensis sp. nov. and Leifsonia antarctica sp. nov.
More LessStrains KFC-22T and SPC-20T are yellow-pigmented, Gram-positive, aerobic, non-motile, rod-shaped bacteria that were isolated from a soil sample near the Kafni glacier in the Himalayan mountain ranges in India, and from a spade core sediment sample from the Antarctic Ocean at Larsemann Hill, respectively. In both cases, the cell-wall peptidoglycan contained 2,4-diaminobutyric acid as the diamino acid, anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0 were the predominant fatty acids and MK-11 was the major isoprenoid quinone in the cell membrane. On the basis of the above-mentioned characteristics, both strains can be assigned to the genus Leifsonia. The strains share 16S rRNA gene sequence similarity of 97.7 % and DNA relatedness of only 10 %, indicating that they represent different species. A blast analysis indicated that Leifsonia pindariensis PON10T was the closest phylogenetic neighbour of strains SPC-20T and KFC-22T, showing 16S rRNA gene sequence similarities of 97.3 and 97.7 %, respectively. However, at the whole-genome level, strains KFC-22T and SPC-20T shared 42 and 11 % DNA–DNA relatedness, respectively, with L. pindariensis PON10T. In addition, both strains exhibited several phenotypic differences with respect to L. pindariensis PON10T. Thus, on the basis of the differences that the two strains exhibited with respect to L. pindariensis, both were identified as representing novel species of the genus Leifsonia, for which the names Leifsonia kafniensis sp. nov. (type strain KFC-22T =NCCB 100216T =LMG 24362T) and Leifsonia antarctica sp. nov. (type strain SPC-20T =NCCB 100227T =LMG 24541T) are proposed.
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Amycolatopsis ultiminotia sp. nov., isolated from rhizosphere soil, and emended description of the genus Amycolatopsis
More LessA novel actinomycete, designated strain RP-AC36T, was isolated from a cliff-associated plant (Peucedanum japonicum Thunb.) in the Republic of Korea and its taxonomic status was determined by using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequence analysis showed that the organism formed a distinct clade within the radiation of the genus Amycolatopsis. The chemotaxonomic properties supported the assignment of the isolate to the genus Amycolatopsis. High levels of 16S rRNA gene sequence similarity were found with Amycolatopsis sulphurea (98.2 %), Amycolatopsis halotolerans (97.5 %) and Amycolatopsis jejuensis (97.1 %). DNA–DNA relatedness data, together with phenotypic differences, clearly distinguished the isolate from its closest relative A. sulphurea. Based on the phenotypic and genotypic evidence, it is suggested that the organism be assigned as representing a novel species of the genus Amycolatopsis, for which the name Amycolatopsis ultiminotia sp. nov. is proposed. The type strain is RP-AC36T (=NRRL B-24662T=DSM 45180T).
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Gordonibacter pamelaeae gen. nov., sp. nov., a new member of the Coriobacteriaceae isolated from a patient with Crohn's disease, and reclassification of Eggerthella hongkongensis Lau et al. 2006 as Paraeggerthella hongkongensis gen. nov., comb. nov.
A strictly anaerobic, Gram-positive, short-rod/coccobacillus-shaped bacterial strain, designated 7-10-1-bT, was isolated from the colon of a patient suffering from acute Crohn's disease. The isolate formed small, pale-white, semi-translucent colonies on solid cultivation media. The strain was catalase-positive and metabolized only a small number of carbon sources. Whole-cell fatty acids consisted predominantly of saturated fatty acids (89 %), of which 15 : 0 anteiso was the major component. The polar lipids phosphatidylglycerol and diphosphatidylglycerol as well as four glycolipids were identified. 16S rRNA gene sequence analysis revealed that the isolate represents a distinct lineage within the family Coriobacteriaceae and has 94.6 % identity to the type strain of [Eggerthella] hongkongensis, the phylogenetically closest bacterial species. On the basis of the analyses performed, the new genus and species Gordonibacter pamelaeae gen. nov., sp. nov. is described, with strain 7-10-1-bT (=DSM 19378T =CCUG 55131T) as the type and only strain of Gordonibacter pamelaeae. Also, based on the chemotaxonomic data obtained for all type strains of the neighbouring genus Eggerthella, we propose that Eggerthella hongkongensis Lau et al. 2006 be transferred to a new genus as Paraeggerthella hongkongensis gen. nov., comb. nov.; the type strain of Paraeggerthella hongkongensis is HKU10T (=DSM 16106T =CCUG 49250T).
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Streptomyces axinellae sp. nov., isolated from the Mediterranean sponge Axinella polypoides (Porifera)
More LessAn actinomycete strain, isolated from the marine sponge Axinella polypoides collected from Banyuls-sur-Mer, France, was characterized using a polyphasic approach. Based on its chemotaxonomic and morphological characteristics, strain Pol001T belongs to the genus Streptomyces. The strain is characterized by ll-diaminopimelic acid in the cell wall, menaquinones MK-9(H4, H6, H8) and a DNA G+C content of 71.0 mol%. It forms a separate phyletic line based on phylogenetic analyses of the nearly complete 16S rRNA gene sequence. Strain Pol001T could be differentiated from other closely related Streptomyces species with validly published names by phenotypic and genotypic analysis. DNA–DNA hybridization between strain Pol001T and closely related reference strains further confirmed that strain Pol001T represents a novel taxon of the genus Streptomyces. Therefore, it is proposed that strain Pol001T represents a novel species in the genus Streptomyces, Streptomyces axinellae sp. nov.; the type strain is Pol001T (=DSM 41948T =CIP 109838T).
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Arcanobacterium abortisuis sp. nov., isolated from a placenta of a sow following an abortion
More LessA Gram-positive, short diphtheroid-shaped organism was isolated from a sow's placenta of an abortion. This novel isolate, strain MurakamiT, was examined physiologically, chemotaxonomically and phylogenetically. Cells had an irregular V-shaped or palisade arrangement. Colonies appeared translucent on TMVL agar. Cells were strictly anaerobic, negative for catalase and gelatin decomposition and positive for nitrate reduction and soluble starch hydrolysis. Fourteen sugars including glucose were utilized as carbon sources for growth, but 15 sugars including arabinose were not. α-Galactosidase, β-galactosidase, α-glucosidase and leucine arylamidase were produced, but β-glucosidase was not. Fermentation products were lactic, succinic and acetic acids. Sugars of whole cells consisted of rhamnose and ribose. The amino-acid composition of the peptidoglycan was glutamic acid, alanine and lysine in the molar ratio of 1 : 2 : 1. The main fatty acid components of whole cells were C14 : 0, C16 : 0, C16 : 1 ω7 and C18 : 1 ω9. The bacterial menaquinone was MK-10(H4). The polar lipids were phosphatidylethanolamine and two unknown phosphatidylinositol mannosides. The G+C content of the genomic DNA of strain MurakamiT was 63.8 mol%. Phylogenetic analysis of 16S rRNA gene sequences from strain MurakamiT and other members of the genus Arcanobacterium supported the phenotypic findings that strain MurakamiT represents a novel species, for which the name Arcanobacterium abortisuis sp. nov. is proposed. The type strain is MurakamiT (=ATCC BAA-1522T =DSM 19515T =JCM 14813T).
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Pseudonocardia acaciae sp. nov., isolated from roots of Acacia auriculiformis A. Cunn. ex Benth.
More LessA novel Gram-positive-staining actinomycete designated strain GMKU095T was isolated from surface-sterilized roots of Acacia auriculiformis A. Cunn. ex Benth. (earpod wattle). The organism produced branching mycelium. The spores were non-motile and had a spiny surface. Growth of strain GMKU095T occurred at 18–42 °C, pH 5.0–8.0 and at NaCl concentrations up to 5 %. Whole-cell hydrolysates contained arabinose and galactose as major characteristic sugars. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The glycan moiety of the murein contained acetyl residues. The menaquinone was MK-8(H4); mycolic acids were not detected. The G+C content of the DNA was 71.6 mol%. iso-C16 : 0 was detected as the major cellular fatty acid. Comparative studies of 16S rRNA gene sequences indicated that the strain was phylogenetically related to members of the genus Pseudonocardia. The most closely related type strain is Pseudonocardia spinosispora IMSNU 50581T, which is 96.2 % similar in 16S rRNA gene sequence. On the basis of the genotypic and phenotypic properties presented, a novel species of the genus Pseudonocardia is proposed, Pseudonocardia acaciae sp. nov. The type strain is strain GMKU095T (=NRRL B-24609T =BCC 28481T =TISTR 1862T =NBRC 104274T).
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Streptomyces sedi sp. nov., isolated from surface-sterilized roots of Sedum sp.
More LessAn endophytic actinomycete, strain YIM 65188T, was isolated from surface-sterilized tissue of Sedum sp. collected from Yunnan province, south-west China, and characterized by using a polyphasic approach. Analysis of the 16S rRNA gene sequence showed that strain YIM 65188T is a member of the genus Streptomyces and exhibited 97.5 and 96.3 % gene sequence similarities to Streptomyces specialis GW41-1564T and Streptomyces hainanensis YIM 47672T, respectively, whereas low sequence similarity values (<95.2 %) distinguished strain YIM 65188T from all other Streptomyces species with validly published names. Strain YIM 65188T had a unique menaquinone composition, with the predominant quinones being MK-11(H6) and MK-10(H6), with moderate amounts of MK-10(H8), MK-11(H8), MK-9(H8), MK-11(H4), MK-9(H6) and MK-10(H4). Similarly, the closest phylogenetic relative, S. specialis GW41-1564T, also had an unusual quinone composition, with the predominant menaquinones MK-10(H4) and MK-10(H6) and minor amounts of MK-9(H4) and MK-9(H6). The DNA–DNA hybridization value between strain YIM 65188T and S. specialis GW41-1564T was 42.7 %. On the basis of phenotypic and phylogenetic characteristics, strain YIM 65188T was identified as a novel species of the genus Streptomyces for which the name Streptomyces sedi sp. nov. is proposed, with YIM 65188T (=CCTCC AA 208020T =DSM 41942T) as the type strain.
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Saccharothrix violaceirubra sp. nov., isolated from soil and plant litter
More LessTwo strains of nocardioform actinomycetes, isolated from soil and plant litter in Yamanashi prefecture, Japan, showed substrate mycelium with purple to dark-red colours. 16S rRNA gene sequence analysis indicated that the organisms belonged to the family Actinosynnemataceae and were related closely to Saccharothrix strains (96.7–98.0 % sequence similarity). The isolates contained MK-9(H4) as the predominant menaquinone, meso-diaminopimelic acid, galactose as the diagnostic whole-cell sugar and phosphatidylethanolamine as the predominant polar lipid. Based on a combination of cultural, physiological and chemotaxonomic properties, in addition to the phylogenetic analysis and DNA–DNA hybridization data, we propose a novel species, Saccharothrix violaceirubra sp. nov., for these strains, with the type strain YU 692-1T (=NBRC 102064T =KCTC 19326T).
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Mycobacterium insubricum sp. nov.
Five independent strains, isolated from clinical samples but probably not responsible for disease, revealed phenotypic and genotypic features that appeared to exclude their belonging to any of the recognized Mycobacterium species. The strains, which are non-pigmented rapid growers, presented a cell-wall lipid pattern resembling those of Mycobacterium brumae and Mycobacterium fallax. Sequencing of the 16S rRNA, hsp65 and rpoB genes and the 16S–23S rRNA gene internal transcribed spacer (ITS) revealed that the strains are clearly distinct from every other Mycobacterium species. While the 16S rRNA and rpoB genes were characterized by a single sequevar, two sequevars were detected in hsp65 and three in the ITS. The divergence shown in the latter region was striking, in which only two short regions (less than 150 bp in all) were comparable with other mycobacteria, apart from Mycobacterium monacense and Mycobacterium gilvum. The PCR restriction analysis pattern of the novel strains also differs from any reported to date. The name Mycobacterium insubricum sp. nov. is proposed for the novel species; the type strain is FI-06250T (=DSM 45132T =CIP 109609T).
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Bifidobacterium mongoliense sp. nov., from airag, a traditional fermented mare's milk product from Mongolia
More LessTwo novel micro-organisms, designated strains YIT 10443T and YIT 10738, were isolated from airag, a traditional fermented mare's milk from Mongolia. The two strains were Gram-positive-staining, non-motile, asporogenous, catalase-negative, facultatively anaerobic rods of various shapes. Comparative analyses of 16S rRNA and ClpC ATPase (clpC) gene sequences and the presence of fructose-6-phosphate phosphoketolase (F6PPK) demonstrated that the novel strains were members of the genus Bifidobacterium. On the basis of 16S rRNA gene sequence similarity, the type strains of Bifidobacterium minimum (96.6 %) and Bifidobacterium psychraerophilum (95.7 %) were the closest neighbours of the novel strains, and DNA–DNA reassociation values with these strains were found to be lower than 15 %. The phenotypic and genotypic features demonstrated that the two strains represent a single, novel Bifidobacterium species, for which the name Bifidobacterium mongoliense sp. nov. is proposed. The type strain is YIT 10443T (=JCM 15461T =DSM 21395T).
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Tsukamurella carboxydivorans sp. nov., a carbon monoxide-oxidizing actinomycete
More LessA Gram-positive, slightly acid–alcohol-fast, carbon monoxide-oxidizing bacterium, strain Y2T, was isolated from a soil sample collected from a roadside in Seoul, Korea. On the basis of 16S rRNA gene sequence comparative analyses, strain Y2T was shown to belong to the genus Tsukamurella and was most closely related to Tsukamurella tyrosinosolvens DSM 44234T (GenBank accession no. AY238514; 99.8 %). The predominant fatty acids were C18 : 1 ω9c and C16 : 0. The cell-wall peptidoglycan of strain Y2T contained meso-diaminopimelic acid as the diagnostic diamino acid. Strain Y2T contained galactose and arabinose as the whole cell sugars. The DNA G+C content was 77 mol%. The DNA–DNA relatedness value between strain Y2T and T. tyrosinosolvens DSM 44234T was 62.7 %. Based on the combination of the carbon source utilization pattern, fatty acid profile, cell-wall chemotype, DNA G+C content and DNA–DNA hybridization experiments, it is proposed that strain Y2T (=KCCM 42885T=JCM 15482T) represents the type strain of a novel species, Tsukamurella carboxydivorans sp. nov.
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Tessaracoccus lubricantis sp. nov., isolated from a metalworking fluid
More LessA Gram-positive-staining, coccoid-shaped, oxidase-negative, non-spore-forming, non-motile bacterium, strain KSS-17SeT, was isolated from a metalworking fluid. On the basis of its major fatty acid (ai-C15 : 0) and 16S rRNA gene sequence similarity, the strain grouped with Tessaracoccus bendigoensis and Tessaracoccus flavescens, sharing 95.3 and 97.4 % 16S rRNA gene sequence similarity with the respective type strains. Similarities with other established species of the genera Luteococcus, Propioniferax and Granulicoccus were lower than 95.5 %. The quinone system was characterized by the major menaquinone MK-9(H4). In the polar lipid profile, diphosphatidylglycerol, phosphatidylglycerol, an unknown glycolipid and an unknown polar lipid were detected as major compounds. Additionally, three unknown glycolipids and minor amounts of phosphatidylethanolamine, two unknown aminolipids and two unknown polar lipids were detected. Phosphatidylinositol was present only in trace amounts. Predominant polyamines were spermine and spermidine. ll-Diaminopimelic acid was identified as the diagnostic diamino acid in the cell wall. The strain showed clear differences in phenotype (including chemotaxonomic features) from both Tessaracoccus species and members of the other above-mentioned genera. DNA–DNA hybridization between KSS-17SeT and T. bendigoensis Ben-106T and T. flavescens SST-39T yielded similarities of 15.1 and 21.0 %, respectively. It is evident that the organism represents a novel species, for which the name Tessaracoccus lubricantis sp. nov. is proposed. The type strain is KSS-17SeT (=DSM 19926T =CCUG 55516T).
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- Bacteroidetes
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Chitinophaga niabensis sp. nov. and Chitinophaga niastensis sp. nov., isolated from soil
Two yellow-coloured bacterial strains, designated JS13-10T and JS16-4T, were isolated from soil from Jeju Island, Republic of Korea. On the basis of 16S rRNA gene sequence analysis, the strains were found to be affiliated with members of the genus Chitinophaga. Phenotypically, the novel strains were identified as being different from each other and from recognized species of the genus Chitinophaga. DNA–DNA hybridization tests between the two novel strains and closely related Chitinophaga reference strains produced DNA relatedness values that were significantly lower (<36 %) than those generally accepted as the highest threshold for the phylogenetic definition of a species. On the basis of their distinct taxonomic characteristics, these strains represent two novel species of the genus Chitinophaga, for which the names Chitinophaga niabensis sp. nov. (type strain JS13-10T=KACC 12952T=JCM 15440T) and Chitinophaga niastensis sp. nov. (type strain JS16-4T=KACC 12954T=JCM 15441T) are proposed.
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Niabella ginsengisoli sp. nov., isolated from soil cultivated with Korean ginseng
More LessThe taxonomic status of a yellow- to light orange-coloured strain isolated from soil of a Korean ginseng field was established based on a polyphasic investigation. The novel isolate, strain GR10-1T, was an obligately aerobic, Gram-staining-negative, non-motile, flexirubin-pigment-producing, short rod-shaped bacterium. The strain grew optimally at 28–30 °C, at pH 7.0 and in the presence of 0–1 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences demonstrated that the new isolate showed the highest sequence similarities with Niabella aurantiaca R2A15-11T (95.1 %) and Niabella soli JS13-8T (94.6 %). The DNA G+C content of strain GR10-1T was 43 mol%. It contained iso-C15 : 1 G (36.4 %) and iso-C15 : 0 (32.8 %) as the major fatty acids (>10 %) and MK-7 as the major isoprenoid quinone. On the basis of evidence from our polyphasic taxonomic study, it was concluded that strain GR10-1T should be classified within a novel species of the genus Niabella, for which the name Niabella ginsengisoli sp. nov. is proposed. The type strain is GR10-1T (=KACC 13021T =JCM 15444T).
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Winogradskyella arenosi sp. nov., a member of the family Flavobacteriaceae isolated from marine sediments from the Sea of Japan
More LessAn aerobic, Gram-negative, yellow-pigmented, gliding bacterial strain, designated R60T, was isolated from a marine sediment sample obtained from the Sea of Japan and was characterized by using a polyphasic approach. 16S rRNA gene sequence analysis showed that strain R60T belonged to the genus Winogradskyella, sharing <97 % sequence similarity with the type strains of recognized Winogradskyella species. The main fatty acids of strain R60T were iso-C15 : 0 3-OH, iso-C16 : 0 3-OH, iso-C17 : 0 3-OH, anteiso-C17 : 0 3-OH and iso-C15 : 0, consistent with its assignment to the genus Winogradskyella. On the basis of phenotypic distinctiveness and phylogenetic divergence, strain R60T is considered to represent a novel species of the genus Winogradskyella, for which the name Winogradskyella arenosi sp. nov. is proposed. The type strain is R60T (=KMM 3968T =NRIC 0748T= JCM 15527T).
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Mucilaginibacter ximonensis sp. nov., isolated from Tibetan soil
More LessStrain XM-003T was isolated from a soil sample that originated from the Ximo region in Tibet. Cells of strain XM-003T were Gram-negative-staining, non-motile, irregular-shaped rods and the strain grew optimally at 28 °C and grew at pH 5–8. It contained MK-7 as the major isoprenoid quinone and iso-C15 : 0 and C16 : 1 ω7c and/or iso-C15 : 0 2-OH as the major fatty acids. Flexirubin-type pigments were absent. The DNA G+C content was 43.4 mol%. The 16S rRNA gene sequence of this strain showed the highest sequence similarity of 96.0 % to Mucilaginibacter kameinonensis SCKT. A number of physiological biochemical tests and chemotaxonomic markers indicate that strain XM-003T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter ximonensis sp. nov. is proposed. The type strain is XM-003T (=CCTCC AB 207094T =KCTC 22437T).
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Mucilaginibacter oryzae sp. nov., isolated from soil of a rice paddy
A Gram-negative-staining, non-spore-forming bacterium devoid of flagella, designated strain B9T, was isolated from rice paddy soil associated with the roots of Oryza sativa collected from Jinju, South Korea. Cells were straight rods, were catalase- and oxidase-positive and were able to hydrolyse pectin, xylan and laminarin. Growth of strain B9T was observed between 15 and 35 °C (optimum 25–30 °C) and between pH 5.0 and 8.0 (optimum pH 6.5–7.5). Strain B9T contained menaquinone-7 (MK-7) as a major isoprenoid quinone and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0 and C16 : 0 as major fatty acids. The G+C content of the genomic DNA was 44.4 mol%. Comparative 16S rRNA gene sequence analysis showed that strain B9T belonged to the genus Mucilaginibacter, a member of the family Sphingobacteriaceae, and was most closely related to Mucilaginibacter kameinonensis SCKT (95.9 % sequence similarity). On the basis of chemotaxonomic data and molecular properties, strain B9T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter oryzae sp. nov. is proposed. The type strain is B9T (=KACC 12816T =DSM 19975T).
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Maribacter antarcticus sp. nov., a psychrophilic bacterium isolated from a culture of the Antarctic green alga Pyramimonas gelidicola
More LessA psychrophilic, Gram-negative, dark orange-pigmented bacterium, designated CL-AP4T, was isolated from a culture of the green alga Pyramimonas gelidicola obtained from the Southern Ocean. Strain CL-AP4T grew optimally at 10 °C, in the presence of 3–4 % sea salts and at pH 8. 16S rRNA gene sequence analysis revealed that strain CL-AP4T belonged to the family Flavobacteriaceae, with Maribacter arcticus KOPRI 20941T as its closest relative (97.2 % similarity). A number of chemotaxonomic characteristics supported affiliation of strain CL-AP4T with the genus Maribacter, i.e. iso-C15 : 0 (17.2 %), iso-C15 : 1 (16.8 %) and iso-C17 : 0 3-OH (14.9 %) were the dominant fatty acids, MK-6 was the major menaquinone and the DNA G+C content was 37.1 mol%. DNA–DNA relatedness between CL-AP4T and M. arcticus KOPRI 20941T was only 10 %, suggesting that they are genomically distinct species. In addition, strain CL-AP4T differed phenotypically from M. arcticus in its optimum growth temperature, its ability to hydrolyse starch, Tween 40 and Tween 80, and production of certain enzymes. On the basis of the results of the polyphasic analysis, strain CL-AP4T was classified in the genus Maribacter as belonging to a novel species, for which the name Maribacter antarcticus sp. nov. is proposed; the type strain is CL-AP4T (=KCCM 90069T=JCM 15445T).
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Winogradskyella echinorum sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from the sea urchin Strongylocentrotus intermedius
More LessThe taxonomic position of a novel marine, yellow-pigmented bacterium, designated strain KMM 6211T, was examined by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain KMM 6211T is a member of the family Flavobacteriaceae, phylum Bacteroidetes. The closest relative of strain KMM 6211T was Winogradskyella eximia KMM 3944T, the sequence similarity being 97.1 %. The DNA G+C content of KMM 6211T was 33.6 mol%. The strain was motile by gliding and grew with 1–6 % NaCl and at 4–37 °C. Aesculin, casein and gelatin were hydrolysed, but agar, starch, DNA and chitin were not degraded. On the basis of phylogenetic data and phenotypic differences between the isolate and recognized Winogradskyella species, strain KMM 6211T represents a novel species of the genus Winogradskyella, for which the name Winogradskyella echinorum sp. nov. is proposed. The type strain is KMM 6211T (=KCTC 22026T=LMG 24757T).
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- Firmicutes And Related Organisms
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Paenibacillus pectinilyticus sp. nov., isolated from the gut of Diestrammena apicalis
During a search for exo-enzyme-producing bacteria in the gut of an insect, Diestrammena apicalis, a novel bacterium capable of degrading pectin was isolated. The isolate, designated strain RCB-08T, comprised Gram-positive, endospore-forming, motile rods capable of growth at 15–30 °C and pH 6.0–8.7. The DNA G+C content of the isolate was 51.5 mol% and the predominant cellular fatty acid was anteiso-C15 : 0 (74.1 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RCB-08T was affiliated with a cluster within the Paenibacillaceae, and was related most closely to Paenibacillus chondroitinus NBRC 15376T, with a sequence similarity of 96.7 %. The DNA–DNA relatedness value for strain RCB-08T with P. chondroitinus NBRC 15376T was 15.0 %. Strain RCB-08T hydrolysed pectin, but not cellulose, casein, starch or xylan. Strain RCB-08T could be clearly distinguished from other Paenibacillus species on the basis of characteristics observed using a polyphasic approach. Therefore strain RCB-08T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus pectinilyticus sp. nov. is proposed. The type strain is RCB-08T (=KCTC 13222T=CECT 7358T).
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Mycoplasma leachii sp. nov. as a new species designation for Mycoplasma sp. bovine group 7 of Leach, and reclassification of Mycoplasma mycoides subsp. mycoides LC as a serovar of Mycoplasma mycoides subsp. capri
More LessThe Mycoplasma mycoides cluster consists of six pathogenic mycoplasmas causing disease in ruminants, which share many genotypic and phenotypic traits. The M. mycoides cluster comprises five recognized taxa: Mycoplasma mycoides subsp. mycoides Small Colony (MmmSC), M. mycoides subsp. mycoides Large Colony (MmmLC), M. mycoides subsp. capri (Mmc), Mycoplasma capricolum subsp. capricolum (Mcc) and M. capricolum subsp. capripneumoniae (Mccp). The group of strains known as Mycoplasma sp. bovine group 7 of Leach (MBG7) has remained unassigned, due to conflicting data obtained by different classification methods. In the present paper, all available data, including recent phylogenetic analyses, have been reviewed, resulting in a proposal for an emended taxonomy of this cluster: (i) the MBG7 strains, although related phylogenetically to M. capricolum, hold sufficient characteristic traits to be assigned as a separate species, i.e. Mycoplasma leachii sp. nov. (type strain, PG50T = N29T = NCTC 10133T = DSM 21131T); (ii) MmmLC and Mmc, which can only be distinguished by serological methods and are related more distantly to MmmSC, should be combined into a single subspecies, i.e. Mycoplasma mycoides subsp. capri, leaving M. mycoides subsp. mycoides (MmmSC) as the exclusive designation for the agent of contagious bovine pleuropneumonia. A taxonomic description of M. leachii sp. nov. and emended descriptions of M. mycoides subsp. mycoides and M. mycoides subsp. capri are presented. As a result of these emendments, the M. mycoides cluster will hereafter be composed of five taxa comprising three subclusters, which correspond to the M. mycoides subspecies, the M. capricolum subspecies and the novel species M. leachii.
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Description of Paenisporosarcina quisquiliarum gen. nov., sp. nov., and reclassification of Sporosarcina macmurdoensis Reddy et al. 2003 as Paenisporosarcina macmurdoensis comb. nov.
More LessIn the course of a study of the prokaryotic diversity of a landfill site in Chandigarh, India, a strain designated SK 55T was isolated and characterized using a polyphasic approach. Its 16S rRNA gene sequence showed closest similarity (98.3 %) to that of Sporosarcina macmurdoensis CMS 21wT. The sequence similarity to strains of other hitherto described species of Sporosarcina was less than 95.5 %. Strain SK 55T contains peptidoglycan of the A4α type (l-Lys–d-Asp), MK-8 and MK-7 as the major menaquinones and iso-C15 : 0 as the major fatty acid. Strain SK 55T, Sporosarcina macmurdoensis and Sporosarcina ureae, the type species of the genus, had some polar lipids in common (diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a phospholipid and an unknown lipid). However, an aminolipid, an aminophospholipid and an unknown lipid found in the former two organisms are similar, though not identical, but quite different from the profile of S. ureae. The genomic DNA G+C contents of strain SK 55T (46.0 mol%) and S. macmurdoensis CMS 21wT (44.0 mol%) are higher than those reported for the majority of species of Sporosarcina (36–42 mol%). As revealed by 16S rRNA gene sequence analysis, strain SK 55T and S. macmurdoensis CMS 21wT form a clade which is distinct from the clade occupied by other species of Sporosarcina. On the basis of phenotypic characteristics including chemotaxonomic data and analysis of the 16S rRNA gene sequence, we conclude that strain SK 55T should be considered as a member of a novel genus and species, for which the name Paenisporosarcina quisquiliarum gen. nov., sp. nov. is proposed. The type strain of Paenisporosarcina quisquiliarum is SK 55T (=MTCC7604T =JCM 14041T). S. macmurdoensis CMS 21wT shows more similarity in its 16S rRNA gene sequence (98.3 %), DNA G+C content and polar lipid profile to strain SK 55T than to S. ureae DSM 2281T. Phylogenetically, it forms a coherent cluster with strain SK 55T which is separate from the Sporosarcina cluster. Moreover, iso-C15 : 0, anteiso-C15 : 0 and C16 : 1 ω7c alcohol are the three major fatty acids in both S. macmurdoensis CMS 21wT and SK 55T. All these data suggest that S. macmurdoensis should be a member of the genus Paenisporosarcina. However, S. macmurdoensis can be differentiated from SK 55T in several physiological and biochemical characteristics, especially in the patterns of oxidation and acid production from carbohydrates. The genomic relatedness of S. macmurdoensis CMS 21wT and strain SK 55T was also very low (18.0 %). It is therefore logical to transfer Sporosarcina macmurdoensis to the newly created genus as Paenisporosarcina macmurdoensis comb. nov. The type strain is CMS 21wT (=MTCC4670T =DSM 15428T).
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Planomicrobium glaciei sp. nov., a psychrotolerant bacterium isolated from a glacier
More LessA novel aerobic, psychrotolerant, yellow-to-orange bacterium (strain 0423T) was isolated from the China No. 1 glacier. Strain 0423T displayed phenotypic and chemotaxonomic features of the genus Planomicrobium, containing anteiso-C15 : 0 and iso-C14 : 0 as the major fatty acids. The temperature range for growth was 4–28 °C, with optimum growth at 20–21 °C. The genomic DNA G+C content was 49 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain 0423T was related to members of the genus Planomicrobium, sharing the highest sequence similarities with the type strains of Planomicrobium chinense, P. mcmeekinii, P. okeanokoites and P. koreense. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, a novel species, Planomicrobium glaciei sp. nov., is proposed. The type strain is 0423T (=CGMCC 1.6846T =JCM 15088T).
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Clostridium tagluense sp. nov., a psychrotolerant, anaerobic, spore-forming bacterium from permafrost
A strictly anaerobic, Gram-positive, psychrotolerant, endospore-forming bacterium (strain A121T) was isolated from a permafrost sample collected in the Canadian High Arctic. Phylogenetic analysis of the 16S rRNA gene sequence of strain A121T showed its affiliation with the group of psychrophilic and psychrotolerant members of cluster I of the genus Clostridium, Clostridium bowmanii DSM 14206T being the closest relative (sequence similarity 98.5 %). Levels of DNA–DNA relatedness between strain A121T and the type strains of phylogenetically related species ranged from 33 to 52 %. Strain A121T grew in PY broth at temperatures between 4 and 28 °C (optimum 15–20 °C), at pH 6.0–8.0 (optimum pH 6.5–7.2) and in NaCl concentrations of 0–10.0 % (optimum 0–2.0 %). The strain utilized a narrow range of carbohydrates as sources of carbon and energy, including glucose, fructose, trehalose, maltose and starch; it also hydrolysed gelatin. Predominant fatty acids were C16 : 1 cis9, C16 : 1 cis9 DMA, C16 : 0 and C14 : 0. The DNA G+C content was 31.5 mol%. On the basis of its overall genotypic and phenotypic characteristics, strain A121T is classified within a novel species of the genus Clostridium, Clostridium tagluense sp. nov. The type strain is A121T (=VKM B-2369T =DSM 17763T).
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Lysinibacillus parviboronicapiens sp. nov., a low-boron-containing bacterium isolated from soil
More LessA spore-forming, Gram-positive-staining, motile, rod-shaped and low-boron-containing bacterium was isolated from soil. The strain, designated BAM-582T, can tolerate 6 % (w/v) NaCl and 50 mM boron, but optimal growth was observed without addition of boron or NaCl. The optimum temperature and pH for growth were 30 °C (range 10–37 °C) and pH 7 (range pH 6–8). A comparative analysis of the 16S rRNA gene sequence demonstrated that the isolated strain was closely related to Lysinibacillus fusiformis DSM 2898T (97.7 % similarity) and Lysinibacillus sphaericus IAM 13420T (98.2 %). Levels of DNA–DNA relatedness were 33.9 % with L. fusiformis DSM 2898T and 29.5 % with L. sphaericus DSM 28T. The genomic DNA G+C content of the novel strain was 38.7 mol%. The major respiratory quinone was MK-7 and the major fatty acids were iso-C15 : 0 (37.4 %) and anteiso-C15 : 0 (19.0 %). Analysis of cell-wall amino acids revealed that the strain contained peptidoglycan with lysine, aspartic acid, alanine and glutamic acid, as is the case with other species of the genus Lysinibacillus. Based upon its distinctive peptidoglycan composition, phylogenetic and genotypic analyses and physiological characteristics, the strain BAM-582T is concluded to represent a novel species in the genus Lysinibacillus, for which the name Lysinibacillus parviboronicapiens sp. nov. is proposed (type strain BAM-582T =NBRC 103144T =KCTC 13154T).
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Bacillus solisalsi sp. nov., a halotolerant, alkaliphilic bacterium isolated from soil around a salt lake
Huan Liu, Yu Zhou, Rui Liu, Ke-Yun Zhang and Ren LaiA novel Gram-positive, motile, rod-shaped bacterium isolated from a saline soil in China was characterized by a polyphasic taxonomic approach. The strain, designated YC1T, was halotolerant [tolerating up to 15 % (w/v) NaCl] and alkaliphilic (growing at a broad pH range of 5–13). 16S rRNA gene sequence analysis revealed that the isolate belonged to the genus Bacillus, showing highest similarity to Bacillus macauensis JCM 13285T (98.0 %). However, DNA–DNA hybridization indicated low levels of genomic relatedness with B. macauensis JCM 13285T (8.5 %). The major isoprenoid quinone was MK-7 and the cellular fatty acid profile consisted of significant amounts of iso-C15 : 0 (38.6 %) and anteiso-C15 : 0 (35.9 %). The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genomic DNA was 41.8 mol%. On the basis of the polyphasic evidence from this study, strain YC1T (=KCTC 13181T=CGMCC 1.6854T) should be classified as the type strain of a novel species of the genus Bacillus, for which the name Bacillus solisalsi sp. nov. is proposed.
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- Other Bacteria
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Deferribacter autotrophicus sp. nov., an iron(III)-reducing bacterium from a deep-sea hydrothermal vent
A thermophilic, anaerobic, chemolithoautotrophic bacterium (designated strain SL50T) was isolated from a hydrothermal sample collected at the Mid-Atlantic Ridge from the deepest of the known World ocean hydrothermal fields, Ashadze field (1 ° 58′ 21″ N 4 ° 51′ 47″ W) at a depth of 4100 m. Cells of strain SL50T were motile, straight to bent rods with one polar flagellum, 0.5–0.6 μm in width and 3.0–3.5 μm in length. The temperature range for growth was 25–75 °C, with an optimum at 60 °C. The pH range for growth was 5.0–7.5, with an optimum at pH 6.5. Growth of strain SL50T was observed at NaCl concentrations ranging from 1.0 to 6.0 % (w/v) with an optimum at 2.5 % (w/v). The generation time under optimal growth conditions for strain SL50T was 60 min. Strain SL50T used molecular hydrogen, acetate, lactate, succinate, pyruvate and complex proteinaceous compounds as electron donors, and Fe(III), Mn(IV), nitrate or elemental sulfur as electron acceptors. The G+C content of the DNA of strain SL50T was 28.7 mol%. 16S rRNA gene sequence analysis revealed that the closest relative of strain SL50T was Deferribacter abyssi JRT (95.5 % similarity). On the basis of its physiological properties and phylogenetic analyses, the isolate is considered to represent a novel species, for which the name Deferribacter autotrophicus sp. nov. is proposed. The type strain is SL50T (=DSM 21529T=VKPM B-10097T). Deferribacter autotrophicus sp. nov. is the first described deep-sea bacterium capable of chemolithoautotrophic growth using molecular hydrogen as an electron donor and ferric iron as electron acceptor and CO2 as the carbon source.
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Deinococcus gobiensis sp. nov., an extremely radiation-resistant bacterium
More LessA Gram-positive, non-motile, spherical, red-pigmented and facultatively anaerobic bacterium, designated strain I-0T, was isolated from a sand sample of the Gobi desert in Xinjiang Autonomous Region, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this isolate represents a novel member of the genus Deinococcus, with low sequence similarities (<94 %) to recognized Deinococcus species. The major cellular fatty acids were C16 : 1 ω7c and C16 : 0. Its polar lipid profile contained several unidentified glycolipids, phosphoglycolipids, phospholipids, pigments and an aminophospholipid. The peptidoglycan type was Orn–Gly2 (A3β) and the predominant respiratory quinone was MK-8. The DNA G+C content was 65.4 mol%. DNA–DNA relatedness between strain I-0T and Deinococcus radiodurans ACCC 10492T was 37 %. The strain was shown to be extremely resistant to gamma radiation (>15 kGy) and UV light (>600 J m−2). On the basis of the phylogenetic, chemotaxonomic and phenotypic data presented, strain I-0T represents a novel species of the genus Deinococcus, for which the name Deinococcus gobiensis sp. nov. is proposed. The type strain is I-0T (=DSM 21396T =CGMCC 1.7299T).
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- Proteobacteria
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Psychromonas agarivorans sp. nov., a novel agarolytic bacterium
More LessTwo heterotrophic, agarolytic bacteria were isolated from marine environments. A 16S rRNA gene sequence analysis showed the isolates (designated strains J42-3AT and 04OZ-AS15-7A) to be positioned in a separate lineage within the genus Psychromonas. Members of the genus Psychromonas are recognized as being psychrophilic or psychrotolerant, whereas none of the currently established Psychromonas species is known to be agarolytic. The DNA G+C contents of the isolates were about 42 mol% and the predominant cellular fatty acids were 16 : 1ω7c and 16 : 0. Based on the results of the phylogenetic and phenotypic analyses and DNA–DNA hybridization data, the isolates represent a novel species, for which the name Psychromonas agarivorans sp. nov. is proposed. The type strain is J42-3AT (=NBRC 104585T=KCTC 22285T).
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Herminiimonas glaciei sp. nov., a novel ultramicrobacterium from 3042 m deep Greenland glacial ice
More LessA Gram-negative ultramicrobacterium (designated strain UMB49T) was isolated from a 120 000-year-old, 3042 m deep Greenland glacier ice core using a 0.2 μm filtration enrichment procedure. Phylogenetic analysis of the 16S rRNA gene sequence indicated that this strain belonged to the genus Herminiimonas of the family Oxalobacteraceae of the class Betaproteobacteria. Strain UMB49T was most closely related to Herminiimonas saxobsidens (99.6 % sequence similarity), Herminiimonas arsenicoxydans (98.4 %), Herminiimonas aquatilis (97.6 %) and Herminiimonas fonticola (97.9 %). Genomic DNA–DNA hybridization showed low levels of relatedness (below 57 %) to H. saxobsidens and H. arsenicoxydans. Cells of strain UMB49T were small thin rods with a mean volume of 0.043 μm3 and possessed 1 or 2 polar and/or 1–3 lateral very long flagella. The original colony pigmentation was brown-purple but after recultivation the colonies were translucent white to tan coloured. Strain UMB49T grew aerobically and under microaerophilic conditions. The strain produced catalase and oxidase, but did not reduce nitrate. Sole carbon sources included citrate, succinate, malate, lactate and alanine. The strain produced acid from l-arabinose, d-arabinose, l-xylose, d-xylose and d-ribose. The DNA G+C content was 59.0 mol%. Based on differential characteristics of strain UMB49T and recognized Herminiimonas species, it was concluded that strain UMB49T represents a novel species of the genus Herminiimonas, for which the name Herminiimonas glaciei sp. nov. is proposed. The type strain is UMB49T (=ATCC BAA-1623T=DSM 21140T).
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Marispirillum indicum gen. nov., sp. nov., isolated from a deep-sea environment
Qiliang Lai, Jun Yuan, Li Gu and Zongze ShaoA taxonomic study was carried out on strain B142T, which was isolated from a crude-oil-degrading microbial consortium via enrichment with deep water from the Indian Ocean. Cells of the isolate were Gram-negative, oxidase-negative, catalase-positive, helical in shape, motile by means of polar flagella (three per cell) and moderately halophilic. Growth was observed at salinities of 0.5–12 % and at temperatures of 10–41 °C. The micro-organism was capable of denitrification, but was unable to degrade Tween 80 or gelatin. The predominant fatty acids were C16 : 1 ω7c and/or iso-C15 :0 2-OH (6.4 %), C16 : 0 (15.7 %), C18 : 1 ω7c (45 %), C18 : 0 (6.8 %) and C19 : 0 ω8c cyclo (6.7 %). The G+C content of the chromosomal DNA was 67.3 mol%. Comparisons of 16S rRNA gene sequences showed that strain B142T was most closely related to the type strains of two Insolitispirillum peregrinum subspecies (93.0–93.1 % sequence similarity), two Novispirillum itersonii subspecies (92.8–92.9 %) and Caenispirillum bisanense (91.7 %); sequence similarities with respect to other taxa were below 90.5 %. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain B142T formed a distinct evolutionary lineage within the family Rhodospirillaceae. Strain B142T was distinguishable from phylogenetically related genera with regard to several phenotypic properties. On the basis of phenotypic and phylogenetic data, therefore, strain B142T represents a novel genus and species, for which the name Marispirillum indicum gen. nov., sp. nov. is proposed. The type strain is B142T (=CCTCC AB 208225T=LMG 24627T=MCCC 1A01235T).
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Pseudomonas xinjiangensis sp. nov., a moderately thermotolerant bacterium isolated from desert sand
A yellow-pigmented, moderately thermotolerant bacterial strain, designated S3-3T, was isolated from desert sand in Xinjiang province, China, and subjected to a polyphasic taxonomic characterization. This isolate was Gram-negative, aerobic and motile. Phylogenetic analyses based on the 16S rRNA gene sequence showed that strain S3-3T is phylogenetically affiliated to the genus Pseudomonas. Strain S3-3T exhibited levels of 16S rRNA gene sequence similarity of less than 96.3 % to the type strains of all Pseudomonas species, making it clear that strain S3-3T represents a species that is separate from previously recognized Pseudomonas species. Its major fatty acids were summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c), summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH) and C19 : 0 cyclo ω8c. The major isoprenoid quinone was Q-9. The DNA G+C content was 60.9 mol%. On the basis of phylogenetic, phenotypic and chemotaxonomic analysis, strain S3-3T should be classified within a novel species of the genus Pseudomonas, for which the name Pseudomonas xinjiangensis sp. nov. is proposed. The type strain is S3-3T (=CCTCC AB 207151T =NRRL B-51270T).
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Halomonas fontilapidosi sp. nov., a moderately halophilic, denitrifying bacterium
More LessWe have made a polyphasic taxonomic study of strain 5CRT, isolated from Fuente de Piedra, Málaga, southern Spain. The strain is a moderately halophilic, Gram-negative rod, oxidase-positive and motile by a single polar flagellum. It does not produce acids from sugars and shows respiratory metabolism, using oxygen, nitrate and nitrite as terminal electron acceptors. It requires NaCl and grows best with 5–7.5 % w/v at temperatures of between 32 and 45 °C within a pH range of 6–8. Its 16S rRNA gene sequence indicates that strain 5CRT belongs to the genus Halomonas in the class Gammaproteobacteria. Its closest relatives are Halomonas alimentaria, H. nitroreducens, H. shengliensis and H. ventosae, with the type strains of which our strain showed 16S rRNA gene sequence similarity values of 96.7–97.8 %. DNA–DNA hybridization studies between strain 5CRT and H. ventosae CECT 5797T, the phylogenetically nearest type strain, showed 40 % relatedness. Its G+C content is 65.7 mol%. Its major fatty acids are C18 : 1 ω7c (31.36 %), C16 : 0 (25.55 %), C16 : 1 ω7c/iso-C15 : 0 2-OH (23.23 %), C19 : 0 cyclo ω8c (8.14 %), C12 : 0 3-OH (5.76 %) and C10 : 0 (2.22 %) and the predominant respiratory lipoquinone is ubiquinone with nine isoprene units (Q-9). The proposed name for the novel species is Halomonas fontilapidosi sp. nov., strain 5CRT (=CECT 7341T =LMG 24455T) being the type strain.
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Nautilia abyssi sp. nov., a thermophilic, chemolithoautotrophic, sulfur-reducing bacterium isolated from an East Pacific Rise hydrothermal vent
A novel strictly anaerobic, thermophilic, sulfur-reducing bacterium, designated PH1209T, was isolated from an East Pacific Rise hydrothermal vent (1 ° N) sample and studied using a polyphasic taxonomic approach. Cells were Gram-negative, motile rods (approx. 1.60×0.40 μm) with a single polar flagellum. Strain PH1209T grew at temperatures between 33 and 65 °C (optimum 60 °C), from pH 5.0 to 8.0 (optimum 6.0–6.5), and between 2 and 4 % (w/v) NaCl (optimum 3 %). Cells grew chemolithoautotrophically with H2 as an energy source, S0 as an electron acceptor and CO2 as a carbon source. Strain PH1209T was also able to use peptone and yeast extract as carbon sources. The G+C content of the genomic DNA was 35 mol%. Phylogenetic analyses based on 16S rRNA gene sequencing showed that strain PH1209T fell within the order Nautiliales, in the class Epsilonproteobacteria. Comparative 16S rRNA gene sequence analysis indicated that strain PH1209T belonged to the genus Nautilia and shared 97.2 and 98.7 % 16S rRNA gene sequence identity, respectively, with the type strains of Nautilia lithotrophica and Nautilia profundicola. It is proposed, from the polyphasic evidence, that the strain represents a novel species, Nautilia abyssi sp. nov.; the type strain is PH1209T (=DSM 21157T=JCM 15390T).
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Pseudidiomarina donghaiensis sp. nov. and Pseudidiomarina maritima sp. nov., isolated from the East China Sea
More LessTwo Gram-negative, aerobic, motile, rod-shaped bacteria, designated strains 908033T and 908087T, were isolated from a seawater sample collected from the East China Sea. Chemotaxonomic characteristics of the two isolates included the presence of iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1 ω9c as the major cellular fatty acids and Q-8 as the predominant ubiquinone. The genomic DNA G+C contents of strains 908033T and 908087T were 45.5 and 45.2 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the new isolates were related to members of the genus Pseudidiomarina, showing levels of similarity of 95.8–96.6 % with the type strains of recognized species of the genus. The results of DNA–DNA hybridization experiments among these two isolates and Pseudidiomarina sediminum CICC 10319T, in combination with chemotaxonomic and phenotypic data, demonstrated that the new isolates represent two novel species of the genus Pseudidiomarina, for which the names Pseudidiomarina donghaiensis sp. nov. (type strain 908033T=CGMCC 1.7284T=JCM 15533T) and Pseudidiomarina maritima sp. nov. (type strain 908087T=CGMCC 1.7285T=JCM 15534T) are proposed.
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Pseudomonas cedrina subsp. fulgida subsp. nov., a fluorescent bacterium isolated from the phyllosphere of grasses; emended description of Pseudomonas cedrina and description of Pseudomonas cedrina subsp. cedrina subsp. nov.
More LessThe taxonomic position of a group of four strains, isolated from the phyllosphere of grasses, within the species Pseudomonas cedrina was investigated. The isolates formed a separate cluster through ribotyping and MALDI-TOF MS, which could be clearly differentiated from the type strain of P. cedrina. The differences found between the patterns of the type strain of P. cedrina and the novel isolates were more distinct than those between the type strain and recognized species of the genus Pseudomonas, which were phylogenetically related by 16S rRNA gene sequence analysis. Physiological characterization also revealed significant differences between the novel grass isolates and the type strain of P. cedrina. Siderotyping of the pyoverdines revealed identical pyoverdine-isoelectrofocusing patterns for the novel isolates and the type strain of P. cedrina. However, pyoverdine-mediated 59Fe cross uptake studies indicated differences in the siderotype. In contrast, phylogenetic analysis based on 16S rRNA gene sequence analysis and DNA–DNA hybridization studies (reassociation value 76.4 %) supported the affiliation of the novel isolates to the species P. cedrina. As a consequence of these observations, the splitting of the species P. cedrina into two novel subspecies Pseudomonas cedrina subsp. cedrina subsp. nov. (type strain CFML 96-198T=CIP 105541T=DSM 17516T) and Pseudomonas cedrina subsp. fulgida subsp. nov. (type strain P 515/12T=DSM 14938T=LMG 21467T) is proposed.
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Sphingomonas aestuarii sp. nov., isolated from tidal flat sediment
More LessA novel bacterium (strain K4T) belonging to the genus Sphingomonas was isolated from tidal flat sediment in Korea. Its morphology, physiology, biochemical features and 16S rRNA gene sequence were characterized. Colonies of this strain are yellow in colour and the cells are rod-shaped, exhibiting negative Gram staining. The strain grows at 0–5 % (w/v) NaCl and 20–35 °C, with optimal growth occurring at 0 % (w/v) NaCl and 30 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain K4T is associated with the genus Sphingomonas. Within the phylogenetic tree, this novel strain shares a branching point with Sphingomonas asaccharolytica Y-345T, with which it shares 97.3 % 16S rRNA gene sequence similarity. The polyamine pattern predominantly contains the Sphingomonas-specific triamine sym-homospermidine. Combined analysis of 16S rRNA gene sequences, DNA–DNA relatedness, physiological and biochemical test results identified genotypic and phenotypic differences between strain K4T and other Sphingomonas species. On the basis of these differentiating features, it is concluded that strain K4T (=KCTC 22050T=DSM 19475T) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas aestuarii sp. nov. is proposed.
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Description of Acinetobacter venetianus ex Di Cello et al. 1997 sp. nov.
The name ‘Acinetobacter venetianus’ has been used previously to designate three marine hydrocarbon-degrading Acinetobacter strains, of which strain RAG-1 (=ATCC 31012) has industrial applications for the production of the bioemulsifier emulsan. However, to date, the name of this taxon has not been validly published. In this study, five strains were examined to corroborate the delineation of this taxon by means of phenotypic characterization, DNA–DNA hybridization, selective restriction fragment amplification (AFLP), amplified rDNA restriction analysis (ARDRA), rpoB gene sequence analysis and tRNA intergenic spacer length polymorphism analysis (tDNA-PCR) and to emend the description of ‘Acinetobacter venetianus’ (ex Di Cello et al. 1997 ). AFLP analysis showed that the five strains formed a tight cluster at 56.8±5.0 % genomic relatedness that was separated from strains of other haemolytic species of the genus Acinetobacter and from the type and reference strains of other Acinetobacter species at ≤27 % relatedness, indicating the distinctiveness of the novel strains. The strains were haemolytic and able to grow on citrate (Simmons), l-histidine and malonate. The strains did not oxidize d-glucose or utilize dl-lactate or l-aspartate. The G+C contents of strains RAG-1 and of VE-C3 were 43.9 % and 43.6 mol%, respectively. The novel strains could be recognized by a characteristic ARDRA pattern (CfoI 1, AluI 3, MboI 2, RsaI 2, MspI 3). The consensus tDNA-PCR pattern for the five strains consisted of amplified fragments of 87.9, 100.2, 134.6 and 248.5 bp and was indistinguishable from that of strains of Acinetobacter genomic species 14BJ. The five strains represent a novel species for which the name Acinetobacter venetianus sp. nov. is proposed. The type strain is RAG-1T (=ATCC 31012T=CCUG 45561T=LMG 19082T=LUH 3904T=NIPH 1925T).
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Saccharospirillum salsuginis sp. nov., a gammaproteobacterium from a subterranean brine
A novel Gram-negative, non-sporulating, moderately halophilic, facultatively alkaliphilic, catalase- and oxidase-positive, obligately aerobic bacterium, strain YIM-Y25T, was isolated from a subterranean brine sample collected from a salt mine in Yunnan, south-west China. Cells were spirilla, motile by monopolar flagella, with meso-diaminopimelic acid in the cell-wall peptidoglycan. Growth occurred with 1–15 % (w/v) NaCl (optimum 5 %), at pH 6.0–10.0 (optimum pH 8.0) and at 15–50 °C (optimum 35–40 °C). Ubiquinone Q-8 was the predominant respiratory quinone. Polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylamine and an unidentified phospholipid. The major cellular fatty acids were C18 : 1 ω7c, iso-C16 : 0, C16 : 0 and C16 : 1. The genomic DNA G+C content was 58.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM-Y25T was most closely related to the type strain of the sole recognized species of the genus Saccharospirillum, Saccharospirillum impatiens EL-105T (sequence similarity 97.0 %), and these two strains formed a robust lineage in the phylogenetic tree. The level of DNA–DNA relatedness between them was 12.6 %. The combination of phylogenetic analysis, phenotypic differences, chemotaxonomic properties and DNA–DNA hybridization data supported the view that this strain represents a novel species of the genus Saccharospirillum, for which the name Saccharospirillum salsuginis sp. nov. is proposed, with YIM-Y25T (=CCTCC AA 207033T =KCTC 22169T) as the type strain.
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Arcobacter mytili sp. nov., an indoxyl acetate-hydrolysis-negative bacterium isolated from mussels
More LessThree Arcobacter isolates, recovered from mussels (genus Mytilus), and one isolate from brackish water in Catalonia (north-east Spain) showed a novel pattern using a recently described identification method for members of the genus Arcobacter, 16S rRNA gene RFLP. Enterobacterial repetitive intergenic consensus PCR fingerprinting demonstrated that the three isolates from mussels belonged to two genotypes and that the fourth isolate from water belonged to a third genotype. Analysis of the 16S rRNA and rpoB gene sequences showed that the new isolates formed a separate lineage within the genus Arcobacter. This was also confirmed by the low DNA–DNA relatedness values (16–30 %) of the isolates with the type strains of recognized Arcobacter species. Hydrolysis of indoxyl acetate, a characteristic trait for all species of the genus Arcobacter, was negative for the novel isolates. The susceptibility of the novel isolates to cefoperazone, together with the lack of urease production and nitrate reduction, further enabled them to be differentiated from recognized Arcobacter species based on physiological characteristics. Genotypic and phenotypic characteristics indicated that the new isolates represent a novel species of the genus Arcobacter, for which the name Arcobacter mytili sp. nov. is proposed, with the type strain F2075T (=CECT 7386T =LMG 24559T). The DNA G+C content of strain F2075T was 26.9 mol%.
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Dyella marensis sp. nov., isolated from cliff soil
More LessA novel, Gram-negative bacterium, designated CS5-B2T, was isolated from soil that had been collected from a cliff on Mara Island, Republic of Korea. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain fell within the radiation of the genus Dyella. The closest relatives were the type strains of Dyella koreensis, Dyella ginsengisoli and Dyella japonica and 16S rRNA gene sequence similarities between strain CS5-B2T and these strains were 99.0, 97.9 and 97.8 %, respectively. The sequence similarities between the novel isolate and other related taxa compared in the phylogenetic analysis were less than 96.7 %. The cells of strain CS5-B2T were aerobic, oxidase-negative, catalase-positive, motile rods. The temperature range for growth was 20–37 °C, with optimal growth at 30–37 °C. Growth occurred at pH 5.1–9.1, with optimal growth at pH 6.1–9.1. NaCl tolerance for growth was from 1 to 2 % (w/v). Ubiquinone-8 was the predominant respiratory lipoquinone. The major fatty acids were iso-C15 : 0 and iso-C17 : 1 ω9c. The G+C content of the DNA was 65.7–66.6 mol%. The level of DNA–DNA relatedness with D. koreensis KCTC 12359T was 20.2 and 29.6 % in duplicate measurements. On the basis of phenotypic features, phylogenetic analysis and DNA–DNA relatedness, a novel species of the genus Dyella is proposed, with the name Dyella marensis sp. nov. The type strain is CS5-B2T (=JCM 14959T =KCTC 22144T).
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Pseudomonas cuatrocienegasensis sp. nov., isolated from an evaporating lagoon in the Cuatro Ciénegas valley in Coahuila, Mexico
Nine Gram-negative, rod-shaped, non-spore-forming isolates with identical or very similar repetitive-sequence-based PCR profiles were recovered from an evaporative lagoon in Mexico. Two strains, designated 1NT and 3N, had virtually identical 16S rRNA gene sequences and, on the basis of these sequences, were identified as members of the genus Pseudomonas, with Pseudomonas peli R-20805T as the closest relative. All nine isolates had practically identical whole-cell protein profiles. The major fatty acids [C16 : 0, C18 : 1 ω7c and summed feature a (C16 : 1 ω7 and/or C16 : 1 ω6c)] of strains 1NT and 3N supported their affiliation with the genus Pseudomonas. The DNA–DNA reassociation values with respect to P. peli LMG 23201T and other closely related Pseudomonas species were <15 %. Physiological and biochemical tests allowed phenotypic differentiation of the strains analysed, including strain 1NT, from the five phylogenetically closest Pseudomonas species. On the basis of the data obtained by using this polyphasic taxonomic approach, the nine strains represent a novel species, for which the name Pseudomonas cuatrocienegasensis sp. nov. is proposed. The type strain is 1NT (=LMG 24676T=CIP 109853T).
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Photobacterium aquimaris sp. nov., a luminous marine bacterium isolated from seawater
More LessTwo luminous marine bacteria, strains LC2-065T and LC2-102, were isolated from seawater at Sagami Bay in Japan. These bacteria were Gram-negative, oxidase-negative, catalase-positive, motile and coccoid-rods. 16S rRNA gene sequence analysis and multilocus sequence analysis (MLSA) using six loci (ftsZ, gapA, gyrB, mreB, pyrH and topA) and sequence analysis of the alpha subunit of luciferase (luxA) gene revealed that these bacteria were distinct from other species of the genus Photobacterium. These novel strains were most closely related to Photobacterium kishitanii. The DNA–DNA hybridization value between strain LC2-065T and Photobacterium kishitanii ATCC BAA-1194T was 42.1 %. The major fatty acids were C12 : 0, C14 : 0, C16 : 0, C18 : 0 and C15 : 0 iso 2-OH and/or C16 : 1 ω7c (summed feature 3). The DNA G+C contents of strains LC2-065T and LC2-086 were 42.2 and 42.9 mol%, respectively. The phenotypic features of the novel strains were similar to those of P. kishitanii and P. phosphoreum, but there were sufficient physiological differences for the novel strains to be easily differentiated. On the basis of these results, these new strains represent a novel species, for which the name Photobacterium aquimaris sp. nov. is proposed. The type strain is LC2-065T (=NBRC 104633T=KCTC 22356T).
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Alcanivorax hongdengensis sp. nov., an alkane-degrading bacterium isolated from surface seawater of the straits of Malacca and Singapore, producing a lipopeptide as its biosurfactant
More LessA taxonomic study was carried out on strain A-11-3T, which was isolated from an oil-enriched consortia from the surface seawater of Hong-Deng dock in the Straits of Malacca and Singapore. Cells were aerobic, Gram-negative, non-spore-forming irregular rods. The strain was catalase- and oxidase-negative. It grew on a restricted spectrum of organic compounds, including some organic acids and alkanes. 16S rRNA gene sequence comparisons showed that strain A-11-3T was most closely related to the type strains of Alcanivorax jadensis (96.8 % sequence similarity), Alcanivorax borkumensis (96.8 %), Alcanivorax dieselolei (94.8 %), Alcanivorax venustensis (94.2 %) and Alcanivorax balearicus (94.0 %). The predominant fatty acids were C16 : 0 (31.2 %), C18 : 1 ω7c (24.8 %), C18 : 0 (9.6 %), C12 : 0 (8.3 %), C16 : 1 ω7c (8.3 %) and C16 : 0 3-OH (5.1 %). The G+C content of the genomic DNA was 54.7 mol%. Moreover, the strain produced lipopeptides as its surface-active compounds. According to physiological and biochemical tests, DNA–DNA hybridization results and sequence comparisons of the 16S–23S internal transcribed spacer, the gyrB gene and the alkane hydroxylase gene alkB1, strain A-11-3T was affiliated with the genus Alcanivorax but could be readily distinguished from recognized Alcanivorax species. Therefore strain A-11-3T represents a novel species of the genus Alcanivorax for which the name Alcanivorax hongdengensis sp. nov. is proposed. The type strain is A-11-3T (=CGMCC 1.7084T=LMG 24624T=MCCC 1A01496T).
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Volumes and issues
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