- Volume 62, Issue Pt_6, 2012
Volume 62, Issue Pt_6, 2012
- Notification List
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Notification that new names and new combinations have appeared in volume 62, part 3, of the IJSEM
More LessThis 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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- Archaea
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Halomicrobium zhouii sp. nov., a halophilic archaeon from a marine solar saltern
Xin Yang and Heng-Lin CuiA halophilic archaeon, strain TBN51T, was isolated from a marine solar saltern in Jiangsu, China. The colonies were red-pigmented and the cells were pleomorphic, motile and Gram-staining-negative. The strain was able to grow at 20–55 °C (optimum 42 °C), in the presence of 1.4–5.1 M NaCl (optimum 2.6 M), with 0–1.0 M MgCl2 (optimum 0.05 M) and at pH 5.5–9.5 (optimum pH 7.0). Cells lysed in distilled water; the minimal NaCl concentration to prevent such lysis was 8 % (w/v). The major polar lipids of strain TBN51T were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and an unidentified glycolipid. The latter lipid and a minor glycolipid also detected in the novel strain were chromatographically identical to sulfated and non-sulfated mannosyl glucosyl diether, respectively. Analysis revealed that strain TBN51T had three dissimilar 16S rRNA genes. Phylogenetic analysis based on the sequences of these genes indicated that the novel strain was most closely related to Halomicrobium mukohataei JCM 9738T (89.2–94.8 % sequence similarity) and Halomicrobium katesii DSM 19301T (88.8–94.8 %). In similar comparisons of rpoB′ gene sequences, strain TBN51T also appeared most closely related to Hmc. mukohataei JCM 9738T (88.5 % sequence similarity) and Hmc. katesii DSM 19301T (88.1 %). The genomic DNA G+C content of strain TBN51T was 69.1 mol%. The results of DNA–DNA hybridizations indicated that strain TBN51T represented a novel species since it showed relatedness values of only 23 % with Hmc. mukohataei JCM 9738T and 21 % with Hmc. katesii DSM 19301T. It was concluded that strain TBN51T represents a novel species of the genus Halomicrobium , for which the name Halomicrobium zhouii sp. nov. is proposed. The type strain is TBN51T ( = CGMCC 1.10457T = JCM 17095T).
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Halobellus limi sp. nov. and Halobellus salinus sp. nov., isolated from two marine solar salterns
More LessTwo halophilic archaea, strains TBN53T and CSW2.24.4T, were characterized to elucidate their taxonomic status. Strain TBN53T was isolated from the Taibei marine solar saltern near Lianyungang city, Jiangsu province, China, whereas strain CSW2.24.4T was isolated from a saltern crystallizer in Victoria, Australia. Cells of the two strains were pleomorphic, stained Gram-negative and produced red-pigmented colonies. Strain TBN53T was able to grow at 25–55 °C (optimum 45 °C), with 1.4–5.1 M NaCl (optimum 2.6–3.9 M NaCl), with 0–1.0 M MgCl2 (optimum 0–0.1 M MgCl2) and at pH 5.5–9.5 (optimum pH 7.0), whereas strain CSW2.24.4T was able to grow at 25–45 °C (optimum 37 °C), with 2.6–5.1 M NaCl (optimum 3.4 M NaCl), with 0.01–0.7 M MgCl2 (optimum 0.05 M MgCl2) and at pH 5.5–9.5 (optimum pH 7.0–7.5). Cells of the two isolates lysed in distilled water. The minimum NaCl concentrations that prevented cell lysis were 8 % (w/v) for strain TBN53T and 12 % (w/v) for strain CSW2.24.4T. The major polar lipids of the two strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate, with two glycolipids chromatographically identical to sulfated mannosyl glucosyl diether and mannosyl glucosyl diether, respectively. Trace amounts of other unidentified lipids were also detected. On the basis of 16S rRNA gene sequence analysis, strains TBN53T and CSW2.24.4T showed 94.1 % similarity to each other and were closely related to Halobellus clavatus TNN18T (95.0 and 94.7 % similarity, respectively). Levels of rpoB′ gene sequence similarity between strains TBN53T and CSW2.24.4T, and between these strains and Halobellus clavatus TNN18T were 88.5, 88.5 and 88.1 %, respectively. The DNA G+C contents of strains TBN53T and CSW2.24.4T were 69.2 and 67.0 mol%, respectively. The level of DNA–DNA relatedness between strain TBN53T and strain CSW2.24.4T was 25 %, and these two strains showed low levels of DNA–DNA relatedness with Halobellus clavatus TNN18T (30 and 29 % relatedness, respectively). Based on these phenotypic, chemotaxonomic and phylogenetic properties, two novel species of the genus Halobellus are proposed to accommodate these two strains, Halobellus limi sp. nov. (type strain TBN53T = CGMCC 1.10331T = JCM 16811T) and Halobellus salinus sp. nov. (type strain CSW2.24.4T = DSM 18730T = CGMCC 1.10710T = JCM 14359T).
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Halovenus aranensis gen. nov., sp. nov., an extremely halophilic archaeon from Aran-Bidgol salt lake
More LessA novel red-pigmented halophilic archaeon, strain EB27T, was isolated from Aran-Bidgol salt lake, a hypersaline playa in Iran. Cells of strain EB27T were non-motile and pleomorphic (rods to triangular or disc-shaped). Strain EB27T required at least 2.5 M NaCl and 0.1 M MgCl2 for growth. Optimal growth was achieved at 4 M NaCl and 0.5 M MgCl2. The optimum pH and temperature for growth were pH 7.5 and 40 °C; it was able to grow at pH 6.0–8.0 and 25–50 °C. 16S rRNA gene sequence analysis showed that strain EB27T is a member of the family Halobacteriaceae ; however, levels of 16S rRNA gene sequence similarity were as low as 90.0, 89.3 and 89.1 % to the most closely related haloarchaeal taxa, namely Halalkalicoccus tibetensis DS12T, Halosimplex carlsbadense 2-9-1T and Halorhabdus utahensis AX-2T, respectively. The DNA G+C content of strain EB27T was 61 mol%. Strain EB27T contained phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, common phospholipids found in haloarchaea, together with two minor phospholipids. The only quinone present was MK-8(II-H2). Physiological, biochemical and phylogenetic differences between strain EB27T and recognized genera of extremely halophilic archaea suggest that this strain represents a novel species in a new genus within the family Halobacteriaceae , for which the name Halovenus aranensis gen. nov., sp. nov. is proposed. The type strain of Halovenus aranensis, the type species of the new genus, is strain EB27T ( = IBRC-M 10015T = CGMCC 1.11001T).
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Methanolinea mesophila sp. nov., a hydrogenotrophic methanogen isolated from rice field soil, and proposal of the archaeal family Methanoregulaceae fam. nov. within the order Methanomicrobiales
A novel mesophilic, hydrogenotrophic methanogen, designated strain TNRT, was isolated from an anaerobic, propionate-degradation enrichment culture that was originally established from a rice field soil sample from Taiwan. Cells were non-motile rods, 2.0–6.5 µm long by 0.3 µm wide. Filamentous (up to about 100 µm) and coccoid (about 1 µm in diameter) cells were also observed in cultures in the late exponential phase of growth. Strain TNRT grew at 20–40 °C (optimally at 37 °C), at pH 6.5–7.4 (optimally at pH 7.0) and in the presence of 0–25 g NaCl l−1 (optimally at 0 g NaCl l−1). The strain utilized H2/CO2 and formate for growth and produced methane. The G+C content of the genomic DNA was 56.4 mol%. Based on sequences of both the 16S rRNA gene and the methanogen-specific marker gene mcrA, strain TNRT was related most closely to Methanolinea tarda NOBI-1T; levels of sequence similarities were 94.8 and 86.4 %, respectively. The 16S rRNA gene sequence similarity indicates that strain TNRT and M. tarda NOBI-1T represent different species within the same genus. This is supported by shared phenotypic properties, including substrate usage and cell morphology, and differences in growth temperature. Based on these genetic and phenotypic properties, strain TNRT is considered to represent a novel species of the genus Methanolinea , for which the name Methanolinea mesophila sp. nov. is proposed; the type strain is TNRT ( = NBRC 105659T = DSM 23604T). In addition, we also suggest family status for the E1/E2 group within the order Methanomicrobiales , for which the name Methanoregulaceae fam. nov. is proposed; the type genus of family is Methanoregula.
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- Actinobacteria
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Nocardia goodfellowii sp. nov. and Nocardia thraciensis sp. nov., isolated from soil
More LessThe taxonomic position of two soil actinomycetes, strains A2012T and A2019T, isolated from Turkish soils, was determined using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that the strains belonged to the family Nocardiaceae . Strains A2012T and A2019T were most closely related to Nocardia caishijiensis DSM 44831T (98.9 %) and Nocardia mexicana CIP 108295T (98.6 %), respectively; similarity to other type strains of the genus Nocardia ranged from 96.9 to 97.9 %. However, DNA–DNA relatedness and phenotypic data demonstrated that strains A2012T and A2019T could be clearly distinguished from members of the most closely related Nocardia species. It is evident from the genotypic and phenotypic data that the two isolates represent two novel species of the genus Nocardia . It is proposed, therefore, that strains A2012T and A2019T be classified in the genus Nocardia as representatives of Nocardia goodfellowii sp. nov. (type strain A2012T = DSM 45516T = NRRL B-24833T = KCTC 19986T) and Nocardia thraciensis sp. nov. (type strain A2019T = DSM 45517T = NRRL B-24834T = KCTC 19985T), respectively.
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Amycolatopsis granulosa sp. nov., Amycolatopsis ruanii sp. nov. and Amycolatopsis thermalba sp. nov., thermophilic actinomycetes isolated from arid soils
The taxonomic positions of three thermophilic actinomycetes isolated from arid soil samples were established by using a polyphasic approach. The organisms had chemical and morphological features that were consistent with their classification in the genus Amycolatopsis . 16S rRNA gene sequence data supported the classification of the isolates in the genus Amycolatopsis and showed that they formed distinct branches in the Amycolatopsis methanolica subclade. DNA–DNA relatedness studies between the isolates and their phylogenetic neighbours showed that they belonged to distinct genomic species. The three isolates were readily distinguished from one another and from the type strains of species classified in the A. methanolica subclade based on a combination of phenotypic properties and by genomic fingerprinting. Consequently, it is proposed that the three isolates be classified in the genus Amycolatopsis as representatives of Amycolatopsis granulosa sp. nov. (type strain GY307T = NCIMB 14709T = NRRL B-24844T), Amycolatopsis ruanii sp. nov. (type strain NMG112T = NCIMB 14711T = NRRL B-24848T) and Amycolatopsis thermalba sp. nov. (type strain SF45T = NCIMB 14705T = NRRL B-24845T).
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Mycobacterium koreense sp. nov., a slowly growing non-chromogenic species closely related to Mycobacterium triviale
A novel slow-growing, non-chromogenic mycobacterium (strain 01-305T) was isolated from a patient with pulmonary dysfunction. Growth characteristics, acid-fastness and the results of 16S rRNA gene sequencing supported the placement of this strain within the genus Mycobacterium . Phenotypically, strain 01-305T was generally similar to Mycobacterium triviale ATCC 23292T, but some unique biochemical characteristics were observed. The 16S rRNA gene sequence of strain 01-305T was similar to those of M. triviale ATCC 23290 (GenBank accession no. AY734996, 99.9 % similarity) and M. triviale ATCC 23291 (AY734995, 99.9 %); however, it differed substantially from that of M. triviale ATCC 23292T (X88924, 98.2 %). Phylogenetic analysis based on 16S rRNA gene sequences placed strain 01-305T in the slow-growing Mycobacterium group close to M. triviale ATCC 23290 and M. triviale ATCC 23291, but not M. triviale ATCC 23292T. Unique mycolic acid profiles and phylogenetic analysis based on two different chronometer molecules, and the hsp65 and rpoB genes, strongly supported the taxonomic status of this strain as representing a distinct species. These data support the conclusion that strain 01-305T represents a novel mycobacterial species, for which the name Mycobacterium koreense sp. nov. is proposed. The type strain is 01-305T ( = DSM 45576T = KCTC 19819T).
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Cryobacterium flavum sp. nov. and Cryobacterium luteum sp. nov., isolated from glacier ice
More LessGram-positive, rod-shaped bacteria, strains Hh8T, Hh15T and Hh40-2, were isolated from the No. 1 glacier in Xinjiang, north-west China. Colonies of strain Hh8T were orange–yellow, convex and round on PYG plates. Strain Hh8T grew at 0–19 °C and pH 5.5–10.5. Colonies of strain Hh15T, which was able to grow at 0–20 °C and pH 5.5–12, were lemon yellow, convex and round on PYG plates. Phylogenetic analysis based on 16S rRNA gene sequences showed that these three strains were related to members of the genus Cryobacterium . The major cellular fatty acids of the novel strains were anteiso-C15 : 0, iso-C16 : 0, iso-C15 : 0 and anteiso-C15 : 1 A. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, two novel species, Cryobacterium flavum sp. nov. (type strain Hh8T = CGMCC 1.11215T = NBRC 107879T) and Cryobacterium luteum sp. nov. (type strain Hh15T = CGMCC 1.11210T = NBRC 107880T), are proposed.
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Nonomuraea jiangxiensis sp. nov., isolated from acidic soil
More LessAn actinomycete, designated FXJ1.102T, was isolated from acidic soil collected in Jiangxi Province, south-east China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain FXJ1.102T belonged to the genus Nonomuraea and was most closely related to Nonomuraea candida HMC10T, Nonomuraea turkmeniaca DSM 43926T, Nonomuraea antimicrobica YIM 61105T and ‘Nonomuraea aegyptia’ S136 (98.9, 98.3, 97.9 and 97.5 % 16S rRNA gene sequence similarities, respectively). The morphological characteristics were typical of the genus Nonomuraea . The chemotaxonomic properties, such as cell-wall chemotype IIIB, phospholipid type IV, MK-9(H4) as the major menaquinone and iso-C16 : 0 (22.2 %) as the major fatty acid, supported the assignment of the strain to the genus Nonomuraea . DNA–DNA relatedness and physiological tests allowed genotypic and phenotypic differentiation of strain FXJ1.102T from its closest phylogenetic relatives. The isolate therefore represents a novel species, for which the name Nonomuraea jiangxiensis sp. nov. is proposed. The type strain is FXJ1.102T ( = CGMCC 4.6533T = NBRC 106679T).
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Williamsia limnetica sp. nov., isolated from a limnetic lake sediment
More LessAn actinomycete, strain L1505T, was isolated from a limnetic lake sediment and found to have morphological, biochemical, physiological and chemotaxonomic properties consistent with its classification in the genus Williamsia . Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain L1505T formed a distinct lineage within the genus Williamsia . The isolate belonged to a cluster containing W. muralis MA140/96T, W. marianensis MT8T and W. faeni N1350T, with which the isolate shared 99.0–98.2 % 16S rRNA gene sequence similarity. Genotypic and phenotypic data also indicated that the isolate was different from known members of the genus Williamsia . On the basis of these data, strain 1505T is considered to represent a novel species of the genus Williamsia , for which the name Williamsia limnetica sp. nov. is proposed (type strain L1505T = DSM 45521T = NRRL B-24829T = KCTC 19981T).
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- Firmicutes and Related Organisms
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Paenibacillus sediminis sp. nov., a xylanolytic bacterium isolated from a tidal flat
More LessA Gram-positive, rod-shaped, xylanolytic, spore-forming bacterium, strain GTH-3T, was isolated from a tidal flat adjacent to Ganghwa Island, Republic of Korea, and was characterized to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain GTH-3T was shown to belong to the family Paenibacillaceae , being most closely related to the type strains of Paenibacillus ginsengisoli (94.9 %), Paenibacillus anaericanus (94.8 %), Paenibacillus urinalis (94.4 %), Paenibacillus cookii (94.2 %), Paenibacillus alvei (94.1 %) and Paenibacillus chibensis (94.0 %). The G+C content of the genomic DNA of strain GTH-3T was 45.9±0.2 mol% (mean±sd). The major menaquinone was MK-7. The major fatty acids were anteiso-C15 : 0 and iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phenotypic and chemotaxonomic data supported the affiliation of strain GTH-3T to the genus Paenibacillus . The results of physiological and biochemical tests allowed strain GTH-3T to be distinguished genotypically and phenotypically from recognized species of the genus Paenibacillus . Strain GTH-3T is therefore considered to represent a novel species of the genus Paenibacillus , for which the name Paenibacillus sediminis sp. nov. is proposed. The type strain is GTH-3T ( = DSM 23491T = LMG 25635T).
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Enterococcus ureasiticus sp. nov. and Enterococcus quebecensis sp. nov., isolated from water
Three enterococcal isolates, CCRI-16620, CCRI-16986T and CCRI-16985T, originating from water were characterized using morphological, biochemical and molecular taxonomic methods. 16S rRNA gene sequence analysis classified all three strains in the Enterococcus faecalis species group. The phylogenetic tree of 16S rRNA gene sequences showed that the three isolates form two separate branches. The first branch is represented by strains CCRI-16620 and CCRI-16986T and the second branch by strain CCRI-16985T. Further sequence analysis of the housekeeping genes rpoA (encoding RNA polymerase α subunit), pheS (phenylalanyl-tRNA synthase), tufA (elongation factor Tu) and atpD (ATP synthase β-subunit) as well as the results of amplified fragment length polymorphism (AFLP) DNA fingerprinting and DNA–DNA hybridization experiments confirmed the distinct status of these strains. Moreover, biochemical tests allowed phenotypic differentiation of the strains from the other species of the E. faecalis species group. On the basis of the results obtained, the names Enterococcus ureasiticus sp. nov. (type strain CCRI-16986T = CCUG 59304T = DSM 23328T = LMG 26304T) and Enterococcus quebecensis sp. nov. (type strain CCRI-16985T = CCUG 59306T = DSM 23327T = LMG 26306T) are proposed for the two hitherto undescribed species.
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Paenibacillus chartarius sp. nov., isolated from a paper mill
The taxonomy of strain CCUG 55240T, a Gram-staining-positive, aerobic, endospore-forming bacterium that was isolated from a paper mill, was investigated using a polyphasic approach. In phylogenetic analysis based on 16S rRNA gene sequences, the novel strain was grouped with established members of the genus Paenibacillus and appeared most closely related to the type strains of Paenibacillus chinjuensis (93.7 % sequence similarity), P. elgii (93.7 %) and P. chitinolyticus (93.6 %). The levels of 16S rRNA gene sequence similarity with other species of the genus Paenibacillus , including the type species of the genus, Paenibacillus polymyxa , were all <93.5 %. The fatty acid profile of strain CCUG 55240T, which showed a predominance of iso- and anteiso-branched fatty acids, supported the allocation of the strain to the genus Paenibacillus . Unusually high amounts of some iso-branched fatty acids, especially iso-C15 : 0 and iso-C16 : 0, allowed differentiation of strain CCUG 55240T from the most closely related species of the genus Paenibacillus . The diagnostic diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The predominant menaquinone was MK-7. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, an unknown glycolipid, an unknown aminophosphoglycolipid and an unknown phospholipid. Spermidine was the major polyamine. The results of some physiological and biochemical tests also allowed the phenotypic differentiation of strain CCUG 55240T from the most closely related recognized species. On the basis of the phylogenetic, phenotypic and molecular evidence, strain CCUG 55240T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus chartarius sp. nov. is proposed. The type strain of the novel species is CCUG 55240T ( = CCM 7759T).
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Fusibacter tunisiensis sp. nov., isolated from an anaerobic reactor used to treat olive-mill wastewater
Strain BELH1T, a novel mesophilic, anaerobic, halotolerant, rod-shaped bacterium, was isolated from a Tunisian wastewater digester. The cells of the strain are motile, measure 0.5×2–5 µm, and occur singly or in pairs. The strain reduced thiosulfate and elemental sulfur (but not sulfate or sulfite) into sulfide. It grew at 15–40 °C (optimum 30 °C), pH 5.8–8.4 (optimum 7) and with 0–10 % (w/v) NaCl (optimum 3.0 %). The genomic DNA G+C content of strain BELH1T was 38.2 mol% and the strain’s predominant cellular fatty acids were C14 : 0, asummed feature that contained iso-C17 : 1 and/or anteiso-C17 : 1 B, and C16 : 0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel strain was most closely related to Fusibacter paucivorans (94.8 % sequence similarity). Based on phenotypic, phylogenetic and taxonomic characteristics, strain BELH1T represents a novel species of the genus Fusibacter , for which the name Fusibacter tunisiensis sp. nov. is proposed. The type strain is BELH1T ( = DSM 24436T = JCM 17481T).
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Pelosinus defluvii sp. nov., isolated from chlorinated solvent-contaminated groundwater, emended description of the genus Pelosinus and transfer of Sporotalea propionica to Pelosinus propionicus comb. nov.
Two anaerobic bacterial strains, designated SHI-1T and SHI-2, were isolated from chlorinated solvent-contaminated groundwater. They were found to be identical in phenotypic properties and shared high (98.5–99.8 %) pairwise 16S rRNA gene sequence similarity. Multiple 16S rRNA genes were found to be present in the isolates as well as Pelosinus fermentans DSM 17108T and Sporotalea propionica DSM 13327T. Strains SHI-1T and SHI-2 could be differentiated from their closest phylogenetic relatives, P. fermentans DSM 17108T and S. propionica DSM 13327T, on the basis of their phenotypic and phylogenetic properties. The isolates were Gram-negative, spore-forming, motile rods with peritrichous flagella. Growth occurred at 10–42 °C and pH 5.5–8.5. Fermentative growth was observed on Casamino acids, fructose, fumarate, glucose, glycerol, pyruvate and yeast extract. The major organic acids produced from glucose and glycerol fermentation were propionate and acetate. The major organic acids produced from fermentation of fumarate were propionate, acetate and succinate. The major cellular fatty acids were summed feature 4 (consisting of C15 : 1ω8c and/or C15 : 2), summed feature 8 (consisting of C17 : 1ω8c and/or C17 : 2) and C14 : 0 dimethyl aldehyde. The polar lipids comprised aminophospholipids, including phosphatidylethanolamine and phosphatidylserine, and an unknown phospholipid. The genomic DNA G+C content was 39.2 mol%. We propose that strains SHI-1T and SHI-2 are assigned to a novel species of the genus Pelosinus , with the name Pelosinus defluvii sp. nov. (type strain SHI-1T = NRRL Y-59407T = LMG 25549T). The description of the genus Pelosinus is emended. We also propose the transfer of S. propionica to the genus Pelosinus as Pelosinus propionicus comb. nov. (type strain TmPN3T = DSM 13327T = ATCC BAA-626T), on the basis of phylogenetic, chemotaxonomic and phenotypic properties.
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Marininema mesophilum gen. nov., sp. nov., a thermoactinomycete isolated from deep sea sediment, and emended description of the family Thermoactinomycetaceae
A novel filamentous bacterium, strain SCSIO 10219T, was isolated from a sediment sample collected from the South China Sea (113° 3.752′ E 18° 1.722′ N) at a depth of 2105 m. Growth was observed at 25–35 °C (optimum 30 °C) and pH 5.0–8.0 (optimum pH 6.0–7.0). The organism formed yellow–white colonies with radial wrinkles. Aerial mycelium was not produced on any of the growth media tested. Phenotypic characterization and 16S rRNA gene sequence analysis indicated that strain SCSIO 10219T belongs to the family Thermoactinomycetaceae . The strain contained ll-diaminopimelic acid in the cell wall. The predominant menaquinone was MK-7. The phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine and five unknown phospholipids. Major fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The DNA G+C content was 46.5 mol%. On the basis of chemotaxonomic properties and phylogenetic analysis based on 16S rRNA gene sequence data, it is proposed that this strain represents a novel species in a new genus, Marininema mesophilum gen. nov., sp. nov., in the family Thermoactinomycetaceae . The type strain of the type species is SCSIO 10219T ( = CCTCC AA 2011006T = DSM 45610T). In addition, we propose that the description of the family Thermoactinomycetaceae should be further emended based on the present study.
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- Proteobacteria
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Sphingomonas polyaromaticivorans sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from an oil port water sample
A bacterial strain (B2-7T) capable of degrading a wide range of polycyclic aromatic hydrocarbon compounds (2–4 rings) was isolated from a water sample taken from Botan Oil Port in Xiamen, China. The isolate was Gram-negative, short-rod-shaped, aerobic, non-motile and formed yellow-pigmented colonies on LB medium. Cells of strain B2-7T were catalase-positive and oxidase-negative. Optimal growth of strain B2-7T was observed at pH 7.0, at 26 °C and in 0.5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain B2-7T grouped with members of the genus Sphingomonas and it showed 16S rRNA gene sequence similarity of 95.40 % to Sphingomonas yunnanensis YIM 003T. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine and sphingoglycolipid. Q-10 and sym-homospermidine were the predominant ubiquinone and polyamine components, respectively. The major fatty acids were C18 : 1ω7c (67.2 %), C14 : 0 2-OH (10.0 %) and C16 : 0 (9.6 %). The G+C content of the genomic DNA was 61.8 mol%. Based on phenotypic properties, and phylogenetic and genomic data, strain B2-7T represents a novel species of the genus Sphingomonas within the class Alphaproteobacteria , for which the name Sphingomonas polyaromaticivorans sp. nov. is proposed. The type strain is B2-7T ( = KCCM 42951T = JCM 16711T).
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Hippea jasoniae sp. nov. and Hippea alviniae sp. nov., thermoacidophilic members of the class Deltaproteobacteria isolated from deep-sea hydrothermal vent deposits
Thirteen novel, obligately anaerobic, thermoacidophilic bacteria were isolated from deep-sea hydrothermal vent sites. Four of the strains, designated EP5-rT, KM1, Mar08-272rT and Mar08-368r, were selected for metabolic and physiological characterization. With the exception of strain EP5-rT, all strains were short rods that grew between 40 and 72 °C, with optimal growth at 60–65 °C. Strain EP5-rT was more ovoid in shape and grew between 45 and 75 °C, with optimum growth at 60 °C. The pH range for growth of all the isolates was between pH 3.5 and 5.5 (optimum pH 4.5 to 5.0). Strain Mar08-272rT could only grow up to pH 5.0. Elemental sulfur was required for heterotrophic growth on acetate, succinate, Casamino acids and yeast extract. Strains EP5-rT, Mar08-272rT and Mar08-368r could also use fumarate, while strains EP5-rT, KM1 and Mar08-272rT could also use propionate. All isolates were able to grow chemolithotrophically on H2, CO2, sulfur and vitamins. Phylogenetic analysis of 16S rRNA gene sequences placed all isolates within the family Desulfurellaceae of the class Deltaproteobacteria , with the closest cultured relative being Hippea maritima MH2 T (~95–98 % gene sequence similarity). Phylogenetic analysis also identified several isolates with at least one intervening sequence within the 16S rRNA gene. The genomic DNA G+C contents of strains EP5-rT, KM1, Mar08-272rT and Mar08-368r were 37.1, 42.0, 35.6 and 37.9 mol%, respectively. The new isolates differed most significantly from H. maritima MH2 T in their phylogenetic placement and in that they were obligate thermoacidophiles. Based on these phylogenetic and phenotypic properties, the following two novel species are proposed: Hippea jasoniae sp. nov. (type strain Mar08-272rT = DSM 24585T = OCM 985T) and Hippea alviniae sp. nov. (type strain EP5-rT = DSM 24586T = OCM 986T).
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Roseivivax isoporae sp. nov., isolated from a reef-building coral, and emended description of the genus Roseivivax
More LessA bacterial strain, isolated from a sample of reef-building coral (Isopora palifera) collected off the coast of southern Taiwan, was characterized using a polyphasic taxonomic approach. The strain, designated sw-2T, was Gram-staining-negative, aerobic, rod-shaped and motile, with subpolar flagella, and formed greyish pink colonies. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain sw-2T was most closely related to Roseivivax halodurans Och 239T (97.4 % sequence similarity) and Roseivivax halotolerans Och 210T (96.4 %). The novel strain did not require NaCl for growth and exhibited optimal growth at 35–40 °C, at pH 7.5–8.0 and with 3–7 % (w/v) NaCl. It produced bacteriochlorophyll a under aerobic conditions. Summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 63.7 %) predominated in the cellular fatty acid profile. The novel strain’s major respiratory quinone was ubiquinone Q-10 and its genomic DNA G+C content was 68.8 mol%. The polar lipid profile consisted of a mixture of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol, phosphatidyldimethylethanolamine, sulfo-quinovosyl diacylglycerol and three uncharacterized phospholipids. The level of DNA–DNA relatedness between strain sw-2T and Roseivivax halodurans Och 239T was only 15.0 %. The results of physiological and biochemical tests allowed the clear phenotypic differentiation of the novel strain from all established species of the genus Roseivivax . Based on the genotypic, phenotypic and chemotaxonomic data, strain sw-2T represents a novel species in the genus Roseivivax , for which the name Roseivivax isoporae sp. nov. is proposed. The type strain is sw-2T ( = LMG 25204T = BCRC 17966T).
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Skermanella stibiiresistens sp. nov., a highly antimony-resistant bacterium isolated from coal-mining soil, and emended description of the genus Skermanella
More LessA Gram-negative, aerobic, motile, rod-shaped, antimony-resistant bacterium, designated strain SB22T, was isolated from soil of Jixi coal mine, China. The major cellular fatty acids (>5 %) were C18 : 1ω7c (63.5 %), summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1 I, 10.8 %) and C16 : 0 (9.9 %). The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unknown aminolipid. The genomic DNA G+C content was 69.6 mol% and Q-10 was the major respiratory quinone. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain SB22T was most closely related to Skermanella aerolata 5416T-32T (97.3 %), Skermanella parooensis ACM 2042T (95.8 %) and Skermanella xinjiangensis 10-1-101T (92.9 %). The DNA–DNA hybridization value between strain SB22T and S. aerolata KACC 11604T ( = 5416T-32T) was 43.3 %. On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics of strain SB22T and related species, it is considered that the isolate represents a novel species of the genus Skermanella , for which the name Skermanella stibiiresistens sp. nov. is proposed. The type strain is SB22T ( = CGMCC 1.10751T = KCTC 23364T). An emended description of the genus Skermanella is provided.
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Cronobacter condimenti sp. nov., isolated from spiced meat, and Cronobacter universalis sp. nov., a species designation for Cronobacter sp. genomospecies 1, recovered from a leg infection, water and food ingredients
A re-evaluation of the taxonomic position of five strains, one assigned to Cronobacter sakazakii (strain 1330T, isolated from spiced meat purchased in Slovakia), two previously assigned to Cronobacter genomospecies 1 (strains NCTC 9529T and 731, isolated from water and a leg infection, respectively) and two previously assigned to Cronobacter turicensis (strains 96 and 1435, isolated from onion powder and rye flour, respectively) was carried out. The analysis included phenotypic characterization, 16S rRNA gene sequencing and multilocus sequence analysis (MLSA) of seven housekeeping genes (atpD, fusA, glnS, gltB, gyrB, infB, ppsA; 3036 bp). 16S rRNA gene sequence analysis and MLSA showed that strain 1330T formed an independent phylogenetic lineage in the MLSA, with Cronobacter dublinensis LMG 23823T as the closest neighbour. DNA–DNA reassociation and phenotypic analysis revealed that strain 1330T represented a novel species, for which the name Cronobacter condimenti sp. nov. is proposed (type strain 1330T = CECT 7863T = LMG 26250T). Strains NCTC 9529T, 731, 96 and 1435 clustered together within an independent phylogenetic lineage, with C. turicensis LMG 23827T as the closest neighbour in the MLSA. DNA–DNA reassociation and phenotypic analysis confirmed that these strains represent a novel species, for which the name Cronobacter universalis sp. nov. is proposed (type strain NCTC 9529T = CECT 7864T = LMG 26249T).
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Herbaspirillum canariense sp. nov., Herbaspirillum aurantiacum sp. nov. and Herbaspirillum soli sp. nov., isolated from volcanic mountain soil, and emended description of the genus Herbaspirillum
Three Gram-negative, motile and slightly curved rod-shaped bacteria, strains SUEMI03T, SUEMI08T and SUEMI10T, were isolated from an old volcanic mountain soil on Tenerife (Canary Islands). The three strains were related phylogenetically to Herbaspirillum seropedicae . 16S rRNA gene sequence similarity was 99.2–99.6 % among strains SUEMI03T, SUEMI08T and SUEMI10T, which presented 97.5, 97.8 and 97.7 % identity, respectively, with respect to H. seropedicae DSM 6445T. The three strains grew optimally in TSB at 28 °C and contained summed features 3 (C16 : 1ω6c and/or C16 : 1ω7c) and 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C16 : 0 as major cellular fatty acids. The DNA G+C contents of strains SUEMI03T, SUEMI08T and SUEMI10T were 61.6, 60.4 and 61.9 mol%, respectively. Strains SUEMI03T, SUEMI08T and SUEMI10T presented less than 60 % interstrain DNA relatedness and less than 30 % relatedness with respect to H. seropedicae DSM 6445T. In spite of their common geographical origin, the three strains isolated in this study presented several phenotypic differences, presenting phenotypic profiles highly divergent from that of H. seropedicae . Therefore, we propose that the strains isolated in this study represent three novel species of the genus Herbaspirillum , named Herbaspirillum canariense sp. nov. (type strain SUEMI03T = LMG 26151T = CECT 7838T), Herbaspirillum aurantiacum sp. nov. (type strain SUEMI08T = LMG 26150T = CECT 7839T) and Herbaspirillum soli sp. nov. (type strain SUEMI10T = LMG 26149T = CECT 7840T).
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Sphingomicrobium lutaoense gen. nov., sp. nov., isolated from a coastal hot spring
A yellowish pigmented, Gram-negative, rod-shaped, non-spore-forming bacterium (strain CC-TBT-3T), was isolated on marine agar 2216 from a coastal hot spring of Green Island (Lutao), located off Taituang, Taiwan. 16S rRNA gene sequence analysis of strain CC-TBT-3T showed a relatively low similarity (<95.5 %) to representatives of the genera Novosphingobium , Sphingosinicella and Sphingomonas of the Sphingomonadaceae , with the most related strain being the type strain of Novosphingobium soli . In addition to the relatively low 16S rRNA gene sequence similarity to members of established species, the isolate also showed some unique chemotaxonomic features, including the presence of some glycolipids with unusual chromatographic behaviour. The major components of the polar lipid profile were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and three unidentified glycolipids. The major respiratory quinone was ubiquinone Q-10. The polyamine pattern was characterized by the triamine sym-homospermidine as a major component. Although the predominant fatty acids were C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), the isolate did not show the typical hydroxyl fatty acids, such as C14 : 0 2-OH, C15 : 0 2-OH and C16 : 0 2-OH, found in members of the genera Novosphingobium , Sphingomonas and Sphingosinicella , but showed instead high amounts of C18 : 1 2-OH (12.0 %). The DNA G+C content of strain CC-TBT-3T was 63.4 mol%. 16S rRNA gene sequence, chemotaxonomic and physiological analyses revealed that strain CC-TBT-3T represents a novel species in a new genus in the family Sphingomonadaceae for which the name Sphingomicrobium lutaoense gen. nov., sp. nov. is proposed; the type strain is of the type species S. lutoaense, CC-TBT-3T ( = DSM 24194T = CCM 7794T).
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Burkholderia zhejiangensis sp. nov., a methyl-parathion-degrading bacterium isolated from a wastewater-treatment system
More LessThe taxonomic status of a methyl-parathion-degrading strain, OP-1T, isolated from a wastewater-treatment system in China, was determined using a polyphasic approach. The rod-shaped cells were Gram-staining-negative, non-spore-forming and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel strain belonged to the genus Burkholderia , as it appeared closely related to Burkholderia glathei ATCC 29195T (97.4 % sequence similarity), Burkholderia sordidicola KCTC 12081T (96.5 %) and Burkholderia bryophila LMG 23644T (96.3 %). The major cellular fatty acids, C16 : 0, C17 : 0 cyclo and C18 : 1ω7c, were also similar to those found in established members of the genus Burkholderia . The genomic DNA G+C content of strain OP-1T was 59.4 mol%. The level of DNA–DNA relatedness between the novel strain and the closest recognized species, Burkholderia glathei ATCC 29195T, was only 30 %. Based on the phenotypic, genotypic and phylogenetic evidence, strain OP-1T represents a novel species of the genus Burkholderia , for which the name Burkholderia zhejiangensis sp. nov. is proposed. The type strain is OP-1T ( = CCTCC AB 2010354T = KCTC 23300T).
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Erythrobacter pelagi sp. nov., a member of the family Erythrobacteraceae isolated from the Red Sea
More LessA novel Gram-negative, aerobic, catalase- and oxidase-positive, non-sporulating, non-motile, rod-shaped bacterium, designated strain UST081027-248T, was isolated from seawater of the Red Sea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain UST081027-248T fell within the genus Erythrobacter . Levels of 16S rRNA gene sequence similarity between the novel strain and the type strains of Erythrobacter species ranged from 95.3 % (with Erythrobacter gangjinensis ) to 98.2 % (with Erythrobacter citreus ). However, levels of DNA–DNA relatedness between strain UST081027-248T and the type strains of closely related species were below 70 %. Optimal growth of the isolate occurred in the presence of 2.0 % NaCl, at pH 8.0–9.0 and at 28–36 °C. The isolate did not produce bacteriochlorophyll a. The predominant cellular fatty acids were C17 : 1ω6c, summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C15 : 0 2-OH. The genomic DNA G+C content of strain UST081027-248T was 60.4 mol%. Phenotypic properties and phylogenetic distinctiveness clearly indicated that strain UST081027-248T represents a novel species of the genus Erythrobacter , for which the name Erythrobacter pelagi sp. nov. is proposed. The type strain is UST081027-248T ( = JCM 17468T = NRRL 59511T).
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Celeribacter baekdonensis sp. nov., isolated from seawater, and emended description of the genus Celeribacter Ivanova et al. 2010
More LessA Gram-stain-negative, non-motile, ovoid or rod-shaped bacterial strain, designated L-6T, was isolated from seawater of Baekdo harbour of the East Sea in Korea and its taxonomic position was investigated by using a polyphasic study. Strain L-6T grew optimally at 30 °C, at pH 7.5–8.0 and in the presence of 2 % (w/v) NaCl. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain L-6T formed a cluster with the type strain of Celeribacter neptunius at a bootstrap resampling value of 100 %. Strain L-6T exhibited 16S rRNA gene sequence similarity values of 97.7 % to C. neptunius H 14T and of less than 96.2 % to the type strains of other species used in the phylogenetic analysis. The G+C content of the chromosomal DNA of strain L-6T was 60.9 mol%. The predominant ubiquinone found in strain L-6T and C. neptunius CIP 109922T was ubiquinone-10 (Q-10). The predominant fatty acid of strain L-6T and C. neptunius CIP 109922T was C18 : 1ω7c. The major polar lipids of strain L-6T were phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. The mean level of DNA–DNA relatedness between strain L-6T and C. neptunius CIP 109922T was 17 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, demonstrated that strain L-6T is distinguishable from C. neptunius . On the basis of the data presented, strain L-6T is considered to represent a novel species of the genus Celeribacter , for which the name Celeribacter baekdonensis sp. nov. is proposed. The type strain is L-6T ( = KCTC 23497T = CCUG 60799T).
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Classification of Pasteurella species B as Pasteurella oralis sp. nov.
More LessPasteurella species B has so far only been reported from the oral cavity of dogs, cats and a ferret. In the present study, information from 15 recent isolates from different sources, including African hedgehogs (Atelerix albiventris), banded mongoose (Mungos mungo), Moholi bushbabies (Galago moholi) and pneumonia of a cat, were compared to five strains investigated previously from bite wounds in humans inflicted by a cat and dog and from gingiva of a cat. rpoB gene sequence comparison showed that 17 isolates, including the reference strain (CCUG 19794T), had identical sequences, whereas two were closely related and demonstrated 97.9 and 99.6 % similarity to strain CCUG 19794T, respectively; the type strain of Pasteurella stomatis was the most closely related strain, with 92.3 % similarity. This is within the mean range (76–100 %) of rpoB gene sequence similarity between species of the same genus within the family Pasteurellaceae . 16S rRNA gene sequencing of four strains selected based on rpoB sequence comparison showed at least 99.7 % similarity between strains of Pasteurella species B, with 96.2 % similarity to the type strain of the closest related species ( Pasteurella canis ), indicating that Pasteurella species B should have separate species status. Separate species status was also documented when recN sequence comparisons were converted to a genome similarity of 93.7 % within Pasteurella species B and 59.0 % to the type strain of the closest related species ( P. canis ). Based on analysis of the phylogenetic and phenotypic data, and since most isolates originate from the oral cavities of a diverse group of animals, it is suggested that these bacteria be classified as Pasteurella oralis sp. nov.; the type strain is P683T ( = CCUG 19794T = CCM 7950T = strain 23193T = MCCM 00102T), obtained from a cat. Previous reports of the type strain have shown ubiquinone-8, demethylmenaquinone-8 and menaquinone-8 as the major quinones. Polyamines in the type strain were reported as diaminopropane, putrescine, cadaverine, sym-norspermidine, spermidine and spermine in a previous investigation, and the major fatty acids of the type strain were reported to be C16 : 0, C16 : 1ω7c and C14 : 0, with minor amounts of C18 : 0 and C18 : 1ω9c. The DNA G+C content of the type strain has been reported to be 40.0 mol%.
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- Bacteroidetes
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Bacteroides sartorii is an earlier heterotypic synonym of Bacteroides chinchillae and has priority
More LessStrains of the recently proposed species Bacteroides chinchillae share more than 99.4 % 16S rRNA gene sequence similarity with the type strain of Bacteroides sartorii although these two species do not appear to be similar from their published descriptions. The aim of this study was to perform phenotypic and genetic analyses of both species to clarify their taxonomic position. B. chinchillae JCM 16497T exhibited high hsp60 gene sequence similarity with B. sartorii JCM 17136T (100 %) as well as B. chinchillae JCM 16498 (100 %). The hsp60 gene sequence analysis and levels of DNA–DNA relatedness observed demonstrated B. sartorii JCM 17136T, B. chinchillae JCM 16497T, and B. chinchillae JCM 16498 are members of a single species. Based on these data, we propose Bacteroides chinchillae as a later heterotypic synonym of Bacteroides sartorii . An emended description of B. sartorii is provided.
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Cellulophaga geojensis sp. nov., a member of the family Flavobacteriaceae isolated from marine sand
More LessA Gram-stain-negative, aerobic, non-flagellated, non-spore-forming, motile (by gliding) bacterial strain, designated M-M6T, was isolated from marine sand of Geoje island, Korea. Strain M-M6T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain M-M6T fell within the clade comprising Cellulophaga species, forming a coherent cluster with Cellulophaga lytica ATCC 23178T and Cellulophaga fucicola NN015860T, with which it shared 16S rRNA gene sequence similarities of 98.1 and 98.2 %, respectively. Sequence similarities between strain M-M6T and the type strains of other recognized Cellulophaga species were in the range 92.4–93.8 %. Strain M-M6T contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, and C16 : 1ω7c and/or iso-C15 : 0 2-OH as the major fatty acids. The major polar lipids detected in strain M-M6T and the type strains of C. lytica and C. fucicola were two unidentified lipids, one unidentified aminolipid and one unidentified aminophospholipid. The DNA G+C content of strain M-M6T was 35.4 mol%. Levels of DNA–DNA relatedness between strain M-M6T and C. lytica JCM 8516T and C. fucicola JCM 21778T were 33 and 35 %, respectively. Differential phenotypic properties and phylogenetic and genetic distinctiveness distinguished strain M-M6T from all recognized Cellulophaga species. On the basis of the data presented, strain M-M6T is considered to represent a novel species of the genus Cellulophaga , for which the name Cellulophaga geojensis sp. nov. is proposed. The type strain is M-M6T ( = KCTC 23498T = CCUG 60801T).
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Flavobacterium chilense sp. nov. and Flavobacterium araucananum sp. nov., isolated from farmed salmonid fish
More LessThree Gram-staining-negative non-endospore-forming strains were isolated from farmed fish in Chile: one (LM-09-FpT) from a rainbow trout (Oncorhynchus mykiss) and the others (LM-19-FpT and LM-20-Fp) from two Atlantic salmon (Salmo salar). Phylogenetic analyses based on 16S rRNA gene sequences indicated that all three isolates belonged to the genus Flavobacterium . In these analyses, strain LM-09-FpT appeared most closely related to the type strains of Flavobacterium chungangense (98.5 % sequence similarity), Flavobacterium glaciei (98.2 %), Flavobacterium aquidurense (97.6 %), Flavobacterium saccharophilum (97.6 %) and Flavobacterium hercynium (97.6 %). The 16S rRNA gene sequences of strains LM-19-FpT and LM-20-Fp were found to be identical and most similar to the corresponding sequences of the type strains of Flavobacterium aquidurense (98.6 %), Flavobacterium frigidimaris (98.5 %), Flavobacterium hercynium (97.9 %), Flavobacterium saccharophilum (97.7 %) and Flavobacterium pectinovorum (97.7 %). For each of the three novel strains, menaquinone (MK-6) was the predominant respiratory quinone and the major compounds in the polar lipid profile were phosphatidylethanolamine, an unidentified aminolipid, phosphatidylserine and two or three unknown lipids. The fatty acid profile of each strain, which comprised major amounts of iso-C15 : 0, C15 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) as well as smaller amounts of various hydroxylated fatty acids (e.g. iso-C16 : 0 3-OH, iso-C17 : 0 3-OH, C16 : 0 3-OH and C15 : 0 3-OH), indicated that each belonged to the genus Flavobacterium . Based on their physiological and biochemical characteristics and the results of DNA–DNA hybridizations, which showed relatively low levels of relatedness between the novel strains and the most closely related Flavobacterium species, strain LM-09-FpT ( = LMG 26360T = CCM 7940T) represents a novel species within the genus Flavobacterium , for which the name Flavobacterium chilense sp. nov. is proposed, and strains LM-19-FpT ( = LMG 26359T = CCM 7939T) and LM-20-Fp ( = LMG 26331) represent a second novel species within the same genus, for which the name Flavobacterium araucananum sp. nov. is proposed.
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- Other Bacteria
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Deinococcus daejeonensis sp. nov., isolated from sludge in a sewage disposal plant
More LessA Gram-stain-positive, strictly aerobic, spherical, non-motile red-pigmented bacterial strain, designated MJ27T, was isolated from a sludge sample of the Daejeon sewage disposal plant in South Korea. A polyphasic approach was used to study the taxonomic position of strain MJ27T. Strain MJ27T shared highest 16S rRNA gene sequence similarity with Deinococcus grandis DSM 3963T (98.8 %), Deinococcus caeni Ho-08T (97.5 %) and Deinococcus aquaticus PB314T (96.6 %.); levels of sequence similarity with the type strains of other Deinococcus species were less than 96.0 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MJ27T belonged to the clade formed by members of the genus Deinococcus in the family Deinococcaceae . The G+C content of the genomic DNA of strain MJ27T was 67.6 mol%. The chemotaxonomic characteristics of strain MJ27T were typical of members of the genus Deinococcus , with MK-8 as the predominant respiratory quinone, C16 : 1ω7c, C15 : 1ω6c, C16 : 0 and C15 : 0 as major fatty acids (>12 %), ornithine as the diamino acid in the cell-wall peptidoglycan and resistance to gamma radiation [D10 (dose required to reduce the bacterial population by tenfold) >9 kGy]. The low levels of DNA–DNA relatedness reported here (5.3±1.5–29.2±2.3 %) indicate that strain MJ27T represents a species that is separate from its closest relatives in the genus Deinococcus . On the basis of phylogenetic inference, fatty acid profile and other phenotypic properties, strain MJ27T is considered to represent a novel species of the genus Deinococcus , for which the name Deinococcus daejeonensis sp. nov. is proposed. The type strain is MJ27T ( = KCTC 13751T = JCM 16918T).
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Mycoplasma neophronis sp. nov., isolated from the upper respiratory tract of Canarian Egyptian vultures (Neophron percnopterus majorensis)
Six strains with the typical characteristics of mycoplasmas were isolated from the tracheae of six Canarian Egyptian vultures (Neophron percnopterus majorensis). The results of biochemical, serological and molecular genetic studies showed that the isolates were nearly identical and that they could be considered as representing a novel species of the genus Mycoplasma . Colonies possessed the typical fried-egg appearance and electron micrographs revealed a pleomorphic cellular morphology with the lack of a cell wall. The isolates hydrolysed arginine and required sterol for growth but did not ferment glucose or hydrolyse urea. We propose that the isolates be assigned to a novel species,Mycoplasma neophronis sp. nov. The type strain is G.A.T ( = DSM 24097T = ATCC BAA-2157T). The antiserum of strain G.A.T has been deposited in the Mollicutes collection at Purdue University (Indiana, USA).
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Defluviitoga tunisiensis gen. nov., sp. nov., a thermophilic bacterium isolated from a mesothermic and anaerobic whey digester
More LessStrain SulfLac1T, a thermophilic, anaerobic and slightly halophilic, rod-shaped bacterium with a sheath-like outer structure (toga), was isolated from a whey digester in Tunisia. The strain’s non-motile cells measured 3–30×1 µm and appeared singly, in pairs or as long chains. The novel strain reduced thiosulfate and elemental sulfur, but not sulfate or sulfite, into sulfide. It grew at 37–65 °C (optimum 55 °C), at pH 6.5–7.9 (optimum pH 6.9) and with 0.2–3 % (w/v) NaCl (optimum 0.5 %). The G+C content of the strain’s genomic DNA was 33.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SulfLac1T was most closely related to Petrotoga mobilis (91.4 % sequence similarity). Based on phenotypic, phylogenetic and chemotaxonomic evidence, strain SulfLac1T represents a novel species of a new genus within the order Thermotogales , for which the name Defluviitoga tunisiensis gen. nov., sp. nov. is proposed. The type strain of the type species is SulfLac1T ( = DSM 23805T = JCM 17210T).
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- Eukaryotic Micro-organisms
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Class Cariacotrichea, a novel ciliate taxon from the anoxic Cariaco Basin, Venezuela
The majority of environmental micro-organisms identified with the rRNA approach have never been visualized. Thus, their reliable classification and taxonomic assignment is often difficult or even impossible. In our preliminary 18S rRNA gene sequencing work from the world’s largest anoxic marine environment, the Cariaco Basin (Caribbean Sea, Venezuela), we detected a ciliate clade, designated previously as CAR_H [Stoeck, S., Taylor, G. T. & Epstein, S. S. (2003). Appl Environ Microbiol 63, 5656–5663]. Here, we combine the traditional rRNA detection method of fluorescent in situ hybridization (FISH) with scanning electron microscopy (SEM) and confirm the phylogenetic separation of the CAR_H sequences from all other ciliate classes by showing an outstanding morphological feature of this group: a unique, archway-shaped kinety surrounding the oral apparatus and extending to the posterior body end in CAR_H cells. Based on this specific feature and the molecular phylogenies, we propose a novel ciliate class, Cariacotrichea nov. cl.
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Kloeckera taiwanica sp. nov., an ascomycetous apiculate yeast species isolated from mushroom fruiting bodies
More LessThree apiculate yeast strains, EJ7M09T, GJ5M15 and GJ15M04, isolated from mushrooms in Taiwan were found to represent a novel species of the genus Kloeckera. The phylogenetically closest relative of this novel species is Hanseniaspora occidentalis, but the type strain of H. occidentalis differed by 4.6 % divergence (25 substitutions; 5 gaps) in the sequence of the D1/D2 domain of the large subunit rRNA gene. This difference clearly suggests that the three strains represent a distinct species. As none of the strains that were examined in this study produced ascospores or exhibited conjugation on common sporulation medium either alone or in a pairwise mixture, this species could be considered as an anamorphic member of the genus Hanseniaspora, and a novel species, Kloeckera taiwanica sp. nov., is proposed, with EJ7M09T ( = BCRC 23182T = CBS 11434T) as the type strain.
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Candida amazonensis sp. nov., an ascomycetous yeast isolated from rotting wood in the Amazonian forest
Five strains of a novel yeast species were isolated from rotting wood samples collected in an Amazonian forest site in the state of Roraima, northern Brazil. The sequences of the D1/D2 domains of the large subunit of the rRNA gene showed that this species belongs to the Scheffersomyces clade and is related to Candida coipomoensis, Candida lignicola and Candida queiroziae. The novel species Candida amazonensis sp. nov. is proposed to accommodate these isolates. The type strain of C. amazonensis sp. nov. is UFMG-HMD-26.3T ( = CBS 12363T = NRRL Y-48762T).
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- Evolution, Phylogeny and Biodiversity
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Phylogenetic analysis of Xanthomonas based on partial rpoB gene sequences and species differentiation by PCR-RFLP
More LessThe rpoB gene was evaluated as an alternative molecular marker for the differentiation of Xanthomonas species and in order to understand better the phylogenetic relationships within the genus. PCR-RFLP experiments using HaeIII allowed differentiation of Xanthomonas species, particularly those that affect the same plant host such as Xanthomonas albilineans and X. sacchari , pathogenic to sugar cane, Xanthomonas cucurbitae and X. melonis , which cause disease in melon, and Xanthomonas gardneri , X. vesicatoria and X. euvesicatoria / X. perforans , pathogenic to tomato. Phylogenetic relationships within the genus Xanthomonas were also examined by comparing partial rpoB gene sequences (612 nt) and the Xanthomonas species were separated into two main groups. Group I, well supported by bootstrap values of 99 %, comprised X. euvesicatoria , X. perforans , X. alfalfae , X. citri , X. dyei , X. axonopodis , X. oryzae , X. hortorum , X. bromi , X. vasicola , X. cynarae , X. gardneri , X. campestris , X. fragariae , X. arboricola , X. cassavae , X. cucurbitae , X. pisi , X. vesicatoria , X. codiaei and X. melonis . Group II, again well supported by bootstrap values of 99 %, comprised X. albilineans , X. sacchari , X. theicola , X. translucens and X. hyacinthi . The rpoB gene sequence similarity observed among the species in this study ranged from 87.8 to 99.7 %. The results of PCR-RFLP of the rpoB gene indicated that this technique can be used for diagnosis and identification of most Xanthomonas strains, including closely related species within the genus. However, species that showed identical profiles could be differentiated clearly only by sequence analysis. The results obtained in our phylogenetic analysis suggested that the rpoB gene can be used as an alternative molecular marker for genetic relatedness in the genus Xanthomonas . The results of PCR-RFLP of the rpoB gene indicate that this technique can be used for diagnosis and identification of closely related species within the genus, representing a rapid and inexpensive tool that can be easily standardized between laboratories.
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- Errata
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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Volume 66 (2016)
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Volume 65 (2015)
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Volume 64 (2014)
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Volume 63 (2013)
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Volume 62 (2012)
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Volume 61 (2011)
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Volume 60 (2010)
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Volume 59 (2009)
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Volume 58 (2008)
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Volume 57 (2007)
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Volume 56 (2006)
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Volume 55 (2005)
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Volume 54 (2004)
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Volume 53 (2003)
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Volume 52 (2002)
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Volume 51 (2001)
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Volume 50 (2000)
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Volume 49 (1999)
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Volume 48 (1998)
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Volume 47 (1997)
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Volume 46 (1996)
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Volume 45 (1995)
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Volume 44 (1994)
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Volume 43 (1993)
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Volume 42 (1992)
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Volume 41 (1991)
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Volume 40 (1990)
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Volume 39 (1989)
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Volume 38 (1988)
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Volume 37 (1987)
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Volume 36 (1986)
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Volume 35 (1985)
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Volume 34 (1984)
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Volume 33 (1983)
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Volume 32 (1982)
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Volume 31 (1981)
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Volume 30 (1980)
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Volume 29 (1979)
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Volume 28 (1978)
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Volume 27 (1977)
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Volume 26 (1976)
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Volume 25 (1975)
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Volume 24 (1974)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 20 (1970)
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Volume 19 (1969)
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Volume 18 (1968)
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Volume 17 (1967)
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Volume 16 (1966)
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Volume 15 (1965)
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Volume 14 (1964)
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Volume 13 (1963)
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Volume 12 (1962)
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Volume 11 (1961)
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Volume 10 (1960)
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Volume 9 (1959)
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Volume 8 (1958)
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Volume 7 (1957)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)