- Volume 59, Issue 10, 2009
Volume 59, Issue 10, 2009
- Notification List
-
-
-
Notification that new names and new combinations have appeared in volume 59, part 7, 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.
-
-
- New Taxa
-
- Actinobacteria
-
-
Micrococcus yunnanensis sp. nov., a novel actinobacterium isolated from surface-sterilized Polyspora axillaris roots
In this study, strain YIM 65004T, isolated from roots of Polyspora axillaris, was shown to represent a novel species of the genus Micrococcus by means of a polyphasic approach. Chemotaxonomic data gathered for peptidoglycan type, menaquinones, phospholipids and fatty acids strongly supported the classification of this strain within the genus Micrococcus: the cell-wall peptidoglycan contained lysine, glutamic acid, alanine, glycine and aspartic acid, the predominant menaquinones were MK-8(H2) (66.97 %) and MK-7(H2) (23.26 %), the phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unknown ninhydrin-negative phospholipid, and the major cellular fatty acids were anteiso-C15 : 0 (61.98 %), iso-C16 : 0 (14.25 %) and iso-C15 : 0 (13.04 %). The G+C content of the genomic DNA was 71.7 mol%. A number of physiological features were found that clearly distinguished strain YIM 65004T from recognized Micrococcus species. DNA–DNA hybridization studies suggested that the novel strain represents a separate genomic species. Based on the above data, a novel species of the genus Micrococcus, Micrococcus yunnanensis sp. nov., is proposed, with the type strain YIM 65004T (=CCTCC AA 208060T=DSM 21948T).
-
-
-
Nocardia iowensis sp. nov., an organism rich in biocatalytically important enzymes and nitric oxide synthase
Nocardia strain NRRL 5646, isolated from a garden soil sample in Osceola, Iowa, USA, was initially of interest as an antibiotic producer. It contained biocatalytically important enzymes and represented the first described nitric oxide synthase enzyme system in bacteria. The present polyphasic taxonomic study was undertaken to differentiate strain NRRL 5646T from related species of the genus Nocardia. Chemotaxonomic analyses included determinations of the fatty acid methyl ester profile (C16 : 1 ω6c/C16 : 1 ω7c, C16 : 0, C18 : 1 ω9c and C18 : 0 10-methyl as major components), quinone [cyclo MK-8(H4) as the major component], polar lipid (diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside as major components) and mycolic acid. These results supported its placement within the genus Nocardia. Biochemical testing and 16S rRNA, 65-kDa heat-shock protein (hsp65) and preprotein translocase (secA1) gene sequence analyses differentiated strain NRRL 5646T from recognized Nocardia species. Previous studies have demonstrated that other genetic sequences (carboxylic acid reductase, Nocardia phosphopantetheinyl transferase and GTP cyclohydrolase I) from strain NRRL 5646T can also be used to substantiate its uniqueness. The level of 16S rRNA gene sequence similarity between strain NRRL 5646T and the type strains of Nocardia tenerifensis and Nocardia brasiliensis was 98.8 %. However, strain NRRL 5646T could be clearly distinguished from these Nocardia species based on DNA–DNA hybridization data. Consequently, strain NRRL 5646T is considered to represent a novel species of the genus Nocardia, for which the name Nocardia iowensis sp. nov. is proposed. The type strain is NRRL 5646T (=UI 122540T=NRRL B-24671T=DSM 45197T).
-
-
-
Nocardioides terrae sp. nov., isolated from forest soil
More LessBacterial strain VA15T was isolated from forest soil of the Changbai Mountains, Heilongjiang Province, China. Cells of strain VA15T were Gram-positive-staining, 0.2–0.3 μm in diameter and 0.3–1.0 μm long, strictly aerobic, non-motile and rod-shaped or coccoid. Growth occurred at 16–34 °C (optimum, 29 °C), at pH 5.5–8.5 (optimum, pH 6.2–6.5) and in the presence of 0–1 % (w/v) NaCl (optimum, 0–0.25 %). Strain VA15T contained MK-8(H4) as the major respiratory quinone and ll-2,6-diaminopimelic acid as the cell-wall diamino acid. The major cellular fatty acids were iso-C16 : 0 (18.1 % of the total), 10-methyl C18 : 0 (11.8 %) and 10-methyl C17 : 0 (10.7 %). The DNA G+C content of strain VA15T was 71.6 mol% (T m). 16S rRNA gene sequence analysis indicated that strain VA15T was phylogenetically related to members of the genus Nocardioides; levels of similarity to the type strains of recognized Nocardioides species ranged from 92.9 to 97.7 %. Levels of DNA–DNA relatedness between strain VA15T and its closest phylogenetic relatives, Nocardioides panacihumi DSM 18660T and Nocardioides marinus DSM 18248T, were 21 and 16 %, respectively. Based on these results, it is concluded that strain VA15T represents a novel species of the genus Nocardioides, for which the name Nocardioides terrae sp. nov. is proposed. The type strain is VA15T (=CGMCC 1.7056T =NBRC 104259T).
-
-
-
Pseudonocardia parietis sp. nov., from the indoor environment
More LessA Gram-positive, rod-shaped, non-endospore-forming, mycelium-forming actinobacterium (04-St-002T) was isolated from the wall of an indoor environment colonized with moulds. On the basis of 16S rRNA gene sequence similarity studies, strain 04-St-002T was shown to belong to the family Pseudonocardiaceae, and to be most closely related to Pseudonocardia antarctica (99.2 %) and Pseudonocardia alni (99.1 %). The major menaquinones were MK-8(H4) and MK-8(H2), the phospholipid type was PIII, and the polar lipid profile consisted of the major lipids diphosphatidylglycerol, phosphatidylmonomethylethanolamine and phosphatidylcholine. Moderate amounts of phosphatidylglycerol and an unknown polar lipid, L1, small or trace amounts of phosphatidylinositol, phosphatidylinositol-mannoside, three unknown lipids, two unknown phospholipids and four unknown glycolipids were also detected. The major fatty acids iso-C16 : 0, iso-C16 : 1, C16 : 0 and C16 : 1 ω7c supported the affiliation of strain 04-St-002T to the genus Pseudonocardia. The results of DNA–DNA hybridization, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 04-St-002T from the two most closely related species, P. alni and P. antarctica. Strain 04-St-002T represents a novel species, for which the name Pseudonocardia parietis sp. nov. is proposed. The type strain is 04-St-002T (=DSM 45256T=CCM 7582T).
-
-
-
Actinomadura flavalba sp. nov., an endophytic actinomycete isolated from leaves of Maytenus austroyunnanensis
More LessAn actinomycete strain, designated YIM 61435T, was isolated from leaves of Maytenus austroyunnanensis collected from a tropical rainforest in Xishuangbanna, Yunnan Province, south-west China. The isolate produced aerial mycelium with long, curved to hooked spore chains. The chemotaxonomic characteristics of the isolate were consistent with its assignment to the genus Actinomadura. Phylogenetic analysis using 16S rRNA gene sequences also indicated that this strain should be classified in the genus Actinomadura; however, it could be separated clearly from its closest neighbour, Actinomadura atramentaria DSM 43919T. Furthermore, a combination of DNA–DNA hybridization results and significant differences in morphological and physiological characteristics indicate that strain YIM 61435T represents a novel species of the genus Actinomadura, for which the name Actinomadura flavalba sp. nov. is proposed. The type strain is YIM 61435T (=DSM 45200T =CCTCC AA 208017T).
-
-
-
Corynebacterium maris sp. nov., a marine bacterium isolated from the mucus of the coral Fungia granulosa
More LessA bacterial strain, designated Coryn-1T, was isolated from mucus of the coral Fungia granulosa (northern Red Sea, Gulf of Eilat, Israel) by growth and enrichment of micro-organisms in agar spheres and subsequent plating. The bacterium was found to be a Gram-positive, non-motile, halotolerant, heterotrophic coccobacillus. Comparative 16S rRNA gene sequence analyses showed that strain Coryn-1T belonged to the genus Corynebacterium, exhibiting the highest levels of similarity (94 %) with the 16S rRNA gene sequence of Corynebacterium halotolerans YIM 70093T. The novel strain grew well at 0.5–4.0 % salinity, at pH 7.2–9.0 and at 30–37 °C. The major cellular fatty acids were oleic acid (C18 : 1 ω9c; 58 %), palmitic acid (C16 : 0; 30 %) and tuberculostearic acid (10-methyl-C18 : 0; 12 %). The DNA G+C content was 66.6 mol%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Coryn-1T represents a novel species, for which the name Corynebacterium maris sp. nov. is proposed. The type strain is Coryn-1T (=DSM 45190T=LMG 24561T).
-
-
-
Streptomonospora amylolytica sp. nov. and Streptomonospora flavalba sp. nov., two novel halophilic actinomycetes isolated from a salt lake
More LessTwo novel halophilic, aerobic, catalase-positive but oxidase-negative, Gram-positive actinomycetes, designated YIM 91353T and YIM 91394T, were isolated from a salt lake in the north-west of China. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the novel isolates should be assigned to the genus Streptomonospora. The phenotypic and chemotaxonomic characteristics of the isolates also matched those described for members of the genus Streptomonospora. The predominant menaquinones were MK-10(H8), MK-10(H6) and MK-9(H8), and meso-diaminopimelic acid was the diagnostic amino acid in the cell walls. The phospholipids of the isolates consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The major fatty acids of strain YIM 91353T were anteiso-C17 : 0 and C18 : 0, and of strain YIM 91394T were anteiso-C17 : 0 and iso-C16 : 0. The DNA G+C contents were 71.2 and 72.5 mol%, respectively. The combination of phylogenetic analysis, DNA–DNA hybridization data, phenotypic characteristics and chemotaxonomic differences supported the view that strains YIM 91353T and YIM 91394T each represent a novel species of the genus Streptomonospora, for which the names Streptomonospora amylolytica sp. nov. and Streptomonospora flavalba sp. nov. are proposed, with type strains YIM 91353T (=DSM 45171T=CCTCC AA 208048T) and YIM 91394T (=DSM 45155T=CCTCC AA 208047T), respectively.
-
-
-
Plantactinospora mayteni gen. nov., sp. nov., a member of the family Micromonosporaceae
More LessA novel Gram-positive, aerobic, spore-forming, endophytic actinomycete, designated strain YIM 61359T, was isolated from the roots of Maytenus austroyunnanensis plants collected from tropical rainforest in Xishuangbanna, Yunnan Province, south-west China. The strain formed single or cluster spores with smooth surfaces from substrate mycelia. The strain contained meso-diaminopimelic acid in the cell wall and arabinose, xylose, galactose and glucose in whole-cell hydrolysates. The acyl type of the cell-wall polysaccharides was glycolyl. MK-10(H6), MK-10(H8) and MK-10(H4) were the predominant menaquinones. The polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol and several unknown phospholipids. The major fatty acids were iso-C15 : 0, anteiso-C15 : 0, C17 : 0, anteiso-C17 : 0 and iso-C16 : 0. The DNA G+C content of strain YIM 61359T was 69.7 mol%. These chemotaxonomic data indicated that the strain belongs to the family Micromonosporaceae. Phylogenetic analysis based on 16S rRNA gene sequences also suggested that strain YIM 61359T fell within the family Micromonosporaceae. On the basis of morphological and chemotaxonomic data, phylogenetic analysis and characteristic patterns of 16S rRNA gene signature nucleotides, strain YIM 61359T is considered to represent a novel species of a new genus within the family Micromonosporaceae, for which the name Plantactinospora mayteni gen. nov., sp. nov. is proposed. The type strain of Plantactinospora mayteni is YIM 61359T (=CCTCC AA 208022T=DSM 45238T).
-
-
-
Streptomyces avicenniae sp. nov., a novel actinomycete isolated from the rhizosphere of the mangrove plant Avicennia mariana
More LessA novel isolate, designated strain MCCC 1A01535T, belonging to the genus Streptomyces was isolated from the rhizosphere of the mangrove plant Avicennia mariana from Fujian Province, south China. Characterization of the isolate was based on a polyphasic approach. Pairwise comparison of 16S rRNA gene sequences revealed that strain MCCC 1A01535T shared 97.7 and 97.5 % sequence similarities to Streptomyces specialis GW41-1564T and Streptomyces hainanensis YIM47672T, respectively, its most closely related neighbours, whereas the DNA–DNA relatedness value between strains MCCC 1A01535T and GW41-1564T was 50.2 %. The major fatty acids of strain MCCC 1A01535T were iso-C16 : 0, C16 : 0 and anteiso-C15 : 0. These differed from the fatty acid compositions of related strains. Strain MCCC 1A01535T exhibited an unusual menaquinone system that comprised MK-10(H6) as the predominant component and moderate amounts of MK-9(H6), MK-9(H8) and MK-10(H8); minor amounts of MK-9(H4), MK-10(H4), MK-9(H10) and MK-10(H10) were also present. Based on its chemotaxonomic, phenotypic and genotypic characteristics, strain MCCC 1A01535T is considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces avicenniae sp. nov. is proposed. The type strain is MCCC 1A01535T (=DSM 41943T=CGMCC 4.5510T).
-
- Bacteroidetes
-
-
Ferruginibacter alkalilentus gen. nov., sp. nov. and Ferruginibacter lapsinanis sp. nov., novel members of the family ‘Chitinophagaceae’ in the phylum Bacteroidetes, isolated from freshwater sediment
More LessSix Gram-negative, non-gliding, rod-shaped bacterial strains isolated from freshwater sediment were subjected to polyphasic analyses to determine their taxonomic positions. Analysis of the 16S rRNA gene sequences of the six strains revealed that they represent two separate genomic species in a new lineage within the phylum Bacteroidetes, related to members of the family ‘Chitinophagaceae’, in which they were most closely related to members of the genus Terrimonas (93.4−90.5 %). Two of the isolates, HU1-GD23T and HU1-HG42T, had a sequence similarity of 96.2 %, with DNA G+C contents of 39.4 and 38.5 mol%, respectively. They possessed MK-7 as the predominant respiratory quinone and contained high amounts of iso-pentadecanoic acid and 3-hydroxy-iso-heptadecanoic acid in their cell envelopes, properties shared by members of the family ‘Chitinophagaceae’. They were well differentiated from other members of the family ‘Chitinophagaceae’ by additional physiological and biochemical characteristics. In conclusion, strains HU1-GD23T (=KCTC 22306T=LMG 24312T) and HU1-HG42T (=KCTC 22305T=LMG 24324T) are considered to represent two novel species of a novel genus, Ferruginibacter gen. nov., for which the names Ferruginibacter alkalilentus sp. nov. and Ferruginibacter lapsinanis sp. nov., are proposed, respectively.
-
-
-
Lishizhenia tianjinensis sp. nov., isolated from coastal seawater
More LessA Gram-negative, non-carbohydrate-utilizing, non-flagellated, motile, flexible, long rod-shaped, orange-pigmented bacterium, strain H6T, was isolated from coastal seawater of Tianjin City, China, and its taxonomic position was investigated by using a polyphasic approach. Strain H6T grew optimally at 30 °C, in the presence of 2.0 % (w/v) NaCl and at pH 7.6. Menaquinone-6 (MK-6) was the sole respiratory quinone and the major fatty acids were iso-C15 : 0 (36.5 % of the total), iso-C15 : 1 (27.3 %) and iso-C17 : 0 3-OH (10.8 %). The DNA G+C content of strain H6T was 34.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain H6T was related most closely to Lishizhenia caseinilytica JCM 13821T (97.8 % similarity). DNA–DNA relatedness between the two strains was 47.4 %. Strain H6T could be further differentiated from L. caseinilytica JCM 13821T based on activity of several enzymes, hydrolysis of casein and Tweens 40, 60 and 80 and production of H2S. On the basis of phenotypic, chemotaxonomic, genomic and phylogenetic data, strain H6T is considered to represent a novel species of the genus Lishizhenia, for which the name Lishizhenia tianjinensis sp. nov. is proposed. The type strain is H6T (=CGMCC 1.7005T =JCM 15141T).
-
-
-
Psychroflexus salinarum sp. nov., isolated from a marine solar saltern
More LessA Gram-negative, non-motile and rod-shaped bacterial strain, ISL-14T, was isolated from a marine solar saltern of the Yellow Sea, Korea, and its taxonomic position was investigated by a polyphasic study. Strain ISL-14T grew optimally at pH 7.0–8.0, 30 °C and in the presence of approximately 2 % (w/v) NaCl. It contained MK-6 as the predominant menaquinone and anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0 3-OH as the major fatty acids. The DNA G+C content was 38.5 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-14T belonged to the genus Psychroflexus. The levels of similarity between the 16S rRNA gene sequence of strain ISL-14T and those of the type strains of recognized Psychroflexus species were 95.8–96.8 %. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain ISL-14T represents a novel species within the genus Psychroflexus, for which the name Psychroflexus salinarum sp. nov. is proposed. The type strain is ISL-14T (=KCTC 22483T=CCUG 56752T).
-
-
-
Description of Chryseobacterium anthropi sp. nov. to accommodate clinical isolates biochemically similar to Kaistella koreensis and Chryseobacterium haifense, proposal to reclassify Kaistella koreensis as Chryseobacterium koreense comb. nov. and emended description of the genus Chryseobacterium
A collection of eight strains, NF 1366T, NF 450, NF 1101, NF 1107, NF 1123, NF 1413, CCUG 15260 and CCUG 15624, from various clinical origins, were characterized biochemically as similar to Kaistella koreensis and Chryseobacterium haifense. They differed from K. koreensis, which is unable to alkalinize acetate, and from C. haifense, which is ONPG-positive (β-galactosidase) and acidifies sucrose, fructose and lactose. Based on 16S rRNA gene sequence comparisons, this collection of strains was most closely related to the type strains of K. koreensis (97.3–97.5 %) and C. haifense (99.1 %). Representative strain NF 1366T showed only 41.8 % DNA–DNA relatedness with K. koreensis DSM 12107T and only 51.9 % with C. haifense DSM 19056T. DNA–DNA hybridization of strains NF 450 and CCUG 15624 to strain NF 1366T was 41.7 and 74.6 %, respectively, and relatedness of these strains with C. haifense DSM 19056T was 72.6 and 70.2 %. With the present information, these two strains must be classified as intermediate between C. haifense and strain NF 1366T. The fatty acid composition and polar lipid profile of strain NF 1366T were similar to those reported for other Chryseobacterium species. Like other chryseobacteria, strain NF 1366T exhibited a polyamine pattern with the predominant compound sym-homospermidine and a quinone system consisting of menaquinone MK-6 only. For this collection of clinical strains, the name Chryseobacterium anthropi sp. nov. is proposed, with NF 1366T (=CCUG 52764T =CIP 109762T) as the type strain. K. koreensis was shown to be very similar genotypically and phenotypically to Chryseobacterium. Its polar lipid profile exhibited the major characteristics shown for recently described Chryseobacterium species and the fatty acid profile of K. koreensis was also very similar to those of the Chryseobacterium species. Hence, no striking genotypic or phenotypic differences could be found that could justify the classification of this species into a separate genus, and we therefore propose to reclassify Kaistella koreensis in the genus Chryseobacterium as Chryseobacterium koreense comb. nov. (type strain Chj707T =IAM 15050T =JCM 21512T =KCTC 12107T =NBRC 103027T). An emended description of the genus Chryseobacterium is also proposed.
-
-
-
Pedobacter oryzae sp. nov., isolated from rice paddy soil
More LessA Gram-stain-negative, strictly aerobic bacterium, designated strain N7T, was isolated from a rice paddy in South Korea. Cells of strain N7T were non-motile, non-spore-forming rods. Growth was observed at 15–35 °C (optimum of 25–30 °C) and between pH 6.0 and 8.0 (optimum of pH 6.5–7.5). The predominant isoprenoid quinone was menaquinone-7. The major cellular fatty acids of strain N7T were summed feature 3 (comprising C16 : 1 ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0, anteiso-C15 : 0, C15 : 0 and iso-C16 : 0. The G+C content of the genomic DNA was 37.7 mol%. Comparative 16S rRNA gene sequence analyses showed that strain N7T formed a distinct phyletic line within the genus Pedobacter. Phylogenetic distances from strains of other Pedobacter species with validly published names were greater than 5.0 % (i.e. <95.0 % 16S rRNA gene sequence similarities). On the basis of phenotypic and molecular data, it is clear that strain N7T represents a novel species within the genus Pedobacter, for which the name Pedobacter oryzae sp. nov. is proposed. The type strain is N7T (=KACC 12821T =DSM 19973T).
-
-
-
Belliella pelovolcani sp. nov., isolated from a mud-volcano in Taiwan
Strain CC-SAL-25T, a non-motile, Gram-negative, red-pigmented bacterium, was isolated from a rare mud-volcano, located in Wandan, Pingtung County, Taiwan. Studies based on 16S rRNA gene sequences showed that the strain clustered closely with Belliella baltica BA143T (95.4 % sequence similarity). A menaquinone with seven isoprene units (MK-7) was the major respiratory quinone. The fatty acid profile was slightly different from that of B. baltica BA143T. The results of the physiological and biochemical tests showed that strain CC-SAL-25T could be clearly differentiated from recognized Belliella species based on phenotypic properties. It was evident from the genotypic and phenotypic data that strain CC-SAL-25T should be classified as representing a second novel species in the genus Belliella. The name proposed for this taxon is Belliella pelovolcani sp. nov., and the type strain is CC-SAL-25T (=BCRC 17883T=KCTC 13248T).
-
-
-
Flectobacillus roseus sp. nov., isolated from freshwater in Taiwan
Two Gram-negative, aerobic, pale pink/rose-coloured, rod-shaped, non-motile bacterial strains, designated GFA-11T and RG-4, were isolated from a freshwater fish culture pond and a freshwater spring sample, respectively. Based on characterization by using a polyphasic approach, the two strains showed highly similar phenotypic, physiological and genetic characteristics. They shared 99.9 % 16S rRNA gene sequence similarity and 89–94 % DNA–DNA relatedness, suggesting that they represent a single genomic species. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains GFA-11T and RG-4 formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Flectobacillus within the family Flexibacteraceae. Their closest neighbours were Flectobacillus major DSM 103T (97.7 % 16S rRNA gene sequence similarity) and Flectobacillus lacus CL-GP79T (95.9 %). Levels of DNA–DNA relatedness between the two novel strains and the type strains of F. major and F. lacus were less than 70 %. The results of physiological and biochemical tests allowed clear phenotypic differentiation of strains GFA-11T and RG-4 from recognized members of the genus Flectobacillus. The predominant fatty acid constituents of strain GFA-11T were C16 : 1 ω5c (40.2 % of the total) and iso-C15 : 0 (15.0 %). The DNA G+C content of strain GFA-11T was 39.7 mol%. On the basis of 16S rRNA gene sequence analysis and chemotaxonomic and physiological data, strains GFA-11T and RG-4 are considered to represent a novel species of the genus Flectobacillus, for which the name Flectobacillus roseus sp. nov. is proposed. The type strain is GFA-11T (=BCRC 17834T=LMG 24501T).
-
-
-
Salisaeta longa gen. nov., sp. nov., a red, halophilic member of the Bacteroidetes
More LessA rod-shaped, 15–30 μm long, red bacterium, affiliated phylogenetically with the phylum Bacteroidetes, was isolated from an experimental mesocosm at Sedom, Israel, filled with a mixture of water from the Dead Sea and the Red Sea. The organism stains Gram-negative and is obligately aerobic, heterotrophic and oxidase- and catalase-positive. Growth is obtained in the presence of 5–20 % NaCl, with an optimum at 10 % NaCl plus 5 % MgCl2 . 6H2O. Temperature and pH optima are 37–46 °C and pH 6.5–8.5. Nitrate is not reduced. Glucose, sucrose, maltose and glycerol stimulate growth with acid formation; no growth stimulation is obtained in the presence of fructose, ribose, xylose, mannitol or sorbitol. The G+C content of the DNA is 62.9 mol% (HPLC). Main fatty acids are 16 : 0 iso and 16 : 1 cis9, followed by 15 : 0 iso and 15 : 0 anteiso. The isolate is sufficiently different from its closest relatives to be classified within a novel species belonging to a new genus, for which we propose the name Salisaeta longa gen. nov., sp. nov. The type strain of Salisaeta longa is strain S4-4T (=DSM 21114T =CECT 7354T).
-
-
-
Flavobacterium rivuli sp. nov., Flavobacterium subsaxonicum sp. nov., Flavobacterium swingsii sp. nov. and Flavobacterium reichenbachii sp. nov., isolated from a hard water rivulet
Strains WB 3.3-2T, WB 3.2-61T, WB 4.1-42T and WB 2.3-68T were isolated from the Westerhöfer Bach hard water rivulet, North Germany. The strains were Gram-staining-negative and catalase-, aminopeptidase- and oxidase-positive. The novel strains lacked flagella and only strain WB3.2-61T showed gliding motility. Isolates WB 3.2-61T, WB 4.1-42T and WB 2.3-68T produced flexirubin pigments. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel strains showed <98.2 % similarity to the type strains of all recognized species of the genus Flavobacterium. Strains WB 3.3-2T and WB 4.1-42T shared 96.3 % sequence similarity and were only distantly related to the type strains of all of the members of the genus Flavobacterium. Strain WB 3.2-61T branched adjacent to Flavobacterium limicola DSM 15094T (98.0 %), while strain WB 2.3-68T was a neighbour of Flavobacterium psychrophilum DSM 3660T (97.1 %). On R2A medium, iso-C15 : 0 was the common major fatty acid; fatty acids C15 : 0, C16 : 0, iso-C15 : 0 3-OH, iso-C17 : 1 ω9c, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1 ω7c and/or iso-C15 : 0 2-OH) occurred in all strains though sometimes in low amounts. Metabolic properties revealed clear differences between the four isolates as well as between the isolates and their nearest phylogenetic neighbours. The lack of close relatedness was confirmed by Riboprinter and MALDI-TOF analyses of cell extracts. On the basis of a high number of phenotypic differentiating properties and phylogenetic uniqueness, four novel Flavobacterium species are proposed with the following names: Flavobacterium rivuli (type strain WB 3.3-2T=DSM 21788T=CIP 109865T), Flavobacterium subsaxonicum (type strain WB 4.1-42T=DSM 21790T=CIP 109867T), Flavobacterium swingsii (type strain WB 2.3-68T=DSM 21789T=CIP 109868T) and Flavobacterium reichenbachii (type strain WB 3.2-61T=DSM 21791T=CIP 109866T).
-
- Firmicutes And Related Organisms
-
-
Alicyclobacillus aeris sp. nov., a novel ferrous- and sulfur-oxidizing bacterium isolated from a copper mine
More LessA novel mesophilic, acidophilic, endospore-forming bacterium, designated strain ZJ-6T, was isolated from Zi-Jin copper mine in Inner Mongolia, China. Cells of strain ZJ-6T were rod-shaped, stained Gram-positive or were Gram-variable, and grew aerobically at 25–35 °C (optimum, 30 °C) and pH 2.0–6.0 (optimum, pH 3.5). 16S rRNA gene sequence analysis showed that strain ZJ-6T was related phylogenetically to members of the genus Alicyclobacillus, with 16S rRNA gene sequence similarities of 89.5–94.2 %. Cells contained MK-7 as the major quinone and the DNA G+C content was 51.2 mol%. Strain ZJ-6T possessed a number of phenotypic characteristics that differentiated it from recognized Alicyclobacillus species, including its growth temperature, assimilation of various carbon sources, production of acids from a range of compounds, and the ability to grow chemoautotrophically using ferrous iron, elemental sulfur and tetrathionate as electron donors. The predominant cellular fatty acids of strain ZJ-6T were anteiso-C15 : 0 (67.1 %), iso-C16 : 0 (7.7 %) and anteiso-C17 : 0 (7.4 %); ω-alicyclic fatty acids were not found. On the basis of these results, it is concluded that strain ZJ-6T represents a novel species within the genus Alicyclobacillus, for which the name Alicyclobacillus aeris sp. nov. is proposed; the type strain is ZJ-6T (=CGMCC 1.7072T=NBRC 104953T).
-
-
-
Phylogeny and molecular taxonomy of the Bacillus subtilis species complex and description of Bacillus subtilis subsp. inaquosorum subsp. nov.
More LessThe Bacillus subtilis species complex is a tight assemblage of closely related species. For many years, it has been recognized that these species cannot be differentiated on the basis of phenotypic characteristics. Recently, it has been shown that phylogenetic analysis of the 16S rRNA gene also fails to differentiate species within the complex due to the highly conserved nature of the gene, yet DNA–DNA hybridization values fall well below 70 % for the same species comparisons. As a complementary approach, we propose that phylogenetic analysis of multiple protein-coding loci can be used as a means to detect and differentiate novel Bacillus taxa. Indeed, our phylogenetic analyses revealed the existence of a previously unknown group of strains closely related to, but distinct from, Bacillus subtilis subsp. spizizenii. Results of matrix-assisted laser desorption ionization-time of flight mass spectrometry analyses revealed that the group produces a novel surfactin-like lipopeptide with mass m/z 1120.8 that is not produced by the other currently recognized subspecies. In addition, the group displayed differences in the total cellular content of the fatty acids C16 : 0 and iso-C17 : 1 ω10c that distinguish it from the closely related B. subtilis subsp. spizizenii. Consequently, the correlation of these novel phenotypic traits with the phylogenetic distinctiveness of this previously unknown subspecies group showed that phylogenetic analysis of multiple protein-coding loci can be used as a means to detect and differentiate novel Bacillus taxa. Therefore, we propose that this new group should be recognized as representing a novel taxon, Bacillus subtilis subsp. inaquosorum subsp. nov., with the type strain NRRL B-23052T (=KCTC 13429T=BGSC 3A28T).
-
-
-
Bavariicoccus seileri gen. nov., sp. nov., isolated from the surface and smear water of German red smear soft cheese
The phylogenetic position and physiological characters of six hitherto-unknown lactic acid bacterial isolates, which form part of the surface microbiota of German red smear soft cheese, are reported. The coccoid cells are aerotolerant, Gram-positive, catalase-negative and non-motile. The cell-wall peptidoglycan contains alanine, glutamic acid, lysine and aspartic acid and is of the A4α type (l-Lys–d-Asp). The sequences of the 16S rRNA, groEL and rpoB genes of the six isolates are identical and reveal that these isolates represent an independent lineage within the radiation of the family Enterococcaceae in the phylum Firmicutes. Their closest phylogenetic neighbour is the lactic acid bacterium Atopobacter phocae M1590/94/2T, with which they share 94.9 % 16S rRNA gene sequence similarity; representatives of other genera such as Granulicatella, Carnobacterium and Trichococcus are more distantly related. DNA–DNA hybridization studies reveal that the six isolates are members of a single species, and this is confirmed by similarities in biochemical characteristics. The six isolates were assigned four different groups by Fourier-transform infrared and randomly amplified polymorphic DNA typing. Therefore, it is formally proposed that these isolates should be classified in a single novel species of a novel genus and be named Bavariicoccus seileri gen. nov., sp. nov. The type strain of Bavariicoccus seileri is WCC 4188T (=DSM 19936T =CCUG 55508T).
-
-
-
‘Candidatus Phytoplasma tamaricis’, a novel taxon discovered in witches'-broom-diseased salt cedar (Tamarix chinensis Lour.)
More LessSalt cedar trees with pronounced witches'-broom symptoms were observed in their natural habitat in China. 16S rRNA gene sequences unique to phytoplasmas were detected in every DNA sample extracted from stem and leaf tissues of the symptomatic trees, revealing a direct association between phytoplasma infection and the salt cedar witches'-broom (SCWB) disease. Phylogenetic analysis of the SCWB phytoplasma 16S rRNA gene sequence indicated that the SCWB phytoplasma belonged to a subclade consisting of several mutually distinct ‘Candidatus Phytoplasma’ taxa including ‘Ca. Phytoplasma prunorum’, ‘Ca. Phytoplasma mali’, ‘Ca. Phytoplasma pyri’ and ‘Ca. Phytoplasma spartii’. Pairwise sequence similarity scores calculated from an alignment of near full-length 16S rRNA genes revealed that SCWB phytoplasma shared 96.6 % or less sequence similarity with each previously described or proposed ‘Ca. Phytoplasma’ taxon, justifying the recognition of SCWB phytoplasma as a novel taxon, ‘Candidatus Phytoplasma tamaricis’. The distinct virtual RFLP pattern derived from the SCWB phytoplasma 16S rRNA gene sequence, together with its lower-than-threshold similarity coefficient values with RFLP patterns of any of the 29 previously established groups, supported the recognition of a new 16Sr group, designated 16SrXXX, salt cedar witches'-broom phytoplasma group.
-
-
-
Halobacillus salsuginis sp. nov., a moderately halophilic bacterium from a subterranean brine
A moderately halophilic, endospore-forming, Gram-positive, catalase- and oxidase-positive, motile, rod-shaped, aerobic bacterium, designated strain JSM 078133T, was isolated from a subterranean brine sample collected from a salt mine in Hunan Province, China. Strain JSM 078133T was able to grow with 1–23 % (w/v) total salts (optimum, 5–10 %) and at pH 6.0–10.0 (optimum, pH 7.5) and 10–45 °C (optimum, 30 °C). meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The predominant respiratory quinone was menaquinone 7 (MK-7) and the major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0. The genomic DNA G+C content of strain JSM 078133T was 42.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain JSM 078133T belongs to the genus Halobacillus, and was related most closely to the type strains of Halobacillus campisalis (97.1 % sequence similarity), Halobacillus alkaliphilus (97.0 %) and Halobacillus yeomjeoni (96.8 %). The combination of phylogenetic analysis, DNA–DNA relatedness data, phenotypic characteristics and chemotaxonomic data supported the view that strain JSM 078133T represents a novel species of the genus Halobacillus, for which the name Halobacillus salsuginis sp. nov. is proposed. The type strain is JSM 078133T (=DSM 21185T=KCTC 13236T).
-
-
-
Thalassobacillus cyri sp. nov., a moderately halophilic Gram-positive bacterium from a hypersaline lake
More LessA Gram-positive, moderately halophilic bacterium, designated strain HS286T, was isolated from water of the hypersaline Lake Howz-Soltan in Iran. Cells were strictly aerobic, rod-shaped, motile and able to produce ellipsoidal endospores at a central-subterminal position in swollen sporangia. Isolate HS286T grew in a complex medium supplemented with 1–15 % (w/v) NaCl, with optimum growth at 8.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that strain HS286T was closely related to Thalassobacillus devorans G-19.1T (99.4 % gene sequence similarity). The other closest species were Halobacillus yeomjeoni MSS-402T (96.9 %) and other species of the genus Halobacillus (with 96.7–93.5 % similarity). Strain HS286T had cell-wall peptidoglycan based on meso-diaminopimelic acid and MK-7 as the respiratory isoprenoid quinone. The major fatty acids were anteiso-C15 : 0 (43.8 %), iso-C16 : 0 (21.4 %), iso-C14 : 0 (9.4 %), anteiso-C17 : 0 (8.7 %) and iso-C15 : 0 (7.0 %) and the polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, two phospholipids and a glycolipid. The DNA G+C content was 43.0 mol%. All of these features confirmed the placement of isolate HS286T within the genus Thalassobacillus. However DNA–DNA hybridization between strain HS286T and the only recognized species of the genus Thalassobacillus, T. devorans G-19.1T, was 27.3 %, showing unequivocally that the novel isolate constituted a new genospecies. Strain HS286T could be clearly differentiated from T. devorans and other phylogenetic neighbours on the basis of several phenotypic, genotypic and chemotaxonomic features. Therefore, strain HS286T constitutes a novel species, for which the name Thalassobacillus cyri sp. nov. is proposed. The type strain is HS286T (=CCM 7597T=JCM 15722T).
-
-
-
Bhargavaea cecembensis gen. nov., sp. nov., isolated from the Chagos–Laccadive ridge system in the Indian Ocean
More LessA novel Gram-positive, rod-shaped, non-motile, non-spore-forming bacterium, strain DSE10T, was isolated from a deep-sea sediment sample collected at a depth of 5904 m from the Chagos–Laccadive ridge system in the Indian Ocean. Cells of strain DSE10T were positive for catalase, oxidase, urease and lipase activities and contained iso-C14 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C15 : 0 as the major fatty acids. The major respiratory quinones were MK-6 and MK-8 and the major lipids were phosphatidylglycerol and diphosphatidylglycerol. The cell-wall peptidoglycan contained diaminopimelic acid as the diagnostic diamino acid. A blast sequence similarity search based on 16S rRNA gene sequences indicated that the genera Planococcus, Planomicrobium, Bacillus and Geobacillus were the nearest phylogenetic neighbours to the novel isolate with gene sequence similarities ranging from 94.9 to 95.2 %. Phylogenetic analyses using neighbour-joining, minimum-evolution and maximum-parsimony methods indicated that strain DSE10T formed a deeply rooted lineage distinct from the clades represented by the genera Planococcus, Planomicrobium, Bacillus and Geobacillus. Further, strain DSE10T could be distinguished from the above-mentioned genera based on the presence of signature nucleotides G, A, C, T, C, A, G, C and T at positions 182, 444, 480, 492, 563, 931, 1253, 1300 and 1391, respectively, in the 16S rRNA gene sequence. Based on the phenotypic and phylogenetic characteristics determined in this study, strain DSE10T was assigned as the type species of a new genus, Bhargavaea gen. nov., as Bhargavaea cecembensis sp. nov. The type strain of Bhargavaea cecembensis gen. nov., sp. nov. is DSE10T (=LMG 24411T=JCM 14375T). The genomic DNA G+C content of strain DSE10T is 59.5±2.5 mol%.
-
- Proteobacteria
-
-
Pseudochrobactrum lubricantis sp. nov., isolated from a metal-working fluid
A Gram-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacterium (KSS 7.8T) was isolated from a water-mixed metal-working fluid. On the basis of 16S rRNA gene and recA sequence similarities, the isolate was clearly grouped in the genus Pseudochrobactrum. This allocation was confirmed by fatty acid data (major fatty acids: C18 : 2 ω7c and C19 : 0 cyclo ω8c), polar lipid profile (major components: phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine, plus moderate amounts of phosphatidylmonomethylethanolamine and unknown aminolipid AL1), quinone system (ubiquinone Q-10) and polyamine pattern (spermidine and putrescine predominant). DNA–DNA pairing with the most closely related Pseudochrobactrum species showed values ranging from 24.2 to 45.7 %, and physiological and biochemical data clearly differentiated this isolate from described Pseudochrobactrum species. This organism represents a novel species of the genus Pseudochrobactrum, for which the name Pseudochrobactrum lubricantis sp. nov. is proposed, with the type strain KSS 7.8T (=CCUG 56963T=CCM 7581T).
-
-
-
Transfer of Defluvibacter lusatiensis to the genus Aquamicrobium as Aquamicrobium lusatiense comb. nov. and description of Aquamicrobium aerolatum sp. nov.
More LessAnalysis of the 16S rRNA gene sequences of the type strains of Aquamicrobium defluvii and Defluvibacter lusatiensis shows a similarity of 98.3 %. There is no evidence for clear phenotypic differences between these organisms that justifies assignment to different genera. Both have ubiquinone Q-10 as the dominant quinone type and very similar fatty acid profiles, with 18 : 1ω7c and 19 : 0 cyclo ω8c predominating. A proposal is made to transfer Defluvibacter lusatiensis to the genus Aquamicrobium as Aquamicrobium lusatiense comb. nov. (type strain S1T =CIP 106844T =DSM 11099T). Furthermore, a novel species within this genus, Aquamicrobium aerolatum sp. nov., is described, with strain Sa14T (=CCUG 57044T =DSM 21857T), isolated from air in a duck shed, as the type strain.
-
-
-
Pseudomonas brassicacearum subsp. neoaurantiaca subsp. nov., orange-pigmented bacteria isolated from soil and the rhizosphere of agricultural plants
A large group of 38 strains of saprophytic bacteria was isolated from soil and the rhizosphere of agricultural plants. The novel organisms were Gram-negative, aerobic, rod-shaped bacteria that produced a green fluorescent pigment, a red–orange diffusible pigment and a complex mixture of phloroglucinol derivates with antimicrobial activity. The latter have not been found in other bacteria, but are peculiar to ferns. The bacteria were vigorous denitrifiers that synthesized levan from sucrose and liquefied gelatin, but were found not to degrade aesculin, starch, agar, Tween 80 or DNA. Bacterial growth was found to occur at 4 °C but not at 40 °C. The predominant cellular fatty acids were 16 : 0, 16 : 1(n-7), 18 : 1(n-7) and 17 : 0 cyclo. The G+C content of the novel bacteria was 61.0–62.9 mol%. 16S rRNA gene sequence analysis indicated that the representative strain CIP 109457T had a clear affiliation with Pseudomonas sensu stricto groups, with the nearest relatives being Pseudomonas brassicacearum, P. thivervalensis, P. corrugata, P. mediterranea and P. kilonensis. DNA–DNA hybridization experiments showed that the group of isolated strains exhibited high levels of genetic relatedness (81–100 %), confirming that they are representatives of the same species. At the same time, they bound at low levels (4−46 %) with DNA of the type strains of their nearest relatives with the exception of P. brassicacearum; DNA binding of 90 % with the DNA of P. brassicacearum CIP 107059T suggested that the bacteria studied belong to this species. Analysis of taxonomic data indicated that the group of novel bacteria maintain a distinct phenotypic profile, allowing the description of novel subspecies within P. brassicacearum, for which the following names are proposed: Pseudomonas brassicacearum subsp. brassicacearum subsp. nov. (type strain DBK11T =CFBP 11706T =CIP 107059T =DSM 13227T =JCM 11938T) and Pseudomonas brassicacearum subsp. neoaurantiaca subsp. nov., with the type strain CIP 109457T (=ATCC 49054T =IMV 387T =VKM B-1524T).
-
-
-
Andreprevotia lacus sp. nov., isolated from a fish-culture pond
A bacterial strain designated GFC-1T was isolated from a fish-culture pond in Taiwan and was characterized by using the polyphasic taxonomic approach. Strain GFC-1T was Gram-negative, aerobic, rod-shaped, motile and non-spore-forming. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belonged to the genus Andreprevotia of the family Neisseriaceae and its closest neighbour was Andreprevotia chitinilytica JS11-7T (97.0 % sequence similarity). The results of physiological and biochemical tests allowed clear phenotypic differentiation of isolate GFC-1T from A. chitinilytica JS11-7T. The major fatty acids were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1 ω7c. The DNA G+C content was 63.0 mol%. On the basis of 16S rRNA gene sequence analysis and chemotaxonomic and physiological data, strain GFC-1T should be classified as representing a novel species and a second member of the genus Andreprevotia, for which the name Andreprevotia lacus sp. nov. is proposed. The type strain is GFC-1T (=BCRC 17832T=LMG 24502T).
-
-
-
Chromobacterium piscinae sp. nov. and Chromobacterium pseudoviolaceum sp. nov., from environmental samples
More LessTwo strains (LMG 3947 and LMG 3953) of motile, Gram-negative, violet-pigmented bacteria, respectively isolated in 1972 and before 1953 from environmental samples and previously assigned to Chromobacterium violaceum, were studied again in detail for their taxonomic position. 16S rRNA gene sequence analysis showed that both strains clustered together with the type strain of Chromobacterium violaceum (99.8 % sequence similarity for strain LMG 3953T and 98.9 % sequence similarity for LMG 3947T). recA sequence similarities were significantly lower (95–96 %), and fatty acid profiles were also different from those reported for C. violaceum and other Chromobacterium species. Both strains exhibit polar-lipid profiles consisting of the major compound phosphatidylethanolamine and moderate amounts of phosphatidylglycerol in addition to some minor lipids. The quinone systems consist of the major compound ubiquinone Q-8 and moderate amounts of Q-7. Polyamine patterns are composed of the major compounds putrescine and 2-hydroxyputrescine, moderate amounts of 1,3-diaminopropane and variable amounts of cadaverine and spermidine. The results of DNA–DNA hybridizations and physiological as well as biochemical tests allowed both genotypic and phenotypic differentiation of the two strains from described Chromobacterium species. It is evident from the genotypic and phenotypic data that both strains represent novel species in the genus Chromobacterium, for which we propose the names Chromobacterium piscinae sp. nov. (type strain LMG 3947T =CCM 3329T) and Chromobacterium pseudoviolaceum sp. nov. (type strain LMG 3953T =CCM 2076T =NCTC 8182T).
-
-
-
Methylovirgula ligni gen. nov., sp. nov., an obligately acidophilic, facultatively methylotrophic bacterium with a highly divergent mxaF gene
Two strains of Gram-negative, aerobic, non-pigmented, non-motile, rod-shaped bacteria were isolated from beechwood blocks during decay by the white-rot fungus Hypholoma fasciculare and were designated strains BW863T and BW872. They are capable of methylotrophic growth and assimilate carbon via the ribulose-bisphosphate pathway. In addition to methanol, the novel isolates utilized ethanol, pyruvate and malate. Strains BW863T and BW872 are obligately acidophilic, mesophilic organisms capable of growth at pH 3.1–6.5 (with an optimum at pH 4.5–5.0) and at 4–30 °C. Phospholipid fatty acid profiles of these bacteria contain unusually large amounts (about 90 %) of C18 : 1 ω7c, thereby resembling the profiles of Methylobacterium strains. The predominant quinone is Q-10. The DNA G+C content of the novel isolates is 61.8–62.8 mol%. On the basis of 16S rRNA gene sequence similarity, strains BW863T and BW872 are most closely related to the acidophilic methanotroph Methylocapsa acidiphila B2T (96.5–97 %). Comparative sequence analysis of mxaF, the gene encoding the large subunit of methanol dehydrogenase, placed the MxaF sequences of the two novel strains in a cluster that is distinct from all previously described MxaF sequences of cultivated methylotrophs. The identity between the MxaF sequences of the acidophilic isolates and those from known alpha-, beta- and gammaproteobacterial methylotrophs was respectively 69–75, 61–63 and 64–67 %. The data therefore suggest that strains BW863T and BW872 represent a novel genus and species of methylotrophic bacteria, for which the name Methylovirgula ligni gen. nov., sp. nov. is proposed. Strain BW863T (=DSM 19998T =NCIMB 14408T) is the type strain of Methylovirgula ligni.
-
-
-
Dissection of the genus Methylibium: reclassification of Methylibium fulvum as Rhizobacter fulvus comb. nov., Methylibium aquaticum as Piscinibacter aquaticus gen. nov., comb. nov. and Methylibium subsaxonicum as Rivibacter subsaxonicus gen. nov., comb. nov. and emended descriptions of the genera Rhizobacter and Methylibium
More Less16S rRNA gene sequenced-based phylogeny indicates that Rhizobacter dauci ATCC 43778T branches within the radiation of Methylibium type strains. A comparative chemotaxonomic study including fatty acid methyl esters, polar lipids and polyamines reveals significant differences that, in combination with the topology of phylogenetic trees, support a dissection of the genus Methylibium. The proposals of this study include the transfer of Methylibium fulvum to the genus Rhizobacter as Rhizobacter fulvus comb. nov. (type strain Gsoil 322T =KCTC 12591T =DSM 19916T) and the reclassification of Methylibium aquaticum as Piscinibacter aquaticus gen. nov., comb. nov. (the type strain of Piscinibacter aquaticus is IMCC1728T =KCCM 42364T =NBRC 102349T =DSM 19915T) and of Methylibium subsaxonicum as Rivibacter subsaxonicus gen. nov., comb. nov. (the type strain of Rivibacter subsaxonicus is BF49T =DSM 19570T =CIP 109700T). As a consequence of these reclassifications, emended descriptions of the genera Methylibium and Rhizobacter are provided.
-
-
-
Salinihabitans flavidus gen. nov., sp. nov., isolated from a marine solar saltern
More LessA Gram-negative, non-motile and rod-shaped bacterial strain, ISL-46T, belonging to the Alphaproteobacteria, was isolated from a marine solar saltern in Korea, and subjected to a polyphasic taxonomic study. Strain ISL-46T grew optimally at pH 7.0–8.0 and 30 °C and in the presence of 7 % (w/v) NaCl. It contained Q-10 as the predominant ubiquinone and C19 : 0 cyclo ω8c, C18 : 1 ω7c and 11-methyl C18 : 1 ω7c as the major fatty acids. The DNA G+C content was 63.5 mol%. Strain ISL-46T exhibited 16S rRNA gene sequence similarity values of 94.1–95.3 % to members of the phylogenetically related genera Roseivivax, Salipiger, Citreicella, Yangia and Citreimonas. Strain ISL-46T could be differentiated from the above-mentioned genera by differences in compositions of the major fatty acids and in some phenotypic properties. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain ISL-46T is considered to represent a novel genus and species, for which the name Salinihabitans flavidus gen. nov., sp. nov. is proposed. The type strain is ISL-46T (=KCTC 22485T=CCUG 56758T).
-
-
-
Fodinicurvata sediminis gen. nov., sp. nov. and Fodinicurvata fenggangensis sp. nov., poly-β-hydroxybutyrate-producing bacteria in the family Rhodospirillaceae
Two Gram-negatively stained, facultatively anaerobic, non-motile, vibrioid and rod-shaped, chemoheterotrophic bacterial strains, designated YIM D82T and YIM D812T, were isolated from a salt mine in Yunnan, south-west China. DNA–DNA hybridization, genomic DNA G+C content and phylogenetic analyses based on 16S rRNA gene sequences divided the two isolates into two distinct genospecies that were also clearly differentiated by fatty acid profiles, carbon source utilization patterns, antibiotic susceptibility and biochemical characteristics. The two isolates grew in the presence of 1.5–20 % NaCl, and optimally at 28 °C and pH 7.5. The genomic DNA G+C contents of strains YIM D82T and YIM D812T were 61.5 and 62.3 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains YIM D82T and YIM D812T were members of the family Rhodospirillaceae and showed 90.5–90.6 % and 90.1–90.2 % similarities with their closest relatives, Rhodovibrio sodomensis and Rhodovibrio salinarum, respectively. Differential phenotypic and genotypic characteristics of the two isolates from recognized genera showed that the two strains should be classified as representing a new genus and two novel species for which the names Fodinicurvata sediminis gen. nov., sp. nov. (type strain YIM D82T=DSM 21159T=KCTC 22351T) and Fodinicurvata fenggangensis sp. nov. (type strain YIM D812T=CCTCC AA 208037T=DSM 21160T) are proposed.
-
-
-
Pseudomonas caeni sp. nov., a denitrifying bacterium isolated from the sludge of an anaerobic ammonium-oxidizing bioreactor
More LessTwo Gram-negative, rod-shaped, motile, aerobic bacterial strains designated HY-14T and HY-24 were isolated from the sludge of an anaerobic ammonium-oxidizing bioreactor. The strains could not grow with 5 % (w/v) NaCl, did not produce acid from d-glucose or utilize d-glucose, gluconate or citrate as a sole carbon source. Summed feature 3 and C16 : 0 were the most abundant fatty acids; hydroxyl fatty acids C12 : 0 3-OH and C10 : 0 3-OH were also present. Fatty acid C12 : 0 2-OH was absent. The DNA G+C contents of strains HY-14T and HY-24 were 50.6±0.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains HY-14T and HY-24 formed a monophyletic clade within the genus Pseudomonas. The highest sequence similarities were to Pseudomonas pseudoalcaligenes DSM 50188T (95.9 %). On the basis of phenotypic and phylogenetic properties, strains HY-14T and HY-24 are proposed as a novel species of the genus Pseudomonas, for which the name Pseudomonas caeni sp. nov. is proposed. The type strain is HY-14T (=KCTC 22292T=CCTCC AB208156T).
-
-
-
Arcobacter thereius sp. nov., isolated from pigs and ducks
More LessDuring a Danish study on the prevalence of campylobacteria in pig abortions and food of animal origin, eight Gram-negative, slightly curved, rod-shaped, non-spore-forming bacteria were clustered by using amplified fragment length polymorphism analysis in a distinct phenon within the genus Arcobacter. In the present study, numerical analysis of whole-cell protein profiles also showed that all isolates clustered in a single group distinct from other recognized Arcobacter species. DNA–DNA hybridization among two representative strains exhibited a mean DNA–DNA relatedness value of 79 %. DNA–DNA hybridization with the type strains of recognized Arcobacter species revealed levels of DNA–DNA relatedness of 41 % or less. The DNA G+C content of the type strain was 28.5 mol%. Pairwise comparison of the 16S rRNA gene sequences with those of the type strains of established species identified Arcobacter cryaerophilus (97.9 %), Arcobacter cibarius (97.5 %) and Arcobacter skirrowii (97.2 %) as the nearest phylogenetic neighbours. The isolates could be distinguished from other Arcobacter species by means of the following biochemical tests: activities of catalase and urease, reduction of nitrate and growth on minimal medium, lack of growth at 37 °C under standardized aerobic and microaerobic conditions, in 4 % NaCl and 1 % glycine media. Finally, DNA fingerprints obtained by using enterobacterial repetitive intergenic consenus-PCR showed that the eight isolates represent eight strains of a single novel Arcobacter species, for which the name Arcobacter thereius sp. nov. is proposed. The type strain is LMG 24486T (=CCUG 56902T).
-
-
-
Marinobacter szutsaonensis sp. nov., isolated from a solar saltern
More LessA Gram-negative, aerobic, non-spore-forming, halophilic bacterial strain, NTU-104T, was isolated from the Szutsao saltern in southern Taiwan, which was previously used as salt production field. The novel isolate grew optimally at 35–40 °C, at pH 7.5–8.0 and in the presence of 5 % (w/v) NaCl. The major fatty acids were C16 : 0, C18 : 1 ω9c, C16 : 1 ω9c, C12 : 0 3-OH and C12 : 0. The predominant quinone was Q-9. Phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine were the predominant polar lipids. The DNA G+C content was 56.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed the affiliation of the novel isolate to the genus Marinobacter. DNA–DNA hybridization results between strain NTU-104T and the type strains of the most closely related species, Marinobacter pelagius and Marinobacter koreensis, were 36.4 % and 33.2 %, respectively. On the basis of phenotypic, phylogenetic and genetic analyses, strain NTU-104T is considered to represent a novel species of the genus Marinobacter. The name Marinobacter szutsaonensis sp. nov. is proposed, with strain NTU-104T (=BCRC 17809T=CGMCC 1.7011T=JCM 15751T) as the type strain.
-
-
-
Vogesella lacus sp. nov., isolated from a soft-shell turtle culture pond
A non-pigmented, Gram-negative, aerobic, rod-shaped bacterium, strain GR13T, was isolated using nutrient agar from a water sample from a pond used for the culture of soft-shell turtles (Trionyx sinensis), Pingtung County, Taiwan. 16S rRNA gene sequence studies indicated that the novel strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Vogesella. Its closest neighbours were Vogesella indigofera ATCC 19706T and Vogesella perlucida DS-28T (both with 97.4 % gene sequence similarity). The novel isolate could be distinguished from these species by several phenotypic characteristics. The predominant fatty acids were summed feature 3 (C16 : 1 ω7c and/or C15 : 0 iso 2-OH; 60 %), C16 : 0 (13.6 %) and C18 : 1 ω7c (12.5 %). The DNA G+C content of strain GR13T was 63 mol%. The DNA–DNA hybridization values for the novel strain with V. indigofera and V. perlucida were <25 %. On the basis of the 16S rRNA gene sequence analysis and the chemotaxonomic and physiological data, it is concluded that strain GR13T represents a novel species in the genus Vogesella, for which the name Vogesella lacus sp. nov. is proposed. The type strain is GR13T (=BCRC 17836T=LMG 24504T).
-
- Evolution, Phylogeny And Biodiversity
-
-
-
Dickeya species relatedness and clade structure determined by comparison of recA sequences
More LessUsing sequences from the recA locus, we have produced a phylogeny of 188 Dickeya strains from culture collections and identified species relatedness and subspecies clade structure within the genus. Of the six recognized species, Dickeya paradisiaca, D. chrysanthemi and D. zeae were discriminated with long branch lengths. The clade containing the D. paradisiaca type strain included just one additional strain, isolated from banana in Colombia. Strains isolated from Chrysanthemum and Parthenium species made up most of the clade containing the D. chrysanthemi type strain, and the host range of this species was extended to include potato. The D. zeae clade had the largest number of sequevars and branched into two major sister clades that contained all of the Zea mays isolates, and were identified as phylotypes PI and PII. The host range was increased from six to 13 species, including potato. The recA sequence of an Australian sugar-cane strain was sufficiently distinct to rank as a new species-level branch. In contrast to these species, Dickeya dadantii, D. dianthicola and D. dieffenbachiae were distinguished with shorter branch lengths, indicating relatively closer relatedness. The recA sequence for the type strain of D. dadantii clustered separately from other strains of the species. However, sequence comparison of three additional loci revealed that the D. dadantii type strain grouped together with the six other D. dadantii strains that were sequenced. Analysis of all four loci indicated that the D. dadantii strains were most closely related to D. dieffenbachiae. Three further branches (DUC-1, -2 and -3) were associated with these three species, which all diverged from a common origin and can be considered as a species complex. The large clade containing the D. dianthicola type strain comprised 58 strains and had little sequence diversity. One sequevar accounted for the majority of these strains, which were isolated nearly exclusively from eight hosts from Europe. Isolation of this sequevar on multiple occasions from Dianthus and (more recently) potato demonstrates that this lineage has become established in these species. The D. dadantii clade comprised 11 sequevars, and the known host range of the species was extended from eight to 19 species. New hosts included several ornamental species and potato. The clade DUC-1 was made up exclusively of potato strains originating from Europe, which had identical sequences, whilst DUC-2 strains were isolated mostly from a variety of monocotyledonous species. A single strain from Aglaonema sp. made up DUC-3. A single sequevar constituted the D. dieffenbachiae clade. The phylogenetic method described will provide a simple means for identification to the species and intraspecies level, which will support efforts to control these pathogens based on monitoring and surveillance.
-
-
-
-
Protein signatures (molecular synapomorphies) that are distinctive characteristics of the major cyanobacterial clades
More LessA combination of phylogenomic and signature sequence-based (or phenetic) approaches was used to understand the evolutionary relationships among cyanobacteria. Phylogenetic trees were constructed for 34 cyanobacteria whose genomes have been sequenced, based on concatenated sequences for 45 conserved proteins and also the 16S rRNA gene. In parallel, sequence alignments of various proteins were examined to identify conserved indels (i.e. molecular signatures or synapomorphies) that are specific for either all cyanobacteria or their various clades in the phylogenetic trees. Of the >40 molecular signatures described in this work, 15 are specific for all cyanobacteria. The other cyanobacterial clades that can now be identified and circumscribed in molecular terms by using these signatures include a deep-branching clade (clade A, corresponding to the subclass Gloeobacterophycidae), consisting of Gloeobacter violaceus and two diazotrophic Synechococcus strains (JA-3-3Ab and JA2-3-B′a) (15 aa insert in EF-G); a clade comprising all other cyanobacteria except those from clade A [18 aa insert in DNA polymerase I (Pol I), 2 aa insert in the DnaX protein, 4 aa insert in TrpRS and 4–5 aa insert in tryptophan synthase beta subunit]; a clade (clade C, corresponding to the subclass Synechococcophycidae) of various marine unicellular Synechococcus and Prochlorococcus cyanobacteria (12 aa insert in Pol I, 3 aa insert in RpoB, 2 aa insert in KgsA, 6 aa insert in TyrRS, 2 aa insert in tRNA-mG1 transferase and 1 aa deletion in the RpoC protein); a clade of the low-B/A ecotype Prochlorococcus strains (5 aa deletion in LeuRS and 1 aa insert in the Ffh protein); a clade consisting of the Nostocales species/strains (subclass Nostocophycidae; 4 aa insert in the PetA protein and 5 aa insert in the ribosomal protein S3); a clade of the order Chroococcales (1 aa insert in RecA); a clade comprising the orders Nostocales, Oscillatoriales and Chroococcales [19 aa insert in DnaE, 13 aa insert in GDP–mannose pyrophosphorylase and 22–27 aa insert in NADP(H)–quinone oxidoreductase subunit D]. Two additional conserved indels in the translation-initiation factor IF-2 and riboflavin synthase alpha subunit suggest an intermediate placement of the Oscillatoriales in between the orders Nostocales and Chroococcales. The unique presence of these molecular signatures in all available sequences from the indicated groups of cyanobacteria, but not in any other cyanobacteria (or bacteria), indicates that these synapomorphies provide novel and potentially useful means for circumscription of several important taxonomic clades of cyanobacteria in more definitive terms. The species-distribution patterns of these synapomorphies also indicate that the plant/plastid homologues are not derived from the clade A or C cyanobacteria.
-
-
-
Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII)
More LessPhytoplasmas, the causal agents of numerous plant diseases, are insect-vector-transmitted, cell-wall-less bacteria descended from ancestral low-G+C-content Gram-positive bacteria in the Bacillus–Clostridium group. Despite their monophyletic origin, widely divergent phytoplasma lineages have evolved in adaptation to specific ecological niches. Classification and taxonomic assignment of phytoplasmas have been based primarily on molecular analysis of 16S rRNA gene sequences because of the inaccessibility of measurable phenotypic characters suitable for conventional microbial characterization. In the present study, an interactive online tool, iPhyClassifier, was developed to expand the efficacy and capacity of the current 16S rRNA gene sequence-based phytoplasma classification system. iPhyClassifier performs sequence similarity analysis, simulates laboratory restriction enzyme digestions and subsequent gel electrophoresis and generates virtual restriction fragment length polymorphism (RFLP) profiles. Based on calculated RFLP pattern similarity coefficients and overall sequence similarity scores, iPhyClassifier makes instant suggestions on tentative phytoplasma 16Sr group/subgroup classification status and ‘Candidatus Phytoplasma’ species assignment. Using iPhyClassifier, we revised and updated the classification of strains affiliated with the peach X-disease phytoplasma group. The online tool can be accessed at http://www.ba.ars.usda.gov/data/mppl/iPhyClassifier.html.
-
- International Committee On Systematics Of Prokaryotes
-
- Minutes
- Errata
Volumes and issues
-
Volume 74 (2024)
-
Volume 73 (2023)
-
Volume 72 (2022 - 2023)
-
Volume 71 (2020 - 2021)
-
Volume 70 (2020)
-
Volume 69 (2019)
-
Volume 68 (2018)
-
Volume 67 (2017)
-
Volume 66 (2016)
-
Volume 65 (2015)
-
Volume 64 (2014)
-
Volume 63 (2013)
-
Volume 62 (2012)
-
Volume 61 (2011)
-
Volume 60 (2010)
-
Volume 59 (2009)
-
Volume 58 (2008)
-
Volume 57 (2007)
-
Volume 56 (2006)
-
Volume 55 (2005)
-
Volume 54 (2004)
-
Volume 53 (2003)
-
Volume 52 (2002)
-
Volume 51 (2001)
-
Volume 50 (2000)
-
Volume 49 (1999)
-
Volume 48 (1998)
-
Volume 47 (1997)
-
Volume 46 (1996)
-
Volume 45 (1995)
-
Volume 44 (1994)
-
Volume 43 (1993)
-
Volume 42 (1992)
-
Volume 41 (1991)
-
Volume 40 (1990)
-
Volume 39 (1989)
-
Volume 38 (1988)
-
Volume 37 (1987)
-
Volume 36 (1986)
-
Volume 35 (1985)
-
Volume 34 (1984)
-
Volume 33 (1983)
-
Volume 32 (1982)
-
Volume 31 (1981)
-
Volume 30 (1980)
-
Volume 29 (1979)
-
Volume 28 (1978)
-
Volume 27 (1977)
-
Volume 26 (1976)
-
Volume 25 (1975)
-
Volume 24 (1974)
-
Volume 23 (1973)
-
Volume 22 (1972)
-
Volume 21 (1971)
-
Volume 20 (1970)
-
Volume 19 (1969)
-
Volume 18 (1968)
-
Volume 17 (1967)
-
Volume 16 (1966)
-
Volume 15 (1965)
-
Volume 14 (1964)
-
Volume 13 (1963)
-
Volume 12 (1962)
-
Volume 11 (1961)
-
Volume 10 (1960)
-
Volume 9 (1959)
-
Volume 8 (1958)
-
Volume 7 (1957)
-
Volume 6 (1956)
-
Volume 5 (1955)
-
Volume 4 (1954)
-
Volume 3 (1953)
-
Volume 2 (1952)
-
Volume 1 (1951)