- Volume 61, Issue 10, 2011
Volume 61, Issue 10, 2011
- Notification List
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Notification that new names and new combinations have appeared in volume 61, 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.
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- New Taxa
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- Actinobacteria
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Leucobacter celer sp. nov., isolated from Korean fermented seafood
More LessA novel, Gram-reaction-positive, aerobic, rod-shaped, non-motile bacterial strain, designated NAL101T, was isolated from gajami-sikhae, a traditional Korean fermented seafood made of flatfish. Growth occurred at 4–45 °C, at pH 5–10 and in 0–12 % (w/v) NaCl. Optimum growth occurred at 30–37 °C, at pH 8 and in 0–1 % (w/v) NaCl. The cell-wall amino acids were 2,4-diaminobutyric acid, alanine, glycine, threonine and glutamic acid and the major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The predominant menaquinone was MK-11. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unknown glycolipid. The 16S rRNA gene sequence of strain NAL101T showed 97.7 % similarity to that of Leucobacter chironomi MM2LBT, its closest relative. The DNA G+C content was 68.8 mol% and DNA–DNA hybridization values with closely related strains were <22 %. Phylogenetic analyses based on 16S rRNA gene sequences as well as differences in its physiological and biochemical characteristics indicated that strain NAL101T represents a novel species of the genus Leucobacter in the family Microbacteriaceae, for which the name Leucobacter celer sp. nov. is proposed. The type strain is NAL101T ( = KACC 14220T = JCM 16465T).
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Dactylosporangium tropicum sp. nov., isolated from soil
More LessTwo novel actinomycete strains, designated KB2-4T and KB9-2, were isolated from soil samples. Both isolates formed finger-shaped sporangia on short sporangiophores that emerged directly from substrate hyphae. The cell-wall peptidoglycan contained glutamic acid, glycine, alanine and meso-diaminopimelic acid; the whole-cell sugars were galactose, glucose, mannose, rhamnose, ribose and xylose. The diagnostic phospholipid was phosphatidylethanolamine. The predominant menaquinones were MK-9(H8) and MK-9(H6). Mycolic acids were not detected. The predominant cellular fatty acids (>20 %) were iso-C16 : 0 and anteiso-C17 : 0. For both strains, the G+C content of the genomic DNA was about 72 mol%. The morphological and chemotaxonomic characteristics of the two strains were typical of members of the genus Dactylosporangium. Phylogenetic analysis using 16S rRNA gene sequences also indicated that these strains should be classified in the genus Dactylosporangium and showed that the closest relative was Dactylosporangium salmoneum NRRL B-16294T (99.1 % 16S rRNA gene sequence similarity). DNA–DNA relatedness and some physiological and biochemical properties indicated that the isolates could be readily distinguished from their closest phylogenetic relatives. On the basis of these phenotypic and genotypic data, the isolates represent a novel species, for which the name Dactylosporangium tropicum sp. nov. is proposed. The type strain is strain KB2-4T ( = BCC 34760T = JCM 15673T).
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Asanoa hainanensis sp. nov., isolated from rhizosphere soil of Acrostichum speciosum in a mangrove, and emended description of the genus Asanoa
A Gram-reaction-positive, non-motile actinobacterium, designated strain 210121T, was isolated from rhizosphere soil of the mangrove fern Acrostichum speciosum. 16S rRNA gene sequence analysis showed that the isolate belonged to the genus Asanoa. DNA–DNA relatedness values between strain 210121T and the type strains of the three recognized species of the genus Asanoa were below the 70 % threshold recommended for distinguishing bacterial genomic species. The novel isolate contained glutamic acid, glycine, alanine and meso-A2pm as cell-wall amino acids, indicating peptidoglycan type A1γ. The characteristic whole-cell sugars were xylose, ribose, glucose and mannose. The predominant menaquinones were MK-9(H4), MK-9(H6) and MK-9(H8). The major fatty acids were iso-C16 : 0 (30.9 %), C17 : 0 (23.0 %), anteiso-C15 : 0 (14.9 %) and iso-C15 : 0 (12.3 %). The phospholipid profile comprised phosphatidylethanolamine, phosphatidylinositol mannosides and phospholipids of unknown structure containing glucosamine. The G+C content of the DNA was 70.3 mol%. On the basis of the phenotypic and genotypic data, strain 210121T ( = CGMCC 4.5593T = DSM 45427T) represents a novel species of the genus Asanoa, for which the name Asanoa hainanensis sp. nov., is proposed. An emended description of the genus Asanoa is also proposed.
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Calidifontibacter indicus gen. nov., sp. nov., a member of the family Dermacoccaceae isolated from a hot spring, and emended description of the family Dermacoccaceae
More LessDuring the course of a study on the bacterial diversity in Western Ghats, India, an actinobacterial strain, designated PC IW02T, was isolated and characterized by a polyphasic taxonomic approach. Strain PC IW02T was a non-motile, Gram-positive, short rod that formed creamish white to yellow coloured colonies. 16S rRNA gene sequence analysis showed that the novel strain showed highest sequence similarity with type strains of members of the genus Dermacoccus: Dermacoccus barathri (96.6 %), Dermacoccus profundi (96.5 %), Dermacoccus abyssi (96.4 %) and Dermacoccus nishinomiyaensis (95.9 %). The phylogenetic tree suggested that strain PC IW02T could represent a member of a new genus of the family Dermacoccaceae with the genus Demetria as closest clade. Pairwise sequence alignment with Demetria terragena HKI 0089T and Kytococcus sedentarius DSM 20547T showed similarities of 94.2 and 93.7 %, respectively. Strain PC IW02T had MK-8(H4) as the major menaquinone. The major fatty acids were iso-C16 : 0 (43.4 %), iso-C16 : 1 H (17.2 %) and anteiso-C17 : 0 (9.9 %). The diagnostic cell-wall amino acid at position 3 of the peptide subunit was lysine; the interpeptide bridge consisted of Gly–Ser–Asp. The polar lipids present were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides and phosphatidylserine, along with two unknown phospholipids. The genomic DNA G+C content of the isolate was 77 mol%. On the basis of phenotypic characteristics, including chemotaxonomic data, and 16S rRNA gene sequence similarities, strain PC IW02T represents a novel species in a new genus of the family Dermacoccaceae for which the name Calidifontibacter indicus gen. nov., sp. nov. is proposed. The type strain of Calidifontibacter indicus is PC IW02T ( = MTCC 8338T = DSM 22967T = JCM 16038T). An emended description of the family Dermacoccaceae is provided.
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Corynebacterium nuruki sp. nov., isolated from an alcohol fermentation starter
More LessA novel Gram-positive, strictly aerobic and non-motile bacterial strain, S6-4T, was isolated from a Korean alcohol fermentation starter. Optimal growth occurred at 37 °C, at pH 8 and in 1 % (w/v) NaCl. The isolate was positive for oxidase and catalase. It assimilated various sugars and acids were produced from several carbohydrates. The major cell-wall sugars were galactose and arabinose. The major fatty acids of strain S6-4T were C16 : 0, C17 : 1ω9c, C18 : 1ω9c and 10-methyl C18 : 0 (tuberculostearic acid). The predominant isoprenoid quinone was menaquinone MK-9(H2) and peptidoglycan amino acids were meso-diaminopimelic acid, alanine, glycine and glutamic acid. The strain contained mycolic acids. According to phylogenetic analysis based on 16S rRNA gene sequences, strain S6-4T was most closely related to Corynebacterium variabile DSM 20132T (98.1 % similarity). The genomic DNA G+C content of strain S6-4T was 73.6 mol% and DNA–DNA hybridization values with related strains were below 33±4 %. On the basis of phenotypic, genotypic and phylogenetic data, strain S6-4T represents a novel species in the genus Corynebacterium, for which the name Corynebacterium nuruki sp. nov. is proposed; the type strain is S6-4T ( = KACC 15032T = JCM 17162T).
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Pseudokineococcus lusitanus gen. nov., sp. nov., and reclassification of Kineococcus marinus Lee 2006 as Pseudokineococcus marinus comb. nov.
More LessA Gram-reaction-positive, motile, coccus-shaped actinobacterium, designated strain T2A-S27T, was isolated from a roof tile in Oporto (Portugal) and studied using a polyphasic approach. The 16S rRNA gene sequence of the novel isolate showed high similarity to that of Kineococcus marinus KST3-3T (97.8 % sequence similarity). Strain T2A-S27T showed lower 16S rRNA gene sequence similarities with other members of the genus Kineococcus and members of the family Kineosporiaceae (<94 %). A phylogenetic tree, based on 16S rRNA gene sequences, showed that strain T2A-S27T formed a coherent clade with the type strain of K. marinus and Quadrisphaera granulorum. The isolate was characterized by the presence of meso-diaminopimelic acid in the cell-wall peptidoglycan, MK-9(H2) as the predominant menaquinone and a polar lipid profile consisting of diphosphatidylglycerol and phosphatidylglycerol. The fatty acid profile was dominated by anteiso-C15 : 0. The DNA G+C content was 76.9 mol%. The low level of DNA–DNA relatedness to K. marinus (46–47 %) and the results of the chemotaxonomic and physiological studies clearly distinguished strain T2A-S27T from recognized species of the genus Kineococcus. On the basis of its phylogenetic position and phenotypic traits, strain T2A-S27T ( = LMG 24148T = CECT 7306T = DSM 23768T) represents a novel species of a new genus in the family Kineosporiaceae, for which the name Pseudokineococcus lusitanus gen. nov., sp. nov. is proposed. The misclassified species K. marinus is transferred to the new genus as Pseudokineococcus marinus comb. nov. The type strain of Pseudokineococcus marinus is KST3-3T ( = KCCM 42250T = NRRL B-24439T).
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- Archaea
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Metallosphaera cuprina sp. nov., an acidothermophilic, metal-mobilizing archaeon
More LessA novel acidothermophilic archaeon, strain Ar-4T, was isolated from a sulfuric hot spring in Tengchong, Yunnan, China. Cells of strain Ar-4T were Gram-staining-negative, irregular cocci and motile by means of flagella. Strain Ar-4T grew over a temperature range of 55–75 °C (optimum, 65 °C), a pH range of 2.5–5.5 (optimum, pH 3.5) and a NaCl concentration range of 0–1 % (w/v). The novel strain was aerobic and facultatively chemolithoautotrophic. The strain could extract metal ions from sulfidic ore. It was also able to oxidize reduced sulfur compounds. In addition, it was able to use heterogeneous organic materials for organotrophic growth. The main cellular lipids were calditoglycerocaldarchaeol (CGTE) and caldarchaeol (DGTE). The DNA G+C content of the strain was 40.2 mol%. Analysis of 16S rRNA gene sequences showed that strain Ar-4T was phylogenetically related to members of the genus Metallosphaera and had sequence similarities of 97.7 %, 97.0 % and 96.8 % with Metallosphaera hakonensis DSM 7519T, Metallosphaera sedula DSM 5348T and Metallosphaera prunae DSM 10039T, respectively. Strain Ar-4T showed DNA–DNA relatedness values of 47.5 %, 30.8 % and 29.1 % with M. hakonensis DSM 7519T, M. sedula DSM 5348T and M. prunae DSM 10039T, respectively. The differences in cell motility, the temperature and pH ranges for growth, the ability to utilize carbon sources, the DNA G+C content, and the low DNA–DNA relatedness values distinguished strain Ar-4T from recognized species of the genus Metallosphaera. On the basis of these results, it was concluded that strain Ar-4T represents a novel species of the genus Metallosphaera, for which the name Metallosphaera cuprina is proposed. The type strain is Ar-4T ( = JCM 15769T = CGMCC 1.7082T).
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Methanosarcina horonobensis sp. nov., a methanogenic archaeon isolated from a deep subsurface Miocene formation
More LessA methanogenic organism, designated strain HB-1T, from the domain Archaea was isolated from groundwater sampled from a subsurface Miocene formation located in Horonobe, Hokkaido, Japan. The strain grew on methanol, dimethylamine, trimethylamine, dimethylsulfide and acetate but not on monomethylamine, H2/CO2, formate, 2-propanol, 2-butanol or cyclopentanol. Cells were Gram-reaction-negative, non-motile, irregular cocci that were 1.4–2.9 µm in diameter and occurred singly or in pairs. The strain grew at 20–42 °C (optimum 37 °C), at pH 6.0–7.75 (optimum pH 7.0–7.25) and in 0–0.35 M NaCl (optimum 0.1 M). The G+C content of the genomic DNA was 41.4 mol%. 16S rRNA gene sequencing revealed that the strain was a member of the genus Methanosarcina but that it clearly differed from all recognized species of this genus (93.1–97.9 % sequence similarity). The phenotypic and phylogenetic features of strain HB-1T indicate that it represents a novel species of the genus Methanosarcina, for which the name Methanosarcina horonobensis sp. nov. is proposed. The type strain is HB-1T ( = DSM 21571T = JCM 15518T = NBRC 102577T).
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- Bacteroidetes
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Aureibacter tunicatorum gen. nov., sp. nov., a marine bacterium isolated from a coral reef sea squirt, and description of Flammeovirgaceae fam. nov.
More LessTwo aerobic, Gram-reaction-negative, golden-yellow pigmented and rod-shaped bacteria, designated strains A5Q-118T and A5Q-27, were isolated from an unidentified sea squirt that thrives in the coral reefs off the coast of Okinawa, Japan. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the novel isolates were affiliated with the family ‘Flammeovirgaceae’ of the phylum Bacteroidetes. Strains A5Q-118T and A5Q-27 shared 100 % sequence similarity with each other and showed <92 % similarity with other cultivated members of the family ‘Flammeovirgaceae’. The novel isolates were phenotypically and physiologically different from strains described previously. The DNA G+C content was 35.5–36.2 mol%, MK-7 was the major menaquinone and iso-C15 : 0 and C16 : 1ω5c were the major fatty acids. Based on the results of this polyphasic taxonomic study, it was concluded that strains A5Q-118T and A5Q-27 represent a novel species in a new genus of the family ‘Flammeovirgaceae’, for which the name Aureibacter tunicatorum gen. nov., sp. nov. is proposed. Proposal for designation of the Flammeovirgaceae fam. nov. is also presented. The type strain of Aureibacter tunicatorum is A5Q-118T ( = KCTC 23232T = NBRC 107587T).
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Chitinophaga eiseniae sp. nov., isolated from vermicompost
More LessA Gram-negative, rod-shaped bacterial strain, YC6729T, was isolated from vermicompost collected at Masan, Korea, and its taxonomic position was investigated by a polyphasic taxonomic approach. Strain YC6729T grew optimally at 30 °C and at pH 6.5–8.5. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YC6729T belongs to the genus Chitinophaga in the family Chitinophagaceae. It was related most closely to Chitinophaga terrae KP01T (96.4 % 16S rRNA gene sequence similarity), Chitinophaga ginsengisegetis Gsoil 040T (96.1 %), Chitinophaga arvensicola IAM 12650T (96.1 %) and Chitinophaga pinensis DSM 2588T (93.3 %). Strain YC6729T contained MK-7 as the major menaquinone and homospermidine as the major polyamine. The fatty acids of strain YC6729T were iso-C15 : 0, C16 : 1ω5c, iso-C17 : 0 3-OH, C16 : 0, anteiso-C18 : 0 and/or C18 : 2ω6,9c, iso-C15 : 0 2-OH and/or C16 : 1ω7c, C14 : 0, iso-C15 : 0 3-OH, iso-C15 : 1 G, C18 : 1ω5c, iso-C15 : 1 I and/or C13 : 0 3-OH, C13 : 0 2-OH, C16 : 0 3-OH and unknown fatty acid ECL 13.565. The polar lipid profile contained phosphatidylethanolamine, unknown aminolipids and unknown lipids. The total DNA G+C content of strain YC6729T was 48.9 mol%. The phenotypic, chemotaxonomic and phylogenetic data showed that strain YC6729T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga eiseniae sp. nov. is proposed. The type strain is YC6729T ( = KACC 13774T = DSM 22224T).
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Aquimarina addita sp. nov., isolated from seawater
Hana Yi and Jongsik ChunAn orange-coloured, rod-shaped, non-motile, Gram-reaction-negative, strictly aerobic bacterial strain, designated JC2680T, was isolated from a seawater sample of Jeju Island, Korea. The isolate required sea salts for growth. Flexirubin-type pigments were absent. 16S rRNA gene sequence analysis indicated that the test strain belonged to the genus Aquimarina within the family Flavobacteriaceae, but shared relatively low levels of similarity (93.6–95.9 %) with the type strains of recognized Aquimarina species. The predominant cellular fatty acids [iso-C17 : 0 3-OH, iso-C15 : 0 and summed feature 9 (comprising 10-methyl C16 : 0 and/or iso-C17 : 1ω9c) and DNA G+C content (35 mol%) were consistent with the assignment of strain JC2680T to the genus Aquimarina. However, a number of phenotypic characteristics, namely inability to grow under microaerophilic conditions, differences in enzyme reactions, and absence of flexirubin-type pigments and gliding motility, clearly distinguished strain JC2680T from recognized species of the genus Aquimarina. The data presented thus indicate that strain JC2680T represents a novel species of the genus Aquimarina, for which the name Aquimarina addita sp. nov. is proposed. The type strain is JC2680T ( = KACC 14156T = JCM 17106T).
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Schleiferia thermophila gen. nov., sp. nov., a slightly thermophilic bacterium of the phylum ‘Bacteroidetes’ and the proposal of Schleiferiaceae fam. nov.
More LessA bacterial isolate, with an optimum growth temperature of about 50 °C and an optimum pH for growth between 7.5 and 8.5, was recovered from a hot spring in the Furnas area of the Island of São Miguel in the Azores. The novel isolate is orange-pigmented, forms non-motile, rod-shaped cells that stain Gram-negative, is strictly aerobic, oxidase-positive and catalase-negative. The major fatty acids of strain TU-20T are 16 : 1ω6c, 17 : 0 iso 3-OH and 15 : 0 iso. Menaquinone 6 is the major respiratory quinone. Based on 16S rRNA gene sequence analysis, physiological and biochemical characteristics, we describe a novel species of a novel genus represented by strain TU-20T ( = DSM 21410T = LMG 24594T) for which we propose the name Schleiferia thermophila gen nov., sp. nov. We also propose the family Schleiferiaceae fam. nov. to accommodate this new genus.
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Snuella lapsa gen. nov., sp. nov., isolated from tidal flat sediment
Hana Yi and Jongsik ChunA yellow-coloured, rod-shaped, Gram-reaction-negative, aerobic bacterial strain, designated JC2132T, was isolated from a tidal flat sediment sample from Ganghwa Island, Korea. The isolate required sea salts for growth. Cells produced non-diffusible carotenoid pigments, but flexirubin-type pigments were absent. Gliding motility was observed. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain JC2132T represented a distinct phyletic line that reflected a novel generic status within the family Flavobacteriaceae with relatively low sequence similarities (<95 %) to members of other genera with validly published names. The predominant isoprenoid quinone (MK-6) and DNA G+C content (35 mol%) were consistent with assignment of the isolate to the family Flavobacteriaceae, but overall phenotypic traits demonstrated that strain JC2132T was not closely affiliated with any previously described genera. Based on taxonomic data obtained using a polyphasic approach, it is proposed that strain JC2132T represents a novel species in a new genus belonging to the family Flavobacteriaceae, for which the name Snuella lapsa gen. nov., sp. nov. is proposed; the type strain of the type species is JC2132T ( = KACC 14152T = JCM 17111T).
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Pontirhabdus pectinivorans gen. nov., sp. nov., isolated from seawater
More LessA yellow-coloured, rod-shaped, Gram-reaction-negative and aerobic bacterial strain, designated JC2675T, was isolated from a seawater sample from Jeju Island, Korea. The isolate required sea salts for growth. Gliding motility was observed. Flexirubin-type pigments were absent. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain JC2675T represented a distinct phyletic line that reflected a novel generic status within the family Flavobacteraceae with relatively low gene sequence similarities (<95.7 %) to other recognized genera. The predominant isoprenoid quinone (MK-6) and DNA G+C content (30 mol%) were consistent with the assignment of the novel strain to the family Flavobacteriaceae, but overall phenotypic traits demonstrated that the novel strain was not closely affiliated with any previously described genus. Based on data from a study using a polyphasic taxonomic approach, it is proposed that strain JC2675T represents a new genus and novel species belonging to the family Flavobacteriaceae, for which the name Pontirhabdus pectinivorans gen. nov., sp. nov. is proposed. The type strain of the type species is JC2675T ( = KACC 14153T = JCM 17107T).
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- Firmicutes And Related Organisms
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Salinicoccus sesuvii sp. nov., isolated from the rhizosphere of Sesuvium portulacastrum
More LessA Gram-staining-positive coccus, designated CC-SPL15-2T, was isolated from the rhizosphere of Sesuvium portulacastrum. By 16S rRNA gene sequence analysis, it was shown that strain CC-SPL15-2T belonged to the genus Salinicoccus. The isolate was most closely related to Salinicoccus hispanicus DSM 5352T (98.3 % 16S rRNA gene sequence similarity) and Salinicoccus roseus DSM 5351T (96.7 %); similarities to all other members of the genus Salinicoccus were <96.5 %. In accordance with characteristics of the genus Salinicoccus, the quinone system was mainly composed of menaquinone MK-6. The polar lipid profile exhibited the major components diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. In the polyamine pattern, spermidine was the predominant compound. The fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0, which supported the affiliation of strain CC-SPL15-2T to the genus Salinicoccus. DNA–DNA relatedness between strain CC-SPL15-2T and S. hispanicus CCUG 43288T was 42 and 32 % (reciprocal analysis). From these data as well as from physiological and biochemical tests, a clear differentiation of strain CC-SPL15-2T from S. hispanicus and other members of the genus Salinicoccus was possible. We propose that strain CC-SPL15-2T be assigned to a novel species, with the name Salinicoccus sesuvii sp. nov. The type strain is CC-SPL15-2T ( = DSM 23267T = CCM 7756T).
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Lactobacillus ozensis sp. nov., isolated from mountain flowers
More LessFive strains (Mizu2-1T, Gon2-7, Koba6-1, Koyu2-2 and Miya2-2) of lactic acid bacteria (LAB) were isolated from flowers in Oze National Park, Japan, using anaerobic cultivation. The five isolates were found to share identical 16S rRNA gene sequences. The isolates exhibited low levels of 16S rRNA gene sequence similarity to known LAB; the closest recognized relatives of strain Mizu2-1T were the type strains of Lactobacillus kunkeei (94.9 %), Lactobacillus kefiri (94.1 %) and Lactobacillus buchneri (93.9 %). Comparative analyses of rpoA and pheS gene sequences demonstrated that the novel isolates did not show significant relationships to other Lactobacillus species. The strains were Gram-stain-positive, catalase-negative and heterofermentative. Anaerobic growth was better than aerobic growth. The isolates utilized a narrow range of carbohydrates as sources of carbon and energy, including glucose and fructose. On the basis of phenotypic characteristics and phylogenetic data, the isolates represent a novel species of the genus Lactobacillus, for which the name Lactobacillus ozensis sp. nov. is proposed. The type strain is Mizu2-1T ( = JCM 17196T = DSM 23829T).
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Reclassification of Lactobacillus catenaformis (Eggerth 1935) Moore and Holdeman 1970 and Lactobacillus vitulinus Sharpe et al. 1973 as Eggerthia catenaformis gen. nov., comb. nov. and Kandleria vitulina gen. nov., comb. nov., respectively
The development of molecular tools and in particular the use of 16S rRNA gene sequencing has had a profound effect on the taxonomy of many bacterial groups. Gram-positive organisms that encompass the genera Lactobacillus and Clostridium within the Firmicutes are examples of taxa that have undergone major revisions based on phylogenetic information. A consequence of these reorganizations is that a number of organisms are now recognized as being misclassified. Previous studies have demonstrated that Lactobacillus catenaformis and Lactobacillus vitulinus are phylogenetically unrelated to Lactobacillus sensu stricto, being placed within the Clostridia rRNA cluster XVII. Based on the phenotypic, chemotaxonomic and phylogenetic data presented, it is proposed that L. catenaformis and L. vitulinus be reclassified in two new genera, named respectively Eggerthia gen. nov., with the type species Eggerthia catenaformis gen. nov., comb. nov. (type strain DSM 20559T = ATCC 25536T = CCUG 48174T = CIP 104817T = JCM 1121T) and Kandleria gen. nov., with the type species Kandleria vitulina gen. nov., comb. nov. (type strain LMG 18931T = ATCC 27783T = CCUG 32236T = DSM 20405T = JCM 1143T).
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Carboxydothermus islandicus sp. nov., a thermophilic, hydrogenogenic, carboxydotrophic bacterium isolated from a hot spring
An anaerobic, thermophilic bacterium, strain SET IS-9T, was isolated from an Icelandic hot spring. Cells of strain SET IS-9T are short, slightly curved, motile rods. The strain grows chemolithotrophically on CO, producing equimolar quantities of H2 and CO2. It also grows fermentatively on lactate or pyruvate in the presence of yeast extract (0.2 g l−1). Products of pyruvate fermentation are acetate, CO2 and H2. Growth occurs at 50–70 °C, with an optimum at 65 °C, and at pH 5.0–8.0, with an optimum at pH 5.5–6.0. The generation time during chemolithotrophic growth on CO under optimal conditions is 2.0 h. 16S rRNA gene sequence analysis suggested that the organism belongs to the genus Carboxydothermus. On the basis of phenotypic features and phylogenetic analysis, Carboxydothermus islandicus sp. nov. is proposed, with the type strain SET IS-9T ( = DSM 21830T = VKM B-2561T). An emended description of the genus Carboxydothermus is also given.
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- Other Bacteria
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Chthonomonas calidirosea gen. nov., sp. nov., an aerobic, pigmented, thermophilic micro-organism of a novel bacterial class, Chthonomonadetes classis nov., of the newly described phylum Armatimonadetes originally designated candidate division OP10
An aerobic, saccharolytic, obligately thermophilic, motile, non-spore-forming bacterium, strain T49T, was isolated from geothermally heated soil at Hell’s Gate, Tikitere, New Zealand. On the basis of 16S rRNA gene sequence similarity, T49T is the first representative of a new class in the newly described phylum Armatimonadetes, formerly known as candidate division OP10. Cells of strain T49T stained Gram-negative and were catalase-positive and oxidase-negative. Cells possessed a highly corrugated outer membrane. The major fatty acids were 16 : 0, i17 : 0 and ai17 : 0. The G+C content of the genomic DNA was 54.6 mol%. Strain T49T grew at 50–73 °C with an optimum temperature of 68 °C, and at pH 4.7–5.8 with an optimum growth pH of 5.3. A growth rate of 0.012 h−1 was observed under optimal temperature and pH conditions. The primary respiratory quinone was MK-8. Optimal growth was achieved in the absence of NaCl, although growth was observed at NaCl concentrations as high as 2 % (w/v). Strain T49T was able to utilize mono- and disaccharides such as cellobiose, lactose, mannose and glucose, as well as branched or amorphous polysaccharides such as starch, CM-cellulose, xylan and glycogen, but not highly linear polysaccharides such as crystalline cellulose or cotton. On the basis of its phylogenetic position and phenotypic characteristics, we propose that strain T49T represents a novel bacterial genus and species within the new class Chthonomonadetes classis nov. of the phylum Armatimonadetes. The type strain of Chthonomonas calidirosea gen. nov., sp. nov. is T49T ( = DSM 23976T = ICMP 18418T).
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- Proteobacteria
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Pseudomonas bauzanensis sp. nov., isolated from soil
More LessA Gram-negative, aerobic, motile rod, designated BZ93T, was isolated from soil from an industrial site. The strain grew at 5–30 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BZ93T was related to members of the genus Pseudomonas and was related most closely to Pseudomonas xiamenensis C10-2T (97.8 % 16S rRNA gene sequence similarity) and Pseudomonas pertucinogena IFO 14163T (97.4 %). The predominant cellular fatty acids of strain BZ93T were C18 : 1ω7c (54.8 %), summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH; 10.3 %), C16 : 0 (9.9 %) and C17 : 0 cyclo (7.4 %). The major quinone was ubiquinone 9. The major phospholipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unknown phospholipid. The genomic DNA G+C content was 61.8 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness, a novel species, Pseudomonas bauzanensis sp. nov., is proposed. The type strain is BZ93T ( = DSM 22558T = CGMCC 1.9095T = LMG 26048T).
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Glaciecola arctica sp. nov., isolated from Arctic marine sediment
A Gram-negative, motile, psychrotolerant, oxidase- and catalase-positive bacterium, designated BSs20135T, was isolated from Arctic marine sediment. Cells were straight or slightly curved rods and formed circular, convex and yellowish-brown colonies. Buds and prosthecae could be produced. The strain grew at 4–28 °C (optimum 25 °C) and with 1–5 % (w/v) NaCl (optimum 2 %) and hydrolysed aesculin and DNA, but did not reduce nitrate to nitrite. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain BSs20135T belonged to the genus Glaciecola and shared 93.6–97.7 % sequence similarity with the type strains of known species of the genus Glaciecola. The major cellular fatty acids of strain BSs20135T were summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C17 : 1ω8c and C18 : 1ω7c. The genomic DNA G+C content was 40.3 mol%. Based on 16S rRNA gene sequence analysis, DNA–DNA hybridization data and phenotypic and chemotaxonomic characterization, strain BSs20135T represents a novel species, for which the name Glaciecola arctica sp. nov. is proposed. The type strain is BSs20135T ( = CCTCC AB 209161T = KACC 14537T).
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Yersinia pekkanenii sp. nov.
The taxonomic position of three strains from water, soil and lettuce samples was studied by using a polyphasic taxonomic approach. The strains were reported to lack the virulence-encoding genes inv and virF in a previous study. Controversially, API 20 E and some other phenotypic tests suggested that the strains belong to Yersinia pseudotuberculosis, which prompted this polyphasic taxonomic study. In both the phylogenetic analyses of four housekeeping genes (glnA, gyrB, recA and HSP60) and numerical analyses of HindIII and EcoRI ribopatterns, the strains formed a separate group within the genus Yersinia. Analysis of the 16S rRNA gene sequences showed that the strains were related to Yersinia aldovae and Yersinia mollaretii, but DNA–DNA hybridization analysis differentiated them from these species. Based on the results of the phylogenetic and DNA–DNA hybridization analyses, a novel species, Yersinia pekkanenii sp. nov., is proposed. The type strain is ÅYV7.1KOH2T ( = DSM 22769T = LMG 25369T).
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Yersinia nurmii sp. nov.
This study was set up to identify three Gram-negative, rod-shaped strains originating from broiler meat packaged under a modified atmosphere. A polyphasic taxonomic approach, including multilocus sequence analysis (MLSA) of five genes (16S rRNA, glnA, gyrB, recA and HSP60), DNA–DNA reassociation between the closest phylogenetic neighbours and determination of relevant phenotypic properties, was applied. Phylogenetic analysis of the 16S rRNA gene sequences grouped these strains together and within the genus Yersinia. MLSA of the 16S rRNA gene and four housekeeping genes showed that the strains formed a monophyletic group separate from other Yersinia species in all phylogenetic trees constructed. The strains had a phenotypic profile different from those of other representatives of the genus Yersinia, but most similar to that of Yersinia ruckeri. Typical virulence markers for pathogenic Yersinia were not detected. Based on phylogenetic, phenotypic and DNA–DNA reassociation data, a novel species, Yersinia nurmii sp. nov., is proposed for the isolated strains. The type strain is APN3a-cT ( = DSM 22296T = LMG 25213T).
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Sphingomonas oryziterrae sp. nov. and Sphingomonas jinjuensis sp. nov. isolated from rhizosphere soil of rice (Oryza sativa L.)
More LessTwo Gram-reaction-negative, yellow–orange-pigmented, rod-shaped bacterial strains, designated YC6722T and YC6723T, were isolated from rhizosphere soil samples collected from rice fields in Jinju, Korea. Strains YC6722T and YC6723T grew optimally at 25–30 °C and at pH 7.0–8.5. Phylogenetic analyses of 16S rRNA gene sequences showed that strain YC6722T was most closely related to Sphingomonas jaspsi TDMA-16T (96.6 % sequence similarity) and strain YC6723T was related most closely to Sphingomonas aquatilis JSS7T (96.9 %). The two strains contained ubiquinone-10 (Q-10) as the major respiratory quinone system and sym-homospermidine as the major polyamine. The G+C contents of the genomic DNA of strains YC6722T and YC6723T were 63.3 and 61.0 mol%, respectively. The major fatty acid was C18 : 1ω7c. The polar lipids detected in the two strains were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, sphingoglycolipid, phosphatidyldimethylethanolamine and other unknown lipids. On the basis of their phylogenetic positions, and their biochemical and phenotypic characteristics, strains YC6722T and YC6723T represent two novel species of the genus Sphingomonas, for which the names Sphingomonas oryziterrae sp. nov. ( = KCTC 22476T = DSM 21455T) and Sphingomonas jinjuensis sp. nov. (KCTC 22477T = DSM 21457T) are proposed.
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Pseudomonas deceptionensis sp. nov., a psychrotolerant bacterium from the Antarctic
More LessDuring the taxonomic investigation of cold-adapted bacteria from samples collected in the Antarctic area of the South Shetland Islands, one Gram-reaction-negative, psychrotolerant, aerobic bacterium, designated strain M1T, was isolated from marine sediment collected on Deception Island. The organism was rod-shaped, catalase- and oxidase-positive and motile by means of a polar flagellum. This psychrotolerant strain grew at temperatures ranging from −4 °C to 34 °C. Phylogenetic studies based on 16S rRNA gene sequences confirmed that Antarctic isolate M1T was a member of the genus Pseudomonas and was located in the Pseudomonas fragi cluster. 16S rRNA gene sequence similarity values were >98 % between 13 type strains belonging to the Pseudomonas fluorescens lineage. However, phylogenetic analysis of rpoD gene sequences showed that strain M1T exhibited high sequence similarity only with respect to Pseudomonas psycrophila (97.42 %) and P. fragi (96.40 %) and DNA–DNA hybridization experiments between the Antarctic isolate M1T and the type strains of these two closely related species revealed relatedness values of 58 and 57 %, respectively. Several phenotypic characteristics, together with the results of polar lipid and cellular fatty acid analyses, were used to differentiate strain M1T from related pseudomonads. Based on the evidence of this polyphasic taxonomic study, strain M1T represents a novel species, for which the name Pseudomonas deceptionensis sp. nov. is proposed. The type strain is M1T ( = LMG 25555T = CECT 7677T).
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Vibrio atlanticus sp. nov. and Vibrio artabrorum sp. nov., isolated from the clams Ruditapes philippinarum and Ruditapes decussatus
Facultatively anaerobic marine bacteria isolated from cultured clams, Ruditapes decussatus and Ruditapes philippinarum, were previously investigated using amplified fragment length polymorphism (AFLP) and 16S rRNA gene sequence analyses. The isolates formed two AFLP clusters and belonged to the genus Vibrio, more precisely to the Splendidus clade. In this study, phylogenetic analyses based on sequences of the housekeeping genes rpoA, rpoD, pyrH, atpA and recA supported their inclusion in that clade forming two well differentiated groups with respect to the rest of the species within the clade, and confirmed that they formed two groups, separated from the rest of the species of the clade. DNA–DNA hybridization demonstrated that the isolates constitute two novel species of the genus Vibrio, which can be phenotypically differentiated from their closest relatives. The names Vibrio atlanticus sp. nov. and Vibrio artabrorum sp. nov. are proposed, with Vb 11.11T ( = CECT 7223T = LMG 24300T) and Vb 11.8T ( = CECT 7226T = LMG 23865T) as the type strains, respectively.
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Thioprofundum hispidum sp. nov., an obligately chemolithoautotrophic sulfur-oxidizing gammaproteobacterium isolated from the hydrothermal field on Suiyo Seamount, and proposal of Thioalkalispiraceae fam. nov. in the order Chromatiales
A novel mesophilic, facultatively anaerobic, sulfur-oxidizing bacterial strain, designated gps61T, was isolated from a surface rock sample collected from the hydrothermal field of Suiyo Seamount on the Izu-Bonin Arc in the Western Pacific Ocean. Cells of the isolate were rod-shaped with a single sheathed polar flagellum. Neither extensive internal membranes nor storage materials were present in the cells. In a 20 % CO2 atmosphere, strain gps61T grew using thiosulfate, sulfur or tetrathionate as electron donors and oxygen or nitrate as electron acceptors. Other substrates, including organic acids and sugars, did not support growth, indicating that strain gps61T was an obligate chemolithoautotroph. 16S rRNA gene sequence analysis revealed that strain gps61T was closely related to Thioprofundum lithotrophicum 106T (98.5 % sequence similarity) in the order Chromatiales. Phylogenetic trees grouped strain gps61T and Thioprofundum lithotrophicum in the same cluster along with Thioalkalispira microaerophila and Thiohalophilus thiocyanoxidans, but it was apparent from the analysis that the novel strain had definitely departed from the family lineage. On the basis of its phylogenetic position along with its morphological and physiological characteristics, strain gps61T ( = NBRC 101261T = DSM 18546T) represents a novel species of the genus Thioprofundum, for which the name Thioprofundum hispidum sp. nov. is proposed. In addition, we propose a novel family name, Thioalkalispiraceae, in the order Chromatiales, to accommodate the genera Thioalkalispira, Thiohalophilus and Thioprofundum.
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Rhizobium pseudoryzae sp. nov., isolated from the rhizosphere of rice
More LessA Gram-stain-negative, aerobic, rod-shaped bacterium, designated strain J3-A127T, was isolated from the roots of fresh rice plants (Oryza sativa). Cells were non-motile and no flagellum was detected. Comparison of 16S rRNA gene sequences indicated that the strain was phylogenetically related to species of the genus Rhizobium, with closest similarity to Rhizobium oryzae Alt 505T (96.4 %). The low levels of 16S rRNA gene sequence similarity (<90 %) found between the gyrB, atpD, recA and glnII gene sequences of strain J3-A127T and the type strains of recognized species of the genus Rhizobium also indicated that it represented a separate species. The temperature range for growth was 10–40 °C (optimum around 28 °C) and the pH range was 6.0–11.0 (optimum pH 7.0–8.0). Strain J3-A127T tolerated NaCl concentrations up to 5.0 % (w/v). The strain was catalase- and oxidase-positive. The main cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6; 46.7 %). The DNA G+C content of strain J3-A127T was 59.5 mol%. Strain J3-A127T did not form any nodules on four different legumes and the nodD and nifH genes were not detected by PCR. According to physiological and biochemical characteristics and genotypic data, strain J3-A127T is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium pseudoryzae sp. nov. is proposed. The type strain is J3-A127T ( = ACCC 10380T = KCTC 23294T).
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Hoeflea anabaenae sp. nov., an epiphytic symbiont that attaches to the heterocysts of a strain of Anabaena
The heterotrophic, epiphytic, symbiotic bacterial strain WH2KT was previously isolated from a two-member culture in which it was attached to the heterocysts of a strain of Anabaena (SSM-00). Analysis of its 16S rRNA gene sequence demonstrated that the symbiont was most closely related to the type strain of Hoeflea marina (96.9 % similarity), which belongs to the family Phyllobacteriaceae within the order Rhizobiales of the class Alphaproteobacteria. A polyphasic taxonomic study was performed on strain WH2KT, which consisted of irregular rods (2–5 µm long, 0.2 µm wide) that appeared to be narrower at one pole. Optimal growth was obtained in complex media with 15 g sea salts l−1, at 18–34 °C (30 °C optimum) and at pH 6.0–8.0 (optimum pH 6.5). Unknown growth requirements were provided by small amounts of yeast extract but not by standard vitamin and trace metal solutions. Of the substrates tested, WH2KT was able to utilize only acetate, pyruvate, malate and fumarate. Growth was observed only under aerobic and microaerobic conditions, and nitrate was not reduced. No photosynthetic pigments were detected under any of the growth conditions tested. The predominant fatty acids were a summed feature that comprises C18 : 1ω7c, C18 : 1ω9t, C18 : 1ω12t or any combination of these (64.0 %) and an unidentified fatty acid of equivalent chain length 17.603 (13.5 %). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphoglycolipid, unknown lipids and an unidentified aminolipid. The only respiratory ubiquinone detected was Q-10. The DNA G+C content of the strain was 58.1 mol%. The organism can form a site-specific attached symbiotic relationship with a species of Anabaena. Based on phylogenetic and phenotypic evidence, it is proposed that strain WH2KT be classified within a novel species of the genus Hoeflea, for which the name Hoeflea anabaenae sp. nov. is proposed. The type strain is WH2KT ( = CCUG 56626T = NRRL B-59520T).
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Methyloferula stellata gen. nov., sp. nov., an acidophilic, obligately methanotrophic bacterium that possesses only a soluble methane monooxygenase
Two strains of aerobic methanotrophic bacteria, AR4T and SOP9, were isolated from acidic (pH 3.8–4.0) Sphagnum peat bogs in Russia. Another phenotypically similar isolate, strain LAY, was obtained from an acidic (pH 4.0) forest soil in Germany. Cells of these strains were Gram-negative, non-pigmented, non-motile, thin rods that multiplied by irregular cell division and formed rosettes or amorphous cell conglomerates. Similar to Methylocella species, strains AR4T, SOP9 and LAY possessed only a soluble form of methane monooxygenase (sMMO) and lacked intracytoplasmic membranes. Growth occurred only on methane and methanol; the latter was the preferred growth substrate. mRNA transcripts of sMMO were detectable in cells when either methane or both methane and methanol were available. Carbon was assimilated via the serine and ribulose-bisphosphate (RuBP) pathways; nitrogen was fixed via an oxygen-sensitive nitrogenase. Strains AR4T, SOP9 and LAY were moderately acidophilic, mesophilic organisms capable of growth between pH 3.5 and 7.2 (optimum pH 4.8–5.2) and at 4–33 °C (optimum 20–23 °C). The major cellular fatty acid was 18 : 1ω7c and the quinone was Q-10. The DNA G+C content was 55.6–57.5 mol%. The isolates belonged to the family Beijerinckiaceae of the class Alphaproteobacteria and were most closely related to the sMMO-possessing methanotrophs of the genus Methylocella (96.4–97.0 % 16S rRNA gene sequence similarity), particulate MMO (pMMO)-possessing methanotrophs of the genus Methylocapsa (96.1–97.0 %), facultative methylotrophs of the genus Methylovirgula (96.1–96.3 %) and non-methanotrophic organotrophs of the genus Beijerinckia (96.5–97.0 %). Phenotypically, strains AR4T, SOP9 and LAY were most similar to Methylocella species, but differed from members of this genus by cell morphology, greater tolerance of low pH, detectable activities of RuBP pathway enzymes and inability to grow on multicarbon compounds. Therefore, we propose a novel genus and species, Methyloferula stellata gen. nov., sp. nov., to accommodate strains AR4T, SOP9 and LAY. Strain AR4T ( = DSM 22108T = LMG 25277T = VKM B-2543T) is the type strain of Methyloferula stellata.
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Novosphingobium sediminicola sp. nov. isolated from freshwater sediment
More LessA yellow-pigmented, Gram-negative, short rod-shaped, non-motile and non-spore-forming bacterial strain, designated HU1-AH51T, was isolated from freshwater sediment and was characterized using a polyphasic approach, in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain HU1-AH51T was shown to belong to the genus Novosphingobium, showing the highest level of sequence similarity with respect to Novosphingobium resinovorum NCIMB 8767T (96.0 %), Novosphingobium naphthalenivorans TUT562T (96.0 %) and Novosphingobium panipatense SM16T (96.0 %). Strain HU1-AH51T had a genomic DNA G+C content of 62.6 mol% and Q-10 as the predominant respiratory quinone. Furthermore, the major polyamine component (spermidine) in the cytoplasm and the presence of sphingoglycolipids suggested that strain HU1-AH51T belongs to the family Sphingomonadaceae. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain HU1-AH51T represents a novel species of the genus Novosphingobium, for which the name Novosphingobium sediminicola sp. nov. is proposed. The type strain is HU1-AH51T ( = LMG 24320T = KCTC 22311T).
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Zobellella aerophila sp. nov., isolated from seashore sand, and emended description of the genus Zobellella
More LessA strictly aerobic, nitrate-reducing, motile, rod-shaped member of the class Gammaproteobacteria, designated strain JC2671T, was isolated from a seashore sand sample from Dokdo, Korea. The isolate reduced nitrate to nitrite, but not to nitrogen, and required NaCl for growth. 16S rRNA gene sequence analysis indicated that the isolate belonged to the genus Zobellella within the order Alteromonadales with sequence similarities of 96.0–97.6 % to strains of Zobellella species with validly published names. However, in DNA–DNA hybridization studies, a low genomic relatedness (43 %) between strain JC2671T and the type strain of Zobellella denitrificans indicated that the isolate represented a novel genomic species. The polar lipid pattern (phosphatidylethanolamine and phosphatidylglycerol), predominant cellular fatty acids [C16 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c)] and the DNA G+C content (59 mol%) of the novel strain were consistent with its assignment to the genus Zobellella. In contrast, a number of phenotypic characteristics, namely a requirement of NaCl for growth, the inability to grow under facultatively anaerobic conditions, the absence of nitrite reduction and differences in carbohydrate utilization and enzymic activities, clearly distinguished the novel isolate from other species of the genus Zobellella. Data from this polyphasic study indicate that strain JC2671T represents a novel species in the genus Zobellella, for which the name Zobellella aerophila sp. nov. is proposed. The type strain is JC2671T ( = KACC 15081T = JCM 17110T). The description of the genus Zobellella has been emended accordingly.
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Bradyrhizobium lablabi sp. nov., isolated from effective nodules of Lablab purpureus and Arachis hypogaea
More LessFive strains isolated from root nodules of Lablab purpureus and Arachis hypogaea grown in the Anhui and Sichuan provinces of China were classified as members of the genus Bradyrhizobium. These strains had identical 16S rRNA gene sequences which shared 99.48 %, 99.48 % and 99.22 % similarity with the most closely related strains of Bradyrhizobium jicamae PAC68T, Bradyrhizobium pachyrhizi PAC48T and Bradyrhizobium elkanii USDA 76T, respectively. A study using a polyphasic approach, including 16S rRNA gene RFLP, IGS-RFLP, BOX-PCR, comparative sequence analysis of the 16S–23S rRNA intergenic spacer (IGS) and the recA, atpD and glnII genes, DNA–DNA hybridization and phenotypic tests, showed that the five strains clustered into a coherent group that differentiated them from all recognized species of the genus Bradyrhizobium. Sequencing of nifH and nodC genes and cross-nodulation tests showed that the representative strains CCBAU 23086T, CCBAU 23160 and CCBAU 61434, isolated from different plants, had identical nifH and nodC gene sequences and were all able to nodulate Lablab purpureus, Arachis hypogaea and Vigna unguiculata. Based upon these results, the name Bradyrhizobium lablabi sp. nov. is proposed for this novel species and strain CCBAU 23086T ( = LMG 25572T = HAMBI 3052T) is designated as the type strain. The DNA G+C mol% is 60.14 (T m).
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Halomonas stenophila sp. nov., a halophilic bacterium that produces sulphate exopolysaccharides with biological activity
We have undertaken a polyphasic taxonomic study of two halophilic, Gram-negative bacterial strains, N12T and B-100, that produce sulphated exopolysaccharides with biological activity. They were isolated from two different saline soil samples. Both strains grow at NaCl concentrations within the range 3–15 % (w/v) [optimum 5–10 % (w/v)], at 15–37 °C (optimum 20–32 °C) and at pH 6–8 (optimum pH 7–8). Their 16S rRNA gene sequences indicate that they belong to the genus Halomonas in the class Gammaproteobacteria. Their closest relative is Halomonas nitroreducens, to which our strains show maximum 16S rRNA gene sequence similarity values of 98.7 % (N12T) and 98.3 % (B-100). Their DNA G+C contents are 61.9 and 63.8 mol%, respectively. The results of DNA–DNA hybridizations showed 43.9 % relatedness between strain N12T and H. nitroreducens CECT 7281T, 30.5 % between N12T and Halomonas ventosae CECT 5797T, 39.2 % between N12T and Halomonas fontilapidosi CECT 7341T, 46.3 % between N12T and Halomonas maura CECT 5298T, 52.9 % between N12T and Halomonas saccharevitans LMG 23976T, 51.3 % between N12T and Halomonas koreensis JCM 12237T and 100 % between strains N12T and B-100. The major fatty acids of strain N12T are C12 : 0 3-OH (5.42 %), C15 : 0 iso 2-OH/C16 : 1ω7c (17.37 %), C16 : 0 (21.62 %) and C18 : 1ω7c (49.19 %). The proposed name for the novel species is Halomonas stenophila sp. nov. Strain N12T ( = CECT 7744T = LMG 25812T) is the type strain.
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- Eukaryotic Micro-Organisms
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Trichosporon xylopini sp. nov., a hemicellulose-degrading yeast isolated from the wood-inhabiting beetle Xylopinus saperdioides
More LessFour arthroconidium-producing yeasts were isolated from the gut of wood-inhabiting tenebrionid and passalid beetles. The rRNA genes of these yeast strains were sequenced, compared and analysed. The sequence results and other taxonomic characterizations placed two of the strains into Trichosporon porosum, and the remaining strains, EH024T and EH026 which were isolated from Xylopinus saperdioides (Coleoptera: Tenebrionidae), into a novel species of the genus Trichosporon in the Porosum clade. Strain EN6S23 was independently isolated from forest soil in Taiwan and was identified as the same novel species based on identical sequences in the internal transcribed spacers (ITS) and the D1/D2 region of the LSU rRNA gene and similar physiological characteristics to those of strains EH024T and EH026. The three strains can assimilate cellulose and xylan as sole carbon source, and are clearly distinguished from their closest taxon, T. porosum, by 14 nt differences in the ITS and D1/D2 region. These strains did not reproduce sexually under the laboratory conditions tested. The novel species is proposed as Trichosporon xylopini sp. nov. (type strain EH024T = ATCC MYA-4670T = CBS 11841T).
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Wickerhamomyces ochangensis sp. nov., an ascomycetous yeast isolated from the soil of a potato field
More LessA novel ascomycetous yeast, designated strain N7a-Y2T, was isolated from soil collected in a potato field in Ochang, Korea, and its taxonomic position was studied. A neighbour-joining tree based on the D1/D2 domain of large-subunit rRNA gene sequences revealed that the isolate was a member of the Wickerhamomyces clade and that it was closely related to Wickerhamomyces bisporus, Candida quercuum, Candida ulmi and Wickerhamomyces alni. Strain N7a-Y2T formed Saturn-shaped ascospores in unconjugated and persistent asci. D1/D2 domain 26S rRNA gene sequence divergences of 11.0–21.1 % between strain N7a-Y2T and other members of the Wickerhamomyces clade indicate that the strain represents a novel species of the genus Wickerhamomyces, for which the name Wickerhamomyces ochangensis sp. nov. is proposed. The type strain is N7a-Y2T ( = KCTC 17870T = CBS 11843T).
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Molecular and morphological analysis of the family Calonymphidae with a description of Calonympha chia sp. nov., Snyderella kirbyi sp. nov., Snyderella swezyae sp. nov. and Snyderella yamini sp. nov.
Calonymphids are a group of multinucleate, multiflagellate protists belonging to the order Cristamonadida (Parabasalia) that are found exclusively in the hindgut of termites from the family Kalotermitidae. Despite their impressive morphological complexity and diversity, few species have been formally described and fewer still have been characterized at the molecular level. In this study, four novel species of calonymphids were isolated and characterized: Calonympha chia and Snyderella yamini spp. nov., from Neotermes castaneus and Calcaritermes nearcticus from Florida, USA, and Snyderella kirbyi and Snyderella swezyae, spp. nov., from Calcaritermes nigriceps and Cryptotermes cylindroceps from Colombia. Each of these species was distinguished from its congeners by residing in a distinct host and by differences at the molecular level. Phylogenetic analyses of small subunit (SSU) rDNA indicated that the genera Calonympha and Stephanonympha were probably not monophyletic, though the genus Snyderella, previously only represented by one sequence in molecular analyses, appeared with these new data to be monophyletic. This was in keeping with the traditional evolutionary view of the group in which the morphology of the genus Snyderella is considered to be derived, while that of the genus Stephanonympha is ancestral and therefore probably plesiomorphic.
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- Evolution, Phylogeny And Biodiversity
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Multilocus sequence analysis of phytopathogenic species of the genus Streptomyces
More LessThe identification and classification of species within the genus Streptomyces is difficult because there are presently 576 species with validly published names and this number increases every year. The value of multilocus sequence analysis applied to the systematics of Streptomyces species has been well demonstrated in several recently published papers. In this study the sequence fragments of four housekeeping genes, atpD, recA, rpoB and trpB, were determined for the type strains of 10 known phytopathogenic species of the genus Streptomyces, including Streptomyces scabiei, Streptomyces acidiscabies, Streptomyces europaeiscabiei, Streptomyces luridiscabiei, Streptomyces niveiscabiei, Streptomyces puniciscabiei, Streptomyces reticuliscabiei, Streptomyces stelliscabiei, Streptomyces turgidiscabies and Streptomyces ipomoeae, as well as six uncharacterized phytopathogenic Streptomyces isolates. The type strains of 52 other species, including 19 species observed to be phylogenetically closely related to these, based on 16S rRNA gene sequence analysis, were also included in the study. Phylogenetic analysis of single gene alignments and a concatenated four-gene alignment demonstrated that the phytopathogenic species are taxonomically distinct from each other in spite of high 16S rRNA gene sequence similarities and provided a tool for the identification of unknown putative phytopathogenic Streptomyces strains at the species level.
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- Methods
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Usefulness of a real-time PCR platform for G+C content and DNA–DNA hybridization estimations in vibrios
More LessThe aim of this study was to evaluate the utility of a real-time PCR platform to estimate the DNA G+C content (mol%) and DNA–DNA hybridization (DDH) values in the genus Vibrio. In total, nine vibrio strains were used to determine the relationship between genomic DNA G+C content and T m (°C). The T m and HPLC datasets fit a linear regression curve with a significant correlation coefficient, corroborating that this methodology has a high correlation with the standard methodology based on HPLC (R2 = 0.94). Analysis of 31 pairs of vibrios provided a wide range of ΔT m values, varying between 0.72 and 12.5 °C. Pairs corresponding to strains of the same species or strains from sister species showed the lowest ΔT m values. For instance, the ΔT m of the sister species Vibrio harveyi LMG 4044T and Vibrio campbellii LMG 11216T was 5.2 °C, whereas the ΔT m of Vibrio coralliilyticus LMG 20984T and Vibrio neptunius LMG 20536T was 8.75 °C. The mean ΔT m values corresponding to pairs of strains with DDH values lower than 60 % or higher than 80 % were, respectively, 8.29 and 2.21 °C (significant difference, P<0.01). The high correlation between DDH values obtained in previous studies and the ΔT m values (R2 = 0.7344) indicates that the fluorimetric methodology is a reliable alternative for the estimation of both DNA G+C content and ΔT m in vibrios. We suggest that strains of the same Vibrio species will have less than 4 °C ΔT m. The use of a real-time PCR platform represents a valuable alternative for the development of the taxonomy of vibrios.
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- International Committee On Systematics Of Prokaryotes
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- Minutes
- Erratum
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Volumes and issues
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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)