- Volume 57, Issue 2, 2007
Volume 57, Issue 2, 2007
- Notification List
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Notification that new names and new combinations have appeared in volume 56, part 11, 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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Smaragdicoccus niigatensis gen. nov., sp. nov., a novel member of the suborder Corynebacterineae
A polyphasic taxonomic approach was applied to determine the taxonomic position of a hydrocarbon-degrading actinomycete, strain Hou_blueT, which was isolated from soil samples collected from an oil spring in Niigata, Japan. The results of 16S rRNA and gyrB gene sequence comparisons indicated that strain Hou_blueT represented a novel lineage in the suborder Corynebacterineae. Colonies were malachite green-like in colour on 1/10 trypticase soy agar and the cell morphology was coccoid in all growth phases. The cell-wall diamino acid and sugar indicated chemotype IV and variation A1γ. The sugars of the peptidoglycan were glycolated. The polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and some unspecified glycolipids. The organism contained two novel cyclic forms of menaquinone, smaragdiquinone A-8(H4, ω-cycl) and smaragdiquinone B-8(H4, dicycl). The major fatty acids were cis-9-18 : 1 (34.46 %) and 16 : 0 (25.1 %). Small amounts of 10-methyl-branched fatty acids were also present (10-methyl-17 : 0, 0.17 %), but not tuberculostearic acid (10-methyl-18 : 0), which has been shown to be present in all nocardiae. Gas-chromatographic analysis of the mycolic acid revealed a carbon-chain length of C43–C49. The DNA G+C content was 63.7 mol%. On the basis of phenotypic and phylogenetic distinctness, the organism is proposed to represent a novel genus and species, Smaragdicoccus niigatensis gen. nov., sp. nov., with the type strain Hou_blueT (=MBIC 06267T=DSM 44881T).
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Aeromicrobium tamlense sp. nov., isolated from dried seaweed
More LessA Gram-positive, non-motile, rod-shaped actinomycete strain, designated SSW1-57T, was isolated from a dried seaweed sample from the coast of Jeju Island, Republic of Korea and subjected to a polyphasic taxonomic study. A neighbour-joining tree based on 16S rRNA gene sequences showed that the organism was related to members of the family Nocardioidaceae and formed a separate branch at the base of a taxon encompassing members of the genus Aeromicrobium, whereas it occupied an intermediate position between Aeromicrobium alkaliterrae–Aeromicrobium marinum and Aeromicrobium erythreum–Aeromicrobium fastidiosum clusters in maximum-parsimony and maximum-likelihood trees. The phylogenetic association of the isolate with the genus Aeromicrobium was supported by the following chemotaxonomic properties: ll-diaminopimelic acid in the peptidoglycan, MK-9(H4) as the major menaquinone and major fatty acids cis-9-octadecenoic acid, hexadecanoic acid, 10-methyl octadecanoic acid and 2-hydroxy hexadecanoic acid. The polar lipid profile contained phosphatidylinositol, diphosphatidylglycerol and phosphatidylglycerol. Levels of 16S rRNA gene sequence similarity between the novel organism and the type strains of the four recognized Aeromicrobium species were in the range 96.5–96.7 %. On the basis of phylogenetic analyses and phenotypic data, it is proposed that the organism should be classified as representing a novel species of the genus Aeromicrobium, with the name Aeromicrobium tamlense sp. nov. The type strain is SSW1-57T (=JCM 13811T=NRRL B-24466T).
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Leifsonia ginsengi sp. nov., isolated from ginseng root
More LessA Gram-positive, rod-shaped, non-motile bacterium, designated strain wged11T, was isolated from the root of ginseng, and its taxonomic position was established using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that this organism formed a robust clade with recognized species of the genus Leifsonia. Strain wged11T was characterized by a high content of ω-cyclohexylundecanoic and anteiso- and iso-branched saturated fatty acids, MK-11 as the major menaquinone and dl-2,4-diaminobutyric acid in its cell-wall peptidoglycan. The DNA G+C content of strain wged11T was 66.4 mol%. Levels of similarity between the 16S rRNA gene sequence of strain wged11T and those of the type strains of other members of the genus Leifsonia ranged from 94.7 to 97.6 %. The mean level of DNA–DNA relatedness between strain wged11T and Leifsonia poae DSM 15202T, its nearest phylogenetic neighbour, was 35.3 %. Based on these findings, strain wged11T (=CGMCC 4.3491T=JCM 13908T) is proposed as the type strain of a novel species of the genus Leifsonia, Leifsonia ginsengi sp. nov.
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- Archaea
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Haloquadratum walsbyi gen. nov., sp. nov., the square haloarchaeon of Walsby, isolated from saltern crystallizers in Australia and Spain
Strains C23T and HBSQ001 were isolated from solar salterns and are novel square-shaped, aerobic, extremely halophilic members of the domain Archaea and family Halobacteriaceae. Cells stained Gram-negative and grew optimally in media containing 18 % salts at around neutral pH. Mg2+ is not required. The DNA G+C content of both isolates was 46.9 mol% and DNA–DNA cross-hybridization showed a relatedness of 80 %. Their 16S rRNA gene sequences showed only 2 nucleotide differences (99.9 % identity) and phylogenetic tree reconstructions with other recognized members of the Halobacteriaceae indicated that they formed a distinct clade, with the closest relative being Halogeometricum borinquense PR 3T (91.2 % sequence identity). The major polar glycolipid of both isolates was the sulfated diglycosyl diether lipid S-DGD-1. Electron cryomicrosopy of whole cells revealed similar internal structures, such as gas vesicles and polyhydroxyalkanoate granules, but the cell wall of isolate HBSQ001 displayed a more complex S-layer compared with that of isolate C23T. The phenotypic characterization and phylogenetic data support the placement of isolates C23T and HBSQ001 in a novel species in a new genus within the Halobacteriaceae, for which we propose the name Haloquadratum walsbyi gen. nov., sp. nov. The type strain of Haloquadratum walsbyi is C23T (=JCM 12705T=DSM 16854T).
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Haloferax prahovense sp. nov., an extremely halophilic archaeon isolated from a Romanian salt lake
More LessA novel halophilic archaeon, strain TL6T, was isolated from Telega Lake, a hypersaline environment in Prahova county, Romania. Strain TL6T was able to grow in media with a salt concentration of between 2.5 and 5.2 M, with optimum growth at a concentration of 3.5 M. The novel strain was able to grow at concentrations of 1 M MgCl2 or less, with an optimum of 0.4 M Mg2+. Growth of the novel strain occurred between pH 6.0 and 8.5, with an optimum of pH 7.0–7.5. The G+C content of the total DNA was 63.7 mol%. The 16S rRNA gene sequence of the novel strain was most closely related to species of the genus Haloferax (97.3–99.3 % sequence similarity). The lipid profile of the novel strain corresponded to that of other species belonging to the genus Haloferax. A comparative analysis of the phenotypic properties and DNA–DNA hybridization between the novel strain and other species of the genus Haloferax strongly supported the conclusion that strain TL6T represents a novel species within this genus, for which the name Haloferax prahovense sp. nov., is proposed. The type strain is TL6T (=JCM 13924T=DSM 18310T).
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- Bacteroidetes
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Salegentibacter catena sp. nov., isolated from sediment of the South China Sea, and emended description of the genus Salegentibacter
More LessA novel marine bacterial strain, HY1T, was isolated from sediment of the South China Sea. The strain was aerobic and heterotrophic and formed saffron yellow-pigmented colonies on marine agar 2216. Cells were non-motile, Gram-negative rods, frequently occurring in chains. blastn searches revealed that the 16S rRNA gene sequence of strain HY1T showed high similarity with those of members of the genera Gillisia (91.7–93.8 %) and Salegentibacter (92.6–93.5 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain clustered with members of both Salegentibacter and Gillisia and phylogenetic trees constructed using three different methods (neighbour-joining, maximum-parsimony and minimum-evolution) indicated that strain HY1T clustered more frequently with members of the genus Salegentibacter. The DNA G+C content of strain HY1T was 44.4 mol% and its major cellular fatty acids (⩾5 % of the total fatty acids) were iso-15 : 1 (5.0 %), iso-15 : 0 (6.8 %), anteiso-15 : 0 (6.4 %), 15 : 0 (10.4 %), iso-16 : 0 (13.5 %), summed feature 3 (comprising iso-15 : 0 2-OH and/or 16 : 1ω7c; 6.3 %), iso-17 : 0 3-OH (5.2 %) and 17 : 0 2-OH (5.0 %). Cells contained menaquinone 6. Based on the phylogenetic and phenotypic analyses, strain HY1T should be classified as representing a novel species within the genus Salegentibacter, for which the name Salegentibacter catena sp. nov. is proposed. The type strain is HY1T (=CGMCC 1.6101T=JCM 14015T). Based on this study and on previously described Salegentibacter species, an emended description of the genus Salegentibacter is given.
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Flavobacterium defluvii sp. nov., isolated from activated sludge
More LessA Gram-negative bacterium, designated strain EMB117T, was isolated from a municipal wastewater treatment plant and characterized by polyphasic taxonomy. The cells were non-spore-forming rods that showed gliding motility. Optimal growth occurred at 25–30 °C and pH 7.0–8.0. Strain EMB117T contained phosphatidylethanolamine as the predominant polar lipid, and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH). The G+C content of the genomic DNA was 33.5 mol% and the major isoprenoid quinone was MK-6. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain EMB117T belonged to the genus Flavobacterium and was most closely related to Flavobacterium johnsoniae DSM 425T (97.8 % sequence similarity). The DNA–DNA relatedness between strain EMB117T and F. johnsoniae ATCC 17061T was about 18 %. On the basis of the phenotypic, chemotaxonomic and molecular data, strain EMB117T represents a novel species within the genus Flavobacterium, for which the name Flavobacterium defluvii sp. nov. is proposed. The type strain is EMB117T (=KCTC 12612T=DSM 17963T).
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Flavobacterium aquidurense sp. nov. and Flavobacterium hercynium sp. nov., from a hard-water creek
More LessTen new Flavobacterium-like strains were isolated from freshwater of the hard-water creek Westerhöfer Bach, northern Germany. These strains formed two phylogenetic groups: strains WB 1.1-56T, WB 1.1-04, WB 1.1-14, WB 1.1-57 and WB 1.1-63; and strains WB 4.2-33T, WB 4.1-86, WB 4.2-34, WB 4.2-32 and WB 4.2-78. Cells were Gram-negative, yellow-pigmented, chemoheterotrophic rods. Their major fatty acid profiles were similar, consisting of iso-C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH). DNA G+C contents for strains WB 1.1-56T and WB 4.2-33T were 33.5 and 37.5 mol%, respectively. Phylogenetic analysis based on almost complete 16S rRNA gene sequences indicated that strain WB 1.1-56T was phylogenetically most closely related to Flavobacterium frigidimaris KUC-1T, and that strain WB 4.2-33T was related most closely to F. frigidimaris KUC-1T and Flavobacterium saccharophilum DSM 1811T. Levels of 16S rRNA gene sequence similarity between strains WB 1.1-56T and WB 4.2-33T and the type strains of recognized members of the genus Flavobacterium were below 98 %. DNA–DNA hybridization experiments confirmed the separate genomic status of strains WB 1.1-56T and WB 4.2-33T. Strains WB 1.1-56T and WB 4.2-33T and their respective relatives differed from phylogenetically related Flavobacterium species based on several phenotypic characteristics. On the basis of their phenotypic and phylogenetic distinctiveness, the two groups of strains are considered to represent two novel species, for which the names Flavobacterium aquidurense sp. nov. (type strain WB 1.1-56T=DSM 18293T=CIP 109242T) and Flavobacterium hercynium sp. nov. (type strain WB 4.2-33T=DSM 18292T=CIP 109241T) are proposed.
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Sediminibacter furfurosus gen. nov., sp. nov. and Gilvibacter sediminis gen. nov., sp. nov., novel members of the family Flavobacteriaceae
More LessTwo Gram-negative, chemoheterotrophic, non-motile strains, Mok-1-36T and MAOS-86T, were isolated from marine-sediment samples collected from the coasts of Okinawa island and the city of Odawara in Japan, respectively. Phylogenetic studies based on 16S rRNA gene sequences indicated that Mok-1-36T and MAOS-86T were members of the family Flavobacteriaceae, clustering with members of the genera Ulvibacter and Vitellibacter, respectively. Strains Mok-1-36T and MAOS-86T shared pairwise 16S rRNA gene sequence similarities of 93.5 and 89.1 % with the type strains of Ulvibacter litoralis and Vitellibacter vladivostokensis, respectively. Phylogenetic distinctiveness and phenotypic differences from their phylogenetic neighbours indicated that these strains represent two novel species and genera within the family Flavobacteriaceae, for which the names Sediminibacter furfurosus gen. nov., sp. nov. (MAOS-86T) and Gilvibacter sediminis gen. nov., sp. nov. (Mok-1-36T) are proposed. The type strain of Sediminibacter furfurosus is MAOS-86T (=NBRC 101622T=CIP 109285T) and the type strain of Gilvibacter sediminis is Mok-1-36T (=NBRC 101626T=CIP 109286T).
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Parabacteroides johnsonii sp. nov., isolated from human faeces
More LessA bacterial strain isolated from human faeces, M-165T, was characterized in terms of its phenotypic and biochemical features, cellular fatty acid profile, menaquinone profile and phylogenetic position (based on 16S rRNA gene sequence analysis). A 16S rRNA gene sequence analysis showed that the isolate was a member of the genus Parabacteroides. Strain M-165T was closely related to Parabacteroides merdae strains, showing 98 % sequence similarity. The strain was obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative, rod-shaped and was able to grow on media containing 20 % bile. Although the phenotypic characteristics of the strain M-165T were similar to those of P. merdae, the isolate could be differentiated from P. merdae by means of API 20A tests for l-arabinose and l-rhamnose fermentation. DNA–DNA hybridization experiments revealed the genomic distinctiveness of the novel strain with respect to P. merdae JCM 9497T (⩽60 % DNA–DNA relatedness). The DNA G+C content of the strain is 47.6 mol%. On the basis of these data, strain M-165T represents a novel species of the genus Parabacteroides, for which the name Parabacteroides johnsonii sp. nov. is proposed. The type strain is M-165T (=JCM 13406T=DSM 18315T).
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Pontibacter akesuensis sp. nov., isolated from a desert soil in China
More LessA Gram-negative, non-motile, rod-shaped bacterium, designated strain AKS 1T, was isolated from a desert soil sample collected from Akesu, XinJiang Province, China. A taxonomic study, including phylogenetic analysis based on 16S rRNA gene sequences and phenotypic characteristics, was performed on the novel isolate. The predominant menaquinone of strain AKS 1T was MK-7. The major fatty acids included i-C15 : 0, ai-C17 : 1 B/i-C17 : 1 I and i-C17 : 0 3-OH. The G+C content of the DNA was 51.4 mol%. Based on the results of phenotypic and genotypic characteristics, strain AKS 1T should be assigned as representing a novel species of the genus Pontibacter, for which the name Pontibacter akesuensis is proposed. The type strain is AKS 1T (=KCTC 12758T=CCTCC AB 206086T).
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Barnesiella viscericola gen. nov., sp. nov., a novel member of the family Porphyromonadaceae isolated from chicken caecum
More LessTwo bacterial strains isolated from chicken caecum, C46T and C47, were characterized using a polyphasic taxonomic approach that included analysis of the phenotypic and biochemical features, cellular fatty acid profiles, menaquinone profiles and phylogenetic position (using 16S rRNA gene sequence analysis). The 16S rRNA gene sequence analysis showed that these strains belonged to the family Porphyromonadaceae. These strains shared 100 % 16S rRNA gene sequence similarity with each other and were related to Parabacteroides distasonis (showing 86 % sequence similarity). The strains were found to be obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative rods. Growth of the strains was inhibited on medium containing 20 % bile. The major menaquinones of the isolates were MK-11 and MK-12. This menaquinone composition was different from those of other genera of the family Porphyromonadaceae, such as Parabacteroides (in which the predominant menaquinones are MK-9 and MK-10), Porphyromonas (MK-9 and MK-10) and Tannerella (MK-10 and MK-11). This is an important chemotaxonomic characteristic of these micro-organisms. The DNA G+C content of strain C46T is 52.0 mol%. On the basis of these data, strains C46T and C47 represent a novel genus and species, for which the name Barnesiella viscericola gen. nov., sp. nov. is proposed. The type strain of Barnesiella viscericola is C46T (=JCM 13660T=DSM 18177T).
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Pedobacter panaciterrae sp. nov., isolated from soil in South Korea
More LessA Gram-negative, facultatively anaerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated Gsoil 042T, was isolated from a soil sample of a ginseng field in Pocheon province (South Korea) and was characterized taxonomically by using a polyphasic approach. The isolate was positive for catalase and oxidase, but negative for gelatinase and production of indole and H2S. The predominant isoprenoid quinone was menaquinone 7 (MK-7). The major cellular fatty acids were summed feature 4 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH; 35.7 %), iso-C15 : 0 (24.3 %) and iso-C17 : 0 3-OH (11.6 %). Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 042T fell within the radiation of the cluster comprising Pedobacter species. On the basis of 16S rRNA gene sequence similarities, the phylogenetically closest recognized species of the genus Pedobacter to strain Gsoil 042T included Pedobacter heparinus DSM 2366T (98.1 %), Pedobacter africanus DSM 12126T (97.8 %) and Pedobacter caeni LMG 22862T (97.2 %). The 16S rRNA gene sequence similarity with other recognized species of the genus Pedobacter was less than 96.1 %. DNA–DNA hybridization experiments showed that the DNA–DNA relatedness between strain Gsoil 042T and its phylogenetically closest neighbours was less than 43 %. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 042T should be classified as representing a novel species in the genus Pedobacter, for which the name Pedobacter panaciterrae sp. nov. is proposed. The type strain is Gsoil 042T (=KCTC 12594T=LMG 23400T).
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Olivibacter sitiensis gen. nov., sp. nov., isolated from alkaline olive-oil mill wastes in the region of Sitia, Crete
More LessA novel, Gram-negative, non-motile, non-sporulating, rod-shaped bacterium isolated from a viscous two-phase olive-oil mill waste (‘alpeorujo’) is described. The strain, designated AW-6T, is an obligate aerobe, forming irregular, pigmented creamy white colonies. The pH and temperature ranges for growth were pH 5–8 and 5–45 °C, with optimal pH and temperature for growth of pH 6–7 and 28–32 °C, respectively. Strain AW-6T was chemo-organotrophic and utilized mostly d(+)-glucose, protocatechuate and d(+)-xylose, followed by l-cysteine, d(−)-fructose, d(+)-galactose, l-histidine, lactose, sorbitol and sucrose. Menaquinone-7 was detected in the respiratory chain of strain AW-6T. The major fatty acids of strain AW-6T were C16 : 1 ω7c and/or iso-C15 : 0 2-OH, iso-C15 : 0, iso-C17 : 0 3-OH and C16 : 0. The closest phylogenetic relative of strain AW-6T was clone BIti35 (89.7 % 16S rRNA gene sequence similarity), while Sphingobacterium thalpophilum DSM 11723T was the closest recognized relative within the Sphingobacteriaceae (88.2 % similarity). Strain AW-6T showed a low level of DNA–DNA relatedness to S. thalpophilum DSM 11723T (33.8–37.0 %). The DNA G+C content of strain AW-6T was 45.6 mol%. Physiological and chemotaxonomic data further confirmed the distinctiveness of strain AW-6T from members of the genera Sphingobacterium and Pedobacter. Thus, strain AW-6T is considered to represent a novel species of a new genus within the family Sphingobacteriaceae, for which the name Olivibacter sitiensis gen. nov., sp. nov. is proposed. The type strain is AW-6T (=DSM 17696T=CECT 7133T).
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- Other Bacteria
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Deinococcus yunweiensis sp. nov., a gamma- and UV-radiation-resistant bacterium from China
A Gram-negative, non-spore-forming, non-motile, rod-shaped, red-pigmented strain, designated YIM 007T, was found as a contaminant on an agar plate in the laboratory of Yunnan Institute of Microbiology, China. The optimum growth pH and temperature for the isolate were 7.0–7.5 and 30 °C, respectively. The predominant respiratory quinone was MK-8. The polar lipid profile consisted mainly of various unknown phosphoglycolipids and glycolipids. The major cellular fatty acids were C16 : 1 ω7c, C16 : 0, C17 : 0 and C17 : 1 ω8c. l-Ornithine was detected in its peptidoglycan. The DNA G+C content was 64.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM 007T showed 16S rRNA gene sequence similarity levels of 86.8–92.1 % to the other described Deinococcus species. Based on the high 16S rRNA gene sequence divergence and phenotypic differences, it is proposed that the unknown strain should be classified as a novel species in the genus Deinococcus with the name Deinococcus yunweiensis sp. nov. The type strain is YIM 007T (=KCTC 3962T=DSM 17005T).
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- Proteobacteria
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Shewanella donghaensis sp. nov., a psychrophilic, piezosensitive bacterium producing high levels of polyunsaturated fatty acid, isolated from deep-sea sediments
More LessA Gram-negative, motile, rod-shaped, psychrophilic bacterium, LT17T, was isolated from deep-sea sediments (3300 m depth) of the East Sea (Sea of Japan). Optimal growth of LT17T requires the presence of 2.5 % (w/v) NaCl, a pH of 7.0–7.5 and a temperature of 17 °C. The isolate grows optimally under a hydrostatic pressure of 10 MPa and growth is possible between 0.1 and <30 MPa. The novel strain is positive in tests for catalase, oxidase, lipase, β-glucosidase and gelatinase activities and reduces nitrate to nitrate. The predominant cellular fatty acids are iso-C13 : 0, iso-C15 : 0, C16 : 0, C16 : 1ω7 and C20 : 5ω3. The DNA G+C content of strain LT17T is 38.8 mol%. Phylogenetic analysis of 16S rRNA gene sequences places this bacterium in the class Gammaproteobacteria, within the genus Shewanella. The closest relatives of strain LT17T are Shewanella japonica (97.8 % gene sequence similarity), Shewanella pacifica (97.5 %), Shewanella olleyana (96.8 %), Shewanella frigidimarina (96.5 %) and Shewanella gelidimarina (95.4 %). The DNA–DNA hybridization levels between the novel isolate and its closest known phylogenetic relatives, S. japonica and S. pacifica, are lower than 14 %. On the basis of this polyphasic evidence, strain LT17T represents a novel species of the genus Shewanella, for which the name Shewanella donghaensis sp. nov. is proposed. The type strain is LT17T (=KCTC 10635BPT=JCM 12524T).
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Helicobacter equorum sp. nov., a urease-negative Helicobacter species isolated from horse faeces
Gram-negative, curved, motile bacteria (strains EqF1T and EqF2) were isolated from faecal samples from two clinically healthy horses. Both strains possessed a single, monopolar, sheathed flagellum and were urease-negative. The novel strains grew at 37 °C under microaerobic conditions and were positive for oxidase, catalase and alkaline phosphatase activities. The isolates reduced nitrate to nitrite, but γ-glutamyl transpeptidase activity was not detected. The novel isolates did not grow at 42 °C or on media containing 1 % glycine. They were resistant to cephalotin and nalidixic acid and susceptible to metronidazole. Analysis of the 16S and 23S rRNA gene sequences of the two novel strains identified them as representing a single species within the genus Helicobacter. In terms of 16S rRNA gene sequence similarity, Helicobacter pullorum and Helicobacter canadensis were the most closely related species (98 % similarity). 23S rRNA gene sequence analysis also classified strains EqF1T and EqF2 within the enterohepatic division of the genus Helicobacter, but only 94 % similarity was detected with H. pullorum and H. canadensis, which are helicobacters with unsheathed flagella. The most closely related species in terms of 23S rRNA gene sequence similarity was Helicobacter canis (95 %). Numerical analysis of whole-cell protein extracts by SDS-PAGE was performed and the novel isolates were clearly differentiated from H. pullorum, H. canadensis, H. canis and other species of the genus Helicobacter. This finding was also confirmed by sequence analysis of the hsp60 gene. On the basis of these genetic, biochemical and protein data, the isolates are classified as representing a novel species, for which the name Helicobacter equorum sp. nov. is proposed (type strain EqF1T=LMG 23362T=CCUG 52199T).
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Rhodovulum imhoffii sp. nov.
More LessA yellowish-brown bacterium was isolated from photoheterotrophic enrichment cultures obtained from water samples of an aquaculture pond at Bhimunipatnam, India. Enrichment and isolation in a medium containing 2 % NaCl (w/v) yielded strain JA125T, the cells of which were rod-shaped and non-motile. On the basis of the 16S rRNA gene sequence, strain JA125T belongs to the class Alphaproteobacteria and is closely related to the type strains of Rhodovulum iodosum (96 %), Rhodovulum adriaticum (95 %), Rhodovulum robiginosum (95 %), Rhodovulum sulfidophilum (94 %) and Rhodovulum marinum (94 %). The cells of strain JA125T contained vesicular internal membranes and bacteriochlorophyll a and carotenoids of the spheroidene series. Strain JA125T grew optimally at 28 °C and at pH 7.0–8.0. The best growth occurred photoheterotrophically with a number of organic compounds serving as carbon sources and electron donors. The strain grew photoautotrophically, but chemoautotrophic growth did not occur. Strain JA125T was able to utilize sulfide, sulfate, thiosulfate and thioglycolate as sulfur sources. Biotin was required as a growth factor. The DNA G+C content was 58 mol%. On the basis of 16S rRNA gene sequence analysis and the morphological and physiological data, strain JA125T is significantly different from other species of the genus Rhodovulum and represents a novel species, for which the name Rhodovulum imhoffii sp. nov. is proposed. The type strain is JA125T (=JCM 13589T=DSM 18064T).
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Marinobacter gudaonensis sp. nov., isolated from an oil-polluted saline soil in a Chinese oilfield
Jun Gu, Hua Cai, Su-Lin Yu, Ri Qu, Bin Yin, Yu-Feng Guo, Jin-Yi Zhao and Xiao-Lei WuTwo novel strains, SL014B61AT and SL014B11A, were isolated from an oil-polluted saline soil from Gudao in the coastal Shengli Oilfield, eastern China. Cells of strains SL014B61AT and SL014B11A were motile, Gram-negative and rod-shaped. Growth occurred at NaCl concentrations of between 0 and 15 % and at temperatures of between 10 and 45 °C. Strain SL014B61AT had Q9 as the major respiratory quinone and C16 : 0 (21.2 %), C18 : 1ω9c (20.3 %), C16 : 1ω7c (7.3 %) and C16 : 1ω9c (6.4 %) as predominant fatty acids. The G+C content of the DNA was 57.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SL014B61AT belonged to the genus Marinobacter in the class Gammaproteobacteria. Strain SL014B61AT showed the highest 16S rRNA gene sequence similarity with Marinobacter bryozoorum (97.9 %) and showed 97.8 % sequence similarity to Marinobacter lipolyticus. DNA–DNA relatedness to the reference strains Marinobacter bryozoorum and Marinobacter lipolyticus was 35.5 % and 33.8 %, respectively. On the basis of these data, it is proposed that strains SL014B61AT and SL014B11A represent a novel species, Marinobacter gudaonensis sp. nov. The type strain is strain SL014B61AT (=DSM 18066T=LMG 23509T=CGMCC 1.6294T).
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Maribius salinus gen. nov., sp. nov., isolated from a solar saltern and Maribius pelagius sp. nov., cultured from the Sargasso Sea, belonging to the Roseobacter clade
More LessTwo strictly aerobic, Gram-negative bacteria, designated strains CL-SP27T and B5-6T, were isolated from the hypersaline water of a solar saltern in Korea and from the surface water of the Sargasso Sea, respectively. The two strains were rod-shaped, non-motile and grew on marine agar 2216 as beige colonies. Phylogenetic analyses of 16S rRNA gene sequences revealed a clear affiliation of the novel strains to the family Rhodobacteraceae. However, the novel strains were only distantly related to members of the Roseobacter clade, forming a distinct lineage. Although the 16S rRNA gene sequence similarity between strains CL-SP27T and B5-6T was very high (99.6 %), DNA–DNA relatedness between the strains was 48.4 %, suggesting that the strains be categorized as two genospecies. Additionally, the two novel strains could be differentiated by DNA G+C contents, fatty acid profiles, carbon source utilization patterns, antibiotic susceptibilities and biochemical characteristics. Based on taxonomic data obtained in this study, strains CL-SP27T and B5-6T represent separate species within a novel genus of the family Rhodobacteraceae, for which the names Maribius salinus gen. nov., sp. nov. (type species) and Maribius pelagius sp. nov. are proposed. The type strains of Maribius salinus and Maribius pelagius are CL-SP27T (=KCCM 42113T=JCM 13037T) and B5-6T (=KCCM 42336T=JCM 14009T), respectively.
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Sulfitobacter marinus sp. nov., isolated from seawater of the East Sea in Korea
More LessA Gram-negative, non-motile, rod- or oval-shaped Sulfitobacter-like bacterial strain, SW-265T, was isolated from seawater at Hwajinpo, Korea, and was subjected to a polyphasic taxonomic study. Strain SW-265T grew optimally at pH 7.0–8.0 and 30 °C in the presence of 2 % (w/v) NaCl. It contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The DNA G+C content was 57.8 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain SW-265T fell within the cluster comprising Sulfitobacter species. The levels of 16S rRNA gene sequence similarity between strain SW-265T and the type strains of Sulfitobacter species ranged from 97.1 to 98.7 %. DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain SW-265T differs from recognized Sulfitobacter species. On the basis of the phenotypic, phylogenetic and genetic data, strain SW-265T represents a novel species of the genus Sulfitobacter, for which the name Sulfitobacter marinus sp. nov. is proposed. The type strain is SW-265T (=KCTC 12738T=JCM 13602T).
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Sphingobium aromaticiconvertens sp. nov., a xenobiotic-compound-degrading bacterium from polluted river sediment
A bacterial strain capable of degrading some monochlorinated dibenzofurans, designated RW16T, was isolated from aerobic River Elbe sediments. The strain was characterized based on 16S rRNA gene sequence analysis, DNA G+C content, physiological characteristics, polyamines, ubiquinone and polar lipid pattern and fatty acid composition. This analysis revealed that strain RW16T represents a novel species of the genus Sphingobium. The DNA G+C content of strain RW16T, 60.7 mol%, is the lowest yet reported for the genus. 16S rRNA gene sequence analysis placed strain RW16T as an outlier in the genus Sphingobium. The name Sphingobium aromaticiconvertens sp. nov. is proposed for this dibenzofuran-mineralizing organism, with type strain RW16T (=DSM 12677T=CIP 109198T).
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Thalassospira xiamenensis sp. nov. and Thalassospira profundimaris sp. nov.
Chenli Liu, Yehui Wu, Li Li, Yingfei Ma and Zongze ShaoTwo bacterial strains, M-5T and WP0211T, were isolated from the surface water of a waste-oil pool in a coastal dock and from a deep-sea sediment sample from the West Pacific Ocean, respectively. Analysis of 16S rRNA gene sequences indicated that both strains belonged to the class Alphaproteobacteria and were closely related to Thalassospira lucentensis (96.1 and 96.2 %, gene sequence similarity, respectively). Based on the results of physiological and biochemical tests, as well as DNA–DNA hybridization experiments, it is suggested that these isolates represent two novel species of the genus Thalassospira. Various traits allow both novel strains to be differentiated from Thalassospira lucentensis, including oxygen requirement, nitrate reduction and denitrification abilities and major fatty acid profiles, as well as their ability to utilize six different carbon sources. Furthermore, the novel strains may be readily distinguished from each other by differences in their motility, flagellation, growth at 4 °C and 40 °C, their ability to hydrolyse Tween 40 and Tween 80, their utilization of 19 different carbon sources and by quantitative differences in their fatty acid contents. It is proposed that the isolates represent two novel species for which the names Thalassospira xiamenensis sp. nov. (type strain, M-5T=DSM 17429T=CGMCC 1.3998T) and Thalassospira profundimaris sp. nov. (type strain, WP0211T=DSM 17430T=CGMCC 1.3997T) are proposed.
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Methylobacterium oryzae sp. nov., an aerobic, pink-pigmented, facultatively methylotrophic, 1-aminocyclopropane-1-carboxylate deaminase-producing bacterium isolated from rice
A pink-pigmented, facultatively methylotrophic bacterium, strain CBMB20T, isolated from stem tissues of rice, was analysed by a polyphasic approach. Strain CBMB20T utilized 1-aminocyclopropane 1-carboxylate (ACC) as a nitrogen source and produced ACC deaminase. It was related phylogenetically to members of the genus Methylobacterium. 16S rRNA gene sequence analysis indicated that strain CBMB20T was most closely related to Methylobacterium fujisawaense, Methylobacterium radiotolerans and Methylobacterium mesophilicum; however, DNA–DNA hybridization values were less than 70 % with the type strains of these species. The DNA G+C content of strain CBMB20T was 70.6 mol%. The study presents a detailed phenotypic characterization of strain CBMB20T that allows its differentiation from other Methylobacterium species. In addition, strain CBMB20T is the only known member of the genus Methylobacterium to be described from the phyllosphere of rice. Based on the data presented, strain CBMB20T represents a novel species in the genus Methylobacterium, for which the name Methylobacterium oryzae sp. nov. is proposed, with strain CBMB20T (=DSM 18207T=LMG 23582T=KACC 11585T) as the type strain.
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Photobacterium lutimaris sp. nov., isolated from a tidal flat sediment in Korea
More LessA Gram-negative, motile, pale-yellow-pigmented, oval-shaped bacterial strain, DF-42T, was isolated from a tidal flat sediment in Korea. Strain DF-42T grew optimally at 25–30 °C and in the presence of 2–3 % (w/v) NaCl. It contained Q-8 as the predominant ubiquinone and C16 : 0, C18 : 1 ω7c and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH) as the major fatty acids. The DNA G+C content was 48.3 mol%. Phylogenetic trees based on 16S rRNA gene sequences showed that strain DF-42T falls within the evolutionary radiation enclosed by the genus Photobacterium. Strain DF-42T exhibited 16S rRNA gene sequence similarity values of 93.8–97.9 % to the type strains of Photobacterium species with validly published names. DNA–DNA relatedness data and differential phenotypic properties made it possible to categorize strain DF-42T as representing a species that is separate from previously described Photobacterium species. The name Photobacterium lutimaris sp. nov. is proposed, with strain DF-42T (=KCTC 12723T=JCM 13586T) as the type strain.
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Description of Shewanella glacialipiscicola sp. nov. and Shewanella algidipiscicola sp. nov., isolated from marine fish of the Danish Baltic Sea, and proposal that Shewanella affinis is a later heterotypic synonym of Shewanella colwelliana
More LessTwo novel species belonging to the genus Shewanella are described on the basis of a polyphasic taxonomic approach. A total of 40 strains of Gram-negative, psychrotolerant, H2S-producing bacteria were isolated from marine fish (cod and plaice) caught in the Baltic Sea off Denmark. Strains belonging to group 1 (seven strains) were a lactate-assimilating variant of Shewanella morhuae with a G+C content of 44 mol%. The strains of group 2 (33 strains) utilized lactate, N-acetylglucosamine and malate but did not produce DNase or ornithine decarboxylase. Their G+C content was 47 mol%. Phylogenetic analysis of the 16S rRNA gene sequence data placed the two novel species within the genus Shewanella. Group 1 showed greatest sequence similarity with S. morhuae ATCC BAA-1205T (99.9 %). However, gyrB gene sequence analysis and DNA–DNA hybridization differentiated these isolates from S. morhuae, with 95.6 % sequence similarity and less than 57 % DNA relatedness, respectively. Group 2 strains shared more than 99 % 16S rRNA gene sequence similarity with the type strains of Shewanella colwelliana and Shewanella affinis, but gyrB sequence similarity (~85 %) and the results of DNA hybridization (~28 %) indicated that the new isolates represented a novel species. Furthermore, when compared to each other, the type strains of S. colwelliana and S. affinis had almost identical gyrB sequences and significantly high DNA reassociation values (76–83 %), indicating that they belonged to the same species. Based on the conclusions of this study, we propose the novel species Shewanella glacialipiscicola sp. nov. (type strain T147T=LMG 23744T=NBRC 102030T) for group 1 strains and Shewanella algidipiscicola sp. nov. (type strain S13T=LMG 23746T=NBRC 102032T) for group 2 strains, and we propose that Shewanella affinis as a later heterotypic synonym of Shewanella colwelliana.
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Nitrogen-fixing and cellulose-producing Gluconacetobacter kombuchae sp. nov., isolated from Kombucha tea
More LessA few members of the family Acetobacteraceae are cellulose-producers, while only six members fix nitrogen. Bacterial strain RG3T, isolated from Kombucha tea, displays both of these characteristics. A high bootstrap value in the 16S rRNA gene sequence-based phylogenetic analysis supported the position of this strain within the genus Gluconacetobacter, with Gluconacetobacter hansenii LMG 1527T as its nearest neighbour (99.1 % sequence similarity). It could utilize ethanol, fructose, arabinose, glycerol, sorbitol and mannitol, but not galactose or xylose, as sole sources of carbon. Single amino acids such as l-alanine, l-cysteine and l-threonine served as carbon and nitrogen sources for growth of strain RG3T. Strain RG3T produced cellulose in both nitrogen-free broth and enriched medium. The ubiquinone present was Q-10 and the DNA base composition was 55.8 mol% G+C. It exhibited low values of 5.2–27.77 % DNA–DNA relatedness to the type strains of related gluconacetobacters, which placed it within a separate taxon, for which the name Gluconacetobacter kombuchae sp. nov. is proposed, with the type strain RG3T (=LMG 23726T=MTCC 6913T).
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Sphingomonas molluscorum sp. nov., a novel marine isolate with antimicrobial activity
An aerobic, Gram-negative, yellow-pigmented, non-motile bacterium, designated strain KMM 3882T, was isolated from a marine bivalve (Anadara broughtoni) collected from Peter the Great Bay, Sea of Japan, and was subjected to phenotypic and phylogenetic analyses. Strain KMM 3882T was found to exert a remarkable inhibitory activity against a number of Gram-positive micro-organisms. Phylogenetic analysis based on 16S rRNA gene sequences placed strain KMM 3882T within the genus Sphingomonas, as an independent lineage adjacent to Sphingomonas dokdonensis DS-4T and Sphingomonas panni DSM 15761T. Strain KMM 3882T showed the highest 16S rRNA gene sequence similarity to Sphingomonas dokdonensis DS-4T (97.3 %); similarities of 96.5–96.7 % were obtained with Sphingomonas pituitosa DSM 13101T, Sphingomonas azotifigens NBRC 15497T, Sphingomonas asaccharolytica NBRC 15499T, Sphingomonas trueperi DSM 7225T and Sphingomonas panni DSM 15761T. Chemotaxonomically, strain KMM 3882T contained sphingoglycolipid, C16 : 0 and C18 : 1 as predominant fatty acids and 2-OH C14 : 0 as a major 2-hydroxy fatty acid, confirming the affiliation of strain KMM 3882T with the genus Sphingomonas. On the basis of phylogenetic analysis, DNA–DNA hybridization and physiological and biochemical characterization, strain KMM 3882T should be classified as representing a novel species of the genus Sphingomonas, for which the name Sphingomonas molluscorum sp. nov. is proposed. The type strain is KMM 3882T (=An 18T=NRIC 0685T=JCM 14122T=CIP 109223T).
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Halomonas indalinina sp. nov., a moderately halophilic bacterium isolated from a solar saltern in Cabo de Gata, Almería, southern Spain
A moderately halophilic bacterium, strain CG2.1T, isolated from a solar saltern at Cabo de Gata, a wildlife reserve located in the province of Almería, southern Spain, was subjected to a polyphasic taxonomic study. This organism was an aerobic, motile, Gram-negative rod that produced orange-pigmented colonies. Strain CG2.1T was able to grow at salinities of 3–25 % (w/v) and at temperatures of 15–40 °C. The pH range for growth was 5–9. Strain CG2.1T was a heterotroph capable of utilizing various carbohydrates as carbon sources. The organism reduced nitrate and showed phenylalanine deaminase activity. The major fatty acids were C18 : 1 ω7c, C16 : 0 and C19 : 0 cyclo ω8c. The DNA G+C content was 60.9 mol%. On the basis of the phenotypic and phylogenetic data, strain CG2.1T appeared to be a member of the genus Halomonas and clustered closely with Halomonas marisflavi (97.1 % 16S rRNA gene sequence similarity). However, the level of DNA–DNA relatedness between the novel isolate and the most closely related Halomonas species was low. On the basis of these data, strain CG2.1T represents a novel member of the genus Halomonas, for which the name Halomonas indalinina is proposed. The type strain is CG2.1T (=CECT 5902T=LMG 23625T).
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- Eukaryotic Micro-Organisms
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Cryptococcus rajasthanensis sp. nov., an anamorphic yeast species related to Cryptococcus laurentii, isolated from Rajasthan, India
More LessTwo novel anamorphic yeast strains (S-15LT and 3-C1) were isolated from the inflorescences of plants collected in two different towns in Rajasthan State, India. Sequencing of the D1/D2 domains of the large-subunit (LSU) rDNA and the internal transcribed spacer (ITS) regions suggested they are strains of the same species. Phenotypic characteristics such as the absence of fermentation, the absence of sexual structures and ballistoconidia, the assimilation of myo-inositol and d-glucuronate, and positive Diazonium blue B and urease reactions indicated that these strains belong to the genus Cryptococcus. The novel strains differed from Cryptococcus laurentii in six physiological tests and differed from other related species in more than six tests. A phylogenetic analysis of the sequences of the D1/D2 domains of the LSU rDNA and the ITS regions placed these strains in the Bulleromyces clade within the order Tremellales, with C. laurentii as their closest described relative. The novel strains showed 1.6 and 7.5 % divergence in the D1/D2 domain of the LSU rDNA and ITS regions, respectively, with respect to C. laurentii. The divergence from other species was more than 3 % for the D1/D2 domain and more than 9 % for the ITS region. On the basis of the phenotypic and molecular data, strains S-15LT and 3-C1 represent a novel species within the genus Cryptococcus, for which the name Cryptococcus rajasthanensis sp. nov. is proposed. The type strain is S-15LT (=MTCC 7075T=CBS 10406T).
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Kazachstania siamensis sp. nov., an ascomycetous yeast species from forest soil in Thailand
More LessTwo strains (S-34T and S-35) of a novel ascomycetous yeast species belonging to the genus Kazachstania were isolated from soil from a mixed deciduous forest in Amphoe Wang Nam Khiao, Nakhon Ratchasima Province, Thailand. The D1/D2 domains of the large-subunit rDNA sequences of the two strains were identical and also indicated a close relationship with respect to Kazachstania aquatica, Kazachstania unispora, Kazachstania aerobia, Kazachstania servazzii and Kazachstania solicola. The most closely related species, K. aquatica, has 14 nucleotide substitutions and three gaps in 566 nt. The phenotypic characteristics of the two strains were typical of those of members of the genus Kazachstania. These characteristics include the formation of a single globose ascospore in an unconjugated and persistent ascus, multilateral budding, the absence of arthrospores and ballistospores, the fermentation of glucose, the inability to assimilate nitrate, negative diazonium blue B and urease reactions, and the presence of ubiquinone Q-6. The novel strains can be distinguished from K. aquatica on the basis of a number of phenotypic characteristics and represent a novel species in the genus Kazachstania, for which the name Kazachstania siamensis sp. nov. is proposed. The type strain is S-34T (=CBS 10361T=NBRC 101968T=BCC 21230T).
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Sergeia podlipaevi gen. nov., sp. nov. (Trypanosomatidae, Kinetoplastida), a parasite of biting midges (Ceratopogonidae, Diptera)
More LessThree strains of a trypanosomatid protozoan were isolated from the midguts of two naturally infected species of biting midges [Culicoides (Oecacta) festivipennis and Culicoides (Oecacta) truncorum] and characterized by light and electron microscopy and by molecular techniques. Morphological characteristics and sequences of the 18S rRNA, 5S rRNA, spliced leader RNA and glycosomal glyceraldehyde-3-phosphate dehydrogenase genes indicate that the studied flagellates represent a novel phylogenetic lineage within the Trypanosomatidae. Based on phylogenetic analyses, the novel endosymbiont-free, monoxenous trypanosomatid was classified as Sergeia podlipaevi gen. nov., sp. nov. Interestingly, it is closely related to another trypanosomatid species that parasitizes the sand fly Lutzomyia evansi, a blood-sucking dipteran from South America. The type strain of S. podlipaevi sp. nov., ICUL/CZ/2000/CER3, was obtained from Malpighian tubes. Of 2518 females of seven species of biting midges trapped in the Czech Republic, more than 1.5 % were infected by trypanosomatid parasites. An unrelated insect species, Culicoides (Monoculicoides) nubeculosus, was experimentally infected with S. podlipaevi, demonstrating that its host range extends to different subgenera of biting midges.
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- Other Gram-Positive Bacteria
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Lactobacillus namurensis sp. nov., isolated from a traditional Belgian sourdough
A biodiversity study on lactic acid bacteria (LAB) occurring in traditional Belgian sourdoughs resulted in the isolation of two Lactobacillus isolates, LMG 23583T and LMG 23584, that could not be assigned to any recognized LAB species. The two isolates were initially investigated by means of phenylalanyl-tRNA synthase (pheS) gene sequence analysis and were found to occupy a separate position relative to recognized Lactobacillus species present in the pheS database. Subsequently, their phylogenetic affiliation was determined by 16S rRNA gene sequence analysis, indicating that the two isolates belong to the Lactobacillus buchneri species group with Lactobacillus zymae, Lactobacillus acidifarinae and Lactobacillus spicheri as closest relatives. Whole-cell protein analysis (SDS-PAGE) and amplified fragment length polymorphism fingerprinting of whole genomes confirmed their separate taxonomic status. DNA–DNA hybridization experiments, DNA G+C content, growth characteristics and biochemical features demonstrated that the two isolates represent a novel Lactobacillus species, for which the name Lactobacillus namurensis sp. nov. is proposed. The type strain is LMG 23583T (=CCUG 52843T).
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Bacillus lehensis sp. nov., an alkalitolerant bacterium isolated from soil
More LessA Gram-positive, endospore-forming, alkalitolerant bacterial strain, designated MLB2T, was isolated from soil from Leh, India, and was subjected to a polyphasic taxonomic study. The strain exhibited phenotypic properties that included chemotaxonomic characteristics consistent with its classification in the genus Bacillus. Growth was observed at pH 7.0–11.0, but not at pH 6.0. The DNA G+C content was 41.4 mol%. The highest level of 16S rRNA gene sequence similarity was with Bacillus oshimensis JCM 12663T (98.8 %). However, DNA–DNA hybridization experiments indicated low levels of genomic relatedness with the type strains of B. oshimensis (62 %), Bacillus patagoniensis (55 %), Bacillus clausii (51 %) and Bacillus gibsonii (34 %), the species with which strain MLB2T formed a coherent cluster (based on the results of the phylogenetic analysis). On the basis of the phenotypic characteristics and genotypic distinctiveness of strain MLB2T, it should be classified within a novel species of Bacillus, for which the name Bacillus lehensis sp. nov. is proposed. The type strain is MLB2T (=MTCC 7633T=JCM 13820T).
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Oceanobacillus chironomi sp. nov., a halotolerant and facultatively alkaliphilic species isolated from a chironomid egg mass
More LessChironomids (Diptera; Chironomidae) are the most abundant insects in freshwater aquatic habitats. Females of the genus Chironomus lay egg masses containing hundreds of eggs embedded in a gelatinous matrix. A bacterial strain, designated T3944DT, was isolated from a chironomid egg mass sampled from a waste-stabilization pond in northern Israel and was found to be Gram-positive, motile by peritrichous flagella, endospore-forming, halotolerant and facultatively alkaliphilic. Comparative 16S rRNA gene sequence analysis showed that strain T3944DT belonged to the genus Oceanobacillus, exhibiting the highest levels of similarity with the sequences of Oceanobacillus oncorhynchi subsp. incaldanensis DSM 16557T (94.9 %), Oceanobacillus oncorhynchi subsp. oncorhynchi JCM 12661T (94.8 %), Oceanobacillus iheyensis JCM 11309T (94.7 %) and Oceanobacillus picturae LMG 19416 (94.5 %). Strain T3944DT grew optimally at 1–3 % NaCl, pH 8.5 and 37 °C. The major cellular fatty acids were anteiso-C15 : 0 (60.0 %) and anteiso-C17 : 0 (12.9 %) and the DNA G+C content was 38.1 mol%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain T3944DT represents a novel species in the genus Oceanobacillus, for which the name Oceanobacillus chironomi sp. nov. is proposed. The type strain is T3944DT (=LMG 23627T=DSM 18262T).
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Thermoanaerobacterium aciditolerans sp. nov., a moderate thermoacidophile from a Kamchatka hot spring
An anaerobic, moderately thermoacidophilic bacterium, strain 761-119T, was isolated from an acidic hot spring in the Orange Field of the Uzon Caldera (Kamchatka, far-eastern Russia). Cells were spore-forming, Gram-positive rods, possessing one polar flagellum. Growth of strain 761-119T was observed between 37 and 68 °C and in the pH20 °C range 3.2–7.1. No growth was observed within 5 days of incubation at or below 35 °C and at or above 70 °C, as well as at or below pH20 °C 2.8 and at or above pH20 °C 7.5. The optimal temperature and pH20 °C for growth were 55 °C and pH20 °C 5.7, respectively. A wide range of carbohydrates and polysaccharides were fermented, as well as peptides and proteinaceous substrates. The main products of glucose fermentation were acetate, ethanol, lactate, H2 and CO2. The DNA G+C content was 34 (±0.5) mol%. 16S rRNA gene sequence analysis indicated that strain 761-119T belonged to the genus Thermoanaerobacterium. The level of 16S rRNA gene sequence similarity with other Thermoanaerobacterium species was 86.5–97.8 %, with the only moderately acidophilic member of this genus, Thermoanaerobacterium aotearoense, being one of its closest relatives. DNA–DNA hybridization with T. aotearoense showed 33 % relatedness. Thus, morphological (one polar flagellum) and physiological characteristics (lower pH limit of growth at pH20 °C 3.2 compared with T. aotearoense) and 16S rRNA gene sequence analyses revealed that strain 761-119T represents a novel species in the genus Thermoanaerobacterium, for which the name Thermoanaerobacterium aciditolerans sp. nov. is proposed, with the type strain 761-119T (=DSM 16487T=VKM B-2363T).
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Exiguobacterium profundum sp. nov., a moderately thermophilic, lactic acid-producing bacterium isolated from a deep-sea hydrothermal vent
A facultatively anaerobic, halotolerant, moderately thermophilic and non-sporulating bacterium, designated strain 10CT, was isolated from deep-sea hydrothermal vent samples collected on the 13° N East Pacific Rise at a depth of approximately 2600 m. Cells of strain 10CT were Gram-positive, motile rods, and grew optimally at 45 °C (range 12–49 °C), pH 7.0 (range pH 5.5–9.5) and 0–2 % NaCl (range 0–11 %). (+)-l-Lactate was the main organic acid detected from carbohydrate fermentation with traces of formate, acetate and ethanol. Strain 10CT was catalase-positive, oxidase-negative and reduced nitrate to nitrite under anaerobic conditions. The DNA G+C content was 50.4 mol%. Its closest phylogenetic relatives were Exiguobacterium aestuarii TF-16T and Exiguobacterium marinum TF-80T (16S rRNA gene sequence similarity >99 %). However, strain 10CT differed genotypically from these two Exiguobacterium species as indicated by DNA–DNA relatedness data. Therefore, on the basis of phenotypic, genotypic and phylogenetic characteristics, strain 10CT is considered to represent a novel species of the genus Exiguobacterium, for which the name Exiguobacterium profundum sp. nov. is proposed. The type strain is 10CT (=CCUG 50949T=DSM 17289T).
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Clostridium aciditolerans sp. nov., an acid-tolerant spore-forming anaerobic bacterium from constructed wetland sediment
More LessAn obligately anaerobic, spore-forming, moderately acid-tolerant bacterium, strain JW/YJL-B3T, was isolated from a sediment sample from a constructed wetland system receiving acid sulfate water. Based on 16S rRNA gene sequence analysis, the isolate belonged to the Firmicutes branch with Clostridium drakei SL1T (96.2 % gene sequence similarity) as its closest relative. The G+C content of the genomic DNA was 30.8 mol% (HPLC). Cells were straight to curved rods, 0.5–1.0 μm in diameter and 3.0–9.0 μm in length. The temperature range for growth was 20–45 °C, with an optimum around 35 °C. Growth was not detected below 18 °C or above 47 °C. The pH range for growth was broad, pH25 °C 3.8–8.9, with an optimum at 7.0–7.5. However at pH 4.5, the strain grew at 52 % of the optimal growth rate. The salinity range was 0–1.5 % NaCl (w/v). Strain JW/YJL-B3T utilized beef extract, Casamino acids, peptone, tryptone, arabinose, cellobiose, fructose, galactose, glucose, lactose, maltose, mannose, raffinose, ribose, sucrose, xylose, pyruvate, glutamate and inulin as a carbon and energy source. There were no indications of growth under aerobic or autotrophic conditions. The isolate produced acetate, butyrate and ethanol as fermentation end products from glucose. Based on these characteristics and other physiological properties, the isolate is placed into the novel taxon, Clostridium aciditolerans sp. nov., with strain JW/YJL-B3T (=DSM 17425T=ATCC BAA-1220T) as the type strain.
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Lentibacillus kapialis sp. nov., from fermented shrimp paste in Thailand
Two strains of strictly aerobic, moderately halophilic Gram-positive rods were isolated from fermented shrimp paste (‘ka-pi’) produced in Thailand. They produced a red pigment and grew optimally in the presence of 5–30 % NaCl. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The predominant menaquinone was MK-7. The major cellular fatty acid was anteiso-C15 : 0. Phosphatidylglycerol, diphosphatidylglycerol and two unidentified glycolipids were found to be the major polar lipid components. The DNA G+C content was 41.2–41.6 mol%. Comparative 16S rRNA gene sequence analyses showed that strain PN7-6T was most closely related to Lentibacillus salarius KCTC 3911T with 96.5 % sequence similarity. On the basis of phenotypic and molecular properties, the two isolates represent a novel species of the genus Lentibacillus, for which the name Lentibacillus kapialis sp. nov. is proposed. The type strain is PN7-6T (=JCM 12580T=PCU 259T=TISTR 1551T).
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Oceanobacillus profundus sp. nov., isolated from a deep-sea sediment core
More LessA halotolerant, facultatively alkaliphilic bacterium, designated CL-MP28T, was isolated from the surface of a sediment core sample collected at a depth of 2247 m in the Ulleung Basin of the East Sea, Korea. Phylogenetic analysis of the 16S rRNA gene sequence of strain CL-MP28T revealed an affiliation with the genus Oceanobacillus. The sequence similarities between the isolate and type strains of members of the genus Oceanobacillus were in the range 95.0–96.0 %, indicating that strain CL-MP28T represented a novel species within the genus. The strain was found to be Gram-positive, rod-shaped and motile by means of peritrichous flagella and was shown to produce ellipsoidal spores. The strain was strictly aerobic and able to grow with NaCl at concentrations in the range 0–14 % (w/v) at pH 7.5. The strain grew at temperatures of 15–42 °C and at pH 6.5–9.5. The major fatty acids were anteiso-C15 : 0 (64.9 %), anteiso-C17 : 0 (11.9 %) and iso-C16 : 0 (7.7 %). The major isoprenoid quinone was MK-7. The DNA G+C content was 40.2 mol%. According to the 16S rRNA gene sequence, DNA–DNA relatedness and physiological data and the fatty acid composition, CL-MP28T could be assigned to the genus Oceanobacillus, but is distinguishable from the recognized species of this genus. Strain CL-MP28T therefore represents a novel species within the genus Oceanobacillus, for which the name Oceanobacillus profundus sp. nov. is proposed. The type strain is CL-MP28T (=KCCM 42318T=DSM 18246T).
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- Evolution, Phylogeny And Biodiversity
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Congruence of evolutionary relationships inside the Leuconostoc–Oenococcus–Weissella clade assessed by phylogenetic analysis of the 16S rRNA gene, dnaA, gyrB, rpoC and dnaK
More LessThe phylogenetic structure of the Leuconostoc–Oenococcus–Weissella clade was evaluated by comparison of 16S rRNA gene, dnaA, gyrB, rpoC and dnaK sequence analysis. Phylogenies obtained with the different genes were in overall good agreement and a well-supported, almost fully resolved phylogenetic tree was obtained when the combined data were analysed in a Bayesian approach. A rapid basal diversification of the three genera is suggested. Evolutionary rates of the 16S rRNA gene in these genera seem to be different and specifically related to the evolution of this group, revealing the importance of this sequence in the constitution of the present taxonomy, but preventing its straightforward use in phylogenetic inference.
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- Letters To The Editor
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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Volume 66 (2016)
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Volume 65 (2015)
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Volume 64 (2014)
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Volume 63 (2013)
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Volume 62 (2012)
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Volume 61 (2011)
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Volume 60 (2010)
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Volume 59 (2009)
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Volume 58 (2008)
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Volume 57 (2007)
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Volume 56 (2006)
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Volume 55 (2005)
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Volume 54 (2004)
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Volume 53 (2003)
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Volume 52 (2002)
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Volume 51 (2001)
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Volume 50 (2000)
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Volume 49 (1999)
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Volume 48 (1998)
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Volume 47 (1997)
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Volume 46 (1996)
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Volume 45 (1995)
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Volume 44 (1994)
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Volume 43 (1993)
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Volume 42 (1992)
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Volume 41 (1991)
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Volume 40 (1990)
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Volume 39 (1989)
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Volume 38 (1988)
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Volume 37 (1987)
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Volume 36 (1986)
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Volume 35 (1985)
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Volume 34 (1984)
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Volume 33 (1983)
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Volume 32 (1982)
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Volume 31 (1981)
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Volume 30 (1980)
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Volume 29 (1979)
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Volume 28 (1978)
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Volume 27 (1977)
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Volume 26 (1976)
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Volume 25 (1975)
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Volume 24 (1974)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 20 (1970)
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Volume 19 (1969)
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Volume 18 (1968)
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Volume 17 (1967)
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Volume 16 (1966)
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Volume 15 (1965)
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Volume 14 (1964)
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Volume 13 (1963)
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Volume 12 (1962)
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Volume 11 (1961)
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Volume 10 (1960)
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Volume 9 (1959)
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Volume 8 (1958)
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Volume 7 (1957)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)