- Volume 58, Issue 6, 2008
Volume 58, Issue 6, 2008
- Obituary
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- Notification List
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Notification that new names and new combinations have appeared in volume 58, part 3, of the IJSEM
This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles). Taxonomic opinions included in this List (i.e. the creation of synonyms or the emendation of circumscriptions) cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission.
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- New Taxa
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- Actinobacteria
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Kocuria flava sp. nov. and Kocuria turfanensis sp. nov., airborne actinobacteria isolated from Xinjiang, China
More LessTwo coloured bacteria were isolated from the same plate for detecting cultivable bacteria from the air of Xinjiang in China. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the isolates were members of the genus Kocuria, in which they represented two novel lineages. Although the two strains presented high 16S rRNA gene sequence similarity (above 97 %), their DNA G+C contents were very different (6 mol%). The G+C contents of strains HO-9041T and HO-9042T are 71 and 65 mol%, respectively. DNA relatedness analysis and other taxonomic evidence supports the placement of the two isolates in the genus Kocuria. The diagnostic diamino acid of the cell-wall peptidoglycan is l-lysine and both strains contain MK-8(H2) and MK-9(H2) as major menaquinones. In addition, they share similar fatty acid patterns containing straight-chain saturated and iso- and anteiso-branched acids, with a major component being anteiso-C15:O. Genotypic, morphological and physiological characteristics are used to describe two novel species of Kocuria, for which the names Kocuria flava sp. nov. (type strain HO-9041T =CCTCC AB 206106T =KCTC 19306T) and Kocuria turfanensis sp. nov. (type strain HO-9042T =CCTCC AB 206107T =KCTC 19307T) are proposed.
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Agromyces terreus sp. nov., isolated from soil
More LessA Gram-positive, non-motile, cream-coloured, curved or straight rod-shaped bacterial strain, DS-10T, was isolated from soil of Dokdo, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain DS-10T grew optimally at 25 °C and pH 7.0–8.0 in the presence of 0.5–1.0 % (w/v) NaCl. Strain DS-10T had peptidoglycan type B2γ [d-Glu–d-Dab (diaminobutyric acid)] and galactose and ribose as whole-cell sugars. Strain DS-10T contained MK-11, MK-12 and MK-10 as predominant menaquinones. Major cellular fatty acids (>10 % of total) were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The DNA G+C content was 71.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-10T belonged to the genus Agromyces. Similarity values between the 16S rRNA gene sequence of strain DS-10T and those of the type strains of recognized Agromyces species ranged from 95.8 to 99.3 %. DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain DS-10T could be differentiated from recognized Agromyces species. On the basis of the data presented, strain DS-10T is considered to represent a novel species of the genus Agromyces, for which the name Agromyces terreus sp. nov. is proposed. The type strain is DS-10T (=KCTC 19216T =JCM 14581T).
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Phycicola gilvus gen. nov., sp. nov., an actinobacterium isolated from living seaweed
More LessA Gram-positive, aerobic, non-mycelium-forming actinomycete, designated strain SSWW-21T, was isolated from a living seaweed sample on the coast of Jeju, Republic of Korea. Cells of the organism were rod-shaped or coccoid depending on culture age. Short rods were observed in young cultures, whereas older cultures predominantly consisted of coccoid cells. Rod-shaped cells were motile by means of flagella, but coccoid cells were non-motile. Budding-like cell division was observed. The temperature and pH for growth were 4–30 °C and pH 6.1–10.1. Growth occurred in the presence of up to 2 % NaCl. Phylogenetic analyses showed that the organism formed a distinct clade within the family Microbacteriaceae. Comparative 16S rRNA gene sequence analyses showed that strain SSWW-21T was related most closely to the type strains of Okibacterium fritillariae (96.8 % similarity), Leifsonia poae (96.8 %) and Agreia bicolorata (96.6 %). Levels of 16S rRNA gene sequence similarity between the new isolate and members of other genera within the family Microbacteriaceae were in the range 93.1–96.3 %. The cell-wall peptidoglycan of strain SSWW-21T was of the B-type (2,4-diaminobutyric acid as the diagnostic diamino acid). The acyl type of the muramic acid was acetyl. The predominant menaquinone was MK-11. The polar lipid profile contained phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol and diphosphatidylglycerol. Mycolic acids were not present. The major cellular fatty acids were saturated branched-chain components (anteiso-C15 : 0 and anteiso-C17 : 0). The G+C content of the DNA was 69.8 mol%. On the basis of the phenotypic and phylogenetic data presented, strain SSWW-21T is considered to represent a novel species of a new genus within the family Microbacteriaceae, for which the name Phycicola gilvus gen. nov., sp. nov. is proposed. The type strain of Phycicola gilvus is SSWW-21T (=KCTC 19185T =DSM 18319T).
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A new member of the family Micromonosporaceae, Planosporangium flavigriseum gen. nov., sp. nov.
A novel actinomycete, designated strain YIM 46034T, was isolated from an evergreen broadleaved forest at Menghai, in southern Yunnan Province, China. Phenotypic characterization and 16S rRNA gene sequence analysis indicated that the strain belonged to the family Micromonosporaceae. Strain YIM 46034T showed more than 3 % 16S rRNA gene sequence divergence from recognized species of genera in the family Micromonosporaceae. Characteristic features of strain YIM 46034T were the production of two types of spores, namely motile spores, which were formed in sporangia produced on substrate mycelia, and single globose spores, which were observed on short sporophores of the substrate mycelia. The cell wall contained meso-diaminopimelic acid, glycine, arabinose and xylose, which are characteristic components of cell-wall chemotype II of actinomycetes. Phosphatidylethanolamine was the major phospholipid (phospholipid type II). Based on morphological, chemotaxonomic, phenotypic and genetic characteristics, strain YIM 46034T is considered to represent a novel species of a new genus in the family Micromonosporaceae, for which the name Planosporangium flavigriseum gen. nov., sp. nov. is proposed. The type strain of Planosporangium flavigriseum is YIM 46034T (=CCTCC AA 205013T =DSM 44991T).
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Nesterenkonia halophila sp. nov., a moderately halophilic, alkalitolerant actinobacterium isolated from a saline soil
A Gram-positive, non-motile, moderately halophilic, alkalitolerant actinobacterium, designated strain YIM 70179T, was isolated from a saline soil sample collected from Xinjiang Province, north-west China, and was subjected to a polyphasic taxonomic study. The cell-wall peptidoglycan type of strain YIM 70179T was A4α, l-Lys–Gly–l-Glu. Cells of the isolate contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unknown glycolipid, MK-8 as major menaquinone and anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0 as major fatty acids. The DNA G+C content was 68.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 70179T fell within the radiation of species of the genus Nesterenkonia. Levels of 16S rRNA gene sequence similarity between strain YIM 70179T and the type strains of recognized Nesterenkonia species were below 97 %, except to Nesterenkonia halobia DSM 20541T (99.6 %), but these two strains exhibited a low level of DNA–DNA relatedness (18.4 %). Based on genetic and phenotypic evidence, it is proposed that strain YIM 70179T represents a novel species of the genus Nesterenkonia, for which the name Nesterenkonia halophila sp. nov. is proposed. The type strain is YIM 70179T (=DSM 16378T =KCTC 19048T).
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Five new members of the Streptomyces violaceusniger 16S rRNA gene clade: Streptomyces castelarensis sp. nov., comb. nov., Streptomyces himastatinicus sp. nov., Streptomyces mordarskii sp. nov., Streptomyces rapamycinicus sp. nov. and Streptomyces ruanii sp. nov.
More LessThe taxonomic status of six strains received as Streptomyces hygroscopicus was established using a polyphasic approach. The organisms had phenotypic and morphological properties consistent with their classification in the genus Streptomyces. Almost complete 16S rRNA gene sequences of the strains were determined and aligned with corresponding sequences of representatives of the genus Streptomyces and phylogenetic trees were inferred using four tree-making algorithms. All of the strains fell within the Streptomyces violaceusniger 16S rRNA gene clade and four of them were considered to merit species status using a combination of genotypic and phenotypic data. These organisms were designated Streptomyces himastatinicus sp. nov. (type strain ATCC 53653T=DSM 41914T), Streptomyces mordarskii sp. nov. (type strain NRRL B-1346T=DSM 40771T), Streptomyces rapamycinicus sp. nov. (type strain NRRL 5491T=ATCC 29253T) and Streptomyces ruanii sp. nov. (type strain ISP 5276T=DSM 40276T). DNA–DNA relatedness and phenotypic data showed that the two remaining strains, ‘Streptomyces hygroscopicus subsp. enhygrus’ NRRL 3664 and Streptomyces hygroscopicus subsp. hygroscopicus NRRL 3111 belong to the same species as the type strain of Streptomyces rutgersensis subsp. castelarensis. This taxon is designated Streptomyces castelarensis sp. nov., comb. nov. (type strain ATCC 15191T=DSM 40830T) following the proposal that Streptomyces rutgersensis subsp. rutgersensis is a heterotypic synonym of Streptomyces albidoflavus.
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Rhodococcus kunmingensis sp. nov., an actinobacterium isolated from a rhizosphere soil
More LessA Gram-positive, aerobic, non-motile actinobacterium strain, designated YIM 45607T, was isolated from a rhizosphere soil sample in Kunming, south-west China. Chemotaxonomically, the isolate contained chemical markers that supported its assignment to the genus Rhodococcus. On the basis of 16S rRNA gene sequence similarity analysis, strain YIM 45607T formed a new subline within the genus Rhodococcus, with Rhodococcus equi as its closest phylogenetic neighbour (98.2 % 16S rRNA gene sequence similarity to the type strain). However, DNA–DNA hybridization demonstrated that strain YIM 45607T was different from R. equi DSM 20307T (35.4 % relatedness). Based on polyphasic analysis, strain YIM 45607T could be clearly distinguished from other species of the genus Rhodococcus. The isolate therefore represents a novel species of Rhodococcus, for which the name Rhodococcus kunmingensis sp. nov. is proposed. The type strain is strain YIM 45607T (=KCTC 19149T =DSM 45001T).
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Proposal for the new genus Allokutzneria gen. nov. within the suborder Pseudonocardineae and transfer of Kibdelosporangium albatum Tomita et al. 1993 as Allokutzneria albata comb. nov.
More LessDuring the course of phylogenetic analyses based on 16S rRNA gene sequences for all currently described taxa within the family Pseudonocardineae, it became evident that Kibdelosporangium albatum DSM 44149T was misplaced within the genus Kibdelosporangium and is phylogenetically most closely related to the genus Kutzneria. Chemotaxonomic analyses revealed that Kibdelosporangium albatum differed from Kutzneria in containing arabinose as well as galactose and mannose as diagnostic whole-cell sugars. The polar lipid pattern was distinct from both Kibdelosporangium and Kutzneria species in containing phosphatidylethanolamine containing 2-hydroxy fatty acids, lyso-phosphatidylethanolamine and lyso-phosphatidylmethylethanolamine as well as phosphatidylethanolamine, phosphatidylmethylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. These data preclude the inclusion of this strain within the genus Kutzneria or Kibdelosporangium and a new genus is proposed, to be named Allokutzneria gen. nov. The type species of this new genus is Allokutzneria albata gen. nov., comb. nov., the type strain of which is R761-7T (=NRRL B-24461T =DSM 44149T =ATCC 55061T).
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Promicromonospora kroppenstedtii sp. nov., isolated from sandy soil
More LessA new actinobacterial strain, RS16T, was isolated from sandy soil collected in Zamora, Spain, and was studied to determine its taxonomic position. A neighbour-joining tree based on 16S rRNA gene sequence analysis revealed that the novel isolate formed an independent branch between Promicromonospora sukumoe DSM 44121T and Promicromonospora citrea DSM 43110T. Levels of 16S rRNA gene sequence similarity between the novel isolate and its phylogenetic neighbours ranged from 98.7 to 98.9 %. Chemotaxonomic properties, such as the predominant menaquinone and polar lipids, supported the assignment of the novel isolate to the genus Promicromonospora, however, a significant number of physiological differences were found between the novel isolate and the other recognized species of the genus Promicromonospora. On the basis of these results, it is proposed that strain RS16T represents a novel species of the genus Promicromonospora, for which the name Promicromonospora kroppenstedtii sp. nov. is proposed. The type strain is RS16T (=DSM 19349T=LMG 24382T).
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- Bacteroidetes
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Balneola alkaliphila sp. nov., a marine bacterium isolated from the Mediterranean Sea
More LessA novel aerobic, Gram-negative bacterium, designated strain CM41_14bT, was isolated from surface waters in the coastal north-western Mediterranean Sea. Cells were non-motile, straight rods, 2.6 μm long and 0.7 μm wide and formed pale-orange colonies on marine agar medium. The G+C content of the genomic DNA was 39 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence placed the strain within the genus Balneola (phylum Bacteroidetes). On the basis of 16S rRNA gene sequence comparisons, and physiological and biochemical characteristics, the isolate represents a novel species for which the name Balneola alkaliphila sp. nov. is proposed. The type strain is CM41_14bT (=DSM 19538T=CIP 109603T=OOB 103T).
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Maribacter arcticus sp. nov., isolated from Arctic marine sediment
More LessA Gram-negative, non-motile, aerobic bacterium, designated strain KOPRI 20941T, was isolated from a sample of marine sediment from Ny Ålesund, Spitsbergen, Norway. A phylogenetic analysis based on 16S rRNA gene sequences revealed that the Arctic isolate nested within the genus Maribacter and showed the highest sequence similarity (98.1 %) with respect to Maribacter orientalis KMM 3947T. Chemotaxonomic data (DNA G+C content of 36 mol%; MK-6 as the major respiratory quinone and iso-C17 : 0 3-OH, C16 : 1 ω7c/iso-C15 : 0 2-OH and iso-C15 : 0 as the major fatty acids) supported the affiliation of strain KOPRI 20941T to the genus Maribacter. The results of phylogenetic analyses, physiological and biochemical tests and a DNA–DNA reassociation test (<54 % relatedness) allowed genotypic and phenotypic differentiation of the strain from the recognized species of the genus Maribacter. Therefore strain KOPRI 20941T represents a novel species of the genus Maribacter, for which the name Maribacter arcticus sp. nov. is proposed. The type strain is KOPRI 20941T (=KCTC 22053T=JCM 14790T).
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Joostella marina gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from the East Sea
A Gram-negative, non-spore-forming, non-motile, yellow-pigmented, strictly aerobic bacterial strain, designated En5T, was isolated from the East Sea of Korea and was subjected to a polyphasic taxonomy study. Strain En5T grew optimally at 30 °C, in the presence of 1–3 % (w/v) NaCl and at pH 5.3–7.6. The major respiratory lipoquinone was MK-6 and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 1 ω9c. The DNA G+C content of strain En5T was 30.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain En5T formed a distinct evolutionary lineage within the family Flavobacteriaceae and shared 93 % sequence similarity with the type strains of both Galbibacter mesophilus and Zhouia amylolytica. On the basis of its phenotypic and phylogenetic properties, strain En5T is suggested to represent a novel species of a new genus in the family Flavobacteriaceae, for which the name Joostella marina gen. nov., sp. nov. is proposed. The type strain is En5T (=KCTC 12518T=DSM 19592T=CGMCC 1.6973T).
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Sphingobacterium siyangense sp. nov., isolated from farm soil
More LessThe taxonomic position of a novel Gram-negative strain, designated SY1T, isolated from a farm-soil sample obtained from Jiangsu Province, PR China, was characterized by using a polyphasic approach. The cells were non-motile, non-spore-forming rods. The organism grew optimally at 30–37 °C and at pH 6.0–8.0. Based on 16S rRNA gene sequence analysis, strain SY1T is a member of the genus Sphingobacterium; Sphingobacterium multivorum JCM 21156T was the nearest relative (98.5 % sequence similarity). The predominant fatty acids of strain SY1T were iso-C15 : 0 (32.9 %), C16 : 0 (10.9 %) and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 24.1 %). The DNA G+C content was 38.5 mol%. The low level of DNA–DNA relatedness (2.2 %) to S. multivorum JCM 21156T in combination with differential morphological and biochemical properties demonstrated that strain SY1T (=KCTC 22131T=CGMCC 1.6855T) should be classified as representing a novel species of the genus Sphingobacterium for which the name Sphingobacterium siyangense sp. nov. is proposed.
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- Proteobacteria
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Presence of specific symbiotic bacteria in flies of the subfamily Tephritinae (Diptera Tephritidae) and their phylogenetic relationships: proposal of ‘Candidatus Stammerula tephritidis’
The presence of symbiotic bacteria in flies belonging to the subfamily Tephritinae, which predominantly infest the flower heads of composite flowers (Asteraceae), was investigated. Twenty-five species of flies, collected mainly in northern Italy, were examined. The bacteria adhered to the midgut epithelium in a space external to the peritrophic membrane and therefore not in direct contact with the gut contents. Specific, unique and live, but unculturable bacteria were consistently found in the majority of the fly species and their presence was also shown to be persistent in flies reared under microbiologically controlled conditions and devoid of any residual culturable intestinal bacteria. Sequencing of the small subunit rRNA gene from the novel bacteria indicated that they belonged to the family Enterobacteriaceae. Three main strongly supported clades were delineated by phylogenetic trees, the first of which featured a coherent set of sequences displaying gene sequence similarities lower than 96 % compared with recognized taxa. The second and third clades featured cases with higher gene sequence similarities to culturable bacteria, including Erwinia persicina and Ewingella americana, respectively. Relative rate tests were supportive of a fast genetic evolution for the majority of the bacterial symbionts of the subfamily Tephritinae. In agreement with the interpretation suggested in 1929 after pioneering observations made by H. J. Stammer, a symbiotic relationship between the novel bacteria and the tephritid flies is postulated. The origin of this apparently polyphyletic relationship is discussed and a novel candidate organism is proposed for the first clade under the designation ‘Candidatus Stammerula tephritidis’.
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Desulfovibrio carbinoliphilus sp. nov., a benzyl alcohol-oxidizing, sulfate-reducing bacterium isolated from a gas condensate-contaminated aquifer
Phenotypic and phylogenetic studies were performed on a novel sulfate-reducing bacterium, strain D41T, isolated as part of a methanogenic syntrophic culture from a gas condensate-contaminated aquifer undergoing intrinsic bioremediation. The bacterium was a Gram-negative, non-spore-forming, curved rod, motile by a single polar flagellum, which oxidized several alcohols incompletely, including methanol, ethanol, 1-propanol, 2-propanol, 1-butanol, 2-butanol, 3-methyl-1-butanol (isoamyl alcohol), ethylene glycol, 1,2-propanediol, 1,3-propanediol, 1,4-butanediol, phenylethanol and benzyl alcohol. Additionally, the strain oxidized H2/CO2, formate, lactate, pyruvate, maleate, malate and fumarate. Sulfate, thiosulfate and sulfite were used as electron acceptors. The DNA G+C content was 63 mol%. Based on phylogenetic and phenotypic evidence, the novel species Desulfovibrio carbinoliphilus sp. nov. is proposed. The type strain is D41T (=ATCC BAA-1241T =DSM 17524T).
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Ponticoccus litoralis gen. nov., sp. nov., a marine bacterium in the family Rhodobacteraceae
More LessA Gram-negative, coccoid to rod-shaped, strictly aerobic bacterium, strain CL-GR66T, was isolated from coastal seawater collected off Korea. The strain grew optimally in the presence of 3–5 % sea salts, at a temperature of 30 °C and at pH 7. The polar lipid profile of strain CL-GR66T comprised phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminolipids, an unidentified glycolipid and an unidentified lipid. The major fatty acids were C18 : 1 ω7c (71.4 %), 11-methyl C18 : 1 ω7c (11.3 %), C16 : 0 (6.4 %), C18 : 0 (4.6 %) and C12 : 1 3-OH (3.0 %). Ubiquinone 10 was the major quinone. The DNA G+C content was 67.9 mol%. 16S rRNA gene sequence analysis revealed that strain CL-GR66T belonged to the Roseobacter clade within the family Rhodobacteraceae. Strain CL-GR66T was related most closely to the type strain of Marinovum algicola (95.5 % 16S rRNA gene sequence similarity), and sequence similarities between strain CL-GR66T and other type species of the Roseobacter clade ranged from 91.8 to 95.4 %. Phylogenetic analyses of 16S rRNA gene sequences showed that strain CL-GR66T was not associated with any known genus in the family Rhodobacteraceae. The distinct phylogenetic position of strain CL-GR66T, its phylogenetic distance from genera of the family Rhodobacteraceae, together with phenotypic data, suggest that the organism represents a novel species of a new genus, for which the name Ponticoccus litoralis gen. nov., sp. nov. is proposed. The type strain of Ponticoccus litoralis is CL-GR66T (=KCCM 90028T =DSM 18986T).
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Pseudomonas panipatensis sp. nov., isolated from an oil-contaminated site
More LessA Gram-negative, motile, rod-shaped, non-sporulating, aerobic bacterial strain (Esp-1T) was isolated from oil-contaminated soil of Panipat Oil Refinery, India, and its taxonomic position was determined using a polyphasic approach. Strain Esp-1T grew in the presence of 2 % NaCl at 30 °C and was characterized chemotaxonomically by having C16 : 0 as the major fatty acid followed by C17 : 0 cyclo and C18 : 1 ω7c. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Esp-1T formed a cluster together with Pseudomonas knackmussii DSM 6978T (98.9 % sequence similarity), Pseudomonas delhiensis MTCC 7601T (98.5 %), Pseudomonas nitroreducens DSM 14399T (98.5 %), Pseudomonas citronellolis DSM 50332T (98.7 %), Pseudomonas multiresinivorans ATCC 700690T (98.9 %) and Pseudomonas jinjuensis DSM 16612T (97.8 %). DNA–DNA hybridization values of strain Esp-1T with P. knackmussii DSM 6978T, P. delhiensis MTCC 7601T, P. jinjuensis DSM 16612T, P. citronellolis DSM 50332T, P. multiresinivorans ATCC 700690T and P. nitroreducens DSM 14399T were 32.9, 30.2, 20.6, 23.4, 23.4 and 20.0 %, respectively. Low levels of DNA–DNA hybridization and phenotypic and chemotaxonomic results are sufficient to delineate strain Esp-1T from other closely related species of Pseudomonas. Phenotypic and chemotaxonomic data confirm that strain Esp-1T represents a novel species, for which the name Pseudomonas panipatensis sp. nov. is proposed. The type strain of Pseudomonas panipatensis sp. nov. is Esp-1T (=MTCC 8990T=CCM 7469T).
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Marinobacter guineae sp. nov., a novel moderately halophilic bacterium from an Antarctic environment
More LessTwo Gram-negative, cold-adapted, moderately halophilic, aerobic bacteria, designated strains M3BT and M3T, were isolated from marine sediment collected from the South Shetland Islands, Antarctica. The organisms were rod-shaped, catalase- and oxidase-positive, and motile by means of polar flagella. These two psychrotolerant strains required Na+ and grew at NaCl concentrations of 1–15 % and temperatures between 4 and 42 °C. 16S rRNA gene sequence analysis placed strains M3BT and M3T within the genus Marinobacter. DNA–DNA hybridization experiments between the Antarctic isolate M3BT and type strains of phylogenetically related species, namely Marinobacter lipolyticus, Marinobacter flavimaris, Marinobacter sediminum, Marinobacter algicola, Marinobacter maritimus and Marinobacter koreensis, revealed levels of relatedness lower than 32 %. Strain M3T showed 99 % DNA relatedness to strain M3BT. The DNA G+C contents of M3BT and M3T were 57.1 and 57.4 mol%, respectively, and their major isoprenoid quinone was ubiquinone-9. Several phenotypic characteristics, together with data on cellular fatty acid composition, served to differentiate strains M3BT and M3T from strains of related Marinobacter species. On the basis of the polyphasic taxonomic evidence presented in this study, it can be concluded that strains M3BT and M3T belong to the same genospecies and represent a novel species of the genus Marinobacter, for which the name Marinobacter guineae sp. nov. is proposed. The type strain is M3BT (=LMG 24048T=CECT 7243T).
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Isolation and characterization of Helicobacter suis sp. nov. from pig stomachs
A new cultivation method was successfully applied for the in vitro isolation of a hitherto uncultured spiral Helicobacter species associated with ulceration of the non-glandular stomach and gastritis in pigs and formerly described as ‘Candidatus Helicobacter suis’. Three isolates, HS1T, HS2 and HS3, were subcultured from the stomach mucosa of three pigs after slaughter and were analysed using a polyphasic taxonomic approach. The novel isolates grew on biphasic culture plates or very moist agar bases in microaerobic conditions and exhibited urease, oxidase and catalase activities. Sequencing of the 16S rRNA gene, the 23S rRNA gene, the partial hsp60 gene and partial ureAB genes confirmed that the strains present in the gastric mucosa of pigs constituted a separate taxon, corresponding to ‘Helicobacter heilmannii’ type 1 strains as detected in the gastric mucosa of humans and other primates. For all genes sequenced, the highest sequence similarities were obtained with Helicobacter felis, Helicobacter bizzozeronii and Helicobacter salomonis, Helicobacter species isolated from the gastric mucosa of dogs and cats, which have also been detected in the human gastric mucosa and which are commonly referred to as ‘Helicobacter heilmannii’ type 2. SDS-PAGE of whole-cell proteins of strains HS1T, HS2 and HS3 differentiated them from other Helicobacter species of gastric origin. The results of the polyphasic taxonomic analysis confirmed that the novel isolates constitute a novel taxon corresponding to ‘Helicobacter heilmannii’ type 1 strains from humans and to ‘Candidatus H. suis’ from pigs. The name Helicobacter suis sp. nov. is proposed for the novel isolates with the type strain HS1T (=LMG 23995T=DSM 19735T).
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Rhizobium miluonense sp. nov., a symbiotic bacterium isolated from Lespedeza root nodules
More LessSeventeen strains of lespedeza rhizobia, a previously defined novel group, were further characterized by comparison with phylogenetically related species using a polyphasic approach, including SDS-PAGE of whole-cell proteins, PCR-based restriction fragment length polymorphism analysis of ribosomal intergenic spacer sequences, determination of DNA G+C contents, DNA–DNA hybridization and analysis of phenotypic features. Based on data obtained in the present and previous studies, a novel species, Rhizobium miluonense sp. nov., is proposed for these strains. The type strain of R. miluonense is CCBAU 41251T (=LMG 24208T=HAMBI 2971T). Strain CCBAU 41251T could form ineffective nodules on Phaseolus vulgaris in addition to its original host Lespedeza chinensis.
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Rhodobacter ovatus sp. nov., a phototrophic alphaproteobacterium isolated from a polluted pond
More LessA novel ovoid, phototrophic, purple non-sulfur bacterium was isolated in pure culture from a sample of sediment from an industrially polluted pond (Noor Mohammad Kunta) in Hyderabad, India. Strain JA234T was found to be Gram-negative and non-motile and grew photoheterotrophically with a number of organic compounds serving as carbon source/electron donor. Photo-organoheterotrophic and chemo-organoheterotrophic growth were demonstrated. Biotin and thiamine were required for growth of strain JA234T. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA234T is most closely related to Rhodobacter azotoformans (97.3 % sequence similarity) and clusters with other species of the genus Rhodobacter of the family Rhodobacteraceae. However, DNA–DNA hybridization with Rba. azotoformans JCM 9340T showed a relatedness of only 31.3 % with respect to strain JA234T. On the basis of 16S rRNA gene sequence analysis, DNA–DNA hybridization data and morphological and physiological characteristics, strain JA234T represents a novel species of the genus Rhodobacter, for which the name Rhodobacter ovatus sp. nov. is proposed. The type strain is JA234T (=JCM 14779T=CCUG 55049T).
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Phaeobacter arcticus sp. nov., a psychrophilic bacterium isolated from the Arctic
More LessA Gram-negative, psychrophilic, motile, rod-shaped bacterium, designated strain 20188T, was isolated from marine samples collected from the Arctic (7 ° 00′ 24″ N 16 ° 59′ 37″ W), and was identified taxonomically by means of a polyphasic study. On the basis of 16S rRNA gene sequence similarity, strain 20188T was closely related to members of the genera Phaeobacter. 16S rRNA gene sequence similarities between strain 20188T and the type strains of Phaeobacter inhibens, Phaeobacter gallaeciensis and Phaeobacter daeponensis were 97.0, 96.8 and 96.2 %, respectively. The temperature range for growth was 0–25 °C, with optimum growth occurring at 19–20 °C and at approximately pH 6.0–9.0. Strain 20188T had ubiquinone-10 as the major respiratory quinone and C18 : 1 ω7c and 11-methyl C18 : 1 ω7c as major fatty acids. The genomic DNA G+C content was 59.6 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain 20188T is considered to represent a novel species of the genus Phaeobacter, for which the name Phaeobacter arcticus sp. nov. is proposed. The type strain is 20188T (=CGMCC 1.6500T=JCM 14644T).
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Chromobacterium haemolyticum sp. nov., a strongly haemolytic species
More LessA Gram-negative bacterium, strain MDA0585T, isolated from a sputum culture, was characterized by a polyphasic approach. The 16S rRNA gene and a conserved portion of the DNA gyrase A gene were sequenced and analysed phylogenetically. Strain MDA0585T showed the closest relationships with Chromobacterium violaceum ATCC 12472T and Chromobacterium subtsugae PRAA4-1T (96.1 % and 96.3 % 16S rRNA gene sequence similarity, respectively). The cellular fatty acids of strain MDA0585T consisted mainly of C16 : 0, C16 : 1 ω7c and C16 : 1 ω6c (summed feature 3) and C18 : 1 ω7c and C18 : 1 ω6c (summed feature 8), a profile that was similar to, but distinguishable from, those of C. violaceum ATCC 12472T and C. subtsugae PRAA4-1T. In culture, strain MDA0585T differed from C. violaceum and C. subtsugae in several ways: lack of violet pigmentation, the ability to haemolyse sheep blood, differences in several biochemical reactions and higher resistance to antibiotics. The culture supernatant of strain MDA0585T also caused remarkable haemolysis of human erythrocytes. These results suggest that strain MDA0585T represents a novel species within the genus Chromobacterium, for which the name Chromobacterium haemolyticum sp. nov. is proposed. The type strain is MDA0585T (=CCUG 53230T=JCM 14163T=DSM 19808T).
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Pseudomonas duriflava sp. nov., isolated from a desert soil
More LessA Gram-negative, rod-shaped, non-motile, non-spore-forming bacterium, designated strain HR2T, was isolated from a soil sample from the Taklimaken Desert in Xinjiang Province, China. Strain HR2T grew optimally at pH 7.0–8.0 and 30–37 °C in the presence of 0–1 % (w/v) NaCl. An analysis of 16S rRNA gene sequences revealed that strain HR2T fell within the radiation of the genus Pseudomonas, the highest level of similarity being found with respect to Pseudomonas luteola IAM 13000T (97.5 %); the levels of sequence similarity with respect to other recognized Pseudomonas species were <96.4 %. DNA–DNA hybridization showed that the genetic relatedness between strain HR2T and P. luteola IAM 13000T was 53.2 %. The G+C content of the genomic DNA of strain HR2T was 55.2 mol%. The major fatty acids were 18 : 1, summed feature 3 and 16 : 0. The hydroxylated fatty acids 10 : 0 3-OH, 12 : 0 3-OH and 12 : 0 2-OH were also present. The data obtained in this polyphasic study indicated that this isolate represents a novel species of the genus Pseudomonas, for which the name Pseudomonas duriflava sp. nov. is proposed. The type strain is HR2T (=KCTC 22129T=CGMCC 1.6858T).
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Shinella kummerowiae sp. nov., a symbiotic bacterium isolated from root nodules of the herbal legume Kummerowia stipulacea
More LessBacterial strain CCBAU 25048T was isolated from root nodules of Kummerowia stipulacea grown in Shandong province of China. Cells of the strain were Gram-negative, strictly aerobic, non-spore-forming, motile short rods. Phylogeny of 16S rRNA gene sequences revealed that the strain belonged to the genus Shinella, a member of family Rhizobiaceae. Its closest phylogenetic relatives were Shinella granuli Ch06T and Shinella zoogloeoides IAM 12669T, respectively showing 98.3 and 98.9 % 16S rRNA gene sequence similarity. Strain CCBAU 25048T had DNA–DNA relatedness of 43.5 and 34.8 %, respectively, with S. zoogloeoides JCM 20728T and S. granuli JCM 13254T. In addition, in TP-RAPD analysis, different patterns were obtained for these three strains and some rhizobial strains. The nifH, nodC and nodD sequences of CCBAU 25048T were identical or very similar to those of bean-nodulating Rhizobium tropici strains. Several phenotypic characteristics, including the use of citrate and d-ribose as carbon sources and growth at pH 11.0, as well as the fatty acid composition, could differentiate CCBAU 25048T from the two defined Shinella species. Therefore, a novel species Shinella kummerowiae sp. nov. is proposed, with strain CCBAU 25048T (=JCM 14778T =LMG 24136T) as the type strain.
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Massilia aerilata sp. nov., isolated from an air sample
A novel aerobic, Gram-negative, rod-shaped, motile bacterium, designated strain 5516S-11T, was isolated from air samples collected in the Suwon region of the Republic of Korea. Analysis of the 16S rRNA gene sequence indicated that the organism belongs to the genus Massilia; the highest sequence similarity (97.2 %) was found with respect to Massilia aurea DSM 18055T. Cells of strain 5516S-11T contained ubiquinone Q-8 as the predominant isoprenoid quinone and possessed summed feature 3 (C16 : 1 ω7c/iso-C15 : 0 2-OH; 35.2 %), C16 : 0 (30.6 %) and C18 : 1 ω7c (11.7 %) as the major fatty acids. DNA–DNA hybridization revealed 32 % relatedness between strain 5516S-11T and M. aurea DSM 18055T. The G+C content of the DNA of strain 5516S-11T was 68.9 mol%. It is clear from the genotypic and phenotypic data presented that strain 5516S-11T represents a novel species of the genus Massilia, for which the name Massilia aerilata sp. nov. is proposed. The type strain is 5516S-11T (=KACC 12505T =DSM 19289T).
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Ochrobactrum rhizosphaerae sp. nov. and Ochrobactrum thiophenivorans sp. nov., isolated from the environment
Two Gram-negative, rod-shaped, non-spore-forming bacteria, PR17T and DSM 7216T, isolated from the potato rhizosphere and an industrial environment, respectively, were studied for their taxonomic allocation. By rrs (16S rRNA) gene sequencing, these strains were shown to belong to the Alphaproteobacteria, most closely related to Ochrobactrum pseudogrignonense (98.4 and 99.3 % similarity to the type strain, respectively). Chemotaxonomic data (major ubiquinone Q-10; major polyamines spermidine, sym-homospermidine and putrescine; major polar lipids phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol and phosphatidylcholine and the Ochrobactrum-specific unidentified aminolipid AL2; major fatty acids C18 : 1 ω7c and C19 : 0 cyclo ω8c) supported the genus affiliation. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of the isolates from all hitherto-described Ochrobactrum species. Hence, both isolates represent novel species of the genus Ochrobactrum, for which the names Ochrobactrum rhizosphaerae sp. nov. (type strain PR17T =CCUG 55411T =CCM 7493T =DSM 19824T) and Ochrobactrum thiophenivorans sp. nov. (type strain DSM 7216T =CCUG 55412T =CCM 7492T) are proposed.
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Cronobacter gen. nov., a new genus to accommodate the biogroups of Enterobacter sakazakii, and proposal of Cronobacter sakazakii gen. nov., comb. nov., Cronobacter malonaticus sp. nov., Cronobacter turicensis sp. nov., Cronobacter muytjensii sp. nov., Cronobacter dublinensis sp. nov., Cronobacter genomospecies 1, and of three subspecies, Cronobacter dublinensis subsp. dublinensis subsp. nov., Cronobacter dublinensis subsp. lausannensis subsp. nov. and Cronobacter dublinensis subsp. lactaridi subsp. nov.
[Enterobacter] sakazakii is an opportunistic pathogen that can cause infections in neonates. This study further clarifies the taxonomy of isolates described as [E.] sakazakii and completes the formal description of the proposed reclassification of these organisms as novel species and subspecies within a proposed novel genus, Cronobacter gen. nov. [E.] sakazakii was first defined in 1980, however recent polyphasic taxonomic analysis has determined that this group of organisms consists of several genomospecies. In this study, the phenotypic descriptions of the proposed novel species are expanded using Biotype 100 and Biolog Phenotype MicroArray data. Further DNA–DNA hybridization experiments showed that malonate-positive strains within the [E.] sakazakii genomospecies represent a distinct species, not a subspecies. DNA–DNA hybridizations also determined that phenotypically different strains within the proposed species, Cronobacter dublinensis sp. nov., belong to the same species and can be considered as novel subspecies. Based on these analyses, the following alternative classifications are proposed: Cronobacter sakazakii gen. nov., comb. nov. [type strain ATCC 29544T (=NCTC 11467T)]; Cronobacter malonaticus sp. nov. [type strain CDC 1058-77T (=LMG 23826T=DSM 18702T)]; Cronobacter turicensis sp. nov. [type strain z3032T (=LMG 23827T=DSM 18703T)]; Cronobacter muytjensii sp. nov. [type strain ATCC 51329T (=CIP 103581T)]; Cronobacter dublinensis sp. nov. [type strain DES187T (=LMG 23823T=DSM 18705T)]; Cronobacter dublinensis subsp. dublinensis subsp. nov. [type strain DES187T (=LMG 23823T=DSM 18705T)]; Cronobacter dublinensis subsp. lausannensis subsp. nov. [type strain E515T (=LMG 23824=DSM 18706T)], and Cronobacter dublinensis subsp. lactaridi subsp. nov. [type strain E464T (=LMG 23825T=DSM 18707T)].
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Marinobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from the Arctic
More LessStrain 20041T was isolated from sea-ice of the Canadian Basin (7 ° 23′ 14″ N 14 ° 06′ 55″ W). Phylogenetic analysis based on 16S rRNA gene homology showed that strain 20041T was related to members of the genus Marinobacter and had highest 16S rRNA gene sequence similarity with the type strain of Marinobacter maritimus. Cells were Gram-negative, rod-shaped, psychrophilic and motile. The temperature range for growth was 0–22 °C, with optimum growth occurring at 16–18 °C and at approximately pH 6.0–9.0. Strain 20041T had ubiquinone-9 as the major respiratory quinone and iso-C15 : 0 2OH and/or C16 : 1 ω7c, C16 : 0, C18 : 1 ω9c and C12 : 0 3OH as major fatty acids. The genomic DNA G+C content was 55.4 mol%. On the basis of the phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain 20041T is considered to represent a novel species, for which the name Marinobacter psychrophilus sp. nov. is proposed. The type strain is 20041T (=CGMCC 1.6499T=JCM 14643T).
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Roseomonas aerilata sp. nov., isolated from an air sample
A polyphasic study was carried out to clarify the taxonomic position of a pink-coloured, Gram-negative bacterium isolated from air in the Suwon region of Korea. The novel strain, 5420S-30T, grew in the temperature range of 5–35 °C (optimum 30 °C) and pH range of 5–9 (optimum pH 6–7). Growth did not occur in the presence of as little as 1 % (w/v) NaCl. It contained Q-10 as the predominant ubiquinone. The major fatty acids were C18 : 1 ω7c, summed feature 3 (C16 : 1 ω7c/iso-C15 : 0 2-OH) and C16 : 0 (together representing 77.7 % of the total). The DNA G+C content was 72.1 mol%. The 16S rRNA gene sequence similarities between strain 5420S-30T and members of the genus Roseomonas were in the range 91.6–95.1 %, with the highest sequence similarities (95.1 and 94.5 %, respectively) to Roseomonas aquatica TR53T and Roseomonas gilardii ATCC 49956T. On the basis of its phenotypic and genotypic characteristics, strain 5420S-30T represents a novel species of the genus Roseomonas, for which the name Roseomonas aerilata sp. nov. is proposed, with 5420S-30T (=KACC 12521T =DSM 19363T) as the type strain.
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- Eukaryotic Micro-Organisms
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Ogataea ganodermae sp. nov., a methanol-assimilating yeast species isolated from basidiocarps of Ganoderma sp.
More LessThree methanol-utilizing yeast strains were isolated from basidiocarps of Ganoderma sp. collected from a tree trunk in Mangshan Mountain, Hunan Province, southern China. These strains formed hat-shaped ascospores in unconjugated and deliquescent asci. Sequence analysis of the large-subunit rRNA gene D1/D2 domain and internal transcribed spacer (ITS) region, electrophoretic karyotype comparison and phenotypic characterization demonstrated that the three strains represent a novel species of the genus Ogataea, which is described as Ogataea ganodermae sp. nov. (type strain SHS 2.1T =CGMCC AS 2.3435T =CBS 10646T). Phylogenetically, the novel species was closely related to Ogataea pini and Ogataea henricii. The latter two taxa with similar D1/D2 sequences were confirmed to represent separate species by ITS sequence and electrophoretic karyotype comparisons.
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- Other Gram-Positive Bacteria
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Ruminococcus gauvreauii sp. nov., a glycopeptide-resistant species isolated from a human faecal specimen
More LessA novel strictly anaerobic, vancomycin-resistant, Gram-positive coccus (strain CCRI-16110T) was isolated from a human faecal specimen. This strain was characterized using morphological, biochemical and molecular taxonomic methods. The organism was unable to hydrolyse aesculin and failed to produce acid from cellobiose, d-lactose and α-raffinose. Acetic acid was the sole product of glucose fermentation by the organism. On the basis of 16S rRNA and tuf gene sequence comparison, strain CCRI-16110T was most closely related to species of the genus Ruminococcus and formed a hitherto unknown sublineage within the Clostridium coccoides rRNA cluster of organisms (cluster XIVa). Based on phenotypic and phylogenetic evidence, a novel species, Ruminococcus gauvreauii sp. nov., is proposed. The type strain is CCRI-16110T (=NML 060141T =CCUG 54292T =JCM 14987T).
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Anaerobranca zavarzinii sp. nov., an anaerobic, alkalithermophilic bacterium isolated from Kamchatka thermal fields
More LessA novel obligately anaerobic, alkalithermophilic, chemo-organotrophic bacterium was isolated from a small and very shallow geothermally heated pool at Pushino (Kamchatka, Far East Russia). The bacterium, designated strain JW/VK-KS5YT, was a Gram staining negative, Gram type positive rod. The cells were sometimes branched, with a tendency to grow in long chains, and were non-sporulating and non-motile. The shortest observed doubling time was 28 min when the novel strain was grown at 54–60 °C in 120 mM sodium carbonate-containing medium at pH25 °C 8.5–9.0. The novel bacterium grew on yeast extract and soytone as sole carbon and energy sources but could also use fumarate, thiosulfate and sulfur as electron acceptors. The DNA G+C content was 32.5 mol%. Based on phylogenetic, DNA–DNA hybridization and phenotypic data, it was concluded that isolate JW/VK-KS5YT (=VKM B-2436T=DSM 18970T) represents the type strain of a novel species, Anaerobranca zavarzinii sp. nov.
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Caldicellulosiruptor kronotskyensis sp. nov. and Caldicellulosiruptor hydrothermalis sp. nov., two extremely thermophilic, cellulolytic, anaerobic bacteria from Kamchatka thermal springs
Five novel strains (2002T, 2902, 2006, 108T and 117) of cellulose-degrading, anaerobic, thermophilic bacteria were isolated from terrestrial hot springs of Kamchatka (Far East, Russia). Strains 2002T and 108T were non-spore-forming bacteria with a Gram-positive type cell wall and peritrichous flagella. Optimum growth of strains 2002T and 108T occurred at pH 7.0 and at temperatures of 70 and 65 °C, respectively. The G+C contents of the DNA of strains 2002T and 108T were 35.1 and 36.4 mol%, respectively. Comparative 16S rRNA gene sequence analysis revealed that the isolates belonged to the genus Caldicellulosiruptor. However, DNA–DNA hybridization experiments indicated that the levels of relatedness between strains 2002T and 108T and those of recognized members of the genus Caldicellulosiruptor ranged between 32 and 54 %. Based on both phenotypic and genomic differences, strains 2002T and 108T are considered to represent two novel species of the genus Caldicellulosiruptor. The names proposed for these organisms are Caldicellulosiruptor kronotskyensis sp. nov. (type strain 2002T=DSM 18902T=VKM B-2412T) and Caldicellulosiruptor hydrothermalis sp. nov. (type strain 108T=DSM 18901T=VKM B-2411T).
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Tumebacillus permanentifrigoris gen. nov., sp. nov., an aerobic, spore-forming bacterium isolated from Canadian high Arctic permafrost
More LessA Gram-positive, aerobic, rod-shaped bacterium (strain Eur1 9.5T) was isolated from a 9-m-deep permafrost sample from the Canadian high Arctic. Strain Eur1 9.5T could not be cultivated in liquid medium and grew over the temperature range 5–37 °C; no growth was observed at 42 °C and only slow growth was observed at 5 °C following 1 month of incubation. Eur1 9.5T grew over the pH range 5.5–8.9 and tolerated NaCl concentrations of 0–0.5 % (w/v). Eur1 9.5T grew heterotrophically on complex carbon substrates and chemolithoautotrophically on inorganic sulfur compounds, as demonstrated by growth on sodium thiosulfate and sulfite as sole electron donors. Eur1 9.5T contained iso-C15 : 0 as the major cellular fatty acid and menaquinone 7 (MK-7) as the major respiratory quinone. The cell-wall peptidoglycan was of type A1γ. The DNA G+C content was 53.1 mol%. The 16S rRNA gene sequence of strain Eur1 9.5T was only distantly related (≤87 % sequence similarity over 1407 bp) to any recognized bacterial species. Based on physiological and phylogenetic analyses, strain Eur1 9.5T is suggested to represent a novel species of a new genus, for which the name Tumebacillus permanentifrigoris gen. nov., sp. nov. is proposed. The type strain of Tumebacillus permanentifrigoris is Eur1 9.5T (=DSM 18773T =JCM 14557T).
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- Evolution, Phylogeny And Biodiversity
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Gene sequences of the pil operon reveal relationships between symbiotic strains of Vibrio fischeri
More LessSymbiosis between the bobtail squid Euprymna scolopes (Mollusca: Cephalopoda) and Vibrio fischeri bacteria has been a well-studied model for understanding the molecular mechanisms of colonization and adherence to host cells. For example, pilin expression has been observed to cause subtle variation in colonization for a number of Gram-negative bacteria with eukaryotic hosts. To investigate variation amongst pil genes of closely related strains of vibrios, we amplified pil genes A, B, C and D to determine orientation and sequence similarity to other symbiotic vibrios. The pilA gene was found to be upstream from all other pil genes, and not contiguous with the rest of the operon. The pilB, pilC and pilD loci were flanked at the 3′ end by yacE, followed by a conserved hypothetical gene. DNA sequences of each pil gene were aligned and analysed phylogenetically using parsimony for both individual and combined gene trees. Results demonstrate that certain pil loci (pilB and pilD) are conserved among strains of V. fischeri, but pilC differs in sequence between symbiotic and free-living strains. Phylogenetic analysis of all pil genes gives better resolution of Indo-west Pacific V. fischeri symbionts compared with analysis of the 16S rRNA gene. Hawaiian and Australian symbiotic strains form one monophyletic tree, supporting the hypothesis that V. fischeri strain specificity is selected by the geographical location of their hosts and is not related to specific squid species.
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The tufB–secE–nusG–rplKAJL–rpoB gene cluster of the liberibacters: sequence comparisons, phylogeny and speciation
More LessThe rplKAJL–rpoBC operon or β operon is a classic bacterial gene cluster, which codes for proteins K, A, J and L of the large ribosomal subunit, as well as proteins B (β subunit) and C (β′ subunit) of RNA polymerase. In the early 1990s, the operon was obtained as a 2.6 kbp DNA fragment (In-2.6) by random cloning of DNA from periwinkle plants infected with the Poona (India) strain of the huanglongbing agent, later named ‘Candidatus (Ca.) Liberibacter asiaticus’. DNA from periwinkle plants infected with the Nelspruit strain (South Africa) of ‘Ca. L. africanus’ was amplified with a primer pair designed from In-2.6 and yielded, after cloning and sequencing, a 1.7 kbp DNA fragment (AS-1.7) of the β operon of ‘Ca. L. africanus’. The β operon of the American liberibacter, as well as the three upstream genes (tufB, secE, nusG), have now also been obtained by the technique of chromosome walking and extend over 4673 bp, comprising the following genes: tufB, secE, nusG, rplK, rplA, rplJ, rplL and rpoB. The sequence of the β operon was also determined for a Brazilian strain of ‘Ca. L. asiaticus’, from nusG to rpoB (3025 bp), and was found to share 99 % identity with the corresponding β operon sequences of an Indian and a Japanese strain. Finally, the β operon sequence of ‘Ca. L. africanus’ was extended from 1673 bp (rplA to rpoB) to 3013 bp (nusG to rpoB), making it possible to compare the β operon sequences of the African, Asian and American liberibacters over a length of ∼3000 bp, from nusG to rpoB. While ‘Ca. L. africanus’ and ‘Ca. L. asiaticus’ shared 81.2 % sequence identity, the percentage for ‘Ca. L. americanus’ and ‘Ca. L. africanus’ was only 72.2 %, and identity for ‘Ca. L. americanus’ and ‘Ca. L. asiaticus’ was only 71.4 %. The ∼3000 bp nusG–rpoB sequence was also used to construct a phylogenetic tree, and this tree was found to be identical to the known 16S rRNA gene sequence-based tree. These results confirm earlier findings that ‘Ca. L. americanus’ is a distinct liberibacter, more distantly related to ‘Ca. L. africanus’ and ‘Ca. L. asiaticus’ than ‘Ca. L. africanus’ is to ‘Ca. L. asiaticus’. The dates of speciation have also been estimated.
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A seven-gene, multilocus, genus-wide approach to the phylogeny of mycobacteria using supertrees
More LessThis is the first study that estimates mycobacterial phylogeny using the maximum-likelihood method (PhyML-aLRT) on a seven-gene concatenate (hsp65, rpoB, 16S rRNA, smpB, sodA, tmRNA and tuf) and the super distance matrix (SDM) supertree method. Two sets of sequences were studied: a complete seven gene sequence set (set R, type strains of 87 species) and an incomplete set (set W, 132 species) with some missing data. Congruencies were computed by using the consense program (phylip package). The evolution rate of each gene was determined, as was the evolution rate of each strain for a given gene. Maximum-likelihood trees resulting from concatenation of the R and W sets resulted in a similar phylogeny, usually showing an early separation between slow-growing (SG) and rapidly growing (RG) mycobacteria. The SDM tree for the W set resulted in a different phylogeny. The separation of SG and RG was still evident, but it was located later in the nodes. The SG were therefore positioned as a subgroup of RG. Maximum-likelihood phylogenetic reconstruction was less affected by increasing the number of strains (with incomplete data), but did seem to cushion the variability of the evolution rate (ER), whereas the SDM method seemed to be more accurate and took into account both the differing ER values and the incomplete data. With regard to ER, it was observed that the 16S rRNA gene was the gene that displayed the slowest evolution, whereas smpB was the most rapidly evolving gene. Surprisingly, these two genes alone accurately separated the SG from the RG on the basis of their ER values. This study focused on the differences in ER between genes and in some cases linked the ER to the phenotypic classification of the mycobacteria.
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Genetic diversity among phytoplasmas infecting Opuntia species: virtual RFLP analysis identifies new subgroups in the peanut witches'-broom phytoplasma group
More LessPhytoplasmas were detected in cactus (Opuntia species) plants exhibiting witches'-broom disease symptoms in Yunnan Province, south-western China. Comparative and phylogenetic analyses of 16S rRNA gene sequences indicated that an overwhelming majority of the cactus-infecting phytoplasmas under study belonged to the peanut witches'-broom phytoplasma group (16SrII). Genotyping through use of computer-simulated restriction fragment length polymorphism (RFLP) analysis of 16S rRNA genes revealed a remarkable genetic diversity among these cactus-infecting phytoplasma strains. Based on calculated coefficients of RFLP pattern similarities, seven new 16SrII subgroups were recognized, bringing the total of described group 16SrII subgroups to 12 worldwide. Geographical areas differed from one another in the extent of genetic diversity among cactus-infecting phytoplasma strains. The findings have implications for relationships between ecosystem distribution and the emergence of group 16SrII subgroup diversity.
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- International Committee On Systematics Of Prokaryotes
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- Request For An Opinion
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The status of the species Pectinatus portalensis Gonzalez et al. 2005. Request for an Opinion
More LessOn the basis of 16S rRNA gene sequence analysis and several key phenotypic features, it was ascertained that the cultures cited as the type strain of the species Pectinatus portalensis, CECT 5841T and LMG 22865T, do not conform to the description, [Gonzalez, J. M., Jurado, V., Laiz, L., Zimmerman, J., Hermosin, B. & Saiz-Jimenez, C. (2004). Antonie van Leeuwenhoek 86, 241–248]. The type strain does not exist in any other established culture collection or with the authors who described this species. Therefore, it cannot be included in any scientific study. It is proposed that the Judicial Commission place the name Pectinatus portalensis on the list of rejected names if a suitable replacement type strain is not found or a neotype is not proposed within two years following the publication of this Request for an Opinion.
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- Taxonomic Note
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Against conservation of specific epithets formed wrongly as nominative nouns in apposition
More LessTogether with 31 other incorrectly formed (i.e. as nominative nouns in apposition) specific epithets, the epithet of Streptomyces scabies was corrected to Streptomyces scabiei in Taxonomic Notes published in 1997 and 1998. A subsequent Request for an Opinion, published in 2001, to reinstate the incorrect epithets for ten of these species was denied by the Judicial Commission in 2002. In 2007, a further Request for an Opinion was submitted to the Judicial Commission which proposed the conservation of the incorrect epithet of Streptomyces ‘scabies’ over the corrected one, scabiei. After having stated once that the corrections made to the epithets were performed according to the correct application of the International Code of Nomenclature of Bacteria (now ‘of Prokaryotes’, ICNP), the Judicial Commission would lose authority and credibility if it were to follow a request to abandon even one of the now correct 32 epithets in favour of its incorrectly formed predecessor. Microbiologists who accept changes in names of genera should also accept the correction of grammatical or orthographical changes in specific epithets.
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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 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)