- Volume 58, Issue 3, 2008
Volume 58, Issue 3, 2008
- Validation List No. 120
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List of new names and new combinations previously effectively, but not validly, published
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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- Notification List
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Notification that new names and new combinations have appeared in volume 57, part 12, 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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Sanguibacter soli sp. nov., isolated from soil of a ginseng field
More LessA Gram-positive, non-spore-forming, rod-shaped, motile bacterium, designated strain DCY22T, was isolated from soil of a ginseng field in South Korea and characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain DCY22T belonged within the family Sanguibacteraceae, and highest levels of sequence similarity were found with Sanguibacter marinus 1-19T (96.8 %), Sanguibacter suarezii ST-26T (96.0 %), Sanguibacter inulinus ST-50T (95.9 %), Sanguibacter keddieii ST-74T (95.5 %), Terrabacter terrae PPLBT (94.0 %) and Terrabacter tumescens DSM 20308T (93.8 %). Chemotaxonomic investigations revealed that strain DCY22T possessed menaquinone MK-9, a common feature of members of the genus Sanguibacter. Predominant fatty acids were unknown ECL 13.961 (45.81 %), 17 : 0 anteiso (23.46 %), 18 : 0 iso (15.42 %) and unknown ECL 14.966 (8.70 %). The results of physiological and biochemical tests clearly demonstrated that strain DCY22T represents a novel species of the genus Sanguibacter, for which the name Sanguibacter soli sp. nov. is proposed. The type strain is DCY22T (=KCTC 13155T=JCM 14841T).
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Saccharomonospora saliphila sp. nov., a halophilic actinomycete from an Indian soil
A Gram-positive, moderately halophilic actinomycete strain, designated YIM 90502T, was isolated from a sample of muddy soil collected from Gulbarga, Karnataka Province, India, and subjected to a polyphasic taxonomical analysis. The isolate grew optimally at 28 °C and in the presence of 10 % (w/v) NaCl. The isolate was characterized chemotaxonomically as having meso-diaminopimelic acid in the cell-wall peptidoglycan and galactose and arabinose as whole-cell sugars. The predominant menaquinone was MK-9(H4), while MK-8(H4) was found in smaller amounts. The phospholipids were phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were iso-C16 : 0 (49.2 %) and C17 : 1 ω6c (9.1 %). The DNA G+C content of the isolate was 71.8 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that the isolate fell within the evolutionary radiation encompassed by the genus Saccharomonospora. 16S rRNA gene sequence similarity between strain YIM 90502T and the type strains of Saccharomonospora species ranged from 92.42 % (with Saccharomonospora xinjiangensis CCTCC AA 97021T) to 97.45 % (with Saccharomonospora azurea KCTC 9693T). Levels of DNA–DNA relatedness between strain YIM 90502T and S. azurea KCTC 9693T, Saccharomonospora halophila DSM 44411T and Saccharomonospora paurometabolica DSM 44619T were 46.0, 41.0 and 42.5 %, respectively. On the basis of phenotypic, phylogenetic and genotypic data, strain YIM 90502T was classified in the genus Saccharomonospora as a member of a novel species, for which the name Saccharomonospora saliphila sp. nov. is proposed, with YIM 90502T (=KCTC 19234T =DSM 45087T) as the type strain.
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Brevibacterium album sp. nov., a novel actinobacterium isolated from a saline soil in China
A novel Gram-positive, rod-shaped actinobacterium, designated strain YIM 90718T, was isolated from a saline soil in Xinjiang province, north-west China, and subjected to polyphasic taxonomy. The peptidoglycan type was A1γ and the cell-wall sugars contained galactose. Phospholipids were phosphatidylglycerol and diphosphatidylglycerol. The predominant menaquinone was MK-8(H2). The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0. All of these chemotaxonomic data assigned the new isolate YIM 90718T consistently to the genus Brevibacterium. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM 90718T formed a distinct phyletic lineage in the genus Brevibacterium and showed the highest sequence similarity (96.2 %) to Brevibacterium samyangense SST-8T and low similarity (<95.5 %) to other species of the genus Brevibacterium. On the based of the polyphasic evidence, a novel species, Brevibacterium album sp. nov., is proposed, with the type strain YIM 90718T (=DSM 18261T =KCTC 19173T =CCTCC AB 206112T).
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Phycicoccus dokdonensis sp. nov., isolated from soil
More LessA Gram-positive, non-motile, coccoid-shaped bacterium, designated strain DS-8T, was isolated from soil from Dokdo, Korea, and its taxonomic position was investigated by using a polyphasic study. Strain DS-8T grew optimally at 30 °C and pH 6.5–7.5 in the presence of 0.5–1.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain DS-8T joined the type strain of Phycicoccus jejuensis, with a bootstrap resampling value of 92.5 %, and shared 96.5 % 16S rRNA gene sequence similarity with P. jejuensis. The cell-wall peptidoglycan type was based on meso-diaminopimelic acid and the acyl type of the muramic acid was acetyl. The predominant menaquinone was MK-8(H4). The major fatty acids were iso-C15 : 0 and iso-C16 : 0. Major polar lipids detected in strain DS-8T were phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol and two unidentified phospholipids. The DNA G+C content was 70.7 mol%. DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness, revealed that strain DS-8T differs from P. jejuensis. On the basis of the data obtained, strain DS-8T is considered to represent a novel species of the genus Phycicoccus, for which the name Phycicoccus dokdonensis sp. nov. is proposed. The type strain is DS-8T (=KCTC 19248T=CCUG 54521T).
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Saccharopolyspora cebuensis sp. nov., a novel actinomycete isolated from a Philippine sponge (Porifera)
More LessThe taxonomic status of a marine actinomycete isolated from the sponge Haliclona sp. collected from Cebu, Philippines, was established using both phenotypic and genotypic data. Strain SPE 10-1T exhibited chemotaxonomic and morphological characteristics that were consistent with those of members of the genus Saccharopolyspora. It showed a strict requirement for salt and is the first obligate marine bacterium of the genus Saccharopolyspora to be isolated. The principal isoprenoid quinone detected was MK-9(H4). The fatty acid pattern consisted mainly of terminally branched iso and anteiso fatty acids. The DNA G+C content was 72.6 mol%. Analysis of the 16S rRNA gene sequence supported affiliation of the strain with the genus Saccharopolyspora; the type strain of Saccharopolyspora gregorii was the closest phylogenetic relative (96 % sequence similarity). Sequence similarities of strain SPE 10-1T to other type strains of this genus were 93–95 %. It is proposed that strain SPE 10-1T should be classified in the genus Saccharopolyspora as a representative of Saccharopolyspora cebuensis sp. nov. The type strain of Saccharopolyspora cebuensis is SPE 10-1T (=DSM 45019T=CIP 109355T).
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Mycobacterium senuense sp. nov., a slowly growing, non-chromogenic species closely related to the Mycobacterium terrae complex
A previously undescribed, slowly growing, non-chromogenic mycobacterium, isolated from a Korean patient with a symptomatic pulmonary infection, is described as representing a novel species. Its 16S rRNA gene sequence was unique and phylogenetic analysis based on 16S rRNA gene sequences showed that this organism belonged to the Mycobacterium terrae subclade. Phenotypically, the strain was generally similar to M. terrae and Mycobacterium nonchromogenicum, but its growth rate was slower than those of other M. terrae complex strains. A unique mycolic acid profile and phylogenetic analysis based on two different alternative chronometer molecules, hsp65 and rpoB, confirm the taxonomic status of this strain as a representative of a novel species. The name Mycobacterium senuense sp. nov. is proposed, with the type strain 05-832T (=DSM 44999T =KCTC 19147T).
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Microbacterium hatanonis sp. nov., isolated as a contaminant of hairspray
More LessAn aerobic, rod-shaped, Gram-positive, oxidase-negative, catalase-positive bacterial isolate, strain FCC-01T, originating as a contaminant of hairspray was characterized using phenotypic and molecular taxonomic methods. A 16S rRNA gene sequence analysis revealed that the isolate belonged to the genus Microbacterium and represented an evolutionary lineage that was distinct from recognized Microbacterium species. Cell-wall hydrolysate from the isolate contained ornithine and the cell-wall sugars consisted of rhamnose and galactose. The main respiratory quinones were MK-12 (38 %) and MK-11 (35 %). The major cellular fatty acids were anteiso-C15 : 0 (48 %), anteiso-C17 : 0 (35 %) and iso-C16 : 0 (11 %). The DNA G+C content was 69 mol%. The isolate showed <98 % 16S rRNA gene sequence similarity with respect to all of the Microbacterium species with validly published names. On the basis of the morphological, physiological and chemotaxonomic data and the results of the comparative 16S rRNA gene sequence analysis, this isolate represents a novel species of the genus Microbacterium, for which the name Microbacterium hatanonis sp. nov. is proposed. The type strain is FCC-01T (=JCM 14558T =DSM 19179T).
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Classification of ‘Streptomyces tenebrarius’ Higgins and Kastner as Streptoalloteichus tenebrarius nom. rev., comb. nov., and emended description of the genus Streptoalloteichus
More LessPhylogenetic analysis of ‘Streptomyces tenebrarius’ NBRC 16177 on the basis of the 16S rRNA gene sequence revealed that this organism was related to Streptoalloteichus hindustanus. It possessed glutamic acid, alanine and meso-diaminopimelic acid as cell-wall amino acids, galactose, mannose and glucose as whole-cell sugars and the menaquinones MK-10(H6), MK-10(H4), MK-9(H6) and MK-9(H4). The chemotaxonomic characteristics of this strain were consistent with those of the genus Streptoalloteichus. DNA–DNA hybridization, physiological, biochemical and chemotaxonomic data revealed that ‘Streptomyces tenebrarius’ can be easily differentiated from the other member of the genus Streptoalloteichus and that it merits separate species status. The phenotypic and genetic evidence reveals that ‘Streptomyces tenebrarius’ represents a novel species of the genus Streptoalloteichus; the name Streptoalloteichus tenebrarius (ex Higgins and Kastner) nom. rev., comb. nov. is proposed for this species. The type strain is NBRC 16177T (=ATCC 17920T =DSM 40477T =JCM 4838T =NRRL B-12390T =ISP 5477T).
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Nocardiopsis quinghaiensis sp. nov., isolated from saline soil in China
A previously unknown Gram-positive, obligately aerobic actinomycete, YIM 28A4T, was isolated from a sample of saline soil collected from the Qaidam Basin in Qinghai Province, north-west China, and was investigated using a polyphasic taxonomic approach. The strain grew well on most of the media tested, producing white to pale-yellow substrate mycelium, white aerial mycelium and straight to flexuous hyphae. The substrate mycelium was well developed and fragmented with age; the aerial mycelium produced long, straight spore chains. The spore chains were composed of non-motile, smooth-surfaced, rod-shaped spores. No diffusible pigments were produced on any of the media tested. The strain grew in the presence of 0–10 % (w/v) NaCl and at pH 6.0–8.0, with optimum growth occurring at 3 % (w/v) NaCl and pH 7.0. It grew at 10–37 °C, the optimum growth temperature being 28 °C. Whole-cell hydrolysates of strain YIM 28A4T contained meso-diaminopimelic acid and no diagnostic sugars. The predominant phospholipids were phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol. The predominant menaquinones were MK-10, MK-10(H2), MK-11 and MK-11(H2). The major cellular fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The DNA G+C content was 67.1 mol%. The morphological and chemotaxonomic characteristics of the isolate matched those described for Nocardiopsis species. A phylogenetic analysis based on 16S rRNA gene sequence comparisons confirmed that strain YIM 28A4T was a member of the genus Nocardiopsis and most closely related to the type strains Nocardiopsis aegyptia DSM 44442T and Nocardiopsis halotolerans DSM 44410T, showing 98.1 and 97.8 % 16S rRNA gene sequence similarity, respectively. Strain YIM 28A4T can be differentiated from these type strains by using phenotypic, phylogenetic and DNA–DNA hybridization data. On the basis of the polyphasic evidence, strain YIM 28A4T represents a novel species of the genus Nocardiopsis, for which the name Nocardiopsis quinghaiensis sp. nov. is proposed. The type strain is YIM 28A4T (=DSM 44739T =CGMCC 4.3494T).
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- Bacteroidetes
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Chryseobacterium aquaticum sp. nov., isolated from a water reservoir
More LessStrains 10-46T and 10-106 were isolated from a water reservoir in Korea. They were Gram-negative, non-motile, non-spore-forming rods, produced yellow-pigmented colonies on nutrient agar, contained MK-6 as the predominant menaquinone and 15 : 0 iso and 17 : 0 iso 3-OH as the major fatty acids and had polar lipid profiles consisting of phosphatidylethanolamine and several unknown aminolipids. Phylogenetic analysis, based on 16S rRNA gene sequencing, showed that the strains were closely related to Chryseobacterium indoltheticum ATCC 27950T, Chryseobacterium scophthalmum LMG 13028T and Chryseobacterium soldanellicola KCTC 12382T (96.9, 96.8 and 96.7 % sequence similarity, respectively) and formed a separate lineage within the genus Chryseobacterium. The combined genotypic and phenotypic data supported the conclusion that the strains represent a novel species of the genus Chryseobacterium, for which the name Chryseobacterium aquaticum sp. nov. is proposed. The type strain is 10-46T (=KCTC 12483T =CECT 7302T).
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Tenacibaculum adriaticum sp. nov., from a bryozoan in the Adriatic Sea
More LessA rod-shaped, translucent yellow-pigmented, Gram-negative bacterium, strain B390T, was isolated from the bryozoan Schizobrachiella sanguinea collected in the Adriatic Sea, near Rovinj, Croatia. 16S rRNA gene sequence analysis indicated affiliation to the genus Tenacibaculum, with sequence similarity levels of 94.8–97.3 % to type strains of species with validly published names. It grew at 5–34 °C, with optimal growth at 18–26 °C, and only in the presence of NaCl or sea salts. In contrast to other type strains of the genus, strain B390T was able to hydrolyse aesculin. The predominant menaquinone was MK-6 and major fatty acids were iso-C15 : 0, iso-C15 : 0 3-OH and iso-C15 : 1. The DNA G+C content was 31.6 mol%. DNA–DNA hybridization and comparative physiological tests were performed with type strains Tenacibaculum aestuarii JCM 13491T and Tenacibaculum lutimaris DSM 16505T, since they exhibit 16S rRNA gene sequence similarities above 97 %. These data, as well as phylogenetic analyses, suggest that strain B390T (=DSM 18961T =JCM 14633T) should be classified as the type strain of a novel species within the genus Tenacibaculum, for which the name Tenacibaculum adriaticum sp. nov. is proposed.
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Nubsella zeaxanthinifaciens gen. nov., sp. nov., a zeaxanthin-producing bacterium of the family Sphingobacteriaceae isolated from freshwater
More LessA yellow-pigmented, Gram-negative, strictly aerobic, rod-shaped bacterium (TDMA-5T) was isolated from a freshwater sample collected at Misasa (Tottori, Japan). The DNA G+C content was 38.6 mol%. Major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 4 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c). MK-7 was the predominant respiratory quinone. Zeaxanthin was the major carotenoid pigment produced; flexirubin-type pigments were not produced. TDMA-5T was sensitive to gamma-irradiation. The strain degraded gelatin, casein, starch, Tween 80 and DNA. Phylogenetic analysis based on the 16S rRNA gene sequence placed TDMA-5T in a distinct lineage in the family Sphingobacteriaceae, sharing 89.4–93.4 % sequence similarity with members of the nearest genus Pedobacter. Strain TDMA-5T could be distinguished from the other members of the family Sphingobacteriaceae by a number of chemotaxonomic and phenotypic characteristics. Based on its unique phenotypic, genotypic and phylogenetic features, strain TDMA-5T represents a novel genus and species, for which the name Nubsella zeaxanthinifaciens gen. nov., sp. nov. is proposed. The type strain of Nubsella zeaxanthinifaciens is TDMA-5T (=NBRC 102579T =CCUG 54348T).
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Chryseobacterium aquifrigidense sp. nov., isolated from a water-cooling system
More LessA non-motile, yellow-pigmented bacterium, designated strain CW9T, was isolated from a water-cooling system in Gwangyang, Republic of Korea. The cells were Gram-negative, catalase- and oxidase-positive, short rods. The major fatty acids were iso-C15 : 0 (45.5 %), iso-C17 : 1 ω9c (14.4 %), iso-C17 : 0 3-OH (13.0 %) and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 8.8 %). The DNA G+C content was 35.6 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain CW9T formed a lineage within the genus Chryseobacterium and was closely related to Chryseobacterium gleum ATCC 35910T (98.4 % sequence similarity) and Chryseobacterium indologenes ATCC 29897T (97.8 % sequence similarity). Phenotypic characteristics and DNA–DNA relatedness data served to distinguish strain CW9T from these two species. On the basis of the evidence presented in this study, strain CW9T represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium aquifrigidense sp. nov. is proposed. The type strain is CW9T (=KCTC 12894T=JCM 14756T).
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- Other Bacteria
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Thermosulfidibacter takaii gen. nov., sp. nov., a thermophilic, hydrogen-oxidizing, sulfur-reducing chemolithoautotroph isolated from a deep-sea hydrothermal field in the Southern Okinawa Trough
More LessA novel thermophilic, sulfur-reducing chemolithoautotroph, strain ABI70S6T, was isolated from a deep-sea hydrothermal field at the Yonaguni Knoll IV, Southern Okinawa Trough. Cells of strain ABI70S6T were motile rods, 0.9–2.0 μm in length and 0.4–0.8 μm in width. Strain ABI70S6T was an obligately anaerobic chemolithotroph, exhibiting hydrogen oxidation coupled with sulfur reduction. Growth was observed at 55–78 °C (optimum, 70 °C), pH 5.0–7.5 (optimum, pH 5.5–6.0) and 0.5–4.5 % NaCl (optimum, 3.0 % NaCl). H2 and elemental sulfur were utilized as electron donor and acceptor, respectively. The major fatty acids were C16 : 0 (40.0 %) and C20 : 1 (60.0 %). The G+C content of genomic DNA was 44.2 mol%. The physiological attributes of strain ABI70S6T are similar to those of species of genera within the family Desulfurobacteriaceae, most of which are thermophilic and chemolithoautotrophic sulfur reducers. However, 16S rRNA gene sequence similarities between the novel isolate and type strains of all species within the family Desulfurobacteriaceae were <87 %, which is close to the similarities found between the novel isolate and members of the family Thermodesulfobacteriaceae (<85 %). Based on physiological and phylogenetic features of the novel isolate, it is proposed that it represents a novel species in a novel genus, Thermosulfidibacter takaii gen. nov., sp. nov., within the phylum Aquificae. The type strain of T. takaii is ABI70S6T (=JCM 13301T=DSM 17441T).
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Hydrogenivirga okinawensis sp. nov., a thermophilic sulfur-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal field, Southern Okinawa Trough
More LessA novel extremely thermophilic sulfur-oxidizing bacterium, strain LS12-2T, was isolated from a deep-sea hydrothermal field at the Yonaguni Knoll IV, Southern Okinawa Trough. Cells of strain LS12-2T were motile rods, 1.5–4.0 μm in length and 0.4–0.5 μm in width. Strain LS12-2T was an obligate chemolithoautotroph that could utilize elemental sulfur or thiosulfate as an electron donor and nitrate or oxygen as an electron acceptor. Growth was observed at 65–85 °C (optimum 70–75 °C), pH 5.8–8.3 (optimum pH 6.9–7.5), 1.0–4.0 % (w/v) NaCl (optimum 2.5 %) and 1.0–7.0 % O2 in the gas phase (optimum 3.0 %). Fatty acids detected were C16 : 0 (8.0 %), C18 : 0 (9.0 %), C18 : 1 (62.5 %) and C20 : 1 (20.5 %). The genomic DNA G+C content was 51.3 mol%. 16S rRNA gene sequence analysis indicated that strain LS12-2T belonged to the genus Hydrogenivirga. Based on physiological and phylogenetic characteristics of the isolate, it is proposed that this strain represents a novel species in the genus Hydrogenivirga, Hydrogenivirga okinawensis sp. nov. The type strain of Hydrogenivirga okinawensis is LS12-2T (=JCM 13302T=DSM 17378T).
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- Proteobacteria
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Sneathiella glossodoripedis sp. nov., a marine alphaproteobacterium isolated from the nudibranch Glossodoris cincta, and proposal of Sneathiellales ord. nov. and Sneathiellaceae fam. nov.
More LessA novel marine bacterium, designated strain MKT133T, was isolated from the foot epidermis of a nudibranch, Glossodoris cincta (Mollusca), collected in seawater off the coast of Japan at a depth of 4 m. This bacterium was Gram-negative, motile, mesophilic and strictly aerobic, with small rod-shaped cells. Colonies of the strain after 4–5 days incubation on marine agar 2216 at 30 °C were less than 1 mm in diameter. The strain required salt for growth and contained Q-10 as the predominant respiratory quinone, C18 : 1 ω7c, C16 : 0 and C17 : 1 as major cellular fatty acids and C14 : 0 3-OH as a hydroxy fatty acid. 16S rRNA gene sequence analysis showed that the isolate had highest similarity to Sneathiella chinensis, with 97.2 % sequence similarity to the type strain. Our phylogenetic analysis also revealed that this clade represents a distinct lineage and forms a deep branch with less than 90 % 16S rRNA gene sequence similarity to the members of the eight known orders within the Alphaproteobacteria. Sufficient differences exist to distinguish this strain from Sneathiella chinensis. The name Sneathiella glossodoripedis sp. nov. is proposed, with the type strain MKT133T (=IAM 15419T =KCTC 12842T). The novel order Sneathiellales ord. nov. and family Sneathiellaceae fam. nov. are proposed for the distinct phyletic line represented by the genus Sneathiella.
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Burkholderia sediminicola sp. nov., isolated from freshwater sediment
More LessA Gram-negative, motile and rod-shaped bacterium, designated HU2-65WT, was isolated from freshwater sediment. The strain possessed ubiquinone 8 as the predominant isoprenoid quinone and contained major amounts of ω7-cis-octadecenoic acid and hexadecanoic acid in its cell envelope, which are properties shared by members of the genus Burkholderia. On the basis of 16S rRNA gene sequence similarity, strain HU2-65WT was most closely related to the type strain of Burkholderia xenovorans (98.4 %). The DNA G+C content of strain HU2-65WT was 61.2 mol%, and DNA–DNA relatedness values to type strains of closely related species were found to be much lower than 70 %, indicating that the strain represents a separate genomic species within the genus Burkholderia. Strain HU2-65WT was also differentiated from other species of the genus by physiological and biochemical characteristics. Consequently, strain HU2-65WT is considered to represent a single, novel species of the genus Burkholderia, for which the name Burkholderia sediminicola sp. nov. is proposed, with the type strain HU2-65WT (=KCTC 22086T =LMG 24238T).
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Nevskia soli sp. nov., isolated from soil cultivated with Korean ginseng
A Gram-negative bacterium, designated strain GR15-1T, was isolated from a field cultivated with Korean ginseng. Cells were strictly aerobic, motile with multipolar flagella and rod-shaped. The strain grew optimally at 25–28 °C and pH 6.0–7.0. The predominant fatty acids of strain GR15-1T were C18 : 1 ω7c, C16 : 0 and summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1 I). The major isoprenoid quinone was ubiquinone 8. The G+C content of the genomic DNA was 63.9 mol%. Phylogenetic analysis showed that strain GR15-1T formed a phyletic cluster with Nevskia ramosa Soe1T, with a 16S rRNA gene sequence similarity of 96.8 %. Based on phenotypic, chemotaxonomic and phylogenetic features, strain GR15-1T represents a novel species within the genus Nevskia, for which the name Nevskia soli sp. nov. is proposed. The type strain is GR15-1T (=KACC 11703T =DSM 19509T).
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Spongiibacter marinus gen. nov., sp. nov., a halophilic marine bacterium isolated from the boreal sponge Haliclona sp. 1
Strain HAL40bT was isolated from the marine sponge Haliclona sp. 1 collected at the Sula Ridge off the Norwegian coast and characterized by physiological, biochemical and phylogenetic analyses. The isolate was a small rod with a polar flagellum. It was aerobic, Gram-negative and oxidase- and catalase-positive. Optimal growth was observed at 20–30 °C, pH 7–9 and in 3 % NaCl. Substrate utilization tests were positive for arabinose, Tween 40 and Tween 80. Enzyme tests were positive for alkaline phosphatase, esterase lipase (C8), leucine arylamidase, acid phosphatase, naphthol-AS-BI-phosphohydrolase and N-acetyl-β-glucosaminidase. The predominant cellular fatty acid was C17 : 1 ω8, followed by C17 : 0 and C18 : 1 ω7. Analysis by matrix-assisted laser desorption/ionization time-of-flight MS was used to characterize the strain, producing a characteristic low-molecular-mass protein pattern that could be used as a fingerprint for identification of members of this species. The DNA G+C content was 69.1 mol%. Phylogenetic analysis supported by 16S rRNA gene sequence comparison classified the strain as a member of the class Gammaproteobacteria. Strain HAL40bT was only distantly related to other marine bacteria including Neptunomonas naphthovorans and Marinobacter daepoensis (type strain sequence similarity >90 %). Based on its phenotypic, physiological and phylogenetic characteristics, it is proposed that the strain should be placed into a new genus as a representative of a novel species, Spongiibacter marinus gen. nov., sp. nov.; the type strain of Spongiibacter marinus is HAL40bT (=DSM 17750T =CCUG 54896T).
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Classification of halo(alkali)philic and halo(alkali)tolerant methanotrophs provisionally assigned to the genera Methylomicrobium and Methylobacter and emended description of the genus Methylomicrobium
The taxonomic positions of four aerobic, obligately halo(alkali)philic/-tolerant, methanotrophic bacteria previously affiliated with the genera Methylobacter (‘Methylobacter alcaliphilus’ strains 20Z and 5Z) and Methylomicrobium (Methylomicrobium strains AMO1 and NI) were investigated. Phylogenetic analysis of 16S rRNA gene sequences indicated that the strains form a separate branch within the type I methanotrophic bacteria and are closely related to Methylomicrobium pelagicum. DNA–DNA hybridization data revealed relatively low levels of relatedness of Methylomicrobium sp. AMO1 and Methylomicrobium sp. N1 with each other and with previously described species of the genera Methylomicrobium and Methylobacter (<55 %), indicating that they may represent novel species. Based on the results presented here and on previously reported morphological and physiological characteristics, we classify these halotolerant and halophilic methanotrophic strains as representing novel species within the genus Methylomicrobium: Methylomicrobium alcaliphilum sp. nov. (type strain 20ZT =VKM B-2133T =NCIMB 14124T; reference strain 5Z =VKM B-2180), Methylomicrobium japanense sp. nov. (type strain NIT =VKM B-2462T =FERM BP-5633T =NBRC 103677T) and Methylomicrobium kenyense sp. nov. (type strain AMO1T =NCCB 97157T =NCIMB 13566T =VKM B-2464T). The genus Methylomicrobium has been emended in its description.
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Devosia geojensis sp. nov., isolated from diesel-contaminated soil in Korea
A Gram-negative, strictly aerobic, non-spore-forming bacterium, designated strain BD-c194T, was isolated from diesel-contaminated soil in Geoje, Korea. The cells were short, motile rods with single polar flagella. Growth of strain BD-c194T was observed between 15 and 45 °C (optimally at 30–35 °C) and between pH 6.0 and 9.5 (optimally at pH 7.5–9.0). The predominant fatty acids were 11-methyl C18 : 1 ω7c, C16 : 0, C18 : 1 ω7c, C18 : 0 and an unknown fatty acid (equivalent chain-length 18.814); a large amount of phosphatidylglycerol and a small amount of diphosphatidylglycerol were present as polar lipids. The G+C content of the genomic DNA was 60.8 mol% and the major isoprenoid quinone was Q-10. A comparative 16S rRNA gene sequence analysis showed that strain BD-c194T formed a well-defined phyletic lineage within the genus Devosia (with 100 % bootstrap support). The levels of 16S rRNA gene sequence similarity with respect to the type strains of other Devosia species ranged from 95.0 to 96.1 %. On the basis of chemotaxonomic data and molecular properties, strain BD-c194T represents a novel species within the genus Devosia, for which the name Devosia geojensis sp. nov. is proposed. The type strain is BD-c194T (=KCTC 22082T =DSM 19414T).
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Marinobacter pelagius sp. nov., a moderately halophilic bacterium
More LessA Gram-negative, aerobic, neutrophilic, moderately halophilic bacterial strain, HS225T, was isolated from seawater samples around the Zhoushan Archipelago, Zhejiang Province, China. The isolate grew optimally in media with 5.0 % NaCl, at pH 7.0–8.0 and at 25–30 °C. The predominant fatty acids were C16 : 0 ω9c, C16 : 0, C12 : 0 3-OH and C18 : 1 ω9c. The genomic DNA G+C content was 59.0 mol%. Based on 16S rRNA gene sequence analysis, the isolate was found to be affiliated to the genus Marinobacter. Strain HS225T exhibited closest phylogenetic affinity to Marinobacter koreensis DD-M3T (98.1 % 16S rRNA gene sequence similarity). DNA–DNA relatedness data and DNA G+C contents as well as physiological and biochemical test results allowed the genotypic and phenotypic differentiation of strain HS225T from closely related species. Therefore, it is proposed that strain HS225T represents a novel species of the genus Marinobacter, for which the name Marinobacter pelagius sp. nov. is proposed. The type strain is HS225T (=CGMCC 1.6775T =JCM 14804T)
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Labrys portucalensis sp. nov., a fluorobenzene-degrading bacterium isolated from an industrially contaminated sediment in northern Portugal
A detailed classification of a novel bacterial strain, designated F11T, capable of degrading fluorobenzene as a sole carbon and energy source, was performed by using a polyphasic approach. This Gram-negative, rod-shaped, non-motile, non-spore-forming, aerobic bacterium was isolated from a sediment sample collected from an industrially contaminated site in northern Portugal. The predominant whole-cell fatty acids were C19 : 0 cyclo ω8c, C16 : 0, C18 : 1 ω7c, C18 : 0, C18 : 0 3-OH and C16 : 0 3-OH. The G+C content of the DNA was 62.9 mol% and the major respiratory quinone was ubiquinone 10 (UQ-10). 16S rRNA gene sequence analysis revealed that strain F11T was a member of the class Alphaproteobacteria and was phylogenetically related to the genus Labrys, having sequence similarities of 95.6 and 93.1 % to the type strains of Labrys monachus and Labrys methylaminiphilus, respectively. DNA–DNA hybridization experiments revealed levels of relatedness of <70 % between strain F11T and the type strains of L. monachus and L. methylaminiphilus (38.6 and 34.1 %, respectively), justifying the classification of strain F11T as representing a novel species of the genus Labrys. The name Labrys portucalensis sp. nov. is proposed for this organism. The type strain is F11T (=LMG 23412T=DSM 17916T).
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Pseudomonas marincola sp. nov., isolated from marine environments
An aerobic, Gram-negative, motile, non-pigmented bacterium, strain KMM 3042T, isolated from a deep-sea brittle star in the Fiji Sea, was subjected to a polyphasic taxonomic study. Phylogenetic analysis based on 16S rRNA gene sequences revealed marine Mn(II)-oxidizing isolate S185-2B as the closest neighbour of strain KMM 3042T (99.9 % sequence similarity). The two strains formed a distinct lineage within the genus Pseudomonas adjacent to the members of the Pseudomonas borbori cluster, sharing highest sequence similarity of 97.4 and 97.0 %, respectively, with P. borbori DSM 17834T and Pseudomonas flavescens DSM 12071T. The DNA–DNA hybridization value (71 %) between strains KMM 3042T and S185-2B confirmed their assignment to the same species. On the basis of phylogenetic analysis, DNA–DNA hybridization and physiological and biochemical characterization, strains KMM 3042T and S185-2B should be assigned to a novel species of the genus Pseudomonas, for which the name Pseudomonas marincola sp. nov. is proposed. The type strain is KMM 3042T (=NRIC 0729T =JCM 14761T).
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Thalassospira tepidiphila sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from seawater
More LessA Gram-negative, mesophilic bacterial strain, designated 1-1BT, which degrades polycyclic aromatic hydrocarbons, was isolated from petroleum-contaminated seawater during a bioremediation experiment. A 16S rRNA gene sequence analysis indicated that the isolate was affiliated with the genus Thalassospira in the Alphaproteobacteria; the sequence was found to be most similar to those of Thalassospira profundimaris WP0211T (99.8 %), Thalassospira xiamenensis M-5T (98.2 %) and Thalassospira lucentensis DSM 14000T (98.1 %). However, the levels of DNA–DNA relatedness between strain 1-1BT and these type strains were 50.7±17.2, 35.7±17.8 and 32.0±21.1 %, respectively. In addition, strain 1-1BT was found to be distinct from the other described species of the genus Thalassospira in terms of some taxonomically important traits, including DNA G+C content, optimum growth temperature, salinity tolerance, utilization of carbon sources and fatty acid composition. Furthermore, strain 1-1BT and T. profundimaris were also different with regard to motility and denitrification capacities. On the basis of physiological and DNA–DNA hybridization data, strain 1-1BT represents a novel species within the genus Thalassospira, for which the name Thalassospira tepidiphila sp. nov. is proposed. The type strain is 1-1BT (=JCM 14578T =DSM 18888T).
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- Eukaryotic Micro-Organisms
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Two novel aflatoxin-producing Aspergillus species from Argentinean peanuts
Two novel species from Aspergillus section Flavi from different species of Arachis (peanuts) in Argentina are described as Aspergillus arachidicola sp. nov. and Aspergillus minisclerotigenes sp. nov. Their novel taxonomic status was determined using a polyphasic taxonomic approach with phenotypic (morphology and extrolite profiles) and molecular (β-tubulin and calmodulin gene sequences) characters. A. minisclerotigenes resembles Aspergillus flavus and Aspergillus parvisclerotigenus in producing aflatoxins B1 and B2, cyclopiazonic acid, kojic acid and aspergillic acid, but in addition it produces aflatoxins G1 and G2, aflavarins, aflatrem, aflavinines, parasiticolides and paspaline. This species also includes several isolates previously assigned to A. flavus group II and three Australian soil isolates. A. arachidicola produces aflatoxins B1, B2, G1 and G2, kojic acid, chrysogine and parasiticolide, and some strains produce aspergillic acid. The type strain of A. arachidicola is CBS 117610T =IBT 25020T and that of A. minisclerotigenes is CBS 117635T =IBT 27196T. The Mycobank accession numbers for Aspergillus minisclerotigenes sp. nov. and Aspergillus arachidicola sp. nov. are respectively MB 505188 and MB 505189 (http://www.mycobank.org).
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Reappraisal of the Sporobolomyces roseus species complex and description of Sporidiobolus metaroseus sp. nov.
More LessHere, we investigate a group of red to pinkish ballistoconidia-forming yeasts that were preliminarily identified as Sporobolomyces roseus or Sporidiobolus pararoseus. Detailed molecular and micromorphological studies revealed that the sexual strains and several conspecific anamorphic isolates belonged to a novel teleomorph that represents the sexual stage of Sporobolomyces roseus. Consequently, a new taxon in the genus Sporidiobolus is here described as Sporidiobolus metaroseus sp. nov. (type strain CBS 7683T). The main characteristics of Sporidiobolus metaroseus are presented and compared with those of the more closely related species. Our studies also led to the clarification of the life cycle of Sporidiobolus pararoseus. We confirm that the teliospores of this species germinate by forming short branches of hyphae, instead of basidia.
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- Other Gram-Positive Bacteria
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Veillonella rogosae sp. nov., an anaerobic, Gram-negative coccus isolated from dental plaque
Strains of a novel anaerobic, Gram-negative coccus were isolated from the supra-gingival plaque of children. Independent strains from each of six subjects were shown, at a phenotypic level and based on 16S rRNA gene sequencing, to be members of the genus Veillonella. Analysis revealed that the six strains shared 99.7 % similarity in their 16S rRNA gene sequences and 99.0 % similarity in their rpoB gene sequences. The six novel strains formed a distinct group and could be clearly separated from recognized species of the genus Veillonella of human or animal origin. The novel strains exhibited 98 and 91 % similarity to partial 16S rRNA and rpoB gene sequences of Veillonella parvula ATCC 10790T, the most closely related member of the genus. The six novel strains could be differentiated from recognized species of the genus Veillonella based on partial 16S rRNA and rpoB gene sequencing. The six novel strains are thus considered to represent a single novel species of the genus Veillonella, for which the name Veillonella rogosae sp. nov. is proposed. The type strain is CF100T (=CCUG 54233T=DSM 18960T).
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Paenibacillus woosongensis sp. nov., a xylanolytic bacterium isolated from forest soil
More LessA novel xylan-degrading bacterium, YB-45T, was isolated from forest soil. The organism is a facultatively anaerobic, Gram-variable, motile, endospore-forming, rod-shaped bacterium. It grew optimally at 37 °C and pH 7.5 in the presence of 3 % (w/v) NaCl. The predominant cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and C16 : 0. The DNA G+C content was 51.7 mol% and the predominant menaquinone was MK-7. Growth was observed with many carbohydrates, including xylan, as sole carbon sources. Strain YB-45T produces a wide variety of hydrolytic enzymes, such as xylanase, cellulase, amylase, β-mannanase, β-mannosidase, β-xylosidase, α-galactosidase, β-galactosidase and β-glucosidase. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain YB-45T belongs to the genus Paenibacillus, sharing sequence similarity that was <96 %. It was related most closely to Paenibacillus jamilae DSM 13815T, with 95.7 % sequence similarity. On the basis of morphological, chemotaxonomic, physiological and phylogenetic properties, strain YB-45T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus woosongensis sp. nov. is proposed. The type strain is YB-45T (=KCTC 3953T=DSM 16971T).
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Halobacillus seohaensis sp. nov., isolated from a marine solar saltern in Korea
More LessA Gram-positive or Gram-variable, motile, moderately halophilic, rod-shaped bacterial strain, ISL-50T, was isolated from a marine solar saltern in Korea and subjected to a polyphasic taxonomic study. Strain ISL-50T grew optimally at pH 7.0–8.0 and 37 °C in the presence of 8 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ISL-50T belonged to the genus Halobacillus. Strain ISL-50T exhibited 16S rRNA gene sequence similarity values of 95.3–98.2 % with respect to the type strains of recognized Halobacillus species. The cell-wall peptidoglycan was based on meso-diaminopimelic acid, the predominant menaquinone was MK-7 and the major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The DNA G+C content was 39.3 mol%. DNA–DNA relatedness data and differential phenotypic properties revealed that strain ISL-50T was distinguishable from the recognized Halobacillus species. On the basis of phenotypic, chemotaxonomic, phylogenetic and genetic data, strain ISL-50T represents a novel species of the genus Halobacillus, for which the name Halobacillus seohaensis sp. nov. is proposed. The type strain is ISL-50T (=KCTC 13145T=CCUG 54358T).
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Virgibacillus kekensis sp. nov., a moderately halophilic bacterium isolated from a salt lake in China
A Gram-positive, moderately halophilic, motile, strictly aerobic, endospore-forming, oxidase- and catalase-positive, rod-shaped bacterium, strain YIM kkny16T, was isolated from a saline mud sample collected from the Keke salt lake in the Qaidam Basin, north-west China. This isolate grew in the presence of 0–25 % (w/v) NaCl and at pH 6.0–10.0 and 10–50 °C; optimum growth was observed with 10 % (w/v) NaCl and at pH 7.0 and 37 °C. Strain YIM kkny16T had meso-diaminopimelic acid as the diagnostic diamino acid, MK-7 as the predominant respiratory quinone, with a significant amount of MK-6, and anteiso-C15 : 0, iso-C14 : 0 and C16 : 1 ω7c alcohol as major fatty acids. Major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C content was 41.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain YIM kkny16T was a member of the genus Virgibacillus, exhibiting sequence similarities of 94.9–97.3 % to the type strains of recognized Virgibacillus species. Strain YIM kkny16T could be differentiated from recognized Virgibacillus species based on phenotypic characteristics, chemotaxonomic differences, phylogenetic analysis and DNA–DNA hybridization data. On the basis of evidence from this polyphasic study, strain YIM kkny16T is considered to represent a novel species of the genus Virgibacillus, for which the name Virgibacillus kekensis sp. nov. is proposed. The type strain is YIM kkny16T (=DSM 17056T=CGMCC 1.6298T).
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Description of Caldanaerobius fijiensis gen. nov., sp. nov., an inulin-degrading, ethanol-producing, thermophilic bacterium from a Fijian hot spring sediment, and reclassification of Thermoanaerobacterium polysaccharolyticum and Thermoanaerobacterium zeae as Caldanaerobius polysaccharolyticus comb. nov. and Caldanaerobius zeae comb. nov.
More LessAn obligately anaerobic, spore-forming, Gram-type-positive but Gram-staining-negative thermophilic bacterium, strain JW/YJL-F3T, was isolated from a Fijian hot spring sediment sample. Cells of strain JW/YJL-F3T were straight to slightly curved rods, 0.5–1.2 μm in diameter and 1.5–19 μm long. The temperature range for growth was between 40 and 67 °C, with an optimum at 60–63 °C. The pH25 °C range for growth was 4.5–8.4 with an optimum of 6.8. The salinity range for growth was 0–0.5 %. Strain JW/YJL-F3T utilized a range of substrates including arabinose, cellobiose, galactose, glucose, inulin, lactose, maltose, mannose, raffinose, ribose, trehalose, xylose and yeast extract as carbon and energy sources. The major fermentation end products from glucose were ethanol, acetate and formate. Strain JW/YJL-F3T converted thiosulfate to elemental sulfur, producing sulfur globules. The DNA G+C content was 37.6 mol% as determined by HPLC. Phylogenetic analysis using the 16S rRNA gene sequence indicated that the isolate is distantly related to the clade of the genus Thermoanaerobacterium. However, Thermoanaerobacterium polysaccharolyticum (96.7 % similarity to the type strain) and Thermoanaerobacterium zeae were the closest relatives, forming a separate, well-supported clade together with the novel isolate. Because Thermoanaerobacterium polysaccharolyticum, Thermoanaerobacterium zeae and strain JW/YJL-F3T have different features from other Thermoanaerobacterium species, including a higher G+C content and formate production, and are placed distantly from the remaining species of Thermoanaerobacterium (greater than 10 % distance) in the 16S rRNA gene sequence analysis, we propose to place the new isolate JW/YJL-F3T and Thermoanaerobacterium polysaccharolyticum and Thermoanaerobacterium zeae into the novel genus Caldanaerobius gen. nov. as Caldanaerobius fijiensis gen. nov., sp. nov. (the type species), Caldanaerobius polysaccharolyticus comb. nov. and Caldanaerobius zeae comb. nov., respectively. The type strain of Caldanaerobius fijiensis is JW/YJL-F3T (=ATCC BAA-1278T =DSM 17918T).
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Bacillus velezensis is a later heterotypic synonym of Bacillus amyloliquefaciens
More LessStrain BCRC 14193, isolated from soil, shared more than 99 % 16S rRNA gene sequence similarity with Bacillus amyloliquefaciens BCRC 11601T and Bacillus velezensis BCRC 17467T. This strain was previously identified as B. amyloliquefaciens, based on DNA–DNA hybridization, but its DNA relatedness value with B. velezensis BCRC 17467T was 89 %. To investigate the relatedness of strain BCRC 14193, B. amyloliquefaciens and B. velezensis, the partial sequence of the gene encoding the subunit B protein of DNA gyrase (gyrB) was determined. B. velezensis BCRC 17467T shared high gyrB gene sequence similarity with B. amyloliquefaciens BCRC 14193 (98.4 %) and all of the B. amyloliquefaciens strains available (95.5–95.6 %). DNA–DNA hybridization experiments revealed high relatedness values between B. velezensis BCRC 17467T and B. amyloliquefaciens BCRC 11601T (74 %) and the B. amyloliquefaciens reference strains (74–89 %). Based on these data and the lack of phenotypic distinctive characteristics, we propose Bacillus velezensis as a later heterotypic synonym of Bacillus amyloliquefaciens.
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Paenibacillus provencensis sp. nov., isolated from human cerebrospinal fluid, and Paenibacillus urinalis sp. nov., isolated from human urine
More LessGram-negative, spore-forming rods were isolated from a human urine sample (strain 5402403T) and a human cerebrospinal fluid sample (strain 4401170T). Based on genotypic characteristics, these strains belonged to the genus Paenibacillus and were closely related. Phylogenetic analysis based on 16S rRNA gene sequence comparison showed that they clustered with Paenibacillus massiliensis 2301065T (95.9 and 94.3 % 16S rRNA gene sequence similarity, respectively, for strains 5402403T and 4401170T), Paenibacillus illinoisensis NRRL NRS-61356T (90.6 and 93.8 %), Paenibacillus xylanilyticus XIL14T (95.3 and 95.4 %), Paenibacillus barcinonensis BP-23T (94.3 and 94.0 %), Paenibacillus pabuli NCIMB 12781T (89.1 and 92.3 %) and Paenibacillus amylolyticus NRRL NRS-290T (94.2 and 93.8 %). The predominant fatty acids were 15 : 0 anteiso (49.0 and 55.3 %, respectively, for strains 5402403T and 4401170T), 16 : 0 iso (15.4 and 13.5 %), 16 : 0 (7.6 and 3.6 %), 15 : 0 (6.3 and 2.8 %), 17 : 0 anteiso (5.7 and 7.5 %), 14 : 0 iso (4.1 and 2.7 %) and 15 : 0 iso (4.1 and 3.4 %). 16S rRNA gene sequence similarity between strain 4401170T and strain 5402403T was 98.4 %, but the DNA–DNA reassociation rate between the two strains was 53.2 %. So, considering the recommendations of the ad hoc committee, they do not belong to the same species. On the basis of phenotypic data and genotypic inference, it is proposed that the strains should be assigned to the novel species Paenibacillus urinalis sp. nov. (type strain 5402403T =CIP 109357T =CCUG 53521T) and Paenibacillus provencensis sp. nov. (type strain 4401170T =CIP 109358T =CCUG 53519T).
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- Evolution, Phylogeny And Biodiversity
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Differential patterns of evolution and distribution of the symbiotic behaviour in nostocacean cyanobacteria
Many cyanobacteria commonly identified as belonging to the genus Nostoc are well-known cyanobionts (symbionts) of a wide variety of plants and fungi. They form symbioses with bryophytes, pteridophytes, gymnosperms and angiosperms that are considerably different in the type of reciprocal interaction between the host and the cyanobiont. The phylogenetic and taxonomic relationships among cyanobionts isolated from different hosts and Nostoc strains isolated from free-living conditions are still not well understood. We compared phylogeny and morphology of symbiotic cyanobacteria originating from different host plants (genera Gunnera, Azolla, Cycas, Dioon, Encephalartos, Macrozamia and Anthoceros) with free-living Nostoc isolates originating from different habitats. After preliminary clustering with ARDRA (amplified rDNA restriction analysis), phylogeny was reconstructed on the basis of 16S rRNA gene sequences and compared with morphological characterization, obtaining several supported clusters. Two main Nostoc clusters harboured almost all cyanobionts of Gunnera, Anthoceros and of several cycads, together with free-living strains of the species Nostoc muscorum, Nostoc calcicola, Nostoc edaphicum, Nostoc ellipsosporum and strains related to Nostoc commune. We suggest that the frequent occurrence of symbiotic strains within these clusters is explained by the intensive hormogonia production that was observed in many of the strains studied. However, no evidence for discrimination between symbiotic and free-living strains, either by molecular or morphological approaches, could be found. Sequences of Azolla cyanobiont filaments, taken directly from leaf cavities, clustered tightly with sequences from the planktic cyanobacterium Cylindrospermopsis raciborskii, from the benthic Anabaena cylindrica 133 and from Anabaena oscillarioides HINDAK 1984/43, with high bootstrap values. The phylogenetic analysis showed that two distinct patterns of evolution of symbiotic behaviour might exist for the nostocacean cyanobacteria, one leading to symbioses of Nostoc species with a wide variety of plants, the other leading to the association of a unique cyanobacterial type with the water fern Azolla.
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Identification of Vibrio cholerae and Vibrio mimicus by multilocus sequence analysis (MLSA)
More LessVibrio cholerae and Vibrio mimicus have similar phenotypes and genomes making rapid differentiation of these two species difficult. The first standard multilocus sequence analysis (MLSA) scheme for the identification of these species is described. A collection of 45 representative isolates from different geographical regions and hosts was examined using segments of the housekeeping genes pyrH, recA and rpoA. Overall, the closest phylogenetic neighbours of these species were Vibrio furnissii and Vibrio fluvialis. V. cholerae and V. mimicus formed separate species clusters on the basis of each gene, suggesting that these genes are useful as identification markers. These species clusters arose by the accumulation of point mutations. The pyrH gene showed the highest resolution for differentiating V. cholerae and V. mimicus. The maximum interspecies pyrH gene sequence similarity was 91 %. Clearly, V. mimicus strains were more heterogeneous than V. cholerae strains at the three loci. It is suggested that vibrio species may be defined on the basis of MLSA data. A vibrio species was defined as a group of strains forming a monophyletic group on the basis of these loci and with an intraspecific sequence similarity of at least 95 %. V. cholerae and V. mimicus isolates can be readily identified through the open database resource ‘The Taxonomy of Vibrios’ (http://www.taxvibrio.lncc.br/).
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Multigene phylogenies of clonal Spumella-like strains, a cryptic heterotrophic nanoflagellate, isolated from different geographical regions
More LessMany nanoflagellate morphospecies comprise an enormous variation of genotypes, probably indicating cryptic species. One of the best-investigated morphospecies with respect to molecular and ecophysiological variation are flagellates of the Spumella morphotype. Here, we have phylogenetically analysed three protein-coding genes (actin, alpha-tubulin, beta-tubulin), internal transcribed spacers (ITS1, ITS2) and the 5.8S rDNA of 17 Spumella-like strains isolated from soil, freshwater and marine samples in order to (i) test the validity of the current Spumella-like phylogenetic classification system based exclusively on small subunit (SSU) rDNA, (ii) elucidate the phylogenetic associations of SSU rDNA-unresolved strains and (iii) evaluate the validity of the assignment of ecophysiological adaptations to previously identified SSU rDNA sequence clades. All single-gene analyses show different patterns of support, are incongruent and identify a number of conflicting nodes. Likewise, a concatenation of all protein genes fails to recover specific SSU rDNA clades. However, a combined analysis of all genes confidently resolved the conflicts of the single genes and the protein-gene concatenations and resulted in a tree topology that is identical to the SSU rDNA analysis, but with enhanced phylogenetic resolution and decisively greater support. We conclude that, depending on the genes concatenated, a ‘supergene’ analysis minimizes artefactual effects of single genes and may be superior in its performance in phylogenetically analysing cryptic species. We confirm the validity of the SSU rDNA Spumella-like phyloclades and support the suggestion that these clades indeed seem to reflect certain ecophysiological adaptations.
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- International Committee On Systematics Of Prokaryotes
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- Taxonomic Note
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Proposal to replace the illegitimate genus name Bryantella Wolin et al. 2004VP with the genus name Marvinbryantia gen. nov. and to replace the illegitimate combination Bryantella formatexigens Wolin et al. 2004VP with Marvinbryantia formatexigens comb. nov.
More LessThe prokaryote generic name Bryantella Wolin et al. 2004VP is illegitimate because it is a later homonym of Bryantella Chickering, 1946 (Animalia, Arthropoda, Arachnida, Araneae, Salticidae, Dendryphantinae, Dendryphantini) and a later homonym of Bryantella Britton, 1957 (Animalia, Arthropoda, Scarabaeoidea, Scarabaeidae, Melolonthinae) [Principle 2, Rule 51b(4) of the Bacteriological Code (1990 Revision)]. Bryantella represents a genus of jumping spiders within the family Salticidae and a genus of melolonthine scarab beetles within the family Scarabaeidae. Therefore, a new genus name, Marvinbryantia gen. nov., is proposed for this taxon. As a result, a new combination, Marvinbryantia formatexigens comb. nov., is required for the type species to replace the illegitimate combination Bryantella formatexigens Wolin et al. 2004VP.
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- Errata
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)