- Volume 57, Issue 9, 2007
Volume 57, Issue 9, 2007
- Validation List No. 117
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Valiation List no. 117
List of new names and new combinations previously effectively, but not validly, publishedThe 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 6, 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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Kribbella aluminosa sp. nov., isolated from a medieval alum slate mine
Three actinomycetes (strains HKI 0478T, HKI 0479 and HKI 0480) isolated from the surfaces of rocks in the Feengrotten medieval alum slate mine (Thuringia, Germany) were examined in a polyphasic taxonomic study. The following morphological and chemotaxonomic features supported their classification as members of the genus Kribbella: the presence of ll-diaminopimelic acid in the cell-wall peptidoglycan; glucose together with minor amounts of mannose and ribose as the whole-cell sugars; polar lipids comprising phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and unknown phospho- and glycolipids; fatty acid profiles characterized by the predominance of anteiso-C15 : 0, iso-C16 : 0 and C16 : 0 9-methyl; and the presence of MK-9(H4) as the main menaquinone. The isolates had almost identical 16S rRNA gene sequences (99.9–100 %) and were most closely related to the type strains of Kribbella jejuensis (98.9 % sequence similarity), Kribbella swartbergensis and Kribbella solani (both 98.8 %). A wide range of genotypic and phenotypic markers as well as the low levels of DNA–DNA relatedness between strain HKI 0478T and the type strains of K. jejuensis (41.3 %), K. swartbergensis (18.6 %) and K. solani (14.2 %) distinguished the novel strains from their closest phylogenetic neighbours. On the basis of these results, strain HKI 0478T represents a novel member of the genus Kribbella, for which the name Kribbella aluminosa sp. nov. is proposed. The type strain is HKI 0478T (=DSM 18824T =JCM 14599T).
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Rhodococcus kyotonensis sp. nov., a novel actinomycete isolated from soil
More LessA polyphasic study was undertaken to establish the taxonomic position of an isolate, strain DS472T, from soil in Kyoto, Japan. Phylogenetic analysis, based on the 16S rRNA gene sequences, revealed that this strain constitutes a new subline within the genus Rhodococcus, with Rhodococcus yunnanensis YIM 70056T and Rhodococcus fascians DSM 20669T as its nearest phylogenetic neighbours (98.2 and 97.8 % sequence similarity, respectively). DNA–DNA hybridization experiments revealed 36 and 29 % relatedness between the isolate and its phylogenetic relatives, R. yunnanensis and R. fascians, respectively. Chemotaxonomic characteristics, including the major quinone MK-8(H2), predominant fatty acids C16 : 0, C18 : 1 ω9c and 10-methyl C18 : 0, the presence of cell-wall chemotype IV and mycolic acids, were consistent with the properties of members of the genus Rhodococcus. The DNA G+C content was 64.5 mol%. On the basis of both phenotypic and genotypic evidence, strain DS472T represents a novel species of the genus Rhodococcus, for which the name Rhodococcus kyotonensis sp. nov. is proposed. The type strain is strain DS472T (=IAM 15415T=CCTCC AB206088T).
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Glycomyces sambucus sp. nov., an endophytic actinomycete isolated from the stem of Sambucus adnata Wall
Qiang Gu, Wen Zheng and Ying HuangAn actinomycete, designated strain E71T, was isolated from the stem of Sambucus adnata Wall, a Chinese medicinal plant, and subjected to a polyphasic taxonomic study. Phylogenetic analyses based on the 16S rRNA gene sequence showed that the organism was a member of the genus Glycomyces, and formed a distinct phyletic line distantly related to recognized species of the genus Glycomyces. Morphological and chemotaxonomic data supported the affiliation of strain E71T to the genus Glycomyces. A number of physiological properties and a unique menaquinone profile allowed differentiation of the strain from related Glycomyces species. It is therefore proposed that strain E71T represents a novel species of the genus Glycomyces, for which the name Glycomyces sambucus sp. nov. is proposed. The type strain is E71T (=CGMCC 4.3147T=DSM 45047T).
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Streptomyces synnematoformans sp. nov., a novel actinomycete isolated from a sand dune soil in Egypt
More LessA polyphasic taxonomic study was undertaken to establish the status of a novel actinomycete, strain S155T, isolated from a sand dune soil in Egypt. The organism formed characteristic synnemata-like structures and exhibited chemical and morphological features consistent with its classification in the genus Streptomyces. An almost-complete 16S rRNA gene sequence of the isolate was compared with corresponding sequences of representative streptomycetes. The 16S rRNA gene sequence data supported the assignment of the strain to the genus Streptomyces and showed that it formed a distinct phyletic line; the organism was most similar to the type strains of Streptomyces ruber (97.0 %), Streptomyces rubiginosus (97.0 %), Streptomyces roseiscleroticus (96.9 %) and Streptomyces thermoalcalitolerans (97.1 %). It was readily distinguished from the type strains of these species using a combination of phenotypic properties. On the basis of these results, strain S155T (=CGMCC 4.2055T =DSM 41902T) is proposed as the type strain of the novel species Streptomyces synnematoformans sp. nov.
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Modestobacter versicolor sp. nov., an actinobacterium from biological soil crusts that produces melanins under oligotrophy, with emended descriptions of the genus Modestobacter and Modestobacter multiseptatus Mevs et al. 2000
More LessA novel isolate, CP153-2T, was obtained from topsoil biological crusts in the Colorado Plateau (USA). Colonies were black in colour due to melanin-like pigments when grown on oligotrophic medium, but not when grown on copiotrophic medium. Induction of melanogenesis was independent of growth phase or illumination conditions, including exposure to UVB and UVA radiation, but exposure to UVB could enhance total pigment production and growth under low nitrogen prevented its synthesis. This mode of regulation was previously unknown among melanin-producing bacteria. Polyphasic characterization of the strain revealed that cells were short, straight to curved or irregular rods that developed into pairs and formed multiseptate short filaments, with rare bud-like cells. Short rods were typically motile by means of flagella; multicellular structures tended to be sessile. Cells stained Gram-positive, grew at 4–30 °C and had a narrow range of pH tolerance (pH 5–9). The major fatty acids were iso-C15:0 iso-C16 : 0, anteiso-C15 : 0 and C18 : 1; MK-9(H4) was the major respiratory quinone. Its peptidoglycan contained meso-diaminopimelic acid. Based on 16S rRNA gene sequence similarity data, its closest relative (98.1 % similarity) was Modestobacter multiseptatus DSM 44406T, which is similar morphologically. Based on the above characteristics, strain CP153-2T was also assigned to the genus Modestobacter. However, CP153-2T had a relatedness of only 49.9 % in whole-genome reassociation comparisons with the type strain of M. multiseptatus and thus formally represents a novel species, for which the name Modestobacter versicolor sp. nov. is proposed. Additional evidence in support of a novel species comes from phenotypic and chemotaxonomic characteristics. Strain CP153-2T (=ATCC BAA-1040T =DSM 16678T) is the type strain of M. versicolor.
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Classification of ‘Sarraceniospora aurea’ Furihata et al. 1989 as Actinocorallia aurea sp. nov.
More LessPhylogenetic analysis of ‘Sarraceniospora aurea’ NBRC 14752 and strain NBRC 15120, based on 16S rRNA gene sequences, revealed that these organisms are related to members of the genus Actinocorallia. These organisms contained glutamic acid, alanine and meso-diaminopimelic acid as cell-wall amino acids and the menaquinones MK-9(H4), MK-9(H6) and MK-9(H8). The chemotaxonomic characteristics of the strains were consistent with those of the genus Actinocorallia. However, DNA–DNA hybridization and phenotypic characteristics revealed that the strains differed from the recognized species of the genus Actinocorallia. Therefore, we propose that ‘Sarraceniospora aurea’ NBRC 14752 and strain NBRC 15120 be reclassified in the genus Actinocorallia as a novel species, Actinocorallia aurea sp. nov. (type strain NBRC 14752T=DSM 44434T).
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Terrabacter aerolatus sp. nov., isolated from an air sample
A Gram-positive, strictly aerobic, motile, rod- or coccoid-shaped bacterium, strain 5516J-36T, was isolated from an air sample from Jeju region, Korea, and its taxonomic position was investigated by a polyphasic approach. The organism grew optimally at 30 °C and pH 7.0–8.0. Comparative 16S rRNA gene sequencing studies demonstrated that this strain was highly related phylogenetically to Terrabacter terrae PPLBT and Terrabacter tumescens DSM 20308T, showing 98.9 % sequence similarity to both strains. However, the DNA–DNA reassociation values between 5516J-36T and the type strains of Terrabacter terrae and Terrabacter tumescens were low (51 and 48 %, respectively). The peptidoglycan type was A3γ, the predominant menaquinone was MK-8(H4), the polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol and an unidentified phosphoglycolipid and the whole-cell sugars were glucose, ribose, rhamnose, xylose and galactose. Mycolic acids were absent. The major fatty acids (>5 % of total fatty acids) were iso-C15 : 0, iso-C16 : 0, iso-C14 : 0, iso-C17 : 0 and anteiso-C15 : 0. The DNA G+C content was 71.7 mol%. On the basis of the above data, it is proposed that strain 5516J-36T represents a novel species, Terrabacter aerolatus sp. nov. The type strain of Terrabacter aerolatus is 5516J-36T (=KACC 20556T =DSM 18562T).
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Aestuariimicrobium kwangyangense gen. nov., sp. nov., an ll-diaminopimelic acid-containing bacterium isolated from tidal flat sediment
More LessFour Gram-positive, catalase-positive, short rod- or coccoid-shaped bacterial strains, R27T, R44, R45 and R47, were isolated from an enrichment culture with diesel oil-degradation activity and their taxonomic positions were investigated using a polyphasic approach. Phenotypic, phylogenetic and genetic similarities indicated that strains R27T, R44, R45 and R47 belong to the same species. Phylogenetic analysis based on 16S rRNA gene sequences showed that the four strains form a distinct evolutionary lineage within the family Propionibacteriaceae. The novel four strains had cell-wall peptidoglycan based on ll-diaminopimelic acid, MK-9(H4) as the predominant menaquinone and anteiso-C15 : 0 as the major cellular fatty acid. The DNA G+C contents were 68.8–69.2 mol%. These chemotaxonomic properties, together with phylogenetic distinctiveness, distinguish the four novel strains from recognized members of the family Propionibacteriaceae. On the basis of phenotypic, chemotaxonomic, phylogenetic and genetic data, strains R27T, R44, R45 and R47 are classified as representatives of a new genus and novel species, Aestuariimicrobium kwangyangense gen. nov., sp. nov., within the family Propionibacteriaceae. The type strain of Aestuariimicrobium kwangyangense sp. nov. is R27T (=KCTC 19182T=JCM 14204T).
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Streptomyces durmitorensis sp. nov., a producer of an FK506-like immunosuppressant
More LessScreening of soil samples from the Durmitor National Park, Serbia and Montenegro, for strains producing immunosuppressants with a similar mechanism of action to FK506 resulted in the isolation of the actinomycete strain MS405T. Isolate MS405T was found to have morphological and phenotypic properties that were consistent with its classification as a Streptomyces strain. The DNA G+C content of strain MS405T was 72 mol%. 16S rRNA gene sequence data confirmed the taxonomic position of the strain, following the generation of phylogenetic trees by using various treeing algorithms. On the basis of 16S rRNA gene sequence similarity, strain MS405T was shown to belong to the Streptomyces albidoflavus ‘supercluster’, being related to Streptomyces aureus DSM 41785T (99.59 % similarity) and Streptomyces kanamyceticus DSM 40500T (99.32 %). The 16S–23S rRNA internally transcribed spacer (ITS) region exhibited variations in length and sequence composition, showing limited usefulness in phylogenetic analyses. However, DNA relatedness values support the classification of this isolate within a novel species. A number of physiological and biochemical tests distinguished strain MS405T from its closest phylogenetic neighbours. Therefore, strain MS405T represents a novel species, for which the name Streptomyces durmitorensis sp. nov. is proposed, with the type strain MS405T (=DSM 41863T =CIP 108995T).
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Nocardioides panacihumi sp. nov., isolated from soil of a ginseng field
More LessA novel bacterial strain designated Gsoil 616T was isolated from a soil sample of a ginseng field in Pocheon province (South Korea) and was characterized taxonomically by using a polyphasic approach. The isolate was Gram-positive, strictly aerobic, non-motile, non-spore-forming and rod- or coccoid-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the genus Nocardioides in the family Nocardioidaceae but was clearly separated from established species of this genus. The 16S rRNA gene sequence similarities between strain Gsoil 616T and the type strains of Nocardioides species with validly published names ranged from 91.8 to 96.1 %. The G+C content of the genomic DNA was 73 mol%. Phenotypic and chemotaxonomic data [major menaquinone MK-8(H4) and major fatty acid iso-C16 : 0] supported the affiliation of strain Gsoil 616T to the genus Nocardioides. However, the results of physiological and biochemical tests allowed phenotypic differentiation of the isolate from other Nocardioides species. Therefore, strain Gsoil 616T represented a novel species within the genus Nocardioides, for which the name Nocardioides panacihumi sp. nov. is proposed. The type strain is Gsoil 616T (=KCTC 19187T =DSM 18660T).
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Humihabitans oryzae gen. nov., sp. nov.
More LessStrain KV-657T was isolated from a paddy field soil sample collected in Japan using GPM agar plates supplemented with catalase. The strain was a Gram-positive, aerobic organism that formed branching hyphae with ll-diaminopimelic acid as the diagnostic peptidoglycan diamino acid. The major menaquinone was MK-8(H4). Mycolic acids were not detected. The G+C content of the DNA was 70 mol%. 16S rRNA gene sequence analysis revealed that this strain is closely related to Intrasporangium calvum DSM 43043T, with a similarity of 97.6 %. Based on the morphological, biochemical and chemotaxonomic properties of this strain and phylogenetic analysis, it was concluded that this isolate represents a new genus and species in the family Intrasporangiaceae, for which the name Humihabitans oryzae gen. nov., sp. nov. is proposed. The type strain of Humihabitans oryzae is KV-657T (=NRRL B-24470T =NBRC 101802T).
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- Archaea
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Natronococcus jeotgali sp. nov., a halophilic archaeon isolated from shrimp jeotgal, a traditional fermented seafood from Korea
A novel halophilic archaeon (strain B1T) belonging to the genus Natronococcus was isolated from shrimp jeotgal, a traditional fermented food from Korea. Colonies of this strain were orange–red and cells were non-motile cocci that stained Gram-variable. Strain B1T grew in 7.5–30.0 % (w/v) NaCl and at 21–50 °C and pH 7.0–9.5, with optimal growth occurring in 23–25 % (w/v) NaCl and at 37–45 °C and pH 7.5. Strain B1T was most closely related to the type strain of Natronococcus occultus, with which it shared 97.91 % 16S rRNA gene sequence similarity. Within the phylogenetic tree, this novel strain shared a branching point with N. occultus and occupied a phylogenetic position that was distinct from the main Natronococcus branch. The degree of DNA–DNA hybridization with the type strain of N. occultus, the most closely related species phylogenetically, was 16.4 %. On the basis of these results, it is concluded that strain B1T represents a novel species of the genus Natronococcus, for which the name Natronococcus jeotgali is proposed. The type strain is B1T (=KCTC 4018T=DSM 18795T=JCM 14583T=CECT 7216T).
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- Bacteroidetes
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Aureispira maritima sp. nov., isolated from marine barnacle debris
A novel gliding marine bacterium (strain 59SAT) was isolated from marine barnacle debris. A phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate formed a distinct lineage within the genus Aureispira in the family ‘Saprospiraceae’. The DNA G+C content of strain 59SAT was 38.7 mol%, the major respiratory quinone was MK-7 and the predominant cellular fatty acids were 20 : 4ω6c and 16 : 0. On the basis of the data from DNA–DNA hybridization, physiological and chemotaxonomic analyses and 16S rRNA gene sequence comparisons, strain 59SAT represents a novel species of the genus Aureispira, for which the name Aureispira maritima sp. nov. is proposed. The type strain is 59SAT (=IAM 15439T=TISTR 1726T).
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Proposal of Algoriphagus vanfongensis sp. nov., transfer of members of the genera Hongiella Yi and Chun 2004 emend. Nedashkovskaya et al. 2004 and Chimaereicella Tiago et al. 2006 to the genus Algoriphagus, and emended description of the genus Algoriphagus Bowman et al. 2003 emend. Nedashkovskaya et al. 2004
A taxonomic study of a novel marine, heterotrophic, non-gliding, halotolerant and light-pink-pigmented bacterium was carried out using a polyphasic approach. 16S rRNA gene sequence analysis revealed that strain KMM 6241T is a member of the phylum Bacteroidetes. Strain KMM 6241T formed a cluster with the genera Algoriphagus, Chimaereicella and Hongiella with sequence similarities of 94.0–98.2 %. Hongiella ornithinivorans was the closest relative of the novel isolate. Comparative analysis of phenotypic, chemotaxonomic and genotypic characteristics of strain KMM 6241T and representatives of the genera Algoriphagus, Chimaereicella and Hongiella revealed many similar features. Consequently, phylogenetic evidence supported by phenotypic and genotypic similarities support the transfer of members of the genera Chimaereicella and Hongiella to the genus Algoriphagus and the establishment of a novel species, Algoriphagus vanfongensis sp. nov., with strain KMM 6241T (=DSM 17529T=KCTC 12716T) as the type strain.
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Pedobacter insulae sp. nov., isolated from soil
More LessA Gram-negative, non-motile, rod-shaped bacterium, DS-139T, was isolated from a soil sample collected from Dokdo, Korea, and subjected to a polyphasic taxonomic analysis. Strain DS-139T grew optimally at 25 °C and pH 6.5–7.5 in the presence of 0–0.5 % (w/v) NaCl. It contained MK-7 as the predominant menaquinone and iso-C15 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH and iso-C17 : 0 3-OH as the major fatty acids. The DNA G+C content was 39.4 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DS-39T belongs to the genus Pedobacter in the family Sphingobacteriaceae. The similarity values between the 16S rRNA gene sequence of strain DS-139T and those of the type strains of recognized Pedobacter species, except Pedobacter saltans, were in the range 93.9–96.7 %. The differential phenotypic properties, together with the phylogenetic distinctiveness, were sufficient to assign strain DS-139T to a species that is separate from recognized Pedobacter species. On the basis of the phenotypic and phylogenetic data, therefore, strain DS-139T represents a novel species of the genus Pedobacter, for which the name Pedobacter insulae sp. nov. is proposed. The type strain is DS-139T (=KCTC 12820T =DSM 18684T).
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Flavobacterium filum sp. nov., isolated from a wastewater treatment plant in Korea
More LessA Gram-negative bacterium, designated strain EMB34T, was isolated from a wastewater treatment plant in Korea. Growth was observed between 10 and 40 °C (optimum, 25–35 °C) and between pH 6.0 and 9.5 (optimum, pH 7.5–8.0). The cells were non-motile rods, linked with extracellular fibrils. The predominant fatty acids of strain EMB34T were iso-C15 : 0, C15 : 0, iso-C15 : 1 G, iso-C16 : 0 3-OH and iso-C15 : 0 3-OH and the strain contained phosphatidylethanolamine and phosphatidylinositol as the polar lipids. The G+C content of the genomic DNA was 34.2 mol% and the major quinone was menaquinone-6. Comparative 16S rRNA gene sequence analyses showed that strain EMB34T formed a distinct phyletic line within the genus Flavobacterium. The levels of 16S rRNA gene sequence similarity with other Flavobacterium species were less than 94.5 %. On the basis of phenotypic, chemotaxonomic and molecular data, it is clear that strain EMB34T represents a novel species within the genus Flavobacterium, for which the name Flavobacterium filum sp. nov. is proposed. The type strain is EMB34T (=KCTC 12610T=DSM 17961T).
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Pedobacter koreensis sp. nov., isolated from fresh water
A motile, rod-shaped bacterium, designated strain WPCB189T, was isolated from fresh water collected from the Woopo wetland (Republic of Korea). The cells were found to be Gram-negative, aerobic and catalase- and oxidase-positive. A phylogenetic analysis based on 16S rRNA gene sequences showed that this isolate forms a lineage within the genus Pedobacter, showing sequence similarities of 89.7–96.4 % with respect to recognized species of the genus, and represents a novel member of this genus. The major fatty acids were iso-C15 : 0 2-OH and/or C16 : 1 ω7c (summed feature 3, 29.7 %), iso-C15 : 0 (26.4 %) and iso-C17 : 1 3-OH (10.1 %). The DNA G+C content was 38.0 mol%. On the basis of data obtained from this polyphasic taxonomic study, strain WPCB189T represents a novel species of the genus Pedobacter, for which the name Pedobacter koreensis sp. nov. is proposed. The type strain is WPCB189T (=KCTC 12536T=NBRC 101153T).
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Pedobacter lentus sp. nov. and Pedobacter terricola sp. nov., isolated from soil
More LessTwo Gram-negative, non-motile, pleomorphic bacterial strains, DS-40T and DS-45T, were isolated from a soil sample collected from Dokdo, Korea, and their exact taxonomic positions were investigated by using a polyphasic approach. Strains DS-40T and DS-45T grew optimally at 25 °C and pH 6.5–7.5 in the presence of 0–1.0 % (w/v) NaCl. They contained MK-7 as the predominant menaquinone and possessed iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH) as the major fatty acids. The DNA G+C contents of strains DS-40T and DS-45T were 36.0 and 36.8 mol%, respectively. Strains DS-40T and DS-45T shared a 16S rRNA gene sequence similarity of 96.7 % and demonstrated a mean DNA–DNA relatedness level of 12 %. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strains DS-40T and DS-45T were most closely phylogenetically affiliated with the genus Pedobacter of the family Sphingobacteriaceae. Strains DS-40T and DS-45T exhibited 16S rRNA gene sequence similarity values of 91.4–93.7 and 89.9–91.6 % with respect to the type strains of Pedobacter and Sphingobacterium species, respectively. Phenotypic and chemotaxonomic properties, together with the phylogenetic data, support the assignment of strains DS-40T and DS-45T as two distinct species within the genus Pedobacter. On the basis of phenotypic, phylogenetic and genetic data, strains DS-40T and DS-45T represent two novel species of the genus Pedobacter, for which the names Pedobacter lentus sp. nov. and Pedobacter terricola sp. nov. are proposed, respectively. The respective type strains are DS-40T (=KCTC 12875T=JCM 14593T) and DS-45T (=KCTC 12876T=JCM 14594T).
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Algibacter mikhailovii sp. nov., a novel marine bacterium of the family Flavobacteriaceae, and emended description of the genus Algibacter
More LessA novel marine bacterium, designated strain KMM 6171T, was subjected to taxonomic analysis by using a polyphasic approach. Colonies were yellow-pigmented and cells were Gram-negative, heterotrophic rods displaying slow gliding motility. 16S rRNA gene sequence analysis indicated that strain KMM 6171T was closely related to the genus Algibacter, a member of the family Flavobacteriaceae, with sequence similarity of 96.7–96.8 %. The predominant cellular fatty acids were iso-C15 : 1, iso-C15 : 0, anteiso-C15 : 0, C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH and summed feature 3, comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH. The DNA G+C content was 35.1 mol%. On the basis of the phenotypic, genotypic, chemotaxonomic and phylogenetic data, strain KMM 6171T represents a novel species of the genus Algibacter, for which the name Algibacter mikhailovii sp. nov. is proposed. The type strain is KMM 6171T (=KCTC 12710T=LMG 23988T). An emended description of the genus Algibacter based on the new data is also given.
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- Other Bacteria
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Cerasicoccus arenae gen. nov., sp. nov., a carotenoid-producing marine representative of the family Puniceicoccaceae within the phylum ‘Verrucomicrobia’, isolated from marine sand
More LessA polyphasic taxonomic study was performed on strain YM26-026T, which was isolated from acid-treated sediment in Kamaishi, Japan. The bacterial cells were pale-pink-pigmented, Gram-negative, obligately aerobic, non-spore-forming, spherical and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel isolate was a member of the phylum ‘Verrucomicrobia’ and shared approximately 84–87 % sequence similarity with strains of the class Opitutae that have been cultivated to date. Strain YM26-026T produced pale-pink pigments of carotenoid. β-Lactam antibiotic susceptibility tests and amino acid analysis of cell-wall hydrolysates indicated that the novel isolate did not contain muramic acid or diaminopimelic acid in the cell wall, suggesting that the strain lacks peptidoglycan. The G+C content of the DNA of strain YM26-026T was 54.0 mol%. Menaquinone-7 was the major quinone and C14 : 0 and C18 : 1 ω9c were the major fatty acids. On the basis of polyphasic taxonomic studies, it was concluded that strain YM26-026T represents a new genus of the family Puniceicoccaceae within the phylum ‘Verrucomicrobia’, for which the name Cerasicoccus arenae gen. nov., sp. nov. is proposed. The type strain is YM26-026T (=MBIC08280T=KCTC 12870T).
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- Proteobacteria
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Pelobacter seleniigenes sp. nov., a selenate-respiring bacterium
More LessStrain KMT is a novel bacterium with the unique metabolic abilities of being able to respire selenate as the electron acceptor using acetate as the carbon substrate and possessing the ability to grow fermentatively on short-chain organic acids such as lactate, citrate and pyruvate. Strain KMT was isolated from a sediment enrichment culture of a highly impacted wetland system in New Jersey, USA. Strain KMT is able to reduce selenate as well as selenite to elemental selenium. The unique metabolic capabilities of strain KMT include the respiration of nitrate, poorly crystalline Fe(III) and anthraquinone disulfonate. Phylogenetic analysis of the 16S rRNA gene of the novel isolate indicates that strain KMT groups within the family Geobacteraceae in the class Deltaproteobacteria with approximately 96–97 % 16S rRNA gene sequence similarity to the closest known organisms Malonomonas rubra Gra Mal 1T, Pelobacter acidigallici Ma Gal 2T and species of the genus Desulfuromusa. Recognized species of the genera Malonomonas and Pelobacter cannot use any inorganic electron acceptors, while strains of the genus Desulfuromusa do not ferment organic substrates. This contrasts with the ability of strain KMT to ferment organic compounds as well as to couple selenate reduction to acetate utilization. Based on 16S rRNA gene phylogeny and metabolic properties, strain KMT represents a novel species for which the name Pelobacter seleniigenes sp. nov. (type strain KMT=DSM 18267T=ATCC BAA-1388T) is proposed. Based on the phylogenetic grouping of species of the genus Pelobacter within the Desulfuromusa cluster, it is suggested that Malonomonas rubra Gra Mal 1T should also be included in this group.
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Pseudovibrio japonicus sp. nov., isolated from coastal seawater in Japan
More LessA Gram-negative, motile, rod-shaped bacterium (WSF2T) was isolated from coastal seawater of the Boso Peninsula in Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain WSF2T represented a separate lineage within the genus Pseudovibrio. The DNA G+C content of strain WSF2T was 51.7 mol%. DNA–DNA hybridization values between strain WSF2T and the type strains of Pseudovibrio species were significantly lower than those accepted as the phylogenetic definition of a species. Furthermore, some biochemical characteristics indicated that strain WSF2T differed from other Pseudovibrio species. Based on these characteristics, it is proposed that the isolate represents a novel species, Pseudovibrio japonicus sp. nov. The type strain is WSF2T (=IAM 15442T=NCIMB 14279T=KCTC 12861T).
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Francisella philomiragia subsp. noatunensis subsp. nov., isolated from farmed Atlantic cod (Gadus morhua L.)
More LessSeven bacterial isolates from farmed Atlantic cod displaying chronic granulomatous disease were characterized by phenotypic and molecular taxonomic methods. The isolates were Gram-negative, facultatively intracellular, non-motile, strictly aerobic coccobacilli which produced H2S from cysteine-supplemented media and are therefore phenotypically consistent with members of the genus Francisella. Comparison of 16S rRNA gene sequences and six partial housekeeping gene sequences (groEL, shdA, rpoB, rpoA, pgm and atpA) confirmed the organism as a member of the genus Francisella, with Francisella philomiragia as its closest relative (99.3 % 16S rRNA gene sequence similarity, 92.2–99.0 % housekeeping gene sequence similarity). Despite the close relationship with F. philomiragia, isolates from Atlantic cod could be readily distinguished phenotypically and genetically from F. philomiragia ATCC 25015T. DNA–DNA hybridization studies revealed a mean reassociation value of 68 %. Thus, on the basis of phenotypic and molecular genetic evidence, we propose that the strains isolated from Atlantic cod should be recognized as Francisella philomiragia subsp. noatunensis subsp. nov. with the type strain 2005/50/F292-6CT (=NCIMB 14265T=LMG 23800T). Francisella philomiragia ATCC 25015T (=DSM 735T) is reclassified as Francisella philomiragia subsp. philomiragia subsp. nov.
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Loktanella atrilutea sp. nov., isolated from seawater in Japan
More LessA Gram-negative, rod-shaped bacterium, IG8T, was isolated from seawater off the Sanriku coast, Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IG8T represented a separate lineage within the genus Loktanella; the highest 16S rRNA gene sequence similarity values were found with the type strains of Loktanella salsilacus (98.6 %) and Loktanella fryxellensis (98.4 %). DNA–DNA hybridization values between strain IG8T and the type strains of L. salsilacus (27.9–36.1 %) and L. fryxellensis (11.3–31.0 %) were clearly below 70 %, the generally accepted limit for species delineation. The DNA G+C content of strain IG8T was 66.3 mol%. On the basis of DNA–DNA hybridization, some biochemical characteristics and 16S rRNA gene sequence comparison, it is proposed that the isolate represents a novel species, Loktanella atrilutea sp. nov. The type strain is IG8T (=IAM 15450T=NCIMB 14280T).
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Marinobacter segnicrescens sp. nov., a moderate halophile isolated from benthic sediment of the South China Sea
More LessA Gram-negative, motile, non-spore-forming and moderately halophilic ellipsoid-shaped marine coccobacillus, designated strain SS011B1-4T, was isolated from benthic sediment of the South China Sea. Optimum growth occurred at 30–37 °C, pH 7.5–8.0 and 4–8 % (w/v) NaCl. Strain SS011B1-4T utilized a variety of organic substrates as sole carbon sources, but did not utilize toluene, n-tetradecane or crude oil. Strain SS011B1-4T had ubiquinone-9 as the major respiratory quinone and C18 : 1 ω9c, C16 : 0 and C12 : 0 3-OH as the predominant fatty acids. The genomic DNA G+C content was 62.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SS011B1-4T belonged to the genus Marinobacter of the Gammaproteobacteria. The results of the phenotypic, phylogenetic and genomic analyses revealed that strain SS011B1-4T represents a novel species of the genus Marinobacter. The name Marinobacter segnicrescens sp. nov. is therefore proposed, with strain SS011B1-4T (=LMG 23928T=CGMCC 1.6489T) as the type strain.
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Halotalea alkalilenta gen. nov., sp. nov., a novel osmotolerant and alkalitolerant bacterium from alkaline olive mill wastes, and emended description of the family Halomonadaceae Franzmann et al. 1989, emend. Dobson and Franzmann 1996
More LessA novel Gram-negative, motile, nonsporulating, rod-shaped bacterium isolated from alkaline sludge-like wastes (‘alpeorujo’ or ‘alperujo’) of two-phase olive oil extraction is described. The strain, designated AW-7T, is an obligate aerobe that is halotolerant (tolerating up to 15 % w/v NaCl), sugar-tolerant (tolerating up to 45 % and 60 % w/v (+)-d-glucose and maltose respectively; these are the highest concentrations tolerated by any known members of the Bacteria domain) and alkalitolerant (growing at a broad pH range of 5–11). Strain AW-7T is chemo-organotrophic. Ubiquinone-9 was detected in the respiratory chain of strain AW-7T. The major fatty acids present are C18 : 1 ω7c, C16 : 0, C19 : 0 cyclo ω8c, C12 : 0 3-OH and C16 : 1 ω7c/iso-C15 : 0 2-OH. Based on 16S rRNA gene sequence analysis, strain AW-7T showed almost equal phylogenetic distances from Zymobacter palmae (95.6 % similarity) and Carnimonas nigrificans (95.4 % similarity). In addition, low DNA–DNA relatedness values were found for strain AW-7T against Carnimonas nigrificans CECT 4437T (22.5–25.4 %) and Z. palmae DSM 10491T (11.9–14.4 %). The DNA G+C content of strain AW-7T is 64.4 mol%. Physiological and chemotaxonomic data further confirmed the differentiation of strain AW-7T from the genera Zymobacter and Carnimonas. Thus, strain AW-7T represents a novel bacterial genus within the family Halomonadaceae, for which the name Halotalea gen. nov. is proposed. Halotalea alkalilenta sp. nov. (type strain AW-7T=DSM 17697T=CECT 7134T) is proposed as the type species of the genus Halotalea gen. nov. A reassignment of the descriptive 16S rRNA signature characteristics of the family Halomonadaceae permitted the placement of the novel genus Halotalea into the family; in contrast, the genus Halovibrio possessed only 12 out of the 18 signature characteristics proposed, and hence it was excluded from the family Halomonadaceae.
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Rhodobacter vinaykumarii sp. nov., a marine phototrophic alphaproteobacterium from tidal waters, and emended description of the genus Rhodobacter
More LessA rod-shaped, phototrophic, purple non-sulfur bacterium was isolated in pure culture from seawater collected from the seashore of Visakhapatnam, on the east coast of India, in a medium that contained 2 % NaCl (w/v). Strain JA123T was Gram-negative and non-motile and had a requirement for NaCl. Photo-organoheterotrophic and chemo-organoheterotrophic growth occurred with organic compounds as carbon sources and electron donors. Photolithoautotrophic, chemolithoautotrophic and fermentative growth could not be demonstrated. Strain JA123T contained vesicular intracellular photosynthetic membrane structures. Bacteriochlorophyll a and probably carotenoids of the spheroidene series were present as photosynthetic pigments. Biotin was required for growth. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA123T clustered with species of the genus Rhodobacter. Based on 16S rRNA gene sequence analysis and morphological and physiological characteristics, strain JA123T is sufficiently different from other Rhodobacter species to propose a novel species, Rhodobacter vinaykumarii sp. nov., to accommodate this strain; the type strain is JA123T (=DSM 18714T =JCM 14544T =CCUG 54311T).
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Stenotrophomonas terrae sp. nov. and Stenotrophomonas humi sp. nov., two nitrate-reducing bacteria isolated from soil
More LessThree Gram-negative, rod-shaped, non-spore-forming, nitrate-reducing isolates (R-32746, R-32768T and R-32729T) were obtained from soil. Analysis of repetitive sequence-based PCR showed that the three isolates represented two different strains. 16S rRNA gene sequence analysis and DNA–DNA hybridization placed them within the genus Stenotrophomonas and revealed that they were genotypically different from each other and from all recognized Stenotrophomonas species. Analysis of the fatty acid composition and physiological and biochemical tests allowed differentiation from their closest phylogenetic neighbours. They are therefore considered to represent two novel species, for which the names Stenotrophomonas terrae sp. nov. and Stenotrophomonas humi sp. nov. are proposed, with strains R-32768T (=LMG 23958T=DSM 18941T) and R-32729T (=LMG 23959T=DSM 18929T), respectively, as the type strains.
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Methylibium fulvum sp. nov., a member of the Betaproteobacteria isolated from ginseng field soil, and emended description of the genus Methylibium
More LessTwo bacterial strains, designated Gsoil 322T and Gsoil 328, were isolated from soil of a ginseng field in Pocheon province (Republic of Korea). The strains were Gram-negative, motile, aerobic rods that showed nearly identical physiological profiles and similar chemotaxonomic profiles. The two strains were oxidase-positive but catalase-negative, reduced nitrate to nitrite and had fatty acid profiles in which C16 : 0, C17 : 0 cyclo and C16 : 1 ω7c/iso-C15 : 0 2-OH were predominant. The DNA G+C contents of Gsoil 322T and Gsoil 328 were 66.6 and 66.7 mol%, respectively. Q-8 was observed as the major quinone. Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 322T belongs to the class Betaproteobacteria and was most closely related to Methylibium petroleiphilum ATCC BAA-1232T (97.5 % sequence similarity). On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 322T (=KCTC 12591T =LMG 23394T) was classified in the genus Methylibium as the type strain of a novel species, for which the name Methylibium fulvum sp. nov. is proposed.
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Photobacterium kishitanii sp. nov., a luminous marine bacterium symbiotic with deep-sea fishes
Six representatives of a luminous bacterium commonly found in association with deep, cold-dwelling marine fishes were isolated from the light organs and skin of different fish species. These bacteria were Gram-negative, catalase-positive, and weakly oxidase-positive or oxidase-negative. Morphologically, cells of these strains were coccoid or coccoid-rods, occurring singly or in pairs, and motile by means of polar flagellation. After growth on seawater-based agar medium at 22 °C for 18 h, colonies were small, round and white, with an intense cerulean blue luminescence. Analysis of 16S rRNA gene sequence similarity placed these bacteria in the genus Photobacterium. Phylogenetic analysis based on seven housekeeping gene sequences (16S rRNA gene, gapA, gyrB, pyrH, recA, rpoA and rpoD), seven gene sequences of the lux operon (luxC, luxD, luxA, luxB, luxF, luxE and luxG) and four gene sequences of the rib operon (ribE, ribB, ribH and ribA), resolved the six strains as members of the genus Photobacterium and as a clade distinct from other species of Photobacterium. These strains were most closely related to Photobacterium phosphoreum and Photobacterium iliopiscarium. DNA–DNA hybridization values between the designated type strain, Photobacterium kishitanii pjapo.1.1T, and P. phosphoreum LMG 4233T, P. iliopiscarium LMG 19543T and Photobacterium indicum LMG 22857T were 51, 43 and 19 %, respectively. In AFLP analysis, the six strains clustered together, forming a group distinct from other analysed species. The fatty acid C17 : 0 cyclo was present in these bacteria, but not in P. phosphoreum, P. iliopiscarium or P. indicum. A combination of biochemical tests (arginine dihydrolase and lysine decarboxylase) differentiates these strains from P. phosphoreum and P. indicum. The DNA G+C content of P. kishitanii pjapo.1.1T is 40.2 %, and the genome size is approximately 4.2 Mbp, in the form of two circular chromosomes. These strains represent a novel species, for which the name Photobacterium kishitanii sp. nov. is proposed. The type strain, pjapo.1.1T (=ATCC BAA-1194T=LMG 23890T), is a luminous symbiont isolated from the light organ of the deep-water fish Physiculus japonicus.
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Methylophaga aminisulfidivorans sp. nov., a restricted facultatively methylotrophic marine bacterium
More LessA novel restricted facultatively methylotrophic marine strain, MPT, possessing the ribulose monophosphate pathway of C1-carbon compound assimilation was isolated from a seawater sample obtained from Mokpo, South Korea. The novel isolate is aerobic, Gram-negative, asporogenous and a non-motile short rod. It grows well on methanol, methylated amines, dimethylsulfide and DMSO. Optimal growth occurs with 3 % NaCl at 30 °C and pH 7.0. Fructose is utilized as a multicarbon source. Growth factors are not required and vitamin B12 does not stimulate growth. The cellular fatty acid profile of the novel strain consists primarily of straight-chain saturated C16 : 0 and unsaturated C16 : 1 acids. The major ubiquinone is Q-8. The dominant phospholipids are phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content is 44.9 mol% (T m). Based on 16S rRNA gene sequence analysis and DNA–DNA relatedness (25–41 %) with the type strains of marine methylotrophs belonging to the genus Methylophaga, it is suggested that isolate MPT represents a novel species, Methylophaga aminisulfidivorans sp. nov. (type strain MPT=KCTC 12909T=VKM B-2441T=JCM 14647T).
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Marinobacter salicampi sp. nov., isolated from a marine solar saltern in Korea
More LessA Gram-negative, motile, rod-shaped, Marinobacter-like bacterial strain, ISL-40T, was isolated from a marine solar saltern of the Yellow Sea in Korea. The taxonomic position of the novel strain was investigated using a polyphasic approach. Strain ISL-40T grew optimally at pH 7.0–8.0 and at 30 °C. It contained Q-9 as the predominant ubiquinone. The major fatty acids were C16 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH and 10-methyl C16 : 0. The DNA G+C content was 58.1 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-40T belongs to the genus Marinobacter. Strain ISL-40T exhibited 16S rRNA gene sequence similarity values of 93.5–96.4 % to the type strains of recognized Marinobacter species. The differential phenotypic properties and phylogenetic distinctiveness of strain ISL-40T revealed that it is separate from recognized Marinobacter species. On the basis of phenotypic, phylogenetic and genetic data, therefore, strain ISL-40T represents a novel species of the genus Marinobacter, for which the name Marinobacter salicampi sp. nov. is proposed. The type strain is ISL-40T (=KCTC 12972T=CCUG 54357T).
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Halochromatium roseum sp. nov., a non-motile phototrophic gammaproteobacterium with gas vesicles, and emended description of the genus Halochromatium
More LessA rod-shaped, marine, phototrophic, purple sulfur bacterium containing gas vesicles was isolated from a marine solar saltern at Kakinada, India. Cells of strain JA134T are Gram-negative, non-motile rods, with vesicular intracytoplasmic membranes, and the strain has an absolute requirement for NaCl for growth. Bacteriochlorophyll a and the carotenoid okenone are present as photosynthetic pigments. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA134T clusters with members of the genus Halochromatium, but is distinctly separated from the species reported so far. The morphological and physiological differences of strain JA134T from other Halochromatium species support the description of strain JA134T (=ATCC BAA-1363T =DSM 18859T =JCM 14151T) as the type strain of a novel species, Halochromatium roseum sp. nov.
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Methylibium aquaticum sp. nov., a betaproteobacterium isolated from a eutrophic freshwater pond
More LessA freshwater bacterium, designated IMCC1728T, was isolated from a eutrophic pond. The strain was Gram-negative, chemoheterotrophic and facultatively aerobic, forming non-motile rods that contained poly-β-hydroxybutyrate granules. Based on 16S rRNA gene sequence comparisons, the most closely related species to strain IMCC1728T was Methylibium petroleiphilum (97.0 % similarity). Phylogenetic trees generated using 16S rRNA gene sequences showed that this isolate formed an independent phyletic line of the genus Methylibium clade of the class Betaproteobacteria. The DNA G+C content of the strain was 66.2±0.4 mol%. The predominant cellular fatty acid constituents were C16 : 1 ω7c and/or iso-C15 : 0 2-OH (43.1 %), C16 : 0 (20.3 %), C12 : 0 (13.4 %) and C10 : 0 3-OH (7.3 %). The strain contained Q-8 as the predominant ubiquinone. Several phenotypic characteristics, including flagellation, temperature range for growth and carbon source utilization patterns, differentiated strain IMCC1728T from species of the genus Methylibium. Therefore, it is proposed that strain IMCC1728T represents a novel species, Methylibium aquaticum sp. nov. The type strain is IMCC1728T (=KCCM 42364T=NBRC 102349T).
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Jannaschia donghaensis sp. nov., isolated from seawater of the East Sea, Korea
More LessA Gram-negative, non-motile and rod-, oval- or coccoid-shaped strain, DSW-17T, was isolated from seawater of the East Sea, Korea, and subjected to a polyphasic taxonomic study. Strain DSW-17T grew optimally at pH 7.0–8.0 and 25 °C. It contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. Major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and an unidentified glycolipid. The DNA G+C content was 65.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DSW-17T was phylogenetically most closely affiliated to the genus Jannaschia. Strain DSW-17T exhibited 16S rRNA gene sequence similarity values of 96.5 % with the type strains of three recognized species of the genus Jannaschia. DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain DSW-17T is distinguishable from the recognized species of the genus Jannaschia. On the basis of phenotypic, phylogenetic and genetic data, strain DSW-17T was classified in the genus Jannaschia as a member of a novel species, for which the name Jannaschia donghaensis sp. nov. is proposed. The type strain is DSW-17T (=KCTC 12862T=JCM 14563T).
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Shewanella canadensis sp. nov. and Shewanella atlantica sp. nov., manganese dioxide- and hexahydro-1,3,5-trinitro-1,3,5-triazine-reducing, psychrophilic marine bacteria
More LessTwo strains belonging to the genus Shewanella, HAW-EB2T and HAW-EB5T, were isolated previously from marine sediment sampled from the Atlantic Ocean, near Halifax harbour in Canada, for their potential to degrade explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). In the present study, strains HAW-EB2T and HAW-EB5T were found to display high 16S rRNA gene sequence similarity (90–99.5 %) to species of Shewanella, but their gyrB sequences were significantly different from each other and from species of Shewanella (79–87.6 %). Furthermore, DNA–DNA hybridization showed that the genomic DNA of the two strains was only 22 % related and showed less than 41 % relatedness to closely related species of Shewanella. In comparison to other species of Shewanella, strains HAW-EB2T and HAW-EB5T were also unique in some phenotypic properties such as activities of β-galactosidase and tyrosine arylamidase and the ability to metabolize certain organic acids and sugars. Both strains HAW-EB2T and HAW-EB5T utilize malate, valerate, peptone and yeast extract as sole carbon and energy sources. The major membrane fatty acids of the two strains were C14 : 0, iso-C15 : 0, C16 : 0, C16 : 1 ω7, C18 : 1 ω7 and C20 : 5 ω3 and their major quinones were Q-7, Q-8 and MK-7. On the basis of these results, strain HAW-EB2T (=NCIMB 14238T =CCUG 54553T) is proposed as the type strain of Shewanella canadensis sp. nov. and strain HAW-EB5T (=NCIMB 14239T =CCUG 54554T) is proposed as the type strain of Shewanella atlantica sp. nov.
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Desulfovibrio marinus sp. nov., a moderately halophilic sulfate-reducing bacterium isolated from marine sediments in Tunisia
More LessTwo novel sulfate-reducing bacterial strains, designated E-2T and IMP-2, were isolated from geographically distinct locations. Strain E-2T was recovered from marine sediments near Sfax (Tunisia), whereas strain IMP-2 originated from oilfield production fluids in the Gulf of Mexico. Cells were Gram-negative, non-sporulated, motile, vibrio-shaped or sigmoid. They were strictly anaerobic, mesophilic and moderately halophilic. Sulfate, sulfite, thiosulfate and elemental sulfur served as electron acceptors, but not nitrate or nitrite. H2 (with acetate as carbon source), formate, fumarate, lactate, malate, pyruvate, succinate and fructose were used as electron donors in the presence of sulfate as terminal electron acceptor. Lactate was oxidized incompletely to acetate. Fumarate and pyruvate were fermented. Desulfoviridin and c-type cytochromes were present. 16S rRNA gene sequence analysis of the two strains showed that they were phylogenetically similar (99.0 % similarity) and belonged to the genus Desulfovibrio, with Desulfovibrio indonesiensis and Desulfovibrio gabonensis as their closest phylogenetic relatives. The G+C content of the DNA was respectively 60.4 and 62.7 mol% for strains E-2T and IMP-2. DNA–DNA hybridization experiments revealed that the novel strains had a high genomic relatedness, suggesting that they belong to the same species. We therefore propose that the two isolates be affiliated to a novel species of the genus Desulfovibrio, Desulfovibrio marinus sp. nov. The type strain is strain E-2T (=DSM 18311T =JCM 14040T).
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- Eukaryotic Micro-Organisms
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Reclassification of Graphium tectonae as Parascedosporium tectonae gen. nov., comb. nov., Pseudallescheria africana as Petriellopsis africana gen. nov., comb. nov. and Pseudallescheria fimeti as Lophotrichus fimeti comb. nov.
More LessDuring a biodiversity survey of Argentinian soil fungi, we recovered a rare Scedosporium-like fungus which was proven to be genetically and morphologically different from known species of Scedosporium (anamorph of Pseudallescheria) and relatives and is proposed here as representing a new genus. This genus is mainly characterized by producing sympodial conidia from denticulate conidiogenous cells. This isolate was morphologically identical to Graphium tectonae and thus the new combination Parascedosporium tectonae gen. nov., comb. nov. is proposed. Sequence analysis of four regions of three genes, i.e. β-tubulin (two loci), calmodulin and the internal transcribed spacer region of the 5.8S rRNA, confirmed our proposal. Both the phylogenetic analysis and morphological studies excluded Pseudallescheria africana and Pseudallescheria fimeti from the genus Pseudallescheria. The former is proposed as a member of the new genus Petriellopsis, and the latter has been accommodated in Lophotrichus. The type strains of Parascedosporium tectonae gen. nov., comb. nov., Petriellopsis africana gen. nov., comb. nov. and Lophotrichus fimeti comb. nov. are respectively CBS 127.84T, CBS 311.72T and CBS 129.78T.
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Rhodotorula psychrophila sp. nov., Rhodotorula psychrophenolica sp. nov. and Rhodotorula glacialis sp. nov., novel psychrophilic basidiomycetous yeast species isolated from alpine environments
More LessThree novel psychrophilic species of the genus Rhodotorula are described. Rhodotorula psychrophila sp. nov. (type strain PB19T=CBS 10440T=DSM 18768T), Rhodotorula psychrophenolica sp. nov. (type strain AG21T=CBS 10438T=DSM 18767T) and Rhodotorula glacialis sp. nov. (type strain A19T=CBS 10436T=DSM 18766T) were isolated from soil collected from an alpine railway area, from mud in the thawing zone of a glacier foot and from glacier cryoconite, respectively. All three species have been assigned to the genus Rhodotorula on the basis of molecular sequence data and physiological and morphological properties. Rhodotorula psychrophila is not able to grow at temperatures above 15 °C. Rhodotorula psychrophenolica and Rhodotorula glacialis degrade high concentrations of phenol (up to 12.5 and 5 mM, respectively) as the sole carbon source at 10 °C. Sequence analyses of the 26S rDNA D1/D2 regions indicated that the novel species are phylogenetically related and belong to a clade that includes other psychrophilic yeasts.
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- Other Gram-Positive Bacteria
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Salinicoccus siamensis sp. nov., isolated from fermented shrimp paste in Thailand
Fifteen strains of moderately halophilic, Gram-positive cocci were isolated from a traditional fermented shrimp paste (‘ka-pi’) produced in Thailand. These bacteria were strictly aerobic, non-motile, non-sporulating and catalase- and oxidase-positive. They produced orange pigment and grew in the presence of 1.5–25 % (w/v) NaCl. They grew optimally in 10 % (w/v) NaCl, at pH 8.5 and at 37 °C. The cell-wall peptidoglycan was of l-Lys type. Menaquinone with six isoprene units (MK-6) was a major component. The dominant cellular fatty acids were anteiso-C15 : 0 and iso-C15 : 0. DNA G+C contents were in the range 44.5–47.5 mol%. Comparative 16S rRNA gene sequence analyses indicated that representative strain PN1-2T was related most closely to Salinicoccus roseus JCM 14630T, with 97.3 % similarity. The other novel strains were included in the same species based on their levels of DNA–DNA relatedness to strain PN1-2T (≥76.6 %) but showed low DNA–DNA relatedness to S. roseus JCM 14630T (21.7 %). On the basis of the phenotypic and molecular data presented, the 15 novel strains are suggested to represent a single novel species of the genus Salinicoccus, for which the name Salinicoccus siamensis sp. nov. is proposed. The type strain is PN1-2T (=JCM 12822T =PCU 242T =TISTR 1562T).
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Halobacillus campisalis sp. nov., containing meso-diaminopimelic acid in the cell-wall peptidoglycan, and emended description of the genus Halobacillus
More LessA Gram-positive or variable, motile and coccoid or oval-shaped bacterial strain, ASL-17T, was isolated from a marine solar saltern of the Yellow Sea in Korea and its exact taxonomic position was investigated by a polyphasic approach. Strain ASL-17T grew optimally at pH 7.0–8.0 and 37 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ASL-17T is most closely affiliated phylogenetically to the genus Halobacillus. Strain ASL-17T exhibited 16S rRNA gene sequence similarity values of 97.7–98.6 % to the type strains of recognized Halobacillus species. Interestingly, strain ASL-17T had cell-wall peptidoglycan based on meso-diaminopimelic acid, unlike other Halobacillus species. It contained MK-7 as the predominant menaquinone. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The DNA G+C content was 42.1 mol%. DNA–DNA relatedness data and differential phenotypic properties demonstrated that strain ASL-17T can be differentiated from recognized Halobacillus species. On the basis of phenotypic, chemotaxonomic, phylogenetic and genetic data, strain ASL-17T represents a novel species of the genus Halobacillus, for which the name Halobacillus campisalis sp. nov. is proposed. The type strain is ASL-17T (=KCTC 13144T =CCUG 54360T).
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Bacillus acidiceler sp. nov., isolated from a forensic specimen, containing Bacillus anthracis pX02 genes
Research at the Center for Biological Defense identified plasmid-borne forms of Bacillus anthracis pXO2 genes in a Gram-positive, endospore-forming rod, isolated from a forensic specimen considered a credible threat of harbouring anthrax. Conventional, commercial and molecular-based methods indicated that the isolate (CBD 119T) was not B. anthracis and considered not to be a member of the Bacillus cereus group. Based on the 16S rRNA gene sequence similarities, strain CBD 119T was most closely related to Bacillus luciferensis LMG 18422T (99.3 %). Phenotyping and fatty acid methyl ester analysis of the isolate were conducted alongside B. luciferensis JCM 12212T. The major cellular fatty acids (anteiso-C15 : 0, iso-C15 : 0, and >7 iso or anteiso forms) supported inclusion of the isolate in the genus Bacillus. Strain CBD 119T was inconsistent with B. luciferensis JCM 12212T for 18 of 96 traits evaluated including motility, degree of endospore-driven swelling and pH optimum; the two were linked by fatty acid methyl ester analysis as separate but closely related species. DNA–DNA relatedness between strain CBD 119T and B. luciferensis JCM 12212T resulted in less than 20 % hybridization. The results of biochemical and physiological characterization, chemotaxonomic analysis and DNA–DNA hybridization differentiated strain CBD 119T both phenotypically and genotypically from the only species with validly published name with greater than 97 % 16S rRNA gene sequence similarity. The isolate has an accelerated doubling time when grown in aerated broth at pH 5.9 relative to that at pH 7.1. Therefore, it is proposed that strain CBD 119T represents a novel species, Bacillus acidiceler sp. nov. The type strain is strain CBD 119T (=NRRL B-41736T=DSM 18954T).
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Bacillus chagannorensis sp. nov., a moderate halophile from a soda lake in Inner Mongolia, China
More LessA Gram-positive, moderately halophilic, spore-forming bacterium, designated strain CG-15T, was isolated from a soda lake, Lake Chagannor, in the Inner Mongolia Autonomous Region, China. The cells were found to be motile short rods with ellipsoidal, terminal and deforming endospores. Strain CG-15T, a facultatively anaerobic bacterium, grew at pH 5.8–11.0 (optimally at pH 8.5), at 6–40 °C (optimally at 37 °C) and at salinities of 3–20 % (w/v) total salts (optimally at 7 % w/v). On the basis of the results of 16S rRNA gene sequence analysis, strain CG-15T was shown to belong to the genus Bacillus (phylum Firmicutes), showing the greatest phylogenetic similarity with respect to Bacillus saliphilus (96.0 %). The DNA G+C content of the novel isolate was found to be 53.8 mol%. The major cellular fatty acids of strain CG-15T were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0, and its polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three different unidentified phospholipids. The analysis of the quinones showed that MK-7 was the major menaquinone. The peptidoglycan type was A1γ, with meso-diaminopimelic acid as the diagnostic diamino acid. On the basis of the data from this polyphasic study, strain CG-15T represents a novel species of the genus Bacillus, for which the name Bacillus chagannorensis sp. nov. is proposed. The type strain is CG-15T (=CCM 7371T=CECT 7153T=CGMCC 1.6292T=DSM 18086T).
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Syntrophomonas palmitatica sp. nov., an anaerobic, syntrophic, long-chain fatty-acid-oxidizing bacterium isolated from methanogenic sludge
More LessA mesophilic, syntrophic, fatty-acid-oxidizing anaerobic strain, designated MPAT, was isolated from granular sludge in a mesophilic upflow anaerobic sludge blanket reactor used to treat palm oil mill effluent. Cells were slightly curved, non-motile rods. Spore formation was not observed. The optimal temperature for growth was around 37 °C and optimal pH for growth was 7.0. Strain MPAT was able to grow on crotonate or pentenoate plus butyrate in pure culture. In co-culture with the hydrogenotrophic methanogen Methanospirillum hungatei, strain MPAT was able to oxidize straight-chain saturated fatty acids with carbon chain lengths of C4–C18. The strain was unable to utilize sulfate, sulfite, thiosulfate, nitrate, fumarate, iron(III) or DMSO as an electron acceptor. The G+C content of the DNA was 45.0 mol%. Based on comparative 16S rRNA gene sequence analysis, strain MPAT was found to be a member of the genus Syntrophomonas and was most closely related to the type strains of Syntrophomonas curvata and Syntrophomonas sapovorans (sequence similarities of 94 %). Genetic and phenotypic characteristics demonstrated that strain MPAT represents a novel species, for which the name Syntrophomonas palmitatica sp. nov. is proposed. The type strain is MPAT (=JCM 14374T=NBRC 102128T=DSM 18709T).
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Enterococcus camelliae sp. nov., isolated from fermented tea leaves in Thailand
More LessA Gram-positive and catalase-negative coccus that formed chains, strain FP15-1T, isolated from fermented tea leaves (‘miang’), was studied systematically. The strain was facultatively anaerobic and produced l-lactic acid from glucose. Demethylmenaquinone (DMK-7) was the major menaquinone. Straight-chain unsaturated fatty acids C16 : 1 and C18 : 1 were the dominant components. The DNA G+C content was 37.8 mol%. On the basis of 16S rRNA and RNA polymerase α subunit (rpoA) gene sequence analysis, strain FP15-1T was closely related to Enterococcus italicus KCTC 5373T, with 99.2 and 93.8 % similarity, respectively. The strain could be clearly distinguished from E. italicus ATCC 5373T by low DNA–DNA relatedness (≤33.8 %) and phenotypic characteristics. Therefore, this strain represent a novel species of the genus Enterococcus, for which the name Enterococcus camelliae sp. nov. is proposed. The type strain is FP15-1T (=KCTC 13133T =NBRC 101868T =NRIC 0105T =TISTR 932T =PCU 277T).
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- Evolution, Phylogeny And Biodiversity
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Ribosomal protein gene-based phylogeny for finer differentiation and classification of phytoplasmas
Extensive phylogenetic analyses were performed based on sequences of the 16S rRNA gene and two ribosomal protein (rp) genes, rplV (rpl22) and rpsC (rps3), from 46 phytoplasma strains representing 12 phytoplasma 16Sr groups, 16 other mollicutes and 28 Gram-positive walled bacteria. The phylogenetic tree inferred from rp genes had a similar overall topology to that inferred from the 16S rRNA gene. However, the rp gene-based tree gave a more defined phylogenetic interrelationship among mollicutes and Gram-positive walled bacteria. Both phylogenies indicated that mollicutes formed a monophyletic group. Phytoplasmas clustered with Acholeplasma species and formed one clade paraphyletic with a clade consisting of the remaining mollicutes. The closest relatives of mollicutes were low-G+C-content Gram-positive bacteria. Comparative phylogenetic analyses using the 16S rRNA gene and rp genes were performed to evaluate their efficacy in resolving distinct phytoplasma strains. A phylogenetic tree was constructed based on analysis of rp gene sequences from 87 phytoplasma strains belonging to 12 16Sr phytoplasma groups. The phylogenetic relationships among phytoplasmas were generally in agreement with those obtained on the basis of the 16S rRNA gene in the present and previous works. However, the rp gene-based phylogeny allowed for finer resolution of distinct lineages within the phytoplasma 16Sr groups. RFLP analysis of rp gene sequences permitted finer differentiation of phytoplasma strains in a given 16Sr group. In this study, we also designed several semi-universal and 16Sr group-specific rp gene-based primers that allow for the amplification of 11 16Sr group phytoplasmas.
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- International Committee On Systematics Of Prokaryotes
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- Taxonomic Note
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On species descriptions based on a single strain: proposal to introduce the status species proponenda (sp. pr.)
More LessA survey of the descriptions of novel bacterial species published in the period 1996–2006 revealed that a large number of taxonomic descriptions are still based on one or a few strains. This situation determines that not only species descriptions, but also proposals to create higher ranks, are actually based on very few strains, which could produce a highly biased scenario. The encouragement to include a reasonable number of strains in species descriptions has been largely disregarded after its proposal, since acceptance of such descriptions relies mainly on editors' and reviewers' opinions. This observation and other considerations lead us to propose the creation of the status species proponenda (sp. pr.), as a compromise between the need for scientific description of biodiversity and exchange of data and the good taxonomic practice of including a sufficient number of strains in descriptions of species and higher taxonomic ranks.
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- Errata
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