- Volume 59, Issue 2, 2009
Volume 59, Issue 2, 2009
- Notification List
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Notification that new names and new combinations have appeared in volume 58, part 11, of the IJSEM
This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles). Taxonomic opinions included in this List (i.e. the creation of synonyms or the emendation of circumscriptions) cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission.
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- New Taxa
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- Actinobacteria
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Sciscionella marina gen. nov., sp. nov., a marine actinomycete isolated from a sediment in the northern South China Sea
The taxonomic position of an actinomycete, designated SCSIO 00231T, isolated from a sediment sample collected from the northern South China Sea, was determined by using a polyphasic approach. The organism formed fragmented substrate hyphae and sparse aerial mycelium on modified ISP 2 medium. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain SCSIO 00231T fell into the family Pseudonocardiaceae, in which it formed a distinct lineage and was loosely associated with Thermocrispum municipale DSM 44069T, with 93 % similarity. The other closest phylogenetic neighbours were Saccharopolyspora erythraea NRRL 2338T (92.6 % similarity) and Amycolatopsis sacchari DSM 44468T (93.1 % similarity). The isolate had cell-wall type IV (meso-diaminopimelic acid and whole-cell sugars arabinose, galactose and glucose) and phospholipid type III. The predominant menaquinone was MK-9(H4). The G+C content of the genomic DNA was 69 mol%. Based on these data, strain SCSIO 00231T can be readily distinguished from previously described organisms and represents a new genus within the family Pseudonocardiaceae. The name Sciscionella gen. nov. is proposed, with the novel species Sciscionella marina sp. nov. The type strain of Sciscionella marina is SCSIO 00231T (=KCTC 19433T =CCTCC AA208009T).
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Nitriliruptor alkaliphilus gen. nov., sp. nov., a deep-lineage haloalkaliphilic actinobacterium from soda lakes capable of growth on aliphatic nitriles, and proposal of Nitriliruptoraceae fam. nov. and Nitriliruptorales ord. nov.
More LessA novel bacterial strain, designated ANL-iso2T, was obtained from an enrichment culture inoculated with a mixture of soda lake sediments by using isobutyronitrile (iBN) as the carbon, energy and nitrogen source at pH 10. The enrichment resulted in a stable binary culture containing iBN-degrading Gram-positive rods and a satellite Gram-negative gammaproteobacterium Marinospirillum sp. strain (ANL-isoa) scavenging the products of nitrile hydrolysis. Cells of the iBN-degrading strain, ANL-iso2T, were short, non-motile, non-spore-forming rods. Strain ANL-iso2T was capable of utilizing propionitrile (C3), butyronitrile (C4), isobutyronitrile (C4), valeronitrile (C5) and capronitrile (C6) as the only growth substrate. Growth on nitriles was biphasic with fast initial hydrolysis of nitriles to the corresponding amides, carboxylic acids and ammonia and slow further utilization of these products resulting in biomass growth. Cells of strain ANL-iso2T grown with iBN were capable of extremely active hydration of a wide range of nitriles into the corresponding amides and much slower hydrolysis of these amides to the corresponding carboxylic acids. This indicated the presence of the nitrile hydratase/amidase pathway of nitrile degradation in the novel bacterium. Strain ANL-iso2T showed obligately alkaliphilic growth on iBN within the pH range 8.4–10.6, with optimum growth at 9.0–9.5. It was moderately salt-tolerant, with a salt range for growth of 0.1–2.0 M Na+ and an optimum salt concentration for growth of 0.2–0.3 M. The dominant fatty acids in the polar lipids were C16 : 0, iso-C14, C14 : 0, iso-C16 and C16 : 1 ω7. The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid. Phylogenetic analysis placed strain ANL-iso2T within the class Actinobacteria as an independent lineage with only uncultured bacteria from soda lakes as its nearest relatives. On the basis of its unique phenotype and distinct phylogeny, strain ANL-iso2T is considered to represent a novel species of a new genus, for which the name Nitriliruptor alkaliphilus gen. nov., sp. nov. is proposed. The type strain of the type species, Nitriliruptor alkaliphilus, is ANL-iso2T (=DSM 45188T=NCCB 100119T=UNIQEM U239T). Phylogenetic data suggest that the novel bacterium forms the basis of a new family Nitriliruptoraceae fam. nov. and a novel order Nitriliruptorales ord. nov. within the class Actinobacteria.
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Streptomyces alni sp. nov., a daidzein-producing endophyte isolated from a root of Alnus nepalensis D. Don
More LessA filamentous actinomycete, designated strain D65T, was isolated from a root of a wild tree, Alnus nepalensis D. Don (Nepalese Alder), collected in Xishuangbanna, China. It produced the bioactive agents daidzein and N-acetyltyramine and had morphological and chemical properties characteristic of streptomycetes. Pink to brownish red diffusible pigments were produced on several ISP media. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain D65T formed a distinct phyletic line that was most closely, albeit loosely, associated with Streptomyces hebeiensis YIM 001T, Streptomyces aurantiogriseus NRRL B-5416T, Streptomyces griseoviridis NBRC 12874T, Streptomyces niveoruber NBRC 15428T and Streptomyces thermovulgaris NBRC 13473. A number of phenotypic properties allowed differentiation of the strain from related Streptomyces species. Therefore strain D65T represents a novel species of the genus Streptomyces, for which the name Streptomyces alni sp. nov. is proposed. The type strain is D65T (=CGMCC 4.3510T=NRRL B-24611T).
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Proposal of Sinomonas flava gen. nov., sp. nov., and description of Sinomonas atrocyanea comb. nov. to accommodate Arthrobacter atrocyaneus
More LessA novel actinomycete strain, designated CW 108T, was isolated from a forest soil in Anhui Province, China. The cells were strictly aerobic, non-motile, bent rods. The strain grew optimally at 30–37 °C and pH 6.0–8.0. Chemotaxonomically, the peptidoglycan type was A3α, the cell-wall sugars contained galactose, mannose and ribose, the polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylmonomethylethanolamine, the major fatty acids were ai-C15 : 0, i-C15 : 0 and ai-C17 : 0 and the predominant respiratory quinone was MK-9(H2), with a moderate amount of MK-8(H2) and a minor amount of MK-6(H2). The G+C content of the genomic DNA was 71.1 mol%. Phylogenetic analysis showed that strain CW 108T formed a deeply separated lineage in the family Micrococcaceae with Arthrobacter atrocyaneus DSM 20127T. The 16S rRNA gene sequence similarity between strain CW 108T and Arthrobacter atrocyaneus DSM 20127T was 99.4 %; sequence similarities between these strains and representatives of other species in the family Micrococcaceae with validly published names were lower than 95.2 %. DNA–DNA hybridization showed a level of relatedness of 52.2 % between the two neighbours. Based on the results of our polyphasic taxonomic study, strain CW 108T and Arthrobacter atrocyaneus DSM 20127T should be assigned to two different species of a novel genus within the family Micrococcaceae, for which the names Sinomonas flava gen. nov., sp. nov. and Sinomonas atrocyanea comb. nov. are proposed. The type strain of Sinomonas flava is CW 108T (=LMG 24447T =KCTC 19388T =CCTCC AB 207194T) and the type strain of Sinomonas atrocyanea is DSM 20127T =JCM 1329T =CGMCC 1.1891T =ATCC 13752T.
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Arthrobacter phenanthrenivorans sp. nov., to accommodate the phenanthrene-degrading bacterium Arthrobacter sp. strain Sphe3
More LessA novel phenanthrene-degrading bacterium, designated strain Sphe3T, was isolated from a creosote-contaminated soil in Greece. Cells were non-motile, Gram-positive, aerobic, and rod- to coccus-shaped. The strain was isolated on the basis of formation of a clear zone on agar plates sprayed with phenanthrene. Optimal growth occurred at 30 °C. The G+C content of the DNA was 65.7 mol%. The polar lipid pattern of strain Sphe3T consisted of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The dominant fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, C16 : 0 and anteiso-C17 : 0, representing >86 % of the total fatty acids. The predominant isoprenoid quinone of strain Sphe3T was menaquinone-8 (MK-8). Based on 16S rRNA gene sequence analysis, strain Sphe3T showed 99 and 98.9 % similarity to the type strains of Arthrobacter oxydans and Arthrobacter polychromogenes, respectively. Strain Sphe3T showed 91 % similarity to homologues of A. oxydans and A. polychromogenes based on recA gene sequence analysis. Based on 16S rRNA and recA gene sequence analysis and DNA–DNA hybridization analysis, as well as physiological and chemotaxonomic characteristics, it is concluded that strain Sphe3T represents a novel species of the genus Arthrobacter, for which the name Arthrobacter phenanthrenivorans sp. nov. is proposed. The type strain is Sphe3T (=DSM 18606T =LMG 23796T).
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Nocardioides sediminis sp. nov., isolated from a sediment sample
More LessA strictly aerobic, motile, short-rod-shaped, Gram-positive-staining actinomycete strain, designated MSL-01T, was isolated from a sediment sample from Bigeum Island of Korea. 16S rRNA gene sequence analysis revealed that the isolate MSL-01T belonged to the genus Nocardioides, with the highest sequence similarity to Nocardioides terrigena DS-17T (98.54 %), but the DNA–DNA relatedness to this type strain was 34 %. The physiological properties of strain MSL-01T differ from those of Nocardioides terrigena DS-17T and other species of Nocardioides. The diamino acid in the cell-wall peptidoglycan of strain MSL-01T is ll-diaminopimelic acid, the major menaquinone is MK-8(H4) and iso-C16 : 0 is the major fatty acid component. The name Nocardioides sediminis sp. nov. is proposed for the novel species, with the type strain MSL-01T (=DSM 19263T =KCTC 19271T).
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Polycyclic aromatic hydrocarbon-degrading species isolated from Hawaiian soils: Mycobacterium crocinum sp. nov., Mycobacterium pallens sp. nov., Mycobacterium rutilum sp. nov., Mycobacterium rufum sp. nov. and Mycobacterium aromaticivorans sp. nov.
More LessPolycyclic aromatic hydrocarbons (PAHs) are widespread environmental contaminants. In this study, both pristine and contaminated soils were sampled as a source of PAH-degrading organisms. Nine strains isolated from these soils were identified as rapidly growing members of the genus Mycobacterium through basic phenotypic characteristics and through sequence similarity of three genes. Because the sequence similarity of the 16S rRNA gene is relatively high among members of this genus, additional conserved genes encoding the β subunit of RNA polymerase (rpoB) and a heat-shock protein (hsp65) were sequenced. Several analyses were completed to differentiate the strains from one another and to determine their species-level taxonomy, including fatty acid methyl ester analysis, biochemical tests and substrate-utilization profiling. A phylogenetic tree incorporating sequences for all three genes was constructed with the isolates and their close described relatives. Results for biochemical tests, substrate-utilization tests and DNA sequencing were compared with those of the phylogenetically similar organisms to establish the isolated strains as representatives of novel species with characteristics unlike those of previously described species of Mycobacterium. Finally, DNA–DNA hybridization was performed between strains and their close relatives to confirm their position within novel species. Our results demonstrated that the isolates represent five novel species, which were named Mycobacterium crocinum sp. nov. (type strain czh-42T =ATCC BAA-1373T =CIP 109262T; reference strains czh-1A =ATCC BAA-1370 =CIP 109266 and czh-3 =ATCC BAA-1371=CIP 109267), Mycobacterium pallens sp. nov. (type strain czh-8T =ATCC BAA-1372T =CIP 109268T), Mycobacterium rutilum sp. nov. (type strain czh-117T =ATCC BAA-1375T =CIP 109271T; reference strains czh-107 =ATCC BAA-1374 =CIP 109270 and czh-132 =ATCC BAA-1376 =CIP 109272), Mycobacterium rufum sp. nov. (type strain JS14T =ATCC BAA-1377T =CIP 109273T) and Mycobacterium aromaticivorans sp. nov. (type strain JS19b1T =ATCC BAA-1378T =CIP 109274T).
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Nocardia jinanensis sp. nov., an amicoumacin B-producing actinomycete
More LessA novel actinomycete, strain 04-5195T, that produces amicoumacin B, which targets bone morphogenetic protein-2, was isolated from a soil sample collected in Jinan, Shandong Province, China. Strain 04-5195T had morphological, biochemical, physiological and chemotaxonomic properties that were consistent with its classification in the genus Nocardia and it formed a phyletic line in the Nocardia 16S rRNA gene tree. It was evident from the phylogenetic data that strain 04-5195T was most closely associated with Nocardia speluncae N2-11T. However, the two organisms were distinguishable from one another using DNA–DNA relatedness and phenotypic data. The isolate was readily differentiated from other related Nocardia strains by a set of phenotypic properties and by its phylogenetic position. Therefore, it is proposed that the isolate represents a novel species in the genus Nocardia, Nocardia jinanensis sp. nov.; the type strain is 04-5195T (=CGMCC 4.3508T =DSM 45048T).
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- Bacteroidetes
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Leptobacterium flavescens gen. nov., sp. nov., a marine member of the family Flavobacteriaceae, isolated from marine sponge and seawater
Six obligately aerobic, Gram-negative, non-motile, pale-yellow-pigmented, rod-shaped bacterial strains, designated YM3-301T, HG868, 04PA2 Co4-8B, 04PA2 Co4-99A, 04PA2 018SW-3 and 04PA2 018SW-18, were isolated from a marine sponge and seawater and were subjected to a polyphasic taxonomic investigation. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the novel isolates were affiliated with the family Flavobacteriaceae (phylum Bacteroidetes) and that they showed the highest sequence similarity (90.3–90.9 %) to members of the genus Leeuwenhoekiella and to Zhouia amylotica. The 16S rRNA gene sequence similarities with respect to members of other related genera were only 86.3–89.1 %. In contrast, the six isolates shared high levels of 16S rRNA gene sequence similarity (99.7–100 %) and DNA-DNA relatedness (72–94 %) with each other. The novel isolates were phenotypically and physiologically different from members of related genera. The G+C content of the DNA was 41.8–43.5 mol%, MK-6 was the major menaquinone and i15 : 0, i15 : 1 and i17 : 0 3-OH were the major fatty acids. On the basis of the data from the taxonomic studies, it was concluded that these six novel strains represent a novel genus and species of the family Flavobacteriaceae, for which the name Leptobacterium flavescens gen. nov., sp. nov. is proposed. The type strain of Leptobacterium flavescens is YM3-301T (=KCTC 22160T=MBIC 06275T=NBRC 104141T).
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Prevotella falsenii sp. nov., a Prevotella intermedia-like organism isolated from monkey dental plaque
Eight anaerobic, pigmented, non-spore-forming, Gram-negative, rod-shaped strains isolated from monkey oral cavities were characterized phenotypically and chemotaxonomically and their phylogenetic positions were determined using 16S rRNA gene sequence analysis. The 16S rRNA gene sequence analysis showed that these isolates represent a single species of the genus Prevotella. These strains were most closely related to Prevotella intermedia ATCC 25611T, with 95.0 % 16S rRNA gene sequence similarity. The next most closely related species were Prevotella pallens and Prevotella nigrescens (92.7 and 92.1 % similarity to the respective type strains). The phenotypic and biochemical characteristics of the isolates were the same as those of P. intermedia JCM 12248T and P. nigrescens JCM 12250T. The isolates could be differentiated from P. pallens JCM 11140T on the basis of mannose fermentation and α-fucosidase activity. The isolates could not be distinguished from P. intermedia or P. nigrescens using conventional biochemical tests. DNA–DNA hybridization experiments revealed the genomic distinctiveness of these eight strains with respect to P. pallens JCM 11140T, P. intermedia JCM 12248T and P. nigrescens JCM 12250T. On the basis of these data, strains 04013, 04021, 04043, 04052T, 0406, 04113, 04111 and 04161 represent a novel Prevotella species, for which the name Prevotella falsenii sp. nov. is proposed. The type strain is 04052T (=JCM 15124T =CCUG 56137T).
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Spirosoma panaciterrae sp. nov., isolated from soil
More LessA Gram-negative, yellowish bacterial strain, designated Gsoil 1519T, was isolated from soil of a ginseng field in Pocheon province (South Korea) and characterized using a polyphasic approach to determine its taxonomic position. Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 1519T belongs to the family ‘Flexibacteraceae’ and is related to Spirosoma rigui KCTC 12531T (91.8 % similarity) and Spirosoma linguale LMG 10896T (91.5 % similarity). Phylogenetic distances from any other recognized species within the family ‘Flexibacteraceae’ were greater than 14.7 %. The G+C content of the genomic DNA of strain Gsoil 1519T was 50.1 %. The detection of MK-7 as the predominant menaquinone and a fatty acid profile with C16 : 1 ω5c, summed feature 4 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0 and C16 : 0 as the major acids supported the affiliation of strain Gsoil 1519T to the genus Spirosoma. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 1519T should be classified in the genus Spirosoma as a representative of a novel species, for which the name Spirosoma panaciterrae sp. nov. is proposed. The type strain is Gsoil 1519T (=KCTC 22263T=DSM 21099T).
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Arcicella rosea sp. nov., isolated from tap water
More LessStrain TW5T, a motile, Gram-negative bacterium that produced pale-pink colonies, was isolated from tap water on R2A agar at 20 °C. 16S rRNA gene sequence studies showed that the strain clustered with Arcicella aquatica (99.0 % sequence similarity to the type strain). The main polyamine present was spermidine, the quinone system comprised menaquinone MK-7 and the polar lipid profile consisted of a mixture of aminophospholipids, aminolipids, glycolipids and uncharacterized polar lipids. The fatty acid profile was slightly different from that reported for A. aquatica. The results of DNA–DNA hybridizations and physiological and biochemical tests clearly allowed both genotypic and phenotypic differentiation of the isolate from A. aquatica. On the basis of these results, it is proposed that the strain should be classified within a novel species of the genus Arcicella. The name proposed for this taxon is Arcicella rosea sp. nov.; the type strain is TW5T (=CCUG 55942T =CCM 7523T).
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Pedobacter composti sp. nov., isolated from compost
More LessA Gram-negative, aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated TR6-06T, was isolated from a compost sample in South Korea and characterized taxonomically by using a polyphasic approach. The organism grew optimally at 30 °C and pH 6.5–7.0. The isolate was positive for catalase and oxidase tests, but negative for gelatinase and urease and for indole and H2S production. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain TR6-06T was most closely affiliated with members of the genus Pedobacter of the family Sphingobacteriaceae. Strain TR6-06T exhibited 16S rRNA gene sequence similarity values of 89.9–93.5 % to the type strains of species of the genus Pedobacter. The G+C content of the genomic DNA of strain TR6-06T was 41.9 mol%. The predominant respiratory quinone was MK-7. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1 ω7c and anteiso-C15 : 0. These chemotaxonomic data support the affiliation of strain TR6-06T to the genus Pedobacter. However, on the basis of its phenotypic properties and phylogenetic distinctiveness, strain TR6-06T (=KCTC 12638T=LMG 23490T) should be classified as the type strain of a novel species, for which the name Pedobacter composti sp. nov. is proposed.
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- Firmicutes And Related Organisms
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Carboxydothermus siderophilus sp. nov., a thermophilic, hydrogenogenic, carboxydotrophic, dissimilatory Fe(III)-reducing bacterium from a Kamchatka hot spring
A novel anaerobic, thermophilic, Fe(III)-reducing, CO-utilizing bacterium, strain 1315T, was isolated from a hot spring of Geyser Valley on the Kamchatka Peninsula. Cells of the new isolate were Gram-positive, short rods. Growth was observed at 52–70 °C, with an optimum at 65 °C, and at pH 5.5–8.5, with an optimum at pH 6.5–7.2. In the presence of Fe(III) or 9,10-anthraquinone 2,6-disulfonate (AQDS), the bacterium was capable of growth with CO and yeast extract (0.2 g l−1); during growth under these conditions, strain 1315T produced H2 and CO2 and Fe(II) or AQDSH2, respectively. Strain 1315T also grew by oxidation of yeast extract, glucose, xylose or lactate under a N2 atmosphere, reducing Fe(III) or AQDS. Yeast extract (0.2 g l−1) was required for growth. Isolate 1315T grew exclusively with Fe(III) or AQDS as an electron acceptor. The generation time under optimal conditions with CO as growth substrate was 9.3 h. The G+C content of the DNA was 41.5±0.5 mol%. 16S rRNA gene sequence analysis placed the organism in the genus Carboxydothermus (97.8 % similarity with the closest relative). On the basis of physiological features and phylogenetic analysis, it is proposed that strain 1315T should be assigned to a novel species, Carboxydothermus siderophilus sp. nov., with the type strain 1315T (=VKPM 9905BT =VKM B-2474T =DSM 21278T).
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Hydrogenoanaerobacterium saccharovorans gen. nov., sp. nov., isolated from H2-producing UASB granules
Lei Song and Xiuzhu DongTwo strictly anaerobic bacterial strains, designated SW512T and W72, were isolated from a laboratory-scale H2-producing up-flow anaerobic sludge blanket (UASB) reactor. Cells were Gram-stain-negative, non-motile and 0.3–0.4×2.0–14.5 μm; they did not form spores. Both strains grew at 24–45 °C (no growth at ≤22 °C or ≥46 °C), with optimum growth at 37 °C. The pH range for growth was 4.5–9.0 (no growth at pH≤4.2 or pH≥9.3), with optimum growth at pH 6.5–7.0. Several kinds of mono-, di- and oligosaccharides supported growth. The main end products of glucose fermentation were ethanol, acetate, hydrogen and carbon dioxide (according to the equation 1 mol glucose→1.1 mol acetate+0.6 mol ethanol+2.6 mol H2+1.6 mol CO2). The DNA G+C contents of strains SW512T and W72 were 41.9±0.5 and 42.8±0.4 mol% (T m method), respectively. Phylogenetic analysis based on 16S rRNA gene sequence similarities indicated that the two strains represent a new phyletic sublineage within the family ‘Ruminococcaceae’, with <91.3 % 16S rRNA gene sequence similarity to recognized species. On the basis of the polyphasic evidence in this study, it is proposed that the two strains represent a novel species in a new genus, for which the name Hydrogenoanaerobacterium saccharovorans gen. nov., sp. nov. is proposed; the type strain of the type species is SW512T (=AS 1.5070T=JCM 14861T).
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- Other Bacteria
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Zavarzinella formosa gen. nov., sp. nov., a novel stalked, Gemmata-like planctomycete from a Siberian peat bog
An aerobic, pink-pigmented, budding and rosette-forming bacterium was isolated from an acidic Sphagnum peat bog and designated strain A10T. The 16S rRNA gene sequence analysis showed that strain A10T was a member of the order Planctomycetales and belonged to a phylogenetic lineage defined by the genus Gemmata, with 90 % sequence similarity to that of Gemmata obscuriglobus, the only taxonomically described organism of this group. Ellipsoid-shaped cells of strain A10T were uniformly covered with crateriform pits and possessed long (up to 10–15 μm) and unusually thick (0.5–0.7 μm) stalks of a unique ultrastructure. Thin sections revealed a complex intracellular membrane system compartmentalizing the cells. Strain A10T was a moderately acidophilic, mesophilic organism capable of growth at pH values between 3.8 and 7.2 (with an optimum at pH 5.5–6.0) and at temperatures between 10 and 30 °C (with an optimum at 20–25 °C). The major fatty acids were C18 : 0, C18 : 1 ω5c and C16 : 1 ω5c and the major quinone was MK-6. Cells of strain A10T contained high amounts of bound saturated and monounsaturated C26–C32 (ω-1) hydroxy fatty acids. The G+C content of the DNA was 62.5 mol%. The unique cell morphology, the capability of growth in acidic conditions and a number of chemotaxonomic and genotypic characteristics served to differentiate strain A10T from G. obscuriglobus. Based on these data, the novel isolate should be considered as representing a novel genus and species of planctomycetes, for which the name Zavarzinella formosa gen. nov., sp. nov. is proposed The type strain is A10T (=DSM 19928T=VKM B-2478T).
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Deinococcus mumbaiensis Shashidhar and Bandekar 2006 is a later heterotypic synonym of Deinococcus ficus Lai et al. 2006
More LessDeinococcus mumbaiensis DSM 17424T was compared with Deinococcus ficus CC-FR2-10T to clarify the taxonomic relationship between the two species. 16S rRNA gene sequence comparisons demonstrated that these strains share 99.5 % sequence similarity. Investigation of fatty acid patterns and substrate utilization profiles displayed no striking differences between the type strains of the two species. DNA–DNA hybridizations between the two strains showed 75.4 % (76.6 %) relatedness. Therefore, the reclassification of Deinococcus mumbaiensis as a later heterotypic synonym of Deinococcus ficus is proposed, based upon the estimated phylogenetic position derived from 16S rRNA gene sequence data, fatty acid and biochemical data and DNA–DNA hybridization results.
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- Proteobacteria
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Diaphorobacter oryzae sp. nov., isolated from a thiosulfate-oxidizing enrichment culture
More LessA taxonomic study was performed on two isolates, strains RF3T and RF21, recovered from a thiosulfate-oxidizing enrichment culture. Comparative 16S rRNA gene sequence analysis showed that these isolates were clearly affiliated with the class Betaproteobacteria. Strains RF3T and RF21 were most closely related to Diaphorobacter nitroreducens NA10BT (97.9 and 98.2 % 16S rRNA gene sequence similarity, respectively). The level of 16S rRNA gene sequence similarity between strains RF3T and RF21 was 99.8 %. The two isolates were Gram-negative, aerobic and denitrifying. Growth was observed at 7–35 °C. Physiological and biochemical properties of strains RF3T and RF21 were different from those of D. nitroreducens NA10BT in that strains RF3T and RF21 were able to utilize l-histidine, 2-ketogluconate and caprate, but unable to utilize suberate. The G+C contents of the genomic DNA of strains RF3T and RF21 were 62.9 and 62.8 mol%, respectively, and the predominant quinone was ubiquinone-8. Strains RF3T and RF21 possessed C16 : 0, C17 : 0 cyclo, and C16 : 1 ω7c and/or iso-C15 : 0 2-OH as major fatty acids. DNA–DNA relatedness data indicated that strains RF3T and RF21 represent a genomic species separate from D. nitroreducens. On the basis of the evidence presented from this polyphasic analysis, it is suggested that strains RF3T and RF21 represent a novel species of the genus Diaphorobacter, for which the name Diaphorobacter oryzae sp. nov. is proposed. The type strain is RF3T (=KCTC 22225T=LMG 24467T).
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Desulfovibrio paquesii sp. nov., a hydrogenotrophic sulfate-reducing bacterium isolated from a synthesis-gas-fed bioreactor treating zinc- and sulfate-rich wastewater
A hydrogenotrophic, sulfate-reducing bacterium, designated strain SB1T, was isolated from sulfidogenic sludge of a full-scale synthesis-gas-fed bioreactor used to remediate wastewater from a zinc smelter. Strain SB1T was found to be an abundant micro-organism in the sludge at the time of isolation. Hydrogen, formate, pyruvate, lactate, malate, fumarate, succinate, ethanol and glycerol served as electron donors for sulfate reduction. Organic substrates were incompletely oxidized to acetate. 16S rRNA gene sequence analysis showed that the closest recognized relative to strain SB1T was Desulfovibrio gigas DSM 1382T (97.5 % similarity). The G+C content of the genomic DNA of strain SB1T was 62.2 mol%, comparable with that of Desulfovibrio gigas DSM 1382T (60.2 mol%). However, the level of DNA–DNA relatedness between strain SB1T and Desulfovibrio gigas DSM 1382T was only 56.0 %, indicating that the two strains are not related at the species level. Strain SB1T could also be differentiated from Desulfovibrio gigas based on phenotypic characteristics, such as major cellular fatty acid composition (anteiso-C15 : 0, iso-C14 : 0 and C18 : 1 cis 9) and substrate utilization. Strain SB1T is therefore considered to represent a novel species of the genus Desulfovibrio, for which the name Desulfovibrio paquesii sp. nov. is proposed. The type strain is SB1T (=DSM 16681T=JCM 14635T).
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Filomicrobium insigne sp. nov., isolated from an oil-polluted saline soil
More LessStrain SLG5B-19T, isolated from an oil-polluted saline soil in Gudao in the coastal Shengli Oilfield, eastern China, was Gram-negative with monoprosthecae or bipolar prosthecae and buds on the prosthecal tips. Growth occurred at NaCl concentrations between 0 and 7 % (w/v), at temperatures between 4 and 45 °C, and at pH 6.0–9.0. Strain SLG5B-19T had Q-9 as the major respiratory quinone and unsaturated C18 : 1 ω7c as the predominant cellular fatty acid. The G+C content of the genomic DNA was 59.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SLG5B-19T belonged to a clade with the genera Filomicrobium and Hyphomicrobium in the class Alphaproteobacteria. However, 16S rRNA gene sequence similarities of strain SLG5B-19T to the phylogenetically most closely related strains, i.e. the type strains of Filomicrobium fusiforme and Hyphomicrobium zavarzinii, were 95.8 and 94.5 %, respectively. In addition, the 16S rRNA gene sequence of strain SLG5B-19T had 24 signature nucleotides that were identical to those of the type strain of F. fusiforme. Based on phylogenetic analysis of 16S rRNA gene sequences, strain SLG5B-19T could be allocated to the genus Filomicrobium. However, distinct phenotypic differences were observed between strain SLG5B-19T and the type strain of F. fusiforme. It is therefore proposed that strain SLG5B-19T represents a novel species in the genus Filomicrobium, Filomicrobium insigne sp. nov. The type strain is SLG5B-19T (=CGMCC 1.6497T=LMG 23927T).
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Polyphasic characterization of xanthomonads pathogenic to members of the Anacardiaceae and their relatedness to species of Xanthomonas
We have used amplified fragment length polymorphism (AFLP), multilocus sequence analysis (MLSA) and DNA–DNA hybridization for genotypic classification of Xanthomonas pathovars associated with the plant family Anacardiaceae. AFLP and MLSA results showed congruent phylogenetic relationships of the pathovar mangiferaeindicae (responsible for mango bacterial canker) with strains of Xanthomonas axonopodis subgroup 9.5. This subgroup includes X. axonopodis pv. citri (synonym Xanthomonas citri). Similarly, the pathovar anacardii, which causes cashew bacterial spot in Brazil, was included in X. axonopodis subgroup 9.6 (synonym Xanthomonas fuscans). Based on the thermal stability of DNA reassociation, consistent with the AFLP and MLSA data, the two pathovars share a level of similarity consistent with their being members of the same species. The recent proposal to elevate X. axonopodis pv. citri to species level as X. citri is supported by our data. Therefore, the causal agents of mango bacterial canker and cashew bacterial spot should be classified as pathovars of X. citri, namely X. citri pv. mangiferaeindicae (pathotype strain CFBP 1716) and X. citri pv. anacardii (pathotype strain CFBP 2913), respectively. Xanthomonas fuscans should be considered to be a later heterotypic synonym of Xanthomonas citri.
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Novosphingobium acidiphilum sp. nov., an acidophilic salt-sensitive bacterium isolated from the humic acid-rich Lake Grosse Fuchskuhle
More LessA yellow- to orange-pigmented, Gram-negative, rod-shaped, motile and non-spore-forming bacterium, strain FSW06-204dT, was isolated from subsurface water of the acidic bog lake, Lake Grosse Fuchskuhle (Brandenburg, Germany). Optimum growth of this strain occurred over a pH range from 5.5 to 6.0 and the growth rate strongly decreased at pH values above 6.5. In addition, the strain exhibited a low tolerance towards NaCl and grew only at a NaCl concentration of up to 0.5 %. 16S rRNA gene sequence analysis of strain FSW06-204dT showed the highest sequence similarity to Novosphingobium hassiacum W-51T (96.7 %) and formed a distinct cluster with Novosphingobium nitrogenifigens DSM 19370T (96.4 %) within the genus Novosphingobium. Strain FSW06-204dT shared a 21 bp signature gap with the latter species, a feature that is absent in all other members of the family Sphingomonadaceae. DNA–DNA hybridization of strain FSW06-204dT and N. nitrogenifigens DSM 19370T showed a low relatedness value of 24 % (reciprocal: 39 %). The major respiratory quinone was ubiquinone Q-10 (91 %) and the predominant fatty acid was C18 : 1 ω7c (43.3 %). Two characteristic 2-hydroxy fatty acids, C14 : 0 2-OH (8.1 %) and C15 : 0 2-OH (6.5 %), were abundant. Polar lipids consisted mainly of phosphatidyldimethylethanolamine and phosphatidylethanolamine; however, only moderate amounts of sphingoglycolipids were present and phosphatidylcholine was lacking. Characterization by 16S rRNA gene sequence, physiological features, pigment analysis and polyamine, ubiquinone, polar lipid and fatty acid contents revealed that strain FSW06-204dT represents a novel species of the genus Novosphingobium within the class Alphaproteobacteria. The name Novosphingobium acidiphilum sp. nov. is proposed for this acidophilic and salt-sensitive species with the type strain FSW06-204dT (=DSM 19966T=CCM 7496T=CCUG 55538T).
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Shewanella vesiculosa sp. nov., a psychrotolerant bacterium isolated from an Antarctic coastal area
More LessTwo strains of psychrotolerant bacteria, designated M7T and M5, isolated from Antarctic coastal marine environments were studied to determine their taxonomic position. The organisms comprised Gram-negative, rod-shaped, facultatively anaerobic cells that were motile by means of single polar flagella. Neither of the bacterial isolates had a requirement for Na+. These two psychrotolerant strains grew at temperatures ranging from −4 to 30 °C. Both strains were capable of producing H2S from thiosulfate and were able to use sodium nitrate and trimethylamine N-oxide as terminal electron acceptors during anaerobic growth. 16S rRNA gene sequence analysis placed M7T and M5 within the genus Shewanella; the strains showed the highest similarity (99.9 and 99.2 % respectively) with respect to the type strains of Shewanella livingstonensis and Shewanella frigidimarina. However the levels of gyrB sequence similarity between strain M7T and the type strains of S. livingstonensis and S. frigidimarina were 87.6 and 87.4 %, respectively. DNA–DNA hybridization experiments performed between the Antarctic isolate M7T and S. livingstonensis LMG 19866T and S. frigidimarina LMG 19475T revealed levels of relatedness of 32 and 35 %, respectively. Strain M5 showed 100 % DNA relatedness with respect to strain M7T. The DNA G+C content of these bacteria was 42 mol%. Several phenotypic characteristics, the cellular fatty acid compositions and the quinone content of strains M7T and M5 served to differentiate them from related shewanellae. On the basis of the data from this polyphasic taxonomic study, M7T and M5 constitute a single genospecies. They represent a novel species of the genus Shewanella, for which the name Shewanella vesiculosa sp. nov. is proposed. The type strain is M7T (=LMG 24424T =CECT 7339T).
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Kiloniella laminariae gen. nov., sp. nov., an alphaproteobacterium from the marine macroalga Laminaria saccharina
More LessA novel alphaproteobacterium, strain LD81T, was isolated from the marine macroalga Laminaria saccharina. The bacterium is mesophilic and shows a typical marine growth response. It is a chemoheterotrophic aerobe with the potential for denitrification. Growth optima are 25 °C, pH 5.5 and 3 % NaCl. Strain LD81T has a unique phylogenetic position, not fitting any of the known families of the Alphaproteobacteria. The 16S rRNA gene sequence revealed a distant relationship to species of several orders of the Alphaproteobacteria, with less than 90 % sequence similarity. Phylogenetically, strain LD81T is related to the type strains of Terasakiella pusilla (88.4 % 16S rRNA gene sequence similarity) and the three Thalassospira species (88.9–89.2 %). It forms a cluster with these bacteria and a novel as-yet undescribed isolate (KOPRI 13522; 96.6 % sequence similarity). Strain LD81T has a relatively low DNA G+C content (51.1 mol%) and, due to its distant phylogenetic position from all other alphaproteobacteria, strain LD81T (=NCIMB 14374T =JCM 14845T) is considered as the type strain of a novel species within a new genus, for which the name Kiloniella laminariae gen. nov., sp. nov. is proposed. The genus Kiloniella represents the type of the new family Kiloniellaceae fam. nov. and order Kiloniellales ord. nov.
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Rhizobium alamii sp. nov., an exopolysaccharide-producing species isolated from legume and non-legume rhizospheres
A group of exopolysaccharide-producing bacteria was isolated from the root environment of Arabidopsis thaliana. The genetic diversity revealed by REP-PCR fingerprinting indicated that the isolates correspond to different strains. 16S rRNA gene sequence analysis showed that the isolates are closely related to the strains Rhizobium sp. YAS34 and USDA 1920, respectively isolated from sunflower roots and Medicago ruthenica nodules. These bacteria belong to the Rhizobium lineage of the Alphaproteobacteria, and the closest known species was Rhizobium sullae. DNA–DNA hybridization experiments and biochemical analysis demonstrated that the nine strains isolated from A. thaliana and Rhizobium strains YAS34 and USDA 1920 constitute a novel species within the genus Rhizobium, for which the name Rhizobium alamii sp. nov. is proposed. The type strain is GBV016T (=CFBP 7146T =LMG 24466T).
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Bermanella marisrubri gen. nov., sp. nov., a genome-sequenced gammaproteobacterium from the Red Sea
A novel heterotrophic, marine, strictly aerobic, motile bacterium was isolated from the Red Sea at a depth of 1 m. Analysis of its 16S rRNA gene sequence, retrieved from the whole-genome sequence, showed that this bacterium was most closely related to the genera Oleispira, Oceanobacter and Thalassolituus, each of which contains a single species, within the class Gammaproteobacteria. Phenotypic, genotypic and phylogenetic analyses supported the creation of a novel genus and species to accommodate this bacterium, for which the name Bermanella marisrubri gen. nov., sp. nov. is proposed. The type strain of Bermanella marisrubri is RED65T (=CECT 7074T =CCUG 52064T).
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Tropicimonas isoalkanivorans gen. nov., sp. nov., a branched-alkane-degrading bacterium isolated from Semarang Port in Indonesia
More LessAn aerobic, Gram-negative, motile bacterium, strain B51T, was isolated from seawater obtained from Semarang Port in Indonesia. Cells of strain B51T were peritrichously flagellated and rod-shaped. Strain B51T was able to degrade alkanes, branched alkanes and alkylnaphthalenes. 16S rRNA gene sequence analysis revealed that strain B51T was affiliated with the family Rhodobacteraceae, and was related most closely to Thioclava pacifica TL 2T (94.6 % similarity). The DNA G+C content of strain B51T was 66.5 mol%. The major cellular fatty acids were C18 : 1 ω7c (84.9 %), C18 : 1 ω9c (13.8 %), C16 : 0 (8.7 %), C18 : 0 (6.4 %) and anteiso-C15 : 0 (5.8 %) and the major quinone was ubiquinone-10. Based on its phenotypic and phylogenetic characteristics, strain B51T is considered to represent a novel species of a new genus, for which the name Tropicimonas isoalcanivorans gen. nov., sp. nov. is proposed. The type strain of the type species is B51T (=JCM 14837T=DSM 19548T).
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Tropicibacter naphthalenivorans gen. nov., sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from Semarang Port in Indonesia
More LessAn aerobic, Gram-negative, motile bacterium, strain C02T, was isolated from seawater obtained from Semarang Port in Indonesia. Cells of strain C02T were peritrichously flagellated and rod-shaped. Strain C02T was able to degrade naphthalene, alkylnaphthalenes and phenanthrene. 16S rRNA gene sequence analysis revealed that this strain was affiliated with the family Rhodobacteraceae in the class Alphaproteobacteria and was related most closely to Marinovum algicola FF3T (95.7 % similarity) and Thalassobius aestuarii JC2049T (95.2 %). The DNA G+C content of strain C02T was 64.6 mol%. The major cellular fatty acids were C18 : 1 ω7c (50.9 % of the total), C16 : 0 (17.9 %), 11 methyl C18 : 1 ω7c (14.7 %), C18 : 1 ω9c (2.9 %) and C19 : 0 cyclo ω8c (2.4 %), and the predominant respiratory lipoquinone was ubiquinone-10. Based on physiological, chemotaxonomic and phylogenetic data, strain C02T is suggested to represent a novel species of a new genus, for which the name Tropicibacter naphthalenivorans gen. nov., sp. nov. is proposed. The type strain of Tropicibacter naphthalenivorans is C02T (=JCM 14838T=DSM 19561T).
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Description of Kushneria aurantia gen. nov., sp. nov., a novel member of the family Halomonadaceae, and a proposal for reclassification of Halomonas marisflavi as Kushneria marisflavi comb. nov., of Halomonas indalinina as Kushneria indalinina comb. nov. and of Halomonas avicenniae as Kushneria avicenniae comb. nov.
An aerobic, moderately halophilic, Gram-negative, motile, non-sporulating rod-shaped bacterium, designated strain A10T, was isolated from the surface of leaves of the black mangrove Avicennia germinans and was subjected to a polyphasic taxonomic study. Strain A10T was able to grow at NaCl concentrations in the range 5–17.5 % (w/v) with optimum growth at 10 % (w/v) NaCl. Growth occurred at temperatures of 20–40 °C (optimal growth at 37 °C) and pH 5.5–8.5 (optimal growth at pH 7.0–8.0). The major respiratory quinone was ubiquinone 9. The major fatty acids were C16 : 0, C18 : 1 ω7c, C19 : 0 cyclo ω8c and C12 : 0 3-OH. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, and unidentified phospholipids, glycolipids and an aminoglycolipid. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain A10T is closely related to Halomonas avicenniae MW2aT (95.7 % sequence similarity), Halomonas marisflavi SW32T (95.2 %) and Halomonas indalinina GC2.1T (95.0 %). Strain A10T formed a coherent phylogenetic branch with these three species, separated from other species of Halomonas and closely related genera (with 16S rRNA gene sequence similarities below 94.0 %). A complete 23S rRNA gene sequence comparison of strain A10T with closely related species confirmed the phylogenetic position of the novel isolate, forming a branch with the species Halomonas avicenniae, Halomonas indalinina and Halomonas marisflavi, separated from other species of the genera belonging to the family Halomonadaceae (showing sequence similarities below 91.7 %). DNA–DNA hybridization studies between strain A10T and Halomonas avicenniae MW2aT, Halomonas marisflavi DSM 15357T and Halomonas indalinina CG2.1T were 21, 17 and 10 %, respectively. These levels of DNA–DNA relatedness were low enough to classify strain A10T as representing a genotypically distinct species. Overall, the phenotypic, genotypic, chemotaxonomic and phylogenetic results demonstrated that strain A10T represents a new genus and species. The name Kushneria aurantia gen. nov., sp. nov. is proposed, with strain A10T (=CCM 7415T=CECT 7220T) as the type strain. This is the type species of the new proposed genus, which belongs to the family Halomonadaceae. In addition, our data support the placement of the species Halomonas marisflavi, Halomonas indalinina and Halomonas avicenniae within this new genus, as Kushneria marisflavi comb. nov., Kushneria indalinina comb. nov. and Kushneria avicenniae comb. nov., respectively.
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Rubellimicrobium aerolatum sp. nov., isolated from an air sample in Korea
A pink-coloured bacterial strain, designated 5715S-9T, was isolated from an air sample collected in Suwon, Republic of Korea. The cells were strictly aerobic, Gram-negative, non-spore-forming, non-flagellated and short-rod-shaped. On the basis of 16S rRNA gene sequence analysis, the organism was a member of the genus Rubellimicrobium, showing the highest sequence similarities with Rubellimicrobium mesophilum MSL-20T (96.2 % sequence similarity) and Rubellimicrobium thermophilum DSM 16684T (93.9 %). The major polar lipids were phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine and an unidentified glycolipid. The major fatty acids (>10 %) were C18 : 1 ω7c, C16 : 0 and 11-methyl C18 : 1 ω7c. The G+C content of the DNA was 69 mol%. On the basis of both phylogenetic and phenotypic evidence, strain 5715S-9T represents a novel species of the genus Rubellimicrobium, for which the name Rubellimicrobium aerolatum sp. nov. is proposed. The type strain is 5715S-9T (=KACC 12504T=DSM 19297T).
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Paramoritella alkaliphila gen. nov., sp. nov., a member of the family Moritellaceae isolated in the Republic of Palau
More LessTwo strains of marine, heterotrophic, alkaliphilic bacteria, designated A3F-7T and ssthio04PA2-7c, were isolated from hard coral and marine sand, respectively, collected in the Republic of Palau. A phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates were related to members of the genus Moritella. However, the sequence similarities between the isolates and the type strains of the Moritella species were less than 93 %. The G+C contents of the isolates were around 57 mol%, the major respiratory quinone was Q-8 and the predominant cellular fatty acids were 16 : 1ω7c, 16 : 0, 18 : 1ω7c and 14 : 0. On the basis of the phylogenetic data, phenotypic characteristics and DNA–DNA hybridization results, strains A3F-7T and ssthio04PA2-7c represent a novel species of a novel genus, for which the name Paramoritella alkaliphila gen. nov., sp. nov. is proposed. The type strain of Paramoritella alkaliphila is A3F-7T (=MBIC06429T =DSM 19956T).
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Alishewanella aestuarii sp. nov., isolated from tidal flat sediment, and emended description of the genus Alishewanella
More LessA Gram-negative strain, B11T, was isolated from tidal flat sediment in Yeosu, Republic of Korea. Strain B11T did not require NaCl for growth and grew between 18 and 44 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B11T was associated with the genus Alishewanella and was closely related to the type strain of Alishewanella fetalis (98.3 % similarity). Within the phylogenetic tree, the novel isolate shared a branching point with A. fetalis. Analysis of 16S rRNA gene sequences and DNA–DNA relatedness, as well as physiological and biochemical tests, indicated genotypic and phenotypic differences between strain B11T and the type strain of A. fetalis. Thus, strain B11T is proposed as a representative of a novel species, Alishewanella aestuarii sp. nov.; the type strain is B11T (=KCTC 22051T =DSM 19476T).
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- Eukaryotic Micro-Organisms
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Synonymy of the yeast genera Moniliella and Trichosporonoides and proposal of Moniliella fonsecae sp. nov. and five new species combinations
Analyses of nucleotide sequences from the D1/D2 domains of the large-subunit rDNA and phenotypic characteristics showed that the genera Moniliella and Trichosporonoides are members of a single, monophyletic clade that would be best represented by a single anamorphic genus. On the basis of taxonomic priority, we propose the transfer of the five species of the genus Trichosporonoides to the genus Moniliella. The description of the genus Moniliella is emended and the following new combinations are proposed: Moniliella madida comb. nov., Moniliella megachiliensis comb. nov., Moniliella nigrescens comb. nov., Moniliella oedocephalis comb. nov. and Moniliella spathulata comb. nov. In addition, ten strains representing a novel yeast species belonging to the Moniliella clade were isolated from flowers in Thailand, Cuba and Brazil. Analysis of the internal transcribed spacer and D1/D2 large-subunit rDNA sequences indicated that the isolates represent a single species that was distinct from other species of the Moniliella clade. The name Moniliella fonsecae sp. nov. is proposed to accommodate these strains. The type strain is BCC 7726T (=CBS 10551T).
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Caryotricha minuta (Xu et al., 2008) nov. comb., a unique marine ciliate (Protista, Ciliophora, Spirotrichea), with phylogenetic analysis of the ambiguous genus Caryotricha inferred from the small-subunit rRNA gene sequence
More LessA population of Kiitricha minuta Xu et al., 2008 , a small kiitrichid ciliate, was isolated from a brackish water sample in Jiaozhou Bay, Qingdao, northern China. After comparison of its morphology and infraciliature, it is believed that this morphotype should be assigned to the genus Caryotricha; hence, a new combination is suggested, Caryotricha minuta ( Xu et al., 2008 ) nov. comb. The small-subunit (SSU) rRNA gene sequence was determined in order to elucidate the phylogenetic position of this poorly known, ambiguous genus. The organism can be clearly separated from its congener, Caryotricha convexa Kahl, 1932, by the extremely shortened ventral cirral rows in the posterior ends. Based on the data available, an improved diagnosis is given for the genus: marine Kiitrichidae with prominent buccal field; two highly developed undulating membranes; non-grouped, uniform cirral rows on both ventral and dorsal sides; enlarged transverse cirri present, which are the only differentiated cirri; marginal cirri not present; one short migratory row located posterior to buccal field; structure of dorsal kineties generally in Kiitricha pattern. The sequence of the SSU rRNA gene of C. minuta differs by 13 % from that of Kiitricha marina. Molecular phylogenetic analyses (Bayesian inference, least squares, neighbour joining, maximum parsimony) indicate that Caryotricha, together with Kiitricha, diverges at a deep level from all other spirotrichs. Its branching position is between Phacodiniidia and Licnophoridia. The results strongly support the distinct separation of the Kiitricha–Caryotricha clade, which always branches basal to the Stichotrichia–Hypotrichia–Oligotrichia–Choreotrichia assemblage. These results also confirm the previous hypothesis that the Kiitricha–Caryotricha group, long assumed to be a close relation to the euplotids, represents a taxon at subclass level within the spirotrichs.
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Does Kiitricha (Protista, Ciliophora, Spirotrichea) belong to Euplotida or represent a primordial spirotrichous taxon? With suggestion to establish a new subclass Protohypotrichia
More LessThe genus Kiitricha was long assumed to be the most primordial taxon in the Stichotrichia [hypotrichs sensu lato (s. l.)] based on its morphological features and was considered to be an intermediate between heterotrichs and the traditional hypotrichous assemblage. In order to evaluate the phylogenetic position of Kiitricha within the Hypotrichia, we sequenced the small-subunit rRNA gene and the alpha-tubulin gene for a Qingdao population of Kiitricha marina. Phylogenetic trees were constructed and compared to morphological and morphogenetic data. The results show that (i) Kiitricha is positioned near Phacodinium, both of which always form a sister clade to the assemblage including Stichotrichia, Hypotrichia, Oligotrichia and Choreotrichia, (ii) Kiitricha, which may represent an intermediate between heterotrichs (s. l.) and the Stichotrichia–Hypotrichia complex, is probably an ancestor-like form of the latter group and (iii) in contrast to morphological characters, both molecular and ontogenetic data support the separation of Kiitricha from the hypotrichs (s. l.). Thus, Kiitricha might be placed in the class Spirotrichea at about subclass level, next to Phaconidiidia, Hypotrichia and Stichotrichia, which supports the establishment of a new subclass Protohypotrichia n. subclass within the class Spirotrichea, with characterizations including slightly differentiated somatic ciliature (i.e. cirri on the ventral side generally uniform and non-grouped, no clearly defined marginal cirral rows, ciliature on the dorsal side mixed with cirri and dikinetids, no clearly differentiated dorsal kineties) and a unique but intermediate morphogenetic pattern of cortical structures between Hypotrichia and Stichotrichia.
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- Evolution, Phylogeny And Biodiversity
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Phylogenomics and protein signatures elucidating the evolutionary relationships among the Gammaproteobacteria
More LessThe class Gammaproteobacteria, which forms one of the largest groups within bacteria, is currently distinguished from other bacteria solely on the basis of its branching in phylogenetic trees. No molecular or biochemical characteristic is known that is unique to the class Gammaproteobacteria or its different subgroups (orders). The relationship among different orders of gammaproteobacteria is also not clear. In this study, we present detailed phylogenomic and comparative genomic analyses on gammaproteobacteria that clarify some of these issues. Phylogenetic trees based on concatenated sequences for 13 and 36 universally distributed proteins were constructed for 45 members of the class Gammaproteobacteria covering 13 of its 14 orders. In these trees, species from a number of the subgroups formed distinct clades and their relative branching order was indicated as follows (from the most recent to the earliest diverging): Enterobacteriales >Pasteurellales >Vibrionales, Aeromonadales >Alteromonadales >Oceanospirillales, Pseudomonadales >Chromatiales, Legionellales, Methylococcales, Xanthomonadales, Cardiobacteriales, Thiotrichales. Four conserved indels in four widely distributed proteins that are specific for gammaproteobacteria are also described. A 2 aa deletion in 5′-phosphoribosyl-5-aminoimidazole-4-carboxamide transformylase (AICAR transformylase; PurH) was a distinctive characteristic of all gammaproteobacteria (except Francisella tularensis). Two other conserved indels (a 4 aa deletion in RNA polymerase β-subunit and a 1 aa deletion in ribosomal protein L16) were found uniquely in various species of the orders Enterobacteriales, Pasteurellales, Vibrionales, Aeromonadales and Alteromonadales, but were not found in other gammaproteobacteria. Lastly, a 2 aa deletion in leucyl-tRNA synthetase was commonly present in the above orders of the class Gammaproteobacteria and also in some members of the order Oceanospirillales. The presence of the conserved indels in these gammaproteobacterial orders indicates that species from these orders shared a common ancestor that was separate from other bacteria, a suggestion that is supported by phylogenetic studies. Systematic blastp searches were also conducted on various open reading frames (ORFs) in the genome of Escherichia coli K-12. These analyses identified 75 proteins that were unique to most members of the class Gammaproteobacteria or were restricted to species from some of its main orders (Enterobacteriales; Enterobacteriales and Pasteurellales; Enterobacteriales, Pasteurellales, Vibrionales, Aeromonadales and Alteromonadales; and the Enterobacteriales, Pasteurellales, Vibrionales, Aeromonadales, Alteromonadales, Oceanospirillales and Pseudomonadales etc.). The genes for these proteins have evolved at various stages during the evolution of gammaproteobacteria and their species distribution pattern, in conjunction with other results presented here, provide valuable information regarding the evolutionary relationships among these bacteria.
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Phylogenetic structure of Xanthomonas determined by comparison of gyrB sequences
More LessPreviously, we have produced a phylogeny of species type strains from the plant-pathogenic genus Xanthomonas based on gyrB sequences. To evaluate this locus further for species and infraspecies identification, we sequenced an additional 203 strains comprising all the pathovar reference strains (which have defined plant hosts), 67 poorly characterized pathovars, currently classified as Xanthomonas campestris, and 59 unidentified xanthomonads. The well-characterized pathovars grouped either in clades containing their respective species type strain or in clades containing species related to Xanthomonas axonopodis. The Xanthomonas euvesicatoria, Xanthomonas perforans and Xanthomonas alfalfae species complex, Xanthomonas fuscans and Xanthomonas citri were discriminated as X. axonopodis-related clades and comprised a large proportion of unidentified strains as well as 80 pathovars representing all the X. axonopodis pathovars and many poorly characterized pathovars, greatly increasing the plant host ranges of the constituent species. Most xanthomonads from these three large clades were isolated from a taxonomically diverse range of plant hosts, including many weed species, from field systems in India, suggesting that these lineages became established and diversified in agricultural areas in this region. The majority of these xanthomonads had minimal sequence diversity, consistent with rapid and highly extensive pathovar diversification that has occurred in relatively recent times. Low-intensity farming practices may have provided conditions conducive to pathovar development, and evidence for pathovar diversification within other regional angiosperm floras is discussed. The gyrB locus was sufficiently discriminating to identify diversity within many species. Seven branches or clades were sufficiently distinct to be considered as potential novel species. This study has provided a comprehensive xanthomonad classification framework and has firmly established gyrB sequencing as a rapid and efficient identification tool.
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Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I)
More LessThe species of Clostridium comprise a very heterogeneous assemblage of bacteria that do not form a phylogenetically coherent group. It has been proposed previously that only a subset of the species of Clostridium that form a distinct cluster in the 16S rRNA tree (cluster I) should be regarded as the true representatives of the genus Clostridium (i.e. Clostridium sensu stricto). However, this cluster is presently defined only in phylogenetic terms, and no biochemical, molecular or phenotypic characteristic is known that is unique to species from this cluster. We report here phylogenomic and comparative analyses based on sequenced clostridial genomes in an attempt to bridge this gap and to clarify the evolutionary relationships among species of clostridia. In phylogenetic trees for species of clostridia based on concatenated sequences for 37 highly conserved proteins, the species of Clostridium cluster I formed a strongly supported clade that was separated from all other clostridia by a long branch. Several other Clostridium species that are not part of this cluster grouped reliably with other species of clostridia in a number of well-resolved clades. Our comparative genomic analyses have identified three conserved indels in three highly conserved proteins (a 4 aa insert in DNA gyrase A, a 1 aa deletion in ATP synthase beta subunit and a 1 aa insert in ribosomal protein S2) that are unique to the species of Clostridium cluster I and are not found in any other bacteria. blastp searches on various proteins in the genomes of Clostridium tetani E88 and Clostridium perfringens SM101 have also identified more than 10 proteins that are found uniquely in the cluster I species. These results provide evidence that the species of Clostridium cluster I not only are phylogenetically distinct but also share many unique molecular characteristics. These newly identified molecular markers provide useful tools to define and circumscribe the genus Clostridium sensu stricto in more definitive terms. We have also identified a 7–9 aa conserved insert in the enzyme phosphoglycerate dehydrogenase that is uniquely found in the Clostridium thermocellum, Thermoanaerobacter pseudethanolicus, Thermoanaerobacter tengcogensis and Caldicellulosiruptor saccharolyticus homologues, and is absent from all other bacteria. These species form a well-defined clade in the phylogenetic trees and this indel provides a potential molecular marker for this clostridial cluster.
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- International Committee On Systematics Of Prokaryotes
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- Taxonomic Note
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Proposal of Frondihabitans gen. nov. to replace the illegitimate genus name Frondicola Zhang et al. 2007
More LessThe prokaryotic generic name Frondicola Zhang et al. 2007 is illegitimate because it is a later homonym of a fungal genus name Frondicola Hyde, 1992 (Fungi, Ascomycota, Sordariomycetes, Xylariomycetidae, Xylariales, Hyponectriaceae) [Principle 2 and Rule 51b(4) of the Bacteriological Code (1990 Revision)]. It is also questionable whether the genus name can be validly published. Therefore, a new genus name, Frondihabitans gen. nov., is proposed for this taxon. As a result, a new name is proposed for the type species, Frondihabitans australicus sp. nov., to replace the illegitimate combination Frondicola australicus Zhang et al. 2007 . The type strain of Frondihabitans australicus is E1HC-02T (=JCM 13598T =DSM 17894T).
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