- Volume 53, Issue 5, 2003
Volume 53, Issue 5, 2003
- Validation List No. 93
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Valid publication of new names and new combinations previously effectively published outside the IJSEM
The purpose of this announcement is to effect the valid publication of the following 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 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 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 53, part 3, of the IJSEM
This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles).
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- New Taxa
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- Archaea
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Methanoculleus bourgensis, Methanoculleus olentangyi and Methanoculleus oldenburgensis are subjective synonyms
More LessMethanoculleus bourgensis, Methanoculleus olentangyi and Methanoculleus oldenburgensis are subjective synonyms on the basis of phenotypic, genotypic and phylogenetic characteristics. Methanoculleus bourgensis must be the name of the united species because it is the type of the genus Methanoculleus.
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Reclassification of Sulfolobus hakonensis Takayanagi et al. 1996 as Metallosphaera hakonensis comb. nov. based on phylogenetic evidence and DNA G+C content
More LessThe taxonomic status of Sulfolobus hakonensis Takayanagi et al. 1996 was re-evaluated by fresh determinations of the 16S rDNA sequence and G+C content of the genomic DNA of the type strain, HO1-1T. The 16S rDNA sequence of strain HO1-1T showed 98 % similarity to those of two Metallosphaera species and only ⩽92 % similarity to those of other Sulfolobus species. The DNA G+C content (46·2 mol%) is in accordance with those of Metallosphaera species. In addition, strain HO1-1T shares some phenotypic properties with Metallosphaera species; however, it can be differentiated from them by its capacity to utilize FeS and tetrathionate and the absence of flagella. Therefore, it is proposed that Sulfolobus hakonensis should be transferred to the genus Metallosphaera as Metallosphaera hakonensis comb. nov.
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- Other Bacteria
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Flavobacterium gelidilacus sp. nov., isolated from microbial mats in Antarctic lakes
More LessTwenty-two isolates from microbial mats in eastern Antarctic lakes showed similar fatty acid compositions and were investigated further using a polyphasic taxonomic approach. Repetitive extragenic palindromic DNA-PCR fingerprinting of the 22 strains revealed three groups, and DNA–DNA hybridizations between representatives showed more than 87 % DNA–DNA reassociation with each other. 16S rRNA gene sequence analysis placed two representative strains, LMG 21477T and LMG 21619, within the genus Flavobacterium, with 95·1 % sequence similarity to Flavobacterium flevense, 95·0 % to Flavobacterium tegetincola, less than 95 % to other Flavobacterium species and less than 90 % to representatives of other genera. The name Flavobacterium gelidilacus sp. nov. is proposed, with LMG 21477T (=DSM 15343T) as the type strain, and a description of the species is given on the basis of morphological, biochemical and physiological characteristics and fatty acid composition. The G+C content of the genomic DNA is 30·0–30·4 mol%.
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Vitellibacter vladivostokensis gen. nov., sp. nov., a new member of the phylum Cytophaga–Flavobacterium–Bacteroides
More LessA novel heterotrophic, yellow-orange-pigmented, non-motile, asporogenic, strictly aerobic, Gram-negative, oxidase and catalase-positive bacterium KMM 3516T was isolated from the holothurian Apostichopus japonicus collected from Troitsa Bay in the Gulf of Peter the Great (Sea of Japan) during November 1997. 16S rDNA sequence analysis revealed that strain KMM 3516T was a member of the family Flavobacteriaceae. The DNA G+C content of KMM 3516T was 41·3 mol%. Major respiratory quinone was MK-6. Predominant fatty acids were i15 : 0 and α15 : 0 (68·8 and 8·4 %, respectively). On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, the novel bacterium has been designated Vitellibacter vladivostokensis gen. nov., sp. nov. The type strain is KMM 3516T (=NBRC 16718T).
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Arenibacter troitsensis sp. nov., isolated from marine bottom sediment
More LessA novel marine, heterotrophic, aerobic, pigmented, non-motile bacterium was isolated from a bottom sediment sample collected from Troitsa Bay in the Gulf of Peter the Great, Sea of Japan, during June 2000. 16S rDNA sequence analysis revealed that this bacterium was a member of the family Flavobacteriaceae. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic analyses, the bacterium was shown to belong to a novel species of the genus Arenibacter, for which the name Arenibacter troitsensis sp. nov. is proposed. The type strain is KMM 3674T (=JCM 11736T).
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Pedobacter cryoconitis sp. nov., a facultative psychrophile from alpine glacier cryoconite
More LessOn the basis of phenotypic and genotypic characteristics, a novel species belonging to the genus Pedobacter is described. A facultatively psychrophilic, Gram-negative, aerobic, rod-shaped strain, A37T, was isolated from alpine glacier cryoconite. The non-flagellated and non-spore-forming isolate grew over a temperature range of 1–25 °C, showed activities of oxidase, catalase, DNase, protease (gelatin, casein), amylase, β-glucosidase, β-galactosidase and β-lactamase and degraded oil hydrocarbons. A distinct optimum temperature of 15 °C was observed for both protease production and oil hydrocarbon biodegradation. Analysis of 16S rDNA revealed that strain A37T represents a distinct taxon within Pedobacter. DNA from strain A37T showed only 19·7 % genetic relatedness to the DNA of Pedobacter piscium. The DNA G+C content was 43·4 mol%. Dominant fatty acids (51 %) were iso-15 : 0 2-OH and 16 : 1ω7c. The strain is assigned to a novel Pedobacter species, for which the name Pedobacter cryoconitis sp. nov. is proposed, with A37T (=DSM 14825T=LMG 21415T) as the type strain.
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Algoriphagus ratkowskyi gen. nov., sp. nov., Brumimicrobium glaciale gen. nov., sp. nov., Cryomorpha ignava gen. nov., sp. nov. and Crocinitomix catalasitica gen. nov., sp. nov., novel flavobacteria isolated from various polar habitats
More LessSeveral cold-adapted strains isolated from a variety of algal-rich Antarctic and Southern Ocean samples formed three distinct groups within the class Flavobacteria, phylogenetically distant from other cultivated species. The first taxon, designated Algoriphagus ratkowskyi gen. nov., sp. nov., was isolated from sea ice and from saline lake cyanobacterial mats and includes non-motile, strictly aerobic, saccharolytic rod-like or serpentine strains that were most closely related to the genus Cyclobacterium according to 16S rDNA sequence analysis (sequence similarity 0·85). The second taxon, designated Brumimicrobium glaciale gen. nov., sp. nov., isolated from sea ice and from continental shelf sediment, formed gliding, rod-like cells that were facultatively anaerobic with a fermentative metabolism. The third taxon, designated Cryomorpha ignava gen. nov., sp. nov., isolated from Southern Ocean particulates and from quartz stone subliths, included strictly aerobic, pleomorphic rod-like cells. Brumimicrobium glaciale and Cryomorpha ignava were most closely allied with ‘Microscilla aggregans var. catalatica’, which, on the basis of its distinctive taxonomic traits, is also proposed as a new genus and species, Crocinitomix catalasitica gen. nov., sp. nov. It is proposed that the three genera Brumimicrobium, Cryomorpha and Crocinitomix belong to a new family, Cryomorphaceae fam. nov. (type genus Cryomorpha), as they possess generally similar morphological and ecophysiological characteristics and form a common and distinct clade within class Flavobacteria.
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Alkanindiges illinoisensis gen. nov., sp. nov., an obligately hydrocarbonoclastic, aerobic squalane-degrading bacterium isolated from oilfield soils
More LessAn alkane-degrading bacterium, designated GTI MVAB Hex1T, was isolated from chronically crude oil-contaminated soil from an oilfield in southern Illinois. The isolate grew very weakly or not at all in minimal or rich media without hydrocarbons. Straight-chain aliphatic hydrocarbons, such as hexadecane and heptadecane, greatly stimulated growth; shorter-chain (⩽C15) hydrocarbons did not (with decane as the sole exception). Growth was also greatly enhanced by the branched aliphatic hydrocarbons pristane and squalane. The latter of these was most intriguing, as catabolism of squalane has hitherto been reported only for Mycobacterium species. Although unable to utilize mono- or polycyclic aromatic hydrocarbons as sole carbon sources, the isolate did show slight fluorene-mineralizing capability in Luria–Bertani medium, which was partially repressed by hexadecane. In contrast, hexadecane supplementation greatly increased mineralization of 14C-dodecane, which was not a growth substrate. Further testing emphasized the isolate's extremely narrow substrate range, as only Tween 40 and Tween 80 supported significant growth. Microscopic examination (by scanning and transmission electron microscopy) revealed a slightly polymorphic coccoidal to bacillar morphology, with hydrocarbon-grown cells tending to be more elongated. When grown with hexadecane, GTI MVAB Hex1T accumulated a large number of electron-transparent intracytoplasmic inclusion bodies. These were also prevalent during growth in the presence of squalane. Smaller inclusion bodies were observed occasionally with pristane supplementation; they were, however, absent during growth on crude oil. On the basis of 16S rRNA gene sequence data and range of growth substrates, classification of this isolate as the type strain of Alkanindiges illinoisensis gen. nov., sp. nov. is proposed, which is most closely related (approx. 94 % sequence similarity) to Acinetobacter junii.
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Deferribacter abyssi sp. nov., an anaerobic thermophile from deep-sea hydrothermal vents of the Mid-Atlantic Ridge
Two strains of thermophilic, anaerobic, chemolithoautotrophic bacteria, designated JRT and DR, were isolated from hydrothermal samples collected on the Mid-Atlantic Ridge from the Rainbow (36° 16′ N, 33° 54′ W) and Menez Gwen (37° 50′ N, 31° 50′ W) vent fields, respectively. Cells of both isolates were short, straight- to vibrio-shaped, motile rods with one polar flagellum, and were Gram-negative and non-sporulating. Strain JRT was characterized in detail. It was found to grow optimally at pH 6·5–6·7, at 60 °C and in the presence of 30 g NaCl l−1. Strain JRT could use molecular hydrogen, acetate, succinate, pyruvate and proteinaceous compounds as electron donors, and elemental sulfur, nitrate or Fe(III) as electron acceptors. No fermentation of organic substrates occurred. The G+C content of the DNA of strain JRT was 30·8 mol%. Strain DR (=DSM 14927) possessed the same morphology and pH, temperature and salinity optima and ranges, and used the same electron acceptors as strain JRT. On the basis of their 16S rDNA sequences (1517 nucleotides), strains JRT and DR were identical and distantly related to Deferribacter thermophilus and Deferribacter desulfuricans (95·3 and 95·2 % sequence similarity, respectively). Based on their phenotypic and phylogenetic characteristics, it is proposed that both strains are members of a new species of the genus Deferribacter, for which the name Deferribacter abyssi (type strain JRT=DSM 14873T=JCM 11955T) is proposed.
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- Proteobacteria
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Methylocella silvestris sp. nov., a novel methanotroph isolated from an acidic forest cambisol
Two strains of Gram-negative, aerobic, non-pigmented, non-motile, rod-shaped, methane-oxidizing bacteria were isolated from an acidic forest cambisol near Marburg, Germany, and were designated as strains BL2T and A1. These bacteria were morphologically and phenotypically similar to Methylocella palustris KT. The cells possess a highly specific bipolar appearance. They lack the intracytoplasmic membranes common to all methane-oxidizing bacteria except Methylocella, but contain a vesicular membrane system connected to the cytoplasmic membrane. A soluble methane monooxygenase was present, but no particulate methane monooxygenase could be detected. These bacteria utilize the serine pathway for carbon assimilation. Strains BL2T and A1 are moderately acidophilic, mesophilic organisms capable of growth at pH values between 4·5 and 7 (with an optimum at pH 5·5) and at temperatures between 4 and 30 °C. Compared with Methylocella palustris KT, these strains have greater tolerance of cold temperatures, dissolved salts and methanol. On the basis of 16S rRNA gene sequence identity, of species with validly published names, strain BL2T is most closely related to Methylocella palustris KT (97·3 % identity), Beijerinckia indica subsp. indica ATCC 9039T (97·1 %) and Methylocapsa acidiphila B2T (96·2 %). The DNA G+C content is 60 mol% and the major phospholipid fatty acid is 18 : 1ω7. Strain BL2T showed only 21–22 % DNA–DNA hybridization with Methylocella palustris KT. The data therefore suggest that strains BL2T and A1 represent a novel species of Methylocella; the name Methylocella silvestris sp. nov. is proposed, with strain BL2T (=DSM 15510T=NCIMB 13906T) as the type strain.
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Bosea minatitlanensis sp. nov., a strictly aerobic bacterium isolated from an anaerobic digester
A strictly aerobic, mesophilic bacterium, strain AMX 51T, was isolated from anaerobic digester sludge. Cells were Gram-negative, motile, non-sporulating, straight to curved rods with one polar flagellum. The isolate had phenotypic traits of the genus Bosea, including cellular fatty acid and substrate utilization profiles. Physiological characteristics and antibiotic susceptibility were determined. Phylogenetic analysis revealed that strain AMX 51T was a member of the α-Proteobacteria, most closely related to Bosea thiooxidans DSM 9653T (similarity of 98·88 %). Methylobacterium organophilum JCM 2833T, Methylobacterium mesophilicum JCM 2829T, Afipia clevelandensis DSM 7315T, Afipia felis DSM 7326T, Afipia broomeae DSM 7327T, Blastobacter denitrificans LMG 8443T and Bradyrhizobium japonicum DSM 30131T showed significant 16S rRNA gene sequence similarities to strain AMX 51T. The DNA G+C composition of strain AMX 51T was 68·5 mol%. DNA–DNA hybridization analysis revealed 44·2 and 15·1 % relatedness between strain AMX 51T and the respective type strains of Bosea thiooxidans and A. felis. Overall results suggest that strain AMX 51T (=DSM 13099T=ATCC 700918T=CIP 106457T) represents a novel species of the genus Bosea; the name Bosea minatitlanensis sp. nov. is proposed.
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Sphingomonas aurantiaca sp. nov., Sphingomonas aerolata sp. nov. and Sphingomonas faeni sp. nov., air- and dustborne and Antarctic, orange-pigmented, psychrotolerant bacteria, and emended description of the genus Sphingomonas
Seven psychrotolerant, Gram-negative bacterial strains, five dust- and airborne isolates (MA101bT, MA306a, MA405/90, MA-olkiT and NW12T) and two from the Antarctic (Ant 20 and M3C203B-B), were subjected to a polyphasic characterization to determine their taxonomic position. High 16S rDNA sequences similarities (99·3–100·0 %) demonstrated that they were closely related to each other. Phylogenetic evaluation of their 16S rDNA sequences revealed that they are members of the genus Sphingomonas sensu stricto, encompassing a separate branch within this genus. They shared 94·4–96·6 % 16S rDNA sequence similarity with species of this genus. All Sphingomonas-specific signature nucleotides were also detected. The presence of the major ubiquinone Q-10, sym-homospermidine as the predominant polyamine, Sphingomonadaceae-specific sphingoglycolipid in the polar lipid patterns and a fatty acid profile containing C14 : 0 2-OH and lacking 3-OH fatty acids were in agreement with identification of these strains as members of the genus Sphingomonas sensu stricto. Results from DNA–DNA hybridizations and comparison of protein patterns indicated that the seven strains are members of three distinct species. One species is represented by strains MA101bT, MA306a and MA405/90, the second by strains NW12T, Ant 20 and M3C203B-B and the third by one strain, MA-olkiT. Their distinction at the species level was also supported by results of biochemical characterization and partly supported by riboprints and genomic fingerprints. On the basis of these results, three novel species of the genus Sphingomonas are proposed: Sphingomonas aurantiaca sp. nov., consisting of strains MA101bT (=DSM 14748T=LMG 21377T), MA306a and MA405/90 (=DSM 14749=LMG 21378), Sphingomonas faeni sp. nov. MA-olkiT (=DSM 14747T=LMG 21379T) and Sphingomonas aerolata sp. nov., represented by strains NW12T (=DSM 14746T=LMG 21376T), Ant 20 (=ICMP 13599) and M3C203B-B (=SMCC M3C203B-B).
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Silicibacter pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments
Three Gram-negative, rod-shaped, aerobic bacteria that were capable of degrading dimethylsulfoniopropionate (DMSP) were isolated from marine waters. These isolates (DSS-3T, DSS-10 and ISMT) exhibited the ability to demethylate and cleave DMSP, as well as to degrade other sulfur compounds related to DMSP that are cycled in marine environments. Intracellular poly-β-hydroxybutyrate inclusions, surface blebs and one polar, complex flagellum that rotated exclusively in the clockwise direction were observed for DSS-3T. The outer membrane of ISMT was separated from the cytoplasm at the poles in a toga-like morphology. The primary fatty acid in both strains was C18 : 1 ω7c. DNA G+C contents for the isolates were 68·0±0·1, 68·1±0·1 and 66·0±0·2 mol% for DSS-3T, DSS-10 and ISMT, respectively. 16S rRNA gene sequence analyses placed these organisms within the Roseobacter lineage of the α-Proteobacteria. Closely related species were Silicibacter lacuscaerulensis and Ruegeria atlantica (DSS-3T and DSS-10) and Roseovarius tolerans (ISMT). Neither DSS-3T nor ISMT exhibited 16S rRNA similarity >97 % or DNA–DNA hybridization values >45 % to their nearest described relatives. Genotypic and phenotypic analyses support the creation of two novel species: Silicibacter pomeroyi sp. nov. with strain DSS-3T (=ATCC 700808T=DSM 15171T) as the type strain, and Roseovarius nubinhibens sp. nov. with strain ISMT (=ATCC BAA-591T=DSM 15170T) as the type strain.
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Desulfonatronum thiodismutans sp. nov., a novel alkaliphilic, sulfate-reducing bacterium capable of lithoautotrophic growth
A novel alkaliphilic, sulfate-reducing bacterium, strain MLF1T, was isolated from sediments of soda Mono Lake, California. Gram-negative vibrio-shaped cells were observed, which were 0·6–0·7×1·2–2·7 μm in size, motile by a single polar flagellum and occurred singly, in pairs or as short spirilla. Growth was observed at 15–48 °C (optimum, 37 °C), >1–7 % NaCl, w/v (optimum, 3 %) and pH 8·0–10·0 (optimum, 9·5). The novel isolate is strictly alkaliphilic, requires a high concentration of carbonate in the growth medium and is obligately anaerobic and catalase-negative. As electron donors, strain MLF1T uses hydrogen, formate and ethanol. Sulfate, sulfite and thiosulfate (but not sulfur or nitrate) can be used as electron acceptors. The novel isolate is a lithoheterotroph and a facultative lithoautotroph that is able to grow on hydrogen without an organic source of carbon. Strain MLF1T is resistant to kanamycin and gentamicin, but sensitive to chloramphenicol and tetracycline. The DNA G+C content is 63·0 mol% (HPLC). DNA–DNA hybridization with the most closely related species, Desulfonatronum lacustre Z-7951T, exhibited 51 % homology. Also, the genome size (1·6×109 Da) and T m value of the genomic DNA (71±2 °C) for strain MLF1T were significantly different from the genome size (2·1×109 Da) and T m value (63±2 °C) for Desulfonatronum lacustre Z-7951T. On the basis of physiological and molecular properties, the isolate was considered to be a novel species of the genus Desulfonatronum, for which the name Desulfonatronum thiodismutans sp. nov. is proposed (the type strain is MLF1T=ATCC BAA-395T=DSM 14708T).
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Ralstonia respiraculi sp. nov., isolated from the respiratory tract of cystic fibrosis patients
More LessFive isolates recovered from the respiratory tract of cystic fibrosis patients were included in a polyphasic taxonomic study that employed 16S rDNA sequence analysis, cellular protein and fatty acid analysis and biochemical characterization. Four isolates were classified as a novel Ralstonia species, for which the name Ralstonia respiraculi sp. nov. is proposed; the other isolate was phylogenetically closely related to R. respiraculi, but is likely to represent another novel Ralstonia species. The type strain of R. respiraculi is AU3313T (=LMG 21510T=CCUG 46809T).
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Transfer of Pseudomonas elongata Humm 1946 to the genus Microbulbifer as Microbulbifer elongatus comb. nov.
More LessPhylogenetic analysis based on 16S rDNA sequences revealed that Pseudomonas elongata Humm 1946 is more closely related to the genus Microbulbifer than to authentic pseudomonads. The type strain of P. elongata (DSM 6810T) exhibited 16S rDNA similarity levels of 97·5 and 98·2 % to the type strains of Microbulbifer hydrolyticus and Microbulbifer salipaludis, respectively, but of less than approximately 92 % to Pseudomonas species with known 16S rDNA sequences. Respiratory lipoquinone and cellular fatty acid analyses showed that the type strain of P. elongata has characteristics similar to those of the genus Microbulbifer, not those of the genus Pseudomonas. P. elongata DSM 6810T contained ubiquinone-8 as the predominant respiratory lipoquinone and iso-C15 : 0 as the major fatty acid. DNA–DNA relatedness data indicate that P. elongata is a species distinct from M. hydrolyticus and M. salipaludis. Therefore, on the basis of these data, P. elongata Humm 1946 should be transferred to the genus Microbulbifer as Microbulbifer elongatus comb. nov.
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Caenibacterium thermophilum gen. nov., sp. nov., isolated from a thermophilic aerobic digester of municipal sludge
More LessA bacterial strain, N2-680T (=DSM 15264T=LMG 21760T), isolated from a thermophilic aerobic digester of municipal sludge, was characterized with respect to its morphology, physiology and taxonomy. Phenotypically, the isolate was a Gram-negative rod with a polar flagellum, catalase- and oxidase-positive, containing cytoplasmic inclusions of poly-β-hydroxybutyrate and had an optimal growth temperature of about 47 °C. Strain N2-680T was unable to reduce nitrate and could use organic acids, amino acids and carbohydrates as single carbon sources. Chemotaxonomic analysis revealed that ubiquinone 8 was the major respiratory quinone of this organism and that phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids. At 50 °C, the major components in fatty acid methyl ester analysis were C16 : 0 and cyclo-C17 : 0. The highest 16S rDNA sequence identity of isolate N2-680T was to Leptothrix mobilis and Ideonella dechloratans (95·7 %) and to Rubrivivax gelatinosus and Aquabacterium commune (95·6 %). 16S rDNA sequence similarities to species of two related thermophilic genera, Caldimonas manganoxidans and Tepidimonas ignava, were lower (93·6 and 94·7 %). On the basis of phylogenetic analyses and physiological and chemotaxonomic characteristics, it is proposed that isolate N2-680T represents a new genus and species, for which the name Caenibacterium thermophilum gen. nov., sp. nov. is proposed.
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Marinobacter lipolyticus sp. nov., a novel moderate halophile with lipolytic activity
More LessIn the course of a screening programme in hypersaline habitats of southern Spain to isolate halophilic bacteria that are able to produce different extracellular enzymes, a novel, moderately halophilic bacterium (strain SM19T) that displays lipolytic activity has been isolated and characterized. Strain SM19T is a Gram-negative rod that grows optimally in culture media that contain 7·5 % NaCl. The DNA G+C content was 57·0 mol%. According to phenotypic and genotypic data, this strain was assigned to the genus Marinobacter. However, 16S rDNA sequence similarity between strain SM19T and species of the genus Marinobacter was <96·7 %; this value is sufficiently low to propose its designation as a novel species. In addition, DNA–DNA hybridization with reference strains of close phylogenetic relatives was between 11 and 19 %. On the basis of these data, the inclusion of strain SM19T in the genus Marinobacter as a novel species is proposed, with the name Marinobacter lipolyticus sp. nov. The type strain of the novel species is SM19T (=DSM 15157T=NCIMB 13907T=CIP 107627T=CCM 7048T).
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Tepidiphilus margaritifer gen. nov., sp. nov., isolated from a thermophilic aerobic digester
More LessA moderately thermophilic bacterium is described, strain N2-214T, that was isolated from an enrichment culture, growing on caprolactone, obtained from a sample from a water-treatment sludge aerobic digester operating at temperatures around 60 °C. The organism was aerobic, Gram-negative, oxidase- and catalase-positive, with a polar flagellum, and capable of growth at temperatures as high as 61 °C. The major fatty acids of strain N2-214T were C16 : 0, C18 : 1 and cyclo-C19 : 0. The phylogenetic relationships of the strain, derived from 16S rRNA gene sequence comparisons, demonstrated it to be a member of the β-subclass of the Proteobacteria. The highest 16S rDNA sequence similarity of isolate N2-214T was to Azoarcus buckelii (91·9 %), Thauera aromatica (92 %) and Hydrogenophilus thermoluteolus (92·7 %). On the basis of phylogenetic analyses and physiological and chemotaxonomic characteristics, it is proposed that isolate N2-214T (=DSM 15129T=LMG 21637T) represents a new genus and species, Tepidiphilus margaritifer gen. nov., sp. nov.
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Taxonomic study of sucrose-positive Aeromonas jandaei-like isolates from faeces, water and eels: emendation of A. jandaei Carnahan et al. 1992
More LessFourteen sucrose-positive Aeromonas jandaei-like isolates from fresh water and reared European eels were subjected to a polyphasic study to determine their taxonomic position. Numerical taxonomy was used to analyse phenotypic data obtained for these isolates and 43 type and reference strains representative of recognized Aeromonas species. The A. jandaei cluster (phenon 1) was defined at 81·6 % similarity (S J); this included the A. jandaei-like isolates, the sucrose-positive strain Aeromonas veronii biogroup sobria CECT 4910 and nearly all A. jandaei reference strains used in the study. Four other reference strains of A. veronii biogroup sobria and the type strain of Aeromonas ichthiosmia were peripheral to the A. jandaei cluster. The supra-group ‘A. jandaei–A.veronii biogroup sobria–A. ichthiosmia’ was linked at 80·7 % similarity (S J) and was clearly segregated from the phenotypic core of the A. veronii biogroup sobria species, which was related to the reference strain Popoff 224 (CECT 4835). DNA relatedness between strains grouped in the A. jandaei cluster (phenon 1) and A. jandaei CECT 4228T ranged from 70 to 100 %, but was below 50 % when DNAs from A. veronii biogroup sobria CECT 4835, A. veronii biogroup veronii CECT 4257T and A. ichthiosmia CECT 4486T were used. In addition, DNA relatedness between peripheral A. veronii biogroup sobria strains and the species A. jandaei (CECT 4228T), A. veronii (CECT 4257T, CECT 4835) and A. ichthiosmia (CECT 4486T) was always below 54 %, as it was between the species A. ichthiosmia (CECT 4486T) and A. veronii (CECT 4257T, CECT 4835). Emendation of A. jandaei is proposed; this taxon now includes sucrose-positive clinical and environmental strains as well as environmental isolates that are pathogenic for fish and humans. Other new traits for this species are the ability to grow at 4–42 °C, acid production from glycerol but not from lactose, d-melibiose or d-raffinose, the use of d-gluconate, l-glutamate or l-proline but not l-lactate, l-alanine, l-arabinose or l-arginine, hydrolytic activity against casein, elastin, starch and lecithin and the inability to lyse arbutin. The DNA G+C content of A. jandaei is also reported for the first time; it ranges from 58·1 to 61·1 mol%. On the other hand, the DNA relatedness data support the classification of peripheral reference strains of A. veronii biogroup sobria outside this taxon, indicating that biogroup sobria requires further revision.
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Proposal of Histophilus somni gen. nov., sp. nov. for the three species incertae sedis ‘Haemophilus somnus’, ‘Haemophilus agni’ and ‘Histophilus ovis’
More LessEarlier investigations have shown that ‘Haemophilus somnus’, ‘Haemophilus agni’ and ‘Histophilus ovis’ represent the same species. In the present investigation, the taxonomic position of this species is explored further by sequencing the 16S rRNA and rpoB genes of strains that were investigated previously by DNA–DNA hybridization. These results clearly support the allocation of this species to a novel genus within the family Pasteurellaceae. The phenotypic separation of Histophilus somni gen. nov., sp. nov. from other members of the family can, for most strains, be based on capnophilia, yellowish pigmentation and indole production. However, due to phenotypic variation, the use of a species-specific PCR test based on the 16S rRNA gene is included in the species description. This is justified by the high sequence similarity of the 16S rRNA gene within the species and the fact that the highest sequence similarity to any other taxon within the family is 93·4 %. The type strain, 8025T=ATCC 43625T=CCUG 36157T, was isolated in the USA from a bovine brain with lesions of thromboembolic meningoencephalitis.
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Aquaspirillum dispar Hylemon et al. 1973 and Microvirgula aerodenitrificans Patureau et al. 1998 are subjective synonyms
More LessThe 16S rDNA sequences of [Aquaspirillum] dispar LMG 4329T and Microvirgula aerodenitrificans SGLY2T (=LMG 18919T) were found to be very similar (>99 %). DNA–DNA hybridizations between the two strains revealed a high level of DNA–DNA binding (84 %), showing that they represent a single species. M. aerodenitrificans and [A.] dispar were also phenotypically very similar. It is concluded that [A.] dispar and M. aerodenitrificans are subjective synonyms. As [A.] dispar was wrongly assigned to the genus Aquaspirillum, we propose that strains of [A.] dispar must be reclassified in the genus Microvirgula. The name Microvirgula aerodenitrificans must be retained for the unified taxon since it is the type of the genus Microvirgula.
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Fluorescent pseudomonads associated with the phyllosphere of grasses; Pseudomonas trivialis sp. nov., Pseudomonas poae sp. nov. and Pseudomonas congelans sp. nov.
More LessStrains of fluorescent pseudomonads, isolated from the phyllosphere of grasses, were analysed by a polyphasic approach in order to clarify their interspecific position. Classification on the basis of ribotyping revealed six genotypes; four of these, which could be differentiated clearly from each other and from Pseudomonas species with validly published names on the basis of phenotypic features, were chosen for detailed phylogenetic analysis. DNA–DNA hybridization studies among representative strains of the four genotypes and closely related Pseudomonas species, determined by comparison of 16S rDNA sequences, showed that three of the studied ribotypes represented novel species. Two of them were related to mainly saprophytic fluorescent pseudomonads and could be easily distinguished by a negative arginine dihydrolase reaction. One ribotype, also characterized by a negative arginine dihydrolase reaction, was closely related to potentially plant-pathogenic fluorescent pseudomonads and differed in certain phenotypic features from its phylogenetic neighbours. As a consequence of the phenotypic and phylogenetic analyses, Pseudomonas trivialis sp. nov. (type strain: P 513/19T=DSM 14937T=LMG 21464T), Pseudomonas poae sp. nov. (type strain: P 527/13T=DSM 14936T=LMG 21465T) and Pseudomonas congelans sp. nov. (type strain: P 538/23T=DSM 14939T=LMG 21466T) are proposed.
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Shewanella waksmanii sp. nov., isolated from a sipuncula (Phascolosoma japonicum)
Two marine bacterial strains, KMM 3823T and KMM 3836, isolated from a sipuncula (Phascolosoma japonicum), a common inhabitant of Troitsa Bay in the Gulf of Peter the Great (Sea of Japan), were studied. Comparative 16S rRNA gene sequence-based phylogenetic analysis placed these bacteria into a separate branch of the ‘Gammaproteobacteria’ within members of the genus Shewanella. KMM 3823T showed the highest similarity (96·6 %) with Shewanella fidelis. The DNA G+C contents of the two strains studied were 43·0 mol%. The level of DNA homology between these two strains was conspecific (93 %), indicating that they represent a single genospecies. These organisms were greenish-brown, Gram-negative, polarly flagellated, facultatively anaerobic, mesophilic (temperature range 4–30 °C), neutrophilic, haemolytic and were able to degrade elastin, gelatin and DNA. They were susceptible to ampicillin, carbenicillin, gentamicin and kanamycin. The predominant fatty acids were characteristic for shewanellas: 13 : 0-i, 15 : 0-i and 16 : 1(n-7); up to 6·7 % of eicosapentaenoic fatty acid, 20 : 5(n-3), was produced during growth at 28 °C. Phylogenetic evidence, confirmed by DNA hybridization and phenotypic characteristics revealed that the two bacteria studied constitute a new species, Shewanella waksmanii sp. nov., the type strain of which is KMM 3823T (=CIP 107701T=ATCC BAA-643T).
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Delftia tsuruhatensis sp. nov., a terephthalate-assimilating bacterium isolated from activated sludge
More LessA terephthalate-assimilating bacterium was isolated from activated sludge collected from a domestic wastewater treatment plant in Japan by enrichment with terephthalate as sole carbon source. The isolate, designated strain T7T, was a Gram-negative, short rod-shaped micro-organism. A phylogenetic study based on 16S rRNA gene sequences indicated that strain T7T should be placed in the genus Delftia. A DNA–DNA hybridization value of 69 % was determined between strain T7T and Delftia acidovorans ATCC 15668T. Major cellular fatty acids of strain T7T were C16 : 0, C16 : 1 and C18 : 1. Substantial amounts of cyclopropanoic acid (C17 : 0), 3-OH C10 : 0, C12 : 0, C15 : 0 and C14 : 0 were also detected. The total DNA G+C content of strain T7T was 66·2 mol%. Strain T7T could utilize the following compounds as carbon sources: acetamide, β-alanine, citrate, d-fructose, glycerol, isobutyrate, isophthalate, d(−)-mannitol, maleate, malonate, phenylacetate, propionate, protocatechuate, terephthalate, d-tryptophan and l-tryptophan. Comparisons of phenotypic and genotypic characteristics with other known species belonging to the genus Delftia suggest that strain T7T represents a novel species, for which the name Delftia tsuruhatensis sp. nov. is proposed; strain T7T is the type strain (=IFO 16741T=ATCC BAA-554T).
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Vibrio fortis sp. nov. and Vibrio hepatarius sp. nov., isolated from aquatic animals and the marine environment
More LessIn this study, the taxonomic positions of 19 Vibrio isolates disclosed in a previous study were evaluated. Phylogenetic analysis based on 16S rDNA sequences partitioned these isolates into groups that were closely related (98·8–99·1 % similarity) to Vibrio pelagius and Vibrio xuii, respectively. DNA–DNA hybridization experiments further showed that these groups had <70 % similarity to other Vibrio species. Two novel Vibrio species are proposed to accommodate these groups: Vibrio fortis sp. nov. (type strain, LMG 21557T=CAIM 629T) and Vibrio hepatarius sp. nov. (type strain, LMG 20362T=CAIM 693T). The DNA G+C content of both novel species is 45·6 mol%. Useful phenotypic features for discriminating V. fortis and V. hepatarius from other Vibrio species include production of indole and acetoin, utilization of cellobiose, fermentation of amygdalin, melibiose and mannitol, β-galactosidase and tryptophan deaminase activities and fatty acid composition.
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Acinetobacter parvus sp. nov., a small-colony-forming species isolated from human clinical specimens
The taxonomic status of seven glucose-non-acidifying, non-proteolytic Acinetobacter strains characterized by forming small colonies on agar media was studied. With one exception, all strains were from human specimens. They could be distinguished from all described Acinetobacter (genomic) species by their ability to grow on ethanol and acetate as sole sources of carbon but not on 22 other substrates tested including dl-lactate or dl-4-aminobutyrate. DNA–DNA hybridization studies, 16S rRNA gene sequence analysis, amplified rDNA restriction analysis and DNA polymorphism analysis by AFLP showed that these strains represent a hitherto unknown species of the genus Acinetobacter, for which the name Acinetobacter parvus (type strain LMG 21765T=LUH 4616T=NIPH 384T=CCM 7030T) is proposed.
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Vibrio pacinii sp. nov., from cultured aquatic organisms
More LessThree strains were isolated from cultured aquatic organisms. They were Gram-negative, oxidase-positive, motile, fermentative, arginine dihydrolase-positive, lysine and ornithine decarboxylase-negative and sensitive to vibriostatic agent O/129. These strains differ from other related Vibrio species by several phenotypic features, which include acetoin and indole production and utilization of amygdalin and d-mannitol. Comparison of 16S rDNA sequences showed a close relationship to the recently described species Vibrio kanaloae (96·6 %) and Vibrio pomeroyi (96·4 %) and to Vibrio furnissii (96·6 %), but DNA–DNA hybridization experiments showed that the three isolates form a tight novel species with ⩽30 % DNA–DNA similarity to its closest phylogenetic neighbours. Vibrio pacinii sp. nov. is proposed, with LMG 19999T (=CAIM 530T=STD3-1057T; DNA G+C content, 44·9 mol%) as the type strain.
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Characterization of rhizobia isolated from legume species within the genera Astragalus and Lespedeza grown in the Loess Plateau of China and description of Rhizobium loessense sp. nov.
More LessTwenty-nine rhizobial isolates from root nodules of Astragalus and Lespedeza spp. growing in the Loess Plateau of China were characterized by numerical taxonomy, RFLP and sequencing of PCR-amplified 16S rRNA genes, measurement of DNA G+C content, DNA–DNA relatedness and cross-nodulation with selected legume species. Based on the results of numerical taxonomy, the isolates formed two clusters (1 and 2) with some single isolates at a similarity level of 82 %. Cluster 1 contained six isolates from Astragalus and Lespedeza spp. Cluster 2 consisted of nine isolates from Astragalus spp. DNA relatedness was greater than 80 % among isolates within cluster 2. Phylogenetic analysis based on 16S rRNA gene sequences showed that CCBAU 7190BT, representing cluster 2, was closely related to Rhizobium galegae and Rhizobium huautlense. DNA–DNA relatedness between CCBAU 7190BT and reference strains of R. galegae, R. huautlense and other related species ranged from 0 to 48·6 %. The cluster 2 isolates could also be differentiated phenotypically from related species. Based on these data, a novel species, Rhizobium loessense sp. nov., is proposed for cluster 2, with the type strain CCBAU 7190BT (=AS1.3401T=LMG 21975T).
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Desulfonauticus submarinus gen. nov., sp. nov., a novel sulfate-reducing bacterium isolated from a deep-sea hydrothermal vent
A novel moderately thermophilic, hydrogenotrophic, sulfate-reducing bacterium, strain 6NT (=DSM 15269T=CIP 107713T), was isolated from matrixes of Alvinella and Riftia originating from deep-sea hydrothermal-vent samples collected on the 13°N East-Pacific Rise at a depth of approximately 2600 m. It was a Gram-negative, non-sporulating, curved rod, motile with one polar flagellum, that did not possess desulfoviridin. It grew at temperatures ranging from 30 to 60 °C, with an optimum at 45 °C, in the presence of 0–5 % NaCl (optimum 2 %). Strain 6NT utilized only H2/CO2 and formate as electron donors with acetate as carbon source. Sulfate, sulfite, thiosulfate and elemental sulfur were used as terminal electron acceptors during hydrogen oxidation. The G+C content of DNA was 34·4 mol%. Strain 6NT grouped with members of the family Desulfohalobiaceae in the δ-subclass of the Proteobacteria. Its closest phylogenetic relative was Desulfonatronovibrio hydrogenovorans, with only 90 % similarity between the sequences of the genes encoding 16S rRNA. Because of significant phylogenetic differences from all sulfate-reducing bacteria described so far in the domain Bacteria, this novel thermophile is proposed to be assigned to a new genus and species, Desulfonauticus submarinus gen. nov., sp. nov.
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Reclassification of Vibrio hollisae as Grimontia hollisae gen. nov., comb. nov.
More LessThe taxonomic positions of three representative strains of Vibrio hollisae (LMG 17719T, LMG 21416 and LMG 21538) were investigated by means of 16S rDNA sequences and phenotypic data. V. hollisae strains (GenBank/EMBL accession nos AJ514909–AJ514911) shared 99·5 % 16S rDNA sequence similarity, but had only 94·6 % similarity to their closest phylogenetic neighbour, Enterovibrio norvegicus. 16S rDNA sequence similarity of V. hollisae and Vibrio cholerae was only 91 %. These results suggest that V. hollisae should be placed into a novel genus, for which the name Grimontia gen. nov. is proposed.
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Alteromonas marina sp. nov., isolated from sea water of the East Sea in Korea
More LessTwo Gram-negative, motile, non-spore-forming and moderately halophilic rods (strains SW-47T and SW-49) were isolated from sea water of the East Sea in Korea and subjected to a polyphasic taxonomic study. The two strains grew optimally between 30 and 37 °C, and grew at 4 and 44 °C but not at temperatures above 45 °C. They grew optimally in the presence of 2–5 % (w/v) NaCl, but did not grow in the absence of NaCl. Strains SW-47T and SW-49 had ubiquinone-8 (Q-8) as the predominant respiratory lipoquinone and C16 : 1 ω7c and/or iso-C15 : 0 2OH, C16 : 0 and C18 : 1 ω7c as the major fatty acids, which are consistent with the corresponding data for Alteromonas macleodii. The DNA G+C contents of strains SW-47T and SW-49 were 45 and 44 mol%, respectively. Strains SW-47T and SW-49 showed a high level of 16S rDNA sequence similarity (99·9 %) and a mean level of DNA–DNA relatedness of 96·5 %. Phylogenetic analyses based on 16S rDNA sequences showed that the two strains form a coherent cluster with A. macleodii. Strains SW-47T and SW-49 exhibited levels of 16S rDNA sequence similarity of 99·3 and 99·1 %, respectively, with A. macleodii DSM 6062T and of less than 89·4 % with other species used in the phylogenetic analyses. Alteromonas fuliginea CIP 105339T was found to be more closely related to the genus Pseudoalteromonas than to the genus Alteromonas. On the basis of phenotypic properties and phylogenetic and genomic data, strains SW-47T and SW-49 represent a new species of the genus Alteromonas, for which the name Alteromonas marina (type strain SW-47T=KCCM 41638T=JCM 11804T) is proposed.
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Burkholderia sordidicola sp. nov., isolated from the white-rot fungus Phanerochaete sordida
More LessTwo bacterial strains associated with the white-rot fungus Phanerochaete sordida were subjected to taxonomic investigation. The isolates, designated KCTC 12081T and KCTC 12082, were Gram-negative, non-motile, non-spore-forming and ovoid to rod-shaped. The strains contained major amounts of hexadecanoic acid, cyclo-heptadecanoic acid and ω-7-cis-octadecenoic acid in their cell envelopes. Strain KCTC 12081T contained ubiquinone-8 as the major isoprenoid quinone and the G+C content of its genomic DNA was 61·3 mol%. Morphological and chemotaxonomic properties of the strains were consistent with classification in the genus Burkholderia. In a comparison of 16S rDNA sequence, KCTC 12081T shared 100 % similarity with KCTC 12082 and both strains formed a distinct phylogenetic lineage within the genus Burkholderia. The two strains were also differentiated from other species of this genus by fatty acid composition and phenotypic properties. DNA–DNA relatedness data further supported the separation of the new isolates from closely related species. It is therefore proposed that strains KCTC 12081T (=JCM 11778T) and KCTC 12082 be recognized as a novel species, for which the name Burkholderia sordidicola sp. nov. is proposed.
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Isolation of thermophilic Desulfotomaculum strains with methanol and sulfite from solfataric mud pools, and characterization of Desulfotomaculum solfataricum sp. nov.
More LessFour strains of thermophilic, endospore-forming, sulfate-reducing bacteria were enriched and isolated from hot solfataric fields in the Krafla area of north-east Iceland, using methanol and sulfite as substrates. Morphologically, these strains resembled thermophilic Desulfotomaculum species. The strains grew with alcohols, including methanol, with glucose and fructose as electron donors, and with sulfate, sulfite or thiosulfate as electron acceptors. For all four strains, the optimum temperature and pH for growth were 60 °C and pH 7·3, respectively; no added NaCl was required. Phylogenetic analysis based on partial 16S rRNA gene sequence comparisons showed high levels of similarity of the novel strains (>92 %) with Desulfotomaculum kuznetsovii and Desulfotomaculum luciae. However, DNA–DNA hybridization studies with D. kuznetsovii revealed that the four strains belonged to one novel species. A representative of this group of isolates, strain V21T, is proposed as the type strain of a novel species of the spore-forming, sulfate-reducing genus Desulfotomaculum, namely Desulfotomaculum solfataricum (type strain V21T=DSM 14956T=CIP 107984T).
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Arthrobacter koreensis sp. nov., a novel alkalitolerant bacterium from soil
More LessTwo Arthrobacter strains, CA15-8T and CA15-9, were isolated from soil, under alkali conditions, and characterized phenotypically, chemotaxonomically and genetically. These alkalitolerant organisms grew over a wide pH range (pH 7·0–12·0), with an optimum at pH 7·0–8·0. The mean G+C content of the DNA of these strains was 63±2 mol%. The strains contained MK-8(H2) and MK-9(H2) as the main respiratory quinones. The cell-wall peptidoglycan was Lys-Thr-Ala2 and the whole-cell sugar was rhamnose. The major cellular fatty acids of the isolates were anteiso-C15 : 0 and iso-C15 : 0. A phylogenetic analysis, based on 16S rDNA sequence data, revealed that strains CA15-8T and CA15-9 formed an evolutionary lineage distinct from other Arthrobacter species. On the basis of morphological, physiological and chemotaxonomic characteristics, 16S rDNA sequence comparisons and DNA–DNA hybridization data, a novel species of Arthrobacter is proposed, namely Arthrobacter koreensis (type strain CA15-8T=KCTC 9922T=IFO 16787T).
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Bacillus marisflavi sp. nov. and Bacillus aquimaris sp. nov., isolated from sea water of a tidal flat of the Yellow Sea in Korea
More LessTwo Gram-positive or Gram-variable, endospore-forming, moderately halophilic rods (strains TF-11T and TF-12T) were isolated from a tidal flat of the Yellow Sea in Korea and were subjected to a polyphasic taxonomic study. Strains TF-11T and TF-12T had cell-wall peptidoglycan based on meso-diaminopimelic acid. The predominant menaquinone found in the two strains was MK-7. The cellular fatty acid profiles of both strains contained large amounts of branched and saturated fatty acids. The major fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The DNA G+C contents of strains TF-11T and TF-12T were respectively 49 and 38 mol%. Phylogenetic analysis based on 16S rDNA sequences showed that strains TF-11T and TF-12T fell within the radiation of the cluster comprising Bacillus species. The level of 16S rDNA sequence similarity between strains TF-11T and TF-12T was 98·3 %. Strains TF-11T and TF-12T exhibited levels of 16S rDNA sequence similarity of less than 96·0 and 96·3 %, respectively, to Bacillus species. The mean level of DNA–DNA relatedness between the two strains was approximately 7 %. On the basis of phenotypic and phylogenetic data and genomic distinctiveness, strains TF-11T and TF-12T should be placed in the genus Bacillus as two distinct novel species, for which the names Bacillus marisflavi sp. nov. (type strain TF-11T=KCCM 41588T=JCM 11544T) and Bacillus aquimaris sp. nov. (type strain TF-12T=KCCM 41589T=JCM 11545T) are proposed.
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Tuberculosis in seals caused by a novel member of the Mycobacterium tuberculosis complex: Mycobacterium pinnipedii sp. nov.
A comparison of Mycobacterium tuberculosis complex isolates from seals (pinnipeds) in Australia, Argentina, Uruguay, Great Britain and New Zealand was undertaken to determine their relationships to each other and their taxonomic position within the complex. Isolates from 30 cases of tuberculosis in six species of pinniped and seven related isolates were compared to representative and standard strains of the M. tuberculosis complex. The seal isolates could be distinguished from other members of the M. tuberculosis complex, including the recently defined ‘Mycobacterium canettii’ and ‘Mycobacterium caprae’, on the basis of host preference and phenotypic and genetic tests. Pinnipeds appear to be the natural host for this ‘seal bacillus’, although the organism is also pathogenic in guinea pigs, rabbits, humans, Brazilian tapir (Tapirus terrestris) and, possibly, cattle. Infection caused by the seal bacillus is predominantly associated with granulomatous lesions in the peripheral lymph nodes, lungs, pleura, spleen and peritoneum. Cases of disseminated disease have been found. As with other members of the M. tuberculosis complex, aerosols are the most likely route of transmission. The name Mycobacterium pinnipedii sp. nov. is proposed for this novel member of the M. tuberculosis complex (the type strain is 6482T=ATCC BAA-688T=NCTC 13288T).
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Anoxybacillus gonensis sp. nov., a moderately thermophilic, xylose-utilizing, endospore-forming bacterium
More LessSeven closely related xylanolytic, thermophilic bacilli were isolated from mud and water samples from the Gonen and Diyadin hot springs, respectively located in the Turkish provinces of Balikesir and Agri. On the basis of morphology and biochemical characteristics, one of the isolates, designated strain G2T, was studied further. Strain G2T is a xylanolytic, sporulating, Gram-positive, rod-shaped bacterium. The isolate is a thermophilic (optimum temperature for growth, 55–60 °C), facultative anaerobe that grows on a wide range of carbon sources, including glucose, starch, xylose and mannitol. It expressed a high level of xylose isomerase activity on xylose and also on glucose. 16S rRNA gene sequence analysis showed that this isolate resembled Anoxybacillus flavithermus DSM 2641T (>97 % similarity), but 16S–23S rDNA internally transcribed spacer polymorphism PCR showed variation between DSM 2641T and isolate G2T. However, it is also known that analysis of 16S rRNA gene sequences may be insufficient to distinguish between some species. In DNA–DNA hybridization, thermophilic isolate G2T showed relatedness of 53·4 % to A. flavithermus and about 45·0 % to Anoxybacillus pushchinoensis, indicating that it is distinct at the species level. On the basis of the evidence presented, it is proposed that strain G2T (=NCIMB 13933T=NCCB 100040T) be designated as the type strain of Anoxybacillus gonensis sp. nov.
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Brevibacterium lutescens sp. nov., from human and environmental samples
Three strains of coryneform rods isolated from clinical samples and one of environmental origin exhibited phenotypic and chemotaxonomic properties characteristic of the genus Brevibacterium and their 16S rRNA gene sequences were closely related (98·5–99·0 %) to that of Brevibacterium otitidis. However, DNA–DNA hybridization of one strain (CF87T) showed only 59·6 % relatedness to the type strain of B. otitidis, DSM 10718T, and 75–82 % relatedness to the three other strains. The four strains could be differentiated from B. otitidis by cellular fatty acid composition and some phenotypic characteristics. These findings suggest that the four strains belong to a novel species, for which the name Brevibacterium lutescens sp. nov. is proposed. The type strain of B. lutescens is CF87T (=DSM 15022T=CCUG 46604T).
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Rhodococcus tukisamuensis sp. nov., isolated from soil
More LessA novel strictly aerobic, heterotrophic, mesophilic bacterium, strain Mb8T, was isolated from soil in Sapporo City, Hokkaido, Japan. The G+C content of strain Mb8T was 66·0 mol%. It had mycolic acids with 44–52 carbon atoms and C16 : 0 and C18 : 1 (9) as the major fatty acids. The major isoprenoid quinone was MK-8(H2). The cell wall contained meso-diaminopimelic acid, arabinose and galactose. 16S rDNA, chemotaxonomic and morphological data indicated that this strain clearly belonged to the genus Rhodococcus. Based on phenotypic properties and DNA–DNA hybridization data, strain Mb8T (=JCM 11308T=NCIMB 13903T) has been assigned to the genus Rhodococcus as the type strain of Rhodococcus tukisamuensis sp. nov.
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Sporosarcina macmurdoensis sp. nov., from a cyanobacterial mat sample from a pond in the McMurdo Dry Valleys, Antarctica
More LessStrain CMS 21wT was isolated from a cyanobacterial mat sample taken from a pond located in the McMurdo Dry Valleys, Antarctica. Based on its phenotypic, chemotaxonomic and phylogenetic properties, strain CMS 21wT was identified as a member of the genus Sporosarcina. At the 16S rRNA gene level, CMS 21wT exhibited about 93–96 % similarity to all reported species of Sporosarcina and exhibited a maximum similarity of 96 % to both Sporosarcina globispora and Sporosarcina psychrophila. Based on more than 3 % difference at the 16S rRNA gene sequence level and the presence of distinct differences with respect to phenotypic, biochemical and chemotaxonomic features, strain CMS 21wT (=MTCC 4670T=DSM 15428T=CIP 107784T) is proposed as the type strain of a novel species of Sporosarcina, Sporosarcina macmurdoensis sp. nov.
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Paenibacillus stellifer sp. nov., a cyclodextrin-producing species isolated from paperboard
The microflora isolated from food-packaging board is dominated by paenibacilli; a number of these micro-organisms have been characterized using a polyphasic approach. The highest 16S rRNA gene similarity was found between these isolates and Paenibacillus azotofixans ATCC 35681T (97·7 %). The main fatty acid of the paperboard isolates was C16 : 0 (34–45 %); straight-chain fatty acids made up 41–60 % of the total cellular fatty acids, thus distinguishing these strains from other Paenibacillus species. The paperboard isolates produced cyclodextrins from starch. The spore surface had a characteristic ribbed ornamentation. Spores and vegetative cells frequently had pilus-like appendages. Based on phylogenetic data and phenotypic and chemotaxonomic characteristics, it is proposed that the isolates represent a novel species, Paenibacillus stellifer sp. nov., with IS 1T (=DSM 14472T=CCUG 45566T) as the type strain.
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Sporomusa aerivorans sp. nov., an oxygen-reducing homoacetogenic bacterium from the gut of a soil-feeding termite
More LessPreviously undescribed, homoacetogenic bacteria were isolated from gut homogenates of the soil-feeding termite Thoracotermes macrothorax. The isolates were slightly curved, banana-shaped rods (0·6–0·7×1·3–7·0 μm) and were motile by one or more lateral flagella. In older cultures, cells formed club-like sporangia that developed into terminal, heat-resistant endospores. Cells stained Gram-positive but were Gram-negative in the KOH test. The isolates were mesophilic and grew homoacetogenically on H2/CO2 and l-lactate. Strain TmAO3T, which was characterized further, also grew homoacetogenically on pyruvate, citrate, l-alanine, d-mannitol, ethanol, formate and methanol. Succinate was decarboxylated to propionate; fumarate, l-malate and oxaloacetate were fermented to propionate and acetate. Hexoses were not used as substrates. Resting cells had a large capacity for hydrogen-dependent oxygen reduction [826 nmol min−1 (mg protein)−1], which enabled them to initiate growth in non-reduced basal medium that originally contained up to 1·5 kPa oxygen in the headspace, although growth commenced only after the medium had been rendered anoxic. Redox difference spectra of cell extracts indicated the presence of membrane-bound b-type cytochrome(s). Comparative 16S rRNA gene sequence analysis revealed that strain TmAO3T belongs to a subgroup of the phylum of Gram-positive bacteria that is characterized by low DNA G+C content and a Gram-negative cell wall. It is related most closely to representatives of the genus Sporomusa. Based on morphological and physiological properties and on 16S rRNA gene sequence similarity of 94–97 % to other Sporomusa species, the isolates are assigned to Sporomusa aerivorans sp. nov. (type strain, TmAO3T=DSM 13326T=ATCC BAA-625T).
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Streptomonospora alba sp. nov., a novel halophilic actinomycete, and emended description of the genus Streptomonospora Cui et al. 2001
A halophilic actinomycete, strain YIM 90003T, was isolated from a soil sample collected from Xinjiang Province, China, by using starch-casein agar with a salt concentration of 20 % (w/v), pH 7·0. The strain grew well on most media tested. No diffusible pigment was produced. Aerial mycelium and substrate mycelium were well developed on most media. The aerial mycelium formed short spore chains, bearing non-motile, straight to flexuous spores with wrinkled surfaces. The cell walls of strain YIM 90003T contained meso-diaminopimelic acid as the diagnostic diamino acid. Cell-wall hydrolysates contained galactose and arabinose. Menaquinone composition varied with the medium used for cell cultivation; on glucose-yeast extract medium supplemented with 10 % NaCl, the major menaquinone was MK-9(H4), while, on vitamin-enriched ISP 2 medium, the major menaquinones were MK-10(H2), MK-9(H8) and MK-10(H4). Phospholipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, diphosphatidyl glycerol, methylphosphatidylethanolamine, phosphatidylserine, phosphatidylcholine and an unidentified phospholipid. 16S rRNA gene sequence analysis showed Streptomonospora salina as the closest phylogenetic neighbour. On the basis of these analyses, strain YIM 90003T is a member of the genus Streptomonospora, though its properties do not match the generic description fully with respect to the menaquinone composition and peptidoglycan amino acid. Analyses of mechanically disrupted cell walls of the type species, Streptomonospora salina DSM 44593T, and strain YIM 90003T, purified by tryptic digestion and subsequent SDS treatment, revealed the exclusive presence of meso-diaminopimelic acid as the diagnostic diamino acid of peptidoglycan. Thus, the genus description of Streptomonospora, indicating the presence of several amino acids usually not found in the peptidoglycan moiety, is therefore emended. DNA–DNA hybridization and comparison of physiological and chemotaxonomic characteristics demonstrated strain YIM 90003T to be different from Streptomonospora salina. The name Streptomonospora alba sp. nov. is proposed, with strain YIM 90003T (=CCTCC AA001013T=DSM 44588T) as the type strain.
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Gordonia sihwensis sp. nov., a novel nitrate-reducing bacterium isolated from a wastewater-treatment bioreactor
More LessA nitrate-reducing bacterium, strain SPR2T, was isolated from a sulphur-oxidizing, autotrophic denitrification reactor used for advanced treatment of wastewater from the lake of Sihwa, Korea. The strain was aerobic but could grow under anaerobic conditions. It was Gram-positive, exhibited rough white colonies on complex nutrient agar, produced elementary branching hyphae that fragmented into rod/coccus-like elements and showed chemotaxonomic markers that were consistent with classification in the genus Gordonia, i.e. meso-diaminopimelic acid, arabinose and galactose in whole-cell hydrolysates, N-glycolylmuramic acid in the peptidoglycan wall, unbranched saturated and monounsaturated fatty acids plus tuberculostearic acid (TBSA), mycolic acids that comprised 48–56 carbon atoms and MK-9(H2) as the predominant menaquinone. The 16S rDNA sequence of strain SPR2T showed highest similarity to Gordonia amicalis DSM 44461T and Gordonia hydrophobica DSM 44015T, with values of 98·2 and 97·9 %, respectively. These values were far below 99·5 % (usually found at the intraspecies level) and they were in the range that separates species at the intrageneric level. The separate phylogenetic position of SPR2T was supported by differences in fatty acid and mycolic acid compositions and in carbon utilization tests that distinguished strain SPR2T from all known Gordonia species. Combined genotypic and phenotypic data show that strain SPR2T merits recognition as a novel species within the genus Gordonia, for which the name Gordonia sihwensis sp. nov. is proposed; the type strain is SPR2T (=DSM 44576T=NRRL B-24155T).
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Agromyces albus sp. nov., isolated from a plant (Androsace sp.)
More LessAgromyces albus sp. nov. is proposed for an aerobic, oxidase- and catalase-positive actinomycete that was isolated from the above-ground part of a plant (Androsace sp., in the family Primulaceae). The strain is characterized by white colonies, fragmenting hyphae that penetrate into agar media and chemotaxonomic properties that are typical of the genus Agromyces. Analysis of 16S rDNA sequences confirmed that the strain belongs to the genus Agromyces and revealed its close phylogenetic relationship with Agromyces ramosus. DNA–DNA pairing studies showed that the strain belongs to a separate genomic species; this is consistent with its distinction from other Agromyces species at the phenotypic level. The G+C content of the DNA was 69·0 mol%. The type strain is VKM Ac-1800T (=UCM Ac-623T).
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Reclassification of Desulfotomaculum auripigmentum as Desulfosporosinus auripigmenti corrig., comb. nov.
More LessThe species Desulfotomaculum auripigmentum is reclassified as Desulfosporosinus auripigmenti corrig., comb. nov. on the basis of morphological and physiological traits, phylogenetic position and chemotaxonomic properties. Characteristics supplementary to those provided in the original description reveal that the type strain, DSM 13351T (=ATCC 700205T), forms oval, subterminal to terminal spores, possesses ll-diaminopimelic acid and contains MK-7 as the predominant menaquinone, while the whole-cell methanolysate contains even-carbon, straight-chain saturated and mono-unsaturated fatty acids and 1,1-dimethylacetals as major components. DNA–DNA reassociation values below 30 % for Desulfosporosinus orientis DSM 765T and Desulfosporosinus meridiei DSM 13257T demonstrate that strain DSM 13351T shows sufficient genomic differences to maintain its species status. Lack of motility, a smaller cell diameter and the ability to use malate and glycerol as electron donors and fumarate and arsenate as electron acceptors are the main properties that differentiate Desulfosporosinus auripigmenti from the other two species of the genus.
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Actinomyces nasicola sp. nov., isolated from a human nose
More LessA previously undescribed facultatively anaerobic, catalase-negative, Actinomyces-like bacterium was isolated from the nose of a human. On the basis of its cellular morphology and the results of biochemical testing, the micro-organism was tentatively identified as a member of the genus Actinomyces, but it did not correspond to any currently recognized species. Comparative 16S rRNA gene sequencing studies showed the bacterium to be a hitherto unknown subline within the genus Actinomyces, displaying sequence divergence values of more than 6 % with respect to recognized species of the genus. On the basis of biochemical, molecular chemical and molecular phylogenetic evidence, it is proposed that the unknown organism, strain R2014T (=CCUG 46092T=CIP 107668T), be classified as the type strain of a novel species, Actinomyces nasicola sp. nov.
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Promicromonospora vindobonensis sp. nov. and Promicromonospora aerolata sp. nov., isolated from the air in the medieval ‘Virgilkapelle’ in Vienna
Two airborne bacterial isolates designated V45T and V54AT were characterized in order to determine their taxonomic position. 16S rDNA sequence analysis showed that the two isolates shared 98·1 % sequence similarity. Highest sequence similarities (98·0–98·5 %) were found to Promicromonospora citrea DSM 43110T and Promicromonospora sukumoe IFO 14650T. Detection of a quinone system with the predominant compound MK-9(H4), a polar lipid pattern containing phosphatidylglycerol, a fatty acid profile with the predominant acids C15 : 0 iso and C15 : 0 anteiso and the diagnostic cell-wall diamino acid l-lysine supported the assignment of the novel isolates to the genus Promicromonospora. The two isolates could be distinguished from P. sukumoe by the presence of glycine in the peptidoglycan, and the detection of the cell-wall sugar galactose differentiates them from the two established species of the genus Promicromonospora. Each of the two isolates displayed a unique biochemical profile. Results from DNA–DNA hybridizations clearly demonstrated that V45T and V54AT represent separate species. Based on these data, it is proposed that V45T (=IFO 16525T=CCM 7044T) and V54AT (=IFO 16526T =CCM 7043T) be classified as the type strains of two novel Promicromonospora species, for which the names Promicromonospora vindobonensis sp. nov. and Promicromonospora aerolata sp. nov. are proposed.
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Garciella nitratireducens gen. nov., sp. nov., an anaerobic, thermophilic, nitrate- and thiosulfate-reducing bacterium isolated from an oilfield separator in the Gulf of Mexico
A novel Gram-positive, anaerobic and thermophilic bacterium, strain MET79T, was isolated from an oil well located in the Gulf of Mexico. Cells were straight rods, motile by a subpolar flagellum. Spores were formed in old cultures. Inner gas vacuoles swelled the cells when exposed to air. The optimum growth conditions were 55 °C, pH 7·5 and 1 % NaCl. Yeast extract was required for growth. Strain MET79T fermented several sugars, some organic acids and Casamino acids. Glucose was fermented into lactate, acetate, butyrate, H2 and CO2. Strain MET79T reduced thiosulfate to hydrogen sulfide and nitrate to ammonium. The DNA G+C content was 30·9 mol%. The closest phylogenetic relative of strain MET79T was Caloranaerobacter azorensis (88·7 % 16S rDNA sequence similarity). As strain MET79T (=DSM 15102T=CIP 107615T) was physiologically and phylogenetically different from its closest relatives, it is assigned as the type strain of a novel species of a new genus, Garciella nitratireducens gen. nov., sp. nov.
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Actinomyces oricola sp. nov., from a human dental abscess
A previously undescribed Actinomyces-like bacterium was isolated from a human dental abscess. Based on its cellular morphology and the results of biochemical testing the organism was tentatively identified as a member of the genus Actinomyces, but it did not correspond to any currently recognized species of this genus. Comparative 16S rRNA gene sequencing studies showed the bacterium represents a hitherto unknown subline within the genus Actinomyces, clustering within a group of species, which includes Actinomyces bovis, the type species of the genus. Based on biochemical and molecular phylogenetic evidence, it is proposed that the unknown organism recovered from a dental abscess be classified as a new species, Actinomyces oricola sp. nov. The type strain of Actinomyces oricola is R5292T (=CCUG 46090T=CIP 107639T).
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Taxonomic re-evaluation of whorl-forming Streptomyces (formerly Streptoverticillium) species by using phenotypes, DNA–DNA hybridization and sequences of gyrB, and proposal of Streptomyces luteireticuli (ex Katoh and Arai 1957) corrig., sp. nov., nom. rev.
More LessThe taxonomic status of 64 strains of whorl-forming Streptomyces (formerly Streptoverticillium) species was re-evaluated and strains were reclassified on the basis of their phenotypes, DNA–DNA hybridization data and partial sequences of gyrB, the structural gene of the B subunit of DNA gyrase. These strains, which consisted of 46 species and eight subspecies with validly published names and 13 species whose names have not been validly published [including 10 strains examined by the International Streptomyces Project (ISP)], were divided into two groups, namely typical and atypical whorl-forming Streptomyces species, based on their phenotypes and gyrB gene sequences. The typical whorl-forming species (59 strains) were divided into six major clusters of three or more species, seven minor clusters of two species and five single-member clusters, based on the threshold value of 97 % gyrB sequence similarity. Major clusters were typified by Streptomyces abikoensis, Streptomyces cinnamoneus, Streptomyces distallicus, Streptomyces griseocarneus, Streptomyces hiroshimensis and Streptomyces netropsis. Phenotypically, members of each cluster resembled each other closely except for the S. distallicus cluster, which was divided phenotypically into the S. distallicus and Streptomyces stramineus subclusters, and the S. netropsis cluster, which was divided into the S. netropsis and Streptomyces eurocidicus subclusters. Strains in each minor cluster closely resembled each other phenotypically. DNA–DNA relatedness between the representative species and others in each major cluster and/or subcluster, and between strains in the minor clusters, was >70 %, indicating that the major clusters and/or subclusters and the minor clusters each comprise a single species. It was concluded that 59 strains of typical whorl-forming Streptomyces species consisted of the following 18 species, including subjective synonym(s): S. abikoensis, Streptomyces ardus, Streptomyces blastmyceticus, S. cinnamoneus, S. eurocidicus, S. griseocarneus, S. hiroshimensis, Streptomyces lilacinus, ‘Streptomyces luteoreticuli’, Streptomyces luteosporeus, Streptomyces mashuensis, Streptomyces mobaraensis, Streptomyces morookaense, S. netropsis, Streptomyces orinoci, S. stramineus, Streptomyces thioluteus and Streptomyces viridiflavus.
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Bacillus krulwichiae sp. nov., a halotolerant obligate alkaliphile that utilizes benzoate and m-hydroxybenzoate
Obligate alkaliphilic strains, AM31DT and AM11D, that utilize benzoate and m-hydroxybenzoate were isolated from soil obtained from Tsukuba, Ibaraki, Japan. The isolates grew at pH 8–10, but not at neutral pH. They were Gram-positive, facultatively anaerobic, straight rods with peritrichous flagella and produced ellipsoidal spores. The isolates reduced nitrate to nitrite and grew in 0–14 % NaCl, but not in higher concentrations. The major isoprenoid quinones were menaquinone-5, -6 and -7, and the cellular fatty acid profile consisted of significant amounts of 15-C branched-chain acids, isoC15 : 0 and anteisoC15 : 0. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain AM31DT was a member of group 6 (alkaliphiles) in the genus Bacillus. DNA–DNA hybridization revealed a low relatedness of the isolates with several phylogenetically close neighbours, including Bacillus alcalophilus and Bacillus pseudalcaliphilus (less than 19·3 %). Based on phenotypic characteristics, phylogenetic data and DNA–DNA relatedness data, it was concluded that these isolates merited classification as a new species, for which the name Bacillus krulwichiae is proposed. The type strain of this species is AM31DT (=NCIMB 13904T=JCM 11691T=IAM 15000T).
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Alicyclobacillus pomorum sp. nov., a novel thermo-acidophilic, endospore-forming bacterium that does not possess ω-alicyclic fatty acids, and emended description of the genus Alicyclobacillus
More LessA thermo-acidophilic endospore-forming bacterium was isolated from a mixed fruit juice. The organism, strain 3AT, was rod-shaped, grew aerobically at 30–60 °C (optimum 45–50 °C), pH 3·0–6·0 (optimum pH 4·0–4·5) and produced acid from various sugars. It contained menaquinone-7 as the major isoprenoid quinone. The G+C content of the DNA was 53·1 mol%. The predominant cellular fatty acids of the strain were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and anteiso-C17 : 0, but ω-alicyclic fatty acids, which are characteristic of the genus Alicyclobacillus, were not found in the strain. Phylogenetic analyses based on both 16S rRNA and gyrB (DNA gyrase B subunit gene) gene sequences showed that strain 3AT falls into the Alicyclobacillus cluster, validated by significant bootstrap values. However, strain 3AT did not show a close relationship to the other species of the cluster. The level of 16S rDNA similarity between strain 3AT and other strains of the cluster was between 92·5 and 95·5 %. The level of gyrB sequence similarity between strain 3AT and other strains of the cluster was between 68·5 and 74·4 %. DNA–DNA hybridization values between strain 3AT and phylogenetically related strains of the genera Alicyclobacillus, Bacillus and Sulfobacillus were under 13 %, indicating that strain 3AT represents a distinct species. On the basis of these results, strain 3AT should be classified as a novel Alicyclobacillus species. The name Alicyclobacillus pomorum is proposed for this organism. The type strain of Alicyclobacillus pomorum is strain 3AT (=DSM 14955T=IAM 14988T).
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Prauserella halophila sp. nov. and Prauserella alba sp. nov., moderately halophilic actinomycetes from saline soil
The actinomycete strains YIM 90001T and YIM 90005T were isolated on starch-casein agar [20 % (w/v) NaCl, pH 7·0] from a soil sample collected from Xinjiang Province in the west of China. The two isolates were aerobic and Gram-positive. The substrate mycelium was fragmented and an aerial mycelium was well developed on Czapek medium. The aerial mycelium formed long spore chains with branched short or long spore chains at maturity, which were straight to flexuous, and spores were non-motile. Based on the results of metabolic, chemotaxonomic and molecular analyses, the two isolates were identified as two new species of the genus Prauserella, for which the names Prauserella halophila for strain YIM 90001T (=DSM 44617T=CCTCC AA001015T) and Prauserella alba for strain YIM 90005T (=DSM 44590T=CCTCC AA001016T) are proposed.
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Longispora albida gen. nov., sp. nov., a novel genus of the family Micromonosporaceae
More LessA novel actinomycete strain was isolated from a soil sample collected in Japan by using gellan gum as a solidifying agent. Spore-chains from the short sporophores were straight and each had more than 20 spores per chain. Spores possessed no motility. Cell-wall peptidoglycan contained meso-diaminopimelic acid, glycine, alanine and glutamic acid; whole-cell hydrolysates contained arabinose, galactose and xylose. The acyl type of the peptidoglycan was glycolyl. The predominant menaquinones were MK-10(H4) and MK-10(H6); MK-10(H8) was a minor component. Mycolic acids were not detected. The diagostic phospholipid was phosphatidylethanolamine. Cellular fatty acids included heptadecenoic (C17 : 1), 14-methylpentadecanoic (i-C16 : 0) and octadecenoic (C18 : 1) acids. The G+C content of the DNA was 70 mol%. On the basis of morphogical and chemotaxonomic properties and phylogenetic analysis based on 16S rDNA sequence data, it is proposed that this strain should be classified in a novel genus and species, Longispora albida gen. nov., sp. nov., in the family Micromonosporaceae. The type strain is K97-0003T (=NRRL B-24201T=JCM 11711T).
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Aerobic growth of Anoxybacillus pushchinoensis K1T: emended descriptions of A. pushchinoensis and the genus Anoxybacillus
More LessIn this work, corrections are made to the descriptions of the species Anoxybacillus pushchinoensis corrig. and the genus Anoxybacillus. Experiments to determine the relationship of A. pushchinoensis K1T to oxygen showed that it was capable of aerobic growth, but preferred to grow anaerobically. During aerobic growth, the redox indicator resazurin was reduced as a result of hydrogen gas production. The facultatively anaerobic nature of K1T was ascertained by cultivation in aerobic liquid medium, where growth began at the bottom of the tube. The anaerobic nature of K1T was also indicated by a negative catalase reaction. This work is submitted to correct the description of the species A. pushchinoensis from obligate anaerobe to aerotolerant anaerobe and to emend the description of the genus Anoxybacillus from obligate anaerobes or facultative anaerobes to aerotolerant anaerobes or facultative anaerobes.
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Saccharomonospora paurometabolica sp. nov., a moderately halophilic actinomycete isolated from soil in China
A novel, moderately halophilic actinomycete, strain YIM 90007T, was isolated from a soil sample collected from the Xinjiang Province, China, and characterized. The optimum growth temperature of the strain was between 35 and 37 °C and growth occurred optimally in 10 % (w/v) NaCl. The cell wall of strain YIM 90007T contained meso-diaminopimelic acid. Whole-cell sugars were galactose, arabinose and ribose. The principal menaquinone was MK-9(H4), while MK-9(H2) was found in smaller amounts. The phospholipids were phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and hydroxyphosphatidylethanolamine. The predominant cellular fatty acids were of the iso- and anteiso-branched and unbranched types; significant amounts of 2-hydroxy fatty acids were also found but 10-methyl-branched fatty acids were missing. The DNA G+C content of strain YIM 900007T was 71 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed strain YIM 90007T to be closely related to Saccharomonospora halophila (98·7 % similarity). DNA–DNA hybridization revealed a relatedness of 53·8 % between strain YIM 90007T and S. halophila DSM 44411T. Based on physiological and biochemical characteristics, phylogenetic analysis (based on 16S rRNA gene sequences) and DNA–DNA relatedness, it is concluded that strain YIM 90007T represents a novel species of the genus Saccharomonospora, for which the name Saccharomonospora paurometabolica (type strain YIM 90007T=CCTCC AA001018T=CCRC 16315T=DSM 44619T) is proposed.
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Nocardia puris sp. nov.
More LessA bacterial isolate (IMMIB R-145T) from a human abscess was subjected to a polyphasic taxonomic study. Chemotaxonomic investigations revealed the isolate to have cell wall chemotype IV and mycolic acids consistent with characteristics of the genus Nocardia. Comparative 16S rRNA gene sequencing showed that the isolate constituted a distinct subline within the genus Nocardia, displaying greater than 1·7 % sequence divergence with established species. However, a DNA–DNA hybridization study demonstrated unambiguously that the isolate was genealogically distinct from closely related species, namely, Nocardia abscessus, Nocardia cyriacigeorgica and Nocardia farcinica, with which it showed high levels of 16S rDNA sequence similarity (97·8, 97·9 and 98·3 %, respectively). Based on phenotypic and phylogenetic data, it is proposed that this isolate be classified as a new species of the genus Nocardia, for which the name Nocardia puris (type strain IMMIB R-145T=DSM 44599T=NRRL B-24204T) is proposed.
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Amycolatopsis kentuckyensis sp. nov., Amycolatopsis lexingtonensis sp. nov. and Amycolatopsis pretoriensis sp. nov., isolated from equine placentas
More LessActinomycete strains isolated from lesions on equine placentas from two horses in Kentucky and one in South Africa were subjected to a polyphasic taxonomic study. Chemotaxonomic and morphological characteristics indicated that the isolates are members of the genus Amycolatopsis. On the basis of phylogenetic analysis of 16S rDNA sequences, the isolates are related most closely to Amycolatopsis mediterranei. Physiological characteristics of these strains indicated that they do not belong to A. mediterranei and DNA relatedness determinations confirmed that these strains represent three novel species of the genus Amycolatopsis, for which the names Amycolatopsis kentuckyensis (type strain, NRRL B-24129T=LDDC 9447-99T=DSM 44652T), Amycolatopsis lexingtonensis (type strain, NRRL B-24131T=LDDC 12275-99T=DSM 44653T) and Amycolatopsis pretoriensis (type strain, NRRL B-24133T=ARC OV1 0181T=DSM 44654T) are proposed.
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Species identification of genus Bifidobacterium based on partial HSP60 gene sequences and proposal of Bifidobacterium thermacidophilum subsp. porcinum subsp. nov.
Lin Zhu, Wei Li and Xiuzhu DongSequence homology of partial 60 kDa heat-shock protein (HSP60) genes was analysed for 50 Bifidobacterium strains that represent 12 Bifidobacterium species and subspecies with validly published names. Sequence similarities were 96·5–100 % within the same species, 95·5–97 % at the subspecies level and 80–96 % (mean, 88 %) at the interspecies level among the 10 Bifidobacterium species. Hence, the HSP60 gene was a more accurate tool for species identification within the genus Bifidobacterium than 16S rDNA. Two new Bifidobacterium strains isolated from piglet faeces were shown to be closely related to the thermophilic bifidobacterial group, based on 16S rDNA sequence analysis: strain P3-14T (=AS 1.3009T=LMG 21689T) exhibited 97·9 % similarity to Bifidobacterium boum JCM 1211T, 97·2 % similarity to Bifidobacterium thermacidophilum AS 1.2282T and 97 % similarity to Bifidobacterium thermophilum JCM 1207T. However, higher levels of DNA–DNA relatedness (83 %) and HSP60 gene sequence similarity (97 %) were determined between B. thermacidophilum AS 1.2282T and strain P3-14T, indicating a closer relationship between them. The new strains differed from B. thermacidophilum AS 1.2282T in some phenotypic characteristics, such as growth at a lower temperature (46·5 °C), as well as different sugar-fermentation patterns. Hence, a novel Bifidobacterium subspecies, Bifidobacterium thermacidophilum subsp. porcinum subsp. nov., is designated.
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Gordonia paraffinivorans sp. nov., a hydrocarbon-degrading actinomycete isolated from an oil-producing well
More LessThe taxonomic position of an actinomycete, strain HD321T, isolated from an oil-producing well of Daqing oilfield, was clarified using a polyphasic taxonomic approach. The strain possessed cell-wall chemotype IV, MK-9(H2) as the predominant menaquinone, relatively long-chain mycolic acids (52–62 carbon atoms) of the Gordonia type, straight-chain saturated and monounsaturated fatty acids and tuberculostearic acid. The G+C content of the DNA was 66 mol%. 16S rDNA analyses as well as chemotaxonomic and physiological properties indicated that strain HD321T represents a novel species within the genus Gordonia, for which the name Gordonia paraffinivorans sp. nov. is proposed; the type strain is HD321T (=AS 4.1730T=DSM 44604T).
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Macrococcus brunensis sp. nov., Macrococcus hajekii sp. nov. and Macrococcus lamae sp. nov., from the skin of llamas
Eight strains of Gram-positive, catalase- and oxidase-positive cocci were isolated from the skin of llamas (Lama glama L.) and characterized using a polyphasic approach. These strains were assigned to the genus Macrococcus on the basis of their phenotypic properties (resistance to bacitracin and sensitivity to furazolidone) and DNA base content (40–42 mol% G+C). Phylogenetic analysis based on 16S rDNA confirmed that the strains are members of the genus Macrococcus. They differed from all hitherto described macrococcal species in their production of phosphatase and reduction of nitrate (most strains) and the inability to produce acid from glycerol or to grow in 7·5 % NaCl. Ribotyping (EcoRI), macrorestriction analysis (XbaI) and fatty acid methyl ester analysis divided the strains from llamas into three stable clusters. Moreover, ribotyping differentiated the strains analysed not only from previously described macrococcal species but also from oxidase-positive staphylococci. DNA–DNA hybridization confirmed that the three clusters represent separate genomic groups (similarity values<54 %). All the results showed that the strains represent three novel species, for which the names Macrococcus hajekii sp. nov. (type strain CCM 4809T=LMG 21711T), Macrococcus brunensis sp. nov. (type strain CCM 4811T=LMG 21712T) and Macrococcus lamae sp. nov. (type strain CCM 4815T=LMG 21713T) are proposed.
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- Unicellular Eukaryotes
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Novel anamorphic mite-associated fungi belonging to the Ustilaginomycetes: Meira geulakonigii gen. nov., sp. nov., Meira argovae sp. nov. and Acaromyces ingoldii gen. nov., sp. nov.
Three novel mite-associated basidiomycetous species are described in two new anamorph genera as Meira geulakonigii gen. nov., sp. nov. (type CBS 110052T=NRRL Y-27483T=AS 004T), Meira argovae sp. nov. (type CBS 110053T=NRRL Y-27482T=AS 005T) and Acaromyces ingoldii gen. nov., sp. nov. (type CBS 110050T=NRRL Y-27484T=AS 001T). Morphologically, these fungi are similar to the yeast-like fungi classified in the Ustilaginales, such as Pseudozyma species. However, analysis of the D1/D2 domain of the LSU rDNA suggests that they belong to two different lineages within the Exobasidiomycetidae of the Ustilaginomycetes (Basidiomycota). Furthermore, these fungi may be of interest for the biocontrol of mites, as they reduced mite numbers by approximately 80 % after inoculation.
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Metschnikowia vanudenii sp. nov. and Metschnikowia lachancei sp. nov., from flowers and associated insects in North America
More LessTwo new species of the ascosporic yeast genus Metschnikowia were isolated from nectaries and associated muscoid flies of flowers from the common milkweed (Asclepias syriaca) in North America, and are described as Metschnikowia vanudenii [type strain=PYCC 4650T=CBS 9134T=NRRL Y-27243T=UWO(PS) 86A4.1T] and Metschnikowia lachancei [type strain=PYCC 4605T=CBS 9131T=NRRL Y-27242T=UWO(PS) 7ASB2.3T]. As with the previously described Metschnikowia gruessii, M. vanudenii has vegetative cells with an ‘aeroplane’ or cross-like configuration, produces ovoid chlamydospores and forms ellipsoidopedunculate asci with two acicular ascospores. Metschnikowia lachancei is distinguished from other Metschnikowia species by formation of club-shaped asci with 1–2 thick clavate ascospores. The phylogenetic positions of the proposed new species within Metschnikowia were determined from sequence analysis of the D1/D2 domain of 26S rDNA. The new species show low nuclear DNA relatedness with neighbouring taxa.
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Hanseniaspora meyeri sp. nov., Hanseniaspora clermontiae sp. nov., Hanseniaspora lachancei sp. nov. and Hanseniaspora opuntiae sp. nov., novel apiculate yeast species
More LessFourteen apiculate yeast strains isolated from various sources in South Africa, North America and the Hawaiian islands were found to be genetically divergent from other Hanseniaspora–Kloeckera species by using randomly amplified polymorphic DNA (RAPD)-PCR. After cluster analysis of the RAPD-PCR fingerprints, five groups were recognized. DNA reassociation values among representatives of these groups and strains of Hanseniaspora–Kloeckera species revealed that the strains represent five novel species. Four are described here as novel species of Hanseniaspora: Hanseniaspora meyeri sp. nov. (type CBS 8734T), Hanseniaspora clermontiae sp. nov. (type CBS 8821T), Hanseniaspora lachancei sp. nov. (type CBS 8818T) and Hanseniaspora opuntiae sp. nov. (type CBS 8733T). The fifth novel species, which is represented by only a single strain, CBS 8772, is not introduced as a new taxon. Phylogenetic analyses of the D1/D2 region of the 26S rDNA and internal transcribed spacer (ITS) regions with 5·8S rDNA sequences placed H. meyeri, H. clermontiae, H. lachancei, H. opuntiae and strain CBS 8772 close to Hanseniaspora uvarum and Hanseniaspora guilliermondii. The key characteristics for standard physiological identification of H. clermontiae and H. lachancei were respectively maximal growth temperature and assimilation of 2-keto-d-gluconate. However, physiological characteristics did not allow the distinction of H. opuntiae and strain CBS 8772 from H. guilliermondii or H. meyeri from H. uvarum. These three novel taxa can be identified by either ITS sequencing or PCR-RFLP of ITS regions using restriction enzymes MboII and HinfI.
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- Evolution, Phylogeny And Biodiversity
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Phylogenetic and physiological characterization of a heterotrophic, chemolithoautotrophic Thiothrix strain isolated from activated sludge
More LessThe sheathed filamentous bacterium known as strain CT3, isolated by micromanipulation from an activated sludge treatment plant in Italy, is a member of the genus Thiothrix in the γ-Proteobacteria according to 16S rDNA sequence analysis. The closest phylogenetic neighbours of strain CT3 are strains I and QT, which were also isolated from activated sludge and belong to the species Thiothrix fructosivorans. These strains have respectively 99·2 and 99·4 % similarity to CT3 by 16S rDNA sequence comparison. CT3 shows 63–67 % DNA–DNA hybridization with strain I, which is the only currently viable strain of T. fructosivorans. CT3 is the second strain in the genus Thiothrix that has been shown to be capable of growing autotrophically with reduced sulfur compounds as the sole energy source; autotrophy was also confirmed in strain I. The first reported chemolithoautotrophic isolate of this genus was a strain of ‘Thiothrix ramosa’ that was isolated from a hydrogen sulfide spring and is morphologically distinguishable from all other described strains of Thiothrix, including CT3. CT3 is an aerobic organism that is non-fermentative, not capable of denitrification and able to grow heterotrophically. Autotrophy in the genus Thiothrix should be investigated more fully to better define the taxonomy of this genus.
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16S rRNA and amoA-based phylogeny of 12 novel betaproteobacterial ammonia-oxidizing isolates: extension of the dataset and proposal of a new lineage within the nitrosomonads
The phylogenetic relationship of 12 ammonia-oxidizing isolates (eight nitrosospiras and four nitrosomonads), for which no gene sequence information was available previously, was investigated based on their genes encoding 16S rRNA and the active site subunit of ammonia monooxygenase (AmoA). Almost full-length 16S rRNA gene sequences were determined for the 12 isolates. In addition, 16S rRNA gene sequences of 15 ammonia-oxidizing bacteria (AOB) published previously were completed to allow for a more reliable phylogeny inference of members of this guild. Moreover, sequences of 453 bp fragments of the amoA gene were determined from 15 AOB, including the 12 isolates, and completed for 10 additional AOB. 16S rRNA gene and amoA-based analyses, including all available sequences of AOB pure cultures, were performed to determine the position of the newly retrieved sequences within the established phylogenetic framework. The resulting 16S rRNA gene and amoA tree topologies were similar but not identical and demonstrated a superior resolution of 16S rRNA versus amoA analysis. While 11 of the 12 isolates could be assigned to different phylogenetic groups recognized within the betaproteobacterial AOB, the estuarine isolate Nitrosomonas sp. Nm143 formed a separate lineage together with three other marine isolates whose 16S rRNA sequences have not been published but have been deposited in public databases. In addition, 17 environmentally retrieved 16S rRNA gene sequences not assigned previously and all originating exclusively from marine or estuarine sites clearly belong to this lineage.
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Flow cytometric sorting, phylogenetic analysis and in situ detection of Oscillospira guillermondii, a large, morphologically conspicuous but uncultured ruminal bacterium
Flow cytometric sorting based on its large cell size enabled an enriched fraction of Oscillospira guillermondii cells to be obtained from the rumen contents of a sheep. Phylogenetic analysis based on cloned 16S rDNA sequences indicated that the bacterium is a member of the low-G+C Gram-positive bacterial cluster. Sporobacter termitidis and Papillibacter cinnamivorans were the most closely related known species, with sequence similarities of only 86·3–88·1 %. Fluorescently labelled 16S rRNA-targeted oligonucleotide probes specific for Oscillospira were designed and applied to the rumen sample from which the enriched fraction was obtained. The probes hybridized specifically with the large, morphologically conspicuous Oscillospira cells.
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- International Committee On Systematics Of Prokaryotes
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- Taxonomic Notes
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Agrobacterium is a definable genus of the family Rhizobiaceae
More LessMembers of the genus Agrobacterium constitute a diverse group of organisms, all of which, when harbouring the appropriate plasmids, are capable of causing neoplastic growths on susceptible host plants. The agrobacteria, which are members of the family Rhizobiaceae, can be differentiated into at least three biovars, corresponding to species divisions based on differential biochemical and physiological tests. Recently, Young et al. [Int J Syst Evol Microbiol 51 (2003), 89–103] proposed to incorporate all members of the genus Agrobacterium into the genus Rhizobium. We present evidence from classical and molecular comparisons that supports the conclusion that the biovar 1 and biovar 3 agrobacteria are sufficiently different from members of the genus Rhizobium to warrant retention of the genus Agrobacterium. The biovar 2 agrobacteria cluster more closely to the genus Rhizobium, but some studies suggest that these isolates differ from species of Rhizobium with respect to their capacity to interact with plants. We conclude that there is little scientific support for the proposal to group the agrobacteria into the genus Rhizobium and consequently recommend retention of the genus Agrobacterium.
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Classification and nomenclature of Agrobacterium and Rhizobium – a reply to Farrand et al. (2003)
More LessFarrand et al. [Int J Syst Evol Microbiol 53 (2003), 1681–1687] have presented a critique of the proposal of Young et al. [Int J Syst Evol Microbiol 51 (2001), 89–103] to revise the nomenclature and classification of Rhizobium. They argued that Young et al. (2001) are mistaken in their reclassification of all Agrobacterium species within Rhizobium, and that the resulting nomenclatural revision is ‘unnecessary and unwarranted’. These objections arise because the authors appear not to understand the role of formal nomenclature, and fail to distinguish between formal and special-purpose nomenclatures (Bacteriological Code, 1990 Revision). The arguments set out by Farrand et al. (2003) can be addressed in terms of (1) the taxonomic status of the genera Agrobacterium and Rhizobium; (2) the status of species and biovars and their nomenclature; and (3) the role of transmissible genomic elements in classification and nomenclature. Finally, an attempt is made to unravel the confusion underpinning their discussion with a consideration of the relationship between formal and special-purpose nomenclatures.
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Taxonomic problems arising in the genera Haloterrigena and Natrinema
More LessData currently available on members of the genera Haloterrigena and Natrinema suggest that some strains of the species Haloterrigena turkmenica that have been shown by DNA–DNA hybridization to belong to this species show a high degree of 16S rDNA sequence similarity to members of the genus Natrinema. However, closer examination of the data presented in the original publications and in subsequent publications suggests that there may be a number of problems associated with some of the published data.
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The nomenclatural type of the genus Deleya and the consequences of Deleya aesta and Alcaligenes aquamarinus being synonyms
More LessThe genus Deleya was created to encompass a number of marine organisms that had previously been classified in diverse genera. Deleya aesta was designated as the type species of the genus. Subsequent work indicated that Deleya aesta, Alcaligenes aquamarinus and Alcaligenes faecalis subsp. homari were heterotypic synonyms. Consequently, Akagawa & Yamasato (Int J Syst Bacteriol 39, 462–466, 1989) concluded that, based on Rules 23a and 51b of the Bacteriological Code (1975 Revision), the oldest legitimate species epithet was aquamarinus and the type species of the genus Deleya should therefore be changed to Deleya aquamarina. Dobson & Franzmann (Int J Syst Bacteriol 46, 550–558, 1996) concluded that it was not possible to distinguish between members of the genus Deleya and members of the genus Halomonas Vreeland et al. 1980 , leading them to transfer members of the genus Deleya to the genus Halomonas and resulting in the creation of a new combination, Halomonas aquamarina. Closer examination of some of these changes indicates that they are not all in accordance with the Rules of the Bacteriological Code (1975 or 1990 Revisions).
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