- Volume 54, Issue 6, 2004
Volume 54, Issue 6, 2004
- Validation List No. 100
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Validation of 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 publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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- Notification List
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Notification that new names and new combinations have appeared in volume 54, part 4, of the IJSEM
This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles). Taxonomic opinions included in this List (i.e. the creation of synonyms or the emendation of circumscriptions) cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission.
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- New Taxa
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- Archaea
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Haloferax sulfurifontis sp. nov., a halophilic archaeon isolated from a sulfide- and sulfur-rich spring
A pleomorphic, extremely halophilic archaeon (strain M6T) was isolated from a sulfide- and sulfur-rich spring in south-western Oklahoma (USA). It formed small (0·8–1·0 mm), salmon pink, elevated colonies on agar medium. The strain grew in a wide range of NaCl concentrations (6 % to saturation) and required at least 1 mM Mg2+ for growth. Strain M6T was able to reduce sulfur to sulfide anaerobically. 16S rRNA gene sequence analysis indicated that strain M6T belongs to the family Halobacteriaceae, genus Haloferax; it showed 96·7–98·0 % similarity to other members of the genus with validly published names and 89 % similarity to Halogeometricum borinquense, its closest relative outside the genus Haloferax. Polar lipid analysis and DNA G+C content further supported placement of strain M6T in the genus Haloferax. DNA–DNA hybridization values, as well as biochemical and physiological characterization, allowed strain M6T to be differentiated from other members of the genus Haloferax. A novel species, Haloferax sulfurifontis sp. nov., is therefore proposed to accommodate the strain. The type strain is M6T (=JCM 12327T=CCM 7217T=DSM 16227T=CIP 108334T).
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- Other Bacteria
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Reclassification of Mesoplasma pleciae as Acholeplasma pleciae comb. nov. on the basis of 16S rRNA and gyrB gene sequence data
More LessGenomic DNA sequence data for the 16S rRNA gene and the gyrB gene of Mesoplasma pleciae PS-1T (=ATCC 49582T=NBRC 100476T) demonstrate a much closer relationship to Acholeplasma laidlawii and Acholeplasma oculi than to other species in the order Entomoplasmatales. In addition, the preferred use of UGG rather than UGA as the codon for tryptophan in the gyrB sequence probably places the organism outside the order Entomoplasmatales. It is proposed that M. pleciae be reclassified in the genus Acholeplasma, as Acholeplasma pleciae comb. nov.
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Thermosipho atlanticus sp. nov., a novel member of the Thermotogales isolated from a Mid-Atlantic Ridge hydrothermal vent
A novel anaerobic, thermophilic and heterotrophic bacterium, designated strain DV1140T, was isolated from a deep-sea hydrothermal vent sample from the Mid-Atlantic Ridge. The cells were non-motile straight rods, 1·8 μm long and 0·4 μm wide, surrounded by an outer sheath-like structure (toga). They grew at 45–80 °C (optimum 65 °C), pH 5·0–9·0 (optimum pH 6·0) and at sea salt concentrations of 20–60 g l−1 (optimum 30 g l−1). Strain DV1140T was able to ferment yeast extract, peptone, brain heart infusion, gelatin, starch, galactose, arabinose, glucose, trehalose and cellobiose. The fermentation products identified on glucose in the presence of yeast extract and peptone were acetate, isovalerate and hydrogen. The G+C content of the genomic DNA was 33 mol%. Phylogenetic analysis of the 16S rRNA gene sequence (GenBank accession number AJ577471) located the strain within the genus Thermosipho in the bacterial domain. On the basis of 16S rRNA gene sequence comparisons, and physiological and biochemical characteristics, the isolate represents a novel species, for which the name Thermosipho atlanticus sp. nov. is proposed. The type strain is DV1140T (=CIP 108053T=DSM 15807T).
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Algoriphagus antarcticus sp. nov., a novel psychrophile from microbial mats in Antarctic lakes
More LessA taxonomic study was performed on six strains isolated from microbial mats of lakes Reid, Fryxell and Ace in Antarctica. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains belonged to the family ‘Flexibacteraceae’ and were closely related to the recently described genera Algoriphagus and Hongiella. The isolates were Gram-negative, chemoheterotrophic, aerobic, psychrophilic, orange–red-pigmented bacteria and their DNA G+C content ranged from 39·9 to 41·0 mol%. Whole-cell fatty acid profiles included mainly branched fatty acids and summed feature 3, comprising 15 : 0 iso 2OH, 16 : 1ω7c or both. On the basis of genotypic, phenotypic, chemotaxonomic and phylogenetic results, the novel strains were classified as Algoriphagus antarcticus sp. nov. The type strain is LMG 21980T (=DSM 15986T=R-10710T).
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Hydrogenivirga caldilitoris gen. nov., sp. nov., a novel extremely thermophilic, hydrogen- and sulfur-oxidizing bacterium from a coastal hydrothermal field
More LessA novel extremely thermophilic, hydrogen- and sulfur-oxidizing bacterium, designated strain IBSK3T, was isolated from a coastal hot spring in Ibusuki, Kagoshima Prefecture, Japan. The cells were motile, straight to slightly curved rods (1·2–3·0 μm long and 0·3–0·4 μm wide). Strain IBSK3T was an obligate chemolithoautotroph growing by respiratory nitrate reduction with H2, forming N2O as an end product. Low concentrations of O2 (0·4–7·7 %, v/v; optimum 2·0 %, v/v) could serve as an alternative electron acceptor to growth. In addition, strain IBSK3T was able to utilize elemental sulfur as a sole electron donor with either nitrate or low concentrations of O2 as an electron acceptor. Growth was observed between 55 and 77·5 °C (optimum 75 °C; 2 h doubling time), pH 5·5 and 8·3 (optimum pH 6·5–7·0), and in the presence of 0·5 and 4·0 % NaCl (optimum 2·0 %). The G+C content of the genomic DNA was 49·2 mol%. On the basis of 16S rRNA gene sequence analysis, strain IBSK3T belonged to the family Aquificaceae, but it only demonstrated a distant phylogenetic relationship with any recognized species within the family (sequence similarity was less than 92 %). On the basis of the physiological and molecular characteristics of the novel isolate, a new genus and novel species are proposed: the type strain of Hydrogenivirga caldilitoris gen. nov., sp. nov. is IBSK3T (=JCM 12173T=ATCC BAA-821T).
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Kaistella koreensis gen. nov., sp. nov., a novel member of the Chryseobacterium–Bergeyella–Riemerella branch
Gram-negative, non-spore-forming, rod-shaped, yellow-pigmented bacteria isolated from a freshwater stream in Korea were investigated to determine their taxonomic position. Complete 16S rRNA gene sequence analysis indicated that the organisms should be placed in the Chryseobacterium–Bergeyella–Riemerella branch in the family Flavobacteriaceae. Phylogenetically, the strains were most closely related to Chryseobacterium balustinum ATCC 33487T and Chryseobacterium scophthalmum LMG 13028T (94·3 and 94·1 % 16S rRNA gene sequence similarity, respectively) and they clustered on a separate well-supported branch. The strains contained menaquinone MK-6 as the predominant respiratory quinone and showed higher G+C contents (41·7 mol%) than other species in the Chryseobacterium–Bergeyella–Riemerella branch and i-C15 : 0 as a major fatty acid (47–52 %). The phylogenetic distances from any species with validly published names and their phenotypic properties confirmed that the strains constitute a separate species in a new genus, for which the name Kaistella koreensis gen. nov., sp. nov. is proposed (type strain Chj707T=KCTC 12107T=IAM 15050T).
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Aquiflexum balticum gen. nov., sp. nov., a novel marine bacterium of the Cytophaga–Flavobacterium–Bacteroides group isolated from surface water of the central Baltic Sea
More LessA bacterial isolate from the Baltic Sea, BA160T, was characterized for its physiological and biochemical features, fatty acid profile, G+C content and phylogenetic position based on 16S rRNA gene sequences. The strain was isolated from the surface water of the central Baltic Sea during the decay of a plankton bloom. Phylogenetic analyses of the 16S rRNA gene sequence revealed a clear affiliation with the family ‘Flexibacteraceae’, and showed the closest phylogenetic relationship with the species Belliella baltica and Cyclobacterium marinum. The G+C content of the DNA was 38·4 mol%. The strain was red-coloured due to carotenoids, Gram-negative, rod-shaped, and catalase- and oxidase-positive. Growth was observed at salinities from 0 to 6 %, with an optimum around 1·5 %. Temperature for growth ranged from 4 to 40 °C, with an optimum around 30 °C. The fatty acids were dominated by branched-chain fatty acids (>87 %), with a high abundance of iso-C15 : 0 (23 %) and anteiso-C15 : 0 (19 %). According to its morphology, physiology, fatty acid composition, G+C content and 16S rRNA gene sequence, strain BA160T is considered to represent a new genus of the family ‘Flexibacteraceae’. Due to its aquatic origin, the name Aquiflexum balticum gen. nov, sp. nov. is suggested for the type species (type strain, BA160T=DSM 16537T=LMG 22565T=CIP 108445T) of the new genus.
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- Proteobacteria
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Chromohalobacter sarecensis sp. nov., a psychrotolerant moderate halophile isolated from the saline Andean region of Bolivia
More LessA moderately halophilic, aerobic, motile, Gram-negative, rod-shaped bacterium (strain LV4T) was isolated from saline soil around the lake Laguna Verde in the Bolivian Andes. The organism is a heterotroph, able to utilize various carbohydrates as a carbon source. It showed tryptophan deaminase, oxidase and catalase activity, but was unable to produce indole or H2S; nitrate was not reduced. The G+C content of the genomic DNA was 56·1 mol%. The pH range for growth was 5–10, temperature range was 0–45 °C and the range of NaCl concentrations was 0–25 % (w/v). On the basis of 16S rRNA gene sequence analysis, strain LV4T was found to be closely related to Chromohalobacter canadensis DSM 6769T and Pseudomonas beijerinckii DSM 7218T; however, its DNA–DNA relatedness with these type strains was low. Strain LV4T resembled other Chromohalobacter species with respect to various physiological, biochemical and nutritional characteristics but also exhibited differences. Thus, a novel species, Chromohalobacter sarecensis sp. nov., is proposed, with LV4T (=CCUG 47987T=ATCC BAA-761T) as the type strain.
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Caenibacterium thermophilum is a later synonym of Schlegelella thermodepolymerans
Recently, two strains of Schlegelella thermodepolymerans Elbanna et al. 2003 and an independently isolated bacterium, Caenibacterium thermophilum Manaia et al. 2003 , were described in parallel as gen. nov., sp. nov. Analysis of the 16S rRNA genes revealed similarity between C. thermophilum and the two strains of S. thermodepolymerans of 99·8 and 99·6 %, respectively. DNA–DNA hybridization experiments revealed mean DNA reassociation levels of 97–98 % among C. thermophilum and the two strains of S. thermodepolymerans, thereby confirming the close relationship and indicating that C. thermophilum is a later synonym of S. thermodepolymerans.
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Shewanella profunda sp. nov., isolated from deep marine sediment of the Nankai Trough
A novel piezotolerant, mesophilic, facultatively anaerobic, organotrophic, polarly flagellated bacterium (strain LT13aT) was isolated from a deep sediment layer in the Nankai Trough (Leg 190, Ocean Drilling Program) off the coast of Japan. This organism used a wide range of organic substrates as sole carbon and energy sources: pyruvate, glutamate, succinate, fumarate, lactate, citrate, peptone and tryptone. Oxygen, nitrate, fumarate, ferric iron and cystine were used as electron acceptors. Maximal growth rates were observed at a hydrostatic pressure of 10 MPa. Hydrostatic pressure for growth was in the range 0·1–50 MPa. Predominant cellular fatty acids were 16 : 1ω7c, 15 : 0 iso, 16 : 0 and 13 : 0 iso. The G+C content of the DNA was 44·9 mol%. On the basis of 16S rRNA gene sequences, strain LT13aT was shown to belong to the γ-Proteobacteria, being closely related to Shewanella putrefaciens (98 %), Shewanella oneidensis (97 %) and Shewanella baltica (96 %). Levels of DNA homology between strain LT13aT and S. putrefaciens, S. oneidensis and S. baltica were <20 %, indicating that strain LT13aT represents a novel species. Genetic evidence and phenotypic characteristics showed that isolate LT13aT constitutes a novel species of the genus Shewanella. Because of the deep origin of the strain, the name Shewanella profunda sp. nov. is proposed, with LT13aT (=DSM 15900T=JCM 12080T) as the type strain.
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Erythrobacter aquimaris sp. nov., isolated from sea water of a tidal flat of the Yellow Sea in Korea
More LessThree Gram-negative, non-motile, non-spore-forming, slightly halophilic rods (strains SW-110T, SW-116 and SW-140) were isolated from sea water of a tidal flat of the Yellow Sea in Korea and subjected to a polyphasic taxonomic study. The three isolates did not produce bacteriochlorophyll a and were characterized chemotaxonomically by having ubiquinone-10 as the predominant respiratory lipoquinone and C18 : 1 ω7c and C17 : 1 ω6c as the major fatty acids. The DNA G+C content of the three isolates was between 62·2 and 62·9 mol%. Strains SW-110T, SW-116 and SW-140 showed no difference in their 16S rRNA gene sequences, and their mean level of DNA–DNA relatedness was 94·8 %. Phylogenetic analyses based on 16S rRNA gene sequences showed that the three strains form a distinct phylogenetic lineage within the cluster comprising Erythrobacter species. Similarities between the 16S rRNA gene sequences of strains SW-110T, SW-116 and SW-140 and the type strains of Erythrobacter species ranged from 98·4 % (with Erythrobacter longus) to 97·7 % (with Erythrobacter flavus). Levels of DNA–DNA relatedness between strains SW-110T, SW-116 and SW-140 and the type strains of all recognized Erythrobacter species were in the range 5·3–12·7 %. On the basis of polyphasic taxonomic data, strains SW-110T, SW-116 and SW-140 were classified as a novel Erythrobacter species, for which the name Erythrobacter aquimaris sp. nov. is proposed. The type strain is SW-110T (=KCCM 41818T=JCM 12189T).
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Mesorhizobium septentrionale sp. nov. and Mesorhizobium temperatum sp. nov., isolated from Astragalus adsurgens growing in the northern regions of China
Ninety-five rhizobial strains isolated from Astragalus adsurgens growing in the northern regions of China were classified into three main groups, candidate species I, II and III, based on a polyphasic approach. Comparative analysis of full-length 16S rRNA gene sequences of representative strains showed that candidate species I and II were Mesorhizobium, while candidate species III, which consisted of non-nodulating strains, was closely related to Agrobacterium tumefaciens. The phylogenetic relationships of the three candidate species and some related strains were also confirmed by the sequencing of glnA genes, which were used as an alternative chromosomal marker. The DNA–DNA relatedness was between 11·3 and 47·1 % among representative strains of candidate species I and II and the type strains of defined Mesorhizobium species. Candidate III had DNA relatedness of between 4·3 and 25·2 % with type strains of Agrobacterium tumefaciens and Agrobacterium rubi. Two novel species are proposed to accommodate candidate species I and II, Mesorhizobium septentrionale sp. nov. (type strain, SDW014T=CCBAU 11014T=HAMBI 2582T) and Mesorhizobium temperatum sp. nov. (type strain, SDW018T=CCBAU 11018T=HAMBI 2583T), respectively. At least two distinct nodA sequences were identified among the strains. The numerically dominant nodA sequence type was most similar to that from the Mesorhizobium tianshanense type strain and was identified in strains belonging to the two novel species as well as other, as yet, undefined genome types. Host range studies indicate that the different nodA sequences correlate with different host ranges. Further comparative studies with the defined Agrobacterium species are needed to clarify the taxonomic identity of candidate species III.
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Halomonas koreensis sp. nov., a novel moderately halophilic bacterium isolated from a solar saltern in Korea
A moderately halophilic bacterium, strain SS20T, capable of growing at salinities of 1–20 % (w/v) NaCl was isolated from a solar saltern of the Dangjin area in Korea and was characterized taxonomically. Strain SS20T was a Gram-negative bacterium comprising motile, short rods. Its major cellular fatty acids were C18 : 1 ω7c, C19 : 0 ω8c cyclo and C16 : 0. The DNA G+C content was 70 mol% and the predominant ubiquinone was Q-9. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SS20T belonged to the genus Halomonas. The levels of 16S rRNA gene sequence similarity to the type strains of Halomonas species were in the range 93·0–97·5 %. The levels of DNA–DNA relatedness between strain SS20T and the type strains of phylogenetically closely related Halomonas species were in the range 5·3–12·3 %. On the basis of physiological and molecular properties, strain SS20T represents a novel species of the genus Halomonas, for which the name Halomonas koreensis sp. nov. is proposed. The type strain is SS20T (=KCTC 12127T=JCM 12237T).
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Aeromonas molluscorum sp. nov., isolated from bivalve molluscs
More LessFive Aeromonas strains (848TT, 93M, 431E, 849T and 869N), which were isolated from bivalve molluscs and were recognized previously by numerical taxonomy as members of an unknown Aeromonas taxon, were subjected to a polyphasic taxonomic study. DNA–DNA hybridization experiments showed that DNA of strain 848TT was <70 % similar (27–45 %) to that of the type/reference strains of the current Aeromonas hybridization groups (HGs), but 93 % similar to that of strain 93M. The DNA G+C content of the five strains ranged from 59·0 to 59·4 mol%. 16S rRNA gene sequence analysis confirmed that the strains belonged to the genus Aeromonas and showed high similarity to Aeromonas encheleia. Amplified fragment length polymorphism fingerprinting clustered the novel strains in a homogeneous group with low genotypic relatedness to other Aeromonas species. Useful phenotypic features for differentiating the five isolates from other Aeromonas species include their negative reactions in tests for indole production, lysine decarboxylase, gas from glucose and starch hydrolysis. From the results of this study, the name Aeromonas molluscorum sp. nov. is proposed for these strains, with the type strain 848TT (=CECT 5864T=LMG 22214T).
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Transfer of Hyphomicrobium indicum to the genus Photobacterium as Photobacterium indicum comb. nov.
More LessHyphomicrobium indicum Johnson and Weisrock 1969 lacks true budding and hyphal branching, and some phenotypic characteristics are in contrast to other true hyphomicrobia. The major quinone system (ubiquinone Q-8), the G+C content of the DNA (40 mol%) and the cellular fatty acid composition (16 : 0, 16 : 1 and 18 : 1 as the major components, and 12 : 0 3-OH and 14 : 0 3-OH as the hydroxy fatty acids) of H. indicum are different from the genus Hyphomicrobium, but similar to the genus Photobacterium. Like the marine bacteria Photobacterium, H. indicum can be tolerant of sea water, while Hyphomicrobium cannot. Phylogenetic analyses of 16S rRNA and gyrB gene sequences revealed that H. indicum is most closely related to the genus Photobacterium of the γ-Proteobacteria. Based on the phylogenetic, phenotypic and chemotaxonomic evidence, the results indicate that H. indicum should be transferred to the genus Photobacterium, and the name Photobacterium indicum comb. nov. (type strain, NBRC 14233T=ATCC 19614T) is proposed.
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Klebsiella singaporensis sp. nov., a novel isomaltulose-producing bacterium
More LessCells of strain LX3T, isolated from soil, were Gram-negative, facultatively anaerobic, non-motile, capsulated and non-endospore-forming straight rods, able to grow at 10 °C, unable to produce gas from lactose at 45 °C and unable to produce indole. The isolate converted sucrose to isomaltulose and did not produce detectable glucose by-products. The G+C content of the DNA was 56·4 mol%. Furthermore, comparison of 16S rRNA and rpoB gene sequences showed that the isolate clearly belongs to the genus Klebsiella. The closest phylogenetic relative was Klebsiella pneumoniae, there being 99·3 and 97·5 % similarity in 16S rRNA and rpoB gene sequences, respectively. DNA–DNA hybridization analysis demonstrated a very low level of relatedness to other members of the genus Klebsiella, indicating that the isolated strain and other species in the genus Klebsiella were not related at the species level. The isolate could be differentiated from other previously described members of the genus Klebsiella on the basis of phenotypic differences and 16S rRNA and rpoB gene sequence divergence, together with DNA–DNA reassociation data. Therefore, it is proposed that strain LX3T (=DSM 16265T=JCM 12419T) should be classified as the type strain of a novel species of genus Klebsiella, Klebsiella singaporensis sp. nov.
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Vibrio crassostreae sp. nov., isolated from the haemolymph of oysters (Crassostrea gigas)
More LessPolyphasic analysis of five new Vibrio isolates originating from the haemolymph of diseased cultured oysters is described. The new isolates were closely related to Vibrio splendidus, having 98 % 16S rRNA gene sequence similarity. gyrB phylogenetic analysis, fluorescent amplified-fragment length polymorphism (FAFLP) fingerprinting and DNA–DNA hybridization experiments clearly showed that the new isolates form a tight genomic group that is different from the currently known Vibrio species. It is proposed to accommodate these isolates in a novel species, Vibrio crassostreae sp. nov. (type strain LGP 7T=LMG 22240T=CIP 108327T). Phenotypic and chemotaxonomic features that differentiate V. crassostreae from other known Vibrio species include arginine dihydrolase, utilization and fermentation of various carbon sources, β-galactosidase activity, NO2 production and the presence of the fatty acids 14 : 0 iso and 16 : 0 iso.
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Phenylobacterium lituiforme sp. nov., a moderately thermophilic bacterium from a subsurface aquifer, and emended description of the genus Phenylobacterium
More LessA facultative anaerobic bacterium, strain FaiI3T, was isolated from samples collected from the free-flowing waters of a bore well (Fairlea Bore, registration number 3768) which taps into the Australian Great Artesian Basin subsurface thermal aquifer. Strain FaiI3T developed yellow to pale-yellow colonies (0·5–1·5 mm) after 48 h. The non-spore forming rods (0·5×1–3 μm) were slightly curved, occurred singly and as pairs and were motile with a single polar flagellum. Cells tended to form clumps in liquid medium and rosettes were commonly observed. The cells stained Gram-negative and electron micrographs of thin sections revealed a multi-layered complex Gram-negative cell wall structure. Strain FaiI3T grew optimally at 40–41 °C, with growth observed at 45 °C but not at 50 °C. The pH growth range was between pH 6 and 9 and optimal growth occurred between pH 6 and 6·5. Strain FaiI3T grew best with yeast extract as the sole carbon and energy source. Peptone, yeast extract, acetate, xylose, sucrose, glucose, glycerol, succinate, butyrate, lactate, fumarate, citrate, l-phenylalanine, cellobiose and gelatin supported growth but maltose, fructose, glycine, ethanol, benzoate and oxalate did not. Tyrosine was produced from l-phenylalanine. Strain FaiI3T was catalase-positive and oxidase-negative and did not hydrolyse starch. Growth was inhibited by neomycin, tetracycline, streptomycin, chloramphenicol, ampicillin, vancomycin and spectinomycin. The G+C content was determined to be 66·5±0·5 mol%. On the basis of the 16S rRNA gene sequence analysis, strain FaiI3T was assigned as a novel species of the genus Phenylobacterium, Phenylobacterium lituiforme sp. nov. in the order Caulobacterales, subclass α-Proteobacteria, class Proteobacteria. The type strain is FaiI3T (=ATCC BAA-294T=DSM 14363T).
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Sphingomonas phyllosphaerae sp. nov., from the phyllosphere of Acacia caven in Argentina
More LessTwo bacterial strains (FA1 and FA2T) were isolated from the phyllosphere of a leguminous tree, Acacia caven, in central Argentina. The strains were Gram-negative, strictly aerobic, rod-shaped, motile and formed yellow-pigmented colonies on nutrient agar. The two-primer RAPD patterns of the two strains were identical, suggesting that they belong to the same species. The complete 16S rRNA gene sequences of the two strains were obtained and comparisons demonstrated that they cluster phylogenetically with the species of the genus Sphingomonas sensu stricto. Strain FA2T was most closely related (97·6 %) to Sphingomonas adhaesiva. 16S rRNA gene sequence similarities to all other established Sphingomonas species ranged from 94·4 % (to Sphingomonas echinoides) to 97·6 % (to S. adhaesiva). Strains FA1 and FA2T were catalase-positive and oxidase-negative. Aesculin was hydrolysed, gelatin and urea were not. β-Galactosidase was produced. From 51 compounds tested 21 were used as single sources of carbon. The major respiratory lipoquinone was ubiquinone-10. The predominant cellular fatty acids were 16 : 0, 18 : 1ω7c and 16 : 1ω7c (from summed feature 3). Hydroxy fatty acids 14 : 0 2-OH and 15 : 0 iso 2-OH were present as well (from summed feature 4). The polar lipids detected in strain FA2T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and two unidentified phospholipids. The DNA G+C content of strain FA2T was 61 mol%. DNA–DNA hybridization experiments showed 27·6 % relatedness between strain FA2T and S. adhaesiva DSM 7418T. Based upon phenotypic and molecular evidence, a novel species of the genus Sphingomonas is proposed, Sphingomonas phyllosphaerae sp. nov., with strain FA2T (=LMG 21958T=CECT 5832T) as the type strain.
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Burkholderia tropica sp. nov., a novel nitrogen-fixing, plant-associated bacterium
In an ecological survey of nitrogen-fixing bacteria isolated from the rhizosphere and as endophytes of sugarcane, maize and teosinte plants in Brazil, Mexico and South Africa, a new phylogenetically homogeneous group of N2-fixing bacteria was identified within the genus Burkholderia. This polyphasic taxonomic study included microscopic and colony morphology, API 20NE tests and growth on different culture media at different pH and temperatures, as well as carbon source assimilation tests and whole-cell protein pattern analysis. Analysis of 16S rRNA gene sequences showed 99·2–99·9 % similarity within the novel species and 97·2 % similarity to the closest related species, Burkholderia sacchari. The novel species was composed of four distinct amplified 16S rDNA restriction analysis groups. The DNA–DNA reassociation values within the novel species were greater than 70 % and less than 42 % for the closest related species, B. sacchari. Based on these results and on many phenotypic characteristics, a novel N2-fixing species is proposed for the genus Burkholderia, Burkholderia tropica sp. nov., with the type strain Ppe8T (=ATCC BAA-831T=LMG 22274T=DSM 15359T). B. tropica was isolated from plants grown in geographical regions with climates ranging from temperate subhumid to hot humid.
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Sphingomonas oligophenolica sp. nov., a halo- and organo-sensitive oligotrophic bacterium from paddy soil that degrades phenolic acids at low concentrations
The taxonomic position of a halo- and organo-sensitive, oligotrophic soil bacterium, strain S213T, was investigated. Cells were Gram-negative, non-motile, strictly aerobic, yellow-pigmented rods of short to medium length on diluted nutrient broth. When 0·1–0·4 % (w/v) NaCl was added to diluted media composed of peptone and meat extract, growth was inhibited with increasing NaCl concentration and the cells became long aberrant forms. When 6 mM CaCl2 was added, the cells grew quite normally and aberrant cells were no longer found at 0·1–0·5 % (w/v) NaCl. Chemotaxonomically, strain S213T contains chemical markers that indicate its assignment to the Sphingomonadaceae: the presence of ubiquinone Q-10 as the predominant respiratory quinone, C18 : 1 and C16 : 0 as major fatty acids, C14 : 0 2-OH as the major 2-hydroxy fatty acid and sphingoglycolipids. 16S rRNA gene sequence analysis indicated that strain S213T belongs to the genus Sphingomonas, exhibiting high sequence similarity to the 16S rRNA gene sequences of Sphingomonas mali IFO 15500T (98·3 %), Sphingomonas pruni IFO 15498T (98·0 %), Sphingomonas asaccharolytica IFO 15499T (97·9 %) and Sphingomonas echinoides DSM 1805T (97·8 %). The results of DNA–DNA hybridization experiments and its phenotypic characteristics clearly distinguished the strain from its nearest neighbours and demonstrate that strain S213T represents a novel Sphingomonas species, for which the name Sphingomonas oligophenolica sp. nov. is proposed. The type strain is S213T (=JCM 12082T=CIP 107926T).
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Description of ‘Candidatus Helicobacter heilmannii’ based on DNA sequence analysis of 16S rRNA and urease genes
While Helicobacter pylori is accepted as the major bacterial agent of gastric disease in humans, some patients and many animals are infected with a larger, tightly helical-shaped bacterium previously referred to as ‘Helicobacter heilmannii’ or ‘Gastrospirillum hominis’. Taxonomic classification of these bacteria has been hampered by the inability to cultivate them in vitro and by the inadequate discriminatory power of 16S rRNA gene sequence analysis. This study describes the detection and phylogenetic analysis of 26 different gastrospirillum isolates from humans and animals, which incorporates sequence data based on the 16S rRNA and urease genes. Fifteen gastrospirilla detected in humans, primates and pigs clustered with ‘Candidatus Helicobacter suis’, thus expanding the host range for this organism. By comparison, based on 16S rRNA data, the remaining 11 gastrospirilla could not be differentiated from Helicobacter felis, Helicobacter bizzozeronii and Helicobacter salomonis. However, urease gene sequence analysis allowed for the discrimination of this latter group into four discrete clusters, three of which contained the above recognized species. The fourth cluster contained isolates from human and feline hosts, and should provisionally be considered a unique bacterial species, for which the name ‘Candidatus Helicobacter heilmannii’ is proposed.
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Erwinia toletana sp. nov., associated with Pseudomonas savastanoi-induced tree knots
Gram-negative bacteria were isolated from knots induced by Pseudomonas savastanoi in olive trees (Olea europaea L.). A total of nine endophytic bacterial strains were isolated, each from inside a different tree knot. Biochemical characterization indicated that all the strains belong to the family Enterobacteriaceae. Phylogenetic analyses of the 16S rRNA genes of these novel isolates revealed that they formed a homogeneous cluster within Erwinia species. DNA signatures of these isolates were identical to those described for the genus Erwinia. The strains formed a homogeneous group as shown by DNA–DNA hybridization analysis and numerical analysis of phenotypic data, clearly differentiated from all species of Erwinia with validly published names. The data provide strong evidence of the differentiation of these strains from the most closely related species. Therefore, these isolates represent a novel species, for which the name Erwinia toletana sp. nov. is proposed. The isolates are available at CFBP, CECT and ATCC. The G+C content is 52±0·5 mol%. The type strain is CFBP 6631T (=A37T=ATCC 700880T=CECT 5263T).
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Proposals of Curvibacter gracilis gen. nov., sp. nov. and Herbaspirillum putei sp. nov. for bacterial strains isolated from well water and reclassification of [Pseudomonas] huttiensis, [Pseudomonas] lanceolata, [Aquaspirillum] delicatum and [Aquaspirillum] autotrophicum as Herbaspirillum huttiense comb. nov., Curvibacter lanceolatus comb. nov., Curvibacter delicatus comb. nov. and Herbaspirillum autotrophicum comb. nov.
More LessTwo strains of curved bacteria, 7-1T and 7-2T, isolated from well water, were phylogenetically examined to determine their taxonomic position. Strain 7-1T is a Gram-negative, slightly curved rod. Analysis of the 16S rRNA gene sequence showed that strain 7-1T formed a cluster with [Aquaspirillum] delicatum and [Pseudomonas] lanceolata. It has some similar characteristics to [A.] delicatum and [P.] lanceolata, but has sufficient distance to separate it from other genera. DNA–DNA hybridization analysis, as well as chemotaxonomic and morphological studies, demonstrated that strain 7-1T, [A.] delicatum and [P.] lanceolata belong to a new genus, Curvibacter gen. nov. Strain 7-1T (=IAM 15033T=ATCC BAA-807T) is classified as the type strain of Curvibacter gracilis gen. nov., sp. nov., and [A.] delicatum and [P.] lanceolata are classified as Curvibacter delicatus comb. nov. and Curvibacter lanceolatus comb. nov., respectively. Strain 7-2T is a Gram-negative spirillum. Phylogenetic study based on the 16S rRNA gene sequences showed that it formed a cluster with the members of the genus Herbaspirillum, [Pseudomonas] huttiensis and [Aquaspirillum] autotrophicum. The classification is therefore proposed of strain 7-2T (=IAM 15032T=ATCC BAA-806T) as the type strain of Herbaspirillum putei sp. nov., and [P.] huttiensis and [A.] autotrophicum are transferred to the genus Herbaspirillum as Herbaspirillum huttiense comb. nov. and Herbaspirillum autotrophicum comb. nov., respectively.
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Porphyrobacter donghaensis sp. nov., isolated from sea water of the East Sea in Korea
More LessTwo Gram-negative, motile, non-spore-forming, bacteriochlorophyll a-containing slightly halophilic strains, SW-132T and SW-158, were isolated from sea water of the East Sea in Korea, and subjected to a polyphasic taxonomic study. The two isolates were characterized chemotaxonomically as having Q-10 as the predominant respiratory lipoquinone and major amounts of unsaturated fatty acids C18 : 1 ω7c and C17 : 1 ω6c. The DNA G+C contents of the two strains were in the range 66·8–65·9 mol%. The 16S rRNA gene sequences of strains SW-132T and SW-158 were 99·9 % (1 nt difference) similar and their mean level of DNA–DNA relatedness was 86 %. The 16S rRNA gene sequence analysis showed that strains SW-132T and SW-158 are phylogenetically closely related to Porphyrobacter species and Erythromicrobium ramosum. Similarities between the 16S rRNA gene sequences of strains SW-132T and SW-158 and the type strains of Porphyrobacter species and E. ramosum ranged from 97·8 to 99·0 %. DNA–DNA relatedness data indicated that strains SW-132T and SW-158 are members of a genomic species that is separate from the four Porphyrobacter species. On the basis of phenotypic and phylogenetic data and genetic distinctiveness, strains SW-132T (=KCTC 12229T=DSM 16220T) and SW-158 (=KCTC 12230) are classified as a novel Porphyrobacter species, for which the name Porphyrobacter donghaensis sp. nov. is proposed.
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‘Candidatus Burkholderia calva’ and ‘Candidatus Burkholderia nigropunctata’ as leaf gall endosymbionts of African Psychotria
More LessPhylogenetic 16S rRNA gene analysis was used to assign the bacterial leaf-nodulating endosymbionts of two tropical African Psychotria species to the genus Burkholderia. The microsymbionts of the different Psychotria hosts were recognized as distinct and novel species of Burkholderia on the basis of relatively low intersequence similarities and sufficiently large evolutionary distances when compared with each other and their closest validly named neighbours. The obligate endosymbiotic nature of the bacteria prevented their in vitro cultivation and the deposition of type strains to culture collections. Therefore, the provisional status Candidatus is assigned to the bacterial partners of Psychotria calva and Psychotria nigropunctata, with the proposal of the names ‘Candidatus Burkholderia calva’ and ‘Candidatus Burkholderia nigropunctata’, respectively.
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Pseudoxanthomonas mexicana sp. nov. and Pseudoxanthomonas japonensis sp. nov., isolated from diverse environments, and emended descriptions of the genus Pseudoxanthomonas Finkmann et al. 2000 and of its type species
Three mesophilic bacteria (strains AMX 26BT, UR374_02 and 12-3T) isolated respectively from an anaerobic digester, human urine and urban riverside soil were characterized. Cells were Gram-negative, motile, non-sporulating, straight to curved rods with one polar flagellum and had a strictly respiratory metabolism with O2 as the preferential terminal electron acceptor. Phylogenetic analysis based on 16S rRNA gene sequences revealed that all strains clustered within the Xanthomonadaceae branch of the Proteobacteria. Isolates AMX 26BT and UR374_02 exhibited 100 % 16S rRNA gene sequence similarity and both were related to strain 12-3T (99·6 % similarity). The closest relative of all the isolates was Pseudoxanthomonas broegbernensis DSM 12573T (similarity 97·1–97·5 %), and they were equidistantly related to Xanthomonas species (95·4–96·6 %), Stenotrophomonas species (95·3–96·1 %) and Pseudoxanthomonas taiwanensis ATCC BAA-4040T (95·3–95·4 %). Chemotaxonomic and biochemical data (branched-chain cellular fatty acid pattern without C13 : 0 iso 3-OH, ubiquinone with eight isoprenoid units, limited range of substrates used, ability to reduce nitrite but not nitrate with the production of N2O) supported their affiliation to the genus Pseudoxanthomonas. The results of DNA–DNA hybridization and/or phenotypic analysis allowed them to be differentiated from the two Pseudoxanthomonas species with validly published names and showed that strain 12-3T was genomically and phenotypically distinct from the other two isolates. On the basis of these results, two novel species of the genus Pseudoxanthomonas are proposed: Pseudoxanthomonas mexicana sp. nov., consisting of strains AMX 26BT (=ATCC 700993T=CIP 106674T=JCM 11524T) (type strain) and UR374_02 (=DSM 15133), and Pseudoxanthomonas japonensis sp. nov., consisting of strain 12-3T (=CCUG 48231T=CIP 107388T=JCM 11525T). The report of these two novel species leads to the emendation of the description of the genus Pseudoxanthomonas and the re-evaluation of the phenotype of P. broegbernensis DSM 12573T necessitates the emendation of its description.
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Saccharibacter floricola gen. nov., sp. nov., a novel osmophilic acetic acid bacterium isolated from pollen
More LessThree Gram-negative, aerobic, rod-shaped bacterial strains were isolated, from the pollen of Japanese flowers, as producers of xylitol; these strains were subjected to a polyphasic taxonomic study. Phylogenetic analyses of the 16S rRNA gene sequences demonstrated that these three isolates formed a new cluster within a group of acetic acid bacteria in the α-Proteobacteria. The characteristics of the three isolates were as follows: (i) their predominant quinone was Q-10; (ii) their cellular fatty acid profile contained major amounts of 2-hydroxy acids and an unsaturated straight-chain acid (C18 : 1 ω7c); and (iii) their DNA G+C contents were in the range 51·9–52·3 mol%, which is around the lower limit of the reported range for the genera of acetic acid bacteria. The negligible or very weak productivity of acetic acid from ethanol and the osmophilic growth properties distinguished these strains from other acetic acid bacteria. The unique phylogenetic and phenotypic characteristics suggest that the three isolates should be classified within a novel genus and species with the proposed name Saccharibacter floricola gen. nov., sp. nov. The type strain is strain S-877T (=AJ 13480T=JCM 12116T=DSM 15669T).
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Methylobacterium nodulans sp. nov., for a group of aerobic, facultatively methylotrophic, legume root-nodule-forming and nitrogen-fixing bacteria
Data on 72 non-pigmented bacterial strains that specifically induce nitrogen-fixing root nodules on the legume species Crotalaria glaucoides, Crotalaria perrottetii and Crotalaria podocarpa are reviewed. By SDS-PAGE analysis of total protein patterns and by 16S rRNA PCR-RFLP, these strains form a homogeneous group that is separate from other legume root-nodule-forming bacteria. The 16S rRNA gene-based phylogeny indicates that these bacteria belong to the genus Methylobacterium. They can grow on C1 compounds such as methanol, formate and formaldehyde but not methylamine as sole carbon source, and carry an mxaF gene, encoding methanol dehydrogenase, which supports their methylotrophic metabolism. Presence of a nodA nodulation gene, and ability to nodulate plants of Crotalaria species and to fix nitrogen are features that separate the strains currently included in this group from other members of the genus Methylobacterium. The present study includes additional genotypic and phenotypic characterization of this novel Methylobacterium species, i.e. nifH gene sequence, morphology, physiology, enzymic and carbon source assimilation tests and antibiotic resistance. The name Methylobacterium nodulans sp. nov. (type strain, ORS 2060T=CNCM I 2342T=LMG 21967T) is proposed for this group of root-nodule-forming bacteria.
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Loktanella hongkongensis sp. nov., a novel member of the α-Proteobacteria originating from marine biofilms in Hong Kong waters
A Gram-negative, non-motile, non-spore-forming, short rod-shaped bacterium (UST950701-009PT) was isolated from a marine biofilm in Hong Kong waters. Colonies are pink in colour, convex with a smooth surface and entire edge. Brown diffusible pigment is produced. Whitish colonies, with otherwise identical morphology, emerge from every culture upon ageing. The white colonies can be maintained as separate cultures (UST950701-009W) without turning pink. UST950701-009PT and UST950701-009W have identical 16S rRNA gene sequences and similar G+C (65·9–66·2 mol%) and fatty acid (86·22–88·52 % 18 : 1ω7c) contents. Phylogenetic analysis of the 16S rRNA gene sequence places UST950701-009PT within the Rhodobacter group of the α-subclass of the Proteobacteria. The nearest neighbours belong to the genus Loktanella, with similarity values ranging from 94·5 to 95·5 %. Data on G+C and fatty acid contents support the affiliation to the genus Loktanella. UST950701-009PT and -009W are heterotrophic, strictly aerobic and require NaCl for growth (2·0–14·0 %). Both grow in pH 5·0–10·0 and at 8–44 °C. Both are positive in oxidase, catalase and β-galactosidase tests, but they differ in the pattern of carbohydrate oxidation and assimilation. Molecular evidence together with phenotypic characteristics shows that UST950701-009PT constitutes a novel species within the genus Loktanella. The name Loktanella hongkongensis sp. nov. is proposed; the type strain is UST950701-009PT (=NRRL B-41039T=JCM 12479T) and a morphovar is UST950701-009W (=NRRL B-41040=JCM 12480).
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Taxonomy of the genus Cupriavidus: a tale of lost and found
More LessDNA–DNA hybridization experiments and an evaluation of phenotypic characteristics, DNA base ratios and 16S rRNA gene sequences demonstrated that Wautersia eutropha (Davies 1969) Vaneechoutte et al. 2004 , the type species of the genus Wautersia, is a later synonym of Cupriavidus necator Makkar and Casida 1987 , the type species of the genus Cupriavidus. In conformity with Rules 15, 17, 23a and 37a(1) of the International Code of Nomenclature of Bacteria, the genus name Cupriavidus has priority over the genus name Wautersia, and all other members of the genus Wautersia are reclassified into Cupriavidus as Cupriavidus basilensis comb. nov. (type strain LMG 18990T=DSM 11853T), Cupriavidus campinensis comb. nov. (type strain LMG 19282T=CCUG 44526T), Cupriavidus gilardii comb. nov. (type strain LMG 5886T=CCUG 38401T), Cupriavidus metallidurans comb. nov. (type strain LMG 1195T=DSM 2839T), Cupriavidus oxalaticus comb. nov. (type strain LMG 2235T=CCUG 2086T=DSM 1105T), Cupriavidus pauculus comb. nov. (type strain LMG 3244T=CCUG 12507T), Cupriavidus respiraculi comb. nov. (type strain LMG 21510T=CCUG 46809T) and Cupriavidus taiwanensis comb. nov. (type strain LMG 19424T=CCUG 44338T).
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Sulfuricurvum kujiense gen. nov., sp. nov., a facultatively anaerobic, chemolithoautotrophic, sulfur-oxidizing bacterium isolated from an underground crude-oil storage cavity
More LessA facultatively anaerobic, chemolithoautotrophic, sulfur-oxidizing bacterium, strain YK-1T, was isolated from an underground crude-oil storage cavity at Kuji in Iwate, Japan. The cells were motile, curved rods and had a single polar flagellum. Optimum growth occurred in a low-strength salt medium at pH 7·0 and 25 °C. It utilized sulfide, elemental sulfur, thiosulfate and hydrogen as the electron donors and nitrate as the electron acceptor under anaerobic conditions, but it did not use nitrite. Oxygen also served as the electron acceptor under the microaerobic condition (O2 in the head space 1 %). It did not grow on sugars, organic acids or hydrocarbons as carbon and energy sources. The DNA G+C content of strain YK-1T was 45 mol%. Phylogenetic analysis, based on the 16S rRNA gene sequence, showed that its closest relative was Thiomicrospira denitrificans in the ‘Epsilonproteobacteria’, albeit with low homology (90 %). On the basis of physiological and phylogenetic data, strain YK-1T should be classified into a novel genus and species, for which the name Sulfuricurvum kujiense gen. nov., sp. nov. is proposed. The type strain is YK-1T (=JCM 11577T=MBIC 06352T=ATCC BAA-921T).
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Pseudovibrio denitrificans gen. nov., sp. nov., a marine, facultatively anaerobic, fermentative bacterium capable of denitrification
More LessTwo denitrifying strains of heterotrophic, facultatively anaerobic, marine bacteria, designated DN34T and DN33, were isolated from sea-water samples collected in Nanwan Bay, Kenting National Park, Taiwan. They were Gram-negative. Cells in late exponential to early stationary phase of growth were predominantly straight or curved rods, but Y- or V-shaped forms were also observed. They were motile by means of one to several lateral or subpolar flagella. Both strains required NaCl for growth and exhibited optimal growth at about 30 °C, pH 8 and 3 % NaCl. They were capable of anaerobic growth by carrying out denitrifying metabolism using nitrate, nitrite or nitrous oxide as terminal electron acceptors or, alternatively, by fermenting glucose, mannose, sucrose or trehalose as substrates. Anaerobic fermentative growth on glucose resulted in formation of various organic acids, including formate, lactate, acetate, pyruvate and fumarate. The major cellular fatty acids were 2-OH-14 : 0, 3-OH-14 : 0 and 16 : 0. DN34T and DN33 had DNA G+C contents of 51·7 and 51·6 mol%, respectively. Physiological characterization, together with phylogenetic analysis based on 16S rRNA gene sequence analysis, revealed that the two denitrifying strains could be accommodated in a novel genus, for which the name Pseudovibrio gen. nov. is proposed. Pseudovibrio denitrificans sp. nov. is the type species, with DN34T (=BCRC 17323T=JCM 12308T) as the type strain.
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Thiomicrospira thermophila sp. nov., a novel microaerobic, thermotolerant, sulfur-oxidizing chemolithomixotroph isolated from a deep-sea hydrothermal fumarole in the TOTO caldera, Mariana Arc, Western Pacific
More LessA novel thermotolerant bacterium, designated strain I78T, was isolated from a self-temperature-recording in situ colonization system deployed in a hydrothermal diffusing flow (maximal temperature 78 °C) at the TOTO caldera in the Mariana Arc, Western Pacific. Cells were highly motile curved rods with a single polar flagellum. Growth was observed at 15–55 °C (optimum 35–40 °C; 60 min doubling time) and pH 5·0–8·0 (optimum pH 6·0). The isolate was a microaerobic chemolithomixotroph capable of using thiosulfate, elemental sulfur or sulfide as the sole energy source, and molecular oxygen as the sole electron acceptor. The isolate was able to grow chemolithoautotrophically with carbon dioxide. Various organic substrates such as complex proteinaceous compounds, carbohydrates, organic acids, amino acids and sugars could also support growth as the carbon source instead of carbon dioxide with sulfur oxidation. The G+C content of the genomic DNA was 43·8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belonged to the genus Thiomicrospira and was most closely related to Thiomicrospira crunogena strain TH-55T and Thiomicrospira sp. strain L-12, while DNA–DNA hybridization demonstrated that the novel isolate could be genetically differentiated from previously described strains of Thiomicrospira. On the basis of its physiological and molecular properties the isolate is representative of a novel Thiomicrospira species, for which the name Thiomicrospira thermophila sp. nov. is proposed (type strain, I78T=JCM 12397T=DSM 16397T).
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Shewanella marisflavi sp. nov. and Shewanella aquimarina sp. nov., slightly halophilic organisms isolated from sea water of the Yellow Sea in Korea
More LessTwo Gram-negative, motile, non-spore-forming, rod-shaped organisms, strains SW-117T and SW-120T, were isolated from sea water of the Yellow Sea in Korea and subjected to a polyphasic taxonomic study. Strains SW-117T and SW-120T simultaneously contained both menaquinones (MK) and ubiquinones (Q) as isoprenoid quinones; the predominant menaquinone was MK-7 and the predominant ubiquinones were Q-7 and Q-8. The major fatty acid detected in the two strains was iso-C15 : 0. The DNA G+C content of strains SW-117T and SW-120T was 51 and 54 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains SW-117T and SW-120T fall within the radiation of the cluster comprising Shewanella species. Strains SW-117T and SW-120T showed a 16S rRNA gene sequence similarity of 97·4 % and a DNA–DNA relatedness level of 10·1 %. Strains SW-117T and SW-120T exhibited 16S rRNA gene sequence similarity levels of 93·8–98·5 % and 92·4–97·0 %, respectively, to Shewanella species. Strain SW-117T exhibited DNA–DNA relatedness levels of 8·3–20·3 % to the type strains of six phylogenetically related Shewanella species. On the basis of phenotypic, phylogenetic and genetic data, strains SW-117T and SW-120T were classified in the genus Shewanella as two distinct novel species, for which the names Shewanella marisflavi sp. nov. (type strain, SW-117T=KCCM 41822T=JCM 12192T) and Shewanella aquimarina sp. nov. (type strain, SW-120T=KCCM 41821T=JCM 12193T) are proposed, respectively.
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Campylobacter insulaenigrae sp. nov., isolated from marine mammals
Phenotypic and phylogenetic studies were performed on four Campylobacter-like organisms recovered from three seals and a porpoise. Comparative 16S rRNA gene sequencing studies demonstrated that the organisms represent a hitherto unknown subline within the genus Campylobacter, associated with a subcluster containing Campylobacter jejuni, Campylobacter coli and Campylobacter lari. DNA–DNA hybridization studies confirmed that the bacteria belonged to a single species, for which the name Campylobacter insulaenigrae sp. nov. is proposed. The type strain of Campylobacter insulaenigrae sp. nov. is NCTC 12927T (=CCUG 48653T).
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- Gram-Positive Bacteria
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Nocardia shimofusensis sp. nov., isolated from soil, and Nocardia higoensis sp. nov., isolated from a patient with lung nocardiosis in Japan
Three actinomycete strains isolated from soils and one strain isolated from a patient with lung nocardiosis in 1999 and 2001 in Japan have been provisionally assigned to the genus Nocardia on the basis of morphological criteria. These isolates were further investigated to determine their specific taxonomic status. Detailed chemotaxonomic characterization and 16S rRNA gene sequence analysis of these isolates confirmed that they belong to the genus Nocardia. The 16S rRNA gene sequences of the four strains were most similar to that of Nocardia farcinica. However, the sequence similarity values between these four strains and N. farcinica were <98·9 %. These four strains were susceptible to 5-fluorouracil, and they have the ability to decompose urea, which is a very characteristic trait. Furthermore, DNA–DNA relatedness data revealed that IFM 10311T, IFM 10312 and IFM 10313 comprise a single novel species of Nocardia, that IFM 10084T represents another novel species of Nocardia and that these two novel species could be distinguished from N. farcinica. The names Nocardia shimofusensis sp. nov. and Nocardia higoensis sp. nov. are proposed, with IFM 10311T (=NBRC 100134T=JCM 12122T=DSM 44733T) and IFM 10084T (=NBRC 100133T=JCM 12121T=DSM 44732T) as the respective type strains.
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Janibacter melonis sp. nov., isolated from abnormally spoiled oriental melon in Korea
More LessTwo Gram-positive bacterial strains, CM2104T and CM2110, isolated from the inner part of abnormally spoiled oriental melon (Cucumis melo) in Korea, were subjected to a polyphasic taxonomic study. The cell-wall peptidoglycan of strains CM2104T and CM2110 contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinone was MK-8(H4). The major fatty acids detected in the two strains were iso-C16 : 0, C17 : 1 ω8c and C18 : 1 ω9c or C17 : 0. The DNA G+C content of the two strains was 73 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strains formed a coherent cluster with a clade comprising two Janibacter species, Janibacter limosus and Janibacter terrae. Strains CM2104T and CM2110 exhibited a 16S rRNA gene sequence similarity value of 99·7 % and a mean DNA–DNA relatedness level of 89 %. Strains CM2104T and CM2110 showed 16S rRNA gene sequence similarity levels of 97·8–98·4 % to the type strains of J. limosus and J. terrae. DNA–DNA relatedness between strains CM2104T and CM2110 and the type strains of these two Janibacter species was 7–11 %. On the basis of the phenotypic and phylogenetic data and genomic distinctiveness, strains CM2104T and CM2110 should be placed within the genus Janibacter as members of a novel species, for which the name Janibacter melonis sp. nov. is proposed. The type strain is CM2104T (=KCTC 9987T=DSM 16063T=JCM 12321T).
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Agromyces ulmi sp. nov., a xylanolytic bacterium isolated from Ulmus nigra in Spain
More LessTwo xylan-degrading bacterial strains were isolated from a decayed Ulmus nigra tree in Spain. The isolates were Gram-positive, non-motile, aerobic and formed substrate mycelium which fragmented into irregular rods. 16S rRNA gene sequence analysis indicated that the isolates form a separate branch within the genus Agromyces phylogenetic cluster, with Agromyces mediolanus DSM 20152T being their closest relative (97·7 and 97·6 % sequence similarity). Catalase, nitrate reduction and urease tests differentiated these strains from A. mediolanus. Cell-wall peptidoglycan composition, major menaquinone, predominant fatty acids and phospholipid pattern were typical of the genus Agromyces. The DNA G+C content determined for the type strain XIL01T was 72 mol%. Based on the data presented, a novel species Agromyces ulmi sp. nov. is proposed. The type strain is XIL01T (=LMG 21954T=DSM 15747T).
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Geobacillus lituanicus sp. nov.
More LessObligately thermophilic, aerobic, proteolytic, endospore-forming strain N-3T was isolated from a high-temperature oilfield in Lithuania. 16S rRNA gene sequence analysis placed this strain in genetic group 5 of the endospore formers. Geobacillus thermoleovorans appeared to be the closest phylogenetic neighbour (99·4 % sequence similarity). The G+C content of strain N-3T was 52·5 mol% and matched the range established for the genus Geobacillus. Studies of DNA–DNA relatedness and morphological and physiological analyses enabled strain N-3T to be described as a member of the genus Geobacillus, but could not assign this strain to any other known species of this genus. Results of this polyphasic study allowed characterization of strain N-3T as a novel species in the genus Geobacillus – Geobacillus lituanicus sp. nov. This species can be distinguished from G. thermoleovorans and Geobacillus stearothermophilus on the basis of 16S rRNA gene PCR-RFLP assays with the restriction endonucleases AluI, HaeIII and TaqI. The type strain of the novel species is N-3T (=DSM 15325T=VKM B-2294T).
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Bacillus asahii sp. nov., a novel bacterium isolated from soil with the ability to deodorize the bad smell generated from short-chain fatty acids
In a screening campaign to isolate strains with the ability to remove the bad smell associated with animal faeces, strain MA001T was isolated from a soil sample obtained from Shizuoka prefecture, Japan. The isolate grew at pH 6–9 but not at pH 10. Cells were Gram-positive, straight rods with peritrichous flagella and produced ellipsoidal spores. The isolate was positive for catalase and oxidase tests but negative for indole production, deamination of phenylalanine and H2S production. The isolate did not produce acid from any carbohydrates tested and could not grow in more than 2 % NaCl. The DNA G+C content was 39·4 mol%. The cellular fatty acids profile consisted of significant amount of C15 branched-chain fatty acids, iso-C15 : 0 and anteiso-C15 : 0. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain MA001T was closely related to Bacillus simplex and Bacillus psychrosaccharolyticus. DNA–DNA hybridization revealed a low relatedness of the isolate to several phylogenetically close neighbours (less than 9 %). On the basis of the phenotypic characteristics observed, phylogenetic data based on 16S rRNA gene sequencing and DNA–DNA relatedness data, it is concluded that the isolate should be classified as representing a novel species, for which the name Bacillus asahii is proposed. The type strain is MA001T (=JCM 12112T=NCIMB 13969T).
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Exiguobacterium oxidotolerans sp. nov., a novel alkaliphile exhibiting high catalase activity
A novel alkaliphile was isolated from a drain of a fish processing plant. The isolate grew at a pH range of 7–10. Cells were Gram-positive, facultatively aerobic, motile rods with peritrichous flagella. Colonies were orange or yellow in colour. Catalase and oxidase reactions were positive. The isolate grew in 0–12 % NaCl but not above 15 % NaCl. Its cell extract exhibited 567 times higher catalase activity than an Escherichia coli cell extract. The major cellular fatty acids were iso-C13 : 0, anteiso-C13 : 0, iso-C15 : 0, iso-C16 : 0, iso-C17 : 0, anteiso-C17 : 0 and iso-C17 : 1. Its DNA G+C content was 46·7 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing and chemotaxonomic data indicated that strain T-2-2T is a member of the genus Exiguobacterium. DNA–DNA hybridization revealed a low relatedness of the isolate to several phylogenetic neighbours (less than 25 %). On the basis of phenotypic characteristics, phylogenetic data and DNA–DNA relatedness data, the isolate merits classification as a novel species, for which the name Exiguobacterium oxidotolerans sp. nov. is proposed. The type strain is T-2-2T (=JCM 12280T=NCIMB 13980T).
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Geobacillus gargensis sp. nov., a novel thermophile from a hot spring, and the reclassification of Bacillus vulcani as Geobacillus vulcani comb. nov.
A novel thermophilic spore-forming strain, GaT, was isolated from the Garga hot spring located in the northern part of the Transbaikal region (Russia). Strain GaT was found to be an aerobic, Gram-positive, rod-shaped, thermophilic (optimum growth temperature is 60–65 °C), chemo-organotrophic bacterium that grows on various sugars, carboxylic acids and hydrocarbons. The G+C content of its DNA is 52·9 mol%. The 16S rRNA gene sequence similarity data show that strain GaT is closely related to members of the genus Geobacillus. Relevant chemotaxonomic data (in particular, the major fatty acid profile of strain GaT, which includes iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0 acids) support the assignment of this strain to the genus Geobacillus. The physiological, biochemical and DNA–DNA hybridization studies of strain GaT showed that it differs both genotypically and phenotypically from the recognized Geobacillus species. Based on these data, strain GaT belongs to a novel species, Geobacillus gargensis sp. nov. (type strain, GaT=VKM B-2300T=DSM 15378T). The analysis of the phenotypic characteristics (additional to those given in the original description) of the type strain of Bacillus vulcani (DSM 13174T) showed that they are very similar to the major phenotypic characteristics of the genus Geobacillus. The low DNA–DNA reassociation values of strain DSM 13174T with various species of this genus (from 38 to 54 %) clearly demonstrate a sufficient genomic distinction of this strain and its taxonomic status as a species. The physiological characteristics, phylogenetic position and DNA–DNA reassociation values of B. vulcani allow this species to be reclassified as Geobacillus vulcani comb. nov. The main properties that differentiate G. vulcani from the other species of the genus are its ability to produce acids from glycerol, lactose and ribose.
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Nocardia araoensis sp. nov. and Nocardia pneumoniae sp. nov., isolated from patients in Japan
Two actinomycete strains isolated from two patients with lung nocardiosis between 1995 and 1997 in Japan were assigned to novel species of the genus Nocardia based on morphological and chemical criteria. Comparative 16S rRNA gene sequence analysis of the two strains revealed that they belong to the genus Nocardia and are most closely related to the species Nocardia beijingensis. Determination of DNA–DNA relatedness indicated that these strains could be assigned to two novel species. Based on their phenotypic and phylogenetic characters, two novel species of the genus Nocardia are proposed: Nocardia araoensis sp. nov. for IFM 0575T (=NBRC 100135T=JCM 12118T=DSM 44729T) and Nocardia pneumoniae sp. nov. for IFM 0784T (=NBRC 100136T=JCM 12119T=DSM 44730T).
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Paenibacillus elgii sp. nov., with broad antimicrobial activity
Two novel spore-forming bacteria with broad antimicrobial activity were isolated from roots of Perilla frutescens. The isolates, SD17T and SD18, were facultatively anaerobic and showed variable Gram reaction. Growth was observed between 20 and 45 °C. DNA G+C content of SD17T was 51·7 mol%, and the major fatty acid was anteiso-C15 : 0 (54·1 %). 16S rRNA gene sequence similarity of SD17T ranged from 98·6 to 91·3 % with other Paenibacillus species. The phylogenetic tree showed that isolate SD17T formed a significant monophyletic clade with Paenibacillus koreensis KCTC 2393T and Paenibacillus ehimensis IFO 15659T. DNA–DNA relatedness values for strain SD17T with Paenibacillus koreensis KCTC 2393T and Paenibacillus ehimensis IFO 15659T were 17·4 and 19·8 %, respectively. These isolates thus merit species status within Paenibacillus, for which the name Paenibacillus elgii sp. nov. is proposed. The type strain is SD17T (=KCTC 10016BPT=NBRC 100335T).
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Clostridium straminisolvens sp. nov., a moderately thermophilic, aerotolerant and cellulolytic bacterium isolated from a cellulose-degrading bacterial community
More LessA novel anaerobic, thermophilic and cellulolytic bacterium (strain CSK1T) was isolated from a cellulose-degrading bacterial community. On the basis of 16S rRNA gene sequence similarity, strain CSK1T was mapped to cluster III of the genus Clostridium. Strain CSK1T is closely related to Clostridium thermocellum (96·2 %) and Clostridium aldrichii (95·1 %). Strain CSK1T is a non-motile, spore-forming, straight or slightly curved rod. The optimum temperature and initial pH for its growth and cellulose degradation are 50–55 °C and pH 7·5. Strain CSK1T grew under a gas phase containing up to 4 % O2. Phylogenetic and phenotypic analyses support the differentiation of strain CSK1T from its closest relatives. Strain CSK1T therefore represents a novel species, for which the name Clostridium straminisolvens sp. nov. is proposed, with CSK1T (=DSM 16021T=IAM 15070T) as the type strain.
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Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description)
More LessSphaerobacter thermophilus was originally classified as the deepest branching member of the phylum Actinobacteria (high-G+C, Gram-positive bacteria) based on 16S rRNA gene comparative analysis. However, the analysis lacked suitable outgroups, and additional 16S rRNA gene sequences indicate that it is most closely related to Thermomicrobium roseum, which it also resembles phenotypically. Furthermore, both species are reproducibly affiliated with the phylum Chloroflexi (green non-sulfur bacteria), despite T. roseum currently being classified in its own phylum, the Thermomicrobia. Transfer of Sphaerobacter to the class Thermomicrobia, and transfer of the class Thermomicrobia to the phylum Chloroflexi, are proposed. Descriptions for the phylum Chloroflexi and the class Thermomicrobia are emended to reflect the proposed changes in classification.
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Planotetraspora silvatica sp. nov. and emended description of the genus Planotetraspora
More LessAn actinomycete that developed sporangia containing four spores in a single row at the ends of short sporangiophores on branched aerial hyphae was isolated from subtropical forest soil. The isolate contained menaquinone MK-9(H4), glutamic acid, alanine and meso-diaminopimelic acid as cell-wall amino acids and madurose in the whole-cell hydrolysate. The 16S rRNA gene sequence indicated that the isolate formed a monophyletic cluster with Planotetraspora mira. On the basis of morphological and chemotaxonomic characteristics, phylogenetic analysis and DNA–DNA relatedness data, a novel species of the genus Planotetraspora is proposed, Planotetraspora silvatica sp. nov. (type strain, TT 00-51T=NBRC 100141T=DSM 44746T).
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 69 (2019)
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