- Volume 54, Issue 6, 2004

Genomic 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.

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).

A 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).

A 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).

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).

A 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.

A 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.

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.

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.

Three 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).

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.

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).

Five 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).

Hyphomicrobium 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.

Cells 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.

Polyphasic 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.

A 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).