Alteromonas-like strains KMM 241T and KMM 642, isolated from marine invertebrate specimens, were investigated to clarify their taxonomic position. The novel isolates were aerobic, Gram-negative, motile, slightly halophilic and heterotrophic and hydrolysed polysaccharides. They did not hydrolyse urea, gelatin or casein and produced acid weakly from carbohydrates. The DNA G+C content ranged between 44·6 and 44·8 mol%. DNA–DNA similarity between the two strains was 71 %. Comparison of the 16S rRNA gene sequence of strain KMM 241T revealed 94·5–94·8 % similarity to Glaciecola species. The novel strains shared several phenotypic and physiological properties with members of Glaciecola, but they differed in their lack of pigment production, their minimal and maximal growth temperatures and their ability to hydrolyse agar and carrageenan and in the utilization of organic compounds. On the basis of phenotypic and physiological characteristics as well as phylogenetic analysis, the isolates should be assigned to a novel species, Glaciecola mesophila sp. nov. The type strain is strain KMM 241T (=DSM 15026T).
Five Gram-negative, motile, aerobic to microaerophilic spirilla were isolated from various depths of the hypersaline, heliothermal and meromictic Ekho Lake (East Antarctica). The strains are oxidase- and catalase-positive, metabolize a variety of sugars and carboxylic acids and have an absolute requirement for sodium ions. The predominant fatty acids of the organisms are C16 : 1 ω7c, C16 : 0 and C18 : 1 ω7c, with C10 : 1 3-OH, C10 : 0 3-OH, C12 : 0 3-OH, C14 : 1 3-OH, C14 : 0 3-OH and C19 : 1 present in smaller amounts. The main polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylmonomethylamine. The DNA base composition of the strains is 54–55 mol% G+C. 16S rRNA gene sequence comparisons show that the isolates are related to the genera Oceanospirillum, Pseudospirillum, Marinospirillum, Halomonas and Chromohalobacter in the γ-Proteobacteria. Morphological, physiological and genotypic differences from these previously described genera support the description of a novel genus and species, Saccharospirillum impatiens gen. nov., sp. nov. The type strain is EL-105T (=DSM 12546T=CECT 5721T).
To further investigate the diversity of micro-organisms capable of conserving energy to support growth from dissimilatory Fe(III) reduction, Fe(III)-reducing micro-organisms were enriched and isolated from subsurface sediments collected in Oyster Bay, VA, USA. A novel isolate, designated T118T, was recovered in a medium with lactate as the sole electron donor and Fe(III) as the sole electron acceptor. Cells of T118T were Gram-negative, motile, short rods with a single polar flagellum. Strain T118T grew between pH 6·7 and 7·1, with a temperature range of 4–30 °C. The optimal growth temperature was 25 °C. Electron donors utilized by strain T118T with Fe(III) as the sole electron acceptor included acetate, lactate, malate, propionate, pyruvate, succinate and benzoate. None of the compounds tested was fermented. Electron acceptors utilized with either acetate or lactate as the electron donor included Fe(III)–NTA (nitrilotriacetic acid), Mn(IV) oxide, nitrate, fumarate and oxygen. Phylogenetic analysis demonstrated that strain T118T is most closely related to the genus Rhodoferax. Unlike other species in this genus, strain T118T is not a phototroph and does not ferment fructose. However, phototrophic genes may be present but not expressed under the experimental conditions tested. No Rhodoferax species have been reported to grow via dissimilatory Fe(III) reduction. Based on these physiological and phylogenetic differences, strain T118T (=ATCC BAA-621T=DSM 15236T) is proposed as a novel species, Rhodoferax ferrireducens sp. nov.
Heterotrophic bacteria were isolated from a water sample taken from the North Sea, 2 km off the coast of the island of Helgoland, by direct plating of the serially diluted sample on complex marine media. Sixteen of 80 strains from the highest sample dilution belonged to the ‘Roseobacter–Sulfitobacter–Silicibacter’ group within the α-subclass of the Proteobacteria on the basis of partial 16S rDNA sequence analysis. Phylogenetic analysis of nearly complete 16S rDNA sequences showed that the closest relative of two strains, Hel 10T and Hel 26, was Ketogulonicigenium vulgare (94·4 % similarity). These strains were Gram-negative, non-motile rods, obligate aerobes, required sodium ions and 1–7 % sea salts for growth and did not produce bacteriochlorophyll. Their optimal growth temperature was 25–30 °C. The strains had Q-10 as the dominant respiratory quinone. Chemotaxonomic analysis showed a combination of ester-linked 3-OH 10 : 0, 12 : 1 and amide-linked 3-oxo 14 : 0 (or 3-OH 14 : 1) and 3-OH 14 : 0 fatty acids, which appears to be a unique feature of strains Hel 10T and Hel 26 within this subsection of the α-subclass of the Proteobacteria. Based on 16S rDNA sequence analysis and chemotaxonomic data, the strains are assigned to a new genus and species, Jannaschia helgolandensis gen. nov., sp. nov., with the type strain Hel 10T (=DSM 14858T=NCIMB 13941T).
The taxonomic position of the fluorescent amplified fragment length polymorphism fingerprinting groups A46 (five isolates), A51 (six isolates), A52 (five isolates) and A53 (seven isolates) obtained in a previous study were further analysed through a polyphasic approach. The 23 isolates were phylogenetically related to Vibrio splendidus, but DNA–DNA hybridization experiments proved that they belong to three novel species. Chemotaxonomic and phenotypic analyses further disclosed several features that differentiate between the 23 isolates and known Vibrio species. The names Vibrio kanaloae sp. nov. (type strain LMG 20539T=CAIM 485T; EMBL accession no. AJ316193; G+C content 44·7 mol%), Vibrio pomeroyi sp. nov. (type strain LMG 20537T=CAIM 578T; EMBL accession no. AJ491290; G+C content 44·1 mol%) and Vibrio chagasii sp. nov. (type strain LMG 21353T=CAIM 431T; EMBL accession no. AJ316199; G+C content 44·6 mol%) are respectively proposed to encompass the five isolates of A46, the six isolates of A51 and the 12 isolates of A52/A53. The three novel species can be distinguished from known Vibrio species by several phenotypic features, including utilization and fermentation of various carbon sources, β-galactosidase activity and fatty acid content (particularly of 12 : 0, 14 : 0, 14 : 0 iso and 16 : 0 iso).
The taxonomic characteristics of two bacterial strains, RB-8T and RB-9, isolated from hydrocarbon-degrading enrichment cultures obtained from Antarctic coastal marine environments (Rod Bay, Ross Sea), were determined. These bacteria were psychrophilic, aerobic and Gram-negative with polar flagella. Growth was not observed in the absence of NaCl, occurred only at concentrations of Na+ above 20 mM and was optimal at an NaCl concentration of 3–5 % (w/v). The major cellular fatty acids were monounsaturated straight-chain fatty acids. The strains were able to synthesize the polyunsaturated fatty acid eicosapentaenoic acid (20 : 5ω3) at low temperatures. The DNA G+C contents were 41–42 mol%. The strains formed a distinct phyletic line within the γ-Proteobacteria, with less than 89·6 % sequence identity to their closest relatives within the Bacteria with validly published names. Both isolates exhibited a restricted substrate profile, with a preference for aliphatic hydrocarbons, that is typical of marine hydrocarbonoclastic micro-organisms such as Alcanivorax, Marinobacter and Oleiphilus. On the basis of ecophysiological properties, G+C content, 16S rRNA gene sequences and fatty acid composition, a novel genus and species within the γ-Proteobacteria are proposed, Oleispira antarctica gen. nov., sp. nov.; strain RB-8T (=DSM 14852T=LMG 21398T) is the type strain.
An anaerobic, halorespiring bacterium (strain PCE-M2T=DSM 13726T=ATCC BAA-583T) able to reduce tetrachloroethene to cis-dichloroethene was isolated from an anaerobic soil polluted with chlorinated aliphatic compounds. The isolate is assigned to the genus Sulfurospirillum as a novel species, Sulfurospirillum halorespirans sp. nov. Furthermore, on the basis of all available data, a related organism, Dehalospirillum multivorans DSM 12446T, is reclassified to the genus Sulfurospirillum as Sulfurospirillum multivorans comb. nov.
Bacterial spot disease of lamb's lettuce [Valerianella locusta (L.) Laterr.] was first observed in fields in 1991. This new bacterial disease is localized in western France in high-technology field production of lamb's lettuce for the preparation of ready-to-use salad. Nineteen strains isolated in 1992 and 1993 from typical black leaf spots of naturally infected lamb's lettuce were characterized and compared with reference strains of Acidovorax and Delftia. The pathogenicity of the 19 strains was confirmed by artificial inoculation. Biochemical and physiological tests, fatty acid profiles, DNA–DNA hybridization and other nucleic acid-based tests were performed. A numerical taxonomic analysis of the 19 lamb's lettuce strains showed a single homogeneous phenon closely related to previously described phytopathogenic taxa of the genus Acidovorax. DNA–DNA hybridization studies showed that the lamb's lettuce strains were 91–100 % related to a representative strain, strain CFBP 4730T, and constituted a discrete DNA hybridization group, indicating that they belong to the same novel species. Results from DNA–rRNA hybridization, 16S rRNA sequence analysis and fatty acid analysis studies confirmed that this novel species belongs to the β-subclass of the Proteobacteria and, more specifically, to the family Comamonadaceae and the genus Acidovorax. The name Acidovorax valerianellae sp. nov. is proposed for this novel taxon of phytopathogenic bacteria. The type strain is strain CFBP 4730T (=NCPPB 4283T).
The taxonomic position of a group of five d-sorbitol- and lactose-negative enterobacterial isolates recovered from diarrhoeal stools of children at the International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B), was investigated by DNA–DNA hybridization, phenotypic characterization and 16S rDNA sequencing. These strains were originally identified as ‘Hafnia alvei-like’ with the API 20E system but, in fact, show more phenotypic and genotypic resemblance to members of the genus Escherichia. By 16S rDNA sequencing, one representative strain of the ICDDR,B group was shown to be closely affiliated to the genera Escherichia and Shigella. Using the fluorimetric microplate hybridization method, the diarrhoeagenic ICDDR,B isolates were found to constitute a homogeneous taxon (⩾82 % internal DNA relatedness), with the closest affiliation to the type strains of Escherichia coli (55–64 %) and Shigella flexneri (54–60 %). The DNA–DNA hybridization levels were much lower with members of other described Escherichia species (16–45 %) and with the type strain of H. alvei (9–17 %). The G+C content of the ICDDR,B strains ranged from 50·5 to 50·7 mol%. Together with the diagnostic characteristics reported previously, including the presence of the eaeA gene of enteropathogenic E. coli and of the E. coli and Shigella-specific phoE gene, it is concluded that the ICDDR,B strains represent a novel taxon in the genus Escherichia, for which the name Escherichia albertii sp. nov. is proposed. Its type strain is Albert 19982T (=LMG 20976T=CCUG 46494T).
Two bacterial strains (KMM 3633T and KMM 3634) were isolated from marine coastal sea-ice and characterized by using phenotypic and molecular methods. The isolates were aerobic, Gram-negative, psychrophilic, halophilic and motile by means of a single polar flagellum. The DNA G+C content was 45·3–45·6 mol%. The major cellular fatty acids were C16 : 0, C16 : 1 ω9c and C18 : 1 ω7c. Comparison of almost-complete 16S rDNA sequences demonstrated that the strains were phylogenetically closely related to each other (99·5 % sequence identity), and related to Marinomonas species (94·4–96·4 % identity). DNA–DNA reassociation between KMM 3633T and KMM 3634 occurred at a level of 92 %. Based on phenotypic, chemotaxonomic and phylogenetic properties, the name Marinomonas primoryensis sp. nov. is proposed for strains KMM 3633T and KMM 3634; the type strain is KMM 3633T (=JCM 11775T=NRIC 523T).
Three clusters of isolates have previously been defined within the species Comamonas terrigena, on the basis of DNA–rRNA and DNA–DNA hybridization data, and of protein electrophoretic patterns and immunotyping. More detailed characterization in the current study shows that representatives of these three groups can also be differentiated phenotypically from each other. Strains of C. terrigena sensu stricto (C. terrigena DNA group 1) are pyrrolidone aminopeptidase-positive, do not grow at 40 °C, are l-alanine-positive and are always negative for 4-hydroxybenzoate. Strains of C. terrigena DNA groups 2 and 3 are pyrrolidone aminopeptidase-negative; the former is the only group that is tyrosine-negative, and only the latter can grow at 42 °C (with an optimal growth temperature of 40 °C). These findings are corroborated by differences in 16S rDNA sequence and tRNA intergenic spacer lengths. Therefore, it is proposed to rename C. terrigena DNA group 2 [containing former Aquaspirillum aquaticum and E. Falsen (EF) group 10 strains] as Comamonas aquatica sp. nov., and C. terrigena DNA group 3 (containing former EF group 10 strains) as Comamonas kerstersii sp. nov.
A group of seven sucrose-negative Aeromonas strains (referred to as group Au) isolated from the internal organs of septicaemic farmed frogs (Rana rugulosa) in Thailand was subjected to a polyphasic taxonomic study including fluorescent amplified fragment length polymorphism (FAFLP) and ERIC-PCR fingerprinting, 16S rDNA sequencing, microplate DNA–DNA hybridizations and extensive phenotypic characterization. Comparison of FAFLP and ERIC-PCR fingerprints indicated that the group Au isolates belonged to the species Aeromonas hydrophila DNA hybridization group (HG) 1 in which they represent a genotypic subgroup closely affiliated to A. hydrophila subsp. hydrophila and subsp. dhakensis. One representative of the Au group exhibited ⩾99·0 % 16S rDNA sequence similarity with the type strains of the two A. hydrophila subspecies. DNA–DNA hybridization with type and reference strains of all known Aeromonas taxa revealed that the Au group represented a homogeneous taxon that exhibited the highest relatedness with members of the two A. hydrophila subspecies, ranging from 75 to 93 %. Phenotypic characterization on the basis of 152 features further revealed that the Au group isolates differed from A. hydrophila subsp. hydrophila or subsp. dhakensis in a total of 13 biochemical properties. Of these, assimilation of l-glycine and isobutyrate as sole carbon source, acid production from salicin and d-sucrose, and aesculin hydrolysis were of diagnostic value. From the results of this study, it can be concluded that the Aeromonas frog isolates of the Au group represent a new subspecies of A. hydrophila, for which the name Aeromonas hydrophila subsp. ranae subsp. nov. is proposed. Its type strain is Au-1D12T (=LMG 19707T=CCUG 46211T).
A format for the description of single novel species is proposed, which should facilitate the reviewing process by assisting the provision of data in a standardized form. The abstract must be short and concise, highlighting phylogenetic position, morphology and chemotaxonomy for genus affiliation, the genotypic and phenotypic basis for species differentiation, and the name and deposition numbers from two public culture collections in different countries for the type strain: A Gram-negative, rod-shaped, non-spore-forming bacterium (Iso 196T) was isolated from chicken faeces. On the basis of 16S rRNA gene sequence similarity, strain Iso 196T was shown to belong to the α-2 subclass of the Proteobacteria related to Ochrobactrum tritici (95·6 %), Ochrobactrum grignonense (95·0 %) and Ochrobactrum anthropi (94·6 %), and the phylogenetic distance from any validly described species within the genus Brucella was less than 95 %. Chemotaxonomic data (major ubiquinone – Q-10; major polyamines – spermidine and putrescine; major polar lipids – phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine; major fatty acids – C18 : 1 ω7c and C19 : 0 cyclo ω8c) supported the affiliation of strain Iso 196T to the genus Ochrobactrum. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain Iso 196T from the four validly published Ochrobactrum species. Iso 196T therefore represents a new species, for which the name Ochrobactrum gallinifaecis sp. nov. is proposed, with the type strain Iso 196T (=DSM 15295T =CIP 107753T).