- Volume 53, Issue 3, 2003

A novel moderately thermophilic, organotrophic, microaerophilic, facultatively chemolithotrophic bacterium, designated strain 506T, was isolated from a deep-sea hydrothermal vent site at 13°N in the East Pacific Rise. Cells were Gram-negative, non-motile rods. The organism grew in the temperature range 40–68 °C, with an optimum at 60 °C, and in the pH range 5·5–8·4, with an optimum around pH 7·5. The NaCl concentration for growth was in the range 10–50 g l−1, with an optimum at 30 g l−1. Strain 506T grew chemoorganoheterotrophically with carbohydrates, proteinaceous substrates, organic acids and alcohols using oxygen or nitrate as electron acceptor. Alternatively, strain 506T was able to grow lithoheterotrophically with molecular hydrogen as the energy source. The G+C content of the genomic DNA was 62·9 mol%. Phylogenetic analysis of the 16S rDNA sequence placed strain 506T in the family Thermaceae. On the basis of phenotypic and phylogenetic data, strain 506T (=DSM 14977T=VKM B-2274T) is proposed as the type strain of a novel species in a new genus, Oceanithermus profundus gen. nov., sp. nov.

Among a large collection of South African dairy isolates, a novel Chryseobacterium taxon (DNA group 3) was previously delineated by a polyphasic taxonomic study ( Hugo et al., Syst Appl Microbiol 22, 586–595, 1999 ). In the present paper, this taxon is further characterized using 16S rDNA sequencing, fatty acid methyl ester analysis and a comparative phenotypic analysis, resulting in the proposal of a novel species, Chryseobacterium joostei sp. nov. (type strain Ix 5aT=LMG 18212T=CCUG 46665T).

A novel, obligately anaerobic, mesophilic, haloalkaliphilic spirochaete, strain ASpG1T, was isolated from sediments of the alkaline, hypersaline Mono Lake in California, USA. Cells of the Gram-negative strain were motile and spirochaete-shaped with sizes of 0·2–0·22×8–18 μm. Growth of the strain was observed between 10 and 44 °C (optimum 37 °C), in 2–12 % (w/v) NaCl (optimum 3 % NaCl) and between pH 8 and 10·5 (optimum pH 9·5). The novel strain was strictly alkaliphilic, required high concentrations of carbonates in the medium and was capable of utilizing d-glucose, fructose, maltose, sucrose, starch and d-mannitol. End products of glucose fermentation were H2, acetate, ethanol and formate. Strain ASpG1T was resistant to kanamycin and rifampicin, but sensitive to gentamicin, tetracycline and chloramphenicol. The G+C content of its DNA was 58·5 mol%. DNA–DNA hybridization analysis of strain ASpG1T with its most closely related species, Spirochaeta alkalica Z-7491T, revealed a hybridization value of only 48·7 %. On the basis of its physiological and molecular properties, strain ASpG1T appears to represent a novel species of the genus Spirochaeta, for which the name Spirochaeta americana is proposed (type strain ASpG1T=ATCC BAA-392T=DSM 14872T).

A polyphasic taxonomic study was performed on a novel facultatively anaerobic, hydrogen- or sulfur/thiosulfate-oxidizing, thermophilic chemolithoautotroph recently isolated from subsurface hot aquifer water in a Japanese gold mine. The cells were straight to slightly curved rods, with a single polar flagellum. Growth was observed at 40–70 °C (optimum 60–65 °C; 80 min doubling time) and at pH 6·4–8·8 (optimum pH 7·5). The isolate was unable to use complex organic compounds, carbohydrates, amino acids or organic acids as sole energy and carbon sources. The G+C content of the genomic DNA was 31·3 mol%. Phylogenetic analysis based on 16S rDNA sequences indicated that the isolate was closely related to an uncultivated group of micro-organisms within the order Aquificales obtained from Icelandic and Japanese hot spring microbial mats, but distantly related to previously identified genera of the Aquificales such as Persephonella, Aquifex and Hydrogenobacter. The name Sulfurihydrogenibium subterraneum gen. nov., sp. nov. is proposed for this novel species; the type strain is HGMK1T (=JCM 11477T=ATCC BAA-562T=DSM 15120T).

A novel anaerobic, heterotrophic thermophile was isolated from a deep-sea hydrothermal vent chimney at the Suiyo Seamount in the Izu-Bonin Arc, Japan. The cells were bent, flexible rods, with a single polar flagellum. Growth was observed between 40 and 70 °C (optimum temperature: 60–65 °C; doubling time, 40 min) and between pH 5·0 and 7·5 (optimum pH 6·5). The isolate was a strictly anaerobic heterotroph capable of using complex organic compounds (yeast extract, tryptone, peptone, casein and Casamino acids), ethanol and various organic acids as energy and carbon sources. Hydrogen could serve as a supplementary energy source. Elemental sulfur (S0), nitrate or arsenate was required for growth as an electron acceptor. The G+C content of the genomic DNA was 38·6 mol%. Phylogenetic analysis based on 16S rDNA sequences indicated that isolate SSM1T is closely related to Deferribacter thermophilus BMAT (98·1 %). However, the novel isolate could be clearly differentiated from D. thermophilus BMAT on the basis of its physiological and genetic properties. The name Deferribacter desulfuricans sp. nov. (type strain SSM1T=JCM 11476T=DSM 14783T) is proposed.

Two novel psychrophilic bacterial strains (ZF-6T and ZF-8T) were isolated from the China No. 1 glacier. Polyphasic taxonomy using physiological and biochemical properties and phylogenetic analysis based on 16S rRNA gene sequences showed that the two isolates belonged to the genus Flavobacterium, and that they were distinct from each other and also from the known species of this genus. Strains ZF-6T and ZF-8T are Gram-negative and both have an optimal growth temperature of 11 °C. Strain ZF-6T is able to grow at 0–20 °C, the G+C content of its genomic DNA is 34·4 mol% and the major fatty acids of ZF-6T are C16 : 1 ω7c (17·7 %) and C15 : 1 ω6c (12·7 %). Strain ZF-8T showed a strong ability to degrade organic macromolecules such as starch, CM-cellulose, pectin and chitin. Its DNA G+C content is 35·1 mol%, and the major fatty acids are C16 : 1 ω7c (18·2 %) and C15 : 0 (9·9 %). Phylogenetic analysis based on 16S rDNA sequences indicated that ZF-6T and ZF-8T belong to the genus Flavobacterium and represent two novel species. DNA–DNA hybridization also supported the status of the two new isolates. The names Flavobacterium xinjiangense sp. nov. (type strain, ZF-6T=AS 1.2749T=JCM 11314T) and Flavobacterium omnivorum sp. nov. (type strain, ZF-8T=AS 1.2747T=JCM 11313T) are proposed for the two new isolates.

A novel thermophilic, hydrogen-oxidizing bacterium, designated 29WT, was isolated from a deep-sea hydrothermal vent chimney sample collected from the Suiyo Seamount in the Izu-Bonin Arc, Japan, at a depth of 1385 m. The cells were cocci (0·9–1·0 μm in diameter) and straight rods (2·3–2·7 μm long) under static and agitated culture conditions, respectively. The new isolate was an obligate chemolithoautotroph growing by respiratory nitrate reduction with H2, forming N2 as a final product. A very low concentration of O2 (optimum 0·6–0·8 %, v/v) was also used as an alternative electron acceptor while reduced sulfur compounds did not serve as electron donors. Anoxic hydrogen-oxidizing growth with nitrate was observed between 50 and 72·5 °C (optimum 70 °C; 40 min doubling time), pH 5·5 and 7·6 (optimum pH 7·2), and in the presence of 1·5 and 5·0 % NaCl (optimum 2·5 %). The G+C content of the genomic DNA was 37·3 mol%. Phylogenetic analysis based on 16S rDNA sequences indicated that the isolate was a member of the recently described genus Persephonella in a potential new family within the order Aquificales. On the basis of the physiological and molecular properties of the new isolate, the name Persephonella hydrogeniphila sp. nov. is proposed. The type strain is strain 29WT (=JCM 11663T=DSM 15103T).

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).