- Volume 53, Issue 5, 2003

The taxonomic status of Sulfolobus hakonensis Takayanagi et al. 1996 was re-evaluated by fresh determinations of the 16S rDNA sequence and G+C content of the genomic DNA of the type strain, HO1-1T. The 16S rDNA sequence of strain HO1-1T showed 98 % similarity to those of two Metallosphaera species and only ⩽92 % similarity to those of other Sulfolobus species. The DNA G+C content (46·2 mol%) is in accordance with those of Metallosphaera species. In addition, strain HO1-1T shares some phenotypic properties with Metallosphaera species; however, it can be differentiated from them by its capacity to utilize FeS and tetrathionate and the absence of flagella. Therefore, it is proposed that Sulfolobus hakonensis should be transferred to the genus Metallosphaera as Metallosphaera hakonensis comb. nov.

Twenty-two isolates from microbial mats in eastern Antarctic lakes showed similar fatty acid compositions and were investigated further using a polyphasic taxonomic approach. Repetitive extragenic palindromic DNA-PCR fingerprinting of the 22 strains revealed three groups, and DNA–DNA hybridizations between representatives showed more than 87 % DNA–DNA reassociation with each other. 16S rRNA gene sequence analysis placed two representative strains, LMG 21477T and LMG 21619, within the genus Flavobacterium, with 95·1 % sequence similarity to Flavobacterium flevense, 95·0 % to Flavobacterium tegetincola, less than 95 % to other Flavobacterium species and less than 90 % to representatives of other genera. The name Flavobacterium gelidilacus sp. nov. is proposed, with LMG 21477T (=DSM 15343T) as the type strain, and a description of the species is given on the basis of morphological, biochemical and physiological characteristics and fatty acid composition. The G+C content of the genomic DNA is 30·0–30·4 mol%.

A novel heterotrophic, yellow-orange-pigmented, non-motile, asporogenic, strictly aerobic, Gram-negative, oxidase and catalase-positive bacterium KMM 3516T was isolated from the holothurian Apostichopus japonicus collected from Troitsa Bay in the Gulf of Peter the Great (Sea of Japan) during November 1997. 16S rDNA sequence analysis revealed that strain KMM 3516T was a member of the family Flavobacteriaceae. The DNA G+C content of KMM 3516T was 41·3 mol%. Major respiratory quinone was MK-6. Predominant fatty acids were i15 : 0 and α15 : 0 (68·8 and 8·4 %, respectively). On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, the novel bacterium has been designated Vitellibacter vladivostokensis gen. nov., sp. nov. The type strain is KMM 3516T (=NBRC 16718T).

A novel marine, heterotrophic, aerobic, pigmented, non-motile bacterium was isolated from a bottom sediment sample collected from Troitsa Bay in the Gulf of Peter the Great, Sea of Japan, during June 2000. 16S rDNA sequence analysis revealed that this bacterium was a member of the family Flavobacteriaceae. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic analyses, the bacterium was shown to belong to a novel species of the genus Arenibacter, for which the name Arenibacter troitsensis sp. nov. is proposed. The type strain is KMM 3674T (=JCM 11736T).

On the basis of phenotypic and genotypic characteristics, a novel species belonging to the genus Pedobacter is described. A facultatively psychrophilic, Gram-negative, aerobic, rod-shaped strain, A37T, was isolated from alpine glacier cryoconite. The non-flagellated and non-spore-forming isolate grew over a temperature range of 1–25 °C, showed activities of oxidase, catalase, DNase, protease (gelatin, casein), amylase, β-glucosidase, β-galactosidase and β-lactamase and degraded oil hydrocarbons. A distinct optimum temperature of 15 °C was observed for both protease production and oil hydrocarbon biodegradation. Analysis of 16S rDNA revealed that strain A37T represents a distinct taxon within Pedobacter. DNA from strain A37T showed only 19·7 % genetic relatedness to the DNA of Pedobacter piscium. The DNA G+C content was 43·4 mol%. Dominant fatty acids (51 %) were iso-15 : 0 2-OH and 16 : 1ω7c. The strain is assigned to a novel Pedobacter species, for which the name Pedobacter cryoconitis sp. nov. is proposed, with A37T (=DSM 14825T=LMG 21415T) as the type strain.

Several cold-adapted strains isolated from a variety of algal-rich Antarctic and Southern Ocean samples formed three distinct groups within the class Flavobacteria, phylogenetically distant from other cultivated species. The first taxon, designated Algoriphagus ratkowskyi gen. nov., sp. nov., was isolated from sea ice and from saline lake cyanobacterial mats and includes non-motile, strictly aerobic, saccharolytic rod-like or serpentine strains that were most closely related to the genus Cyclobacterium according to 16S rDNA sequence analysis (sequence similarity 0·85). The second taxon, designated Brumimicrobium glaciale gen. nov., sp. nov., isolated from sea ice and from continental shelf sediment, formed gliding, rod-like cells that were facultatively anaerobic with a fermentative metabolism. The third taxon, designated Cryomorpha ignava gen. nov., sp. nov., isolated from Southern Ocean particulates and from quartz stone subliths, included strictly aerobic, pleomorphic rod-like cells. Brumimicrobium glaciale and Cryomorpha ignava were most closely allied with ‘Microscilla aggregans var. catalatica’, which, on the basis of its distinctive taxonomic traits, is also proposed as a new genus and species, Crocinitomix catalasitica gen. nov., sp. nov. It is proposed that the three genera Brumimicrobium, Cryomorpha and Crocinitomix belong to a new family, Cryomorphaceae fam. nov. (type genus Cryomorpha), as they possess generally similar morphological and ecophysiological characteristics and form a common and distinct clade within class Flavobacteria.

An alkane-degrading bacterium, designated GTI MVAB Hex1T, was isolated from chronically crude oil-contaminated soil from an oilfield in southern Illinois. The isolate grew very weakly or not at all in minimal or rich media without hydrocarbons. Straight-chain aliphatic hydrocarbons, such as hexadecane and heptadecane, greatly stimulated growth; shorter-chain (⩽C15) hydrocarbons did not (with decane as the sole exception). Growth was also greatly enhanced by the branched aliphatic hydrocarbons pristane and squalane. The latter of these was most intriguing, as catabolism of squalane has hitherto been reported only for Mycobacterium species. Although unable to utilize mono- or polycyclic aromatic hydrocarbons as sole carbon sources, the isolate did show slight fluorene-mineralizing capability in Luria–Bertani medium, which was partially repressed by hexadecane. In contrast, hexadecane supplementation greatly increased mineralization of 14C-dodecane, which was not a growth substrate. Further testing emphasized the isolate's extremely narrow substrate range, as only Tween 40 and Tween 80 supported significant growth. Microscopic examination (by scanning and transmission electron microscopy) revealed a slightly polymorphic coccoidal to bacillar morphology, with hydrocarbon-grown cells tending to be more elongated. When grown with hexadecane, GTI MVAB Hex1T accumulated a large number of electron-transparent intracytoplasmic inclusion bodies. These were also prevalent during growth in the presence of squalane. Smaller inclusion bodies were observed occasionally with pristane supplementation; they were, however, absent during growth on crude oil. On the basis of 16S rRNA gene sequence data and range of growth substrates, classification of this isolate as the type strain of Alkanindiges illinoisensis gen. nov., sp. nov. is proposed, which is most closely related (approx. 94 % sequence similarity) to Acinetobacter junii.

Two strains of thermophilic, anaerobic, chemolithoautotrophic bacteria, designated JRT and DR, were isolated from hydrothermal samples collected on the Mid-Atlantic Ridge from the Rainbow (36° 16′ N, 33° 54′ W) and Menez Gwen (37° 50′ N, 31° 50′ W) vent fields, respectively. Cells of both isolates were short, straight- to vibrio-shaped, motile rods with one polar flagellum, and were Gram-negative and non-sporulating. Strain JRT was characterized in detail. It was found to grow optimally at pH 6·5–6·7, at 60 °C and in the presence of 30 g NaCl l−1. Strain JRT could use molecular hydrogen, acetate, succinate, pyruvate and proteinaceous compounds as electron donors, and elemental sulfur, nitrate or Fe(III) as electron acceptors. No fermentation of organic substrates occurred. The G+C content of the DNA of strain JRT was 30·8 mol%. Strain DR (=DSM 14927) possessed the same morphology and pH, temperature and salinity optima and ranges, and used the same electron acceptors as strain JRT. On the basis of their 16S rDNA sequences (1517 nucleotides), strains JRT and DR were identical and distantly related to Deferribacter thermophilus and Deferribacter desulfuricans (95·3 and 95·2 % sequence similarity, respectively). Based on their phenotypic and phylogenetic characteristics, it is proposed that both strains are members of a new species of the genus Deferribacter, for which the name Deferribacter abyssi (type strain JRT=DSM 14873T=JCM 11955T) is proposed.

Two strains of Gram-negative, aerobic, non-pigmented, non-motile, rod-shaped, methane-oxidizing bacteria were isolated from an acidic forest cambisol near Marburg, Germany, and were designated as strains BL2T and A1. These bacteria were morphologically and phenotypically similar to Methylocella palustris KT. The cells possess a highly specific bipolar appearance. They lack the intracytoplasmic membranes common to all methane-oxidizing bacteria except Methylocella, but contain a vesicular membrane system connected to the cytoplasmic membrane. A soluble methane monooxygenase was present, but no particulate methane monooxygenase could be detected. These bacteria utilize the serine pathway for carbon assimilation. Strains BL2T and A1 are moderately acidophilic, mesophilic organisms capable of growth at pH values between 4·5 and 7 (with an optimum at pH 5·5) and at temperatures between 4 and 30 °C. Compared with Methylocella palustris KT, these strains have greater tolerance of cold temperatures, dissolved salts and methanol. On the basis of 16S rRNA gene sequence identity, of species with validly published names, strain BL2T is most closely related to Methylocella palustris KT (97·3 % identity), Beijerinckia indica subsp. indica ATCC 9039T (97·1 %) and Methylocapsa acidiphila B2T (96·2 %). The DNA G+C content is 60 mol% and the major phospholipid fatty acid is 18 : 1ω7. Strain BL2T showed only 21–22 % DNA–DNA hybridization with Methylocella palustris KT. The data therefore suggest that strains BL2T and A1 represent a novel species of Methylocella; the name Methylocella silvestris sp. nov. is proposed, with strain BL2T (=DSM 15510T=NCIMB 13906T) as the type strain.

A strictly aerobic, mesophilic bacterium, strain AMX 51T, was isolated from anaerobic digester sludge. Cells were Gram-negative, motile, non-sporulating, straight to curved rods with one polar flagellum. The isolate had phenotypic traits of the genus Bosea, including cellular fatty acid and substrate utilization profiles. Physiological characteristics and antibiotic susceptibility were determined. Phylogenetic analysis revealed that strain AMX 51T was a member of the α-Proteobacteria, most closely related to Bosea thiooxidans DSM 9653T (similarity of 98·88 %). Methylobacterium organophilum JCM 2833T, Methylobacterium mesophilicum JCM 2829T, Afipia clevelandensis DSM 7315T, Afipia felis DSM 7326T, Afipia broomeae DSM 7327T, Blastobacter denitrificans LMG 8443T and Bradyrhizobium japonicum DSM 30131T showed significant 16S rRNA gene sequence similarities to strain AMX 51T. The DNA G+C composition of strain AMX 51T was 68·5 mol%. DNA–DNA hybridization analysis revealed 44·2 and 15·1 % relatedness between strain AMX 51T and the respective type strains of Bosea thiooxidans and A. felis. Overall results suggest that strain AMX 51T (=DSM 13099T=ATCC 700918T=CIP 106457T) represents a novel species of the genus Bosea; the name Bosea minatitlanensis sp. nov. is proposed.

Seven psychrotolerant, Gram-negative bacterial strains, five dust- and airborne isolates (MA101bT, MA306a, MA405/90, MA-olkiT and NW12T) and two from the Antarctic (Ant 20 and M3C203B-B), were subjected to a polyphasic characterization to determine their taxonomic position. High 16S rDNA sequences similarities (99·3–100·0 %) demonstrated that they were closely related to each other. Phylogenetic evaluation of their 16S rDNA sequences revealed that they are members of the genus Sphingomonas sensu stricto, encompassing a separate branch within this genus. They shared 94·4–96·6 % 16S rDNA sequence similarity with species of this genus. All Sphingomonas-specific signature nucleotides were also detected. The presence of the major ubiquinone Q-10, sym-homospermidine as the predominant polyamine, Sphingomonadaceae-specific sphingoglycolipid in the polar lipid patterns and a fatty acid profile containing C14 : 0 2-OH and lacking 3-OH fatty acids were in agreement with identification of these strains as members of the genus Sphingomonas sensu stricto. Results from DNA–DNA hybridizations and comparison of protein patterns indicated that the seven strains are members of three distinct species. One species is represented by strains MA101bT, MA306a and MA405/90, the second by strains NW12T, Ant 20 and M3C203B-B and the third by one strain, MA-olkiT. Their distinction at the species level was also supported by results of biochemical characterization and partly supported by riboprints and genomic fingerprints. On the basis of these results, three novel species of the genus Sphingomonas are proposed: Sphingomonas aurantiaca sp. nov., consisting of strains MA101bT (=DSM 14748T=LMG 21377T), MA306a and MA405/90 (=DSM 14749=LMG 21378), Sphingomonas faeni sp. nov. MA-olkiT (=DSM 14747T=LMG 21379T) and Sphingomonas aerolata sp. nov., represented by strains NW12T (=DSM 14746T=LMG 21376T), Ant 20 (=ICMP 13599) and M3C203B-B (=SMCC M3C203B-B).

Three Gram-negative, rod-shaped, aerobic bacteria that were capable of degrading dimethylsulfoniopropionate (DMSP) were isolated from marine waters. These isolates (DSS-3T, DSS-10 and ISMT) exhibited the ability to demethylate and cleave DMSP, as well as to degrade other sulfur compounds related to DMSP that are cycled in marine environments. Intracellular poly-β-hydroxybutyrate inclusions, surface blebs and one polar, complex flagellum that rotated exclusively in the clockwise direction were observed for DSS-3T. The outer membrane of ISMT was separated from the cytoplasm at the poles in a toga-like morphology. The primary fatty acid in both strains was C18 : 1 ω7c. DNA G+C contents for the isolates were 68·0±0·1, 68·1±0·1 and 66·0±0·2 mol% for DSS-3T, DSS-10 and ISMT, respectively. 16S rRNA gene sequence analyses placed these organisms within the Roseobacter lineage of the α-Proteobacteria. Closely related species were Silicibacter lacuscaerulensis and Ruegeria atlantica (DSS-3T and DSS-10) and Roseovarius tolerans (ISMT). Neither DSS-3T nor ISMT exhibited 16S rRNA similarity >97 % or DNA–DNA hybridization values >45 % to their nearest described relatives. Genotypic and phenotypic analyses support the creation of two novel species: Silicibacter pomeroyi sp. nov. with strain DSS-3T (=ATCC 700808T=DSM 15171T) as the type strain, and Roseovarius nubinhibens sp. nov. with strain ISMT (=ATCC BAA-591T=DSM 15170T) as the type strain.

A novel alkaliphilic, sulfate-reducing bacterium, strain MLF1T, was isolated from sediments of soda Mono Lake, California. Gram-negative vibrio-shaped cells were observed, which were 0·6–0·7×1·2–2·7 μm in size, motile by a single polar flagellum and occurred singly, in pairs or as short spirilla. Growth was observed at 15–48 °C (optimum, 37 °C), >1–7 % NaCl, w/v (optimum, 3 %) and pH 8·0–10·0 (optimum, 9·5). The novel isolate is strictly alkaliphilic, requires a high concentration of carbonate in the growth medium and is obligately anaerobic and catalase-negative. As electron donors, strain MLF1T uses hydrogen, formate and ethanol. Sulfate, sulfite and thiosulfate (but not sulfur or nitrate) can be used as electron acceptors. The novel isolate is a lithoheterotroph and a facultative lithoautotroph that is able to grow on hydrogen without an organic source of carbon. Strain MLF1T is resistant to kanamycin and gentamicin, but sensitive to chloramphenicol and tetracycline. The DNA G+C content is 63·0 mol% (HPLC). DNA–DNA hybridization with the most closely related species, Desulfonatronum lacustre Z-7951T, exhibited 51 % homology. Also, the genome size (1·6×109 Da) and T m value of the genomic DNA (71±2 °C) for strain MLF1T were significantly different from the genome size (2·1×109 Da) and T m value (63±2 °C) for Desulfonatronum lacustre Z-7951T. On the basis of physiological and molecular properties, the isolate was considered to be a novel species of the genus Desulfonatronum, for which the name Desulfonatronum thiodismutans sp. nov. is proposed (the type strain is MLF1T=ATCC BAA-395T=DSM 14708T).

Five isolates recovered from the respiratory tract of cystic fibrosis patients were included in a polyphasic taxonomic study that employed 16S rDNA sequence analysis, cellular protein and fatty acid analysis and biochemical characterization. Four isolates were classified as a novel Ralstonia species, for which the name Ralstonia respiraculi sp. nov. is proposed; the other isolate was phylogenetically closely related to R. respiraculi, but is likely to represent another novel Ralstonia species. The type strain of R. respiraculi is AU3313T (=LMG 21510T=CCUG 46809T).

Phylogenetic analysis based on 16S rDNA sequences revealed that Pseudomonas elongata Humm 1946 is more closely related to the genus Microbulbifer than to authentic pseudomonads. The type strain of P. elongata (DSM 6810T) exhibited 16S rDNA similarity levels of 97·5 and 98·2 % to the type strains of Microbulbifer hydrolyticus and Microbulbifer salipaludis, respectively, but of less than approximately 92 % to Pseudomonas species with known 16S rDNA sequences. Respiratory lipoquinone and cellular fatty acid analyses showed that the type strain of P. elongata has characteristics similar to those of the genus Microbulbifer, not those of the genus Pseudomonas. P. elongata DSM 6810T contained ubiquinone-8 as the predominant respiratory lipoquinone and iso-C15 : 0 as the major fatty acid. DNA–DNA relatedness data indicate that P. elongata is a species distinct from M. hydrolyticus and M. salipaludis. Therefore, on the basis of these data, P. elongata Humm 1946 should be transferred to the genus Microbulbifer as Microbulbifer elongatus comb. nov.

A bacterial strain, N2-680T (=DSM 15264T=LMG 21760T), isolated from a thermophilic aerobic digester of municipal sludge, was characterized with respect to its morphology, physiology and taxonomy. Phenotypically, the isolate was a Gram-negative rod with a polar flagellum, catalase- and oxidase-positive, containing cytoplasmic inclusions of poly-β-hydroxybutyrate and had an optimal growth temperature of about 47 °C. Strain N2-680T was unable to reduce nitrate and could use organic acids, amino acids and carbohydrates as single carbon sources. Chemotaxonomic analysis revealed that ubiquinone 8 was the major respiratory quinone of this organism and that phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids. At 50 °C, the major components in fatty acid methyl ester analysis were C16 : 0 and cyclo-C17 : 0. The highest 16S rDNA sequence identity of isolate N2-680T was to Leptothrix mobilis and Ideonella dechloratans (95·7 %) and to Rubrivivax gelatinosus and Aquabacterium commune (95·6 %). 16S rDNA sequence similarities to species of two related thermophilic genera, Caldimonas manganoxidans and Tepidimonas ignava, were lower (93·6 and 94·7 %). On the basis of phylogenetic analyses and physiological and chemotaxonomic characteristics, it is proposed that isolate N2-680T represents a new genus and species, for which the name Caenibacterium thermophilum gen. nov., sp. nov. is proposed.

In the course of a screening programme in hypersaline habitats of southern Spain to isolate halophilic bacteria that are able to produce different extracellular enzymes, a novel, moderately halophilic bacterium (strain SM19T) that displays lipolytic activity has been isolated and characterized. Strain SM19T is a Gram-negative rod that grows optimally in culture media that contain 7·5 % NaCl. The DNA G+C content was 57·0 mol%. According to phenotypic and genotypic data, this strain was assigned to the genus Marinobacter. However, 16S rDNA sequence similarity between strain SM19T and species of the genus Marinobacter was <96·7 %; this value is sufficiently low to propose its designation as a novel species. In addition, DNA–DNA hybridization with reference strains of close phylogenetic relatives was between 11 and 19 %. On the basis of these data, the inclusion of strain SM19T in the genus Marinobacter as a novel species is proposed, with the name Marinobacter lipolyticus sp. nov. The type strain of the novel species is SM19T (=DSM 15157T=NCIMB 13907T=CIP 107627T=CCM 7048T).