- Volume 55, Issue 3, 2005

The 16S rRNA gene sequence of [Methanogenium] frittonii DSM 2832T was determined and was found to be 99·9 % similar to the sequence of Methanoculleus thermophilus DSM 2373T. DNA–DNA hybridizations between both strains revealed 86 % DNA–DNA binding, indicating that both strains belong to the same species. The determination of the DNA G+C content of both type strains, DSM 2832T and DSM 2373T, revealed values of 56·1 and 59·1 mol%, respectively. Based on the phenotypic and genotypic characteristics, it is proposed to unite the species [Methanogenium] frittonii and Methanoculleus thermophilus under the name Methanoculleus thermophilus, which is the earlier synonym and hence has priority. Emended descriptions of the species Methanoculleus thermophilus and the genus Methanogenium are also given.

A novel extremely halophilic strain, AJ2T, was isolated from Ayakekum salt lake located in the Altun Mountain National Nature Reserve in Xinjiang, China. This isolate was neutrophilic, motile and grew in a wide range of MgCl2 concentrations (0·005–1·0 M). The major polar lipids of the isolate were C20C20 and C20C25 derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate. A comprehensive 16S rRNA gene sequence analysis revealed that the isolate shared 96·6–97·7 % sequence identity with Natrinema species. The isolate, however, could be genetically differentiated from these species by DNA–DNA hybridization analysis and on the basis of its physiological properties. On the basis of the polyphasic evidence, strain AJ2T (=AS 1.3731T=JCM 12890T) represents the type strain of a novel species, for which the name Natrinema altunense sp. nov. is proposed.

Four Gram-negative, non-spore-forming, slightly halophilic rods (strains SW-62T, SW-74, SW-63T and SW-72) with appendages were isolated from a salt lake near Hwajinpo Beach on the East Sea in Korea, and subjected to a polyphasic taxonomic analysis. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains SW-62T, SW-74, SW-63T and SW-72 formed a coherent cluster with Muricauda ruestringensis. Strains SW-62T and SW-74 had the same 16S rRNA gene sequence, as did strains SW-63T and SW-72. The level of 16S rRNA gene sequence similarity between strains SW-62T and SW-63T was 97·0 %. Strains SW-62T and SW-63T exhibited 16S rRNA gene similarity levels of 96·5 and 98·3 %, respectively, with respect to M. ruestringensis DSM 13258T. The predominant isoprenoid quinone found in the four isolates and M. ruestringensis DSM 13258T was MK-6. The four strains contained iso-C17 : 0 3-OH, iso-C15 : 1 and iso-C15 : 0 as the major fatty acids. Their DNA G+C contents were 44·1–45·4 mol%. The levels of DNA–DNA relatedness indicated that strains SW-62T and SW-74 and strains SW-63T and SW-72 were members of two species that were different from M. ruestringensis. On the basis of phenotypic and phylogenetic data and genomic distinctiveness, strains SW-62T and SW-74 and strains SW-63T and SW-72 were placed in the genus Muricauda as two distinct novel species, for which the names Muricauda flavescens sp. nov. (type strain, SW-62T=KCCM 41645T=JCM 11812T) and Muricauda aquimarina sp. nov. (type strain, SW-63T=KCCM 41646T=JCM 11811T), respectively, are proposed.

Five heterotrophic, aerobic, halotolerant and pigmented bacterial strains with gliding motility were isolated from Antarctic sea water; one other isolate was collected from the sea urchin Strongylocentrotus intermedius in the Gulf of Peter the Great in the Sea of Japan. 16S rRNA gene sequence analysis indicated that the strains are members of the family Flavobacteriaceae, the nearest neighbour (with 97·1 % sequence similarity) being the misclassified species [Cytophaga] marinoflava. DNA–DNA hybridization experiments and chemotaxonomic and phenotypic analyses demonstrated that the six novel isolates represent a single species distinct from [C.] marinoflava. On the basis of its separate phylogenetic lineage (the nearest neighbours show 92 % sequence similarity), [C.] marinoflava is reclassified as Leeuwenhoekiella marinoflava gen. nov., comb. nov. A second species of this new genus, Leeuwenhoekiella aequorea sp. nov., is proposed for the six novel isolates, with strain LMG 22550T (=CCUG 50091T) as the type strain.

An aerobic, Gram-negative, non-fermentative, rod-shaped, motile, orange-pigmented bacterium, UST20020801T, was isolated from sea-water samples collected from Port Shelter, Hong Kong, S.A.R., China, in August 2002. The full 16S rRNA gene sequence of this strain shared only 87·5 % similarity with its nearest relative, Crocinitomix catalasitica, a species of the family Cryomorphaceae. However, strain UST20020801T possessed menaquinone-6, a major respiratory quinone of members of the family Flavobacteriaceae. This strain contains unique fatty acids such as i15 : 1G, i17 : 1ω9c, 2-OH 15 : 0, 15 : 1ω6c and three unknown fatty acids of equivalent chain-length of 11·543, 13·565 and 16·582. Further analysis of its ecophysiology and biochemistry suggests that this strain represents a new genus in the phylum ‘Bacteroidetes’. The name Owenweeksia hongkongensis gen. nov., sp. nov. is proposed. The type strain is UST20020801T (=NRRL B-23963T=JCM 12287T).

Strain HHS 22T was isolated from a glacial water sample from the snout of the Hamta glacier located in the Himalayan mountain ranges of India. Phenotypic, chemotaxonomic and phylogenetic analyses established the affiliation of the isolate to the genus Pedobacter. HHS 22T exhibits high 16S rRNA gene sequence similarity with Pedobacter cryoconitis (98 %). However, the level of DNA–DNA relatedness between HHS 22T and P. cryoconitis is only 42 %. Furthermore, HHS 22T differs from P. cryoconitis and the four other recognized species of Pedobacter in a number of phenotypic characteristics. These data suggest that HHS 22T represents a novel species of the genus Pedobacter, for which the name Pedobacter himalayensis sp. nov. is proposed. The type strain is HHS 22T (=JCM 12171T=MTCC 6384T).

A mesophilic, anaerobic, fermentative bacterium, strain BN3T, was isolated from a producing well of a biodegraded oil reservoir in Canada. Cells were Gram-negative, non-motile rods that did not form spores. The temperature range for growth was 15–40 °C, with optimum growth at 37–40 °C. The strain grew with up 4 % NaCl, with optimum growth in the absence of NaCl. Tryptone was required for growth. Yeast extract and elemental sulfur stimulated growth. Growth was also enhanced during fermentation of glucose, arabinose, galactose, maltose, mannose, rhamnose, lactose, ribose, fructose, sucrose, cellobiose, lactate, mannitol and glycerol. Acetate, hydrogen and CO2 were produced during glucose fermentation. Elemental sulfur and nitrate were used as electron acceptors and were reduced to sulfide and ammonium, respectively. The G+C content of the genomic DNA was 40·8 mol%. Phylogenetic analyses of the 16S rRNA gene sequence indicated that the strain was a member of the phylum ‘Bacteroidetes’, distantly related to the genera Bacteroides and Tannerella (similarity values of less than 90 %). The chemotaxonomic data (fatty acids, polar lipids and quinones composition) also indicated that strain BN3T could be clearly distinguished from its closest cultivated relatives. This novel organism possesses phenotypic, chemotaxonomic and phylogenetic traits that do not allow its classification as a member of any previously described genus; therefore, it is proposed that this isolate should be described as a member of a novel species of a new genus, Petrimonas gen. nov., of which Petrimonas sulfuriphila sp. nov. is the type species. The type strain is BN3T (=DSM 16547T=JCM 12565T).

The mammalian gastrointestinal tract is covered by a layer of mucus that can harbour a range of bacterial species specifically adapted to colonize this ecological niche. Examination of 110 bacterial isolates cultivated from the gastrointestinal tract of 23 mice revealed the presence of a subgroup of 30 isolates that did not correspond genetically with genera commonly associated with this site, i.e. members of the ε-Proteobacteria such as Helicobacter and Campylobacter species. Instead this group of isolates was found to lie within the phylum Deferribacteres, a completely distinct lineage in the domain Bacteria. There was a high level of consensus in results obtained from the phenotypic and genotypic characterization of a number of the isolates, which showed they were distinct from other members of the Deferribacteres. As such, they are proposed to constitute a new genus and species, Mucispirillum schaedleri gen. nov., sp. nov. These organisms are anaerobic, Gram-negative, spiral-shaped rods with bipolar flagella. The type strain is HRI I17T (=ATCC BAA-1009T=ACM 5223T).

A novel, thermophilic, anaerobic bacterium that is able to tolerate hydrogen was isolated from a deep-sea hydrothermal chimney collected at the Rainbow field on the Mid-Atlantic Ridge. Cells were rod-shaped and surrounded by a sheath-like outer structure (toga); they were weakly motile by means of a polar flagellum. They appeared singly, in pairs or in short chains. They grew at 35–65 °C (optimum 60 °C), pH 4·5–8·5 (optimum pH 6·0) and 10–65 g sea salts l−1 (optimum 30–40 g l−1). The isolate was organotrophic, and able to grow on various carbohydrates or complex proteinaceous substrates. Growth was not inhibited under 100 % hydrogen or in the presence of 2 % oxygen in the gas phase. The isolate reduces sulfur, although sulfur reduction is not required for growth. The fermentation products identified on glucose were acetate, ethanol, formate, hydrogen and CO2. The G+C content of the genomic DNA was 28±1 mol%. Phylogenetic analysis of the 16S rRNA gene placed the strain within the genus Marinitoga, order Thermotogales, in the bacterial domain. On the basis of the 16S rRNA gene sequence comparisons and physiological characteristics, the isolate is considered to represent a novel species, for which the name Marinitoga hydrogenitolerans sp. nov. is proposed. The type strain is AT1271T (=DSM 16785T=JCM 12826T).

The taxonomic positions of six strains (including the type strain) of Chryseobacterium meningosepticum ( King 1959 ) Vandamme et al. 1994 and the type strain of Chryseobacterium miricola Li et al. 2004 were re-evaluated by using a polyphasic taxonomic approach. Phylogenetic analysis, based on 16S rRNA gene sequencing, showed that the strains represent a separate lineage from the type strains of the Chryseobacterium–Bergeyella–Riemerella branch within the family Flavobacteriaceae (90·7–93·9 % similarities), which was supported by phenotypic differences. Combined phylogenetic and phenotypic data showed that C. meningosepticum and C. miricola should be transferred to a new genus, Elizabethkingia gen. nov., with the names Elizabethkingia meningoseptica comb. nov. (type strain, ATCC 13253T=NCTC 10016T=LMG 12279T=CCUG 214T) and Elizabethkingia miricola comb. nov. (type strain, DSM 14571T=JCM 11413T=GTC 862T) proposed.

Bacterial strain CP183-8T was isolated from biological soil crusts collected in the Colorado Plateau, USA. Cells of this strain were aerobic, non-motile, Gram-negative, psychrotolerant and formed beaded chains in the stationary growth phase. They contained C16 : 1 ω5c and C16 : 1 ω7c as major fatty acids. 16S rRNA gene sequence analysis assigned the strain to the genus Dyadobacter. However, it shared a sequence similarity of only 95·88 % with the type strain of Dyadobacter fermentans, NS114T. Because it also exhibited a significant number of phenotypic and chemotaxonomic differences from D. fermentans, it is described as a novel second species in the genus Dyadobacter, with the name Dyadobacter crusticola sp. nov. The type strain is CP183-8T (=DSM 16708T=ATCC BAA-1036T).

A bacterial strain (CC-TWGS1-8T) isolated from a tar-contaminated soil in Taiwan was studied in a detailed taxonomic study. The cells were Gram-negative, rod-shaped and non-spore-forming. Phylogenetic analyses using the 16S rRNA gene sequence of the strain clearly revealed an affiliation to the genus Chryseobacterium, the highest sequence similarities being to the type strain of Chryseobacterium indologenes (96·8 %), to Chryseobacterium gleum (96·8 %) and to Chryseobacterium joostei (96·4 %). The 16S rRNA gene sequence similarities to all other Chryseobacterium species were below 96 %. The major whole-cell fatty acids were 15 : 0 iso (35·4 %) and 17 : 0 iso 3OH (22·5 %). DNA–DNA hybridization values and the biochemical and chemotaxonomic properties demonstrate that strain CC-TWGS1-8T represents a novel species, for which the name Chryseobacterium taichungense sp. nov. is proposed. The type strain is CC-TWGS1-8T (=CCUG 50001T=CIP 108519T).

A Gram-negative, rod-shaped, non-spore-forming bacterium was isolated from a nitrifying inoculum. On the basis of 16S rRNA gene sequence similarity, LMG 22862T was shown to belong to the family Sphingobacteriaceae, related to Pedobacter africanus (98·0 %) and Pedobacter heparinus (97·6 %). The results of 16S rRNA gene sequence analysis, DNA–DNA hybridization, SDS-PAGE, analysis of the fatty acid composition and physiological and biochemical tests allowed genotypic and phenotypic differentiation of LMG 22862T from Pedobacter species with validly published names. LMG 22862T therefore represents a novel species within this genus, for which the name Pedobacter caeni sp. nov. is proposed, with the type strain LMG 22862T (=DSM 16990T).

Gram-negative anaerobic rods were isolated from blood culture of a healthy baby born at term. Based on phylogenetic analysis and specific phenotypic characteristics, this strain was included within the Bacteroides cluster. The novel bile-resistant anaerobic species was designated Bacteroides massiliensis and it has 92·8 % 16S rRNA similarity to Bacteroides vulgatus and a DNA G+C content of 49 mol%. The major cellular fatty acid is anteiso-branched C15 : 0. The type strain of B. massiliensis sp. nov. is B84634T (=CIP 107942T=CCUG 48901T).

A novel alkaliphilic, sulfate-reducing bacterium was isolated from a syntrophic acetate-decomposing community enriched from samples of the soda lake Khadin, Tuva, Russia; the isolate was designated strain Z-7999T. Cells of strain Z-7999T were vibrioid, Gram-negative, 0·4–0·5×1·0–2·5 μm and motile by means of a polar flagellum. The temperature range for growth was 15–40 °C, with an optimum of 35–38 °C. The pH range for growth was 6·7–10·3, with an optimum of pH 8·0–9·0. The NaCl concentration range for growth was 1–80 g l−1. The novel isolate was obligately anaerobic, was alkaliphilic with a broad pH range and had an obligate requirement for carbonate ions in the growth medium. In the presence of sulfate as electron acceptor, it grew with hydrogen, formate and lactate. It was not able to ferment sugars, organic acids, amino acids or peptides. During growth on formate, strain Z-7999T reduced sulfite and thiosulfate to sulfide. It was able to grow lithoheterotrophically with sulfate and formate when acetate was added as a carbon source for biosynthesis of biomass. The G+C content of the genomic DNA of strain Z-7999T was 56·5 mol%. Results of comparative 16S rRNA gene sequence analyses revealed that strain Z-7999T was part of the δ-Proteobacteria and clustered with other members of the genus Desulfonatronum (similarity values of 95·2 and 95·3 % to Desulfonatronum lacustre and Desulfonatronum thiodismutans, respectively). DNA–DNA hybridization with D. lacustre was 37 %. On the basis of physiological and phylogenetic data, it is proposed that strain Z-7999T (=DSM 16749T=VKM B-2329T) should be placed in the genus Desulfonatronum as a representative of a novel species, Desulfonatronum cooperativum sp. nov.

Two Gram-negative, non-motile, non-spore-forming, slightly halophilic bacterial strains, SW-210T and SW-242T, were isolated from sea water of the South Sea in Korea, and were characterized taxonomically by means of a polyphasic approach. The two isolates grew optimally at 25–30 °C and in the presence of 2–3 % (w/v) NaCl. Strains SW-210T and SW-242T contained Q-8 as the predominant respiratory lipoquinone and C18 : 1 ω9c as the major fatty acid. The DNA G+C contents of strains SW-210T and SW-242T were 43·2 and 45·3 mol%, respectively. The 16S rRNA gene sequences of strains SW-210T and SW-242T were 98·9 % similar, and the mean DNA–DNA relatedness value between them was 24 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains SW-210T and SW-242T form distinct phylogenetic lineages within the radiation of the cluster comprising Psychrobacter species, having 16S rRNA gene sequence similarity levels of 95·9–99·2 % with respect to the type strains of Psychrobacter species. The levels of DNA–DNA relatedness between the two isolates and the type strains of 15 phylogenetically related Psychrobacter species were well below 70 %. On the basis of phenotypic and phylogenetic data and genomic distinctiveness, strains SW-210T and SW-242T were classified in the genus Psychrobacter as representing two distinct novel species, for which the names Psychrobacter aquimaris sp. nov. (type strain, SW-210T=KCTC 12254T=DSM 16329T) and Psychrobacter namhaensis sp. nov. (type strain, SW-242T=KCTC 12255T=DSM 16330T) are proposed, respectively.

A novel mesophilic, chemolithoautotrophic, sulfur-oxidizing bacterium, designated strain SO07T, was isolated from a microaerobic waste-water biofilm. Chemolithoautotrophic growth was observed with elemental sulfur, sulfide and thiosulfate as sole electron donors and oxygen as electron acceptor. Anaerobic and heterotrophic growth were not observed. Nitrate was not used as a terminal electron acceptor. The optimum pH and temperature for growth were pH 7·5 and 30 °C, respectively. The major isoprenoid quinone was Q-8. The DNA G+C content of strain SO07T was 47·1 mol%. Phylogenetic analysis of 16S rRNA gene sequences demonstrated that strain SO07T formed a monophyletic group in the γ-Proteobacteria with only 89 % similarity to members of the genus Halothiobacillus, its nearest phylogenetic neighbours. In addition, the isolate differed from members of the genus Halothiobacillus in its requirement for and tolerance of NaCl; strain SO07T was unable to grow in NaCl concentrations of more than 180 mM. On the basis of phylogenetic, chemotaxonomic and physiological data, it is proposed that isolate SO07T (=JCM 12417T=ATCC BAA-1033T) represents the type strain of a novel species in a new genus, Thiovirga sulfuroxydans gen. nov., sp. nov.