- Volume 56, Issue 7, 2006

A buff-yellow-pigmented bacterium, strain K22-20T, which was isolated from a cold desert of the Indian Himalayas, was subjected to a polyphasic taxonomic study. Phenotypic and chemical properties of strain K22-20T were consistent with its classification in the genus Ornithinimicrobium. The major fatty acids of the strain were iso-C17 : 1 ω9c (cis-15-methyl 7-hexadecenoic acid), iso-C15 : 0 (13-methyl tetradecanoic acid), iso-C16 : 0 (14-methyl pentadecanoic acid) and iso-C17 : 0 (15-methyl hexadecanoic acid). The G+C content of the genomic DNA was 71 mol%. According to 16S rRNA gene sequence analysis, strain K22-20T was closely related to Ornithinimicrobium humiphilum HKI 0124T (97.7 %). However, genomic relatedness between strain K22-20T and O. humiphilum MTCC 6406T, as revealed by DNA–DNA hybridization, was 64.5 %. Based on the polyphasic data, strain K22-20T (=MTCC 6545T=DSM 17687T=JCM 12763T) represents a novel species of the genus Ornithinimicrobium, for which the name Ornithinimicrobium kibberense sp. nov. is proposed.

A coral-red-pigmented actinobacterium, strain K30-10T, was isolated from a soil sample from a cold desert of the Indian Himalayas. Chemical and phenotypic properties of strain K30-10T were consistent with its classification in the genus Dietzia. It showed 97.9 % 16S rRNA gene sequence similarity to Dietzia maris MTCC 7011T; similarities to the type strains of three other species of the genus, Dietzia natronolimnaea, Dietzia psychralcaliphila and Dietzia cinnamea, were 94.4–96.0 %. The DNA–DNA relatedness between K30-10T and the closely related strain D. maris MTCC 7011T was 59.2 %. The DNA G+C content of strain K30-10T was 67.0 mol%. Based on physiological and biochemical tests and genotypic differences between strain K30-10T and its closest phylogenetic relatives, it is proposed that this strain represents a novel species, Dietzia kunjamensis sp. nov.; the type strain is K30-10T (=MTCC 7007T=DSM 44907T=JCM 13325T).

An extremely halophilic archaeon (strain 7-3T) was isolated from Aibi salt lake in Xin-Jiang, China. It formed small (<1.0 mm), red, elevated colonies on salt-milk agar medium. Strain 7-3T was able to grow at pH 6.5–9.5 (optimum pH 8.0) and at 20–50 °C (optimum 45 °C). Analysis of its 16S rRNA gene sequence indicated that strain 7-3T was phylogenetically related to members of the genus Natronorubrum, with sequence similarities of 97.0 % to Natronorubrum bangense A33T and 95.2 % to Natronorubrum tibetense GA33T. The G+C content of its DNA was 61.2 mol% (T m). Levels of DNA–DNA relatedness to Nrr. bangense and Nrr. tibetense were 45 and 37 %, respectively. It is concluded that strain 7-3T (=CGMCC 1.4299T=JCM 13488T) should be classified as the type strain of a novel species of the genus Natronorubrum, for which the name Natronorubrum aibiense sp. nov. is proposed. Based on the properties of Nrr. aibiense given here and of those of Nrr. bangense and Nrr. tibetense described previously, an emended description of the genus Natronorubrum is presented.

Strain XH-48T was isolated from the sediment of Lake Xilinhot, a saline lake in Inner Mongolia (China). The organism is pleomorphic, neutrophilic and requires at least 2.5 M (15 %) NaCl, but not MgCl2, for growth; it exhibits optimal growth at 3.4 M (20 %) NaCl. The G+C content of its DNA is 61 mol%. 16S rRNA gene sequence analysis revealed that strain XH-48T is a member of the family Halobacteriaceae, but there were low levels of similarity with other members of this family. The highest sequence similarity values (94.5 and 93.3 %) were obtained with the 16S rRNA genes of Natrialba aegyptiaca and Natrialba asiatica, respectively. Polar lipid analyses revealed that strain XH-48T contains phosphatidylglycerol and phosphatidylglyceromethylphosphate, derived from both C20C20 and C20C25 glycerol diethers, and two unidentified glycolipids. On the basis of the data obtained, the novel isolate cannot be classified within any recognized genus. Strain XH-48T should be placed within a novel genus and species within the family Halobacteriaceae, order Halobacteriales, for which the name Halostagnicola larsenii gen. nov., sp. nov. is proposed. The type strain of Halostagnicola larsenii is strain XH-48T (=DSM 17691T=CGMCC 1.5338T=JCM 13463T=CECT 7116T).

Three strains of CO2-reducing methanogens were isolated from marine sediments. Strain PL-15/HP was isolated from marine sediments of the Lipari Islands, near Sicily and the other two strains, Nankai-2 and Nankai-3T, were isolated from deep marine sediments of the Nankai Trough, about 50 km from the coast of Japan. Analysis of the cellular proteins and 16S rRNA gene sequences indicated that these three strains represented a single novel species that formed a deep branch of the mesophilic methanococci. Phylogenetic analysis indicated that the three strains were most closely related to Methanothermococcus okinawensis (95 % 16S rRNA gene sequence similarity). However, strains PL-15/HP, Nankai-2 and Nankai-3T grew at temperatures that were more similar to those of recognized species within the genus Methanococcus. Strain Nankai-3T grew fastest at 46 °C. Results of physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strains PL-15/HP, Nankai-2 and Nankai-3T from closely related species. The name Methanococcus aeolicus sp. nov. is proposed, with strain Nankai-3T (=OCM 812T=DSM 17508T) as the type strain.

A novel extremely halophilic archaeon was isolated from Ezzemoul sabkha, Algeria. The strain, designated 5.1T, was neutrophilic, motile and Gram-negative. At least 15 % (w/v) NaCl was required for growth. The isolate grew at pH 6.5–9.0, with optimum growth at pH 7.0–7.5. Mg2+ was required for growth. Polar lipids were C20C20 derivatives of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, and phosphatidylglycerol sulfate and sulfated diglycosyl diether. The genomic DNA G+C content of strain 5.1T was 61.9 mol% (T m). Phylogenetic analysis based on comparison of 16S rRNA gene sequences revealed that strain 5.1T clustered with Halorubrum species. The results of DNA–DNA hybridization and biochemical tests allowed genotypic and phenotypic differentiation of strain 5.1T from other Halorubrum species. The name Halorubrum ezzemoulense sp. nov. (type strain 5.1T=CECT 7099T=DSM 17463T) is proposed.

Two extremely halophilic archaea, strains 9-3T and 31-hongT, were isolated from Aibi salt lake and Aiding salt lake in Xin-Jiang, China. Their morphology, physiology, biochemical features, polar lipid compositions and 16S rRNA gene sequences were characterized in order to elucidate their taxonomic status. The results from this study indicated that strains 9-3T and 31-hongT are members of the genus Halorubrum. Their physiological properties and polar lipid compositions are clearly different from those of the currently described species of Halorubrum. DNA–DNA relatedness values for strain 9-3T with respect to its closely related neighbours Halorubrum saccharovorum JCM 8865T and Halorubrum lacusprofundi JCM 8891T were 51.6 and 25.1 %, respectively, DNA–DNA relatedness values for strain 31-hongT with respect to its closely related neighbours Hrr. saccharovorum JCM 8865T and Hrr. lacusprofundi JCM 8891T were 29.4 and 44.9 %, respectively, and DNA–DNA relatedness between strains 9-3T and 31-hongT was 54 %. Thus, two novel species of the genus Halorubrum are proposed, Halorubrum lipolyticum sp. nov. (type strain 9-3T=CGMCC 1.5332T=JCM 13559T) and Halorubrum aidingense sp. nov. (type strain 31-hongT=CGMCC 1.2670T=JCM 13560T).

Bacteria in the family Flavobacteriaceae are increasingly recognized to play important roles in the degradation of organic matter during and following algal blooms. A novel heterotrophic, rod-shaped, aerobic, yellow-pigmented and gliding bacterium was isolated from a seawater sample collected in the Bay of Blanes in the north-western Mediterranean Sea. Analysis of its 16S rRNA gene sequence, retrieved from the whole-genome sequence, showed that the bacterium was closely related to members of the genus Leeuwenhoekiella within the family Flavobacteriaceae, phylum Bacteroidetes. Phenotypic, genotypic, chemotaxonomic and phylogenetic analyses supported the creation of a novel species to accommodate this bacterium, for which the name Leeuwenhoekiella blandensis sp. nov. is proposed. The type strain is MED 217T (=CECT 7118T=CCUG 51940T).

A taxonomic study was performed on strain R2A10-2T, isolated from greenhouse soil cultivated with lettuce (Lactuca sativa L.), collected in Wanju Province, Korea. The bacterial cells were Gram-negative, aerobic, short rods. The growth temperature and pH were 5–35 °C and 5.0–9.0, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that this isolate had 93.3–97.7 % similarity to Chryseobacterium species: the highest sequence similarities were to the type strains of Chryseobacterium daecheongense (97.7 %), Chryseobacterium formosense (97.1 %) and Chryseobacterium defluvii (96.9 %). Low levels of DNA–DNA relatedness were found between strain R2A10-2T and the type strains of these three species (<28 %). Differences in phenotypic properties were found with respect to Chryseobacterium species with validly published names. The predominant cellular fatty acids were iso-15 : 0 (40.0 %), iso-17 : 0 3-OH (21.9 %), iso-17 : 1ω9c (11.7 %) and summed feature 4 (iso-15 : 0 2-OH and/or 16 : 1ω7c/t, 11.0 %). Menaquinone MK-6 was detected as the sole respiratory quinone. The G+C content of the genomic DNA was 37.8 mol%. On the basis of the genomic and phenotypic evidence, this isolate represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium wanjuense sp. nov. is proposed. The type strain is R2A10-2T (=KACC 11468T=DSM 17724T).

A novel Tenacibaculum-like bacterial strain, SMK-4T, was isolated from a tidal flat sediment in Korea. Strain SMK-4T was Gram-negative, pale yellow-pigmented and rod-shaped. It grew optimally at 30–37 °C and in the presence of 2–3 % (w/v) NaCl. It contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C16 : 0 3-OH and C16 : 1 ω7c and/or iso-C15 : 0 2-OH as the major fatty acids (>10 % of total fatty acids). The DNA G+C content was 33.6 mol%. Phylogenetic trees based on 16S rRNA gene sequences showed that strain SMK-4T fell within the evolutionary radiation encompassed by the genus Tenacibaculum. Strain SMK-4T exhibited 16S rRNA gene sequence similarity levels of 95.2–98.6 % with respect to the type strains of recognized Tenacibaculum species. DNA–DNA relatedness levels and differential phenotypic properties made it possible to categorize strain SMK-4T as a species that is separate from previously described Tenacibaculum species. On the basis of phenotypic properties and phylogenetic and genetic distinctiveness, strain SMK-4T (=KCTC 12569T=JCM 13491T) should be classified as a novel Tenacibaculum species, for which the name Tenacibaculum aestuarii sp. nov. is proposed.

Strain VP48T was isolated from drinking water during a screening programme to monitor the bacterial population present in the water distribution system of Sevilla (Spain). A polyphasic taxonomic study of the isolate resulted in its identification as a member of the genus Chryseobacterium, members of which are widely distributed in soil, water and clinical sources. However, the 16S rRNA gene sequence similarity values of strain VP48T to the type strains of Chryseobacterium species were 96 % or lower. Furthermore, phenotypic characteristics clearly indicated that the isolate represents a novel Chryseobacterium species, for which the name Chryseobacterium hispanicum sp. nov. is proposed; strain VP48T (=CECT 7129T=CCM 7359T=JCM 13554T) is the type strain. The DNA G+C content of this strain is 34.3 mol%.

The characteristics of three Bacteroides species, Bacteroides distasonis, Bacteroides goldsteinii and Bacteroides merdae, were examined. 16S rRNA gene sequence analysis showed that B. distasonis, B. goldsteinii and B. merdae should not be classified as species within the genus Bacteroides. Although B. distasonis, B. goldsteinii and B. merdae were phylogenetically related to Tannerella forsythensis, the ratios of anteiso-C15 : 0 to iso-C15 : 0 in whole-cell methanolysates of the three species were different from that of T. forsythensis. In addition, whereas the major menaquinones of T. forsythensis were MK-10 and MK-11, the major menaquinones of B. distasonis, B. goldsteinii and B. merdae were MK-9 and MK-10. The three species were phenotypically similar to Bacteroides sensu stricto, but phylogenetically distinct. Furthermore, B. distasonis, B. goldsteinii and B. merdae could be differentiated from Bacteroides sensu stricto (predominant menaquinones: MK-10 and MK-11) by the menaquinone composition. This is an important chemotaxonomic characteristic of the three species. On the basis of these data, a novel genus, Parabacteroides gen. nov., is proposed for B. distasonis, B. goldsteinii and B. merdae, with three species, Parabacteroides distasonis gen. nov., comb. nov. (the type species), Parabacteroides goldsteinii comb. nov. and Parabacteroides merdae comb. nov. The type strains of P. distasonis, P. goldsteinii and P. merdae are JCM 5825T (=CCUG 4941T=DSM 20701T=ATCC 8503T), JCM 13446T (=CCUG 48944T) and JCM 9497T (=CCUG 38734T=ATCC 43184T), respectively.

A marine bacterium, designated strain KMM 6038T, was subjected to taxonomic analysis via a polyphasic approach. Cells of the strain were heterotrophic, orange-pigmented, Gram-negative and motile by means of gliding. 16S rRNA gene sequence analysis indicated that strain KMM 6038T was closely related to the type species of the genera Algibacter and Yeosuana, members of the family Flavobacteriaceae, with sequence similarities of 93.8 and 93.6 % to the respective type strains. However, several chemotaxonomic and phenotypic characteristics, such as the cellular fatty acid profile (iso-C15 : 0, anteiso-C15 : 0, iso-C15 : 1, C15 : 0, C15 : 1 ω6c, iso-C15 : 0 3-OH and iso-C17 : 0 3-OH) and the low G+C content of the DNA (35.7 mol%), indicated that the strain should be separated from these two genera. From the results of phenotypic, genotypic, chemotaxonomic and phylogenetic analyses, the bacterium should be classified as representing a novel genus and species, for which the name Mariniflexile gromovii gen. nov., sp. nov. is proposed. The type strain of Mariniflexile gromovii is KMM 6038T (=KCTC 12570T=LMG 22578T).

Two Gram-negative, anaerobic, non-spore-forming rod-shaped organisms were isolated from human faeces. These isolates were tentatively identified as Bacteroides based on morphological and biochemical criteria and appeared closely related to Bacteroides vulgatus ATCC 8482T. The 16S rRNA gene sequence analysis showed that the isolates were highly related to each other (99.5 %) and confirmed their placement in the genus Bacteroides. 16S rRNA gene sequence similarity values with close phylogenetic neighbours Bacteroides vulgatus ATCC 8482T (96 %) and Bacteroides massiliensis CCUG 48901T (93 %) preliminarily demonstrated that the organisms represented a novel species. The results of phenotypic, chemotaxonomic and 16S rRNA gene sequence analyses, and DNA–DNA homology values provided evidence that these two unknown isolates represent a single species and should be assigned to a novel species of the genus Bacteroides, as Bacteroides dorei sp. nov. The type strain is JCM 13471T (=DSM 17855T).

Two yellow-pigmented, Gram-negative, rod-shaped bacterial strains, GH1-10T and GH29-5T, were isolated from greenhouse soils in Korea. 16S rRNA gene sequence analysis indicated that these strains were related to members of the genus Flavobacterium. Strain GH1-10T was most closely related to Flavobacterium psychrolimnae and Flavobacterium denitrificans, with sequence similarities of 95.9 and 95.2 %, respectively. Strain GH29-5T was most closely related to ‘Flavobacterium saliodium’, F. denitrificans and Flavobacterium frigoris, with sequence similarities of 94.3, 92.5 and 92.5 %, respectively. The major cellular fatty acids of GH1-10T were iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c) and iso-C17 : 0 3-OH, and those of GH29-5T were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G and iso-C15 : 0 3-OH. Both strains contained menaquinone with six isoprene units (MK-6) as the sole quinone. The DNA G+C contents of GH1-10T and GH29-5T were 35 and 39 mol%, respectively. Based on the phylogenetic and phenotypic data presented, it is concluded that the two bacteria represent two separate novel species of the genus Flavobacterium. The names proposed to accommodate these organisms are Flavobacterium daejeonense sp. nov., with type strain GH1-10T (=KACC 11422T=DSM 17708T), and Flavobacterium suncheonense sp. nov., with type strain GH29-5T (=KACC 11423T=DSM 17707T).

Bacteria-like endosymbionts of females of the plant-parasitic nematodes Globodera rostochiensis and Heterodera goettingiana and juveniles of Heterodera glycines were first observed during transmission electron microscopy (TEM) studies conducted in the 1970s. These organisms were characterized as being rod-shaped, ranging in size from 0.3 to 0.5 μm in diameter and 1.8 to 3 μm in length and containing structures labelled as striated inclusion bodies or tubular structures. A population of H. glycines was obtained from the soybean field where infected nematodes were first discovered in order to conduct TEM studies of females and males and to determine the phylogenetic position of the H. glycines endosymbiont among bacteria by studying the 16S rRNA and gyrB gene sequences. The bacterium was observed in the pseudocoelom and intestine of juveniles, females and males, in hypodermal chords of juveniles and males, in ovary walls and in oocytes and spermatozoa. The bacterium was polymorphic, measuring 0.4–0.8×2.5–4.5 μm, and many specimens contained an array of microfilament-like structures similar to those observed in ‘Candidatus Cardinium hertigii’, the endosymbiont of Encarsia spp. wasps. Phylogenetic analysis of the 16S rRNA and gyrB genes of the H. glycines-infecting bacterium revealed 93 % and 81 % sequence identity, respectively, to the homologous genes in ‘Candidatus C. hertigii’. Thus, the name ‘Candidatus Paenicardinium endonii’ is proposed for the bacterial endosymbiont of the plant-parasitic nematode H. glycines.

A Gram-negative bacterial isolate (designated SRC-1T) was isolated from an occasional drainage system and characterized by a polyphasic approach to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequences affiliated strain SRC-1T with the family ‘Flexibacteraceae’ of the phylum Bacteroidetes. It showed greatest sequence similarity to Pontibacter actiniarum KMM 6156T (95.5 %) followed by Adhaeribacter aquaticus MBRG1.5T (89.0 %) and Hymenobacter roseosalivarius DSM 11622T (88.9 %), but it differed from these micro-organisms in many phenotypic characteristics. Strain SRC-1T was an obligate aerobe and its cells were non-motile, irregular rods. The major fatty acids included mainly unsaturated and hydroxy fatty acids, including 17 : 1 iso I/anteiso B (36.7 %), 15 : 0 iso (15.8 %) and 17 : 0 iso 3-OH (10.3 %), and the DNA G+C content was 59.5 mol%. From the phenotypic and genotypic analyses it was clear that strain SRC-1T was quite different from members other genera in the family ‘Flexibacteraceae’. Therefore we conclude that strain SRC-1T represents a novel genus, for which the name Effluviibacter gen. nov., containing a single species Effluviibacter roseus sp. nov., is proposed. The type species of the genus is Effluviibacter roseus, the type strain of which is strain SRC-1T (=MTCC 7260T=DSM 17521T).

A novel anaerobic, moderately thermophilic bacterium, strain Cas60314T, was isolated from hot oil-well production water obtained from an oil reservoir in the North Sea. The cells were Gram-negative, motile, straight rods. The salinity and pH growth optima were 2.0–3.0 % NaCl and 6.5–7.0, respectively. The optimum temperature was 58 °C. Strain Cas60314T had a fermentative type of metabolism and utilized proteinous substrates, some single amino acids and a limited number of organic acids, but not sugars, fatty acids or alcohols. Cystine and elemental sulfur were reduced to sulfide. The G+C content of the DNA was 46.6 mol%. On the basis of phenotypic and phylogenetic features, it is proposed that this isolate represents a novel genus and species with the name Thermovirga lienii gen. nov., sp. nov. within the family Syntrophomonadaceae. The proposed type strain is strain Cas60314T (=DSM 17291T=ATTC BAA-1197T).

Desulfovibrio vulgaris subsp. oxamicus (type strain, DSM 1925T) was found to use nitrate as a terminal electron acceptor, the latter being reduced to ammonium. Phylogenetic studies indicated that strain DSM 1925T was distantly related to the type strain of Desulfovibrio vulgaris (95.4 % similarity of the small-subunit rRNA gene) and had as its closest phylogenetic relatives two other nitrate- and sulfate-reducing bacteria, namely Desulfovibrio termitidis (99.4 % similarity) and Desulfovibrio longreachensis (98.4 % similarity). Additional experiments were conducted to characterize better strain DSM 1925T. This strain incompletely oxidized lactate and ethanol to acetate. It also oxidized butanol, pyruvate and citrate, but not glucose, fructose, acetate, propionate, butyrate, methanol, glycerol or peptone. The optimum temperature for growth was 37 °C (range 16–50 °C) and the optimum NaCl concentration for growth was 0.1 % (range 0–5 %). Because of significant genotypic and phenotypic differences from Desulfovibrio termitidis and Desulfovibrio longreachensis, reclassification of Desulfovibrio vulgaris subsp. oxamicus as Desulfovibrio oxamicus sp. nov., comb. nov., is proposed. The type strain is strain Monticello 2T (=DSM 1925T=NCIMB 9442T=ATCC 33405T).

A Gram-negative, motile, denitrifying bacterium (strain AcBE2-1T) was isolated from activated sludge of a municipal wastewater treatment plant using 17β-oestradiol (E2) as sole source of carbon and energy. Cells were curved rods, 0.4–0.8×0.8–2.0 μm in size, non-fermentative, non-spore-forming, oxidase-positive and catalase-negative. E2 was oxidized completely to carbon dioxide and water by reduction of nitrate to a mixture of dinitrogen monoxide and dinitrogen, with the intermediate accumulation of nitrite. Electron recoveries were between 90 and 100 %, taking assimilated E2 into account. With nitrate as the electron acceptor, the bacterium also grew on fatty acids (C2 to C6), isobutyrate, crotonate, dl-lactate, pyruvate, fumarate and succinate. Phylogenetic analysis of its 16S rRNA gene sequence revealed that strain AcBE2-1T represents a separate line of descent within the family Rhodocyclaceae (Betaproteobacteria). The closest relatives are the cholesterol-degrading, denitrifying bacteria Sterolibacterium denitrificans DSM 13999T and strain 72Chol (=DSM 12783), with <93.9 % sequence similarity. The G+C content of the DNA was 61.4 mol%. Detection of a quinone system with ubiquinone Q-8 as the predominant compound and a fatty acid profile that included high concentrations of C16 : 1 ω7c/iso-C15 : 0 2-OH and C16 : 0, in addition to C18 : 1 ω7c and small amounts of C8 : 0 3-OH, supported the results of the phylogenetic analysis. On the basis of 16S rRNA gene sequence data in combination with chemotaxonomic and physiological data, strain AcBE2-1T (=DSM 16959T=JCM 12830T) is placed in a new genus Denitratisoma gen. nov. as the type strain of the type species Denitratisoma oestradiolicum gen. nov., sp. nov.

A Gram-negative, microaerophilic helical rod, isolated from the gastric mucosa of a dog and designated strain JKM4T, was subjected to a polyphasic taxonomic study. The tightly coiled organism, measuring 10–18 μm long and up to 1 μm wide, was motile by means of multiple sheathed flagella located at both ends of the cell and by a periplasmic fibril running along the external side of the helix. Strain JKM4T grew preferably on biphasic culture plates or on very moist agar. Coccoid forms predominated in cultures older than 4 days as well as in growth obtained on dry agar plates. The strain grew at 30 and 37 °C, but not at 25 or 42 °C and exhibited urease, oxidase and catalase activities. On the basis of 16S rRNA gene sequence analysis, the novel isolate was identified as a member of the genus Helicobacter and showed > 97 % similarity to Helicobacter felis, Helicobacter bizzozeronii and Helicobacter salomonis, three species previously isolated from the canine gastric mucosa. Protein profiling of strain JKM4T using SDS-PAGE revealed a pattern different from those of other Helicobacter species of mammalian gastric origin and from Helicobacter canis. Additionally, the urease gene sequence of strain JKM4T was different from those of urease genes of H. felis, H. bizzozeronii, H. salomonis and ‘Candidatus Helicobacter heilmannii’. It is thus proposed that strain JKM4T (=LMG 23188T) represents a novel species within this genus, Helicobacter cynogastricus sp. nov.

Six strains representing three novel species were isolated from deep-sea sediment in Suruga Bay, Japan, at a depth of 2406–2409 m. On the basis of 16S rRNA gene sequence analysis, the isolated strains, c931T, c941T, d943, c952, d954 and c959T, are closely affiliated with members of the genus Shewanella. The hybridization values for DNA–DNA relatedness between these strains and Shewanella reference strains were significantly lower than that which is accepted as the phylogenetic definition of a species. On the basis of their distinct taxonomic characteristics, the isolated strains represent three novel Shewanella species, for which the names Shewanella kaireitica sp. nov. (three strains, type strain c931T=JCM 11836T=DSM 17170T), Shewanella abyssi sp. nov. (two strains, type strain c941T=JCM 13041T=DSM 17171T) and Shewanella surugensis sp. nov. (type strain c959T=JCM 11835T=DSM 17177T) are proposed.

A Gram-negative, non-spore-forming, rod-shaped, motile bacterium, strain Ko06T, was isolated from soil from a ginseng field in South Korea and was characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain Ko06T belongs to the Gammaproteobacteria, and the highest levels of sequence similarity were with Thermomonas brevis LMG 21746T (98.4 %), Thermomonas fusca LMG 21737T (97.7 %), Thermomonas haemolytica A50-7-3T (96.5 %) and Thermomonas hydrothermalis SGM-6T (95.8 %). Chemotaxonomic data revealed that strain Ko06T possesses ubiquinone Q-8 and that the predominant fatty acids are C15 : 0 iso, C11 : 0 iso and C11 : 0 iso 3-OH, all of which corroborated assignment of the strain to the genus Thermomonas. The results of DNA–DNA hybridization and physiological and biochemical tests clearly demonstrated that strain Ko06T represents a distinct species. On the basis of these data, strain Ko06T (=KCTC 12540T=NBRC 101155T) should be classified as the type strain of a novel Thermomonas species, for which the name Thermomonas koreensis sp. nov. is proposed.

A yellowish-brown bacterium was isolated from enrichment cultures inoculated with seawater samples from the eastern coast of India (Visakhapatnam) under photoheterotrophic conditions. Enrichment and isolation in a medium containing 2 % NaCl (w/v) yielded strain JA128T, which has ovoid to rod-shaped cells, also forms chains and is non-motile. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA128T clusters with the Alphaproteobacteria and the sequence similarity with its closest relatives, Rhodovulum iodosum and Rhodovulum sulfidophilum, was 95 %. Strain JA128T contained vesicular intracytoplasmic membranes, bacteriochlorophyll a and carotenoids of the spheroidene series. Strain JA128T was mesophilic, slightly acidophilic, slightly halophilic and grew photoheterotrophically with a number of organic compounds as carbon source and electron donor. It was unable to grow photoautotrophically, chemoautotrophically or by fermentative modes. It did not utilize sulfide, thiosulfate or hydrogen as electron donors. Thiamine was required as a growth factor. Based on the 16S rRNA gene sequence analysis, morphological and physiological characteristics, strain JA128T was significantly different from other species of the genus Rhodovulum and was recognized as a novel species for which the name Rhodovulum marinum sp. nov. is proposed. The type strain is JA128T (=ATCC BAA 1215T=CCUG 52183T=JCM 13300T).

A Gram-negative, non-motile, non-spore-forming, rod-shaped bacterium (strain Y9T) was isolated from a contaminated culture of the phototrophic bacterium Rhodopseudomonas palustris, and was investigated using a polyphasic taxonomic approach. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain Y9T belonged to the order Rhizobiales in the Alphaproteobacteria. Comparison of phylogenetic data indicated that it was most closely related to Pleomorphomonas oryzae (98.5 % similarity of 16S rRNA gene sequence), and the phylogenetic distance from any other species of the order Rhizobiales with a validly published name was greater than 7.5 % (i.e. less than 92.5 % similarity). The predominant ubiquinone was Q-10 and the major fatty acids were C18 : 1, C16 : 0, C19 : 0 cyclo ω8c and C18 : 0. The G+C content of genomic DNA of strain Y9T was 65.1 mol%. The results of DNA–DNA hybridization in combination with chemotaxonomic and physiological data demonstrated that strain Y9T represents a novel species within the genus Pleomorphomonas, for which the name Pleomorphomonas koreensis sp. nov. is proposed. The type strain is Y9T (=KCTC 12246T=NBRC 100803T)

Rickettsia sp. strain AT-1T was isolated from Amblyomma testudinarium ticks in Japan in 1993. Comparative analysis of sequences obtained from 16S rRNA, gltA, ompA, ompB and sca4 gene fragments demonstrated those from AT-1T to be markedly different from those of other members of the spotted fever group. Using mouse serotyping, it was also observed that Rickettsia sp. strain AT-1T was different from other Rickettsia species with validly published names. Such genotypic and phenotypic characteristics warrant its classification as a representative of a novel species, for which the name Rickettsia tamurae sp. nov. is proposed, with the type strain AT-1T (=CSUR R1T).

A non-pigmented, motile, Gram-negative bacterium designated MTCC 4195T was isolated from surface-sterilized seeds and plant tissue from deep-water rice (Oryza sativa) cultivated in Suraha Tal Lake in northern India. This isolate was shown to reinfect and colonize deep-water rice endophytically. The highest level of 16S rRNA sequence similarity (96.8 %) to strain MTCC 4195T was shown by Ochrobactrum gallinifaecis DSM 15295T. Strain MTCC 4195T utilized γ-hydroxybutyric acid, adonitol, d-glucosaminic acid and arabinose as carbon sources, but failed to use gentiobiose or citrate. The cell-wall fatty acids of strain MTCC 4195T were characterized by the presence of a relatively large proportion of C18 : 1 ω7c and a relative small proportion of C16 : 0 in comparison with Ochrobactrum species. DNA–DNA relatedness studies showed less than 52 % binding with the DNAs of type strains of other species of the genus Ochrobactrum. On the basis of phenotypic and genotypic characteristics and the results of 16S rRNA gene sequence analysis, the novel species Ochrobactrum oryzae sp. nov. is proposed, with MTCC 4195T (=DSM 17471T) as the type strain.

Six strains of extremely halophilic bacteria were isolated from several crystallizer ponds of the Maras solar salterns in the Peruvian Andes. On the basis of 16S rRNA gene sequence similarity, G+C contents and DNA–DNA hybridization results, the six isolates constituted a genomically homogeneous group affiliated with the Gammaproteobacteria. The closest relatives were members of the halophilic genera Halovibrio and Halospina, which showed 16S rRNA gene sequence similarities below 97 % and whole-genome hybridization levels below 33 % for the type strain, 7Sm5T. From the genomic and phenotypic properties of the six novel isolates and phylogenetic reconstruction based on 16S rRNA gene sequence analysis, they can be considered to represent a novel genus within the Gammaproteobacteria. On the basis of the taxonomic study, a novel genus, Salicola gen. nov., is proposed containing the single species Salicola marasensis sp. nov., which is the type species. The type strain of Salicola marasensis is 7Sm5T (=CECT 7107T=CIP 108835T).

Four novel bacterial strains were isolated from cryogenic tubes used to collect air samples at altitudes of 24, 28 and 41 km. The four strains, 24KT, 28KT, 41KF2aT and 41KF2bT, were identified as members of the genus Bacillus. Phylogenetic analysis based on 16S rRNA gene sequences indicated that three of the strains, 24KT, 28KT and 41KF2aT, are very similar to one another (>98 % sequence similarity) and show a similarity of 98–99 % with Bacillus licheniformis and 98 % with Bacillus sonorensis. DNA–DNA hybridization studies showed that strains 24KT, 28KT and 41KF2aT exhibit <70 % similarity with each other and with B. licheniformis and B. sonorensis. Differences in phenotypic and chemotaxonomic characteristics between the novel strains and B. licheniformis and B. sonorensis further confirmed that these three isolates are representatives of three separate novel species. Strain 41KF2bT showed 100 % 16S rRNA gene sequence similarity to Bacillus pumilus, but differed from its nearest phylogenetic neighbour in a number of phenotypic and chemotaxonomic characteristics and showed only 55 % DNA–DNA relatedness. Therefore, the four isolates represent four novel species for which the names Bacillus aerius sp. nov. (type strain, 24KT=MTCC 7303T=JCM 13348T), Bacillus aerophilus sp. nov. (type strain, 28KT=MTCC 7304T=JCM 13347T), Bacillus stratosphericus sp. nov. (type strain, 41KF2aT=MTCC 7305T=JCM 13349T) and Bacillus altitudinis sp. nov. (type strain, 41KF2bT=MTCC 7306T=JCM 13350T) are proposed.

A Gram-positive, spore-forming bacillus was isolated from a sample taken from an approximately 2000-year-old shaft-tomb located in the Mexican state of Jalisco, near the city of Tequila. Tentative identification using conventional biochemical analysis consistently identified the isolate as Bacillus subtilis. DNA isolated from the tomb isolate, strain 10bT, and closely related species was used to amplify a Bacillus-specific portion of the highly conserved 16S rRNA gene and an internal region of the superoxide dismutase gene (sodA int). Trees derived from maximum-likelihood methods applied to the sodA int sequences yielded non-zero branch lengths between strain 10bT and its closest relative, whereas a comparison of a Bacillus-specific 546 bp amplicon of the 16S rRNA gene demonstrated 99 % similarity with B. subtilis. Although the 16S rRNA gene sequences of strain 10bT and B. subtilis were 99 % similar, PFGE of NotI-digested DNA of strain 10bT revealed a restriction profile that was considerably different from those of B. subtilis and other closely related species. Whereas qualitative differences in whole-cell fatty acids were not observed, significant quantitative differences were found to exist between strain 10bT and each of the other closely related Bacillus species examined. In addition, DNA–DNA hybridization studies demonstrated that strain 10bT had a relatedness value of less than 70 % with B. subtilis and other closely related species. Evidence from the sodA int sequences, whole-cell fatty acid profiles and PFGE analysis, together with results from DNA–DNA hybridization studies, justify the classification of strain 10bT as representing a distinct species, for which the name Bacillus tequilensis sp. nov. is proposed. The type strain is 10bT (=ATCC BAA-819T=NCTC 13306T).

An unidentified Gram-negative-staining, aerobic, rod-shaped, spore-forming bacterium was isolated from a sample of cerebrospinal fluid. Based on comparative analysis of 16S rRNA gene sequences and phenotypic characteristics, the novel isolate was included in the Bacillus sphaericus-like group. The isolate was closely related to Bacillus odysseyi and Bacillus silvestris, with 96.2 and 94.4 % 16S rRNA gene sequence similarity, respectively. The major fatty acid was iso-C15 : 0 (48 %). The name Bacillus massiliensis sp. nov. is proposed for the novel isolate, with strain 4400831T (=CIP 108446T=CCUG 49529T) as the type strain.

The National Antimicrobial Resistance Monitoring System Laboratory at the Centers for Disease Control and Prevention (CDC) isolated two enterococcus-like strains that were referred to the CDC Streptococcus Laboratory for further identification. The isolates were recovered from human stool samples collected on different occasions from the same individual in Portland (OR, USA) in July 2000. Conventional physiological tests distinguished these strains from all known species of enterococci. Analyses of whole-cell-protein electrophoretic profiles showed the same unique profile for the two isolates, being most similar those of Enterococcus moraviensis and Enterococcus haemoperoxidus albeit not close enough to allow conclusive inclusion in any enterococcal species. Both isolates gave positive results in tests using the AccuProbe Enterococcus genetic probe, and Lancefield extracts reacted with CDC group D antiserum. Comparative 16S rRNA gene sequencing studies also revealed that these strains were closely related to the species E. moraviensis (99.6 % identity). The results of DNA–DNA relatedness experiments confirmed that these strains represented a single novel taxon. The highest level of DNA–DNA relatedness found between the novel taxon and any of the currently recognized species of Enterococcus was 32 %, for both E. moraviensis and E. haemoperoxidus. On the basis of this evidence, it is proposed that these stool isolates constitute a novel species, for which the name Enterococcus caccae sp. nov. is proposed. The type strain is 2215-02T (=SS-1777T=ATCC BAA-1240T=CCUG 51564T).

Two novel spore-forming, Gram-positive, mesophilic, heterotrophic bacteria representing two novel species were isolated from the Jet Propulsion Laboratory Spacecraft Assembly Facility (JPL-SAF) at Pasadena, CA, USA. The incidence of similar strains was examined by screening the growing collection of isolates (~400 strains) obtained from the JPL-SAF using species-specific PCR primer sets designed from the 16S rRNA gene sequences of strains SAFN-016T and SAFN-007T. Phylogenetic analysis of 16S rRNA gene sequences placed these novel isolates within the genus Paenibacillus. Two strains, SAFN-016T and SAFN-125, shared 98 % 16S rRNA gene sequence similarity with Paenibacillus timonensis and 97 % similarity with Paenibacillus macerans. Strain SAFN-007T showed 95.2 % 16S rRNA gene sequence similarity with Paenibacillus kobensis, its nearest phylogenetic neighbour. The results of DNA–DNA hybridization, physiological tests and biochemical analysis allowed genotypic and phenotypic differentiation of the isolates from currently recognized Paenibacillus species. Strain SAFN-007T and strains SAFN-016T and SAFN-125 are representatives of two separate novel species, for which the names Paenibacillus pasadenensis sp. nov. (type strain SAFN-007T=ATCC BAA-1211T=NBRC 101214T) and Paenibacillus barengoltzii sp. nov. (type strain SAFN-016T=ATCC BAA-1209T=NBRC 101215T) are proposed.

A novel thermophilic bacterium, strain KW1T, was isolated from a coastal hydrothermal field on the Satsuma Peninsula, Kagoshima Prefecture, Japan. The variably Gram-stained cells were motile rods with flagella, did not form spores and proliferated at 52–78 °C (optimum, 70 °C), pH 5–8 (optimum, pH 7) and 0–4.5 % NaCl (optimum, 1.0 %). The novel isolate was a strictly aerobic heterotroph that utilized complex proteinaceous substrates as well as a variety of carboxylic acids and amino acids. The G+C content of the genomic DNA was 70.8 mol%. Analysis of 16S rRNA gene sequences indicated that strain KW1T is closely related to Thermaerobacter subterraneus C21T (98.4 % sequence similarity). However, the DNA–DNA hybridization value for strain KW1T and T. subterraneus ATCC BAA-137T was below 46 %. On the basis of the molecular and physiological traits of strain KW1T, it represents a novel species of the genus Thermaerobacter, for which the name Thermaerobacter litoralis sp. nov. is proposed. The type strain is KW1T (=JCM 13210T=DSM 17372T).

A polyphasic study revealed taxonomic heterogeneity among reference strains of the species Lactobacillus brevis. Representative strains of L. brevis and related taxa were investigated by partial sequence analysis of the housekeeping gene encoding the alpha-subunit of phenylalanyl-tRNA synthase (pheS). Species-specific clusters were delineated for all taxa studied except for two L. brevis strains, LMG 11494 and LMG 11984, respectively isolated from cheese and wheat, which occupied a distinct position. Their phylogenetic affiliation was determined using 16S rRNA gene sequence analysis and it was found that both strains (with 99.9 % gene sequence similarity between them) belonged to the Lactobacillus buchneri group, with nearest neighbours Lactobacillus hammesii and L. brevis (gene sequence similarities of 99.2 and 98.1 %, respectively). Further genotypic and phenotypic studies, including fluorescent amplified fragment length polymorphism, DNA–DNA hybridization and DNA G+C content, clearly demonstrated that the two strains represent a single novel taxon for which the name Lactobacillus parabrevis sp. nov. is proposed (type strain LMG 11984T=ATCC 53295T).

Potato purple top wilt (PPT) is a devastating disease that occurs in various regions of North America and Mexico. At least three distinct phytoplasma strains belonging to three different phytoplasma groups (16SrI, 16SrII and 16SrVI) have been associated with this disease. A new disease with symptoms similar to PPT was recently observed in Texas and Nebraska, USA. Two distinct phytoplasma strain clusters were identified. One belongs to the 16SrI phytoplasma group, subgroup A, and the other is a novel phytoplasma that is most closely related to, and shares 96.6 % 16S rRNA gene sequence similarity with, a member of group 16SrXII. Phylogenetic analysis of 16S rRNA gene sequences of the novel PPT-associated phytoplasma strains, previously described ‘Candidatus Phytoplasma’ organisms and other distinct unnamed phytoplasmas indicated that the novel phytoplasma, termed American potato purple top wilt (APPTW) phytoplasma, represents a distinct lineage and shares a common ancestor with stolbur phytoplasma, ‘Candidatus Phytoplasma australiense’, ‘Candidatus Phytoplasma japonicum’, ‘Candidatus Phytoplasma fragariae’, bindweed yellows phytoplasma (IBS), ‘Candidatus Phytoplasma caricae’ and ‘Candidatus Phytoplasma graminis’. On the basis of unique 16S rRNA gene sequences and biological properties, it is proposed that the APPTW phytoplasma represents ‘Candidatus Phytoplasma americanum’, with APPTW12-NE as the reference strain.

Three anaerobic, moderately thermophilic, syntrophic primary alcohol- and lactate-degrading microbes, designated strains JLT, JE and OL, were isolated from sludges of thermophilic (55 °C) digesters that decomposed either municipal solid wastes or sewage sludge. The strains were strictly anaerobic organisms. All three strains grew at 25–60 °C and pH 5.5–8.5 and optimum growth was observed at 45–50 °C and pH 6.0–7.0. The three organisms grew chemo-organotrophically on a number of carbohydrates in the presence of yeast extract. In co-culture with the hydrogenotrophic methanogen Methanothermobacter thermautotrophicus, all strains could utilize ethanol, glycerol and lactate syntrophically for growth, although these compounds were not metabolized in pure culture without additional external electron acceptors. All strains could reduce thiosulphate. Quinones were not detected. The DNA G+C contents of strains JLT, JE and OL were 38.0, 37.3 and 37.7 mol%, respectively. Major cellular fatty acids of the strains were iso-C15 : 0, C16 : 0 and unsaturated species of C15 : 1. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the strains belong to a deeply branched lineage of the phylum Firmicutes; the most closely related species was Thermovenabulum ferriorganovorum (16S rRNA gene sequence similarity of 88 %). The three strains were phylogenetically very closely related to each other (99–100 % 16S rRNA gene sequence similarity) and were physiologically and chemotaxonomically similar. These genetic and phenotypic properties suggest that the strains should be classified as representatives of a novel species and genus; the name Tepidanaerobacter syntrophicus gen. nov., sp. nov. is proposed. The type strain of Tepidanaerobacter syntrophicus is strain JLT (=JCM 12098T=NBRC 100060T=DSM 15584T).

The applicability of a multilocus sequence analysis (MLSA)-based identification system for lactobacilli was evaluated. Two housekeeping genes that code for the phenylalanyl-tRNA synthase α-subunit (pheS) and RNA polymerase α-subunit (rpoA) were sequenced and analysed for members of the Lactobacillus salivarius species group. The type strains of Lactobacillus acidipiscis and Lactobacillus cypricasei were investigated further using a third gene that encodes the α-subunit of ATP synthase (atpA). The MLSA data revealed close relatedness between L. acidipiscis and L. cypricasei, with 99.8–100 % pheS, rpoA and atpA gene sequence similarities. Comparison of the 16S rRNA gene sequences of the type strains of the two species confirmed the close relatedness (99.8 % gene sequence similarity) between the two taxa. Similar phenotypes and high DNA–DNA binding values in the range of 84 to 97.5 % confirmed that L. acidipiscis and L. cypricasei are synonymous species. On the basis of the present study, it is proposed that Lactobacillus cypricasei is a later heterotypic synonym of Lactobacillus acidipiscis.

A Gram-positive, rod-shaped, non-endospore-forming bacterium, strain ASB1T, able to degrade tannin, was isolated from faeces of the Japanese large wood mouse, Apodemus speciosus. Comparative analysis of the 16S rRNA gene sequence revealed that the strain could be assigned as a member of the genus Lactobacillus. The nearest phylogenetic neighbours were determined as Lactobacillus animalis DSM 20602T (98.9 % 16S rRNA gene sequence similarity) and Lactobacillus murinus ASF 361 (98.9 %). Subsequent polyphasic analysis, including automated ribotyping and DNA–DNA hybridization experiments, confirmed that the isolate represents a novel species, for which the name Lactobacillus apodemi sp. nov. is proposed. The DNA G+C content of the novel strain is 38.5 mol%. The cell-wall peptidoglycan is of type A4α l-lys–d-Asp. The type strain is ASB1T (=DSM 16634T=CIP 108913T).

The order Trentepohliales is a widespread group of terrestrial green algae. As currently circumscribed, it includes six genera (Cephaleuros, Phycopeltis, Physolinum, Printzina, Stomatochroon and Trentepohlia), the phylogenetic affinities of which are poorly understood. Sequences for the small subunit rRNA gene (18S rDNA) were obtained for several representatives of the order and phylogenetic analyses based on these sequences were compared with the traditional system of classification based on morphological characters. The results indicate that the morphological criteria used for the circumscription of genera and species of the Trentepohliales do not match phylogenetic patterns. Whereas isolates of Cephaleuros form a well-supported monophyletic clade, Trentepohlia is polyphyletic and strains of Trentepohlia, Phycopeltis, Printzina and Physolinum are mixed together in several different lineages. A reassessment of the generic boundaries and a narrower circumscription of some genera (in particular Trentepohlia) will be necessary. Subcuticular habit, heteromorphic life history and occurrence of zoosporangia in clusters are shown to be phylogenetically significant features, whereas other characters commonly used for separation of species and genera (shape and size of the cells, prostrate/erect habit, substratum colonized) have no phylogenetic relevance.