4 Lipid and Cell-Wall Analysis in Bacterial Systematics

Marinibacillus campisalis sp. nov., a moderate halophile isolated from a marine solar saltern in Korea, with emended description of the genus Marinibacillus

A Gram-positive, motile, round to ellipsoidal, endospore-forming, rod-shaped bacterial strain, SF-57T, was isolated from a marine solar saltern in Korea. This organism grew between 4 and 39 degrees C, with optimum growth at 30 degrees C. Strain SF-57T grew in the presence of 0.5-15.0% NaCl, with optimum growth at 2-3% NaCl. The peptidoglycan type of strain SF-57T was A1alpha linked directly through l-Lys. In strain SF-57TT, menaquinone-7 (MK-7) was the predominant isoprenoid quinone and anteiso-C(15 : 0) was the major fatty acid. The DNA G+C content was 41.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SF-57T formed a coherent cluster with Marinibacillus marinus, with a bootstrap resampling value of 100%. The level of 16S rRNA gene sequence similarity between strain SF-57T and M. marinus DSM 1297T was 98.9%. The mean DNA-DNA relatedness level between strain SF-57T and the type strain of M. marinus was 20.6%. Based on phenotypic properties, phylogenetic analyses and genomic data, strain SF-57T merits placement in the genus Marinibacillus as a representative of a novel species, for which the name Marinibacillus campisalis sp. nov. is proposed. The type strain is SF-57T (=KCCM 41644T=JCM 11810T).

Isolation of Lentibacillus salicampi strains and Lentibacillus juripiscarius sp. nov. from fish sauce in Thailand

Eight strains of aerobic, spore-forming, Gram-positive, moderately halophilic bacteria were isolated from sauce (nam-pla and bu-du) produced in Thailand by the fermentation of fish. They grew optimally in the presence of 10 % NaCl, at 37 °C and pH 7·0. A diagnostic diamino acid, meso-diaminopimelic acid, was present in the cell-wall peptidoglycan. The predominant menaquinone was MK-7. The major cellular fatty acids were anteiso-C15 : 0 and iso-C16 : 0. Phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid were found to be the major polar lipid components. The DNA G+C content was 42–43 mol%. These bacteria were further divided into two groups based on phenotypic characteristics and DNA–DNA similarities. Three strains of Group I were highly affiliated to the type strain of Lentibacillus salicampi in terms of phenotypic characterization and DNA–DNA similarities (96–102 %); accordingly, they were identified as strains of L. salicampi. A representative strain of Group II, strain IS40-3T, was most closely related to L. salicampi in terms of 16S rRNA-based phylogenetic analysis, although five strains of Group II could be distinguished from L. salicampi by means of several phenotypic properties, low 16S rRNA gene sequence similarity (95·2 %) and low DNA–DNA similarities (12–32 %). Therefore, the Group II strains should be included in a novel species of the genus Lentibacillus, for which the name Lentibacillus juripiscarius sp. nov. is proposed. The type strain is IS40-3T (=JCM 12147T=PCU 229T=TISTR 1535T).

Silanimonas lenta gen. nov., sp. nov., a slightly thermophilic and alkaliphilic gammaproteobacterium isolated from a hot spring

A moderately thermophilic aerobic bacterium, strain 25-4T, was isolated from a hot spring at Baekdoo Mountain in Korea. The cells were Gram-negative, motile rods each having a polar flagellum. Analysis of the 16S rRNA gene sequence indicated that the strain represented a new lineage within the family ‘Xanthomonadaceae’ of the ‘Gammaproteobacteria’, being most closely related to the genera Thermomonas, Xanthomonas, Luteimonas, Pseudoxanthomonas, Stenotrophomonas and Xylella and having 16S rRNA gene sequence similarities to the most related species of the genera of between 92·9 and 94·4 %. The strain contained Q-8 as the major isoprenoid quinone and had a fatty acid profile with predominant iso-branched fatty acids. Growth occurred at pH 6·0–10, with an optimum at pH 9·0, and at 25–53 °C, with an optimum at 47 °C. The G+C content of the genomic DNA was 50·7 mol%. On the basis of phylogenetic analyses and its phenotypic characteristics, strain 25-4T belongs to a new genus, Silanimonas gen. nov., within the ‘Gammaproteobacteria’. The sole species of this genus is Silanimonas lenta sp. nov. (type strain, 25-4T=DSM 16282T=KCTC 12236T).

Erythrobacter seohaensis sp. nov. and Erythrobacter gaetbuli sp. nov., isolated from a tidal flat of the Yellow Sea in Korea

Two Gram-negative, non-spore-forming, slightly halophilic strains, SW-135T and SW-161T, which were isolated from a tidal flat of the Yellow Sea in Korea, were subjected to a polyphasic taxonomic study. The two isolates lacked bacteriochlorophyll a and contained ubiquinone-10 (Q-10) as the predominant respiratory lipoquinone and C18 : 1 ω7c and C17 : 1 ω6c as the major fatty acids. The DNA G+C contents of strains SW-135T and SW-161T were 62·2 and 64·5 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that the two strains fall within the radiation of the cluster comprising Erythrobacter species. Strains SW-135T and SW-161T exhibited a 16S rRNA gene sequence similarity value of 96·9 % and a mean DNA–DNA relatedness level of 12·3 %. Sequence similarities between strains SW-135T and SW-161T and the type strains of recognized Erythrobacter species ranged from 96·7 to 98·5 %. Levels of DNA–DNA relatedness were low enough to indicate that strains SW-135T and SW-161T represent members of two species separate from all recognized Erythrobacter species. On the basis of polyphasic taxonomic data, strains SW-135T (=KCTC 12228T=DSM 16221T) and SW-161T (=KCTC 12227T=DSM 16225T) were classified as two novel Erythrobacter species, for which the names Erythrobacter seohaensis sp. nov. and Erythrobacter gaetbuli sp. nov. are proposed, respectively.

Psychrobacter alimentarius sp. nov., isolated from squid jeotgal, a traditional Korean fermented seafood

Two Gram-negative, non-motile, non-spore-forming, moderately halophilic strains, JG-100T and JG-102, were isolated from squid jeotgal, a traditional Korean fermented seafood. The two strains grew optimally at 30 °C and in the presence of 2–3 % (v/w) NaCl. Strains JG-100T and JG-102 were characterized chemotaxonomically; they both had ubiquinone-8 as the predominant respiratory lipoquinone and C18 : 1 ω9c as the major fatty acid. Their DNA G+C content was 44 mol%. Strains JG-100T and JG-102 showed 1 bp difference in their 16S rRNA gene sequences and a mean DNA–DNA relatedness level of 88 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains JG-100T and JG-102 form a distinct phylogenetic lineage within the cluster comprising Psychrobacter species. The 16S rRNA gene sequences of strains JG-100T and JG-102 had similarity levels of 95·2–98·4 % to sequences of the type strains of recognized Psychrobacter species. Levels of DNA–DNA relatedness between strains JG-100T and JG-102 and the type strains of some phylogenetically related Psychrobacter species were 6–24 %. On the basis of phenotypic and phylogenetic data and genomic distinctiveness, strains JG-100T and JG-102 should be placed in the genus Psychrobacter as a novel species, for which the name Psychrobacter alimentarius sp. nov. (type strain, JG-100T=KCTC 12186T=DSM 16065T) is proposed.

Sphingopyxis flavimaris sp. nov., isolated from sea water of the Yellow Sea in Korea

A Gram-negative, motile, yellow-pigmented, slightly halophilic bacterial strain, SW-151T, was isolated from sea water of the Yellow Sea in Korea, and subjected to a polyphasic taxonomic study. The isolate grew optimally at 30 °C and in the presence of 2–3 % NaCl. Strain SW-151T was characterized chemotaxonomically as having Q-10 as the predominant respiratory lipoquinone and C18 : 1 ω7c, C16 : 1 ω7c and/or iso-C15 : 0 2-OH and C17 : 1 ω6c as the major fatty acids. Sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were the major polar lipids. The DNA G+C content was 58 mol%. 16S rRNA gene sequence analysis showed that strain SW-151T joins the evolutionary radiation enclosed by the genus Sphingopyxis. Similarities between the 16S rRNA gene sequences of strain SW-151T and the type strains of Sphingopyxis species ranged from 92·3 to 94·3 %, which is low enough to categorize strain SW-151T as a species distinct from previously described Sphingopyxis species. On the basis of phenotypic properties and phylogenetic distinctiveness, strain SW-151T (=KCTC 12232T=DSM 16223T) should be classified as a novel Sphingopyxis species, for which the name Sphingopyxis flavimaris sp. nov. is proposed.

Pontibacillus chungwhensis gen. nov., sp. nov., a moderately halophilic Gram-positive bacterium from a solar saltern in Korea

Three moderately halophilic, spore-forming strains, designated BH030062T, BH030049 and BH030080, were isolated from a solar saltern in Korea. Phylogenetic analyses and comparative 16S rRNA gene sequence studies revealed that the isolates represent a novel distinct monophyletic lineage within the phyletic group classically defined as the genus Bacillus and are most closely related to members of the genera Gracilibacillus (93·7–95·1 % similarity), Virgibacillus (93·5–94·8 %), Halobacillus (94·8–95·9 %), Filobacillus (94·4–94·8 %) and Lentibacillus (93·3–93·7 %). Strain BH030062T was strictly aerobic, rod-shaped, Gram-positive and motile by means of peritrichous flagella. It grew in the presence of 1–15 % (w/v) NaCl and at temperatures of 15–45 °C. The cell wall peptidoglycan contained A1γ-meso-diaminopimelic acid as the diagnostic diamino acid. The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0. DNA G+C content was about 41 mol% and the major isoprenoid quinone was MK-7. On the basis of their physiological and molecular properties, the isolates represent a new genus, Pontibacillus gen. nov., and novel species, Pontibacillus chungwhensis sp. nov. The type strain is BH030062T (=KCTC 3890T=DSM 16287T).

Salinimonas chungwhensis gen. nov., sp. nov., a moderately halophilic bacterium from a solar saltern in Korea

A halophilic non-spore-forming bacterium of the γ-Proteobacteria, designated strain BH030046T, was isolated from a solar saltern in Korea. Cells were Gram-negative, chemoheterotrophic, short rod-shaped and motile with a polar flagellum. Comparative 16S rRNA gene sequence analysis revealed that strain BH030046T formed a distinct lineage in the family Alteromonadaceae and was distinguished from its closest related genera Alteromonas (91·4–94·8 %), Aestuariibacter (92·1–93·5 %) and Glaciecola (92·1–93·5 %) on the basis of low 16S rRNA gene sequence similarities. Physiological and biochemical data also showed that the isolate was different from members of these three genera. The predominant cellular fatty acids were C16 : 0 and C18 : 1 ω7c. DNA G+C content was 48 mol% and the major isoprenoid quinone was Q-8. The strain grew optimally at 30–35 °C, pH 7·0–8·0 and 2–5 % NaCl. On the basis of physiological and molecular properties, strain BH030046T (=KCTC 12239T=DSM 16280T) represents a novel genus and species in the family Alteromonadaceae, for which the name Salinimonas chungwhensis gen. nov., sp. nov. is proposed.

Proposal of the genus Thermoactinomyces sensu stricto and three new genera, Laceyella, Thermoflavimicrobium and Seinonella, on the basis of phenotypic, phylogenetic and chemotaxonomic analyses

Phylogenetic analysis based on 16S rRNA gene sequences revealed that Thermoactinomyces species with validly published names can be assigned to four clusters or lineages. The type strains of Thermoactinomyces sacchari and Thermoactinomyces putidus were differentiated from the type strains of Thermoactinomyces vulgaris and Thermoactinomyces intermedius by the predominant menaquinone and fatty acid profiles. The type strains of Thermoactinomyces dichotomicus and Thermoactinomyces peptonophilus formed lines of descent distinct from other Thermoactinomyces species. Thermoactinomyces dichotomicus KCTC 3667T was distinguishable from the type strains of Thermoactinomyces vulgaris and Thermoactinomyces intermedius by the contents of two fatty acids, iso-C16 : 0 and iso-C17 : 0. Thermoactinomyces dichotomicus could be distinguished from other Thermoactinomyces species by DNA G+C content and some phenotypic properties, particularly its property of forming a yellow colour. The type strain of Thermoactinomyces peptonophilus was distinguishable from other Thermoactinomyces species by differences in menaquinone profile, major fatty acids, DNA G+C content and some physiological properties including optimal growth temperature. On the basis of these data, the creation of three new genera, Laceyella, Thermoflavimicrobium and Seinonella, is proposed in addition to the genus Thermoactinomyces sensu stricto. The genus Laceyella gen. nov. is proposed to accommodate Thermoactinomyces sacchari and Thermoactinomyces putidus as Laceyella sacchari comb. nov. and Laceyella putida comb. nov., the genus Thermoflavimicrobium gen. nov. is proposed for Thermoactinomyces dichotomicus as Thermoflavimicrobium dichotomicum comb. nov. and the genus Seinonella gen. nov. is proposed for Thermoactinomyces peptonophilus as Seinonella peptonophila comb. nov.

Photobacterium lipolyticum sp. nov., a bacterium with lipolytic activity isolated from the Yellow Sea in Korea

A Gram-negative, motile, non-spore-forming, pleomorphic and lipolytic bacterial strain, M37T, was isolated from an intertidal sediment of the Yellow Sea in Korea. This organism grew optimally at 25–28 °C and in the presence of 1–2 % NaCl. It did not grow without NaCl or in the presence of more than 6 % NaCl. Strain M37T was characterized chemotaxonomically by having Q-8 as the predominant respiratory lipoquinone and C16 : 1 ω7c and/or iso-C15 : 0 2-OH and C16 : 0 as the major fatty acids. The DNA G+C content was 47 mol%. Phylogenetic analyses based on 16S rRNA gene sequences placed strain M37T within the clade comprising Photobacterium species, forming a coherent cluster with the type strains of Photobacterium profundum and Photobacterium indicum (16S rRNA gene similarity levels of 97·5–98·0 %). The mean DNA–DNA relatedness levels between strain M37T and P. profundum JCM 10084T and P. indicum DSM 5151T were in the range 12–15 %. Similarities between 16S rRNA gene sequences of strain M37T and those of the type strains of the other Photobacterium species ranged from 93·9 % (with Photobacterium fischeri) to 96·2 % (with Photobacterium phosphoreum). On the basis of phenotypic properties and phylogenetic and genomic distinctiveness, strain M37T (=KCTC 10562BPT=DSM 16190T) should be placed in the genus Photobacterium as a novel species, for which the name Photobacterium lipolyticum sp. nov. is proposed.

Porphyrobacter donghaensis sp. nov., isolated from sea water of the East Sea in Korea

Two Gram-negative, motile, non-spore-forming, bacteriochlorophyll a-containing slightly halophilic strains, SW-132T and SW-158, were isolated from sea water of the East Sea in Korea, and subjected to a polyphasic taxonomic study. The two isolates were characterized chemotaxonomically as having Q-10 as the predominant respiratory lipoquinone and major amounts of unsaturated fatty acids C18 : 1 ω7c and C17 : 1 ω6c. The DNA G+C contents of the two strains were in the range 66·8–65·9 mol%. The 16S rRNA gene sequences of strains SW-132T and SW-158 were 99·9 % (1 nt difference) similar and their mean level of DNA–DNA relatedness was 86 %. The 16S rRNA gene sequence analysis showed that strains SW-132T and SW-158 are phylogenetically closely related to Porphyrobacter species and Erythromicrobium ramosum. Similarities between the 16S rRNA gene sequences of strains SW-132T and SW-158 and the type strains of Porphyrobacter species and E. ramosum ranged from 97·8 to 99·0 %. DNA–DNA relatedness data indicated that strains SW-132T and SW-158 are members of a genomic species that is separate from the four Porphyrobacter species. On the basis of phenotypic and phylogenetic data and genetic distinctiveness, strains SW-132T (=KCTC 12229T=DSM 16220T) and SW-158 (=KCTC 12230) are classified as a novel Porphyrobacter species, for which the name Porphyrobacter donghaensis sp. nov. is proposed.

Halomonas koreensis sp. nov., a novel moderately halophilic bacterium isolated from a solar saltern in Korea

A moderately halophilic bacterium, strain SS20T, capable of growing at salinities of 1–20 % (w/v) NaCl was isolated from a solar saltern of the Dangjin area in Korea and was characterized taxonomically. Strain SS20T was a Gram-negative bacterium comprising motile, short rods. Its major cellular fatty acids were C18 : 1 ω7c, C19 : 0 ω8c cyclo and C16 : 0. The DNA G+C content was 70 mol% and the predominant ubiquinone was Q-9. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SS20T belonged to the genus Halomonas. The levels of 16S rRNA gene sequence similarity to the type strains of Halomonas species were in the range 93·0–97·5 %. The levels of DNA–DNA relatedness between strain SS20T and the type strains of phylogenetically closely related Halomonas species were in the range 5·3–12·3 %. On the basis of physiological and molecular properties, strain SS20T represents a novel species of the genus Halomonas, for which the name Halomonas koreensis sp. nov. is proposed. The type strain is SS20T (=KCTC 12127T=JCM 12237T).

Erythrobacter aquimaris sp. nov., isolated from sea water of a tidal flat of the Yellow Sea in Korea

Three Gram-negative, non-motile, non-spore-forming, slightly halophilic rods (strains SW-110T, SW-116 and SW-140) were isolated from sea water of a tidal flat of the Yellow Sea in Korea and subjected to a polyphasic taxonomic study. The three isolates did not produce bacteriochlorophyll a and were characterized chemotaxonomically by having ubiquinone-10 as the predominant respiratory lipoquinone and C18 : 1 ω7c and C17 : 1 ω6c as the major fatty acids. The DNA G+C content of the three isolates was between 62·2 and 62·9 mol%. Strains SW-110T, SW-116 and SW-140 showed no difference in their 16S rRNA gene sequences, and their mean level of DNA–DNA relatedness was 94·8 %. Phylogenetic analyses based on 16S rRNA gene sequences showed that the three strains form a distinct phylogenetic lineage within the cluster comprising Erythrobacter species. Similarities between the 16S rRNA gene sequences of strains SW-110T, SW-116 and SW-140 and the type strains of Erythrobacter species ranged from 98·4 % (with Erythrobacter longus) to 97·7 % (with Erythrobacter flavus). Levels of DNA–DNA relatedness between strains SW-110T, SW-116 and SW-140 and the type strains of all recognized Erythrobacter species were in the range 5·3–12·7 %. On the basis of polyphasic taxonomic data, strains SW-110T, SW-116 and SW-140 were classified as a novel Erythrobacter species, for which the name Erythrobacter aquimaris sp. nov. is proposed. The type strain is SW-110T (=KCCM 41818T=JCM 12189T).

Bacillus vietnamensis sp. nov., a moderately halotolerant, aerobic, endospore-forming bacterium isolated from Vietnamese fish sauce

Five strains of Gram-positive, endospore-forming, moderately halotolerant bacteria were studied taxonomically. Four were isolated from Vietnamese fish sauce and one from the Gulf of Mexico. Phylogenetic analysis based on 16S rRNA gene sequences showed that these strains clustered within the radiation of the genus Bacillus but separately from recognized Bacillus species. DNA G+C composition of the isolates ranged from 43 to 44 mol%. Strains 15-1T and NRRL B-14850 showed high levels of DNA–DNA relatedness (82–100 %) to each other and to the other strains isolated here; they displayed low levels of DNA–DNA relatedness (<29 %) to the type strains of selected recognized Bacillus species. They grew in 15 % NaCl and optimally in 1 % NaCl, which is characteristic of moderately halotolerant bacteria. The isolates grew at pH 6·5 to 10·0 but not at pH 6·0. Their cell walls contained meso-diaminopimelic acid. The major isoprenoid quinone was MK-7 and the principal cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. Based on these results, the strains tested were regarded as members of a novel Bacillus species for which the name Bacillus vietnamensis sp. nov. is proposed. The type strain is 15-1T (=JCM 11124T=NRIC 0531T=NRRL 23890T).

Sphingomonas oligophenolica sp. nov., a halo- and organo-sensitive oligotrophic bacterium from paddy soil that degrades phenolic acids at low concentrations

The taxonomic position of a halo- and organo-sensitive, oligotrophic soil bacterium, strain S213T, was investigated. Cells were Gram-negative, non-motile, strictly aerobic, yellow-pigmented rods of short to medium length on diluted nutrient broth. When 0·1–0·4 % (w/v) NaCl was added to diluted media composed of peptone and meat extract, growth was inhibited with increasing NaCl concentration and the cells became long aberrant forms. When 6 mM CaCl2 was added, the cells grew quite normally and aberrant cells were no longer found at 0·1–0·5 % (w/v) NaCl. Chemotaxonomically, strain S213T contains chemical markers that indicate its assignment to the Sphingomonadaceae: the presence of ubiquinone Q-10 as the predominant respiratory quinone, C18 : 1 and C16 : 0 as major fatty acids, C14 : 0 2-OH as the major 2-hydroxy fatty acid and sphingoglycolipids. 16S rRNA gene sequence analysis indicated that strain S213T belongs to the genus Sphingomonas, exhibiting high sequence similarity to the 16S rRNA gene sequences of Sphingomonas mali IFO 15500T (98·3 %), Sphingomonas pruni IFO 15498T (98·0 %), Sphingomonas asaccharolytica IFO 15499T (97·9 %) and Sphingomonas echinoides DSM 1805T (97·8 %). The results of DNA–DNA hybridization experiments and its phenotypic characteristics clearly distinguished the strain from its nearest neighbours and demonstrate that strain S213T represents a novel Sphingomonas species, for which the name Sphingomonas oligophenolica sp. nov. is proposed. The type strain is S213T (=JCM 12082T=CIP 107926T).

Shewanella marisflavi sp. nov. and Shewanella aquimarina sp. nov., slightly halophilic organisms isolated from sea water of the Yellow Sea in Korea

Two Gram-negative, motile, non-spore-forming, rod-shaped organisms, strains SW-117T and SW-120T, were isolated from sea water of the Yellow Sea in Korea and subjected to a polyphasic taxonomic study. Strains SW-117T and SW-120T simultaneously contained both menaquinones (MK) and ubiquinones (Q) as isoprenoid quinones; the predominant menaquinone was MK-7 and the predominant ubiquinones were Q-7 and Q-8. The major fatty acid detected in the two strains was iso-C15 : 0. The DNA G+C content of strains SW-117T and SW-120T was 51 and 54 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains SW-117T and SW-120T fall within the radiation of the cluster comprising Shewanella species. Strains SW-117T and SW-120T showed a 16S rRNA gene sequence similarity of 97·4 % and a DNA–DNA relatedness level of 10·1 %. Strains SW-117T and SW-120T exhibited 16S rRNA gene sequence similarity levels of 93·8–98·5 % and 92·4–97·0 %, respectively, to Shewanella species. Strain SW-117T exhibited DNA–DNA relatedness levels of 8·3–20·3 % to the type strains of six phylogenetically related Shewanella species. On the basis of phenotypic, phylogenetic and genetic data, strains SW-117T and SW-120T were classified in the genus Shewanella as two distinct novel species, for which the names Shewanella marisflavi sp. nov. (type strain, SW-117T=KCCM 41822T=JCM 12192T) and Shewanella aquimarina sp. nov. (type strain, SW-120T=KCCM 41821T=JCM 12193T) are proposed, respectively.

Marinobacter flavimaris sp. nov. and Marinobacter daepoensis sp. nov., slightly halophilic organisms isolated from sea water of the Yellow Sea in Korea

Two Gram-negative, motile, non-spore-forming and slightly halophilic rods (strains SW-145T and SW-156T) were isolated from sea water of the Yellow Sea in Korea. Strains SW-145T and SW-156T grew optimally at 37 and 30–37 °C, respectively, and in the presence of 2–6 % (w/v) NaCl. Strains SW-145T and SW-156T were chemotaxonomically characterized as having ubiquinone-9 as the predominant respiratory lipoquinone and C16 : 0, C18 : 1 ω9c, C16 : 1 ω9c and C12 : 0 3-OH as the major fatty acids. The DNA G+C contents of strains SW-145T and SW-156T were 58 and 57 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains SW-145T and SW-156T fell within the evolutionary radiation enclosed by the genus Marinobacter. The 16S rRNA gene sequences of strains SW-145T and SW-156T were 94·8 % similar. Strains SW-145T and SW-156T exhibited 16S rRNA gene sequence similarity levels of 94·3–98·1 and 95·4–97·7 %, respectively, with respect to the type strains of all Marinobacter species. Levels of DNA–DNA relatedness, together with 16S rRNA gene sequence similarity values, indicated that strains SW-145T and SW-156T are members of two species that are distinct from seven Marinobacter species with validly published names. On the basis of phenotypic properties and phylogenetic and genotypic distinctiveness, strains SW-145T (=KCTC 12185T=DSM 16070T) and SW-156T (=KCTC 12184T=DSM 16072T) should be placed in the genus Marinobacter as the type strains of two distinct novel species, for which the names Marinobacter flavimaris sp. nov. and Marinobacter daepoensis sp. nov. are proposed.

Kangiella koreensis gen. nov., sp. nov. and Kangiella aquimarina sp. nov., isolated from a tidal flat of the Yellow Sea in Korea

Two Gram-negative, non-motile, non-spore-forming, rod-shaped organisms, strains SW-125T and SW-154T, were isolated from tidal flat sediment of the Yellow Sea in Korea, and subjected to a polyphasic taxonomic study. Strains SW-125T and SW-154T grew optimally at 30–37 °C and in the presence of 2–3 % (w/v) NaCl. They contained ubiquinone-8 (Q-8) as the predominant respiratory lipoquinone and iso-C15 : 0 as the major fatty acid. The DNA G+C contents of strains SW-125T and SW-154T were 44 mol%. Phylogenetic trees based on 16S rRNA gene sequences revealed that the two strains form deep evolutionary lineages of descent within the γ-Proteobacteria. Strains SW-125T and SW-154T exhibited 16S rRNA gene sequence similarity levels of less than 90 % to members of the γ-Proteobacteria used in this analysis. Strains SW-125T and SW-154T showed a 16S rRNA gene sequence similarity level of 98·5 % and a mean DNA–DNA relatedness level of 9·4 %. Therefore, on the basis of phenotypic, phylogenetic and genomic data, a new genus, Kangiella gen. nov., is proposed to accommodate the novel strains, comprising two novel species, Kangiella koreensis sp. nov. (type strain, SW-125T=KCTC 12182T=DSM 16069T) and Kangiella aquimarina sp. nov. (type strain, SW-154T=KCTC 12183T=DSM 16071T).

Sulfurovum lithotrophicum gen. nov., sp. nov., a novel sulfur-oxidizing chemolithoautotroph within the ε-Proteobacteria isolated from Okinawa Trough hydrothermal sediments

A novel mesophilic sulfur- and thiosulfate-oxidizing bacterium, strain 42BKTT, was isolated from the gas-bubbling sediment at the Iheya North hydrothermal system in the mid-Okinawa Trough, Japan. The isolate was a Gram-negative, non-motile and coccoid to oval-shaped bacterium. Growth was observed at 10–40 °C (optimum 28–30 °C) and in the pH range 5·0–9·0 (optimum 6·5–7·0). Strain 42BKTT grew chemolithoautotrophically with elemental sulfur or thiosulfate as a sole electron donor and oxygen (optimum 5 % in gas phase) or nitrate as an electron acceptor. The G+C content of the genomic DNA was 48·0 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the isolate belonged to the previously uncultivated Group F within the ε-Proteobacteria, which includes phylotypes of vent epibiont and environmental sequences from global deep-sea cold seep and hydrothermal vent fields. On the basis of the physiological and molecular characteristics of this isolate, the type species of a novel genus, Sulfurovum lithotrophicum gen. nov., sp. nov., is proposed. The type strain is 42BKTT (=ATCC BAA-797T=JCM 12117T).

Hongiella marincola sp. nov., isolated from sea water of the East Sea in Korea

Two Gram-negative, non-motile, non-spore-forming, rod-shaped strains, SW-2T and SW-26, were isolated from sea water of the East Sea in Korea. These organisms grew optimally at 37 °C and in the presence of 2–3 % (w/v) NaCl. They did not grow without NaCl or in the presence of >9 % (w/v) NaCl. Strains SW-2T and SW-26 were characterized chemotaxonomically as having MK-7 as the predominant isoprenoid quinone and iso-C15 : 0 as the major fatty acid. The DNA G+C content of strains SW-2T and SW-26 was 43 mol%. A neighbour-joining tree based on 16S rRNA gene sequences showed that strains SW-2T and SW-26 fell within the Cytophaga–Flavobacterium–Bacteroides group and formed a coherent cluster with Hongiella species. Strains SW-2T and SW-26 showed a 16S rRNA gene sequence similarity value of 99·9 % and a mean DNA–DNA relatedness level of 87 % to each other. Levels of 16S rRNA gene sequence similarity between strains SW-2T and SW-26 and the type strains of two Hongiella species ranged from 94·2 to 96·6 %. On the basis of phenotypic and chemotaxonomic properties and phylogenetic distinctiveness, strains SW-2T and SW-26 should be placed in the genus Hongiella as members of a novel species, for which the name Hongiella marincola sp. nov. is proposed. The type strain is SW-2T (=KCTC 12180T=DSM 16067T).

Deinococcus indicus sp. nov., an arsenic-resistant bacterium from an aquifer in West Bengal, India

An arsenic- and radiation-resistant bacterium, strain Wt/1a(T), was isolated from water from an arsenic-contaminated aquifer located in the Chakdah district of West Bengal, India. The bacterium stains Gram-negative and is rod-shaped, non-motile, non-sporulating and red-pigmented. Cell-wall peptidoglycan contains ornithine as the diamino acid, MK-8 is the major menaquinone, C(15 : 1) and C(16 : 1) are the major fatty acids and the DNA G+C content of the organism is 65.8 mol%. Based on these phenotypic and chemotaxonomic characteristics, strain Wt/1a(T) was identified as a member of the genus Deinococcus. Strain Wt/1a(T) exhibited maximum 16S rRNA gene sequence similarity (95 %) with Deinococcus grandis; however, strain Wt/1a(T) exhibited only 14 % similarity to D. grandis IAM 13005(T) at the DNA-DNA level. Furthermore, strain Wt/1a(T) (compared to D. grandis IAM 13005(T)) is more resistant to arsenate and arsenite, is positive for arginine dihydrolase, utilizes a number of carbon sources and exhibits quantitative differences in fatty acid composition and qualitative differences in lipid composition. Strain Wt/1a(T) is identified as a novel species of the genus Deinococcus, for which the name Deinococcus indicus sp. nov. is proposed. The type strain of Deinococcus indicus is Wt/1a(T) (=MTCC 4913(T)=DSM 15307(T)).

Alteromonas litorea sp. nov., a slightly halophilic bacterium isolated from an intertidal sediment of the Yellow Sea in Korea

A Gram-negative, motile, non-spore-forming, rod-shaped bacterium, designated strain TF-22T, was isolated from an intertidal sediment in Korea. This organism grew optimally at 30–37 °C and in the presence of 2–5 % (w/v) NaCl. It did not grow without NaCl or in the presence of more than 14 % (w/v) NaCl. Strain TF-22T was characterized chemotaxonomically as having ubiquinone-8 as the predominant respiratory lipoquinone and C16 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH and C18 : 1 ω7c as the major fatty acids. The DNA G+C content of strain TF-22T was 46·0 mol%. Phylogenetic analyses based on 16S rDNA sequences showed that strain TF-22T falls within the γ-subclass of the Proteobacteria and forms a coherent cluster with Alteromonas macleodii and Alteromonas marina. Levels of 16S rDNA similarity between strain TF-22T and the type strains of two Alteromonas species were in the range 98·1–98·6 %. The level of DNA–DNA relatedness between strain TF-22T and the type strains of two Alteromonas species was 15·7–18·5 %. Therefore, on the basis of phenotypic properties, phylogeny and genomic distinctiveness, strain TF-22T should be placed in the genus Alteromonas as a novel species, for which the name Alteromonas litorea sp. nov. is proposed. The type strain is TF-22T (=KCCM 41775T=JCM 12188T).

Microbulbifer maritimus sp. nov., isolated from an intertidal sediment from the Yellow Sea, Korea

A Gram-negative, rod-shaped, non-spore-forming, slightly halophilic bacterium (strain TF-17T) was isolated from an intertidal sediment from the Yellow Sea, Korea. Pigment of strain TF-17T was similar to that of Microbulbifer elongatus, but different from those of Microbulbifer hydrolyticus and Microbulbifer salipaludis. Strain TF-17T was distinguishable from M. elongatus by some phenotypic properties, including motility, optimal growth temperature and others. Phylogenetic analysis based on 16S rDNA sequences showed that strain TF-17T clustered with the type strains of the three Microbulbifer species with validly published names. Strain TF-17T exhibited 16S rDNA sequence similarity levels of 95·1–95·7 % to the type strains of the three Microbulbifer species. The predominant respiratory lipoquinone found in strain TF-17T was ubiquinone-8. The major fatty acid was iso-C15 : 0 and significant amounts of iso-C11 : 0 3-OH and iso-C17 : 1 ω9c were also present. The DNA G+C content of strain TF-17T was 59·9 mol%. Levels of DNA–DNA relatedness between strain TF-17T and the type strains of the three Microbulbifer species were in the range 10·0–13·0 %. On the basis of phenotypic and phylogenetic data and genotypic distinctiveness, strain TF-17T (=KCCM 41774T=JCM 12187T) is proposed as the type strain of a novel species of the genus Microbulbifer, Microbulbifer maritimus sp. nov.

Bacillus indicus sp. nov., an arsenic-resistant bacterium isolated from an aquifer in West Bengal, India

Strain Sd/3T (=MTCC 4374T=DSM 15820T), an arsenic-resistant bacterium, was isolated from a sand sample obtained from an arsenic-contaminated aquifer in Chakdah district in West Bengal, India (23° 3′ N 88° 35′ E). The bacterium was Gram-positive, rod-shaped, non-motile, endospore-forming and yellowish-orange pigmented. It possessed all the characteristics that conform to the genus Bacillus, such as it had A4 β murein type (l-orn-d-Asp) peptidoglycan variant, MK-7 as the major menaquinone and iso-C15 : 0 and anteiso-C15 : 0 as the major fatty acids. Based on its chemotaxonomic and phylogenetic characteristics, strain Sd/3T was identified as a species of the genus Bacillus. It exhibited maximum similarity (95 %) at the 16S rRNA gene level with Bacillus cohnii; however, DNA–DNA similarity with B. cohnii was 60·7 %. Strain Sd/3T also exhibited a number of phenotypic differences from B. cohnii (DSM 6307T). These data suggest that Sd/3T represents a novel species of the genus Bacillus. The name Bacillus indicus sp. nov. is proposed.

Genomic characterization of thermophilic Geobacillus species isolated from the deepest sea mud of the Mariana Trench

The thermophilic strains HTA426 and HTA462 isolated from the Mariana Trench were identified as Geobacillus kaustophilus and G. stearothermophilus, respectively, based on physiologic and phylogenetic analyses using 16S rDNA sequences and DNA-DNA relatedness. The genome size of HTA426 and HTA462 was estimated at 3.23-3.49 Mb and 3.7-4.49 Mb, respectively. The nucleotide sequences of three independent lambda-phage inserts of G. stearothermophilus HTA462 have been determined. The organization of protein coding sequences (CDSs) in the two lambda-phage inserts was found to differ from that in the contigs corresponding to each lambda insert assembled by the shotgun clones of the G. kaustophilus HTA426 genome, although the CDS organization in another lambda insert is identical to that in the HTA426 genome.

Prevotella shahii sp. nov. and Prevotella salivae sp. nov., isolated from the human oral cavity

Two bacterial strains, EHS11T and EPSA11T, which were isolated from the human oral cavity, were characterized in terms of phenotypic and biochemical characteristics, cellular fatty acid profiles and phylogenetic position based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that each of the isolates belonged to a novel species of the genus Prevotella. Strain EHS11T was related to Prevotella loescheii (about 95 % similarity), whereas strain EPSA11T was related to Prevotella oris (about 94 % similarity). Both strains were obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative rods. The cellular fatty acid composition of strain EPSA11T was very similar to that of P. oris JCM 8540T. On the other hand, the cellular fatty acid composition of strain EHS11T was significantly different from those of other Prevotella species. The predominant fatty acids in strain EHS11T are C18 : 1 ω9c, C16 : 0 and C16 : 0 3-OH, whereas other Prevotella species, except for P. loescheii JCM 8530T, possess anteiso-C15 : 0, iso-C17 : 0 3-OH and C18 : 1 ω9c. The predominant fatty acids in P. loescheii JCM 8530T are anteiso-C15 : 0, C16 : 0 and C18 : 1 ω9c. DNA–DNA hybridization experiments revealed a genomic distinction of strains EHS11T and EPSA11T from P. loescheii JCM 8530T and P. oris JCM 8540T. On the basis of these data, two novel Prevotella species are proposed: Prevotella shahii sp. nov. and Prevotella salivae sp. nov. The type strains of P. shahii and P. salivae are EHS11T (=JCM 12083T=DSM 15611T) and EPSA11T (=JCM 12084T=DSM 15606T), respectively.

Rothia aeria sp. nov., Rhodococcus baikonurensis sp. nov. and Arthrobacter russicus sp. nov., isolated from air in the Russian space laboratory Mir

Four Gram-positive bacteria, strains A1-17BT, A1-22T, A1-3T and A1-8, isolated from the air in the Russian space laboratory Mir, were subjected to a polyphasic taxonomic study. Phylogenetic analysis of the bacteria based on their 16S rDNA sequence showed that they belong to the genera Rothia (A1-17BT), Rhodococcus (A1-22T) and Arthrobacter (A1-3T and A1-8). Morphological, physiological, chemotaxonomic and genomic characteristics supported the assignments of these strains to these genera, but they could not be classified as any existing species within each respective genus. 16S rDNA similarity values between strain A1-17BT and its neighbours, Rothia dentocariosa genomovar II, Rothia dentocariosa, Rothia mucilaginosa and Rothia nasimurium, were respectively 99·8, 98·0, 96·4 and 95·4 %. Polyphasic taxonomic evidence indicated that strain A1-17BT should be categorized together with the unofficially named Rothia dentocariosa genomovar II, but clearly differentiated them from the established species of the genus Rothia. Strain A1-22T formed a coherent cluster with Rhodococcus erythropolis, Rhodococcus globerulus, Rhodococcus marinonascens and Rhodococcus percolatus in 16S rDNA sequence analysis, but DNA–DNA relatedness values were only 45·5, 35·3, 18·9 and 21·9 %. Strains A1-3T and A1-8 shared 99·9 % 16S rDNA sequence similarity, and strain A1-3T showed the highest level of 16S rDNA similarity, 96·6 %, to Arthrobacter polychromogenes. Contrasting biochemical characteristics were also identified. Finally, as a result of the polyphasic taxonomic study, three of the strains are proposed as type strains of novel species: Rothia aeria sp. nov. (A1-17BT=GTC 867T=JCM 11412T=DSM 14556T), Rhodococcus baikonurensis sp. nov. (A1-22T=GTC 1041T=JCM 11411T=DSM 44587T) and Arthrobacter russicus sp. nov. (A1-3T=GTC 863T=JCM 11414T=DSM 14555T).

Nesterenkonia halotolerans sp. nov. and Nesterenkonia xinjiangensis sp. nov., actinobacteria from saline soils in the west of China

The taxonomic position of two Gram-positive strains, YIM 70084T and YIM 70097T, isolated from hypersaline soils was determined by a polyphasic approach. Cells of strain YIM 70084T are motile cocci, whereas those of strain YIM 70097T are non-motile rods. The G+C contents of their DNA are 64·4 and 66·7 mol%. Both strains had chemotaxonomic markers typical of the genus Nesterenkonia and formed a coherent cluster with Nesterenkonia species in a phylogenetic inference based on 16S rDNA sequence analysis, exhibiting less than 97 % similarity to each other and to the other two type strains of the genus. Phylogenetic distinction and differences in the peptidoglycan type, composition of cell-wall sugars, phospholipid patterns, the major menaquinones and other phenotypic characteristics indicate that the strains under study represent two novel species, Nesterenkonia halotolerans sp. nov. (type strain YIM 70084T=CCTCC AA 001022T=DSM 15474T) and Nesterenkonia xinjiangensis sp. nov. (type strain YIM 70097T=CCTCC AA 001025T=DSM 15475T).

Bacillus hwajinpoensis sp. nov. and an unnamed Bacillus genomospecies, novel members of Bacillus rRNA group 6 isolated from sea water of the East Sea and the Yellow Sea in Korea

Two Gram-positive or -variable, endospore-forming, slightly halophilic strains (SW-72T and SW-93) were isolated from sea water of the East Sea and the Yellow Sea in Korea, respectively, and subjected to polyphasic taxonomic study. Both strains had cell-wall peptidoglycan that was based on meso-diaminopimelic acid and MK-7 as the predominant menaquinone. The two strains contained large amounts of saturated and branched fatty acids, with anteiso-C15 : 0 as the major fatty acid. The DNA G+C contents of strains SW-72T and SW-93 were 40·9 and 41·0 mol%, respectively. Phylogenetic analysis based on 16S rDNA sequences showed that strains SW-72T and SW-93 fall within the radiation of the cluster that comprises members of the genus Bacillus, particularly Bacillus rRNA group 6. There were five nucleotide differences between the 16S rDNA sequences of strains SW-72T and SW-93. The mean level of DNA–DNA relatedness between strains SW-72T and SW-93 was 21·5 %. Strains SW-72T and SW-93 showed 93·1–95·2 % 16S rDNA sequence similarity to the type strains of Bacillus species that are assigned to rRNA group 6. Strains SW-72T and SW-93 could not be differentiated clearly by using their phenotypic properties. On the basis of phenotypic properties, phylogeny and genomic data, it is proposed that strain SW-72T (=KCCM 41641T=JCM 11807T) should be placed in the genus Bacillus as the type strain of a novel species, Bacillus hwajinpoensis sp. nov., and that strain SW-93 (=KCCM 41640=JCM 11806) should be placed in the genus Bacillus as an unnamed Bacillus genomospecies.

Herbaspirillum chlorophenolicum sp. nov., a 4-chlorophenol-degrading bacterium

A 4-chlorophenol-degrading bacterial strain, formerly designated as a strain of Comamonas testosteroni, was reclassified as a member of the genus Herbaspirillum based on its phenotypic and chemotaxonomic characteristics, as well as phylogenetic analysis using 16S rDNA sequences. Phylogenetic inference based on 16S rDNA sequences showed that strain CPW301T clusters in a phylogenetic branch that contains Herbaspirillum species. 16S rDNA sequence similarity of strain CPW301T to species of the genus Herbaspirillum with validly published names is in the range 98·7–98·9 %. Despite the considerably high 16S rDNA sequence similarity, strain CPW301T could be distinguished clearly from type strains of Herbaspirillum species with validly published names by DNA–DNA relatedness values, which were <15·7 %. The genomic DNA G+C content of strain CPW301T is 61·3 mol%. The predominant ubiquinone is Q-8 and the major cellular fatty acids are C16 : 0 and cyclo-C17 : 0. The strain does not fix nitrogen and is not plant-associated. It is an aerobic rod with one unipolar flagellum. On the basis of these characteristics, a novel Herbaspirillum species, Herbaspirillum chlorophenolicum sp. nov., is proposed. The type strain of the novel species is strain CPW301T (=KCTC 12096T=IAM 15024T).

Emendation of the genus Acidomonas Urakami, Tamaoka, Suzuki and Komagata 1989

The genus Acidomonas and the species Acidomonas methanolica were recharacterized by using the type strain (NRIC 0498T), three reference strains and 10 methanol-utilizing bacteria that were isolated from activated sludge from three different sewage-treatment plants in Tokyo. Based on 16S rDNA sequences, all strains formed a single cluster within the Acetobacteraceae that was clearly different from the genera Acetobacter, Gluconobacter, Gluconacetobacter, Asaia and Kozakia. The 14 strains were identified as a single species, Acidomonas methanolica, by DNA–DNA similarities, showed DNA G+C contents that ranged from 62 to 63 mol% and had Q-10 as the major quinone, accounting for >87 % of total ubiquinones. Cells of Acidomonas methanolica had a single polar flagellum (or occasionally polar tuft flagella); this differs from a previous study that described peritrichous flagella. Oxidation of acetate was positive for all strains, but oxidation of lactate was weakly positive and varied with strains. Dihydroxyacetone was not produced from glycerol. Pantothenic acid was an essential requirement for growth. The strains tested grew at mostly the same extent at pH 3·0–8·0. Therefore, Acidomonas methanolica should be regarded as acidotolerant, not acidophilic. The descriptions of the genus Acidomonas and the species Acidomonas methanolica Urakami, Tamaoka, Suzuki and Komagata 1989 are emended with newly obtained data.

Pseudonocardia chloroethenivorans sp. nov., a chloroethene-degrading actinomycete

A bacterial strain, SL-1T, capable of degrading trichloroethene was isolated from a laboratory enrichment in the Department of Civil and Environmental Engineering, University of Washington, USA. The material in the enrichments was derived from a soil sample from Seattle, WA, USA. Strain SL-1T was capable of using phenol as a source of carbon and energy. Chemotaxonomic, morphological, physiological and phylogenetic analyses showed that strain SL-1T is a member of the genus Pseudonocardia. The ability of strain SL-1T to utilize phenol and degrade trichloroethene, as well as other phenotypic properties and the results from a 16S rRNA phylogenetic analysis, led to the proposal of a novel species, Pseudonocardia chloroethenivorans sp. nov. The type strain is SL-1T (=ATCC BAA-742T=DSM 44698T). Trichloroethene and other chloroethenes are major pollutants at many environmental sites, and P. chloroethenivorans has biodegradation properties that should be of interest to environmental microbiologists and engineers.

Shewanella gaetbuli sp. nov., a slight halophile isolated from a tidal flat in Korea

A Gram-negative, motile, non-spore-forming, rod-shaped strain, TF-27T (=KCCM 41648T=JCM 11814T), was isolated from a tidal flat in Korea. This organism grew well at 25–35 °C, with optimum growth at 30 °C. Strain TF-27T grew optimally in the presence of 2 % NaCl; it did not grow without NaCl or in the presence of >8 % NaCl. Strain TF-27T simultaneously contained both menaquinones and ubiquinones as isoprenoid quinones. The predominant menaquinone was MK-7 and the predominant ubiquinones were Q-7 and Q-8. The major fatty acids in strain TF-27T were iso-C15 : 0 (20·6 %) and iso-C15 : 0 2-OH and/or C16 : 1 ω7c (21·1 %). The DNA G+C content of strain TF-27T was 42 mol%. Phylogenetic analyses based on 16S rDNA sequences showed that strain TF-27T falls within the radiation of the cluster that is encompassed by the genus Shewanella. Levels of 16S rDNA sequence similarity between strain TF-27T and the type strains of Shewanella species were 93·2–96·8 %. On the basis of phenotypic properties and phylogenetic data, strain TF-27T should be placed in the genus Shewanella as a novel species, for which the name Shewanella gaetbuli sp. nov. is proposed.

Nocardioides aquiterrae sp. nov., isolated from groundwater in Korea

A bacterial strain, GW-9T, which was isolated from groundwater in Korea, was subjected to a polyphasic taxonomic study using phenotypic characterization and phylogenetic and genetic methods. Phylogenetic analysis based on 16S rDNA sequences showed that strain GW-9T forms an evolutionary lineage within the radiation enclosing Nocardioides species and, in particular, a coherent cluster with Nocardioides pyridinolyticus. The cell-wall peptidoglycan type of strain GW-9T was based on ll-diaminopimelic acid as the diamino acid, indicating wall chemotype I. The predominant menaquinone was MK-8(H4). Strain GW-9T had a cellular fatty acid profile containing straight-chain, branched, unsaturated and 10-methyl fatty acids. The major fatty acid was iso-C16 : 0. The DNA G+C content of strain GW-9T was 73 mol%. The 16S rDNA of strain GW-9T was 99·2 % similar to that of the type strain of Nocardioides pyridinolyticus and 94·9–96·0 % similar to sequences of the type strains of other Nocardioides species. Differences in phenotypic characteristics and genetic distinctiveness indicate that strain GW-9T is separate from previously described Nocardioides species. Therefore, on the basis of the data presented, a novel species of the genus Nocardioides, Nocardioides aquiterrae sp. nov., is proposed. The type strain is strain GW-9T (=KCCM 41647T=JCM 11813T).

Polaromonas naphthalenivorans sp. nov., a naphthalene-degrading bacterium from naphthalene-contaminated sediment

Strain CJ2T, capable of growth on naphthalene as a sole carbon and energy source, was isolated from coal-tar-contaminated freshwater sediment. The Gram reaction of strain CJ2Twas negative. The cells were non-spore-forming, non-motile cocci (without flagella). The isolate was found to be an aerobic heterotroph capable of utilizing glucose and other simple sugars. Growth was observed between 4 and 25 °C (optimum, 20 °C) and between pH 6·0 and 9·0 (optimum, pH 7·0–7·5). The G+C content of the genomic DNA was 61·5 mol% and the major quinone was ubiquinone-8. The peptidoglycan of strain CJ2Twas determined as belonging to type A1-γ,meso-diaminopimelic acid. The major fatty acids of strain CJ2Twere 16 : 1ω7c(67·0 %), 16 : 0 (19·6 %), 18 : 1ω7c(∼7·9 %) and 10 : 0 3-OH (∼2·5 %). The polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Mycolic acid and glycolipids could not be detected. Comparative 16S rDNA analysis indicated that strain CJ2Tis related to the familyComamonadaceaeand that the nearest phylogenetic relative wasPolaromonas vacuolata34-PT(97·1 % similarity). On the basis of the physiological and molecular properties, the naphthalene-degrading isolate was designatedPolaromonas naphthalenivoranssp. nov. The type strain is CJ2T(=ATCC BAA-779T=DSM 15660T).

Delftia tsuruhatensis sp. nov., a terephthalate-assimilating bacterium isolated from activated sludge

A terephthalate-assimilating bacterium was isolated from activated sludge collected from a domestic wastewater treatment plant in Japan by enrichment with terephthalate as sole carbon source. The isolate, designated strain T7(T), was a Gram-negative, short rod-shaped micro-organism. A phylogenetic study based on 16S rRNA gene sequences indicated that strain T7(T) should be placed in the genus DELFTIA: A DNA-DNA hybridization value of 69 % was determined between strain T7(T) and Delftia acidovorans ATCC 15668(T). Major cellular fatty acids of strain T7(T) were C(16 : 0), C(16 : 1) and C(18 : 1). Substantial amounts of cyclopropanoic acid (C(17 : 0)), 3-OH C(10 : 0), C(12 : 0), C(15 : 0) and C(14 : 0) were also detected. The total DNA G+C content of strain T7(T) was 66.2 mol%. Strain T7(T) could utilize the following compounds as carbon sources: acetamide, beta-alanine, citrate, D-fructose, glycerol, isobutyrate, isophthalate, D(-)-mannitol, maleate, malonate, phenylacetate, propionate, protocatechuate, terephthalate, D-tryptophan and L-tryptophan. Comparisons of phenotypic and genotypic characteristics with other known species belonging to the genus Delftia suggest that strain T7(T) represents a novel species, for which the name Delftia tsuruhatensis sp. nov. is proposed; strain T7(T) is the type strain (=IFO 16741(T)=ATCC BAA-554(T)).

Gordonia paraffinivorans sp. nov., a hydrocarbon-degrading actinomycete isolated from an oil-producing well

The taxonomic position of an actinomycete, strain HD321(T), isolated from an oil-producing well of Daqing oilfield, was clarified using a polyphasic taxonomic approach. The strain possessed cell-wall chemotype IV, MK-9(H(2)) as the predominant menaquinone, relatively long-chain mycolic acids (52-62 carbon atoms) of the Gordonia type, straight-chain saturated and monounsaturated fatty acids and tuberculostearic acid. The G+C content of the DNA was 66 mol%. 16S rDNA analyses as well as chemotaxonomic and physiological properties indicated that strain HD321(T) represents a novel species within the genus Gordonia, for which the name Gordonia paraffinivorans sp. nov. is proposed; the type strain is HD321(T) (=AS 4.1730(T)=DSM 44604(T)).

Alteromonas marina sp. nov., isolated from sea water of the East Sea in Korea

Two Gram-negative, motile, non-spore-forming and moderately halophilic rods (strains SW-47(T) and SW-49) were isolated from sea water of the East Sea in Korea and subjected to a polyphasic taxonomic study. The two strains grew optimally between 30 and 37 degrees C, and grew at 4 and 44 degrees C but not at temperatures above 45 degrees C. They grew optimally in the presence of 2-5 % (w/v) NaCl, but did not grow in the absence of NaCl. Strains SW-47(T) and SW-49 had ubiquinone-8 (Q-8) as the predominant respiratory lipoquinone and C(16 : 1) omega7c and/or iso-C(15 : 0) 2OH, C(16 : 0) and C(18 : 1) omega7c as the major fatty acids, which are consistent with the corresponding data for Alteromonas macleodii. The DNA G+C contents of strains SW-47(T) and SW-49 were 45 and 44 mol%, respectively. Strains SW-47(T) and SW-49 showed a high level of 16S rDNA sequence similarity (99.9 %) and a mean level of DNA-DNA relatedness of 96.5 %. Phylogenetic analyses based on 16S rDNA sequences showed that the two strains form a coherent cluster with A. macleodii. Strains SW-47(T) and SW-49 exhibited levels of 16S rDNA sequence similarity of 99.3 and 99.1 %, respectively, with A. macleodii DSM 6062(T) and of less than 89.4 % with other species used in the phylogenetic analyses. Alteromonas fuliginea CIP 105339(T) was found to be more closely related to the genus Pseudoalteromonas than to the genus ALTEROMONAS: On the basis of phenotypic properties and phylogenetic and genomic data, strains SW-47(T) and SW-49 represent a new species of the genus Alteromonas, for which the name Alteromonas marina (type strain SW-47(T)=KCCM 41638(T)=JCM 11804(T)) is proposed.

Rhodococcus tukisamuensis sp. nov., isolated from soil

A novel strictly aerobic, heterotrophic, mesophilic bacterium, strain Mb8(T), was isolated from soil in Sapporo City, Hokkaido, Japan. The G+C content of strain Mb8(T) was 66.0 mol%. It had mycolic acids with 44-52 carbon atoms and C16 : 0 and C18 : 1 (9) as the major fatty acids. The major isoprenoid quinone was MK-8(H(2)). The cell wall contained meso-diaminopimelic acid, arabinose and galactose. 16S rDNA, chemotaxonomic and morphological data indicated that this strain clearly belonged to the genus RHODOCOCCUS: Based on phenotypic properties and DNA-DNA hybridization data, strain Mb8(T) (=JCM 11308(T)=NCIMB 13903(T)) has been assigned to the genus Rhodococcus as the type strain of Rhodococcus tukisamuensis sp. nov.

Sporosarcina macmurdoensis sp. nov., from a cyanobacterial mat sample from a pond in the McMurdo Dry Valleys, Antarctica

Strain CMS 21w(T) was isolated from a cyanobacterial mat sample taken from a pond located in the McMurdo Dry Valleys, Antarctica. Based on its phenotypic, chemotaxonomic and phylogenetic properties, strain CMS 21w(T) was identified as a member of the genus SPOROSARCINA: At the 16S rRNA gene level, CMS 21w(T) exhibited about 93-96 % similarity to all reported species of Sporosarcina and exhibited a maximum similarity of 96 % to both Sporosarcina globispora and Sporosarcina psychrophila. Based on more than 3 % difference at the 16S rRNA gene sequence level and the presence of distinct differences with respect to phenotypic, biochemical and chemotaxonomic features, strain CMS 21w(T) (=MTCC 4670(T)=DSM 15428(T)=CIP 107784(T)) is proposed as the type strain of a novel species of Sporosarcina, Sporosarcina macmurdoensis sp. nov.

Bacillus marisflavi sp. nov. and Bacillus aquimaris sp. nov., isolated from sea water of a tidal flat of the Yellow Sea in Korea

Two Gram-positive or Gram-variable, endospore-forming, moderately halophilic rods (strains TF-11(T) and TF-12(T)) were isolated from a tidal flat of the Yellow Sea in Korea and were subjected to a polyphasic taxonomic study. Strains TF-11(T) and TF-12(T) had cell-wall peptidoglycan based on meso-diaminopimelic acid. The predominant menaquinone found in the two strains was MK-7. The cellular fatty acid profiles of both strains contained large amounts of branched and saturated fatty acids. The major fatty acids were anteiso-C(15 : 0) and iso-C(15 : 0). The DNA G+C contents of strains TF-11(T) and TF-12(T) were respectively 49 and 38 mol%. Phylogenetic analysis based on 16S rDNA sequences showed that strains TF-11(T) and TF-12(T) fell within the radiation of the cluster comprising Bacillus species. The level of 16S rDNA sequence similarity between strains TF-11(T) and TF-12(T) was 98.3 %. Strains TF-11(T) and TF-12(T) exhibited levels of 16S rDNA sequence similarity of less than 96.0 and 96.3 %, respectively, to Bacillus species. The mean level of DNA-DNA relatedness between the two strains was approximately 7 %. On the basis of phenotypic and phylogenetic data and genomic distinctiveness, strains TF-11(T) and TF-12(T) should be placed in the genus Bacillus as two distinct novel species, for which the names Bacillus marisflavi sp. nov. (type strain TF-11(T)=KCCM 41588(T)=JCM 11544(T)) and Bacillus aquimaris sp. nov. (type strain TF-12(T)=KCCM 41589(T)=JCM 11545(T)) are proposed.

Transfer of Pseudomonas elongata Humm 1946 to the genus Microbulbifer as Microbulbifer elongatus comb. nov

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 6810(T)) 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 6810(T) contained ubiquinone-8 as the predominant respiratory lipoquinone and iso-C(15 : 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.

Leifsonia rubra sp. nov. and Leifsonia aurea sp. nov., psychrophiles from a pond in Antarctica

Two unique psychrophilic strains (CMS 76rT and CMS 81yT) were isolated from a cyanobacterial mat sample from a pond in Wright Valley, McMurdo, Antarctica. Both isolates were assigned to the genus Leifsonia, since they were gram-positive, curved rods, non-motile, catalase-positive, contained DL-2,4-diaminobutyric acid, menaquinone MK-11, phosphatidylglycerol and diphosphatidylglycerol, had a high content of anteiso- and iso-branched fatty acids and had a DNA G + C content of 64-66 mol%. In addition, both isolates were related to the five reported species of Leifsonia at a level of about 95-96% 16S rDNA sequence similarity and differed from one another by 2.5%. Strains CMS 76rT and CMS 81yT also differed from one another in many other phenotypic characteristics and exhibited only 30% relatedness at the DNA-DNA level, thus indicating that they represent two different species. Furthermore, these two isolates also showed many distinct differences with respect to the reported species of Leifsonia in terms of their phenotypic characteristics, biochemical properties, chemotaxonomic features, sensitivity to various antibiotics and 16S rDNA similarity, clearly indicating that strains CMS 76rT (= MTCC 4210T = DSM 15304T = CIP 107783T) and CMS 81yT (= MTCC 4657T = DSM 15303T = CIP 107785T) represent the type strains of two novel species of Leifsonia, for which the names Leifsonia rubra sp. nov. and Leifsonia aurea sp. nov. are proposed.

Alicyclobacillus sendaiensis sp. nov., a novel acidophilic, slightly thermophilic species isolated from soil in Sendai, Japan

An acidophilic, slightly thermophilic bacterium, designated strain NTAP-1T, that produces a thermostable extracellular acid collagenase activity with potential industrial applications was isolated from soil of Aoba-yama Park, Sendai, Japan. The temperature range for growth was 40-65 degrees C, with an optimum at 55 degrees C, and the pH range for growth was 2.5-6.5, with an optimum at pH 5.5. Analysis of the 16S rDNA sequence of strain NTAP-1T showed that it is most closely related to strains of the genus Alicyclobacillus. Consistently, the major constituents of the cell-membrane lipid of strain NTAP-1T were omega-alicyclic fatty acids. However, DNA-DNA reassociation studies showed only low similarities (less than 33%) to any type strain of Alicyclobacillus. On the basis of the phenotypic and genotypic properties, a novel species is proposed, Alicyclobacillus sendaiensis sp. nov., represented by strain NTAP-1T (=JCM 11817T=ATCC BAA-609T).

Erythrobacter flavus sp. nov., a slight halophile from the East Sea in Korea

Two gram-negative, motile, non-spore-forming, yellow-pigmented and slightly halophilic strains (SW-46T and SW-52) were isolated from sea water of the East Sea, Korea, and subjected to a polyphasic taxonomic study. Strains SW-46T and SW-52 were characterized chemotaxonomically by having ubiquinone-10 (Q-10) as the predominant respiratory lipoquinone and C18:1 omega7c as the major fatty acid. Their DNA G + C content was 64.0-64.1 mol%. Strains SW-46T and SW-52 showed 1 bp difference in their 16S rDNA sequences and a mean DNA-DNA relatedness level of 94.4%. Phylogenetic analysis based on 16S rDNA sequences showed that strains SW-46T and SW-52 fall within the alpha-subclass of the Proteobacteria and form a coherent cluster with Erythrobacter longus, Erythrobacter litoralis and Erythrobacter citreus. Levels of 16S rDNA similarity between strains SW-46T and SW-52 and the type strains of these three Erythrobacter species were 96.5-97.9%. Levels of DNA-DNA relatedness between strains SW-46T and SW-52 and the type strains of E. longus, E. litoralis and E. citreus were 3.6-14.7%. Therefore, on the basis of phenotypic properties, phylogeny and genomic data, strains SW-46T and SW-52 should be placed in the genus Erythrobacter as a novel species, for which the name Erythrobacter flavus sp. nov. is proposed. The type strain is SW-46T (= KCCM 41642T = JCM 11808T).

Gemmatimonas aurantiaca gen. nov., sp. nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov

A phylogenetically novel aerobic bacterium was isolated from an anaerobic-aerobic sequential batch reactor operated under enhanced biological phosphorus removal conditions for wastewater treatment. The isolation strategy used targeted slowly growing polyphosphate-accumulating bacteria by combining low-speed centrifugations and prolonged incubation on a low-nutrient medium. The isolate, designated strain T-27T, was a gram-negative, rod-shaped aerobe. Cells often appeared to divide by budding replication. Strain T-27T grew at 25-35 degrees C with an optimum growth temperature of 30 degrees C, whilst no growth was observed below 20 degrees C or above 37 degrees C within 20 days incubation. The pH range for growth was 6.5-9.5, with an optimum at pH 7.0. Strain T-27T was able to utilize a limited range of substrates, such as yeast extract, polypepton, succinate, acetate, gelatin and benzoate. Neisser staining was positive and 4,6-diamidino-2-phenylindole-stained cells displayed a yellow fluorescence, indicative of polyphosphate inclusions. Menaquinone 9 was the major respiratory quinone. The cellular fatty acids of the strain were mainly composed of iso-C15:0, C16:1 and C14:0. The G + C content of the genomic DNA was 66 mol%. Comparative analyses of 16S rRNA gene sequences indicated that strain T-27T belongs to candidate division BD (also called KS-B), a phylum-level lineage in the bacterial domain, to date comprised exclusively of environmental 16S rDNA clone sequences. Here, a new genus and species are proposed, Gemmatimonas aurantiaca (type strain T-27T=JCM 11422T=DSM 14586T) gen. nov., sp. nov., the first cultivated representative of the Gemmatimonadetes phyl. nov. Environmental sequence data indicate that this phylum is widespread in nature and has a phylogenetic breadth (19% 16S rDNA sequence divergence) that is greater than well-known phyla such as the Actinobacteria (18% divergence).

Marinilactibacillus psychrotolerans gen. nov., sp. nov., a halophilic and alkaliphilic marine lactic acid bacterium isolated from marine organisms in temperate and subtropical areas of Japan

A novel marine lactic acid rod bacterium has been described for eight strains isolated from living and decomposing marine organisms collected from temperate and subtropical areas of Japan. The isolates were Gram-positive, catalase-negative, non-sporulating and motile with peritrichous flagella. They were slightly halophilic, highly halotolerant and alkaliphilic; the optimum NaCl concentration for growth was 2.0-3.75% (w/v) with a range from 0 to 17.0-20.5% (depending on the strain); the optimum pH was between 8.0 and 9.5 with a range from 6.0 to 10.0. They were psychrotolerant, growing well at -1.8 degrees C with a maximum at 40-45 degrees C and the optimum at 37-40 degrees C. Lactate yields were 87-100% per consumed glucose; the residual products were formate, acetate and ethanol with a molar ratio of approximately 2 : 1 : 1. The product composition was markedly affected by the pH of fermentation medium; at higher pH, the yield of lactate decreased (60-65% at pH 9.0) and that of other products increased conversely. The cell-wall peptidoglycan type was type A4beta, Orn-D-Glu, whereas that of the genus Alkalibacterium, the phylogenetically closest lactic acid bacterium, was type A4beta, Orn-D-Asp. The major cellular fatty acids were C16 : 0, C16 : 1delta9, C18 : 0 and C18 : 1delta9 (oleic acid). The G + C content of the DNA was 34.6-36.2 mol%. The eight isolates were phenotypically homogeneous and formed a single genomic species. The 16S rRNA gene sequence analysis indicated that the isolates constituted an independent phylogenetic lineage within the radiation of lactic acid bacteria with 96.2% similarity to the genus Alkalibacterium. The secondary structure and the nucleotide sequence of the V6 region of the 16S rRNA were characteristic of the organism among other related lactic acid genera. On the bases of phenotypic and phylogenetic distinctness, the organism was proposed to belong to a new genus and species, Marinilactibacillus psychrotolerans gen. nov., sp. nov. The type strain, M13-2(T) (G + C = 36.2 mol%), has been deposited in the IAM, NBRC, NCIMB and NRIC culture collections as IAM 14980(T), NBRC 100002(T), NCIMB 13873(T) and NRIC 0510(T), respectively.

Halobacillus salinus sp. nov., isolated from a salt lake on the coast of the East Sea in Korea

A Gram-positive, rod-shaped, endospore-forming, halophilic bacterium (strain HSL-3(T)) was isolated from a salt lake near Hwajinpo beach on the East Sea in Korea and was subjected to a polyphasic taxonomic study. Strain HSL-3(T) grew optimally in the presence of 2-10% (w/v) NaCl. Strain HSL-3(T) showed poor growth in the absence of NaCl and grew in the presence of less than 23% NaCl. The cell wall peptidoglycan type of strain HSL-3(T) was A4beta based on L-Orn-D-Asp. The predominant menaquinone found in strain HSL-3(T) was menaquinone-7 (MK-7). Strain HSL-3(T) had a cellular fatty acid profile containing large amounts of branched fatty acids; the major fatty acids were anteiso-C(15 : 0), iso-C(15 : 0) and iso-C(16 : 0). The DNA G + C content of strain HSL-3(T) was 45 mol%. Phylogenetic analysis based on 16S rDNA sequences showed that strain HSL-3(T) falls within the radiation of the cluster comprising Halobacillus species. Strain HSL-3(T) exhibited levels of 16S rDNA similarity of 97.4-98.4% to the type strains of Halobacillus species. Levels of DNA-DNA relatedness between strain HSL-3(T) and the type strains of all validly named Halobacillus species were in the range 7.3-9.2%. On the basis of phenotypic and phylogenetic data and the genomic distinctiveness, strain HSL-3(T) (= KCCM 41590(T) = JCM 11546(T)) should be placed in the genus Halobacillus as the type strain of a novel species, for which the name Halobacillus salinus sp. nov. is proposed.

Marinobacter lutaoensis sp. nov., a thermotolerant marine bacterium isolated from a coastal hot spring in Lutao, Taiwan

A heterotrophic and thermotolerant marine bacterium, designated strain T5054, was isolated from a hot spring on the coast of Lutao, Taiwan. It was a strictly aerobic, Gram-negative rod. Cells grown in broth cultures were non-spore-forming and motile by means of one to several polar flagella. It seems that pilus-like structures were produced from both poles of the cells. Strain T5054 required Na+ for growth and exhibited optimal growth at about 45 degrees C, pH 7, and 3-5% NaCl. It contained iso-C15:0 as the most abundant fatty acid and ubiquinone-8 as the only isoprenoid quinone. Its genomic DNA G+C content was 63.5 mol%. The strain did not require vitamins or other organic growth factors, and it grew on glucose, mannitol, and a variety of organic acids and amino acids as sole carbon sources. Characterization data, together with the results of a 16S rDNA-based phylogenetic analysis, indicated that strain T5054 could be classified as a new species in the genus Marinobacter. The name Marinobacter lutaoensis sp. nov. is proposed for this new bacterium. The type strain is T5054 (CCRC 17087; JCM 11179).

Jeotgalicoccus halotolerans gen. nov., sp. nov. and Jeotgalicoccus psychrophilus sp. nov., isolated from the traditional Korean fermented seafood jeotgal

Two Gram-positive, non-motile, non-spore-forming, halotolerant and moderately halophilic cocci (strains YKJ-101T and YKJ-115T) were isolated from the traditional Korean fermented seafood jeotgal, and were investigated using a polyphasic taxonomic approach. Phylogenetic analysis of 16S rDNA sequences showed that strains YKJ-101T and YKJ-115T are most closely related to the cluster comprising two Salinicoccus species. The peptidoglycan type of the strains is A3alpha, based on L-Lys-Gly(3-4)-L-Ala(Gly), and the predominant menaquinone is MK-7. Strains YKJ-101T and YKJ-115T have cellular fatty acid profiles containing major amounts of saturated, unsaturated and branched fatty acids; the major fatty acids are anteiso-C15 : 0 and iso-C15 : 0. The cellular polar lipids are phosphatidylglycerol, diphosphatidylglycerol and unidentified phospholipids. Strains YKJ-101T and YKJ-115T have identical DNA G + C contents of 42 mol%. The 16S rDNA similarity between strains YKJ-101T and YKJ-115T is 98% and the mean level of DNA-DNA relatedness between the two strains is 13.4%. On the basis of phenotypic and phylogenetic data and genomic distinctiveness, it is proposed that strains YKJ-101T and YKJ-115T should be placed in a new genus, Jeotgalicoccus gen. nov., as two distinct new species, for which the names Jeotgalicoccus halotolerans sp. nov. and Jeotgalicoccus psychrophilus sp. nov. are proposed. The type strains are YKJ-101T (=KCCM 41448T =JCM 11198T) and YKJ-115T (=KCCM 41449T =JCM 11199T), respectively.