- Volume 60, Issue 6, 2010

A motile, rod-shaped, yellow-pigmented bacterium, designated strain CW1T, was isolated from a water-cooling system in the Republic of Korea. Cells were Gram-stain-positive, aerobic, catalase-positive and oxidase-negative. Strain CW1T formed slender rods with unusual bulbous protuberances. The major fatty acids were iso-C16 : 1 (33.7 %), anteiso-C15 : 0 (27.2 %), iso-C14 : 0 (13.3 %) and C16 : 0 (10.8 %). The cell-wall peptidoglycan was of type B2β, containing lysine as the diamino acid. The respiratory quinones were menaquinones with 12, 13 and 14 isoprene units. A phylogenetic tree based on 16S rRNA gene sequences showed that strain CW1T formed an evolutionary lineage within the radiation enclosing members of the family Microbacteriaceae and was related to, but distant from, members of the genera Microcella and Yonghaparkia. On the basis of the evidence presented, strain CW1T is considered to represent a novel species of a new genus in the family Microbacteriaceae, for which the name Chryseoglobus frigidaquae gen. nov., sp. nov. is proposed. The type strain of Chryseoglobus frigidaquae is CW1T (=KCTC 13142T =JCM 14730T).

A Gram-stain-positive actinobacterium, designated strain YIM 93316T, was isolated from a salt lake in Xinjiang Province, north-west China, and was subjected to a polyphasic taxonomic study. The isolate grew at 10–45 °C, at pH 6–9 and in the presence of 1–15 % (w/v) NaCl, but no growth was observed in the absence of NaCl. The cell-wall diamino acid contained alanine, glutamine and lysine with peptidoglycan type A4α. Polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, an unknown glycolipid and an unknown phospholipid. The predominant menaquinone was MK-8(H4). The major fatty acids were anteiso-C15 : 0 and anteiso-C15 : 1. The DNA G+C content of strain YIM 93316T was 70.1 mol%. Chemotaxonomic properties supported the affiliation of strain YIM 93316T to the genus Georgenia, and this was supported by phylogenetic analysis based on 16S rRNA gene sequences. Levels of 16S rRNA gene sequence similarity between strain YIM 93316T and Georgenia thermotolerans TT02-04T, Georgenia ruanii YIM 004T and Georgenia muralis 1A-CT were 96.6, 96.5 and 96.3 %, respectively. Data from fatty acid, physiological and biochemical tests allowed the clear phenotypic differentiation of strain YIM 93316T from recognized members of the genus Georgenia. On the basis of evidence from the present polyphasic study, strain YIM 93316T is considered to represent a novel species of the genus Georgenia, for which the name Georgenia halophila sp. nov. is proposed. The type strain is YIM 93316T (=DSM 21365T =CCTCC AB 208144T).

Two yellow-pigmented, Gram-stain-positive, aerobic, motile, short rod-shaped bacteria were isolated from natural teak tree rhizosphere soil and their taxonomic positions were determined by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strains TG-S248T and TG-S240 formed a distinct phyletic line within the genus Leifsonia. 16S rRNA gene sequence analysis of strain TG-S248T with sequences from Leifsonia shinshuensis DB 102T, L. poae VKM Ac-1401T, L. naganoensis DB 103T, L. aquatica DSM 20146T and L. xyli subsp. cynodontis JCM 9733T revealed pairwise similarities ranging from 98.7 to 99.1 %. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The G+C content of the DNA of the type strain was 69.4 mol%. DNA–DNA hybridization experiments revealed low levels of DNA–DNA relatedness (32 % or less) between strain TG-S248T and its closest relatives. Based on differences in phenotypic and genotypic characteristics, strain TG-S248T (=LMG 24767T =JCM 15679T) is designated the type strain of a novel species of the genus Leifsonia, for which the name Leifsonia soli sp. nov. is proposed.

A novel actinomycete, strain TVU1T, was isolated from leaves of the indigenous South African plant Tulbaghia violacea. Applying a polyphasic approach, the isolate was identified as a member of the genus Micromonospora. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain TVU1T was most closely related to Micromonospora echinospora DSM 43816T. However, phylogenetic analysis based on gyrB gene sequences showed that strain TVU1T was most closely related to the type strains of Micromonospora aurantiaca and Micromonospora chalcea. DNA–DNA relatedness values between strain TVU1T and the type strains of M. echinospora, M. aurantiaca and M. chalcea were 7.6±4.5, 45.9±2.0 and 60.9±4.5 %, respectively. Strain TVU1T could be distinguished from the type strains of all three of these species by several physiological characteristics, such as colony colour, NaCl tolerance, growth temperature range and sole carbon source utilization pattern. Strain TVU1T (=DSM 45142T=NRRL B-24576T) therefore represents a novel species for which the name Micromonospora tulbaghiae sp. nov. is proposed.

A Gram-positive, non-motile and rod- or coccoid-shaped bacterial strain, MDN22T, was isolated from a soil sample from Korea. Strain MDN22T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 0–0.5 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain MDN22T was phylogenetically most closely related to the genera Nocardioides and Marmoricola. In the neighbour-joining phylogenetic tree, strain MDN22T was most closely related to Nocardioides jensenii KCTC 9134T, with which it exhibited 98.3 % 16S rRNA gene sequence similarity. The strain exhibited 93.1–96.9 % and 95.3–95.9 % 16S rRNA gene sequence similarities to the type strains of other species of the genera Nocardioides and Marmoricola, respectively. The chemotaxonomic properties of strain MDN22T were consistent with those of the genus Nocardioides; the cell-wall peptidoglycan type was based on ll-2,6-diaminopimelic acid, the predominant menaquinone was MK-8(H4) and the major fatty acids were iso-C16 : 0 and C17 : 1. The DNA G+C content was 68.7 mol%. DNA–DNA relatedness data and differential phenotypic properties suggested that strain MDN22T could be differentiated from N. jensenii and Nocardioides dubius. On the basis of the data obtained, strain MDN22T is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides daedukensis sp. nov., is proposed. The type strain is MDN22T (=KCTC 19601T=CCUG 57505T).

The species Amycolatopsis fastidiosa (ex Celmer et al. 1977) Henssen et al. 1987 was proposed, based on morphological and chemotaxonomic observations, for a strain originally described as ‘Pseudonocardia fastidiosa’ Celmer et al. 1977 in a US patent. In the course of a phylogenetic study of the taxa with validly published names within the suborder Pseudonocardineae based on 16S rRNA gene sequences, it became apparent that this species was misplaced in the genus Amycolatopsis. After careful evaluation of the phylogeny, morphology, chemotaxonomy and physiology of the type strain, it was concluded that this strain represents a species of the genus Actinokineospora that is unable to produce motile spores. The description of the genus Actinokineospora is therefore emended to accommodate species that do not produce motile spores, and it is proposed that Amycolatopsis fastidiosa be transferred to the genus Actinokineospora as Actinokineospora fastidiosa comb. nov. The type strain is NRRL B-16697T =ATCC 31181T =DSM 43855T =JCM 3276T =NBRC 14105T =VKM Ac-1419T.

Two extremely halophilic archaea, strains RO2-11T and HO2-1, were isolated from two Chinese marine solar salterns, Rudong solar saltern and Haimen solar saltern, respectively. Cells of the two strains were polymorphic and Gram-stain-negative; colonies were red-pigmented. The two strains grew at NaCl concentrations of 2.6–4.3 M (optimum 3.9 M) and required at least 0.1 M Mg2+ for growth. They were able to grow over a pH range of 6.0–8.0 and a temperature range of 20–50 °C, with optimal pH of 7.5 and optimal temperature of 37 °C. The major polar lipids of strain RO2-11T and strain HO2-1 were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and three glycolipids, two of them chromatographically identical to S-DGD-1 and DGD-1, the third unidentified. The 16S rRNA gene sequence similarity of strain RO2-11T and strain HO2-1 was 99.3 % and highest sequence similarity with the closest relative (Haloferax larsenii) was 91.4 %. Based on the data obtained, the two isolates could not be classified in any recognized genus of the family Halobacteriaceae. Strain RO2-11T and strain HO2-1 are thus considered to represent a novel species of a new genus within the family Halobacteriaceae, for which the name Halogranum rubrum gen. nov., sp. nov. is proposed. The type strain is RO2-11T (=CGMCC 1.7738T =JCM 15772T).

Two anaerobic, non-spore-forming, non-motile, Gram-negative-staining bacteria, strains YIT 12060T and YIT 12061T, were isolated from human faeces. Cells of strain YIT 12060T were coccoid to rod-shaped with round ends, positive for catalase, negative for indole and oxidase production, produced succinic and acetic acids as end products of glucose metabolism in peptone/yeast extract/glucose medium and had a DNA G+C content of 55.2 mol%. The main respiratory quinones were MK-10 (40 %) and MK-11 (57 %). Fatty acid analysis demonstrated the presence of a high concentration of iso-C15 : 0 (56 %). Following 16S rRNA gene sequence analysis, this strain was found to be most closely related to species of the genus Alistipes, with 90.9–92.6 % gene sequence similarities to type strains of this species. Phylogenetic analysis and biochemical data supported the affiliation of strain YIT 12060T to the genus Alistipes of the family ‘Rikenellaceae’. Strain YIT 12060T therefore represents a novel species of the genus Alistipes for which the name Alistipes indistinctus sp. nov. is proposed; the type strain is YIT 12060T (=DSM 22520T=JCM 16068T). Cells of the other isolate, strain YIT 12061T, were pleomorphic rods that were asaccharolytic, catalase- and oxidase-negative, positive for gelatin hydrolysis and indole production, produced small amounts of succinic, acetic and iso-valeric acids as end products of metabolism in peptone/yeast extract medium and had a DNA G+C content of approximately 42.4 mol%. On the basis of 16S rRNA gene sequence similarity values, this strain was shown to belong to the family ‘Porphyromonadaceae’ and related to the type strains of Odoribacter splanchnicus (89.6 %) and Odoribacter denticanis (86.2 %); similarity values with strains of recognized species within the family ‘Porphyromonadaceae’ were less than 84 %. Biochemical data supported the affiliation of strain YIT 12061T to the genus Odoribacter. Strain YIT 12061T therefore represents a novel species for which the name Odoribacter laneus sp. nov. is proposed; the type strain is YIT 12061T (=DSM 22474T=JCM 16069T).

Four Gram-stain-positive, aerobic or facultatively anaerobic, motile, endospore-forming, rod-shaped bacteria, designated strains FeL05T, FeL11, Fek19 and Fek21, were isolated from seeds of hybrid rice (Oryza sativa L. Jinyou 611), and their taxonomic positions were determined using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that the four strains were members of the genus Paenibacillus. They showed 95.4 % sequence similarity or less with strains of other Paenibacillus species. The G+C content of strain FeL05T was found to be 53.3 mol%. Its predominant respiratory quinone was MK-7. The predominant cellular fatty acids were anteiso-C15 : 0 (61.7 %), C16 : 0 (10.9 %), iso-C16 : 0 (7.0 %), anteiso-C17 : 0 (6.7 %) and iso-C15 : 0 (5.2 %). On the basis of its phenotypic properties and phylogenetic distinctiveness, strain FeL05T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus hunanensis sp. nov. is proposed. The type strain is strain FeL05T (=ACCC 10718T =CGMCC 1.8907T =DSM 22170T).

Three strains of a hitherto unknown, Gram-negative, tiny, anaerobic coccus were collected from human clinical samples originating from skin and soft tissues. The three isolates displayed at least 99.9 % identity in their 16S rRNA gene sequences and more than 99.8 % identity in their dnaK gene sequences. The isolates were affiliated to the family Veillonellaceae, the coccobacillus Dialister micraerophilus being the most closely related species, but there was no more than 91.1 % identity in the 16S rRNA gene sequence between this species and the three isolates. Phylogeny based on the 16S rRNA gene confirmed that the three strains represent a novel and robust lineage within the current family Veillonellaceae. A similar genomic structure was demonstrated for the three isolates by PFGE-based analysis. Morphology and metabolic end products, as well as genotypic and phylogenetic data supported the proposal of the novel genus Negativicoccus gen. nov., with the novel species Negativicoccus succinicivorans sp. nov. [type strain ADV 07/08/06-B-1388T (=AIP 149.07T=CIP 109806T=DSM 21255T=CCUG 56017T) as type species]. Phylogenetic analyses based on the 16S rRNA gene sequences of members of the phylum Firmicutes and other phyla indicated that the family Veillonellaceae forms a robust lineage clearly separated from those of the classes ‘Bacilli’, ‘Clostridia’, Thermolithobacteria and ‘Erysipelotrichi’ in the phylum Firmicutes. Therefore, we propose that this family is a class-level taxon in the phylum Firmicutes, for which the name Negativicutes classis nov. is proposed, based on the Gram-negative type of cell wall of its members, with the type order Selenomonadales ord. nov. In this order, a novel family, Acidaminococcaceae fam. nov., is proposed and description of the family Veillonellaceae is emended.

Four isolates (FSL S4-120T, FSL S4-696, FSL S4-710, and FSL S4-965) of Gram-positive, motile, facultatively anaerobic, non-spore-forming bacilli that were phenotypically similar to species of the genus Listeria were isolated from soil, standing water and flowing water samples obtained from the natural environment in the Finger Lakes National Forest, New York, USA. The four isolates were closely related to one another and were determined to be the same species by whole genome DNA–DNA hybridization studies (>82 % relatedness at 55 °C and >76 % relatedness at 70 °C with 0.0–0.5 % divergence). 16S rRNA gene sequence analysis confirmed their close phylogenetic relatedness to Listeria monocytogenes and Listeria innocua and more distant relatedness to Listeria welshimeri, L. seeligeri, L. ivanovii and L. grayi. Phylogenetic analysis of partial sequences for sigB, gap, and prs showed that these isolates form a well-supported sistergroup to L. monocytogenes. The four isolates were sufficiently different from L. monocytogenes and L. innocua by DNA–DNA hybridization to warrant their designation as a new species of the genus Listeria. The four isolates yielded positive reactions in the AccuProbe test that is purported to be specific for L. monocytogenes, did not ferment l-rhamnose, were non-haemolytic on blood agar media, and did not contain a homologue of the L. monocytogenes virulence gene island. On the basis of their phenotypic characteristics and their genotypic distinctiveness from L. monocytogenes and L. innocua, the four isolates should be classified as a new species within the genus Listeria, for which the name Listeria marthii sp. nov. is proposed. The type strain of L. marthii is FSL S4-120T (=ATCC BAA-1595T =BEIR NR 9579T =CCUG 56148T). L. marthii has not been associated with human or animal disease at this time.

A Gram-stain-positive, oxidase- and catalase-positive, non-motile, non-spore-forming, halotolerant, coccoid bacterium, designated strain NY-2T, was isolated from a seaside soil sample from Shandong Province, China. Strain NY-2T was able to grow in the presence of 0–23 % (w/v) NaCl and at pH 4.5–10.0 and 5–42 °C; optimum growth was observed with 3–8 % (w/v) total salts and at pH 6.5–8.0 and 28–37 °C. Chemotaxonomic analyses, including fatty acid profiles, menaquinones and polar lipids, supported the affiliation of strain NY-2T to the genus Jeotgalicoccus. The predominant menaquinone of strain NY-2T was menaquinone 7 (MK-7) (100 %) and the major cellular fatty acids were iso-C15 : 0 (49.0 %) and anteiso-C15 : 0 (19.6 %). Cellular polar lipids were phosphatidylglycerol, diphosphatidylglycerol and several unidentified phospholipids. The DNA G+C content of strain NY-2T was 36.8 mol%. Based on 16S rRNA gene sequence analysis, strain NY-2T formed a coherent cluster with Jeotgalicoccus marinus JSM 076033T, Jeotgalicoccus halotolerans YKJ-101T and Jeotgalicoccus psychrophilus YKJ-115T. Phylogenetic analysis, DNA–DNA relatedness data, phenotypic characteristics and chemotaxonomic data indicated that strain NY-2T (=CCTCC AB 208288T =JCM 15687T) should be classified as the type strain of a novel species of the genus Jeotgalicoccus, for which the name Jeotgalicoccus huakuii sp. nov. is proposed.

A Gram-stain-positive, rod-shaped, endospore-forming, halophilic, alkalitolerant bacterium, designated halo-1T, was isolated from sediment of Xiarinaoer soda lake, located in the Inner Mongolia Autonomous Region of China. Strain halo-1T grew in the presence of 9–30 % (w/v) NaCl (optimum 19 %) and at pH 5–10 (optimum pH 9). The cell-wall peptidoglycan contained meso-diaminopimelic acid and the major respiratory isoprenoid quinone was MK-7. The predominant cellular fatty acids of the isolate were anteiso-C15 : 0 (58.35 %), anteiso-C17 : 0 (12.89 %) and C16 : 0 (6.52 %). The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, glycolipid and a phospholipid of unknown structure. The DNA G+C content of the strain was 46.4 mol%. On the basis of 16S rRNA gene sequence similarity, strain halo-1T showed the highest similarity (93.9 %) to Salsuginibacillus kocurii CH9dT. Strain halo-1T could be clearly differentiated from its closest phylogenetic relative on the basis of several phenotypic, genotypic and chemotaxonomic features. Therefore, strain halo-1T represents a novel species, for which the name Salsuginibacillus halophilus sp. nov. is proposed, with the type strain halo-1T (=CGMCC 1.7653T =NBRC 104934T).

A novel xylan-degrading bacterium, YT-1101T, was isolated from fresh water. The isolate was a Gram-reaction-negative, aerobic, motile, endospore-forming and rod-shaped bacterium. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain YT-1101T belonged to the genus Cohnella, sharing sequence similarities of less than 94 % with the type species. The genomic G+C content was 58.6 mol%. The predominant menaquinone was MK-7. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and iso-C15 : 0. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. On the basis of morphological, physiological and phylogenetic properties, strain YT-1101T represents a novel species of the genus Cohnella, for which the name Cohnella fontinalis sp. nov. is proposed. The type strain is YT-1101T (=NBRC 104957T =DSM 21753T).

The taxonomic position of a Gram-stain-positive, endospore-forming, halophilic strain, designated CAU 348T, isolated from sea sand was investigated using a polyphasic approach. Colony morphology, biochemical tests and chemotaxonomic investigations revealed that strain CAU 348T had the characteristics of the genus Bacillus. Comparative 16S rRNA gene sequence analysis showed that the organism formed a hitherto unknown subline within the genus Bacillus. Sequence divergence values of more than 4.3 % from other described Bacillus species, together with phenotypic differences, showed that the unidentified bacterium represents a previously unrecognized member of this genus. The genotypic and phenotypic data indicated that strain CAU 348T represents a novel species of the genus Bacillus, for which the name Bacillus chungangensis sp. nov. is proposed. The type strain is CAU 348T (=KCTC 13566T =CCUG 57835T).

The taxonomic positions of two Gram-positive, endospore-forming rods, strains CCUG 53915T and CCUG 53480T, isolated from an industrial clean-room floor and from a human blood sample, respectively, were studied. 16S rRNA gene sequence similarity studies revealed that both isolates clearly clustered with Sporosarcina species. Strain CCUG 53915T was most closely related to Sporosarcina koreensis and Sporosarcina soli, showing 99.4 and 99.2 % 16S rRNA gene sequence similarities to the type strains of these species, respectively. Strain CCUG 53480T showed the highest 16S rRNA gene sequence similarities to the type strains of S. koreensis (98.7 %) and Sporosarcina saromensis (98.6 %). Strains CCUG 53915T and CCUG 53480T had peptidoglycan type A4α l-Lys–d-Glu. The quinone systems of both strains were composed predominantly of menaquinone MK-7, with small amounts of MK-8. The polar lipid profiles of both strains consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and three unidentified phospholipids. The fatty acid profiles, which comprise anteiso- and iso-branched fatty acids, supported affiliation of the two isolates to the genus Sporosarcina. The results of physiological and biochemical tests and DNA–DNA hybridization data allowed a clear phenotypic and genotypic differentiation of both strains from the most closely related Sporosarcina species. For this reason, it is proposed that strains CCUG 53915T (=DSM 22204T) and CCUG 53480T (=DSM 22203T) represent two novel species in the genus Sporosarcina, with the names Sporosarcina contaminans sp. nov. and Sporosarcina thermotolerans sp. nov., respectively.

An anaerobic thermophilic bacterium, strain K67T, was isolated from a terrestrial hot spring of Uzon Caldera, Kamchatka Peninsula. Analysis of the 16S rRNA gene sequence revealed that the novel isolate belongs to the genus Caldanaerobacter, with 95 % 16S rRNA gene sequence similarity to Caldanaerobacter subterraneus subsp. subterraneus SEBR 7858T, suggesting that it represents a novel species of the genus Caldanaerobacter. Strain K67T was characterized as an obligate anaerobe, a thermophile (growth at 50–75 °С; optimum 68–70 °C), a neutrophile (growth at pH25 °C 4.8–8.0; optimum pH25 °C 6.8) and an obligate organotroph (growth by fermentation of various sugars, peptides and polysaccharides). Major fermentation products were acetate, H2 and CO2; ethanol, lactate and l-alanine were formed in smaller amounts. Thiosulfate stimulated growth and was reduced to hydrogen sulfide. Nitrate, sulfate, sulfite and elemental sulfur were not reduced and did not stimulate growth. Thus, according to the strain's phylogenetic position and phenotypic novelties (lower upper limit of temperature range for growth, the ability to grow on arabinose, the inability to reduce elemental sulfur and the formation of alanine as a minor fermentation product), the novel species Caldanaerobacter uzonensis sp. nov. is proposed, with the type strain K67T (=DSM 18923T =VKM В-2408T).

A Gram-stain-positive, halotolerant, neutrophilic, rod-shaped bacterium, strain MF38T, was isolated from a saline–alkaline soil in China and subjected to a polyphasic taxonomic characterization. The isolate grew in the presence of 0–15 % (w/v) NaCl and at pH 6.5–8.5; optimum growth was observed with 3.0 % (w/v) NaCl and at pH 7.0. Chemotaxonomic analysis showed menaquinone MK-7 as the predominant respiratory quinone and anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, C17 : 0 and C16 : 0 as major fatty acids. The genomic DNA G+C content was 35.3 mol%. 16S rRNA gene sequence similarities of strain MF38T with type strains of described Gracilibacillus species ranged from 95.3 to 97.7 %. Strain MF38T exhibited the closest phylogenetic affinity to the type strain of Gracilibacillus dipsosauri, with 97.7 % 16S rRNA gene sequence similarity. The DNA–DNA reassociation between strain MF38T and G. dipsosauri DSM 11125T was 45 %. On the basis of phenotypic and genotypic data, strain MF38T represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus ureilyticus sp. nov. (type strain MF38T =CGMCC 1.7727T =JCM 15711T) is proposed.