- Volume 62, Issue Pt_11, 2012

A novel actinomycete strain, designated YIM 75904T, was isolated from a soil sample that had been collected from a dry and hot river valley in Dongchuan county, Yunnan province, south-western China. The taxonomic position of the novel strain was investigated by a polyphasic approach. In phylogenetic analyses based on 16S rRNA gene sequences, strain YIM 75904T formed a distinct clade within the genus Amycolatopsis and appeared to be closely related to Amycolatopsis sacchari K24T (99.3 % sequence similarity). Strain YIM 75904T had a type-IV cell wall, with no detectable mycolic acids, and had MK-9(H4) as its predominant menaquonine. Its cell wall contained meso-diaminopimelic acid, galactose, glucose and arabinose, and its major cellular fatty acids were iso-C16 : 0, iso-C15 : 0, anteiso-C17 : 0 and anteiso-C15 : 0. The genomic DNA G+C content of the novel strain was 68.5 mol%. Based on the results of physiological and biochemical tests and DNA–DNA hybridizations, strain YIM 75904T represents a novel species of the genus Amycolatopsis for which the name Amycolatopsis dongchuanensis sp. nov. is proposed. The type strain is YIM 75904T ( = CCTCC AA 2011016T  = JCM 18054T).

A Gram-positive rod, designated 01-Gi-001T, was isolated from a wall colonized with moulds. The 16S rRNA gene sequence analysis clearly showed that the isolate belonged to the genus Microbacterium . On the basis of pairwise comparisons of 16S rRNA gene sequences, strain 01-Gi-001T was most closely related to Microbacterium hydrocarbonoxydans DSM 16089T (98.9 % sequence similarity), Microbacterium profundi Shh49T (98.7 %), Microbacterium phyllosphaerae DSM 13468T (98.3 %) and Microbacterium foliorum DSM 12966T (98.1 %). The diagnostic diamino acid of the peptidoglycan was ornithine. The major menaquinones detected were MK-13 and MK-12. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, one unknown phospholipid and one unknown glycolipid. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0, which were in agreement with those reported for other members of the genus Microbacterium . Physiological and biochemical characteristics and DNA–DNA relatedness between strain 01-Gi-001T and the type strains of its closest phylogenetic neighbours showed clear differences. For this reason, strain 01-Gi-001T ( = DSM 22178T = CCM 7640T) is proposed as the type strain of a novel species, Microbacterium murale sp. nov.

The taxonomic position of a Streptomyces strain isolated from an extreme hyper-arid soil sample collected from the Atacama Desert was determined using a polyphasic approach. The strain, isolate C60T, had chemical and morphological features typical of members of the genus Streptomyces and formed a distinct phyletic line in the Streptomyces 16S rRNA gene tree, together with the type strain of Streptomyces radiopugnans . The two strains were distinguished readily using a combination of phenotypic properties and by a DNA–DNA relatedness value of 23.17 (±0.95) %. On the basis of these genotypic and phenotypic data, it is proposed that isolate C60T ( = CGMCC 4.7018T = KACC 15492T) be classified in the genus Streptomyces as Streptomyces atacamensis sp. nov.

A novel Gram-stain-positive, aerobic, rod-shaped bacterium, designated strain D94-1T, was isolated from soil collected in Liancheng county, Fujian province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain D94-1T was a member of the genus Nocardioides and was most closely related to Nocardioides salarius DSM 18239T (98.54 % 16S rRNA gene sequence similarity), Nocardioides marinisabuli DSM 18965T (98.30 %), Nocardioides basaltis KCTC 19365T (98.10 %) and Nocardioides dokdonensis KCTC 19309T (97.76 %). Phenotypic characteristics and DNA–DNA relatedness data served to distinguish strain D94-1T from N. salarius , N. marinisabuli , N. basaltis and N. dokdonensis . The chemotaxonomic properties of strain D94-1T were consistent with those of the genus Nocardioides : the cell-wall peptidoglycan type was based on ll-diaminopimelic acid, the predominant menaquinone was MK-8(H4) and the major fatty acids were iso-C16 : 0 (29.15 %) and anteiso-C17 : 0 (21.0 %). The DNA G+C content was 71.8 mol%. On the basis of the evidence presented in this study, strain D94-1T represents a novel species of the genus Nocardioides , for which the name Nocardioides lianchengensis sp. nov. is proposed. The type strain is D94-1T ( = DSM 24663T = CGMCC 4.6858T).

A Gram-stain-positive, strictly aerobic, short-rod-shaped, non-motile strain (designated MJ32T) was isolated from a sludge sample of the Daejeon sewage disposal plant in South Korea. A polyphasic approach was applied to study the taxonomic position of strain MJ32T. Strain MJ32T showed highest 16S rRNA gene sequence similarity to Gordonia hirsuta DSM 44140T (98.1 %) and Gordonia hydrophobica DSM 44015T (97.0 %); levels of sequence similarity to the type strains of other recognized Gordonia species were less than 97.0 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MJ32T belonged to the clade formed by members of the genus Gordonia in the family Gordoniaceae . The G+C content of the genomic DNA of strain MJ32T was 69.2 mol%. Chemotaxonomically, strain MJ32T showed features typical of the genus Gordonia . The predominant respiratory quinone was MK-9(H2), the mycolic acids present had C56–C60 carbon atoms, and the major fatty acids were C16 : 0 (34.6 %), tuberculostearic acid (21.8 %), C16 : 1ω7c (19.5 %) and C18 : 1ω9c (12.7 %). The peptidoglycan type was based on meso-2,6-diaminopimelic acid as the diagnostic diamino acid with glycolated sugars. On the basis of phylogenetic inference, fatty acid profile and other phenotypic properties, strain MJ32T is considered to represent a novel species of the genus Gordonia , for which the name Gordonia caeni sp. nov. is proposed. The type strain is MJ32T ( = KCTC 19771T = JCM 16923T).

A novel actinobacterium, designated strain YIM 100590T, was isolated from Panthera tigris amoyensis faeces collected from Yunnan Wild Animal Park in Yunnan province, south-west China. Phylogenetic analysis based on 16S rRNA gene sequence data showed that strain YIM 100590T is a member of the family Micrococcaceae . Cells were coccoid to oval (0.7–1.5 µm in diameter) occurring singly or in clusters. Growth was observed at 10–37 °C (optimum 28 °C) and at pH 7.0–11.0 (optimum pH 8.0). The major fatty acids were iso-C15 : 0 (32.22 %), anteiso-C15 : 0 (31.64 %) and iso-C16 : 0 (17.38 %). The peptidoglycan was of A4α type (l-Lys–Gly–l-Glu). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, dimannosyl diacylglycerol, an unknown glycolipid and two unknown phospholipids. The quinone system comprised menaquinones MK-7 (91.9 %) and MK-8 (8.3 %). The DNA G+C content of strain YIM 100590T was 56.2 mol%. Chemotaxonomic data indicated that the strain belongs to the family Micrococcaceae . On the basis of morphological and chemotaxonomic data and phylogenetic analysis, strain YIM 100590T is considered to represent a novel species of a new genus within the family Micrococcaceae , for which the name Enteractinococcus coprophilus gen. nov., sp. nov. is proposed. The type strain of Enteractinococcus coprophilus is YIM 100590T ( = DSM 24083T = JCM 17352T). Yaniella fodinae DSM 22966T was transferred to the new genus as Enteractinococcus fodinae comb. nov. (type strain G5T = DSM 22966T = JCM 17931T = MTCC 9846T).

An actinomycete strain, designated K09-0627T, was isolated from the roots of an orchid collected in Okinawa Prefecture, Japan. Two actinomycete strains K11-0047T and K11-0057T were isolated from the roots of Rumex acetosa and Houttuynia cordata collected in Kanagawa Prefecture, Japan. 16S rRNA gene sequence analyses indicated that the isolates belonged to the genus Phytohabitans, and that they were closely related to each other and to Phytohabitans suffuscus K07-0523T. The DNA–DNA relatedness values between the three isolates and Phytohabitans suffuscus were below 70 %. On the basis of phylogenetic analysis, DNA–DNA relatedness values and phenotypic characteristics, the strains should be classified as novel species in the genus Phytohabitans , for which the names Phytohabitans flavus sp. nov. (type strain, K09-0627T = JCM 17387T = NBRC 107702T = DSM 45551T), Phytohabitans rumicis sp. nov. (type strain, K11-0047T = JCM 17829T = NBRC 108638T = BCC 48146T) and Phytohabitans houttuyneae sp. nov. (type strain, K11-0057T = JCM 17830T = NBRC 108639T = BCC 48147T) are proposed.

A Gram-type positive, Gram-reaction variable, non-motile, psychrophilic actinobacterium, designated Cr8-25T, was isolated from alpine glacier cryoconite and was able to grow well over a temperature range of 1–15 °C. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Cr8-25T belonged to the family Microbacteriaceae and showed highest 16S rRNA gene sequence similarity with Klugiella xanthotipulae 44C3T (97.0 %). However, strain Cr8-25T could be differentiated from the type strain of K. xanthotipulae on the level of genomospecies by a DNA–DNA relatedness value of only 37.2 %. Strain Cr8-25T contained a cell-wall peptidoglycan that was cross-linked according to the B-type, which is based on 2,4-diaminobutyric acid. The cell wall contained the sugars galactose, fucose and rhamnose. The predominant cellular fatty acids of strain Cr8-25T were C15 : 0 anteiso (64.6 %) and iso-C16 : 0 (22.5 %) and the major menaquinones were MK-11 and MK-10. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and unknown glycolipids. The G+C content of the genomic DNA was 58.8 mol%. On the basis of the phenotypic characteristics, phylogenetic and chemotaxonomic analyses and DNA–DNA relatedness data, strain Cr8-25T represents a novel species of a new genus in the family Microbacteriaceae , for which the name Alpinimonas psychrophila gen. nov., sp. nov. is proposed. The type strain is Cr8-25T ( = DSM 23737T = LMG 26215T).

An actinobacterial strain, designated D48T, was isolated from the rhizosphere soil of a cypress tree collected from Mianyang in Sichuan province, China. The strain was Gram-stain-positive, catalase-positive, oxidase-negative and non-motile, with lysine as the peptidoglycan diagnostic diamino acid and acetyl as the peptidoglycan acyl type. The predominant menaquinone was MK-9(H2); small amounts of MK-7(H2), MK-10(H2) and MK-6 were also present. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The isolate underwent a rod–coccus morphological cycle, had a high DNA G+C content, was aerobic and grew between 12 and 37 °C (optimum, 28 °C). On the basis of the phenotypic and chemotaxonomic analyses, 16S rRNA gene sequence comparisons and DNA–DNA hybridization data, the isolate represents a novel species of the genus Arthrobacter , for which the name Arthrobacter cupressi sp. nov. is proposed. The type strain is D48T ( = DSM 24664T = CGMCC 1.10783T).

Although four strains of bacteria isolated from sunki, a traditional Japanese, non-salted pickle, were initially identified as Lactobacillus delbrueckii , the molecular and phenotypic characteristics of the strains did not match those of any of the four recognized subspecies of L. delbrueckii . Together, the results of phenotypic characterization, DNA–DNA hybridizations (in which the relatedness values between the novel strains and type strains of the recognized subspecies of L. delbrueckii were all >88.7 %) and 16S rRNA gene sequence, amplified fragment length polymorphism (AFLP) and whole-cell MALDI-TOF/MS spectral pattern analyses indicated that the four novel strains represented a single, novel subspecies, for which the name Lactobacillus delbrueckii subsp. sunkii subsp. nov. is proposed. The type strain is YIT 11221T ( = JCM 17838T  = DSM 24966T).

Two novel obligately anaerobic, Gram-stain-positive, saccharolytic and non-proteolytic spore-forming bacilli (strains CD3 : 22T and N1T) are described. Strain CD3 : 22T was isolated from a biopsy of the small intestine of a child with coeliac disease, and strain N1T from the saliva of a healthy young man. The cells of both strains were observed to be filamentous, approximately 5 to >20 µm long, some of them curving and with swellings. The novel organisms produced H2S, NH3, butyric acid and acetic acid as major metabolic end products. Phylogenetic analyses, based on comparative 16S rRNA gene sequencing, revealed close relationships (98 % sequence similarity) between the two isolates, as well as the type strain of Eubacterium saburreum and four other Lachnospiraceae bacterium-/ E. saburreum -like organisms. This group of bacteria were clearly different from any of the 19 known genera in the family Lachnospiraceae . While Eubacterium species are reported to be non-spore-forming, reanalysis of E. saburreum CCUG 28089T confirmed that the bacterium is indeed able to form spores. Based on 16S rRNA gene sequencing, phenotypic and biochemical properties, strains CD3 : 22T and N1T represent novel species of a new and distinct genus, named Lachnoanaerobaculum gen. nov., in the family Lachnospiraceae [within the order Clostridiales , class Clostridia , phylum Firmicutes ]. Strain CD3 : 22T ( = CCUG 58757T  = DSM 23576T) is the type strain of the type species, Lachnoanaerobaculum umeaense gen. nov., sp. nov., of the proposed new genus. Strain N1T ( = CCUG 60305T = DSM 24553T) is the type strain of Lachnoanaerobaculum orale sp. nov. Moreover, Eubacterium saburreum is reclassified as Lachnoanaerobaculum saburreum comb. nov. (type strain CCUG 28089T  = ATCC 33271T  = CIP 105341T  = DSM 3986T  = JCM 11021T  = VPI 11763T).

A novel Gram-stain-positive, moderately halophilic bacterium, designated strain P4BT, was isolated from water of the hypersaline Aran-Bidgol lake in Iran and characterized taxonomically by using a polyphasic approach. Cells of strain P4BT were non-motile rods producing ellipsoidal endospores at a central position in non-swollen sporangia. Strain P4BT was strictly aerobic and catalase- and oxidase-positive. It was able to grow at NaCl concentrations of 0.5–12.5 % (w/v), with optimum growth occurring at 5–7.5 % (w/v) NaCl. The optimum temperature and pH for growth were 35 °C and pH 7.0. On the basis of 16S rRNA gene sequence analysis, strain P4BT was shown to belong to the phylum Firmicutes and shared highest similarity with Bacillus persepolensis HS136T (97.1 %) and Bacillus salarius BH169T (95.1 %). However, it shared only 91.3 % 16S rRNA gene sequence similarity with Bacillus subtilis subsp. subtilis DSM 10T, indicating that strain P4BT might not be a member of the genus Bacillus . The DNA G+C content of this new isolate was 38.9 mol%. DNA–DNA hybridization experiments revealed a low level of relatedness between strain P4BT and B. persepolensis HS136T (6 %). The major cellular fatty acids of strain P4BT were iso-C15 : 0 and anteiso-C15 : 0, as for B. persepolensis HS136T but in contrast to B. salarius DSM 16461T and B. subtilis subsp. subtilis DSM 10T. Its polar lipid pattern consisted of phosphatidylglycerol, an aminoglycolipid and an unknown phospholipid. This polar lipid profile was similar to that obtained for B. persepolensis DSM 21632T but different from those of B. salarius DSM 16461T and B. subtilis subsp. subtilis DSM 10T. The isoprenoid quinones were MK-7 (88 %) and MK-8 (2 %). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. All these features indicate placement of strain P4BT within the Firmicutes , closely related to B. persepolensis but with features clearly distinct from those of the genus Bacillus and other related genera. On the basis of these data, strain P4BT is considered to represent a novel species of a new genus, for which the name Alteribacillus bidgolensis gen. nov., sp. nov. is proposed. The type strain of Alteribacillus bidgolensis is P4BT ( = CCM 7963T = CECT 7998T = DSM 25260T = IBRC-M 10614T = KCTC 13821T). It is also suggested to transfer B. persepolensis to this new genus, as Alteribacillus persepolensis comb. nov. The type strain of Alteribacillus persepolensis is HS136T ( = CCM 7595T = DSM 21632T = JCM 15720T = LMG 25222T).

A total of 27 bacterial isolates from California sea lions and a walrus tentatively classified within the family Pasteurellaceae was further characterized by genotypic and phenotypic tests. Phylogenetic analysis of partial 16S rRNA and rpoB gene sequences showed that the isolates investigated formed a monophyletic group, tentatively designated Bisgaard taxon 57. According to 16S rRNA gene sequences, the most closely related species with a validly published name was Bisgaardia hudsonensis and the most closely related species based on rpoB sequence comparison was Pasteurella multocida subsp. multocida; highest similarities between the isolates and the type strains of B. hudsonensis and P. multocida subsp. multocida were 95.0 and 88.2%. respectively. All isolates of Bisgaard taxon 57 exhibit the phenotypic characters of the family Pasteurellaceae . Members of Bisgaard taxon 57 can be separated from existing genera of the Pasteurellaceae by the following tests: positive reactions for catalase, oxidase, Voges–Proskauer and indole; no X- or V-factor dependency; and acid production from l-arabinose (slow), l-fucose, maltose and trehalose, but not from dulcitol, d-mannitol, d-mannose or sucrose. The main fatty acids of Bisgaard taxon 57 (CCUG 59994T) are C14 : 0, C16 : 0, C16 : 1ω7c and the summed feature C14 : 0 3-OH/iso-C16 : 1 I. This fatty acid profile is characteristic of members of the Pasteurellaceae . The quinone profile of Bisgaard taxon 57 (DSM 23800T) was similar to that of other genera in the Pasteurellaceae . The DNA G+C content of strain Baika1T is 36.2 mol%, which is at the lower end of the range for members of the family Pasteurellaceae . On the basis of both phylogenetic and phenotypic evidence, it is proposed that members of Bisgaard taxon 57 should be classified as representatives of a novel species in a new genus, Otariodibacter oris gen. nov., sp. nov. The type strain of Otariodibacter oris is Baika1T ( = CCUG 59994T = DSM 23800T), which was isolated from the oral cavity of a healthy California sea lion in Copenhagen Zoo, Denmark, in 2007.

Strains of Gram-negative, rod-shaped, non-spore-forming bacteria were isolated from nitrogen-fixing nodules of the native legumes Listia angolensis (from Zambia) and Lupinus texensis (from Texas, USA). Phylogenetic analysis of the 16S rRNA gene showed that the novel strains belong to the genus Microvirga , with ≥96.1 % sequence similarity with type strains of this genus. The closest relative of the representative strains Lut6T and WSM3557T was Microvirga flocculans TFBT, with 97.6–98.0 % similarity, while WSM3693T was most closely related to Microvirga aerilata 5420S-16T, with 98.8 % similarity. Analysis of the concatenated sequences of four housekeeping gene loci (dnaK, gyrB, recA and rpoB) and cellular fatty acid profiles confirmed the placement of Lut6T, WSM3557T and WSM3693T within the genus Microvirga . DNA–DNA relatedness values, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of Lut6T, WSM3557T and WSM3693T from each other and from other Microvirga species with validly published names. The nodA sequence of Lut6T was placed in a clade that contained strains of Rhizobium , Mesorhizobium and Sinorhizobium , while the 100 % identical nodA sequences of WSM3557T and WSM3693T clustered with Bradyrhizobium , Burkholderia and Methylobacterium strains. Concatenated sequences for nifD and nifH show that the sequences of Lut6T, WSM3557T and WSM3693T were most closely related to that of Rhizobium etli CFN42T nifDH. On the basis of genotypic, phenotypic and DNA relatedness data, three novel species of Microvirga are proposed: Microvirga lupini sp. nov. (type strain Lut6T  = LMG 26460T  = HAMBI 3236T), Microvirga lotononidis sp. nov. (type strain WSM3557T  = LMG 26455T  = HAMBI 3237T) and Microvirga zambiensis sp. nov. (type strain WSM3693T  = LMG 26454T  = HAMBI 3238T).

A pink-pigmented, facultatively methylotrophic bacterium, strain 23eT, was isolated from the leaves of Gnaphalium spicatum (cudweed). The cells of strain 23eT were Gram-reaction negative, motile and non-spore-forming rods. On the basis of 16S rRNA gene sequence similarities, strain 23eT was related to Methylobacterium organophilum ATCC 27886T (97.1 %) and Methylobacterium marchantiae JT1T (97 %), and the phylogenetic similarities to all other Methylobacterium species with validly published names were less than 97 %. Major cellular fatty acids were C18 : 1ω7c, C16 : 00 and C18 : 0. The results of DNA–DNA hybridization, phylogenetic analyses based on 16S rRNA and cpn60 gene sequences, fatty acid profiles, whole-cell matrix-assisted laser desorption/ionization time of flight/MS analysis, physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 23eT from the phylogenetically closest relatives. We propose that strain 23eT represents a novel species within the genus Methylobacterium , for which the name Methylobacterium gnaphalii sp. nov. is proposed. The type strain is 23eT ( = DSM 24027T = NBRC 107716T).

A Gram-stain-negative, rod-shaped, non-motile, non-spore-forming bacterium, designated strain BY-1T, was isolated from a soil sample from the city of Qiqihar in Heilongjiang Province, PR China. Strain BY-1T grew optimally at pH 7.0 and 30–35 °C in the presence of 0.5 % (w/v) NaCl. Analysis of 16S rRNA gene sequences revealed that strain BY-1T fell within the radiation of the genus Pseudomonas , and showed highest 16S rRNA gene sequence similarities to Pseudomonas luteola IAM 13000T (99.5 %) and Pseudomonas duriflava HR2T (97.3 %); the levels of sequence similarity with respect to other recognized species of the genus Pseudomonas were <96.7 %. Strain BY-1T showed low DNA–DNA relatedness values with Pseudomonas luteola IAM 13000T (29±3.1 %) and Pseudomonas duriflava HR2T (21±1.5 %). The G+C content of the genomic DNA of strain BY-1T was 55.3 mol%. The major fatty acids were C18 : 1, C16 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and the major ubiquinone was Q-9. Data obtained in this study indicated that this isolate represents a novel species of the genus Pseudomonas , for which the name Pseudomonas zeshuii sp. nov. is proposed. The type strain is BY-1T ( = KACC 15471T = ACCC 05688T).