- Volume 63, Issue Pt_7, 2013

An actinomycete, strain 2602GPT1-05T, was isolated from a composite mangrove soil sample collected from Wenchang, Hainan province, China. Strain 2602GPT1-05T showed closest 16S rRNA gene sequence similarity to Micromonospora haikouensis 232617T (99.05 %), and phylogenetically clustered with Micromonospora haikouensis 232617T, Micromonospora matsumotoense IMSNU 22003T (98.7 %) and Micromonospora rifamycinica AM105T (98.6 %) based on the 16S rRNA and gyrB gene sequence phylogenetic analysis. The strain harboured meso-DAP and glycine as major cell-wall amino acids, and MK-10(H6) and MK-9(H6) as predominant menaquinones. The characteristic whole-cell sugars were xylose, arabinose, glucose and galactose. The polar lipid profile comprised phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylglycerol, phosphatidylinositol mannosides, unknown phospholipid and an unknown phosphoglycolipid. The major cellular fatty acids were C18 : 1ω9c, iso-C15 : 0, 10-methyl C18 : 0 (tuberculostearic acid), C16 : 0, C18 : 0 and iso-C16 : 0. The DNA G+C content was 71.7 mol%. Furthermore, some physiological and biochemical properties and low DNA–DNA relatedness values enabled the strain to be differentiated from members of closely related species. On the basis of these phenotypic, genotypic and chemotaxonomic data, strain 2602GPT1-05T represents a novel species of the genus Micromonospora , for which the name Micromonospora wenchangensis sp. nov. is proposed. The type strain is 2602GPT1-05T ( = CCTCC AA 2012002T = DSM 45709T).

A novel actinomycete, designated strain NEAU-Z6T, was isolated from eggplant (Solanum melongena L.) root. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain NEAU-Z6T belonged to the genus Nonomuraea , with highest sequence similarity to Nonomuraea monospora PT 708T (98.83 %), Nonomuraea rosea GW 12687T (98.55 %) and Nonomuraea rhizophila YIM 67092T (98.02 %). Sequence similarities between strain NEAU-Z6T and other species of the genus Nonomuraea ranged from 97.94 % ( Nonomuraea candida HMC10T) to 96.30 % ( Nonomuraea wenchangensis 210417T). Key morphological, physiological and chemotaxonomic characteristics of strain NEAU-Z6T were congruent with the description of the genus Nonomuraea . The G+C content of the genomic DNA was 64.51 mol%. DNA–DNA relatedness and comparative analysis of physiological, biochemical and chemotaxonomic data allowed genotypic and phenotypic differentiation of strain NEAU-Z6T from closely related species. Thus, strain NEAU-Z6T represents a novel species of the genus Nonomuraea , for which the name Nonomuraea solani sp. nov. is proposed. The type strain is NEAU-Z6T ( = CGMCC 4.7037T = DSM 45729T).

A Gram-positive, aerobic, rod-shaped bacterial strain, 5116S-4T, was isolated from an air sample collected in Suwon city, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain was a new member of the family Microbacteriaceae . The sequence similarities of this strain to the members of the family Microbacteriaceae were less than 97 %, with the highest values observed with Cryobacterium mesophilum MSL-15T (96.3 %), Cryobacterium roopkundense RuGl7T (96.2 %), Labedella gwakjiensis KSW2-17T (96.2 %), Cryobacterium luteum Hh15T (96.2 %), Cryobacterium psychrophilum DSM 4854T (96.2 %), Klugiella xanthotipulae 44C3T (96.0 %) and Amnibacterium kyonggiense KSL51201-037T (96.0 %). According to the phylogenetic tree, strain 5116S-4T formed a cluster with A. kyonggiense KSL51201-037T, Labedella gwakjiensis KSW2-17T and Lysinimonas soli SGM3-12T (95.3 % sequence similarity) on the support of high bootstrap values. Cells were motile with single polar flagellum and showed optimum growth at 30 °C and pH 7 without NaCl. Predominant cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Polar lipids were diphosphatidylglycerol, dimannosyldiacylglycerol, phosphatidylglycerol, one unknown glycolipid, one unknown phospholipid and one unknown lipid. The acyl type of the cell-wall muramic acid was the acetyl type. Peptidoglycan was supposed to be the type B1 with 2,4-diaminobutyric acid on position 3. Strain 5116S-4T was clearly distinguishable from the phylogenetically related genera in the family Microbacteriaceae in terms of chemotaxonomic characteristics. On the basis of the chemotaxonomic and phylogenetic characteristics, a novel genus and species are proposed, Naasia aerilata gen. nov., sp. nov. The type strain of Naasia aerilata is 5116S-4T ( = KACC 15517T  = NBRC 108725T).

A novel aerobic soil actinobacterium (strain MB10T) belonging to the genus Microbacterium was isolated from rice field soil samples collected from Jagatpur, Orissa, India. Cells were Gram-stain positive, short rod-shaped and motile. The strain was oxidase-negative and catalase-positive. Heterotrophic growth was observed at pH 5.0–11.0 and at 16–37 °C; optimum growth was observed at 28 °C and pH 7.0–9.0. The DNA G+C content was 71.6 mol%. Predominant cellular fatty acids of strain MB10T were iso-C14 : 0, anteiso-C15 : 0, C16 : 0, iso-C16 : 0 and anteiso-C17 : 0. Cell wall sugars were galactose, glucose and rhamnose. The major isoprenoid quinones were MK-9 (10 %), MK-10 (43 %) and MK-11 (36 %). The peptidoglycan represents the peptidoglycan type B2β. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipid and unknown glycolipids. 16S rRNA gene sequence identity revealed the strain MB10T clustered within the radiation of the genus Microbacterium and showed 99.2 % similarity with Microbacterium barkeri DSM 20145T. However, DNA–DNA similarity study was 37.0 % with Microbacterium barkeri DSM 20145T, the nearest phylogenetic relative. On the basis of phenotypic and chemotaxonomic properties, 16S rRNA gene sequence analysis and DNA–DNA reassociation studies, it is proposed that strain MB10T represents a novel species of the genus Microbacterium , for which the name Microbacterium oryzae sp. nov. is proposed; the type strain is MB10T ( = JCM 16837T = DSM 23396 T ).

Two strains of aerobic, non-motile, Gram-reaction-positive cocci were independently isolated from geographically distinct spacecraft assembly clean room facilities (Kennedy Space Center, Florida, USA and Centre Spatial Guyanais, Kourou, French Guiana). A polyphasic study was carried out to delineate the taxonomic identity of these two isolates (1P05MAT and KO_PS43). The 16S rRNA gene sequences exhibited a high similarity when compared to each other (100 %) and lower than 96.7 % relatedness with Arthrobacter crystallopoietes ATCC 15481T, Arthrobacter luteolus ATCC BAA-272T, Arthrobacter tumbae DSM 16406T and Arthrobacter subterraneus DSM 17585T. In contrast with previously described Arthrobacter species, the novel isolates maintained their coccidal morphology throughout their growth and did not exhibit the rod–coccus life cycle typically observed in nearly all Arthrobacter species, except A. agilis . The distinct taxonomic identity of the novel isolates was confirmed based on their unique cell-wall peptidoglycan type (A.11.20; Lys-Ser-Ala2) and polar lipid profile (presence of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, an unknown phospholipid and two unknown glycolipids). The G+C content of the genomic DNA was 70.6 mol%. The novel strains revealed MK-9(H2) and MK-8(H2) as dominant menaquinones and exhibited fatty acid profiles consisting of major amounts of anteiso-C15 : 0 and anteiso-C17 : 0 and moderate amounts of iso-C15 : 0 discriminating them again from closely related Arthrobacter species. Based on these observations, the authors propose that strains 1P05MAT and KO_PS43 be assigned into a separate genus Tersicoccus gen. nov. For this new taxon, comprising strains 1P05MAT and KO_PS43, we propose the name Tersicoccus phoenicis gen. nov., sp. nov. (the type species of Tersicoccus), represented by the type strain Tersicoccus phoenicis 1P05MAT ( = NRRL B-59547T = DSM 30849T).

A Gram-positive, non-spore-forming bacterium (GW-12028T) of unknown origin showing filamentous growth and producing spherical sporangia was studied for its taxonomic allocation. The 16S rRNA gene sequence analysis and subsequent similarity studies showed that strain GW-12028T belongs to the genus Streptosporangium , and is most closely related to Streptosporangium pseudovulgare DSM 43181T (99.9 %) and Streptosporangium nondiastaticum DSM 43848T (99.6 %) and more distantly related to Streptosporangium fragile IFO 14311T (98.4 %) and other species of the genus Streptosporangium (95.8 to 98 %). Chemotaxonomic analyses showed that the peptidoglycan diamino acid was meso-diaminopimelic acid. Whole-cell hydrolysates contained madurose as the diagnostic sugar and exhibited a quinone system that contained predominantly menaquinones with nine isoprenoic units in the side chain [MK-9, MK-9(H2), MK-9(H4)]. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phoshatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol-mannosides, four unidentified glycolipids, a phospholipid and an aminolipid. The polyamine pattern contained the major compounds spermine and spermidine. The major fatty acids were 10-methyl C17 : 0, iso-C16 : 0 and C15 : 0. These chemotaxonomic traits are common to other species of the genus Streptosporangium . DNA–DNA hybridizations and physiological and biochemical tests in comparison with the type strains of the most closely related species, S. nondiastaticum and S. pseudovulgare , allowed genotypic and phenotypic differentiation of strain GW-12028T. This strain represents a novel species, for which we propose the name Streptosporangium sandarakinum sp. nov., with the type strain GW-12028T ( = LMG 27062T  = DSM 45763T).

A micro-organism resembling members of the genus Dermatophilus , strain W254T, which was isolated from the submandibular lymph node of a pig, and an additional 16 strains isolated from swine tonsils, were studied to establish their taxonomic status. Although all 17 strains were isolated anaerobically under an atmosphere of 100 % CO2, all of them were aerotolerant anaerobes. The micro-organisms showed at least five cellular morphologies: (i) a radially protrusive thallus, which proliferated into tuber-like cells; (ii) segmentation in both tubers and thallus followed by multilocule formation, (iii) development of coccoid forms in the locules; (iv) a change from the coccoid forms to zoospores; (v) resting cells, which were able to develop into protrusive thalli again. The micro-organisms were positive for nitrate reduction, but negative for catalase, indole production, hydrolysis of urea and gelatin liquefaction. Milk was not decomposed and none of the strains was haemolytic. A total of 16 compounds, including glucose, were utilized as sole carbon sources and seven compounds, including l-arabinose, were not utilized. Three out of the 17 strains were subjected to further studies. The micro-organisms had meso-diaminopimelic acid in their peptidoglycan and galactose, glucose, madurose and a trace of mannose in their whole-cell sugar patterns. The major phospholipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol.Cellular fatty acids were C15 : 0 (35.7–23.1 %), C16 : 0 (5.9–2.4 %) C17 : 0 (62.9–39.5 %), C17 : 1 (24.4–0 %) and C18 : 0 (3–1.6 %). The predominant menaquinone was MK-8 (H4). The G+C content of the DNA was 69.6–71.8 mol%. Analysis of the 16S rRNA gene sequences showed that the strains clustered with the type strains of members of the family Dermatophilaceae . Based on the polyphasic taxonomic characterization carried out, all 17 strains are considered to belong to a novel species in a new genus, for which the name Tonsilliphilus suis gen. nov., sp. nov. is proposed. The type strain of the type species is W254T ( = ATCC 35846T = CCM 3774T = DSM 21880T = JCM 15727T).

Three isolates of a slow-growing, non-chromogenic mycobacterium were grown from three sputum samples of a patient from the north-eastern Ceará state in Brazil. Identification at species level could not be obtained with PCR restriction analysis of the hsp65 gene. In order to characterize the isolates we carried out phenotypic and genotypic tests. We sequenced the nearly complete 16S rRNA gene and obtained partial sequences of the hsp65 (encoding the hypervariable region of the 65 kDa heat-shock protein) and rpoB (encoding the beta-subunit of RNA polymerase) genes. The three isolates turned out to be identical and most closely related to the species Mycobacterium celatum and Mycobacterium kyorinense . The results, however, showed significant differences between these species and the isolates studied, which led us to consider them members of a novel species for which we propose the name Mycobacterium fragae. The type strain is HF8705T ( = Fiocruz-INCQS/CMRVS P4051T = DSM 45731T).

A Gram-positive, aerobic, non-motile, non-endospore-forming rod-shaped bacterium with ibuprofen-degrading capacity, designated strain I11T, was isolated from activated sludge from a wastewater treatment plant. The major respiratory quinone was demethylmenaquinone DMK-7, C18 : 1 cis9 was the predominant fatty acid, phosphatidylglycerol was the predominant polar lipid, the cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid and the G+C content of the genomic DNA was 74.1 mol%. On the basis of 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of strain I11T were Patulibacter ginsengiterrae CECT 7603T (96.8 % similarity), Patulibacter minatonensis DSM 18081T (96.6 %) and Patulibacter americanus DSM 16676T (96.6 %). Phenotypic characterization supports the inclusion of strain I11T within the genus Patulibacter (phylum Actinobacteria) . However, distinctive features and 16S rRNA gene sequence analysis suggest that is represents a novel species, for which the name Patulibacter medicamentivorans sp. nov. is proposed. The type strain is I11T ( = DSM 25962T = CECT 8141T).

A Gram-stain-positive, non-motile, strictly aerobic, non-spore-forming and short rod-shaped bacterial strain, CL-GY44T, was isolated from coastal seawater, Korea. Analysis of the 16S rRNA gene sequence of strain CL-GY44T revealed a clear affiliation with the genus Nocardioides . Based on phylogenetic analysis, strain CL-GY44T showed the closest phylogenetic relationship with Nocardioides ginsengagri BX5-10T and Nocardioides plantarum NCIMB 12834T. Strain CL-GY44T was not able to grow in the presence of NaCl but grew with 0–5.5 % sea salts. The optimum temperature and pH for growth were 30 °C and pH 7.0. The major cellular fatty acids of strain CL-GY44T were C17 : 1ω6c, iso-C16 : 0, C16 : 0 and iso-C15 : 0 and the major menaquinone was MK-8(H4). The cell-wall analysis showed that strain CL-GY44T contained ll-diaminopimelic acid. The genomic DNA G+C content was 71.6 mol%. The combined phenotypic, chemotaxonomic and phylogenetic data showed that strain CL-GY44T could be clearly distinguished from members of the genus Nocardioides . Thus, strain CL-GY44T should be classified as representing a novel species in the genus Nocardioides , for which the name Nocardioides marinquilinus sp. nov. is proposed. The type strain is CL-GY44T ( = KCCM 90109T = JCM 18459T).

An actinobacterial strain, designated ViU22T, was isolated from a natural uranium-rich soil and was studied using a polyphasic approach. Cells formed orange-pigmented colonies, were rod-shaped, Gram-positive (non-staining method), non-motile and non-spore-forming. This organism grew in 0–4.5 % (w/v) NaCl and at 15–37 °C, with optimal growth occurring in 0.5 % (w/v) NaCl and at 30 °C. Comparative 16S rRNA gene sequence analysis revealed that the strain ViU22T belonged to the genus Microbacterium . It exhibited highest 16S rRNA gene sequence similarity with the type strains of Microbacterium testaceum (98.14 %) and Microbacterium binotii (98.02 %). The DNA–DNA relatedness of strains ViU22T with the most closely related type strains Microbacterium testaceum and Microbacterium binotii DSM 19164T was 20.10 % (±0.70) and 28.05 % (±0.35), respectively. Strain ViU22T possessed a type B2β peptidoglycan with partial substitution of glutamic acid by 3-hydroxy glutamic acid. The major menaquinones were MK-11 and MK-12. Major polar lipids detected in the strain ViU22T were diphosphatidylglycerol, phosphatidylglycerol, an unknown phospholipid and unknown glycolipids. The predominant fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0, a pattern reported for other Microbacterium species. The major cell-wall sugars were galactose, xylose and mannose and the DNA G+C content was 71 mol%. Together, the DNA–DNA hybridization results and the differentiating phenotypic characteristics, showed that strain ViU22T should be classified as the type strain of a novel species within the genus Microbacterium , for which the name Microbacterium lemovicicum sp. nov. is proposed. The type strain is ViU22T ( = ATCC BAA-2396T = CCUG 62198T = DSM 25044T).

Two strains, PB34T and PB261T, were isolated from grass soil sampled in Daejeon, Republic of Korea. Comparative 16S rRNA gene sequence studies showed the two bacteria to be clearly affiliated with the phylum Actinobacteria and most closely related to the genus Geodermatophilus , showing 16S rRNA gene sequence similarities to the type strains of species of the genus Geodermatophilus of 95.0–96.3 % and sharing 98.5 % similarity between the two strains. The two strains were Gram-stain-positive, aerobic, motile and rod-shaped bacteria. The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinones were MK-9(H4) and MK-9(H0). The major fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) for strain PB34T and iso-C14 : 0, iso-C15 : 0, iso-C16 : 0 and C16 : 0 for strain PB261T. The G+C contents of the genomic DNA of strains PB34T and PB261T were 73.2 mol% and 74.1 mol%, respectively. Thus, based on the evidence of a polyphasic study, it is proposed that strains PB34T and PB261T represent two novel species, for which the names Geodermatophilus soli sp. nov. (type strain PB34T = KCTC 19880T = JCM 17785T) and Geodermatophilus terrae sp. nov. (type strain PB261T = KCTC 19881T = JCM 17786T) are proposed.

A novel Gram-stain-positive actinobacterium, designated H25-14T, was isolated from a sea sediment sample, and its taxonomic position was investigated by a polyphasic approach. The peptidoglycan type of strain H25-14T was A4α and lysine was the diagnostic diamino acid of the peptidoglycan. The predominant menaquinone was MK-9(H4) and the major fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The DNA G+C content was 73.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain H25-14T was closely related to Paraoerskovia marina NBRC 104352T (98.3 %). However, DNA–DNA hybridization data and phenotypic characteristics revealed that strain H25-14T differed from P. marina NBRC 104352T. Therefore, strain H25-14T represents a novel species of the genus Paraoerskovia , for which the name Paraoerskovia sediminicola sp. nov. is proposed. The type strain is H25-14T ( = NBRC 108565T = DSM 25477T). An emended description of the genus Paraoerskovia is also proposed.

A single strain, NR06T, was isolated from the intestine of a TNFdeltaARE mouse. Based on phylogenetic analysis of partial 16S rRNA gene sequences, strain NR06T belongs in the family Coriobacteriaceae within the Actinobacteria . The most closely related species with validly published names are members of the genera Adlercreutzia , Asaccharobacter and Enterorhabdus (<96 % sequence similarity). Strain NR06T was characterized by a high prevalence of monomethylmenaquinone-6 (MMK-6; 76 %) and the presence of meso-diaminopimelic acid in the cell wall. One of the major cellular fatty acids of strain NR06T was C15 : 0 ISO. Glucose was detected as a whole cell sugar. Strain NR06T was resistant to the antibiotic colistin and was positive for arginine and leucine arylamidase activity. Based on these characteristics, strain NR06T differed from related described bacteria. Therefore, the name Parvibacter caecicola gen. nov., sp. nov. is proposed to accommodate the novel bacterium. The type strain of the type species is NR06T ( = DSM 22242T = CCUG 57646T).