- Volume 63, Issue Pt_10, 2013

A novel extremely halophilic archaeon KCY07-B2T was isolated from a salt mine in Kuche county, Xinjiang province, China. Colonies were cream-pigmented and cells were pleomorphic rod-shaped. Strain KCY07-B2T was able to grow at 25–50 °C (optimum 37–45 °C) and pH 6.0–8.0 (optimum 7.0). The strain required at least 1.9 M NaCl for growth. MgCl2 was not required. Cells lysed in distilled water. Polar lipid analysis revealed the presence of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, derived from both C20C20 and C20C25 glycerol diethers, together with five glyolipids. The bis-sulfated glycolipid S2-DGD-1 was present. The DNA G+C content was 62.5 mol%. Analysis of the 16S rRNA gene sequence revealed that strain KCY07-B2T was closely related to Halopiger xanaduensis SH-6T and Halopiger aswanensis 56T (95.8 % and 95.5 % similarity, respectively). On the basis of its phenotypic, chemotaxonomic and genotypic characteristics, strain KCY07-B2T is considered to represent a novel species of the genus Halopiger , for which the name Halopiger salifodinae sp. nov. is proposed. The type strain is KCY07-B2T ( = JCM 18547T = CGMCC 1.12284T).

A thermotolerant, extremely halophilic archaeon, BC12-B1T, was isolated from a salt mine in Baicheng county, Xinjiang province, China. Colonies were off-white–grey. The cells stained Gram-negative, were motile and irregularly long-rod-shaped (variation in both width and length) with abundant gas vesicles. The strain was able to grow at 20–55 °C (optimum, 48 °C), at pH 6.0–8.0 (optimum, 7.0–7.3), with 1.8–6.0 M NaCl (optimum, 3.0–3.5 M) and with 0.02–2.2 M Mg2+ (optimum, 0.1–0.2 M). Cells lysed in distilled water and the minimal NaCl concentration to prevent cell lysis was 8 % (w/v). Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain BC12-B1T was most closely related to Halopelagius inordinatus RO5-2T (98.5 %) with less than 95 % sequence similarity to other described species. The genomic DNA G+C content of strain BC12-B1T was 64.0 mol%. The DNA–DNA hybridization value between strain BC12-B1T and Hpl. inordinatus RO5-2T was 43.6 %. The major polar lipids of strain BC12-B1T were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, four glycolipids and an unknown lipid. Based on phenotypic, chemotaxonomic and genotypic characteristics, strain BC12-B1T represents a novel species of the genus Halopelagius , for which the name Halopelagius longus sp. nov. is proposed. The type strain is BC12-B1T ( = CGMCC 1.12397T = JCM 18758T). An emended description of the genus Halopelagius is also provided.

A novel ikarugamycin-producing actinomycete, designated strain NEAU-Da3T, was isolated from soybean root [Glycine max (L.) Merr.] and characterized using a polyphasic approach. 16S rRNA gene sequence similarity studies showed that strain NEAU-Da3T belonged to the genus Streptomyces , and was most closely related to Streptomyces carpaticus NRRL B-16359T (99.5 %), Streptomyces cheonanensis VC-A46T (99.3 %) and Streptomyces xiamenensis MCCC 1A01550T (97.2 %); similarities to other type strains of species of the genus Streptomyces were lower than 97.1 %. The maximum-likelihood phylogenetic tree based on 16S rRNA gene sequences showed that the isolate formed a distinct phyletic line with S. carpaticus NRRL B-16359T, S. cheonanensis VC-A46T and S. xiamenensis MCCC 1A01550T. This branching pattern was also supported by the tree reconstructed with the neighbour-joining method. A comparative study between strain NEAU-Da3T and the type strains of the closest related species of the genus Streptomyces revealed that it differed from them in morphological, physiological and biochemical characteristics. Therefore, it is proposed that strain NEAU-Da3T represents a novel species of the genus Streptomyces , for which the name Streptomyces harbinensis sp. nov. is proposed. The type strain is NEAU-Da3T ( = CGMCC 4.7047T = DSM 42076T).

A novel actinobacterium, strain BC640T, was isolated from a biofilm sample collected in 2009 in the Saint Callistus Roman catacombs. Analysis of the 16S rRNA gene sequence showed that the strain belonged to the genus Kribbella . Phylogenetic analysis using the 16S rRNA gene and concatenated gyrB, rpoB, relA, recA and atpD gene sequences showed that strain BC640T was most closely related to the type strains of Kribbella yunnanensis and Kribbella sandramycini . Based on gyrB genetic distance analysis, strain BC640T was shown to be distinct from all Kribbella type strains. DNA–DNA hybridization experiments confirmed that strain BC640T represents a genomic species distinct from its closest phylogenetic relatives, K. yunnanensis DSM 15499T (53.5±7.8 % DNA relatedness) and K. sandramycini DSM 15626T (33.5±5.0 %). Physiological comparisons further showed that strain BC640T is phenotypically distinct from the type strains of K. yunnanensis and K. sandramycini . Strain BC640T ( = DSM 26744T = NRRL B-24917T) is thus presented as the type strain of a novel species, for which the name Kribbella albertanoniae sp. nov. is proposed.

A novel Gram-stain-positive actinobacterium, designated HR08-44T, was isolated from a sea-sediment sample collected from the foreshore of Rishiri Island, Japan, and its taxonomic position was investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain HR08-44T was closely related to the members of the genus Janibacter , with pairwise sequence similarities of 97.3–98.8 %. Strain HR08-44T had peptidoglycan type A1γ, with meso-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinone was MK-8(H4) and the major fatty acids were iso-C16 : 0, C17 : 1ω8c, C17 : 0 and C18 : 1ω9c. These data supported the affiliation of the novel strain to the genus Janibacter . Meanwhile, the results of DNA–DNA hybridization and physiological and biochemical tests indicated that strain HR08-44T can be distinguished from recognized species of the genus Janibacter . Therefore, strain HR08-44T represents a novel species of the genus Janibacter , for which the name Janibacter cremeus sp. nov. is proposed; the type strain is HR08-44T ( = NBRC 107693T = DSM 26154T).

A Gram-reaction-positive, rod-shaped, non-spore-forming bacterium (strain 2C1-5T) was isolated from activated sludge of an industrial wastewater treatment plant in Daegu, South Korea. Its taxonomic position was investigated by using a polyphasic approach. On the basis of 16S rRNA gene sequence similarity, the closest phylogenetic relatives were the type strains of Nocardioides nitrophenolicus (98.6 % similarity), N. kongjuensis (98.5 %), N. caeni (98.4 %), N. simplex (98.3 %), N. aromaticivorans (98.1 %) and N. ginsengisoli (97.5 %); the phylogenetic distance from other species with validly published names within the genus Nocardioides was greater than 3 %. Strain 2C1-5T was characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-8(H4) as the predominant menaquinone and iso-C16 : 0, C16 : 0 and C17 : 1ω6c as the major fatty acids. The G+C content of the genomic DNA was 74.9 mol%. These chemotaxonomic properties and phenotypic characteristics supported the affiliation of strain 2C1-5T to the genus Nocardioides . The results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 2C1-5T from existing species with validly published names. Therefore, strain 2C1-5T represents a novel species of the genus Nocardioides , for which the name Nocardioides daeguensis sp. nov. is proposed, with the type strain 2C1-5T ( = JCM 17460T = KCTC 19799T).

A spore-forming streptomycete designated strain SUK12T was isolated from a Malaysian ethnomedicinal plant. Its taxonomic position, established using a polyphasic approach, indicates that it is a novel species of the genus Streptomyces . Morphological and chemical characteristics of the strain were consistent with those of members of the genus Streptomyces . Analysis of the almost complete 16S rRNA gene sequence placed strain SUK12T in the genus Streptomyces where it formed a distinct phyletic line with recognized species of this genus. The strain exhibited highest sequence similarity to Streptomyces corchorusii DSM 40340T (98.2 %) followed by Streptomyces chrestomyceticus NRRL B-3310T (98.1 %). The G+C content of the genomic DNA was 74 mol%. Chemotaxonomic data [MK-9(H8) as the major menaquinone; LL-diaminopimelic acid as a component of cell-wall peptidoglycan; C12 : 0, C14 : 0, C15 : 0 and C17 : 1 as the major fatty acids; phospholipid type II] supported the affiliation of strain SUK12T to the genus Streptomyces . The results of the phylogenetic analysis and phenotypic data derived from this and previous studies allowed the genotypic and phenotypic differentiation of strain SUK12T from the related species of the genus Streptomyces . The DNA–DNA relatedness value between strain SUK12T and S. corchorusii DSM 40340T is 18.85±4.55 %. Strain SUK12T produces phenazine-1-carboxylic acid, known as tubermycin B, an antibacterial agent. It is proposed, therefore, that strain SUK12T ( = DSM 42048T = NRRL B-24860T) be classified in the genus Streptomyces as the type strain of Streptomyces kebangsaanensis sp. nov.

A novel halotolerant actinomycete, designated strain BNT52T, was isolated from soil collected from Cihanbeyli Salt Mine in the central Anatolia region of Turkey, and examined using a polyphasic taxonomic approach. The isolate was found to have chemical and morphological properties typical of the genus Amycolatopsis and formed a distinct phyletic line in the 16S rRNA gene tree. Strain BNT52T was most closely related to Amycolatopsis nigrescens CSC17Ta-90T (96.7 %), Amycolatopsis magusensis KT2025T (96.6 %), Amycolatopsis sulphurea DSM 46092T (96.6 %), Amycolatopsis dongchuanensis YIM 75904T (96.5 %), Amycolatopsis ultiminotia RP-AC36T (96.4 %) and Amycolatopsis sacchari DSM 44468T (96.4 %). Sequence similarities with other strains of species of the genus Amycolatopsis were lower than 96.2 %. The isolate grew at 20–37 °C, pH 6–12 and in the presence of 0–10 % (w/v) NaCl. The cell wall of the novel strain contained meso-diaminopimelic acid and arabinose and galactose as the diagnostic sugars. Major fatty acids were iso-C16 : 0 2-OH and iso-C16 : 0. The predominant menaquinone was MK-9(H4). The polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylmethylethanolamine. The genomic DNA G+C content was 68.8 mol%. On the basis of the data from this polyphasic taxonomic study, strain BNT52T represents a novel species within the genus Amycolatopsis for which the name Amycolatopsis cihanbeyliensis sp. nov. is proposed (type strain BNT52T = KCTC 29065T = NRRL B-24886T = DSM 45679T).

The taxonomic position of a novel actinomycete, strain SA152T, isolated from a sample of Algerian Saharan soil, was determined using a polyphasic taxonomic approach. The strain produced abundant aerial mycelium and fragmented substrate mycelium on most media tested. Chemotaxonomically and phylogenetically, the strain was related to the members of the genus Saccharothrix . Results of 16S rRNA gene sequence comparison revealed that strain SA152T shared the highest degree of 16S rRNA gene sequence similarity with Saccharothrix xinjiangensis NBRC 101911T (99.3 %) and Saccharothrix texasensis NRRL B-16134T (98.9 %). However, DNA–DNA hybridization studies showed only 16.2 % relatedness with S. xinjiangensis DSM 44896T and 33.9 % relatedness with S. texasensis DSM 44231T. Based upon genotypic and phenotypic differences from other members of the genus, a novel species, Saccharothrix saharensis sp. nov., is proposed, with SA152T ( = DSM 45456T = CCUG 60213T) as the type strain.

A novel actinobacterium, designated strain NJ2035T, was isolated from soil collected from Abuja, Nigeria and was characterized to determine its taxonomic position. The isolate was found to have chemical and morphological properties associated with members of the genus Lechevalieria . Phylogenetic analyses based on almost-complete 16S rRNA gene sequences indicated that the isolate was closely related to members of the genus Lechevalieria , and was shown to form a distinct phyletic line in the Lechevalieria phylogenetic tree. Strain NJ2035T was most closely related to Lechevalieria roselyniae C81T, Lechevalieria atacamensis C61T and Lechevalieria deserti C68T (98.5 % 16S rRNA gene sequence similarity). Sequence similarities with other members of the genus Lechevalieria were less than 98.2 %. The cell wall of the novel strain contained meso-diaminopimelic acid, and galactose, mannose and rhamnose as the diagnostic sugars. The predominant menaquinone was MK-9(H4). The polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol. DNA–DNA relatedness and phenotypic data showed that the novel isolate and L. roselyniae C81T, L. atacamensis C61T and L. deserti C68T belong to distinct genomic species. On the basis of data from this taxonomic study using a polyphasic approach, strain NJ2035T represents a novel species of the genus Lechevalieria , for which the name Lechevalieria nigeriaca sp. nov. is proposed. The type strain is NJ2035T ( = DSM 45680T = KCTC 29057T = NRRL B-24881T).

A novel actinomycete, strain DS3030T, was isolated from a deep sediment sample, collected from the southern Black Sea coast, Turkey, and was examined using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain DS3030T was shown to belong to the genus Saccharomonospora and to be related most closely to Saccharomonospora marina XMU15T (99.6 % similarity). Sequence similarities with other strains of the genus Saccharomonospora were lower than 97.0 %. The organism had chemical and morphological features typical of the genus Saccharomonospora . The cell wall of the novel strain contained meso-diaminopimelic acid, arabinose and galactose as diagnostic sugars. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The predominant menaquinone was MK-9(H4). Major fatty acids were iso-C16 : 0, iso-C16 : 0 2-OH and C16 : 1 cis 9. Phenotypic data clearly distinguished the new isolate from its closest relative, S. marina XMU15T. The combined genotypic and phenotypic data and low DNA–DNA relatedness with its closest related strain reveal that strain DS3030T represents a novel species of the genus, for which the name Saccharomonospora amisosensis sp. nov. is proposed. The type strain is DS3030T ( = DSM 45685T = KCTC 29069T = NRRL B-24885T).

A halophilic actinomycete strain, designated H55T, was isolated from Saharan soil sampled in the Mzab region (Ghardaïa, southern Algeria) and was characterized in a taxonomic study using a polyphasic approach. The cell wall was determined to contain meso-diaminopimelic acid and the characteristic whole-cell sugars were arabinose and galactose. The predominant menaquinones were found to be MK-10(H4) and MK-9(H4). The predominant cellular fatty acids were determined to be anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0. The diagnostic phospholipid detected was phosphatidylcholine. The morphological and chemotaxonomic characteristics of the strain were consistent with those of members of the genus Actinopolyspora , and 16S rRNA gene sequence analysis confirmed that strain H55T was a member of this genus. DNA–DNA hybridization values between strain H55T and the type strains of the nearest species of the genus Actinopolyspora , Actinopolyspora erythraea and A. alba , were clearly below the 70 % threshold. The genotypic and phenotypic data showed that the organism represents a novel species of the genus Actinopolyspora , for which the name Actinopolyspora mzabensis sp. nov. is proposed, with the type strain H55T ( = DSM 45460T = CCUG 62965T).

A Gram-staining-positive, non-motile, aerobic, non-spore-forming and short rod-shaped bacterial strain, PAMC 26527T, was isolated from biofilm formed in coastal seawater of the Norwegian Sea. Analysis of the 16S rRNA gene sequence of strain PAMC 26527T revealed a clear affiliation with the genus Nocardioides . Based on phylogenetic analysis, strain PAMC 26527T showed the closest phylogenetic relationship with Nocardioides caricicola YC6903T with 16S rRNA gene sequence similarity of 96.3 %. Strain PAMC 26527T grew in the presence of 0–5.0 % sea salts. The optimum temperature and pH for growth were 20 °C and pH 7.5. The major cellular fatty acids of strain PAMC 26527T were iso-C16 : 0, C17 : 1ω8c and C18 : 1ω9c and the major isoprenoid quinone was MK-8(H4). Cell-wall analysis showed that strain PAMC 26527T contained ll-diaminopimelic acid. The genomic DNA G+C content was 69.3 mol%. The combined phenotypic, chemotaxonomic and phylogenetic data showed that strain PAMC 26527T could be clearly distinguished from recognized members of the genus Nocardioides . Thus, strain PAMC 26527T should be classified as representing a novel species in the genus Nocardioides , for which the name Nocardioides salsibiostraticola sp. nov. is proposed. The type strain is PAMC 26527T ( = KCTC 29158T = JCM 18743T).

A Gram-stain-positive, spore-forming actinomycete strain (HKI0641T) was isolated from a soil sample collected in the Black Forest, Germany. During screening for antimicrobial natural products this bacterium was identified as a producer of the antibiotic telomycin. Morphological characteristics and chemotaxonomic data indicated that the strain belonged to the genus Micromonospora . The peptidoglycan of strain HKI0641T contained meso-diaminopimelic acid, and the fatty acid profile consisted predominantly of anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and C16 : 0. MK-10(H4), MK-10(H2) and MK-10 were identified as the major menaquinones. To determine the taxonomic positioning of strain HKI0641T, we computed a binary tanglegram of two rooted phylogenetic trees that were based upon 16S rRNA and gyrB gene sequences. The comparative analysis of the two common classification methods strongly supported the phylogenetic affiliation with the genus Micromonospora , but it also revealed discrepancies in the assignment at the level of the genomic species. 16S rRNA gene sequence analysis identified Micromonospora coxensis DSM 45161T (99.1 % sequence similarity) and Micromonospora marina DSM 45555T (99.0 %) as the nearest taxonomic neighbours, whereas the gyrB sequence of strain HKI0641T indicated a closer relationship to Micromonospora aurantiaca DSM 43813T (95.1 %). By means of DNA–DNA hybridization experiments, it was possible to resolve this issue and to clearly differentiate strain HKI0641T from other species of the genus Micromonospora . The type strains of the aforementioned species of the genus Micromonospora could be further distinguished from strain HKI0641T by several phenotypic properties, such as colony colour, NaCl tolerance and the utilization of carbon sources. The isolate was therefore assigned to a novel species of the genus Micromonospora , for which the name Micromonospora schwarzwaldensis sp. nov. is proposed. The type strain is HKI0641T ( = DSM 45708T = CIP 110415T).

A rod-shaped actinobacterium, designated strain RS-16T, was isolated from a rhizosphere soil and its taxonomic position was determined by a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis indicated that strain RS-16T was most closely related to the type strain of Motilibacter peucedani (98.3 % sequence similarity). The cell-wall peptidoglycan contained ll-diaminopimelic acid as the diagnostic diamino acid and N-glycolylated murein. The major whole-cell sugars were glucose, galactose and mannose. The predominant menaquinone was MK-9(H4). The major fatty acids were C18 : 1ω9c and C16 : 0. The DNA G+C content was 73.1 mol%. The phenotypic and DNA–DNA hybridization data showed that strain RS-16T ( = KACC 16209T = DSM 45622T) represents a novel species of the genus Motilibacter , for which Motilibacter rhizosphaerae sp. nov. is proposed. Based on the phylogenetic position determined by 16S rRNA gene analysis and the signature nucleotide set of the 16S rRNA sequence, the genus Motilibacter represents a novel family of the suborder Frankineae , for which the name Motilibacteraceae fam. nov. is proposed.

A Gram-stain-positive, aerobic, motile, rod-shaped bacterium, designated strain Mn1-7T, was isolated from manganese mining soil in Tianjin, China. The closest phylogenetic relatives were Lysinibacillus massiliensis CCUG 49529T (97.2 % 16S rRNA gene sequence similarity), L. xylanilyticus XDB9T (96.7 %), L. sinduriensis JCM 15800T (96.2 %), L. odysseyi NBRC 100172T (95.9 %) and L. boronitolerans NBRC 103108T (95.4 %) (the type species of the genus). DNA–DNA hybridization values for strain Mn1-7T with the type strains of L. massiliensis and L. sinduriensis were 24.9 and 27.7 %, respectively. The genomic DNA G+C content was 38.4 mol%. The major menaquinone was MK-7 and the major fatty acids were iso-C15 : 0, iso-C16 : 0 and iso-C14 : 0. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The cell-wall peptidoglycan was type A4α (l-Lys–d-Asp), and the predominant cell-wall sugar was xylose. DNA–DNA hybridization results and comparison of phenotypic and chemotaxonomic characters between strain Mn1-7T and the phylogenetically most closely related strains revealed that the isolate represents a novel species of the genus Lysinibacillus , for which the name Lysinibacillus manganicus sp. nov. is proposed. The type strain is Mn1-7T ( = DSM 26584T = CCTCC AB 2012916T).

A novel spore-forming, sulfate-reducing bacterium, strain SR45T, was isolated from sediment of a freshwater lake, Lake Mizugaki, in Japan. Cells of strain SR45 were rod-shaped (1.0–1.5×2.0–5.0 µm) and weakly motile; Gram staining and the KOH lysis test were negative. For growth, the optimum pH was 6.4–6.8 and the optimum temperature was 42–45 °C. Strain SR45T used sulfate, thiosulfate, sulfite and elemental sulfur as electron acceptors but not Fe(III). The G+C content of the genomic DNA was 41.1 mol%. Phylogenetic analyses based on genes for the 16S rRNA and DNA gyrase (gyrB) revealed that the isolated strain belonged to the family Peptococcaceae in the class Clostridia . The closest relative is Desulfotomaculum acetoxidans 5575T, with 16S rRNA gene sequence similarity of 92–94 %. It is suggested that the strain is the second isolated member of Desulfotomaculum subcluster Ie. The isolate had multiple 16S rRNA gene copies, with 13 different sequences. On the basis of phylogenetic and phenotypic characterization, the name Desulfotomaculum intricatum sp. nov. is proposed, with the type strain SR45T ( = NBRC 109411T = DSM 26801T).

A hydrogenogenic, carboxydotrophic marine bacterium, strain KKC1T, was isolated from a sediment core sample taken from a submerged marine caldera. Cells were non-motile, Gram-stain-negative, 1.0–3.0 µm straight rods, often observed with round endospores. Strain KKC1T grew at 55–68 °C, pH 5.2–9.2 and 0.8–14 % (w/v) salinity. Optimum growth occurred at 65 °C, pH 7.0–7.5 and 2.46 % salinity with a doubling time of 3.7 h. The isolate grew chemolithotrophically, producing H2 from carbon monoxide (CO) oxidation with reduction of various electron acceptors, e.g. sulfite, thiosulfate, fumarate, ferric iron and AQDS (9,10-anthraquinone 2,6-disulfonate). KKC1T grew heterotrophically on pyruvate, lactate, fumarate, glucose, fructose and mannose with thiosulfate as an electron acceptor. When grown mixotrophically on CO and pyruvate, C16 : 0 constituted almost half of the total cellular fatty acids. The DNA G+C content was 50.6 mol%. The 16S rRNA gene sequence of KKC1T was most closely related to those of members of the genus Moorella with similarity ranging from 91 to 89 %. Based on physiological and phylogenetic novelty, we propose the isolate as a representative of a new genus and novel species with the name Calderihabitans maritimus gen. nov., sp. nov.; the type strain of the type species is KKC1T ( = DSM 26464T = NBRC 109353T).