- Volume 63, Issue Pt_11, 2013

A novel haloalkaliphilic archaeon, strain B23T was isolated from the former lake Texcoco in Mexico. The strain was Gram-stain-negative, the cells coccoid to ovoid rods, red pigmented and aerobic. Strain B23T grew in 1.7–4.3 M NaCl, at pH 6.5–9.5 and at 25–45 °C with optimal growth at 2.6–3.4 M NaCl, pH 7.5–8.5 and 37 °C. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain B23T was most closely related to Natronobacterium gregoryi SP2T with 97.3 % sequence similarity. The polar lipids of strain B23T were phosphatidylglycerol and several unidentified phospholipids. The G+C content of the DNA of the strain was 62.5 mol%. Levels of DNA–DNA relatedness between strain B23T and Natronobacterium gregoryi DSM 3393T was 32.3 %. The name Natronobacterium texcoconense sp. nov. is proposed. The type strain is B23T ( = CECT 8068T = JCM 17655T).

Three strictly anaerobic, methanogenic strains JH1T, JH4 and JH8 were isolated from rumen of the Korean native cattle (HanWoo; Bos taurus coreanae) in South Korea. The colonies were circular, opaque, and slightly yellowish. Phylogenetic analyses of 16S rRNA gene and mcrA (encoding α subunit of methyl-coenzyme M reductase) sequences confirmed the affiliation of the novel strains with the Methanobacteriales , and Methanobrevibacter wolinii SHT was the most closely related species. The 16S rRNA gene and mcrA sequence similarities between strains JH1T, JH4 and JH8 and M. wolinii SHT were 96.2 and 89.0 % respectively, and DNA–DNA hybridization of the isolates and M. wolinii DSM 11976T showed a 20 % reassociation. Strain JH1T exhibited 92 % DNA–DNA relatedness with strains JH4 and JH8, and their 16S rRNA gene and mcrA sequences were identical. Cells stained Gram-positive and were non-motile rods, 1.5–1.8 µm long and 0.6 µm wide. The strains were able to use H2/CO2 and formate. The optimum temperature and pH ranges for growth were 37–40 °C and pH 6.5–7.0. The DNA G+C content of strain JH1T was 28 mol%. Based on data from this study using a polyphasic approach, the three strains represent a novel species of genus Methanobrevibacter , for which the name Methanobrevibacter boviskoreani sp. nov. is proposed. The type strain is JH1T ( = KCTC 4102T = JCM 18376T).

Two halophilic moderately acidophilic archaeal strains, MH1-136-2T and MH1-370-1 were isolated from commercial salt samples made from seawater in Japan and Indonesia, respectively. Cells of the two strains were pleomorphic and Gram-stain-negative. Strain MH1-136-2T was pink pigmented, while MH1-370-1 was orange–red pigmented. Strain MH1-136-2T was able to grow at 9–30 % (w/v) NaCl (with optimum, 21 % NaCl, w/v) at pH 4.5–6.2 (optimum, pH 5.2–5.5) and at 18–55 °C (optimum, 45 °C). Strain MH1-370-1 was able to grow at 12–30 % (w/v) NaCl (optimum, 18 %, w/v) at pH 4.2–6.0 (optimum, pH 5.2–5.5) and 20–50 °C (optimum, 45 °C). Strain MH1-136-2T required at least 1 mM Mg2+, while MH1-370-1 required at least 10 mM for growth. Both strains reduced nitrate and nitrite under aerobic conditions. The 16S rRNA gene sequences of strains MH1-136-2T and MH1-370-1 were identical, and the closest relative was Halarchaeum rubridurum MH1-16-3T with 98.3 % similarity. The level of DNA–DNA relatedness between these strains was 90.9 % and 92.4 % (reciprocally), while that between MH1-136-2T and Halarchaeum acidiphilum MH1-52-1T, Halarchaeum salinum MH1-34-1T and Halarchaeum rubridurum MH1-16-3T was 37.7 %, 44.3 % and 41.1 % (each an average), respectively. Based on the phenotypic, genotypic and phylogenetic analyses, it is proposed that the isolates represent a novel species of the genus Halarchaeum , for which the name Halarchaeum nitratireducens sp. nov. is proposed. The type strain is MH1-136-2T ( = JCM 16331T = CECT 7573T) isolated from solar salt produced in Japan.

A methanogenic organism from the domain Archaea , designated strain T10T, was isolated from groundwater sampled from a deep diatomaceous shale formation located in Horonobe, Hokkaido, Japan. The strain utilized H2/CO2 and formate as substrates for methanogenesis. Cells were strictly anaerobic, Gram-negative-staining, flagellated, irregular coccoids, 0.7–1.6 µm in diameter, and occurred singly. The strain grew at 25–45 °C (optimum 37–42 °C), at pH 5.8–8.2 (optimum pH 6.7–6.8) and in the presence of 0–1.3 M NaCl (optimum 0.1–0.2 M NaCl). The G+C content of the genomic DNA was 62.9 mol%. 16S rRNA gene sequencing revealed that, although the strain is a member of the genus Methanoculleus , it clearly differed from all described species of this genus (95.5–98.3 % sequence similarity). Values for DNA–DNA hybridization with type strains of closely related Methanoculleus species were less than 50 %. Phenotypic and phylogenetic features of strain T10T clearly indicate that it represents a novel species of the genus Methanoculleus , for which the name Methanoculleus horonobensis sp. nov. is proposed. The type strain is T10T ( = DSM 21626T = JCM 15517T).

A novel Gram-stain-positive, non-endospore-forming, coccoid actinobacterium, designated strain D3-40T, was isolated from the soil of a natural cave and characterized by means of a polyphasic taxonomic analysis. 16S rRNA gene sequence analysis showed that strain D3-40T is a member of the suborder Micrococcineae and forms a distinct branch at the base of a Brevibacteriaceae cluster. Its closest relative is the type strain of Brevibacterium samyangense (95.7 % sequence similarity). The chemotaxonomic characteristics were as follows: the cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid; the major menaquinone was MK-9(H2); the polar lipids consisted of phosphatidylglycerol, phosphatidylinositol, an unknown glycolipid and an unknown phospholipid; the major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, C16 : 0 and cyclohexyl-C17 : 0; mycolic acids were absent. The G+C content of the DNA was 64.3 mol%. On the basis of morphological, chemotaxonomic and phylogenetic data, it is suggested that the organism represents a novel species of a new genus within the family Brevibacteriaceae , for which the name Spelaeicoccus albus gen. nov., sp. nov. is proposed. The type strain of the type species is D3-40T ( = KCTC 29141T = DSM 26341T).

A novel endophytic actinobacterium, designated strain YIM 67072T, was isolated from healthy roots of Dysophylla stellata (Lour.) Benth. Cells of this aerobic, cream–yellow-coloured strain occurred singly, in pairs or in tetrads, were Gram-stain-positive and ovoid- to spherical-shaped. Strain YIM 67072T grew at 4–45 °C, pH 5.0–10.0 and in the presence of 0–7 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 67072T belonged to the genus Rothia . The isolate contained MK-7 as the major component of the quinone system. The peptidoglycan type was A3α. The polar lipid profile consisted predominantly of diphosphatidylglycerol and glycolipids. The major fatty acids were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The DNA G+C content was 53.2 mol%. However, strain YIM 67072T differed from its closest relatives Rothia nasimurium CCUG 35957T (98.5 % 16S rRNA gene sequence similarity), Rothia amarae JCM 11375T (97.6 %) and Rothia terrae L-143T (97.3 %) in many phenotypic characteristics. Moreover, the levels of DNA–DNA relatedness between the novel isolate and the three above-mentioned type strains were 28.7±1.3 %, 36.5±1.2 %, 46.8±1.5 %, respectively. Based on comparative analysis of physiological and chemotaxonomic data, strain YIM 67072T represents a novel species of the genus Rothia , for which the name Rothia endophytica sp. nov. is proposed. The type strain is YIM 67072T ( = DSM 26247T = JCM 18541T).

An actinomycete strain, SP03-05T, was isolated from a marine sponge sample (Xestospongia sp.) collected from Phuket Province of Thailand. The strain was aerobic, Gram-stain-positive and produced single spores at the tips of the substrate mycelium. Strain SP03-05T contained meso-diaminopimelic acid in the peptidoglycan; whole-cell sugars were arabinose, galactose, glucose, rhamnose, ribose and xylose. The polar lipid profile of strain SP03-05T consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides and unknown polar lipids. Morphological and chemotaxonomic characteristics of the strain identified it as a member of the family Micromonosporaceae . Phylogenetic analysis based on 16S rRNA gene sequences showed similarity of the strain to Verrucosispora lutea YIM 013T (96.90 %), Verrucosispora sediminis MS426T (96.90 %), Verrucosispora gifhornensis DSM 44337T (96.80 %), Verrucosispora maris AB-18-032T (96.80 %) and Verrucosispora qiuiae RtIII47T (95.40 %). The DNA G+C content was 72.4 mol%. The phenotypic, genotypic and DNA–DNA hybridization results supported the classification of this strain as a representative of a novel species in the genus Verrucosispora , for which the name Verrucosispora andamanensis sp. nov. is proposed. The type strain is SP03-05T ( = BCC 45620T = NBRC 109075T).

A novel actinomycete strain, designed MW4-36T, was isolated from tropical forest soil in Nakhon Sawan Province, Thailand. Morphological and chemotaxonomic characteristics of this strain clearly demonstrated that it belongs to the genus Dactylosporangium . The strain formed finger-shaped sporangia on short sporangiophores that emerged directly from substrate hyphae. The cell-wall peptidoglycan contained glutamic acid, glycine, alanine and meso-diaminopimelic acid including 3-hydroxy-meso-diaminopimelic acid; arabinose, glucose, rhamnose, ribose and xylose were found as whole-cell sugars. The diagnostic phospholipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol; no phosphatidylcholine was found. The predominant menaquinones were MK-9(H8) and MK-9(H6). Mycolic acids were not detected. The predominant cellular fatty acids were iso-C15 : 0, iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The G+C content of the genomic DNA was 72.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences also indicated that the strain should be classified in the genus Dactylosporangium and showed that the closest relative was Dactylosporangium maewongense JCM 15933T (99.4 % similarity). These taxonomic data revealed that strain MW4-36T could be readily distinguished from its phylogenetically closest relative. On the basis of these phenotypic and genotypic data, strain MW4-36T is considered to represent a novel species, for which the name Dactylosporangium siamense sp. nov. is proposed. The type strain is MW4-36T ( = BCC 34901T = NBRC 106093T).

Dermatophilus -like bacteria were observed in histological examinations of samples of diseased foot skin from greater flamingos (Phoenicopterus roseus) living in zoological gardens in Switzerland. When grown on TSA-SB containing polymyxin B, the bacteria isolated from these skin samples formed hyphae, as is typical for Dermatophilus congolensis , but these bacteria were non-haemolytic. The closest relatives based on 16S rRNA gene sequences were the two members of the genus Arsenicicoccus , Arsenicicoccus bolidensis and Arsenicicoccus piscis . A representative of the isolated strains shared 34.3 % DNA–DNA relatedness with the type strain of A. bolidensis , 32.3 % with the type strain of A. piscis and 34.5 % with the type strain of D. congolensis , demonstrating that these strains do not belong to any of these species. The phenotypic characteristics differed from those of members of the genus Arsenicicoccus as well as from those of D. congolensis . The G+C content of strain KM 894/11T was 71.6 mol%. The most abundant fatty acids were iso-C15 : 0, summed feature 3 (including C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C18 : 1ω9c. MK-8(H4) was the predominant menaquinone. Cell-wall structure analysis revealed that the peptidoglycan type was A3γ ll-Dpm–Gly (type A41.1). Based on genotypic and chemotaxonomic characteristics, the isolated strains represent a novel species within the genus Arsenicicoccus , for which the name Arsenicicoccus dermatophilus sp. nov. is proposed. The type strain is KM 894/11T ( = DSM 25571T = CCUG 62181T = CCOS 690T), and strain KM 1/12 ( = DSM 25572 = CCUG 62182 = CCOS 691) is a reference strain.

A novel Gram-stain-positive, non-motile, rod-shaped bacterium, designated 5GHs34-4T, was isolated from greenhouse soil in Yongin, Republic of Korea. Growth occurred in the temperature range of 10–37 °C (optimum 28–30 °C) and at pH 5.0–9.0 (optimum pH 7.0). It can tolerate up to 3 % (w/v) NaCl. The strain showed 16S rRNA gene sequence similarity levels of 95.1–97.0 % with species of the genus Leifsonia , 95.7–96.7 % with species of the genus Herbiconiux , 95.1–96.4 % with species of the genus Salinibacterium and 96.1 % with Labedella gwakjiensis and Homoserinimonas aerilata . The highest sequence similarities (97.0 %) were with Leifsonia aquatica JCM 1368T, Leifsonia poae VKM Ac-1401T and Leifsonia psychrotolerans LI1T. The peptidoglycan type determined for strain 5GHs34-4T was B2γ with dl-2,4-diaminobutyric acid at position 3. The murein was of the acetyl type. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The menaquinones detected were MK-13, MK-12 and MK-14, and the major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), anteiso-C17 : 0 and anteiso-C15 : 0. The phenotypic and phylogenetic traits of strain 5GHs34-4T differed in some respects from those of members of the family Microbacteriaceae . Therefore, strain 5GHs34-4T is considered to represent a novel species of a new genus in the family Microbacteriaceae , for which the name Rudaibacter terrae gen. nov., sp. nov. is proposed. The type strain is 5GHs34-4T ( = KACC 15523T = NBRC 108754T).

Two novel isolates of rapidly growing, Gram-stain-positive, non-chromogenic species of the genus Mycobacterium , strain YIM M13028T from a sediment sample collected from the South China Sea (19° 30.261′ N 111° 0.247′ E) at a depth of 42 m and strain YIM 121001T from a coastal zone sand sample collected in Dubai, United Arab Emirates, were obtained in our laboratory. Their taxonomic positions were determined by a polyphasic approach. Good growth of the two strains was observed at 28 °C and pH 7.0 with 0–2 % NaCl on tryptic soy agar medium. Both strains formed round orange–red colonies, strain YIM M13028T had a rough surface, while YIM 121001T was smooth. Cellular fatty acids, whole-cell protein profiles and TLC analysis of their mycolic acids show significant differences from reference stains. Phenotypic characteristics and multilocus sequence analysis (MLSA) of 16S rRNA gene, hsp65, rpoB and 16S–23S internal transcribed spacer (ITS) sequences indicated that both strains YIM M13028T and YIM 121001T belong to the genus Mycobacterium . DNA–DNA hybridization values revealed a low relatedness (<70 %) of the two isolates with the type strains Mycobacterium neoaurum DSM 44074T and Mycobacterium hodleri DSM 44183T. The low DNA–DNA hybridization values (40.4±3.5 %) between strains YIM M13028T and YIM 121001T and phenotypic distinctiveness indicated that the two strains were representatives of different novel species of the genus Mycobacterium . The names proposed for these novel species are Mycobacterium sediminis sp. nov. and Mycobacterium arabiense sp. nov., and the type strains are YIM M13028T ( = DSM 45643T = KCTC 19999T) and YIM 121001T ( = DSM 45768T = JCM 18538T), respectively.

A novel actinobacterial strain, 3-wff-81T, was isolated from interfacial sediment of the eutrophic Taihu Lake in Jiangsu Province (China) and subjected to polyphasic taxonomic characterization. The strain formed pale orange-pigmented colonies comprising rod-shaped cells on R2A agar. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain 3-wff-81T belonged to the genus Geodermatophilus , with Geodermatophilus soli PB34T (99.1 % similarity) and Geodermatophilus terrae PB261T (98.3 % similarity) as closest relatives. The major fatty acids were 16 : 0 iso, 15 : 0 iso, 17 : 1ω8c and 14 : 0 iso. The predominant menaquinones were MK-9(H4) and MK-9. Polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides. The genomic DNA G+C content was 73.2 mol%. DNA–DNA relatedness values with G. soli PB34T and G. terrae PB261T were 42.8 % and 39.6 %, respectively. Based on the physiological, biochemical and chemotaxonomic data, it is proposed that strain 3-wff-81T represents a novel species named Geodermatophilus taihuensis sp. nov. with 3-wff-81T ( = CGMCC 1.12303T = NBRC 109416T) as the type strain.

Two actinobacterial strains, CPCC 203464T and CPCC 203448, isolated from surface-sterilized stems of medicinal plants were subjected to a polyphasic taxonomic study. These two aerobic organisms formed pale yellow colonies on tryptic soy agar (TSA). Cells were Gram-stain-positive, non-acid-fast, non-motile, rod- or coccoid-like elements. Comparative 16S rRNA gene sequence analysis indicated that strains CPCC 203464T and CPCC 203448 were most closely related to the type strains of the species of the genus Williamsia . Chemotaxonomic properties such as containing meso-diaminopimelic acid in the cell wall, arabinose, galactose and ribose being the whole-cell hydrolysate sugars, phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylinositol (PI) as the phospholipids, and C16 : 0, 10-methyl C18 : 0, C18 : 1ω9c, C16 : 1ω7c and/or iso-C15 : 0 2-OH as major fatty acids supported the affiliation of strains CPCC 203464T and CPCC 203448 to the genus Williamsia . The DNA–DNA hybridization values in combination with differentiating chemotaxonomic and physiological characteristics strongly suggested that these two isolates should be classified as representatives of a novel species of the genus Williamsia . The name Williamsia sterculiae sp. nov. is proposed, with strain CPCC 203464T ( = DSM 45741T = KCTC 29118T) as the type strain.

A novel desiccation-tolerant, xeroprotectant-producing bacterium, designated strain 4J27T, was isolated from a Nerium oleander rhizosphere subjected to seasonal drought in Granada, Spain. Phylogenetic analysis based on 16S rRNA gene sequencing placed the isolate within the genus Arthrobacter , its closest relative being Arthrobacter phenanthrenivorans Shep3 DSM 18606T, with which it showed 99.23 % 16S rRNA gene sequence similarity. DNA–DNA hybridization measurements showed less than 25 % relatedness between strain 4J27T and Arthrobacter phenanthrenivorans DSM 18606T. The DNA base composition of strain 4J27T was 65.3 mol%. The main fatty acids were anteiso C15 : 0, anteiso C17 : 0, C16 : 0 and iso C16 : 0 and the major menaquinone was MK-9 (H2). The peptidoglycan type was A3α with an l-Lys–l-Ser–l-Thr–l-Ala interpeptide bridge. The bacterium tested positive for catalase activity and negative for oxidase activity. Phylogenetic, chemotaxonomic and phenotypic analyses indicated that the desiccation-tolerant strain 4J27T represents a novel species within the genus Arthrobacter , for which the name Arthrobacter siccitolerans is proposed. The type strain is 4J27T ( = CECT 8257T = LMG 27359T).

A Gram-stain-positive actinobacterium, designated strain SCSIO 15020T, was isolated from sediment of the South China Sea, and characterized by using a polyphasic approach. The temperature range for growth was 24–60 °C, with optimal growth occurring at 50 °C. The pH range for growth was 6–10 (optimum pH 8–9). The NaCl concentration range for growth was 0–5 % (w/v). The peptidoglycan type was A4α. Polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and an unknown polar lipid. The major menaquinone was MK-8(H4); MK-7(H4) was present as a minor component. The major fatty acids (>5 %) were anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0. The DNA G+C content of strain SCSIO 15020T was 73.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SCSIO 15020T belonged to the genus Georgenia , with the closest neighbours being Georgenia muralis 1A-CT (96.3 % similarity), Georgenia thermotolerans TT02-04T (95.7 %) and Georgenia ruanii YIM 004T (95.6 %). Based on evidence from the present polyphasic study, strain SCSIO 15020T is considered to represent a novel species of the genus Georgenia , for which the name Georgenia sediminis sp. nov. is proposed. The type strain is SCSIO 15020T ( = DSM 25884T = NBRC 108941T).

An actinomycete with well-branched mycelia, designated strain YIM 120521T, was isolated from soil collected from the banks of the Nujiang River, Yunnan Province, south-west China. Both aerial and substrate mycelia were white and non-pigmented. Growth was observed at 4–40 °C (optimum 28 °C), pH 6.0–9.0 (optimum 7.0) and in 0–4 % (w/v) NaCl (optimum 0 %). Analysis of the 16S rRNA gene sequence revealed that strain YIM 120521T belongs to the genus Allokutzneria with the highest sequence similarity to Allokutzneria albata DSM 44149T (98.4 %). However, the mean DNA–DNA relatedness value between the two strains was below 70 %. Chemotaxonomic characteristics supported the inclusion of strain YIM 120521T in the genus Allokutzneria , with rhamnose, arabinose, glucose, galactose and mannose as the whole-cell sugars, meso-diaminopimelic acid as the cell-wall diamino acid and MK-9(H4) as the predominant menaquinone. On the basis of physiological, biochemical and chemotaxonomic characteristics, strain YIM 120521T is considered to represent a novel species of the genus Allokutzneria , for which the name Allokutzneria multivorans sp. nov. is proposed. The type strain is YIM 120521T ( = JCM 17342T = DSM 45532T).

A novel high DNA G+C content bacterium, designated strain D7-27T, was isolated from clay soils collected inside a natural cave in Jeju, Republic of Korea. The cells of the organism were aerobic, Gram-stain-positive, non-motile rods; its colonies were white, circular and entire in margin. Phylogenetic analyses based on 16S rRNA gene sequence comparison showed that strain D7-27T formed a coherent cluster with Humibacter albus of the family Microbacteriaceae (97.6 % sequence similarity). The cell-wall peptidoglycan contained ornithine and 2,4-diaminobutyric acid as the diagnostic diamino acids. The major menaquinones were MK-12 and MK-11, with MK-10 as a minor component. The polar lipids consisted mainly of phosphatidylglycerol and an unknown glycolipid. Mycolic acids were not present. The predominant fatty acids were anteiso-C17 : 0 and cyclohexyl-C17 : 0. The DNA G+C content was 66.3 mol%. DNA–DNA relatedness between strain D7-27T and H. albus DSM 18994T was 28.6 % (17.6 % in a reciprocal test). On the basis of the phenotypic, chemotaxonomic and DNA–DNA hybridization data, strain D7-27T ( = KCTC 33009T = DSM 25738T) is considered as the type strain of a novel species of the genus Humibacter , for which the name Humibacter antri sp. nov. is proposed. An emended description of the genus Humibacter is also provided.