- Volume 60, Issue 12, 2010

A marine bacterium, strain KME 001T, was isolated from the siphon tissue of a marine ascidian, Halocynthia roretzi, collected off the coast of Gangneung, Korea. Strain KME 001T was a Gram-positive, aerobic, non-spore-forming, rod-shaped and non-motile bacterium. Phylogenetic analysis using 16S rRNA gene sequences revealed that strain KME 001T clustered with the genus Aeromicrobium and was closely related to Aeromicrobium ginsengisoli, Aeromicrobium erythreum and Aeromicrobium ponti with 97.7, 97.6 and 97.5 % sequence similarities, respectively. The strain was capable of growth at a variety of temperatures (10–42 °C) and over a broad pH range (5.0–10.0). NaCl was required for robust growth of the strain. The diagnostic diamino acid of the cell-wall peptidoglycan was ll-diaminopimelic acid. The predominant menaquinone was MK-9(H4). The predominant fatty acids were C18 : 1 ω9c, C16 : 0 and 10-methyl C18 : 0. The DNA–DNA hybridization analyses showed that DNA–DNA relatedness values between strain KME 001T and its nearest neighbours, A. ginsengisoli KCTC 19207T, A. erythreum KCCM 41104T and A. ponti KACC 20565T, were 49.6, 57.1 and 63.5 %, respectively. The DNA G+C content of strain KME 001T was 75.9 mol%. Chemical investigation of the liquid culture medium of strain KME 001T led to the isolation of taurocholic acid as a major secondary metabolite. On the basis of phylogenetic and phenotypic data, strain KME 001T is classified as representing a novel species of the genus Aeromicrobium, for which the name Aeromicrobium halocynthiae sp. nov. is proposed. The type strain is KME 001T (=JCM 15749T=KCCM 90079T).

Gram-reaction-positive, aerobic, non-spore-forming, irregular rod-shaped bacteria, designated AHU1821T and AHU1820, were isolated from an ice wedge in the Fox permafrost tunnel, Alaska. The strains were psychrophilic, growing at −5 to 27 °C. Phylogenetic analysis of the 16S rRNA and gyrB gene sequences indicated that the ice-wedge isolates formed a clade distinct from other mycolic-acid-containing bacteria within the suborder Corynebacterineae. The cell wall of strains AHU1821T and AHU1820 contained meso-diaminopimelic acid, arabinose and galactose, indicating chemotype IV. The muramic acids in the peptidoglycan were glycolated. The predominant menaquinone was MK-9(H2). The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and an unidentified glycolipid. The major fatty acids were hexadecenoic acid (C16 : 1), hexadecanoic acid (C16 : 0), octadecenoic acid (C18 : 1) and tetradecanoic acid (C14 : 0). Tuberculostearic acid was present in relatively small amounts (1 %). Strains AHU1821T and AHU1820 contained mycolic acids with 42–52 carbons. The DNA G+C content of the two strains was 69.3–71.6 mol% (T m). 16S rRNA, rpoB and recA gene sequences were identical between strains AHU1821T and AHU1820 and those of the gyrB gene showed 99.9 % similarity. Based on phylogenetic and phenotypic evidence, strains AHU1821T and AHU1820 represent a single novel species of a novel genus, for which the name Tomitella biformata gen. nov., sp. nov. is proposed. The type strain of Tomitella biformata is AHU1821T (=DSM 45403T =NBRC 106253T).

Strain DCY37T was isolated from a soil sample of a ginseng field in the Republic of Korea and characterized in order to determine its taxonomic position. Cells were Gram-staining-positive, heterotrophic, strictly aerobic, non-motile short rods. 16S rRNA gene sequence analysis revealed that strain DCY37T belongs to the genus Microbacterium. According to 16S rRNA gene sequence analysis, it is closely related to Microbacterium aerolatum DSM 14217T (98.8 %), Microbacterium hydrocarbonoxydans DSM 16089T (98.5 %), Microbacterium natoriense JCM 12611T (98.5 %), Microbacterium foliorum (98.4 %) and Microbacterium phyllosphaerae (98.3 %). However, DNA–DNA hybridization studies showed reassociation values of less than 70 % between representative strains and DCY37T. The DNA G+C content was 64.5 mol%. Strain DCY37T possessed chemotaxonomic markers that were consistent with classification in the genus Microbacterium, i.e. MK-12 and MK-13 as the major menaquinones and anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0 as the predominant cellular fatty acids. The major cell wall sugars were ribose, xylose and galactose. The diamino acid in cell-wall hydrolysates of strain DCY37T was ornithine and major cell-wall amino acids were alanine, glycine, d-glutamic acid and serine. The major polar lipids were glycolipid, phosphatidylglycerol, diphosphatidylglycerol and unknown aminolipids. Based on these data, DCY37T (=KCTC 19526T =JCM 15516T) should be classified as the type strain of a novel species of the genus Microbacterium, for which the name Microbacterium ginsengiterrae sp. nov. is proposed.

An aerobic, actinobacterial strain with rod-shaped spores, EUM 221T, which was isolated from the surface-sterilized stem of a grey box tree (Eucalyptus microcarpa), is described. Phylogenetic evaluation based on 16S rRNA gene sequence similarity showed that this isolate belongs to the family Pseudonocardiaceae, with the closest neighbour being Pseudonocardia zijingensis 6330T (98.7 %). The level of 16S rRNA gene sequence similarity between the isolate and species of the genus Pseudonocardia with validly published names ranged from 95 to 98 %. Chemotaxonomic data (meso-diaminopimelic acid; major menaquinone MK-8(H4); major fatty acid iso-C16 : 0) confirmed the affiliation of strain EUM 221T to the genus Pseudonocardia. The results of the phylogenetic analysis, including physiological and biochemical studies in combination with DNA–DNA hybridization, allowed the genotypic and phenotypic differentiation of strain EUM 221T from the closest described species. Therefore, this strain represented a novel species and the name proposed is Pseudonocardia adelaidensis sp. nov. The type strain is EUM 221T (=DSM 45352T =ACM 5286T).

Strain Eg1T, an anaerobic, Gram-stain-positive, non-motile and non-spore-forming bacterium, was isolated from human faeces. The optimal temperature for growth was 37 °C and tests for oxidase and catalase activities gave negative results. Fructose-6-phosphate phosphoketolase activity was detected. Acid was produced during fermentation of several substrates, including glucose. The end products of glucose fermentation were acetic acid and lactic acid, which were produced in a molar ratio of 1.76 : 1 (approximately 3 : 2). The G+C content was 57.8 mol%. Comparative analysis of 16S rRNA gene sequences showed that strain Eg1T was closely related to Bifidobacterium adolescentis YIT 4011T (98.36 % 16S rRNA gene sequence similarity) and Bifidobacterium ruminantium JCM 8222T (97.93 %) and analysis of hsp60 sequences showed that strain Eg1T was closely related to B. adolescentis JCM 1275T (99.35 % hsp60 sequence similarity) and B. ruminantium JCM 8222T (92.13 %). However, despite these degrees of similarity being high enough for strain Eg1T to be included at the same species level as B. adolescentis and B. ruminantium (96.5–100 % for the genus Bifidobacterium), the isolate could be distinguished from B. adolescentis KCTC 3216T and B. ruminantium KCTC 3425T by low levels of DNA–DNA relatedness (41 and 17 %, respectively). Based on phenotypic, genotypic and phylogenetic analyses, we propose that strain Eg1T is classified in a novel species, Bifidobacterium stercoris sp. nov. The type strain is Eg1T (=KCTC 5756T =JCM 15918T).

A Gram-positive, non-spore-forming actinobacterium (Sj 10T) was isolated on tryptone soy agar from the air of a duck barn after filter sampling. Based on 16S rRNA gene sequence similarity studies, strain Sj 10T was shown to belong to the genus Leucobacter and was closely related to Leucobacter chromiireducens subsp. chromiireducens L-1T (97.8 %), Leucobacter tardus DSM 19811T (97.3 %) and Leucobacter luti RF6T (97.3 %). The peptidoglycan of strain Sj 10T contained 2,4-diaminobutyric acid in combination with a lower amount of lysine as diagnostic diamino acids. In addition, threonine, glycine, alanine and glutamic acid were found. Menaquinone MK-11 was the major respiratory quinone; MK-12 and MK-10 were detected in minor amounts. The polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol and one unknown component each of a phospholipid, glycolipid and aminoglycolipid. Strain Sj 10T contained the major fatty acids anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0, like other members of the genus Leucobacter. Results of DNA–DNA hybridization, physiological and biochemical tests enabled strain Sj 10T to be differentiated genotypically and phenotypically from the most closely related Leucobacter species. Strain Sj 10T represents a novel species of the genus Leucobacter, for which the name Leucobacter aerolatus sp. nov. is proposed, with Sj 10T (=DSM 22806T =CCM 7705T) as the type strain.

An actinomycete strain, designated YU1183-22T, was isolated from a compost sample collected in Nikko, Japan. The isolate formed white aerial mycelium with relatively long aerial hyphae showing chains of arthrospores. Strain YU1183-22T grew with 0–10 % (w/v) NaCl, at pH 6–11 and at 10–37 °C (optimum 30 °C). Strain YU1183-22T contained meso-diaminopimelic acid and no diagnostic sugars. The predominant menaquinones were MK-10(H10) and MK-10(H8). The polar lipids were phosphatidylcholine and phosphatidylglycerol. The major cellular fatty acids were iso-C16 : 0, anteiso-C17 : 0 and tuberculostearic acid. The G+C content of the DNA was 72.3 mol%. Chemotaxonomic and morphological characterization clearly demonstrated that strain YU1183-22T belonged to the genus Nocardiopsis. Phylogenetic analysis using 16S rRNA gene sequences showed that the isolate was closely related to Nocardiopsis salina YIM 90010T (98.0 % 16S rRNA gene sequence similarity), Nocardiopsis xinjiangensis YIM 90004T (97.9 %) and Nocardiopsis kunsanensis HA-9T (97.3 %). However, DNA–DNA relatedness as well as physiological and biochemical analyses showed that strain YU1183-22T could be differentiated from its closest phylogenetic relatives. It is proposed that this strain be classified as a representative of a novel species of the genus Nocardiopsis, with the name Nocardiopsis nikkonensis sp. nov. The type strain is YU1183-22T (=NBRC 102170T =KCTC 19666T).

A novel bacterium, designated TRM 415T, belonging to the genus Brevibacterium, was isolated from a sediment sample from a salt lake in Xinjiang province, China. Comparative 16S rRNA gene sequence analysis indicated that strain TRM 415T was phylogenetically most closely related to Brevibacterium album YIM 90718T (98.4 % sequence similarity) and had low similarity (<95.5 %) to other species of the genus Brevibacterium; however, DNA–DNA hybridization studies between strain TRM 415T and B. album YIM 90718T showed only 41.3 % relatedness. Strain TRM 415T possessed meso-diaminopimelic acid as the diagnostic cell-wall diamino acid, MK-8(H2) as the major menaquinone and polar lipids including phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids were anteiso-C17 : 0 and anteiso-C15 : 0. The genomic DNA G+C content was 69 mol%. Based on the evidence from this polyphasic study, strain TRM 415T represents a novel species of the genus Brevibacterium, for which the name Brevibacterium salitolerans sp. nov. is proposed. The type strain is TRM 415T (=JCM 15900T =CCTCC AB 208328T =KCTC 19616T).

A novel thermophilic and lithoautotrophic sulfate-reducing archaeon was isolated from black rust formed on the steel surface of a borehole observatory (CORK 1026B) retrieved during IODP Expedition 301 on the eastern flank of Juan de Fuca Ridge, eastern Pacific Ocean. Cells of the strain were lobe-shaped or triangular. The optimum temperature, pH and NaCl concentration for growth were 75 °C, pH 7 and 2 % (w/v), respectively. The isolate was strictly anaerobic, growing lithoautotrophically on H2 and CO2 using sulfate, sulfite or thiosulfate as electron acceptors. Lactate and pyruvate could serve as alternative energy and carbon sources. The G+C content of the genomic DNA was 42 mol%. Phylogenetic analyses of the 16S rRNA gene indicated that the isolate was closely related to members of the family Archaeoglobaceae, with sequence similarities of 90.3–94.4 %. Physiological and molecular properties showed that the isolate represents a novel species of the genus Archaeoglobus. The name Archaeoglobus sulfaticallidus sp. nov. is proposed; the type strain is PM70-1T (=DSM 19444T=JCM 14716T).

A novel extremely halophilic archaeon, strain 194-10T, was isolated from a solar salt sample imported into Japan from the Philippines. Strain 194-10T was pleomorphic, neutrophilic and mesophilic and required at least 10 % (w/v) NaCl but no MgSO4 . 7H2O for growth; it exhibited optimal growth at 15 % (w/v) NaCl and 60 mM MgSO4 . 7H2O. Strain 194-10T grew at 20–45 °C (optimum, 30 °C) and pH 6.0–9.0 (optimum, pH 6.5–7.0). The G+C content of its DNA was 59.8 mol%. 16S rRNA gene sequence analysis revealed closest proximity to Halostagnicola larsenii XH-48T (98.5 % similarity), the sole representative of the genus Halostagnicola. Polar lipid analysis revealed that strain 194-10T contained phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester (the latter derived from both C20C20 and C20C25 archaeol) and several unidentified glycolipids. The results of DNA–DNA hybridization (20.7 % relatedness between Hst. larsenii JCM 13463T and strain 194-10T) and physiological and biochemical characteristics allowed differentiation of strain 194-10T from Hst. larsenii XH-48T. Therefore, strain 194-10T represents a novel species of the genus Halostagnicola, for which the name Halostagnicola kamekurae sp. nov. is proposed, with the type strain 194-10T (=DSM 22427T =JCM 16110T =CECT 7536T).

A novel hydrogenotrophic methanogen, designated strain MRE50T, was isolated from a methanogenic consortium, which was originally established from an Italian rice field soil. Cells were non-motile rods, 1.3–2.8 μm long and 0.4–0.7 μm wide. Coccoid cells were also observed in cultures at the late-exponential phase of growth. Strain MRE50T grew at 37–55 °C (optimally at 45 °C), at pH 6–7.8 (optimally at pH 7.0) and in the presence of 0–20 g NaCl l−1. The isolate utilized H2/CO2 and formate for growth and methane production. Phylogenetic analyses of the 16S rRNA gene and the methanogen-specific marker gene mcrA showed that strain MRE50T is affiliated with the order Methanocellales, previously known as uncultured archaeal group Rice Cluster I. Based on both 16S rRNA gene and mcrA gene sequences, strain MRE50T was related most closely to Methanocella paludicola SANAET. Levels of sequence similarity were 92.5 and 86.1 %, respectively, indicating that strains MRE50T and Methanocella paludicola SANAET represent different species within the genus Methanocella. In addition, although these strains shared phenotypic properties including cell morphology and substrate utilization, they differed with respect to susceptibility to antibiotics, and temperature and NaCl ranges for growth. Given the phenotypic differences and the distinct phylogenetic placement of the new isolate relative to the type species of the genus Methanocella, strain MRE50T is considered to represent a novel species of the genus Methanocella, for which the name Methanocella arvoryzae sp. nov. is proposed. The type strain is MRE50T (=NBRC 105507T =DSM 22066T).

A yellow-pigmented bacterial strain, designated RIB1-6T, was isolated from a freshwater spring in Taiwan. Strain RIB1-6T was aerobic, Gram-negative, rod-shaped, non-motile and non-spore-forming. Growth occurred at 10–37 °C, at pH 7–8 and with 0–1 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain RIB1-6T belonged to the genus Terrimonas and its two closest neighbours were Terrimonas ferruginea ATCC 13524T and Terrimonas lutea DYT (16S rRNA gene sequence similarity 97.4 % and 93.5 %, respectively). Strain RIB1-6T contained iso-C15 : 0 (33.4 %), iso-C17 : 0 3-OH (18.2 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 14.7 %) and iso-C15 : 1 (11.5 %) as the predominant fatty acids. The major isoprenoid quinone was MK-7. The DNA G+C content of strain RIB1-6T was 47.3 mol%. On the basis of the genotypic and phenotypic data, strain RIB1-6T represents a novel species in the genus Terrimonas, for which the name Terrimonas aquatica sp. nov. is proposed. The type strain is RIB1-6T (=BCRC 17941T=LMG 24825T).

The taxonomic position of a novel Gram-stain-negative, aerobic, heterotrophic, gliding, yellow–orange-pigmented bacterium, isolated from the sea urchin Strongylocentrotus intermedius and designated strain KMM 6048T, was established. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the isolate was a member of the family Flavobacteriaceae affiliated with recognized species of the genus Gramella, forming a distinct lineage within the genus. 16S rRNA gene sequence similarities between strain KMM 6048T and the type strains of species of the genus Gramella were 97.4–98.4 %. In line with representative members of the genus Gramella, strain KMM 6048T was oxidase- and catalase-positive, hydrolysed gelatin and starch, utilized carbohydrates and possessed a DNA G+C content of 40.0 mol%. However, differentiating phenotypic traits and phylogenetic distinctiveness clearly indicated that the strain represented a novel species within the genus Gramella, for which the name Gramella marina sp. nov. is proposed; the type strain is KMM 6048T (=KCTC 12366T=LMG 25418T).

Five cold-adapted bacteria belonging to the genus Mucilaginibacter were isolated from lichen and soil samples collected from Finnish Lapland and investigated in detail by phenotypic and phylogenetic analyses. Based on 16S rRNA gene phylogeny, the novel strains represent three new branches within the genus Mucilaginibacter. The strains were aerobic, chemo-organotrophic, non-motile rods and formed pigmented, smooth, mucoid colonies on solid media. The strains grew between 0 and 33 °C (optimum growth at 25 °C) and at pH 4.5–8.0 (optimum growth at pH 6.0). The main cellular fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1 ω7c/iso-C15 : 0 2-OH) and iso-C17 : 0 3-OH and the major respiratory quinone was MK-7. The DNA G+C contents were 44.0–46.5 mol%. Based on phylogenetic, phenotypic and chemotaxonomic data, the strains represent three novel species of the genus Mucilaginibacter for which the names Mucilaginibacter frigoritolerans sp. nov. (type strain FT22T =ATCC BAA-1854T =LMG 25359T), Mucilaginibacter lappiensis sp. nov. (type strain ANJLI2T =ATCC BAA-1855T =LMG 25358T) and Mucilaginibacter mallensis sp. nov. (type strain MP1X4T =ATCC BAA-1856T =LMG 25360T) are proposed.

A Gram-negative, rod-shaped bacterial strain, NII-0905T, that was motile by gliding was isolated from soil of a dense forest collected from the Western Ghats of India and its taxonomic position was established. Strain NII-0905T contained MK-7 as the major menaquinone and anteiso-C17 : 0, anteiso-C15 : 0, iso-C16 : 0 and iso-C15 : 0 as the major cellular fatty acids. The DNA G+C content of strain NII-0905T was 51.47 mol%. 16S rRNA gene sequence-based phylogenetic analysis confirmed the placement of strain NII-0905T in the genus Pontibacter and strain NII-0905T exhibited 93.9–96.3 % 16S rRNA sequence similarity with type strains of species of the genus Pontibacter. On the basis of genotypic and phenotypic evidence, strain NII-0905T is considered to represent a novel species of the genus Pontibacter, for which the name Pontibacter niistensis sp. nov. is proposed. The type strain is NII-0905T (=NCIM 5339T =CCTCC AA 209057T).

Strain 7SM30T , an aerobic marine, Gram-negative, heterotrophic and yellow- to orange-pigmented bacterium isolated from seawater from Castellón, Spain, was characterized using a polyphasic approach. Analysis of the 16S rRNA gene sequence showed that the isolate represented a novel lineage within the family Flavobacteriaceae. The most closely related genera were Pseudozobellia, Zobellia and Kriegella. Cells of strain 7SM30T were non-motile rods that required sea salts for growth, used a wide variety of carbohydrates as sole carbon and energy sources and, unlike species of the genera Pseudozobellia and Zobellia, did not possess flexirubin-type pigment or hydrolyse agar. Strain 7SM30T contained MK6 as the sole respiratory quinone. Phosphatidylethanolamine (PE) was the only identifiable polar lipid, although other lipids were also detected. The predominant cellular fatty acids were saturated C15 and monounsaturated C15. The DNA G+C content was around 40 mol%. On the basis of extensive phenotypic and phylogenetic comparative analysis, it is concluded that the new strain represents a novel genus and species, for which the name Euzebyella saccharophila gen. nov., sp. nov., is proposed. The type strain of the type species is 7SM30T (=CECT 7477T=KCTC 22655T).

A Gram-negative, non-spore-forming, yellow-pigmented bacterium, strain LQY-7T, was isolated from activated sludge treating synthetic pyrethroid-manufacturing wastewater. The taxonomic status of the strain was determined using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain LQY-7T was a member of the genus Flavobacterium but had low similarities with other species of this genus (95.0 % similarity with Flavobacterium indicum GPTSA100-9T and <94 % similarities with other Flavobacterium species). On the basis of phenotypic, genetic and phylogenetic data, strain LQY-7T should be classified as a representative of a novel species of the genus Flavobacterium, for which the name Flavobacterium haoranii sp. nov. is proposed; the type strain is LQY-7T (=ACCC 05409T =KCTC 23008T).

A novel aerobic, heterotrophic bacterium, designated BiosLi39T, was isolated from the South East Pacific Ocean. Cells were Gram-negative gliding rods forming yellow colonies on marine agar. The isolate was oxidase-, catalase- and alkaline phosphatase-positive and β-galactosidase-negative. Strain BiosLi39T grew at 20-37 °C (optimum 30 °C), at pH 7.0–9.0 (optimum pH 8.0) and with 20–60 g NaCl l−1 (optimum 30–50 g NaCl l−1). The fatty acids (>1 %) comprised iso-C14 : 0, iso-C15 : 1 G, iso-C15 : 0, anteiso-C15 : 0, C15 : 1 G, C15 : 0, iso-C15 : 0 2-OH, iso-C16 : 1 G, iso-C16 : 0, iso-C16 : 0 3-OH, iso-C16 : 0 2-OH, iso-C17 : 0 3-OH, C17 : 0 2-OH and three unidentified components with equivalent chain lengths of 17.87, 18.10 and 18.71. A significant proportion of the hydroxylated fatty acids are amide-linked. The lipid pattern indicated the presence of phosphatidylethanolamine, two unidentified aminolipids and three unidentified polar lipids. The strain contained menaquinone 7 as the sole respiratory lipoquinone and did not produce flexirubin-type pigments. The G+C content of the genomic DNA was 37.2 mol%. Comparative 16S rRNA gene sequence analysis indicated that strain BiosLi39T was distantly related to all of the representatives of the phylum Bacteroidetes. Its closest relative was Marinoscillum furvescens IFO 15994T, with which it shared 92.5 % 16S rRNA gene sequence similarity. On the basis of genotypic, phenotypic and chemotaxonomic characteristics, we propose a novel genus and species, Ekhidna gen. nov., sp. nov., with type strain BiosLi39T (=DSM 19307T =CIP 109600T =OOB 398T).