- Volume 59, Issue 1, 2009

A coryneform bacterium isolated from a cow with a profound ulceration was characterized by using phenotypic and molecular taxonomic methods. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV and short-chain mycolic acids consistent with the genus Corynebacterium. Comparative 16S rRNA gene sequencing showed that the organism formed a hitherto unknown subline within the genus Corynebacterium. Sequence divergence values of greater than 3.6 % from recognized Corynebacterium species, together with phenotypic differences, showed that the unidentified bacterium represents a new member of this genus. On the basis of phenotypic and phylogenetic considerations, it is proposed that the novel bacterium be classified as representing a novel species of the genus Corynebacterium, with the name Corynebacterium ulceribovis sp. nov. The type strain is IMMIB L-1395T (=DSM 45146T=CCUG 55727T).

A novel Gram-positive, aerobic, short-rod-shaped bacterium, designated strain J112T, was isolated from black sand collected from Soesoggak, Jeju Island, Korea. The strain was found to be oxidase-negative and catalase-positive. Cells grew at 10–37 °C, at pH 5.5–8.0 and with 1–10 % NaCl. Growth occurred on marine agar but not on R2A or trypticase soy agar. A phylogenetic analysis based on 16S rRNA gene sequences showed that the strain belongs to the radiation of the genus Nocardioides. Strain J112T shared the highest 16S rRNA gene sequence similarities with Nocardioides marinisabuli SBS-12T (99.2 %), Nocardioides terrigena DS-17T (97.3 %), Nocardioides kribbensis KCTC 19038T (97.1 %) and type strains of other Nocardioides species with validly published names (<97 %). The DNA–DNA hybridization values between strain J112T and the three most closely related strains were low enough to justify the assignment of this strain to a novel species. On the basis of these phenotypic, phylogenetic and chemotaxonomic data, strain J112T represents a novel species of the genus Nocardioides, for which the name Nocardioides basaltis sp. nov. is proposed. The type strain is J112T (=KCTC 19365T=JCM 14945T).

Two bacterial strains, CP153-3 and CP177-2T, were isolated from biological soil crusts on the Colorado Plateau, USA, and assigned to the genus Patulibacter, according to 16S rRNA gene sequence analysis and phenotypic characteristics. The strains were Gram-positive, aerobic and psychrotolerant and showed positive catalase and negative oxidase reactions. Cells were motile in young cultures, motility consisting of subtle jerking motions, but no flagella could be detected. The strains shared high 16S rRNA gene sequence similarity (99.7 %) and DNA–DNA relatedness (99 %). They contained meso-diaminopimelic acid in the cell wall, the major menaquinone was MK-7(H2) and the predominant fatty acids were C18 : 1 ω9c and iso-C15 : 0. A low DNA–DNA hybridization value of 20 % with the type strain of the type species of the genus Patulibacter, Patulibacter minatonensis, as well as phenotypic differences, indicated that the isolates belong to a novel species, for which the name Patulibacter americanus sp. nov. is proposed. Strain CP177-2T (=ATCC BAA-1038T =DSM 16676T) was chosen as the type strain. An emended description of the genus Patulibacter is also presented. Further, two new orders are created to accommodate several families previously classified in the order Rubrobacterales Rainey et al. 1997. The first, Solirubrobacterales ord. nov., encompasses the families Solirubrobacteraceae, Conexibacteraceae and Patulibacteraceae, and the second, Thermoleophilales ord. nov., includes the family Thermoleophilaceae.

Actinobacteria comprise a substantial fraction of the bacterioplankton in freshwater lakes and streams. Numerous cultivation-independent investigations have retrieved actinobacterial 16S rRNA gene sequences from such habitats. The taxa detected in freshwater habitats are usually absent from terrestrial and marine systems. So far, none of the indigenous freshwater lineages is represented by a taxon with a validly published name. The seven organisms for which Candidatus status is described here were isolated from freshwater lakes and ponds located in tropical, subtropical and temperate climatic zones. Phylogenetic analyses demonstrated that they are affiliated with one of the actinobacterial lineages indigenous to freshwater bacterioplankton. The seven novel taxa could only be cultivated to date as mixed cultures that also contain non-actinobacterial strains. Due to the lack of pure cultures, I propose to establish the candidate species ‘Candidatus Planktoluna difficilis’, ‘Candidatus Aquiluna rubra’, ‘Candidatus Flaviluna lacus’, ‘Candidatus Rhodoluna limnophila’, ‘Candidatus Rhodoluna planktonica’, ‘Candidatus Rhodoluna lacicola’ and ‘Candidatus Limnoluna rubra’ for these taxa.

A polyphasic taxonomic approach was used to study strain 12116T, which was isolated from desert sand in Xinjiang, China. Cells of the isolate were Gram-negative, non-motile, rod-shaped and aerobic. MK-7 was the predominant respiratory menaquinone. The DNA G+C content was 46.3 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate was most closely related to the members of the genus Dyadobacter, with similarities ranging from 94.7 to 96.6 %. Therefore, on the basis of genotypic and phenotypic data, strain 12116T represents a novel species of the genus Dyadobacter, for which the name Dyadobacter alkalitolerans sp. nov. is proposed. The type strain is 12116T (=CCTCC AB 207176T =NRRL B-51268T).

A marine bacterium, designated IMCC3223T, was isolated from Antarctic coastal seawater and subjected to a polyphasic taxonomic investigation. Cells of the strain were Gram-negative, short to elongated rods that were orange-coloured but negative for flexirubin-type pigments, obligately aerobic, chemoheterotrophic and devoid of gliding or flagellar motility. On the basis of 16S rRNA gene sequence comparisons, the strain was closely related to members of the genus Lewinella (86.3–93.1 %) of the family ‘Saprospiraceae’ in the phylum Bacteroidetes; the most closely related species was Lewinella lutea (93.1 % similarity to the type strain). The DNA G+C content of the strain was 50.3 mol% and the major respiratory quinone was MK-7. The predominant cellular fatty acids were C16 : 1 ω7c/iso-C15 : 0 2-OH (39.4 %), iso-C15 : 0 (15.9 %), C17 : 1 ω7c (10.5 %) and C15 : 1 ω6c (8.9 %). 16S rRNA gene sequence analyses and the phenotypic and chemotaxonomic tests allowed the differentiation of strain IMCC3223T from all recognized species of the genus Lewinella. Therefore, strain IMCC3223T represents a novel species of the genus Lewinella, for which the name Lewinella antarctica sp. nov. is proposed. The type strain is IMCC3223T (=KCCM 42688T =NBRC 103142T).

A novel bacterial strain, designated Dae 13T, was isolated from sediment from a freshwater lake in Daejeon, South Korea, and was characterized taxonomically by using a polyphasic approach. The isolate was Gram-negative, aerobic, non-motile, non-spore-forming and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belonged to the genus Pedobacter in the family Sphingobacteriaceae but was clearly separate from established species of this genus. The 16S rRNA gene sequence similarities between strain Dae 13T and type strains of Pedobacter species with validly published names ranged from 91.6 to 97.5 %. The G+C content of the genomic DNA was 33.8 mol%. Chemotaxonomic data, i.e. the presence of MK-7 as the major menaquinone and iso-C15 : 0, C16 : 0 and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c) as the major fatty acids, supported the affiliation of strain Dae 13T to the genus Pedobacter. However, the results of physiological and biochemical tests allowed phenotypic differentiation of the isolate with respect to Pedobacter species with validly published names. Therefore, strain Dae 13T represents a novel species within the genus Pedobacter, for which the name Pedobacter daechungensis sp. nov. is proposed. The type strain is Dae 13T (=KCTC 12637T=LMG 23489T).

A Gram-negative, rod-shaped, non-motile and pink-pigmented bacterium, designated strain ZLB-3T, was isolated from a desert soil sample collected from Xinjiang Province, China, and characterized by using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the phylum Bacteroidetes and is related to the genus Hymenobacter. 16S rRNA gene sequence similarities between strain ZLB-3T and the type strains of Hymenobacter species with validly published names ranged from 90.0 to 94.6 %. No other taxa in the phylum Bacteroidetes showed more than 90 % sequence similarity to the isolate. The strain contained MK-7 as the predominant menaquinone. The major fatty acids were iso-C15 : 0 (27.8 %), anteiso-C17 : 1 B/iso-C17 : 1 I (25.2 %), iso-C17 : 0 3-OH (9.6 %) and C16 : 1 ω7c/iso-C15 : 0 2-OH (8.5 %). Phosphatidylethanolamine, two unknown aminophospholipids, an unknown aminolipid, an unknown glycolipid and six unknown polar lipids were detected in the polar lipid profile. The DNA G+C content was 58.6 mol%. These chemotaxonomic data supported the affiliation of strain ZLB-3T to the genus Hymenobacter. However, the results of physiological and biochemical tests allowed phenotypic differentiation of the isolate from recognized Hymenobacter species. On the basis of the evidence presented, it is proposed that strain ZLB-3T represents a novel species, Hymenobacter deserti sp. nov. The type strain is ZLB-3T (=CCTCC AB 207171T =NRRL B-51267T).

Two Gram-positive bacterial strains, LMG 24284T and LMG 24285T, were isolated from different spontaneous cocoa bean heap fermentations in Ghana. Analysis of their 16S rRNA gene sequences indicated that they were members of the Lactobacillus plantarum and Lactobacillus salivarius species groups, respectively. DNA–DNA hybridization experiments with their nearest phylogenetic neighbours demonstrated that both strains represented novel species that could be differentiated from their nearest neighbours by pheS sequence analysis, whole-cell protein electrophoresis, fluorescent amplified fragment length polymorphism analysis and biochemical characterization. Therefore, two novel Lactobacillus species are proposed, Lactobacillus fabifermentans sp. nov. (type strain LMG 24284T =DSM 21115T) and Lactobacillus cacaonum sp. nov. (type strain LMG 24285T =DSM 21116T).

A Gram-positive, endospore-forming, rod-shaped bacterium, designated strain B519T, was isolated from a desert sand sample of Gansu Province, China. Strain B519T was strictly aerobic and cells were motile by means of peritrichous flagella. The strain grew optimally at 32–35 °C and pH 6.5–7.0. Chemotaxonomic data supported the affiliation of the new isolate to the genus Paenibacillus, including menaquinone-7 (MK-7) as the major isoprenoid quinone, DNA G+C content of 49.9 mol%, cell-wall type A1γ (meso-diaminopimelic acid as the diagnostic diamino acid) and anteiso-C15 : 0, iso-C15 : 0, C16 : 0 and iso-C16 : 0 as the major fatty acids. Comparative 16S rRNA gene sequence analysis showed that strain B519T was most closely related to Paenibacillus alkaliterrae KSL-134T (98.0 % similarity). DNA–DNA relatedness between strain B519T and P. alkaliterrae KSL-134T was about 12.3 %. On the basis of phenotypic characteristics and molecular properties, strain B519T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus harenae sp. nov. is proposed. The type strain is B519T (=KCTC 3951T =DSM 16969T).

A Gram-positive, moderately halophilic, endospore-forming, catalase- and oxidase-positive, obligately aerobic bacterium, designated strain YIM-C158T, was isolated from sediment of a salt lake in the Qaidam Basin, north-west China. Cells were motile with peritrichous flagella and rod-shaped, with meso-diaminopimelic acid in the cell-wall peptidoglycan. Strain YIM-C158T grew in the presence of 1–20 % (w/v) NaCl and pH 6.0–10.0, with optimum growth at 5 % (w/v) NaCl and pH 8.0. The strain grew at 4–50 °C, with optimum growth at 37 °C. The major cellular fatty acids were anteiso-C15 : 0, iso-C14 : 0, C16 : 0, anteiso-C17 : 0, iso-C16 : 0, C16 : 1 ω7c alcohol and C16 : 1 ω11c. Strain YIM-C158T contained menaquinone MK-7 as the sole respiratory quinone and phosphatidylmethylethanolamine and phosphatidylcholine as the polar lipids. The genomic DNA G+C content was 39.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM-C158T was most closely related to Paraliobacillus ryukyuensis DSM 15140T (96.8 % similarity), and the two strains formed a distinct branch in the phylogenetic tree. The level of DNA–DNA relatedness between the two strains was 15.6 %. The combination of phylogenetic analysis, phenotypic characteristics, chemotaxonomic differences and DNA–DNA hybridization data supported the view that strain YIM-C158T represents a novel species of the genus Paraliobacillus, for which the name Paraliobacillus quinghaiensis sp. nov. is proposed. The type strain is YIM-C158T (=DSM 17857T=CGMCC 1.6333T).

Gram-positive, rod-shaped, non-motile lactic acid bacteria, strains iz4b-1T, iz4b-2 and iz4c-1, were isolated in an attempt to study the composition of the Lactobacillus flora of Japanese pickles. Analysis of their 16S rRNA gene sequences revealed that the strains clustered in the Lactobacillus alimentarius group, and comparatively high similarities were shown to ‘Lactobacillus tucceti’ CECT 5920 (97.0 %), Lactobacillus versmoldensis KU-3T (96.4 %) and Lactobacillus nantensis LP33T (94.4 %). DNA–DNA hybridization assays clearly revealed that the isolates represented a novel taxon. The DNA G+C content was 40.6 mol% and the peptidoglycan type was l-Lys–d-Asp. Thus, these isolates represent a novel Lactobacillus species, for which the name Lactobacillus nodensis sp. nov. is proposed. The type strain is iz4b-1T (=DSM 19682T =JCM 14932T).

A strictly anaerobic, thermophilic bacterium, designated strain RC3T, was isolated from microbial mats colonizing thermal waters of a run-off channel formed by free-flowing waters from a bore well (registered no. 17263) of the Great Artesian Basin, Australia. The slightly curved rods (2.5–4.2×0.8–1.0 μm) of strain RC3T stained Gram-positive and grew optimally in tryptone-yeast extract-glucose medium at 60 °C (range 45–70 °C) and pH 7 (range pH 5–9). Strain RC3T grew poorly on yeast extract (0.2 %) but did not grow on tryptone (0.2 %) as a sole carbon source; yeast extract was required for growth on other energy sources, which included glucose, fructose, galactose, xylose, maltose, sucrose, raffinose, mannose, cellobiose, cellulose, starch, amylopectin, xylan, peptone, amyl media (Research Achievement), threonine and pyruvate but did not include arabinose, ribose, lactose, CM-cellulose, myo-inositol, mannitol, chitin, casein, formate, acetate, succinate, propionate, lactate, benzoate, glycerol, ethanol, Casamino acids, arginine, alanine, serine, glycine, glutamine, leucine, isoleucine, methionine or aspartate. The end products of glucose fermentation were ethanol and acetate. In the presence of 0.2 % yeast extract, iron(III), manganese(IV) and elemental sulfur were reduced but not sulfate, sulfite, thiosulfate, nitrate or nitrite. Iron(III) was also reduced in the presence of peptone, tryptone, amyl media, threonine and glycerol but not chitin, xylan, pectin, starch, pyruvate, acetate, benzoate, lactate, propionate, succinate, inositol, ethanol, mannitol, arginine, glutamine or serine. Strain RC3T was not able to utilize molecular hydrogen and/or carbon dioxide in the presence or absence of iron(III). In the presence of iron(III) and glycerol, increased concentrations of Fe(II) corresponded to increased cell numbers, demonstrating that strain RC3T was able to conserve energy to support growth from the reduction of Fe(III) to Fe(II). Chloramphenicol, streptomycin, tetracycline, penicillin and ampicillin and NaCl concentrations greater than 2 % inhibited growth. The G+C content of the DNA was 34±1 mol% as determined by the thermal denaturation (T m) method. 16S rRNA gene sequence analysis indicated that strain RC3T was affiliated to Caloramator fervidus (95.8 % similarity to the type strain) and to other Caloramator species (average similarity of 91.6 %) within the phylum Firmicutes. On the basis of phylogenetic and phenotypic characteristics, it is proposed that strain RC3T should be classified in the genus Caloramator as a representative of a novel species, Caloramator australicus sp. nov. The type strain is RC3T (=JCM 1508T =KCTC 5601T).

A bacterial strain, designated CKOBP-6T, isolated from a contaminated laboratory plate, was characterized by using a polyphasic taxonomic approach. Chemotaxonomic and morphological properties of the strain were consistent with its classification in the genus Paenibacillus. Cells were Gram-variable, aerobic, sporulating, motile rods. 16S rRNA gene sequence analysis demonstrated that this novel isolate was unique, showing 94.6 % sequence similarity to Paenibacillus chitinolyticus NBRC 15660T and lower levels of similarity to Paenibacillus gansuensis KCTC 3950T (93.8 %) and Paenibacillus terrigena A35T (93.8 %). The novel isolate could be distinguished from the type strains of all of these species based on a range of phenotypic data. The major cellular phospholipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and one unknown phosphoglycolipid. The predominant isoprenologue was an unsaturated menaquinone with seven isoprene units (MK-7). The major fatty acids of strain CKOBP-6T were C16 : 0 (12.0 %), anteiso-C15 : 0 (52.0 %) and iso-C16 : 0 (16.4 %). The G+C content of the genomic DNA was 51.2 mol%. It is evident from the genotypic and phenotypic data that strain CKOBP-6T should be classified as a representative of a novel species of the genus Paenibacillus, for which the name Paenibacillus contaminans sp. nov. is proposed. The type strain is CKOBP-6T (=BCRC 17728T=LMG 24216T).

Three strains of xylanase-producing bacteria, S5-3T, X13-1T and MXC2-2T, isolated from soils in Thailand, were characterized taxonomically based on their phenotypic and chemotaxonomic characteristics and 16S rRNA gene sequence comparisons. They were Gram-positive, facultatively anaerobic, spore-forming, rod-shaped bacteria. They contained meso-diaminopimelic acid in the cell-wall peptidoglycan. The DNA G+C contents were respectively 45.8, 47.3 and 48.8 mol%. The predominant isoprenoid quinone was MK-7, and anteiso-C15 : 0 and C16 : 0 were the dominant cellular fatty acids. Phylogenetic analyses based on 16S rRNA gene sequence comparison showed that they were affiliated to the genus Paenibacillus. Strains S5-3T, X13-1T and MXC2-2T were closely related to Paenibacillus granivorans A30T and Paenibacillus agaridevorans DSM 1355T (94.7–98.6 % 16S rRNA gene sequence similarity). The similarity between the three novel strains ranged from 96.3 to 98.4 %. DNA–DNA relatedness, DNA G+C contents and some phenotypic characteristics could clearly distinguish the strains from each other and from related Paenibacillus species. Therefore, strains S5-3T, X13-1T and MXC2-2T represent novel species of the genus Paenibacillus, for which the names Paenibacillus siamensis sp. nov. (type strain S5-3T =KCTC 13038T =PCU 279T =TISTR 1831T), Paenibacillus septentrionalis sp. nov. (type strain X13-1T =KCTC 13039T =PCU 280T =TISTR 1830T) and Paenibacillus montaniterrae sp. nov. (type strain MXC2-2T =KCTC 13036T =PCU 281T =TISTR 1836T) are proposed.

A polyphasic taxonomic study was performed on six strains of an unknown Gram-positive, non-motile, spore-forming, short oval to rod-shaped bacterium isolated from a swine-manure storage pit. In addition to these strains, an isolate deposited in the Culture Collection of the University of Göteborg (Sweden) was found to be biochemically related to the manure strains. The major end products of metabolism included acetate and succinate but not butyrate. Comparative 16S rRNA gene sequencing confirmed that all these isolates were closely related to each other and formed a hitherto unknown lineage within the clostridial rRNA XIVa cluster of organisms. On the basis of phylogenetic, biochemical and phenotypic evidence, it is proposed that the unknown bacterium represents a novel genus and species, for which the name Robinsoniella peoriensis gen. nov., sp. nov. is proposed. The type strain of Robinsoniella peoriensis is PPC31T (=CCUG 48729T =NRRL B-23985T).