- Volume 58, Issue 5, 2008

A novel actinomycete, designated strain LR-26T, was isolated from a small stone collected from an agricultural field in Jeju, Republic of Korea. Cells of the organism were strictly aerobic, Gram-positive, non-motile, short rods. Colonies were bright yellow, circular, smooth and translucent. The organism was characterized chemotaxonomically as having ll-diaminopimelic acid in the cell wall, MK-8(H4) as major menaquinone, a polar lipid profile including diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and unknown phospholipids, iso-C15 : 0 as the predominant fatty acid and a DNA G+C content of 72.6 mol%. Comparative 16S rRNA gene sequence analysis showed that the organism was related to the genera Intrasporangium, Terracoccus and Terrabacter within the family Intrasporangiaceae. The closest phylogenetic relatives of strain LR-26T were the type strains of Terrabacter terrae (99.4 % 16S rRNA gene sequence similarity), Terrabacter aerolatus (99.3 %) and Terrabacter tumescens (99.3 %). DNA–DNA hybridization experiments showed that strain LR-26T shared low levels of DNA–DNA relatedness with Terrabacter terrae LMG 22921T (17.6 and 22.8 % from reciprocal experiments) and with Terrabacter tumescens IMSNU 21313T (27.6 and 34.9 %). The phenotypic data and low levels of DNA–DNA relatedness readily distinguished strain LR-26T from the type strains of recognized species of the genus Terrabacter, and showed that it therefore represents a novel species. The name Terrabacter lapilli sp. nov. is proposed for this novel actinomycete. The type strain is LR-26T (=JBRI 2002T =KCTC 19199T =DSM 18583T).

A novel actinomycete strain, DAS-139T, was isolated from a soil sample collected from Gulbarga, Karnataka Province, India. The isolate was characterized by white to grey aerial mycelium. Long spore chains were found on the aerial mycelium and the aerial mycelium was composed of non-motile spores with hairy surfaces. The cell wall of strain DAS-139T contained ll-diaminopimelic acid isomer as the diagnostic diaminoacid indicating that the cell wall was of chemotype-I. The predominant menaquinones were MK-9(H6) (76 %), MK-9(H4) (14 %) and MK-9(H8) (10 %). Phosphatidylethanolamine was the diagnostic phospholipid. On the basis of 16S rRNA gene sequence, phenotypic and phylogenetic analyses, the novel strain was identified as a member of the genus Streptomyces. The novel strain grew optimally at 28 °C and pH 9.0. The G+C content of the genomic DNA was 71.8 mol%. 16S rRNA gene sequence analysis showed that the novel isolate had 99.4 % sequence similarity with Streptomyces scabiei ATCC 49173T and 99.2 % similarity with Streptomyces diastachromogenes ATCC 12309T. Furthermore, DNA–DNA hybridization with these two Streptomyces species showed 36.0 and 43.0 % relatedness, respectively. Based on these observations, strain DAS-139T is proposed to represent a novel species of the genus Streptomyces, for which the name Streptomyces deccanensis sp. nov. is proposed with the type strain DAS-139T (=KCTC 19241T=CCTCC AA 207004T).

A polyphasic study was undertaken to establish the taxonomic status of a wheat-field soil isolate. The organism, strain 88T, was found to have a range of chemical and morphological properties consistent with its classification in the genus Saccharopolyspora. Phylogenetic analysis based on an almost-complete 16S rRNA gene sequence of the strain showed that it formed a monophyletic clade with the type strain of Saccharopolyspora spinosa. However, the two strains shared low DNA–DNA relatedness. Strain 88T also had a profile of phenotypic properties that readily distinguished it from representatives of the species of Saccharopolyspora with validly published names. It is evident from the combination of genotypic and phenotypic data that the organism should be classified within a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora shandongensis sp. nov. is proposed. The type strain is strain 88T (=CGMCC 4.3530T =JCM 14614T).

A mycelium-forming actinomycete, designated strain D8-87T, was isolated from a soil collected from a cave in Jeju, Republic of Korea. Comparative 16S rRNA gene sequence analysis showed that the organism was closely related to the type and only species of the genus Jiangella. The level of 16S rRNA gene sequence similarity between strain D8-87T and the type strain of Jiangella gansuensis was 99.2 %. The novel organism produced extensively branched aerial and substrate mycelia, which fragmented into short or elongated rod-shaped cells. Whole-cell hydrolysates of the isolate contained ll-diaminopimelic acid, glucose, mannose and arabinose. The predominant menaquinone was MK-9(H4). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannoside and an unknown phospholipid. The predominant fatty acids were anteiso-C15 : 0, iso-C16 : 0 and iso-C14 : 0. The DNA G+C content of strain D8-87T was 71.5 mol%. Levels of DNA–DNA relatedness between strain D8-87T and J. gansuensis KCTC 19044T were 23.4 and 34.6 %. On the basis of the phenotypic and DNA–DNA hybridization data presented, strain D8-87T is considered to represent a novel species of the genus Jiangella, for which the name Jiangella alkaliphila is proposed. The type strain is D8-87T (=JBRI 2008T=KCTC 19222T=DSM 45079T).

Three Gram-positive, aerobic, non-motile, non-acid–alcohol-fast strains, designated I05-00051, I05-00074T and I03-00808, were isolated from different soil samples in Beijing and Sichuan, China. Phylogenetic analysis based on 16S rRNA gene sequences and DNA–DNA hybridization experiments revealed that these three isolates represented the same genospecies. These three strains showed <97.0 % 16S rRNA gene sequence similarity with the type strains of recognized species of the genus Saccharopolyspora, with the exception of Saccharopolyspora hirsuta subsp. hirsuta DSM 43463T (98.1 % gene sequence similarity) and Saccharopolyspora spinosa DSM 44228T (98.0 % similarity). Chemotaxonomic data, including meso-diaminopimelic acid as the diagnostic diamino acid, arabinose and galactose as predominant sugars, iso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and anteiso-C17 : 0 as major fatty acids, MK-9(H4) as predominant menaquinone and polar lipids dominated by diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol and phosphatidylinositol, supported the affiliation of these three organisms to the genus Saccharopolyspora. The genomic DNA G+C contents of the three isolates were 68.2–69.9 mol%. The results of DNA–DNA hybridization experiments among these three isolates and S. hirsuta subsp. hirsuta DSM 43463T and S. spinosa DSM 44228T, in combination with chemotaxonomic and physiological data, demonstrated that the three new isolates represent a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora antimicrobica sp. nov. is proposed. The type strain is I05-00074T (=CCM 7463T=KCTC 19303T).

Nine strains capable of metabolizing isoflavones to equol were isolated from human faeces. Four of the strains were characterized by determining phenotypic and biochemical features and their phylogenetic position based on 16S rRNA gene sequence analysis. These strains were related to Eggerthella sinensis HKU14T with about 93 % 16S rRNA gene sequence similarity; they were asaccharolytic, obligately anaerobic, non-spore-forming, non-motile and Gram-positive coccobacilli. In enzyme activity tests, arginine dihydrolase, arginine and leucine arylamidases were positive but nitrate reduction, urease and β-glucosidase were negative. The major menaquinone was DMMK-6 (dimethylmenaquinone-6), while that of members of the genus Eggerthella was MMK-6 (methylmenaquinone-6). Furthermore, the cell-wall peptidoglycan type of these strains was A1γ, while that of members of the genus Eggerthella was A4γ. On the basis of these data, a new genus, Adlercreutzia gen. nov., is proposed with one species, Adlercreutzia equolifaciens sp. nov. The type strain of Adlercreutzia equolifaciens is FJC-B9T (=JCM 14793T =DSM 19450T =CCUG 54925T).

An obligately anaerobic and equol-producing bacterium, designated strain do03T, was isolated from the caecal content of a rat. Cells were Gram-positive, non-spore-forming rods. The results from a phylogenetic analysis based on 16S rRNA gene sequences showed that strain do03T formed a separate line of descent in the phylogenetic cluster of the family Coriobacteriaceae. The strain was unable to metabolize glucose or other carbohydrates as sole carbon sources; growth was enhanced in the presence of arginine. The cell wall contained meso-diaminopimelic acid. The major fatty acid was C18 : 1 cis9 (54.0 %). The strain had one unidentified predominant (91.9 %) quinone that was not menaquinone, methylmenaquinone, demethylmenaquinone, ubiquinone or rhodoquinone. The DNA G+C content was 63 mol%. The data presented in this work show that strain do03T differs from members of the related recognized genera Eggerthella and Denitrobacterium at both the phylogenetic and phenotypic level. Therefore, the strain constitutes a novel genus and species, for which the name Asaccharobacter celatus gen. nov., sp. nov. is proposed. The type strain of the type species is do03T (=JCM 14811T=DSM 18785T=AHU 1763T).

A novel mesophilic, Gram-positive, cream- to pale yellow-pigmented, aerobic bacterium, designated MSL-15T, was isolated from a soil sample collected from Bigeum Island, South Korea. The cells were catalase-positive, motile and irregular rods. The diamino acid content of the cell-wall peptidoglycan was determined to be 2,4-diaminobutyric acid. Strain MSL-15T grew well between 20 and 28 °C, with optimum growth occurring at 25–28 °C. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and iso-C15 : 0. The genomic DNA G+C content was 70.0 mol%. A phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MSL-15T was associated with the genus Cryobacterium and exhibited 96.6 % sequence similarity to Cryobacterium psychrotolerans JCM 13925T and 94.8 % similarity to Cryobacterium psychrophilum JCM 1463T. Phenotypic, chemotaxonomic and phylogenetic data revealed that strain MSL-15T represents a novel species within the genus Cryobacterium, for which the name Cryobacterium mesophilum is proposed. The type strain is MSL-15T (=DSM 19267T=KCTC 19270T).

In this study, strain P 461/12T, isolated from decaying plant material after mulching a pasture, was shown to represent a novel species of the genus Chryseobacterium by means of a polyphasic approach. The closest phylogenetic neighbours to the novel strain, as determined by 16S rRNA gene sequence analysis, were Chryseobacterium daeguense K105T and Chryseobacterium soldanellicola PSD1-4T with gene sequence similarities of 97.4 % and 97.2 %, respectively. Strain P 461/12T could be differentiated by means of its RiboPrint pattern from the type strains of all recognized Chryseobacterium species belonging to the same cluster as determined by 16S rRNA gene sequence comparisons. The nearest phylogenetic neighbours, and in particular the closest relatives C. daeguense and C. soldanellicola, could be distinguished from the novel isolate by means of several physiological features and also by the remarkably lower proportion of anteiso-C15 : 0 in the whole-cell fatty acid profile. Based on these findings, the new isolate represents a novel species, for which the name Chryseobacterium gregarium sp. nov. is proposed. The type strain is P 461/12T (=DSM 19109T=LMG 24052T).

A taxonomic study was carried out on Gsoil 085T, a bacterial strain isolated from a soil sample from a ginseng field in Pocheon Province (South Korea). Comparative 16S rRNA gene sequence studies showed a clear affiliation of this bacterium to the family ‘Flexibacteraceae’ and indicated that the closest relative was Emticicia oligotrophica GPTSA100-15T (94.6 % sequence similarity). Lower sequence similarities (<83.0 %) were found with respect to all other recognized species of the family ‘Flexibacteraceae’. Strain Gsoil 085T was found to be Gram-negative, strictly aerobic, non-motile and rod-shaped. It grew well on half-strength R2A medium but did not utilize a broad range of carbon sources. The G+C content of the genomic DNA was 40.5 mol%. The major fatty acids were summed feature 4 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c, 45.4 %), iso-C15 : 0 (13.9 %), C16 : 1 ω5c (8.6 %) and C16 : 0 (8.2 %). On the basis of evidence from the polyphasic study, strain Gsoil 085T represents a novel species of the genus Emticicia, for which the name Emticicia ginsengisoli sp. nov. is proposed. The type strain is Gsoil 085T (=KCTC 12588T =LMG 23396T).

Three novel strains, designated Gsoil 034T, Gsoil 060T and Jip13T, isolated from soil from a ginseng field and compost in South Korea, were characterized using a polyphasic approach to clarify their taxonomic positions. These isolates were found to be Gram-negative, aerobic and heterotrophic, non-spore-forming, non-motile and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these three isolates formed a cluster with the monospecific genus Olivibacter within the family Sphingobacteriaceae but were clearly separated from Olivibacter sitiensis. The 16S rRNA gene sequence similarities between these isolates and the type strain of O. sitiensis were in the range 88.5–90.1 %. Phenotypic and chemotaxonomic data (MK-7 as the major isoprenoid quinone and iso-C15 : 0 2-OH and/or C16 : 1 ω7c, iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids) supported the affiliation of these strains to the genus Olivibacter. However, the results of physiological and biochemical tests allowed phenotypic differentiation of the isolates from Olivibacter species with validly published names. Therefore strains Gsoil 034T, Gsoil 060T and Jip13T represent three novel species of the genus Olivibacter, for which the names Olivibacter soli sp. nov. (type strain Gsoil 034T =KCTC 12645T =LMG 23492T), Olivibacter ginsengisoli sp. nov. (type strain Gsoil 060T =KCTC 12646T =LMG 23491T) and Olivibacter terrae sp. nov. (type strain Jip13T =KCTC 12644T =LMG 23494T) are proposed.

The precise taxonomic position of Roseivirga seohaensis strain SW-152T, formerly [Marinicola] seohaensis, was established. On the basis of data from DNA–DNA reassociation experiments and phenotypic analysis, it is proposed that this strain should be considered as a later heterotypic synonym of Roseivirga ehrenbergii KMM 6017T Nedashkovskaya et al. 2005. Emended descriptions for Roseivirga ehrenbergii and for the genus Roseivirga are also given.

Two Gram-negative, rod-shaped, gliding and pink-pigmented bacterial strains, X14-1T and X19-1, were isolated from a mixture of sand samples collected from the desert of Xinjiang, China, and characterized by using a polyphasic taxonomic approach. Strains X14-1T and X19-1 contained MK-7 as the predominant menaquinone. The major cellular fatty acids included iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 and summed feature 4. The DNA G+C contents of strains X14-1T and X19-1 were 48.2 and 48.9 mol%, respectively. 16S rRNA gene sequence analysis showed that the isolates were highly related to each other (99.2 %) and confirmed their placement in the genus Pontibacter. Strains X14-1T and X19-1 exhibited 16S rRNA gene similarity levels of 95.0–97.2 % to the type strains of the two Pontibacter species with validly published names. DNA–DNA hybridization experiments revealed a high level of relatedness between the two new isolates (82 %), but low levels of relatedness between strain X14-1T and the phylogenetically most closely related species Pontibacter actiniarum KMM 6156T (51 %). On the basis of genotypic and phenotypic evidence, strains X14-1T and X19-1 are considered to represent a novel species of the genus Pontibacter, for which the name Pontibacter korlensis sp. nov. is proposed. The type strain is X14-1T (=CCTCC AB 206081T=NRRL B-51097T).

A psychrotolerant bacterium, designated strain Tibet-IIU11T, was isolated from the Qinghai--Tibet Plateau permafrost region, China. A taxonomic study was conducted using a polyphasic approach, with determination of physiological and biochemical properties and phylogenetic analysis based on 16S rRNA gene sequences. The novel isolate was found to belong to the genus Hymenobacter and was distinct from the recognized species of this genus. The major fatty acids were iso-C15 : 0 (24.5 %), summed feature 3 (C16 : 1 ω7c and/or iso C15 : 0 2-OH; 20.0 %), summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B; 14.0 %), C16 : 1 ω5c (12.7 %) and anteiso-C15 : 0 (8.4 %). Phosphatidylethanolamine and an unknown aminophospholipid were predominant in the polar lipid profile. The quinone system consisted exclusively of menaquinone MK-7 and sym-homospermidine was the major polyamine present. These chemotaxonomic traits are in good agreement with the characteristics of the genus Hymenobacter. The assignment of the novel isolate to this genus was further supported by a DNA G+C content of 60 mol%. On the basis of the polyphasic evidence presented in this study, it is proposed that strain Tibet-IIU11T (=DSM 18569T=CGMCC 1.6365T) represents a novel species, Hymenobacter psychrotolerans sp. nov.

A novel spirochaete, Treponema sp. strain SPIT5T, was isolated from hindgut contents of the drywood termite Incisitermes tabogae (Snyder). The cells of strain SPIT5T were motile, helical in shape, 0.4–0.5 μm in diameter and generally 12–20 μm long. The strain is obligately anaerobic and ferments different mono-, di- and oligosaccharides by forming ethanol as the main liquid fermentation end product. Furthermore, strain SPIT5T was able to grow anaerobically with yeast extract as sole carbon and energy source. Fastest growth was obtained at 30 °C, the temperature at which the termites were also grown. The optimum pH for growth was 7.2, with a range of pH 6.5–8.0. The cells possessed various enzyme activities that are involved in the degradation of lignocellulose in the termite hindgut, such as β-d-glucosidase, α-l-arabinosidase and β-d-xylosidase. The G+C content of the DNA was 47.7 mol%. Based on 16S rRNA gene sequence analysis, strain SPIT5T was shown to belong to the so-called ‘termite cluster I’ of the genus Treponema. The closest relative of strain SPIT5T was Treponema primitia ZAS-2T, with 92.3 % sequence similarity. On the basis of its phenotypic and genotypic properties, strain SPIT5T can be distinguished from other described species of the genus Treponema. Therefore, strain SPIT5T represents a novel species of Treponema, for which the name Treponema isoptericolens sp. nov. is proposed. The type strain is strain SPIT5T (=DSM 18056T =JCM 13955T).

The phylum Acidobacteria is currently represented mostly by environmental 16S rRNA gene sequences, and the phylum so far contains only four species with validly published names, Holophaga foetida, Geothrix fermentans, Acidobacterium capsulatum and Terriglobus roseus. In the present study, two novel strains of acidobacteria were isolated. High-throughput enrichments were set up with the MicroDrop technique using an alpine calcareous soil sample and a mixture of polymeric carbon compounds supplemented with signal compounds. This approach yielded a novel, previously unknown acidobacterium, strain Jbg-1T. The second strain, Wbg-1T, was recovered from a co-culture with a methanotrophic bacterium established from calcareous forest soil. Both strains represent members of subdivision 1 of the phylum Acidobacteria and are closely related to each other (98.0 % 16S rRNA gene sequence similarity). At a sequence similarity of 93.8–94.7 %, strains Jbg-1T and Wbg-1T are only distantly related to the closest described relative, Terriglobus roseus KBS 63T, and accordingly are described as members of the novel genus Edaphobacter gen. nov. Based on the DNA–DNA relatedness between strains Jbg-1T and Wbg-1T of 11.5–13.6 % and their chemotaxonomic and phenotypic characteristics, the two strains are assigned to two separate species, Edaphobacter modestus sp. nov. (the type species), with strain Jbg-1T (=ATCC BAA-1329T =DSM 18101T) as the type strain, and Edaphobacter aggregans sp. nov., with strain Wbg-1T (=ATCC BAA-1497T =DSM 19364T) as the type strain. The two novel species are adapted to low carbon concentrations and to neutral to slightly acidic conditions.

Four thermophilic, sulfur-oxidizing, chemolithoautotrophic strains with >99 % 16S rRNA gene sequence similarity were isolated from terrestrial hot springs in the Geyser Valley and the Uzon Caldera, Kamchatka, Russia. One strain, designated UZ3-5T, was characterized fully. Cells of UZ3-5T were Gram-negative, motile, slightly oval rods (about 0.7 μm wide and 1.0 μm long) with multiple polar flagella. All four strains were obligately microaerophilic chemolithoautotrophs and could use elemental sulfur or thiosulfate as electron donors and oxygen (1–14 %, v/v) as the electron acceptor. Strain UZ3-5T grew at temperatures between 55 and 80 °C (optimally at 75 °C; 1.1 h doubling time), at pH 5.0–7.2 (optimally at pH 6.0–6.3) and at 0–0.9 % NaCl (optimally in the absence of NaCl). The G+C content of the genomic DNA of strain UZ3-5T was 35 mol%. Phylogenetic analysis revealed that strain UZ3-5T was a member of the genus Sulfurihydrogenibium, its closest relative in culture being Sulfurihydrogenibium azorense Az-Fu1T (98.3 % 16S rRNA gene sequence similarity). On the basis of its physiological and molecular characteristics, strain UZ3-5T represents a novel species of the genus Sulfurihydrogenibium, for which the name Sulfurihydrogenibium rodmanii sp. nov. is proposed. The type strain is UZ3-5T (=OCM 900T =ATCC BAA-1536T =DSM 19533T).