- Volume 59, Issue 2, 2009

A novel bacterial strain, designated ANL-iso2T, was obtained from an enrichment culture inoculated with a mixture of soda lake sediments by using isobutyronitrile (iBN) as the carbon, energy and nitrogen source at pH 10. The enrichment resulted in a stable binary culture containing iBN-degrading Gram-positive rods and a satellite Gram-negative gammaproteobacterium Marinospirillum sp. strain (ANL-isoa) scavenging the products of nitrile hydrolysis. Cells of the iBN-degrading strain, ANL-iso2T, were short, non-motile, non-spore-forming rods. Strain ANL-iso2T was capable of utilizing propionitrile (C3), butyronitrile (C4), isobutyronitrile (C4), valeronitrile (C5) and capronitrile (C6) as the only growth substrate. Growth on nitriles was biphasic with fast initial hydrolysis of nitriles to the corresponding amides, carboxylic acids and ammonia and slow further utilization of these products resulting in biomass growth. Cells of strain ANL-iso2T grown with iBN were capable of extremely active hydration of a wide range of nitriles into the corresponding amides and much slower hydrolysis of these amides to the corresponding carboxylic acids. This indicated the presence of the nitrile hydratase/amidase pathway of nitrile degradation in the novel bacterium. Strain ANL-iso2T showed obligately alkaliphilic growth on iBN within the pH range 8.4–10.6, with optimum growth at 9.0–9.5. It was moderately salt-tolerant, with a salt range for growth of 0.1–2.0 M Na+ and an optimum salt concentration for growth of 0.2–0.3 M. The dominant fatty acids in the polar lipids were C16 : 0, iso-C14, C14 : 0, iso-C16 and C16 : 1 ω7. The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid. Phylogenetic analysis placed strain ANL-iso2T within the class Actinobacteria as an independent lineage with only uncultured bacteria from soda lakes as its nearest relatives. On the basis of its unique phenotype and distinct phylogeny, strain ANL-iso2T is considered to represent a novel species of a new genus, for which the name Nitriliruptor alkaliphilus gen. nov., sp. nov. is proposed. The type strain of the type species, Nitriliruptor alkaliphilus, is ANL-iso2T (=DSM 45188T=NCCB 100119T=UNIQEM U239T). Phylogenetic data suggest that the novel bacterium forms the basis of a new family Nitriliruptoraceae fam. nov. and a novel order Nitriliruptorales ord. nov. within the class Actinobacteria.

A filamentous actinomycete, designated strain D65T, was isolated from a root of a wild tree, Alnus nepalensis D. Don (Nepalese Alder), collected in Xishuangbanna, China. It produced the bioactive agents daidzein and N-acetyltyramine and had morphological and chemical properties characteristic of streptomycetes. Pink to brownish red diffusible pigments were produced on several ISP media. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain D65T formed a distinct phyletic line that was most closely, albeit loosely, associated with Streptomyces hebeiensis YIM 001T, Streptomyces aurantiogriseus NRRL B-5416T, Streptomyces griseoviridis NBRC 12874T, Streptomyces niveoruber NBRC 15428T and Streptomyces thermovulgaris NBRC 13473. A number of phenotypic properties allowed differentiation of the strain from related Streptomyces species. Therefore strain D65T represents a novel species of the genus Streptomyces, for which the name Streptomyces alni sp. nov. is proposed. The type strain is D65T (=CGMCC 4.3510T=NRRL B-24611T).

A novel actinomycete strain, designated CW 108T, was isolated from a forest soil in Anhui Province, China. The cells were strictly aerobic, non-motile, bent rods. The strain grew optimally at 30–37 °C and pH 6.0–8.0. Chemotaxonomically, the peptidoglycan type was A3α, the cell-wall sugars contained galactose, mannose and ribose, the polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylmonomethylethanolamine, the major fatty acids were ai-C15 : 0, i-C15 : 0 and ai-C17 : 0 and the predominant respiratory quinone was MK-9(H2), with a moderate amount of MK-8(H2) and a minor amount of MK-6(H2). The G+C content of the genomic DNA was 71.1 mol%. Phylogenetic analysis showed that strain CW 108T formed a deeply separated lineage in the family Micrococcaceae with Arthrobacter atrocyaneus DSM 20127T. The 16S rRNA gene sequence similarity between strain CW 108T and Arthrobacter atrocyaneus DSM 20127T was 99.4 %; sequence similarities between these strains and representatives of other species in the family Micrococcaceae with validly published names were lower than 95.2 %. DNA–DNA hybridization showed a level of relatedness of 52.2 % between the two neighbours. Based on the results of our polyphasic taxonomic study, strain CW 108T and Arthrobacter atrocyaneus DSM 20127T should be assigned to two different species of a novel genus within the family Micrococcaceae, for which the names Sinomonas flava gen. nov., sp. nov. and Sinomonas atrocyanea comb. nov. are proposed. The type strain of Sinomonas flava is CW 108T (=LMG 24447T =KCTC 19388T =CCTCC AB 207194T) and the type strain of Sinomonas atrocyanea is DSM 20127T =JCM 1329T =CGMCC 1.1891T =ATCC 13752T.

A novel phenanthrene-degrading bacterium, designated strain Sphe3T, was isolated from a creosote-contaminated soil in Greece. Cells were non-motile, Gram-positive, aerobic, and rod- to coccus-shaped. The strain was isolated on the basis of formation of a clear zone on agar plates sprayed with phenanthrene. Optimal growth occurred at 30 °C. The G+C content of the DNA was 65.7 mol%. The polar lipid pattern of strain Sphe3T consisted of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The dominant fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, C16 : 0 and anteiso-C17 : 0, representing >86 % of the total fatty acids. The predominant isoprenoid quinone of strain Sphe3T was menaquinone-8 (MK-8). Based on 16S rRNA gene sequence analysis, strain Sphe3T showed 99 and 98.9 % similarity to the type strains of Arthrobacter oxydans and Arthrobacter polychromogenes, respectively. Strain Sphe3T showed 91 % similarity to homologues of A. oxydans and A. polychromogenes based on recA gene sequence analysis. Based on 16S rRNA and recA gene sequence analysis and DNA–DNA hybridization analysis, as well as physiological and chemotaxonomic characteristics, it is concluded that strain Sphe3T represents a novel species of the genus Arthrobacter, for which the name Arthrobacter phenanthrenivorans sp. nov. is proposed. The type strain is Sphe3T (=DSM 18606T =LMG 23796T).

A strictly aerobic, motile, short-rod-shaped, Gram-positive-staining actinomycete strain, designated MSL-01T, was isolated from a sediment sample from Bigeum Island of Korea. 16S rRNA gene sequence analysis revealed that the isolate MSL-01T belonged to the genus Nocardioides, with the highest sequence similarity to Nocardioides terrigena DS-17T (98.54 %), but the DNA–DNA relatedness to this type strain was 34 %. The physiological properties of strain MSL-01T differ from those of Nocardioides terrigena DS-17T and other species of Nocardioides. The diamino acid in the cell-wall peptidoglycan of strain MSL-01T is ll-diaminopimelic acid, the major menaquinone is MK-8(H4) and iso-C16 : 0 is the major fatty acid component. The name Nocardioides sediminis sp. nov. is proposed for the novel species, with the type strain MSL-01T (=DSM 19263T =KCTC 19271T).

Polycyclic aromatic hydrocarbons (PAHs) are widespread environmental contaminants. In this study, both pristine and contaminated soils were sampled as a source of PAH-degrading organisms. Nine strains isolated from these soils were identified as rapidly growing members of the genus Mycobacterium through basic phenotypic characteristics and through sequence similarity of three genes. Because the sequence similarity of the 16S rRNA gene is relatively high among members of this genus, additional conserved genes encoding the β subunit of RNA polymerase (rpoB) and a heat-shock protein (hsp65) were sequenced. Several analyses were completed to differentiate the strains from one another and to determine their species-level taxonomy, including fatty acid methyl ester analysis, biochemical tests and substrate-utilization profiling. A phylogenetic tree incorporating sequences for all three genes was constructed with the isolates and their close described relatives. Results for biochemical tests, substrate-utilization tests and DNA sequencing were compared with those of the phylogenetically similar organisms to establish the isolated strains as representatives of novel species with characteristics unlike those of previously described species of Mycobacterium. Finally, DNA–DNA hybridization was performed between strains and their close relatives to confirm their position within novel species. Our results demonstrated that the isolates represent five novel species, which were named Mycobacterium crocinum sp. nov. (type strain czh-42T =ATCC BAA-1373T =CIP 109262T; reference strains czh-1A =ATCC BAA-1370 =CIP 109266 and czh-3 =ATCC BAA-1371=CIP 109267), Mycobacterium pallens sp. nov. (type strain czh-8T =ATCC BAA-1372T =CIP 109268T), Mycobacterium rutilum sp. nov. (type strain czh-117T =ATCC BAA-1375T =CIP 109271T; reference strains czh-107 =ATCC BAA-1374 =CIP 109270 and czh-132 =ATCC BAA-1376 =CIP 109272), Mycobacterium rufum sp. nov. (type strain JS14T =ATCC BAA-1377T =CIP 109273T) and Mycobacterium aromaticivorans sp. nov. (type strain JS19b1T =ATCC BAA-1378T =CIP 109274T).

A novel actinomycete, strain 04-5195T, that produces amicoumacin B, which targets bone morphogenetic protein-2, was isolated from a soil sample collected in Jinan, Shandong Province, China. Strain 04-5195T had morphological, biochemical, physiological and chemotaxonomic properties that were consistent with its classification in the genus Nocardia and it formed a phyletic line in the Nocardia 16S rRNA gene tree. It was evident from the phylogenetic data that strain 04-5195T was most closely associated with Nocardia speluncae N2-11T. However, the two organisms were distinguishable from one another using DNA–DNA relatedness and phenotypic data. The isolate was readily differentiated from other related Nocardia strains by a set of phenotypic properties and by its phylogenetic position. Therefore, it is proposed that the isolate represents a novel species in the genus Nocardia, Nocardia jinanensis sp. nov.; the type strain is 04-5195T (=CGMCC 4.3508T =DSM 45048T).

Six obligately aerobic, Gram-negative, non-motile, pale-yellow-pigmented, rod-shaped bacterial strains, designated YM3-301T, HG868, 04PA2 Co4-8B, 04PA2 Co4-99A, 04PA2 018SW-3 and 04PA2 018SW-18, were isolated from a marine sponge and seawater and were subjected to a polyphasic taxonomic investigation. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the novel isolates were affiliated with the family Flavobacteriaceae (phylum Bacteroidetes) and that they showed the highest sequence similarity (90.3–90.9 %) to members of the genus Leeuwenhoekiella and to Zhouia amylotica. The 16S rRNA gene sequence similarities with respect to members of other related genera were only 86.3–89.1 %. In contrast, the six isolates shared high levels of 16S rRNA gene sequence similarity (99.7–100 %) and DNA-DNA relatedness (72–94 %) with each other. The novel isolates were phenotypically and physiologically different from members of related genera. The G+C content of the DNA was 41.8–43.5 mol%, MK-6 was the major menaquinone and i15 : 0, i15 : 1 and i17 : 0 3-OH were the major fatty acids. On the basis of the data from the taxonomic studies, it was concluded that these six novel strains represent a novel genus and species of the family Flavobacteriaceae, for which the name Leptobacterium flavescens gen. nov., sp. nov. is proposed. The type strain of Leptobacterium flavescens is YM3-301T (=KCTC 22160T=MBIC 06275T=NBRC 104141T).

Eight anaerobic, pigmented, non-spore-forming, Gram-negative, rod-shaped strains isolated from monkey oral cavities were characterized phenotypically and chemotaxonomically and their phylogenetic positions were determined using 16S rRNA gene sequence analysis. The 16S rRNA gene sequence analysis showed that these isolates represent a single species of the genus Prevotella. These strains were most closely related to Prevotella intermedia ATCC 25611T, with 95.0 % 16S rRNA gene sequence similarity. The next most closely related species were Prevotella pallens and Prevotella nigrescens (92.7 and 92.1 % similarity to the respective type strains). The phenotypic and biochemical characteristics of the isolates were the same as those of P. intermedia JCM 12248T and P. nigrescens JCM 12250T. The isolates could be differentiated from P. pallens JCM 11140T on the basis of mannose fermentation and α-fucosidase activity. The isolates could not be distinguished from P. intermedia or P. nigrescens using conventional biochemical tests. DNA–DNA hybridization experiments revealed the genomic distinctiveness of these eight strains with respect to P. pallens JCM 11140T, P. intermedia JCM 12248T and P. nigrescens JCM 12250T. On the basis of these data, strains 04013, 04021, 04043, 04052T, 0406, 04113, 04111 and 04161 represent a novel Prevotella species, for which the name Prevotella falsenii sp. nov. is proposed. The type strain is 04052T (=JCM 15124T =CCUG 56137T).

A Gram-negative, yellowish bacterial strain, designated Gsoil 1519T, was isolated from soil of a ginseng field in Pocheon province (South Korea) and characterized using a polyphasic approach to determine its taxonomic position. Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 1519T belongs to the family ‘Flexibacteraceae’ and is related to Spirosoma rigui KCTC 12531T (91.8 % similarity) and Spirosoma linguale LMG 10896T (91.5 % similarity). Phylogenetic distances from any other recognized species within the family ‘Flexibacteraceae’ were greater than 14.7 %. The G+C content of the genomic DNA of strain Gsoil 1519T was 50.1 %. The detection of MK-7 as the predominant menaquinone and a fatty acid profile with C16 : 1 ω5c, summed feature 4 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0 and C16 : 0 as the major acids supported the affiliation of strain Gsoil 1519T to the genus Spirosoma. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 1519T should be classified in the genus Spirosoma as a representative of a novel species, for which the name Spirosoma panaciterrae sp. nov. is proposed. The type strain is Gsoil 1519T (=KCTC 22263T=DSM 21099T).

Strain TW5T, a motile, Gram-negative bacterium that produced pale-pink colonies, was isolated from tap water on R2A agar at 20 °C. 16S rRNA gene sequence studies showed that the strain clustered with Arcicella aquatica (99.0 % sequence similarity to the type strain). The main polyamine present was spermidine, the quinone system comprised menaquinone MK-7 and the polar lipid profile consisted of a mixture of aminophospholipids, aminolipids, glycolipids and uncharacterized polar lipids. The fatty acid profile was slightly different from that reported for A. aquatica. The results of DNA–DNA hybridizations and physiological and biochemical tests clearly allowed both genotypic and phenotypic differentiation of the isolate from A. aquatica. On the basis of these results, it is proposed that the strain should be classified within a novel species of the genus Arcicella. The name proposed for this taxon is Arcicella rosea sp. nov.; the type strain is TW5T (=CCUG 55942T =CCM 7523T).

A Gram-negative, aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated TR6-06T, was isolated from a compost sample in South Korea and characterized taxonomically by using a polyphasic approach. The organism grew optimally at 30 °C and pH 6.5–7.0. The isolate was positive for catalase and oxidase tests, but negative for gelatinase and urease and for indole and H2S production. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain TR6-06T was most closely affiliated with members of the genus Pedobacter of the family Sphingobacteriaceae. Strain TR6-06T exhibited 16S rRNA gene sequence similarity values of 89.9–93.5 % to the type strains of species of the genus Pedobacter. The G+C content of the genomic DNA of strain TR6-06T was 41.9 mol%. The predominant respiratory quinone was MK-7. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1 ω7c and anteiso-C15 : 0. These chemotaxonomic data support the affiliation of strain TR6-06T to the genus Pedobacter. However, on the basis of its phenotypic properties and phylogenetic distinctiveness, strain TR6-06T (=KCTC 12638T=LMG 23490T) should be classified as the type strain of a novel species, for which the name Pedobacter composti sp. nov. is proposed.

A novel anaerobic, thermophilic, Fe(III)-reducing, CO-utilizing bacterium, strain 1315T, was isolated from a hot spring of Geyser Valley on the Kamchatka Peninsula. Cells of the new isolate were Gram-positive, short rods. Growth was observed at 52–70 °C, with an optimum at 65 °C, and at pH 5.5–8.5, with an optimum at pH 6.5–7.2. In the presence of Fe(III) or 9,10-anthraquinone 2,6-disulfonate (AQDS), the bacterium was capable of growth with CO and yeast extract (0.2 g l−1); during growth under these conditions, strain 1315T produced H2 and CO2 and Fe(II) or AQDSH2, respectively. Strain 1315T also grew by oxidation of yeast extract, glucose, xylose or lactate under a N2 atmosphere, reducing Fe(III) or AQDS. Yeast extract (0.2 g l−1) was required for growth. Isolate 1315T grew exclusively with Fe(III) or AQDS as an electron acceptor. The generation time under optimal conditions with CO as growth substrate was 9.3 h. The G+C content of the DNA was 41.5±0.5 mol%. 16S rRNA gene sequence analysis placed the organism in the genus Carboxydothermus (97.8 % similarity with the closest relative). On the basis of physiological features and phylogenetic analysis, it is proposed that strain 1315T should be assigned to a novel species, Carboxydothermus siderophilus sp. nov., with the type strain 1315T (=VKPM 9905BT =VKM B-2474T =DSM 21278T).

Two strictly anaerobic bacterial strains, designated SW512T and W72, were isolated from a laboratory-scale H2-producing up-flow anaerobic sludge blanket (UASB) reactor. Cells were Gram-stain-negative, non-motile and 0.3–0.4×2.0–14.5 μm; they did not form spores. Both strains grew at 24–45 °C (no growth at ≤22 °C or ≥46 °C), with optimum growth at 37 °C. The pH range for growth was 4.5–9.0 (no growth at pH≤4.2 or pH≥9.3), with optimum growth at pH 6.5–7.0. Several kinds of mono-, di- and oligosaccharides supported growth. The main end products of glucose fermentation were ethanol, acetate, hydrogen and carbon dioxide (according to the equation 1 mol glucose→1.1 mol acetate+0.6 mol ethanol+2.6 mol H2+1.6 mol CO2). The DNA G+C contents of strains SW512T and W72 were 41.9±0.5 and 42.8±0.4 mol% (T m method), respectively. Phylogenetic analysis based on 16S rRNA gene sequence similarities indicated that the two strains represent a new phyletic sublineage within the family ‘Ruminococcaceae’, with <91.3 % 16S rRNA gene sequence similarity to recognized species. On the basis of the polyphasic evidence in this study, it is proposed that the two strains represent a novel species in a new genus, for which the name Hydrogenoanaerobacterium saccharovorans gen. nov., sp. nov. is proposed; the type strain of the type species is SW512T (=AS 1.5070T=JCM 14861T).

An aerobic, pink-pigmented, budding and rosette-forming bacterium was isolated from an acidic Sphagnum peat bog and designated strain A10T. The 16S rRNA gene sequence analysis showed that strain A10T was a member of the order Planctomycetales and belonged to a phylogenetic lineage defined by the genus Gemmata, with 90 % sequence similarity to that of Gemmata obscuriglobus, the only taxonomically described organism of this group. Ellipsoid-shaped cells of strain A10T were uniformly covered with crateriform pits and possessed long (up to 10–15 μm) and unusually thick (0.5–0.7 μm) stalks of a unique ultrastructure. Thin sections revealed a complex intracellular membrane system compartmentalizing the cells. Strain A10T was a moderately acidophilic, mesophilic organism capable of growth at pH values between 3.8 and 7.2 (with an optimum at pH 5.5–6.0) and at temperatures between 10 and 30 °C (with an optimum at 20–25 °C). The major fatty acids were C18 : 0, C18 : 1 ω5c and C16 : 1 ω5c and the major quinone was MK-6. Cells of strain A10T contained high amounts of bound saturated and monounsaturated C26–C32 (ω-1) hydroxy fatty acids. The G+C content of the DNA was 62.5 mol%. The unique cell morphology, the capability of growth in acidic conditions and a number of chemotaxonomic and genotypic characteristics served to differentiate strain A10T from G. obscuriglobus. Based on these data, the novel isolate should be considered as representing a novel genus and species of planctomycetes, for which the name Zavarzinella formosa gen. nov., sp. nov. is proposed The type strain is A10T (=DSM 19928T=VKM B-2478T).

Deinococcus mumbaiensis DSM 17424T was compared with Deinococcus ficus CC-FR2-10T to clarify the taxonomic relationship between the two species. 16S rRNA gene sequence comparisons demonstrated that these strains share 99.5 % sequence similarity. Investigation of fatty acid patterns and substrate utilization profiles displayed no striking differences between the type strains of the two species. DNA–DNA hybridizations between the two strains showed 75.4 % (76.6 %) relatedness. Therefore, the reclassification of Deinococcus mumbaiensis as a later heterotypic synonym of Deinococcus ficus is proposed, based upon the estimated phylogenetic position derived from 16S rRNA gene sequence data, fatty acid and biochemical data and DNA–DNA hybridization results.

A taxonomic study was performed on two isolates, strains RF3T and RF21, recovered from a thiosulfate-oxidizing enrichment culture. Comparative 16S rRNA gene sequence analysis showed that these isolates were clearly affiliated with the class Betaproteobacteria. Strains RF3T and RF21 were most closely related to Diaphorobacter nitroreducens NA10BT (97.9 and 98.2 % 16S rRNA gene sequence similarity, respectively). The level of 16S rRNA gene sequence similarity between strains RF3T and RF21 was 99.8 %. The two isolates were Gram-negative, aerobic and denitrifying. Growth was observed at 7–35 °C. Physiological and biochemical properties of strains RF3T and RF21 were different from those of D. nitroreducens NA10BT in that strains RF3T and RF21 were able to utilize l-histidine, 2-ketogluconate and caprate, but unable to utilize suberate. The G+C contents of the genomic DNA of strains RF3T and RF21 were 62.9 and 62.8 mol%, respectively, and the predominant quinone was ubiquinone-8. Strains RF3T and RF21 possessed C16 : 0, C17 : 0 cyclo, and C16 : 1 ω7c and/or iso-C15 : 0 2-OH as major fatty acids. DNA–DNA relatedness data indicated that strains RF3T and RF21 represent a genomic species separate from D. nitroreducens. On the basis of the evidence presented from this polyphasic analysis, it is suggested that strains RF3T and RF21 represent a novel species of the genus Diaphorobacter, for which the name Diaphorobacter oryzae sp. nov. is proposed. The type strain is RF3T (=KCTC 22225T=LMG 24467T).

A hydrogenotrophic, sulfate-reducing bacterium, designated strain SB1T, was isolated from sulfidogenic sludge of a full-scale synthesis-gas-fed bioreactor used to remediate wastewater from a zinc smelter. Strain SB1T was found to be an abundant micro-organism in the sludge at the time of isolation. Hydrogen, formate, pyruvate, lactate, malate, fumarate, succinate, ethanol and glycerol served as electron donors for sulfate reduction. Organic substrates were incompletely oxidized to acetate. 16S rRNA gene sequence analysis showed that the closest recognized relative to strain SB1T was Desulfovibrio gigas DSM 1382T (97.5 % similarity). The G+C content of the genomic DNA of strain SB1T was 62.2 mol%, comparable with that of Desulfovibrio gigas DSM 1382T (60.2 mol%). However, the level of DNA–DNA relatedness between strain SB1T and Desulfovibrio gigas DSM 1382T was only 56.0 %, indicating that the two strains are not related at the species level. Strain SB1T could also be differentiated from Desulfovibrio gigas based on phenotypic characteristics, such as major cellular fatty acid composition (anteiso-C15 : 0, iso-C14 : 0 and C18 : 1 cis 9) and substrate utilization. Strain SB1T is therefore considered to represent a novel species of the genus Desulfovibrio, for which the name Desulfovibrio paquesii sp. nov. is proposed. The type strain is SB1T (=DSM 16681T=JCM 14635T).