<Emphasis Type="Italic">Ancylobacter abiegnus</Emphasis> sp. nov., an oligotrophic member of the xylotrophic mycobacterial community

A new species of the genus Ancylobacter, exemplified by strain Z-0056, was isolated from dystrophic humified waters formed by xylotrophic fungi grown on decaying spruce wood. The cells of strain Z-0056 (0.65–0.9 μm) are coccoid, gram-negative, with fimbriae, and nonmotile. The strain is pleomorphic and reproduces by nonuniform division. Strain Z-0056 is an aerobic organoheterotroph and a mesophilic and moderately acidophilic oligotrophic microorganism. As an inhabitant of dystrophic ultrafresh waters, strain Z-0056 is sensitive to NaCl. The bacterium utilizes organic acids (acetate, pyruvate, oxalate, gluconate, malate, succinate, and citrate), as well as xylose and xylan. The microorganism grows in a pH range of 4.0–8.0, with an optimum at pH 5.5. The temperature range for growth is 15–25°C, with an optimum at 20°C. According to its ecophysiological properties, strain Z-0056 belongs to the group of ombrophilic dissipotrophs. The DNA G+C base content is 66.8 mol %. According to phylogenetic analysis, strain Z-0056 belongs to the genus Ancylobacter. Strain Z-0056 showed the highest similarity (98.3%) with the type strain of the species A. oerskovii. The phenotypic and phylogenetic properties of strain Z-0056 support classification of this microorganism within the genus Ancylobacter as the novel species Ancylobacter abiegnus sp. nov.     

Spirosoma xylofaga sp. nov., an oligotrophic pleomorphic bacterium from a myco-bacterial community of freshwater ecosystems

A novel aerobic bacterial strain Z-0088 was assigned to the genus Spirosoma on the basis of 16S rRNA analysis; it was isolated from a bacterial community of moderately acidic (pH 5.0) dystrophic, slightly humified water formed by xylotrophic fungi grown on decaying spruce wood. The cells are nonmotile, gramnegative, straight or curved rods, 0.5–1.5 × 1.0–6.0 μm; they may also be toroidal. The cells are usually single but can form spiral filaments containing from 4 to 13 coils; their reproduction is by division. Strain Z-0088 is an organoheterotroph utilizing xylan, inulin, xylose, sucrose, and N-acetylglucosamine as organic growth substrates. The bacterium is oligotrophic (the optimum substrate concentration is 0.5 g/L). It is characterized by high sensitivity to NaCl concentration; growth was completely suppressed at 1% NaCl. The strain grows in a pH range of 3.8–7.5 with the optimum at pH 5.5–6.5. The temperature range for growth was 13–35°C with the optimum at 28°C. The DNA G+C base content was 50.2 mol %. The ecophysiological features of strain Z-0088, such as oligotrophic, mesophilic, moderate acidophilic properties, and sensitivity to NaCl, support its designation as a representative of ombrophilic dissipotrophs. The strain is assigned to a novel species Spirosoma xylofaga sp. nov.     

A psychrotolerant Caulobacter sp. from Russian polar tundra soil

train Z-0024, a psychrotolerant aerobic heterotrophic representative of the prosthecate bacteria of the genus Caulobacter, was isolated from a methanotrophic enrichment obtained from Russian polar tundra soil. The cells of the new isolate are vibrios (0.5–0.6 × 1.3–1.8 mm) with a polar stalk. The organism grows in a temperature range from 5 to 36°C, with an optimum at 20°C. The pH range for growth is from 4.5 to 7.0 with an optimum at pH 6.0. Strain Z-0024 utilizes a wide range of organic compounds: sugars, amino acids, volatile fatty acids, and primary alcohols. It tolerates a NaCl concentration in the medium of up to 15 g/l. The G+C content of DNA is 66.6 mol %. The 16S rRNA gene sequence analysis revealed that strain Z-0024 belongs to the cluster of Caulobacter species, showing a 98.8–99.2% sequence similarity to them. DNA-DNA hybridization revealed a low level of homology (24%) between strain Z-0024 and C. vibrioides ATCC 15252. The new isolate is described as Caulobacter sp. Z-0024.     

Natroniella acetigena gen. nov. sp. nov., an Extremely Haloalkaliphilic,Homoacetic Bacterium: A New Member of Haloanaerobiales

A new extremely haloalkaliphilic, chemoorganotrophic, homoacetogenic bacterium strain Z-7937^T(T-type strain) was isolated from the bottom mud of the soda-depositing Lake Magadi, Kenya. It is an obligately anaerobic, motile, Gram-negative, spore-forming rod growing in the pH range pH 8.1 to 10.7 and optimally in the range pH 9.7 to 10.0 under conditions of high alkalinity caused by saturation with trona. It has an obligate requirement for sodium carbonate and chloride ions. The optimum salt concentration for growth is in the range 12–15% wt/vol, and growth occurs within the range from 10% to 26%. Strain Z-7937^T is a mesophile with an optimal temperature for growth of 37°C, and a maximum of 42°C. The G + C content of strain Z-7937^T is 31.9 mol%. A limited number of compounds are utilized, including lactate, ethanol, pyruvate, glutamate, and propanol. Acetate is the main end product. 16S rDNA sequence analysis shows strain Z-7937^T to be a member of the order Haloanaerobiales and to represent a new branch within the family Halobacteroidaceae. On the basis of its novel physiology and phylogenetic position, we propose strain Z-7937 as a new species of a new genus, Natroniella acetigena gen. nov. sp. nov. The type strain is Z-7937^T (= DSM 9952).     

A novel thermophilic anaerobic bacteria producing cyclodextrin glycosyltransferase

A novel thermophilic anaerobic, rod-shaped, non-spore forming, gram positive bacterium was isolated from an oil field in Turkey, that produces cyclodextrin glycosyltransferase (CGTase) from starch. According to the some morphological, biochemical and 16S rRNA analysis, the strain belongs to the genus Thermoanaerobacter. The strain mainly utilizes starch and derivatives, glucose and fructose as carbon source between 45 and 75 °C, optimally at 65 °C. Optimum pH for growth is 7.5. 16S RNA studies indicate that the bacterium has a similarity of 98.3% to homoacetogenic Thermoanaerobacter kivui and the main fermentation product is acetic acid as in the case with homoacetogenic bacteria. The main difference between the bacterium and T. kivui concerns the utilization of starch. Based on the phylogenetic and biochemical analysis, it is proposed that the species are a new member of the genus Thermoanaerobacter. The strain has CGTase activity optimum at 80 °C and pH 7.0–8.0.     

Isolation of Paenibacillus pinesoli sp. nov. from forest soil in Gyeonggi-Do,Korea

Using a new culture method for unculturable soil bacteria, strain NB5^T was isolated from forest soil at Kyonggi University, and characterized taxonomically on the basis of 16S rRNA gene sequence as well as phenotypic and chemotaxonomic characteristics. The novel strain was a Gram- and catalase-positive, rod-shaped bacterium, which grew in the pH range 6.0–9.5 (optimum, 6.5–9.5) and at temperatures between 15°C and 45°C (optimum, 25–40°C). Growth was possible at 0–5% NaCl (optimum, 0% to 3%) in nutrient, Luria-Bertani, and trypticase soy broths (TSB), as well as R2A medium (with optimal growth in TSB). A phylogenetic analysis of the 16S rRNA gene sequence showed that the novel strain was affiliated with the genus Paenibacillus and had 96.8% and 96.5% similarity to P. nanensis MX2-3^T and P. agaridevorans DSM 1355^T, respectively. The predominant menaquinone in NB5^T was MK-7; the major fatty acids were anteiso-C_15:0 and iso-C_16:0; and the DNA G+C content was 54.5 mol%. We propose this strain as a novel species of the genus Paenibacillus, and suggest the name Paenibacillus pinesoli sp. nov. (type strain, KACC 17472^T=KEMB 9005-025^T=JCM 19203^T).     

Lysobacter thermophilus sp. nov., isolated from a geothermal soil sample in Tengchong, south-west China

A Gram-negative and aerobic bacterium, designated YIM 77875^T, was isolated from a geothermal soil sample collected at Rehai National Park, Tengchong, Yunnan Province, south-west China. Bacterial growth occurred from 37 to 65 °C (optimum 50 °C), pH 6.0–8.0 (optimum pH 7.0) and 0–1 % NaCl (w/v). Cells were rod-shaped and colonies were convex, circular, smooth, yellow and non-transparent. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain YIM 77875^T belongs to the genus Lysobacter. The 16S rRNA gene sequence similarity values between strain YIM 77875^T and other species of the genus Lysobacter were all below 94.7 %. The polar lipids of strain YIM 77875^T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and five unknown phospholipids. The predominant respiratory quinone was Q-8 and the G+C content was 68.8 mol%. Major fatty acids were iso-C_16:0, iso-C_15:0 and iso-C_11:0. On the basis of the morphological and chemotaxonomic characteristics, as well as genotypic data, strain YIM 77875^T represents a novel species, Lysobacter thermophilus sp. nov., in the genus Lysobacter. The type strain is YIM 77875^T (CCTCC AB 2012064^T = KCTC 32020^T).     

Geoalkalibacter ferrihydriticus gen. nov. sp. nov., the first alkaliphilic representative of the family Geobacteraceae, isolated from a soda lake

Investigation of iron reduction in bottom sediments of alkaline soda lakes resulted in the isolation of a new obligately anaerobic iron-reducing bacterium, strain Z-0531, from Lake Khadyn (Tuva, Russia) sediment samples. The cells of strain Z-0531 are short (1.0–1.5 by 0.3–0.5 μm), motile, non-spore-forming, gram-negative rods. The isolate is an obligate alkaliphile, developing in the pH range of 7.8–10.0, with an optimum at pH 8.6. It does not require NaCl but grows at NaCl concentrations of 0–50 g/l. It can oxidize acetate with such electron acceptors as amorphous Fe(III) hydroxide (AFH), EDTA-Fe(III), anthraquinone-2,6-disulfonate (quinone), Mn(IV), and S⁰. On medium with EDTA-Fe(III), the isolate can oxidize, apart from acetate, ethanol, pyruvate, oxalate, arginine, tartrate, lactate, propionate, and serine. H₂ is not utilized. The reduced products formed during growth with AFH are siderite or magnetite, depending on the growth conditions. The isolate is incapable of fermenting sugars, peptides, and amino acids. Yeast extract or vitamins are required as growth factors. The organism is capable of dinitrogen fixation and harbors the nifH gene. The DNA G+C content is 55.3 mol %. 16S rRNA analysis places strain Z-0531 into the family Geobacteraceae. Its closest relative (93% similarity) is Desulfuromonas palmitatis. Based on phenotypic distinctions and phylogenetic position, it is proposed that this strain be assigned to the new genus and species Geoalkalibacter ferrihydriticus gen. nov., sp. nov. (Z-0531^T-DSMZ-17813-VKMB-2401). Original Russian Text ? D.G. Zavarzina, T.V. Kolganova, E.S. Boulygina, N.A. Kostrikina, T.P. Tourova, G.A. Zavarzin, 2006, published in Mikrobiologiya, 2006, Vol. 75, No. 6, pp. 775–785.     

Themoanaerobacterium calidifontis sp. nov., a novel anaerobic, thermophilic, ethanol-producing bacterium from hot springs in China

A novel thermophilic Gram staining positive strain Rx1 was isolated from hot springs in Baoshan of Yunnan Province, China. The strain was characterized as a hemicellulose-decomposing obligate anaerobe bacterium that is rod-shaped (diameter: 0.5–0.7 μm; length: 2.0–6.7 μm), spore-forming, and motile. Its growth temperature range is 38–68 °C (optimum 50–55 °C) and pH range is 4.5–8.0 (optimum 7.0). The maximum tolerance concentration of NaCl was 3 %. Rx1 converted thiosulfate to elemental sulfur and reduced sulfite to hydrogen sulfide. The bacterium grew by utilizing xylan and starch, as well as a wide range of monosaccharide and polysaccharides, including glucose and xylose. The main products of fermentation were ethanol, lactate, acetate, CO₂, and H₂. The maximum xylanase activity in the culture supernatant after 30 h of incubation at 55 °C was 16.2 U/ml. Rx1 DNA G + C content was 36 mol %. 16S rRNA gene sequence analysis indicated that strain Rx1 belonged to the genus Thermoanaerobacterium of the family ‘Thermoanaerobacteriaceae’ (Firmicutes), with Thermoanaerobacterium aciditolerans 761–119 (99.2 % 16S rRNA gene sequence similarity) being its closest relative. DNA–DNA hybridization between Rx1 and T. aciditolerans 761–119 showed 36 % relatedness. Based on its physiological and biochemical tests and DNA–DNA hybridization analyses, the isolate is considered to represent a novel species in the genus Thermoanaerobacterium, for which the name Thermoanaerobacterium calidifontis sp. nov. is proposed, with the type strain is Rx1 (=JCM 18270 = CCTCC M 2011109).     

Halonatronomonas betaini gen. nov., sp. nov., a haloalkaliphilic isolate from soda lake capable of betaine degradation and proposal of Halarsenatibacteraceae fam. nov. and Halothermotrichaceae fam. nov. within the order Halanaerobiales

A search for the organisms responsible for anaerobic betaine degradation in soda lakes resulted in isolation of a novel bacterial strain, designated Z-7014^T. The cells were Gram-stain-negative, non-endospore-forming rods. Growth occurred at 8–52 °C (optimum 40–45 °C), pH 7.1–10.1 (optimum pH 8.1–8.8) and 1.0–3.5 M Na⁺ (optimum 1.8 M), i.e. it can be regarded as a haloalkaliphile. The strain utilized a limited range of substrates, mostly peptonaceous but not amino acids, and was able to degrade betaine. Growth on betaine occurred only in the presence of peptonaceous substances which could not be replaced by vitamins. The G + C content of the genomic DNA of strain Z-7014^T was 36.1 mol%. The major cellular fatty acids (>5% of the total) were C_16:0 DMA, C_{18: 0} DMA, C_16:1ω8, C_16:0, C_18:1 DMA, C_16:1 DMA, C_18:1ω9, and C_18:0. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain Z-7014^T formed a distinct evolutionary lineage in the order Halanaerobiales with the highest similarity to Halarsenitibacter silvermanii SLAS-1^T (83.6%), Halothermothrix orenii H168^T (85.6%), and Halocella cellulosilytica DSM 7362^T (85.6%). AAI and POCP values between strain Z-7014^T and type strains of the order Halanaerobiales were 51.7–57.8%, and 33.8–58.3%, respectively. Based on polyphasic results including phylogenomic data, the novel strain could be distinguished from other genera, which suggests that strain Z-7014^T represents a novel species of a new genus, for which the name Halonatronomonas betaini gen. nov., sp. nov. is proposed. The type strain is Z-7014^T (=KCTC 25237^T = VKM B-3506^T). On the basis of phylogenomic data, it is also proposed to evolve two novel families Halarsenitibacteraceae fam. nov. and Halothermotrichaceae fam. nov. within the current order Halanaerobiales.     

Petrotoga japonica sp. nov., a thermophilic,fermentative bacterium isolated from Yabase Oilfield in Japan

A gram-negative, motile, fermentative, thermophilic bacterium, designated AR80^T, was isolated from a high-temperature oil reservoir in Yabase Oilfield in Akita, Japan. Cells were rod-shaped, motile by means of polar flagella, and formed circular, convex, white colonies. The strain grew at 40–65 °C (optimum 60 °C), 0.5–9 % (w/v) NaCl (optimum 0.5–1 %), pH 6–9 (optimum pH 7.5), and elemental sulfur or thiosulfate serves as terminal electron acceptor. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain AR80^T belonged to the genus Petrotoga and shared approximately 94.5 % sequence similarity with the type species of this genus. The G + C content of genomic DNA was 32.4 mol% while the value of DNA–DNA hybridization between the closest relative species Petrotoga miotherma and AR80^T was 58.1 %. The major cellular fatty acids of strain AR80^T consisted of 18:1 w9c, 16:0, and 16:1 w9c. Based on genetic and phenotypic properties, strain AR80^T was different with other identified Petrotoga species and represents as a novel species, for which the name Petrotoga japonica sp. nov. is proposed. The type strain is AR80^T (=NBRC 108752^T = KCTC 15103^T = HUT 8122^T).     

Paenibacillus cucumis sp. nov. isolated from greenhouse soil

Strain CO 4–7^T was isolated from greenhouse soil used for cultivation of cucumbers in Korea. The 16S rRNA gene sequence of strain CO 4–7^T showed the highest sequence similarity with Paenibacillus contaminans CKOBP-6^T (94.2%) among the type strains. Strain CO 4–7^T was a strictly aerobic, Gram-staining-positive, endospore-forming, and motile rodshaped bacterium. Strain CO 4–7^T grew at 10–45°C (optimum, 30°C), at pH 6.0–7.5 (optimum, pH 6.5) and in the presence of 0–5% NaCl (optimum, 0.5%). The DNA G+C content of strain CO 4–7^T was 48.5 mol%. It contained MK-7 as the major isoprenoid quinone and anteiso-C15:0 (51.8%), C16:0 (12.7%), and iso-C16:0 (8.6%) as the major fatty acids. The cell wall contained meso-diaminopimelic acid. Based on evidence from our polyphasic taxonomic study, it was concluded that strain CO 4-7T should be classified as a novel species of the genus Paenibacillus, for which, the name Paenibacillus cucumis sp. nov. is proposed. The type strain is CO 4–7^T (=KACC 17444^T=JCM 19515^T).     

Niabella terrae sp. nov. isolated from greenhouse soil

An orange-colored bacterial strain, ICM 1–15^T, was isolated from greenhouse soil. The 16S rRNA gene sequence of this strain showed the highest sequence similarity with Niabella ginsengisoli GR10-1^T (95.2%) and Niabella yanshanensis CCBAU 05354^T (95.0%) among the type strains. The strain ICM 1–15^T was a strictly aerobic, Gram-negative, non-spore-forming, non-motile, flexirubin pigment-producing, short rod-shaped bacterium. The strain grew at 15–35°C (optimum, 25°C), at a pH of 5.0–8.5 (optimum, pH 6.5), and in the presence of 0–3% NaCl (optimum, 1%). The DNA G+C content of strain ICM 1–15^T was 43.6 mol%. It contained MK-7 as the major isoprenoid quinone and iso-C_15:0 (38.9%), iso-C_15:1 G (20.3%), and iso-C_17:0 3-OH (12.9%) as the major fatty acids. On the basis of evidence from our polyphasic taxonomic study, we concluded that strain ICM 1–15^T should be classified within a novel species of the genus Niabella, for which the name Niabella terrae sp. nov. is proposed. The type strain is ICM 1–15^T (=KACC 17443^T =JCM 19502^T).     

Desulfotomaculum tongense sp. nov., a moderately thermophilic sulfate-reducing bacterium isolated from a hydrothermal vent sediment collected from the Tofua Arc in the Tonga Trench

A novel, strictly anaerobic, moderately thermophilic, endospore-forming, sulfate-reducing bacterium, designated TGB60-1^T, was isolated from a hydrothermal sediment vent collected from the Tofua Arc in the Tonga Trench. The strain was characterized phenotypically and phylogenetically. The isolated strain was observed to be Gram-positive, with slightly curved rod-shaped cells and a polar flagellum. Strain TGB60-1^T was found to grow anaerobically at 37–60 °C (optimum, 50 °C), at pH 6.0–8.5 (optimum, pH 7.0) and with 1.0–4.0 % (w/v) NaCl (optimum, 3.0 %). The electron acceptors utilised were determined to be sulfate, sulfite, and thiosulfate. Strain TGB60-1^T was found to utilise pyruvate and H₂ as electron donors. Strain TGB60-1^T was determined to be related to representatives of the genus Desulfotomaculum and the closest relatives within this genus were identified as Desulfotomaculum halophilum SEBR 3139^T, Desulfotomaculum alkaliphilum S1^T and Desulfotomaculum peckii LINDBHT1^T (92.7, 92.1, and 91.8 % 16S rRNA gene sequence similarity, respectively). The major fatty acids (>20 %) were identified as C_16:0 and C_18:1 ω7c. The G+C content of the genomic DNA of this novel bacterium was determined to be 53.9 mol%. Based on this polyphasic taxonomic study, strain TGB60-1^T is considered to represent a novel species in the genus Desulfotomaculum, for which the name Desulfotomaculum tongense sp. nov. is proposed. The type strain of D. tongense is strain TGB60-1^T (= KTCT 4534^T = JCM 18733^T).     

Thermus tengchongensis sp. nov., isolated from a geothermally heated soil sample in Tengchong, Yunnan, south-west China

A Gram-stain negative aerobic bacterium, designated YIM 77924^T, was isolated from a geothermally heated soil sample collected at Rehai National Park, Tengchong, Yunnan province, south-west China. Growth was found to occur from 55 to 75 °C (optimum 65 °C), pH 6.0–8.0 (optimum pH 7.0) and 0–1 % NaCl (w/v). Cells were observed to be rod-shaped and the colonies convex, circular, smooth, yellow and non-transparent. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain YIM 77924^T belongs to the genus Thermus. The 16S rRNA gene sequence similarity values between strain YIM 77924^T and other species of the genus Thermus were all below 97 %. The polar lipids of strain YIM 77924^T were determined to be aminophospholipid, phospholipid and glycolipid. The predominant respiratory quinone was determined to be MK-8 and the G+C content was 66.64 mol%. The major fatty acids identified were iso-C_16:0, iso-C_15:0, iso-C_17:0 and C_16:0. On the basis of the morphological and chemotaxonomic characteristics as well as genotypic data, strain YIM 77924^T is proposed to represent a novel species, Thermus tengchongensis sp. nov., in the genus Thermus. The type strain is YIM 77924^T (=KCTC 32025^T = CCTCC AB2012063^T).     

Paenibacillus beijingensis sp. nov., a novel nitrogen-fixing species isolated from jujube garden soil

A novel Gram-positive, rod-shaped, motile, spore-forming, nitrogen-fixing bacterium, designated strain 7188^T, was isolated from jujube rhizosphere soil in Beijing, China. The strain grew at 4–40 °C and pH 6–12, with an optimum of 30 °C and pH 7.0, respectively. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain 7188^T is a member of the genus Paenibacillus. Levels of 16S rRNA gene sequence similarities between strain 7188^T and the type strains of all recognized members of the genus Paenibacillus were below 96 %. The major cellular fatty acids were anteiso-C_15:0, anteiso-C_17:0 and C_16:0. The predominant menaquinone was MK-7. The DNA G+C content of strain 7188^T was 60.3 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and unknown aminophospholipids. The diamino acid in the cell wall peptidoglycan is meso-diaminopimelic acid. On the basis of these results, strain 7188^T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus beijingensis sp. nov. is proposed. The type strain is 7188^T (=ACCC 03082^T = DSM 24997^T).     

Novel halotolerant bacterium from cryopeg in permafrost: Description of <Emphasis Type="Italic">Psychrobacter muriicola</Emphasis> sp. nov.

A novel halotolerant psychrotrophic gram-negative bacterium, strain 2pS, was isolated from lenses of water brine in Arctic permafrost (cryopeg). The optimal growth of the new strain was observed at 16–18°C; the maximal and minimal growth temperatures were 37°C and ?2°C, respectively. The pH growth range was 5.8 to 8.5 (optimum 6.5–7.5) and the range of medium salinity was 0 to 100 g/l (optimum 3–8 g/l NaCl). The strain 2pS did not produce acid from carbohydrates and utilized acetate, yeast extract, pyruvate, glutarate, fumarate, caproate, heptanoate, butyrate, malate, DL-lactate, citrate, L-proline, L-tyrosine, butanol, and dulcitol as the sole carbon and energy sources. The major fatty acids of the cell wall at optimal growth temperature were C_18:1ω7 and C_18:1ω9. The G+C DNA base content was 46.0 mol.%. Phylogenetic analysis of the 16S rRNA gene sequences showed that the studied strain was the closest (97% similarity) to Psychrobacter nivimaris DSM 16093^T, a halotolerant psychrotrophic bacterium isolated from the Arctic sea’s ice. Genotypic and phenotypic differences of the new bacterium from closely related species lead to the conclusion that strain 2pS belongs to a novel species of the genus Psychrobacter: Psychrobacter muriicola sp. nov.