Rhizobium halotolerans sp. nov., Isolated from Chloroethylenes Contaminated Soil

The strain designated as AB21^T was isolated from chloroethylenes contaminated soil. Cells are gram-negative, aerobic, non-spore-forming, and motile rods. Phylogenetic analysis based on 16S rRNA gene sequence showed that it belonged to the genus Rhizobium, and was closely related to Rhizobium sullae IS 123^T (97.4 %), Rhizobium yanglingense SH 22623^T (97.2 %), Rhizobium gallicum R 602sp^T (97.1 %), Rhizobium alamii GBV 016^T (97.0 %), and Rhizobium monogolense USDA 1844^T (97.0 %). It showed less than 97 % identity with the remaining Rhizobium species. This novel isolate grew optimally at 25–37 °C (optimum, 30 °C) and pH 6–9 (optimum, pH 8.0). It grew in the presence of 0–4 % (w/v) NaCl, tolerating a 4 % (w/v) NaCl. DNA–DNA hybridization experiment shows less than 53 % binding with closely related Rhizobium. Predominant quinone is ubiquinone (Q-10). The major fatty acids were summed feature 8 (composed of C_18:1 ω7c/C_18:1 ω6c), C_19:0 cyclo ω8c, and C_16:0. The G+C molar content is 62.5 mol%. Based on the polyphasic analysis, strain AB21^T is referred to be a novel species of the genus Rhizobium for which the name Rhizobium halotolerans sp. nov. is proposed. The type strain is AB21^T (=KEMC 224-056^T = JCM 17536^T).     

Pedobacter hainanensis sp. nov., Isolated from Seaside Soil

A Gram-negative, aerobic, rod-shaped, motile, non-spore-forming bacterial strain, designated 13-Q^T, was isolated from seaside soil under the stacks of the red algae in Hainan province in China. Identification was carried out on the basis of polyphasic taxonomy. Phylogenetic analysis of 16S rRNA gene sequences showed that strain 13-Q^T belonged to the genus Pedobacter, and the highest similarity was 94.4 % with Pedobacter terricola KCTC 12876^T. Strain 13-Q^T was able to grow at 10–40 °C, in pH 5.0–10.0, in the presence of 0–2.0 % NaCl. The major fatty acids were iso-C_15:0 (40.4 %), summed feature 3 (comprising iso-C_15:0 2-OH and/or C_16:1 ω7c) (18.9 %) and iso-C_17:0 3-OH (18.4 %). The predominant menaquinone was MK-7. The G+C content of the genomic DNA was 42.7 mol%. Strain 13-Q^T could be distinguished from the nearest phylogenetic neighbors by various chemotaxonomic and phenotypic properties. The results of the polyphasic analyses suggested that strain 13-Q^T should be considered to represent a novel species of the genus Pedobacter, for which the name Pedobacter hainanensis sp. nov. is proposed. The type strain is 13-Q^T (=CCTCC AB 2012076^T = NRRL B-59850^T).     

Pontibacter humi sp. nov., Isolated from Mountain Soil

A Gram-negative, aerobic, non-motile, rod-shaped bacterial strain, designated as SWU8^T, was isolated from a mountain soil collected in Seoul Women’s University campus at South Korea. Phylogenic analysis, using 16S rRNA gene sequence of the new isolate, showed that strain SWU8^T belongs to the genus Pontibacter. The highest sequence similarities were 96.2 % with Pontibacter saemangeumensis GCM0142^T, 95.5 % with Pontibacter toksunensis ZLD-7^T, 95.3 % with Pontibacter roseus DSM 17521^T, and 95.1 % with Pontibacter odishensis JC130^T. Chemotaxonomic data showed that the most abundant fatty acids were summed feature 4 (comprising iso-C_17:1 I/anteiso-C_17:1 B; 26.9 %), iso-C_15:0 (25.6 %), and iso-C_17:0 3OH (10.6 %), and major polar lipid was phosphatidylethanolamine. The DNA G+C content of strain SWU8^T was 48.5 mol%. Together, the phenotypic, phylogenetic, and chemotaxonomic data supported that strain SWU8^T presents a novel species of the genus Pontibacter, for which the name Pontibacter humi sp. nov. is proposed. The type strain is SWU8^T (=KEMC 9004-131^T = JCM 19178^T).     

Cohnella humi sp. nov., Isolated from Russian Soil

A Gram-positive, catalase and oxidase positive, rod-shaped bacteria, and spore-forming, designated as J20-3^T was isolated from a peat soil, collected near a coal mine at Prokopyevsk, (GPS; N53°52′51″, E86°43′39″) Kemerovo Oblast, Russia. A polyphasic taxonomy study using phenotypic, phylogenetic, and genotypic method was performed to characterize strain J20-3^T. Comparative 16S rRNA gene sequence analysis indicated that strain J20-3^T represented a novel subline within the genus Cohnella in the family Paenibacillaceae. According to 16S rRNA gene sequence, strain J20-3^T showed 93.7–97.2 % similarity levels with other Cohnella species. Strain J20-3^T exhibited relatively low level of DNA–DNA hybridization value with type strains KACC 11643^T (40 %), KACC 11771^T (37.5 %), and KACC 15372^T (30.5 %). The strain showed typical chemotaxonomic characteristic of the genus Cohnella, with the presence of predominant respiratory quinone MK-7; major fatty acids are C_15:0, C_16:0, iso, and C_16:0. The DNA G+C content of the strain J20-3^T was 56.3 mol%. The polar lipid profile of the strain J20-3^T included major amount of diphosphatidylglycerol, phosphatidylglycerol, and phosphoatidylethanolamine. On the basis of its phenotypic and genotypic properties, and its phylogenetic distinctiveness, strain J20-3^T should be classified as a novel species in the genus Cohnella, for which the name Cohnella humi sp. nov. is proposed.     

Nitratireductor shengliensis sp. nov., Isolated from an Oil-Polluted Saline Soil

Two Gram-negative, non-motile, short-rod-shaped bacterial isolates, designated 110399^T and 110248, were isolated from an oil-polluted saline soil in Shengli Oilfield, Eastern China. The two strains shared 99.9 % 16S rRNA gene sequence similarity with the DNA–DNA relatedness value being 80.0 %. They were both capable to grow at 20–40 °C, pH 7–9, and 1–9 % (w/v) NaCl with the optimum growth happened at 30 °C, pH 8, and 2–6 % (w/v) NaCl. The phylogenetic analysis based on 16S rRNA gene sequences revealed that the two strains were members of Nitratireductor and most closely related to Nitratireductor pacificus pht-3B^T and N. basaltis J3^T with the 16S rRNA gene sequence similarities being 97.1 and 97.0 %. The DNA–DNA relatedness between the novel strains and two type strains were below 27 ± 7 %. The strains 110399^T and 110248 also differed from N. pacificus and N. basaltis in nitrate reduction, salt tolerance, enzyme activities, and utilization of carbon sources. The major cellular fatty acids of strain 110399^T were C_19:0ω8c cyclo (10.5 %) and Summed Feature 8 (C_18:1ω7c and/or C_18:1ω6c, 41.5 %) which are typical in the genus Nitratireductor. The predominant ubiquinone was Q-10. The genome DNA G+C content of strain 110399^T and 110248 was 61.1 and 61.7 mol%. On the basis of genetic, phenotypic, and chemotaxonomic analyses, strains 110399^T and 110248 represent a novel species within the genus Nitratireductor, for which the name Nitratireductor shengliensis sp. nov. is proposed. The type strain is 110399^T (=CGMCC 1.12519^T = LMG 27405^T).     

Hymenobacter swuensis sp. nov., a Gamma-Radiation-Resistant Bacteria Isolated from Mountain Soil

Gram stain-negative and non-motile bacteria, designated as DY53^T and DY43, were isolated from mountain soil in South Korea prior exposure with 5 kGy gamma radiation. Phylogenetic analysis based on 16S rRNA gene sequence revealed that the strains belonged to the family Cytophagaceae in the class Cytophagia. 16S rRNA gene sequence similarity of strains DY53^T and DY43 was 100 %. The highest degrees of sequence similarities of strains DY53^T and DY43 were found with Hymenobacter perfusus A1-12^T (98.8 %), Hymenobacter rigui WPCB131^T (98.5 %), H. yonginensis HMD1010^T (97.9 %), H. xinjiangensis X2-1g^T (96.6 %), and H. gelipurpurascens Txg1^T (96.5 %). The DNA G+C content of the novel strains DY53^T and DY43 were 59.5 mol%. Chemotaxonomic data revealed that strains possessed major fatty acids such as C_15:0 iso, C_15:0 anteiso, C_16:1 ω5c, summed feature 3 (16:1 ω7c/ω6c), summed feature 4 (17:1 anteiso B/iso I) and C_17:0 iso, and major polar lipid was phosphatidylethanolamine. The novel strains showed resistance to gamma radiation, with a D10 value (i.e., the dose required to reduce the bacterial population by tenfold) in excess of 5 kGy. Based on these data, strains DY53^T and DY43 should be classified as representing a novel species, for which the name Hymenobacter swuensis sp. nov. is proposed, with the type strain DY53^T (=KCTC 32018^T = JCM 18582^T) and DY43 (=KCTC 32010).     

Deinococcus soli sp. nov., a Gamma-Radiation-Resistant Bacterium Isolated from Rice Field Soil

A Gram-negative, non-motile, short rod-shaped bacterial strain, designated N5^T, was isolated from a rice field soil in South Korea. Phylogenetic analysis based on the 16S rRNA gene sequence of the new isolate showed that strain N5^T belongs to the genus Deinococcus, family Deinococcaceae, showing the highest sequence similarity to Deinococcus grandis KACC 11979^T (98.4 %) and Deinococcus daejeonensis KCTC 13751^T (97.5 %). Strain N5^T exhibits resistance to gamma-radiation similar to that of other members of the genus Deinococcus, with a D₁₀ value in excess of 4 kGy. Chemotaxonomic data showed that the most abundant fatty acids are C_16:1 ω7c (25.25 %), C_15:1 ω6c (19.77 %), C_17:1 ω6c (11.87 %), and C_17:0 (9.41 %), and the major polar lipid is an unknown phosphoglycolipid. The predominant respiratory quinone is menaquinone MK-8. The DNA G+C content is 71.4 mol%. Phenotypic, phylogenetic, and chemotaxonomic data support designation of strain N5^T as a novel species of the genus Deinococcus, for which the name Deinococcus soli sp. nov. is proposed. The type strain is N5^T (=KCTC 33153^T = JCM 19176^T).     

Pseudomonas hunanensis sp. nov., Isolated from Soil Subjected to Long-Term Manganese Pollution

A Gram-negative, polar flagella, rod-shaped bacterium LV ^T was isolated from a soil sample subjected to long-term manganese pollution in Hunan Province, China. Cells grow optimally on Luria–Bertani agar medium at 30 °C in the presence of 0–5.0 % (w/v) NaCl and pH 7–8. 16S rRNA gene sequence analysis revealed that strain LV ^T belonged to the genus Pseudomonas, with sequence similarity values of 98.6, 98.2, 98.7, and 97.3 % to Pseudomonas monteilii BCRC 17520 ^T , Pseudomonas putida BCRC 10459 ^T , Pseudomonas plecoglossicida BCRC 17517 ^T , and Pseudomonas asplenii BCRC 17131 ^T , respectively. The level of DNA–DNA relatedness between the five strains was <30 %. The DNA G+C content of strain LV ^T is 68.8 mol%. Chemotaxonomic data revealed that the strain LV^T possesses ubiquinone Q-9. The polar lipid profile of strain LV ^T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and phosphatidylethanolamine. The major cellular fatty acids present are C_10:03-OH (12.33 %), C_16:0 (23.99 %), summed feature 3(C_16:1ω7c and/or C_16:1ω6c), and summed feature 8(C_{18:1 ω7c} and C_{18:1 ω6c}). Based on the genotypic, chemotaxonomic and phenotypic data, strain LV ^T is distinguishable from related members of the genus Pseudomonas. Thus, strain LV ^T represents a novel species of the genus Pseudomonas, for which the name Pseudomonas hunanensis sp. nov. is proposed. The type strain is LV ^T (=CICC 10558^T = NCCB 100446^T).     

Spirosoma radiotolerans sp. nov., a Gamma-Radiation-Resistant Bacterium Isolated from Gamma Ray-Irradiated Soil

A Gram-negative, short-rod-shaped bacterial strain with gliding motility, designated as DG5A^T, was isolated from a rice field soil in South Korea. Phylogenic analysis using 16S rRNA gene sequence of the new isolate showed that strain DG5A^T belong to the genus Spirosoma in the family Spirosomaceae, and the highest sequence similarities were 95.5 % with Spirosoma linguale DSM 74^T, 93.4 % with Spirosoma rigui WPCB118^T, 92.8 % with Spirosoma luteum SPM-10^T, 92.7 % with Spirosoma spitsbergense SPM-9^T, and 91.9 % with Spirosoma panaciterrae Gsoil 1519^T. Strain DG5A^T revealed resistance to gamma and UV radiation. Chemotaxonomic data showed that the most abundant fatty acids were summed feature C_16:1 ω7c/C_16:1 ω6c (36.90 %), C_16:1 ω5c (29.55 %), and iso-C_15:0 (14.78 %), and the major polar lipid was phosphatidylethanolamine (PE). The DNA G+C content of strain DG5A^T was 49.1 mol%. Together, the phenotypic, phylogenetic, and chemotaxonomic data supported that strain DG5A^T presents a novel species of the genus Spirosoma, for which the name Spirosoma radiotolerans sp. nov., is proposed. The type strain is DG5A^T (=KCTC 32455^T = JCM19447^T).     

Mrakia terrae sp. nov. and Mrakia soli sp. nov., Two Novel Basidiomycetous Yeast Species Isolated from Soil in Korea

Three strains, YP416^T, YP421^T, and Y422, were isolated from soil samples in Pocheon City, Gyeonggi province, South Korea. The strains belong to two novel yeast species in the genus Mrakia. Molecular phylogenetic analysis showed that the strain YP416^T was closely related to Mrakia niccombsii. Still, it differed by 9 nucleotide substitutions with no gap (1.51%) in the D1/D2 domain of the LSU rRNA gene and 14 nucleotide substitutions with 7 gaps (2.36%) in the ITS region. The strain YP421^T differed from the type strain of the most closely related species, Mrakia aquatica, by 5 nucleotide substitutions with no gap (0.81%) in the D1/D2 domain of the LSU rRNA gene and 9 nucleotide substitutions with one gap (1.43%) in the ITS region. The names Mrakia terrae sp. nov. and Mrakia soli sp. nov. are proposed, with type strains YP416^T (KCTC 27886^T) and YP421^T (KCTC 27890^T), respectively. MycoBank numbers of the strains YP416^T and YP421^T are MB 836844 and MB 836847, respectively.     

Acinetobacter refrigeratorensis sp. nov., Isolated from a Domestic Refrigerator

A Gram-negative bacterial strain, designated WB1^T, was isolated from a domestic refrigerator in Guangzhou, PR China. Cells of strain WB1^T were oxidase-negative, catalase-positive, strictly aerobic, non-spore-forming and non-motile coccobacilli with peritrichous fimbriae-like structures. The strain was able to grow at 10–40 °C with optimum growth at 28–30 °C, pH 6.0–8.0 (optimum, pH 7.0) and 0–6 % NaCl (w/v, optimum, 0.5 %). Phylogenetic analyses based on 16S rRNA gene and rpoB gene sequences revealed that strain WB1^T belonged to the genus Acinetobacter and was most closely related to A. indicus DSM 25388^T (97.2 % 16S rRNA gene sequence similarity) and A. radioresistens NBRC 102413^T (96.8 %). The DNA G + C content of strain WB1^T was 46.74 ± 0.04 mol % and the major fatty acids comprised summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c), C_18:1 ω9c, C_16:0 and C_12:0. The predominant respiratory quinone was identified as Q-9 and the polar lipids as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and an unidentified phospholipid. Phenotypic, phylogenetic and chemotaxonomic data, including low DNA–DNA relatedness with closely related type strains, supported that strain WB1^T represents a distinct novel species in the genus Acinetobacter, for which the name Acinetobacter refrigeratorensis sp. nov. was proposed. The type strain is WB1^T (=GIMCC 1.663^T = CCTCC AB 2014197^T = KCTC 42011^T).     

Comamonas faecalis sp. nov., Isolated from Domestic Pig Feces

A new bacterial strain, designated as FF42^T, was isolated from feces of domestic pigs—collected from Suwon, Korea—and was characterized to determine its taxonomic position. Strain FF42^T was observed to be Gram negative, aerobic, non-spore forming, motile, and rod-shaped cells. Based on the phylogenetic and 16S rRNA sequence analyses, it was revealed that strain FF42^T belonged to the genus Comamonas. The highest degree of sequence similarities was determined to be with Comamonas zonglianii BF-3^T (96.3 %), Comamonas composti CC-YY287^T (96.1 %), and Comamonas nitrativorans 23310^T (95.9 %), while showing less than 95.6 % identity with the remaining Comamonas species. Growth of strain FF42^T occurred between 25 and 40 °C (optimum, 28 °C) and at pH of 5-9 (optimum, pH 6.0). It grew in the presence of 0–3 % (w/v) NaCl while minimally tolerating at 3 % (w/v) NaCl. Biochemical and physiological tests revealed phenotypic differentiation of strain FF42^T to other members of the genus Comamonas. The predominant quinone is ubiquinone (Q-8). The major cellular fatty acids were C_10:0 3OH, C_16:0, summed feature 3 (C_16:1 ω7c/C_16:1 ω6c), and summed feature 8 (C_18:1 ω6c/C_18:1 ω7c), all of which have previously been reported to occur in the species of the genus Comamonas. The G+C molar content for strain FF42^T is 60.2 mol %. Based on phylogenetic and phenotypic analyses, strain FF42^T (=KEMC 1002-058^T=JCM 17561^T) is clearly referred to be a novel species for the genus Comamonas, for which the name Comamonas faecalis sp. nov. is proposed.     

A Novel Protein-Deamidating Enzyme from Chryseobacterium proteolyticum sp. nov., a Newly Isolated Bacterium from Soil

A novel protein-deamidating enzyme, which has potential for industrial applications, was purified from the culture supernatant of Chryseobacterium proteolyticum strain 9670^T isolated from rice field soil in Tsukuba, Japan. The deamidating activities on carboxybenzoxy (Cbz)-Gln-Gly and caseins and protease activity were produced synchronously by the isolate. Both deamidating activities were eluted as identical peaks separated from several proteases by phenyl-Sepharose chromatography of the culture supernatant. The enzyme catalyzed the deamidation of native caseins with no protease and transglutaminase activities. Phenotypic characterization and DNA analyses of the isolate were performed to determine its taxonomy. Physiological and biochemical characteristics, 16S rRNA gene sequence analysis, and DNA-DNA relatedness data indicated that the isolate should be placed as a new species belonging to the genus Chryseobacterium. The isolate showed no growth on MacConkey agar and produced acid from sucrose. The levels of DNA-DNA relatedness between the isolate and other related strains were less than 17%. The name Chryseobacterium proteolyticum is proposed for the new species; strain 9670 is the type strain (=FERM P-17664).