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Sample records for achromabacter sp isolated

  1. Mineralization of a Malaysian crude oil by Pseudomonas sp. and Achromabacter sp. isolated from coastal waters

    SciTech Connect

    Ahmad, J.; Ahmad, M.F.

    1995-12-31

    Regarded as being a potentially effective tool to combat oil pollution, bioremediation involves mineralization, i.e., the conversion of complex hydrocarbons into harmless CO{sub 2} and water by action of microorganisms. Therefore, in achieving optimum effectiveness from the application of these products on crude oil in local environments, the capability of the bacteria to mineralize hydrocarbons was evaluated. The microbial laboratory testing of mineralization on local oil degraders involved, first, isolation of bacteria found at a port located on the west coast of Peninsular Malaysia. Subsequently, these bacteria were identified by means of Biomereux`s API 20E and 20 NE systems and later screened by their growth on a Malaysian crude oil. Selected strains of Pseudomonas sp. and Achromabacter sp. were then exposed individually to a similar crude oil in a mineralization unit and monitored for 16 days for release of CO{sub 2}. Pseudomonas paucimobilis was found to produce more CO{sub 2} than Achromobacter sp. When tested under similar conditions, mixed populations of these two taxa produced more CO{sub 2} than that produced by any individual strain. Effective bioremediation of local crude in Malaysian waters can therefore be achieved from biochemically developed Pseudomonas sp. strains.

  2. Janibacter alkaliphilus sp. nov., isolated from coral Anthogorgia sp.

    PubMed

    Li, Jie; Long, Li-Juan; Yang, Ling-Ling; Xu, Ying; Wang, Fa-Zuo; Li, Qing-Xin; Zhang, Si; Li, Wen-Jun

    2012-06-01

    A novel actinobacterium, designated strain SCSIO 10480(T), was isolated from a gorgonian coral sample of Anthogorgia sp. Phylogenetic and phenotypic properties of the organism supported that it belonged to the genus Janibacter. Phylogenetic analysis indicated that the levels of 16S rRNA gene sequence similarity between strain SCSIO 10480(T) and other type strains of recognized members of the genus Janibacter were 96.0-97.8 %. Growth in the presence of up to 17 % (w/v) NaCl and optimally at pH 9.0-10.0 was a distinctive characteristic of strain SCSIO 10480(T). Other biochemical and physiological properties and the fatty acid profile also differentiated the isolate from other members of Janibacter species. Based on the results obtained in this study, we propose that strain SCSIO 10480(T) should be classified within a novel species of the genus Janibacter, for which the name Janibacter alkaliphilus sp. nov. is proposed, with SCSIO 10480(T) (=CCTCC AB 2011027(T) = DSM 24723(T)) as the type strain.

  3. Listeria fleischmannii sp. nov., isolated from cheese.

    PubMed

    Bertsch, David; Rau, Jörg; Eugster, Marcel R; Haug, Martina C; Lawson, Paul A; Lacroix, Christophe; Meile, Leo

    2013-02-01

    A study was performed on three isolates (LU2006-1(T), LU2006-2 and LU2006-3), which were sampled independently from cheese in western Switzerland in 2006, as well as a fourth isolate (A11-3426), which was detected in 2011, using a polyphasic approach. The isolates could all be assigned to the genus Listeria but not to any known species. Phenotypic and chemotaxonomic data were compatible with the genus Listeria and phylogenetic analysis based on 16S rRNA gene sequences confirmed that the closest relationships were with members of this genus. However, DNA-DNA hybridization demonstrated that the isolates did not belong to any currently described species. Cell-wall-binding domains of Listeria monocytogenes bacteriophage endolysins were able to attach to the isolates, confirming their tight relatedness to the genus Listeria. Although PCR targeting the central portion of the flagellin gene flaA was positive, motility was not observed. The four isolates could not be discriminated by Fourier transform infrared spectroscopy or pulsed-field gel electrophoresis. This suggests that they represent a single species, which seems to be adapted to the environment in a cheese-ripening cellar as it was re-isolated from the same type of Swiss cheese after more than 5 years. Conjugation experiments demonstrated that the isolates harbour a transferable resistance to clindamycin. The isolates did not exhibit haemolysis or show any indication of human pathogenicity or virulence. The four isolates are affiliated with the genus Listeria but can be differentiated from all described members of the genus Listeria and therefore they merit being classified as representatives of a novel species, for which we propose the name Listeria fleischmannii sp. nov.; the type strain is LU2006-1(T) ( = DSM 24998(T)  = LMG 26584(T)).

  4. Clostridium jejuense sp. nov., isolated from soil.

    PubMed

    Jeong, Hyunyoung; Yi, Hana; Sekiguchi, Yuji; Muramatsu, Mizuho; Kamagata, Yoichi; Chun, Jongsik

    2004-09-01

    A strictly anaerobic, mesophilic, endospore-forming bacterium, designated strain HY-35-12T, was isolated from a soil sample in Jeju, Korea. Cells of this isolate were Gram-positive, motile rods that formed oval to spherical terminal spores. Strain HY-35-12T grew optimally at 30 degrees C, pH 7.0 and 0-0.5 % (w/v) NaCl. The isolate produced pyruvate, lactate, acetate, formate and hydrogen as fermentation end products from glucose. The G + C content of DNA of the isolate was 41 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism formed a monophyletic clade with Clostridium xylanovorans and Clostridium aminovalericum in cluster XIVa of the genus Clostridium. The closest phylogenetic neighbour was C. xylanovorans, with 96.65 % 16S rRNA gene sequence similarity. Several physiological and chemotaxonomic properties were identified that enable strain HY-35-12T to be distinguished from phylogenetically related clostridia. On the basis of polyphasic characteristics, it is proposed that strain HY-35-12T (= IMSNU 40003T = KCTC 5026T = DSM 15929T) represents a novel species, Clostridium jejuense sp. nov.

  5. Paenibacillus tianmuensis sp. nov., isolated from soil.

    PubMed

    Wu, Xuechang; Fang, Haihuan; Qian, Chaodong; Wen, Yanping; Shen, Xiaobo; Li, Ou; Gao, Haichun

    2011-05-01

    Two closely related, Gram-stain-negative, rod-shaped, spore-forming strains, B27(T) and F6-B70, were isolated from soil samples of Tianmu Mountain National Natural Reserve in Zhejiang, China. Phylogenetic analysis based on 16S rRNA gene and rpoB sequences indicated that the isolates were members of the genus Paenibacillus. Both isolates were closely related to Paenibacillus ehimensis IFO 15659(T), Paenibacillus elgii SD17(T) and Paenibacillus koreensis YC300(T) (≥ 95.2 % 16S rRNA gene sequence similarity). DNA-DNA relatedness between strain B27(T) and P. ehimensis DSM 11029(T), P. elgii NBRC 100335(T) and P. koreensis KCTC 2393(T) was 21.2, 28.6 and 16.8 %, respectively. The major cellular fatty acids of strains B27(T) and F6-B70 were anteiso-C(15 : 0) and iso-C(15 : 0). The cell wall contained meso-diaminopimelic acid. The two isolates differed from their closest neighbours in terms of phenotypic characteristics and cellular fatty acid profiles (such as variable for oxidase, negative for methyl red test, unable to produce acid from d-fructose and glycogen and relatively higher amounts of iso-C(15 : 0) and lower amounts of C(16 : 0) and iso-C(16 : 0)). Strains B27(T) and F6-B70 represent a novel species of the genus Paenibacillus, for which the name Paenibacillus tianmuensis sp. nov. is proposed. The type strain is B27(T) ( = DSM 22342(T)  = CGMCC 1.8946(T)).

  6. Pontibacter yuliensis sp. nov., isolated from soil.

    PubMed

    Cao, Hanjun; Nie, Yao; Zeng, Xian-Chun; Xu, Linghua; He, Zancan; Luo, Xuesong; Wu, Rina

    2014-03-01

    A Gram-staining-negative, rod-shaped and pink bacterium was isolated from the soil of a Populus euphratica forest in the Taklamakan desert, Xinjiang, China. It was designated strain H9X(T). A 16S rRNA gene sequence homology search indicated that the isolate was most closely related to the family Cytophagaceae. The 16S rRNA gene of strain H9X(T) displayed 94.2-96.3 % sequence identities to those of type strains of other species of the genus Pontibacter. It only possessed menaquinone-7. The major cellular fatty acids of the novel isolate were iso-C15 : 0, C16 : 1ω5c summed feature 3 (containing C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 4 (comprising anteiso-C17 : 1 B and/or iso-C17 : 1 I). The major polar lipids were phosphatidylethanolamine, one unknown aminophospholipid, one unknown glycophospholipid and several unknown phospholipids. The DNA G+C content of this bacterium was 55.2 mol%. Based on the phenotypic and genotypic data presented, it can be concluded that this isolate represents a novel species of the genus Pontibacter, for which the name Pontibacter yuliensis sp. nov. is proposed. The type strain is H9X(T) ( = CCTCC AB 2013047(T) = KCTC 32396(T)).

  7. Sphingobium vermicomposti sp. nov., isolated from vermicompost.

    PubMed

    Vaz-Moreira, Ivone; Faria, Cátia; Lopes, Ana R; Svensson, Liselott; Falsen, Enevold; Moore, Edward R B; Ferreira, António C Silva; Nunes, Olga C; Manaia, Célia M

    2009-12-01

    Strain VC-230(T) was isolated from homemade vermicompost produced from kitchen waste. The isolate was a Gram-negative-staining, catalase- and oxidase-positive, motile rod-shaped bacterium able to grow at 15-37 degrees C and pH 6-8. On the basis of 16S rRNA gene sequence analysis, strain VC-230(T) was determined to belong to the family Sphingomonadaceae by its clustering with type strains of the genus Sphingobium, with Sphingobium chlorophenolicum ATCC 33790(T) (97.7 %) and Sphingobium herbicidovorans DSM 11019(T) (97.4 %) as its closest neighbours. The polar lipid pattern, the presence of spermidine and ubiquinone 10, the predominance of the cellular fatty acids C(18 : 1)omega7c/9t/12t, C(16 : 1)omega7c and C(16 : 0) and the G+C content of the genomic DNA supported the affiliation of this organism to the genus Sphingobium. The phylogenetic, chemotaxonomic, phenotypic and DNA-DNA hybridization analyses verify that strain VC-230(T) represents a novel species, for which the name Sphingobium vermicomposti sp. nov. is proposed. The type strain is VC-230(T) (=CCUG 55809(T) =DSM 21299(T)).

  8. Campylobacter iguaniorum sp. nov., isolated from reptiles.

    PubMed

    Gilbert, Maarten J; Kik, Marja; Miller, William G; Duim, Birgitta; Wagenaar, Jaap A

    2015-03-01

    During sampling of reptiles for members of the class Epsilonproteobacteria, strains representing a member of the genus Campylobacter not belonging to any of the established taxa were isolated from lizards and chelonians. Initial amplified fragment length polymorphism, PCR and 16S rRNA sequence analysis showed that these strains were most closely related to Campylobacter fetus and Campylobacter hyointestinalis. A polyphasic study was undertaken to determine the taxonomic position of five strains. The strains were characterized by 16S rRNA and atpA sequence analysis, matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry and conventional phenotypic testing. Whole-genome sequences were determined for strains 1485E(T) and 2463D, and the average nucleotide and amino acid identities were determined for these strains. The strains formed a robust phylogenetic clade, divergent from all other species of the genus Campylobacter. In contrast to most currently known members of the genus Campylobacter, the strains showed growth at ambient temperatures, which might be an adaptation to their reptilian hosts. The results of this study clearly show that these strains isolated from reptiles represent a novel species within the genus Campylobacter, for which the name Campylobacter iguaniorum sp. nov. is proposed. The type strain is 1485E(T) ( = LMG 28143(T) = CCUG 66346(T)).

  9. Actinomyces weissii sp. nov., isolated from dogs.

    PubMed

    Hijazin, Muaz; Alber, Jörg; Lämmler, Christoph; Kämpfer, Peter; Glaeser, Stefanie P; Busse, Hans-Jürgen; Kassmannhuber, Johannes; Prenger-Berninghoff, Ellen; Förnges, Thorsten; Hassan, Abdulwahed Ahmed; Abdulmawjood, Amir; Zschöck, Michael

    2012-08-01

    Two Gram-positive, rod-shaped, non-spore-forming bacteria were isolated from the oral cavities of two dogs. On the basis of 16S rRNA gene sequence similarities both strains were shown to belong to the genus Actinomyces and were most closely related to Actinomyces bovis (97.3% and 97.5%, respectively). The polyamine profile of the two isolates and Actinomyces bovis DSM 43014(T) was composed of spermidine and spermine as the major components. Menaquinone MK-9 was the major compound in the quinone system of the two strains and Actinomyces bovis. The polar lipid profiles of strains 2298(T) and 4321 were almost identical, containing diphosphatidylglycerol as the major compound, and moderate to trace amounts of phosphatidylcholine, phosphatidylinositol, phosphatidylinositol-mannoside, phosphatidylglycerol and several unidentified lipids. A highly similar polar lipid profile was detected in Actinomyces bovis DSM 43014(T) supporting the affiliation of strains 2298(T) and 4321 to the genus Actinomyces. The typical major fatty acids were C(16:0), C(18:0) and C(18:1)ω9c. Fatty acids C(14:0) and C(18:2)ω6,9c were found in minor amounts. The results of physiological and biochemical analyses revealed clear differences between both strains and the most closely related species of the genus Actinomyces. Thus, strains 2298(T) and 4321 represent a novel species, for which the name Actinomyces weissii sp. nov., is proposed, with strain 2298(T) ( = CIP 110333(T) = LMG 26472(T) = CCM 7951(T) = CCUG 61299(T)) as the type strain.

  10. Noviherbaspirillum humi sp. nov., isolated from soil.

    PubMed

    Sundararaman, Aravind; Srinivasan, Sathiyaraj; Lee, Sang-Seob

    2016-05-01

    Two novel Gram-stain negative, motile, non-spore forming, facultative aerobic and short rod shaped bacterial strains, designated U15(T) and U32, were isolated from soil obtained from Ukraine. The sequence similarity of the 16S rRNA gene between strains U15(T) and U32 was found to be 99.5 %. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that new bacteria belong to the genus Noviherbaspirillum. The closest member of the genus was found to be Noviherbaspirillum malthae (97.0 %) followed by Noviherbaspirillum suwonensis (96.3 %). The novel isolates was observed to grow optimally at 30 °C and pH 7.0. The major fatty acids present in the two strains were identified as summed feature 3 (C16:1 ω7c/C16:1 ω6c), C16:0, and summed feature 8 (C18:1 ω7c/C18:1 ω6c). Ubiquinone 8 was identified as the respiratory quinone component for both the strains. The polar lipid (L) profile contained phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, aminophospholipid, unidentified aminolipid and unidentified Ls, and putrescine and 2-hydroxyputrescine as major polyamines. The G+C content of the DNA for the strain U15(T) was found to be 61.2 mol%. The DNA-DNA relatedness between U15(T) and U32 and closely related species was less than 40 %. Based on the polyphasic taxonomic analysis, a new species, Noviherbaspirillum humi sp. nov., is proposed. The type strain is strain U15(T) = JCM 19873(T) = KEMB 7305-102(T). PMID:26940744

  11. Friedmanniella aerolata sp. nov., isolated from air.

    PubMed

    Kim, Soo-Jin; Hamada, Moriyuki; Ahn, Jae-Hyung; Weon, Hang-Yeon; Suzuki, Ken-Ichiro; Kwon, Soon-Wo

    2016-05-01

    A novel bacterium, strain 7515T-26T, was isolated from an air sample collected in Taean region, Republic of Korea. Cells were aerobic, Gram-stain-positive, non-flagellated cocci, growing in the temperature, pH and NaCl ranges of 10-33 °C, pH 5.0-9.0 and 0-2 % (w/v). It shared high 16S rRNA gene sequence similarity with Friedmanniella lacustris EL-17AT (97.6 %), Friedmanniella lucida FA2T (96.9 %) and Friedmanniella luteola FA1T (96.9 %), showing high sequence similarities of 96.5-97.6 % with members of the genus Friedmanniella. Phylogenetic trees based on 16S rRNA gene sequences showed that strain 7515T-26T and members of the genus Friedmanniella formed a compact cluster separable from other genera. The isolate contained anteiso-C15 : 0, iso-C14 : 0 3-OH and iso-C15 : 0 as the major cellular fatty acids, and MK-9(H4) as the predominant isoprenoid quinone. Polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unknown phospholipids and one unknown lipid, and the DNA G+C content was 73.1 mol%. The peptidoglycan type was A3γ. It showed DNA-DNA hybridization values of less than 70 % with F. lacustris EL-17AT. On the basis of the evidence from this polyphasic study, a novel species, Friedmanniella aerolata sp. nov., is proposed. The type strain is 7515T-26T ( = KACC 17306T = DSM 27139T). PMID:26873462

  12. Sinosporangium fuscum sp. nov., isolated from soil.

    PubMed

    Suriyachadkun, Chanwit; Ngaemthao, Wipaporn; Chunhametha, Suwanee; Thawai, Chitti; Sanglier, Jean-Jacques

    2015-06-01

    A novel actinomycete, A-T 8343T was isolated from a moist evergreen forest soil sample collected in the Trat Province, Thailand. Based on 16S rRNA gene sequence analysis, strain A-T 8343T belonged to the genus Sinosporangium and was closely related to Sinosporangium siamense A-T 1946T (98.81 %) and Sinosporangium album 6014T (98.54 %). The DNA-DNA relatedness values were 21.8-27 % with S. siamense A-T 1946T and 31.1-31.9 % with S. album 6014T, which were significantly below 70 %. The result differentiated A-T 8343T from the closest species. The organism developed spherical sporangia containing non-motile spores on aerial mycelia. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars contained rhamnose, ribose, madurose and glucose. The predominant menaquinones were MK-9(H2) and MK-9(H4). The diagnostic phospholipids were phosphatidylmethylethanolamine, phosphatidylethanolamine, hydroxyl-phosphatidylethanolamine, diphosphatidylglycerol, lyso-phosphatidylethanolamine, N-acetylglucosamine-containing phospholipids, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol-mannosides, aminophosphoglycolipid and one unknown phospholipid. The major cellular fatty acids were saturated C16 : 0, iso C16 : 0, unsaturated C16 : 1 and C18 : 1. Following an evaluation of phenotypic, chemotaxonomic and genotypic characteristics, the new isolate is proposed as a representative novel species of the genus Sinosporangium to be named Sinosporangiumfuscum sp. nov. The type strain is A-T 8343T ( = BCC 52770T = NBRC 109516T). PMID:25744582

  13. Pseudogulbenkiania gefcensis sp. nov., isolated from soil.

    PubMed

    Lee, Dong-Geol; Im, Dong-Moon; Kang, HeeCheol; Yun, Pyeong; Park, Sun-Ki; Hyun, Seung-Su; Hwang, Dong-Youn

    2013-01-01

    A novel strain, yH16, was isolated on nutrient agar from soil samples collected at KyungHee University, Suwon City, Republic of Korea. Cells of strain yH16(T) were short rods, Gram-negative-staining, motile and non-spore-forming, with a polar flagellum. Biochemical and molecular characterization revealed that this strain was most similar to Pseudogulbenkiania subflava BP-5(T). Further 16S rRNA gene sequencing studies revealed that the new strain clustered with Pseudogulbenkiania subflava BP-5(T) (95.9 % similarity), Paludibacterium yongneupense 5YN8-15(T) (95.2 % similarity), Gulbenkiania mobilis E4FC31-5(T) (94.6 % similarity) and Chromobacterium aquaticum CC-SE-YA-1(T) (93.9 % similarity). The isolate was able to grow at 25-40 °C, 0.3-2 % NaCl and pH 5.5-7. The DNA G+C content was 65.9 ± 1.0 mol%. The predominant fatty acids were summed feature 3 (C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH) and C(16:0). Ubiquinone 8 was the major respiratory quinone. It was evident from the data obtained that the strain should be classified as a novel species of the genus Pseudogulbenkiania. The name proposed for this taxon is Pseudogulbenkiania gefcensis sp. nov., and the type strain is yH16(T) (=KCCM 90100(T) = JCM 17850(T)). PMID:22389280

  14. Deinococcus antarcticus sp. nov., isolated from soil.

    PubMed

    Dong, Ning; Li, Hui-Rong; Yuan, Meng; Zhang, Xiao-Hua; Yu, Yong

    2015-02-01

    A pink-pigmented, non-motile, coccoid bacterial strain, designated G3-6-20(T), was isolated from a soil sample collected in the Grove Mountains, East Antarctica. This strain was resistant to UV irradiation (810 J m(-2)) and slightly more sensitive to desiccation as compared with Deinococcus radiodurans. Phylogenetic analyses based on the 16S rRNA gene sequence of the isolate indicated that the organism belongs to the genus Deinococcus. Highest sequence similarities were with Deinococcus ficus CC-FR2-10(T) (93.5 %), Deinococcus xinjiangensis X-82(T) (92.8 %), Deinococcus indicus Wt/1a(T) (92.5 %), Deinococcus daejeonensis MJ27(T) (92.3 %), Deinococcus wulumuqiensis R-12(T) (92.3 %), Deinococcus aquaticus PB314(T) (92.2 %) and Deinococcus radiodurans DSM 20539(T) (92.2 %). Major fatty acids were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), anteiso-C15 : 0 and C16 : 0. The G+C content of the genomic DNA of strain G3-6-20(T) was 63.1 mol%. Menaquinone 8 (MK-8) was the predominant respiratory quinone. Based on its phylogenetic position, and chemotaxonomic and phenotypic characteristics, strain G3-6-20(T) represents a novel species of the genus Deinococcus, for which the name Deinococcus antarcticus sp. nov. is proposed. The type strain is G3-6-20(T) ( = DSM 27864(T) = CCTCC AB 2013263(T)).

  15. Loktanella aquimaris sp. nov., Isolated from Seawater.

    PubMed

    Kim, Kunho; Srinivasan, Sathiyaraj; Lee, Sang-Seob

    2016-02-01

    Two novel bacterial strains, designated C5(T) and C9 were isolated from a fish cage at Tongyeong, South Korea and were characterized to determine their taxonomic position. The strains were Gram-negative, non-motile, strictly aerobic and short rod shaped. Growth occurred between 20 and 32 °C (optimum 30 °C) and at pH 6.0-9.0 (optimum pH 8.0) and at 0-10 % NaCl (optimum at 2 % NaCl). Based on the 16S rRNA gene sequence analysis, they were identified as a member of the genus Loktanella that belongs to the phylum Proteobacteria. Strains C5(T) and C9 were analyzed by a polyphasic approach, revealing variations in their phenotypic characters but reciprocal DNA-DNA hybridization values confirmed that they belong to the same species. Phylogenetic analysis of the 16S rRNA gene sequences of closely related species indicated their similarities were below 97 %. The predominant isoprenoid quinone is ubiquinone-10 (Q-10). The major cellular fatty acids were C16:0, and C18:1 ω7c. Major polar lipid contained phosphatidylglycerol (PG), phosphatidycholine (PC), diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), unidentified amino lipid (AL) and unidentified lipids (L1-3). Based on phylogenetic and phenotypic data, the isolated strains represent a novel species of the genus Loktanella, for which the name Loktanella aquimaris sp. nov. is proposed. The type strains were C5(T) (=KEMB 3-892(T) = JCM 30382(T)), and a second strain is C9 (=KEMB 3-893 = JCM 30383). PMID:26607359

  16. Sphingomonas sanxanigenens sp. nov., isolated from soil.

    PubMed

    Huang, Hai-Dong; Wang, Wei; Ma, Ting; Li, Guo-Qiang; Liang, Feng-Lai; Liu, Ru-Lin

    2009-04-01

    Strain NX02(T), a Gram-negative, non-spore-forming, rod-shaped bacterium, was isolated from soil, and its taxonomic position was investigated using a polyphasic approach. Chemotaxonomic analysis revealed that strain NX02(T) possessed Q-10 as the predominant ubiquinone, sym-homospermidine as the major polyamine and C(18 : 1)omega7c, C(16 : 0) and C(14 : 0) 2-OH as the major fatty acids. The main polar lipids were sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine and an unidentified glycolipid. The DNA G+C content was 66.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NX02(T) belongs to the alpha-4 subgroup of the Proteobacteria, exhibiting the highest sequence similarity with respect to Sphingomonas azotifigens NBRC 15497(T) (95.9 %), Sphingomonas pituitosa DSM 13101(T) (95.8 %) and Sphingomonas dokdonensis KCTC 12541(T) (95.8 %). On the basis of these results, strain NX02(T) represents a novel species of the genus Sphingomonas sensu stricto, for which the name Sphingomonas sanxanigenens sp. nov. is proposed. The type strain is NX02(T) (=DSM 19645(T) =CGMCC 1.6417(T)).

  17. Sphingomonas dokdonensis sp. nov., isolated from soil.

    PubMed

    Yoon, Jung-Hoon; Lee, Mi-Hwa; Kang, So-Jung; Lee, Soo-Young; Oh, Tae-Kwang

    2006-09-01

    A Gram-negative, rod-shaped, Sphingomonas-like bacterial strain, DS-4(T), was isolated from soil of Dokdo, Korea, and its taxonomic position was investigated using a polyphasic approach. Strain DS-4(T) grew optimally on trypticase soy agar medium without NaCl at pH 6.0-6.5 and 25 degrees C. It contained Q-10 as the predominant ubiquinone and C(18 : 1)omega7c, C(16 : 0), C(14 : 0) 2-OH and C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH as the major fatty acids. Sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and unidentified phospholipid were the major polar lipids. The DNA G+C content was 66.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-4(T) fell within the evolutionary radiation comprising Sphingomonas species. Levels of 16S rRNA gene sequence similarity between strain DS-4(T) and the type strains of Sphingomonas species ranged from 93.0 to 97.6 %. DNA-DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain DS-4(T) differs from the recognized Sphingomonas species. On the basis of phenotypic, phylogenetic and genetic data, this strain represents a novel species of the genus Sphingomonas, for which the name Sphingomonas dokdonensis sp. nov. is proposed, with DS-4(T) (=KCTC 12541(T)=CIP 108841(T)) as the type strain.

  18. Dokdonia pacifica sp. nov., isolated from seawater.

    PubMed

    Zhang, Zenghu; Gao, Xin; Wang, Long; Zhang, Xiao-Hua

    2015-07-01

    A Gram-stain-negative, aerobic, non-flagellated, non-gliding, oxidase- and catalase-positive, rod-shaped, yellow-pigmented bacterium, designated strain SW230(T), was isolated from a surface seawater sample collected from the South Pacific Gyre. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SW230(T) shared highest similarity with members of the genus Dokdonia (95.0-94.5%), exhibiting 95.0% sequence similarity to Dokdonia genika NBRC 100811(T). Optimal growth occurred in the presence of 2-3% (w/v) NaCl, at pH 8.0 and at 28 °C. The DNA G+C content of strain SW230(T) was 36 mol%. The major fatty acids (>10% of the total) were iso-C15:1 G, iso-C15:0, iso-C17:0 3-OH, and C16:1 ω7c and/or C16:1ω6c. The major respiratory quinone was menaquinone-6. The major polar lipids were phosphatidylethanolamine, two unidentified aminolipids and two unidentified lipids. On the basis of data from the present polyphasic study, strain SW230(T) is considered to represent a novel species of the genus Dokdonia, for which the name Dokdonia pacifica sp. nov. is proposed. The type strain is SW230(T) ( = CGMCC 1.12184(T) = JCM 18216(T)). PMID:25862384

  19. Citrobacter bitternis sp. nov. isolated from bitterns.

    PubMed

    Ko, Kwan Soo; Choi, Ji-Young; Kim, Joo; Park, Myoung Kyu

    2015-06-01

    In this study, we reported two gram-negative bacteria that were isolated from bitterns, designated as SKKU-TP7(T) and SKKU-TP20, representing a novel species of Citrobacter. Based on the 16S rRNA gene sequences, the two strains were found to be closely related and showed the highest pairwise similarity with Citrobacter farmeri CDC 2992-81(T) (97.1-97.3 %) and other Citrobacter species. Cellular fatty acid analysis revealed that the profiles of strains SKKU-TP7(T) and SKKU-TP20 were similar to those of related species of Citrobacter. The major cellular fatty acids were C16:0 (31.5 %), summed feature 3 (C16:1 ω7c, C16:1 ω6c, 19.7 %), summed feature 8 (C18:1 ω7c, C18:1 ω6c, 11.9 %), C17:0 cyclo (10.7 %), and summed feature 2 (C12:0 aldehyde/unknown 10928, 9.5 %). Although the strains could utilize sucrose and raffinose as a carbon source, they did not produce ornithine decarboxylase and urease. The biochemical and genotypic characteristics indicate that strains SKKU-TP7(T) and SKKU-TP20 represent a novel species of Citrobacter, for which the name Citrobacter bitterns sp. nov. is proposed. The type strain is SKKU-TP7(T) (=KCTC 42139(T) = JCM 30009(T)).

  20. Loktanella tamlensis sp. nov., isolated from seawater.

    PubMed

    Lee, Soon Dong

    2012-03-01

    An aerobic, Gram-reaction-negative, chemo-organotrophic bacterium, designated strain SSW-35(T), was isolated from seawater in Jeju, Republic of Korea. Cells were motile, short rods; colonies were circular, smooth, convex, translucent and beige in colour. No diffusible pigment formed on any of the media tested. The bacterium grew at 4-30 °C and pH 7.1-10.1. Phylogenetic analysis based on 16S rRNA gene sequences showed that the organism was related to members of the genus Loktanella, its closest recognized relatives being Loktanella rosea Fg36(T) (98.1% sequence similarity) and Loktanella maricola DSW-18(T) (97.8%). Levels of 16S rRNA gene similarity between strain SSW-35(T) and other recognized species of the genus Loktanella were all <97%. Polar lipid analysis revealed the presence of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unknown lipid as major components, as well as small amounts of two unknown phospholipids. The predominant ubiquinone was Q-10. The major cellular fatty acid was C(18:1) (summed feature 7), and the 3-hydroxy fatty acids detected were C(12:1) 3-OH and C(10:0) 3-OH. The genomic DNA G+C content was 55.0 mol%. In DNA-DNA hybridization experiments, the relatedness values between strain SSW-35(T) and the type strains of the phylogenetically closest recognized species were all <11%. On the basis of the phenotypic and genotypic characteristics, phylogenetic analysis and DNA-DNA relatedness, a novel species, Loktanella tamlensis sp. nov., is proposed. The type strain is SSW-35(T) (=KCTC 12722(T)=JCM 14020(T)).

  1. Actibacterium ureilyticum sp. nov., isolated from seawater.

    PubMed

    Lin, Shih-Yao; Young, Chiu-Chung; Hameed, Asif; Liu, You-Cheng; Hsu, Yi-Han; Chung, Wei-Ching; Young, Li-Sen

    2016-08-01

    A polyphasic approach was used to characterize a novel marine bacterial strain, designated LS-811T, isolated from seawater of the South China Sea (Taiwan). Cells of strain LS-811Twere Gram-staining negative, aerobic and rod-shaped with polar flagella. The 16S rRNA gene sequence analysis of strain LS-811T showed highest sequence similarity to Actibacterium mucosum (96.5 %) and Actibacterium atlanticum (95.6 %), and lower sequence similarity (<96.0 %) to members of all other related genera. Strain LS-811Twas able to grow at 15-40 °C and pH 5.0-9.0. The quinone system was ubiquinone (Q-10), and the DNA G+C content was 60.1 mol%. The major fatty acids (>5 %) found in strain LS-811T were C18 : 0, C10 : 0 3-OH, C19 : 0 cyclo ω8c and C18 : 1ω7c/C18 : 1ω6c. The major polar lipid profile consisted of glycolipids, phosphatidylglycerol and one unidentified aminolipid. Based on the distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence analysis, strain LS-811T is considered to represent a novel species in the genus Actibacterium, for which the name Actibacterium ureilyticum sp. nov. is proposed. The type strain is LS-811T (=BCRC 80823T=JCM 30681T). PMID:27031530

  2. Xenophilus aerolatus sp. nov., isolated from air.

    PubMed

    Kim, Soo-Jin; Kim, Yi-Seul; Weon, Hang-Yeon; Anandham, Rangasamy; Noh, Hyung-Jun; Kwon, Soon-Wo

    2010-02-01

    A novel aerobic, Gram-negative, motile, rod-shaped bacterial strain designated 5516S-2(T) was isolated from an air sample taken in Suwon, Republic of Korea. Colonies were yellow-pigmented and circular with entire margins. 16S rRNA gene sequence analysis showed that strain 5516S-2(T) was closely related to Xylophilus ampelinus DSM 7250(T) (97.6 % sequence similarity), Variovorax soli KACC 11579(T) (97.5 %) and Xenophilus azovorans DSM 13620(T) (97.1 %). However, the phylogenetic tree indicated that strain 5516S-2(T) formed a separate clade from Xenophilus azovorans. Strain 5516S-2(T) displayed 42, 31 and 30 % DNA-DNA relatedness to the type strains of Xenophilus azovorans, Xylophilus ampelinus and V. soli, respectively. The major fatty acids (>10 % of total fatty acids) were C(16 : 0) (33.3 %), C(17 : 0) cyclo (18.8 %), C(18 : 1)omega7c (17.5 %) and summed feature 3 (comprising C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH; 13.0 %). The DNA G+C content was 69 mol%. The major quinone was ubiquinone Q-8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two unknown aminophospholipids. Genotypic and phenotypic characteristics clearly distinguished strain 5516S-2(T) from closely related species and indicated that it represents a novel species within the genus Xenophilus, for which the name Xenophilus aerolatus sp. nov. is proposed. The type strain is 5516S-2(T) (=KACC 12602(T)=DSM 19424(T)).

  3. Tsukamurella soli sp. nov., isolated from soil.

    PubMed

    Weon, Hang-Yeon; Yoo, Seung-Hee; Anandham, Rangasamy; Schumann, Peter; Kroppenstedt, Reiner M; Kwon, Soon-Wo; Stackebrandt, Erko

    2010-07-01

    A Gram-positive, rod-shaped, catalase-positive, oxidase-negative, white-coloured bacterium, designated strain JS18-1(T), was isolated from a soil sample collected from Halla mountain, Jeju island, Korea. 16S rRNA gene sequence analysis revealed that the strain was most closely related to members of the genus Tsukamurella with levels of sequence similarity of 95.4-96.5 %. Strain JS18-1(T) shared highest 16S rRNA gene sequence similarity with Tsukamurella strandjordii DSM 44573(T) (96.5 %), Tsukamurella carboxydivorans Y2(T) (96.4 %) and Tsukamurella tyrosinosolvens DSM 44234(T) (96.4 %). The G+C content of the total DNA of strain JS18-1(T) was 70 mol%. The cell-wall peptidoglycan type was A1gamma and mycolic acids were also detected. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The major quinone was menaquinone-9 (MK-9) and major cell-wall sugars were arabinose, ribose and glucose. The major fatty acids (>10 % of the total fatty acids) were C(16 : 0), C(18 : 1)omega9c, C(18 : 0) 10-methyl and summed feature 3 (C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH). Phylogenetic analysis based on 16S rRNA gene sequences and chemotaxonomic, biochemical and physiological characteristics indicate that strain JS18-1(T) represents a novel species of the genus Tsukamurella, for which the name Tsukamurella soli sp. nov. is proposed. The type strain is JS18-1(T) (=KACC 20764(T)=DSM 45046(T)).

  4. Shewanella dokdonensis sp. nov., isolated from seawater.

    PubMed

    Sung, Hye-Ri; Yoon, Jung-Hoon; Ghim, Sa-Youl

    2012-07-01

    A novel bacterial strain, designated UDC329(T), was isolated from a sample of seawater collected at Dong-do, on the coast of Dokdo Island, in the East Sea of the Republic of Korea. The Gram-staining-negative, motile, facultatively anaerobic, non-spore-forming rods of the strain developed into dark orange-yellow colonies. The strain grew optimally between 25 and 30 °C, with 1% (w/v) NaCl and at pH 7. It grew in the absence of NaCl, but not with NaCl at >7% (w/v). The predominant menaquinone was MK-7, the predominant ubiquinones were Q-7 and Q-8, and the major fatty acids were iso-C(15:0) (33.52%) and C(17:1)ω8c (11.73%). The genomic DNA G+C content of strain UDC329(T) was 50.2 mol%. In phylogenetic analyses based on 16S rRNA and gyrB gene sequences, strain UDC329(T) was grouped with members of the genus Shewanella and appeared most closely related to Shewanella fodinae JC15(T) (97.9% 16S rRNA gene sequence similarity), Shewanella indica KJW27(T) (95.0%), Shewanella algae ATCC 51192(T) (94.8%), Shewanella haliotis DW01(T) (94.5%) and Shewanella chilikensis JC5(T) (93.9%). The level of DNA-DNA relatedness between strain UDC329(T) and S. fodinae JC15(T) was, however, only 27.4%. On the basis of phenotypic, genotypic and DNA-DNA relatedness data, strain UDC329(T) represents a novel species in the genus Shewanella, for which the name Shewanella dokdonensis sp. nov. is proposed. The type strain is UDC329(T) (=KCTC 22898(T)=DSM 23626(T)).

  5. Marinicella pacifica sp. nov., isolated from seawater.

    PubMed

    Wang, Yanan; Liu, Yan; Zhang, Zenghu; Zheng, Yanfen; Zhang, Xiao-Hua

    2016-06-01

    A Gram-stain-negative, strictly aerobic, non-motile, non-gliding, oxidase-positive, catalase-positive, rod-shaped bacterium, designated strain sw153T, was isolated from surface seawater of the South Pacific Gyre (39° 19' S 139° 48' W) during Integrated Ocean Drilling Program Expedition 329. Growth occurred at 10-42 °C (optimum 28 °C), in the presence of 1-8 % (w/v) NaCl (optimum 2 %) and at pH 6.0-10.0 (optimum pH 7.5-8.5). The major fatty acids (>10 %) were iso-C15:0 and summed feature 3 (C16:1ω6c and/or C16:1ω7c). The major polar lipids comprised phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphatidylglycerol, an unidentified polar lipid and an unidentified phospholipid. The major respiratory quinone was ubiquinone-8 (Q-8). The DNA G+C content of strain sw153T was 44.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed strain sw153T within the genus Marinicella, class Gammaproteobacteria. The most closely related species was Marinicella litoralis KMM 3900T (96.6 % 16S rRNA gene sequence similarity). Based on the polyphasic analyses in this study, strain sw153T is considered to represent a novel species of the genus Marinicella, for which the name Marinicella pacifica sp. nov. is proposed. The type strain is sw153T (=JCM 18208T=CGMCC 1.12181T).

  6. Actinokineospora guangxiensis sp. nov., isolated from soil.

    PubMed

    Wu, Hao; Liu, Bin

    2015-12-01

    A novel actinomycete, designated strain GK-6T, was isolated from a soil sample from Nanning, Guangxi province, PR China. The strain grew at 20-40 °C, pH 6.0-11.0 and with 0-7.0 % NaCl. It formed well-developed aerial and vegetative mycelia. The aerial mycelium was white and the vegetative mycelium was yellow. The long branching aerial mycelia yielded rod-shaped arthrospores, the spores had smooth surfaces and were non-motile. Strain Gk-6T contained meso-diaminopimelic acid as the diagnostic diamino acid, the whole-cell sugars were galactose, glucose and arabinose. Major fatty acids were iso-C16 : 0, iso-C15 : 0 and C17 : 0. MK-9(H4) was the predominant menaquinone. The polar phospholipids were phosphatidylethanolamine, phosphatidylethanolamine-containing hydroxylated fatty acids, diphosphatidylglycerol, ninhydrin-positive glycophospholipid and an unknown phospholipid. The G+C content of the genomic DNA was 73.4 mol%. The 16S rRNA gene sequence analysis indicated that the organism was a member of the genus Actinokineospora and its closest relative among recognized species was Actinokineospora soli JCM 17695T (97.7 % sequence similarity). But the phenotypic characteristics of strain Gk-6T were significantly different from those of A. soli JCM 17695T, and DNA-DNA hybridization showed low relatedness (22.6-28.3 %) between strain Gk-6T and JCM 17695T. On the basis of the phenotypic and phylogenetic data, strain Gk-6T represents a novel species of the genus Actinokineospora, and the name Actinokineospora guangxiensis sp. nov. is proposed. The type strain is Gk-6T ( = DSM 46779 T = CGMCC 4.7154T). PMID:26410559

  7. Planomonospora corallina sp. nov., isolated from soil.

    PubMed

    Suriyachadkun, Chanwit; Ngaemthao, Wipaporn; Chunhametha, Suwanee

    2016-08-01

    A novel actinomycete strain, A-T 11038T, was isolated from bamboo rhizospheric soil collected in Thailand. Based on a polyphasic approach, the novel strain was characterized as a member of the genus Planomonospora, which developed cylindrical to clavate sporangia containing a single motile spore on aerial mycelium. The 16S rRNA gene sequence and phylogenetic analysis indicated that strain A-T 11038T was closely related to Planomonospora sphaerica JCM 9374T (98.82 %), P.lanomonospora parontospora subsp. parontospora NBRC 13880T and P.parontospora subsp. antibiotica JCM 3094T (98.54 %), Planomonospora alba JCM 9373T (98.41 %) and Planomonospora venezuelensis JCM 3167T (97.51 %). The DNA-DNA relatedness values that distinguished strain A-T 11038T from the most closely related species were below 45 %. The novel strain contained meso-diaminopimelic acid in cell-wall hydrolysates, and rhamnose, ribose, madurose and glucose in whole-cell hydrolysates. The predominant menaquinone was MK-9(H2). The diagnostic phospholipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol mannosides, phosphatidylinositol and aminophosphoglycolipids. The predominant cellular fatty acids were unsaturated fatty acids C17 : 1 and C16 : 1 and saturated fatty acid C16 : 0. The G+C content of the genomic DNA was 73.5 mol%. Following the evidence obtained using a polyphasic approach, the novel strain is proposed as a representative of a novel species to be named Planomonospora corallina sp. nov. The type strain is A-T 11038T (=BCC 67829T=TBRC 4489T=NBRC 110609T). PMID:27217033

  8. Marinicella pacifica sp. nov., isolated from seawater.

    PubMed

    Wang, Yanan; Liu, Yan; Zhang, Zenghu; Zheng, Yanfen; Zhang, Xiao-Hua

    2016-06-01

    A Gram-stain-negative, strictly aerobic, non-motile, non-gliding, oxidase-positive, catalase-positive, rod-shaped bacterium, designated strain sw153T, was isolated from surface seawater of the South Pacific Gyre (39° 19' S 139° 48' W) during Integrated Ocean Drilling Program Expedition 329. Growth occurred at 10-42 °C (optimum 28 °C), in the presence of 1-8 % (w/v) NaCl (optimum 2 %) and at pH 6.0-10.0 (optimum pH 7.5-8.5). The major fatty acids (>10 %) were iso-C15:0 and summed feature 3 (C16:1ω6c and/or C16:1ω7c). The major polar lipids comprised phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphatidylglycerol, an unidentified polar lipid and an unidentified phospholipid. The major respiratory quinone was ubiquinone-8 (Q-8). The DNA G+C content of strain sw153T was 44.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed strain sw153T within the genus Marinicella, class Gammaproteobacteria. The most closely related species was Marinicella litoralis KMM 3900T (96.6 % 16S rRNA gene sequence similarity). Based on the polyphasic analyses in this study, strain sw153T is considered to represent a novel species of the genus Marinicella, for which the name Marinicella pacifica sp. nov. is proposed. The type strain is sw153T (=JCM 18208T=CGMCC 1.12181T). PMID:26978647

  9. Aquimarina megaterium sp. nov., isolated from seawater.

    PubMed

    Yu, Tong; Zhang, Zenghu; Fan, Xiaoyang; Shi, Xiaochong; Zhang, Xiao-Hua

    2014-01-01

    A novel Gram-stain-negative, rod-shaped, non-flagellated, strictly aerobic strain with gliding motility, designated XH134(T), was isolated from surface seawater of the South Pacific Gyre (45° 58' S 163° 11' W) during the Integrated Ocean Drilling Program Expedition 329. The major respiratory quinone of strain XH134(T) was MK-6. The dominant fatty acids of strain XH134(T) were iso-C15 : 0, iso-C15 : 1 G, C16 : 1ω6c and/or C16 : 1ω7c, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH and 10-methyl C16 : 0 and/or iso-C17 : 1ω9c. The polar lipids of strain XH134(T) comprised phosphatidylethanolamine, one unknown aminolipid and three unknown polar lipids. The DNA G+C content of strain XH134(T) was 32.4 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that the novel strain was related most closely to Aquimarina macrocephali JAMB N27(T) with 96.9 % sequence similarity. A number of phenotypic characteristics distinguished strain XH134(T) from described members of the genus Aquimarina. On the basis of combined phenotypic and phylogenetic analyses, strain XH134(T) represents a novel species of the genus Aquimarina, for which the name Aquimarina megaterium sp. nov. is proposed. The type strain is XH134(T) ( = CGMCC 1.12186(T) = JCM 18215(T)). PMID:24030690

  10. Belliella marina sp. nov., isolated from seawater.

    PubMed

    Song, Lei; Liu, Hongcan; Wang, Jian; Huang, Ying; Dai, Xin; Han, Xiqiu; Zhou, Yuguang

    2015-12-01

    Gram-stain-negative, rod-shaped bacterium, strain SW112T, was isolated from a seawater sample collected from the Indian Ocean. The strain was strictly aerobic and catalase- and oxidase-positive. Strain SW112T grew at 4-42 °C (optimum 30 °C), at pH 5.5-9.5 (optimum pH 7.5) and in the presence of 0-9.0 % (w/v) NaCl (optimum 2.0-3.0 %). The predominant cellular fatty acids were iso-C15 : 0 (29.7 %), iso-C17 : 03-OH (14.3 %) and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c, 15.1 %). The major menaquinone was menaquinone-7 and the major polar lipid was phosphatidylethanolamine. The genomic DNA G+C content of strain SW112T was 39 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain SW112T was related to members of the genus Belliella, showing the highest similarity with Belliella aquatica TS-T86T and Belliella baltica DSM 15883T (96.5 % and 96.4 %sequence similarity, respectively). On the basis of phylogenetic inference and phenotypic characteristics, it is proposed that strain SW112T represents a novel species of the genus Belliella, for which the name Belliella marina sp. nov. is proposed. The type strain is SW112T(=CGMCC 1.15180T=KCTC 33694T). PMID:26346194

  11. Actibacterium ureilyticum sp. nov., isolated from seawater.

    PubMed

    Lin, Shih-Yao; Young, Chiu-Chung; Hameed, Asif; Liu, You-Cheng; Hsu, Yi-Han; Chung, Wei-Ching; Young, Li-Sen

    2016-08-01

    A polyphasic approach was used to characterize a novel marine bacterial strain, designated LS-811T, isolated from seawater of the South China Sea (Taiwan). Cells of strain LS-811Twere Gram-staining negative, aerobic and rod-shaped with polar flagella. The 16S rRNA gene sequence analysis of strain LS-811T showed highest sequence similarity to Actibacterium mucosum (96.5 %) and Actibacterium atlanticum (95.6 %), and lower sequence similarity (<96.0 %) to members of all other related genera. Strain LS-811Twas able to grow at 15-40 °C and pH 5.0-9.0. The quinone system was ubiquinone (Q-10), and the DNA G+C content was 60.1 mol%. The major fatty acids (>5 %) found in strain LS-811T were C18 : 0, C10 : 0 3-OH, C19 : 0 cyclo ω8c and C18 : 1ω7c/C18 : 1ω6c. The major polar lipid profile consisted of glycolipids, phosphatidylglycerol and one unidentified aminolipid. Based on the distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence analysis, strain LS-811T is considered to represent a novel species in the genus Actibacterium, for which the name Actibacterium ureilyticum sp. nov. is proposed. The type strain is LS-811T (=BCRC 80823T=JCM 30681T).

  12. Aquimarina pacifica sp. nov., isolated from seawater.

    PubMed

    Zhang, Zenghu; Yu, Tong; Xu, Tingting; Zhang, Xiao-Hua

    2014-06-01

    A Gram-stain-negative, rod-shaped, non-flagellated, strictly aerobic bacterium with gliding motility, designated strain SW150(T), was isolated from surface seawater of the South Pacific Gyre (39° 19' S 139° 48' W) during the Integrated Ocean Drilling Program Expedition 329. Optimal growth occurred in the presence of 2-4% (w/v) NaCl, at pH 7-8 and at 28-30 °C. The dominant fatty acids were iso-C(15 : 0), iso-C(17 : 0) 3-OH, iso-C(15 : 1) G, C(16 : 1)ω6c and/or C(16 : 1)ω7c and 10-methyl C(16 : 0) and/or iso-C(17 : 1)ω9c. The polar lipids of strain SW150(T) comprised phosphatidylethanolamine, three unknown polar lipids and one unknown aminolipid. The major respiratory quinone was MK-6. The DNA G+C content of strain SW150(T) was 33.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel strain was related most closely to Aquimarina macrocephali JAMB N27(T) and Aquimarina muelleri KMM 6020(T) with 97.8 and 96.8% sequence similarities, respectively. The estimated DNA-DNA hybridization values were 21.00±2.33% between strain SW150(T) and A. macrocephali JAMB N27(T) and 20.60±2.32% between strain SW150(T) and Aquimarina megaterium XH134(T). On the basis of polyphasic analyses, strain SW150(T) represents a novel species of the genus Aquimarina, for which the name Aquimarina pacifica sp. nov. is proposed. The type strain is SW150(T) ( = JCM 18214(T) = CGMCC 1.12180(T)). PMID:24626966

  13. Bacillus luteus sp. nov., isolated from soil.

    PubMed

    Subhash, Y; Sasikala, Ch; Ramana, Ch V

    2014-05-01

    Two bacterial strains (JC167T and JC168) were isolated from a soil sample collected from Mandpam, Tamilnadu, India. Colonies of both strains were orange and cells Gram-stain-positive. Cells were small rods, and formed terminal endospores of ellipsoidal to oval shape. Both strains were positive for catalase, oxidase and hydrolysis of starch/gelatin, and negative for chitin hydrolysis, H2S production, indole production and nitrate reduction activity. Major fatty acids of both strains (>5%) were anteiso-C15:0, iso-C16:0, iso-C15:0, anteiso-C17:0, iso-C14:0 and C16:0 with minor (<5 but >1%) amounts of iso-C17:0, anteiso-C17:0 B/iso-C17:0 I and C16:1ω11c. Diphosphatydilglycerol, phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids of both strains. Cell wall amino acids were L-alanine, D-alanine, D-glutamic acid and meso-diaminopimelic acid. β-Carotene and five unidentified carotenoids were present in both strains. Mean genomic DNA G+C content was 53.4±1 mol% and the two strains were closely related (mean DNA-DNA hybridization>90%). 16S rRNA gene sequence comparisons of both strains indicated that they represent species of the genus Bacillus within the family Bacillaceae of the phylum Firmicutes. Both strains had a sequence similarity of 97.6% with Bacillus saliphilus 6AGT and <96.8% with other members of the genus Bacillus. Sequence similarity between strain JC167T and 168 was 100%. Strain JC167T showed 25.8±1% reassociation (based on DNA-DNA hybridization) with B. saliphilus DSM 15402T (=6AGT). Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain JC167T as a representative of a novel species of the genus Bacillus, for which the name Bacillus luteus sp. nov. is proposed. The type strain is JC167T (=KCTC 33100T=LMG 27257T). PMID:24478212

  14. Chitinophaga eiseniae sp. nov., isolated from vermicompost.

    PubMed

    Yasir, Muhammad; Chung, Eu Jin; Song, Geun Cheol; Bibi, Fehmida; Jeon, Che Ok; Chung, Young Ryun

    2011-10-01

    A Gram-negative, rod-shaped bacterial strain, YC6729(T), was isolated from vermicompost collected at Masan, Korea, and its taxonomic position was investigated by a polyphasic taxonomic approach. Strain YC6729(T) grew optimally at 30 °C and at pH 6.5-8.5. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YC6729(T) belongs to the genus Chitinophaga in the family Chitinophagaceae. It was related most closely to Chitinophaga terrae KP01(T) (96.4 % 16S rRNA gene sequence similarity), Chitinophaga ginsengisegetis Gsoil 040(T) (96.1 %), Chitinophaga arvensicola IAM 12650(T) (96.1 %) and Chitinophaga pinensis DSM 2588(T) (93.3 %). Strain YC6729(T) contained MK-7 as the major menaquinone and homospermidine as the major polyamine. The fatty acids of strain YC6729(T) were iso-C(15 : 0), C(16 : 1)ω5c, iso-C(17 : 0) 3-OH, C(16 : 0), anteiso-C(18 : 0) and/or C(18 : 2)ω6,9c, iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c, C(14 : 0), iso-C(15 : 0) 3-OH, iso-C(15 : 1) G, C(18 : 1)ω5c, iso-C(15 : 1) I and/or C(13 : 0) 3-OH, C(13 : 0) 2-OH, C(16 : 0) 3-OH and unknown fatty acid ECL 13.565. The polar lipid profile contained phosphatidylethanolamine, unknown aminolipids and unknown lipids. The total DNA G+C content of strain YC6729(T) was 48.9 mol%. The phenotypic, chemotaxonomic and phylogenetic data showed that strain YC6729(T) represents a novel species of the genus Chitinophaga, for which the name Chitinophaga eiseniae sp. nov. is proposed. The type strain is YC6729(T) ( = KACC 13774(T)  = DSM 22224(T)).

  15. Direct transesterification of Oedogonium sp. oil be using immobilized isolated novel Bacillus sp. lipase.

    PubMed

    Sivaramakrishnan, Ramachandran; Muthukumar, Karuppan

    2014-01-01

    This work emphasizes the potential of the isolated Bacillus sp. lipase for the production of fatty acid methyl ester by the direct transesterification of Oedogonium sp. of macroalgae. Dimethyl carbonate was used as the extraction solvent and also as the reactant. The effect of solvent/algae ratio, water addition, catalyst, temperature, stirring and time on the direct transesterification was studied. The highest fatty acid methyl ester yield obtained under optimum conditions (5 g Oedogonium sp. powder, 7.5 ml of solvent (dimethyl carbonate)/g of algae, 8% catalyst (%wt/wt of oil), distilled water 1% (wt/wt of algae), 36 h, 55°C and 180 rpm) was 82%. Final product was subjected to thermogravimetric analysis and (1)H NMR analysis. The results showed that the isolated enzyme has good potential in catalyzing the direct transesterification of algae, and the dimethyl carbonate did not affect the activity of the isolated lipase. PMID:23890544

  16. Direct transesterification of Oedogonium sp. oil be using immobilized isolated novel Bacillus sp. lipase.

    PubMed

    Sivaramakrishnan, Ramachandran; Muthukumar, Karuppan

    2014-01-01

    This work emphasizes the potential of the isolated Bacillus sp. lipase for the production of fatty acid methyl ester by the direct transesterification of Oedogonium sp. of macroalgae. Dimethyl carbonate was used as the extraction solvent and also as the reactant. The effect of solvent/algae ratio, water addition, catalyst, temperature, stirring and time on the direct transesterification was studied. The highest fatty acid methyl ester yield obtained under optimum conditions (5 g Oedogonium sp. powder, 7.5 ml of solvent (dimethyl carbonate)/g of algae, 8% catalyst (%wt/wt of oil), distilled water 1% (wt/wt of algae), 36 h, 55°C and 180 rpm) was 82%. Final product was subjected to thermogravimetric analysis and (1)H NMR analysis. The results showed that the isolated enzyme has good potential in catalyzing the direct transesterification of algae, and the dimethyl carbonate did not affect the activity of the isolated lipase.

  17. Diversity of culturable actinobacteria isolated from marine sponge Haliclona sp.

    PubMed

    Jiang, Shumei; Sun, Wei; Chen, Minjie; Dai, Shikun; Zhang, Long; Liu, Yonghong; Lee, Kyung Jin; Li, Xiang

    2007-11-01

    This study describes actinobacteria isolated from the marine sponge Haliclona sp. collected in shallow water of the South China Sea. A total of 54 actinobacteria were isolated using media selective for actinobacteria. Species diversity and natural product diversity of isolates from marine sponge Haliclona sp. were analysed. Twenty-four isolates were selected on the basis of their morphology on different media and assigned to the phylum Actinobacteria by a combination of 16S rRNA gene based restriction enzymes digestion and 16S rRNA gene sequence analysis. The 16S rRNA genes of 24 isolates were digested by restriction enzymes TaqI and MspI and assigned to different groups according to their restriction enzyme pattern. The phylogenetic analysis based on 16S rRNA gene sequencing showed that the isolates belonged to the genera Streptomyces, Nocardiopsis, Micromonospora and Verrucosispora; one other isolate was recovered that does not belong to known genera based on its unique 16S rRNA gene sequence. To our knowledge, this is the first report of a bacterium classified as Verrucosispora sp. that has been isolated from a marine sponge. The majority of the strains tested belong to the genus Streptomyces and three isolates may be new species. All of the 24 isolates were screened for genes encoding polyketide synthases (PKS) and nonribosomal peptide synthetases (NRPS). PKS and NRPS sequences were detected in more than half of the isolates and the different "PKS-I-PKS-II-NRPS" combinations in different isolates belonging to the same species are indicators of their potential natural product diversity and divergent genetic evolution.

  18. Agarivorans gilvus sp. nov. Isolated From Seaweed

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A novel agarase-producing, non-endospore-forming marine bacterium WH0801T was isolated from a fresh seaweed sample collected from the coast of Weihai, China. Preliminary characterization based on 16S rRNA gene sequence analysis showed that WH0801T shared 96.1% identity with Agarivorans albus MKT 10...

  19. Campylobacter iguaniorum sp. nov., isolated from reptiles

    Technology Transfer Automated Retrieval System (TEKTRAN)

    During samplings of reptiles for Epsilonproteobacteria, Campylobacter strains were isolated from lizards and chelonians not belonging to any of the established taxa. Initial AFLP, PCR, and 16S rRNA sequence analysis showed that these strains were most closely related to Campylobacter fetus and Campy...

  20. Streptomyces erringtonii sp. nov. and Streptomyces kaempferi sp. nov., isolated from a hay meadow soil.

    PubMed

    Santhanam, Rakesh; Rong, Xiaoying; Huang, Ying; Goodfellow, Michael

    2013-01-01

    Two filamentous actinomycetes isolated from a hay meadow soil were provisionally assigned to the genus Streptomyces based on morphological features. The isolates were found to have chemical and morphological properties typical of the genus Streptomyces and formed distinct phyletic lines in the 16S rRNA gene tree. Isolate I36(T) was most closely related to Streptomyces glauciniger NBRC 100913(T) and isolate I37(T) to Streptomyces mirabilis NBRC 13450(T). Low DNA:DNA relatedness values were recorded between each of the isolates and their closest phylogenetic neighbour. The isolates were also distinguished from their nearest phylogenetic neighbour, and from one another, using a combination of phenotypic properties. These data indicate that the isolates should be recognised as new species in the genus Streptomyces. The names proposed for these new taxa are Streptomyces erringtonii sp. nov. and Streptomyces kaempferi sp. nov. with isolate I36(T) (=CGMCC 4.7016(T) = KACC 15424(T)) and isolate I37(T) (=CGMCC 4.7020(T) = KACC 15428(T)) as the respective type strains.

  1. Indirect Manganese Removal by Stenotrophomonas sp. and Lysinibacillus sp. Isolated from Brazilian Mine Water.

    PubMed

    Barboza, Natália Rocha; Amorim, Soraya Sander; Santos, Pricila Almeida; Reis, Flávia Donária; Cordeiro, Mônica Mendes; Guerra-Sá, Renata; Leão, Versiane Albis

    2015-01-01

    Manganese is a contaminant in the wastewaters produced by Brazilian mining operations, and the removal of the metal is notoriously difficult because of the high stability of the Mn(II) ion in aqueous solutions. To explore a biological approach for removing excessive amounts of aqueous Mn(II), we investigated the potential of Mn(II) oxidation by both consortium and bacterial isolates from a Brazilian manganese mine. A bacterial consortium was able to remove 99.7% of the Mn(II). A phylogenetic analysis of isolates demonstrated that the predominant microorganisms were members of Stenotrophomonas, Bacillus, and Lysinibacillus genera. Mn(II) removal rates between 58.5% and 70.9% were observed for Bacillus sp. and Stenotrophomonas sp. while the Lysinibacillus isolate 13P removes 82.7%. The catalytic oxidation of Mn(II) mediated by multicopper oxidase was not properly detected; however, in all of the experiments, a significant increase in the pH of the culture medium was detected. No aggregates inside the cells grown for a week were found by electronic microscopy. Nevertheless, an energy-dispersive X-ray spectroscopy of the isolates revealed the presence of manganese in Stenotrophomonas sp. and Lysinibacillus sp. grown in K medium. These results suggest that members of Stenotrophomonas and Lysinibacillus genera were able to remove Mn(II) by a nonenzymatic pathway. PMID:26697496

  2. Indirect Manganese Removal by Stenotrophomonas sp. and Lysinibacillus sp. Isolated from Brazilian Mine Water

    PubMed Central

    Barboza, Natália Rocha; Amorim, Soraya Sander; Santos, Pricila Almeida; Reis, Flávia Donária; Cordeiro, Mônica Mendes; Guerra-Sá, Renata; Leão, Versiane Albis

    2015-01-01

    Manganese is a contaminant in the wastewaters produced by Brazilian mining operations, and the removal of the metal is notoriously difficult because of the high stability of the Mn(II) ion in aqueous solutions. To explore a biological approach for removing excessive amounts of aqueous Mn(II), we investigated the potential of Mn(II) oxidation by both consortium and bacterial isolates from a Brazilian manganese mine. A bacterial consortium was able to remove 99.7% of the Mn(II). A phylogenetic analysis of isolates demonstrated that the predominant microorganisms were members of Stenotrophomonas, Bacillus, and Lysinibacillus genera. Mn(II) removal rates between 58.5% and 70.9% were observed for Bacillus sp. and Stenotrophomonas sp. while the Lysinibacillus isolate 13P removes 82.7%. The catalytic oxidation of Mn(II) mediated by multicopper oxidase was not properly detected; however, in all of the experiments, a significant increase in the pH of the culture medium was detected. No aggregates inside the cells grown for a week were found by electronic microscopy. Nevertheless, an energy-dispersive X-ray spectroscopy of the isolates revealed the presence of manganese in Stenotrophomonas sp. and Lysinibacillus sp. grown in K medium. These results suggest that members of Stenotrophomonas and Lysinibacillus genera were able to remove Mn(II) by a nonenzymatic pathway. PMID:26697496

  3. Properties of Polyhydroxyalkanoate Granules and Bioemulsifiers from Pseudomonas sp. and Burkholderia sp. Isolates Growing on Glucose.

    PubMed

    Sacco, Laís Postai; Castellane, Tereza Cristina Luque; Lopes, Erica Mendes; de Macedo Lemos, Eliana Gertrudes; Alves, Lúcia Maria Carareto

    2016-03-01

    A Burkholderia and Pseudomonas species designated as AB4 and AS1, respectively, were isolated from soil containing decomposing straw or sugar cane bagasse collected from Brazil. This study sought to evaluate the capacities of culture media, cell-free medium, and crude lysate preparations (containing PHB inclusion bodies) from bacterial cell cultures to stabilize emulsions with several hydrophobic compounds. Four conditions showed good production of bioemulsifiers (E24 ≥ 50 %), headed by substantially cell-free media from bacterial cell cultures in which bacterial isolates from Burkholderia sp. strain AB4 and Pseudomonas sp. strain AS1 were grown. Our results revealed that the both isolates (AB4 and AS1 strains) exhibited high emulsification indices (indicating usefulness in bioremediation) and good stabilities. PMID:26578147

  4. Wickerhamiella slavikovae sp. nov. and Wickerhamiella goesii sp. nov., two yeast species isolated from natural substrates.

    PubMed

    Hagler, Allen N; Ribeiro, José R A; Pinotti, T; Brandão, Luciana R; Pimenta, Raphael S; Lins, U; Lee, Ching-Fu; Hsieh, Chin-Wen; Lachance, Marc-André; Rosa, Carlos A

    2013-08-01

    Two novel yeast species were isolated during three independent studies of yeasts associated with natural substrates in Brazil and Taiwan. Analysis of the sequences of the D1/D2 domains of the large subunit rRNA gene showed that these novel species belong to the Wickerhamiella clade. The first was isolated from freshwater and a leaf of sugar cane (Saccharum officinarum) in Brazil and from leaves of Wedelia biflora in Taiwan. Described here as Wickerhamiella slavikovae sp. nov., it differs by 56 nucleotide substitutions and 19 gaps in the D1/D2 region of the large subunit rRNA gene from Candida sorbophila, the least divergent species. The second species, named Wickerhamiella goesii sp. nov., was isolated from leaves and the rhizosphere of sugar cane collected in Rio de Janeiro, Brazil. The species differs by 54 nucleotide substitutions and nine gaps in the D1/D2 domains from Candida drosophilae, its least divergent relative. The type strains are Wickerhamiella slavikovae sp. nov. IMUFRJ 52096(T) (= CBS 12417(T) = DBVPG 8032(T)) and Wickerhamiella goesii sp. nov. IMUFRJ 52102(T) (= CBS 12419(T) = DBVPG 8034(T)). PMID:23710055

  5. Lactobacillus apinorum sp. nov., Lactobacillus mellifer sp. nov., Lactobacillus mellis sp. nov., Lactobacillus melliventris sp. nov., Lactobacillus kimbladii sp. nov., Lactobacillus helsingborgensis sp. nov. and Lactobacillus kullabergensis sp. nov., isolated from the honey stomach of the honeybee Apis mellifera.

    PubMed

    Olofsson, Tobias C; Alsterfjord, Magnus; Nilson, Bo; Butler, Eile; Vásquez, Alejandra

    2014-09-01

    We previously discovered a symbiotic lactic acid bacterial (LAB) microbiota in the honey stomach of the honeybee Apis mellifera. The microbiota was composed of several phylotypes of Bifidobacterium and Lactobacillus. 16S rRNA gene sequence analyses and phenotypic and genetic characteristics revealed that the phylotypes isolated represent seven novel species. One grouped with Lactobacillus kunkeei and the others belong to the Lactobacillus buchneri and Lactobacillus delbrueckii subgroups of Lactobacillus. We propose the names Lactobacillus apinorum sp. nov., Lactobacillus mellifer sp. nov., Lactobacillus mellis sp. nov., Lactobacillus melliventris sp. nov., Lactobacillus kimbladii sp. nov., Lactobacillus helsingborgensis sp. nov. and Lactobacillus kullabergensis sp. nov. for these novel species, with the respective type strains being Fhon13N(T) ( = DSM 26257(T) = CCUG 63287(T)), Bin4N(T) ( = DSM 26254(T) = CCUG 63291(T)), Hon2N(T) ( = DSM 26255(T) = CCUG 63289(T)), Hma8N(T) ( = DSM 26256(T) = CCUG 63629(T)), Hma2N(T) ( = DSM 26263(T) = CCUG 63633(T)), Bma5N(T) ( = DSM 26265(T) = CCUG 63301(T)) and Biut2N(T) ( = DSM 26262(T) = CCUG 63631(T)).

  6. Lactobacillus apinorum sp. nov., Lactobacillus mellifer sp. nov., Lactobacillus mellis sp. nov., Lactobacillus melliventris sp. nov., Lactobacillus kimbladii sp. nov., Lactobacillus helsingborgensis sp. nov. and Lactobacillus kullabergensis sp. nov., isolated from the honey stomach of the honeybee Apis mellifera

    PubMed Central

    Alsterfjord, Magnus; Nilson, Bo; Butler, Èile; Vásquez, Alejandra

    2014-01-01

    We previously discovered a symbiotic lactic acid bacterial (LAB) microbiota in the honey stomach of the honeybee Apis mellifera. The microbiota was composed of several phylotypes of Bifidobacterium and Lactobacillus. 16S rRNA gene sequence analyses and phenotypic and genetic characteristics revealed that the phylotypes isolated represent seven novel species. One grouped with Lactobacillus kunkeei and the others belong to the Lactobacillus buchneri and Lactobacillus delbrueckiisubgroups of Lactobacillus. We propose the names Lactobacillus apinorum sp. nov., Lactobacillus mellifer sp. nov., Lactobacillus mellis sp. nov., Lactobacillus melliventris sp. nov., Lactobacillus kimbladii sp. nov., Lactobacillus helsingborgensis sp. nov. and Lactobacillus kullabergensis sp. nov. for these novel species, with the respective type strains being Fhon13NT ( = DSM 26257T = CCUG 63287T), Bin4NT ( = DSM 26254T = CCUG 63291T), Hon2NT ( = DSM 26255T = CCUG 63289T), Hma8NT ( = DSM 26256T = CCUG 63629T), Hma2NT ( = DSM 26263T = CCUG 63633T), Bma5NT ( = DSM 26265T = CCUG 63301T) and Biut2NT ( = DSM 26262T = CCUG 63631T). PMID:24944337

  7. Nocardia zapadnayensis sp. nov., isolated from soil.

    PubMed

    Ozdemir-Kocak, Fadime; Saygin, Hayrettin; Saricaoglu, Salih; Cetin, Demet; Pötter, Gabriele; Spröer, Cathrin; Guven, Kiymet; Isik, Kamil; Klenk, Hans-Peter; Sahin, Nevzat

    2016-01-01

    A novel Gram-stain positive, rod-shaped, non-motile and mycolic acid containing strain, FMN18(T), isolated from soil, was characterised using a polyphasic approach. The organism showed a combination of 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. The cell wall contained meso-diaminopimelic acid (type IV) and whole cell sugars were galactose, glucose, arabinose and ribose. The predominant menaquinone was MK-8(H4ω-cyclo). The major phospholipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides. Major fatty acids are C16:0, 10-methyl C18:0 (TBSA), C18:1 cis9 and C16:1 trans9. These chemotaxonomic traits are in good agreement with those known for representatives of the genus Nocardia. The phylogenetic analysis based on the 16S rRNA gene sequence of strain FMN18(T) showed it to be closely related to Nocardia grenadensis GW5-5797(T) (99.2 %), Nocardia speluncae N2-11(T) (99.1 %), Nocardia jinanensis 04-5195(T) (99.0 %) and Nocardia rhamnosiphila 202GMO(T) (98.3 %). The phylogenetic analysis based on the gyrB gene sequence of strain FMN18(T) showed it to be closely related to N. rhamnosiphila 202GMO(T) (99.0 %), N. grenadensis DSM 45869(T) (96.6 %), N. jinanensis DSM 45048(T) (93.1 %), N. carnea IFM 0237(T) (89.7 %) and N. speluncae DSM 45078(T) (89.1 %). A combination of DNA-DNA hybridization results and phenotypic properties demonstrated that strain FMN18(T) was clearly distinguished from all closely related Nocardia species. It is proposed that the organism be classified as representing a novel species of the genus Nocardia, for which the name Nocardia zapadnayensis (type strain FMN18(T) = DSM 45872(T) = KCTC 29234(T)) is proposed.

  8. Streptomyces chlorus sp. nov. and Streptomyces viridis sp. nov., isolated from soil.

    PubMed

    Kim, Byung-Yong; Rong, Xiaoying; Zucchi, Tiago D; Huang, Ying; Goodfellow, Michael

    2013-05-01

    Two actinomycete strains, BK125(T) and BK199(T), isolated from a hay meadow soil sample were investigated to determine their taxonomic position using a polyphasic approach. The isolates produced greenish-yellow and light green aerial mycelium on oatmeal agar, respectively. They contained anteiso-C15 : 0, iso-C15 : 0 and C16 : 0 as the major fatty acids, and MK-9 (H6) and MK-9 (H8) as the predominant isoprenoid quinones. Phylogenetic analysis of the 16S rRNA gene sequences showed that the isolates formed distinct phyletic lines towards the periphery of the Streptomyces prasinus subclade. Analysis of DNA-DNA relatedness between the two isolates showed that they belonged to different genomic species. The organisms were also distinguished from one another and from type strains of species classified in the S. prasinus subclade using a combination of genotypic and phenotypic properties. On the basis of these data, it is proposed that the isolates be assigned to the genus Streptomyces as Streptomyces chlorus sp. nov. and Streptomyces viridis sp. nov. with isolates BK125(T) ( = KACC 20902(T) = CGMCC 4.5798(T)) and BK199(T) ( = KACC 21003(T) = CGMCC 4.6824(T)) as the respective type strains. PMID:22922536

  9. Morphology of Blastocystis sp. isolated from circus animals.

    PubMed

    Stenzel, D J; Cassidy, M F; Boreham, P F

    1993-08-01

    Blastocystis sp. is reported for the first time from faecal samples collected from a camel, a llama, a highland bull and a lion in a travelling circus. Fresh faecal specimens were examined by light and electron microscopy, and vacuolar and cyst forms of similar morphology were present in all three ungulates. These cells were smaller than cultured vacuolar cells of Blastocystis hominis isolated from humans and contained only a single vacuole in comparison to the multivacuolar cell found in fresh human faeces. The taxonomic relationship of Blastocystis isolated from humans and ungulates remains to be determined. The number of parasites present in the lion sample was too small to make valid comparisons.

  10. Streptococcus loxodontisalivarius sp. nov. and Streptococcus saliviloxodontae sp. nov., isolated from oral cavities of elephants.

    PubMed

    Saito, Masanori; Shinozaki-Kuwahara, Noriko; Hirasawa, Masatomo; Takada, Kazuko

    2014-09-01

    Four Gram-stain-positive, catalase-negative, coccoid-shaped organisms were isolated from elephant oral cavities. The isolates were tentatively identified as streptococcal species based on the results of biochemical tests. Comparative 16S rRNA gene sequencing studies confirmed the organisms to be members of the genus Streptococcus. Two isolates (NUM 6304(T) and NUM 6312) were related most closely to Streptococcus salivarius with 96.8 % and 93.1 % similarity based on the 16S rRNA gene and the RNA polymerase β subunit encoding gene (rpoB), respectively, and to Streptococcus vestibularis with 83.7 % similarity based on the 60 kDa heat-shock protein gene (groEL). The other two isolates (NUM 6306(T) and NUM 6318) were related most closely to S. vestibularis with 97.0 % and 82.9 % similarity based on the 16S rRNA and groEL genes, respectively, and to S. salivarius with 93.5 % similarity based on the rpoB gene. Based on phylogenetic and phenotypic evidence, these isolates are suggested to represent novel species of the genus Streptococcus, for which the names Streptococcus loxodontisalivarius sp. nov. (type strain NUM 6304(T) = JCM 19287(T) = DSM 27382(T)) and Streptococcus saliviloxodontae sp. nov. (type strain NUM 6306(T) = JCM 19288(T) = DSM 27513(T)) are proposed.

  11. Lactobacillus ceti sp. nov., isolated from beaked whales (Ziphius cavirostris).

    PubMed

    Vela, A I; Fernandez, A; Espinosa de los Monteros, A; Goyache, J; Herraez, P; Tames, B; Cruz, F; Domínguez, L; Fernández-Garayzábal, J F

    2008-04-01

    Biochemical and molecular genetic studies were performed on three isolates of an unknown Gram-positive, catalase-negative and rod-shaped organism isolated from the lungs and liver of two beaked whales. The organisms were tentatively identified as Lactobacillus spp. based on cellular morphology and biochemical tests. 16S rRNA gene sequencing studies confirmed the provisional identification of the novel isolates as members of the genus Lactobacillus, but the isolates did not correspond to any recognized species of this genus. The novel strains shared the same phenotypic characteristics and exhibited 100 % 16S rRNA gene sequence similarity. The nearest phylogenetic relatives of the novel isolates were Lactobacillus satsumensis DSM 16230T (94.2 % 16S rRNA gene sequence similarity), Lactobacillus salivarius JCM 1047 (94.0 %), Lactobacillus nagelii ATCC 700692T (94.0 %) and Lactobacillus saerimneri DSM 16049T (93.8 %). The novel isolates could be distinguished from these species and other related species of the genus Lactobacillus by physiological and biochemical tests. On the basis of these phenotypic, physiological and phylogenetic findings, it is proposed that the new isolates from whales be classified as a novel species of the genus Lactobacillus, Lactobacillus ceti sp. nov. The type strain is 142-2T (=CECT 7185T=CCUG 53626T).

  12. Acinetobacter sp. HM746599 isolated from leatherback turtle blood.

    PubMed

    Soslau, Gerald; Russell, Jacob A; Spotila, James R; Mathew, Andrew J; Bagsiyao, Pamela

    2011-09-01

    A newly described bacterial isolate, Acinetobacter sp. HM746599, has been obtained from leatherback sea turtle hatchling blood. The implication is that the hatchling was infected during development in the egg, which is substantiated by other studies to be reported by us in the future. The 16S rRNA gene sequence of the bacterium (GenBank accession number: HM746599) showed the greatest similarity to the identified species, Acinetobacter beijerinckii (97.6-99.78%) and Acinetobacter venetianus (99.78%). Acinetobacter sp. HM746599 are gram-negative, rod-shaped coccobacilli and are hemolytic/cytotoxic to human and sea turtle red blood cells (RBCs). Hemolysis is not the result of any detectable soluble toxin. Acinetobacter beijerinckii and A. venetianus hemolyze sheep RBCs while Acinetobacter sp. HM746599 does not, and unlike A. venetianus, the growth of Acinetobacter sp. HM746599 and A. beijerinckii is not supported by l-arginine. Many Acinetobacter species, especially hemolytic ones, are pathogenic to immunologically compromised humans and it is possible that, in addition to sea turtles, this bacterium might also be a danger to susceptible humans who handle infected hatchlings. The bacteria are available from CCUG (Culture Collection, University Gothenburg, Göteborg, Sweden) and from NRRL (Agricultural Research Service Culture Collection, Peoria, IL). PMID:21707734

  13. Streptomyces glycovorans sp. nov., Streptomyces xishensis sp. nov. and Streptomyces abyssalis sp. nov., isolated from marine sediments.

    PubMed

    Xu, Ying; He, Jie; Tian, Xin-Peng; Li, Jie; Yang, Ling-Ling; Xie, Qiong; Tang, Shu-Kun; Chen, Yi-Guang; Zhang, Si; Li, Wen-Jun

    2012-10-01

    Strains YIM M 10366(T), YIM M 10378(T) and YIM M 10400(T) were isolated from marine sediments collected from the Xisha Islands in the South China Sea. All three isolates were able to grow optimally at pH 7.0, 28-37 °C and 0-3% (w/v) NaCl. Comparison of 16S rRNA gene sequences showed that these strains are members of the genus Streptomyces, exhibiting moderately high 16S rRNA gene sequence similarities of 97.0-98.8% to members of the most closely related Streptomyces species. Morphological characteristics, physiological characteristics and compositions of whole-cell sugars and phospholipids are consistent with the diagnostic characteristics of the genus Streptomyces, but still allowed differentiation amongst the three strains and their neighbours. Based on 16S rRNA gene sequence analysis, DNA-DNA relatedness, phenotypic characteristics and chemotaxonomic data, strains YIM M 10366(T), YIM M 10378(T) and YIM M 10400(T) were identified as members of three novel species of the genus Streptomyces, for which the names Streptomyces glycovorans sp. nov. (type strain YIM M 10366(T)  =DSM 42021(T)  =CCTCC AA2010005(T)), Streptomyces xishensis sp. nov. (type strain YIM M 10378(T)  = DSM 42022(T)  =CCTCC AA 2010006(T)) and Streptomyces abyssalis sp. nov. (type strain YIM M 10400(T)  =DSM 42024(T)  = CCTCC AA 2010008(T)) are proposed.

  14. Novel linear megaplasmid from Brevibacterium sp. isolated from extreme environment.

    PubMed

    Dib, Julián Rafael; Wagenknecht, Martin; Hill, Russell T; Farías, María Eugenia; Meinhardt, Friedhelm

    2010-06-01

    Brevibacterium sp. Ap13, isolated from flamingo's feces in Laguna Aparejos, a high-altitude lake located at approximately 4,200 m in the northwest of Argentina was previously found to be resistant to multiple antibiotics, and was therefore screened for plasmids that may be implicated in antibiotic resistance. Brevibacterium sp. Ap13 was found to contain two plasmids of approximately 87 and 436 kb, designated pAP13 and pAP13c, respectively. Only pAP13 was stably maintained and was extensively characterized by pulsed-field gel electrophoresis to reveal that this plasmid is linear and likely has covalently linked terminal proteins associated with its 5' ends. This is the first report of a linear plasmid in the genus Brevibacterium and may provide a new tool for genetic manipulation of this commercially important genus. PMID:20473959

  15. Dechlorination of Atrazine by a Rhizobium sp. Isolate

    PubMed Central

    Bouquard, C.; Ouazzani, J.; Prome, J.; Michel-Briand, Y.; Plesiat, P.

    1997-01-01

    A Rhizobium sp. strain, named PATR, was isolated from an agricultural soil and found to actively degrade the herbicide atrazine. Incubation of PATR in a basal liquid medium containing 30 mg of atrazine liter(sup-1) resulted in the rapid consumption of the herbicide and the accumulation of hydroxyatrazine as the only metabolite detected after 8 days of culture. Experiments performed with ring-labeled [(sup14)C]atrazine indicated no mineralization. The enzyme responsible for the hydroxylation of atrazine was partially purified and found to consist of four 50-kDa subunits. Its synthesis in PATR was constitutive. This new atrazine hydrolase demonstrated 92% sequence identity through a 24-amino-acid fragment with atrazine chlorohydrolase AtzA produced by Pseudomonas sp. strain ADP. PMID:16535552

  16. Streptococcus orisasini sp. nov. and Streptococcus dentasini sp. nov., isolated from the oral cavity of donkeys.

    PubMed

    Takada, Kazuko; Saito, Masanori; Tsudukibashi, Osamu; Hiroi, Takachika; Hirasawa, Masatomo

    2013-08-01

    Four Gram-positive, catalase-negative, coccoid isolates that were obtained from donkey oral cavities formed two distinct clonal groups when characterized by phenotypic and phylogenetic studies. From the results of biochemical tests, the organisms were tentatively identified as a streptococcal species. Comparative 16S rRNA gene sequencing studies confirmed the organisms to be members of the genus Streptococcus. Two of the isolates were related most closely to Streptococcus ursoris with 95.6 % similarity based on the 16S rRNA gene and to Streptococcus ratti with 92.0 % similarity based on the 60 kDa heat-shock protein gene (groEL). The other two isolates, however, were related to Streptococcus criceti with 95.0 and 89.0 % similarities based on the 16S rRNA and groEL genes, respectively. From both phylogenetic and phenotypic evidence, the four isolates formed two distinct clonal groups and are suggested to represent novel species of the genus Streptococcus. The names proposed for these organisms are Streptococcus orisasini sp. nov. (type strain NUM 1801(T) = JCM 17942(T) = DSM 25193(T)) and Streptococcus dentasini sp. nov. (type strain NUM 1808(T) = JCM 17943(T) = DSM 25137(T)).

  17. Aquamicrobium ahrensii sp. nov. and Aquamicrobium segne sp. nov., isolated from experimental biofilters.

    PubMed

    Lipski, André; Kämpfer, Peter

    2012-10-01

    Two groups of Gram-negative, aerobic bacterial strains previously isolated from experimental biofilters were investigated to determine their taxonomic position. Based on their 16S rRNA gene sequences, these isolates formed two distinct groups within the genus Aquamicrobium. The gene sequence similarities of the new isolates to the type strains of Aquamicrobium species were below 98.3 %. The presence of ubiquinone-10, C(18 : 1) cis 11 as the predominant fatty acid and a polar lipid pattern with phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol and phosphatidylethanolamine was in accordance with the characteristics of this genus. The results of DNA-DNA hybridization, biochemical tests and chemotaxonomic properties allowed genotypic and phenotypic differentiation of the strains from all recognized species of the genus Aquamicrobium. Therefore, the isolates were assigned to two novel species of this genus for which the names Aquamicrobium ahrensii sp. nov. (type strain 905/1(T) = DSM 19730(T) = CCUG 55251(T)) and Aquamicrobium segne sp. nov. (type strain 1006/1(T) = DSM 19714(T) = CCUG 55250(T)) are proposed. An emended description of the genus Aquamicrobium is also presented.

  18. Flavobacterium ceti sp. nov., isolated from beaked whales (Ziphius cavirostris).

    PubMed

    Vela, A I; Fernandez, A; Sánchez-Porro, C; Sierra, E; Mendez, M; Arbelo, M; Ventosa, A; Domínguez, L; Fernández-Garayzábal, J F

    2007-11-01

    Three isolates of a Gram-negative, catalase- and oxidase-positive, rod-shaped bacterium, isolated from the lung and liver of two beaked whales, were characterized by phenotypic and molecular genetic methods. Based on cellular morphology and biochemical criteria, the isolates were tentatively assigned to the family Flavobacteriaceae, although they did not appear to correspond to any recognized species. Comparative 16S rRNA gene sequencing showed that the three new isolates shared 100% sequence similarity. The unknown bacterium was phylogenetically closely related to, but distinct from the type strains of Flavobacterium johnsoniae (93.7% sequence similarity), Flavobacterium frigidimaris (93.4%), Flavobacterium aquidurense (93.4%), Flavobacterium hibernum (93.4%) and Flavobacterium degerlachei (93.4%). The novel isolates were readily distinguished from these and other related Flavobacterium species by physiological and biochemical tests. On the basis of phenotypic and phylogenetic evidence, it is proposed that the unknown isolates from whales are classified as a novel species of the genus Flavobacterium, Flavobacterium ceti sp. nov. The type strain is 454-2T (=CECT 7184T=CCUG 52969T).

  19. Burkholderia humisilvae sp. nov., Burkholderia solisilvae sp. nov. and Burkholderia rhizosphaerae sp. nov., isolated from forest soil and rhizosphere soil.

    PubMed

    Lee, Jae-Chan; Whang, Kyung-Sook

    2015-09-01

    Strains Y-12(T) and Y-47(T) were isolated from mountain forest soil and strain WR43(T) was isolated from rhizosphere soil, at Daejeon, Korea. The three strains grew at 10-55 °C (optimal growth at 28-30 °C), at pH 3.0-8.0 (optimal growth at pH 6.0) and in the presence of 0-4.0% (w/v) NaCl, growing optimally in the absence of added NaCl. On the basis of 16S rRNA gene sequence analysis, the three strains were found to belong to the genus Burkholderia, showing the closest phylogenetic similarity to Burkholderia diazotrophica JPY461(T) (97.2-97.7%); the similarity between the three sequences ranged from 98.3 to 98.7%. Additionally, the three strains formed a distinct group in phylogenetic trees based on the housekeeping genes recA and gyrB. The predominant ubiquinone was Q-8, the major fatty acids were C16 : 0 and C17  : 0 cyclo and the DNA G+C content of the novel isolates was 61.6-64.4 mol%. DNA-DNA relatedness among the three strains and the type strains of the closest species of the genus Burkholderia was less than 50%. On the basis of 16S rRNA, recA and gyrB gene sequence similarities, chemotaxonomic and phenotypic data, the three strains represent three novel species within the genus Burkholderia, for which the names Burkholderia humisilvae sp. nov. (type strain Y-12(T)= KACC 17601(T) = NBRC 109933(T) = NCAIM B 02543(T)), Burkholderia solisilvae sp. nov. (type strain Y-47(T) = KACC 17602(T)= NBRC 109934(T) = NCAIM B 02539(T)) and Burkholderia rhizosphaerae sp. nov. (type strain WR43(T) = KACC 17603(T) = NBRC 109935(T) = NCAIM B 02541(T)) are proposed.

  20. Moraxella pluranimalium sp. nov., isolated from animal specimens.

    PubMed

    Vela, A I; Arroyo, E; Aragón, V; Sánchez-Porro, C; Latre, M V; Cerdà-Cuéllar, M; Ventosa, A; Domínguez, L; Fernández-Garayzábal, J F

    2009-04-01

    Four unusual Gram-negative, catalase-positive, oxidase-positive, coccus-shaped bacteria isolated from one sheep and three pigs were characterized using phenotypic and molecular genetic methods. On the basis of cellular morphology and biochemical criteria, the isolates were tentatively assigned to the genus Moraxella, although the organisms did not appear to correspond to any recognized species. Comparative 16S rRNA gene sequencing studies demonstrated that the isolates represent a novel subline within the genus Moraxella. The most closely related species in phylogenetic terms was Moraxella cuniculi, with 16S rRNA gene sequence similarity of 97.9 % to the type strain CCUG 2154(T), although the DNA-DNA relatedness value was only 29 %. The novel isolates were readily distinguished from all recognized Moraxella species by means of physiological and biochemical tests. On the basis of molecular genetic and phenotypic evidence, therefore, the four isolates represent a novel species of the genus Moraxella, for which the name Moraxella pluranimalium sp. nov. is proposed. The type strain is 248-01(T) (=CECT 7295(T) =CCUG 54913(T)).

  1. Legionella tunisiensis sp. nov. and Legionella massiliensis sp. nov., isolated from environmental water samples.

    PubMed

    Campocasso, Angélique; Boughalmi, Mondher; Fournous, Ghislain; Raoult, Didier; La Scola, Bernard

    2012-12-01

    Two isolates of intra-amoeba-growing bacteria, LegA(T) ( = DSM 24804(T) = CSUR P146(T)) and LegM(T) ( = DSM 24805(T) = CSUR P145(T)), were characterized on the basis of microscopic appearance, staining characteristics, axenic growth at different temperatures and the sequences of the mip, rpoB, 16S rRNA and rnpb genes, as well as the 23S-5S region. Phylogenetic analysis showed that these two isolates lay within the radius of the family Legionellaceae. Furthermore, the analysis of these genes yielded congruent data that indicated that, although strain LegM(T) clusters specifically with Legionella feeleii ATCC 35072(T) and LegA(T) clusters with Legionella nautarum ATCC 49596(T), the divergence observed between these species was greater than that observed between other members of the family. Taken together, these results support the proposal that these two isolates represent novel members of the genus Legionella, and we propose to name them Legionella tunisiensis sp. nov. for LegM(T) ( = DSM 24805(T) = CSUR P145(T)) and Legionella massiliensis sp. nov. for LegA(T) ( = DSM 24804(T) = CSUR P146(T)).

  2. Lactococcus hircilactis sp. nov. and Lactococcus laudensis sp. nov., isolated from milk.

    PubMed

    Meucci, Aurora; Zago, Miriam; Rossetti, Lia; Fornasari, Maria Emanuela; Bonvini, Barbara; Tidona, Flavio; Povolo, Milena; Contarini, Giovanna; Carminati, Domenico; Giraffa, Giorgio

    2015-07-01

    Two strains of lactic acid bacteria, designated 117(T) and 4195(T), were isolated from goat milk in Valtellina, Italy and from cow milk in Valle Trompia, Italy, respectively, and characterized taxonomically by a polyphasic approach. The strains were Gram-stain-positive, coccoid, non-spore-forming and catalase-negative bacteria. Morphological, physiological and phylogenetic data indicated that these isolates belonged to the genus Lactococcus. Strain 117(T) was closely related to Lactococcus fujiensis, Lactococcus lactis subsp. lactis, L. lactis subsp. cremoris, L. lactis subsp. hordniae, L. lactis subsp. tructae and Lactococcus taiwanensis, showing 93-94% and 82-89% 16S rRNA and rpoB gene sequence similarities, respectively. Strain 4195(T) was closely related to Lactococcus chungangensis, Lactococcus raffinolactis, Lactococcus plantarum and Lactococcus piscium, showing 92-98% and 86-99% 16S rRNA and rpoB gene sequence similarities, respectively. Based on this evidence and the data obtained in the present study, the milk isolates represent two novel species of the genus Lactococcus, for which the names Lactococcushircilactis sp. nov., and Lactococcuslaudensis sp. nov. are proposed. The respective type strains are 117(T) ( = LMG 28352(T) = DSM 28960(T)) and 4195(T )( = LMG 28353(T) = DSM 28961(T)). PMID:25833154

  3. Legionella tunisiensis sp. nov. and Legionella massiliensis sp. nov., isolated from environmental water samples.

    PubMed

    Campocasso, Angélique; Boughalmi, Mondher; Fournous, Ghislain; Raoult, Didier; La Scola, Bernard

    2012-12-01

    Two isolates of intra-amoeba-growing bacteria, LegA(T) ( = DSM 24804(T) = CSUR P146(T)) and LegM(T) ( = DSM 24805(T) = CSUR P145(T)), were characterized on the basis of microscopic appearance, staining characteristics, axenic growth at different temperatures and the sequences of the mip, rpoB, 16S rRNA and rnpb genes, as well as the 23S-5S region. Phylogenetic analysis showed that these two isolates lay within the radius of the family Legionellaceae. Furthermore, the analysis of these genes yielded congruent data that indicated that, although strain LegM(T) clusters specifically with Legionella feeleii ATCC 35072(T) and LegA(T) clusters with Legionella nautarum ATCC 49596(T), the divergence observed between these species was greater than that observed between other members of the family. Taken together, these results support the proposal that these two isolates represent novel members of the genus Legionella, and we propose to name them Legionella tunisiensis sp. nov. for LegM(T) ( = DSM 24805(T) = CSUR P145(T)) and Legionella massiliensis sp. nov. for LegA(T) ( = DSM 24804(T) = CSUR P146(T)). PMID:22307511

  4. Actinomyces hominis sp. nov., isolated from a wound swab.

    PubMed

    Funke, Guido; Englert, Ralf; Frodl, Reinhard; Bernard, Kathryn A; Stenger, Steffen

    2010-07-01

    A coryneform bacterium (strain 1094(T)) was isolated from a wound swab taken from an 89-year-old female patient. Chemotaxonomic investigations suggested that this bacterium was related to the genera Actinomyces, Arcanobacterium and Actinobaculum. Phylogenetic analysis of 16S rRNA gene sequences showed that strain 1094(T) was most closely related to Actinomyces europaeus CCUG 32789 A(T) (94.3 % similarity). Phenotypically, the isolate could be separated from its closest phylogenetic neighbours on the basis of being positive for catalase, CAMP reaction, acid phosphatase, N-acetyl-beta-glucosaminidase and raffinose fermentation. Based on the data presented, it is proposed that strain 1094(T) should be classified in a novel species, Actinomyces hominis sp. nov. The type strain is 1094(T) (=CCUG 57540(T) =DSM 22168(T)).

  5. Penicillium koreense sp. nov., isolated from various soils in Korea.

    PubMed

    You, Young-Hyun; Cho, Hye Sun; Song, Jaekyeong; Kim, Dae-Ho; Houbraken, Jos; Hong, Seung-Beom

    2014-12-28

    During an investigation of the fungal diversity of Korean soils, four Penicillium strains could not be assigned to any described species. The strains formed monoverticillate conidiophores with occasionally a divaricate branch. The conidia were smooth or finely rough-walled, globose to broadly ellipsoidal and 2.5-3.5 × 2.0-3.0 μm in size. Their taxonomic novelty was determined using partial β-tubulin gene sequences and the ribosomal internal transcribed spacer region. The phylogenetic analysis showed that the isolates belonged to section Lanata- Divaricata and were most closely related to Penicillium raperi. Phenotypically, the strains differed from P. raperi in having longer and thicker stipes and thicker phialides. Strain KACC 47721(T) from bamboo field soil was designated as the type strain of the new species, and the species was named Penicillium koreense sp. nov., as it was isolated from various regions in Korea.

  6. Draft genome sequence of a Sphingomonas sp., an endosymbiotic bacterium isolated from an arctic lichen Umbilicaria sp.

    PubMed

    Lee, Jungeun; Shin, Seung Chul; Kim, Su Jin; Kim, Bum-Keun; Hong, Soon Gyu; Kim, Eun Hye; Park, Hyun; Lee, Hyoungseok

    2012-06-01

    Sphingomonas sp. strain PAMC 26617 has been isolated from an Arctic lichen Umbilicaria sp. on the Svalbard Islands. Here we present the draft genome sequence of this strain, which represents a valuable resource for understanding the symbiotic mechanisms between endosymbiotic bacteria and lichens surviving in extreme environments.

  7. Luteimonas abyssi sp. nov., isolated from deep-sea sediment.

    PubMed

    Fan, Xiaoyang; Yu, Tong; Li, Zhao; Zhang, Xiao-Hua

    2014-02-01

    Three Gram-stain-negative, strictly aerobic, rod-shaped with single polar flagellum, yellow-pigmented bacteria, designated strains XH031(T), XH038-3 and XH80-1, were isolated from deep-sea sediment of the South Pacific Gyre (41° 51' S 153° 6' W) during the Integrated Ocean Drilling Program (IODP) Expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolates belonged to the genus Luteimonas and showed the highest 16S rRNA gene sequence similarity with Luteimonas aestuarii B9(T) (96.95%), Luteimonas huabeiensis HB2(T) (96.93%) and Xanthomonas cucurbitae LMG 690(T) (96.92 %). The DNA G+C contents of the three isolates were 70.2-73.9 mol%. The major fatty acids were iso-C(15 : 0), iso-C(16 : 0), iso-C(11 : 0) and C16 : 010-methyl and/or iso-C(17 : 1)ω9c. The major respiratory quinone was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one unknown phospholipid. On the basis of data from polyphasic analysis, the three isolates represent a novel species of the genus Luteimonas, for which the name Luteimonas abyssi sp. nov. is proposed. The type strain is XH031(T) ( = DSM 25880(T) = CGMCC 1.12611(T)). PMID:24170776

  8. Microbispora bryophytorum sp. nov., an actinomycete isolated from moss (Bryophyta).

    PubMed

    Li, Chuang; Zhang, Yuejing; Liu, Chongxi; Wang, Haiyan; Zhao, Junwei; Li, Lianjie; Zhang, Zhongwen; Wang, Xiangjing; Xiang, Wensheng

    2015-04-01

    A novel endophytic actinomycete, designated strain NEAU-TX2-2(T), was isolated from moss and characterized using a polyphasic approach. The isolate was found to have morphological characteristics typical of the genus Microbispora . The isolate formed longitudinally paired spores on the tips of short sporophores that branched from aerial hyphae. Analysis of the 16S rRNA gene sequence supported the assignment of the novel strain to the genus Microbispora , and strain NEAU-TX2-2(T) exhibited 99.08 and 98.62% gene sequence similarities to Microbispora amethystogenes JCM 3021(T) and Microbispora rosea subsp. rosea JCM 3006(T), respectively. However two tree-making algorithms supported the position that strain NEAU-TX2-2(T) formed a distinct clade with M. rosea subsp. rosea JCM 3006(T). A low level of DNA-DNA relatedness allowed the isolate to be differentiated from M. amethystogenes JCM 3021(T) and M. rosea subsp. rosea JCM 3006(T). Moreover, strain NEAU-TX2-2(T) could also be distinguished from its closest phylogenetic relatives by morphological and physiological characteristics. Therefore, it is proposed that strain NEAU-TX2-2(T) represents a novel species of the genus Microbispora for which the name Microbispora bryophytorum sp. nov. is proposed. The type strain is NEAU-TX2-2(T) ( = CGMCC 4.7138(T) = DSM 46710(T)).

  9. Dyadobacter tibetensis sp. nov., isolated from glacial ice core.

    PubMed

    Shen, Liang; Liu, Yongqin; Yao, Tandong; Wang, Ninglian; Xu, Baiqing; Jiao, Nianzhi; Liu, Hongcan; Zhou, Yuguang; Liu, Xiaobo; Wang, Yanan

    2013-10-01

    A Gram-stain-negative, rod-shaped, aerobic, non-motile bacterium, designated Y620-1(T), was isolated from a glacier on the Tibetan Plateau, China. The 16S rRNA gene sequence of the novel isolate shared 93.6-95.1 % similarity with type strains of species of the genus Dyadobacter. The major fatty acids of strain Y620-1(T) were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0, C16 : 1ω5c and iso-C17 : 0 3-OH. The predominant isoprenoid quinone and polar lipid were MK-7 and phosphatidylethanolamine (PE), respectively. The DNA G+C content was 44.4±0.3 mol% (Tm). Flexirubin-type pigment was produced. The novel isolate was classified in the genus Dyadobacter, but a number of phenotypic characteristics distinguished the novel isolate from type strains of species of the genus Dyadobacter. From these genotypic and phenotypic data, it is evident that strain Y620-1(T) represents a novel species of the genus Dyadobacter, for which the name Dyadobacter tibetensis sp. nov. is proposed. The type strain is Y620-1(T) ( = JCM 18589(T) = CGMCC 1.12215(T)).

  10. Luteimonas abyssi sp. nov., isolated from deep-sea sediment.

    PubMed

    Fan, Xiaoyang; Yu, Tong; Li, Zhao; Zhang, Xiao-Hua

    2014-02-01

    Three Gram-stain-negative, strictly aerobic, rod-shaped with single polar flagellum, yellow-pigmented bacteria, designated strains XH031(T), XH038-3 and XH80-1, were isolated from deep-sea sediment of the South Pacific Gyre (41° 51' S 153° 6' W) during the Integrated Ocean Drilling Program (IODP) Expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolates belonged to the genus Luteimonas and showed the highest 16S rRNA gene sequence similarity with Luteimonas aestuarii B9(T) (96.95%), Luteimonas huabeiensis HB2(T) (96.93%) and Xanthomonas cucurbitae LMG 690(T) (96.92 %). The DNA G+C contents of the three isolates were 70.2-73.9 mol%. The major fatty acids were iso-C(15 : 0), iso-C(16 : 0), iso-C(11 : 0) and C16 : 010-methyl and/or iso-C(17 : 1)ω9c. The major respiratory quinone was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one unknown phospholipid. On the basis of data from polyphasic analysis, the three isolates represent a novel species of the genus Luteimonas, for which the name Luteimonas abyssi sp. nov. is proposed. The type strain is XH031(T) ( = DSM 25880(T) = CGMCC 1.12611(T)).

  11. Bacillus oceanisediminis sp. nov., isolated from marine sediment.

    PubMed

    Zhang, Jianli; Wang, Jiewei; Fang, Caiyuan; Song, Fei; Xin, Yuhua; Qu, Lei; Ding, Kai

    2010-12-01

    A Gram-stain-positive, spore-forming, rod-shaped and aerobic bacterium was isolated from a sediment sample from the South Sea in China. The isolate, designated H2(T), grew at 4-45 °C (optimum 37 °C) and pH 6-10 (optimum pH 7.0). The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major isoprenoid quinone was MK-7 and the polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unknown aminophospholipid. The major fatty acid was iso-C(15 : 0). The genomic DNA G+C content of strain H2(T) was 44.8mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate formed a monophyletic clade with Bacillus firmus IAM 12464(T). DNA-DNA relatedness between the isolate and B. firmus ATCC 14575(T) was low (27.5 %). Strain H2(T) also had a phenotypic profile that readily distinguished it from its closest phylogenetic neighbours. It is evident from the combination of genotypic and phenotypic data that the organism should be classified in a novel species of the genus Bacillus, for which the name Bacillus oceanisediminis sp. nov. is proposed. The type strain is H2(T) (=CGMCC 1.10115(T) =JCM 16506(T)).

  12. Paenibacillus oenotherae sp. nov. and Paenibacillus hemerocallicola sp. nov., isolated from the roots of herbaceous plants.

    PubMed

    Kim, Tae-Su; Han, Ji-Hye; Joung, Yochan; Kim, Seung Bum

    2015-08-01

    Two Gram-staining-positive, aerobic, endospore-forming, motile bacteria, strains DT7-4T and DLE-12T, were isolated from roots of evening primrose (Oenothera biennis) and day lily (Hemerocallis fulva), respectively, and subjected to taxonomic characterization. Analysis of 16S rRNA gene sequences indicated that the two strains fell into two distinct phylogenetic clusters belonging to the genus Paenibacillus. Strain DT7-4T was most closely related to Paenibacillus phyllosphaerae PALXIL04T and Paenibacillus taihuensis THMBG22T, with 96.3% 16S rRNA gene sequence similarity to each, and strain DLE-12T was most closely related to Paenibacillus ginsengarvi Gsoil 139T and Paenibacillus hodogayensis SGT, with 96.6 and 93.3% sequence similarity, respectively. Both isolates contained anteiso-C15 : 0 as the dominant fatty acid, meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan and MK-7 as the respiratory menaquinone. The cellular polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and unidentified polar lipids. The DNA G+C contents of strains DT7-4T and DLE-12T were 50.1 ± 0.7 and 55.2 ± 0.5 mol%, respectively. The chemotaxonomic properties of both isolates were typical of members of the genus Paenibacillus. However, our biochemical and phylogenetic analyses distinguished each isolate from related species. Based on our polyphasic taxonomic analysis, strains DT7-4T and DLE-12T should be recognized as representatives of novel species of Paenibacillus, for which the names Paenibacillus oenotherae sp. nov. (type strain DT7-4T = KCTC 33186T = JCM 19573T) and Paenibacillus hemerocallicola sp. nov. (type strain DLE-12T = KCTC 33185T = JCM 19572T) are proposed. PMID:25977281

  13. Glycomyces fuscus sp. nov. and Glycomyces albus sp. nov., actinomycetes isolated from a hypersaline habitat.

    PubMed

    Han, Xiao-Xue; Luo, Xiao-Xia; Zhang, Li-Li

    2014-07-01

    Two actinomycete strains, designated TRM 49117(T) and TRM 49136(T), were isolated from a hypersaline habitat in Xinjiang Province, north-west China and were characterized taxonomically by using a polyphasic study. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain TRM 49117(T) had 93.93% similarity with the type strain Glycomyces halotolerans TRM 40137(T) (GenBank accession no. HQ651156) and TRM 49136(T) had 94.32% similarity with G. halotolerans TRM 40137(T). The 16S rRNA gene sequence similarity between the two new isolates was 93%. The isolates contained meso-diaminopimelic acid as the diagnostic diamino acid and anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as major cellular fatty acids. The predominant menaquinones of the isolates were MK-9(H4) and MK-9(H6). The whole-cell sugar patterns of these strains contained xylose and ribose, and strain TRM 49136(T) also contained arabinose. The polar lipid pattern of strain TRM 49117(T) comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol mannosides, phosphatidylcholine, phosphatidylinositol and three additional unknown phospholipids. The polar lipid pattern of strain TRM 49136(T) comprised phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, glycolipids and two phosphoglycolipids of unknown composition. Genotypic and phenotypic data confirmed that strains TRM 49117(T) and TRM 49136(T) represent two novel species, clearly different from related species of the genus Glycomyces, for which the names Glycomyces fuscus sp. nov. (type strain TRM 49117(T) = CCTCC AA 2013003(T) = NRRL B-59998(T) = KACC 17682(T)) and Glycomyces albus sp. nov. (type strain TRM 49136(T) = CCTCC AA 2013004(T) = NRRL B-24927(T) = KACC 17681(T)) are proposed. PMID:24776532

  14. Glycomyces fuscus sp. nov. and Glycomyces albus sp. nov., actinomycetes isolated from a hypersaline habitat.

    PubMed

    Han, Xiao-Xue; Luo, Xiao-Xia; Zhang, Li-Li

    2014-07-01

    Two actinomycete strains, designated TRM 49117(T) and TRM 49136(T), were isolated from a hypersaline habitat in Xinjiang Province, north-west China and were characterized taxonomically by using a polyphasic study. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain TRM 49117(T) had 93.93% similarity with the type strain Glycomyces halotolerans TRM 40137(T) (GenBank accession no. HQ651156) and TRM 49136(T) had 94.32% similarity with G. halotolerans TRM 40137(T). The 16S rRNA gene sequence similarity between the two new isolates was 93%. The isolates contained meso-diaminopimelic acid as the diagnostic diamino acid and anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as major cellular fatty acids. The predominant menaquinones of the isolates were MK-9(H4) and MK-9(H6). The whole-cell sugar patterns of these strains contained xylose and ribose, and strain TRM 49136(T) also contained arabinose. The polar lipid pattern of strain TRM 49117(T) comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol mannosides, phosphatidylcholine, phosphatidylinositol and three additional unknown phospholipids. The polar lipid pattern of strain TRM 49136(T) comprised phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, glycolipids and two phosphoglycolipids of unknown composition. Genotypic and phenotypic data confirmed that strains TRM 49117(T) and TRM 49136(T) represent two novel species, clearly different from related species of the genus Glycomyces, for which the names Glycomyces fuscus sp. nov. (type strain TRM 49117(T) = CCTCC AA 2013003(T) = NRRL B-59998(T) = KACC 17682(T)) and Glycomyces albus sp. nov. (type strain TRM 49136(T) = CCTCC AA 2013004(T) = NRRL B-24927(T) = KACC 17681(T)) are proposed.

  15. Idiomarina maris sp. nov., a marine bacterium isolated from sediment.

    PubMed

    Zhang, Yan-Jiao; Zhang, Xi-Ying; Zhao, Hui-Lin; Zhou, Ming-Yang; Li, Hui-Juan; Gao, Zhao-Ming; Chen, Xiu-Lan; Dang, Hong-Yue; Zhang, Yu-Zhong

    2012-02-01

    A protease-producing marine bacterium, designated CF12-14(T), was isolated from sediment of the South China Sea. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain CF12-14(T) formed a separate lineage within the genus Idiomarina (Gammaproteobacteria). The isolate showed the highest 16S rRNA gene sequence similarity with Idiomarina salinarum ISL-52(T) (94.7 %), Idiomarina seosinensis CL-SP19(T) (94.6 %) and other members of the genus Idiomarina (91.9-94.6 %). Cells were gram-negative, aerobic, flagellated, straight or slightly curved, and often formed buds and prosthecae. Strain CF12-14(T) grew at 4-42 °C (optimum 30-35 °C) and with 0.1-15 % (w/v) NaCl (optimum 2-3 %). The isolate reduced nitrate to nitrite and hydrolysed DNA, but did not produce acids from sugars. The predominant cellular fatty acids were iso-C(15 : 0) (27.4 %), iso-C(17 : 0) (16.0 %) and iso-C(17 : 1)ω9c (15.8 %). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major respiratory quinone was ubiquinone 8. The DNA G+C content was 50.4 mol%. The phylogenetic, phenotypic and chemotaxonomic data supported the conclusion that CF12-14(T) represents a novel species of the genus Idiomarina, for which the name Idiomarina maris sp. nov. is proposed. The type strain is CF12-14(T) ( = CCTCC AB 208166(T) = KACC 13974(T)).

  16. Microsphaerol and seimatorone: two new compounds isolated from the endophytic fungi, Microsphaeropsis sp. and Seimatosporium sp.

    PubMed

    Hussain, Hidayat; Root, Natalia; Jabeen, Farah; Al-Harrasi, Ahmed; Ahmad, Manzoor; Mabood, Fazal; Hassan, Zahid; Shah, Afzal; Green, Ivan R; Schulz, Barbara; Krohn, Karsten

    2015-02-01

    A new polychlorinated triphenyl diether named microsphaerol (1), has been isolated from the endophtic fungus Microsphaeropsis sp. An intensive phytochemical investigation of the endophytic fungus Seimatosporium sp., led to the isolation of a new naphthalene derivative named seimatorone (2) and eight known compounds, i.e., 1-(2,6-dihydroxyphenyl)-3-hydroxybutan-1-one (3), 1-(2,6-dihydroxyphenyl)butan-1-one (4), 1-(2-hydroxy-6-methoxyphenyl)butan-1-one (5), 5-hydroxy-2-methyl-4H-chromen-4-one (6), 2,3-dihydro-5-hydroxy-2-methyl-4H-chromen-4-one (7), 8-methoxynaphthalen-1-ol (8), nodulisporins A and B (9 and 10, resp.), and daldinol (11). The structures of 1 and 2 were elucidated by detailed spectroscopic analysis including (1) H- and (13) C-NMR, COSY, HMQC, HMBC, and HR-EI-MS, while the structures of the known compounds were deduced from comparison of their spectral data with those in the literature. Preliminary studies revealed that microsphaerol (1) showed good antibacterial activities against B. Megaterium and E. coli, and good antilagal and antifungal activities against C. fusca, M. violaceum, respectively. On the other hand, seimatorone (2) exhibited moderate antibacterial, antialgal, and antifungal activities.

  17. Aminobacter ciceronei sp. nov. and Aminobacter lissarensis sp. nov., isolated from various terrestrial environments

    USGS Publications Warehouse

    McDonald, I.R.; Kampfer, P.; Topp, E.; Warner, K.L.; Cox, M.J.; Connell, Hancock T.L.; Miller, L.G.; Larkin, M.J.; Ducrocq, V.; Coulter, C.; Harper, D.B.; Murrell, J.C.; Oremland, R.S.

    2005-01-01

    The bacterial strains IMB-1T and CC495T, which are capable of growth on methyl chloride (CH3Cl, chloromethane) and methyl bromide (CH3Br, bromomethane), were isolated from agricultural soil in California fumigated with CH3Br, and woodland soil in Northern Ireland, respectively. Two pesticide- /herbicide-degrading bacteria, strains ER2 and C147, were isolated from agricultural soil in Canada. Strain ER2 degrades N-methyl carbamate insecticides, and strain C147 degrades triazine herbicides widely used in agriculture. On the basis of their morphological, physiological and genotypic characteristics, these four strains are considered to represent two novel species of the genus Aminobacter, for which the names Aminobacter ciceronei sp. nov. (type strain IMB-1T=ATCC 202197T=CIP 108660T=CCUG 50580T; strains ER2 and C147) and Aminobacter lissarensis sp. nov. (type strain CC495T=NCIMB 13798T=CIP 108661T=CCUG 50579T) are proposed. ?? 2005 IUMS.

  18. Planotetraspora kaengkrachanensis sp. nov. and Planotetraspora phitsanulokensis sp. nov., isolated from soil.

    PubMed

    Suriyachadkun, Chanwit; Chunhametha, Suwanee; Thawai, Chitti; Tamura, Tomohiko; Potacharoen, Wanchern; Kirtikara, Kanyawim; Sanglier, Jean-Jacques; Kitpreechavanich, Vichien

    2010-09-01

    Two novel bacterial strains were isolated from tropical rain forest soil from Thailand. Strains A-T 0875(T) and A-T 1383(T) stained Gram-positive and were filamentous bacteria that developed cylindrical sporangia containing four oval- to rod-shaped spores at the ends of short sporangiophores on branched aerial mycelium. The cell-wall peptidoglycan contained meso-diaminopimelic acid, glutamic acid and alanine as cell-wall amino acids; whole-cell hydrolysates contained rhamnose, madurose, glucose, galactose and 3-O-methylmannose as whole-cell sugars. The predominant menaquinone was MK-9(H(4)). Mycolic acids were not detected. The diagnostic phospholipid was phosphatidylethanolamine. The predominant cellular fatty acids were iso-C(16 : 0) and 10-methyl-C(17 : 0). For both strains, the G+C content of the genomic DNA was 71 mol%. Phenotypic and chemotaxonomic analyses showed that the characteristics of the two isolates were typical of members of the genus Planotetraspora. Furthermore, 16S rRNA gene sequence analysis also indicated that the strains belonged to the genus Planotetraspora but as representatives of two novel species. Following an evaluation of our phenotypic, chemotaxonomic and genotypic studies, two novel species are proposed, Planotetraspora kaengkrachanensis sp. nov. (type strain A-T 0875(T)=BCC 24832(T)=NBRC 104272(T)) and Planotetraspora phitsanulokensis sp. nov. (type strain A-T 1383(T)=BCC 26045(T)=NBRC 104273(T)).

  19. Neisseria wadsworthii sp. nov. and Neisseria shayeganii sp. nov., isolated from clinical specimens.

    PubMed

    Wolfgang, William J; Carpenter, Andrea N; Cole, Jocelyn A; Gronow, Sabine; Habura, Andrea; Jose, Sherly; Nazarian, Elizabeth J; Kohlerschmidt, Donna J; Limberger, Ronald; Schoonmaker-Bopp, Dianna; Spröer, Cathrin; Musser, Kimberlee A

    2011-01-01

    An analysis of 16S rRNA gene sequences from archived clinical reference specimens has identified two novel Neisseria species. For each species, two strains from independent sources were identified. Amongst species with validly published names, the closest species to the newly identified organisms were Neisseria canis, N. dentiae, N. zoodegmatis, N. animaloris and N. weaveri. DNA-DNA hybridization studies demonstrated that the newly identified isolates represent species that are distinct from these nearest neighbours. Analysis of partial 23S rRNA gene sequences for the newly identified strains and their nearest neighbours provided additional support for the species designation. Bayesian analysis of 16S rRNA gene sequences suggested that the newly identified isolates belong to distinct but related species of the genus Neisseria, and are members of a clade that includes N. dentiae, N. bacilliformis and N. canis. The predominant cellular fatty acids [16 : 0, summed feature 3 (16 : 1ω7c and/or iso-15 : 0 2-OH) and 18 : 1ω7c], as well as biochemical and morphological analyses further support the designation of Neisseria wadsworthii sp. nov. (type strain 9715(T) =DSM 22247(T) =CIP 109934(T)) and Neisseria shayeganii sp. nov. (type strain 871(T) =DSM 22246(T) =CIP 109933(T)).

  20. Gracilibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi.

    PubMed

    Oh, Young Joon; Lee, Hae-Won; Lim, Seul Ki; Kwon, Min-Sung; Lee, Jieun; Jang, Ja-Young; Park, Hae Woong; Nam, Young-Do; Seo, Myung-Ji; Choi, Hak-Jong

    2016-09-01

    A novel halophilic bacterium, strain K7(T), was isolated from kimchi, a traditional Korean fermented food. The strain is Gram-positive, motile, and produces terminal endospores. The isolate is facultative aerobic and grows at salinities of 0.0-25.0% (w/v) NaCl (optimum 10-15% NaCl), pH 5.5-8.5 (optimum pH 7.0-7.5), and 15-42°C (optimum 37°C). The predominant isoprenoid quinone in the strain is menaquinone-7 and the peptidoglycan of the strain is meso-diaminopimelic acid. The major fatty acids of the strain are anteisio-C15:0, iso-C15:0, and, C16:0 (other components were < 10.0%), while the major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and three unidentified lipids. A phylogenetic analysis of 16S rRNA gene sequence similarity showed that the isolated strain was a cluster of the genus Gracilibacillus. High levels of gene sequence similarity were observed between strain K7(T) and Gracilibacillus orientalis XH-63(T) (96.5%), and between the present strain and Gracilibacillus xinjiangensis (96.5%). The DNA G+C content of this strain is 37.7 mol%. Based on these findings, strain K7(T) is proposed as a novel species: Gracilibacillus kimchii sp. nov. The type strain is K7(T) (KACC 18669(T); JCM 31344(T)).

  1. Paenibacillus periandrae sp. nov., isolated from nodules of Periandra mediterranea.

    PubMed

    Menéndez, Esther; Ramírez-Bahena, Martha-Helena; Carro, Lorena; Fernández-Pascual, Mercedes; Peter Klenk, Hans; Velázquez, Encarna; Mateos, Pedro F; Peix, Alvaro; Rita Scotti, Maria

    2016-04-01

    A bacterial strain designated PM10T was isolated from root nodules of Periandra mediterranea in Brazil. Phylogenetic analyses based on 16S rRNA gene sequences placed the isolate in the genus Paenibacillus with its closest relatives being Paenibacillus vulneris CCUG 53270T and Paenibacillus yunnanensis YN2T with 95.6 and 95.9% 16S rRNA gene sequence similarity, respectively. The isolate was a Gram-stain-variable, motile, sporulating rod that was catalase-negative and oxidase-positive. Caseinase was positive, amylase was weakly positive and gelatinase was negative. Growth was supported by many carbohydrates and organic acids as carbon sources. MK-7 was the only menaquinone detected and anteiso-C15 : 0 was the major fatty acid. Major polar lipids were diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol and two unidentified lipids. meso-Diaminopimelic acid was detected in the peptidoglycan. The DNA G+C content was 52.9 mol%. Phylogenetic, chemotaxonomic and phenotypic analyses showed that strain PM10T should be considered representative of a novel species of the genus Paenibacillus, for which the name Paenibacillus periandrae sp. nov. is proposed. The type strain is PM10T (=LMG 28691T=CECT 8827T).

  2. Fontibacillus phaseoli sp. nov. isolated from Phaseolus vulgaris nodules.

    PubMed

    Flores-Félix, José David; Mulas, Rebeca; Ramírez-Bahena, Martha-Helena; Cuesta, María José; Rivas, Raúl; Brañas, Javier; Mulas, Daniel; González-Andrés, Fernando; Peix, Alvaro; Velázquez, Encarna

    2014-01-01

    A bacterial strain, designated BAPVE7BT, was isolated from root nodules of Phaseolus vulgaris in Spain. Phylogenetic analysis based on its 16S rRNA gene sequence placed the isolate into the genus Fontibacillus with Fontibacillus panacisegetis KCTC 13564T its closest relative with 97.1 % identity. The isolate was observed to be a Gram-positive, motile and sporulating rod. The catalase test was negative and oxidase was weak. The strain was found to reduce nitrate to nitrite and to produce β-galactosidase but the production of gelatinase, caseinase, urease, arginine dehydrolase, ornithine or lysine decarboxylase was negative. Acetoin production and aesculin hydrolysis were found to be positive. Growth was observed to be supported by many carbohydrates and organic acids as carbon source. MK-7 was identified as the predominant menaquinone and the major fatty acid (43.7 %) as anteiso-C15:0, as occurs in the other species of the genus Fontibacillus. Strain BAPVE7BT displayed a complex lipid profile consisting of diphosphatidylglycerol, phosphatidylglycerol, four glycolipids, four phospholipids, two lipids, two aminolipids and an aminophospholipid. Mesodiaminopimelic acid was detected in the peptidoglycan. The G+C content was determined to be 45.6 mol% (Tm). Phylogenetic, chemotaxonomic and phenotypic analyses showed that strain BAPVE7BT should be considered a new species of genus Fontibacillus, for which the name Fontibacillus phaseoli sp. nov. is proposed (type strain, LMG 27589T, CECT 8333T).

  3. Saccharibacillus sacchari gen. nov., sp. nov., isolated from sugar cane.

    PubMed

    Rivas, Raúl; García-Fraile, Paula; Zurdo-Piñeiro, José Luis; Mateos, Pedro F; Martínez-Molina, Eustoquio; Bedmar, Eulogio J; Sánchez-Raya, Juan; Velázquez, Encarna

    2008-08-01

    A bacterial strain designated GR21T was isolated from apoplastic fluid of Saccharum officinarum (sugar cane). Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate forms a separate branch within the family 'Paenibacillaceae', with Paenibacillus as the closest related genus. Within this genus, the closest related species is Paenibacillus xylanilyticus, with 93.4 % similarity to the sequence of the type strain. The isolate has Gram-variable, facultatively anaerobic, rod-shaped cells, motile by polar and subpolar flagella. Round, non-ornamented, central or subterminal spores are formed in unswollen sporangia. The strain is catalase-positive and oxidase-negative on nutrient agar medium. Cellulose and aesculin were hydrolysed, whereas xylan, starch and gelatin were not. Growth was supported by many carbohydrates as carbon sources. Strain GR21T displayed a lipid profile consisting of diphosphatidylglycerol, phosphatidylglycerol, an unknown aminophospholipid, two unknown glycolipids and an unknown phosphoglycolipid. MK-7 was the predominant menaquinone and anteiso-C15: 0 was the major fatty acid. The DNA G+C content was 57.8 mol%. Phylogenetic and phenotypic analyses, including assimilation of carbon sources and exoenzyme production commonly used for classification within the family 'Paenibacillaceae', showed that strain GR21T belongs to a new genus within this family, for which the name Saccharibacillus sacchari gen. nov., sp. nov. is proposed. The type strain of Saccharibacillus sacchari is GR21T (=LMG 24085T =DSM 19268T).

  4. Arcobacter defluvii sp. nov., isolated from sewage samples.

    PubMed

    Collado, Luis; Levican, Arturo; Perez, Jessica; Figueras, Maria José

    2011-09-01

    A study employing a polyphasic taxonomic approach was undertaken to clarify the position of 12 isolates recovered from sewage samples. These isolates were recognized as a potential novel species because a new and specific pattern was produced with the 16S rRNA-RFLP Arcobacter identification method. The sequences of the 16S rRNA gene not only supported the classification of these novel strains as members of the genus Arcobacter, but also showed that they formed a separate phylogenetic line. Strain SW28-11(T), chosen as the representative of these strains, showed 16S rRNA gene sequence similarity of 95.6 % with the closest related species Arcobacter nitrofigilis. The phylogenetic position of the novel strains was further confirmed by analysis of the housekeeping genes hsp60, rpoB and, for the first time, gyrB. The latter proved to be an excellent additional gene for establishing the phylogeny of this genus. These data, together with phenotypic characterization, revealed that this group of isolates represent a novel species of the genus Arcobacter. The name Arcobacter defluvii sp. nov., is proposed, with the type strain SW28-11(T) ( = CECT 7697(T) = LMG 25694(T)).

  5. Gracilibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi.

    PubMed

    Oh, Young Joon; Lee, Hae-Won; Lim, Seul Ki; Kwon, Min-Sung; Lee, Jieun; Jang, Ja-Young; Park, Hae Woong; Nam, Young-Do; Seo, Myung-Ji; Choi, Hak-Jong

    2016-09-01

    A novel halophilic bacterium, strain K7(T), was isolated from kimchi, a traditional Korean fermented food. The strain is Gram-positive, motile, and produces terminal endospores. The isolate is facultative aerobic and grows at salinities of 0.0-25.0% (w/v) NaCl (optimum 10-15% NaCl), pH 5.5-8.5 (optimum pH 7.0-7.5), and 15-42°C (optimum 37°C). The predominant isoprenoid quinone in the strain is menaquinone-7 and the peptidoglycan of the strain is meso-diaminopimelic acid. The major fatty acids of the strain are anteisio-C15:0, iso-C15:0, and, C16:0 (other components were < 10.0%), while the major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and three unidentified lipids. A phylogenetic analysis of 16S rRNA gene sequence similarity showed that the isolated strain was a cluster of the genus Gracilibacillus. High levels of gene sequence similarity were observed between strain K7(T) and Gracilibacillus orientalis XH-63(T) (96.5%), and between the present strain and Gracilibacillus xinjiangensis (96.5%). The DNA G+C content of this strain is 37.7 mol%. Based on these findings, strain K7(T) is proposed as a novel species: Gracilibacillus kimchii sp. nov. The type strain is K7(T) (KACC 18669(T); JCM 31344(T)). PMID:27572507

  6. Lactobacillus suntoryeus sp. nov., isolated from malt whisky distilleries.

    PubMed

    Cachat, Elise; Priest, Fergus G

    2005-01-01

    Eight strains of Lactobacillus with identical partial 16S rRNA gene sequences and similar randomly amplified polymorphic DNA patterns were isolated from fermentation samples from Japanese and Scottish malt whisky distilleries. Phylogenetic analysis of almost complete 16S rRNA gene sequences from three representative strains (two from Japan, one from Scotland) placed them in the genus Lactobacillus as members of the Lactobacillus acidophilus group. Lactobacillus helveticus and Lactobacillus gallinarum were the most closely related species, with 16S rRNA gene similarities of 99.3 and 98.1 %, respectively. A similar phylogeny was derived from partial sequences of elongation factor Tu (tuf) genes in which the alleles from the three distillery isolates were identical and shared 99.0 % similarity with L. helveticus and L. gallinarum tuf genes. S-layer (slp) gene sequences suggested different relationships among the strains and the distillery isolates no longer formed a monophyletic group. The alleles from the Japanese and Scottish strains shared only 54 % similarity. Chromosomal DNA from the distillery strains gave DNA-DNA hybridization values between 79 and 100 % but showed less than 43 and 22 % reassociation with L. helveticus and L. gallinarum DNA, respectively. The name Lactobacillus suntoryeus sp. nov. is proposed for this novel taxon; the type strain is strain SAT (=LMG 22464T=NCIMB 14005T).

  7. Paenibacillus periandrae sp. nov., isolated from nodules of Periandra mediterranea.

    PubMed

    Menéndez, Esther; Ramírez-Bahena, Martha-Helena; Carro, Lorena; Fernández-Pascual, Mercedes; Peter Klenk, Hans; Velázquez, Encarna; Mateos, Pedro F; Peix, Alvaro; Rita Scotti, Maria

    2016-04-01

    A bacterial strain designated PM10T was isolated from root nodules of Periandra mediterranea in Brazil. Phylogenetic analyses based on 16S rRNA gene sequences placed the isolate in the genus Paenibacillus with its closest relatives being Paenibacillus vulneris CCUG 53270T and Paenibacillus yunnanensis YN2T with 95.6 and 95.9% 16S rRNA gene sequence similarity, respectively. The isolate was a Gram-stain-variable, motile, sporulating rod that was catalase-negative and oxidase-positive. Caseinase was positive, amylase was weakly positive and gelatinase was negative. Growth was supported by many carbohydrates and organic acids as carbon sources. MK-7 was the only menaquinone detected and anteiso-C15 : 0 was the major fatty acid. Major polar lipids were diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol and two unidentified lipids. meso-Diaminopimelic acid was detected in the peptidoglycan. The DNA G+C content was 52.9 mol%. Phylogenetic, chemotaxonomic and phenotypic analyses showed that strain PM10T should be considered representative of a novel species of the genus Paenibacillus, for which the name Paenibacillus periandrae sp. nov. is proposed. The type strain is PM10T (=LMG 28691T=CECT 8827T). PMID:26843192

  8. Bradyrhizobium pachyrhizi sp. nov. and Bradyrhizobium jicamae sp. nov., isolated from effective nodules of Pachyrhizus erosus.

    PubMed

    Ramírez-Bahena, Martha Helena; Peix, Alvaro; Rivas, Raúl; Camacho, María; Rodríguez-Navarro, Dulce N; Mateos, Pedro F; Martínez-Molina, Eustoquio; Willems, Anne; Velázquez, Encarna

    2009-08-01

    Several strains isolated from the legume Pachyrhizus erosus were characterized on the basis of diverse genetic, phenotypic and symbiotic approaches. These novel strains formed two groups closely related to Bradyrhizobium elkanii according to their 16S rRNA gene sequences. Strains PAC48T and PAC68T, designated as the type strains of these two groups, presented 99.8 and 99.1% similarity, respectively, in their 16S rRNA gene sequences with respect to B. elkanii USDA 76T. In spite of these high similarity values, the analysis of additional phylogenetic markers such as atpD and glnII genes and the 16S-23S intergenic spacer (ITS) showed that strains PAC48T and PAC68T represented two separate novel species of the genus Bradyrhizobium with B. elkanii as their closest relative. Phenotypic differences among the novel strains isolated from Pachyrhizus and B. elkanii were found regarding the assimilation of carbon sources and antibiotic resistance. All these differences were congruent with DNA-DNA hybridization analysis which revealed 21% genetic relatedness between strains PAC48T and PAC68T and 46% and 25%, respectively, between these strains and B. elkanii LMG 6134T. The nodD and nifH genes of strains PAC48T and PAC68T were phylogenetically divergent from those of bradyrhizobia species that nodulate soybean. Soybean was not nodulated by the novel Pachyrhizus isolates. Based on the genotypic and phenotypic data obtained in this study, the new strains represent two novel species for which the names Bradyrhizobium pachyrhizi sp. nov. (type strain PAC48T=LMG 24246T=CECT 7396T) and Bradyrhizobium jicamae sp. nov. (type strain PAC68T=LMG 24556T=CECT 7395T) are proposed. PMID:19567584

  9. Rhodopirellula lusitana sp. nov. and Rhodopirellula rubra sp. nov., isolated from the surface of macroalgae.

    PubMed

    Bondoso, Joana; Albuquerque, Luciana; Lobo-da-Cunha, Alexandre; da Costa, Milton S; Harder, Jens; Lage, Olga Maria

    2014-05-01

    Twenty two strains of Rhodopirellula were isolated from the epiphytic community of several marine macroalgae and separated into two groups, designated as group B and group C. In this study, we characterized these groups as two novel species belonging to the genus Rhodopirellula. These strains were represented by pleomorphic cells that were arranged in rosettes and formed pink- or red-pigmented colonies. The organisms were chemoorganotrophic and required vitamin B12 for growth. Their optimal temperature for growth was around 25°C. Major fatty acids were C18:1 ω9c, C16:0 and C16:1 ω7c/C16:1 ω6c. Phosphatidylcholine and phosphatidylglycerol were the major polar lipids. Unidentified phospholipids were also present. The 16S rDNA sequence analysis confirmed the affiliation of these organisms to the order Planctomycetales, genus Rhodopirellula, with R. baltica as the closest phylogenetic relative. The analysis of a partial sequence of the gene encoding the β-subunit of RNA polymerase (rpoB) confirmed the phylogenetic separation of the isolates into two different species of the genus Rhodopirellula. The 16S rRNA sequences from strains of group B revealed their widespread occurrence across the world, whereas strains of group C were not observed before. On the basis of physiological, biochemical, chemotaxonomic and genetic characteristics we propose that our isolates represent two new species of Rhodopirellula, Rhodopirellula rubra sp. nov. (type strain is LF2(T)=DSM 25,459=CECT 8075) and Rhodopirellula lusitana sp. nov. (type strain is UC17(T)=DSM 25,457=LMG 27,777). PMID:24631661

  10. Actinomyces massiliensis sp. nov., isolated from a patient blood culture.

    PubMed

    Renvoise, Aurélie; Raoult, Didier; Roux, Véronique

    2009-03-01

    Gram-positive, non-spore-forming rods (strain 4401292(T)) were isolated from a human blood sample. Based on cellular morphology and the results of biochemical tests, this strain was tentatively identified as belonging to an undescribed species of the genus Actinomyces. Phylogenetic analysis based on 16S rRNA gene sequence comparison showed that the bacterium was related closely to Actinomyces gerencseriae (95.1 % 16S rRNA gene sequence similarity), Actinomyces israelii (95.2 %), Actinomyces oricola (95.2 %), Actinomyces ruminicola (93.3 %) and Actinomyces dentalis (91.4 %). The predominant fatty acids were C18 : 1omega9c and C16 : 0. On the basis of phenotypic data and phylogenetic inference, the novel species Actinomyces massiliensis sp. nov. is proposed; the type strain is 4401292(T) (=CSUR P18(T)=CCUG 53522(T)).

  11. Actinomyces suimastitidis sp. nov., isolated from pig mastitis.

    PubMed

    Hoyles, L; Falsen, E; Holmström, G; Persson, A; Sjödén, B; Collins, M D

    2001-07-01

    An unusual Actinomyces-like bacterium originating from a pig with mastitis was subjected to a polyphasic taxonomic investigation. The morphological and biochemical characteristics of the organism were consistent with its preliminary assignment to the genus Actinomyces but it did not appear to correspond to any recognized species. PAGE analysis of whole-cell proteins confirmed the phenotypic distinctiveness of the bacterium and 16S rRNA gene sequence analysis demonstrated that it represents a hitherto unknown sub-line amongst a cluster of Actinomyces species which embraces Actinomyces canis, Actinomyces georgiae, Actinomyces hyovaginalis, Actinomyces meyeri, Actinomyces odontolyticus, Actinomyces radingae and Actinomyces turicensis. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium isolated from pig mastitis be classified as Actinomyces suimastitidis sp. nov. The type strain of Actinomyces suimastitidis is CCUG 39279T (= CIP 106779T). PMID:11491328

  12. Photobacterium sanguinicancri sp. nov. isolated from marine animals.

    PubMed

    Gomez-Gil, Bruno; Roque, Ana; Rotllant, Guiomar; Romalde, Jesus L; Doce, Alejandra; Eggermont, Mieke; Defoirdt, Tom

    2016-06-01

    Six strains were isolated from the hemolymph of the spider crab Maja brachydactyla, captured in Spain, and one from a diseased blue mussel, Mytilus edulis. The 16S rRNA gene sequences showed close similarity to the recently described Photobacterium swingsii (98.1 %) and to a lesser degree to Photobacterium aquimaris (97.8 %). MLSA analyses showed a monophyletic group including P. swingsii that form a new subclade. All genomic analyses (Average Nucleotide Identity, Average Amino Acid Identity, and in silico DNA-DNA) clearly separate the strains analysed from P. swingsii with values below the thresholds to delimit a new species. The phenotypic, genotypic and genomic data presented here clearly place these strains as a coherent group within the genus Photobacterium, for which we propose the name Photobacterium sanguinicancri sp. nov. Strain CAIM 1827(T) (=CECT 7579(T), =DSM 24670(T)) is proposed as the type strain of the species. PMID:27048242

  13. Isolation and structure elucidation of a new antifungal and antibacterial antibiotic produced by Streptomyces sp. 201.

    PubMed

    Bordoloi, G N; Kumari, B; Guha, A; Bordoloi, M; Yadav, R N; Roy, M K; Bora, T C

    2001-08-01

    An antibacterial and antifungal antibiotic was isolated from the culture filtrate of Streptomyces sp. 201, and its structure was determined as 2-methyl-heptyl isonicotinate by extensive use of NMR spectroscopy. The compound exhibited marked antimicrobial activity against Bacillus subtilis, Shigella sp., Klebsiella sp., E. coli, Proteus mirabilis, and the pathogenic fungi, Fusarium moniliforme, F. semitectum, F. oxysporum, F. solani and Rhizoctonia solani.

  14. Adhaeribacter aerophilus sp. nov., Adhaeribacter aerolatus sp. nov. and Segetibacter aerophilus sp. nov., isolated from air samples.

    PubMed

    Weon, Hang-Yeon; Kwon, Soon-Wo; Son, Jung-A; Kim, Soo-Jin; Kim, Yi-Seul; Kim, Byung-Yong; Ka, Jong-Ok

    2010-10-01

    Three bacterial isolates from air samples in Korea, designated strains 6424S-25(T), 6515J-31(T) and 6424S-61(T), were characterized using a polyphasic approach. The cells were strictly aerobic, Gram-stain-negative, non-motile, non-spore-forming and rod-shaped. Phylogenetic analysis of their 16S rRNA gene sequences revealed a clear affiliation with the phylum Bacteroidetes. Strains 6424S-25(T) and 6515J-31(T) showed 16S rRNA gene sequence similarities of 92.7-94.8 % to type strains of recognized species of the genus Adhaeribacter and strain 6424S-61(T) was closely related to Segetibacter koreensis Gsoil 664(T) (93.9 % similarity). The G+C contents of the DNA of strains 6424S-25(T), 6515J-31(T) and 6424S-61(T) were 44.5, 43.9 and 38.4 mol%, respectively. Major fatty acids of strains 6424S-25(T) and 6515J-31(T) were summed feature 4 (iso-C₁₇:₁ I and/or anteiso-C₁₇ :₁ B), iso-C₁₅:₀ and C₁₆:₁ω5c. The fatty acid content of strain 6424S-61(T) mainly comprised iso-C₁₅ :₁ G and iso-C₁₅:₀. Comparative analysis of phenotypic and phylogenetic traits indicated that strains 6424S-25(T) and 6515J-31(T) represented two novel species of the genus Adhaeribacter and that strain 6424S-61(T) should be considered as a novel species of the genus Segetibacter. The names Adhaeribacter aerophilus sp. nov. (type strain 6424S-25(T) =KACC 14118(T) =NBRC 106134(T)), Adhaeribacter aerolatus sp. nov. (type strain 6515J-31(T) =KACC 14117(T) =NBRC 106133(T)) and Segetibacter aerophilus sp. nov. (type strain 6424S-61(T) =KACC 14119(T) =NBRC 106135(T)) are proposed for these organisms.

  15. Leisingera nanhaiensis sp. nov., isolated from marine sediment.

    PubMed

    Sun, Fengqin; Wang, Baojiang; Liu, Xiupian; Lai, Qiliang; Du, Yaping; Li, Guangyu; Luo, Jie; Shao, Zongze

    2010-02-01

    An aerobic, Gram-staining-negative, motile, rod-shaped bacterium, strain NH52F(T), was isolated from a sandy sediment sample taken from the South China Sea. On M2 agar medium (a complex medium), colonies were beige in colour. The isolate showed highest 16S rRNA gene sequence similarities to members of the genera Leisingera (96.7 % similarity), Phaeobacter (95.4-96.0 %) and Marinovum (94.1 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NH52F(T) formed a distinct cluster with Leisingera methylohalidivorans MB2(T) and Leisingera aquimarina LMG 24366(T). Optimal growth was observed at pH 7.0-8.5 and 25 degrees C and the new isolate required the presence of 1-4 % (w/v) NaCl. The major fatty acids were C(18 : 1)omega7c, C(16 : 0) 2-OH, C(10 : 0) 3-OH, C(12 : 0) 3-OH, C(16 : 0) and 11-methyl C(18 : 1)omega7c. The DNA G+C content was 60.5 mol%. The phylogenetic and chemotaxonomic characteristics of strain NH52F(T) were similar to those of the genus Leisingera. However, the differences in phenotypic properties and the 16S rRNA gene similarity values demonstrated that the new isolate differed from recognized species of the genus Leisingera. On the basis of phenotypic, chemotaxonomic and phylogenetic data, this organism should be classified as a representative of a novel species in the genus Leisingera, for which the name Leisingera nanhaiensis sp. nov. is proposed. The type strain is NH52F(T) (=LMG 24841(T)=CCTCC AB 208316(T)=MCCC 1A04178(T)).

  16. Staphylococcus massiliensis sp. nov., isolated from a human brain abscess.

    PubMed

    Al Masalma, Mouhamad; Raoult, Didier; Roux, Véronique

    2010-05-01

    Gram-positive, catalase-positive, coagulase-negative, non-motile, non-fermentative and novobiocin-susceptible cocci were isolated from a human brain abscess sample (strain 5402776(T)). This novel strain was analysed by a polyphasic taxonomic approach. The respiratory quinones detected were MK-7 (93 %) and MK-6 (7 %) and the major fatty acids were C(15 : 0) iso (60.5 %), C(17 : 0) iso (8.96 %) C(15 : 0) anteiso (7.93 %) and C(19 : 0) iso (6.78 %). The peptidoglycan type was A3alpha l-Lys-Gly(2-3)-l-Ser-Gly. Based on cellular morphology and biochemical criteria, the new isolate was assigned to the genus Staphylococcus, although it did not correspond to any recognized species. The G+C content of the DNA was 36.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the new isolate was most closely related to Staphylococcus piscifermentans, Staphylococcus condimenti, Staphylococcus carnosus subsp. carnosus, S. carnosus subsp. utilis and Staphylococcus simulans (97.7 %, 97.6 %, 97.6 %, 97.6 % and 96.5 % sequence similarity, respectively). Comparison of tuf, hsp60, rpoB, dnaJ and sodA gene sequences was also performed. In phylogenetic analysis inferred from tuf, dnaJ and rpoB gene sequence comparisons, strain 5402776(T) clustered with Staphylococcus pettenkoferi (93.7 %, 82.5 % and 89 % sequence similarity, respectively) and on phylogenetic analysis inferred from sodA gene sequence comparisons, it clustered with Staphylococcus chromogenes (82.8 %). On the basis of phenotypic and genotypic data, this isolate represents a novel species for which the name Staphylococcus massiliensis sp. nov. is proposed (type strain 5402776(T)=CCUG 55927(T)=CSUR P23(T)). PMID:19666814

  17. Streptococcus moroccensis sp. nov. and Streptococcus rifensis sp. nov., isolated from raw camel milk.

    PubMed

    Kadri, Zaina; Amar, Mohamed; Ouadghiri, Mouna; Cnockaert, Margo; Aerts, Maarten; El Farricha, Omar; Vandamme, Peter

    2014-07-01

    Two catalase- and oxidase-negative Streptococcus-like strains, LMG 27682(T) and LMG 27684(T), were isolated from raw camel milk in Morocco. Comparative 16S rRNA gene sequencing assigned these bacteria to the genus Streptococcus with Streptococcus rupicaprae 2777-2-07(T) as their closest phylogenetic neighbour (95.9% and 95.7% similarity, respectively). 16S rRNA gene sequence similarity between the two strains was 96.7%. Although strains LMG 27682(T) and LMG 27684(T) shared a DNA-DNA hybridization value that corresponded to the threshold level for species delineation (68%), the two strains could be distinguished by multiple biochemical tests, sequence analysis of the phenylalanyl-tRNA synthase (pheS), RNA polymerase (rpoA) and ATP synthase (atpA) genes and by their MALDI-TOF MS profiles. On the basis of these considerable phenotypic and genotypic differences, we propose to classify both strains as novel species of the genus Streptococcus, for which the names Streptococcus moroccensis sp. nov. (type strain, LMG 27682(T)  = CCMM B831(T)) and Streptococcus rifensis sp. nov. (type strain, LMG 27684(T)  = CCMM B833(T)) are proposed.

  18. Cellulomonas soli sp. nov. and Cellulomonas oligotrophica sp. nov., isolated from soil.

    PubMed

    Hatayama, Kouta; Esaki, Kouji; Ide, Teruhiko

    2013-01-01

    Two novel bacterial strains, designated Kc1(T) and Kc5(T), were isolated from soil in Japan. Cells of the novel strains were Gram-reaction-positive, aerobic or facultatively anaerobic, motile rods. Phylogenetic analyses based on 16S rRNA gene sequences indicated that both strains belonged to the genus Cellulomonas. The 16S rRNA gene sequences of strains Kc1(T) and Kc5(T) showed closest similarity to that of Cellulomonas terrae DB5(T) (98.1 % and 98.4 % similarity, respectively), and the 16S rRNA gene similarity between the two novel strains was 97.8 %. In both strains, the major menaquinone was MK-9(H(4)), the predominant polar lipids were diphosphatidylglycerol and phosphatidylinositol mannosides, and the peptidoglycan contained ornithine and glutamic acid. Cell-wall sugars were identified as rhamnose, galactose and mannose in strain Kc1(T) and rhamnose and glucose in strain Kc5(T). The DNA G+C contents of strains Kc1(T) and Kc5(T) were 73.6 mol% and 75.8 mol%, respectively. Based on the chemotaxonomic and physiological data and the results of DNA-DNA hybridizations, the two strains represent two novel species within the genus Cellulomonas, for which the names Cellulomonas soli sp. nov. (type strain Kc1(T) =DSM 24484(T) =JCM 17535(T)) and Cellulomonas oligotrophica sp. nov. (type strain Kc5(T) =DSM 24482(T) =JCM 17534(T)) are proposed.

  19. Vibrio hispanicus sp. nov., isolated from Artemia sp. and sea water in Spain.

    PubMed

    Gomez-Gil, B; Thompson, F L; Thompson, C C; Garcia-Gasca, A; Roque, A; Swings, J

    2004-01-01

    Three Gram-negative, small, motile, rod-shaped bacteria were isolated from Artemia sp. and sea water in Barcelona, Spain, during 1990 and 1991. They were fermentative, oxidase-positive, sensitive to vibriostatic agent O/129, arginine dihydrolase-positive, lysine and ornithine decarboxylase-negative and grew in the absence of NaCl. They differed from phenotypically related species by their ability to grow at 4 degrees C and utilize L-rhamnose. Cloning of the 16S rRNA gene of the type strain produced two different 16S rRNA gene sequences, which differed by 15 bases (0.99%); comparison of these sequences with those deposited in GenBank showed close relationships with Vibrio proteolyticus (97.6% similarity), Vibrio diazotrophicus (97.9%), Vibrio campbellii (96.8%) and Vibrio alginolyticus (96.8%), among others. DNA-DNA hybridization levels with the closest phylogenetically related Vibrio species were <26.4%. Sufficient evidence is provided to support the identity of the three strains analysed as members of a novel species of the genus Vibrio, for which the name Vibrio hispanicus sp. nov. is proposed, with the type strain LMG 13240T (=CAIM 525T=VIB 213T).

  20. Streptomyces graminisoli sp. nov. and Streptomyces rhizophilus sp. nov., isolated from bamboo (Sasa borealis) rhizosphere soil.

    PubMed

    Lee, Hyo-Jin; Whang, Kyung-Sook

    2014-05-01

    Four strains of actinomycete, designated strains JR-19T, JR-12, JR-29 and JR-41T were isolated from bamboo (Sasa borealis) rhizosphere soil. Phylogenetic, morphological, chemotaxonomic and phenotypic analysis demonstrated that the four strains belong to the genus Streptomyces. Microscopic observation revealed that the four strains produced spirales spore chains with spiny surfaces. The cell-wall peptidoglycan of the four strains contained ll-diaminopimelic acid, glutamic acid, alanine and glycine. Whole-cell hydrolysates mainly contained glucose and ribose. The predominant menaquinones were MK-9 (H6) and MK-9 (H8). Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that these strains and the members of the genus Streptomyces exhibited moderately high 16S rRNA gene sequence similarities of 98.3-99.3%, with the most closely related strains being Streptomyces shenzhenensis 172115T and Streptomyces gramineus JR-43T. Based on the phenotypic and genotypic data, the four strains are considered to represent two novel species of the genus Streptomyces, for which the names Streptomyces graminisoli sp. nov. [to accommodate strains JR-19T (type strain; =KACC 16472T=NBRC 108883T), JR-12 (=KACC 16471) and JR-29 (=KACC 16473)] and Streptomyces rhizophilus sp. nov. [for strain JR-41T (=KACC 16580T=NBRC 108885T)] are proposed. PMID:24478213

  1. Lactobacillus plajomi sp. nov. and Lactobacillus modestisalitolerans sp. nov., isolated from traditional fermented foods.

    PubMed

    Miyashita, Mika; Yukphan, Pattaraporn; Chaipitakchonlatarn, Winai; Malimas, Taweesak; Sugimoto, Masako; Yoshino, Mayumi; Kamakura, Yuki; Potacharoen, Wanchern; Tanasupawat, Somboon; Tanaka, Naoto; Nakagawa, Yasuyoshi; Suzuki, Ken-ichiro

    2015-08-01

    Three Lactobacillus-like strains, NB53T, NB446T and NB702, were isolated from traditional fermented food in Thailand. Comparative 16S rRNA gene sequence analysis indicated that these strains belong to the Lactobacillus plantarum group. Phylogenetic analysis based on the dnaK, rpoA, pheS and recA gene sequences indicated that these three strains were distantly related to known species present in the L. plantarum group. DNA-DNA hybridization with closely related strains demonstrated that these strains represented two novel species; the novel strains could be differentiated based on chemotaxonomic and phenotypic characteristics. Therefore, two novel species of the genus Lactobacillus, Lactobacillus plajomi sp. nov. (NB53T) and Lactobacillus modestisalitolerans sp. nov. (NB446T and NB702), are proposed with the type strains NB53T ( = NBRC 107333T = BCC 38054T) and NB446T ( = NBRC 107235T = BCC 38191T), respectively.

  2. Oceanobacillus damuensis sp. nov. and Oceanobacillus rekensis sp. nov., isolated from saline alkali soil samples.

    PubMed

    Long, Xiufeng; Ye, Renyuan; Zhang, Shuai; Liu, Bo; Zhang, Yuqin; Zeng, Zhigang; Tian, Yongqiang

    2015-09-01

    Two moderately halophilic strains, PT-11(T) and PT-20(T), were isolated from saline alkali soil samples collected in Shache County, Xinjiang Province, China. Both strains are aerobic, Gram-positive, motile rods. Strain PT-11(T) grows at 15-40 °C and at pH 6.5-10.0, while PT-20(T) grows at 15-40 °C and at pH 6.5-11.0. The major cellular fatty acids in both strains include anteiso-C15:0, anteiso-C17:0 and iso-C15:0. For both strains, the polar lipids consist of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and several unidentified lipids. In addition, strain PT-20(T) also contains phosphatidylcholine. The major isoprenoid quinone for both strains is MK-7. The genomic G+C content is 36.7 % for PT-11(T) and 39.2 % for PT-20(T). Phylogenetic analyses of 16S rRNA gene sequences indicated that these two isolates are members of the genus Oceanobacillus. DNA-DNA hybridization indicated that strains PT-11(T) and PT-20(T) should be considered two distinct species. On the basis of both phylogenetic and chemotaxonomic data analyses, therefore, we conclude that PT-11(T) and PT-20(T) represent two novel species within the genus Oceanobacillus, for which we propose the names Oceanobacillus rekensis sp. nov. and Oceanobacillus damuensis sp. nov., respectively. The type strains are PT-11(T) (=KCTC 33144(T) = DSM 26900(T)) and PT-20(T) (=KCTC 33146(T) = DSM 26901(T)).

  3. Methanobacterium petrolearium sp. nov. and Methanobacterium ferruginis sp. nov., mesophilic methanogens isolated from salty environments.

    PubMed

    Mori, Koji; Harayama, Shigeaki

    2011-01-01

    Two methane-producing archaea, designated Mic5c12(T) and Mic6c05(T), were isolated from sludge deposited in a crude oil storage tank and a tubercle on the interior of a pipe transporting natural gas-containing brine, respectively. The isolates were Gram-staining-variable, non-motile rods and grew only on H(2)/CO(2). Strain Mic6c05(T) produced methane from some alcohols without showing any growth; strain Mic5c12(T) did not utilize alcohols. The optimum growth conditions for strain Mic5c12(T) were 35 °C, pH 6.5 and 0-0.68 M NaCl and for strain Mic6c05(T) were 40 °C, pH 6.0-7.5 and 0.34 M NaCl. Strain Mic5c12(T) was halotolerant and strain Mic6c05(T) was halophilic. Comparative 16S rRNA gene sequence analysis revealed that strains Mic5c12(T) and Mic6c05(T) belonged to the genus Methanobacterium and their closest relative was Methanobacterium subterraneum A8p(T) (97.3 and 97.9 % 16S rRNA gene sequence similarity, respectively). The findings from the 16S rRNA gene sequence analyses were supported by analysis of McrA, the alpha subunit of methyl-coenzyme M reductase. On the basis of phylogenetic analyses and phenotypic characteristics, two novel species are proposed, Methanobacterium petrolearium sp. nov. and Methanobacterium ferruginis sp. nov., with type strains Mic5c12(T) (=NBRC 105198(T) =DSM 22353(T)) and Mic6c05(T) (=NBRC 105197(T) =DSM 21974(T)), respectively.

  4. Serratia myotis sp. nov. and Serratia vespertilionis sp. nov., isolated from bats hibernating in caves.

    PubMed

    García-Fraile, P; Chudíčková, M; Benada, O; Pikula, J; Kolařík, M

    2015-01-01

    During the study of bacteria associated with bats affected by white-nose syndrome hibernating in caves in the Czech Republic, we isolated two facultatively anaerobic, Gram-stain-negative bacteria, designated strains 12(T) and 52(T). Strains 12(T) and 52(T) were motile, rod-like bacteria (0.5-0.6 µm in diameter; 1-1.3 µm long), with optimal growth at 20-35 °C and pH 6-8. On the basis of the almost complete sequence of their 16S rRNA genes they should be classified within the genus Serratia; the closest relatives to strains 12(T) and 52(T) were Serratia quinivorans DSM 4597(T) (99.5 % similarity in 16S rRNA gene sequences) and Serratia ficaria DSM 4569(T) (99.5% similarity in 16S rRNA gene sequences), respectively. DNA-DNA relatedness between strain 12(T) and S. quinivorans DSM 4597(T) was only 37.1% and between strain 52(T) and S. ficaria DSM 4569(T) was only 56.2%. Both values are far below the 70% threshold value for species delineation. In view of these data, we propose the inclusion of the two isolates in the genus Serratia as representatives of Serratia myotis sp. nov. (type strain 12(T) =CECT 8594(T) =DSM 28726(T)) and Serratia vespertilionis sp. nov. (type strain 52(T) =CECT 8595(T) =DSM 28727(T)). PMID:25281728

  5. Hymenobacter latericoloratus sp. nov. and Hymenobacter luteus sp. nov., isolated from freshwater sediment.

    PubMed

    Liu, Lan; Zhou, En-Min; Jiao, Jian-Yu; Manikprabhu, Deene; Ming, Hong; Liu, Wei-Hong; Hozzein, Wael N; Shu, Wen-Sheng; Li, Wen-Jun

    2015-01-01

    Two novel Gram-stain negative, non-motile, rod-shaped and aerobic bacterial strains, designated YIM 77920(T) and YIM 77921(T), were isolated from freshwater sediment of Jiuxiang cave, a tourism cave located in Yiliang county, Yunnan province, south-west China. The 16S rRNA gene sequences of strains YIM 77920(T) and YIM 77921(T) exhibited sequence similarities of 96.59 and 96.66 % to Hymenobacter xinjiangensis X2-Y(T), respectively, and indicated that the two isolates belong to the genus Hymenobacter. The major fatty acids present in the two strains were identified as C16:1 ω5c, iso-C15:0 and Summed Feature 4 (C17:1 anteiso B/iso I). MK-7 was identified as the respiratory quinone component for both strains. The polar lipids profile of strain YIM 77920(T) was found to consist of phosphatidylethanolamine, four unidentified polar lipids, three unidentified aminophospholipids, two unidentified phospholipids and two unidentified aminolipids, while that of strain YIM 77921(T) consisted of phosphatidylethanolamine, four unidentified polar lipids, two unidentified aminolipids, one unidentified phospholipid and four unidentified aminophospholipids. The DNA G+C contents of strains YIM 77920(T) and YIM 77921(T) were determined to be 57.5 and 59.6 mol%, respectively. DNA-DNA hybridization between them had a low value (56.55 %). Based on the morphological and physiological properties, and phylogenetic analyses, strains YIM 77920(T) and YIM 77921(T) are considered to represent two novel species of the genus Hymenobacter, for which the names Hymenobacter latericoloratus sp. nov. (type strain YIM 77920(T) = JCM 30327(T) = CCTCC AB 2012949(T)) and Hymenobacter luteus sp. nov. (type strain YIM 77921(T) = JCM 30328(T) = CCTCC AB 2012947(T)) are proposed. PMID:25348876

  6. Phaeodactylibacter luteus sp. nov., isolated from the oleaginous microalga Picochlorum sp.

    PubMed

    Lei, Xueqian; Li, Yi; Wang, Guanghua; Chen, Yao; Lai, Qiliang; Chen, Zhangran; Zhang, Jingyan; Liao, Pingping; Zhu, Hong; Zheng, Wei; Zheng, Tianling

    2015-08-01

    A Gram-staining-negative, orange-pigmented, non-motile, aerobic bacterial strain, designated GYP20T, was isolated from a culture of the alga Picochlorum sp., a promising feedstock for biodiesel production, which was isolated from the India Ocean. Growth was observed at temperatures from 20 to 37 °C, salinities from 0 to 3% and pH from 5 to 9.Mg2+ and Ca2+ ions were required for growth. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the strain was a member of the genus Phaeodactylibacter, which belongs to the family Saprospiraceae. Strain GYP20T was most closely related to Phaeodactylibacter xiamenensis KD52T (95.5% sequence similarity). The major fatty acids were iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3. The predominant respiratory quinone was menaquinone-7 (MK-7). The polar lipids of strain GYP20T were found to consist of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, four unidentified glycolipids, two unidentified phospholipids and three unidentified aminolipids. According to its morphology, physiology, fatty acid composition and 16S rRNA sequence data, the novel strain most appropriately belongs to the genus Phaeodactylibacter, but can readily be distinguished from Phaeodactylibacter xiamenensis GYP20T. The name Phaeodactylibacter luteus sp. nov. is proposed with the type strain GYP20T ( = MCCC 1F01222T = KCTC 42180T).

  7. Paenibacillus cisolokensis sp. nov., isolated from litter of a geyser.

    PubMed

    Yokota, Akira; Ningsih, Fitria; Nurlaili, Dafina Ghossani; Sakai, Yasuteru; Yabe, Shuhei; Oetari, Ariyanti; Santoso, Iman; Sjamsuridzal, Wellyzar

    2016-08-01

    A Gram-stain-positive, endospore-forming, aerobic and thermophilic bacterium, designated strain LC2-13AT, was isolated from Cisolok geyser, West Java, Indonesia, at 50 °C. The isolate was rod-shaped and motile by means of peritrichous flagella. The major cellular fatty acids were iso-C16 : 0, C16 : 0 and anteiso-C15 : 0 and the major quinone was menaquinone 7. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The genomic DNA G+C content was 56.6 mol% and the major diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain LC2-13AT is related most closely to Paenibacillus kobensis DSM 10249T (94.86 % similarity), Paenibacillus tarimensis SA-7-6T (94.77 %) and Paenibacillus barengoltzii SAFN-016T (94.77 %). On the basis of phenotypic, chemotaxonomic and phylogenetic evidence, strain LC2-13AT is affiliated to the genus Paenibacillus, but could be distinguished from recognized species of this genus. A novel species with the name Paenibacillus cisolokensis sp. nov. is thus proposed. The type strain is LC2-13AT (=UICC B-42T=NRRL B-65368T=DSM 101873T).

  8. Streptococcus rubneri sp. nov., isolated from the human throat.

    PubMed

    Huch, Melanie; De Bruyne, Katrien; Cleenwerck, Ilse; Bub, Achim; Cho, Gyu-Sung; Watzl, Bernhard; Snauwaert, Isabel; Franz, Charles M A P; Vandamme, Peter

    2013-11-01

    The novel, Gram-stain-positive, ovoid, lactic acid bacterial isolates LMG 27205, LMG 27206, LMG 27207(T) and MRI-F 18 were obtained from throat samples of healthy humans. 16S rRNA gene sequence analyses indicated that these isolates belong to the genus Streptococcus, specifically the Streptococcus mitis group, with Streptococcus australis and Streptococcus mitis as the nearest neighbours (99.45 and 98.56 % 16S rRNA gene sequence similarity to the respective type strains). Genotypic fingerprinting by fluorescent amplified fragment length polymorphism (FAFLP) and pulsed-field gel electrophoresis (PFGE), DNA-DNA hybridizations, comparative sequence analysis of pheS, rpoA and atpA and physiological and biochemical tests revealed that these bacteria formed a taxon well separated from its nearest neighbours and other species of the genus Streptococcus with validly published names and, therefore, represent a novel species, for which the name Streptococcus rubneri sp. nov. is proposed, with LMG 27207(T) ( = DSM 26920(T)) as the type strain.

  9. Cellulomonas aerilata sp. nov., isolated from an air sample.

    PubMed

    Lee, Chang-Muk; Weon, Hang-Yeon; Hong, Seung-Beom; Jeon, Young-Ah; Schumann, Peter; Kroppenstedt, Reiner M; Kwon, Soon-Wo; Stackebrandt, Erko

    2008-12-01

    A Gram-positive, aerobic, motile, coccoid or short rod-shaped bacterium, 5420S-23(T), was isolated from an air sample collected in the Republic of Korea. According to phylogenetic analysis based on 16S rRNA gene sequences, strain 5420S-23(T) revealed 97.5, 97.3, 97.3 and 97.2 % similarity, respectively, to Cellulomonas biazotea DSM 20112(T), Cellulomonas cellasea DSM 20118(T), Cellulomonas fimi DSM 20113(T) and Cellulomonas chitinilytica X.bu-b(T). The peptidoglycan type of strain 5420S-23(T) was A4beta, containing l-ornithine-d-glutamic acid. The cell-wall sugars were galactose, glucose and xylose. The major fatty acids were anteiso-C(15 : 0) (49.7 %) and C(16 : 0) (20.0 %). The major menaquinone was MK-9(H(4)) and major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C content was 74 mol%. The results of DNA-DNA hybridization with strains of closely related Cellulomonas species, in combination with chemotaxonomic and physiological data, demonstrated that isolate 5420S-23(T) represents a novel Cellulomonas species, for which the name Cellulomonas aerilata sp. nov. is proposed, with strain 5420S-23(T) (=KACC 20692(T) =DSM 18649(T)) as the type strain.

  10. Nonomuraea soli sp. nov., an actinomycete isolated from soil

    PubMed Central

    Cao, Yan-Ru; Jin, Rong-Xian; He, Wen-Xiang; Jiang, Cheng-Lin

    2012-01-01

    A straight-chain, spore-forming actinobacterium, strain YIM 120770T, was isolated from soil. Phylogenetic analysis on the basis of 16S rRNA gene sequence comparisons revealed that the isolate represents a distinct cluster within the clade comprising the genus Nonomuraea and is related most closely to Nonomuraea rhizophila YIM 67092T (96.5 % similarity). Cells of strain YIM 120770T grew in the presence of 0–3 % (w/v) NaCl, at 15–37 °C and at pH 7.0–8.0. The diagnostic amino acid was meso-diaminopimelic acid, cell hydrolysates contained madurose, glucose, mannose, ribose and galactose, the predominant cellular fatty acids were 10-methyl C17 : 0 and iso-C16 : 0, and the DNA G+C content was 66.4 mol%, data consistent with affiliation of strain YIM 120770T to the genus Nonomuraea. Strain YIM 120770T shared low levels of 16S rRNA gene sequence similarity (<97 %) with the type strains of recognized species of the genus Nonomuraea and could be differentiated from its closest phylogenetic relative based on phenotypic characteristics. These results suggested that strain YIM 120770T represents a novel species of the genus Nonomuraea, for which the name Nonomuraea soli sp. nov. is proposed. The type strain is YIM 120770T ( = DSM 45533T = JCM 17347T). PMID:21890732

  11. Williamsia sterculiae sp. nov., isolated from a Chinese medicinal plant.

    PubMed

    Fang, Xiao-Mei; Su, Jing; Wang, Hao; Wei, Yu-Zhen; Zhang, Tao; Zhao, Li-Li; Liu, Hong-Yu; Ma, Bai-Ping; Klenk, Hans-Peter; Zhang, Yu-Qin; Yu, Li-Yan

    2013-11-01

    Two actinobacterial strains, CPCC 203464(T) and CPCC 203448, isolated from surface-sterilized stems of medicinal plants were subjected to a polyphasic taxonomic study. These two aerobic organisms formed pale yellow colonies on tryptic soy agar (TSA). Cells were Gram-stain-positive, non-acid-fast, non-motile, rod- or coccoid-like elements. Comparative 16S rRNA gene sequence analysis indicated that strains CPCC 203464(T) and CPCC 203448 were most closely related to the type strains of the species of the genus Williamsia. Chemotaxonomic properties such as containing meso-diaminopimelic acid in the cell wall, arabinose, galactose and ribose being the whole-cell hydrolysate sugars, phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylinositol (PI) as the phospholipids, and C16 : 0, 10-methyl C18 : 0, C18 : 1ω9c, C16 : 1ω7c and/or iso-C15 : 0 2-OH as major fatty acids supported the affiliation of strains CPCC 203464(T) and CPCC 203448 to the genus Williamsia. The DNA-DNA hybridization values in combination with differentiating chemotaxonomic and physiological characteristics strongly suggested that these two isolates should be classified as representatives of a novel species of the genus Williamsia. The name Williamsia sterculiae sp. nov. is proposed, with strain CPCC 203464(T) ( = DSM 45741(T) = KCTC 29118(T)) as the type strain.

  12. Isolation, Purification, and Characterization of Fungal Laccase from Pleurotus sp.

    PubMed Central

    More, Sunil S.; P. S., Renuka; K., Pruthvi; M., Swetha; Malini, S.; S. M., Veena

    2011-01-01

    Laccases are blue copper oxidases (E.C. 1.10.3.2 benzenediol: oxygen oxidoreductase) that catalyze the one-electron oxidation of phenolics, aromatic amines, and other electron-rich substrates with the concomitant reduction of O2 to H2O. They are currently seen as highly interesting industrial enzymes because of their broad substrate specificity. A positive strain was isolated and characterized as nonspore forming Basidiomycetes Pleurotus sp. Laccase activity was determined using ABTS as substrate. Laccase was purified by ionexchange and gel filtration chromatography. The purified laccase was a monomer showed a molecular mass of 40 ± 1 kDa as estimated by SDS-PAGE and a 72-fold purification with a 22% yield. The optimal pH and temperature were 4.5 and 65°C, respectively. The Km and Vmax values are 250 (mM) and 0.33 (μmol/min), respectively, for ABTS as substrate. Metal ions like CuSO4, BaCl2, MgCl2, FeCl2, ZnCl2 have no effect on purified laccase whereas HgCl2 and MnCl2 moderately decrease enzyme activity. SDS and sodium azide inhibited enzyme activity, whereas Urea, PCMB, DTT, and mercaptoethanol have no effect on enzyme activity. The isolated laccase can be used in development of biosensor for detecting the phenolic compounds from the effluents of paper industries. PMID:21977312

  13. Actinomadura darangshiensis sp. nov., isolated from a volcanic cone.

    PubMed

    Lee, Soon Dong; Kim, Seung Bum

    2015-05-01

    An actinobacterium, designated strain DLS-70(T), was isolated from a soil sample from the surface of a rock on the peak of Darangshi Oreum (a volcanic cone) in Jeju, Republic of Korea. Substrate mycelium was produced abundantly on most of the media tested. Spiral chains of spores with warty surface developed on the aerial hyphae. A phylogenetic tree based on 16S rRNA gene sequences showed that strain DLS-70(T) belonged to the genus Actinomadura and was most closely related to Actinomadura bangladeshensis DSM 45347(T) (98.9% sequence similarity), Actinomadura madurae DSM 43067(T) (98.8%) and Actinomadura chokoriensis DSM 45346(T) (98.6%). Chemotaxonomic observations supported the assignment of the isolate to the genus Actinomadura . DNA-DNA relatedness values between strain DLS-70(T) and the type strains of the closest phylogenetic relatives were less than 20%. On the basis of data from this polyphasic study, strain DLS-70(T) ( =KCTC 29224(T) =DSM 45941(T)) is considered to represent a novel species of the genus Actinomadura , for which the name Actinomadura darangshiensis sp. nov. is proposed.

  14. Actinomadura meridiana sp. nov., isolated from mountain soil.

    PubMed

    Lee, Soon Dong

    2012-01-01

    A novel actinomycete, designated strain DLS-45(T), was isolated from soil from the surface of a rock collected from the peak of Darangshi Oreum (Small Mountain) in Jeju, Republic of Korea. Substrate mycelium was well developed, but aerial mycelium was scant on most of the media tested. Spherical to subspherical spores on the aerial mycelium were in chains that were arranged in hooks and their surfaces were warty. The combination of morphological and chemical features supported the classification of the new isolate in the genus Actinomadura. The neighbour-joining tree based on 16S rRNA gene sequences showed that the strain belonged to the family Thermomonosporaceae and formed a coherent cluster with Actinomadura pelletieri IMSNU 22169(T) (98.0% sequence similarity). The other closest relatives were Actinomadura bangladeshensis 3-46-b(3)(T) (98.2%) and Actinomadura chokoriensis 3-25-a(11)(T) (97.9%). Levels of DNA-DNA relatedness between strain DLS-45(T) and the type strains of the phylogenetic relatives were less than 17%. A battery of phenotypic, genotypic and DNA-DNA relatedness data indicated that strain DLS-45(T) represented a novel species of the genus Actinomadura, for which the name Actinomadura meridiana sp. nov. is proposed. The type strain is strain DLS-45(T) (=KCTC 19558(T)=DSM 45252(T)).

  15. Pelistega suis sp. nov., isolated from domestic and wild animals.

    PubMed

    Vela, Ana I; Perez Sancho, Marta; Domínguez, Lucas; Busse, Hans-Jürgen; Fernández-Garayzábal, Jose F

    2015-12-01

    Biochemical and molecular genetic studies were performed on three novel Gram-stain-negative, catalase- and oxidase-positive, bacilli-shaped organisms isolated from the tonsils of two pigs and one wild boar. The micro-organism was identified as a species of the genus Pelistega based on its cellular morphological and biochemical tests. The closest phylogenetic relative of the novel bacilli was Pelistega indica HM-7T (98.2 % 16S rRNA gene sequence similarity to the type strain). groEL and gyrB sequence analysis showed interspecies divergence from the closest 16S rRNA gene phylogenetic relative, P. indica of 87.0.% and 69 %, respectively. The polyamine pattern contains predominantly putrescine and 2-hydroxyputrescine. The major quinone is ubiquinone Q-8 and in the polar lipid profile, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid and an unidentified lipid are predominant. The novel bacterial isolate can be distinguished from P. indica by several biochemical characteristics, such as the production of l-pyrrolydonil arylamidase but not gamma-glutamyl-transferase, and the utilization of different carbon sources. Based on both phenotypic and phylogenetic findings, the novel bacterium is classified as representing a novel species of the genus Pelistega, for which the name Pelistega suis sp. nov. is proposed. The type strain is 3340-03T ( = CECT 8400T = CCUG 64465T). PMID:26449759

  16. Paenibacillus cisolokensis sp. nov., isolated from litter of a geyser.

    PubMed

    Yokota, Akira; Ningsih, Fitria; Nurlaili, Dafina Ghossani; Sakai, Yasuteru; Yabe, Shuhei; Oetari, Ariyanti; Santoso, Iman; Sjamsuridzal, Wellyzar

    2016-08-01

    A Gram-stain-positive, endospore-forming, aerobic and thermophilic bacterium, designated strain LC2-13AT, was isolated from Cisolok geyser, West Java, Indonesia, at 50 °C. The isolate was rod-shaped and motile by means of peritrichous flagella. The major cellular fatty acids were iso-C16 : 0, C16 : 0 and anteiso-C15 : 0 and the major quinone was menaquinone 7. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The genomic DNA G+C content was 56.6 mol% and the major diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain LC2-13AT is related most closely to Paenibacillus kobensis DSM 10249T (94.86 % similarity), Paenibacillus tarimensis SA-7-6T (94.77 %) and Paenibacillus barengoltzii SAFN-016T (94.77 %). On the basis of phenotypic, chemotaxonomic and phylogenetic evidence, strain LC2-13AT is affiliated to the genus Paenibacillus, but could be distinguished from recognized species of this genus. A novel species with the name Paenibacillus cisolokensis sp. nov. is thus proposed. The type strain is LC2-13AT (=UICC B-42T=NRRL B-65368T=DSM 101873T). PMID:27188601

  17. Burkholderia monticola sp. nov., isolated from mountain soil.

    PubMed

    Baek, Inwoo; Seo, Boram; Lee, Imchang; Yi, Hana; Chun, Jongsik

    2015-02-01

    An ivory/yellow, Gram-stain-negative, short-rod-shaped, aerobic bacterial strain, designated JC2948(T), was isolated from a soil sample taken from Gwanak Mountain, Republic of Korea. 16S rRNA gene sequence analysis indicated that strain JC2948(T) belongs to the genus Burkholderia. The test strain showed highest sequence similarities to Burkholderia tropica LMG 22274(T) (97.6 %), Burkholderia acidipaludis NBRC 101816(T) (97.5 %), Burkholderia tuberum LMG 21444(T) (97.5 %), Burkholderia sprentiae LMG 27175(T) (97.4 %), Burkholderia terricola LMG 20594(T) (97.3 %) and Burkholderia diazotrophica LMG 26031(T) (97.1 %). Based on average nucleotide identity (ANI) values, the new isolate represents a novel genomic species as it shows less than 90 % ANI values with other closely related species. Also, other phylosiological and biochemical comparisons allowed the phenotypic differentiation of strain JC2948(T) from other members of the genus Burkholderia. Therefore, we suggest that this strain should be classified as the type strain of a novel species of the genus Burkholderia. The name Burkholderia monticola sp. nov. (type strain, JC2948(T) = JCM 19904(T) = KACC 17924(T)) is proposed.

  18. Pelistega suis sp. nov., isolated from domestic and wild animals.

    PubMed

    Vela, Ana I; Perez Sancho, Marta; Domínguez, Lucas; Busse, Hans-Jürgen; Fernández-Garayzábal, Jose F

    2015-12-01

    Biochemical and molecular genetic studies were performed on three novel Gram-stain-negative, catalase- and oxidase-positive, bacilli-shaped organisms isolated from the tonsils of two pigs and one wild boar. The micro-organism was identified as a species of the genus Pelistega based on its cellular morphological and biochemical tests. The closest phylogenetic relative of the novel bacilli was Pelistega indica HM-7T (98.2 % 16S rRNA gene sequence similarity to the type strain). groEL and gyrB sequence analysis showed interspecies divergence from the closest 16S rRNA gene phylogenetic relative, P. indica of 87.0.% and 69 %, respectively. The polyamine pattern contains predominantly putrescine and 2-hydroxyputrescine. The major quinone is ubiquinone Q-8 and in the polar lipid profile, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid and an unidentified lipid are predominant. The novel bacterial isolate can be distinguished from P. indica by several biochemical characteristics, such as the production of l-pyrrolydonil arylamidase but not gamma-glutamyl-transferase, and the utilization of different carbon sources. Based on both phenotypic and phylogenetic findings, the novel bacterium is classified as representing a novel species of the genus Pelistega, for which the name Pelistega suis sp. nov. is proposed. The type strain is 3340-03T ( = CECT 8400T = CCUG 64465T).

  19. Sphingomonas arantia sp. nov., isolated from Hoh Xil basin, China.

    PubMed

    Jia, Li; Zheng, Zhong; Feng, Xiaomin; Nogi, Yuichi; Yang, Aichen; Zhang, Yali; Han, Lu; Lu, Zhenquan; Lv, Jie

    2015-12-01

    A Gram-negative, rod-shaped, non-motile, non-spore forming, aerobic, orange-pigmented bacterium, designated strain 6P(T), was isolated from a soil sample collected from the Hoh Xil basin, China. Strain 6P(T) grew optimally at 25 °C, pH 7.0-7.5 and NaCl concentration of 0-1 % (w/v). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 6P(T) belongs to the genus Sphingomonas, with high sequence similarity (97.1 %) to Sphingomonas fennica. The DNA-DNA hybridization homology with S. fennica DSM 13665(T) was 45.3 %. The DNA G+C content of the novel strain is 65.3 mol%. The isolate contained Q-10 as the only respiratory quinone. The major polar lipids are diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC) and sphingoglycolipid (SGL). C18:1 ω7c and C16:1 ω7c are the major fatty acids. On the basis of the polyphasic evidence presented, strain 6P(T) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas arantia sp. nov. is proposed. The type strain is 6P(T) (=CGMCC 1.12702(T) = JCM 19855(T)). PMID:26363912

  20. Virgibacillus halotolerans sp. nov., isolated from a dairy product.

    PubMed

    Seiler, Herbert; Wenning, Mareike

    2013-09-01

    A Gram-stain-positive, strictly aerobic, rod-shaped and weakly motile bacterium, designated WS 4627(T), was isolated from a dairy product sample collected in southern Germany. Spherical to slightly ellipsoidal endospores were formed centrally or subterminally in sometimes slightly swollen sporangia. The isolate was able to grow at 8-35 °C, at pH 6.5-8.5 and with 0.5-16.5% (w/v) NaCl. The diamino acid of the cell wall was meso-diaminopimelic acid (peptidoglycan type A1γ) and the genomic DNA G+C content was 39.1 mol%. The major menaquinone was MK-7, the cellular fatty acid profile contained major amounts of anteiso-C(15:0) and anteiso-C(17:0) and the major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. Strain WS 4627(T) was most closely related to 'Virgibacillus natachei' FarD (96.5% 16S rRNA gene sequence similarity) and 'Virgibacillus zhanjiangensis' JSM 079157 (96.0%). Based on the data presented, strain WS 4627(T) represents a novel species of the genus Virgibacillus, for which the name Virgibacillus halotolerans sp. nov. is proposed. The type strain is WS 4627(T) ( =DSM 25060(T) =LMG 26644(T)). PMID:23504972

  1. Myroides guanonis sp. nov., isolated from prehistoric paintings.

    PubMed

    Tomova, Anna; Tomova, Iva; Vasileva-Tonkova, Evgenia; Lazarkevich, Irina; Stoilova-Disheva, Margarita; Lyutskanova, Dimitrinka; Kambourova, Margarita

    2013-11-01

    A novel psychrotolerant, strictly aerobic, non-motile, rod-shaped bacterial strain, designated IM13(T), was isolated from a sample taken from prehistoric guano paintings in Magura Cave, northwest Bulgaria and subjected to a polyphasic taxonomic study. Strain IM13(T) formed yellow colonies on LB agar plates and was Gram-staining-negative, heterotrophic and alkalitolerant. It grew optimally at pH 7.5 and 30 °C in the absence of NaCl. Phylogenetic analysis of the whole 16S rRNA gene revealed that strain IM13(T) branched with representatives of the genus Myroides with sequence similarity of 93-94 % with other species of the genus. The novel isolate contained iso-C15 : 0 (49.1 %), iso-C17 : 1ω9c (18.2 %) and iso-C17 : 0 3-OH (14.0 %) as dominant fatty acids. The DNA G+C content of strain IM13(T) was 33.5 mol%. Based on phylogenetic inference and phenotypic characteristics, it was concluded that strain IM13(T) represents a novel species of the genus Myroides, for which the name Myroides guanonis sp. nov. is proposed. The type strain is IM13(T) ( = DSM 26542(T) = NBIMCC 8736(T)).

  2. Bartonella jaculi sp. nov., Bartonella callosciuri sp. nov., Bartonella pachyuromydis sp. nov. and Bartonella acomydis sp. nov., isolated from wild Rodentia.

    PubMed

    Sato, Shingo; Kabeya, Hidenori; Fujinaga, Yuta; Inoue, Kai; Une, Yumi; Yoshikawa, Yasuhiro; Maruyama, Soichi

    2013-05-01

    Four novel strains of members of the genus Bartonella, OY2-1(T), BR11-1(T), FN15-2(T) and KS2-1(T), were isolated from the blood of wild-captured greater Egyptian jerboa (Jaculus orientalis), plantain squirrel (Callosciurus notatus), fat-tailed gerbil (Pachyuromys duprasi) and golden spiny mouse (Acomys russatus). All the animals were imported to Japan as pets from Egypt, Thailand and the Netherlands. The phenotypic characterization (growth conditions, incubation periods, biochemical properties and cell morphologies), DNA G+C contents (37.4 mol% for strain OY2-1(T), 35.5 mol% for strain BR11-1(T), 35.7 mol% for strain FN15-2(T) and 37.2 mol% for strain KS2-1(T)), and sequence analyses of the 16S rRNA genes indicated that those strains belong to the genus Bartonella. Sequence comparisons of gltA and rpoB genes suggested that all of the strains should be classified as novel species of the genus Bartonella. In phylogenetic trees based on the concatenated sequences of five loci, including the 16S rRNA, ftsZ, gltA and rpoB genes and the ITS region, and on the concatenated deduced amino acid sequences of three housekeeping genes (ftsZ, gltA and rpoB), all strains formed distinct clades and had unique mammalian hosts that could be discriminated from other known species of the genus Bartonella. These data strongly support the hypothesis that strains OY2-1(T), BR11-1(T), FN15-2(T) and KS2-1(T) should be classified as representing novel species of the genus Bartonella. The names Bartonella jaculi sp. nov., Bartonella callosciuri sp. nov., Bartonella pachyuromydis sp. nov. and Bartonella acomydis sp. nov. are proposed for these novel species. Type strains of Bartonella jaculi sp. nov., Bartonella callosciuri sp. nov., Bartonella pachyuromydis sp. nov. and Bartonella acomydis sp. nov. are OY2-1(T) ( = JCM 17712(T) = KCTC 23655(T)), BR11-1(T) ( = JCM 17709(T) = KCTC 23909(T)), FN15-2(T) ( = JCM 17714(T) = KCTC 23657(T)) and KS2-1(T) ( = JCM 17706(T

  3. Polaromonas glacialis sp. nov. and Polaromonas cryoconiti sp. nov., isolated from alpine glacier cryoconite.

    PubMed

    Margesin, Rosa; Spröer, Cathrin; Zhang, De-Chao; Busse, Hans-Jürgen

    2012-11-01

    The taxonomic positions of two Gram-staining-negative, psychrophilic bacteria, which were isolated from alpine glacier cryoconite and designated strains Cr4-12(T) and Cr4-35(T), were investigated using a polyphasic approach. Both novel strains contained ubiquinone Q-8 as the sole quinone, summed feature 3 (C(16:1)ω7c and/or C(16:1)ω6c) and C(16:0) as the dominant cellular fatty acids, putrescine and 2-hydroxyputrescine as the major polyamines, and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. The genomic DNA G+C contents of strains Cr4-12(T) and Cr4-35(T) were 61.3 mol% and 60.7 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two strains belonged to the genus Polaromonas. Although the 16S rRNA gene sequences of strains Cr4-12(T) and Cr4-35(T) were very similar (98.7% sequence similarity), hybridizations indicated a DNA-DNA relatedness value of only 26.9% between the two novel strains. In pairwise comparisons with the type strains of recognized Polaromonas species, strains Cr4-12(T) and Cr4-35(T) showed 16S rRNA gene sequence similarities of 96.4-98.5% and 96.5-98.4%, respectively. Based on the phenotypic and phylogenetic evidence and DNA-DNA relatedness data, strains Cr4-12(T) and Cr4-35(T) represent two novel species within the genus Polaromonas, for which the names Polaromonas glacialis sp. nov. and Polaromonas cryoconiti sp. nov., respectively, are proposed. The type strain of Polaromonas glacialis sp. nov. is Cr4-12(T) (=DSM 24062(T) =LMG 26049(T) =KACC 15089(T)) and that of Polaromonas cryoconiti sp. nov. is Cr4-35(T) (=DSM 24248(T) =LMG 26050(T) =KACC 15090(T)).

  4. Lysobacter tyrosinelyticus sp. nov. isolated from Gyeryongsan national park soil.

    PubMed

    Du, Juan; Singh, Hina; Ngo, Hien T T; Won, KyungHwa; Kim, Ki-Young; Yi, Tae-Hoo

    2015-06-01

    A novel Gram-negative, rod-shaped (0.2-0.5 μm × 1.5-2.5 μm), aerobic, non-motile bacterium was isolated from Gyeryongsan national park soil, Republic of Korea. The novel isolate was designated as THG-DN8.2(T). The strain grows optimally at 28 °C, at pH 7 and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequence showed that the novel isolate shared the highest sequence similarity with Lysobacter oryzae KCTC 22249(T) followed by Lysobacter yangpyeongensis KACC 11407(T) and Lysobacter niabensis KACC 11587(T). The DNA G+C content of strain THG-DN8.2T is 66.0 mol% and ubiquinone Q-8 is the main isoprenoid quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidyl-N-methylethanolamine. The major fatty acids of strain THG-DN8.2(T) were identified as iso-C15:0, iso-C16:0, and C16:1 ω7с alcohol. The phylogenetic distinctiveness and phenotypic characteristics differentiated strain THG-DN8.2(T) from closely related Lysobacter species. The results of polyphasic taxonomic analysis suggest that strain THG-DN8.2(T) represents a novel species of the genus Lysobacter, for which the name Lysobacter tyrosinelyticus sp. nov. is proposed. The type strain is THG-DN8.2(T) (= KCTC 42235(T) = JCM 30320(T)).

  5. Pseudomonas chengduensis sp. nov., isolated from landfill leachate.

    PubMed

    Tao, Yong; Zhou, Yan; He, Xiaohong; Hu, Xiaohong; Li, Daping

    2014-01-01

    Strain MBR(T) was isolated from landfill leachate in a solid-waste disposal site in Chengdu, Sichuan, China. An analysis of 16S rRNA gene sequences revealed that the isolate was closely related to members of the genus Pseudomonas, sharing the highest sequence similarities with Pseudomonas toyotomiensis HT-3(T) (99.8 %), Pseudomonas alcaliphila AL15-21(T) (99.7 %) and Pseudomonas oleovorans ATCC 8062(T) (99.4 %). Multi-locus sequence analysis based on three housekeeping genes (gyrB, rpoB and rpoD) provided higher resolution at the species level than that based on 16S rRNA gene sequences, which was further confirmed by less than 70 % DNA-DNA relatedness between the new isolate and P. toyotomiensis HT-3(T) (61.3 %), P. alcaliphila AL15-21(T) (51.5 %) and P. oleovorans ATCC 8062(T) (57.8 %). The DNA G+C content of strain MBR(T) was 61.9 mol% and the major ubiquinone was Q-9. The major cellular fatty acids (>10 %) were C18 : 1ω7c and/or C18 : 1ω6c, C16 : 0, and C16 : 1ω7c and/or C16 : 1ω6c. Polyphasic analysis indicates that strain MBR(T) represents a novel species of the genus Pseudomonas, for which the name Pseudomonas chengduensis sp. nov. is proposed. The type strain is MBR(T) ( = CGMCC 2318(T) = DSM 26382(T)). PMID:24021726

  6. Arthrobacter deserti sp. nov., isolated from a desert soil sample.

    PubMed

    Hu, Qing-Wen; Chu, Xiao; Xiao, Min; Li, Chang-Tian; Yan, Zheng-Fei; Hozzein, Wael N; Kim, Chang-Jin; Zhi, Xiao-Yang; Li, Wen-Jun

    2016-05-01

    A Gram-stain-positive, non-motile, rod-shaped, catalase-positive and oxidase-negative bacterium, designated YIM CS25T, was isolated from a soil sample collected from Turpan desert in Xinjiang Uyghur Autonomous Region, north-western China. The isolate grew at 15-40 °C, at pH 6.0-8.0 and with 0-6 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences revealed that strain YIM CS25T belonged to the genus Arthrobacter and was closely related to Arthrobacter halodurans JSM 078085T (95.89 % similarity). The peptidoglycan type contained lysine, alanine and glutamic acid. The major whole-cell sugars were galactose, glucose and ribose. The isolate contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol as the major polar lipids and MK-9 (H2) as the predominant menaquinone. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and anteiso-C17 : 1ω9c. The genomic DNA G+C content was 68.3 mol%. On the basis of phylogenetic, phenotypic and chemotaxonomic analysis, strain YIM CS25T is considered to represent a novel species of the genus Arthrobacter, for which the name Arthrobacter deserti sp. nov. is proposed. The type strain is YIM CS25T ( = KCTC 39544T = CGMCC 1.15091T). PMID:26908080

  7. Dermabacter vaginalis sp. nov., isolated from human vaginal fluid.

    PubMed

    Chang, Dong-Ho; Rhee, Moon-Soo; Kim, Byoung-Chan

    2016-04-01

    A novel actinobacterial strain, AD1-86T, was isolated from the vaginal fluid of a Korean female and was characterized by a polyphasic approach. The strain was a facultatively anaerobic, Gram-stain-positive, non-spore-forming, non-motile, catalase-positive and oxidase-negative short rod. Colonies were creamy white, of low convexity and 1-2 mm in diameter after growth on DSM 92 agar plates at 37 °C for 2 days. The most closely related strains were Dermabacter hominis DSM 7083T and Helcobacillus massiliensis 6401990T (98.3 and 96.3 % 16S rRNA gene sequence similarity, respectively). The isolate grew optimally at 37 °C and pH 7 in the presence of 0.5% (w/v) NaCl. The cell-wall peptidoglycan contained meso-diaminopimelic acid and the cell-wall hydrolysates contained ribose, galactose and glucose. The DNA G+C content was 62.6 mol% and the mean DNA-DNA relatedness value of the isolate to D. hominis DSM 7083T was 31.1±3.0% (reciprocal: 48.2±5.3%). The major cellular fatty acids (>10%) were anteiso-C17:0, anteiso-C15:0 and iso-C16:0, and the menaquinones were MK-9, MK-8 and MK-7. The polar lipid profile of strain AD1-86T consisted of diphosphatidylglycerol, phosphatidylglycerol, two aminolipids and a glycolipid. Data from this polyphasic study indicate that strain AD1-86T represents a novel species of the genus Dermabacter, for which the name Dermabacter vaginalis sp. nov. is proposed; the type strain is AD1-86T (=KCTC 39585T=DSM 100050T). PMID:26867728

  8. Bacillus vini sp. nov. isolated from alcohol fermentation pit mud.

    PubMed

    Ma, Kedong; Chen, Xiaorong; Guo, Xiang; Wang, Yanwei; Wang, Huimin; Zhou, Shan; Song, Jinlong; Kong, Delong; Zhu, Jie; Dong, Weiwei; He, Mingxiong; Hu, Guoquan; Zhao, Bingqiang; Ruan, Zhiyong

    2016-08-01

    A novel aerobic, Gram-stain-positive, sporogenous, rod-shaped bacterium, designated LAM0415(T), was isolated from an alcohol fermentation pit mud sample collected from Sichuan Luzhou-flavour liquor enterprise in China. The isolate was found to be able to grow at NaCl concentrations of 0-10 % (w/v) (optimum: 1.0 %), 10-50 °C (optimum: 30-35 °C) and pH 3.0-10.0 (optimum: 7.0-8.0). Phylogenetic analysis of 16S rRNA gene sequences indicated that the new isolate belonged to the genus Bacillus and was closely related to Bacillus sporothermodurans DSM 10599(T) and Bacillus oleronius DSM 9356(T), with 98.4 and 97.2 % sequence similarity, respectively. The DNA-DNA hybridization values between strain LAM0415(T) and the two reference strains were 33.3 ± 1.2 and 42.8 ± 0.8 %, respectively. The genomic DNA G+C content was 35.2 mol% as determined by the T m method. The major fatty acids were determined to be iso-C15:0, anteiso-C15:0 and anteiso-C17:0. The predominant menaquinones were identified as MK7 and MK8. The major polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid and four unidentified glycolipids. The diagnostic amino acid of the cell wall peptidoglycan was determined to be meso-diaminopimelic acid. On the basis of its phenotypic, phylogenetic and chemotaxonomic characteristics, strain LAM0415(T) (=ACCC 06413(T) = JCM 19841(T)) represents the type strain of a novel species of the genus Bacillus, for which the name Bacillus vini sp. nov. is proposed. PMID:27055557

  9. Streptomyces aidingensis sp. nov., an actinomycete isolated from lake sediment.

    PubMed

    Xia, Zhan-Feng; Ruan, Ji-Sheng; Huang, Ying; Zhang, Li-Li

    2013-09-01

    A novel actinomycete strain, designated TRM 46012(T), was isolated from sediment of Aiding Lake in Tulufan Basin (42° 64' N 89° 26' E), north-west China. The strain was aerobic and Gram-staining-positive with an optimum NaCl concentration for growth of 0-5% (w/v). The isolate had sparse aerial mycelium and produced bud-shaped spores at the end of the aerial mycelium on ISP medium 4. The isolate contained ll-diaminopimelic acid as the diagnostic diamino acid and ribose as the major whole-cell sugar. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannoside, one unidentified phospholipid and three unidentified glycolipids. The predominant menaquinones were MK-9(H₆), MK-9(H₈) and MK-9(H₄). The major fatty acids were iso-C(16:0), anteiso-C(17:0) and anteiso-C(15:0). The G+C content of the DNA was 74.4 mol%. Phylogenetic analysis showed that strain TRM 46012(T) had 16S rRNA gene sequence similarity of 95.7% with the most closely related species with a validly published name, Streptomyces cheonanensis, and it could be distinguished from all species in the genus Streptomyces by using the data from this polyphasic taxonomic study. On the basis of these data, strain TRM 46012(T) should be designated as a representative of a novel species of the genus Streptomyces, for which the name Streptomyces aidingensis sp. nov. is proposed. The type strain is TRM 46012(T) ( =CGMCC 4.5739(T) =NBRC 108211(T)). PMID:23456804

  10. Paenibacillus lupini sp. nov., isolated from nodules of Lupinus albus.

    PubMed

    Carro, Lorena; Flores-Félix, José David; Ramírez-Bahena, Martha-Helena; García-Fraile, Paula; Martínez-Hidalgo, Pilar; Igual, José M; Tejedor, Carmen; Peix, Alvaro; Velázquez, Encarna

    2014-09-01

    A bacterial strain designated RLAHU15(T) was isolated from root nodules of Lupinus albus in Spain. Phylogenetic analyses based on 16S rRNA gene sequences placed the isolate in the genus Paenibacillus, with its closest relatives being Paenibacillus catalpae D75(T), Paenibacillus glycanilyticus DS-1(T), Paenibacillus endophyticus PECAE04(T) and Paenibacillus xinjiangensis B538(T) with 98.8 %, 98.9 %, 97.4 % and 97.4 % similarity, respectively. DNA-DNA hybridization studies showed values lower than 45 % between the strain RLAHU15(T) and any of these species. The isolate was a Gram-stain positive, motile and sporulating rod. Catalase activity was weak and oxidase activity was positive. Casein and starch were hydrolysed but gelatin was not. Growth was supported by many carbohydrates and organic acids as carbon sources. MK-7 was the only menaquinone detected and anteiso-C15 : 0 and iso-C16 : 0 were the major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified phospholipids and an unidentified lipid. meso-Diaminopimelic acid was detected in the peptidoglycan. The DNA G+C content was 54.4 mol%. Phylogenetic, chemotaxonomic and phenotypic analyses showed that strain RLAHU15(T) represents a novel species of the genus Paenibacillus, for which the name Paenibacillus lupini sp. nov. is proposed. The type strain is RLAHU15(T) ( = LMG 27296(T) = CECT 8235(T)).

  11. Streptomyces aidingensis sp. nov., an actinomycete isolated from lake sediment.

    PubMed

    Xia, Zhan-Feng; Ruan, Ji-Sheng; Huang, Ying; Zhang, Li-Li

    2013-09-01

    A novel actinomycete strain, designated TRM 46012(T), was isolated from sediment of Aiding Lake in Tulufan Basin (42° 64' N 89° 26' E), north-west China. The strain was aerobic and Gram-staining-positive with an optimum NaCl concentration for growth of 0-5% (w/v). The isolate had sparse aerial mycelium and produced bud-shaped spores at the end of the aerial mycelium on ISP medium 4. The isolate contained ll-diaminopimelic acid as the diagnostic diamino acid and ribose as the major whole-cell sugar. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannoside, one unidentified phospholipid and three unidentified glycolipids. The predominant menaquinones were MK-9(H₆), MK-9(H₈) and MK-9(H₄). The major fatty acids were iso-C(16:0), anteiso-C(17:0) and anteiso-C(15:0). The G+C content of the DNA was 74.4 mol%. Phylogenetic analysis showed that strain TRM 46012(T) had 16S rRNA gene sequence similarity of 95.7% with the most closely related species with a validly published name, Streptomyces cheonanensis, and it could be distinguished from all species in the genus Streptomyces by using the data from this polyphasic taxonomic study. On the basis of these data, strain TRM 46012(T) should be designated as a representative of a novel species of the genus Streptomyces, for which the name Streptomyces aidingensis sp. nov. is proposed. The type strain is TRM 46012(T) ( =CGMCC 4.5739(T) =NBRC 108211(T)).

  12. Rhodanobacter umsongensis sp. nov., isolated from a Korean ginseng field.

    PubMed

    Kim, Yi-Seul; Kim, Soo-Jin; Anandham, Rangasamy; Weon, Hang-Yeon; Kwon, Soon-Wo

    2013-04-01

    A bacterial isolate designated GR24-2(T) was isolated from Korean soil used for cultivating ginseng (Panax ginseng C. A. Meyer). The strain was aerobic, Gram-negative, motile, and rod-shaped. It grew optimally at 28-30°C, pH 7.0, and in a range of 0-1% NaCl. Phylogenetically, the strain clustered with members of the genus Rhodanobacter. The strain exhibited the highest sequence similarities (>98%) with R. panaciterrae LnR5-47(T) (98.4%), R. soli DCY45(T) (98.2%), and R. ginsengisoli GR17-7(T) (98.0%). However, it also showed high sequence similarities (>97%) with some other Rhodanobacter and Dyella species. The strain contained Q-8 as the predominant respiratory quinone. The major fatty acids (greater than 10% of the total fatty acids) were iso-C17:1 ω9c (24.5%), iso-C16:0 (22.8%), anteiso-C15:0 (10.5%), and iso-C15:0 (10.1%). Its major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and an unknown aminophospholipid. The DNA G+C content of strain GR24-2(T) was 65.6 mol%. The strain showed less than 70% DNA relatedness values between the closely related Rhodanobacter and Dyella species. The phylogeny, phenotype, DNA-DNA hybridization, and chemotaxonomic data generated in this study reveal that the isolate is a novel species of the genus Rhodanobacter. The name proposed for this strain is Rhodanobacter umsongensis sp. nov. (type strain GR24-2(T) =KACC 12917(T) =DSM 21300(T)).

  13. Massilia yuzhufengensis sp. nov., isolated from an ice core.

    PubMed

    Shen, Liang; Liu, Yongqin; Wang, Ninglian; Yao, Tandong; Jiao, Nianzhi; Liu, Hongcan; Zhou, Yuguang; Xu, Baiqing; Liu, Xiaobo

    2013-04-01

    A gram-negative, rod-shaped, aerobic, motile bacterium, strain Y1243-1(T), was isolated from an ice core drilled from Yuzhufeng Glacier, Tibetan Plateau, China. Cells had polar flagella. The novel strain shared 94.7-97.6 % 16S rRNA gene sequence similarity with the type strains of species of the genus Massilia. The novel isolate is thus classified in the genus Massilia. The major fatty acids of strain Y1243-1(T) were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) (43.98 %), C16 : 0 (27.86 %), C10 : 0 3-OH (7.10 %), C18 : 0 (6.95 %) and C18 : 1ω7c (5.01 %). The predominant isoprenoid quinone was Q-8. The DNA G+C content of strain Y1243-1(T) was 65.7 mol% (Tm). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. A number of phenotypic characteristics distinguished the novel isolate from the type strains of recognized Massilia species. Furthermore, in DNA-DNA hybridization tests, strain Y1243-1(T) shared 45 % relatedness with its closest phylogenetic relative, Massilia consociata CCUG 58010(T). From the genotypic and phenotypic data, it is evident that strain Y1243-1(T) represents a novel species of the genus Massilia, for which the name Massilia yuzhufengensis sp. nov. is proposed. The type strain is Y1243-1(T) ( = KACC 16569(T) = CGMCC 1.12041(T)).

  14. Pseudonocardia sediminis sp. nov., isolated from marine sediment.

    PubMed

    Zhang, Dao-Feng; Jiang, Zhao; Li, Li; Liu, Bing-Bing; Zhang, Xiao-Mei; Tian, Xin-Peng; Zhang, Si; Li, Wen-Jun

    2014-03-01

    A Gram-stain-positive, aerobic actinomycete, designated strain YIM M13141(T), was isolated from a marine sediment sample from the South China Sea, and its taxonomic position was determined using a polyphasic approach. The strain produced branched substrate mycelium and aerial hyphae, but no diffusible pigments were produced on the media tested. At maturity, substrate mycelium was fragmented and spore chains were formed on aerial hyphae and substrate mycelium. Optimum growth occurred at 28 °C, 1-3% (w/v) NaCl and pH 7.0. Comparative analysis of the 16S rRNA gene sequence showed that the isolate belongs to the genus Pseudonocardia, showing highest levels of similarity with respect to Pseudonocardia sichuanensis KLBMP 1115(T) (97.1%), Pseudonocardia tetrahydrofuranoxydans K1(T) (97.1%) and Pseudonocardia kunmingensis YIM 63158(T) (97.0%). Whole-organism hydrolysates of the strain contained meso-diaminopimelic acid and the sugars galactose, glucose, mannose and arabinose. The predominant menaquinone was MK-8(H4). The polar lipids detected were diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, phosphatidylmethylethanolamine, phosphatidylethanolamine, two unknown phosphoglycolipids and two glycolipids. The major fatty acid was iso-C16 : 0. The G+C content of the genomic DNA was 73.1 mol%. DNA-DNA relatedness with P. tetrahydrofuranoxydans DSM 44239(T) was 42.8 ± 3.5% (mean±sd). Based on phylogenetic analysis, phenotypic and genotypic data, it is concluded that the isolate represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia sediminis sp. nov. is proposed. The type strain is YIM M13141(T) ( = DSM 45779(T) = JCM 18540(T)).

  15. Draft Genome Sequences of the Antimicrobial Producers Pseudomonas sp. TAA207 and Pseudomonas sp. TAD18 Isolated from Antarctic Sediments

    PubMed Central

    Presta, Luana; Inzucchi, Ilaria; Bosi, Emanuele; Fondi, Marco; Perrin, Elena; Maida, Isabel; Miceli, Elisangela; Tutino, Maria Luisa; Lo Giudice, Angelina; de Pascale, Donatella

    2016-01-01

    We report here the draft genome sequence of the Pseudomonas sp. TAA207 and Pseudomonas sp. TAD18 strains, isolated from Antarctic sediments during a summer campaign near coastal areas of Terra Nova Bay (Antarctica). Genome sequence knowledge allowed the identification of genes associated with the production of bioactive compounds and antibiotic resistance. Furthermore, it will be instrumental for comparative genomics and the fulfillment of both basic and application-oriented investigations. PMID:27469957

  16. Draft Genome Sequences of the Antimicrobial Producers Pseudomonas sp. TAA207 and Pseudomonas sp. TAD18 Isolated from Antarctic Sediments.

    PubMed

    Presta, Luana; Inzucchi, Ilaria; Bosi, Emanuele; Fondi, Marco; Perrin, Elena; Maida, Isabel; Miceli, Elisangela; Tutino, Maria Luisa; Lo Giudice, Angelina; de Pascale, Donatella; Fani, Renato

    2016-01-01

    We report here the draft genome sequence of the Pseudomonas sp. TAA207 and Pseudomonas sp. TAD18 strains, isolated from Antarctic sediments during a summer campaign near coastal areas of Terra Nova Bay (Antarctica). Genome sequence knowledge allowed the identification of genes associated with the production of bioactive compounds and antibiotic resistance. Furthermore, it will be instrumental for comparative genomics and the fulfillment of both basic and application-oriented investigations. PMID:27469957

  17. Isolation of Indole Utilizing Bacteria Arthrobacter sp. and Alcaligenes sp. From Livestock Waste.

    PubMed

    Kim, Minsu; Lee, Jin-Hyung; Kim, Eonmi; Choi, Hyukjae; Kim, Younghoon; Lee, Jintae

    2016-06-01

    Indole is an interspecies and interkingdom signaling molecule widespread in different environmental compartment. Although multifaceted roles of indole in different biological systems have been established, little information is available on the microbial utilization of indole in the context of combating odor emissions from different types of waste. The present study was aimed at identifying novel bacteria capable of utilizing indole as the sole carbon and energy source. From the selective enrichment of swine waste and cattle feces, we identified Gram-positive and Gram-negative bacteria belonging to the genera Arthrobacter and Alcaligenes. Bacteria belonging to the genus Alcaligenes showed higher rates of indole utilization than Arthrobacter. Indole at 1.0 mM for growth was completely utilized by Alcaligenes sp. in 16 h. Both strains produced two intermediates, anthranilic acid and isatin, during aerobic indole metabolism. These isolates were also able to grow on several indole derivatives. Interestingly, an adaptive response in terms of a decrease in cell size was observed in both strains in the presence of indole. The present study will help to explain the degradation of indole by different bacteria and also the pathways through which it is catabolized. Furthermore, these novel bacterial isolates could be potentially useful for the in situ attenuation of odorant indole and its derivatives emitted from different types of livestock waste. PMID:27570307

  18. Marinomonas gallaica sp. nov. and Marinomonas atlantica sp. nov., isolated from reared clams (Ruditapes decussatus).

    PubMed

    Lasa, Aide; Pichon, Phillip; Diéguez, Ana L; Romalde, Jesús L

    2016-08-01

    Three Gram-negative bacterial strains (Cmf 17.2T, Rd 20.33 and Cmf 18.22T) isolated from reared clams in Galicia were subjected to a taxonomic study, based on genetic and phenotypic characterization. Analysis of the 16S rRNA gene allowed the identification of the strains as members of the genus Marinomonas, sharing the highest similarity with Marinomonas aquimarina CECT 5080T (97.8 %-98.5 % 16S rRNA gene sequence similarity). Phylogenetic analysis of the sequences showed that the three isolates formed two different groups distantly related to their closest relative, M. aquimarina. DNA-DNA hybridizations were performed to confirm the taxonomic position and the results were below the recommended threshold for species delimitation, specifically 44.5 % (Cmf 17.2T with M. aquimarina CECT 5080T) and 55 % (Cmf 18.22Twith M. aquimarina CECT 5080T). Furthermore, the average nucleotide identity (ANIb, ANIm and OrthoANI) and in silico estimated DNA-DNA reassociation values among Cmf 17.2T, Cmf 18.22T and M. aquimarina CECT 5080T were in all cases below the respective threshold for species differentiation. The estimated G+C content of the genomic DNA was found to be 45.3 % (Cmf 17.2T) and 44.6 % (Cmf 18.22T). The principal fatty acids of the strains were found to be summed feature 3 (C16 : 1 ω7c/C16 : 1ω6c), summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), C16 : 0, C12 : 0 and C10 : 0 3-OH. The results obtained on the characterization of the clam isolates indicate that they represent two novel species of the genus Marinomonas, for which the names Marinomonas gallaica sp. nov. (type strain Cmf 17.2T=CECT 9049T=LMG 29243T) and Marinomonas atlantica sp. nov. (type strain Cmf 18.22T=CECT 9050T=LMG 29244T) are proposed. PMID:27199280

  19. Bifidobacterium reuteri sp. nov., Bifidobacterium callitrichos sp. nov., Bifidobacterium saguini sp. nov., Bifidobacterium stellenboschense sp. nov. and Bifidobacterium biavatii sp. nov. isolated from faeces of common marmoset (Callithrix jacchus) and red-handed tamarin (Saguinus midas).

    PubMed

    Endo, Akihito; Futagawa-Endo, Yuka; Schumann, Peter; Pukall, Rüdiger; Dicks, Leon M T

    2012-03-01

    Five strains of bifidobacteria were isolated from faeces of a common marmoset (Callithrix jacchus) and a red-handed tamarin (Saguinus midas). The five isolates clustered inside the phylogenetic group of the genus Bifidobacterium but did not show high sequence similarities between the isolates and to known species in the genus by phylogenetic analysis based on 16S rRNA gene sequences. Sequence analyses of dnaJ1 and hsp60 also indicated their independent phylogenetic positions to each other in the Bifidobacterium cluster. DNA G+C contents of the species ranged from 57.3 to 66.3 mol%, which is within the values recorded for Bifidobacterium species. All isolates showed fructose-6-phosphate phosphoketolase activity. Based on the data provided, the five isolates represent five novel species, for which the names Bifidobacterium reuteri sp. nov. (type strain: AFB22-1(T) = JCM 17295(T) = DSM 23975(T)), Bifidobacterium callitrichos sp. nov. (type strain: AFB22-5(T) = JCM 17296(T) = DSM 23973(T)), Bifidobacterium saguini sp. nov. (type strain: AFB23-1(T) = JCM 17297(T) = DSM 23967(T)), Bifidobacterium stellenboschense sp. nov. (type strain: AFB23-3(T) = JCM 17298(T) = DSM 23968(T)) and Bifidobacterium biavatii sp. nov. (type strain: AFB23-4(T) = JCM 17299(T) = DSM 23969(T)) are proposed. PMID:22225994

  20. Brucella papionis sp. nov., isolated from baboons (Papio spp.).

    PubMed

    Whatmore, Adrian M; Davison, Nicholas; Cloeckaert, Axel; Al Dahouk, Sascha; Zygmunt, Michel S; Brew, Simon D; Perrett, Lorraine L; Koylass, Mark S; Vergnaud, Gilles; Quance, Christine; Scholz, Holger C; Dick, Edward J; Hubbard, Gene; Schlabritz-Loutsevitch, Natalia E

    2014-12-01

    Two Gram-negative, non-motile, non-spore-forming coccoid bacteria (strains F8/08-60(T) and F8/08-61) isolated from clinical specimens obtained from baboons (Papio spp.) that had delivered stillborn offspring were subjected to a polyphasic taxonomic study. On the basis of 16S rRNA gene sequence similarities, both strains, which possessed identical sequences, were assigned to the genus Brucella. This placement was confirmed by extended multilocus sequence analysis (MLSA), where both strains possessed identical sequences, and whole-genome sequencing of a representative isolate. All of the above analyses suggested that the two strains represent a novel lineage within the genus Brucella. The strains also possessed a unique profile when subjected to the phenotyping approach classically used to separate species of the genus Brucella, reacting only with Brucella A monospecific antiserum, being sensitive to the dyes thionin and fuchsin, being lysed by bacteriophage Wb, Bk2 and Fi phage at routine test dilution (RTD) but only partially sensitive to bacteriophage Tb, and with no requirement for CO2 and no production of H2S but strong urease activity. Biochemical profiling revealed a pattern of enzyme activity and metabolic capabilities distinct from existing species of the genus Brucella. Molecular analysis of the omp2 locus genes showed that both strains had a novel combination of two highly similar omp2b gene copies. The two strains shared a unique fingerprint profile of the multiple-copy Brucella-specific element IS711. Like MLSA, a multilocus variable number of tandem repeat analysis (MLVA) showed that the isolates clustered together very closely, but represent a distinct group within the genus Brucella. Isolates F8/08-60(T) and F8/08-61 could be distinguished clearly from all known species of the genus Brucella and their biovars by both phenotypic and molecular properties. Therefore, by applying the species concept for the genus Brucella suggested by the ICSP

  1. Brucella papionis sp. nov., isolated from baboons (Papio spp.)

    PubMed Central

    Davison, Nicholas; Cloeckaert, Axel; Al Dahouk, Sascha; Zygmunt, Michel S.; Brew, Simon D.; Perrett, Lorraine L.; Koylass, Mark S.; Vergnaud, Gilles; Quance, Christine; Scholz, Holger C.; Dick, Edward J.; Hubbard, Gene; Schlabritz-Loutsevitch, Natalia E.

    2014-01-01

    Two Gram-negative, non-motile, non-spore-forming coccoid bacteria (strains F8/08-60T and F8/08-61) isolated from clinical specimens obtained from baboons (Papio spp.) that had delivered stillborn offspring were subjected to a polyphasic taxonomic study. On the basis of 16S rRNA gene sequence similarities, both strains, which possessed identical sequences, were assigned to the genus Brucella. This placement was confirmed by extended multilocus sequence analysis (MLSA), where both strains possessed identical sequences, and whole-genome sequencing of a representative isolate. All of the above analyses suggested that the two strains represent a novel lineage within the genus Brucella. The strains also possessed a unique profile when subjected to the phenotyping approach classically used to separate species of the genus Brucella, reacting only with Brucella A monospecific antiserum, being sensitive to the dyes thionin and fuchsin, being lysed by bacteriophage Wb, Bk2 and Fi phage at routine test dilution (RTD) but only partially sensitive to bacteriophage Tb, and with no requirement for CO2 and no production of H2S but strong urease activity. Biochemical profiling revealed a pattern of enzyme activity and metabolic capabilities distinct from existing species of the genus Brucella. Molecular analysis of the omp2 locus genes showed that both strains had a novel combination of two highly similar omp2b gene copies. The two strains shared a unique fingerprint profile of the multiple-copy Brucella-specific element IS711. Like MLSA, a multilocus variable number of tandem repeat analysis (MLVA) showed that the isolates clustered together very closely, but represent a distinct group within the genus Brucella. Isolates F8/08-60T and F8/08-61 could be distinguished clearly from all known species of the genus Brucellaand their biovars by both phenotypic and molecular properties. Therefore, by applying the species concept for the genus Brucellasuggested by the ICSP Subcommittee on

  2. Halopolyspora alba gen. nov., sp. nov., isolated from sediment.

    PubMed

    Lai, Hangxian; Wei, Xiaomin; Jiang, Yingying; Chen, Xiu; Li, Qinyuan; Jiang, Yi; Jiang, Chenglin; Gillerman, Leionid

    2014-08-01

    A novel halophilic, filamentous actinomycete, designated strain AFM 10251(T), was isolated from a sediment sample collected from the Dead Sea, Israel. The isolate grew with 10-35% multi-salts, and did not grow without NaCl or MgCl2. The isolate formed a white aerial mycelium, and long chains of arthrospores with more than 10 spores per chain. The spores were spherical or oval with warty surfaces, and sterile mycelium was present between individual spores. The isolate contained meso-diaminopimelic acid and a small proportion of LL-diaminopimelic acid as cell-wall diamino acids, and galactose and arabinose as whole-cell sugars. The major menaquinone was MK-9(H4). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol and three unknown phospholipids. Major fatty acids were iso-C(16 : 0), iso-C(17 : 0), iso-C(15 : 0) and anteiso-C(17 : 0). The DNA G+C content of strain AFM 10251(T) was 66.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AFM 10251(T) and the genus Actinopolyspora formed a distinct lineage. Analysis of the secondary structures of variable areas of the 16S rRNA gene showed that strain AFM 10251(T) was different from all recognized species of the genus Actinopolyspora and members of the family Pseudonocardiaceae. Analysis of the signature nucleotides of the 16S rRNA gene showed that strain AFM 10251(T) and Actinopolyspora halophila formed a single group, but with base pair differences at positions 127 : 234 and 183 : 194. On the basis of analysis of chemical and molecular characteristics, strain AFM 10251(T) is considered to represent a novel species of a new genus in the family Actinopolysporaceae, for which the name Halopolyspora alba gen. nov., sp. nov. is proposed. The type strain of Halopolyspora alba is AFM 10251(T) ( = DSM 45976(T) = CGMCC 4.7114(T)). PMID:24860112

  3. Flavobacterium daejeonense sp. nov. and Flavobacterium suncheonense sp. nov., isolated from greenhouse soils in Korea.

    PubMed

    Kim, Byung-Yong; Weon, Hang-Yeon; Cousin, Sylvie; Yoo, Seung-Hee; Kwon, Soon-Wo; Go, Seung-Joo; Stackebrandt, Erko

    2006-07-01

    Two yellow-pigmented, Gram-negative, rod-shaped bacterial strains, GH1-10(T) and GH29-5(T), were isolated from greenhouse soils in Korea. 16S rRNA gene sequence analysis indicated that these strains were related to members of the genus Flavobacterium. Strain GH1-10(T) was most closely related to Flavobacterium psychrolimnae and Flavobacterium denitrificans, with sequence similarities of 95.9 and 95.2 %, respectively. Strain GH29-5(T) was most closely related to "Flavobacterium saliodium", F. denitrificans and Flavobacterium frigoris, with sequence similarities of 94.3, 92.5 and 92.5 %, respectively. The major cellular fatty acids of GH1-10(T) were iso-C(15 : 0), summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c) and iso-C(17 : 0) 3-OH, and those of GH29-5(T) were iso-C(15 : 0), iso-C(17 : 0) 3-OH, iso-C(15 : 1) G and iso-C(15 : 0) 3-OH. Both strains contained menaquinone with six isoprene units (MK-6) as the sole quinone. The DNA G+C contents of GH1-10(T) and GH29-5(T) were 35 and 39 mol%, respectively. Based on the phylogenetic and phenotypic data presented, it is concluded that the two bacteria represent two separate novel species of the genus Flavobacterium. The names proposed to accommodate these organisms are Flavobacterium daejeonense sp. nov., with type strain GH1-10(T) (=KACC 11422(T)=DSM 17708(T)), and Flavobacterium suncheonense sp. nov., with type strain GH29-5(T) (=KACC 11423(T)=DSM 17707(T)).

  4. Parapedobacter luteus sp. nov. and Parapedobacter composti sp. nov., isolated from cotton waste compost.

    PubMed

    Kim, Soo-Jin; Weon, Hang-Yeon; Kim, Yi-Seul; Yoo, Seung-Hee; Kim, Byung-Yong; Anandham, Rangasamy; Kwon, Soon-Wo

    2010-08-01

    Two aerobic, Gram-reaction-negative, non-spore-forming bacterial strains, 4M29T and 4M40T, were isolated from cotton composts. The two strains grew in the presence of 0-5% (w/v) NaCl (optimum growth in the absence of NaCl), at pH 6.0-8.0 (optimum, pH 7.0) and at 15-45 degrees C (optimum, 30 degrees C). The strains shared 97.1% 16S rRNA gene sequence similarity. Strains 4M29T and 4M40T showed the next highest levels of 16S rRNA gene sequence similarity to Parapedobacter koreensis Jip14T (95.6 and 94.4%, respectively) and Parapedobacter soli DCY14T (95.2 and 93.8%). The level of DNA-DNA relatedness between strains 4M29T and 4M40T was 38%. The two strains contained iso-C15:0, summed feature 3 (comprising iso-C15:0 2-OH and/or C16:1omega7c) and iso-C17:0 3-OH as major fatty acids, MK-7 as the major respiratory quinone, homospermidine as the only polyamine and phosphatidylethanolamine as the major polar lipid. The DNA G+C contents of strains 4M29T and 4M40T were 47.6 and 48.6 mol%, respectively. On the basis of phylogenetic and phenotypic data, strains 4M29T and 4M40T are considered to represent two novel species of the genus Parapedobacter, for which the names Parapedobacter luteus sp. nov. (type strain 4M29T =KACC 10955T =JCM 15977T) and Parapedobacter composti sp. nov. (type strain 4M40T =KACC 10972T =JCM 15978T) are proposed.

  5. Deinococcus aerolatus sp. nov. and Deinococcus aerophilus sp. nov., isolated from air samples.

    PubMed

    Yoo, Seung-Hee; Weon, Hang-Yeon; Kim, Soo-Jin; Kim, Yi-Seul; Kim, Byung-Yong; Kwon, Soon-Wo

    2010-05-01

    Two strains of pink-coloured bacteria, 5516T-9(T) and 5516T-11(T), were isolated from an air sample collected in Korea. The taxonomic status of these novel strains was investigated by means of a polyphasic approach. The novel strains were Gram-positive, aerobic, non-spore-forming and coccus-shaped bacteria. The DNA G+C contents of strains 5516T-9(T) and 5516T-11(T) were 61.0 and 59.3 mol%, respectively. The major isoprenoid quinone for both strains was MK-8. Strain 5516T-9(T) contained summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c), C(16 : 0) and iso-C(17 : 1)omega9c, and strain 5516T-11(T) contained summed feature 3, iso-C(17 : 1)omega9c, C(17 : 1)omega8c and C(15 : 1)omega6c as the major fatty acids (>10 %). The polar lipid patterns of both strains were similar, comprising one phospholipid and one aminophospholipid as the major components. Phylogenetic analyses using 16S rRNA gene sequences showed that both novel strains were affiliated to the genus Deinococcus. Strain 5516T-9(T) exhibited the highest sequence similarity with Deinococcus marmoris DSM 12784(T) (96.8 %) and strain 5516T-11(T) showed the highest sequence similarity with Deinococcus saxicola DSM 15974(T) (94.5 %). The sequence similarity between strains 5516T-9(T) and 5516T-11(T) was 94.7 %. On the basis of the data presented, it is evident that both strains represent separate novel species of the genus Deinococcus for which the names Deinococcus aerolatus sp. nov. (type strain 5516T-9(T)=KACC 12745(T)=JCM 15442(T)) and Deinococcus aerophilus sp. nov. (type strain 5516T-11(T)=KACC 12746(T)=JCM 15443(T)) are proposed.

  6. Massilia jejuensis sp. nov. and Naxibacter suwonensis sp. nov., isolated from air samples.

    PubMed

    Weon, Hang-Yeon; Yoo, Seung-Hee; Kim, Soo-Jin; Kim, Yi-Seul; Anandham, Rangasamy; Kwon, Soon-Wo

    2010-08-01

    Two Gram-negative, motile, rod-shaped bacteria (strains 5317J-18T and 5414S-25T) were isolated from air samples collected in the Jeju Island and Suwon region of Korea, respectively. Phylogenetically, strain 5317J-18T was grouped with the genus Massilia with Massilia brevitalea byr23-80T as the closest relative (98.8% sequence similarity). Strain 5414S-25T was affiliated with the genus Naxibacter with Naxibacter haematophilus CCUG 38318T as the closest relative (98.8% sequence similarity). The mean DNA-DNA relatedness values between strain 5317J-18T and M. brevitalea DSM 18925T and Massilia aurea DSM 18055T were 43 and 36%, respectively. The mean DNA-DNA hybridization values between strain 5414S-25T and N. haematophilus KACC 13771T, M. brevitalea DSM 18925T, Massilia timonae DSM 16850T, Naxibacter varians KACC 13770T, M. aurea DSM 18055T, Massilia lutea DSM 17473T and Massilia albidiflava DSM 17472T ranged from 33 to 42%. Both novel strains had ubiquinone Q-8 as the predominant isoprenoid quinone and summed feature 3 (comprising iso-C15:0 2-OH and/or C16:1 omega7c) and C16:0 as the major fatty acids. Both strains also showed similar polar lipid profiles with phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as the major polar lipids. The DNA G+C contents of strains 5317J-18T and 5414S-25T were 66.1 and 67.8%, respectively. On the basis of their phenotypic, chemotaxonomic and genotypic characteristics, the new strains represent novel species in the genera Massilia and Naxibacter. Strain 5317J-18T (=KACC 12634T=DSM 21309T) is proposed as the type strain of Massilia jejuensis sp. nov. and strain 5414S-25T (=KACC 12635T=DSM 21311T) is proposed as the type strain of Naxibacter suwonensis sp. nov.

  7. Methylobacterium haplocladii sp. nov. and Methylobacterium brachythecii sp. nov., isolated from bryophytes.

    PubMed

    Tani, Akio; Sahin, Nurettin

    2013-09-01

    Pink-pigmented, facultatively methylotrophic bacteria, strains 87e(T) and 99b(T), were isolated from the bryophytes Haplocladium microphyllum and Brachythecium plumosum, respectively. The cells of both strains were Gram-reaction-negative, motile, non-spore-forming rods. On the basis of 16S rRNA gene sequence similarity, strains 87e(T) and 99b(T) were found to be related to Methylobacterium organophilum ATCC 27886(T) (97.1% and 97.7%, respectively). Strains 87e(T) and 99b(T) showed highest 16S rRNA gene similarity to Methylobacterium gnaphalii 23e(T) (98.3 and 99.0%, respectively). The phylogenetic similarities to all other species of the genus Methylobacterium with validly published names were less than 97%. Major cellular fatty acids of both strains were C(18:1)ω7c and C(18:0). The results of DNA-DNA hybridization, phylogenetic analyses based on 16S rRNA and cpn60 gene sequences, fatty acid profiles, whole-cell matrix-assisted, laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) analysis, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains 87e(T) and 99b(T) from their phylogenetically closest relatives. We propose that strains 87e(T) and 99b(T) represent novel species within the genus Methylobacterium, for which the names Methylobacterium haplocladii sp. nov. (type strain 87e(T) =DSM 24195(T) =NBRC 107714(T)) and Methylobacterium brachythecii sp. nov. (type strain 99b(T) =DSM 24105(T) =NBRC 107710(T)) are proposed.

  8. Humibacter ginsengiterrae sp. nov., and Humibacter ginsengisoli sp. nov., isolated from soil of a ginseng field.

    PubMed

    Kim, Eul-Kon; Hoang, Van-An; Kim, Yeon-Ju; Nguyen, Ngoc-Lan; Sukweenadhi, Johan; Kang, Jong-Pyo; Yang, Deok-Chun

    2015-08-01

    Two novel Gram-staining-positive bacteria, designated DCY60T and DCY90T, were isolated from soil of a ginseng field in the Republic of Korea. 16S rRNA gene sequence comparisons showed the two novel strains were closely related to members of the genus Humibacter with greatest similarity to Humibacter antri KCTC 33009T (98.8 and 98.4% for DCY60T and DCY90T, respectively). The predominant menaquinones present were MK-11 and MK-12. The major fatty acids were anteiso-C17 : 0 and summed feature 8 containing C18 : 1ω7c and/or C18 : 1ω6c. The DNA G+C contents of strains DCY60T and DCY90T were 62.8 and 66.8 mol%, respectively. The peptidoglycan of both strains contained the amino acids ornithine, 2,4-diaminobutyric acid, alanine, glutamic acid and glycine. The cell-wall sugars of strain DCY60T comprised glucose, galactose, rhamnose and xylose, while strain DCY90T contained glucose, galactose, rhamnose and ribose. The major polar lipids of both strains were phosphatidylglycerol, an unidentified glycolipid, and an unknown phospholipid. On the basis of the phenotypic analysis strains DCY60T and DCY90T represent novel species of the genus Humibacter, for which names Humibacter ginsengiterrae sp. nov. (type strain DCY60T = KCTC 33520T = JCM 30079T) and Humibacter ginsengisoli sp. nov. (type strain DCY90T = KCTC 33521T = JCM 30080T) are proposed.

  9. Paenibacillus nicotianae sp. nov., isolated from a tobacco sample.

    PubMed

    Li, Qing-Qing; Zhou, Xing-Kui; Dang, Li-Zhi; Cheng, Juan; Hozzein, Wael N; Liu, Min-Jiao; Hu, Qun; Li, Wen-Jun; Duan, Yan-Qing

    2014-12-01

    A Gram-stain positive, facultative anaerobic endospore-forming bacterium, designated strain YIM h-19(T), was isolated from a tobacco sample. Cells were observed to be motile rods by means of peritrichous flagella and colonies were observed to be convex, yellow, circular and showed catalase-positive and oxidase-negative reactions. Strain YIM h-19(T) was able to grow at 4-45 °C, pH 6.0-8.0 and 0-3 % NaCl (w/v). The predominant respiratory quinone was identified as MK-7. Major fatty acids were identified as anteiso-C15:0, anteiso-C17:0 and C16:0. The polar lipids were found to be phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and two unidentified polar lipids. The genomic DNA G+C content was determined to be 54 mol%. 16S rRNA gene sequence analysis showed the strain YIM h-19(T) was most closely related to Paenibacillus hordei RH-N24(T) and Paenibacillus hunanensis FeL05(T) with similarities of 98.30 and 94.64 % respectively. However, DNA-DNA hybridization data indicated that the isolate represented a novel genomic species with the genus Paenibacillus. All data from genotypic and phenotypic analyses support the conclusion that strain YIM h-19(T) represents a novel species of the genus Paenibacillus, for which the name Paenibacillus nicotianae sp. nov. is proposed. The type strain is YIM h-19(T) (=CGMCC1.12819(T) = NRRL B-59112(T)). PMID:25239270

  10. Cellulomonas carbonis sp. nov., isolated from coal mine soil.

    PubMed

    Shi, Zunji; Luo, Guosheng; Wang, Gejiao

    2012-08-01

    A Gram-positive, aerobic, motile, rod-shaped bacterium, designated strain T26(T), was isolated from subsurface soil of Tianjin coal mine, China. Colonies were yellow-white, convex, circular, smooth and non-transparent on R2A agar. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain T26(T) was closely related to members of the genus Cellulomonas and a member of the genus Actinotalea with 96.8-94.7% and 96.7% gene sequence similarities, respectively. The peptidoglycan type of strain T26(T) was A4β, containing l-ornithine-d-glutamic acid as the interpeptide bridge. The cell-wall sugars were rhamnose, galactose, xylose and inositol. The major fatty acids (>10%) were anteiso-C(15:0) (33.6%), anteiso-C(15:1) A (22.1%), C(16:0) (14.4%) and C(14:0) (12.1%). The predominant respiratory quinone was MK-9(H(4)) and the genomic DNA G+C content was 74.4 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol-mannosides and phosphatidylinositol. Comparison of phenotypic and phylogenetic characteristics between strain T26(T) and related organisms revealed that the new isolate represented a novel species of the genus Cellulomonas, for which the name Cellulomonas carbonis sp. nov. is proposed. The type strain is T26(T) ( = CGMCC 1.10786(T) = KCTC 19824(T) = CCTCC AB2010450(T)).

  11. Erythrobacter luteus sp. nov., isolated from mangrove sediment.

    PubMed

    Lei, Xueqian; Zhang, Huajun; Chen, Yao; Li, Yi; Chen, Zhangran; Lai, Qiliang; Zhang, Jingyan; Zheng, Wei; Xu, Hong; Zheng, Tianling

    2015-08-01

    A Gram-staining-negative, orange-pigmented, aerobic bacterial strain, designated KA37T, was isolated from a mangrove sediment sample collected from Yunxiao mangrove National Nature Reserve, Fujian Province, China. Growth was observed at 4-37 °C, 0-3% (w/v) NaCl and pH 5-10. Mg2+ ions were required for growth. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the isolate was a member of the genus Erythrobacter, which belongs to the family Erythrobacteraceae. Strain KA37T was most closely related to Erythrobacter gangjinensis KCTC 22330T (96.9% sequence similarity), followed by Erythrobacter marinus KCTC 23554T (96.8%); similarity to other members of the genus was below 96.6%. The major fatty acids were C17 : 1ω6c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). Strain KA37T did not produce bacteriochlorophyll a. The predominant respiratory quinone was ubiquinone 10 (Q-10). The polar lipids of strain KA37T were sphingoglycolipid, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, five unknown lipids and one unidentified phospholipid. According to its morphology, physiology, fatty acid composition and 16S rRNA sequence, the novel strain most appropriately belongs to the genus Erythrobacter, but can be distinguished readily from species of the genus Erythrobacter with validly published names. The name Erythrobacter luteus sp. nov. is proposed, with strain KA37T ( = MCCC 1F01227T = KCTC 42179T) as the type strain. PMID:25911535

  12. Motiliproteus sediminis gen. nov., sp. nov., isolated from coastal sediment.

    PubMed

    Wang, Zong-Jie; Xie, Zhi-Hong; Wang, Chao; Du, Zong-Jun; Chen, Guan-Jun

    2014-10-01

    A novel Gram-stain-negative, rod-to-spiral-shaped, oxidase- and catalase- positive and facultatively aerobic bacterium, designated HS6(T), was isolated from marine sediment of Yellow Sea, China. It can reduce nitrate to nitrite and grow well in marine broth 2216 (MB, Hope Biol-Technology Co., Ltd) with an optimal temperature for growth of 30-33 °C (range 12-45 °C) and in the presence of 2-3% (w/v) NaCl (range 0.5-7%, w/v). The pH range for growth was pH 6.2-9.0, with an optimum at 6.5-7.0. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that the novel isolate was 93.3% similar to the type strain of Neptunomonas antarctica, 93.2% to Neptunomonas japonicum and 93.1% to Marinobacterium rhizophilum, the closest cultivated relatives. The polar lipid profile of the novel strain consisted of phosphatidylethanolamine, phosphatidylglycerol and some other unknown lipids. Major cellular fatty acids were summed feature 3 (C(16:1) ω7c/iso-C15:0 2-OH), C(18:1) ω7c and C(16:0) and the main respiratory quinone was Q-8. The DNA G+C content of strain HS6(T) was 61.2 mol%. Based on the phylogenetic, physiological and biochemical characteristics, strain HS6(T) represents a novel genus and species and the name Motiliproteus sediminis gen. nov., sp. nov., is proposed. The type strain is HS6(T) (=ATCC BAA-2613(T)=CICC 10858(T)).

  13. Burkholderia megalochromosomata sp. nov., isolated from grassland soil.

    PubMed

    Baek, Inwoo; Seo, Boram; Lee, Imchang; Lee, Kihyun; Park, Sang-Cheol; Yi, Hana; Chun, Jongsik

    2015-03-01

    A Gram-stain negative, rod-shaped, non-spore-forming, obligate aerobic bacterial strain, JC2949(T), was isolated from grassland soil in Gwanak Mountain, Seoul, Republic of Korea. Phylogenetic analysis, based on 16S rRNA sequences, indicated that strain JC2949(T) belongs to the genus Burkholderia, showing highest sequence similarities with Burkholderia grimmiae R27(T) (98.8 %), Burkholderia cordobensis LMG 27620(T) (98.6 %), Burkholderia jiangsuensis MP-1T(T) (98.6 %), Burkholderia zhejiangensis OP-1(T) (98.5 %), Burkholderia humi LMG 22934(T) (97.5 %), Burkholderia terrestris LMG 22937(T) (97.3 %), Burkholderia telluris LMG 22936(T) (97.2 %) and Burkholderia glathei ATCC 29195(T) (97.0 %). The major fatty acids of strain JC2949(T) were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. Its predominant polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unknown amino phospholipid. The dominant isoprenoid quinone was ubiquinone Q-8. The pairwise average nucleotide identity values between strain JC2949(T) and the genomes of 30 other species of the genus Burkholderia ranged from 73.4-90.4 %, indicating that the isolate is a novel genomic species within this genus. Based on phenotypic and chemotaxonomic comparisons, it is clear that strain JC2949(T) represents a novel species of the genus Burkholderia. We propose the name for this novel species to be Burkholderia megalochromosomata sp. nov. The type strain is JC2949(T) ( = KACC 17925(T) = JCM 19905(T)).

  14. Flavobacterium palustre sp. nov., isolated from wetland soil.

    PubMed

    Feng, Hao; Zeng, Yanhua; Huang, Yili

    2015-03-01

    A Gram-staining-negative, non-motile, yellow-coloured, rod-shaped bacterium, designated S44(T), was isolated from bankside soil of Xixi wetland, located in Zhejiang province, China. Growth of strain S44(T) was observed at 6-37 °C (optimum, 28 °C) and at pH 6.0-9.0 (optimum, 7.0). No growth occurred in the presence of >2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain S44(T) represented a member of the genus Flavobacterium, showing the highest sequence similarities to the sequences from Flavobacterium succinicans DSM 4002(T) (96.9 %), Flavobacterium reichenbachii WB 3.2-61(T) (96.6 %) and Flavobacterium glycines NCBI 105008(T) (96.5 %). The G+C content of the genomic DNA was 33.6 mol%. The predominant cellular fatty acids were C15 : 0, iso-C15 : 0, anteiso-C15 : 0 and summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), and the major respiratory quinone was menaquinone 6 (MK-6). The major polar lipids were phosphatidylethanolamine, two unknown aminolipids, two unknown aminophospholipids and four unknown polar lipids. On the basis of the phenotypic and genotypic data, it is proposed that the isolate S44(T) be classified as representing a novel species of the genus Flavobacterium, for which the name Flavobacterium palustre sp. nov. is proposed. The type strain is S44(T) ( = CGMCC 1.12811(T) = NBRC 110389(T)). PMID:25563922

  15. Lysobacter agri sp. nov., a bacterium isolated from soil.

    PubMed

    Singh, Hina; Won, KyungHwa; Du, Juan; Yang, Jung-Eun; Akter, Shahina; Kim, Ki-Young; Yi, Tae-Hoo

    2015-09-01

    A bacterial strain, designated as THG-SKA3(T), was isolated from field soil of Kyung Hee University, South Korea. Cells of the isolate were observed to be Gram-negative, aerobic, rod-shaped and motile by gliding. The strain was found to grow optimally at 28 °C, at pH 7 and in absence of NaCl. Based on 16S rRNA gene sequence comparisons, strain THG-SKA3(T) shared highest sequence similarity with Lysobacter niastensis KACC 11588(T) followed by Lysobacter panacisoli KACC 17502(T), Lysobacter enzymogenes LMG 8762(T) and Lysobacter oryzae KCTC 22249(T). The G+C content of THG-SKA3(T) was determined to be 68.9 mol%. The DNA-DNA relatedness values between strain THG-SKA3(T) and its closest phylogenetic neighbors were below 25.0 %.The major polar lipids of strain THG-SKA3(T) were determined to be diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant respiratory quinone was identified as ubiquinone 8 (Q-8). The major cellular fatty acids were identified as branched chain iso-C15:0, iso-C16:0 and unsaturated iso-C17:1 ω9c. On the basis of polyphasic data presented, it is evident that strain THG-SKA3(T) represents a novel species of the genus Lysobacter, for which the name Lysobacter agri sp. nov. (type strain THG-SKA3(T) = KACC 18283(T) = CSCTCC AB 2015126(T)) is proposed. PMID:26111851

  16. Arcanobacterium pinnipediorum sp. nov., isolated from a harbour seal.

    PubMed

    Sammra, Osama; Balbutskaya, Anna; Ülbegi-Mohyla, Hivda; Nagib, Samy; Lämmler, Christoph; Kämpfer, Peter; Glaeser, Stefanie P; Golke, Jan; Busse, Hans-Jürgen; Prenger-Berninghoff, Ellen; Siebert, Ursula; Abdulmawjood, Amir; Klein, Günter

    2015-12-01

    A polyphasic taxonomic study was performed on an unidentified Arcanobacterium-like, Gram-stain-positive bacterium, strain 2710T, isolated from a harbour seal. Comparative 16S rRNA gene sequence analysis showed that this bacterial strain belonged to the genus Arcanobacterium and was related most closely to the type strains of Arcanobacterium phocae (98.4 % similarity) and Arcanobacterium phocisimile (97.5 %). 16S rRNA gene sequence similarities to the type strains of other Arcanobacterium species were between 95.3 and 96.9 %. DNA-DNA hybridization values between strain 2710T and A. phocae DSM 10002T and A. phocisimile LMG 27073T were 4.7 % (reciprocal 56 %) and 23 % (reciprocal 7.7 %), respectively. The presence of the major menaquinone MK-9(H4) and a polar lipid profile with the major compounds diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside supported the affiliation of strain 2710T to the genus Arcanobacterium. The major fatty acids were C16:0, C18:1ω9c, C18:0 and C18:2ω6,9c/anteiso-C18:0. The peptidoglycan structure was of cross-linkage type A5α (l-Lys-l-Lys-d-Glu). Physiological and biochemical tests clearly distinguished the isolate from other members of the genus Arcanobacterium. Based on these tests, it is proposed that this unknown bacterium should be classified as a novel species of the genus Arcanobacterium, with the name Arcanobacterium pinnipediorum sp. nov. The type strain is 2710T ( = DSM 28752T = LMG 28298T). PMID:26373578

  17. Lactobacillus insicii sp. nov., isolated from fermented raw meat.

    PubMed

    Ehrmann, Matthias A; Kröckel, Lothar; Lick, Sonja; Radmann, Pia; Bantleon, Annegret; Vogel, Rudi F

    2016-01-01

    The analysis of the bacterial microbiota of retain samples of pork salami revealed an isolate (strain TMW 1.2011T) that could neither be assigned to typical genera of starter organisms nor to any other known meat-associated species. Cells were Gram-stain-positive, short, straight rods occurring singly, in pairs or short chains. Phylogenetic analysis of the 16S rRNA gene sequence and specific phenotypic characteristics showed that strain TMW 1.2011T belonged to the phylogenetic Lactobacillus alimentarius group, and the closest neighbours were Lactobacillus nodensis JCM 14932T (97.8 % 16S rRNA gene sequence similarity), Lactobacillus tucceti DSM 20183T (97.4 %), 'Lactobacillus ginsenosidimutans' EMML 3041 (97.3 %), Lactobacillus versmoldensis DSM 14857T (96.9 %) and Lactobacillus furfuricola JCM 18764T (97.2 %). Similarities using partial gene sequences of the alternative chronometers pheS, dnaK and rpoA also support these relationships. DNA-DNA relatedness between the novel isolate and L. nodensis JCM 14932T, L. versmoldensis DSM 14857T and L. tucceti DSM 20183T, L. furfuricola JCM 18764T and 'L. ginsenosidimutans' EMML 3041 were below 70 % and the DNA G+C content was 36.3 mol%. The cell-wall peptidoglycan type is l-Lys-Gly-d-Asp. Based on phylogenetic, chemotaxonomic and physiological evidence, strain TMW 1.2011T represents a novel species of the genus Lactobacillus, for which the name Lactobacillus insicii sp. nov. is proposed. The type strain is TMW 1.2011T ( = CECT 8802T = DSM 29801T).

  18. Cohnella saccharovorans sp. nov., isolated from ginseng soil.

    PubMed

    Choi, Jung-Hye; Seok, Ji-Hye; Jang, Ho-Jin; Cha, Ju-Hee; Cha, Chang-Jun

    2016-04-01

    A novel bacterial strain, CJ22T, was isolated from soil of a ginseng field located in Anseong, Korea. Cells of strain CJ22T were aerobic, Gram-stain-positive, endospore-forming, motile, oxidase- and catalase-positive and rod-shaped. The isolate grew optimally at pH 7 and 30 °C. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain CJ22T belonged to the genus Cohnella, displaying highest sequence similarity of 97.3% with Cohnella panacarvi Gsoil 349T. DNA-DNA relatedness between strain CJ22T and its closest relative was 35.5 % (reciprocal value, 23.8%). The phenotypic features of strain CJ22T also distinguished it from related species of the genus Cohnella. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major isoprenoid quinone was menaquinone MK-7 and the major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, lysyl-phosphatidylglycerol, two unidentified phospholipids and two unidentified aminophospholipids. The predominant cellular fatty acids of strain CJ22T were anteiso-C15 : 0, iso-C16:0 and C16:0. The DNA G+C content was 63.1 mol%. Based on data from this polyphasic taxonomic study, strain CJ22T is considered to represent a novel species of the genus Cohnella, for which the name Cohnella saccharovorans sp. nov. is proposed. The type strain is CJ22T (=KACC 17501T=JCM 19227T).

  19. Chryseobacterium panacis sp. nov., isolated from ginseng soil.

    PubMed

    Singh, Priyanka; Kim, Yeon-Ju; Farh, Mohamed El-Agamy; Dan, Wang Dan; Kang, Chang Ho; Yang, Deok-Chun

    2016-02-01

    A novel strain, DCY107(T), was isolated from soil collected from a ginseng field in Gochang, Republic of Korea. Strain DCY107(T) is Gram-negative, yellow pigmented, non-motile, non-flagellate, rod-shaped and aerobic. The strain was found to grow optimally at 25-30 °C and pH 6.5-7. Phylogenetically, strain DCY107(T) is closely related to Chryseobacterium polytrichastri DSM 26899(T) (98.49 % 16S rRNA gene sequence similarity), Chryseobacterium yeoncheonense JCM 18516(T) (97.78 %), Chryseobacterium aahli LMG 27338(T) (97.74 %), Chryseobacterium limigenitum LMG28734(T) (97.74 %), Chryseobacterium ginsenosidimutans JCM 16719(T) (97.47 %) and Chryseobacterium gregarium LMG 24052(T) (97.31 %). The DNA-DNA relatedness values between strain DCY107(T) and reference strains were found to be clearly below 70 %. The DNA G+C content of strain DCY107(T) was determined to be 34.2 mol%. The predominant quinone was identified menaquinone 6 (MK-6). The major polar lipids were identified as phosphatidylethanolamine and unidentified lipids: aminolipids AL1, AL2 and lipid L2. C16:00, iso-C15:00, iso-C15:02OH, iso-C17:03OH and summed feature 9 (iso-C17:1 ω9c and/or C16:0 10-methyl) were identified as the major fatty acids present in strain DCY107(T). The results of physiological and biochemical tests allowed strain DCY107(T) to be differentiated phenotypically from other recognised species belonging to the genus Chryseobacterium. Therefore, it is suggested that the newly isolated organism represents a novel species, for which the name Chryseobacterium panacis sp. nov. is proposed, with the type strain designated as DCY107(T) (=CCTCC AB 2015195(T) = KCTC 42750(T)).

  20. Bacillus panacisoli sp. nov., isolated from ginseng soil.

    PubMed

    Choi, Jung-Hye; Cha, Chang-Jun

    2014-03-01

    A Gram-staining-positive, motile, facultatively anaerobic, endospore-forming and rod-shaped bacterium, designated strain CJ32(T), was isolated from ginseng soil at Geumsan in Korea. The isolate grew optimally at 30 °C, 2% (w/v) NaCl and pH 7.0. Colonies of strain CJ32(T) were beige and circular with an entire margin on LB agar plates. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CJ32(T) was associated with the genus Bacillus and was most closely related to Bacillus graminis YC6957(T) (97.3% similarity) and Bacillus lentus IAM 12466(T) (97.1%). DNA-DNA hybridization with closely related strains was below 31.3%. The major respiratory isoprenoid quinone was MK-7. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The polar lipid profile of strain CJ32(T) consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several unidentified lipids, including phospholipids, aminolipids and aminophospholipids. The predominant fatty acids of strain CJ32(T) were iso-C15:0 and anteiso-C15:0. The G+C content of the genomic DNA was 35.1 mol%. Based on phenotypic, genotypic and phylogenetic data, strain CJ32(T) should be classified within a novel species of the genus Bacillus, for which the name Bacillus panacisoli sp. nov. is proposed. The type strain is strain CJ32(T) ( = KACC 17503(T) = JCM 19226(T)).

  1. Chitinophaga ginsengihumi sp. nov., isolated from soil of ginseng rhizosphere.

    PubMed

    Lee, Jae-Chan; Whang, Kyung-Sook

    2014-08-01

    A novel strain designated SR18(T) was isolated from the rhizosphere soil of a ginseng in Korea. Cells were Gram-staining-negative, motile by gliding, catalase-positive and oxidase-negative, non-spore-forming rods. The isolate grew aerobically at 15-45 °C (optimum 28 °C), pH 5.5-7.5 (optimum pH 7.0) and with 0-3.0% (w/v) NaCl (optimum 1.5% NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain SR18(T) belongs to the genus Chitinophaga with sequence similarity of 97.2% and 97.0% to Chitinophaga japonensis 758(T) and Chitinophaga rupis CS5-B1(T), respectively. Similarity to other species of the genus Chitinophaga was 92.8-95.5%. The predominant menaquinone was MK-7. Major fatty acids were iso-C(15 : 0) and C(16 : 1)ω5c. The polar lipids included phosphatidylethanolamine, unidentified phospholipids, unknown aminolipids and unknown lipids. The genomic DNA G+C content was 45.3 mol%. DNA-DNA relatedness between strain SR18(T) and C. japonensis NBRC 16041(T) was 29-32%. On the basis of polyphasic analysis from this study, strain SR18(T) represents a novel species of the genus Chitinophaga, for which the name Chitinophaga ginsengihumi sp. nov. is proposed. The type strain is SR18(T) ( = KACC 17604(T) = NBRC 109832(T)).

  2. Sphingomonas panacis sp. nov., isolated from rhizosphere of rusty ginseng.

    PubMed

    Singh, Priyanka; Kim, Yeon-Ju; Hoang, Van-An; Farh, Mohamed El-Agamy; Yang, Deok-Chun

    2015-09-01

    The type strain DCY99(T) was isolated from soil collected from a ginseng field in Hwacheon, Republic of Korea. Strain DCY99(T) is Gram-negative, non-spore forming, motile, rod-shaped, and strictly aerobic. The bacteria grow optimally at 25-30 °C and pH 6.0-6.5. Phylogenetically, strain DCY99(T) is most closely related to Sphingomonas oligophenolica JCM 12082(T), followed by Sphingomonas asaccharolytica KCTC 2825(T), Sphingomonas mali KCTC 2826(T), Sphingomonas cynarae JCM17498(T), Sphingomonas pruni KCTC 2824(T), and Sphingomonas glacialis DSM 22294(T). The DNA-DNA relatedness between strain DCY99(T) and S. oligophenolica JCM 12082(T) was 15.6 ± 0.4 %, and the DNA G+C content of strain DCY99(T) was 64.4 mol%. An isoprenoid quinone was detected and identified as ubiquinone Q-10, and sym-homospermidine was identified as the major polyamine of DCY99(T). The major polar lipids were identified as sphingoglycolipid, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylcholine. C14:02OH, C16:0, and summed feature 8 (C18:1 ω7c:/C18:1 ω6c) were identified as the major fatty acids present in DCY99(T). The results of physiological and biochemical tests allowed strain DCY99(T) to be differentiated phenotypically from other recognized species belonging to the genus Sphingomonas. Therefore, it is suggested that the newly isolated organism represents a novel species, for which the name Sphingomonas panacis sp. nov. is proposed with the type strain designated as DCY99(T) (=JCM 30806(T) =KCTC 42347(T)).

  3. Chryseobacterium carnipullorum sp. nov., isolated from raw chicken.

    PubMed

    Charimba, George; Jooste, Piet; Albertyn, Jacobus; Hugo, Celia

    2013-09-01

    Three Gram-staining-negative, rod-shaped, non-spore-forming, non-motile, oxidase-positive, yellow pigmented and aerobic bacterial isolates designated 8_R23573, 9_R23581(T) and 10_R23577 were isolated from raw chicken at a broiler processing plant in Bloemfontein, South Africa. A polyphasic taxonomic approach was used to determine their exact taxonomic identities. Phylogenetic analysis of the 16S rRNA gene sequences showed that the three strains belonged to the genus Chryseobacterium, exhibiting the highest similarities to Chryseobacterium shigense DSM 17126(T) (98.6-99.2%) and Chryseobacterium luteum DSM 18605(T) (98.3-98.7%). The most abundant quinone was menaquinone MK-6 and the predominant cellular fatty acids were iso-15:0, iso-17:1ω9c, iso-17:0 3-OH and summed feature 3 (iso-16:1ω7c and/or iso-15:0 2-OH), which supported the affiliation of the strains to the genus Chryseobacterium. The DNA G+C contents of the strains were 36.9, 36.7 and 36.6 mol% respectively. The DNA-DNA hybridization results gave relatedness values ranging from 78.8 to 87.2% among the three strains and 23.4 to 56.1% to the two nearest phylogenetic neighbours C. shigense DSM 17126(T) and C. luteum LMG 23785(T). On the basis of the data from this polyphasic study, the three strains are concluded to represent a novel species of the genus Chryseobacterium for which the name Chryseobacterium carnipullorum sp. nov. is proposed. The type strain is 9_R23581(T) ( = LMG 26732(T) =DSM 25581(T)).

  4. Algoriphagus aquaeductus sp. nov., isolated from a freshwater pipe.

    PubMed

    Rau, Jan Erik; Blotevogel, Karl-Heinz; Fischer, Ulrich

    2012-03-01

    A Gram-staining-negative, aerobic to microaerophilic, rod-shaped, red-coloured bacterium, strain T4(T), was isolated from a freshwater pipe on Tenerife island. A polyphasic taxonomic study was performed in order to characterize the strain in detail. The isolate is surrounded by a slime capsule, occurs singly, in the form of short chains, or in aggregates, and exhibits catalase and oxidase activities. Growth was observed at 15-42 °C. Optimum growth occurred at pH 8 with mono- and disaccharides, followed by polysaccharides and deoxysaccharides, but the bacterium utilized only a restricted spectrum of alcohols, alditols, amides, amines, carboxylic acids and amino acids. Strain T4(T) tolerated concentrations of 0-4% (w/v) NaCl and contained MK-7 as predominant isoprenoid quinone as well as carotenoids, but lacked pigments of the flexirubin type. The predominant fatty acids were iso-C(15:0) (32.2%), summed feature 3 (C(16:1)ω6c and/or C(16:1)ω7c; 22.5%), and iso-C(17:0) 3-OH (7.9%). Major polar lipids were phosphatidylethanolamine, phospholipids, aminophospholipids and other lipids of unknown character. The DNA G+C content was approximately 41.8 mol%. The sequence of the 16S-rRNA gene assigned strain T4(T) to the CFB group, forming a coherent cluster with species of the genus Algoriphagus with the highest similarity of 98.8% to Algoriphagus aquatilis A8-7(T). DNA-DNA hybridization revealed 37.5% relatedness to strain A8-7(T). Based on morphological, physiological and molecular properties as well as on phylogenetic distinctiveness, strain T4(T) should be placed into the genus Algoriphagus as a novel species, for which the name Algoriphagus aquaeductus sp. nov. (type strain T4(T) =DSM 19759(T) =LMG 24398(T) =NCIMB 14399(T)) is proposed.

  5. Streptomyces calidiresistens sp. nov., isolated from a hot spring sediment.

    PubMed

    Duan, Yan-Yan; Ming, Hong; Dong, Lei; Yin, Yi-Rui; Zhang, Yi; Zhou, En-Min; Liu, Lan; Nie, Guo-Xing; Li, Wen-Jun

    2014-08-01

    A Streptomyces-like actinomycete strain, designated as YIM 78087(T), was isolated from a sediment sample collected from Hehua hot spring in Tengchong, Yunnan province, south-west China. The taxonomic position of strain YIM 78087(T) was investigated by a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain YIM 78087(T) belongs to the genus Streptomyces and is closely related to Streptomyces fimbriatus DSM 40942(T), Streptomyces marinus DSM 41968(T) and Streptomyces qinglanensis DSM 42035(T) (97.18, 97.05 and 97.1 % similarity, respectively). Combined with the low values of DNA-DNA hybridization between strain YIM 78087(T) and its closest neighbours, these analyses indicated that this new isolate represents a different genomic species in the genus Streptomyces. The predominant menaquinones of strain YIM 78087(T) were identified as MK-9 (H4) and MK-9 (H6). The major fatty acids were identified as anteiso-C15:0 (28.4 %), anteiso-C17:0 (23.0 %) and iso-C16:0 (15.1 %). The whole-cell hydrolysates found to contain glucose, mannose and ribose. The DNA G+C content was determined to be 73.0 mol%. Based on the comparative analysis of phenotypic and genotypic characteristics, it is proposed that strain YIM 78087(T) represents a novel species of the genus Streptomyces, for which the name Streptomyces calidiresistens sp. nov., is proposed. The type strain is YIM 78087(T) (=BCRC 16955(T)=DSM 42108(T)=JCM 19629(T)).

  6. Deinococcus enclensis sp. nov., isolated from a marine sediment sample.

    PubMed

    Thorat, Meghana N; Mawlankar, Rahul; Sonalkar, Vidya V; Venkata Ramana, V; Joseph, Neetha; Shouche, Yogesh S; Dastager, Syed G

    2015-01-01

    A novel pale-pink coloured strain, designated NIO-1023(T), was isolated from a marine sediment sample from Chorao Island, Goa, India. The taxonomic position of strain NIO-1023(T) was investigated by using a polyphasic approach. The cells were observed to be Gram-stain positive, coccal shaped and non-spore forming. Phylogenetic analyses using the 16S rRNA gene sequence of the isolate indicated that the organism belongs to the genus Deinococcus. The strain NIO-1023(T) showed highest 16S rRNA gene sequence similarities with Deinococcus ficus (97.8 %), whereas other Deinococcus species showed less than 95 % sequence similarity. The DNA-DNA relatedness with respect to D. ficus CC-FR2-10(T) was 23.9 %. Chemotaxonomic data revealed that strain NIO-1023(T) contains only menaquinone MK-8 as the respiratory quinone and a complex polar lipid profile consisting of different unidentified glycolipids and polar lipids, two unknown phospholipids and three unknown phosphoglycolipids. As in other deinococci, one of these phosphoglycolipids was predominant in the profile. The predominant fatty acids were identified as C17:1 w8c, C16:1 w6c/w7c, C15:1 w6c and C17:1 w9c. The genomic DNA G + C content of strain NIO-1023(T) was determined to be 67.2 mol%. The biochemical and chemotaxonomic properties demonstrate that strain NIO-1023(T) represents a novel species, for which the name Deinococcus enclensis sp. nov. is proposed. The type strain is NIO-1023(T) (=DSM 25127(T) = NCIM 5456(T)).

  7. Hymenobacter terrae sp. nov., a bacterium isolated from soil.

    PubMed

    Srinivasan, Sathiyaraj; Lee, Jae-Jin; Park, Kyoung Ryun; Park, Se-Hee; Jung, Hee-Young; Kim, Myung Kyum

    2015-05-01

    A Gram-negative, UV tolerant bacterial strain, DG7A(T), was isolated from soil samples collected in Seoul city, South Korea. The cells were grown on R2A agar at 25 °C and were pink to red in color. The DNA G+C content of the novel strain DG7A was 63.5 mol%. Chemotaxonomic data revealed that the strains contain the major fatty acids iso-C15:0, anteiso-C15:0, and summed feature 3 (16:1 ω7c/16:1 ω6c), with phosphatidylethanolamine as the major polar lipid. Phylogenetic analysis of the 16S rRNA gene sequences showed that strain DG7A(T) formed a distinct phylogenetic line along with Hymenobacter soli PB17(T), and they shared approximately 98.35 % 16S rRNA gene sequence similarity. However, these two strains shared only 5.3 % pairwise similarity (reciprocal analysis, 36.3 %) in their genomic DNA. The next highest degree of 16S rRNA gene sequence similarity after H. soli PB17(T) was found with H. glaciei VUG-A130(T) (96.78 %), H. antarcticus VUG-A42aa(T) (96.66 %), and H. saemangeumensis GSR0100(T) (96.57 %). Based on the phylogenetic analysis and analysis of the physiological and biochemical characteristics, this isolate was considered to represent a novel species, for which we propose the name Hymenobacter terrae sp. nov., with type strain DG7A(T) (= KCTC 32554(T) = KEMB 9004-164(T )= JCM 30007(T)). PMID:25572492

  8. Lactobacillus mixtipabuli sp. nov. isolated from total mixed ration silage.

    PubMed

    Tohno, Masanori; Kitahara, Maki; Irisawa, Tomohiro; Ohmori, Hideyuki; Masuda, Takaharu; Ohkuma, Moriya; Tajima, Kiyoshi

    2015-06-01

    Using a polyphasic taxonomic approach, we investigated three bacterial strains - IWT30T, IWT8 and IWT75 - isolated from total mixed ration silage prepared in Hachimantai, Iwate, Japan. The isolates comprised Gram-stain positive, non-motile, non-spore-forming, catalase-negative, rod-shaped bacteria. Good growth occurred at 15-45 °C and at pH 4.0-7.5. Their major cellular fatty acids were C18:1ω9c and C19:1 cyclo 9,10.The G+C content of genomic DNA of strain IWT30T was 44.6 mol%. Comparative 16S rRNA gene sequence analysis showed that these novel strains belonged to the genus Lactobacillus. These strains shared 100 % 16S rRNA gene sequence similarity and were most closely related to the type strains of Lactobacillus silagei, Lactobacillus odoratitofui, Lactobacillus similis, Lactobacillus collinoides, Lactobacillus paracollinoides and Lactobacillus kimchicus, with sequence similarity values of 99.5, 98.8, 98.7, 97.8, 97.8 and 96.8 %, respectively. The level of DNA-DNA relatedness between these strains and their closest phylogenetic neighbours was less than 30 %. On the basis of additional phylogenetic analysis of pheS and rpoA gene sequences and phenotypic and chemotaxonomic characteristics, we conclude that these three strains represent a novel species of the genus Lactobacillus, for which we propose the name Lactobacillus mixtipabuli sp. nov. The type strain is IWT30T ( = JCM 19805T = DSM 28580T).

  9. Altererythrobacter aurantiacus sp. nov., isolated from deep-sea sediment.

    PubMed

    Zhang, Gaiyun; Yang, Yanliu; Wang, Lina

    2016-09-01

    A Gram-negative, aerobic, coccoid bacterium, strain O30(T), was isolated from a deep-sea sediment sample collected from the west Pacific. 16S rRNA gene sequence analysis revealed that this strain is affiliated with the family Erythrobacteraceae in the class Alphaproteobacteria, and is closely related to the members of the genera Erythromicrobium (96.6 %), Porphyrobacter (95.5-96.3 %), Altererythrobacter (94.1-96.2 %) and Erythrobacter (94.2-96.2 %). Phylogenetic analysis including all described species of the family Erythrobacteraceae revealed that the isolate forms a clade in the cluster of the genus Altererythrobacter. Strain O30(T) was found to grow at 4-40 °C, pH 6.0-10.0 and in the presence of 0.5-7.0 % (w/v) NaCl. Chemotaxonomic analysis revealed ubiquinones Q-8, Q-9 and Q-10 as the predominant respiratory quinones, summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C17:1 ω6c and C16:0 as major fatty acids, and diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid as the major polar lipids. The DNA G + C content was determined to be 56.9 mol %. On the basis of phenotypic and genotypic data presented in this study, strain O30(T) represents a novel species within the genus Altererythrobacter, for which the name Altererythrobacter aurantiacus sp. nov. is proposed; the type strain is O30(T) (= CGMCC 1.12762(T) = JCM 19853(T) = LMG 28110(T) = MCCC 1A09962(T)). PMID:27371378

  10. Sphingomonas faucium sp. nov., isolated from canyon soil.

    PubMed

    Liu, Dongmei; Jin, Xin; Sun, Xuelian; Song, Yali; Feng, Liling; Wang, Gejiao; Li, Mingshun

    2016-08-01

    A Gram-stain-negative, strictly aerobic, non-motile, yellow, rod-shaped bacterium, designated strain E62-3T, was isolated from soil of Enshi Grand Canyon, Hubei province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain E62-3T was most closely related to Sphingomonas laterariae LNB2T. Strain E62-3T exhibited the highest 16S rRNA gene sequence similarity to Sphingosinicella vermicomposti YC7378T (96.0 %), Sphingobium xanthum NL9T (95.8 %), Sphingobium boeckii 469T (95.7 %) and Sphingomonas laterariae LNB2T (95.5 %) within the family Sphingomonadaceae. The major fatty acids (>5 %) of strain E62-3T were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C14 : 0 2-OH. The predominant respiratory quinone and polyamine were ubiquinone Q-10 and homospermidine, respectively. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The genomic DNA G+C content was 66.4 mol%. The genotypic, chemotaxonomic and phenotypic data revealed that the isolate represents a novel species of the genus Sphingomonas, for which the name Sphingomonas faucium sp. nov. is proposed. The type strain is E62-3T (=KCTC 42834T=CCTCC AB 2015300T).

  11. Paenibacillus physcomitrellae sp. nov., isolated from the moss Physcomitrella patens.

    PubMed

    Zhou, Xun; Nan Guo, Guan; Qi Wang, Le; Lan Bai, Su; Li Li, Chun; Yu, Rong; Hong Li, Yan

    2015-10-01

    A Gram-stain-positive, facultatively anaerobic and rod-shaped bacterium, designated strain XBT, was isolated from Physcomitrella patens growing in Beijing, China. The isolate was identified as a member of the genus Paenibacillus based on phenotypic characteristics and phylogenetic inferences. The novel strain was spore-forming, motile, catalase-negative and weakly oxidase-positive. Optimal growth of strain XBT occurred at 28°C and pH 7.0-7.5. The major polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and several unidentified components, including one phospholipid, two aminophospholipids, three glycolipids, one aminolipid and one lipid. The predominant isoprenoid quinone was MK-7. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major fatty acid components (>5 %) were anteiso-C15 : 0 (51.2 %), anteiso-C17 : 0 (20.6 %), iso-C16 : 0 (8.3 %) and C16 : 0 (6.7 %). The G+C content of the genomic DNA was 53.3 mol%. Phylogenetic analysis, based on the 16S rRNA gene sequence, showed that strain XBT fell within the evolutionary distances encompassed by the genus Paenibacillus; its closest phylogenetic neighbour was Paenibacillus yonginensis DCY84T (96.6 %). Based on phenotypic, chemotaxonomic and phylogenetic properties, strain XBT is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus physcomitrellae sp. nov., is proposed. The type strain is XBT ( = CGMCC 1.15044T = DSM 29851T).

  12. Virgibacillus oceani sp. nov. isolated from ocean sediment.

    PubMed

    Yin, Xijie; Yang, Yanliu; Wang, Shuang; Zhang, Gaiyun

    2015-01-01

    A Gram-stain-positive, moderately halophilic, motile, strictly aerobic, endospore-forming, rod-shaped bacterium, strain MY11(T), was isolated from a sediment sample collected from the Western Pacific. This isolate grew in the presence of 0.5-18% (w/v) NaCl and at pH 6.0-10.0 and 15-45 °C; optimum growth was observed with 3.5% (w/v) NaCl and at pH 8.0-9.0 and 35-37 °C. Strain MY11(T) had menaquinone 7 (MK-7) as the predominant respiratory quinone and anteiso-C15:0 and anteiso-C17:0 as major fatty acids. Major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C content was 34.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain MY11(T) was a member of the genus Virgibacillus, exhibiting sequence similarities of 95.3-97.6% to the type strains of recognized Virgibacillus species. Strain MY11(T) could be differentiated from recognized species of the genus Virgibacillus based on phenotypic characteristics, chemotaxonomic differences, phylogenetic analysis and DNA-DNA hybridization data. On the basis of the data presented, strain MY11(T) is considered to represent a novel species of the genus Virgibacillus, for which the name Virgibacillus oceani sp. nov. is proposed. The type strain is MY11(T) ( =LMG 28105(T) =CGMCC 1.12754(T) =MCCC 1A09973(T)). PMID:25301543

  13. Sphingomonas faucium sp. nov., isolated from canyon soil.

    PubMed

    Liu, Dongmei; Jin, Xin; Sun, Xuelian; Song, Yali; Feng, Liling; Wang, Gejiao; Li, Mingshun

    2016-08-01

    A Gram-stain-negative, strictly aerobic, non-motile, yellow, rod-shaped bacterium, designated strain E62-3T, was isolated from soil of Enshi Grand Canyon, Hubei province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain E62-3T was most closely related to Sphingomonas laterariae LNB2T. Strain E62-3T exhibited the highest 16S rRNA gene sequence similarity to Sphingosinicella vermicomposti YC7378T (96.0 %), Sphingobium xanthum NL9T (95.8 %), Sphingobium boeckii 469T (95.7 %) and Sphingomonas laterariae LNB2T (95.5 %) within the family Sphingomonadaceae. The major fatty acids (>5 %) of strain E62-3T were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C14 : 0 2-OH. The predominant respiratory quinone and polyamine were ubiquinone Q-10 and homospermidine, respectively. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The genomic DNA G+C content was 66.4 mol%. The genotypic, chemotaxonomic and phenotypic data revealed that the isolate represents a novel species of the genus Sphingomonas, for which the name Sphingomonas faucium sp. nov. is proposed. The type strain is E62-3T (=KCTC 42834T=CCTCC AB 2015300T). PMID:27054358

  14. Pedobacter pituitosus sp. nov., isolated from a waterfall.

    PubMed

    Chun, Jeesun; Kang, Ji Young; Jahng, Kwang Yeop

    2014-11-01

    A taxonomic study was carried out on a novel bacterial strain, designated MIC2002(T), which was isolated from Wibong falls in Korea. Cells were Gram-stain-negative, aerobic, non-motile and rods, 0.3-0.5 µm wide and 4.0-5.0 µm long. The optimum temperature and pH range for growth were 25 °C and pH 6.5-7.0, respectively. Catalase and oxidase activities were positive. Flexirubin pigments were not produced. Comparison of the 16S rRNA gene sequences indicated that the isolate belonged to the genus Pedobacter, with Pedobacter daechungensis as its closest relative, with a similarity of 94.4%. It contained iso-C(15:0), anteiso-C(15:0), C(16:0), summed feature 3 (C(16:1)ω6c and/or C(16:1)ω7c) and iso-C(17:0) 3-OH as the major fatty acids and menaquinone MK-7 as isoprenoid quinone. The polar lipid profile of strain MIC2002(T) revealed the presence of phosphatidylethanolamine and an unknown lipid. The DNA G+C content of the strain was 34.7 mol%. On the basis of the evidences presented, it was concluded that strain MIC2002(T) represents a novel species of the genus Pedobacter within the family Sphingobacteriaceae, for which the name Pedobacter pituitosus sp. nov. is proposed. The type strain is MIC2002(T) ( =KACC 17064(T) =JCM 18729(T)). PMID:25168612

  15. Pedobacter pituitosus sp. nov., isolated from a waterfall.

    PubMed

    Chun, Jeesun; Kang, Ji Young; Jahng, Kwang Yeop

    2014-11-01

    A taxonomic study was carried out on a novel bacterial strain, designated MIC2002(T), which was isolated from Wibong falls in Korea. Cells were Gram-stain-negative, aerobic, non-motile and rods, 0.3-0.5 µm wide and 4.0-5.0 µm long. The optimum temperature and pH range for growth were 25 °C and pH 6.5-7.0, respectively. Catalase and oxidase activities were positive. Flexirubin pigments were not produced. Comparison of the 16S rRNA gene sequences indicated that the isolate belonged to the genus Pedobacter, with Pedobacter daechungensis as its closest relative, with a similarity of 94.4%. It contained iso-C(15:0), anteiso-C(15:0), C(16:0), summed feature 3 (C(16:1)ω6c and/or C(16:1)ω7c) and iso-C(17:0) 3-OH as the major fatty acids and menaquinone MK-7 as isoprenoid quinone. The polar lipid profile of strain MIC2002(T) revealed the presence of phosphatidylethanolamine and an unknown lipid. The DNA G+C content of the strain was 34.7 mol%. On the basis of the evidences presented, it was concluded that strain MIC2002(T) represents a novel species of the genus Pedobacter within the family Sphingobacteriaceae, for which the name Pedobacter pituitosus sp. nov. is proposed. The type strain is MIC2002(T) ( =KACC 17064(T) =JCM 18729(T)).

  16. Bacillus nanhaiensis sp. nov., isolated from an oyster.

    PubMed

    Chen, Yi-Guang; Zhang, Li; Zhang, Yu-Qin; He, Jian-Wu; Klenk, Hans-Peter; Tang, Shu-Kun; Zhang, You-Xiang; Li, Wen-Jun

    2011-04-01

    A novel Gram-stain-positive, slightly halophilic, facultatively alkaliphilic, catalase-positive, oxidase-negative, endospore-forming, motile, rod-shaped, aerobic bacterium, designated strain JSM 082006(T), was isolated from an oyster collected from Naozhou Island in the South China Sea. The isolate grew in 0-18 % (w/v) NaCl (optimum, 0.5-4.0 %), at pH 6.0-10.5 (optimum, pH 8.0) and at 15-45 °C (optimum, 30 °C). meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The major cellular fatty acids were anteiso-C(15 : 0), iso-C(15 : 0) and C(16 : 0). Strain JSM 082006(T) contained MK-7 as the predominant respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. The genomic DNA G+C content was 40.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain JSM 082006(T) should be assigned to the genus Bacillus and that it was most closely related to the type strains of Bacillus barbaricus (sequence similarity 99.1 %) and Bacillus arsenicus (97.5 %), followed by those of Bacillus rigui (96.6 %) and Bacillus solisalsi (96.1 %). Phylogenetic analysis, DNA-DNA relatedness values, phenotypic characteristics and chemotaxonomic data support the view that strain JSM 082006(T) represents a novel species of the genus Bacillus, for which the name Bacillus nanhaiensis sp. nov. is proposed; the type strain is JSM 082006(T) ( = DSM 23009(T)  = KCTC 13712(T)).

  17. Marinirhabdus gelatinilytica gen. nov., sp. nov., isolated from seawater.

    PubMed

    Wu, Yue-Hong; Xamxidin, Maripat; Meng, Fan-Xu; Zhang, Xin-Qi; Wang, Chun-Sheng; Tohty, Dilbar; Xu, Xue-Wei

    2016-08-01

    A Gram-stain-negative, aerobic and slightly halophilic bacterium was isolated from the South China Sea, and was subjected to characterization using a polyphasic taxonomic approach. Cells of the isolate, designated NH83T, were non-motile and rod-shaped. On the basis of 16S rRNA gene sequence analysis, strain NH83Twas closely related to members of the genera Aureisphaera (with sequence similarity of 92.9 %), Jejudonia (92.8 %), Marixanthomonas (92.6 %), Altuibacter (92.6 %), Ulvibacter (91.5-91.9 %), Gilvibacter (91.8 %) and Aequorivita (89.6-91.2 %), all of which belong to the family Flavobacteriaceae. Phylogenetic analysis indicated that it represented an independent lineage and its closest relatives belonged to the genus Marixanthomonas. The sole respiratory quinone was MK-6. The major polar lipids were phosphatidylethanolamine, two aminolipids, one aminophospholipid and one unidentified lipid. The principal fatty acids were branched fatty acids, including iso-C15 : 0, iso-C17 : 0 3-OH, iso-C16 : 0, iso-C15 : 1 G and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c). The genomic DNA G+C content was 41.0 mol%. Strain NH83T was positive for hydrolysis of aesculin, gelatin and Tween 60. Phylogenetic distinctiveness and chemotaxonomic differences, together with differential phenotypic properties, revealed that strain NH83T could be differentiated from closely related genera. Therefore, it is proposed that strain NH83T represents a novel species in a new genus, for which the name Marinirhabdus gelatinilytica gen. nov., sp. nov. (type strain NH83T=CGMCC 1.15462T=DSM 101478T) is proposed.

  18. Altererythrobacter aurantiacus sp. nov., isolated from deep-sea sediment.

    PubMed

    Zhang, Gaiyun; Yang, Yanliu; Wang, Lina

    2016-09-01

    A Gram-negative, aerobic, coccoid bacterium, strain O30(T), was isolated from a deep-sea sediment sample collected from the west Pacific. 16S rRNA gene sequence analysis revealed that this strain is affiliated with the family Erythrobacteraceae in the class Alphaproteobacteria, and is closely related to the members of the genera Erythromicrobium (96.6 %), Porphyrobacter (95.5-96.3 %), Altererythrobacter (94.1-96.2 %) and Erythrobacter (94.2-96.2 %). Phylogenetic analysis including all described species of the family Erythrobacteraceae revealed that the isolate forms a clade in the cluster of the genus Altererythrobacter. Strain O30(T) was found to grow at 4-40 °C, pH 6.0-10.0 and in the presence of 0.5-7.0 % (w/v) NaCl. Chemotaxonomic analysis revealed ubiquinones Q-8, Q-9 and Q-10 as the predominant respiratory quinones, summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C17:1 ω6c and C16:0 as major fatty acids, and diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid as the major polar lipids. The DNA G + C content was determined to be 56.9 mol %. On the basis of phenotypic and genotypic data presented in this study, strain O30(T) represents a novel species within the genus Altererythrobacter, for which the name Altererythrobacter aurantiacus sp. nov. is proposed; the type strain is O30(T) (= CGMCC 1.12762(T) = JCM 19853(T) = LMG 28110(T) = MCCC 1A09962(T)).

  19. Paracoccus beibuensis sp. nov., isolated from the South China Sea.

    PubMed

    Zheng, Qiang; Wang, Yanan; Chen, Chuang; Wang, Yu; Xia, Xiaomin; Fu, Yingnan; Zhang, Rui; Jiao, Nianzhi

    2011-03-01

    A Gram-negative, non-motile, short rod-shaped or spherical bacterial strain that accumulates poly-β-hydroxybutyrate (PHB) granules was isolated from the Beibu Gulf in the South China Sea. Cells have no polar or subpolar flagella, dividing by binary fission. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Paracoccus, family Rhodobacteraceae, order Rhodobacterales, class Alphaproteobacteria. The closest neighbours were Paracoccus aestuarii strain B7(T) (97.2% similarity), Paracoccus zeaxanthinifaciens ATCC 21588(T) (97.1% similarity) and Paracoccus homiensis DD-R11(T) (96.8%). The predominant fatty acids were C(18:1) ω7c (82.1%), and significant amounts of C(18:0) (5.6%), C(10:0) 3-OH (2.3%) and C(16:0) (1.5%) were present. The predominant respiratory ubiquinone of strain JLT1284(T) was Q-10 and the DNA G+C content of strain JLT1284(T) was 67.0 mol%. The isolate was also distinguishable from members of the genus Paracoccus on the basis of phenotypic and biochemical characteristics. It is evident from the genotypic, chemotaxonomic and phenotypic data, therefore, that strain JLT1284(T) represents a novel species of the genus Paracoccus, for which the name Paracoccus beibuensis sp. nov. is proposed. The type strain is JLT1284(T)=LMG 24871(T)=CGMCC 1.7295(T)).

  20. Arcanobacterium pinnipediorum sp. nov., isolated from a harbour seal.

    PubMed

    Sammra, Osama; Balbutskaya, Anna; Ülbegi-Mohyla, Hivda; Nagib, Samy; Lämmler, Christoph; Kämpfer, Peter; Glaeser, Stefanie P; Golke, Jan; Busse, Hans-Jürgen; Prenger-Berninghoff, Ellen; Siebert, Ursula; Abdulmawjood, Amir; Klein, Günter

    2015-12-01

    A polyphasic taxonomic study was performed on an unidentified Arcanobacterium-like, Gram-stain-positive bacterium, strain 2710T, isolated from a harbour seal. Comparative 16S rRNA gene sequence analysis showed that this bacterial strain belonged to the genus Arcanobacterium and was related most closely to the type strains of Arcanobacterium phocae (98.4 % similarity) and Arcanobacterium phocisimile (97.5 %). 16S rRNA gene sequence similarities to the type strains of other Arcanobacterium species were between 95.3 and 96.9 %. DNA-DNA hybridization values between strain 2710T and A. phocae DSM 10002T and A. phocisimile LMG 27073T were 4.7 % (reciprocal 56 %) and 23 % (reciprocal 7.7 %), respectively. The presence of the major menaquinone MK-9(H4) and a polar lipid profile with the major compounds diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside supported the affiliation of strain 2710T to the genus Arcanobacterium. The major fatty acids were C16:0, C18:1ω9c, C18:0 and C18:2ω6,9c/anteiso-C18:0. The peptidoglycan structure was of cross-linkage type A5α (l-Lys-l-Lys-d-Glu). Physiological and biochemical tests clearly distinguished the isolate from other members of the genus Arcanobacterium. Based on these tests, it is proposed that this unknown bacterium should be classified as a novel species of the genus Arcanobacterium, with the name Arcanobacterium pinnipediorum sp. nov. The type strain is 2710T ( = DSM 28752T = LMG 28298T).

  1. Paenibacillus baekrokdamisoli sp. nov., isolated from soil of crater lake.

    PubMed

    Lee, Keun Chul; Kim, Kwang Kyu; Kim, Jong-Shik; Kim, Dae-Shin; Ko, Suk-Hyung; Yang, Seung-Hoon; Lee, Jung-Sook

    2016-05-01

    A novel bacterial strain, Back-11T, was isolated from sediment soil of a crater lake, Baekrokdam, Hallasan, Jeju, Republic of Korea. Cells of strain Back-11T were Gram-stain-positive, motile, endospore-forming, rod-shaped and oxidase- and catalase-positive. It contained anteiso-C15 : 0 as the major fatty acid, menaquinone-7 (MK-7) as the predominant isoprenoid quinone, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and four unidentified aminophospholipids as the main polar lipids, and meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The DNA G+C content was 45.3 mol%. Phylogenetic analysis, based on 16S rRNA gene sequencing, showed that strain Back-11T was most closely related to Paenibacillus taihuensis THMBG22T (95.5 % similarity) and fell into a clade in the genus Paenibacillus. On the basis of phylogenetic, chemotaxonomic and phenotypic data, strain Back-11T represents a novel species in the genus Paenibacillus, for which the name Paenibacillus baekrokdamisoli sp. nov. is proposed. The type strain is Back-11T ( = KCTC 33723T = CECT 8890T). PMID:26868819

  2. Methylobacterium dankookense sp. nov., isolated from drinking water.

    PubMed

    Lee, Si-Won; Oh, Hyun-Woo; Lee, Kang-Hyun; Ahn, Tae-Young

    2009-12-01

    A pink-pigmented bacterium, designated SW08-7(T) was isolated from the drinking water of a water purifier. Cells were Gram-negative, rod-shaped, strictly aerobic, and non-spore-forming. It grew optimally at 25 degrees C, pH 6 approximately 7. Phylogenese analysis based on 16S rRNA gene sequence showed that strain SW08-7(T) belongs to the genus Methylobacterium. The highest 16S rRNA gene sequence similarities were found to Methylobacterium mesophilicum JCM 2829(T) (96.9%), Methylobacterium brachiatum B0021(T) (96.9%), Methylobacterium phyllosphaerae CBMB27(T) (96.6%), Methylobacterium radiotolerans JCM 2831(T) (96.6%), and Methylobacterium hispanicum GP34(T) (96.5%). DNA-DNA hybridization experiment revealed low-level (28.5%) of DNA-DNA relatedness between strain SW08-7(T) and Methylobacterium hispanicum. The genomic DNA G+C content was 68.9 mol% and the major isoprenoid quinone was Q-10. The major cellular fatty acid of strain SW08-7(T) was C(18:1) omega7c (79.8+/-2.1%). Results of phylogenetic, phenotypic, and biochemical analyses revealed that strain SW08-7(T) could be classified as representing a novel species of genus Methylobacterium, for which the name Methylobacterium dankookense sp. nov. is proposed. The type strain is SW08-7(T) (=KCTC 22512(T) =DSM 22415(1)). PMID:20127465

  3. Tumebacillus soli sp. nov., isolated from non-rhizosphere soil.

    PubMed

    Kim, Jong-Hwa; Kim, Wonyong

    2016-06-01

    A Gram-stain-positive, strictly aerobic, motile, spore-forming, rod-shaped bacterial strain, CAU 11108T, was isolated from soil in Danghangpo, Republic of Korea, and its taxonomic position was investigated using a polyphasic approach. The bacterium grew optimally at 37 °C, at pH 8, and in the presence of 1 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence similarity revealed that strain CAU 11108T formed a distinct lineage within the genus Tumebacillus and was most closely related to Tumebacillus luteolus U13T (98.2 %). The strain contained menaquinone-7 (MK-7) as the major respiratory quinone and iso-C15 : 0 and anteiso-C15 : 0 as the major fatty acids. The DNA G+C content was 54.6 mol%. On the basis of phenotypic differentiation, phylogenetic and chemotaxonomic data, strain CAU 11108T represents a novel species of the genus Tumebacillus, for which the name Tumebacillus soli sp. nov. is proposed. The type strain is CAU 11108T (=KCTC 33141T=CECT 8918T). PMID:26956136

  4. Prevotella colorans sp. nov., isolated from a human wound.

    PubMed

    Buhl, Michael; Willmann, Matthias; Liese, Jan; Autenrieth, Ingo B; Marschal, Matthias

    2016-08-01

    A strain of obligately anaerobic, Gram-stain-negative and non-spore-forming rod-shaped bacterium was isolated from a human wound and characterized both phenotypically and genotypically. The strain was moderately saccharolytic and proteolytic. Phylogenetic analysis was based on full-length 16S rRNA gene sequence analysis and revealed the strain to represent a member of the genus Prevotella, but to be different from the described species, with the closest relationship to Prevotella bergensis and Prevotella multisaccharivorax. The genomic DNA G+C content was 43.2 mol%. The most abundant cellular long-chain fatty acids were 3-OH iso-C17 : 0, anteiso-C15 : 0 and iso-C15 : 0. In view of phenotypical and biochemical characteristics as well as gene sequencing, strain A1336T is considered to represent a novel species within the genus Prevotella, for which the name Prevotella colorans sp. nov. is proposed. The type strain is A1336T (=DSM 100333T =CCUG 67421T =CCOS 902T). PMID:27150727

  5. Dinghuibacter silviterrae gen. nov., sp. nov., isolated from forest soil.

    PubMed

    Lv, Ying-Ying; Wang, Jia; Chen, Mei-Hong; You, Jia; Qiu, Li-Hong

    2016-04-01

    A novel Gram-stain negative, non-motile, rod-shaped, aerobic bacterial strain, designated DHOA34T, was isolated from forest soil of Dinghushan Biosphere Reserve, Guangdong Province, China. Comparative 16S rRNA gene sequence analysis showed that it exhibited highest similarity with Flavisolibacter ginsengiterrae Gsoil 492T and Flavitalea populi HY-50RT, at 90.89 and 90.83%, respectively. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, DHOA34T formed an independent lineage within the family Chitinophagaceae but was distinct from all recognized species and genera of the family. The major cellular fatty acids of DHOA34T included iso-C15:0, anteiso-C15:0, iso-C17:0 3-OH and summed feature 3 (C16:1ω6c and/or C16:1ω7c). The DNA G+C content was 51.6 mol% and the predominant quinone was menaquinone 7 (MK-7). Flexirubin pigments were produced. The phenotypic, chemotaxonomic and phylogenetic data demonstrate consistently that strain DHOA34T represents a novel species of a new genus in the family Chitinophagaceae, for which the name Dinghuibacter silviterrae gen. nov., sp. nov. is proposed. The type strain of Dinghuibacter silviterrae is DHOA34T (=CGMCC 1.15023T=KCTC 42632T). PMID:26828023

  6. Rhodococcus aerolatus sp. nov., isolated from subarctic rainwater.

    PubMed

    Hwang, C Y; Lee, I; Cho, Y; Lee, Y M; Baek, K; Jung, Y-J; Yang, Y Y; Lee, T; Rhee, T S; Lee, H K

    2015-02-01

    A Gram-stain-positive, rod-shaped and non-motile strain, designated PAMC 27367(T), was isolated from rainwater collected on the Bering Sea. Analysis of the 16S rRNA gene sequence of the strain showed an affiliation with the genus Rhodococcus. Phylogenetic analyses revealed that strain PAMC 27367(T) formed a robust clade with the type strains of Rhodococcus rhodnii, Rhodococcus aetherivorans and Rhodococcus ruber with 16S rRNA gene sequence similarities of 96.3 %, 95.8 % and 95.5 %, respectively. Cells of the strain grew optimally at 25 °C and at pH 6.5-7.0 in the presence of 0-2 % (w/v) sea salts. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and three unknown phospholipids. The major cellular fatty acids (>10 %) were iso-C16 : 0, C17 : 1ω8c and 10-methyl C17 : 0. Cell wall analysis showed that strain PAMC 27367(T) contained meso-diaminopimelic acid. The genomic DNA G+C content was 77.1 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data presented here, we propose a novel species with the name Rhodococcus aerolatus sp. nov., with PAMC 27367(T) ( = KCTC 29240(T) = JCM 19485(T)) as the type strain.

  7. Saccharothrix carnea sp. nov., an actinobacterium isolated from soil.

    PubMed

    Liu, Chongxi; Guan, Xuejiao; Wang, Shurui; Zhao, Junwei; Wang, Haiyan; He, Hairong; Xiang, Wensheng; Wang, Xiangjing

    2014-12-01

    A novel actinobacterium, designated strain NEAU-yn17(T), was isolated from a soil sample collected at the wastewater discharge site of a pesticide factory in Harbin, northern China, and characterized using a polyphasic approach. Morphological and chemotaxonomic properties of strain NEAU-yn17(T) were consistent with the description of the genus Saccharothrix, such as the spore arrangement, the diamino acid of the peptidoglycan, the whole-cell hydrolysates, the predominant menaquinone and the phospholipid profile. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain NEAU-yn17(T) should also be classified in the genus Saccharothrix, with Saccharothrix saharensis DSM 45456(T) (99.52 % sequence similarity) and Saccharothrix xinjiangensis JCM 12329(T) (99.04 %) as the nearest phylogenetic relatives. A combination of DNA-DNA hybridization results and some phenotypic characteristics indicated that strain NEAU-yn17(T) can be distinguished from its closest relatives. Therefore, strain NEAU-yn17(T) represents a novel species of the genus Saccharothrix, for which the name Saccharothrix carnea sp. nov. is proposed. The type strain is NEAU-yn17(T) ( = CGMCC 4.7097(T) = DSM 45878(T)). PMID:25256705

  8. Cellulomonas marina sp. nov., isolated from deep-sea water.

    PubMed

    Zhang, Limin; Xi, Lijun; Qiu, Danheng; Song, Lei; Dai, Xin; Ruan, Jisheng; Huang, Ying

    2013-08-01

    A bacterial strain FXJ8.089(T) was isolated from deep-sea water collected from the southwest Indian Ocean (49° 39' E 37° 47' S) at a depth of 2800 m, and its taxonomic position was investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain FXJ8.089(T) belonged to the genus Cellulomonas and had the highest similarities with Cellulomonas oligotrophica (96.9 %) and Cellulomonas aerilata (96.6 %). It contained MK-9(H4) as the predominant menaquinone. The polar lipids were diphosphatidylglycerol and phosphatidylinositol mannosides. The cell-wall peptidoglycan type was A4β with an interpeptide bridge L-Orn-D-Glu. The cell-wall sugars were glucose, mannose and ribose. The DNA G+C content was 70.3 mol%. The strain also showed a number of physiological and biochemical characteristics that were distinct from the closely related species. Based on phenotypic and genotypic data, strain FXJ8.089(T) (= CGMCC 4.6945(T) = DSM 24960(T)) represents a novel species of the genus Cellulomonas, for which the name Cellulomonas marina sp. nov. is proposed.

  9. Paenibacillus baekrokdamisoli sp. nov., isolated from soil of crater lake.

    PubMed

    Lee, Keun Chul; Kim, Kwang Kyu; Kim, Jong-Shik; Kim, Dae-Shin; Ko, Suk-Hyung; Yang, Seung-Hoon; Lee, Jung-Sook

    2016-05-01

    A novel bacterial strain, Back-11T, was isolated from sediment soil of a crater lake, Baekrokdam, Hallasan, Jeju, Republic of Korea. Cells of strain Back-11T were Gram-stain-positive, motile, endospore-forming, rod-shaped and oxidase- and catalase-positive. It contained anteiso-C15 : 0 as the major fatty acid, menaquinone-7 (MK-7) as the predominant isoprenoid quinone, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and four unidentified aminophospholipids as the main polar lipids, and meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The DNA G+C content was 45.3 mol%. Phylogenetic analysis, based on 16S rRNA gene sequencing, showed that strain Back-11T was most closely related to Paenibacillus taihuensis THMBG22T (95.5 % similarity) and fell into a clade in the genus Paenibacillus. On the basis of phylogenetic, chemotaxonomic and phenotypic data, strain Back-11T represents a novel species in the genus Paenibacillus, for which the name Paenibacillus baekrokdamisoli sp. nov. is proposed. The type strain is Back-11T ( = KCTC 33723T = CECT 8890T).

  10. Nocardiopsis mangrovei sp. nov., isolated from mangrove sediment.

    PubMed

    Huang, Hui-qin; Xing, Shan-shan; Yuan, Wei-dao; Wang, Ying; Liu, Min; Sun, Qian-guang; Lin, Xiang-zhi; Bao, Shi-xiang

    2015-06-01

    Two Gram-positive actinobacterial strains, designated HA11166(T) and HA12420, were isolated from mangrove sediments in Hainan, China. The bacterial cells grew with 0-9 % (w/v) NaCl, at 15-40 °C and pH 5.0-10.0, with the optimum growth at 1 % NaCl, 30-37 °C and pH 7.0. The organisms had a range of chemical and morphological properties consistent with their classification in the genus Nocardiopsis. Phylogenetic analysis of the 16S rRNA gene sequences indicated that strains HA11166(T) and HA12420 can be affiliated to the genus Nocardiopsis and most closely related to Nocardiopsis trehalosi VKM Ac-942(T) (with the similarity of 97.2 and 97.5 %, respectively). The value of DNA-DNA relatedness between type strain HA11166(T), selected as the representative strain, and N. trehalosi VKM Ac-942(T) was 38.8 %. The DNA G+C content of strain HA11166(T) was 73.7 %. On the basis of these phenotypic and genotypic data, strains HA11166(T) and HA12420 are proposed to represent a novel species of the genus Nocardiopsis, for which the name Nocardiopsis mangrovei sp. nov. is proposed. The type strain is HA11166(T) (=CGMCC 4.7119(T)=DSM 46665(T)). PMID:25969384

  11. Marinomonas mangrovi sp. nov., isolated from mangrove sediment.

    PubMed

    Zhang, De-Chao; Margesin, Rosa

    2015-05-01

    A Gram-stain-negative, Na(+)-requiring bacterial strain, designated B20-1(T), was isolated from soil of the root system of mangrove forest. Cells were curved rods and motile by means of a polar flagellum. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B20-1(T) belonged to the genus Marinomonas , sharing highest sequence similarities with Marinomonas rhizomae IVIA-Po-145(T) (97.6%), Marinomonas dokdonensis DSW10-10(T) (97.0%) and Marinomonas foliarum IVIA-Po-155(T) (96.9%). The predominant cellular fatty acids of strain B20-1(T) were C10 : 0 3-OH, C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16 : 0. Phosphatidylethanolamine and phosphatidylglycerol were identified as the predominant phospholipids. The predominant ubiquinone was Q-8. The genomic DNA G+C content of strain B20-1(T) was 46.6 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness, a novel species, Marinomonas mangrovi sp. nov., is proposed with B20-1(T) ( =DSM 28136(T) =LMG 28077(T)) as the type strain. PMID:25713041

  12. Acetobacter oeni sp. nov., isolated from spoiled red wine.

    PubMed

    Silva, Luis R; Cleenwerck, Ilse; Rivas, Raúl; Swings, Jean; Trujillo, Martha E; Willems, Anne; Velázquez, Encarna

    2006-01-01

    A bacterial strain, designated B13T, was isolated from spoiled red wine from the Dão region, Portugal. The strain was Gram-negative, strictly aerobic, rod-shaped and motile. Phylogenetic analysis on the basis of 16S rRNA gene sequences indicated that B13T belonged to the genus Acetobacter within the Alphaproteobacteria. The closest related species was Acetobacter aceti, with 98.4 % 16S rRNA gene sequence similarity. DNA-DNA hybridization showed that B13T constituted a taxon separate from the Acetobacter species with validly published names. The DNA G+C content of B13T was 58.1 mol%. Phenotypic characteristics of B13T allowed its differentiation from the recognized Acetobacter species. B13T produced 5-ketogluconic acid from glucose, but no 2-ketogluconic acid. It produced catalase, but no oxidase. It utilized glycerol, but not maltose, ethanol or methanol as carbon sources. On the basis of the results obtained, B13T represents a novel species for which the name Acetobacter oeni sp. nov. is proposed. The type strain is B13T (= LMG 21952T = CECT 5830T).

  13. Arthrobacter psychrophenolicus sp. nov., isolated from an alpine ice cave.

    PubMed

    Margesin, Rosa; Schumann, Peter; Spröer, Cathrin; Gounot, Anne-Monique

    2004-11-01

    On the basis of phenotypic, genotypic and chemotaxonomic characteristics, a novel species belonging to the genus Arthrobacter is described. A facultatively psychrophilic bacterium, strain AG31(T), was isolated from an alpine ice cave. The aerobic, Gram-positive, non-spore-forming, non-motile strain exhibited a rod-coccus growth cycle and produced a yellow pigment. Good growth and phenol biodegradation occurred at a temperature range of 1-25 degrees C. Up to 10 mM phenol was utilized as a sole carbon source. Glucose was not assimilated. Analysis of the 16S rRNA gene revealed that strain AG31(T) represents a distinct lineage within the genus Arthrobacter, being most closely related to Arthrobacter sulfureus. The level of DNA-DNA relatedness to the type strain of A. sulfureus was 29.9 %. Anteiso-C(15 : 0) was the predominant fatty acid (72 %). Strain AG31(T) exhibited A4alpha l-lys-l-Glu-type peptidoglycan and contained glucose as the only cell-wall sugar. MK-10 was the predominant menaquinone, and the polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and an unidentified glycolipid. Strain AG31(T) (=DSM 15454(T)=LMG 21914(T)) is assigned as the type strain of a novel Arthrobacter species, Arthrobacter psychrophenolicus sp. nov.

  14. Biodegradation of indole by a newly isolated Cupriavidus sp. SHE.

    PubMed

    Qu, Yuanyuan; Shen, E; Ma, Qiao; Zhang, Zhaojing; Liu, Ziyan; Shen, Wenli; Wang, Jingwei; Li, Duanxing; Li, Huijie; Zhou, Jiti

    2015-08-01

    Indole, a typical nitrogen heterocyclic aromatic pollutant, is extensively spread in industrial wastewater. Microbial degradation has been proven to be a feasible approach to remove indole, whereas the microbial resources are fairly limited. A bacterial strain designated as SHE was isolated and found to be an efficient indole degrader. It was identified as Cupriavidus sp. according to 16S rRNA gene analysis. Strain SHE could utilize indole as the sole carbon source and almost completely degrade 100mg/L of indole within 24hr. It still harbored relatively high indole degradation capacity within pH4-9 and temperature 25°C-35°C. Experiments also showed that some heavy metals such as Mn(2+), Pb(2+) and Co(2+) did not pose severe inhibition on indole degradation. Based on high performance liquid chromatography-mass spectrum analysis, isatin was identified as a minor intermediate during the process of indole biodegradation. A major yellow product with m/z 265.0605 (C15H8N2O3) was generated and accumulated, suggesting a novel indole conversion pathway existed. Genome analysis of strain SHE indicated that there existed a rich set of oxidoreductases, which might be the key reason for the efficient degradation of indole. The robust degradation ability of strain SHE makes it a promising candidate for the treatment of indole containing wastewater. PMID:26257355

  15. Enterococcus Xinjiangensis sp. nov., Isolated from Yogurt of Xinjiang, China.

    PubMed

    Ren, Xiaopu; Li, Mingyang; Guo, Dongqi

    2016-09-01

    A Gram-strain-positive bacterial strain 48(T) was isolated from traditional yogurt in Xinjiang Province, China. The bacterium was characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, polymerase α subunit (rpoA) gene sequence analysis, determination of DNA G+C content, DNA-DNA hybridization with the type strain of Enterococcus ratti and analysis of phenotypic features. Strain 48(T) accounted for 96.1, 95.8, 95.8, and 95.7 % with Enterococcus faecium CGMCC 1.2136(T), Enterococcus hirae ATCC 9790(T), Enterococcus durans CECT 411(T), and E. ratti ATCC 700914(T) in the 16S rRNA gene sequence similarities, respectively. The sequence of rpoA gene showed similarities of 99.0, 96.0, 96.0, and 96 % with that of E. faecium ATCC 19434(T), Enterococcus villorum LMG12287, E. hirae ATCC 9790(T), and E. durans ATCC 19432(T), respectively. Based upon of polyphasic characterization data obtained in the study, a novel species, Enterococcus xinjiangensis sp. nov., was proposed and the type strain was 48(T)(=CCTCC AB 2014041(T) = JCM 30200(T)). PMID:27260143

  16. Aneurinibacillus soli sp. nov., isolated from mountain soil.

    PubMed

    Lee, Keun Chul; Kim, Kwang Kyu; Eom, Mi Kyung; Kim, Jong-Shik; Kim, Dae-Shin; Ko, Suk-Hyung; Lee, Jung-Sook

    2014-11-01

    A novel bacterial strain designated CB4(T) was isolated from soil from the Hallasan, Jeju, Korea. Strain CB4(T) was found to be strictly aerobic, Gram-stain-positive, rod-shaped, motile and formed creamy greyish colonies on nutrient agar. The major fatty acids were identified as iso-C(15:0) and iso-C(16:0), and the predominant isoprenoid quinone as MK-7. The cell-wall peptidoglycan contained glycine and alanine as the diagnostic amino acids and phosphatidyl-N-methylethanolamine, phosphatidylethanolamine, diphosphatidylglycerol and an unidentified aminophospholipid as the polar lipids. The genomic DNA G+C content of strain CB4(T) was 46.5 mol%. Phylogenetic analysis, based on 16S rRNA gene sequence similarities, showed that strain CB4(T) forms a deep branch within the genus Aneurinibacillus, sharing the highest level of sequence homology with Aneurinibacillus aneurinilyticus DSM 5562(T) (96.5%). On the basis of the phenotypic, chemotaxonomic and phylogenetic characteristics, strain CB4(T) is considered to represent a novel species within the genus Aneurinibacillus, for which the name Aneurinibacillus soli sp. nov. is proposed. The type strain is CB4(T) ( =KCTC 33505(T) =CECT 8566(T)). An emended description of the genus Aneurinibacillus is also proposed.

  17. Chryseobacterium taichungense sp. nov., isolated from contaminated soil.

    PubMed

    Shen, Fo-Ting; Kämpfer, Peter; Young, Chiu-Chung; Lai, Wei-An; Arun, A B

    2005-05-01

    A bacterial strain (CC-TWGS1-8(T)) isolated from a tar-contaminated soil in Taiwan was studied in a detailed taxonomic study. The cells were Gram-negative, rod-shaped and non-spore-forming. Phylogenetic analyses using the 16S rRNA gene sequence of the strain clearly revealed an affiliation to the genus Chryseobacterium, the highest sequence similarities being to the type strain of Chryseobacterium indologenes (96.8 %), to Chryseobacterium gleum (96.8 %) and to Chryseobacterium joostei (96.4 %). The 16S rRNA gene sequence similarities to all other Chryseobacterium species were below 96 %. The major whole-cell fatty acids were 15 : 0 iso (35.4 %) and 17 : 0 iso 3OH (22.5 %). DNA-DNA hybridization values and the biochemical and chemotaxonomic properties demonstrate that strain CC-TWGS1-8(T) represents a novel species, for which the name Chryseobacterium taichungense sp. nov. is proposed. The type strain is CC-TWGS1-8(T) (= CCUG 50001(T) = CIP 108519(T)).

  18. Burkholderia sprentiae sp. nov., isolated from Lebeckia ambigua root nodules.

    PubMed

    De Meyer, Sofie E; Cnockaert, Margo; Ardley, Julie K; Maker, Garth; Yates, Ron; Howieson, John G; Vandamme, Peter

    2013-11-01

    Seven Gram-stain-negative, rod-shaped bacteria were isolated from Lebeckia ambigua root nodules and authenticated on this host. Based on the 16S rRNA gene phylogeny, they were shown to belong to the genus Burkholderia, with the representative strain WSM5005(T) being most closely related to Burkholderia tuberum (98.08 % sequence similarity). Additionally, these strains formed a distinct group in phylogenetic trees based on the housekeeping genes gyrB and recA. Chemotaxonomic data including fatty acid profiles and analysis of respiratory quinones supported the assignment of the strains to the genus Burkholderia. Results of DNA-DNA hybridizations, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of our strains from the closest species of the genus Burkholderia with a validly published name. Therefore, these strains represent a novel species for which the name Burkholderia sprentiae sp. nov. (type strain WSM5005(T) = LMG 27175(T) = HAMBI 3357(T)) is proposed.

  19. Burkholderia rhynchosiae sp. nov., isolated from Rhynchosia ferulifolia root nodules.

    PubMed

    De Meyer, Sofie E; Cnockaert, Margo; Ardley, Julie K; Trengove, Robert D; Garau, Giovanni; Howieson, John G; Vandamme, Peter

    2013-11-01

    Two strains of Gram-stain-negative, rod-shaped bacteria were isolated from root nodules of the South African legume Rhynchosia ferulifolia and authenticated on this host. Based on phylogenetic analysis of the 16S rRNA gene, strains WSM3930 and WSM3937(T) belonged to the genus Burkholderia, with the highest degree of sequence similarity to Burkholderia terricola (98.84 %). Additionally, the housekeeping genes gyrB and recA were analysed since 16S rRNA gene sequences are highly similar between closely related species of the genus Burkholderia. The results obtained for both housekeeping genes, gyrB and recA, showed the highest degree of sequence similarity of the novel strains towards Burkholderia caledonica LMG 19076(T) (94.2 % and 94.5 %, respectively). Chemotaxonomic data, including fatty acid profiles and respiratory quinone data supported the assignment of strains WSM3930 and WSM3937(T) to the genus Burkholderia. DNA-DNA hybridizations, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains WSM3930 and WSM3937(T) from the most closely related species of the genus Burkholderia with validly published names. We conclude, therefore, that these strains represent a novel species for which the name Burkholderia rhynchosiae sp. nov. is proposed, with strain WSM3937(T) ( = LMG 27174(T) = HAMBI 3354(T)) as the type strain.

  20. Burkholderia dilworthii sp. nov., isolated from Lebeckia ambigua root nodules.

    PubMed

    De Meyer, Sofie E; Cnockaert, Margo; Ardley, Julie K; Van Wyk, Ben-Erik; Vandamme, Peter A; Howieson, John G

    2014-04-01

    Three strains of Gram-stain-negative, rod-shaped bacteria were isolated from Lebeckia ambigua root nodules and authenticated on this host. Based on the 16S rRNA gene sequence phylogeny, they were shown to belong to the genus Burkholderia, with the representative strain WSM3556(T) being most closely related to Burkholderia caledonica LMG 23644(T) (98.70 % 16S rRNA gene sequence similarity) and Burkholderia rhynchosiae WSM3937(T) (98.50 %). Additionally, these strains formed a distinct group in phylogenetic trees of the housekeeping genes gyrB and recA. Chemotaxonomic data, including fatty acid profiles and analysis of respiratory quinones, supported the assignment of our strains to the genus Burkholderia. Results of DNA-DNA hybridizations, MALDI-TOF MS analysis and physiological and biochemical tests allowed genotypic and phenotypic differentiation of our strains from their nearest neighbour species. Therefore, these strains represent a novel species, for which the name Burkholderia dilworthii sp. nov. is proposed, with the type strain WSM3556(T) ( = LMG 27173(T) = HAMBI 3353(T)).

  1. Sphingobacterium paludis sp. nov., isolated from wetland soil.

    PubMed

    Feng, Hao; Zeng, Yanhua; Huang, Yili

    2014-10-01

    A novel Gram-stain-negative bacteria, designated S37(T), was isolated from soil of the Xixi wetland, Zhejiang province, China. Cells of strain S37(T) were aerobic, non-motile rods. Growth occurred at 10-37 °C (optimum, 25 °C), pH 5.0-9.7 (optimum, pH 7.5) and with 0-6% (w/v) NaCl (optimum, 0.5%). Based on 16S rRNA gene sequence analysis, strain S37(T) was found to be a member of the genus Sphingobacterium and shared highest similarity with Sphingobacterium composti 4M24(T) (95.78%). The major fatty acids were summed feature 3 (iso-C15:0 2-OH and/or C16:1ω7c), iso-C15:0 and iso-C17:0 3-OH, and the DNA G+C content was 43.8 mol%. The predominant respiratory quinone was MK-7. Based on its phenotypic and chemotaxonomic characteristics and phylogenetic data, strain S37(T) represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium paludis sp. nov. (type strain S37(T) = CGMCC 1.12801(T) = NBRC 110386(T)) is proposed. PMID:25048213

  2. Dokdonella fugitiva sp. nov., a Gammaproteobacterium isolated from potting soil.

    PubMed

    Cunha, Sofia; Tiago, Igor; Luísa Pires, Ana; da Costa, Milton S; Veríssimo, António

    2006-04-01

    A Gram-negative bacterium designated A3(T) was isolated from a potting soil produced in Portugal. This organism formed rod-shaped cells, was non-motile and strictly aerobic. Strain A3(T) was catalase-negative, weakly oxidase positive, with an optimum growth temperature of 40 degrees C and an optimum pH value for growth of 7.0. The predominant cellular fatty acids detected were iso-17:1 omega9c, iso-17:0, iso-15:0, iso-16:0 and iso-11:0 3OH and the major respiratory quinone was ubiquinone 8. The G+C content of DNA was 68.3%. The phylogenetic analyses based on the 16S rRNA sequencing showed that the closest relative of strain A3(T) was the type strain of Dokdonella koreensis indicating that the organism is a member of the family Xanthomonadaceae, class Gammaproteobacteria. Based on the phylogenetic analyses and distinct phenotypic characteristics, we are of the opinion that strain A3(T), represents a novel species of the genus Dokdonella for which we propose the name Dokdonella fugitiva sp.nov.

  3. Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus

    PubMed Central

    Sánchez, Maximo; Ramírez-Bahena, Martha-Helena; Peix, Alvaro; Lorite, María J.; Sanjuán, Juan; Monza, Jorge

    2014-01-01

    Strain S658T was isolated from a Lotus corniculatus nodule in a soil sample obtained in Uruguay. Phylogenetic analysis of the 16S rRNA gene and atpD gene showed that this strain clustered within the genus Phyllobacterium. The closest related species was, in both cases, Phyllobacterium trifolii PETP02T with 99.8 % sequence similarity in the 16S rRNA gene and 96.1 % in the atpD gene. The 16S rRNA gene contains an insert at the beginning of the sequence that has no similarities with other inserts present in the same gene in described rhizobial species. Ubiquinone Q-10 was the only quinone detected. Strain S658T differed from its closest relatives through its growth in diverse culture conditions and in the assimilation of several carbon sources. It was not able to reproduce nodules in Lotus corniculatus. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain should be classified as a representative of a novel species of the genus Phyllobacterium, for which the name Phyllobacterium loti sp. nov. is proposed. The type strain is S658T( = LMG 27289T = CECT 8230T). PMID:24271211

  4. Streptomyces hyaluromycini sp. nov., isolated from a tunicate (Molgula manhattensis).

    PubMed

    Harunari, Enjuro; Hamada, Moriyuki; Shibata, Chiyo; Tamura, Tomohiko; Komaki, Hisayuki; Imada, Chiaki; Igarashi, Yasuhiro

    2016-03-01

    A novel Gram-stain-positive actinomycete, designated MB-PO13(T), was isolated from a tunicate (Molgula manhattensis) collected in Tokyo Bay, Japan, and its taxonomic position was studied by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain MB-PO13(T) was closely related to Streptomyces graminisoli JR-12(T) (99.72% 16S rRNA gene sequence similarity) and Streptomyces shenzhenensis 172115(T) (99.23%). The strain contained LL-diaminopimelic acid in the whole-cell hydrolysate. The predominant menaquinones were MK-9(H8) and MK-9(H6) and the major fatty acids were anteiso-C15:0, iso-C16:0, iso-C14:0 and C16:0. These data supported the affiliation of the novel strain to the genus Streptomyces. Meanwhile, results of DNA-DNA hybridization and physiological and biochemical tests indicated that strain MB-PO13(T) was distinguished from known Streptomyces type strains. Therefore, strain MB-PO13(T) represents a novel species of the genus Streptomyces for which the name Streptomyces hyaluromycini sp. nov. is proposed; the type strain is MB-PO13(T) (=NBRC 110483(T) =DSM 100105(T)). PMID:26531686

  5. Streptomyces graminifolii sp. nov., isolated from bamboo (Sasa borealis) litter.

    PubMed

    Lee, Hyo-Jin; Whang, Kyung-Sook

    2014-08-01

    The taxonomic position of strain JL-22(T), isolated from litter of a bamboo (Sasa borealis) forest, was determined using a polyphasic approach. The organism had phenotypic and morphological properties consistent with it being a member of the genus Streptomyces. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain JL-22(T) was closely related to Streptomyces prunicolor NRRL B-12281(T) (99.2%), Streptomyces galilaeus JCM 4757(T) (99.0%) and Streptomyces chartreusis NBRC 12753(T) (99.0%). However, the results of DNA-DNA hybridization and physiological and biochemical tests showed that strain JL-22(T) could be differentiated from its closest phylogenetic relatives both genotypically and phenotypically. Based on phenotypic and genotypic data, strain JL-22(T) represents a novel species of the genus Streptomyces, for which the name Streptomyces graminifolii sp. nov. is proposed. The type strain is JL-22(T) ( = KACC 17180(T) = NBRC 109806(T)). PMID:24812360

  6. Enterococcus Xinjiangensis sp. nov., Isolated from Yogurt of Xinjiang, China.

    PubMed

    Ren, Xiaopu; Li, Mingyang; Guo, Dongqi

    2016-09-01

    A Gram-strain-positive bacterial strain 48(T) was isolated from traditional yogurt in Xinjiang Province, China. The bacterium was characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, polymerase α subunit (rpoA) gene sequence analysis, determination of DNA G+C content, DNA-DNA hybridization with the type strain of Enterococcus ratti and analysis of phenotypic features. Strain 48(T) accounted for 96.1, 95.8, 95.8, and 95.7 % with Enterococcus faecium CGMCC 1.2136(T), Enterococcus hirae ATCC 9790(T), Enterococcus durans CECT 411(T), and E. ratti ATCC 700914(T) in the 16S rRNA gene sequence similarities, respectively. The sequence of rpoA gene showed similarities of 99.0, 96.0, 96.0, and 96 % with that of E. faecium ATCC 19434(T), Enterococcus villorum LMG12287, E. hirae ATCC 9790(T), and E. durans ATCC 19432(T), respectively. Based upon of polyphasic characterization data obtained in the study, a novel species, Enterococcus xinjiangensis sp. nov., was proposed and the type strain was 48(T)(=CCTCC AB 2014041(T) = JCM 30200(T)).

  7. Biodegradation of indole by a newly isolated Cupriavidus sp. SHE.

    PubMed

    Qu, Yuanyuan; Shen, E; Ma, Qiao; Zhang, Zhaojing; Liu, Ziyan; Shen, Wenli; Wang, Jingwei; Li, Duanxing; Li, Huijie; Zhou, Jiti

    2015-08-01

    Indole, a typical nitrogen heterocyclic aromatic pollutant, is extensively spread in industrial wastewater. Microbial degradation has been proven to be a feasible approach to remove indole, whereas the microbial resources are fairly limited. A bacterial strain designated as SHE was isolated and found to be an efficient indole degrader. It was identified as Cupriavidus sp. according to 16S rRNA gene analysis. Strain SHE could utilize indole as the sole carbon source and almost completely degrade 100mg/L of indole within 24hr. It still harbored relatively high indole degradation capacity within pH4-9 and temperature 25°C-35°C. Experiments also showed that some heavy metals such as Mn(2+), Pb(2+) and Co(2+) did not pose severe inhibition on indole degradation. Based on high performance liquid chromatography-mass spectrum analysis, isatin was identified as a minor intermediate during the process of indole biodegradation. A major yellow product with m/z 265.0605 (C15H8N2O3) was generated and accumulated, suggesting a novel indole conversion pathway existed. Genome analysis of strain SHE indicated that there existed a rich set of oxidoreductases, which might be the key reason for the efficient degradation of indole. The robust degradation ability of strain SHE makes it a promising candidate for the treatment of indole containing wastewater.

  8. Belliella buryatensis sp. nov., isolated from alkaline lake water.

    PubMed

    Kozyreva, Lyudmila; Egorova, Darya; Anan'ina, Lyudmila; Plotnikova, Elena; Ariskina, Elena; Prisyazhnaya, Natalya; Radnaeva, Larisa; Namsaraev, Bair

    2016-01-01

    Two bacterial isolates from water of the alkaline brackish Lake Solenoe (Buryatia, Russia), 2C and 5CT, were characterized by using a polyphasic taxonomic approach. The strains were small, non-motile, Gram-stain-negative rods that formed small orange-red colonies on the surface of marine agar. Studies based on 16S rRNA gene sequences showed that the strains were related closely to Belliella pelovolcani CC-SAL-25T (98.7 % sequence similarity). The G+C content of the DNA was 38-40 mol%. DNA-DNA hybridization values between strains 2C and 5CT and B. pelovolcani CC-SAL-25T were 56-58 mol%. A menaquinone with seven isoprene units (MK-7) was the major respiratory quinone. The fatty acid profiles were slightly different from that of B. pelovolcani CC-SAL-25T. The novel strains could be distinguished from the phylogenetically closest species B. pelovolcani CC-SAL-25T based on matrix-assisted laser desorption ionization time-of-flight mass spectra of whole cells and a range of physiological and biochemical characteristics. The data obtained suggest that strains 2C and 5CT represent a novel species of the genus Belliella, for which the name Belliella buryatensis sp. nov. is proposed. The type strain is 5CT ( = VKM B-2724T = KCTC 32194T). PMID:26474559

  9. Amycolatopsis dongchuanensis sp. nov., an actinobacterium isolated from soil.

    PubMed

    Nie, Guo-Xing; Ming, Hong; Li, Shuai; Zhou, En-Min; Cheng, Juan; Tang, Xia; Feng, Hui-Gen; Tang, Shu-Kun; Li, Wen-Jun

    2012-11-01

    A novel actinomycete strain, designated YIM 75904(T), was isolated from a soil sample that had been collected from a dry and hot river valley in Dongchuan county, Yunnan province, south-western China. The taxonomic position of the novel strain was investigated by a polyphasic approach. In phylogenetic analyses based on 16S rRNA gene sequences, strain YIM 75904(T) formed a distinct clade within the genus Amycolatopsis and appeared to be closely related to Amycolatopsis sacchari K24(T) (99.3% sequence similarity). Strain YIM 75904(T) had a type-IV cell wall, with no detectable mycolic acids, and had MK-9(H(4)) as its predominant menaquonine. Its cell wall contained meso-diaminopimelic acid, galactose, glucose and arabinose, and its major cellular fatty acids were iso-C(16:0), iso-C(15:0), anteiso-C(17:0) and anteiso-C(15:0). The genomic DNA G+C content of the novel strain was 68.5 mol%. Based on the results of physiological and biochemical tests and DNA-DNA hybridizations, strain YIM 75904(T) represents a novel species of the genus Amycolatopsis for which the name Amycolatopsis dongchuanensis sp. nov. is proposed. The type strain is YIM 75904(T) (=CCTCC AA 2011016(T) =JCM 18054(T)).

  10. Chitinophaga vermicomposti sp. nov., with antifungal activity, isolated from vermicompost.

    PubMed

    Yasir, Muhammad; Aslam, Zubair; Song, Geun Cheol; Bibi, Fehmida; Jeon, Che Ok; Chung, Young Ryun

    2010-01-01

    A Gram-negative, rod-shaped bacterial strain, YC6729T, was isolated from the vermicompost (VC) collected at Masan, Korea and its taxonomic position was investigated by a polyphasic taxonomic approach. Strain YC6729T grew optimally at 30 degrees C and at pH 6.5-8.5. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YC6729T belongs to the genus Chitinophaga in the family Chitinophagaceae. Most closely related species are Chitinophaga terra KP01T (96.4 %), Chitinophaga ginsengisegetis Gsoil 040T (96.1 %) and Chitinophaga arvensicola IAM 12650T (96.1 %). Strain YC6729T contained MK-7 as the major menaquinone and homospermidine as the major polyamine. The major fatty acids of strain YC6729T C15:0 iso, C16:1omega5c and C17:0 iso 3-OH. The total DNA G+C content was 48.9 mol%. The phenotypic, chemotaxonomic and phylogenetic data showed that strain YC6729T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga vermicomposti sp. nov. is proposed. The type strain is YC6729T (= KACC 13774T = DSM 22224T).

  11. Arcticibacter pallidicorallinus sp. nov. isolated from glacier ice.

    PubMed

    Liu, Qing; Kim, Song-gun; Liu, Hong-can; Xin, Yu-hua; Zhou, Yu-guang

    2014-07-01

    A Gram-stain-negative, rod-shaped bacterium (strain Hh36(T)) was isolated from the No. 1 glacier in Xinjiang, north-west China. Colonies of strain Hh36(T) were pink, convex and round on PYG medium plates. Strain Hh36(T) was able to grow at 4-30 °C and pH 6.0-8.0. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Hh36(T) was related to members of the genus Arcticibacter. The major cellular fatty acids of the novel strain were iso-C15 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and iso-C17 : 0 3-OH. The G+C content of the genomic DNA was 44.0 mol%. On the basis of phenotypic characteristics and phylogenetic analysis, strain Hh36(T) is considered to represent a novel species of the genus Arcticibacter, for which the name Arcticibacter pallidicorallinus sp. nov. is proposed. The type strain is Hh36(T) ( = CGMCC 1.9313(T)  = KCTC 32542(T)).

  12. Arcticibacter eurypsychrophilus sp. nov., isolated from ice core.

    PubMed

    Shen, Liang; Liu, Yongqin; Gu, Zhengquan; Yao, Tandong; Xu, Baiqing; Wang, Ninglian; Jiao, Nianzhi; Liu, Hongcan; Zhou, Yuguang

    2015-02-01

    A Gram-stain-negative, rod-shaped, non-flagellated bacterium, strain MJ9-5(T), was isolated from ice core of Muji Glacier. Colonies of strain MJ9-5(T) were pink, convex and round on R2A agar. Strain MJ9-5(T) grew between -1 to 25 °C with an optimum growth temperature of 10-15 °C. The strain tolerated 0-1.2 % (w/v) NaCl with an optimum of 1 %. The major cellular fatty acids of strain MJ9-5(T) were iso-C15 : 0, summed feature 3 (C16 : 1ω6c and/or C1 6 : 1ω7c). The G+C content of the genomic DNA was 38.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MJ9-5(T) was related to members of the genus Arcticibacter. On the basis of the phenotypic characteristics and phylogenetic analysis, a novel species of this genus, Arcticibacter eurypsychrophilus sp. nov., is proposed. The type strain is MJ9-5(T) ( = KCTC 42008(T) = JCM 19862(T)).

  13. Streptomyces ziwulingensis sp. nov., isolated from grassland soil.

    PubMed

    Lin, Yan Bing; Wang, Xin Ye; Wang, Ting Ting; An, Shao Shan; Shi, Peng; Wei, Ge Hong

    2013-04-01

    A novel actinobacterium, designated strain F22(T), was isolated from grassland soil collected from the Ziwuling area on the Loess Plateau, China. The novel strain was found to have morphological and chemotaxonomic characteristics typical of members of the genus Streptomyces. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain F22(T) belonged to the genus Streptomyces, being most closely related to Streptomyces resistomycificus NBRC 12814(T) (98.28 % sequence similarity), Streptomyces ciscaucasicus NBRC 12872(T) (98.14 %), Streptomyces chartreusis NBRC 12753(T) (98.14 %) and Streptomyces canus NRRL B-1989(T) (98.14 %). In DNA-DNA hybridizations and comparisons of morphological and phenotypic data, strain F22(T) could be distinguished from all of its closest phylogenetic relatives. Strain F22(T) exhibited antibacterial and antifungal activity, especially against Staphylococcus aureus, Bacillus subtilis and Cylindrocarpon destructans. Based on the DNA-DNA hybridization data and morphological, phenotypic and phylogenetic evidence, strain F22(T) represents a novel species of the genus Streptomyces, for which the name Streptomyces ziwulingensis sp. nov. is proposed. The type strain is F22(T) ( = CCNWFX 0001(T) = JCM 18081(T) = ACCC41875(T)).

  14. Virgibacillus soli sp. nov., isolated from mountain soil.

    PubMed

    Kämpfer, P; Arun, A B; Busse, H-J; Langer, S; Young, C-C; Chen, W-M; Syed, A A; Rekha, P D

    2011-02-01

    A Gram-positive bacterium (strain CC-YMP-6(T)) was isolated from soil samples collected from Yang-Ming Mountain, Taiwan. On the basis of 16S rRNA gene sequence analysis, strain CC-YMP-6(T) clearly belonged to the genus Virgibacillus and was most closely related to the type strains of Virgibacillus halophilus (96.2 % similarity) and Virgibacillus kekensis (96.3 %). The predominant isoprenoid quinone was menaquinone MK-7 and the polar lipid profile was composed of the major components diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and one unidentified phospholipid plus moderate amounts of two unidentified aminophospholipids and a phospholipid. The polyamine pattern comprised spermidine as the single major component with spermine and putrescine present in minor amounts. The major fatty acids of strain CC-YMP-6(T) were iso-C(15 : 0) and anteiso-C(15 : 0). The results of physiological and biochemical tests allowed the clear phenotypic differentiation of strain CC-YMP-6(T) from all recognized species of the genus Virgibacillus. Strain CC-YMP-6(T) is therefore considered to represent a novel species of the genus Virgibacillus, for which the name Virgibacillus soli sp. nov. is proposed. The type strain is CC-YMP-6(T) (=DSM 22952(T)=CCM 7714(T)). PMID:20228217

  15. Shewanella fidelis sp. nov., isolated from sediments and sea water.

    PubMed

    Ivanova, Elena P; Sawabe, Tomoo; Hayashi, Karin; Gorshkova, Nataliya M; Zhukova, Natalia V; Nedashkovskaya, Olga I; Mikhailov, Valery V; Nicolau, Dan V; Christen, Richard

    2003-03-01

    Two marine bacterial strains, KMM 3582T and KMM 3589, isolated respectively from sediments of the South China Sea and sea water of the Sea of Japan, have been characterized. Comparative 16S rDNA sequence-based phylogenetic analysis placed the two strains in a separate branch of the gamma-Proteobacteria within the members of the genus Shewanella. KMM 3582T showed the highest similarity (97.1 and 97.4%, respectively) to Shewanella pealeana and Shewanella gelidimarina. The G + C contents of the DNAs of the two strains studied were 45.0 mol%. The level of DNA-DNA relatedness between the two strains was 82%, indicating that they represent a single genospecies. These organisms were slightly pinkish, Gram-negative, polarly flagellated, facultatively anaerobic, mesophilic (with temperature range from 4 to 30 degrees C), neutrophilic and haemolytic and were able to degrade alginate, gelatin and DNA. The novel organisms were susceptible to gentamicin, lincomycin, oleandomycin, streptomycin and polymyxin. The predominant fatty acids were characteristic for shewanellae: 13 : 0-i, 15 : 0-i, 16 : 0 and 16 : 1omega7. Eicosapentaenoic acid, 20 : 5omega3, was not detected. Phylogenetic evidence, together with phenotypic characteristics, showed that the two bacteria constitute a novel species of the genus Shewanella. The name Shewanella fidelis sp. nov. is proposed, with the type strain KMM 3582T (=LMG 20551T =ATCC BAA-318T).

  16. Micromonospora yangpuensis sp. nov., isolated from a sponge.

    PubMed

    Zhang, Limin; Xi, Lijun; Ruan, Jisheng; Huang, Ying

    2012-02-01

    An actinomycete, strain FXJ6.011(T), was isolated from a cup-shaped sponge collected at Dachan reef, Yangpu in the South China Sea. The strain had morphological characteristics of members of the family Micromonosporaceae. Phylogenetic analysis of the 16S rRNA gene sequence of strain FXJ6.011(T) indicated the highest similarity (98.7 %) to Micromonospora auratinigra JCM 12357(T), Micromonospora chaiyaphumensis JCM 12873(T) and Micromonospora echinofusca JCM 3327(T). Analysis of the gyrB gene sequence also showed that strain FXJ6.011(T) should be assigned to the genus Micromonospora. It contained DD-diaminopimelic acid as the major cell-wall diamino acid and MK-10(H(2)) as predominant menaquinone. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidyl mannosides and phosphatidylinositol dimannoside. The major cellular fatty acids were iso-C(16 : 0), C(17 : 1)ω8c and C(16 : 0). Physiological and biochemical data and low DNA-DNA relatedness values enabled the strain to be differentiated from members of closely related species. Based on phenotypic and genotypic data, strain FXJ6.011(T) represents a novel Micromonospora species, for which the name Micromonospora yangpuensis sp. nov. is proposed; the type strain is FXJ6.011(T) ( = CGMCC 4.5736(T) = NBRC 107727(T)).

  17. Devosia pacifica sp. nov., isolated from deep-sea sediment.

    PubMed

    Jia, Yan-Yu; Sun, Cong; Pan, Jie; Zhang, Wei-Yan; Zhang, Xin-Qi; Huo, Ying-Yi; Zhu, Xu-Fen; Wu, Min

    2014-08-01

    A novel bacterial strain, NH131(T), was isolated from deep-sea sediment of South China Sea. Cells were strictly aerobic, Gram-stain negative, short rod-shaped and motile with a single lateral flagellum. Strain NH131(T) grew optimally at pH 6.5-7.0 and 25-30 °C. 16S rRNA gene sequence analysis revealed that strain NH131(T) belonged to the genus Devosia, sharing the highest sequence similarity with the type strain, Devosia geojensis BD-c194(T) (96.2%). The predominant fatty acids were C(18 : 1)ω7c, 11-methyl C(18 : 1)ω7c, C(18 : 0) and C(16 : 0). Ubiquinone 10 was the predominant ubiquinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipid, three glycolipids and two unknown lipids. The DNA G+C content of strain NH131(T) was 63.0 mol%. On the basis of the results of polyphasic identification, it is suggested that strain NH131(T) represents a novel species of the genus Devosia for which the name Devosia pacifica sp. nov. is proposed. The type strain is NH131(T) ( = JCM 19305(T) = KCTC 32437(T)).

  18. Bacillus lehensis sp. nov., an alkalitolerant bacterium isolated from soil.

    PubMed

    Ghosh, A; Bhardwaj, M; Satyanarayana, T; Khurana, M; Mayilraj, S; Jain, R K

    2007-02-01

    A Gram-positive, endospore-forming, alkalitolerant bacterial strain, designated MLB2T, was isolated from soil from Leh, India, and was subjected to a polyphasic taxonomic study. The strain exhibited phenotypic properties that included chemotaxonomic characteristics consistent with its classification in the genus Bacillus. Growth was observed at pH 7.0-11.0, but not at pH 6.0. The DNA G+C content was 41.4 mol%. The highest level of 16S rRNA gene sequence similarity was with Bacillus oshimensis JCM 12663T (98.8 %). However, DNA-DNA hybridization experiments indicated low levels of genomic relatedness with the type strains of B. oshimensis (62 %), Bacillus patagoniensis (55 %), Bacillus clausii (51 %) and Bacillus gibsonii (34 %), the species with which strain MLB2T formed a coherent cluster (based on the results of the phylogenetic analysis). On the basis of the phenotypic characteristics and genotypic distinctiveness of strain MLB2T, it should be classified within a novel species of Bacillus, for which the name Bacillus lehensis sp. nov. is proposed. The type strain is MLB2T (=MTCC 7633T=JCM 13820T). PMID:17267957

  19. Isolation of Paenibacillus sp. and Variovorax sp. strains from decaying woods and characterization of their potential for cellulose deconstruction

    PubMed Central

    Ghio, Silvina; Lorenzo, Gonzalo Sabarís Di; Lia, Verónica; Talia, Paola; Cataldi, Angel; Grasso, Daniel; Campos, Eleonora

    2012-01-01

    Prospection of cellulose-degrading bacteria in natural environments allows the identification of novel cellulases and hemicellulases that could be useful in second-generation bioethanol production. In this work, cellulolytic bacteria were isolated from decaying native forest soils by enrichment on cellulose as sole carbon source. There was a predominance of Gram positive isolates that belonged to the phyla Proteobacteria and Firmicutes. Many primary isolates with cellulolytic activity were not pure cultures. From these consortia, isolation of pure constituents was attempted in order to test the hypothesis whether microbial consortia are needed for full degradation of complex substrates. Two isolates, CB1-2-A-5 and VG-4-A-2, were obtained as the pure constituents of CB1-2 and VG-4 consortia, respectively. Based on 16S RNA sequence, they could be classified as Variovorax paradoxus and Paenibacillus alvei. Noteworthy, only VG-4 consortium showed measurable xylan degrading capacity and signs of filter paper degradation. However, no xylan or filter paper degrading capacities were observed for the pure cultures isolated from it, suggesting that other members of this consortium were necessary for these hydrolyzing activities. Our results indicated that Paenibacillus sp. and Variovorax sp. as well as VG-4 consortium, might be a useful source of hydrolytic enzymes. Moreover, although Variovorax sp. had been previously identified in metagenomic studies of cellulolytic communities, this is the first report on the isolation and characterization of this microorganism as a cellulolytic genus. PMID:23301200

  20. Isolation of Paenibacillus sp. and Variovorax sp. strains from decaying woods and characterization of their potential for cellulose deconstruction.

    PubMed

    Ghio, Silvina; Lorenzo, Gonzalo Sabarís Di; Lia, Verónica; Talia, Paola; Cataldi, Angel; Grasso, Daniel; Campos, Eleonora

    2012-01-01

    Prospection of cellulose-degrading bacteria in natural environments allows the identification of novel cellulases and hemicellulases that could be useful in second-generation bioethanol production. In this work, cellulolytic bacteria were isolated from decaying native forest soils by enrichment on cellulose as sole carbon source. There was a predominance of Gram positive isolates that belonged to the phyla Proteobacteria and Firmicutes. Many primary isolates with cellulolytic activity were not pure cultures. From these consortia, isolation of pure constituents was attempted in order to test the hypothesis whether microbial consortia are needed for full degradation of complex substrates. Two isolates, CB1-2-A-5 and VG-4-A-2, were obtained as the pure constituents of CB1-2 and VG-4 consortia, respectively. Based on 16S RNA sequence, they could be classified as Variovorax paradoxus and Paenibacillus alvei. Noteworthy, only VG-4 consortium showed measurable xylan degrading capacity and signs of filter paper degradation. However, no xylan or filter paper degrading capacities were observed for the pure cultures isolated from it, suggesting that other members of this consortium were necessary for these hydrolyzing activities. Our results indicated that Paenibacillus sp. and Variovorax sp. as well as VG-4 consortium, might be a useful source of hydrolytic enzymes. Moreover, although Variovorax sp. had been previously identified in metagenomic studies of cellulolytic communities, this is the first report on the isolation and characterization of this microorganism as a cellulolytic genus.

  1. Isolation of Paenibacillus sp. and Variovorax sp. strains from decaying woods and characterization of their potential for cellulose deconstruction.

    PubMed

    Ghio, Silvina; Lorenzo, Gonzalo Sabarís Di; Lia, Verónica; Talia, Paola; Cataldi, Angel; Grasso, Daniel; Campos, Eleonora

    2012-01-01

    Prospection of cellulose-degrading bacteria in natural environments allows the identification of novel cellulases and hemicellulases that could be useful in second-generation bioethanol production. In this work, cellulolytic bacteria were isolated from decaying native forest soils by enrichment on cellulose as sole carbon source. There was a predominance of Gram positive isolates that belonged to the phyla Proteobacteria and Firmicutes. Many primary isolates with cellulolytic activity were not pure cultures. From these consortia, isolation of pure constituents was attempted in order to test the hypothesis whether microbial consortia are needed for full degradation of complex substrates. Two isolates, CB1-2-A-5 and VG-4-A-2, were obtained as the pure constituents of CB1-2 and VG-4 consortia, respectively. Based on 16S RNA sequence, they could be classified as Variovorax paradoxus and Paenibacillus alvei. Noteworthy, only VG-4 consortium showed measurable xylan degrading capacity and signs of filter paper degradation. However, no xylan or filter paper degrading capacities were observed for the pure cultures isolated from it, suggesting that other members of this consortium were necessary for these hydrolyzing activities. Our results indicated that Paenibacillus sp. and Variovorax sp. as well as VG-4 consortium, might be a useful source of hydrolytic enzymes. Moreover, although Variovorax sp. had been previously identified in metagenomic studies of cellulolytic communities, this is the first report on the isolation and characterization of this microorganism as a cellulolytic genus. PMID:23301200

  2. Bacillus invictae sp. nov., isolated from a health product.

    PubMed

    Branquinho, Raquel; Sousa, Clara; Osório, Hugo; Meirinhos-Soares, Luís; Lopes, João; Carriço, João A; Busse, Hans-Jürgen; Abdulmawjood, Amir; Klein, Günter; Kämpfer, Peter; Pintado, Manuela E; Peixe, Luísa V

    2014-11-01

    A Gram-positive, rod-shaped, endospore-forming Bacillus isolate, Bi.(FFUP1) (T), recovered in Portugal from a health product was subjected to a polyphasic study and compared with the type strains of Bacillus pumilus, Bacillus safensis, Bacillus altitudinis and Bacillus xiamenensis, the phenotypically and genotypically most closely related species. Acid production from cellobiose, D-glucose and D-mannose and absence of acid production from D-arabinose, erythritol, inositol, maltose, mannitol, raffinose, rhamnose, sorbitol, starch and L-tryptophan discriminated this new isolate from the type strains of the most closely related species. Additionally, a significant different protein and carbohydrate signature was evidenced by spectroscopic techniques, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and Fourier transform IR spectroscopy with attenuated total reflectance. Using a chemometric approach, the score plot generated by principal component analysis clearly delineated the isolate as a separate cluster. The quinone system for strain Bi.(FFUP1) (T) comprised predominantly menaquinone MK-7 and major polar lipids were diphosphatidylglycerol, an unidentified phospholipid and an unidentified glycolipid. Strain Bi.(FFUP1) (T) showed ≥ 99% 16S rRNA gene sequence similarity to B. safensis FO-036b(T), B. pumilus (7061(T) and SAFR-032), B. altitudinis 41KF2b(T) and B. xiamenensis HYC-10(T). Differences in strain Bi.FFUP1 (T) gyrB and rpoB sequences in comparison with the most closely related species and DNA-DNA hybridization experiments with Bi.FFUP1 (T) and B. pumilus ATCC 7061(T), B. safensis FO-036b(T), B. altitudinis 41KF2b(T) and B. xiamenensis HYC-10(T) gave relatedness values of 39.6% (reciprocal 38.0%), 49.9% (reciprocal 42.9%), 61.9% (reciprocal 52.2%) and 61.7% (reciprocal 49.2%), respectively, supported the delineation of strain Bi.(FFUP1) (T) as a representative of a novel species of the genus Bacillus, for which the name Bacillus

  3. Candida baotianmanensis sp. nov. and Candida pseudoviswanathii sp. nov., two ascosporic yeast species isolated from the gut of beetles.

    PubMed

    Ren, Yong-Cheng; Xu, Long-Long; Zhang, Lin; Hui, Feng-Li

    2015-10-01

    Four yeast strains were isolated from the gut of beetles collected on Baotianman Mountain and People's Park of Nanyang in Henan Province, China. These strains produced unconjugated asci with one or two ellipsoidal to elongate ascospores in a persistent ascus. Phylogenetic analysis of the D1/D2 domains of the LSU rRNA gene sequences indicated that the isolates represent two novel sexual species in the Candida/Lodderomyces clade. Candida baotianmanensis sp. nov. was located in a statistically well-supported branch together with Candida maltosa. Candida pseudoviswanathii sp. nov. formed a subclade with its closest relative Candida viswanathii supported by a strong bootstrap value. The two novel species were distinguished from their most closely related described species, Candida maltosa and Candida viswanathii, in the D1/D2 LSU rRNA gene and internal transcribed spacer (ITS) sequences and in phenotypic traits. The type strain of Candida baotianmanensis sp. nov. is NYNU 14719T ( = CBS 13915T = CICC 33052T), and the type strain of Candida pseudoviswanathii sp. nov. is NYNU 14772T ( = CBS 13916T = CICC 33053T). The MycoBank numbers for Candida baotianmanensis sp. nov. and Candida pseudoviswanathii sp. nov. are MB 812621 and MB 812622.

  4. Whole-genome sequence of Enterobacter sp. strain SST3, an endophyte isolated from Jamaican sugarcane (Saccharum sp.) stalk tissue.

    PubMed

    Gan, Han Ming; McGroty, Sean E; Chew, Teong Han; Chan, Kok Gan; Buckley, Larry J; Savka, Michael A; Hudson, André O

    2012-11-01

    Enterobacter sp. strain SST3 is an endophytic bacterium isolated from Saccharum spp. Here we present its annotated draft genome that may shed light on its role as a bacterial endophyte of sugarcane. To our knowledge, this is the first genome announcement of a sugarcane-associated bacterium from the genus Enterobacter.

  5. Nitrincola nitratireducens sp. nov. isolated from a haloalkaline crater lake.

    PubMed

    Singh, Aditya; Vaidya, Bhumika; Tanuku, Naga Radha Srinivas; Pinnaka, Anil Kumar

    2015-12-01

    The novel, cream coloured, Gram-negative-staining, rod-shaped, motile bacteria, designated strains AK23(T) and AK28, were isolated from sediment samples collected from Lonar Lake, Buldhana district, India. The predominant fatty acids were C18:1ω7c, C16:0, C10:0 3OH and C16:1ω7c and/or iso-C15:0 2OH (summed feature 3). Polar lipid content of strains AK23(T) and AK28 were found to be phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphotidylserine (PS), one unidentified phospholipid (PL) and two unidentified lipids (L1 and L2). The 16S rRNA gene sequence analysis indicated strains AK23(T) and AK28 as the members of the genus Nitrincola and closely related to the type strain Nitrincola lacisaponensis with pair-wise sequence similarity of 97.67% and 97.62% respectively. DNA-DNA hybridization between strain AK23(T) and AK28 showed a relatedness of 91%. Genome of strains AK23(T) and N. lacisaponensis DSM 16316(T) were sequenced. A comparative genomics approach was used to study strains AK23(T), N. lacisaponensis DSM 16316(T) and five other phylogenetic neighbours. The genome size of N. lacisaponensis DSM 16316(T) was found to be 614,784bp smaller than that of the strain AK23(T). This variation could be due to multiple reasons, gene uptake, evolution, mutation, genome reduction phenomenon and draft nature of sequencing. Based on data from the current polyphasic study, strains AK23(T) and AK28 are proposed as novel species of the genus Nitrincola, for which the name Nitrincola nitratireducens sp. nov. is proposed. The type strain of N. nitratireducens is AK23(T) (=JCM 18788(T)=MTCC 11628(T)). PMID:26481633

  6. Pantoea theicola sp. nov., isolated from black tea.

    PubMed

    Kato Tanaka, Yuko; Horie, Nobuhiro; Mochida, Kaoru; Yoshida, Yoshihiro; Okugawa, Eri; Nanjo, Fumio

    2015-10-01

    A Gram-negative, facultatively anaerobic strain was isolated from black tea. On the basis of 16S rRNA gene sequence similarity comparisons, strain QC88-366T was grouped into the genus Pantoea, being related most closely to the type strains of Pantoea gaviniae (98.5 %) and Pantoea calida (98.3 %); sequence similarities were ≤ 97.0 % to the type strains of other species of the genus Pantoea. Multilocus sequence analysis based on partial sequences of the gyrB, rpoB, infB and atpD genes also revealed P. gaviniae and P. calida as the closest phylogenetic relatives. The fatty acid profile showed the major fatty acids of strain QC88-366T were C16 : 0, C16 : 1 and C18 : 1, the same as those of its closest related species. However, the ratio of C16 : 1, C17 : 0 cyclo, C18 : 1 and C18 : 2 differed slightly compared with those of the related neighbours. In addition, the results of physiological and biochemical tests also allowed the phenotypic differentiation of strain QC88-366T from its closest phylogenetic neighbours. The G+C content of the DNA was 57.2 mol%. Strain QC88-366T therefore represents a novel species of the genus Pantoea, for which the name Pantoea theicola sp. nov. is proposed. The type strain is QC88-366T ( = DSM 29212T = NBRC 110557T).

  7. Chitinophaga qingshengii sp. nov., isolated from weathered rock surface.

    PubMed

    Cheng, Cheng; Wang, Qi; He, Lin-Yan; Huang, Zhi; Sheng, Xia-Fang

    2015-01-01

    A novel mineral-weathering bacterium was isolated from weathered rock (potassic trachyte) surfaces collected from Nanjing (Jiangsu, PR China). Cells of strain JN246(T) were Gram-stain-negative, rod-shaped and non-motile. Strain JN246(T) was aerobic, catalase- and oxidase-positive, and grew optimally at 28 °C and pH 7.0. On the basis of 16S rRNA gene sequence analysis, strain JN246(T) belonged to the genus Chitinophaga and the closest phylogenetic relatives were Chitinophaga eiseniae YC6729(T) (98.5% 16S rRNA gene sequence similarity), Chitinophaga terrae KP01(T) (96.8%), and Chitinophaga jiangningensis JN53(T) (96.3 %). The major respiratory quinone was MK-7 and the major polyamine was homospermidine. The major fatty acids were iso-C15:0, C16:1ω5c, C16:0 and iso-C17:0 3-OH. The polar lipid profile of strain JN246(T) consisted of phosphatidylethanolamine, unknown aminolipids and unknown lipids. The genomic DNA G+C content of strain JN246(T) was 48.8 mol%. Based on the low level of DNA-DNA relatedness of strain JN246(T) (ranging from 22.6% to 42.4%) to the type strains of other species of the genus Chitinophaga and unique phenotypic characteristics, strain JN246(T) represents a novel species of the genus Chitinophaga, for which the name Chitinophaga qingshengii sp. nov. is proposed. The type strain is JN246(T) ( = CCTCC AB 2014201(T) = JCM 30026(T)).

  8. Novosphingobium colocasiae sp. nov., isolated from a taro field.

    PubMed

    Chen, Wen-Ming; Chen, Jhen-Ci; Huang, Cheng-Wen; Young, Chiu-Chung; Sheu, Shih-Yi

    2016-02-01

    A novel bacterial strain, designated Teta-03T, was isolated from a taro field in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain Teta-03T were aerobic, Gram-stain-negative, rod-shaped and non-motile and formed bright yellow colonies. Growth occurred at 10-37 °C (optimum, 20 °C), with 0-1.0 % (w/v) NaCl (optimum, 0 %) and at pH 3.0-9.0 (optimum, pH 7.0-8.0). The major fatty acids (>10 %) of strain Teta-03T were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, sphingoglycolipid, phosphatidylcholine, an uncharacterized glycolipid and an uncharacterized aminolipid. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 65.0 mol%. On the basis of 16S rRNA gene sequence analysis, strain Teta-03T was shown to belong to the genus Novosphingobium and showed highest similarity to Novosphingobium barchaimii LL02T (96.8 %). Phenotypic characteristics of the novel strain also differed from those of the closest related species of the genus Novosphingobium. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Teta-03T represents a novel species of the genus Novosphingobium, for which the name Novosphingobium colocasiae sp. nov. is proposed. The type strain is Teta-03T ( = LMG 27385T = KCTC 32255T).

  9. Halomonas xiaochaidanensis sp. nov., isolated from a salt lake sediment.

    PubMed

    Liu, Wen; Zhang, Guojing; Xian, Wendong; Yang, Jian; Yang, Lingling; Xiao, Min; Jiang, Hongchen; Li, Wen-Jun

    2016-10-01

    A short-rod-shaped moderately halophilic bacterium, designated CUG 00002(T), was isolated from the sediment of Xiaochaidan salt lake in Qinghai Province, China by using R2A medium. The cells were Gram-staining negative, aerobic, forming creamy and circular colonies with diameters of 2-3 mm on R2A agar when incubated at 30 °C for 3 days. 16S rRNA gene-based phylogenetic analysis indicated that strain CUG 00002(T) belonged to the genus Halomonas in the class Gammaproteobacteria, showing highest sequence similarity of 97.1 and 96.7 % to Halomonas mongoliensis Z-7009(T) (=DSM 17332=VKM B2353) and Halomonas shengliensis SL014B-85(T) (=CGMCC 1.6444(T)=LMG 23897(T)), respectively. The predominant isoprenoid quinone was ubiquinone-9 (Q9), and the major fatty acids were C16:0, summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c) and summed feature 8 (comprising C18:1 ω7c or C18:1 ω6c). The genomic DNA G+C content of strain CUG 00002(T) was 61.8 mol%. The above characteristics were consistent with the placement of the organism in the genus Halomonas. The level of DNA-DNA relatedness between CUG 00002(T) and its most closely related strain H. mongoliensis Z-7009(T) was 41.0 ± 1.6 %. Based on the results of phenotypic, phylogenetic and biochemical analyses, strain CUG 00002(T) represents a novel species of the genus Halomonas, for which the name Halomonas xiaochaidanensis sp. nov. is proposed. The type strain is CUG 00002(T) (=CCTCC AB 2014152(T)=KCTC 42685(T)). PMID:27177899

  10. Terrilactibacillus laevilacticus gen. nov., sp. nov., isolated from soil.

    PubMed

    Prasirtsak, Budsabathip; Thongchul, Nuttha; Tolieng, Vasana; Tanasupawat, Somboon

    2016-03-01

    A Gram-stain-positive, catalase-positive, facultatively anaerobic, spore-forming, rod-shaped bacterium, strain NK26-11T, was isolated from soil in Thailand. This strain produced d-lactic acid from glucose homofermentatively, and grew at 20-45 °C and pH 5-8.5. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major respiratory quinone was menaquinone 7 (MK-7), the DNA G+C content was 42.6 mol%, and the major cellular fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. On the basis of 16S rRNA gene sequences analysis, strain NK26-11T was closely related to Bacillus solimangrovi JCM 18994T (93.89 % 16S rRNA gene sequence similarity), Pullulanibacillus naganoensis LMG 12887T (93.32 %), Sporolactobacillus inulinus NRIC 1133T (92.99 %), Tuberibacillus calidus JCM 13397T (92.98 %) and Thalassobacillus devorans DSM 16966T ( < 90.93 %). Strain NK26-11T could be clearly distinguished from the closely related genera based on phenotypic characteristics and DNA G+C content, and thus represents a novel species of a new genus between the Bacillus and Sporolactobacillus cluster, for which the name Terrilactibacillus laevilacticus gen. nov., sp. nov. is proposed. The type strain of the type species is NK26-11T ( = LMG 27803T = TISTR 2241T = PCU 335T). PMID:26843374

  11. Taibaiella soli sp. nov., isolated from pine forest soil.

    PubMed

    Kim, Min-Kyeong; Kim, Tae-Su; Joung, Yochan; Han, Ji-Hye; Kim, Seung Bum

    2016-08-01

    A Gram-stain-negative, motile by gliding, non-spore-forming and oval-shaped bacterial strain designated T1-10T was isolated from pine forest soil, and its taxonomic position was investigated using a polyphasic approach. Growth occurred at 10-37 °C (optimum, 30 °C), at pH 6-7 and in the presence of 0-1 % (w/v) (optimum, 0 %) NaCl. Flexirubin-type pigments were produced. On the basis of 16S rRNA gene sequence similarity, strain T1-10T was assigned to the genus Taibaiella of the phylum Bacteroidetes, and the most closely related species was Taibaiella koreensis THG-DT86T with 97.11 % sequence similarity, but the strain formed an independent lineage in the phylogenetic tree. The genomic DNA G+C content of strain T1-10T was 42.5 mol%. The main cellular fatty acids were iso-C15 : 1 G, iso-C15 : 0 and iso-C17 : 0 3-OH. The only isoprenoid quinone detected in the strain was MK-7, and the major polyamine was homospermidine. The major polar lipids were phosphatidylethanolamine and unidentified aminophospholipids. Strain T1-10T could be distinguished from related species by physiological and biochemical properties. Phenotypic and phylogenetic data supported that strain T1-10T represents a novel species of the genus Taibaiella, for which the name Taibaiella soli sp. nov. is proposed (type strain T1-10T=KCTC 42277T=JCM 31014T). PMID:27222401

  12. Tumebacillus lipolyticus sp. nov., isolated from river water.

    PubMed

    Prasad, R V; Bhumika, V; Anil Kumar, P; Srinivas, N R T

    2015-12-01

    An aerobic, endospore-forming, alkali-tolerant, Gram-stain-positive, non-motile, rod-shaped bacterium, designated strain NIO-S10T, was isolated from a surface water sample collected from the Godavari River, Kapileswarapuram, India. Colonies on nutrient agar were circular, 3-4 mm in diameter, creamish and raised after incubation for 36 h at 37 °C. Growth occurred at 20-40 °C, at pH 6-9 and in the presence of 0-2 % (w/v) NaCl. Strain NIO-S10T was positive for oxidase, caseinase, DNase, gelatinase, lipase and urease activities, and negative for catalase, aesculinase, amylase and cellulase activities. The fatty acids were dominated by branched and saturated fatty acids, with a high abundance of iso-C15 : 0, anteiso-C15 : 0 and C18 : 0.The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid, and MK-7 was the major menaquinone. The DNA G+C content of strain NIO-S10T was 54.4 mol%. A blast sequence similarity search based on 16S rRNA gene sequences indicated that Tumebacillus ginsengisoli Gsoil 1105T was the nearest phylogenetic neighbour to strain NIO-S10T, with a pairwise sequence similarity of 94.9 %. Phylogenetic analysis showed that strain NIO-S10T was clustered with members of the genus Tumebacillus and together with members of the genus Effusibacillus. Based on phenotypic characteristics and phylogenetic inference, strain NIO-S10T represents a novel species of the genus Tumebacillus, for which the name Tumebacillus lipolyticus sp. nov. is proposed. The type strain is NIO-S10T ( = KCTC 32289T = MTCC 12483T). PMID:26956705

  13. Polaromonas eurypsychrophila sp. nov., isolated from an ice core.

    PubMed

    Xing, Tingting; Yao, Tandong; Liu, Yongqin; Wang, Ninglian; Xu, Bainqing; Shen, Liang; Gu, Zhengquan; Gu, Bixi; Liu, Hongcan; Zhou, Yuguang

    2016-07-01

    A Gram-stain-negative, aerobic, rod-shaped, beige bacterium, strain B717-2T, was isolated from an ice core drilled from Muztagh Glacier on the Tibetan Plateau, China. According to phylogenetic analyses based on 16S rRNA gene sequences, the novel strain was related most closely to Polaromonas vacuolataand shared 97.7 % similarity with the type strain of this species. It grew optimally at pH 7, at 15 °C and with 2 % (w/v) NaCl. Major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), summed feature 8 (C18 : 1ω7c, C18 : 1ω6c) and C16 : 0. The sole respiratory quinone was Q-8. The DNA G+C content was 63.4 mol %. In DNA-DNA hybridization tests, strain B717-2T shared 37.0±1.9, 30.0±1.7, 26.0±0.9, 23.4±0.5 and 18.4±1.9 % DNA-DNA relatedness with Polaromonas jejuensisJS12-13T, P. vacuolata 34-PT, Polaromonas aquatica CCUG 39402T, Polaromonas glacialisCr4-12T and Polaromonas cryoconitiCr4-35T, respectively. Based on the phenotypic, phylogenetic and genetic characteristics, strain B717-2T represents a novel species of the genus Polaromonas, for which the name Polaromonaseurypsychrophila sp. nov. is proposed. The type strain is B717-2T (=CGMCC 1.15322T=JCM 31171T). PMID:27082956

  14. Luteimonas tolerans sp. nov., isolated from hexachlorocyclohexane-contaminated soil.

    PubMed

    Rani, Pooja; Mukherjee, Udita; Verma, Helianthous; Kamra, Komal; Lal, Rup

    2016-04-01

    A Gram-stain-negative, aerobic, rod-shaped, non-spore-forming, yellow pigmented bacterial strain (UM1T) was isolated from the hexachlorocyclohexane (HCH)-contaminated dumpsite located at Ummari village in Lucknow, India. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain UM1T belongs to the genus Luteimonas with Luteimonas aestuarii B9T as the closest neighbour (97.2% 16S rRNA gene sequence similarity). The DNA G+C content of strain UM1T was 64.3 mol%. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). Main fatty acids were iso-C15:0, iso-C11:0, iso-C11:0 3-OH, iso-C17:0 and summed feature 9 (C16:0 10-methyl and/or iso-C17:1ω9c). Ubiquinone (Q-8) was the only respiratory quinone. Spermidine was detected as the major polyamine. The DNA-DNA relatedness value of strain UM1T with respect to its closest neighbour Luteimonas aestuarii B9T was well below 70 % (∼49%). Thus, data obtained from phylogenetic analysis, DNA-DNA hybridization, and chemotaxonomical and biochemical analyses supports classification of strain UM1T as representative of a novel species of the genus Luteimonas, for which the name Luteimonas tolerans sp. nov. is proposed. The type strain is UM1T (=DSM 28473T=MCC 2572T=KCTC 42936T). PMID:26869334

  15. Winogradskyella sediminis sp. nov., isolated from marine sediment.

    PubMed

    Zhang, De-Chao; Liu, Yan-Xia; Huang, Hai-Jun; Weber, Karin; Margesin, Rosa

    2016-08-01

    A Gram-stain-negative, rod-shaped, yellow-pigmented, gliding bacterial strain, designated S5-23-3T, was isolated from a sediment sample of the Yellow Sea in China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S5-23-3T was related to the genus Winogradskyella and had highest 16S rRNA gene sequence similarities with Winogradskyella arenosi JCM 15527T (97.6 %), Winogradskyella rapida CECT 7392T (97.4 %) and Winogradskyella undariae KCTC 32261T (97.2 %). The predominant cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C15 : 0 3-OH and iso-C17 : 0 3-OH. Strain S5-23-3T contained MK-6 as the predominant menaquinone. The polar lipid profile contained phosphatidylethanolamine, two aminolipids, one aminoglycolipid, one aminophospholipid, one unidentified phospholipid and seven unidentified polar lipids. The genomic DNA G+C content of strain S5-23-3T was 36.1 mol%. Combined data from phenotypic, chemotaxonomic, phylogenetic and DNA-DNA relatedness studies demonstrated that strain S5-23-3T is a representative of a novel species of the genus Winogradskyella, for which the name Winogradskyellasediminis sp. nov. (type strain S5-23-3T=LMG 28075T=DSM 28134T) is proposed. PMID:27189204

  16. Xanthomarina gelatinilytica gen. nov., sp. nov., isolated from seawater.

    PubMed

    Vaidya, Bhumika; Kumar, Ravinder; Sharma, Gunjan; Srinivas, Tanuku Naga Radha; Kumar, Pinnaka Anil

    2015-11-01

    A novel Gram-stain-negative, rod-shaped, yellow-pigmented, non-sporulating, non-motile bacterium, designated strain AK20T, was isolated from seawater collected from Kochi city, Kerala state, India. Colonies on marine agar were circular, yellow, shiny, translucent, 2-3 mm in diameter, convex and with entire margin. Flexirubin-type pigment was present. The fatty acids were dominated by iso-branched units with a high abundance of iso-C15:0, iso-C15:1 G, iso-C17:0 3-OH, summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH) and iso-C15:0 3-OH. Polar lipids included phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified phospholipids and four unidentified lipids. Menaquinone 6 (MK-6) was the predominant respiratory quinone. The DNA G+C content of strain AK20T was 38.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain AK20T was closely related to Formosa spongicola A2T and Bizionia paragorgiae KMM 6029T (pair-wise sequence similarities of 95.9 and 95.7%, respectively), forming a distinct branch within the family Flavobacteriaceae and clustering with the clade comprising species of the genus Bizionia. Based on phenotypic and chemotaxonomic characteristics and phylogenetic analysis, strain AK20T is different from the existing genera in the family Flavobacteriaceae, and is therefore considered to represent a novel species of a new genus, for which the name Xanthomarina gelatinilytica gen. nov., sp. nov. is proposed. The type strain of Xanthomarina gelatinilytica is AK20T ( = MTCC 11705T = JCM 18821T). PMID:26956595

  17. Thalassobius litorarius sp. nov., isolated from a tidal flat.

    PubMed

    Park, Inhye; Cha, In-Tae; Seo, Myung-Ji

    2016-04-01

    A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium, belonging to the family Rhodobacteraceae, designated strain MME-075T, was isolated from a tidal flat. Strain MME-075T grew with 1-5% (w/v) NaCl at 20-35 °C and at pH 7-9. Optimal growth occurred with 2% (w/v) NaCl at 25-30 °C and at pH 7. The dominant respiratory quinone was ubiquinone-10, whereas summed feature 8 (C18:1ω7c and/or C18:1ω6c), 11-methyl C18:1ω7c, and C16:0 were the major fatty acids. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unidentified lipid. The genomic DNA G+C content was 62.1 mol%. The highest 16S rRNA gene sequence similarity values were between strain MME-075T and Thalassobius aestuarii, Thalassococcus lentus, Thalassobius maritimus and Shimia marina and were 97.6, 97.5, 97.2 and 96.2%, respectively. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees, based on 16S rRNA gene sequences, revealed that strain MME-075T clustered with species of the genus Thalassobius. Based on phenotypic and phylogenetic taxonomic properties, this strain is proposed as a representative of a novel species of the genus Thalassobius, for which the name Thalassobius litorarius sp. nov. is proposed. The type strain is MME-075T (=KCCM 43143T=JCM 30758T). PMID:26821920

  18. Maribacter lutimaris sp. nov., isolated from marine sediment.

    PubMed

    Kim, Kyung Hyun; Jin, Hyun Mi; Jeong, Hye Im; Jeon, Che Ok

    2016-04-01

    A Gram-staining-negative, moderately halophilic and strictly aerobic bacterium, designated strain KJ4T, was isolated from marine sediment at Gangjin in South Korea. Cells were catalase- and oxidase-positive long rods with gliding motility. Growth of strain KJ4T was observed at 4-37 °C (optimum, 15-25 °C), at pH 6.0-9.0 (optimum, pH 7.0-8.5) and in the presence of 1.0-7.0% (w/v) NaCl (optimum, 2.0-5.0%). Menaquinone 6 (MK-6) was the only isoprenoid quinone detected and iso-C15:0, iso-C17:0 3-OH, iso-C15:1 G and summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c) were the major cellular fatty acids. The polar lipids of strain KJ4T consisted of phosphatidylethanolamine, an unidentified aminophospholipid and five unidentified lipids. The G+C content of the genomic DNA was 38.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KJ4T formed a distinct phylogenetic lineage within the genus Maribacter. Strain KJ4T was most closely related to Maribacter orientalis KMM 3947T with 97.4% 16S rRNA gene sequence similarity. On the basis of phenotypic, chemotaxonomic and molecular features, strain KJ4T clearly represents a novel species of the genus Maribacter, for which the name Maribacter lutimaris sp. nov. is proposed. The type strain is KJ4T (=KACC 16438T=JCM 31154T). PMID:26828017

  19. Escherichia marmotae sp. nov., isolated from faeces of Marmota himalayana.

    PubMed

    Liu, Sha; Jin, Dong; Lan, Ruiting; Wang, Yiting; Meng, Qiong; Dai, Hang; Lu, Shan; Hu, Shoukui; Xu, Jianguo

    2015-07-01

    The taxonomic position of a group of seven closely related lactose-negative enterobacterial strains, which were isolated from fresh faecal samples of Marmota himalayana collected from the Qinghai-Tibetan plateau, China, was determined by using a polyphasic approach. Cells were Gram-reaction-negative, non-sporulating, non-motile, short rods (0.5-1 × 1-2.5 μm). By 16S rRNA gene sequences, the representative strain, HT073016(T), showed highest similarity values with Escherichia fergusonii ATCC 35469(T) at 99.3%, Escherichia coli ATCC 11775(T) at 99.2%, Escherichia albertii LMG 20976(T) at 98.9%, Escherichia hermannii CIP 103176(T) at 98.4%, and Escherichia vulneris ATCC 33821(T) at 97.7%. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the seven strains formed a monophyletic group with five other species of the genus Escherichia. Digital DNA-DNA hybridization studies between strain HT073016(T) and five other species of the genus Escherichia showed that it shared less than 70% DNA-DNA relatedness with all known species of the genus Escherichia, supporting the novel species status of the strain. The DNA G+C content of strain HT073016(T) was 53.8 mol%. On the basis of phenotypic and phylogenetic characteristics, strain HT073016(T) and the six other HT073016(T)-like strains were clearly distinct from the type strains of other recognized species of the genus Escherichia and represent a novel species of the genus Escherichia, for which the name Escherichia marmotae sp. nov. is proposed, with HT073016(T) ( = CGMCC 1.12862(T) = DSM 28771(T)) as the type strain.

  20. Nitrincola nitratireducens sp. nov. isolated from a haloalkaline crater lake.

    PubMed

    Singh, Aditya; Vaidya, Bhumika; Tanuku, Naga Radha Srinivas; Pinnaka, Anil Kumar

    2015-12-01

    The novel, cream coloured, Gram-negative-staining, rod-shaped, motile bacteria, designated strains AK23(T) and AK28, were isolated from sediment samples collected from Lonar Lake, Buldhana district, India. The predominant fatty acids were C18:1ω7c, C16:0, C10:0 3OH and C16:1ω7c and/or iso-C15:0 2OH (summed feature 3). Polar lipid content of strains AK23(T) and AK28 were found to be phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphotidylserine (PS), one unidentified phospholipid (PL) and two unidentified lipids (L1 and L2). The 16S rRNA gene sequence analysis indicated strains AK23(T) and AK28 as the members of the genus Nitrincola and closely related to the type strain Nitrincola lacisaponensis with pair-wise sequence similarity of 97.67% and 97.62% respectively. DNA-DNA hybridization between strain AK23(T) and AK28 showed a relatedness of 91%. Genome of strains AK23(T) and N. lacisaponensis DSM 16316(T) were sequenced. A comparative genomics approach was used to study strains AK23(T), N. lacisaponensis DSM 16316(T) and five other phylogenetic neighbours. The genome size of N. lacisaponensis DSM 16316(T) was found to be 614,784bp smaller than that of the strain AK23(T). This variation could be due to multiple reasons, gene uptake, evolution, mutation, genome reduction phenomenon and draft nature of sequencing. Based on data from the current polyphasic study, strains AK23(T) and AK28 are proposed as novel species of the genus Nitrincola, for which the name Nitrincola nitratireducens sp. nov. is proposed. The type strain of N. nitratireducens is AK23(T) (=JCM 18788(T)=MTCC 11628(T)).

  1. Actinomadura rayongensis sp. nov., isolated from peat swamp forest soil.

    PubMed

    Phongsopitanun, Wongsakorn; Tanasupawat, Somboon; Suwanborirux, Khanit; Ohkuma, Moriya; Kudo, Takuji

    2015-03-01

    A novel actinomycete strain RY35-68(T), isolated from a peat swamp forest soil sample in Rayong Province, Thailand, was characterized using a polyphasic approach. The strain belonged to the genus Actinomadura based on morphological and chemotaxonomic characteristics. Cell-wall analysis revealed the presence of meso-diaminopimelic acid and N-acetylmuramic acid in the peptidoglycan layer. The diagnostic sugar in whole-cell hydrolysates was identified as madurose. The predominant menaquinones were MK-9(H6), MK-9(H8) and MK-9(H4). The major cellular fatty acids were C16 : 0 and iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. The genomic DNA G+C content was 73.7 mol%. On the basis of 16S rRNA gene sequence similarity analysis, strain RY35-68(T) was closely related to the species Actinomadura atramentaria JCM 6250(T) (97.5 %). The value of DNA-DNA relatedness between strain RY35-68(T) and A. atramentaria JCM 6250(T) was 37.6-42.6 %. On the basis of its phenotypic characteristics and these results mentioned, this strain could be distinguished from the closely related type strain and represents a novel species of the genus Actinomadura, for which the name Actinomadura rayongensis sp. nov. (type strain RY35-68(T) = JCM 19830(T) = TISTR 2211(T) = PCU 332(T)) is proposed.

  2. Escherichia marmotae sp. nov., isolated from faeces of Marmota himalayana.

    PubMed

    Liu, Sha; Jin, Dong; Lan, Ruiting; Wang, Yiting; Meng, Qiong; Dai, Hang; Lu, Shan; Hu, Shoukui; Xu, Jianguo

    2015-07-01

    The taxonomic position of a group of seven closely related lactose-negative enterobacterial strains, which were isolated from fresh faecal samples of Marmota himalayana collected from the Qinghai-Tibetan plateau, China, was determined by using a polyphasic approach. Cells were Gram-reaction-negative, non-sporulating, non-motile, short rods (0.5-1 × 1-2.5 μm). By 16S rRNA gene sequences, the representative strain, HT073016(T), showed highest similarity values with Escherichia fergusonii ATCC 35469(T) at 99.3%, Escherichia coli ATCC 11775(T) at 99.2%, Escherichia albertii LMG 20976(T) at 98.9%, Escherichia hermannii CIP 103176(T) at 98.4%, and Escherichia vulneris ATCC 33821(T) at 97.7%. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the seven strains formed a monophyletic group with five other species of the genus Escherichia. Digital DNA-DNA hybridization studies between strain HT073016(T) and five other species of the genus Escherichia showed that it shared less than 70% DNA-DNA relatedness with all known species of the genus Escherichia, supporting the novel species status of the strain. The DNA G+C content of strain HT073016(T) was 53.8 mol%. On the basis of phenotypic and phylogenetic characteristics, strain HT073016(T) and the six other HT073016(T)-like strains were clearly distinct from the type strains of other recognized species of the genus Escherichia and represent a novel species of the genus Escherichia, for which the name Escherichia marmotae sp. nov. is proposed, with HT073016(T) ( = CGMCC 1.12862(T) = DSM 28771(T)) as the type strain. PMID:25851592

  3. Micromonospora zhanjiangensis sp. nov., isolated from mangrove forest soil.

    PubMed

    Zhang, Li; Li, Lei; Deng, Zixin; Hong, Kui

    2015-12-01

    A novel actinomycete, designated strain 2902at01T was isolated from soil collected at a mangrove forest in Zhanjiang, Guangdong province, China. The strain was identified using a polyphasic classification method. The 16S rRNA gene sequence of strain 2902at01T showed the highest similarity to Micromonospora equina Y22T (98.3 %) and Micromonospora pattaloongensis TJ2-2T (98.1 %). Phylogenetic analysis based on the gyrB gene sequence also clearly showed that the strain was different from any previously discovered species of the genus Micromonospora. The characteristic whole-cell sugars were ribose and xylose. The cell-wall hydrolysates contained alanine, asparagine, glycine and meso-diaminopimelic acid. MK-10(H6) and MK-10(H8) were the major menaquinones of the novel strain. The predominant fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0. The characteristic polar lipids of strain 2902at01T were phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and diphosphatidylglycerol. The DNA G+C content was 70.2 mol%. DNA-DNA hybridization data combined with other physiological and biochemical features could distinguish strain 2902at01T from the reference strains M. equina Y22T and M. pattaloongensis TJ2-2 T. On the basis of these phenotypic and genotypic data, strain 2902at01T represents a novel species of the genus Micromonospora, for which the name Micromonospora zhanjiangensis sp. nov. is proposed. The type strain is 2902at01T ( = CCTCC AA2014018T = DSM 45902T). PMID:26446196

  4. Streptomyces ferrugineus sp. nov., isolated from mangrove soil in Thailand.

    PubMed

    Ruan, Chang-ying; Zhang, Li; Ye, Wan-wan; Xie, Xiu-chao; Srivibool, Rattanaporn; Duangmal, Kannika; Pathom-aree, Wasu; Deng, Zi-xin; Hong, Kui

    2015-01-01

    Bacterial strain HV38(T) was isolated from mangrove soil, which was collected from Thailand. Chemotaxonomic and morphological characteristics were found to be typical of members of the genus Streptomyces. The strain was found to form a distinct phyletic line in the Streptomyces 16S rRNA gene tree and to be closely associated with the type strains of Streptomyces coeruleofuscus CGMCC 4.1667(T) (98.84 % sequence similarity), Streptomyces chromofuscus CGMCC 4.1451(T) (98.63 %) and Streptomyces albidoflavus CGMCC 4.1291(T) (98.56 %). The major menaquinones were identified as MK-9(H8) and MK-9(H10). Its major cellular fatty acids were found to be iso-C14:0, iso-C15:0, anteiso-C15:0, iso-C16:1ω8c, C16:0, anteiso-C16:1ω8c, iso-C16:0 and anteiso-C16:0. The DNA-DNA hybridization values between strain HV38(T) with S. coeruleofuscus CGMCC 4.1667(T), S. chromofuscus CGMCC 4.1451(T) and S. albidoflavus CGMCC 4.1291(T) were 32.7 ± 0.9, 21.8 ± 0.3 and 19.9 ± 0.9 %, respectively, which clearly supported the conclusion that they belong to separate genomic species. Cumulatively, the data indicated that strain HV38(T) represents a novel species of the genus Streptomyces, for which the name Streptomyces ferrugineus sp. nov. is proposed. The type strain is HV38(T) (=CCTCC AA2014009(T )= DSM 42152(T)). PMID:25331336

  5. Dactylosporangium darangshiense sp. nov., isolated from rock soil.

    PubMed

    Seo, Seong Hae; Lee, Soon Dong

    2010-06-01

    A novel actinomycete was isolated from soil of a rock surface collected from the peak of Darangshi Oreum (Small Mountain) in Jeju, Republic of Korea. Phylogenetic analyses based on 16S rRNA gene sequences demonstrated that strain DLS-44(T) belonged to the genus Dactylosporangium, with the type strains of Dactylosporangium roseum (99.1 % sequence similarity) and Dactylosporangium fulvum (99.0 %) as the nearest phylogenetic relatives. Substrate mycelium was abundant, irregularly branched, twisted and vivid orange-yellow in colour. Aerial mycelium was not produced on most media tested. Finger-shaped sporangia and globose bodies were formed directly from the vegetative mycelium. The combination of morphological and chemotaxonomic characteristics supported assignment of the actinomycete to the genus Dactylosporangium. Strain DLS-44(T) could be distinguished clearly from all type strains of the genus based on its physiological properties (utilization of methyl alpha-d-mannoside and glycerol, nitrate reduction and growth at 20 degrees C and pH 9.1) and some chemotaxonomic characteristics (absence of unsaturated fatty acids). DNA-DNA relatedness values between strain DLS-44(T) and its closest phylogenetic relatives were 12.2-14.8 % with D. roseum DSM 43916(T) and 2.5-3.6 % with D. fulvum IMSNU 22055(T). On the basis of phenotypic, phylogenetic and DNA-DNA hybridization data, strain DLS-44(T) represents a novel species of the genus Dactylosporangium, for which the name Dactylosporangium darangshiense sp. nov. is proposed. The type strain is strain DLS-44(T) (=KCTC 19560(T) =DSM 45260(T)).

  6. Streptosporangium saharense sp. nov., an actinobacterium isolated from Saharan soil.

    PubMed

    Chaabane Chaouch, Fawzia; Bouras, Noureddine; Mokrane, Salim; Zitouni, Abdelghani; Schumann, Peter; Spröer, Cathrin; Sabaou, Nasserdine; Klenk, Hans-Peter

    2016-03-01

    A novel actinobacterium, designated strain SG20T, was isolated from a Saharan soil sample collected from Béni-isguen (Mzab), Ghardaïa province, southern Algeria. The micro-organism developed small roundish sporangia on aerial mycelium that were sessile or carried by very short sporangiophores. The cell-wall peptidoglycan contained meso-diaminopimelic acid and the whole-cell sugars comprised glucose, ribose and mannose, but madurose was not detected. The predominant menaquinones were MK-9(H4), MK-9(H6) and MK-9(H2). The major fatty acids were iso-C16 : 0 and C16 : 0. The phospholipids detected were diphosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine and unknown lipids. The phenotypic and chemotaxonomic characteristics of the novel strain resembled those of recognized members of the genus Streptosporangium. Moreover, phylogenetic analysis based on a 16S rRNA gene sequence generated from the strain identified its closest relative as Streptosporangium jomthongense BCC 53154T (98.5 % similarity), which produces single spores on aerial mycelium, but no sporangia. In hybridization experiments, the DNA-DNA relatedness values recorded between strain SG20T and S. jomthongense DSM 46822T fell well below 70 %. On the basis of phenotypic and genotypic data, strain SG20T can be distinguished as representing a novel species of the genus Streptosporangium, for which the name Streptosporangium saharense sp. nov. is proposed. The type strain is SG20T ( = DSM 46743T = CECT 8840T). PMID:26755450

  7. Chitinophaga qingshengii sp. nov., isolated from weathered rock surface.

    PubMed

    Cheng, Cheng; Wang, Qi; He, Lin-Yan; Huang, Zhi; Sheng, Xia-Fang

    2015-01-01

    A novel mineral-weathering bacterium was isolated from weathered rock (potassic trachyte) surfaces collected from Nanjing (Jiangsu, PR China). Cells of strain JN246(T) were Gram-stain-negative, rod-shaped and non-motile. Strain JN246(T) was aerobic, catalase- and oxidase-positive, and grew optimally at 28 °C and pH 7.0. On the basis of 16S rRNA gene sequence analysis, strain JN246(T) belonged to the genus Chitinophaga and the closest phylogenetic relatives were Chitinophaga eiseniae YC6729(T) (98.5% 16S rRNA gene sequence similarity), Chitinophaga terrae KP01(T) (96.8%), and Chitinophaga jiangningensis JN53(T) (96.3 %). The major respiratory quinone was MK-7 and the major polyamine was homospermidine. The major fatty acids were iso-C15:0, C16:1ω5c, C16:0 and iso-C17:0 3-OH. The polar lipid profile of strain JN246(T) consisted of phosphatidylethanolamine, unknown aminolipids and unknown lipids. The genomic DNA G+C content of strain JN246(T) was 48.8 mol%. Based on the low level of DNA-DNA relatedness of strain JN246(T) (ranging from 22.6% to 42.4%) to the type strains of other species of the genus Chitinophaga and unique phenotypic characteristics, strain JN246(T) represents a novel species of the genus Chitinophaga, for which the name Chitinophaga qingshengii sp. nov. is proposed. The type strain is JN246(T) ( = CCTCC AB 2014201(T) = JCM 30026(T)). PMID:25342110

  8. Microbacterium hydrothermale sp. nov., an actinobacterium isolated from hydrothermal sediment.

    PubMed

    Zhang, Yubian; Ren, Huihui; Zhang, Gaiyun

    2014-10-01

    A Gram-stain-positive, aerobic, non-motile, rod-shaped bacterium, strain 0704C9-2(T), was isolated from hydrothermal sediment of the Indian Ocean. The organism grew with 0-5% (w/v) NaCl and at 10-37 °C, with optimal growth occurring with 1% NaCl and at 28-30 °C. Comparative 16S rRNA gene sequence analysis revealed that strain 0704C9-2(T) belonged to the genus Microbacterium. It exhibited highest 16S rRNA gene sequence similarity with Microbacterium testaceum DSM 20166(T) (98.4%). Levels of similarity with the type strains of all other recognized species of the genus Microbacterium were less than 98.0%. DNA-DNA hybridization experiments with strain 0704C9-2(T) and its closest relative, M. testaceum DSM 20166(T), revealed a low reassociation value of 42.9%. The DNA G+C content of strain 0704C9-2(T) was 73.3 mol%. The cell-wall peptidoglycan contained ornithine and the acyl type was glycolyl. The major whole-cell sugars were mannose, galactose, rhamnose and glucose. The major cellular fatty acids were anteiso-C15:0, anteiso-C17:0, iso-C16:0 and iso-C15:0. The predominant menaquinones were MK-11, MK-10 and MK-12. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two unknown glycolipids and an unknown phospholipid. On the basis of phenotypic, phylogenetic and genotypic data, strain 0704C9-2(T) represents a novel species within the genus Microbacterium, for which the name Microbacterium hydrothermale sp. nov. is proposed. The type strain is 0704C9-2(T) ( = LMG 27542(T) = CGMCC 1.12512(T)).

  9. Terrabacter aeriphilus sp. nov., isolated from an air sample.

    PubMed

    Weon, Hang-Yeon; Son, Jung-A; Yoo, Seung-Hee; Kim, Byung-Yong; Kwon, Soon-Wo; Schumann, Peter; Kroppenstedt, Reiner; Stackebrandt, Erko

    2010-05-01

    A novel actinomycete, designated strain 5414T-18(T), was isolated from an air sample collected from the Taean region, Korea. The strain contained oxidase and grew in the presence of 7 % NaCl. A neighbour-joining tree constructed on the basis of the 16S rRNA gene sequence showed that strain 5414T-18(T) is a member of the genus Terrabacter, sharing 97.8-98.3 % 16S rRNA gene sequence similarities to type strains of species of the genus Terrabacter (98.3 % sequence similarity with Terrabacter lapilli LR-26(T)). It contained peptidoglycan containing ll-diaminopimelic acid of A3gamma type, with three glycine residues as the interpeptide bridge. Whole-cell sugars were glucose, mannose and ribose. Mycolic acids were absent. The predominant menaquinone was MK-8(H(4)). The major fatty acids (>7 % of total fatty acids) were iso-C(15 : 0), iso-C(16 : 0), C(17 : 1)omega8c and iso-C(14 : 0). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol and an unidentified phosphoglycolipid. The DNA G+C content of the type strain was 73 mol%. Strain 5414T-18(T) exhibited DNA-DNA relatedness levels of 44, 43, 39, 34 and 34 % to the type strains of Terrabacter lapilli, Terrabacter aerolatus, Terrabacter terrae, Terrabacter tumescens and Terracoccus luteus, respectively. These findings suggest that strain 5414T-18(T) represents a novel species within the genus Terrabacter. The name Terrabacter aeriphilus sp. nov. is proposed for this novel species, with the type strain 5414T-18(T) (=KACC 20693(T)=DSM 18563(T)).

  10. Roseomonas eburnea sp. nov., isolated from activated sludge.

    PubMed

    Wang, Chenghong; Deng, Shikai; Liu, Xin; Yao, Li; Shi, Chao; Jiang, Jin; Kwon, Soon-Wo; He, Jian; Li, Jiayou

    2016-01-01

    A Gram-stain-negative, aerobic, short rod-shaped, non-endospore-forming, ivory-pigmented and non-motile bacterium, designated strain BUT-5T, was isolated from activated sludge of an herbicides-manufacturing wastewater treatment facility in Jiangsu Province, China. The major fatty acids (>5 % of total fatty acids) were C16 : 0, C18 : 1 2-OH and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The predominant respiratory quinone was ubiquinone Q-10. The polar lipids profile of strain BUT-5T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and two unknown aminolipids. The DNA G+C content was 67.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BUT-5T showed the highest sequence similarities to Roseomonas soli 5N26T (97.5 % 16S rRNA gene sequence similarity), followed by Roseomonas lacus TH-G33T (97.3 %) and Roseomonas terrae DS-48T (97.1 %). Strain BUT-5T showed low DNA-DNA relatedness with Roseomonas soli KACC 16376T (41 %), Roseomonas lacus KACC 11678T (46 %) and Roseomonas terrae KACC 12677T (42 %), respectively. On the basis of phenotypic and genotypic properties, as well as chemotaxonomic data, strain BUT-5T represents a novel species of the genus Roseomonas, for which the name Roseomonas eburnea sp. nov. is proposed. The type strain is BUT-5T ( = CCTCC AB2013276T = KACC 17166T).

  11. Kaistia terrae sp. nov., isolated from a wetland in Korea.

    PubMed

    Kim, Soo-Jin; Weon, Hang-Yeon; Kim, Yi-Seul; Anandham, Rangasamy; Yoo, Seung-Hee; Park, In-Cheol; Kwon, Soon-Wo

    2010-04-01

    An ivory-coloured bacterium, designated strain 5YN7-3(T), was isolated from a wetland, Yongneup, Korea. Cells of the strain were aerobic, Gram-stain-negative, non-motile and short rods. 16S rRNA gene sequence analysis demonstrated that strain 5YN7-3(T) belongs to the order Rhizobiales of the class Alphaproteobacteria and is closely related to Kaistia soli 5YN9-8(T) (97.8 %), Kaistia granuli Ko04(T) (97.6 %) and Kaistia adipata Chj404(T) (97.4 %). Strain 5YN7-3(T) showed DNA-DNA hybridization values of 28, 22 and 35 % with K. granuli Ko04(T), K. soli 5YN9-8(T) and K. adipata Chj404(T), respectively. The major fatty acids were C(18 : 1)omega7c (51.2 %), C(19 : 0) cyclo omega8c (25.0 %), C(18 : 0) (12.9 %) and C(16 : 0) (10.8 %) (>10 % of total fatty acids). Ubiquinone-10 was the major isoprenoid quinone and the DNA G+C content was 66.5 mol%. The phenotypic characteristics in combination with 16S rRNA gene sequence analysis and DNA-DNA hybridization data clearly define strain 5YN7-3(T) as a novel species of the genus Kaistia, for which the name Kaistia terrae sp. nov. is proposed. The type strain is 5YN7-3(T) (=KACC 12910(T) =DSM 21341(T)).

  12. Streptomyces lopnurensis sp. nov., an actinomycete isolated from soil.

    PubMed

    Zheng, Bei; Han, Xiao-Xue; Xia, Zhan-Feng; Wan, Chuan-Xing; Zhang, Li-Li

    2014-12-01

    A novel actinomycete, designated strain TRM 49590(T), was isolated from a soil sample from Lop Nur in Xinjiang Province, China. Strain TRM 49590(T) was aerobic, Gram-staining-positive, with an optimum NaCl concentration for growth of 1.5 % (w/v) and an optimum temperature for growth of 28-37 °C. The aerial mycelium was sparse, cylindrical and smooth-surfaced with irregular branches on ISP medium 4. The whole-cell sugars of strain TRM 49590(T) were ribose and glucose. The diagnostic diamino acid contained ll-diaminopimelic acid. The predominant menaquinones were MK-9(H6) and MK-9(H8), with MK-9(H4) and MK-10(H6) present in smaller amounts. The major fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The G+C content of the genomic DNA was 62.2 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol and phosphatidylinositol mannoside. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain TRM 49590(T) belongs to the genus Streptomyces with a sequence similarity of 97.16 % with the most closely related species Streptomyces sodiiphilus. Based on these observations, strain TRM 49590(T) is proposed to represent a novel species of the genus Streptomyces for which the name Streptomyces lopnurensis sp. nov. is suggested. The type strain is TRM 49590(T) ( = CCTCC AA 2013018(T) = NRRL B59109(T)). PMID:25253072

  13. Shewanella seohaensis sp. nov., isolated from a tidal flat sediment.

    PubMed

    Yoon, Jung-Hoon; Park, Sooyeon; Jung, Yong-Taek; Lee, Jung-Sook

    2012-06-01

    A Gram-negative, motile and rod-shaped bacterial strain, designated S7-3(T), was isolated from a tidal flat sediment at Saemankum on the western coast of Korea. Phylogenetic analyses based on 16S rRNA gene and gyrB sequences showed that strain S7-3(T) belonged to the genus Shewanella, clustering with Shewanella decolorationis S12(T). Strain S7-3(T) exhibited 98.8 % 16S rRNA gene sequence similarity and 96.8 % gyrB sequence similarity to S. decolorationis S12(T), respectively. The 16S rRNA gene sequence similarity values between strain S7-3(T) and other members of the genus Shewanella were in the range of 93.0-98.0 %. Strain S7-3(T) contained simultaneously both menaquinones (MK) and ubiquinones (Q); the predominant menaquinone was MK-7 and the predominant ubiquinones were Q-7 and Q-8. The fatty acid profiles of strain S7-3(T) and S. decolorationis JCM 21555(T) were similar; major components were C(17:1) ω8c, iso-C(15:0) and iso-C(15:0) 2-OH and/or C(16:1) ω7c. The DNA G+C content of strain S7-3(T) was 51.8 mol% and its mean DNA-DNA relatedness value with S. decolorationis JCM 21555(T) was 43 %. Differential phenotypic properties of strain S7-3(T), together with the phylogenetic and genetic distinctiveness, revealed that this strain is distinguishable from recognized Shewanella species. On the basis of the data presented, strain S7-3(T) is considered to represent a novel Shewanella species, for which the name Shewanella seohaensis sp. nov. is proposed. The type strain is S7-3(T) (=KCTC 23556(T) = CCUG 60900(T)).

  14. Nocardioides gilvus sp. nov., isolated from Namtso Lake.

    PubMed

    Zhang, Heng-Xi; Wang, Kan; Xu, Zhen-Xing; Chen, Guan-Jun; Du, Zong-Jun

    2016-10-01

    A Gram-stain positive, facultatively anaerobic, non-motile and rod to coccoid-shaped bacterium, designated XZ17(T), was isolated from Namtso Lake of Tibet, China. Strain XZ17(T) grew optimally at pH 8.0-9.0, at 30-33 °C and in the presence of 0-1.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain XZ17(T) belongs to the genus Nocardioides in the family Nocardioidaceae. Strain XZ17(T) shared pairwise 16S rRNA gene sequence similarities of 97.2, 96.8, 96.5, 96.4 and <96.0 % to Nocardioides solisilvae KCTC 39528(T), Nocardioides daejeonensis JCM 16922(T), Nocardioides jensenii NCIB 9770(T), Nocardioides dubius KCTC 9992(T) and other Nocardioides species, respectively. It contained MK-8 (H4) as the predominant menaquinone and C17:1 ω8c, C15:0, C17:0 and C18:1 ω9c as the major fatty acid. The strain had cell wall peptidoglycan based on LL-2,6-diaminopimelic acid. The polar lipids of strain XZ17(T) comprised diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids, three unidentified glycolipids and two unidentified lipids. The DNA G+C content of strain XZ17(T) was 68.9 mol%. Based on distinctive phenotypic characteristics, phylogenetic analysis and chemotaxonomic data, it can be concluded that strain XZ17(T) represents a novel species within the genus Nocardioides, for which the name Nocardioides gilvus sp. nov. is proposed. The type strain is strain XZ17(T) (=KCTC 39561(T) = MCCC 1H00114(T)).

  15. Halomonas xiaochaidanensis sp. nov., isolated from a salt lake sediment.

    PubMed

    Liu, Wen; Zhang, Guojing; Xian, Wendong; Yang, Jian; Yang, Lingling; Xiao, Min; Jiang, Hongchen; Li, Wen-Jun

    2016-10-01

    A short-rod-shaped moderately halophilic bacterium, designated CUG 00002(T), was isolated from the sediment of Xiaochaidan salt lake in Qinghai Province, China by using R2A medium. The cells were Gram-staining negative, aerobic, forming creamy and circular colonies with diameters of 2-3 mm on R2A agar when incubated at 30 °C for 3 days. 16S rRNA gene-based phylogenetic analysis indicated that strain CUG 00002(T) belonged to the genus Halomonas in the class Gammaproteobacteria, showing highest sequence similarity of 97.1 and 96.7 % to Halomonas mongoliensis Z-7009(T) (=DSM 17332=VKM B2353) and Halomonas shengliensis SL014B-85(T) (=CGMCC 1.6444(T)=LMG 23897(T)), respectively. The predominant isoprenoid quinone was ubiquinone-9 (Q9), and the major fatty acids were C16:0, summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c) and summed feature 8 (comprising C18:1 ω7c or C18:1 ω6c). The genomic DNA G+C content of strain CUG 00002(T) was 61.8 mol%. The above characteristics were consistent with the placement of the organism in the genus Halomonas. The level of DNA-DNA relatedness between CUG 00002(T) and its most closely related strain H. mongoliensis Z-7009(T) was 41.0 ± 1.6 %. Based on the results of phenotypic, phylogenetic and biochemical analyses, strain CUG 00002(T) represents a novel species of the genus Halomonas, for which the name Halomonas xiaochaidanensis sp. nov. is proposed. The type strain is CUG 00002(T) (=CCTCC AB 2014152(T)=KCTC 42685(T)).

  16. Uruburuella testudinis sp. nov., isolated from tortoise (Testudo).

    PubMed

    Kuhnert, Peter; Thomann, Andreas; Brodard, Isabelle; Haefeli, Willi; Korczak, Bożena M

    2015-04-01

    A polyphasic taxonomic analysis was carried out on 11 uncommon Gram-stain-negative, non-motile, catalase- and oxidase-positive, but indole-negative, bacterial strains isolated from tortoises. Phenotypically and genetically they represented a homogeneous group of organisms most closely related to, but distinct from, Uruburuella suis. In a reconstructed 16S rRNA gene tree they clustered on a monophyletic branch next to U. suis with gene similarities between strains of 99.5-100%, and of up to 98.2% with U. suis . DNA-DNA hybridization indicated the organisms represented a novel species with only 40% DNA-DNA similarity with U. suis . Partial sequencing of rpoB resulted in two subclusters confirming the 16S rRNA gene phylogeny; both genes allowed clear separation and identification of the novel species. Furthermore, they could be unambiguously identified by matrix-assisted laser desorption ionization time-of-flight MS, where, again, they formed a highly homogeneous cluster separate from U. suis and other members of the family Neisseriaceae . The major fatty acids were C(16 : 0) and summed feature C(16 : 1)ω7c/iso-C(15 : 0) 2-OH. The DNA G+C content was 54.4 mol%. Based on phenotypic and genetic data we propose classifying these organisms as representatives of a novel species named Uruburuella testudinis sp. nov. The type strain is 07_OD624(T) ( = DSM 26510(T) = CCUG 63373(T)).

  17. Corynebacterium guangdongense sp. nov., isolated from a contaminated plate.

    PubMed

    Li, Yan-Xuan; Yang, Song-Zhen; Feng, Guang-Da; Wang, Yong-Hong; Zhu, Hong-Hui

    2016-08-01

    A novel Gram-reaction-positive, non-motile and facultatively anaerobic bacterium, designated strain S01T, was isolated from a nutrient agar plate kept on a laboratory clean bench at Guangdong Institute of Microbiology, PR China, which was contaminated from an unknown source. Strain S01T was found to be catalase-positive and oxidase-negative. Similarity searches revealed that the strain shared the highest 16S rRNA gene similarity with Corynebacterium humireducens MFC-5T (95.9 %). However, phylogenetic analysis based on the 16S rRNA gene sequences showed that strain S01T was closely related to Corynebacteriumdoosanense JCM 17317T (94.8 %) and Corynebacterium maris JCM 17018T (94.8 %). The major fatty acids were C18:1ω9c, C16:0, 10-methyl C18:0 and C18:0. The respiratory quinones predominantly consisted of MK-8(H2), with small amounts of MK-8 and MK-9(H2). Polar lipids contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, an unidentified aminolipid, two unidentified glycolipids and two unidentified lipids. Mycolic acids were present. The cell-wall peptidoglycan contained meso-diaminopimelic acid and the major cell-wall sugars were galactose, arabinose and glucose. The genomic DNA G+C content of strain S01T was 70.7±0.1 mol%. The results of phenotypic, phylogenetic and chemotaxonomic analyses indicated that strain S01T represents a novel species of the genus Corynebacterium, for which the name Corynebacterium guangdongense sp. nov. is proposed. The type strain is S01T (=GDMCC 1.1022T=CCTCC AB 2015423T=KCTC 39608T).

  18. Arthrobacter pityocampae sp. nov., isolated from Thaumetopoea pityocampa (Lep., Thaumetopoeidae).

    PubMed

    İnce, İkbal Agah; Demirbağ, Zihni; Katı, Hatice

    2014-10-01

    A bacterium (strain Tp2(T)) was isolated from a caterpillar of the pine processionary moth, Thaumetopoea pityocampa (Den. & Schiff.) (Lepidoptera: Thaumetopoeidae), a destructive pine forest pest. The bacterium is a Gram-stain-positive, red-pigmented coccus, oxidase-negative, nitrate-reducing, non-motile and non-spore-forming. Strain Tp2(T) was subjected to a taxonomic study using polyphasic approach that included morphological and biochemical characterizations, 16S rRNA gene sequence analysis, DNA-DNA hybridization, DNA G+C content analysis, comparative fatty acid profiles, and analyses of quinones and polar lipids. The 16S rRNA gene sequence of strain Tp2(T) revealed that Arthrobacter agilis DSM 20550(T) was the closest known strain (98% 16S rRNA gene sequence similarity). DNA-DNA hybridization of A. agilis DSM 20550(T) and strain Tp2(T) resulted in a DNA-DNA relatedness value of 11.9% (20.2% reciprocal). The DNA base composition of strain Tp2(T) was 69.5 mol%, which is consistent with the other recognized members of Actinobacteria that have a high G+C content in their genome. The polar lipid pattern of strain Tp2(T) consisted of diphosphatidylglycerol (major), phosphatidylglycerol and phosphatidylinositol and unknown glycolipids. The cellular fatty acids were anteiso C15:0 and anteiso C17:0 and the major menaquinone was MK-9(II-H2). The peptidoglycan type was A3α with an L-Lys-L-Thr-L-Ala3 interpeptide bridge. The above-mentioned characterization qualifies strain Tp2(T) as genotypically and phenotypically distinct from closely related species of the genus Arthrobacter with validly published names. Strain Tp2(T) is therefore proposed to represent a novel species of the genus Arthrobacter, described as Arthrobacter pityocampae sp. nov. The type strain is Tp2(T) ( = DSM 21719(T) = NCCB 100254(T)).

  19. Paenibacillus arachidis sp. nov., isolated from groundnut seeds.

    PubMed

    Sadaf, K; Tushar, L; Nirosha, P; Podile, A R; Sasikala, Ch; Ramana, Ch V

    2016-08-01

    A Gram-stain-positive, endospore-forming, rod-shaped, facultatively anaerobic bacterium, designated as strain E3T, was isolated from groundnut seeds. Based on the 16S rRNA gene sequence analysis, strain E3T belongs to the genus Paenibacillus with Paenibacillus thailandensis S3-4AT (96.0 %), Paenibacillus xanthinilyticus 11N27T (95.7 %), Paenibacillus mendelii C/2T (95.7 %) and other members of the genus Paenibacillus (<95.5 %) as its closest phylogenetic neighbours. The DNA G+C content of strain E3T was 53 mol%. Strain E3T was positive for gelatin hydrolysis, ammonification, catalase, chitinase production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, HCN production, siderophore production, biofilm formation, and urea and starch hydrolysis. Strain E3T had phosphatidylethanolamine, diphosphotidylglycerol, phosphatidylcholine, an unidentified aminophospholipid, two unidentified aminolipids and two unidentified lipids as polar lipids. Strain E3T had diploptene, deplopterol and bacteriohopaneterol as major hopanoids. anteiso-C15 : 0 was the predominant cellular fatty acid with significant proportions of iso-C16 : 0, C16 : 0, C17 : 0, anteiso-C17 : 0, C18 : 1ω9c and iso-C14 : 0. Strain E3T had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. On the basis of physiological, biochemical, chemotaxonomic and molecular analysis, strain E3T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus arachidis sp. nov. is proposed. The type strain is E3T (=KCTC 33574T=LMG 28417T).

  20. Terrilactibacillus laevilacticus gen. nov., sp. nov., isolated from soil.

    PubMed

    Prasirtsak, Budsabathip; Thongchul, Nuttha; Tolieng, Vasana; Tanasupawat, Somboon

    2016-03-01

    A Gram-stain-positive, catalase-positive, facultatively anaerobic, spore-forming, rod-shaped bacterium, strain NK26-11T, was isolated from soil in Thailand. This strain produced d-lactic acid from glucose homofermentatively, and grew at 20-45 °C and pH 5-8.5. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major respiratory quinone was menaquinone 7 (MK-7), the DNA G+C content was 42.6 mol%, and the major cellular fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. On the basis of 16S rRNA gene sequences analysis, strain NK26-11T was closely related to Bacillus solimangrovi JCM 18994T (93.89 % 16S rRNA gene sequence similarity), Pullulanibacillus naganoensis LMG 12887T (93.32 %), Sporolactobacillus inulinus NRIC 1133T (92.99 %), Tuberibacillus calidus JCM 13397T (92.98 %) and Thalassobacillus devorans DSM 16966T ( < 90.93 %). Strain NK26-11T could be clearly distinguished from the closely related genera based on phenotypic characteristics and DNA G+C content, and thus represents a novel species of a new genus between the Bacillus and Sporolactobacillus cluster, for which the name Terrilactibacillus laevilacticus gen. nov., sp. nov. is proposed. The type strain of the type species is NK26-11T ( = LMG 27803T = TISTR 2241T = PCU 335T).

  1. Burkholderia humi sp. nov., isolated from peat soil.

    PubMed

    Srinivasan, Sathiyaraj; Kim, Jinsoo; Kang, Sang-Rim; Jheong, Weon-Hwa; Lee, Sang-Seob

    2013-03-01

    A Gram-negative, aerobic, short-rod-shaped, non-motile bacterium designated Rs7(T), was isolated from peat soil collected from Russia and was characterized to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that the strain Rs7(T) belongs to the class Betaproteobacteria. The highest degree of sequence similarities were determined to be with Burkholderia tropica Ppe8(T) (98.4 %), Burkholderia unamae MTI-641(T) (97.8 %), Burkholderia bannensis E25(T) (97.7 %), Burkholderia heleia SA41(T) (97.0 %), and Burkholderia sacchari IPT101(T) (97.0 %). Chemotaxonomic data revealed that the strain Rs7(T) possesses ubiquinone Q-8. The polar lipid profile of strain Rs7(T) contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, and an unknown amino phospholipid. The predominant fatty acids were C(16:0), C(19:0) cyclo ω8c, and C(17:0) cyclo, all of which corroborated the assignment of the strain to the genus Burkholderia. The DNA G+C content was 63.2 mol%. DNA-DNA hybridization experiments showed less than 37.8 % DNA relatedness with closely related type strains, thus confirming separate species status. The results of physiological and biochemical tests allowed phenotypic differentiation of strain Rs7(T) from the members of the genus Burkholderia. Based on these data, Rs7(T) (=KEMC 7302-068(T) = JCM 18069(T)) should be classified as the type strain for a novel Burkholderia species, for which the name Burkholderia humi sp. nov. is proposed.

  2. Burkholderia eburnea sp. nov., isolated from peat soil.

    PubMed

    Kang, Sang Rim; Srinivasan, Sathiyaraj; Lee, Sang Seob

    2014-04-01

    A novel aerobic bacterium, designated strain RR11(T), was isolated from peat soil and was characterized by using a polyphasic taxonomic approach and identified in order to determine its taxonomic position. Strain RR11(T) is a Gram-negative, non-sporulating, motile, short-rod-shaped bacterium. 16S rRNA gene sequence analysis identified this strain as a member of the genus Burkholderia of the class Betaproteobacteria. The highest degrees of gene sequence similarity were found with Burkholderia tropica Ppe8(T) (98.0 %), B. bannensis E25(T) (97.3 %), B. ferrariae FeGI01(T) (97.1 %), B. unamae MTI-641(T) (97.1 %) and B. heleia SA41(T) (97.1 %). Strain RR11(T) had the following chemotaxonomic characteristics: the major ubiquinone was Q-8, the DNA G+C content was 60.8 mol%, the major fatty acids were C16 : 0, C19 : 0 cyclo ω8c and C17 : 0 cyclo and the polar lipid profile contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unknown aminophospholipid. Based on its morphological, physiological and chemotaxonomic characteristics, together with 16S rRNA gene sequence comparison results, strain RR11(T) represents a novel species, for which the name Burkholderia eburnea sp. nov. is proposed. The type strain is strain RR11(T) ( = KEMC 7302-065(T) = JCM 18070(T)).

  3. Bacillus vanillea sp. nov., Isolated from the Cured Vanilla Bean.

    PubMed

    Chen, Yong-gan; Gu, Feng-lin; Li, Ji-hua; Xu, Fei; He, Shu-zhen; Fang, Yi-ming

    2015-02-01

    A Gram-positive bacterium, designated strain XY18(T), was isolated from a cured vanilla bean in Hainan province, China. Cells were rod-shaped, endospore producing, and peritrichous flagella. Strain XY18(T) grew at salinities of 0-8 % (w/v) NaCl (optimally 1-4 %), pH 4.0-8.0 (optimally 5.0-7.0 %) and temperature range 20-45 °C (optimally 28-35 °C). The predominant menaquinone was MK-7. The major cellular fatty acids were anteiso-C15:0, iso-C15:0, anteiso-C17:0, and iso-C17:0. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain XY18(T) was a member of the genus Bacillus, and closely related to B. amyloliquefaciens NBRC 15535(T) and B. siamensis PD-A10(T), with 99.1 and 99.2 % sequence similarity, respectively. However, the DNA-DNA hybridization value between strain XY18(T) and B. amyloliquefaciens NBRC 15535(T) was 35.7 %. The genomic DNA G+C content of strain XY18(T) was 46.4 mol%, significantly differed from B. siamensis PD-A10(T) (41.4 %), which was higher than the range of 4 % indicative of species. On the basis of polyphasic taxonomic study, including phenotypic features, chemotaxonomy, and phylogenetic analyses, strain XY18(T) represents a novel species within the genus Bacillus, for which the name Bacillus vanillea sp. nov. is proposed. The type strain is XY18(T) (=CGMCC 8629 = NCCB 100507). PMID:25292250

  4. Sphingomonas hengshuiensis sp. nov., isolated from lake wetland.

    PubMed

    Wei, Shuzhen; Wang, Tingting; Liu, Hongliang; Zhang, Caifeng; Guo, Jiping; Wang, Qian; Liang, Kuijing; Zhang, Zhiqiang

    2015-12-01

    A polyphasic taxonomic study was undertaken to establish the status of a novel bacterium, designated strain WHSC-8T, which was isolated from soil of Hengshui Lake Wetland Reserve in Hebei province, northern China. Colonies of this strain were yellow and cells were rod-shaped, polar-flagellated and obligately aerobic, exhibiting negative Gram reaction. The strain was able to grow at 0-1 % (w/v) NaCl, pH 5-10 and 20-35 °C, with optimal growth occurring at pH 7.0 and 28 °C without NaCl. Chemotaxonomic data revealed that strain WHSC-8T possesses ubiquinone Q-10 as the predominant respiratory quinone, C18 : 1ω7c, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) as the major fatty acids, and sym-homospermidine as the major polyamine. Sphingomonadaceae-specific sphingoglycolipid was detected in the polar lipid patterns. The G+C content of the genomic DNA was 68.7 mol%. All of the above characters corroborated the assignment of the novel strain to the genus Sphingomonas. Strain WHSC-8T shared less than 97.0 % 16S rRNA gene sequence similarity with the type strains of other species of the genus Sphingomonas, except for Sphingomonas asaccharolytica DSM 10564T (97.5 %). The low DNA-DNA relatedness value and distinct phenotypic and chemotaxonomic characteristics distinguished strain WHSC-8T from closely related species of the genus Sphingomonas. Therefore, strain WHSC-8T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas hengshuiensis sp. nov. is proposed. The type strain is WHSC-8T ( = KCTC 42455T = CCTCC AB 2015265T). PMID:26410379

  5. Pedobacter xixiisoli sp. nov., isolated from bank soil.

    PubMed

    Zeng, Yanhua; Feng, Hao; Huang, Yili

    2014-11-01

    A Gram-stain-negative, rod-shaped, yellow, non-motile, aerobic bacterium (strain S27(T)) was isolated from bank soil of the Xixi wetland in Zhejiang province, PR China. Phylogenetic analysis, based on its 16S rRNA gene sequence, revealed that strain S27(T) could represent a novel species of the genus Pedobacter showing highest similarity to Pedobacter koreensis WPCB189(T) (95.45%), followed by 'Pedobacter zeaxanthinifaciens' TDMA-5 (95.22%). The temperature, pH and NaCl concentration ranges for growth were 6-37 °C (optimum 28 °C), pH 5.0-9.0 (optimum pH 7.5) and 0-3% (w/v) [optimum 0.5% (w/v)], respectively. The DNA G+C content was 36.1 mol%, MK-7 was the only respiratory quinone, and iso-C(15:0), iso-C(17:0) 3-OH and summed feature 3 (C(16:1)ω7c and/or iso-C(15:0) 2-OH) were the major fatty acids. These data all support the affiliation of strain S27(T) to the genus Pedobacter. The polar lipids of strain S27(T) comprised phosphatidylethanolamine, one unidentified aminophospholipid, four unidentified aminolipids and three unidentified lipids. However, strain S27(T) could be distinguished from other members of the genus Pedobacter due to its physiological and biochemical characteristics. Therefore, strain S27(T) represents a novel species of the genus Pedobacter, for which the name Pedobacter xixiisoli sp. nov. is proposed; the type strain is S27(T) ( =CGMCC 1.12803(T) =NBRC 110388(T)). PMID:25106922

  6. Pedobacter humi sp. nov., isolated from a playground soil.

    PubMed

    Trinh, Huan; Yi, Tae-Hoo

    2016-06-01

    A Gram-stain-negative, aerobic, non-motile, rod-shaped and yellow-pigmented bacterium, designated strain THG S15-2T, was isolated from playground soil in Sindorim-dong, Guro-gu, Seoul, South Korea. According to 16S rRNA gene sequence comparisons, strain THG S15-2T was found to be related most closely to Pedobacter ginsengisoli Gsoil 104T (97.5 % similarity), Pedobacter panaciterrae Gsoil 042T (97.4 %), Pedobacter seoulensis THG-G12T (97.1 %) and Pedobacter caeni LMG 22862T (97.1 %). The level of DNA-DNA relatedness between strain THG S15-2T and its phylogenetically closest neighbours was below 30.0 %. The only isoprenoid quinone detected in strain THG S15-2T was menaquinone-7. The DNA G+C content was 45.9 mol%. The major polar lipid was phosphatidylethanolamine. The major component in the polyamine pattern was sym-homospermidine. The major fatty acids were identified as summed feature 3 (C16:1ω7c and/or C16:1ω6c), iso-C15:0 and C16:0. These data supported the affiliation of strain THG S15-2T to the genus Pedobacter. Strain THG S15-2T was distinguished from related Pedobacter species by physiological and biochemical tests. Therefore, strain THG S15-2T represents a novel species, for which the name Pedobacter humi sp. nov. is proposed. The type strain is THG S15-2T (= KCTC 42735T = CCTCC AB 2015293T).

  7. Roseovarius antarcticus sp. nov., isolated from a decayed whale bone.

    PubMed

    Deng, Sangsang; Jiang, Fan; Chang, Xulu; Qu, Zhihao; Ren, Lvzhi; Zhang, Yumin; Kan, Wenjing; Da, Xuyang; Qiu, Xia; Kim, Myongchol; Fang, Chengxiang; Peng, Fang

    2015-07-01

    A pale yellow, ovoid- to rod-shaped and budding bacterium, designated strain M-S13-148(T), was isolated from a decayed bone of whale from the eastern coast of King George Island, South Shetlands, Antarctica. Strain M-S13-148(T) exhibited motility, aerobic growth and was Gram-stain-negative. Strain M-S13-148(T) was positive for catalase and oxidase. Growth was observed at pH 6.0-9.0, at 4-42 °C and with 0-14% (w/v) NaCl. The novel strain contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unknown phospholipid as the major polar lipids. The dominant cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), (58.8%) and C16 : 0 (11.7%). The respiratory quinone was Q-10 and the DNA G + C content was 60.9 mol%. Neighbour-joining, maximum-likelihood and minimum-evolution phylogenetic trees, based on 16S rRNA gene sequences, indicated that strain M-S13-148(T) belonged to the genus Roseovarius and was most closely related to Roseovarius nanhaiticus CCTCC AB 208317(T) (93.72% 16S rRNA gene sequence similarity). The 16S rRNA gene sequence similarity with respect to members of the genus Roseovarius ranged from 91.81 to 93.94%. On the basis of phenotypic, molecular and chemotaxonomic characteristics, strain M-S13-148 is considered to represent a novel species of the genus Roseovarius, for which the name Roseovarius antarcticus sp. nov., is proposed. The type strain is M-S13-148(T) ( = CCTCC AB2014072(T) = LMG 28420(T)).

  8. Cellulosimicrobium aquatile sp. nov., isolated from Panagal reservoir, Nalgonda, India.

    PubMed

    Sultanpuram, Vishnuvardhan Reddy; Mothe, Thirumala; Chintalapati, Sasikala; Chintalapati, Venkata Ramana

    2015-12-01

    A Gram-stain positive, non-spore forming, non-motile, yellow-pigmented, rod shaped and coccoid aerobic strain designated 3bp(T) was isolated from Panagal reservoir, at Nalgonda, Telangana, India. Based on 16S rRNA gene sequence analysis it was identified that strain 3bp(T) belongs to the class Actinobacteria and is closely related to Cellulosimicrobium funkei VTT E-072700(T), Cellulosimicrobium cellulans LMG16221(T) and Cellulosimicrobium terreum KCTC 19206(T). The DNA-DNA relatedness data demonstrated that strain 3bp(T) is distinguishable from the above three species of the genus. Further, the chemotaxonomic properties of strain 3bp(T) were consistent with those of the genus Cellulosimicrobium: MK-9(H4) was the predominant menaquinone, anteiso-C15 : 0, iso-C15:0,  anteiso-C17 : 0 and iso- C16:0 were the predominant cellular fatty acids and the cell-wall peptidoglycan contains L-lysine. The DNA G+C content of strain 3bp(T) was 73.8 mol%. The results of the polyphasic analysis allowed a clear differentiation of strain 3bp(T) from all other members of the genus Cellulosimicrobium. Strain 3bp(T) is thus considered to represent a novel member of the genus Cellulosimicrobium, for which the name Cellulosimicrobium aquatile sp. nov. is proposed. The type strain is 3bp(T) (=KCTC 39527(T) = MCC 2761(T) = LMG 28646(T)).

  9. Cryptosporangium cibodasense sp. nov., isolated from leaf litter in Indonesia.

    PubMed

    Nurkanto, Arif; Lisdiyanti, Puspita; Hamada, Moriyuki; Ratnakomala, Shanti; Shibata, Chiyo; Tamura, Tomohiko

    2015-12-01

    A novel actinomycete strain, designated LIPI11-2-Ac046T, was isolated from a leaf litter sample obtained from Cibodas Botanical Garden, West Java, Indonesia, using the rehydration and centrifugation method. The taxonomic status of this organism was established using a polyphasic approach. Comparative 16S rRNA gene sequence analysis revealed that strain LIPI11-2-Ac046T had the closest sequence similarities with members of the genus Cryptosporangium (97.99-98.90 %). The strain grew well on ISP 4 and ISP 5 media and formed sporangia. Spores of this strain were motile. The strain grew in the presence of 0-2 % (w/v) NaCl and the temperature range of 15-28 8C. The cell-wall hydrolysate contained meso-diaminopimelic acid as the diagnostic diamino acid and the whole-cell hydrolysate contained mannose, glucose, galactose, ribose and xylose, together with one unidentified O-methyl-pentose. The predominant menaquinones were MK-9(H4), MK-9(H6) and MK-9(H8), and the major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were C18 : 1ω9c, iso-C16 : 0, C16 : 0 andC17 : 1ω9c. These phenotypic characteristics corresponded to those of the genus Cryptosporangium. Meanwhile, the results of DNA-DNA hybridization as well as physiological and biochemical analyses distinguished strain LIPI11-2-Ac046T from known members of the genus Cryptosporangium. On the basis of these data, it is proposed that strain LIPI11-2-Ac046T represents a novel species of the genus Cryptosporangium, with the name Cryptosporangium cibodasense sp. nov. The type strain is LIPI11-2-Ac046T (=InaCC A457T=NBRC 110976T).

  10. Nocardioides opuntiae sp. nov., isolated from soil of a cactus.

    PubMed

    Lee, Soon Dong; Seong, Chi Nam

    2014-06-01

    A novel high G+C actinobacterium, designated strain OS1-21(T), was isolated from the rhizosphere soil of a cactus (Opuntia fiscus-indica var. sanboten) and the taxonomic status was investigated using a polyphasic approach. Cells of strain OS1-21(T) were aerobic, Gram-stain-positive, non-endospore-forming, non-motile rods; colonies of the cells were circular, translucent, smooth and moderate yellow in colour. LL-Diaminopimelic acid was the diagnostic diamino acid in cell-wall peptidoglycan. The predominant menaquinone was MK-8(H4). The major fatty acids were iso-C(16 : 0), iso-C(16 : 0) 2-OH, 10-methyl C(17 : 0), 10-methyl C(18 : 0) and C(17 : 1)cis9. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two unknown phospholipids. The DNA G+C content was 73.7 mol%. Based on 16S rRNA gene sequence analysis, the closest phylogenetic neighbours were Nocardioides panacihumi Gsoil 616(T) (98.7% sequence similarity) and Nocardioides terrae VA15(T) (97.8%), followed by Nocardioides marinus CL-DD14(T) (97.1%). DNA-DNA relatedness values of strain OS1-21(T) with the type strains of the closest phylogenetic neighbours were low (<16.0%). Combined data of polyphasic taxonomic analyses revealed that the organism could be assigned to a novel species of the genus Nocardioides, for which the name Nocardioides opuntiae sp. nov. is proposed. The type strain is OS1-21(T) ( = KCTC 19804(T) = NBRC 107915(T)).

  11. Fusobacterium hwasookii sp. nov., Isolated from a Human Periodontitis Lesion.

    PubMed

    Cho, Eugene; Park, Soon-Nang; Lim, Yun Kyong; Shin, Yeseul; Paek, Jayoung; Hwang, Cheol Ho; Chang, Young-Hyo; Kook, Joong-Ki

    2015-02-01

    In this study, we classified the five strains (ChDC F128(T), ChDC F145, ChDC F174, ChDC F206, and ChDC F300) as a novel species of genus Fusobacterium by DNA-DNA hybridization and multi-locus phylogenetic analysis (MLPA), based on a single sequence (24,715 bp) of 22 concatenated housekeeping genes, with morphological and chemotaxonomic characteristics. DNA-DNA hybridization data showed that the values of genomic relatedness between ChDC F128(T) and each of the other novel strains were ranged from 79.0 to 82.6 %, while those of genomic relatedness between ChDC F128(T) and type strain of each of subspecies of F. nucleatum or Fusobacterium periodonticum were ranged from 40.9 to 54.4 %. MLPA revealed that the 5 strains were clustered as one group and clearly discriminated with F. nucleatum and F. periodonticum with 100 % bootstrap value. The DNA G+C content of the five novel strains were ranged from 26.9 to 27.0 mol%. The cellular fatty acid analysis of clinical isolates and type strains revealed C14:0, C16:0, and cis-9 C16:1 as the major fatty acids. The cell wall peptidoglycan of the 5 strains was comprised of meso-lanthionine. These results show that the 5 strains are novel species and belong to the genus Fusobacterium. Strain ChDC F128(T) (=KCOM 1249(T) = KCTC 5108(T) = JCM 30218(T)) is suggested to be the type strain of a novel species of genus Fusobacterium, for which the name Fusobacterium hwasookii sp. nov. is proposed.

  12. Aeromicrobium halotolerans sp. nov., isolated from desert soil sample.

    PubMed

    Yan, Zheng-Fei; Lin, Pei; Chu, Xiao; Kook, MooChang; Li, Chang-Tian; Yi, Tae-Hoo

    2016-07-01

    A Gram-positive, aerobic, and non-motile, rod-shaped actinomycete strain, designated YIM Y47(T), was isolated from soils collected from Turpan desert, China, and subjected to a polyphasic taxonomic study. Phylogenetic analysis indicated that strain YIM Y47(T) belonged to the genus Aeromicrobium. YIM Y47(T) shared highest 16S rRNA gene sequence similarities with Aeromicrobium massiliense JC14(T) (96.47 %). Growth occurs at 20-45 °C (optimum at 30 °C), pH 6.0-8.0 (optimum at pH 7.0), and salinities of 0-7.0 % NaCl (optimum at 4.0 %). The strain YIM Y47(T) exhibits chemotaxonomic features with menaquinone-7 (MK-7) as the predominant quinone, C16:0, C18:1 ω9c and 10-methyl C18:0 (>10 %) as major fatty acids. The cell-wall peptidoglycan of strain YIM Y47(T) contained LL-diaminopimelic acid as the diagnostic diamino acid. The polar lipids were found to consist of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and unknown phospholipids. The G+C content of the genomic DNA of strain YIM Y47(T) was found to be 44.7 mol%. On the basis of phylogenetic analyses and phenotypic data, it is proposed that strain YIM Y47(T) should be classified as representing a novel species of the genus Aeromicrobium, with the name Aeromicrobium halotolerans sp. nov. The type strain is YIM Y47(T) (=KCTC 39113(T)=CGMCC 1.15063(T)=DSM 29939(T)=JCM 30627(T)).

  13. Microbacterium enclense sp. nov., isolated from sediment sample.

    PubMed

    Mawlankar, Rahul R; Mual, Poonam; Sonalkar, Vidya V; Thorat, Meghana N; Verma, Ashish; Srinivasan, Krishnamurthi; Dastager, Syed G

    2015-07-01

    A novel bacterium (strain NIO-1002(T)) belonging to the genus Microbacterium was isolated from a marine sediment sample in Chorao Island, Goa Province, India. Its morphology, physiology, biochemical features and 16S rRNA gene sequence were characterized. Cells of this strain were Gram-stain-positive, non-motile, non-spore-forming rods that formed yellow-pigmented colonies. It grew in 0-12% (w/v) NaCl and at 25-37 °C, with optimal growth at 30 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NIO-1002(T) is associated with members of the genus Microbacterium, with highest sequence similarity with Microbacterium hominis CIP 105731(T) (98.1%) and Microbacterium testaceum KCTC 9103(T) (98.0%). Within the phylogenetic tree, this novel strain shared a branching point with M. hominis CIP 105731(T). The DNA G+C content was 66.5 mol% and DNA-DNA hybridization relatedness between NIO-1002(T), M. hominis CIP 105731(T) and M. testaceum KCTC 9103(T) was 39.0 ± 2.0% and 41.0 ± 2.0%, respectively. The major fatty acids were ai-C15 : 0, i-C16 : 0 and ai-C17 : 0 and the diamino acid in the cell-wall peptidoglycan of NIO-1002(T) was lysine. Data obtained from DNA-DNA hybridization and chemotaxonomic phenotypic analysis support the conclusion that strain NIO-1002(T) represents a novel species within the genus Microbacterium. The name Microbacterium enclense sp. nov. is proposed, with NIO-1002(T) ( = NCIM 5454(T) = DSM 25125(T) = CCTCC AB 2011120(T)) as the type strain. PMID:25829331

  14. Streptomyces graminilatus sp. nov., isolated from bamboo litter.

    PubMed

    Lee, Hyo-Jin; Whang, Kyung-Sook

    2014-02-01

    A Gram-stain-positive, novel actinobacterium, designated strain JL-6(T), was isolated from the litter of a bamboo (Sasa borealis) forest in Damyang, Korea. Strain JL-6(T) had white-grey, smooth, cylindrical spores that were borne in straight, long spore-chains. The novel strain grew aerobically at 15-28 °C (optimum, 28 °C), pH 4.0-8.0 (optimum, pH 5.5) and with 0-1.5% (w/v) NaCl. The cell-wall peptidoglycan contained ll-diaminopimelic acid, glutamic acid, alanine and glycine. The predominant menaquinones were MK-9(H6) and MK-9(H8). Whole-cell hydrolysates mainly contained glucose and ribose. Phosphatidylinositol and phosphatidylcholine were the diagnostic phospholipids. The G+C content of the genomic DNA was 72.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JL-6(T) belonged to the genus Streptomyces with sequence similarities ranging from 97.3% to 98.3%. However, DNA-DNA hybridization between JL-6(T) and the closest related strain, Streptomyces turgidiscabies, ATCC 700248(T) and other closely related species in the genus Streptomyces showed <50% relatedness. Based on these observations, strain JL-6(T) is proposed to represent a novel species of the genus Streptomyces, for which the name Streptomyces graminilatus sp. nov. is proposed. The type strain is JL-6(T) ( = KACC 16470(T) = NBRC 108882(T)). PMID:24123200

  15. Bacillus vanillea sp. nov., Isolated from the Cured Vanilla Bean.

    PubMed

    Chen, Yong-gan; Gu, Feng-lin; Li, Ji-hua; Xu, Fei; He, Shu-zhen; Fang, Yi-ming

    2015-02-01

    A Gram-positive bacterium, designated strain XY18(T), was isolated from a cured vanilla bean in Hainan province, China. Cells were rod-shaped, endospore producing, and peritrichous flagella. Strain XY18(T) grew at salinities of 0-8 % (w/v) NaCl (optimally 1-4 %), pH 4.0-8.0 (optimally 5.0-7.0 %) and temperature range 20-45 °C (optimally 28-35 °C). The predominant menaquinone was MK-7. The major cellular fatty acids were anteiso-C15:0, iso-C15:0, anteiso-C17:0, and iso-C17:0. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain XY18(T) was a member of the genus Bacillus, and closely related to B. amyloliquefaciens NBRC 15535(T) and B. siamensis PD-A10(T), with 99.1 and 99.2 % sequence similarity, respectively. However, the DNA-DNA hybridization value between strain XY18(T) and B. amyloliquefaciens NBRC 15535(T) was 35.7 %. The genomic DNA G+C content of strain XY18(T) was 46.4 mol%, significantly differed from B. siamensis PD-A10(T) (41.4 %), which was higher than the range of 4 % indicative of species. On the basis of polyphasic taxonomic study, including phenotypic features, chemotaxonomy, and phylogenetic analyses, strain XY18(T) represents a novel species within the genus Bacillus, for which the name Bacillus vanillea sp. nov. is proposed. The type strain is XY18(T) (=CGMCC 8629 = NCCB 100507).

  16. Kordia antarctica sp. nov., isolated from Antarctic seawater.

    PubMed

    Baek, Kiwoon; Choi, Ahyoung; Kang, Ilnam; Lee, Kiyoung; Cho, Jang-Cheon

    2013-10-01

    A Gram-staining-negative, chemoheterotrophic, yellow-pigmented, non-motile, flexirubin-negative, facultatively anaerobic bacterium, designated strain IMCC3317(T), was isolated from a coastal seawater sample from the Antarctic Penninsula. Optimal growth of strain IMCC3317(T) was observed at 20 °C, pH 8.0 and in the presence of 2-3 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IMCC3317(T) belonged to the genus Kordia and was closely related to Kordia algicida OT-1(T) (96.7 % sequence similarity) and Kordia periserrulae IMCC1412(T) (96.1 % sequence similarity). The major fatty acids were 10-methyl C16 : 0 and/or iso-C16 : 1ω9c, iso-C17 : 0 3-OH, iso-C15 : 0 and anteiso-C15 : 0. The G+C content of the genomic DNA was 35.1 mol%. The strain contained menaquinone-6 (MK-6) as the respiratory quinone. The polar lipids detected in the strain were phosphatidylethanolamine and unknown aminophospholipids, aminolipids and polar lipids. On the basis of phylogenetic distinction and differential phenotypic characteristics, it is suggested that strain IMCC3317(T) ( = KCTC 32292(T) = NBRC 109401(T)) be assigned to the genus Kordia as the type strain of a novel species, for which the name Kordia antarctica sp. nov. is proposed.

  17. Terrimonas arctica sp. nov., isolated from Arctic tundra soil.

    PubMed

    Jiang, Fan; Qiu, Xia; Chang, Xulu; Qu, Zhihao; Ren, Lvzhi; Kan, Wenjing; Guo, Youhao; Fang, Chengxiang; Peng, Fang

    2014-11-01

    A novel, Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium, designated R9-86(T), was isolated from tundra soil collected near Ny-Ålesund, Svalbard Archipelago, Norway (78° N). Growth occurred at 4-28 °C (optimum, 22-25 °C) and at pH 6.0-9.0 (optimum, pH 7.0). Flexirubin-type pigments were absent. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R9-86(T) belonged to the genus Terrimonas in the family Chitinophagaceae. 16S rRNA gene sequence similarities between strain R9-86(T) and the type strains of species of the genus Terrimonas with validly published names ranged from 93.7 to 95.0%. Strain R9-86(T) contained iso-C(15:1)-G (25.7%), iso-C(15:0) (24.5%), iso-C(17:0)-3OH (18.3%) and summed feature 3 (C(16:1)ω7c and/or C(16:1)ω6c, 8.7%) as its major cellular fatty acids; phosphatidylethanolamine and an unknown polar lipid as its main polar lipids, and MK-7 as its predominant respiratory quinone. The DNA G+C content was 48.4 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain R9-86(T) is considered to represent a novel species of the genus Terrimonas, for which the name Terrimonas arctica sp. nov. is proposed. The type strain is R9-86(T) ( =CCTCC AB 2011004(T) =NRRL B-59114(T)).

  18. Tropicimonas sediminicola sp. nov., isolated from marine sediment.

    PubMed

    Shin, Na-Ri; Roh, Seong Woon; Kim, Min-Soo; Yun, Bora; Whon, Tae Woong; Kim, Young-Ok; Bae, Jin-Woo

    2012-10-01

    A novel Gram-negative, obligately aerobic, non-motile, rod-shaped bacterium, strain M97(T), was isolated from marine sediment of a cage-cultured ark clam farm on the south coast of Korea. Strain M97(T) was positive for oxidase and catalase. Optimal growth occurred at 37 °C, with 1-2 % (w/v) NaCl and at pH 7-8. The main cellular fatty acids were C(16 : 0), C(18 : 1)ω7c, C(12 : 0) 3-OH and cyclo-C(19 : 0)ω8c. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an unknown aminolipid and three unknown lipids. The predominant respiratory quinone was ubiquinone-10 (Q-10). Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain M97(T) belongs to the genus Tropicimonas, with highest sequence similarity to Tropicimonas aquimaris DPG-21(T) (99.0 %). The DNA G+C content of strain M97(T) was 68.5 mol%. Mean DNA-DNA relatedness between strain M97(T) and T. aquimaris DPG-21(T) was 46 ± 10 %. Based on phylogenetic, phenotypic and genotypic analyses, strain M97(T) is considered to represent a novel species of the genus Tropicimonas, for which the name Tropicimonas sediminicola sp. nov. is proposed. The type strain is M97(T) ( = KACC 15544(T) = JCM 17731(T)). PMID:22140172

  19. Lysobacter panacisoli sp. nov., isolated from ginseng soil.

    PubMed

    Choi, Jung-Hye; Seok, Ji-Hye; Cha, Ju-Hee; Cha, Chang-Jun

    2014-07-01

    A novel bacterial strain, designated CJ29(T), was isolated from ginseng soil of Anseong in South Korea. Cells of strain CJ29(T) were Gram-stain-negative, facultatively anaerobic, rod-shaped and non-motile. Strain CJ29(T) grew optimally at 28-30 °C and pH 7.0. Based on 16S rRNA gene sequence analysis, strain CJ29(T) was shown to belong to the genus Lysobacter within the class Gammaproteobacteria and was related most closely to Lysobacter soli DCY21(T) (98.5% similarity) and Lysobacter niastensis GH41-7(T) (98.2%). DNA-DNA relatedness between strain CJ29(T) and its closest relatives was below 55.6%. The predominant cellular fatty acids of strain CJ29(T) were iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1ω9c. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The major isoprenoid quinone was ubiquinone 8 (Q-8). The G+C content of the genomic DNA was 65.6 mol%. Phenotypic, genotypic and phylogenetic characteristics strongly supported the differentiation of strain CJ29(T) from related species of the genus Lysobacter. On the basis of data from this polyphasic taxonomic study, strain CJ29(T) is considered to represent a novel species of the genus Lysobacter, for which the name Lysobacter panacisoli sp. nov. is proposed. The type strain is CJ29(T) ( = KACC 17502(T) = JCM 19212(T)).

  20. Microbacterium panaciterrae sp. nov., isolated from the rhizosphere of ginseng.

    PubMed

    Nguyen, Ngoc-Lan; Kim, Yeon-Ju; Hoang, Van-An; Min, Jin-Woo; Hwang, Kyu-Hyon; Yang, Deok-Chun

    2015-03-01

    Strain DCY56(T) was isolated from a soil sample taken from a ginseng field. The strain was Gram-reaction positive, catalase-positive, oxidase-negative, aerobic and non-motile. Phylogenetic analysis, based on 16S rRNA gene sequence analysis, indicated that strain DCY56(T) belonged to the genus Microbacterium. The closest relatives were Microbacterium azadirachtae AI-S262(T), Microbacterium aerolatum V-73(T) and Microbacterium phyllosphaerae DSM 13468(T) (98.0 %, 98.0 % and 97.5 % gene sequence similarity, respectively). The G+C content of the genomic DNA of strain DCY56(T) was 68.5 mol%. The DNA-DNA relatedness values between strain DCY56(T) and the most closely related type strains were lower than 36 %. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid. The predominant fatty acids contained iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The menaquinones were MK-12 and MK-13. The diagnostic diamino acid of strain DCY56(T) was ornithine. The dominant whole-cell sugars were glucose, rhamnose and ribose. The results of the genotypic analysis, in combination with chemotaxonomic and physiological data, demonstrate that strain DCY56(T) represents a novel species within the genus Microbacterium, for which the name Microbacterium panaciterrae sp. nov. is proposed. The type strain is DCY56(T) ( = KCTC 19884(T) = JCM 17839(T)).

  1. Duganella ginsengisoli sp. nov., isolated from ginseng soil.

    PubMed

    Zhang, Jinglou; Kim, Yeon-Ju; Hoang, Van-An; Lan Nguyen, Ngoc; Wang, Chao; Kang, Jong-Pyo; Wang, Dandan; Yang, Deok-Chun

    2016-01-01

    A Gram-stain-negative, rod-shaped bacterium, designated DCY83T, was isolated from soil of a ginseng field in Gwangju Province, Republic of Korea. Cells were motile by means of flagella. Growth occurred at 4-40 °C (optimum 30 °C), at pH 6-8 (optimum pH 7.0) and with ≤ 0.4 % NaCl. Strain DCY83T was able to produce siderophore and was positive for phosphate solubilization. Indole-3-acetic acid production was 12.9 μg ml- 1 after 3 days in culture. 16S rRNA gene sequence analysis showed that strain DCY83T belonged to the genus Duganella and was related most closely to Duganella sacchari Sac-22T (97.4 % similarity), Duganella zoogloeoides IAM 12670T (97.1 %) and Duganella radicis Sac-41T (97.1 %). The major fatty acids were C16 : 0 and summed feature 3 (containing C16 : 1ω7c and/or C16 : 1ω6c). The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. The only quinone was ubiquinone 8. The genomic DNA G+C content was 55.3 mol%. DNA-DNA relatedness between strain DCY83T and D. sacchari KCTC 22381T, D. zoogloeoides JCM 20729T and D. radicis KCTC 22382T was 27.7, 22.4 and 35.5 %, respectively. On the basis of the phenotypic and genotypic analysis, DCY83T is classified as representing a novel species in the genus Duganella, for which the name Duganella ginsengisoli sp. nov. is proposed. The type strain is DCY83T ( = KCTC 42409T = JCM 30745T).

  2. Natronomonas gomsonensis sp. nov., isolated from a solar saltern.

    PubMed

    Kim, Tae-Yoon; Kim, So-Jeong; Park, Soo-Je; Kim, Jong-Geol; Cha, In-Tae; Jung, Man-Young; Lee, Sang-A; Roh, Seong Woon; Yim, Kyung June; Itoh, Takashi; Rhee, Sung-Keun

    2013-11-01

    A halophilic archaeal strain, SA3(T), was isolated from sediment of a solar saltern in Gomso Bay, Republic of Korea. Cells of strain SA3(T) were observed to be coccoid-shaped, to lyse in distilled water, Gram stain-negative and to form red-pigmented colonies. Strain SA3(T) was found to require at least 18 % (w/v) NaCl for growth. Optimal growth was observed at 24 % (w/v) NaCl and 6 % (w/v) MgCl2. The optimum pH and temperature for growth were determined to be pH 7.0 and 40 °C, respectively, while the strain was found to grow within pH and temperature ranges of 5.5-8.0 and 20-45 °C, respectively. The polar lipids were determined to consist of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, unidentified phosphoglycolipids and unidentified phospholipids. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SA3(T) was most closely related to the members of the genus Natronomonas, Natronomonas moolapensis JCM 14361(T) (95.2 %) and Natronomonas pharaonis JCM 8858(T) (95.1 %). The genomic DNA G+C content (61.8 mol%) determined for strain SA3(T) was slightly lower than those of N. moolapensis JCM 14361(T) (63.4 mol%) and N. pharaonis JCM 8858(T) (64.3 mol%). DNA-DNA hybridization values between N. moolapensis JCM 14361(T) and N. pharaonis JCM 8858(T) and strain SA3(T) were <20 %. Based on phenotypic, chemotaxonomic and phylogenetic properties, we describe a new species of the genus Natronomonas, represented by strain SA3(T) (=JCM 17867(T) = KCTC 4088(T)), for which we propose the name Natronomonas gomsonensis sp. nov.

  3. Halorussus amylolyticus sp. nov., isolated from an inland salt lake.

    PubMed

    Yuan, Pan-Pan; Ye, Wei-Tao; Pan, Jia-Xiang; Han, Dong; Zhang, Wen-Jiao; Cui, Heng-Lin

    2015-10-01

    A halophilic archaeal strain, YC93T, was isolated from Yuncheng salt lake in Shanxi Province, China. Cells were pleomorphic rods, stained Gram-negative and formed light-red-pigmented colonies on agar plates. Strain YC93T was able to grow at 25–50 °C (optimum 37 °C), with 1.4–4.8 M NaCl (optimum 2.0 M), with 0–1.0 M MgCl2 (optimum 0.05 M) and at pH 6.0–9.5 (optimum pH 7.0). Cells lysed in distilled water and the minimal NaCl concentration to prevent cell lysis was 8 % (w/v). 16S rRNA gene sequence analysis revealed that strain YC93T had two dissimilar 16S rRNA genes both of which were phylogenetically related to those of the two recognized members of the genus Halorussus (93.0–95.3 % similarity). The rpoB′ gene of strain YC93T was phylogenetically related to the corresponding gene of Halorussus rarus TBN4T (91.3 % similarity) and Halorussus ruber YC25T (90.5 %). The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and five glycolipids chromatographically identical to those of Halorussus rarus CGMCC 1.10122T. The DNA G+C content of strain YC93T was 64.6 mol%. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strain YC93T represents a novel species of the genus Halorussus, for which the name Halorussus amylolyticus sp. nov. is proposed. The type strain is YC93T ( = CGMCC 1.12126T = JCM 18367T). PMID:26228463

  4. Novosphingobium colocasiae sp. nov., isolated from a taro field.

    PubMed

    Chen, Wen-Ming; Chen, Jhen-Ci; Huang, Cheng-Wen; Young, Chiu-Chung; Sheu, Shih-Yi

    2016-02-01

    A novel bacterial strain, designated Teta-03T, was isolated from a taro field in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain Teta-03T were aerobic, Gram-stain-negative, rod-shaped and non-motile and formed bright yellow colonies. Growth occurred at 10-37 °C (optimum, 20 °C), with 0-1.0 % (w/v) NaCl (optimum, 0 %) and at pH 3.0-9.0 (optimum, pH 7.0-8.0). The major fatty acids (>10 %) of strain Teta-03T were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, sphingoglycolipid, phosphatidylcholine, an uncharacterized glycolipid and an uncharacterized aminolipid. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 65.0 mol%. On the basis of 16S rRNA gene sequence analysis, strain Teta-03T was shown to belong to the genus Novosphingobium and showed highest similarity to Novosphingobium barchaimii LL02T (96.8 %). Phenotypic characteristics of the novel strain also differed from those of the closest related species of the genus Novosphingobium. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Teta-03T represents a novel species of the genus Novosphingobium, for which the name Novosphingobium colocasiae sp. nov. is proposed. The type strain is Teta-03T ( = LMG 27385T = KCTC 32255T). PMID:26582085

  5. Halomarina salina sp. nov., isolated from a marine solar saltern.

    PubMed

    Xu, Wen-Mei; Xu, Jia-Qi; Zhou, Yao; Li, Yang; Lü, Zhen-Zhen; Hou, Jing; Zhu, Lin; Cui, Heng-Lin

    2016-08-01

    A halophilic archaeal strain, designated ZS-57-S(T), was isolated from Zhoushan marine solar saltern, China. Cells were observed to be pleomorphic, stained Gram-negative and formed red pigmented colonies on agar plates. Optimal growth was obtained at 3.9 M NaCl (range 1.4-4.8 M), 0.3 M MgCl2 (range 0-1.0 M), 30 °C (range 20-55 °C) and pH 6.5-7.5 (range 5.5-9.0). The cells were found to lyse in distilled water and the minimal NaCl concentration to prevent cell lysis was determined to be 5 % (w/v). The major polar lipids were identified as C20C20 and C20C25 diether derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, glucosyl mannosyl glucosyl diether and two unidentified glycolipids. The 16S rRNA gene and rpoB' gene of strain ZS-57-S(T) were phylogenetically related to the corresponding genes of Halomarina oriensis JCM 16495(T) (98.2 and 93.7 % similarities, respectively). The DNA G+C content of strain ZS-57-S(T) was determined to be 67.1 mol% (T m). The phenotypic, chemotaxonomic and phylogenetic properties suggested that strain ZS-57-S(T) (=CGMCC 1.12543(T) = JCM 30039(T)) represents a new species of the genus Halomarina, for which the name Halomarina salina sp. nov. is proposed. PMID:27198657

  6. Polaromonas eurypsychrophila sp. nov., isolated from an ice core.

    PubMed

    Xing, Tingting; Yao, Tandong; Liu, Yongqin; Wang, Ninglian; Xu, Bainqing; Shen, Liang; Gu, Zhengquan; Gu, Bixi; Liu, Hongcan; Zhou, Yuguang

    2016-07-01

    A Gram-stain-negative, aerobic, rod-shaped, beige bacterium, strain B717-2T, was isolated from an ice core drilled from Muztagh Glacier on the Tibetan Plateau, China. According to phylogenetic analyses based on 16S rRNA gene sequences, the novel strain was related most closely to Polaromonas vacuolataand shared 97.7 % similarity with the type strain of this species. It grew optimally at pH 7, at 15 °C and with 2 % (w/v) NaCl. Major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), summed feature 8 (C18 : 1ω7c, C18 : 1ω6c) and C16 : 0. The sole respiratory quinone was Q-8. The DNA G+C content was 63.4 mol %. In DNA-DNA hybridization tests, strain B717-2T shared 37.0±1.9, 30.0±1.7, 26.0±0.9, 23.4±0.5 and 18.4±1.9 % DNA-DNA relatedness with Polaromonas jejuensisJS12-13T, P. vacuolata 34-PT, Polaromonas aquatica CCUG 39402T, Polaromonas glacialisCr4-12T and Polaromonas cryoconitiCr4-35T, respectively. Based on the phenotypic, phylogenetic and genetic characteristics, strain B717-2T represents a novel species of the genus Polaromonas, for which the name Polaromonaseurypsychrophila sp. nov. is proposed. The type strain is B717-2T (=CGMCC 1.15322T=JCM 31171T).

  7. Aneurinibacillus humi sp. nov., Isolated from Soil Collected in Ukraine.

    PubMed

    Lee, Kalam; Lee, Sang Seob

    2016-02-01

    A novel bacterium, designated U33(T), was isolated from a soil sample collected in Mykhailyky, Poltavs'ka oblast, Ukraine. The bacterium was aerobic, Gram-positive, spore-forming, and consists of motile rods. The taxonomic position of strain U33(T) was studied by a polyphasic approach, and the results clearly showed that the phenotypic and chemotaxonomic properties are consistent with those of the genus Aneurinibacillus. The phylogenic analysis with 16S rRNA gene sequence of strains U33(T) showed the highest sequence similarity to those of Aneurinibacillus aneuriniticus ATCC 12856(T) (96.7 %), Aneurinibacillus migulanus DSM 2895(T) (96.7 %), Aneurinibacillus danicus NCIMB 13288(T) (95.8 %), and lower sequence similarity with other members of the genus Aneurinibacillus. Growth was observed at 20-55 °C (optimum, 37 °C) at pH 5.0-9.0 (optimum, pH 7) and with 0-5 % (w/v) NaCl (optimum, 2 % NaCl). The predominant menaquinone was MK-7 and the cell wall peptidoglycan consist of meso-diaminopimelic acid. The major cellular fatty acids are iso-C15:0 (58.0 %) and anteiso-C15:0 (13.2 %). The DNA G+C content of the strain U33(T) was 45.8 %. The physiological and chemotaxonomic characteristics distinguish strain U33(T) from the validly published species of genus Aneurinibacillus, and therefore, we consider this strain to represent a novel species of the genus Aneurinibacillus. The name Aneurinibaciilus humi sp. nov. is proposed with strain U33(T) (= KEMC7305-119(T) = JCM19865(T)) as the type strain. PMID:26542530

  8. Pseudovibrio stylochi sp. nov., isolated from a marine flatworm.

    PubMed

    Zhang, Yu; Li, Qi; Tian, Renmao; Lai, Qiliang; Xu, Ying

    2016-05-01

    A Gram-stain-negative, motile, rod-shaped bacterial strain, designated UST20140214-052T, was isolated from a marine flatworm (polyclad). The bacterium was found to be catalase-positive and weakly oxidase-positive, and motile by means of several peritrichous or subpolar flagella. Strain UST20140214-052T grew optimally at 28 °C, at pH 7.0 and in the presence of 3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain UST20140214-052T belongs to the genus Pseudovibrio, with highest sequence similarity to Pseudovibrio hongkongensis UST20140214-015BT (98.8 %), followed by Pseudovibrio japonicus WSF2T (96.2 %), Pseudovibrio ascidiaceicola F423T (96.2 %), Pseudovibrio denitrificans DN34T (95.9 %), Pseudovibrio axinellae Ad2T (95.9 %). All the other species shared < 95.5 % sequence similarity. The DNA-DNA hybridization estimate value between strain UST20140214-052T and P. hongkongensis UST20140214-015BT was 24.7 ± 2.4 %. The major fatty acid was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c, as defined by the MIDI system; 62.6 %). The DNA G+C content was 47.0 mol%. The combined genotypic and phenotypic data show that strain UST20140214-052T represents a novel species within the genus Pseudovibrio, for which the name Pseudovibrio stylochi sp. nov. is proposed, with the type strain UST20140214-052T ( = KCTC 42384T = MCCC 1K00452T).

  9. Pseudovibrio hongkongensis sp. nov., isolated from a marine flatworm.

    PubMed

    Xu, Ying; Li, Qi; Tian, Renmao; Lai, Qiliang; Zhang, Yu

    2015-07-01

    A Gram-negative, motile, rod-shaped bacterial strain, designated UST20140214-015B(T), was isolated from a marine flatworm (Polyclad). The bacterium was found to be Gram-negative, oxidase and catalase positive, long-rod shaped, and motile by means of several peritrichous or subpolar flagella. Strain UST20140214-015B(T) grew optimally at 28 °C, at pH 7.0 and in the presence of 3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain UST20140214-015B(T) belongs to the genus Pseudovibrio, with highest sequence similarity to Pseudovibrio japonicus WSF2(T) (96.9 %), followed by P. ascidiaceicola F423(T) (96.7 %), P. denitrificans DN34(T) (96.6 %), P. axinellae Ad2(T) (96.3 %). All the other species shared <95.5 % sequence similarity. The principal fatty acids were identified as summed feature 8 (C18:1 ω7c/ω6c, as defined by the MIDI system; 70.8 %), C16:0 (9.1 %), summed feature 3 (C16:1 ω6c/C16:1 ω7c; 5.7 %). The G+C content of the chromosomal DNA was determined to be 53.3 mol%. The combined genotypic and phenotypic data show that strain UST20140214-015B(T) represents a novel species within the genus Pseudovibrio, for which the name Pseudovibrio hongkongensis sp. nov. is proposed, with the type strain UST20140214-015B(T) (=KCTC 42383(T) = MCCC 1K00451(T)).

  10. Fusobacterium hwasookii sp. nov., Isolated from a Human Periodontitis Lesion.

    PubMed

    Cho, Eugene; Park, Soon-Nang; Lim, Yun Kyong; Shin, Yeseul; Paek, Jayoung; Hwang, Cheol Ho; Chang, Young-Hyo; Kook, Joong-Ki

    2015-02-01

    In this study, we classified the five strains (ChDC F128(T), ChDC F145, ChDC F174, ChDC F206, and ChDC F300) as a novel species of genus Fusobacterium by DNA-DNA hybridization and multi-locus phylogenetic analysis (MLPA), based on a single sequence (24,715 bp) of 22 concatenated housekeeping genes, with morphological and chemotaxonomic characteristics. DNA-DNA hybridization data showed that the values of genomic relatedness between ChDC F128(T) and each of the other novel strains were ranged from 79.0 to 82.6 %, while those of genomic relatedness between ChDC F128(T) and type strain of each of subspecies of F. nucleatum or Fusobacterium periodonticum were ranged from 40.9 to 54.4 %. MLPA revealed that the 5 strains were clustered as one group and clearly discriminated with F. nucleatum and F. periodonticum with 100 % bootstrap value. The DNA G+C content of the five novel strains were ranged from 26.9 to 27.0 mol%. The cellular fatty acid analysis of clinical isolates and type strains revealed C14:0, C16:0, and cis-9 C16:1 as the major fatty acids. The cell wall peptidoglycan of the 5 strains was comprised of meso-lanthionine. These results show that the 5 strains are novel species and belong to the genus Fusobacterium. Strain ChDC F128(T) (=KCOM 1249(T) = KCTC 5108(T) = JCM 30218(T)) is suggested to be the type strain of a novel species of genus Fusobacterium, for which the name Fusobacterium hwasookii sp. nov. is proposed. PMID:25257648

  11. Hafnia psychrotolerans sp. nov., isolated from lake water.

    PubMed

    Gu, Zhengquan; Liu, Yongqin; Shen, Liang; Liu, Xiaobo; Xiao, Na; Jiao, Nianzhi; Liu, Hongcan; Zhou, Yuguang; Zhang, Shuhong

    2015-03-01

    A psychrotolerant, Gram-stain-negative, motile, aerobic, peritrichous bacterium, strain DJC1-1(T), was isolated from Lake Dajiaco, Tibetan Plateau, China. The strain was negative for citrate utilization, lipase activity and α-glucosidase, but positive for the Voges-Proskauer reaction and N-acetyl-β-glucosaminidase. 16S rRNA gene sequence analysis indicated that Hafnia paralvei ATCC 29927(T), Hafnia alvei ATCC 13337(T), Serratia grimesii DSM 30063(T) and Serratia plymuthica DSM 4540(T) were the closest relatives of strain DJC1-1(T), with similarities of 97.76, 96.80, 97.71 and 97.58 %, respectively. The DNA G+C content of strain DJC1-1(T) was 53.9 mol%. The predominant fatty acids were C16 : 0 and C17 : 0 cyclo. Based on these characteristics, strain DJC1-1(T) can be assigned to the genus Hafnia. In DNA-DNA hybridization tests, strain DJC1-1(T) shared 50.6, 35.1, 36.5 and 18.1 % DNA-DNA relatedness with the type strains of H. paralvei, H. alvei, S. grimesii and S. plymuthica, respectively. The growth temperature ranged from 0 to 40 °C, with optimum growth at 15 °C. Physiological and biochemical tests differentiated strain DJC1-1(T) from the type strains of recognized species of the genus Hafnia. Therefore, strain DJC1-1(T) is identified as representing a novel species of the genus Hafnia, for which the name Hafnia psychrotolerans sp. nov. is proposed. The type strain is DJC1-1(T) ( = JCM 30077(T) = CGMCC1.12806(T)). PMID:25563917

  12. Virgibacillus byunsanensis sp. nov., isolated from a marine solar saltern.

    PubMed

    Yoon, Jung-Hoon; Kang, So-Jung; Jung, Yong-Taek; Lee, Keun Chul; Oh, Hyun Woo; Oh, Tae-Kwang

    2010-02-01

    A Gram-variable, motile, endospore-forming and rod-shaped bacterial strain, ISL-24(T), was isolated from a marine solar saltern of the Yellow Sea, Korea, and its taxonomic position was investigated by a polyphasic study. Strain ISL-24(T) grew optimally at pH 7.0-8.0, at 30-37 degrees C and in the presence of 8 % (w/v) NaCl. It contained MK-7 as the predominant menaquinone and anteiso-C(15 : 0) as the predominant fatty acid. The DNA G+C content was 37.6 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-24(T) fell within the genus Virgibacillus, clustering with Virgibacillus carmonensis LMG 20964(T) and Virgibacillus necropolis LMG 19488(T), with a bootstrap resampling value of 92.3 %, and exhibiting 97.3 and 97.4 % 16S rRNA gene sequence similarity, respectively, to these strains. Strain ISL-24(T) exhibited 94.8-96.8 % 16S rRNA gene sequence similarity to the type strains of the other Virgibacillus species. Mean DNA-DNA relatedness values between strain ISL-24(T) and V. carmonensis DSM 14868(T) and V. necropolis DSM 14866(T) were 11 and 19 %, respectively. Differential phenotypic properties of strain ISL-24(T), together with the phylogenetic and genetic distinctiveness, revealed that this strain is different from recognized Virgibacillus species. On the basis of phenotypic, phylogenetic and genetic data, strain ISL-24(T) represents a novel species of the genus Virgibacillus, for which the name Virgibacillus byunsanensis sp. nov. is proposed. The type strain is ISL-24(T) (=KCTC 13259(T) =CCUG 56754(T)). PMID:19651717

  13. Virgibacillus alimentarius sp. nov., isolated from a traditional Korean food.

    PubMed

    Kim, Jandi; Jung, Mi-Ja; Roh, Seong Woon; Nam, Young-Do; Shin, Kee-Sun; Bae, Jin-Woo

    2011-12-01

    A novel, Gram-positive, rod-shaped, motile, endospore-forming, halophilic bacterial strain, J18(T), was isolated from a traditional salt-fermented seafood made of gizzard shad in Korea. Colonies were convex, cream-coloured and 1.0-2.0 mm in diameter after incubation for 3 days on marine agar. Growth occurred at pH 7.0-11.0 (optimum, pH 10.0), at 4-40 °C (optimum, 37 °C) and in the presence of 0-30% NaCl (optimum, 9-10%). On the basis of 16S rRNA gene sequence analysis, strain J18(T) was related most closely to Virgibacillus byunsanensis ISL-24(T) (96.3% similarity), Virgibacillus carmonensis LMG 20964(T) (96.2%), Virgibacillus halodenitrificans DSM 10037(T) (96.0%), Virgibacillus arcticus Hal 1(T) (95.5%) and Virgibacillus necropolis LMG 19488(T) (95.5%). The major fatty acids were anteiso-C(15:0) and anteiso-C(17:0). The DNA G+C content of strain J18(T) was 37.0 mol%. The cell-wall peptidoglycan was of the meso-diaminopimelic acid type. The major quinone was menaquinone 7 (MK-7). Based on phenotypic, chemotaxonomic and phylogenetic data, strain J18(T) is considered to represent a novel species of the genus Virgibacillus, for which the name Virgibacillus alimentarius sp. nov. is proposed. The type strain is J18(T) (=KACC 14624(T) =JCM 16994(T)). PMID:21239563

  14. Tenacibaculum litoreum sp. nov., isolated from tidal flat sediment.

    PubMed

    Choi, Dong Han; Kim, Yoon-Gon; Hwang, Chung Yeon; Yi, Hana; Chun, Jongsik; Cho, Byung Cheol

    2006-03-01

    A rod-shaped bacterium, designated CL-TF13T, was isolated from a tidal flat in Ganghwa, Korea. Analysis of the 16S rRNA gene sequence revealed an affiliation with the genus Tenacibaculum. The sequence similarities between CL-TF13T and type strains of members of the genus Tenacibaculum were from 94.2 to 97.4%. Cells were motile by means of gliding. Strain CL-TF13T grew on solid medium as pale-yellow colonies with an irregular spreading edge. The strain was able to grow in NaCl at a range of 3-5%. They grew within a temperature range of 5-40 degrees C and at pH range of 6-10. The major fatty acids were summed feature 3 (C(16:1)omega7c and/or iso-C(15:0) 2-OH, 19.6%), iso-C(15:0) (18.8%) and iso-C(17:0) 3-OH (13.6%). Fatty acids such as C(18:3)omega6c (6,9,12) (1.5%) and summed feature 4 (iso I- and/or anteiso B-C(17:1), 1.3%) were uniquely found in minor quantities in CL-TF13T among Tenacibaculum species. The DNA G + C content was 30 mol%. According to physiological data, fatty-acid composition and 16S rRNA gene sequence, CL-TF13T could be assigned to the genus Tenacibaculum but distinguished from the recognized species of the genus. Therefore, strain CL-TF13T (= KCCM 42115T = JCM 13039T) represents a novel species, for which the name Tenacibaculum litoreum sp. nov. is proposed.

  15. Gluconobacter cerevisiae sp. nov., isolated from the brewery environment.

    PubMed

    Spitaels, Freek; Wieme, Anneleen; Balzarini, Tom; Cleenwerck, Ilse; Van Landschoot, Anita; De Vuyst, Luc; Vandamme, Peter

    2014-04-01

    Three strains, LMG 27748(T), LMG 27749 and LMG 27882 with identical MALDI-TOF mass spectra were isolated from samples taken from the brewery environment. Analysis of the 16S rRNA gene sequence of strain LMG 27748(T) revealed that the taxon it represents was closely related to type strains of the species Gluconobacter albidus (100 % sequence similarity), Gluconobacter kondonii (99.9 %), Gluconobacter sphaericus (99.9 %) and Gluconobacter kanchanaburiensis (99.5 %). DNA-DNA hybridization experiments on the type strains of these species revealed moderate DNA relatedness values (39-65 %). The three strains used d-fructose, d-sorbitol, meso-erythritol, glycerol, l-sorbose, ethanol (weakly), sucrose and raffinose as a sole carbon source for growth (weak growth on the latter two carbon sources was obtained for strains LMG 27748(T) and LMG 27882). The strains were unable to grow on glucose-yeast extract medium at 37 °C. They produced acid from meso-erythritol and sucrose, but not from raffinose. d-Gluconic acid, 2-keto-d-gluconic acid and 5-keto-d-gluconic acid were produced from d-glucose, but not 2,5-diketo-d-gluconic acid. These genotypic and phenotypic characteristics distinguish strains LMG 27748(T), LMG 27749 and LMG 27882 from species of the genus Gluconobacter with validly published names and, therefore, we propose classifying them formally as representatives of a novel species, Gluconobacter cerevisiae sp. nov., with LMG 27748(T) ( = DSM 27644(T)) as the type strain. PMID:24368694

  16. Microbacterium nanhaiense sp. nov., an actinobacterium isolated from sea sediment.

    PubMed

    Yan, Lien; Wang, Jingjing; Chen, Zhirong; Guan, Yingying; Li, Jing

    2015-10-01

    A Gram-staining-positive, heterotrophic, anaerobic, non-spore-forming, non-motile, rod-shaped strain, OAct400T, belonging to the genus Microbacterium was isolated from a sediment collected from a depth of 2093 m in the South China Sea, China. The strain was identified using a polyphasic taxonomic approach. The strain grew well on yeast extract/malt extract agar (ISP 2) and nutrient agar media, and formed no aerial mycelium and no diffusible pigments on any media tested. The strain grew in the presence of 0-8 % (w/v) NaCl (optimum, 2-4 %), at pH 5.0-10.0 (optimum, pH 7.0) and at 4-37 °C (optimum, 28 °C). Strain OAct400T contained ornithine as the diagnostic diamino acid. The whole-cell sugars were dominated by glucose and galactose. The predominant menaquinones were MK-11 (51 %) and MK-10 (24 %). The major phospholipids were phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids were anteiso-C15 : 0 (59.35 %), iso-C16 : 0 (17.89 %) and anteiso-C17 : 0 (16.09 %). DNA-DNA relatedness with Microbacterium amylolyticum DSM 24221T and Microbacterium gubbeenense CIP 107184T, the nearest phylogenetic relatives (97.73 and 97.44 % 16S rRNA gene sequence similarity, respectively) was 31.3 ± 2.1 and 28.7 ± 1.2 %, respectively. On the basis of phenotypic, phylogenetic and genotypic data, a novel species, Microbacterium nanhaiense sp. nov., is proposed. The type strain is OAct400T ( = CGMCC 4.7181T = DSM 26811T = KCTC 29185T).

  17. Bacillus tianshenii sp. nov., isolated from a marine sediment sample.

    PubMed

    Jiang, Zhao; Zhang, Dao-Feng; Khieu, Thi-Nhan; Son, Chu Ky; Zhang, Xiao-Mei; Cheng, Juan; Tian, Xin-Peng; Zhang, Si; Li, Wen-Jun

    2014-06-01

    A novel Gram-stain-positive, motile, catalase- and oxidase-positive, aerobic, endospore-forming, peritrichous, rod-shaped bacterium, designated YIM M13235(T), was isolated from a marine sediment sample collected from the South China Sea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM M13235(T) belonged to the genus Bacillus. The strain grew optimally at 30 °C, pH 7.0 and in the presence of 2-4% (w/v) NaCl. meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. Strain YIM M13235(T) exhibited a menaquinone system with MK-7, and the major polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unknown phospholipids and one unknown glycolipid. The major fatty acids (>5%) were iso-C(15 : 0), anteiso-C(15 : 0), anteiso-C(17 : 0), iso-C(17 : 1)ω10c and summed feature 4 (anteiso-C(17 : 1) and/or iso-C(17 : 1)). The genomic DNA G+C content was 42.1 mol%. The DNA-DNA relatedness values between strain YIM M13235(T) and its close relatives (16S rRNA gene sequence similarities >97%) including Bacillus halmapalus DSM 8723(T), Bacillus horikoshii DSM 8719(T) and Bacillus zhanjiangensis JSM 099021(T) were 41%, 44% and 44%, respectively. On the basis of genotypic, phenotypic and DNA-DNA relatedness data, it is apparent that strain YIM M13235(T) represents a novel species of the genus Bacillus, for which the name Bacillus tianshenii sp. nov. is proposed. The type strain is YIM M13235(T) ( = DSM 25879(T) = KCTC 33044(T)).

  18. Roseivivax marinus sp. nov., isolated from deep water.

    PubMed

    Dai, Xiaofeng; Shi, Xiaochong; Gao, Xin; Liu, Jingli; Zhang, Xiao-Hua

    2014-08-01

    A Gram-stain-negative, strictly aerobic, non-motile, cream, long rod-shaped bacterium, designated strain ZL136(T), was isolated from deep water of the South China Sea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain belonged to the genus Roseivivax with highest sequence similarity to Roseivivax halodurans OCh 239(T) (97.0%), followed by Roseivivax isoporae sw-2(T) (96.9%). Growth occurred at 4-37 °C (optimum 32 °C), pH 6.0-10.0 (optimum 8.0) and in the presence of 0-12% (w/v) NaCl (optimum 3-4%) in marine broth 2216. Strain ZL136(T) did not produce bacteriochlorophyll a. The predominant fatty acids were C(18 : 1)ω7c and/or C(18 : 1)ω6c, C(18 : 0), C(16 : 0) and 11-methyl C(18 : 1)ω7c. The major polar lipids of ZL136(T) were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unidentified lipid. The major respiratory quinone was ubiquinone Q-10. The genomic DNA G+C content of strain ZL136(T) was 67.0 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic analysis, strain ZL136(T) was classified as a representative of a novel species in the genus of Roseivivax, for which the name Roseivivax marinus sp. nov. is proposed. The type strain is ZL136(T) ( = JCM 19386(T) = KCTC 32470(T)).

  19. Bacillus crassostreae sp. nov., isolated from an oyster (Crassostrea hongkongensis).

    PubMed

    Chen, Jin-Hua; Tian, Xiang-Rong; Ruan, Ying; Yang, Ling-Ling; He, Ze-Qiang; Tang, Shu-Kun; Li, Wen-Jun; Shi, Huazhong; Chen, Yi-Guang

    2015-05-01

    A novel Gram-stain-positive, motile, catalase- and oxidase-positive, endospore-forming, facultatively anaerobic rod, designated strain JSM 100118(T), was isolated from an oyster (Crassostrea hongkongensis) collected from the tidal flat of Naozhou Island in the South China Sea. Strain JSM 100118(T) was able to grow with 0-13% (w/v) NaCl (optimum 2-5%), at pH 5.5-10.0 (optimum pH 7.5) and at 5-50 °C (optimum 30-35 °C). The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant respiratory quinone was menaquinone-7 and the major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C16 : 0 and C16 : 1ω11c. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown glycolipid and an unknown phospholipid. The genomic DNA G+C content was 35.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 100118(T) belonged to the genus Bacillus , and was most closely related to Bacillus litoralis SW-211(T) (98.9% 16S rRNA gene sequence similarity), Bacillus halosaccharovorans E33(T) (98.3%), Bacillus niabensis 4T19(T) (97.8%) and Bacillus herbersteinensis D-1,5a(T) (97.1%). The combination of results from the phylogenetic analysis, DNA-DNA hybridization, and phenotypic and chemotaxonomic characterization supported the conclusion that strain JSM 100118(T) represents a novel species of the genus Bacillus , for which the name Bacillus crassostreae sp. nov. is proposed. The type strain is JSM 100118(T) ( = CTCC AB 2010452(T) =DSM 24486(T) =JCM 17523(T)).

  20. Microbacterium marinum sp. nov., isolated from deep-sea water.

    PubMed

    Zhang, Limin; Xi, Lijun; Ruan, Jisheng; Huang, Ying

    2012-03-01

    Two Gram-positive, rod-shaped bacterial strains, H101(T) and H207, were isolated from deep sea water collected from South-West Indian Ocean. Phylogenetic analysis of 16S rRNA gene sequences showed that the two strains were closely related to one another (100% similarity), and had the closest relationship with Microbacterium hominis NBRC 15708(T) and Microbacterium insulae KCTC 19247(T) (98.2-98.3% similarities). DNA-DNA hybridization value between strains H101(T) and H207 was 87.2 ± 3.7%, and the values between the two strains and the closely related type strains were well below 70%. The two strains also shared a number of physiological and biochemical characteristics that were distinct from the closely related species, and grew at 2-37 ° C, pH 5-11 and 0-8% (w/v) NaCl. Both strains contained MK-12, MK-13 and MK-11 as the detected menaquinones. The peptidoglycan was of type B1γ with an interpeptide bridge D-Glu(Hyg)→ Gly(2)→ l-Lys. The major cellular fatty acids were anteiso-C(15:0), anteiso-C(17:0), and iso-C(16:0). Based on the genetic and phenotypic properties, it is proposed that strains H101(T) and H207 be classified as representatives of a novel species of the genus Microbacterium, with the name Microbacterium marinum sp. nov. The type strain is H101(T) (= CGMCC 4.6941(T) = DSM 24947(T)).

  1. Citreicella marina sp. nov., isolated from deep-sea sediment.

    PubMed

    Lai, Qiliang; Fu, Yuanyuan; Wang, Jianning; Chen, Shuangxi; Zhong, Huanzi; Sun, Fengqin; Shao, Zongze

    2011-04-01

    A taxonomic study was carried out on a novel strain, designated CK-I3-6(T), which was isolated from deep-sea sediment of the south-west Indian Ocean Ridge. Cells were Gram-reaction-negative, oxidase- and catalase-positive, rod-shaped and non-motile. Growth was observed at 4-38 °C and in 1-12 % (w/v) NaCl. Cells were able to degrade gelatin and oxidize thiosulfate but did not reduce nitrate. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CK-I3-6(T) belonged to the genus Citreicella with a sequence similarity of 97.3 % to Citreicella thiooxidans CHLG 1(T), while similarities with other taxa were <95.7 %. DNA-DNA hybridization showed that strain CK-I3-6(T) and C. thiooxidans CHLG 1(T) showed a low DNA-DNA relatedness (48±3 %). The principal fatty acids were C(16 : 0) (7.8 %), C(18 : 1)ω7c (66.6 %), summed feature 3 (C(16 : 1)ω6c and/or C(16 : 1)ω7c; 6.3 %) and C(19 : 0)ω8c cyclo (10.0 %). The chromosomal DNA G+C content was 67.5 mol%. On the basis of the combined genotypic and phenotypic data, strain CK-I3-6(T) represents a novel species of the genus Citreicella, for which the name Citreicella marina sp. nov. is proposed. The type strain is CK-I3-6(T) ( = CCTCC AB 209064(T)  = LMG 25230(T)  = MCCC 1A03060(T)).

  2. Oceanobacillus halophilum sp. nov. isolated from a mangrove forest soil.

    PubMed

    Tang, Jia; Yang, Guiqin; Wang, Yueqiang; Wu, Chu; Zhou, Shungui

    2014-05-01

    A halophilic, aerobic bacterium, designated GD01(T), was isolated from a mangrove forest soil near the South China Sea. Cells of strain GD01(T) were Gram staining positive, oxidase positive, and catalase positive. The strain was rod shaped and motile by means of peritrichous flagella and produced ellipsoidal endospores. The strain was able to grow with NaCl at concentrations of 0.5-12 % (optimum 3-5 %, w/v), at temperatures of 20-50 °C (optimum 30 °C), and at pH 6.0-8.5 (optimum pH 7.0). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain GD01(T) formed a cluster with O. profundus DSM 18246(T) (96.4 % 16S rRNA gene sequence similarity), O. caeni KCTC 13061(T) (95.4 %), and O. oncorhynchi JCM 12661(T) (94.5 %). The G+C content of strain GD01(T) was 38.7 mol%. The major respiratory quinone was MK-7. The major cellular fatty acids (>5 %) were anteiso-C15:0, iso-C16:0 (13.7 %), anteiso-C17:0 (12.6 %), iso-C15:0 (9.9 %), iso-C14:0 (9.5 %), and C16:0 (5.0 %). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, glycolipid, four unknown lipids, and four unknown phospholipids. Based on phenotypic characteristics, chemotaxonomic features, and phylogenetic analysis based on 16S rRNA gene sequences, the strain was identified to represent a distinct novel species in the genus Oceanobacillus, and the name proposed is Oceanobacillus halophilum sp. nov. with type train GD01(T) (=CCTCC AB 2012863(T) = KCTC 33101(T)).

  3. Kangiella profundi sp. nov., isolated from deep-sea sediment.

    PubMed

    Xu, Fang-di; Li, Xue-gong; Xiao, Xiang; Xu, Jun

    2015-07-01

    A taxonomic study employing a polyphasic approach was carried out on strain FT102(T), which was isolated from a deep-sea sediment sample collected in the south-west Indian Ocean at a depth of 2784 m. The strain was Gram-stain-negative, non-motile, rod-shaped and non-spore-forming. It grew optimally at 37-42 °C, pH 6.5-8.5 and in the presence of 1-4% (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene sequences confirmed the separation of the novel strain from recognized members of the genus Kangiella that are available in public databases. Strain FT102(T) exhibited 95.5-98.6% 16S rRNA gene sequence similarity to the type strains of the eight recognized species of the genus Kangiella. The chemotaxonomically characteristic fatty acid iso-C15:0 and ubiquinone Q-8 were also detected. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine. The DNA G + C content of strain FT102(T) was 45.0 mol%. The mean DNA-DNA relatedness values between strain FT102(T) and the type strains of Kangiella aquimarina and Kangiella koreensis were 47.3% and 13.7%, respectively. The combined results of phylogenetic, physiological and chemotaxonomic studies indicated that strain FT102(T) was affiliated with the genus Kangiella but differed from the recognized species of the genus Kangiella. Therefore, strain FT102T represents a novel species of the genus Kangiella, for which the name Kangiella profundi sp. nov. is proposed. The type strain is FT102(T) ( = CGMCC 1.12959(T) = KCTC 42297(T) = JCM 30232(T)).

  4. Prauserella coralliicola sp. nov., isolated from the coral Galaxea fascicularis.

    PubMed

    Wu, Jia-Fa; Li, Jie; You, Zhi-Qing; Zhang, Si

    2014-10-01

    A novel Gram-stain-positive actinobacterium, designated strain SCSIO 11529(T), was isolated from tissues of the stony coral Galaxea fascicularis, and characterized by using a polyphasic approach. The temperature range for growth was 22-50 °C (optimum 28-45 °C), the pH range for growth was 6.0-8.0 (optimum pH 7.0), and the NaCl concentration range for growth was 0-7% (w/v) NaCl. The polar lipid profile contained diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine and an unknown polar lipid. The predominant menaquinone was MK-9(H4). The major fatty acids (>10%) were iso-C16:0, iso-C17:1ω6c, iso-C16:1 H and C16:1ω7c/iso-C15:0 2-OH. The DNA G+C content of strain SCSIO 11529(T) was 70.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SCSIO 11529(T) belongs to the genus Prauserella, with the closest neighbours being Prauserella marina MS498(T) (97.0% 16S rRNA gene sequence similarity), Prauserella rugosa DSM 43194(T) (96.4%) and Prauserella flava YIM 90630(T) (95.9%). Based on the evidence of the present study, strain SCSIO 11529(T) is considered to represent a novel species of the genus Prauserella, for which the name Prauserella coralliicola sp. nov. is proposed. The type strain is SCSIO 11529(T) ( = DSM 45821(T) = NBRC 109418(T)).

  5. Bacillus glycinifermentans sp. nov., isolated from fermented soybean paste.

    PubMed

    Kim, Soo-Jin; Dunlap, Christopher A; Kwon, Soon-Wo; Rooney, Alejandro P

    2015-10-01

    Two independent isolates of a Gram-stain-positive, facultatively anaerobic, motile, rod-shaped bacterium were recovered from cheonggukjang, a Korean fermented soybean paste food product. Preliminary sequencing analysis of the 16S rRNA gene indicated that these strains were related most closely to Bacillus sonorensis KCTC-13918T and Bacillus licheniformis DSM 13T. In phenotypic characterization, the novel strains were found to grow between 15 and 55 °C and to tolerate up to 8 % (w/v) NaCl. Furthermore, the strains grew in media of pH 5-10 (optimal growth at pH 7.0). The predominant cellular fatty acids were anteiso-C15 : 0 and iso-C15 : 0.The isoprenoid quinone was menaquinone 7 (MK-7). The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unknown glycolipid. Draft genomes of the two strains were determined and in silico DNA-DNA hybridizations with their nearest neighbour (B. sonorensis KCTC-13918T) revealed 29.9 % relatedness for both strains. Phylogenomic analysis of the genomes was conducted with the core genome (799 genes) of all strains in the Bacillus subtilis group and the two strains formed a distinct monophyletic cluster. In addition, the strains differed from the two most closely related species in that they did not metabolize maltose, d-galactose, d-sorbitol or d-gluconic acid. The DNA G+C content was 45.9 mol%. Based upon the consensus of phylogenetic and phenotypic analyses, these strains represent a novel species of the genus Bacillus, for which the name Bacillus glycinifermentans sp. nov. is proposed. The type strain is GO-13T ( = KACC 18425T = NRRL B-65291T). PMID:26297378

  6. Pseudorhodobacter sinensis sp. nov. and Pseudorhodobacter aquaticus sp. nov., isolated from crater lakes.

    PubMed

    Li, Ai-Hua; Liu, Hong-Can; Hou, Wei-Guo; Zhou, Yu-Guang

    2016-08-01

    Three Gram-stain negative, aerobic, non-motile, rod-shaped bacterial strains, Y1R2-4T, Y3R2-3 and DC2N1-10T, isolated from two crater lakes of the Daxinganling Mountains, northern China, were studied to determine their taxonomic position. They grew at 4-30 °C (optimally at 20-25 °C), at pH 6.0-7.5 (optimally at pH 7.0) and in the presence of 0-0.5 % (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, these strains showed 95.3-96.6 % similarity to members of the genus Pseudorhodobacter, including Pseudorhodobacter ferrugineus DSM 5888T, Pseudorhodobacter wandonensis WT-MW11T, Pseudorhodobacter antarcticus ZS3-33T and Pseudorhodobacter aquimaris HDW-19T. All strains contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The main polar lipids for strains Y1R2-4T and Y3R2-3 were phosphatidylglycerol, phosphatidylcholine, one unidentified aminophospholipid, one unidentified aminolipid, three unidentified phospholipids and two unidentified lipids, and those for strain DC2N1-10T were phosphatidylglycerol, phosphatidylcholine, one unidentified aminophospholipid, one unidentified aminolipid, one unidentified phospholipid and several unidentified lipids. The DNA G+C contents of strains Y1R2-4T, Y3R2-3 and DC2N1-10T were 61.9, 61.0 and 60.0 mol%, respectively. In addition, strain Y1R2-4T shared less than 50 % DNA-DNA relatedness to strain DC2N1-10T. Based on these differences in genetic, physiological and chemotaxonomic properties, strains Y1R2-4T, Y3R2-3 and DC2N1-10T were considered to represent two novel species of the genus Pseudorhodobacter, for which the names Pseudorhodobacter sinensis sp. nov. (type strain Y1R2-4T=CGMCC1.14435T=KCTC 52039T) and Pseudorhodobacter aquaticus sp. nov. (type strain DC2N1-10T=CGMCC1.14433T=KCTC 52040T) are proposed. PMID:27045957

  7. Pseudorhodobacter sinensis sp. nov. and Pseudorhodobacter aquaticus sp. nov., isolated from crater lakes.

    PubMed

    Li, Ai-Hua; Liu, Hong-Can; Hou, Wei-Guo; Zhou, Yu-Guang

    2016-08-01

    Three Gram-stain negative, aerobic, non-motile, rod-shaped bacterial strains, Y1R2-4T, Y3R2-3 and DC2N1-10T, isolated from two crater lakes of the Daxinganling Mountains, northern China, were studied to determine their taxonomic position. They grew at 4-30 °C (optimally at 20-25 °C), at pH 6.0-7.5 (optimally at pH 7.0) and in the presence of 0-0.5 % (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, these strains showed 95.3-96.6 % similarity to members of the genus Pseudorhodobacter, including Pseudorhodobacter ferrugineus DSM 5888T, Pseudorhodobacter wandonensis WT-MW11T, Pseudorhodobacter antarcticus ZS3-33T and Pseudorhodobacter aquimaris HDW-19T. All strains contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The main polar lipids for strains Y1R2-4T and Y3R2-3 were phosphatidylglycerol, phosphatidylcholine, one unidentified aminophospholipid, one unidentified aminolipid, three unidentified phospholipids and two unidentified lipids, and those for strain DC2N1-10T were phosphatidylglycerol, phosphatidylcholine, one unidentified aminophospholipid, one unidentified aminolipid, one unidentified phospholipid and several unidentified lipids. The DNA G+C contents of strains Y1R2-4T, Y3R2-3 and DC2N1-10T were 61.9, 61.0 and 60.0 mol%, respectively. In addition, strain Y1R2-4T shared less than 50 % DNA-DNA relatedness to strain DC2N1-10T. Based on these differences in genetic, physiological and chemotaxonomic properties, strains Y1R2-4T, Y3R2-3 and DC2N1-10T were considered to represent two novel species of the genus Pseudorhodobacter, for which the names Pseudorhodobacter sinensis sp. nov. (type strain Y1R2-4T=CGMCC1.14435T=KCTC 52039T) and Pseudorhodobacter aquaticus sp. nov. (type strain DC2N1-10T=CGMCC1.14433T=KCTC 52040T) are proposed.

  8. Actinomadura amylolytica sp. nov. and Actinomadura cellulosilytica sp. nov., isolated from geothermally heated soil.

    PubMed

    Jiao, Jian-Yu; Liu, Lan; Zhou, En-Min; Wei, Da-Qiao; Ming, Hong; Xian, Wen-Dong; Yuan, Chang-Guo; Zhong, Jing-Mei; Li, Wen-Jun

    2015-07-01

    Two aerobic, Gram-positive actinomycetes, designated YIM 77502(T) and YIM 77510(T), were isolated from geothermally heated soil of Tengchong county, Yunnan province, south-west China. The taxonomic position of strains YIM 77502(T) and YIM 77510(T) were investigated by a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains YIM 77502(T) and YIM 77510(T) belong to the genus Actinomadura. Both strains form extensively-branched substrate and aerial mycelia which differentiated into short spore chains. The cell wall of the two strains contained meso-diaminopimelic acid, while the whole-cell sugars detected were glucose, madurose, mannose and rhamnose. The polar lipid profile of strain YIM 77502(T) was found to consist of diphosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylinositol, two unidentified phospholipids and an unidentified polar lipid, while strain YIM 77510(T) consisted of diphosphatidylglycerol, phosphatidylinositol mannoside and phosphatidylinositol. The respiratory quinones of strains YIM 77502(T) and YIM 77510(T) were MK-9(H6) and MK-9(H8). The major fatty acids (>10 %) of strain YIM 77502(T) were C17:0, iso-C16:0, C17:010-methyl and iso-C18:0, and those of strain YIM 77510(T) were iso-C16:0, C17:010-methyl and iso-C18:0. The G+C contents of strains YIM 77502(T) and YIM 77510(T) were determined to be 71.3 and 70.2 mol%, respectively. The DNA-DNA hybridization values of strains YIM 77502(T), YIM 77510(T) and their closest phylogenetic neighbours Actinomadura echinospora BCRC 12547(T) and Actinomadura umbrina KCTC 9343(T) were less than 70 %. Based on the morphological and physiological properties, and phylogenetic analyses, strains YIM 77502(T) and YIM 77510(T) are considered to represent two novel species of the genus Actinomadura, for which the names Actinomadura amylolytica sp. nov. (type strain YIM 77502(T) = DSM 45822(T) = CCTCC AA 2012024(T)) and Actinomadura cellulosilytica sp. nov. (type

  9. Psychroflexus salis sp. nov. and Psychroflexus planctonicus sp. nov., isolated from a salt lake.

    PubMed

    Zhong, Zhi-Ping; Liu, Ying; Wang, Fang; Zhou, Yu-Guang; Liu, Hong-Can; Liu, Zhi-Pei

    2016-01-01

    Two Gram-stain-negative, catalase- and oxidase-positive, strictly aerobic, non-motile, moderately halophilic bacteria (strains X15M-6T and X15M-8T) were isolated from Lake Xiaochaidan, a salt lake in Qaidam basin, Qinghai Province, China. Cells of X15M-6T were rod-like or coccoid, 0.5-0.9 μm wide and 0.9-1.5 μm long; cells of X15M-8T were rods, 0.3-0.6 μm wide and 1.2-2.2 μm long. Growth was observed in the presence of 0.5-14.0 % (w/v) NaCl (optimum, 3.0 %) and at pH 6.5-10.0 (optimum, pH 7.0-7.5) for both. X15M-6T and X15M-8T grew at 10-35 °C (optimum, 20-25 °C) and 4-35 °C (optimum, 25 °C), respectively. Both contained iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids, phosphatidylethanolamine and an unknown lipid as the major polar lipids, and menaquinone MK-6 as the major respiratory quinone. The DNA G+C contents were 32.8 and 35.0 mol% for X15M-6T and X15M-8T, respectively. Phylogenetic trees based on 16S rRNA gene sequences showed that both strains belonged to the genus Psychroflexus and formed a separate lineage. In addition, strains X15M-6T and X15M-8T shared 96.8 % 16S rRNA gene sequence similarity and showed highest similarities to members of the genus Psychroflexus (92.7-93.5 and 91.8-93.1 %, respectively). Based on the above data, it is concluded that strains X15M-6T and X15M-8T represent two novel species of the genus Psychroflexus, for which the names Psychroflexus salis sp. nov. (type strain X15M-6T = CGMCC 1.12925T = JCM 30615T) and Psychroflexus planctonicus sp. nov. (type strain X15M-8T = CGMCC 1.12931T = JCM 30616T) are proposed. PMID:26475261

  10. Cohnella yongneupensis sp. nov. and Cohnella ginsengisoli sp. nov., isolated from two different soils.

    PubMed

    Kim, Soo-Jin; Weon, Hang-Yeon; Kim, Yi-Seul; Anandham, Rangasamy; Jeon, Young-Ah; Hong, Seung-Beom; Kwon, Soon-Wo

    2010-03-01

    Two aerobic, Gram-positive, rod-shaped bacterial strains, 5YN10-14(T) and GR21-5(T), were isolated from the Yongneup wetland and ginseng soil in Korea, respectively. The two strains formed ellipsoidal or oval spores positioned centrally or paracentrally in swollen sporangia. On the basis of 16S rRNA gene sequence analysis, these strains were related to members of the genus Cohnella. 16S rRNA gene sequence similarity between strains 5YN10-14(T) and GR21-5(T) was 95.9 %. Strains 5YN10-14(T) and GR21-5(T) showed, respectively, 94.3 and 95.2 % 16S rRNA gene sequence similarity to Cohnella thermotolerans CCUG 47242(T), 94.6 and 94.4 % to Cohnella hongkongensis HKU3(T), 94.7 and 94.7 % to Cohnella laeviribosi RI-39(T), and 95.4 and 94.8 % to Cohnella phaseoli GSPC1(T). The major fatty acids of strain 5YN10-14(T) were anteiso-C(15 : 0) (51.1 %), iso-C(16 : 0) (18.5 %) and C(16 : 0) (13.2 %), and the major fatty acids of strain GR21-5(T) were anteiso-C(15 : 0 ) (48.9 %), iso-C(16 : 0) (15.0 %) and iso-C(15 : 0) (12.2 %). The two strains contained menaquinone with seven isoprene units (MK-7) as the predominant quinone, and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as major polar lipids; however, strain 5YN10-14(T) also contained lysylphosphatidylglycerol as a major polar lipid, whereas strain GR21-5(T) had an unknown aminophospholipid as another major polar lipid. The DNA G+C contents of strains 5YN10-14(T) and GR21-5(T) were 58.8 and 61.3 mol%, respectively. Based on the results of the phylogenetic and phenotypic data presented, it was concluded that the two strains represent two novel species of the genus Cohnella , for which the names Cohnella yongneupensis sp. nov. (type strain 5YN10-14(T)=KACC 11768(T)=DSM 18998(T)) and Cohnella ginsengisoli sp. nov. (type strain GR21-5(T)=KACC 11771(T)=DSM 18997(T)) are proposed.

  11. Psychroflexus salis sp. nov. and Psychroflexus planctonicus sp. nov., isolated from a salt lake.

    PubMed

    Zhong, Zhi-Ping; Liu, Ying; Wang, Fang; Zhou, Yu-Guang; Liu, Hong-Can; Liu, Zhi-Pei

    2016-01-01

    Two Gram-stain-negative, catalase- and oxidase-positive, strictly aerobic, non-motile, moderately halophilic bacteria (strains X15M-6T and X15M-8T) were isolated from Lake Xiaochaidan, a salt lake in Qaidam basin, Qinghai Province, China. Cells of X15M-6T were rod-like or coccoid, 0.5-0.9 μm wide and 0.9-1.5 μm long; cells of X15M-8T were rods, 0.3-0.6 μm wide and 1.2-2.2 μm long. Growth was observed in the presence of 0.5-14.0 % (w/v) NaCl (optimum, 3.0 %) and at pH 6.5-10.0 (optimum, pH 7.0-7.5) for both. X15M-6T and X15M-8T grew at 10-35 °C (optimum, 20-25 °C) and 4-35 °C (optimum, 25 °C), respectively. Both contained iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids, phosphatidylethanolamine and an unknown lipid as the major polar lipids, and menaquinone MK-6 as the major respiratory quinone. The DNA G+C contents were 32.8 and 35.0 mol% for X15M-6T and X15M-8T, respectively. Phylogenetic trees based on 16S rRNA gene sequences showed that both strains belonged to the genus Psychroflexus and formed a separate lineage. In addition, strains X15M-6T and X15M-8T shared 96.8 % 16S rRNA gene sequence similarity and showed highest similarities to members of the genus Psychroflexus (92.7-93.5 and 91.8-93.1 %, respectively). Based on the above data, it is concluded that strains X15M-6T and X15M-8T represent two novel species of the genus Psychroflexus, for which the names Psychroflexus salis sp. nov. (type strain X15M-6T = CGMCC 1.12925T = JCM 30615T) and Psychroflexus planctonicus sp. nov. (type strain X15M-8T = CGMCC 1.12931T = JCM 30616T) are proposed.

  12. Actinomadura amylolytica sp. nov. and Actinomadura cellulosilytica sp. nov., isolated from geothermally heated soil.

    PubMed

    Jiao, Jian-Yu; Liu, Lan; Zhou, En-Min; Wei, Da-Qiao; Ming, Hong; Xian, Wen-Dong; Yuan, Chang-Guo; Zhong, Jing-Mei; Li, Wen-Jun

    2015-07-01

    Two aerobic, Gram-positive actinomycetes, designated YIM 77502(T) and YIM 77510(T), were isolated from geothermally heated soil of Tengchong county, Yunnan province, south-west China. The taxonomic position of strains YIM 77502(T) and YIM 77510(T) were investigated by a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains YIM 77502(T) and YIM 77510(T) belong to the genus Actinomadura. Both strains form extensively-branched substrate and aerial mycelia which differentiated into short spore chains. The cell wall of the two strains contained meso-diaminopimelic acid, while the whole-cell sugars detected were glucose, madurose, mannose and rhamnose. The polar lipid profile of strain YIM 77502(T) was found to consist of diphosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylinositol, two unidentified phospholipids and an unidentified polar lipid, while strain YIM 77510(T) consisted of diphosphatidylglycerol, phosphatidylinositol mannoside and phosphatidylinositol. The respiratory quinones of strains YIM 77502(T) and YIM 77510(T) were MK-9(H6) and MK-9(H8). The major fatty acids (>10 %) of strain YIM 77502(T) were C17:0, iso-C16:0, C17:010-methyl and iso-C18:0, and those of strain YIM 77510(T) were iso-C16:0, C17:010-methyl and iso-C18:0. The G+C contents of strains YIM 77502(T) and YIM 77510(T) were determined to be 71.3 and 70.2 mol%, respectively. The DNA-DNA hybridization values of strains YIM 77502(T), YIM 77510(T) and their closest phylogenetic neighbours Actinomadura echinospora BCRC 12547(T) and Actinomadura umbrina KCTC 9343(T) were less than 70 %. Based on the morphological and physiological properties, and phylogenetic analyses, strains YIM 77502(T) and YIM 77510(T) are considered to represent two novel species of the genus Actinomadura, for which the names Actinomadura amylolytica sp. nov. (type strain YIM 77502(T) = DSM 45822(T) = CCTCC AA 2012024(T)) and Actinomadura cellulosilytica sp. nov. (type

  13. Paenibacillus salinicaeni sp. nov., isolated from saline silt sample.

    PubMed

    Guo, Xiang; Zhou, Shan; Wang, Yan-Wei; Wang, Hui-Min; Kong, De-Long; Zhu, Jie; Dong, Wei-Wei; He, Ming-Xiong; Zhao, Bing-Qiang; Hu, Guo-Quan; Ruan, Zhi-Yong

    2016-05-01

    A novel facultatively anaerobic bacterium, designated strain LAM0A28(T), was isolated from a saline silt sample collected from the Chinese Sea of Death located in Suining city, Sichuan province, China. Cells of strain LAM0A28(T) were observed to be Gram-stain positive, motile, endospore-forming and straight-rod shaped. Strain LAM0A28(T) was found to be able to grow at 15-45 °C (optimum: 30-35 °C), pH 5.0-10.0 (optimum: 7.5) and 0-5 % NaCl (w/v) (optimum: 0.5 %). The 16S rRNA gene sequence similarity analysis showed that strain LAM0A28(T) is closely related to Paenibacillus jilunlii DSM 23019(T) (97.5 %) and Paenibacillus graminis DSM 15220(T) (97.2 %). The DNA-DNA hybridization values between the isolate and P. jilunlii DSM 23019(T), P. graminis DSM 15220(T) were 30.2 ± 1.6 % and 44.7 ± 2.1 %, respectively. The DNA G+C content was found to be 51.2 mol% as determined by the T m method. The major cellular fatty acids were identified as anteiso-C15:0, C16:0, iso-C16:0 and C14:0. The major isoprenoid quinone was identified as MK-7. The cell wall peptidoglycan was found to contain meso-diaminopimelic acid. The major polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two aminophospholipids and six unidentified lipids. Based on the phylogenetic, phenotypic and chemotaxonomic characteristics, strain LAM0A28(T) is concluded to represent a novel species within the genus Paenibacillus, for which the name Paenibacillus salinicaeni sp. nov. is proposed. The type strain is LAM0A28(T) (=ACCC 00741(T) = JCM 30850(T)). PMID:26979511

  14. Asticcacaulis solisilvae sp. nov., isolated from forest soil.

    PubMed

    Kim, Seil; Gong, Gyeongtaek; Park, Tai Hyun; Um, Youngsoon

    2013-10-01

    An obligately aerobic, chemoheterotrophic, mesophilic prosthecate bacterium, designated strain CGM1-3EN(T), was isolated from the enrichment cultures of forest soil from Cheonggyesan Mountain, Republic of Korea. Cells were Gram-reaction-negative, motile rods (1.3-2.4 µm long by 0.30-0.75 µm wide) with single flagella. The strain grew at 10-37 °C (optimum 25-30 °C) and at pH 4.5-9.5 (optimum 5.0-7.0). The major cellular fatty acids were C16 : 0, C18 : 1ω7c 11-methyl, C12 : 1 3-OH and summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c). The genomic DNA G+C content of strain CGM1-3EN(T) was 63.7 mol%. The closest phylogenetic neighbour to strain CGM1-3EN(T) was identified as Asticcacaulis biprosthecium DSM 4723(T) (97.2 % 16S rRNA gene sequence similarity) and the DNA-DNA hybridization value between strain CGM1-3EN(T) and A. biprosthecium DSM 4723(T) was less than 24.5 %. Strain CGM1-3EN(T) used d-glucose, d-fructose, sucrose, maltose, trehalose, d-mannose, d-mannitol, d-sorbitol, d-galactose, cellobiose, lactose, raffinose, fumarate, pyruvate, dl-alanine and glycerol as carbon sources. Based on data from the present polyphasic study, the forest soil isolate CGM1-3EN(T) is considered to represent a novel species of the genus Asticcacaulis, for which the name Asticcacaulis solisilvae sp. nov. is proposed. The type strain is CGM1-3EN(T) ( = AIM0088(T) = KCTC 32102(T) = JCM 18544(T)). PMID:23687055

  15. Hymenobacter sedentarius sp. nov., isolated from a soil.

    PubMed

    Lee, Jae-Jin; Kang, Myung-Suk; Joo, Eun Sun; Jung, Hee-Young; Kim, Myung Kyum

    2016-04-01

    A novel Gram-negative and red-pinkish bacterium designated DG5B(T) was isolated from a dry soil. Cells were rods that were catalase- and oxidase-positive, and non-motile. The strain was found to grow at temperatures from 10 to 30°C (optimum 25°C) and pH 6.0-8.0, (optimum pH 7) on R2A broth. 16S rRNA gene sequence (1,452 bp) analysis of this strain identified it as a member of the genus Hymenobacter that belongs to the class Cytophagia. The highest gene sequence similarities were with Hymenobacter arizonensis OR362-8(T) (98.3%), Hymenobacter humi DG31A(T) (97.6%), and Hymenobacter glaciei VUG-A130(T) (96.6%). Strain DG5B(T) exhibited <70% DNA-DNA relatedness with H. arizonensis (34.7 ± 7.0%; reciprocally, 29.7 ± 1.2%) and H. humi (39.4 ± 4.3%; reciprocally, 39.5 ± 3.3%) as a different genomic species, and its genomic DNA G+C content was 59.8%. Strain DG5B(T) had the following chemotaxonomic characteristics: the major fatty acids are iso-C15:0, anteiso-C15:0, C16:1 ω5c, and summed feature 3 (C16:1 ω7c / C16:1 ω6c); polar lipid profile contained phosphatidylethanolamine (PE), unknown aminophospholipid (APL), unknown glycolipids (GL), unknown phospholipids (PL), and unknown polar lipids (L); the major quinone is MK-7. The absorbance peak of pigment is at 481.0 nm. Strain DG5B(T) showed low-level resistance to gamma-ray irradiation. Phenotypic, chemotaxonomic, and genotypic properties indicated that isolate DG5B(T) represents a novel species within the genus Hymenobacter for which the name Hymenobacter sedentarius sp. nov. is proposed. The type strain is DG5B(T) (=KCTC 32524(T) =JCM 19636(T)). PMID:27033203

  16. Terrisporobacter petrolearius sp. nov., isolated from an oilfield petroleum reservoir.

    PubMed

    Deng, Yu; Guo, Xiang; Wang, Yanwei; He, Mingxiong; Ma, Kedong; Wang, Huimin; Chen, Xiaorong; Kong, Delong; Yang, Zhirong; Ruan, Zhiyong

    2015-10-01

    A Gram-staining-positive, spore-forming, strictly anaerobic bacterium, designated strain LAM0A37T, was isolated from enrichment samples collected from a petroleum reservoir in Shengli oilfield. Cells of strain LAM0A37T were rod-shaped and motile by peritrichous flagella. The optimal temperature and pH for growth were 40 °C and 7.0–7.5, respectively. The strain did not require NaCl for growth but tolerated up to 3 % (w/v) NaCl. Strain LAM0A37T was able to utilize glucose, fructose, maltose, xylose, sorbitol, cellobiose, melibiose and melezitose as sole carbon sources. Sulfite was used as an electron acceptor. The main products of glucose fermentation were acetate and CO2. The predominant fatty acid was C16 : 0 (23.6 %). The main polar lipid profile comprised of five glycolipids, six phospholipids and two lipids. No menaquinone was detected. The genomic DNA G+C content was 27.1 ± 0.2 mol% as determined by the T m method. Analysis of the 16S rRNA gene sequence indicated that the isolate was a member of the genus Terrisporobacter, and was most closely related to Terrisporobacter glycolicus JCM 1401T and Terrisporobacter mayombei DSM 6539T with 98.3 % 16S rRNA gene sequence similarity to both. DNA–DNA hybridization values between strain LAM0A37T and type strains of Terrisporobacter glycolicus and Terrisporobacter mayombei were 45.6 ± 0.3 % and 38.3 ± 0.4 %, respectively. Based on phenotypic, phylogenetic and chemotaxonomic characteristics, strain LAM0A37T is suggested to represent a novel species of the genus Terrisporobacter, for which the name Terrisporobacter petrolearius sp. nov. is proposed. The type strain is LAM0A37T ( = ACCC 00740T = JCM 19845T).

  17. Paenibacillus salinicaeni sp. nov., isolated from saline silt sample.

    PubMed

    Guo, Xiang; Zhou, Shan; Wang, Yan-Wei; Wang, Hui-Min; Kong, De-Long; Zhu, Jie; Dong, Wei-Wei; He, Ming-Xiong; Zhao, Bing-Qiang; Hu, Guo-Quan; Ruan, Zhi-Yong

    2016-05-01

    A novel facultatively anaerobic bacterium, designated strain LAM0A28(T), was isolated from a saline silt sample collected from the Chinese Sea of Death located in Suining city, Sichuan province, China. Cells of strain LAM0A28(T) were observed to be Gram-stain positive, motile, endospore-forming and straight-rod shaped. Strain LAM0A28(T) was found to be able to grow at 15-45 °C (optimum: 30-35 °C), pH 5.0-10.0 (optimum: 7.5) and 0-5 % NaCl (w/v) (optimum: 0.5 %). The 16S rRNA gene sequence similarity analysis showed that strain LAM0A28(T) is closely related to Paenibacillus jilunlii DSM 23019(T) (97.5 %) and Paenibacillus graminis DSM 15220(T) (97.2 %). The DNA-DNA hybridization values between the isolate and P. jilunlii DSM 23019(T), P. graminis DSM 15220(T) were 30.2 ± 1.6 % and 44.7 ± 2.1 %, respectively. The DNA G+C content was found to be 51.2 mol% as determined by the T m method. The major cellular fatty acids were identified as anteiso-C15:0, C16:0, iso-C16:0 and C14:0. The major isoprenoid quinone was identified as MK-7. The cell wall peptidoglycan was found to contain meso-diaminopimelic acid. The major polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two aminophospholipids and six unidentified lipids. Based on the phylogenetic, phenotypic and chemotaxonomic characteristics, strain LAM0A28(T) is concluded to represent a novel species within the genus Paenibacillus, for which the name Paenibacillus salinicaeni sp. nov. is proposed. The type strain is LAM0A28(T) (=ACCC 00741(T) = JCM 30850(T)).

  18. Cupriavidus yeoncheonense sp. nov., isolated from soil of ginseng.

    PubMed

    Singh, Priyanka; Kim, Yeon-Ju; Nguyen, Ngoc-Lan; Hoang, Van-An; Sukweenadhi, Johan; Farh, Mohamed El-Agamy; Yang, Deok-Chun

    2015-03-01

    A novel bacterial strain, DCY86(T) (=KCTC 42053(T) = JCM 19890(T)) was isolated from soil of a ginseng field in Yeoncheon province (38°04'00″N 126°57'00″E), Republic of Korea using a serial dilution method. Strain DCY86(T) was observed to be Gram-stain negative, strictly aerobic, to grow optimally at 25-30 °C, at pH 7-7.5 and on tryptic soya agar medium. The cells were found to be sensitive to ceftazidine and tetracycline. Based on 16S rRNA gene sequence comparisons, strain DCY86(T) was found to be most closely related to Cupriavidus basilensis LMG 18990(T) (98.48 %), Cupriavidus numazensis LMG 26411(T) (98.34 %), Cupriavidus pinatabonesis KCTC 22125(T) (98.34 %) and Cupriavidus laharis KCTC 22126(T) (98.00 %). The G+C content was determined to be 64.23 mol %. The only isoprenoid quinone detected in strain DCY86(T) was ubiquinone Q-8. The major polar lipids were identified as diphosphatidylglycerol, phosphtidylethanolamine, phosphatidylglycerol, unidentified aminophosphoglycolipids and unidentified phospholipids. The major fatty acids were identified as C16:0 summed feature 3 (C16:1 ω7c/ω6c and/or iso-C15 : 0 2-OH) and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). These data support the affiliation of strain DCY86(T) to the genus Cupriavidus. Strain DCY86(T) was also found to be able to solubilize phosphate and produce siderophores. The results of physiological and biochemical tests enabled strain DCY86(T) to be differentiated genotypically and phenotypically from the recognized species of the genus Cupriaividus. Therefore, the novel isolate can be considered to represent a novel species, for which the name Cupriavidus yeoncheonense sp. nov. is proposed here. The type strain is DCY86(T) (=KCTC 42053(T) = JCM 19890(T)).

  19. Flavobacterium panacis sp. nov., isolated from rhizosphere of Panax ginseng.

    PubMed

    Kim, Dong Hyun; Singh, Priyanka; Farh, Mohamed El-Agamy; Kim, Yeon-Ju; Nguyen, Ngoc-Lan; Lee, Hyun A; Yang, Deok-Chun

    2016-09-01

    A novel bacterial strain, designated DCY106(T), was isolated from soil collected from the rhizosphere of ginseng (Panax ginseng), in Gochang, Republic of Korea. Strain DCY106(T) is Gram-negative, yellow-pigmented, non-flagellate, motile, non-spore-forming, rod-shaped, and strictly aerobic. The strain grows optimally at 25-30 °C and pH 6.5-7.5. Phylogenetically, strain DCY106(T) is closely related to Flavobacterium arsenitoxidans KCTC 22507(T) (98.41 %), followed by Flavobacterium cutihirudini LMG 26922(T) (97.67 %), Flavobacterium nitrogenifigens LMG 28694(T) (97.59 %), Flexibacter auranticus LMG 3987(T) (97.38 %), Flavobacterium defluvi KCTC 12612(T) (97.21 %) and Flavobacterium chilense LMG 26360(T) (97.05 %). The 16S rRNA gene sequence similarities to all other Flavobacterium species were below 97 %. The DNA G+C content of strain DCY106(T) is 34.2 mol% and the DNA-DNA relatedness between strain DCY106(T) and F. cutihirudini LMG 26922(T), F. auranticus LMG 3987(T), F. defluvi KCTC 12612(T) and F. chilense LMG 26360(T) were below 40.0 %. The menaquinone of the type MK-6 was found to be the predominant respiratory quinone. The major polar lipids were identified as phosphatidylethanolamine, phosphatidylserine, two unidentified aminolipids (APL1, APL6) and one unidentified lipid L2. C15:0, iso-C15:0 and summed feature 3 (iso-C15:0 2OH/C16:1 ω7c) were identified as the major fatty acids present in DCY106(T). The results of physiological and biochemical tests allowed strain DCY106(T) to be differentiated phenotypically from other recognized species belonging to the genus Flavobacterium. Therefore, it is suggested that the newly isolated organism represents a novel species, for which the name Flavobacterium panacis sp. nov. is proposed with the type strain designated as DCY106(T) (= JCM 31468(T)= KCTC 42747(T)).

  20. Nocardioides albidus sp. nov., an actinobacterium isolated from garden soil.

    PubMed

    Singh, Hina; Du, Juan; Trinh, Huan; Won, KyungHwa; Yang, Jung-Eun; Yin, ChangShik; Kook, MooChang; Yi, Tae-Hoo

    2016-01-01

    A novel bacterial strain, designated THG-S11.7T, was isolated from garden soil in Incheon, South Korea. Cells of the strain were Gram-stain-positive, aerobic, non-motile cocci, and were catalase- and oxidase-positive. Colonies of the strain were white. Strain THG-S11.7T grew optimally at 28 °C, at pH 7.0 and in the presence of 2.0 % NaCl. 16S rRNA gene sequence analysis indicated that the strain was a member of the genus Nocardioides. Strain THG-S11.7T showed a 16S rRNA gene sequence similarity of 98.2 % to Nocardioides kongjuensis KCTC 19054T, 98.0 % to Nocardioides caeni KCTC 19600T, 97.9 % to Nocardioides daeguensis KCTC 19799T, 97.8 % to Nocardioides nitrophenolicus KCTC 047BPT, 97.6 % to Nocardioides aromaticivorans KACC 20613T, 97.5 % to Nocardioides simplex KACC 20620T and 97.0 % to Nocardioides ginsengisoli KCTC 19135T. DNA-DNA relatedness values between strain THG-S11.7T and the closest phylogenetic neighbours were below 45.0 % and the DNA G+C content of strain THG-S11.7T was 72.2 mol%. Strain THG-S11.7T was characterized chemotaxonomically as having ll-diaminopimelic acid in the cell-wall peptidoglycan and menaquinone MK-8(H4) as the predominant isoprenoid quinone. The major phospholipid was determined to be diphosphatidylglycerol. The major cellular fatty acids of strain THG-S11.7T were iso-C15 : 0, C16 : 0 and iso-C16 : 0. Based on the phenotypic, genotypic and phylogenetic analyses, it is proposed that the isolate represents a novel species of the genus Nocardioides, for which the name Nocardioides albidus sp. nov. is proposed. The type strain is THG-S11.7T ( = KCTC 39607T = CCTCC AB 2015297T).

  1. Aestuariivita atlantica sp. nov., isolated from deep-sea sediment.

    PubMed

    Li, Guizhen; Lai, Qiliang; Du, Yaping; Liu, Xiupian; Sun, Fengqin; Shao, Zongze

    2015-10-01

    A novel strain, 22II-S11-z3T, was isolated from the deep-sea sediment of the Atlantic Ocean. The bacterium was aerobic, Gram-staining-negative, oxidase-positive and catalase-negative, oval- to rod-shaped, and non-motile. Growth was observed at salinities of 1-9 % NaCl and temperatures of 10-45 °C. The isolate could hydrolyse aesculin and Tweens 20, 40 and 80, but not gelatin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 22II-S11-z3T belonged to the genus Aestuariivita, with highest sequence similarity to Aestuariivita boseongensis KCTC 42052T (97.5 %). The average nucleotide identity and digital DNA-DNA hybridization values between strain 22II-S11-z3T and A. boseongensis KCTC 42052T were 71.5 % and 20.0 ± 2.3 %, respectively. The G+C content of the chromosomal DNA was 65.5 mol%. The principal fatty acids (>5 %) were summed feature 8 (C18 : 1ω7c/ω6c) (35.2 %), C19 : 0 cyclo ω8c (20.9 %), C16 : 0 (11.8 %), 11-methyl C18 : 1ω7c (11.4 %) and C12 : 1 3-OH (9.4 %). The respiratory quinone was determined to be Q-10. Diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, nine unidentified phospholipids, one unidentified aminolipid and two unidentified lipids were present. The combined genotypic and phenotypic data show that strain 22II-S11-z3T represents a novel species of the genus Aestuariivita, for which the name Aestuariivita atlantica sp. nov. is proposed, with the type strain 22II-S11-z3T ( = KCTC 42276T = MCCC 1A09432T).

  2. Evidence for cooperative mineralization of diuron by Arthrobacter sp. BS2 and Achromobacter sp. SP1 isolated from a mixed culture enriched from diuron exposed environments.

    PubMed

    Devers-Lamrani, Marion; Pesce, Stéphane; Rouard, Nadine; Martin-Laurent, Fabrice

    2014-12-01

    Diuron was found to be mineralized in buffer strip soil (BS) and in the sediments (SED) of the Morcille river in the Beaujolais vineyard repeatedly treated with this herbicide. Enrichment cultures from BS and SED samples led to the isolation of three bacterial strains transforming diuron to 3,4-dichloroaniline (3,4-DCA) its aniline derivative. 16S rRNA sequencing revealed that they belonged to the genus Arthrobacter (99% of similarity to Arthrobacter globiformis strain K01-01) and were designated as Arthrobacter sp. BS1, BS2 and SED1. Diuron-degrading potential characterized by sequencing of the puhA gene, characterizing the diuron-degradaing potential, revealed 99% similarity to A. globiformis strain D47 puhA gene isolated a decade ago in the UK. These isolates were also able to use chlorotoluron for their growth. Although able to degrade linuron and monolinuron to related aniline derivatives they were not growing on them. Enrichment cultures led to the isolation of a strain from the sediments entirely degrading 3,4-DCA. 16S rRNA sequence analysis showed that it was affiliated to the genus Achromobacter (99% of similarity to Achromobacter sp. CH1) and was designated as Achromobacter sp. SP1. The dcaQ gene encoding enzyme responsible for the transformation of 3,4-DCA to chlorocatechol was found in SP1 with 99% similarity to that of Comamonas testosteroni WDL7. This isolate also used for its growth a range of anilines (3-chloro-4-methyl-aniline, 4-isopropylaniline, 4-chloroaniline, 3-chloroaniline, 4-bromoaniline). The mixed culture composed of BS2 and SP1 strains entirely mineralizes (14)C-diuron to (14)CO2. Diuron-mineralization observed in the enrichment culture could result from the metabolic cooperation between these two populations. PMID:25061887

  3. Draft Genome Sequence of Pseudomonas sp. LAB-08 Isolated from Trichloroethene-Contaminated Aquifer Soil

    PubMed Central

    Aziz, Fatma A. A.; Inuzuka, Yuma; Tashiro, Yosuke

    2016-01-01

    Pseudomonas sp. LAB-08 was isolated from a phenol-fed bioreactor constructed with contaminated aquifer soil as the inoculum. Strain LAB-08 utilized phenol as a sole carbon and energy source. Here, we report the genome sequence and annotation of Pseudomonas sp. LAB-08. PMID:27660772

  4. Draft Genome Sequence of Pseudomonas sp. LAB-08 Isolated from Trichloroethene-Contaminated Aquifer Soil.

    PubMed

    Suzuki, Kenshi; Aziz, Fatma A A; Inuzuka, Yuma; Tashiro, Yosuke; Futamata, Hiroyuki

    2016-01-01

    Pseudomonas sp. LAB-08 was isolated from a phenol-fed bioreactor constructed with contaminated aquifer soil as the inoculum. Strain LAB-08 utilized phenol as a sole carbon and energy source. Here, we report the genome sequence and annotation of Pseudomonas sp. LAB-08. PMID:27660772

  5. Draft Genome Sequence of Micromonospora sp. Strain HK10, Isolated from Kaziranga National Park, India

    PubMed Central

    Talukdar, Madhumita; Das, Dhrubajyoti; Borah, Chiranjeeta; Deka Boruah, Hari Prasanna; Bora, Tarun Chandra

    2016-01-01

    We report the 6.92-Mbp genome sequence of Micromonospora sp. HK10, isolated from soil samples collected from Kaziranga National Park, Assam, India. The full genome of strain Micromonospora sp. strain HK10 consists of 6,911,179 bp with 73.39% GC content, 6,196 protein-coding genes, and 86 RNAs. PMID:27516496

  6. Draft Genome Sequence of Pedobacter sp. Strain Hv1, an Isolate from Medicinal Leech Mucosal Castings

    PubMed Central

    Ott, Brittany M.; Beka, Lidia; Graf, Joerg

    2015-01-01

    The Pedobacter sp. Hv1 strain was isolated from the medicinal leech, Hirudo verbana, mucosal castings. These mucosal sheds have been demonstrated to play a role in horizontal symbiont transmission. Here, we report the draft 4.9 Mbp genome sequence of Pedobacter sp. strain Hv1. PMID:26679583

  7. Complete Genome Sequence of Photobacterium sp. Strain J15, Isolated from Seawater of Southwestern Johor, Malaysia

    PubMed Central

    Roslan, Noordiyanah Nadhirah; Oslan, Siti Nurbaya; Baharum, Syarul Nataqain; Leow, Thean Chor

    2016-01-01

    Here, we report the genome sequences of Photobacterium sp. strain J15, isolated from seawater in Johor, Malaysia, with the ability to produce lipase and asparaginase. The PacBio genome sequence analysis of Photobacterium sp. strain J15 generated revealed its potential in producing enzymes with different catalytic functions. PMID:27469962

  8. Complete Genome Sequence of Photobacterium sp. Strain J15, Isolated from Seawater of Southwestern Johor, Malaysia.

    PubMed

    Roslan, Noordiyanah Nadhirah; Sabri, Suriana; Oslan, Siti Nurbaya; Baharum, Syarul Nataqain; Leow, Thean Chor

    2016-01-01

    Here, we report the genome sequences of Photobacterium sp. strain J15, isolated from seawater in Johor, Malaysia, with the ability to produce lipase and asparaginase. The PacBio genome sequence analysis of Photobacterium sp. strain J15 generated revealed its potential in producing enzymes with different catalytic functions. PMID:27469962

  9. Genome sequence of Pedobacter arcticus sp. nov., a sea ice bacterium isolated from tundra soil.

    PubMed

    Yin, Ye; Yue, Guidong; Gao, Qiang; Wang, Zhiyong; Peng, Fang; Fang, Chengxiang; Yang, Xu; Pan, Li

    2012-12-01

    Pedobacter arcticus sp. nov. was originally isolated from tundra soil collected from Ny-Ålesund, in the Arctic region of Norway. It is a Gram-negative bacterium which shows bleb-shaped appendages on the cell surface. Here, we report the draft annotated genome sequence of Pedobacter arcticus sp. nov., which belongs to the genus Pedobacter.

  10. Draft Genome Sequence of Serratia sp. Strain DD3, Isolated from the Guts of Daphnia magna.

    PubMed

    Poehlein, Anja; Freese, Heike M; Daniel, Rolf; Simeonova, Diliana D

    2014-01-01

    We report the draft genome sequence of Serratia sp. strain DD3, a gammaproteobacterium from the family Enterobacteriaceae. It was isolated from homogenized guts of Daphnia magna. The genome size is 5,274 Mb.

  11. Draft Genome Sequence of Serratia sp. Strain DD3, Isolated from the Guts of Daphnia magna

    PubMed Central

    Poehlein, Anja; Freese, Heike M.; Daniel, Rolf

    2014-01-01

    We report the draft genome sequence of Serratia sp. strain DD3, a gammaproteobacterium from the family Enterobacteriaceae. It was isolated from homogenized guts of Daphnia magna. The genome size is 5,274 Mb. PMID:25212623

  12. Modestobacter lapidis sp. nov. and Modestobacter muralis sp. nov., isolated from a deteriorated sandstone historic building in Salamanca, Spain.

    PubMed

    Trujillo, Martha E; Goodfellow, Michael; Busarakam, Kanungnid; Riesco, Raul

    2015-08-01

    A polyphasic study was undertaken to establish the taxonomic status of two Modestobacter strains isolated from the surface of deteriorated sandstone of a historic building in Salamanca, Spain. The strains, isolates MDVD1(T) and MON 3.1(T), were found to have chemotaxonomic and morphological properties consistent with their classification in the genus Modestobacter and to form distinct phyletic lines in the Modestobacter 16S rRNA gene tree. Isolate MDVD1(T) was found to be closely related to the type strain of Modestobacter versicolor (98.7 % similarity) and isolate MON 3.1(T) to the type strain of Modestobacter multiseptatus (98.6 % similarity). The isolates were distinguished readily from one another and from the Modestobacter type strains by a broad range of phenotypic properties, by qualitative and quantitative differences in fatty acid profiles and by BOX fingerprint patterns. On the basis of these data, it is proposed that the isolates be classified in the genus Modestobacter as Modestobacter lapidis sp. nov. and Modestobacter muralis sp. nov., with isolates MON 3.1(T) (CECT 8844(T) = DSM 100206(T)) and MDVD1(T) (CECT 8845(T) = DSM 100205(T)) as the respective type strains.

  13. Draft Genome Sequence of Methylobacterium sp. ME121, Isolated from Soil as a Mixed Single Colony with Kaistia sp. 32K

    PubMed Central

    Fujinami, Shun; Takeda-Yano, Kiyoko; Onodera, Takefumi; Satoh, Katsuya; Shimizu, Tetsu; Wakabayashi, Yuu; Narumi, Issay; Nakamura, Akira

    2015-01-01

    Methylobacterium sp. ME121 was isolated from soil as a mixed single colony with Kaistia sp. 32K, and its growth was enhanced by coculture. Here, we report the draft genome sequence of Methylobacterium sp. ME121, which may contribute to the study of the molecular mechanisms underlying this phenomenon. PMID:26337893

  14. Pseudomonas zhaodongensis sp. nov., isolated from saline and alkaline soils.

    PubMed

    Zhang, Lei; Pan, Yuanyuan; Wang, Kaibiao; Zhang, Xiaoxia; Zhang, Cheng; Zhang, Shuang; Fu, Xiaowei; Jiang, Juquan

    2015-03-01

    Strain NEAU-ST5-21(T) was isolated from saline and alkaline soils in Zhaodong City, Heilongjiang Province, China. It was aerobic, Gram-stain-negative, rod-shaped and motile with a polar flagellum. It produced yellow-orange colonies with a smooth surface, and grew in the presence of 0-5 % (w/v) NaCl (optimum 0 %, w/v), at temperatures of 20-40 °C (optimum 28 °C) and at pH 7-11 (optimum pH 7). Phylogenetic analyses based on the separate 16S rRNA gene sequences and concatenated 16S rRNA, gyrB and rpoD gene sequences indicated that strain NEAU-ST5-21(T) belongs to the genus Pseudomonas in the class Gammaproteobacteria. The most closely related species is Pseudomonas xanthomarina, whose type strain (KMM 1447(T)) showed gene sequence similarities of 99.0 % for 16S rRNA, 81.8 % for gyrB and 85.0 % for rpoD with strain NEAU-ST5-21(T). DNA-DNA hybridization values between strain NEAU-ST5-21(T) and P. xanthomarina DSM 18231(T), Pseudomonas kunmingensis CGMCC 1.12273(T), Pseudomonas stutzeri DSM 5190(T), Pseudomonas oleovorans subsp. lubricantis DSM 21016(T), Pseudomomas chengduensis CGMCC 2318(T), Pseudomonas alcaliphila DSM 17744(T) and Pseudomonas toyotomiensis DSM 26169(T) were 52±0 % to 25±2 %. The DNA G+C content of strain NEAU-ST5-21(T) was 65 mol%. The major fatty acids (>10 %) were C18 : 1ω7c and/or C18 : 1ω6c, C16 : 1ω7c and/or C16 : 1ω6c and C16 : 0, the predominant respiratory quinone was ubiquinone 9, and polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, one unknown phospholipid, phosphatidylglycerol, one unknown aminolipid, one unknown lipid and a glycolipid. The proposed name is Pseudomonas zhaodongensis sp. nov., NEAU-ST5-21(T) ( = ACCC 06362(T) = DSM 27559(T)) being the type strain. PMID:25574037

  15. Rhodobacter sediminis sp. nov., isolated from lagoon sediments.

    PubMed

    Subhash, Y; Lee, Sang-Seob

    2016-08-01

    Two Gram-stain-negative, rod-shaped phototrophic bacteria (designated strains N1T and C7) were isolated from lagoon sediments. Both strains were positive for catalase and oxidase activity. Casein, starch, urea and Tween 20 were hydrolysed by both strains while chitin, gelatin and Tween 80 were not. In both strains, C16 : 0, C18 : 0,C16 : 1ω6c/C16 : 1ω7c and C18 : 1ω6c/ C18 : 1ω7c were the predominant fatty acids, with minor amounts of C8 : 0 3-OH, anteiso-C14 : 0, C17 : 0, C14 : 1ω5c, C17 : 1 10-methyl and C18 : 1ω5c. Strains N1T and C7 contained phosphatidylglycerol and phosphatidylethanolamine as major polar lipids with minor amounts of phosphatidylcholine, unidentified lipids and an unidentified phospholipid. The mean genomic DNA G+C content was 70.6±1 mol% and the two strains were closely related (mean DNA-DNA hybridization >90 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that the two strains clustered with species of the genus Rhodobacter belonging to the family Rhodobacteraceae of the class Alphaproteobacteria. Strain N1T has a 16S rRNA gene sequence similarity of 99.2 % with Rhodobacter capsulatus ATCC 11166T, 99.1 % with Rhodobacter viridis JA737T and <96.6 % with other members of the genus Rhodobacter. Strain N1T and C7 shared 100 % 16S rRNA gene sequence similarity. DNA- DNA hybridization values between strain N1T and the type strains of the nearest species were clearly below the 70 % threshold. On the basis of phenotypic and genotypic data, it is proposed that strain N1T represents a novel species of the genus Rhodobacter, for which the name Rhodobacter sediminis sp. nov. is proposed. The type strain is N1T (=KEMB 563-471T=JCM 31175T), and strain C7 is an additional strain of the species. PMID:27150292

  16. Marinobacterium aestuariivivens sp. nov., isolated from a tidal flat.

    PubMed

    Park, Sooyeon; Jung, Yong-Taek; Kim, Sona; Yoon, Jung-Hoon

    2016-04-01

    A Gram-stain-negative, motile, aerobic, rod- or ovoid-shaped bacterium, designated DB-1T, was isolated from a tidal flat on the Yellow Sea in South Korea and subjected to a taxonomic study using a polyphasic approach. Strain DB-1T grew optimally at 30 °C, at pH 7.0-8.0 and in the presence of 0.5-2.0% (w/v) NaCl. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain DB-1T falls within the clade comprising species of the genus Marinobacterium, clustering coherently with the type strain of Marinobacterium nitratireducens and showing a sequence similarity value of 98.4 %. The novel strain exhibited 16S rRNA gene sequence similarities of 91.5-94.4 % to the type strains of other species of the genus Marinobacterium. Strain DB-1T contained Q-8 as the predominant ubiquinone and C18:1ω7c, summed feature 3 (C16:1ω7c and/or C16:1ω6c) and C16:0 as the major fatty acids. The major polar lipids detected in strain DB-1T were phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminolipid, one unidentified glycolipid, one unidentified phospholipid and two unidentified lipids. The DNA G+C content of strain DB-1T was 62.3 mol% and the mean DNA-DNA relatedness value with the type strain of M. nitratireducens was 21±4.6%. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain DB-1T is separated from recognized species of the genus Marinobacterium. On the basis of the data presented, strain DB-1T is considered to represent a novel species of the genus Marinobacterium, for which the name Marinobacterium aestuariivivens sp. nov. is proposed. The type strain is DB-1T (=KCTC 42778T=NBRC 111756T). PMID:26812956

  17. Novosphingobium malaysiense sp. nov. isolated from mangrove sediment.

    PubMed

    Lee, Learn-Han; Azman, Adzzie-Shazleen; Zainal, Nurullhudda; Eng, Shu-Kee; Fang, Chee-Mun; Hong, Kui; Chan, Kok-Gan

    2014-04-01

    A novel bacterium, strain MUSC 273(T), was isolated from mangrove sediments of the Tanjung Lumpur river in the state of Pahang in peninsular Malaysia. The bacterium was yellow-pigmented, Gram-negative, rod-shaped and non-spore-forming. The taxonomy of strain MUSC 273(T) was studied by a polyphasic approach and the organism showed a range of phenotypic and chemotaxonomic properties consistent with those of the genus Novosphingobium. The 16S rRNA gene sequence of strain MUSC 273(T) showed the highest sequence similarity to those of Novosphingobium indicum H25(T) (96.8 %), N. naphthalenivorans TUT562(T) (96.4 %) and N. soli CC-TPE-1(T) (95.9 %) and lower sequence similarity to members of all other species of the genus Novosphingobium. Furthermore, in phylogenetic analyses based on the 16S rRNA gene sequence, strain MUSC 273(T) formed a distinct cluster with members of the genus Novosphingobium. DNA-DNA relatedness of strain MUSC 273(T) to the type strains of the most closely related species, N. indicum MCCC 1A01080(T) and N. naphthalenivorans DSM 18518(T), was 29.2 % (reciprocal 31.0 %) and 17 % (reciprocal 18 %), respectively. The major respiratory quinone was ubiquinone Q-10, the major polyamine was spermidine and the DNA G+C content was 63.3±0.1 mol%. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine and sphingoglycolipid. The major fatty acids were C18 : 1ω7c, C17 : 1ω6c, C16 : 0, C15 : 0 2-OH and C16 : 1ω7c. Comparison of BOX-PCR fingerprints indicated that strain MUSC 273(T) represented a unique DNA profile. The combined genotypic and phenotypic data showed that strain MUSC 273(T) represents a novel species of the genus Novosphingobium, for which the name Novosphingobium malaysiense sp. nov. is proposed. The type strain is MUSC 273(T) ( = DSM 27798(T) = MCCC 1A00645(T

  18. Francisella guangzhouensis sp. nov., isolated from air-conditioning systems.

    PubMed

    Qu, Ping-Hua; Chen, Shou-Yi; Scholz, Holger C; Busse, Hans-Jürgen; Gu, Quan; Kämpfer, Peter; Foster, Jeffrey T; Glaeser, Stefanie P; Chen, Cha; Yang, Zhi-Chong

    2013-10-01

    Four strains (08HL01032(T), 09HG994, 10HP82-6 and 10HL1960) were isolated from water of air-conditioning systems of various cooling towers in Guangzhou city, China. Cells were Gram-stain-negative coccobacilli without flagella, catalase-positive and oxidase-negative, showing no reduction of nitrate, no hydrolysis of urea and no production of H2S. Growth was characteristically enhanced in the presence of l-cysteine, which was consistent with the properties of members of the genus Francisella. The quinone system was composed of ubiquinone Q-8 with minor amounts of Q-9. The polar lipid profile consisted of the predominant lipids phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, two unidentified phospholipids (PL2, PL3), an unidentified aminophospholipid and an unidentified glycolipid (GL2). The polyamine pattern consisted of the major compounds spermidine, cadaverine and spermine. The major cellular fatty acids were C10 : 0, C14 : 0, C16 : 0, C18 : 1ω9c and C18 : 1 3-OH. A draft whole-genome sequence of the proposed type strain 08HL01032(T) was generated. Comparative sequence analysis of the complete 16S and 23S rRNA genes confirmed affiliation to the genus Francisella, with 95 % sequence identity to the closest relatives in the database, the type strains of Francisella philomiragia and Francisella noatunensis subsp. orientalis. Full-length deduced amino acid sequences of various housekeeping genes, recA, gyrB, groEL, dnaK, rpoA, rpoB, rpoD, rpoH, fopA and sdhA, exhibited similarities of 67-92 % to strains of other species of the genus Francisella. Strains 08HL01032(T), 09HG994, 10HP82-6 and 10HL1960 exhibited highly similar pan-genome PCR profiles. Both the phenotypic and molecular data support the conclusion that the four strains belong to the genus Francisella but exhibit considerable divergence from all recognized Francisella species. Therefore, we propose the name Francisella guangzhouensis sp

  19. Lysinibacillus halotolerans sp. nov., isolated from saline-alkaline soil.

    PubMed

    Kong, Delong; Wang, Yanwei; Zhao, Bingqiang; Li, Yanting; Song, Jinlong; Zhai, Yi; Zhang, Chi; Wang, Huimin; Chen, Xiaorong; Zhao, Bin; Ruan, Zhiyong

    2014-08-01

    A novel aerobic, halotolerant bacterium, designated strain LAM612(T), was isolated from saline-alkaline soil samples from Lingxian County, Shandong Province, China. Cells of strain LAM612(T) were Gram-reaction-positive, endospore-forming, motile and rod-shaped. The optimal temperature and pH for growth were 35 °C and pH 6.0, respectively. Strain LAM612(T) could grow in the presence of up to 10% (w/v) NaCl. The genomic DNA G+C conten was 36.4 mol% as detected by the T(m) method. Comparative analysis of 16S rRNA gene sequences revealed that LAM612(T) was closely related to Lysinibacillus sinduriensis KACC 16611(T) (98.0%), L. chungkukjangi KACC 16626(T) (97.5%), L. massiliensis KCTC 13178(T) (97.4%), L. xylanilyticus KACC 15113(T) (97.2%), L. macroides DSM 54(T) (97.0%) and L. manganicus DSM 26584(T) (96.5%). The DNA-DNA hybridization values between strain LAM612(T) and its closest relatives ranged from 20.6% to 41.9%. The major fatty acids of strain LAM612(T) were iso-C(15 : 0) (40.8%), iso-C(16 : 0) (15.2%) and anteiso-C(15 : 0) (10.8%). The cell-wall peptidoglycan content was A4α (L-Lys-D-Asp). The predominant menaquinone was MK-7 and the main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown phospholipids, five unknown glycolipids and an unknown lipid. Based on the DNA-DNA hybridization results and phenotypic, phylogenetic and chemotaxonomic properties, strain LAM612(T) could be distinguished from the recognized species of the genus Lysinibacillus, and was suggested to represent a novel species of this genus, for which the name Lysinibacillus halotolerans sp. nov. is proposed. The type strain is LAM612(T) ( = ACCC 00718(T) = JCM 19611(T)). PMID:24814335

  20. Halosimplex litoreum sp. nov., isolated from a marine solar saltern.

    PubMed

    Yuan, Pan-Pan; Xu, Jia-Qi; Xu, Wen-Mei; Wang, Zhao; Yin, Shuai; Han, Dong; Zhang, Wen-Jiao; Cui, Heng-Lin

    2015-08-01

    A halophilic archaeal strain, YGH94(T), was isolated from the Yinggehai marine solar saltern near the Shanya city of Hainan Province, China. Cells of the strain were observed to be short rods, stain Gram-negative and to form red-pigmented colonies on solid media. Strain YGH94(T) was found to grow at 25-50 °C (optimum 40 °C), at 0.9-4.8 M NaCl (optimum 3.1 M), at 0-1.0 M MgCl2 (optimum 0.05 M) and at pH 5.0-9.0 (optimum pH 7.5). The cells were found to lyse in distilled water and the minimal NaCl concentration to prevent cell-lysis was determined to be 5 % (w/v). The major polar lipids were identified as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and four major glycolipids (disulfated mannosyl glucosyl diether, sulfated mannosyl glucosyl diether and two unidentified glycolipids chromatographically identical to glycolipids in Halosimplex carlsbadense JCM 11222(T)). Strain YGH94(T) was found to possess two heterogeneous 16S rRNA genes (rrnA and rrnB) and both are related to those of Hsx. carlsbadense JCM 11222(T) (92.7-98.6 % similarities), Halosimplex pelagicum R2(T) (94.6-99.2 % similarities) and Halosimplex rubrum R27(T) (92.9-98.8 % similarities). The rpoB' gene similarity between strain YGH94(T) and Hsx. carlsbadense JCM 11222(T), Hsx. pelagicum R2(T) and Hsx. rubrum R27(T) are 95.4, 94.9 and 95.1 %, respectively. The DNA G+C content of strain YGH94(T) was determined to be 64.0 mol%. Strain YGH94(T) showed low DNA-DNA relatedness (35-39 %) with the current three members of the genus Halosimplex. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strain YGH94(T) (=CGMCC 1.12235(T) = JCM 18647(T)) represents a new species of the genus Halosimplex, for which the name Halosimplex litoreum sp. nov. is proposed.

  1. Deinococcus citri sp. nov., isolated from citrus leaf canker lesions.

    PubMed

    Ahmed, Iftikhar; Abbas, Saira; Kudo, Takuji; Iqbal, Muhammad; Fujiwara, Toru; Ohkuma, Moriya

    2014-12-01

    A Gram-stain-positive, strictly aerobic, non-motile, coccoid bacterium, designated NCCP-154(T), was isolated from citrus leaf canker lesions and was subjected to a polyphasic taxonomic study. Strain NCCP-154(T) grew at 10-37 °C (optimum 30 °C) and at pH 7.0-8.0 (optimum pH 7.0). The novel strain exhibited tolerance of UV irradiation (>1000 J m(-2)). Based on 16S rRNA gene sequence analysis, strain NCCP-154(T) showed the highest similarity to Deinococcus gobiensis CGMCC 1.7299(T) (98.8 %), and less than 94 % similarity to other closely related taxa. The chemotaxonomic data [major menaquinone, MK-8; cell-wall peptidoglycan type, A3β (Orn-Gly2); major fatty acids, summed feature 3 (C16 : 1ω7c/iso-C15 : 0 2-OH; 35.3 %) followed by C16 : 0 (12.7 %), iso-C17 : 1ω9c (9.2 %), C17 : 1ω8c (7.4 %) and iso-C17 : 0 (6.9 %); major polar lipids made up of several unidentified phosphoglycolipids and glycolipids and an aminophospholipid, and mannose as the predominant whole-cell sugar] also supported the affiliation of strain NCCP-154(T) to the genus Deinococcus. The level of DNA-DNA relatedness between strain NCCP-154(T) and D. gobiensis JCM 16679(T) was 63.3±3.7 %. The DNA G+C content of strain NCCP-154(T) was 70.0 mol%. Based on the phylogenetic analyses, DNA-DNA hybridization and physiological and biochemical characteristics, strain NCCP-154(T) can be differentiated from species with validly published names. Therefore, it represents a novel species of the genus Deinococcus. The name Deinococcus citri sp. nov. is proposed, with the type strain NCCP-154(T) ( = JCM 19024(T) = DSM 24791(T) = KCTC 13793(T)).

  2. Idiomarina planktonica sp. nov., isolated from a saline lake.

    PubMed

    Zhong, Zhi-Ping; Liu, Ying; Liu, Hong-Can; Wang, Fang; Song, Lei; Liu, Zhi-Pei

    2014-10-01

    A Gram-stain-negative bacterium, strain TS-T11(T), was isolated from Tuosu lake, a saline lake (salinity 5.4%, w/v) in the Qaidam basin, Qinghai province, China. Its taxonomic position was determined by using a polyphasic approach. Cells of strain TS-T11(T) were non-spore-forming rods, 0.6-0.8 µm wide and 0.8-2.2 µm long, and motile by means of a single polar flagellum. Strain TS-T11(T) was strictly heterotrophic and aerobic. Cells were positive for catalase and oxidase. Growth was observed in the presence of 0.5-11.0% (w/v) NaCl (optimum 4.0-6.0%), at 4-40 °C (optimum 30-35 °C) and at pH 6.0-10.5 (optimum pH 7.5-8.5). Strain TS-T11(T) contained iso-C15:0, iso-C17:0 and iso-C17:1ω9c as the predominant fatty acids (>10%). The major respiratory quinone was Q-8. The polar lipids consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and nine uncharacterized phospholipids. The G+C content of genomic DNA was 46.8 mol% (Tm). Phylogenetic trees based on 16S rRNA gene sequences showed that strain TS-T11(T) was associated with the genus Idiomarina, and showed highest 16S rRNA gene sequence similarity to Idiomarina aestuarii KYW314(T) (97.4%) and Idiomarina salinarum ISL-52(T) (97.4%). DNA-DNA relatedness of strain TS-T11(T) to I. aestuarii JCM 16344(T) and I. salinarum DSM 21900(T) was 22.2 ± 2.4 and 11.5 ± 1.6%, respectively. Based on the data presented above, it was concluded that strain TS-T11(T) represents a novel species of the genus Idiomarina, for which the name Idiomarina planktonica sp. nov. is proposed. The type strain is TS-T11(T) ( = CGMCC 1.12458(T) = JCM 19263(T)).

  3. Belliella aquatica sp. nov., isolated from a saline lake.

    PubMed

    Zhong, Zhi-Ping; Liu, Ying; Hou, Ting-Ting; Zhou, Yu-Guang; Liu, Hong-Can; Liu, Zhi-Pei

    2015-05-01

    A Gram-staining-negative bacterium, strain TS-T86(T), was isolated from Lake Tuosu, a saline lake (salinity 5.4%, w/w) in Qaidam basin, China. Its taxonomic position was determined by using a polyphasic approach. Strain TS-T86(T) was strictly heterotrophic, aerobic and catalase- and oxidase-positive. Cells were non-spore-forming, non-motile rods, 0.4-0.6 µm wide and 1.2-2.3 µm long. Growth was observed in the presence of 0-9.0% (w/v) NaCl (optimum, 2.0%), at 4-35 °C (optimum, 25 °C) and at pH 7.0-10.5 (optimum, pH 8.5-9.0). Strain TS-T86(T) contained MK-7 as the predominant respiratory quinone. The major fatty acids (>10%) were iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 1ω9c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The polar lipids consisted of phosphatidylethanolamine, an unknown phospholipid, six unidentified aminolipids and two uncharacterized lipids. The DNA G+C content was 35 mol% (T m). Phylogenetic trees based on 16S rRNA gene sequences showed that strain TS-T86(T) was associated with the genus Belliella, and showed the highest sequence similarity to Belliella baltica BA134(T) (98.5 %) and then to Belliella kenyensis No.164(T) (95.7%) and Belliella pelovolcani CC-SAL-25(T) (95.3 %). DNA-DNA relatedness of strain TS-T86(T) to Belliella baltica DSM 15883(T) was 32 ± 3%. It is concluded that strain TS-T86(T) represents a novel species of the genus Belliella, for which the name Belliella aquatica sp. nov. is proposed. The type strain is TS-T86(T) ( = CGMCC 1.12479(T) = JCM 19468(T)). PMID:25716953

  4. Bacillus paralicheniformis sp. nov., isolated from fermented soybean paste.

    PubMed

    Dunlap, Christopher A; Kwon, Soon-Wo; Rooney, Alejandro P; Kim, Soo-Jin

    2015-10-01

    An isolate of a Gram-stain-positive, facultatively anaerobic, motile, rod-shaped, endospore-forming bacterium was recovered from soybean-based fermented paste. Phylogenetic analysis of the 16S rRNA gene indicated that the strain was most closely related to Bacillus sonorensis KCTC-13918T (99.5 % similarity) and Bacillus licheniformis DSM 13T (99.4 %). In phenotypic characterization, the novel strain was found to grow at 15–60 °C and to tolerate up to 10 % (w/v) NaCl. Furthermore, the strain grew in media with pH 6–11 (optimal growth at pH 7.0–8.0). The predominant cellular fatty acids were anteiso-C15 : 0 (37.7 %) and iso-C15 : 0 (31.5 %). The predominant isoprenoid quinone was menaquinone 7 (MK-7). The cell-wall peptidoglycan contained meso-diaminopimelic acid. A draft genome sequence of the strain was completed and used for phylogenetic analysis. Phylogenomic analysis of all published genomes of species in the B. licheniformis group revealed that strains belonging to B. licheniformis clustered into two distinct groups, with group 1 consisting of B. licheniformis DSM 13T and 11 other strains and group 2 consisting of KJ-16T and four other strains. The DNA G+C content of strain KJ-16T was 45.9 % (determined from the genome sequence). Strain KJ-16T and another strain from group 2 were subsequently characterized using a polyphasic taxonomic approach and compared with strains from group 1 and another closely related species of the genus Bacillus. Based upon the consensus of phylogenetic and phenotypic analyses, we conclude that this strain represents a novel species within the genus Bacillus, for which the name Bacillus paralicheniformis sp. nov. is proposed, with type strain KJ-16T ( = KACC 18426T = NRRL B-65293T). PMID:26296568

  5. Marinobacter salarius sp. nov. and Marinobacter similis sp. nov., isolated from sea water.

    PubMed

    Ng, Hooi Jun; López-Pérez, Mario; Webb, Hayden K; Gomez, Daniela; Sawabe, Tomoo; Ryan, Jason; Vyssotski, Mikhail; Bizet, Chantal; Malherbe, François; Mikhailov, Valery V; Crawford, Russell J; Ivanova, Elena P

    2014-01-01

    Two non-pigmented, motile, Gram-negative marine bacteria designated R9SW1T and A3d10T were isolated from sea water samples collected from Chazhma Bay, Gulf of Peter the Great, Sea of Japan, Pacific Ocean, Russia and St. Kilda Beach, Port Phillip Bay, the Tasman Sea, Pacific Ocean, respectively. Both organisms were found to grow between 4 °C and 40 °C, between pH 6 to 9, and are moderately halophilic, tolerating up to 20% (w/v) NaCl. Both strains were found to be able to degrade Tween 40 and 80, but only strain R9SW1T was found to be able to degrade starch. The major fatty acids were characteristic for the genus Marinobacter including C16:0, C16:1ω7c, C18:1ω9c and C18:1ω7c. The G+C content of the DNA for strains R9SW1T and A3d10T were determined to be 57.1 mol% and 57.6 mol%, respectively. The two new strains share 97.6% of their 16S rRNA gene sequences, with 82.3% similarity in the average nucleotide identity (ANI), 19.8% similarity in the in silico genome-to-genome distance (GGD), 68.1% similarity in the average amino acid identity (AAI) of all conserved protein-coding genes, and 31 of the Karlin's genomic signature dissimilarity. A phylogenetic analysis showed that R9SW1T clusters with M. algicola DG893T sharing 99.40%, and A3d10T clusters with M. sediminum R65T sharing 99.53% of 16S rRNA gene sequence similarities. The results of the genomic and polyphasic taxonomic study, including genomic, genetic, phenotypic, chemotaxonomic and phylogenetic analyses based on the 16S rRNA, gyrB and rpoD gene sequence similarities, the analysis of the protein profiles generated using MALDI-TOF mass spectrometry, and DNA-DNA relatedness data, indicated that strains R9SW1T and A3d10(T) represent two novel species of the genus Marinobacter. The names Marinobacter salarius sp. nov., with the type strain R9SW1(T) ( =  LMG 27497(T)  =  JCM 19399(T)  =  CIP 110588(T)  =  KMM 7502(T)) and Marinobacter similis sp. nov., with the type strain A3d10(T) ( =  JCM

  6. Flavobacterium xueshanense sp. nov. and Flavobacterium urumqiense sp. nov., two psychrophilic bacteria isolated from glacier ice.

    PubMed

    Dong, Kun; Liu, Hongcan; Zhang, Jianli; Zhou, Yuguang; Xin, Yuhua

    2012-05-01

    Two Gram-stain-negative, rod-shaped bacteria, designated strains Sr22(T) and Sr25(T), were isolated from water of melted ice from the China No.1 glacier, Xinjiang Uygur Autonomous Region, China. Cells formed yellow, circular, convex colonies. 16S rRNA gene sequence analysis indicated that strains Sr22(T) and Sr25(T) belong to the genus Flavobacterium, sharing ≤99.1  and ≤99.6 % similarity, respectively, with the type strains of recognized species of the genus. Strain Sr22(T) shared highest 16S rRNA gene sequence similarity with Flavobacterium tiangeerense CGMCC 1.6847(T) (98.6 %), Flavobacterium fryxellicola LMG 22022(T) (98.1 %) and Flavobacterium omnivorum CGMCC 1.2747(T) (99.1 %). Strain Sr25(T) shared highest similarity with Flavobacterium sinopsychrotolerans CGMCC 1.8704(T) (98.5 %), Flavobacterium degerlachei NBRC 102677(T) (98.4 %) and Flavobacterium xinjiangense CGMCC 1.2749(T) (99.5 %). The predominant fatty acids of strain Sr22(T) were iso-C(15 : 1) G (6.01 %), iso-C(15 : 0) (8.93 %), iso-C(16 : 1) H (12.68 %), iso-C(16 : 0) (10.4 %), C(15 : 1)ω6c (8.97 %), C(17 : 1)ω6c (5.96 %), iso-C(16 : 0) 3-OH (11.14 %) and summed feature 3 (comprising C(16 : 1)ω7c and/or C(16 : 1)ω6c, 12.33 %). The major fatty acids of strain Sr25(T) were iso-C(15 : 0) (10.8 %), anteiso-C(15 : 0) (5.23 %), C(15 : 1)ω6c (11.79 %), C(17 : 1)ω6c (5.43 %), iso-C(16 : 0) 3-OH (7.04 %) and summed feature 3 (20.42 %). The genomic DNA G+C contents of strains Sr22(T) and Sr25(T) were 37.2 and 35.1 mol%. On the basis of differential phenotypic and phylogenetic characteristics, these strains are considered to represent two novel species of the genus Flavobacterium, for which the names Flavobacterium xueshanense sp. nov. (type strain Sr22(T)  = CGMCC 1.9227(T)  = NBRC 106479(T)) and Flavobacterium urumqiense sp. nov. (type strain Sr25(T)  = CGMCC 1.9230(T)  = NBRC 106480

  7. Marinobacter salarius sp. nov. and Marinobacter similis sp. nov., Isolated from Sea Water

    PubMed Central

    Ng, Hooi Jun; López-Pérez, Mario; Webb, Hayden K.; Gomez, Daniela; Sawabe, Tomoo; Ryan, Jason; Vyssotski, Mikhail; Bizet, Chantal; Malherbe, François; Mikhailov, Valery V.; Crawford, Russell J.; Ivanova, Elena P.

    2014-01-01

    Two non-pigmented, motile, Gram-negative marine bacteria designated R9SW1T and A3d10T were isolated from sea water samples collected from Chazhma Bay, Gulf of Peter the Great, Sea of Japan, Pacific Ocean, Russia and St. Kilda Beach, Port Phillip Bay, the Tasman Sea, Pacific Ocean, respectively. Both organisms were found to grow between 4°C and 40°C, between pH 6 to 9, and are moderately halophilic, tolerating up to 20% (w/v) NaCl. Both strains were found to be able to degrade Tween 40 and 80, but only strain R9SW1T was found to be able to degrade starch. The major fatty acids were characteristic for the genus Marinobacter including C16:0, C16:1ω7c, C18:1ω9c and C18:1ω7c. The G+C content of the DNA for strains R9SW1T and A3d10T were determined to be 57.1 mol% and 57.6 mol%, respectively. The two new strains share 97.6% of their 16S rRNA gene sequences, with 82.3% similarity in the average nucleotide identity (ANI), 19.8% similarity in the in silico genome-to-genome distance (GGD), 68.1% similarity in the average amino acid identity (AAI) of all conserved protein-coding genes, and 31 of the Karlin's genomic signature dissimilarity. A phylogenetic analysis showed that R9SW1T clusters with M. algicola DG893T sharing 99.40%, and A3d10T clusters with M. sediminum R65T sharing 99.53% of 16S rRNA gene sequence similarities. The results of the genomic and polyphasic taxonomic study, including genomic, genetic, phenotypic, chemotaxonomic and phylogenetic analyses based on the 16S rRNA, gyrB and rpoD gene sequence similarities, the analysis of the protein profiles generated using MALDI-TOF mass spectrometry, and DNA-DNA relatedness data, indicated that strains R9SW1T and A3d10T represent two novel species of the genus Marinobacter. The names Marinobacter salarius sp. nov., with the type strain R9SW1T ( =  LMG 27497T  =  JCM 19399T  =  CIP 110588T  =  KMM 7502T) and Marinobacter similis sp. nov., with the type strain A3d10T ( =  JCM 19398T  =  CIP

  8. Marinobacter salarius sp. nov. and Marinobacter similis sp. nov., isolated from sea water.

    PubMed

    Ng, Hooi Jun; López-Pérez, Mario; Webb, Hayden K; Gomez, Daniela; Sawabe, Tomoo; Ryan, Jason; Vyssotski, Mikhail; Bizet, Chantal; Malherbe, François; Mikhailov, Valery V; Crawford, Russell J; Ivanova, Elena P

    2014-01-01

    Two non-pigmented, motile, Gram-negative marine bacteria designated R9SW1T and A3d10T were isolated from sea water samples collected from Chazhma Bay, Gulf of Peter the Great, Sea of Japan, Pacific Ocean, Russia and St. Kilda Beach, Port Phillip Bay, the Tasman Sea, Pacific Ocean, respectively. Both organisms were found to grow between 4 °C and 40 °C, between pH 6 to 9, and are moderately halophilic, tolerating up to 20% (w/v) NaCl. Both strains were found to be able to degrade Tween 40 and 80, but only strain R9SW1T was found to be able to degrade starch. The major fatty acids were characteristic for the genus Marinobacter including C16:0, C16:1ω7c, C18:1ω9c and C18:1ω7c. The G+C content of the DNA for strains R9SW1T and A3d10T were determined to be 57.1 mol% and 57.6 mol%, respectively. The two new strains share 97.6% of their 16S rRNA gene sequences, with 82.3% similarity in the average nucleotide identity (ANI), 19.8% similarity in the in silico genome-to-genome distance (GGD), 68.1% similarity in the average amino acid identity (AAI) of all conserved protein-coding genes, and 31 of the Karlin's genomic signature dissimilarity. A phylogenetic analysis showed that R9SW1T clusters with M. algicola DG893T sharing 99.40%, and A3d10T clusters with M. sediminum R65T sharing 99.53% of 16S rRNA gene sequence similarities. The results of the genomic and polyphasic taxonomic study, including genomic, genetic, phenotypic, chemotaxonomic and phylogenetic analyses based on the 16S rRNA, gyrB and rpoD gene sequence similarities, the analysis of the protein profiles generated using MALDI-TOF mass spectrometry, and DNA-DNA relatedness data, indicated that strains R9SW1T and A3d10(T) represent two novel species of the genus Marinobacter. The names Marinobacter salarius sp. nov., with the type strain R9SW1(T) ( =  LMG 27497(T)  =  JCM 19399(T)  =  CIP 110588(T)  =  KMM 7502(T)) and Marinobacter similis sp. nov., with the type strain A3d10(T) ( =  JCM

  9. Novel lactic acid bacteria isolated from the bumble bee gut: Convivina intestini gen. nov., sp. nov., Lactobacillus bombicola sp. nov., and Weissella bombi sp. nov.

    PubMed

    Praet, Jessy; Meeus, Ivan; Cnockaert, Margo; Houf, Kurt; Smagghe, Guy; Vandamme, Peter

    2015-05-01

    Twelve isolates of lactic acid bacteria (LAB) were obtained in the course of a bumble bee gut microbiota study and grouped into four matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry clusters. Comparative 16S rRNA gene sequence analysis revealed that cluster 1 isolates, represented by strain LMG 28288(T), are most closely related to Lactobacillus apis (97.0% sequence similarity to that of L. apis LMG 26964(T)). Cluster 2 isolates represented by strain LMG 28290(T) are most closely related to Weissella hellenica (99.6% sequence similarity to that of W. hellenica LMG 15125(T)). The single cluster 3 and 4 isolates had identical 16S rRNA gene sequences which were 94.8% similar to that of Leuconostoc mesenteroides subsp. mesenteroides LMG 6893(T), their nearest phylogenetic neighbour. A polyphasic taxonomic study additionally including comparative pheS sequence analysis, DNA-DNA hybridization experiments, DNA G+C content analysis, (GTG)5-PCR fingerprinting and a biochemical characterization, demonstrated that cluster 1 isolates represent a novel Lactobacillus species for which we propose the name Lactobacillus bombicola sp. nov. with LMG 28288(T) (= DSM 28793(T)) as the type strain; and that cluster 2 isolates represent a novel Weissella species for which we propose the name Weissella bombi sp. nov. with LMG 28290(T) (= DSM 28794(T)) as the type strain. Cluster 3 and 4 isolates, in contrast, represented a very distinct, novel taxon that could be distinguished from members of the genera Leuconostoc and Fructobacillus, its nearest phylogenetic neighbours, by its cellular morphology, non-fructophilic metabolism and DNA G+C content. We therefore classify both isolates into a novel species representing a novel LAB genus for which the name Convivina intestini gen. nov., sp. nov. is proposed with LMG 28291(T) (= DSM 28795(T)) as the type strain.

  10. Genome sequence of Oceanicaulis sp. strain HTCC2633, isolated from the Western Sargasso Sea.

    PubMed

    Oh, Hyun-Myung; Kang, Ilnam; Vergin, Kevin L; Lee, Kiyoung; Giovannoni, Stephen J; Cho, Jang-Cheon

    2011-01-01

    The genus Oceanicaulis represents dimorphic rods that were originally isolated from a marine dinoflagellate. Here, we announce the genome sequence of Oceanicaulis sp. strain HTCC2633, isolated by dilution-to-extinction culturing from the Sargasso Sea. The genome information of strain HTCC2633 indicates a chemoorganotrophic way of life of this strain.

  11. Pseudomonas seleniipraecipitatus sp. nov.: A selenite reducing -proteobacteria isolated from soil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Abstract: A Gram-negative, yellow pigmented bacterium designated strain CA5 that reduced selenite to elemental red selenium (Se0) was isolated from soil. 16S rRNA gene sequence alignment identified the isolate as a novel Pseudomonas sp. with P. argentinensis, P. flavescens and P. straminea as its c...

  12. Genome sequence of Oceanicaulis sp. strain HTCC2633, isolated from the Western Sargasso Sea.

    PubMed

    Oh, Hyun-Myung; Kang, Ilnam; Vergin, Kevin L; Lee, Kiyoung; Giovannoni, Stephen J; Cho, Jang-Cheon

    2011-01-01

    The genus Oceanicaulis represents dimorphic rods that were originally isolated from a marine dinoflagellate. Here, we announce the genome sequence of Oceanicaulis sp. strain HTCC2633, isolated by dilution-to-extinction culturing from the Sargasso Sea. The genome information of strain HTCC2633 indicates a chemoorganotrophic way of life of this strain. PMID:21036991

  13. Rhizobium selenireducens sp. nov.: A selenite reducing a-Proteobacteria isolated from a bioreactor

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A Gram-negative, non-pigmented bacterium designated strain B1 was isolated from a laboratory bioreactor that reduced selenate to elemental red selenium (Se0). 16S rRNA gene sequence alignment identified the isolate as a Rhizobium sp. belonging to the Rhizobium clade that includes R. daejeonense, R....

  14. First report of the blaVIM gene in environmental isolates of Buttiauxella sp.

    PubMed

    Pitondo-Silva, André; Martins, Vinicius Vicente; Stehling, Eliana Guedes

    2015-04-01

    Several works have demonstrated the presence of metallo-β-lactamases (MBLs) in clinical bacteria. However, in environmental isolates, few works have reported on these enzymes. In this study, we report for the first time two environmental isolates of Buttiauxella sp. recovered from chrysanthemum plantations in Brazil containing blaVIM gene and producing MBLs.

  15. Draft Genome Sequence of Ureolytic Environmental Isolate Staphylococcus sp. NA309

    PubMed Central

    Gaiero, Jonathan R.; Hsiang, Tom; Nicol, Rob W.

    2016-01-01

    We report the 2.7 Mb draft genome sequence of Staphylococcus sp. NA309 isolated from poultry litter. The isolate was a dominant member of the cultivable aerobic bacteria identified to have ureolytic activity, responsible for ammonia generation in poultry litter residue. PMID:27795244

  16. Maribacter spongiicola sp. nov. and Maribacter vaceletii sp. nov., isolated from marine sponges, and emended description of the genus Maribacter.

    PubMed

    Jackson, Stephen A; Kennedy, Jonathan; Morrissey, John P; O'Gara, Fergal; Dobson, Alan D W

    2015-07-01

    Two Gram-stain-negative, rod-shaped, orange, catalase- and oxidase-positive, non-motile bacteria, designated W13M1A(T) and W15M10(T), were isolated from the marine sponges Suberites carnosus and Leucosolenia sp., respectively, which were sampled from Lough Hyne, Co. Cork, Ireland. Analysis of the 16S rRNA gene sequences of these isolates revealed that they are members of the genus Maribacter, in the family Flavobacteriaceae of the phylum Bacteroidetes. The type strain most closely related to strain W13M1A(T) is Maribacter forsetii DSM 18668(T) with a gene sequence similarity of 96.5%. The closest related type strain to strain W15M10(T) is Maribacter orientalis DSM 16471(T) with a gene sequence similarity of 98.3%. Phylogenetic inference and phenotypic data combined indicate that the isolates represent two novel species of the genus Maribacter, for which the names Maribacter spongiicola sp. nov. with type strain W15M10(T) ( = NCIMB 14725(T) = DSM 25233(T)) and Maribacter vaceletii sp. nov. with type strain W13M1A(T) ( = NCIMB 14724(T) = DSM 25230(T)), are proposed.

  17. Phytohabitans flavus sp. nov., Phytohabitans rumicis sp. nov. and Phytohabitans houttuyneae sp. nov., isolated from plant roots, and emended description of the genus Phytohabitans.

    PubMed

    Inahashi, Yuki; Matsumoto, Atsuko; Omura, Satoshi; Takahashi, Yoko

    2012-11-01

    An actinomycete strain, designated K09-0627(T), was isolated from the roots of an orchid collected in Okinawa Prefecture, Japan. Two actinomycete strains K11-0047(T) and K11-0057(T) were isolated from the roots of Rumex acetosa and Houttuynia cordata collected in Kanagawa Prefecture, Japan. 16S rRNA gene sequence analyses indicated that the isolates belonged to the genus Phytohabitans, and that they were closely related to each other and to Phytohabitans suffuscus K07-0523(T). The DNA-DNA relatedness values between the three isolates and Phytohabitans suffuscus were below 70%. On the basis of phylogenetic analysis, DNA-DNA relatedness values and phenotypic characteristics, the strains should be classified as novel species in the genus Phytohabitans, for which the names Phytohabitans flavus sp. nov. (type strain, K09-0627(T)=JCM 17387(T)=NBRC 107702(T)=DSM 45551(T)), Phytohabitans rumicis sp. nov. (type strain, K11-0047(T)=JCM 17829(T)=NBRC 108638(T)=BCC 48146(T)) and Phytohabitans houttuyneae sp. nov. (type strain, K11-0057(T)=JCM 17830(T)=NBRC 108639(T)=BCC 48147(T)) are proposed. PMID:22228668

  18. Isolation of high-salinity-tolerant bacterial strains, Enterobacter sp., Serratia sp., Yersinia sp., for nitrification and aerobic denitrification under cyanogenic conditions.

    PubMed

    Mpongwana, N; Ntwampe, S K O; Mekuto, L; Akinpelu, E A; Dyantyi, S; Mpentshu, Y

    2016-01-01

    Cyanides (CN(-)) and soluble salts could potentially inhibit biological processes in wastewater treatment plants (WWTPs), such as nitrification and denitrification. Cyanide in wastewater can alter metabolic functions of microbial populations in WWTPs, thus significantly inhibiting nitrifier and denitrifier metabolic processes, rendering the water treatment processes ineffective. In this study, bacterial isolates that are tolerant to high salinity conditions, which are capable of nitrification and aerobic denitrification under cyanogenic conditions, were isolated from a poultry slaughterhouse effluent. Three of the bacterial isolates were found to be able to oxidise NH(4)-N in the presence of 65.91 mg/L of free cyanide (CN(-)) under saline conditions, i.e. 4.5% (w/v) NaCl. The isolates I, H and G, were identified as Enterobacter sp., Yersinia sp. and Serratia sp., respectively. Results showed that 81% (I), 71% (G) and 75% (H) of 400 mg/L NH(4)-N was biodegraded (nitrification) within 72 h, with the rates of biodegradation being suitably described by first order reactions, with rate constants being: 4.19 h(-1) (I), 4.21 h(-1) (H) and 3.79 h(-1) (G), respectively, with correlation coefficients ranging between 0.82 and 0.89. Chemical oxygen demand (COD) removal rates were 38% (I), 42% (H) and 48% (G), over a period of 168 h with COD reduction being highest at near neutral pH. PMID:27148718

  19. Identification of Acetobacter strains isolated from Indonesian sources, and proposals of Acetobacter syzygii sp. nov., Acetobacter cibinongensis sp. nov., and Acetobacter orientalis sp. nov.

    PubMed

    Lisdiyanti, Puspita; Kawasaki, Hiroko; Seki, Tatsuji; Yamada, Yuzo; Uchimura, Tai; Komagata, Kazuo

    2001-06-01

    Forty-six strains of acetic acid bacteria newly isolated from flowers, fruits, and fermented foods collected in Indonesia were taxonomically studied. They were Gram-negative rods, produced acetic acid from ethanol, oxidized acetate and lactate to CO(2) and H(2)O, and had Q-9 as the major ubiquinone system. On the basis of DNA-DNA similarity, all strains studied, including type strains and reference strains of the genus Acetobacter, were separated into eleven groups (Groups I to XI). Of the 46 isolates, two isolates were included in Group II and identified as Acetobacter pasteurianus, five in Group IV as A. orleanensis, 16 in Group V as A. lovaniensis, five in Group VII as A. indonesiensis, and three in Group VIII as A. tropicalis. The remaining 15 isolates constituted three new groups based on DNA-DNA similarity; four isolates were included in Group IX, two in Group X, and nine in Group XI. No isolates were identified as A. aceti (Group I), A. peroxydans (Group III), and A. estunensis (Group VI). Phylogenetic analysis based on 16S rDNA sequences of representative strains of the Groups indicated belonging to the strains of the genus Acetobacter. On the basis of DNA base composition, DNA-DNA similarity, and 16S rDNA sequences, three new species of the genus Acetobacter are proposed: Acetobacter syzygii sp. nov. for Group IX, Acetobacter cibinongensis sp. nov. for Group X, and Acetobacter orientalis sp. nov. for Group XI. The distribution of Acetobacter strains in Indonesia is discussed in light of isolation sources.

  20. Whole genome analyses of marine fish pathogenic isolate, Mycobacterium sp. 012931.

    PubMed

    Kurokawa, Satoru; Kabayama, Jun; Hwang, Seong Don; Nho, Seong Won; Hikima, Jun-ichi; Jung, Tae Sung; Kondo, Hidehiro; Hirono, Ikuo; Takeyama, Haruko; Mori, Tetsushi; Aoki, Takashi

    2014-10-01

    Mycobacterium is a genus within the order Actinomycetales that comprises of a large number of well-characterized species, several of which includes pathogens known to cause serious disease in human and animal. Here, we report the whole genome sequence of Mycobacterium sp. strain 012931 isolated from the marine fish, yellowtail (Seriola quinqueradiata). Mycobacterium sp. 012931 is a fish pathogen causing serious damage to aquaculture farms in Japan. DNA dot plot analysis showed that Mycobacterium sp. 012931 was more closely related to Mycobacterium marinum when compared across several Mycobacterium species. However, little conservation of the gene order was observed between Mycobacterium sp. 012931 and M. marinum genome. The annotated 5,464 genes of Mycobacterium sp. 012931 was classified into 26 subsystems. The insertion/deletion gene analysis shows Mycobacterium sp. 012931 had 643 unique genes that were not found in the M. marinum strains. In the virulence, disease, and defense subsystem, both insertion and deletion genes of Mycobacterium sp. 012931 were associated with the PPE gene cluster of Mycobacteria. Of seven plcB genes in Mycobacterium sp. 012931, plcB_2 and plcB_3 showed low identities with those of M. marinum strains. Therefore, Mycobacterium sp. 012931 has differences on genetic and virulence from M. marinum and may induce different interaction mechanisms between host and pathogen. PMID:24879010

  1. Whole genome analyses of marine fish pathogenic isolate, Mycobacterium sp. 012931.

    PubMed

    Kurokawa, Satoru; Kabayama, Jun; Hwang, Seong Don; Nho, Seong Won; Hikima, Jun-ichi; Jung, Tae Sung; Kondo, Hidehiro; Hirono, Ikuo; Takeyama, Haruko; Mori, Tetsushi; Aoki, Takashi

    2014-10-01

    Mycobacterium is a genus within the order Actinomycetales that comprises of a large number of well-characterized species, several of which includes pathogens known to cause serious disease in human and animal. Here, we report the whole genome sequence of Mycobacterium sp. strain 012931 isolated from the marine fish, yellowtail (Seriola quinqueradiata). Mycobacterium sp. 012931 is a fish pathogen causing serious damage to aquaculture farms in Japan. DNA dot plot analysis showed that Mycobacterium sp. 012931 was more closely related to Mycobacterium marinum when compared across several Mycobacterium species. However, little conservation of the gene order was observed between Mycobacterium sp. 012931 and M. marinum genome. The annotated 5,464 genes of Mycobacterium sp. 012931 was classified into 26 subsystems. The insertion/deletion gene analysis shows Mycobacterium sp. 012931 had 643 unique genes that were not found in the M. marinum strains. In the virulence, disease, and defense subsystem, both insertion and deletion genes of Mycobacterium sp. 012931 were associated with the PPE gene cluster of Mycobacteria. Of seven plcB genes in Mycobacterium sp. 012931, plcB_2 and plcB_3 showed low identities with those of M. marinum strains. Therefore, Mycobacterium sp. 012931 has differences on genetic and virulence from M. marinum and may induce different interaction mechanisms between host and pathogen.

  2. Isolation and characterization of diesel degrading bacteria, Sphingomonas sp. and Acinetobacter junii from petroleum contaminated soil

    NASA Astrophysics Data System (ADS)

    Zhang, Qiuzhuo; Wang, Duanchao; Li, Mengmeng; Xiang, Wei-Ning; Achal, Varenyam

    2014-03-01

    Two indigenous bacteria of petroleum contaminated soil were characterized to utilize diesel fuel as the sole carbon and energy sources in this work. 16S rRNA gene sequence analysis identified these bacteria as Sphingomonas sp. and Acinetobacter junii. The ability to degrade diesel fuel has been demonstrated for the first time by these isolates. The results of IR analyses showed that Sphingomonas sp. VA1 and A. junii VA2 degraded up to 82.6% and 75.8% of applied diesel over 15 days, respectively. In addition, Sphingomonas sp. VA1 possessed the higher cellular hydrophobicities of 94% for diesel compared to 81% by A. junii VA2. The isolates Sphingomonas sp. VA1 and A. junii VA2 exhibited 24% and 18%, respectively emulsification activity. This study reports two new diesel degrading bacterial species, which can be effectively used for bioremediation of petroleum contaminated sites.

  3. Whole genome sequence of Oscheius sp. TEL-2014 entomopathogenic nematodes isolated from South Africa

    PubMed Central

    Lephoto, Tiisetso E.; Mpangase, Phelelani T.; Aron, Shaun; Gray, Vincent M.

    2016-01-01

    We present the annotation of the draft genome sequence of Oscheius sp. TEL-2014 (Genbank accession number KM492926). This entomopathogenic nematode was isolated from grassland in Suikerbosrand Nature Reserve near Johannesburg in South Africa. Oscheius sp. Strain TEL has a genome size of 110,599,558 bp and a GC content of 42.24%. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession number LNBV00000000. PMID:27054091

  4. [A STUDY OF THE ISOLATED BACTERIOPHAGE ΦAB-SP7 ADSORPTION ON THE CELL SURFACE OF THE AZOSPIRILLUM BRASILENSE SP7].

    PubMed

    Guliy, O I; Karavaeva, O A; Velikov, V A; Sokolov, O I; Pavily, S A; Larionova, O S; Burov, A M; Ignatov, O V

    2016-01-01

    The bacteriophage ΦAb-Sp7 was isolated from the cells of the Azospirillum brasilense Sp7. The morphology, size of the gram-negative colonies, and range of lytic activity against other strains and species of the genus Azospirillum was tested. The isolated phage DNA was examined using electrophoretic and restriction analysis, and the size of the genome were established. The electron microscopy. resuIts show that the phage (capsid) has a strand-like form. The electron microscopy study of the bacteriophage ΦAb-Sp7 adsorption on the A. brasilense Sp7 bacterial surface was performed. PMID:27145602

  5. [A STUDY OF THE ISOLATED BACTERIOPHAGE ΦAB-SP7 ADSORPTION ON THE CELL SURFACE OF THE AZOSPIRILLUM BRASILENSE SP7].

    PubMed

    Guliy, O I; Karavaeva, O A; Velikov, V A; Sokolov, O I; Pavily, S A; Larionova, O S; Burov, A M; Ignatov, O V

    2016-01-01

    The bacteriophage ΦAb-Sp7 was isolated from the cells of the Azospirillum brasilense Sp7. The morphology, size of the gram-negative colonies, and range of lytic activity against other strains and species of the genus Azospirillum was tested. The isolated phage DNA was examined using electrophoretic and restriction analysis, and the size of the genome were established. The electron microscopy. resuIts show that the phage (capsid) has a strand-like form. The electron microscopy study of the bacteriophage ΦAb-Sp7 adsorption on the A. brasilense Sp7 bacterial surface was performed.

  6. Knoellia sinensis gen. nov., sp. nov. and Knoellia subterranea sp. nov., two novel actinobacteria isolated from a cave.

    PubMed

    Groth, Ingrid; Schumann, Peter; Schütze, Barbara; Augsten, Kurt; Stackebrandt, Erko

    2002-01-01

    Two novel strains of the class Actinobacteria were isolated from a cave in China. Cells of both strains were gram-positive, non-motile, non-spore-forming and not acid-fast and exhibited a rod/coccus growth cycle. Both isolates grew well on complex organic media under aerobic conditions. Their cell wall peptidoglycan contained meso-diaminopimelic acid as diagnostic diamino acid. The acyl type of the glycan chain of peptidoglycan was acetyl. The major respiratory quinone was MK-8(H4). The cellular fatty acid profile was characterized by the predominance of 13-methyltetradecanoic (i-C15:0), 15-methylhexadecanoic (i-C17:0), 14-methylpentadecanoic (i-C16:0) and 14-methylhexadecanoic (ai-C17:0) acids. The major polar lipids were phosphatidylethanolamine, phosphatidylinositol and diphosphatidylglycerol. Mycolic acids were absent. The DNA G+C composition was 68-69 mol%. 16S rDNA-based phylogenetic analysis revealed an intermediate phylogenetic position of the cave isolates between the genera Janibacter and Tetrasphaera, which did not permit their unambiguous affiliation to either genus. Differences in morphological, physiological and chemotaxonomic properties between the two isolates and their closest phylogenetic neighbours support the proposal of a new genus and two novel species, Knoellia sinensis gen. nov., sp. nov. and Knoellia subterranea sp. nov. The type and only strains of the species are respectively HKI 0119T (= DSM 12331T = CIP 106775T) and HKI 0120T (= DSM 12332T = CIP 106776T).

  7. Streptomonospora amylolytica sp. nov. and Streptomonospora flavalba sp. nov., two novel halophilic actinomycetes isolated from a salt lake.

    PubMed

    Cai, Man; Tang, Shu-Kun; Chen, Yi-Guang; Li, Yan; Zhang, Yu-Qin; Li, Wen-Jun

    2009-10-01

    Two novel halophilic, aerobic, catalase-positive but oxidase-negative, Gram-positive actinomycetes, designated YIM 91353(T) and YIM 91394(T), were isolated from a salt lake in the north-west of China. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the novel isolates should be assigned to the genus Streptomonospora. The phenotypic and chemotaxonomic characteristics of the isolates also matched those described for members of the genus Streptomonospora. The predominant menaquinones were MK-10(H(8)), MK-10(H(6)) and MK-9(H(8)), and meso-diaminopimelic acid was the diagnostic amino acid in the cell walls. The phospholipids of the isolates consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The major fatty acids of strain YIM 91353(T) were anteiso-C(17 : 0) and C(18 : 0), and of strain YIM 91394(T) were anteiso-C(17 : 0) and iso-C(16 : 0). The DNA G+C contents were 71.2 and 72.5 mol%, respectively. The combination of phylogenetic analysis, DNA-DNA hybridization data, phenotypic characteristics and chemotaxonomic differences supported the view that strains YIM 91353(T) and YIM 91394(T) each represent a novel species of the genus Streptomonospora, for which the names Streptomonospora amylolytica sp. nov. and Streptomonospora flavalba sp. nov. are proposed, with type strains YIM 91353(T) (=DSM 45171(T)=CCTCC AA 208048(T)) and YIM 91394(T) (=DSM 45155(T)=CCTCC AA 208047(T)), respectively.

  8. Bacillus paralicheniformis sp. nov., isolated from fermented soybean paste

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An isolate of a Gram-positive, facultatively anaerobic, motile, rod-shaped, endospore forming bacterium was recovered from soybean-based fermented paste. It was isolated from cheonggukjang, a Korean fermented soybean food product. Phylogenetic analysis of the 16S rRNA gene indicated that the strain ...

  9. Bacillus glycinifermentans sp. nov., isolated from fermented soybean paste

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two independent isolates of a Gram-positive, aerobic, motile rod-shaped bacterium were recovered from soybean-based fermented foodstuffs. Two were isolated from cheonggukjang, a Korean fermented soybean food product. Multilocus sequencing analysis of the 16S rRNA gene and 5 protein coding genes indi...

  10. Potential virulence of Klebsiella sp. isolates from enteral diets

    PubMed Central

    Pereira, S.C.L.; Vanetti, M.C.D.

    2015-01-01

    We aimed to evaluate the potential virulence of Klebsiella isolates from enteral diets in hospitals, to support nosocomial infection control measures, especially among critical-care patients. Phenotypic determination of virulence factors, such as capsular expression on the external membrane, production of aerobactin siderophore, synthesis of capsular polysaccharide, hemolytic and phospholipase activity, and resistance to antibiotics, which are used therapeutically, were investigated in strains of Klebsiella pneumoniae and K. oxytoca. Modular industrialized enteral diets (30 samples) as used in two public hospitals were analyzed, and Klebsiella isolates were obtained from six (20%) of them. The hypermucoviscous phenotype was observed in one of the K. pneumoniae isolates (6.7%). Capsular serotypes K1 to K6 were present, namely K5 and K4. Under the conditions of this study, no aerobactin production, hemolytic activity or lecithinase activity was observed in the isolates. All isolates were resistant to amoxicillin and ampicillin and sensitive to cefetamet, imipenem, chloramphenicol, gentamicin and sulfamethoxazole-trimethoprim. Most K. pneumoniae isolates (6/7, 85.7%) from hospital B presented with a higher frequency of resistance to the antibiotics tested in this study, and multiple resistance to at least four antibiotics (3/8; 37.5%) compared with isolates from Hospital A. The variations observed in the antibiotic resistance profiles allowed us to classify the Klebsiella isolates as eight antibiotypes. No production of broad-spectrum β-lactamases was observed among the isolates. Our data favor the hypothesis that Klebsiella isolates from enteral diets are potential pathogens for nosocomial infections. PMID:26176307

  11. Bullera vrieseae sp. nov., a tremellaceous yeast species isolated from bromeliads.

    PubMed

    Landell, Melissa Fontes; Brandão, Luciana R; Safar, Silvana V B; Gomes, Fatima C O; Félix, Ciro R; Santos, Ana Raquel O; Pagani, Danielle M; Ramos, Jesus P; Broetto, Leonardo; Mott, Tamí; Vainstein, Marilene H; Valente, Patricia; Rosa, Carlos A

    2015-08-01

    Two independent surveys of yeasts associated with different bromeliads in different Brazilian regions led to the proposal of a novel yeast species, Bullera vrieseae sp. nov., belonging to the Tremellales clade (Agaricomycotina, Basidiomycota). Analysis of the sequences in the internal transcribed spacer (ITS) region and D1/D2 domain of the LSU rRNA gene suggested affinity to a phylogenetic lineage that includes Bullera miyagiana and Bullera sakaeratica. Six isolates of the novel species were obtained from different bromeliads and regions in Brazil. Sequence analysis of the D1/D2 domains of the large subunit of the rRNA gene showed that the novel species differs from B. miyagiana and B. sakaeratica by 85 and 64 nt substitutions, respectively and by more than 75 nt substitutions in the ITS region. Phenotypically, Bullera vrieseae sp. nov. can be distinguished from both species based on the assimilation of meso-erythritol, which was negative for B. vrieseae sp. nov. but positive for the others, assimilation of d-glucosamine, which was positive for B. vrieseae sp. nov. but negative for B. miyagiana and of l-sorbose, which was negative for B. vrieseae sp. nov. but positive for B. sakaeratica. The novel species Bullera vrieseae sp. nov. is proposed to accommodate these isolates. The type strain of Bullera vrieseae sp. nov. is UFMG-CM-Y379T (BRO443T; ex-type CBS 13870T). PMID:25911536

  12. Isolation, antimicrobial activity, and metabolites of fungus Cladosporium sp. associated with red alga Porphyra yezoensis.

    PubMed

    Ding, Ling; Qin, Song; Li, Fuchao; Chi, Xiaoyuan; Laatsch, Hartmut

    2008-03-01

    Cladosporium sp. isolate N5 was isolated as a dominant fungus from the healthy conchocelis of Porphyra yezoensis. In the re-infection test, it did not cause any pathogenic symptoms in the alga. Twenty-one cultural conditions were chosen to test its antimicrobial activity in order to obtain the best condition for large-scale fermentation. Phenylacetic acid, p-hydroxyphenylethyl alcohol, and L-beta-phenyllactic acid were isolated from the crude extract as strong antimicrobial compounds and they are the first reported secondary metabolites for the genus Cladosporium. In addition, the Cladosporium sp. produced the reported Porphyra yezoensis growth regulators phenylacetic acid and p-hydroxyphenylacetic acid. No cytotoxicity was found in the brine shrimp lethality test, which indicated that the environmental-friendly Cladosporium sp. could be used as a potential biocontrol agent to protect the alga from pathogens.

  13. Legionella tucsonensis sp. nov. isolated from a renal transplant recipient.

    PubMed Central

    Thacker, W L; Benson, R F; Schifman, R B; Pugh, E; Steigerwalt, A G; Mayberry, W R; Brenner, D J; Wilkinson, H W

    1989-01-01

    A Legionella-like organism (strain 1087-AZ-H) was isolated from a pleural-fluid specimen from a renal transplant patient undergoing immunosuppressive therapy. Growth characteristics and gas-liquid chromatography profiles of the isolate were consistent with those for Legionella spp. The isolate fluoresced blue-white under long-wave UV light. Strain 1087-AZ-H was serologically distinct in the slide agglutination test with absorbed antisera. DNA hybridization studies placed it in a new Legionella species, Legionella tucsonensis (ATCC 49180). PMID:2671032

  14. Perkinsus sp. infections and in vitro isolates from Anadara trapezia (mud arks) of Queensland, Australia.

    PubMed

    Dang, Cécile; Dungan, Christopher F; Scott, Gail P; Reece, Kimberly S

    2015-02-10

    Perkinsus sp. protists were found infecting Anadara trapezia mud ark cockles at 6 sites in Moreton Bay, Queensland, Australia, at prevalences of 4 to 100% during 2011 as determined by surveys using Ray's fluid thioglycollate medium. Perkinsus sp. lesions were found among gill and visceral connective tissues in histological samples from several cockles, where basophilic, eccentrically vacuolated Perkinsus sp. signet ring trophozoites and proliferating, Perkinsus sp. schizont cells were documented. Two Perkinsus sp. isolates were propagated in vitro during August 2013 from gill tissues of a single infected A. trapezia cockle from Wynnum in Moreton Bay. DNA from those isolate cells amplified universally by a Perkinsus genus-specific PCR assay, and rDNA-internal transcribed spacer sequences respectively grouped them with P. olseni and P. chesapeaki in phylogenetic analyses. This is the first report of P. chesapeaki in Australia, and the first report of a P. chesapeaki in vitro isolate from an Australian mollusc host. Although P. olseni was originally described in 1981 as a pathogen of abalone in South Australia, and has subsequently been identified as a prevalent pathogen of numerous other molluscs worldwide, this is also the first report of a P. olseni-like in vitro isolate from an Australian mollusc host.

  15. Perkinsus sp. infections and in vitro isolates from Anadara trapezia (mud arks) of Queensland, Australia.

    PubMed

    Dang, Cécile; Dungan, Christopher F; Scott, Gail P; Reece, Kimberly S

    2015-02-10

    Perkinsus sp. protists were found infecting Anadara trapezia mud ark cockles at 6 sites in Moreton Bay, Queensland, Australia, at prevalences of 4 to 100% during 2011 as determined by surveys using Ray's fluid thioglycollate medium. Perkinsus sp. lesions were found among gill and visceral connective tissues in histological samples from several cockles, where basophilic, eccentrically vacuolated Perkinsus sp. signet ring trophozoites and proliferating, Perkinsus sp. schizont cells were documented. Two Perkinsus sp. isolates were propagated in vitro during August 2013 from gill tissues of a single infected A. trapezia cockle from Wynnum in Moreton Bay. DNA from those isolate cells amplified universally by a Perkinsus genus-specific PCR assay, and rDNA-internal transcribed spacer sequences respectively grouped them with P. olseni and P. chesapeaki in phylogenetic analyses. This is the first report of P. chesapeaki in Australia, and the first report of a P. chesapeaki in vitro isolate from an Australian mollusc host. Although P. olseni was originally described in 1981 as a pathogen of abalone in South Australia, and has subsequently been identified as a prevalent pathogen of numerous other molluscs worldwide, this is also the first report of a P. olseni-like in vitro isolate from an Australian mollusc host. PMID:25667336

  16. Isolation and characterization of Babesia pecorum sp. nov. from farmed red deer (Cervus elaphus).

    PubMed

    Jouglin, Maggy; Fernández-de-Mera, Isabel G; de la Cotte, Nathalie; Ruiz-Fons, Francisco; Gortázar, Christian; Moreau, Emmanuelle; Bastian, Suzanne; de la Fuente, José; Malandrin, Laurence

    2014-01-01

    The diversity of Babesia species infecting cervids in parts of central and southern Spain was analyzed by collecting blood from farmed red deer (Cervus elaphus). Babesia sp. was isolated in vitro from two red deer herds in Cádiz and Ciudad Real. The number of Babesia sp. carriers differed between the two herds: 36/77 in Cádiz and 1/35 in Ciudad Real. Hyalomma lusitanicum was the most prevalent tick species identified on the Cádiz farm vegetation and on sampled animals, and is therefore a candidate vector. The molecular characteristics of 21 isolates were determined by complete (8 isolates) or partial (13 isolates) 18S rRNA gene sequencing. The sequences were highly similar (over 99.4% identity) and 6 sequence types were identified at the level of one herd only, demonstrating a rather high genetic diversity. They formed a monophyletic clade, and members of the three main sequence types shared a similar morphology and the same erythrocyte susceptibility pattern. This clade also included Babesia sp. Xinjiang isolated from sheep in China and Babesia sp. identified in giraffe in South Africa, with identities higher than 98.3% and statistically relevant phylogenetic support. None of the biological properties analyzed for both Babesia from red deer and Babesia sp. Xinjiang allowed their differentiation (ability to develop in vitro in erythrocytes from cattle and sheep, as well as in erythrocytes from different cervids, unsuccessful infection of calves). We propose the Babesia isolated from red deer as a new species named B. pecorum. Whether Babesia sp. Xinjiang and the Babesia characterized in South Africa belong to the same species is debated. PMID:25155988

  17. Bacteroides acidifaciens sp. nov., isolated from the caecum of mice.

    PubMed

    Miyamoto, Y; Itoh, K

    2000-01-01

    During studies of the bacterial flora in the intestines of mice, we isolated characteristic strains which lowered the pH of peptone-yeast broth containing Fildes' digest. Based on 16S rRNA sequence comparison, these isolates were considered to belong to the Bacteroides cluster in the bacteroides subgroup of the Cytophaga-Flavobacterium-Bacteroides phylum, and were divided into two groups. Their phenotypic characteristics, i.e. growth in 20% bile, aesculin hydrolysis, and glucose-6-phosphate dehydrogenase (G6PDH) and 6-phosphogluconate dehydrogenase (6PGDH) activity, were the same as those of the 'Bacteroides fragilis group'. The low level of DNA-DNA hybridization with type strains in the Bacteroides cluster confirmed the novel species status of these isolates. It is proposed that these isolates be named Bacteroides acidifaciens, the type strain of which is A40T (= JCM 10556T). PMID:10826798

  18. Antifungal activity of Bacillus sp. isolated from compost.

    PubMed

    Czaczyk, K; Stachowiak, B; Trojanowska, K; Gulewicz, K

    2000-01-01

    Four strains of Bacillus isolated from lupine compost exhibited an antifungal activity against six plant fungal pathogens (Rhizoctonia solani, Bipolaris sorokiniana, Sclerotinia sclerotiorum, Trichothecium roseum, Fusarium solani, Fusarium oxysporum). It was significantly influenced by the composition of the cultivation media.

  19. Wickerhamiella dulcicola sp. nov. and Wickerhamiella cachassae sp. nov., yeasts isolated from cachaça fermentation in Brazil.

    PubMed

    Badotti, Fernanda; Silva, Pollyana A B; Mendonça, Michelle C; Gomes, Fatima C O; Morais, Paula B; Lachance, Marc-André; Rosa, Carlos A

    2013-03-01

    Six strains of two novel yeast species were isolated from sugar-cane juice and fermentation vats of cachaça production in Brazil. The sequences of the D1/D2 domains of the large-subunit rRNA gene showed that these species belong to the Wickerhamiella clade, and their closest described relative in terms of sequence similarity is Candida (iter. nom. Wickerhamiella) drosophilae. The type strain of Wickerhamiella cachassae sp. nov. is UFMG-D5L7(T) ( = CBS 12587(T)  = CBMAI 1469(T)) and the type strain of Wickerhamiella dulcicola sp. nov. is UFMG-TOL15(T) ( = CBS 12588(T)  = CBMAI 1468(T)). PMID:23203623

  20. Moniliella carnis sp. nov. and Moniliella dehoogii sp. nov., two novel species of black yeasts isolated from meat processing environments.

    PubMed

    Thanh, Vu Nguyen; Hai, Dao Anh; Hien, Dinh Duc; Takashima, Masako; Lachance, Marc-André

    2012-12-01

    Thirteen strains of yeasts typical of the genus Moniliella were isolated from fermenting meat and meat processing tools in Vietnam. PCR fingerprints generated by primer (GAC)(5) subdivided the strains into two distinctive genetic groups. In a phylogenetic tree based on D1/D2 large subunit rRNA gene sequences, the strains formed a well-supported clade with Moniliella spathulata and Moniliella suaveolens but represented two new lineages. The names Moniliella carnis sp. nov. and Moniliella dehoogii sp. nov. are proposed. The two novel species can be distinguished from each other and from known species of Moniliella based on phenotypic characteristics. It is assumed that the yeasts were associated with fatty substances that contaminated the meat processing tools. The type strain of Moniliella carnis is KFP 246(T) ( = CBS 126447(T) = NRRL Y-48681(T)) and the type strain of Moniliella dehoogii is KFP 211(T) ( = CBS 126564(T) = NRRL Y-48682(T)). PMID:22863989

  1. Psychroflexus saliphilus sp. nov., isolated from a marine solar saltern

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A Gram-stain-negative, non-motile, rod-shaped, orange pigmented strain, WDS4A13**T, was isolated from a marine solar saltern in Weihai, China. WDS4A13**T grows optimally at pH at 7.0-8.0, 33°C, with 6% (w/v) NaCl. The polar lipid profile of the novel isolate consisted of two unidentified phospholipi...

  2. Nocardiopsis potens sp. nov., isolated from household waste.

    PubMed

    Yassin, A F; Spröer, C; Hupfer, H; Siering, C; Klenk, H-P

    2009-11-01

    The taxonomic position of an actinomycete, designated strain IMMIB L-21(T), was determined using a polyphasic taxonomic approach. The organism, which had phenotypic properties consistent with its classification in the genus Nocardiopsis, formed a distinct clade in the 16S rRNA gene sequence tree together with the type strain of Nocardiopsis composta, but was readily distinguished from this species using DNA-DNA relatedness and phenotypic data. The genotypic and phenotypic data show that the organism represents a novel species of the genus Nocardiopsis, for which the name Nocardiopsis potens sp. nov. is proposed. The type strain is IMMIB L-21(T) (=DSM 45234(T)=CCUG 56587(T)).

  3. Atpenins, new antifungal antibiotics produced by Penicillium sp. Production, isolation, physico-chemical and biological properties.

    PubMed

    Omura, S; Tomoda, H; Kimura, K; Zhen, D Z; Kumagai, H; Igarashi, K; Imamura, N; Takahashi, Y; Tanaka, Y; Iwai, Y

    1988-12-01

    Penicillium sp. FO-125, a soil isolate, was found to produce a new antifungal antibiotic complex named atpenin. Three components A4, A5 and B were isolated from the fermentation broth of the producing strain by solvent extraction, silica gel column chromatography and HPLC. The molecular formula of atpenins A4, A5 and B were determined to be C15H22NO5Cl, C15H21NO5Cl2 and C15H23NO5, respectively, on the basis of high resolution electron impact mass spectrometry and elemental analysis. They are active against filamentous fungi, especially, Trichophyton sp. PMID:3209470

  4. Lactobacillus arizonensis sp. nov., isolated from jojoba meal.

    PubMed

    Swezey, J L; Nakamura, L K; Abbott, T P; Peterson, R E

    2000-09-01

    Five strains of simmondsin-degrading, lactic-acid-producing bacteria were isolated from fermented jojoba meal. These isolates were facultatively anaerobic, gram-positive, non-motile, non-spore-forming, homofermentative, rod-shaped organisms. They grew singly and in short chains, produced lactic acid but no gas from glucose, and did not exhibit catalase activity. Growth occurred at 15 and 45 degrees C. All strains fermented cellobiose, D-fructose, D-galactose, D-glucose, lactose, maltose, D-mannitol, D-mannose, melibiose, D-ribose, salicin, D-sorbitol, sucrose and trehalose. Some strains fermented L-(-)-arabinose and L-rhamnose. D-Xylose was not fermented and starch was not hydrolysed. The mean G+C content of the DNA was 48 mol%. Phylogenetic analyses of 16S rDNA established that the isolates were members of the genus Lactobacillus. DNA reassociation of 45% or less was obtained between the new isolates and the reference strains of species with G+C contents of about 48 mol%. The isolates were differentiated from other homofermentative Lactobacillus spp. on the basis of 16S rDNA sequence divergence, DNA relatedness, stereoisomerism of the lactic acid produced, growth temperature and carbohydrate fermentation. The data support the conclusion that these organisms represent strains of a new species, for which the name Lactobacillus arizonensis is proposed. The type strain of L. arizonensis is NRRL B-14768T (= DSM 13273T).

  5. Magnetospirillum caucaseum sp. nov., Magnetospirillum marisnigri sp. nov. and Magnetospirillum moscoviense sp. nov., freshwater magnetotactic bacteria isolated from three distinct geographical locations in European Russia.

    PubMed

    Dziuba, Marina; Koziaeva, Veronika; Grouzdev, Denis; Burganskaya, Ekaterina; Baslerov, Roman; Kolganova, Tatjana; Chernyadyev, Alexander; Osipov, Georgy; Andrianova, Ekaterina; Gorlenko, Vladimir; Kuznetsov, Boris

    2016-05-01

    Three strains of helical, magnetotactic bacteria, SO-1T, SP-1T and BB-1T, were isolated from freshwater sediments collected from three distinct locations in European Russia. Phylogenetic analysis showed that the strains belong to the genus Magnetospirillum. Strains SO-1T and SP-1T showed the highest 16S rRNA gene sequence similarity to Magnetospirillum magnetotacticum MS-1T (99.3 and 98.1 %, respectively), and strain BB-1T with Magnetospirillum gryphiswaldense MSR-1T (97.3 %). The tree based on concatenated deduced amino acid sequences of the MamA, B, K, M, O, P, Q and T proteins, which are involved in magnetosome formation, was congruent with the tree based on 16S rRNA gene sequences. The genomic DNA G+C contents of strains SO-1T, SP-1T and BB-1T were 65.9, 63.0 and 65.2 mol%, respectively. As major fatty acids, C18 : 1ω9, C16 : 1ω7c, C16 : 0 and C18 : 0 were detected. DNA-DNA hybridization values between the novel strains and their closest relatives in the genus Magnetospirillum were less than 51.7 ± 2.3 %. In contrast to M. magnetotacticum MS-1T, the strains could utilize butyrate and propionate; strains SO-1T and BB-1T could also utilize glycerol. Strain SP-1T showed strictly microaerophilic growth, whereas strains SO-1T and BB-1T were more tolerant of oxygen. The results of DNA-DNA hybridization and physiological tests allowed genotypic and phenotypic differentiation of the strains from each other as well as from the two species of Magnetospirillum with validly published names. Therefore, the strains represent novel species, for which we propose the names Magnetospirillum caucaseum sp. nov. (type strain SO-1T = DSM 28995T = VKM B-2936T), Magnetospirillum marisnigri sp. nov. (type strain SP-1T = DSM 29006T = VKM B-2938T) and Magnetospirillum moscoviense sp. nov. (type strain BB-1T = DSM 29455T = VKM B-2939T). PMID:26921147

  6. Draft Genome Sequence of Halomonas sp. HG01, a Polyhydroxyalkanoate-Accumulating Strain Isolated from Peru

    PubMed Central

    Cardinali-Rezende, Juliana; Nahat, Rafael Augusto Teodoro Pereira de Souza; Guzmán Moreno, César Wilber; Carreño Farfán, Carmen Rosa; Silva, Luiziana Ferreira; Taciro, Marilda Keico

    2016-01-01

    Halomonas sp. strain HG01, isolated from a salt mine in Peru, is a halophilic aerobic heterotrophic bacterium accumulating poly-3-hydroxybutyrate and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) from different carbon sources. Here, we report the draft genome sequence of this isolate, which was found to be 3,665,487 bp long, with a G+C content of 68%. PMID:26798101

  7. Pestaloporonins: Caryophyllene-Derived Sesquiterpenoids from a Fungicolous Isolate of Pestalotiopsis sp.

    PubMed

    Hwang, In Hyun; Swenson, Dale C; Gloer, James B; Wicklow, Donald T

    2015-09-01

    Three new sesquiterpenoids (pestaloporonins A-C; 1-3) related to the caryophyllene-derived punctaporonins were isolated from cultures of a fungicolous isolate of Pestalotiopsis sp. The structures of 1-3 were determined by analysis of NMR and HRMS data, and the structure of 1, including its absolute configuration, was confirmed by X-ray crystallographic analysis. Compounds 1 and 2 contain new bicyclic and tricyclic ring systems, respectively. PMID:26287562

  8. Peptoniphilus duerdenii sp. nov. and Peptoniphilus koenoeneniae sp. nov., isolated from human clinical specimens.

    PubMed

    Ulger-Toprak, Nurver; Lawson, Paul A; Summanen, Paula; O'Neal, Lindsey; Finegold, Sydney M

    2012-10-01

    Two previously uncharacterized strains of Gram-reaction-positive, anaerobic, coccus-shaped bacteria, designated strains WAL 18896(T) and WAL 18898(T), were recovered from human wound specimens and characterized using phenotypic, chemotaxonomic and molecular taxonomic methods. Comparative 16S rRNA gene sequence analysis and chemotaxonomic and biochemical characteristics demonstrated that these organisms are genotypically and phenotypically distinct and represent previously unidentified sublines within the order Clostridiales in the phylum Firmicutes. Pairwise sequence analysis demonstrated that the novel organisms had 91.9% sequence similarity to each other and were most closely related to members of the genus Peptoniphilus. The major long-chain fatty acids of both strains were C(16:0,) C(18:0), C(18:1)ω9c and C(18:2)ω6,9c. Based on the phenotypic and phylogenetic findings, strains WAL 18896(T) ( = CCUG 56065(T)  = ATCC BAA-1640(T)) and WAL 18898(T) ( = CCUG 56067(T)  = ATCC BAA-1638(T)  = DSM 22616(T)) represent two novel species, for which the names Peptoniphilus duerdenii sp. nov. and Peptoniphilus koenoeneniae sp. nov. are proposed, respectively. PMID:22140159

  9. Prauserella endophytica sp. nov., an endophytic actinobacterium isolated from Tamarix taklamakanensis.

    PubMed

    Liu, Jia-Meng; Habden, Xugela; Guo, Lin; Tuo, Li; Jiang, Zhong-Ke; Liu, Shao-Wei; Liu, Xian-Fu; Chen, Li; Li, Rong-Feng; Zhang, Yu-Qin; Sun, Cheng-Hang

    2015-06-01

    A novel endophytic actinobacterium, designated strain SP28S-3(T), was isolated from a surface-sterilized stem of Tamarix taklamakanensis collected from the southern edge of Taklamakan desert, Xinjiang, China. Strain SP28S-3(T) was found to show chemotaxonomic and morphological properties consistent with its classification in the genus Prauserella. The polar lipids were found to consist of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphoglycolipid, phosphatidylcholine, phosphatidylinositol, a glycolipid, an aminolipid and unidentified phospholipids. The major fatty acids (>10 %) were identified as iso-C16:0 and C16:0. The genomic DNA G+C content was determined to be 69.7 mol%. Phylogenetic analysis of strain SP28S-3(T) clearly showed that the strain had the highest similarity of 16S rRNA gene sequence with Prauserella coralliicola SCSIO 11529(T) (99.9 %), followed by Prauserella marina DSM 45268(T) (97.0 %) and is affiliated with the genus Prauserella. The low level (47.8 ± 5.5 %) of DNA-DNA relatedness between strain SP28S-3(T) and P. coralliicola SCSIO 11529(T) combined with other polyphasic taxonomic evidence clearly support the conclusion that strain SP28S-3(T) represents a novel Prauserella species, for which the name Prauserella endophytica sp. nov. is proposed. The type strain is SP28S-3(T) (=DSM 46655(T) = CGMCC 4.7182 (T)).

  10. Complete genome sequence of carotenoid-producing Microbacterium sp. strain PAMC28756 isolated from an Antarctic lichen.

    PubMed

    Han, So-Ra; Kim, Ki-Hwa; Ahn, Do-Hwan; Park, Hyun; Oh, Tae-Jin

    2016-05-20

    Microbacterium sp. strain PAMC28756, of the family Microbacteriaceae, was isolated from Stereocaulon sp., an Antarctic lichen. Complete genome sequencing of Microbacterium sp. PAMC28756 revealed, for the first time in the genus Microbacterium, a series of key genes involved in C50 carotenoid biosynthesis. An analysis of the Microbacterium sp. PAMC28756 genome will lead to a better understanding of the carotenoid biosynthesis pathway. Furthermore, the sequence data will provide novel insight into UV radiation resistance in extremely cold environments. PMID:27015978

  11. Genome Sequence of Marinobacter sp. Strain MCTG268 Isolated from the Cosmopolitan Marine Diatom Skeletonema costatum

    PubMed Central

    Whitman, William B.; Huntemann, Marcel; Copeland, Alex; Chen, Amy; Kyrpides, Nikos; Markowitz, Victor; Pillay, Manoj; Ivanova, Natalia; Mikhailova, Natalia; Ovchinnikova, Galina; Andersen, Evan; Pati, Amrita; Stamatis, Dimitrios; Reddy, T. B. K.; Ngan, Chew Yee; Chovatia, Mansi; Daum, Chris; Shapiro, Nicole; Cantor, Michael N.; Woyke, Tanja

    2016-01-01

    Marinobacter sp. strain MCTG268 was isolated from the cosmopolitan marine diatom Skeletonema costatum and can degrade oil hydrocarbons as sole sources of carbon and energy. Here, we present the genome sequence of this strain, which is 4,449,396 bp with 4,157 genes and an average G+C content of 57.0%. PMID:27609918

  12. Draft Genome Sequence of Shewanella sp. ECSMB14101, Isolated from the East China Sea.

    PubMed

    Yang, Jin-Long; Guo, Xing-Pan; Ding, De-Wen

    2015-01-01

    Shewanella sp. ECSMB14101 was isolated from marine biofilms formed on the East China Sea. The draft genome sequence comprises 4,272,451 bp with a G+C content of 49.82%. Information on this draft genome will contribute to the understanding of bacterium-animal interactions. PMID:25593251

  13. Draft Genome Sequence of Pseudoalteromonas sp. Strain ECSMB14103, Isolated from the East China Sea.

    PubMed

    Guo, Xing-Pan; Ding, De-Wen; Bao, Wei-Yang; Yang, Jin-Long

    2015-01-01

    Pseudoalteromonas sp. strain ECSMB14103 was isolated from marine biofilms formed on the East China Sea. The draft genome sequence comprises 4.11 Mp with a G+C content of 39.7%. The information from the draft genome will contribute to an understanding of bacteria-animal interaction. PMID:25908138

  14. Draft Genome Sequence of Lysinibacillus sp. Strain A1, Isolated from Malaysian Tropical Soil

    PubMed Central

    Chen, Jian Woon; Chang, Chien-Yi; Yin, Wai-Fong; Chan, Xin-Yue

    2015-01-01

    In this work, we describe the genome of Lysinibacillus sp. strain A1, which was isolated from tropical soil. Analysis of its genome sequence shows the presence of a gene encoding for a putative peptidase responsible for nitrogen compounds. PMID:25814592

  15. Genome Sequence of Gluconacetobacter sp. Strain SXCC-1, Isolated from Chinese Vinegar Fermentation Starter▿

    PubMed Central

    Du, Xin-jun; Jia, Shi-ru; Yang, Yue; Wang, Shuo

    2011-01-01

    Gluconacetobacter strains are prominent bacteria during traditional vinegar fermentation. Here, we report a draft genome sequence of Gluconacetobacter sp. strain SXCC-1. This strain was isolated from a fermentation starter (Daqu) used for commercial production of Shanxi vinegar, the best-known vinegar of China. PMID:21551293

  16. Draft Genome Sequence of Rhizobium sp. GHKF11, Isolated from Farmland Soil in Pecan Grove, Texas

    PubMed Central

    Damania, Ashish

    2016-01-01

    Rhizobium sp. GHKF11 is an organophosphate-degrading bacterial strain that was isolated from farmland soil in Pecan Grove, Texas, USA. In addition to a capacity for pesticide degradation, GHKF11 shares conserved traits with other Rhizobium spp., including heavy metal resistance and transport genes that may have significant agricultural biotechnology applications. PMID:27445376

  17. Draft Genome Sequence of an Oceanobacillus sp. Strain Isolated from Soil in a Burial Crypt

    PubMed Central

    Arizaga, Ylenia; Bikandi, Joseba; Garaizar, Javier; Ganau, Giulia; Paglietti, Bianca; Deligios, Massimo; Rubino, Salvatore

    2016-01-01

    We present the draft genome of an Oceanobacillus sp. strain isolated from spores found in soil samples from a burial crypt of the Cathedral of Sant'Antonio Abate in Castelsardo, Italy. The data obtained indicated the closest relation of the strain with Oceanobacillus caeni. PMID:27469952

  18. Complete Genome Sequence of Marinobacter sp. CP1, Isolated from a Self-Regenerating Biocathode Biofilm

    PubMed Central

    Wang, Zheng; Eddie, Brian J.; Malanoski, Anthony P.; Hervey, W. Judson; Lin, Baochuan

    2015-01-01

    Marinobacter sp. CP1 was isolated from a self-regenerating and self-sustaining biocathode biofilm that can fix CO2 and generate electric current. We present the complete genome sequence of this strain, which consists of a circular 4.8-Mbp chromosome, to understand the mechanism of extracellular electron transfer in a microbial consortium. PMID:26404584

  19. Draft Genome Sequence of Rhizobium sp. GHKF11, Isolated from Farmland Soil in Pecan Grove, Texas.

    PubMed

    Iyer, Rupa; Damania, Ashish

    2016-01-01

    Rhizobium sp. GHKF11 is an organophosphate-degrading bacterial strain that was isolated from farmland soil in Pecan Grove, Texas, USA. In addition to a capacity for pesticide degradation, GHKF11 shares conserved traits with other Rhizobium spp., including heavy metal resistance and transport genes that may have significant agricultural biotechnology applications. PMID:27445376

  20. Complete Genome Sequence of Hemolysin-Containing Carnobacterium sp. Strain CP1 Isolated from the Antarctic

    PubMed Central

    Zhu, Sidong; Wang, Xing; Zhang, Di; Jing, Xiaohuan; Zhang, Ning

    2016-01-01

    Carnobacterium sp. strain CP1 was isolated from Antarctic sandy soil and predicted to be a novel species belonging to the genus Carnobacterium. Herein, we report the complete genome sequence, which consists of a circular 2,605,518-bp chromosome and an 8,883-bp plasmid with G+C contents of 38.13% and 31.63%, respectively. PMID:27445381

  1. Genome sequence of Shinella sp. strain DD12, isolated from homogenized guts of starved Daphnia magna.

    PubMed

    Poehlein, Anja; Freese, Heike; Daniel, Rolf; Simeonova, Diliana D

    2016-01-01

    Shinella sp. strain DD12, a novel phosphite assimilating bacterium, has been isolated from homogenized guts of 4 days starved zooplankton Daphnia magna. Here we report the draft genome of this bacterium, which comprises 7,677,812 bp and 7505 predicted protein-coding genes.

  2. Draft Genome Sequence of Achromobacter sp. Strain AR476-2, Isolated from a Cellulolytic Consortium

    PubMed Central

    Kurth, Daniel; Romero, Cintia M.; Fernandez, Pablo M.; Ferrero, Marcela A.

    2016-01-01

    Achromobacter sp. AR476-2 is a noncellulolytic strain previously isolated from a cellulolytic consortium selected from samples of insect gut. Its genome sequence could contribute to the unraveling of the complex interaction of microorganisms and enzymes involved in the biodegradation of lignocellulosic biomass in nature. PMID:27340069

  3. Draft Genome Sequence of Achromobacter sp. Strain AR476-2, Isolated from a Cellulolytic Consortium.

    PubMed

    Kurth, Daniel; Romero, Cintia M; Fernandez, Pablo M; Ferrero, Marcela A; Martinez, M Alejandra

    2016-01-01

    Achromobacter sp. AR476-2 is a noncellulolytic strain previously isolated from a cellulolytic consortium selected from samples of insect gut. Its genome sequence could contribute to the unraveling of the complex interaction of microorganisms and enzymes involved in the biodegradation of lignocellulosic biomass in nature. PMID:27340069

  4. Whole-Genome Sequence of Bacillus sp. SDLI1, Isolated from the Social Bee Scaptotrigona depilis

    PubMed Central

    Paludo, Camila R.; Silva-Junior, Eduardo A.; Pishchany, Gleb; Currie, Cameron R.; Nascimento, Fábio S.; Kolter, Roberto G.

    2016-01-01

    We announce the complete genome sequence of Bacillus sp. strain SDLI1, isolated from larval gut of the stingless bee Scaptotrigona depilis. The 4.13-Mb circular chromosome harbors biosynthetic gene clusters for the production of antimicrobial compounds. PMID:27013050

  5. Genome sequence of Janthinobacterium sp. strain PAMC 25724, isolated from alpine glacier cryoconite.

    PubMed

    Kim, Su Jin; Shin, Seung Chul; Hong, Soon Gyu; Lee, Yung Mi; Lee, Hyoungseok; Lee, Jungeun; Choi, In-Geol; Park, Hyun

    2012-04-01

    The draft genome of Janthinobacterium sp. strain PAMC 25724, which is a violacein-producing psychrotolerant bacterium, was determined. The strain was isolated from glacier cryoconite of the Alps mountain permafrost region. The sequence will allow identification and characterization of the genetic determination of its cold-adaptive properties.

  6. Genome sequence of Pseudomonas sp. strain PAMC 25886, isolated from alpine glacial cryoconite.

    PubMed

    Shin, Seung Chul; Kim, Su Jin; Hong, Soon Gyu; Ahn, Do Hwan; Lee, Yung Mi; Lee, Hyoungseok; Lee, Jungeun; Park, Hyun

    2012-04-01

    Pseudomonas spp. have shown characteristics of efficiently metabolizing environmental pollutants and also producing exopolysaccharides known as biofilms. Here we present the draft genome sequence of Pseudomonas sp. strain PAMC 25886, which was isolated from glacier cryoconite in the Alps mountain permafrost region and which may provide further insight into biodegradative and/or biofilm-producing mechanisms in a cold environment.

  7. Draft Genome Sequence of Rheinheimera sp. Strain SA_1 Isolated from Iron Backwash Sludge in Germany.

    PubMed

    Schröder, Josephin; Braun, Burga; Liere, Karsten; Szewzyk, Ulrich

    2016-01-01

    Rheinheimera sp. strain SA_1 is an iron-depositing bacterium for which we report a draft genome sequence. Strain SA_1 was isolated from iron backwash sludge of a waterworks in Germany. The Illumina MiSeq technique was used to sequence the genome of the strain. PMID:27540074

  8. Draft Genome Sequence of Rheinheimera sp. Strain SA_1 Isolated from Iron Backwash Sludge in Germany

    PubMed Central

    Schröder, Josephin; Liere, Karsten; Szewzyk, Ulrich

    2016-01-01

    Rheinheimera sp. strain SA_1 is an iron-depositing bacterium for which we report a draft genome sequence. Strain SA_1 was isolated from iron backwash sludge of a waterworks in Germany. The Illumina MiSeq technique was used to sequence the genome of the strain. PMID:27540074

  9. Genome Sequence of Marinobacter sp. Strain MCTG268 Isolated from the Cosmopolitan Marine Diatom Skeletonema costatum.

    PubMed

    Gutierrez, Tony; Whitman, William B; Huntemann, Marcel; Copeland, Alex; Chen, Amy; Kyrpides, Nikos; Markowitz, Victor; Pillay, Manoj; Ivanova, Natalia; Mikhailova, Natalia; Ovchinnikova, Galina; Andersen, Evan; Pati, Amrita; Stamatis, Dimitrios; Reddy, T B K; Ngan, Chew Yee; Chovatia, Mansi; Daum, Chris; Shapiro, Nicole; Cantor, Michael N; Woyke, Tanja

    2016-01-01

    Marinobacter sp. strain MCTG268 was isolated from the cosmopolitan marine diatom Skeletonema costatum and can degrade oil hydrocarbons as sole sources of carbon and energy. Here, we present the genome sequence of this strain, which is 4,449,396 bp with 4,157 genes and an average G+C content of 57.0%. PMID:27609918

  10. Actinokineospora bangkokensis sp. nov., isolated from rhizospheric soil.

    PubMed

    Intra, Bungonsiri; Matsumoto, Atsuko; Inahashi, Yuki; Omura, Satoshi; Takahashi, Yoko; Panbangred, Watanalai

    2013-07-01

    A novel actinomycete, strain 44EHW(T), was isolated from rhizospheric soil under an Elephant ear plant (Colocasia esculenta) in Bangkok, Thailand. Strain 44EHW(T) produced long branching hyphae and abundant aerial mycelia with chains of rod-shaped spores. Whole-cell hydrolysates contained galactose, glucose, arabinose, ribose, mannose and rhamnose as diagnostic sugars. meso-Diaminopimelic acid was the diamino acid and glycine, alanine and glutamic acid were present in the cell-wall peptidoglycan with the acyl type of the peptidoglycan being acetyl. Phospholipids consisted of phosphatidylethanolamine, phosphatidylethanolamine with hydroxy fatty acids and diphosphatidylglycerol, as well as other unknown phospholipids; however, no mycolic acids were detected. The predominant menaquinone observed was MK-9(H4) and major fatty acids were iso-C16 : 0 and 2-OH iso-C16 : 0. The G+C content of genomic DNA was 74 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that this isolate was most similar to Actinokineospora enzanensis NBRC 16517(T). However, DNA-DNA hybridization revealed a low relatedness between this isolate and A. enzanensis NBRC 16517(T), indicating that this isolate represented a novel species in the genus Actinokineospora. On the basis of 16S rRNA gene sequence analysis, phenotypic characteristics and DNA-DNA hybridization data, we propose that strain 44EHW(T) represents a novel species in the genus Actinokineospora, Actinokineospora bangkokensis. The type strain is 44EHW(T) ( = BCC 53155(T) = NBRC 108932(T)). PMID:23291892

  11. Arsenic biotransformation by Streptomyces sp. isolated from rice rhizosphere.

    PubMed

    Kuramata, Masato; Sakakibara, Futa; Kataoka, Ryota; Abe, Tadashi; Asano, Maki; Baba, Koji; Takagi, Kazuhiro; Ishikawa, Satoru

    2015-06-01

    Isolation and functional analysis of microbes mediating the methylation of arsenic (As) in paddy soils is important for understanding the origin of dimethylarsinic acid (DMA) in rice grains. Here, we isolated from the rice rhizosphere a unique bacterium responsible for As methylation. Strain GSRB54, which was isolated from the roots of rice plants grown in As-contaminated paddy soil under anaerobic conditions, was classified into the genus Streptomyces by 16S ribosomal RNA sequencing. Sequence analysis of the arsenite S-adenosylmethionine methyltransferase (arsM) gene revealed that GSRB54 arsM was phylogenetically different from known arsM genes in other bacteria. This strain produced DMA and monomethylarsonic acid when cultured in liquid medium containing arsenite [As(III)]. Heterologous expression of GSRB54 arsM in Escherichia coli promoted methylation of As(III) by converting it into DMA and trimethylarsine oxide. These results demonstrate that strain GSRB54 has a strong ability to methylate As. In addition, DMA was detected in the shoots of rice grown in liquid medium inoculated with GSRB54 and containing As(III). Since Streptomyces are generally aerobic bacteria, we speculate that strain GSRB54 inhabits the oxidative zone around roots of paddy rice and is associated with DMA accumulation in rice grains through As methylation in the rice rhizosphere. PMID:25039305

  12. Syntrophic biodegradation of butachlor by Mycobacterium sp. J7A and Sphingobium sp. J7B isolated from rice paddy soil.

    PubMed

    Kim, Nam Hyun; Kim, Dong-Uk; Kim, Ijung; Ka, Jong-Ok

    2013-07-01

    Two bacterial strains involved in syntrophic degradation of chloroacetamide herbicide butachlor were isolated from a rice paddy soil. Analysis of 16S rRNA gene sequences indicated that the two isolates were related to members of the genera Mycobacterium and Sphingobium, respectively. Thus, a pair consisted of Mycobacterium sp. J7A and Sphingobium sp. J7B could rapidly degrade butachlor (100 mg L(-1)) at 28 °C within 24 h, while each isolate alone was not able to completely degrade butachlor. The isolate Mycobacterium sp. J7A was observed to grow slightly on butachlor, possibly utilizing the alkyl side chain of butachlor as its carbon and energy source, but the isolate Sphingobium sp. J7B alone could not grow on butachlor at all. Gas chromatography-mass spectrometry on catabolic intermediates revealed that the strain J7A produced and accumulated 2-chloro-N-(2,6-diethylphenyl) acetamide (CDEPA) during growth on butachlor. This intermediate was not further degraded by strain J7A, but strain J7B was observed to be able to completely degrade and grow on it through 2,6-diethylaniline (DEA). The results showed that butachlor was completely degraded by the two isolates by syntrophic metabolism, in which strain Mycobacterium sp. J7A degraded butachlor to CDEPA, which was subsequently degraded by strain Sphingobium sp. J7B through DEA.

  13. Alistipes inops sp. nov. and Coprobacter secundus sp. nov., isolated from human faeces.

    PubMed

    Shkoporov, Andrei N; Chaplin, Andrei V; Khokhlova, Ekaterina V; Shcherbakova, Victoria A; Motuzova, Oksana V; Bozhenko, Vladimir K; Kafarskaia, Lyudmila I; Efimov, Boris A

    2015-12-01

    Culture-based study of the faecal microbiome in two adult female subjects revealed the presence of two obligately anaerobic, non-spore-forming, rod-shaped, non-motile, Gram-negative bacterial strains that represent novel species. The first strain, designated 627T, was a fastidious, slow-growing, indole-positive bacterium with a non-fermentative type of metabolism.The strain was characterized by the production of acetic and succinic acids as metabolic end products, the prevalence of iso-C15 : 0 fatty acid and the presence of menaquinones MK-10 and MK-11. The DNA G+C content was found to be 56.6 mol%. The second strain, designated 177T, was capable of fermenting a rich collection of carbohydrate substrates, producing acetic acid as a terminal product. The strain was indole-negative and resistant to bile. The major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0 (in a 1 : 1 ratio) and the predominant menaquinone was MK-11.The DNA G+C content was 37.8 mol%. A phylogenomic analysis of the draft genomes of strains 627T and 177T placed these bacteria in the genera Alistipes(family Rikenellaceae) and Coprobacter (family Porphyromonadaceae), respectively.On the basis of the phenotypic and genotypic properties of strains 627T and 177T, we conclude that these strains from human faeces represent two novel bacterial species, for which the names Alistipes inops sp. nov. (type strain 627T5DSM 28863T5VKM B-2859T) and Coprobacter secundus sp. nov. (type strain 177T=DSM 28864T=VKM B-2857T) are proposed.

  14. Metschnikowia noctiluminum sp. nov., Metschnikowia corniflorae sp. nov., and Candida chrysomelidarum sp. nov., isolated from green lacewings and beetles.

    PubMed

    Nguyen, Nhu H; Suh, Sung-Oui; Erbil, Cennet K; Blackwell, Meredith

    2006-03-01

    Fourteen yeast isolates belonging to the Metschnikowia clade were isolated from the digestive tracts of lacewings (Neuroptera: Chrysopidae), soldier beetles and leaf beetles (Coleoptera: Cantharidae and Chrysomelidae), and a caddisfly (Trichoptera: Hydropsychidae). The insect hosts were associated with sugary substances of plants, a typical habitat for yeasts in this clade. Based on DNA sequence comparisons and phenetic characters, the yeasts were identified as Candida picachoensis, Candida pimensis, and four undescribed taxa. Among the undescribed taxa, three yeasts were distinguished from one another and from other described taxa by nucleotide differences in the ribosomal DNA repeat, which were sufficient to consider them as new species. Two of the novel yeast species are described as Metschnikowia noctiluminum (NRRL Y-27753(T)) and M. cornifloraespp. nov. (NRRL Y-27750(T)) based in part on production of needle-shaped ascospores, which are found in most Metschnikowia species. Sexual reproduction was not observed in the third new yeast, Candida chrysomelidarumsp. nov. (NRRL Y-27749(T)). A fourth isolate, NRRL Y-27752, was not significantly distinct from Metschnikowia viticola and Candida kofuensis to be described as a new species. Phylogenetic analysis of the D1/D2 loop sequences placed M. noctiluminum within the M. viticola clade, while C. chrysomelidarum was a sister taxon of Candida rancensis. Metschnikowia corniflorae was phylogenetically distinct from other new species and fell outside of the large-spored Metschnikowia group.

  15. Aspergillus pragensis sp. nov. discovered during molecular reidentification of clinical isolates belonging to Aspergillus section Candidi.

    PubMed

    Hubka, Vit; Lyskova, Pavlina; Frisvad, Jens C; Peterson, Stephen W; Skorepova, Magdalena; Kolarik, Miroslav

    2014-08-01

    The identity of nine clinical isolates recovered from Czech patients and presumptively identified as Aspergillus sp. section Candidi based on colony morphology was revised using sequences of β-tubulin, calmodulin gene sequence, and internal transcribed spacer rDNA. Six isolates were from suspected and proven onychomycosis, one from otitis externa, and two associated with probable invasive aspergillosis. The results showed that one Aspergillus candidus isolate was the cause of otitis externa, and both isolates obtained from sputa of patients with probable invasive aspergillosis were reidentified as A. carneus (sect. Terrei) and A. flavus (sect. Flavi). Three isolates from nail scrapings were identified as A. tritici, a verified agent of nondermatophyte onychomycosis. One isolate from toenail was determined to be A. candidus and the two isolates belonged to a hitherto undescribed species, Aspergillus pragensis sp. nov. This species is well supported by phylogenetic analysis based on β-tubulin and calmodulin gene and is distinguishable from other members of sect. Candidi by red-brown reverse on malt extract agar, slow growth on Czapek-Dox agar and inability to grow at 37°C. A secondary metabolite analysis was also provided with comparison of metabolite spectrum to other species. Section Candidi now encompasses five species for which a dichotomous key based on colony characteristics is provided. All clinical isolates were tested for susceptibilities to selected antifungal agents using the Etest and disc diffusion method. Overall sect. Candidi members are highly susceptible to common antifungals.

  16. Isolation and characterization of "Methanosphaera cuniculi" sp. nov.

    PubMed Central

    Biavati, B; Vasta, M; Ferry, J G

    1988-01-01

    A nonmotile, gram-positive, spherical organism was isolated from the intestinal tracts of rabbits. Both hydrogen and methanol were required for growth. No methane was produced from hydrogen-carbon dioxide, formate, acetate, methylamines, ethanol, or isopropanol. The optimum pH was 6.8, and the optimum temperature was 35 to 40 degrees C. The DNA G+C content is 23 mol%. The pseudomurein cell wall contained serine. These characteristics and the immunological fingerprinting results are consistent with its placement in the genus Methanosphaera as a new species. Images PMID:3132100

  17. Rickettsia lusitaniae sp. nov. isolated from the soft tick Ornithodoros erraticus (Acarina: Argasidae).

    PubMed

    Milhano, Natacha; Palma, Mariana; Marcili, Arlei; Núncio, Maria Sofia; de Carvalho, Isabel Lopes; de Sousa, Rita

    2014-05-01

    In this study a novel Rickettsia from the spotted fever group, isolated from Ornithodoros erraticus soft ticks collected from pigpens in the south of Portugal, is described. After initial screening revealed Rickettsia-positive ticks, isolation attempts were then performed. Successful isolates were achieved by shell-vial technique using Vero E6 cells at 28°C. Molecular characterization of the isolate was performed based on analysis of five rickettsial genes gltA, ompA, ompB, sca1 and htr with their subsequent concatenation along with other rickettsial species resulting in a clustering of the new isolate with Rickettsia felis and Rickettsia hoogstraalii. The degree of nucleotide sequence similarity with other rickettsiae fulfills the criteria for classification of our isolate as a novel species. The name Rickettsia lusitaniae sp. nov. (=CEVDI PoTiRo) is proposed for this new species found in O. erraticus.

  18. Isolation and Molecular Characterization of Five Marine Cyanophages Propagated on Synechococcus sp. Strain WH7803

    PubMed Central

    Wilson, William H.; Joint, Ian R.; Carr, Noel G.; Mann, Nicholas H.

    1993-01-01

    Five marine cyanophages propagated on Synechococcus sp. strain WH7803 were isolated from three different oceanographic provinces during the months of August and September 1992: coastal water from the Sargasso Sea, Bermuda; Woods Hole harbor, Woods Hole, Mass.; and coastal water from the English Channel, off Plymouth Sound, United Kingdom. The five cyanophage isolates were found to belong to two families, Myoviridae and Styloviridae, on the basis of their morphology observed in the transmission electron microscope. DNA purified from each of the cyanophage isolates was restricted with a selection of restriction endonucleases, and three distinguishably different patterns were observed. DNA isolated from Myoviridae isolates from Bermuda and the English Channel had highly related restriction patterns, as did DNA isolated from Styloviridae isolates from Bermuda and the English Channel. DNA isolated from the Myoviridae isolate from Woods Hole had a unique restriction pattern. The genome size for each of the Myoviridae isolates was ca. 80 to 85 kb, and it was ca. 90 to 100 kb for each of the Styloviridae isolates. Southern blotting analysis revealed that there was a limited degree of homology among all cyanophage DNAs probed, but clear differences were observed between cyanophage DNA from the Myoviridae and that from the Styloviridae isolates. Polypeptide analysis revealed a clear difference between Myoviridae and Styloviridae polypeptide profiles, although the major, presumably structural, protein in each case was ca. 53 to 54 kDa. Images PMID:16349088

  19. Maribacter gen. nov., a new member of the family Flavobacteriaceae, isolated from marine habitats, containing the species Maribacter sedimenticola sp. nov., Maribacter aquivivus sp. nov., Maribacter orientalis sp. nov. and Maribacter ulvicola sp. nov.

    PubMed

    Nedashkovskaya, Olga I; Kim, Seung Bum; Han, Suk Kyun; Lysenko, Anatoly M; Rohde, Manfred; Rhee, Moon-Soo; Frolova, Galina M; Falsen, Enevold; Mikhailov, Valery V; Bae, Kyung Sook

    2004-07-01

    Six novel gliding, heterotrophic, Gram-negative, yellow-pigmented, aerobic, oxidase- and catalase-positive bacteria were isolated from the green alga Ulva fenestrata, sea water and a bottom sediment sample collected in the Gulf of Peter the Great, Sea of Japan. 16S rRNA gene sequence analysis revealed that the strains studied were members of the family Flavobacteriaceae. On the basis of their phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, the novel bacteria have been assigned to the new genus Maribacter gen. nov., as Maribacter sedimenticola sp. nov., Maribacter orientalis sp. nov., Maribacter aquivivus sp. nov. and Maribacter ulvicola sp. nov., with the type strains KMM 3903T (=KCTC 12966T=CCUG 47098T), KMM 3947T (=KCTC 12967T=CCUG 48008T), KMM 3949T (=KCTC 12968T=CCUG 48009T) and KMM 3951T (=KCTC 12969T=DSM 15366T), respectively.

  20. Jiangella mangrovi sp. nov., isolated from mangrove soil.

    PubMed

    Suksaard, Paweena; Duangmal, Kannika; Srivibool, Rattanaporn; Xie, Qingyi; Hong, Kui; Pathom-aree, Wasu

    2015-08-01

    An aerobic, Gram-stain-positive actinomycete, designated strain 3SM4-07T, was characterized using a polyphasic taxonomic approach. The strain produced branching mycelium which fragmented into short or elongated rods. The whole-cell hydrolysates contained ll-2,6-diaminopimelic acid as the diagnostic diamino acid, with glucose and ribose as the main sugars. The predominant cellular fatty acids were anteiso-C15  :  0, iso-C15  :  0 and iso-C16  :  0.The predominant menaquinone was MK-9(H4). Phospholipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol and phosphatidylinositol mannoside. Mycolic acids were absent. The DNA G+C content was 72.3 mol%. Strain 3SM4-07T formed a phylogenetic line within the genus Jiangella and its 16S rRNA gene sequence was related most closely to Jiangella alkaliphila D8-87T (99.0% similarity), Jiangella muralis 15-Je-017T (98.8%), Jiangella alba YIM 61503T (98.6%) and Jiangella gansuensis YIM 002T (98.6%). However, mean DNA-DNA hybridization values revealed that strain 3SM4-07T differed from the closest species previously described in this genus. Data from phenotypic, chemotaxonomic and molecular analyses between strain 3SM4-07T and recognized species of the genus Jiangella indicate that strain 3SM4-07T is a representative of a novel species of the genus Jiangella, for which the name Jiangella mangrovi sp. nov. is proposed. The type strain is 3SM4-07T ( = BCC 60398T = NBRC 109648T). PMID:25948618

  1. Flavobacterium tistrianum sp. nov., a gliding bacterium isolated from soil.

    PubMed

    Suwannachart, Chatrudee; Rueangyotchanthana, Kanjana; Srichuay, Suksan; Pheng, Sophea; Fungsin, Bundit; Phoonsiri, Chantara; Kim, Song-Gun

    2016-06-01

    A novel gliding bacterial strain, GB 56.1T, was obtained from soil at the Sakaerat Biosphere Reserve, in Nakhon Ratchasima province, Thailand; the strain was characterized using a polyphasic approach. Cells were Gram-stain-negative, yellow, rod shaped and devoid of flagella, but showed gliding motility. Phylogenetic analysis based on 16S rRNA gene sequences found that GB 56.1T was a member of the genus Flavobacterium and that the strain shared the highest sequence similarities with Flavobacterium nitrogenifigens (98.4 %), Flavobacterium anhuiense(98.3 %) and Flavobacterium ginsenosidimutans (97.9 %). The similarities of the sequences of all other species of the genus Flavobacterium were below 97.4 %. The major respiratory quinone of strain GB 56.1T was MK-6; fatty acids were iso-C15:0, C16:1ω6c/C16:1ω7c, C16:0 and C16:0 3-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylserine, an unidentified amino lipid and four polar lipids. The DNA G+C content of this strain was 34.2 mol%. The DNA-DNA relatedness of GB 56.1T was highest against F.anhuiense, with a value of 37.6 %. On the basis of morphological, physiological and chemotaxonomic characteristics, DNA-DNA hybridization relatedness and 16S rRNA gene sequence analysis, we conclude that strain GB 56.1T represents a novel species, for which the name Flavobacterium tistrianum sp. nov. is proposed. The type strain is GB 56.1T (=TISTR 1612T =KCTC 42679T). PMID:26970735

  2. Morphological and molecular characterization of a fungus, Hirsutella sp., isolated from planthoppers and psocids in Argentina.

    PubMed

    Toledo, Andrea V; Simurro, María E; Balatti, Pedro A

    2013-01-01

    A mycosed planthopper, Oliarus dimidiatus Berg (Hemiptera: Cixiidae), and two psocids, Heterocaecilius sp. (Psocodea: Pseudocaeciliidae) and Ectopsocus sp. (Ectopsocidae), were collected from Los Hornos and La Plata, Buenos Aires, Argentina between February and September 2007. Observations of mycelia growing on the host revealed that the putative fungal parasite had synnemata supporting monophialidic conidiogenous cells. Likewise, in vitro fungal cultures presented characteristics typical of the fungus Hirsutella citriformis Speare (Ascomycota: Hypocreales: Clavicipitaceae). The identity of the isolated fungi characterized based on morphological aspects was complemented by means of the internal transcribed spacer sequences. The sequences of both isolates were highly homologous to those of Cordyceps sp. (Fries) Link and Ophiocordyceps sinensis (Berkely) G.H. Sung, J.M. Sung, Hywel-Jones, and Spatafora (Ophiocordycipitaceae). We additionally confirmed that both isolates had the ability to infect and kill adults of Delphacodes kuscheli Fennah (Hemiptera: Delphacidae) after 10 days. Therefore, based on the morphology of the isolated fungi, their ribosomal internal transcribed spacer sequence, and their ability to parasite insects, we conclude that the fungi isolated belong to the genus Hirsutella and might have biotechnological potential. PMID:23885970

  3. Morphological and Molecular Characterization of a Fungus, Hirsutella sp., Isolated from Planthoppers and Psocids in Argentina

    PubMed Central

    Toledo, Andrea V.; Simurro, María E.; Balatti, Pedro A.

    2013-01-01

    A mycosed planthopper, Oliarus dimidiatus Berg (Hemiptera: Cixiidae), and two psocids, Heterocaecilius sp. (Psocodea: Pseudocaeciliidae) and Ectopsocus sp. (Ectopsocidae), were collected from Los Hornos and La Plata, Buenos Aires, Argentina between February and September 2007. Observations of mycelia growing on the host revealed that the putative fungal parasite had synnemata supporting monophialidic conidiogenous cells. Likewise, in vitro fungal cultures presented characteristics typical of the fungus Hirsutella citriformis Speare (Ascomycota: Hypocreales: Clavicipitaceae). The identity of the isolated fungi characterized based on morphological aspects was complemented by means of the internal transcribed spacer sequences. The sequences of both isolates were highly homologous to those of Cordyceps sp. (Fries) Link and Ophiocordyceps sinensis (Berkely) G.H. Sung, J.M. Sung, Hywel-Jones, and Spatafora (Ophiocordycipitaceae). We additionally confirmed that both isolates had the ability to infect and kill adults of Delphacodes kuscheli Fennah (Hemiptera: Delphacidae) after 10 days. Therefore, based on the morphology of the isolated fungi, their ribosomal internal transcribed spacer sequence, and their ability to parasite insects, we conclude that the fungi isolated belong to the genus Hirsutella and might have biotechnological potential. PMID:23885970

  4. Detection of Leptomonas sp. parasites in clinical isolates of Kala-azar patients from India

    PubMed Central

    Srivastava, Pankaj; Prajapati, Vijay Kumar; Vanaerschot, Manu; Van der Auwera, Gert; Dujardin, Jean Claude; Sundar, Shyam

    2010-01-01

    We report here nine unusual cases of Kala-azar, of which parasites were isolated and found by 18S rRNA gene sequencing to be most similar to Leptomonas species. One of these isolates was used to inoculate Balb/c mice; organs were collected and directly submitted to a genus-specific rDNA-ITS1 PCR analysis: this revealed the presence of both Leptomonas sp. and Leishmania donovani. Therefore, we conclude that there was a mixed infection of Leptomonas sp. and L. donovani in this isolate. We consider that mixed infection may be present in the patients themselves, Leptomonas persisting in them because of the immuno-suppression associated with Kala-azar. PMID:20633704

  5. Beta-lactamase-free penicillin amidase from Alcaligenes sp.: isolation strategy, strain characteristics, and enzyme immobilization.

    PubMed

    Pal, A; Samanta, T B

    1999-11-01

    Isolation and characterization of a beta-lactamase (EC 3.5.2.6)-free, penicillin amidase (penicillin amidohydrolase, EC 3.5.1. 11)-producing organism is reported. The test strain was isolated by an enrichment technique with a substrate other than penicillins. The isolated strain belongs to the genus Alcaligenes. Phenylacetic acid was found to be the inducer of penicillin amidase. The amidase has a broad substrate spectrum. It is very active against penicillin G and semisynthetic cephalosporins, whereas penicillin V and semisynthetic penicillins acted moderately as a substrate. Immobilized cells of Alcaligenes sp. were shown to act as a reversible enzyme. PMID:10489431

  6. Isolation and characterization of a thermophilic Bacillus sp. with protease activity isolated from hot spring of Tarabalo, Odisha, India

    PubMed Central

    Panda, Mrunmaya Kumar; Sahu, Mahesh Kumar; Tayung, Kumananda

    2013-01-01

    Background and Objectives Thermophilic bacteria are less studied but important group of microorganisms due to their ability to produce industrial enzymes. Materials and Methods In this study, thermophilic bacteria were isolated from hot spring of Tarabalo, India. A bacterium that could tolerate high temperatures was characterized by morphology, biochemistry and sequencing of its 16S rRNA gene. The isolate was screened for protease and amylase activity. Phylogenetic affiliations and G+C content of the isolate was studied. Results The bacterium with the ability to tolerate high temperatures was identified as Bacillus sp. both by morphology, biochemistry and sequencing of its 16S rRNA gene. BLAST search analysis of the sequence showed maximum identity with Bacillus amyloliquefaciens (99% similarity). Strain exhibited considerable protease activity. Phylogenetic analysis of the isolate revealed close affiliation with thermophilic Bacillus species. The G+C content was found to be 54.7%. Conclusion The study confirmed that the isolated Bacillus sp. to be a true thermophile and could be a source of thermostable protease which can be exploited for pharmaceutical and industrials applications. PMID:23825735

  7. Corynebacterium timonense sp. nov. and Corynebacterium massiliense sp. nov., isolated from human blood and human articular hip fluid.

    PubMed

    Merhej, Vicky; Falsen, Enevold; Raoult, Didier; Roux, Véronique

    2009-08-01

    Gram-positive, facultatively anaerobic, rod-shaped bacteria were isolated from the blood of a patient with endocarditis (strain 5401744T) and from the hip joint fluid of a patient with an infected orthopaedic prosthesis (strain 5402485T). These strains were characterized by using a polyphasic taxonomic approach. Based on cellular morphology and biochemical criteria the two isolates were tentatively assigned to the genus Corynebacterium, although they did not correspond to any recognized species. The predominant fatty acids were a mix of C18:2omega6,9c and anteiso-C18:0 (32.1% of the total), C16:0 (26.3%) and C18:1omega9c (22.5%) for strain 5402485T and C18:1omega9c (36.4%), C17:1omega9c (27.1%) and C16:0 (10.9%) for strain 5401744T. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that strain 5401744T was closely related to the type strains of Corynebacterium auris, Corynebacterium capitovis, Corynebacterium lipophiloflavum and Corynebacterium mycetoides (97.0, 96.6, 96.5 and 96.3% similarity, respectively) and strain 5402485T was closely related to the type strains of Corynebacterium macginleyi, Corynebacterium accolens, Corynebacterium tuberculostearicum, Corynebacterium confusum, Corynebacterium mastitidis and Corynebacterium renale (95.6, 95.3, 95.3, 94.5, 94.0 and 93.5%, respectively). On the basis of phenotypic data and phylogenetic inference, these isolates are considered to represent two novel species of the genus Corynebacterium, for which the names Corynebacterium timonense sp. nov. (type strain, 5401744T=CSUR P20T=CIP 109424T=CCUG 53856T) and Corynebacterium massiliense sp. nov. (type strain, 5402485T=CSUR P19T=CIP 109423T=CCUG 53857T) are proposed.

  8. Rhodotorula psychrophila sp. nov., Rhodotorula psychrophenolica sp. nov. and Rhodotorula glacialis sp. nov., novel psychrophilic basidiomycetous yeast species isolated from alpine environments.

    PubMed

    Margesin, Rosa; Fonteyne, Pierre-Alain; Schinner, Franz; Sampaio, José Paulo

    2007-09-01

    Three novel psychrophilic species of the genus Rhodotorula are described. Rhodotorula psychrophila sp. nov. (type strain PB19(T)=CBS 10440(T)=DSM 18768(T)), Rhodotorula psychrophenolica sp. nov. (type strain AG21(T)=CBS 10438(T)=DSM 18767(T)) and Rhodotorula glacialis sp. nov. (type strain A19(T)=CBS 10436(T)=DSM 18766(T)) were isolated from soil collected from an alpine railway area, from mud in the thawing zone of a glacier foot and from glacier cryoconite, respectively. All three species have been assigned to the genus Rhodotorula on the basis of molecular sequence data and physiological and morphological properties. Rhodotorula psychrophila is not able to grow at temperatures above 15 degrees C. Rhodotorula psychrophenolica and Rhodotorula glacialis degrade high concentrations of phenol (up to 12.5 and 5 mM, respectively) as the sole carbon source at 10 degrees C. Sequence analyses of the 26S rDNA D1/D2 regions indicated that the novel species are phylogenetically related and belong to a clade that includes other psychrophilic yeasts.

  9. Rasamsonia pulvericola sp. nov., isolated from house dust.

    PubMed

    Tanney, Joey B; Seifert, Keith A

    2013-12-01

    In the course of a global survey of the indoor mycobiota, we sampled and analysed settled dust from 87 buildings from 14 countries, using both a modified dilution-to-extinction method and 454-pyrosequencing. Rasamsonia is a recently established genus including thermotolerant or thermophilic species, five of which have been isolated from humans, including the emerging pathogen R. argillacea. A new species, R. pulvericola, was recovered from one residence in Songkhla, Thailand, and is morphologically characterised and compared phylogenetically with other members of the genus. Rasamsonia pulvericola forms a clade with R. brevistipitata and shares morphological characters such as usually biverticillate and never terverticillate conidiophores, and subglobose to ellipsoidal conidia. It has a lower maximum growth temperature and is the first mesophilic species added to the genus. The ITS sequence of R. pulvericola was not detected in the 454-pyrosequencing data for Thailand or other countries, but a similar ITS sequence was detected in Micronesia, probably representing another undescribed Rasamsonia species.

  10. Thalassospira australica sp. nov. isolated from sea water.

    PubMed

    Ivanova, Elena P; López-Pérez, Mario; Webb, Hayden K; Ng, Hooi Jun; Dang, Thi Hoang Yen; Zhukova, Natalia V; Mikhailov, Valery V; Crawford, Russell J; Rodriguez-Valera, Francisco

    2016-08-01

    Two Gram-negative, non-pigmented, motile bacteria were isolated from a sea water sample collected at St. Kilda Beach, Port Philip Bay, Victoria, Australia. The two strains were found to grow between 4 and 40 °C, pH 5-10 and tolerate up to 10 % NaCl. A phylogenetic study, based on a 16S rRNA gene sequence analysis indicated that strains NP 3b2(T) and H 94 belong to the genus Thalassospira. The sequence similarity of the 16S rRNA gene between the two new isolates is 99.8 % and between these strains and all validly named Thalassospira species was found to be in the range of 95-99.4 %. The DNA-DNA relatedness between the two strains was found to be 80.2 %, while relatedness with other validly named species of the genus Thalassospira was between 53 and 65 %. The average nucleotide identity (ANI) and the in silico genome-to-genome distance (GGD) between the two bacteria and T. profundimaris WP0211(T), T. xiamenensis M-5(T), 'T. permensis' NBRC 106175(T) and T. lucentensis QMT2(T) was 76-82 % and 21-25 %, respectively. The results of phylogenetic and genomic analysis, together with physiological and biochemical properties, indicated that the two strains represent a new species of the genus Thalassospira. Based on these data, a new species, Thalassospira australica, is proposed with strain NP 3b2(T) (=KMM 6365(T) = JCM 31222(T)) as the type strain. PMID:27180097

  11. Sphingomonas starnbergensis sp. nov., isolated from a prealpine freshwater lake.

    PubMed

    Chen, Hong; Jogler, Mareike; Tindall, Brian J; Klenk, Hans-Peter; Rohde, Manfred; Busse, Hans-Jürgen; Overmann, Jörg

    2013-03-01

    A novel type of freshwater bacterium was isolated from the prealpine mesotrophic Starnberger See (Bavaria, southern Germany). Cells of strain 382(T) were Gram-negative and rod-shaped, motile and creamy-white. The isolate was strictly aerobic, catalase- and oxidase-positive, and grew at pH values of 6-9 (optimum, pH 7) and temperatures of 10-37 °C (optimum, 28 °C). The genomic G+C content of strain 382(T) was 64.1 mol%. Based on 16S rRNA gene sequence analyses, strain 382(T) belongs to the family Sphingomonadaceae and clusters within the genus Sphingomonas. Sphingomonas histidinilytica UM 2(T) and Sphingomonas wittichii DSM 6014(T) were the closest relatives, as indicated by the highest 16S rRNA gene sequence similarities (97.1 % and 96.8 %, respectively). Sphingomonas paucimobilis DSM 1098(T) (the type species of the genus Sphingomonas) exhibited 95.3 % sequence similarity. This affiliation of strain 382(T) to the genus Sphingomonas is confirmed by the presence of Q-10 as the major respiratory quinone, two sphingoglycolipids, C14 : 0 2-OH as the major 2-hydroxy fatty acid and sym-homospermidine as the major polyamine. The main cellular fatty acids of strain 382(T) were C18 : 1ω7c (39 %), C16 : 1ω7c (21 %), C16 : 0 (10 %) and C14 : 0 2-OH (10 %). Based on the phylogenetic distance from other species of the genus Sphingomonas and its unusually high C16 : 1ω7c content, strain 382(T) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas starnbergensis is proposed. The type strain is 382(T) ( = DSM 25077(T)  = LMG 26763(T)).

  12. Bacillus rubiinfantis sp. nov. strain mt2T, a new bacterial species isolated from human gut

    PubMed Central

    Tidjiani Alou, M.; Rathored, J.; Khelaifia, S.; Michelle, C.; Brah, S.; Diallo, B.A.; Raoult, D.; Lagier, J.-C.

    2015-01-01

    Bacillus rubiinfantis sp. nov. strain mt2T is the type strain of B. rubiinfantis sp. nov., isolated from the fecal flora of a child with kwashiorkor in Niger. It is Gram-positive facultative anaerobic rod belonging to the Bacillaceae family. We describe the features of this organism alongside the complete genome sequence and annotation. The 4 311 083 bp long genome (one chromosome but no plasmid) contains 4028 protein-coding gene and 121 RNA genes including nine rRNA genes. PMID:27076912

  13. Bacillus niameyensis sp. nov., a new bacterial species isolated from human gut

    PubMed Central

    Tidjani Alou, M.; Rathored, J.; Traore, S.I.; Khelaifia, S.; Michelle, C.; Brah, S.; Diallo, B.A.; Raoult, D.; Lagier, J.-C.

    2015-01-01

    Bacillus niameyensis sp. nov. strain SIT3T (= CSUR P1266 = DSM 29725) is the type strain of B. niameyensis sp. nov. This Gram-positive strain was isolated from the digestive flora of a child with kwashiorkor and is a facultative anaerobic rod and a member of the Bacillaceae family. This organism is hereby described alongside its complete genome sequence and annotation. The 4  286  116 bp long genome (one chromosome but no plasmid) contains 4130 protein-coding and 66 RNA genes including five rRNA genes. PMID:27076913

  14. Alteromonas australica sp. nov., isolated from the Tasman Sea.

    PubMed

    Ivanova, Elena P; Ng, Hooi Jun; Webb, Hayden K; Kurilenko, Valeriya V; Zhukova, Natalia V; Mikhailov, Valery V; Ponamoreva, Olga N; Crawford, Russell J

    2013-04-01

    A non-pigmented, motile, Gram-negative bacterium designated H 17(T) was isolated from a seawater sample collected in Port Phillip Bay (the Tasman Sea, Pacific Ocean). The new organism displayed optimal growth between 4 and 37 °C, was found to be neutrophilic and slightly halophilic, tolerating salt water environments up to 10 % NaCl. Strain H 17(T) was found to be able to degrade starch and Tween 80 but unable to degrade gelatin or agar. Phosphatidylglycerol (27.7 %) and phosphatidylethanolamine (72.3 %) were found to be the only associated phospholipids. The major fatty acids identified are typical for the genus Alteromonas and include C16:0, C16:1ω7, C17:1ω8 and C18:1ω7. The G+C content of the DNA was found to be 43.4 mol%. A phylogenetic study, based on the 16S rRNA gene sequence analysis and Multilocus Phylogenetic Analysis, clearly indicated that strain H 17(T) belongs to the genus Alteromonas. The DNA-DNA relatedness between strain H 17(T) and the validly named Alteromonas species was between 30.7 and 46.4 mol%. Based on these results, a new species, Alteromonas australica, is proposed. The type strain is H 17(T) (= KMM 6016(T) = CIP 109921(T)). PMID:23291832

  15. Alteromonas australica sp. nov., isolated from the Tasman Sea.

    PubMed

    Ivanova, Elena P; Ng, Hooi Jun; Webb, Hayden K; Kurilenko, Valeriya V; Zhukova, Natalia V; Mikhailov, Valery V; Ponamoreva, Olga N; Crawford, Russell J

    2013-04-01

    A non-pigmented, motile, Gram-negative bacterium designated H 17(T) was isolated from a seawater sample collected in Port Phillip Bay (the Tasman Sea, Pacific Ocean). The new organism displayed optimal growth between 4 and 37 °C, was found to be neutrophilic and slightly halophilic, tolerating salt water environments up to 10 % NaCl. Strain H 17(T) was found to be able to degrade starch and Tween 80 but unable to degrade gelatin or agar. Phosphatidylglycerol (27.7 %) and phosphatidylethanolamine (72.3 %) were found to be the only associated phospholipids. The major fatty acids identified are typical for the genus Alteromonas and include C16:0, C16:1ω7, C17:1ω8 and C18:1ω7. The G+C content of the DNA was found to be 43.4 mol%. A phylogenetic study, based on the 16S rRNA gene sequence analysis and Multilocus Phylogenetic Analysis, clearly indicated that strain H 17(T) belongs to the genus Alteromonas. The DNA-DNA relatedness between strain H 17(T) and the validly named Alteromonas species was between 30.7 and 46.4 mol%. Based on these results, a new species, Alteromonas australica, is proposed. The type strain is H 17(T) (= KMM 6016(T) = CIP 109921(T)).

  16. Mycetocola manganoxydans sp. nov., an actinobacterium isolated from the Taklamakan desert.

    PubMed

    Luo, Xuesong; Wang, Jun; Zeng, Xian-Chun; Wang, Yaqiong; Zhou, Lingli; Nie, Yao; Dai, Jun; Fang, Chengxiang

    2012-12-01

    Two Gram-staining-positive, aerobic, non-sporulating bacteria forming short rods and cocci, designated MB1-7 and MB1-14(T), were isolated from the Taklamakan desert. The isolates could oxidize manganese (II) ions. The isolates shared 95.4-98.0% 16S rRNA gene sequence similarity with members of the genus Mycetocola. Although the isolates possessed chemotaxonomic properties similar to those of Mycetocola reblochoni, they were readily distinguished from this taxon by DNA-DNA relatedness and phenotypic characters. According to morphological and chemotaxonomic characteristics, as well as phylogenetic analysis and DNA-DNA relatedness, the two isolates represent a novel species of the genus Mycetocola, for which the name Mycetocola manganoxydans sp. nov. is proposed. The type strain is MB1-14(T) ( = CCTCC AB 209002(T)  = KCTC 19753(T)).

  17. Spirosoma aerophilum sp. nov., isolated from an air sample.

    PubMed

    Kim, Soo-Jin; Ahn, Jae-Hyung; Weon, Hang-Yeon; Hong, Seung-Beom; Seok, Soon-Ja; Kim, Jeong-Seon; Kwon, Soon-Wo

    2016-06-01

    A rod-shaped, yellow, Gram-stain-negative, non-flagellated, aerobic bacterium, designated 5516J-17T, was isolated from an air sample collected from Jeju Island, Republic of Korea. It grew in the temperature range of 10-37 °C (optimum 28-30 °C), pH 6.0-11.0 (optimum, pH 7.0) and 0-1 % NaCl (w/v). Phylogenetic trees generated using 16S rRNA gene sequences revealed that strain 5516J-17T belongs to the genus Spirosoma, showing 96.9 % sequence similarity to the most closely related species, Spirosoma linguale DSM 74T. The cellular fatty acids comprised large amounts (>10 % of total fatty acids) of summed feature 3 (C16:1ω7c and/or C16:1ω6c) and C16:1ω5c, and moderate amounts (5-10 % of total fatty acids) of iso-C17:0 3-OH, iso-C15:0 and C16:0. The DNA G+C content was 55.7 mol % and MK-7 was the predominant isoprenoid quinone. Polar lipids were phosphatidylethanolamine, two unknown aminophospholipids, one unknown aminolipid and one unknown lipid. On the basis of this phenotypic and polyphasic taxonomy study, it is suggested that strain 5516J-17T represents a novel species within the genus Spirosoma, with the proposed name Spirosoma aerophilum. The type strain is 5516J-17T (= KACC 17323T = DSM 28388T = JCM 19950T). PMID:27031168

  18. Paralcaligenes ginsengisoli sp. nov., isolated from ginseng cultivated soil.

    PubMed

    Kang, Jong-Pyo; Nguyen, Ngoc-Lan; Kim, Yeon-Ju; Hoang, Van-An; Bae, Kwi-Sik; Yang, Deok-Chun

    2015-09-01

    A novel bacterial strain DCY104(T) isolated from soil of a ginseng field in Yeoncheon County, Republic of Korea is described in this study. Cells were short rod-shaped, motile by mean of one polar flagellum, strictly aerobic, Gramreaction negative, oxidase and catalase-positive. 16S rRNA gene sequence analysis showed that strain DCY104(T) shared highest similarity 98.2 % to Paralcaligenes ureilyticus GR24-5(T), and from 97.7 to 97.1 % with other type strains belong to the genera Candidimonas, Pusillimonas and Parapusillimonas Otherwise, phylogenetic trees analyses indicated that strain DCY104(T) belongs to a single group with P. ureilyticus GR24-5(T) that was distinct to other genera. The major polar lipids were phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The major cellular fatty acids consisted of C16:0, cyclo-C17:0, and summed feature 8 (comprising C18:1 ω7c and/or C18:1 ω6c). The predominant polyamine was putrescine. The ubiquinone was Q-8. The genomic DNA G+C content was 55.9 mol%. These data in combination with the presence of one polar flagellum and positive activity of urease confirmed the placement of strain DCY104(T) in the genus Paralcaligenes. DNA-DNA relatedness between strain DCY104(T) and P. ureilyticus KACC 13888(T) was 40 %. The differences in the profiles of polar lipids, fatty acids and phenotypic characteristics in combination with DNA-DNA relatedness delineated strain DCY104(T) and P. ureilyticus KACC 13888(T). In summary, taxonomic analyses in this study demonstrated that strain DCY104(T) represents a novel species within the genus Paralcaligenes, for which we propose the name Paralcaligenes ginsengisoli. The type strain is DCY104(T) (= KCTC 42406(T) = JCM 30746(T)).

  19. Rhodococcus nanhaiensis sp. nov., an actinobacterium isolated from marine sediment.

    PubMed

    Li, Jie; Zhao, Guo-Zhen; Long, Li-Juan; Wang, Fa-Zuo; Tian, Xin-Peng; Zhang, Si; Li, Wen-Jun

    2012-10-01

    In this study, two strains (SCSIO 10187(T) and SCSIO 10197) were isolated from a sediment sample collected from the South China Sea and characterized by using a polyphasic approach. Growth was observed at 15-35 °C (optimum 28 °C) and pH 5.0-8.0 (optimum pH 6.0). Based on 16S rRNA gene sequence analysis, the strains were identified as members of the genus Rhodococcus. Phylogenetic analysis showed that the two strains clustered together and the 16S rRNA gene sequence similarities between them and other members of the genus Rhodococcus were 93.2-97.7 %. The menaquinone type was MK-8(H(2)). Major cellular fatty acids were C(16 : 0), C(18 : 1)ω9c, C(17 : 0), 10-methyl C(18 : 0), C(18 : 0), C(19 : 0) and C(17 : 1)ω8c. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The DNA G+C contents of strains SCSIO 10187(T) and SCSIO 10197 were 63.7 and 63.2 mol%, respectively. The combined genotypic and phenotypic data showed that the two strains represent a novel species of the genus Rhodococcus, for which the name Rhodococcus nanhaiensis is proposed; the type strain is SCSIO 10187(T) ( = DSM 45608(T) = CCTCC AB 2011024(T)), with SCSIO 10197 ( = DSM 45609 = CCTCC AB 2011025) as a reference strain.

  20. Bifidobacterium myosotis sp. nov., Bifidobacterium tissieri sp. nov. and Bifidobacterium hapali sp. nov., isolated from faeces of baby common marmosets (Callithrix jacchus L.).

    PubMed

    Michelini, Samanta; Oki, Kaihei; Yanokura, Emiko; Shimakawa, Yasuhisa; Modesto, Monica; Mattarelli, Paola; Biavati, Bruno; Watanabe, Koichi

    2016-01-01

    In a previous study on bifidobacterial distribution in New World monkeys, six strains belonging to the Bifidobacteriaceae were isolated from faecal samples of baby common marmosets (Callithrix jacchus L.). All the isolates were Gram-positive-staining, anaerobic, asporogenous and fructose-6-phosphate phosphoketolase-positive. Comparative analysis of 16S rRNA gene sequences revealed relatively low levels of similarity (maximum identity 96 %) to members of the genus Bifidobacterium, and placed the isolates in three independent clusters: strains of cluster I (MRM_5.9T and MRM_5.10) and cluster III (MRM_5.18T and MRM_9.02) respectively showed 96.4 and 96.7 % 16S rRNA gene sequence similarity to Bifidobacterium callitrichos DSM 23973T, while strains of cluster II (MRM_8.14T and MRM_9.14) showed 95.4 % similarity to Bifidobacterium stellenboschense DSM 23968T. Phylogenetic analysis of partial hsp60 and clpC gene sequences supported an independent phylogenetic position of each cluster from each other and from the related type strains B. callitrichos DSM 23973T and B. stellenboschense DSM 23968T. Clusters I, II and III respectively showed DNA G+C contents of 64.9-65.1, 56.4-56.7 and 63.1-63.7 mol%. The major cellular fatty acids of MRM_5.9T were C14 : 0, C16 : 0 and C18 : 1ω9c dimethylacetal, while C16 : 0 was prominent in strains MRM_5.18T and MRM_8.14T, followed by C18 : 1ω9c and C14 : 0. Biochemical profiles and growth parameters were recorded for all the isolates. Based on the data provided, the clusters represent three novel species, for which the names Bifidobacterium myosotis sp. nov. (type strain MRM_5.9T = DSM 100196T = JCM 30796T), Bifidobacterium hapali sp. nov. (type strain MRM_8.14T = DSM 100202T = JCM 30799T) and Bifidobacterium tissieri sp. nov. (type strain MRM_5.18T = DSM 100201T = JCM 30798T) are proposed. PMID:26515885

  1. H2, N2, and O2 metabolism by isolated heterocysts from Anabaena sp. strain CA.

    PubMed Central

    Smith, R L; Kumar, D; Zhang, X K; Tabita, F R; Van Baalen, C

    1985-01-01

    Metabolically active heterocysts isolated from wild-type Anabaena sp. strain CA showed high rates of light-dependent acetylene reduction and hydrogen evolution. These rates were similar to those previously reported in heterocysts isolated from the mutant Anabaena sp. strain CA-V possessing fragile vegetative cell walls. Hydrogen production was observed with isolated heterocysts. The ratio of C2H4 to H2 produced ranged from 0.9 to 1.2, and H2 production exhibited unique biphasic kinetics consisting of a 1 to 2-min burst of hydrogen evolution followed by a lower, steady-state rate of hydrogen production. This burst was found to be dependent upon the length of the dark period immediately preceding illumination and may be related to dark-to-light ATP transients. The presence of 100 nM NiCl2 in the growth medium exerted an effect on both acetylene reduction and hydrogen evolution in the isolated heterocysts from strain CA. H2-stimulated acetylene reduction was increased from 2.0 to 3.2 mumol of C2H4 per mg (dry weight) per h, and net hydrogen production was abolished. A phenotypic Hup- mutant (N9AR) of Anabaena sp. strain CA was isolated which did not respond to nickel. In isolated heterocysts from N9AR, ethylene production rates were the same under both 10% C2H2-90% Ar and 10% C2H2-90% H2 with or without added nickel, and net hydrogen evolution was not affected by the presence of 100 nM Ni2+. Isolated heterocysts from strain CA were shown to have a persistent oxygen uptake of 0.7 mumol of O2 per mg (dry weight) per h, 35% of the rate of whole filaments, at air saturating O2 levels, indicating that O2 impermeability is not a requirement for active heterocysts. PMID:3921524

  2. Streptococcus tangierensis sp. nov. and Streptococcus cameli sp. nov., two novel Streptococcus species isolated from raw camel milk in Morocco.

    PubMed

    Kadri, Zaina; Vandamme, Peter; Ouadghiri, Mouna; Cnockaert, Margo; Aerts, Maarten; Elfahime, El Mostafa; Farricha, Omar El; Swings, Jean; Amar, Mohamed

    2015-02-01

    Biochemical and molecular genetic studies were performed on two unidentified Gram-stain positive, catalase and oxidase negative, non-hemolytic Streptococcus-like organisms recovered from raw camel milk in Morocco. Phenotypic characterization and comparative 16S rRNA gene sequencing demonstrated that the two strains were highly different from each other and that they did not correspond to any recognized species of the genus Streptococcus. Phylogenetic analysis based on 16S rRNA gene sequences showed the unidentified organisms each formed a hitherto unknown sub-line within the genus Streptococcus, displaying a close affinity with Streptococcus moroccensis, Streptococcus minor and Streptococcus ovis. DNA G+C content determination, MALDI-TOF mass spectrometry and biochemical tests demonstrated the bacterial isolates represent two novel species. Based on the phenotypic distinctiveness of the new bacteria and molecular genetic evidence, it is proposed to classify the two strains as Streptococcus tangierensis sp. nov., with CCMM B832(T) (=LMG 27683(T)) as the type strain, and Streptococcus cameli sp. nov., with CCMM B834(T) (=LMG 27685(T)) as the type strain.

  3. Wickerhamomyces edaphicus sp. nov. and Pichia jaroonii sp. nov., two ascomycetous yeast species isolated from forest soil in Thailand.

    PubMed

    Limtong, Savitree; Yongmanitchai, Wichien; Kawasaki, Hiroko; Fujiyama, Kazuhito

    2009-05-01

    Four yeast strains were isolated from soil in a mixed deciduous forest in Amphoe Wang Nam Khiao, Nakhon Ratchasima province, Thailand. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, and the sequence analyses of the D1/D2 domain of the large-subunit (LSU) rRNA gene, small-subunit rRNA gene and internal transcribed spacer (ITS) region, the three strains (S-29, S-63 and S-80) were found to represent a single species of the genus Wickerhamomyces, which were named Wickerhamomyces edaphicus sp. nov. The type strain is S-29(T) (BCC 21231(T)=NBRC 101969(T)=CBS 10408(T)). Strain S-75 represented a novel species of the genus Pichia on the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, and the sequence analyses of the D1/D2 domain of the LSU rRNA gene, for which the name Pichia jaroonii sp. nov. is proposed. The type strain is S-75(T) (BCC 23061(T), NRBC 102180(T)=CBS 10930(T)).

  4. Galbibacter marinus sp. nov., isolated from deep-sea sediment.

    PubMed

    Li, Chongping; Lai, Qiliang; Fu, Yuanyuan; Chen, Shuangxi; Shao, Zongze

    2013-04-01

    A taxonomic study was carried out on a novel bacterium, designated strain ck-I2-15(T), which was isolated from deep-sea sediment collected from the South-west Indian Ocean Ridge. Cells of strain ck-I2-15(T) were Gram-reaction-negative, rod-shaped, non-motile, moderately halophilic and capable of denitrification. Growth was observed with 0-9 % (w/v) NaCl and at temperatures of 10-37 °C. The novel strain was unable to degrade gelatin. The dominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0). The major respiratory quinone was MK6 and the polar lipid profile comprised phosphatidylethanolamine, one unidentified phospholipid, two unidentified aminolipids, one unidentified glycolipid and four other unidentified lipids. The G+C content of the genomic DNA was 38 mol%. 16S rRNA gene sequence comparison indicated that strain ck-I2-15(T) was most closely related to Galbibacter mesophilus Mok-17(T) (92.9 % sequence similarity), followed by 'Joostella atrarenae' M1-2 (92.8 %), Joostella marina En5(T) (92.7 %) and Zhouia amylolytica HN-171(T) (91.6 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ck-I2-15(T) formed a clade with the genus Galbibacter, within the family Flavobacteriaceae. Several phenotypic properties allowed strain ck-I2-15(T) to be distinguished from its closest phylogenetic relatives. On the basis of the phenotypic and phylogenetic data, strain ck-I2-15(T) represents a novel species of the genus Galbibacter, for which the name Galbibacter marinus is proposed. The type strain is ck-I2-15(T) ( = CCTCC AB 209062(T) = LMG 25228(T) = MCCC 1A03044(T)).

  5. BbrzSP-32, the first serine protease isolated from Bothrops brazili venom: Purification and characterization.

    PubMed

    Zaqueo, Kayena D; Kayano, Anderson M; Domingos, Thaisa F S; Moura, Laura A; Fuly, André L; da Silva, Saulo L; Acosta, Gerardo; Oliveira, Eliandre; Albericio, Fernando; Zanchi, Fernando B; Zuliani, Juliana P; Calderon, Leonardo A; Stábeli, Rodrigo G; Soares, Andreimar M

    2016-05-01

    Snake venom toxins are related not only in detention, death and the promotion of initial digestion of prey but also due to their different biochemical, structural and pharmacological effects they can result in new drugs. Among these toxins snake venom serine proteases (SVSPs) should be highlighted because they are responsible for inducing changes in physiological functions such as blood coagulation, fibrinolysis, and platelet aggregation. This article presents the first serine protease (SP) isolated from Bothrops brazili: BbrzSP-32. The new SP showed 36 kDa of relative molecular mass and its absolute mass was confirmed by mass spectrometry as 32,520 Da. It presents 79.48% identity when compared to other SVSPs and was able to degrade the α-chain of fibrinogen, in in vitro models, because of this it is considered a SVTLE-A. It showed dose-dependent activity in the process of degradation of fibrin networks demonstrating greater specificity for this activity when compared to its thrombolytic action. BbrzSP-32 demonstrated proteolytic activity on gelatin and chromogenic substrates for serine proteases and thrombin-like enzymes (S-2288 and S-2238 respectively), besides having coagulant activity on human plasma. After pre-incubation with PMSF and benzamidine the coagulant and proteolytic activities on the S-2288 and S-2238 substrates were reduced. BbrzSP-32 shows stability against pH and temperature variations, demonstrating optimum activity between 30 and 40 °C and in the pH range 7.5 to 8.5. A new SP with potential biotechnological application was isolated. PMID:26827743

  6. Streptomyces chiangmaiensis sp. nov. and Streptomyces lannensis sp. nov., isolated from the South-East Asian stingless bee (Tetragonilla collina).

    PubMed

    Promnuan, Yaowanoot; Kudo, Takuji; Ohkuma, Moriya; Chantawannakul, Panuwan

    2013-05-01

    Two novel actinomycetes, strains TA4-1(T) and TA4-8(T,) were isolated from the South-East Asian stingless bee (Tetragonilla collina Smith 1857), collected from Chiang Mai Province, Thailand. The morphological and chemotaxonomic properties of strains TA4-1(T) and TA4-8(T) were consistent with the genus Streptomyces, i.e. the formation of aerial mycelia bearing spiral spore chains, the presence of the ll-isomer of diaminopimelic acid in cell walls, iso- and anteiso-branched fatty acids with carbon chain lengths 14-17 atoms as the major fatty acids and MK-9(H8) as the predominant menaquinone plus minor amounts of MK-9(H6) and MK-9(H10). Analysis of 16S rRNA gene sequences showed that strains TA4-1(T) and TA4-8(T) exhibited 98.8 and 98.1% sequence similarity, respectively, with Streptomyces chromofuscus NRRL B-12175(T) and 98.9% sequence similarity with each other. This study suggested that strains TA4-1(T) and TA4-8(T) were distinct from previously described species of the genus Streptomyces. In addition, the low degrees of DNA-DNA relatedness between the isolates and S. chromofuscus JCM 4354(T) warranted assigning strains TA4-1(T) and TA4-8(T) to two novel species. The names Streptomyces chiangmaiensis sp. nov. (type strain TA4-1(T)  = JCM 16577(T)  = TISTR 1981(T)) and Streptomyces lannensis sp. nov. (type strain TA4-8(T)  = JCM 16578(T)  = TISTR 1982(T)) are proposed. The species names indicate the geographical locations where the stingless bees reside.

  7. Thermotoga profunda sp. nov. and Thermotoga caldifontis sp. nov., anaerobic thermophilic bacteria isolated from terrestrial hot springs.

    PubMed

    Mori, Koji; Yamazoe, Atsushi; Hosoyama, Akira; Ohji, Shoko; Fujita, Nobuyuki; Ishibashi, Jun-ichiro; Kimura, Hiroyuki; Suzuki, Ken-ichiro

    2014-06-01

    Two thermophilic, strictly anaerobic, Gram-negative bacteria, designated strains AZM34c06(T) and AZM44c09(T), were isolated from terrestrial hot springs in Japan. The optimum growth conditions for strain AZM34c06(T) were 60 °C, pH 7.4 and 0% additional NaCl, and those for strain AZM44c09(T) were 70 °C, pH 7.4 and 0% additional NaCl. Complete genome sequencing was performed for both strains, revealing genome sizes of 2.19 Mbp (AZM34c06(T)) and 2.01 Mbp (AZM44c09(T)). Phylogenetic analyses based on 16S rRNA gene sequences and the concatenated predicted amino acid sequences of 33 ribosomal proteins showed that both strains belonged to the genus Thermotoga. The closest relatives of strains AZM34c06(T) and AZM44c09(T) were the type strains of Thermotoga lettingae (96.0% similarity based on the 16S rRNA gene and 84.1% similarity based on ribosomal proteins) and Thermotoga hypogea (98.6 and 92.7% similarity), respectively. Using blast, the average nucleotide identity was 70.4-70.5% when comparing strain AZM34c06(T) and T. lettingae TMO(T) and 76.6% when comparing strain AZM44c09(T) and T. hypogea NBRC 106472(T). Both values are far below the 95% threshold value for species delineation. In view of these data, we propose the inclusion of the two isolates in the genus Thermotoga within two novel species, Thermotoga profunda sp. nov. (type strain AZM34c06(T) = NBRC 106115(T) = DSM 23275(T)) and Thermotoga caldifontis sp. nov. (type strain AZM44c09(T) = NBRC 106116(T) = DSM 23272(T)).

  8. Spongiibacter marinus gen. nov., sp. nov., a halophilic marine bacterium isolated from the boreal sponge Haliclona sp. 1.

    PubMed

    Graeber, Ingeborg; Kaesler, Ines; Borchert, Martin S; Dieckmann, Ralf; Pape, Thomas; Lurz, Rudi; Nielsen, Preben; von Döhren, Hans; Michaelis, Walter; Szewzyk, Ulrich

    2008-03-01

    Strain HAL40b(T) was isolated from the marine sponge Haliclona sp. 1 collected at the Sula Ridge off the Norwegian coast and characterized by physiological, biochemical and phylogenetic analyses. The isolate was a small rod with a polar flagellum. It was aerobic, Gram-negative and oxidase- and catalase-positive. Optimal growth was observed at 20-30 degrees C, pH 7-9 and in 3 % NaCl. Substrate utilization tests were positive for arabinose, Tween 40 and Tween 80. Enzyme tests were positive for alkaline phosphatase, esterase lipase (C8), leucine arylamidase, acid phosphatase, naphthol-AS-BI-phosphohydrolase and N-acetyl-beta-glucosaminidase. The predominant cellular fatty acid was C(17 : 1) omega8, followed by C(17 : 0) and C(18 : 1) omega7. Analysis by matrix-assisted laser desorption/ionization time-of-flight MS was used to characterize the strain, producing a characteristic low-molecular-mass protein pattern that could be used as a fingerprint for identification of members of this species. The DNA G+C content was 69.1 mol%. Phylogenetic analysis supported by 16S rRNA gene sequence comparison classified the strain as a member of the class Gammaproteobacteria. Strain HAL40b(T) was only distantly related to other marine bacteria including Neptunomonas naphthovorans and Marinobacter daepoensis (type strain sequence similarity >90 %). Based on its phenotypic, physiological and phylogenetic characteristics, it is proposed that the strain should be placed into a new genus as a representative of a novel species, Spongiibacter marinus gen. nov., sp. nov.; the type strain of Spongiibacter marinus is HAL40b(T) (=DSM 17750(T) =CCUG 54896(T)).

  9. Tsukamurella hongkongensis sp. nov. and Tsukamurella sinensis sp. nov., isolated from patients with keratitis, catheter-related bacteraemia and conjunctivitis.

    PubMed

    Teng, Jade L L; Tang, Ying; Wong, Samson S Y; Ngan, Antonio H Y; Huang, Yi; Tsang, Chi-Ching; Choi, Garnet K Y; Lau, Susanna K P; Woo, Patrick C Y

    2016-01-01

    Three bacterial strains, HKU51T, HKU52T and HKU53, were isolated from a conjunctival swab, corneal scraping and blood culture of three patients in Hong Kong with conjunctivitis, keratitis and catheter-related bacteraemia, respectively. Cells were Gram-stain-positive, aerobic, catalase-positive, non-sporulating and non-motile bacilli. The three strains had unique biochemical profiles that were distinguishable from those of closely related species of the genus Tsukamurella. Fatty acids, mycolic acids, cell-wall sugars and peptidoglycan analyses showed that they were typical of members of Tsukamurella. 16S rRNA gene sequence analysis revealed 100 % sequence identity between HKU52T and HKU53, and the two strains shared 99.5 % sequence identity with Tsukamurella sunchonensis JCM 15929T and Tsukamurella pseudospumae JCM 13375T; HKU51T shared 99.6 % sequence identity with Tsukamurella pulmonis CCUG 35732T. The DNA G+C contents of strains HKU51T, HKU52T and HKU53 were 70.9 ± 2.2, 71.3 ± 2.1 and 71.2 ± 2.3 mol% (mean ± sd; n = 3), respectively. DNA-DNA hybridization confirmed that the novel strains were distinct from other known species of the genus Tsukamurella ( ≤ 50.1 ± 3.7 % DNA-DNA relatedness); two of the isolates, HKU52T and HKU53, represented the same species ( ≥ 94.6 ± 5.6 % DNA-DNA relatedness), while the third isolate, HKU51T, represented another species. The novel species Tsukamurella hongkongensis sp. nov. is proposed to accommodate strains HKU52T and HKU53, with HKU52T ( = JCM 30715T = DSM 100208T) as the type strain; whilst another novel species, Tsukamurella sinensis sp. nov., is proposed to accommodate the third isolate, HKU51T ( = JCM 30714T = DSM 100207T), which is designated the type strain.

  10. Detoxification of Atrazine by Endophytic Streptomyces sp. Isolated from Sugarcane and Detection of Nontoxic Metabolite.

    PubMed

    Mesquini, Josiane A; Sawaya, Alexandra C H F; López, Begonã G C; Oliveira, Valéria M; Miyasaka, Natalia R S

    2015-12-01

    Atrazine is still one of the most used agricultural pesticides worldwide and it has been recognized as a major contaminant of surface and ground water. The aims of this research were to isolate an endophytic microorganism from leaves of sugarcane, evaluate its ability to degrade atrazine, and investigate the formation of metabolites. By sequencing of the 16S rRNA gene, the endophytic isolate atz2 was identified as Streptomyces sp. The reduction in atrazine concentration by Streptomyces sp. atz2 was 98 % and UHPLC-MS/MS analyses showed the appearance of an unknown metabolite observed as m/z 311. Ecotoxicity tests with an aquatic organism, Daphnia similis, confirmed that this metabolite was nontoxic. This mechanism of detoxification of atrazine is different from the ones of other free-living microorganisms that inhabit the soil or rhizosphere. The results show new aspects of atrazine detoxification, highlighting a new role of endophytic bacteria in plants. PMID:26467569

  11. Saturnispora quitensis sp. nov., a yeast species isolated from the Maquipucuna cloud forest reserve in Ecuador.

    PubMed

    James, Stephen A; Cadet, Geneviève M; Barriga, Enrique Javier Carvajal; Barahona, Patricia Portero; Cross, Kathryn; Bond, Christopher J; Roberts, Ian N

    2011-12-01

    A single strain, CLQCA-10-114(T), representing a novel yeast species belonging to the genus Saturnispora was isolated from the fruit of an unidentified species of bramble (Rubus sp.), collected from the Maquipucuna cloud forest reserve, near Quito, in Ecuador. Sequence analyses of the D1/D2 domains of the large-subunit rRNA gene and ribosomal internal transcribed spacer region indicated that the novel species is most closely related to the recently described species Saturnispora gosingensis, isolated from the fruiting body of a mushroom collected in Taiwan, and Saturnispora hagleri, a Drosophila-associated yeast found in Brazil. The name Saturnispora quitensis sp. nov. is proposed to accommodate this strain; the type strain is CLQCA-10-114(T) (=CBS 12184(T)=NCYC 3744(T)). PMID:21335499

  12. Detoxification of Atrazine by Endophytic Streptomyces sp. Isolated from Sugarcane and Detection of Nontoxic Metabolite.

    PubMed

    Mesquini, Josiane A; Sawaya, Alexandra C H F; López, Begonã G C; Oliveira, Valéria M; Miyasaka, Natalia R S

    2015-12-01

    Atrazine is still one of the most used agricultural pesticides worldwide and it has been recognized as a major contaminant of surface and ground water. The aims of this research were to isolate an endophytic microorganism from leaves of sugarcane, evaluate its ability to degrade atrazine, and investigate the formation of metabolites. By sequencing of the 16S rRNA gene, the endophytic isolate atz2 was identified as Streptomyces sp. The reduction in atrazine concentration by Streptomyces sp. atz2 was 98 % and UHPLC-MS/MS analyses showed the appearance of an unknown metabolite observed as m/z 311. Ecotoxicity tests with an aquatic organism, Daphnia similis, confirmed that this metabolite was nontoxic. This mechanism of detoxification of atrazine is different from the ones of other free-living microorganisms that inhabit the soil or rhizosphere. The results show new aspects of atrazine detoxification, highlighting a new role of endophytic bacteria in plants.

  13. Draft genome sequence of Thermoactinomyces sp. strain AS95 isolated from a Sebkha in Thamelaht, Algeria.

    PubMed

    Bezuidt, Oliver K I; Gomri, Mohamed A; Pierneef, Rian; Van Goethem, Marc W; Kharroub, Karima; Cowan, Don A; Makhalanyane, Thulani P

    2016-01-01

    The members of the genus Thermoactinomyces are known for their protein degradative capacities. Thermoactinomyces sp. strain AS95 is a Gram-positive filamentous bacterium, isolated from moderately saline water in the Thamelaht region of Algeria. This isolate is a thermophilic aerobic bacterium with the capacity to produce extracellular proteolytic enzymes. This strain exhibits up to 99 % similarity with members of the genus Thermoactinomyces, based on 16S rRNA gene sequence similarity. Here we report on the phenotypic features of Thermoactinomyces sp. strain AS95 together with the draft genome sequence and its annotation. The genome of this strain is 2,558,690 bp in length (one chromosome, but no plasmid) with an average G + C content of 47.95 %, and contains 2550 protein-coding and 60 RNA genes together with 64 ORFs annotated as proteases. PMID:27617058

  14. Draft Genome Sequence of Burkholderia sp. Strain CCA53, Isolated from Leaf Soil

    PubMed Central

    Kimura, Zen-ichiro; Yusoff, Mohd Zulkhairi Mohd; Nakashima, Nobutaka; Hoshino, Tamotsu

    2016-01-01

    Burkholderia sp. strain CCA53 was isolated from leaf soil collected in Higashi-Hiroshima City in Hiroshima Prefecture, Japan. Here, we present a draft genome sequence of this strain, which consists of a total of 4 contigs containing 6,647,893 bp, with a G+C content of 67.0% and comprising 9,329 predicted coding sequences. PMID:27389268

  15. Isolation and structural elucidation of chondrosterins F-H from the marine fungus Chondrostereum sp.

    PubMed

    Li, Hou-Jin; Chen, Ting; Xie, Ying-Lu; Chen, Wen-Dan; Zhu, Xiao-Feng; Lan, Wen-Jian

    2013-02-01

    The marine fungus Chondrostereum sp. was collected from a soft coral of the species Sarcophyton tortuosum from the South China Sea. Three new compounds, chondrosterins F-H (1, 4 and 5), together with three known compounds, incarnal (2), arthrosporone (3), and (2E)-decene-4,6,8-triyn-1-ol (6), were isolated. Their structures were elucidated primarily based on NMR and MS data. Incarnal (2) exhibited potent cytotoxic activity against various cancer cell lines.

  16. Draft Genome Sequence of Burkholderia sp. Strain CCA53, Isolated from Leaf Soil.

    PubMed

    Akita, Hironaga; Kimura, Zen-Ichiro; Yusoff, Mohd Zulkhairi Mohd; Nakashima, Nobutaka; Hoshino, Tamotsu

    2016-01-01

    Burkholderia sp. strain CCA53 was isolated from leaf soil collected in Higashi-Hiroshima City in Hiroshima Prefecture, Japan. Here, we present a draft genome sequence of this strain, which consists of a total of 4 contigs containing 6,647,893 bp, with a G+C content of 67.0% and comprising 9,329 predicted coding sequences. PMID:27389268

  17. Draft genome sequence of Kocuria sp. SM24M-10 isolated from coral mucus

    PubMed Central

    Palermo, Bruna Rafaella Z.; Castro, Daniel B.A.; Pereira, Letícia Bianca; Cauz, Ana Carolina G.; Magalhães, Beatriz L.; Carlos, Camila; da Costa, Fernanda L.P.; Scagion, Guilherme P.; Higa, Juliana S.; Almeida, Ludimila D.; das Neves, Meiriele da S.; Cordeiro, Melina Aparecida; do Prado, Paula F.V.; da Silva, Thiago M.; Balsalobre, Thiago Willian A.; Paulino, Luciana C.; Vicentini, Renato; Ferraz, Lúcio F.C.; Ottoboni, Laura M.M.

    2015-01-01

    Here, we describe the genomic features of the Actinobacteria Kocuria sp. SM24M-10 isolated from mucus of the Brazilian endemic coral Mussismilia hispida. The sequences are available under accession number LDNX01000000 (http://www.ncbi.nlm.nih.gov/nuccore/LDNX00000000). The genomic analysis revealed interesting information about the adaptation of bacteria to the marine environment (such as genes involved in osmotic and oxidative stress) and to the nutrient-rich environment provided by the coral mucus. PMID:26981384

  18. Cytotoxic prodigiosin family pigments from Pseudoalteromonas sp. 1020R isolated from the Pacific coast of Japan.

    PubMed

    Wang, Yi; Nakajima, Aya; Hosokawa, Kakushi; Soliev, Azamjon B; Osaka, Issey; Arakawa, Ryuichi; Enomoto, Keiichi

    2012-01-01

    Pseudoalteromonas sp. 1020R, isolated from the Pacific coast of Japan, produces prodigiosin family pigments. Structural analysis indicated that these are prodigiosin (2-methyl-3-pentyl-prodiginine) and three other prodigiosin congeners which differ only in the lengths of the alkyl side chains. These compounds exhibited different extents of cytotoxicity against U937 leukemia cells, and cell death was accompanied by typical features of apoptosis.

  19. Virgibacillus senegalensis sp. nov., a new moderately halophilic bacterium isolated from human gut

    PubMed Central

    Seck, E.; Rathored, J.; Khelaifia, S.; Croce, O.; Robert, C.; Couderc, C.; Di Pinto, F.; Sokhna, C.; Raoult, D.; Lagier, J.-C.

    2015-01-01

    Virgibacillus senegalensis SK-1T (= CSUR P1101 = DSM 28585) is the type strain of V. senegalensis sp. nov. It is an aerobic, Gram positive, moderately halophilic, motile bipolar flagellum isolated from a healthy Senegalese man. Here we describe the genomic and phenotypic characteristics of this isolate. The 3 755 098 bp long genome (one chromosome, no plasmid) exhibits a G + C content of 42.9% and contains 3738 protein-coding and 95 RNA genes. PMID:26693281

  20. Virgibacillus senegalensis sp. nov., a new moderately halophilic bacterium isolated from human gut.

    PubMed

    Seck, E; Rathored, J; Khelaifia, S; Croce, O; Robert, C; Couderc, C; Di Pinto, F; Sokhna, C; Raoult, D; Lagier, J-C

    2015-11-01

    Virgibacillus senegalensis SK-1(T) (= CSUR P1101 = DSM 28585) is the type strain of V. senegalensis sp. nov. It is an aerobic, Gram positive, moderately halophilic, motile bipolar flagellum isolated from a healthy Senegalese man. Here we describe the genomic and phenotypic characteristics of this isolate. The 3 755 098 bp long genome (one chromosome, no plasmid) exhibits a G + C content of 42.9% and contains 3738 protein-coding and 95 RNA genes. PMID:26693281

  1. Kazachstania rupicola sp. nov., a yeast species isolated from water tanks of a bromeliad in Brazil.

    PubMed

    Safar, Silvana Vilas Boas; Gomes, Fátima C O; Marques, Andréa R; Lachance, Marc-André; Rosa, Carlos A

    2013-03-01

    Two isolates of a novel yeast species were obtained from water tanks (phytotelmata) of the bromeliad Vriesea minarum collected in a tableland ('campo rupestre') ecosystem in Brazil. The sequences of the D1/D2 domains of the large-subunit rRNA gene showed that this species is related to Kazachstania exigua and others, from which it differs by 8-10 nucleotide substitutions. The novel species Kazachstania rupicola sp. nov. is proposed to accommodate these isolates. The type strain is UFMG-BRO-80(T) ( = CBS 12684(T)  = CBMAI 1466(T)).

  2. Five sesquiterpenoids from a marine-derived fungus Aspergillus sp. isolated from a gorgonian Dichotella gemmacea.

    PubMed

    Wei, Mei-Yan; Wang, Chang-Yun; Liu, Qing-Ai; Shao, Chang-Lun; She, Zhi-Gang; Lin, Yong-Cheng

    2010-01-01

    Three new phenolic bisabolane-type sesquiterpenoids: (+)-methyl sydowate (1), 7-deoxy-7,14-didehydrosydonic acid (2), and 7-deoxy-7,8-didehydrosydonic acid (3), together with two known fungal metabolites were isolated from the fermentation broth of a marine-derived fungus Aspergillus sp., which was isolated in turn from a gorgonian Dichotella gemmacea collected from the South China Sea. Their structures were elucidated by combined spectroscopic methods, and the structure of 1 was further confirmed by single-crystal X-ray data.

  3. Isolation and application of Gordonia sp. JC11 for removal of boat lubricants.

    PubMed

    Chanthamalee, Jirapat; Luepromchai, Ekawan

    2012-01-01

    Boat lubricants are continuously released into the marine environment and thereby cause chronic oil pollution. This study aims to isolate lubricant-degrading microorganisms from Thai coastal areas as well as to apply a selected strain for removal of boat lubricants. Ten microorganisms in the genera of Gordonia, Microbacterium, Acinetobacter, Pseudomonas, Brucella, Enterococcus and Candida were initially isolated by crude oil enrichment culture techniques. The lubricant-removal activity of these isolates was investigated with mineral-based lubricants that had been manufactured for the 4-stroke diesel engines of fishing boats. Gordonia sp. JC11, the most effective strain was able to degrade 25-55% of 1,000 mg L(-1) total hydrocarbons in six tested lubricants, while only 0-15% of the lubricants was abiotically removed. The bacterium had many characteristics that promoted lubricant degradation such as hydrocarbon utilization ability, emulsification activity and cell surface hydrophobicity. For bioaugmentation treatment of lubricant contaminated seawater, the inoculum of Gordonia sp. JC11 was prepared by immobilizing the bacterium on polyurethane foam (PUF). PUF-immobilized Gordonia sp. JC11 was able to remove 42-56% of 100-1,000 mg L(-1) waste lubricant No. 2 within 5 days. This lubricant removal efficiency was higher than those of free cells and PUF without bacterial cells. The bioaugmentation treatment significantly increased the number of lubricant-degrading microorganisms in the fishery port seawater microcosm and resulted in rapid removal of waste lubricant No. 2.

  4. Impacts of varying light regimes on phycobiliproteins of Nostoc sp. HKAR-2 and Nostoc sp. HKAR-11 isolated from diverse habitats.

    PubMed

    Kannaujiya, Vinod K; Sinha, Rajeshwar P

    2015-11-01

    The adaptability of cyanobacteria in diverse habitats is an important factor to withstand harsh conditions. In the present investigation, the impacts of photosynthetically active radiation (PAR; 400-700 nm), ultraviolet-B (UV-B; 280-315 nm), and PAR + UV-B radiations on two cyanobacteria viz., Nostoc sp. HKAR-2 and Nostoc sp. HKAR-11 inhabiting diverse habitats such as hot springs and rice fields, respectively, were studied. Cell viability was about 14 % in Nostoc sp. HKAR-2 and <10 % in Nostoc sp. HKAR-11 after 48 h of UV-B exposure. PAR had negligible negative impact on the survival of both cyanobacteria. The continuous exposure of UV-B and PAR + UV-B showed rapid uncoupling, bleaching, fragmentation, and degradation in both phycocyanin (C-PC) and phycoerythrin (C-PE) subunits of phycobiliproteins (PBPs). Remarkable bleaching effect of C-PE and C-PC was not only observed with UV-B or PAR + UV-B radiation, but longer period (24-48 h) of exposure with PAR alone also showed noticeable negative impact. The C-PE and C-PC subunits of the rice field isolate Nostoc sp. HKAR-11 were severely damaged in comparison to the hot spring isolate Nostoc sp. HKAR-2 with rapid wavelength shifting toward shorter wavelengths denoting the bleaching of both the accessory light harvesting pigments. The results indicate that PBPs of the hot spring isolate Nostoc sp. HKAR-2 were more stable under various light regimes in comparison to the rice field isolate Nostoc sp. HKAR-11 that could serve as a good source of valuable pigments to be used in various biomedical and biotechnological applications.

  5. Impacts of varying light regimes on phycobiliproteins of Nostoc sp. HKAR-2 and Nostoc sp. HKAR-11 isolated from diverse habitats.

    PubMed

    Kannaujiya, Vinod K; Sinha, Rajeshwar P

    2015-11-01

    The adaptability of cyanobacteria in diverse habitats is an important factor to withstand harsh conditions. In the present investigation, the impacts of photosynthetically active radiation (PAR; 400-700 nm), ultraviolet-B (UV-B; 280-315 nm), and PAR + UV-B radiations on two cyanobacteria viz., Nostoc sp. HKAR-2 and Nostoc sp. HKAR-11 inhabiting diverse habitats such as hot springs and rice fields, respectively, were studied. Cell viability was about 14 % in Nostoc sp. HKAR-2 and <10 % in Nostoc sp. HKAR-11 after 48 h of UV-B exposure. PAR had negligible negative impact on the survival of both cyanobacteria. The continuous exposure of UV-B and PAR + UV-B showed rapid uncoupling, bleaching, fragmentation, and degradation in both phycocyanin (C-PC) and phycoerythrin (C-PE) subunits of phycobiliproteins (PBPs). Remarkable bleaching effect of C-PE and C-PC was not only observed with UV-B or PAR + UV-B radiation, but longer period (24-48 h) of exposure with PAR alone also showed noticeable negative impact. The C-PE and C-PC subunits of the rice field isolate Nostoc sp. HKAR-11 were severely damaged in comparison to the hot spring isolate Nostoc sp. HKAR-2 with rapid wavelength shifting toward shorter wavelengths denoting the bleaching of both the accessory light harvesting pigments. The results indicate that PBPs of the hot spring isolate Nostoc sp. HKAR-2 were more stable under various light regimes in comparison to the rice field isolate Nostoc sp. HKAR-11 that could serve as a good source of valuable pigments to be used in various biomedical and biotechnological applications. PMID:25772678

  6. Microbispora corallina sp. nov., a new species of the genus Microbispora isolated from Thai soil.

    PubMed

    Nakajima, Y; Kitpreechavanich, V; Suzuki, K; Kudo, T

    1999-10-01

    Two actinomycete strains, DF-28 and DF-32T, were isolated from soil samples collected in a deciduous dipterocarp forest in Thailand. They produced longitudinally paired spores on the tips of short sporophores alternately branched from aerial hyphae, and the chemotaxonomic properties of the isolates were the same as those of members of the family Streptosporangiaceae. These phenotypic properties, together with the results of a phylogenetic analysis based on 16S rRNA gene sequences, indicated that these isolates should be assigned to the genus Microbispora. The two isolates showed more than 93% DNA relatedness to each other, but their relatedness to any previously described species of the genus Microbispora was only 45% or less. They were distinguishable from previously described Microbispora spp. by a combination of physiological and biochemical properties. Therefore, a new species is proposed for these strains, under the name Microbispora corallina sp. nov. The type strain is strain DF-32T (= JCM 10267T).

  7. Mesorhizobium shonense sp. nov., Mesorhizobium hawassense sp. nov. and Mesorhizobium abyssinicae sp. nov., isolated from root nodules of different agroforestry legume trees.

    PubMed

    Degefu, Tulu; Wolde-Meskel, Endalkachew; Liu, Binbin; Cleenwerck, Ilse; Willems, Anne; Frostegård, Åsa

    2013-05-01

    A total of 18 strains, representing members of the genus Mesorhizobium, obtained from root nodules of woody legumes growing in Ethiopia, have been previously shown, by multilocus sequence analysis (MLSA) of five housekeeping genes, to form three novel genospecies. In the present study, the phylogenetic relationship between representative strains of these three genospecies and the type strains of their closest phylogenetic neighbours Mesorhizobium plurifarium, Mesorhizobium amorphae, Mesorhizobium septentrionale and Mesorhizobium huakuii was further evaluated using a polyphasic taxonomic approach. In line with our earlier MLSA of other housekeeping genes, the phylogenetic trees derived from the atpD and glnII genes grouped the test strains into three well-supported, distinct lineages that exclude all defined species of the genus Mesorhizobium. The DNA-DNA relatedness between the representative strains of genospecies I-III and the type strains of their closest phylogenetic neighbours was low (≤59 %). They differed from each other and from their closest phylogenetic neighbours by the presence/absence of several fatty acids, or by large differences in the relative amounts of particular fatty acids. While showing distinctive features, they were generally able to utilize a wide range of substrates as sole carbon and nitrogen sources. The strains belonging to genospecies I, II and III therefore represent novel species for which we propose the names Mesorhizobium shonense sp. nov., Mesorhizobium hawassense sp. nov. and Mesorhizobium abyssinicae sp. nov. The isolates AC39a(T) ( = LMG 26966(T) = HAMBI 3295(T)), AC99b(T) ( = LMG 26968(T) = HAMBI 3301(T)) and AC98c(T) ( = LMG 26967(T) = HAMBI 3306(T)) are proposed as type strains for the respective novel species.

  8. Megasphaera paucivorans sp. nov., Megasphaera sueciensis sp. nov. and Pectinatus haikarae sp. nov., isolated from brewery samples, and emended description of the genus Pectinatus.

    PubMed

    Juvonen, Riikka; Suihko, Maija-Liisa

    2006-04-01

    Seven unidentified strictly anaerobic, Gram-negative, non-spore-forming bacteria from spoiled beer or the brewery environment were characterized. Based on 16S rRNA gene sequence analyses, all strains were affiliated to the Sporomusa sub-branch of the class 'Clostridia'. Three of the strains were non-motile cocci, on average 1.5 x 1.2 microm or 1.2 x 1.0 microm, occurring mainly singly or in pairs. They shared nearly identical (>99 %) 16S rRNA gene sequences, being most closely related to the species of the Megasphaera-Anaeroglobus group (< or =93.9 % similarity). According to DNA-DNA hybridization results, the coccoid strains represented two genospecies, neither of which was related to any of the recognized Megasphaera species. Several phenotypic characteristics and/or DNA G+C content also differentiated the strains from each other and from their closest relatives. The other four novel strains were motile, slightly curved to helical rods, 0.6-0.8 x 3-50 microm or more in size. They shared identical 16S rRNA gene sequences and ribofragment patterns. The highest 16S rRNA gene similarity was found between these isolates and Pectinatus cerevisiiphilus ATCC 29359T (95.6 %) and Pectinatus frisingensis ATCC 33332T (93.6 %). The novel strains also differed from recognized Pectinatus species in their sugar utilization, proteolytic activity, catalase activity, antibiotic resistance and temperature tolerance. The results suggest that the bacteria belong to three novel species, for which the names Megasphaera paucivorans sp. nov. (type strain VTT E-032341T = DSM 16981T), Megasphaera sueciensis sp. nov. (type strain VTT E-97791T = DSM 17042T) and Pectinatus haikarae sp. nov. (type strain VTT E-88329T = DSM 16980T) are proposed.

  9. Corynebacterium tapiri sp. nov. and Corynebacterium nasicanis sp. nov., isolated from a tapir and a dog, respectively.

    PubMed

    Baumgardt, Sandra; Loncaric, Igor; Kämpfer, Peter; Busse, Hans-Jürgen

    2015-11-01

    Two Gram-stain-positive bacterial isolates, strain 2385/12T and strain 2673/12T were isolated from a tapir and a dog's nose, respectively. The two strains were rod to coccoid-shaped, catalase-positive and oxidase-negative. The highest 16S rRNA gene sequence similarity identified Corynebacterium singulare CCUG 37330T (96.3% similarity) as the nearest relative of strain 2385/12T and suggested the isolate represented a novel species. Corynebacterium humireducens DSM 45392T (98.7% 16S rRNA gene sequence similarity) was identified as the nearest relative of strain 2673/12T. Results from DNA-DNA hybridization with the type strain of C. humireducens demonstrated that strain 2673/12T also represented a novel species. Strain 2385/12T showed a quinone system consisting predominantly of menaquinones MK-8(H2) and MK-9(H2) whereas strain 2673/12T contained only MK-8(H2) as predominant quinone. The polar lipid profiles of the two strains showed the major compounds phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid. Phosphatidylinositol was identified as another major lipid in 2673/12T whereas it was only found in moderate amounts in strain 2385/12T. Furthermore, moderate to minor amounts of phosphatidylinositol-mannoside, β-gentiobiosyl diacylglycerol and variable counts of several unidentified lipids were detected in the two strains. Both strains contained corynemycolic acids. The polyamine patterns were characterized by the major compound putrescine in strain 2385/12T and spermidine in strain 2673/12T. In the fatty acid profiles, predominantly C18:1ω9c and C16:0 were detected. The two strains are distinguishable from each other and the nearest related established species of the genus Corynebacterium phylogenetically and phenotypically. In conclusion, two novel species of the genus Corynebacterium are proposed, namely Corynebacterium tapiri sp. nov. (type strain, 2385/12T = CCUG 65456T = LMG 28165T) and Corynebacterium nasicanis sp. nov. (type

  10. Corynebacterium tapiri sp. nov. and Corynebacterium nasicanis sp. nov., isolated from a tapir and a dog, respectively.

    PubMed

    Baumgardt, Sandra; Loncaric, Igor; Kämpfer, Peter; Busse, Hans-Jürgen

    2015-11-01

    Two Gram-stain-positive bacterial isolates, strain 2385/12T and strain 2673/12T were isolated from a tapir and a dog's nose, respectively. The two strains were rod to coccoid-shaped, catalase-positive and oxidase-negative. The highest 16S rRNA gene sequence similarity identified Corynebacterium singulare CCUG 37330T (96.3% similarity) as the nearest relative of strain 2385/12T and suggested the isolate represented a novel species. Corynebacterium humireducens DSM 45392T (98.7% 16S rRNA gene sequence similarity) was identified as the nearest relative of strain 2673/12T. Results from DNA-DNA hybridization with the type strain of C. humireducens demonstrated that strain 2673/12T also represented a novel species. Strain 2385/12T showed a quinone system consisting predominantly of menaquinones MK-8(H2) and MK-9(H2) whereas strain 2673/12T contained only MK-8(H2) as predominant quinone. The polar lipid profiles of the two strains showed the major compounds phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid. Phosphatidylinositol was identified as another major lipid in 2673/12T whereas it was only found in moderate amounts in strain 2385/12T. Furthermore, moderate to minor amounts of phosphatidylinositol-mannoside, β-gentiobiosyl diacylglycerol and variable counts of several unidentified lipids were detected in the two strains. Both strains contained corynemycolic acids. The polyamine patterns were characterized by the major compound putrescine in strain 2385/12T and spermidine in strain 2673/12T. In the fatty acid profiles, predominantly C18:1ω9c and C16:0 were detected. The two strains are distinguishable from each other and the nearest related established species of the genus Corynebacterium phylogenetically and phenotypically. In conclusion, two novel species of the genus Corynebacterium are proposed, namely Corynebacterium tapiri sp. nov. (type strain, 2385/12T = CCUG 65456T = LMG 28165T) and Corynebacterium nasicanis sp. nov. (type

  11. Nocardiopsis oceani sp. nov. and Nocardiopsis nanhaiensis sp. nov., actinomycetes isolated from marine sediment of the South China Sea.

    PubMed

    Pan, Hua-Qi; Zhang, Dao-Feng; Li, Li; Jiang, Zhao; Cheng, Juan; Zhang, Yong-Guang; Wang, Hong-Fei; Hu, Jiang-Chun; Li, Wen-Jun

    2015-10-01

    Two actinomycete strains, designated 10A08AT and 10A08BT, were isolated from marine sediment samples of the South China Sea and their taxonomic positions were determined by a polyphasic approach. The two Gram-stain-positive, aerobic strains produced branched substrate mycelium and aerial hyphae, and no diffusible pigment was produced in the media tested. At maturity, spore chains were formed on aerial hyphae and all mycelium fragmented with age. Whole-cell hydrolysates of both strains contained meso-diaminopimelic acid and no diagnostic sugars. Their predominant menaquinones (>10 %) were MK-9(H4), MK-9(H6) and MK-10(H6) for strain 10A08AT and MK-9(H4), MK-9(H6), MK-10(H4) and MK-10(H6) for strain 10A08BT. The polar lipids detected from the two strains were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and unknown phosphoglycolipids and phospholipids. The major fatty acids (>10 %) of both strains were iso-C16 : 0 and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The genomic DNA G+C contents of strains 10A08AT and 10A08BT were 70.9 and 71.6 mol%, respectively. On the basis of 16S rRNA gene sequence similarities, the two strains were shown to be most closely related to species of the genus Nocardiopsis. DNA–DNA hybridization relatedness values of < 70 % between these two isolates and their closest neighbour, Nocardiopsis terrae YIM 90022T, and between the two strains supported the conclusion that they represent two novel species. Based on phylogenetic analysis and phenotypic and genotypic data, it is concluded that the two isolates belong to the genus Nocardiopsis, and the names Nocardiopsis oceani sp. nov. (type strain 10A08AT = DSM 45931T = BCRC 16951T) and Nocardiopsis nanhaiensis sp. nov. (type strain 10A08BT = CGMCC 47227T = BCRC 16952T) are proposed.

  12. Biodegradation of 4-chloronitrobenzene by biochemical cooperation between Sphingomonas sp. strain CNB3 and Burkholderia sp. strain CAN6 isolated from activated sludge.

    PubMed

    Zhang, Longjiang; Wang, Xin; Jiao, Yiying; Chen, Xu; Zhou, Lingyan; Guo, Kun; Ge, Feng; Wu, Jun

    2013-05-01

    Two bacterial strains were isolated from activated sludge by using 4-chloronitrobenzene (4-CB) as the sole source of carbon for enrichment. One of the isolates was identified as Sphingomonas sp. strain CNB3 and the other as Burkholderia sp. strain CAN6, mainly through morphological and physiological characteristics and 16S rRNA gene sequence analysis. Sphingomonas sp. strain CNB3 could transform 4-CB to 4-chloroaniline, which accumulated in the medium. Burkholderia sp. strain CAN6 could transform 4-chloroaniline but not 4-CB. The co-culture of Sphingomonas sp. strain CNB3 and Burkholderia sp. strain CAN6 could degrade 4-CB completely by the biochemical cooperation of two strains to overcome the degradative limitations of each species alone. In addition, the biochemical pathway of 4-chloroaniline transformation by Burkholderia sp. strain CAN6 was proposed based on the determined related enzyme activities. The results suggested that 4-chloroaniline was completely transformed via the ortho-cleavage and modified ortho-cleavage pathways.

  13. Candida aechmeae sp. nov. and Candida vrieseae sp. nov., novel yeast species isolated from the phylloplane of bromeliads in Southern Brazil.

    PubMed

    Landell, Melissa Fontes; Billodre, Raisa; Ramos, Jesus P; Leoncini, Orílio; Vainstein, Marilene H; Valente, Patrícia

    2010-01-01

    Two novel yeast species, Candida aechmeae sp. nov. and Candida vrieseae sp. nov., were isolated from bromeliads in Itapuã Park, Rio Grande do Sul, Brazil. These species are genetically isolated from all other currently recognized ascomycetous yeasts based on their sequence divergence in the D1/D2 domain of the LSU rRNA gene. C. aechmeae sp. nov. is phylogenetically close to Candida ubatubensis, a species also isolated from bromeliads in Brazil, but the novel species can be differentiated on the basis of differences in the D1/D2 domain and positive results for the assimilation of l-arabinose, raffinose, inulin and citrate. Candida vrieseae sp. nov. is phylogenetically placed in a clade near Candida membranifaciens that is composed of several species associated with insects, but the novel species can be differentiated from them by the D1/D2 and ITS gene sequences, positive results for the assimilation of nitrite and a negative result for the assimilation of ethylamine. The type strain for Candida aechmeae sp. nov. is BI153(T) (=CBS 10831(T)=NRRL Y-48456(T)) and the type strain for C. vrieseae sp. nov. is BI146(T) (=CBS 10829(T)=NRRL Y-48461(T)).

  14. Permanent Draft Genome Sequence of Nocardia sp. BMG111209, an Actinobacterium Isolated from Nodules of Casuarina glauca

    PubMed Central

    Ghodhbane-Gtari, Faten; Beauchemin, Nicholas; Gueddou, Abdellatif; Hezbri, Karima; Ktari, Amir; Louati, Moussa; Nouioui, Imen; Chen, Amy; Huntemann, Marcel; Ivanova, Natalia; Kyrpides, Nikos; Markowitz, Victor; Mavrommatis, Kostas; Pagani, Ioanna; Sen, Arnab; Wall, Luis; Woyke, Tanja

    2016-01-01

    Nocardia sp. strain BMG111209 is a non-Frankia actinobacterium isolated from root nodules of Casuarina glauca in Tunisia. Here, we report the 9.1-Mbp draft genome sequence of Nocardia sp. strain BMG111209 with a G + C content of 69.19% and 8,122 candidate protein-encoding genes. PMID:27491997

  15. Permanent Draft Genome Sequence of Nocardia sp. BMG111209, an Actinobacterium Isolated from Nodules of Casuarina glauca.

    PubMed

    Ghodhbane-Gtari, Faten; Beauchemin, Nicholas; Gueddou, Abdellatif; Hezbri, Karima; Ktari, Amir; Louati, Moussa; Nouioui, Imen; Chen, Amy; Huntemann, Marcel; Ivanova, Natalia; Kyrpides, Nikos; Markowitz, Victor; Mavrommatis, Kostas; Pagani, Ioanna; Sen, Arnab; Wall, Luis; Woyke, Tanja; Gtari, Maher; Tisa, Louis S

    2016-01-01

    Nocardia sp. strain BMG111209 is a non-Frankia actinobacterium isolated from root nodules of Casuarina glauca in Tunisia. Here, we report the 9.1-Mbp draft genome sequence of Nocardia sp. strain BMG111209 with a G + C content of 69.19% and 8,122 candidate protein-encoding genes. PMID:27491997

  16. Complete Genome Sequence of Pseudoalteromonas sp. Strain OCN003, Isolated from Kāne'ohe Bay, O'ahu, Hawaii.

    PubMed

    Beurmann, Silvia; Videau, Patrick; Ushijima, Blake; Smith, Ashley M; Aeby, Greta S; Callahan, Sean M; Belcaid, Mahdi

    2015-01-01

    Pseudoalteromonas sp. strain OCN003 is a marine gammaproteobacterium that was isolated from a diseased colony of the common Hawaiian reef coral, Montipora capitata, found on a reef surrounding Moku o Lo'e in Kāne'ohe Bay, Hawaii. Here, we report the complete genome of Pseudoalteromonas sp. strain OCN003. PMID:25593253

  17. Complete Genome Sequence of Labrenzia sp. Strain CP4, Isolated from a Self-Regenerating Biocathode Biofilm

    PubMed Central

    Wang, Zheng; Eddie, Brian J.; Malanoski, Anthony P.; Hervey, W. Judson; Lin, Baochuan

    2016-01-01

    Here, we present the complete genome sequence of Labrenzia sp. strain CP4, isolated from an electricity-consuming marine biocathode biofilm. Labrenzia sp. strain CP4 consists of a circular 5.2 Mbp chromosome and an 88 Kbp plasmid. PMID:27174270

  18. Draft Genome Sequence of a Phthalate Ester-Degrading Bacterium, Rhizobium sp. LMB-1, Isolated from Cultured Soil

    PubMed Central

    Tang, Wen-Juan

    2015-01-01

    Rhizobium sp. LMB-1, newly isolated from greenhouse soil, can effectively degrade phthalate. Here, we present a 5.2-Mb assembly of this Rhizobium sp. genome for the first time. It may provide abundant molecular information for the transformation of phthalates. PMID:25953182

  19. Draft Genome Sequence of a Tetrabromobisphenol A–Degrading Strain, Ochrobactrum sp. T, Isolated from an Electronic Waste Recycling Site

    PubMed Central

    Liang, Zhishu; Li, Guiying; Zhang, Guoxia; Das, Ranjit

    2016-01-01

    Ochrobactrum sp. T was previously isolated from a sludge sample collected from an electronic waste recycling site and characterized as a unique tetrabromobisphenol A (TBBPA)–degrading bacterium. Here, the draft genome sequence (3.9 Mb) of Ochrobactrum sp. T is reported to provide insights into its diversity and its TBBPA biodegradation mechanism in polluted environments. PMID:27445374

  20. Whole-Genome Sequence of Enteractinococcus helveticum sp. nov. Strain UASWS1574 Isolated from Industrial Used Waters

    PubMed Central

    Crovadore, Julien; Calmin, Gautier; Chablais, Romain; Cochard, Bastien

    2016-01-01

    We report here the whole-genome shotgun sequences of the strain UASWS1574 of the undescribed Enteractinococcus helveticum sp. nov., isolated from used water. This is the first genome registered for the whole genus. PMID:27469945

  1. Neptunomonas phycophila sp. nov. isolated from a culture of Symbiodinium sp., a dinoflagellate symbiont of the sea anemone Aiptasia tagetes.

    PubMed

    Frommlet, Jörg; Guimarães, Bárbara; Sousa, Lígia; Serôdio, João; Alves, Artur

    2015-03-01

    A Gram-stain-negative, facultatively anaerobic, oxidase- and catalase-positive, rod-shaped bacterium, strain SYM1(T), was isolated from a culture of Symbiodinium sp., an algal symbiont of the sea anemone Aiptasia tagetes collected in Puerto Rico. Growth was observed at 4-40 °C (optimum 30 °C), at pH 5.0-11.0 (optimum pH 8.0) and with 0.5-8 % (optimum 2 %) (w/v) NaCl. Phylogenetic analyses of 16S rRNA gene sequences showed that strain SYM1(T) was a member of the genus Neptunomonas with the type strain of Neptunomonas naphthovorans as the closest phylogenetic relative with a pairwise sequence similarity of 98.15 %. However, DNA-DNA relatedness between strain SYM1(T) and N. naphthovorans CIP 106451(T) was 24 %. Moreover, strain SYM1(T) could be distinguished from its closest relative by several phenotypic characteristics such as NaCl, pH and temperature tolerance, nitrate reduction and utilization of carbon substrates. The major cellular fatty acids were C16 : 0, C18 : 1ω7c and summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH). The genomic DNA G+C content of strain SYM1(T) was 45 mol%. Ubiquinone-8 (Q-8) was the only respiratory quinone detected. Based on a polyphasic taxonomic characterization, strain SYM1(T) represents a novel species of the genus Neptunomonas, for which the name Neptunomonas phycophila sp. nov. is proposed. The type strain is SYM1(T) ( = LMG 28329(T) = CECT 8716(T)). PMID:25563909

  2. Deinococcus metallilatus sp. nov. and Deinococcus carri sp. nov., isolated from a car air-conditioning system.

    PubMed

    Kim, Dong-Uk; Lee, Hyosun; Lee, Ji-Hyeong; Ahn, Jae-Hyung; Lim, Sangyong; Jeong, Sunwook; Park, So Yoon; Seong, Chi Nam; Ka, Jong-Ok

    2015-09-01

    Two bacterial strains, designated MA1002(T) and MA1003(T), were isolated from the air-conditioning system of a car. Cells of both strains were Gram-reaction-positive, non-motile, non-spore-forming coccoids, catalase- and oxidase-positive and UV-radiation resistant. The major fatty acids of strain MA1002(T) were iso-C17 : 0 and iso-C15 : 0 and those of strain MA1003(T) were iso-C16 : 0 and iso-C16 : 1 H. The polar lipid profile of MA1002(T) contained phosphatidylethanolamine, two unidentified phosphoglycolipids, an unidentified phospholipid, an unidentified aminophospholipid, an unidentified aminolipid and an unidentified lipid. MA1003(T) had three unidentified phosphoglycolipids, six unidentified phospholipids, two unidentified glycolipids and two unidentified polar lipids as the polar lipids. The G+C contents of the genomic DNA of MA1002(T) and MA1003(T) were 70.5 and 76.0 mol%, respectively. MK-8 was the predominant respiratory quinone for both strains. 16S rRNA gene sequence analysis showed that strain MA1002(T) was phylogenetically related to Deinococcus apachensis DSM 19763(T), D. geothermalis DSM 11300(T), D. aerius TR0125(T) and D. aetherius ST0316(T) (92.9, 92.6, 92.0 and 91.9% sequence similarity, respectively), and MA1003(T) showed the highest sequence similarity to Deinococcus hopiensis KR-140(T) (92.9%) and D. xinjiangensis X-82(T) (91.4%). The results of genotypic and phenotypic characterizations showed that both strains could be distinguished from phylogenetically related species, and that the strains represented novel species within the genus Deinococcus, for which we propose the names Deinococcus metallilatus sp. nov. (type strain MA1002(T) = KACC 17964(T) = NBRC 110141(T)) and Deinococcus carri sp. nov. (type strain is MA1003(T) = KACC 17965(T) = NBRC 110142(T)). PMID:26297510

  3. Deinococcus metallilatus sp. nov. and Deinococcus carri sp. nov., isolated from a car air-conditioning system.

    PubMed

    Kim, Dong-Uk; Lee, Hyosun; Lee, Ji-Hyeong; Ahn, Jae-Hyung; Lim, Sangyong; Jeong, Sunwook; Park, So Yoon; Seong, Chi Nam; Ka, Jong-Ok

    2015-09-01

    Two bacterial strains, designated MA1002(T) and MA1003(T), were isolated from the air-conditioning system of a car. Cells of both strains were Gram-reaction-positive, non-motile, non-spore-forming coccoids, catalase- and oxidase-positive and UV-radiation resistant. The major fatty acids of strain MA1002(T) were iso-C17 : 0 and iso-C15 : 0 and those of strain MA1003(T) were iso-C16 : 0 and iso-C16 : 1 H. The polar lipid profile of MA1002(T) contained phosphatidylethanolamine, two unidentified phosphoglycolipids, an unidentified phospholipid, an unidentified aminophospholipid, an unidentified aminolipid and an unidentified lipid. MA1003(T) had three unidentified phosphoglycolipids, six unidentified phospholipids, two unidentified glycolipids and two unidentified polar lipids as the polar lipids. The G+C contents of the genomic DNA of MA1002(T) and MA1003(T) were 70.5 and 76.0 mol%, respectively. MK-8 was the predominant respiratory quinone for both strains. 16S rRNA gene sequence analysis showed that strain MA1002(T) was phylogenetically related to Deinococcus apachensis DSM 19763(T), D. geothermalis DSM 11300(T), D. aerius TR0125(T) and D. aetherius ST0316(T) (92.9, 92.6, 92.0 and 91.9% sequence similarity, respectively), and MA1003(T) showed the highest sequence similarity to Deinococcus hopiensis KR-140(T) (92.9%) and D. xinjiangensis X-82(T) (91.4%). The results of genotypic and phenotypic characterizations showed that both strains could be distinguished from phylogenetically related species, and that the strains represented novel species within the genus Deinococcus, for which we propose the names Deinococcus metallilatus sp. nov. (type strain MA1002(T) = KACC 17964(T) = NBRC 110141(T)) and Deinococcus carri sp. nov. (type strain is MA1003(T) = KACC 17965(T) = NBRC 110142(T)).

  4. Natribaculum breve gen. nov., sp. nov. and Natribaculum longum sp. nov., halophilic archaea isolated from saline soil.

    PubMed

    Liu, Qin; Ren, Min; Zhang, Li-Li

    2015-02-01

    Two halophilic archaeal strains, TRM20010(T) and TRM20345(T), were isolated from saline soil of the Lop Nur region in Xinjiang, north-west China. Cells from the two strains were pleomorphic rods, stained Gram-negative and produced red-pigmented colonies. Strains TRM20010(T) and TRM20345(T) were able to grow at 30-62 °C (optimum 37 °C), 0.9-5.1 M NaCl (optimum 2.6 and 3.4 M, respectively) and pH 6.0-10.0 (optimum pH 7.0-7.5) and neither strain required Mg(2+) for growth. The major polar lipids of the two strains were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), two glycolipids chromatographically identical to galactosyl mannosyl glucosyl diether (TGD-1) and disulfated mannosyl glucosyl diether (S2-DGD). Phylogenetic analysis based on 16S rRNA and rpoB' genes revealed that strains TRM20010(T) and TRM20345(T) clustered together and formed a distinct clade separated from the related genera Halovivax, Haloterrigena, Halostagnicola, Natronolimnobius and Natrinema. The DNA G+C contents of strains TRM20010(T) and TRM20345(T) were 63.9 and 63.8 mol%, respectively. The DNA-DNA hybridization value between strain TRM20010(T) and strain TRM20345(T) was 42.8 %. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strains TRM20010(T) and TRM20345(T) represent two novel species in a new genus within the family Halobacteriaceae, for which the names Natribaculum breve gen. nov., sp. nov. (type strain TRM20010(T) = CCTCC AB2013112(T) = NRRL B-59996(T)) and Natribaculum longum sp. nov. (type strain TRM20345(T) = CCTCC AB2013113(T) = NRRL B-59997(T)) are proposed. PMID:25406237

  5. Natribaculum breve gen. nov., sp. nov. and Natribaculum longum sp. nov., halophilic archaea isolated from saline soil.

    PubMed

    Liu, Qin; Ren, Min; Zhang, Li-Li

    2015-02-01

    Two halophilic archaeal strains, TRM20010(T) and TRM20345(T), were isolated from saline soil of the Lop Nur region in Xinjiang, north-west China. Cells from the two strains were pleomorphic rods, stained Gram-negative and produced red-pigmented colonies. Strains TRM20010(T) and TRM20345(T) were able to grow at 30-62 °C (optimum 37 °C), 0.9-5.1 M NaCl (optimum 2.6 and 3.4 M, respectively) and pH 6.0-10.0 (optimum pH 7.0-7.5) and neither strain required Mg(2+) for growth. The major polar lipids of the two strains were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), two glycolipids chromatographically identical to galactosyl mannosyl glucosyl diether (TGD-1) and disulfated mannosyl glucosyl diether (S2-DGD). Phylogenetic analysis based on 16S rRNA and rpoB' genes revealed that strains TRM20010(T) and TRM20345(T) clustered together and formed a distinct clade separated from the related genera Halovivax, Haloterrigena, Halostagnicola, Natronolimnobius and Natrinema. The DNA G+C contents of strains TRM20010(T) and TRM20345(T) were 63.9 and 63.8 mol%, respectively. The DNA-DNA hybridization value between strain TRM20010(T) and strain TRM20345(T) was 42.8 %. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strains TRM20010(T) and TRM20345(T) represent two novel species in a new genus within the family Halobacteriaceae, for which the names Natribaculum breve gen. nov., sp. nov. (type strain TRM20010(T) = CCTCC AB2013112(T) = NRRL B-59996(T)) and Natribaculum longum sp. nov. (type strain TRM20345(T) = CCTCC AB2013113(T) = NRRL B-59997(T)) are proposed.

  6. Genetic and Pathogenic Variability of Fusarium oxysporum f. sp. cepae Isolated from Onion and Welsh Onion in Japan.

    PubMed

    Sasaki, Kazunori; Nakahara, Katsuya; Tanaka, Shuhei; Shigyo, Masayoshi; Ito, Shin-ichi

    2015-04-01

    Fusarium oxysporum f. sp. cepae causes Fusarium basal rot in onion (common onion) and Fusarium wilt in Welsh onion. Although these diseases have been detected in various areas in Japan, knowledge about the genetic and pathogenic variability of F. oxysporum f. sp. cepae is very limited. In this study, F. oxysporum f. sp. cepae was isolated from onion and Welsh onion grown in 12 locations in Japan, and a total of 55 F. oxysporum f. sp. cepae isolates (27 from onion and 28 from Welsh onion) were characterized based on their rDNA intergenic spacer (IGS) and translation elongation factor-1α (EF-1α) nucleotide sequences, vegetative compatibility groups (VCGs), and the presence of the SIX (secreted in xylem) homologs. Phylogenetic analysis of IGS sequences showed that these isolates were grouped into eight clades (A to H), and 20 onion isolates belonging to clade H were monophyletic and assigned to the same VCG. All the IGS-clade H isolates possessed homologs of SIX3, SIX5, and SIX7. The SIX3 homolog was located on a 4 Mb-sized chromosome in the IGS-clade H isolates. Pathogenicity tests using onion seedlings showed that all the isolates with high virulence were in the IGS-clade H. These results suggest that F. oxysporum f. sp. cepae isolates belonging to the IGS-clade H are genetically and pathogenically different from those belonging to the other IGS clades.

  7. Mycobacterium minnesotense sp. nov., a photochromogenic bacterium isolated from sphagnum peat bogs.

    PubMed

    Hannigan, Geoffrey D; Krivogorsky, Bogdana; Fordice, Daniel; Welch, Jacqueline B; Dahl, John L

    2013-01-01

    Several intermediate-growing, photochromogenic bacteria were isolated from sphagnum peat bogs in northern Minnesota, USA. Acid-fast staining and 16S rRNA gene sequence analysis placed these environmental isolates in the genus Mycobacterium, and colony morphologies and PCR restriction analysis patterns of the isolates were similar. Partial sequences of hsp65 and dnaJ1 from these isolates showed that Mycobacterium arupense ATCC BAA-1242(T) was the closest mycobacterial relative, and common biochemical characteristics and antibiotic susceptibilities existed between the isolates and M. arupense ATCC BAA-1242(T). However, compared to nonchromogenic M. arupense ATCC BAA-1242(T), the environmental isolates were photochromogenic, had a different mycolic acid profile and had reduced cell-surface hydrophobicity in liquid culture. The data reported here support the conclusion that the isolates are representatives of a novel mycobacterial species, for which the name Mycobacterium minnesotense sp. nov. is proposed. The type strain is DL49(T) (=DSM 45633(T) = JCM 17932(T) = NCCB 100399(T)).

  8. Isolation, identification and screening of antimicrobial thermophilic Streptomyces sp. Al-Dhabi-1 isolated from Tharban hot spring, Saudi Arabia.

    PubMed

    Al-Dhabi, Naif Abdullah; Esmail, Galal Ali; Duraipandiyan, Veeramuthu; Valan Arasu, Mariadhas; Salem-Bekhit, Mounir M

    2016-01-01

    The strain Streptomyces sp. Al-Dhabi-1 was isolated from soil sediments collected from Tharban hot spring in the southern west of Saudi Arabia using actinomycetes isolation agar and starch casein agar at 55 °C. Identification of the isolate was done according to morphological, physiological and biochemical characteristics and 16S rRNA sequence similarity as well. 16S rRNA sequence and blast analyses confirmed that the isolate belonging to the genus Streptomyces. The sequence was submitted to GenBank with accession number (KF815080). Ethyl acetate extract of Streptomyces sp. Al-Dhabi-1 showed good antimicrobial activities against tested pathogenic microbes. Minimum inhibitory concentration results showed that the best values were observed against S. agalactiae (<0.039 mg/ml) and Klebsiella pneumonia (0.125 mg/ml). Minimum inhibitory concentration of Al-Dhabi-1 against fungi; Cryptococcus neoformans (0.078 mg/ml), C. albicans (0.156 mg/ml), A. niger (0.625 mg/ml), and T. mentagrophytes (0.156 mg/ml). GC-MS analysis was used for the chemical profile of ethyl acetate extract. Benzeneacetic acid (16.02 %) and acetic acid 2-phenylethyl ester (10.35 %) were the major compounds among 31 substances found the ethyl acetate extract. According to the results of antimicrobial activity against pathogenic microbes, it is clear that the actinomycetes from hot springs with extreme environments are promising source for antimicrobial compounds. PMID:26515082

  9. Isolation, identification and screening of antimicrobial thermophilic Streptomyces sp. Al-Dhabi-1 isolated from Tharban hot spring, Saudi Arabia.

    PubMed

    Al-Dhabi, Naif Abdullah; Esmail, Galal Ali; Duraipandiyan, Veeramuthu; Valan Arasu, Mariadhas; Salem-Bekhit, Mounir M

    2016-01-01

    The strain Streptomyces sp. Al-Dhabi-1 was isolated from soil sediments collected from Tharban hot spring in the southern west of Saudi Arabia using actinomycetes isolation agar and starch casein agar at 55 °C. Identification of the isolate was done according to morphological, physiological and biochemical characteristics and 16S rRNA sequence similarity as well. 16S rRNA sequence and blast analyses confirmed that the isolate belonging to the genus Streptomyces. The sequence was submitted to GenBank with accession number (KF815080). Ethyl acetate extract of Streptomyces sp. Al-Dhabi-1 showed good antimicrobial activities against tested pathogenic microbes. Minimum inhibitory concentration results showed that the best values were observed against S. agalactiae (<0.039 mg/ml) and Klebsiella pneumonia (0.125 mg/ml). Minimum inhibitory concentration of Al-Dhabi-1 against fungi; Cryptococcus neoformans (0.078 mg/ml), C. albicans (0.156 mg/ml), A. niger (0.625 mg/ml), and T. mentagrophytes (0.156 mg/ml). GC-MS analysis was used for the chemical profile of ethyl acetate extract. Benzeneacetic acid (16.02 %) and acetic acid 2-phenylethyl ester (10.35 %) were the major compounds among 31 substances found the ethyl acetate extract. According to the results of antimicrobial activity against pathogenic microbes, it is clear that the actinomycetes from hot springs with extreme environments are promising source for antimicrobial compounds.

  10. Boron bioremoval by a newly isolated Chlorella sp. and its stimulation by growth stimulators.

    PubMed

    Taştan, Burcu Ertit; Duygu, Ergin; Dönmez, Gönül

    2012-01-01

    It has been well documented that excess concentrations of boron (B) causes toxic effects on many of the environmental systems. Although Chlorella sp. has been studied to remove pollutants from water, its capacity to remove B has not been investigated yet. Boron removal levels of newly isolated Chlorella sp. were investigated in BG 11 media with stimulators as triacontanol (TRIA) and/or sodium bicarbonate (NaHCO(3)) and without them, to test if they could increase the removal efficiency by increasing biomass. The assays were performed to determine the effect of different medial compositions, B concentrations, pH and biomass concentrations onto removal efficiency. Boron removal was investigated at 5-10 mg/L range at pH 8 in different medial compositions and maximum removal yield was found as 32.95% at 5.45 mg/L B in media with TRIA and NaHCO(3). The effect of different pH values on the maximum removal yield was investigated at pH 5-9, and the optimum pH was found again 8. The interactive effect of biomass concentration and B removal yield was also investigated at 0.386-1.061 g wet weight/L biomass. The highest removal yield was found as 38.03% at the highest biomass range. This study highlights the importance of using new isolate Chlorella sp. as a new biomaterial for B removal process of waters containing B.

  11. Phylogenetic characterization of a microsporidium (Nosema sp.) isolated from the mulberry pest, Hemerophila atrilineata.

    PubMed

    Guan, Rui; Shen, Zhongyuan; Zhu, Feng; Chen, Darui; Zhang, Jiao; Hou, Jiange; Dong, Shinan; Tang, Xudong; Xu, Li

    2012-06-01

    Microsporidia are a group of obligate intracellular unicellular eukaryotes that can parasitize a wide variety of other eukaryotes ranging from protists to invertebrates and vertebrates. In this study, we examined the microsporidium Nosema sp. isolated from the mulberry pest, Hemerophila atrilineata Butler, 1881, named herein "Nosema sp. HA". The fresh spores were long oval in shape, 3.8 +/- 0.4 microm in length and 1.9 +/- 0.3 microm in width. Analysis of tissue infection of silkworm, Bombyx mori Linnaeus, 1758, indicated that the midgut, Malpighian tubules, muscle, fat body, silk glands, hemocytes, nerve tissue and gonads of silkworm were infected with Nosema sp. HA. The complete rRNA gene sequence of this microsporidium contained 4 305 base pairs (GenBank Accession JN882299), including the large subunit rRNA (2492 bp), the internal transcribed spacer (187 bp), the small subunit rRNA (1232 bp), the intergenic spacer (279 bp) and the 5S region (115 bp). The organization of the rRNA gene is 5'-LSU-ITS-SSU-IGS-5S-3'. Phylogenetic analysis, comparison of sequence identities and the arrangement in the rRNA gene subunits suggested that this isolate is separate from other Nosema species.

  12. Actinomadura flavalba sp. nov., an endophytic actinomycete isolated from leaves of Maytenus austroyunnanensis.

    PubMed

    Qin, Sheng; Zhao, Guo-Zhen; Li, Jie; Zhu, Wen-Yong; Xu, Li-Hua; Li, Wen-Jun

    2009-10-01

    An actinomycete strain, designated YIM 61435(T), was isolated from leaves of Maytenus austroyunnanensis collected from a tropical rainforest in Xishuangbanna, Yunnan Province, south-west China. The isolate produced aerial mycelium with long, curved to hooked spore chains. The chemotaxonomic characteristics of the isolate were consistent with its assignment to the genus Actinomadura. Phylogenetic analysis using 16S rRNA gene sequences also indicated that this strain should be classified in the genus Actinomadura; however, it could be separated clearly from its closest neighbour, Actinomadura atramentaria DSM 43919(T). Furthermore, a combination of DNA-DNA hybridization results and significant differences in morphological and physiological characteristics indicate that strain YIM 61435(T) represents a novel species of the genus Actinomadura, for which the name Actinomadura flavalba sp. nov. is proposed. The type strain is YIM 61435(T) (=DSM 45200(T) =CCTCC AA 208017(T)).

  13. Cellulomonas xylanilytica sp. nov., a cellulolytic and xylanolytic bacterium isolated from a decayed elm tree.

    PubMed

    Rivas, Raúl; Trujillo, Martha E; Mateos, P F; Martínez-Molina, E; Velázquez, Encarna

    2004-03-01

    A Gram-positive, aerobic, non-motile bacterium was isolated from a decayed elm tree. Phylogenetic analysis based on 16S rDNA sequences revealed 99.0 % similarity to Cellulomonas humilata. Chemotaxonomic data that were determined for this isolate included cell-wall composition, fatty acid profiles and polar lipids; the results supported the placement of strain XIL11(T) in the genus Cellulomonas. The DNA G+C content was 73 mol%. The results of DNA-DNA hybridization with C. humilata ATCC 25174(T), in combination with chemotaxonomic and physiological data, demonstrated that isolate XIL11(T) should be classified as a novel Cellulomonas species. The name Cellulomonas xylanilytica sp. nov. is proposed, with strain XIL11(T) (=LMG 21723(T)=CECT 5729(T)) as the type strain.

  14. Rhodotorula portillonensis sp. nov., a basidiomycetous yeast isolated from Antarctic shallow-water marine sediment.

    PubMed

    Laich, Federico; Vaca, Inmaculada; Chávez, Renato

    2013-10-01

    During the characterization of the mycobiota associated with shallow-water marine environments from Antarctic sea, a novel pink yeast species was isolated. Sequence analysis of the D1/D2 domain of the LSU rDNA gene and 5.8S-ITS regions revealed that the isolated yeast was closely related to Rhodotorula pallida CBS 320(T) and Rhodotorula benthica CBS 9124(T). On the basis of morphological, biochemical and physiological characterization and phylogenetic analyses, a novel basidiomycetous yeast species, Rhodotorula portillonensis sp. nov., is proposed. The type strain is Pi2(T) ( = CBS 12733(T)  = CECT 13081(T)) which was isolated from shallow-water marine sediment in Fildes Bay, King George Island, Antarctica. PMID:23934251

  15. Quorum Sensing Activity of Mesorhizobium sp. F7 Isolated from Potable Water

    PubMed Central

    Yong, Pei-Ling; Chan, Kok-Gan

    2014-01-01

    We isolated a bacterial isolate (F7) from potable water. The strain was identified as Mesorhizobium sp. by 16S rDNA gene phylogenetic analysis and screened for N-acyl homoserine lactone (AHL) production by an AHL biosensor. The AHL profile of the isolate was further analyzed using high resolution triple quadrupole liquid chromatography mass spectrometry (LC/MS) which confirmed the production of multiple AHLs, namely, N-3-oxo-octanoyl-L-homoserine lactone (3-oxo-C8-HSL) and N-3-oxo-decanoyl-L-homoserine lactone (3-oxo-C10-HSL). These findings will open the perspective to study the function of these AHLs in plant-microbe interactions. PMID:25177734

  16. Pantoea sp. isolated from tropical fresh water exhibiting N-acyl homoserine lactone production.

    PubMed

    Tan, Wen-Si; Muhamad Yunos, Nina Yusrina; Tan, Pui-Wan; Mohamad, Nur Izzati; Adrian, Tan-Guan-Sheng; Yin, Wai-Fong; Chan, Kok-Gan

    2014-01-01

    N-Acyl homoserine lactone (AHL) serves as signaling molecule for quorum sensing (QS) in Gram-negative bacteria to regulate various physiological activities including pathogenicity. With the aim of isolating freshwater-borne bacteria that can cause outbreak of disease in plants and portrayed QS properties, environmental water sampling was conducted. Here we report the preliminary screening of AHL production using Chromobacterium violaceum CV026 and Escherichia coli [pSB401] as AHL biosensors. The 16S rDNA gene sequence of isolate M009 showed the highest sequence similarity to Pantoea stewartii S9-116, which is a plant pathogen. The isolated Pantoea sp. was confirmed to produce N-3-oxohexanoyl-L-HSL (3-oxo-C6-HSL) through analysis of high resolution mass tandem mass spectrometry.

  17. Pantoea sp. Isolated from Tropical Fresh Water Exhibiting N-Acyl Homoserine Lactone Production

    PubMed Central

    Tan, Wen-Si; Tan, Pui-Wan; Adrian, Tan-Guan-Sheng; Yin, Wai-Fong; Chan, Kok-Gan

    2014-01-01

    N-Acyl homoserine lactone (AHL) serves as signaling molecule for quorum sensing (QS) in Gram-negative bacteria to regulate various physiological activities including pathogenicity. With the aim of isolating freshwater-borne bacteria that can cause outbreak of disease in plants and portrayed QS properties, environmental water sampling was conducted. Here we report the preliminary screening of AHL production using Chromobacterium violaceum CV026 and Escherichia coli [pSB401] as AHL biosensors. The 16S rDNA gene sequence of isolate M009 showed the highest sequence similarity to Pantoea stewartii S9-116, which is a plant pathogen. The isolated Pantoea sp. was confirmed to produce N-3-oxohexanoyl-L-HSL (3-oxo-C6-HSL) through analysis of high resolution mass tandem mass spectrometry. PMID:25197715

  18. Chryseobacterium ureilyticum sp. nov., Chryseobacterium gambrini sp. nov., Chryseobacterium pallidum sp. nov. and Chryseobacterium molle sp. nov., isolated from beer-bottling plants.

    PubMed

    Herzog, Peter; Winkler, Ilka; Wolking, Dorothee; Kämpfer, Peter; Lipski, André

    2008-01-01

    Four Gram-negative, rod-shaped, non-spore-forming and non-motile bacterial strains were isolated from surfaces and biofilms associated with beer-bottling plants. Based on their 16S rRNA gene sequences these isolates were allocated to the genus Chryseobacterium. The sequence similarities of the isolates to the next most closely related type strains of this genus ranged from 96.4 to 98.3%. The presence of menaquinone MK-6 and predominant fatty acids 15:0 iso, 17:1 iso cis9, 15:0 iso 2-OH and 17:0 iso 3-OH supported the affiliation of these strains to the genus. The results of DNA-DNA hybridization, biochemical tests and chemotaxonomic properties allowed genotypic and phenotypic differentiation of the strains from the next most closely related Chryseobacterium species with validly published names. Therefore, the isolates represent four novel species for which the names Chryseobacterium ureilyticum (type strain F-Fue-04IIIaaaa(T)=DSM 18017(T)=CCUG 52546(T)), Chryseobacterium gambrini (type strain 5-1St1a(T)=DSM 18014(T)=CCUG 52549(T)), Chryseobacterium pallidum (type strain 26-3St2b(T)=DSM 18015(T)=CCUG 52548(T)) and Chryseobacterium molle (type strain DW3(T)=DSM 18016(T)=CCUG 52547(T)) are proposed. PMID:18175677

  19. Differentiation Among Blumeria graminis f. sp. tritici Isolates Originating from Wild Versus Domesticated Triticum Species in Israel.

    PubMed

    Ben-David, Roi; Parks, Ryan; Dinoor, Amos; Kosman, Evsey; Wicker, Thomas; Keller, Beat; Cowger, Christina

    2016-08-01

    Israel and its vicinity constitute a center of diversity of domesticated wheat species (Triticum aestivum and T. durum) and their sympatrically growing wild relatives, including wild emmer wheat (T. dicoccoides). We investigated differentiation within the forma specialis of their obligate powdery mildew pathogen, Blumeria graminis f. sp. tritici. A total of 61 B. graminis f. sp. tritici isolates were collected from the three host species in four geographic regions of Israel. Genetic relatedness of the isolates was characterized using both virulence patterns on 38 wheat lines (including 21 resistance gene differentials) and presumptively neutral molecular markers (simple-sequence repeats and single-nucleotide polymorphisms). All isolates were virulent on at least some genotypes of all three wheat species tested. All assays divided the B. graminis f. sp. tritici collection into two distinct groups, those from domesticated hosts and those from wild emmer wheat. One-way migration was detected from the domestic wheat B. graminis f. sp. tritici population to the wild emmer B. graminis f. sp. tritici population at a rate of five to six migrants per generation. This gene flow may help explain the overlap between the distinct domestic and wild B. graminis f. sp. tritici groups. Overall, B. graminis f. sp. tritici is significantly differentiated into wild-emmer and domesticated-wheat populations, although the results do not support the existence of a separate f. sp. dicocci.

  20. Thermolongibacillus altinsuensis gen. nov., sp. nov. and Thermolongibacillus kozakliensis sp. nov., aerobic, thermophilic, long bacilli isolated from hot springs.

    PubMed

    Cihan, Arzu Coleri; Koc, Melih; Ozcan, Birgul; Tekin, Nilgun; Cokmus, Cumhur

    2014-01-01

    Two novel endospore-forming, aerobic bacilli, strains E173a(T) and E265(T), were isolated from soil and sediment samples from Kozakli and Altinsu hot springs, Nevsehir (Turkey). Their young cells in the exponential phase of growth were motile, Gram-stain-positive, straight rods, 0.6-1.1×3.0-8.0 µm in size, but they became strikingly long, approximately 0.6-1.2 by 9.0-35.0 µm, after the stationary phase of growth. Cells varied in tests for oxidase, and had a weakly positive reaction for catalase. Both strains could grow between 40 and 70 °C, with optimal growth at 60 °C (E173a(T)) and 55 °C (E265(T)). Growth occurred within the range pH 5.0-11.0 with optimal growth at pH 9.0 (E173a(T)) and pH 8.5 (E265(T)). Strain E173a(T) grew within a salinity range from 0 to1.5 % (w/v) NaCl with optimal growth at 0.5 %, while strain E265(T) grew within the range 0-5.0 % (w/v), with an optimum at 3.0 %. The new isolates differed from each other in some phenotypic and chemotaxonomic characters as well as repetitive extragenic palindromic element PCR (rep-PCR) fingerprints. 16S rRNA gene sequence similarities suggested distant relationships with other members of the family Bacillaceae (<95.8 %), although the two strains showed 97.5 % sequence similarity between them, and had 55 % relatedness by DNA-DNA hybridization. The DNA G+C contents were 44.8 (E173a(T)) and 43.5 mol% (E265(T)). Moreover, the chemotaxonomic data of E173a(T) and E265(T) [presence of low amounts of meso-diaminopimelic acid, A1γ to A1γ' cross-linkage types in peptidoglycan, fatty acids including iso-C15 : 0 (>60 %), iso-C17 : 0 and C16 : 0] supported the consideration of these isolates as members of a novel genus. Based upon phenotypic, phylogenetic and chemotaxonomic characteristics, it is proposed that new isolates represent a novel genus, Thermolongibacillus gen. nov., with two novel species: Thermolongibacillus altinsuensis sp. nov. (type strain E265(T) = DSM 24979(T