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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

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

    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)). PMID:19643879

  3. Actinoplanes lichenis sp. nov., isolated from lichen.

    Phongsopitanun, Wongsakorn; Matsumoto, Atsuko; Inahashi, Yuki; Kudo, Takuji; Mori, Mihoko; Shiomi, Kazuro; Takahashi, Yoko; Tanasupawat, Somboon

    2016-01-01

    A novel species of the genus Actinoplanes, strain LDG1-22T, for which we propose the name Actinoplanes lichenis sp. nov., was isolated from a lichen sample collected from tree bark in Thailand. The taxonomic position of the species has been described based on a polyphasic approach. Strain LDG1-22T produced irregular sporangia on agar media. It contained meso-diaminopimelic acid in the cell-wall peptidoglycan. The major menaquinone was MK-9(H4); the polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and phosphatidylglycerol. Whole-cell hydrolysates contained ribose, glucose, mannose and small amounts of arabinose and xylose. The major cellular fatty acids were anteiso-C15 : 0 (31.2 %) and iso-C16 : 0 (14.2 %). Mycolic acids were absent. The G+C content was 73.6 %. 16S rRNA gene sequence analysis of strain LDG1-22T showed highest similarity (98.8 %) to Actinoplanes friuliensis DSM 45797T and it clustered with Actinoplanes nipponensis JCM 3264T and Actinoplanes missouriensis JCM 3121T in phylogenetic tree analysis. On the basis of the phenotypic characteristics and DNA-DNA relatedness, strain LDG1-22T could be distinguished from related species of the genus Actinoplanes and so represents a novel species of this genus. The type strain of Actinoplanes lichenis sp. nov. is LDG1-22T ( = JCM 30485T = TISTR 2343T = PCU 344T). PMID:26552374

  4. Tenacibaculum geojense sp. nov., isolated from seawater.

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

    2012-01-01

    A Gram-negative, non-flagellated, non-spore-forming bacterium, designated YCS-6(T), that was motile by gliding, was isolated from seawater on the southern coast of Korea. Strain YCS-6(T) grew optimally at 30 °C and with 2% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YCS-6(T) fell within the genus Tenacibaculum and was most closely associated with Tenacibaculum litopenaei B-I(T), with which the isolate exhibited 95.9% 16S rRNA gene sequence similarity. Sequence similarity between strain YCS-6(T) and other members of the genus Tenacibaculum was 93.8-95.7%. Strain YCS-6(T) contained menaquinone-6 (MK-6) as the predominant respiratory quinone and iso-C(15:0), summed feature 3 (iso-C(15:0) 2-OH and/or C(16:1)ω7c), iso-C(15:0) 3-OH and iso-C(15:1) G as the major fatty acids. The DNA G+C content was 32.7 mol%. Differential phenotypic properties and phylogenetic distinctiveness distinguished strain YCS-6(T) from all other members of the genus Tenacibaculum. On the basis of our phenotypic, chemotaxonomic and phylogenetic data, strain YCS-6(T) is considered to represent a novel species of the genus Tenacibaculum, for which the name Tenacibaculum geojense sp. nov. is proposed. The type strain is YCS-6(T) (=KCTC 23423(T) =CCUG 60527(T)). PMID:21257684

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

    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

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

    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)). PMID:25351880

  7. Flavobacterium shanxiense sp. nov., isolated from soil.

    Yang, Fan; Liu, Hong-Ming; Zhang, Rong; Chen, Ding-Bin; Wang, Xiang; Yan, Xin; Hong, Qing; Li, Shun-Peng

    2015-06-01

    Strain YF-2(T), a Gram-staining-negative, non-motile, non-spore-forming, light-yellow-pigmented bacterium, was isolated from soil samples collected in the city of Yuncheng, Shanxi province of China. Strain YF-2(T) grew over a temperature range of 25-37 °C, at pH 5.0-8.0 and with 0-5 % (w/v) NaCl. Phylogenetic analysis based on sequence of the 16S rRNA gene showed that strain YF-2(T) was closely related to strains Flavobacterium akiainvivens CIP 110358(T) and Flavobacterium hauense KCTC 32147(T) with 95.99 and 95.92 % sequence similarity, respectively. The dominant fatty acids of strain YF-2(T) were Summed Feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c) (21.97 %), iso-C15:0 (18.65 %), iso-C17:0 3OH (11.41 %), C16:0 (9.92 %), and anteiso-C15:0 (6.21 %). It contained phosphatidylethanolamine and menaquinone MK-6 as major polar lipid and respiratory quinone, respectively. Strain YF-2(T) differs from other Flavobacterium species in many characteristics and represents a novel species, for which the name Flavobacterium shanxiense sp. nov. is proposed. The type strain is strain YF-2(T) (=CCTCC AB 2014079(T) = JCM 30153(T)). PMID:25726422

  8. Flavobacterium procerum sp. nov., isolated from freshwater.

    Feng, Qingqing; Han, Lu; Yuan, Xin; Tan, Xu; Gao, Yuan; Lv, Jie

    2015-08-01

    A Gram-reaction-negative, strictly aerobic, yellow-pigmented, rod-shaped bacterium, designated strain T3T, was isolated from freshwater of Chishui River flowing through Maotai town, Guizhou, south-west China. Analysis of the16S rRNA gene sequence indicated that strain T3T was a member of the genus Flavobacterium and closely related to Flavobacterium resistens DSM 19382T (96.8 %). The novel strain was able to grow at 10-34 °C (optimum 28 °C), pH 6.0-11.0 (optimum pH 8.0-9.0) and with 0-2.0 % (w/v) NaCl (optimum 0 %). The major polar lipids were phosphatidylethanolamine, two unknown glycolipids, five unknown aminolipids and four unidentified lipids, and the major respiratory quinone was MK-6. The predominant fatty acids were C16  :  1ω7c and/or C16  :  1ω6c and iso-C15  :  0. The DNA G+C content of the strain was 36 mol  %. Based on these data, strain T3T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium procerum sp. nov. is proposed. The type strain is T3T ( = CGMCC 1.12926T = JCM 30113T). PMID:25969476

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

    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

  10. Streptomyces andamanensis sp. nov., isolated from soil.

    Sripreechasak, Paranee; Tamura, Tomohiko; Shibata, Chiyo; Suwanborirux, Khanit; Tanasupawat, Somboon

    2016-05-01

    A novel actinomycete, strain KC-112T, was isolated from soil collected from Similan Islands, Phang-Nga Province, Thailand. The strain exhibited morphological and chemotaxonomic characteristics consistent with those of members of the genus Streptomyces. The formation of smooth spiral spore chains was observed on aerial mycelia. ll-Diaminopimelic acid was detected in whole-cell hydrolysates, but no diagnostic sugars were detected and the strain lacked mycolic acids. The N-acyl type of muramic acid was acetyl. The major menaquinones were MK-9(H8), MK-9(H6) and MK-9(H2). The predominant cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unknown phospholipid, an unknown aminolipid, unknown lipids and an unknown glycolipid. The DNA G+C content was 73 mol%. On the basis of 16S rRNA gene sequence analysis, strain KC-112T was closely related to Streptomyces fumanus NBRC 13042T (98.8 % 16S rRNA gene sequence similarity), Streptomyces anandii NBRC 13438T (98.8 %) and Streptomyces capillispiralis NBRC 14222T (98.8 %). DNA-DNA relatedness values among strain KC-112T and type strains of closely related species were lower than 70 %. On the basis of evidence from this taxonomic study using a polyphasic approach, strain KC-112T represents a novel species of the genus Streptomyces, namely Streptomyces andamanensis sp. nov. The type strain is KC-112T ( = KCTC 29502T = NBRC 110085T = PCU 347T = TISTR 2401T). PMID:26908169

  11. Massilia flava sp. nov., isolated from soil.

    Wang, Jiewei; Zhang, Jianli; Pang, Huancheng; Zhang, Yabo; Li, Yuyi; Fan, Jinping

    2012-03-01

    A Gram-stain-negative, rod-shaped bacterium, designated strain Y9(T), was isolated from a soil sample collected in Ningxia Province in China and was characterized to determine its taxonomic position. Strain Y9(T) contained Q-8 as the predominant ubiquinone. Major fatty acid components were summed feature 3 (C(16:1)ω7c and/or iso-C(15:0) 2-OH) and C(16:0). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The G+C content of the genomic DNA of strain Y9(T) was 68.7 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that the strain fell within the evolutionary radiation encompassed by the genus Massilia. Levels of 16S rRNA gene sequence similarity between strain Y9(T) and the type strains of recognized Massilia species ranged from 95.2 to 98.2%, the highest values being with Massilia albidiflava 45(T) (98.2%) and Massilia lutea 101(T) (98.0%). However, levels of DNA-DNA relatedness between strain Y9(T) and M. albidiflava KCTC 12343(T) and M. lutea KCTC 12345(T) were 37 and 26%, respectively. Strain Y9(T) was clearly differentiated from its nearest phylogenetic relatives in the genus Massilia based on phenotypic, chemotaxonomic and phylogenetic properties. Therefore, strain Y9(T) is considered to represent a novel species of the genus Massilia, for which the name Massilia flava sp. nov. is proposed. The type strain is Y9(T) (=CGMCC 1.10685(T) =KCTC 23585(T)). PMID:21515701

  12. Emulsion properties of algae soluble protein isolate from Tetraselmis sp.

    Schwenzfeier, A.; Helbig, A.; Wierenga, P.A.; Gruppen, H.

    2013-01-01

    To study possible applications of microalgae proteins in foods, a colourless, protein-rich fraction was isolated from Tetraselmis sp. In the present study the emulsion properties of this algae soluble protein isolate (ASPI) were investigated. Droplet size and droplet aggregation of ASPI stabilized o

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

    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

  14. Isolation of C11 Cyclopentenones from Two Didemnid Species, Lissoclinum sp. and Diplosoma sp.

    Katsuhiro Ueda

    2009-12-01

    Full Text Available A series of new C11 cyclopentenones 1-7 was isolated, together with four known metabolites 9/10, 12 and 13, from the extract of the didemnid ascidian Lissoclinum sp. The other didemnid ascidian Diplosoma sp. contained didemnenones 1, 2 and 5, and five known metabolites 8-12. The structures of 1-7 were elucidated by spectroscopic analyses. Cytotoxicity of the isolated compounds was evaluated against three human cancer cell lines (HCT116, A431 and A549.

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

    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...

  16. Photobacterium swingsii sp. nov., isolated from marine organisms.

    Gomez-Gil, Bruno; Roque, Ana; Rotllant, Guiomar; Peinado, Lauro; Romalde, Jesus L; Doce, Alejandra; Cabanillas-Beltrán, Hector; Chimetto, Luciane A; Thompson, Fabiano L

    2011-02-01

    Six Gram-negative coccobacilli were isolated from Pacific oysters (Crassostrea gigas) from Mexico and haemolymph of spider crabs (Maja brachydactyla) from Spain. All of the isolates grew as small green colonies on thiosulphate-citrate-bile salts-sucrose (TCBS) agar and were facultatively anaerobic, oxidase-positive and sensitive to the vibriostatic agent O/129. Repetitive palindromic PCR analysis revealed a high degree of genomic homogeneity among the isolates. Several phenotypic traits differentiated the isolates from the type strains of species of the genus Photobacterium. DNA-DNA relatedness between two representative isolates and their closest phylogenetic neighbours by 16S rRNA gene sequence similarity, Photobacterium aplysiae CAIM 14(T) and Photobacterium frigidiphilum CAIM 20(T), was 44.01-53.85 %. We propose a novel species of the genus Photobacterium to accommodate the six isolates, with the name Photobacterium swingsii sp. nov. The type strain is CAIM 1393(T) (=CECT 7576(T)). PMID:20228205

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

    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

  18. Analysis of Chromobacterium sp. natural isolates from different Brazilian ecosystems

    Nascimento Andréa MA; Santos Fabrício R; Astolfi-Filho Spartaco; Chartone-Souza Edmar; Lima-Bittencourt Cláudia I

    2007-01-01

    Abstract Background Chromobacterium violaceum is a free-living bacterium able to survive under diverse environmental conditions. In this study we evaluate the genetic and physiological diversity of Chromobacterium sp. isolates from three Brazilian ecosystems: Brazilian Savannah (Cerrado), Atlantic Rain Forest and Amazon Rain Forest. We have analyzed the diversity with molecular approaches (16S rRNA gene sequences and amplified ribosomal DNA restriction analysis) and phenotypic surveys of anti...

  19. Pantoea allii sp. nov., isolated from onion plants and seed.

    Brady, Carrie L; Goszczynska, Teresa; Venter, Stephanus N; Cleenwerck, Ilse; De Vos, Paul; Gitaitis, Ronald D; Coutinho, Teresa A

    2011-04-01

    Eight yellow-pigmented, Gram-negative, rod-shaped, oxidase-negative, motile, facultatively anaerobic bacteria were isolated from onion seed in South Africa and from an onion plant exhibiting centre rot symptoms in the USA. The isolates were assigned to the genus Pantoea on the basis of phenotypic and biochemical tests. 16S rRNA gene sequence analysis and multilocus sequence analysis (MLSA), based on gyrB, rpoB, infB and atpD sequences, confirmed the allocation of the isolates to the genus Pantoea. MLSA further indicated that the isolates represented a novel species, which was phylogenetically most closely related to Pantoea ananatis and Pantoea stewartii. Amplified fragment length polymorphism analysis also placed the isolates into a cluster separate from P. ananatis and P. stewartii. Compared with type strains of species of the genus Pantoea that showed >97 % 16S rRNA gene sequence similarity with strain BD 390(T), the isolates exhibited 11-55 % whole-genome DNA-DNA relatedness, which confirmed the classification of the isolates in a novel species. The most useful phenotypic characteristics for the differentiation of the isolates from their closest phylogenetic neighbours are production of acid from amygdalin and utilization of adonitol and sorbitol. A novel species, Pantoea allii sp. nov., is proposed, with type strain BD 390(T) ( = LMG 24248(T)). PMID:20495023

  20. Bifidobacterium commune sp. nov. isolated from the bumble bee gut.

    Praet, Jessy; Meeus, Ivan; Cnockaert, Margo; Aerts, Maarten; Smagghe, Guy; Vandamme, Peter

    2015-05-01

    Bifidobacteria were isolated from the gut of Bombus lapidarius, Bombus terrestris and Bombus hypnorum bumble bees by direct isolation on modified trypticase phytone yeast extract agar. The MALDI-TOF MS profiles of four isolates (LMG 28292(T), R-53560, R-53124, LMG 28626) were found to be identical and did not cluster with the profiles of established Bifidobacterium species. Analysis of the 16S rRNA gene sequence of strain LMG 28292(T) revealed that LMG 28292(T) is most closely related to the Bifidobacterium bohemicum type strain (96.8%), which was also isolated from bumble bee gut specimens. The hsp60 gene of strain LMG 28292(T) shows 85.8% sequence similarity to that of the B. bohemicum type strain. The (GTG)5-PCR profiles and the hsp60 sequences of all four isolates were indistinguishable; however, three different phenotypes were observed among the four isolates by means of the API 50CHL microtest system. Based on the phylogenetic, genotypic and phenotypic data, we propose to classify the four isolates within the novel species Bifidobacterium commune sp. nov., with LMG 28292(T) (= DSM 28792(T)) as the type strain. PMID:25753540

  1. Streptomyces mangrovi sp. nov., isolated from mangrove forest sediment.

    Yousif, Ghada; Busarakam, Kanungnid; Kim, Byung-Yong; Goodfellow, Michael

    2015-09-01

    A Streptomyces strain isolated from a mangrove sediment was classified using a polyphasic approach. The organism, isolate GY1(T), was found to have chemical and morphological properties typical of members of the genus Streptomyces. The isolate was shown to form a distinct phyletic line within the Streptomyces radiopugnans 16S rRNA gene subclade and to be closely related to the type strain of Streptomyces fenhuangensis (98.7 % similarity). It is also closely related to the type strain of Streptomyces bakulensis which was also closely related to members of the Streptomyces glaucosporus 16S rRNA gene subclade. Isolate GY1(T) was distinguished readily from the S. barkulensis type strain and from species classified in the S. radiopugnans clade using a combination of morphological and physiological properties, including a requirement for seawater for growth. Based on the genotypic and phenotypic data, it is proposed that isolate GY1(T) (=NCIMB 14980(T), NRRL B-69296(T)) be classified in the genus Streptomyces as Streptomyces mangrovi sp. nov. PMID:26187116

  2. Treponema berlinense sp. nov. and Treponema porcinum sp. nov., novel spirochaetes isolated from porcine faeces.

    Nordhoff, Marcel; Taras, David; Macha, Moritz; Tedin, Karsten; Busse, Hans-Jürgen; Wieler, Lothar H

    2005-07-01

    Limit-dilution procedures were used to isolate seven, helically coiled bacterial strains from faeces of swine that constituted two unidentified taxa. Comparative 16S rRNA gene sequence analysis showed highest similarity values with species of the genus Treponema indicating that the isolates are members of this genus. Strain 7CPL208(T), as well as five further isolates, and 14V28(T) displayed the highest 16S rRNA gene sequence similarities with Treponema pectinovorum ATCC 33768(T) (92.3%) and Treponema parvum OMZ 833(T) (89.9%), respectively. Polar lipid profiles distinguished 7CPL208(T) and 14V28(T) from each other as well as from related species. Based on their phenotypic and genotypic distinctiveness, strains 7CPL208(T) and 14V28(T) are suggested to represent two novel species of the genus Treponema, for which the names Treponema berlinense sp. nov. and Treponema porcinum sp. nov. are proposed. The type strain for Treponema berlinense is 7CPL208(T) (=ATCC BAA-909(T)=CIP 108244(T)=JCM 12341(T)) and for Treponema porcinum 14V28(T) (=ATCC BAA-908(T)=CIP 108245(T)=JCM 12342(T)). PMID:16014500

  3. Janibacter corallicola sp. nov., isolated from coral in Palau.

    Kageyama, Akiko; Takahashi, Yoko; Yasumoto-Hirose, Mina; Kasai, Hiroaki; Shizuri, Yoshikazu; Omura, Satoshi

    2007-06-01

    A novel Janibacter species is described on the basis of phenotypic, chemotaxonomic and genotypic data. Two bacterial strains were isolated in Palau, which were both Gram-positive, catalase-positive bacteria with meso-diaminopimelic acid as the diagnostic diamino acid of the peptidoglycan. The major menaquinone was MK-8(H(4)). Mycolic acids were not detected. The G+C content of the DNA was 70-71 mol%. Comparative 16S rDNA studies of the two isolated strains revealed that they both belonged to the genus Janibacter. DNA-DNA relatedness data revealed that 04PA2-Co5-61(T) and 02PA-Ca-009 belong to the same species, a new species of the genus Janibacter. From these results, Janibacter corallicola sp. nov. is proposed, with the type strain 04PA2-Co5-61(T) (=MBIC 08265(T), DSM 18906(T)). PMID:17726299

  4. Aeromonas aquariorum sp. nov., isolated from aquaria of ornamental fish.

    Martínez-Murcia, A J; Saavedra, M J; Mota, V R; Maier, T; Stackebrandt, E; Cousin, S

    2008-05-01

    During a survey to determine the prevalence of Aeromonas strains in water and skin of imported ornamental fish, 48 strains presumptively identified as Aeromonas were isolated but they could not be identified as members of any previously described Aeromonas species. These strains were subjected to a polyphasic approach including phylogenetic analysis derived from gyrB, rpoD and 16S rRNA gene sequencing, DNA-DNA hybridization, MALDI-TOF MS analysis, genotyping by RAPD and extensive biochemical and antibiotic susceptibility tests in order to determine their taxonomic position. Based on the results of the phylogenetic analyses and DNA-DNA hybridization data, we describe a novel species of the genus Aeromonas, for which the name Aeromonas aquariorum sp. nov. is proposed, with strain MDC47T (=DSM 18362T =CECT 7289T) as the type strain. This is the first Aeromonas species description based on isolations from ornamental fish. PMID:18450708

  5. Aeromonas lusitana sp. nov., Isolated from Untreated Water and Vegetables.

    Martínez-Murcia, Antonio; Beaz-Hidalgo, Roxana; Navarro, Aaron; Carvalho, M João; Aravena-Román, Max; Correia, Antonio; Figueras, M José; Saavedra, M José

    2016-06-01

    During previous studies to evaluate the phylogenetic diversity of Aeromonas from untreated waters and vegetables intended for human consumption, a group of isolates formed a unique gyrB phylogenetic cluster, separated from those of all other species described so far. A subsequent extensive phenotypic characterization, DNA-DNA hybridization, 16S rRNA gene sequencing, multi-locus phylogenetic analysis of the concatenated sequence of seven housekeeping genes (gyrB, rpoD, recA, dnaJ, gyrA, dnaX, and atpD; 4705 bp), and ERIC-PCR, were performed in an attempt to ascertain the taxonomy position of these isolates. This polyphasic approach confirmed that they belonged to a novel species of the genus Aeromonas, for which the name Aeromonas lusitana sp. nov. is proposed, with strain A.11/6(T) (=DSMZ 24095(T), =CECT 7828(T)) as the type strain. PMID:26868258

  6. Belliella kenyensis sp. nov., isolated from an alkaline lake.

    Akhwale, Juliah Khayeli; Göker, Markus; Rohde, Manfred; Schumann, Peter; Klenk, Hans-Peter; Boga, Hamadi Iddi

    2015-02-01

    A red-pigmented, Gram-reaction-negative, aerobic bacterial strain, designated No.164(T), was isolated from sediment sample from the alkaline Lake Elmenteita located in the Kenyan Rift Valley. Results of 16S rRNA gene sequence analysis indicated that the isolate represented a member of the genus Belliella, with the highest sequence similarity (97 %) to Belliella pelovolcani DSM 46698(T). Optimal growth temperature was 30-35 °C, at pH 7.0-12.0 in the presence of 0-4 % (w/v) NaCl. Flexirubins were absent. The respiratory menaquinone (MK-7), predominant cellular fatty acids (iso-C15 : 0, anteiso-C15 : 0 and a mixture of C16 : 1ω7c and/or iso-C15 : 0 2-OH) and DNA G+C content (38.1 mol%) of strain No.164(T) were consistent with those of other members of the genus Belliella. The polar lipids consisted of phosphatidylethanolamine, eight unspecified lipids and one unspecified phospholipid. Several phenotypic characteristics can be used to differentiate this isolate from those of other species of the genus Belliella. The results of polyphasic analyses presented in this study indicated that this isolate should be classified as representing a novel species of the genus Belliella. The name Belliella kenyensis sp. nov. is therefore proposed; the type strain is strain No.164(T) ( = DSM 46651(T) = CECT 8551(T)). PMID:25385994

  7. Bacillus cellulasensis sp. nov., isolated from marine sediment.

    Mawlankar, Rahul; Thorat, Meghana N; Krishnamurthi, Srinivasan; Dastager, Syed G

    2016-01-01

    A novel bacterial strain NIO-1130(T) was isolated from sediment sample taken from Chorao Island, Goa Province, India, and subjected to a taxonomic investigation. The strain was Gram-positive, aerobic, and motile. Phylogenetic analysis based on 16S rRNA gene sequences placed the isolate within the genus Bacillus and strain NIO-1130(T) showed highest sequence similarity with Bacillus halosaccharovorans DSM 25387(T) (98.4%) and Bacillus niabensis CIP 109816(T) (98.1%), whereas other Bacillus species showed <97.0% similarity. Tree based on gyrB gene sequence revealed that strain bacillus group. The major menaquinone was MK-7 and the predominant cellular fatty acids were iso-C15:0, anteiso-C15:0, iso-C17:0, and anteiso-C17:0. The strain showed a DNA G+C content of 39.9 mol%. DNA-DNA hybridization studies revealed that strain NIO-1130(T) exhibits 70% similarity with Bacillus halosaccharovorans DSM 25387(T) and Bacillus niabensis CIP 109816(T). On the basis of physiological, biochemical, chemotaxonomic and phylogenetic analyses, we consider the isolate to represent a novel species of the genus Bacillus, for which the name Bacillus cellulasensis sp. nov., is proposed. The type strain is NIO-1130(T) (=NCIM 5461(T)=CCTCC AB 2011126(T)). PMID:26410293

  8. Tenacibaculum litopenaei sp. nov., isolated from a shrimp mariculture pond.

    Sheu, Shih-Yi; Lin, Kuan-Yin; Chou, Jui-Hsing; Chang, Poh-Shing; Arun, A B; Young, Chiu-Chung; Chen, Wen-Ming

    2007-05-01

    A yellow-coloured, aerobic, Gram-negative, rod-shaped bacterial strain, designated B-I(T), was isolated from the water of a shrimp (Litopenaeus vannamei) mariculture pond in Taiwan. No species with a validly published name showed 16S rRNA gene sequence similarity of more than 96.5 % to this novel isolate. The highest sequence similarities displayed by strain B-I(T) (93.2-96.1 %) were to members of the genus Tenacibaculum. The phenotypic properties of this organism were consistent with its classification in the genus Tenacibaculum. The novel isolate could be distinguished from all Tenacibaculum species by several phenotypic characteristics. The major fatty acids were iso-C(15 : 0) (22 %), summed feature 3 (C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH; 21.3 %), iso-C(17 : 0) 3-OH (12.7 %) and iso-C(15 : 1) (8.7 %). The G+C content of the genomic DNA was 35.2 mol%. Hence, genotypic and phenotypic data demonstrate that strain B-I(T) should be classified within a novel species in the genus Tenacibaculum, for which the name Tenacibaculum litopenaei sp. nov. is proposed. The type strain is B-I(T) (=BCRC 17590(T)=LMG 23706(T)). PMID:17473274

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

    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). PMID:24122118

  10. Azospirillum rugosum sp. nov., isolated from oil-contaminated soil.

    Young, C C; Hupfer, H; Siering, C; Ho, M-J; Arun, A B; Lai, W-A; Rekha, P D; Shen, F-T; Hung, M-H; Chen, W-M; Yassin, A F

    2008-04-01

    The taxonomic status of a light-orange-coloured bacterial isolate from an oil-contaminated soil sample was characterized by using a polyphasic taxonomic approach. Comparative analysis of 16S rRNA gene sequences demonstrated that the isolate belonged phylogenetically to the genus Azospirillum, with Azospirillum canadense, Azospirillum brasilense and Azospirillum doebereinerae as its closest phylogenetic relatives (97.3, 97.0 and 97.0 % similarity, respectively). DNA-DNA pairing studies showed that the unidentified organism displayed 25.0, 17.0 and 19.0 % relatedness to the type strains of A. brasilense, A. canadense and A. doebereinerae, respectively. The generic assignment was confirmed by chemotaxonomic data, which revealed a fatty acid profile that was characteristic of the genus Azospirillum, consisting of straight-chain saturated and unsaturated fatty acids with C18 : 1 omega 7c as the major fatty acid, and ubiquinone with ten isoprene units (Q-10) as the predominant respiratory quinone. On the basis of both the phenotypic and molecular genetic evidence, it is proposed that the unknown isolate be classified as a representative of a novel species of the genus Azospirillum, for which the name Azospirillum rugosum sp. nov. is proposed. The type strain is IMMIB AFH-6T (=CCUG 53966T=DSM 19657T). PMID:18398202

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

    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

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

    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). PMID:25964516

  13. Niastella vici sp. nov., isolated from farmland soil.

    Chen, Lu; Wang, Dan; Yang, Sining; Wang, Gejiao

    2016-04-01

    Strain DJ57T is a Gram-reaction-negative, filamentous-shaped, non-flagellated, aerobic bacterium isolated from farmland soil in Hunan province of China. 16S rRNA gene sequence analysis demonstrated that this isolate belonged to the genus Niastella, with 95.83 % nucleotide identity to Niastella populi THYL-44T, while the similarities to other type strains of species of the genus Niastella were less than 95.76 %. The major isoprenoid quinone was menaquinone-7 and the major fatty acids (>5 %) were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G, anteiso-C15 : 0 and iso-C16 : 0. The DNA G+C content was 44 mol%. Polar lipids were phosphatidylethanolamine, three unknown aminophospholipids, three unknown phospholipids and six unknown lipids. The chemotaxonomic, phenotypic and genotypic data indicated that strain DJ57T represents a novel species of the genus Niastella, for which the name Niastella vici sp. nov. is proposed. The type strain is DJ57T ( = KCTC 42474T = CCTCC AB 2015052T). PMID:26828035

  14. Hymenobacter sedentarius sp. nov., isolated from a soil.

    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 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

  15. Paenibacillus terreus sp. nov., isolated from forest soil.

    Huang, Zhi; Dai, Wenjuan; Zhou, Zhijun; Wang, Guoxiang; Lin, Guoqing; Yan, Xixue; Zhao, Fei

    2016-01-01

    A Gram-stain-positive, rod-shaped, endospore-forming, motile bacterium, designated D33T, was isolated from a forest soil sample. The strain grew optimally at 30-37 °C, pH 8.0 and with 1 % (w/v) NaCl. The 16S rRNA gene sequence of the isolate showed similarities lower than 97 % with respect to species of the genus Paenibacillus. Strain D33T contained meso-diaminopimelic acid in the cell-wall peptidoglycan, and ribose and lower amounts of glucose and galactose as the whole-cell sugars. The major cellular fatty acid was anteiso-C15 : 0, and menaquinone-7 (MK-7) was the only respiratory quinone. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmethylethanolamine, two glycolipids and an unknown lipid. The DNA G+C content was 51.1 mol%. The low DNA-DNA relatedness values between strain D33T and recognized species of the genus Paenibacillus, together with many phenotypic properties supported the classification of strain D33T as representative of a novel species of the genus Paenibacillus, for which the name Paenibacillus terreus sp. nov. is proposed. The type strain is D33T ( = KACC 18491T = DSM 100035T = CCTCC AB 2015273T). PMID:26493172

  16. Lactococcus nasutitermitis sp. nov. isolated from a termite gut.

    Yan Yang, Shu; Zheng, Ying; Huang, Zhou; Min Wang, Xue; Yang, Hong

    2016-01-01

    Bacterial strain M19T was isolated from the gut of a wood-feeding termite, Nasutitermes hainanensis. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain M19T was related to members of the genus Lactococcus, with sequence similarities ranging from 84.8 to 95.5 %. Comparison of housekeeping gene ropB sequences revealed that strain M19T was well separated from Lactococcus fujiensis JCM 16395T and Lactococcus hircilactis 117T. The isolate was Gram-stain-positive, catalase-negative and non-motile. Cells were coccoid or ovoid-shaped, and occurred singly, in pairs or as short chains. Growth of strain M19T occurred at 10-40 °C and at pH 5.0-7.5. The DNA G+C content of strain M19T was 39.6 mol% and the major fatty acids were C16 : 0, cyclo-C19 : 0ω8c, C18 : 1ω9c, summed feature 7 and summed feature 8. Based on the phylogenetic, chemotaxonomic and phenotypic data presented, strain M19T represents a novel species of the genus Lactococcus, for which the name Lactococcus nasutitermitis sp. nov. is proposed. The type strain is M19T ( = CGMCC 1.15204T = NBRC 111537T). PMID:26546382

  17. Knoellia flava sp. nov., isolated from pig manure.

    Yu, Xiang; Du, Yan; Wang, Gejiao

    2012-02-01

    A gram-positive, aerobic, non-spore-forming actinobacterial strain, designated strain TL1(T), was isolated from pig manure in Wuhan, China. The cell wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were phosphatidylethanolamine, phosphatidylinositol and diphosphatidylglycerol. The predominant menaquinone was MK-8(H(4)). The major fatty acids (>10 %) were iso-C(16 : 0), iso-C(15 : 0) and C(17 : 1)ω8c. The genomic DNA G+C content was 70.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain TL1(T) was most closely related to the type strains of Knoellia sinensis (98.5 %), Knoellia subterranea (98.2 %) and Knoellia aerolata (96.9 %). DNA-DNA relatedness values of strain TL1(T) with the type strains of K. sinensis and K. subterranea were 27.3 and 34.0 %, respectively. Comparison of phenotypic, chemotaxonomic and phylogenetic characteristics among strain TL1(T) and related organisms revealed that the isolate represents a novel species of the genus Knoellia, for which the name Knoellia flava sp. nov. is proposed; the type strain is TL1(T) ( = CGMCC 1.10749(T) = KCTC 19810(T)). PMID:21441369

  18. Paenibacillus relictisesami sp. nov., isolated from sesame oil cake.

    Shimoyama, Takefumi; Johari, Nurziha Binti; Tsuruya, Atsuki; Nair, Arun; Nakayama, Toru

    2014-05-01

    A facultatively anaerobic, Gram-stain-positive, rod-shaped bacterium, designated strain KB0549T, was isolated from sesame oil cake. Cells were motile, round-ended rods, and produced central or terminal spores. The cell wall peptidoglycan contained meso-diaminopimelic acid as the diamino acid. The major fatty acids were anteiso-C15:0 and anteiso-C17:0. The DNA G+C content of strain KB0549T was 51.9 mol%. On the basis of 16S rRNA gene sequence phylogeny, strain KB0549T was affiliated with the genus Paenibacillus in the phylum Firmicutes and was most closely related to Paenibacillus cookii with 97.4% sequence similarity. Strain KB0549T was physiologically differentiated from P. cookii by the high content of anteiso-C17:0, inability to grow at 50 °C, spore position, and negative Voges-Proskauer reaction. Based on these unique physiological and phylogenetic characteristics, it is proposed that the isolate represents a novel species, Paenibacillus relictisesami sp. nov.; the type strain is KB0549T (=JCM 18068T=DSM 25385T). PMID:24478207

  19. Chromobacterium aquaticum sp. nov., isolated from spring water samples.

    Young, Chiu-Chung; Arun, A B; Lai, Wei-An; Chen, Wen-Ming; Chou, Jui-Hsing; Chao, Jiu-Hsing; Shen, Fo-Ting; Rekha, P D; Kämpfer, Peter

    2008-04-01

    Strain CC-SEYA-1T, a motile, Gram-negative, non-violet-pigmented bacterium, was isolated on nutrient agar from spring-water samples collected from Yang-Ming Mountain, Taipei County, Taiwan. 16S rRNA gene sequence studies showed that the strain clustered with Chromobacterium violaceum (96.8 % similarity) and Chromobacterium subtsugae (96.5 % similarity), followed by Aquitalea magnusonii (95.8 % similarity). The fatty acid profile was slightly different from those reported for C. violaceum, C. subtsugae and A. magnusonii. The results of DNA-DNA hybridization, and physiological and biochemical tests allowed both genotypic and phenotypic differentiation of the isolate from the described Chromobacterium species. It is evident from the data obtained that the strain should be classified as a novel species in the genus Chromobacterium. The name proposed for this taxon is Chromobacterium aquaticum sp. nov.; the type strain is CC-SEYA-1T (=CCUG 55175T=BCRC 17769T). PMID:18398186

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

    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

  1. Paenibacillus endophyticus sp. nov., isolated from nodules of Cicer arietinum.

    Carro, Lorena; Flores-Félix, José David; Cerda-Castillo, Eugenia; Ramírez-Bahena, Martha-Helena; Igual, José M; Tejedor, Carmen; Velázquez, Encarna; Peix, Alvaro

    2013-12-01

    A bacterial strain, designated PECAE04(T), was isolated from root nodules of Cicer arietinum in Spain. Phylogenetic analysis based on 16S rRNA gene sequence placed the isolate into the genus Paenibacillus with its closest relative being Paenibacillus castaneae Ch-32(T) with 98.4 % 16S rRNA gene sequence similarity followed by Paenibacillus glycanilyticus DS-1(T), Paenibacillus prosopidis PW21(T), Paenibacillus xinjiangensis B538(T) and Paenibacillus catalpae D75(T) with similarities ranging from 97.9 to 96.8 %. DNA-DNA hybridization measurements showed values lower than 20 % between the strain PECAE04(T) and any of these species. The isolate was a Gram-stain-positive, motile, sporulating rod. Catalase and oxidase activities were positive. Aesculin was hydrolysed but casein and gelatin were not. Acetoin production, H2S production, nitrate reduction and urease and caseinase production were negative. Growth was supported by many carbohydrates and organic acids as carbon sources. MK-7 was the predominant menaquinone and anteiso-C15 : 0, iso-C16 : 0 and C16 : 0 were the major fatty acids. Major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, a glycolipid, three phospholipids and an unidentified lipid. Meso-diaminopimelic acid was not detected in the peptidoglycan. The DNA G+C content was 52.9 mol%. Phylogenetic, chemotaxonomic and phenotypic analyses showed that strain PECAE04(T) should be considered to be a representative of a novel species of the genus Paenibacillus, for which the name Paenibacillus endophyticus sp. nov. is proposed. The type strain is PECAE04(T) ( = LMG 27297(T) = CECT 8234(T)). PMID:23852155

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

    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)). PMID:24928428

  3. A Newly Isolated Thermostable Lipase from Bacillus sp.

    Abu Bakar Salleh

    2011-05-01

    Full Text Available A thermophilic lipolytic bacterium identified as Bacillus sp. L2 via 16S rDNA was previously isolated from a hot spring in Perak, Malaysia. Bacillus sp. L2 was confirmed to be in Group 5 of bacterial classification, a phylogenically and phenotypically coherent group of thermophilic bacilli displaying very high similarity among their 16S rRNA sequences (98.5–99.2%. Polymerase chain reaction (PCR cloning of L2 lipase gene was conducted by using five different primers. Sequence analysis of the L2 lipase gene revealed an open reading frame (ORF of 1251 bp that codes for 417 amino acids. The signal peptides consist of 28 amino acids. The mature protein is made of 388 amino acid residues. Recombinant lipase was successfully overexpressed with a 178-fold increase in activity compared to crude native L2 lipase. The recombinant L2 lipase (43.2 kDa was purified to homogeneity in a single chromatography step. The purified lipase was found to be reactive at a temperature range of 55–80 °C and at a pH of 6–10. The L2 lipase had a melting temperature (Tm of 59.04 °C when analyzed by circular dichroism (CD spectroscopy studies. The optimum activity was found to be at 70 °C and pH 9. Lipase L2 was strongly inhibited by ethylenediaminetetraacetic acid (EDTA (100%, whereas phenylmethylsulfonyl fluoride (PMSF, pepstatin-A, 2-mercaptoethanol and dithiothreitol (DTT inhibited the enzyme by over 40%. The CD spectra of secondary structure analysis showed that the L2 lipase structure contained 38.6% α-helices, 2.2% ß-strands, 23.6% turns and 35.6% random conformations.

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

    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

  5. Marmoricola ginsengisoli sp. nov. and Marmoricola pocheonensis sp. nov. isolated from a ginseng-cultivating field.

    Lee, Hye-Yeon; Liu, Qingmei; Kang, Myung-Suk; Kim, Soo-Ki; Lee, Soon-Youl; Im, Wan-Taek

    2016-05-01

    Two novel actinobacteria, designated strains Gsoil 097T and Gsoil 818T, isolated from soil of a ginseng field, South Korea, were characterized by a polyphasic approach to clarify their taxonomic positions. They were Gram-reaction-positive, aerobic, non-spore-forming and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that both isolates belong to the genus Marmoricola and were related most closely to Marmicola solisilvae KIS18-7T (99.1 and 98.3 % similarity, respectively), Marmicola terrae JOS5-1T (97.9 and 97.9 %), Marmicola scoriae Sco-D01T (97.8 and 97.1 %) and Marmicola aequoreus SST-45T (97.5 and 97.0 %). The G+C content of the genomic DNA was 68.8 and 70.0 mol%, respectively. Both strains were characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-8(H4) as the predominant menaquinone and C17 : 1ω6c, C18 : 1ω9c, C18 : 0 10-methyl and iso-C16 : 0 as major fatty acids. These chemotaxonomic data supported the affiliation of both strains to the genus Marmoricola. However, levels of DNA-DNA relatedness between the two strains and closely related type strains of Marmoricola species were less than 30 %. Moreover, the results of physiological and biochemical tests allowed the phenotypic differentiation of strains Gsoil 097T and Gsoil 818T from other Marmoricola species with validly published names. Therefore, the two isolates represent two novel species, for which the names Marmoricola ginsengisoli sp. nov. (type strain Gsoil 097T = KACC 14267T = DSM 22772T) and Marmoricola pocheonensis sp. nov. (type strain Gsoil 818T = KACC 14275T = DSM 22773T) are proposed. PMID:26883120

  6. 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).

    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

  7. Kroppenstedtia pulmonis sp. nov. and Kroppenstedtia sanguinis sp. nov., isolated from human patients.

    Bell, Melissa E; Lasker, Brent A; Klenk, Hans-Peter; Hoyles, Lesley; Spröer, Catherine; Schumann, Peter; Brown, June M

    2016-05-01

    Three human clinical strains (W9323(T), X0209(T) and X0394) isolated from a lung biopsy, blood and cerebral spinal fluid, respectively, were characterised using a polyphasic taxonomic approach. Comparative analysis of the 16S rRNA gene sequences showed the three strains belong to two novel branches within the genus Kroppenstedtia: 16S rRNA gene sequence analysis of W9323(T) showed close sequence similarity to Kroppenstedtia eburnea JFMB-ATE(T) (95.3 %), Kroppenstedtia guangzhouensis GD02(T) (94.7 %) and strain X0209(T) (94.6 %); sequence analysis of strain X0209(T) showed close sequence similarity to K. eburnea JFMB-ATE(T) (96.4 %) and K. guangzhouensis GD02(T) (96.0 %). Strains X0209(T) and X0394 were 99.9 % similar to each other by 16S rRNA gene sequence analysis. The DNA-DNA relatedness was 94.6 %, confirming that X0209(T) and X0394 belong to the same species. Chemotaxonomic data for strains W9323(T) and X0209(T) were consistent with those described for the members of the genus Kroppenstedtia: the peptidoglycan was found to contain LL-diaminopimelic acid; the major cellular fatty acids were identified as iso-C15 and anteiso-C15; and the major menaquinone was identified as MK-7. Differences in endospore morphology, carbon source utilisation profiles, and cell wall sugar patterns of strains W9323(T) and X0209(T), supported by phylogenetic analysis, enabled us to conclude that the strains each represent a new species within the genus Kroppenstedtia, for which the names Kroppenstedtia pulmonis sp. nov. (type strain W9323(T) = DSM 45752(T) = CCUG 68107(T)) and Kroppenstedtia sanguinis sp. nov. (type strain X0209(T) = DSM 45749(T) = CCUG 38657(T)) are proposed. PMID:26910402

  8. Pseudomonas helleri sp. nov. and Pseudomonas weihenstephanensis sp. nov., isolated from raw cow's milk.

    von Neubeck, M; Huptas, C; Glück, C; Krewinkel, M; Stoeckel, M; Stressler, T; Fischer, L; Hinrichs, J; Scherer, S; Wenning, M

    2016-03-01

    Analysis of the microbiota of raw cow's milk and semi-finished milk products yielded seven isolates assigned to the genus Pseudomonas that formed two individual groups in a phylogenetic analysis based on partial rpoD and 16S rRNA gene sequences. The two groups could be differentiated from each other and also from their closest relatives as well as from the type species Pseudomonas aeruginosa by phenotypic and chemotaxonomic characterization and average nucleotide identity (ANIb) values calculated from draft genome assemblies. ANIb values within the groups were higher than 97.3 %, whereas similarity values to the closest relatives were 85 % or less. The major cellular lipids of strains WS4917T and WS4993T were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol; the major quinone was Q-9 in both strains, with small amounts of Q-8 in strain WS4917T. The DNA G+C contents of strains WS4917T and WS4993T were 58.08 and 57.30 mol%, respectively. Based on these data, strains WS4917T, WS4995 ( = DSM 29141 = LMG 28434), WS4999, WS5001 and WS5002 should be considered as representatives of a novel species of the genus Pseudomonas, for which the name Pseudomonas helleri sp. nov. is proposed. The type strain of Pseudomonas helleri is strain WS4917T ( = DSM 29165T = LMG 28433T). Strains WS4993T and WS4994 ( = DSM 29140 = LMG 28438) should be recognized as representing a second novel species of the genus Pseudomonas, for which the name Pseudomonas weihenstephanensis sp. nov. is proposed. The type strain of Pseudomonas weihenstephanensis is strain WS4993T ( = DSM 29166T = LMG 28437T). PMID:26675012

  9. Acidipila dinghuensis sp. nov., an acidobacterium isolated from forest soil.

    Jiang, Ya-Wen; Wang, Jia; Chen, Mei-Hong; Lv, Ying-Ying; Qiu, Li-Hong

    2016-01-01

    An aerobic, chemoheterotrophic, non-motile, capsule-forming bacterium designated DHOF10T was isolated from a soil sample collected from the forest of Dinghushan Biosphere Reserve, Guangdong Province, PR China. Strain DHOF10T was able to grow at pH 3.5-8.0 (optimum pH 4.0-4.5) and at 10-37 °C (optimum 28-37 °C). NaCl tolerance was up to 1.0 % (w/v). Major fatty acids consisted of iso-C15 : 0, C18 : 1ω9c and C16 : 1ω7c. The quinone was MK-8 and the DNA G+C content was 56.3 mol%. The polar lipids consisted of phosphatidylethanolamine, an unidentified aminolipid, an unidentified phospholipid, two unidentified aminophospholipids and two unidentified polar lipids. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was a member of genus Acidipila of the phylum Acidobacteria, with the highest 16S rRNA gene sequence similarity of 97.3 % to Acidipila rosea AP8T. On the basis of phylogenetic, phenotypic, physiological and chemotaxonomic distinctiveness, strain DHOF10T represents a novel species of the genus Acidipila, for which the name Acidipila dinghuensis sp. nov. is proposed. The type strain is DHOF10T ( = CGMCC 1.13007T = KCTC 42631T). PMID:26475169

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

    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). PMID:26813106

  11. Chitinimonas prasina sp. nov., isolated from lake water.

    Li, Yi; Zhu, Hong; Lai, Qiliang; Lei, Xueqian; Chen, Zhangran; Zhang, Huajun; Tian, Yun; Zheng, Wei; Zheng, Tianling

    2014-09-01

    A Gram-stain-negative, elongated rod-shaped, motile by gliding, green-pigmented, aerobic bacterial strain, designated LY03(T), was isolated from lake water in Xiamen, Fujian Province, China. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the isolate was a member of the genus Chitinimonas, which belongs to the family Burkholderiaceae. Strain LY03(T) was most closely related to Chitinimonas taiwanensis LMG 22011(T) (96.02 % 16S rRNA gene sequence similarity), followed by Chitinimonas koreensis KACC 11467(T) (94.85 %), and the three strains formed a distinct lineage from other strains in the phylogenetic analyses. Optimum conditions for growth were 37 °C, pH 7-9 and without NaCl. The major fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and C10 : 0 3-OH. The DNA G+C content of strain LY03(T) was 63.6 mol% and the major respiratory quinone was ubiquinone-8 (Q-8). The polar lipids were found to consist of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unknown polar lipids and unidentified phospholipids. Differential phenotypic properties and phylogenetic distinctiveness distinguished strain LY03(T) from all other members of the genus Chitinimonas. On the basis of its morphology, physiology, fatty acid composition and 16S rRNA gene sequence data, strain LY03(T) represents a novel species of the genus Chitinimonas, for which the name Chitinimonas prasina sp. nov. is proposed. The type strain is LY03(T) ( = MCCC 1F01209(T) = KCTC 32574(T)). PMID:24907265

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

    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

  13. Mariniphaga sediminis sp. nov., isolated from coastal sediment.

    Wang, Feng-Qing; Shen, Qi-Yao; Chen, Guan-Jun; Du, Zong-Jun

    2015-09-01

    A Gram-stain-negative and facultatively anaerobic bacterium, SY21(T), was isolated from marine sediments of the coastal area in Weihai, China (122° 0' 37" E 37° 31' 33" N). Cells of strain SY21(T) were 0.3-0.5 μm wide and 1.5-2.5 μm long, catalase- and oxidase-positive. Colonies on 2216E agar were transparent, beige- to pale-brown-pigmented, and approximately 0.5 mm in diameter. Growth occurred optimally at 33-37 °C, pH 7.0-7.5 and in the presence of 2-3% (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene indicated that strain SY21(T) was a member of the genus Mariniphaga within the family Prolixibacteraceae. The closest described neighbour in terms of 16S rRNA gene sequences identity was Mariniphaga anaerophila Fu11-5(T) (94.7%). The major respiratory quinone of strain SY21(T) was MK-7, and the dominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and anteiso-C15 : 0. The major polar lipids were phosphatidylethanolamine, aminolipid and an unidentified lipid, and the DNA G+C content was 37.9 mol%. The distinct phylogenetic position and phenotypic traits distinguished the novel isolate from M. anaerophila Fu11-5(T). Phenotypic and genotypic analysis indicated that strain SY21(T) could be assigned to the genus Mariniphaga. The name Mariniphaga sediminis sp. nov. is proposed, with the type strain SY21(T) ( = KCTC 42260(T) = MCCC 1H00107(T)). PMID:26012581

  14. Lysobacter novalis sp. nov., isolated from fallow farmland soil.

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

    2015-09-01

    A novel bacterial strain, designated THG-PC7(T), was isolated from fallow farmland soil in Yongin, South Korea. Cells of strain THG-PC7(T) were Gram-stain-negative, dark yellow, aerobic, rod-shaped and had gliding motility. Strain THG-PC7(T) grew optimally at 25-35 °C, at pH 7 and in the absence of NaCl. Comparative 16S rRNA gene sequence analysis identified strain THG-PC7(T) as belonging to the genus Lysobacter, exhibiting highest sequence similarity with Lysobacter ximonensis KCTC 22336(T) (98.7%) followed by Lysobacter niastensis KACC 11588(T) (95.7%). In DNA-DNA hybridization tests, DNA relatedness between strain THG-PC7(T) and its closest phylogenetic neighbour L. ximonensis was below 25%. The DNA G+C content of the novel isolate was determined to be 62.5 mol%. Flexirubin-type pigments were found to be present. The major cellular fatty acids were determined to be iso-C15 : 0, iso-C16 : 0, anteiso-C15 : 0 and iso-C17 : 1ω9c. The major respiratory quinone was identified as ubiquonone-8 (Q8). The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospolipid. On the basis of results from DNA-DNA hybridization and the polyphasic data, strain THG-PC7(T) represents a novel species of the genus Lysobacter, for which the name Lysobacter novalis sp. nov. is proposed. The type strain is THG-PC7(T)( = KACC 18276(T) = CCTCC AB 2014319(T)). PMID:26296792

  15. Parafilimonas terrae gen. nov., sp. nov., isolated from greenhouse soil.

    Kim, Soo-Jin; Park, Joo-Hyeon; Lim, Jun-Muk; Ahn, Jae-Hyung; Anandham, Rangasamy; Weon, Hang-Yeon; Kwon, Soon-Wo

    2014-09-01

    A Gram-stain-negative, short rod-shaped, non-flagellated, yellow bacterium, designated strain 5GHs7-2(T), was isolated from a greenhouse soil sample in South Korea. 16S rRNA gene sequence analysis of strain 5GHs7-2(T) indicated that the isolate belonged to the family Chitinophagaceae, and exhibited the highest sequence similarities with members of the genera Terrimonas (89.2-92.6 %), Sediminibacterium (90.8-91.4 %) and Chitinophaga (89.2-91.7 %), Filimonas lacunae YT21(T) (91.7 %), members of the genus Segetibacter (90.2-91.6 %), Parasegetibacter luojiensis RHYL-37(T) (90.9 %) and Flavihumibacter petaseus T41(T) (91.2 %). Flexirubin-type pigments were present. The major cellular fatty acids of the novel strain were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The polar lipid profile consisted of a large amount of phosphatidylethanolamine, and moderate and small amounts of several unknown aminolipids and lipids. The only respiratory quinone of strain 5GHs7-2(T) was MK-7, and the DNA G+C content was 47.6 mol%. On the basis of the evidence presented, it is concluded that strain 5GHs7-2(T) represents a novel species of a new genus in the family Chitinophagaceae, for which the name Parafilimonas terrae gen. nov., sp. nov. is proposed. The type strain of the type species is 5GHs7-2(T) ( = KACC 17343(T) = DSM 28286(T)). PMID:24925599

  16. Kocuria koreensis sp. nov., isolated from fermented seafood.

    Park, Eun-Jin; Roh, Seong Woon; Kim, Min-Soo; Jung, Mi-Ja; Shin, Kee-Sun; Bae, Jin-Woo

    2010-01-01

    A Gram-positive, aerobic, non-motile and coccoid actinobacterium, designated P31(T), was isolated from a traditional, fermented seafood. The strain was catalase-positive and oxidase-negative. Cells grew in the presence of 0-15.0 % (w/v) NaCl, and at pH 5-10 and 15-37 degrees C. Major cellular fatty acids were anteiso-C(15 : 0), anteiso-C(17 : 0) and iso-C(16 : 0). Strain P31(T) contained MK-7 as the predominant menaquinone. The DNA G+C content of the genomic DNA of strain P31(T) was 65.2 mol%. A phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain P31(T) was most closely related to Kocuria kristinae DSM 20032(T), with 96.9 % similarity, and these two strains clustered together in constructed phylogenetic trees. The DNA-DNA hybridization value between strain P31(T) and K. kristinae DSM 20032(T) was 21.1 %. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, it is suggested that strain P31(T) represents a novel species of the genus Kocuria, for which the name Kocuria koreensis sp. nov. is proposed. The type strain is P31(T) (=KCTC 19595(T)=JCM 15915(T)). PMID:19648328

  17. Salinimicrobium soli sp. nov., isolated from soil of reclaimed land.

    Kim, Jong-Hwa; Yoon, Jung-Hoon; Kim, Wonyong

    2016-01-01

    A Gram-stain-negative, facultatively anaerobic, non-gliding, rod-shaped bacterial strain, designated CAU 1287T, was isolated from a soil sample of reclaimed land and its taxonomic position was investigated using a polyphasic approach. Strain CAU 1287T grew optimally at 30 °C, at pH 5.5 and in the presence of up to 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CAU 1287T formed a distinct lineage within the genus Salinimicrobium and shared the highest 16S rRNA gene sequence similarity of 98.0 % with Salinimicrobium gaetbulicola KCTC 23579T. Similar to other species of the genus Salinimicrobium, menaquinone-6 (MK-6) was the only isoprenoid quinone and iso-C15:0 and anteiso-C15:0 were the major cellular fatty acid detected in strain CAU 1287T. The polar lipid pattern of strain CAU 1287T consisted of phosphatidylethanolamine and various unidentified lipids including three aminolipids, one aminophospholipid, one phosphoglycolipid, one glycolipid, and three lipids. The DNA G+C content of CAU 1287T was 43.4 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain CAU 1287T represents a novel species of the genus Salinimicrobium, for which the name Salinimicrobium soli sp. nov. is proposed. The type strain is CAU 1287T ( = KCTC 32163T = CCUG 64794T). PMID:26541463

  18. Nocardia altamirensis sp. nov., isolated from Altamira cave, Cantabria, Spain.

    Jurado, Valme; Boiron, Patrick; Kroppenstedt, Reiner M; Laurent, Frédéric; Couble, Andrée; Laiz, Leonila; Klenk, Hans-Peter; González, Juan M; Saiz-Jimenez, Cesareo; Mouniée, Delphine; Bergeron, Emanuelle; Rodríguez-Nava, Verónica

    2008-09-01

    A novel actinomycete strain, OFN S17(T), was isolated from a sample collected from Altamira Cave, Cantabria, Spain. This strain was identified by using a polyphasic taxonomic approach. The 16S rRNA, hsp65 and sod gene sequences of the strain were determined and compared with those of representative Nocardia species. The results showed that strain OFN S17(T) should be assigned to the genus Nocardia. Phylogenetic analysis indicated that strain OFN S17(T) was most closely related to the type strain of Nocardia tenerifensis (98.6, 96.2 and 96% similarity, respectively, for the 16S rRNA, hsp65 and sod gene sequences). The DNA G+C content was 64.4 mol%. DNA-DNA hybridization analyses revealed 29% relative reassociation between the DNA of strain OFN S17(T) and N. tenerifensis DSM 44704(T). The phenotypic and genotypic data show that strain OFN S17(T) merits recognition as a representative of a novel species of the genus Nocardia, for which the name Nocardia altamirensis sp. nov. is proposed. The type strain is OFN S17(T) (=CIP 109606(T) =DSM 44997(T)). PMID:18768631

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

    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

  20. Fretibacter rubidus gen. nov., sp. nov., isolated from seawater.

    Cho, Yong-Joon; Yi, Hana; Seo, Boram; Cho, Kyeung Hee; Chun, Jongsik

    2013-12-01

    A brick-red-coloured, curved-rod-shaped, prostheca-bearing and non-motile bacterial strain, designated JC2236(T), was isolated from a seawater sample of Jeju Island, Republic of Korea. 16S rRNA gene sequence analysis indicated that this strain belongs to the family Hyphomonadaceae and represents a distinct phyletic line that reflects a novel genus status within a clade containing the genera Litorimonas, Hellea, Robiginitomaculum and Algimonas. The predominant isoprenoid quinone (Q10) and polar lipid profile (phosphatidylglycerol, glucuronopyranosyl diglyceride and monoglycosyl diglyderide) were in line with those of most members of the family. However, the DNA G+C content (49.3 mol%), the abundance of C16 : 0, the requirement of sea salts for growth and absence of cell motility differentiated strain JC2236(T) from other closely related genera. Overall enzyme traits also demonstrated that the novel strain is not closely affiliated with any of the previously described genera. Thus, based on data from the present polyphasic taxonomic study, strain JC2236(T) is considered to represent a novel species of a new genus belonging to the family Hyphomonadaceae, for which the name Fretibacter rubidus gen. nov., sp. nov. is proposed. The type strain of Fretibacter rubidus is JC2236(T) ( = KACC 16935(T) = JCM 15585(T)). PMID:23934249

  1. Micromonospora humi sp. nov., isolated from peat swamp forest soil.

    Songsumanus, Apakorn; Tanasupawat, Somboon; Thawai, Chitti; Suwanborirux, Khanit; Kudo, Takuji

    2011-05-01

    A novel actinomycete, strain P0402(T), was isolated from peat swamp forest soil collected in Thailand. Its taxonomic position was determined by using a polyphasic taxonomic approach. The chemotaxonomic characteristics of this strain matched those of the genus Micromonospora, i.e. the presence of meso-diaminopimelic acid and N-glycolyl muramic acid in the peptidoglycan, whole-cell sugar pattern D, phospholipid type II, and cellular fatty acid type 3b. Phylogenetic analysis based on 16S rRNA gene sequences revealed a close relationship between strain P0402(T) and Micromonospora coxensis JCM 13248(T) (99.0 % similarity), Micromonospora eburnea JCM 12345(T) (99.0 %), Micromonospora marina JCM 12870(T) (98.9 %), Micromonospora halophytica JCM 3125(T) (98.7 %), Micromonospora chalcea JCM 3031(T) (98.7 %), Micromonospora purpureochromogenes JCM 3156(T) (98.6 %) and Micromonospora aurantiaca JCM 10878(T) (98.5 %). It could be clearly distinguished from these type strains based on low levels of DNA-DNA relatedness and phenotypic differences. On the basis of the data presented, strain P0402(T) is suggested to represent a novel species of the genus Micromonospora, for which the name Micromonospora humi sp. nov. is proposed. The type strain is P0402(T) ( = JCM 15292(T)  = PCU 315(T)  = TISTR 1883(T)). PMID:20562246

  2. Alicyclobacillus fodiniaquatilis sp. nov., isolated from acid mine water.

    Zhang, Bo; Wu, Yu-Fan; Song, Jin-Long; Huang, Zhong-Sheng; Wang, Bao-Jun; Liu, Shuang-Jiang; Jiang, Cheng-Ying

    2015-12-01

    Two novel, Gram-stain-variable, moderately thermophilic, acidophilic, rod-shaped, endospore-forming bacteria, G45-16T and G45-17, were isolated from acid mine water of Zijin copper mine in Fujian Province, China. Phylogenetic analysis of 16S rRNA gene sequences showed that they were closely related to Alicyclobacillus acidoterrestris ATCC 49025T with sequence similarities of 96.8 %. Cells grew aerobically at 20-45 °C (optimum, 40 °C), at pH 2.5-5.5(optimum, pH 3.5) and in the presence of 0-4.0 % (w/v) NaCl. Strains contained MK-7 as the major menaquinone and the major cellular fatty acids were ω-cyclohexane C19 : 0 and ω-cyclohexane C17 : 0. The DNA G+C content was 51.3 and 49.8 mol% (Tm) for G45-16T and G45-17, respectively. On the basis of phenotypic, chemotaxonomic and phylogenetic comparisons with their relatives and DNA-DNA relatedness values, it is concluded that strains G45-16T and G45-17 represent a novel species within the genus Alicyclobacillus, for which the name Alicyclobacillus fodiniaquatilis sp. nov. is proposed; the type strain is G45-16T(=CGMCC 1.15049T=NBRC 111483T). PMID:26476812

  3. Microbacterium gilvum sp. nov., isolated from civet faeces.

    Chen, Xiu; Li, Qin-Yuan; Li, Gui-Ding; Xu, Fang-Ji; Jiang, Yi; Han, Li; Jiang, Cheng-Lin; Huang, Xue-Shi

    2016-09-01

    A novel aerobic, non-motile, Gram-positive, rod-shaped actinobacterium, designated YIM 100951(T), was isolated from the faeces of civets (Viverra zibetha) living in the National Nature Protect Region in Selangor, Malaysia. Strain YIM 100951(T) shows high similarities with Microbacterium barkeri DSM 20145(T) (97.6 %), Microbacterium oryzae MB10(T) (97.3 %), Microbacterium lemovicicum ViU22(T) (97.1 %) and Microbacterium indicum BBH6(T) (97.0 %) based on their 16S rRNA genes. However, phylogenetic analysis showed that strain YIM 100951(T) formed a clade with Microbacterium halotolerans YIM 70130(T) (96.7 %), Microbacterium populi 10-107-8(T) (96.7 %) and Microbacterium sediminis YLB-01(T) (96.9 %). DNA-DNA hybridization was carried out between strains YIM 100951(T) and M. barkeri DSM 20145(T), the result showed a value of 23.2 ± 4.5 %. In addition, some of the physiological, biochemical and chemotaxonomic characteristics of strain YIM 100951(T) are different from the closely related strains. Thus, we suggest that strain YIM 100951(T) represents a novel species of the genus Microbacterium, for which the name Microbacterium gilvum sp. nov. is proposed. The type strain is YIM 100951(T) (=DSM 26235(T) = CCTCC AB 2012971(T)). PMID:27260265

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

    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

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

    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

  6. Molecular characterization of Cryptosporidium sp. isolated from northern Alaskan caribou (Rangifer tarandus).

    Siefker, C; Rickard, L G; Pharr, G T; Simmons, J S; O'Hara, T M

    2002-02-01

    Cryptosporidium sp. was found in 3 out of 49 caribou (Rangifer tarandus) from northern Alaska. Segments of both the 18S ribosomal RNA and the heat shock protein genes were amplified from the caribou isolate and compared with that obtained from an isolate from a wild white-tailed deer (Odocoileus virginianus) in Virginia as well as other species and isolates available from GenBank. Analyses showed the white-tailed deer isolate to be identical with the C. parvum cattle genotype; however, the caribou isolate represents a new genotype closely related to C. serpentis, C. muris, and C. andersoni. Giardia sp. was not detected in any of the caribou samples nor was Cryptosporidium sp. or Giardia sp. detected in any of the 42 moose (Alces alces) samples examined. PMID:12053974

  7. Roseovarius sediminilitoris sp. nov., isolated from seashore sediment.

    Park, Sooyeon; Yoon, Jung-Hoon

    2013-05-01

    A Gram-negative, motile and ovoid- to rod-shaped bacterial strain, designated M-M10(T), was isolated from a seashore sediment collected from the South Sea, South Korea. Strain M-M10(T) grew optimally at pH 7.0-8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences revealed that strain M-M10(T) clustered with the type strains of Roseovarius crassostreae, Roseovarius halocynthiae and Roseovarius marinus, with which it exhibited sequence similarities of 97.4, 97.3 and 95.1 %, respectively. It exhibited 93.2-95.1 % sequence similarity to the type strains of the other species of the genus Roseovarius. Strain M-M10(T) contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and C16 : 0 as the major fatty acids, as observed in the genus Roseovarius. The polar lipid profile of strain M-M10(T) was similar to that of Roseovarius tolerans DSM 11457(T). The DNA G+C content of strain M-M10(T) was 63.0 mol% and its mean DNA-DNA relatedness values with Roseovarius crassostreae DSM 16950(T) and Roseovarius halocynthiae MA1-10(T) were 16 % and 22 %, respectively. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, demonstrated that strain M-M10(T) is distinct from other species of the genus Roseovarius. On the basis of the data presented, strain M-M10(T) is considered to represent a novel species of the genus Roseovarius, for which the name Roseovarius sediminilitoris sp. nov. is proposed. The type strain is M-M10(T) ( = KCTC 23959(T) = CCUG 62413(T)). PMID:22941298

  8. Micromonospora fluostatini sp. nov., isolated from marine sediment.

    Phongsopitanun, Wongsakorn; Kudo, Takuji; Mori, Mihoko; Shiomi, Kazuro; Pittayakhajonwut, Pattama; Suwanborirux, Khanit; Tanasupawat, Somboon

    2015-12-01

    The novel actinomycete strain PWB-003T, which produced fluostatins B and C antibiotics, was isolated from nearshore sediment collected from Panwa Cape, Phuket Province, Thailand. Data from the present polyphasic study indicated that strain PWB-003T represented a member of the genus Micromonospora. It produced single spores on substrate mycelia and contained meso-diaminopimelic acid in the cell-wall peptidoglycan. Whole-cell hydrolysate contained ribose, xylose, arabinose, mannose and glucose. The predominant menaquinone was MK-10 (H4). Cellular fatty acids comprised C18 : 1ω9c, iso-C16 : 0, anteiso-C17 : 0, iso-C15 : 0 and iso-C17 : 0. On the basis of 16S rRNA gene sequence similarity analysis, the novel strain was closely related to Micromonospora eburnea LK2-10T (99.38 %), Micromonospora chaiyaphumensis MC5-1T (99.16 %), Micromonospora yangpuensis FXJ6.011T (98.97 %), Micromonospora echinaurantiaca DSM 43904T (98.97 %), Micromonospora pallida DSM 43817T (98.97 %), Micromonospora sagamiensis DSM 43912T and Micromonospora auratinigra JCM 12357T (both 98.97 %). The G+C content of the DNA was 74.5 mol%. DNA-DNA relatedness values among strain PWB-003T and related type strains ranged from 11.3 ± 1.3 to 38.8 ± 1.1 %. On the basis of these observations, strain PWB-003T could be distinguished from its closely related type strains and is considered to represent a novel species of the genus Micromonospora, for which the name Micromonospora fluostatini sp. nov. (type strain PWB-003T = JCM 30529T = PCU 341T = TISTR 2345T) is proposed. PMID:26358439

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

    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

  10. Micromonospora mangrovi sp. nov., isolated from mangrove soil.

    Xie, Qing-Yi; Ren, Jian; Li, Lei; Li, Yu; Deng, Zi-Xin; Hong, Kui

    2016-04-01

    A novel actinomycete strain 2803GPT1-18(T) was isolated from a composite mangrove soil sample collected from Beihai, Guangxi province, China. Phylogenetic analysis of the 16S rRNA gene sequence of strain 2803GPT1-18(T) indicated high similarity with 'Micromonospora harpali' NEAU-JC6(T) (99.2 %), Micromonospora haikouensis 232617(T) (99.1 %), Micromonospora wenchangensis 2602GPT1-05(T) (99.1 %), Micromonospora schwarzwaldensis HKI0641(T) (99.1 %). The gyrB gene sequence analysis also indicated that strain 2803GPT1-18(T) should be assigned to the genus Micromonospora but different from any established Micromonospora species. The strain harbored meso-DAP and glycine as major cell wall amino acids, MK-10(H6) (53.5 %), MK-9(H6) (25.1 %) and MK-9(H4) (13.4 %) as predominant menaquinones. The characteristic whole cell sugars are arabinose, xylose, glucose, galactose and mannose. The polar lipid profile comprises phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol and unidentified polar lipids. The major cellular fatty acids present are iso-C16:0 (44.2 %) and iso-C15:0 (12.4 %). The DNA G+C content is 71.2 mol%. Furthermore, a combination of DNA-DNA relatedness and some physiological and biochemical properties indicated that the novel strain could be readily distinguished from the closely related species. On the basis of these phenotypic and genotypic data, strain 2803GPT1-18(T) represents a novel species of the genus Micromonospora, for which the name Micromonospora mangrovi sp. nov. is proposed. The type strain is 2803GPT1-18(T) (=CCTCC AA2012012(T) = DSM45761(T)). PMID:26942919

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

    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

  12. Saccharibacillus deserti sp. nov., isolated from desert soil.

    Sun, Ji-Quan; Wang, Xin-Ying; Wang, Li-Juan; Xu, Lian; Liu, Min; Wu, Xiao-Lei

    2016-02-01

    A Gram-stain-positive, facultatively anaerobic bacterial strain, designated WLJ055T, with polar and subpolar flagella was isolated from the top layer of desert soil from Erdos, Inner Mongolia, northern China. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain WLJ055T was a member of the genus Saccharibacillus, and shared 97.17-97.24 % 16S rRNA gene sequence similarities with Saccharibacillus sacchari GR21T and Saccharibacillus kuerlensis HR1T. The major polar lipids of strain WLJ055T were diphosphatidylglycerol, phosphatidylglycerol, an unknown aminophospholipid, two unknown glycolipids and an unknown phosphoglycolipid. MK-7 was the predominant menaquinone, while anteiso-C15 : 0, C16 : 0, iso-C16 : 0, and anteiso-C17 : 0 were the major cellular fatty acids. Its genomic DNA G+C content was 55.5 mol%. DNA-DNA hybridization revealed that strain WLJ055T showed 45 ± 5 % and 40 ± 5 % genomic DNA relatedness with its two closest relatives, S. sacchari GR21T and S. kuerlensis HR1T, respectively. The results of physiological and biochemical tests allowed the discrimination of strain WLJ055T from its phylogenetic relatives. Saccharibacillus deserti sp. nov. is therefore proposed to be a novel species of the genus Saccharibacillus, with strain WLJ055T ( = CGMCC 1.15276T = KCTC 33693T) as the type strain. PMID:26559492

  13. Mucilaginibacter yixingensis sp. nov., isolated from vegetable soil.

    Jing, Yi-Ting; Wang, Ping; Zhang, Hao; Dong, Wei-Liang; Jing, Yin-Juan; Xiao, Yong-Liang; Cao, Hui

    2016-04-01

    A Gram-reaction-negative, aerobic, non-motile, non-spore-forming, rod-shaped bacterium, designated YX-36T, was isolated from a vegetable plot in Yixing, Jiangsu province, China. The strain grew at 15-37 °C (optimally at 37 °C), at pH 6.0-9.5 (optimally at pH 6.5) and in the presence of 0-1 % (w/v) NaCl (optimally without NaCl). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YX-36T was related most closely to Mucilaginibacter herbaticus DR-9T (96.88 % similarity), followed by Mucilaginibacter sabulilitoris SMS-12T (95.78 %), Mucilaginibacter polysacchareus DR-f3T (95.77 %) and Mucilaginibacter polysacchareus DRP28T (95.77 %). The DNA G+C content of strain YX-36T was 47.2 mol%. The only isoprenoid quinone was menaquinone 7 (MK-7). The major polar lipids were phosphatidylethanolamine and aminophospholipid. The major fatty acids were iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH/C16 : 1ω7c) and iso-C17 : 0 3-OH. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain YX-36T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter yixingensis sp. nov. is proposed. The type strain is YX-36T ( = DSM 26809T = CCTCC AB 2012880T). PMID:26827674

  14. Massilia violacea sp. nov., isolated from riverbank soil.

    Embarcadero-Jiménez, Salvador; Peix, Álvaro; Igual, José Mariano; Rivera-Orduña, Flor N; Tao Wang, En

    2016-02-01

    A bacterial strain designated CAVIOT was isolated during the course of a study of culturable bacteria in a riverbank soil sample from Tlaxcala, Mexico. The strain was subjected to a polyphasic taxonomic characterization. Strain CAVIOT was aerobic, Gram-stain-negative, non-spore-forming and rod-shaped. Colonies grown on R2A agar at 28 °C were pale violet, mucoid, rounded, smooth and glossy. The strain was motile and catalase- and oxidase-positive, and maximum growth temperature was 35 °C. Strain CAVIOT was classified within the genus Massilia as its 16S rRNA gene sequence was closely related to those of Massilia umbonata LP01T (97.5 % similarity), Massilia dura 16T (97.2 %) and Massilia plicata 76T (97.1 %). The predominant respiratory quinone was Q8. The major fatty acids were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1ω7c/C18 : 1ω6c). The predominant polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and an unknown phospholipid. The DNA G+C content was 65.0 mol% (Tm). DNA-DNA hybridization results showed values below 25 % with respect to the type strains of the closest related species. Therefore, strain CAVIOT can be differentiated from previously described species of the genus Massilia and represents a novel species, for which the name Massilia violacea sp. nov. is proposed. The type strain is CAVIOT ( = CECT 8897T = LMG 28941T). PMID:26611862

  15. Tenacibaculum litoreum sp. nov., isolated from tidal flat sediment.

    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. PMID:16514041

  16. Tenacibaculum jejuense sp. nov., isolated from coastal seawater.

    Oh, You-Sung; Kahng, Hyung-Yeel; Lee, Dong-Heon; Lee, Sun Bok

    2012-02-01

    A Gram-staining-negative, strictly aerobic and rod-shaped bacterium, designated strain CNURIC013(T), was isolated from seawater collected on the coast of Jeju Island, South Korea. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CNURIC013(T) belonged to the genus Tenacibaculum, within the family Flavobacteriaceae. Sequence similarities between the novel strain and the type strains of recognized species of the genus Tenacibaculum were 93.6-96.0 %, the highest value being with Tenacibaculum litopenaei B-I(T) (96 %). The DNA G+C content of the novel strain was 34.5 mol% and the major respiratory quinone was menaquinone-6. The major fatty acids were summed feature 3 (comprising C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH; 26.0 %), iso-C(15 : 0) (24.4 %), iso-C(15 : 1) G (18.5 %) and iso-C(17 : 0) 3-OH (8.1 %). The polar lipids consisted of phosphatidylethanolamine, one unknown aminophospholipid and nine unknown polar lipids. On the basis of the phenotypic, phylogenetic and genotypic data, strain CNURIC013(T) represents a novel species within the genus Tenacibaculum, for which the name Tenacibaculum jejuense sp. nov. is proposed. The type strain is CNURIC013(T) ( = KCTC 22618(T) = JCM 15975(T)). PMID:21460140

  17. Acinetobacter refrigeratoris [corrected] sp. nov., isolated from a domestic refrigerator.

    Feng, Guangda; Yang, Songzhen; Wang, Yonghong; Yao, Qing; Zhu, Honghui

    2014-12-01

    A Gram-negative bacterial strain, designated WB1(T), was isolated from a domestic refrigerator in Guangzhou, PR China. Cells of strain WB1(T) were oxidase-negative, catalase-positive, strictly aerobic, non-spore-forming and non-motile coccobacilli with peritrichous fimbriae-like structures. The strain was able to grow at 10-40 °C with optimum growth at 28-30 °C, pH 6.0-8.0 (optimum, pH 7.0) and 0-6 % NaCl (w/v, optimum, 0.5 %). Phylogenetic analyses based on 16S rRNA gene and rpoB gene sequences revealed that strain WB1(T) belonged to the genus Acinetobacter and was most closely related to A. indicus DSM 25388(T) (97.2 % 16S rRNA gene sequence similarity) and A. radioresistens NBRC 102413(T) (96.8 %). The DNA G + C content of strain WB1(T) was 46.74 ± 0.04 mol % and the major fatty acids comprised summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C18:1 ω9c, C16:0 and C12:0. The predominant respiratory quinone was identified as Q-9 and the polar lipids as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and an unidentified phospholipid. Phenotypic, phylogenetic and chemotaxonomic data, including low DNA-DNA relatedness with closely related type strains, supported that strain WB1(T) represents a distinct novel species in the genus Acinetobacter, for which the name Acinetobacter refrigeratorensis sp. nov. was proposed. The type strain is WB1(T) (=GIMCC 1.663(T) = CCTCC AB 2014197(T) = KCTC 42011(T)). PMID:25103126

  18. Altererythrobacter buctense sp. nov., isolated from mudstone core.

    Zhang, Wei; Yuan, Xin; Feng, Qingqing; Zhang, Rengang; Zhao, Xingmin; Lv, Jie

    2016-06-01

    A yellow-pigmented, Gram-negative, non-flagellated, rod-shaped bacterial strain, designated M0322(T), was isolated from a mudstone core sample of the Mohe Basin, China. Growth of strain M0322(T) was observed at 15-40 °C (optimum, 30 °C), at pH 5.0-10.0, (optimum, pH 6.0-7.0) and in the presence 0-4 % NaCl (optimum, 0 %). Phylogenetic analyses of 16S rRNA gene sequences revealed that strain M0322(T) formed a distinct phyletic lineage with the members of the genus Altererythrobacter and is closely related to Altererythrobacter aestuarii JCM 16339(T) (96.1 %) and Altererythrobacter namhicola JCM 16345(T) (95.7 %). The only isoprenoid quinone was identified as ubiquinone 10 (Q-10), major polar lipids were determined to be phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified glycolipid and three unidentified phospholipids, while major cellular fatty acids were summed feature 8 (C18:1 ω6c and/or C18:1 ω7c), summed feature 3 (C16:1 ω6c and/or C16:1 ω7c) and 11-Methyl C18:1 ω7c. The DNA G+C content of strain M0322(T) was determined to be 64.6 mol%. Based on the results of the polyphasic taxonomic study, strain M0322(T) is considered to represent a novel species of the genus Altererythrobacter, for which the name Altererythrobacter buctense sp. nov. is proposed. The type strain is M0322(T) (=CGMCC 1.12871(T) = JCM 30112(T)). PMID:26984353

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

    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)). PMID:26892181

  20. Ornithinimicrobium pekingense sp. nov., isolated from activated sludge.

    Liu, Xing-Yu; Wang, Bao-Jun; Jiang, Cheng-Ying; Liu, Shuang-Jiang

    2008-01-01

    The bacterial strain LW6(T) was isolated from activated sludge of a wastewater treatment bioreactor. Cells of strain LW6(T) are Gram-positive, irregular, short rods and cocci, 0.5-0.8x1.0-1.6 microm. Colonies are light-yellow, smooth, circular and 0.2-1.0 mm in diameter after 3 days incubation. Strain LW6(T) is aerobic and heterotrophic. It grows at a temperature range of 26-38 degrees C and pH range of 6-9, with optimal growth at 33-37 degrees C and pH 7.8-8.2. The predominant cellular fatty acids of strain LW6(T) are iso-C(15:0) (38.9%) and iso-C(17:1)omega9c (18.8%). Strain LW6(T) has the major respiratory menaquinones MK-8(H(4)) and MK-8(H(2)) and polar lipids phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol and unknown glycolipid/phospholipids. The cell wall peptidoglycan of strain LW6(T) contained the amino acids ornithine, lysine, glutamic acid, alanine, glycine and aspartic acid. Its molar DNA G+C content is 69 mol% (T(m)). Analysis of 16S rRNA gene sequences indicated that strain LW6(T) was related phylogenetically to members of the genus Ornithinimicrobium, with similarities ranging from 98.3 to 98.7%. The DNA-DNA relatedness of strain LW6(T) to Ornithinimicrobium humiphilum DSM 12362(T) and Ornithinimicrobium kibberense K22-20(T) was respectively 31.5 and 15.2%. Based on these results, it is concluded that strain LW6(T) represents a novel species of the genus Ornithinimicrobium, for which the name Ornithinimicrobium pekingense sp. nov. is proposed. The type strain is strain LW6(T) (=CGMCC 1.5362(T) =JCM 14001(T)). PMID:18175694

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

    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

  2. Pseudomonas helmanticensis sp. nov., isolated from forest soil.

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

    2014-07-01

    A bacterial strain, OHA11(T), was isolated during the course of a study of phosphate-solubilizing bacteria occurring in a forest soil from Salamanca, Spain. The 16S rRNA gene sequence of strain OHA11(T) shared 99.1% similarity with respect to Pseudomonas baetica a390(T), and 98.9% similarity with the type strains of Pseudomonas jessenii, Pseudomonas moorei, Pseudomonas umsongensis, Pseudomonas mohnii and Pseudomonas koreensis. The analysis of housekeeping genes rpoB, rpoD and gyrB confirmed its phylogenetic affiliation to the genus Pseudomonas and showed similarities lower than 95% in almost all cases with respect to the above species. Cells possessed two polar flagella. The respiratory quinone was Q9. The major fatty acids were C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c/iso-C15 : 0 2-OH). The strain was oxidase-, catalase- and urease-positive, positive for arginine dihydrolase but negative for nitrate reduction, β-galactosidase production and aesculin hydrolysis. It was able to grow at 31 °C and at pH 11. The DNA G+C content was 58.1 mol%. DNA-DNA hybridization results showed values lower than 49% relatedness with respect to the type strains of the seven closest related species. Therefore, the combined genotypic, phenotypic and chemotaxonomic data support the classification of strain OHA11(T) to a novel species of the genus Pseudomonas, for which the name Pseudomonas helmanticensis sp. nov. is proposed. The type strain is OHA11(T) ( = LMG 28168(T) = CECT 8548(T)). PMID:24744015

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

    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)). PMID:25142212

  4. Mucilaginibacter auburnensis sp. nov., isolated from a plant stem.

    Kämpfer, Peter; Busse, Hans-Jürgen; McInroy, John A; Glaeser, Stefanie P

    2014-05-01

    A yellow-pigmented, Gram-negative, rod-shaped, non-spore-forming bacterium (strain JM-1070T) was isolated as a presumptive endophyte from internal stem tissue of a healthy corn stem. Phylogenetic analyses based on the 16S rRNA gene sequence placed strain JM-1070T in the monophyletic cluster of the genus Mucilaginibacter, with closest affiliation to the type strains of Mucilaginibacter composti (98% similarity) and Mucilaginibacter calamicampi (97.2%). 16S rRNA gene sequence similarity to type strains of other species of the genus Mucilaginibacter was 93.4-96.0%. DNA-DNA hybridizations between strain JM-1070T and the type strains M. composti LMG 23497T and M. calamicampi CCUG 63418T showed low relatedness values of 13% (reciprocal 18%) and 52% (reciprocal 54.4%). Major respiratory quinones were menaquinones MK-6 and MK-7. The predominant fatty acids (>15%) were iso-C15:0, iso-C15:0 2-OH/C16:1ω7c (measured as summed feature 3) and iso-C17:0 3-OH. Several other iso-branched and hydroxylated fatty acids were detected. The polar lipid profile was composed of the major components phosphatidylethanolamine and an unidentified aminophospholipid. The polyamine pattern contained predominantly sym-homospermidine. Characterization by 16S rRNA gene sequencing, physiological parameters and polyamine, ubiquinone, polar lipid and fatty acid compositions revealed that strain JM-1070T represents a novel species of the genus Mucilaginibacter. For this reason, we propose the name Mucilaginibacter auburnensis sp. nov., with the type strain JM-1070T (=CIP 110694T=LMG 28078T). PMID:24554635

  5. Microvirga makkahensis sp. nov., and Microvirga arabica sp. nov., isolated from sandy arid soil.

    Veyisoglu, Aysel; Tatar, Demet; Saygin, Hayrettin; Inan, Kadriye; Cetin, Demet; Guven, Kiymet; Tuncer, Munir; Sahin, Nevzat

    2016-02-01

    The taxonomic positions of two Gram-negative strains, SV1470(T) and SV2184P(T), isolated from arid soil samples, were determined using a polyphasic approach. Analysis of the 16S rRNA gene and the concatenated sequences of three housekeeping gene loci (dnaK, rpoB and gyrB) confirmed that the strains belong to the genus Microvirga. Strain SV1470(T) was found to be closely related to Microvirga vignae BR3299(T) (98.8 %), Microvirga flocculans TFB(T) (98.3 %) and Microvirga lupini Lut6(T) (98.2 %), whilst similarity to other type strains of the genus ranged from 97.8 to 96.3 %; strain SV2184P(T) was found to be closely related to Microvirga aerilata 5420S-16(T) (98.0 %), Microvirga zambiensis WSM3693(T) (97.8 %) and M. flocculans ATCC BAA-817(T) (97.4 %), whilst similarity to other type strains of the genus ranged from 97.2 to 95.9 %. The G + C content of the genomic DNA was determined to be 61.5 mol % for strain SV1470(T) and 62.1 mol % for strain SV2184P(T). Both strains were found to have the same quinone system, with Q-10 as the major ubiquinone. The polar lipid profile of strain SV1470(T) was found to consist of phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid and one unidentified aminolipid, while that of strain SV2184P(T) consisted of phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, one unidentified aminolipid, one unidentified aminophospholipid and two unidentified phospholipids. DNA-DNA relatedness studies showed that the two strains belong to different genomic species. The strains were also distinguished using a combination of phenotypic properties. Based on the genotypic and phenotypic data, the novel species Microvirga makkahensis sp. nov. (type strain SV1470(T) = DSM 25394(T) = KCTC 23863(T) = NRRL-B 24875(T)) and Microvirga arabica sp. nov. (type strain SV2184P(T) = DSM 25393(T) = KCTC 23864(T) = NRRL-B 24874(T)) are proposed. PMID:26671415

  6. Sphingomonas aerophila sp. nov. and Sphingomonas naasensis sp. nov., isolated from air and soil, respectively.

    Kim, Soo-Jin; Moon, Ji-Young; Lim, Jun-Muk; Ahn, Jae-Hyung; Weon, Hang-Yeon; Ahn, Tae-Young; Kwon, Soon-Wo

    2014-03-01

    Two strains, designated 5413J-26(T) and KIS18-15(T), were isolated from the air and forest soil, respectively, in South Korea. Cells of the two strains were Gram-stain-negative, aerobic, polar-flagellated and rod-shaped. According to the phylogenetic tree, strains 5413J-26(T) and KIS18-15(T) fell into the cluster of Sphingomonas sensu stricto. Strain 5413J-26(T) showed the highest sequence similarities with Sphingomonas trueperi LMG 2142(T) (96.6%), Sphingomonas molluscorum KMM 3882(T) (96.5%), Sphingomonas azotifigens NBRC 15497(T) (96.3 %) and Sphingomonas pituitosa EDIV(T) (96.1 %), while strain KIS18-15(T) had the highest sequence similarity with Sphingomonas soli T5-04(T) (96.8%), Sphingomonas pituitosa EDIV(T) (96.6%), Sphingomonas leidyi ATCC 15260(T) (96.6 %), Sphingomonas asaccharolytica NBRC 15499(T) (96.6 %) and Sphingomonas koreensis JSS26(T) (96.6 %). The 16S rRNA gene sequence similarity between strains 5413J-26(T) and KIS18-15(T) was 95.4 %. Ubiquinone 10 was the predominant respiratory quinone and homospermidine was the major polyamine. The major polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and several unidentified phospholipids and lipids. The main cellular fatty acids (>10% of the total fatty acids) of strain 5413J-26(T) were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c), summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C14 : 0 2-OH, and those of strain KIS18-15(T) were summed feature 8 and C16 : 0. Based on the results of 16S rRNA gene sequence analysis, and physiological and biochemical characterization, two novel species with the suggested names Sphingomonas aerophila sp. nov. (type strain 5413J-26(T) = KACC 16533(T) = NBRC 108942(T)) and Sphingomonas naasensis sp. nov. (type strain KIS18-15(T) = KACC 16534(T) = NBRC 108943(T)) are proposed. PMID:24425812

  7. Rhizobacter profundi sp. nov., isolated from freshwater sediment.

    Jin, Long; Ko, So-Ra; Ahn, Chi-Yong; Lee, Hyung-Gwan; Oh, Hee-Mock

    2016-05-01

    Three bacterial strains, designated DS48-6-5T, DS48-6-7 and DS48-6-9, were isolated from a sediment sample taken from Daechung Reservoir (Republic of Korea) at a water depth of 48 m. Cells of the strains were Gram-stain-negative, aerobic, rod-shaped and motile with a single polar flagellum. Comparative 16S rRNA gene sequence studies showed that the three isolates had clear affiliation with Betaproteobacteria and the closest relatives were Rhizobacter bergeniae KCTC 32299T, Rhizobacter dauci DSM 11587T and Rhizobacter fulvus KCTC 12591T with 97.2-97.9 % 16S rRNA gene sequence similarities; the 16S rRNA gene sequence similarities between the three strains were 99.5-100 %. The only isoprenoid quinone of the three strains was ubiquinone-8, and the major fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and C16 : 0. The G+C content of the genomic DNA of strains DS48-6-5T, DS48-6-7 and DS48-6-9 was 66.7, 67.0 and 66.8 mol%, respectively. DNA-DNA hybridization values of the novel strains with R. bergeniae KCTC 32299T, R. dauci DSM 11587T and R. fulvus KCTC 12591T were 19.3-48.5 %. Based on the evidence from this taxonomic study using a polyphasic approach, it is proposed that strains, DS48-6-5T, DS48-6-7 and DS48-6-9, represent a novel species of the genus Rhizobacter, for which the name Rhizobacter profundi sp. nov. is proposed. The type strain is DS48-6-5T ( = KCTC 42645T = NBRC 111169T). PMID:26868002

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

    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)). PMID:26573006

  9. Georgenia daeguensis sp. nov., isolated from 4-chlorophenol enrichment culture.

    Woo, Sung-Geun; Cui, Yingshun; Kang, Myung-Suk; Jin, Long; Kim, Kwang Kyu; Lee, Sung-Taik; Lee, Myungjin; Park, Joonhong

    2012-07-01

    During screening for 4-chlorophenol-degrading micro-organisms in activated sludge from industrial wastewater treatment, a Gram-positive, rod-shaped, aerobic bacterial strain, designated 2C6-43(T), was isolated and characterized taxonomically by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain 2C6-43(T) belongs to the family Bogoriellaceae, class Actinobacteria, and is related most closely to Georgenia soli CC-NMPT-T3(T) (98.8% sequence similarity), Georgenia muralis 1A-C(T) (97.6%), Georgenia thermotolerans TT02-04(T) (96.8%), Georgenia ruanii YIM 004(T) (96.6%) and Georgenia halophila YIM 93316(T) (96.0%). The G+C content of the genomic DNA of strain 2C6-43(T) was 66.2 mol%. Sugars from whole-cell hydrolysates found in strain 2C6-43(T) were rhamnose, ribose and galactose. The menaquinone MK-8(H(4)) was detected as the predominant quinone. Polar lipid analysis of 2C6-43(T) revealed diphosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylinositol and phosphatidylglycerol. An aromatic compound ring cleavage enzyme of catechol 1,2-dioxygenase was detected but catechol 2,3-dioxygenase was not detected in 2C6-43(T). A fatty acid profile with anteiso-C(15:0), iso-C(15:0) and C(16:0) as the major components supported the affiliation of strain 2C6-43(T) to the genus Georgenia. However, the DNA-DNA relatedness between strain 2C6-43(T) and the type strains of five species of the genus Georgenia ranged from 17 to 40%, clearly showing that the isolate constitutes a new genospecies. Strain 2C6-43(T) could be clearly differentiated from its phylogenetic neighbours on the basis of some phenotypic, genotypic and chemotaxonomic features. Therefore, strain 2C6-43(T) is considered to represent a novel species of the genus Georgenia, for which the name Georgenia daeguensis sp. nov. is proposed; the type strain is 2C6-43(T) (=KCTC 19801(T)=JCM 17459(T)). PMID:21930682

  10. Flavobacterium panacis sp. nov., isolated from rhizosphere of Panax ginseng.

    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)). PMID:27357576

  11. Draft Genome Sequence of Lysinibacillus sp. Strain A1, Isolated from Malaysian Tropical Soil

    Chan, Kok-Gan; 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.

  12. Pseudoalteromonas aestuariivivens sp. nov., isolated from a tidal flat.

    Park, Sooyeon; Jung, Yong-Taek; Park, Doo-Sang; Yoon, Jung-Hoon

    2016-05-01

    A Gram-stain-negative, aerobic, motile, rod-shaped or ovoid bacterial strain, designated DB-2T, was isolated from a tidal flat of the Yellow Sea in South Korea, and subjected to a taxonomic study using a polyphasic approach. Strain DB-2T grew optimally at 30 °C, at pH 7.0-8.0 and in the presence of 2.0-3.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain DB-2T belonged to the genus Pseudoalteromonas. Strain DB-2T exhibited 16S rRNA gene sequence similarities of 97.17-97.36 % to the type strains of Pseudoalteromonas mariniglutinosa, Pseudoalteromonas spongiae and Pseudoalteromonas tetraodonis and of 93.79-96.99 % to the type strains of the other species of the genus Pseudoalteromonas. Strain DB-2T contained Q-8 as the predominant ubiquinone and C16 : 0, C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C12 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain DB-2T were phosphatidylglycerol, phosphatidylethanolamine, two unidentified glycolipids, an unidentified phospholipid and an unidentified aminolipid. The DNA G+C content of strain DB-2T was 54.9 ± 0.2 mol% and mean DNA-DNA relatedness values with the type strains of P. mariniglutinosa, P. spongiae and P. tetraodonis were 10-17 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain DB-2T is separated from recognized species of the genus Pseudoalteromonas. On the basis of these data, strain DB-2T is considered to represent a novel species of the genus Pseudoalteromonas, for which the name Pseudoalteromonas aestuariivivens sp. nov. is proposed. The type strain is DB-2T ( = KCTC 42779T = CECT 8945T). PMID:26921230

  13. Flavobacterium brevivitae sp. nov., isolated from river water.

    Chen, Wen-Ming; Chen, Yi-Ling; Sheu, Shih-Yi

    2016-04-01

    A bacterial strain, designated TTM-43T, was isolated from a water sample taken from the Caohu River in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain TTM-43T were Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped and surrounded by a thick capsule. The strain formed bright-yellow colonies. Growth occurred at 15-30 °C (optimum, 20 °C), at pH 5-9 (optimum, pH 6) and with 0-0.3 % NaCl (optimum growth in the absence of added NaCl). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TTM-43T belonged to the genus Flavobacterium and was most closely related to Flavobacterium terrae R2A1-13T, with 97.8 % sequence similarity. Strain TTM-43T contained iso-C15 : 0 (24.9 %), iso-C15 : 1 G (12.6 %), summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0; 12.2 %), iso-C17 : 0 3-OH (10.9 %), iso-C15 : 0 3-OH (7.3 %) and iso-C16 : 0 (6.7 %) as the predominant fatty acids. The major isoprenoid quinone was MK-6. The polar lipid profile consisted of phosphatidylethanolamine and several uncharacterized aminophospholipids and phospholipids. The major polyamine was homospermidine. The genomic DNA G+C content of strain TTM-43T was 31 mol%. DNA-DNA relatedness of strain TTM-43T with respect to type strains of recognized species of the genus Flavobacterium was less than 70 %. On the basis of phylogenetic inference and phenotypic data, strain TTM-43T should be assigned to a novel species, for which the name Flavobacterium brevivitae sp. nov. is presented. The type strain is TTM-43T ( = BCRC 80913T = KCTC 42744T = LMG 29004T). PMID:26812967

  14. Marinobacterium aestuariivivens sp. nov., isolated from a tidal flat.

    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

  15. Epilithonimonas psychrotolerans sp. nov., isolated from alpine permafrost.

    Ge, Liang; Zhao, Qi; Sheng, Hongmei; Wu, Jianmin; An, Lizhe

    2015-11-01

    A bacterial strain, designated TSBY 57T, was isolated during a study on the phylogenetic diversity of culturable bacteria from alpine permafrost in Tianshan Mountains, China, and was classified by means of a polyphasic taxonomic approach. The novel strain was found to belong to the genus Epilithonimonas and was distinguished from recognized species of this genus. Strain TSBY 57T grew aerobically, at 0-30 °C, with 0-1.5% (w/v) NaCl and at pH 6-8.Cells were Gram-stain-negative, non-motile, non-spore-forming rods. Compared with the reference strains, the novel strain was psychrotolerant. The predominant fatty acids were summed feature 3 (consisting of C16:1ω7c and/or C16:1ω6c), anteiso-C15:0 and iso-C15:0.The sole respiratory quinone was MK-6.Phosphatidylethanolamine was predominant in the polar lipid profile of strain TSBY 57T. These chemotaxonomic traits were in good agreement with the characteristics of the genus Epilithonimonas. On the basis of 16S rRNA gene sequence similarity, strain TSBY 57T was a member of the genus Epilithonimonas and was closely related to Epilithonimonas tenax DSM 16811T (99.0%), Epilithonimonas ginsengisoli DCY78T (98.6%) and Epilithonimonas lactis H1T (98.5%). However, DNA-DNA reassociation values between strain TSBY 57T and E. tenax DSM 16811T, E. ginsengisoli DCY78T and E. lactis H1T were 39.5 ± 2.6, 37.7 ± 1.0 and 37.3 ± 1.1%, respectively. The G+C content of the DNA was 34.4 ± 0.2  mol%. Based on data from this polyphasic taxonomic study, strain TSBY 57T represents a novel species of the genus Epilithonimonas, for which the name Epilithonimonas psychrotolerans sp. nov. is proposed. The type strain is TSBY 57T ( = NRRL B-51307T=CCTCC AB 207182T). PMID:26233482

  16. Rudaibacter terrae gen. nov., sp. nov., isolated from greenhouse soil.

    Kim, Soo-Jin; Moon, Ji-Young; Hamada, Moriyuki; Tamura, Tomohiko; Weon, Hang-Yeon; Suzuki, Ken-ichiro; Kwon, Soon-Wo

    2013-11-01

    A novel Gram-stain-positive, non-motile, rod-shaped bacterium, designated 5GHs34-4(T), was isolated from greenhouse soil in Yongin, Republic of Korea. Growth occurred in the temperature range of 10-37 °C (optimum 28-30 °C) and at pH 5.0-9.0 (optimum pH 7.0). It can tolerate up to 3 % (w/v) NaCl. The strain showed 16S rRNA gene sequence similarity levels of 95.1-97.0 % with species of the genus Leifsonia, 95.7-96.7 % with species of the genus Herbiconiux, 95.1-96.4 % with species of the genus Salinibacterium and 96.1 % with Labedella gwakjiensis and Homoserinimonas aerilata. The highest sequence similarities (97.0 %) were with Leifsonia aquatica JCM 1368(T), Leifsonia poae VKM Ac-1401(T) and Leifsonia psychrotolerans LI1(T). The peptidoglycan type determined for strain 5GHs34-4(T) was B2γ with dl-2,4-diaminobutyric acid at position 3. The murein was of the acetyl type. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The menaquinones detected were MK-13, MK-12 and MK-14, and the major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), anteiso-C17 : 0 and anteiso-C15 : 0. The phenotypic and phylogenetic traits of strain 5GHs34-4(T) differed in some respects from those of members of the family Microbacteriaceae. Therefore, strain 5GHs34-4(T) is considered to represent a novel species of a new genus in the family Microbacteriaceae, for which the name Rudaibacter terrae gen. nov., sp. nov. is proposed. The type strain is 5GHs34-4(T) ( = KACC 15523(T) = NBRC 108754(T)). PMID:23728372

  17. Luteimonas soli sp. nov., isolated from farmland soil.

    Wang, Xiang; Yang, Hong-Xing; Zhang, Ying-Kun; Zhu, Shi-Jun; Liu, Xiao-Wei; Zhang, Hao; Zhang, Chen-Fei; Zhao, Chao-Ran; Hu, Gang; Hong, Qing

    2015-12-01

    A yellow-pigmented bacterial strain, designated Y2T, was isolated from farmland soil in Bengbu, Anhui province, China. Cells of strain Y2T were Gram-stain-negative, strictly aerobic, non-motile and rod-shaped. Strain Y2T grew optimally at pH 7.0, 30 °C and in the presence of 2 % (w/v) NaCl. The DNA G+C content was 68.9 mol%. The major fatty acids (>5 %) were iso-C15 : 0, iso-C17 : 0, summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1ω9c), iso-C11 : 0 3-OH and iso-C11 : 0. The major respiratory quinone was ubiquinone-8 (Q-8), and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Phylogenetic analysis of the 16S rRNA gene sequences showed that strain Y2T was most closely related to Luteimonas mephitis B1953/27.1T (99.1 % 16S rRNA gene sequence similarity), followed by Luteimonas lutimaris G3T (98.6 %), Luteimonas abyssi XH031T (96.2 %) and Luteimonas aquatica RIB1-20T (96.0 %). Strain Y2T exhibited low DNA-DNA relatedness with Luteimonas mephitis B1953/27.1T (43.6 ± 0.5 %) and Luteimonas lutimaris G3T (43.9 ± 2.1 %). On the basis of phenotypic, genotypic and phylogenetic evidence, strain Y2T represents a novel species of the genus Luteimonas, for which the name Luteimonas soli sp. nov. is proposed. The type strain is Y2T ( = ACCC 19799T = KCTC 42441T). PMID:26437920

  18. Novosphingobium fluoreni sp. nov., isolated from rice seeds.

    Gao, Shumei; Zhang, Yingjun; Jiang, Na; Luo, Laixin; Li, Qing X; Li, Jianqiang

    2015-05-01

    A yellow-pigmented, Gram-stain-negative, rod-shaped, non-spore-forming bacterium designated strain HLJ-RS18(T), which could degrade fluorene, was isolated from rice seeds collected from Heilongjiang Province, China. Similarities of full-length of 16S rRNA gene sequences between strain HJL-RS18(T) and the type strains of the genus Novosphingobium with validly published names ranged from 93.8 to 97.1%. Phylogenetic analysis with maximum-likelihood and neighbour-joining methods revealed that strain HLJ-RS18(T) belonged to genus Novosphingobium and strain HLJ-RS18(T) formed a distinct clade to Novosphingobium chloroacetimidivorans BUT-14(T) (96.9% similarity based on 16S rRNA gene). DNA-DNA hybridization of HLJ-RS18(T) and BUT-14(T) showed a low relatedness value of 22.4 ± 0.9%, which indicated that strain HLJ-RS18(T) represents a novel species of the genus Novosphingobium. The genomic DNA G+C content of strain HLJ-RS18(T) was 62 mol%. Ubiquinone Q-10 was the major respiratory quinone. Spermidine was the predominant polyamine. Polar lipids consisted mainly of aminophospholipid, phosphatidylglycerol, phosphatidylethanolamine, phospholipid and sphingoglycolipid. The predominant fatty acid composition of HLJ-RS18(T) were summed 8 (C(18:1)ω7c and/or C(18:1)ω6c, 61.5%), C(16 : 0) (14.2%), summed 3 (C(16:1)ω7c and/or C(16:1)ω6c, 13.5%) and C14:0 2-OH (6.8%). Phylogenetic analysis, DNA-DNA hybridization, chemotaxonomic data and phenotypic characteristics support the conclusion that HLJ-RS18(T) represents a novel species within the genus Novosphingobium. Therefore, we propose the species Novosphingobium fluoreni sp. nov. with HLJ-RS18(T) ( = DSM 27568(T) = ACCC19180(T)) as the type strain. PMID:25667393

  19. Sphingomonas gei sp. nov., isolated from roots of Geum aleppicum.

    Zhu, Lingfang; Si, Meiru; Li, Changfu; Xin, Kaiyun; Chen, Chaoqiong; Shi, Xu; Huang, Ruijun; Zhao, Liang; Shen, Xihui; Zhang, Lei

    2015-04-01

    A yellow-pigmented bacterium, designated strain ZFGT-11(T), was isolated from roots of Geum aleppicum Jacq. collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. Cells of strain ZFGT-11(T) were Gram-stain-negative, strictly aerobic rods that were surrounded by a thick capsule and were motile by means of a single polar flagellum. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ZFGT-11(T) was a member of the genus Sphingomonas and was closely related to Sphingomonas naasensis KACC 16534(T) (97.6% similarity), Sphingomonas kyeonggiense JCM 18825(T) (96.8%), Sphingomonas asaccharolytica IFO 15499(T) (96.7%) and Sphingomonas leidyi DSM 4733(T) (96.6%). The predominant respiratory quinone was ubiquinone-10 (Q-10) and the major cellular fatty acids were summed feature 8 (comprising C(18 : 1)ω7c and/or C(18 : 1)ω6c), C(17 : 1)ω6c, C(14 : 0) 2-OH, C(16 : 0) and C(15 : 0) 2-OH. The major polyamine of strain ZFGT-11(T) was sym-homospermidine. Phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, sphingoglycolipid, two unidentified aminoglycolipids, two unidentified phospholipids and two unidentified lipids were detected in the polar lipid profile. The DNA G+C content was 66.8 mol%. DNA-DNA relatedness for strain ZFGT-11(T) with respect to its closest phylogenetic relative S. naasensis KACC 16534(T) was 26.2±4.8% (mean±SD). On the basis of data from the present polyphasic taxonomic study, strain ZFGT-11(T) is considered to represent a novel species of the genus Sphingomonas , for which the name Sphingomonas gei sp. nov. is proposed. The type strain is ZFGT-11(T) ( = CCTCC AB 2013306(T) = KCTC 32449(T) = LMG 27608(T)). PMID:25604345

  20. Ornithinimicrobium tianjinense sp. nov., isolated from a recirculating aquaculture system.

    Liu, Liang-Zi; Liu, Ying; Chen, Zhu; Liu, Hong-Can; Zhou, Yu-Guang; Liu, Zhi-Pei

    2013-12-01

    A Gram-positive, strictly aerobic and heterotrophic, non-spore-forming actinobacterium (strain B2(T)) isolated from a recirculating aquaculture system was studied for its taxonomic position. Strain B2(T) formed a rudimentary substrate-mycelium that fragmented into short rod-shaped to coccoid cells (0.5 µm×0.5-2.2 µm or 0.5-1.0 µm in diameter). Colonies were yellow, smooth, circular and 1.5-2.0 mm in diameter after incubation on TSA for 3 days at 30 °C. Strain B2(T) grew at 20-40 °C (optimal, 30 °C) and pH 5.5-9.5 (optimal, 6.5-7.0) and in the presence of 0-9% (w/v) NaCl (optimal, 1%). The predominant menaquinone of strain B2(T) was MK-8(H4). The cell-wall peptidoglycan of strain B2(T) contained the amino acids ornithine, glutamic acid, alanine, glycine and aspartic acid. The major polar lipids were phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids were iso-C15 : 0, iso-C16 : 0 and summed feature 9. Its DNA G+C content was 68.3 mol% (Tm). Analysis of 16S rRNA gene sequences indicated that strain B2(T) was related phylogenetically to members of the genus Ornithinimicrobium with highest similarity (96.6 %) to Ornithinimicrobium kibberense DSM 17687(T), followed by Ornithinimicrobium humiphilum DSM 12362(T) (96.3 %), Ornithinimicrobium pekingense LW6(T) (96.2%) and Ornithinimicrobium murale 01-Gi-040(T) (94.8%). On basis of phenotypic, chemotaxonomic and phylogenetic data, it was concluded that strain B2(T) represents a novel species of the genus Ornithinimicrobium, for which the name Ornithinimicrobium tianjinense sp. nov. is proposed. The type strain is B2(T) ( =CGMCC 1.12160(T) =JCM 18464(T)). PMID:23907216

  1. Rhizobium ipomoeae sp. nov., isolated from a water convolvulus field.

    Sheu, Shih-Yi; Chen, Zih-Han; Young, Chiu-Chung; Chen, Wen-Ming

    2016-04-01

    A bacterial strain, designated shin9-1T, was isolated from a water sample taken from a water convolvulus field in Taiwan and characterized using a polyphasic taxonomical approach. Cells of strain shin9-1T were aerobic, Gram-stain-negative, rod-shaped and surrounded by a thick capsule and formed cream-coloured colonies. Growth occurred at 10-45 °C (optimum, 30 °C), with 0-3.0 % NaCl (optimum, 0.5 %) and at pH 7.0-9.0 (optimum, pH 7.0). Strain shin9-1T did not form nodules on a legume plant, Macroptilium atropurpureum, and the nodulation genes nodA, nodC and the nitrogenase reductase gene nifH were not detected by PCR. Phylogenetic analyses based on 16S rRNA and three housekeeping gene sequences (recA, atpD and rpoB) showed that strain shin9-1T belonged to the genus Rhizobium. Strain shin9-1T had the highest level of 16S rRNA gene sequence similarity with respect to Rhizobium daejeonense L61T (97.6 %). The major fatty acid of strain shin9-1T was C18 : 1ω7c. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, phosphatidylmonomethylethanolamine and several uncharacterized lipids. The DNA G+C content was 58.3 mol%. The DNA-DNA relatedness of strain shin9-1T with respect to recognized species of the genus Rhizobium was less than 70 %. Phenotypic characteristics of the novel strain also differed from those of the most closely related species of the genus Rhizobium. On the basis of the phylogenetic inference and phenotypic data, strain shin9-1T should be classified as a representative of a novel species, for which the name Rhizobium ipomoeae sp. nov. is proposed. The type strain is shin9-1T ( = LMG 27163T = KCTC 32148T). PMID:26739022

  2. Genome Sequences of the Lignin-Degrading Pseudomonas sp. Strain YS-1p and Rhizobium sp. Strain YS-1r Isolated from Decaying Wood

    Prabhakaran, Madhu; Couger, Matthew B.; Jackson, Colin A.; Weirick, Tyler; Fathepure, Babu Z.

    2015-01-01

    Pseudomonas sp. strain YS-1p and Rhizobium sp. strain YS-1r were isolated from a lignin-degrading enrichment culture. The isolates degraded lignin-derived monomers, dimers, alkali lignin, and, to a smaller extent (3% to 5%), lignin in switch grass and alfalfa. Genome analysis revealed the presence of a variety of lignin-degrading genes.

  3. Genome sequence of Oceanicaulis sp. strain HTCC2633, isolated from the Western Sargasso Sea.

    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

  4. Genome Sequence of Oceanicaulis sp. Strain HTCC2633, Isolated from the Western Sargasso Sea ▿

    Oh, Hyun-Myung; Kang, Ilnam; Vergin, Kevin L.; Lee, Kiyoung; Giovannoni, Stephen J.; Cho, Jang-Cheon

    2010-01-01

    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.

  5. Rhizobium selenireducens sp. nov.: A selenite reducing a-Proteobacteria isolated from a bioreactor

    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....

  6. Pseudomonas seleniipraecipitatus sp. nov.: A selenite reducing -proteobacteria isolated from soil

    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...

  7. Halomonas saccharevitans sp. nov., Halomonas arcis sp. nov. and Halomonas subterranea sp. nov., halophilic bacteria isolated from hypersaline environments of China.

    Xu, Xue-Wei; Wu, Yue-Hong; Zhou, Zhen; Wang, Chun-Sheng; Zhou, Yu-Guang; Zhang, Hui-Bin; Wang, Yong; Wu, Min

    2007-07-01

    Three strains of Gram-negative, aerobic, neutrophilic and halophilic bacteria were isolated from samples of a salt lake on the Qinghai-Tibet Plateau and a subterranean saline well in the Si-Chuan Basin of China. These isolates, designated AJ275(T), AJ282(T) and ZG16(T), were investigated using a polyphasic approach. Based on 16S rRNA gene sequence analysis, the isolates could be affiliated to the genus Halomonas. Genomic DNA G+C contents were 65.9 mol% for AJ275(T), 56.7 mol% for AJ282(T) and 57.6 mol% for ZG16(T). The results of DNA-DNA hybridizations, fatty acid analysis and physiological and biochemical tests allowed the isolates to be differentiated genotypically and phenotypically from closely related species. It is proposed that strains AJ275(T) (=CGMCC 1.6493(T)=JCM 14606(T)=LMG 23976(T)), AJ282(T) (=CGMCC 1.6494(T)=JCM 14607(T)=LMG 23978(T)) and ZG16(T) (=CGMCC 1.6495(T)=JCM 14608(T)=LMG 23977(T)) represent the type strains of three novel species in the genus Halomonas: Halomonas saccharevitans sp. nov., Halomonas arcis sp. nov. and Halomonas subterranea sp. nov., respectively. PMID:17625205

  8. Isolation, Identification, and Characterization of Cadmium Resistant Pseudomonas sp. M3 from Industrial Wastewater

    Syed Zaghum Abbas; Mohd. Rafatullah; Norli Ismail; Japareng Lalung

    2014-01-01

    The present study deals with the isolation, identification, and characterization of the cadmium resistant bacteria from wastewater collected from industrial area of Penang, Malaysia. The isolate was selected based on high level of the cadmium and antibiotic resistances. On the basis of morphological, biochemical characteristics, 16S rDNA gene sequencing and phylogeny analysis revealed that the strain RZCd1 was authentically identified as Pseudomonas sp. M3. The industrial isolate showed more ...

  9. Infectivity of Trichinella sp. isolated from Crocodylus niloticus to the indigenous Zimbabwean pig (Mukota).

    Mukaratirwa, S; Foggin, C M

    1999-07-01

    An experimental infection of the indigenous Zimbabwean pig (Mukota) with a Trichinella sp. derived from crocodile (Crocodylus niloticus) was performed. The same larval isolates of Trichinella were infected to rats as a control. The muscles of both pigs and rats were found to be heavily infected with the first-stage larvae. The present study constitutes the first report of a successful experimental infection of the pig with Trichinella sp. originating from crocodile. PMID:10501623

  10. Aspergillus saccharolyticus sp. nov., a new black Aspergillus species isolated in Denmark

    Sørensen, Annette; Lübeck, Peter S.; Lübeck, Mette; Nielsen, Kristian Fog; Ahring, Birgitte K.; Teller, Philip J.; Frisvad, Jens Christian

    2011-01-01

    A novel species, Aspergillus saccharolyticus sp. nov., belonging to the Aspergillus section Nigri group is described. This species was isolated in Denmark from treated hardwood. Its taxonomic status was determined using a polyphasic taxonomic approach including phenotypic (morphology and extrolite...... Aspergillus species that is morphologically similar to Aspergillus japonicus and Aspergillus aculeatus, but has a totally different extrolite profile compared to any known Aspergillus species. The type strain of A. saccharolyticus sp. nov. is CBS 127449T ( = IBT 28509T)....

  11. Production of lipopeptides in Bacillus sp. CS93 isolated from Pozol

    Moran, Stephen; Robertson, Keith; Paradisi, Francesca; Dilip K. Rai; Murphy, Cormac D.

    2010-01-01

    Bacillus sp. strain CS93, which was previously isolated from Pozol, was previously shown to produce iturin A, bacilysin and chlorotetaine. To investigate the biosynthetic mechanism of chlorotetaine production, the bac genes were amplified from genomic DNA of Bacillus sp. CS93 by PCR and sequenced. The genes bacABCDE were determined, but no gene that might code for a halogenating enzyme was detected either within the gene cluster or in the flanking sequences. Following further analysis of cult...

  12. [A STUDY OF THE ISOLATED BACTERIOPHAGE ΦAB-SP7 ADSORPTION ON THE CELL SURFACE OF THE AZOSPIRILLUM BRASILENSE SP7].

    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

  13. Candida materiae sp. nov., a yeast species isolated from rotting wood in the Atlantic Rain Forest.

    Barbosa, Anne C; Cadete, Raquel M; Gomes, Fátima C O; Lachance, Marc-André; Rosa, Carlos A

    2009-08-01

    Three strains of a novel yeast species, Candida materiae sp. nov., were isolated from rotting wood in an Atlantic rain forest site in Brazil. Analysis of the sequences of the D1/D2 domains of the large-subunit rDNA showed that this species belonged to the Spathaspora clade and was related to Candida jeffriesii and Spathaspora passalidarum. Unlike C. jeffriesii and S. passalidarum, C. materiae sp. nov. did not ferment xylose. The type strain of C. materiae sp. nov. is UFMG-07-C15.1BT (=CBS 10975T=CBMAI 956T). PMID:19605715

  14. The Newly Isolated Endophytic Fungus Paraconiothyrium sp. LK1 Produces Ascotoxin

    Sang-Mo Kang

    2012-01-01

    Full Text Available We have isolated five endophytic fungi from the roots of Capsicum annuum, Cucumis sativus and Glycine max. The culture filtrates (CF of these endophytes were screened on dwarf mutant rice (Waito-C and normal rice (Dongjin-byeo. Endophyte CAC-1A significantly inhibited the growth of Waito-C and Dongjin-byeo. Endophyte CAC-1A was identified as Paraconiothyrium sp. by sequencing the ITS rDNA region and phylogenetic analysis. The ethyl acetate fraction of Paraconiothyrium sp. suppressed the germination of Lactuca sativa and Echinochloa crus-galli seeds. The ethyl acetate fraction of the endophyte was subjected to bioassay-guided isolation and we obtained the phytotoxic compound ascotoxin (1 which was characterized through NMR and GC/MS techniques. Ascotoxin revealed 100% inhibitory effects on seed germination of Echinochloa crus-galli. Compound (1 was isolated for the first time from Paraconiothyrium sp.

  15. Isolation and Purifi cation of Chitinase Bacillus sp. D2 Isolated from Potato Rhizosfer

    Sebastian Margino

    2015-11-01

    Full Text Available Normal 0 false false false EN-US X-NONE X-NONE MicrosoftInternetExplorer4 Potato Cyst Nematodes (Globodera rostochiensis is one of the important potato’s pests and caused economic looses up to 70% in the several centrals of potato plantations in Indonesia. Potato Cyst Nematodes (PCN shell component of egg shell containing chitin (inner layer and vitelline/protein (outer layer, so the purpose of research was to fi nd out of chitin degrading bacteria for controlling of egg’s PCN by cutting of their life cycle. The results showed that Bacillus sp. D2 isolated from potato rhizosphere could produce extra cellular chitinase in the medium containing of 0.20% colloidal chitin and fermented for 72 hours. Result of chitinase purifi cation using ammonium sulphate precipitation and DEAE-Cellulose ion-exchange chromatography showed a specifi c activity 2691,052 U/mg and analyzing using SDS-PAGE 12.5% resulted in molecular weight 30 kDa. The apparent Km and Vmax of chitinase towards colloidal chitin were 2 mg/ml and 2.2 μg/h, respectively.  

  16. ε-Caprolactam Utilization by Proteus sp. and Bordetella sp. Isolated From Solid Waste Dumpsites in Lagos State, Nigeria, First Report.

    Sanuth, Hassan Adeyemi; Yadav, Amit; Fagade, Obasola Ezekiel; Shouche, Yogesh

    2013-06-01

    The ε-caprolactam is the monomer of the synthetic non-degradable nylon-6 and often found as nonreactive component of nylon-6 manufacturing waste effluent. Environmental consequences of its toxicity to natural habitats and humans pose a global public concern. Soil samples were collected from three designated solid waste dumpsites, namely, Abule-Egba, Olusosun and Isheri-Igando in Lagos State, Nigeria. Sixteen bacteria isolated from these samples were found to utilize the ε-caprolactam as a sole source of carbon and nitrogen at concentration of ≤20 g l(-1). The isolates were characterized using their 16S rRNA gene sequence and showed similarity with Pseudomonas sp., Proteus sp., Providencia sp., Corynebacterium sp., Lysinibacillus sp., Leucobacter sp., Alcaligenes sp. and Bordetella sp. Their optimal growth conditions were found to be at temperature range of 30 to 35 °C and pH range of 7.0-7.5. High Performance liquid chromatography analysis of the ε-caprolactam from supernatant of growth medium revealed that these isolates have potential to remove 31.6-95.7 % of ε-caprolactam. To the best of our knowledge, this study is first to report the ability of Proteus sp. and Bordetella sp. for ε-caprolactam utilization. PMID:24426112

  17. Characterization of cellulase enzyme produced by Chaetomium sp. isolated from books and archives

    Moza Mohammed AL-Kharousi

    2015-12-01

    Full Text Available Background: Cellulase is an important industrial enzyme used to degrade cellulosic biomass. The demand for cellulase enzyme is continuously increasing because of its applications in various industries. Hence, screening of cellulase producing microorganisms from different sources has gained significant importance. Material and Methods: In this study, fungi isolated from books and archives were screened for their cellulase producing abilities. Four different fungi were isolated from books and archives using potato dextrose agar. Screening of these isolates for cellulase production was carried out using carboxymethyl cellulose broth. The most efficient fungus was subjected to cellulase fermentation and enzymes produced were purified and partially characterized. Results: Four different fungi, Chaetomium sp., Aspergillus niger, Aspergillus nidulans and Penicillium sp., were isolated from books and archives. All the isolates were tested for their ability to producecellulase enzyme. During the primary screening Chaetomium sp. showed good growth and highercellulase activity (155.3±25.6 U/mL in carboxymethyl cellulose medium than the other fungi. The cellulase fermentation study was conducted with Chaetomium sp. using carboxymethyl cellulose asa substrate. During the stationary phase (144 h of the growth, the cellulase activity of Chaetomium sp. was significantly high. The maximum mycelial weight of this fungi was obtained at 168 h. Viscosity of the Chaetomium sp. inoculated fermentation medium continuously decreased until 144 h because of the degradation of carboxymethyl cellulose. During cellulase fermentation, pHincreased from the initial neutral pH to 8.5. Purified cellulase showed a specific activity of 7.3 U/mg. It exhibited maximum activity at 20°C and was stable between pH 5 and 9. Conclusions: Books and archives could be a good source for the isolation of cellulase producing fungi.

  18. Pichia sporocuriosa sp. nov., a new yeast isolated from rambutan.

    Péter, G; Tornai-Lehoczki, J; Dlauchy, D; Vitányi, G

    2000-01-01

    A strain of a hitherto undescribed yeast species with a unique ascospore morphology was isolated from rambutan (Nephelium lappaceum). A description of the new species, Pichia sporocuriosa, is given. PMID:10696876

  19. Reduction of Chromium(VI) by Locally Isolated Pseudomonas sp. C-171

    Rahman, Mujeeb Ur; GUL, Shereen; HAQ, Mohammad Zahoor UL

    2007-01-01

    A strain of Pseudomonas sp. C-171 capable of tolerating hexavalent chromium (Cr+6) up to 2000 ppm as potassium dichromate was isolated from domestic sewage. The Cr+6 reduction was checked by growing the isolated strain in a medium containing potassium dichromate as Cr+6 source. The rate of growth of Pseudomonas sp. C-171 decreased with the increase in Cr+6 concentration of the medium. The maximum rate of chromium reduction was observed during the log phase of bacterium growth. The reduction o...

  20. Polyunsaturated fatty acids production by Schizochytrium sp. isolated from mangrove

    K.W. Fan

    2003-09-01

    Full Text Available Five Schizochytrium strains (N-1, N-2, N-5, N-6, and N-9 were isolated from fallen, senescent leaves of mangrove tree (Kandelia candel in Hong Kong. The fungi were cultivated in glucose yeast extract medium containing 60 g of glucose, 10 g of yeast extract and 1 L of 15‰ artificial seawater, initial pH 6.0, with shaking for 52 hr at 25ºC. Biomass yields of 5 isolates ranged from 10.8 to 13.2 g/l. Isolate N-2 yielding the highest dried cell mass at 13.2 g/l and isolate N-9 grew poorly with 10.8 g/l of biomass. EPA (Eicosapentaenoic acid, 20:5n-3 yield was low in most strains, while DHA (Docosahexaenoic acid, 22:6n-3 was high on the same medium. The contents of DHA in biomass varied: 174.9, 203.6, 186.1, 171.3 and 157.9 mg/g of dried-biomass for Schizochytrium isolate N-1, N-2, N-5, N-6, and N-9, respectively. Isolate N-2 had the highest proportion of DHA in fatty acid profile with 15:0, 28.7%; 16:0, 21.3%; 18:0, 0.9%; 18:3, 0.2%; 20:4, 0.3%; 20:5, 0.9%; 22:4, 6.7%; 22:6, 36.1%; and others, 9.3%. The salinity range for growth of Schizochytrium isolates was from 0-30‰ with optimum salinity for growth between 20-30‰.

  1. Buwchfawromyces eastonii gen. nov., sp. nov.: a new anaerobic fungus (Neocallimastigomycota isolated from buffalo faeces

    Tony Martin Callaghan

    2015-03-01

    Full Text Available The novel anaerobic fungus Buwchfawromyces eastonii gen. nov., sp. nov., belonging to order Neocallimastigales (phylum Neocallimastigomycota is described. Morphologically similar to Piromyces but genetically quite distinct, this fungus (isolate GE09 was first isolated from buffalo faeces in west Wales and then subsequently isolated from sheep, cattle and horse in the same area. Phylogenetic analysis of LSU and ITS sequence confirmed that B. eastonii isolates formed a distinct clade close to the polycentric Anaeromyces spp. The morphology of GE09 is monocentric with monoflagellate zoospores. However, the sporangial stalk (sporangiophore is often distinctly swollen and the proximal regions of the rhizoidal system twisted in appearance.

  2. 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.

    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

  3. Neiella marinum gen. nov., sp. nov., isolated from sea cucumber

    A novel strain, designated J221**T, was isolated from the intestine of a sea cucumber, Apostichopus japonicus, collected from earthen ponds in Qingdao, China. The strain is Gram-negative, oxidase-positive, aerobic, and rod-shaped cell. Growth of strain J221T was observed at temperatures between 10...

  4. Arcobacter cibarius sp nov., isolated from broiler carcasses

    Houf, K.; On, Stephen L.W.; Coenye, T.; Mast, J.; Van Hoof, J.; Vandamme, P.

    2005-01-01

    Twenty Gram-negative, rod-shaped, slightly curved, non-spore-forming bacteria that gave a negative result in Arcobacter species-specific PCR tests but that yielded an amplicon in an Arcobacter genus-specific PCR test were isolated from 13 unrelated broiler carcasses. Numerical analysis of the...

  5. Arthrobacter enclensis sp. nov., isolated from sediment sample

    Dastager, S.G.; Qin, L.; Tang, S.K.; Krishnamurthi, S.; Lee, J.C.; Li, W.J.

    A novel bacterial strain designated as NIO-1008(T) was isolated from marine sediments sample in Chorao Island India. Cells of the strains were gram positive and non-motile, displayed a rod-coccus life cycle and formed cream to light grey colonies...

  6. Characterization of a bioflocculant from a newly isolated Vagococcus sp. W31*

    Gao, Jie; Bao, Hua-Ying; Xin, Ming-Xiu; Liu, Yuan-Xia; Li, Qian; Zhang, Yan-Fen

    2006-01-01

    Screening of microorganisms producing flocculating substances was carried out. A strain secreting a large amount of bioflocculant was isolated from wastewater samples collected from the Little Moon River in Beijing. Based on the morphological properties and 16S rDNA sequence analysis, the isolate (designated W31) was classified as Vagococcus sp. A bioflocculant (named MBFW31) produced by W31 was extracted from the culture broth by ethanol precipitation and purified by gel chromatography. MBFW...

  7. A Morphological, Biochemical and Biological Studies of Halophilic Streptomyces sp. Isolated from Saltpan Environment

    Deepika T. Lakshmipathy

    2009-01-01

    Full Text Available Problem statement: Dermatophytes have developed resistance to the existing antifungal antibiotics. As a part of our continuous search we had isolated, identified and characterized actinomycetes from the halophilic environment having antagonistic activity against the dermatophytes namely Trichophyton, Microsporum and Epidermophyton. Approach: Actinomycetes were isolated from the soil sample collected from the Ennore saltpan region, Chennai, India and screened for antidermatophytic secondary metabolite production by well diffusion method. Four dermatophytes Trichophyton rubrum [MTCC 3272], Trichophyton mentagrophytes [MTCC 7687], Microsporum gypseum [MTCC 2819] and Epidermophyton floccosum [MTCC 7880] were used to study its susceptibility to the isolated actinomycetes. Actinomycetes which showed antidermatophytic activity were subjected to cultural characterization with respect to aerial and substrate mycelia color, diffusible and melanin pigment production and the growth of the organisms on different media. Further the micro morphological characteristics such as spore surface ornamentation and spore chain morphology determined by Scanning Electron Microscopic (SEM analysis also suggested that the isolates belonged to the genus Streptomyces. The isolates were also tested for utilization of various carbon and nitrogen sources, degradation of complex compounds, sensitivity to antibiotics and inhibitory compounds. Results: All the 3 isolates exhibited different cultural and morphological characteristics. Based on the cultural characters and morphology they were assigned to the genus Streptomyces. The three isolates produced an inhibition zone of 30-31 mm on an average, utilized a wide range of carbon and nitrogen sources, degraded almost all the complex compounds and exhibited a broad spectrum of antibiotic resistance. They were designated as Streptomyces sp. DKDVIT1, Streptomyces sp. DKDVIT2 and

  8. Endophytic Phoma sp. isolated from medicinal plants promote the growth of Zea mays

    ASHWINI KEDAR; DNYANESHWAR RATHOD; ALKA YADAV; GAURAVI AGARKAR; MAHENDRA RAI

    2014-01-01

    Kedar A, Rathod D, Yadav A, Agarkar G, Rai M. 2014. Endophytic Phoma sp. isolated from medicinal plants promote the growth of Zea mays. Nusantara Bioscience 6: 132-139. Fungal endophytes are reported as rich sources of valuable secondary metabolites and could be used as bio-fertilizers. In the present study, we report growth promotion potential of two Phoma species isolated from Tinospora cordifolia and Calotropis procera on maize. The fungal endophytes enhanced growth in inoculated maize pla...

  9. Draft Genome Sequence of Halomonas sp. HG01, a Polyhydroxyalkanoate-Accumulating Strain Isolated from Peru.

    Cardinali-Rezende, Juliana; Nahat, Rafael Augusto Teodoro Pereira de Souza; Guzmán Moreno, César Wilber; Carreño Farfán, Carmen Rosa; Silva, Luiziana Ferreira; Taciro, Marilda Keico; Gomez, José Gregório Cabrera

    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

  10. Draft Genome Sequence of Halomonas sp. HG01, a Polyhydroxyalkanoate-Accumulating Strain Isolated from Peru

    Cardinali-Rezende, Juliana; Nahat, Rafael Augusto Teodoro Pereira de Souza; Guzmán Moreno, César Wilber; Carreño Farfán, Carmen Rosa; Silva, Luiziana Ferreira; Taciro, Marilda Keico; Gomez, José Gregório Cabrera

    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%.

  11. Complete genome sequence of carotenoid-producing Microbacterium sp. strain PAMC28756 isolated from an Antarctic lichen.

    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

  12. Draft Genome Sequence of Lactobacillus sp. Strain TCF032-E4, Isolated from Fermented Radish

    Chen, Meng; Horvath, Philippe

    2015-01-01

    Here, we report the draft genome sequence of Lactobacillus sp. strain TCF032-E4 (= CCTCC AB2015090 = DSM 100358), isolated from a Chinese fermented radish. The total length of the 57 contigs is about 2.9 Mb, with a G+C content of 43.5 mol% and 2,797 predicted coding sequences (CDSs). PMID:26227596

  13. Genome of Rhizobium sp. UR51a, Isolated from Rice Cropped in Southern Brazilian Fields.

    de Souza, Rocheli; Sant'Anna, Fernando Hayashi; Ambrosini, Adriana; Tadra-Sfeir, Michele; Faoro, Helisson; Pedrosa, Fabio Oliveira; Souza, Emanuel Maltempi; Passaglia, Luciane M P

    2015-01-01

    Rhizobium sp. UR51a is a Gram-negative bacterium isolated from roots of rice plants, and it presents plant growth-promoting abilities. The nutrient uptake in rice plants inoculated with UR51a was satisfactory. The genome of strain UR51a is composed of 5,233,443-bp and harbors 5,079 coding sequences. PMID:25838497

  14. Genome of Rhizobium sp. UR51a, Isolated from Rice Cropped in Southern Brazilian Fields

    de Souza, Rocheli; Sant’Anna, Fernando Hayashi; Ambrosini, Adriana; Tadra-Sfeir, Michele; Faoro, Helisson; Pedrosa, Fabio Oliveira; Souza, Emanuel Maltempi; Passaglia, Luciane M. P.

    2015-01-01

    Rhizobium sp. UR51a is a Gram-negative bacterium isolated from roots of rice plants, and it presents plant growth-promoting abilities. The nutrient uptake in rice plants inoculated with UR51a was satisfactory. The genome of strain UR51a is composed of 5,233,443-bp and harbors 5,079 coding sequences.

  15. Draft Genome Sequence of Rhizobium sp. GHKF11, Isolated from Farmland Soil in Pecan Grove, Texas

    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

  16. Whole-Genome Sequence of Bacillus sp. SDLI1, Isolated from the Social Bee Scaptotrigona depilis

    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

  17. Isolation of 2-deoxyecdysterone, a novel oxytocic agent, from a marine Zoanthus sp.

    Parameswaran, P.S.; Naik, C.G.; Gonsalves, C.; Achuthankutty, C.T.

    The insect-moulting hormone 2-deoxyecdysterone (2-deoxy-20-hydroxyecdysone 1) has been isolated for the first time and in relatively high yield (0.016%) from a marine Zoanthus sp. The compound exhibited promising oxytocic activity in guinea pig...

  18. Draft Genome Sequence of Clostridium sp. Maddingley, Isolated from Coal-Seam Gas Formation Water

    Rosewarne, Carly P.; Greenfield, Paul; Li, Dongmei; Tran-Dinh, Nai; Bradbury, Mark I.; Midgley, David J.; Hendry, Philip

    2013-01-01

    Clostridium sp. Maddingley was isolated as an axenic culture from a brown coal-seam formation water sample collected from Victoria, Australia. It lacks the solventogenesis genes found in closely related clostridial strains. Metabolic reconstructions suggest that volatile fatty acids are the main fermentation end products.

  19. Draft Genome Sequence of Clostridium sp. Maddingley, Isolated from Coal-Seam Gas Formation Water.

    Rosewarne, Carly P; Greenfield, Paul; Li, Dongmei; Tran-Dinh, Nai; Bradbury, Mark I; Midgley, David J; Hendry, Philip

    2013-01-01

    Clostridium sp. Maddingley was isolated as an axenic culture from a brown coal-seam formation water sample collected from Victoria, Australia. It lacks the solventogenesis genes found in closely related clostridial strains. Metabolic reconstructions suggest that volatile fatty acids are the main fermentation end products. PMID:23405323

  20. Genome Sequence of Pseudomonas sp. HUK17, Isolated from Hexachlorocyclohexane-Contaminated Soil

    Gasc , Cyrielle; Richard, Jean-Yves; Peyret, Pierre

    2016-01-01

    Pseudomonas sp. HUK17 has been isolated from hexachlorocyclohexane (HCH) long-term contaminated soil. The genome of strain HUK17 was sequenced to elucidate its adaptation toward HCH and to evaluate the presence of pesticide degradation pathways. Here, we report the annotated draft genome sequence (~2.6 Mbp) of this strain.

  1. Isolation of Ochrobactrum sp.QZ2 from sulfide and nitrite treatment system.

    Mahmood, Qaisar; Hu, Baolan; Cai, Jing; Zheng, Ping; Azim, Muhammad Rashid; Jilani, Ghulam; Islam, Ejazul

    2009-06-15

    A bacterial strain QZ2 was isolated from sludge of anoxic sulfide-oxidizing (ASO) reactor. Based on 16S rDNA sequence analysis and morphology, the isolate was identified as Ochrobactrum sp. QZ2. The strain was facultative chemolithotroph, able of using sulfide to reduce nitrite anaerobically. It produced either elemental sulfur or sulfate as the product of sulfide oxidation, depending on the initial sulfide and nitrite concentrations. The optimum growth pH and temperature for Ochrobactrum sp. QZ2 were found as 6.5-7.0 and 30 degrees C, respectively. The specific growth rate (micro) was found as 0.06 h(-1) with a doubling time of 19.75h; the growth seemed more sensitive to highly alkaline pH. Ochrobactrum sp. QZ2 catalyzed sulfide oxidation to sulfate was more sensitive to sulfide compared with nitrite as indicated by IC(50) values for sulfide and nitrite utilization implying that isolate was relatively more tolerant to nitrite. The comparison of physiology of Ochrobactrum sp. QZ2 with those of other known sulfide-oxidizing bacteria suggested that the present isolate resembled to Ochrobactrum anthropi in its denitrification ability. PMID:19010594

  2. Genome Sequence of Streptomyces sp. Strain TOR3209, a Rhizosphere Microecology Regulator Isolated from Tomato Rhizosphere

    Hu, Dong; Li, Xiaozhi; Chang, Yueli; He, Huan; Zhang, Cuimian; Jia, Nan; Li, Hongtao; Wang, Zhanwu

    2012-01-01

    Streptomyces sp. strain TOR3209, isolated from tomato rhizosphere, can regulate the rhizosphere microecology of a variety of crops. Strain TOR3209 could improve plant systemic resistance and promote plant growth. Here, the genome sequence of strain TOR3209 is reported, providing the molecular biological basis of the regulation mechanism of rhizosphere microecology.

  3. Structural elucidation of the EPS of slime producing Brevundimonas vesicularis sp isolated from a paper machine

    Verhoef, R.P.; Waard, de P.; Schols, H.A.; Ratto, M.; Siika-aho, M.; Voragen, A.G.J.

    2002-01-01

    The slime forming bacteria Brevundimonas vesicularis sp. was isolated from a paper mill and its EPS was produced on laboratory scale. After production, the exopolysaccharide (EPS) was purified and analysed for its purity and homogeneity, HPSEC revealed one distinct population with a molecular mass o

  4. Complete Genome Sequence of Algoriphagus sp. Strain M8-2, Isolated from a Brackish Lake

    Muraguchi, Yusuke; Kushimoto, Koya; Ohtsubo, Yoshiyuki; Suzuki, Tomohiro; Dohra, Hideo; Kimbara, Kazuhide

    2016-01-01

    Algoriphagus sp. strain M8-2 was isolated from a brackish lake, Lake Sanaru, in Hamamatsu, Japan, as a filterable bacterium through a 0.22-µm-pore-size membrane filter. We report here the complete nucleotide sequence of the M8-2 genome (a 3,882,610-bp chromosome). PMID:27174266

  5. Genome Sequence of Gluconacetobacter sp. Strain SXCC-1, Isolated from Chinese Vinegar Fermentation Starter▿

    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.

  6. Isolation of Ochrobactrum sp.QZ2 from sulfide and nitrite treatment system

    Mahmood, Qaisar, E-mail: mahmoodzju@gmail.com [Department of Environmental Engineering, Zhejiang University Hangzhou 310029 (China); Department of Environmental Sciences, COMSATS Institute of Information Technology Abbottabad (Pakistan); Hu Baolan; Cai Jing [Department of Environmental Engineering, Zhejiang University Hangzhou 310029 (China); Zheng Ping, E-mail: pzheng@zju.edu.cn [Department of Environmental Engineering, Zhejiang University Hangzhou 310029 (China); Azim, Muhammad Rashid [Department of Botany, Federal Government Post Graduate College H-8 Islamabad (Pakistan); Jilani, Ghulam [Department of Soil Science and Soil and Water Conservation, PMAS Arid Agriculture University, Rawalpindi (Pakistan); Islam, Ejazul [Department of Environmental Engineering, Zhejiang University Hangzhou 310029 (China)

    2009-06-15

    A bacterial strain QZ2 was isolated from sludge of anoxic sulfide-oxidizing (ASO) reactor. Based on 16S rDNA sequence analysis and morphology, the isolate was identified as Ochrobactrum sp. QZ2. The strain was facultative chemolithotroph, able of using sulfide to reduce nitrite anaerobically. It produced either elemental sulfur or sulfate as the product of sulfide oxidation, depending on the initial sulfide and nitrite concentrations. The optimum growth pH and temperature for Ochrobactrum sp. QZ2 were found as 6.5-7.0 and 30 deg. C, respectively. The specific growth rate ({mu}) was found as 0.06 h{sup -1} with a doubling time of 19.75 h; the growth seemed more sensitive to highly alkaline pH. Ochrobactrum sp. QZ2 catalyzed sulfide oxidation to sulfate was more sensitive to sulfide compared with nitrite as indicated by IC{sub 50} values for sulfide and nitrite utilization implying that isolate was relatively more tolerant to nitrite. The comparison of physiology of Ochrobactrum sp. QZ2 with those of other known sulfide-oxidizing bacteria suggested that the present isolate resembled to Ochrobactrum anthropi in its denitrification ability.

  7. Knoellia sinensis gen. nov., sp. nov. and Knoellia subterranea sp. nov., two novel actinobacteria isolated from a cave.

    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). PMID:11837319

  8. Isolation and characterization of "Methanosphaera cuniculi" sp. nov.

    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...

  9. Candidimonas nitroreducens gen. nov., sp nov and Candidimonas humi sp nov., isolated from sewage sludge compost

    Vaz-Moreira, Ivone; Figueira, Vânia; Lopes, Ana R.; De Brandt, Evie; Vandamme, Peter; Nunes, Olga C.; Manaia, Célia M.

    2011-01-01

    Two bacterial strains (SC-089(T) and SC-092(T)) isolated from sewage sludge compost were characterized by using a polyphasic approach. The isolates were Gram-negative short rods, catalase- and oxidase-positive, and showed good growth at 30 degrees C, at pH 7 and with 1% (w/v) NaCl. Ubiquinone 8 was the major respiratory quinone, and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol were amongst the major polar lipids. On the basis of 16S rRNA gene sequence analysis, th...

  10. Algoriphagus shivajiensis sp. nov., isolated from Cochin back water, India

    AnilKumar, P.; Bhumika, V.; Ritika, C.; VijayaBhaskar, Y.; Priyashanth, P.; Aravind, R.; Bindu, E.; Srinivas, T.N.R.

    in Algoriphagus jejuensis, Algoriphagus aquatilis, Algoriphagus faecimaris and Algoriphagus boritolerans (Lee et al., 2012; Liu et al., 2009; Nedashkovskaya et al., 2007b; Li et al., 2011). Two isolates differed with the type species of the genus Algoriphagus... habitats. Int. J. Syst. Evol. Microbiol. 53, 1343-1355. [7] Chun, J., Lee, J.-H., Jung, Y., Kim, M., Kim, S., Kim, B.K., Lim, Y.W. (2007). EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int. J...

  11. Physico-chemical and techno-functional properties of proteins isolated from the green microalgae Tetraselmis sp.

    Schwenzfeier, A.

    2013-01-01

    In this thesis, the mild isolation of an algae soluble protein isolate (ASPI) and the characterisation of its techno-functional properties are described. The ASPI was isolated from the green microalgae Tetraselmis sp. by beadmilling and subsequent anion exchange adsorption. The isolate obtained cont

  12. Impacts of varying light regimes on phycobiliproteins of Nostoc sp. HKAR-2 and Nostoc sp. HKAR-11 isolated from diverse habitats.

    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 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

  13. Antimicrobial activity of endophytic fungus Fusarium sp. isolated from medicinal honeysuckle plant

    Zhang Huiru

    2016-01-01

    Full Text Available Endophytes of plants have a wide range of strains comprising important sources of various bioactive metabolites. An endophytic fungus was isolated from honeysuckle, an important Chinese medicinal plant. The phylogenetic and physiological characterization indicated that the isolated strain JY2corresponded to Fusarium sp. The culture filtrate of JY2displayed antagonism activity against some pathogenic bacteria owing to the existence of antimicrobial compounds. The filtrate revealed the strongest in vitro antimicrobial activity on Pseudomonas aeruginosa by increasing the permeability of cell membranes. The antibacterial extract was fractionated and purifiedusing silica gel chromatography. Five different bioactive compounds were isolated by bioactivity-guided fractionation from the culture extracts of JY2, and preliminarily identified by HPLC-MS spectral data. These results suggest that Fusarium sp. features a potentially remarkable antimicrobial activity and could be valuable to discover the new drugs or agents for antimicrobial purposes.

  14. Bioactive secondary metabolites from the endophytic fungus Chaetomium sp. isolated from Salvia officinalis growing in Morocco

    Ebel R.

    2009-01-01

    Full Text Available This study reports the chemical investigation and cytotoxic activity of the secondary metabolites produced by the endophytic fungus Chaetomium sp. isolated from Salvia officinalis growing in Morocco. This plant was collected from the Beni-Mellal Mountain in Morocco and belongs to the Lamiaceae family and is named in Morocco “Salmia”. The endophytic fungus Chaetomium sp. was isolated from the tissues of the stem of this plant. The fungal strain was identified by PCR. The crude organic extract of the fungal strain was proven to be active when tested for cytotoxicity against L5178Y mouse lymphoma cells. Chemical investigation of the secondary metabolites showed that cochliodinol is the main component beside isocochliodinol. The structures of the isolated compounds were determined on the basis of NMR analysis (1H, 13C, COSY and HMBC as well as by mass spectrometry using ESI (Electron Spray Ionisation as source.

  15. Thalassospira australica sp. nov. isolated from sea water.

    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

  16. Rhizobium helianthi sp. nov., isolated from the rhizosphere of sunflower.

    Wei, Xuexin; Yan, Shouwei; Li, Dai; Pang, Huancheng; Li, Yuyi; Zhang, Jianli

    2015-12-01

    A Gram-stain-negative, non-spore-forming, rod-shaped and aerobic bacterium, designated Xi19T, was isolated from a soil sample collected from the rhizosphere of sunflower (Helianthus annuus) in Wuyuan county of Inner Mongolia, China and was characterized taxonomically by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolate was related to species of the genus Rhizobium, sharing the greatest 16S rRNA gene sequence similarity with Rhizobium rhizoryzae J3-AN59T (98.4 %), followed by Rhizobium pseudoryzae J3-A127T (97.4 %). There were low similarities ( < 91 %) between the atpD, recA and glnII gene sequences of the novel strain and those of members of the genus Rhizobium. DNA-DNA hybridization values between strain Xi19T and the most related strain Rhizobium rhizoryzae J3-AN59T were low. The major cellular fatty acids of strain Xi19T were C16 : 0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C19 : 0 cyclo ω8c. Q-10 was identified as the predominant ubiquinone and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The DNA G+C content of strain Xi19T was 60.2 mol%. On the basis of physiological and biochemical characteristics, coupled with genotypic data obtained in this work, strain Xi19T represents a novel species of the genus Rhizobium, for which the name Rhizobium helianthi is proposed. The type strain is Xi19T ( = CGMCC 1.12192T = KCTC 23879T). PMID:26364048

  17. Aspergillus uvarum sp. nov., an uniseriate black Aspergillus species isolated from grapes in Europe

    Perrone, Giancarlo; Varga, János; Susca, Antonia;

    2008-01-01

    A novel species, Aspergillus uvarum sp. nov., is described within Aspergillus section Nigri. This species can be distinguished from other black aspergilli based on internal transcribed spacers (ITS), beta-tubulin and calmodulin gene sequences, by AFLP analysis and by extrolite profiles. Aspergill...... atypical strains of Aspergillus aculeatus, CBS 114.80 and CBS 620.78, and was isolated from grape berries in Portugal, Italy, France, Israel, Greece and Spain. The type strain of Aspergillus uvarum sp. nov. is IMI 388523(T)=CBS 127591(T)= ITEM 4834(T)= IBT26606(T)....

  18. Isolation of an exopolysaccharide-producing heavy metal-resistant Halomonas sp. MG.

    Govarthanan, Muthusamy; Shim, Jaehong; Praburaman, Loganathan; Kim, Seol Ah; Oh, Byung-Taek

    2016-03-01

    An exopolysaccharide (EPS)-producing heavy metal-resistant Gram-negative bacterium was isolated from ore-contaminated soil. The selected strain was identified by 16S rDNA sequencing and designated as Halomonas sp. MG. Phylogenetic analysis of the gene sequence showed its close similarity with Halomonas sp. Field emission scanning electron microscopy analysis revealed that the EPS had a porous structure with small pores. X-ray diffractograms showed the non-crystalline nature of the EPS. Further, FTIR spectroscopic analysis revealed the presence of carboxyl, hydroxyl and amide groups corresponding to a typical EPS. PMID:26581416

  19. Isolation and characterization of Babesia pecorum sp. nov. from farmed red deer (Cervus elaphus)

    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 cand...

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

    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 ( PCU 335T). PMID:26843374

  1. Rhizobium petrolearium sp. nov., isolated from oil-contaminated soil.

    Zhang, Xiaoxia; Li, Baoming; Wang, Haisheng; Sui, Xinhua; Ma, Xiaotong; Hong, Qing; Jiang, Ruibo

    2012-08-01

    Two Gram-negative, aerobic, rod-shaped bacteria, designated strains SL-1(T) and F11, which had the ability to decompose polycyclic aromatic hydrocarbons (PAHs), were isolated from soil samples contaminated by oil. The cells were motile by polar or lateral flagella. According to comparison of 16S rRNA gene sequences, strains SL-1(T) and F11 were identical and showed the greatest degree of similarity (96.8%) to both Rhizobium oryzae Alt505(T) and Rhizobium mesosinicum CCBAU 25010(T); however, only Rhizobium oryzae with SL-1(T) and F11 formed a separate clade. There were low similarities (SL-1(T) showed 29 and 0% DNA-DNA relatedness, respectively, with the most related strains R. oryzae Alt505(T) and R. mesosinicum CCBAU 25010(T) according to phylogenic analysis of the 16S rRNA gene. According to physiological and biochemical characteristics and genotypic data obtained in this work, the bacteria represent a novel species of the genus Rhizobium, and the name Rhizobium petrolearium is proposed. The type strain is SL-1(T) ( = ACCC 11238(T) = KCTC 23288(T)) and it could nodulate Medicago sativa in nodulation tests. PMID:21984664

  2. Degradation of Phenolic Compounds in Coal Gasification Wastewater by Biofilm Reactor with Isolated Klebsiella sp

    Fang Fang; HongJun Han; ChunYan Xu; Qian Zhao; LingHan Zhang

    2014-01-01

    This study was conducted to evaluate the degradation of phenolic compounds by one strain isolated from coal gasification wastewater ( CGW ) . 16S rRNA gene sequences homology and phylogenetic analysis showed that the isolate is belonged to the genus Klebsiella sp. The effect of different phenolic compounds on the isolate was investigated by determining OD600 and phenoloxidase activity, of which the results showed that the isolate can utilize phenol, 4-methyl phenol, 3, 5-dimethyl phenol and resorcinol as carbon resources. The biofilm reactor ( formed by the isolate) can resist the influent concentration of phenolic compounds as high as 750 mg/L when fed with synthetic CGW and incubated at optimum conditions. The capacity of improving the biodegradability of CGW through degrading phenolic compounds was testified with fed the biofilm reactor with real CGW. Thus, it might be an effective strain for bioaugmentation of CGW treatment.

  3. Aspergillus pragensis sp nov discovered during molecular reidentification of clinical isolates belonging to Aspergillus section Candidi

    Lyskova, Pavlina; Hubka, Vit; Kolarik, Miroslav;

    2014-01-01

    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 beta-tubulin, calmodulin gene sequence, and internal transcribed spacer rDNA. Six isolates were from...... 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...... 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...

  4. Application of Oligonucleotide Microarrays for Bacterial Source Tracking of Environmental Enterococcus sp. Isolates

    John S. Furey

    2005-04-01

    Full Text Available In an effort towards adapting new and defensible methods for assessing and managing the risk posed by microbial pollution, we evaluated the utility of oligonucleotide microarrays for bacterial source tracking (BST of environmental Enterococcus sp. isolates derived from various host sources. Current bacterial source tracking approaches rely on various phenotypic and genotypic methods to identify sources of bacterial contamination resulting from point or non-point pollution. For this study Enterococcus sp. isolates originating from deer, bovine, gull, and human sources were examined using microarrays. Isolates were subjected to Box PCR amplification and the resulting amplification products labeled with Cy5. Fluorescent-labeled templates were hybridized to in-house constructed nonamer oligonucleotide microarrays consisting of 198 probes. Microarray hybridization profiles were obtained using the ArrayPro image analysis software. Principal Components Analysis (PCA and Hierarchical Cluster Analysis (HCA were compared for their ability to visually cluster microarray hybridization profiles based on the environmental source from which the Enterococcus sp. isolates originated. The PCA was visually superior at separating origin-specific clusters, even for as few as 3 factors. A Soft Independent Modeling (SIM classification confirmed the PCA, resulting in zero misclassifications using 5 factors for each class. The implication of these results for the application of random oligonucleotide microarrays for BST is that, given the reproducibility issues, factor-based variable selection such as in PCA and SIM greatly outperforms dendrogram-based similarity measures such as in HCA and K-Nearest Neighbor KNN.

  5. Antifungal activity of indigenous bacillus sp. isolate Q3 against marshmallow mycobiota

    Jošić Dragana Lj.

    2011-01-01

    Full Text Available Marshmallow is a host of a number of saprophytic and parasitic fungi in Serbia. The seeds of marshmallow are contaminated with fungi from different genera, especially Alternaria and Fusarium, which significantly reduced seed germination and caused seedling decay. In this study we investigate antagnonism of indigenous Bacillus sp. isolate Q3 against marshmallow mycopopulation. Bacillus sp. Q3 was isolated from maize rhizosphere, characterized by polyphasic approch and tested for plant growth promoting treats. Bacillus sp. Q3 produced antifungal metabolites with growth inhibition activity against numerous fungi in dual culture: 61.8% of Alternaria alternata, 74.8% of Myrothecium verrucaria and 33.6% of Sclerotinia sclerotiorum. That effect could be caused by different antifungal metabolites including siderophores, hydrolytic enzymes, organic acids and indole acetic acid (IAA. Suppression of natural marshmallow seed infection by Q3 isolate was observed. The seeds were immersed in different concentrations of bacterial suspension during 2h and their infections by phytopathogenic fungi were estimated. The results showed significant reduction of seed infection by Alternaria spp. The presented results indicate possible application of this isolate as promising biological agent for control of marshmallow seed pathogenic fungi.

  6. Photobacterium aphoticum sp. nov., isolated from coastal water.

    Lucena, Teresa; Ruvira, María A; Pascual, Javier; Garay, Esperanza; Macián, M Carmen; Arahal, David R; Pujalte, María J

    2011-07-01

    A facultatively anaerobic marine gammaproteobacterium, designated strain M46(T), was isolated from Mediterranean seawater at Malvarrosa beach, Valencia, Spain. The strain was characterized by using a polyphasic approach and was found to be situated within the genus Photobacterium in the family Vibrionaceae. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain M46(T) was closely related to P. rosenbergii CECT 7644(T), P. halotolerans CECT 5860(T) and P. ganghwense CECT 7641(T), showing sequence similarities of 96.8, 96.4 and 96.2 %, respectively. According to the results of phylogenetic analyses based on recA and gyrB gene sequences, the most closely related taxon was P. ganghwense CECT 7641(T) with 87.4 and 85.0 % sequence similarity, respectively. Regardless of the gene used in phylogenetic analysis, strain M46(T) always formed a separate and stable clade containing these three species of the genus Photobacterium. Strain M46(T) was not luminescent and produced a diffusible brown pigment. It required NaCl to grow, reduced nitrate to nitrite and oxidized a small number of substrates in Biolog GN plates. Strain M46(T) was positive for arginine dihydrolase (ADH), β-galactosidase, aesculin hydrolysis and DNase activity. In API ZYM tests, the novel strain was positive for alkaline phosphatase, leucine arylamidase and acidic phosphatase activities. The major cellular fatty acids were unsaturated C(18) and C(16), as in other members of the genus Photobacterium, but their relative amounts and the presence or absence of other fatty acids differentiated strain M46(T) from its closest relatives. Based on the results of this polyphasic taxonomic study, strain M46(T) represents a novel species of the genus Photobacterium, for which the name Photobacterium aphoticum is proposed. The type strain is M46(T) ( = CECT 7614(T)  = KCTC 23057(T)). PMID:20675441

  7. BbrzSP-32, the first serine protease isolated from Bothrops brazili venom: Purification and characterization.

    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 36kDa of relative molecular mass and its absolute mass was confirmed by mass spectrometry as 32,520Da. 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

  8. Tenacibaculum discolor sp. nov. and Tenacibaculum gallaicum sp. nov., isolated from sole (Solea senegalensis) and turbot (Psetta maxima) culture systems.

    Piñeiro-Vidal, Maximino; Riaza, Ana; Santos, Ysabel

    2008-01-01

    Two Gram-negative, rod-shaped, gliding bacterial strains, designated strain LL04 11.1.1(T) and strain A37.1(T), were isolated from a diseased sole (Solea senegalensis) and from seawater from a holding tank for turbot (Psetta maxima), respectively. The strains grew on solid media as bright yellow colonies with uneven edges; the colonies did not adhere to the agar. The bacteria were able to grow at temperatures in the range 14 to 38 degrees C and from pH 6.0 to pH 8.0. The DNA G+C contents of strains LL04 11.1.1(T) and A37.1(T) were 32.1 and 32.7 mol%, respectively. Analysis of the 16S rRNA gene sequences indicated that strains LL04 11.1.1(T) and A37.1(T) were members of the genus Tenacibaculum in the family Flavobacteriaceae. The sequence similarities of the two isolates with respect to the type strains of recognized members of the genus ranged from 94.2 to 99.4%. DNA-DNA hybridization studies revealed that the strains studied represent two distinct novel species of the genus Tenacibaculum, for which the names Tenacibaculum discolor sp. nov. [type strain LL04 11.1.1(T) (=NCIMB 14278(T)=DSM 18842(T))] and Tenacibaculum gallaicum sp. nov. [type strain A37.1(T) (=NCIMB 14147(T)=DSM 18841(T))] are proposed. PMID:18175676

  9. Draft genome sequence of Thermoactinomyces sp. strain AS95 isolated from a Sebkha in Thamelaht, Algeria.

    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

  10. MORPHOLOGICAL IDENTIFICATION OF DIAPORTHE/PHOMOPSIS SP. ISOLATED FROM XANTHIUM ITALICUM

    Draženka Jurković

    2007-12-01

    Full Text Available Diaporthe/Phomopsis sp. was isolated from Xanthium italicum (Italian cockleburr for the first time in Eastern Croatia during 2004 year. As Diaporthe/Phomopsis species are known as pathogens of soybean, sunflower and other arable crops, it is important to study alternative hosts as a possible source of inoculum from an epidemiological point of view. This paper describes symptoms of infection on X. italicum, pathogen morphological and cultural characters on potato-dextrose agar (PDA, biometrical values of reproductive structures (pycnidia, beta conidia, perithecia, asci and ascospores of naturally infected plants and of cultures grown on PDA. Results obtained from undertaken studies indicate that our Phomopsis sp. isolates from X. italicum belong to the group of P. helianthi.

  11. Detoxification of Atrazine by Endophytic Streptomyces sp. Isolated from Sugarcane and Detection of Nontoxic Metabolite.

    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

  12. Mechanism of thorium biosorption by the cells of the soil fungal isolate Geotrichum sp. dwc-1

    In order to understand the impact of microorganisms on the fate of thorium in soils, we investigated the thorium biosorption behavior and the corresponding mechanisms by the cells of Geotrichum sp. dwc-1, one of the dominant species of fungal group isolated from 3.5 m depth soil layer in Southwest China. It was observed that fast thorium adsorption onto cells of G. sp. dwc-1 could take place, with a high distribution coefficient Kd (0.93 mL/mg) obtained, when Geotrichum sp. dwc-1and thorium concentrations were 5 g/L and 10 mg/L, respectively. The thorium biosorption behavior was dependent on the pH value, and the lower pH could disrupt cell membrane of G. sp. dwc-1. At pH 1, thorium was accumulated in the cytoplasmic region of the cells. When pH was higher than 1, thorium was adsorbed on the cell surface of G. sp. dwc-1, like in periplasmic region or in the outer membrane. FTIR study combined with biosorption experiments further indicated that the thorium distribution and binding behavior on cell surface were associated with amino, hydroxyl groups and phosphate or sulphur functional groups, and might also be governed by electrostatic interaction. Moreover, PIXE and EPBS showed that ion-exchange mechanism contributed to the thorium biosorption process, in which the tetravalent thorium ions replaced smaller counter-ions (K+, Ca2+ and Fe3+) occuring on the cell surface. (orig.)

  13. Isolation and Structural Elucidation of Chondrosterins F–H from the Marine Fungus Chondrostereum sp.

    Wen-Jian Lan

    2013-02-01

    Full Text Available 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.

  14. Isolation and characterization of Burkholderia sp. strain CCA53 exhibiting ligninolytic potential

    Akita, Hironaga; Kimura, Zen-ichiro; Mohd Yusoff, Mohd Zulkhairi; Nakashima, Nobutaka; Hoshino, Tamotsu

    2016-01-01

    Microbial degradation of lignin releases fermentable sugars, effective utilization of which could support biofuel production from lignocellulosic biomass. In the present study, a lignin-degrading bacterium was isolated from leaf soil and identified as Burkholderia sp. based on 16S rRNA gene sequencing. This strain was named CCA53, and its lignin-degrading capability was assessed by observing its growth on medium containing alkali lignin or lignin-associated aromatic monomers as the sole carbo...

  15. Application of Oligonucleotide Microarrays for Bacterial Source Tracking of Environmental Enterococcus sp. Isolates

    Furey, John S.; Kelley Betts; Indest, Karl J.

    2005-01-01

    In an effort towards adapting new and defensible methods for assessing and managing the risk posed by microbial pollution, we evaluated the utility of oligonucleotide microarrays for bacterial source tracking (BST) of environmental Enterococcus sp. isolates derived from various host sources. Current bacterial source tracking approaches rely on various phenotypic and genotypic methods to identify sources of bacterial contamination resulting from point or non-point pollution. For this study Ent...

  16. Hexavalent Chromium Removal by a Paecilomyces sp. Fungal Strain Isolated from Environment

    Cárdenas-González, Juan F.; Ismael Acosta-Rodríguez

    2010-01-01

    A resistant and capable fungal strain in removing hexavalent chromium was isolated from an environment near of Chemical Science Faculty, located in the city of San Luis Potosí, Mexico. The strain was identified as Paecilomyces sp., by macro- and microscopic characteristics. Strain resistance of the strain to high Cr (VI) concentrations and its ability to reduce chromium were studied. When it was incubated in minimal medium with glucose, another inexpensive commercial carbon source like unrefi...

  17. Draft genome sequence of Kocuria sp. SM24M-10 isolated from coral mucus

    Bruna Rafaella Z. Palermo

    2016-03-01

    Full Text Available 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.

  18. Draft genome sequence of Kocuria sp. SM24M-10 isolated from coral mucus.

    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

    2016-03-01

    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

  19. Draft genome sequence of Kocuria sp. SM24M-10 isolated from coral mucus

    Palermo, Bruna Rafaella Z.; Castro, Daniel B.A.; Pereira, Letícia Bianca; Cauz, Ana Carolina G.; Beatriz L. Magalhães; Carlos, Camila; da Costa, Fernanda L.P.; Guilherme P. Scagion; Higa, Juliana S.; Almeida, Ludimila D.; das Neves, Meiriele da S.; Cordeiro, Melina Aparecida; Paula F.V. do Prado; da Silva, Thiago M.; Balsalobre, Thiago Willian A.

    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 cora...

  20. Draft genome sequence of Kocuria sp. SM24M-10 isolated from coral mucus

    Palermo, Bruna Rafaella Z.; Castro, Daniel B.A.; Letícia Bianca Pereira; Cauz, Ana Carolina G.; Beatriz L. Magalhães; Camila Carlos; da Costa, Fernanda L.P.; Guilherme P. Scagion; Higa, Juliana S.; Almeida, Ludimila D.; das Neves, Meiriele da S.; Melina Aparecida Cordeiro; Paula F.V. do Prado; da Silva, Thiago M.; Balsalobre, Thiago Willian A.

    2016-01-01

    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 cora...

  1. Draft Genome Sequence of Burkholderia sp. Strain CCA53, Isolated from Leaf Soil

    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

  2. Cytochalasin H2, a New Cytochalasin, Isolated from the Endophytic Fungus Xylaria sp. A23

    Yu Li

    2012-01-01

    Full Text Available A new natural product, cytochalasin H2 (1, together with cytochalasin H (2 were obtained from the agar cultures of the strain Xylaria sp. A23, which was isolated from Annona squamosa. The chemical structures of them were elucidated by spectroscopic and mass spectrometric analyses, including 1D-, 2D-NMR and HR FTMS. Compound 1 showed week cytotoxicity against HeLa and 293T cell lines by MTT assay.

  3. Antifungal compounds of Xylaria sp., an endophytic fungus isolated from Palicourea marcgravii (Rubiaceae)

    Five compounds, 2-hexyl-3-methyl-butanodioic acid (1), cytochalasin D (2), 7-dechlorogriseofulvin (3), cytochalasin B (4) and griseofulvin (5), have been isolated from the endophytic fungus Xylaria sp., and their structures were elucidated on the basis of spectroscopic data. In the bioautography assay against Cladosporium cladosporioides and Cladosporium sphaerospermum, compounds 1 and 2 were found to be active while compounds 3, 4 and 5 did not show antifungal activity. (author)

  4. Preferential desulfurization of dibenzyl sulfide by an isolated Gordonia sp. IITR100

    Ahmad, Abrar; Chauhan, Ashok Kumar; Kushwaha, Hari Narayan; Javed, Saleem; Kumar, Ashwani

    2014-01-01

    Several organosulfur compounds are present in the crude oil, and are required to be removed before its processing into transport fuel. For this reason, biodesulfurization of thiophenic compounds has been studied extensively. However, studies on the sulfide compounds are scarce. In this paper, we describe desulfurization of a model sulfidic compound, dibenzyl sulfide (DBS) by an isolated Gordonia sp. IITR100. The reaction was accompanied with the formation of metabolites dibenzyl sulfoxide, di...

  5. Seminibacterium arietis gen. nov., sp. nov., isolated from the semen of rams.

    Vela, A I; Bueso, J P; Domínguez, L; Busse, H-J; Fernández-Garayzábal, J F

    2013-05-01

    Two gram-negative, catalase- and oxidase-positive, bacillus-shaped bacterial strains were isolated from the semen of two rams. 16S rRNA gene sequencing demonstrated that both isolates represented a distinct subline within the family Pasteurellaceae with traits and a combination of signature amino acids in the RpoB protein sequence. On the basis of these results we describe a new genus and species for which we propose the name of Seminibacterium arietis gen. nov., sp. nov. (DICM11-00342(T)=CCUG 61707(T)=CECT 8033(T)). PMID:23415481

  6. A Novel Radiation-Resistant Strain of Filobasidium sp. Isolated from the West Sea of Korea

    A novel radiation-resistant Filobasidium sp. yeast strain was isolated from seawater. Along with this strain, a total of 656 yeast isolates were purified from seawater samples collected from three locations in the West Sea of Korea and assessed for their radiation tolerance. Among these isolates, five were found to survive a 5 kGy radiation dose. The most radiation resistant strain was classified as Filobasidium sp. based on 18S rDNA sequence analysis and hence was named Filobasidium RRY1 (Radiation-Resistant Yeast 1). RRY1 differed from F. elegans, which is closely related to RRY1, in terms of the optimal growth temperature and radiation resistance, and was resistant to high doses of γ-ionizing radiation (D10: 6-7 kGy). When exposed to a high dose of 3 kGy irradiation, the RRY1 cells remained intact and undistorted, with negligible cell death. When these irradiated cells were allowed to recover, the cells fully repaired their genomic DNA within 3 h of growth recovery. This is the first report in which a radiation-resistant response has been investigated at the physiological, morphological, and molecular levels in a strain of Filobasidium sp. (author)

  7. Comparative study on biochemical activity of the intestinal isolates Lactobacillus sp. V3 and Bifidobacterium sp. A71 in different substrates

    JOSIP BARAS; SUZANA DIMITRIJEVIC-BRANKOVIC

    2001-01-01

    The two intestinal isolates Lactobacillus sp. V3 and Bifidobacterium sp. A71 were selected for soymilk fermentation according to their acidification activity in soymilk. Beetroot juice and carrot juice were chosen for soymilk supplementation as additional sources of carbohydrates and brewer's yeast as an extra source of nitrogen. The fermentation was carried out for eight hours at 42°C. The fermentation was monitored by standard analytical and microbiological tests for changes of acidity (dec...

  8. Pantoea beijingensis sp. nov., isolated from the fruiting body of Pleurotus eryngii.

    Liu, Yu; Wang, Shouxian; Zhang, Dianpeng; Wei, Shujun; Zhao, Shuang; Chen, Sanfeng; Xu, Feng

    2013-12-01

    Four Gram-negative-staining, facultatively anaerobic bacterial isolates were obtained from a fruiting body of the edible mushroom Pleurotus eryngii showing symptoms of soft rot disease in Beijing, China. Partial 16S rRNA gene sequencing, together with partial rpoB sequencing, placed these isolates in the genus Pantoea. Multilocus sequence analysis based on the partial sequences of gyrB, rpoB, infB and atpD revealed Pantoea dispersa and Pantoea gaviniae as their closest phylogenetic relatives and indicated that these isolates constituted a possible novel species. DNA-DNA hybridization studies confirmed the classification of the new isolates as a novel species and phenotypic tests allowed for differentiation from the closest phylogenetic neighbours. The name Pantoea beijingensis sp. nov. [type strain LMG 27579(T) = KCTC 32406(T) = JZB2120001(T) (deposited at Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences)] is proposed. PMID:24013967

  9. Pantoea hericii sp. nov., Isolated from the Fruiting Bodies of Hericium erinaceus.

    Rong, Chengbo; Ma, Yuanwei; Wang, Shouxian; Liu, Yu; Chen, Sanfeng; Huang, Bin; Wang, Jing; Xu, Feng

    2016-06-01

    Three Gram-negative, facultatively anaerobic bacterial isolates were obtained from the fruiting bodies of the edible mushroom Hericium erinaceus showing symptoms of soft rot disease in Beijing, China. Sequences of partial 16S rRNA gene placed these isolates in the genus Pantoea. Multilocus sequence analysis based on the partial sequences of atpD, gyrB, infB and rpoB revealed P. eucalypti and P. anthophila as their closest phylogenetic relatives and indicated that these isolates constituted a possible novel species. DNA-DNA hybridization studies confirmed the classification of these isolates as a novel species and phenotypic tests allowed for differentiation from the closest phylogenetic neighbours. The name Pantoea hericii sp. nov. [Type strain LMG 28847(T) = CGMCC 1.15224(T) = JZB 2120024(T)] is proposed. PMID:26897127

  10. Complete genome sequence of the xylan-degrading Mucilaginibacter sp. strain PAMC26640 isolated from an Arctic lichen.

    Oh, Tae-Jin; Han, So-Ra; Kang, Seunghyun; Park, Hyun; Kim, Augustine Yonghwi

    2016-06-10

    Mucilaginibacter sp. PAMC26640 is a xylan-degrading bacterium isolated from the Arctic lichen Stereocaulon sp. Here, we present the first complete genome sequence of Mucilaginibacter sp. strain PAMC26640, which contains several genes involved in xylan utilization. This genome information provides new insights into the genetic basis of its physiology and further analysis of key metabolic genes related to the xylan degradation pathway. PMID:27080447

  11. Biodegradation of 4-chloronitrobenzene by biochemical cooperation between Sphingomonas sp. strain CNB3 and Burkholderia sp. strain CAN6 isolated from activated sludge.

    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. PMID:23473429

  12. Permanent Draft Genome Sequence of Nocardia sp. BMG111209, an Actinobacterium Isolated from Nodules of Casuarina glauca.

    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

  13. Draft Genome Sequence of a Tetrabromobisphenol A–Degrading Strain, Ochrobactrum sp. T, Isolated from an Electronic Waste Recycling Site

    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

  14. Draft Genome Sequence of the Lignin-Degrading Burkholderia sp. Strain LIG30, Isolated from Wet Tropical Forest Soil

    Woo, Hannah L.; Utturkar, Sagar; Klingeman, Dawn; Simmons, Blake A.; DeAngelis, Kristen M; Brown, Steven D.; Hazen, Terry C.

    2014-01-01

    Burkholderia species are common soil Betaproteobacteria capable of degrading recalcitrant aromatic compounds and xenobiotics. Burkholderia sp. strain LIG30 was isolated from wet tropical forest soil and is capable of utilizing lignin as a sole carbon source. Here we report the draft genome sequence of Burkholderia sp. strain LIG30.

  15. Genome Sequence of Pseudomonas sp. Strain S9, an Extracellular Arylsulfatase-Producing Bacterium Isolated from Mangrove Soil ▿

    Long, Mengxian; Ruan, Lingwei; Yu, Ziniu; Xu, Xun

    2011-01-01

    Pseudomonas sp. strain S9 was originally isolated from mangrove soil in Xiamen, China. It is an aerobic bacterium which shows extracellular arylsulfatase activity. Here, we describe the 4.8-Mb draft genome sequence of Pseudomonas sp. S9, which exhibits novel cysteine-type sulfatases.

  16. Draft Genome Sequence of a Phthalate Ester-Degrading Bacterium, Rhizobium sp. LMB-1, Isolated from Cultured Soil

    Tang, Wen-Juan; Ying ZHOU; Ye, Bang-Ce

    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.

  17. Complete Genome Sequence of Labrenzia sp. Strain CP4, Isolated from a Self-Regenerating Biocathode Biofilm

    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 Paenibacillus sp. Strain MSt1 with Broad Antimicrobial Activity, Isolated from Malaysian Tropical Peat Swamp Soil

    Aw, Yoong Kit; Ong, Kuan Shion; Catherine M Yule; Gan, Han Ming; Lee, Sui Mae

    2014-01-01

    We report the draft genome sequence of Paenibacillus sp. strain MSt1, which has broad-range antimicrobial activity, isolated from tropical peat swamp soil. Genes involved in antimicrobial biosynthesis are found to be present in this genome.

  19. Isolation of (-)-avenaciolide as the antifungal and antimycobacterial constituent of a Seimatosporium sp. Endophyte from the medicinal plant Hypericum perforatum .

    Clark, Trevor N; Bishop, Amanda I; McLaughlin, Mark; Calhoun, Larry A; Johnson, John A; Gray, Christopher A

    2014-10-01

    An extract of Seimatosporium sp., an endophyte from the Canadian medicinal plant Hypericum perforatum, exhibited significant antifungal and antimycobacterial activity against Candida albicans and Mycobacterium tuberculosis H37Ra. Bioassay guided fractionation led to the isolation of (-)-avenaciolide as the only bioactive constituent of the extract. This is the first report of both the antimycobacterial activity of avenaciolide and its isolation from a Seimatosporium sp. fungus. PMID:25522544

  20. Isolation of a psychrotrophic Exiguobacterium sp. SKPB5 (MTCC 7803) and characterization of its alkaline protease.

    Kasana, Ramesh C; Yadav, Sudesh K

    2007-03-01

    Out of nine psychrotrophic bacterial strains isolated from cold environments of the Western Himalayas, SKPB5 was selected for protease purification and characterization because it had the largest zone of clearance on plate assay. On the basis of the phenotypic and biochemical characterization and 16S rRNA gene-sequencing studies, isolate was identified as Exiguobacterium sp. SKPB5. The protease was purified near to homogeneity with a purification fold of 7.1, and its molecular weight was determined to be 36 kDa. The enzyme exhibited maximum stability at 50 degrees C and an optimal pH of 8.0. Metal ions Mg2+, Ca2+, Zn2+, and Mn2+ enhanced the enzyme activity, whereas Cu2+ had no effect. Phenylmethanesulfonyl fluoride and ethylenediaminetetraacetic acid did not show any effect on the activity of the enzyme, whereas a 20% increase in activity was observed when it was incubated in presence of reducing agents such as beta-mercaptoethanol and dithiothreitol. This suggests that the protease isolated from psychrotrophic Exiguobacterium sp. SKPB5 belongs to the cysteine family. The results highlight the relevance of unexplored microbes from cold environments of Western Himalayas for the isolation of protease enzymes active at wide range of temperature and pH. PMID:17294327

  1. Pantoea sp. isolated from tropical fresh water exhibiting N-acyl homoserine lactone production.

    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. PMID:25197715

  2. Pantoea sp. Isolated from Tropical Fresh Water Exhibiting N-Acyl Homoserine Lactone Production

    Wen-Si Tan

    2014-01-01

    Full Text Available 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.

  3. Endophytic Phoma sp. isolated from medicinal plants promote the growth of Zea mays

    ASHWINI KEDAR

    2014-11-01

    Full Text Available Kedar A, Rathod D, Yadav A, Agarkar G, Rai M. 2014. Endophytic Phoma sp. isolated from medicinal plants promote the growth of Zea mays. Nusantara Bioscience 6: 132-139. Fungal endophytes are reported as rich sources of valuable secondary metabolites and could be used as bio-fertilizers. In the present study, we report growth promotion potential of two Phoma species isolated from Tinospora cordifolia and Calotropis procera on maize. The fungal endophytes enhanced growth in inoculated maize plants compared to non-inoculated plants. The main aim of this work was to assess the growth promotion activity of endophytic Phoma species on maize isolated from T. cordifolia and C. procera.

  4. Amylase production by endophytic fungi Cylindrocephalum sp. isolated from medicinal plant Alpinia calcarata (Haw. Roscoe

    V. H. Sunitha.

    2012-09-01

    Full Text Available Amylases are among the most important enzymes used in modern biotechnology particularly in the process involving starch hydrolysis. Fungal amylase has large applications in food and pharmaceutical industries. Considering these facts, endophytic fungi isolated from the plant Alpinia calcarata (Haw. Roscoe were screened for amylolytic activity on glucose yeast extract peptone agar (GYP medium. Among thirty isolates of endophytic fungi, isolate number seven identified as Cylindrocephalum sp. (Ac-7 showed highest amylolytic activity and was taken for further study. Influence of various physical and chemical factors such as pH, temperature, carbon and nitrogen sources on amylase production in liquid media were studied. The maximal amylase production was found to be at 30ºC and at pH 7.0 of the growth medium. Among the various carbon and nitrogen sources tested, maltose at 1.5% and Sodium nitrate at 0.3% respectively gave optimum amylase production.

  5. Pantoea pleuroti sp. nov., Isolated from the Fruiting Bodies of Pleurotus eryngii.

    Ma, Yuanwei; Yin, Yonggang; Rong, Chengbo; Chen, Sanfeng; Liu, Yu; Wang, Shouxian; Xu, Feng

    2016-02-01

    Four Gram-negative-staining, facultatively anaerobic bacterial isolates were obtained from the fruiting bodies of the edible mushroom Pleurotus eryngii showing symptoms of bacterial blight disease in Beijing, China. Nearly complete 16S rRNA gene sequencing placed these isolates in the genus Pantoea. Multilocus sequence analysis based on the partial sequences of atpD, gyrB, infB and rpoB revealed Pantoea agglomerans as their closest phylogenetic relatives. DNA-DNA hybridization and phenotypic tests confirmed the classification of the new isolates as a novel species. The name Pantoea pleuroti sp. nov. [type strain KCTC 42084(T) = CGMCC 1.12894(T) = JZB 2120015(T)] is proposed. PMID:26581526

  6. Isolation and Characterization of Multi-Metal-Resistant Halomonas sp. MG from Tamil Nadu Magnesite Ore Soil in India.

    Govarthanan, Muthusamy; Shim, Jaehong; Kim, Seol Ah; Kamala-Kannan, Seralathan; Oh, Byung-Taek

    2015-11-01

    The aim of the study was to isolate and characterize potential multi-metal-resistant bacteria from ore soils. A total of three bacteria were isolated and assayed for resistance to arsenic (As), copper (Cu), and lead (Pb). Isolate Halomonas sp. MG exhibited maximum resistance to 1000 mg Pb/L, 800 mg As/L, and 500 mg Cu/L and it was identified as Halomonas sp. based on the partial 16S rDNA sequences. The metal(loid)s resistance mechanisms were further confirmed by amplification of arsC (As) copAU (Cu), and pbrT (Pb) genes. Biological transmission electron micrographs and XRD studies showed that the isolate Halomonas sp. MG transformed and/or biomineralized the metals either intracellularly or extracellularly. These results suggest that the isolate could be used as a potential candidate for the bioremediation of As, Cu, and Pb. PMID:26298269

  7. Cadmium(II) removal by a hyperaccumulator fungus Phoma sp. F2 isolated from blende soil.

    Yuan, HonGli; Li, ZhiJian; Ying, JiaoYan; Wang, EnTao

    2007-09-01

    A cadmium(II)-resistant fungus, strain F2, isolated from blende soil was identified as Phoma sp. by morphological study and internal transcribed spacer sequencing. This strain could accumulate 280 mg of Cd(II)/g dry weight mycelium. In liquid medium containing 163.8 mg Cd(II)/L, 96% of Cd(II) was removed by the actively growing mycelium. In addition, both oven-dried and lyophilized mycelium could effectively adsorb Cd(II). There were removed 91% and 46.2% of Cd(II) from 51.6 mg Cd(II)/L solution by lyophilized biomass and oven-dried biomass respectively. Transmission electron microscopy and energy-dispersive X-ray analysis showed the accumulation of Cd(II) in the mycelium cell walls. Our results demonstrated that Phoma sp. F2 was a hyperaccumulator for the removal of Cd(II) from contaminated soil and water. PMID:17657529

  8. Isolation of Streptomyces sp. strain capable of butyltin compounds degradation with high efficiency.

    Bernat, Przemysław; Długoński, Jerzy

    2009-11-15

    Dibutyltin (DBT), a widely used plastic stabilizer, has been detected in the environment as well as in human tissues. DBT is considered to be highly neurotoxic and immunotoxic. Hence, DBT needs to be considered as a potential toxic chemical. Degradation of butyltin compounds by Streptomyces sp. isolated from plant waste composting heaps was studied. Glucose grown cells degraded organotin from 10 to 40 mg l(-1). After 1 day of incubation 90% of DBT (added at 20 mg l(-1)) was converted to less toxic derivative--monobutyltin (MBT). DBT metabolism was inhibited by metyrapone addition, a known cytochrome P-450 inhibitor. It could provide evidence that cytochrome P-450 system is involved in DBT metabolism in Streptomyces sp. IM P102. Moreover, according to our knowledge, the degradation of DBT by actinobacterium has not been previously described. PMID:19592163

  9. Chemical investigation of metabolites produced by an endophytic Aspergillus sp. isolated from Limonia acidissima.

    Siriwardane, A M D A; Kumar, N Savitri; Jayasinghe, Lalith; Fujimoto, Yoshinori

    2015-01-01

    Endophytic fungi are considered as a good source to produce important secondary metabolites with interesting bioactivities. In a continuation of our studies towards the search for environmentally friendly bioactive compounds from Sri Lankan flora, we investigated the secondary metabolites produced by the endophytic fungi Aspergillus sp. isolated from the seeds of the popular edible fruit Limonia acidissima L. of the family Rutaceae. The pure culture of the Aspergillus sp. was grown on potato dextrose broth media. After 4 weeks fermentation, fungal media were extracted with organic solvents. Chromatographic separation of the fungal extracts over silica gel, Sephadex LH-20 and RP-HPLC furnished flavasperone (1), rubrofusarin B (2), aurasperone A (3), fonsecinone D (4) and aurasperone B (5). Compounds 1-4 showed moderate activities in brine shrimp toxicity assay. This is the first report of the (13)C NMR data of compounds 4 and 5. PMID:25809933

  10. Mechanism of thorium biosorption by the cells of the soil fungal isolate Geotrichum sp. dwc-1

    Ding, Congcong; Feng, Su [Sichuan Univ., Chengdu (China). Key Laboratory of Biological Resource and Ecological Environment; Li, Xiaolong [Sichuan Univ., Chengdu (China). Key Laboratory of Radiation Physics and Technology; and others

    2014-04-01

    In order to understand the impact of microorganisms on the fate of thorium in soils, we investigated the thorium biosorption behavior and the corresponding mechanisms by the cells of Geotrichum sp. dwc-1, one of the dominant species of fungal group isolated from 3.5 m depth soil layer in Southwest China. It was observed that fast thorium adsorption onto cells of G. sp. dwc-1 could take place, with a high distribution coefficient K{sub d} (0.93 mL/mg) obtained, when Geotrichum sp. dwc-1and thorium concentrations were 5 g/L and 10 mg/L, respectively. The thorium biosorption behavior was dependent on the pH value, and the lower pH could disrupt cell membrane of G. sp. dwc-1. At pH 1, thorium was accumulated in the cytoplasmic region of the cells. When pH was higher than 1, thorium was adsorbed on the cell surface of G. sp. dwc-1, like in periplasmic region or in the outer membrane. FTIR study combined with biosorption experiments further indicated that the thorium distribution and binding behavior on cell surface were associated with amino, hydroxyl groups and phosphate or sulphur functional groups, and might also be governed by electrostatic interaction. Moreover, PIXE and EPBS showed that ion-exchange mechanism contributed to the thorium biosorption process, in which the tetravalent thorium ions replaced smaller counter-ions (K{sup +}, Ca{sup 2+} and Fe{sup 3+}) occuring on the cell surface. (orig.)

  11. Biosurfactan Production by Bacillus sp. Isolated from Petroleum Contaminated Soils of Sirri Island

    M. G. Jazeh

    2012-01-01

    Full Text Available Problem statement: Biosurfactants are active surface components produced by some bacteria and fungi. These molecules reduce surface and interfacial tension in aqueous solutions and hydrocarbon mixtures. The most important application of biosurfactants is in oil industry to enhance oil quality and facilitate oil extraction. The aim of this study was to isolate biosurfactant producing bacteria and optimize the conditions like temperature and pH for maximum biosurfactant production. Approach: Samples were collected from 8 selected points of oil contaminated soils in Sirri Island-Iran. Primary screening tests including hemolytic activity, Drop collapse technique and Oil Spreading method were preformed and species with the best results were picked for complementary screening tests like emulsification activity, foaming and surface tension measurement. Results: Totally, 160 bacteria species were isolated. During primary and complementary screening tests, 59 species showed hemolytic activity, 46 had drop collapsing ability and 18 species showed positive results in emulsification, foaming and surface tension reduction. Finally, two Bacillus sp. were found to be able to reduce surface tension more than 30 mNm-1. Conclusion: Two strains with a high amount of biosurfactant production and emulsification ability were resulted from the present study. According to the high potential of Bacillus sp. especially for Microbial Enhanced Oil Recovery (MEOR and Bioremediation of oil contamination we can hope that further study of the isolates characteristics and looking for new local strains can play an important role in their application in oil industry.

  12. Analysis of an Effective Antibiotic (Chaetomacin) Isolated from a Thermophilic Bacillus sp. Against Olive Green Mold

    Tautorus, T. E.; Townsley, P. M.

    1984-01-01

    Successful methods to control the damaging weed mold Chaetomium olivaceum (olive green mold) in mushroom beds are not known. An effective antibiotic (named chaetomacin) against C. olivaceum was isolated from a thermophilic Bacillus sp. This compound was shown to be an extremely potent and stable antibiotic, effective over a wide range of both pH (2 to 10) and temperature (−15 to 150°C). Chaetomacin is soluble in most polar solvents and insoluble in nonpolar solvents. It is produced only at me...

  13. [Isolation and purification of Mn-peroxidase from Azospirillum brasilense Sp245].

    Kupriashina, M A; Selivanov, N Iu; Nikitina, V E

    2012-01-01

    Homogenous Mn-peroxidase of a 26-fold purity grade was isolated from a culture of Azospirillum brasilense Sp245 cultivated on a medium containing 0.1 mM pyrocatechol. The molecular weight of the enzyme is 43 kD as revealed by electrophoresis in SDS-PAAG. It was shown that the use of pyrocatechol and 2,2'-azino-bis(3-ethylbenzotiazoline-6-sulfonate) at concentrations of 0.1 and I mM as inductors increased the Mn-peroxidase activity by a factor of 3. PMID:22567881

  14. Biodegradation of Di-n-Butyl Phthalate by a Newly Isolated Halotolerant Sphingobium sp.

    Decai Jin; Xiao Kong; Bingjian Cui; Zhihui Bai; Hongxun Zhang

    2013-01-01

    A Gram-negative strain (TJ) capable of growing aerobically on mixed phthalate esters (PAEs) as the sole carbon and energy source was isolated from the Haihe estuary, Tianjin, China. It was identified as belonging to the Sphingobium genus on the basis of morphological and physiological characteristics and 16S rRNA and gyrb gene sequencing. The batch tests for biodegradation of di-n-butyl phthalate (DBP) by the Sphingobium sp. TJ showed that the optimum conditions were 30 °C, pH 7.0, and the ab...

  15. Isolation and identification of a novel alginate-degrading bacterium, Ochrobactrum sp.

    Xiao-wei Zhao

    2008-03-01

    Full Text Available An alginate-degrading bacterium, identified as Ochrobactrum sp. on the basis of 16S rDNA gene sequencing, was isolated from brown algal samples collected from the waters in close vicinity to the Dongtou Isles in the East China Sea. The strain, designated WZUH09-1, is a short rod, gram-negative, obligatory aerobic, grows under the following conditions: 5-40oC, pH 3-9, and 0-2 times of the seawater concentration, and is able to depolymerize alginates with higher enzyme activity than that of others reported so far.

  16. The sodium/proton antiport system in a newly isolated alkalophilic Bacillus sp.

    Kitada, M; Onda, K.; Horikoshi, K

    1989-01-01

    The pH homeostasis and the sodium/proton antiport system have been studied in the newly isolated alkalophilic Bacillus sp. strain N-6, which could grow on media in a pH range from 7 to 10, and in its nonalkalophilic mutant. After a quick shift in external pH from 8 to 10 by the addition of Na2CO3, the delta pH (inside acid) in the cells of strain N-6 was immediately established, and the pH homeostatic state was maintained for more than 20 min in an alkaline environment. However, under the sam...

  17. Candida wangnamkhiaoensis sp. nov., an anamorphic yeast species in the Hyphopichia clade isolated in Thailand.

    Limtong, Savitree; Kaewwichian, Rungluk; Jindamorakot, Sasitorn; Yongmanitchai, Wichien; Nakase, Takashi

    2012-06-01

    Two strains representing a single novel yeast species were isolated from a flower of Calycoopteris floribunda Lame (SK170(T)) and insect frass (ST-122) collected in Thailand. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, and the sequence analysis of the D1/D2 domain of the large subunit rRNA gene and the internal transcribed spacer region, the two strains were assigned as a single novel Candida species in the Hyphopichia clade for which the name Candida wangnamkhiaoensis sp. nov. is proposed. The type strain is SK170(T)=BCC 39604(T)=NBRC 106724(T)=CBS 11695(T)). PMID:22331449

  18. A Sterol and Spiroditerpenoids from a Penicillium sp. Isolated from a Deep Sea Sediment Sample

    Chengbin Cui; Yongsheng Che; Dezan Ye; Zongze Shao; Yan Li

    2012-01-01

    A new polyoxygenated sterol, sterolic acid (1), three new breviane spiroditerpenoids, breviones I–K (2–4), and the known breviones (5–8), were isolated from the crude extract of a Penicillium sp. obtained from a deep sea sediment sample that was collected at a depth of 5115 m. The structures of 1–4 were elucidated primarily by NMR experiments, and 1 was further confirmed by X-ray crystallography. The absolute configurations of 2 and 3 were deduced by comparison of their CD spectra with those ...

  19. Draft Genome Sequence of Insecticidal Streptomyces sp. Strain PCS3-D2, Isolated from Mangrove Soil in Philippines

    Bayot-Custodio, Aileen N.; Alcantara, Edwin P.; Zulaybar, Teofila O.

    2014-01-01

    A draft genome sequence of a Streptomyces sp. isolated from mangrove soil in Cebu, Philippines, is described here. This isolate produced compounds with contact insecticidal activity against important corn pests. The genome contains 7,479,793 bp (in 27 scaffolds), 6,297 predicted genes, and 29 secondary metabolite biosynthetic gene clusters.

  20. Characterization of Francisella sp., GM2212, the first Francisella isolate from marine fish, Atlantic cod (Gadus morhua)

    Ottem, Karl F; Nylund, Are; Karlsbakk, Egil; Friis-Møller, Alice; Krossøy, Bjørn

    2007-01-01

    A Francisella sp., isolate GM2212(T), previously isolated from diseased farmed Atlantic cod Gadus morhua in Norway is characterized. The complete 16S rDNA, 16S-23S intergenic spacer, 23S rDNA, 23S-5S intergenic spacer, 5S rDNA, FopA, lipoprotein TUL4 (LpnA), malate dehydrogenase and a hypothetica...

  1. Isolation of Antioxidant Compound from Endophytic Fungi Acremonium sp. from the Twigs of Kandis Gajah

    Rizki

    2012-04-01

    Full Text Available The endophytic fungi Chrisonilia sitophila, Acremonium sp., and Penicillium sp. have been isolated from the tissues ofthe twigs of kandis gajah. All of the fungi strains were grown in 3 L potatoe dextrose broth medium (PDB at a roomtemperature for 28 days. To extract the antioxidant compounds, the culture broth were filtered for mycelia removalfollowed by extraction and evaporation. All of the extracts were evaluated for their antioxidant activities by using 1,1-diphenyl-2-picrylhydrazyl (DPPH radical scavenging activity. The extract of Acremonium sp. have strong activity withIC50 value of 10.3 μg/mL, which is equivalent to ascorbic acid activity with IC50 value of 9.8 μg/mL. The extract wassubjected to column chromatography on Si gel twice to obtain a high purity antioxidant compound in the form of yellowoil. The molecular structure was determined based on spectroscopic data, including 1H-NMR, 13C-NMR, HMQC,HMBC, and COSY. The compound was determined as sesquiterpene 3,5-dihydroxy-2,5-dimethyltrideca-2,9,11-triene-4,8-dione.

  2. Sympodiomycopsis yantaiensis sp. nov., a basidiomycetous yeast isolated from insect frass.

    Chen, Liang; Zhang, Lin; Li, Zhi-Hui; Hui, Feng-Li

    2013-09-01

    Two strains (NYNU 121010(T) and NYNU 121032) of a novel basidiomycetous yeast species belonging to the genus Sympodiomycopsis were isolated from insect frass collected from trunks of a pagoda tree (Sophora japonica L.) in Yantai, Shandong province, east China. The sequence analyses of the D1/D2 domain of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region indicated that the closest relatives were Sympodiomycopsis kandeliae FIRDI 007(T), Sympodiomycopsis paphiopedili CBS 7429(T) and Sympodiomycopsis sp. S6A. The D1/D2 sequences of the novel strains differed by 12 nt substitutions (2%) from the type strain of S. kandeliae, and by 13 nt substitutions (2.2%) from the type strain of S. paphiopedili and from Sympodiomycopsis sp. S6A. The novel strains differed from closely related species by more than 4.6% substitutions in the ITS region. The novel strains can also be distinguished from S. kandeliae and S. paphiopedili on the basis of a number of morphological and physiological characteristics and represent a novel species in the genus Sympodiomycopsis, for which the name Sympodiomycopsis yantaiensis sp. nov. is proposed. The type strain is NYNU 121010(T) ( =CICC 32998(T) = CBS 12813(T)). The Mycobank deposit number is MB 804119. PMID:23838443

  3. Aurantimonas altamirensis sp. nov., a member of the order Rhizobiales isolated from Altamira Cave.

    Jurado, Valme; Gonzalez, Juan M; Laiz, Leonila; Saiz-Jimenez, Cesareo

    2006-11-01

    A bacterial strain, S21BT, was isolated from Altamira Cave (Cantabria, Spain). The cells were Gram-negative, short rods growing aerobically. Comparative 16S rRNA gene sequence analysis revealed that strain S21BT represented a separate subline of descent within the family 'Aurantimonadaceae' (showing 96% sequence similarity to Aurantimonas coralicida) in the order Rhizobiales (Alphaproteobacteria). The major fatty acids detected were C16:0 and C18:1omega7c. The G+C content of the DNA from strain S21BT was 71.8 mol%. Oxidase and catalase activities were present. Strain S21BT utilized a wide range of substrates for growth. On the basis of the results of this polyphasic study, isolate S21BT represents a novel species of the genus Aurantimonas, for which the name Aurantimonas altamirensis sp. nov. is proposed. The type strain is S21BT (=CECT 7138T=LMG 23375T). PMID:17082395

  4. Tenacibaculum skagerrakense sp. nov., a marine bacterium isolated from the pelagic zone in Skagerrak, Denmark.

    Frette, Lone; Jørgensen, Niels O G; Irming, Heidi; Kroer, Niels

    2004-03-01

    A number of bacteria were isolated from sea water in Skagerrak, Denmark, at 30 m depth. Two of the isolates, strains D28 and D30(T), belonged to the Flavobacteriaceae within the Cytophaga-Flavobacterium-Bacteroides group. Sequencing of 16S rRNA genes of the two strains indicated strongly that they belonged to the genus Tenacibaculum and that they showed greatest similarity to the species Tenacibaculum amylolyticum and Tenacibaculum mesophilum. DNA-DNA hybridization values, DNA base composition and phenotypic characteristics separated the Skagerrak strains from the other species within TENACIBACULUM: Thus, it is concluded that the strains belong to a novel species within the genus Tenacibaculum, for which the name Tenacibaculum skagerrakense sp. nov. is proposed, with strain D30(T) (=ATCC BAA-458(T)=DSM 14836(T)) as the type strain. PMID:15023969

  5. Nocardia kroppenstedtii sp. nov., an actinomycete isolated from a lung transplant patient with a pulmonary infection.

    Jones, Amanda L

    2014-03-01

    A novel actinomycete, strain N1286(T), isolated from a lung transplant patient with a pulmonary infection, was provisionally assigned to the genus Nocardia. The strain had chemotaxonomic and morphological properties typical of members of the genus Nocardia and formed a distinct phyletic line in the Nocardia 16S rRNA gene tree. Isolate N1286(T) was most closely related to Nocardia farcinica DSM 43665(T) (99.8% gene sequence similarity) but could be distinguished from the latter by the low level of DNA-DNA relatedness. These strains were also distinguishable on the basis of a broad range of phenotypic properties. It is concluded that strain N1286(T) represents a novel species of the genus Nocardia for which the name Nocardia kroppenstedtii sp. nov. is proposed. The type strain is N1286(T) ( = DSM 45810(T) = NCTC 13617(T)).

  6. Characterization of a bioflocculant from a newly isolated Vagococcus sp. W31

    2006-01-01

    Screening of microorganisms producing flocculating substances was carried out. A strain secreting a large amount of bioflocculant was isolated from wastewater samples collected from the Little Moon River in Beijing. Based on the morphological properties and 16S rDNA sequence analysis, the isolate (designated W31) was classified as Vagococcus sp. A bioflocculant (named MBFW31) produced by W31 was extracted from the culture broth by ethanol precipitation and purified by gel chromatography. MBFW31 was heat-stable and had strong flocculating activity in a wide range of pH with relatively low dosage requirement. MBFW31 was identified as a polysaccharide with molecular weight over 2 × 106. It contained neutral sugar and uronic acid as its major and minor components, respectively. Infrared spectra showed the presence of hydroxyl, carboxyl and methoxyl group in its molecules. The present results suggested that MBFW31 had potential application in wastewater treatment.

  7. Isolation and Characterization of a Methomyl-Degrading Paracoccus sp.mdw-1

    XU Jing-Liang; WU Jun; WANG Zhi-Chun; WANG Kun; LI Meng-Ying; JIANG Jian-Dong; HE Jian; LI Shun-Peng

    2009-01-01

    Methomyl,an extremely toxic pesticide,is widely used in agriculture.A strain named mdw-1 capable of degrading methomyl rapidly was successfully isolated from activated sludge in this study.It could utilize methomyl as the sole carbon or nitrogen source.The optimal temperature and medium pH for its growth and methomyl biodegradation were 30 ℃ and 7.0,respectively.It was identified as a Paracoeeus sp.according to its morphological features,physiological and biochemical characteristics,and phylogenetic analysis based on the sequence of 16S rDNA.Gas chromatography-mass spectrometry (GC-MS) analysis showed that methomyl could be completcly transformed to S-methyl-N-hydroxythioacetamidate in 10 h of incubation with the isolate mdw-1.

  8. Cellular fatty acid composition, protein profile and antimicrobial activity of Bacillus sp., isolated from fish gut

    Pushparaj Sujith

    2014-01-01

    Full Text Available Objective: To purify and partially characterize the antimicrobial compounds from bacteria Bacillus sp., isolated from fish gut. Methods: Protein and fatty acids were isolated from the bacteria and checked for the presence of antibacterial activity. Protein has been purified to apparent homogeneity from the supernatants of culture by means of ammonium sulphate precipitation followed by dialysis. Fourier transform infrared spectroscopy analyses were performed for proteins to identify the functional groups. Results: Protein showed an apparent molecular mass 56, 47 and 39 kDa on sodium dodecyl sulfate polyacrylamide gel electrophoresis. Fatty acids were extracted and subjected to gas chromatographic analysis. Conclusions: The antimicrobial activity of the bacteria might be due to the presence of fatty acids and proteins which holds promise for the development of new drugs.

  9. Cellular fatty acid composition, protein profile and antimicrobial activity of Bacillus sp., isolated from fish gut

    Pushparaj Sujith; Baskaran Rohini; Singaram Jayalakshmi

    2014-01-01

    Objective: To purify and partially characterize the antimicrobial compounds from bacteriaBacillus sp., isolated from fish gut. Methods: Protein and fatty acids were isolated from the bacteria and checked for the presence of antibacterial activity. Protein has been purified to apparent homogeneity from the supernatants of culture by means of ammonium sulphate precipitation followed by dialysis. Fourier transform infrared spectroscopy analyses were performed for proteins to identify the functional groups.Results:sulfate polyacrylamide gel electrophoresis. Fatty acids were extracted and subjected to gas chromatographic analysis.Conclusions:Protein showed an apparent molecular mass 56, 47 and 39 kDa on sodium dodecyl acids and proteins which holds promise for the development of new drugs. The antimicrobial activity of the bacteria might be due to the presence of fatty acids and proteins which holds promise for the development of new drugs.

  10. Screening of Pseudomonas sp. Isolated from Rhizosphere of Soybean Plant as Plant Growth Promoter and Biocontrol Agent

    Aris T. Wahyudi

    2011-01-01

    Full Text Available Problem statement: Pseudomonas spesies are one of the rihizobacterial group that have an important role in plant growth promoter and plant health. To prepare them as inoculants, they must have a range of characters as growth promoter such as Indole Acetic Acid (IAA producers which can promote the growth of plants and solubilize phosphates. In addition, they must also have the various characters that act as biocontrol agents such as siderofor, chitinase and anti-fungal compound producers. Approach: Pseudomonas sp isolated from soybeans rhizospere and identified based on physiological reactions and 16S rRNA gene sequences. Various tests for the determination of the growth promoter were based on IAA production, phosphate solubilization and growth promoter of length of root and stems and number of lateral roots of soybean sprouts. Test of siderophore, chitinase, as well as anti anti-fungal compounds productions to inhibit the growth of Fusarium oxysporum, Rhizoctonia solani and Sclerotium rolfsii, were used as a biocontrol agent determination. Hypersensitivity test was used to screen for Pseudomonas sp classified as non-pathogenic rhizobacteria. Results: Fourteen isolates identified as a non-pathogenic Pseudomonas sp that produced IAA and Promoted enhancement of root length, shoot length, or number of lateral root. Among those 14 isolates, 8 isolates showed phosphate solubilizing activity, 12 isolates capable of producing siderophore and six isolates were observed to have chitinolytic activity. Only three isolates were able to inhibit the growth of Fusarium oxysporum in high level. While one and two isolates inhibited Sclerotium rolfsii and Rhizoctonia solani in high level, respectively. Conclusion: On the basis of excellent growth promoter and biocontrol activities, we recommended 5 isolates of Pseudomonas sp which were Crb-3, Crb-16, Crb-17, Crb-44 and Crb-94 as potential isolates of Pseudomonas sp that could be applied as

  11. Plant growth promoting potential of pseudomonas sp. SP0113 isolated from potable water from a closed water well

    Przemieniecki Wojciech Sebastian; Kurowski Paweł Tomasz; Karwowska Anna

    2015-01-01

    The Pseudomonas sp. SP0113 strain from a partially closed aquatic environment was identified as a plant growth promoting bacterium (PGPB). Laboratory tests revealed that PS0113 has multiple plant growth promoting traits, including mineral phosphate solubilizing ability, ammonifying ability that increases nitrogen availability for plants via the root system, and phosphatase activity that plays an important role in organic phosphorus mineralization. Tricalciu...

  12. Single Cystosorus Isolate Production and Restriction Fragment Length Polymorphism Characterization of the Obligate Biotroph Spongospora subterranea f. sp. subterranea.

    Qu, Xinshun; Christ, Barbara J

    2006-10-01

    ABSTRACT Spongospora subterranea f. sp. subterranea causes powdery scab in potatoes and is distributed worldwide. Genetic studies of this pathogen have been hampered due, in part, to its obligate parasitism and the lack of molecular markers for this pathogen. In this investigation, a single cystosorus inoculation technique was developed to produce large amounts of S. subterranea f. sp. subterranea plasmodia or zoosporangia in eastern black nightshade (Solanum ptycanthum) roots from which DNA was extracted. Cryopreservation of zoosporangia was used for long-term storage of the isolates. S. subterranea f. sp. subterranea-specific restriction fragment length polymorphism (RFLP) markers were developed from randomly amplified polymorphic DNA (RAPD) fragments. Cystosori of S. subterranea f. sp. subterranea were used for RAPD assays and putative pathogen-specific RAPD fragments were cloned and sequenced. The fragments were screened for specificity by Southern hybridization and subsequent DNA sequence BLAST search. Four polymorphic S. subterranea f. sp. subterranea-specific probes containing repetitive elements, and one containing single copy DNA were identified. These RFLP probes were then used to analyze 24 single cystosorus isolates derived from eight geographic locations in the United States and Canada. Genetic variation was recorded among, but not within, geographic locations. Cluster analysis separated the isolates into two major groups: group I included isolates originating from western North America, with the exception of those from Colorado, and group II included isolates originating from eastern North America and from Colorado. The techniques developed in this study, i.e., production of single cystosorus isolates of S. subterranea f. sp. subterranea and development of RFLP markers for this pathogen, provide methods to further study the genetic structure of S. subterranea f. sp. subterranea. PMID:18943505

  13. Cyberlindnera xylosilytica sp. nov., a xylitol-producing yeast species isolated from lignocellulosic materials.

    Cadete, Raquel M; Cheab, Monaliza A M; Santos, Renata O; Safar, Silvana V B; Zilli, Jerri E; Vital, Marcos J S; Basso, Luiz C; Lee, Ching-Fu; Kurtzman, Cletus P; Lachance, Marc-André; Rosa, Carlos A

    2015-09-01

    Independent surveys of yeasts associated with lignocellulosic-related materials led to the discovery of a novel yeast species belonging to the Cyberlindnera clade (Saccharomycotina, Ascomycota). Analysis of the sequences of the internal transcribed spacer (ITS) region and the D1/D2 domains of the large subunit rRNA gene showed that this species is related to C. japonica, C. maesa and C. easanensis. Six isolates were obtained from different sources, including rotting wood, tree bark and sugar cane filter cake in Brazil, frass from white oak in the USA and decayed leaf in Taiwan. A novel species is suggested to accommodate these isolates, for which the name C. xylosilytica sp. nov. is proposed. The type strain of C. xylosilytica sp. nov. is NRRL YB-2097(T) ( = CBS 13984(T) = UFMG-CM-Y347(T)) and the allotype is UFMG-CM-Y409 ( = CBS 14083). The novel species is heterothallic and complementary mating types are represented by the type and allotype strains. The MycoBank number is MB 811428. PMID:26025941

  14. In vitro and in vivo antitumor activity of crude extracts obtained from Brazilian Chromobacterium sp isolates

    Natural products produced by microorganisms have been an important source of new substances and lead compounds for the pharmaceutical industry. Chromobacterium violaceum is a Gram-negative β-proteobacterium, abundant in water and soil in tropical and subtropical regions and it produces violacein, a pigment that has shown great pharmaceutical potential. Crude extracts of five Brazilian isolates of Chromobacterium sp (0.25, 2.5, 25, and 250 µg/mL) were evaluated in an in vitro antitumor activity assay with nine human tumor cells. Secondary metabolic profiles were analyzed by liquid chromatography and electrospray ionization mass spectrometry resulting in the identification of violacein in all extracts, whereas FK228 was detected only in EtCE 308 and EtCE 592 extracts. AcCE and EtCE 310 extracts showed selectivity for NCI/ADR-RES cells in the in vitro assay and were evaluated in vivo in the solid Ehrlich tumor model, resulting in 50.3 and 54.6% growth inhibition, respectively. The crude extracts of Chromobacterium sp isolates showed potential and selective antitumor activities for certain human tumor cells, making them a potential source of lead compounds. Furthermore, the results suggest that other compounds, in addition to violacein, deoxyviolacein and FK228, may be involved in the antitumor effect observed

  15. Isolation and Characterization of a Dichlorvos-Degrading Strain DDV-1 of Ochrobactrum sp.

    ZHANG Xiao-Hua; ZHANG Guo-Shun; ZHANG Zhong-Hui; XU Jian-Hong; LI Shun-Peng

    2006-01-01

    The objective of this research was to isolate a dichlorvos (2,2-dichlorovinyl dimethyl phosphate)-degrading strain of Ochrobactrum sp., and determine its effectiveness in remediation of a dichlorvos-contaminated soil. A dichlorvos-degrading bacterium (strain DDV-1) was successfully isolated and identified as an Ochrobactrum sp. based on its 16S rDNA sequence analysis. Strain DDV-1 was able to utilize dichlorvos as a sole carbon source, and the optimal pH and temperature for its cell growth and degradation were 7.0 and 30 ℃, respectively. Also, the growth and degradation of strain DDV-1 showed the same response to dissolved oxygen. In addition, the soil degradation test indicated that in soil spiked with 100 mg L-1 or 500 mg L-1 dichlorvos and inoculated with 0.5% or 1.0% (v/v) strain DDV-1, complete degradation of dichlorvos could be achieved in 24 h. The present study showed that strain DDV-1 was a fast dichlorvos-degrading bacterium in soil. However, further research will be needed to clarify the degradation pathway and the properties of the key enzymes involved in its biodegradation.

  16. Pelagitalea pacifica gen. nov., sp. nov., a new marine bacterium isolated from seawater.

    Lee, Hyunsang; Yoshizawa, Susumu; Kogure, Kazuhiro; Kim, Hyun Soo; Yoon, Jaewoo

    2015-04-01

    A strictly aerobic, Gram-negative, beige-pigmented, short-rod-shaped, non-motile and chemoheterotrophic bacteria, designated K2-48(T) was isolated from seawater collected in the Western North Pacific Ocean near Japan. Preliminary analysis based on the 16S rRNA gene sequence revealed that the novel isolate was affiliated with the family Oceanospirillaceae within the class Gammaproteobacteria and that it showed the highest sequence similarity (93.7 %) to Neptunomonas qingdaonensis P10-2-4(T). The strain could be differentiated phenotypically from recognized members of the family Oceanospirillaceae. The major fatty acids of strain K2-48(T) were identified as summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH) and C16:0 as defined by the MIDI system. The DNA G+C content was determined to be 43.2 mol%, the major respiratory quinone was identified as ubiquinone 9 and a polar lipid profile was present consisting of phosphatidylethanolamine, a phosphatidylglycerol and an unidentified phospolipid. On the basis of polyphasic taxonomic studies, it was concluded that strain K2-48(T) represents a novel genus sp. We propose the name Pelagitalea pacifica gen. nov., sp. nov. for this strain; its type strain is K2-48(T) (=KCCM 90119(T)). PMID:25487119

  17. Isolation and characterization of a biosurfactant-producing Fusarium sp. BS-8 from oil contaminated soil.

    Qazi, Muneer A; Kanwal, Tayyaba; Jadoon, Muniba; Ahmed, Safia; Fatima, Nighat

    2014-01-01

    This study reports characterization of a biosurfactant-producing fungal isolate from oil contaminated soil of Missa Keswal oil field, Pakistan. It was identified as Fusarium sp. BS-8 on the basis of macroscopic and microscopic morphology, and 18S rDNA gene sequence homology. The biosurfactant-producing capability of the fungal isolates was screened using oil displacement activity, emulsification index assay, and surface tension (SFT) measurement. The optimization of operational parameters and culture conditions resulted in maximum biosurfactant production using 9% (v/v) inoculum at 30°C, pH 7.0, using sucrose and yeast extract, as carbon and nitrogen sources, respectively. A C:N ratio of 0.9:0.1 (w/w) was found to be optimum for growth and biosurfactant production. At optimal conditions, it attained lowest SFT (i.e., 32 mN m(-1) ) with a critical micelle concentration of ≥ 1.2 mg mL(-1) . During 5 L shake flask fermentation experiments, the biosurfactant productivity was 1.21 g L(-1) pure biosurfactant having significant emulsifying index (E24 , 70%) and oil-displacing activity (16 mm). Thin layer chromatography and Fourier transform infrared spectrometric analyses indicated a lipopeptide type of the biosurfactant. The Fusarium sp. BS-8 has substantial potential of biosurfactant production, yet it needs to be fully characterized with possibility of relatively new class of biosurfactants. PMID:24850435

  18. In vitro and in vivo antitumor activity of crude extracts obtained from Brazilian Chromobacterium sp isolates

    C.B.A. Menezes

    2013-01-01

    Full Text Available Natural products produced by microorganisms have been an important source of new substances and lead compounds for the pharmaceutical industry. Chromobacterium violaceum is a Gram-negative β-proteobacterium, abundant in water and soil in tropical and subtropical regions and it produces violacein, a pigment that has shown great pharmaceutical potential. Crude extracts of five Brazilian isolates of Chromobacterium sp (0.25, 2.5, 25, and 250 µg/mL were evaluated in an in vitro antitumor activity assay with nine human tumor cells. Secondary metabolic profiles were analyzed by liquid chromatography and electrospray ionization mass spectrometry resulting in the identification of violacein in all extracts, whereas FK228 was detected only in EtCE 308 and EtCE 592 extracts. AcCE and EtCE 310 extracts showed selectivity for NCI/ADR-RES cells in the in vitro assay and were evaluated in vivo in the solid Ehrlich tumor model, resulting in 50.3 and 54.6% growth inhibition, respectively. The crude extracts of Chromobacterium sp isolates showed potential and selective antitumor activities for certain human tumor cells, making them a potential source of lead compounds. Furthermore, the results suggest that other compounds, in addition to violacein, deoxyviolacein and FK228, may be involved in the antitumor effect observed.

  19. In vitro and in vivo antitumor activity of crude extracts obtained from Brazilian Chromobacterium sp isolates

    Menezes, C.B.A.; Silva, B.P. [Universidade Estadual de Campinas, Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas, Campinas, SP (Brazil); Universidade de São Paulo, Interunidades em Biotecnologia, São Paulo, SP (Brazil); Sousa, I.M.O.; Ruiz, A.L.T.G.; Spindola, H.M. [Universidade Estadual de Campinas, Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas, Campinas, SP (Brazil); Cabral, E.; Eberlin, M.N. [Instituto de Química, Universidade Estadual de Campinas, Laboratório Thomson Mass Spectrometry, Campinas, SP (Brazil); Tinti, S.V.; Carvalho, J.E. [Universidade Estadual de Campinas, Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas, Campinas, SP (Brazil); Foglio, M.A.; Fantinatti-Garboggini, F. [Universidade Estadual de Campinas, Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas, Campinas, SP (Brazil); Universidade de São Paulo, Interunidades em Biotecnologia, São Paulo, SP (Brazil)

    2012-10-23

    Natural products produced by microorganisms have been an important source of new substances and lead compounds for the pharmaceutical industry. Chromobacterium violaceum is a Gram-negative β-proteobacterium, abundant in water and soil in tropical and subtropical regions and it produces violacein, a pigment that has shown great pharmaceutical potential. Crude extracts of five Brazilian isolates of Chromobacterium sp (0.25, 2.5, 25, and 250 µg/mL) were evaluated in an in vitro antitumor activity assay with nine human tumor cells. Secondary metabolic profiles were analyzed by liquid chromatography and electrospray ionization mass spectrometry resulting in the identification of violacein in all extracts, whereas FK228 was detected only in EtCE 308 and EtCE 592 extracts. AcCE and EtCE 310 extracts showed selectivity for NCI/ADR-RES cells in the in vitro assay and were evaluated in vivo in the solid Ehrlich tumor model, resulting in 50.3 and 54.6% growth inhibition, respectively. The crude extracts of Chromobacterium sp isolates showed potential and selective antitumor activities for certain human tumor cells, making them a potential source of lead compounds. Furthermore, the results suggest that other compounds, in addition to violacein, deoxyviolacein and FK228, may be involved in the antitumor effect observed.

  20. ASSESSMENT OF PROBIOTIC POTENTIAL OF LACTOBACILLUS SP. ISOLATED FROM CHEESE AND PREPARATION OF PROBIOTIC ICE-CREAM

    Patil Liladhar Shivram; Pandav Parag Vishwanath

    2012-01-01

    Probiotic microorganisms are naturally present in milk and fermented milk products such as different kinds of cheese, yogurt, butter etc. The aim of the present study was isolation and taxonomic determination of lactic acid bacteria (LAB) from cheese (wild type). Lactobacillus sp. was isolated from indigenous cheese sample, identified and characterized on the basis of their morphological and biochemical characteristics at genus level. The pure isolated Lactobacillus was assessed for various p...

  1. Extracellular Synthesis of Silver Nanoparticles by Ralstonia sp. SM8 Isolated from the Sarcheshmeh Copper Mine

    Morahem Ashengroph

    2014-04-01

    Full Text Available Introduction: The biological synthesis of nanoparticles has gained enormous importance due to the development of clean and environmentally-friendly processes. Silver is highly toxic to microbial cells, Nevertheless, it has been reported that several microorganisms are silver resistance and corroborate the microbial reduction of water soluble Ag+ to Ag0 nanoparticles. In this study, native strains of bacteria screen for use as biocatalysts for extracellular synthesis of silver nanoparticles. Materials and methods: Eight different strains of bacteria exhibiting high silver tolerance were isolated from collecting soil samples from copper and gold mines and characterized using morphological observations and preliminary biochemical tests. The bacterial strains in the presence of 1 g/l Ag+ solution at pH 7 were incubated at 28º C for 48 h in an orbital shaker. The silver nanoparticles formation was investigated by visual observations (changing the color of the reaction solution, spectroscopic techniques and microscopic observations. Results: Among the 8 strains giving high Ag+ tolerance, the strain SM8, isolated from the Sarcheshmeh Copper Mine, Kerman, showed the capability of promoting the formation extracellular Ag nanoparticles. The strain was selected and identified as Ralstonia sp. SM8 (GenBank accession number KF264453 based on morphological and biochemical characteristics and its molecular phylogenetic analysis. Results obtained by visual observations, spectral data achieved from UV–vis, XRD spectrum and SEM micrographs revealed the extracellular formation of spherical silver nanoparticles in the size range of 20-50 nm with the culture supernatants of Ralstonia sp. SM8. Discussion and conclusion: Based on the results obtained, fast and extracellular synthesis of silver nanoparticles, without the need for complicated extraction steps, can be taken by using the culture supernatants of Ralstonia sp. SM8. The current study is the first report

  2. OTYPIC CHARACTERIZATION AND ANTIFUNGAL SUSCEPTIBILITY PATTERN OF CANDIDA SP ISOLATED FROM A TERTIARY CARE CENTER

    Rudramurthy

    2014-02-01

    Full Text Available ACT: Candida , a yeast like ubiquitous fungus , is an endogenous species which produces commonest fungal infection; Candidiasis. Resistance to antifungal agents is an alarming sign for the emerging common nosocomial candidiasis. MATERIALS AND METHODS: Various types of specimens we re collected from the c linically suspected cases of candidiasis. Isolation and characterization of candida sp . was done by standard procedures. Antifungal susceptibility was done by disc diffusion method. RESULT: The candida was isolated from various clinical specimens , vaginal swab (24.66% , skin scraping (13.33% oral swabs (12.66% , ear swabs ( 11.33% , nail scraping (10% , and pus from diabetes foot ulcer and post - operative wound infection ( 8% , sputum ( 6% , urine (4.66% , stool ( 4% , blood ( 2.66% , and eye swabs ( 2.66%. Amon g different species of candida isolated C.albicans was the predominant species (79.33% followed by C tropicalis (19.33% and C.Guilliermondii (1.33%. Antifungal resistance of different species of candida was higher to fluconazole . The least resistance wa s seen with amphotericin - B (1.33%. CONCLUSION: The increased isolation of candida species and development of resistance to commonly used antifungal drugs requires careful interpretation and the in vitro susceptibility testing. This facilitates better pat ient care.

  3. Mageeibacillus indolicus gen. nov., sp. nov.: a novel bacterium isolated from the female genital tract.

    Austin, Michele N; Rabe, Lorna K; Srinivasan, Sujatha; Fredricks, David N; Wiesenfeld, Harold C; Hillier, Sharon L

    2015-04-01

    Three isolates of a bacterium recovered from human endometrium using conventional culture methods were characterized biochemically and subjected to 16S rRNA gene sequencing and phylogenetic analysis. Isolates were non-motile, obligately anaerobic, non-spore forming, asaccharolytic, non-cellulolytic, indole positive, Gram positive rods. Cell wall fatty acid profiling revealed C14:0, C16:0, C18:2 ω6, 9c, C18:1 ω9c and C18:0 to be the major fatty acid composition. The DNA mol % G+C was determined to be 44.2%. 16S rRNA gene sequence analysis revealed only 91% sequence similarity with the closest cultivated bacterial isolate, Saccharofermentans acetigenes. Based on genotypic and phenotypic data, all three isolates are considered to be members of the same species and data suggest it represents a novel genus and species in the order Clostridiales with an association with Clostridium rRNA cluster III within the family Ruminococcaceae. We propose the name, Mageeibacillus indolicus gen. nov., sp. nov. The type strain is BAA-2120(T) and CCUG 59143(T). PMID:25482717

  4. Enterococcus bulliens sp. nov., a novel lactic acid bacterium isolated from camel milk.

    Kadri, Zaina; Spitaels, Freek; Cnockaert, Margo; Praet, Jessy; El Farricha, Omar; Swings, Jean; Vandamme, Peter

    2015-11-01

    Four lactic acid bacteria isolates obtained from fresh dromedary camel milk produced in Dakhla, a city in southern Morocco, were characterised in order to determine their taxonomic position. The four isolates had highly similar MALDI-TOF MS and RAPD fingerprints and identical 16S rRNA gene sequences. Comparative sequence analysis revealed that the 16S rRNA gene sequence of the four isolates was most similar to that of Enterococcus sulfureus ATCC 49903(T) and Enterococcus italicus DSM 15952(T) (99.33 and 98.59% similarity, respectively). However, sequence analysis of the phenylalanyl-tRNA synthase (pheS), RNA polymerase (rpoA) and ATP synthase (atpA) genes revealed that the taxon represented by strain LMG 28766(T) was well separated from E. sulfureus LMG 13084(T) and E. italicus LMG 22039(T), which was further confirmed by DNA-DNA hybridization values that were clearly below the species demarcation threshold. The novel taxon was easily differentiated from its nearest neighbour species through sequence analysis of protein encoding genes, MALDI-TOF mass spectrometry and multiple biochemical tests, but had a similar percentage G+C content of about 39%. We therefore propose to formally classify these isolates as Enterococcus bulliens sp. nov., with LMG 28766(T) (=CCMM B1177(T)) as the type strain. PMID:26346480

  5. Hanseniaspora jakobsenii sp. nov., a yeast isolated from Bandji, a traditional palm wine of Borassus akeassii.

    Ouoba, Labia Irène I; Nielsen, Dennis S; Anyogu, Amarachukwu; Kando, Christine; Diawara, Bréhima; Jespersen, Lene; Sutherland, Jane P

    2015-10-01

    Investigation of the microbial diversity of Bandji, a traditional palm wine from Burkina Faso (West Africa) revealed the presence of two yeast isolates (YAV16 and YAV17T) with unusual phenotypic and genotypic characteristics. The isolates divide by bipolar budding with no production of ascospores. Phylogenetic analysis of concatenated sequences of the 26S rRNA gene D1/D2 and internal transcribed spacer (ITS) regions indicated that the novel species was most closely related to Kloeckera lindneri and Hanseniaspora valbyensis. The new isolates differed from K. lindneri NRRL Y-17531T and H. valbyensis CBS 479T by substitutions in the D1/D2 region of 12 and 16 nt respectively. The divergence in the ITS region from the closely related species was characterized by substitutions of 45-46 nt. Repetitive palindromic PCR (rep-PCR) profiles of YAV16 and YAV17T were also significantly different from those of K. lindneri MUCL 31146T ( = NRRL Y-17531T), H. valbyensis NCYC 17T ( = CBS 479T) and other species of the genus Hanseniaspora. Based on the results of the phenotypic and genotypic characterizations, it was concluded that the new isolates represent a novel species for which the name Hanseniaspora jakobsenii sp. nov. is proposed with YAV17T ( = CBS 12942T = DSM 26339T = NCYC 3828T; MycoBank number MB 805785) as the type strain. PMID:26297247

  6. Pathogenicity of Aeromonas hydrophila isolated from the Malaysian Sea against coral (Turbinaria sp.) and sea bass (Lates calcarifer).

    Hamid, Rahimi; Ahmad, Asmat; Usup, Gires

    2016-09-01

    A study was carried out to determine the pathogenicity (hemolytic activity) on corals (Turbinaria sp.) and sea bass (Lates calcarifer) of Aeromonas hydrophila from water, sediment, and coral. Samples were collected from coastal water and coral reef areas. One hundred and sixty-two isolates were successfully isolated. Out of 162, 95 were from seawater, 49 from sediment, and 18 from coral. Sixteen isolates were picked and identified. Isolates were identified using a conventional biochemical test, the API 20NE kit, and 16S rRNA nucleotide sequences. Hemolytic activity was determined. Out of 16 isolates, 14 isolates were β-hemolytic and two isolates were non-hemolytic. Corals infected with A. hydrophila suffered bleaching. Similar effect was observed for both hemolytic and non-hemolytic isolates. Intramuscular injection of A. hydrophila into sea bass resulted in muscular bleeding and death. Higher infection rates were obtained from hemolytic compared to non-hemolytic strains of A. hydrophila isolates. PMID:27221587

  7. Uptake of radioiodide by Paenibacillus sp., Pseudomonas sp., Burkholderia sp. and Rhodococcus sp. isolated from a boreal nutrient-poor bog.

    Lusa, Merja; Lehto, Jukka; Aromaa, Hanna; Knuutinen, Jenna; Bomberg, Malin

    2016-06-01

    Radionuclides, like radioiodine ((129)I), may escape deep geological nuclear waste repositories and migrate to the surface ecosystems. In surface ecosystems, microorganisms can affect their movement. Iodide uptake of six bacterial strains belonging to the genera Paenibacillus, Pseudomonas, Burkholderia and Rhodococcus isolated from an acidic boreal nutrient-poor bog was tested. The tests were run in four different growth media at three temperatures. All bacterial strains removed iodide from the solution with the highest efficiency shown by one of the Paenibacillus strains with >99% of iodide removed from the solution in one of the used growth media. Pseudomonas, Rhodococcus and one of the two Paenibacillus strains showed highest iodide uptake in 1% yeast extract with maximum values for the distribution coefficient (Kd) ranging from 90 to 270L/kg DW. The Burkholderia strain showed highest uptake in 1% Tryptone (maximum Kd 170L/kg DW). The Paenibacillus strain V0-1-LW showed exceptionally high uptake in 0.5% peptone +0.25% yeast extract broth (maximum Kd>1,000,000L/kg DW). Addition of 0.1% glucose to the 0.5% peptone +0.25% yeast extract broth reduced iodide uptake at 4°C and 20°C and enhanced iodide uptake at 37°C compared to the uptake without glucose. This indicates that the uptake of glucose and iodide may be competing processes in these bacteria. We estimated that in in situ conditions of the bog, the bacterial uptake of iodide accounts for approximately 0.1%-0.3% of the total sorption of iodide in the surface, subsurface peat, gyttja and clay layers. PMID:27266299

  8. Complete genome sequence of Burkholderia sp. strain PAMC28687, a potential octopine-utilizing bacterium isolated from Antarctica lichen.

    Han, So-Ra; Yu, Sang-Cheol; Ahn, Do-Hwan; Park, Hyun; Oh, Tae-Jin

    2016-05-20

    We report the complete genome sequence of Burkholderia sp. PAMC28687, which was isolated from the Antarctica lichen Useea sp., for better understanding of its catabolic traits in utilizing octopine as a source of carbon/nitrogen between Burkholderia and lichen. The genome consists of three circular chromosomes with five circular plasmids for the total 6,881,273bp sized genome with a G+C content of 58.14%. PMID:27034021

  9. Bioaccumulation of Cadmium by Pseudomonas Sp. Isolated From Metal Polluted Industrial Region

    Rinoy Varghese

    2012-10-01

    Full Text Available In the present study, bacterial strains were isolated from soil, sediment and water samples of metal contaminated industrial area and investigated the heavy metal resistance and bioaccumulation potential of the isolates. Cadmium analysis of the samples revealed that Cd concentration varying from 2.31µg L-1 to 8.96 µg L-1 in water, 0.55µg g-1 to 25.44µg g-1 in soil and 0.45µg g-1 to 22.90µg g-1 in sediment. Cadmium resistance studies of the bacterial isolates showed that out of 164 isolates collected most of them showed  low resistance (<500µg/ml and many isolates showed high resistance of  >1500µg/ml. Ten bacterial genera were represented in soil and 11 from water, while only 5 bacterial genera were recorded from sediment samples.  Bacillus, pseudomonas and Enterobacter were found in soil, sediment and water samples. Results of cadmium removal study revealed that with increase in time, the biomass of the selected Pseudomonas sp. increased. Correspondingly, with increase in biomass, the cadmium bioaccumulation was also increased. Relatively an Increased removal of cadmium was observed in the first day of the experiment. About 40% of the cadmium in the experimental flask was reduced while only 5% reduction occurs in the control flasks till the end of the experiment (74hours. Comparatively cadmium showed higher reduction at pH 7. From the results, it could be concluded that the selected bacterial isolates possessed potential in respect of bioaccumulation activity and thus, appeared to be an appropriate nominee in bioremediation processes.DOI: http://dx.doi.org/10.5755/j01.erem.61.3.1268

  10. [Morphological and molecular characterization of the antagonistic interaction between the endophyte Diaporthe sp. isolated from frailejón (Espeletia sp.) and the plant pathogen Phytophthora infestans].

    Prada, Harold; Avila, Laura; Sierra, Roberto; Bernal, Adriana; Restrepo, Silvia

    2009-09-30

    Endophytic fungi produce a great variety of secondary metabolites both in vivo and in vitro. In this study, we characterized the ability of a sterile-mycelium endophytic fungus isolated from Espeletia sp. to control the growth of Phytophthora infestans in Petri dishes. Sequence from the ITS regions (internal transcribed spacer) of the endophyte showed 94% similarity to Diaporthe phaseolorum's. The antagonistic interaction between Diaporthe sp. and P. infestans was evaluated in three different culture media. Diaporthe sp. showed an antagonistic effect towards P. infestans, with some variation depending on which medium was used. In an attempt to identify possible genes involved in this antagonism, we detected a gene from the endophyte encoding an amylase, which was differentially expressed during this biotic interaction. PMID:19635440

  11. Isolation of enriched-yielders and fed-batch production of alkaline protease from the newly isolated Bacillus sp. BHA

    Bhawana Agarwal; Brajesh S. Katiyar

    2013-01-01

    An alkalophilc and thermophilic Bacillus sp. BHA that produced a thermostable alkaline protease was isolated from decaying protein substrates. The isolate was found to grow in pH range 7 - 11 with an optimum pH 9.0 and temperature up to 55℃. The activity of alkaline protease of Bacillus sp. BHA (68.98 APU/ml) was found higher than the standard strains of Bacillus amyloliquefaciens MTCC 610 (8.98 APU/ml) and Bacillus subtilis MTCC 8349 (12.14 APU/ml, used in this study, and was comparable (68...

  12. Biodegradation of cyanide using Serratia sp. isolated from contaminated soil of gold mine in Takab

    Mojtaba Mohseni

    2014-07-01

    Full Text Available   Introduction : Cyanide is a toxic and hazardous compound for all organisms which is produced enormously by human being and causes the environment pollution. Biodegradation is the best method for cyanide elimination in industrial wastewater. The aims of this study were isolation of cyanide degrading bacteria from contaminated soil and investigation of their ability for cyanide degradation.   Materials and methods: After soil samples collection, enrichment of cyanide degrading bacteria was performed in a minimal medium containing 0.5 mM potassium cyanide. The ability of isolated bacterium to utilize the cyanide as sole carbon and nitrogen source was investigated. Cyanide degradation and ammonium production was determined in growth medium using picric acid and Nessler’s regent methods. Toxicity effect of different cyanide compounds on bacterial growth was determined using minimum inhibitory concentration. In addition, the ability of the isolated bacterium to utilize different cyanide compounds was investigated . Identification of the isolate was undertaken using morphological, physiological and biochemical characteristics and molecular analysis .   Results : A bacterium with ability to degrade cyanide as sole carbon and nitrogen source was isolated from soil. This bacterium named as isolate MF1. MF1 degraded cyanide in growth medium in alkaline condition after 40 hours. Moreover this isolate tolerated more than 7 mM potassium cyanide. The results showed that there was a direct relation between decreasing of cyanide concentration, increasing of ammonia concentration and growth of MF1. In addition, the isolated bacterium demonstrated the ability to utilize different cyanide compounds as sole carbon and nitrogen source. The results of morphological and physiological characteristics showed that this bacterium belonged to the Serratia sp. Moreover, 16S rDNA sequencing and phylogenetic analyses exhibited that MF1 strain was similar to Serratia

  13. Biodegradation of chlorpyrifos by Klebsiella sp. isolated from an activated sludge sample of waste water treatment plant in Damascus.

    Ghanem, I; Orfi, M; Shamma, M

    2007-01-01

    A chlorpyrifos (CPY)-degrading bacterial strain was isolated from an activated sludge sample collected from the Damascus Wastewater Treatment Plant, Syria. The isolation of Klebsiella sp. was facilitated by the addition of CPY at a rate of 3.84 g/L of sludge weekly (selection pressure). Identification of Klebsiella sp. was done using major staining and biochemical differentiation tests (Gram stain, cytochrome oxidase and some relevant saccharide fermentation tests using biochemical assays). Klebsiella sp. was maintained by culturing in a poor medium consisting of mineral salts and CPY as the sole carbon source. When 3 activated sludge samples were incubated in the presence of CPY (13.9 g/L sludge), 46% of added CPY were degraded within 4 d. By comparison, within 4 d the isolated Klebsiella sp. was found to break down 92% of CPY when co-incubated in a poor mineral medium in which CPY was the sole carbon source (13.9 g/L poor medium). Isolated Klebsiella sp. was able to tolerate up to 17.3 g of CPY in the poor medium. PMID:18062192

  14. Comparative study on biochemical activity of the intestinal isolates Lactobacillus sp. V3 and Bifidobacterium sp. A71 in different substrates

    JOSIP BARAS

    2001-09-01

    Full Text Available The two intestinal isolates Lactobacillus sp. V3 and Bifidobacterium sp. A71 were selected for soymilk fermentation according to their acidification activity in soymilk. Beetroot juice and carrot juice were chosen for soymilk supplementation as additional sources of carbohydrates and brewer's yeast as an extra source of nitrogen. The fermentation was carried out for eight hours at 42°C. The fermentation was monitored by standard analytical and microbiological tests for changes of acidity (decreasing pH and increasing acid content, the contents of soluble dry substances, sugars and a-amino acids as well as changes in the number of viable cells. The samples were collected at the beginning and subsequently every two hours until the end of the fermentation. The results showed that there were differences between the tested isolates in terms of their ability to ferment soymilk. The mix with brewer's yeast had a better stimulating effect on the growth of both strains compared to those with juices alone. In addition, the carrot juice stimulated the growth of Bifidobacterium sp. A71 better than beetroot juice, while the opposite effect was found for the growth of Lactobacillus sp. V3.

  15. Isolement d'une chrysophyte amylolytique, Poterioochromonas sp., de l'intestin du termite Reticulitermes santonensis

    Tarayre, C.

    2014-01-01

    Full Text Available Isolation of an amylolytic chrysophyte, Poterioochromonas sp., from the digestive tract of the termite Reticulitermes santonensis. The aim of this work was the isolation and cultivation of amylolytic protists living in the digestive tract of the termite Reticulitermes santonensis (Feytaud. A chrysophyte identified as Poterioochromonas sp. was isolated in a special medium containing rice grains as a source of carbon and nitrogen. Then, the protist was grown in a medium containing starch as a carbon source, tryptone, and a phosphate buffer at different pH values (5, 6 and 7. Yeast extract was added or not. Ciprofloxacin was used to avoid the bacterial development. Other antibiotics were also tested but showed an inhibitive effect on the growth of Poterioochromonas sp. Yeast extract allowed reaching 1.9 (pH 5, 2.3 (pH 6 and 2.2 (pH 7 times higher final cell concentrations, and 2.8 (pH 5, 2.8 (pH 6 and 2.2 (pH 7 times higher biomass yields. The starch concentration did not decrease in the medium until 3 and 4 days of culture, with and without yeast extract, respectively. Eight days of culture were necessary for hydrolyzing the starch completely, with and without yeast extract. Maltose and maltotriose were detected in the culture media and were hydrolyzed progressively. Maximal maltose concentrations were 0.68, 0.66 and 0.51 g·l-1 in the medium containing yeast extract. Maltotriose concentrations were only 0.17, 0.14 and 0.12 g·l-1. Other glucose oligomers were also detected but in lower quantities. It was determined that the protist developed a weak amylase activity, particularly at a weakly acidic pH (5-6. Such a pH also allowed a better growth of the protist. A maximal amylase activity of 112 nkat·l-1 was measured with yeast extract at pH 5. No other enzymatic activity (protease, cellulase or xylanase was detected except amylase. The degradation products of starch, which were obtained by enzymatic hydrolysis, allow the identification of

  16. Antifungal compounds of Xylaria sp., an endophytic fungus isolated from Palicourea marcgravii (Rubiaceae); Substancias antifungicas de Xylaria sp., um fungo endofitico isolado de Palicourea marcgravii (Rubiaceae)

    Cafeu, Mariana C.; Silva, Geraldo H.; Teles, Helder L.; Bolzani, Vanderlan da S.; Araujo, Angela R. [UNESP, Araraquara, SP (Brazil). Inst. de Quimica]. E-mail: araujoar@iq.unesp.br; Young, Maria Claudia M. [Instituto de Botanica, Sao Paulo, SP (Brazil). Secao de Fisiologia e Bioquimica de Plantas; Pfenning, Ludwig H. [Universidade Federal de Lavras, MG (Brazil). Dept. de Fitopatologia

    2005-11-15

    Five compounds, 2-hexyl-3-methyl-butanodioic acid (1), cytochalasin D (2), 7-dechlorogriseofulvin (3), cytochalasin B (4) and griseofulvin (5), have been isolated from the endophytic fungus Xylaria sp., and their structures were elucidated on the basis of spectroscopic data. In the bioautography assay against Cladosporium cladosporioides and Cladosporium sphaerospermum, compounds 1 and 2 were found to be active while compounds 3, 4 and 5 did not show antifungal activity. (author)

  17. Isolation, Identification, and Characterization of Cadmium Resistant Pseudomonas sp. M3 from Industrial Wastewater

    Syed Zaghum Abbas

    2014-01-01

    Full Text Available The present study deals with the isolation, identification, and characterization of the cadmium resistant bacteria from wastewater collected from industrial area of Penang, Malaysia. The isolate was selected based on high level of the cadmium and antibiotic resistances. On the basis of morphological, biochemical characteristics, 16S rDNA gene sequencing and phylogeny analysis revealed that the strain RZCd1 was authentically identified as Pseudomonas sp. M3. The industrial isolate showed more than 70% of the cadmium removal in log phase. The cadmium removal capacity of strain RZCd1 was affected by temperature and pH. At pH 7.0 and 35°C, strain RZCd1 showed maximum cadmium removal capacity. The minimal inhibitory concentration of strain RZCd1 against the cadmium was 550 µg/mL. The resistance against the cadmium was associated with resistance to multiple antibiotics: amoxicillin, penicillin, cephalexin, erythromycin, and streptomycin. The strain RZCd1 also gave thick bands of proteins in front of 25 kDa in cadmium stress condition after 3 h of incubation. So the identified cadmium resistant bacteria may be useful for the bioremediation of cadmium contaminated industrial wastewater.

  18. Tenacibaculum dicentrarchi sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from European sea bass.

    Piñeiro-Vidal, Maximino; Gijón, Daniel; Zarza, Carles; Santos, Ysabel

    2012-02-01

    A novel Gram-stain-negative rod-shaped gliding bacterial strain, designated 35/09(T), was isolated from diseased European sea bass (Dicentrarchus labrax L.) in Spain. Colonies were pale-yellow-pigmented with uneven edges and did not adhere to the agar. The DNA G+C content of the isolate was 31.3 mol%. 16S rRNA gene sequence analysis indicated affiliation to the genus Tenacibaculum (family Flavobacteriaceae, phylum 'Bacteroidetes'). Sequence similarities between the isolate and type strains of other members of the genus were 93.1-97.3 %. The major fatty acids (>5 % of the total fatty acids) were iso-C(15 : 0) (24.8 %), iso-C(15 : 0) 3-OH (18.0 %), anteiso-C(15 : 0) (8.1 %), C(15 : 1)ω6c (6.9 %) and iso-C(15 : 1) (6.2 %). Genotypic and phenotypic data indicate that strain 35/09(T) should be classified as a representative of a novel species in the genus Tenacibaculum, for which the name Tenacibaculum dicentrarchi sp. nov. is proposed; the type strain is 35/09(T) ( = CECT 7612(T) = NCIMB 14598(T)). PMID:21460137

  19. Abyssisolibacter fermentans gen. nov. sp. nov., isolated from deep sub-seafloor sediment.

    Kim, Wonduck; Lee, Jung-Hyun; Kwon, Kae Kyoung

    2016-05-01

    A Gram-staining-negative, thin rod-shaped, anaerobic bacterium designated MCWD3(T) was isolated from sediment of the deep sea in Ulleung Basin, East Sea, Korea. The ranges of temperature, pH and NaCl for growth of this strain were 15-40°C (optimum 29°C), 5.0-10.0 (optimum pH 6.5), and 1-5%, respectively. The major fatty acids were iso-C15:0 (30%) and iso-C15:0 dimethyl acetal (17%). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and unidentified aminophospholipids, phospholipids, and aminolipids. The fermentation product from yeast extract was acetate. Phylogenetic analysis based on 16S rRNA genes indicated that the isolate was related to Sporosalibacterium faouarense (92.8% sequence identity), Clostridiisalibacter paucivorans (92.6%), and Brassicibacter mesophilus (92.4%). However, the isolate was differentiated from these genera by both physiological and chemotaxonomical properties. On the basis of a polyphasic taxonomic analysis, we propose that MCWD3(T) represents a novel taxon with the name Abyssisolibacter fermentans gen. nov. sp. nov. PMID:27095453

  20. Pararhizobium polonicum sp. nov. isolated from tumors on stone fruit rootstocks.

    Puławska, Joanna; Kuzmanović, Nemanja; Willems, Anne; Pothier, Joël F

    2016-05-01

    Five Gram-negative, rod-shaped, non-spore-forming bacteria were isolated from galls on different stone fruit rootstocks in Poland: strains F5.1(T) and F5.3 from Prunus avium F12/1, strains CP3.5 and CP17.2.1 from Prunus avium and strain AL5.1.8 from Prunus cerasifera. On the basis of 16S rDNA phylogeny, the strains cluster together and belong to the genus Pararhizobium with type strain of Pararhizobium herbae (99.6-99.8%) as their closest relative. Phylogenetic analysis of the novel strains using housekeeping genes atpD, recA and rpoB revealed their distinct position separate from other known Rhizobium species and confirmed their relation to P. herbae. DNA-DNA hybridization of strains F5.1(T), with the type strain of P. herbae LMG 25718(T) and Pararhizobium giardinii R-4385(T) revealed 28.3% and 27.9% of DNA-DNA relatedness, respectively. Phenotypic and physiological properties differentiate the novel isolates from other closely related species. On the basis of the results obtained, the five isolates are considered to represent a novel species of the genus Pararhizobium, for which the name Pararhizobium polonicum sp. nov. (type strain F5.1(T)=LMG 28610(T)=CFBP 8359(T)) is proposed. PMID:27026286

  1. Ruegeria mobilis sp. nov., a member of the Alphaproteobacteria isolated in Japan and Palau.

    Muramatsu, Yuki; Uchino, Yoshihito; Kasai, Hiroaki; Suzuki, Ken-ichiro; Nakagawa, Yasuyoshi

    2007-06-01

    The taxonomic positions of two bacterial strains, MBIC01146(T) and MBIC01099, isolated from marine environments of Japan and Palau, respectively, were determined by using a polyphasic approach. The bacteria were aerobic, motile, Gram-negative rods and formed star-shaped aggregations. The G+C content of the genomic DNA ranged from 58.5 to 58.7 mol%. The major respiratory quinone was ubiquinone-10 and the predominant cellular fatty acids were C(16 : 0), C(18 : 1)omega6c and C(18 : 1)omega7c. 16S rRNA gene sequence analyses based on both neighbour-joining and maximum-parsimony methods revealed that strains MBIC01146(T) and MBIC01099 were positioned within the cluster comprising Ruegeria atlantica and Silicibacter lacuscaerulensis within subgroup alpha-3 of the Proteobacteria. The phenotypic and chemotaxonomic characteristics of the novel strains were similar to those of Ruegeria atlantica; however, DNA-DNA hybridization tests showed that the isolates represented an independent species. The isolates could be differentiated from Ruegeria atlantica based on several characteristics. Therefore, strains MBIC01146(T) and MBIC01099 are considered to represent a novel species of the genus Ruegeria, for which the name Ruegeria mobilis sp. nov. is proposed. The type strain is MBIC01146(T) (=NBRC 101030(T)=CIP 109181(T)). An emended description of Ruegeria atlantica Uchino et al. 1999 is also given. PMID:17551047

  2. Gordonia otitidis sp. nov., isolated from a patient with external otitis.

    Iida, Soji; Taniguchi, Hiroko; Kageyama, Akiko; Yazawa, Katsukiyo; Chibana, Hiroji; Murata, Shota; Nomura, Fumio; Kroppenstedt, Reiner M; Mikami, Yuzuru

    2005-09-01

    The taxonomic positions of two clinically isolated actinomycetes were established using a polyphasic approach. The two strains, IFM 10032(T), isolated from ear discharge of a 28-year-old Japanese female patient with external otitis, and IFM 10148, isolated from pleural fluid of a 60-year-old Japanese male patient with bronchitis, possessed meso-diaminopimelic acid as the diagnostic amino acid, MK-9(H(2)) as the predominant menaquinone and mycolic acids ranging from 58 to 64 carbons. The 16S rRNA gene sequences of the two strains were most closely related to those of Gordonia aichiensis, Gordonia sputi and 'Gordonia jacobaea'. Differences in several phenotypic characteristics together with genotypic distinctiveness distinguish strains IFM 10032(T) and IFM 10148 from these three species. DNA-DNA hybridization results and the combination of genotypic and phenotypic data showed that the two strains belong to a single species, and merit recognition of a novel species within the genus Gordonia. The name proposed for this taxon is Gordonia otitidis sp. nov.; the type strain is IFM 10032(T) (=DSM 44809(T)=JCM 12355(T)=NBRC 100426(T)). PMID:16166681

  3. Roseimarinus sediminis gen. nov., sp. nov., a facultatively anaerobic bacterium isolated from coastal sediment.

    Wu, Wen-Jie; Liu, Qian-Qian; Chen, Guan-Jun; Du, Zong-Jun

    2015-07-01

    A Gram-stain-negative, facultatively anaerobic, non-motile and pink-pigmented bacterium, designated strain HF08(T), was isolated from marine sediment of the coast of Weihai, China. Cells were rod-shaped, and oxidase- and catalase-positive. The isolate grew optimally at 33 °C, at pH 7.5-8.0 and with 2-3% (w/v) NaCl. The dominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C14 : 0. Menaquinone 7 (MK-7) was the major respiratory quinone and the DNA G+C content was 44.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was a member of the class Bacteroidia, and shared 88-90% sequence similarity with the closest genera Sunxiuqinia, Prolixibacter, Draconibacterium, Mariniphaga and Meniscus. Based on the phylogenetic and phenotypic evidence presented, a novel species in a new genus of the family Prolixibacteraceae is proposed, with the name Roseimarinus sediminis gen. nov., sp. nov. The type strain of Roseimarinus sediminis is HF08(T) ( = KCTC 42261(T) = CICC 10901(T)). PMID:25866024

  4. Paenibacillus castaneae sp. nov., isolated from the phyllosphere of Castanea sativa Miller.

    Valverde, Angel; Peix, Alvaro; Rivas, Raúl; Velázquez, Encarna; Salazar, Sergio; Santa-Regina, Ignacio; Rodríguez-Barrueco, Claudino; Igual, José M

    2008-11-01

    A bacterial strain, designated Ch-32(T), was isolated from the phyllosphere of Castanea sativa in Spain. Phylogenetic analysis based on 16S rRNA gene sequences placed the isolate in the genus Paenibacillus within the same subgroup as Paenibacillus xinjiangensis and Paenibacillus glycanilyticus, with similarities of 96.3 and 96.8 %, respectively. DNA-DNA hybridization values for strain Ch-32(T) with these two species were lower than 20 %. The novel isolate was a Gram-variable, motile, sporulating rod. It produced catalase and oxidase and hydrolysed cellulose, gelatin and aesculin. Acetoin and urease production, nitrate reduction and starch hydrolysis were negative. Growth was supported by many carbohydrates and organic acids as carbon sources. MK-7 was the only menaquinone detected and anteiso-C(15 : 0), iso-C(16 : 0) and C(16 : 0) were the major fatty acids. The DNA G+C content was 46 mol%. Phylogenetic, DNA relatedness and phenotypic analyses showed that strain Ch-32(T) should be classified as a novel species of the genus Paenibacillus, for which the name Paenibacillus castaneae sp. nov. is proposed; the type strain is Ch-32(T) (=CECT 7279(T)=DSM 19417(T)). PMID:18984693

  5. Biodegradation of stored jet fuel by a Nocardia sp. isolated from contaminated soil

    Edelvio de Barros Gomes

    2009-10-01

    Full Text Available The aim of this study was to investigate the potential of degradation of an autochthonous bacterial strain, isolated from petroleum derivatives contaminated soil samples against jet fuel hydrocarbons. The autochthonous bacterial strain was characterized as Nocardia sp. Evaluation of their degrading abilities was carried out by presumptive assays as redox indicator test and by observations of surface tension decreases in aqueous medium. Degradation of jet fuel hydrocarbons was evaluated by chromatographic methods. Experiments were performed in flasks at two biostimulation rates. A bacterial strain of Pseudomonas aeruginosa UFPEDA 39 was utilized as a reference microorganism. The bacterial strain, identified as Nocardia sp, demonstrate high ability to degrade jet fuel compounds as well as to produce surface active compounds when compared to the reference microrganism.O presente estudo objetivou a investigação da capacidade degradadora de uma linhagem bacteriana autóctone (isolada de amostras de solo contaminadas com derivados de petróleo contra hidrocarbonetos de querosene de aviação. A linhagem foi caracterizada como Nocardia sp. A avaliação do seu potencial degradador deu-se realizada mediante testes com indicador redox e observações na redução da tensão superficial na fase aquosa. A degradação do querosene foi avaliada por métodos cromatográficos. Os experimentos foram realizados utilizando-se duas taxas de bioestímulo. Uma linhagem bacteriana Pseudomonas aeruginosa UFPEDA 39 foi utilizada como referência. A linhagem autóctone demonstrou alta eficiência na degradação de hidrocarbonetos do querosene bem como para produzir compostos ativos de superfície quando comparada com a linhagem de referência.

  6. Biosorption behavior and mechanism of thorium on Bacillus sp. dwc-2 isolated from soil

    兰图; 刘宁; 张东; 杨吉军; 罗顺忠; 安竹; 邬琦琦; 杨远友; 冯更生; 唐军

    2015-01-01

    To develop a microbe-based bioremediation strategy for cleaning up thorium-contaminated sites, we have investigated the biosorption behavior and mechanism of thorium on Bacillus sp. dwc-2, one of the dominant species of bacterial groups isolated from soils in Southwest China. Thorium biosorption depended on the pH of environment, and its rapid biosorption reached a maximum of up to 10.75 mg Th per gram of the bacteria (wet wt.) at pH 3.0. The biosorption agreed bettter with Langmuir isotherm model than Freundlich model, indicating that thorium biosorption was a monolayer adsorption. The thermodynamic parameters, negative change in Gibbs free energy and positive value in enthalpy and entropy, suggested that the biosorption was spontaneous, more favorable at higher temperature and endothermic process with an increase of entropy. Scanning electron microscopy (SEM) indicated that thorium initially binded with the cell surface, while transmission electron microscopy (TEM) revealed that Th deposited in the cytoplasm and served as cores for growth of element precipitation (e.g., phosphate minerals) or by self-precipitation of hydroxides, which is probably controlled by ion-exchange, as evidenced by particle induced X-ray emission (PIXE) and enhanced proton backscattering spectrometry (EPBS). Fourier Transform Infrared (FTIR) further indicated that thorium biosorption involved carboxyl and phosphate groups and protein in complexation or electrostatic interaction. Overall results indicated that a combined electrostatic interaction-complexation-ion exchange mechanism could be involved in thorium biosorption by Bacillus sp. dwc-2.

  7. Exopolysaccharide production by a marine Pseudoalteromonas sp. strain isolated from Madeira Archipelago ocean sediments.

    Roca, Christophe; Lehmann, Mareen; Torres, Cristiana A V; Baptista, Sílvia; Gaudêncio, Susana P; Freitas, Filomena; Reis, Maria A M

    2016-06-25

    Exopolysaccharides (EPS) are polymers excreted by some microorganisms with interesting properties and used in many industrial applications. A new Pseudoalteromonas sp. strain, MD12-642, was isolated from marine sediments and cultivated in bioreactor in saline culture medium containing glucose as carbon source. Its ability to produce EPS under saline conditions was demonstrated reaching an EPS production of 4.4g/L within 17hours of cultivation, corresponding to a volumetric productivity of 0.25g/Lh, the highest value so far obtained for Pseudoalteromonas sp. strains. The compositional analysis of the EPS revealed the presence of galacturonic acid (41-42mol%), glucuronic acid (25-26mol%), rhamnose (16-22mol%) and glucosamine (12-16mol%) sugar residues. The polymer presents a high molecular weight (above 1000kDa). These results encourage the biotechnological exploitation of strain MD12-642 for the production of valuable EPS with unique composition, using saline by-products/wastes as feedstocks. PMID:26923806

  8. Identification of New Lactone Derivatives Isolated from Trichoderma sp., An Endophytic Fungus of Brotowali (Tinaspora crispa

    Elfita

    2014-03-01

    Full Text Available Endophytic fungi is a rich source of novel organic compounds with interesting biological activities and a high level of structural diversity. As a part of our systematic search for new bioactive lead structures and specific profiles from endophytic fungi, an endophytic fungus was isolated from roots of brotowali (Tinaspora crispa, an important medicinal plant. Colonial morphological trait and microscopic observation revealed that the endophytic fungus was Trichoderma sp. The pure fungal strain was cultivated on 7 L Potatos Dextose Broth (PDB medium under room temperature (no shaking for 8 weeks. The ethyl acetate were added to cultur medium and left overnight to stop cell growth. The culture filtrates were collected and extracted with EtOAc and then taken to evaporation. Two new lactone derivatives, 5-hydroxy-4-hydroxymethyl-2H-pyran-2-one (1 and (5-hydroxy-2-oxo-2H pyran-4-yl methyl acetate (2 were obtained from the EtOAc extracts of Trichoderma sp. Their structures were determined on the basic of spectroscopic methods including UV, IR, 1H-NMR, 13C-NMR, HMQC, and HMBC.

  9. Heterotrophic nitrogen removal by Acinetobacter sp. Y1 isolated from coke plant wastewater.

    Liu, YuXiang; Hu, Tingting; Song, Yujie; Chen, Hongping; Lv, YongKang

    2015-11-01

    A strain of Acinetobacter sp. Y1, which exhibited an amazing ability to remove ammonium, nitrite and nitrate, was isolated from the activated sludge of a coking wastewater treatment plant. The aim of this work was to study the ability, influence factors and possible pathway of nitrogen removal by Acinetobacter sp. Y1. Results showed that maximum removal rate of NH4(+)-N by the strain was 10.28 mg-N/L/h. Carbon source had significant influence on the growth and ammonium removal efficiencies of strain Y1. Pyruvate, citrate and acetate were favourable carbon sources for the strain. Temperature, pH value and shaking speed could affect the growth and nitrogen removal ability. Nitrate or nitrite could be used as a sole nitrogen source for the growth and removed efficiently by the strain. N2 levels increased to 53.74%, 50.21% and 55.13% within 36 h when 100 mg/L NH4(+)-N, NO2(-)-N or NO3(-) -N was used as sole nitrogen source in the gas detection experiment. The activities of hydroxylamine oxidoreductase (HAO), nitrate reductase (NR) and nitrite reductase (NiR), which are key enzymes in heterotrophic nitrification and aerobic denitrification, were all detectable in the strain. Consequently, a possible pathway for ammonium removal by the strain was also suggested. PMID:25910961

  10. Production and characterization of cyclodextrin glycosyltransferase from Bacillus sp. isolated from Cuban

    Kárel Hernández Sánchez

    2014-12-01

    Full Text Available A cyclodextrin glycosyltransferase (CGTase from an alkaliphilic Bacillus sp. strain, isolated from Cuban soil, was purified with Sephadex G-50 with a yield of 66.5%. The CGTase was stable over a very wide pH range, 6.0–10, at 25°C and was most active at pH 7.5. The enzyme exhibited an optimum temperature of 60°C and was stable to 50°C for at least 8 h. The T50 value – defined as the temperature at which 50% of the initial activity was retained–was 63°C in this enzyme. The influence of substrate or product concentration on the initial rate of CD production was studied, and the kinetic parameters were determined. The analysis of kinetic parameters Km and Vmax was obtained by the action of CGTase on the starch of corn with respect to β-CD, and the values were 4.1 g/L and 5.2 μM β-CD/min ml, respectively. The purified CGTase from Bacillus sp. could be used for an efficient cyclodextrin (CD production which is the significant yield of γ- CDs.

  11. Isolation and characterization of a fungus Aspergillus sp. strain F-3 capable of degrading alkali lignin.

    Yang, Y S; Zhou, J T; Lu, H; Yuan, Y L; Zhao, L H

    2011-09-01

    A fungus strain F-3 was selected from fungal strains isolated from forest soil in Dalian of China. It was identified as one Aspergillus sp. stain F-3 with its morphologic, cultural characteristics and high homology to the genus of rDNA sequence. The budges or thickened node-like structures are peculiar structures of hyphae of the strain. The fungus degraded 65% of alkali lignin (2,000 mg l(-1)) after day 8 of incubation at 30°C at pH 7. The removal of colority was up to 100% at 8 days. The biodegradation of lignin by Aspergillus sp. F-3 favored initial pH 7.0. Excess acid or alkali conditions were not propitious to lignin decomposing. Addition of ammonium L: -tartrate or glucose delayed or repressed biodegradation activities. During lignin degradation, manganese peroxidase (28.2 U l(-1)) and laccase (3.5 U l(-1))activities were detected after day 7 of incubation. GC-MS analysis of biodegraded products showed strain F-3 could convert alkali lignin into small molecules or other utilizable products. Strain F-3 may co-culture with white rot fungus and decompose alkali lignin effectively. PMID:21350882

  12. Crude bacterial extracts of two new Streptomyces sp. isolates as bio-colorants for textile dyeing.

    Kramar, Ana; Ilic-Tomic, Tatjana; Petkovic, Milos; Radulović, Niko; Kostic, Mirjana; Jocic, Dragan; Nikodinovic-Runic, Jasmina

    2014-08-01

    Renewed demand for incorporation of natural dyes (bio-colorants) in textile industry could be met through biotechnological production of bacterial pigments. Two new Streptomyces strains (NP2 and NP4) were isolated for the remarkable ability to produce diffusible deep blue and deep red pigment into fermentation medium. Crude mycelial extracts of both strains were used as bio-colorants in conventional textile dyeing procedures avoiding downstream purification procedures. The yields of bio-colorants obtained in this way were 62 and 84 mg per g of mycelia for Streptomyces sp. NP2 and Streptomyces sp. NP4, respectively. Through nuclear magnetic resonance analysis of crude extracts before and after dyeing procedures, it was shown that both extracts contained prodigiosin-like family of compounds that exhibited different dyeing capabilities towards different textile fibers. Polyamide and acrylic fibers were colored to the deepest shade, polyester and triacetate fibers to a noticeable, but much lower shade depth, while cotton and cellulosic fibers stained weakly. These results confirmed that crude bacterial extracts had the characteristics similar to those of ionic and disperse dyes, which was consistent with the identified polypyrrolic prodigiosin-like structures. PMID:24671299

  13. Biosorption and biotransformation of chromium by Serratia sp. isolated from tannery effluent.

    Srivastava, Shaili; Thakur, Indu Shekhar

    2012-01-01

    A bacterium isolated from soil and sediment ofa leather tanning mill's effluent was identified as Serratia sp. by the analysis of 16S rDNA. Scanning electron microscopy-energy dispersive X-ray analysis (SEM-EDX) and transmission electron microscopy (TEM) were used to assess morphological changes and confirm chromium biosorption in Serratia sp. both in a shake-flask culture containing chromium and in a tannery wastewater. The SEMEDX and the elemental analysis of the chromate-containing samples confirmed the binding of chromium with the bacterial biomass. The TEM exhibited chromium accumulation throughout the bacterial cell, with some granular deposits in the cell periphery and in the cytoplasm. X-ray diffraction analysis (XRD) was used to quantify the chromium and to determine the chemical nature of the metal-microbe interaction. The XRD data showed the crystalline character of the precipitates, which consisted of mainly calcium chromium oxide, chromium fluoride phosphate and related organo-Cr(III) complex crystals. The XRD data also revealed a strong involvement of cellular carboxyl and phosphate groups in chromium binding by the bacterial biomass. The results of the study indicated that a combined mechanism of ion-exchange, complexation, croprecipitation and immobilization was involved in the biosorption of chromium by bacterial cells in contaminated environments. PMID:22519094

  14. Evaluation of secretome of highly efficient lignocellulolytic Penicillium sp. Dal 5 isolated from rhizosphere of conifers.

    Rai, Rohit; Kaur, Baljit; Singh, Surender; Di Falco, Macros; Tsang, Adrian; Chadha, B S

    2016-09-01

    Penicillium sp. (Dal 5) isolated from rhizosphere of conifers from Dalhousie (Himachal Pradesh, India) was found to be an efficient cellulolytic strain. The culture under shake flask on CWR (cellulose, wheat bran and rice straw) medium produced appreciably higher levels of endoglucanase (35.69U/ml), β-glucosidase (4.20U/ml), cellobiohydrolase (2.86U/ml), FPase (1.2U/ml) and xylanase (115U/ml) compared to other Penicillium strains reported in literature. The mass spectroscopy analysis of Penicillium sp. Dal 5 secretome identified 108 proteins constituting an array of CAZymes including glycosyl hydrolases (GH) belonging to 24 different families, polysaccharide lyases (PL), carbohydrate esterases (CE), lytic polysaccharide mono-oxygenases (LPMO) in addition to swollenin and a variety of carbohydrate binding modules (CBM) indicating an elaborate genetic potential of this strain for hydrolysis of lignocellulosics. Further, the culture extract was evaluated for hydrolysis of alkali treated rice straw, wheat straw, bagasse and corn cob at 10% substrate loading rate. PMID:27341464

  15. Isospora dromaii n. sp. (Apicomplexa, Eimeriidae) isolated from emus, Dromaius novaehollandiae (Casuariiformes, Casuariidae).

    dos Santos Teixeira, Carina; Gallo, Samira Salim Mello; Ederli, Nicole Brand; Berto, Bruno Pereira; de Oliveira, Francisco Carlos Rodrigues

    2014-11-01

    A new species of Coccidia (Protozoa: Apicomplexa: Eimeriidae) isolated from emus, Dromaius novaehollandiae, which was observed in Brazil is described and named. Oocysts of Isospora dromaii n. sp. are subspheroidal to ovoid in shape, measure 21.6 × 19.8 μm, and have a double and smooth wall thickness of approximately 1.4 μm. In this species, micropyle, oocyst residuum, and polar granules are absent. The sporocysts are slightly ovoid in shape and measure 13.7 × 10.0 μm. Nipple-like Stieda body and prominent sub-Stieda body are present. The sporocyst residuum is composed of small dispersed granules of varying sizes. The sporozoites are characterized by an oblong refractile body and one centrally located nucleus. This is the first description of isosporid coccidia infecting birds of the family Dromaiidae. PMID:25195056

  16. Physicochemical parameters optimization, and purification of phycobiliproteins from the isolated Nostoc sp.

    Johnson, Eldin M; Kumar, Kanhaiya; Das, Debabrata

    2014-08-01

    The present study investigated the effects of several physicochemical parameters on the improvement of phycobiliproteins (especially phycocyanin) synthesis in a newly isolated species of Nostoc sp. Standard BG11₀ medium was modified to enhance the biomass productivity in different photobioreactors. The initial pH of 8, light intensity of 40 μmol m(-2)s(-1), temperature of 35 °C, diurnal cycle of 16:8 h (light:dark regime), 75.48 μM Na₂CO₃ and 17.65 mM NaNO₃ were found most suitable for the phycobiliproteins synthesis. Cyanobacteria exhibited chromatic adaptation, causing overexpression of phycocyanin in red and phycoerythrin in green light. The maximum phycobiliproteins yield of 0.13 gg(-1) dry cell weight was obtained in green light. Phycocyanin was further purified using thin layer chromatography (TLC), anion exchange chromatography and SDS-PAGE (denaturing gel) electrophoresis. PMID:24951941

  17. Cylindrospermopsin Biodegradation Abilities of Aeromonas sp. Isolated from Rusałka Lake.

    Dziga, Dariusz; Kokocinski, Mikolaj; Maksylewicz, Anna; Czaja-Prokop, Urszula; Barylski, Jakub

    2016-03-01

    The occurrence of the cyanobacterial toxin cylindrospermopsin (CYN) in freshwater reservoirs is a common phenomenon. However, the biodegradation of this toxin in environmental samples has been observed only occasionally. In this work the biodegradation ability of cylindrospermopsin was investigated based on isolates from lakes with previous cyanotoxin history. Bacterial strains were identified based on the 16S rDNA and rpoD gene comparison. CYN biodegradation was monitored using the HPLC method. The R6 strain identified as Aeromonas sp. was documented as being capable of CYN removal. This biodegradation was dependent on the pH and temperature. Additionally, the stimulation of the growth of the R6 strain in the presence of CYN was indicated. Our discovery supports the hypothesis that (in analogy to the well-known phenomenon of microcystin biodegradation) in lakes dominated by potential CYN-producing cyanobacteria, the processes of microbial utilization of this toxin may occur. PMID:26927173

  18. Saprolegnia bulbosa sp. nov. isolated from an Argentine stream: taxonomy and comparison with related species.

    Steciow, Mónica Mirta; Paul, Alan; Bala, Kanak

    2007-03-01

    Saprolegnia bulbosa sp. nov. was isolated from floating and decaying twigs and leaves in El Gato stream, Partido de La Plata, Buenos Aires Province, Argentina. The distinctive characteristics of S. bulbosa are the product of smooth oogonia and predominantly contorted monoclinous, androgynous and diclinous antheridia. The oogonial stalks are usually bent, curved or once coiled; oospores are subcentric, (1) 2-15 (45) per oogonium and are variable in size. Taxonomical description of this new species, its comparison with related oomycetes of the genus and the nucleotide sequences of the internal transcribed region (spacers ITS1, ITS2 and the gene 5.8S) of its rRNA gene are given here. PMID:17328749

  19. Cylindrospermopsin Biodegradation Abilities of Aeromonas sp. Isolated from Rusałka Lake

    Dziga, Dariusz; Kokocinski, Mikolaj; Maksylewicz, Anna; Czaja-Prokop, Urszula; Barylski, Jakub

    2016-01-01

    The occurrence of the cyanobacterial toxin cylindrospermopsin (CYN) in freshwater reservoirs is a common phenomenon. However, the biodegradation of this toxin in environmental samples has been observed only occasionally. In this work the biodegradation ability of cylindrospermopsin was investigated based on isolates from lakes with previous cyanotoxin history. Bacterial strains were identified based on the 16S rDNA and rpoD gene comparison. CYN biodegradation was monitored using the HPLC method. The R6 strain identified as Aeromonas sp. was documented as being capable of CYN removal. This biodegradation was dependent on the pH and temperature. Additionally, the stimulation of the growth of the R6 strain in the presence of CYN was indicated. Our discovery supports the hypothesis that (in analogy to the well-known phenomenon of microcystin biodegradation) in lakes dominated by potential CYN-producing cyanobacteria, the processes of microbial utilization of this toxin may occur. PMID:26927173

  20. A Sterol and Spiroditerpenoids from a Penicillium sp. Isolated from a Deep Sea Sediment Sample

    Chengbin Cui

    2012-02-01

    Full Text Available A new polyoxygenated sterol, sterolic acid (1, three new breviane spiroditerpenoids, breviones I–K (2–4, and the known breviones (5–8, were isolated from the crude extract of a Penicillium sp. obtained from a deep sea sediment sample that was collected at a depth of 5115 m. The structures of 1–4 were elucidated primarily by NMR experiments, and 1 was further confirmed by X-ray crystallography. The absolute configurations of 2 and 3 were deduced by comparison of their CD spectra with those of the model compounds. Compounds 2 and 5 showed significant cytotoxicity against MCF-7 cells, which is comparable to the positive control cisplatin.

  1. Nocardia pigrifrangens sp. nov., a novel actinomycete isolated from a contaminated agar plate.

    Wang, Liming; Zhang, Yamei; Huang, Ying; Maldonado, Luis A; Liu, Zhiheng; Goodfellow, Michael

    2004-09-01

    A polyphasic study was undertaken to establish the taxonomic position of an actinomycete strain isolated from a contaminated agar plate. The strain, designated 7031T, had morphological and chemotaxonomic properties typical of the genus Nocardia. An almost-complete 16S rRNA gene sequence determined for the strain was aligned with available sequences for nocardiae, and phylogenetic trees were inferred using three tree-generating algorithms. Strain 7031T clustered with the type strains of Nocardia carnea and Nocardia flavorosea, showing low 16S rRNA gene sequence similarities to these species (97.2 and 97.5 %, respectively). The strain was also distinguished from the closest species by a range of phenotypic properties. It is proposed that the strain be recognized as a novel species of Nocardia, Nocardia pigrifrangens sp. nov., the type strain of which is 7031T (= AS 4.1808T = JCM 11884T). PMID:15388728

  2. Isolation and optimization of production of Astaxanthin from Antarctic yeast Rhodotorula sp.NJ298

    Liu Junling; Miao Jinlai; Sun Xiuqin; Wang Quanfu; Li Guangyou

    2007-01-01

    Rhodotorula sp. NJ298 which could produce carotenoids was isolated from Antarctic sea ice. The major carotenoid was identified as astaxanthin by Liquid Chromatography/Mass Spectrometry(LC/MS), and its content accounted for 87.62% of total carotenoids (1,786 μg/g). High Performance Liquid Chromatogrephy(HPLC)analysis showed that the purity of the astaxanthin reached about 96.16% through a simple purification. Maximum astaxanthin production(1,908/μg/g)was obtained when the yeast was grown at 10℃ in seawater medium containing 5g/L sodium acetate, 5g/L peptone, 0.5g/L NaCl, 0.01g/L KH2P04;0.01g/L MgS04·7H2O and 0.001 g/L FeS04·7H20 at pH 7.5.

  3. Legionella thermalis sp. nov., isolated from hot spring water in Tokyo, Japan.

    Ishizaki, Naoto; Sogawa, Kazuyuki; Inoue, Hiroaki; Agata, Kunio; Edagawa, Akiko; Miyamoto, Hiroshi; Fukuyama, Masafumi; Furuhata, Katsunori

    2016-03-01

    Strain L-47(T) of a novel bacterial species belonging to the genus Legionella was isolated from a sample of hot spring water from Tokyo, Japan. The 16S rRNA gene sequences (1477 bp) of this strain (accession number AB899895) had less than 95.0% identity with other Legionella species. The dominant fatty acids of strain L-47(T) were a15:0 (29.6%) and the major ubiquinone was Q-12 (71.1%). It had a guanine-plus-cytosine content of 41.5 mol%. The taxonomic description of Legionella thermalis sp. nov. is proposed to be type strain L-47(T) (JCM 30970(T)  = KCTC 42799(T)). PMID:26865126

  4. Bipolamides A and B, triene amides isolated from the endophytic fungus Bipolaris sp. MU34.

    Siriwach, Ratklao; Kinoshita, Hiroshi; Kitani, Shigeru; Igarashi, Yasuhiro; Pansuksan, Kanokthip; Panbangred, Watanalai; Nihira, Takuya

    2014-02-01

    As a result of the continued screening for new metabolites produced by endophytic fungi from Thai medicinal plants, two new triene fatty acid amides, bipolamides A (1) and B (2), were discovered from the endophytic fungus Bipolaris sp. MU34. The structures of all of the isolated compounds were elucidated on the basis of the spectroscopic data of NMR and MS. An antimicrobial assay revealed that bipolamide B (2) had moderate antifungal activity against Cladosporium cladosporioides FERMS-9, Cladosporium cucumerinum NBRC 6370, Saccharomyces cerevisiae ATCC 9804, Aspergillus niger ATCC 6275 and Rhisopus oryzae ATCC 10404, with Minimum inhibitory concentration (MIC) values of 16, 32, 32, 64 and 64 μg ml(-1), respectively. PMID:24192556

  5. Characterization of Francisella sp., GM2212, the first Francisella isolate from marine fish, Atlantic cod (Gadus morhua)

    Ottem, Karl F; Nylund, Are; Karlsbakk, Egil;

    2007-01-01

    A Francisella sp., isolate GM2212(T), previously isolated from diseased farmed Atlantic cod Gadus morhua in Norway is characterized. The complete 16S rDNA, 16S-23S intergenic spacer, 23S rDNA, 23S-5S intergenic spacer, 5S rDNA, FopA, lipoprotein TUL4 (LpnA), malate dehydrogenase and a hypothetica......; but is susceptible to ceftazidime, tetracycline, gentamicin, ciprofloxacin. Based on the molecular and phenotypical characteristics, we suggest that this GM2212 isolate, may represent a new species of Francisella. Isolate GM2212(T) (=CNCM I-3481(T) = CNCM I-3511(T) = DSM 18777(T))....

  6. Co-metabolism of DDT by the newly isolated bacterium, Pseudoxanthomonas sp. wax

    Guangli Wang

    2010-06-01

    Full Text Available Microbial degradation of 1,1,1-trichloro-2,2-bis(p-chlorophenylethane (DDT is the most promising way to clean up DDT residues found in the environment. In this paper, a bacterium designated as wax, which was capable of co-metabolizing DDT with other carbon sources, was isolated from a long-term DDT-contaminated soil sample by an enrichment culture technique. The new isolate was identified as a member of the Pseudoxanthomonas sp., based on its morphological, physiological and biochemical properties, as well as by 16S rRNA gene analysis. In the presence of 100 mg l-1 glucose, the wax strain could degrade over 95% of the total DDT, at a concentration of 20 mg l-1, in 72 hours, and could degrade over 60% of the total DDT, at a concentration of 100 mg l-1, in 144 hours. The wax strain had the highest degradation efficiency among all of the documented DDT-degrading bacteria. The wax strain could efficiently degrade DDT at temperatures ranging from 20 to 37ºC, and with initial pH values ranging from 7 to 9. The bacterium could also simultaneously co-metabolize 1,1-dichloro-2,2-bis(p-chlorophenylethane (DDD, 2,2-bis(p-chlorophenyl-1,1-dichlorethylene (DDE, and other organochlorine compounds. The wax strain could also completely remove 20 mg kg-1 of DDT from both sterile and non-sterile soils in 20 days. This study demonstrates the significant potential use of Pseudoxanthomonas sp. wax for the bioremediation of DDT in the environment.

  7. Low molecular weight human pulmonary surfactant protein (SP5): isolation, characterization, and cDNA and amino acid sequences

    Pulmonary surfactant is a lipid-protein complex that promotes alveolar stability by lowering the surface tension at the air-fluid interface in the peripheral air spaces. A group of hydrophobic surfactant-associated proteins has been shown to be essential for rapid surface film formation by surfactant phospholipids. The authors have purified a hydrophobic surfactant protein of ≅ 5kDa that they term SP5 from bronchopulmonary lavage fluid from a patient with alveolar proteinosis and shown that it promotes rapid surface film formation by simple mixtures of phospholipids. They have derived the full amino acid sequence of human SP5 from the nucleotide sequence of cDNAs identified with oligonucleotide probes based on the NH2-terminal sequence of SP5. SP5 isolated from surfactant is a fragment of a much larger precursor protein (21 kDa). The precursor contains an extremely hydrophobic region of 34 amino acids that comprises most the mature SP5. This hydrophobicity explains the unusual solubility characteristics of SP5 and the fact that it is lipid-associated when isolated from lung

  8. Low molecular weight human pulmonary surfactant protein (SP5): isolation, characterization, and cDNA and amino acid sequences

    Warr, R.G.; Hawgood, S.; Buckley, D.I.; Crisp, T.M.; Schilling, J.; Benson, B.J.; Ballard, P.L.; Clements, J.A.; White, R.T.

    1987-11-01

    Pulmonary surfactant is a lipid-protein complex that promotes alveolar stability by lowering the surface tension at the air-fluid interface in the peripheral air spaces. A group of hydrophobic surfactant-associated proteins has been shown to be essential for rapid surface film formation by surfactant phospholipids. The authors have purified a hydrophobic surfactant protein of approx. = 5kDa that they term SP5 from bronchopulmonary lavage fluid from a patient with alveolar proteinosis and shown that it promotes rapid surface film formation by simple mixtures of phospholipids. They have derived the full amino acid sequence of human SP5 from the nucleotide sequence of cDNAs identified with oligonucleotide probes based on the NH/sub 2/-terminal sequence of SP5. SP5 isolated from surfactant is a fragment of a much larger precursor protein (21 kDa). The precursor contains an extremely hydrophobic region of 34 amino acids that comprises most the mature SP5. This hydrophobicity explains the unusual solubility characteristics of SP5 and the fact that it is lipid-associated when isolated from lung.

  9. Streptomonospora tuzyakensis sp. nov., a halophilic actinomycete isolated from saline soil.

    Tatar, Demet; Guven, Kiymet; Inan, Kadriye; Cetin, Demet; Belduz, Ali Osman; Sahin, Nevzat

    2016-01-01

    A novel actinobacterium, designated strain BN506(T), was isolated from soil collected from Tuz (Salt) Lake, Konya, Turkey, and was characterised to determine its taxonomic position. The isolate was found to have morphological and chemotaxonomic properties associated with members of the genus Streptomonospora. The isolate was found to grow optimally at 37 °C and in the presence of 10 % (w/v) NaCl but not in the absence of NaCl. Phylogenetic analyses based on an almost-complete 16S rRNA gene sequences indicated that isolate is closely related to members of the genus Streptomonospora and forms a distinct phyletic line in the Streptomonospora phylogenetic tree. Strain BN506(T) is closely related to Streptomonospora halophila YIM 91355(T) (98.1 % sequence similarity). Sequence similarities with other type strains of the genus Streptomyces were lower than 98.0 %. The cell wall of the novel strain was found to contain meso-diaminopimelic acid. Whole cell hydrolysates were found to contain galactose, glucose and ribose. The predominant menaquinone was identified as MK-10(H8) (57.0 %). The polar lipids detected were identified as diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine. The major fatty acids were found to be anteiso-C17:0, iso-C16:0 and 10 methyl C18:0. Based on 16S rRNA gene sequence analysis, DNA-DNA relatedness, phenotypic characteristics and chemotaxonomic data, strain BN506(T) was identified as a member of a novel species of the genus Streptomonospora, for which the name Streptomonospora tuzyakensis sp. nov. (type strain BN506(T) = DSM 45930(T) = KCTC 29210(T)) is proposed. PMID:26459342

  10. Nitrincola lacisaponensis gen. nov., sp. nov., a novel alkaliphilic bacterium isolated from an alkaline, saline lake.

    Dimitriu, Pedro A; Shukla, Sanjay K; Conradt, Jennifer; Márquez, M Carmen; Ventosa, Antonio; Maglia, Anne; Peyton, Brent M; Pinkart, Holly C; Mormile, Melanie R

    2005-11-01

    A novel alkaliphilic bacterium, strain 4CAT, was isolated from decomposing wood taken from the shore of Soap Lake, a saline, alkaline lake in Grant County, WA, USA. Cells of the isolate were Gram-negative, asporogenous, short, motile rods that utilized only a limited range of organic acids as sole carbon and energy sources. In addition to oxygen, the strain possessed the ability to reduce in the presence of acetate. Strain 4CAT was oxidase- and catalase-positive; it degraded Tween 60, but not DNA, urea, gelatin or starch. It grew at pH values from 7.5 to 11.0, with optimum growth occurring at pH 9.0, and growth was observed in NaCl concentrations of 0.2-1.3 M, with optimum growth at 0.8 M NaCl. The optimum temperature for growth was 37 degrees C. Strain 4CAT was resistant to erythromycin, bacitracin, novobiocin, polymyxin B, neomycin, gentamicin, streptomycin, carbenicillin, rifampicin and tetracycline, and was susceptible to nalidixic acid, chloramphenicol, ampicillin and penicillin. The isolate's 16S rRNA gene sequence indicated that it belonged to the gamma-Proteobacteria, showing 90-94 % similarity to its closest relatives. Maximum-likelihood phylogenetic inferences placed strain 4CAT within a novel lineage related to the marine bacterial genera Neptunomonas and Marinobacterium. The DNA G+C content of the isolate was 47.4 mol%. On the basis of genotypic and phenotypic characterization, it was concluded that strain 4CAT should be placed in a separate taxon as a novel genus and species, with the proposed name Nitrincola lacisaponensis gen. nov., sp. nov. The type strain is 4CAT (=ATCC BAA-920T=DSM 16316T). PMID:16280482

  11. Mycoavidus cysteinexigens gen. nov., sp. nov., an endohyphal bacterium isolated from a soil isolate of the fungus Mortierella elongata.

    Ohshima, Shoko; Sato, Yoshinori; Fujimura, Reiko; Takashima, Yusuke; Hamada, Moriyuki; Nishizawa, Tomoyasu; Narisawa, Kazuhiko; Ohta, Hiroyuki

    2016-05-01

    An endohyphal bacterium (strain B1-EBT) living in association with the fungus Mortierella elongata FMR23-6 I-B1 was isolated from a fungal cell homogenate and studied for its taxonomic allocation. Cells were Gram-stain-negative, rod-shaped, non-spore-forming, non-motile, and negative for oxidase and catalase. Strain B1-EBT required cysteine for growth and grew at temperatures between 4 and 35 °C. A comparative analysis of 16S rRNA gene sequences revealed that strain B1-EBT forms a distinct clade in the family Burkholderiaceae, encompassing a group of endosymbionts associated with several soil isolates of M. elongata. The most closely related genus is 'Candidatus Glomeribacter gigasporarum', an endosymbiont of the arbuscular mycorrhizal fungus Gigaspora margarita. The major cellular fatty acids of strain B1-EBT were C16 : 0, summed feature 3 (C16 : 1ω7c and C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c or C18 : 1ω6c). Ubiquinone Q-8 was the only quinone detected. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminophospholipid and two unknown aminolipids. The DNA G+C content was 49.8 mol%. On the basis of phenotypic, chemotaxonomic, and phylogenetic characteristics, strain B1-EBT represents a novel genus and novel species in the family Burkholderiaceae, for which the name Mycoavidus cysteinexigens gen. nov., sp. nov. is proposed. The type strain is B1-EBT ( = JCM 30646T = LMG 28693T = NBRC 110909T). PMID:26920389

  12. Complete genome sequence of Hymenobacter sp. strain PAMC26554, an ionizing radiation-resistant bacterium isolated from an Antarctic lichen.

    Oh, Tae-Jin; Han, So-Ra; Ahn, Do-Hwan; Park, Hyun; Kim, Augustine Yonghwi

    2016-06-10

    A Gram-negative, rod-shaped, red-pink in color, and UV radiation-resistant bacterium Hymenobacter sp. strain PAMC26554 was isolated from Usnea sp., an Antarctic lichen, and belongs to the class of Cytophagia and the phylum of Bacteroidetes. The complete genome of Hymenobacter sp. PAMC26554 consists of one chromosome (5,244,843bp) with two plasmids (199,990bp and 6421bp). The genomic sequence indicates that Hymenobacter sp. strain PAMC26554 possesses several genes involved in the nucleotide excision repair pathway that protects damaged DNA. This complete genome information will help us to understand its adaptation and novel survival strategy in the Antarctic extreme cold environment. PMID:27063139

  13. Draft Genome Sequence of Thauera sp. Strain SWB20, Isolated from a Singapore Wastewater Treatment Facility Using Gel Microdroplets

    Davenport, Karen W.; Li, Po-E; Ahmed, Sanaa A.; Daligault, Hajnalka; Gleasner, Cheryl D.; Kunde, Yuliya; McMurry, Kim; Lo, Chien-Chi; Reitenga, Krista G.; Daughton, Ashlynn R.; Shen, Xiaohong; Frietze, Seth; Wang, Dongping; Drautz-Moses, Daniela I.; Schuster, Stephan; Chain, Patrick S.; Han, Cliff

    2015-01-01

    We report here the genome sequence of Thauera sp. strain SWB20, isolated from a Singaporean wastewater treatment facility using gel microdroplets (GMDs) and single-cell genomics (SCG). This approach provided a single clonal microcolony that was sufficient to obtain a 4.9-Mbp genome assembly of an ecologically relevant Thauera species. PMID:25792053

  14. Draft Genome Sequence of Thauera sp. Strain SWB20, Isolated from a Singapore Wastewater Treatment Facility Using Gel Microdroplets

    Dichosa, Armand E. K.; Davenport, Karen W.; Li, Po-E; Ahmed, Sanaa A.; Daligault, Hajnalka; Gleasner, Cheryl D.; Kunde, Yuliya; McMurry, Kim; Lo, Chien-Chi; Reitenga, Krista G.; Daughton, Ashlynn R.; Shen, Xiaohong; Frietze, Seth; WANG, Dongping; Johnson, S. L.

    2015-01-01

    We report here the genome sequence of Thauera sp. strain SWB20, isolated from a Singaporean wastewater treatment facility using gel microdroplets (GMDs) and single-cell genomics (SCG). This approach provided a single clonal microcolony that was sufficient to obtain a 4.9-Mbp genome assembly of an ecologically relevant Thauera species.

  15. Draft Genome Sequence of Frankia sp. Strain BMG5.12, a Nitrogen-Fixing Actinobacterium Isolated from Tunisian Soils.

    Nouioui, Imen; Beauchemin, Nicholas; Cantor, Michael N; Chen, Amy; Detter, J Chris; Furnholm, Teal; Ghodhbane-Gtari, Faten; Goodwin, Lynne; Gtari, Maher; Han, Cliff; Han, James; Huntemann, Marcel; Hua, Susan Xinyu; Ivanova, Natalia; Kyrpides, Nikos; Markowitz, Victor; Mavrommatis, Kostas; Mikhailova, Natalia; Nordberg, Henrik P; Ovchinnikova, Galina; Pagani, Ioanna; Pati, Amrita; Sen, Arnab; Sur, Saubashya; Szeto, Ernest; Thakur, Subarna; Wall, Luis; Wei, Chia-Lin; Woyke, Tanja; Tisa, Louis S

    2013-01-01

    Members of the actinomycete genus Frankia form a nitrogen-fixing symbiosis with 8 different families of actinorhizal plants. We report a draft genome sequence for Frankia sp. strain BMG5.12, a nitrogen-fixing actinobacterium isolated from Tunisian soils with the ability to infect Elaeagnus angustifolia and Myrica gale. PMID:23846272

  16. Draft Genome Sequence of Frankia sp. Strain DC12, an Atypical, Noninfective, Ineffective Isolate from Datisca cannabina.

    Tisa, Louis S; Beauchemin, Nicholas; Cantor, Michael N; Furnholm, Teal; Ghodhbane-Gtari, Faten; Goodwin, Lynne; Copeland, Alex; Gtari, Maher; Huntemann, Marcel; Ivanova, Natalia; Kyrpides, Nikos; Markowitz, Victor; Mavrommatis, Kostas; Mikhailova, Natalia; Nouioui, Imen; Oshone, Rediet; Ovchinnikova, Galina; Pagani, Ioanna; Palaniappan, Krishnaveni; Pati, Amrita; Sen, Arnab; Shapiro, Nicole; Szeto, Ernest; Wall, Luis; Wishart, Jessie; Woyke, Tanja

    2015-01-01

    Frankia sp. strain DC12, isolated from root nodules of Datisca cannabina, is a member of the fourth lineage of Frankia, which is unable to reinfect actinorhizal plants. Here, we report its 6.88-Mbp high-quality draft genome sequence, with a G+C content of 71.92% and 5,858 candidate protein-coding genes. PMID:26251504

  17. Draft genome sequence of Frankia sp. strain CN3, an atypical, noninfective (Nod-) ineffective (Fix-) isolate from Coriaria nepalensis.

    Ghodhbane-Gtari, Faten; Beauchemin, Nicholas; Bruce, David; Chain, Patrick; Chen, Amy; Walston Davenport, Karen; Deshpande, Shweta; Detter, Chris; Furnholm, Teal; Goodwin, Lynne; Gtari, Maher; Han, Cliff; Han, James; Huntemann, Marcel; Ivanova, Natalia; Kyrpides, Nikos; Land, Miriam L; Markowitz, Victor; Mavrommatis, Kostas; Nolan, Matt; Nouioui, Imen; Pagani, Ioanna; Pati, Amrita; Pitluck, Sam; Santos, Catarina L; Sen, Arnab; Sur, Saubashya; Szeto, Ernest; Tavares, Fernando; Teshima, Hazuki; Thakur, Subarna; Wall, Luis; Woyke, Tanja; Tisa, Louis S

    2013-01-01

    We report here the genome sequence of Frankia sp. strain CN3, which was isolated from Coriaria nepalensis. This genome sequence is the first from the fourth lineage of Frankia, strains of which are unable to reinfect actinorhizal plants. At 10 Mb, it represents the largest Frankia genome sequenced to date. PMID:23516212

  18. Draft Genome Sequence of Frankia sp. Strain BCU110501, a Nitrogen-Fixing Actinobacterium Isolated from Nodules of Discaria trinevis.

    Wall, Luis G; Beauchemin, Nicholas; Cantor, Michael N; Chaia, Eugenia; Chen, Amy; Detter, J Chris; Furnholm, Teal; Ghodhbane-Gtari, Faten; Goodwin, Lynne; Gtari, Maher; Han, Cliff; Han, James; Huntemann, Marcel; Hua, Susan Xinyu; Ivanova, Natalia; Kyrpides, Nikos; Markowitz, Victor; Mavrommatis, Kostas; Mikhailova, Natalia; Nordberg, Henrik P; Nouioui, Imen; Ovchinnikova, Galina; Pagani, Ioanna; Pati, Amrita; Sen, Arnab; Sur, Saubashya; Szeto, Ernest; Thakur, Subarna; Wei, Chia-Lin; Woyke, Tanja; Tisa, Louis S

    2013-01-01

    Frankia forms a nitrogen-fixing symbiosis with actinorhizal plants. We report a draft genome sequence for Frankia sp. strain BCU110501, a nitrogen-fixing actinobacterium isolated from nodules of Discaria trinevis grown in the Patagonia region of Argentina. PMID:23846281

  19. Whole-Genome Shotgun Sequence of the Keratinolytic Bacterium Lysobacter sp. A03, Isolated from the Antarctic Environment

    Pereira, Jamile Queiroz; Ambrosini, Adriana; Sant’Anna, Fernando Hayashi; Tadra-Sfeir, Michele; Faoro, Helisson; Pedrosa, Fábio de Oliveira; Souza, Emanuel Maltempi; Adriano BRANDELLI; Passaglia, Luciane M. P.

    2015-01-01

    Lysobacter sp. strain A03 is a protease-producing bacterium isolated from decomposing-penguin feathers collected in the Antarctic environment. This strain has the ability to degrade keratin at low temperatures. The A03 genome sequence provides the possibility of finding new genes with biotechnological potential to better understand its cold-adaptation mechanism and survival in cold environments.

  20. Whole-Genome Shotgun Sequence of the Keratinolytic Bacterium Lysobacter sp. A03, Isolated from the Antarctic Environment.

    Pereira, Jamile Queiroz; Ambrosini, Adriana; Sant'Anna, Fernando Hayashi; Tadra-Sfeir, Michele; Faoro, Helisson; Pedrosa, Fábio Oliveira; Souza, Emanuel Maltempi; Brandelli, Adriano; Passaglia, Luciane M P

    2015-01-01

    Lysobacter sp. strain A03 is a protease-producing bacterium isolated from decomposing-penguin feathers collected in the Antarctic environment. This strain has the ability to degrade keratin at low temperatures. The A03 genome sequence provides the possibility of finding new genes with biotechnological potential to better understand its cold-adaptation mechanism and survival in cold environments. PMID:25838495

  1. Draft Genome Sequence of Tatumella sp. Strain UCD-D_suzukii (Phylum Proteobacteria) Isolated from Drosophila suzukii Larvae

    Dunitz, Madison I.; James, Pamela M.; Jospin, Guillaume; Eisen, Jonathan A.; Coil, David A.; Chandler, James Angus

    2014-01-01

    Here we present the draft genome of Tatumella sp. strain UCD-D_suzukii, the first member of this genus to be sequenced. The genome contains 3,602,931 bp in 72 scaffolds. This strain was isolated from Drosophila suzukii larvae as part of a larger project to study the microbiota of D. suzukii.

  2. Draft Genome Sequence of Tatumella sp. Strain UCD-D_suzukii (Phylum Proteobacteria) Isolated from Drosophila suzukii Larvae.

    Dunitz, MI; James, PM; Jospin, G; Eisen, JA; Coil, DA; Chandler, JA

    2014-01-01

    Here we present the draft genome of Tatumella sp. strain UCD-D_suzukii, the first member of this genus to be sequenced. The genome contains 3,602,931 bp in 72 scaffolds. This strain was isolated from Drosophila suzukii larvae as part of a larger project to study the microbiota of D. suzukii.

  3. Draft Genome Sequence of Tatumella sp. Strain UCD-D_suzukii (Phylum Proteobacteria) Isolated from Drosophila suzukii Larvae.

    Dunitz, Madison I; James, Pamela M; Jospin, Guillaume; Eisen, Jonathan A; Coil, David A; Chandler, James Angus

    2014-01-01

    Here we present the draft genome of Tatumella sp. strain UCD-D_suzukii, the first member of this genus to be sequenced. The genome contains 3,602,931 bp in 72 scaffolds. This strain was isolated from Drosophila suzukii larvae as part of a larger project to study the microbiota of D. suzukii. PMID:24762940

  4. Draft Genome Sequence of Streptomyces sp. Strain Wigar10, Isolated from a Surface-Sterilized Garlic Bulb

    Klassen, Jonathan L.; Adams, Sandye M; Bramhacharya, Shanti; Giles, Steven S.; Goodwin, Lynne A.; Woyke, Tanja; Currie, Cameron R

    2011-01-01

    Streptomyces sp. strain Wigar10 was isolated from a surface-sterilized garlic bulb (Allium sativum var. Purple Stripe). Its genome encodes several novel secondary metabolite biosynthetic gene clusters and provides a genetic basis for further investigation of this strain's chemical biology and potential for interaction with its garlic host.

  5. Draft Genome Sequence of MCPA-Degrading Sphingomonas sp. Strain ERG5, Isolated from a Groundwater Aquifer in Denmark

    Nielsen, Tue Kjærgaard; Kot, Witold; Sørensen, Sebastian R;

    2015-01-01

    Sphingomonas sp. strain ERG5 was isolated from a bacterial community, originating from a groundwater aquifer polluted with low pesticide concentrations. This bacterium degrades 2-methyl-4-chlorophenoxyacetic acid (MCPA) in a wide spectrum of concentrations and has been shown to function in...

  6. Genome Sequence of Halomonas sp. Strain A3H3, Isolated from Arsenic-Rich Marine Sediments

    Koechler, Sandrine; Plewniak, Frédéric; Barbe, Valérie; Battaglia-Brunet, Fabienne; Jost, Bernard; Joulian, Catherine; Philipps, Muriel; Vicaire, Serge; Vincent, Stéphanie; Ye, Tao; Bertin, Philippe N.

    2013-01-01

    We report the genome sequence of Halomonas sp. strain A3H3, a bacterium with a high tolerance to arsenite, isolated from multicontaminated sediments of the l’Estaque harbor in Marseille, France. The genome is composed of a 5,489,893-bp chromosome and a 157,085-bp plasmid.

  7. Draft Genome Sequence of Nitrosospira sp. Strain APG3, a Psychrotolerant Ammonia-Oxidizing Bacterium Isolated from Sandy Lake Sediment

    Garcia, Juan C.; Urakawa, Hidetoshi; Le, Vang Q.; Stein, Lisa Y.; Klotz, Martin G; Nielsen, Jeppe L.

    2013-01-01

    Bacteria in the genus Nitrosospira play vital roles in the nitrogen cycle. Nitrosospira sp. strain APG3 is a psychrotolerant betaproteobacterial ammonia-oxidizing bacterium isolated from freshwater lake sediment. The draft genome revealed that it represents a new species of cluster 0 Nitrosospira, which is presently not represented by described species.

  8. Draft Genome Sequence of Anaeromyxobacter sp. Strain PSR-1, an Arsenate-Respiring Bacterium Isolated from Arsenic-Contaminated Soil

    Tonomura, Mimori; Ehara, Ayaka; Suzuki, Haruo; Amachi, Seigo

    2015-01-01

    Here, we report a draft genome sequence of Anaeromyxobacter sp. strain PSR-1, an arsenate-respiring bacterium isolated from arsenic-contaminated soil. It contained three distinct arsenic resistance gene clusters (ars operons), while no respiratory arsenate reductase gene (arr) was identified.

  9. Draft Genome Sequence of Ralstonia sp. MD27, a Poly(3-Hydroxybutyrate)-Degrading Bacterium, Isolated from Compost

    Zhu, Morgan; McCully, Lucy M.; Silby, Mark W; Charles-Ogan, Tamunonengiyeofori I.; Huang, Jean; Brigham, Christopher J.

    2015-01-01

    Ralstonia sp. strain MD27, a novel biopolymer-degrading betaproteobacterium, was isolated from compost samples. This organism has been shown to utilize the biopolymer poly(3-hydroxybutyrate) [P(3HB)] as a carbon source for growth. We report the draft genome sequence of MD27 with an estimated total sequence length of 5.9 Mb.

  10. Atkinsiella hamanaensis sp. nov isolated from cultivated ova of the mangrove crab, Scylla serrata ( Forsskal )

    B.Z.BIAN; S.EGUSA

    1986-01-01

    Atkinsiella hamanaensis sp. nov. a marine mastigomycete isolated from ova of the mangrove crab. scylla serrata (Forsskal). is described and illustrated The fungus grew over a temperature range of 15-32℃. with an optimum of 29-32℃ Its growth was observed in peptone-yeast extract glucose broth containing 1-5%NaCl.

  11. Draft Genome Sequence of Methylobacterium sp. Strain ARG-1 Isolated from the White-Rot Fungus Armillaria gallica

    Collins, Caitlin; Kowalski, Caitlin; Zebrowski, Jessica; Tulchinskaya, Yevgeniya; Tai, Albert K.; James-Pederson, Magdalena

    2016-01-01

    Methylobacterium sp. strain ARG-1 was isolated from a cell culture of hyphal tips of the white-rot fungus Armillaria gallica. We describe here the sequencing, assembly, and annotation of its genome, confirming the presence of genes involved in methylotrophy. This is the first genome announcement of a strain of Methylobacterium associated with A. gallica. PMID:27257212

  12. Production and characterization of bacterial cellulose by Leifsonia sp. CBNU-EW3 isolated from the earthworm, Eisenia fetida

    A total of five bacterial strains were isolated from earthworm, Eisenia fetida and examined for bacterial cellulose (BC) production in Hestrin–Schramm medium (HS). Among the five strains tested, CBNU-EW3 exhibited excellent BC production and was identified as Leifsonia sp. by 16S rDNA sequence analy...

  13. Genome sequence of Acinetobacter sp. strain HA, isolated from the gut of the polyphagous insect pest Helicoverpa armigera.

    Malhotra, Jaya; Dua, Ankita; Saxena, Anjali; Sangwan, Naseer; Mukherjee, Udita; Pandey, Neeti; Rajagopal, Raman; Khurana, Paramjit; Khurana, Jitendra P; Lal, Rup

    2012-09-01

    In this study, Acinetobacter sp. strain HA was isolated from the midgut of a fifth-instar larva of Helicoverpa armigera. Here, we report the draft genome sequence (3,125,085 bp) of this strain that consists of 102 contigs, 2,911 predicted coding sequences, and a G+C content of 41%. PMID:22933775

  14. Brucella microti sp. nov., isolated from the common vole Microtus arvalis.

    Scholz, Holger C; Hubalek, Zdenek; Sedlácek, Ivo; Vergnaud, Gilles; Tomaso, Herbert; Al Dahouk, Sascha; Melzer, Falk; Kämpfer, Peter; Neubauer, Heinrich; Cloeckaert, Axel; Maquart, Marianne; Zygmunt, Michel S; Whatmore, Adrian M; Falsen, Enevold; Bahn, Peter; Göllner, Cornelia; Pfeffer, Martin; Huber, Birgit; Busse, Hans-Jürgen; Nöckler, Karsten

    2008-02-01

    Two Gram-negative, non-motile, non-spore-forming, coccoid bacteria (strains CCM 4915(T) and CCM 4916), isolated from clinical specimens of the common vole Microtus arvalis during an epizootic in the Czech Republic in 2001, were subjected to a polyphasic taxonomic study. On the basis of 16S rRNA (rrs) and recA gene sequence similarities, both isolates were allocated to the genus Brucella. Affiliation to Brucella was confirmed by DNA-DNA hybridization studies. Both strains reacted equally with Brucella M-monospecific antiserum and were lysed by the bacteriophages Tb, Wb, F1 and F25. Biochemical profiling revealed a high degree of enzyme activity and metabolic capabilities not observed in other Brucella species. The omp2a and omp2b genes of isolates CCM 4915(T) and CCM 4916 were indistinguishable. Whereas omp2a was identical to omp2a of brucellae from certain pinniped marine mammals, omp2b clustered with omp2b of terrestrial brucellae. Analysis of the bp26 gene downstream region identified strains CCM 4915(T) and CCM 4916 as Brucella of terrestrial origin. Both strains harboured five to six copies of the insertion element IS711, displaying a unique banding pattern as determined by Southern blotting. In comparative multilocus VNTR (variable-number tandem-repeat) analysis (MLVA) with 296 different genotypes, the two isolates grouped together, but formed a separate cluster within the genus Brucella. Multilocus sequence typing (MLST) analysis using nine different loci also placed the two isolates separately from other brucellae. In the IS711-based AMOS PCR, a 1900 bp fragment was generated with the Brucella ovis-specific primers, revealing that the insertion element had integrated between a putative membrane protein and cboL, encoding a methyltransferase, an integration site not observed in other brucellae. Isolates CCM 4915(T) and CCM 4916 could be clearly distinguished from all known Brucella species and their biovars by means of both their phenotypic and molecular

  15. Actinoalloteichus nanshanensis sp. nov., isolated from the rhizosphere of a fig tree (Ficus religiosa).

    Xiang, Wensheng; Liu, Chongxi; Wang, Xiangjing; Du, Jing; Xi, Lijun; Huang, Ying

    2011-05-01

    A Gram-positive, aerobic actinomycete, designated strain NEAU 119(T), was isolated from the rhizosphere of a fig tree and was characterized using a polyphasic approach. The isolate formed branching, non-fragmenting vegetative hyphae and produced black pigment on yeast extract/malt extract (ISP medium 2). The G+C content of the DNA was 76.6 mol%. The organism had chemotaxonomic characteristics typical of the genus Actinoalloteichus and was closely related to the type strains of Actinoalloteichus cyanogriseus, Actinoalloteichus spitiensis and Actinoalloteichus hymeniacidonis, currently the only three recognized species of the genus Actinoalloteichus, sharing 16S rRNA gene similarities of 96.4, 96.6 and 98.1 %, respectively. However, the results of DNA-DNA hybridization studies demonstrated that the novel strain showed only 46.8 % relatedness with the type strain of A. hymeniacidonis. In addition, a set of phenotypic characteristics also readily distinguished strain NEAU 119(T) from the type strains of recognized species of the genus Actinoalloteichus. According to the above data, it is proposed that strain NEAU 119(T) represents a novel species, Actinoalloteichus nanshanensis sp. nov. The type strain of Actinoalloteichus nanshanensis is NEAU 119(T) ( = CGMCC 4.5714(T) = NBRC 106685(T)). PMID:20562245

  16. Kocuria halotolerans sp. nov., an actinobacterium isolated from a saline soil in China.

    Tang, Shu-Kun; Wang, Yun; Lou, Kai; Mao, Pei-Hong; Xu, Li-Hua; Jiang, Cheng-Lin; Kim, Chang-Jin; Li, Wen-Jun

    2009-06-01

    A Gram-positive actinobacterium, designated strain YIM 90716(T), was isolated from a saline soil sample collected from Ganjiahu Suosuo Forest National Nature Reserve in Xinjiang Province, north-west China. The new isolate contained lysine, glutamic acid and alanine with peptidoglycan type Lys-Ala(3) (variation A3alpha). The major phospholipids were phosphatidylglycerol and diphosphatidylglycerol. The predominant menaqinone was MK-7(H(2)). The major fatty acids were anteiso-C(15 : 0), iso-C(16 : 0) and anteiso-C(17 : 0). The DNA G+C content of strain YIM 90716(T) was 68.0 mol%. Chemotaxonomic properties supported the affiliation of strain YIM 90716(T) to the genus Kocuria. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism was related most closely to Kocuria kristinae DSM 20032(T) (96.8 % similarity) and showed lower levels of 16S rRNA gene similarity (Kocuria. The results of fatty acid analysis and physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain YIM 90716(T) from its closest relatives. On the basis of data from the present polyphasic study, strain YIM 90716(T) is considered to represent a novel species of the genus Kocuria, for which the name Kocuria halotolerans sp. nov. is proposed. The type strain is YIM 90716(T) (=DSM 18442(T)=KCTC 19172(T)=CCTCC AB 206069(T)). PMID:19502308

  17. Corynebacterium uropygiale sp. nov., isolated from the preen gland of Turkeys (Meleagris gallopavo).

    Braun, Markus Santhosh; Zimmermann, Stefan; Danner, Maria; Rashid, Harun-Or; Wink, Michael

    2016-03-01

    A novel species of fastidious, lipophilic, club-shaped, Gram-positive bacteria was recovered from the preen glands of healthy Turkeys (Meleagris gallopavo) from two different locations. Phylogenetic analysis of the 16S rRNA gene showed highest similarity to Corynebacterium spheniscorum DSM 44757(T) (96.8%) with a 3.2kb stretch of rpoB sharing 82.4% sequence similarity to the same species. DNA fingerprinting by ERIC-PCR and polar lipid profiles clearly differentiated the Turkey isolates from the most closely related Corynebacteria, as did MALDI-TOF MS analysis. Chemotaxonomic tests revealed the presence of corynemycolic acids with C16:0, C18:0, C18:1ω9c and tuberculostearic acid as the major cellular fatty acids. The G+C content of the type strain was 60.7mol%. The species was susceptible to ampicillin, kanamycin A, streptomycin, amikacin, polymyxin B and vancomycin. From our results, it becomes evident that the isolated organisms represent a new species, for which the name Corynebacterium uropygiale sp. nov. is proposed. The type strain is Iso10(T) (=DSM 46817(T)=LMG 28616(T)). PMID:26776107

  18. Massilia humi sp. nov. isolated from soil in Incheon, South Korea.

    Du, Juan; Yin, Chang Shik

    2016-05-01

    A Gram-negative, strictly aerobic, non-motile, rod-shaped bacterium, designated THG-S6.8(T), was isolated from soil in Incheon, South Korea. Based on 16S rRNA gene sequence, strain THG-S6.8(T) was moderately related to Massilia plicata 76(T) (97.3 %), Massilia dura 16(T) (97.2 %) and Massilia albidiflava 45(T) (96.9 %). Chemotaxonomic data revealed that strain THG-S6.8(T) possesses ubiquinone-8 as the predominant respiratory quinone, and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) and C16:0 as the major fatty acids. The major polar lipids were found to be phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA-DNA relatedness between strain THG-S6.8(T) and Massilia plicata KCTC 12344(T) and Massilia dura KACC 12342(T) was 38.7 and 40.5 %, respectively. The DNA G+C content was 66.8 %. These data, together with phenotypic characterization, suggest the isolate represents a novel species, for which the name Massilia humi sp. nov. is proposed, with THG-S6.8(T) as the type strain (=KCTC 42737(T) = CCTCC AB 2015296(T)). PMID:26846918

  19. Devosia humi sp. nov., isolated from soil of a Korean pine (Pinus koraiensis) garden.

    Du, Juan; Kook, MooChang; Akter, Shahina; Singh, Hina; Won, KyungHwa; Ngo, Hien T T; Yi, Tae-Hoo

    2016-01-01

    A bacterial isolate, designated strain THG-MM1T, was isolated from soil in Yongin region, Republic of Korea. Strain THG-MM1T was Gram-stain-negative, aerobic, non-motile and rod-shaped. Based on 16S rRNA gene sequence comparisons, strain THG-MM1T was most closely related to Devosia insulae DS-56T (96.5 % 16S rRNA gene sequence similarity), followed by Devosia yakushimensis Yak96BT (95.7 %) and Devosia albogilva IPL15T (95.2 %). The G+C content of the genomic DNA was 63.7 mol%. The major cellular fatty acids were C16 : 0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C18 : 0. The predominant isoprenoid quinone was ubiquinone-10 (Q-10). The major polar lipids were phosphatidylglycerol and an unidentified lipid. The combined phenotypic, chemotaxonomic and phylogenetic data showed that strain THG-MM1T represents a novel species of the genus Devosia, for which the name Devosia humi sp. nov. is proposed, with strain THG-MM1T ( = KACC 18281T = CCTCC AB 2015121T) as the type strain. PMID:26514816

  20. Microbacterium horti sp. nov., a bacterium isolated from Cucurbita maxima cultivating soil.

    Akter, Shahina; Park, Jae Hee; Yin, Chang Shik

    2016-04-01

    A novel bacterial strain THG-SL1(T) was isolated from a soil sample of Cucurbita maxima garden and was characterized by using a polyphasic approach. Cells were Gram-reaction-positive, non-motile and rod-shaped. The strain was aerobic, catalase positive and weakly positive for oxidase. Phylogenetic analysis based on 16S rRNA gene sequence analysis but it shared highest similarity with Microbacterium ginsengisoli KCTC 19189(T) (96.6 %), indicating that strain THG-SL1(T) belongs to the genus Microbacterium. The DNA G + C content of the isolate was 68.9 mol %. The major fatty acids were anteiso-C15: 0 (39.7 %), anteiso-C17: 0 (24.4 %) and iso-C16: 0 (18.5 %). The major polar lipids of strain THG-SL1(T) were phosphatidylglycerol (PG) and an unidentified glycolipid (GL). The predominant respiratory isoprenoid quinones were menaquinone-11 and menaquinone-12. The diamino acid in the cell-wall peptidoglycan was ornithine. Based on the results of polyphasic characterization, strain THG-SL1(T) represented a novel species within the genus Microbacterium, for which the name Microbacterium horti sp. nov. is proposed. The type strain is THG-SL1(T) (=KACC 18286(T)=CCTCC AB 2015117(T)). PMID:26757723

  1. Biodegradation of di-n-Butyl Phthalate by Achromobacter sp. Isolated from Rural Domestic Wastewater

    Decai Jin

    2015-10-01

    Full Text Available A bacterial strain W-1, isolated from rural domestic wastewater, can utilize the environmental hormone di-n-butyl phthalate (DBP as the sole carbon and energy source. The isolated bacterium species was confirmed to belong to the genus Achromobacter based on its 16S rRNA gene sequence. The results of substrate utilization tests showed that the strain W-1 could utilize other common phthalates and phenol. High-performance liquid chromatography analysis revealed that the optimal conditions for DBP degradation were pH 7.0, 35 °C, and an agitation rate of 175 rpm. Under these conditions, 500 mg/L of DBP was completely degraded within 30 h. The effects of heavy metals (50 mg/L Cu2+ and 500 mg/L Pb2+ and surfactants (100 mg/L SDS and 500 mg/L Tween 20 on DBP degradation were investigated. The results demonstrated that Cu2+ and SDS severely inhibited DBP degradation and Pb2+ weakly inhibited DBP degradation, while Tween 20 greatly enhanced DBP degradation. Furthermore, phthalate degradation genes were found to be located on a plasmid present in Achromobacter sp. W-1.

  2. Actinorugispora endophytica gen. nov., sp. nov., an actinomycete isolated from Daucus carota.

    Liu, Min-Jiao; Zhu, Wen-Yong; Li, Jie; Zhao, Guo-Zhen; Xiong, Zhi; Park, Dong-Jin; Hozzein, Wael N; Kim, Chang-Jin; Li, Wen-Jun

    2015-08-01

    An actinomycete strain, designated YIM 690008T, was isolated from Daucus carota collected from South Korea and its taxonomic position was investigated by using a polyphasic approach. The strain grew well on most media tested and no diffusible pigment was produced. The aerial mycelium formed wrinkled single spores and short spore chains, some of which were branched. The whole-cell hydrolysates contained meso-diaminopimelic acid, glucose, mannose, ribose, galactose and rhamnose. The predominant menaquinones were MK-10(H4), MK-10(H6), MK-10(H8) and MK-10(H2). The polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannosides, some unknown phospholipids, glycolipids and polar lipids. The major fatty acids were i-C16 : 0, ai-C17 : 0 and C18 : 1ω9c. The DNA G+C content of the genomic DNA was 63.1 mol%. Phylogenetic analysis indicated that the isolate belongs to the family Nocardiopsaceae. However, based on phenotypic, chemotaxonomic and genotypic data, it was concluded that strain YIM 690008T represents a novel genus and novel species of the family Nocardiopsaceae, for which the name Actinorugispora endophytica gen. nov., sp. nov. (type strain YIM 690008T = DSM 46770T = JCM 30099T = KCTC 29480T) is proposed. PMID:25948617

  3. Peptoniphilus catoniae sp. nov., isolated from a human faecal sample from a traditional Peruvian coastal community.

    Patel, Nisha B; Tito, Raul Y; Obregón-Tito, Alexandra J; O'Neal, Lindsey; Trujillo-Villaroel, Omar; Marin-Reyes, Luis; Troncoso-Corzo, Luzmila; Guija-Poma, Emilio; Lewis, Cecil M; Lawson, Paul A

    2016-05-01

    A novel Gram-stain-positive, coccus-shaped, obligately anaerobic bacterium was isolated from a faecal sample obtained from an individual in a traditional community located off the southern coast of Peru. Comparative 16S rRNA gene sequence analysis showed the novel bacterium belonged to the genus Peptoniphilus but showed no particular relationship with any species, demonstrating less than 91 % 16S rRNA gene sequence similarity with all members of the genus. The major cellular fatty acids of the novel isolate were determined to be C10 : 0, C14 : 0, C16 : 0, C18 : 1ω9c and C18 : 2ω6,9c/anteiso-C18 : 0. The DNA G+C content was 34.4 mol%. End-products of metabolism from peptone-yeast-glucose broth (PYG) were determined to be acetate and butyrate. Based on the phenotypic, chemotaxonomic and phylogenetic results, the organism represents a novel species of the genus Peptoniphilus, for which the name Peptoniphilus catoniae sp. nov. is proposed. The type strain is M6.X2DT ( = DSM 29874T = CCUG 66798T). PMID:26907921

  4. Fulvibacter tottoriensis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from marine sediment.

    Khan, Shams Tabrez; Nakagawa, Yasuyoshi; Harayama, Shigeaki

    2008-07-01

    A novel bacterium, MTT-39(T), was isolated from a sample of marine sediment collected at Tottori on the coast of the Sea of Japan. Cells were Gram-negative, rod-shaped and non-motile. The bacterium formed yellowish brown colonies on marine agar 2216. Although the 16S rRNA gene sequence of strain MTT-39(T) classified this strain as a member of the family Flavobacteriaceae, the maximum sequence similarity obtained was only 91.5 % (with Kordia algicida OT-1(T)). In the maximum-likelihood tree based on 16S rRNA gene sequences, the novel bacterium clustered with the type strains of Kordia algicida, Lutibacter litoralis, Tenacibaculum maritimum and Polaribacter filamentus. The novel strain exhibited the following characteristics: the predominant fatty acids in cells grown on artificial seawater-based tryptic soya agar were iso-C(15 : 1), iso-C(15 : 0) and iso-C(15 : 0) 3-OH, the major respiratory quinone was MK-6 and the DNA G+C content was 35 mol%. On the basis of its distinct phenotypic traits and the phylogenetic distance between this marine isolate and other recognized taxa, strain MTT-39(T) represents a novel genus and species of the family Flavobacteriaceae, for which the name Fulvibacter tottoriensis gen. nov., sp. nov. is proposed. The type strain of the type species is MTT-39(T) (=NBRC 102624(T)=KCTC 22214(T)=CGMCC 1.7058(T)). PMID:18599714

  5. Tenacibaculum soleae sp. nov., isolated from diseased sole (Solea senegalensis Kaup).

    Piñeiro-Vidal, Maximino; Carballas, Cristina G; Gómez-Barreiro, Oscar; Riaza, Ana; Santos, Ysabel

    2008-04-01

    A novel Gram-negative, rod-shaped, gliding bacterial strain designated LL04 12.1.7T was isolated from diseased sole (Solea senegalensis Kaup) in Galicia, Spain. Colonies were yellow-pigmented with uneven edges and did not adhere to the agar. The DNA G+C content of the strain was 29.8 mol%. 16S rRNA gene sequence similarity analysis indicated that strain LL04 12.1.7T is a member of the genus Tenacibaculum in the family Flavobacteriaceae. Sequence similarities between the isolate and the type strains of other members of the genus were 96.7-94.8 %. The major fatty acids (>10 % of total fatty acids) were iso-C15 : 0 (23.1 %), iso-C15 : 0 3-OH (10.6 %), C15 : 1 omega 6c (12.2 %) and summed feature 3 (comprising C16 : 1 omega 7c and/or iso-C15 : 0 2-OH, 11.0 %). Genotypic and phenotypic data distinguished strain LL04 12.1.7T from the 11 recognized Tenacibaculum species, indicating that it represents a novel species, for which the name Tenacibaculum soleae sp. nov. is proposed. The type strain is strain LL04 12.1.7T (=CECT 7292T =NCIMB 14368T). PMID:18398187

  6. Hannaella pagnoccae sp. nov., a tremellaceous yeast species isolated from plants and soil.

    Landell, Melissa Fontes; Brandão, Luciana R; Barbosa, Anne C; Ramos, Jesus P; Safar, Silvana V B; Gomes, Fatima C O; Sousa, Francisca M P; Morais, Paula B; Broetto, Leonardo; Leoncini, Orílio; Ribeiro, José Roberto; Fungsin, Bundit; Takashima, Masako; Nakase, Takashi; Lee, Ching-Fu; Vainstein, Marilene H; Fell, Jack W; Scorzetti, Gloria; Vishniac, Helen S; Rosa, Carlos A; Valente, Patricia

    2014-06-01

    Several independent surveys of yeasts associated with different plant materials and soil led to the proposal of a novel yeast species belonging to the Tremellales clade (Agaricomycotina, Basidiomycota). Analysis of the sequences of the D1/D2 domains and internal transcribed spacer region of the large subunit of the rRNA gene suggested affinity to a phylogenetic lineage that includes Hannaella coprosmaensis, Hannaella oryzae and Hannaella sinensis. Thirty-two isolates were obtained from different sources, including bromeliads, nectar of Heliconia psittacorum (Heliconiaceae), flowers of Pimenta dioica (Myrtaceae), roots and leaves of sugar cane (Saccharum spp.) in Brazil, leaves of Cratoxylum maingayi, Arundinaria pusilla and Vitis vinifera in Thailand, soil samples in Taiwan, and prairie soil in the USA. Sequence analysis of the D1/D2 domains of the large subunit of the rRNA gene showed that the novel species differs from Hannaella coprosmaensis and Hannaella oryzae by 36 and 46 nt substitutions, respectively. A novel species is suggested to accommodate these isolates, for which the name Hannaella pagnoccae sp. nov. is proposed. The type strain is BI118(T) ( = CBS 11142(T) = ATCC MYA-4530(T)). PMID:24614844

  7. Isolation and classification of a novel marine Bacteroidetes as Frondibacter aureus gen. nov., sp. nov.

    Yoon, Jaewoo; Adachi, Kyoko; Kasai, Hiroaki

    2015-02-01

    A facultatively anaerobic, Gram-stain negative, golden-yellow pigmented, non-motile and rod-shaped bacterium, designated strain A5Q-67(T) was isolated from leaf litter collected at the mangrove estuary of Nakama River, Japan. Phylogenetic analysis based on the 16S rRNA gene sequence revealed the novel isolate was affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (94.2 %) to Imtechella halotolerans K1(T). The strain could be differentiated phenotypically from recognized members of the family Flavobacteriaceae. The major fatty acids of strain A5Q-67(T) were identified as iso-C17:0 3-OH, summed feature 1 (iso-C15:1 H and/or C13:0 3-OH) and iso-C15:0 as defined by the MIDI system. The DNA G+C content was determined to be 36.7 mol%, the major respiratory quinone was identified as menaquinone 6 (MK-6) and a polar lipid profile was present consisting of phosphatidylethanolamine, two unidentified aminolipids and an unidentified lipid. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus for which the name Frondibacter aureus gen. nov., sp. nov. is proposed. The type strain of F. aureus is A5Q-67(T) (=KCTC 32991(T) = NBRC 110021(T)). PMID:25385000

  8. Isolation and identification of an endophytic fungus Pezicula sp. in Forsythia viridissima and its secondary metabolites.

    Wang, Jiaying; Wang, Guoping; Zhang, Yalei; Zheng, Biqiang; Zhang, Chulong; Wang, Liwei

    2014-10-01

    In a survey of endophytic fungal biodiversity, an antimicrobial endophytic isolate zjwcf069 was obtained from twigs of Forsythia viridissima, Zhejiang Province, Southeast China. Zjwcf069 was then identified as Pezicula sp. through combination of morphological and phylogenetic analysis based on ITS-rDNA. Zjwcf069 here represented the first endophytic fungus in Pezicula isolated from host F. viridissima. From the fermentation broth, four compounds were obtained through silica gel column chromatography and Sephadex LH-20 under the guide of bioassay. Their structures were elucidated by spectroscopic analysis as mellein (1), ramulosin (2), butanedioic acid (3), and 4-methoxy-1(3H)-isobenzofuranone (4). Compound 4 here stood for the very first time as natural product from microbes. In vitro antifungal assay showed that compound 1 displayed growth inhibition against 9 plant pathogenic fungi, especially Botrytis cinerea and Fulvia fulva with EC50 values below 50 μg/mL. Endophytic fungi in medicinal plants were good resources for bioactive secondary metabolites. PMID:24928260

  9. Cloning and Expression of the PHA Synthase Gene From a Locally Isolated Chromobacterium sp. USM2

    Bhubalan, K.

    2010-01-01

    Full Text Available Chromobacterium sp. USM2, a locally isolated bacterium was found to synthesize poly(3-hydroxybutyrate-co-3-hydroxyvalerate, P(3HB-co-3HV copolymer with high 3HV monomer composition. The PHA synthase gene was cloned and expressed in Cupriavidus necator PHB¯4 to investigate the possibilities of incorporating other monomer. The recombinant successfully incorporated 3-hydroxyhexanoate (3HHx monomer when fed with crude palm kernel oil (CPKO as the sole carbon source. Approximately 63 ± 2 wt% of P(3HB-co-3HHx copolymer with 4 mol% of 3HHx was synthesized from 5 g/L of oil after 48 h of cultivation. In addition, P(3HB-co-3HV-co-3HHx terpolymer with 9 mol% 3HV and 4 mol% 3HHx could be synthesized with a mixture of CPKO and sodium valerate. The presence of 3HV and 3HHx monomers in the copolymer and terpolymer was further confirmed with +H-NMR analysis. This locally isolated PHA synthase has demonstrated its ability to synthesize P(3HB-co-3HHx copolymer from a readily available and renewable carbon source; CPKO, without the addition of 3HHx precursors.

  10. Biodecolorization and biodegradation potential of recalcitrant triphenylmethane dyes by Coriolopsis sp. isolated from compost.

    Chen, Si Hui; Yien Ting, Adeline Su

    2015-03-01

    Triphenylmethane dyes (TPM) are recalcitrant colorants brought into the environment. In this study, a lesser-known white rot fungus Coriolopsis sp. (1c3), isolated from compost of Empty Fruit Bunch (EFB) of oil palm, was explored for its decolorization potential of TPM dyes. The isolate 1c3 demonstrated good decolorization efficiencies in the treatment of Crystal Violet (CV; 100 mg l(-1)), Methyl Violet (MV; 100 mg l(-1)) and Cotton Blue (CB; 50 mg(-1)), with 94%, 97% and 91%, within 7, 7 and 1 day(s), respectively. Malachite Green (MG; 100 mg l(-1)) was the most recalcitrant dye, with 52% decolorization after 9 days. Dye removal by 1c3 was presumably via biosorption, whereby the process was determined to be influenced by fungal biomass, initial dye concentrations and oxygen requirements. Biodegradation was also a likely mechanism responsible for dye removal by 1c3, occurred as indicated by the reduction of dye spectra peaks. Detection of laccase, lignin peroxidase and NADH-DCIP reductase activities further substantiate the possible occurrence of biodegradation of TPM dyes by 1c3. PMID:25527986

  11. Biodegradation of dimethyl phthalate by Sphingomonas sp. isolated from phthalic-acid-degrading aerobic granules.

    Zeng, Ping; Moy, Benjamin Yan-Pui; Song, Yong-Hui; Tay, Joo-Hwa

    2008-10-01

    Phthalic acid esters (PAEs) contamination in water, air, and soil is one of the major environmental concerns in many countries. Besides the PAE biodegradation process, the PAE degrading bacteria have become one of the focuses of study. This study reports the successful isolation of one kind of indigenous bacterium PA-02 from phthalic acid (PA)-degrading aerobic granules. Based on its 16S ribosomal DNA sequence, isolate PA-02 was identified as Sphingomonas genus with 100% similarity to Sphingomonas sp. strain D84532. Strain PA-02 was a Gram-negative, rod-shaped bacterium with strong auto-aggregation ability. In particular, the strain PA-02 possessed PAE-degrading ability without acclimation. Results of growth tests showed that strain PA-02 could degrade dimethyl phthalate (DMP), dibutyl phthalate, and diethylhexyl phthalate. The specific degradation rates of DMP and PA were concentration-dependent with maximum values of 0.4 g-DMP g(-1) biomass h(-1) and 1.3 g-PA g(-1) biomass h(-1), respectively. Kinetic studies also revealed that PA-02 was robust under high concentrations of DMP and PA. Even when the PA concentration was increased to 1,000.0 mg l(-1), the specific PA degradation rate was about 0.25 g-PA g(-1) biomass h(-1). The corresponding value for DMP was 0.067 g-DMP g(-1) biomass h(-1) at 1,000 mg l(-1). PMID:18751698

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

    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 no...

  13. Phytoactinopolyspora alkaliphila sp. nov., an alkaliphilic actinomycete isolated from a saline-alkaline soil.

    Zhang, Yong-Guang; Lu, Xin-Hua; Ding, Yan-Bo; Zhou, Xing-Kui; Li, Li; Guo, Jian-Wei; Wang, Hong-Fei; Duan, Yan-Qing; Li, Wen-Jun

    2016-05-01

    An alkaliphilic, filamentous actinomycete, designated EGI 80629T, was isolated from a soil sample of Xinjiang, north-west China. Strain EGI 80629T grew at pH 6.0-11.0 (optimum pH 9.0-10.0) and in the presence of 0-13.0 % NaCl (optimum 3.0-5.0 %). The isolate formed fragmented substrate mycelia, and aerial hyphae with short spore chains with rod-like spores. Whole-cell hydrolysates of the isolate contained ll-diaminopimelic acid as the diagnostic diamino acid, and mannose and rhamnose as diagnostic sugars. The major fatty acids identified were iso-C15 : 0, iso-C16 : 0, anteiso-C15 : 0 and iso-C17 : 0. The predominant menaquinone was MK-9(H4), while the polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two phosphatidylinositol mannosides, five unknown phospholipids, three unknown phosphoglycolipids, one unknown glycolipid, four unknown polar lipids and one unknown aminophospholipid. The G+C content of the genomic DNA was 67.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain EGI 80629T clustered with the genus Phytoactinopolyspora. The 16S rRNA gene sequence similarity between strain EGI 80629T and Phytoactinopolyspora endophytica EGI 60009T was 96.8 %. Based on morphological, chemotaxonomic and phylogenetic characteristics, strain EGI 80629T represents a novel species of the genus Phytoactinopolyspora, for which the name Phytoactinopolyspora alkaliphila sp. nov. is proposed. The type strain is EGI 80629T ( = CGMCC 4.7225T = KCTC 39701T). PMID:26920762

  14. Pseudorhodoplanes sinuspersici gen. nov., sp. nov., isolated from oil-contaminated soil.

    Tirandaz, Hassan; Dastgheib, Seyed Mohammad Mehdi; Amoozegar, Mohammad Ali; Shavandi, Mahmoud; de la Haba, Rafael R; Ventosa, Antonio

    2015-12-01

    Strain RIPI 110T was isolated from a soil sample collected from an oil-contaminated site on Siri Island, Persian Gulf, Iran. Cells of the novel isolate were Gram-stain-negative, facultatively anaerobic, non-motile and rod-shaped. Cells divided asymmetrically by budding and formed rosette-like clusters. The optimum pH and temperature for growth were pH 7 and 30 °C, while the strain was able to grow at pH 5.5-8 and 15-35 °C. Strain RIPI 110T utilized only complex carbon sources and pyruvate as the sole carbon source and could not grow under photoautotrophic conditions. The highest 16S rRNA gene sequence similarities, 93.9, 93.9 and 93.5 %, were obtained with Variibacter gotjawalensis GJW-30T, Rhodoplanes roseus 941T and Rhodoplanes elegans AS130T, respectively. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c/ω6c), C16 : 0 and C19 : 0 cyclo ω8c. Polar lipid analyses revealed that strain RIPI 110T contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, an unknown aminophospholipid and four unknown phospholipids. Ubiquinone-10 was the predominant quinone component. The DNA G+C content was 59.4 mol%. On the basis of the 16S rRNA gene sequence analysis, in combination with chemotaxonomic and physiological data, the novel isolate could not be classified in any recognized genera. Strain RIPI 110T is thus considered to represent a novel species of a new genus within the order Rhizobiales, for which the name Pseudorhodoplanes sinuspersici gen. nov., sp. nov. is proposed. The type strain of the type species is RIPI 110T ( = IBRC-M 10770T = CECT 8374T). PMID:26420766

  15. Erythrobacter pelagi sp. nov., a member of the family Erythrobacteraceae isolated from the Red Sea

    Wu, H.-x.

    2011-08-05

    A novel Gram-negative, aerobic, catalase- and oxidase-positive, non-sporulating, non-motile, rod-shaped bacterium, designated strain UST081027-248(T), was isolated from seawater of the Red Sea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain UST081027-248(T) fell within the genus Erythrobacter. Levels of 16S rRNA gene sequence similarity between the novel strain and the type strains of Erythrobacter species ranged from 95.3% (with Erythrobacter gangjinensis) to 98.2% (with Erythrobacter citreus). However, levels of DNA-DNA relatedness between strain UST081027-248(T) and the type strains of closely related species were below 70%. Optimal growth of the isolate occurred in the presence of 2.0% NaCl, at pH 8.0-9.0 and at 28-36 degrees C. The isolate did not produce bacteriochlorophyll a. The predominant cellular fatty acids were C-17:1 omega 6c, summed feature 8 (C-18:1 omega 6c and/or C-18:1 omega 7c) and C-15:0 2-OH. The genomic DNA G+C content of strain UST081027-248(T) was 60.4 mol%. Phenotypic properties and phylogenetic distinctiveness clearly indicated that strain UST081027-248(T) represents a novel species of the genus Erythrobacter, for which the name Erythrobacter pelagi sp. nov. is proposed. The type strain is UST081027-248(T) (=JCM 17468(T)=NRRL 59511(T)).

  16. Psychroglaciecola arctica gen. nov., sp. nov., isolated from Arctic glacial foreland soil.

    Qu, Zhihao; Jiang, Fan; Chang, Xulu; Qiu, Xia; Ren, Lvzhi; Fang, Chengxiang; Peng, Fang

    2014-05-01

    A novel pink-pigmented, facultatively methylotrophic strain, designated M6-76T, was isolated from glacial foreland soil near Ny-Ålesund, Svalbard Archipelago, Norway. Cells of strain M6-76T were rod-shaped (0.4-0.7×0.8-2.0 µm), Gram-stain-negative, aerobic and motile by a single polar flagellum. Growth occurred at 4-28 °C (optimum 18 °C) and at pH 5-8 (optimum pH 7). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain M6-76T belonged to the family Methylobacteriaceae. The 16S rRNA gene sequence of the novel strain showed 94.6%, 94.0% and 93.9% sequence similarity to those of Methylobacterium salsuginis MRT, Methylobacterium organophilum ATCC 27886T and Microvirga subterranea FaiI4T, respectively. Cells could utilize methanol as the sole source of carbon and energy but not formate. The major respiratory quinone was Q-10. The polar lipids were phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and two unknown polar lipids. The predominant cellular fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c), summed feature 3 (C16:1ω6c and/or C16:1ω7c) and C16:0. The DNA G+C content was 67 mol%. The polyphasic data presented in this study indicated that the isolate should be classified as representing a novel species of a new genus within the family Methylobacteriaceae. The name Psychroglaciecola arctica gen. nov., sp. nov. is therefore proposed for the isolate. The type strain of the type species is M6-76T (=CCTCC AB 2013033T=KACC 17684T). PMID:24556636

  17. Isolation and characterization of Pseudoalteromonas sp. from fermented Korean food, as an antagonist to Vibrio harveyi.

    Morya, V K; Choi, Wooyoung; Kim, Eun-Ki

    2014-02-01

    The microbial intervention for sustainable management of aquaculture, especially use of probiotics, is one of the most popular and practical approaches towards controlling pathogens. Vibrio harveyi is a well-known pathogenic bacterium, which is associated to a huge economic loss in the aquaculture system by causing vibriosis. The present study is crafted for screening and characterization of anti-Vibrio strains, which were isolated from various traditional fermented Korean foods. A total of 196 strains have been isolated from soybean paste (78 strains), red chili paste (49 strains), soy sauce (18 strains), jeotgal-a salted fish (34 strains), and the gazami crab-Portunus trituberculatus (17 strains). Fifteen strains showed an inhibitory effect on the growth of V. harveyi when subjected to coculture condition. Among the strains isolated, one has been identified as a significant anti-Vibrio strain. Further biochemical characterization and 16S rDNA sequencing revealed it as Pseudoalteromonas aliena, which had been deposited at the Korean Culture Center of Microorganisms (KCCM), Korea and designated as KCCM 11207P. The culture supernatants did not have any antimicrobial properties either in pure or in coculture condition. The culture supernatant was not toxic when supplemented to the swimming crab, Zoea, and Artemia larvae in aquaculture system. The results were very encouraging and showed a significant reduction in accumulated mortality. Here, we reported that pathogenic vibriosis can be controlled by Pseudoalteromonas sp. under in vitro and in vivo conditions. The results indicated that the biotic treatment offers a promising alternative to the use of antibiotics in crab aquaculture. PMID:23793257

  18. Isolation and characterization of Bradyrhizobium sp. SR1 degrading two β-triketone herbicides.

    Romdhane, Sana; Devers-Lamrani, Marion; Martin-Laurent, Fabrice; Calvayrac, Christophe; Rocaboy-Faquet, Emilie; Riboul, David; Cooper, Jean-François; Barthelmebs, Lise

    2016-03-01

    In this study, a bacterial strain able to use sulcotrione, a β-triketone herbicide, as sole source of carbon and energy was isolated from soil samples previously treated with this herbicide. Phylogenetic study based on16S rRNA gene sequence showed that the isolate has 100 % of similarity with several Bradyrhizobium and was accordingly designated as Bradyrhizobium sp. SR1. Plasmid profiling revealed the presence of a large plasmid (>50 kb) in SR1 not cured under nonselective conditions. Its transfer to Escherichia coli by electroporation failed to induce β-triketone degrading capacity, suggesting that degrading genes possibly located on this plasmid cannot be expressed in E. coli or that they are not plasmid borne. The evaluation of the SR1 ability to degrade various synthetic (mesotrione and tembotrione) and natural (leptospermone) triketones showed that this strain was also able to degrade mesotrione. Although SR1 was able to entirely dissipate both herbicides, degradation rate of sulcotrione was ten times higher than that of mesotrione, showing a greater affinity of degrading-enzyme system to sulcotrione. Degradation pathway of sulcotrione involved the formation of 2-chloro-4-mesylbenzoic acid (CMBA), previously identified in sulcotrione degradation, and of a new metabolite identified as hydroxy-sulcotrione. Mesotrione degradation pathway leads to the accumulation of 4-methylsulfonyl-2-nitrobenzoic acid (MNBA) and 2-amino-4 methylsulfonylbenzoic acid (AMBA), two well-known metabolites of this herbicide. Along with the dissipation of β-triketones, one could observe the decrease in 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibition, indicating that toxicity was due to parent molecules, and not to the formed metabolites. This is the first report of the isolation of bacterial strain able to transform two β-triketones. PMID:25903192

  19. Meiothermus roseus sp. nov., a thermophilic bacterium isolated from a geothermal area.

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

    2015-10-01

    Two closely related thermophilic bacterial strains, designated YIM 71031(T) and YIM 71039, were isolated from a hot spring in Tengchong county, Yunnan province, south-western China. The novel isolates were observed to be Gram-negative, aerobic, rod-shaped and yellow-pigmented bacteria. The strains were found to be able to grow at 37-65 °C, pH 6.0-9.0 and with a NaCl tolerance up to 1.0 % (w/v). Phylogenetic analysis based on 16S rRNA gene sequences placed these two isolates in the genus Meiothermus. They were found to be closely related to Meiothermus timidus DSM 17022(T) (98.6 % similarity), and formed a cluster with this species. The predominant menaquinone was identified as MK-8 and the major fatty acids (>10 %) as anteiso-C15:0, iso-C15:0, anteiso-C17:0, iso-C16:0 and C16:0. The genomic DNA G+C contents of strains YIM 71031(T) and YIM 71039 were determined to be 64.0 and 65.4 mol%, respectively. DNA-DNA hybridizations showed low values between strains YIM 71031(T) and YIM 71039 and their closely related neighbour M. timidus DSM 17022(T). Morphological phylogenetic and chemotaxonomic results suggest that strains YIM 71031(T) and YIM 71039 are representatives of a new species within the genus Meiothermus, for which the name Meiothermus roseus sp. nov. is proposed. The type strain is YIM 71031(T) (=KCTC 42495(T) =NBRC 110900(T)). PMID:26219565

  20. A potent fish pathogenic bacterial killer Streptomyces sp. isolated from the soils of east coast region, South India

    Durairaj Thirumurugan; Ramasamy Vijayakumar

    2013-01-01

    Objective: To investigate the potentiality of the marine actinobacteria isolated from marine soil against fish pathogenic bacteria.Methods:east coast region (ECR) of Tamilnadu, South India. Then they were used for the isolation of actinobacteria by using conventional serial dilution technique on starch casein agar medium. The antibacterial activities of the actinobacteria were screened primarily by using cross streak plate method against fish pathogenic bacteria namely Vibrio alginolyticus, Vibrio parahaemolyticus,Vibrio cholera, Aeromonas sp. and Pseudomonas sp. The antimicrobial efficacy of the selected isolates was carried out with various organic solvents, and finally the active compound was subjected to chromatographic techniques including TLC and GC-MS.Results:In the present study, a total of 33 soil samples were collected from the Bay of Bengal, against fish pathogenic bacteria. Out of 21 antibacterial isolates, the isolate ECR77 was selected for further study based on its potential activity against fish pathogenic bacteria. Of the various solvents tested, the ethyl acetate extract had good antibacterial activity against the tested bacterial pathogens. The isolate ECR77 grew well on oat meal agar medium with 2% salt level at 35 °C. GC-MS study found that the presence of bioactive compounds namely tetradecanoic acid,n-hexadecanoic acid and octadecanoic acid. The morphological, physiological, biochemical and cultural characteristics of the potential isolate were supported the identity up to generic level asStreptomyces sp. ECR77. Conclusions: The results obtained from this study concludes that the ECR soils of South India is a hot spot of novel bioactive compound producing marine actinobacteria with great pharmaceutical values. Of the 82 actinobacteria isolated, 21 (26%) isolates were possessed antibacterial activity.

  1. Cloning and characterization of newly isolated lipase from Enterobacter sp. Bn12.

    Farrokh, Parisa; Yakhchali, Bagher; Karkhane, Ali Asghar

    2014-01-01

    A mesophilic Enterobacter sp. Bn12 producing an alkaline thermostable lipase was isolated from soil in Tehran, Iran. The lipase gene (ELBn12) was identified from a genomic library. Sequence analysis of the DNA fragment revealed an open reading frame of 879 bp encoding a lipase with a molecular mass of 31.3 kDa. The deduced amino acid sequence showed 96% identity with a lipase of Enterobacter sp. Ag1 and the identity of their DNA sequences was 88.9%. ELBn12 belongs to the lipase subfamily I.1 and its catalytic triad consists of Ser82, Asp237 and His259. The lipase was expressed in Escherichia coli (BL21) pLysS and partially purified by anion exchange chromatography. The maximum activity of ELBn12 was obtained at temperature of 60 °C and pH 8.0 towards tricaprylin (C8) and its specific activity was around 2900 U/mg. ELBn12 was stable within a broad pH range from 6.0 to 11.0. The enzyme showed high stability in both polar and nonpolar organic solvents at 50% (v/v). The lipase activity was enhanced in the presence of 10 mM of Ca(2+), Mg(2+) and K(+), while heavy metals (Fe(3+) and Zn(2+)) had strong inhibitory effect. ELBn12 showed high activity in the presence of 1% (w/v) nonionic surfactants, however ionic surfactants inhibited the lipolytic activity. ELBn12 characteristics show that it has a potential to be used in various industrial processes. PMID:25242958

  2. Isolation and characterization of Staphylococcus sp. strain NBRIEAG-8 from arsenic contaminated site of West Bengal

    Srivastava, Shubhi; Singh, Namrata; Singh, Nandita [CSIR - National Botanical Research Institute, Lucknow, UP (India). Eco-auditing Lab.; Verma, Praveen C.; Singh, Ankit; Mishra, Manisha [CSIR - National Botanical Research Institute, Lucknow, UP (India). Plant Molecular Biology and Genetic Engineering; Sharma, Neeta [Lucknow Univ., UP (India). Plant Pathology Lab.

    2012-09-15

    Arsenic contaminated rhizospheric soils of West Bengal, India were sampled for arsenic resistant bacteria that could transform different arsenic forms. Staphylococcus sp. NBRIEAG-8 was identified by16S rDNA ribotyping, which was capable of growing at 30,000 mg l{sup -1} arsenate [As(V)] and 1,500 mg l{sup -1} arsenite [As(III)]. This bacterial strain was also characterized for arsenical resistance (ars) genes which may be associated with the high-level resistance in the ecosystems of As-contaminated areas. A comparative proteome analysis was conducted with this strain treated with 1,000 mg l{sup -1} As(V) to identify changes in their protein expression profiles. A 2D gel analysis showed a significant difference in the proteome of arsenic treated and untreated bacterial culture. The change in pH of cultivating growth medium, bacterial growth pattern (kinetics), and uptake of arsenic were also evaluated. After 72 h of incubation, the strain was capable of removing arsenic from the culture medium amended with arsenate and arsenite [12% from As(V) and 9% from As(III)]. The rate of biovolatilization of As(V) was 23% while As(III) was 26%, which was determined indirectly by estimating the sum of arsenic content in bacterial biomass and medium. This study demonstrates that the isolated strain, Staphylococcus sp., is capable for uptake and volatilization of arsenic by expressing ars genes and 8 new upregulated proteins which may have played an important role in reducing arsenic toxicity in bacterial cells and can be used in arsenic bioremediation. (orig.)

  3. Pseudozyma vetiver sp. nov., a novel anamorphic ustilaginomycetous yeast species isolated from the phylloplane in Thailand.

    Chamnanpa, Thunnicha; Limtong, Pitayakon; Srisuk, Nantana; Limtong, Savitree

    2013-11-01

    Three strains representing one novel yeast species were isolated from the phylloplanes of the vetiver grasses (DMKU-LV90 and DMKU-LV99(T)) and sugarcane (DMKU-SP260) collected in Thailand by leaf washing followed by a plating technique. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics and the sequence analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer region (ITS), the three strains were found to represent a single novel anamorphic ustilaginomycetous yeast species in the genus Pseudozyma. The name Pseudozyma vetiver sp. nov. is proposed for this novel species. The type strain is DMKU-LV99(T) (BCC 61021 = CBS 12824). The novel species showed phylogenetic relationships to the other members of the genus Pseudozyma and to teleomorphic fungal genera, namely Ustilago, Sporisorium and Anomalomyces in Ustilaginaceae, Ustilaginales. The three strains showed identical sequences both in the D1/D2 and ITS regions. The Pseudozyma species closest to the novel species in terms of pairwise sequence similarity in the D1/D2 region was Pseudozyma pruni but with 2.3 % nucleotide substitutions (14 nucleotide substitutions and no gaps out of 606 nt). The novel species and P. pruni differed by 10.9 % nucleotide substitutions (75 nucleotide substitutions and 31 gaps out of 691 nt) in the ITS region. The phylogenetic analysis based on the combined sequences of the ITS region and the D1/D2 region of the LSU rRNA gene showed that the novel species was found to be most closely related to Pseudozyma fusiformata but with 2.9 % nucleotide substitutions in the D1/D2 region and 7.4 % nucleotide substitutions in the ITS region. PMID:23877892

  4. Bradyrhizobium ingae sp. nov., isolated from effective nodules of Inga laurina grown in Cerrado soil.

    da Silva, Krisle; De Meyer, Sofie E; Rouws, Luc F M; Farias, Eliane N C; dos Santos, Marco A O; O'Hara, Graham; Ardley, Julie K; Willems, Anne; Pitard, Rosa Maria; Zilli, Jerri E

    2014-10-01

    Root-nodule bacteria were isolated from Inga laurina (Sw.) Willd. growing in the Cerrado Amazon region, State of Roraima, Brazil. The 16S rRNA gene sequences of six strains (BR 10250(T), BR 10248, BR 10249, BR 10251, BR 10252 and BR 10253) showed low similarities with currently described species of the genus Bradyrhizobium. Phylogenetic analyses of sequences of five housekeeping genes (dnaK, glnII, gyrB, recA and rpoB) revealed Bradyrhizobium iriomotense EK05(T) to be the closest type strain (97.4% sequence similarity or less). Chemotaxonomic data, including fatty acid profiles [with the major components C16:0 and summed feature 8 (C18:1ω6c/C18:1ω7c)], the slow growth rate and carbon compound utilization patterns supported the assignment of our strains to the genus Bradyrhizobium. Results from DNA-DNA hybridizations and physiological traits differentiated our strains from the closest related species of the genus Bradyrhizobium with validly published names. Sequences of symbiosis-related genes for nodulation (nodC) and nitrogen fixation (nifH) grouped together with those of B. iriomotense EK05(T) and Bradyrhizobium sp. strains BR 6610 (used as a commercial inoculant for Inga marginata in Brazil) and TUXTLAS-10 (previously observed in Central America). Based on these data, the six strains represent a novel species, for which the name Bradyrhizobium ingae sp. nov. is proposed. The type strain is BR 10250(T) ( = HAMBI 3600(T)). PMID:25013231

  5. Isolation and characterization of fatty acid methyl ester (FAME)-producing Streptomyces sp. S161 from sheep (Ovis aries) faeces.

    Lu, Y; Wang, J; Deng, Z; Wu, H; Deng, Q; Tan, H; Cao, L

    2013-09-01

    An actinomycete producing oil-like mixtures was isolated and characterized. The strain was isolated from sheep faeces and identified as Streptomyces sp. S161 based on 16S rRNA gene sequence analysis. The strain showed cellulase and xylanase activities. The (1) H nuclear magnetic resonance (NMR) spectra of the mixtures showed that the mixtures were composed of fatty acid methyl esters (52·5), triglycerides (13·7) and monoglycerides (9·1) (mol.%). Based on the gas chromatography-mass spectrometry (GC-MS) analysis, the fatty acid methyl esters were mainly composed of C14-C16 long-chain fatty acids. The results indicated that Streptomyces sp. S161 could produce fatty acid methyl esters (FAME) directly from starch. To our knowledge, this is the first isolated strain that can produce biodiesel (FAME) directly from starch. PMID:23692633

  6. Molecular Characterization of Isolated Xanthomonas sp. From Rice Rhizosphere Soil and their Inhibition using Clerodendrum viscosum Vent

    In this study, we characterized some Xanthomonas sp. from rice rhizosphere soil by 16S rDNA sequence analysis and the potentiality tested of oil and extracts of Clerodendrum viscosum Vent. leaves against those isolated bacteria. The essential oil compositions were evaluated by GC-MS analysis and identified twenty four compounds as 94.37% of the total essential oil, where cyclohepta-1,3,5,-triene (16.07%), 2H-1,4-pyridoxazin-3(4H)-one (12.27%), L-carvenol (8.04%), p-cymene (9.15%), alpha-terpineol (7.98%), beta-sitosterol (6.76%), tyranton (6.42%), mesityl oxide (6.34%), gamma-terpinene (5.42%) and beta-linalool (3.74%) were the major constituents. According to the 16S rDNA sequences analysis, Hb28 and Xb43 isolates have shown the 100% similarity for Xanthomonas retroflexus and Xanthomonas theicola. In addition, isolates Ha18, Xb33 and Jb30 also have shown the maximum similarity of 98% for Xanthomonas sp. TB8-9-II, Xanthomonas campestris and Xanthomonas sp. BBCT38. Furthermore, in vitro studies showed that the oil have the inhibitory effect on Xanthomonas sp. TB8-9-II, X. campestris, X. retroflexus, Xanthomonas sp. BBCT38, and X. theicola, where the zone of inhibition and MIC values were 18.8 to 25.9 mm and 62.5 to 125 meu g ml/sup -1/, respectively. However, organic extracts showed the zone of inhibition and MIC values were 13.4 to 22.9 and 62.5 to 500 meu g ml-1, respectively. Our findings suggested that the essential oil and extracts of C. viscosum Vent. leaves might be the effective source to control Xanthomonas sp. biologically. (author)

  7. Simultaneous heterotrophic nitrification and aerobic denitrification at high initial phenol concentration by isolated bacterium Diaphorobacter sp. PD-7

    Qilong Ge; Xiuping Yue; Guoying Wang

    2015-01-01

    A strain capable of phenol degradation, heterotrophic nitrification and aerobic denitrification was isolated from activated sludge of coking-plant wastewater ponds under aerobic condition. Based on its morphology, physiology, biochemical analysis and phylogenetic characteristics, the isolate was identified as Diaphorobacter sp. PD-7. Biodegradation tests of phenol showed that the maximum phenol degradation occurred at the late phase of exponential growth stages, with 1400 mg·L-1 phenol completely degraded within 85 h. Diaphorobacter sp. PD-7 accumulated a vast quantity of phenol hydroxylase in this physiological phase, ensuring that the cel s quickly utilize phenol as a sole carbon and energy source. The kinetic behavior of Diaphorobacter sp. PD-7 in batch cultures was investigated over a wide range of initial phenol concentrations (0–1400 mg·L-1) by using the Haldane model, which adequately describes the dynamic behavior of phenol biodegradation by strain Diaphorobacter sp. PD-7. At initial phenol concentration of 1400 mg·L-1, batch experiments (0.25 L flask) of nitrogen removal under aerobic condition gave almost entirely removal of 120.69 mg·L-1 ammonium nitrogen within 75 h, while nitrate nitrogen removal reached 91%within 65 h. Moreover, hydroxylamine oxidase, periplasmic nitrate reductase and nitrite reductase were successful y expressed in the isolate.

  8. Cloning of Thermostable DNA Polymerase Gene from a Thermophilic Brevibacillus sp. Isolated from Sikidang Crater, Dieng Plateu, Central Java

    Lucia Dhiantika Witasari

    2015-11-01

    Full Text Available Thermostable DNA polymerase has an important role for amplifying small amount of DNA through polymerase chain reaction (PCR. Thermophillic bacteria Brevibacillus sp. was isolated from Sikidang Crater, Dieng Plateu, Central Java. Previous study showed that crude protein of the isolate could be used in PCR. Unfortunately, like most native thermostable enzymes, the thermostable DNA polymerase of the isolate is synthesized in a very low level and therefore is cumbersome to purify. The purpose of this research is to clone thermostable DNA polymerase gene of the isolate. The DNA polymerase gene was amplified by means of PCR using spesific primers. The amplified fragment was then isolated, purified, and ligated into the pGEM-T cloning vector. The recombinant plasmid was then transformed to competent E. coli JM109 cells using heat shock method. The cloned thermostable DNA polymerase gene from the thermophilic isolate was then characterized for its nucleotide base sequence. The result showed that the DNA Pol I gene was successfully be amplified from the isolate DNA genom, resulting in ± 2,7 kb DNA fragment in length. Sequence analysis of segment of targeted gene showed high similarity to that of thermostable DNA polymerase genes from other Bacillus.Key words : Thermostable DNA Pol I, Brevibacillus sp., PCR, cloning

  9. Complete genome sequence of the novel thermophilic polyhydroxyalkanoates producer Aneurinibacillus sp. XH2 isolated from Gudao oilfield in China.

    Xi, Lijun; Zhang, Zhenchong; Qiao, Nenghu; Zhang, Yu; Li, Jing; Zhao, Jing-Yi; Xiao, Zijun

    2016-06-10

    Aneurinibacillus sp. XH2 (CGMCC 1.15535) was isolated from Gudao oilfield in China. It is able to use simple carbon resources to accumulate Polyhydroxyalkanoates (PHAs) in a thermophilic fashion. Here, we describe the genomic features of this strain. The total genome size of Aneurinibacillus sp. XH2 is 3,664,835bp and contains 3441 coding sequences and 114 tRNAs. The annotated genome sequence of this strain provides the genetic basis for revealing its role as a themophilic PHAs producing bacterium. PMID:27046067

  10. Halomonas sp. BS4, A biosurfactant producing halophilic bacterium isolated from solar salt works in India and their biomedical importance

    Donio, Mariathason Birdilla Selva; Ronica, Fernando Arul; Viji, Vijayaragavan Thanga; Velmurugan, Subramanian; Jenifer, John Selesteen Charles Adlin; Michaelbabu, Mariavincent; Dhar, Prasenjit; Citarasu, Thavasimuthu

    2013-01-01

    Halophilic bacteria were isolated from Thamaraikulam solar salt works in India. After routine biosurfactant screening by various methods, the biosurfactant producing bacteria, Halomonas sp BS4 was confirmed by 16 S rRNA sequencing. The growth optimization of Halomonas sp BS4 revealed their optimum growth at 8% NaCl and 6-8 pH in the growth medium. Further the partially purified biosurfactants were characterized by TLC, FTIR and GC-MS analysis. GC-MS results revealed that, the partial purified...

  11. Antagonistic activities of some Bifidobacterium sp. strains isolated from resident infant gastrointestinal microbiota on Gram-negative enteric pathogens.

    Delcaru, Cristina; Alexandru, Ionela; Podgoreanu, Paulina; Cristea, Violeta Corina; Bleotu, Coralia; Chifiriuc, Mariana Carmen; Bezirtzoglou, Eugenia; Lazar, Veronica

    2016-06-01

    The gastrointestinal microbiota contributes to the consolidation of the anti-infectious barrier against enteric pathogens. The purpose of this study was to investigate the influence of Bifidobacterium sp. strains, recently isolated from infant gastrointestinal microbiota on the in vitro growth and virulence features expression of enteropathogenic bacterial strains. The antibacterial activity of twelve Bifidobacterium sp. strains isolated from human feces was examined in vitro against a wide range of Gram negative pathogenic strains isolated from 30 infant patients (3 days to 5 years old) with diarrhea. Both potential probiotic strains (Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bifidobacterium catenulatum, Bifidobacterium breve, Bifidobacterium ruminantium) and enteropathogenic strains (EPEC, EIEC, Klebsiella pneumoniae, Salmonella sp., Yersinia enterocolitica, Pseudomonas aeruginosa) were identified by MALDI-TOF and confirmed serologically when needed. The bactericidal activity, growth curve, adherence to the cellular HEp-2 substratum and production of soluble virulence factors have been assessed in the presence of different Bifidobacterium sp. cultures and fractions (whole culture and free-cell supernatants). Among the twelve Bifidobacterium sp. strains, the largest spectrum of antimicrobial activity against 9 of the 18 enteropathogenic strains was revealed for a B. breve strain recently isolated from infant intestinal feces. The whole culture and free-cell supernatant of B. breve culture decreased the multiplication rate, shortened the log phase and the total duration of the growth curve, with an earlier entrance in the decline phase and inhibited the adherence capacity to a cellular substratum and the swimming/swarming motility too. These results indicate the significant probiotic potential of the B. breve strain. PMID:26921694

  12. Marinobacterium coralli sp. nov., isolated from mucus of coral (Mussismilia hispida).

    Chimetto, Luciane A; Cleenwerck, Ilse; Brocchi, Marcelo; Willems, Anne; De Vos, Paul; Thompson, Fabiano L

    2011-01-01

    A Gram-negative, aerobic bacterium, designated R-40509(T), was isolated from mucus of the reef builder coral (Mussismilia hispida) located in the São Sebastião Channel, São Paulo, Brazil. The strain was oxidase-positive and catalase-negative, and required Na(+) for growth. Its phylogenetic position was in the genus Marinobacterium and the closest related species were Marinobacterium sediminicola, Marinobacterium maritimum and Marinobacterium stanieri; the isolate exhibited 16S rRNA gene sequence similarities of 97.5-98.0 % with the type strains of these species. 16S rRNA gene sequence similarities with other type strains of the genus Marinobacterium were below 96 %. DNA-DNA hybridizations between strain R-40509(T) and the type strains of the phylogenetically closest species of the genus Marinobacterium revealed less than 70 % DNA-DNA relatedness, supporting the novel species status of the strain. Phenotypic characterization revealed that the strain was able to grow at 15-42 °C and in medium containing up to 9 % NaCl. The isolate could be differentiated from phenotypically related species by several features, including its ability to utilize d-alanine, l-alanine, bromosuccinic acid, β-hydroxybutyric acid and α-ketovaleric acid, but not acetate or l-arabinose. It produced acetoin (Voges-Proskauer), but did not have esterase lipase (C8) or catalase activities. It possessed C(18 : 1)ω7c (35 %), summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c; 25 %) and C(16 : 0) (22 %) as major cellular fatty acids. The DNA G+C content was 58.5 mol%. The name Marinobacterium coralli sp. nov. is proposed to accommodate this novel isolate; the type strain is R-40509(T) (=LMG 25435(T) =CAIM 1449(T)). PMID:20154332

  13. Virgibacillus kapii sp. nov., isolated from Thai shrimp paste (Ka-pi).

    Daroonpunt, Rungsima; Tanasupawat, Somboon; Kudo, Takuji; Ohkuma, Moriya; Itoh, Takashi

    2016-04-01

    A Gram-reaction-positive and rod-shaped bacterium, designated KN3-8-4T, was isolated from shrimp paste collected from a market in Nakhon Sri Thammarat province, Thailand. Strain KN3-8-4T was a strictly aerobic, motile bacterium that produced ellipsoidal endospores at a terminal position. The isolate grew at pH 4.5-10 (optimum pH 7.5), at 11-42 °C (optimum 37 °C) and in the presence of 0-15 % (w/v) NaCl (optimum 1-5 %). On the basis of 16S rRNA gene sequences, strain KN3-8-4T belonged to the genus Virgibacillus and showed highest similarity with Virgibacillus olivae JCM 30551T (97.85 % 16S rRNA gene sequence similarity). The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid and the major isoprenoid quinone was MK-7. Strain KN3-8-4T contained anteiso-C15 : 0 and anteiso-C17 : 0 as major cellular fatty acids and had phosphatidylglycerol, diphosphatidylglycerol, two unknown phospholipids and one glycolipid as polar lipids. The DNA G+C content was 43.5 mol%. Strain KN3-8-4T showed low DNA-DNA relatedness (20.44 %) with V. olivae JCM 30551T. On the basis of phenotypic and chemotaxonomic data and phylogenetic analyses, strain KN3-8-4T represents a novel species of the genus Virgibacillus for which the name Virgibacillus kapii sp. nov. is proposed. The type strain is KN3-8-4T ( = JCM 30071T = LMG 28282T = TISTR 2279T = PCU 345T). PMID:26869011

  14. Bacillus depressus sp. nov., isolated from soil of a sunflower field.

    Wei, Xuexin; Xin, Di; Xin, Yuhua; Zhang, Hao; Wang, Tianying; Zhang, Jianli

    2016-01-01

    A Gram-stain positive, rod-shaped, endospore-forming and aerobic bacterium, designated BZ1(T), was isolated from a soil sample collected from a sunflower field in Wuyuan county, Inner Mongolia, China. On the basis of 16S rRNA gene sequence analysis, the isolate was found to be a member of the genus Bacillus and the close phylogenetic relatives to be Bacillus gottheilii WCC 4585(T), Bacillus oceanisediminis H2(T), Bacillus mesonae FJAT-13985(T) and Bacillus horneckiae DSM 23495(T) with 98.3, 98.1, 98.0 and 97.6 % sequence similarity, respectively. Strain BZ1(T) was found to grow at 6-40 °C (optimum 30-33 °C), pH 6.0-9.0 (optimum pH 7.0) and 0-5.5 % (w/v) NaCl (optimum 0.5 %). The cell wall diamino acid of the peptidoglycan of strain BZ1(T) was identified as meso-diaminopimelic acid and the predominant respiratory quinone as MK-7. The major cellular fatty acids were found to be iso-C15:0, anteiso-C15:0 and iso-C14:0, and the polar lipids to consist of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The novel strain was found to have a DNA G + C content 44.5 mol%. DNA-DNA hybridization with closely related strains was low. Based on phenotypic, phylogenetic and chemotaxonomic results, it is concluded that strain BZ1(T) represents a novel species within the genus Bacillus, for which we propose the name Bacillus depressus sp. nov. The type strain is BZ1(T) (= CGMCC 1.15124(T) = KCTC 33643(T)). PMID:26452774

  15. Tenacibaculum aiptasiae sp. nov., isolated from a sea anemone Aiptasia pulchella.

    Wang, Jih-Terng; Chou, Yi-Ju; Chou, Jui-Hsing; Chen, Chaolun Allen; Chen, Wen-Ming

    2008-04-01

    A novel bacterial strain, designated a4T, isolated from a sea anemone (Aiptasia pulchella) in Taiwan, was characterized using a polyphasic taxonomic approach. Strain a4T was aerobic, Gram-negative, pale-yellow-pigmented and rod-shaped. It grew optimally at 30-35 degrees C, in the presence of 3-4 % (w/v) NaCl and at pH 8.0. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belonged to the genus Tenacibaculum (family Flavobacteriaceae, phylum Bacteroidetes). The closest neighbours were Tenacibaculum lutimaris TF-26T (97.6 % similarity) and Tenacibaculum aestuarii SMK-4T (97.7 % similarity). The novel isolate could be distinguished from all Tenacibaculum species by several phenotypic characteristics. The major fatty acids were summed feature 3 (comprising C16 : 1 omega 7c and/or iso-C15 : 0 2-OH, 19.6 %), iso-C15 : 0 (12.9 %), iso-C16 : 0 3-OH (10.2 %), iso-C17 : 0 3-OH (9.9 %) and iso-C15 : 1 (9.5 %). The DNA G+C content was 35.0 mol%. Hence, genotypic and phenotypic data demonstrate that strain a4(T) should be classified as a representative of a novel species in the genus Tenacibaculum, for which the name Tenacibaculum aiptasiae sp. nov. is proposed. The type strain is a4T (=BCRC 17655T =LMG 24004T). PMID:18398166

  16. Description of Rhodanobacter denitrificans sp. nov., isolated from nitrate-rich zones of a contaminated aquifer

    Prakash, Om [Florida State University, Tallahassee; Green, Stefan [Florida State University, Tallahassee; Jasrotia, Puja [Florida State University, Tallahassee; Overholt, Will [Florida State University, Tallahassee; Canion, Andy [Florida State University, Tallahassee; Watson, David B [ORNL; Brooks, Scott C [ORNL; Kostka, [Georgia Institute of Technology, Atlanta

    2012-01-01

    Bacterial strains 2APBS1T and 116-2 were isolated from the subsurface of a nuclear legacy waste site where sediments are co-contaminated with large amounts of acidity, nitrate, metal radionuclides and other heavy metals. A combination of physiological and genetic assays indicated that these strains represent the first members of the Rhodanobacter genus shown to be capable of complete denitrification. Cells of strain 2APBS1T and 116-2 were Gram negative, non-spore-forming, rods, 3-5 micro;m long and 0.25-0.5 m in diameter. The isolates were facultative anaerobes, and had temperature and pH optima for growth at 30 C and pH 6.5, respectively, and could tolerate up to 2.0 % NaCl, though growth improved in its absence. Strains 2APBS1T and 116-2 contained fatty acid profiles and 100 % Q-8 ubiquinone, that are characteristic features of the genus Rhodanobacter. Although strains 2APBS1T and 116-2 share high SSU rRNA gene sequence similarity to R. thiooxydans (>99%), DNA-DNA hybridization values were substantially below the 70% threshold used to designate novel species. Thus, based on genotypic, phylogenetic, chemotaxonomic and physiological differences, strains 2APBS1T and 116-2 are considered to represent a novel species of the genus Rhodanobacter, for which the name Rhodanobacter denitrificans sp. nov is proposed. The type strain is 2APBS1T (=DSM 23569T =JCM 17641T). Strain 116-2 (=DSM 24678 = JCM 17642) is a reference strain.

  17. Lentibacillus kimchii sp. nov., an extremely halophilic bacterium isolated from kimchi, a Korean fermented vegetable.

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

    2016-06-01

    A Gram-positive, aerobic, non-motile and extremely halophilic bacterial strain, designated K9(T), was isolated from kimchi, a Korean fermented food. The strain was observed as endospore-forming rod-shaped cells showing oxidase and catalase activity. It was found to grow at 10.0-30.0 % (w/v) NaCl (optimum, 15.0-20.0 %), pH 7.0-8.0 (optimum, pH 7.5) and 15-40 °C (optimum, 30 °C). The polar lipids of strain K9(T) were identified as phosphatidylglycerol, three unidentified phospholipids and an unidentified glycolipid. The isoprenoid quinone was identified as menaquinone-7. The major cellular fatty acids (>20 % of the total) were found to be anteisio-C15:0 and anteisio-C17:0. The cell wall peptidoglycan composition was determined to contain meso-diaminopimelic acid. The G + C content of genomic DNA was determined to be 48.2 mol %. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolated strain is closely related to Lentibacillus salinarum AHS-1(T) (96.7 % sequence similarity). Based on its phenotypic, chemotaxonomic and phylogenetic data, strain K9(T) is considered to represent a novel species of the genus Lentibacillus, for which the name Lentibacillus kimchii sp. nov., is proposed. The type strain is K9(T) (=KACC 18490(T) = JCM 30234(T)). PMID:27002961

  18. Salinicoccus sesuvii sp. nov., isolated from the rhizosphere of Sesuvium portulacastrum.

    Kämpfer, P; Arun, A B; Busse, H-J; Young, Chiu-Chung; Lai, W-A; Rekha, P D; Chen, Wen-Ming

    2011-10-01

    A Gram-staining-positive coccus, designated CC-SPL15-2(T), was isolated from the rhizosphere of Sesuvium portulacastrum. By 16S rRNA gene sequence analysis, it was shown that strain CC-SPL15-2(T) belonged to the genus Salinicoccus. The isolate was most closely related to Salinicoccus hispanicus DSM 5352(T) (98.3 % 16S rRNA gene sequence similarity) and Salinicoccus roseus DSM 5351(T) (96.7 %); similarities to all other members of the genus Salinicoccus were <96.5 %. In accordance with characteristics of the genus Salinicoccus, the quinone system was mainly composed of menaquinone MK-6. The polar lipid profile exhibited the major components diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. In the polyamine pattern, spermidine was the predominant compound. The fatty acids were anteiso-C(15 : 0), iso-C(15 : 0), iso-C(16 : 0) and anteiso-C(17 : 0), which supported the affiliation of strain CC-SPL15-2(T) to the genus Salinicoccus. DNA-DNA relatedness between strain CC-SPL15-2(T) and S. hispanicus CCUG 43288(T) was 42 and 32 % (reciprocal analysis). From these data as well as from physiological and biochemical tests, a clear differentiation of strain CC-SPL15-2(T) from S. hispanicus and other members of the genus Salinicoccus was possible. We propose that strain CC-SPL15-2(T) be assigned to a novel species, with the name Salinicoccus sesuvii sp. nov. The type strain is CC-SPL15-2(T) ( = DSM 23267(T)  = CCM 7756(T)). PMID:21037029

  19. Sphingomonas qilianensis sp. nov., Isolated from Surface Soil in the Permafrost Region of Qilian Mountains, China.

    Piao, Ai-Lian; Feng, Xiao-Min; Nogi, Yuichi; Han, Lu; Li, Yonghong; Lv, Jie

    2016-04-01

    A Gram-stain-negative, strictly aerobic, non-motile and rod-shaped bacterial strain, designated X1(T), was isolated from the permafrost region of Qilian Mountains in northwest of China. Phylogenetic analyses of 16S rRNA gene sequence revealed that strain X1(T) was a member of the genus Sphingomonas and shared the highest 16S rRNA gene sequence similarity with Sphingomonas oligophenolica JCM 12082(T) (96.9%), followed by Sphingomonas glacialis CGMCC 1.8957(T) (96.7%) and Sphingomonas alpina DSM 22537(T) (96.4%). Strain X1(T) was able to grow at 15-30 °C, pH 6.0-10.0 and with 0-0.3% NaCl (w/v). The DNA G+C content of the isolate was 64.8 mol%. Strain X1(T)-contained Q-10 as the dominant ubiquinone and C(18:1)ω7c, C(16:1)ω7c, C(16:0) and C(14:0) 2-OH as the dominant fatty acids. The polar lipid profile of strain XI(T)-contained sphingoglycolipid, phosphatidylglycerol, phosphatidylethanolamine, one unidentified glycolipid and two unidentified phospholipid. Due to the phenotypic and genetic distinctiveness and other characteristic studied in this article, we consider X1(T) as a novel species of the genus Sphingomonas and propose to name it Sphingomonas qilianensis sp. nov. The type strain is X1(T) (=CGMCC 1.15349(T) = KCTC 42862(T)). PMID:26676296

  20. Knoellia aerolata sp. nov., isolated from an air sample in Korea.

    Weon, Hang-Yeon; Kim, Byung-Yong; Schumann, Peter; Kroppenstedt, Reiner M; Noh, Hyung-Jun; Park, Chan-Won; Kwon, Soon-Wo

    2007-12-01

    An aerobic, Gram-positive, non-motile, non-spore-forming, rod-coccus-shaped bacterium, strain 5317S-21(T), was isolated from an air sample from Suwon city, Republic of Korea. The isolate was able to grow within a pH range of 5.0-9.0 and a temperature range of 5-35 degrees C and it tolerated up to 2 % (w/v) NaCl. The cell-wall peptidoglycan contained meso-diaminopimelic acid as diagnostic diamino acid. The predominant isoprenoid quinone was MK-8(H(4)). The major polar lipids were phosphatidylinositol, phosphatidylethanolamine and diphosphatidylglycerol; phosphatidylglycerol and several unknown phospholipids were also detected. Mycolic acids were absent. The only whole-cell sugar was glucose. The major cellular fatty acids were iso-C(16 : 0), C(17 : 1)omega8c and iso-C(15 : 0). 16S rRNA gene sequence analysis indicated that strain 5317S-21(T) was related phylogenetically to members of the genus Knoellia, with 97.4 % sequence similarity to the type strains of Knoellia sinensis and Knoellia subterranea. The G+C content of the genomic DNA of strain 5317S-21(T) was 73 mol%. Levels of DNA-DNA relatedness between strain 5317S-21(T) and the type strains of Knoellia sinensis and Knoellia subterranea were 37 and 41 %, respectively. It was concluded that strain 5317S-21(T) represents a novel species of the genus Knoellia, for which the name Knoellia aerolata sp. nov. is proposed. The type strain is 5317S-21(T) (=KACC 20583(T) =DSM 18566(T)). PMID:18048739

  1. Pontibacter amylolyticus sp. nov., isolated from a deep-sea sediment hydrothermal vent field.

    Wu, Yue-Hong; Zhou, Peng; Jian, Shu-Ling; Liu, Zhen-Sheng; Wang, Chun-Sheng; Oren, Aharon; Xu, Xue-Wei

    2016-04-01

    A Gram-stain-negative, short rod-shaped bacterium, designated 9-2T, was isolated from a sediment sample collected from a hydrothermal vent field on the south-west Indian Ridge. It formed red colonies, produced carotenoid-like pigments and did not produce bacteriochlorophyll a. Strain 9-2T was positive for hydrolysis of DNA, gelatin and starch, but negative for hydrolysis of aesculin and Tween 60. The sole respiratory quinone was menaquinone-7 (MK-7). The main polar lipids consisted of phosphatidylethanolamine, one unidentified phospholipid and two unidentified polar lipids. The principal fatty acids (>5%) were summed feature 4 (iso-C17:1 I and/or anteiso-C17:1 B), iso-C15:0 and iso-C17:0 3-OH. The genomic DNA G+C content was 49.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 9-2T should be assigned to the genus Pontibacter. Levels of 16S rRNA gene sequence similarity between the new isolate and the type strains of Pontibacter species with validly published names were in the range 94.0-96.5%. On the basis of phenotypic and genotypic data, strain 9-2T represents a novel species of the genus Pontibacter, for which the name Pontibacter amylolyticus sp. nov. is proposed. The type strain is 9-2T (=CGMCC 1.12749T=JCM 19653T=MCCC 1K00278T). PMID:26827710

  2. Streptomyces xinjiangensis sp. nov., an actinomycete isolated from Lop Nur region.

    Cheng, Cong; Li, Yu-Qian; Asem, Mipeshwaree Devi; Lu, Chun-Yan; Shi, Xiao-Han; Chu, Xiao; Zhang, Wan-Qin; Di An, Deng-; Li, Wen-Jun

    2016-10-01

    A novel actinobacterial strain, designated LPA192(T), was isolated from a soil sample collected from Lop Nur, Xinjiang Uygur Autonomous Region, Northwest China. A polyphasic approach was used to investigate the taxonomic position of strain LPA192(T). The isolate showed morphological and chemotaxonomic characteristics typical of members of the genus Streptomyces. Peptidoglycan was found to contain LL-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinones were MK-9(H6) and MK-10(H4). Polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylinositol. Major cellular fatty acids consist of C16:0, anteiso-C15:0 and C18:1 ω9c. The sugar in whole-cell hydrolysates was mannose. Phylogenetic analysis indicated that strain LPA192(T) is closely related to Streptomyces tanashiensis LMG 20274(T) (99.3 %), Streptomyces gulbargensis DAS131(T) (99.3 %), Streptomyces nashvillensis NBRC 13064(T) (99.3 %), Streptomyces roseolus NBRC 12816(T) (99.2 %) and Streptomyces filamentosus NBRC 12767(T) (99.1 %) while showing below 98.5 % sequencing similarities with other validly published Streptomyces species. However, DNA-DNA relatedness values between LPA192(T) and the closely related type strains were below 40 %, which are much lower than 70 % threshold value for species delineation. The genomic DNA G + C content of strain LPA192(T) was 69.3 mol %. Based on the differences in genotypic and phenotypic characteristics from the closely related strains, strain LPA192(T) is considered to represent a novel species of the genus Streptomyces for which the name Streptomyces xinjiangensis sp. nov. is proposed. The type strain is LPA192(T) (=KCTC 39601(T) = CGMCC 4.7288(T)). PMID:27209413

  3. Brevibacterium daeguense sp. nov., a nitrate-reducing bacterium isolated from a 4-chlorophenol enrichment culture.

    Cui, Yingshun; Kang, Myung-Suk; Woo, Sung-Geun; Jin, Long; Kim, Kwang Kyu; Park, Joonhong; Lee, Myungjin; Lee, Sung-Taik

    2013-01-01

    A Gram-reaction-positive, non-spore-forming, aerobic actinobacterial strain (2C6-41(T)) was isolated from the activated sludge from an industrial wastewater treatment plant in Daegu, South Korea. Its taxonomic position was investigated by using a polyphasic approach. On the basis of 16S rRNA gene sequence similarity, closest phylogenetic relatives to strain 2C6-41(T) were Brevibacterium pityocampae DSM 21720(T) (97.2 %), Brevibacterium salitolerans KCTC 19616(T) (96.7 %), Brevibacterium album KCTC 19173(T) (96.2 %) and Brevibacterium samyangense KCCM 42316(T) (96.2 %). The DNA G+C content of strain 2C6-41(T) was 66.4 mol%. Chemotaxonomic data, which included MK-8(H(2)) as the major menaquinone; meso-diaminopimelic acid, glutamic acid and alanine as cell-wall amino acids; ribose, mannose and glucose as major cell-wall sugars; and anteiso-C(15 : 0), anteiso-C(17 : 0), C(16 : 0) and iso-C(15 : 0) as major fatty acids, supported the affiliation of strain 2C6-41(T) to the genus Brevibacterium. The aromatic ring cleavage enzyme catechol 1,2-dioxygenase was not detected in strain 2C6-41(T), but catechol 2,3-dioxygenase was detected. The results of physiological and biochemical tests, and the low level of DNA-DNA relatedness to the closest phylogenetic relative enabled strain 2C6-41(T) to be differentiated genotypically and phenotypically from recognized species of the genus Brevibacterium. The isolate is therefore considered to represent a novel species in the genus Brevibacterium, for which the name Brevibacterium daeguense sp. nov. is proposed. The type strain is 2C6-41(T) (=KCTC 19800(T) = JCM 17458(T)). PMID:22368170

  4. Brucella vulpis sp. nov., isolated from mandibular lymph nodes of red foxes (Vulpes vulpes).

    Scholz, Holger C; Revilla-Fernández, Sandra; Al Dahouk, Sascha; Hammerl, Jens A; Zygmunt, Michel S; Cloeckaert, Axel; Koylass, Mark; Whatmore, Adrian M; Blom, Jochen; Vergnaud, Gilles; Witte, Angela; Aistleitner, Karin; Hofer, Erwin

    2016-05-01

    Two slow-growing, Gram-negative, non-motile, non-spore-forming, coccoid bacteria (strains F60T and F965), isolated in Austria from mandibular lymph nodes of two red foxes (Vulpes vulpes), were subjected to a polyphasic taxonomic analysis. In a recent study, both isolates were assigned to the genus Brucella but could not be attributed to any of the existing species. Hence, we have analysed both strains in further detail to determine their exact taxonomic position and genetic relatedness to other members of the genus Brucella. The genome sizes of F60T and F965 were 3 236 779 and 3 237 765 bp, respectively. Each genome consisted of two chromosomes, with a DNA G+C content of 57.2 %. A genome-to-genome distance of >80 %, an average nucleotide identity (ANI) of 97 % and an average amino acid identity (AAI) of 98 % compared with the type species Brucella melitensis confirmed affiliation to the genus. Remarkably, 5 % of the entire genetic information of both strains was of non-Brucella origin, including as-yet uncharacterized bacteriophages and insertion sequences as well as ABC transporters and other genes of metabolic function from various soil-living bacteria. Core-genome-based phylogenetic reconstructions placed the novel species well separated from all hitherto-described species of the genus Brucella, forming a long-branched sister clade to the classical species of Brucella. In summary, based on phenotypic and molecular data, we conclude that strains F60T and F965 are members of a novel species of the genus Brucella, for which the name Brucella vulpis sp. nov. is proposed, with the type strain F60T ( = BCCN 09-2T = DSM 101715T). PMID:26928956

  5. Asticcacaulis endophyticus sp. nov., a prosthecate bacterium isolated from the root of Geum aleppicum.

    Zhu, Lingfang; Long, Mingxiu; Si, Meiru; Wei, Linfang; Li, Changfu; Zhao, Liang; Shen, Xihui; Wang, Yao; Zhang, Lei

    2014-12-01

    A strictly aerobic, light-yellow-coloured, stalked bacterium, designated strain ZFGT-14(T), was isolated from the root of Geum aleppicum Jacq. collected from Taibai Mountain in Shaanxi province, north-west China, and was subjected to a taxonomic study using a polyphasic approach. This novel isolate grew at 7-33 °C (optimum 25-28 °C) and pH 6.0-10.0 (optimum pH 7.0-8.0). Flexirubin-type pigments were not produced. Cells were Gram-stain-negative, rod-shaped and motile with a single polar flagellum. The predominant respiratory quinone was Q-10. The major cellular fatty acids were summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c), C16 : 0, C19 : 0 cyclo ω8c and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and the major polar lipids were phosphatidylglycerol and glycolipids. The DNA G+C content was 57.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZFGT-14(T) was most closely related to the genus Asticcacaulis and had low sequence similarity (95.0-95.9 %) with all species with validly published names within the genus Asticcacaulis. Based on the phenotypic, phylogenetic and genotypic data, strain ZFGT-14(T) is considered to represent a novel species of the genus Asticcacaulis, for which the name Asticcacaulis endophyticus sp. nov. is proposed. The type strain is ZFGT-14(T) ( = CCTCC AB 2013012(T) = KCTC 32296(T) = LMG 27605(T)). PMID:25205798

  6. Marimicrobium arenosum gen. nov., sp. nov., a moderately halophilic bacterium isolated from sea sand.

    Konkit, Maytiya; Kim, Jong-Hwa; Kim, Wonyong

    2016-02-01

    A Gram-stain-negative, non-pigmented, non-spore-forming, non-motile, strictly aerobic bacterial strain, designated CAU 1038T, was isolated from a sea sand sample in Modo, Republic of Korea, and its taxonomic position was examined using a polyphasic approach. Cells of strain CAU 1038T grew optimally at 30 °C, pH 7.5 in 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CAU 1038T formed a distinct lineage within the class Gammaproteobacteria as a separate deep branch, with 95.2 % or lower sequence similarity to representatives of the genera Haliea, Halioglobus and Chromatocurvus, and 92.3 % or lower with Luminiphilus, Pseudohaliea and Congregibacter. The major cellular fatty acids of strain CAU 1038T were C16 : 0, C16 : 1ω7c and C18 : 1ω7c. The polar lipid pattern of the isolate consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid and two unidentified lipids. The strain contained lipoquinone (Q-8) as the sole respiratory quinone. The G+C content of the genomic DNA was 65 mol%. On the basis of phenotypic and chemotaxonomic data, and phylogenetic inference, strain CAU 1038T represents a novel species of a new genus in the family Halieaceae, for which the name Marimicrobium arenosum gen. nov., sp. nov. is proposed. The type strain of the type species is CAU 1038T ( = KCTC 42300T = NBRC 110727T). PMID:26611676

  7. Methylocapsa palsarum sp. nov., a methanotroph isolated from a subArctic discontinuous permafrost ecosystem.

    Dedysh, Svetlana N; Didriksen, Alena; Danilova, Olga V; Belova, Svetlana E; Liebner, Susanne; Svenning, Mette M

    2015-10-01

    An aerobic methanotrophic bacterium was isolated from a collapsed palsa soil in northern Norway and designated strain NE2T. Cells of this strain were Gram-stain-negative, non-motile, non-pigmented, slightly curved thick rods that multiplied by normal cell division. The cells possessed a particulate methane monooxygenase enzyme (pMMO) and utilized methane and methanol. Strain NE2T grew in a wide pH range of 4.1–8.0 (optimum pH 5.2–6.5) at temperatures between 6 and 32 °C (optimum 18–25 °C), and was capable of atmospheric nitrogen fixation under reduced oxygen tension. The major cellular fatty acids were C18 : 1ω7c, C16 : 0 and C16 : 1ω7c, and the DNA G+C content was 61.7 mol%. The isolate belonged to the family Beijerinckiaceae of the class Alphaproteobacteria and was most closely related to the facultative methanotroph Methylocapsa aurea KYGT (98.3 % 16S rRNA gene sequence similarity and 84 % PmoA sequence identity). However, strain NE2T differed from Methylocapsa aurea KYGT by cell morphology, the absence of pigmentation, inability to grow on acetate, broader pH growth range, and higher tolerance to NaCl. Therefore, strain NE2T represents a novel species of the genus Methylocapsa, for which we propose the name Methylocapsa palsarum sp. nov. The type strain is NE2T ( = LMG 28715T = VKM B-2945T). PMID:26297585

  8. A Comparative biochemical study on two marine endophytes, Bacterium SRCnm and Bacillus sp. JS, Isolated from red sea algae.

    Ahmed, Eman Fadl; Hassan, Hossam Mokhtar; Rateb, Mostafa Ezzat; Abdel-Wahab, Noha; Sameer, Somayah; Aly Taie, Hanan Anwar; Abdel-Hameed, Mohammed Sayed; Hammouda, Ola

    2016-01-01

    Two marine endophytic bacteria were isolated from the Red Sea algae; a red alga; Acanthophora dendroides and the brown alga Sargassum sabrepandum. The isolates were identified based on their 16SrRNA sequences as Bacterium SRCnm and Bacillus sp. JS. The objective of this study was to investigate the potential anti-microbial and antioxidant activities of the extracts of the isolated bacteria grown in different nutrient conditions. Compared to amoxicillin (25μg/disk) and erythromycin (15μg/disk), the extracts of Bacterium SRCn min media II, III, IV and V were potent inhibitors of the gram-positive bacterium Sarcina maxima even at low concentrations. Also, the multidrug resistant Staphylococcus aureus(MRSA) was more sensitive to the metabolites produced in medium (II) of the same endophyte than erythromycin (15μg/disk). A moderate activity of the Bacillus sp. JS extracts of media I and II was obtained against the same pathogen. The total compounds (500ug/ml) of both isolated endophytes showed moderate antioxidant activities (48.9% and 46.1%, respectively). LC/MS analysis of the bacterial extracts was carried out to investigate the likely natural products produced. Cyclo(D-cis-Hyp-L-Leu), dihydrosphingosine and 2-Amino-1,3-hexadecanediol were identified in the fermentation medium of Bacterium SRCnm, whereas cyclo (D-Pro-L-Tyr) and cyclo (L-Leu-L-Pro) were the suggested compounds of Bacillus sp. JS. PMID:26826831

  9. Deinococcus ficus sp. nov., isolated from the rhizosphere of Ficus religiosa L.

    Lai, Wei-An; Kämpfer, Peter; Arun, A B; Shen, Fo-Ting; Huber, Birgit; Rekha, P D; Young, Chiu-Chung

    2006-04-01

    A pale-pink strain (CC-FR2-10T) from the rhizosphere of the sacred tree Ficus religiosa L. in Taiwan was investigated by using a polyphasic taxonomic approach. The cells were Gram-positive, rod-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 highest sequence similarities being found with Deinococcus grandis (96.1 %), Deinococcus radiodurans (94.3 %), Deinococcus radiopugnans (93.2 %), Deinococcus indicus (93.0 %), Deinococcus proteolyticus (92.5 %), Deinococcus murrayi (92.4 %) and Deinococcus geothermalis (90.7 %). The DNA-DNA relatedness with respect to D. grandis DSM 3963T was 17.9 %. Chemotaxonomic data revealed that strain CC-FR2-10T contains only menaquinone MK-8 as the respiratory quinone, unknown phosphoglycolipids as the predominant polar lipids and 16 : 1omega7c, 17 : 1omega8c and 17 : 1omega9c iso as the predominant fatty acids. The biochemical and chemotaxonomic properties demonstrate that strain CC-FR2-10T represents a novel species, for which the name Deinococcus ficus sp. nov. is proposed. The type strain is CC-FR2-10T (=CCUG 51391T [corrected] = CIP 108832T). PMID:16585695

  10. Streptomyces actinomycinicus sp. nov., isolated from soil of a peat swamp forest.

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

    2016-01-01

    A novel actinomycete, strain RCU-197T, was isolated from soil of a peat swamp forest in Rayong Province, Thailand. Using a polyphasic approach, the strain was classified in the genus Streptomyces. It contained ll-diaminopimelic acid in the cell-wall peptidoglycan. No diagnostic sugars were detected in whole-cell hydrolysates and there was a lack of mycolic acids. The major menaquinones were MK-9(H6) and MK-9(H8). The predominant cellular fatty acids were iso-C14 : 0, iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0. The polar lipids profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol and phosphatidylinositol mannoside, an unknown aminolipid and two unknown phospholipids. Phylogenetic analysis of 16S rRNA gene sequences showed the strain formed distinct clade within the genus Streptomyces and was closely related to Streptomyces echinatus NBRC 12763T (98.78 % 16S rRNA gene sequence similarity). According to the polyphasic approach as well as DNA-DNA relatedness, the strain could be clearly differentiated from closely related species and represents a novel species of the genus Streptomyces, for which the name Streptomyces actinomycinicus sp. nov. is proposed. The type strain is RCU-197T ( = JCM 30864T = TISTR 2208T = PCU 342T). PMID:26510888

  11. Pontibacter locisalis Sy30T sp. nov. isolated from soil collected from an abandoned saltern.

    Zhou, Yan-Xia; Xie, Zhi-Hong; Zhao, Jin-Xin; Du, Zong-Jun; Chen, Guan-Jun

    2016-03-01

    A novel Gram-stain negative, red, rod-shaped, non-motile and aerobic bacterial strain, designated Sy30(T), was isolated from dry soils of an abandoned marine saltern at Weihai, China. 16S rRNA sequence analysis indicated that strain Sy30(T) belongs to the genus Pontibacter in the family Cytophagaceae, with sequence similarities ranging from 93.3 to 96.4 % with other type species of the genus Pontibacter. The predominant cellular fatty acids were iso-C15:0 and summed feature 4 (iso-C17:1 I and/or anteiso-C17:1 B). The major menaquinone was MK-7. The major polyamine was sym-homospermidine. The DNA G+C content was 47.7 mol%. The major polar lipids consisted of phosphatidylethanolamine, phosphoaminolipid and two unidentified polar lipid. Based on phenotypic, chemotaxonomic and phylogenetic analysis, strain Sy30(T) represents a novel species of the genus Pontibacter in the family Cytophagaceae, phylum Bacteroidetes, for which the name Pontibacter locisalis sp. nov. is proposed. The type strain is Sy30(T) (=KCTC 42498(T) = CICC AB 2015060(T)). PMID:26833190

  12. Wohlfahrtiimonas larvae sp. nov., isolated from the larval gut of Hermetia illucens (Diptera: Stratiomyidae).

    Lee, Jae Kook; Lee, Youn Yeop; Park, Kwan Ho; Sim, Jeonggu; Choi, Youngcheol; Lee, Sung-Jae

    2014-01-01

    A novel, Gram-negative, facultative anaerobic, motile and short rod-shaped bacterium, strain KBL006(T) was isolated from the larval gut of Hermetia illucens, Black soldier fly. The 16S rRNA gene sequence of strain KBL006(T) showed 96.4 % similarity to that of Wohlfahrtiimonas chitiniclastica S5(T). Strain KBL006(T) grew optimally at 30 °C, at pH 8.0 and in the presence of 1-2 % (w/v) NaCl. Oxidase activity and catalase activity were positive. The major fatty acids were C18:1 ω7c, C14:0, and C16:0. The major respiratory quinone was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol, and two phospholipids. The G+C content of the genomic DNA was 45.2 mol%. Based on these polyphasic data, strain KBL006(T) is considered to represent a novel species in the genus Wohlfahrtiimonas, for which the name Wohlfahrtiimonas larvae sp. nov. is proposed. The type strain is KBL006(T) (= KACC 16839(T) = JCM 18424(T)). PMID:24126466

  13. Biodegradation of Di-n-Butyl Phthalate by a Newly Isolated Halotolerant Sphingobium sp.

    Decai Jin

    2013-12-01

    Full Text Available A Gram-negative strain (TJ capable of growing aerobically on mixed phthalate esters (PAEs as the sole carbon and energy source was isolated from the Haihe estuary, Tianjin, China. It was identified as belonging to the Sphingobium genus on the basis of morphological and physiological characteristics and 16S rRNA and gyrb gene sequencing. The batch tests for biodegradation of di-n-butyl phthalate (DBP by the Sphingobium sp. TJ showed that the optimum conditions were 30 °C, pH 7.0, and the absence of NaCl. Stain TJ could tolerate up to 4% NaCl in minimal salt medium supplemented with DBP, although the DBP degradation rates slowed as NaCl concentration increased. In addition, substrate tests showed that strain TJ could utilize shorter side-chained PAEs, such as dimethyl phthalate and diethyl phthalate, but could not metabolize long-chained PAEs, such as di-n-octyl phthalate, diisooctyl phthalate, and di-(2-ethyl-hexyl phthalate. To our knowledge, this is the first report on the biodegradation characteristics of DBP by a member of the Sphingobium genus.

  14. Tenacibaculum aestuarii sp. nov., isolated from a tidal flat sediment in Korea.

    Jung, Seo-Youn; Oh, Tae-Kwang; Yoon, Jung-Hoon

    2006-07-01

    A novel Tenacibaculum-like bacterial strain, SMK-4(T), was isolated from a tidal flat sediment in Korea. Strain SMK-4(T) was Gram-negative, pale yellow-pigmented and rod-shaped. It grew optimally at 30-37 degrees C and in the presence of 2-3 % (w/v) NaCl. It contained MK-6 as the predominant menaquinone and iso-C(15 : 0), iso-C(16 : 0) 3-OH and C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH as the major fatty acids (>10 % of total fatty acids). The DNA G+C content was 33.6 mol%. Phylogenetic trees based on 16S rRNA gene sequences showed that strain SMK-4(T) fell within the evolutionary radiation encompassed by the genus Tenacibaculum. Strain SMK-4(T) exhibited 16S rRNA gene sequence similarity levels of 95.2-98.6 % with respect to the type strains of recognized Tenacibaculum species. DNA-DNA relatedness levels and differential phenotypic properties made it possible to categorize strain SMK-4(T) as a species that is separate from previously described Tenacibaculum species. On the basis of phenotypic properties and phylogenetic and genetic distinctiveness, strain SMK-4(T) (=KCTC 12569(T)=JCM 13491(T)) should be classified as a novel Tenacibaculum species, for which the name Tenacibaculum aestuarii sp. nov. is proposed. PMID:16825632

  15. Bacillus lonarensis sp. nov., an alkalitolerant bacterium isolated from a soda lake.

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

    2015-01-01

    A novel Gram-stain-positive, rod-shaped, motile and endospore-forming novel bacterial strain 25nlg(T) was isolated from Lonar soda lake, in India. Based on the 16S rRNA gene sequence analysis, it was identified as a member of Firmicutes, being most closely related to Bacillus patagoniensis PAT 05(T) (96.6 %) and other members in the genus Bacillus (APL2) and three unknown lipids (L2-4). The predominant isoprenoid quinone was MK-7. iso-C15:0 (41.7 %) was the predominant fatty acid, and significant proportions of anteiso-C15:0 (20.8 %), C12:0 (5.5 %), anteiso-C17:0 (4.9 %), iso-C17:0 (4.5 %) were also detected in the strain 25nlg(T). The DNA G+C content of the strain 25nlg(T) was 40.5 mol%. The results of molecular, physiological and biochemical tests allowed a clear phenotypic differentiation of strain 25nlg(T) from all other members of the genus Bacillus. Strain 25nlg(T) represents a novel member of the genus Bacillus, for which the name Bacillus lonarensis sp. nov. is proposed. The type strain is 25nlg(T) (=KCTC 33413(T) = LMG 27974(T) = CGMCC = 1.12817(T)). PMID:25294189

  16. Methanolobus zinderi sp nov., a methylotrophic methanogen isolated from a deep subsurface coal seam

    Doerfert, S.N.; Reichlen, M.; Iyer, P.; Wang, M.Y.; Ferry, J.G. [Penn State University, University Park, PA (United States)

    2009-05-15

    A methanogenic organism from the domain Archaea (SD1{sup T}) was isolated from saline water released from a coal seam located 926 m below the surface via a methane-producing well near Monroe, Louisiana, USA. Growth and methanogenesis were supported with methanol, monomethylamine, dimethylamine or trimethylamine, but not with dimethylsulfide, formate, acetate or H{sub 2}/CO{sub 2}. Cells grew in high-salt minimal medium but growth was stimulated with yeast extract or tryptone. Cells were single, non-motile, irregular coccoids 0.5-1.0 {mu} m in diameter and the cell wall contained protein. Conditions for the maximum rate of growth were 40-50{sup o}C, 0.2-0.6 M NaCl, 100- {ge} 200 mM MgCl{sub 2}, and pH 7.0-8.0. The G + C content of the genomic DNA was 42 {+-} 1 mol%. A comparison of 16S rRNA gene sequences indicated that strain SD1{sup T} was most closely related to Methanolobus oregonensis DSM 5435{sup T} with 96% gene sequence similarity. It is proposed that strain SD1{sup T} represents a novel species, Methanolobus zinderi sp. nov. The type strain is SD1{sup T} (=ATCC BAA-1601P{sup T}=DSM 21339{sup T}).

  17. Production of cellobiose dehydrogenase from a newly isolated white rot fungus Termitomyces sp. OE147.

    Gupta, Gupteshwar; Gangwar, Rishabh; Gautam, Ashwani; Kumar, Lalit; Dhariwal, Anuj; Sahai, Vikram; Mishra, Saroj

    2014-08-01

    Class I cellobiose dehydrogenases (CDHs) are extracellular hemoflavo enzymes produced at low levels by the Basidiomycetes (white rot fungi). In presence of suitable electron acceptors, e.g., cytochrome c, 2,6-dichlorophenol-indophenol, or metal ions, it oxidizes cellobiose to cellobionolactone. A stringent requirement for disaccharides makes CDH also useful for conversion of lactose to lactobionic acid, an important ingredient in pharma and detergent industry. In this work, class I CDH was produced using a newly identified white rot fungus Termitomyces sp. OE147. Four media were evaluated for CDH production, and maximum enzyme activity of 0.92 international unit (IU)/ml was obtained on Ludwig medium under submerged conditions. Statistical optimization of N source, which had significant effect on CDH production, using Box-Behnken design followed by optimization of inoculum size and age resulted in an increase in activity to 2.9 IU/ml and a productivity of ~25 IU/l/h. The nearly purified CDH exhibited high activity of 26.4 IU/mg protein on lactose indicating this enzyme to be useful for lactobionic acid synthesis. Some of the internal peptide sequences bore 100 % homology to the CDH produced in Myceliophthora thermophila. The fungal isolate was amenable to scale up, and an overall productivity of ~18 IU/l/h was obtained at 14-l level. PMID:24929309

  18. Starmerella orientalis f.a., sp. nov., an ascomycetous yeast species isolated from flowers.

    Alimadadi, Nayyereh; Soudi, Mohammad Reza; Wang, Shi-An; Wang, Qi-Ming; Talebpour, Zahra; Bai, Feng-Yan

    2016-03-01

    Four strains of a novel ascomycetous yeast species were isolated from flowers in Iran and China. Phylogenetic analysis of the sequences of the ITS region (including 5.8S rRNA gene) and the LSU rRNA gene D1/D2 domains indicated that these strains belong to the Starmerella clade and show divergence from previously described species in this clade. Growth reactions on carbon and nitrogen sources were similar to those observed in related species of the Starmerella clade. Sexual reproduction was not observed after mating tests on different sporulation media. Based on physiological characteristics and phylogeny of rRNA gene sequences, the novel species is most closely related to Candida (iter. nom. Starmerella) powellii and Candida (iter. nom. Starmerella) floricola. It is therefore assigned to the genus Starmerella and described as Starmerella orientalis f.a., sp. nov. The type strain is SAM09T ( = IBRC-M 30204T = CBS 14142T). The MycoBank accession number is MB 814379. PMID:26780917

  19. Nocardia casuarinae sp. nov., an actinobacterial endophyte isolated from root nodules of Casuarina glauca.

    Ghodhbane-Gtari, Faten; Nouioui, Imen; Salem, Karima; Ktari, Amir; Montero-Calasanz, Maria del Carmen; Tisa, Louis S; Klenk, Hans-Peter; Gtari, Maher

    2014-06-01

    An actinobacterium strain BMG51109a was isolated from surface sterilized root nodules of Casuarina glauca collected in Tunisia. The 16S rRNA gene sequence of strain BMG51109a showed most similarity (96.53-96.55 %) to the type strains of Nocardia transvalensis, N. aobensis and N. elegans. Chemotaxonomic analysis supported the assignment of the strain to Nocardia genus. The major menaquinone was MK-8(H4c) while the polar lipid profile contained diphosphatidylglycerol, phosphatidylmonomethylethanolamine, glycophospholipid, phosphatidylinositol, one uncharacterized phospholipid and three glycolipids. Whole-cell sugar analysis revealed the presence of meso-diaminopimelic acid, arabinose and galactose as diagnostic sugars, complemented by glucose, mannose and ribose. The major cellular fatty acids were tuberculostearic, oleic, palmitoleic and stearic acids. Physiological and biochemical tests showed that strain BMG51109a could be clearly distinguished from its closest phylogenetic neighbours. On the basis of these results, strain BMG51109a(T) (= DSM 45978(T) = CECT 8469(T)) is proposed as the type strain of the novel species Nocardia casuarinae sp. nov. PMID:24715251

  20. Actinomadura gamaensis sp. nov., a novel actinomycete isolated from soil in Gama, Chad.

    Abagana, Adam Yacoub; Sun, Pengyu; Liu, Chongxi; Cao, Tingting; Zheng, Weiwei; Zhao, Shanshan; Xiang, Wensheng; Wang, Xiangjing

    2016-06-01

    A novel single spore-producing actinomycete, designated strain NEAU-Gz5(T), was isolated from a soil sample from Gama, Chad. A polyphasic taxonomic study was carried out to establish the status of this strain. The diamino acid present in the cell wall is meso-diaminopimelic acid. Glucose, mannose and madurose occur in whole cell hydrolysates. The polar lipids were found to consist of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannoside and an unidentified glycolipid. The predominant menaquinones were identified as MK-9(H8) and MK-9(H6). The predominant cellular fatty acids were found to be C16:0, iso-C15:0, iso-C16:0 and C18:0 10-methyl. Phylogenetic analysis based on the 16S rRNA gene showed that strain NEAU-Gz5(T) belongs to the genus Actinomadura and is closely related to Actinomadura oligospora JCM 10648(T) (ATCC 43269(T); 98.3 % similarity). However, the low level of DNA-DNA relatedness and some different phenotypic characteristics allowed the strain to be distinguished from its close relatives. Therefore, it is concluded that strain NEAU-Gz5(T) represents a novel species of the genus of Actinomadura, for which the name Actinomadura gamaensis sp. nov. is proposed. The type strain is NEAU-Gz5(T) (= CGMCC 4.7301(T) = DSM 100815(T)). PMID:27010208

  1. Raoultella electrica sp. nov., isolated from anodic biofilms of a glucose-fed microbial fuel cell.

    Kimura, Zen-ichiro; Chung, Kyung Mi; Itoh, Hiroaki; Hiraishi, Akira; Okabe, Satoshi

    2014-04-01

    A Gram-stain-negative, non-spore-forming, rod-shaped bacterium, designated strain 1GB(T), was isolated from anodic biofilms of a glucose-fed microbial fuel cell. Strain 1GB(T) was facultatively anaerobic and chemo-organotrophic, having both a respiratory and a fermentative type of metabolism, and utilized a wide variety of sugars as carbon and energy sources. Cells grown aerobically contained Q-8 as the major quinone, but excreted Q-9 and a small amount of Q-10 when cultured with an electrode serving as the sole electron acceptor. The G+C content of the genomic DNA of 1GB(T) was 54.5 mol%. Multilocus sequence typing (MLST) analysis showed that strain 1GB(T) represented a distinct lineage within the genus Raoultella (98.5-99.4 % 16S rRNA gene sequence similarity and 94.0-96.5 % sequence similarity based on the three concatenated housekeeping genes gyrA, rpoB and parC. Strain 1GB(T) exhibited DNA-DNA hybridization relatedness of 7-43 % with type strains of all established species of the genus Raoultella. On the basis of these phenotypic, phylogenetic and genotypic data, the name Raoultella electrica sp. nov. is proposed for strain 1GB(T). The type strain is 1GB(T) ( = NBRC 109676(T) = KCTC 32430(T)). PMID:24449794

  2. Marinicola seohaensis gen. nov., sp. nov., isolated from sea water of the Yellow Sea, Korea.

    Yoon, Jung-Hoon; Kang, So-Jung; Lee, Choong-Hwan; Oh, Tae-Kwang

    2005-03-01

    A Gram-negative, non-flagellated, non-spore-forming and rod-shaped bacterial strain, SW-152(T), was isolated from sea water of the Yellow Sea in Korea, and subjected to a polyphasic taxonomic study. Strain SW-152(T) grew optimally at 30 degrees C and in the presence of 2-3 % (w/v) NaCl. It contained MK-7 as the predominant menaquinone and iso-C(15 : 0) and iso-C(15 : 1) as the major fatty acids. Polar lipids detected in strain SW-152(T) were phosphatidylethanolamine, diphosphatidylglycerol and unidentified lipids. The DNA G+C content was 40.3 mol%. Phylogenetic trees based on 16S rRNA gene sequences exhibited that strain SW-152(T) forms a distinct evolutionary lineage within the Cytophaga-Flavobacterium-Bacteroides (CFB) group. Strain SW-152(T) exhibited low 16S rRNA similarity levels of less than 89.4 % to members belonging to the CFB group. Phenotypic properties of strain SW-152(T) differentiate it from phylogenetically related taxa. On the basis of phenotypic and phylogenetic data, strain SW-152(T) (=KCTC 12312(T)=JCM 12600(T)) was classified in a novel genus and species, Marinicola seohaensis gen. nov., sp. nov. PMID:15774675

  3. Leifsonia soli sp. nov., a yellow-pigmented actinobacterium isolated from teak rhizosphere soil.

    Madhaiyan, Munusamy; Poonguzhali, Selvaraj; Lee, Jung-Sook; Senthilkumar, Murugaiyan; Lee, Keun Chul; Sundaram, Subbiah

    2010-06-01

    Two yellow-pigmented, Gram-stain-positive, aerobic, motile, short rod-shaped bacteria were isolated from natural teak tree rhizosphere soil and their taxonomic positions were determined by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strains TG-S248(T) and TG-S240 formed a distinct phyletic line within the genus Leifsonia. 16S rRNA gene sequence analysis of strain TG-S248(T) with sequences from Leifsonia shinshuensis DB 102(T), L. poae VKM Ac-1401(T), L. naganoensis DB 103(T), L. aquatica DSM 20146(T) and L. xyli subsp. cynodontis JCM 9733(T) revealed pairwise similarities ranging from 98.7 to 99.1 %. The major fatty acids were anteiso-C(15 : 0), anteiso-C(17 : 0) and iso-C(16 : 0). The G+C content of the DNA of the type strain was 69.4 mol%. DNA-DNA hybridization experiments revealed low levels of DNA-DNA relatedness (32 % or less) between strain TG-S248(T) and its closest relatives. Based on differences in phenotypic and genotypic characteristics, strain TG-S248(T) (=LMG 24767(T) =JCM 15679(T)) is designated the type strain of a novel species of the genus Leifsonia, for which the name Leifsonia soli sp. nov. is proposed. PMID:19667370

  4. Marinomonas ushuaiensis sp. nov., isolated from coastal sea water in Ushuaia, Argentina, sub-Antarctica.

    Prabagaran, S R; Suresh, K; Manorama, Ruth; Delille, Daniel; Shivaji, S

    2005-01-01

    A Gram-negative, rod-shaped, psychrophilic, motile, non-spore-forming bacterium, strain U1T, was isolated from Ushuaia located at the southernmost tip of Argentina. On the basis of 16S rRNA gene sequence similarity, strain U1T was found to be closely related to Marinomonas communis (DSM 5604T) and Marinomonas primoryensis (IAM 15010T). At the DNA-DNA level, however, the values for similarity were 41 and 25 %, respectively. The major fatty acids present were iso-C(16 : 0), C(16 : 1)omega7c, iso-C(17 : 1) and C(18 : 1)omega7c and the G+C content of the DNA was 43.6 mol%. All of the above characteristics support the affiliation of strain U1T to the genus Marinomonas. Furthermore, on the basis of phenotypic features, chemotaxonomic characteristics and phylogenetic analysis of the 16S rRNA gene sequence, it appears that strain U1T is distinct from the four Marinomonas species with validly published names. Strain U1T, therefore, represents a novel species, for which the name Marinomonas ushuaiensis sp. nov. is proposed. The type strain of M. ushuaiensis is U1T (=MTCC 6143T=DSM 15871T=JCM 12170T). PMID:15653892

  5. Novosphingobium sediminis sp. nov., isolated from the sediment of a eutrophic lake.

    Li, Hai-Feng; Zou, Zhuo-Tao; Li, Bao-Zhen; Wang, Xin; Yang, Jin-Shui; Yuan, Hong-Li

    2012-01-01

    A Gram-negative, rod-shaped, aerobic, non-motile, bacterium (YG-17(T)) was isolated from eutrophic Taihu lake sediment. Colonies grown on YG agar plates were circular, convex, and yellow-colored. On the basis of 16S rRNA gene sequence similarity, strain YG-17(T) was shown to be closely related to Novosphingobium aromaticivorum (97.9%), followed by Novosphingobium stygium (97.5%), Novosphingobium subterranea (96.9%) and Novosphingobium taihuense (96.7%). The DNA-DNA relatedness values of strain YG-17(T) to the most phylogenetically related species N. aromaticivorum and N. stygium were 14% and 21%, respectively. The G+C content of the genomic DNA was 63.2 mol%. The major respiratory quinone was ubiquinone-10 and major fatty acids were C(18:1 ω7c), C(17:1 ω6c) and C(14:0)2-OH. Sphingoglycolipids were present, and spermidine was detected as the major polyamine. According to comparative physiological and chemotaxonomic analysis, strain YG-17(T) is proposed to be a novel species of the genus Novosphingobium, with the name of Novosphingobium sediminis sp. nov. The type strain is YG-17(T) (NBRC 106119(T)= CGMCC 1.9114(T)). PMID:23149680

  6. Methanosarcina subterranea sp. nov., a methanogenic archaeon isolated from a deep subsurface diatomaceous shale formation.

    Shimizu, Satoru; Ueno, Akio; Naganuma, Takeshi; Kaneko, Katsuhiko

    2015-04-01

    A methanogenic archaeon, strain HC-2(T), was isolated from a deep diatomaceous shale formation. The strain grew on methanol, monomethylamine, dimethylamine, trimethylamine and dimethylsulphide, but not on acetate, H2/CO2, formate, 2-propanol, 2-butanol or cyclopentanol. Cells were Gram-stain-negative, non-motile, and coccus-like, 0.9-1.4 µm in diameter, and occurred singly, in pairs, or as aggregates. The strain grew at 10-40 °C (optimum 35 °C), pH 5.9-7.4 (optimum pH 6.6-6.8) and in 0-0.6 M NaCl (optimum 0.1-0.2 M). The genomic DNA G+C content was 41.5 mol% and the 16S rRNA gene sequence was closely related to those of Methanosarcina lacustris DSM 13486(T) (99.1%) and Methanosarcina siciliae DSM 3028(T) (98.3%). Values for DNA-DNA hybridization with these strains were less than 30%. The phenotypic and phylogenetic features of HC-2(T) indicate that it represents a novel species of the genus Methanosarcina , for which the name Methanosarcina subterranea sp. nov. is proposed. The type strain is HC-2(T) ( = DSM 22503(T) = JCM 15540(T) = NBRC 102578(T)). PMID:25604340

  7. Nickel adsorption by wild type and nickel resistant isolate of chlorella sp

    Use of unicellular green microalgae has several advantages over conventional methods for removing heavy metals from contaminated sites. Here, a comparative study was made to investigate nickel detoxification mechanisms between a wild type(WT) Chlorella sp. and a nickel resistant, EMS-5 cell line isolated from the same species by EMS (Ethyl Methane Sulphonate) mutagenesis. Results showed that the growth rate of the tested algal cells was inhibited with increasing nickel concentrations in the liquid growth medium. Higher ID/sub 50/ value of EMS-5 compared to the WT revealed some degree of resistance to nickel. Removal and adsorption of Ni/sub 2+/ were found rapid during the first few hours in both the algal cultures when exposed to 50 microM Ni/sub 2+/. However, kinetic experiments showed significantly higher removal and adsorption of Ni by EMS-5 compared to the WT throughout the treatment hours. Besides, the total nickel accumulation, surface bound and intracellular nickel in EMS-5 was significantly higher to that of the WT. Hence the EMS-5 appeared more resistant to nickel. (author)

  8. Sphingomonas zeae sp. nov., isolated from the stem of Zea mays.

    Kämpfer, Peter; Busse, Hans-Jürgen; McInroy, John A; Glaeser, Stefanie P

    2015-08-01

    A yellow-pigmented bacterial isolate (strain JM-791T) obtained from the healthy internal stem tissue of 1-month-old corn (Zea mays, cultivar 'Sweet Belle') grown at the Plant Breeding Unit of the E.V. Smith Research Center in Tallassee (Elmore county), Alabama, USA, was taxonomically characterized. The study employing a polyphasic approach, including 16S RNA gene sequence analysis, physiological characterization, estimation of the ubiquinone and polar lipid patterns, and fatty acid composition, revealed that strain JM-791T shared 16S rRNA gene sequence similarities with type strains of Sphingomonas paucimobilis (98.3%), Sphingomonas pseudosanguinis (97.5%) and Sphingomonas yabuuchiae (97.4%), but also showed pronounced differences, both genotypically and phenotypically. On the basis of these results, a novel species of the genus Sphingomonas is described, for which we propose the name Sphingomonas zeae sp. nov. with the type strain JM-791T ( = LMG 28739T = CCM 8596T). PMID:25944808

  9. Pedobacter roseus sp. nov., isolated from a hypertrophic pond, and emended description of the genus Pedobacter.

    Hwang, Chung Yeon; Choi, Dong Han; Cho, Byung Cheol

    2006-08-01

    A Gram-negative, pink-coloured, rod-shaped, non-flagellated bacterium, designated CL-GP80(T), was isolated from a hypertrophic pond located within the campus of Seoul National University, Korea. Analysis of its 16S rRNA gene sequence revealed that strain CL-GP80(T) belongs to the family Sphingobacteriaceae and is closely related to Pedobacter heparinus ATCC 13125(T) (95.8 % sequence similarity) and to other members of the genus Pedobacter (90.8-95.3 % similarity). Temperature and pH ranges for growth were 5-33 degrees C and pH 6-8, respectively. The DNA G+C content was 41.3 mol%. The major fatty acids were iso-C(15 : 0) (37.0 %), iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c (24.5 %), and iso-C(17 : 0) 3-OH (11.3 %). Phenotypic, chemotaxonomic and phylogenetic analyses indicated that strain CL-GP80(T) could be assigned to the genus Pedobacter, but distinguished from recognized species of the genus. Strain CL-GP80(T) (=KCCM 42272(T)=JCM 13399(T)) is therefore proposed as the type strain of a novel species, for which the name Pedobacter roseus sp. nov. is proposed. PMID:16902016

  10. Emulsification potential of a newly isolated biosurfactant-producing bacterium, Rhodococcus sp. strain TA6.

    Shavandi, Mahmoud; Mohebali, Ghasemali; Haddadi, Azam; Shakarami, Heidar; Nuhi, Ashrafossadat

    2011-02-01

    An indigenous biosurfactant producing bacterium, Rhodococcus sp. strain TA6 was isolated from Iranian oil contaminated soil using an efficient enrichment and screening method. During growth on sucrose and several hydrocarbon substrates as sole carbon source, the bacterium could produce biosurfactants. As a result of biosurfactant synthesis, the surface tension of the growth medium was reduced from 68mNm(-1) to values below 30mNm(-1). The biosurfactant was capable of forming stable emulsions with various hydrocarbons ranging from pentane to light motor oil. Preliminary chemical characterization revealed that the TA6 biosurfactant consisted of extracellular lipids and glycolipids. The biosurfactant was stable during exposure to high salinity (10% NaCl), elevated temperatures (120°C for 15min) and within a wide pH range (4.0-10.0). The culture broth was effective in recovering up to 70% of the residual oil from oil-saturated sand packs which indicates the potential value of the biosurfactant in enhanced oil recovery. PMID:21030223

  11. Novel degradation pathway and kinetic analysis for buprofezin removal by newly isolated Bacillus sp.

    Wang, Guangli; Xu, Dayong; Xiong, Minghua; Zhang, Hui; Li, Feng; Liu, Yuan

    2016-09-15

    Given the intensive and widespread application of the pesticide, buprofezin, its environmental residues potentially pose a problem; yet little is known about buprofezin's kinetic and metabolic behaviors. In this study, a novel gram-positive strain, designated BF-5, isolated from aerobic activated sludge, was found to be capable of metabolizing buprofezin as its sole energy, carbon, and nitrogen source. Based on its physiological and biochemical characteristics, other aspects of its phenotype, and a phylogenetic analysis, strain BF-5 was identified as Bacillus sp. This study investigated the effect of culture conditions on bacterial growth and substrate degradation, such as pH, temperature, initial concentration, different nitrogen source, and additional nitrogen sources as co-substrates. The degradation rate parameters, qmax, Ks, Ki and Sm were determined to be 0.6918 h(-1), 105.4 mg L(-1), 210.5 mg L(-1), and 148.95 mg L(-1) respectively. The capture of unpublished potential metabolites by gas chromatography-mass spectrometry (GC-MS) analysis has led to the proposal of a novel degradation pathway. Taken together, our results clarify buprofezin's biodegradation pathway(s) and highlight the promising potential of strain BF-5 in bioremediation of buprofezin-contaminated environments. PMID:27208995

  12. Antioxidative and radioprotective activities of semiquinone glucoside derivative (SQGD) isolated from Bacillus sp. INM-1.

    Kumar, Raj; Bansal, Deen Dayal; Patel, Dev Dutt; Mishra, Saurabh; Karamalakova, Yana; Zheleva, A; Gadjeva, Vessilina; Sharma, Rakesh Kumar

    2011-03-01

    A semiquinone glucoside derivative (SQGD) was isolated from a radioresistant bacterium Bacillus sp. INM-1 and its antioxidant and radioprotective activities were evaluated using in vitro assays. Natural stable free radical properties of SQGD in solid as well as in solution form were estimated using Electron Paramagnetic Resonance (EPR) spectrometry. Results of the study were demonstrated high reducing power (1.267 ± 0.03356 U(abs)) and nitric oxide radicals scavenging activity (34.684 ± 2.132%) of SQGD. Maximum lipid peroxidation inhibitory activity of SQGD was found to be 74.09 ± 0.08% at 500 μg/ml concentration. Similarly, significant (39.54%; P EPR spectroscopic analysis of the SQGD indicated ~80% reduction of DPPH radicals at 6.4% concentration. EPR spectral analysis of SQGD was revealed an appearance of very strong EPR signal of 2.00485 (crystalline form) and 2.00520 (solution form) g(y) tensor value, which were an established characteristic of o-semiquinone radicals. Therefore, it can be concluded that SQGD is a natural stable o-semiquinone-type radical, possessing strong antioxidant activities and can effectively neutralize radiation induced free radicals in biological system. PMID:21116688

  13. Flaviaesturariibacter amylovorans gen. nov., sp. nov., a starch-hydrolysing bacterium, isolated from estuarine water.

    Kang, Ji Young; Chun, Jeesun; Seo, Jeong-Woo; Kim, Chul Ho; Jahng, Kwang Yeop

    2015-07-01

    A novel bacterial strain, designated GCR0105(T), was isolated from a water sample of the Mangyung estuary enclosed by the Saemangeum Embankment, located in JEOLlabuk-do, South Korea. Cells of strain GCR0105(T) were Gram-stain-negative, non-motile and rod-shaped. Colonies of strain GCR0105(T) were pale yellow-pigmented on R2A agar and nutrient agar media, and were able to grow at 15-30 °C (optimum 25 °C) and pH 6.5-8.5 (optimum pH 7.5). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain GCR0105(T) was related most closely to Flavisolibacter ginsengisoli Gsoil 643(T) (93.14% similarity). The polar lipid profile of strain GCR0105(T) comprised phosphatidylethanolamine, two unknown aminolipids, an unknown aminophospholipid and four unknown lipids. The DNA G+C content of strain GCR0105(T) was 42.9 mol% and the respiratory quinone was MK-7.On the basis of phenotypic, chemotaxonomic and phylogenetic properties, strain GCR0105(T) represents a novel species in a new genus within the family Chitinophagaceae, for which the name Flaviaesturariibacter amylovorans gen. nov., sp. nov. is proposed. The type strain of Flaviaesturariibacter amylovorans is GCR0105(T) ( = KACC 16454(T) = JCM 17919(T)). PMID:25858251

  14. Mycobacterium alsense sp. nov., a scotochromogenic slow grower isolated from clinical respiratory specimens.

    Tortoli, Enrico; Richter, Elvira; Borroni, Emanuele; Cabibbe, Andrea M; Capitolo, Eleonora; Cittaro, Davide; Engel, Regina; Hendricks, Oliver; Hillemann, Doris; Kristiansen, Jette E; Mariottini, Alessandro; Schubert, Sabine; Cirillo, Daniela M

    2016-01-01

    The name 'Mycobacterium alsiense', although reported in 2007, has not been validly published. Polyphasic characterization of three available strains of this species led us to the conclusion that they represent a distinct species within the genus Mycobacterium. The proposed novel species grows slowly and presents pale yellow-pigmented colonies. Differentiation from other mycobacteria is not feasible on the basis of biochemical and cultural features alone while genetic analysis, extended to eight housekeeping genes and one spacer region, reveals its clear distinction from all other mycobacteria. Mycobacterium asiaticum is the most closely related species on the basis of 16S rRNA gene sequences (similarity 99.3 %); the average nucleotide identity between the genomes of the two species is 80.72 %, clearly below the suggested cut-off (95-96 %). The name Mycobacterium alsense sp. nov. is proposed here for the novel species and replaces the name 'M. alsiense', ex Richter et al. 2007, given at the time of isolation of the first strain. The type strain is TB 1906T ( = DSM 45230T = CCUG 56586T). PMID:26545358

  15. Acaricomes phytoseiuli gen. nov., sp. nov., isolated from the predatory mite Phytoseiulus persimilis.

    Pukall, Rüdiger; Schumann, Peter; Schütte, Conny; Gols, Rieta; Dicke, Marcel

    2006-02-01

    A Gram-positive, rod-shaped, non-spore-forming bacterium, strain CSCT, was isolated from diseased, surface-sterilized specimens of the predatory mite Phytoseiulus persimilis Athias-Henriot and subjected to polyphasic taxonomic analysis. Comparative analysis of the 16S rRNA gene sequence revealed that the strain was a new member of the family Micrococcaceae. Nearest phylogenetic neighbours were determined as Renibacterium salmoninarum (94.0%), Arthrobacter globiformis (94.8%) and Arthrobacter russicus (94.6%). Although the predominant fatty acids (anteiso C15:0), cell-wall sugars (galactose, glucose) and polar lipids (diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol) are in accordance with those of members of the genus Arthrobacter, strain CSCT can be distinguished from members of the genus Arthrobacter by biochemical tests, the absence of a rod-coccus life cycle and the occurrence of the partially saturated menaquinone MK-10(H2) as the predominant menaquinone. The DNA G+C content is 57.7 mol%. On the basis of morphological, chemotaxonomic and phylogenetic differences from other species of the Micrococcaceae, a novel genus and species are proposed, Acaricomes phytoseiuli gen. nov., sp. nov. The type strain is CSCT (=DSM 14247T=CCUG 49701T). PMID:16449459

  16. Geminicoccus roseus gen. nov., sp. nov., an aerobic phototrophic Alphaproteobacterium isolated from a marine aquaculture biofilter.

    Foesel, Bärbel U; Gössner, Anita S; Drake, Harold L; Schramm, Andreas

    2007-12-01

    A Gram-negative, strictly aerobic, diplococcoid bacterium (strain D2-3(T)) was isolated from the biofilter of a recirculating marine aquaculture system. Phylogenetic analysis of the 16S rRNA gene sequence of D2-3(T) indicated that the new organism occupied a novel lineage within the alpha-1 subclass of Proteobacteria and was related to the genera Rhodothalassium, Azospirillum, Craurococcus, Acidiphilium, and Tistrella. The highest sequence similarity (90.8%) of the 16S rRNA gene sequence of D2-3(T) was to that of Candidatus "Alysiosphaera europaea". D2-3(T) was mesophilic, heterotrophic, required sea salt, and had a pH optimum of 8.0. Growth in the presence of light resulted in the formation of pink colonies, a 25% increased cell yield, and a slightly increased growth rate. D2-3(T) contained carotenoids and low amounts of bacteriochlorophyll a. Membranes of D2-3(T) contained b-type cytochromes. The G+C content of the DNA was 60.3+/-0.1mol%. Phylogenetic, morphological, physiological, and biochemical analyses demonstrated that D2-3(T) represented a new aerobic phototrophic genus, for which the name Geminicoccus roseus gen. nov., sp. nov. is proposed for the type species (D2-3(T)=DSM 18922(T)=ATCC BAA-1445(T)). PMID:17643894

  17. Deinococcus mumbaiensis sp. nov., a radiation-resistant pleomorphic bacterium isolated from Mumbai, India.

    Shashidhar, Ravindranath; Bandekar, Jayant R

    2006-01-01

    A radiation-resistant, Gram-negative and pleomorphic bacterium (CON-1) was isolated from a contaminated tryptone glucose yeast extract agar plate in the laboratory. It was red pigmented, nonmotile, nonsporulating, and aerobic, and contained MK-8 as respiratory quinone. The cell wall of this bacterium contained ornithine. The major fatty acids were C16:0, C16:1, C17:0, C18:1 and iso C18:0. The DNA of CON-1 had a G+C content of 70 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that CON-1 exhibited a maximum similarity (94.72%) with Deinococcus grandis. Based on the genotypic, phenotypic and chemotaxonomic characteristics, the bacterium CON-1 was identified as a new species of the genus Deinococcus, for which the name Deinococcus mumbaiensis sp. nov. is proposed. The type strain of D. mumbaiensis is CON-1 (MTCC 7297(T)=DSM 17424(T)). PMID:16445756

  18. The chloroplast genome of a symbiodinium sp. clade C3 isolate

    Barbrook, Adrian C.

    2014-01-01

    Dinoflagellate algae of the genus Symbiodinium form important symbioses within corals and other benthic marine animals. Dinoflagellates possess an extremely reduced plastid genome relative to those examined in plants and other algae. In dinoflagellates the plastid genes are located on small plasmids, commonly referred to as \\'minicircles\\'. However, the chloroplast genomes of dinoflagellates have only been extensively characterised from a handful of species. There is also evidence of considerable variation in the chloroplast genome organisation across those species that have been examined. We therefore characterised the chloroplast genome from an environmental coral isolate, in this case containing a symbiont belonging to the Symbiodinium sp. clade C3. The gene content of the genome is well conserved with respect to previously characterised genomes. However, unlike previously characterised dinoflagellate chloroplast genomes we did not identify any \\'empty\\' minicircles. The sequences of this chloroplast genome show a high rate of evolution relative to other algal species. Particularly notable was a surprisingly high level of sequence divergence within the core polypeptides of photosystem I, the reasons for which are currently unknown. This chloroplast genome also possesses distinctive codon usage and GC content. These features suggest that chloroplast genomes in Symbiodinium are highly plastic. © 2013 Adrian C. Barbrook.

  19. Plant growth promoting potential of pseudomonas sp. SP0113 isolated from potable water from a closed water well

    Przemieniecki Wojciech Sebastian

    2015-01-01

    Full Text Available The Pseudomonas sp. SP0113 strain from a partially closed aquatic environment was identified as a plant growth promoting bacterium (PGPB. Laboratory tests revealed that PS0113 has multiple plant growth promoting traits, including mineral phosphate solubilizing ability, ammonifying ability that increases nitrogen availability for plants via the root system, and phosphatase activity that plays an important role in organic phosphorus mineralization. Tricalcium phosphate (Ca3(PO42 solubilizing ability was described as average (2-3 mm after 7 days of incubation and as high (>3 mm after 14 days of incubation. The analyzed bacterium was an antagonist of major crop pathogenic fungi. A high degree of pathogen growth inhibition was reported with regard to Rhizoctonia solani (38%, whereas the tested strain's ability to inhibit the growth of fungi of the genera Fusarium and Microdochium nivalis was somewhat lower at 20-29%. The bacterium proliferated in Roundup 360 SL solutions with concentrations of 0.1, 1 and 10 mg•ml-1.

  20. Cytotoxicity of three new triazolo-pyrimidine derivatives against the plant trypanosomatid: Phytomonas sp. isolated from Euphorbia characias

    Rosa Magán

    2004-10-01

    Full Text Available There is no effective chemotherapy against diseases caused by Phytomonas sp., a plant trypanosomatid responsible for economic losses in major crops. We tested three triazolo-pyrimidine complexes [two with Pt(II, and another with Ru(III] against promastigotes of Phytomonas sp. isolated from Euphorbia characias. The incorporation of radiolabelled precursors, ultrastructural alterations and changes in the pattern of metabolite excretion were examined. Different degrees of toxicity were found for each complex: the platinun compound showed an inhibition effect on nucleic acid synthesis, provoking alterations on the levels of mitochondria, nucleus and glycosomes. These results, together with others reported previously in our laboratory about the activity of pyrimidine derivatives, reflect the potential of these compounds as agents in the treatment of Phytomonas sp.

  1. THE RESISTANCE TO ANTIBIOTICS IN STRAINS OF E. COLI AND ENTEROCOCCUS SP. ISOLATED FROM RECTAL SWABS OF LAMBS AND CALVES

    IVANA NOVÁKOVÁ

    2013-07-01

    Full Text Available he aim of this study was to determine the prevalence and antibiotic resistance of enterococcii and E. coli strains isolated from dairy calves and lambs. Susceptibilities of isolated enterococci were tested using the disk diffusion method. The interpretation of inhibition zones around the disks was according to CLSI 2004 Performance standards for antimicrobial susceptibility testing. In our study, all isolates (E. coli and enterococci were multiresistant (100% to tetracycline, streptomycin and compound sulphonamides. Lower levels of resistance to enrofloxacin were noted. Antimicrobial resistance profiles of Enterococcus sp. isolated from lambs indicated that the highest percentage of susceptibility was exhibited to tetracycline (100% and streptomycin (100% and compound sulphonamides (100%. The intermediate resistance was exhibited against compound enrofloxacin (80%. The high frequencies of resistant isolates of Enterococcus sp. from calves were documented in tetracycline (100%, streptomycin (100% and compound sulphonamides (100% and enrofloxacin (50%. The high percentage (compound sulphonamides-100%, tetracycline-100% and streptomycin- 100% of multiresistant E. coli (isolates from dairy calves was noticed. There were no significant correlations between groups.

  2. Eksopolisakarida dari Lactobacillus sp. Isolat Susu Kuda Sumbawa dan Potensinya sebagai Prebiotik (EXOPOLYSACCHARIDES FROM LACTOBACILLUS SP. ISOLATED FROM SUMBAWA MARE’S MILK AND ITS POTENTIAL APPLICATION AS PREBIOTICS)

    I Nengah Sujaya; Ni Putu Desy Aryantini; Ni Wayan Nursini; Cok. Istri Dewiyani Cakrawati; Ni Luh Made Ema Juliasari; Ni Made Utami Dwipayanti; Yan Ramona

    2014-01-01

    This research aimed to isolate exopolysaccharides (EPS) producing Lactobacilli isolated fromsumbawa mare’s milk and its potential as prebiotics for modulating the growth of Bifidobacteriumbreve. Nine strains of Lactobacillus sp. were screened for their capabilities to produce EPS usingmodified MRS medium containing sucrose. Prebiotics potential of the EPS was verified by culturingB. breve JCM1273 in TOS medium containing EPS. The results showed that all strains ofLactobacillus sp. produced EP...

  3. Hamadaea flava sp. nov., isolated from a soil sample and emended description of the genus Hamadaea.

    Chu, Xiao; Li, Shuai; Chen, Wei; Devi Asem, Mipeshwaree; Duan, Yan-Qing; Nie, Guo-Xing; Hozzein, Wael N; Zhi, Xiao-Yang; Li, Wen-Jun

    2016-04-01

    A Gram-stain-positive, aerobic and non-motile actinobacterial strain, designated YIM C0533T, was isolated from a soil sample collected from Shiling county, Yunnan province, south-west China. The isolate grew at 15-37 °C, pH 6.0-8.0 and in the presence of 0-3 % (w/v) NaCl. The whole-cell hydrolysates contained meso-diaminopimelic acid, xylose, galactose, mannose, ribose, arabinose, glucose and rhamnose. The acyl type of muramic acid was glycolyl. The polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and an unidentified phospholipid. The major cellular fatty acids were iso-C16 : 0, 10-methyl C17 : 0 and iso-C15 : 0.MK-9(H6) was the predominant menaquinone. The genomic DNA G+C content was determined to be 69.4 mol%. These chemotaxonomic data and the morphological properties were consistent with those of the genus Hamadaea. The strain showed highest sequence similarities to Hamadaea tsunoensis CGMCC 4.1403T on phylogenetic analysis of 16S rRNA gene sequences and was found to form a coherent cluster in the neighbour-joining tree. The DNA-DNA hybridization experiment indicated that the DNA-DNA relatedness value between strain YIM C0533T and H. tsunoensis CGMCC 4.1403T was 34.4 ± 1.3 %. In addition, the results of physiological and biochemical tests allowed the isolate to be differentiated phenotypically from H. tsunoensis CGMCC 4.1403T. On the basis of data from this polyphasic study, strain YIM C0533T is characterized as a novel species of the genus Hamadaea, for which the name Hamadaea flava sp. nov. is proposed. The type strain is YIM C0533T ( = CPCC 204160T = KCTC 39591T = CGMCC 4.7289T). An emended description of the genus Hamadaea is also provided. PMID:26842996

  4. Pseudomonas yamanorum sp. nov., a psychrotolerant bacterium isolated from a subantarctic environment.

    Arnau, Víctor Gonzalo; Sánchez, Leandro Arturo; Delgado, Osvaldo Daniel

    2015-02-01

    A psychrotolerant strain, 8H1(T), was isolated from soil samples collected in Isla de los Estados, Ushuaia, Argentina. Cells were Gram-negative, aerobic, straight rods, occurring singly or in pairs, non-spore-forming and motile by means of two polar flagella. The isolate was able to grow in the range 4-35 °C, with optimum growth at 28 °C. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The polar lipid pattern of strain 8H1(T) comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unknown phospholipid. Ubiquinone 9 (Q-9) was the predominant lipoquinone. The DNA G+C content was 59.8 mol%. 16S rRNA gene sequence-based phylogeny suggested the affiliation of strain 8H1(T) to the 'Pseudomonas fluorescens group', displaying ≥98.5 % sequence similarity to 29 type strains. A multilocus sequence analysis (MLSA) study performed by concatenating 16S rRNA, gyrB, rpoD and rpoB gene sequences showed that isolate 8H1(T) could be discriminated from closely related species of the genus Pseudomonas and placed in the 'Pseudomonas gessardii subgroup', including the species with the highest MLSA sequence similarities: Pseudomonas brenneri (96.2 %), P. gessardii (96.1 %), P. proteolytica (96.0 %), P. meridiana (96.0 %) and P. mucidolens (95.4 %). DNA-DNA hybridization analysis between 8H1(T) and the type strains of these closely related species revealed relatedness values of 27.0, 8.8, 41.2, 39.7 and 46.1 %, respectively. These results, together with differences in several phenotypic features, support the classification of a novel species, for which the name Pseudomonas yamanorum sp. nov. is proposed. The type strain is 8H1(T) ( = DSM 26522(T) = CCUG 63249(T) = LMG 27247(T)). PMID:25385990

  5. Desulfurella amilsii sp. nov., a novel acidotolerant sulfur-respiring bacterium isolated from acidic river sediments.

    Florentino, Anna P; Brienza, Claudio; Stams, Alfons J M; Sánchez-Andrea, Irene

    2016-03-01

    A novel acidotolerant and moderately thermophilic sulfur-reducing bacterium was isolated from sediments of the Tinto River (Spain), an extremely acidic environment. Strain TR1T stained Gram-negative, and was obligately anaerobic, non-spore-forming and motile. Cells were short rods (1.5-2 × 0.5-0.7 μm), appearing singly or in pairs. Strain TR1T was catalase-negative and slightly oxidase-positive. Urease activity and indole formation were absent, but gelatin hydrolysis was present. Growth was observed at 20-52 °C with an optimum close to 50 °C, and a pH range of 3-7 with optimum between pH 6 and 6.5. Yeast extract was essential for growth, but extra vitamins were not required. In the presence of sulfur, strain TR1T grew with acetate, formate, lactate, pyruvate, stearate, arginine and H2/CO2. All substrates were completely oxidized and H2S and CO2 were the only metabolic products detected. Besides elemental sulfur, thiosulfate was used as an electron acceptor. The isolate also grew by disproportionation of elemental sulfur. The predominant cellular fatty acids were saturated components: C16 : 0, anteiso-C17 : 0 and C18 : 0. The only quinone component detected was menaquinone MK-7(H2). The G+C content of the genomic DNA was 34 mol%. The isolate is affiliated to the genus Desulfurella of the class Deltaproteobacteria, sharing 97 % 16S rRNA gene sequence similarity with the four species described in the genus Desulfurella. Considering the distinct physiological and phylogenetic characteristics, strain TR1T represents a novel species within the genus Desulfurella, for which the name Desulfurella amilsii sp. nov. is proposed. The type strain is TR1T ( = DSM 29984T = JCM 30680T). PMID:26704766

  6. Blastomonas aquatica sp. nov., a bacteriochlorophyll-containing bacterium isolated from lake water.

    Xiao, Na; Liu, Yongqin; Liu, Xiaobo; Gu, Zhengquan; Jiao, Nianzhi; Liu, Hongcan; Zhou, Yuguang; Shen, Liang

    2015-05-01

    Yellow or orange-to-brown pigmented, ovoid or rod-shaped, Gram-negative staining, aerobic strains PE 4-5(T) and N5-10 m-1 were isolated from brackish water in Lake Peng Co and fresh to brackish water in Lake Namtso on the Tibetan Plateau, China. Bacteriochlorophyll a was produced by the isolates. The predominant cellular fatty acids were C16 : 1, C17 : 1 and C18 : 1 unsaturated fatty acids, C17 : 1ω6c (55.3%), C17 : 1ω8c (13.0%) and C18 : 1ω7c (10.4%) for PE 4-5(T) and C18 : 1ω7c (54.7%) and C16 : 1ω7c (18.0%) for N5-10 m-1. The polar lipid profiles of strains PE 4-5(T) and N5-10 m-1 were composed of diphosphatidylglycerol, phosphatidylcholine (not detected in N5-10 m-1), phosphatidyldimethylethanolamine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, sphingoglycolipid and an unknown phospholipid. The predominant respiratory quinone was ubiquinone Q10 and the DNA G+C content was 66.0 mol% for both strains. The16S rRNA gene sequence of strain PE 4-5(T) shared 99.0% similarity with that of N5-10 m-1, and 97.56% similarity with those of Blastomonas natatoria LMG 17322(T) and Blastomonas ursincola DSM 9006(T), respectively. The DNA-DNA hybridization relatedness between strains PE 4-5(T) and N5-10 m-1 was 79.0 ± 1.0%, but below 70% with the type strains in the genus Blastomonas . Based on the variability of phylogenetic and phenotypic characteristics, the isolates should be classified as representatives of a novel species of the genus Blastomonas; the name Blastomonas aquatica sp. nov. is proposed. The type strain is PE 4-5(T) ( =JCM 30179(T) =CGMCC 1.12851(T)). PMID:25724744

  7. Phaeobacterium nitratireducens gen. nov., sp. nov., a phototrophic gammaproteobacterium isolated from a mangrove forest sediment sample.

    Nupur; Tanuku, Naga Radha Srinivas; Shinichi, Takaichi; Pinnaka, Anil Kumar

    2015-08-01

    A novel brown-coloured, Gram-negative-staining, rod-shaped, motile, phototrophic, purple sulfur bacterium, designated strain AK40T, was isolated in pure culture from a sediment sample collected from Coringa mangrove forest, India. Strain AK40T contained bacteriochlorophyll a and carotenoids of the rhodopin series as major photosynthetic pigments. Strain AK40T was able to grow photoheterotrophically and could utilize a number of organic substrates. It was unable to grow photoautotrophically and did not utilize sulfide or thiosulfate as electron donors. Thiamine and riboflavin were required for growth. The dominant fatty acids were C12 : 0, C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The polar lipid profile of strain AK40T was found to contain diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and eight unidentified lipids. Q-10 was the predominant respiratory quinone. The DNA G+C content of strain AK40T was 65.5 mol%. 16S rRNA gene sequence comparisons indicated that the isolate represented a member of the family Chromatiaceae within the class Gammaproteobacteria. 16S rRNA gene sequence analysis indicated that strain AK40T was closely related to Phaeochromatium fluminis, with 95.2% pairwise sequence similarity to the type strain; sequence similarity to strains of other species of the family was 90.8-94.8%. Based on the sequence comparison data, strain AK40T was positioned distinctly outside the group formed by the genera Phaeochromatium, Marichromatium, Halochromatium, Thiohalocapsa, Rhabdochromatium and Thiorhodovibrio. Distinct morphological, physiological and genotypic differences from previously described taxa supported the classification of this isolate as a representative of a novel species in a new genus, for which the name Phaeobacterium nitratireducens gen. nov., sp. nov. is proposed. The type strain of Phaeobacterium nitratireducens is AK40T ( = JCM 19219T = MTCC 11824T

  8. Effect of pretreatments on enhanced degradation of polyisoprene rubber by newly isolated bacillus sp, strain S10

    The present investigation was conducted to isolate polyisoprene rubber (latex gloves) degrading microorganisms from soil. Twelve bacterial species were isolated through enrichment technique and were screened for their capacity to degrade rubber. Best growth was observed with Bacillus sp. S 10 in terms of diameter of the spot on latex overlay mineral salt agar plates and increase in optical density as determined at 600 nm for liquid culture. The effect of different pretreatments like extraction of rubber pieces with organic solvent (acetone), pretreatment with UV and sunlight, effect of temperature and pH were optimized for Bacillus sp. S10 in liquid MSM with pieces of gloves as the only source of carbon In case of pretreated rubber best growth was observed in case of acetone pretreated rubber shown by increase in optical density. Bacillus sp. S10 grew best at pH 7 at 37 degree C Qualitative analysis of degradation of pretreated rubbers, after incubation in liquid MSM with Bacillus sp. S I 0 was done through FTIR which showed marked differences in transmittance spectra of test and control due to changes in the functional groups Present study on biodegradation may provide an opportunity for further studies on the applications of biotechnological processes as a tool for rubber waste management. (author)

  9. Molecular characterization of clinical multiresistant isolates of Acinetobacter sp. from hospitals in Porto Alegre, State of Rio Grande do Sul, Brazil

    Alessandra Einsfeld Ferreira

    2011-12-01

    Full Text Available INTRODUCTION: Hospitals around the world have presented multiresistant Acinetobacter sp. outbreaks. The spread of these isolates that harbor an increasing variety of resistance genes makes the treatment of these infections and their control within the hospital environment more difficult. This study aimed to evaluate the occurrence and dissemination of Acinetobacter sp. multiresistant isolates and to identify acquired resistance genes. METHODS: We analyzed 274 clinical isolates of Acinetobacter sp. from five hospitals in Porto Alegre, RS, Brazil. We evaluated the susceptibility to antimicrobial, acquired resistance genes from Ambler's classes B and D, and performed molecular typing of the isolates using enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR technique. RESULTS: A high (68% percentage of multiresistant isolates of Acinetobacter sp. was observed, and 69% were resistant to carbapenems. We identified 84% of isolates belonging to species A. baumannii because they presented the gene blaOXA-51. The gene blaOXA-23 was detected in 62% of the isolates, and among these, 98% were resistant to carbapenems. Using the ERIC-PCR technique, we identified clones of Acinetobacter sp. spread among the four hospitals analyzed during the sampling period. CONCLUSIONS: The data indicate the dissemination of Acinetobacter sp. isolates among hospitals and their permanence in the hospital after one year.

  10. Characterization of Klebsiella sp. strain 10982, a colonizer of humans that contains novel antibiotic resistance alleles and exhibits genetic similarities to plant and clinical Klebsiella isolates.

    Hazen, Tracy H; Zhao, LiCheng; Sahl, Jason W; Robinson, Gwen; Harris, Anthony D; Rasko, David A; Johnson, J Kristie

    2014-01-01

    A unique Klebsiella species strain, 10982, was cultured from a perianal swab specimen obtained from a patient in the University of Maryland Medical Center intensive care unit. Klebsiella sp. 10982 possesses a large IncA/C multidrug resistance plasmid encoding a novel FOX AmpC β-lactamase designated FOX-10. A novel variant of the LEN β-lactamase was also identified. Genome sequencing and bioinformatic analysis demonstrated that this isolate contains genes associated with nitrogen fixation, allantoin metabolism, and citrate fermentation. These three gene regions are typically present in either Klebsiella pneumoniae clinical isolates or Klebsiella nitrogen-fixing endophytes but usually not in the same organism. Phylogenomic analysis of Klebsiella sp. 10982 and sequenced Klebsiella genomes demonstrated that Klebsiella sp. 10982 is present on a branch that is located intermediate between the genomes of nitrogen-fixing endophytes and K. pneumoniae clinical isolates. Metabolic features identified in the genome of Klebsiella sp. 10982 distinguish this isolate from other Klebsiella clinical isolates. These features include the nitrogen fixation (nif) gene cluster, which is typically present in endophytic Klebsiella isolates and is absent from Klebsiella clinical isolates. Additionally, the Klebsiella sp. 10982 genome contains genes associated with allantoin metabolism, which have been detected primarily in K. pneumoniae isolates from liver abscesses. Comparative genomic analysis of Klebsiella sp. 10982 demonstrated that this organism has acquired genes conferring new metabolic strategies and novel antibiotic resistance alleles, both of which may enhance its ability to colonize the human body. PMID:24395222

  11. Efficient biodegradation of phenanthrene by a novel strain Massilia sp. WF1 isolated from a PAH-contaminated soil.

    Wang, Haizhen; Lou, Jun; Gu, Haiping; Luo, Xiaoyan; Yang, Li; Wu, Laosheng; Liu, Yong; Wu, Jianjun; Xu, Jianming

    2016-07-01

    A novel phenanthrene (PHE)-degrading strain Massilia sp. WF1, isolated from PAH-contaminated soil, was capable of degrading PHE by using it as the sole carbon source and energy in a range of pH (5.0-8.0), temperatures (20-35 °C), and PHE concentrations (25-400 mg L(-1)). Massilia sp. WF1 exhibited highly effective PHE-degrading ability that completely degraded 100 mg L(-1) of PHE over 2 days at optimal conditions (pH 6.0, 28 °C). The kinetics of PHE biodegradation by Massilia sp. WF1 was well represented by the Gompertz model. Results indicated that PHE biodegradation was inhibited by the supplied lactic acid but was promoted by the supplied carbon sources of glucose, citric acid, and succinic acid. Salicylic acid (SALA) and phthalic acid (PHTA) were not utilized by Massilia sp. WF1 and had no obvious effect on PHE biodegradation. Only two metabolites, 1-hydroxy-2-naphthoic acid (1H2N) and PHTA, were identified in PHE biodegradation process. Quantitatively, nearly 27.7 % of PHE was converted to 1H2N and 30.3 % of 1H2N was further metabolized to PHTA. However, the PHTA pathway was broken and the SALA pathway was ruled out in PHE biodegradation process by Massilia sp. WF1. PMID:27026540

  12. A low cost fermentation medium for potential fibrinolytic enzyme production by a newly isolated marine bacterium, Shewanella sp. IND20

    Vijayaraghavan, P; S.G. Prakash Vincent

    2015-01-01

    Agro-residues were used as the substrate for the production of fibrinolytic enzyme in solid state fermentation. In this study, two-level full factorial design (25) and response surface methodology were applied to optimize a fermentation medium for the production of fibrinolytic enzyme from the marine isolate Shewanella sp. IND20. The 25 factorial design demonstrated that the physical factors (pH and moisture) and nutrient factors (trehalose, casein, and sodium dihydrogen phosphate) had signif...

  13. Isolation and identification of berberine and berberrubine metabolites by berberine-utilizing bacterium Rhodococcus sp. strain BD7100.

    Ishikawa, Kazuki; Takeda, Hisashi; Wakana, Daigo; Sato, Fumihiko; Hosoe, Tomoo

    2016-05-01

    Based on the finding of a novel berberine (BBR)-utilizing bacterium, Rhodococcus sp. strain BD7100, we investigated the degradation of BBR and its analog berberrubine (BRU). Resting cells of BD7100 demethylenated BBR and BRU, yielding benzeneacetic acid analogs. Isolation of benzeneacetic acid analogs suggested that BD7100 degraded the isoquinoline ring of the protoberberine skeleton. This work represents the first report of cleavage of protoberberine skeleton by a microorganism. PMID:26882131

  14. Whole genome sequencing of Halomonas sp. SUBG004 isolated from Little Rann of Kutch, a desert of India

    Jigna H. Patel; Thaker, Vrinda S.

    2015-01-01

    A salt tolerant strain, designated as SUBG004, was isolated from the desert of India, Little Rann of Kutch. The organism is a Gram-negative, facultatively anaerobic and rod shaped bacterium. Chemotaxonomic and phylogenetic properties were consistent with its classification in the genus Halomonas. Here we report the whole genome sequence of Halomonas sp. SUBG004 deposited in DDBJ/EMBL/GenBank under accession number JPEU0100000 which provides insights for salt stress adaptation through betaine ...

  15. Whole genome sequencing of Halomonas sp. SUBG004 isolated from Little Rann of Kutch, a desert of India.

    Patel, Jigna H; Thaker, Vrinda S

    2015-12-01

    A salt tolerant strain, designated as SUBG004, was isolated from the desert of India, Little Rann of Kutch. The organism is a Gram-negative, facultatively anaerobic and rod shaped bacterium. Chemotaxonomic and phylogenetic properties were consistent with its classification in the genus Halomonas. Here we report the whole genome sequence of Halomonas sp. SUBG004 deposited in DDBJ/EMBL/GenBank under accession number JPEU0100000 which provides insights for salt stress adaptation through betaine synthesis. PMID:26697321

  16. Whole genome sequencing of Halomonas sp. SUBG004 isolated from Little Rann of Kutch, a desert of India

    Jigna H. Patel

    2015-12-01

    Full Text Available A salt tolerant strain, designated as SUBG004, was isolated from the desert of India, Little Rann of Kutch. The organism is a Gram-negative, facultatively anaerobic and rod shaped bacterium. Chemotaxonomic and phylogenetic properties were consistent with its classification in the genus Halomonas. Here we report the whole genome sequence of Halomonas sp. SUBG004 deposited in DDBJ/EMBL/GenBank under accession number JPEU0100000 which provides insights for salt stress adaptation through betaine synthesis.

  17. High biodegradation levels of 4,5,6-trichloroguaiacol by Bacillus sp. isolated from cellulose pulp mill effluent

    Tondo E.C.; Andretta C.W.S.; Souza C.F.V.; Monteiro A.L.; Henriques J.A.P.; Ayub M.A.Z.

    1998-01-01

    An aerobic Gram positive spore-forming bacterium was isolated from cellulose pulp mill effluent. This microorganism, identified as Bacillus sp. and named IS13, was able to rapidly degrade the organic chlorinated compound 4,5,6-trichloroguaiacol (4,5,6-TCG) from a culture containing 50 mg/l, which corresponds to about 3x104 times the concentration found in the original effluent. The biodegradation of this compound, usually found in cellulose pulp mill effluents, was evaluated by spectrophotome...

  18. Growth temperature of different local isolates of Bacillus sp. in the solid state affects production of raw starch digesting amylases

    Šokarda-Slavić Marinela; Božić Nataša; Vujčić Z.

    2014-01-01

    Natural amylase producers, wild type strains of Bacillus sp., were isolated from different regions of Serbia. Strains with the highest amylase activity based on the starch-agar plate test were grown on solid-state fermentation (SSF) on triticale. The influence of the substrate and different cultivation temperature (28 and 37°C) on the production of amylase was examined. The tested strains produced α-amylases when grown on triticale grains both at 28 and at ...

  19. Radamycin, a novel thiopeptide produced by streptomyces sp. RSP9. I. Taxonomy, fermentation, isolation and biological activities

    González Holgado Gloria; Castro Rodríguez, Julian; Díaz, Margarita; Fernández-Ábalos, José M.; Santamaría, Ramón I

    2002-01-01

    The newly isolated strain Streptomyces sp. RSP9 produces two thiopeptides; one of them is methylsulfomycin I, which shows potent antibiotic activity against several gram-positive bacteria such as Micrococcus luteus and Staphylococcus aureus. The other is a new thiopeptide named radamycin. In the present work, this compound was purified and tested against several microorganisms and no antibiotic activity was detected in the assays. However, it does have a very strong capacity as an inducer of ...

  20. Scytalidium parasiticum sp. nov., a New Species Parasitizing on Ganoderma boninense Isolated from Oil Palm in Peninsular Malaysia

    Goh, Yit Kheng; Goh, Teik Khiang; Marzuki, Nurul Fadhilah; Tung, Hun Jiat; Goh, You Keng; Goh, Kah Joo

    2015-01-01

    A mycoparasite, Scytalidium parasiticum sp. nov., isolated from the basidiomata of Ganoderma boninense causing basal stem rot of oil palm in Johor, Malaysia, is described and illustrated. It is distinct from other Scytalidium species in having smaller asci and ascospores (teleomorphic stage), longer arthroconidia (anamorphic stage), hyaline to yellowish chlamydospores, and producing a fluorescent pigment. The phylogenetic position of S. parasiticum was determined by sequence analyses of the i...

  1. Extracellular cold active lipase from the psychrotrophic Halomonas sp. BRI 8 isolated from the Antarctic sea water

    Vipra Vijay Jadhav; Swanandi Suresh Pote; Amit Yadav; Shouche, Yogesh S.; Rama Kaustubh Bhadekar

    2013-01-01

    An extracellular cold active lipase-producing psychrotrophic bacterium (BRI 8) was isolated from the Antarctic sea water sample. The 16s rRNA sequence study revealed that the isolate belongs to the genus Halomonas (929 bp). The present paper reports optimization of fermentation conditions for production of lipase (EC 3.1.1.3) from Halomonas sp. BRI 8. Highest lipase production was observed in the medium containing olive oil and peptone. The optimum pH and temperature for enzyme catalysis were...

  2. An antimicrobial alkaloid and other metabolites produced by Penicillium sp. An endophytic fungus isolated from Mauritia flexuosa L. f.

    Hector Henrique Ferreira Koolen; Elzalina Ribeiro Soares; Felipe Moura Araújo da Silva; Richardson Alves de Almeida; Afonso Duarte Leão de Souza; Lívia Soman de Medeiros; Edson Rodrigues Filho; Antonia Queiroz Lima de Souza

    2012-01-01

    The alkaloid glandicoline B (1) and six other compounds: ergosterol (2), brassicasterol (3), ergosterol peroxide (4), cerevisterol (5), mannitol (6) and 1-O-α-D-glucopyranoside (7) were isolated from Penicillium sp. strain PBR.2.2.2, a fungus from Mauritia flexuosa roots. The structures of the isolated metabolites were established by spectral analysis. MeOH extract of the fungal mycelium at 500 µg mL-1 exhibited antimicrobial activity against Staphylococcus aureus and the compound 1 at 100 µg...

  3. Poly-β-Hydroxybutyrate (PHB Production By Amylolytic Micrococcus sp. PG1 Isolated From Soil Polluted Arrowroot Starch Waste

    Sebastian Margino

    2015-12-01

    Full Text Available Poly-β-hydroxybutyrate (PHB production from amylolytic Micrococcus sp. PG1. Poly-β-hydroxybutyrate(PHB is an organic polymer, which synthesized by many bacteria and serves as internal energy. PHB ispotential as future bioplastic but its price is very expensive due to glucose usage in PHB industry. Thedevelopment of PHB production using starch as an alternative carbon source has been conducted to reducethe dependence of glucose in PHB production. In this study, amylolytic bacteria from arrowroot processingsite were screened quantitavely based on amylase specifi c activity and PHB producing ability. The result of thestudy showed that among of 24 amylolytic isolates, 12 isolates of them were able to accumulate PHB rangedfrom 0,68-11,65% (g PHB/g cdw. The highest PHB production from substrate arrowroot starch was PG1 andafter optimization resulted in increasing of PHB production up to 16,8% (g PHB/g cdw 40 hours incubationtime. Based on morphological, biochemical and physiological characters, the PG1 isolate was identifi ed asMicrococcus sp. PG1. Result of the FTIR analysis of produced polymer by Micrococcus sp. PG1 was indicatedas poly-β- hydroxybutyrate (PHB

  4. Unusual Multiple Production of N-Acylhomoserine Lactones a by Burkholderia sp. Strain C10B Isolated from Dentine Caries

    Share Yuan Goh

    2014-05-01

    Full Text Available Bacteria realize the ability to communicate by production of quorum sensing (QS molecules called autoinducers, which regulate the physiological activities in their ecological niches. The oral cavity could be a potential area for the presence of QS bacteria. In this study, we report the isolation of a QS bacterial isolate C10B from dentine caries. Preliminary screening using Chromobacterium violaceum CV026 biosensor showed that isolate C10B was able to produce N-acylhomoserine lactones (AHLs. This bacterium was further identified as a member of Burkholderia, an opportunistic pathogen. The isolated Burkholderia sp. was confirmed to produce N-hexanoyl-L-homoserine lactone (C6-HSL, N-octanoyl-L-homoserine lactone (C8-HSL, N-decanoyl-L-homoserine lactone (C10-HSL and N-dodecanoyl-L-homoserine lactone (C12-HSL.

  5. Frigidibacter albus gen. nov., sp. nov., a novel member of the family Rhodobacteraceae isolated from lake water.

    Li, Ai-Hua; Zhou, Yu-Guang

    2015-04-01

    Three Gram-staining-negative, strictly aerobic, non-pigmented, non-motile, rod-shaped bacterial strains, SP32(T) ( = SLM-1(T)), SR68 ( = SLM-3) and SP95 ( = SLM-2), were isolated from two water samples of a cold-water lake in Xinjiang province, China. Growth was observed at 4-25 °C and pH 6.0-9.0, and optimum growth occurred at 18-20 °C and at pH 7.0-7.5. Phylogenetic analysis of 16S rRNA gene sequences revealed that these isolates belonged to the family Rhodobacteraceae , but formed an evolutionary lineage distinct from other species of this family with validly published names. Strain SP32(T) showed the highest 16S rRNA gene sequence similarity (96.7%) to Rhodobacter veldkampii ATCC 35703(T), and the similarity to members of the genera Defluviimonas , Haematobacter and Pseudorhodobacter was respectively 95.8-96.4, 96.0-96.1 and 95.3-96.1%. The genomic DNA G+C content of strain SP32(T) was 67.6 mol%. The major fatty acids (>5%) were summed feature 8 (C(18 : 1)ω7c/C(18 : 1)ω6c) and11-methyl C(18 : 1)ω7c. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, one unidentified glycolipid and one unidentified polar lipid were the main polar lipids. Ubiquinone 10 (Q-10) was the sole respiratory quinone. Strain SP32(T) did not produce photosynthetic pigments and did not contain the gene pufM, by which it differed from the phototrophic species of the family Rhodobacteraceae . Based on its distinct phenotypic, chemotaxonomic and phylogenetic properties, strain SP32(T) represents a novel species in a novel genus within the family Rhodobacteraceae , for which we propose the name Frigidibacter albus gen. nov., sp. nov. The type strain of Frigidibacter albus is strain SP32(T) ( = SLM-1(T) = CGMCC 1.13995(T) = NBRC 109671(T)). PMID:25609677

  6. Metalloid reducing bacteria isolated from deep ocean hydrothermal vents of the Juan de Fuca Ridge, Pseudoalteromonas telluritireducens sp. nov. and Pseudoalteromonas spiralis sp. nov.

    Rathgeber, Christopher; Yurkova, Natalia; Stackebrandt, Erko; Schumann, Peter; Humphrey, Elaine; Beatty, J Thomas; Yurkov, Vladimir

    2006-11-01

    Five strains of Gram-negative, rod, curved rod and spiral-shaped bacteria were isolated from the vicinity of deep ocean hydrothermal vents along the Main Endeavour Segment of the Juan de Fuca Ridge in the Pacific Ocean. All strains showed remarkable resistance to high levels of toxic metalloid oxyanions, and were capable of reducing the oxyanions tellurite and selenite to their less toxic elemental forms. Phylogenetic analysis of four strains identified these isolates as close relatives of the genus Pseudoalteromonas within the class Gammaproteobacteria. Pseudoalteromonas agarivorans was the closest relative of strains Te-1-1 and Se-1-2-redT, with, respectively, 99.5 and 99.8% 16S rDNA sequence similarity. Strain Te-2-2T was most closely related to Pseudoalteromonas paragorgicola, with 99.8% 16S rDNA sequence similarity. The DNA G+C base composition was 39.6 to 41.8 mol%, in agreement with other members of the genus Pseudoalteromonas. However, the isolates showed important morphological and physiological differences from previously described species of this genus, with one group forming rod-shaped bacteria typical of Pseudoalteromonas and the other forming vibrioid- to spiral-shaped cells. Based on these differences, and on phylogenetic data, we propose the creation of the new species Pseudoalteromonas telluritireducens sp. nov., with strain Se-1-2-redT (DSMZ = 16098T = VKM B-2382T) as the type strain, and Pseudoalteromonas spiralis sp. nov., with strain Te-2-2T (DSMZ = 16099T = VKM B-2383T) as the type strain. PMID:17066332

  7. Vallitalea pronyensis sp. nov., isolated from a marine alkaline hydrothermal chimney.

    Ben Aissa, Fatma; Postec, Anne; Erauso, Gaël; Payri, Claude; Pelletier, Bernard; Hamdi, Moktar; Ollivier, Bernard; Fardeau, Marie-Laure

    2014-04-01

    A novel thermotolerant, anaerobic, Gram-stain-positive, spore-forming bacterium was isolated from a hydrothermal chimney in Prony Bay, New Caledonia. This strain, designated FatNI3(T), grew at 15-55 °C (optimum 30 °C) and at pH 5.8-8.9 (optimum 7.7). It was slightly halophilic, requiring at least 0.5 % NaCl for growth (optimum 2.5-3.0 %), and was able to grow at up to 6 % NaCl. Sulfate, thiosulfate, elemental sulfur, sulfite, nitrate and nitrite were not used as terminal electron acceptors. Growth of strain FatNI3(T) was inhibited in the presence of sulfite (2 mM) or nitrite (2 mM). Strain FatNI3(T) fermented cellobiose, glucose, mannose, maltose, sucrose, galactose, lactose, ribose, fructose, rhamnose, raffinose, xylose, yeast extract, peptone and biotrypticase. The main fermentation products from glucose metabolism were acetate, ethanol, H2 and CO2. The predominant cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The main polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, and unknown glycolipids and phospholipids. The G+C content of the genomic DNA was 36.6 mol%. On the basis of phylogenetic and physiological properties, strain FatNI3(T) ( = DSM 25904 = JCM 18391) belonging to the phylum Firmicutes, class Clostridia, order Clostridiales, is proposed as the type strain of a novel species of the genus Vallitalea, for which the name Vallitalea pronyensis sp. nov. is proposed. PMID:24408522

  8. Fusibacter bizertensis sp. nov., isolated from a corroded kerosene storage tank.

    Smii, Latifa; Ben Hania, Wajdi; Cayol, Jean-Luc; Joseph, Manon; Hamdi, Moktar; Ollivier, Bernard; Fardeau, Marie-Laure

    2015-01-01

    Strain LTF Kr01(T), a novel mesophilic, anaerobic, halotolerant, rod-shaped bacterium, was isolated from a drain at the bottom of a corroded kerosene storage tank of the Société Tunisienne des Industries de Raffinage (STIR), Bizerte, northern Tunisia. Cells were Gram-positive-staining rods, occurred singly or in pairs, and were motile by one lateral flagellum. Strain LTF Kr01(T) grew at temperatures between 15 and 40 °C (optimum 30 °C), between pH 5.5 and 8.2 (optimum pH 7.2) and at NaCl concentrations between 0 and 50 g l(-1) (optimum 5 g l(-1)). It reduced thiosulfate and elemental sulfur into sulfide, but did not reduce sulfate or sulfite. It utilized a wide range of carbohydrates (cellobiose, d-glucose, d-fructose, d-mannitol, d-ribose, sucrose, d-xylose, maltose, d-galactose, starch and trehalose) and produced acetate, CO2 and H2 as end products from glucose fermentation. The DNA G+C content was 37.4 mol%. The predominant cellular fatty acids were C14:0 and C16:0. Phylogenetic analysis of the 16S rRNA gene sequence suggested that Fusibacter tunisiensis was the closest relative of strain LTF Kr01(T) (gene sequence similarity of 94.6%). Based on phenotypic, phylogenetic and genotypic taxonomic characteristics, strain LTF Kr01(T) is proposed to represent a novel species of the genus Fusibacter, order Clostridiales, for which the name Fusibacter bizertensis sp. nov. is proposed. The type strain is LTF Kr01(T) ( = DSM 28034(T) = JCM 19376(T)). PMID:25294821

  9. Bioactive metabolites from the endophytic fungus Ampelomyces sp. isolated from the medicinal plant Urospermum picroides.

    Aly, Amal H; Edrada-Ebel, Ruangelie; Wray, Victor; Müller, Werner E G; Kozytska, Svitlana; Hentschel, Ute; Proksch, Peter; Ebel, Rainer

    2008-05-01

    Extracts of cultures grown in liquid or on solid rice media of the fungal endophyte Ampelomyces sp. isolated from the medicinal plant Urospermum picroides exhibited considerable cytotoxic activity when tested in vitro against L5178Y cells. Chromatographic separation yielded 14 natural products that were unequivocally identified based on their 1H and 13C NMR as well as mass spectra and comparison with previously published data. Six compounds (2, 4, 5, 7, 9 and 11) were natural products. Both fungal extracts differed considerably in their secondary metabolites. The extract obtained from liquid cultures afforded a pyrone (2) and sulfated anthraquinones (7 and 9) along with the known compounds 1, 3, 6 and 8. When grown on solid rice medium the fungus yielded three compounds 4, 5 and 11 in addition to several known metabolites including 6, 8, 10, 12, 13 and 14. Compounds 4, 8 and 10 showed the strongest cytotoxic activity against L5178Y cells with EC50 values ranging from 0.2-7.3microg/ml. Furthermore, 8 and 10 displayed antimicrobial activity against the Gram-positive pathogens, Staphylococcus aureus, S. epidermidis and Enterococcus faecalis at minimal inhibitory concentrations (MIC) of 12.5microg/ml and 12.5-25microg/ml, respectively. Interestingly, 6 and 8 were also identified as constituents of an extract derived from a healthy plant sample of the host plant U. picroides thereby indicating that the production of bioactive natural products by the endophyte proceeds also under in situ conditions within the host plant. PMID:18400237

  10. Actinopolyspora salinaria sp. nov., a halophilic actinomycete isolated from solar saltern soil.

    Duangmal, Kannika; Suksaard, Paweena; Pathom-Aree, Wasu; Mingma, Ratchanee; Matsumoto, Atsuko; Takahashi, Yoko

    2016-04-01

    The taxonomic position of the halophilic actinobacterial strain, HS05-03T, isolated from solar saltern soil, was determined using a polyphasic approach. Phylogenetic analysis based on the 16S rRNA gene sequence of the strain showed that it formed a distinct evolutionary lineage in the genus Actinopolyspora. The organism was most closely related to the type strains of the species Actinopolyspora xinjiangensis (98.0 % similarity), Actinopolyspora righensis (97.9 % similarity), Actinopolyspora lacussalsi (97.9 % similarity) and Actinopolyspora erythraea (97.8 % similarity). The whole-organism hydrolysates contained meso-diaminopimelic acid, arabinose, galactose and ribose. The predominant menaquinones were found to be MK-9(H4) and MK-10(H4). The acyl type of the peptidoglycan was N-acetyl. The diagnostic phospholipid detected was phosphatidylcholine. The predominant cellular fatty acids were iso-C16 : 0, anteiso-C17 : 0 and iso-C15 : 0. The G+C content of the genomic DNA was 69.9 mol%. DNA-DNA hybridization values between strain HS05-03T and the type strains of the most closely related species were below the 70 % threshold. On the basis of the phenotypic and genotypic data, it is proposed that strain HS05-03T represents a novel species of the genus Actinopolyspora, with the name Actinopolyspora salinaria sp. nov. The type strain is HS05-03T ( = BCC 51286T = NBRC 109078T). PMID:26812900

  11. Paenibacillus puernese sp. nov., a β-glucosidase-producing bacterium isolated from Pu'er tea.

    Wang, Dan-Dan; Kim, Yeon-Ju; Hoang, Van-An; Nguyen, Ngoc-Lan; Singh, Priyanka; Wang, Chao; Chun-Yang, Deok

    2016-04-01

    A Gram-staining-positive, endospore-forming, aerobic, rod-shaped bacterium, designated as DCY97(T), was isolated from ripened Pu'er tea and was identified by using a polyphasic approach. 16S rRNA gene sequence analysis showed that strain DCY97(T) was closely related to Paenibacillus dongdonensis KUDC0114(T) (98.0 %), Paenibacillus oceanisediminis L10(T) (97.7 %), and Paenibacillus barcinonensis BP-23(T) (97.2 %). The phenotypic and chemotaxonomic characteristics of strain DCY97(T) matched with the characteristics of members belonging to the genus Paenibacillus. The major identified polar lipids included phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol. The predominant quinone was MK-7. The major fatty acids were anteiso-C15:0 (35.1 %), anteiso-C16:0 (19.0 %), and iso-C16:0 (13.9 %). The peptidoglycan cell wall was composed of meso-diaminopimelic acids, alanine, and D-glutamic acid. The genomic DNA G + C content was determined to be 46.7 mol%. The DNA-DNA relatedness between strain DCY97(T) and Paenibacillus dongdonensis KCTC 33221(T), Paenibacillus oceanisediminis KACC 16023(T), Paenibacillus barcinonensis KCTC 13019(T) were 27, 19, and 10 %, respectively. Based on the genotypic, phenotypic, and chemotaxonomic characteristics, strain DCY97(T) is considered as a novel species of the genus Paenibacillus, for which the name Paenibacillus puernese sp. nov. is proposed. The type strain is DCY97(T) (=KCTC 33596(T) = JCM 140369(T)). PMID:26721586

  12. Bacillus nitroreducens sp. nov., a humus-reducing bacterium isolated from a compost.

    Guo, Junhui; Wang, Yue Qiang; Yang, Guiqin; Chen, Yunqi; Zhou, Shungui; Zhao, Yong; Zhuang, Li

    2016-05-01

    A Gram-staining-positive, facultative anaerobic, motile and rod-shaped bacterium, designated GSS08(T), was isolated from a windrow compost pile and characterized by means of a polyphasic approach. Growth occurred with 0-4 % (w/v) NaCl (optimum 1 %), at pH 6.5-9.5 (optimum pH 7.5) and at 20-45 °C (optimum 37 °C). Anaerobic growth occurred with anthraquinone-2,6-disulphonate, fumarate and NO3 (-) as electron acceptor. The main respiratory quinone was MK-7. The predominant polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. The major fatty acids (>5 %) were iso-C15:0 (43.1 %), anteiso-C15:0 (27.4 %) and iso-C16:0 (8.3 %). The DNA G + C content was 39.6 mol%. The phylogenetic analysis based on 16S rRNA gene sequences revealed that strain GSS08(T) formed a phyletic lineage with the type strain of Bacillus humi DSM 16318(T) with a high sequence similarity of 97.5 %, but it displayed low sequence similarity with other valid species in the genus Bacillus (<96.0 %). The DNA-DNA relatedness between strains GSS08(T) and B. humi DSM 16318(T) was 50.8 %. The results of phenotypic, chemotaxonomic and genotypic analyses clearly indicated that strain GSS08(T) represents a novel species, for which the name Bacillus nitroreducens sp. nov. is proposed. The type strain is GSS08(T) (=KCTC 33699(T) = MCCC 1K01091(T)). PMID:26832132

  13. Paradonghicola geojensis gen. nov., sp. nov., isolated from seawater, Geoje-si, South Korea.

    Lee, Kalam; Srinivasan, Sathiyaraj; Lee, Sang-Seob

    2016-08-01

    A Gram-negative, non-motile, non-spore-forming and aerobic bacterium, designated FJ12(T), was isolated from seawater, Geoje-si, South Korea. Strain FJ12(T) was catalase and oxidase positive. Growth of strain FJ12(T) was optimally observed at 30 °C and pH 6 and grew in the presence of 0-11 % (w/v) NaCl (optimum 2-3 % NaCl). The phylogenic analysis based on 16S rRNA gene sequence of strains FJ12(T) showed the highest sequence similarity to those of Doghicola eburneus KCTC 12735(T) (95.4 %), Aestuariihabitans beolgyonensis KTCT 32324(T) (95.3 %), Sulfitobacter pontiacus KCTC 32185(T) (94.9 %), Roseisalinus antarcticus DSM 11466(T) (94.8 %) and Loktanella soesokkaensis KCTC 32425(T) (94.7 %). The major polar lipids of FJ12(T) were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, an unidentified aminolipid and unidentified lipids. It contained Q-10 as the predominant ubiquinone, and major fatty acid is C18:1 ω7c (51.7 %), C16:0 (24.0 %). The DNA G+C content of the strain FJ12(T) was 60 mol%. Based on physiological and chemotaxonomic characteristics, strain FJ12(T) should be regarded as the type species of a novel genus in the family Rhodobacteraceae for which the name Paradonghicola geojensis sp. nov. is proposed. The type strain FJ12(T) (=KEMB 3001-336(T)=JCM 30384(T)). PMID:26971334

  14. Roseovarius halocynthiae sp. nov., isolated from the sea squirt Halocynthia roretzi.

    Kim, Young-Ok; Kong, Hee Jeong; Park, Sooyeon; Kang, So-Jung; Kim, Woo-Jin; Kim, Kyung-Kil; Oh, Tae-Kwang; Yoon, Jung-Hoon

    2012-04-01

    A Gram-negative, motile, ovoid- to rod-shaped bacterial strain, designated MA1-10T, was isolated from a sea squirt (Halocynthia roretzi) collected from the South Sea, Korea. Strain MA1-10T grew optimally at pH 7.0-8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain MA1-10T clustered with Roseovarius crassostreae CV919-312T, with which it exhibited 97.1 % sequence similarity, at a bootstrap resampling value of 96.2 %. It exhibited 93.3-95.8 % 16S rRNA gene sequence similarity to the type strains of other recognized Roseovarius species. Strain MA1-10T contained Q-10 as the predominant ubiquinone and C18:1ω7c as the major fatty acid, which is consistent with data for the genus Roseovarius. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid and an unidentified lipid. The DNA G+C content of strain MA1-10T was 55.4 mol%. Mean DNA-DNA relatedness between strain MA1-10T and R. crassostreae DSM 16950T was 13 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, demonstrated that strain MA1-10T could be distinguished from all recognized Roseovarius species. On the basis of the data presented, strain MA1-10T is considered to represent a novel species of the genus Roseovarius, for which the name Roseovarius halocynthiae sp. nov. is proposed; the type strain is MA1-10T (=KCTC 23462T=CCUG 60745T). PMID:21669917

  15. Colwellia meonggei sp. nov., a novel gammaproteobacterium isolated from sea squirt Halocynthia roretzi.

    Kim, Young-Ok; Park, Sooyeon; Nam, Bo-Hye; Jung, Yong-Taek; Kim, Dong-Gyun; Yoon, Jung-Hoon

    2013-12-01

    A Gram-negative, non-spore-forming, aerobic, motile and rod-shaped or ovoid bacterial strain, designated MA1-3(T), was isolated from a sea squirt (Halocynthia roretzi) collected from the South sea in South Korea. Strain MA1-3(T) was found to grow optimally at 25 °C, at pH 7.0-8.0 and in the presence of 2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain MA1-3(T) fell within the clade comprising Colwellia species, clustering coherently with the type strains of Colwellia aestuarii, Colwellia polaris and Colwellia chukchiensis, showing sequence similarity values of 97.2, 96.4 and 95.6 %, respectively. It exhibited 16S rRNA gene sequence similarity values of 93.9-96.1 % to the type strains of the other Colwellia species. Strain MA1-3(T) was found to contain Q-8 as the predominant ubiquinone and C16:1 ω7c and/or C16:1 ω6c, C16:0 and C16:1 ω9c as the major fatty acids. The DNA G+C content of strain MA1-3(T) was determined to be 39.1 mol% and its mean DNA-DNA relatedness value with the type strain of C. aestuarii was 13 ± 5.4 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that the novel strain is separated from other Colwellia species. On the basis of the data presented, strain MA1-3(T) is considered to represent a novel species of the genus Colwellia, for which the name Colwellia meonggei sp. nov. is proposed. The type strain is MA1-3(T) (=KCTC 32380(T) = CECT 8302(T)). PMID:24006188

  16. Ruegeria halocynthiae sp. nov., isolated from the sea squirt Halocynthia roretzi.

    Kim, Young-Ok; Park, Sooyeon; Nam, Bo-Hye; Kang, So-Jung; Hur, Young Baek; Lee, Sang-Jun; Oh, Tae-Kwang; Yoon, Jung-Hoon

    2012-04-01

    A Gram-negative, non-motile, rod-shaped bacterial strain, designated MA1-6T, was isolated from a sea squirt (Halocynthia roretzi) collected from the South Sea, Korea, and was characterized to determine its taxonomic position. Strain MA1-6T grew optimally at pH 7.0-8.0, at 30 °C and in the presence of 2-3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MA1-6T fell within the clade comprising Ruegeria species and exhibited 95.3-96.5 % similarity to the type strains of recognized Ruegeria species. Strain MA1-6T contained Q-10 as the predominant ubiquinone and C18:1ω7c as the major fatty acid, which is consistent with data for Ruegeria species. The major polar lipids detected in strain MA1-6T and Ruegeria atlantica KCTC 12424T were phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and an unidentified lipid. The DNA G+C content of strain MA1-6T was 58.6 mol%. Differential phenotypic properties, together with phylogenetic distinctiveness, demonstrated that strain MA1-6T can be distinguished from recognized Ruegeria species. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain MA1-6T is considered to represent a novel species of the genus Ruegeria, for which the name Ruegeria halocynthiae sp. nov. is proposed; the type strain is MA1-6T (=KCTC 23463T=CCUG 60744T). PMID:21669923

  17. Nocardia rayongensis sp. nov., isolated from Thai peat swamp forest soil.

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

    2016-05-01

    An actinomycete strain, RY45-3T, isolated from a peat swamp forest soil in Rayong Province, Thailand, was characterized using a polyphasic approach. The strain belonged to the genus Nocardia on the basis of morphological, physiological, biochemical and chemotaxonomic properties. Cell-wall peptidoglycan contained meso-diaminopimelic acid. The N-acyl group of muramic acid in the cell wall was glycolyl type. The diagnostic sugars in whole-cell hydrolysates were galactose and arabinose. MK-8 (H4ω-cycl) was the major menaquinone. The major fatty acids were C16 : 0 and C18 : 1ω9c. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides. The genomic DNA G+C content was 71 mol%. On the basis of 16S rRNA gene sequence similarity analysis, strain RY45-3T was closely related to Nocardia jiangxiensis JCM 12861T (98.9 %), Nocardia nova JCM 6044T (98.8 %) and Nocardia pseudobrasiliensis JCM 9894T (98.6 %). The strain showed low levels of DNA-DNA relatedness with N. jiangxiensis JCM 12861T, N. nova JCM 6044T and N. pseudobrasiliensis JCM 9894T (range from 3.6 to 55.3 %). On the basis of the phenotypic characteristics and the results mentioned, this strain could be differentiated from closely related type strains and represents a novel species of the genus Nocardia, for which the name Nocardia rayongensis sp. nov. (type strain RY45-3T = JCM 19832T = TISTR 2213T = PCU 334T) is proposed. PMID:26873179

  18. Rufibacter glacialis sp. nov., a psychrotolerant bacterium isolated from glacier soil.

    Liu, Qing; Liu, Hong-Can; Zhang, Jian-Li; Zhou, Yu-Guang; Xin, Yu-Hua

    2016-01-01

    A Gram-stain-negative, rod-shaped, red-pigmented bacterium (MDT1-10-3T) was isolated from Midui glacier in Tibet, China. Cells were aerobic and psychrotolerant (growth occurred at 4-25 °C). Phylogenetic analysis based on 16S rRNA gene sequences indicated that it was a member of the genus Rufibacter, with Rufibacter immobilis MCC P1T (96.7 % similarity) as its closest phylogenetic relative. MK-7 was the predominant respiratory menaquinone. The major cellular fatty acids were summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C17 : 1ω6c, iso-C16 : 0, iso-C15 : 0 and C16 : 1ω5c. The predominant polar lipids were phosphatidylethanolamine, two unidentified aminophospholipids, one glycolipid and four unidentified lipids. The G+C content of the genomic DNA was 49 mol%. On the basis of the phenotypic characteristics and phylogenetic analysis, strain MDT1-10-3T represents a novel species of the genus Rufibacter, for which the name Rufibacter glacialis sp. nov. is proposed. The type strain is MDT1-10-3T ( = CGMCC 1.9789T = NBRC 109705T). PMID:26510965

  19. Edaphobacter dinghuensis sp. nov., an acidobacterium isolated from lower subtropical forest soil.

    Wang, Jia; Chen, Mei-Hong; Lv, Ying-Ying; Jiang, Ya-Wen; Qiu, Li-Hong

    2016-01-01

    An aerobic bacterium, designated DHF9T, was isolated from a soil sample collected from the lower subtropical forest of Dinghushan Biosphere Reserve, Guangdong Province, PR China. Cells were Gram-stain-negative, non-motile, short rods that multiplied by binary division. Strain DHF9T was an obligately acidophilic, mesophilic bacterium capable of growth at pH 3.5-5.5 (optimum pH 4.0) and at 10-33 °C (optimum 28-33 °C). Growth was inhibited at NaCl concentrations above 2.0 % (w/v). The major fatty acids were iso-C15 : 0, C16 : 0 and C16 : 1ω7c. The polar lipids consist of phosphatidylethanolamine, two unidentified aminolipids, two unidentified phospholipids, two unidentified polar lipids and an unidentified glycolipid. The DNA G+C content was 57.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belongs to the genus Edaphobacter in subdivision 1 of the phylum Acidobacteria, with the highest 16S rRNA gene sequence similarity of 97.0 % to Edaphobacter modestus Jbg-1T. Based on phylogenetic, chemotaxonomic and physiological analyses, it is proposed that strain DHF9T represents a novel species of the genus Edaphobacter, named Edaphobacter dinghuensis sp. nov. The type strain is DHF9T ( = DSM 29920T = CGMCC 1.12997T). PMID:26503862

  20. Luteimonas terrae sp. nov., isolated from rhizosphere soil of Radix ophiopogonis.

    Ngo, Hien T T; Yin, Chang Shik

    2016-05-01

    A Gram-staining-negative, strictly aerobic, rod-shaped and bright-yellow-pigmented bacterium, motile by means of a single polar flagellum, designated THG-MD21T, was isolated from rhizosphere soil of Radix ophiopogonis in Henan province, PR China. On the basis of 16S rRNA gene sequence similarity, strain THG-MD21T belongs to the genus Luteimonas and was most closely related to Luteimonas aestuarii B9T (98.2 % sequence similarity), Lysobacter panaciterrae Gsoil 068T (97.2 %) and Luteimonas marina FR1330T (97.0 %). The DNA G+C content was 64.4 mol%. The DNA-DNA relatedness between strain THG-MD21T and its closest phylogenetic neighbours was below 30.0 %. The only isoprenoid quinone detected in strain THG-MD21T was ubiquinone-8.The major polar lipids were found to be phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol, and the predominant fatty acids were iso-C11 : 0, iso-C15 : 0, iso-C16 : 0, C16 : 0 and iso-C17 : 1ω9c. The DNA-DNA hybridization result and characteristics revealed by a polyphasic study showed that strain THG-MD21T represents a novel species, for which the name Luteimonas terrae sp. nov. is proposed. The type strain is THG-MD21T ( = KACC 18131T = JCM 30122T). PMID:26782356

  1. Chryseobacterium chengduensis sp. nov. isolated from the air of captive giant panda enclosures in Chengdu, China.

    Wen, Cai-Fang; Xi, Li-Xin; Zhao, Shan; Hao, Zhong-Xiang; Luo, Lu; Liao, Hong; Chen, Zhen-Rong; She, Rong; Han, Guo-Quan; Cao, San-Jie; Wu, Rui; Yan, Qi-Gui; Hou, Rong

    2016-08-01

    A Gram-negative, aerobic, non-motile, rod-shaped bacterial strain, designated 25-1(T), was isolated from the air inside giant panda enclosures at the Chengdu Research Base of Giant Panda Breeding, China. Strain 25-1(T) grew optimally at pH 7.0-8.0, at 28-30 °C and in the presence of NaCl concentrations from 0.0% to 0.5 %. 16S rRNA gene sequence analysis indicated that strain 25-1(T) belongs to the genus Chryseobacterium within the family Flavobacteriaceae and is related most closely to C. carnis G81(T) (96.4% similarity), C. lathyri RBA2-6(T) (95.8% similarity), and C. zeae JM1085(T) (95.8% similarity). Its genomic DNA G+C molar composition was 36.2%. The major cellular fatty acids were iso-C15:0 (44.0%), iso-C17:0 3OH (19.8%) and C16:1 ω7c/16:1 ω6c (12.7%). The only isoprenoid quinone was menaquinone 6 (MK-6). The major polar lipids were phosphatidylethanolamine, two unidentified amino lipids and two unidentified lipids. The DNA-DNA relatedness between strain 25-1(T) and C. lathyri RBA2-6(T) was 38%. Phenotypic, genotypic, and phylogenetic characteristics indicated that strain 25-1(T) is a novel member of the genus Chryseobacterium, for which the name C. chengduensis sp. nov. is proposed. The type strain is 25-1(T) (CCTCC AB2015133(T)=DSM 100396(T)). PMID:27487806

  2. Microbacterium oryzae sp. nov., an actinobacterium isolated from rice field soil.

    Kumari, Prabla; Bandyopadhyay, Saumya; Das, Subrata K

    2013-07-01

    A novel aerobic soil actinobacterium (strain MB10(T)) belonging to the genus Microbacterium was isolated from rice field soil samples collected from Jagatpur, Orissa, India. Cells were Gram-stain positive, short rod-shaped and motile. The strain was oxidase-negative and catalase-positive. Heterotrophic growth was observed at pH 5.0-11.0 and at 16-37 °C; optimum growth was observed at 28 °C and pH 7.0-9.0. The DNA G+C content was 71.6 mol%. Predominant cellular fatty acids of strain MB10(T) were iso-C14 : 0, anteiso-C15 : 0, C16 : 0, iso-C16 : 0 and anteiso-C17 : 0. Cell wall sugars were galactose, glucose and rhamnose. The major isoprenoid quinones were MK-9 (10 %), MK-10 (43 %) and MK-11 (36 %). The peptidoglycan represents the peptidoglycan type B2β. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipid and unknown glycolipids. 16S rRNA gene sequence identity revealed the strain MB10(T) clustered within the radiation of the genus Microbacterium and showed 99.2 % similarity with Microbacterium barkeri DSM 20145(T). However, DNA-DNA similarity study was 37.0 % with Microbacterium barkeri DSM 20145(T), the nearest phylogenetic relative. On the basis of phenotypic and chemotaxonomic properties, 16S rRNA gene sequence analysis and DNA-DNA reassociation studies, it is proposed that strain MB10(T) represents a novel species of the genus Microbacterium, for which the name Microbacterium oryzae sp. nov. is proposed; the type strain is MB10(T) ( = JCM 16837(T) = DSM 23396(T)). PMID:23203624

  3. Tenacibaculum finnmarkense sp. nov., a fish pathogenic bacterium of the family Flavobacteriaceae isolated from Atlantic salmon.

    Småge, Sverre Bang; Brevik, Øyvind Jakobsen; Duesund, Henrik; Ottem, Karl Fredrik; Watanabe, Kuninori; Nylund, Are

    2016-02-01

    A novel Gram-stain negative, aerobic, non-flagellated, rod-shaped gliding bacterial strain, designated HFJ(T), was isolated from a skin lesion of a diseased Atlantic salmon (Salmo salar L.) in Finnmark, Norway. Colonies were observed to be yellow pigmented with entire and/or undulating margins and did not adhere to the agar. The 16S rRNA gene sequence showed that the strain belongs to the genus Tenacibaculum (family Flavobacteriaceae, phylum 'Bacteroidetes'). Strain HFJ(T) exhibits high 16S rRNA gene sequence similarity values to Tenacibaculum dicentrarchi NCIMB 14598(T) (97.2 %). The strain was found to grow at 2-20 °C and only in the presence of sea salts. The respiratory quinone was identified as menaquinone 6 and the major fatty acids were identified as summed feature 3 (comprising C16:1 ω7c and/or iso-C15:0 2-OH), iso-C15:0, anteiso-C15:0, iso-C15:1 and iso-C15:0 3-OH. The DNA G+C content was determined to be 34.1 mol%. DNA-DNA hybridization and comparative phenotypic and genetic tests were performed with the phylogenetically closely related type strains, T. dicentrarchi NCIMB 14598(T) and Tenacibaculum ovolyticum NCIMB 13127(T). These data, as well as phylogenetic analyses, suggest that strain HFJ(T) should be classified as a representative of a novel species in the genus Tenacibaculum, for which the name Tenacibaculum finnmarkense sp. nov. is proposed; the type strain is HFJ (T) = (DSM 28541(T) = NCIMB 42386(T)). PMID:26662517

  4. Tenacibaculum caenipelagi sp. nov., a member of the family Flavobacteriaceae isolated from tidal flat sediment.

    Park, Sooyeon; Yoon, Jung-Hoon

    2013-08-01

    A Gram-stain-negative, non-spore-forming, aerobic, non-flagellated, gliding and rod-shaped bacterial strain, designated HJ-26M(T), was isolated from a tidal flat sediment in the Korean peninsula. It grew optimally at 25-30 °C, at pH 7.0-8.0 and in the presence of 2 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that the strain fell within the clade comprising Tenacibaculum species, clustering coherently with the type strains of Tenacibaculum lutimaris and Tenacibaculum aestuarii. Strain HJ-26M(T) exhibited the highest 16S rRNA gene sequence similarity values of 98.4 and 98.2 % to T. lutimaris TF-26(T) and T. aestuarii SMK-4(T), respectively, and of 94.9-97.4 % to the type strains of the other Tenacibaculum species. Strain HJ-26M(T) contained MK-6 as the predominant menaquinone and iso-C15:0 and iso-C17:0 3-OH as the major fatty acids. The DNA G+C content of strain HJ-26M(T) was 34.5 mol% and its mean DNA-DNA relatedness values with the type strains of T. lutimaris and T. aestuarii were 19 and 23 %, respectively. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain HJ-26M(T) is separate from other Tenacibaculum species. On the basis of the data presented, strain HJ-26M(T) is considered to represent a novel species of the genus Tenacibaculum, for which the name Tenacibaculum caenipelagi sp. nov. is proposed. The type strain is HJ-26M(T) (= KCTC 32323(T) = CECT 8283(T)). PMID:23733002

  5. Tenacibaculum lutimaris sp. nov., isolated from a tidal flat in the Yellow Sea, Korea.

    Yoon, Jung-Hoon; Kang, So-Jung; Oh, Tae-Kwang

    2005-03-01

    Four Gram-negative, rod-shaped bacterial strains, TF-26(T), TF-28, TF-42 and TF-53, were isolated from a tidal flat in the Yellow Sea, Korea, and their taxonomic positions were determined by a polyphasic characterization. The strains grew optimally in the presence of 2-3 % (w/v) NaCl and at 30-37 degrees C. The predominant menaquinone detected in the four strains was MK-6. These strains contained large amounts of fatty acids C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH, iso-C(15 : 0), iso-C(16 : 0) 3-OH, C(15 : 0) and iso-C(17 : 0) 3-OH. The DNA G+C contents of the four strains were 32.3-32.8 mol%. Strains TF-26(T), TF-28, TF-42 and TF-53 showed 16S rRNA gene sequence similarity levels of 99.8-100 % and DNA-DNA relatedness levels of 82-87 %. The four strains exhibited 16S rRNA gene sequence similarity levels of 95.0-98.0 % to the type strains of the five current Tenacibaculum species, and DNA-DNA relatedness levels between the four strains and two phylogenetic relatives, Tenacibaculum mesophilum DSM 13764(T) and Tenacibaculum skagerrakense DSM 14836(T), were less than 21 %. On the basis of phenotypic, phylogenetic and genetic data, strains TF-26(T), TF-28, TF-42 and TF-53 were classified in the genus Tenacibaculum as members of a novel species, for which the name Tenacibaculum lutimaris sp. nov. (type strain, TF-26(T)=KCTC 12302(T)=DSM 16505(T)) is proposed. PMID:15774664

  6. Tenacibaculum xiamenense sp. nov., an algicidal bacterium isolated from coastal seawater.

    Li, Yi; Wei, Jun; Yang, Caiyun; Lai, Qiliang; Chen, Zhangran; Li, Dong; Zhang, Huajun; Tian, Yun; Zheng, Wei; Zheng, Tianling

    2013-09-01

    A Gram-stain-negative, elongated rod-shaped, yellow-pigmented, aerobic bacterial strain, designated WJ-1(T), was isolated from coastal seawater in Xiamen, Fujian province, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain WJ-1(T) fell within the genus Tenacibaculum and was most closely associated with Tenacibaculum aestuarii SMK-4(T) (96.7% 16S rRNA gene sequence similarity); lower similarities were shown to other members of the genus Tenacibaculum (Tenacibaculum litopenaei B-I(T) (96.0%), Tenacibaculum geojense YCS-6(T) (94.5%) and Tenacibaculum jejuense CNURIC 013(T) (95.4%). Growth was observed at temperatures from 16 to 38 °C, at salinities from 2 to 4% and at pH 6-9. The major fatty acids were summed feature 3 (C(16:1)ω6c and/or C(16 1)ω7c), iso-C(17:0) 3-OH, iso-C(15:0) and iso-C(15:0) 3-OH. The DNA G+C content of strain WJ-1(T) was 33.2 mol% and the major respiratory quinone was menaquinone-6 (MK-6). Differential phenotypic properties and phylogenetic distinctiveness in this study distinguished strain WJ-1(T) from all other members of the genus Tenacibaculum. According to the morphology, physiology, fatty acid composition and 16S rRNA gene sequence data, strain WJ-1(T) represents a novel species of the genus Tenacibaculum, for which the name Tenacibaculum xiamenense sp. nov. is proposed. The type strain is WJ-1(T) ( =CGMCC 1.12378(T) =LMG 27422(T)). PMID:23543502

  7. Tenacibaculum crassostreae sp. nov., isolated from the Pacific oyster, Crassostrea gigas.

    Lee, Young Sun; Baik, Keun Sik; Park, So Yeon; Kim, Eun Mi; Lee, Dong-Heon; Kahng, Hyung-Yeel; Jeon, Che Ok; Jung, Jae Sung

    2009-07-01

    A rod-shaped, yellow-pigmented, aerobic, Gram-negative bacterium, designated strain JO-1(T), was isolated from an apparently healthy Pacific oyster, Crassostrea gigas, collected at Wan Island, Korea. It grew at 15-37 degrees C (optimum 30 degrees C) only in the presence of sea salts. Strain JO-1(T) hydrolysed casein, Tween 80 and starch. The major fatty acids were iso-C(15 : 0) (23.8 %), summed feature 3 (comprising C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH; 14.5 %) and iso-C(15 : 1) G (14.1 %). Analysis of the 16S rRNA gene sequence indicated that strain JO-1(T) was a member of the genus Tenacibaculum in the family Flavobacteriaceae, with sequence similarity of 94.6-97.8 % to the type strains of recognized members of the genus. The G+C content of the genomic DNA was 31.4 mol%. DNA-DNA relatedness levels between strain JO-1(T) and the five closest relatives, Tenacibaculum litoreum KCCM 42115(T), T. lutimaris KCTC 12302(T), T. aestuarii KCTC 12569(T), T. mesophilum DSM 13764(T) and T. adriaticum JCM 14633(T), were less than 28 %. Phylogenetic analyses and differences in physiological and biochemical characteristics suggested that strain JO-1(T) (=KCTC 22329(T) =JCM 15428(T)) should be classified as the type strain of a novel species within the genus Tenacibaculum, for which the name Tenacibaculum crassostreae sp. nov. is proposed. PMID:19542127

  8. Sphingobacterium psychroaquaticum sp. nov., a psychrophilic bacterium isolated from Lake Michigan water.

    Albert, Richard A; Waas, Nancy E; Pavlons, Shawn C; Pearson, Jamie L; Ketelboeter, Laura; Rosselló-Móra, Ramon; Busse, Hans-Jürgen

    2013-03-01

    A psychrophilic, Gram-negative bacterium, designated MOL-1(T), was isolated from water of Lake Michigan. 16S rRNA gene sequence analysis revealed that the sequence of strain MOL-1(T) has sequence similarity of 95.6, 94.8, 94.3, 94.3, 94.2 and 93.9 %, respectively, to the 16S rRNA gene sequences of Sphingobacterium shayense HS39(T), S. lactis WCC 4512(T), S. composti T5-12(T), S. daejeonense TR6-04(T), S. bambusae IBFC2009(T) and S. alimentarium WCC 4521(T). The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c). Menaquinone MK-7 is the predominant respiratory quinone, while sym-homospermidine is the predominant polyamine. The polar lipid profile is composed of the predominant lipids phosphatidylethanolamine and unidentified polar lipid L2, with moderate amounts of unidentified polar lipids L1, L5 and L6 and unidentified aminophospholipids APL1 and APL2 and minor to trace amounts of unidentified polar lipids L3, L4, L7, L8, L9 and L10, unidentified phospholipid PL4 and unidentified aminophospholipid APL3. After molecular and phenotypic studies, including chemotaxonomic analyses, it was concluded that strain MOL-1(T) represents a novel Sphingobacterium species, for which the name Sphingobacterium psychroaquaticum sp. nov. is proposed. The type strain is MOL-1(T) ( = NRRL B-59232(T)  = DSM 22418(T)). PMID:22659507

  9. Thermocrinis jamiesonii sp. nov., a thiosulfate-oxidizing, autotropic thermophile isolated from a geothermal spring

    Dodsworth, Jeremy A.; Ong, John C.; Williams, Amanda; Dohnalkova, Alice; Hedlund, Brian P.

    2015-12-12

    An obligately thermophilic, chemolithotrophic, microaerophilic bacterium, designated strain GBS1T, was isolated from the water column of Great Boiling Spring, Nevada, USA. Thiosulfate was required for growth. Although capable of autotrophy, growth of GBS1T was enhanced in the presence of acetate, peptone, or Casamino acids. Growth occurred at 70-85 °C with an optimum at 80 °C, at pH 6.5-7.75 with an optimum at pH 7.25, at 0.5-8% oxygen with an optimum at 1-2%, and at ≤200 mM sodium chloride. The doubling time under optimal growth conditions was 1.3 hrs, with a final cell density of 6.2±0.5 x 107 cells/mL. Non-motile, rod-shaped cells 1.4-2.4 x 0.4-0.6 µm occurred singly or in pairs. Major cellular fatty acids (>5% of total) were C20:1ω9c (44.8%), C18:0 (26.0%), C16:0 (9.9%) and C20:0 (5.4%). Phylogenetic analysis of the GBS1T 16S rRNA gene sequence indicated an affiliation with Thermocrinis ruber and other Thermocrinis spp., but comparisons of 16S rRNA gene identity (≤97.10%) and in silico estimated DNA-DNA hybridization values (≤18.4%) with Thermocrinis spp. indicate that his strain is distinct from described species. Based on phenotypic, genotypic, and phylogenetic characteristics, the name Thermocrinis jamiesonii sp. nov. is proposed, with GBS1T (= JCM 19133T = DSM 27162T) as the type strain.

  10. Sphingomonas morindae sp. nov., isolated from Noni (Morinda citrifolia L.) branch.

    Liu, Yang; Yao, Su; Lee, Yong-Jae; Cao, Yanhua; Zhai, Lei; Zhang, Xin; Su, Jiaojiao; Ge, Yuanyuan; Kim, Song-Gun; Cheng, Chi

    2015-09-01

    Two yellow bacterial strains, designated NBD5(T) and NBD8, isolated from Noni (Morinda citrifolia L.) branch were investigated using a polyphasic taxonomic approach. Cells were Gram-stain-negative, aerobic, non-spore-forming, non-motile and short rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the strains were members of a novel species of the genus Sphingomonas, the seven closest neighbours being Sphingomonas oligoaromativorans SY-6(T) (96.9% similarity), Sphingomonas polyaromaticivorans B2-7(T) (95.8%), Sphingomonas yantingensis 1007(T) (94.9%), Sphingomonas sanguinis IFO 13937(T) (94.7%), Sphingomonas ginsenosidimutans Gsoil 1429(T) (94.6%), Sphingomonas wittichii RW1(T) (94.6%) and Sphingomonas formosensis CC-Nfb-2(T) (94.5%). Strains NBD5T and NBD8 had sphingoglycolipid, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine as the major polar lipids, ubiquinone 10 as the predominant respiratory quinone, and sym-homospermidine as the major polyamine. Strains NBD5(T) and NBD8 were clearly distinguished from reference type strains based on phylogenetic analysis, DNA-DNA hybridization, fatty acid composition data analysis, and comparison of a range of physiological and biochemical characteristics. It is evident from the genotypic and phenotypic data that strains NBD5(T) and NBD8 represent a novel species of the genus Sphingomonas, for which the name Sphingomonas morindae sp. nov. is proposed. The type strain is NBD5(T) ( = DSM 29151(T) = KCTC 42183(T) = CICC 10879(T)). PMID:25985831

  11. Eoetvoesia caeni gen. nov., sp. nov., isolated from an activated sludge system treating coke plant effluent.

    Felföldi, Tamás; Vengring, Anita; Kéki, Zsuzsa; Márialigeti, Károly; Schumann, Peter; Tóth, Erika M

    2014-06-01

    A novel bacterium, PB3-7B(T), was isolated on phenol-supplemented inorganic growth medium from a laboratory-scale wastewater purification system that treated coke plant effluent. 16S rRNA gene sequence analysis revealed that strain PB3-7B(T) belonged to the family Alcaligenaceae and showed the highest pairwise sequence similarity to Parapusillimonas granuli Ch07(T) (97.5%), Candidimonas bauzanensis BZ59(T) (97.3%) and Pusillimonas noertemannii BN9(T) (97.2%). Strain PB3-7B(T) was rod-shaped, motile and oxidase- and catalase-positive. The predominant fatty acids were C(16 : 0), C(17 : 0) cyclo, C(19 : 0) cyclo ω8c and C(14 : 0) 3-OH, and the major respiratory quinone was Q-8. The G+C content of the genomic DNA of strain PB3-7B(T) was 59.7 mol%. The novel bacterium can be distinguished from closely related type strains based on its urease activity and the capacity for assimilation of glycerol and amygdalin. On the basis of the phenotypic, chemotaxonomic and molecular data, strain PB3-7B(T) is considered to represent a new genus and species, for which the name Eoetvoesia caeni gen. nov., sp. nov. is proposed. The type strain of Eoetvoesia caeni is PB3-7B(T) ( = DSM 25520(T) = NCAIM B 02512(T)). PMID:24585374

  12. Aquamicrobium terrae sp. nov., isolated from the polluted soil near a chemical factory.

    Wu, Zhi-Guo; Wang, Fang; Gu, Cheng-Gang; Zhang, Yin-Ping; Yang, Zong-Zheng; Wu, Xiao-Wei; Jiang, Xin

    2014-06-01

    A Gram-negative, aerobic, non-motile bacterial strain hun6(T) isolated from the polluted soil near a chemical factory in northern Nanjing, China was investigated to clarify its taxonomic position. Growth of strain hun6(T) occurred between 10 and 45 °C (optimum, 30 °C) and between pH 6.0 and 8.0 (optimum, pH 7.0). No growth occurred at NaCl concentrations greater than 5 % (w/v). The 16S rRNA gene sequence analysis indicated that strain hun6(T) belongs to the genus Aquamicrobium. The sequence similarities of strain hun6(T) to other type strains of Aquamicrobium genus were all below 98.5 %. The presence of ubiquinone-10, the predominant fatty acid summed feature 8 (C18:1 ω7c and/or C18:1 ω6c) and C19:0 cyclo ω8c, a polar lipid pattern with phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine and phophatidylmonomethylethanoamine were in accord with the characteristics of the genus Aquamicrobium. The G+C content of the genomic DNA was determined to be 63.5 mol%. The results of DNA-DNA hybridization, physiological and biochemical tests and chemotaxonomic properties allowed genotypic and phenotypic differentiation of strain hun6(T) from all known Aquamicrobium species. Therefore, strain hun6(T) can be assigned to a new species of this genus for which the name Aquamicrobium terrae sp. nov. is proposed. The type strain is hun6(T) (= CICC 10733(T) = DSM 27865(T)). PMID:24788880

  13. Cupriavidus nantongensis sp. nov., a novel chlorpyrifos-degrading bacterium isolated from sludge.

    Sun, Le-Ni; Wang, Dao-Sheng; Yang, En-Dong; Fang, Lian-Cheng; Chen, Yi-Fei; Tang, Xin-Yun; Hua, Ri-Mao

    2016-06-01

    A Gram-stain-negative, aerobic, coccoid to small rod-shaped bacterium, designated X1T, was isolated from sludge collected from the vicinity of a pesticide manufacturer in Nantong, Jiangsu Province, China. Based on 16S rRNA gene sequence analysis, strain X1T belonged to the genus Cupriavidus, and was most closely related to Cupriavidus taiwanensis LMG 19424T (99.1 % 16S rRNA gene sequence similarity) and Cupriavidus alkaliphilus LMG 26294T (98.9 %). Strain X1T showed 16S rRNA gene sequence similarities of 97.2-98.2 % with other species of the genus Cupriavidus. The major cellular fatty acids of strain X1T were C16 : 0, C16 : 1ω7c and/or iso-C15 : 0 2-OH (summed feature 3), C18 : 1ω7c and C17 : 0 cyclo, and the major respiratory quinone was ubiquinone Q-8. The major polar lipids of strain X1T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid, phospholipid and hydroxyphosphatidylethanolamine. The DNA G+C content was 66.6 mol%. The DNA-DNA relatedness values of strain X1T with the five reference strains C. taiwanensis LMG 19424T, C. alkaliphilus LMG 26294T, Cupriavidus necator LMG 8453T, Cupriavidus gilardii LMG 5886T and 'Cupriavidus yeoncheonense' KCTC 42053 were lower than 70 %. The results obtained from phylogenetic analysis, phenotypic characterization and DNA-DNA hybridization indicated that strain X1T should be proposed to represent a novel species of the genus Cupriavidus, for which the name Cupriavidus nantongensis sp. nov. is proposed. The type strain is X1T (=KCTC 42909T=LMG 29218T). PMID:27001671

  14. Dactylosporangium solaniradicis sp. nov., a novel actinobacterium isolated from a root of tomato (Solanum lycopersicum L.).

    Fan, Jianlong; Liu, Chongxi; Ma, Zhaoxu; Zhou, Shuyu; Li, Wenchao; Li, Jiansong; Chu, Liyang; Wang, Xiangjing; Xiang, Wensheng

    2016-07-01

    A novel actinobacterium, designated strain NEAU-FJL2(T), was isolated from a tomato root (Solanum lycopersicum L.) and characterised using a polyphasic approach. Morphological and chemotaxonomic properties of strain NEAU-FJL2(T) are consistent with the description of the genus Dactylosporangium. Finger-shaped sporangia were observed to form on short sporangiophores branching from the substrate hyphae. The cell wall peptidoglycan was found to contain meso- and 3-hydroxy-diaminopimelic acids; arabinose, mannose, rhamnose and xylose were found as whole-cell sugars. The phospholipid profile was found to consist of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol. The predominant menaquinones were identified as MK-9(H8) and MK-9(H6). The major fatty acids were identified as iso-C16:0, C16:1 ω7c and iso-C15:0. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain NEAU-FJL2(T) belongs to the genus Dactylosporangium, with Dactylosporangium sucinum JCM 19831(T) (99.3 % 16S rRNA gene sequence similarity), Dactylosporangium darangshiense JCM 17441(T) (99.2 %), Dactylosporangium fulvum JCM 5631(T) (98.9 %) and Dactylosporangium roseum JCM 3364(T) (98.8 %) as the nearest phylogenetic relatives. However, a combination of DNA-DNA hybridization results and some phenotypic characteristics demonstrated that strain NEAU-FJL2(T) can be distinguished from them. Consequently, it is proposed that strain NEAU-FJL2(T) represents a novel species of the genus Dactylosporangium, for which the name Dactylosporangium solaniradicis sp. nov. is proposed. The type strain is NEAU-FJL2(T) (=CGMCC 4.7302(T) = DSM 100814(T)). PMID:27091125

  15. Bowmanella dokdonensis sp. nov., a novel exoelectrogenic bacterium isolated from the seawater of Dokdo, Korea.

    Kim, Marie; Hwang, Ye-Ji; Jung, Hyun-Ju; Park, Hyunwoong; Ghim, Sa-Youl

    2016-07-01

    A Gram-negative, motile, and rod-shaped bacterial strain, UDC354(T), was isolated from the seawater of Dokdo, Korea. The strain UDC354(T) displayed optimal growth at 30-37 °C in the presence of 0-2 % (w/v) NaCl at pH 8. Strain UDC354(T) was found to contain Q-8 and 9 as isoprenoid ubiquinones; C16:0 (22.9 %), summed feature 3 (iso-C15:0 2-OH and C16:1 ω7c) (21.4 %) and C18:1 ω7c (12.2 %) as the major fatty acids; and diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine as the major polar lipids. The DNA G+C content was found to be 54.1 mol %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain UDC354(T) belongs to the genus Bowmanella, of the family Alteromonadaceae, and is closely related to Bowmanella pacifica W3-3A(T) (95.2 %) and Bowmanella denitrificans BD1(T) (95.0 %). It was found that strain UDC354(T) is exoelectrogenic and is capable of generating 6.6 μW/cm(3) in marine broth in the microbial fuel cells. Based on the analysis of the phenotypic, chemotypic and phylogenetic characteristics, a new species, Bowmanella dokdonensis sp. nov. is proposed. The type strain is UDC354(T) (=KCTC 42147(T)=JCM 30855(T)). PMID:27040554

  16. Dankookia rubra gen. nov., sp. nov., an alphaproteobacterium isolated from sediment of a shallow stream.

    Kim, Wan-Hoe; Kim, Do-Hak; Kang, Keunsoo; Ahn, Tae-Young

    2016-06-01

    WS-10(T)-a Gram-negative, non-motile, and aerobic bacterial strain-was isolated from the sediment of a shallow stream in Korea. The optimum ranges of temperature and pH for growth were 20-40°C (optimum 28°C) and pH 6.0-8.0 (optimum pH 7.0), respectively. The DNA G+C content of strain WS-10(T) was 72.7 mol%. The major fatty acids (>5%) were summed feature 8 (C18:1 ω7c), summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:0, and C18:1 2-OH. The major polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, and unidentified aminolipids. Q-10 was the predominant respiratory quinone. The highest similarities in the 16S rRNA gene sequence were shown with Paracraurococcus ruber (95.3%), Belnapia soli (95.3%), B. moabensis (95.1%), and B. rosea (95.0%). A phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that strain WS-10T formed a distinct line within a clade containing the genera Paracraurococcus, Craurococcus, and Belnapia in the family Acetobacteraceae. On the basis of polyphasic evidence, strain WS-10(T) represents a novel species of a new genus in the family Acetobacteraceae, for which the name Dankookia rubra gen. nov., sp. nov. is proposed. The type strain of the type species is WS-10(T) (= KACC 18533(T) = JCM 30602(T)). PMID:27225458

  17. Clostridium chromiireducens sp. nov., isolated from Cr(VI)-contaminated soil.

    Inglett, K S; Bae, H S; Aldrich, H C; Hatfield, K; Ogram, A V

    2011-11-01

    A Cr(VI)-resistant, Gram-positive, spore-forming, obligate anaerobe, designated GCAF-1(T), was isolated from chromium-contaminated soil by its ability to reduce Cr(VI) in low concentrations. Mixed acid fermentation during growth on glucose resulted in accumulation of acetate, butyrate, formate and lactate. Morphological studies indicated the presence of peritrichous flagella, pili and an S-layer. The major cellular fatty acids (>5 %) were C(16 : 0), C(14 : 0), summed feature 3 (comprising iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c), C(18 : 1)ω7c, C(16 : 1)ω9c, summed feature 4 (comprising iso-C(17 : 1) I and/or anteiso-C(17 : 1) B) and C(18 : 1)ω9c. The DNA G+C content of strain GCAF-1(T) was 30.7 mol%. Phylogenetic interference indicated that strain GCAF-1(T) clustered with group I of the genus Clostridium. Of strains within this cluster, strain GCAF-1(T) shared the highest 16S rRNA gene sequence similarities (98.1-98.9 %) with Clostridium beijerinckii DSM 791(T), C. saccharobutylicum NCP 262(T), C. saccharoperbutylacetonicum N1-4(T), C. puniceum DSM 2619(T) and C. roseum DSM 51(T). However, strain GCAF-1(T) could be clearly distinguished from its closest phylogenetic neighbours by low levels of DNA-DNA relatedness (Clostridium, for which the name Clostridium chromiireducens sp. nov. is proposed. PMID:21148674

  18. Marinobacter xestospongiae sp. nov., isolated from the marine sponge Xestospongia testudinaria collected from the Red Sea

    Lee, O. O.

    2011-10-14

    A Gram-negative, catalase- and oxidase-positive, non-sporulating, rod-shaped and slightly halophilic bacterial strain, designated UST090418-1611(T), was isolated from the marina sponge Xestospongia testudinaria collected from the Red Sea coast of Saudi Arabia. Phylogenetic trees based on the 16S rRNA gene sequence placed strain UST090418-1611(T) in the family Alteromonadaceae with the closest relationship to the genus Marinobacter. The 16S rRNA gene sequence similarity between the strain and the type strains of recognized Marinobacter species ranged from 92.9 to 98.3%. Although strain UST090418-1611(T) shared high 16S rRNA gene sequence similarity with Marinobacter mobilis CN46(T), M. zhejiangensis CN74(T) and M. sediminum R65(T) (98.3, 97.4 and 97.3%, respectively), the relatedness of the strain to these three strains in DNA DNA hybridization was only 58, 56 and 33%, respectively, supporting the novelty of the strain. In contrast to most strains in the genus Marinobacter, strain UST090418-1611(T) tolerated only 6% (w/v) NaCl, and optimal growth occurred at 2.0% (w/v) NaCl, pH 7.0-8.0 and 28-36 degrees C. The predominant cellular fatty acids were C-12:0 3-OH, C-16:0, C-12:0 and summed feature 3 (C-16.1 omega 6c and/or C-16:1 omega 7c) The genomic DNA G+C content was 57.1 mol%. Based on the physiological, phylogenetic and chemotaxonomic characteristics presented in this study, we suggest that the strain represents a novel species in the genus Marinobacter, for which the name Marinobacter xestospongiae sp. nov. is proposed, with UST090418-1611(T) (=JCM 17469(T) =NRRL B-59512(T)) as the type strain.

  19. Ideonella sakaiensis sp. nov., isolated from a microbial consortium that degrades poly(ethylene terephthalate).

    Tanasupawat, Somboon; Takehana, Toshihiko; Yoshida, Shosuke; Hiraga, Kazumi; Oda, Kohei

    2016-08-01

    A Gram-stain-negative, aerobic, non-spore-forming, rod-shaped bacterium, designed strain 201-F6T, was isolated from a microbial consortium that degrades poly(ethylene terephthalate) (PET) collected in Sakai city, Japan, and was characterized on the basis of a polyphasic taxonomic study. The cells were motile with a polar flagellum. The strain contained cytochrome oxidase and catalase. It grew within the pH range 5.5-9.0 (optimally at pH 7-7.5) and at 15-42 ºC (optimally at 30-37 ºC). The major isoprenoid quinone was ubiquinone with eight isoprene units (Q-8). C16 : 0, C17 : 0 cyclo, C18 :1ω7c and C12 : 0 2-OH were the predominant cellular fatty acids. The major polar lipids were phosphatidylethanolamine, lyso-phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The G+C content of genomic DNA was 70.4 mol%. Phylogenetic analysis using the 16S rRNA gene sequences showed that strain 201-F6T was affiliated to the genus Ideonella, and was closely related to Ideonella dechloratans LMG 28178T (97.7 %) and Ideonella azotifigens JCM 15503T (96.6 %). Strain 201-F6T could be clearly distinguished from the related species of the genus Ideonella by its physiological and biochemical characteristics as well as by its phylogenetic position and DNA-DNA relatedness. Therefore, the strain represents a novel species of the genus Ideonella, for which the name Ideonella sakaiensis sp. nov. (type strain 201-F6T=NBRC 110686T=TISTR 2288T) is proposed. PMID:27045688

  20. Hyphomonas pacifica sp. nov., isolated from deep sea of the Pacific Ocean.

    Li, Xi; Li, Chongping; Lai, Qiliang; Li, Guizhen; Sun, Fengqin; Shao, Zongze

    2016-08-01

    Three Gram-negative, aerobic, non-spore-forming, oval- to pear-shaped bacterial strains (T16B2(T), T24B3, and C76AD) were isolated from petroleum-degrading microbial communities through an enrichment of sediments and seawater samples from the Pacific Ocean. Phylogenetic analysis showed strains T16B2(T), T24B3, and C76AD to form a robust clade together with Hyphomonas atlanticus 22II1-22F38(T) and Hyphomonas beringensis 25B14_1(T) (16S rRNA identity ≥99.6 %). Genomic average nucleotide identity and DNA-DNA hybridization estimate values between strain T16B2(T) and nine type strains of the genus Hyphomonas are in the range of 82.9-88.2 and 18.3-33.6 %, respectively. The major cellular fatty acids in strains T16B2(T), T24B3, and C76AD are C16:0, C17:0, C18:1 ω7c-methyl, and summed feature 8 (C18:1 ω6c/ω7c). The DNA G+C content of strain T16B2(T) is 58.5 %. The predominant respiratory quinone of strain T16B2(T) is Q-11. Polar lipids comprise three unidentified glycolipids, one unidentified phospholipid, and two polar lipids. Combined phenotypic and genotypic data show strains T16B2(T), T24B3, and C76AD to represent a novel species of the genus Hyphomonas, for which the name Hyphomonas pacifica sp. nov. is proposed, with type strain T16B2(T) (=LMG 27911(T) = MCCC 1A04387(T)). PMID:27255138

  1. Halorhabdus rudnickae sp. nov., a halophilic archaeon isolated from a salt mine borehole in Poland.

    Albuquerque, Luciana; Kowalewicz-Kulbat, Magdalena; Drzewiecka, Dominika; Stączek, Paweł; d'Auria, Giuseppe; Rosselló-Móra, Ramon; da Costa, Milton S

    2016-03-01

    Two halophilic archaea, designated strains WSM-64(T) and WSM-66, were isolated from a sample taken from a borehole in the currently unexploited Barycz mining area belonging to the "Wieliczka" Salt Mine Company, in Poland. Strains are red pigmented and form non-motile cocci that stain Gram-negative. Strains WSM-64(T) and WSM-66 showed optimum growth at 40°C, in 20% NaCl and at pH 6.5-7.5. The strains were facultative anaerobes. The major polar lipids of the two strains were phosphatidylglycerol (PG2), phosphatidylglycerol phosphate methyl ester (PGP-Me) and sulfated diglycosyl diether (S-DGD). Menaquinone MK-8 was the major respiratory quinone. The DNA G+C content of strain WSM-64(T) was 61.2mol% by HPLC method; 61.0mol% by genome sequencing. Analysis of the almost complete 16S rRNA gene sequence indicated that the strains WSM-64(T) and WSM-66 (99.7% identity) represented a member of the genus Halorhabdus in the family Halobacteriaceae. Both strains formed a distinct cluster and were most closely related to Halorhabdus tiamatea SARL4B(T) and Halorhabdus utahensis AX-2(T) (DSM 12940(T)) (95.4% and 95.6%, respectively). ANI values of WSM-64(T) with the closest relative type strains were <78.5%. Based on 16S rRNA gene sequence and whole genome analyses, physiological and biochemical characteristics we describe a new species represented by strain WSM-64(T) (=DSM 29498(T) =CECT 8673(T)) for which we propose the name Halorhabdus rudnickae sp. nov. PMID:26749115

  2. Chryseobacterium chengduensis sp. nov. isolated from the air of captive giant panda enclosures in Chengdu, China* #

    Wen, Cai-fang; Xi, Li-xin; Zhao, Shan; Hao, Zhong-xiang; Luo, Lu; Liao, Hong; Chen, Zhen-rong; She, Rong; Han, Guo-quan; Cao, San-jie; Wu, Rui; Yan, Qi-gui; Hou, Rong

    2016-01-01

    A Gram-negative, aerobic, non-motile, rod-shaped bacterial strain, designated 25-1T, was isolated from the air inside giant panda enclosures at the Chengdu Research Base of Giant Panda Breeding, China. Strain 25-1T grew optimally at pH 7.0–8.0, at 28–30 °C and in the presence of NaCl concentrations from 0.0% to 0.5 %. 16S rRNA gene sequence analysis indicated that strain 25-1T belongs to the genus Chryseobacterium within the family Flavobacteriaceae and is related most closely to C. carnis G81T (96.4% similarity), C. lathyri RBA2-6T (95.8% similarity), and C. zeae JM1085T (95.8% similarity). Its genomic DNA G+C molar composition was 36.2%. The major cellular fatty acids were iso-C15:0 (44.0%), iso-C17:0 3OH (19.8%) and C16:1 ω7c/16:1 ω6c (12.7%). The only isoprenoid quinone was menaquinone 6 (MK-6). The major polar lipids were phosphatidylethanolamine, two unidentified amino lipids and two unidentified lipids. The DNA–DNA relatedness between strain 25-1T and C. lathyri RBA2-6T was 38%. Phenotypic, genotypic, and phylogenetic characteristics indicated that strain 25-1T is a novel member of the genus Chryseobacterium, for which the name C. chengduensis sp. nov. is proposed. The type strain is 25-1T (CCTCC AB2015133T=DSM 100396T). PMID:27487806

  3. Bacillus sp.CDB3 isolated from cattle dip-sites possesses two ars gene clusters

    Somanath Bhat; Xi Luo; Zhiqiang Xu; Lixia Liu; Ren Zhang

    2011-01-01

    Contamination of soil and water by arsenic is a global problem.In Australia, the dipping of cattle in arsenic-containing solution to control cattle ticks in last centenary has left many sites heavily contaminated with arsenic and other toxicants.We had previously isolated five soil bacterial strains (CDB1-5) highly resistant to arsenic.To understand the resistance mechanism, molecular studies have been carried out.Two chromosome-encoded arsenic resistance (ars) gene clusters have been cloned from CDB3 (Bacillus sp.).They both function in Escherichia coli and cluster 1 exerts a much higher resistance to the toxic metalloid.Cluster 2 is smaller possessing four open reading frames (ORFs) arsRorf2BC, similar to that identified in Bacillus subtilis Skin element.Among the eight ORFs in cluster 1 five are analogs of common ars genes found in other bacteria, however, organized in a unique order arsRBCDA instead of arsRDABC.Three other putative genes are located directly downstream and designated as arsTIP based on the homologies of their theoretical translation sequences respectively to thioredoxin reductases, iron-sulphur cluster proteins and protein phosphatases.The latter two are novel of any known ars operons.The arsD gene from Bacillus species was cloned for the first time and the predict protein differs from the well studied E.coli ArsD by lacking two pairs of C-terrninal cysteine residues.Its functional involvement in arsenic resistance has been confirmed by a deletion experiment.There exists also an inverted repeat in the intergenic region between arsC and arsD implying some unknown transcription regulation.

  4. Kordiimonas sediminis sp. nov., isolated from a sea cucumber culture pond.

    Zhang, Heng-Xi; Zhao, Jin-Xin; Chen, Guan-Jun; Du, Zong-Jun

    2016-05-01

    A marine bacterium, designated strain N39(T), was isolated from a sediment sample collected at a sea cucumber culture pond in Weihai, China. Cells of strain N39(T) were observed to be Gram-stain negative, facultatively anaerobic, motile rods showing catalase and oxidase negative reactions. Strain N39(T) was found to grow optimally at pH 8.0-8.5, 35-37 °C and in the presence of approximately 3.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain N39(T) belongs to the genus Kordiimonas in the family Kordiimonadaceae, appearing closely related to Kordiimonas lacus JCM 16261(T) (95.9 %), Kordiimonas aquimaris MEBiC06554(T) (95.1 %), Kordiimonas gwangyangensis JCM 12864(T) (94.2 %) and Kordiimonas aestuarii 101-1(T) (93.8 %). Ubiquinone 10 (Q-10) was found to be the major respiratory quinone. The dominant cellular fatty acids were identified as iso-C17:1 ω9c, iso-C17:0, iso-C15:0 and C17:1 ω6c. The predominant polar lipids were found to be phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. The DNA G + C content of strain N39(T) is 50.8 %. On the basis of genotypic, chemotaxonomic and phenotypic data, strain N39(T) is concluded to represent a novel species within the genus Kordiimonas, for which the name Kordiimonas sediminis sp. nov. is proposed. The type strain is N39(T) (=KCTC 42590(T) = MCCC 1H00112(T)). PMID:26936256

  5. Deinococcus arenae sp. nov., a novel species isolated from sand in South Korea.

    Lee, Dongwook; Cha, Seho; Jang, Jun Hyeong; Seo, Taegun

    2016-07-01

    A Gram-negative strain, designated SA1(T), was isolated from a sand specimen from Yangyang Beach, South Korea. The cells of SA1(T) were observed to be red pigmented, strictly aerobic, non-motile rods. Strain SA1(T) was found to grow optimally at 30 °C and pH 7 (pH growth range, pH 7-9). Phylogenetic analyses of the 16S rRNA gene sequence of SA1(T) showed that the organism belongs to the phylum Deinococcus-Thermus and forms a branch within the genus Deinococcus, with Deinococcus actinosclerus BM2(T) as a close relative (99.8   % sequence similarity). The strain was found to be catalase positive and oxidase negative and to metabolise 2-ketogluconate, acetate, D,L-3-hydroxybutyrate, D-glucose, D-maltose, D-mannitol, D-mannose, D-melibiose, D-sorbitol, D-sucrose, glycogen, L-alanine, L-histidine, L-malate, L-proline and n-valerate. The guanine plus cytosine (G + C) base composition of the DNA was 69.5 mol %, as determined by the thermal denaturation method. The predominant respiratory quinone was identified as menaquinone with eight isoprene units (MK-8). The polar lipid profile of strain SA1(T) showed the presence of several unidentified glycolipids, phosphoglycolipids, phospholipids, aminophospholipids and unidentified lipids. In addition, the most abundant fatty acids of strain SA1(T) were identified as C15:1 ω6c, C16:1 ω7c and C17:0. On the basis of phylogenetic analyses, DNA-DNA hybridisation and biochemical characteristics, strain SA1(T) (=KCTC 33741(T) = JCM 31047(T)) is concluded to represent a novel species of the genus Deinococcus, for which the name Deinococcus arenae sp. nov. is proposed. PMID:27147067

  6. Mucilaginibacter carri sp. nov., isolated from a car air conditioning system.

    Kim, Dong-Uk; Lee, Hyosun; Kim, Hyun; Kim, Song-Gun; Park, So Yoon; Ka, Jong-Ok

    2016-04-01

    A Gram-stain-negative, pink bacterial strain, designated PR0008KT, was isolated from an automobile evaporator core in Korea. The cells were obligately aerobic and rod-shaped. The strain grew at 10-40 °C (optimum, 20 °C), at pH 5-8 (optimum, 7), and in the presence of 0-1.5% (w/v) NaCl. Phylogenetically, the strain was closely related to members of the genus Mucilaginibacter (93.4-97.0% 16S rRNA sequence similarities) and showed a high sequence similarity with Mucilaginibacter litoreus BR-18T, Mucilaginibacter lutimaris BR-3T and Mucilaginibacter soli R9-65T (97.0%, 96.9% and 96.9% 16S rRNA sequence similarity, respectively). It contained summed feature 3 (C16:1ω7c and/or C16:1ω6c), C16 : 0, iso-C17:0 3-OH and C16:0 as the predominant fatty acids and MK-7 as the major menaquinone. The polar lipids were phosphatidylethanolamine, one unknown aminophospholipid, two unknown aminolipids and two unknown polar lipids. The DNA G+C content of this strain was 47.4 mol%. Based on the phenotypic, genotypic and chemotaxonomic data, strain PR0008KT represents a novel species in the genus Mucilaginibacter, for which the name Mucilaginibacter carri sp. nov. (=KACC 17938T=NBRC 111539T) is proposed. PMID:26827708

  7. Spirosoma aerolatum sp. nov., isolated from a motor car air conditioning system.

    Kim, Dong-Uk; Lee, Hyosun; Kim, Song-Gun; Ahn, Jae-Hyung; Park, So Yoon; Ka, Jong-Ok

    2015-11-01

    A Gram-stain-negative, yellow-pigmented bacterial strain, designated PR1012KT, was isolated from a motor car evaporator core collected in Korea. Cells of the strain were facultatively anaerobic, non-spore-forming and rod-shaped. The strain grew at 10-40 °C (optimum, 25 °C), at pH 6.5-8.0 (optimum, pH 7.0-8.0) and in the presence of 0-1% (w/v) NaCl. Phylogenetically, the strain was closely related to members of the genus Spirosoma (97.50-90.74% 16S rRNA gene sequence similarities) and showed highest sequence similarity to Spirosoma panaciterrae DSM 21099T (97.50%). Its predominant fatty acids included summed feature 3 (C16:1ω7c and/or C16:1ω6c), C16:1ω5c, iso-C15:0 and summed feature 4 (iso-C17:1 I and/or anteiso B) and it had MK-7 as the major menaquinone. The polar lipids present included phosphatidylethanolamine, one unknown aminophospholipid, two unknown aminolipids and five unknown polar lipids. The DNA G+C content of this strain was 54 mol%. Based on phenotypic, genotypic and chemotaxonomic data, strain PR1012KT represents a novel species in the genus Spirosoma, for which the name Spirosoma aerolatum sp. nov. is proposed. The type strain is PR1012KT ( = KACC 17939T = NBRC 110794T). PMID:26956596

  8. Filimonas endophytica sp. nov., isolated from surface-sterilized root of Cosmos bipinnatus.

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

    2015-12-01

    A Gram-stain-negative, yellow, motile by gliding, filamentous bacterium, designated SR 2-06T, was isolated from surface-sterilized root of garden cosmos. 16S rRNA gene sequence analysis indicated that SR 2-06T was related most closely to Filimonas lacunae YT21T of the family Chitinophagaceae at a sequence similarity of 96.90 %, while levels of similarity to other related taxa were less than 93.08 %. Strain SR 2-06T exhibited similar features to F. lacunae in that it contained MK-7 as the major respiratory quinone, and iso-C15 : 1 G, iso-C15 : 0 and a summed feature consisting of C16 : 1ω6c and/or C16 : 1ω7c as the major fatty acids. However, strain SR 2-06T was distinguished from F. lacunae using a combination of physiological and biochemical properties. The cellular polar lipids were phosphatidylethanolamine, unknown aminophospholipids, unknown aminolipids, an unknown phospholipid and unidentified polar lipids. The DNA G+C content was 46.0 mol%. The phenotypic and phylogenetic evidence clearly indicates that strain SR 2-06T represents a novel species of the genus Filimonas, for which the name Filimonas endophytica sp. nov. is proposed. The type strain is SR 2-06T ( = KCTC 42060T = JCM 19844T). PMID:26443022

  9. Proteocatella sphenisci gen. nov., sp. nov., a psychrotolerant, spore-forming anaerobe isolated from penguin guano.

    Pikuta, Elena V; Hoover, Richard B; Marsic, Damien; Whitman, William B; Lupa, Boguslaw; Tang, Jane; Krader, Paul

    2009-09-01

    A novel, obligately anaerobic, psychrotolerant bacterium, designated strain PPP2T, was isolated from guano of the Magellanic penguin (Spheniscus magellanicus) in Chilean Patagonia. Cells were Gram-stain-positive, spore-forming, straight rods (0.7-0.8x3.0-5.0 microm) that were motile by means of peritrichous flagella. Growth was observed at pH 6.7-9.7 (optimum pH 8.3) and 2-37 degrees C (optimum 29 degrees C). Growth was observed between 0 and 4% (w/v) NaCl with optimum growth at 0.5% (w/v). Strain PPP2T was a catalase-negative chemo-organoheterotroph that was capable of fermentative metabolism. Peptone, bacto-tryptone, Casamino acids, oxalate, starch, chitin and yeast extract were utilized as substrates. The major metabolic products were acetate, butyrate and ethanol. Strain PPP2T was resistant to ampicillin, but sensitive to tetracycline, chloramphenicol, rifampicin, kanamycin, vancomycin and gentamicin. The DNA G+C content of strain PPP2T was 39.5 mol%. Phylogenetic analysis revealed that strain PPP2T was related most closely to Clostridium sticklandii SR (approximately 90% 16S rRNA gene sequence similarity). On the basis of phylogenetic analysis and phenotypic characteristics, strain PPP2T is considered to represent a novel species of a new genus, for which the name Proteocatella sphenisci gen. nov., sp. nov. is proposed. The type strain of Proteocatella sphenisci is PPP2T (=ATCC BAA-755T=JCM 12175T=CIP 108034T). PMID:19620379

  10. Epilithonimonas xixisoli sp. nov., isolated from wetland bank-side soil.

    Feng, Hao; Zeng, Yanhua; Huang, Yili

    2014-12-01

    A novel Gram-staining-negative, non-motile and rod-shaped bacterial strain containing flexirubin-type pigments, designated S31(T), was isolated from bank-side soil of the Xixi wetland in Zhejiang province, China. Growth occurred at 10-37 °C (optimum, 32 °C), pH 6-8 (optimum, pH 7) and with 0-2 % (w/v) NaCl (optimum, 1 %). Strain S31(T) shared highest 16S rRNA gene sequence similarities with Epilithonimonas lactis H1(T) (96.2 %) and Chryseobacterium molle DW3(T) (96.4 %). Phylogenetic analysis suggested that strain S31(T) was a member of the genus Epilithonimonas. The dominant respiratory quinone was MK-6 and the DNA G+C content was 33.3 mol%. The major fatty acids were iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) and anteiso-C15 : 0. The major polar lipids of strain S31(T) were phosphatidylethanolamine, three unidentified aminolipids and four unidentified polar lipids. Based on its phenotypic and chemotaxonomic characteristics and phylogenetic data, strain S31(T) represents a novel species of the genus Epilithonimonas, for which the name Epilithonimonas xixisoli sp. nov. (type strain S31(T) = CGMCC 1.12802(T) = NBRC 110387(T)) is proposed. PMID:25256707

  11. Bizionia arctica sp. nov., isolated from Arctic fjord seawater, and emended description of the genus Bizionia.

    Li, Hai; Zhang, Xi-Ying; Liu, Chang; Liu, Ang; Qin, Qi-Long; Su, Hai-Nan; Shi, Mei; Zhou, Bai-Cheng; Chen, Xiu-Lan; Zhang, Yu-Zhong; Xie, Bin-Bin

    2015-09-01

    A Gram-stain-negative, yellow-pigmented, aerobic, non-flagellated, non-gliding bacterial strain, designated SM1203(T), was isolated from surface seawater of Kongsfjorden, Svalbard. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SM1203(T) was affiliated with the genus Bizionia in the family Flavobacteriaceae. The strain shared the highest 16S rRNA gene sequence similarity (>96%) with the type strains of Formosa spongicola (96.8%), Bizionia paragorgiae (96.3%), B. saleffrena (96.3%) and B. echini (96.1%) and 95.4-95.7% sequence similarity with the type strains of other known species of the genus Bizionia. The strain grew at 4-30 °C and in the presence of 1.0-5.0% (w/v) NaCl. The major fatty acids of strain SM1203(T) were iso-C15 : 0, iso-C15 : 1, anteiso-C15 : 0 and C15 : 0 and the main polar lipids were phosphatidylethanolamine and an unidentified lipid. The major respiratory quinone of strain SM1203(T) was menaquinone 6 (MK-6). The genomic DNA G+C content of strain SM1203(T) was 34.8 mol%. Based on the polyphasic characterization of strain SM1203(T) in this study, the strain represents a novel species in the genus Bizionia, for which the name Bizionia arctica sp. nov. is proposed. The type strain is SM1203(T) ( = CGMCC 1.12751(T) = JCM 30333(T)). An emended description of the genus Bizionia is also given. PMID:26016491

  12. Chitinophaga longshanensis sp. nov., a mineral-weathering bacterium isolated from weathered rock.

    Gao, Shan; Zhang, Wen-Bin; Sheng, Xia-Fang; He, Lin-Yan; Huang, Zhi

    2015-02-01

    A Gram-stain-negative, aerobic, yellow-pigmented, non-motile, non-spore-forming, rod-shaped bacterial strain, Z29(T), was isolated from the surface of weathered rock (potassic trachyte) from Nanjing, Jiangsu Province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences suggested that strain Z29(T) belongs to the genus Chitinophaga in the family Chitinophagaceae. Levels of 16S rRNA gene sequence similarity between strain Z29(T) and the type strains of recognized species of the genus Chitinophaga ranged from 92.7 to 98.2 %. The main fatty acids of strain Z29(T) were iso-C15 : 0, C16 : 1ω5c and iso-C17 : 0 3-OH. It also contained menaquinone 7 (MK-7) as the respiratory quinone and homospermidine as the main polyamine. The polar lipid profile contained phosphatidylethanolamine, unknown aminolipids, unknown phospholipids and unknown lipids. The total DNA G+C content of strain Z29(T) was 51.3 mol%. Phenotypic properties and chemotaxonomic data supported the affiliation of strain Z29(T) with the genus Chitinophaga. The low level of DNA-DNA relatedness (ranging from 14.6 to 29.8 %) to the type strains of other species of the genus Chitinophaga and differential phenotypic properties demonstrated that strain Z29(T) represents a novel species of the genus Chitinophaga, for which the name Chitinophaga longshanensis sp. nov. is proposed. The type strain is Z29(T) ( = CCTCC AB 2014066(T) = LMG 28237(T)). PMID:25376849

  13. Marivirga atlantica sp. nov., isolated from seawater and emended description of the genus Marivirga.

    Lin, Chao-Yi; Zhang, Xi-Ying; Liu, Ang; Liu, Chang; Song, Xiao-Yan; Su, Hai-Nan; Qin, Qi-Long; Xie, Bin-Bin; Zhang, Yu-Zhong

    2015-05-01

    A novel Gram-stain-negative, aerobic, orange-pigmented, non-flagellated, gliding, rod-shaped bacterium, designated strain SM1354(T) was isolated from surface seawater of the Atlantic Ocean. The strain hydrolysed gelatin and DNA but did not reduce nitrate. It grew at 4-40 °C and with 0.5-11% (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene sequences revealed that strain SM1354(T) belonged to the genus Marivirga with 96.0-96.2% sequence similarities to known species of the genus Marivirga . The major fatty acids of strain SM1354(T) were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 03-OH and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 02-OH). Polar lipids of strain SM1354(T) included phosphatidylethanolamine, three unidentified lipids and one unidentified aminolipid and aminophospholipid. The major respiratory quinone of strain SM1354(T) was menaquinone 7 (MK-7). The genomic DNA G+C content of strain SM1354(T) was 33.9 ± 0.4 mol%. On the basis of the results of the polyphasic characterization in this study, it is proposed that strain SM1354(T) represents a novel species of the genus Marivirga , namely Marivirga atlantica sp. nov. The type strain of Marivirga atlantica is SM1354(T) ( =CCTCC AB 2014242(T) =JCM 30305(T)). An emended description of the genus Marivirga is also proposed. PMID:25701845

  14. Roseomonas elaeocarpi sp. nov., isolated from olive (Elaeocarpus hygrophilus Kurz.) phyllosphere.

    Damtab, Jenjira; Nutaratat, Pumin; Boontham, Wanatchaporn; Srisuk, Nantana; Duangmal, Kannika; Yurimoto, Hiroya; Sakai, Yasuyoshi; Muramatsu, Yuki; Nakagawa, Yasuyoshi

    2016-01-01

    An aerobic, Gram-stain-negative, coccobacillus-shaped, non-endospore-forming, pink-pigmented bacterium, designated PN2T, was isolated from an olive leaf. The strain grew at 15-35 °C with an optimum temperature for growth at 30 °C, and at pH 5.0-7.5 with an optimum pH for growth at 6.0. Growth was observed in the presence of up to 1.02 % (w/v) NaCl. The major fatty acids were C19 : 0 cyclo ω8c, C16 : 0 and C18 : 1ω7c. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, unknown aminolipids, an unknown phospholipid and an unknown lipid. The respiratory quinone was ubiquinone-10. The DNA G+C content of strain PN2T was 70.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain PN2T was closely related to members of the genus Roseomonas and shared highest similarity with Roseomonas mucosa ATCC BAA-692T (96.5 %), Roseomonas gilardii subsp. gilardii ATCC 49956T (96.2 %) and Roseomonas gilardii subsp. rosea ATCC BAA-691T (96.2 %). Furthermore, the DNA-DNA relatedness value between strain PN2T and the closest related species R. mucosa ATCC BAA-692T was 27 %. These data allowed the phenotypic and genotypic differentiation of strain PN2T from its closest phylogenetic neighbour (R. mucosa ATCC BAA-692T). Based on phenotypic and genotypic characteristics, strain PN2T is classified as representing a novel species of the genus Roseomonas for which the name Roseomonas elaeocarpi sp. nov. is proposed. The type strain is PN2T ( = BCC 44864T = NBRC 107871T). PMID:26552692

  15. Sphingobium endophyticus sp. nov., isolated from the root of Hylomecon japonica.

    Zhu, Lingfang; Xin, Kaiyun; Chen, Chaoqiong; Li, Changfu; Si, Meiru; Zhao, Liang; Shi, Xu; Zhang, Lei; Shen, Xihui

    2015-04-01

    A yellow-pigmented bacterium, designated strain GZGR-4(T), was isolated from the root of Hylomecon japonica (Thunb.) Prantl et Kündig collected from Taibai Mountain in Shaanxi Province, north-west China. Cells of strain GZGR-4(T) were Gram-negative, rod-shaped, strictly aerobic, non-endospore-forming and non-motile. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GZGR-4(T) is a member of the genus Sphingobium, exhibiting the highest sequence similarity to Sphingobium aromaticiconvertens DSM 12677(T) (97.3 %). 16S rRNA gene sequence similarities between strain GZGR-4(T) and the type strains of other Sphingobium species with validly published names ranged from 93.4-96.5 %. The predominant respiratory quinone of strain GZGR-4(T) was ubiquinone-10 (Q-10) and the major cellular fatty acids were summed feature 8 (comprising C18:1 ω7c and/or C18:1 ω6c), summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c), C16:0 and C14:0 2-OH. Spermidine was the major polyamine. The polar lipid profile consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid, one unidentified phosphoglycolipid, one unidentified phospholipid, one unidentified aminolipid and one unidentified lipid. The DNA G+C content was 63.6 mol%. DNA-DNA relatedness for strain GZGR-4(T) with respect to its closest phylogenetic relative S. aromaticiconvertens DSM 12677(T) was 22.6 ± 5.3 %. On the basis of the polyphasic taxonomic data presented, strain GZGR-4(T) is considered to represent a novel species of the genus Sphingobium, for which the name Sphingobium endophyticus sp. nov. is proposed. The type strain is GZGR-4(T) (=CCTCC AB 2013305(T) = KCTC 32447(T)). PMID:25623892

  16. Carboxylicivirga linearis sp. nov., isolated from a sea cucumber culture pond.

    Wang, Feng-Qing; Zhou, Yan-Xia; Lin, Xue-Zheng; Chen, Guan-Jun; Du, Zong-Jun

    2015-10-01

    A yellow-pigmented, Gram-stain-negative and facultatively anaerobic bacterium, designated FB218T, was isolated from a sediment sample collected from a sea cucumber culture pond in Rongcheng, China (36° 54′ 36″ N 122° 14′ 34″ E). Cells of strain FB218T were slender, gliding, catalase-positive and oxidase-negative. Optimal growth occurred at 30 °C, pH 6.5–7.0 and in medium containing 2–3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain FB218T belonged to the genus Carboxylicivirga, family Marinilabiliaceae. The predominant fatty acids were iso-C15 : 0 and anteiso-C15 : 0. MK-7 was the main respiratory quinone. The major polar lipids of strain FB218T were two unidentified lipids and a phospholipid. The genomic DNA G+C content was 40.0 mol%. Based on the distinct phylogenetic position and the combination of physiological and phenotypic characteristics, strain FB218T represents a novel species of the genus Carboxylicivirga, for which the name Carboxylicivirga linearis sp. nov. is proposed. The type strain is FB218T ( = KCTC 42254T = MCCC 1H00106T). An emended description of the genus Carboxylicivirga is also provided. PMID:26297036

  17. Hyunsoonleella pacifica sp. nov., isolated from seawater of South Pacific Gyre.

    Gao, Xin; Zhang, Zenghu; Dai, Xiaofeng; Zhang, Xiao-Hua

    2015-04-01

    A Gram-stain-negative, strictly aerobic, non-flagellated, non-gliding, oxidase- and catalase-positive and rod-shaped yellow-pigmented bacterium, designated strain SW033(T) was isolated from a surface seawater sample collected from the South Pacific Gyre (GPS position: 26° 29' S 137° 56' W) during the Integrated Ocean Drilling Program, expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SW033(T) belonged to the genus Hyunsoonleella and showed the highest 16S rRNA gene sequence similarity with Hyunsoonleella jejuensis CNU004(T) (96.8%). It showed 94.7-95.8% 16S rRNA gene sequence similarity with respect to members of the genera Jejuia , Arenitalea and Algibacter in the family Flavobacteriaceae . Optimal growth occurred in the presence of 2-3% (w/v) NaCl, at pH 8.0 and at 28 °C. The genomic DNA G+C content of strain SW033(T) was 36.1 mol%. The major fatty acids were iso-C(15 : 1) G, iso-C(15 : 0), iso-C(17 : 0) 3-OH, iso-C(15 : 0) 3-OH and summed feature 3 (comprising C(16 : 1)ω7c and/or C(16 : 1)ω6c). The major respiratory quinone was menaquinone-6. The major polar lipids were phosphatidylethanolamine, two unidentified aminolipids and four unidentified lipids. On the basis of the polyphasic analyses, strain SW033(T) is considered to represent a member of a novel species in the genus Hyunsoonleella , for which the name Hyunsoonleella pacifica sp. nov. is proposed. The type strain is SW033(T) ( = CGMCC 1.11009(T) = JCM 17860(T)). PMID:25604336

  18. Zooshikella marina sp. nov. a cycloprodigiosin- and prodigiosin-producing marine bacterium isolated from beach sand.

    Ramaprasad, E V V; Bharti, Dave; Sasikala, Ch; Ramana, Ch V

    2015-12-01

    A red-pigmented bacterium producing a metallic green sheen, designated strain JC333T, was isolated from a sand sample collected from Shivrajpur-Kachigad beach, Gujarat, India. Phylogenetic analyses based on the 16S rRNA gene sequence of strain JC333T showed highest sequence similarity to Zooshikella ganghwensis JC2044T (99.24 %) and less than 91.94 % similarity with other members of the class Gammaproteobacteria. DNA-DNA hybridizations between JC333T and Z. ganghwensis JC2044T showed low relatedness values of 19 ± 1.3 % (reciprocal 21 ± 2.2 %). The major respiratory quinone was ubiquinone-9 (Q9) and the polar lipid profile was composed of the major components diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid and an unidentified lipid. The presence of C16 : 1ω7c/C16 : 1ω6c, C16 : 0, C18 : 1ω7c and C12 : 0 as major fatty acids supported the affiliation of strain JC333T to the genus Zooshikella. Prodigiosin, cycloprodigiosin and eight other prodigiosin analogues were the pigments of JC333T. Characterization based on 16S rRNA gene sequence analysis, physiological parameters, pigment analysis, ubiquinone, and polar lipid and fatty acid compositions revealed that JC333T represents a novel species of the genus Zooshikella, for which the name Zooshikella marina sp. nov. is proposed. The type strain is JC333T ( = KCTC 42659T = LMG 28823T). PMID:26409875

  19. Cohnella rhizosphaerae sp. nov., isolated from the rhizosphere environment of Zea mays.

    Kämpfer, Peter; Glaeser, Stefanie P; McInroy, John A; Busse, Hans-Jürgen

    2014-05-01

    A Gram-staining-positive, aerobic, non-endospore forming organism, isolated as a seed endophyte (colonizing the internal healthy tissue of plant seed) of sweet corn (Zea mays), strain CSE-5610T, was studied for its taxonomic allocation. On the basis of 16S rRNA gene sequence comparisons, strain CSE-5610T was grouped into the genus Cohnella, most closely related to Cohnella ginsengisoli GR21-5T (98.1%) and 'Cohnella plantaginis' YN-83 (97.5%). The 16S rRNA gene sequence similarity to other members of the genus Cohnella was <96.6%. DNA-DNA hybridization of strain CSE-5610T with C. ginsengisoli DSM 18997T and 'C. plantaginis' DSM 25424 was 58% (reciprocal 24%) and 30% (reciprocal 27%), respectively. The fatty acid profile from whole cell hydrolysates supported the allocation of the strain to the genus Cohnella; iso- and anteiso-branched fatty acids were found as major compounds. meso-Diaminopimelic acid was identified as the cell-wall diamino acid. The quinone system consisted predominantly of menaquinone MK-7. The polar lipid profile was composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two aminophospholipids, a phospholipid and minor amounts of two polar lipids. In the polyamine pattern, spermidine was the major polyamine. The G+C content of the genomic DNA was 60 mol%. In addition, the results of physiological and biochemical tests also allowed phenotypic differentiation of strain CSE-5610T from the two closely related strains. Hence, CSE-5610T represents a novel species of the genus Cohnella, for which we propose the name Cohnella rhizosphaerae sp. nov., with CSE-5610T (=LMG 28080T=CIP 110695T) as the type strain. PMID:24556632

  20. Description of Micrococcus aloeverae sp. nov., an endophytic actinobacterium isolated from Aloe vera.

    Prakash, Om; Nimonkar, Yogesh; Munot, Hitendra; Sharma, Avinash; Vemuluri, Venkata Ramana; Chavadar, Mahesh S; Shouche, Yogesh S

    2014-10-01

    A yellow Gram-stain-positive, non-motile, non-endospore -forming, spherical endophytic actinobacterium, designated strain AE-6(T), was isolated from the inner fleshy leaf tissues of Aloe barbadensis (Aloe vera) collected from Pune, Maharashtra, India. Strain AE-6(T) grew at high salt concentrations [10% (w/v) NaCl], temperatures of 15-41 °C and a pH range of 5-12. It showed highest (99.7%) 16S rRNA gene sequence similarity with Micrococcus yunnanensis YIM 65004(T) followed by Micrococcus luteus NCTC 2665(T) (99.6%) and Micrococcus endophyticus YIM 56238(T) (99.0%). Ribosomal protein profiling by MALDI-TOF/MS also showed it was most closely related to M. yunnanensis YIM 65004(T) and M. luteus NCTC 2665(T). Like other members of the genus Micrococcus, strain AE-6(T) had a high content of branched chain fatty acids (iso-C15:0 and anteiso-C15:0). MK-8(H2) and MK-8 were the predominant isoprenoid quinones. Cell wall analysis showed an 'A2 L-Lys-peptide subunit' type of peptidoglycan and ribose to be the major cell wall sugar. The DNA G+C content was 70 mol%. Results of DNA-DNA hybridization of AE-6(T) with its closest relatives from the genus Micrococcus produced a value of less than 70%. Based on the results of this study, strain AE-6(T) could be clearly differentiated from other members of the genus Micrococcus. We propose that it represents a novel species of the genus Micrococcus and suggest the name Micrococcus aloeverae sp. nov., with strain AE-6(T) ( = MCC 2184(T) = DSM 27472(T)) as the type strain of the species. PMID:25048212

  1. Micrococcus cohnii sp. nov., isolated from the air in a medical practice.

    Rieser, Gernot; Scherer, Siegfried; Wenning, Mareike

    2013-01-01

    Three Gram-reaction-positive bacteria, isolated from the air in a medical practice (strains WS4601(T), WS4602) or a pharmaceutical clean room (strain WS4599), were characterized using a polyphasic approach. Phylogenetic analyses based on 16S rRNA and recA gene sequences of the three novel strains showed that they formed a distinct lineage within the genus Micrococcus, sharing 16S rRNA gene sequence similarities of 96.1-98.0 % with other species of this genus. Chemotaxonomic features also supported the classification of the three novel strains within the genus Micrococcus. The major cellular fatty acids of strain WS4601(T) were anteiso-C(15 : 0) and iso-C(15 : 0), the cell-wall peptidoglycan was of type A3α (L-Lys-L-Ala), and the predominant respiratory quinones were MK-7(H(2)) and MK-8(H(2)). The polar lipid profile contained diphosphatidylglycerol and phosphatidylglycerol, but no phosphatidylinositol. The G+C content of the genomic DNA was 70.4 mol%. Numerous physiological properties were found that clearly distinguished strains WS4599, WS4601(T) and WS4602 from established members of the genus Micrococcus. Based on the phenotypic and phylogenetic data, strains WS4599, WS4601(T) and WS4602 are considered to represent three different strains of a novel species of the genus Micrococcus, for which the name Micrococcus cohnii sp. nov. is proposed. The type strain is WS4601(T) (=DSM 23974(T)=LMG 26183(T)). PMID:22328614

  2. Antifungal and antibacterial activities of Streptomyces polymachus sp. nov. isolated from soil.

    Nguyen, Tuan Manh; Kim, Jaisoo

    2015-08-01

    Strain T258T was isolated from forest soil at Bongnae Falls, South Korea. The strain exhibited antimicrobial and antifungal activity against the following strains: Bacillus subtilis, Staphylococcus aureus, Pseudomonas aeruginosa, Paenibacillus larvae, Escherichia coli, Candida albicans and Aspergillus niger. Growth occurred on all ISP media tested (2, 3, 4, 5, 6 and 7), Czapek-Dox agar, potato dextrose agar, trypticase soy agar, Bennett's modified agar and nutrient agar at 28 °C. Aerial spores were produced solely on ISP Medium 4; the colour of the aerial mycelium was white and the substrate mycelium was ivory. Melanin production was negative on peptone-yeast extract iron agar (ISP Medium 6). The cell-wall peptidoglycan contained ll-diaminopimelic acid, glutamic acid, alanine and glycine. Whole-cell hydrolysates contained glucose, ribose and galactose. The predominant menaquinones were MK-9(H6) and MK-9(H8) while the minor menaquinone was MK-10(H2). The polar lipids included diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The major fatty acids (>10%) were C16 : 0 (29.8%), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) (15.1%), anteiso-C15 : 0 (13.5%) and iso-C15 : 0 (10.3%). DNA-DNA similarity with other strains ranged between 37.84 ± 1.15% and 50.25 ± 1.91 %. On the basis of these data, we suggest that strain T258T represents a novel species that belong to the genus Streptomyces, for which we propose a name Streptomyces polymachus sp. nov. The type strain is T258T ( = KACC 18247T = KEMB 9005-212T = NBRC 110905T). PMID:25899502

  3. Stackebrandtia cavernae sp. nov., a novel actinobacterium isolated from a karst cave sample.

    Zhang, Wan-Qin; Li, Yu-Qian; Liu, Lan; Salam, Nimaichand; Fang, Bao-Zhu; Wei, Dao-Qiao; Han, Ming-Xian; Li, Wen-Jun

    2016-03-01

    A novel actinobacterial strain, YIM ART06T, was isolated from a rock sample of karst cave located at Guizhou province, south-west China, and was characterized by a polyphasic taxonomic approach. The morphological and chemotaxonomic properties of strain YIM ART06T were in accordance with those of the genus Stackebrandtia. The 16S rRNA gene sequence of strain YIM ART06T showed highest similarity to Stackebrandtia nassauensis JCM 14905T (98.0 %). The DNA-DNA hybridization value between strains YIM ART06T and S. nassauensis JCM 14905T was, however, moderately high (62.9 %) but below the 70 % limit for species identification. Strain YIM ART06T contained meso-diaminopimelic acid as the diagnostic diamino acid, and mannose, ribose and xylose in the whole-cell hydrolysates. The predominant menaquinones detected were MK-10(H4), MK-10(H6), MK-11(H4) and MK-11(H6), while the cell membrane polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmethylethanolamine and three unidentified phospholipids. The genomic DNA G+C content of strain YIM ART06T was 71 mol%. The major fatty acids were anteiso-C17 : 0, iso-C17 : 0, iso-C16 : 0 and iso-C15 : 0. Based on the taxonomic characteristics from the genotypic and phenotypic results, strain YIM ART06T merits recognition as a representative of a novel species of the genus Stackebrandtia, for which the name Stackebrandtia cavernae sp. nov. is proposed. The type strain is YIM ART06T ( = KCTC 39599T = CCTCC AA 2015021T = DSM 100594T). PMID:26703216

  4. Streptomyces formicae sp. nov., a novel actinomycete isolated from the head of Camponotus japonicus Mayr.

    Bai, Lu; Liu, Chongxi; Guo, Lifeng; Piao, Chenyu; Li, Zhilei; Li, Jiansong; Jia, Feiyu; Wang, Xiangjing; Xiang, Wensheng

    2016-02-01

    During a screening for novel and biotechnologically useful actinobacteria in insects, a novel actinomycete with antifungal activity, designated strain 1H-GS9(T), was isolated from the head of a Camponotus japonicus Mayr ant, which were collected from Northeast Agricultural University (Harbin, Heilongjiang, China). Strain 1H-GS9(T) was characterised using a polyphasic approach. The organism was found to have morphological and chemotaxonomic characteristics typical of members of the genus Streptomyces. 16S rRNA gene sequence similarity studies showed that strain 1H-GS9(T) belongs to the genus Streptomyces with high sequence similarities to Streptomyces scopuliridis DSM 41917(T) (98.8 %) and Streptomyces mauvecolor JCM 5002(T) (98.6 %). However, phylogenetic analysis based on the 16S rRNA gene sequence indicated that it forms a monophyletic clade with Streptomyces kurssanovii JCM 4388(T) (98.6 %), Streptomyces xantholiticus JCM 4282(T) (98.6 %) and Streptomyces peucetius JCM 9920(T) (98.5 %). Thus, a combination of DNA-DNA hybridization experiments and phenotypic tests were carried out between strain 1H-GS9(T) and the above-mentioned five strains, which further clarified their relatedness and demonstrated that strain 1H-GS9(T) could be distinguished from these strains. Therefore, the strain is concluded to represent a novel species of the genus Streptomyces, for which the name Streptomyces formicae sp. nov. is proposed. The type strain is 1H-GS9(T) (=CGMCC 4.7277(T) = DSM 100524(T)). PMID:26608172

  5. Streptomyces humi sp. nov., an actinobacterium isolated from soil of a mangrove forest.

    Zainal, Nurullhudda; Ser, Hooi-Leng; Yin, Wai-Fong; Tee, Kok-Keng; Lee, Learn-Han; Chan, Kok-Gan

    2016-03-01

    A novel Streptomyces strain, MUSC 119(T), was isolated from a soil collected from a mangrove forest. Cells of MUSC 119(T) stained Gram-positive and formed light brownish grey aerial mycelium and grayish yellowish brown substrate mycelium on ISP 2 medium. A polyphasic approach was used to determine the taxonomic status of strain MUSC 119(T), which shows a range of phylogenetic and chemotaxonomic properties consistent with those of the genus Streptomyces. The cell wall peptidoglycan consisted of LL-diaminopimelic acid. The predominant menaquinones were identified as MK-9(H8), MK-9(H6) and MK-9(H4). The polar lipid profile consisted of phosphatidylinositol, phosphatidylethanolamine, glycolipids, diphosphatidylglycerol and four phospholipids. The predominant cellular fatty acids were anteiso-C15:0, iso-C16:0, and anteiso-C17:0. The cell wall sugars were glucose, mannose, ribose and rhamnose. The phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain MUSC119(T) to be closely related to Streptomyces rhizophilus JR-41(T) (99.0 % sequence similarity), S. panaciradicis 1MR-8(T) (98.9 %), S. gramineus JR-43(T) (98.8 %) and S. graminisoli JR-19(T) (98.7 %). These results suggest that MUSC 119(T) should be placed within the genus Streptomyces. DNA-DNA relatedness values between MUSC 119(T) to closely related strains ranged from 14.5 ± 1.3 to 27.5 ± 0.7 %. The G+C content was determined to be 72.6 mol  %. The polyphasic study of MUSC 119(T) showed that this strain represents a novel species, for which the name Streptomyces humi sp. nov. is proposed. The type strain of S. humi is MUSC 119(T) (=DSM 42174(T) = MCCC 1K00505(T)). PMID:26786500

  6. Celeribacter persicus sp. nov., a polycyclic-aromatic-hydrocarbon-degrading bacterium isolated from mangrove soil.

    Jami, Mansooreh; Lai, Qiliang; Ghanbari, Mahdi; Moghadam, Mohsen Shahriari; Kneifel, Wolfgang; Domig, Konrad J

    2016-04-01

    A Gram-stain-negative, mesophilic bacterial strain, designated SBU1T, which degrades polycyclic aromatic hydrocarbons was isolated from the sediments of the mangrove forests of Nayband Bay in the Iranian Persian Gulf during a bioremediation experiment. The 16S rRNA gene sequence of strain SBU1T exhibited highest similarities with Celeribacter indicus P73T (98.52 %) and Celeribacter neptunius H 14T (97.05 %). Phylogenetic analysis, based on 16S rRNA gene sequences, demonstrated that strain SBU1T fell within a cluster consisting of the type strains of species of the genus Celeribacter and formed a stable clade with C. indicus P73T in trees generated with three algorithms. The fatty acid profile of strain SBU1T consisted of the major fatty acids C18 : 1ω7c/ω6c and C18 : 1ω7c 11-methyl. The major compounds in the polar lipid profile were one phosphatidylglycerol and four unidentified phospholipids. The quinone system exclusively comprised ubiquinone (Q-10). The DNA G+C content was 60.4 mol%. A combination of phylogenetic analysis, DNA-DNA hybridization estimation, average nucleotide identity results and differential phenotypic and chemotaxonomic characteristics demonstrated that strain SBU1T could be distinguished from its close relatives. Therefore, strain SBU1T is considered to represent a novel species of the genus Celeribacter for which the name Celeribacter persicus sp. nov. is proposed. The type strain is SBU1T ( = MCCC 1A00672T = DSM 100434T). PMID:26867899

  7. Morphological and Molecular Characterization of a Fungus, Hirsutella sp., Isolated from Planthoppers and Psocids in Argentina

    Toledo, Andrea V.; Simurro, María E.; Pedro A. Balatti

    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 ...

  8. Draft Genome of Janthinobacterium sp. RA13 Isolated from Lake Washington Sediment.

    McTaggart, Tami L; Shapiro, Nicole; Woyke, Tanja; Chistoserdova, Ludmila

    2015-01-01

    Sequencing the genome of Janthinobacterium sp. RA13 from Lake Washington sediment is announced. From the genome content, a versatile life-style is predicted, but not bona fide methylotrophy. With the availability of its genomic sequence, Janthinobacterium sp. RA13 presents a prospective model for studying microbial communities in lake sediments. PMID:25676775

  9. Draft Genome of Pseudomonas sp. Strain 11/12A, Isolated from Lake Washington Sediment.

    McTaggart, Tami L; Shapiro, Nicole; Woyke, Tanja; Chistoserdova, Ludmila

    2015-01-01

    We announce here the genome sequencing of Pseudomonas sp. strain 11/12A from Lake Washington sediment. From the genome content, a versatile lifestyle is predicted but not one of bona fide methylotrophy. With the availability of its genomic sequence, Pseudomonas sp. 11/12A presents a prospective model for studying microbial communities in lake sediments. PMID:25700412

  10. Draft Genome of Pseudomonas sp. Strain 11/12A, Isolated from Lake Washington Sediment

    McTaggart, Tami L.; Shapiro, Nicole; Woyke, Tanja; Chistoserdova, Ludmila

    2015-01-01

    We announce here the genome sequencing of Pseudomonas sp. strain 11/12A from Lake Washington sediment. From the genome content, a versatile lifestyle is predicted but not one of bona fide methylotrophy. With the availability of its genomic sequence, Pseudomonas sp. 11/12A presents a prospective model for studying microbial communities in lake sediments.

  11. Draft Genome of Janthinobacterium sp. RA13 Isolated from Lake Washington Sediment

    McTaggart, Tami L.; Shapiro, Nicole; Woyke, Tanja; Chistoserdova, Ludmila

    2015-01-01

    Sequencing the genome of Janthinobacterium sp. RA13 from Lake Washington sediment is announced. From the genome content, a versatile life-style is predicted, but not bona fide methylotrophy. With the availability of its genomic sequence, Janthinobacterium sp. RA13 presents a prospective model for studying microbial communities in lake sediments.

  12. Isolation of Endoglucanase Genes from Pseudomonas fluorescens subsp. cellulosa and a Pseudomonas sp

    Wolff, Bruce R.; Mudry, Terry A.; Glick, Bernard R.; Pasternak, J J

    1986-01-01

    Endoglucanase genes from Pseudomonas fluorescens subsp. cellulosa and Pseudomonas sp. were cloned and characterized. DNA hybridization studies showed that these genes are homologous and that each species has one copy of the gene per genome. The DNA fragment from Pseudomonas sp. codes for, at most, a 23-kilodalton endoglucanase.

  13. Isolation and characterization of human trophoblast side-population (SP cells in primary villous cytotrophoblasts and HTR-8/SVneo cell line.

    Tomoka Takao

    Full Text Available Recently, numerous studies have identified that immature cell populations including stem cells and progenitor cells can be found among "side-population" (SP cells. Although SP cells isolated from some adult tissues have been reported elsewhere, isolation and characterization of human trophoblast SP remained to be reported. In this study, HTR-8/SVneo cells and human primary villous cytotrophoblasts (vCTBs were stained with Hoechst 33342 and SP and non-SP (NSP fractions were isolated using a cell sorter. A small population of SP cells was identified in HTR-8/SVneo cells and in vCTBs. SP cells expressed several vCTB-specific markers and failed to express syncytiotrophoblast (STB or extravillous cytotrophopblast (EVT-specific differentiation markers. SP cells formed colonies and proliferated on mouse embryonic fibroblast (MEF feeder cells or in MEF conditioned medium supplemented with heparin/FGF2, and they also showed long-term repopulating property. SP cells could differentiate into both STB and EVT cell lineages and expressed several differentiation markers. Microarray analysis revealed that IL7R and IL1R2 were exclusively expressed in SP cells and not in NSP cells. vCTB cells sorted as positive for both IL7R and IL1R2 failed to express trophoblast differentiation markers and spontaneously differentiated into both STB and EVT in basal medium. These features shown by the SP cells suggested that IL7R and IL1R2 are available as markers to detect the SP cells and that vCTB progenitor cells and trophoblast stem cells were involved in the SP cell population.

  14. Tenacibaculum holothuriorum sp. nov., isolated from the sea cucumber Apostichopus japonicus intestine.

    Wang, Liping; Li, Xiaoyi; Hu, Dong; Lai, Qiliang; Shao, Zongze

    2015-12-01

    A novel bacterial strain, designated S2-2T, was isolated from the intestine of a sea cucumber Apostichopus japonicus in Xiapu, Fujian province, China. Strain S2-2T was found to be aerobic, Gram-stain-negative, pale yellow, rod-shaped, oxidase- and catalase-positive. Growth occurred at 15-36 °C (optimum, 25-32 °C), in the presence of 2-7% sea salt (w/v, optimum, 3-5%) and at pH 6-9 (optimum, pH 7.0). The isolate was able to hydrolyse gelatin, casein and DNA, but unable to degrade Tween 20, 40 and 80, starch and cellulose. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S2-2T represented a member of the genus Tenacibaculum, with highest sequence similarity to Tenacibaculum aiptasiae a4T (96.9% similarity), followed by Tenacibaculum xiamenense WJ-1T (96.5% similarity) and showed lower similarities (93.3-95.9%) with other members of the genus Tenacibaculum. The major cellular fatty acids were summed feature 3 (comprising C16 : 1ω6c/C16 : 1ω7c, 33.8%), iso-C15 : 0 (13.7%), iso-C15 : 1G (8.6%), iso-C15 : 0 3-OH (5.3%) and C15 : 0 3-OH (5.1%). The DNA G+C content of the chromosomal DNA was determined to be 31.8 mol%. The respiratory quinone was determined to be MK-6. Phosphatidylethanolamine, phosphatidylglycerol, one unknown aminophospholipid, one unknown phospholipid, one unknown glycolipid and five unknown lipids were detected as major polar lipids. Hence, the combined genotypic and phenotypic data indicated that strain S2-2T represents a novel species of the genus Tenacibaculum, for which the name Tenacibaculum holothuriorum sp. nov. is proposed. The type strain is S2-2T ( = MCCC 1A09872T = LMG 27758T). PMID:26345588

  15. Halomonas heilongjiangensis sp. nov., a novel moderately halophilic bacterium isolated from saline and alkaline soil.

    Dou, Guiming; He, Wei; Liu, Hongcan; Ma, Yuchao

    2015-08-01

    A moderately halophilic bacterium, designated strain 9-2(T), was isolated from saline and alkaline soil collected in Lindian county, Heilongjiang province, China. The strain was observed to be strictly aerobic, Gram-negative, rod-shaped, oxidase-positive, catalase-positive and motile. It was found to require NaCl for growth and to grow at NaCl concentrations of 0.5-14 % (w/v) (optimum, 7-10 %, w/v), at temperatures of 10-45 °C (optimum 25-30 °C) and at pH 5.0-10.0 (optimum pH 8.0). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 9-2(T) is a member of the genus Halomonas and is closely related to Halomonas desiderata DSM 9502(T) (96.68 %), Halomonas campaniensis DSM 1293(T) (96.46 %), Halomonas ventosae DSM 15911(T) (96.27 %) and Halomonas kenyensis DSM 17331(T) (96.27 %). The DNA-DNA hybridization value was 38.9 ± 0.66 % between the novel isolate 9-2(T) and H. desiderata DSM 9502(T). The predominant ubiquinones were identified as Q9 (75.1 %) and Q8 (24.9 %). The major fatty acids were identified as C16:0 (22.0 %), Summed feature 8 (C18:1 ω6c/C18:1 ω7c, 19.6 %), Summed feature 3 (C16:1 ω6c/C16:1 ω7c, 12.6 %), C12:0 3-OH (12.0 %) and C10:0 (11.7 %). The DNA G+C content was determined to be 69.7 mol%. On the basis of the evidence presented in this study, strain 9-2(T) is considered to represent a novel species of the genus Halomonas, for which the name Halomonas heilongjiangensis sp. nov. is proposed. The type strain is 9-2(T) (=DSM 26881(T) = CGMCC 1.12467(T)). PMID:26036672

  16. Halomonas salicampi sp. nov., a halotolerant and alkalitolerant bacterium isolated from a saltern soil.

    Lee, Jae-Chan; Kim, Young-Sook; Yun, Bong-Sik; Whang, Kyung-Sook

    2015-12-01

    A Gram-stain-negative, halotolerant and alkalitolerant bacterium, designated strain BH103T, was isolated from saltern soil in Gomso, Korea. Cells of strain BH103T were strictly aerobic, motile, straight rods and grew at pH 7.0-10.8 (optimum, pH 8.5), at 10-55 °C (optimum, 28 °C) and at salinities of 0-23 % (w/v) NaCl (optimum, 14 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain BH103T belongs to the genus Halomonas, showing highest sequence similarity to Halomonas boliviensis LC1T (97.7 %), Halomonas neptunia Eplume1T (97.7 %), Halomonas variabilis IIIT (97.7 %), Halomonas alkaliantarctica CRSST (97.7 %), Halomonas olivaria TYRC17T (97.5 %), Halomonas titanicae BH1T (97.2 %) and Halomonas sulfidaeris Esulfide1T (96.2 %). The predominant ubiquinone was Q-9. The major fatty acids were C18 : 1ω7c, C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C12 : 0 3-OH. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and an unknown phospholipid. The DNA G+C content of this novel isolate was 54.7 mol%. DNA-DNA relatedness between strain BH103T and H. boliviensis KACC 16615T, H. neptunia KCTC 2888T, H. variabilis KCTC 2889T, H. alkaliantarctica KCTC 22844T, H. olivaria DSM 19074T, H. titanicae JCM 16411T and H. sulfidaeris DSM 15722T was 45, 41, 39, 32, 38, 45 and 35 %, respectively. On the basis of polyphasic analysis from this study, strain BH103T represents a novel species of the genus Halomonas, for which the name Halomonas salicampi sp. nov. is proposed. The type strain is BH103T ( = KACC 17609T = NBRC 109914T = NCAIM B 02528T). PMID:26431725

  17. Steroidobacter flavus sp. nov., a microcystin-degrading Gammaproteobacterium isolated from soil.

    Gong, Zhi-Lian; Zhang, Chang-Feng; Jin, Rong; Zhang, Yu-Qin

    2016-08-01

    A microcystin-degrading strain, designated CPCC 100154(T), was isolated from a forest soil sample collected from Hainan Island, South China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CPCC 100154(T) is affiliated to the family Sinobacteraceae in Gammaproteobacteria, with high 16S rRNA gene sequence similarities of 98.1, 96.6 and 96.6 % to Steroidobacter agariperforans JCM 18477(T), S. denitrificansis DSM 18526(T), and Povalibacter uvarum JCM 18749(T), respectively. In the phylogenetic tree based on 16S rRNA gene sequences, strain CPCC 100154(T) formed a stable phylogenetic subclade with S. agariperforans JCM 18477(T), which indicated that strain CPCC 100154(T) should be identified as a member of the genus Steroidobacter. The phylogenetic analysis based on partial gyrB gene sequences confirmed the affiliation of strain CPCC 100154(T) to the genus Steroidobacter. While the DNA-DNA hybridization value (47.0 ± 1.7 %) between the new isolate and its near phylogenetic neighbor S. agariperforans JCM 18477(T) was far below 70 %, which demonstrated that strain CPCC 100154(T) represents a different genomic species from S. agariperforans. The strain CPCC 100154(T) was found to be a Gram-stain negative, rod-shaped, motile with a polar flagellum, non-endospore-forming bacterium. Good growth was observed at 28-32 °C and pH 7.0-7.5. Polar lipids were identified to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, a unidentified phospholipid, an aminophospholipid and an unidentified aminolipid. The polyamine pattern was determined to contain spermidine as the predominant polyamine, moderate amounts of putrescine as well as traces of sym-homospermidine and spermine. The respiratory quinone was identified as ubiquinone-8. The major cellular fatty acids were found to include summed feature 3 (C16: 1 ω7C/C16: 1 ω6C) (46.1 %) and C16: 0 (29.6 %). The genomic DNA G+C content was determined to be 64.4 mol%. On the

  18. Streptomyces zhihengii sp. nov., isolated from rhizospheric soil of Psammosilene tunicoides.

    Huang, Mei-Juan; Fei, Jing-Jing; Salam, Nimaichand; Kim, Chang-Jin; Hozzein, Wael N; Xiao, Min; Huang, Hai-Quan; Li, Wen-Jun

    2016-10-01

    An actinomycete strain, designated YIM T102(T), was isolated from the rhizospheric soil of Psammosilene tunicoides W. C. Wu et C. Y. Wu collected from Lijiang, Yunnan Province, China. The taxonomic position of the new isolate was investigated by a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain YIM T102(T) belongs to the genus Streptomyces. Strain YIM T102(T) was most closely related to Streptomyces eurocidicus NRRL B-1676(T) with a pairwise 16S rRNA gene sequence similarity of 98.9 %. However, DNA-DNA relatedness value between strain YIM T102(T) and S. eurocidicus NBRC 13491(T) was found to be 37.8 ± 1.8 %. The menaquinone composition detected for strain YIM T102(T) was MK-9 (H6) and MK-9 (H8), while the major fatty acids were summed feature 4 (38.0 %), anteiso-C15:0 (13.1 %), iso-C16:0 (10.1 %), summed feature 3 (9.8 %) and C16:0 (9.0 %) and iso-C15:0 (5.2 %). The whole-cell hydrolysates contained galactose, glucose, ribose and mannose, along with LL-diaminopimelic acid as the diagnostic diamino acid in the peptidoglycan. The DNA G+C content was 70.7 mol%. Strain YIM T102(T) also exhibited antagonistic activity against Alternaria alternata, Alternaria brassicae and Colletotrichum nicotianae Averna, based on the findings from the comparative analyses of phenotypic and genotypic characteristics; it is proposed that strain YIM T102 represents a novel species of the genus Streptomyces, for which the name Streptomyces zhihengii sp. nov. is proposed. The type strain is YIM T102(T) (=KCTC 39115(T) = DSM 42176(T) = CGMCC 4.7248(T)). PMID:27169711

  19. Bizionia fulviae sp. nov., isolated from the gut of an egg cockle, Fulvia mutica.

    Kim, Hyun Sik; Hyun, Dong-Wook; Kim, Pil Soo; Lee, June-Young; Shin, Na-Ri; Yun, Ji-Hyun; Whon, Tae Woong; Kim, Min-Soo; Jung, Mi-Ja; Bae, Jin-Woo

    2015-09-01

    A novel Gram-staining-negative, non-spore-forming, non-flagellated, non-motile, aerobic, saffron-coloured, rod-shaped bacterium that did not produce flexirubin-type pigments was designated strain EM7(T) and was distinct from other members of the genus Bizionia by produce carotenoid-type pigments and being able to grow independently of NaCl. Strain EM7(T) was isolated from the intestinal tract of an egg cockle, Fulvia mutica, which had been collected from the West Sea in Korea. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain EM7(T) belonged to the genus Bizionia, and showed sequence similarity to Bizionia paragorgiae KMM 6029(T) (97.9%) and Bizionia saleffrena HFD(T) (97.73%). Growth occurred on marine agar 2216 at 0-25 °C (optimum, 20 °C) and at pH 6-9 (optimum, pH 7). Growth occurred in the presence of 0-10% (w/v) NaCl (optimum, 2%, w/v, NaCl). The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C15 : 1 G, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH and iso-C16 : 0 3-OH. The major respiratory quinone was menaquinone MK-6. The polar lipids of strain EM7(T) comprised phosphatidylethanolamine, three unidentified aminolipids, an unidentified aminophospholipid and two unidentified lipids. The genomic DNA G+C content was 34.8 mol%. Bizionia paragorgiae KMM 6029(T) and Bizionia saleffrena HFD(T) to Bizionia paragorgiae KCTC 12304(T) and Bizionia saleffrena CIP 108534(T), respectively. Thus, it is proposed that the isolate represents a novel species, Bizionia fulviae sp. nov., with strain EM7(T) ( = KACC 18255(T) = JCM 30417(T)) as the type strain. PMID:26297143

  20. Myceligenerans cantabricum sp. nov., a barotolerant actinobacterium isolated from a deep cold-water coral.

    Sarmiento-Vizcaíno, Aida; González, Verónica; Braña, Alfredo F; Molina, Axayacatl; Acuña, José L; García, Luis A; Blanco, Gloria

    2015-04-01

    An actinobacterium strain (M-201(T)) was isolated from a deep-sea scleractinian coral (Fam. Caryophillidae) collected at 1500 m depth in the Avilés Canyon in the Cantabrian Sea, Asturias, Spain. Strain M-201(T) grew at pH 6.0-9.0 (optimum pH 7.0), between 4 and 37 °C (optimum 28 °C) and at salinities of 0.5-10.5% (w/v) NaCl (optimum 0.5-3.0%). The peptidoglycan contained the amino acids Lys, Ala, Thr, Glu and one unknown amino acid component, and belonged to type A4α, and the cell-wall sugars are glucose, mannose and galactose. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, an unknown phosphoglycolipid and seven unknown glycolipids. The predominant menaquinones were MK-9(H4) and MK-9(H6). Major cellular fatty acids were anteiso-C(15 : 0), iso-C(15 : 0) and anteiso-C(17 : 0). The genomic DNA G+C content was 72.4 mol%. The chemotaxonomic properties supported the affiliation of strain M-201(T) to the genus Myceligenerans . Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism was most closely related to Myceligenerans crystallogenes CD12E2-27(T) (98.2% 16S rRNA gene sequence similarity). However, it had a relatively low DNA-DNA relatedness value with the above strain (48%). The isolate showed antibiotic activity against Escherichia coli , Micrococcus luteus ATCC 14452 and Saccharomyces cerevisiae var. carlsbergensis. To the best of our knowledge, this is the first report of antibiotic production in the genus Myceligenerans . The differences in phenotypic, metabolic, ecological and phylogenetic characteristics justify the proposal of a novel species of the genus Myceligenerans , Myceligenerans cantabricum sp. nov., with M-201(T) ( = CECT 8512(T) = DSM 28392(T)) as the type strain. PMID:25667397