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Sample records for burkholderia sp bacterium

  1. Burkholderia susongensis sp. nov., a mineral-weathering bacterium isolated from weathered rock surface.

    Science.gov (United States)

    Gu, Jia-Yu; Zang, Sheng-Gang; Sheng, Xia-Fang; He, Lin-Yan; Huang, Zhi; Wang, Qi

    2015-03-01

    A novel type of mineral-weathering bacterium was isolated from the weathered surface of rock (mica schist) collected from Susong (Anhui, China). Cells of strain L226(T) were Gram-stain-negative. The strain grew optimally at 30 °C, with 1 % (w/v) NaCl and at pH 7.0 in trypticase soy broth. On the basis of 16S rRNA gene phylogeny, strain L226(T) was shown to belong to the genus Burkholderia and the closest phylogenetic relatives were Burkholderia sprentiae WSM5005(T) (98.3 %), Burkholderia acidipaludis NBRC 101816(T) (98.2 %), Burkholderia tuberum STM678(T) (97.2 %) and Burkholderia diazotrophica JPY461(T) (97.1 %). The DNA G+C content was 63.5 mol% and the respiratory quinone was Q-8. The major fatty acids were C16 : 0, C17 : 0 cyclo and C19 : 0 cyclo ω8c. The polar lipid profile of strain L226(T) consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, unknown lipids and unidentified aminophospholipids. Based on the low level of DNA-DNA relatedness (ranging from 25.8 % to 34.4 %) to the tested type strains of species of the genus Burkholderia and unique phenotypic characteristics, it is suggested that strain L226(T) represents a novel species of the genus Burkholderia, for which the name Burkholderia susongensis sp. nov., is proposed. The type strain is L226(T) ( = CCTCC AB2014142(T) = JCM 30231(T)). © 2015 IUMS.

  2. Burkholderia jiangsuensis sp. nov., a methyl parathion degrading bacterium, isolated from methyl parathion contaminated soil.

    Science.gov (United States)

    Liu, Xu-Yun; Li, Chun-Xiu; Luo, Xiao-Jing; Lai, Qi-Liang; Xu, Jian-He

    2014-09-01

    A methyl parathion (MP) degrading bacterial strain, designated MP-1(T), was isolated from a waste land where pesticides were formerly manufactured in Jiangsu province, China. Polyphasic taxonomic studies showed that MP-1(T) is a Gram-stain-negative, non-spore-forming, rod-shaped and motile bacterium. The bacterium could grow at salinities of 0-1 % (w/v) and temperatures of 15-40 °C. Strain MP-1(T) could reduce nitrate to nitrite, utilize d-glucose and l-arabinose, but not produce indole, or hydrolyse gelatin. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that MP-1(T) belongs to the genus Burkholderia, showing highest sequence similarity to Burkholderia grimmiae DSM 25160(T) (98.5 %), and similar strains including Burkholderia zhejiangensis OP-1(T) (98.2 %), Burkholderia choica LMG 22940(T) (97.5 %), Burkholderia glathei DSM 50014(T) (97.4 %), Burkholderia terrestris LMG 22937(T) (97.2 %) and Burkholderia telluris LMG 22936(T) (97.0 %). In addition, the gyrB and recA gene segments of strain MP-1(T) exhibited less than 89.0 % and 95.1 % similarities with the most highly-related type strains indicated above. The G+C content of strain MP-1(T) was 62.6 mol%. The major isoprenoid quinone was ubiquinone Q-8. The predominant polar lipids comprised phosphatidyl ethanolamine, phosphatidyl glycerol, aminolipid and phospholipid. The principal fatty acids in strain MP-1(T) were C18 : 1ω7c/C18 : 1ω6c (23.3 %), C16 : 0 (16.8 %), cyclo-C17 : 0 (15.0 %), C16 : 1ω7c/C16 : 1ω6 (8.5 %), cyclo-C19 : 0ω8c (8.1 %), C16 : 1 iso I/C14 : 0 3-OH (5.7 %), C16 : 0 3-OH (5.6 %) and C16 : 02-OH (5.1 %). The DNA-DNA relatedness values between strain MP-1(T) and the three type strains (B. grimmiae DSM 25160(T), B. zhejiangensis OP-1(T) and B. glathei DSM 50014(T)) ranged from 24.6 % to 37.4 %. In accordance with phenotypic and genotypic characteristics, strain MP-1(T) represents a novel

  3. Proteogenomic Characterization of Monocyclic Aromatic Hydrocarbon Degradation Pathways in the Aniline-Degrading Bacterium Burkholderia sp. K24.

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    Sang-Yeop Lee

    Full Text Available Burkholderia sp. K24, formerly known as Acinetobacter lwoffii K24, is a soil bacterium capable of utilizing aniline as its sole carbon and nitrogen source. Genomic sequence analysis revealed that this bacterium possesses putative gene clusters for biodegradation of various monocyclic aromatic hydrocarbons (MAHs, including benzene, toluene, and xylene (BTX, as well as aniline. We verified the proposed MAH biodegradation pathways by dioxygenase activity assays, RT-PCR, and LC/MS-based quantitative proteomic analyses. This proteogenomic approach revealed four independent degradation pathways, all converging into the citric acid cycle. Aniline and p-hydroxybenzoate degradation pathways converged into the β-ketoadipate pathway. Benzoate and toluene were degraded through the benzoyl-CoA degradation pathway. The xylene isomers, i.e., o-, m-, and p-xylene, were degraded via the extradiol cleavage pathways. Salicylate was degraded through the gentisate degradation pathway. Our results show that Burkholderia sp. K24 possesses versatile biodegradation pathways, which may be employed for efficient bioremediation of aniline and BTX.

  4. Proteogenomic Characterization of Monocyclic Aromatic Hydrocarbon Degradation Pathways in the Aniline-Degrading Bacterium Burkholderia sp. K24.

    Science.gov (United States)

    Lee, Sang-Yeop; Kim, Gun-Hwa; Yun, Sung Ho; Choi, Chi-Won; Yi, Yoon-Sun; Kim, Jonghyun; Chung, Young-Ho; Park, Edmond Changkyun; Kim, Seung Il

    2016-01-01

    Burkholderia sp. K24, formerly known as Acinetobacter lwoffii K24, is a soil bacterium capable of utilizing aniline as its sole carbon and nitrogen source. Genomic sequence analysis revealed that this bacterium possesses putative gene clusters for biodegradation of various monocyclic aromatic hydrocarbons (MAHs), including benzene, toluene, and xylene (BTX), as well as aniline. We verified the proposed MAH biodegradation pathways by dioxygenase activity assays, RT-PCR, and LC/MS-based quantitative proteomic analyses. This proteogenomic approach revealed four independent degradation pathways, all converging into the citric acid cycle. Aniline and p-hydroxybenzoate degradation pathways converged into the β-ketoadipate pathway. Benzoate and toluene were degraded through the benzoyl-CoA degradation pathway. The xylene isomers, i.e., o-, m-, and p-xylene, were degraded via the extradiol cleavage pathways. Salicylate was degraded through the gentisate degradation pathway. Our results show that Burkholderia sp. K24 possesses versatile biodegradation pathways, which may be employed for efficient bioremediation of aniline and BTX.

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

    Science.gov (United States)

    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%. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Burkholderia insulsa sp. nov., a facultatively chemolithotrophic bacterium isolated from an arsenic-rich shallow marine hydrothermal system.

    Science.gov (United States)

    Rusch, Antje; Islam, Shaer; Savalia, Pratixa; Amend, Jan P

    2015-01-01

    Enrichment cultures inoculated with hydrothermally influenced nearshore sediment from Papua New Guinea led to the isolation of an arsenic-tolerant, acidophilic, facultatively aerobic bacterial strain designated PNG-April(T). Cells of this strain were Gram-stain-negative, rod-shaped, motile and did not form spores. Strain PNG-April(T) grew at temperatures between 4 °C and 40 °C (optimum 30-37 °C), at pH 3.5 to 8.3 (optimum pH 5-6) and in the presence of up to 2.7% NaCl (optimum 0-1.0%). Both arsenate and arsenite were tolerated up to concentrations of at least 0.5 mM. Metabolism in strain PNG-April(T) was strictly respiratory. Heterotrophic growth occurred with O2 or nitrate as electron acceptors, and aerobic lithoautotrophic growth was observed with thiosulfate or nitrite as electron donors. The novel isolate was capable of N2-fixation. The respiratory quinones were Q-8 and Q-7. Phylogenetically, strain PNG-April(T) belongs to the genus Burkholderia and shares the highest 16S rRNA gene sequence similarity with the type strains of Burkholderia fungorum (99.8%), Burkholderia phytofirmans (98.8%), Burkholderia caledonica (98.4%) and Burkholderia sediminicola (98.4%). Differences from these related species in several physiological characteristics (lipid composition, carbohydrate utilization, enzyme profiles) and DNA-DNA hybridization suggested the isolate represents a novel species of the genus Burkholderia, for which we propose the name Burkholderia insulsa sp. nov. The type strain is PNG-April(T) ( = DSM 28142(T) = LMG 28183(T)). © 2015 IUMS.

  7. Ocurrence of the antibiotic producing bacterium Burkholderia sp. in colonies of the leaf-cutting ant Atta sexdens rubropilosa.

    Science.gov (United States)

    Santos, Adão Valmir; Dillon, Rod J; Dillon, Viv M; Reynolds, Stuart E; Samuels, Richard I

    2004-10-15

    Fungus garden material from recently established Atta sexdens rubropilosa colonies (6-12 months old) was sampled to detect antibiotic producing microorganisms that inhibited the growth of pathogens of insects and of the fungus gardens but did not affect their mutualistic fungus. A bacterium with activity against the entomopathogenic fungus Beauveria bassiana was isolated from 56% of the gardens tested (n=57) and identified from its biochemical profile and from 16S and 23S ribosomal DNA sequences as a member of the genus Burkholderia. The ant-associated Burkholderia isolates secreted a potent, anti-fungal agent that inhibited germination of conidia of the entomopathogenic fungi B. bassiana, Metarhizium anisopliae, of the saprophytic Verticillium lecanii, and also of a specialist fungus garden Escovopsis weberi. Growth of the ant's mutualist fungus was unaffected.

  8. Burkholderia humi sp. nov., Burkholderia choica sp. nov., Burkholderia telluris sp. nov., Burkholderia terrestris sp. nov. and Burkholderia udeis sp. nov.: Burkholderia glathei-like bacteria from soil and rhizosphere soil.

    Science.gov (United States)

    Vandamme, Peter; De Brandt, Evie; Houf, Kurt; Salles, Joana Falcão; Dirk van Elsas, Jan; Spilker, Theodore; Lipuma, John J

    2013-12-01

    Analysis of partial gyrB gene sequences revealed six taxa in a group of 17 Burkholderia glathei-like isolates which were further examined by (GTG)5-PCR fingerprinting, 16S rRNA gene sequence analysis, DNA-DNA hybridizations, determination of the DNA G+C content, whole-cell fatty acid analysis and an analysis of cell and colony morphology and more than 180 biochemical characteristics. The results demonstrated that one taxon consisting of three human clinical isolates represented Burkholderia zhejiangensis, a recently described methyl-parathion-degrading bacterium isolated from a wastewater-treatment system in China. The remaining taxa represented five novel species isolated from soil or rhizosphere soil samples, and could be distinguished by both genotypic and phenotypic characteristics. We therefore propose to formally classify these bacteria as Burkholderia humi sp. nov. (type strain, LMG 22934(T) = CCUG 63059(T)), Burkholderia choica sp. nov. (type strain, LMG 22940(T) = CCUG 63063(T)), Burkholderia telluris sp. nov. (type strain, LMG 22936(T) = CCUG 63060(T)), Burkholderia udeis sp. nov. (type strain, LMG 27134(T) = CCUG 63061(T)) and Burkholderia terrestris sp. nov. (type strain, LMG 22937(T) = CCUG 63062(T)).

  9. Burkholderia latens sp. nov., Burkholderia diffusa sp. nov., Burkholderia arboris sp. nov., Burkholderia seminalis sp. nov. and Burkholderia metallica sp. nov., novel species within the Burkholderia cepacia complex.

    Science.gov (United States)

    Vanlaere, Elke; Lipuma, John J; Baldwin, Adam; Henry, Deborah; De Brandt, Evie; Mahenthiralingam, Eshwar; Speert, David; Dowson, Chris; Vandamme, Peter

    2008-07-01

    The taxonomic position of five recA gene clusters of Burkholderia cepacia complex (Bcc) isolates was determined using a polyphasic taxonomic approach. The levels of 16S rRNA and recA gene sequence similarity, multilocus sequence typing (MLST) data and the intermediate DNA-DNA binding values demonstrated that these five clusters represented five novel species within the Bcc. Biochemical identification of these species is difficult, as is the case for most Bcc species. However, identification of these novel species can be accomplished through recA gene sequence analysis, MLST and BOX-PCR profiling and by recA RFLP analysis. For diagnostic laboratories, recA gene sequence analysis offers the best combination of accuracy and simplicity. Based on these results, we propose five novel Bcc species, Burkholderia latens sp. nov. (type strain FIRENZE 3(T) =LMG 24064(T) =CCUG 54555(T)), Burkholderia diffusa sp. nov. (type strain AU1075(T) =LMG 24065(T) =CCUG 54558(T)), Burkholderia arboris sp. nov. (type strain ES0263A(T) =LMG 24066(T) =CCUG 54561(T)), Burkholderia seminalis sp. nov. (type strain AU0475(T) =LMG 24067(T) =CCUG 54564(T)) and Burkholderia metallica sp. nov. (type strain AU0553(T) =LMG 24068(T) =CCUG 54567(T)). In the present study, we also demonstrate that Burkholderia ubonensis should be considered a member of the Bcc.

  10. Isolation and Characterization of Burkholderia rinojensis sp. nov., a Non-Burkholderia cepacia Complex Soil Bacterium with Insecticidal and Miticidal Activities

    Science.gov (United States)

    Fernandez, Lorena E.; Koivunen, Marja; Yang, April; Flor-Weiler, Lina; Marrone, Pamela G.

    2013-01-01

    Isolate A396, a bacterium isolated from a Japanese soil sample demonstrated strong insecticidal and miticidal activities in laboratory bioassays. The isolate was characterized through biochemical methods, fatty acid methyl ester (FAME) analysis, sequencing of 16S rRNA, multilocus sequence typing and analysis, and DNA-DNA hybridization. FAME analysis matched A396 to Burkholderia cenocepacia, but this result was not confirmed by 16S rRNA or DNA-DNA hybridization. 16S rRNA sequencing indicated closest matches with B. glumae and B. plantarii. DNA-DNA hybridization experiments with B. plantarii, B. glumae, B. multivorans, and B. cenocepacia confirmed the low genetic similarity (11.5 to 37.4%) with known members of the genus. PCR-based screening showed that A396 lacks markers associated with members of the B. cepacia complex. Bioassay results indicated two mechanisms of action: through ingestion and contact. The isolate effectively controlled beet armyworms (Spodoptera exigua; BAW) and two-spotted spider mites (Tetranychus urticae; TSSM). In diet overlay bioassays with BAW, 1% to 4% (vol/vol) dilution of the whole-cell broth caused 97% to 100% mortality 4 days postexposure, and leaf disc treatment bioassays attained 75% ± 22% mortality 3 days postexposure. Contact bioassays led to 50% larval mortality, as well as discoloration, stunting, and failure to molt. TSSM mortality reached 93% in treated leaf discs. Activity was maintained in cell-free supernatants and after heat treatment (60°C for 2 h), indicating that a secondary metabolite or excreted thermostable enzyme might be responsible for the activity. Based on these results, we describe the novel species Burkholderia rinojensis, a good candidate for the development of a biocontrol product against insect and mite pests. PMID:24096416

  11. Non-obligate predatory bacterium Burkholderia casidae and uses thereof

    OpenAIRE

    2001-01-01

    A novel predator bacterium Burkholderia casidae is disclosed. The invention is directed to the isolation and use of Burkholderia casidae to control microbial diseases of plants. The genetic, biochemical and physiological characteristics of Burkholderia casidae are described. Biocontrol compositions comprising Burkholderia casidae, and antimicrobial compounds and antimicrobial preparations prepared from Burkholderia casidae are also disclosed, as are methods for accomplishing all of the forego...

  12. Non-obligate predatory bacterium burkholderia casidaeand uses thereof

    OpenAIRE

    1998-01-01

    A novel predator bacterium Burkholderia casidae is disclosed. The invention is directed to the isolation and use of Burkholderia casidae to control microbial diseases of plants. The genetic, biochemical and physiological characteristics of Burkholderia casidae are described. Biocontrol compositions comprising Burkholderia casidae, and antimicrobial compounds and antimicrobial preparations prepared from Burkholderia casidae are also disclosed, as are methods for accomplishing all of the forego...

  13. Comparative Genomics of Burkholderia singularis sp. nov., a Low G+C Content, Free-Living Bacterium That Defies Taxonomic Dissection of the Genus Burkholderia

    Science.gov (United States)

    Vandamme, Peter; Peeters, Charlotte; De Smet, Birgit; Price, Erin P.; Sarovich, Derek S.; Henry, Deborah A.; Hird, Trevor J.; Zlosnik, James E. A.; Mayo, Mark; Warner, Jeffrey; Baker, Anthony; Currie, Bart J.; Carlier, Aurélien

    2017-01-01

    Four Burkholderia pseudomallei-like isolates of human clinical origin were examined by a polyphasic taxonomic approach that included comparative whole genome analyses. The results demonstrated that these isolates represent a rare and unusual, novel Burkholderia species for which we propose the name B. singularis. The type strain is LMG 28154T (=CCUG 65685T). Its genome sequence has an average mol% G+C content of 64.34%, which is considerably lower than that of other Burkholderia species. The reduced G+C content of strain LMG 28154T was characterized by a genome wide AT bias that was not due to reduced GC-biased gene conversion or reductive genome evolution, but might have been caused by an altered DNA base excision repair pathway. B. singularis can be differentiated from other Burkholderia species by multilocus sequence analysis, MALDI-TOF mass spectrometry and a distinctive biochemical profile that includes the absence of nitrate reduction, a mucoid appearance on Columbia sheep blood agar, and a slowly positive oxidase reaction. Comparisons with publicly available whole genome sequences demonstrated that strain TSV85, an Australian water isolate, also represents the same species and therefore, to date, B. singularis has been recovered from human or environmental samples on three continents. PMID:28932212

  14. Transcriptional responses of the bacterium Burkholderia terrae BS001 to the fungal host Lyophyllum sp strain Karsten under soil-mimicking conditions

    NARCIS (Netherlands)

    Ul Haq, Irshad; Dini-Andreote, Francisco; van Elsas, Jan Dirk

    In this study, the mycosphere isolate Burkholderia terrae BS001 was confronted with the soil fungus Lyophyllum sp. strain Karsten on soil extract agar plates in order to examine its transcriptional responses over time. At the initial stages of the experiment (T1-day 3; T2-day 5), contact between

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

    Science.gov (United States)

    Lee, Jae-Chan; Whang, Kyung-Sook

    2015-09-01

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

  16. Burkholderia cordobensis sp. nov., from agricultural soils.

    Science.gov (United States)

    Draghi, Walter O; Peeters, Charlotte; Cnockaert, Margo; Snauwaert, Cindy; Wall, Luis G; Zorreguieta, Angeles; Vandamme, Peter

    2014-06-01

    Two Gram-negative, rod-shaped bacteria were isolated from agricultural soils in Córdoba province in central Argentina. Their 16S rRNA gene sequences demonstrated that they belong to the genus Burkholderia, with Burkholderia zhejiangensis as most closely related formally named species; this relationship was confirmed through comparative gyrB sequence analysis. Whole-cell fatty acid analysis supported their assignment to the genus Burkholderia. Burkholderia sp. strain YI23, for which a whole-genome sequence is available, represents the same taxon, as demonstrated by its highly similar 16S rRNA (100% similarity) and gyrB (99.1-99.7%) gene sequences. The results of DNA-DNA hybridization experiments and physiological and biochemical characterization further substantiated the genotypic and phenotypic distinctiveness of the Argentinian soil isolates, for which the name Burkholderia cordobensis sp. nov. is proposed, with strain MMP81(T) ( = LMG 27620(T) = CCUG 64368(T)) as the type strain. © 2014 IUMS.

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

    National Research Council Canada - National Science Library

    Lee, Jae-Chan; Whang, Kyung-Sook

    2015-01-01

    .... On the basis of 16S rRNA gene sequence analysis, the three strains were found to belong to the genus Burkholderia, showing the closest phylogenetic similarity to Burkholderia diazotrophica JPY461(T) (97.2-97.7...

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

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

    2015-02-01

    An ivory/yellow, Gram-stain-negative, short-rod-shaped, aerobic bacterial strain, designated JC2948(T), was isolated from a soil sample taken from Gwanak Mountain, Republic of Korea. 16S rRNA gene sequence analysis indicated that strain JC2948(T) belongs to the genus Burkholderia. The test strain showed highest sequence similarities to Burkholderia tropica LMG 22274(T) (97.6 %), Burkholderia acidipaludis NBRC 101816(T) (97.5 %), Burkholderia tuberum LMG 21444(T) (97.5 %), Burkholderia sprentiae LMG 27175(T) (97.4 %), Burkholderia terricola LMG 20594(T) (97.3 %) and Burkholderia diazotrophica LMG 26031(T) (97.1 %). Based on average nucleotide identity (ANI) values, the new isolate represents a novel genomic species as it shows less than 90 % ANI values with other closely related species. Also, other phylosiological and biochemical comparisons allowed the phenotypic differentiation of strain JC2948(T) from other members of the genus Burkholderia. Therefore, we suggest that this strain should be classified as the type strain of a novel species of the genus Burkholderia. The name Burkholderia monticola sp. nov. (type strain, JC2948(T) = JCM 19904(T) = KACC 17924(T)) is proposed. © 2015 IUMS.

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

    Science.gov (United States)

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

    2015-03-01

    A Gram-stain negative, rod-shaped, non-spore-forming, obligate aerobic bacterial strain, JC2949(T), was isolated from grassland soil in Gwanak Mountain, Seoul, Republic of Korea. Phylogenetic analysis, based on 16S rRNA sequences, indicated that strain JC2949(T) belongs to the genus Burkholderia, showing highest sequence similarities with Burkholderia grimmiae R27(T) (98.8 %), Burkholderia cordobensis LMG 27620(T) (98.6 %), Burkholderia jiangsuensis MP-1T(T) (98.6 %), Burkholderia zhejiangensis OP-1(T) (98.5 %), Burkholderia humi LMG 22934(T) (97.5 %), Burkholderia terrestris LMG 22937(T) (97.3 %), Burkholderia telluris LMG 22936(T) (97.2 %) and Burkholderia glathei ATCC 29195(T) (97.0 %). The major fatty acids of strain JC2949(T) were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. Its predominant polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unknown amino phospholipid. The dominant isoprenoid quinone was ubiquinone Q-8. The pairwise average nucleotide identity values between strain JC2949(T) and the genomes of 30 other species of the genus Burkholderia ranged from 73.4-90.4 %, indicating that the isolate is a novel genomic species within this genus. Based on phenotypic and chemotaxonomic comparisons, it is clear that strain JC2949(T) represents a novel species of the genus Burkholderia. We propose the name for this novel species to be Burkholderia megalochromosomata sp. nov. The type strain is JC2949(T) ( = KACC 17925(T) = JCM 19905(T)). © 2015 IUMS.

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

    Science.gov (United States)

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

    2013-11-01

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

  1. Burkholderia stagnalis sp. nov. and Burkholderia territorii sp. nov., two novel Burkholderia cepacia complex species from environmental and human sources

    National Research Council Canada - National Science Library

    De Smet, Birgit; Mayo, Mark; Peeters, Charlotte; Zlosnik, James E A; Spilker, Theodore; Hird, Trevor J; LiPuma, John J; Kidd, Timothy J; Kaestli, Mirjam; Ginther, Jennifer L; Wagner, David M; Keim, Paul; Bell, Scott C; Jacobs, Jan A; Currie, Bart J; Vandamme, Peter

    2015-01-01

    Nine Burkholderia cepacia complex (Bcc) bacteria were isolated during environmental surveys for the ecological niche of Burkholderia pseudomallei, the aetiological agent of melioidosis, in the Northern Territory of Australia...

  2. Burkholderia aspalathi sp. nov., isolated from root nodules of the South African legume Aspalathus abietina Thunb.

    Science.gov (United States)

    Mavengere, Natasha R; Ellis, Allan G; Le Roux, Johannes J

    2014-06-01

    During a study to investigate the diversity of rhizobia associated with native legumes in South Africa's Cape Floristic Region, a Gram-negative bacterium designated VG1C(T) was isolated from the root nodules of Aspalathus abietina Thunb. Based on phylogenetic analyses of the 16S rRNA and recA genes, VG1C(T) belongs to the genus Burkholderia, with the highest degree of sequence similarity to the type strain of Burkholderia sediminicola (98.5% and 98%, respectively). The DNA G+C content of strain VG1C(T) was 60.1 mol%, and DNA-DNA relatedness values to the type strain of closely related species were found to be substantially lower than 70%. As evidenced by results of genotypic, phenotypic and chemotaxonomic tests provided here, we conclude that isolate VG1C(T) represents a novel rhizosphere-associated species in the genus Burkholderia, for which the name Burkholderia aspalathi sp. nov. is proposed, with the type strain VG1C(T) ( = DSM 27239(T) = LMG 27731(T)). © 2014 IUMS.

  3. Burkholderia humi sp nov., Burkholderia choica sp nov., Burkholderia telluris sp nov., Burkholderia terrestris sp nov and Burkholderia udeis sp nov. : Burkholderia glathei-like bacteria from soil and rhizosphere soil

    NARCIS (Netherlands)

    Vandamme, Peter; De Brandt, Evie; Houf, Kurt; Salles, Joana Falcao; van Elsas, Jan Dirk; Spilker, Theodore; LiPuma, John J.

    2013-01-01

    Analysis of partial gyrB gene sequences revealed six taxa in a group of 17 Burkholderia glathei-like isolates which were further examined by (GTG)(5)-PCR fingerprinting, 16S rRNA gene sequence analysis, DNA-DNA hybridizations, determination of the DNA G+C content, whole-cell fatty acid analysis and

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

    Science.gov (United States)

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

    2013-11-01

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

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

    Science.gov (United States)

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

    2014-04-01

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

  6. HemX is required for production of 2-ketogluconate, the predominant organic anion required for inorganic phosphate solubilization by Burkholderia sp. Ha185.

    Science.gov (United States)

    Hsu, Pei-Chun Lisa; Condron, Leo; O'Callaghan, Maureen; Hurst, Mark R H

    2015-12-01

    The bacterium Burkholderia sp. Ha185 readily solubilizes inorganic phosphate by releasing the low molecular weight organic anion, 2-ketogluconate. Using random transposon mutagenesis and in silico analysis, a mutation that caused almost complete abolition of phosphate solubilization was located within hemX, which is part of the hem operon. Burkholderia sp. Ha185 HemX is a multidomain protein, predicted to encode a bifunctional uroporphyrinogen-III synthetase/uroporphyrin-III C-methyltransferase, which has not previously been implicated in phosphate solubilization. Complementation of hemX restored the ability of the mutant to solubilize phosphate in both plate and liquid cultures. Based on a combination of organic-anion profiling, quantitative polymerase chain reaction and in silico analyses, hemX was confirmed to be solely responsible for hydroxyapatite solubilization in Burkholderia sp. Ha185. It is proposed that the biosynthesis of a yet to be determined redox cofactor by HemX is the main pathway for generating 2-ketogluconate via a haem-dependent gluconate 2-dehydrogenase in Burkholderia sp. Ha185. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  7. Herminiimonas arsenicoxydans sp. nov., a metalloresistant bacterium.

    Science.gov (United States)

    Muller, Daniel; Simeonova, Diliana D; Riegel, Philippe; Mangenot, Sophie; Koechler, Sandrine; Lièvremont, Didier; Bertin, Philippe N; Lett, Marie-Claire

    2006-08-01

    An arsenite-oxidizing bacterium, designated strain ULPAs1(T), was isolated from industrial sludge heavily contaminated with arsenic. Cells of this isolate were Gram-negative, curved rods, motile by means of a polar flagellum. The strain was positive for oxidase and catalase activities, was able to reduce nitrate to nitrite, used acetate, lactate and peptone as organic carbon sources under aerobic conditions and was able to oxidize arsenite (As[III]) to arsenate (As[V]). 16S rRNA gene sequence analysis and the absence of dodecanoic fatty acids suggested that this strain represents a member of the genus Herminiimonas of the family Oxalobacteraceae, order Burkholderiales in the Betaproteobacteria. Genomic DNA-DNA hybridization between strain ULPAs1(T) and Herminiimonas fonticola S-94(T) and between strain ULPAs1(T) and Herminiimonas aquatilis CCUG 36956(T) revealed levels of relatedness of <10 %, well below the recommended 70 % species cut-off value. Thus, strain ULPAs1(T) (=CCM 7303(T)=DSM 17148(T)=LMG 22961(T)) is the type strain of a novel species of Herminiimonas, for which the name Herminiimonas arsenicoxydans sp. nov. is proposed.

  8. Multiphasic characterization of a plant growth promoting bacterial strain, Burkholderia sp, 7016 and its effect on tomato growth in the field

    Institute of Scientific and Technical Information of China (English)

    GAO Miao[1; ZHOU Jian-jiao[1; WANG En-tao[2; CHEN Qian[1; XU Jing[1; SUN Jian-guana[1

    2015-01-01

    Aiming at searching for plant growth promoting rhizobacteria (PGPR), a bacterium strain coded as 7016 was isolated from soybean rhizosphere and was characterized in the present study. It was identified as Burkholderia sp. based on 16S rDNA sequence analysis, as well as phenotypic and biochemical characterizations. This bacterium presented nitrogenase activity, 1-aminocyclopropane-l-carboxylic acid (ACC) deaminase activity and phosphate solubilizing ability; inhibited the growth of Sclerotinia sclerotiorum, Gibberella zeae and Verticillium dahliae; and produced small quantities of indole acetic acid (IAA). In green house experiments, significant increases in shoot height and weight, root length and weight, and stem diameter were observed on tomato plants in 30 d after inoculation with strain 7016. Result of 16S rDNA PCR-DGGE showed that 7016 survived in the rhizosphere of tomato seedlings. In the field experiments, Burkholderia sp. 7016 enhanced the tomato yield and significantly promoted activities of soil urease, phosphatase, sucrase, and catalase. All these results demonstrated Burkholderia sp. 7016 as a valuable PGPR and a candidate of biofertilizer.

  9. Bioremediation of refinery wastewater using immobilised Burkholderia cepacia and Corynebacterium sp and their transconjugants

    Directory of Open Access Journals (Sweden)

    Abdullahi T. Ajao

    2013-07-01

    Full Text Available When oil spill occurs, it poses serious toxic hazards to all forms of life. Mixed culture of Burkholderia cepacia and Corynebacterium sp isolated from refinery sludge using selective enrichment technique was used for bioremediation of refinery wastewater in a laboratoryscale bioreactor. Physicochemical parameters of both raw and treated water were as determined and compared with Federal Environ - mental Protection Agency (FEPA-limit, Abuja, Nigeria to asses the efficiency of the bioremediation process. Each of the bacterium was screened for the presence of plasmid DNA and for the involvement or otherwise of plasmid in the bioremediation of wastewater. The immobilised cells showed percentage decrease in chemical oxygen demand (97%, biochemical oxygen demand (94%, phenol (98%, total petroleum hydrocarbon (79%, oil and grease (90% of the refinery waste water after 20 days of treatment while their transconjugants showed the multiplicative effect by achieving the same percentage after 10 days of treatment. Therefore, the findings revealed that bioaugmentation of wastewater using transmissible catabolic plasmid will enhance efficiency of the bioremediation by spreading the plasmid among indigenous microbial community either through horizontal gene transfer or transformation.

  10. Phosphorus uptake of an arbuscular mycorrhizal fungus is not effected by the biocontrol bacterium ¤Burkholderia cepacia¤

    DEFF Research Database (Denmark)

    Ravnskov, S.; Larsen, J.; Jakobsen, I.

    2002-01-01

    The biocontrol bacterium Burkholderia cepacia is known to suppress a broad range of root pathogenic fungi, while its impact on other beneficial non-target organisms such as arbuscular mycorrhizal (AM) fungi is unknown. Direct interactions between five B. cepacia strains and the AM fungus, Glomus...... (NLFAs), respectively. Hyphal P transport was also unaffected by the biocontrol bacterium, which either stimulated, reduced or had no effect on length of the external mycelium of G. intraradices. The cyclic PLFAs cy17:0 and cy19:0 were suggested to be useful markers for estimation of biomass of B...

  11. What drives the occurrence of the melioidosis bacterium Burkholderia pseudomallei in domestic gardens?

    Science.gov (United States)

    Kaestli, Mirjam; Harrington, Glenda; Mayo, Mark; Chatfield, Mark D; Harrington, Ian; Hill, Audrey; Munksgaard, Niels; Gibb, Karen; Currie, Bart J

    2015-03-01

    Melioidosis is an often fatal infectious disease affecting humans and animals in tropical regions and is caused by the saprophytic environmental bacterium Burkholderia pseudomallei. Domestic gardens are not only a common source of exposure to soil and thus to B. pseudomallei, but they also have been found to contain more B. pseudomallei than other environments. In this study we addressed whether anthropogenic manipulations common to gardens such as irrigation or fertilizers change the occurrence of B. pseudomallei. We conducted a soil microcosm experiment with a range of fertilizers and soil types as well as a longitudinal interventional study over three years on an experimental fertilized field site in an area naturally positive for B. pseudomallei. Irrigation was the only consistent treatment to increase B. pseudomallei occurrence over time. The effects of fertilizers upon these bacteria depended on soil texture, physicochemical soil properties and biotic factors. Nitrates and urea increased B. pseudomallei load in sand while phosphates had a positive effect in clay. The high buffering and cation exchange capacities of organic material found in a commercial potting mix led to a marked increase in soil salinity with no survival of B. pseudomallei after four weeks in the potting mix sampled. Imported grasses were also associated with B. pseudomallei occurrence in a multivariate model. With increasing population density in endemic areas these findings inform the identification of areas in the anthropogenic environment with increased risk of exposure to B. pseudomallei.

  12. Taxon K, a complex within the Burkholderia cepacia complex, comprises at least two novel species, Burkholderia contaminans sp. nov. and Burkholderia lata sp. nov

    National Research Council Canada - National Science Library

    Vanlaere, Elke; Baldwin, Adam; Gevers, Dirk; Henry, Deborah; De Brandt, Evie; LiPuma, John J; Mahenthiralingam, Eshwar; Speert, David P; Dowson, Chris; Vandamme, Peter

    2009-01-01

    ... (also known as group K) within the Burkholderia cepacia complex (Bcc). For this purpose, a representative set of strains was examined by a traditional polyphasic taxonomic approach, by multilocus sequence typing (MLST...

  13. Identification of volatile compounds produced by the bacterium Burkholderia tropica that inhibit the growth of fungal pathogens

    Science.gov (United States)

    Tenorio-Salgado, Silvia; Tinoco, Raunel; Vazquez-Duhalt, Rafael; Caballero-Mellado, Jesus; Perez-Rueda, Ernesto

    2013-01-01

    It has been documented that bacteria from the Burkholderia genera produce different kinds of compounds that inhibit plant pathogens, however in Burkholderia tropica, an endophytic diazotrophic and phosphate-solubilizing bacterium isolated from a wide diversity of plants, the capacity to produce antifungal compounds has not been evaluated. In order to expand our knowledge about Burkholderia tropica as a potential biological control agent, we analyzed 15 different strains of this bacterium to evaluate their capacities to inhibit the growth of four phytopathogenic fungi, Colletotrichum gloeosporioides, Fusarium culmorum, Fusarium oxysporum and Sclerotium rolffsi. Diverse analytical techniques, including plant root protection and dish plate growth assays and gas chromatography-mass spectroscopy showed that the fungal growth inhibition was intimately associated with the volatile compounds produced by B. tropica and, in particular, two bacterial strains (MTo293 and TTe203) exhibited the highest radial mycelial growth inhibition. Morphological changes associated with these compounds, such as disruption of fungal hyphae, were identified by using photomicrographic analysis. By using gas chromatography-mass spectroscopy technique, 18 volatile compounds involved in the growth inhibition mechanism were identified, including α-pinene and limonene. In addition, we found a high proportion of bacterial strains that produced siderophores during growth with different carbon sources, such as alanine and glutamic acid; however, their roles in the antagonism mechanism remain unclear. PMID:23680857

  14. Burkholderia paludis sp. nov., an Antibiotic-Siderophore Producing Novel Burkholderia cepacia Complex Species, Isolated from Malaysian Tropical Peat Swamp Soil.

    Science.gov (United States)

    Ong, Kuan Shion; Aw, Yoong Kit; Lee, Learn Han; Yule, Catherine M; Cheow, Yuen Lin; Lee, Sui Mae

    2016-01-01

    A novel Gram negative rod-shaped bacterium, designated strain MSh1T, was isolated from Southeast Pahang tropical peat swamp forest soil in Malaysia and characterized using a polyphasic taxonomy approach. The predominant cellular fatty acids (>10.0%) were C16:0 (31.7%), C17:0 cyclo (26.6%), and C19:0 cyclo ω8c (16.1%). The polar lipids detected were phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol. The predominant ubiquinone was Q-8. This revealed that strain MSh1T belongs to the genus Burkholderia. The type strain MSh1T can be differentiated from other Burkholderia cepacia complex (Bcc) species by phylogenetic analysis of 16S rRNA gene sequence, multilocus sequence analysis (MLSA), average nucleotide identity (ANI) and biochemical tests. DNA-DNA relatedness values between strain MSh1T and closely related type strains were below the 70% threshold value. Based on this polyphasic study of MSh1T, it can be concluded that this strain represents a novel species within the Bcc, for which the name Burkholderia paludis sp. nov. is proposed. The type strain is MSh1T (= DSM 100703T = MCCC 1K01245T). The dichloromethane extract of MSh1T exhibited antimicrobial activity against four Gram positive bacteria (Enterococcus faecalis ATCC 29212, E. faecalis ATCC 700802, Staphylococcus aureus ATCC 29213, S. aureus ATCC 700699) and a Gram negative bacteria (Escherichia coli ATCC 25922). Further purification work has led to the isolation of Compound 1, pyochelin. Pyochelin demonstrated antimicrobial activity against four S. aureus strains and three E. faecalis strains with MIC-values of 3.13 μg/ml and 6.26 μg/ml, respectively. SEM analysis showed that the cellular morphology of E. faecalis ATCC 700802 was not affected by pyochelin; suggesting that it might target the intracellular components. Pyochelin, a siderophore with antimicrobial activity might be useful in treating bacterial infections caused by S. aureus and E. faecalis, however further work has to

  15. Burkholderia ginsengiterrae sp. nov. and Burkholderia panaciterrae sp. nov., antagonistic bacteria against root rot pathogen Cylindrocarpon destructans, isolated from ginseng soil.

    Science.gov (United States)

    Farh, Mohamed El-Agamy; Kim, Yeon-Ju; Van An, Hoang; Sukweenadhi, Johan; Singh, Priyanka; Huq, Md Amdadul; Yang, Deok-Chun

    2015-04-01

    Strain DCY85(T) and DCY85-1(T), isolated from rhizosphere of ginseng, were rod-shaped, Gram-reaction-negative, strictly aerobic, catalase positive and oxidase negative. 16S rRNA gene sequence analysis revealed that strain DCY85(T) as well as DCY85-1(T) belonged to the genus Burkholderia and were closely related to Burkholderia fungorum KACC 12023(T) (98.1 and 98.0 % similarity, respectively). The major polar lipids of strain DCY85(T) and DCY85-1(T) were phosphatidylethanolamine, one unidentified aminolipid and two unidentified phospholipids. The major fatty acids of both strains are C16:0, C18:1 ω7c and summed feature 3 (C16:1 ω6c and/or C16:1 ω7c). The predominant isoprenoid quinone of each strain DCY85(T) and DCY85-1(T) was ubiquinone (Q-8) and the G+C content of their genomic DNA was 66.0 and 59.4 mol%, respectively, which fulfill the characteristic range of the genus Burkholderia. The polyamine content of both DCY85(T) and DCY85-1(T) was putrescine. Although both DCY85(T) and DCY85-1(T) have highly similar 16S rRNA and identical RecA and gyrB sequences, they show differences in phenotypic and chemotaxonomic characteristics. DNA-DNA hybridization results proved the consideration of both strains as two different species. Based on the results from our polyphasic characterization, strain DCY85(T) and DCY85-1(T) are considered novel Burkholderia species for which the name Burkholderia ginsengiterrae sp. nov and Burkholderia panaciterrae sp. nov are, respectively, proposed. An emended description of those strains is also proposed. DCY85(T) and DCY85-1(T) showed antagonistic activity against the common root rot pathogen of ginseng, Cylindrocarpon destructans. The proposed type strains are DCY85(T) (KCTC 42054(T) = JCM 19888(T)) and DCY85-1(T) (KCTC 42055(T) = JCM 19889(T)).

  16. Draft Genome Sequence of the Soil Bacterium Burkholderia terrae Strain BS001, Which Interacts with Fungal Surface Structures

    DEFF Research Database (Denmark)

    Nazir, Rashid; Hansen, Martin A.; Sorensen, Soren

    2012-01-01

    Burkholderia terrae BS001 is a soil bacterium which was originally isolated from the mycosphere of the ectomycorrhizal fungus Laccaria proxima. It exhibits a range of fungus-interacting traits which reveal its propensity to actively interact at fungal interfaces. Here, we present the approximately...... 11.5-Mb (G+C content, 61.52 draft genome sequence of B. terrae BS001 with the aim of providing insight into the genomic basis of its ecological success in fungus-affected soil settings....

  17. Enhanced bioconversion of ethylene glycol to glycolic acid by a newly isolated Burkholderia sp. EG13.

    Science.gov (United States)

    Gao, Xiaoxin; Ma, Zhengfei; Yang, Limin; Ma, Jiangquan

    2014-10-01

    Burkholderia sp. EG13 with high ethylene glycol-oxidizing activity was isolated from soil, which could be used for the synthesis of glycolic acid from the oxidation of ethylene glycol. Using the resting cells of Burkholderia sp. EG13 as biocatalysts, the optimum reaction temperature and pH were 30 °C and 6.0, respectively. After 24 h of biotransformation, the yield of glycolic acid from 200 mM ethylene glycol was 98.8 %. Furthermore, an integrated bioprocess for the production of glycolic acid which involved in situ product removal (ISPR) was investigated. Using fed-batch method with ISPR, a total of 793 mM glycolic acid has been accumulated in the reaction mixture after the 4th feed.

  18. Burkholderia metalliresistens sp. nov., a multiple metal-resistant and phosphate-solubilising species isolated from heavy metal-polluted soil in Southeast China.

    Science.gov (United States)

    Guo, Jun Kang; Ding, Yong Zhen; Feng, Ren Wei; Wang, Rui Gang; Xu, Ying Ming; Chen, Chun; Wei, Xiu Li; Chen, Wei Min

    2015-06-01

    A metal-resistant and phosphate-solubilising bacterium, designated as strain D414(T), was isolated from heavy metal (Pb, Cd, Cu and Zn)-polluted paddy soils at the surrounding area of Dabao Mountain Mine in Southeast China. The minimum inhibitory concentrations of heavy metals for strain D414(T) were 2000 mg L(-1) (Cd), 800 mg L(-1) (Pb), 150 mg L(-1) (Cu) and 2500 mg L(-1) (Zn). The strain possessed plant growth-promoting properties, such as 1-aminocyclopropane-1-carboxylate assimilation, indole production and phosphate solubilisation. Analysis of 16S rRNA gene sequence indicated that the isolate is a member of the genus Burkholderia where strain D414(T) formed a distinct phyletic line with validly described Burkholderia species. Strain D414(T) is closely related to Burkholderia tropica DSM 15359(T), B. bannensis NBRC E25(T) and B. unamae DSM 17197(T), with 98.5, 98.3 and 98.3 % sequence similarities, respectively. Furthermore, less than 34 % DNA-DNA relatedness was detected between strain D414(T) and the type strains of the phylogenetically closest species of Burkholderia. The dominant fatty acids of strain D414(T) were C14:0, C16:0, C17:0 cyclo and C18:1 ω7c. The DNA G+C content was 62.3 ± 0.5 mol%. On the basis of genotypic, phenotypic and phylogenetic data, strain D414(T) represents a novel species, for which the name Burkholderia metalliresistens sp. nov. is proposed, with D414(T) (=CICC 10561(T) = DSM 26823(T)) as the type strain.

  19. Biodegradation of PAHs by Burkholderia sp. VITRSB1 Isolated from Marine Sediments

    Directory of Open Access Journals (Sweden)

    T. Revathy

    2015-01-01

    Full Text Available The polycyclic aromatic hydrocarbons (PAHs pollution to the environment is a major threat to the living organisms, and hence the degradation of these PAHs is necessary. Studies on PAHs degrading bacteria have focussed on terrestrial microbes and the potential of marine derived microbes is undermined. Herein we report the isolation and characterization of PAHs degrading Burkholderia sp. from lagoon sediments collected at the Southern coast of India. The strain was Gram negative, rod-shaped, motile, and ∼2–5 μm in length. Based on the phylogenetic data the strain was identified as Burkholderia and designated as VITRSB1. Initial PAHs degradation ability of the strain was assessed using basal salt medium supplemented with diesel, kerosene, toluene, aniline, naphthalene, and phenol. The strain was found to be effectively degrading kerosene, diesel, toluene, and aniline even at higher concentration (1%. However, naphthalene and aniline were degraded only at lower concentration (0.1% and phenol, camphor, and DAP inhibited the growth of the strain. Furthermore, the degraded end products of the PAHs were determined using FTIR. Notably, none of the end products were found to be toxic to the biosphere. Our results indicate that the isolated Burkholderia sp. could be a prospective candidate for the effective degradation of selective PAHs.

  20. High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Burkholderia sp. strain UYPR1.413.

    Science.gov (United States)

    De Meyer, Sofie E; Fabiano, Elena; Tian, Rui; Van Berkum, Peter; Seshadri, Rekha; Reddy, Tbk; Markowitz, Victor; Ivanova, Natalia; Pati, Amrita; Woyke, Tanja; Howieson, John; Kyrpides, Nikos; Reeve, Wayne

    2015-01-01

    Burkholderia sp. strain UYPR1.413 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Parapiptadenia rigida collected at the Angico plantation, Mandiyu, Uruguay, in December 2006. A survey of symbionts of P. rigida in Uruguay demonstrated that this species is nodulated predominantly by Burkholderia microsymbionts. Moreover, Burkholderia sp. strain UYPR1.413 is a highly efficient nitrogen fixing symbiont with this host. Currently, the only other sequenced isolate to fix with this host is Cupriavidus sp. UYPR2.512. Therefore, Burkholderia sp. strain UYPR1.413 was selected for sequencing on the basis of its environmental and agricultural relevance to issues in global carbon cycling, alternative energy production, and biogeochemical importance, and is part of the GEBA-RNB project. Here we describe the features of Burkholderia sp. strain UYPR1.413, together with sequence and annotation. The 10,373,764 bp high-quality permanent draft genome is arranged in 336 scaffolds of 342 contigs, contains 9759 protein-coding genes and 77 RNA-only encoding genes.

  1. Burkholderia sp. induces functional nodules on the South African invasive legume Dipogon lignosus (Phaseoleae) in New Zealand soils.

    Science.gov (United States)

    Liu, Wendy Y Y; Ridgway, Hayley J; James, Trevor K; James, Euan K; Chen, Wen-Ming; Sprent, Janet I; Young, J Peter W; Andrews, Mitchell

    2014-10-01

    The South African invasive legume Dipogon lignosus (Phaseoleae) produces nodules with both determinate and indeterminate characteristics in New Zealand (NZ) soils. Ten bacterial isolates produced functional nodules on D. lignosus. The 16S ribosomal RNA (rRNA) gene sequences identified one isolate as Bradyrhizobium sp., one isolate as Rhizobium sp. and eight isolates as Burkholderia sp. The Bradyrhizobium sp. and Rhizobium sp. 16S rRNA sequences were identical to those of strains previously isolated from crop plants and may have originated from inocula used on crops. Both 16S rRNA and DNA recombinase A (recA) gene sequences placed the eight Burkholderia isolates separate from previously described Burkholderia rhizobial species. However, the isolates showed a very close relationship to Burkholderia rhizobial strains isolated from South African plants with respect to their nitrogenase iron protein (nifH), N-acyltransferase nodulation protein A (nodA) and N-acetylglucosaminyl transferase nodulation protein C (nodC) gene sequences. Gene sequences and enterobacterial repetitive intergenic consensus (ERIC) PCR and repetitive element palindromic PCR (rep-PCR) banding patterns indicated that the eight Burkholderia isolates separated into five clones of one strain and three of another. One strain was tested and shown to produce functional nodules on a range of South African plants previously reported to be nodulated by Burkholderia tuberum STM678(T) which was isolated from the Cape Region. Thus, evidence is strong that the Burkholderia strains isolated here originated in South Africa and were somehow transported with the plants from their native habitat to NZ. It is possible that the strains are of a new species capable of nodulating legumes.

  2. Rhizonin A from Burkholderia sp. KCTC11096 and Its Growth Promoting Role in Lettuce Seed Germination

    Directory of Open Access Journals (Sweden)

    Sang-Mo Kang

    2012-07-01

    Full Text Available We isolated and identified a gibberellin-producing Burkholderia sp. KCTC 11096 from agricultural field soils. The culture filtrate of plant growth promoting rhizobacteria (PGPR significantly increased the germination and growth of lettuce and Chinese cabbage seeds. The ethyl acetate extract of the PGPR culture showed significantly higher rate of lettuce seed germination and growth as compared to the distilled water treated control. The ethyl acetate fraction of the Burkholderia sp. was subjected to bioassay-guided isolation and we obtained for the first time from a Burkholderia sp. the plant growth promoting compound rhizonin A (1, which was characterized through NMR and MS techniques. Application of various concentrations of 1 significantly promoted the lettuce seed germination as compared to control.

  3. Burkholderia novacaledonica sp. nov. and B. ultramafica sp. nov. isolated from roots of Costularia spp. pioneer plants of ultramafic soils in New Caledonia.

    Science.gov (United States)

    Guentas, Linda; Gensous, Simon; Cavaloc, Yvon; Ducousso, Marc; Amir, Hamid; De Georges de Ledenon, Benjamin; Moulin, Lionel; Jourand, Philippe

    2016-05-01

    The taxonomic status of eleven rhizospheric bacterial strains belonging to the genus Burkholderia and isolated from roots of Costularia (Cyperaceae), tropical herbaceous pioneer plants growing on ultramafic soils in New Caledonia, was investigated using a polyphasic taxonomic approach. The genetic analyses (16S rRNA genes, gyrB, recA, nreB and cnr) confirmed that all strains are Burkholderia and cluster into two separated groups. The DNA hybridization results showed low relatedness values to the closest relatives Burkholderia species. The phenotypic analyses confirmed that the two groups of strains could be differentiated from each other and from other known Burkholderia species. This polyphasic study revealed that these two groups of strains represent each a novel species of Burkholderia, for which the names Burkholderia novacaledonica sp. nov. (type strain STM10272(T)=LMG28615(T)=CIP110887(T)) and B. ultramafica sp. nov. (type strain STM10279(T)=LMG28614(T)=CIP110886(T)) are proposed, respectively. These strains of Burkholderia presented specific ecological traits such as the tolerance to the extreme edaphic constraints of ultramafic soils: they grew at pH between 4 and 8 and tolerate the strong unbalanced Ca/Mg ratio (1/19) and the high concentrations of heavy metals i.e. Co, Cr, Mn and Ni. Noteworthy B. ultramafica tolerated nickel until 10mM and B. novacaledonica up to 5mM. The presence of the nickel (nreB) and cobalt/nickel (cnr) resistance determinants encoding for protein involved in metal tolerance was found in all strains of both groups. Moreover, most of the strains were able to produce plant growth promoting molecules (ACC, IAA, NH3 and siderophores). Such ecological traits suggest that these new species of Burkholderia might be environmentally adaptable plant-associated bacteria and beneficial to plants. Copyright © 2016 Elsevier GmbH. All rights reserved.

  4. Burkholderia caballeronis sp. nov., a nitrogen fixing species isolated from tomato (Lycopersicon esculentum) with the ability to effectively nodulate Phaseolus vulgaris.

    Science.gov (United States)

    Martínez-Aguilar, Lourdes; Salazar-Salazar, Corelly; Méndez, Rafael Díaz; Caballero-Mellado, Jesús; Hirsch, Ann M; Vásquez-Murrieta, María Soledad; Estrada-de los Santos, Paulina

    2013-12-01

    During a survey of Burkholderia species with potential use in agrobiotechnology, a group of 12 strains was isolated from the rhizosphere and rhizoplane of tomato plants growing in Mexico (Nepantla, Mexico State). A phylogenetic analysis of 16S rRNA gene sequences showed that the strains are related to Burkholderia kururiensis and Burkholderia mimosarum (97.4 and 97.1 %, respectively). However, they induced effective nitrogen-fixing nodules on roots of Phaseolus vulgaris. Based on polyphasic taxonomy, the group of strains represents a novel species for which the name Burkholderia caballeronis sp. nov. is proposed. The type species is TNe-841(T) (= LMG 26416(T) = CIP 110324(T)).

  5. Comparison of the Sulfonamide Inhibition Profiles of the β- and γ-Carbonic Anhydrases from the Pathogenic Bacterium Burkholderia pseudomallei

    Directory of Open Access Journals (Sweden)

    Daniela Vullo

    2017-03-01

    Full Text Available We have cloned, purified, and characterized a β-carbonic anhydrase (CA, EC 4.2.1.1, BpsCAβ, from the pathogenic bacterium Burkholderia pseudomallei, responsible for the tropical disease melioidosis. The enzyme showed high catalytic activity for the physiologic CO2 hydration reaction to bicarbonate and protons, with the following kinetic parameters: kcat of 1.6 × 105 s−1 and kcat/KM of 3.4 × 107 M−1 s−1. An inhibition study with a panel of 38 sulfonamides and one sulfamate—including 15 compounds that are used clinically—revealed an interesting structure–activity relationship for the interaction of this enzyme with these inhibitors. Many simple sulfonamides and clinically used agents such as topiramate, sulpiride, celecoxib, valdecoxib, and sulthiame were ineffective BpsCAβ inhibitors (KI > 50 µM. Other drugs, such as ethoxzolamide, dorzolamide, brinzolamide, zonisamide, indisulam, and hydrochlorothiazide were moderately potent micromolar inhibitors. The best inhibition was observed with benzene-1,3-disulfonamides—benzolamide and its analogs acetazolamide and methazolamide—which showed KI in the range of 185–745 nM. The inhibition profile of BpsCAβ is very different from that of the γ-class enzyme from the same pathogen, BpsCAγ. Thus, identifying compounds that would effectively interact with both enzymes is relatively challenging. However, benzolamide was one of the best inhibitors of both of these CAs with KI of 653 and 185 nM, respectively, making it an interesting lead compound for the design of more effective agents, which may be useful tools for understanding the pathogenicity of this bacterium.

  6. Optimization of Lipase Production by Burkholderia sp. Using Response Surface Methodology

    Directory of Open Access Journals (Sweden)

    Shiow-Ling Lee

    2012-11-01

    Full Text Available Response surface methodology (RSM was employed to optimize the extracellular lipase production by Burkholderia sp. HL-10. Preliminary tests showed that olive oil, tryptone and Tween-80 exhibited significant effects on the lipase production. The optimum concentrations of these three components were determined using a faced-centered central composite design (FCCCD. The analysis of variance revealed that the established model was significant (p < 0.01. The optimized medium containing 0.65% olive oil (v/v, 2.42% tryptone (w/v and 0.15% Tween-80 (v/v resulted in a maximum activity of 122.3 U/mL, about three fold higher than that in basal medium. Approximately 99% of validity of the predicted value was achieved.

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

    Science.gov (United States)

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

    2016-09-01

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

  8. Burkholderia humptydooensis sp. nov., A Burkholderia thailandensis-Like Species and the Fifth Member of the pseudomallei Complex

    Science.gov (United States)

    2016-06-02

    2012). The type strain, MSMB43T, has been previously referred to as B. 312 Page 14 of 23 thailandensis-like species in multiple studies (Currie...closely related species were used to reconstruct the phylogenetic relationships. 339 Genomes from this study in bold and assembly numbers in...The In Vitro Antibiotic Susceptibility of Malaysian 379 Isolates of Burkholderia pseudomallei. Int J Microbiol, 2013, 121845. 380 BARNES, J. L

  9. Porphyrobacter algicida sp. nov., an algalytic bacterium isolated from seawater.

    Science.gov (United States)

    Kristyanto, Sylvia; Lee, Sang Don; Kim, Jaisoo

    2017-11-01

    A novel Gram-stain-negative, yellow-pigmented, catalase- and oxidase-positive, non-endospore-forming, flagellated bacterium, designated strain Yeonmyeong 2-22 T , was isolated from surface seawater of Geoje Island, Republic of Korea. Strain Yeonmyeong 2-22 T showed algalytic activity against the seven strains tested: Cochlodinium polykrikoides, Chattonella marina, Heterosigma akashiwo, Scrippsiella trochoidea, Heterocapsa triquetra, Prorocentrum minimum and Skeletonema costatum. A taxonomic study was carried out based on a polyphasic approach to characterize the exact taxonomic position of strain Yeonmyeong 2-22 T . The bacterium was able to grow at 10-40 °C, at salinities from 0 to 9 %, at pH from 4.0 to 9.0 and was not able to degrade gelatin or casein. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain Yeonmyeong 2-22 T was considered to represent a novel species of the genus Porphyrobacter, which belongs to the family Erythrobacteraceae, and was related most closely to Porphyrobacter dokdonensis DSW-74 T with 97.23 % 16S rRNA gene sequence similarity. The dominant cellular fatty acids of strain Yeonmyeong 2-22 T were C18 : 1ω7c (49.7 %), C16 : 0 (12.0 %) and 11-methyl C18 : 1ω7c (11.5 %), and ubiquinone-10 (Q-10) was the predominant respiratory lipoquinone. The genomic DNA G+C content of strain Yeonmyeong 2-22 T was calculated to be 63.0 mol%. Phenotypic characteristics of the novel strain also differed from other members of the genus Porphyrobacter. On the basis of polyphasic taxonomic data, strain Yeonmyeong 2-22 T represents as a novel species of the genus Porphyrobacter, for which the name of Porphyrobacter algicida sp. nov. is proposed. The type strain is Yeonmyeong 2-22 T (=KEMB 9005-328 T =JCM 31499 T ).

  10. High-quality permanent draft genome sequence of the Lebeckia ambigua-nodulating Burkholderia sp. strain WSM4176.

    Science.gov (United States)

    De Meyer, Sofie E; Tian, Rui; Seshadri, Rekha; Reddy, Tbk; Markowitz, Victor; Ivanova, Natalia; Pati, Amrita; Woyke, Tanja; Kyrpides, Nikos; Yates, Ron; Howieson, John; Reeve, Wayne

    2015-01-01

    Burkholderia sp. strain WSM4176 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective N2-fixing root nodule of Lebeckia ambigua collected in Nieuwoudtville, Western Cape of South Africa, in October 2007. This plant persists in infertile, acidic and deep sandy soils, and is therefore an ideal candidate for a perennial based agriculture system in Western Australia. Here we describe the features of Burkholderia sp. strain WSM4176, which represents a potential inoculant quality strain for L. ambigua, together with sequence and annotation. The 9,065,247 bp high-quality-draft genome is arranged in 13 scaffolds of 65 contigs, contains 8369 protein-coding genes and 128 RNA-only encoding genes, and is part of the GEBA-RNB project proposal (Project ID 882).

  11. Bioformulation of Burkholderia sp. MSSP with a multispecies consortium for growth promotion of Cajanus cajan.

    Science.gov (United States)

    Pandey, Piyush; Maheshwari, D K

    2007-02-01

    The present work was undertaken to formulate an effective bioformulation using Burkholderia sp. strain MSSP, a known plant-growth-promoting rhizobacterium. MSSP was tagged with the reporter gene of green fluorescent protein (gfp) to monitor its population in cost-effective solid carriers, including sugarcane-bagasse, sawdust, cocoa peat, rice husk, wheat bran, charcoal, and rock phosphate, and paneer-whey as liquid carrier. Physical and chemical properties of different low-cost carrier materials were studied. The viability of the green fluorescent tagged variant of MSSP was estimated in different sterile carrier materials. Whey and wheat bran proved to be efficient carrier materials for the bioformulation. Sawdust, rock phosphate, rice husk, and cocoa peat were average, while charcoal and sugarcane-bagasse proved to be inferior carriers. The viability of strain MSSP was also assessed in wheat bran and whey-based consortium, having three other bacterial strains, namely Sinorhizobium meliloti PP3, Rhizobium leguminosarum Pcc, and Bacillus sp. strain B1. Presence of other plant-growth-promoting bacteria did not have any detrimental effect on the viability of MSSP. Efficiency of the wheat-bran-based multispecies consortium was studied on the growth of pigeonpea in field conditions. A considerable increase in plant biomass, nodule number and weight, and number of pods was recorded as compared with individual trials and with the control.

  12. Virgibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi.

    Science.gov (United States)

    Oh, Young Joon; Jang, Ja-Young; Lim, Seul Ki; Kwon, Min-Sung; Lee, Jieun; Kim, NamHee; Shin, Mi-Young; Park, Hyo Kyeong; Seo, Myung-Ji; Choi, Hak-Jong

    2017-12-01

    A Gram-stain-positive, halophilic, rod-shaped, non-motile, spore forming bacterium, strain NKC1-2 T , was isolated from kimchi, a Korean fermented food. Comparative analysis based on 16S rRNA gene sequence demonstrated that the isolated strain was a species of the genus Virgibacillus. Strain NKC1-2 T exhibited high level of 16S rRNA gene sequence similarity with the type strains of Virgibacillus xinjiangensis SL6-1 T (96.9%), V. sediminis YIM kkny3 T (96.8%), and V. salarius SA-Vb1 T (96.7%). The isolate grew at pH 6.5-10.0 (optimum, pH 8.5-9.0), 0.0-25.0% (w/v) NaCl (optimum, 10-15% NaCl), and 15-50°C (optimum, 37°C). The major menaquinone in the strain was menaquinone-7, and the main peptidoglycan of the strain was meso-diaminopimelic acid. The predominant fatty acids of the strain were iso-C 14:0 , anteisio-C 15:0 , iso- C 15:0 , and iso-C 16:0 (other components were < 10.0%). The polar lipids consisted of diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G + C content of NKC1-2 T was 42.5 mol%. On the basis of these findings, strain NKC1-2 T is proposed as a novel species in the genus Virgibacillus, for which the name Virgibacillus kimchii sp. nov. is proposed (=KACC 19404 T =JCM 32284 T ). The type strain of Virgibacillus kimchii is NKC1-2T.

  13. Burkholderia tropica as a Potential Microalgal Growth-Promoting Bacterium in the Biosorption of Mercury from Aqueous Solutions.

    Science.gov (United States)

    ZÁrate, Ana; Florez, July; Angulo, Edgardo; Varela-Prieto, Lourdes; Infante, Cherlys; Barrios, Fredy; Barraza, Beatriz; Gallardo, D I; Valdés, Jorge

    2017-06-28

    The use of microalgal biomass is an interesting technology for the removal of heavy metals from aqueous solutions owing to its high metal-binding capacity, but the interactions with bacteria as a strategy for the removal of toxic metals have been poorly studied. The goal of the current research was to investigate the potential of Burkholderia tropica co-immobilized with Chlorella sp. in polyurethane discs for the biosorption of Hg(II) from aqueous solutions and to evaluate the influence of different Hg(II) concentrations (0.041, 1.0, and 10 mg/l) and their exposure to different contact times corresponding to intervals of 1, 2, 4, 8, 16, and 32 h. As expected, microalgal bacterial biomass adhered and grew to form a biofilm on the support. The biosorption data followed pseudo-second-order kinetics, and the adsorption equilibrium was well described by either Langmuir or Freundlich adsorption isotherm, reaching equilibrium from 1 h. In both bacterial and microalgal immobilization systems in the coimmobilization of Chlorella sp. and B. tropica to different concentrations of Hg(II), the kinetics of biosorption of Hg(II) was significantly higher before 60 min of contact time. The highest percentage of biosorption of Hg(II) achieved in the co-immobilization system was 95% at pH 6.4, at 3.6 g of biosorbent, 30 ± 1°C, and a mercury concentration of 1 mg/l before 60 min of contact time. This study showed that co-immobilization with B. tropica has synergistic effects on biosorption of Hg(II) ions and merits consideration in the design of future strategies for the removal of toxic metals.

  14. Cell-bound lipases from Burkholderia sp. ZYB002: gene sequence analysis, expression, enzymatic characterization, and 3D structural model.

    Science.gov (United States)

    Shu, Zhengyu; Lin, Hong; Shi, Shaolei; Mu, Xiangduo; Liu, Yanru; Huang, Jianzhong

    2016-05-03

    The whole-cell lipase from Burkholderia cepacia has been used as a biocatalyst in organic synthesis. However, there is no report in the literature on the component or the gene sequence of the cell-bound lipase from this species. Qualitative analysis of the cell-bound lipase would help to illuminate the regulation mechanism of gene expression and further improve the yield of the cell-bound lipase by gene engineering. Three predictive cell-bound lipases, lipA, lipC21 and lipC24, from Burkholderia sp. ZYB002 were cloned and expressed in E. coli. Both LipA and LipC24 displayed the lipase activity. LipC24 was a novel mesophilic enzyme and displayed preference for medium-chain-length acyl groups (C10-C14). The 3D structural model of LipC24 revealed the open Y-type active site. LipA displayed 96 % amino acid sequence identity with the known extracellular lipase. lipA-inactivation and lipC24-inactivation decreased the total cell-bound lipase activity of Burkholderia sp. ZYB002 by 42 % and 14 %, respectively. The cell-bound lipase activity from Burkholderia sp. ZYB002 originated from a multi-enzyme mixture with LipA as the main component. LipC24 was a novel lipase and displayed different enzymatic characteristics and structural model with LipA. Besides LipA and LipC24, other type of the cell-bound lipases (or esterases) should exist.

  15. Endophytic colonization of rice (Oryza sativa L. by the diazotrophic bacterium Burkholderia kururiensis and its ability to enhance plant growth

    Directory of Open Access Journals (Sweden)

    Katherine A. Mattos

    2008-09-01

    Full Text Available Burkholderia kururiensis is a diazotrophic bacterium originally isolated from a polluted aquifer environment and presents a high level of similarity with the rice endophyte "B. brasilensis" species. This work assessed the ability of B. kururiensis to endophytically colonize rice plantlets by monitoring different tissues of root-inoculated plants for the presence of bacterial growth in different media, electron microscopy and by 16S rDNA analysis. Observations of roots, stems and leaves of inoculated rice plantlets by electron microscopy revealed B. kururiensis colonization predominantly on root hair zones, demonstrating endophytic colonization primarily through the endodermis, followed by spreading into xylem vessels, a possible pathway leading to aerial parts. Although indifferent for the bacterial growth itself, addition of a nitrogen source was a limiting factor for endophytic colonization. As endophytic colonization was directly associated to an enhanced plant development, production of phytohormone auxin/indole-3-acetic acid by B. kururiensis was assayed with transgenic rice plantlets containing an auxin-responsive reporter (DR5-GUS. Our findings suggest the ability of auxin production by plant-associated B. kururiensis which may have a stimulatory effect on plant development, as evidenced by activation of DR5-GUS. We hereby demonstrate, for the first time, the ability of B. kururiensis to endophytically colonize rice, promoting both plant growth and rice grain yield.Burkholderia kururiensis é uma bactéria diazotrófica, originalmente isolada de um ambiente aquático poluído e apresenta alto nível de similaridade com a espécie endofítica "B. brasilensis" encontrada na planta de arroz. Este artigo demonstrou a habilidade de B. kururiensis colonizar endofiticamente plântulas de arroz, após esta bactéria ter sido inoculada na raiz das plantas. Esta capacidade foi confirmada pelo crescimento bacteriano em diferentes tecidos da planta

  16. The Role of Hydrophobicity and Surface Receptors at Hyphae of Lyophyllum sp. Strain Karsten in the Interaction with Burkholderia terrae BS001 – Implications for Interactions in Soil

    Science.gov (United States)

    Vila, Taissa; Nazir, Rashid; Rozental, Sonia; dos Santos, Giulia M. P.; Calixto, Renata O. R.; Barreto-Bergter, Eliana; Wick, Lukas Y.; van Elsas, Jan Dirk

    2016-01-01

    The soil bacterium Burkholderia terrae strain BS001 can interact with varying soil fungi, using mechanisms that range from the utilization of carbon/energy sources such as glycerol to the ability to reach novel territories in soil via co-migration with growing fungal mycelia. Here, we investigate the intrinsic properties of the B. terrae BS001 interaction with the basidiomycetous soil fungus Lyophyllum sp. strain Karsten. In some experiments, the ascomycetous Trichoderma asperellum 302 was also used. The hyphae of Lyophyllum sp. strain Karsten were largely hydrophilic on water-containing media versus hydrophobic when aerial, as evidenced by contact angle analyses (CA). Co-migration of B. terrae strain BS001 cells with the hyphae of the two fungi occurred preferentially along the - presumably hydrophilic - soil-dwelling hyphae, whereas aerial hyphae did not allow efficient migration, due to reduced thickness of their surrounding mucous films. Moreover, the cell numbers over the length of the hyphae in soil showed an uneven distribution, i.e., the CFU numbers increased from minima at the inoculation point to maximal numbers in the middle of the extended hyphae, then decreasing toward the terminal side. Microscopic analyses of the strain BS001 associations with the Lyophyllum sp. strain Karsten hyphae in the microcosms confirmed the presence of B. terrae BS001 cells on the mucous matter that was present at the hyphal surfaces of the fungi used. Cell agglomerates were found to accumulate at defined sites on the hyphal surfaces, which were coined ‘fungal-interactive’ hot spots. Evidence was further obtained for the contention that receptors for a physical bacterium-fungus interaction occur at the Lyophyllum sp. strain Karsten hyphal surface, in which the specific glycosphingolipid ceramide monohexoside (CMH) plays an important role. Thus, bacterial adherence may be mediated by heterogeneously distributed fungal-specific receptors, implying the CMH moieties. This

  17. Draft Genome Sequence of the Antitrypanosomally Active Sponge-Associated Bacterium Actinokineospora sp. Strain EG49

    KAUST Repository

    Harjes, Janno

    2014-03-06

    The marine sponge-associated bacterium Actinokineospora sp. strain EG49 produces the antitrypanosomal angucycline-like compound actinosporin A. The draft genome of Actinokineospora sp. EG49 has a size of 7.5 megabases and a GC content of 72.8% and contains 6,629 protein-coding sequences (CDS). antiSMASH predicted 996 genes residing in 36 secondary metabolite gene clusters.

  18. Phylogenomic Study of Burkholderia glathei-like Organisms, Proposal of 13 Novel Burkholderia Species and Emended Descriptions of Burkholderia sordidicola, Burkholderia zhejiangensis, and Burkholderia grimmiae

    Science.gov (United States)

    Peeters, Charlotte; Meier-Kolthoff, Jan P.; Verheyde, Bart; De Brandt, Evie; Cooper, Vaughn S.; Vandamme, Peter

    2016-01-01

    Partial gyrB gene sequence analysis of 17 isolates from human and environmental sources revealed 13 clusters of strains and identified them as Burkholderia glathei clade (BGC) bacteria. The taxonomic status of these clusters was examined by whole-genome sequence analysis, determination of the G+C content, whole-cell fatty acid analysis and biochemical characterization. The whole-genome sequence-based phylogeny was assessed using the Genome Blast Distance Phylogeny (GBDP) method and an extended multilocus sequence analysis (MLSA) approach. The results demonstrated that these 17 BGC isolates represented 13 novel Burkholderia species that could be distinguished by both genotypic and phenotypic characteristics. BGC strains exhibited a broad metabolic versatility and developed beneficial, symbiotic, and pathogenic interactions with different hosts. Our data also confirmed that there is no phylogenetic subdivision in the genus Burkholderia that distinguishes beneficial from pathogenic strains. We therefore propose to formally classify the 13 novel BGC Burkholderia species as Burkholderia arvi sp. nov. (type strain LMG 29317T = CCUG 68412T), Burkholderia hypogeia sp. nov. (type strain LMG 29322T = CCUG 68407T), Burkholderia ptereochthonis sp. nov. (type strain LMG 29326T = CCUG 68403T), Burkholderia glebae sp. nov. (type strain LMG 29325T = CCUG 68404T), Burkholderia pedi sp. nov. (type strain LMG 29323T = CCUG 68406T), Burkholderia arationis sp. nov. (type strain LMG 29324T = CCUG 68405T), Burkholderia fortuita sp. nov. (type strain LMG 29320T = CCUG 68409T), Burkholderia temeraria sp. nov. (type strain LMG 29319T = CCUG 68410T), Burkholderia calidae sp. nov. (type strain LMG 29321T = CCUG 68408T), Burkholderia concitans sp. nov. (type strain LMG 29315T = CCUG 68414T), Burkholderia turbans sp. nov. (type strain LMG 29316T = CCUG 68413T), Burkholderia catudaia sp. nov. (type strain LMG 29318T = CCUG 68411T) and Burkholderia peredens sp. nov. (type strain LMG 29314T = CCUG

  19. A marine bacterium, Oceanobacillus sp. Pinky, isolated from Algoa ...

    African Journals Online (AJOL)

    In this study, we report on the bioflocculant production potential of an Oceanobacillus sp. isolated from the marine sediments of Algoa Bay. The bacteria produced an extracellular bioflocculant optimally in the presence of sodium carbonate as source of carbon with flocculating activity of about 95.5%. Other optimal culture ...

  20. Burkholderia dipogonis sp. nov., isolated from root nodules of Dipogon lignosus in New Zealand and Western Australia.

    Science.gov (United States)

    Sheu, Shih-Yi; Chen, Ming-Hui; Liu, Wendy Y Y; Andrews, Mitchell; James, Euan K; Ardley, Julie K; De Meyer, Sofie E; James, Trevor K; Howieson, John G; Coutinho, Bruna G; Chen, Wen-Ming

    2015-12-01

    Seven strains, ICMP 19430T, ICMP 19429, ICMP 19431, WSM4637, WSM4638, WSM4639 and WSM4640, were isolated from nitrogen-fixing nodules on roots of the invasive South African legume Dipogon lignosus (subfamily Papilionoideae, tribe Phaseoleae) in New Zealand and Western Australia, and their taxonomic positions were investigated by using a polyphasic approach. All seven strains grew at 10-37 °C (optimum, 25-30 °C), at pH 4.0-9.0 (optimum, pH 6.0-7.0) and with 0-2 % (w/v) NaCl (optimum growth in the absence of NaCl). On the basis of 16S rRNA gene sequence analysis, the strains showed 99.0-99.5 % sequence similarity to the closest type strain, Burkholderia phytofirmans PsJNT, and 98.4-99.7 % sequence similarity to Burkholderia caledonica LMG 19076T. The predominant fatty acids were C18 : 1ω7c (21.0 % of the total fatty acids in strain ICMP 19430T), C16 : 0 (19.1 %), C17 : 0 cyclo (18.9 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 10.7 %) and C19 : 0 cyclov ω8c (7.5 %). The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized aminophospholipids and phospholipids. The major isoprenoid quinone was Q-8 and the DNA G+C content of strain ICMP 19430T was 63.2 mol%. The DNA–DNA relatedness of the novel strains with respect to the closest neighbouring members of the genus Burkholderia was 55 % or less. On the basis of 16S rRNA and recA gene sequence similarities and chemotaxonomic and phenotypic data,these strains represent a novel symbiotic species in the genus Burkholderia, for which the name Burkholderia dipogonis sp. nov. is proposed, with the type strain ICMP 19430T (=LMG28415T=HAMBI 3637T).

  1. Draft Genome Sequences of Two Antimicrobial-Producing Burkholderia sp. Strains, MSh1 and MSh2, Isolated from Malaysian Tropical Peat Swamp Forest Soil

    Science.gov (United States)

    Aw, Yoong Kit; Gan, Han Ming; Yule, Catherine M.; Lee, Sui Mae

    2014-01-01

    We report the draft genome sequences of two antimicrobial-producing isolates, Burkholderia sp. strains MSh1 and MSh2, which were isolated from tropical peat swamp forest soil. Putative genes related to different antimicrobial production have been annotated in both genome sequences. PMID:25301661

  2. Yersinia ruckeri sp. nov., the redmouth (RM) bacterium

    Science.gov (United States)

    Ewing, W.H.; Ross, A.J.; Brenner, Don J.; Fanning, G. R.

    1978-01-01

    Cultures of the redmouth (RM) bacterium, one of the etiological agents of redmouth disease in rainbow trout (Salmo gairdneri) and certain other fishes, were characterized by means of their biochemical reactions, by deoxyribonucleic acid (DNA) hybridization, and by determination of guanine-plus-cytosine (G+C) ratios in DNA. The DNA relatedness studies confirmed the fact that the RM bacteria are members of the family Enterobacteriaceae and that they comprise a single species that is not closely related to any other species of Enterobacteriaceae. They are about 30% related to species of both Serratia and Yersinia. A comparison of the biochemical reactions of RM bacteria and serratiae indicated that there are many differences between these organisms and that biochemically the RM bacteria are most closely related to yersiniae. The G+C ratios of RM bacteria were approximated to be between 47.5 and 48.5% These values are similar to those of yersiniae but markedly different from those of serratiae. On the basis of their biochemical reactions and their G+C ratios, the RM bacteria are considered to be a new species of Yersinia, for which the name Yersinia ruckeri is proposed. Strain 2396-61 (= ATCC 29473) is designated the type strain of the species.

  3. Rhizobium yantingense sp. nov., a mineral-weathering bacterium.

    Science.gov (United States)

    Chen, Wei; Sheng, Xia-Fang; He, Lin-Yan; Huang, Zhi

    2015-02-01

    A Gram-stain-negative, rod-shaped bacterial strain, H66(T), was isolated from the surfaces of weathered rock (purple siltstone) found in Yanting, Sichuan Province, PR China. Cells of strain H66(T) were motile with peritrichous flagella. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain H66(T) belongs to the genus Rhizobium. It is closely related to Rhizobium huautlense SO2(T) (98.1 %), Rhizobium alkalisoli CCBAU 01393(T) (98.0 %) and Rhizobium cellulosilyticum ALA10B2(T) (98.0 %). Analysis of the housekeeping genes, recA, glnII and atpD, showed low levels of sequence similarity (Rhizobium. The predominant components of the cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The G+C content of strain H66(T) was 60.3 mol%. Strain H66(T) is suggested to be a novel species of the genus Rhizobium based on the low levels of DNA-DNA relatedness (ranging from 14.3 % to 40.0 %) with type strains of species of the genus Rhizobium and on its unique phenotypic characteristics. The namehttp://dx.doi.org/10.1601/nm.1279Rhizobium yantingense sp. nov. is proposed for this novel species. The type strain is H66(T) ( = CCTCC AB 2014007(T) = LMG 28229(T)). © 2015 IUMS.

  4. Permanent draft genome of the malachite-green-tolerant bacterium Rhizobium sp. MGL06.

    Science.gov (United States)

    Liu, Yang; Wang, Runping; Zeng, Runying

    2014-12-01

    Rhizobium sp. MGL06, the first Rhizobium isolate from a marine environment, is a malachite-green-tolerant bacterium with a broader salinity tolerance (range: 0.5% to 9%) than other rhizobia. This study sequences and annotates the draft genome sequence of this strain. Genome sequence information provides a basis for analyzing the malachite green tolerance, broad salinity adaptation, nitrogen fixation properties, and taxonomic classification of the isolate. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. Acidovorax anthurii sp. nov., a new phytopathogenic bacterium which causes bacterial leaf-spot of anthurium.

    Science.gov (United States)

    Gardan, L; Dauga, C; Prior, P; Gillis, M; Saddler, G S

    2000-01-01

    The bacterial leaf-spot of anthurium emerged during the 1980s, in the French West Indies and Trinidad. This new bacterial disease is presently wide spread and constitutes a serious limiting factor for commercial anthurium production. Twenty-nine strains isolated from leaf-spots of naturally infected anthurium were characterized and compared with reference strains belonging to the Comamonadaceae family, the genera Ralstonia and Burkholderia, and representative fluorescent pseudomonads. From artificial inoculations 25 out of 29 strains were pathogenic on anthurium. Biochemical and physiological tests, fatty acid analysis, DNA-DNA hybridization, 16S rRNA gene sequence analysis, DNA-16S RNA hybridization were performed. The 25 pathogenic strains on anthurium were clustered in one phenon closely related to phytopathogenic strains of the genus Acidovorax. Anthurium strains were 79-99% (deltaTm range 0.2-1.6) related to the strain CFBP 3232 and constituted a discrete DNA homology group indicating that they belong to the same species. DNA-rRNA hybridization, 16S rRNA sequence and fatty acid analysis confirmed that this new species belongs to the beta-subclass of Proteobacteria and to rRNA superfamily III, to the family of Comamonadaceae and to the genus Acidovorax. The name Acidovorax anthurii is proposed for this new phytopathogenic bacterium. The type strain has been deposited in the Collection Française des Bactéries Phytopathogènes as CFBP 3232T.

  6. Metabolism of 4-chloro-2-nitrophenol in a Gram-positive bacterium, Exiguobacterium sp. PMA

    Directory of Open Access Journals (Sweden)

    Arora Pankaj

    2012-11-01

    Full Text Available Abstract Background Chloronitrophenols (CNPs are widely used in the synthesis of dyes, drugs and pesticides, and constitute a major group of environmental pollutants. 4-Chloro-2-nitrophenol (4C2NP is an isomer of CNPs that has been detected in various industrial effluents. A number of physicochemical methods have been used for treatment of wastewater containing 4C2NP. These methods are not as effective as microbial degradation, however. Results A 4C2NP-degrading bacterium, Exiguobacterium sp. PMA, which uses 4C2NP as the sole carbon and energy source was isolated from a chemically-contaminated site in India. Exiguobacterium sp. PMA degraded 4C2NP with the release of stoichiometeric amounts of chloride and ammonium ions. The effects of different substrate concentrations and various inoculum sizes on degradation of 4C2NP were investigated. Exiguobacterium sp. PMA degraded 4C2NP up to a concentration of 0.6 mM. High performance liquid chromatography and gas chromatography–mass spectrometry identified 4-chloro-2-aminophenol (4C2AP and 2-aminophenol (2AP as possible metabolites of the 4C2NP degradation pathway. The crude extract of 4C2NP-induced PMA cells contained enzymatic activity for 4C2NP reductase and 4C2AP dehalogenase, suggesting the involvement of these enzymes in the degradation of 4C2NP. Microcosm studies using sterile and non-sterile soils spiked with 4C2NP were carried out to monitor the bioremediation potential of Exiguobacterium sp. PMA. The bioremediation of 4C2NP by Exiguobacterium sp. PMA was faster in non-sterilized soil than sterilized soil. Conclusions Our studies indicate that Exiguobacterium sp. PMA may be useful for the bioremediation of 4C2NP-contaminated sites. This is the first report of (i the formation of 2AP in the 4C2NP degradation pathway by any bacterium and (iii the bioremediation of 4C2NP by any bacterium.

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

    Directory of Open Access Journals (Sweden)

    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.

  8. Genome sequence of the plant growth promoting endophytic bacterium Enterobacter sp. 638.

    Directory of Open Access Journals (Sweden)

    Safiyh Taghavi

    2010-05-01

    Full Text Available Enterobacter sp. 638 is an endophytic plant growth promoting gamma-proteobacterium that was isolated from the stem of poplar (Populus trichocarpaxdeltoides cv. H11-11, a potentially important biofuel feed stock plant. The Enterobacter sp. 638 genome sequence reveals the presence of a 4,518,712 bp chromosome and a 157,749 bp plasmid (pENT638-1. Genome annotation and comparative genomics allowed the identification of an extended set of genes specific to the plant niche adaptation of this bacterium. This includes genes that code for putative proteins involved in survival in the rhizosphere (to cope with oxidative stress or uptake of nutrients released by plant roots, root adhesion (pili, adhesion, hemagglutinin, cellulose biosynthesis, colonization/establishment inside the plant (chemiotaxis, flagella, cellobiose phosphorylase, plant protection against fungal and bacterial infections (siderophore production and synthesis of the antimicrobial compounds 4-hydroxybenzoate and 2-phenylethanol, and improved poplar growth and development through the production of the phytohormones indole acetic acid, acetoin, and 2,3-butanediol. Metabolite analysis confirmed by quantitative RT-PCR showed that, the production of acetoin and 2,3-butanediol is induced by the presence of sucrose in the growth medium. Interestingly, both the genetic determinants required for sucrose metabolism and the synthesis of acetoin and 2,3-butanediol are clustered on a genomic island. These findings point to a close interaction between Enterobacter sp. 638 and its poplar host, where the availability of sucrose, a major plant sugar, affects the synthesis of plant growth promoting phytohormones by the endophytic bacterium. The availability of the genome sequence, combined with metabolome and transcriptome analysis, will provide a better understanding of the synergistic interactions between poplar and its growth promoting endophyte Enterobacter sp. 638. This information can be further

  9. Mancha bacteriana em Ruscus sp. causada por Burkholderia andropogonis no Brasil

    OpenAIRE

    Almeida, Irene M.G; Beriam, Luís O.S; Sannazzaro, Ana M; Rodrigues Neto, Júlio

    2009-01-01

    Em abril de 2008 foram recebidas folhas de Ruscus sp. originárias de plantios localizados na região de Santo Antonio de Posse SP com sintomas de manchas arredondadas, com 5 a 8 mm de diâmetro, de coloração marrom escura, com centro necrótico e circundadas por halo clorótico. Dos isolamentos realizados, foram obtidas colônias bacterianas de cor creme, de crescimento lento, com células Gram-negativas, oxidativas e não fluorescentes. Inoculações artificiais em Ruscus sp. reproduziram os sintomas...

  10. Characterization of acetonitrile-tolerant marine bacterium Exiguobacterium sp. SBH81 and its tolerance mechanism.

    Science.gov (United States)

    Kongpol, Ajiraporn; Kato, Junichi; Tajima, Takahisa; Vangnai, Alisa S

    2012-01-01

    A Gram-positive marine bacterium, Exiguobacterium sp. SBH81, was isolated as a hydrophilic organic-solvent tolerant bacterium, and exhibited high tolerance to various types of toxic hydrophilic organic solvents, including acetonitrile, at relatively high concentrations (up to 6% [v/v]) under the growing conditions. Investigation of its tolerance mechanisms illustrated that it does not rely on solvent inactivation processes or modification of cell surface characteristics, but rather, increase of the cell size lowers solvent partitioning into cells and the extrusion of solvents through the efflux system. A test using efflux pump inhibitors suggested that secondary transporters, i.e. resistance nodulation cell division (RND) and the multidrug and toxic compound extrusion (MATE) family, are involved in acetonitrile tolerance in this strain. In addition, its acetonitrile tolerance ability could be stably and significantly enhanced by repetitive growth in the presence of toxic acetonitrile. The marked acetonitrile tolerance of Exiguobacterium sp. SBH81 indicates its potential use as a host for biotechnological fermentation processes as well as bioremediation.

  11. Optimization of olive oil hydrolysis process using immobilized Lipase from Burkholderia cepacia sp. in Polyurethane

    Directory of Open Access Journals (Sweden)

    Nádia Ligianara Dewes Nyari

    2017-09-01

    Full Text Available The aim of this study was to achieve the best conditions for the  olive oil hydrolysis process at optimal pH and temperature using Burkholderia cepacia lipase immobilized in situ in rigid polyurethane support. The influences of the temperature (13.85 to 56.5ºC and pH (4.18 to 9.82 were evaluated by a central composite rotational experimental design 22. The operational stability and storage conditions were also studied. The olive oil hydrolysis process was optimized in pH 7.0, at 40°C and 15 min of reaction, with 66 and 93 U g-1 of hydrolysis activity in free and immobilized lipase, respectively, with > 700% yield. The immobilized remained stable for up to 40 days of storage at temperatures of 60oC, and for 100 days from 4 to 25°C. The operational stability of the immobilized was 6 continuous cycles. In this way, immobilization showed to be a promising alternative for its application in olive oil hydrolysis, having storage stability and reuse capability.

  12. Isolation and Characterization of a Novel Electrogenic Bacterium, Dietzia sp. RNV-4.

    Directory of Open Access Journals (Sweden)

    Natalia J Sacco

    Full Text Available Electrogenic bacteria are organisms that can transfer electrons to extracellular electron acceptors and have the potential to be used in devices such as bioelectrochemical systems (BES. In this study, Dietzia sp. RNV-4 bacterium has been isolated and identified based on its biochemical, physiological and morphological characteristics, as well as by its 16S rRNA sequence analysis. Furthermore, the current density production and electron transfer mechanisms were investigated using bioelectrochemical methods. The chronoamperometric data showed that the biofilm of Dietzia sp. RNV-4 grew as the current increased with time, reaching a maximum of 176.6 ± 66.1 mA/m2 at the end of the experiment (7 d; this highly suggests that the current was generated by the biofilm. The main electron transfer mechanism, indicated by the cyclic voltammograms, was due to secreted redox mediators. By high performance liquid chromatography, canthaxanthin was identified as the main compound involved in charge transfer between the bacteria and the solid electrodes. Dietzia sp. RNV-4 was used as biological material in a microbial fuel cell (MFC and the current density production was 299.4 ± 40.2 mA/m2. This is the first time that Dietzia sp. RNV-4 has been electrochemically characterized and identified as a new electrogenic strain.

  13. Genome Sequence of the Plant Growth Promoting Endophytic Bacterium Enterobacter sp. 638

    Energy Technology Data Exchange (ETDEWEB)

    Taghavi, S.; van der Lelie, D.; Hoffman, A.; Zhang, Y.-B.; Walla, M. D.; Vangronsveld, J.; Newman, L.; Monchy, S.

    2010-05-13

    Enterobacter sp. 638 is an endophytic plant growth promoting gamma-proteobacterium that was isolated from the stem of poplar (Populus trichocarpa x deltoides cv. H11-11), a potentially important biofuel feed stock plant. The Enterobacter sp. 638 genome sequence reveals the presence of a 4,518,712 bp chromosome and a 157,749 bp plasmid (pENT638-1). Genome annotation and comparative genomics allowed the identification of an extended set of genes specific to the plant niche adaptation of this bacterium. This includes genes that code for putative proteins involved in survival in the rhizosphere (to cope with oxidative stress or uptake of nutrients released by plant roots), root adhesion (pili, adhesion, hemagglutinin, cellulose biosynthesis), colonization/establishment inside the plant (chemiotaxis, flagella, cellobiose phosphorylase), plant protection against fungal and bacterial infections (siderophore production and synthesis of the antimicrobial compounds 4-hydroxybenzoate and 2-phenylethanol), and improved poplar growth and development through the production of the phytohormones indole acetic acid, acetoin, and 2,3-butanediol. Metabolite analysis confirmed by quantitative RT-PCR showed that, the production of acetoin and 2,3-butanediol is induced by the presence of sucrose in the growth medium. Interestingly, both the genetic determinants required for sucrose metabolism and the synthesis of acetoin and 2,3-butanediol are clustered on a genomic island. These findings point to a close interaction between Enterobacter sp. 638 and its poplar host, where the availability of sucrose, a major plant sugar, affects the synthesis of plant growth promoting phytohormones by the endophytic bacterium. The availability of the genome sequence, combined with metabolome and transcriptome analysis, will provide a better understanding of the synergistic interactions between poplar and its growth promoting endophyte Enterobacter sp. 638. This information can be further exploited to

  14. [Isolation, identification and characterization of a microcystin-degrading bacterium Paucibacter sp. strain CH].

    Science.gov (United States)

    You, Di-Jie; Chen, Xiao-Guo; Xiang, Hui-Yi; Ouyang, Liao; Yang, Bing

    2014-01-01

    A bacterium capable of degrading microcystin (MC), strain CH, was isolated from the sediment of Lake Chaohu, China. Strain CH was tentatively identified as Paucibacter sp. based on the analysis of 16S rRNA gene sequences. Paucibacter sp. strain CH can use microcystin LR (MCLR) as the sole carbon and energy sources, and 11.6 microg x mL(-1) of MCLR was degraded to below the detection limit within 10 hours with the first-order reaction rate constant of 0.242 h(-1). The optimum temperature and initial pH for MC degradation were 25-30 degrees C and pH 6-9, respectively. A novel intermediate product containing the Adda residue was detected during the degradation of MCLR, which is different from those produced by strain ACM-3962, and Adda was recognized as the final product of the degradation process. Furthermore, no homologue to any of the four genes, mlrA, mlrB, mlrC and mlrD previously associated with the degradation of MCLR by strain ACM-3962 was found in strain CH. These findings suggest that Paucibacter sp. strain CH mighe degrade MC through a different pathway from that of strain ACM-3962.

  15. Nesterenkonia sp. strain F, a halophilic bacterium producing acetone, butanol, and ethanol under aerobic conditions.

    Science.gov (United States)

    Amiri, Hamid; Azarbaijani, Reza; Parsa Yeganeh, Laleh; Shahzadeh Fazeli, Abolhassan; Tabatabaei, Meisam; Salekdeh, Ghasem Hosseini; Karimi, Keikhosro

    2016-01-04

    The moderately halophilic bacterium Nesterenkonia sp. strain F, which was isolated from Aran-Bidgol Lake (Iran), has the ability to produce acetone, butanol, and ethanol (ABE) as well as acetic and butyric acids under aerobic and anaerobic conditions. This result is the first report of ABE production with a wild microorganism from a family other than Clostridia and also the first halophilic species shown to produce butanol under aerobic cultivation. The cultivation of Nesterenkonia sp. strain F under anaerobic conditions with 50 g/l of glucose for 72 h resulted in the production of 105 mg/l of butanol, 122 mg/l of acetone, 0.2 g/l of acetic acid, and 2.5 g/l of butyric acid. Furthermore, the strain was cultivated on media with different glucose concentrations (20, 50, and 80 g/l) under aerobic and anaerobic conditions. Through fermentation with a 50 g/l initial glucose concentration under aerobic conditions, 66 mg/l of butanol, 125 mg/l of acetone, 291 mg/l of ethanol, 5.9 g/l of acetic acid, and 1.2 g/l of butyric acid were produced. The enzymes pertaining to the fermentation pathway in the strain were compared with the enzymes of Clostridium spp., and the metabolic pathway of fermentation used by Nesterenkonia sp. strain F was investigated.

  16. Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations

    OpenAIRE

    Bollmann, A.; Sedlacek, C.J.; Norton, J.; Laanbroek, H.J.; Suwa, Y.; Stein, L.Y.; Klotz, M.G.; Arp, D.; Sayavedra-Soto, L.; Lu, M.; Bruce, D.; Detter, C.; Tapia, R.; Han, J.; Woyke, T.

    2013-01-01

    Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production of nitrate. Nitrosomonas sp. Is79 is an ammonia oxidizer of high interest because it is adapted to low ammonium and can be found in freshwater environments around the world. The 3,783,444-bp chromos...

  17. Cellulomonas xylanilytica sp. nov., a cellulolytic and xylanolytic bacterium isolated from a decayed elm tree.

    Science.gov (United States)

    Rivas, Raúl; Trujillo, Martha E; Mateos, P F; Martínez-Molina, E; Velázquez, Encarna

    2004-03-01

    A Gram-positive, aerobic, non-motile bacterium was isolated from a decayed elm tree. Phylogenetic analysis based on 16S rDNA sequences revealed 99.0 % similarity to Cellulomonas humilata. Chemotaxonomic data that were determined for this isolate included cell-wall composition, fatty acid profiles and polar lipids; the results supported the placement of strain XIL11(T) in the genus Cellulomonas. The DNA G+C content was 73 mol%. The results of DNA-DNA hybridization with C. humilata ATCC 25174(T), in combination with chemotaxonomic and physiological data, demonstrated that isolate XIL11(T) should be classified as a novel Cellulomonas species. The name Cellulomonas xylanilytica sp. nov. is proposed, with strain XIL11(T) (=LMG 21723(T)=CECT 5729(T)) as the type strain.

  18. Exopolysaccharide of Antarctic bacterium Pseudoaltermonas sp. S-5 induces apoptosis in K562 cells.

    Science.gov (United States)

    Chen, Guochuang; Qian, Wen; Li, Jing; Xu, Yanghui; Chen, Kaoshan

    2015-05-05

    The aim of this study was to investigate the anticancer activity of exopolysaccharide (PEP) of Antarctic bacterium Pseudoaltermonas sp. S-5 and elucidate the underlying molecular mechanisms. PEP significantly inhibited the growth of human leukemia K562 cells. Results of morphological characterization showed that PEP-treated cells displayed typical morphological characteristics of apoptosis such as condensation of chromatin and formation of apoptotic bodies. Flow cytometry analyses and colorimetric assay demonstrated that PEP induced collapse of mitochondrial membrane potential and activation of caspase-9, which indicated that intrinsic apoptotic signaling pathway was involved in apoptosis induced by PEP in K562 cells. Western blot analysis showed that PEP increased the ratio of Bax/Bcl-2. In addition, calcium signal might contribute to the cytotoxicity of PEP against K562 cells. These findings suggest that PEP may be potentially effective drug against human leukemia. Copyright © 2014 Elsevier Ltd. All rights reserved.

  19. Proteomics of early and late cold shock stress on thermophilic bacterium, Thermus sp. GH5.

    Science.gov (United States)

    Yousefi-Nejad, Masoumeh; Manesh, Hossein Naderi-; Khajeh, Khosro

    2011-09-06

    Thermus sp. GH5 is an aerobic thermophilic bacterium with optimal growth at 70-75°C isolated from a hot spring in Ardabil, North West province of Iran. Due to industrial and biotechnological applications of thermophils, it is very important to know more about their proteomes and metabolomes. Since thermophils live in stressful environments it will be very useful to study their survival mechanisms. There are many reports on stress induced proteins, particularly the well characterized heat shock proteins, but little is known about the functions of proteins induced after a decrease in temperature. In this study, the proteomes of the thermophilic bacterium after a temperature down shift from 75°C to 45°C for 2h and 5h were investigated. We also compared protein profiles of early and late cold shock processes to that of cells grown at 75°C and identified a set of proteins, some of which are involved in metabolic processes such as fatty acid synthesis, pentose phosphate pathway, aromatic component degradation and signal transduction. Our data showed this organism could be tolerating the stress conditions by changing its metabolism and physiology. Copyright © 2011 Elsevier B.V. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    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.

  1. Global microarray analysis of carbohydrate use in alkaliphilic hemicellulolytic bacterium Bacillus sp. N16-5.

    Science.gov (United States)

    Song, Yajian; Xue, Yanfen; Ma, Yanhe

    2013-01-01

    The alkaliphilic hemicellulolytic bacterium Bacillus sp. N16-5 has a broad substrate spectrum and exhibits the capacity to utilize complex carbohydrates such as galactomannan, xylan, and pectin. In the monosaccharide mixture, sequential utilization by Bacillus sp. N16-5 was observed. Glucose appeared to be its preferential monosaccharide, followed by fructose, mannose, arabinose, xylose, and galactose. Global transcription profiles of the strain were determined separately for growth on six monosaccharides (glucose, fructose, mannose, galactose, arabinose, and xylose) and four polysaccharides (galactomannan, xylan, pectin, and sodium carboxymethylcellulose) using one-color microarrays. Numerous genes potentially related to polysaccharide degradation, sugar transport, and monosaccharide metabolism were found to respond to a specific substrate. Putative gene clusters for different carbohydrates were identified according to transcriptional patterns and genome annotation. Identification and analysis of these gene clusters contributed to pathway reconstruction for carbohydrate utilization in Bacillus sp. N16-5. Several genes encoding putative sugar transporters were highly expressed during growth on specific sugars, suggesting their functional roles. Two phosphoenolpyruvate-dependent phosphotransferase systems were identified as candidate transporters for mannose and fructose, and a major facilitator superfamily transporter was identified as a candidate transporter for arabinose and xylose. Five carbohydrate uptake transporter 1 family ATP-binding cassette transporters were predicted to participate in the uptake of hemicellulose and pectin degradation products. Collectively, microarray data improved the pathway reconstruction involved in carbohydrate utilization of Bacillus sp. N16-5 and revealed that the organism precisely regulates gene transcription in response to fluctuations in energy resources.

  2. Global microarray analysis of carbohydrate use in alkaliphilic hemicellulolytic bacterium Bacillus sp. N16-5.

    Directory of Open Access Journals (Sweden)

    Yajian Song

    Full Text Available The alkaliphilic hemicellulolytic bacterium Bacillus sp. N16-5 has a broad substrate spectrum and exhibits the capacity to utilize complex carbohydrates such as galactomannan, xylan, and pectin. In the monosaccharide mixture, sequential utilization by Bacillus sp. N16-5 was observed. Glucose appeared to be its preferential monosaccharide, followed by fructose, mannose, arabinose, xylose, and galactose. Global transcription profiles of the strain were determined separately for growth on six monosaccharides (glucose, fructose, mannose, galactose, arabinose, and xylose and four polysaccharides (galactomannan, xylan, pectin, and sodium carboxymethylcellulose using one-color microarrays. Numerous genes potentially related to polysaccharide degradation, sugar transport, and monosaccharide metabolism were found to respond to a specific substrate. Putative gene clusters for different carbohydrates were identified according to transcriptional patterns and genome annotation. Identification and analysis of these gene clusters contributed to pathway reconstruction for carbohydrate utilization in Bacillus sp. N16-5. Several genes encoding putative sugar transporters were highly expressed during growth on specific sugars, suggesting their functional roles. Two phosphoenolpyruvate-dependent phosphotransferase systems were identified as candidate transporters for mannose and fructose, and a major facilitator superfamily transporter was identified as a candidate transporter for arabinose and xylose. Five carbohydrate uptake transporter 1 family ATP-binding cassette transporters were predicted to participate in the uptake of hemicellulose and pectin degradation products. Collectively, microarray data improved the pathway reconstruction involved in carbohydrate utilization of Bacillus sp. N16-5 and revealed that the organism precisely regulates gene transcription in response to fluctuations in energy resources.

  3. Draft Genome Sequence of Enterobacter sp. Sa187, an Endophytic Bacterium Isolated from the Desert Plant Indigofera argentea

    KAUST Repository

    Lafi, Feras Fawzi

    2017-02-17

    Enterobacter sp. Sa187 is a plant endophytic bacterium, isolated from root nodules of the desert plant Indigofera argentea, collected from the Jizan region of Saudi Arabia. Here, we report the genome sequence of Sa187, highlighting several genes involved in plant growth–promoting activity and environmental adaption.

  4. Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations

    NARCIS (Netherlands)

    Bollmann, A.; Sedlacek, C.J.; Norton, J.; Laanbroek, H.J.; Suwa, Y.; Stein, L.Y.; Klotz, M.G.; Arp, D.; Sayavedra-Soto, L.; Lu, M.; Bruce, D.; Detter, C.; Tapia, R.; Han, J.; Woyke, T.; Lucas, S.; Pitluck, S.; Pennacchio, L.; Nolan, M.; Land, M.L.; Huntemann, M.; Deshpande, S.; Han, C.; Chen, A.; Kyrpides, N.; Mavromatis, K.; Markowitz, V.; Szeto, E.; Ivanova, N.; Mikhailova, N.; Pagani, I.; Pati, A.; Peters, L.; Ovchinnikova, G.; Goodwin, L.

    2013-01-01

    Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production

  5. Draft Genome Sequence of Chryseobacterium sp. Strain GSE06, a Biocontrol Endophytic Bacterium Isolated from Cucumber (Cucumis sativus)

    Science.gov (United States)

    Jeong, Jin-Ju; Park, Byeong Hyeok; Park, Hongjae

    2016-01-01

    Chryseobacterium sp. strain GSE06 is a biocontrol endophytic bacterium against the destructive soilborne oomycete Phytophthora capsici, which causes Phytophthora blight of pepper. Here, we present its draft genome sequence, which contains genes related to biocontrol traits, such as colonization, antimicrobial activity, plant growth promotion, and abiotic or biotic stress adaptation. PMID:27313310

  6. Development of vaccines against burkholderia pseudomallei

    National Research Council Canada - National Science Library

    Patel, Natasha; Conejero, Laura; De Reynal, Melanie; Easton, Anna; Bancroft, Gregory J; Titball, Richard W

    2011-01-01

    Burkholderia pseudomallei is a Gram-negative bacterium which is the causative agent of melioidosis, a disease which carries a high mortality and morbidity rate in endemic areas of South East Asia and Northern Australia...

  7. Propionate-Degrading Bacterium, Syntrophobacter wolinii sp. nov. gen. nov., from Methanogenic Ecosystems

    Science.gov (United States)

    Boone, David R.; Bryant, Marvin P.

    1980-01-01

    A new genus and species of a nonmotile gram-negative rod, Syntrophobacter wolinii, is the first bacterium described which degrades propionate only in coculture with an H2-using organism and in the absence of light or exogenous electron acceptors such as O2, sulfate, or nitrate. It was isolated from methanogenic enrichments from an anaerobic municipal sewage digestor, using anaerobic roll tubes containing a medium with propionate as the energy source in association with an H2-using, sulfate-reducing Desulfovibrio sp. which cannot utilize fatty acids other than formate. S. wolinii produced acetate and, presumably, CO2 and H2 (or formate) from propionate. In media without sulfate and with Methanospirillum hungatei, a methanogen that uses only H2-CO2 or formate as an energy source, acetate, methane, and, presumably, CO2 were produced from propionate and only small amounts of Desulfovibrio sp. were present. Isolation in coculture with the methanogen was not successful. S. wolinii does not use other saturated fatty acids as energy sources. Images PMID:16345640

  8. Novel Acetone Metabolism in a Propane-Utilizing Bacterium, Gordonia sp. Strain TY-5▿

    Science.gov (United States)

    Kotani, Tetsuya; Yurimoto, Hiroya; Kato, Nobuo; Sakai, Yasuyoshi

    2007-01-01

    In the propane-utilizing bacterium Gordonia sp. strain TY-5, propane was shown to be oxidized to 2-propanol and then further oxidized to acetone. In this study, the subsequent metabolism of acetone was studied. Acetone-induced proteins were found in extracts of cells induced by acetone, and a gene cluster designated acmAB was cloned on the basis of the N-terminal amino acid sequences of acetone-induced proteins. The acmA and acmB genes encode a Baeyer-Villiger monooxygenase (BVMO) and esterase, respectively. The BVMO encoded by acmA was purified from acetone-induced cells of Gordonia sp. strain TY-5 and characterized. The BVMO exhibited NADPH-dependent oxidation activity for linear ketones (C3 to C10) and cyclic ketones (C4 to C8). Escherichia coli expressing the acmA gene oxidized acetone to methyl acetate, and E. coli expressing the acmB gene hydrolyzed methyl acetate. Northern blot analyses revealed that polycistronic transcription of the acmAB gene cluster was induced by propane, 2-propanol, and acetone. These results indicate that the acmAB gene products play an important role in the metabolism of acetone derived from propane oxidation and clarify the propane metabolism pathway of strain TY-5 (propane → 2-propanol → acetone → methyl acetate → acetic acid + methanol). This paper provides the first evidence for BVMO-dependent acetone metabolism. PMID:17071761

  9. The complete genome sequence of the plant growth-promoting bacterium Pseudomonas sp. UW4.

    Directory of Open Access Journals (Sweden)

    Jin Duan

    Full Text Available The plant growth-promoting bacterium (PGPB Pseudomonas sp. UW4, previously isolated from the rhizosphere of common reeds growing on the campus of the University of Waterloo, promotes plant growth in the presence of different environmental stresses, such as flooding, high concentrations of salt, cold, heavy metals, drought and phytopathogens. In this work, the genome sequence of UW4 was obtained by pyrosequencing and the gaps between the contigs were closed by directed PCR. The P. sp. UW4 genome contains a single circular chromosome that is 6,183,388 bp with a 60.05% G+C content. The bacterial genome contains 5,423 predicted protein-coding sequences that occupy 87.2% of the genome. Nineteen genomic islands (GIs were predicted and thirty one complete putative insertion sequences were identified. Genes potentially involved in plant growth promotion such as indole-3-acetic acid (IAA biosynthesis, trehalose production, siderophore production, acetoin synthesis, and phosphate solubilization were determined. Moreover, genes that contribute to the environmental fitness of UW4 were also observed including genes responsible for heavy metal resistance such as nickel, copper, cadmium, zinc, molybdate, cobalt, arsenate, and chromate. Whole-genome comparison with other completely sequenced Pseudomonas strains and phylogeny of four concatenated "housekeeping" genes (16S rRNA, gyrB, rpoB and rpoD of 128 Pseudomonas strains revealed that UW4 belongs to the fluorescens group, jessenii subgroup.

  10. Novel alginate lyases from marine bacterium Alteromonas sp. strain H-4.

    Science.gov (United States)

    Sawabe, T; Ohtsuka, M; Ezura, Y

    1997-10-28

    A bacterium Alteromonas sp. strain H-4 isolated from Laminaria fronds produced extra- and intra-cellular alginate lyases and utilized alginate as its sole carbon source. An extracellular alginate lyase was purified from the culture supernatant of the strain and its substrate specificity was characterized. The estimated molecular mass of the enzyme was 32 kDa and the isoelectric point was 4.7. Both polyM and polyG block degrading activities were observed using the substrate-containing gel overlay technique after isoelectric focusing of the enzyme. By analyzing the reaction products from the polyM block, polyG block, MG random block and intact alginate, three major peaks containing unsaturated tri-uronide through octa-uronide were detected for each substrate. The results indicate that the enzyme of Alteromonas sp. H-4 can degrade both polyM and polyG blocks with a K(m) in mg/mL 20-times higher for the polyM block.

  11. Rapid Aggregation of Biofuel-Producing Algae by the Bacterium Bacillus sp. Strain RP1137

    Science.gov (United States)

    Powell, Ryan J.

    2013-01-01

    Algal biofuels represent one of the most promising means of sustainably replacing liquid fuels. However, significant challenges remain before alga-based fuels become competitive with fossil fuels. One of the largest challenges is the ability to harvest the algae in an economical and low-energy manner. In this article, we describe the isolation of a bacterial strain, Bacillus sp. strain RP1137, which can rapidly aggregate several algae that are candidates for biofuel production, including a Nannochloropsis sp. This bacterium aggregates algae in a pH-dependent and reversible manner and retains its aggregation ability after paraformaldehyde fixation, opening the possibility for reuse of the cells. The optimal ratio of bacteria to algae is described, as is the robustness of aggregation at different salinities and temperatures. Aggregation is dependent on the presence of calcium or magnesium ions. The efficiency of aggregation of Nannochloropsis oceanica IMET1 is between 70 and 95% and is comparable to that obtained by other means of harvest; however, the rate of harvest is fast, with aggregates forming in 30 s. PMID:23892750

  12. Evaluation of dna extraction methods of the Salmonella sp. bacterium in artificially infected chickens eggs

    Directory of Open Access Journals (Sweden)

    Ana Cristina dos Reis Ferreira

    2015-06-01

    Full Text Available ABSTRACT. Ferreira A.C.dosR. & dos Santos B.M. [Evaluation of dna extraction methods of the Salmonella sp. bacterium in artificially infected chickens eggs.] Avaliação de três métodos de extração de DNA de Salmonella sp. em ovos de galinhas contaminados artificialmente. Revista Brasileira de Medicina Veterinária, 37(2:115-119, 2015. Departamento de Veterinária, Universidade Federal de Viçosa, Campus Universitário, Av. Peter Henry Rolfs, s/n, Viçosa, MG 36571-000, Brasil. E-mail: bmsantos@ufv.br The present study evaluated the efficiency of different protocols for the genomic DNA extraction of Salmonella bacteria in chicken eggs free of specific pathogens – SPF. Seventy-five eggs were used and divided into five groups with fifteen eggs each. Three of the five groups of eggs were inoculated with enteric Salmonella cultures. One of the five groups was inoculated with Escherichia coli bacterium culture. And another group of eggs was the negative control that received saline solution 0.85% infertile. The eggs were incubated on a temperature that varied from 20 to 25°C during 24, 48 and 72 hours. Five yolks of each group were collected every 24 hours. These yolks were homogenized and centrifuged during 10 minutes. The supernatant was rejected. After the discard, PBS ph 7.2 was added and centrifuged again. The sediment obtained of each group was used for the extraction of bacterial genomic DNA. Silica particles and a commercial kit were utilized as the extraction methods. The extracted DNA was kept on a temperature of 20°C until the evaluation through PCR. The primers utilized were related with the invA gene and they were the following: 5’ GTA AAA TTA TCG CCA CGT TCG GGC AA 3’ and 5’ TCA TCG CAC CGT CAA AGG AAC C 3’. The amplification products were visualized in transilluminator with ultraviolet light. The obtained results through the bacterial DNA extractions demonstrated that the extraction method utilizing silica particles was

  13. Increased hyphal branching and growth of ectomycorrhizal fungus Lactarius rufus by the helper bacterium Paenibacillus sp.

    Science.gov (United States)

    Aspray, T J; Jones, E E; Davies, M W; Shipman, M; Bending, G D

    2013-07-01

    Paenibacillus sp. EJP73 has been previously demonstrated as a mycorrhization helper bacterium (MHB) for the Lactarius rufus-Pinus sylvestris symbiosis in both laboratory and glasshouse experiments. In the present study, the effect of Paenibacillus sp. EJP73 metabolites on L. rufus EO3 pre-symbiotic growth was tested in two agar plate-based systems. Specifically, volatile metabolites were investigated using a dual plate system, in which the presence of strain EJP73 resulted in a significant negative effect on L. rufus EO3 hyphal radial growth but enhanced hyphal branching and reduced internode distance. Soluble metabolites produced by strain EJP73 were tested on L. rufus EO3 growth in single-agar plate assays by incorporating bacterial cell-free whole or molecular weight fraction spent broth into the agar. Whole spent broth had a negative effect on hyphal growth, whereas a low molecular weight fraction (100-1,000) promoted colony radial growth. Headspace and spent broth analysis of strain EJP73 cultures revealed 2,5-diisopropylpyrazine to be the most significant component. Synthesised 2,5-diisopropylpyrazine and elevated CO2 (2,000 ppm) were tested as specific volatile metabolites in the dual plate system, but neither produced the response shown when strain EJP73 was present. Increased pre-symbiotic hyphal branching leading to increased likelihood of plant infection may be an important MHB mechanism for strain EJP73. Although the precise signal molecules could not be identified, the work suggests a number of metabolites may work synergistically to increase L. rufus root colonisation.

  14. Colwellia polaris sp. nov., a psychrotolerant bacterium isolated from Arctic sea ice.

    Science.gov (United States)

    Zhang, De-Chao; Yu, Yong; Xin, Yu-Hua; Liu, Hong-Can; Zhou, Pei-Jin; Zhou, Yu-Guang

    2008-08-01

    A novel psychrotolerant, Gram-negative, aerobic bacterium, designated strain 537T, was isolated from sea-ice samples from the Arctic. Strain 537T was able to grow at 4-26 degrees C, with optimum growth occurring at 20-21 degrees C. Strain 537T had Q-8 as the major respiratory quinone and contained iso-C15:0 2-OH and/or C16:1 omega7c (22.95 %), C15:1 (17.64 %) and C17:1 omega8c (13.74 %) as the predominant cellular fatty acids. The genomic DNA G+C content was 38.9 mol%. A phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 537T formed a coherent cluster within the genus Colwellia. The highest level of 16S rRNA gene sequence similarity (97.5 %) exhibited by strain 537T was obtained with respect to the type strain of Colwellia aestuarii. On the basis of phenotypic, chemotaxonomic and phylogenetic properties and DNA-DNA relatedness data, strain 537T represents a novel species of the genus Colwellia, for which the name Colwellia polaris sp. nov. is proposed. The type strain is 537T (=CGMCC 1.6132T =JCM 13952T).

  15. Cellulomonas composti sp. nov., a cellulolytic bacterium isolated from cattle farm compost.

    Science.gov (United States)

    Kang, Myung-Suk; Im, Wan-Taek; Jung, Hae-Min; Kim, Myung Kyum; Goodfellow, Michael; Kim, Kwang Kyu; Yang, Hee-Chan; An, Dong-Shan; Lee, Sung-Taik

    2007-06-01

    A bacterial strain, TR7-06(T), which has cellulase and beta-glucosidase activities, was isolated from compost at a cattle farm near Daejeon, Republic of Korea. It was a Gram-positive, aerobic or facultatively anaerobic, non-motile, rod-shaped bacterium. Phylogenetic analysis based on 16S rRNA gene sequences showed that this strain belongs to the genus Cellulomonas, with highest sequence similarity to Cellulomonas uda DSM 20107(T) (98.5 %). Cell wall analysis revealed the presence of type A4beta, L-orn-D-Glu peptidoglycan. The cell-wall sugars detected were mannose and glucose. The predominant menaquinone was MK-9(H(4)); MK-8(H(4)) was detected in smaller quantities. The major fatty acids were anteiso-C(15 : 0), C(16 : 0), C(14 : 0) and C(18 : 0). The polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The results of DNA-DNA hybridization and physiological and biochemical tests clearly demonstrated that TR7-06(T) represents a novel species. The combined genotypic and phenotypic data show that strain TR7-06(T) (=KCTC 19030(T)=NBRC 100758(T)) merits description as the type strain of a novel Cellulomonas species, Cellulomonas composti sp. nov.

  16. Pectinatus brassicae sp. nov., a Gram-negative, anaerobic bacterium isolated from salty wastewater.

    Science.gov (United States)

    Zhang, Wen-wu; Fang, Ming-xu; Tan, Hai-qin; Zhang, Xin-qi; Wu, Min; Zhu, Xu-fen

    2012-09-01

    A novel Gram-negative, non-spore-forming, strictly anaerobic, heterotrophic bacterium, strain TY(T), was isolated from salty pickle wastewater. Cells were rod-shaped with comb-like flagella, slightly curved and very variable in length. Optimal growth occurred at 28 °C and pH 6.5. Cells were resistant to up to 50 g NaCl l(-1). Strain TY(T) produced acid from glycerol, sucrose, glucose, fructose and mannitol. The main fermentation products from glucose were acetic and propionic acids. Tests for acid phosphatase and naphthol-AS-BI-phosphohydrolase activities were positive. The major fatty acids were C(14 : 0) DMA (18.7 %), C(15 : 0) (15.4 %), anteiso-C(18 : 1) (15.2 %), C(11 : 0) (13.3 %) and summed feature 5 (C(17 : 1)ω7c and/or C(17 : 2)) (11.0 %). The DNA G+C content was 35.9 mol%. 16S rRNA gene sequence-based phylogenetic analysis indicated that strain TY(T) represented a novel species of the genus Pectinatus (sequence similarity to other members of the genus ranged from 93.2 to 94.8 %). Based on its phenotypic, genotypic and phylogenetic characteristics, strain TY(T) is proposed to represent a novel species, named Pectinatus brassicae sp. nov. (type strain TY(T) = JCM 17499(T) = DSM 24661(T)).

  17. Sulfuriflexusmobilis gen. nov., sp. nov., a sulfur-oxidizing bacterium isolated from a brackish lake sediment.

    Science.gov (United States)

    Kojima, Hisaya; Fukui, Manabu

    2016-09-01

    A chemolithotrophic sulfur-oxidizing bacterium, strain aks1T, was isolated from sediment of a brackish lake in Japan. The cells were curved rod-shaped and Gram-stain-negative. The G+C content of the genomic DNA was 53 mol%. The major components in the cellular fatty acid profile were C16 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). As electron donor for chemolithoautotrophic growth, strain aks1T oxidized thiosulfate, sulfide, and elemental sulfur. The strain could utilize oxygen and nitrate as an electron acceptor for thiosulfate oxidation. Growth was observed at a temperature range of 5-34 °C, with optimum growth at 30-32 °C. Growth of the strain was observed at a pH range of 6.4-8.7. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain is related to members of the family Granulosicoccaceae within the order Chromatiales, with sequence similarities around 92 %. On the basis of phylogenetic and phenotypic properties, strain aks1T represents a novel species of a new genus, for which the name Sulfuriflexus mobilis gen. nov., sp. nov. is proposed. The type strain of the type species is aks1T (=DSM 102939T=NBRC 111889T).

  18. Methylobacterium soli sp. nov. a methanol-utilizing bacterium isolated from the forest soil.

    Science.gov (United States)

    Cao, Yan-Ru; Wang, Qian; Jin, Rong-Xian; Tang, Shu-Kun; Jiang, Yi; He, Wen-Xiang; Lai, Hang-Xian; Xu, Li-Hua; Jiang, Cheng-Lin

    2011-03-01

    A Gram-negative, pink-pigmented, non-spore-forming rod shaped, methanol-utilizing bacterium, strain YIM 48816(T), was isolated from forest soil collected from Sichuan province, China. Strain YIM 48816(T) can grow at 4-37 °C, pH 5.0-7.0 and 0% NaCl (w/v). Based on 16S rRNA gene sequence similarity studies, it belonged to the genus Methylobacterium, and formed a phyletic line. The 16S rRNA gene sequence similarities were 96.2% to Methylobacterium mesophilicum DSM 1708(T) and 96.0% to Methylobacterium brachiatum DSM 19569(T), and the phylogenetic similarities to all other Methylobacterium species with validly published names were less than 96.0%. The major menaquinones detected were Q-10 (97.14%) and Q-9 (2.86%). The major fatty acids were C18:1 ω7c (80.84%). The DNA G + C content was 66.2 mol%. It is apparent from the genotypic and phenotypic data that strain YIM 48816(T) belongs to a novel species of the genus Methylobacterium, for which the name Methylobacterium soli sp. nov. is proposed. The type strain is YIM 48816(T) (CCTCC AA 208027(T) = KCTC 22810(T)).

  19. Bacillus notoginsengisoli sp. nov., a novel bacterium isolated from the rhizosphere of Panax notoginseng.

    Science.gov (United States)

    Zhang, Meng-Yue; Cheng, Juan; Cai, Ying; Zhang, Tian-Yuan; Wu, Ying-Ying; Manikprabhu, Deene; Li, Wen-Jun; Zhang, Yi-Xuan

    2017-08-01

    A Gram-stain-positive, rod-shaped, motile bacterium designated as SYP-B691T was isolated from rhizospheric soil of Panax notoginseng. Phylogenetic analysis indicated that SYP-B691T clearly represented a member of the genus Bacillus and showed 16S rRNA gene similarity lower than 97.0 % with the type strains of species of the genus Bacillus, which indicates that it should be considered as a candidate novel species within this genus. The optimum growth of the strain was found to occur at 37 °C and pH 7.0-9.0. The genomic DNA G+C content was determined to be 45.2 mol%. It contained meso-2,6-diaminopimelic acid in the cell-wall peptidoglycan. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unknown phospholipid. MK-7 was the only menaquinone identified. The major cellular fatty acids of SYP-B691T were identified as iso-C15 : 0 and anteiso-C15 : 0. On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics, SYP-B691T merits recognition as a representative of a novel species of the genus Bacillus, for which the name Bacillus notoginsengisoli sp. nov. is proposed, with SYP-B691T(=DSM 29196T=JCM 30743T) as the type strain.

  20. Sphingomonas psychrolutea sp. nov., a psychrotolerant bacterium isolated from glacier ice.

    Science.gov (United States)

    Liu, Qing; Liu, Hong-Can; Zhang, Jian-Li; Zhou, Yu-Guang; Xin, Yu-Hua

    2015-09-01

    A Gram-stain-negative, rod-shaped, orange bacterium (strain MDB1-A(T)) was isolated from ice samples collected from Midui glacier in Tibet, south-west China. Cells were aerobic and psychrotolerant (growth occurred at 0-25 °C). Phylogenetic analysis based on 16S rRNA gene sequences showed that it was a member of the genus Sphingomonas, with its closest relative being Sphingomonas glacialis C16y(T) (98.9% similarity). Q-10 was the predominant ubiquinone. C17 : 1ω6c and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) were the major cellular fatty acids. The predominant polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and sphingoglycolipid. The polyamines detected were sym-homospermidine, spermidine and spermine. The G+C content of the genomic DNA was 63.6%. Based on data from this polyphasic analysis, strain MDB1-A(T) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas psychrolutea sp. nov. is proposed. The type strain is MDB1-A(T) ( = CGMCC 1.10106(T) = NBRC 109639(T)).

  1. Exopolysaccharides play a role in the swarming of the benthic bacterium Pseudoalteromonas sp. SM9913

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    Ang eLiu

    2016-04-01

    Full Text Available Most marine bacteria secrete exopolysaccharide (EPS, which is important for bacterial survival in the marine environment. However, it is still unclear whether the self-secreted EPS is involved in marine bacterial motility. Here we studied the role of EPS in the lateral flagella-driven swarming motility of benthic bacterium Pseudoalteromonas sp. SM9913 (SM9913 by a comparison of wild SM9913 and ΔepsT, an EPS synthesis defective mutant. Reduction of EPS production in ΔepsT did not affect the growth rate or the swimming motility, but significantly decreased the swarming motility on a swarming plate, suggesting that the EPS may play a role in SM9913 swarming. However, the expression and assembly of lateral flagella in ΔepsT were not affected. Instead, ΔepsT had a different swarming behavior from wild SM9913. The swarming of ΔepsT did not have an obvious rapid swarming period, and its rate became much lower than that of wild SM9913 after 35 h incubation. An addition of surfactin or SM9913 EPS on the surface of the swarming plate could rescue the swarming level. These results indicate that the self-secreted EPS is required for the swarming of SM9913. This study widens our understanding of the function of the EPS of benthic bacteria.

  2. Clostridium amazonense sp. nov. an obliqately anaerobic bacterium isolated from a remote Amazonian community in Peru.

    Science.gov (United States)

    O'Neal, Lindsey; Obregón-Tito, Alexandra J; Tito, Raul Y; Ozga, Andrew T; Polo, Susan I; Lewis, Cecil M; Lawson, Paul A

    2015-10-01

    A strictly anaerobic Gram-stain positive, spore-forming, rod-shaped bacterium designated NE08V(T), was isolated from a fecal sample of an individual residing in a remote Amazonian community in Peru. Phylogenetic analysis based on the 16S rRNA gene sequence showed the organism belonged to the genus Clostridium and is most closely related to Clostridium vulturis (97.4% sequence similarity) and was further characterized using biochemical and chemotaxonomic methods. The major cellular fatty acids were anteiso C13:0 and C16:0 with a genomic DNA G + C content of 31.6 mol%. Fermentation products during growth with PYG were acetate and butyrate. Based on phylogenetic, phenotypic and chemotaxonomic information, strain NE08V was identified as representing a novel species of the genus Clostridium, for which the name Clostridium amazonense sp. nov. is proposed. The type strain is NE08V(T) (DSM 23598(T) = CCUG 59712(T)). Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Desulfovibrio alkalitolerans sp. nov., a novel alkalitolerant, sulphate-reducing bacterium isolated from district heating water.

    Science.gov (United States)

    Abildgaard, Lone; Nielsen, Marie Bank; Kjeldsen, Kasper Urup; Ingvorsen, Kjeld

    2006-05-01

    A novel alkalitolerant, sulphate-reducing bacterium (strain RT2T) was isolated from alkaline district heating water. Strain RT2T was a motile vibrio (0.5-0.8 microm wide and 1.4-1.9 microm long) and grew at pH 6.9-9.9 (optimum at pH 9.0-9.4) and at 16-47 degrees C (optimum at 43 degrees C). The genomic DNA G+C content was 64.7 mol%. A limited number of compounds were used as electron donors with sulphate as electron acceptor, including lactate, pyruvate, formate and hydrogen/acetate. Sulphite and thiosulphate also served as electron acceptors. Based on physiological and genotypic properties, the isolate was considered to represent a novel species of the genus Desulfovibrio, for which the name Desulfovibrio alkalitolerans sp. nov. is proposed. The type strain is RT2T (=DSM 16529T=JCM 12612T). The strain is the first alkali-tolerant member of the genus Desulfovibrio to be described.

  4. Microbacterium xylanilyticum sp. nov., a xylan-degrading bacterium isolated from a biofilm.

    Science.gov (United States)

    Kim, Kwang Kyu; Park, Hye Yoon; Park, Wooshin; Kim, In S; Lee, Sung-Taik

    2005-09-01

    A novel xylan-degrading bacterium, S3-E(T), was isolated from the biofilm of a membrane bioreactor. The cells of this strain were Gram-positive, non-motile, non-spore-forming rods, produced primary branches and formed yellow colonies on nutrient agar. The strain had chemotaxonomic markers that were consistent with classification in the genus Microbacterium, i.e. MK-12, MK-11 and MK-13 as the major menaquinones, predominant iso- and anteiso-branched cellular fatty acids, glucose and galactose as the cell-wall sugars, peptidoglycan-type B2beta with glycolyl residues and a DNA G+C content of 69.7 mol%. Phylogenetic analysis, based on 16S rRNA gene sequencing, showed that strain S3-E(T) is most similar to Microbacterium hominis IFO 15708(T) and Microbacterium foliorum DSM 12966(T) (97.6 and 97.4% sequence similarity, respectively), and that it forms a separate lineage with M. hominis in the genus Microbacterium. DNA-DNA hybridization results and phenotypic properties showed that strain S3-E(T) could be distinguished from all known Microbacterium species and represented a novel species, for which the name Microbacterium xylanilyticum sp. nov. is proposed; the type strain is S3-E(T) (=DSM 16914(T)=KCTC 19079(T)).

  5. Actinomyces haliotis sp. nov., a bacterium isolated from the gut of an abalone, Haliotis discus hannai.

    Science.gov (United States)

    Hyun, Dong-Wook; Shin, Na-Ri; Kim, Min-Soo; Kim, Pil Soo; Kim, Joon Yong; Whon, Tae Woong; Bae, Jin-Woo

    2014-02-01

    A novel, Gram-staining-positive, facultatively anaerobic, non-motile and coccus-shaped bacterium, strain WL80(T), was isolated from the gut of an abalone, Haliotis discus hannai, collected from the northern coast of Jeju in Korea. Optimal growth occurred at 30 °C, pH 7-8 and with 1% (w/v) NaCl. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that strain WL80(T) fell within the cluster of the genus Actinomyces, with highest sequence similarity to the type strains of Actinomyces radicidentis (98.8% similarity) and Actinomyces urogenitalis (97.0% similarity). The major cellular fatty acids were C18 : 1ω9c and C16 : 0. Menaquinone-10 (H4) was the major respiratory quinone. The genomic DNA G+C content of the isolate was 70.4 mol%. DNA-DNA hybridization values with closely related strains indicated less than 7.6% genomic relatedness. The results of physiological, biochemical, chemotaxonomic and genotypic analyses indicated that strain WL80(T) represents a novel species of the genus Actinomyces, for which the name Actinomyces haliotis sp. nov. is proposed. The type strain is WL80(T) ( = KACC 17211(T) = JCM 18848(T)).

  6. Tuwongella immobilis gen. nov., sp. nov., a novel non-motile bacterium within the phylum Planctomycetes.

    Science.gov (United States)

    Seeger, Christian; Butler, Margaret K; Yee, Benjamin; Mahajan, Mayank; Fuerst, John A; Andersson, Siv G E

    2017-10-31

    A gram-negative, budding, catalase negative, oxidase positive and non-motile bacterium (MBLW1(T)) with a complex endomembrane system has been isolated from a freshwater lake in southeast Queensland, Australia. Phylogeny based on 16S rRNA gene sequence analysis places the strain within the family Planctomycetaceae, related to Zavarzinella formosa (93.3 %), Telmatocola sphagniphila (93.3 %) and Gemmata obscuriglobus (91.9 %). Phenotypic and chemotaxonomic analysis demonstrates considerable differences to the type strains of the related genera. MBLW1(T) displays modest salt tolerance and grows optimally at pH values of 7.5-8.0 and at temperatures of 32-36 °C. Transmission electron microscopy analysis demonstrates the presence of a complex endomembrane system, however, without the typically condensed nucleoid structure found in related genera. The major fatty acids are 16 : 1 ω5c, 16 : 0 and 18 : 0. Based on discriminatory results from 16S rRNA gene sequence analysis, phenotypic, biochemical and chemotaxonomic analysis, MBLW1(T) should be considered as a new genus and species, for which the name Tuwongella immobilis gen. nov., sp. nov. is proposed. The type strain is MBLW1(T) (=CCUG 69661(T)=DSM 105045(T)).

  7. Characterization of the N2O-producing soil bacterium Rhizobium azooxidifex sp. nov.

    Science.gov (United States)

    Behrendt, Undine; Kämpfer, Peter; Glaeser, Stefanie P; Augustin, Jürgen; Ulrich, Andreas

    2016-06-01

    In the context of studying the bacterial community involved in nitrogen transformation processes in arable soils exposed to different extents of erosion and sedimentation in a long-term experiment (CarboZALF), a strain was isolated that reduced nitrate to nitrous oxide without formation of molecular nitrogen. The presence of the functional gene nirK, encoding the respiratory copper-containing nitrite reductase, and the absence of the nitrous oxide reductase gene nosZ indicated a truncated denitrification pathway and that this bacterium may contribute significantly to the formation of the important greenhouse gas N2O. Phylogenetic analysis based on the 16S rRNA gene sequence and the housekeeping genes recA and atpD demonstrated that the investigated soil isolate belongs to the genus Rhizobium. The closest phylogenetic neighbours were the type strains of Rhizobium. subbaraonis and Rhizobium. halophytocola. The close relationship with R. subbaraonis was reflected by similarity analysis of the recA and atpD genes and their amino acid positions. DNA-DNA hybridization studies revealed genetic differences at the species level, which were substantiated by analysis of the whole-cell fatty acid profile and several distinct physiological characteristics. Based on these results, it was concluded that the soil isolate represents a novel species of the genus Rhizobium, for which the name Rhizobium azooxidifex sp. nov. (type strain Po 20/26T=DSM 100211T=LMG 28788T) is proposed.

  8. Purification and Characterization of Catalase from Marine Bacterium Acinetobacter sp. YS0810

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    Xinhua Fu

    2014-01-01

    Full Text Available The catalase from marine bacterium Acinetobacter sp. YS0810 (YS0810CAT was purified and characterized. Consecutive steps were used to achieve the purified enzyme as follows: ethanol precipitation, DEAE Sepharose ion exchange, Superdex 200 gel filtration, and Resource Q ion exchange. The active enzyme consisted of four identical subunits of 57.256 kDa. It showed a Soret peak at 405 nm, indicating the presence of iron protoporphyrin IX. The catalase was not apparently reduced by sodium dithionite but was inhibited by 3-amino-1,2,4-triazole, hydroxylamine hydrochloride, and sodium azide. Peroxidase-like activity was not found with the substrate o-phenylenediamine. So the catalase was determined to be a monofunctional catalase. N-terminal amino acid of the catalase analysis gave the sequence SQDPKKCPVTHLTTE, which showed high degree of homology with those of known catalases from bacteria. The analysis of amino acid sequence of the purified catalase by matrix-assisted laser desorption ionization time-of-flight mass spectrometry showed that it was a new catalase, in spite of its high homology with those of known catalases from other bacteria. The catalase showed high alkali stability and thermostability.

  9. Mechanism of biosynthesis of unsaturated fatty acids in Pseudomonas sp. strain E-3, a psychrotrophic bacterium

    Energy Technology Data Exchange (ETDEWEB)

    Wada, M.; Fukunaga, N.; Sasaki, S. (Hokkaido Univ., Sapporo (Japan))

    1989-08-01

    Biosynthesis of palmitic, palmitoleic, and cis-vaccenic acids in Pseudomonas sp. strain E-3 was investigated with in vitro and in vivo systems. (1-{sup 14}C)palmitic acid was aerobically converted to palmitoleate and cis-vaccenate, and the radioactivities on their carboxyl carbons were 100 and 43%, respectively, of the total radioactivity in the fatty acids. Palmitoyl coenzyme A desaturase activity was found in the membrane fraction. (1-{sup 14}C)stearic acid was converted to octadecenoate and C16 fatty acids. The octadecenoate contained oleate and cis-vaccenate, but only oleate was produced in the presence of cerulenin. (1-{sup 14}C)lauric acid was aerobically converted to palmitate, palmitoleate, and cis-vaccenate. Under anaerobic conditions, palmitate (62%), palmitoleate (4%), and cis-vaccenate (34%) were produced from (1-{sup 14}C)acetic acid, while they amounted to 48, 39, and 14%, respectively, under aerobic conditions. In these incorporation experiments, 3 to 19% of the added radioactivity was detected in released {sup 14}CO{sub 2}, indicating that part of the added fatty acids were oxidatively decomposed. Partially purified fatty acid synthetase produced saturated and unsaturated fatty acids with chain lengths of C10 to C18. These results indicated that both aerobic and anaerobic mechanisms for the synthesis of unsaturated fatty acid are operating in this bacterium.

  10. Detection and differentiation of Burkholderia pseudomallei, Burkholderia mallei and Burkholderia thailandensis by multiplex PCR.

    Science.gov (United States)

    Lee, May-Ann; Wang, Dongling; Yap, Eu Hian

    2005-03-01

    Burkholderia pseudomallei, a Gram-negative bacterium that causes melioidosis may be differentiated from closely related species of Burkholderia mallei that causes glanders and non-pathogenic species of Burkholderia thailandensis by multiplex PCR. The multiplex PCR consists of primers that flank a 10-bp repetitive element in B. pseudomallei and B. mallei amplifying PCR fragment of varying sizes between 400-700 bp, a unique sequence in B. thailandensis amplifying a PCR fragment of 308 bp and the metalloprotease gene amplifying a PCR fragment of 245 bp in B. pseudomallei and B. thailandensis. The multiplex PCR not only can differentiate the three Burkholderia species but can also be used for epidemiological typing of B. pseudomallei and B. mallei strains.

  11. Structural characteristics of alkaline phosphatase from the moderately halophilic bacterium Halomonas sp. 593

    Energy Technology Data Exchange (ETDEWEB)

    Arai, Shigeki; Yonezawa, Yasushi [Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195 (Japan); Ishibashi, Matsujiro [Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065 (Japan); Matsumoto, Fumiko; Adachi, Motoyasu; Tamada, Taro [Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195 (Japan); Tokunaga, Hiroko [Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065 (Japan); Blaber, Michael [Florida State University, 1115 West Call Street, Tallahassee, FL 32306-4300 (United States); Tokunaga, Masao [Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065 (Japan); Kuroki, Ryota, E-mail: kuroki.ryota@jaea.go.jp [Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195 (Japan)

    2014-03-01

    In order to clarify the structural basis of the halophilic characteristics of an alkaline phosphatase derived from the moderate halophile Halomonas sp. 593 (HaAP), the tertiary structure of HaAP was determined to 2.1 Å resolution by X-ray crystallography. The structural properties of surface negative charge and core hydrophobicity were shown to be intermediate between those characteristic of halophiles and non-halophiles, and may explain the unique functional adaptation to a wide range of salt concentrations. Alkaline phosphatase (AP) from the moderate halophilic bacterium Halomonas sp. 593 (HaAP) catalyzes the hydrolysis of phosphomonoesters over a wide salt-concentration range (1–4 M NaCl). In order to clarify the structural basis of its halophilic characteristics and its wide-range adaptation to salt concentration, the tertiary structure of HaAP was determined by X-ray crystallography to 2.1 Å resolution. The unit cell of HaAP contained one dimer unit corresponding to the biological unit. The monomer structure of HaAP contains a domain comprised of an 11-stranded β-sheet core with 19 surrounding α-helices similar to those of APs from other species, and a unique ‘crown’ domain containing an extended ‘arm’ structure that participates in formation of a hydrophobic cluster at the entrance to the substrate-binding site. The HaAP structure also displays a unique distribution of negatively charged residues and hydrophobic residues in comparison to other known AP structures. AP from Vibrio sp. G15-21 (VAP; a slight halophile) has the highest similarity in sequence (70.0% identity) and structure (C{sup α} r.m.s.d. of 0.82 Å for the monomer) to HaAP. The surface of the HaAP dimer is substantially more acidic than that of the VAP dimer (144 exposed Asp/Glu residues versus 114, respectively), and thus may enable the solubility of HaAP under high-salt conditions. Conversely, the monomer unit of HaAP formed a substantially larger hydrophobic interior

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

    Science.gov (United States)

    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. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Draft Genome Sequence of a Sulfide-Oxidizing, Autotrophic Filamentous Anoxygenic Phototrophic Bacterium, Chloroflexus sp. Strain MS-G (Chloroflexi).

    Science.gov (United States)

    Thiel, Vera; Hamilton, Trinity L; Tomsho, Lynn P; Burhans, Richard; Gay, Scott E; Schuster, Stephan C; Ward, David M; Bryant, Donald A

    2014-09-04

    The draft genome sequence of the thermophilic filamentous anoxygenic phototrophic bacterium Chloroflexus sp. strain MS-G (Chloroflexi), isolated from Mushroom Spring (Yellowstone National Park, WY, USA) was sequenced and comprises 4,784,183 bp in 251 contigs. The draft genome is predicted to encode 4,059 protein coding genes, 49 tRNA encoding genes, and 3 rRNA operons. Copyright © 2014 Thiel et al.

  14. Complete Genome Sequence of Magnetospirillum sp. ME-1, a Novel Magnetotactic Bacterium Isolated from East Lake, Wuhan, China.

    Science.gov (United States)

    Ke, Linfeng; Liu, Pengming; Liu, Shan; Gao, Meiying

    2017-08-24

    A novel spiral magnetotactic bacterium, Magnetospirillum sp. ME-1, was isolated from East Lake in China. Here we report the complete genome of ME-1, which contains a 4,551,873-bp circular chromosome and a 5,222-bp circular plasmid. The magnetosome biogenesis-specific genes are located in a 97,664-bp magnetosome genomic island. Copyright © 2017 Ke et al.

  15. Syntrophaceticus schinkii gen. nov., sp. nov., an anaerobic, syntrophic acetate-oxidizing bacterium isolated from a mesophilic anaerobic filter.

    Science.gov (United States)

    Westerholm, Maria; Roos, Stefan; Schnürer, Anna

    2010-08-01

    A mesophilic, syntrophic acetate-oxidizing bacterium, designated strain Sp3(T), was isolated from sludge from a mesophilic methanogenic digestor operating at a high ammonium concentration (6.4 g L(-1) NH(4)(+)-N). The strain showed acetate-oxidizing ability in cocultivation with a hydrogen-consuming methanogen. Comparative 16S rRNA gene sequence analysis confirmed that strain Sp3(T) belonged to the Firmicutes-Clostridia class. The most closely related species was Thermacetogenium phaeum (16S rRNA gene sequence identity 92%). Strain Sp3(T) used ethanol, betaine and lactate as carbon and electron sources and showed growth between 25 and 40 degrees C and pH 6.0 and 8.0. Based on the phylogenetic position and the physiological characteristics of strain Sp3(T), this new syntrophic, acetate-oxidizing bacterium is proposed as the new genus and species Syntrophaceticus schinkii, with Sp3(T) (=JCM 16669(T)) as the type strain. An isolate (strain Esp=JCM 16670) with high 16S rRNA gene sequence identity (99%) to syntrophic acetate-oxidizing Clostridium ultunense was also retrieved from the methanogenic digestor.

  16. Bacillus halosaccharovorans sp. nov., a moderately halophilic bacterium from a hypersaline lake.

    Science.gov (United States)

    Mehrshad, Maliheh; Amoozegar, Mohammad Ali; Didari, Maryam; Bagheri, Maryam; Fazeli, Seyed Abolhassan Shahzadeh; Schumann, Peter; Spröer, Cathrin; Sánchez-Porro, Cristina; Ventosa, Antonio

    2013-08-01

    A novel Gram-stain-positive, moderately halophilic bacterium, designated strain E33(T), was isolated from water of the hypersaline lake Aran-Bidgol in Iran and characterized taxonomically using a polyphasic approach. Cells of strain E33(T) were motile rods and produced ellipsoidal endospores at a central or subterminal position in swollen sporangia. Strain E33(T) was a strictly aerobic bacterium, catalase- and oxidase-positive. The strain was able to grow at NaCl concentrations of 0.5-25 % (w/v), with optimum growth occurring at 5-15 % (w/v) NaCl. The optimum temperature and pH for growth were 40 °C and pH 7.5-8.0, respectively. On the basis of 16S rRNA gene sequence analysis, strain E33(T) was shown to belong to the genus Bacillus within the phylum Firmicutes and showed the closest phylogenetic similarity with the species Bacillus niabensis 4T19(T) (99.2 %), Bacillus herbersteinensis D-1-5a(T) (97.3 %) and Bacillus litoralis SW-211(T) (97.2 %). The DNA G+C content of the type strain of the novel species was 42.6 mol%. The major cellular fatty acids of strain E33(T) were anteiso-C15 : 0 and iso-C15 : 0, and the polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, two unknown glycolipids, an unknown lipid and an unknown phospholipid. The isoprenoid quinones were MK-7 (97 %), MK-6 (2 %) and MK-8 (0.5 %). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. All these features confirm the placement of isolate E33(T) within the genus Bacillus. DNA-DNA hybridization experiments revealed low levels of relatedness between strain E33(T) and Bacillus niabensis IBRC-M 10590(T) (22 %), Bacillus herbersteinensis CCM 7228(T) (38 %) and Bacillus litoralis DSM 16303(T) (19 %). On the basis of polyphasic evidence from this study, a novel species of the genus Bacillus, Bacillus halosaccharovorans sp. nov. is proposed, with strain E33(T) (= IBRC-M 10095(T) = DSM 25387(T)) as the type strain.

  17. Bacillus persicus sp. nov., a halophilic bacterium from a hypersaline lake.

    Science.gov (United States)

    Didari, Maryam; Amoozegar, Mohammad Ali; Bagheri, Maryam; Mehrshad, Maliheh; Schumann, Peter; Spröer, Cathrin; Sánchez-Porro, Cristina; Ventosa, Antonio

    2013-04-01

    A novel gram-positive, slightly halophilic bacterium, designated strain B48(T), was isolated from soil around the hypersaline lake Aran-Bidgol in Iran and characterized taxonomically using a polyphasic approach. Cells of strain B48(T) were non-motile rods and produced ellipsoidal endospores at a central or subterminal position in swollen sporangia. Strain B48(T) was a strictly aerobic bacterium, catalase- and oxidase-positive. The strain was able to grow at NaCl concentrations of 0.5-10.0 % (w/v), with optimum growth occurring at 2.5 % (w/v) NaCl. The optimum temperature and pH for growth were 35 °C and pH 7.5-8.0, respectively. On the basis of 16S rRNA gene sequence analysis, strain B48(T) was shown to belong to the genus Bacillus within the phylum Firmicutes and showed the closest phylogenetic similarity to the species Bacillus foraminis CV53(T) (97.4 %) and Bacillus purgationiresistens DS22(T) (96.9 %). The DNA G+C content of this new isolate was 40.1 mol%. The major cellular fatty acids of strain B48(T) were iso-C15 : 0 and anteiso-C15 : 0, and its polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an aminophospholipid and two unknown phospholipids. The only quinone present was menaquinone 7 (MK-7). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. All these features confirm the placement of isolate B48(T) within the genus Bacillus. DNA-DNA hybridization experiments revealed a low level of relatedness between strain B48(T) and Bacillus foraminis IBRC-M 10625(T) (8.1 %). On the basis of polyphasic evidence from this study, a new species of the genus Bacillus, Bacillus persicus sp. nov., is proposed, with strain B48(T) ( = IBRC-M 10115(T) = DSM 25386(T) = CECT 8001(T)) as the type strain.

  18. Saliterribacillus persicus gen. nov., sp. nov., a moderately halophilic bacterium isolated from a hypersaline lake.

    Science.gov (United States)

    Amoozegar, Mohammad Ali; Bagheri, Maryam; Didari, Maryam; Shahzedeh Fazeli, Seyed Abolhassan; Schumann, Peter; Sánchez-Porro, Cristina; Ventosa, Antonio

    2013-01-01

    A novel Gram-positive, moderately halophilic bacterium, designated strain X4B(T), was isolated from soil around the hypersaline lake Aran-Bidgol in Iran and characterized taxonomically using a polyphasic approach. Cells of strain X4B(T) were motile rods and formed ellipsoidal endospores at a terminal or subterminal position in swollen sporangia. Strain X4B(T) was a strictly aerobic bacterium, catalase- and oxidase-positive. The strain was able to grow at NaCl concentrations of 0.5-22.5 % (w/v), with optimum growth occurring at 7.5 % (w/v) NaCl. The optimum temperature and pH for growth were 35 °C and pH 7.0. Analysis of 16S rRNA gene sequence revealed that strain X4B(T) is a member of the family Bacillaceae, constituting a novel phyletic lineage within this family. Highest sequence similarities were obtained with the 16S rRNA gene sequences of the type strains of Sediminibacillus albus (96.0 %), Paraliobacillus ryukyuensis (95.9 %), Paraliobacillus quinghaiensis (95.8 %) and Sediminibacillus halophilus (95.7 %), respectively. The DNA G+C content of this novel isolate was 35.2 mol%. The major cellular fatty acids of strain X4B(T) were anteiso-C(15 : 0) and anteiso-C(17 : 0) and its polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, two aminolipids, an aminophospholipid and an unknown phospholipid. The isoprenoid quinones were MK-7 (89 %) and MK-6 (11 %). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. On the basis of 16S rRNA gene sequence analysis in combination with chemotaxonomic and phenotypic data, strain X4B(T) represents a novel species in a new genus in the family Bacillaceae, order Bacillales for which the name Saliterribacillus persicus gen. nov., sp. nov. is proposed. The type strain of the type species (Saliterribacillus persicus) is X4B(T) ( = IBRC-M 10629(T) = KCTC 13827(T)).

  19. Paenibacillus populi sp. nov., a novel bacterium isolated from the rhizosphere of Populus alba.

    Science.gov (United States)

    Han, Tong-Yan; Tong, Xiao-Mei; Wang, Yan-Wei; Wang, Hui-Min; Chen, Xiao-Rong; Kong, De-Long; Guo, Xiang; Ruan, Zhi-Yong

    2015-09-01

    A novel aerobic bacterium, designated strain LAM0705(T), was isolated from the rhizosphere of Populus alba in the Peking University Third Hospital. Cells of strain LAM0705(T) were observed to be Gram-stain positive, motile, spore-forming and rod-shaped. The optimal temperature and pH for growth were found to be 30 °C and pH 7.5, respectively. Strain LAM0705(T) was found to be able to grow in the presence 0-5 % NaCl (w/v) (optimum 1.0 %). The major fatty acids of strain LAM0705(T) were identified as anteiso-C15:0, C16:0 and iso-C16:0. The dominant polar lipids were found to consist of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The cell wall peptidoglycan of strain LAM0705(T) was found to contain meso-diaminopimelic acid. The predominant menaquinone was identified as MK-7. The G+C content of genomic DNA was found to be 48 mol% when determined by the T m method. The 16S rRNA gene sequence similarity analysis indicated that strain LAM0705(T) is closely related to Paenibacillus agaridevorans DSM 1355(T) and Paenibacillus thailandensis KCTC 13043(T) with 97.8 and 96.1 % sequence similarity, respectively. The DNA-DNA hybridization value between strain LAM0705(T) and P. agaridevorans DSM 1355(T) was 47 ± 0.8 %. On the basis of its phenotypic, phylogenetic and chemotaxonomic characteristics, strain LAM0705(T) is concluded to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus populi sp. nov. is proposed. The type strain is LAM0705(T) (=ACCC 06427(T) = JCM 19843(T)).

  20. Bacillus capparidis sp. nov., an endophytic bacterium isolated from roots of Capparis spinosa L.

    Science.gov (United States)

    Wang, Hong-Fei; Li, Qiu-Li; Zhang, Yong-Guang; Xiao, Min; Zhou, Xing-Kui; Guo, Jian-Wei; Duan, Yan-Qing; Li, Wen-Jun

    2017-02-01

    A novel endophytic bacterium, designated strain EGI 6500252T, was isolated from the surface-sterilized roots of a medicinal plant (Capparis spinosa L.) collected from Urumqi city, Xinjiang, north-west China. Cells were Gram-stain-positive, non-motile, aerobic, catalase- and oxidase-positive, rod-shaped and did not display spore formation. Strain EGI 6500252T grew at 10-40 °C (optimum 25-30 °C), at pH 6.0-8.0 (optimum pH 7.0) and in the presence of 0-10 % (w/v) NaCl (optimum 0-3 %). The major cellular fatty acids (>10 %) were identified as iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0 and summed feature 4. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, four unknown phospholipids, one unknown glycolipid and one unknown lipid. The dominant isoprenoid quinone was menaquinone 7 (MK-7). The DNA G+C content was 39.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain EGI 6500252T belonged to the genus Bacillus, and exhibited a highest 16S rRNA gene sequence similarity (96.2 %) that was lower than the suggested threshold (97.0 %) for separating bacterial species. On the basis of the phylogenetic analysis, chemotaxonomic data and physiological characteristics, strain EGI 6500252T represents a novel species of the genus Bacillus, for which the name Bacillus capparidis sp. nov. is proposed. The type strain is EGI 6500252T (=CGMCC 1.12820T=KCTC 33514T).

  1. Cohnella formosensis sp. nov., a xylanolytic bacterium isolated from the rhizosphere of Medicago sativa L.

    Science.gov (United States)

    Hameed, Asif; Hung, Mei-Hua; Lin, Shih-Yao; Hsu, Yi-Han; Liu, You-Cheng; Shahina, Mariyam; Lai, Wei-An; Huang, Hsin-Chieh; Young, Li-Sen; Young, Chiu-Chung

    2013-08-01

    A Gram-positive, spore-forming, aerobic, rod-shaped, xylanolytic bacterium designated strain CC-Alfalfa-35(T) was isolated from the rhizosphere of Medicago sativa L. in Taiwan. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain CC-Alfalfa-35(T) was affiliated to the genus Cohnella. Strain CC-Alfalfa-35(T) shared 95.3 % pairwise 16S rRNA gene sequence similarity to the type strain of the type species of the genus Cohnella (Cohnella thermotolerans DSM 17683(T)) besides showing a similarity of 97.4-93.6 % with other recognized species of the genus Cohnella. The DNA-DNA hybridization value between CC-Alfalfa-35(T) and Cohnella thailandensis KCTC 22296(T) was 37.7 % ± 1.7 % (reciprocal value, 55.7 % ± 3.0 %). Predominant cellular fatty acids were iso-C16 : 0 and anteiso-C15 : 0. The polar lipid profile constituted diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, lysyl-phosphatidylglycerol, three unidentified phospholipids and three unidentified aminophospholipids. The major respiratory quinone was MK-7 and the DNA G+C content was 58.3 mol%. Strain CC-Alfalfa-35(T) contained meso-diaminopimelic acid as the major diamino acid in the cell-wall peptidoglycan. Based on the polar lipid and fatty acid profiles, which were in line with those of C. thermotolerans DSM 17683(T), coupled with additional distinguishing genotypic, phenotypic and chemotaxonomic features, strain CC-Alfalfa-35(T) is proposed to represent a novel species within the genus Cohnella, for which the name Cohnella formosensis sp. nov. is proposed. The type strain is CC-Alfalfa-35(T) ( = JCM 18405(T) = BCRC 80428(T)).

  2. Antibiofilm activity of an exopolysaccharide from marine bacterium Vibrio sp. QY101.

    Directory of Open Access Journals (Sweden)

    Peng Jiang

    Full Text Available Bacterial exopolysaccharides have always been suggested to play crucial roles in the bacterial initial adhesion and the development of complex architecture in the later stages of bacterial biofilm formation. However, Escherichia coli group II capsular polysaccharide was characterized to exert broad-spectrum biofilm inhibition activity. In this study, we firstly reported that a bacterial exopolysaccharide (A101 not only inhibits biofilm formation of many bacteria but also disrupts established biofilm of some strains. A101 with an average molecular weight of up to 546 KDa, was isolated and purified from the culture supernatant of the marine bacterium Vibrio sp. QY101 by ethanol precipitation, iron-exchange chromatography and gel filtration chromatography. High performance liquid chromatography traces of the hydrolyzed polysaccharides showed that A101 is primarily consisted of galacturonic acid, glucuronic acid, rhamnose and glucosamine. A101 was demonstrated to inhibit biofilm formation by a wide range of Gram-negative and Gram-positive bacteria without antibacterial activity. Furthermore, A101 displayed a significant disruption on the established biofilm produced by Pseudomonas aeruginosa, but not by Staphylococcus aureus. Importantly, A101 increased the aminoglycosides antibiotics' capability of killing P. aeruginosa biofilm. Cell primary attachment to surfaces and intercellular aggregates assays suggested that A101 inhibited cell aggregates of both P. aeruginosa and S. aureus, while the cell-surface interactions inhibition only occurred in S. aureus, and the pre-formed cell aggregates dispersion induced by A101 only occurred in P. aeruginosa. Taken together, these data identify the antibiofilm activity of A101, which may make it potential in the design of new therapeutic strategies for bacterial biofilm-associated infections and limiting biofilm formation on medical indwelling devices. The found of A101 antibiofilm activity may also promote a

  3. Bacillus endozanthoxylicus sp. nov., an endophytic bacterium isolated from Zanthoxylum bungeanum Maxim leaves.

    Science.gov (United States)

    Ma, Li; Xi, Jia-Qin; Cao, Yong-Hong; Wang, Xiao-Yan; Zheng, Shuai-Chao; Yang, Cheng-Gang; Yang, Ling-Ling; Mi, Qi-Li; Li, Xue-Mei; Zhu, Ming-Liang; Mo, Ming-He

    2017-10-01

    A Gram-stain-positive, rod-shaped, motile bacterium, designated as 1404 T , was isolated from leaves of Chinese red pepper (Huajiao) (Zanthoxylum bungeanum Maxim) collected from Gansu, north-west China. Spores were not observed under a range of conditions. Strain 1404 T was observed to grow at 15-45 °C and pH 6.0-10.0 and in presence of 0-5 % (w/v) NaCl concentration. The cell wall of strain 1404 T was found to contain meso-diaminopimelic acid, and the predominant respiratory quinone was identified as MK-7. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as well as three unidentified polar lipids. The major fatty acids profile of strain 1404 T consisted of iso-C15 : 0 (25.6 %), anteiso-C15 : 0 (18.4 %) and iso-C14 : 0 (12.1 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 1404 T was affiliated to the genus Bacillus and was closely related to Bacillusoryzisoli 1DS3-10 T , Bacillusbenzoevorans DSM 5391 T and Bacilluscirculans DSM 11 T with sequence similarity of 98.3, 98.2 and 96.9 %, respectively. The G+C content of the genomic DNA was determined to be 39.4 mol%. DNA-DNA hybridization values indicated that relatedness between strain 1404 T and the type strains of closely related species of the genus Bacillus was below 41 %. Therefore, on the basis of the data from the polyphasic taxonomic study presented, strain 1404 T represents a novel species of the genus Bacillus, for which the name proposed is Bacillus endozanthoxylicus sp. nov. The type strain is 1404 T (=CCTCC AB 2017021 T =KCTC 33827 T ).

  4. A new purple sulfur bacterium isolated from a littoral microbial mat, Thiorhodococcus drewsii sp. nov.

    Science.gov (United States)

    Zaar, Annette; Fuchs, Georg; Golecki, Jochen R; Overmann, Jörg

    2003-03-01

    A new strain of purple sulfur bacterium was isolated from a marine microbial mat sampled in Great Sippewissett Salt Marsh at the Atlantic coast (Woods Hole, Mass., USA). Single cells of strain AZ1 were coccus-shaped, highly motile by means of a single flagellum, and did not contain gas vesicles. Intracellular membranes were of the vesicular type. However, additional concentric membrane structures were present. The photosynthetic pigments were bacteriochlorophyll a and carotenoids of the normal spirilloxanthin series, with rhodopin as the dominant carotenoid. Hydrogen sulfide (up to 11 mM), sulfur, thiosulfate, and molecular hydrogen were used as electron donors during anaerobic phototrophic growth. During growth on sulfide, elemental sulfur globules were transiently stored inside the cells. Strain AZ1 is much more versatile than most other Chromatiaceae with respect to electron donor and organic substrates. In the presence of CO(2), it is capable of assimilating C(1)-C(5) fatty acids, alcohols, and intermediates of the tricarboxylic acid cycle. Strain AZ1 could also grow photoorganotrophically with acetate as the sole photosynthetic electron donor. Chemotrophic growth in the dark under microoxic conditions was not detected. Optimum growth occurred at pH 6.5-6.7, 30-35 degrees C, > or =50 micro mol quanta m(-2) s(-1), and 2.4-2.6% NaCl. The DNA base composition was 64.5 mol% G+C. Comparative sequence analysis of the 16S rRNA gene confirmed that the isolate is a member of the family Chromatiaceae. Sequence similarity to the most closely related species, Thiorhodococcus minor DSMZ 11518(T), was 97.8%; however, the value for DNA-DNA hybridization between both strains was only 20%. Because of the low genetic similarity and since strain AZ1 physiologically differs considerably from all other members of the Chromatiaceae, including Trc. minor, the new isolate is described as a new species of the genus Thiorhodococcus, Thiorhodococcus drewsii sp. nov.

  5. A Novel Exopolysaccharide with Metal Adsorption Capacity Produced by a Marine Bacterium Alteromonas sp. JL2810

    Science.gov (United States)

    Zhang, Zilian; Cai, Ruanhong; Zhang, Wenhui; Fu, Yingnan; Jiao, Nianzhi

    2017-01-01

    Most marine bacteria can produce exopolysaccharides (EPS). However, very few structures of EPS produced by marine bacteria have been determined. The characterization of EPS structure is important for the elucidation of their biological functions and ecological roles. In this study, the structure of EPS produced by a marine bacterium, Alteromonas sp. JL2810, was characterized, and the biosorption of the EPS for heavy metals Cu2+, Ni2+, and Cr6+ was also investigated. Nuclear magnetic resonance (NMR) analysis indicated that the JL2810 EPS have a novel structure consisting of the repeating unit of [-3)-α-Rhap-(1→3)-α-Manp-(1→4)-α-3OAc-GalAp-(1→]. The biosorption of the EPS for heavy metals was affected by a medium pH; the maximum biosorption capacities for Cu2+ and Ni2+ were 140.8 ± 8.2 mg/g and 226.3 ± 3.3 mg/g at pH 5.0; however, for Cr6+ it was 215.2 ± 5.1 mg/g at pH 5.5. Infrared spectrometry analysis demonstrated that the groups of O-H, C=O, and C-O-C were the main function groups for the adsorption of JL2810 EPS with the heavy metals. The adsorption equilibrium of JL2810 EPS for Ni2+ was further analyzed, and the equilibrium data could be better represented by the Langmuir isotherm model. The novel EPS could be potentially used in industrial applications as a novel bio-resource for the removal of heavy metals. PMID:28604644

  6. Akkermansia glycaniphila sp. nov., an anaerobic mucin-degrading bacterium isolated from reticulated python faeces.

    Science.gov (United States)

    Ouwerkerk, Janneke P; Aalvink, Steven; Belzer, Clara; de Vos, Willem M

    2016-11-01

    A Gram-stain-negative, non-motile, strictly anaerobic, oval-shaped, non-spore-forming bacterium (strain PytT) was isolated from reticulated python faeces. Strain PytT was capable of using mucin as sole carbon, energy and nitrogen source. Cells could grow singly, in pairs, and were also found to aggregate. Scanning electron microscopy revealed the presence of filamentous structures connecting individual bacterial cells. Strain PytT could grow on a limited number of single sugars, including N-acetylglucosamine, N-acetylgalactosamine, glucose, lactose and galactose, but only when a plentiful protein source was provided. Phylogenetic analysis based on 16S rRNA gene sequencing showed strain PytT to belong to the Verrucomicrobiae class I, family Akkermansiaceae, genus Akkermansia, with Akkermansia muciniphila MucT as the closest relative (94.4 % sequence similarity). DNA-DNA hybridization revealed low relatedness of 28.3 % with A. muciniphila MucT. The G+C content of DNA from strain PytT was 58.2 mol%. The average nucleotide identity (ANI) of the genome of strain PytT compared to the genome of strain MucT was 79.7 %. Chemotaxonomic data supported the affiliation of strain PytT to the genus Akkermansia. Based on phenotypic, phylogenetic and genetic characteristics, strain PytT represents a novel species of the genus Akkermansia, for which the name Akkermansia glycaniphila sp. nov. is proposed. The type strain is PytT (=DSM 100705T=CIP 110913T).

  7. Thermus anatoliensis sp. nov., a thermophilic bacterium from geothermal waters of Buharkent, Turkey.

    Science.gov (United States)

    Kacagan, Murat; Inan, Kadriye; Canakci, Sabriye; Guler, Halil Ibrahim; Belduz, Ali Osman

    2015-12-01

    A Gram-stain-negative, lack of motility, catalase- and oxidase- positive bacterium (strain MT1(T)) was isolated from Buharkent hot spring in Aydin, Turkey. Its taxonomy was investigated using a polyphasic approach. The strain was able to grow at 45-80 °C, pH 5.5-10.5 and with a NaCI tolerance up to 2.0% (w/v). Strain MT1(T) was able to utilize d-mannitol and l-arabinose, not able to utilize d-cellobiose as sole carbon source. 16S rRNA gene sequence analysis revealed that the strain belonged to the genus Thermus; strain MT1(T) detected low-level similarities of 16S rRNA gene sequences (below 97%) compared with all other species in this genus. The predominant fatty acids of strain MT1(T) were iso-C(15:0) (43.0%) and iso-C(17:0) (27.4%). Polar lipid analysis revealed a major phospholipid, one major glycolipid, one major aminophospholipid, two minor aminolipids, one minor phospholipid, and several minor glycolipids. The major isoprenoid quinone was MK-8. The DNA G+C content of MT1(T) was 69.6 mol%. On the basis of a taxonomic study using a polyphasic approach, strain MT1(T) is considered to represent a novel species of the genus Thermus, for which the name Thermus anatoliensis sp. nov. is proposed. The type strain is MT1(T) (=NCCB 100425(T) =LMG 26880(T)). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Acinetobacter halotolerans sp. nov., a novel halotolerant, alkalitolerant, and hydrocarbon degrading bacterium, isolated from soil.

    Science.gov (United States)

    Dahal, Ram Hari; Chaudhary, Dhiraj Kumar; Kim, Jaisoo

    2017-07-01

    A novel aerobic, non-motile, halotolerant, alkalitolerant, hydrocarbon degrading, and rod shaped bacterium, designated strain R160(T), was isolated from soil in South Korea. Cells were Gram-staining-negative, catalase-positive, and oxidase-negative. This strain grew up to 7% of NaCl and in the pH range of 6-11 (optimum 7.0-10.0). The isolate degraded 51.7 ± 1.3% of hydrocarbon components (C-18, C-20, and C-22) and 45.8 ± 1.4% oil components (kerosene, diesel, and gasoline). Phylogenetic analysis based on 16 S rRNA gene sequences revealed that strain R160(T) formed a lineage within the genus Acinetobacter, and was closely related to 'Acinetobacter oleivorans' DR1(T) (97.47%, sequence similarity). Other closely related members have sequence similarity between 97.47 to 96.52%. The predominant respiratory lipoquinones of strain R160(T) were ubiquinone 9 (Q-9) and ubiquinone 8 (Q-8). The major polar lipids were phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and phosphatidylcholine (PC). The major cellular fatty acids were 9-octadecenoic acid (C18:1 ω9c), hexadecanoic acid (C16:0), and summed feature (comprising C16:1 ω7c and/or C16:1 ω6c). The DNA G + C content of strain R160(T) was 44.9 mol%. On the basis of phenotypic, genotypic, chemotaxonomic, and phylogenetic characteristics, strain R160(T) represents a novel species of the genus Acinetobacter, for which the name Acinetobacter halotolerans sp. nov. is proposed. The type strain is R160(T) (= KEMB 9005-333(T) = KACC 18453(T) = JCM 31009(T)).

  9. Methylobacterium pseudosasae sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the bamboo phyllosphere.

    Science.gov (United States)

    Madhaiyan, Munusamy; Poonguzhali, Selvaraj

    2014-02-01

    A pink-pigmented, Gram negative, aerobic, facultatively methylotrophic bacterium, strain BL44(T), was isolated from bamboo leaves and identified as a member of the genus Methylobacterium. Phylogenetic analysis based on 16S rRNA gene sequences showed similarity values of 98.7-97.0 % with closely related type strains and showed highest similarity to Methylobacterium zatmanii DSM 5688(T) (98.7 %) and Methylobacterium thiocyanatum DSM 11490(T) (98.7 %). Methylotrophic metabolism in this strain was confirmed by PCR amplification and sequencing of the mxaF gene coding for the α-subunit of methanol dehydrogenase. Strain BL44(T) produced three known quorum sensing signal molecules with similar retention time to C8, C10 and C12-HSLs when characterized by GC-MS. The fatty acid profiles contained major amounts of C18:1 ω7c, iso-3OH C17:0 and summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH), which supported the grouping of the isolate in the genus Methylobacterium. The DNA G+C content was 66.9 mol%. DNA relatedness of the strain BL44(T) to its most closely related strains ranged from 12-43.3 %. On the basis of the phenotypic, phylogenetic and DNA-DNA hybridization data, strain BL44(T) is assigned to a novel species of the genus Methylobacterium for which the name Methylobacterium pseudosasae sp. nov. is proposed (type strain BL44(T) = NBRC 105205(T) = ICMP 17622(T)).

  10. Martelella endophytica sp. nov., an antifungal bacterium associated with a halophyte.

    Science.gov (United States)

    Bibi, Fehmida; Chung, Eu Jin; Khan, Ajmal; Jeon, Che Ok; Chung, Young Ryun

    2013-08-01

    A Gram-staining-negative, non-spore-forming endophytic bacterium, designated strain YC6887(T), was isolated from a root sample of a halophyte, Rosa rugosa, collected from a tidal flat area of Namhae Island, located at the southern end of Korea. Strain YC6887(T) was found to exhibit inhibitory activity against oomycete plant pathogens. The cells were non-motile and aerobic rods. The strain was able to grow at 4-40 °C (optimum 28-30 °C) and at pH 5.0-9.0 (optimum pH 7.0-8.5). Strain YC6887(T) was able to grow at NaCl concentrations of 0-9 % (w/v) with optimum growth at 4-5 % (w/v) NaCl, but NaCl is not essential for growth. Comparison of 16S rRNA gene sequences showed that the strain was a member of the genus Martelella, a member of order Rhizobiales, exhibiting highest similarity with Martelella mediterranea (98.6 %). The DNA-DNA relatedness between strain YC6887(T) and M. mediterranea MACL11(T) was 19.8 ± 6.8. Chemotaxonomically, strain YC6887(T) contained C19 : 0 cyclo ω8c (28.0 %) and C18 : 1ω7c (17.9 %) as predominant fatty acids, confirming the affiliation of strain YC6887(T) with the genus Martelella. The major respiratory quinone was Q-10 and the DNA G+C content was 62.1 mol%. On the basis of phylogenetic analysis, physiological and biochemical characterization and DNA-DNA hybridization data, strain YC6887(T) should be classified as representing a novel species of the genus Martelella, for which the name Martelella endophytica sp. nov. is proposed. The type strain is YC6887(T) ( = KCCM 43011(T) = NBRC 109149(T)).

  11. Bacillus mesophilum sp. nov., strain IITR-54T, a novel 4-chlorobiphenyl dechlorinating bacterium.

    Science.gov (United States)

    Manickam, Natesan; Singh, Nitin Kumar; Bajaj, Abhay; Kumar, Rajendran Mathan; Kaur, Gurwinder; Kaur, Navjot; Bala, Monu; Kumar, Anand; Mayilraj, Shanmugam

    2014-07-01

    The taxonomic position of a Gram-positive, endospore-forming bacterium isolated from soil sample collected from an industrial site was analyzed by a polyphasic approach. The strain designated as IITR-54T matched most of the phenotypic and chemical characteristics of the genus Bacillus and represents a novel species. It was found to biodegrade 4-chlorobiphenyl through dechlorination and was isolated through enrichment procedure from an aged polychlorinated biphenyl-contaminated soil. Both resting cell assay and growth under aerobic liquid conditions using 4-chlorobiphenyl as sole source of carbon along with 0.01% yeast extract, formation of chloride ions was measured. 16S rRNA (1,489 bases) nucleotide sequence of isolated strain was compared with those of closely related Bacillus type strains and confirmed that the strain belongs to the genus Bacillus. Strain IITR-54T differs from all other species of Bacillus by at least 2.1% at the 16S rRNA level, and the moderately related species are Bacillus oceanisediminis (97.9%) followed by Bacillus infantis (97.7%), Bacillus firmus (97.4%), Bacillus drentensis (97.3%), Bacillus circulans (97.2%), Bacillus soli (97.1%), Bacillus horneckiae (97.1%), Bacillus pocheonensis (97.1%) and Bacillus bataviensis (97.1%), respectively. The cell wall peptidoglycan contained meso-diaminopimelic acid and the major isoprenoid quinone was MK-7. Major fatty acids are iso-C15:0 (32.4%) and anteiso-C15:0 (27.4%). Predominant polar lipids are diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The results of physiological and biochemical tests allowed the genotypic and phenotypic distinctiveness of strain IITR-54T with its phylogenetic relatives and suggest that the strain IITR-54T should be recognized as a novel species, for which the name Bacillus mesophilum sp. nov. is proposed. The type strain is IITR-54T (=MTCC 11060T=JCM 19208T).

  12. Cyclobacterium halophilum sp. nov., a marine bacterium isolated from a coastal-marine wetland.

    Science.gov (United States)

    Shahinpei, Azadeh; Amoozegar, Mohammad Ali; Sepahy, Abbas Akhavan; Schumann, Peter; Ventosa, Antonio

    2014-03-01

    A novel Gram-stain-negative, slightly halophilic bacterium, designated strain GASx41(T), was isolated from soil of the coastal-marine wetland Gomishan in Iran. Cells of strain GASx41(T) were curved, ring-like or horseshoe-shaped rods and non-motile. Strain GASx41(T) was strictly aerobic, and catalase- and oxidase-positive. The strain was able to grow at NaCl concentrations of 1-10% (w/v), with optimum growth occurring at 2.5-3% (w/v) NaCl. The optimum temperature and pH for growth were 25-30 °C and pH 7.5-8.0. On the basis of 16S rRNA gene sequence analysis, strain GASx41(T) was shown to belong to the genus Cyclobacterium within the phylum Bacteroidetes and showed closest phylogenetic similarity to 'Cyclobacterium jeungdonense' HMD3055 (98.0%). The DNA G+C content of strain GASx41(T) was 48.1 mol%. The major cellular fatty acids of strain GASx41(T) were iso-C15 : 0, summed feature 4 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), anteiso-C15 : 0 2-OH, anteiso-C15 : 0 and iso-C17 : 0 3-OH, and its polar lipid pattern consisted of phosphatidylethanolamine, phosphatidylcholine and 12 unknown lipids. The only quinone present was menaquinone 7 (MK-7). All these features confirmed the placement of isolate GASx41(T) within the genus Cyclobacterium. On the basis of evidence from this study, a novel species of the genus Cyclobacterium, Cyclobacterium halophilum sp. nov., is proposed, with strain GASx41(T) ( = IBRC-M 10761(T) = CECT 8341(T)) as the type strain.

  13. Salinispirillum marinum gen. nov., sp. nov., a haloalkaliphilic bacterium in the family 'Saccharospirillaceae'.

    Science.gov (United States)

    Shahinpei, Azadeh; Amoozegar, Mohammad Ali; Fazeli, Seyed Abolhassan Shahzadeh; Schumann, Peter; Ventosa, Antonio

    2014-11-01

    A novel Gram-staining-negative, motile, non-pigmented, facultatively anaerobic, spirillum-shaped, halophilic and alkaliphilic bacterium, designated strain GCWy1(T), was isolated from water of the coastal-marine wetland Gomishan in Iran. The strain was able to grow at NaCl concentrations of 1-10% (w/v) and optimal growth was achieved at 3% (w/v). The optimum pH and temperature for growth were pH 8.5 and 30 °C, while the strain was able to grow at pH 7.5-10 and 4-40 °C. Phylogenetic analysis based on the comparison of the 16S rRNA gene sequence placed the isolate within the class Gammaproteobacteria as a separate deep branch, with 92.1% or lower sequence similarity to representatives of the genera Saccharospirillum and Reinekea and less than 91.0% sequence similarity with other remotely related genera. The major cellular fatty acids of the isolate were C(18 : 1)ω7c, C(16:0) and C(17 : 0), and the major components of its polar lipid profile were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The cells of strain GCWy1(T) contained the isoprenoid quinones Q-9 and Q-8 (81% and 2%, respectively). The G+C content of the genomic DNA of this strain was 52.3 mol%. On the basis of 16S rRNA gene sequence analysis in combination with chemotaxonomic and phenotypic data, strain GCWy1(T) represents a novel species in a new genus in the family 'Saccharospirillaceae', order Oceanospirillales, for which the name Salinispirillum marinum gen. nov., sp. nov. is proposed. The type strain of the type species is GCWy1(T) ( = IBRC-M 10765(T) =CECT 8342(T)). © 2014 IUMS.

  14. Limimonas halophila gen. nov., sp. nov., an extremely halophilic bacterium in the family Rhodospirillaceae.

    Science.gov (United States)

    Amoozegar, Mohammad Ali; Makhdoumi-Kakhki, Ali; Ramezani, Mohadaseh; Nikou, Mahdi Moshtaghi; Fazeli, Seyed Abolhassan Shahzadeh; Schumann, Peter; Ventosa, Antonio

    2013-04-01

    A novel, Gram-staining-negative, non-pigmented, rod-shaped, strictly aerobic, extremely halophilic bacterium, designated strain IA16(T), was isolated from the mud of the hypersaline Lake Aran-Bidgol, in Iran. Cells of strain IA16(T) were not motile. Growth occurred with 2.5-5.2 M NaCl (optimum 3.4 M), at pH 6.0-8.0 (optimum pH 7.0) and at 30-50 °C (optimum 40 °C). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain IA16(T) belonged in the family Rhodospirillaceae and that its closest relatives were Rhodovibrio sodomensis DSM 9895(T) (91.6 % sequence similarity), Rhodovibrio salinarum NCIMB 2243(T) (91.2 %), Pelagibius litoralis CL-UU02(T) (88.9 %) and Fodinicurvata sediminis YIM D82(T) (88.7 %). The novel strain's major cellular fatty acids were C19 : 0 cyclo ω7c and C18 : 0 and its polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, four unidentified phospholipids, three unidentified aminolipids and two other unidentified lipids. The cells of strain IA16(T) contained the ubiquinone Q-10. The G+C content of the novel strain's genomic DNA was 67.0 mol%. The physiological, biochemical and phylogenetic differences between strain IA16(T) and other previously described taxa indicate that the strain represents a novel species in a new genus within the family Rhodospirillaceae, for which the name Limimonas halophila gen. nov., sp. nov. is proposed. The type strain of Limimonas halophila is IA16(T) ( = IBRC-M 10018(T)  = DSM 25584(T)).

  15. Rhizobium hidalgonense sp. nov., a nodule endophytic bacterium of Phaseolus vulgaris in acid soil.

    Science.gov (United States)

    Yan, Jun; Yan, Hui; Liu, Li Xue; Chen, Wen Feng; Zhang, Xiao Xia; Verástegui-Valdés, Myrthala M; Wang, En Tao; Han, Xiao Zeng

    2017-01-01

    One Gram-negative, aerobic, motile, rod-shaped bacterium, designated as FH14 T , was isolated from nodules of Phaseolus vulgaris grown in Hidalgo State of Mexico. Results based upon 16S rRNA gene (≥99.8 % similarities to known species), concatenated sequence (recA, atpD and glnII) analysis of three housekeeping genes (≤93.4 % similarities to known species) and average nucleotide identity (ANI) values of genome sequence (ranged from 87.6 to 90.0 % to related species) indicated the distinct position of strain FH14 T within the genus Rhizobium. In analyses of symbiotic genes, only nitrogen fixation gene nifH was amplified that had nucleotide sequence identical to those of the bean-nodulating strains in R. phaseoli and R. vallis, while nodulation gene nodC gene was not amplified. The failure of nodulation to its original host P. vulgaris and other legumes evidenced the loss of its nodulation capability. Strain FH14 T contained summed feature 8 (C 18:1 ω6c/C 18:1 ω7c, 59.96 %), C 16:0 (10.6 %) and summed feature 2 (C 12:0 aldehyde/unknown 10.928, 10.24 %) as the major components of cellular fatty acids. Failure to utilize alaninamide, and utilizing L-alanine, L-asparagine and γ-amino butyric acid as carbon source, distinguished the strain FH14 T from the type strains for the related species. The genome size and DNA G+C content of FH14 T were 6.94 Mbp and 60.8 mol %, respectively. Based on those results, a novel specie in Rhizobium, named Rhizobium hidalgonense sp. nov., was proposed, with FH14 T (=HAMBI 3636 T  = LMG 29288 T ) as the type strain.

  16. Aliidiomarina iranensis sp. nov., a haloalkaliphilic bacterium from a coastal-marine wetland.

    Science.gov (United States)

    Ali Amoozegar, Mohammad; Shahinpei, Azadeh; Abolhassan Shahzadeh Fazeli, Seyed; Schumann, Peter; Spröer, Cathrin; Ventosa, Antonio

    2016-05-01

    A novel Gram-stain-negative, straight rod-shaped, non-pigmented, slightly halophilic and alkaliphilic bacterium, designated strain GBPy7T, was isolated from a sample of the coastal-marine wetland Gomishan in Iran. Cells of strain GBPy7T were motile. Growth occurred on media with 1-15 % (w/v) NaCl (optimum 3 %), at pH 7-10 (optimum pH 8.5) and at 4-45 °C (optimum 37 °C). Phylogenetic analysis based on 16S rRNA gene sequence comparison indicated that strain GBPy7T belonged to the family Idiomarinaceae. Its closest relatives were Aliidiomarina shirensis AIST (98.1 % 16S rRNA gene sequence similarity) and other Aliidiomarina species (95.9-94.2 %), together with Idiomarina seosinensis CL-SP19T (94.3 %) and Idiomarina fontislapidosi F23T (94.3 %). The major cellular fatty acids of the isolate were iso-C15 : 0, iso-C17 : 0, iso-C17 : 1ω9c and C18 : 1ω7c and its polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, one unknown phospholipid and one unknown aminophospholipid. Cells of strain GBPy7T contained ubiquinone Q-8. The G+C content of the genomic DNA of this strain was 51.6 mol%. The level of DNA-DNA relatedness between strain GBPy7T and A. shirensis IBRC-M 10414T was 21 %. The physiological, biochemical, genotypic and phylogenetic differences between strain GBPy7T and other previously described taxa indicate that the strain represents a novel species of the genus Aliidiomarina within the family Idiomarinaceae, for which the name Aliidiomarina iranensis sp. nov. is proposed. The type strain is GBPy7T ( = IBRC-M 10763T = CECT 8339T).

  17. Acute toxicity evaluation of explosive wastewater by bacterial bioluminescence assays using a freshwater luminescent bacterium, Vibrio qinghaiensis sp. Nov.

    Science.gov (United States)

    Ye, Zhengfang; Zhao, Quanlin; Zhang, Mohe; Gao, Yuchen

    2011-02-28

    The compositions of explosive wastewater generated from TNT (2,4,6-trinitrotoluene) purification stage were characterized by using UV-vis spectroscopy, Fourier transform infrared spectroscopy (FTIR), high performance liquid chromatograph (HPLC) and gas chromatograph/mass spectroscopy (GC/MS). The acute toxicity was evaluated by bacterium bioluminescence assay using a freshwater luminescent bacterium (Vibrio qinghaiensis sp. Nov.) and a marine luminescent bacterium (Photobacterium phosphoreum). The results showed that the wastewater's biodegradability was poor due to the high amount of chemical oxygen demand (COD). The main organic components were dinitrotoluene sulfonates (DNTS) with small amount of TNT, dinitrotoluene (DNT), mononitrotoluene (MNT) and other derivatives of nitrobenzene. It was highly toxic to luminescent bacteria P. phosphoreum and V. qinghaiensis sp. Nov. After reaction time of 15 min, the relative concentration of toxic pollutants (expressed as reciprocal of dilution ratio of wastewater) at 50% of luminescence inhibition ratio was 5.32×10(-4) for P. phosphoreu, while that was 4.34×10(-4) for V. qinghaiensis. V. qinghaiensis is more sensitive and suitable for evaluating the wastewater's acute toxicity than P. phosphoreum. After adsorption by resin, the acute toxicity can be greatly reduced, which is helpful for further treatment by biological methods. Copyright © 2010 Elsevier B.V. All rights reserved.

  18. Rheinheimera aestuari sp. nov., a marine bacterium isolated from coastal sediment.

    Science.gov (United States)

    Baek, Kyunghwa; Jeon, Che Ok

    2015-08-01

    A Gram-stain-negative, strictly aerobic, non-pigmented, motile bacterium with a single polar flagellum, designated H29T, was isolated from coastal sediment of Jeju Island, South Korea. Cells were non-spore-forming rods showing catalase- and oxidase-positive reactions. Growth of strain H29T was observed at 10-40 °C (optimum, 20-25 °C) and pH 6.0-9.0 (optimum, pH 7.0-8.0), and in the presence of 1-4% (w/v) NaCl (optimum, 2-3%). Strain H29T contained C16 : 0, iso-C15 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c) as the major fatty acids and ubiquinone-8 (Q-8) as the sole isoprenoid quinone. Phosphatidylethanolamine and phosphatidylglycerol were identified as the major polar lipids. The G+C content of the genomic DNA was 46.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain H29T formed a phyletic lineage with Rheinheimera hassiensis E48T within the genus Rheinheimera of the family Chromatiaceae. Strain H29T was most closely related to Rheinheimera pacifica KMM 1406T, Rheinheimera muenzenbergensis E49T, Rheinheimera hassiensis E48T and Rheinheimera baltica OSBAC1T with 97.8%, 97.6%, 97.4% and 97.2% 16S rRNA gene sequence similarities, respectively. However, DNA-DNA hybridization values of strain H29T with type strains of these species were lower than 70%. On the basis of the phenotypic, chemotaxonomic and molecular properties, strain H29T represents a novel species of the genus Rheinheimera, for which the name Rheinheimeraaestuarii sp. nov. is proposed. The type strain is H29T ( = KACC 18251T = JCM 30404T).

  19. Rheinheimera gaetbuli sp. nov., a Marine Bacterium Isolated from a Tidal Flat.

    Science.gov (United States)

    Baek, Kyunghwa; Jeon, Che Ok

    2016-03-01

    A gram-staining-negative, strictly aerobic, rod-shaped, and motile bacterium with a single polar flagellum, designated H26(T), was isolated from tidal flat sediment in Jeju Island, South Korea. Growth of strain H26(T) was observed at 4-35 °C (optimum, 20-25 °C), pH 6.0-9.0 (optimum, pH 7.0-8.0), and 1-4 % NaCl (optimum, 2-3 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain H26(T) formed a phyletic lineage within the genus Rheinheimera, family Chromatiaceae. Strain H26(T) was most closely related to Rheinheimera baltica OSBAC1(T), Rheinheimera aestuarii H29(T), Rheinheimera muenzenbergensis E49(T), and Rheinheimera aquimaris SW-353(T) with 98.5, 98.1, 97.8, and 97.5 % of 16S rRNA gene sequence similarities, respectively. The DNA-DNA relatedness levels between strain H26(T) and the type strains of R. baltica, R. aestuarii, R. muenzenbergensis, and R. aquimaris were 35.5 ± 3.2, 33.4 ± 1.5, 31.2 ± 2.2, and 28.7 ± 0.9 %, respectively. The major fatty acids of strain H26(T) were iso-C15:0 3-OH, summed feature 3 (comprising C16:1 ω7c/C16:1 ω6c), C16:0, summed feature 8 (comprising C18:1 ω7c/C18:1 ω6c), iso-C17:0 3-OH, and C12:0 3-OH and the strain contained ubiquinone (Q-8) as the sole isoprenoid quinone. Phosphatidylethanolamine, phosphatidylglycerol, and an aminolipid were identified as the major polar lipids and the G + C content of the genomic DNA was 52.0 mol%. Based on the phenotypic, chemotaxonomic, and molecular properties, strain H26(T) represents a novel species of the genus Rheinheimera, for which the name Rheinheimera gaetbuli sp. nov. is proposed. The type strain was H26(T) (=KACC 18254(T) = JCM 30403(T)).

  20. Photobacterium kishitanii sp. nov., a luminous marine bacterium symbiotic with deep-sea fishes.

    Science.gov (United States)

    Ast, Jennifer C; Cleenwerck, Ilse; Engelbeen, Katrien; Urbanczyk, Henryk; Thompson, Fabiano L; De Vos, Paul; Dunlap, Paul V

    2007-09-01

    Six representatives of a luminous bacterium commonly found in association with deep, cold-dwelling marine fishes were isolated from the light organs and skin of different fish species. These bacteria were Gram-negative, catalase-positive, and weakly oxidase-positive or oxidase-negative. Morphologically, cells of these strains were coccoid or coccoid-rods, occurring singly or in pairs, and motile by means of polar flagellation. After growth on seawater-based agar medium at 22 degrees C for 18 h, colonies were small, round and white, with an intense cerulean blue luminescence. Analysis of 16S rRNA gene sequence similarity placed these bacteria in the genus Photobacterium. Phylogenetic analysis based on seven housekeeping gene sequences (16S rRNA gene, gapA, gyrB, pyrH, recA, rpoA and rpoD), seven gene sequences of the lux operon (luxC, luxD, luxA, luxB, luxF, luxE and luxG) and four gene sequences of the rib operon (ribE, ribB, ribH and ribA), resolved the six strains as members of the genus Photobacterium and as a clade distinct from other species of Photobacterium. These strains were most closely related to Photobacterium phosphoreum and Photobacterium iliopiscarium. DNA-DNA hybridization values between the designated type strain, Photobacterium kishitanii pjapo.1.1(T), and P. phosphoreum LMG 4233(T), P. iliopiscarium LMG 19543(T) and Photobacterium indicum LMG 22857(T) were 51, 43 and 19 %, respectively. In AFLP analysis, the six strains clustered together, forming a group distinct from other analysed species. The fatty acid C(17 : 0) cyclo was present in these bacteria, but not in P. phosphoreum, P. iliopiscarium or P. indicum. A combination of biochemical tests (arginine dihydrolase and lysine decarboxylase) differentiates these strains from P. phosphoreum and P. indicum. The DNA G+C content of P. kishitanii pjapo.1.1(T) is 40.2 %, and the genome size is approximately 4.2 Mbp, in the form of two circular chromosomes. These strains represent a novel species, for

  1. Chloroflexus islandicus sp. nov., a thermophilic filamentous anoxygenic phototrophic bacterium from a geyser.

    Science.gov (United States)

    Gaisin, Vasil A; Kalashnikov, Alexander M; Grouzdev, Denis S; Sukhacheva, Marina V; Kuznetsov, Boris B; Gorlenko, Vladimir M

    2017-05-01

    A novel, thermophilic filamentous anoxygenic phototrophic bacterium, strain isl-2T, was isolated from the Strokkur Geyser, Iceland. Strain isl-2T formed unbranched multicellular filaments with gliding motility. The cells formed no spores and stained Gram-negative. The existence of pili was described in a species of the genus Chloroflexus for the first time, to our knowledge. Optimal growth occurred at a pH range of 7.5-7.7 and at a temperature of 55 °C. Strain isl-2T grew photoheterotrophically under anaerobic conditions in the light and chemoheterotrophically under aerobic conditions in the dark. The major cellular fatty acids were C18 : 1ω9, C16 : 0, C18 : 0 and C18 : 0-OH. The major quinone was menaquinone-10. The photosynthetic pigments were bacteriochlorophylls c and a as well as β- and γ-carotenes. The results of phylogenetic analysis of the 16S rRNA gene sequences placed strain isl-2T into the genus Chloroflexus of the phylum Chloroflexi with Chloroflexus aggregans DSM 9485T as the closest relative (97.0 % identity). The whole-genome sequence of isl-2T was determined. Average nucleotide identity values obtained for isl-2T in comparison to available genomic sequences of other strains of members of the genus Chloroflexus were 81.4 % or less and digital DNA-DNA hybridisation values 22.8 % or less. The results of additional phylogenetic analysis of the PufLM and BchG amino acid sequences supported the separate position of the isl-2T phylotype from the phylotypes of other members of the genus Chloroflexus. On the basis of physiological and phylogenetic data as well as genomic data, it was suggested that isl-2T represents a novel species within the genus Chloroflexus, with the proposed name Chloroflexus islandicus sp. nov. The type strain of the species is isl-2T (=VKM B-2978T,=DSM 29225T,=JCM 30533T).

  2. Fodinicurvata halophila sp. nov., a moderately halophilic bacterium from a marine saltern.

    Science.gov (United States)

    Infante-Dominguez, Carmen; Lawson, Paul A; Johnson, Crystal N; Sánchez-Porro, Cristina; Ventosa, Antonio

    2015-03-01

    A Gram-stain-negative, rod-shaped, facultatively anaerobic, moderately halophilic bacterium, designated strain BA45AL(T), was isolated from water of a saltern located in Santa Pola, Alicante, Spain. Cells were motile, and catalase- and oxidase-positive. Strain BA45AL(T) grew at temperatures in the range 14-45 °C (optimally at 37 °C), at pH 5.0-9.0 (optimally at pH 7.5), and in media containing 5-20 % (w/v) salts [optimally in media containing 10 % (w/v) salts]. Phylogenetic analysis based on the comparison of 16S rRNA gene sequences revealed that strain BA45AL(T) is a member of the genus Fodinicurvata. The closest relatives to the novel strain were Fodinicurvata fenggangensis YIM D812(T) and Fodinicurvata sediminis YIM D82(T) with sequence similarities of 98.2 % and 97.4 %, respectively. DNA-DNA hybridization between the novel isolate and these phylogenetically related species revealed relatedness values of 30 % and 15 %, respectively, with respect to the aforementioned species. The major cellular fatty acids of strain BA45AL(T) were C18 : 1ω7c, C16 : 0 and iso-C15 : 0. The G+C content of the genomic DNA of strain BA45AL(T) was 58.0 mol%, and the polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylmethylethanolamine and a number of unknown phospholipids and lipids. Based on phenotypic, chemotaxonomic and phylogenetic data presented in this study, strain BA45AL(T) constituted a novel species of the genus Fodinicurvata, for which the name Fodinicurvata halophila sp. nov. is suggested. The type strain is BA45AL(T) ( = CCM 8504(T) = CECT 8472(T) = JCM 19075(T) = LMG 27945(T)). © 2015 IUMS.

  3. Aquisalimonas lutea sp. nov., a moderately halophilic bacterium from a saltern.

    Science.gov (United States)

    Infante-Domínguez, Carmen; Sánchez-Porro, Cristina; Ventosa, Antonio

    2015-04-01

    A yellow-pigmented, motile, Gram-stain-negative, moderately halophilic and strictly aerobic bacterium, designated BA42AL-1(T), was isolated from water of a saltern of Santa Pola, Alicante, Spain. Strain BA42AL-1(T) grew in media containing 5-20% (w/v) salts (optimum 7.5% salts). It grew between pH 6.0 and 9.0 (optimally at pH 7.5) and at 15-45 °C (optimally at 37 °C). Phylogenetic analysis based on the comparison of 16S rRNA gene sequences revealed that strain BA42AL-1(T) is a member of the genus Aquisalimonas . The closest relatives to this strain were Aquisalimonas halophila YIM 95345(T) and Aquisalimonas asiatica CG12(T) with sequence similarities of 99.4% and 97.0%, respectively. DNA-DNA hybridization between the novel isolate and Aquisalimonas halophila YIM 95345(T) revealed a relatedness of 54%. The major fatty acids of strain BA42AL-1(T) were C(18 : 1)ω6c/C(18 : 1)ω7c, C(19 : 0) cyclo ω8c and C(16 : 0), and lower contents of C12 : 0 and C18 : 0. The polar lipid pattern of strain BA42AL-1(T) consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine, two glycolipids, a lipid and four unknown phospholipids. The G+C content of the genomic DNA of this strain was 65.0 mol%. Based on the DNA-DNA hybridization, phenotypic, chemotaxonomic and phylogenetic data presented in this study, strain BA42AL-1(T) is proposed as a novel species of the genus Aquisalimonas , for which the name Aquisalimonas lutea sp. nov. is suggested. The type strain is BA42AL-1(T) ( = CCM 8472(T) = CECT 8326(T) = LMG 27614(T)). © 2015 IUMS.

  4. Aliidiomarina sedimenti sp. nov., a haloalkaliphilic bacterium in the family Idiomarinaceae.

    Science.gov (United States)

    Shahinpei, Azadeh; Amoozegar, Mohammad Ali; Shahzadeh Fazeli, Seyed Abolhassan; Schumann, Peter; Spröer, Cathrin; Ventosa, Antonio

    2017-07-01

    A novel Gram-staining-negative straight or curved rod-shaped, moderately halophilic and alkaliphilic bacterium, designated strain GBSy1T, was isolated from a sediment sample from the coastal-marine wetland Gomishan in Iran. GBSy1T was motile, and formed non-pigmented, mucoid colonies. Growth occurred with between 1 and 15 % (w/v) NaCl and the isolate grew optimally with 5 % (w/v) NaCl. The optimum pH and temperature for growth were 8.5 and 34 °C, while the strain was able to grow at pH 7.0-10 and 4-40 °C. On the basis of the results of 16S rRNA gene sequence analysis, GBSy1T was shown to represent a member of the genus Aliidiomarina within the class Gammaproteobacteria, family Idiomarinaceae and showed closest phylogenetic similarity to Aliidiomarina marisCF12-14T (97.7 %). The DNA G+C content of GBSy1T was 51.2 mol%. The cells of GBSy1T contained the isoprenoid ubiquinones Q-8, Q-9 and Q-10 (92, 2 and 2 %, respectively). The major cellular fatty acids of the isolate were iso-C11 : 0 3-OH, iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω9c and its polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and three unknown phospholipids. The level of DNA-DNA relatedness between GBSy1T and Aliidiomarina marisDSM 22154T was 31 %. All these features confirmed the placement of GBSy1T within the genus Aliidiomarina. On the basis of evidence from this study, a novel species of the genus Aliidiomarina, Aliidiomarina sedimenti sp. nov., is proposed, with GBSy1T (=IBRC-M 10764T=CECT 8340T) as the type strain.

  5. Oceanobacillus halophilus sp. nov., a novel moderately halophilic bacterium from a hypersaline lake.

    Science.gov (United States)

    Amoozegar, Mohammad Ali; Bagheri, Maryam; Makhdoumi, Ali; Nikou, Mahdi Moshtaghi; Fazeli, Seyed Abolhassan Shahzadeh; Schumann, Peter; Spröer, Cathrin; Sánchez-Porro, Cristina; Ventosa, Antonio

    2016-03-01

    A moderately halophilic bacterium was isolated from a brine sample of a hypersaline lake, Aran-Bidgol, in Iran. The strain, designated J8BT, was Gram-stain-positive, endospore-forming, rod-shaped, strictly aerobic, motile and produced cream colonies. Strain J8BT grew in NaCl at between 3.0-15.0 % (w/v) (optimally at 7.5 % NaCl, w/v), between pH 6.5-9.0 (optimally at pH 8.0) and between 20-45 °C (optimally at 35 °C). Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain J8BT is a member of the genus Oceanobacillus and most closely related to Oceanobacillus profundus CL-MP28T, Oceanobacillus polygoni SA9T and Oceanobacillus oncorhynchi R-2T (96.9 %, 96.3 % and 96.2 % similarities, respectively). The level of DNA-DNA relatedness between the novel isolate and O. profundus IBRC-M 10567T was 10 %. The major cellular fatty acids of the isolate were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. The polar lipid pattern of strain J8BT consisted of phosphatidylglycerol, diphosphatidylglycerol, five phospholipids, two aminolipids and two glycoaminolipids. It contained MK-7 as the predominant menaquinone and meso-diaminopimelic acid in the cell-wall peptidoglycan. The G+C content of the genomic DNA of this strain was 39.2 mol%. Phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data suggest that this strain represents a novel species of the genus Oceanobacillus, for which the name Oceanobacillus halophilus sp. nov. is proposed. The type strain is strain J8BT ( = IBRC-M 10444T = DSM 23996T).

  6. Oceanobacillus longus sp. nov., a moderately halophilic bacterium isolated from a salt lake.

    Science.gov (United States)

    Amoozegar, Mohammad Ali; Bagheri, Maryam; Makhdoumi, Ali; Mehrshad, Maliheh; Didari, Maryam; Schumann, Peter; Spröer, Cathrin; Sánchez-Porro, Cristina; Ventosa, Antonio

    2016-10-01

    A Gram-stain-positive, endospore-forming, long rod-shaped, strictly aerobic, moderately halophilic bacterium, designated strain T9BT, was isolated from a brine sample of the hypersaline lake Aran-Bidgol in Iran. Cells of strain T9BT were motile and produced colonies with a brown pigment. Growth occurred between 1.0 and 20 % (w/v) NaCl and the isolate grew optimally at 5.0 % (v/w) NaCl. The optimum pH and temperature for growth of the strain were pH 7.0 and 35 °C, while it was able to grow over pH and temperature ranges of pH 6.0-9.0 and 25-45 °C. Phylogenetic analysis based on the comparison of 16S rRNA gene sequences revealed that strain T9BT is a member of the genus Oceanobacillus. The closest relative to this strain was Oceanobacillus rekensis PT-11T with a similarity of 97.4 %, followed by Oceanobacillus profundus CL-MP28T and Oceanobacillus polygoni SA9T with 97.3 and 97.1 % similarity, respectively. The major cellular fatty acids of the isolate were anteiso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. The polar lipids of strain T9BT consisted of phosphatidylglycerol, diphosphatidylglycerol, three phospholipids and one aminoglycolipid. It contained MK-7 as the predominant menaquinone and meso-diaminopimelic acid in the cell-wall peptidoglycan. The G+C content of the genomic DNA of this strain was 42.9 mol%. Phylogenetic analysis, DNA-DNA hybridization data and phenotypic characteristics allowed strain T9BT to be differentiated from other members of the genus Oceanobacillus. A novel species, Oceanobacillus longus sp. nov., is therefore proposed to accommodate this strain. The type strain is T9BT (=IBRC-M 10703T=LMG 29250T).

  7. Bacillus salsus sp. nov., a halophilic bacterium from a hypersaline lake.

    Science.gov (United States)

    Amoozegar, Mohammad Ali; Didari, Maryam; Bagheri, Maryam; Fazeli, Seyed Abolhassan Shahzadeh; Schumann, Peter; Spröer, Cathrin; Sánchez-Porro, Cristina; Ventosa, Antonio

    2013-09-01

    A Gram-staining-positive, endospore-forming, rod-shaped, strictly aerobic, slightly halophilic bacterium, designated strain A24(T), was isolated from the hypersaline lake Aran-Bidgol in Iran. Cells of strain A24(T) were motile rods and produced oval endospores at a terminal position in swollen sporangia. Strain A24(T) was catalase and oxidase positive. Growth occurred with between 0.5 and 7.5% (w/v) NaCl and the isolate grew optimally at 3% (v/w) NaCl. The optimum temperature and pH for growth were 35 °C and pH 8.0, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain A24(T) belonged to the genus Bacillus within the phylum Firmicutes and showed the closest phylogenetic similarity with the species Bacillus alkalitelluris BA288(T) (97.2%), Bacillus herbersteinensis D-1,5a(T) (96.0%) and Bacillus litoralis SW-211(T) (95.6%). The G+C content of the genomic DNA of this strain was 35.9 mol%. The polar lipid pattern of strain A24(T) consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and two unknown phospholipids. The major cellular fatty acids of strain A24(T) were anteiso-C(15:0) and iso-C(15:0). The respiratory quinones were MK-7 (94%) and MK-6 (4%). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. All these features confirm the placement of isolate A24(T) within the genus Bacillus. DNA-DNA hybridization experiments revealed a relatedness of 8% between strain A24(T) and Bacillus alkalitelluris IBRC-M 10596(T), supporting its placement as a novel species. Phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data suggest that this strain represents a novel species of the genus Bacillus, for which the name Bacillus salsus sp. nov. is proposed. The type strain is strain A24(T) ( = IBRC-M 10078 (T) = KCTC 13816(T)).

  8. Marinobacter persicus sp. nov., a moderately halophilic bacterium from a saline lake in Iran.

    Science.gov (United States)

    Bagheri, Maryam; Amoozegar, Mohammad Ali; Didari, Maryam; Makhdoumi-Kakhki, Ali; Schumann, Peter; Spröer, Cathrin; Sánchez-Porro, Cristina; Ventosa, Antonio

    2013-07-01

    A Gram-negative, non-endospore-forming, rod shaped, strictly aerobic, moderately halophilic bacterium, designated strain M9B(T), was isolated from the hypersaline lake Aran-Bidgol in Iran. Cells of strain M9B(T) were found to be motile and produce colonies with an orange-yellow pigment. Growth was determined to occur between 5 and 20 % (w/v) NaCl and the isolate grew optimally at 7.5-10 % (v/w) NaCl. The optimum pH and temperature for growth of the strain were determined to be pH 7.0 and 35 °C, respectively, while it was able to grow over pH and temperature ranges of 6-8 and 25-45 °C, respectively. Phylogenetic analysis based on the comparison of 16S rRNA gene sequences revealed that strain M9B(T) is a member of the genus Marinobacter. The closest relative to this strain was found to be Marinobacter hydrocarbonoclasticus MBIC 1303(T) with a similarity level of 97.7 %. DNA-DNA hybridization between the novel isolate and this phylogenetically related species was 13 ± 2 %. The major cellular fatty acids of the isolate were identified as C16:0, C19:1 ω6c, C18:1 ω9c and C16:1 ω9c. The polar lipid pattern of strain M9B(T) was determined to consist of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine and three phospholipids. Ubiquinone 9 (Q-9) was the only lipoquinone detected. The G+C content of the genomic DNA of this strain was determined to be 58.6 mol%. Phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data suggest that this strain represents a novel species of the genus Marinobacter, for which the name Marinobacter persicus sp. nov. is proposed. The type strain of Marinobacter persicus is strain M9B(T) (=IBRC-M 10445(T) = CCM 7970(T) = CECT 7991(T) = KCTC 23561(T)).

  9. Marinobacter aquaticus sp. nov., a moderately halophilic bacterium from a solar saltern.

    Science.gov (United States)

    León, María José; Sánchez-Porro, Cristina; Ventosa, Antonio

    2017-08-01

    A moderately halophilic bacterium designated strain M6-53T was isolated from water of a pond from a marine saltern located in Huelva, south-west Spain. Cells of the strain were Gram-stain-negative, strictly aerobic, motile, slightly curved rods, able to grow in media containing 5-25 % (w/v) NaCl (optimal growth at 10 %, w/v), at temperatures from 20 to 40 °C (optimally at 37 °C) and at pH 6.5-9 (optimally at pH 7.0). Phylogenetic analysis based on 16S rRNA gene sequences placed the new isolate within the genus Marinobacter, with the type strains of the most closely related species being Marinobacter persicus IBRC-M 10445T (98.5 % similarity), Marinobacter oulmenensis Set74T (97.2 %) and Marinobacter hydrocarbonoclasticus ATCC 49840T (97.1 %). The major fatty acids present in strain M6-53T were C18 : 1ω9c (29.5 %), C16 : 0 (26.7 %), C12 : 0 3-OH (15.1 %), C18 : 0 (10.2 %) and C16 : ω9c (9.6 %). The G+C content of the genomic DNA for this strain was determined to be 56.4 mol%. The DNA-DNA hybridization values between strain M6-53T and M. persicus CECT 7991T, M. oulmenensis CECT 7499T and M. hydrocarbonoclasticus DSM 50418 were 8, 41 and 38 %, respectively. These values are lower than the accepted 70 % threshold and showed that the new isolate represented a different species within the genus Marinobacter. Phylogenetic analysis based on the 16S rRNA gene sequence and the phenotypic, genotypic and chemotaxonomic features of this new isolate support the placement of strain M6-53T as a representative of a novel species of the genus Marinobacter, for which we propose the name Marinobacter aquaticus sp. nov., with strain M6-53T (=CECT 9228T=LMG 30006T) as the type strain.

  10. Oceanobacillus limi sp. nov., a moderately halophilic bacterium from a salt lake.

    Science.gov (United States)

    Amoozegar, Mohammad Ali; Bagheri, Maryam; Makhdoumi-Kakhki, Ali; Didari, Maryam; Schumann, Peter; Spröer, Cathrin; Sánchez-Porro, Cristina; Ventosa, Antonio

    2014-04-01

    A Gram-stain-positive, endospore-forming, rod-shaped, strictly aerobic, moderately halophilic bacterium, designated strain H9B(T), was isolated from a mud sample of the hypersaline lake Aran-Bidgol in Iran. Cells of strain H9B(T) were motile and produced colonies with a yellowish-grey pigment. Growth occurred between 2.5 and 10 % (w/v) NaCl and the isolate grew optimally at 7.5 % (w/v) NaCl. The optimum pH and temperature for growth of the strain were pH 7.0 and 35 °C, respectively, while it was able to grow over pH and temperature ranges of pH 6-10 and 25-45 °C, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain H9B(T) is a member of the genus Oceanobacillus. The closest relative to this strain was Oceanobacillus profundus CL-MP28(T) with 97.1 % 16S rRNA gene sequences similarity. The level of DNA-DNA relatedness between the novel isolate and this phylogenetically related species was 17 %. The major cellular fatty acids of the isolate were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0 and iso-C16 : 0. The polar lipid pattern of strain H9B(T) consisted of phosphatidylglycerol, diphosphatidylglycerol, four phospholipids and an aminolipid. It contained MK-7 as the predominant menaquinone and meso-diaminopimelic acid in the cell-wall peptidoglycan. The G+C content of the genomic DNA of this strain was 37.1 mol%. Phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data suggest that this strain represents a novel species of the genus Oceanobacillus, for which the name Oceanobacillus limi sp. nov. is proposed. The type strain of Oceanobacillus limi is strain H9B(T) ( = IBRC-M 10780(T) = KCTC 13823(T) = CECT 7997(T)).

  11. Rhizobium populi sp. nov., an endophytic bacterium isolated from Populus euphratica.

    Science.gov (United States)

    Rozahon, Manziram; Ismayil, Nurimangul; Hamood, Buayshem; Erkin, Raziya; Abdurahman, Mehfuzem; Mamtimin, Hormathan; Abdukerim, Muhtar; Lal, Rup; Rahman, Erkin

    2014-09-01

    An endophytic bacterium, designated K-38(T), was isolated from the storage liquid in the stems of Populus euphratica trees at the ancient Ugan River in Xinjiang, PR China. Strain K-38(T) was found to be rod-shaped, Gram-stain-negative, aerobic, non-motile and non-spore-forming. Strain K-38(T) grew at temperatures of 25-37 °C (optimum, 28 °C), at pH 6.0-9.0 (optimum, pH 7.5) and in the presence of 0-3 % (w/v) NaCl with 1 % as the optimum concentration for growth. According to phylogenetic analysis based on 16S rRNA gene sequences, strain K-38(T) was assigned to the genus Rhizobium with highest 16S rRNA gene sequence similarity of 97.2 % to Rhizobium rosettiformans W3(T), followed by Rhizobium nepotum 39/7(T) (96.5 %) and Rhizobium borbori DN316(T) (96.2 %). Phylogenetic analysis of strain K-38(T) based on the protein coding genes recA, atpD and nifH confirmed (similarities were less than 90 %) it to be a representative of a distinctly delineated species of the genus Rhizobium. The DNA G+C content was determined to be 63.5 mol%. DNA-DNA relatedness between K-38(T) and R. rosettiformans W3(T) was 48.4 %, indicating genetic separation of strain K-38(T) from the latter strain. The major components of the cellular fatty acids in strain K-38(T) were revealed to be summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c; 57.2 %), C16 : 0 (13.6 %) and summed feature 2 (comprising C12 : 0 aldehyde, C14 : 0 3-OH/iso-C16 : 1 I and/or unknown ECL 10.928; 11.0 %). Polar lipids of strain K-38(T) include phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminophospholipids and two unidentified phospholipids. Q-10 was the major quinone in strain K-38(T). Based on phenotypic, chemotaxonomic and phylogenetic properties, strain K-38(T) represents a novel species of the genus Rhizobium, for which the name Rhizobium populi sp. nov. is proposed

  12. Colwellia echini sp. nov., an agar- and carrageenan-solubilizing bacterium isolated from sea urchin.

    Science.gov (United States)

    Christiansen, Line; Bech, Pernille Kjersgaard; Schultz-Johansen, Mikkel; Martens, Helle Juel; Stougaard, Peter

    2018-02-01

    A novel bacterial strain, A3T, was isolated from the intestines of the sea urchin Strongylocentrotus droebachiensis collected in Øresund, Denmark. The strain was Gram-reaction-negative, rod-shaped and facultatively anaerobic, and displayed growth at 5-25 °C (optimum 20 °C), pH 7-9 (optimum at pH 7) and 1-6 % (w/v) NaCl (optimum 3 %). Furthermore, strain A3T grew on agar, agarose, κ-carrageenan, alginate and laminarin as sole carbon source. Complete liquefaction of agar and κ-carrageenan was observed on solid plate media as a result of enzymatic activities. Major fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The respiratory quinones were determined to be ubiquinones Q-8 (92 %) and Q-7 (8 %), and polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 36.9 mol%. Phylogenetical analyses based on the 16S rRNA gene showed that the bacterium was affiliated with the genus Colwellia within the Alteromonadaceae of the Gammaproteobacteria. The level of 16S rRNA gene sequence similarity between strain A3T and its closest relatives in the genus Colwellia (C. psychrerythraea ATCC 27364T and C. asteriadis KMD 002T) was 97.5 %. The average nucleotide identity between strain A3T and other members of Colwellia was 78.6-80.5 %, and DNA-DNA hybridization prediction revealed values of less than 23 % relatedness between strain A3T and other Colwellia species. The phenotypic, phylogenetic and genomic analyses support the hypothesis that strain A3T represents a novel species of the genus Colwellia, for which the name Colwellia echini sp. nov. is proposed. The type strain is A3T (=LMG 30125T=NCIMB 15095T).

  13. Geobacillus zalihae sp. nov., a thermophilic lipolytic bacterium isolated from palm oil mill effluent in Malaysia

    Directory of Open Access Journals (Sweden)

    Salleh Abu

    2007-08-01

    Full Text Available Abstract Background Thermophilic Bacillus strains of phylogenetic Bacillus rRNA group 5 were described as a new genus Geobacillus. Their geographical distribution included oilfields, hay compost, hydrothermal vent or soils. The members from the genus Geobacillus have a growth temperatures ranging from 35 to 78°C and contained iso-branched saturated fatty acids (iso-15:0, iso-16:0 and iso-17:0 as the major fatty acids. The members of Geobacillus have similarity in their 16S rRNA gene sequences (96.5–99.2%. Thermophiles harboring intrinsically stable enzymes are suitable for industrial applications. The quest for intrinsically thermostable lipases from thermophiles is a prominent task due to the laborious processes via genetic modification. Results Twenty-nine putative lipase producers were screened and isolated from palm oil mill effluent in Malaysia. Of these, isolate T1T was chosen for further study as relatively higher lipase activity was detected quantitatively. The crude T1 lipase showed high optimum temperature of 70°C and was also stable up to 60°C without significant loss of crude enzyme activity. Strain T1T was a Gram-positive, rod-shaped, endospore forming bacterium. On the basic of 16S rDNA analysis, strain T1T was shown to belong to the Bacillus rRNA group 5 related to Geobacillus thermoleovorans (DSM 5366T and Geobacillus kaustophilus (DSM 7263T. Chemotaxonomic data of cellular fatty acids supported the affiliation of strain T1T to the genus Geobacillus. The results of physiological and biochemical tests, DNA/DNA hybridization, RiboPrint analysis, the length of lipase gene and protein pattern allowed genotypic and phenotypic differentiation of strain T1T from its validly published closest phylogenetic neighbors. Strain T1T therefore represents a novel species, for which the name Geobacillus zalihae sp. nov. is proposed, with the type strain T1T (=DSM 18318T; NBRC 101842T. Conclusion Strain T1T was able to secrete extracellular

  14. Ponticoccus marisrubri sp. nov., a moderately halophilic marine bacterium of the family Rhodobacteraceae

    KAUST Repository

    Zhang, Guishan

    2017-10-06

    Strain SJ5A-1T, a Gram-stain-negative, coccus-shaped, non-motile, aerobic bacterium, was isolated from the brine-seawater interface of the Erba Deep in the Red Sea, Saudi Arabia. The colonies of strain SJ5A-1T have a beige to pale-brown pigmentation, are approximately 0.5-0.7 µm in diameter, and are catalase and oxidase positive. Growth occurred optimally at 30-33 °C, pH 7.0-7.5, and in the presence of 9.0-12.0 % NaCl (w/v). Phylogenetic analysis of the 16S rRNA gene indicates that strain SJ5A-1T is a member of the genus Ponticoccus within the family Rhodobacteraceae. Ponticoccus litoralis DSM 18986T is the most closely related described species based on 16S rRNA gene sequence identity (96.7 %). The DNA-DNA hybridization value between strain SJ5A-1T and P. litoralis DSM 18986T was 36.7 %. The major respiratory quinone of strain SJ5A-1T is Q-10; it predominantly uses the fatty acids C18 : 1 (54.2 %), C18 : 0 (11.2 %), C16 : 0 (8.6 %), 11-methyl C18 : 1ω7c (7.7 %), C19 : 0cyclo ω8c (3.3 %), and C12 : 1 3-OH (3.5 %), and its major polar lipids are phosphatidylethanolamine, phosphatidylglycerol, phosphocholine, an unknown aminolipid, an unknown phospholipid and two unknown lipids. The genome draft of strain SJ5A-1T as presented here is 4 562 830 bp in size and the DNA G+C content is 68.0 mol %. Based on phenotypic, phylogenetic and genotypic data, strain SJ5A-1T represents a novel species in the genus Ponticoccus, for which we propose the name Ponticoccus marisrubri sp. nov. The type strain of P. marisrubri is SJ5A-1T (=JCM 19520T=ACCC19863T).

  15. Biotransformation of citrinin to decarboxycitrinin using an organic solvent-tolerant marine bacterium, Moraxella sp. (MB1)

    Digital Repository Service at National Institute of Oceanography (India)

    PrabhaDevi; Naik, C.G.; Rodrigues, C.

    of organic solvents. Hence they may be successfully employed as biocatalysts in non-aqueous conditions (Bont, 1998). In the present study, we use Moraxella sp. MB1 from a marine source as an organic solvent tolerant bacterium. This culture was used... yellow in color, poorly soluble in water but soluble in organic solvents. 2.2. Culture medium During this study two different media namely nutrient agar and nutrient broth medium was used (HiMedia). The nutrient agar medium comprised of 5 g...

  16. Isolation and Characterization of a Thermotolerant Ammonia-Oxidizing Bacterium Nitrosomonas sp. JPCCT2 from a Thermal Power Station

    OpenAIRE

    Itoh, Yoshikane; Sakagami, Keiko; Uchino, Yoshihito; Boonmak, Chanita; Oriyama, Tetsuro; Tojo, Fuyumi; Matsumoto, Mitsufumi; Morikawa, Masaaki

    2013-01-01

    A thermotolerant ammonia-oxidizing bacterium strain JPCCT2 was isolated from activated sludge in a thermal power station. Cells of JPCCT2 are short non-motile rods or ellipsoidal. Molecular phylogenetic analysis of 16S rRNA gene sequences demonstrated that JPCCT2 belongs to the genus Nitrosomonas with the highest similarity to Nitrosomonas nitrosa Nm90 (100%), Nitrosomonas sp. Nm148 (99.7%), and Nitrosomonas communis Nm2 (97.7%). However, G+C content of JPCCT2 DNA was 49.1 mol% and clearly di...

  17. Isolation, purification and spectrometric analysis of PSP toxins from moraxella sp., a bacterium associated with a toxic dinoflagellate

    Energy Technology Data Exchange (ETDEWEB)

    Boyce, S.D.; Doucette, G.J.

    1994-12-31

    Paralytic shellfish poisoning (PSP) is a seafood intoxication syndrome caused by the injestion of shellfish contaminated with toxins produced by algae known as dinoflagellates. The PSP toxins, saxitoxin and its derivatives, act to block voltage-dependent sodium channels and can cause paralysis and even death at higher doses. It is well documented that bacteria coexist with many harmful or toxic algal species, though the exact nature of the association in relation to toxin production is unknown. Recently, the bacterium Moraxella sp. was isolated from the PSP toxin producing dinoflagellate Alexandrium tamarense. Through HPLC analysis and saxitoxin receptor binding assays performed on crude bacterial extracts, it appears that Moraxella sp. is capable of producing saxitoxin and several of its derivatives. However, physical confirmation (e.g. mass spectrometry) of these results is still needed.

  18. Desulfovirga adipica gen. nov., sp. nov., an adipate-degrading, gram-negative, sulfate-reducing bacterium.

    Science.gov (United States)

    Tanaka, K; Stackebrandt, E; Tohyama, S; Eguchi, T

    2000-03-01

    A novel, mesophilic, Gram-negative bacterium was isolated from an anaerobic digestor for municipal wastewater. The bacterium degraded adipate in the presence of sulfate, sulfite, thiosulfate and elemental sulfur. (E)-2-Hexenedioate accumulated transiently in the degradation of adipate. (E)-2-Hexenedioate, (E)-3-hexenedioate, pyruvate, lactate, C1-C12 straight-chain fatty acids and C2-C10 straight-chain primary alcohols were also utilized as electron donors. 3-Phenylpropionate was oxidized to benzoate. The G + C content of the DNA was 60 mol%. 16S rDNA sequence analysis revealed that the new isolate clustered with species of the genus Syntrophobacter and Desulforhabdus amnigenus. Strain TsuAS1T resembles Desulforhabdus amnigenus DSM 10338T with respect to the ability to utilize acetate as an electron donor and the inability to utilize propionate without sulfate in co-culture with Methanospirillum hungatei DSM 864. Strains TsuAS1T and DSM 10338T form a 'non-syntrophic subcluster' within the genus Syntrophobacter. Desulfovirga adipica gen. nov., sp. nov. is proposed for the newly isolated bacterium, with strain TsuAS1T (= DSM 12016T) as the type strain.

  19. Effects of Bacterial Community Members on the Proteome of the Ammonia-Oxidizing Bacterium Nitrosomonas sp. Strain Is79.

    Science.gov (United States)

    Sedlacek, Christopher J; Nielsen, Susanne; Greis, Kenneth D; Haffey, Wendy D; Revsbech, Niels Peter; Ticak, Tomislav; Laanbroek, Hendrikus J; Bollmann, Annette

    2016-08-01

    Microorganisms in the environment do not exist as the often-studied pure cultures but as members of complex microbial communities. Characterizing the interactions within microbial communities is essential to understand their function in both natural and engineered environments. In this study, we investigated how the presence of a nitrite-oxidizing bacterium (NOB) and heterotrophic bacteria affect the growth and proteome of the chemolithoautotrophic ammonia-oxidizing bacterium (AOB) Nitrosomonas sp. strain Is79. We investigated Nitrosomonas sp. Is79 in co-culture with Nitrobacter winogradskyi, in co-cultures with selected heterotrophic bacteria, and as a member of the nitrifying enrichment culture G5-7. In batch culture, N. winogradskyi and heterotrophic bacteria had positive effects on the growth of Nitrosomonas sp. Is79. An isobaric tag for relative and absolute quantification (iTRAQ) liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics approach was used to investigate the effect of N. winogradskyi and the co-cultured heterotrophic bacteria from G5-7 on the proteome of Nitrosomonas sp. Is79. In co-culture with N. winogradskyi, several Nitrosomonas sp. Is79 oxidative stress response proteins changed in abundance, with periplasmic proteins increasing and cytoplasmic proteins decreasing in abundance. In the presence of heterotrophic bacteria, the abundance of proteins directly related to the ammonia oxidation pathway increased, while the abundance of proteins related to amino acid synthesis and metabolism decreased. In summary, the proteome of Nitrosomonas sp. Is79 was differentially influenced by the presence of either N. winogradskyi or heterotrophic bacteria. Together, N. winogradskyi and heterotrophic bacteria reduced the oxidative stress for Nitrosomonas sp. Is79, which resulted in more efficient metabolism. Aerobic ammonia-oxidizing microorganisms play an important role in the global nitrogen cycle, converting ammonia to nitrite. In their

  20. Inhibitory activity of an extract from a marine bacterium Halomonas sp. HSB07 against the red-tide microalga Gymnodinium sp. (Pyrrophyta)

    Science.gov (United States)

    Liu, Juan; Li, Fuchao; Liu, Ling; Jiang, Peng; Liu, Zhaopu

    2013-11-01

    In recent years, red tides occurred frequently in coastal areas worldwide. Various methods based on the use of clay, copper sulfate, and bacteria have been successful in controlling red tides to some extent. As a new defensive agent, marine microorganisms are important sources of compounds with potent inhibitory bioactivities against red-tide microalgae, such as Gymnodinium sp. (Pyrrophyta). In this study, we isolated a marine bacterium, HSB07, from seawater collected from Hongsha Bay, Sanya, South China Sea. Based on its 16S rRNA gene sequence and biochemical characteristics, the isolated strain HSB07 was identified as a member of the genus Halomonas. A crude ethyl acetate extract of strain HSB07 showed moderate inhibition activity against Gymnodinium sp. in a bioactive prescreening experiment. The extract was further separated into fractions A, B, and C by silica gel column chromatography. Fractions B and C showed strong inhibition activities against Gymnodinium. This is the first report of inhibitory activity of secondary metabolites of a Halomonas bacterium against a red-tide-causing microalga.

  1. Draft Genome Sequence of Chloroflexus sp. Strain isl-2, a Thermophilic Filamentous Anoxygenic Phototrophic Bacterium Isolated from the Strokkur Geyser, Iceland.

    Science.gov (United States)

    Gaisin, Vasil A; Ivanov, Timophey M; Kuznetsov, Boris B; Gorlenko, Vladimir M; Grouzdev, Denis S

    2016-07-21

    We report here the draft genome sequence of the thermophilic filamentous anoxygenic phototrophic bacterium Chloroflexus sp. strain isl-2, which was isolated from the Strokkur geyser, Iceland, and contains 5,222,563 bp with a G+C content of 59.65%. The annotated genome sequence offers the genetic basis for understanding the strain's ecological role as a phototrophic bacterium within the bacterial community. Copyright © 2016 Gaisin et al.

  2. Flavobacterium nitratireducens sp. nov., an amylolytic bacterium of the family Flavobacteriaceae isolated from coastal surface seawater

    Digital Repository Service at National Institute of Oceanography (India)

    Nupur; Bhumika, V.; Srinivas, T.N.R.; AnilKumar, P.

    A novel Gram-negative, rod-shaped, non-motile bacterium, designated strain N1 sup(T), was isolated from a marine water sample collected from the sea shore, Bay of Bengal, Visakhapatnam, India. The strain was positive for starch hydrolysis, nitrate...

  3. Marinilabilia nitratireducens sp. nov., a lipolytic bacterium of the family Marinilabiliaceae isolated from marine solar saltern

    Digital Repository Service at National Institute of Oceanography (India)

    Shalley, S.; PradipKumar; Srinivas, T.N.R.; Suresh, K.; AnilKumar, P.

    A Gram-negative, rod shaped, motile bacterium, was isolated from a marine solar saltern sample collected from Kakinada, India. Strain AK2 sup(T) was determined to be positive for nitrate reduction, catalase, Ala-Phe-Pro-arylamidase, beta...

  4. (Per)chlorate reduction by an acetogenic bacterium, Sporomusa sp., isolated from an underground gas storage

    NARCIS (Netherlands)

    Balk, M.; Mehboob, F.; Gelder, van A.H.; Rijpstra, I.; Sinninghe-Damsté, J.S.; Stams, A.J.M.

    2010-01-01

    A mesophilic bacterium, strain An4, was isolated from an underground gas storage reservoir with methanol as substrate and perchlorate as electron acceptor. Cells were Gram-negative, spore-forming, straight to curved rods, 0.5-0.8 microm in diameter, and 2-8 microm in length, growing as single cells

  5. Pseudomonas chloritidismutans sp. nov., a non-denitrifying chlorate-reducing bacterium

    NARCIS (Netherlands)

    Wolterink, A.F.W.M.; Jonker, A.B.; Kengen, S.W.M.; Stams, A.J.M.

    2002-01-01

    A Gram-negative, facultatively anaerobic, rod-shaped, dissimilatory chlorate-reducing bacterium, strain AW-1(T), was isolated from biomass of an anaerobic chlorate-reducing bioreactor. Phylogenetic analysis of the 16S rDNA sequence showed 100␜equence similarity to Pseudomonas stutzeri DSM 50227 and

  6. Genome Sequence of the Acidophilic Bacterium Acidocella sp. Strain MX-AZ02

    DEFF Research Database (Denmark)

    Servín-Garcidueñas, Luis E.; Garrett, Roger A.; Amils, Ricardo

    2013-01-01

    Here, we report the draft genome sequence of Acidocella sp. strain MX-AZ02, an acidophilic and heterotrophic alphaproteobacterium isolated from a geothermal lake in western Mexico.......Here, we report the draft genome sequence of Acidocella sp. strain MX-AZ02, an acidophilic and heterotrophic alphaproteobacterium isolated from a geothermal lake in western Mexico....

  7. The grapevine flagellin receptor VvFLS2 differentially recognizes flagellin-derived epitopes from the endophytic growth-promoting bacterium Burkholderia phytofirmans and plant pathogenic bacteria.

    Science.gov (United States)

    Trdá, Lucie; Fernandez, Olivier; Boutrot, Freddy; Héloir, Marie-Claire; Kelloniemi, Jani; Daire, Xavier; Adrian, Marielle; Clément, Christophe; Zipfel, Cyril; Dorey, Stéphan; Poinssot, Benoit

    2014-03-01

    • The role of flagellin perception in the context of plant beneficial bacteria still remains unclear. Here, we characterized the flagellin sensing system flg22-FLAGELLIN SENSING 2 (FLS2) in grapevine, and analyzed the flagellin perception in the interaction with the endophytic plant growth-promoting rhizobacterium (PGPR) Burkholderia phytofirmans. • The functionality of the grapevine FLS2 receptor, VvFLS2, was demonstrated by complementation assays in the Arabidopsis thaliana fls2 mutant, which restored flg22-induced H₂O₂ production and growth inhibition. Using synthetic flg22 peptides from different bacterial origins, we compared recognition specificities between VvFLS2 and AtFLS2. • In grapevine, flg22-triggered immune responses are conserved and led to partial resistance against Botrytis cinerea. Unlike flg22 peptides derived from Pseudomonas aeruginosa or Xanthomonas campestris, flg22 peptide derived from B. phytofirmans triggered only a small oxidative burst, weak and transient defense gene induction and no growth inhibition in grapevine. Although, in Arabidopsis, all the flg22 epitopes exhibited similar biological activities, the expression of VvFLS2 into the fls2 background conferred differential flg22 responses characteristic for grapevine. • These results demonstrate that VvFLS2 differentially recognizes flg22 from different bacteria, and suggest that flagellin from the beneficial PGPR B. phytofirmans has evolved to evade this grapevine immune recognition system. No claim to original European Union works. New Phytologist © 2013 New Phytologist Trust.

  8. Zoospore homing and infection events: effects of the biocontrol bacterium Burkholderia cepacia AMMDR1 on two oomycete pathogens of pea (Pisum sativum L.).

    Science.gov (United States)

    Heungens, K; Parke, J L

    2000-12-01

    Burkholderia cepacia AMMDR1 is a biocontrol agent that protects pea and sweet corn seeds from Pythium damping-off in field experiments. The goal of this work was to understand the effect of B. cepacia AMMDR1 on Pythium aphanidermatum and Aphanomyces euteiches zoospore homing events and on infection of pea seeds or roots. In vitro, B. cepacia AMMDR1 caused zoospore lysis, prevented cyst germination, and inhibited germ tube growth of both oomycetes. B. cepacia AMMDR1 also reduced the attractiveness of seed exudates to Pythium zoospores to nondetectable levels. However, when present at high levels on seeds, B. cepacia AMMDR1 had little net effect on zoospore attraction, probably because it also enhanced seed exudation. Seed-applied B. cepacia AMMDR1 dramatically reduced the incidence of infection by Pythium zoospores in situ compared with an antibiosis-deficient Tn5 mutant strain. This mutant strain also decreased Pythium infection incidence to some extent, but only when the pathogen inoculum potential was low. B. cepacia AMMDR1 did not affect attraction of Aphanomyces zoospores or Aphanomyces root rot incidence. These results suggest that B. cepacia AMMDR1 controls P. aphanidermatum largely through antibiosis, but competition for zoospore-attracting compounds can contribute to the effect. Differences in suppression of Aphanomyces and Pythium are discussed in relation to differences in the ecology of the two pathogens.

  9. An extremely thermophilic anaerobic bacterium Caldicellulosiruptor sp. F32 exhibits distinctive properties in growth and xylanases during xylan hydrolysis.

    Science.gov (United States)

    Ying, Yu; Meng, Dongdong; Chen, Xiaohua; Li, Fuli

    2013-08-15

    An anaerobic, extremely thermophilic, and cellulose- and xylan-degrading bacterium F32 was isolated from biocompost. Sequence analysis of the 16S rRNA gene of this strain showed that it was closely related to Caldicellulosiruptor saccharolyticus DSM 8903 (99.0% identity). Physiological and biochemical data also supported that identification of strain F32 as a Caldicellulosiruptor species. The proteins secreted by Caldicellulosiruptor sp. F32 grown on xylan showed a xylanase activity of 7.74U/mg, which was 2.5 times higher than that of C. saccharolyticus DSM 8903. Based on the genomic sequencing data, 2 xylanase genes, JX030400 and JX030401, were identified in Caldicellulosiruptor sp. F32. The xylanase encoded by JX030401 shared 97% identity with Csac_0696 of C. saccharolyticus DSM 8903, while that encoded by JX030400 shared 94% identity with Athe_0089 of C. bescii DSM 6725, which was not found in the genome of strain DSM 8903. Xylanse encoded by JX030400 had 9-fold higher specific activity than JX030401. Our results indicated that although the 2 strains shared high identity, the xylanase system in Caldicellulosiruptor sp. F32 was more efficient than that in C. saccharolyticus DSM 8903. Copyright © 2013 Elsevier Inc. All rights reserved.

  10. The novel oleaginous bacterium Sphingomonas sp. EGY1 DSM 29616: a value added platform for renewable biodiesel.

    Science.gov (United States)

    Amer, Nehad N; Elbahloul, Yasser; Embaby, Amira M; Hussein, Ahmed

    2017-07-01

    Oleaginous microorganisms are regarded as efficient, renewable cell factories for lipid biosynthesis, a biodiesel precursor, to overwhelm the cosmopolitan energy crisis with affordable investment capital costs. Present research highlights production and characterization of lipids by a newly isolated oleaginous bacterium, Sphingomonas sp. EGY1 DSM 29616 through an eco-friendly approach. Only sweet whey [42.1% (v/v)] in tap water was efficiently used as a growth medium and lipid production medium to encourage cell growth and trigger lipid accumulation simultaneously. Cultivation of Sphingomonas sp. EGY1 DSM 29616 in shake flasks resulted in the accumulation of 8.5 g L(-1) lipids inside the cells after 36 h at 30 °C. Triglycerides of C16:C18 saturated and unsaturated fatty acids showed a similar pattern to tripalmitin or triolein; deduced from gas chromatography (GC), thin layer chromatography (TLC), and Matrix-assisted laser desorption/ionization time-of-flight-mass spectra analysis (MALDI-TOF-MS) analyses. Batch cultivation 2.5 L in a laboratory scale fermenter led to 13.8 g L(-1) accumulated lipids after 34 h at 30 °C. Present data would underpin the potential of Sphingomonas sp. EGY1 DSM 29616 as a novel renewable cell factory for biosynthesis of biodiesel.

  11. Genome Sequence of the Dichloromethane-Degrading Bacterium Hyphomicrobium sp. Strain GJ21

    NARCIS (Netherlands)

    Bringel, Françoise; Postema, Christiaan P; Mangenot, Sophie; Bibi-Triki, Sabrina; Chaignaud, Pauline; Farhan Ul Haque, Muhammad; Gruffaz, Christelle; Hermon, Louis; Louhichi, Yousra; Maucourt, Bruno; Muller, Emilie E L; Nadalig, Thierry; Lajus, Aurélie; Rouy, Zoé; Médigue, Claudine; Barbe, Valérie; Janssen, Dick B; Vuilleumier, Stéphane

    2017-01-01

    The genome sequence of Hyphomicrobium sp. strain GJ21, isolated in the Netherlands from samples of environments contaminated with halogenated pollutants and capable of using dichloromethane as its sole carbon and energy source, was determined.

  12. Kinetics of transesterification of olive oil with methanol catalyzed by immobilized lipase derived from an isolated Burkholderia sp. strain.

    Science.gov (United States)

    Tran, Dang-Thuan; Lin, Yi-Jan; Chen, Ching-Lung; Chang, Jo-Shu

    2013-10-01

    This work was carried out to investigate the acyl migration phenomena which has been considered as the factor having significant impact on kinetics of transesterification of oils catalyzed by a Burkholderia lipase with 1,3-regioselectivity. Transesterification of olive oil with methanol catalyzed by the immobilized lipase produces various intermediates, including 1-monoglyceride, 2-monoglyceride, 1,2-diglyceride, and 1,3-diglyceride. Migration kinetics of fatty acid groups from sn-2 of 2-monoglyceride and 1,2-diglyceride to 1-monoglyceride and 1,3-diglyceride were investigated for the temperature range of 25-65°C. The kinetics of transesterification of olive oil with methanol involving acyl migration in the presence of water was also systematically studied at 25, 40, and 65°C. Increasing temperature could increase the acyl migration rate. The overall biodiesel conversion was improved from 73.4% (at 25°C) to 90.0% and 92.4% when conducting at 40 and 65°C, respectively. Thermodynamics aspects of equilibrium state of the immobilized lipase-catalyzed transesterification were also discussed. Copyright © 2013 Elsevier Ltd. All rights reserved.

  13. Noncontiguous finished genome sequence and description of Virgibacillus massiliensis sp. nov., a moderately halophilic bacterium isolated from human gut

    Directory of Open Access Journals (Sweden)

    S. Khelaifia

    2015-11-01

    Full Text Available Strain Vm-5T was isolated from the stool specimen of a 10-year-old Amazonian boy. This bacterium is a Gram-positive, strictly aerobic rod, motile by a polar flagellum. Here we describe its phenotypic characteristics and complete genome sequence. The 4 353 177 bp long genome exhibits a G + C content of 36.87% and contains 4394 protein-coding and 125 predicted RNA genes. Phylogenetically and genetically, strain Vm-c is a member of the genus Virgibacillus but is distinct enough to be classified as a new species. We propose the creation of V. massiliensis sp. nov., whose type strain is strain Vm-5T (CSUR P971 = DSM 28587.

  14. Enhancement of cadmium bioremediation by endophytic bacterium Bacillus sp. L14 using industrially used metabolic inhibitors (DCC or DNP)

    Energy Technology Data Exchange (ETDEWEB)

    Luo Shenglian, E-mail: sllou@hnu.cn [College of Environmental Science and Engineering, Hunan University, Changsha 410082 (China); Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082 (China); State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082 (China); Key Laboratory of Jiangxi Province for Ecological Diagnosis-Remediation and Pollution Control, Nanchang 330063 (China); Xiao Xiao [College of Environmental Science and Engineering, Hunan University, Changsha 410082 (China); Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082 (China); Xi Qiang [State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082 (China); Wan Yong; Chen Liang; Zeng Guangming [College of Environmental Science and Engineering, Hunan University, Changsha 410082 (China); Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082 (China); Liu Chengbin [State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082 (China); Guo Hanjun; Chen Jueliang [College of Environmental Science and Engineering, Hunan University, Changsha 410082 (China); Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082 (China)

    2011-06-15

    Bioremediations of cadmium by endophytic bacterium (EB) L14 (Bacillus sp.) in the presence of industrially used metabolic inhibitors (DCC or DNP) were investigated. In the presence of DCC or DNP, the biomass population of EB L14 was greatly inhibited. However, the cadmium removal of EB L14 increased from 73.6% (in the absence of DCC or DNP) to 93.7% and 80.8%, respectively. The analysis of total and intracellular cadmium concentrations during 24 h of incubation indicated that this enhanced cadmium removal was the inhibition effect of DCC or DNP on the cations export resistance system of EB L14. This unique property strongly indicated the superiority of this endophyte for practical application in cadmium bioremediation in the presence of industrially used metabolic inhibitors.

  15. Cloning and biochemical characterization of a glucosidase from a marine bacterium Aeromonas sp. HC11e-3.

    Science.gov (United States)

    Huang, Xiaoluo; Zhao, Yan; Dai, Yunjing; Wu, Gaobing; Shao, Zongze; Zeng, Qinglan; Liu, Ziduo

    2012-12-01

    By constructing the genomic library, a β-glucosidase gene, with a length of 2,382 bp, encoding 793 amino acids, designated bgla, is cloned from a marine bacterium Aeromonas sp. HC11e-3. The enzyme is expressed successfully in the recombinant host Escherichia coli BL21 (DE3) and purified using glutathione affinity purification system. It shows the optimal activity at pH 6, 55 °C and hydrolyzes aryl-glucoside specially. Ca(2+), Mn(2+), Zn(2+), Ba(2+), Pb(2+), Sr(2+) can activate the enzyme activity, whereas SDS, EDTA, DTT show slight inhibition to the enzyme activity. Homologous comparing shows that the enzyme belongs to glycosyl hydrolase family 3, exhibiting 46 % identity with a fully characterized glucosidase from Thermotoga neapolitana DSM 4359. Such results provide useful references for investigating other glucosidases in the glycosyl family 3 as well as developing glucosidases using in suitable industrial area.

  16. Complete Genome Sequence Analysis of Enterobacter sp. SA187, a Plant Multi-Stress Tolerance Promoting Endophytic Bacterium

    KAUST Repository

    Andres-Barrao, Cristina

    2017-10-20

    Enterobacter sp. SA187 is an endophytic bacterium that has been isolated from root nodules of the indigenous desert plant Indigofera argentea. SA187 could survive in the rhizosphere as well as in association with different plant species, and was able to provide abiotic stress tolerance to Arabidopsis thaliana. The genome sequence of SA187 was obtained by using Pacific BioScience (PacBio) single-molecule sequencing technology, with average coverage of 275X. The genome of SA187 consists of one single 4,429,597 bp chromosome, with an average 56% GC content and 4,347 predicted protein coding DNA sequences (CDS), 153 ncRNA, 7 rRNA, and 84 tRNA. Functional analysis of the SA187 genome revealed a large number of genes involved in uptake and exchange of nutrients, chemotaxis, mobilization and plant colonization. A high number of genes were also found to be involved in survival, defense against oxidative stress and production of antimicrobial compounds and toxins. Moreover, different metabolic pathways were identified that potentially contribute to plant growth promotion. The information encoded in the genome of SA187 reveals the characteristics of a dualistic lifestyle of a bacterium that can adapt to different environments and promote the growth of plants. This information provides a better understanding of the mechanisms involved in plant-microbe interaction and could be further exploited to develop SA187 as a biological agent to improve agricultural practices in marginal and arid lands.

  17. Isolation and characterization of a thermotolerant ammonia-oxidizing bacterium Nitrosomonas sp. JPCCT2 from a thermal power station.

    Science.gov (United States)

    Itoh, Yoshikane; Sakagami, Keiko; Uchino, Yoshihito; Boonmak, Chanita; Oriyama, Tetsuro; Tojo, Fuyumi; Matsumoto, Mitsufumi; Morikawa, Masaaki

    2013-01-01

    A thermotolerant ammonia-oxidizing bacterium strain JPCCT2 was isolated from activated sludge in a thermal power station. Cells of JPCCT2 are short non-motile rods or ellipsoidal. Molecular phylogenetic analysis of 16S rRNA gene sequences demonstrated that JPCCT2 belongs to the genus Nitrosomonas with the highest similarity to Nitrosomonas nitrosa Nm90 (100%), Nitrosomonas sp. Nm148 (99.7%), and Nitrosomonas communis Nm2 (97.7%). However, G+C content of JPCCT2 DNA was 49.1 mol% and clearly different from N. nitrosa Nm90, 47.9%. JPCCT2 was capable of growing at temperatures up to 48 °C, while N. nitrosa Nm90 and N. communis Nm2 could not grow at 42°C. Moreover, JPCCT2 grew similarly at concentrations of carbonate 0 and 5 gL(-1). This is the first report that Nitrosomonas bacterium is capable of growing at temperatures higher than 37°C.

  18. Anoxynatronum buryatiense sp. nov., an anaerobic alkaliphilic bacterium from a low mineralization soda lake in Buryatia, Russia.

    Science.gov (United States)

    Ryzhmanova, Yana; Oshurkova, Victoria; Troshina, Olga; Abashina, Tatyana; Ariskina, Elena; Avtukh, Alexander; Shcherbakova, Viktoria

    2017-11-01

    An anaerobic alkaliphilic, proteolytic bacterium, strain Su22T, was isolated from the bottom sediment of the alkaline low mineralization lake Sulphatnoe (Selenginsky district, Buryatia, Russia). A comparative analysis of the 16S rRNA gene sequence revealed that this bacterium was closely related to Anoxynatronum sibiricum Z-7981T with a similarity of 98.1 %. Strain Su22T differed from A. sibiricum Z-7981T in its inability to use carbohydrates, peptone and amino acids as carbon sources. Strain Su22T grew over a temperature range of 20-40 °C with an optimum at 30 °C and within the pH range 7.4-11.0 with an optimum at pH 9.6. Sodium cations stimulated the growth of the strain considerably with an optimal concentration at 0.76-1.09 M. The whole-cell fatty acid profile included C16 : 1ω7c, C16 : 0 and C16 : 0 ALDE. The G+C content was 46.1 mol%. Based on the DNA-DNA hybridization level (53.2 %) and phenotypical differences between strains Su22T and Z-7981T, the new isolate is thus considered to represent a novel species, for which the name Anoxynatronumburyatiense sp. nov. is proposed. The type strain is Su22Т (=VKM B-2510T=CECT 8731T).

  19. Study on human intestinal bacterium Blautia sp. AUH-JLD56 for the conversion of arctigenin to (-)-3'-desmethylarctigenin.

    Science.gov (United States)

    Liu, Ming-Yue; Li, Meng; Wang, Xiu-Ling; Liu, Peng; Hao, Qing-Hong; Yu, Xiu-Mei

    2013-12-11

    Arctium lappa L. (A. lappa) is a popularly used vegetable as well as herbal medicine. Human intestinal microflora was reported to convert arctiin, the lignan compound with highest content in the dried fruits of Arctium lappa, to a series of metabolites. However, the specific bacterium responsible for the formation of 3'-desmethylarctigenin (3'-DMAG), the most predominant metabolite of arctiin by rat or human intestinal microflora, has not been isolated yet. In the present study, we isolated one single bacterium, which we named Blautia sp. AUH-JLD56, capable of solely biotransforming arctiin or arctigenin to (-)-3'-DMAG. The structure of the metabolite 3'-DMAG was elucidated by electrospray ionization mass spectrometry (ESI-MS) and (1)H and (13)C nuclear magnetic resonance spectroscopy. The biotransforming kinetics and maximum biotransforming capacity of strain AUH-JLD56 was investigated. In addition, the metabolite 3'-DMAG showed significantly higher 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging activity than that of the substrate arctigenin at the concentrations tested.

  20. Microbacterium natoriense sp. nov., a novel D-aminoacylase-producing bacterium isolated from soil in Natori, Japan.

    Science.gov (United States)

    Liu, Jian; Nakayama, Toru; Hemmi, Hisashi; Asano, Yu; Tsuruoka, Naoki; Shimomura, Kengo; Nishijima, Miyuki; Nishino, Tokuzo

    2005-03-01

    A rod-shaped, Gram-positive bacterium, strain TNJL143-2(T), having N-acyl-D-amino acid amidohydrolase (D-aminoacylase) activity, was isolated from a soil sample from Natori, Japan. It was a non-spore-forming, strictly aerobic bacterium without motility, showing a temperature optimum for growth of 30 degrees C and a pH optimum for growth of 5-7. The 16S rRNA gene sequence of the strain showed the highest similarities to members of the genus Microbacterium, in particular, Microbacterium aerolatum, Microbacterium foliorum and Microbacterium phyllosphaerae. The chemotaxonomic characteristics, including the compositions of cellular menaquinones, cellular fatty acids and cell-wall amino acids, were consistent with those described for the genus Microbacterium. The G+C content of the genomic DNA was determined as 69.1 mol%. DNA-DNA hybridization studies using type strains of M. aerolatum, M. foliorum and M. phyllosphaerae showed only low levels of relatedness (11-12 %). On the basis of these phenotypic and genotypic results, a novel species, Microbacterium natoriense sp. nov., is proposed, with TNJL143-2(T) (=JCM 12611(T)=ATCC BAA-1032(T)) as the type strain.

  1. The death mechanism of the harmful algal bloom species Alexandrium tamarense induced by algicidal bacterium Deinococcus sp. Y35

    Directory of Open Access Journals (Sweden)

    Yi eLi

    2015-09-01

    Full Text Available Abstract: Harmful algal blooms (HABs cause a variety of deleterious effects on aquatic ecosystems, especially the toxic dinoflagellate Alexandrium tamarense, which poses a serious threat to marine economic and human health based on releasing paralytic shellfish poison into the environment. The algicidal bacterium Deinococcus sp. Y35 which can induce growth inhibition on A. tamarense was used to investigate the functional mechanism. The growth status, reactive oxygen species (ROS content, photosynthetic system and the nuclear system of algal cells were determined under algicidal activity. A culture of strain Y35 not only induced overproduction of ROS in algal cells within only 0.5 h of treatment, also decrease the total protein content as well as the response of the antioxidant enzyme. Meanwhile, lipid peroxidation was induced and cell membrane integrity was lost. Photosynthetic pigments including chlorophyll a and carotenoid decreased along with the photosynthetic efficiency being significantly inhibited. At the same time, photosynthesis-related gene expression showed down-regulation. More than, the destruction of cell nuclear structure and inhibition of proliferating cell nuclear antigen related gene expression were confirmed. The potential functional mechanism of the algicidal bacterium on A. tamarense was investigated and provided a novel viewpoint which could be used in HABs control.

  2. The death mechanism of the harmful algal bloom species Alexandrium tamarense induced by algicidal bacterium Deinococcus sp. Y35.

    Science.gov (United States)

    Li, Yi; Zhu, Hong; Lei, Xueqian; Zhang, Huajun; Cai, Guanjing; Chen, Zhangran; Fu, Lijun; Xu, Hong; Zheng, Tianling

    2015-01-01

    Harmful algal blooms (HABs) cause a variety of deleterious effects on aquatic ecosystems, especially the toxic dinoflagellate Alexandrium tamarense, which poses a serious threat to marine economic and human health based on releasing paralytic shellfish poison into the environment. The algicidal bacterium Deinococcus sp. Y35 which can induce growth inhibition on A. tamarense was used to investigate the functional mechanism. The growth status, reactive oxygen species (ROS) content, photosynthetic system and the nuclear system of algal cells were determined under algicidal activity. A culture of strain Y35 not only induced overproduction of ROS in algal cells within only 0.5 h of treatment, also decrease the total protein content as well as the response of the antioxidant enzyme. Meanwhile, lipid peroxidation was induced and cell membrane integrity was lost. Photosynthetic pigments including chlorophyll a and carotenoid decreased along with the photosynthetic efficiency being significantly inhibited. At the same time, photosynthesis-related gene expression showed down-regulation. More than, the destruction of cell nuclear structure and inhibition of proliferating cell nuclear antigen (PCNA) related gene expression were confirmed. The potential functional mechanism of the algicidal bacterium on A. tamarense was investigated and provided a novel viewpoint which could be used in HABs control.

  3. Phosphate Solubilization and Gene Expression of Phosphate-Solubilizing Bacterium Burkholderia multivorans WS-FJ9 under Different Levels of Soluble Phosphate.

    Science.gov (United States)

    Zeng, Qingwei; Wu, Xiaoqin; Wang, Jiangchuan; Ding, Xiaolei

    2017-04-28

    Phosphate-solubilizing bacteria (PSB) have the ability to dissolve insoluble phosphate and enhance soil fertility. However, the growth and mineral phosphate solubilization of PSB could be affected by exogenous soluble phosphate and the mechanism has not been fully understood. In the present study, the growth and mineral phosphate-solubilizing characteristics of PSB strain Burkholderia multivorans WS-FJ9 were investigated at six levels of exogenous soluble phosphate (0, 0.5, 1, 5, 10, and 20 mM). The WS-FJ9 strain showed better growth at high levels of soluble phosphate. The phosphate-solubilizing activity of WS-FJ9 was reduced as the soluble phosphate concentration increased, as well as the production of pyruvic acid. Transcriptome profiling of WS-FJ9 at three levels of exogenous soluble phosphate (0, 5, and 20 mM) identified 446 differentially expressed genes, among which 44 genes were continuously up-regulated when soluble phosphate concentration was increased and 81 genes were continuously down-regulated. Some genes related to cell growth were continuously up-regulated, which would account for the better growth of WS-FJ9 at high levels of soluble phosphate. Genes involved in glucose metabolism, including glycerate kinase, 2-oxoglutarate dehydrogenase, and sugar ABC-type transporter, were continuously down-regulated, which indicates that metabolic channeling of glucose towards the phosphorylative pathway was negatively regulated by soluble phosphate. These findings represent an important first step in understanding the molecular mechanisms of soluble phosphate effects on the growth and mineral phosphate solubilization of PSB.

  4. Draft Genome Sequence of a Chitinase-producing Biocontrol Bacterium Serratia sp. C-1

    Directory of Open Access Journals (Sweden)

    Seur Kee Park

    2015-09-01

    Full Text Available The chitinase-producing bacterial strain C-1 is one of the key chitinase-producing biocontrol agents used for effective bioformulations for biological control. These bioformulations are mixed cultures of various chitinolytic bacteria. However, the precise identification, biocontrol activity, and the underlying mechanisms of the strain C-1 have not been investigated so far. Therefore, we evaluated in planta biocontrol efficacies of C-1 and determined the draft genome sequence of the strain in this study. The bacterial C-1 strain was identified as a novel Serratia sp. by a phylogenic analysis of its 16S rRNA sequence. The Serratia sp. C-1 bacterial cultures showed strong in planta biocontrol efficacies against some major phytopathogenic fungal diseases. The draft genome sequence of Serratia sp. C-1 indicated that the C-1 strain is a novel strain harboring a subset of genes that may be involved in its biocontrol activities.

  5. (Per)chlorate reduction by an acetogenic bacterium, Sporomusa sp., isolated from an underground gas storage.

    KAUST Repository

    Balk, Melike

    2010-08-03

    A mesophilic bacterium, strain An4, was isolated from an underground gas storage reservoir with methanol as substrate and perchlorate as electron acceptor. Cells were Gram-negative, spore-forming, straight to curved rods, 0.5-0.8 microm in diameter, and 2-8 microm in length, growing as single cells or in pairs. The cells grew optimally at 37 degrees C, and the pH optimum was around 7. Strain An4 converted various alcohols, organic acids, fructose, acetoin, and H(2)/CO(2) to acetate, usually as the only product. Succinate was decarboxylated to propionate. The isolate was able to respire with (per)chlorate, nitrate, and CO(2). The G+C content of the DNA was 42.6 mol%. Based on the 16S rRNA gene sequence analysis, strain An4 was most closely related to Sporomusa ovata (98% similarity). The bacterium reduced perchlorate and chlorate completely to chloride. Key enzymes, perchlorate reductase and chlorite dismutase, were detected in cell-free extracts.

  6. Genome Sequence of the Dichloromethane-Degrading Bacterium Hyphomicrobium sp. Strain GJ21.

    Science.gov (United States)

    Bringel, Françoise; Postema, Christiaan P; Mangenot, Sophie; Bibi-Triki, Sabrina; Chaignaud, Pauline; Farhan Ul Haque, Muhammad; Gruffaz, Christelle; Hermon, Louis; Louhichi, Yousra; Maucourt, Bruno; Muller, Emilie E L; Nadalig, Thierry; Lajus, Aurélie; Rouy, Zoé; Médigue, Claudine; Barbe, Valérie; Janssen, Dick B; Vuilleumier, Stéphane

    2017-07-27

    The genome sequence of Hyphomicrobium sp. strain GJ21, isolated in the Netherlands from samples of environments contaminated with halogenated pollutants and capable of using dichloromethane as its sole carbon and energy source, was determined. Copyright © 2017 Bringel et al.

  7. Genome of Cupriavidus sp. HMR-1, a Heavy Metal-Resistant Bacterium

    OpenAIRE

    Li, Li-Guan; Cai, Lin; Zhang, Tong

    2013-01-01

    Cupriavidus sp. HMR-1 was isolated from a heavy metal-enriched culture of activated sludge from a wastewater treatment plant in Hong Kong. Here, we release the HMR-1 genome to provide basic genetic characteristics for a better understanding of its multiple heavy metal resistance properties.

  8. Herpetosiphon gulosus sp. nov., a filamentous predatory bacterium isolated from sandy soil and Herpetosiphon giganteus sp. nov., nom. rev.

    Science.gov (United States)

    Pan, Xinli; Kage, Hirokazu; Martin, Karin; Nett, Markus

    2017-07-01

    Three filamentous gliding bacteria from the German Collection of Microorganisms and Cell Cultures, Hp g11, Hp g471 and Hp g472, were subjected to a phylogenetic analysis. These organisms had previously been classified as members of the genus Herpetosiphon based on their growth physiology and morphology. However, a taxonomic assignment at the species level had not been carried out. Analysis of 16S rRNA sequences now confirmed the close relationship of strain Hp g472 to Herpetosiphon aurantiacus DSM 785T (98.6 % nucleotide identity) and Herpetosiphon geysericola DSM 7119T (97.7 %). The results of DNA-DNA hybridization experiments further implied that strain Hp g472 should be classified as a distinct species. The DNA G+C content of strain Hp g472 was 49.9 mol%. The major quinone was MK-10 and the predominant cellular fatty acids were C18 : 1, C16 : 1 and C16 : 0. Based on phenotypic, chemotaxonomic and phylogenetic data it was concluded that strain Hp g472 represents a novel species of the genus Herpetosiphon, for which the name Herpetosiphon gulosus sp. nov. is proposed. The type strain is Hp g472T (=DSM 52871T=NBRC 112829T). In contrast to Hp g472T, the strains Hp g11 and Hp g471 exhibited closest 16S rRNA gene sequence similarity (>99 %) with 'Herpetosiphon giganteus' Hp a2. The distinctive genotypic and phenotypic properties of the latter supported the revival of the name as Herpetosiphon giganteus (ex Reichenbach & Golecki, 1975) sp. nov., nom. rev. We propose the previously deposited reference strain DSM 589T=NBRC 112828T as the type strain.

  9. Wenzhouxiangella marina gen. nov, sp. nov, a marine bacterium from the culture broth of Picochlorum sp. 122, and proposal of Wenzhouxiangellaceae fam. nov. in the order Chromatiales.

    Science.gov (United States)

    Wang, Guanghua; Tang, Mingxing; Li, Tao; Dai, Shikun; Wu, Huanlian; Chen, Chenghao; He, Hui; Fan, Jiewei; Xiang, Wenzhou; Li, Xiang

    2015-06-01

    A Gram-stain negative, non-motile, non-phototrophic, non-alkaliphilic, obligately aerobic, chemoheterotrophic, and rod-shaped bacterium, designated strain Ma-11(T), was isolated from the culture broth of a marine microalga, Picochloruma sp. 122. Phylogenetic analyses showed that strain Ma-11(T) has less than 91 % similarity to its closest relative, Thioalkalivibrio sulfidiphilus HL-EbGR7(T), represents a distinct phylogenetic lineage in the order Chromatiales, and could not be assigned to any defined families in this order. Chemotaxonomic, genetic and physiological characteristics, including major fatty acids, genomic G+C content, lack of motility, aerophilicity and chemoheterotrophicity, could readily distinguish strain Ma-11(T) from any established members of the order Chromatiales. Based on the 16S rRNA gene sequence analysis and its signature nucleotide pattern, a new family Wenzhouxiangellaceae fam. nov. comprising the genus Wenzhouxiangella gen. nov. and species Wenzhouxiangella marina sp. nov. is proposed. The type strain is Ma-11(T) (=CGMCC 1.14936(T) = KCTC 42284(T) = MCCC 1K00261(T)).

  10. Characterization of a fluoride-resistant bacterium Acinetobacter sp. RH5 towards assessment of its water defluoridation capability

    Science.gov (United States)

    Mukherjee, Shraboni; Yadav, Vaibhav; Mondal, Madhumanti; Banerjee, Soumya; Halder, Gopinath

    2017-07-01

    The present study investigates the defluoridation capability of fluoride-resistant bacteria from contaminated groundwater collected from Asanjola and Madhabpur, West Bengal, India. Seven strains of fluoride-resistant bacteria were isolated employing culture media containing 10-250 mg/L of fluoride to evaluate their ability in reducing fluoride concentration in water. Five isolates exhibited significant amount of reduction in fluoride. Isolate RH5 achieved a maximum fluoride removal of 25.7 % from the media at 30 °C and pH 7 after 8 days of incubation. Based on morphological, physiological characteristics and analysis of 16S rDNA gene sequence, isolate RH5 was identified as Acinetobacter sp. RH5. Growth of RH5 was analysed at a diverse pH range, and it could thrive at pH 5-10. The present investigation revealed that the selective pressure of fluoride results in growth of fluoride-resistant bacteria capable of secreting high-affinity anion-binding compounds. This bacterium played a dominant bioremediative role by concentrating the anions so that they become less available. Hence, the fluoride-resistant bacteria, Acinetobacter sp. RH5, could be used as a promising strain for application in water defluoridation from contaminated sites.

  11. Aerobic-heterotrophic nitrogen removal through nitrate reduction and ammonium assimilation by marine bacterium Vibrio sp. Y1-5.

    Science.gov (United States)

    Li, Yating; Wang, Yanru; Fu, Lin; Gao, Yizhan; Zhao, Haixia; Zhou, Weizhi

    2017-04-01

    An aerobic marine bacterium Vibrio sp. Y1-5 was screened to achieve efficient nitrate and ammonium removal simultaneously and fix nitrogen in cells without N loss. Approximately 98.0% of nitrate (100mg/L) was removed in 48h through assimilatory nitrate reduction and nitrate reductase was detected in the cytoplasm. Instead of nitrification, the strain assimilated ammonium directly, and it could tolerate as high as 1600mg/L ammonium concentration while removing 844.6mg/L. In addition, ammonium assimilation occurred preferentially in the medium containing nitrate and ammonium with a total nitrogen (TN) removal efficiency of 80.4%. The results of nitrogen balance and Fourier infrared spectra illustrated that the removed nitrogen was all transformed to protein or stored as organic nitrogen substances in cells and no N was lost in the process. Toxicological studies with the brine shrimp species Artemia naupliia indicated that Vibrio sp. Y1-5 can be applied in aquatic ecosystems safely. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Co-inoculation of an antibiotic-producing bacterium and a lytic enzyme-producing bacterium for the biocontrol of tomato wilt caused by Fusarium oxysporum f. sp. lycopersici.

    Science.gov (United States)

    Someya, Nobutaka; Tsuchiya, Kenichi; Yoshida, Takanobu; Noguchi, Masako T; Akutsu, Katsumi; Sawada, Hiroyuki

    2007-03-01

    The antifungal compound 2,4-diacetylphloroglucinol-producing bacterium, Pseudomonas fluorescens strain LRB3W1, inhibits the growth of Fusarium oxysporum f. sp. lycopersici, and controls Fusarium wilt of tomato caused by F. oxysporum f. sp. lycopersici. On the other hand, Serratia marcescens strain B2, which produces cell wall-degrading enzyme chitinases, did not inhibit fungal growth and the suppressive effect of strain B2 against tomato Fusarium wilt was less than that of strain LRB3W1. Combined inoculation of strain LRB3W1 with strain B2 was more effective than treatment with strain LRB3W1 alone. When 2,4-diacetylphloroglucinol and the chitinolytic enzymes were applied in combination, a synergistic inhibitory effect against the pathogen was observed. It was possible that bacteria which produce cell wall-degrading enzymes enhanced the biocontrol effect of the antibiotic-producing bacterium against tomato Fusarium wilt.

  13. Isolation and characterization of a chromium-resistant bacterium Serratia sp. Cr-10 from a chromate-contaminated site

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Kundi; Li, Fuli [Chinese Academy of Sciences, Qingdao (China). Qingdao Inst. of Bioenergy and Bioprocess Technology

    2011-05-15

    A novel bacterium, Cr-10, was isolated from a chromium-contaminated site and capable of removing toxic chromium species from solution by reducing hexavalent chromium to an insoluble precipitate. Sequence analysis of 16S rRNA gene of strain Cr-10 showed that it was most closely related to Serratia rubidaea JCM 1240{sup T} (97.68%). Physiological and chemotaxonomic data also supported that strain Cr-10 was identified as Serratia sp., a genus which was never specially reported chromate-resistant before. Serratia sp., Cr-10 was tolerant to a concentration of 1,500 mg Cr(VI) L{sup -1}, which was the highest level reported until now. The optimum pH and temperature for reduction of Cr(VI) by Serratia sp. Cr-10 were found to be 7.0 and 37 C, respectively. The Cr(VI) reduction was significantly influenced by additional carbon sources, and among them fructose and lactose offered maximum reduction, with a rate of 0.28 and 0.25 mg Cr(VI) L{sup -1} h{sup -1}, respectively. The cell-free extracts and filtrate of the culture were able to reduce Cr(VI) while concentration of total chromium remained stable in the process, indicating that the enzyme-catalyzed mechanism was applied in Cr(VI) reduction by the isolate. Additionally, it was found that there was hardly any chromium on the cell surface of the strain, further supporting that reduction, rather than bioadsorption, plays a major role in the Cr(VI) removal. (orig.)

  14. Enterobacter sacchari sp. nov., a nitrogen-fixing bacterium associated with sugar cane (Saccharum officinarum L.).

    Science.gov (United States)

    Zhu, Bo; Zhou, Qing; Lin, Li; Hu, Chunjin; Shen, Ping; Yang, Litao; An, Qianli; Xie, Guanlin; Li, Yangrui

    2013-07-01

    Five nitrogen-fixing bacterial strains (SP1(T), NN143, NN144, NN208 and HX148) were isolated from stem, root or rhizosphere soil of sugar cane (Saccharum officinarum L.) plants. Cells were Gram-negative, motile, rods with peritrichous flagella. DNA G+C content was 55.0 ± 0.5 mol%. Sequence determinations and phylogenetic analysis of 16S rRNA gene and rpoB indicated that the strains were affiliated with the genus Enterobacter and most closely related to E. radicincitans DSM 16656(T) and E. oryzae LMG 24251(T). Fluorimetric determination of thermal denaturation temperatures after DNA-DNA hybridization, enterobacterial repetitive intergenic consensus PCR and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry differentiated the whole-genome, genotype and protein profiles from those of E. radicincitans and E. oryzae. The strains' cell fatty acid composition differentiated them from E. radicincitans and E. oryzae by containing a higher level of summed feature 2 (C16 : 1ω7c and/or C16 : 1ω6c) and a lower level of C17 : 0 cyclo. Their physiological and biochemical profiles differentiated them from E. radicincitans by being positive for methyl red test, ornithine decarboxylase and utilization of putrescine, D-arabitol, L-fucose and methyl α-D-glucoside and being negative for arginine dihydrolase, and differentiated them from E. oryzae by being positive for aesculin hydrolysis and utilization of putrescine, D-arabitol and L-rhamnose and being negative for arginine dihydrolase, lysine decarboxylase and utilization of mucate. The five strains therefore represent a novel species, for which the name Enterobacter sacchari sp. nov. is proposed, with the type strain SP1(T) ( = CGMCC 1.12102(T) = LMG 26783(T)).

  15. Does S-metolachlor affect the performance of Pseudomonas sp. strain ADP as bioaugmentation bacterium for atrazine-contaminated soils?

    Directory of Open Access Journals (Sweden)

    Cristina A Viegas

    Full Text Available Atrazine (ATZ and S-metolachlor (S-MET are two herbicides widely used, often as mixtures. The present work examined whether the presence of S-MET affects the ATZ-biodegradation activity of the bioaugmentation bacterium Pseudomonas sp. strain ADP in a crop soil. S-MET concentrations were selected for their relevance in worst-case scenarios of soil contamination by a commercial formulation containing both herbicides. At concentrations representative of application of high doses of the formulation (up to 50 µg g(-1 of soil, corresponding to a dose approximately 50× higher than the recommended field dose (RD, the presence of pure S-MET significantly affected neither bacteria survival (~10(7 initial viable cells g(-1 of soil nor its ATZ-mineralization activity. Consistently, biodegradation experiments, in larger soil microcosms spiked with 20× or 50 × RD of the double formulation and inoculated with the bacterium, revealed ATZ to be rapidly (in up to 5 days and extensively (>96% removed from the soil. During the 5 days, concentration of S-MET decreased moderately to about 60% of the initial, both in inoculated and non-inoculated microcosms. Concomitantly, an accumulation of the two metabolites S-MET ethanesulfonic acid and S-MET oxanilic acid was found. Despite the dissipation of almost all the ATZ from the treated soils, the respective eluates were still highly toxic to an aquatic microalgae species, being as toxic as those from the untreated soil. We suggest that this high toxicity may be due to the S-MET and/or its metabolites remaining in the soil.

  16. Does S-Metolachlor Affect the Performance of Pseudomonas sp. Strain ADP as Bioaugmentation Bacterium for Atrazine-Contaminated Soils?

    Science.gov (United States)

    Viegas, Cristina A.; Costa, Catarina; André, Sandra; Viana, Paula; Ribeiro, Rui; Moreira-Santos, Matilde

    2012-01-01

    Atrazine (ATZ) and S-metolachlor (S-MET) are two herbicides widely used, often as mixtures. The present work examined whether the presence of S-MET affects the ATZ-biodegradation activity of the bioaugmentation bacterium Pseudomonas sp. strain ADP in a crop soil. S-MET concentrations were selected for their relevance in worst-case scenarios of soil contamination by a commercial formulation containing both herbicides. At concentrations representative of application of high doses of the formulation (up to 50 µg g−1 of soil, corresponding to a dose approximately 50× higher than the recommended field dose (RD)), the presence of pure S-MET significantly affected neither bacteria survival (∼107 initial viable cells g−1 of soil) nor its ATZ-mineralization activity. Consistently, biodegradation experiments, in larger soil microcosms spiked with 20× or 50×RD of the double formulation and inoculated with the bacterium, revealed ATZ to be rapidly (in up to 5 days) and extensively (>96%) removed from the soil. During the 5 days, concentration of S-MET decreased moderately to about 60% of the initial, both in inoculated and non-inoculated microcosms. Concomitantly, an accumulation of the two metabolites S-MET ethanesulfonic acid and S-MET oxanilic acid was found. Despite the dissipation of almost all the ATZ from the treated soils, the respective eluates were still highly toxic to an aquatic microalgae species, being as toxic as those from the untreated soil. We suggest that this high toxicity may be due to the S-MET and/or its metabolites remaining in the soil. PMID:22615921

  17. From metagenomics to pure culture: isolation and characterization of the moderately halophilic bacterium Spiribacter salinus gen. nov., sp. nov.

    Science.gov (United States)

    León, María José; Fernández, Ana B; Ghai, Rohit; Sánchez-Porro, Cristina; Rodriguez-Valera, Francisco; Ventosa, Antonio

    2014-07-01

    Recent metagenomic studies on saltern ponds with intermediate salinities have determined that their microbial communities are dominated by both Euryarchaeota and halophilic bacteria, with a gammaproteobacterium closely related to the genera Alkalilimnicola and Arhodomonas being one of the most predominant microorganisms, making up to 15% of the total prokaryotic population. Here we used several strategies and culture media in order to isolate this organism in pure culture. We report the isolation and taxonomic characterization of this new, never before cultured microorganism, designated M19-40(T), isolated from a saltern located in Isla Cristina, Spain, using a medium with a mixture of 15% salts, yeast extract, and pyruvic acid as the carbon source. Morphologically small curved cells (young cultures) with a tendency to form long spiral cells in older cultures were observed in pure cultures. The organism is a Gram-negative, nonmotile bacterium that is strictly aerobic, non-endospore forming, heterotrophic, and moderately halophilic, and it is able to grow at 10 to 25% (wt/vol) NaCl, with optimal growth occurring at 15% (wt/vol) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparison showed that strain M19-40(T) has a low similarity with other previously described bacteria and shows the closest phylogenetic similarity with species of the genera Alkalilimnicola (94.9 to 94.5%), Alkalispirillum (94.3%), and Arhodomonas (93.9%) within the family Ectothiorhodospiraceae. The phenotypic, genotypic, and chemotaxonomic features of this new bacterium showed that it constitutes a new genus and species, for which the name Spiribacter salinus gen. nov., sp. nov., is proposed, with strain M19-40(T) (= CECT 8282(T) = IBRC-M 10768(T) = LMG 27464(T)) being the type strain. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  18. Photobacterium galatheae sp. nov., a bioactive bacterium isolated from a mussel in the Solomon Sea

    DEFF Research Database (Denmark)

    Machado, Henrique; Giubergia, Sonia; Mateiu, Ramona Valentina

    2015-01-01

    A novel, Gram-negative marine bacterium, S2753T, was isolated from a mussel of the Solomon Sea, Solomon Islands. Analysis of the 16S rRNA gene sequence and whole genome sequence data placed strain S2753T in the genus Photobacterium with the closest relative being Photobacterium halotolerans...... DSM 18316T (97.7 % 16S rRNA gene similarity). Strain S2753T was able to grow from 15 to 40 °C and in NaCl concentrations of 0.5 to 9 % (w/v). The predominant fatty acids were 16 : 1ω7c/16 : 1ω6c (27.9 %), 16 : 0 (22.1 %) and 18 : 1ω7c/8 : 1ω6c (21.4 %). The genomic DNA G+C mol content was 49.5 mol%. Based...

  19. Desulfuromonas thiophila sp. nov., a new obligately sulfur-reducing bacterium from anoxic freshwater sediment

    Science.gov (United States)

    Finster, K.; Coates, J.D.; Liesack, W.; Pfennig, N.

    1997-01-01

    A mesophilic, acetate-oxidizing, sulfur-reducing bacterium, strain NZ27(T), was isolated from anoxic mud from a freshwater sulfur spring. The cells were ovoid, motile, and gram negative. In addition to acetate, the strain oxidized pyruvate, succinate, and fumarate. Sulfur flower could be replaced by polysulfide as an electron acceptor. Ferric nitrilotriacetic acid was reduced in the presence of pyruvate; however, this reduction did not sustain growth. These phenotypic characteristics suggested that strain NZ27(T) is affiliated with the genus Desulfuromonas. A phylogenetic analysis based on the results of comparative 16S ribosomal DNA sequencing confirmed that strain NZ27(T) belongs to the Desulfuromonas cluster in the recently proposed family 'Geobacteraceae' in the delta subgroup of the Proteobacteria. In addition, the results of DNA-DNA hybridization studies confirmed that strain NZ27(T) represents a novel species. Desulfuromonas thiophila, a name tentatively used in previous publications, is the name proposed for strain NZ27(T) in this paper.

  20. Purification and characterization of chitinase B from moderately thermophilic bacterium Ralstonia sp. A-471.

    Science.gov (United States)

    Ueda, Mitsuhiro; Kotani, Yukiko; Sutrisno, Aji; Nakazawa, Masami; Miyatake, Kazutaka

    2005-04-01

    Chitinase B was purified from a culture medium of Ralstonia sp. A-471 by precipitation with (NH4)2SO4 and column chromatography with DEAE-Toyopearl 650 M and Sephacryl S-200. The purified enzyme was homogeneous on SDS-PAGE. The molecular weight was 45,000 by SDS-PAGE. The optimum pH was 5.0 and stable pH was from 5.0 to 10.0. In the early stage of the reaction, chitinase B produced beta-anomer of (GlcNAc)2 from the substrate (GlcNAc)6, whereas (GlcNAc)4 produced almost at equilibrium, indicating that the enzyme predominantly hydrolyzes the second glycosidic linkage from the nonreducing end of (GlcNAc)6.

  1. NMR structural study of fructans produced by Bacillus sp. 3B6, bacterium isolated in cloud water.

    Science.gov (United States)

    Matulová, Mária; Husárová, Slavomíra; Capek, Peter; Sancelme, Martine; Delort, Anne-Marie

    2011-03-01

    Bacillus sp. 3B6, bacterium isolated from cloud water, was incubated on sucrose for exopolysaccharide production. Dialysis of the obtained mixture (MWCO 500) afforded dialyzate (DIM) and retentate (RIM). Both were separated by size exclusion chromatography. RIM afforded eight fractions: levan exopolysaccharide (EPS), fructooligosaccharides (FOSs) of levan and inulin types with different degrees of polymerization (dp 2-7) and monosaccharides fructose:glucose=9:1. Levan was composed of two components with molecular mass ~3500 and ~100kDa in the ratio 2.3:1. Disaccharide fraction contained difructose anhydride DFA IV. 1-Kestose, 6-kestose, and neokestose were identified as trisaccharides in the ratio 2:1:3. Fractions with dp 4-7 were mixtures of FOSs of levan (2,6-βFruf) and inulin (1,2-βFruf) type. DIM separation afforded two dominant fractions: monosaccharides with fructose: glucose ratio 1:3; disaccharide fraction contained sucrose only. DIM trisaccharide fraction contained 1-kestose, 6-kestose, and neokestose in the ratio1.5:1:2, penta and hexasaccharide fractions contained FOSs of levan type (2,6-βFruf) containing α-glucose. In the pentasaccharide fraction also the presence of a homopentasaccharide composed of 2,6-linked βFruf units only was identified. Nystose, inulin (1,2-βFruf) type, was identified as DIM tetrasaccharide. Identification of levan 2,6-βFruf and inulin 1,2-βFruf type oligosaccharides in the incubation medium suggests both levansucrase and inulosucrase enzymes activity in Bacillus sp. 3B6. Copyright © 2010 Elsevier Ltd. All rights reserved.

  2. Thiocapsa imhoffii, sp. nov., an alkaliphilic purple sulfur bacterium of the family Chromatiaceae from Soap Lake, Washington (USA).

    Science.gov (United States)

    Asao, Marie; Takaichi, Shinichi; Madigan, Michael T

    2007-12-01

    An alkaliphilic purple sulfur bacterium, strain SC5, was isolated from Soap Lake, a soda lake located in east central Washington state (USA). Cells of strain SC5 were gram-negative, non-motile, and non-gas vesiculate cocci, often observed in pairs or tetrads. In the presence of sulfide, elemental sulfur was deposited internally. Liquid cultures were pink to rose red in color. Cells contained bacteriochlorophyll a and spirilloxanthin as major photosynthetic pigments. Internal photosynthetic membranes were of the vesicular type. Optimal growth of strain SC5 occurred in the absence of NaCl (range 0-4%), pH 8.5 (range pH 7.5-9.5), and 32 degrees C. Photoheterotrophic growth occurred in the presence of sulfide or thiosulfate with only a limited number of organic carbon sources. Growth factors were not required, and cells could fix N2. Dark, microaerobic growth occurred in the presence of both an organic carbon source and thiosulfate. Sulfide and thiosulfate served as electron donors for photoautotrophy, which required elevated levels of CO2. Phylogenetic analysis placed strain SC5 basal to the clade of the genus Thiocapsa in the family Chromatiaceae with a 96.7% sequence similarity to its closest relative, Thiocapsa roseopersicina strain 1711T (DSM217T). The unique assemblage of physiological and phylogenetic properties of strain SC5 defines it as a new species of the genus Thiocapsa, and we describe strain SC5 herein as Tca. imhoffii, sp. nov.

  3. Isolation of cellulase-producing bacteria and characterization of the cellulase from the isolated bacterium Cellulomonas sp. YJ5.

    Science.gov (United States)

    Yin, Li-Jung; Huang, Po-Shin; Lin, Hsin-Hung

    2010-09-08

    A cellulase-producing bacterium was isolated from soil and identified as Cellulomonas sp. YJ5. Maximal cellulase activity was obtained after 48 h of incubation at 30 degrees C in a medium containing 1.0% carboxymethyl cellulose (CMC), 1.0% algae powder, 1.0% peptone, 0.24% (NH4)2SO4, 0.20% K2HPO4, and 0.03% MgSO(4).7H2O. The cellulase was purified after Sephacryl S-100 chromatography twice with a recovery of 27.9% and purification fold of 17.5. It was, with N-terminal amino acids of AGTKTPVAK, stable at pH 7.5-10.5 and 20-50 degrees C with optimal pH and temperature of 7.0 and 60 degrees C, respectively. Cu2+, Fe2+, Hg2+, Cr3+, and SDS highly inhibited, but cysteine and beta-mercaptoethanol activated, its activity. Substrate specificity indicated it to be an endo-beta-1,4-glucanase.

  4. Isolation and Characterization of Two Cryptic Plasmids in the Ammonia-Oxidizing Bacterium Nitrosomonas sp. Strain ENI-11

    Science.gov (United States)

    Yamagata, Akira; Kato, Junichi; Hirota, Ryuichi; Kuroda, Akio; Ikeda, Tsukasa; Takiguchi, Noboru; Ohtake, Hisao

    1999-01-01

    Two plasmids were discovered in the ammonia-oxidizing bacterium Nitrosomonas sp. strain ENI-11, which was isolated from activated sludge. The plasmids, designated pAYS and pAYL, were relatively small, being approximately 1.9 kb long. They were cryptic plasmids, having no detectable plasmid-linked antibiotic resistance or heavy metal resistance markers. The complete nucleotide sequences of pAYS and pAYL were determined, and their physical maps were constructed. There existed two major open reading frames, ORF1 in pAYS and ORF2 in pAYL, each of which was more than 500 bp long. The predicted product of ORF2 was 28% identical to part of the replication protein of a Bacillus plasmid, pBAA1. However, no significant similarity to any known protein sequences was detected with the predicted product of ORF1. pAYS and pAYL had a highly homologous region, designated HHR, of 262 bp. The overall identity was 98% between the two nucleotide sequences. Interestingly, HHR-homologous sequences were also detected in the genomes of ENI-11 and the plasmidless strain Nitrosomonas europaea IFO14298. Deletion analysis of pAYS and pAYL indicated that HHR, together with either ORF1 or ORF2, was essential for plasmid maintenance in ENI-11. To our knowledge, pAYS and pAYL are the first plasmids found in the ammonia-oxidizing autotrophic bacteria. PMID:10348848

  5. Caldicellulosiruptor obsidiansis sp. nov., an anaerobic, extremely thermophilic, cellulolytic bacterium isolated from Obsidian Pool, Yellowstone National Park.

    Science.gov (United States)

    Hamilton-Brehm, Scott D; Mosher, Jennifer J; Vishnivetskaya, Tatiana; Podar, Mircea; Carroll, Sue; Allman, Steve; Phelps, Tommy J; Keller, Martin; Elkins, James G

    2010-02-01

    A novel, obligately anaerobic, extremely thermophilic, cellulolytic bacterium, designated OB47(T), was isolated from Obsidian Pool, Yellowstone National Park, WY. The isolate was a nonmotile, non-spore-forming, Gram-positive rod approximately 2 microm long by 0.2 microm wide and grew at temperatures between 55 and 85 degrees C, with the optimum at 78 degrees C. The pH range for growth was 6.0 to 8.0, with values of near 7.0 being optimal. Growth on cellobiose produced the fastest specific growth rate at 0.75 h(-1). The organism also displayed fermentative growth on glucose, maltose, arabinose, fructose, starch, lactose, mannose, sucrose, galactose, xylose, arabinogalactan, Avicel, xylan, filter paper, processed cardboard, pectin, dilute acid-pretreated switchgrass, and Populus. OB47(T) was unable to grow on mannitol, fucose, lignin, Gelrite, acetate, glycerol, ribose, sorbitol, carboxymethylcellulose, and casein. Yeast extract stimulated growth, and thiosulfate, sulfate, nitrate, and sulfur were not reduced. Fermentation end products were mainly acetate, H2, and CO2, although lactate and ethanol were produced in 5-liter batch fermentations. The G+C content of the DNA was 35 mol%, and sequence analysis of the small subunit rRNA gene placed OB47(T) within the genus Caldicellulosiruptor. Based on its phylogenetic and phenotypic properties, the isolate is proposed to be designated Caldicellulosiruptor obsidiansis sp. nov. and OB47 is the type strain (ATCC BAA-2073).

  6. Thermodesulfobacterium geofontis sp. nov., a hyperthermophilic, sulfate-reducing bacterium isolated from Obsidian Pool, Yellowstone National Park.

    Science.gov (United States)

    Hamilton-Brehm, Scott D; Gibson, Robert A; Green, Stefan J; Hopmans, Ellen C; Schouten, Stefan; van der Meer, Marcel T J; Shields, John P; Damsté, Jaap S S; Elkins, James G

    2013-03-01

    A novel sulfate-reducing bacterium designated OPF15(T) was isolated from Obsidian Pool, Yellowstone National Park, Wyoming. The phylogeny of 16S rRNA and functional genes (dsrAB) placed the organism within the family Thermodesulfobacteriaceae. The organism displayed hyperthermophilic temperature requirements for growth with a range of 70-90 °C and an optimum of 83 °C. Optimal pH was around 6.5-7.0 and the organism required the presence of H2 or formate as an electron donor and CO2 as a carbon source. Electron acceptors supporting growth included sulfate, thiosulfate, and elemental sulfur. Lactate, acetate, pyruvate, benzoate, oleic acid, and ethanol did not serve as electron donors. Membrane lipid analysis revealed diacyl glycerols and acyl/ether glycerols which ranged from C14:0 to C20:0. Alkyl chains present in acyl/ether and diether glycerol lipids ranged from C16:0 to C18:0. Straight, iso- and anteiso-configurations were found for all lipid types. The presence of OPF15(T) was also shown to increase cellulose consumption during co-cultivation with Caldicellulosiruptor obsidiansis, a fermentative, cellulolytic extreme thermophile isolated from the same environment. On the basis of phylogenetic, phenotypic, and structural analyses, Thermodesulfobacterium geofontis sp. nov. is proposed as a new species with OPF15(T) representing the type strain.

  7. Desulfohalophilus alkaliarsenatis gen. nov., sp. nov., an extremely halophilic sulfate- and arsenate-respiring bacterium from Searles Lake, California

    Science.gov (United States)

    Blum, Jodi Switzer; Kulp, Thomas R.; Han, Sukkyun; Lanoil, Brian; Saltikov, Chad W.; Stolz, John F.; Miller, Laurence G.; Oremland, Ronald S.

    2012-01-01

    A haloalkaliphilic sulfate-respiring bacterium, strain SLSR-1, was isolated from a lactate-fed stable enrichment culture originally obtained from the extreme environment of Searles Lake, California. The isolate proved capable of growth via sulfate-reduction over a broad range of salinities (125–330 g/L), although growth was slowest at salt-saturation. Strain SLSR-1 was also capable of growth via dissimilatory arsenate-reduction and displayed an even broader range of salinity tolerance (50–330 g/L) when grown under these conditions. Strain SLSR-1 could also grow via dissimilatory nitrate reduction to ammonia. Growth experiments in the presence of high borate concentrations indicated a greater sensitivity of sulfate-reduction than arsenate-respiration to this naturally abundant anion in Searles Lake. Strain SLSR-1 contained genes involved in both sulfate-reduction (dsrAB) and arsenate respiration (arrA). Amplicons of 16S rRNA gene sequences obtained from DNA extracted from Searles Lake sediment revealed the presence of close relatives of strain SLSR-1 as part of the flora of this ecosystem despite the fact that sulfate-reduction activity could not be detected in situ. We conclude that strain SLSR-1 can only achieve growth via arsenate-reduction under the current chemical conditions prevalent at Searles Lake. Strain SLSR-1 is a deltaproteobacterium in the family Desulfohalobiacea of anaerobic, haloalkaliphilic bacteria, for which we propose the name Desulfohalophilus alkaliarsenatis gen. nov., sp. nov.

  8. Exiguobacterium indicum sp. nov., a psychrophilic bacterium from the Hamta glacier of the Himalayan mountain ranges of India.

    Science.gov (United States)

    Chaturvedi, Preeti; Shivaji, S

    2006-12-01

    Strain HHS 31(T), a Gram-positive, motile, rod-shaped, non-spore-forming, alkaliphilic bacterium, was isolated from the melt water of a glacier. Phenotypic and chemotaxonomic characteristics indicate that strain HHS 31(T) is related to species of the genus Exiguobacterium. The 16S rRNA gene sequence similarities between HHS 31(T) and strains of known species confirm that it is closely related to members of the genus Exiguobacterium (93-99 %) and that it exhibits >97 % similarity with Exiguobacterium acetylicum DSM 20416(T) (98.9 %), Exiguobacterium antarcticum DSM 14480(T) (98.0 %), Exiguobacterium oxidotolerans JCM 12280(T) (97.9 %) and Exiguobacterium undae DSM 14481(T) (97.4 %). Phylogenetic analysis based on the 16S rRNA gene sequence further confirms the affiliation of HHS 31(T) with the genus Exiguobacterium. However, the levels of DNA-DNA relatedness between HHS 31(T) and E. oxidotolerans JCM 12280(T), E. acetylicum DSM 20416(T), E. undae DSM 14481(T) and E. antarcticum DSM 14480(T) are 50, 63, 67 and 28 %, respectively. Strain HHS 31(T) also differs from these four closely related species in terms of a number of phenotypic traits. The phenotypic, chemotaxonomic and phylogenetic data suggest that HHS 31(T) merits the status of a novel species, for which the name Exiguobacterium indicum sp. nov. is proposed. The type strain is HHS 31(T) (=LMG 23471(T)=IAM 15368(T)).

  9. Methylobacterium marchantiae sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the thallus of a liverwort.

    Science.gov (United States)

    Schauer, S; Kämpfer, P; Wellner, S; Spröer, C; Kutschera, U

    2011-04-01

    A pink-pigmented, facultatively methylotrophic bacterium, designated strain JT1(T), was isolated from a thallus of the liverwort Marchantia polymorpha L. and was analysed by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis placed the strain in a clade with Methylobacterium adhaesivum AR27(T), Methylobacterium fujisawaense DSM 5686(T), Methylobacterium radiotolerans JCM 2831(T) and Methylobacterium jeotgali S2R03-9(T), with which it showed sequence similarities of 97.8, 97.7, 97.2 and 97.4 %, respectively. However, levels of DNA-DNA relatedness between strain JT1(T) and these and the type strains of other closely related species were lower than 70 %. Cells of JT1(T) stained Gram-negative and were motile, rod-shaped and characterized by numerous fimbriae-like appendages on the outer surface of their wall (density up to 200 µm(-2)). Major fatty acids were C(18 : 1)ω7c and C(16 : 0). Based on the morphological, physiological and biochemical data presented, strain JT1(T) is considered to represent a novel species of the genus Methylobacterium, for which the name Methylobacterium marchantiae sp. nov. is proposed. The type strain is JT1(T) ( = DSM 21328(T)  = CCUG 56108(T)).

  10. Caldimicrobium rimae gen. nov., sp. nov., an extremely thermophilic, facultatively lithoautotrophic, anaerobic bacterium from the Uzon Caldera, Kamchatka.

    Science.gov (United States)

    Miroshnichenko, Margarita L; Lebedinsky, Alexander V; Chernyh, N A; Tourova, Tatyana P; Kolganova, Tatyana V; Spring, Stefan; Bonch-Osmolovskaya, Elizaveta A

    2009-05-01

    An extremely thermophilic, strictly anaerobic, facultatively chemolithoautotrophic bacterium designated strain DS(T) was isolated from Treshchinnyi Spring, one of the hottest springs of the Uzon Caldera (Kamchatka, Russia). Cells of the novel organism were Gram-negative rods, about 1.0-1.2 microm long and 0.5 microm wide. The temperature range for growth was 52-82 degrees C, with an optimum at 75 degrees C. Growth was observed at pH 6.8-7.4, and the optimum pH was 7.0-7.2. Strain DS(T) was able to grow lithoautotrophically with hydrogen in the presence of CO(2) as a carbon source and thiosulfate or elemental sulfur as an electron acceptor. It also grew well with ethanol, fumarate, succinate or malate in the presence of thiosulfate. Yeast extract was not required for growth and did not stimulate growth. The genomic DNA G+C content was 35.2 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that the novel organism was a member of the family Thermodesulfobacteriaceae. On the basis of phylogenetic and physiological considerations, it is proposed that strain DS(T) represents a new genus and species, Caldimicrobium rimae gen. nov., sp. nov. The type strain of Caldimicrobium rimae is DS(T) (=DSM 19393(T) =VKM B-2460(T)).

  11. Gilvimarinus agarilyticus sp. nov., a new agar-degrading bacterium isolated from the seashore of Jeju Island.

    Science.gov (United States)

    Kim, Byung-Chun; Kim, Mi Na; Lee, Kang Hyun; Kim, Hyun Soon; Min, Sung Ran; Shin, Kee-Sun

    2011-06-01

    An agarolytic bacterium, designated as strain M5c(T), was isolated from sea sand in Jeju Island, Korea. This isolate was Gram-negative, positive for catalase and oxidase, rod and motile by means of monotrichous flagella. Strain M5c(T) has translucent or dark ivory colonies, forms a dent on an agar plate under colonies, and grows in the presence of 1-12% (w/v) NaCl and at 10-37°C. This isolate hydrolyzes agar, alginic acid, carboxymethyl (CM)-cellulose and starch. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain M5c(T) can be considered as a species within the genus Gilvimarinus, being most closely related to Gilvimarinus chinensis QM42(T), with a 16S rRNA gene sequence similarity of 95.6%. The major cellular fatty acids were C16:1ω7c and/or iso-C15:0 2OH (33.5%), C16:0 (26.5%) and C18:1ω7c (14.1%). The DNA G+C content was 53.8 mol%. Based on these polyphasic data, strain M5c(T) should be classified as a novel species, for which the name Gilvimarinus agarilyticus sp. nov. is proposed. The type strain for the novel species is M5c(T) (= KCTC 23325(T) = NCAIM B 02425(T)).

  12. Marinobacterium mangrovicola sp. nov., a marine nitrogen-fixing bacterium isolated from mangrove roots of Rhizophora mangle.

    Science.gov (United States)

    Alfaro-Espinoza, Gabriela; Ullrich, Matthias S

    2014-12-01

    A nitrogen-fixing marine bacterium, designated strain Gal22(T), was isolated from mangrove roots of Rhizophora mangle. Cells were Gram-stain-negative rods, motile with a single polar flagellum. Growth was observed at 4-42 °C, pH 5.5 to 10 and with 0-18 % (w/v) NaCl. Strain Gal22(T) was positive for catalase and oxidase. Q-8 was the predominant lipoquinone. The DNA G+C content was 57.0 mol%. Based on phylogenetic analysis of 16S rRNA gene, strain Gal22(T) belongs to the genus Marinobacterium. The closely related strains were shown to be Marinobacterium lutimaris DSM 22012(T) and Marinobacterium litorale IMCC1877(T) with 99 % and 96 % 16S rRNA gene sequence similarity, respectively. DNA-DNA relatedness analysis indicated that strain Gal22(T) was different from M. lutimaris DSM 22012(T). On the basis of genotypic, morphological and biochemical characteristics, a novel species, Marinobacterium mangrovicola sp. nov. (type strain, Gal22(T) = DSM 27697(T) = CIP 110653(T)), is proposed. © 2014 IUMS.

  13. Phototrophic Growth and Accumulation of Poly(3-hydroxybutyrate-co-3-hydroxyvalerate by Purple Nonsulfur Bacterium Rhodopseudomonas palustris SP5212

    Directory of Open Access Journals (Sweden)

    M. Mukhopadhyay

    2013-01-01

    Full Text Available The ability of the phototrophic bacterium Rhodopseudomonas palustris SP5212 to produce polyhydroxyalkanoates (PHAs, poly(3-hydroxybutyrate-co-3-hydroxyvalerate [P(3HB-co-3HV] in particular was, assessed in acetate medium supplemented with hydroxybutyrate and valerate as cosubstrates. The isolate accumulated the polymer accounting for some 49.06% and 30% of cell dry weight when grown in hydroxybutyrate and valerate, respectively. PHA accumulation as well as 3HV monomer incorporation (30 mol% was maximum at 0.1% hydroxybutyrate, while valerate at 0.1% and 0.3% was suitable for total polymer accumulation and 3HV monomer incorporation, respectively. Cosupplementation of hydroxybutyrate and valerate in the ratio of 3 : 1 led to the accumulation of PHA accounting for 54% of cell dry weight, which contained more than 50 mol% of 3HV monomer. Moreover, the biphasic cultivation conditions with hydroxybutyrate as cosubstrate have improved the quality as well as quantity of the accumulated copolymer significantly.

  14. Cloning, Expression, Purification, and Characterization of Glutaredoxin from Antarctic Sea-Ice Bacterium Pseudoalteromonas sp. AN178

    Directory of Open Access Journals (Sweden)

    Quanfu Wang

    2014-01-01

    Full Text Available Glutaredoxins (Grxs are small ubiquitous redox enzymes that catalyze glutathione-dependent reactions to reduce protein disulfide. In this study, a full-length Grx gene (PsGrx with 270 nucleotides was isolated from Antarctic sea-ice bacterium Pseudoalteromonas sp. AN178. It encoded deduced 89 amino acid residues with the molecular weight 9.8 kDa. Sequence analysis of the amino acid sequence revealed the catalytic motif CPYC. Recombinant PsGrx (rPsGrx stably expressed in E. coli BL21 was purified to apparent homogeneity by Ni-affinity chromatography. rPsGrx exhibited optimal activity at 30°C and pH 8.0 and showed 25.5% of the activity at 0°C. It retained 65.0% of activity after incubation at 40°C for 20 min and still exhibited 37.0% activity in 1.0 M NaCl. These results indicated that rPsGrx was a typical cold active protein with low thermostability.

  15. Thermodesulfobacterium geofontis sp. nov., a hyperthermophilic, sulfate-reducing bacterium isolated from Obsidian Pool, Yellowstone National Park

    Energy Technology Data Exchange (ETDEWEB)

    Hamilton-Brehm, Scott D.; Gibson, Robert A.; Green, Stefan J.; Hopmans, Ellen C.; Schouten, Stefan; van der Meer, Marcel T. J.; Shields, John P.; Damsté, Jaap S. S.; Elkins, James G.

    2013-01-24

    A novel sulfate-reducing bacterium designated OPF15T was isolated from Obsidian Pool, Yellowstone National Park, Wyoming. The phylogeny of 16S rRNA and functional genes (dsrAB) placed the organism within the family Thermodesulfobacteriaceae. The organism displayed hyperthermophilic temperature requirements for growth with a range of 70 90 C and an optimum of 83 C. Optimal pH was around 6.5 7.0 and the organism required the presence of H2 or formate as an electron donor and CO2 as a carbon source. Electron acceptors supporting growth included sulfate, thiosulfate, and elemental sulfur. Lactate, acetate, pyruvate, benzoate, oleic acid, and ethanol did not serve as electron donors. Membrane lipid analysis revealed diacyl glycerols and acyl/ether glycerols which ranged from C14:0 to C20:0. Alkyl chains present in acyl/ether and diether glycerol lipids ranged from C16:0 to C18:0. Straight, iso- and anteiso-configurations were found for all lipid types. The presence of OPF15T was also shown to increase cellulose consumption during co-cultivation with Caldicellulosiruptor obsidiansis, a fermentative, cellulolytic extreme thermophile isolated from the same environment. On the basis of phylogenetic, phenotypic, and structural analyses, Thermodesulfobacterium geofontis sp. nov. is proposed as a new species with OPF15T representing the type strain.

  16. Simultaneous heterotrophic nitrification and aerobic denitrification by the marine origin bacterium Pseudomonas sp. ADN-42.

    Science.gov (United States)

    Jin, Ruofei; Liu, Tianqi; Liu, Guangfei; Zhou, Jiti; Huang, Jianyu; Wang, Aijie

    2015-02-01

    Recent research has highlighted the existence of some bacteria that are capable of performing heterotrophic nitrification and have a phenomenal ability to denitrify their nitrification products under aerobic conditions. A high-salinity-tolerant strain ADN-42 was isolated from Hymeniacidon perleve and found to display high heterotrophic ammonium removal capability. This strain was identified as Pseudomonas sp. via 16S rRNA gene sequence analysis. Gene cloning and sequencing analysis indicated that the bacterial genome contains N2O reductase function (nosZ) gene. NH3-N removal rate of ADN-42 was very high. And the highest removal rate was 6.52 mg/L · h in the presence of 40 g/L NaCl. Under the condition of pure oxygen (DO >8 mg/L), NH3-N removal efficiency was 56.9 %. Moreover, 38.4 % of oxygen remained in the upper gas space during 72 h without greenhouse gas N2O production. Keeping continuous and low level of dissolved oxygen (DO <3 mg/L) was helpful for better denitrification performance. All these results indicated that the strain has heterotrophic nitrification and aerobic denitrification abilities, which guarantee future application in wastewater treatment.

  17. Cellulomonas terrae sp. nov., a cellulolytic and xylanolytic bacterium isolated from soil.

    Science.gov (United States)

    An, Dong-Shan; Im, Wan-Taek; Yang, Hee-Chan; Kang, Myung Suk; Kim, Kwang Kyu; Jin, Long; Kim, Myung Kyum; Lee, Sung-Taik

    2005-07-01

    A bacterial strain (DB5(T)), with polysaccharide-degrading activities, was isolated from garden soil in Daejeon, Republic of Korea. The cells were Gram-positive, aerobic or facultatively anaerobic, non-motile straight rods. Phylogenetic analysis based on 16S rRNA gene sequences showed that this strain belongs to the genus Cellulomonas and that it is most closely related to Cellulomonas xylanilytica LMG 21723(T) and Cellulomonas humilata ATCC 25174(T) (98.0 and 97.9% similarity, respectively). Chemotaxonomic data also supported the classification of strain DB5(T) in the genus Cellulomonas, i.e. L-ornithine as the cell-wall diamino acid, anteiso-C(15:0) and iso-C(15:0) as the major fatty acids, MK-9(H(4)) as the predominant menaquinone and the presence of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol mannosides in the polar lipid profile. The results of DNA-DNA hybridization in combination with chemotaxonomic and physiological data demonstrated that strain DB5(T) (=KCTC 19081(T)=NBRC 100819(T)) should be classified as the type strain of a novel species within the genus Cellulomonas, for which the name Cellulomonas terrae sp. nov. is proposed.

  18. Inoculating plants with the endophytic bacterium Pseudomonas sp. Ph6-gfp to reduce phenanthrene contamination.

    Science.gov (United States)

    Sun, Kai; Liu, Juan; Gao, Yanzheng; Sheng, Yuehui; Kang, Fuxing; Waigi, Michael Gatheru

    2015-12-01

    Plant organic contamination poses a serious threat to the safety of agricultural products and human health worldwide, and the association of endophytic bacteria with host plants may decrease organic pollutants in planta. In this study, we firstly determined the growth response and biofilm formation of endophytic Pseudomonas sp. Ph6-gfp, and then systematically evaluated the performance of different plant colonization methods (seed soaking (SS), root soaking (RS), leaf painting (LP)) for circumventing the risk of plant phenanthrene (PHE) contamination. After inoculation for 48 h, strain Ph6-gfp grew efficiently with PHE, oxalic acid, or malic acid as the sole sources of carbon and energy. Moreover, strain Ph6-gfp could form robust biofilms in LB medium. In greenhouse hydroponic experiments, strain Ph6-gfp could actively colonize inoculated plants internally, and plants colonized with Ph6-gfp showed a higher capacity for PHE removal. Compared with the Ph6-gfp-free treatment, the accumulations of PHE in Ph6-gfp-colonized plants via SS, RS, and LP were 20.1, 33.1, and 7.1 %, respectively, lower. Our results indicate that inoculating plants with Ph6-gfp could lower the risk of plant PHE contamination. RS was most efficient for improving PHE removal in whole plant bodies by increasing the cell numbers of Ph6-gfp in plant roots. The findings in this study provide an optimized method to strain Ph6-gfp reduce plant PAH residues, which may be applied to agricultural production in PAH-contaminated soil.

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

    Science.gov (United States)

    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.

  20. Mycobacterium minnesotense sp. nov., a photochromogenic bacterium isolated from sphagnum peat bogs.

    Science.gov (United States)

    Hannigan, Geoffrey D; Krivogorsky, Bogdana; Fordice, Daniel; Welch, Jacqueline B; Dahl, John L

    2013-01-01

    Several intermediate-growing, photochromogenic bacteria were isolated from sphagnum peat bogs in northern Minnesota, USA. Acid-fast staining and 16S rRNA gene sequence analysis placed these environmental isolates in the genus Mycobacterium, and colony morphologies and PCR restriction analysis patterns of the isolates were similar. Partial sequences of hsp65 and dnaJ1 from these isolates showed that Mycobacterium arupense ATCC BAA-1242(T) was the closest mycobacterial relative, and common biochemical characteristics and antibiotic susceptibilities existed between the isolates and M. arupense ATCC BAA-1242(T). However, compared to nonchromogenic M. arupense ATCC BAA-1242(T), the environmental isolates were photochromogenic, had a different mycolic acid profile and had reduced cell-surface hydrophobicity in liquid culture. The data reported here support the conclusion that the isolates are representatives of a novel mycobacterial species, for which the name Mycobacterium minnesotense sp. nov. is proposed. The type strain is DL49(T) (=DSM 45633(T) = JCM 17932(T) = NCCB 100399(T)).

  1. Chromobacterium sphagni sp. nov., an insecticidal bacterium isolated from Sphagnum bogs.

    Science.gov (United States)

    Blackburn, Michael B; Farrar, Robert R; Sparks, Michael E; Kuhar, Daniel; Mitchell, Ashaki; Gundersen-Rindal, Dawn E

    2017-09-01

    Sixteen isolates of Gram-reaction-negative, motile, violet-pigmented bacteria were isolated from Sphagnum bogs in West Virginia and Maine, USA. 16S rRNA gene sequences and fatty acid analysis revealed a high degree of relatedness among the isolates, and genome sequencing of two isolates, IIBBL 14B-1T and IIBBL 37-2 (from West Virginia and Maine, respectively), revealed highly similar genomic sequences. The average nucleotide identity (gANI) calculated for these two isolates was found to be in excess of 99 %, but did not exceed 88 % when comparing either isolate with genomic sequences of Chromobacterium violaceum ATCC 12472T, C. haemolyticum DSM 19808T, C. piscinae ND17, C. subtsugae PRAA4-1T, C. vaccinii MWU205T or C. amazonense CBMAI 310T. Collectively, gANI and 16S rRNA gene sequence comparisons suggested that isolates IIBBL 14B-1T and IIBBL 37-2 were most closely related to C. subtsugae, but represented a distinct species. We propose the name Chromobacterium sphagni sp. nov. for this taxon; the type strain is IIBBL 14B-1T (=NRRL B-67130T=JCM 31882T).

  2. Methylobacterium gossipiicola sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the cotton phyllosphere.

    Science.gov (United States)

    Madhaiyan, Munusamy; Poonguzhali, Selvaraj; Senthilkumar, Murugaiyan; Lee, Jung-Sook; Lee, Keun-Chul

    2012-01-01

    A pink, aerobic, facultatively methylotrophic, motile, Gram-negative rod, designated Gh-105(T), was isolated from the phyllosphere of cotton from Coimbatore (Tamilnadu, India). 16S rRNA gene sequence analysis showed clearly that the isolate belonged to the Methylobacterium cluster. Strain Gh-105(T) was most closely related to Methylobacterium adhaesivum AR27(T) (99% 16S rRNA gene sequence similarity) and Methylobacterium iners 5317S-33(T) (97.5%). The isolate grew with C(1) compounds such as methanol and dichloromethane, but not with formaldehyde, formate, methylamine, trimethylamine or methane, as sole carbon sources and carried mxaF, which encodes methanol dehydrogenase and supports methylotrophic metabolism. The major fatty acid was C(18:1)ω7c and the G+C content of the genomic DNA was 64.2 mol%. Physiological and biochemical data and DNA-DNA relatedness with M. adhaesivum KACC 12195(T) and M. iners KACC 11765(T) revealed clear phenotypic and genotypic differences. For this reason, we propose that strain Gh-105(T) (=CCM 7572(T) =NRRL B-51692(T)) represents the type strain of a novel species, with the name Methylobacterium gossipiicola sp. nov.

  3. Methylobacterium bullatum sp. nov., a methylotrophic bacterium isolated from Funaria hygrometrica.

    Science.gov (United States)

    Hoppe, Thomas; Peters, Karsten; Schmidt, Friedrich

    2011-11-01

    A novel, pink-pigmented aerobic, facultatively methylotrophic bacterial strain (F3.2(T)) isolated from the phyllosphere of Funaria hygrometrica, was analyzed using a polyphasic approach. Cells were Gram-negative, motile rods, strictly aerobic and non-spore-forming and exhibited surface structures varying in quantity, distribution and morphology. The isolate grew at 10-33°C over a pH range of 5.5-8.0 and in the presence of less than 1.0% NaCl. Strain F3.2(T) shared less than 70% DNA-DNA binding to the next type strain of the genus Methylobacterium (M. adhaesivum DSM 17169(T)). In addition to the major cellular fatty acid C(18:1)ω7c (81.7%), present in all Methylobacterium species (and also members of the genus Alphaproteobacteria), a high value (11.7%) of the fatty acids (summed feature) C(16:1)ω7c and/or iso-C(15:0)2OH was determined. Phylogenetic analyses based on 16S rDNA and methanol dehydrogenase gene sequences, DNA-DNA hybridization values, chemotaxonomic and phenotypic characteristics indicate that the strain F3.2(T) represents a novel species within the genus Methylobacterium. We propose the name Methylobacterium bullatum sp. nov. for this species. The type strain is the strain F3.2(T) (DSM 21893(T)=LMG 24788(T)). Copyright © 2011 Elsevier GmbH. All rights reserved.

  4. Cryobacterium levicorallinum sp. nov., a psychrophilic bacterium isolated from glacier ice.

    Science.gov (United States)

    Liu, Qing; Liu, Hongcan; Zhang, Jianli; Zhou, Yuguang; Xin, Yuhua

    2013-08-01

    In this study, two psychrophilic bacterial strains were isolated from the China No. 1 glacier in Xinjiang, north-west China. Cells were Gram-positive rods. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strains belonged to the genus Cryobacterium. Phylogenetic analysis showed that they clustered together and are most closely related to Cryobacterium luteum CGMCC 1.11210(T), Cryobacterium flavum CGMCC 1.11215(T), Cryobacterium psychrophilum CGMCC 1.4292(T), Cryobacterium psychrotolerans CGMCC 1.5382(T) and Cryobacterium roopkundense CGMCC 1.10672(T). The major cellular fatty acids of the novel strains were anteiso-C15 : 0, anteiso-C15 : 1 A, iso-C16 : 0 and iso-C15 : 0. Both strains contained diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid in the cell membrane. The results of DNA-DNA hybridization and physiological tests allowed the genotypic and phenotypic differentiation of strains Hh34(T) and Hh28 from related species. However, their high DNA-DNA relatedness showed that they belong to the same novel species. Strain Hh34(T) (= NBRC 107883(T) = CGMCC 1.11211(T)) was selected as the type strain to represent this novel species, for which the name Cryobacterium levicorallinum sp. nov. is proposed.

  5. Description of Pseudomonas gregormendelii sp. nov., a Novel Psychrotrophic Bacterium from James Ross Island, Antarctica.

    Science.gov (United States)

    Kosina, Marcel; Švec, Pavel; Černohlávková, Jitka; Barták, Miloš; Snopková, Kateřina; De Vos, Paul; Sedláček, Ivo

    2016-07-01

    During the microbiological research performed within the scope of activities of Czech expeditions based at the Johann Gregor Mendel Station at James Ross Island, Antarctica, two psychrotrophic gram-stain negative non-fluorescent strains CCM 8506T and CCM 8507 from soil were extensively characterized using genotypic and phenotypic methods. Initial characterization using ribotyping with HindIII restriction endonuclease and phenotyping implies that both isolates belong to a single Pseudomonas species. Sequencing of rrs, rpoB, rpoD and glnA genes of strain CCM 8506(T) confirmed affiliation of investigated strains within the genus Pseudomonas. Further investigation using automated ribotyping with EcoRI (RiboPrinter(®) Microbial Characterisation System), whole-cell protein profiling using the Agilent 2100 Bioanalyzer system, extensive biochemical testing and DNA-DNA hybridization experiments confirmed that both investigated strains are members of a single taxon which is clearly separated from all hitherto described Pseudomonas spp. Based on all findings, we describe a novel species Pseudomonas gregormendelii sp. nov. with the type strain CCM 8506(T) (=LMG 28632T).

  6. Mycobacterium celeriflavum sp. nov., a rapidly growing scotochromogenic bacterium isolated from clinical specimens.

    Science.gov (United States)

    Shahraki, Abdolrazagh Hashemi; Çavuşoğlu, Cengiz; Borroni, Emanuele; Heidarieh, Parvin; Koksalan, Orhan Kaya; Cabibbe, Andrea Maurizio; Hashemzadeh, Mohamad; Mariottini, Alessandro; Mostafavi, Ehsan; Cittaro, Davide; Feizabadi, Mohamad Mehdi; Lazarevic, Dejan; Yaghmaei, Farhad; Molinari, Gian Lorenzo; Camaggi, Anna; Tortoli, Enrico

    2015-02-01

    Six strains of a rapidly growing scotochromogenic mycobacterium were isolated from pulmonary specimens of independent patients. Biochemical and cultural tests were not suitable for their identification. The mycolic acid pattern analysed by HPLC was different from that of any other mycobacterium. Genotypic characterization, targeting seven housekeeping genes, revealed the presence of microheterogeneity in all of them. Different species were more closely related to the test strains in various regions: the type strain of Mycobacterium moriokaense showed 99.0 % 16S rRNA gene sequence similarity, and 91.5-96.5 % similarity for the remaining six regions. The whole genome sequences of the proposed type strain and that of M. moriokaense presented an average nucleotide identity (ANI) of 82.9 %. Phylogenetic analysis produced poorly robust trees in most genes with the exception of rpoB and sodA where Mycobacterium flavescens and Mycobacterium novocastrense were the closest species. This phylogenetic relatedness was confirmed by the tree inferred from five concatenated genes, which was very robust. The polyphasic characterization of the test strains, supported by the ANI value, demonstrates that they belong to a previously unreported species, for which the name Mycobacterium celeriflavum sp. nov. is proposed. The type strain is AFPC-000207(T) ( = DSM 46765(T) = JCM 18439(T)). © 2015 IUMS.

  7. Mycobacterium aquiterrae sp. nov., a rapidly growing bacterium isolated from groundwater.

    Science.gov (United States)

    Lee, Jae-Chan; Whang, Kyung-Sook

    2017-10-01

    A strain representing a rapidly growing, Gram-stain-positive, aerobic, rod-shaped, non-motile, non-sporulating and non-pigmented species of the genus Mycobacterium, designated strain S-I-6T, was isolated from groundwater at Daejeon in Korea. The strain grew at temperatures between 10 and 37 °C (optimal growth at 25 °C), between pH 4.0 and 9.0 (optimal growth at pH 7.0) and at salinities of 0-5 % (w/v) NaCl, growing optimally with 2 % (w/v) NaCl. Phylogenetic analyses based on multilocus sequence analysis of the 16S rRNAgene, hsp65, rpoB and the 16S-23S internal transcribed spacer indicated that strain S-I-6T belonged to the rapidly growing mycobacteria, being most closely related to Mycobacterium sphagni. On the basis of polyphasic taxonomic analysis, the bacterial strain was distinguished from its phylogenetic neighbours by chemotaxonomic properties and other biochemical characteristics. DNA-DNA relatedness among strain S-I-6T and the closest phylogenetic neighbour strongly support the proposal that this strain represents a novel species within the genus Mycobacterium, for which the name Mycobacterium aquiterrae sp. nov. is proposed. The type strain is S-I-6T (=KACC 17600T=NBRC 109805T=NCAIM B 02535T).

  8. Brevibacterium siliguriense sp. nov., a facultatively oligotrophic bacterium isolated from river water.

    Science.gov (United States)

    Kumar, Arvind; Ince, İkbal Agah; Katı, Ahmet; Chakraborty, Ranadhir

    2013-02-01

    A Gram-positive-staining, rod-shaped, facultatively oligotrophic bacterial strain, designated MB18(T), was isolated from a water sample collected from the River Mahananda at Siliguri (26° 44' 23.20' N, 88° 25' 22.89' E), West-Bengal, India. On the basis of 16S rRNA gene sequence similarity, the closest relative of this strain was Brevibacterium epidermidis NCDO 2286(T) (96 % similarity). The DNA G+C content of strain MB18(T) was 64.6 mol%. Chemotaxonomic data [MK-8(H(2)) as the major menaquinone, galactose as the sole cell-wall sugar, meso-diaminopimelic acid as the diagnostic cell-wall diamino acid, phosphatidylglycerol and diphosphatidylglycerol as constituents of the polar lipids, anteiso-C(15 : 0), anteiso-C(17 : 0) and iso-C(15 : 0) as the major fatty acids] supported the affiliation of strain MB18(T) to the genus Brevibacterium. The results of DNA G+C content, 16S rRNA gene sequence analysis and biochemical and physiological analyses allowed genotypic and phenotypic differentiation of strain MB18(T) from its nearest neighbour B. epidermidis. The isolate therefore represents a novel species, for which the name Brevibacterium siliguriense sp. nov. is proposed; the type strain is MB18(T) ( = DSM 23676(T) = LMG 25772(T)).

  9. Rhizobium helanshanense sp. nov., a bacterium that nodulates Sphaerophysa salsula (Pall.) DC. in China.

    Science.gov (United States)

    Qin, Wei; Deng, Zhen Shan; Xu, Lin; Wang, Na Na; Wei, Ge Hong

    2012-05-01

    Studying rhizobia in the root nodules of Sphaerophysa salsula (Pall.) DC in the northwest of China, we obtained five strains classified as genus Rhizobium on the basis of their 16S rRNA gene sequences. The sequence similarity of strain CCNWQTX14(T) with the most related species was 99.0%. Further phylogenetic analysis of housekeeping genes (recA and atpD) suggested the five strains comprised a novel lineage within Rhizobium. The nifH and nodD gene sequences of CCNWQTX14(T) were phylogenetically closely related with those of Sinorhizobium kummerowiae and R. sphaerophysae, respectively. The five strains isolated from different places were also distinct from related Rhizobium species using ERIC fingerprint profiles. The DNA-DNA hybridization value was 41.8% between CCNWQTX14(T) and Rhizobium sphaerophysae CCNWGS0238(T). Our novel strains were only able to form effective nodules on its original host Sphaerophysa salsula. Our data showed that the five Rhizobium strains formed a unique genomic species, for which a novel species Rhizobium helanshanense sp. nov. is proposed. The type strain is CCNWQTX14(T) (=ACCC 16237(T) =HAMBI 3083(T)).

  10. Lactobacillus uvarum sp. nov.--a new lactic acid bacterium isolated from Spanish Bobal grape must.

    Science.gov (United States)

    Mañes-Lázaro, Rosario; Ferrer, Sergi; Rosselló-Mora, Ramón; Pardo, Isabel

    2008-12-01

    Five strains isolated from grape musts in Spain in 1997, have been characterized by several molecular techniques, and three of them have been identified as pertaining to a new species. All strains are Gram-positive rods, aerotolerant and homofermentative bacteria that do not exhibit catalase activity. Phylogenetic analysis based on 16S rRNA gene sequences placed these strains within the genus Lactobacillus, closely related to Lactobacillus mali. DNA-DNA hybridization experiments confirmed that strain 71 belongs to the lately described species L. satsumensis, strain 88 belongs to L. mali and the other three isolates have an independent status at species level. Restriction analysis of the amplified 16S rRNA gene (16S-ARDRA), internal spacer region (ISR) analysis, random amplified polymorphism DNA (RAPD) and ribotyping were performed in order to establish genotypic similarities and differences between the new species and their closest species. The three isolates can be genetically differentiated from their closest relatives by RAPD analysis and ribotyping. Phenotypically, they can be distinguished by several traits such as their ability to grow at pH 3.3 and NaCl 5% (w/v) and by certain carbohydrate fermentations. The name L. uvarum sp. nov. is proposed. The type strain is 8T (=DSM 19971T = colección española de cultivos tipo (CECT) 7335T).

  11. Cohnella lupini sp. nov., an endophytic bacterium isolated from root nodules of Lupinus albus.

    Science.gov (United States)

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

    2014-01-01

    A bacterial strain designated RLAHU4B(T) was isolated from root nodules of Lupinus albus in León (Spain). The 16S rRNA gene sequence of this strain showed similarities lower than 97 % with respect to species of the genus Cohnella. The strain was a Gram-variable, sporulating rod, motile by means of peritrichous flagella, and facultatively anaerobic. It was positive for oxidase, catalase and β-galactosidase production but negative for urease, amylase and gelatinase. Strain RLAHU4B(T) grew in the presence of 5 % NaCl. MK-7 was the predominant menaquinone and meso-diaminopimelic acid was present in the peptidoglycan. anteiso-C15 : 0, iso-C16 : 0, iso-C15 : 0 and C16 : 0 were the major fatty acids. Major polar lipids of strain RLAHU4B(T) were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown phospholipids, two unknown aminophospholipids and one unknown lipid. The DNA G+C content was 57.8 mol%. Strain RLAHU4B(T) presented phenotypic differences from all recognized species of the genus Cohnella. The phylogenetic, chemotaxonomic and phenotypic data indicated that strain RLAHU4B(T) belongs to a novel species of the genus Cohnella, for which the name Cohnella lupini sp. nov. is proposed, with strain RLAHU4B(T) ( = LMG 27416(T) = CECT 8236(T)) as the type strain.

  12. Flavihumibacter stibioxidans sp. nov., an antimony-oxidizing bacterium isolated from antimony mine soil.

    Science.gov (United States)

    Han, Yushan; Zhang, Fujun; Wang, Qian; Zheng, Shixue; Guo, Wei; Feng, Liang; Wang, Gejiao

    2016-11-01

    A Gram-stain-positive, strictly aerobic, non-motile and rod-shaped bacterial strain, designated YS-17T, was isolated from soil in the Lengshuijiang antimony mine, Hunan Province, China. Comparative 16S rRNA gene sequencing analysis clustered it with Flavihumibacter strains, and strain YS-17T was most closely related to Flavihumibacter cheonanensis WS16T (97.2 % similarity), Flavihumibacter petaseus T41T (96.6 %) and Flavihumibacter solisilvae 3-3T (96.5 %). The level of DNA-DNA relatedness between strain YS-17T and F. cheonanensis JCM 19322T was 35.5±0.1 % (n=2). The major respiratory quinone of strain YS-17T was menaquinone-7 and the major polar lipids were phosphatidylethanolamine, two unidentified lipids, two unidentified amino lipids and phospholipid. The major fatty acids (≥5 %) were iso-C15 : 0, iso-C15 : 1 G, unknown ECL 13.565, iso-C17 : 0 3-OH, C15 : 0, C16 : 1ω5c and anteiso-C15 : 0. The DNA G+C content was 47.8 mol%. Compared with other Flavihumibacter strains, strain YS-17T showed major biophysical and biochemical differences, with the ability to hydrolyse gelatin and to assimilate salicin and l-proline. The results demonstrated that strain YS-17T belongs to the genus Flavihumibacter and represents a novel species, for which the name Flavihumibacter stibioxidans sp. nov. is proposed. The type strain is YS-17T (=CCTCC AB 2016053T=KCTC 52205T).

  13. Dickeya solani sp. nov., a pectinolytic plant-pathogenic bacterium isolated from potato (Solanum tuberosum).

    Science.gov (United States)

    van der Wolf, Jan M; Nijhuis, Els H; Kowalewska, Malgorzata J; Saddler, Gerry S; Parkinson, Neil; Elphinstone, John G; Pritchard, Leighton; Toth, Ian K; Lojkowska, Ewa; Potrykus, Marta; Waleron, Malgorzata; de Vos, Paul; Cleenwerck, Ilse; Pirhonen, Minna; Garlant, Linda; Hélias, Valérie; Pothier, Joël F; Pflüger, Valentin; Duffy, Brion; Tsror, Leah; Manulis, Shula

    2014-03-01

    Pectinolytic bacteria have been recently isolated from diseased potato plants exhibiting blackleg and slow wilt symptoms found in a number of European countries and Israel. These Gram-reaction-negative, motile, rods were identified as belonging to the genus Dickeya, previously the Pectobacterium chrysanthemi complex (Erwinia chrysanthemi), on the basis of production of a PCR product with the pelADE primers, 16S rRNA gene sequence analysis, fatty acid methyl esterase analysis, the production of phosphatases and the ability to produce indole and acids from α-methylglucoside. Differential physiological assays used previously to differentiate between strains of E. chrysanthemi, showed that these isolates belonged to biovar 3. Eight of the isolates, seven from potato and one from hyacinth, were analysed together with 21 reference strains representing all currently recognized taxa within the genus Dickeya. The novel isolates formed a distinct genetic clade in multilocus sequence analysis (MLSA) using concatenated sequences of the intergenic spacer (IGS), as well as dnaX, recA, dnaN, fusA, gapA, purA, rplB, rpoS and gyrA. Characterization by whole-cell MALDI-TOF mass spectrometry, pulsed field gel electrophoresis after digestion of whole-genome DNA with rare-cutting restriction enzymes, average nucleotide identity analysis and DNA-DNA hybridization studies, showed that although related to Dickeya dadantii, these isolates represent a novel species within the genus Dickeya, for which the name Dickeya solani sp. nov. (type strain IPO 2222(T) = LMG25993(T) = NCPPB4479(T)) is proposed.

  14. Lentibacillus kimchii sp. nov., an extremely halophilic bacterium isolated from kimchi, a Korean fermented vegetable.

    Science.gov (United States)

    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)).

  15. Thermus islandicus sp. nov., a mixotrophic sulfur-oxidizing bacterium isolated from the Torfajokull geothermal area.

    Science.gov (United States)

    Bjornsdottir, Snaedis H; Petursdottir, Solveig K; Hreggvidsson, Gudmundur O; Skirnisdottir, Sigurlaug; Hjorleifsdottir, Sigridur; Arnfinnsson, Johann; Kristjansson, Jakob K

    2009-12-01

    Strains PRI 2268 and PRI 3838(T) were isolated from two separate hot springs in the Torfajokull geothermal area of South Iceland. The cells were non-motile rods, approximately 0.3 microm in width and 1.5-2.5 microm in length. Electron microscopy revealed a Gram-negative cell-wall structure. The strains grew at 45-79 degrees C (optimum, 65 degrees C) and pH 5.5-10.5 (optimum, pH 6.0-7.0). 16S rRNA gene sequence analysis indicated that they formed a separate branch within the genus Thermus with 'Thermus kawarayensis' KW11 as their closest cultured relative (96.5 % similarity). The gene sequence similarities of both new isolates to Thermus aquaticus YT-1(T) and Thermus igniterrae RF-4(T) were 96.1 % and 95.5 %, respectively. DNA-DNA relatedness between strain PRI 3838(T) and 'T. kawarayensis' was 46.1 %. The DNA G+C content of strain PRI 3838(T) was 69.0 mol%. The predominant menaquinones, pigmentation, fatty acid profiles and phospholipid profiles of the novel strains were similar to those of other members of the genus Thermus. However, the new strains could be differentiated from the type strains of all other species of the genus Thermus by their lack of catalase activity and their utilization of only a few carbon sources. Furthermore, the novel strains exhibited mixotrophic growth with sulfur oxidation. On the basis of 16S rRNA gene sequence comparisons, DNA-DNA hybridization and physiological and biochemical characteristics, the new isolates represent a novel species. Since the species appears to be ubiquitous in Icelandic hot springs, the name Thermus islandicus sp. nov. is proposed. The type strain is PRI 3838(T) (=DSM 21543(T)=ATCC BAA-1677(T)).

  16. Photobacterium aquimaris sp. nov., a luminous marine bacterium isolated from seawater.

    Science.gov (United States)

    Yoshizawa, Susumu; Wada, Minoru; Kita-Tsukamoto, Kumiko; Yokota, Akira; Kogure, Kazuhiro

    2009-06-01

    Two luminous marine bacteria, strains LC2-065(T) and LC2-102, were isolated from seawater at Sagami Bay in Japan. These bacteria were Gram-negative, oxidase-negative, catalase-positive, motile and coccoid-rods. 16S rRNA gene sequence analysis and multilocus sequence analysis (MLSA) using six loci (ftsZ, gapA, gyrB, mreB, pyrH and topA) and sequence analysis of the alpha subunit of luciferase (luxA) gene revealed that these bacteria were distinct from other species of the genus Photobacterium. These novel strains were most closely related to Photobacterium kishitanii. The DNA-DNA hybridization value between strain LC2-065(T) and Photobacterium kishitanii ATCC BAA-1194(T) was 42.1 %. The major fatty acids were C(12 : 0,) C(14 : 0), C(16 : 0), C(18 : 0) and C(15 : 0) iso 2-OH and/or C(16 : 1)omega7c (summed feature 3). The DNA G+C contents of strains LC2-065(T) and LC2-086 were 42.2 and 42.9 mol%, respectively. The phenotypic features of the novel strains were similar to those of P. kishitanii and P. phosphoreum, but there were sufficient physiological differences for the novel strains to be easily differentiated. On the basis of these results, these new strains represent a novel species, for which the name Photobacterium aquimaris sp. nov. is proposed. The type strain is LC2-065(T) (=NBRC 104633(T)=KCTC 22356(T)).

  17. Photobacterium toruni sp. nov., a bacterium isolated from diseased farmed fish.

    Science.gov (United States)

    Labella, Alejandro M; Arahal, David R; Lucena, Teresa; Manchado, Manuel; Castro, Dolores; Borrego, Juan J

    2017-11-01

    Three bacterial strains were isolated from liver and spleen of diseased farmed redbanded seabream (Pagrus auriga) in south-west Spain. Their partial 16S rRNA gene sequences clustered within those of the genus Photobacterium, showing high similarity (98.6-99.3 %) to the type strains of Photobacterium iliopiscarium, P. piscicola, P. kishitanii, P. aquimaris and P. phosphoreum. Multilocus sequence analysis using six housekeeping genes (gapA, topA, mreB, ftsZ, gyrB and 16S rRNA) confirmed the new strains as forming an independent branch with a bootstrap value of 100, likely to represent a novel species. To confirm this, we used whole genome sequencing and genomic analysis (ANIb, ANIm and in silico DNA-DNA hybridization) obtaining values well below the thresholds for species delineation. In addition, a phenotypic characterization was performed to support the description and differentiation of the novel strains from related taxa. Cells were Gram-stain-negative, motile bacilli, chemo-organotrophic and facultatively anaerobic. They fermented glucose, as well as galactose and d-mannose, without production of gas. Oxidase and catalase were positive. The predominant cellular fatty acids were C16 : 1ω7c/C16 : 1ω6c and C16  :  0. The predominant respiratory quinone (Q-8) and major polar lipids (phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol) were inferred from annotated genes in the genome of strain H01100410BT, which had a G+C content of 38.6 mol%. The results obtained demonstrate that the three strains represent a novel species, for which the name Photobacterium toruni sp. nov. is proposed. The type strain is H01100410BT (=CECT 9189T=LMG 29991T).

  18. Photobacterium lipolyticum sp. nov., a bacterium with lipolytic activity isolated from the Yellow Sea in Korea.

    Science.gov (United States)

    Yoon, Jung-Hoon; Lee, Jung-Kee; Kim, Young-Ok; Oh, Tae-Kwang

    2005-01-01

    A Gram-negative, motile, non-spore-forming, pleomorphic and lipolytic bacterial strain, M37T, was isolated from an intertidal sediment of the Yellow Sea in Korea. This organism grew optimally at 25-28 degrees C and in the presence of 1-2 % NaCl. It did not grow without NaCl or in the presence of more than 6 % NaCl. Strain M37T was characterized chemotaxonomically by having Q-8 as the predominant respiratory lipoquinone and C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH and C(16 : 0) as the major fatty acids. The DNA G+C content was 47 mol%. Phylogenetic analyses based on 16S rRNA gene sequences placed strain M37T within the clade comprising Photobacterium species, forming a coherent cluster with the type strains of Photobacterium profundum and Photobacterium indicum (16S rRNA gene similarity levels of 97.5-98.0 %). The mean DNA-DNA relatedness levels between strain M37T and P. profundum JCM 10084T and P. indicum DSM 5151T were in the range 12-15 %. Similarities between 16S rRNA gene sequences of strain M37T and those of the type strains of the other Photobacterium species ranged from 93.9 % (with Photobacterium fischeri) to 96.2 % (with Photobacterium phosphoreum). On the basis of phenotypic properties and phylogenetic and genomic distinctiveness, strain M37T (=KCTC 10562BPT=DSM 16190T) should be placed in the genus Photobacterium as a novel species, for which the name Photobacterium lipolyticum sp. nov. is proposed.

  19. Methylobacterium indicum sp. nov., a facultative methylotrophic bacterium isolated from rice seed.

    Science.gov (United States)

    Chaudhry, Vasvi; Baindara, Piyush; Pal, Vijay Kumar; Chawla, Niharika; Patil, Prabhu B; Korpole, Suresh

    2016-02-01

    Two pink pigmented, Gram-negative, motile, aerobic, rod shaped endophytic bacteria designated as SE2.11(T) and SE3.6 were isolated in different experiments from surface sterilized rice seeds. Both strains grew optimally at 28°C temperature. They were positive for catalase and nitrate reduction. The 16S rRNA gene sequence of the strains SE2.11(T) and SE3.6 displayed between 98.1% and 97.2% similarities with the validly published species of the genus Methylobacterium. The major cellular fatty acid was C18:1 ω7c in both the strains, a characteristic feature observed for members of the genus Methylobacterium. The predominant polar lipids were phospholipids including phosphatidylglycerol (PG), phosphatidylethanolamine (PE) and diphosphatidylglycerol (DPG). Phylogenetic analysis of 16S rRNA gene sequences resulted in the formation of a coherent cluster of strains SE2.11(T) and SE3.6 with closest relative Methylobacterium platani JCM 14648(T). However, digital DNA-DNA hybridization (dDDH) of strains SE2.11(T) and SE3.6 with the closest type strain M. platani JCM 14648(T) revealed similarity of 35.5% and 35.4%, respectively. Further, the ANI analysis of strains SE2.11(T) and SE3.6 genomes revealed only 87.9% identity with M. platani JCM 14648(T). Based on differences in biochemical, chemotaxonomic characteristics along with low identity at whole genome level we conclude that both strains represent a novel species of the genus Methylobacterium, for which the name Methylobacterium indicum sp. nov., is proposed. The type strain Methylobacterium indicum is SE2.11(T) (=MTCC 12298(T)=JCM 30761(T)) and SE3.6 (=MTCC 12299=JCM 30762) is another strain. Copyright © 2015 Elsevier GmbH. All rights reserved.

  20. Bacillus kiskunsagensis sp. nov., a novel alkaliphilic and moderately halophilic bacterium isolated from soda soil.

    Science.gov (United States)

    Borsodi, Andrea K; Tóth, Erika; Aszalós, Júlia M; Bárány, Ágnes; Schumann, Peter; Spröer, Cathrin; Kovács, Attila L; Márialigeti, Károly; Szili-Kovács, Tibor

    2017-09-01

    An alkaliphilic and moderately halophilic strain characterized by optimal growth at pH 9.0-10.0 and 7 % (w/v) NaCl, and designated B16-24T, was isolated from the rhizosphere soil of the bayonet grass Bolboschoenus maritimus at a soda pond in the Kiskunság National Park, Hungary. Cells of the strain were Gram-staining-positive, non-motile, straight rods, and formed central, ellipsoidal endospores with slightly swollen sporangia. The isolate was facultative anaerobic, catalase positive, oxidase negative, and contained a peptidoglycan of type A1γ based on meso-diaminopimelic acid. Menaquinone-7 (MK-7) was the predominant isoprenoid quinone, and anteiso-C15 : 0 the major cellular fatty acid. The DNA G+C content of strain B16-24T was 36.6 mol%. The 16S rRNA gene-based phylogenetic analysis revealed that the novel isolate had the greatest similarities to the type strains of Bacillus okhensis Kh10-101T (97.8 %), B. akibai 1139T (97.4 %), B. alkalisediminis K1-25T (97.3 %) and B. wakoensis N-1T (97.1 %). The DNA-DNA relatedness of strain B16-24T and the closely related Bacillus species ranged between 24±6 % and 35±3 %. The distinctive phenotypic and genetic results of this study confirmed that strain B16-24T represents a novel species within the genus Bacillus, for which the name Bacillus kiskunsagensis sp. nov. is proposed. The type strain is B16-24T (=DSM 29791T=NCAIM B.02610T).

  1. Salinithrix halophila gen. nov., sp. nov., a halophilic bacterium in the family Thermoactinomycetaceae.

    Science.gov (United States)

    Zarparvar, Parisa; Amoozegar, Mohammad Ali; Nikou, Mahdi Moshtaghi; Schumann, Peter; Ventosa, Antonio

    2014-12-01

    A halophilic actinomycete, strain R4S8(T), was isolated from soil of Inche-Broun hypersaline wetland in the north of Iran. The isolate grew aerobically at temperatures of 30-50 °C (optimum 40 °C), pH 6-10 (optimum pH 7.0) and in the presence of 1-15 % (w/v) NaCl (optimum 3-5 %). It formed short and straight to moderately flexuous aerial mycelium without motile elements. The cell wall of strain R4S8(T) contained meso-diaminopimelic acid as the diamino acid without any diagnostic sugars. The polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, phosphatidylmonomethylethanolamine two unknown phospholipids and one unknown aminophospholipid. It synthesized anteiso-C15 : 0 (44.8 %), iso-C15 : 0 (28.8 %) and iso-C14 : 0 (8.5 %) as major fatty acids. MK-6 was the predominant respiratory quinone. The G+C content of the genomic DNA was 52.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain R4S8(T) belongs to the family Thermoactinomycetaceae and showed the closest 16S rRNA gene sequence similarity with Desmospora activa IMMIB L-1269(T) (95.5 %) and Marininema mesophilum SCSIO 10219(T) (95.3 %). On the basis of phylogenetic analysis and phenotypic characteristics, strain R4S8(T) represents a novel species in a new genus within the family Thermoactinomycetaceae, for which the name Salinithrix halophila gen. nov., sp. nov. is proposed. The type strain of the type species is R4S8(T) ( = IBRC-M 10813(T) = CECT 8506(T)). © 2014 IUMS.

  2. Brevibacterium daeguense sp. nov., a nitrate-reducing bacterium isolated from a 4-chlorophenol enrichment culture.

    Science.gov (United States)

    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)).

  3. Rhizobium wenxiniae sp. nov., an endophytic bacterium isolated from maize root.

    Science.gov (United States)

    Gao, Jun-Lian; Sun, Pengbo; Wang, Xu-Ming; Lv, Fan-Yang; Mao, Xiao-Jie; Sun, Jian-Guang

    2017-08-01

    A novel Gram-stain-negative, aerobic, rod-shaped strain designated 166T was isolated from surface-sterilized root tissue of maize planted in the Fangshan District of Beijing, PR China. The 16S rRNA gene sequence analysis indicated that strain 166T belongs to the genus Rhizobium and is closely related to Rhizobium cellulosilyticum ALA10B2T and Rhizobium yantingense H66T with sequence similarities of 98.8 and 98.3 %, respectively. According to atpD and recA sequence analysis, the highest sequence similarity between strain 166T and R. cellulosilyticum ALA10B2T is 93.8 and 84.7 %, respectively. However, the new isolate exhibited relatively low levels of DNA-DNA relatedness with respect to R. cellulosilyticum DSM 18291T (20.8±2.3 %) and Rhizobium yantingense CCTCC AB 2014007T (47.2±1.4 %). The DNA G+C content of strain 166T was 59.8 mol%. The main polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, an unidentified aminophospholipid and an unidentified aminolipid. The major fatty acids of strain 166T were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The results of the physiological and biochemical tests and minor differences in the fatty acid profiles allowed a clear phenotypic differentiation of strain 166T from the type strains of closely related species, R. cellulosilyticum DSM 18291T and R. yantingense CCTCC AB 2014007T. Strain 166T represents a novel species within the genus Rhizobium, for which the name Rhizobium wenxiniae sp. nov. is proposed, with the type strain 166T (=CGMCC 1.15279T=DSM 100734T).

  4. Rhizobium smilacinae sp. nov., an endophytic bacterium isolated from the leaf of Smilacina japonica.

    Science.gov (United States)

    Zhang, Lei; Shi, Xu; Si, Meiru; Li, Changfu; Zhu, Lingfang; Zhao, Liang; Shen, Xihui; Wang, Yao

    2014-10-01

    During a study of endophytic bacteria from traditional Chinese medicinal plants, a bacterial strain, designated PTYR-5(T), was isolated from the leaf of Smilacina japonica A. Gray collected from Taibai Mountain in Shaanxi Province, north-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PTYR-5(T) is a member of the genus Rhizobium, exhibiting the highest sequence similarities to R. cellulosilyticum LMG 23642(T) (97.2%), R. huautlense LMG 18254(T) (97.2%) and R. alkalisoli CCBAU 01393(T) (97.1%). The levels of 16S rRNA gene sequence similarity with respect to other Rhizobium species with validly published names were less than 97.0%. Phylogenies of the housekeeping genes atpD, recA and glnII confirmed its distinct position, showing low similarity with respect to those of recognized Rhizobium species (no more than 94.1, 90.0 and 88.0% similarity, respectively). The DNA-DNA relatedness values of strain PTYR-5(T) with R. cellulosilyticum LMG 23642(T), R. huautlense LMG 18254(T) and R. alkalisoli CCBAU 01393(T) were 33.6, 21.4 and 29.5 %, respectively. Based on phenotypic, phylogenetic and genotypic data, strain PTYR-5(T) is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium smilacinae sp. nov. is proposed. The type strain is PTYR-5(T) (=CCTCC AB 2013016(T)=KCTC 32300(T)=LMG 27604(T)).

  5. Rhizobium azibense sp. nov., a nitrogen fixing bacterium isolated from root-nodules of Phaseolus vulgaris.

    Science.gov (United States)

    Mnasri, Bacem; Liu, Tian Yan; Saidi, Sabrine; Chen, Wen Feng; Chen, Wen Xin; Zhang, Xiao Xia; Mhamdi, Ridha

    2014-05-01

    Three microbial strains isolated from common beans, 23C2T (Tunisia), Gr42 (Spain) and IE4868 (Mexico), which have been identified previously as representing a genomic group closely related to Rhizobium gallicum, are further studied here. Their 16S rRNA genes showed 98.5-99% similarity with Rhizobium loessense CCBAU 7190BT, R. gallicum R602spT, Rhizobium mongolense USDA 1844T and Rhizobium yanglingense CCBAU 71623T. Phylogenetic analysis based on recA, atpD, dnaK and thrC sequences showed that the novel strains were closely related and could be distinguished from the four type strains of the closely related species. Strains 23C2T, Gr42 and IE4868 could be also differentiated from their closest phylogenetic neighbours by their phenotypic and physiological properties and their fatty acid contents. All three strains harboured symbiotic genes specific to biovar gallicum. Levels of DNA-DNA relatedness between strain 23C2T and the type strains of R. loessense, R. mongolense, R. gallicum and R. yanglingense ranged from 58.1 to 61.5%. The DNA G+C content of the genomic DNA of strain 23C2T was 59.52%. On the basis of these data, strains 23C2T, Gr42 and IE4868 were considered to represent a novel species of the genus Rhizobium for which the name Rhizobium azibense is proposed. Strain 23C2T (=CCBAU 101087T=HAMBI3541T) was designated as the type strain.

  6. Bradyrhizobium ottawaense sp. nov., a symbiotic nitrogen fixing bacterium from root nodules of soybeans in Canada

    Science.gov (United States)

    Yu, Xiumei; Cloutier, Sylvie; Tambong, James T.

    2014-01-01

    Sixteen strains of symbiotic bacteria from root nodules of Glycine max grown in Ottawa, Canada, were previously characterized and placed in a novel group within the genus Bradyrhizobium. To verify their taxonomic status, these strains were further characterized using a polyphasic approach. All strains possessed identical 16S rRNA gene sequences that were 99.79 % similar to the closest relative, Bradyrhizobium liaoningense LMG 18230T. Phylogenetic analysis of concatenated atpD, glnII, recA, gyrB, rpoB and dnaK genes divided the 16 strains into three multilocus sequence types that were placed in a highly supported lineage distinct from named species of the genus Bradyrhizobium consistent with results of DNA–DNA hybridization. Based on analysis of symbiosis gene sequences (nodC and nifH), all novel strains were placed in a phylogenetic group with five species of the genus Bradyrhizobium that nodulate soybeans. The combination of phenotypic characteristics from several tests including carbon and nitrogen source utilization and antibiotic resistance could be used to differentiate representative strains from recognized species of the genus Bradyrhizobium. Novel strain OO99T elicits effective nodules on Glycine max, Glycine soja and Macroptilium atropurpureum, partially effective nodules on Desmodium canadense and Vigna unguiculata, and ineffective nodules on Amphicarpaea bracteata and Phaseolus vulgaris. Based on the data presented, we conclude that our strains represent a novel species for which the name Bradyrhizobium ottawaense sp. nov. is proposed, with OO99T ( = LMG 26739T = HAMBI 3284T) as the type strain. The DNA G+C content is 62.6 mol%. PMID:24969302

  7. Genome sequence of the photoarsenotrophic bacterium Ectothiorhodospira sp. strain BSL-9, isolated from a hypersaline alkaline arsenic-rich extreme environment

    Science.gov (United States)

    Hernandez-Maldonado, Jaime; Stoneburner, Brendon; Boren, Alison; Miller, Laurence; Rosen, Michael R.; Oremland, Ronald S.; Saltikov, Chad W

    2016-01-01

    The full genome sequence of Ectothiorhodospira sp. strain BSL-9 is reported here. This purple sulfur bacterium encodes an arxA-type arsenite oxidase within the arxB2AB1CD gene island and is capable of carrying out “photoarsenotrophy” anoxygenic photosynthetic arsenite oxidation. Its genome is composed of 3.5 Mb and has approximately 63% G+C content.

  8. Dyadobacter jiangsuensis sp. nov., a methyl red degrading bacterium isolated from a dye-manufacturing factory.

    Science.gov (United States)

    Wang, Li; Chen, Liang; Ling, Qi; Li, Chen-chen; Tao, Yong; Wang, Min

    2015-04-01

    A Gram-stain-negative, non-motile, rod-shaped bacterial strain, L-1(T), which was capable of degrading methyl red was isolated from a dye-manufacturing factory in China. Phenotypic, chemotaxonomic and phylogenetic analyses established affiliation of the isolate to the genus Dyadobacter . Cells occurred in pairs in young cultures but became chains of coccoid cells in old cultures, and produced a flexirubin-like yellow pigment. Strain L-1(T) could not hydrolyse cellulose, and had a DNA G+C content of 51.3 mol%. The major cellular fatty acids were iso-C(15 : 0), C(16 : 1)ω5c, iso-C(17 : 0) 3-OH and summed feature 3 (C(16 : 1)ω7c and/or C(16 : 1)ω6c). C(16 : 0), iso-C(15 : 0) 3-OH and C(16 : 0) 3-OH were the other major fatty acid components. Comparative 16S rRNA gene sequence analysis showed that strainL-1(T) was most closely related to Dyadobacter fermentans DSM 18053(T) (99.2%), Dyadobacter soli JCM 16232(T) (98.9%) and Dyadobacter beijingensis CGMCC 1.6375(T) (98.7%). However, the new isolate exhibited relatively low levels of DNA-DNA relatedness with respect to JCM 16232(T) (41.2±1.8%), DSM 18053(T) (38.6±2.6%) and CGMCC 1.6375(T) (35.0±2.1%). Strain L-1(T) could also be differentiated from its closest phylogenetic relatives based on differences in several phenotypic characteristics. These data suggest that strain L-1(T) represents a novel species of the genus Dyadobacter , for which the name Dyadobacter jiangsuensis sp. is proposed. The type strain is L-1(T) (DSM 29057(T) = CGMCC 1.12969(T)). © 2015 IUMS.

  9. Salimicrobium salexigens sp. nov., a moderately halophilic bacterium from salted hides.

    Science.gov (United States)

    de la Haba, Rafael R; Yilmaz, Pinar; Sánchez-Porro, Cristina; Birbir, Meral; Ventosa, Antonio

    2011-09-01

    Two Gram-positive, moderately halophilic bacteria, designated strains 29CMI(T) and 53CMI, were isolated from salted hides. Both strains were non-motile, strictly aerobic cocci, growing in the presence of 3-25% (w/v) NaCl (optimal growth at 7.5-12.5% [w/v] NaCl), between pH 5.0 and 10.0 (optimal growth at pH 7.5) and at temperatures between 15 and 40°C (optimal growth at 37°C). Phylogenetic analysis based on 16S rRNA gene sequence comparison showed that both strains showed a similarity of 98.7% and were closely related to species of the genus Salimicrobium, within the phylum Firmicutes. Strains 29CMI(T) and 53CMI exhibited 16S rRNA gene sequence similarity values of 97.9-97.6% with Salimicrobium album DSM 20748(T), Salimicrobium halophilum DSM 4771(T), Salimicrobium flavidum ISL-25(T) and Salimicrobium luteum BY-5(T). The DNA G+C content was 50.7mol% and 51.5mol% for strains 29CMI(T) and 53CMI, respectively. The DNA-DNA hybridization between both strains was 98%, whereas the values between strain 29CMI(T) and the species S. album CCM 3517(T), S. luteum BY-5(T), S. flavidum ISL-25(T) and S. halophilum CCM 4074(T) were 45%, 28%, 15% and 10%, respectively, showing unequivocally that strains 29CMI(T) and 53CMI constitute a new genospecies. The major cellular fatty acids were anteiso-C(15:0), anteiso-C(17:0), iso-C(15:0) and iso-C(14:0). The main respiratory isoprenoid quinone was MK-7, although small amounts of MK-6 were also found. The polar lipids of the type strain consist of diphosphatidylglycerol, phosphatidylglycerol, one unidentified phospholipid and one glycolipid. The peptidoglycan type is A1γ, with meso-diaminopimelic acid as the diagnostic diamino acid. On the basis of the phylogenetic analysis, and phenotypic, genotypic and chemotaxonomic characteristics, we propose strains 29CMI(T) and 53CMI as a novel species of the genus Salimicrobium, with the name Salimicrobium salexigens sp. nov. The type strain is 29CMI(T) (=CECT 7568(T)=JCM 16414(T)=LMG 25386(T

  10. Cellulomonas chitinilytica sp. nov., a chitinolytic bacterium isolated from cattle-farm compost.

    Science.gov (United States)

    Yoon, Min-Ho; Ten, Leonid N; Im, Wan-Taek; Lee, Sung-Taik

    2008-08-01

    A bacterial strain, designated X.bu-b T, with chitin-, xylan-, cellulose- and starch-degrading activities, was isolated from compost at a cattle farm near Daejeon, Republic of Korea. The strain comprised Gram-positive, aerobic or facultatively anaerobic, non-motile, rod-shaped bacteria. On the basis of an analysis of 16S rRNA gene sequences, the phylogenetic position of X.bu-b T was within the genus Cellulomonas, and the strain exhibited relatively high sequence similarities with respect to Cellulomonas biazotea DSM 20112T (98.1 %), C. cellasea DSM 20118T (98.1 %), C. fimi DSM 20113T (98.0 %), C. terrae DB5T (97.9 %), C. humilata ATCC 25174T (97.7 %), C. xylanilytica XIL11 T (97.5 %), C. uda DSM 20107T (97.4 %), C. gelida DSM 20111 T (97.3 %), C. iranensis OT (97.3 %) and C. flavigena DSM 20109T (97.0 %). The phylogenetic distance from other Cellulomonas species with validly published names was greater than 3 % (i.e. less than 97.0 % sequence similarity). Chemotaxonomic data also supported the classification of strain X.bu-b T within the genus Cellulomonas: L-ornithine was the cell-wall diamino acid, anteiso-C15:0 and anteiso-C17:0 were the major fatty acids, rhamnose, galactose, xylose and ribose were the cell-wall sugars, MK-9(H4) was the predominant menaquinone and diphosphatidylglycerol and phosphatidylglycerol were present in the polar lipids. The G+C content of the genomic DNA was 73.6 mol%. DNA-DNA hybridization experiments showed that the values for DNA-DNA relatedness between strain X.bu-b T and the phylogenetically closest neighbours were below 23 %. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain X.bu-b T represents a novel species of the genus Cellulomonas, for which the name Cellulomonas chitinilytica sp. nov. is proposed. The type strain is X.bu-b T (=KCTC 19133T =DSM 17922T).

  11. Thermus caldifontis sp. nov., a thermophilic bacterium isolated from a hot spring.

    Science.gov (United States)

    Khan, Inam Ullah; Habib, Neeli; Hussain, Firasat; Xian, Wen-Dong; Amin, Arshia; Zhou, En-Min; Ahmed, Iftikhar; Zhi, Xiao-Yang; Li, Wen-Jun

    2017-08-01

    A thermophilic bacterial strain, designated YIM 73026T was isolated from a sediment sample collected from a hot spring in Tibet, PR China. The taxonomic position of the novel isolate was investigated by a polyphasic approach. The novel isolate was Gram-stain-negative, aerobic and rod-shaped. Colonies were circular, convex, opaque and yellow. The strain grew at 50-70 °C (optimum, 60 °C), pH 6.0-8.0 (optimum, pH 7.0) and in the presence of up to 1.0 % NaCl (w/v). Comparison of the 16S rRNA gene sequences of YIM 73026T and those of other members of the genus Thermus showed sequence similarities ranging from 91.2 to 97.5 %, with YIM 73026T showing closest sequence similarity to Thermus scotoductus SE-1T (97.5 %). DNA-DNA hybridization results, however, revealed that DNA-DNA reassociation values between YIM 73026T and T. scotoductus DSM 8553T (37.6 %), Thermusamyloliquefaciens YIM 77409T (34.5 %), Thermusantranikianii DSM 12462T (30.3 %), Thermuscaliditerrae YIM 77925T (28.6 %) and Thermustengchongensis YIM 77924T (27.3 %) were well below the 70 % limit for species identification. YIM 73026T contained MK-8 as the respiratory quinone, and iso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and anteiso-C15 : 0 as the major cellular fatty acids (>10 %). The polar lipids consisted of one aminophospholipid, one phospholipid and two glycolipids. The genomic DNA G+C content of YIM 73026T was 65.4 mol%. On the basis of morphological, chemotaxonomic and genotypic characteristics, it is proposed that the isolate represents a novel species of the genus Thermus, for which the name Thermus caldifontis sp. nov. is proposed. The type strain is YIM 73026T (=NBRC 112415T=CCTCC AB 2016305T).

  12. Geobacter lovleyi sp. nov. strain SZ, a novel metal-reducing and tetrachloroethene-dechlorinating bacterium.

    Science.gov (United States)

    Sung, Youlboong; Fletcher, Kelly E; Ritalahti, Kirsti M; Apkarian, Robert P; Ramos-Hernández, Natalia; Sanford, Robert A; Mesbah, Noha M; Löffler, Frank E

    2006-04-01

    A bacterial isolate, designated strain SZ, was obtained from noncontaminated creek sediment microcosms based on its ability to derive energy from acetate oxidation coupled to tetrachloroethene (PCE)-to-cis-1,2-dichloroethene (cis-DCE) dechlorination (i.e., chlororespiration). Hydrogen and pyruvate served as alternate electron donors for strain SZ, and the range of electron acceptors included (reduced products are given in brackets) PCE and trichloroethene [cis-DCE], nitrate [ammonium], fumarate [succinate], Fe(III) [Fe(II)], malate [succinate], Mn(IV) [Mn(II)], U(VI) [U(IV)], and elemental sulfur [sulfide]. PCE and soluble Fe(III) (as ferric citrate) were reduced at rates of 56.5 and 164 nmol min(-1) mg of protein(-1), respectively, with acetate as the electron donor. Alternate electron acceptors, such as U(VI) and nitrate, did not inhibit PCE dechlorination and were consumed concomitantly. With PCE, Fe(III) (as ferric citrate), and nitrate as electron acceptors, H(2) was consumed to threshold concentrations of 0.08 +/- 0.03 nM, 0.16 +/- 0.07 nM, and 0.5 +/- 0.06 nM, respectively, and acetate was consumed to 3.0 +/- 2.1 nM, 1.2 +/- 0.5 nM, and 3.6 +/- 0.25 nM, respectively. Apparently, electron acceptor-specific acetate consumption threshold concentrations exist, suggesting that similar to the hydrogen threshold model, the measurement of acetate threshold concentrations offers an additional diagnostic tool to delineate terminal electron-accepting processes in anaerobic subsurface environments. Genetic and phenotypic analyses classify strain SZ as the type strain of the new species, Geobacter lovleyi sp. nov., with Geobacter (formerly Trichlorobacter) thiogenes as the closest relative. Furthermore, the analysis of 16S rRNA gene sequences recovered from PCE-dechlorinating consortia and chloroethene-contaminated subsurface environments suggests that Geobacter lovleyi belongs to a distinct, dechlorinating clade within the metal-reducing Geobacter group. Substrate

  13. Salinivibrio kushneri sp. nov., a moderately halophilic bacterium isolated from salterns.

    Science.gov (United States)

    López-Hermoso, Clara; de la Haba, Rafael R; Sánchez-Porro, Cristina; Ventosa, Antonio

    2017-12-21

    Ten Gram-strain-negative, facultatively anaerobic, moderately halophilic bacterial strains, designated AL184T, IB560, IB563, IC202, IC317, MA421, ML277, ML318, ML328A and ML331, were isolated from water ponds of five salterns located in Spain. The cells were motile, curved rods and oxidase and catalase positive. All of them grew optimally at 37°C, at pH 7.2-7.4 and in the presence of 7.5% (w/v) NaCl. Based on phylogenetic analyses of the 16S rRNA, the isolates were most closely related to Salinivibrio sharmensis BAGT (99.6-98.2% 16S rRNA gene sequence similarity) and Salinivibrio costicola subsp. costicola ATCC 35508T (99.0-98.1%). According to the MLSA analyses based on four (gyrB, recA, rpoA and rpoD) and eight (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA and topA) concatenated gene sequences, the most closely relatives were S. siamensis JCM 14472T (96.8-95.4% and 94.9-94.7%, respectively) and S. sharmensis DSM 18182T (94.0-92.6% and 92.9-92.7%, respectively). In silico DNA-DNA hybridization (GGDC) and average nucleotide identity (ANI) showed values of 23.3-44.8% and 80.2-91.8%, respectively with the related species demonstrating that the ten isolates constituted a single novel species of the genus Salinivibrio. Its pangenome and core genome consist of 6041 and 1230 genes, respectively. The phylogeny based on the concatenated orthologous core genes revealed that the ten strains form a coherent phylogroup well separated from the rest of the species of the genus Salinivibrio. The major cellular fatty acids of strain AL184T were C16:0 and C18:1. The DNA G+C content range was 51.9-52.5mol% (Tm) and 50.2-50.9mol% (genome). Based on the phylogenetic-phylogenomic, phenotypic and chemotaxonomic data, the ten isolates represent a novel species of the genus Salinivibrio, for which the name Salinivibrio kushneri sp. nov. is proposed. The type strain is AL184T (=CECT 9177T=LMG 29817T). Copyright © 2017 Elsevier GmbH. All rights reserved.

  14. Rhizobium marinum sp. nov., a malachite-green-tolerant bacterium isolated from seawater.

    Science.gov (United States)

    Liu, Yang; Wang, Run-Ping; Ren, Chong; Lai, Qi-Liang; Zeng, Run-Ying

    2015-12-01

    A motile, Gram-stain-negative, non-pigmented bacterial strain, designated MGL06T, was isolated from seawater of the South China Sea on selection medium containing 0.1 % (w/v) malachite green. Strain MGL06T showed highest 16S rRNA gene sequence similarity to Rhizobium vignae CCBAU 05176T (97.2 %), and shared 93.2-96.9 % with the type strains of other recognized Rhizobium species. Phylogenetic analyses based on 16S rRNA and housekeeping gene sequences showed that strain MGL06T belonged to the genus Rhizobium. Mean levels of DNA-DNA relatedness between strain MGL06T and R. vignae CCBAU 05176T, Rhizobium huautlense S02T and Rhizobium alkalisoli CCBAU 01393T were 20 ± 3, 18 ± 2 and 14 ± 3 %, respectively, indicating that strain MGL06T was distinct from them genetically. Strain MGL06T did not form nodules on three different legumes, and the nodD and nifH genes were also not detected by PCR or based on the draft genome sequence. Strain MGL06T contained Q-10 as the predominant ubiquinone. The major fatty acid was C18 : 1ω7c/C18 : 1ω6c with minor amounts of C19 : 0 cyclo ω8c, C16 : 0 and C18 : 1ω7c 11-methyl. Polar lipids of strain MGL06T included unknown glycolipids, phosphatidylcholine, aminolipid, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, an unknown polar lipid and aminophospholipid. Based on its phenotypic and genotypic data, strain MGL06T represents a novel species of the genus Rhizobium, for which the name Rhizobium marinum sp. nov. is proposed. The type strain is MGL06T ( = MCCC 1A00836T = JCM 30155T).

  15. Halomonas titanicae sp. nov., a halophilic bacterium isolated from the RMS Titanic.

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    Sánchez-Porro, Cristina; Kaur, Bhavleen; Mann, Henrietta; Ventosa, Antonio

    2010-12-01

    A Gram-negative, heterotrophic, aerobic, non-endospore-forming, peritrichously flagellated and motile bacterial strain, designated BH1(T), was isolated from samples of rusticles, which are formed in part by a consortium of micro-organisms, collected from the RMS Titanic wreck site. The strain grew optimally at 30-37°C, pH 7.0-7.5 and in the presence of 2-8 % (w/v) NaCl. We carried out a polyphasic taxonomic study in order to characterize the strain in detail. Phylogenetic analyses based on 16S rRNA gene sequence comparison indicated that strain BH1(T) clustered within the branch consisting of species of Halomonas. The most closely related type strains were Halomonas neptunia (98.6 % 16S rRNA sequence similarity), Halomonas variabilis (98.4 %), Halomonas boliviensis (98.3 %) and Halomonas sulfidaeris (97.5 %). Other closely related species were Halomonas alkaliphila (96.5 % sequence similarity), Halomonas hydrothermalis (96.3 %), Halomonas gomseomensis (96.3 %), Halomonas venusta (96.3 %) and Halomonas meridiana (96.2 %). The major fatty acids of strain BH1(T) were C(18 : 1)ω7c (36.3 %), C(16 : 0) (18.4 %) and C(19 : 0) cyclo ω8c (17.9 %). The DNA G+C content was 60.0 mol% (T(m)). Ubiquinone 9 (Q-9) was the major lipoquinone. The phenotypic features, fatty acid profile and DNA G+C content further supported the placement of strain BH1(T) in the genus Halomonas. DNA-DNA hybridization values between strain BH1(T) and H. neptunia CECT 5815(T), H. variabilis DSM 3051(T), H. boliviensis DSM 15516(T) and H. sulfidaeris CECT 5817(T) were 19, 17, 30 and 29 %, respectively, supporting the differential taxonomic status of BH1(T). On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain BH1(T) is considered to represent a novel species, for which the name Halomonas titanicae sp. nov. is proposed. The type strain is BH1(T) (=ATCC BAA-1257(T) =CECT 7585(T) =JCM 16411(T) =LMG 25388(T)).

  16. Genes involved in degradation of para-nitrophenol are differentially arranged in form of non-contiguous gene clusters in Burkholderia sp. strain SJ98.

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    Surendra Vikram

    Full Text Available Biodegradation of para-Nitrophenol (PNP proceeds via two distinct pathways, having 1,2,3-benzenetriol (BT and hydroquinone (HQ as their respective terminal aromatic intermediates. Genes involved in these pathways have already been studied in different PNP degrading bacteria. Burkholderia sp. strain SJ98 degrades PNP via both the pathways. Earlier, we have sequenced and analyzed a ~41 kb fragment from the genomic library of strain SJ98. This DNA fragment was found to harbor all the lower pathway genes; however, genes responsible for the initial transformation of PNP could not be identified within this fragment. Now, we have sequenced and annotated the whole genome of strain SJ98 and found two ORFs (viz., pnpA and pnpB showing maximum identity at amino acid level with p-nitrophenol 4-monooxygenase (PnpM and p-benzoquinone reductase (BqR. Unlike the other PNP gene clusters reported earlier in different bacteria, these two ORFs in SJ98 genome are physically separated from the other genes of PNP degradation pathway. In order to ascertain the identity of ORFs pnpA and pnpB, we have performed in-vitro assays using recombinant proteins heterologously expressed and purified to homogeneity. Purified PnpA was found to be a functional PnpM and transformed PNP into benzoquinone (BQ, while PnpB was found to be a functional BqR which catalyzed the transformation of BQ into hydroquinone (HQ. Noticeably, PnpM from strain SJ98 could also transform a number of PNP analogues. Based on the above observations, we propose that the genes for PNP degradation in strain SJ98 are arranged differentially in form of non-contiguous gene clusters. This is the first report for such arrangement for gene clusters involved in PNP degradation. Therefore, we propose that PNP degradation in strain SJ98 could be an important model system for further studies on differential evolution of PNP degradation functions.

  17. Skin infection caused by Burkholderia thailandensis: Case report with review

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    AbdelRahman Mohammad Zueter, Mahmoud Abumarzouq, Chan Yean Yean, Azian Harun

    2016-06-01

    Full Text Available Burkholderia thailandensis is genetically closed to Burkholderia pseudomallei, which causes melioidosis. The bacterium inhabits the environments of tropical regions including those in Southeast Asia and the Northern part of Australia. B. thailandensis is considered avirulent and extremely uncommon to cause disease. We report the first case of foot abscess with skin cellulitis and ankle swelling caused by B. thailandensis in Malaysia. J Microbiol Infect Dis 2016;6(2: 92-95

  18. Taxonomic characterization and metabolic analysis of the Halomonas sp. KM-1, a highly bioplastic poly(3-hydroxybutyrate)-producing bacterium.

    Science.gov (United States)

    Kawata, Yoshikazu; Shi, Lian-Hua; Kawasaki, Kazunori; Shigeri, Yasushi

    2012-04-01

    In a brief previous report, the gram-negative moderately halophilic bacterium, Halomonas sp. KM-1, that was isolated in our laboratory was shown to produce the bioplastic, poly(3-hydroxybutyrate) (PHB), using biodiesel waste glycerol (Kawata and Aiba, Biosci. Biotechnol. Biochem., 74, 175-177, 2010). Here, we further characterized this KM-1 strain and compared it to other Halomonas strains. Strain KM-1 was subjected to a polyphasic taxonomic study. Strain KM-1 was rod-shaped and formed colonies on a plate that were cream-beige in color, smooth, opaque, and circular with entire edges. KM-1 grew under environmental conditions of 0.1%-10% (w/v) NaCl, pH 6.5-10.5 and at temperatures between 10°C and 45°C. The G+C content of strain KM-1 was 63.9 mol%. Of the 16 Halomonas strains examined in this study, the strain KM-1 exhibited the highest production of PHB (63.6%, w/v) in SOT medium supplemented with 10% glycerol, 10.0 g/L sodium nitrate and 2.0 g/L dipotassium hydrogen phosphate. The intracellular structures within which PHB accumulated had the appearance of intracellular granules with a diameter of approximately 0.5 μm, as assessed by electron microscopy. The intra- and extra-cellular metabolites of strain KM-1 were analyzed by capillary electrophoresis mass spectrometry. In spite of the high amount of PHB stored intra-cellularly, as possible precursors for PHB only a small quantity of 3-hydroxybutyric acid and acetyl CoA, and no quantity of 3-hydroxybutyl CoA, acetoacetyl CoA and acetoacetate were detected either intra- or extra-cellularly, suggesting highly efficient conversion of these precursors to PHB. Copyright © 2011 The Society for Biotechnology, Japan. All rights reserved.

  19. Optimization of culture conditions and medium composition for the marine algicidal bacterium Alteromonas sp. DH46 by uniform design

    Science.gov (United States)

    Lin, Jing; Zheng, Wei; Tian, Yun; Wang, Guizhong; Zheng, Tianling

    2013-09-01

    Harmful algal blooms (HABs) have led to extensive ecological and environmental issues and huge economic losses. Various HAB control techniques have been developed, and biological methods have been paid more attention. Algicidal bacteria is a general designation for bacteria which inhibit algal growth in a direct or indirect manner, and kill or damage the algal cells. A metabolite which is strongly toxic to the dinoflagellate Alexandrium tamarense was produced by strain DH46 of the alga-lysing bacterium Alteromonas sp. The culture conditions were optimized using a single-factor test method. Factors including carbon source, nitrogen source, temperature, initial pH value, rotational speed and salinity were studied. The results showed that the cultivation of the bacteria at 28°C and 180 r min-1 with initial pH 7 and 30 salt contcentration favored both the cell growth and the lysing effect of strain DH46. The optimal medium composition for strain DH46 was determined by means of uniform design experimentation, and the most important components influencing the cell density were tryptone, yeast extract, soluble starch, NaNO3 and MgSO4. When the following culture medium was used (tryptone 14.0g, yeast extract 1.63g, soluble starch 5.0 g, NaNO3 1.6 g, MgSO4 2.3 g in 1L), the largest bacterial dry weight (7.36 g L-1) was obtained, which was an enhancement of 107% compared to the initial medium; and the algal lysis rate was as high as 98.4% which increased nearly 10% after optimization.

  20. Photobacterium panuliri sp. nov., an alkalitolerant marine bacterium isolated from eggs of spiny lobster, Panulirus penicillatus from Andaman Sea.

    Science.gov (United States)

    Deep, Kamal; Poddar, Abhijit; Das, Subrata K

    2014-11-01

    A facultative anaerobe, alkalitolerant, gram-negative marine bacterium strain LBS5(T), was isolated from eggs carried on the pleopods of female spiny lobster (Panulirus penicillatus) in Andaman Sea from a depth of 3.5 m. Heterotrophic growth was observed at 15-38 °C and pH 5.5-11. Optimum growth occurred at 28 °C and pH 7.5. It can grow in the presence of 0.5-7 % NaCl (w/v), and the optimal NaCl required for growth was 2-4 %. 16S rRNA gene sequence analysis revealed the strain LBS5(T) belongs to the genus Photobacterium and showed 99.6 % similarity with P. aquae AE6(T), 98.2 % with P. aphoticum M46(T), 97 % with P. rosenbergii CC1(T), 96.9 % with P. lutimaris DF-42(T), and 96.6 % with P. halotolerans MACL01(T). The DNA-DNA similarities between strains LBS5(T) with other closely related strains were well below 70 %. The DNA G + C content was 50.52 (±0.9) mol%. The major fatty acids were C16:1w7c/w6c, C18:1w6c/w7c, C16:0, C15:0 iso, C16:0 10-methyl/17:1 iso w9c, C17:0 iso. Polar lipids included a phosphatidylglycerol, a diphosphatidylglycerol, a phosphatidylethanolamine, and one unidentified lipid. Based on the polyphasic evidences, strain LBS5(T) represents a novel species of the genus Photobacterium for which Photobacterium panuliri sp. nov. is proposed. The type strain is LBS5(T) (=DSM 27646(T) = LMG 27617(T) = JCM 19199(T)).

  1. Tailoring nutritional and process variables for hyperproduction of catalase from a novel isolated bacterium Geobacillus sp. BSS-7.

    Science.gov (United States)

    Kauldhar, Baljinder Singh; Sooch, Balwinder Singh

    2016-01-14

    Catalase (EC 1.11.1.6) is one of the important industrial enzyme employed in diagnostic and analytical methods in the form of biomarkers and biosensors in addition to their enormous applications in textile, paper, food and pharmaceutical sectors. The present study demonstrates the utility of a newly isolated and adapted strain of genus Geobacillus possessing unique combination of several industrially important extremophilic properties for the hyper production of catalase. The bacterium can grow over a wide range of pH (3-12) and temperature (10-90 °C) with extraordinary capability to produce catalase. A novel extremophilic strain belonging to genus Geobacillus was exploited for the production of catalase by tailoring its nutritional requirements and process variables. One variable at a time traditional approach followed by computational designing was applied to customize the fermentation process. A simple fermentation media containing only three components namely sucrose (0.55 %, w/v), yeast extract (1.0 %, w/v) and BaCl2 (0.08 %, w/v) was designed for the hyperproduction of catalase. A controlled and optimum air supply caused a tremendous increase in the enzyme production on moving the bioprocess from the flask to bioreactor level. The present paper reports high quantum of catalase production (105,000 IU/mg of cells) in a short fermentation time of 12 h. To the best of our knowledge, there is no report in the literature that matches the performance of the developed protocol for the catalase production. This is the first serious study covering intracellular catalase production from thermophilic genus Geobacillus. An increase in intracellular catalase production by 214.72 % was achieved in the optimized medium when transferred from the shake flask to the fermenter level. The extraordinary high production of catalase from Geobacillus sp. BSS-7 makes the isolated strain a prospective candidate for bulk catalase production on an industrial scale.

  2. Virgibacillus albus sp. nov., a novel moderately halophilic bacterium isolated from Lop Nur salt lake in Xinjiang province, China.

    Science.gov (United States)

    Zhang, Yun-Jiao; Zhou, Yu; Ja, Man; Shi, Rong; Chun-Yu, Wei-Xun; Yang, Ling-Ling; Tang, Shu-Kun; Li, Wen-Jun

    2012-11-01

    A Gram-positive, moderately halophilic, strictly aerobic bacterium, designated YIM 93624(T), was isolated from a salt lake in Xinjiang province of China and subjected to a polyphasic taxonomic study. Strain YIM 93624(T) grew at 15-45 °C (optimum 25-30 °C), 1-17% (w/v) NaCl (optimum 5-10 %, w/v) and pH 4.0-9.0 (optimum pH 7.0). The predominant menaquinone was found to be MK-7. The major fatty acids were anteiso-C(15:0) and C(16:0). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, a glycolipid and two unidentified phospholipids. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The G+C content of the genomic DNA was 37.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 93624(T) was a member of the genus Virgibacillus and exhibited the highest similarity of 97.0 % to Virgibacillus koreensis KCTC 3823(T). However, the level of DNA-DNA relatedness between strain YIM 93624(T) and V. koreensis KCTC 3823(T) was 32.5 %. On the basis of phylogenetic, physiological and chemotaxonomic analysis data, the isolate is concluded to represent a novel species of the genus Virgibacillus, for which the name Virgibacillus albus sp. nov., is proposed, with type strain of YIM 93624(T) (=DSM 23711(T) = JCM 17364(T)).

  3. Desulfovibrio legallis sp. nov.: a moderately halophilic, sulfate-reducing bacterium isolated from a wastewater digestor in Tunisia.

    Science.gov (United States)

    Thabet, Olfa Ben Dhia; Wafa, Terres; Eltaief, Khelifi; Cayol, Jean-Luc; Hamdi, Moktar; Fauque, Guy; Fardeau, Marie-Laure

    2011-02-01

    A new moderately halophilic sulfate-reducing bacterium (strain H₁(T) ) was enriched and isolated from a wastewater digestor in Tunisia. Cells were curved, motile rods (2-3 x 0.5 μm). Strain H₁(T) grew at temperatures between 22 and 43°C (optimum 35°C), and at pH between 5.0 and 9.2 (optimum 7.3-7.5). Strain H₁(T) required salt for growth (1-45 g of NaCl/l), with an optimum at 20-30 g/l. Sulfate, sulfite, thiosulfate, and elemental sulfur were used as terminal electron acceptors but not nitrate and nitrite. Strain H₁(T) utilized lactate, pyruvate, succinate, fumarate, ethanol, and hydrogen (in the presence of acetate and CO₂) as electron donors in the presence of sulfate as electron acceptor. The main end-products from lactate oxidation were acetate with H₂ and CO₂. The G + C content of the genomic DNA was 55%. The predominant fatty acids of strain H₁(T) were C(15:0) iso (38.8%), C(16:0) (19%), and C(14:0) iso 3OH (12.2%), and menaquinone MK-6 was the major respiratory quinone. Phylogenetic analysis of the small-subunit (SSU) ribosomal RNA (rRNA) gene sequence indicated that strain H₁(T) was affiliated to the genus Desulfovibrio. On the basis of SSU rRNA gene sequence comparisons and physiological characteristics, strain H₁(T) is proposed to be assigned to a novel species of sulfate reducers of the genus Desulfovibrio, Desulfovibrio legallis sp. nov. (= DSM 19129(T) = CCUG 54389(T)).

  4. Methylobacterium jeotgali sp. nov., a non-pigmented, facultatively methylotrophic bacterium isolated from jeotgal, a traditional Korean fermented seafood.

    Science.gov (United States)

    Aslam, Zubair; Lee, Chang Soo; Kim, Kyoung-Ho; Im, Wan-Taek; Ten, Leonid N; Lee, Sung-Taik

    2007-03-01

    A novel facultatively methylotrophic, Gram-negative, rod-shaped bacterium, designated strain S2R03-9(T), was isolated from jeotgal, a traditional Korean fermented seafood. The organism was strictly aerobic, motile by means of a single polar flagellum, non-sporulating and catalase- and oxidase-positive. Strain S2R03-9(T) grew in the presence of 0-1 % (w/v) NaCl and at pH 6.0-10.0, with optimum growth in the absence of NaCl and at pH 7.0. It grew at temperatures in the range 20.0-30.0 degrees C, with optimum growth at 30 degrees C. Colonies grown on R2A medium were non-pigmented, opaque and creamy white. Phylogenetic analysis based on 16S rRNA gene sequences indicated that it was most closely related to Methylobacterium organophilum JCM 2833(T) (96.6 % similarity) and the phylogenetic similarities to all other Methylobacterium species with validly published names were less than 95.0 %. The DNA G+C content was 64.9 mol%. The phylogenetic analysis, the phenotypic assessment and the chemotaxonomic data (major ubiquinone, Q-10; major fatty acids, C(18 : 1) and C(18 : 0)) showed that S2R03-9(T) represents a novel species within the genus Methylobacterium in the class Alphaproteobacteria, for which the name Methylobacterium jeotgali sp. nov. is proposed. The type strain is S2R03-9(T) (=KCTC 12671(T)=LMG 23639(T)).

  5. Bacillus piscis sp. nov., a novel bacterium isolated from the muscle of the antarctic fish Dissostichus mawsoni.

    Science.gov (United States)

    Lee, Jae-Bong; Jeon, Seon Hwa; Choi, Seok-Gwan; Jung, Hee-Young; Kim, Myung Kyum; Srinivasan, Sathiyaraj

    2016-12-01

    In this paper, a new bacterial strain designated as 16MFT21(T) is isolated from the muscle of a fish caught in the Antarctic Ocean. Strain 16MFT21(T) is a Gram-staining-positive, catalase-oxidase-positive, rod-shaped facultative-aerobic bacterium. The phylogenetic analysis that is based on the 16S-rRNA gene sequence of strain 16MFT21(T) revealed that it belongs to the genus Bacillus in the family Bacillaceae in the class Bacilli. The highest degrees of the sequence similarity of the strain 16MFT21(T) is with Bacillus licheniformis ATCC 14580(T) (96.6%) and Bacillus sonorensis NBRC 101234(T) (96.6%). The isolate formed a pale-yellow pigment, and it grew in the presence of 0% to 10% (w/v) NaCl (optimum at 2% NaCl), a pH of 6.0 to 10.0 (optimum pH from 7.0 to 8.0), and from 4°C to 30°C (optimum at 30°C). The major polar lipids consist of diphosphatidylglycerol (DPG) and phosphatidylglycerol (PG). The predominant fatty acids are iso-C15:0, anteiso-C15:0, iso-C17:0, and anteiso-C17:0. The main respiratory quinone is menaquinone-7 (MK-7), and based on the use of the meso-diaminopimelic acid as the diagnostic diamino acid, the peptidoglycan cell-wall type is A1γ. Based on the phylogenetic, phenotypic, and chemotaxonomic data, strain 16MFT21(T) (=KCTC 18866(T) =JCM 31664(T)) for which the name Bacillus piscis sp. nov. is proposed should be classified as a new species.

  6. Desulfitibacter alkalitolerans gen. nov., sp. nov., an anaerobic, alkalitolerant, sulfite-reducing bacterium isolated from a district heating plant.

    Science.gov (United States)

    Nielsen, Marie Bank; Kjeldsen, Kasper Urup; Ingvorsen, Kjeld

    2006-12-01

    A novel alkalitolerant, anaerobic bacterium, designated strain sk.kt5(T), was isolated from a metal coupon retrieved from a corrosion-monitoring reactor of a Danish district heating plant (Skanderborg, Jutland). The cells of strain sk.kt5(T) were motile, rod-shaped (0.4-0.6 x 2.5-9.6 microm), stained Gram-positive and formed endospores. Strain sk.kt5(T) grew at pH 7.6-10.5 (with optimum growth at pH 8.0-9.5), at temperatures in the range 23-44 degrees C (with optimum growth at 35-37 degrees C), at NaCl concentrations in the range 0-5 % (w/v) (with optimum growth at 0-0.5 %) and required yeast extract for growth. Only a limited number of substrates were utilized as electron donors, including betaine, formate, lactate, methanol, choline and pyruvate. Elemental sulfur, sulfite, thiosulfate, nitrate and nitrite, but not sulfate or Fe(III) citrate, were used as electron acceptors. The G+C content of the DNA was 41.6 mol%. Phylogenetic analyses of the sequence data for the dsrAB genes [encoding the major subunits of dissimilatory (bi)sulfite reductase] and the 16S rRNA gene placed strain sk.kt5(T) within a novel lineage in the class Clostridia of the phylum Firmicutes. Taken together, the physiological and genotypic data suggest that strain sk.kt5(T) represents a novel species within a novel genus, for which the name Desulfitibacter alkalitolerans gen. nov., sp. nov. is proposed. The type strain of Desulfitibacter alkalitolerans is sk.kt5(T) (=JCM 12761(T)=DSM 16504(T)).

  7. Bacillus eiseniae sp. nov., a swarming, moderately halotolerant bacterium isolated from the intestinal tract of an earthworm (Eisenia fetida L.).

    Science.gov (United States)

    Hong, Sung Wook; Park, Jung Min; Kim, Soo-Jin; Chung, Kun Sub

    2012-09-01

    A swarming and moderately halotolerant bacterium, designated strain A1-2(T), was isolated from the intestinal tract of the earthworm Eisenia fetida L. Cells were endospore-forming rods that were facultatively anaerobic, catalase-positive, oxidase-negative and motile by peritrichous flagella. The isolate grew optimally at 30 °C and pH 7.0, and could grow with up to 9 % (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain A1-2(T) belonged to the genus Bacillus and exhibited 16S rRNA gene sequence similarities of 96.8, 96.0, 96.0, 96.4 and 96.7 % with Bacillus drentensis LMG 21831(T), B. horneckiae PT-45(T), B. niacini BAC 1015, B. infantis SMC 4352-1(T) and B. shackletonii LMG 18435(T), respectively. DNA-DNA relatedness values between the isolate and the reference strains were ≤ 38.3 %. The DNA G+C content of strain A1-2(T) was 38.5 mol%. The predominant menaquinone was MK-7 and the major polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids were iso-C(15 : 0) (51.5 %) and anteiso-C(15 : 0) (29.6 %) and the cell-wall diamino acid was meso-diaminopimelic acid. On the basis of 16S rRNA gene sequence analysis and chemotaxonomic and phenotypic characteristics, it is concluded that strain A1-2(T) represents a novel species of the genus Bacillus, for which we propose the name Bacillus eiseniae sp. nov. The type strain is A1-2(T) (= KCCM 90092(T) = JCM 16993(T)).

  8. Brevibacterium ammoniilyticum sp. nov., an ammonia-degrading bacterium isolated from sludge of a wastewater treatment plant.

    Science.gov (United States)

    Kim, Jinsoo; Srinivasan, Sathiyaraj; You, Taek; Bang, John J; Park, Sujeong; Lee, Sang-Seob

    2013-03-01

    A Gram-stain-positive, non-motile, chemo-organotrophic, mesophilic, aerobic bacterium, designated A1(T), was isolated from sludge of a wastewater treatment plant. Strain A1(T) showed good ability to degrade ammonia and grew well on media amended with methanol and ammonia. Strain A1(T) grew with 0-11 % (w/v) NaCl, at 20-42 °C, but not 45 °C and at pH 6-10 (optimum pH 8.0-9.0). The isolate was catalase-positive and oxidase-negative. The DNA G+C content was 70.7 mol%. A comparative analysis of 16S rRNA gene sequences revealed that strain A1(T) formed a distinct phyletic lineage in the genus Brevibacterium and showed high sequence similarity with Brevibacterium casei NCDO 2048(T) (96.9 %), Brevibacterium celere KMM 3637(T) (96.9 %) and Brevibacterium sanguinis CF63(T) (96.4 %). DNA-DNA hybridization revealed Brevibacterium was supported by the chemotaxonomic data: predominant quinone menaquinone MK-7(H2); polar lipid profile containing diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid; characteristic cell-wall diamino acid meso-diaminopimelic acid; whole-cell sugars galactose, xylose and ribose; absence of mycolic acids; and major fatty acids iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The results of physiological and biochemical tests allowed phenotypic differentiation of strain A1(T) from members of the genus Brevibacterium. On the basis of the results in this study, a novel species, Brevibacterium ammoniilyticum sp. nov., is proposed. The type strain is A1(T) ( = KEMC 41-098(T)  = JCM 17537(T)  = KACC 15558(T)).

  9. Bacillus daqingensis sp. nov., a halophilic, alkaliphilic bacterium isolated from saline-sodic soil in Daqing, China.

    Science.gov (United States)

    Wang, Shuang; Sun, Lei; Wei, Dan; Zhou, Baoku; Zhang, Junzheng; Gu, Xuejia; Zhang, Lei; Liu, Ying; Li, Yidan; Guo, Wei; Jiang, Shuang; Pan, Yaqing; Wang, Yufeng

    2014-07-01

    An alkaliphilic, moderately halophilic, bacterium, designated strain X10-1(T), was isolated from saline-alkaline soil in Daqing, Heilongjiang Province, China. Strain X10-1(T) was determined to be a Gram-positive aerobe with rod-shaped cells. The isolate was catalase-positive, oxidase-negative, non-motile, and capable of growth at salinities of 0-16% (w/v) NaCl (optimum, 3%). The pH range for growth was 7.5-11.0 (optimum, pH 10.0). The genomic DNA G+C content was 47.7 mol%. Its major isoprenoid quinone was MK-7 and its cellular fatty acid profile mainly consisted of anteiso-C15:0, anteiso-C17:0, iso-C15:0, C16:0, and iso-C16:0. The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. Phylogenetic analysis based on 16S rRNA gene sequences showed that X10-1(T) is a member of the genus Bacillus, being most closely related to B. saliphilus DSM15402(T) (97.8% similarity) and B. agaradhaerens DSM 8721(T) (96.2%). DNA-DNA relatedness to the type strains of these species was less than 40%. On the basis of the phylogenetic, physiological, and biochemical data, strain X10-1(T) represents a novel species of the genus Bacillus, for which the name Bacillus daqingensis sp. nov. is proposed. The type strain is X10-1(T) (=NBRC 109404(T) = CGMCC 1.12295(T)).

  10. Genetic and Biochemical Characterization of 2-Chloro-5-Nitrophenol Degradation in a Newly Isolated Bacterium, Cupriavidus sp. Strain CNP-8

    Directory of Open Access Journals (Sweden)

    Jun Min

    2017-09-01

    Full Text Available Compound 2-chloro-5-nitrophenol (2C5NP is a typical chlorinated nitroaromatic pollutant. To date, the bacteria with the ability to degrade 2C5NP are rare, and the molecular mechanism of 2C5NP degradation remains unknown. In this study, Cupriavidus sp. strain CNP-8 utilizing 2-chloro-5-nitrophenol (2C5NP and meta-nitrophenol (MNP via partial reductive pathways was isolated from pesticide-contaminated soil. Biodegradation kinetic analysis indicated that 2C5NP degradation by this strain was concentration dependent, with a maximum specific degradation rate of 21.2 ± 2.3 μM h−1. Transcriptional analysis showed that the mnp genes are up-regulated in both 2C5NP- and MNP-induced strain CNP-8. Two Mnp proteins were purified to homogeneity by Ni-NTA affinity chromatography. In addition to catalyzing the reduction of MNP, MnpA, a NADPH-dependent nitroreductase, also catalyzes the partial reduction of 2C5NP to 2-chloro-5-hydroxylaminophenol via 2-chloro-5-nitrosophenol, which was firstly identified as an intermediate of 2C5NP catabolism. MnpC, an aminohydroquinone dioxygenase, is likely responsible for the ring-cleavage reaction of 2C5NP degradation. Gene knockout and complementation indicated that mnpA is necessary for both 2C5NP and MNP catabolism. To our knowledge, strain CNP-8 is the second 2C5NP-utilizing bacterium, and this is the first report of the molecular mechanism of microbial 2C5NP degradation.

  11. Alkanindiges illinoisensis gen. nov., sp. nov., an obligately hydrocarbonoclastic, aerobic squalane-degrading bacterium isolated from oilfield soils.

    Science.gov (United States)

    Bogan, Bill W; Sullivan, Wendy R; Kayser, Kevin J; Derr, K D; Aldrich, Henry C; Paterek, J Robert

    2003-09-01

    An alkane-degrading bacterium, designated GTI MVAB Hex1(T), was isolated from chronically crude oil-contaminated soil from an oilfield in southern Illinois. The isolate grew very weakly or not at all in minimal or rich media without hydrocarbons. Straight-chain aliphatic hydrocarbons, such as hexadecane and heptadecane, greatly stimulated growth; shorter-chain (squalane. The latter of these was most intriguing, as catabolism of squalane has hitherto been reported only for Mycobacterium species. Although unable to utilize mono- or polycyclic aromatic hydrocarbons as sole carbon sources, the isolate did show slight fluorene-mineralizing capability in Luria-Bertani medium, which was partially repressed by hexadecane. In contrast, hexadecane supplementation greatly increased mineralization of (14)C-dodecane, which was not a growth substrate. Further testing emphasized the isolate's extremely narrow substrate range, as only Tween 40 and Tween 80 supported significant growth. Microscopic examination (by scanning and transmission electron microscopy) revealed a slightly polymorphic coccoidal to bacillar morphology, with hydrocarbon-grown cells tending to be more elongated. When grown with hexadecane, GTI MVAB Hex1(T) accumulated a large number of electron-transparent intracytoplasmic inclusion bodies. These were also prevalent during growth in the presence of squalane. Smaller inclusion bodies were observed occasionally with pristane supplementation; they were, however, absent during growth on crude oil. On the basis of 16S rRNA gene sequence data and range of growth substrates, classification of this isolate as the type strain of Alkanindiges illinoisensis gen. nov., sp. nov. is proposed, which is most closely related (approx. 94 % sequence similarity) to Acinetobacter junii.

  12. Antimicrobial and antibiofilm activity of LL-37 and its truncated variants against Burkholderia pseudomallei

    NARCIS (Netherlands)

    Kanthawong, S.; Bolscher, J.G.M.; Veerman, E.C.I.; van Marle, J.; de Soet, H.J.J.; Nazmi, K.; Wongratanacheewin, S.; Taweechaisupapong, S.

    2012-01-01

    The Gram-negative bacterium Burkholderia pseudomallei is the aetiological agent of melioidosis, which is an endemic disease in tropical areas of Southeast Asia and Northern Australia. Burkholderia pseudomallei has intrinsic resistance to a number of commonly used antibiotics and has also been

  13. Structural flexibility in the Burkholderia mallei genome.

    Science.gov (United States)

    Nierman, William C; DeShazer, David; Kim, H Stanley; Tettelin, Herve; Nelson, Karen E; Feldblyum, Tamara; Ulrich, Ricky L; Ronning, Catherine M; Brinkac, Lauren M; Daugherty, Sean C; Davidsen, Tanja D; Deboy, Robert T; Dimitrov, George; Dodson, Robert J; Durkin, A Scott; Gwinn, Michelle L; Haft, Daniel H; Khouri, Hoda; Kolonay, James F; Madupu, Ramana; Mohammoud, Yasmin; Nelson, William C; Radune, Diana; Romero, Claudia M; Sarria, Saul; Selengut, Jeremy; Shamblin, Christine; Sullivan, Steven A; White, Owen; Yu, Yan; Zafar, Nikhat; Zhou, Liwei; Fraser, Claire M

    2004-09-28

    The complete genome sequence of Burkholderia mallei ATCC 23344 provides insight into this highly infectious bacterium's pathogenicity and evolutionary history. B. mallei, the etiologic agent of glanders, has come under renewed scientific investigation as a result of recent concerns about its past and potential future use as a biological weapon. Genome analysis identified a number of putative virulence factors whose function was supported by comparative genome hybridization and expression profiling of the bacterium in hamster liver in vivo. The genome contains numerous insertion sequence elements that have mediated extensive deletions and rearrangements of the genome relative to Burkholderia pseudomallei. The genome also contains a vast number (>12,000) of simple sequence repeats. Variation in simple sequence repeats in key genes can provide a mechanism for generating antigenic variation that may account for the mammalian host's inability to mount a durable adaptive immune response to a B. mallei infection.

  14. Burkholderia thailandensis: Growth and Laboratory Maintenance.

    Science.gov (United States)

    Garcia, Erin C; Cotter, Peggy A

    2016-08-12

    Burkholderia thailandensis is a nonpathogenic Gram-negative bacterium found in tropical soils. Closely related to several human pathogens, its ease of genetic manipulation, rapid growth in the laboratory, and low virulence make B. thailandensis a commonly used model organism. This unit describes the fundamental protocols for in vitro growth and maintenance of B. thailandensis in the laboratory. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

  15. Structural flexibility in the Burkholderia mallei genome

    OpenAIRE

    William C. Nierman; DeShazer, David; Kim, H Stanley; Tettelin, Herve; Nelson, Karen E.; Feldblyum, Tamara; Ulrich, Ricky L.; Ronning, Catherine M.; Brinkac, Lauren M.; Daugherty, Sean C.; Davidsen, Tanja D.; DeBoy, Robert T.; Dimitrov, George; Dodson, Robert J.; Durkin, A. Scott

    2004-01-01

    The complete genome sequence of Burkholderia mallei ATCC 23344 provides insight into this highly infectious bacterium's pathogenicity and evolutionary history. B. mallei, the etiologic agent of glanders, has come under renewed scientific investigation as a result of recent concerns about its past and potential future use as a biological weapon. Genome analysis identified a number of putative virulence factors whose function was supported by comparative genome hybridization and expression prof...

  16. Neoasaia chiangmaiensis gen. nov., sp. nov., a novel osmotolerant acetic acid bacterium in the alpha-Proteobacteria.

    Science.gov (United States)

    Yukphan, Pattaraporn; Malimas, Taweesak; Potacharoen, Wanchern; Tanasupawat, Somboon; Tanticharoen, Morakot; Yamada, Yuzo

    2005-10-01

    An acetic acid bacterium, designated as isolate AC28(T), was isolated from a flower of red ginger (khing daeng in Thai; Alpinia purpurata) collected in Chiang Mai, Thailand, at pH 3.5 by use of a glucose/ethanol/acetic acid (0.3%, w/v) medium. A phylogenetic tree based on 16S rRNA gene sequences for 1,376 bases showed that isolate AC28(T) constituted a cluster along with the type strain of Kozakia baliensis. However, the isolate formed an independent cluster in a phylogenetic tree based on 16S-23S rDNA internal transcribed spacer (ITS) region sequences for 586 bases. Pair-wise sequence similarities of the isolate in 16S rRNA gene sequences for 1,457 bases were 93.0-88.3% to the type strains of Asaia, Kozakia, Swaminathania, Acetobacter, Gluconobacter, Gluconacetobacter, Acidomonas, and Saccharibacter species. Restriction analysis of 16S-23S rDNA ITS regions discriminated isolate AC28(T) from the type strains of Asaia and Kozakia species. Cells were non-motile. Colonies were pink, shiny, and smooth. The isolate produced acetic acid from ethanol. Oxidation of acetate and lactate was negative. The isolate grew on glutamate agar and mannitol agar. Growth was positive on 30% D-glucose (w/v) and in the presence of 0.35% acetic acid (w/v), but not in the presence of 1.0% KNO(3) (w/v). Ammoniac nitrogen was hardly assimilated on a glucose medium or a mannitol medium. Production of dihydroxyacetone from glycerol was weakly positive. The isolate did not produce a levan-like polysaccharide on a sucrose medium. Major isoprenoid quinone was Q-10. DNA base composition was 63.1 mol% G+C. On the basis of the results obtained, Neoasaia gen. nov. was proposed with Neoasaia chiangmaiensis sp. nov. The type strain was isolate AC28(T) (=BCC 15763(T) =NBRC 101099(T)).

  17. Ornithinibacillus halophilus sp. nov., a moderately halophilic, Gram-stain-positive, endospore-forming bacterium from a hypersaline lake.

    Science.gov (United States)

    Bagheri, Maryam; Amoozegar, Mohammad Ali; Schumann, Peter; Didari, Maryam; Mehrshad, Malihe; Spröer, Cathrin; Sánchez-Porro, Cristina; Ventosa, Antonio

    2013-03-01

    A novel Gram-stain-positive, moderately halophilic bacterium, designated strain G8B(T), was isolated from water of the hypersaline lake Aran-Bidgol in Iran and characterized taxonomically using a polyphasic approach. Cells of strain G8B(T) were rod-shaped, motile and produced oval endospores at a terminal position in swollen sporangia. Strain G8B(T) was strictly aerobic, catalase-positive and oxidase-negative. The strain was able to grow at NaCl concentrations of 0.5-12.5 % (w/v), with optimum growth occurring at 5-7.5 % (w/v) NaCl. The optimum temperature and pH for growth were 35-40 °C and pH 7.5-8.0, respectively. On the basis of 16S rRNA gene sequence analysis, strain G8B(T) was shown to belong to the genus Ornithinibacillus within the phylum Firmicutes and showed closest phylogenetic similarity with Ornithinibacillus bavariensis WSBC 24001(T) (97.6 %). The DNA G+C content of strain G8B(T) was 36.9 mol%. The major cellular fatty acids of strain G8B(T) were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0 and iso-C16 : 0, and its polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol, four unknown phospholipids and an unknown aminolipid. The isoprenoid quinones were MK-7 (98 %) and MK-8 (2 %). Strain G8B(T) contained a peptidoglycan of type A4β, l-Orn-d-Asp. All these features confirmed the placement of isolate G8B(T) within the genus Ornithinibacillus. DNA-DNA hybridization experiments revealed a low level of relatedness (6 %) between strain G8B(T) and Ornithinibacillus bavariensis DSM 15681(T). On the basis of evidence from this study, a novel species of the genus Ornithinibacillus, Ornithinibacillus halophilus sp. nov., is proposed, with strain G8B(T) ( = IBRC-M 10683(T) = KCTC 13822(T)) as the type strain.

  18. An arsenate-reducing and alkane-metabolizing novel bacterium, Rhizobium arsenicireducens sp. nov., isolated from arsenic-rich groundwater.

    Science.gov (United States)

    Mohapatra, Balaram; Sarkar, Angana; Joshi, Swati; Chatterjee, Atrayee; Kazy, Sufia Khannam; Maiti, Mrinal Kumar; Satyanarayana, Tulasi; Sar, Pinaki

    2017-03-01

    A novel arsenic (As)-resistant, arsenate-respiring, alkane-metabolizing bacterium KAs 5-22 T , isolated from As-rich groundwater of West Bengal was characterized by physiological and genomic properties. Cells of strain KAs 5-22 T were Gram-stain-negative, rod-shaped, motile, and facultative anaerobic. Growth occurred at optimum of pH 6.0-7.0, temperature 30 °C. 16S rRNA gene affiliated the strain KAs 5-22 T to the genus Rhizobium showing maximum similarity (98.4 %) with the type strain of Rhizobium naphthalenivorans TSY03b T followed by (98.0 % similarity) Rhizobium selenitireducens B1 T . The genomic G + C content was 59.4 mol%, and DNA-DNA relatedness with its closest phylogenetic neighbors was 50.2 %. Chemotaxonomy indicated UQ-10 as the major quinone; phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol as major polar lipids; C 16:0 , C 17:0 , 2-OH C 10:0 , 3-OH C 16:0 , and unresolved C 18:1 ɷ7C/ɷ9C as predominant fatty acids. The cells were found to reduce O 2 , As 5+ , NO 3 - , SO 4 2- and Fe 3+ as alternate electron acceptors. The strain's ability to metabolize dodecane or other alkanes as sole carbon source using As 5+ as terminal electron acceptor was supported by the presence of genes encoding benzyl succinate synthase (bssA like) and molybdopterin-binding site (mopB) of As 5+ respiratory reductase (arrA). Differential phenotypic, chemotaxonomic, genotypic as well as physiological properties revealed that the strain KAs 5-22 T is separated from its nearest recognized Rhizobium species. On the basis of the data presented, strain KAs 5-22 T is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium arsenicireducens sp. nov. is proposed as type strain (=LMG 28795 T =MTCC 12115 T ).

  19. Rhizobium metallidurans sp. nov., a symbiotic heavy metal resistant bacterium isolated from the Anthyllis vulneraria Zn-hyperaccumulator.

    Science.gov (United States)

    Grison, Claire M; Jackson, Stephen; Merlot, Sylvain; Dobson, Alan; Grison, Claude

    2015-05-01

    A Gram-stain-negative, aerobic, rod-shaped, non-spore-forming bacterium (ChimEc512(T)) was isolated from 56 host seedlings of the hyperaccumulating Anthyllis vulneraria legume, which was on an old zinc mining site at Les Avinières, Saint-Laurent-Le-Minier, Gard, South of France. On the basis of 16S rRNA gene sequence similarities, strain ChimEc512(T) was shown to belong to the genus Rhizobium and to be most closely related to Rhizobium endophyticum CCGE 2052(T) (98.4%), Rhizobium tibeticum CCBAU 85039(T) (98.1%), Rhizobium grahamii CCGE 502(T) (98.0%) and Rhizobium mesoamericanum CCGE 501(T) (98.0%). The phylogenetic relationships of ChimEc512(T) were confirmed by sequencing and analyses of recA and atpD genes. DNA-DNA relatedness values of strain ChimEc512(T) with R. endophyticum CCGE 2052(T), R. tibeticum CCBAU 85039(T), R. mesoamericanum CCGE 52(T), Rhizobium grahamii CCGE 502(T), Rhizobium etli CCBAU 85039(T) and Rhizobium radiobacter KL09-16-8-2(T) were 27, 22, 16, 18, 19 and 11%, respectively. The DNA G+C content of strain ChimEc512(T) was 58.9 mol%. The major cellular fatty acid was C18 : 1ω7c, characteristic of the genus Rhizobium . The polar lipid profile included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol and phosphatidylcholine and moderate amounts of aminolipids, phospholipid and sulfoquinovosyl diacylglycerol. Although ChimEc512(T) was able to nodulate A. vulneraria, the nodC and nifH genes were not detected by PCR. The rhizobial strain was tolerant to high concentrations of heavy metals: up to 35 mM Zn and up to 0.5 mM Cd and its growth kinetics was not impacted by Zn. The results of DNA-DNA hybridizations and physiological tests allowed genotypic and phenotypic differentiation of strain ChimEc512(T) from species of the genus Rhizobium with validly published names. Strain ChimEc512(T), therefore, represents a novel species, for which the name Rhizobium metallidurans sp. nov. is proposed, with the type strain

  20. Gene Inactivation in the Cyanobacterium Synechococcus sp. PCC 7002 and the Green Sulfur Bacterium Chlorobium tepidum Using In Vitro-Made DNA Constructs and Natural Transformation

    DEFF Research Database (Denmark)

    Frigaard, Niels-Ulrik; Sakuragi, Yumiko; Bryant, Donald A

    2004-01-01

    Inactivation of a chromosomal gene is a useful approach to study the function of the gene in question and can be used to produce a desired phenotype in the organism. This chapter describes how to generate such mutants of the cyanobacterium Synechococcus sp. PCC 7002 and the green sulfur bacterium...... Chlorobium tepidum by natural transformation with synthetic DNA constructs. Two alternative methods to generate the DNA constructs, both performed entirely in vitro and based on the polymerase chain reaction (PCR), are also presented. These methods are ligation of DNA fragments with T4 DNA ligase...

  1. Isolation and Characterization of a Human Intestinal Bacterium Eggerthella sp. AUH-JLD49s for the Conversion of (-)-3'-Desmethylarctigenin.

    Science.gov (United States)

    Wang, Ye; Yu, Fei; Liu, Ming-Yue; Zhao, Yi-Kai; Wang, Dong-Ming; Hao, Qing-Hong; Wang, Xiu-Ling

    2017-05-24

    Arctiin is the most abundant bioactive compound contained in the Arctium lappa plant. In our previous study, we isolated one single bacterium capable of bioconverting arctigenin, an aglycone of arctiin, to 3'-desmethylarctigenin (3'-DMAG) solely. However, to date, a specific bacterium capable of producing other arctiin metabolites has not been reported. In this study, we isolated one single bacterium, which we named Eggerthella sp. AUH-JLD49s, capable of bioconverting 3'-DMAG under anaerobic conditions. The metabolite of 3'-DMAG by strain AUH-JLD49s was identified as 3'-desmethyl-4'-dehydroxyarctigenin (DMDH-AG) based on electrospray ionization mass spectrometry (ESI-MS) and 1H and 13C nuclear magnetic resonance spectroscopy. The bioconversion kinetics and bioconversion capacity of strain AUH-JLD49s were investigated. In addition, the metabolite DMDH-AG showed an inhibitory effect on cell growth of human colon cancer cell line HCT116 and human breast cancer cell line MDA-MB-231.

  2. Glaciihabitans tibetensis gen. nov., sp. nov., a psychrotolerant bacterium of the family Microbacteriaceae, isolated from glacier ice water.

    Science.gov (United States)

    Li, Ai-Hua; Liu, Hong-Can; Xin, Yu-Hua; Kim, Song-Gun; Zhou, Yu-Guang

    2014-02-01

    A Gram-stain-positive, aerobic, non-spore-forming, short-rod-shaped bacterium, designated strain MP203(T), was isolated from ice water of Midui Glacier in Tibet Autonomous Region, China. The strain was psychrotolerant, growing at 0-25 °C. 16S rRNA gene sequence analysis showed that strain MP203(T) was most similar to Frigoribacterium faeni NBRC 103066(T), Compostimonas suwonensis KACC 13354(T), Frigoribacterium mesophilum KCTC 19311(T), Marisediminicola antarctica CCTCC AB 209077(T) and Alpinimonas psychrophila JCM 18951(T), with similarities of 97.4, 97.2, 97.2, 97.1 and 97.1%, respectively. The maximum-likelihood phylogenetic tree indicated that strain MP203(T) clustered with nine genera of the family Microbacteriaceae, namely Frigoribacterium, Compostimonas, Marisediminicola, Alpinimonas, Frondihabitans, Clavibacter, Subtercola, Klugiella and Agreia. However, bootstrap analysis showed that there was no significance in the branching pattern of the linage comprising strain MP203(T) and any existing generic lineage of the family Microbacteriaceae. DNA-DNA hybridization results indicated levels of relatedness between strain MP203(T) and Marisediminicola antarctica CCTCC AB 209077(T), Frigoribacterium faeni NBRC 103066(T), Frigoribacterium mesophilum KCTC 19311(T), Compostimonas suwonensis KACC 13354(T) and Alpinimonas psychrophila JCM 18951(T) were 25.8 ± 7.3, 29.6 ± 7.6, 19.7 ± 6.7, 16.0 ± 4.2 and 12.4 ± 5.1 % (mean ± SD), respectively. The G+C content of the genomic DNA was 64.1 mol%. Analysis of the cell-wall peptidoglycan revealed that the peptidoglycan structure of strain MP203(T) was B10 type with Gly[l-Hse]-D-Glu-D-DAB, containing 2, 4-diaminobutyric acid (DAB) as a diagnostic amino acid. The cell-wall sugars were rhamnose, ribose, mannose and glucose. The major fatty acids were anteiso-C(15 : 0), iso-C(16 : 0) and anteiso A-C(15 : 1). An unusual compound identified as anteiso-C(15 : 0)-DMA (1,1-dimethoxy-anteiso-pentadecane) was also present in strain

  3. A sequential statistical approach towards an optimized production of a broad spectrum bacteriocin substance from a soil bacterium Bacillus sp. YAS 1 strain.

    Science.gov (United States)

    Embaby, Amira M; Heshmat, Yasmin; Hussein, Ahmed; Marey, Heba S

    2014-01-01

    Bacteriocins, ribosomally synthesized antimicrobial peptides, display potential applications in agriculture, medicine, and industry. The present study highlights integral statistical optimization and partial characterization of a bacteriocin substance from a soil bacterium taxonomically affiliated as Bacillus sp. YAS 1 after biochemical and molecular identifications. A sequential statistical approach (Plackett-Burman and Box-Behnken) was employed to optimize bacteriocin (BAC YAS 1) production. Using optimal levels of three key determinants (yeast extract (0.48% (w/v), incubation time (62 hrs), and agitation speed (207 rpm)) in peptone yeast beef based production medium resulted in 1.6-fold enhancement in BAC YAS 1 level (470 AU/mL arbitrary units against Erwinia amylovora). BAC YAS 1 showed activity over a wide range of pH (1-13) and temperature (45-80 °C). A wide spectrum antimicrobial activity of BAC YAS 1 against the human pathogens (Clostridium perfringens, Staphylococcus epidermidis, Campylobacter jejuni, Enterobacter aerogenes, Enterococcus sp., Proteus sp., Klebsiella sp., and Salmonella typhimurium), the plant pathogen (E. amylovora), and the food spoiler (Listeria innocua) was demonstrated. On top and above, BAC YAS 1 showed no antimicrobial activity towards lactic acid bacteria (Lactobacillus bulgaricus, L. casei, L. lactis, and L. reuteri). Promising characteristics of BAC YAS 1 prompt its commercialization for efficient utilization in several industries.

  4. Isolation, Identification, and Optimization of Culture Conditions of a Bioflocculant-Producing Bacterium Bacillus megaterium SP1 and Its Application in Aquaculture Wastewater Treatment.

    Science.gov (United States)

    Luo, Liang; Zhao, Zhigang; Huang, Xiaoli; Du, Xue; Wang, Chang'an; Li, Jinnan; Wang, Liansheng; Xu, Qiyou

    2016-01-01

    A bioflocculant-producing bacterium, Bacillus megaterium SP1, was isolated from biofloc in pond water and identified by using both 16S rDNA sequencing analysis and a Biolog GEN III MicroStation System. The optimal carbon and nitrogen sources for Bacillus megaterium SP1 were 20 g L-1 of glucose and 0.5 g L-1 of beef extract at 30°C and pH 7. The bioflocculant produced by strain SP1 under optimal culture conditions was applied into aquaculture wastewater treatment. The removal rates of chemical oxygen demand (COD), total ammonia nitrogen (TAN), and suspended solids (SS) in aquaculture wastewater reached 64, 63.61, and 83.8%, respectively. The volume of biofloc (FV) increased from 4.93 to 25.97 mL L-1. The addition of Bacillus megaterium SP1 in aquaculture wastewater could effectively improve aquaculture water quality, promote the formation of biofloc, and then form an efficient and healthy aquaculture model based on biofloc technology.

  5. Isolation, Identification, and Optimization of Culture Conditions of a Bioflocculant-Producing Bacterium Bacillus megaterium SP1 and Its Application in Aquaculture Wastewater Treatment

    Directory of Open Access Journals (Sweden)

    Liang Luo

    2016-01-01

    Full Text Available A bioflocculant-producing bacterium, Bacillus megaterium SP1, was isolated from biofloc in pond water and identified by using both 16S rDNA sequencing analysis and a Biolog GEN III MicroStation System. The optimal carbon and nitrogen sources for Bacillus megaterium SP1 were 20 g L−1 of glucose and 0.5 g L−1 of beef extract at 30°C and pH 7. The bioflocculant produced by strain SP1 under optimal culture conditions was applied into aquaculture wastewater treatment. The removal rates of chemical oxygen demand (COD, total ammonia nitrogen (TAN, and suspended solids (SS in aquaculture wastewater reached 64, 63.61, and 83.8%, respectively. The volume of biofloc (FV increased from 4.93 to 25.97 mL L−1. The addition of Bacillus megaterium SP1 in aquaculture wastewater could effectively improve aquaculture water quality, promote the formation of biofloc, and then form an efficient and healthy aquaculture model based on biofloc technology.

  6. A Sequential Statistical Approach towards an Optimized Production of a Broad Spectrum Bacteriocin Substance from a Soil Bacterium Bacillus sp. YAS 1 Strain

    Directory of Open Access Journals (Sweden)

    Amira M. Embaby

    2014-01-01

    Full Text Available Bacteriocins, ribosomally synthesized antimicrobial peptides, display potential applications in agriculture, medicine, and industry. The present study highlights integral statistical optimization and partial characterization of a bacteriocin substance from a soil bacterium taxonomically affiliated as Bacillus sp. YAS 1 after biochemical and molecular identifications. A sequential statistical approach (Plackett-Burman and Box-Behnken was employed to optimize bacteriocin (BAC YAS 1 production. Using optimal levels of three key determinants (yeast extract (0.48% (w/v, incubation time (62 hrs, and agitation speed (207 rpm in peptone yeast beef based production medium resulted in 1.6-fold enhancement in BAC YAS 1 level (470 AU/mL arbitrary units against Erwinia amylovora. BAC YAS 1 showed activity over a wide range of pH (1–13 and temperature (45–80°C. A wide spectrum antimicrobial activity of BAC YAS 1 against the human pathogens (Clostridium perfringens, Staphylococcus epidermidis, Campylobacter jejuni, Enterobacter aerogenes, Enterococcus sp., Proteus sp., Klebsiella sp., and Salmonella typhimurium, the plant pathogen (E. amylovora, and the food spoiler (Listeria innocua was demonstrated. On top and above, BAC YAS 1 showed no antimicrobial activity towards lactic acid bacteria (Lactobacillus bulgaricus, L. casei, L. lactis, and L. reuteri. Promising characteristics of BAC YAS 1 prompt its commercialization for efficient utilization in several industries.

  7. Marinimicrobium haloxylanilyticum sp. nov., a new moderately halophilic, polysaccharide-degrading bacterium isolated from Great Salt Lake, Utah

    DEFF Research Database (Denmark)

    Fogh Møller, Mette; Kjeldsen, Kasper Urup; Ingvorsen, Kjeld

    2010-01-01

    A new moderately halophilic, strictly aerobic, Gram-negative bacterium, strain SX15T, was isolated from hypersaline surface sediment of the southern arm of Great Salt Lake (Utah, USA). The strain grew on a number of carbohydrates and carbohydrate polymers such as xylan, starch, carboxymethyl...

  8. Lactobacillus diolivorans sp nov., a 1,2-propanediol-degrading bacterium isolated from aerobically stable maize silage

    NARCIS (Netherlands)

    Krooneman, J; Faber, F; Alderkamp, AC; Elferink, SJHWO; Driehuis, F; Cleenwerck, [No Value; Swings, J; Gottschal, JC; Vancanneyt, M

    Inoculation of maize silage with Lactobacillus buchneri (5 x 10(5) c.f.u. g(-1) of maize silage) prior to ensiling results in the formation of aerobically stable silage. After 9 months, lactic acid bacterium counts are approximately 10(10) c.f.u. g(-1) in these treated silages. An important

  9. Microbacter margulisiae gen. nov., sp. nov., a novel propionigenic bacterium isolated from sediments of an acid rock drainage pond

    NARCIS (Netherlands)

    Sanchez Andrea, I.; Luis Sanz, J.; Stams, A.J.M.

    2014-01-01

    A novel anaerobic propionigenic bacterium, strain ADRIT, was isolated from sediment of an acid rock drainage environment (Tinto River, Spain). Cells were small (0.4-0.6 x 1-1.7 µm), non-motile and non-spore forming rods. Cells possessed a Gram-negative cell wall structure and were vancomycin

  10. Genome-centric evaluation of Burkholderia sp. strain SRS-W-2-2016 resistant to high concentrations of uranium and nickel isolated from the Savannah River Site (SRS, USA

    Directory of Open Access Journals (Sweden)

    Ashish Pathak

    2017-06-01

    Full Text Available Savannah River Site (SRS, an approximately 800-km2 former nuclear weapons production facility located near Aiken, SC remains co-contaminated by heavy metals and radionuclides. To gain a better understanding on microbially-mediated bioremediation mechanisms, several bacterial strains resistant to high concentrations of Uranium (U and Nickel (Ni were isolated from the Steeds Pond soils located within the SRS site. One of the isolated strains, designated as strain SRS-W-2-2016, grew robustly on both U and Ni. To fully understand the arsenal of metabolic functions possessed by this strain, a draft whole genome sequence (WGS was obtained, assembled, annotated and analyzed. Genome-centric evaluation revealed the isolate to belong to the Burkholderia genus with close affiliation to B. xenovorans LB400, an aggressive polychlorinated biphenyl-degrader. At a coverage of 90×, the genome of strain SRS-W-2-2016 consisted of 8,035,584 bases with a total number of 7071 putative genes assembling into 191 contigs with an N50 contig length of 134,675 bases. Several gene homologues coding for resistance to heavy metals/radionuclides were identified in strain SRS-W-2-2016, such as a suite of outer membrane efflux pump proteins similar to nickel/cobalt transporter regulators, peptide/nickel transport substrate and ATP-binding proteins, permease proteins, and a high-affinity nickel-transport protein. Also noteworthy were two separate gene fragments in strain SRS-W-2-2016 homologous to the spoT gene; recently correlated with bacterial tolerance to U. Additionally, a plethora of oxygenase genes were also identified in the isolate, potentially involved in the breakdown of organic compounds facilitating the strain's successful colonization and survival in the SRS co-contaminated soils. The WGS project of Burkholderia sp. strain SRS-W-2-2016 is available at DDBJ/ENA/GenBank under the accession #MSDV00000000.

  11. Genome-centric evaluation of Burkholderia sp. strain SRS-W-2-2016 resistant to high concentrations of uranium and nickel isolated from the Savannah River Site (SRS), USA.

    Science.gov (United States)

    Pathak, Ashish; Chauhan, Ashvini; Stothard, Paul; Green, Stefan; Maienschein-Cline, Mark; Jaswal, Rajneesh; Seaman, John

    2017-06-01

    Savannah River Site (SRS), an approximately 800-km2 former nuclear weapons production facility located near Aiken, SC remains co-contaminated by heavy metals and radionuclides. To gain a better understanding on microbially-mediated bioremediation mechanisms, several bacterial strains resistant to high concentrations of Uranium (U) and Nickel (Ni) were isolated from the Steeds Pond soils located within the SRS site. One of the isolated strains, designated as strain SRS-W-2-2016, grew robustly on both U and Ni. To fully understand the arsenal of metabolic functions possessed by this strain, a draft whole genome sequence (WGS) was obtained, assembled, annotated and analyzed. Genome-centric evaluation revealed the isolate to belong to the Burkholderia genus with close affiliation to B. xenovorans LB400, an aggressive polychlorinated biphenyl-degrader. At a coverage of 90 ×, the genome of strain SRS-W-2-2016 consisted of 8,035,584 bases with a total number of 7071 putative genes assembling into 191 contigs with an N50 contig length of 134,675 bases. Several gene homologues coding for resistance to heavy metals/radionuclides were identified in strain SRS-W-2-2016, such as a suite of outer membrane efflux pump proteins similar to nickel/cobalt transporter regulators, peptide/nickel transport substrate and ATP-binding proteins, permease proteins, and a high-affinity nickel-transport protein. Also noteworthy were two separate gene fragments in strain SRS-W-2-2016 homologous to the spoT gene; recently correlated with bacterial tolerance to U. Additionally, a plethora of oxygenase genes were also identified in the isolate, potentially involved in the breakdown of organic compounds facilitating the strain's successful colonization and survival in the SRS co-contaminated soils. The WGS project of Burkholderia sp. strain SRS-W-2-2016 is available at DDBJ/ENA/GenBank under the accession #MSDV00000000.

  12. Draft genome sequence of Paenisporosarcina sp. strain TG-20, a psychrophilic bacterium isolated from the basal ice of Taylor Glacier.

    Science.gov (United States)

    Lee, Jun Hyuck; Koh, Hye Yeon; Lee, Sung Gu; Doyle, Shawn; Christner, Brent C; Kim, Hak Jun

    2012-12-01

    We report the draft genome sequence of Paenisporosarcina sp. strain TG-20, which is 4.12 Mb in size and consists of 4,071 protein-coding genes and 76 RNA genes. The genome sequence of Paenisporosarcina sp. TG-20 may provide useful information about molecular adaptations that enhance survival in icy subsurface environments.

  13. Development of a multiplex PCR assay for rapid identification of Burkholderia pseudomallei, Burkholderia thailandensis, Burkholderia mallei and Burkholderia cepacia complex.

    Science.gov (United States)

    Koh, Seng Fook; Tay, Sun Tee; Sermswan, Rasana; Wongratanacheewin, Surasakdi; Chua, Kek Heng; Puthucheary, Savithri D

    2012-09-01

    We have developed a multiplex PCR assay for rapid identification and differentiation of cultures for Burkholderia pseudomallei, Burkholderia thailandensis, Burkholderia mallei and Burkholderia cepacia complex. The assay is valuable for use in clinical and veterinary laboratories, and in a deployable laboratory during outbreaks. Copyright © 2012 Elsevier B.V. All rights reserved.

  14. Genome sequence of the marine bacterium Marinobacter hydrocarbonoclasticus SP17, which forms biofilms on hydrophobic organic compounds.

    Science.gov (United States)

    Grimaud, Regis; Ghiglione, Jean-François; Cagnon, Christine; Lauga, Béatrice; Vaysse, Pierre-Joseph; Rodriguez-Blanco, Arturo; Mangenot, Sophie; Cruveiller, Stephane; Barbe, Valérie; Duran, Robert; Wu, Long-Fei; Talla, Emmanuel; Bonin, Patricia; Michotey, Valerie

    2012-07-01

    Marinobacter hydrocarbonoclasticus SP17 forms biofilms specifically at the interface between water and hydrophobic organic compounds (HOCs) that are used as carbon and energy sources. Biofilm formation at the HOC-water interface has been recognized as a strategy to overcome the low availability of these nearly water-insoluble substrates. Here, we present the genome sequence of SP17, which could provide further insights into the mechanisms of enhancement of HOCs assimilation through biofilm formation.

  15. Inoculation of hybrid poplar with the endophytic bacterium Enterobacter sp. 638 increases biomass but does not impact leaf level physiology

    Energy Technology Data Exchange (ETDEWEB)

    Rogers, A.; McDonald, K.; Muehlbauer, M. F.; Hoffman, A.; Koenig, K.; Newman, L.; Taghavi, S.; Van Der Lelie, D.

    2011-01-01

    Endophytic bacteria have been shown to provide several advantages to their host, including enhanced growth. Inoculating biofuel species with endophytic bacteria is therefore an attractive option to increase the productivity of biofuel feedstocks. Here, we investigated the effect of inoculating hard wood cuttings of Populus deltoides Bartr. x Populus. nigra L. clone OP367 with Enterobacter sp. 638. After 17 weeks, plants inoculated with Enterobacter sp. 638 had 55% greater total biomass than un-inoculated control plants. Study of gas exchange and fluorescence in developing and mature leaves over a diurnal cycle and over a 5 week measurement campaign revealed no effects of inoculation on photosynthesis, stomatal conductance, photosynthetic water use efficiency or the maximum and operating efficiency of photosystem II. However, plants inoculated with Enterobacter sp. 638 had a canopy that was 39% larger than control plants indicating that the enhanced growth was fueled by increased leaf area, not by improved physiology. Leaf nitrogen content was determined at two stages over the 5 week measurement period. No effect of Enterobacter sp. 638 on leaf nitrogen content was found indicating that the larger plants were acquiring sufficient nitrogen. Enterobacter sp. 638 lacks the genes for N{sub 2} fixation, therefore the increased availability of nitrogen likely resulted from enhanced nitrogen acquisition by the 84% larger root system. These data show that Enterobacter sp. 638 has the potential to dramatically increase productivity in poplar. If fully realized in the production environment, these results indicate that an increase in the environmental and economic viability of poplar as a biofuel feedstock is possible when inoculated with endophytic bacteria like Enterobacter sp. 638.

  16. Genome sequencing and annotation of Geobacillus sp. 1017, a hydrocarbon-oxidizing thermophilic bacterium isolated from a heavy oil reservoir (China

    Directory of Open Access Journals (Sweden)

    Vitaly V. Kadnikov

    2017-03-01

    Full Text Available The draft genome sequence of Geobacillus sp. strain 1017, a thermophilic aerobic oil-oxidizing bacterium isolated from formation water of the Dagang high-temperature oilfield, China, is presented here. The genome comprised 3.6 Mbp, with the G + C content of 51.74%. The strain had a number of genes responsible for numerous metabolic and transport systems, exopolysaccharide biosynthesis, and decomposition of sugars and aromatic compounds, as well as the genes related to resistance to metals and metalloids. The genome sequence is available at DDBJ/EMBL/GenBank under the accession no MQMG00000000. This genome is annotated for elucidation of the genomic and phenotypic diversity of new thermophilic alkane-oxidizing bacteria of the genus Geobacillus.

  17. A novel marine bacterium Isoptericola sp. JS-C42 with the ability to saccharifying the plant biomasses for the aid in cellulosic ethanol production.

    Science.gov (United States)

    Santhi, Velayudhan Satheeja; Gupta, Ashutosh; Saranya, Somasundaram; Jebakumar, Solomon Robinson David

    2014-06-01

    The ever growing demands for food products such as starch and sugar produces; there is a need to find the sources for saccharification for cellulosic bioethanol production. This study provides the first evidence of the lignocellulolytic and saccharifying ability of a marine bacterium namely Isoptericola sp. JS-C42, a Gram positive actinobacterium with the cocci cells embedded on mycelia isolated from the Arabian Sea, India. It exhibited highest filter paper unit effect, endoglucanase, exoglucanase, cellobiohydrolase, β-glucosidase, xylanase and ligninase effect. The hydrolytic potential of the enzymes displayed the efficient saccharification capability of steam pretreated biomass. It was also found to degrade the paddy, sorghum, Acacia mangium and Ficus religiosa into simple reducing sugars by its efficient lignocellulose enzyme complex with limited consumption of sugars. Production of ethanol was also achieved with the Saccharomyces cerevisiae. Overall, it offers a great potential for the cellulosic ethanol production in an economically reliable and eco-friendly point-of-care.

  18. Genome sequencing and annotation of Geobacillus sp. 1017, a hydrocarbon-oxidizing thermophilic bacterium isolated from a heavy oil reservoir (China).

    Science.gov (United States)

    Kadnikov, Vitaly V; Mardanov, Andrey V; Poltaraus, Andrey B; Sokolova, Diyana S; Semenova, Ekaterina M; Ravin, Nikolay V; Tourova, Tatiyana P; Nazina, Tamara N

    2017-03-01

    The draft genome sequence of Geobacillus sp. strain 1017, a thermophilic aerobic oil-oxidizing bacterium isolated from formation water of the Dagang high-temperature oilfield, China, is presented here. The genome comprised 3.6 Mbp, with the G + C content of 51.74%. The strain had a number of genes responsible for numerous metabolic and transport systems, exopolysaccharide biosynthesis, and decomposition of sugars and aromatic compounds, as well as the genes related to resistance to metals and metalloids. The genome sequence is available at DDBJ/EMBL/GenBank under the accession no MQMG00000000. This genome is annotated for elucidation of the genomic and phenotypic diversity of new thermophilic alkane-oxidizing bacteria of the genus Geobacillus.

  19. Identification of the Antibacterial Compound Produced by the Marine Epiphytic Bacterium Pseudovibrio sp. D323 and Related Sponge-Associated Bacteria

    Directory of Open Access Journals (Sweden)

    Suhelen Egan

    2011-08-01

    Full Text Available Surface-associated marine bacteria often produce secondary metabolites with antagonistic activities. In this study, tropodithietic acid (TDA was identified to be responsible for the antibacterial activity of the marine epiphytic bacterium Pseudovibrio sp. D323 and related strains. Phenol was also produced by these bacteria but was not directly related to the antibacterial activity. TDA was shown to effectively inhibit a range of marine bacteria from various phylogenetic groups. However TDA-producers themselves were resistant and are likely to possess resistance mechanism preventing autoinhibition. We propose that TDA in isolate D323 and related eukaryote-associated bacteria plays a role in defending the host organism against unwanted microbial colonisation and, possibly, bacterial pathogens.

  20. Phenotypic and genomic properties of Chitinispirillum alkaliphilum gen. nov., sp. nov., a haloalkaliphilic anaerobic chitinolytic bacterium representing a novel class in the phylum Fibrobacteres

    Directory of Open Access Journals (Sweden)

    Dimitry eSorokin

    2016-03-01

    Full Text Available Anaerobic enrichment from sediments of hypersaline alkaline lakes in Wadi el Natrun (Egypt with chitin resulted in the isolation of a fermentative haloalkaliphilic bacterium, strain ACht6-1, growing exclusively with insoluble chitin as the substrate in a sodium carbonate-based medium at pH 8.5-10.5 and total Na+ concentrations from 0.4 to 1.75 M. The isolate had a Gram-negative cell wall and formed lipid cysts in old cultures. The chitinolytic activity was associated with cells. Analysis of the 4.4 Mb draft genome identified pathways for chitin utilization, particularly, secreted chitinases linked to the cell surface, as well as genes for the hydrolysis of other polysaccharides and fermentation of sugars, while the genes needed for aerobic and anaerobic respiration were absent. Adaptation to a haloalkaliphilic lifestyle was reflected by the gene repertoire encoding sodium rather than proton-dependent membrane-bound ion pumps, including the Rnf-type complex, oxaloacetate decarboxylase, V-type ATPase and pyrophosphatase. The phylogenetic analysis using 16S rRNA gene and ribosomal proteins indicated that ACht6-1 forms a novel deep lineage at the class level within the bacterial candidate division TG3. Based on phylogenetic, phenotypic and genomic analyses, the novel chitinolytic bacterium is described as Chitinispirillum alkaliphilum gen. nov., sp. nov., within a novel class Chitinispirillia that could be included into the phylum Fibrobacteres.

  1. Phenotypic and Genomic Properties of Chitinispirillum alkaliphilum gen. nov., sp. nov., A Haloalkaliphilic Anaerobic Chitinolytic Bacterium Representing a Novel Class in the Phylum Fibrobacteres.

    Science.gov (United States)

    Sorokin, Dimitry Y; Rakitin, Andrey L; Gumerov, Vadim M; Beletsky, Alexey V; Sinninghe Damsté, Jaap S; Mardanov, Andrey V; Ravin, Nikolai V

    2016-01-01

    Anaerobic enrichment from sediments of hypersaline alkaline lakes in Wadi el Natrun (Egypt) with chitin resulted in the isolation of a fermentative haloalkaliphilic bacterium, strain ACht6-1, growing exclusively with insoluble chitin as the substrate in a sodium carbonate-based medium at pH 8.5-10.5 and total Na(+) concentrations from 0.4 to 1.75 M. The isolate had a Gram-negative cell wall and formed lipid cysts in old cultures. The chitinolytic activity was associated with cells. Analysis of the 4.4 Mb draft genome identified pathways for chitin utilization, particularly, secreted chitinases linked to the cell surface, as well as genes for the hydrolysis of other polysaccharides and fermentation of sugars, while the genes needed for aerobic and anaerobic respiration were absent. Adaptation to a haloalkaliphilic lifestyle was reflected by the gene repertoire encoding sodium rather than proton-dependent membrane-bound ion pumps, including the Rnf-type complex, oxaloacetate decarboxylase, V-type ATPase, and pyrophosphatase. The phylogenetic analysis using 16S rRNA gene and ribosomal proteins indicated that ACht6-1 forms a novel deep lineage at the class level within the bacterial candidate division TG3. Based on phylogenetic, phenotypic and genomic analyses, the novel chitinolytic bacterium is described as Chitinispirillum alkaliphilum gen. nov., sp. nov., within a novel class Chitinispirillia that could be included into the phylum Fibrobacteres.

  2. Proton efflux coupled to dark H2 oxidation in whole cells of a marine sulfur photosynthetic bacterium (Chromatium sp. strain Miami PBS1071).

    Science.gov (United States)

    Kumazawa, S; Izawa, S; Mitsui, A

    1983-04-01

    Whole cells of photoanaerobically grown Chromatium sp. strain Miami PBS1071, a marine sulfur purple bacterium, oxidized H2 in the dark through the oxyhydrogen reaction at rates of up to 59 nmol of H2 per mg (dry weight) per min. H2 oxidation was routinely measured in H2 pulse experiments with air-equilibrated cells. The reaction was accompanied by a reversible H+ efflux from the cells, suggesting an outward H+ translocation reaction coupled to H2 oxidation. The H+/e- ratio, calculated from simultaneous measurements of H2, O2, and H+ changes in the medium, varied with the cultures from 0.7 to 1.2. The ratio increased considerably when the backflow of H+ was taken into account. Anaerobic H2 uptake with 2,5-dimethyl-p-benzoguinone as an oxidant also showed a weak H+-translocating activity. No H+-translocating activity was detected with methylene blue as an oxidant. Carbonylcyanide 3-chlorophenylhydrazone (1 microM) stimulated H2 oxidation and abolished the associated H+ changes when H2 oxidation was observed in O2 pulse experiments with H2-Ar-equilibrated cells. However, the uncoupler inhibited both H2 oxidation and H+ changes when measurements were made in H2 pulse experiments with air-equilibrated cells. It is suggested that in this bacterium the susceptibility of hydrogenase to reversible O2 inactivation in situ is enhanced by the presence of uncoupling agents.

  3. Proton efflux coupled to dark H/sub 2/ oxidation in whole cells of a marine sulfur photosynthetic bacterium (Chromatium sp. strain Miami PBS1071)

    Energy Technology Data Exchange (ETDEWEB)

    Kumazawa, S.; Izawa, S.; Mitsui, A.

    1983-04-01

    Whole cells of photoanaerobically grown Chromatium sp. strain Miami PBS1071, a marine sulfur purple bacterium, oxidized H/sub 2/ in the dark through the oxyhydrogen reaction at rates of up to 59 nmol of H/sub 2/ per mg (dry weight) per min. H/sub 2/ oxidation was routinely measured in H/sub 2/ pulse experiments with air-equilibrated cells. The reaction was accompanied by a reversible H/sup +/ efflux from the cells, suggesting an outward H/sup +/ translocation reaction coupled to H/sub 2/ oxidation. Anaerobic H/sub 2/ uptake with 2,5-dimethyl-p-benzoguinone as an oxidant also showed a weak H/sup +/-translocating activity. Carbonylcyanide 3-chlorophenylhydrazone (1 ..mu..M) stimulated H/sub 2/ oxidation and abolished the associated H/sup +/ changes when H/sub 2/ oxidation was observed in O/sub 2/ pulse experiments with H/sub 2/-Ar-equilibrated cells. However, the uncoupler inhibited both H/sub 2/ oxidation and H/sup +/ changes when measurements were made in H/sub 2/ pulse experiments with air-equilibrated cells. It is suggested that in this bacterium the susceptibility of hydrogenase to reversible O/sub 2/ inactivation in situ is enhanced by the presence of uncoupling agents.

  4. Elemental sulfur and thiosulfate disproportionation by Desulfocapsa sulfoexigens sp. nov., a new anaerobic bacterium isolated from marine surface sediment

    DEFF Research Database (Denmark)

    Finster, Kai; Liesack, Werner; Thamdrup, Bo

    1998-01-01

    A mesophilic, anaerobic, gram-negative bacterium, strain SB164P1, was enriched and isolated from oxidized marine surface sediment with elemental sulfur as the sole energy substrate in the presence of ferrihydrite. Elemental sulfur was disproportionated to hydrogen sulfide and sulfate. Growth...... chemolithoautotrophically exclusively by the disproportionation of inorganic sulfur compounds. Comparative 16S rDNA sequencing analysis placed strain SB164P1 into the delta subclass of the class Proteobacteria. Its closest relative is Desulfocapsa thiozymogenes, and slightly more distantly related are Desulfofustis...

  5. Sulfuriflexus mobilis gen. nov., sp nov., a sulfur-oxidizing bacterium isolated from a brackish lake sediment

    OpenAIRE

    Kojima, Hisaya; Fukui, Manabu

    2016-01-01

    A chemolithotrophic sulfur-oxidizing bacterium, strain aks1(T), was isolated from sediment of a brackish lake in Japan. The cells were curved rod-shaped and Gram-stain-negative. The G+C content of the genomic DNA was 53 mol%. The major components in the cellular fatty acid profile were C-16:0 and summed feature 3 (C-16 (: 1)omega 7c and/or C-16 (: 1)omega 6c). As electron donor for chemolithoautotrophic growth, strain aks1(T) oxidized thiosulfate, sulfide, and elemental sulfur. The strain cou...

  6. PENAPISAN LIMBAH PERTANIAN (SABUT KELAPA DAN ARANG SEKAM DALAM PENINGKATAN KETAHANAN BIBIT PISANG BARANGAN BERMIKORIZA TERHADAP BLOOD DISEASE BACTERIUM DAN FUSARIUM OXYSPORUM F.SP. CUBENSE

    Directory of Open Access Journals (Sweden)

    Suswati .

    2015-03-01

    Full Text Available Agricultural waste screening (coconut fibre and chaff charcoal in improving the resistance of Mychorrizae Barangan seedling to Blood diseases bacterium and Fusarium oxysporum f. sp. cubense. The application of soil and compost are very general in Barangan banana seedling. However, those media always contaminated by BDB and Foc propagul. This research was intended to examine the influence of planting media composition (soil, coconut fibre and chuff charcoal in improving the resistance of Mychorrizae Barangan banana seedling to blood diseases bacterium dan Fusarium oxysporum f sp.cubense. Some experiments conducted in wirehouse using a randomized complete block design application of two subtracts for soil substitution included to either coconut fibre (A or chuff charcoal (B (v:v completed by 6 treatments of each: A0 = 100% soil media, A1 = 50% soil + 50% chuff charcoal, A2 = 50% soil + 25% chuff charcoal + 25% sand, A3 = 25% soil + 50% chuff charcoal + 25% sand; A4 = 75% chuff charcoal + 25% sand, A5 = 100% chuff charcoal, B0 = 100% soil, B1 = 50% soil + 50 % chuff charcoal; B2 = 50% soil + 25 % coconut fiber + 25% sand, B3 = 25% soil +50% coconut fiber +25% sand; B4 = 75% coconut fiber + 25% sand, B5 = 100% coconut fiber. The soil generated from banana seedling area of Sempakata village that seriously infected BDB and Foc. The observation variables encompassed percentage of disease attack, density of BDB and Foc. population, period of pathogen incubation and measurement of Barangan seed and AMF colonization resistance development. The results indicated the planting of Mychorrizae Barangan banana seeds applied diminishing soil media as much as 25–100% substituted by chuff charcoal or coconut fiber increased the seed resistance of BDB and Foc.

  7. Antifouling Activity towards Mussel by Small-Molecule Compounds from a Strain of Vibrio alginolyticus Bacterium Associated with Sea Anemone Haliplanella sp.

    Science.gov (United States)

    Wang, Xiang; Huang, Yanqiu; Sheng, Yanqing; Su, Pei; Qiu, Yan; Ke, Caihuan; Feng, Danqing

    2017-03-28

    Mussels are major fouling organisms causing serious technical and economic problems. In this study, antifouling activity towards mussel was found in three compounds isolated from a marine bacterium associated with the sea anemone Haliplanella sp. This bacterial strain, called PE2, was identified as Vibrio alginolyticus using morphology, biochemical tests, and phylogenetic analysis based on sequences of 16S rRNA and four housekeeping genes (rpoD, gyrB, rctB, and toxR). Three small-molecule compounds (indole, 3-formylindole, and cyclo (Pro-Leu)) were purified from the ethyl acetate extract of V. alginolyticus PE2 using column chromatography techniques. They all significantly inhibited byssal thread production of the green mussel Perna viridis, with EC50 values of 24.45 μg/ml for indole, 50.07 μg/ml for 3-formylindole, and 49.24 μg/ml for cyclo (Pro-Leu). Previous research on the antifouling activity of metabolites from marine bacteria towards mussels is scarce. Indole, 3-formylindole and cyclo (Pro-Leu) also exhibited antifouling activity against settlement of the barnacle Balanus albicostatus (EC50 values of 8.84, 0.43, and 11.35 μg/ml, respectively) and the marine bacterium Pseudomonas sp. (EC50 values of 42.68, 69.68, and 39.05 μg/ml, respectively). These results suggested that the three compounds are potentially useful for environmentally friendly mussel control and/or the development of new antifouling additives that are effective against several biofoulers.

  8. Bacterial Cell Wall Synthesis Gene uppP Is Required for Burkholderia Colonization of the Stinkbug Gut

    Science.gov (United States)

    Kim, Jiyeun Kate; Lee, Ho Jin; Kikuchi, Yoshitomo; Kitagawa, Wataru; Nikoh, Naruo

    2013-01-01

    To establish a host-bacterium symbiotic association, a number of factors involved in symbiosis must operate in a coordinated manner. In insects, bacterial factors for symbiosis have been poorly characterized at the molecular and biochemical levels, since many symbionts have not yet been cultured or are as yet genetically intractable. Recently, the symbiotic association between a stinkbug, Riptortus pedestris, and its beneficial gut bacterium, Burkholderia sp., has emerged as a promising experimental model system, providing opportunities to study insect symbiosis using genetically manipulated symbiotic bacteria. Here, in search of bacterial symbiotic factors, we targeted cell wall components of the Burkholderia symbiont by disruption of uppP gene, which encodes undecaprenyl pyrophosphate phosphatase involved in biosynthesis of various bacterial cell wall components. Under culture conditions, the ΔuppP mutant showed higher susceptibility to lysozyme than the wild-type strain, indicating impaired integrity of peptidoglycan of the mutant. When administered to the host insect, the ΔuppP mutant failed to establish normal symbiotic association: the bacterial cells reached to the symbiotic midgut but neither proliferated nor persisted there. Transformation of the ΔuppP mutant with uppP-encoding plasmid complemented these phenotypic defects: lysozyme susceptibility in vitro was restored, and normal infection and proliferation in the midgut symbiotic organ were observed in vivo. The ΔuppP mutant also exhibited susceptibility to hypotonic, hypertonic, and centrifugal stresses. These results suggest that peptidoglycan cell wall integrity is a stress resistance factor relevant to the successful colonization of the stinkbug midgut by Burkholderia symbiont. PMID:23747704

  9. Pathogenesis of Burkholderia pseudomallei and Burkholderia mallei.

    Science.gov (United States)

    Larsen, Joseph C; Johnson, Nathan H

    2009-06-01

    Burkholderia pseudomallei and mallei are biological agents of military significance. There has been significant research in recent years to develop medical countermeasures for these organisms. This review summarizes work which details aspects of the pathogenesis of B. pseudomallei and mallei and discusses key scientific questions and directions for future research.

  10. Draft genome sequence of Paenisporosarcina sp. strain TG-14, a psychrophilic bacterium isolated from sediment-laden stratified basal ice from Taylor Glacier, McMurdo Dry Valleys, Antarctica.

    Science.gov (United States)

    Koh, Hye Yeon; Lee, Sung Gu; Lee, Jun Hyuck; Doyle, Shawn; Christner, Brent C; Kim, Hak Jun

    2012-12-01

    The psychrophilic bacterium Paenisporosarcina sp. TG-14 was isolated from sediment-laden stratified basal ice from Taylor Glacier, McMurdo Dry Valleys, Antarctica. Here we report the draft genome sequence of this strain, which may provide useful information on the cold adaptation mechanism in extremely variable environments.

  11. Molecular cloning of the gene which encodes beta-N-acetylglucosaminidase from a marine bacterium, Alteromonas sp. strain O-7.

    Science.gov (United States)

    Tsujibo, H; Fujimoto, K; Tanno, H; Miyamoto, K; Kimura, Y; Imada, C; Okami, Y; Inamori, Y

    1995-01-01

    The gene encoding the periplasmic beta-N-acetylglucosaminidase (GlcNAcase B) from a marine Alteromonas sp. strain, O-7, was cloned and sequenced. The protein sequence of GlcNAcase B revealed a highly significant homology with Vibrio GlcNAcase and alpha- and beta-chains of human beta-hexosaminidase. PMID:7574618

  12. Molecular cloning of the gene which encodes beta-N-acetylglucosaminidase from a marine bacterium, Alteromonas sp. strain O-7.

    OpenAIRE

    Tsujibo, H; Fujimoto, K; Tanno, H; Miyamoto, K.; Kimura, Y.; Imada, C; Okami, Y; Inamori, Y

    1995-01-01

    The gene encoding the periplasmic beta-N-acetylglucosaminidase (GlcNAcase B) from a marine Alteromonas sp. strain, O-7, was cloned and sequenced. The protein sequence of GlcNAcase B revealed a highly significant homology with Vibrio GlcNAcase and alpha- and beta-chains of human beta-hexosaminidase.

  13. Genome sequence of Methylobacterium sp. strain GXF4, a xylem-associated bacterium isolated from Vitis vinifera L. grapevine.

    Science.gov (United States)

    Gan, Han Ming; Chew, Teong Han; Hudson, André O; Savka, Michael A

    2012-09-01

    Methylobacterium sp. strain GXF4 is an isolate from grapevine. Here we present the sequence, assembly, and annotation of its genome, which may shed light on its role as a grapevine xylem inhabitant. To our knowledge, this is the first genome announcement of a plant xylem-associated strain of the genus Methylobacterium.

  14. Flux coupling and transcriptional regulation within the metabolic network of the photosynthetic bacterium Synechocystis sp. PCC6803

    DEFF Research Database (Denmark)

    Montagud, Arnau; Zelezniak, Aleksej; Navarro, Emilio

    2011-01-01

    Synechocystis sp. PCC6803 is a model cyanobacterium capable of producing biofuels with CO2 as carbon source and with its metabolism fueled by light, for which it stands as a potential production platform of socio-economic importance. Compilation and characterization of Synechocystis genome...

  15. Crystal structure of the inactive state of the receiver domain of Spo0A from Paenisporosarcina sp. TG-14, a psychrophilic bacterium isolated from an Antarctic glacier.

    Science.gov (United States)

    Lee, Chang Woo; Park, Sun-Ha; Lee, Sung Gu; Shin, Seung Chul; Han, Se Jong; Kim, Han-Woo; Park, Hyun Ho; Kim, Sunghwan; Kim, Hak Jun; Park, Hyun; Park, HaJeung; Lee, Jun Hyuck

    2017-06-01

    The two-component phosphorelay system is the most prevalent mechanism for sensing and transducing environmental signals in bacteria. Spore formation, which relies on the two-component phosphorelay system, enables the long-term survival of the glacial bacterium Paenisporosarcina sp. TG-14 in the extreme cold environment. Spo0A is a key response regulator of the phosphorelay system in the early stage of spore formation. The protein is composed of a regulatory N-terminal phospho-receiver domain and a DNA-binding C-terminal activator domain. We solved the three-dimensional structure of the unphosphorylated (inactive) form of the receiver domain of Spo0A (PaSpo0A-R) from Paenisporosarcina sp. TG-14. A structural comparison with phosphorylated (active form) Spo0A from Bacillus stearothermophilus (BsSpo0A) showed minor notable differences. A molecular dynamics study of a model of the active form and the crystal structures revealed significant differences in the α4 helix and the preceding loop region where phosphorylation occurs. Although an oligomerization study of PaSpo0A-R by analytical ultracentrifugation (AUC) has shown that the protein is in a monomeric state in solution, both crosslinking and crystal-packing analyses indicate the possibility of weak dimer formation by a previously undocumented mechanism. Collectively, these observations provide insight into the mechanism of phosphorylation-dependent activation unique to Spo0A.

  16. Antibacterial activity of the Antarctic bacterium Janthinobacterium sp. SMN 33.6 against multi-resistant Gram-negative bacteria

    Directory of Open Access Journals (Sweden)

    Geraldine Asencio

    2014-01-01

    Conclusions: The ethanolic extract of Janthinobacterium sp. SMN 33.6 possesses antibacterial activity against a chromosomal AmpC beta-lactamase-producing strain of Serratia marcescens, an extended-spectrum beta-lactamase-producing Escherichia coli and also against carbapenemase-producing strains of Acinetobacter baumannii and Pseudomonas aeruginosa. This becomes a potential and interesting biotechnological tool for the control of bacteria with multi-resistance to commonly used antibiotics.

  17. Draft Genome Sequence of Shewanella sp. ECSMB14102, a Mussel Recruitment-Promoting Bacterium Isolated from the East China Sea

    Science.gov (United States)

    Guo, Xing-Pan; Chen, Yu-Ru; Gao, Wei; Ding, De-Wen

    2015-01-01

    Shewanella sp. ECSMB14102, which promotes recruitment of the mussel Mytilus coruscus, was isolated from natural biofilms formed on glass slides submerged in the East China Sea. Here, we present the draft genome sequence, which comprises 4.41 Mb with a G+C content of 52.2%. The genomic information in this strain will contribute to deepening our understanding of bacteria-animal interaction. PMID:26089429

  18. A novel goose-type lysozyme gene with chitinolytic activity from the moderately thermophilic bacterium Ralstonia sp. A-471: cloning, sequencing, and expression.

    Science.gov (United States)

    Ueda, Mitsuhiro; Ohata, Konomi; Konishi, Toshiaki; Sutrisno, Aji; Okada, Hitomi; Nakazawa, Masami; Miyatake, Kazutaka

    2009-01-01

    In this study, we cloned the gene encoding goose-type (G-type) lysozyme with chitinase (Ra-ChiC) activity from Ralstonia sp. A-471 genomic DNA library. This is the first report of another type of chitinase after the previously reported chitinases ChiA (Ra-ChiA) and ChiB (Ra-ChiB) in the chitinase system of the moderately thermophilic bacterium, Ralstonia sp. A-471 and also the first such data in Ralstonia sp. G-type lysozyme gene. It consisted of 753 bp nucleotides, which encodes 251 amino acids including a putative signal peptide. This ORF was modular enzyme composed of a signal sequence, chitin-binding domain, linker, and catalytic domain. The catalytic domain of Ra-ChiC showed homologies to those of G-type lysozyme (glycoside hydrolases (GH) family 23, 16.8%) and lysozyme-like enzyme from Clostridium beijerincki (76.1%). Ra-ChiC had activities against ethylene glycol chitin, carboxyl methyl chitin, and soluble chitin but not against the cell wall of Micrococcus lysodeikticus. The enzyme produced alpha-anomer by hydrolyzing beta-1,4-glycosidic linkage of the substrate, indicating that the enzyme catalyzes the hydrolysis through an inverting mechanism. When N-acetylglucosamine hexasaccharide [(GlcNAc)6] was hydrolyzed by the enzyme, the second and third glycosidic linkage from the non-reducing end were split producing (GlcNAc)2 + (GlcNAc)4 and (GlcNAc)3 + (GlcNAc)3 of almost the same concentration in the early stage of the reaction. The G-type lysozyme hydrolyzed (GlcNAc)6 in an endo-splitting manner, which produced (GlcNAc)3 + (GlcNAc)3 predominating over that to (GlcNAc)2 + (GlcNAc)4. Thus, Ra-ChiC was found to be a novel enzyme in its structural and functional properties.

  19. Functional Characterization of a Novel Member of the Amidohydrolase 2 Protein Family, 2-Hydroxy-1-Naphthoic Acid Nonoxidative Decarboxylase from Burkholderia sp. Strain BC1.

    Science.gov (United States)

    Pal Chowdhury, Piyali; Basu, Soumik; Dutta, Arindam; Dutta, Tapan K

    2016-06-15

    The gene encoding a nonoxidative decarboxylase capable of catalyzing the transformation of 2-hydroxy-1-naphthoic acid (2H1NA) to 2-naphthol was identified, recombinantly expressed, and purified to homogeneity. The putative gene sequence of the decarboxylase (hndA) encodes a 316-amino-acid protein (HndA) with a predicted molecular mass of 34 kDa. HndA exhibited high identity with uncharacterized amidohydrolase 2 proteins of various Burkholderia species, whereas it showed a modest 27% identity with γ-resorcylate decarboxylase, a well-characterized nonoxidative decarboxylase belonging to the amidohydrolase superfamily. Biochemically characterized HndA demonstrated strict substrate specificity toward 2H1NA, whereas inhibition studies with HndA indicated the presence of zinc as the transition metal center, as confirmed by atomic absorption spectroscopy. A three-dimensional structural model of HndA, followed by docking analysis, identified the conserved metal-coordinating and substrate-binding residues, while their importance in catalysis was validated by site-directed mutagenesis. Microbial nonoxidative decarboxylases play a crucial role in the metabolism of a large array of carboxy aromatic chemicals released into the environment from a variety of natural and anthropogenic sources. Among these, hydroxynaphthoic acids are usually encountered as pathway intermediates in the bacterial degradation of polycyclic aromatic hydrocarbons. The present study reveals biochemical and molecular characterization of a 2-hydroxy-1-naphthoic acid nonoxidative decarboxylase involved in an alternative metabolic pathway which can be classified as a member of the small repertoire of nonoxidative decarboxylases belonging to the amidohydrolase 2 family of proteins. The strict substrate specificity and sequence uniqueness make it a novel member of the metallo-dependent hydrolase superfamily. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  20. Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp. SH-C52 for antimicrobial compounds

    Directory of Open Access Journals (Sweden)

    Menno evan der Voort

    2015-07-01

    Full Text Available The plant microbiome represents an enormous untapped resource for discovering novel genes and bioactive compounds. Previously, we isolated Pseudomonas sp. SH-C52 from the rhizosphere of sugar beet plants grown in a soil suppressive to the fungal pathogen Rhizoctonia solani and showed that its antifungal activity is, in part, attributed to the production of the chlorinated 9-amino-acid lipopeptide thanamycin (Mendes et al. 2011. Science. To get more insight into its biosynthetic repertoire, the genome of Pseudomonas sp. SH-C52 was sequenced and subjected to in silico, mutational and functional analyses. The sequencing revealed a genome size of 6.3 Mb and 5,579 predicted ORFs. Phylogenetic analysis placed strain SH-C52 within the Pseudomonas corrugata clade. In silico analysis for secondary metabolites revealed a total of six nonribosomal peptide synthetase (NRPS gene clusters, including the two previously described NRPS clusters for thanamycin and the 2-amino acid antibacterial lipopeptide brabantamide. Here we show that thanamycin also has activity against an array of other fungi and that brabantamide A exhibits anti-oomycete activity and affects phospholipases of the late blight pathogen Phytophthora infestans. Most notably, mass spectrometry led to the discovery of a third LP, designated thanapeptin, with a 22-amino-acid peptide moiety. Seven structural variants of thanapeptin were found with varying degrees of activity against P. infestans. Of the remaining four NRPS clusters, one was predicted to encode for yet another and unknown lipopeptide with a predicted peptide moiety of 8-amino acids. Collectively, these results show an enormous metabolic potential for Pseudomonas sp. SH-C52, with at least three structurally diverse lipopeptides, each with a different antimicrobial activity spectrum.

  1. Serpentinicella alkaliphila gen. nov., sp. nov., a novel alkaliphilic anaerobic bacterium isolated from the serpentinite-hosted Prony hydrothermal field, New Caledonia.

    Science.gov (United States)

    Mei, Nan; Postec, Anne; Erauso, Gael; Joseph, Manon; Pelletier, Bernard; Payri, Claude; Ollivier, Bernard; Quéméneur, Marianne

    2016-11-01

    A novel anaerobic, alkaliphilic, Gram-stain-positive, spore-forming bacterium was isolated from a carbonaceous hydrothermal chimney in Prony Bay, New Caledonia. This bacterium, designated strain 3bT, grew at temperatures from 30 to 43 °C (optimum 37 °C) and at pH between 7.8 and 10.1 (optimum 9.5). Added NaCl was not required for growth (optimum 0-0.2 %, w/v), but was tolerated at up to 4 %. Yeast extract was required for growth. Strain 3bT utilized crotonate, lactate and pyruvate, but not sugars. Crotonate was dismutated to acetate and butyrate. Lactate was disproportionated to acetate and propionate. Pyruvate was degraded to acetate plus trace amounts of hydrogen. Growth on lactate was improved by the addition of fumarate, which was used as an electron acceptor and converted to succinate. Sulfate, thiosulfate, elemental sulfur, sulfite, nitrate, nitrite, FeCl3, Fe(III)-citrate, Fe(III)-EDTA, chromate, arsenate, selenate and DMSO were not used as terminal electron acceptors. The G+C content of the genomic DNA was 33.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the isolate is a member of the family Clostridiaceae, order Clostridiales within the phylum Firmicutes. Strain 3bT was most closely related to 'Alkaliphilus hydrothermalis' FatMR1T (92.2 % 16S rRNA gene sequence similarity), and was positioned approximately equidistantly between the genera Alkaliphilus, Anaerovirgula and Natronincola. On the basis of phylogenetic, genetic, chemotaxonomic and physiological properties, strain 3bT is proposed to represent a novel species of a new genus, for which the name Serpentinicella alkaliphila gen. nov., sp. nov. is proposed. The type strain of Serpentinicella alkaliphila is 3bT (=DSM 100013T=JCM 30645T).

  2. Removal of multi-heavy metals using biogenic manganese oxides generated by a deep-sea sedimentary bacterium - Brachybacterium sp. strain Mn32.

    Science.gov (United States)

    Wang, Wenming; Shao, Zongze; Liu, Yanjun; Wang, Gejiao

    2009-06-01

    A deep-sea manganese-oxidizing bacterium, Brachybacterium sp. strain Mn32, showed high Mn(II) resistance (MIC 55 mM) and Mn(II)-oxidizing/removing abilities. Strain Mn32 removed Mn(II) by two pathways: (1) oxidizing soluble Mn(II) to insoluble biogenic Mn oxides - birnessite (delta-MnO(2) group) and manganite (gamma-MnOOH); (2) the biogenic Mn oxides further adsorb more Mn(II) from the culture. The generated biogenic Mn oxides surround the cell surfaces of strain Mn32 and provide a high capacity to adsorb Zn(II) and Ni(II). Mn(II) oxidation by strain Mn32 was inhibited by both sodium azide and o-phenanthroline, suggesting the involvement of a metalloenzyme which was induced by Mn(II). X-ray diffraction analysis showed that the crystal structures of the biogenic Mn oxides were different from those of commercial pyrolusite (beta-MnO(2) group) and fresh chemically synthesized vernadite (delta-MnO(2) group). The biogenic Mn oxides generated by strain Mn32 showed two to three times higher Zn(II) and Ni(II) adsorption abilities than commercial and fresh synthetic MnO(2). The crystal structure and the biogenic MnO(2) types may be important factors for the high heavy metal adsorption ability of strain Mn32. This study provides potential applications of a new marine Mn(II)-oxidizing bacterium in heavy metal bioremediation and increases our basic knowledge of microbial manganese oxidation mechanisms.

  3. The Growth of Steroidobacter agariperforans sp. nov., a Novel Agar-Degrading Bacterium Isolated from Soil, is Enhanced by the Diffusible Metabolites Produced by Bacteria Belonging to Rhizobiales

    Science.gov (United States)

    Sakai, Masao; Hosoda, Akifumi; Ogura, Kenjiro; Ikenaga, Makoto

    2014-01-01

    An agar-degrading bacterium was isolated from soil collected in a vegetable cropping field. The growth of this isolate was enhanced by supplying culture supernatants of bacteria belonging to the order Rhizobiales. Phylogenetic analysis based on 16S rRNA gene sequences indicated the novel bacterium, strain KA5–BT, belonged to the genus Steroidobacter in Gammaproteobacteria, but differed from its closest relative, Steroidobacter denitrificans FST, at the species level with 96.5% similarity. Strain KA5–BT was strictly aerobic, Gram-negative, non-motile, non-spore forming, and had a straight to slightly curved rod shape. Cytochrome oxidase and catalase activities were positive. The strain grew on media containing culture supernatants in a temperature range of 15–37°C and between pH 4.5 and 9.0, with optimal growth occurring at 30°C and pH 6.0–8.0. No growth occurred at 10 or 42°C or at NaCl concentrations more than 3% (w/v). The main cellular fatty acids were iso–C15:0, C16:1ω7c, and iso–C17:1ω9c. The main quinone was ubiquinone-8 and DNA G+C content was 62.9 mol%. In contrast, strain FST was motile, did not grow on the agar plate, and its dominant cellular fatty acids were C15:0 and C17:1ω8c. Based on its phylogenetic and phenotypic properties, strain KA5–BT (JCM 18477T = KCTC 32107T) represents a novel species in genus Steroidobacter, for which the name Steroidobacter agariperforans sp. nov. is proposed. PMID:24621511

  4. Draft genome sequence of Halomonas sp. strain KM-1, a moderately halophilic bacterium that produces the bioplastic poly(3-hydroxybutyrate).

    Science.gov (United States)

    Kawata, Yoshikazu; Kawasaki, Kazunori; Shigeri, Yasushi

    2012-05-01

    We report the draft genome sequence of Halomonas sp. strain KM-1, which was isolated in Ikeda City, Osaka, Japan, and which produces the bioplastic poly(3-hydroxybutyrate). The total length of the assembled genome is 4,992,811 bp, and 4,220 coding sequences were predicted within the genome. Genes encoding proteins that are involved in the production and depolymerization of poly(3-hydroxybutyrate) were identified. The identification of these genes might be of use in the production of the bioplastic poly(3-hydroxybutyrate) and its monomer 3-hydroxybutyrate.

  5. Ageloline A, new antioxidant and antichlamydial quinolone from the marine sponge-derived bacterium Streptomyces sp. SBT345

    OpenAIRE

    Cheng, Cheng; Othman, Eman M.; Reimer, Anastasija; Grüne, Matthias; Kozjak-Pavlovic, Vera; Stopper, Helga; Hentschel, Ute; Abdelmohsen, Usama R.

    2016-01-01

    A new chlorinated quinolone, ageloline A, was isolated from the broth culture of Streptomyces sp. SBT345 that was cultivated from the Mediterranean sponge Agelas oroides. The structure of this compound was determined by spectroscopic analysis including 1D and 2D NMR as well as HR-ESI-MS experiments. Ageloline A exhibited antioxidant potential using cell-free and cell-based assays and was further able to reduce oxidative stress and genomic damage induced by the oxidative stress inducer 4-nitro...

  6. Draft Genome Sequence of Halomonas sp. Strain KM-1, a Moderately Halophilic Bacterium That Produces the Bioplastic Poly(3-Hydroxybutyrate)

    Science.gov (United States)

    Kawasaki, Kazunori; Shigeri, Yasushi

    2012-01-01

    We report the draft genome sequence of Halomonas sp. strain KM-1, which was isolated in Ikeda City, Osaka, Japan, and which produces the bioplastic poly(3-hydroxybutyrate). The total length of the assembled genome is 4,992,811 bp, and 4,220 coding sequences were predicted within the genome. Genes encoding proteins that are involved in the production and depolymerization of poly(3-hydroxybutyrate) were identified. The identification of these genes might be of use in the production of the bioplastic poly(3-hydroxybutyrate) and its monomer 3-hydroxybutyrate. PMID:22535927

  7. Desulfovibrio brasiliensis sp. nov., a moderate halophilic sulfate-reducing bacterium from Lagoa Vermelha (Brazil) mediating dolomite formation.

    Science.gov (United States)

    Warthmann, Rolf; Vasconcelos, Crisogono; Sass, Henrik; McKenzie, Judith A

    2005-06-01

    A novel halotolerant sulfate-reducing bacterium, Desulfovibrio brasiliensis strain LVform1, was isolated from sediments of a dolomite-forming hypersaline coastal lagoon, Lagoa Vermelha, in the state of Rio de Janeiro, Brazil. The cells are vibrio-shaped and 0.30 to 0.45 microm by 1.0 to 3.5 microm in size. These bacteria mediate the precipitation of dolomite [CaMg(CO3)2] in culture experiments. The strain was identified as a member of the genus Desulfovibrio in the delta-subclass of the Proteobacteria on the basis of its 16S rRNA gene sequence, its physiological and morphological properties. Strain LVform1 is obligate sodium-dependent and grows at NaCl concentrations of up to 15%. The 16S rRNA sequence revealed that this strain is closely related to Desulfovibrio halophilus (96.2% similarity) and to Desulfovibrio oxyclinae (96.8% similarity), which were both isolated from Solar Lake, a hypersaline coastal lake in the Sinai, Egypt. Strain LVform1 is barotolerant, growing under pressures of up to 370 bar (37 MPa). We propose strain LVform1 to be the type strain of a novel species of the genus Desulfovibrio, Desulfovibrio brasiliensis (type strain LVform1 = DSMZ No. 15816 and JCM No. 12178). The GenBank/EMBL accession number for the 16S rDNA sequence of strain LVform1 is AJ544687.

  8. Kocuria polaris sp. nov., an orange-pigmented psychrophilic bacterium isolated from an Antarctic cyanobacterial mat sample.

    Science.gov (United States)

    Reddy, Gundlapally S N; Prakash, Jogadhenu S S; Prabahar, Vadivel; Matsumoto, Genki I; Stackebrandt, Erko; Shivaji, Sisinthy

    2003-01-01

    Strain CMS 76orT, an orange-pigmented bacterium, was isolated from a cyanobacterial mat sample from a pond located in McMurdo Dry Valley, Antarctica. On the basis of chemotaxonomic and phylogenetic properties, strain CMS 76orT was identified as a member of the genus Kocuria. It exhibited a 16S rDNA similarity of 99.8% and DNA-DNA similarity of 71% with Kocuria rosea (ATCC 186T). Phenotypic traits confirmed that strain CMS 78orT and K. rosea were well differentiated. Furthermore, strain CMS 76orT could be differentiated from the other reported species of Kocuria, namely Kocuria kristinae (ATCC 27570T), Kocuria varians (ATCC 15306T), Kocuria rhizophila (DSM 11926T) and Kocuria palustris (DSM 11025T), on the basis of a number of phenotypic features. Therefore, it is proposed that strain CMS 76orT (= MTCC 3702T = DSM 14382T) be assigned to a novel species of the genus Kocuria, as Kocuria polaris.

  9. Virgibacillus ainsalahensis sp. nov., a Moderately Halophilic Bacterium Isolated from Sediment of a Saline Lake in South of Algeria.

    Science.gov (United States)

    Amziane, Meriam; Darenfed-Bouanane, Amel; Abderrahmani, Ahmed; Selama, Okba; Jouadi, Lydia; Cayol, Jean-Luc; Nateche, Farida; Fardeau, Marie-Laure

    2017-02-01

    A Gram-positive, moderately halophilic, endospore-forming bacterium, designated MerVT, was isolated from a sediment sample of a saline lake located in Ain Salah, south of Algeria. The cells were rod shaped and motile. Isolate MerVT grew at salinity interval of 0.5-25% NaCl (optimum, 5-10%), pH 6.0-12.0 (optimum, 8.0), and temperature between 10 and 40 °C (optimum, 30 °C).The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, a glycolipid, a phospholipid, and two lipids, and MK-7 is the predominant menaquinone. The predominant cellular fatty acids were anteiso C15:0 and anteiso C17:0. The DNA G+C content was 45.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain MerVT was most closely related to Virgibacillus halodenitrificans (gene sequence similarity of 97.0%). On the basis of phenotypic, chemotaxonomic properties, and phylogenetic analyses, strain MerVT (=DSM = 28944T) should be placed in the genus Virgibacillus as a novel species, for which the name Virgibacillus ainsalahensis is proposed.

  10. Reuse of red seaweed waste by a novel bacterium, Bacillus sp. SYR4 isolated from a sandbar.

    Science.gov (United States)

    Kang, Soyeon; Kim, Joong Kyun

    2015-01-01

    A potent bacterial strain was isolated from a sandbar and identified as Bacillus sp. SYR4 for the reuse of red seaweed waste. The isolate possessed both agarase and carrageenase activities. The optimal pH and temperature for the degradation of both agar and carrageenan by the isolate were found to be pH 7.5 and 30 °C, respectively. The effects of cations on cell growth and degradation ability of the isolate were significant in comparison with controls. The isolate produced 0.27 and 0.29 g l(-1) of reducing sugars from 1 g l(-1) of agar and carrageenan, respectively. When the isolate was cultivated in red seaweed powder medium for 10 days, the yield of reducing sugars was 24 %. As a result, the eco-friendly reuse of red seaweed waste by this isolate appears to be feasible for the production of reducing sugars and could be a valuable resource. To the best of our knowledge, this is the first study to directly demonstrate the ability of Bacillus sp. SYR4 to degrade both agar and carrageenan.

  11. Identification of a 4-Deoxy-l-erythro-5-hexoseulose Uronic Acid Reductase, FlRed, in an Alginolytic Bacterium Flavobacterium sp. Strain UMI-01

    Directory of Open Access Journals (Sweden)

    Akira Inoue

    2015-01-01

    Full Text Available In alginate-assimilating bacteria, alginate is depolymerized to unsaturated monosaccharide by the actions of endolytic and exolytic alginate lyases (EC 4.2.2.3 and EC 4.2.2.11. The monosaccharide is non-enzymatically converted to 4-deoxy-l-ery thro-5-hexoseulose uronic acid (DEH, then reduced to 2-keto-3-deoxy-d-gluconate (KDG by a specific reductase, and metabolized through the Entner–Doudoroff pathway. Recently, the NADPH-dependent reductase A1-R that belongs to short-chain dehydrogenases/reductases (SDR superfamily was identified as the DEH-reductase in Sphingomonas sp. A1. We have subsequently noticed that an SDR-like enzyme gene, flred, occurred in the genome of an alginolytic bacterium Flavobacterium sp. strain UMI-01. In the present study, we report on the deduced amino-acid sequence of flred and DEH-reducing activity of recombinant FlRed. The deduced amino-acid sequence of flred comprised 254 residues and showed 34% amino-acid identities to that of A1-R from Sphingomonas sp. A1 and 80%–88% to those of SDR-like enzymes from several alginolytic bacteria. Common sequence motifs of SDR-superfamily enzymes, e.g., the catalytic tetrad Asn-Lys-Tyr-Ser and the cofactor-binding sequence Thr-Gly-x-x-x-Gly-x-Gly in Rossmann fold, were completely conserved in FlRed. On the other hand, an Arg residue that determined the NADPH-specificity of Sphingomonas A1-R was replaced by Glu in FlRed. Thus, we investigated cofactor-preference of FlRed using a recombinant enzyme. As a result, the recombinant FlRed (recFlRed was found to show high specificity to NADH. recFlRed exhibited practically no activity toward variety of aldehyde, ketone, keto ester, keto acid and aldose substrates except for DEH. On the basis of these results, we conclude that FlRed is the NADH-dependent DEH-specific SDR of Flavobacterium sp. strain UMI-01.

  12. Bacillus oryzicola sp. nov., an Endophytic Bacterium Isolated from the Roots of Rice with Antimicrobial, Plant Growth Promoting, and Systemic Resistance Inducing Activities in Rice

    Directory of Open Access Journals (Sweden)

    Eu Jin Chung

    2015-06-01

    Full Text Available Biological control of major rice diseases has been attempted in several rice-growing countries in Asia during the last few decades and its application using antagonistic bacteria has proved to be somewhat successful for controlling various fungal diseases in field trials. Two novel endophytic Bacillus species, designated strains YC7007 and YC7010T, with anti-microbial, plant growth-promoting, and systemic resistance-inducing activities were isolated from the roots of rice in paddy fields at Jinju, Korea, and their multifunctional activities were analyzed. Strain YC7007 inhibited mycelial growth of major rice fungal pathogens strongly in vitro. Bacterial blight and panicle blight caused by Xanthomonas oryzae pv. oryzae (KACC 10208 and Burkholderia glumae (KACC 44022, respectively, were also suppressed effectively by drenching a bacterial suspension (10⁷ cfu/ml of strain YC7007 on the rhizosphere of rice. Additionally, strain YC7007 promoted the growth of rice seedlings with higher germination rates and more tillers than the untreated control. The taxonomic position of the strains was also investigated. Phylogenetic analyses based on 16S rRNA gene sequences indicated that both strains belong to the genus Bacillus, with high similarity to the closely related strains, Bacillus siamensis KACC 15859T (99.67%, Bacillus methylotrophicus KACC 13105T (99.65%, Bacillus amyloliquefaciens subsp. plantarum KACC 17177T (99.60%, and Bacillus tequilensis KACC 15944T (99.45%. The DNA-DNA relatedness value between strain YC7010T and the most closely related strain, B. siamensis KACC 15859T was 50.4±3.5%, but it was 91.5±11.0% between two strains YC7007 and YC7010T, indicating the same species. The major fatty acids of two strains were anteiso-C15:0 and iso C15:0. Both strains contained MK-7 as a major respiratory quinone system. The G+C contents of the genomic DNA of two strains were 50.5 mol% and 51.2 mol%, respectively. Based on these polyphasic studies, the

  13. Wenyingzhuangia gracilariae sp. nov., a novel marine bacterium of the phylum Bacteroidetes isolated from the red alga Gracilaria vermiculophylla.

    Science.gov (United States)

    Yoon, Jaewoo; Oku, Naoya; Kasai, Hiroaki

    2015-06-01

    A Gram-negative, strictly aerobic, beige-pigmented, non-motile, rod-shaped bacterial strain designated N5DB13-4(T) was isolated from the red alga Gracilaria vermiculophylla (Rhodophyta) collected at Sodegaura Beach, Chiba, Japan. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the novel isolate is affiliated with the family Flavobacteriaceae within the phylum Bacteroidetes and that it showed highest sequence similarity (97.3 %) to Wenyingzhuangia heitensis H-MN17(T). The hybridization values for DNA-DNA relatedness between the strains N5DB13-4(T) and W. heitensis H-MN17(T) were 34.1 ± 3.5 %, which is below the threshold accepted for the phylogenetic definition of a novel prokaryotic species. The DNA G+C content of strain N5DB13-4(T) was determined to be 31.8 mol%; MK-6 was identified as the major menaquinone; and the presence of iso-C15:0, iso-C15:0 3-OH and iso-C17:0 3-OH as the major (>10 %) cellular fatty acids. A complex polar lipid profile was present consisting of phosphatidylethanolamine, two unidentified glycolipids and four unidentified lipids. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel species of the genus Wenyingzhuangia for which the name Wenyingzhuangia gracilariae sp. nov. is proposed. The type strain of W. gracilariae sp. nov. is N5DB13-4(T) (=KCTC 42246 (T)=NBRC 110602(T)).

  14. DNA microarray-based detection and identification of Burkholderia mallei, Burkholderia pseudomallei and Burkholderia spp.

    Science.gov (United States)

    Schmoock, Gernot; Ehricht, Ralf; Melzer, Falk; Rassbach, Astrid; Scholz, Holger C; Neubauer, Heinrich; Sachse, Konrad; Mota, Rinaldo Aparecido; Saqib, Muhammad; Elschner, Mandy

    2009-01-01

    We developed a rapid oligonucleotide microarray assay based on genetic markers for the accurate identification and differentiation of Burkholderia (B.) mallei and Burkholderia pseudomallei, the agents of glanders and melioidosis, respectively. These two agents were clearly identified using at least 4 independent genetic markers including 16S rRNA gene, fliC, motB and also by novel species-specific target genes, identified by in silico sequence analysis. Specific hybridization signal profiles allowed the detection and differentiation of up to 10 further Burkholderia spp., including the closely related species Burkholderia thailandensis and Burkholderia-like agents, such as Burkholderia cepacia, Burkholderia cenocepacia, Burkholderia vietnamiensis, Burkholderia ambifaria, and Burkholderia gladioli, which are often associated with cystic fibrosis (CF) lung disease. The assay was developed using the easy-to-handle and economical ArrayTube (AT) platform. A representative strain panel comprising 44 B. mallei, 32 B. pseudomallei isolates, and various Burkholderia type strains were examined to validate the test. Assay specificity was determined by examination of 40 non-Burkholderia strains.

  15. Tepidibacillus infernus sp. nov., a moderately thermophilic, selenate- and arsenate-respiring hydrolytic bacterium isolated from a gold mine, and emended description of the genus Tepidibacillus.

    Science.gov (United States)

    Podosokorskaya, Olga A; Merkel, Alexander Y; Gavrilov, Sergey N; Fedoseev, Igor; Heerden, Esta van; Cason, Errol D; Novikov, Andrey A; Kolganova, Tatyana V; Korzhenkov, Aleksei A; Bonch-Osmolovskaya, Elizaveta A; Kublanov, Ilya V

    2016-08-01

    A novel aerotolerant anaerobic, moderately thermophilic, organotrophic bacterium, strain MBL-TLPT, was isolated from a sample of microbial mat, developed under the flow of subsurface water in TauTona gold mine, South Africa. Cells of the new isolate were flagellated, spore-forming rods, 0.25-0.5 µm in width and 3-15 µm in length. Strain MBL-TLPT grew in the temperature range from 25 to 58 °C, pH range from 5.6 to 8.8 and at NaCl concentration from 0 to 85 g l-1. The isolate was able to ferment yeast extract and mono-, oligo- and polysaccharides, including starch and xanthan gum. The G+C content of the DNA was 35 mol%. Phylogenetic analysis of 16S rRNA gene sequences of strain MBL-TLPT and relatives showed its affiliation to the genus Tepidibacillus. Tepidibacillus fermentans STGHT was its closest relative (97.1 % identity of 16S rRNA gene sequences). Based on phylogenetic analysis and the physiological properties of the novel isolate, we propose a novel species, Tepidibacillus infernus sp. nov., with MBL-TLPT(=DSM 28123T=VKM В-2949T) as the type strain.

  16. Interaction with mycorrhiza helper bacterium Streptomyces sp. AcH 505 modifies organisation of actin cytoskeleton in the ectomycorrhizal fungus Amanita muscaria (fly agaric).

    Science.gov (United States)

    Schrey, Silvia D; Salo, Vanamo; Raudaskoski, Marjatta; Hampp, Rüdiger; Nehls, Uwe; Tarkka, Mika T

    2007-08-01

    The actin cytoskeleton (AC) of fungal hyphae is a major determinant of hyphal shape and morphogenesis, implicated in controlling tip structure and secretory vesicle delivery. Hyphal growth of the ectomycorrhizal fungus Amanita muscaria and symbiosis formation with spruce are promoted by the mycorrhiza helper bacterium Streptomyces sp. AcH 505 (AcH 505). To investigate structural requirements of growth promotion, the effect of AcH 505 on A. muscaria hyphal morphology, AC and actin gene expression were studied. Hyphal diameter and mycelial density decreased during dual culture (DC), and indirect immunofluorescence microscopy revealed that the dense and polarised actin cap in hyphal tips of axenic A. muscaria changes to a loosened and dispersed structure in DC. Supplementation of growth medium with cell-free bacterial supernatant confirmed that reduction in hyphal diameter and AC changes occurred at the same stage of growth. Transcript levels of both actin genes isolated from A. muscaria remained unaltered, indicating that AC changes are regulated by reorganisation of the existing actin pool. In conclusion, the AC reorganisation appears to result in altered hyphal morphology and faster apical extension. The thus improved spreading of hyphae and increased probability to encounter plant roots highlights a mechanism behind the mycorrhiza helper effect.

  17. Sediminibacillus massiliensis sp. nov., a moderately halophilic, Gram-positive bacterium isolated from a stool sample of a young Senegalese man.

    Science.gov (United States)

    Senghor, Bruno; Bassène, Hubert; Khelaifia, Saber; Robert, Catherine; Fournier, Pierre-Edouard; Ruimy, Raymond; Sokhna, Cheikh; Raoult, Didier; Lagier, Jean-Christophe

    2018-02-07

    A Gram-positive, moderately halophilic bacterium, referred to as strain Marseille-P3518 T , was isolated from a stool sample with 2% NaCl concentration from a healthy 15-year-old male living in Dielmo, a village in Senegal. Cells are aerobic, rod-shaped and motile and display endospore formation. Strain Marseille-P3518 T can grow in a medium with 0-20% (w/v) sodium chloride (optimally at 5-7.5% w/v). The major fatty acids were 12-methyl-tetradecanoic acid (45.8%), 13-methyl-tetradecanoic acid (26.9%) and 12-methyl-tridecanoic acid (12.8%). The genome is 4,347,479 bp long with 42.1% G+C content. It contains 4282 protein-coding and 107 RNA genes. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that strain Marseille-P3518 T is a member of the Bacillaceae family and is closely related to Sediminibacillus albus (97.4% gene sequence similarity). Strain Marseille-P3518 T was clearly differentiated from its phylogenetic neighbors on the basis of phenotypic and genotypic features. Strain Marseille-P3518 T is, therefore, considered to be a novel representative of the genus Sediminibacillus, for which the name Sediminibacillus massiliensis sp. nov. is proposed, and the type strain is Marseille-P3518 T (CSUR P3518T, DSM69894).

  18. Biochemical characterization and sequence analysis of a xylanase produced by an exo-symbiotic bacterium of Gryllotalpa orientalis, Cellulosimicrobium sp. HY-12.

    Science.gov (United States)

    Oh, Hyun-Woo; Heo, Sun-Yeon; Kim, Do Young; Park, Doo-Sang; Bae, Kyung Sook; Park, Ho-Yong

    2008-05-01

    An exo-symbiotic bacterium capable of hydrolyzing xylan was isolated from the gut of the mole cricket, Gryllotalpa orientalis, and identified as Cellulosimicrobium sp. HY-12. The xylanase (XylA( CspHY-12)) of this organism bound tightly to both DEAE and mono Q resins, and its molecular mass (M(r)) was about 39.0 kDa. The highest xylanase activity was observed at pH 6.0 and 60 degrees C. The enzyme was greatly suppressed by Ca(2+), Cu(2+), Co(2+), and Fe(2+) ions but not by Mg(2+) and Mn(2+). Although XylA( CspHY-12) was capable of hydrolyzing various types of xylosic compounds, it could not decompose carboxymethyl cellulose or xylobiose. The xylA (CspHY-12 ) gene consisted of an 1,188 bp open reading frame that encoded a polypeptide of 395 amino acids with a deduced molecular mass of 42,925 Da. The domain structure of XylA( CspHY-12) was most similar to those of the glycoside hydrolase (GH) family 10 endoxylanases. However its sequence identity with any of the enzymes in this family was below 52%. The results of this study suggest that the XylA( CspHY-12) is a new cellulase-free endo-beta-1,4-xylanase with some properties that are distinct from those of GH family 10.

  19. Pilot-Scale Production and Thermostability Improvement of the M23 Protease Pseudoalterin from the Deep Sea Bacterium Pseudoalteromonas sp. CF6-2

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    Jie Yang

    2016-11-01

    Full Text Available Pseudoalterin is the most abundant protease secreted by the marine sedimental bacterium Pseudoalteromonas sp. CF6-2 and is a novel cold-adapted metalloprotease of the M23 family. Proteases of the M23 family have high activity towards peptidoglycan and elastin, suggesting their promising biomedical and biotechnological potentials. To lower the fermentive cost and improve the pseudoalterin production of CF6-2, we optimized the fermentation medium by using single factor experiments, added 0.5% sucrose as a carbon source, and lowered the usage of artery powder from 1.2% to 0.6%. In the optimized medium, pseudoalterin production reached 161.15 ± 3.08 U/mL, 61% greater than that before optimization. We further conducted a small-scale fermentation experiment in a 5-L fermenter and a pilot-scale fermentation experiment in a 50-L fermenter. Pseudoalterin production during pilot-scale fermentation reached 103.48 ± 8.64 U/mL, 77% greater than that before the medium was optimized. In addition, through single factor experiments and orthogonal tests, we developed a compound stabilizer for pseudoalterin, using medically safe sugars and polyols. This stabilizer showed a significant protective effect for pseudoalterin against enzymatic thermal denaturation. These results lay a solid foundation for the industrial production of pseudoalterin and the development of its biomedical and biotechnological potentials.

  20. Characterization of Alkaliphilus hydrothermalis sp. nov., a novel alkaliphilic anaerobic bacterium, isolated from a carbonaceous chimney of the Prony hydrothermal field, New Caledonia.

    Science.gov (United States)

    Ben Aissa, Fatma; Postec, Anne; Erauso, Gaël; Payri, Claude; Pelletier, Bernard; Hamdi, Moktar; Fardeau, Marie-Laure; Ollivier, Bernard

    2015-01-01

    A novel anaerobic, alkaliphilic, Gram-positive staining bacterium was isolated from a hydrothermal chimney in the Prony Bay, New Caledonia. This strain designated FatMR1(T) grew at temperatures from 20 to 55 °C (optimum 37 °C) and at pH between 7.5 and 10.5 (optimum 8.8-9). NaCl is not required for growth (optimum 0.2-0.5%), but is tolerated up to 3%. Sulfate, thiosulfate, elemental sulfur, sulfite, nitrate and nitrite are not used as terminal electron acceptors. Strain FatMR1(T) fermented pyruvate, yeast extract, peptone and biotrypcase and used fructose as the only sugar. The main fermentation products from fructose and proteinaceous compounds (e.g. peptone and biotrypcase) were acetate, H2 and CO2. Crotonate was disproportionated to acetate and butyrate. The predominant cellular fatty acids were C14:0 and C16:0. The G + C content of the genomic DNA was 37.1 mol%. On the basis of phylogenetic, genetic, and physiological properties, strain FatMR1(T) (=DSM 25890(T), =JCM 18390(T)) belonging to the phylum Firmicutes, class Clostridia, order Clostridiales, is proposed as a novel species of the genus Alkaliphilus, A. hydrothermalis sp. nov.

  1. Methylobacterium oryzae sp. nov., an aerobic, pink-pigmented, facultatively methylotrophic, 1-aminocyclopropane-1-carboxylate deaminase-producing bacterium isolated from rice.

    Science.gov (United States)

    Madhaiyan, Munusamy; Kim, Byung-Yong; Poonguzhali, Selvaraj; Kwon, Soon-Wo; Song, Myung-Hee; Ryu, Jeoung-Hyun; Go, Seung-Joo; Koo, Bon-Sung; Sa, Tong-Min

    2007-02-01

    A pink-pigmented, facultatively methylotrophic bacterium, strain CBMB20T, isolated from stem tissues of rice, was analysed by a polyphasic approach. Strain CBMB20T utilized 1-aminocyclopropane 1-carboxylate (ACC) as a nitrogen source and produced ACC deaminase. It was related phylogenetically to members of the genus Methylobacterium. 16S rRNA gene sequence analysis indicated that strain CBMB20T was most closely related to Methylobacterium fujisawaense, Methylobacterium radiotolerans and Methylobacterium mesophilicum; however, DNA-DNA hybridization values were less than 70 % with the type strains of these species. The DNA G+C content of strain CBMB20T was 70.6 mol%. The study presents a detailed phenotypic characterization of strain CBMB20T that allows its differentiation from other Methylobacterium species. In addition, strain CBMB20T is the only known member of the genus Methylobacterium to be described from the phyllosphere of rice. Based on the data presented, strain CBMB20T represents a novel species in the genus Methylobacterium, for which the name Methylobacterium oryzae sp. nov. is proposed, with strain CBMB20T (=DSM 18207T=LMG 23582T=KACC 11585T) as the type strain.

  2. Structural and functional characterization of mature forms of metalloprotease E495 from Arctic sea-ice bacterium Pseudoalteromonas sp. SM495.

    Directory of Open Access Journals (Sweden)

    Hai-Lun He

    Full Text Available E495 is the most abundant protease secreted by the Arctic sea-ice bacterium Pseudoalteromonas sp. SM495. As a thermolysin family metalloprotease, E495 was found to have multiple active forms in the culture of strain SM495. E495-M (containing only the catalytic domain and E495-M-C1 (containing the catalytic domain and one PPC domain were two stable mature forms, and E495-M-C1-C2 (containing the catalytic domain and two PPC domains might be an intermediate. Compared to E495-M, E495-M-C1 had similar affinity and catalytic efficiency to oligopeptides, but higher affinity and catalytic efficiency to proteins. The PPC domains from E495 were expressed as GST-fused proteins. Both of the recombinant PPC domains were shown to have binding ability to proteins C-phycocyanin and casein, and domain PPC1 had higher affinity to C-phycocyanin than domain PPC2. These results indicated that the domain PPC1 in E495-M-C1 could be helpful in binding protein substrate, and therefore, improving the catalytic efficiency. Site-directed mutagenesis on the PPC domains showed that the conserved polar and aromatic residues, D26, D28, Y30, Y/W65, in the PPC domains played key roles in protein binding. Our study may shed light on the mechanism of organic nitrogen degradation in the Arctic sea ice.

  3. Antimicrobial activity of PVP from an Antarctic bacterium, Janthinobacterium sp. Ant5-2, on multi-drug and methicillin resistant Staphylococcus aureus

    KAUST Repository

    Huang, Jonathan P.

    2012-04-11

    Multiple drug resistant (MDR) and methicillin-resistant Staphylococcus aureus (MRSA) have become increasingly prevalent as a community acquired infection. As a result limited treatment options are available with conventional synthetic antibiotics. Bioprospecting natural products with potent antimicrobial activity show promise for developing new drugs against this pathogen. In this study, we have investigated the antimicrobial activity of a purple violet pigment (PVP) from an Antarctic bacterium, Janthinobacterium sp. Ant5-2 on 15 clinical MDR and MRSA strains. The colorimetric resazurin assay was employed to determine the minimum inhibitory concentration (MIC90) of PVP against MDR and MRSA. The MIC90 ranged between 1.57 µg/mL and 3.13 µg/mL, which are significantly lower than many antimicrobials tested from natural sources against this pathogen. The spectrophotometrically determined growth analysis and total microscopic counts using Live/dead® BacLight™ fluorescent stain exhibited a steady decrease in viability of both MDR and MRSA cultures following treatment with PVP at the MIC levels. In silico predictive molecular docking study revealed that PVP could be a DNA-targeting minor groove binding antimicrobial compound. The continued development of novel antimicrobials derived from natural sources with the combination of a suite of conventional antibiotics could stem the rising pandemic of MDR and MRSA along with other deadly microbial pathogens.

  4. A novel marine bacterium Isoptericola sp. JS-C42 with the ability to saccharifying the plant biomasses for the aid in cellulosic ethanol production

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    Velayudhan Satheeja Santhi

    2014-06-01

    Full Text Available The ever growing demands for food products such as starch and sugar produces; there is a need to find the sources for saccharification for cellulosic bioethanol production. This study provides the first evidence of the lignocellulolytic and saccharifying ability of a marine bacterium namely Isoptericola sp. JS-C42, a Gram positive actinobacterium with the cocci cells embedded on mycelia isolated from the Arabian Sea, India. It exhibited highest filter paper unit effect, endoglucanase, exoglucanase, cellobiohydrolase, β-glucosidase, xylanase and ligninase effect. The hydrolytic potential of the enzymes displayed the efficient saccharification capability of steam pretreated biomass. It was also found to degrade the paddy, sorghum, Acacia mangium and Ficus religiosa into simple reducing sugars by its efficient lignocellulose enzyme complex with limited consumption of sugars. Production of ethanol was also achieved with the Saccharomyces cerevisiae. Overall, it offers a great potential for the cellulosic ethanol production in an economically reliable and eco-friendly point-of-care.

  5. Enterobacter arachidis sp. nov., a plant-growth-promoting diazotrophic bacterium isolated from rhizosphere soil of groundnut.

    Science.gov (United States)

    Madhaiyan, Munusamy; Poonguzhali, Selvaraj; Lee, Jung-Sook; Saravanan, Venkatakrishnan Sivaraj; Lee, Keun-Chul; Santhanakrishnan, Palani

    2010-07-01

    A methylotrophic nitrogen-fixing bacterial strain, Ah-143(T), isolated from the rhizosphere soil of field-grown groundnut was analysed by a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis combined with rpoB gene sequence analysis allocated strain Ah-143(T) to the family Enterobacteriaceae, with Enterobacter radicincitans and Enterobacter cowanii as the closest relatives. The strain is Gram-stain-negative, non-spore-forming, aerobic and motile, having straight rod-shaped cells with a DNA G+C content of approximately 53.2 mol%. The strain utilizes methanol as a carbon source and the mxaF gene was closely related to the mxaF gene of members of the genus Methylobacterium. The fatty acid profile consisted of C(16 : 0), C(17 : 0) cyclo, C(18 : 1)omega7c, summed feature 2 (iso-C(16 : 1) I and/or C(14 : 0) 3-OH) and summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c) as the major components. DNA-DNA relatedness of strain Ah-143(T) with its close relatives was less than 20 %. On the basis of the phylogenetic analyses, DNA-DNA hybridization data, and unique physiological and biochemical characteristics, it is proposed that the strain represents a novel species of the genus Enterobacter and should be named Enterobacter arachidis sp. nov. The type strain is Ah-143(T) (=NCIMB 14469(T) =KCTC 22375(T)).

  6. Enterobacter oryzae sp. nov., a nitrogen-fixing bacterium isolated from the wild rice species Oryza latifolia.

    Science.gov (United States)

    Peng, Guixiang; Zhang, Wu; Luo, Huifen; Xie, Hongwei; Lai, Weihao; Tan, Zhiyuan

    2009-07-01

    Twelve facultatively anaerobic, endophytic diazotrophs were isolated from surface-sterilized roots of the wild rice species Oryza latifolia and characterized by phenotypic and molecular methods. Six isolates were grouped together as group A by phenotypic characters, and this grouping was confirmed by SDS-PAGE whole-cell protein patterns and insertion sequence-based PCR (IS-PCR) methods. Phylogenetic analysis of the 16S rRNA gene sequence indicated that group A, represented by strain Ola 51(T), is closely related to Enterobacter radicincitans D5/23(T) (98.9 % similarity, except that E. radicincitans D5/23(T) has a 70 bp insertion) and Enterobacter cloacae (98.0 % similarity to the type strain). rpoB gene sequence analysis also showed strain Ola 51(T) has the highest sequence similarity to E. radicincitans DSM 16656(T) (98.3 %), but supported the distinct position. Biological and biochemical tests, protein patterns, genomic DNA fingerprinting, antibiotic resistance and comparison of cellular fatty acids showed differences among group A, E. radicincitans DSM 16656(T) and E. cloacae ATCC 13047(T). DNA-DNA hybridization distinguished strain Ola 51(T) from closely phylogenetically related Enterobacter species. Based on these data, the novel species Enterobacter oryzae sp. nov. is proposed, with strain Ola 51(T) (=LMG 24251(T) =CGMCC 1.7012(T)) as the type strain.

  7. Permianibacter aggregans gen. nov., sp. nov., a bacterium of the family Pseudomonadaceae capable of aggregating potential biofuel-producing microalgae.

    Science.gov (United States)

    Wang, Hui; Zheng, Tianling; Hill, Russell T; Hu, Xiaoke

    2014-10-01

    A novel bacterial strain, capable of aggregating potential biofuel-producing microalgae, was isolated from the phycosphere of an algal culture and designated HW001(T). The novel bacterial strain was identified on the basis of its phylogenetic, genotypic, chemotaxonomic and phenotypic characteristics in this study. Cells were aerobic, Gram-negative rods. 16S rRNA gene-based phylogenetic analysis revealed that strain HW001(T) is affiliated with the family Pseudomonadaceae in the phylum Proteobacteria, but forms a distinct clade within this family. The DNA G+C content of strain HW001(T) was 55.4 mol%. The predominant cellular fatty acids were iso-C15:0, summed feature 9 (iso-C17:1ω9c), C16:0 and summed feature 3 (C16:1ω7c/C16:1ω6c). Q-8 was the main respiratory quinone. The polar lipid profile contained phosphatidylethanolamine, an unidentified aminophospholipid and some unidentified lipids. Based on the extensive polyphasic analysis, strain HW001(T) represents a novel species of a new genus in the family Pseudomonadaceae, for which the name Permianibacter aggregans gen. nov., sp. nov., is proposed. The type strain of the type species is HW001(T) ( = CICC 10856(T) = KCTC 32485(T)). IUMS.

  8. Gluconacetobacter sp. gel_SEA623-2, bacterial cellulose producing bacterium isolated from citrus fruit juice

    Directory of Open Access Journals (Sweden)

    S.S. Kim

    2017-02-01

    Full Text Available Cellulose producing bacterial strain was isolated from citrus fruit juice fungus. The isolated strain was identified as Gluconacetobacter sp. gel_SEA623-2 based on several morphological characteristics, biochemical tests, and 16S rRNA conducted. Culture conditions for bacterial cellulose production by SEA623-2 were screened in static trays. Conditions were extensively optimized by varying the kind of fruit juice, pH, sugar concentration, and temperature for maximum cellulose production. SEA623-2 has a high productive capacity in citrus processing medium, but not in other fruits. The optimal combination of the media constituents for bacterial cellulose production is as follows: 10% citrus juice, 10% sucrose, 1% acetic acid, and 1% ethanol at 30 °C, pH 3.5. Bacterial cellulose produced by SEA623-2 has soft physical properties, high tensile strength, and high water retention value. The cellulose produced by the selected bacteria is suitable as a cosmetic and medical material.

  9. Methylomusa anaerophila gen. nov., sp. nov., an anaerobic methanol-utilizing bacterium isolated from a microbial fuel cell.

    Science.gov (United States)

    Amano, Nanako; Yamamuro, Ayaka; Miyahara, Morio; Kouzuma, Atsushi; Abe, Takashi; Watanabe, Kazuya

    2018-02-15

    Abacterial strain, designated MMFC1 T , was isolated from a methanol-fed microbial fuel cell that had been inoculated with sludge obtained from a wastewater-treatmentfacility in a chemical plant. The strain grows by fermenting methanol to produce acetate under anaerobic conditions, while homoacetogenic growth is not observed. MMFC1 T also grows on pyruvate and lactate but not on sugars and other organic acids. Cells are curved rods and motile, have peritrichous flagella, and form endospores. The genome sequence of strain MMFC1 T supports the physiological data. Phylogenetic analysis based on the 16S rRNA gene sequence shows that strain MMFC1 T is affiliated with the family Sporomusaceae, while the closest relative is Sporomusa ovata with nucleotide-sequencesimilarity of 93.5 %. Major fatty acids are iso-C13 : 0 3-OH, C16 : 1ω9 and iso-C17 : 0. On the basis of its physiological, genomic and phylogenetic features, a novel genus and species are proposed to accommodate strain MMFC1 T , with the name Methylomusa anaerophila gen. nov., sp. nov. The type strain of Methylomusa anaerophila is MMFC1 T (=JCM 31821 T = KCTC 15592 T ).

  10. Taxonomic characterisation of Proteus terrae sp. nov., a N2O-producing, nitrate-ammonifying soil bacterium.

    Science.gov (United States)

    Behrendt, Undine; Augustin, Jürgen; Spröer, Cathrin; Gelbrecht, Jörg; Schumann, Peter; Ulrich, Andreas

    2015-12-01

    In the context of studying the influence of N-fertilization on N2 and N2O flux rates in relation to the soil bacterial community composition in fen peat grassland, a group of bacterial strains was isolated that performed dissimilatory nitrate reduction to ammonium and concomitantly produced N2O. The amount of nitrous oxide produced was influenced by the C/N ratio of the medium. The potential to generate nitrous oxide was increased by higher availability of nitrate-N. Phylogenetic analysis based on the 16S rRNA and the rpoB gene sequences demonstrated that the investigated isolates belong to the genus Proteus, showing high similarity with the respective type strains of Proteus vulgaris and Proteus penneri. DNA-DNA hybridization studies revealed differences at the species level. These differences were substantiated by MALDI-TOF MS analysis and several distinct physiological characteristics. On the basis of these results, it was concluded that the soil isolates represent a novel species for which the name Proteus terrae sp. nov. (type strain N5/687(T) =DSM 29910(T) =LMG 28659(T)) is proposed.

  11. The role of exochitinase type A1 in the fungistatic activity of the rhizosphere bacterium Paenibacillus sp. M4

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    Jankiewicz Urszula

    2016-01-01

    Full Text Available The aim of the study was to detect the activity and characterize potentially fungistatic chitinases synthesized by rhizosphere bacteria identified as Paenibacillus sp. M4. Maximum chitinolytic activity was achieved on the fifth day of culturing bacteria in a growth medium with 1% colloidal chitin. Analysis of a zymogram uncovered the presence of four activity bands in the crude bacterial extract. The used three-stage protein purification procedure resulted in a single band of chitinase activity on the zymogram. The purified enzyme exhibited maximum activity at pH 6.5 and temperature 45oC, and thermal stability at 40oC for 4 h. In terms of substrate specificity, it is an exochitinase (chitobiose. The amino acid sequence obtained after mass spectrometry showed similarity to chitinase A1 synthesized by Bacillus circulans. The M4 isolate demonstrated the highest growth inhibiting activity against plant pathogens belonging to the genera Fusarium, Rhizoctonia and Alternaria. Fungistatic activity, although to a somewhat lesser degree, was also demonstrated by purified chitinase. The obtained results confirm the participation of the studied exochitinase in antagonism towards pathogenic molds. However, the lower fungistatic effectiveness of the chitinases points to the synergistic action of different metabolites in biocontrol by these bacteria.

  12. Biochemical characterization of a bifunctional acetaldehyde-alcohol dehydrogenase purified from a facultative anaerobic bacterium Citrobacter sp. S-77.

    Science.gov (United States)

    Tsuji, Kohsei; Yoon, Ki-Seok; Ogo, Seiji

    2016-03-01

    Acetaldehyde-alcohol dehydrogenase (ADHE) is a bifunctional enzyme consisting of two domains of an N-terminal acetaldehyde dehydrogenase (ALDH) and a C-terminal alcohol dehydrogenase (ADH). The enzyme is known to be important in the cellular alcohol metabolism. However, the role of coenzyme A-acylating ADHE responsible for ethanol production from acetyl-CoA remains uncertain. Here, we present the purification and biochemical characterization of an ADHE from Citrobacter sp. S-77 (ADHE(S77)). Interestingly, the ADHE(S77) was unable to be solubilized from membrane with detergents either 1% Triton X-100 or 1% Sulfobetaine 3-12. However, the enzyme was easily dissociated from membrane by high-salt buffers containing either 1.0 M NaCl or (NH(4))(2)SO(4) without detergents. The molecular weight of a native protein was estimated as approximately 400 kDa, consisting of four identical subunits of 96.3 kDa. Based on the specific activity and kinetic analysis, the ADHES77 tended to have catalytic reaction towards acetaldehyde elimination rather than acetaldehyde formation. Our experimental observation suggests that the ADHES77 may play a pivotal role in modulating intracellular acetaldehyde concentration. Copyright © 2015 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  13. A low cost fermentation medium for potential fibrinolytic enzyme production by a newly isolated marine bacterium, Shewanella sp. IND20

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    P. Vijayaraghavan

    2015-09-01

    Full Text Available 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 significant effect on fibrinolytic enzyme production. Central composite design was employed to search for the optimal concentration of the three factors, namely moisture, pH, and trehalose, and the experimental results were fitted with a second-order polynomial model at 99% level (p < 0.0001. The optimized medium showed 2751 U/mL of fibrinolytic activity, which was 2.5-fold higher than unoptimized medium. The molecular weight of fibrinolytic enzyme was found to be 55.5 kDa. The optimum pH and temperature were 8.0 and 50 °C, respectively.

  14. Pandoraea thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soils of sesame (Sesamum indicum L.).

    Science.gov (United States)

    Anandham, Rangasamy; Indiragandhi, Pandiyan; Kwon, Soon Wo; Sa, Tong Min; Jeon, Che Ok; Kim, Yong Ki; Jee, Hyeong Jin

    2010-01-01

    A facultatively chemolithoautotrophic, thiosulfate-oxidizing, Gram-negative, aerobic, motile, rod-shaped bacterial strain, designated ATSB16(T), was isolated from rhizosphere soils of sesame (Sesamum indicum L.). 16S rRNA gene sequence analysis demonstrated that this strain was closely related to Pandoraea pnomenusa LMG 18087(T) (96.7 % similarity), P. pulmonicola LMG 18016(T) (96.5 %), P. apista LMG 16407(T) (96.2 %), P. norimbergensis LMG 18379(T) (96.1 %) and P. sputorum LMG 18819(T) (96.0 %). Strain ATSB16(T) shared 96.0-96.4 % sequence similarity with four unnamed genomospecies of Pandoraea. The major cellular fatty acids of the strain ATSB16(T) were C(17 : 0) cyclo (33.0 %) and C(16 : 0) (30.6 %). Q-8 was the predominant respiratory quinone. The major polar lipids were phosphatidylmethylethanolamine, diphosphatidylglycerol, phosphatidylethanolamine and two unidentified aminophospholipids. Hydroxyputrescine and putrescine were the predominant polyamines. The genomic DNA G+C content of the strain was 64.0 mol%. On the basis of the results obtained from this study, strain ATSB16(T) represents a novel species of the genus Pandoraea, for which the name Pandoraea thiooxydans sp. nov. is proposed. The type strain is ATSB16(T) (=KACC 12757(T) =LMG 24779(T)).

  15. Identification of a Putative P-Transporter Operon in the Genome of a Burkholderia Strain Living inside the Arbuscular Mycorrhizal Fungus Gigaspora margarita

    Science.gov (United States)

    Ruiz-Lozano, J. M.; Bonfante, P.

    1999-01-01

    This article reports the identification of a putative P-transporter operon in the genome of a Burkholderia sp. living in the cytoplasm of the arbuscular mycorrhizal fungus Gigaspora margarita. Its presence suggests that Burkholderia sp. has the potential for P uptake from this environment. This finding raises new questions concerning the importance of intracellular bacteria for mycorrhizal symbiosis. PMID:10383982

  16. DBSecSys: a database of Burkholderia mallei secretion systems

    OpenAIRE

    Memišević, Vesna; Kumar, Kamal; Cheng, Li; Zavaljevski, Nela; DeShazer, David; Wallqvist, Anders; Reifman, Jaques

    2014-01-01

    Background Bacterial pathogenicity represents a major public health concern worldwide. Secretion systems are a key component of bacterial pathogenicity, as they provide the means for bacterial proteins to penetrate host-cell membranes and insert themselves directly into the host cells’ cytosol. Burkholderia mallei is a Gram-negative bacterium that uses multiple secretion systems during its host infection life cycle. To date, the identities of secretion system proteins for B. mallei are not we...

  17. Symbiotic effects of a lipase-secreting bacterium, Burkholderia arboris SL1B1, and a glycerol-assimilating yeast, Candida cylindracea SL1B2, on triacylglycerol degradation.

    Science.gov (United States)

    Matsuoka, Hiroshi; Miura, Atsuto; Hori, Katsutoshi

    2009-04-01

    Although microbial degradation of oils and fats has been developed for application in wastewater treatment, microbial degraders are not always effective in the field, for example, in grease-traps installed for the treatment of wastewater from restaurants and food industries. Wastewater in grease-traps is usually in a pH range of 5.5 to 6.5 due to hydrolysis of triacylglycerol (TAG). Because many microorganisms commercialized for use in grease-traps cannot grow at pH 6.0, we screened oil-degrading microorganisms from the environment by growing in a medium at pH 6.0 containing canola oil as the sole carbon source. We succeeded in isolating the bacterial strain Burkholderia arboris SL1B1, which secretes lipase and assimilates fatty acids, and the yeast strain Candida cylindracea SL1B2, which assimilates glycerol. The former cannot utilize glycerol as a carbon source while the latter shows only faint lipase activity that cannot support its active growth on TAG. Canola oil was degraded rapidly by a pure culture of SL1B1 at pH 6.0. However, the degradation was markedly enhanced by a mixed culture of SL1B1 and SL1B2, although lipase activity during cultivation was similar between the pure and mixed cultures. This suggests that the reversible reaction proceeds in the direction of hydrolysis of TAG due to consumption of the reaction product, glycerol, by the symbiotic yeast strain. The optimum pH and temperature of lipase secreted by B. arboris SL1B1 were 8.0 and 60 degrees C, respectively. This lipase showed highly thermal stability; the residual activity after incubation at 70 degrees C for 2 h did not decline.

  18. Cellulomonas macrotermitis sp. nov., a chitinolytic and cellulolytic bacterium isolated from the hindgut of a fungus-growing termite.

    Science.gov (United States)

    Sun, Xinxin; Li, Jingjing; Du, Jiao; Xiao, Hesheng; Ni, Jinfeng

    2018-03-01

    To investigate the symbiotic roles of the gut microbiota in the fungus-growing termite Macrotermes barneyi, a novel strain with chitinolytic and cellulolytic activity, designated strain an-chi-1 T , was isolated from the hindgut of M. barneyi. Strain an-chi-1 T grows optimally at 28-30 °C, pH 8.0 in PYG medium. On the basis of 16S rRNA gene sequence analysis, this isolate belongs to the genus Cellulomonas with high sequence similarity to Cellulomonas iranensis (99.4%), followed by Cellulomonas flavigena (98.4%), Cellulomonas phragmiteti (97.4%), Cellulomonas oligotrophica (97.2%) and Cellulomonas terrae (97.0%). The DNA-DNA relatedness between an-chi-1 T and the type strains of C. iranensis and C. flavigena DSM20109 T are 35.4% and 23.7%, respectively. The major cellular fatty acids are anteiso-C 15:0 and C 14:0 . The polar lipid profile consists of diphosphatidylglycerol, phosphatidylinositol mannosides, phosphatidylinositol dimannosides and one unidentified phospholipid. The cell-wall sugar is ribose. The peptidoglycan contains glutamic acid, aspartic acid and alanine. The DNA G+C content is 67.3 mol%. Based on its distinctive phenotypic, phylogenetic, and chemotaxonomic characteristics, an-chi-1 T represents a novel species of the genus Cellulomonas, for which the name Cellulomonas macrotermitis sp. nov. is proposed. The type strain is an-chi-1 T (= JCM 31923 T  = CICC 24195 T ).

  19. Cellulomonas phragmiteti sp. nov., a cellulolytic bacterium isolated from reed (Phragmites australis) periphyton in a shallow soda pond.

    Science.gov (United States)

    Rusznyák, Anna; Tóth, Erika M; Schumann, Peter; Spröer, Cathrin; Makk, Judit; Szabó, Gitta; Vladár, Péter; Márialigeti, Károly; Borsodi, Andrea K

    2011-07-01

    An alkalitolerant and moderately halophilic strain, designated KB23(T), characterized by optimal growth at pH 8.0-9.0 and in the presence of 5-7 % (w/v) NaCl, was isolated from a reed (Phragmites australis) periphyton sample originating from an extremely shallow, alkaline soda pond located in Hungary. Cells of strain KB23(T) were Gram-stain-positive, motile straight rods. Strain KB23(T) was facultatively anaerobic, catalase-positive, oxidase-negative and contained peptidoglycan type A4β (L-Orn-D-Asp). MK-9(H4) was the predominant isoprenoid quinone and anteiso-C(15 : 0), C(16 : 0) and anteiso-C(15 : 1) were the major cellular fatty acids. The DNA G+C content of strain KB23(T) was 74.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that this strain belongs to the genus Cellulomonas and that it is related most closely to Cellulomonas flavigena DSM 20109(T) (97.35 % similarity), Cellulomonas terrae DB5(T) (96.81 %), Cellulomonas iranensis O(T) (96.75), Cellulomonas chitinilytica X.bu-b(T) (96.60 %), Cellulomonas persica I(T) (96.53 %), Cellulomonas composti TR7-06(T) (96.45 %), Cellulomonas biazotea DSM 20112(T) (96.34 %) and Cellulomonas fimi DSM 20113(T) (96.20 %). According to these results, together with DNA-DNA hybridization and physiological data, strain KB23(T) is considered to represent a novel species of the genus Cellulomonas, for which the name Cellulomonas phragmiteti sp. nov. is proposed. The type strain is KB23(T) ( = DSM 22512(T)  = NCAIM B002303(T)).

  20. Acetoanaerobium pronyense sp. nov., an anaerobic alkaliphilic bacterium isolated from a carbonate chimney of the Prony Hydrothermal Field (New Caledonia).

    Science.gov (United States)

    Bes, Méline; Merrouch, Mériem; Joseph, Manon; Quéméneur, Marianne; Payri, Claude; Pelletier, Bernard; Ollivier, Bernard; Fardeau, Marie-Laure; Erauso, Gaël; Postec, Anne

    2015-08-01

    A novel anaerobic bacterial strain, ST07-YET, was isolated from a carbonate chimney of the Prony Hydrothermal Field (PHF) in New Caledonia. Cells were Gram-stain-positive, straight rods (0.7-0.8 × 3.0-5.0 μm) and motile by means of lateral flagella. Strain ST07-YET was mesophilic (optimum 35 °C), moderately alkaliphilic and halotolerant (optimum pH 8.7 and 5 g l- 1 NaCl). Elemental sulfur, sulfate, thiosulfate, sulfite, nitrate and nitrite were not used as terminal electron acceptors. Yeast extract, peptone, tryptone, Casamino acids, crotonate, pyruvate, galactose, maltose, sucrose, ribose, trehalose and glucose were used as carbon sources. Glucose fermentation led to acetate, H2 and CO2 formation. Arginine, serine, histidine, lysine, methionine and cysteine improved growth, but the Stickland reaction was negative for the combinations of amino acids tested. The major metabolic products from yeast extract fermentation were H2, CO2, acetate, butyrate, isobutyrate, isovalerate and propionate. The predominant cellular fatty acids were C16  :  0, C16  :  1cis9, C14  :  0 and C16  :  1cis7 (>5 % of total fatty acids). The G+C content of the genomic DNA was 32.9 mol%. Phylogenetic analysis revealed that strain ST07-YET was most closely related to Clostridium sticklandii DSM 519T and Acetoanaerobium noterae NOT-3T (96.7 % and 96.8 % 16S rRNA gene sequence similarity, respectively). On the basis of phylogenetic, chemotaxonomic and physiological properties, strain ST07-YET is proposed to represent a novel species of the genus Acetoanaerobium (order Clostridiales, phylum Firmicutes) with the name Acetoanaerobium pronyense sp. nov. The type strain is ST07-YET ( = DSM 27512T = JCM 19400T).

  1. Microbacterium ginsengiterrae sp. nov., a beta-glucosidase-producing bacterium isolated from soil of a ginseng field.

    Science.gov (United States)

    Kim, Yeon-Ju; Kim, Myung Kyum; Bui, Thi Phuong Nam; Kim, Ho-Bin; Srinivasan, Sathiyaraj; Yang, Deok-Chun

    2010-12-01

    Strain DCY37(T) was isolated from a soil sample of a ginseng field in the Republic of Korea and characterized in order to determine its taxonomic position. Cells were Gram-staining-positive, heterotrophic, strictly aerobic, non-motile short rods. 16S rRNA gene sequence analysis revealed that strain DCY37(T) belongs to the genus Microbacterium. According to 16S rRNA gene sequence analysis, it is closely related to Microbacterium aerolatum DSM 14217(T) (98.8 %), Microbacterium hydrocarbonoxydans DSM 16089(T) (98.5 %), Microbacterium natoriense JCM 12611(T) (98.5 %), Microbacterium foliorum (98.4 %) and Microbacterium phyllosphaerae (98.3 %). However, DNA-DNA hybridization studies showed reassociation values of less than 70 % between representative strains and DCY37(T). The DNA G+C content was 64.5 mol%. Strain DCY37(T) possessed chemotaxonomic markers that were consistent with classification in the genus Microbacterium, i.e. MK-12 and MK-13 as the major menaquinones and anteiso-C(15 : 0), anteiso-C(17 : 0) and iso-C(16 : 0) as the predominant cellular fatty acids. The major cell wall sugars were ribose, xylose and galactose. The diamino acid in cell-wall hydrolysates of strain DCY37(T) was ornithine and major cell-wall amino acids were alanine, glycine, d-glutamic acid and serine. The major polar lipids were glycolipid, phosphatidylglycerol, diphosphatidylglycerol and unknown aminolipids. Based on these data, DCY37(T) (=KCTC 19526(T) =JCM 15516(T)) should be classified as the type strain of a novel species of the genus Microbacterium, for which the name Microbacterium ginsengiterrae sp. nov. is proposed.

  2. Rhizobium flavum sp. nov., a triazophos-degrading bacterium isolated from soil under the long-term application of triazophos.

    Science.gov (United States)

    Gu, Tao; Sun, Li Na; Zhang, Jun; Sui, Xin Hua; Li, Shun Peng

    2014-06-01

    A Gram-stain-negative, non-motile, pale yellow, rod-shaped bacterial strain, YW14(T), was isolated from soil and its taxonomic position was investigated by a polyphasic study. Strain YW14(T) did not form nodules on three different legumes, and the nodD and nifH genes were not detected by PCR. Strain YW14(T) contained Q-10 as the predominant ubiquinone. The major cellular fatty acid was C(18 : 1)ω7c. Phylogenetic analyses based on 16S rRNA gene sequences and seven housekeeping gene sequences (recA, atpD, glnII, gyrB, rpoB, dnaK and thrC) showed that strain YW14(T) belonged to the genus Rhizobium. Strain YW14(T) showed 16S rRNA gene sequence similarity of 93.4-97.3% to the type strains of recognized species of the genus Rhizobium. DNA-DNA relatedness between strain YW14(T) and the type strains of Rhizobium sullae IS123(T) and Rhizobium yanglingense CCBAU 71623(T) was 19.6-25.7%, indicating that strain YW14(T) was distinct from them genetically. Strain YW14(T) could also be differentiated from these phylogenetically related species of the genus Rhizobium by various phenotypic properties. On the basis of phenotypic properties, phylogenetic distinctiveness and genetic data, strain YW14(T) is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium flavum sp. nov. is proposed. The type strain is YW14(T) ( = KACC 17222(T) = CCTCC AB2013042(T)). © 2014 IUMS.

  3. Arsenicicoccus dermatophilus sp. nov., a hypha-forming bacterium isolated from the skin of greater flamingos (Phoenicopterus roseus) with pododermatitis.

    Science.gov (United States)

    Gobeli, Stefanie; Thomann, Andreas; Wyss, Fabia; Kuehni-Boghenbor, Kathrin; Brodard, Isabelle; Perreten, Vincent

    2013-11-01

    Dermatophilus-like bacteria were observed in histological examinations of samples of diseased foot skin from greater flamingos (Phoenicopterus roseus) living in zoological gardens in Switzerland. When grown on TSA-SB containing polymyxin B, the bacteria isolated from these skin samples formed hyphae, as is typical for Dermatophilus congolensis, but these bacteria were non-haemolytic. The closest relatives based on 16S rRNA gene sequences were the two members of the genus Arsenicicoccus, Arsenicicoccus bolidensis and Arsenicicoccus piscis. A representative of the isolated strains shared 34.3 % DNA-DNA relatedness with the type strain of A. bolidensis, 32.3 % with the type strain of A. piscis and 34.5 % with the type strain of D. congolensis, demonstrating that these strains do not belong to any of these species. The phenotypic characteristics differed from those of members of the genus Arsenicicoccus as well as from those of D. congolensis. The G+C content of strain KM 894/11(T) was 71.6 mol%. The most abundant fatty acids were iso-C15 : 0, summed feature 3 (including C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C18 : 1ω9c. MK-8(H4) was the predominant menaquinone. Cell-wall structure analysis revealed that the peptidoglycan type was A3γ ll-Dpm-Gly (type A41.1). Based on genotypic and chemotaxonomic characteristics, the isolated strains represent a novel species within the genus Arsenicicoccus, for which the name Arsenicicoccus dermatophilus sp. nov. is proposed. The type strain is KM 894/11(T) ( = DSM 25571(T) = CCUG 62181(T) = CCOS 690(T)), and strain KM 1/12 ( = DSM 25572 = CCUG 62182 = CCOS 691) is a reference strain.

  4. Agrobacterium salinitolerans sp. nov., a saline-alkaline-tolerant bacterium isolated from root nodule of Sesbania cannabina.

    Science.gov (United States)

    Yan, Jun; Li, Yan; Yan, Hui; Chen, Wen Feng; Zhang, Xiaoxia; Wang, En Tao; Han, Xiao Zeng; Xie, Zhi Hong

    2017-06-01

    Two Gram-staining-negative, aerobic bacteria (YIC 5082T and YIC4104) isolated from root nodules of Sesbania cannabina grown in a high-salt and alkaline environment were identified as a group in the genus Agrobacterium because they shared 100 and 99.7 % sequence similarities of 16S rRNA and recA+atpD genes, respectively. These two strains showed 99.2/100 % and 93.9/95.4 % 16S rRNA and recA+atpD gene sequence similarities to Agrobacterium radiobacter LMG140T and Agrobacterium. pusense NRCPB10T, respectively. The average nucleotide identities (ANI) of genome sequences were 89.95 % or lower between YIC 5082T and the species of the genus Agrobacterium examined. Moreover, these two test strains formed a unique nifH lineage deeply separated from other rhizobia. Although the nodC gene was not detected in YIC 5082T and YIC4104, they could form effective root nodules on S. cannabina plants. The main cellular fatty acids in YIC 5082T were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), C19 : 0cyclo ω8c, summed feature 2 (C12 : 0 aldehyde/unknown equivalent chain length 10.9525) and C16 : 0. The DNA G+C content of YIC 5082T was 59.3 mol%. The failure to utilize d-sorbitol as a carbon source distinguished YIC 5082T from the type strains of related species. YIC 5082T could grow in presence of 5.0 % (w/v) NaCl and at a pH of up to 10.0. Based on results regarding the genetic and phenotypic properties of YIC 5082T and YIC4104 the name Agrobacterium salinitolerans sp. nov. is proposed and YIC 5082T (=HAMBI 3646T=LMG 29287T) is designed as the type strain.

  5. Cupriavidus malaysiensis sp. nov., a novel poly(3-hydroxybutyrate-co-4-hydroxybutyrate) accumulating bacterium isolated from the Malaysian environment.

    Science.gov (United States)

    Ramachandran, Hema; Shafie, Nur Asilla Hani; Sudesh, Kumar; Azizan, Mohamad Noor; Majid, Mohamad Isa Abdul; Amirul, Al-Ashraf Abdullah

    2017-10-11

    Bacterial classification on the basis of a polyphasic approach was conducted on three poly(3 hydroxybutyrate-co-4-hydroxybutyrate) [P(3HB-co-4HB)] accumulating bacterial strains that were isolated from samples collected from Malaysian environments; Kulim Lake, Sg. Pinang river and Sg. Manik paddy field. The Gram-negative, rod-shaped, motile, non-sporulating and non-fermenting bacteria were shown to belong to the genus Cupriavidus of the Betaproteobacteria on the basis of their 16S rRNA gene sequence analyses. The sequence similarity value with their near phylogenetic neighbour, Cupriavidus pauculus LMG3413T, was 98.5%. However, the DNA-DNA hybridization values (8-58%) and ribotyping analysis both enabled these strains to be differentiated from related Cupriavidus species with validly published names. The RiboPrint patterns of the three strains also revealed that the strains were genetically related even though they displayed a clonal diversity. The major cellular fatty acids detected in these strains included C15:0 ISO 2OH/C16:1 ω7c, hexadecanoic (16:0) and cis-11-octadecenoic (C18:1 ω7c). Their G+C contents ranged from 68.0  to 68.6 mol%, and their major isoprenoid quinone was Ubiquinone Q-8. Of these three strains, only strain USMAHM13 (= DSM 25816 = KCTC 32390) was discovered to exhibit yellow pigmentation that is characteristic of the carotenoid family. Their assembled genomes also showed that the three strains were not identical in terms of their genome sizes that were 7.82, 7.95 and 8.70 Mb for strains USMAHM13, USMAA1020 and USMAA2-4, respectively, which are slightly larger than that of Cupriavidus necator H16 (7.42 Mb). The average nucleotide identity (ANI) results indicated that the strains were genetically related and the genome pairs belong to the same species. On the basis of the results obtained in this study, the three strains are considered to represent a novel species for which the name Cupriavidus malaysiensis sp. nov. is proposed. The

  6. Removal of Soluble Strontium via Incorporation into Biogenic Carbonate Minerals by Halophilic Bacterium Bacillus sp. Strain TK2d in a Highly Saline Solution.

    Science.gov (United States)

    Horiike, Takumi; Dotsuta, Yuma; Nakano, Yuriko; Ochiai, Asumi; Utsunomiya, Satoshi; Ohnuki, Toshihiko; Yamashita, Mitsuo

    2017-10-15

    Radioactive strontium ( 90 Sr) leaked into saline environments, including the ocean, from the Fukushima Daiichi Nuclear Power Plant after a nuclear accident. Since the removal of 90 Sr using general adsorbents (e.g., zeolite) is not efficient at high salinity, a suitable alternative immobilization method is necessary. Therefore, we incorporated soluble Sr into biogenic carbonate minerals generated by urease-producing microorganisms from a saline solution. An isolate, Bacillus sp. strain TK2d, from marine sediment removed >99% of Sr after contact for 4 days in a saline solution (1.0 × 10 -3 mol liter -1 of Sr, 10% marine broth, and 3% [wt/vol] NaCl). Transmission electron microscopy and energy-dispersive X-ray spectroscopy showed that Sr and Ca accumulated as phosphate minerals inside the cells and adsorbed at the cell surface at 2 days of cultivation, and then carbonate minerals containing Sr and Ca developed outside the cells after 2 days. Energy-dispersive spectroscopy revealed that Sr, but not Mg, was present in the carbonate minerals even after 8 days. X-ray absorption fine-structure analyses showed that a portion of the soluble Sr changed its chemical state to strontianite (SrCO 3 ) in biogenic carbonate minerals. These results indicated that soluble Sr was selectively solidified into biogenic carbonate minerals by the TK2d strain in highly saline environments. IMPORTANCE Radioactive nuclides ( 134 Cs, 137 Cs, and 90 Sr) leaked into saline environments, including the ocean, from the Fukushima Daiichi Nuclear Power Plant accident. Since the removal of 90 Sr using general adsorbents, such as zeolite, is not efficient at high salinity, a suitable alternative immobilization method is necessary. Utilizing the known concept that radioactive 90 Sr is incorporated into bones by biomineralization, we got the idea of removing 90 Sr via incorporation into biominerals. In this study, we revealed the ability of the isolated ureolytic bacterium to remove Sr under high

  7. Marinilactibacillus psychrotolerans gen. nov., sp. nov., a halophilic and alkaliphilic marine lactic acid bacterium isolated from marine organisms in temperate and subtropical areas of Japan.

    Science.gov (United States)

    Ishikawa, Morio; Nakajima, Kazuyuki; Yanagi, Miyoko; Yamamoto, Yasushi; Yamasato, Kazuhide

    2003-05-01

    A novel marine lactic acid rod bacterium has been described for eight strains isolated from living and decomposing marine organisms collected from temperate and subtropical areas of Japan. The isolates were Gram-positive, catalase-negative, non-sporulating and motile with peritrichous flagella. They were slightly halophilic, highly halotolerant and alkaliphilic; the optimum NaCl concentration for growth was 2.0-3.75% (w/v) with a range from 0 to 17.0-20.5% (depending on the strain); the optimum pH was between 8.0 and 9.5 with a range from 6.0 to 10.0. They were psychrotolerant, growing well at -1.8 degrees C with a maximum at 40-45 degrees C and the optimum at 37-40 degrees C. Lactate yields were 87-100% per consumed glucose; the residual products were formate, acetate and ethanol with a molar ratio of approximately 2 : 1 : 1. The product composition was markedly affected by the pH of fermentation medium; at higher pH, the yield of lactate decreased (60-65% at pH 9.0) and that of other products increased conversely. The cell-wall peptidoglycan type was type A4beta, Orn-D-Glu, whereas that of the genus Alkalibacterium, the phylogenetically closest lactic acid bacterium, was type A4beta, Orn-D-Asp. The major cellular fatty acids were C16 : 0, C16 : 1delta9, C18 : 0 and C18 : 1delta9 (oleic acid). The G + C content of the DNA was 34.6-36.2 mol%. The eight isolates were phenotypically homogeneous and formed a single genomic species. The 16S rRNA gene sequence analysis indicated that the isolates constituted an independent phylogenetic lineage within the radiation of lactic acid bacteria with 96.2% similarity to the genus Alkalibacterium. The secondary structure and the nucleotide sequence of the V6 region of the 16S rRNA were characteristic of the organism among other related lactic acid genera. On the bases of phenotypic and phylogenetic distinctness, the organism was proposed to belong to a new genus and species, Marinilactibacillus psychrotolerans gen. nov., sp. nov

  8. Mangrovibacter plantisponsor gen. nov., sp. nov., a nitrogen-fixing bacterium isolated from a mangrove-associated wild rice (Porteresia coarctata Tateoka).

    Science.gov (United States)

    Rameshkumar, N; Lang, Elke; Nair, Sudha

    2010-01-01

    A facultatively anaerobic, nitrogen-fixing bacterium, strain MSSRF40(T), was isolated from roots of mangrove-associated wild rice (Porteresia coarctata Tateoka). On the basis of 16S rRNA gene sequence similarities, strain MSSRF40(T) was shown to belong to the family Enterobacteriaceae, most closely related to Cronobacter muytjensii E603(T) (97.2 % sequence similarity), Enterobacter cloacae subsp. dissolvens LMG 2683(T) (97.1 %), E. radicincitans D5/23(T) (97.1 %) and E. ludwigii EN-119(T) (97.0 %). Sequence analysis of rpoB, gyrB and hsp60 genes showed that strain MSSRF40(T) had relatively low sequence similarity (<91, <84 and <90 %) to recognized species of different genera of the family Enterobacteriaceae and formed an independent phyletic lineage in all phylogenetic analyses using the 16S rRNA, rpoB, gyrB and hsp60 genes, clearly indicating that strain MSSRF40(T) could not be affiliated to any of the recognized genera within the family Enterobacteriaceae. The dominant cellular fatty acids were C(16 : 0), C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH and C(18 : 1)omega7c, similar to those of other members of the Enterobacteriaceae. The DNA G+C content was 50.1 mol%. Phylogenetic distinctiveness and phenotypic differences from its phylogenetic neighbours indicated that strain MSSRF40(T) represents a novel species and genus within the family Enterobacteriaceae, for which the name Mangrovibacter plantisponsor gen. nov., sp. nov. is proposed. The type strain of Mangrovibacter plantisponsor is strain MSSRF40(T) (=LMG 24236(T) =DSM 19579(T)).

  9. Sporosalibacterium tautonense sp. nov., a thermotolerant, halophilic, hydrolytic bacterium isolated from a gold mine, and emended description of the genus Sporosalibacterium.

    Science.gov (United States)

    Podosokorskaya, Olga A; Merkel, Alexander Y; Heerden, Esta van; Cason, Errol D; Kopitsyn, Dmitry S; Vasilieva, Maria; Bonch-Osmolovskaya, Elizaveta A; Kublanov, Ilya V

    2017-05-01

    A novel strictly anaerobic, thermotolerant, moderately halophilic, organotrophic bacterium, strain MRo-4T, was isolated from a sample of a microbial mat, developed under the flow of subsurface water in TauTona gold mine, South Africa. Cells of the novel isolate stained Gram-positive and were motile, spore-forming rods, 0.2-0.3 µm in width and 5-20 µm in length. Strain MRo-4T grew at 25-50 °C, at pH 7.0-8.8 and at an NaCl concentration of 5-100 g l-1. The isolate was able to ferment yeast extract, peptone and mono-, oligo- and polysaccharides, including cellulose and chitin. Elemental sulfur, thiosulfate, sulfate, sulfite, nitrate, nitrite, fumarate and arsenate were not reduced. The major fatty acids were iso-C15 : 0, iso-C15 : 0 dimethyl acetyl and anteiso-C15 : 0. The G+C content of the DNA was 32.9 mol%. Phylogenetic analysis of 16S rRNA gene sequences of strain MRo-4T and its nearest relatives showed its affiliation to the genus Sporosalibacterium. Sporosalibacteriumfaouarense SOL3f37T, the only valid published representative of the genus, appeared to be its closest relative (96.8 % 16S rRNA gene sequence similarity). However, strains MRo-4T and S. faouarense SOL3f37T differed in temperature, pH and salinity ranges for growth, requirement for yeast extract and substrate profiles. Based on the phylogenetic analysis and physiological properties of the novel isolate, we propose a novel species, Sporosalibacterium tautonense sp. nov. The type strain is MRo-4T (=DSM 28179T=VKM B-2948T).

  10. Proteus cibarius sp. nov., a swarming bacterium from Jeotgal, a traditional Korean fermented seafood, and emended description of the genus Proteus.

    Science.gov (United States)

    Hyun, Dong-Wook; Jung, Mi-Ja; Kim, Min-Soo; Shin, Na-Ri; Kim, Pil Soo; Whon, Tae Woong; Bae, Jin-Woo

    2016-06-01

    A novel Proteus-like, Gram-stain-negative, facultatively anaerobic, rod-shaped bacterium, designated strain JS9T, was isolated from Korean fermented seafood, Jeotgal. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain JS9T belonged to the genus Proteus in the family Enterobacteriaceae. The highest 16S rRNA gene sequence similarity of strain JS9T was to Proteus vulgaris KCTC 2579T (98.98 %) and the genomic DNA G+C content is 39.0 mol%. DNA-DNA hybridization values were measured and strain JS9T showed Proteus. The isolate showed bacterial motility and swarming activity similar to those of pathogenic Proteus mirabilis but distinct from those of other species of the genus Proteus. The isolate grows optimally at 30 °C, at pH 7, and in the presence of 2 % (w/v) NaCl. The main respiratory quinones are ubiquinone Q-8 and Q-10, and the major cellular fatty acids are C16 : 0, summed feature 3 and summed feature 8. The polar lipids comprise phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, an unidentified amino lipid, two unidentified amino-phospholipids, and three unidentified lipids. Based on phylogenetic, phenotypic, chemotaxonomic and genotypic analyses, strain JS9T represents a novel species of the genus Proteus, for which the name Proteus cibarius sp. nov. is proposed. The type strain is JS9T (=KACC 18404T=JCM 30699T). An emended description of the genus Proteus is also provided.

  11. Aquichromatium aeriopus gen. nov., sp. nov., A Non-phototrophic Aerobic Chemoheterotrophic Bacterium, and Proposal of Aquichromatiaceae fam. nov. in the Order Chromatiales.

    Science.gov (United States)

    Yang, Liqiang; Tang, Lili; Liu, Lan; Salam, Nimaichand; Li, Wen-Jun; Zhang, Yongyu

    2017-08-01

    A gram-staining negative, non-motile, aerobic chemoheterotrophic, ovoid or short rod-shaped bacterium, designated as J89T, was isolated from a seawater sample collected from the coast of Yellow Sea in Qingdao, China. The strain grew at salinities of 1.0-6.0% (w/v) NaCl (optimum, 3.0%). Growth occurred at pH 6.0-9.0 (optimum, pH 7.0) and at 10-35 °C (optimum, 25-30 °C). The genomic DNA G+C content was determined to be 59.3 mol%. Q-8 was detected as the respiratory quinone. The major fatty acids (>10%) were summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), and C16:0. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, two unidentified phospholipids, and an unidentified polar lipid. Comparison of the 16S rRNA gene sequence indicated that the strain was most closely related (Chromatiales in the class Gammaproteobacteria. Phylogenetic analyses showed that this strain represented a distinct phylogenetic lineage in the order Chromatiales and could not be assigned to any of the defined families in the order. On the basis of low sequence similarities and differential characteristics of strain J89T from the genera of neighboring families, the strain is proposed to be a representative of a novel genus Aquichromatium gen. nov. A new family Aquichromatiaceae with the type genus Aquichromatium is proposed. Strain J89T (=MCCC 1K03281T=CMRC C2017206T) is the type strain of the type species Aquichromatium aeriopus sp. nov.

  12. Caldicellulosiruptor obsidiansis sp. nov., an anaerobic, extremely thermophilic, cellulolytic bacterium isolated from Obsidian Pool, Yellowstone National Park

    Energy Technology Data Exchange (ETDEWEB)

    Hamilton-Brehm, Scott D. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Elkins, James G. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Phelps, Tommy Joe [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Keller, Martin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Carroll, Sue L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Allman, Steve L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Podar, Mircea [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Mosher, Jennifer J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Vishnivetskaya, Tatiana A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2010-02-01

    Here, a novel, obligately anaerobic, extremely thermophilic, cellulolytic bacterium, designated OB47T, was isolated from Obsidian Pool, Yellowstone National Park, WY, USA. The isolate was a non-motile, non-spore forming, Gram-positive rod approximately 2 μm long by 0.2 μm wide and grew at temperatures between 55-85oC with the optimum at 78oC. The pH range for growth was 6.0-8.0 with values of near 7.0 being optimal. Growth on cellobiose produced the fastest specific growth rates at 0.75 hr-1. The organism also displayed fermentative growth on glucose, maltose, arabinose, fructose, starch, lactose, mannose, sucrose, galactose, xylose, arabinogalactan, Avicel, xylan, filter paper, processed cardboard, pectin, dilute acid-pretreated switchgrass and Populus. OB47T was unable to grow on mannitol, fucose, lignin, Gelrite, acetate, glycerol, ribose, sorbital, carboxymethylcellulose and casein. Yeast extract stimulated growth and thiosulfate, sulfate, nitrate, and sulfur were not reduced. Fermentation end products were mainly acetate, H2, and CO2 although lactate and ethanol were produced in 5 l batch fermentations. The G+C content of the DNA was 35 mol% and sequence analysis of the small subunit ribosomal RNA gene placed OB47T within the genus Caldicellulosiruptor. Based on its phylogenetic and phenotypic properties, the isolate is proposed to be designated Caldicellulosiruptor obsidiansis sp. nov. and OB47T is the type stain (ATCC BAA-2073).

  13. Nonlabens antarcticus sp. nov., a psychrophilic bacterium isolated from glacier ice, and emended descriptions of Nonlabens marinus Park et al. 2012 and Nonlabens agnitus Yi and Chun 2012.

    Science.gov (United States)

    Kwon, Yong Min; Yang, Sung-Hyun; Kwon, Kae Kyoung; Kim, Sang-Jin

    2014-02-01

    A Gram-negative, proteorhodopsin-containing, orange pigmented, rod-shaped and strictly aerobic bacterium, designated strain AKS622(T), was isolated from a glacier core collected from the coast of King George Island, Antarctica. 16S rRNA gene sequence analysis revealed that strain AKS622(T) was affiliated to the genus Nonlabens of the family Flavobacteriaceae and showed highest similarity to Nonlabens marinus S1-08(T) (97.9%). The level of DNA-DNA relatedness between strain AKS622(T) and N. marinus S1-08(T) was 46%. Optimal growth of strain AKS622(T) was observed at pH 7.0, at 15 °C and with 2.0% NaCl. The predominant cellular fatty acids were anteiso-C(15 : 0), iso-C(16 : 0), iso-C(16 : 0) 3-OH, C17:0 2-OH and summed feature 3 (comprising C(16 : 1)ω7c and/or C(16 : 1)ω6c). The DNA G+C content was 37.9 mol%. The major respiratory quinone was MK-6. Phosphatidylethanolamine, four unidentified glycolipids, three unidentified aminolipids and one unidentified lipid were detected as major polar lipids. On the basis of the data from this polyphasic taxonomic study, it was concluded that strain AKS622(T) represents a novel species within the genus Nonlabens, for which the name Nonlabens antarcticus sp. nov. is proposed. The type strain is AKS622(T) ( = KCCM 43019(T) = JCM 14068(T)). Emended descriptions of N. marinus Park et al. 2012 and Nonlabens agnitus Yi and Chun 2012 are given.

  14. Desulfobulbus oligotrophicus sp. nov., a sulfate-reducing and propionate-oxidizing bacterium isolated from a municipal anaerobic sewage sludge digester.

    Science.gov (United States)

    El Houari, Abdelaziz; Ranchou-Peyruse, Magali; Ranchou-Peyruse, Anthony; Dakdaki, Adrien; Guignard, Marion; Idouhammou, Lahcen; Bennisse, Rhizlane; Bouterfass, Radia; Guyoneaud, Rémy; Qatibi, Abdel-Illah

    2017-02-01

    A novel, mesophilic, strictly anaerobic, sulfate-reducing and propionate-oxidizing bacterium, strain Prop6T, was enriched and isolated from a municipal anaerobic sewage sludge digester. Cells were Gram-stain-negative, catalase-positive, oval rods, motile by means of amphitrichous flagella, non-spore-forming and contained menaquinone MK-5(H2) as the major respiratory quinone. The genomic DNA G+C content was 51.7 mol%. The optimal NaCl concentration, temperature and pH were 2-5 g l-1, 35 °C and pH 7.6, respectively. Strain Prop6T could only oxidize propionate, lactate and pyruvate (weakly) with sulfate, sulfite or thiosulfate, mainly to acetate. Strain Prop6T fermented pyruvate and lactate to acetate and propionate. The predominant cellular fatty acids were C14 : 0, C16 : 0, C16 : 1ω7, C16 : 1ω5, C17 : 1ω6 and C18 : 1ω7. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the newly isolated strain was a member of the genus Desulfobulbus, with Desulfobulbus elongatus DSM 2908T, Desulfobulbus propionicus DSM 2032T and Desulfobulbus rhabdoformis DSM 8777T as closest relatives among species with validly published names. On the basis of genotypic, phenotypic and chemotaxonomic characteristics, it is proposed that the isolate represents a novel species, Desulfobulbus oligotrophicus sp. nov. The type strain is Prop6T (=DSM 103420T=JCM 31535T).

  15. Aminobacterium thunnarium sp. nov., a mesophilic, amino acid-degrading bacterium isolated from an anaerobic sludge digester, pertaining to the phylum Synergistetes.

    Science.gov (United States)

    Hamdi, Olfa; Ben Hania, Wajdi; Postec, Anne; Bouallagui, Hassib; Hamdi, Moktar; Bonin, Patricia; Ollivier, Bernard; Fardeau, Marie-Laure

    2015-02-01

    A new Gram-staining-positive, non-sporulating, mesophilic, amino acid-degrading anaerobic bacterium, designated strain OTA 102(T), was isolated from an anaerobic sequencing batch reactor treating wastewater from cooking tuna. The cells were curved rods (0.6-2.5×0.5 µm) and occurred singly or in pairs. The strain was motile by means of one lateral flagellum. Strain OTA 102(T) grew at temperatures between 30 and 45 °C (optimum 40 °C), between pH 6.0 and 8.4 (optimum pH 7.2) and NaCl concentrations between 1 and 5 % (optimum 2 %, w/v). Strain OTA 102(T) required yeast extract for growth. Serine, threonine, glycine, cysteine, citrate, fumarate, α-ketoglutarate and pyruvate were fermented. When co-cultured with Methanobacterium formicicum as the hydrogen scavenger, strain OTA 102(T) oxidized alanine, valine, leucine, isoleucine, aspartate, tyrosine, methionine, histidine and asparagine. The genomic DNA G+C content of strain OTA 102(T) was 41.7 mol%. The main fatty acid was iso-C15 : 0. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain OTA 102(T) was related to Aminobacterium colombiense and Aminobacterium mobile (95.5 and 95.2 % similarity, respectively), of the phylum Synergistetes. On the basis of phylogenetic, genetic and physiological characteristics, strain OTA 102(T) is proposed to represent a novel species of the genus Aminobacterium, Aminobacterium thunnarium sp. nov. The type strain is OTA 102(T) ( = DSM 27500(T) = JCM 19320(T)). © 2015 IUMS.

  16. Haloferula luteola sp. nov., an endophytic bacterium isolated from the root of a halophyte, Rosa rugosa, and emended description of the genus Haloferula.

    Science.gov (United States)

    Bibi, Fehmida; Chung, Eu Jin; Yoon, Hwan Sik; Song, Geun Cheol; Jeon, Che Ok; Chung, Young Ryun

    2011-08-01

    A Gram-negative, non-spore-forming, endophytic bacterium, strain YC6886(T), was isolated from the root of a halophyte, Rosa rugosa, which inhabits coastal areas of Namhae Island off the southern coast of Korea. Cells were non-motile, obligately aerobic rods and formed pale-yellow colonies. The isolate grew at 4-32 °C (optimum 25-28 °C) and at pH 6.5-9.5 (optimum pH 7.5) and grew optimally with 2-3 % (w/v) NaCl, but NaCl was not an absolute requirement for growth. Strain YC6886(T) produced yellow carotenoid pigments. Strain YC6886(T) exhibited the highest 16S rRNA gene sequence similarity with Haloferula sargassicola MN1-1037(T) (97.4 %). Sequence similarities between strain YC6886(T) and other members of the genus Haloferula were 93.9-94.7 %. DNA-DNA relatedness between strain YC6886(T) and H. sargassicola KCTC 22202(T) and Haloferula rosea KCTC 22201(T) was 27 and 15 %, respectively. The major fatty acids were iso-C(14 : 0), C(16 : 0) and C(16 : 1)ω9c and minor components were C(14 : 0), C(18 : 0) and anteiso-C(15 : 0). The major respiratory quinone was menaquinone 9 and the DNA G+C content was 58.5 mol%. The polar lipid profile was composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown phospholipid and an unknown phosphoglycolipid. On the basis of phenotypic, chemotaxonomic, DNA-DNA hybridization and phylogenetic analysis, strain YC6886(T) represents a novel species in the genus Haloferula, for which the name Haloferula luteola sp. nov. is proposed. The type strain is YC6886(T) ( = KCTC 22447(T)  = DSM 21608(T)). An emended description of the genus Haloferula is also presented.

  17. A thermophilic, hydrogenogenic and carboxydotrophic bacterium, Calderihabitans maritimus gen. nov., sp. nov., from a marine sediment core of an undersea caldera.

    Science.gov (United States)

    Yoneda, Yasuko; Yoshida, Takashi; Yasuda, Hisato; Imada, Chiaki; Sako, Yoshihiko

    2013-10-01

    A hydrogenogenic, carboxydotrophic marine bacterium, strain KKC1(T), was isolated from a sediment core sample taken from a submerged marine caldera. Cells were non-motile, Gram-stain-negative, 1.0-3.0 µm straight rods, often observed with round endospores. Strain KKC1(T) grew at 55-68 °C, pH 5.2-9.2 and 0.8-14 % (w/v) salinity. Optimum growth occurred at 65 °C, pH 7.0-7.5 and 2.46 % salinity with a doubling time of 3.7 h. The isolate grew chemolithotrophically, producing H2 from carbon monoxide (CO) oxidation with reduction of various electron acceptors, e.g. sulfite, thiosulfate, fumarate, ferric iron and AQDS (9,10-anthraquinone 2,6-disulfonate). KKC1(T) grew heterotrophically on pyruvate, lactate, fumarate, glucose, fructose and mannose with thiosulfate as an electron acceptor. When grown mixotrophically on CO and pyruvate, C16 : 0 constituted almost half of the total cellular fatty acids. The DNA G+C content was 50.6 mol%. The 16S rRNA gene sequence of KKC1(T) was most closely related to those of members of the genus Moorella with similarity ranging from 91 to 89 %. Based on physiological and phylogenetic novelty, we propose the isolate as a representative of a new genus and novel species with the name Calderihabitans maritimus gen. nov., sp. nov.; the type strain of the type species is KKC1(T) ( = DSM 26464(T) = NBRC 109353(T)).

  18. Brevibacterium metallicus sp. nov., an endophytic bacterium isolated from roots of Prosopis laegivata grown at the edge of a mine tailing in Mexico.

    Science.gov (United States)

    Román-Ponce, Brenda; Li, Yong Hua; Vásquez-Murrieta, María Soledad; Sui, Xin Hua; Chen, Wen Feng; Estrada-de Los Santos, Paulina; Wang, En Tao

    2015-12-01

    A Gram-positive, aerobic, nonmotile strain, NM2E3(T) was identified as Brevibacterium based on the 16S rRNA gene sequence analysis and had the highest similarities to Brevibacterium jeotgali SJ5-8(T) (97.3 %). This novel bacterium was isolated from root tissue of Prosopis laegivata grown at the edge of a mine tailing in San Luis Potosí, Mexico. Its cells were non-spore-forming rods, showing catalase and oxidase activities and were able to grow in LB medium added with 40 mM Cu(2+), 72 mM As(5+) and various other toxic elements. Anteiso-C15:0 (41.6 %), anteiso-C17:0 (30 %) and iso-C15:0 (9.5 %) were the major fatty acids. MK-8(H2) (88.4 %) and MK-7(H2) (11.6 %) were the major menaquinones. The DNA G + C content of the strain NM2E3(T) was 70.8 mol % (Tm). DNA-DNA hybridization showed that the strain NM2E3(T) had 39.8, 21.7 and 20.3 % relatedness with B. yomogidense JCM 17779(T), B. jeotgali JCM 18571(T) and B. salitolerans TRM 45(T), respectively. Based on the phenotypic and genotypic analyses, the strain NM2E3(T) (=CCBAU 101093(T) = HAMBI 3627(T) = LMG 8673(T)) is reported as a novel species of the genus Brevibacterium, for which the name Brevibacterium metallicus sp. nov., is proposed.

  19. Protozoa graze on the 2,6-dichlorobenzamide (BAM)-degrading bacterium Aminobacter sp. MSH1 introduced into waterworks sand filters.

    Science.gov (United States)

    Ellegaard-Jensen, Lea; Albers, Christian N; Aamand, Jens

    2016-10-01

    Groundwater contamination by pesticide residues often leads to the closure of drinking water wells, making the development of new techniques to remediate drinking water resources of considerable interest. Pesticide-degrading bacteria were recently added to a waterworks sand filter in an attempt to remediate pesticide-polluted drinking water. The density of the introduced bacteria, however, decreased rapidly, which was partly attributed to predation by protozoa in the sand filter. This study investigated the effects of indigenous sand filter protozoa on the population density and degradation efficiency of degrader bacteria introduced into sand from a waterworks sand filter. The 2,6-dichlorobenzamide (BAM)-degrading bacterium Aminobacter sp. MSH1 was used as a model organism. The introduction of MSH1 at high cell densities was followed by a >1000-fold increase in the protozoan population size and at the same time a 29 % reduction in Aminobacter cell numbers. The protozoan population in the systems that had MSH1 added at a lower density only increased 50-fold, and a decrease in Aminobacter numbers was not detectable. Furthermore, a reduction in the number of Aminobacter and in BAM degradation efficiency was seen in flow-through sand filter columns inoculated with MSH1 and fed BAM-contaminated water, when comparing sand columns containing the indigenous microbial filter community, i.e. containing protozoa, to columns with sterilised sand. These results suggest that degrader bacteria introduced into waterworks sand filters are adversely affected by grazing from the indigenous protozoa, reducing the size of the degrader population and the sand filter degradation efficiency.

  20. Culturing and Characterization of Gut Symbiont Burkholderia spp. from the Southern Chinch Bug, Blissus insularis (Hemiptera: Blissidae).

    Science.gov (United States)

    Xu, Yao; Buss, Eileen A; Boucias, Drion G

    2016-06-01

    The phloem-feeding Southern chinch bug, Blissus insularis, harbors a high density of the exocellular bacterial symbiont Burkholderia in the lumen of specialized midgut crypts. Here we developed an organ culture method that initially involved incubating the B. insularis crypts in osmotically balanced insect cell culture medium. This approach enabled the crypt-inhabiting Burkholderia spp. to make a transition to an in vitro environment and to be subsequently cultured in standard bacteriological media. Examinations using ribotyping and BOX-PCR fingerprinting techniques demonstrated that most in vitro-produced bacterial cultures were identical to their crypt-inhabiting Burkholderia counterparts. Genomic and physiological analyses of gut-symbiotic Burkholderia spp. that were isolated individually from two separate B. insularis laboratory colonies revealed that the majority of individual insects harbored a single Burkholderia ribotype in their midgut crypts, resulting in a diverse Burkholderia community within each colony. The diversity was also exhibited by the phenotypic and genotypic characteristics of these Burkholderia cultures. Access to cultures of crypt-inhabiting bacteria provides an opportunity to investigate the interaction between symbiotic Burkholderia spp. and the B. insularis host. Furthermore, the culturing method provides an alternative strategy for establishing in vitro cultures of other fastidious insect-associated bacterial symbionts. An organ culture method was developed to establish in vitro cultures of a fastidious Burkholderia symbiont associated with the midgut crypts of the Southern chinch bug, Blissus insularis The identities of the resulting cultures were confirmed using the genomic and physiological features of Burkholderia cultures isolated from B. insularis crypts, showing that host insects maintained the diversity of Burkholderia spp. over multiple generations. The availability of characterized gut-symbiotic Burkholderia cultures provides

  1. Desulfitobacterium sp strain PCE1, an anaerobic bacterium that can grow by reductive dechlorination of tetrachloroethene or ortho-chlorinated phenols

    NARCIS (Netherlands)

    Gerritse, J; Renard, [No Value; Gomes, TMP; Lawson, PA; Collins, MD; Gottschal, JC

    A strictly anaerobic bacterium, strain PCE1, was isolated from a tetrachloroethene-dechlorinating enrichment culture. Cells of the bacterium were motile curved rods, with approximately four lateral flagella. They possessed a gram-positive type of cell wall and contained cytochrome c. Optimum growth

  2. Dehalobacter restrictus gen. nov. and sp. nov., a strictly anaerobic bacterium that reductively dechlorinates tetra- and trichloroethene in an anaerobic respiration

    NARCIS (Netherlands)

    Holliger, C; Hahn, D; Harmsen, H; Ludwig, W; Schumacher, W; Tindall, B; Vazquez, F; Weiss, N; Zehnder, AJB

    The highly enriched anaerobic bacterium that couples the reductive dechlorination of tetrachloroethene to growth, previously referred to as PER-K23, was obtained in pure culture and characterized. The bacterium, which does not form spores, is a small, gram-negative rod with one lateral flagellum. It

  3. Growth and cesium uptake responses of Phytolacca americana Linn. and Amaranthus cruentus L. grown on cesium contaminated soil to elevated CO{sub 2} or inoculation with a plant growth promoting rhizobacterium Burkholderia sp. D54, or in combination

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Shirong, E-mail: tangshir@hotmail.com [Centre for Research in Ecotoxicology and Environmental Remediation, Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191 (China); Key Laboratory of Production Environment and Agro-product Safety of Ministry of Agriculture, Tianjin (China); Liao, Shangqiang; Guo, Junkang; Song, Zhengguo; Wang, Ruigang [Centre for Research in Ecotoxicology and Environmental Remediation, Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191 (China); Key Laboratory of Production Environment and Agro-product Safety of Ministry of Agriculture, Tianjin (China); Zhou, Xiaomin [Plant Science Department, McGill University, Macdonald Campus, 21111 Lakeshore Road, Ste. Anne de Bellevue, Quebec, Canada H9X 3V9 (Canada)

    2011-12-30

    Highlights: Black-Right-Pointing-Pointer Elevated CO{sub 2} and microbial inoculation, alone or in combination, significantly promoted growth of P. americana, and A. cruentus. Black-Right-Pointing-Pointer Total tissue Cs in plants was significantly increased. Black-Right-Pointing-Pointer A. cruentus had higher tissue Cs concentration, Cs transfer factors and concentration ratios than P. americana. Black-Right-Pointing-Pointer The two plants had slightly different contents of antioxidant enzymes. Black-Right-Pointing-Pointer Combined effects of elevated CO{sub 2} and microbial inoculation can be explored for CO{sub 2}- and microbe-assisted phytoextraction technology. - Abstract: Growth and cesium uptake responses of plants to elevated CO{sub 2} and microbial inoculation, alone or in combination, can be explored for clean-up of contaminated soils, and this induced phytoextraction may be better than the natural process. The present study used open-top chambers to investigate combined effects of Burkholderia sp. D54 inoculation and elevated CO{sub 2} (860 {mu}L L{sup -1}) on growth and Cs uptake by Phytolacca americana and Amaranthus cruentus grown on soil spiked with various levels of Cs (0-1000 mg kg{sup -1}). Elevated CO{sub 2} and bacterial inoculation, alone or in combination, significantly increased biomass production with increased magnitude, ranging from 22% to 139% for P. americana, and 14% to 254% for A. cruentus. Total tissue Cs in both plants was significantly greater for bacterial inoculation treatment singly, and combined treatments of bacterial inoculation and elevated CO{sub 2} than for the control treatment in most cases. Regardless of CO{sub 2} concentrations and bacterial inoculation, A. cruentus had higher tissue Cs concentration, Cs transfer factors and concentration ratios than P. americana, but they had slightly different contents of antioxidant enzymes. It is concluded that combined effects of elevated CO{sub 2} and microbial inoculation with

  4. Preparation of Burkholderia pseudomallei Polysaccharide-CRM197 Conjugate, a Potential Vaccine Candidate for Glanders and Melioidosis

    Science.gov (United States)

    2005-10-01

    Glanders Glanders is an infectious disease that is caused by the bacterium Burkholderia mallei The types of infection include localized, pus- forming...Glanders Burkholderia mallei and B. pseudomallei are the causative agents for glanders and melioidosis, respectively Both of these organisms have... virulence factor : – Dave DeShazer prepared a capsule mutant (DD3008) and demonstrated that the mouse aerosol LD50 was at least 103 times greater than the

  5. Study of the mode of action of a polygalacturonase from the phytopathogen Burkholderia cepacia

    DEFF Research Database (Denmark)

    Massa, C.; Clausen, Mads Hartvig; Stojan, J.

    2007-01-01

    We have recently isolated and heterologously expressed BcPeh28A, an endopolygalacturonase from the phytopathogenic Gram-negative bacterium Burkholderia cepacia. Endopolygalacturonases belong to glycoside hydrolase family 28 and are responsible for the hydrolysis of the non-esterified regions of p...

  6. Competition between Burkholderia pseudomallei and B. thailandensis.

    Science.gov (United States)

    Ngamdee, Wikanda; Tandhavanant, Sarunporn; Wikraiphat, Chanthiwa; Reamtong, Onrapak; Wuthiekanun, Vanaporn; Salje, Jeanne; Low, David A; Peacock, Sharon J; Chantratita, Narisara

    2015-03-03

    Burkholderia pseudomallei is a Gram-negative bacterium that causes melioidosis, an often fatal disease in tropical countries. Burkholderia thailandensis is a non-virulent but closely related species. Both species are soil saprophytes but are almost never isolated together. We identified two mechanisms by which B. pseudomallei affects the growth of B. thailandensis. First, we found that six different isolates of B. pseudomallei inhibited the growth of B. thailandensis on LB agar plates. Second, our results indicated that 55% of isolated strains of B. pseudomallei produced a secreted compound that inhibited the motility but not the viability of B. thailandensis. Analysis showed that the active compound was a pH-sensitive and heat-labile compound, likely a protein, which may affect flagella processing or facilitate their degradation. Analysis of bacterial sequence types (STs) demonstrated an association between this and motility inhibition. The active compound was produced from B. pseudomallei during the stationary growth phase. Taken together, our results indicate that B. pseudomallei inhibits both the growth and motility of its close relative B. thailandensis. The latter phenomenon appears to occur via a previously unreported mechanism involving flagellar processing or degradation.

  7. sp

    African Journals Online (AJOL)

    Vihar

    adopted as the first line drug. SP has few untoward effects if used carefully in therapeutic doses. Nausea, vomiting, generalized body weakness; diarrhea, skin rashes and hematological reactions are some of the associated side effects. The drug can cause severe skin reactions such as Steven Johnson's syndrome. This.

  8. Phylogeography of Burkholderia pseudomallei Isolates, Western Hemisphere.

    Science.gov (United States)

    Gee, Jay E; Gulvik, Christopher A; Elrod, Mindy G; Batra, Dhwani; Rowe, Lori A; Sheth, Mili; Hoffmaster, Alex R

    2017-07-01

    The bacterium Burkholderia pseudomallei causes melioidosis, which is mainly associated with tropical areas. We analyzed single-nucleotide polymorphisms (SNPs) among genome sequences from isolates of B. pseudomallei that originated in the Western Hemisphere by comparing them with genome sequences of isolates that originated in the Eastern Hemisphere. Analysis indicated that isolates from the Western Hemisphere form a distinct clade, which supports the hypothesis that these isolates were derived from a constricted seeding event from Africa. Subclades have been resolved that are associated with specific regions within the Western Hemisphere and suggest that isolates might be correlated geographically with cases of melioidosis. One isolate associated with a former World War II prisoner of war was believed to represent illness 62 years after exposure in Southeast Asia. However, analysis suggested the isolate originated in Central or South America.

  9. Low nitrogen stress stimulating the indole-3-acetic acid biosynthesis of Serratia sp. ZM is vital for the survival of the bacterium and its plant growth-promoting characteristic.

    Science.gov (United States)

    Ouyang, Liming; Pei, Haiyan; Xu, Zhaohui

    2017-04-01

    Serratia sp. ZM is a plant growth-promoting (PGP) bacterial strain isolated from the rhizospheric soil of Populus euphratica in northwestern China. In this study, low nitrogen supply significantly stimulated the production of indole-3-acetic acid (IAA) in Serratia sp.ZM. The inoculation of the bacterium to wheat seedlings improved plant growth compared with the uninoculated group, and the stimulating effect was more prominent under low nitrogen stress. Inactivation of the predicted key gene in the IAA biosynthesis pathway impaired IAA production and significantly hampered mutant growth in poor medium. Furthermore, the IAA-deficient mutant lost the PGP effect under either normal or low nitrogen conditions in plant experiments. This study revealed the significant impact of environmental nitrogen levels on IAA production in the PGP strain and the vital effect of IAA on resistance physiology of both the bacterium and host plant. The characteristics of Serratia sp. ZM also indicated its application potential as a biofertilizer for plants, especially those suffering from poor nitrogen soil.

  10. Reclassification of Bacillus saliphilus as Alkalicoccus saliphilus gen. nov., comb. nov., and description of Alkalicoccus halolimnae sp. nov., a moderately halophilic bacterium isolated from a salt lake.

    Science.gov (United States)

    Zhao, Baisuo; Lu, Weidong; Zhang, Shanshan; Liu, Kang; Yan, Yanchun; Li, Jun

    2017-05-01

    A Gram-stain-positive, cocci-shaped, non-spore-forming and moderately halophilic bacterium, designed BZ-SZ-XJ29T, was isolated from a salt lake of China. On the basis of 16S rRNA gene sequence similarity, the closest phylogenetic relatives were Bacillus saliphilus 6AGT (97.3 % 16S rRNA gene sequence similarity) and five other species of the genus Bacillus(95.4-96.3 %). However, strain BZ-SZ-XJ29T shared only 89.5 % 16S rRNA gene sequence similarity with Bacillus subtilis subsp. subtilis DSM 10T, indicating that this isolate might not be a member of the genus Bacillus. The genomic DNA G+C content was 40.0 mol% (Tm). The DNA-DNA relatedness value with B. saliphilus 6AGT was 45±2 %. Strain BZ-SZ-XJ29T formed yellow pigment and grew in the presence of 0.74-4.15 M Na+ [optimum 1.42-2.10 M Na+], at pH 6.0-10.5 (optimum pH 7.5), and at 5-41 °C (optimum 33 °C). The predominant (>10 %) fatty acids were anteiso-C15 : 0 and anteiso-C15 : 0. The dominant polar lipids consisted of diphosphatidylglycerol and the respiratory quinone was menaquinone-7 (MK-7). The peptidoglycan type of the cell wall was A1γ, based on meso-diaminopimelic acid as the diagnostic diamino acid. On the basis of the combined phylogenetic data, phenotypic features and chemotaxonomic properties, it is proposed that B. saliphilus and strain BZ-SZ-XJ29T should be assigned to a single novel genus as two separate species. Bacillus. saliphilus is reclassified in a new genus, Alkalicoccus gen. nov., as Alkalicoccus saliphilus comb. nov., and is the type species of the new genus; the type strain of the type species is 6AGT (=DSM 15402T=ATCC BAA-957T). Strain BZ-SZ-XJ29T (=DSM 29191T=JCM 30193T=CGMCC 1.12936T) is placed in the genus Alkalicoccus as a novel species, Alkalicoccus halolimnae sp. nov.

  11. Defluviitalea raffinosedens sp. nov., a thermophilic, anaerobic, saccharolytic bacterium isolated from an anaerobic batch digester treating animal manure and rice straw.

    Science.gov (United States)

    Ma, Shichun; Huang, Yan; Wang, Cong; Fan, Hui; Dai, Lirong; Zhou, Zheng; Liu, Xing; Deng, Yu

    2017-05-01

    A thermophilic, anaerobic, fermentative bacterium, strain A6T, was obtained from an anaerobic batch digester treating animal manure and rice straw. Cells were Gram-stain-positive, slightly curved rods with a size of 0.6-1×2.5-8.2 µm, non-motile and produced terminal spores. The temperature, pH and NaCl concentration ranges for growth were 40-60 °C, 6.5-8.0 and 0-15.0 g l-1, with optimum growth noted at 50-55 °C, pH 7.5 and in the absence of NaCl, respectively. Yeast extract was required for growth. d-Glucose, maltose, d-xylose, d-galactose, d-fructose, d-ribose, lactose, raffinose, sucrose, d-arabinose, cellobiose, d-mannose and yeast extract were used as carbon and energy sources. The fermentation products from glucose were ethanol, lactate, acetate, propionate, butyrate, valerate, iso-butyrate, iso-valerate, H2 and CO2. The G+C content of the genomic DNA was 36.6 mol%. The predominant fatty acids were C16 : 0, iso-C17 : 1, C14 : 0, C16 : 1ω7c, C16 : 0 N-alcohol and C13 : 0 3-OH. Respiratory quinones were not detected. The polar lipid profile comprised phosphoglycolipids, phospholipids, glycolipids, a diphosphatidylglycerol, a phosphatidylglycerol and an unidentified lipid. Phylogenetic analyses of the 16S rRNA gene sequence indicated that the strain was closely related to Defluviitalea saccharophila DSM 22681T with a similarity of 96.0 %. Based on the morphological, physiological and taxonomic characterization, strain A6T is considered to represent a novel species of the genus Defluviitalea, for which the name Defluviitalea raffinosedens sp. nov. is proposed. The type strain is A6T (=DSM 28090T=ACCC 19951T).

  12. Moorella humiferrea sp. nov., a thermophilic, anaerobic bacterium capable of growth via electron shuttling between humic acid and Fe(III).

    Science.gov (United States)

    Nepomnyashchaya, Y N; Slobodkina, G B; Baslerov, R V; Chernyh, N A; Bonch-Osmolovskaya, E A; Netrusov, A I; Slobodkin, A I

    2012-03-01

    An anaerobic, thermophilic, spore-forming bacterium (strain 64-FGQ(T)) was isolated from a terrestrial hydrothermal spring from the Kamchatka peninsula, Russia. This strain utilized lactate as an electron donor, insoluble poorly crystalline Fe(III) oxide incorporated into alginate beads as a potential electron acceptor and 9,10-anthraquinone-2,6-disulfonate (AQDS) as an electron-shuttling compound. Vegetative cells of strain 64-FGQ(T) were Gram-stain-positive, peritrichously flagellated, motile, straight rods, 0.3-0.5 µm in diameter and 2.0-5.0 µm long, growing singly or forming short chains. Cells formed round refractive endospores in terminal swollen sporangia. The temperature range for growth was 46-70 °C, with an optimum at 65 °C. The pH range for growth was 5.5-8.5, with an optimum at pH 7.0. The substrates utilized by strain 64-FGQ(T) in the presence of AQDS as an electron acceptor included lactate, malate, succinate, glycerol and yeast extract. The strain fermented galactose, fructose, maltose, sucrose, pyruvate and peptone. Strain 64-FGQ(T) used AQDS, humic acid, thiosulfate, nitrate and perchlorate as electron acceptors for growth. Fe(III) was not directly reduced, but strain 64-FGQ(T) was able to grow and reduce Fe(III) oxide in the presence of small amounts of AQDS or humic acid as electron-shuttling compounds. The G+C content of the DNA of strain 64-FGQ(T) was 51 mol%. 16S rRNA gene sequence analysis placed the isolate in the genus Moorella, with the type strain of Moorella glycerini as its closest relative (97.2% similarity). Based on phylogenetic analysis and physiological characteristics, strain 64-FGQ(T) is considered to represent a novel species of the genus Moorella, for which the name Moorella humiferrea sp. nov. is proposed; the type strain is 64-FGQ(T) (=DSM 23265(T)=VKM B-2603(T)).

  13. Sulfuriferula thiophila sp. nov., a chemolithoautotrophic sulfur-oxidizing bacterium, and correction of the name Sulfuriferula plumbophilusWatanabe, Kojima and Fukui 2015 to Sulfuriferula plumbiphila corrig.

    Science.gov (United States)

    Watanabe, Tomohiro; Kojima, Hisaya; Fukui, Manabu

    2016-05-01

    A novel sulfur-oxidizing bacterium designated strain mst6T was isolated from spring water of Masutomi hot spring in Japan. The cells were rod-shaped (1.2-4.0 × 0.5-0.7 μm) and Gram-stain-negative. The G+C content of genomic DNA was around 52.6 mol%. The isolate possessed summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C12 : 0 as major cellular fatty acids. Strain mst6T grew by inorganic carbon fixation and oxidation of inorganic sulfur compounds with oxygen as an electron acceptor. The isolate grew over a temperature range of 5-34 °C, a NaCl concentration range of 0-110 mM and a pH range of 4.6-8.1. Optimum growth occurred at 32 °C, in the absence of NaCl and at pH 5.9-6.2. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain mst6T belongs to the family Sulfuricellaceae in the class Betaproteobacteria. The closest cultured relative was Sulfuriferula multivorans TTNT with a 16S rRNA gene sequence similarity of 97.0 %. On the basis of the data obtained in this study, strain mst6T represents a novel species of the genus Sulfuriferula, for which the name Sulfuriferula thiophila sp. nov. is proposed. The type strain is mst6T ( = NBRC 111150T = DSM 101871T). In addition, we propose correcting the name Sulfuriferula plumbophilus Watanabe, Kojima and Fukui 2015 to Sulfuriferula plumbiphila corrig. based on Rule 12c, Rule 61 and Appendix 9 of the International Code of Nomenclature of Prokaryotes.

  14. Accurate and rapid identification of the Burkholderia pseudomallei near-neighbour, Burkholderia ubonensis, using real-time PCR.

    Science.gov (United States)

    Price, Erin P; Sarovich, Derek S; Webb, Jessica R; Ginther, Jennifer L; Mayo, Mark; Cook, James M; Seymour, Meagan L; Kaestli, Mirjam; Theobald, Vanessa; Hall, Carina M; Busch, Joseph D; Foster, Jeffrey T; Keim, Paul; Wagner, David M; Tuanyok, Apichai; Pearson, Talima; Currie, Bart J

    2013-01-01

    Burkholderia ubonensis is an environmental bacterium belonging to the Burkholderia cepacia complex (Bcc), a group of genetically related organisms that are associated with opportunistic but generally nonfatal infections in healthy individuals. In contrast, the near-neighbour species Burkholderia pseudomallei causes melioidosis, a disease that can be fatal in up to 95% of cases if left untreated. B. ubonensis is frequently misidentified as B. pseudomallei from soil samples using selective culturing on Ashdown's medium, reflecting both the shared environmental niche and morphological similarities of these species. Additionally, B. ubonensis shows potential as an important biocontrol agent in B. pseudomallei-endemic regions as certain strains possess antagonistic properties towards B. pseudomallei. Current methods for characterising B. ubonensis are laborious, time-consuming and costly, and as such this bacterium remains poorly studied. The aim of our study was to develop a rapid and inexpensive real-time PCR-based assay specific for B. ubonensis. We demonstrate that a novel B. ubonensis-specific assay, Bu550, accurately differentiates B. ubonensis from B. pseudomallei and other species that grow on selective Ashdown's agar. We anticipate that Bu550 will catalyse research on B. ubonensis by enabling rapid identification of this organism from Ashdown's-positive colonies that are not B. pseudomallei.

  15. Accurate and rapid identification of the Burkholderia pseudomallei near-neighbour, Burkholderia ubonensis, using real-time PCR.

    Directory of Open Access Journals (Sweden)

    Erin P Price

    Full Text Available Burkholderia ubonensis is an environmental bacterium belonging to the Burkholderia cepacia complex (Bcc, a group of genetically related organisms that are associated with opportunistic but generally nonfatal infections in healthy individuals. In contrast, the near-neighbour species Burkholderia pseudomallei causes melioidosis, a disease that can be fatal in up to 95% of cases if left untreated. B. ubonensis is frequently misidentified as B. pseudomallei from soil samples using selective culturing on Ashdown's medium, reflecting both the shared environmental niche and morphological similarities of these species. Additionally, B. ubonensis shows potential as an important biocontrol agent in B. pseudomallei-endemic regions as certain strains possess antagonistic properties towards B. pseudomallei. Current methods for characterising B. ubonensis are laborious, time-consuming and costly, and as such this bacterium remains poorly studied. The aim of our study was to develop a rapid and inexpensive real-time PCR-based assay specific for B. ubonensis. We demonstrate that a novel B. ubonensis-specific assay, Bu550, accurately differentiates B. ubonensis from B. pseudomallei and other species that grow on selective Ashdown's agar. We anticipate that Bu550 will catalyse research on B. ubonensis by enabling rapid identification of this organism from Ashdown's-positive colonies that are not B. pseudomallei.

  16. Alteribacillus bidgolensis gen. nov., sp. nov., a moderately halophilic bacterium from a hypersaline lake, and reclassification of Bacillus persepolensis as Alteribacillus persepolensis comb. nov.

    Science.gov (United States)

    Didari, Maryam; Amoozegar, Mohammad Ali; Bagheri, Maryam; Schumann, Peter; Spröer, Cathrin; Sánchez-Porro, Cristina; Ventosa, Antonio

    2012-11-01

    A novel Gram-stain-positive, moderately halophilic bacterium, designated strain P4B(T), was isolated from water of the hypersaline Aran-Bidgol lake in Iran and characterized taxonomically by using a polyphasic approach. Cells of strain P4B(T) were non-motile rods producing ellipsoidal endospores at a central position in non-swollen sporangia. Strain P4B(T) was strictly aerobic and catalase- and oxidase-positive. It was able to grow at NaCl concentrations of 0.5-12.5% (w/v), with optimum growth occurring at 5-7.5% (w/v) NaCl. The optimum temperature and pH for growth were 35 °C and pH 7.0. On the basis of 16S rRNA gene sequence analysis, strain P4B(T) was shown to belong to the phylum Firmicutes and shared highest similarity with Bacillus persepolensis HS136(T) (97.1%) and Bacillus salarius BH169(T) (95.1%). However, it shared only 91.3% 16S rRNA gene sequence similarity with Bacillus subtilis subsp. subtilis DSM 10(T), indicating that strain P4B(T) might not be a member of the genus Bacillus. The DNA G+C content of this new isolate was 38.9 mol%. DNA-DNA hybridization experiments revealed a low level of relatedness between strain P4B(T) and B. persepolensis HS136(T) (6%). The major cellular fatty acids of strain P4B(T) were iso-C(15:0) and anteiso-C(15:0), as for B. persepolensis HS136(T) but in contrast to B. salarius DSM 16461(T) and B. subtilis subsp. subtilis DSM 10(T). Its polar lipid pattern consisted of phosphatidylglycerol, an aminoglycolipid and an unknown phospholipid. This polar lipid profile was similar to that obtained for B. persepolensis DSM 21632(T) but different from those of B. salarius DSM 16461(T) and B. subtilis subsp. subtilis DSM 10(T). The isoprenoid quinones were MK-7 (88%) and MK-8 (2%). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. All these features indicate placement of strain P4B(T) within the Firmicutes, closely related to B. persepolensis but with features clearly distinct from those of the

  17. Burkholderia pseudomallei transcriptional adaptation in macrophages

    Directory of Open Access Journals (Sweden)

    Chieng Sylvia

    2012-07-01

    Full Text Available Abstract Background Burkholderia pseudomallei is a facultative intracellular pathogen of phagocytic and non-phagocytic cells. How the bacterium interacts with host macrophage cells is still not well understood and is critical to appreciate the strategies used by this bacterium to survive and how intracellular survival leads to disease manifestation. Results Here we report the expression profile of intracellular B. pseudomallei following infection of human macrophage-like U937 cells. During intracellular growth over the 6 h infection period, approximately 22 % of the B. pseudomallei genome showed significant transcriptional adaptation. B. pseudomallei adapted rapidly to the intracellular environment by down-regulating numerous genes involved in metabolism, cell envelope, motility, replication, amino acid and ion transport system and regulatory function pathways. Reduced expression in catabolic and housekeeping genes suggested lower energy requirement and growth arrest during macrophage infection, while expression of genes encoding anaerobic metabolism functions were up regulated. However, whilst the type VI secretion system was up regulated, expression of many known virulence factors was not significantly modulated over the 6hours of infection. Conclusions The transcriptome profile described here provides the first comprehensive view of how B. pseudomallei survives within host cells and will help identify potential virulence factors and proteins that are important for the survival and growth of B. pseudomallei within human cells.

  18. Phenotypic and genomic properties of Chitinispirillum alkaliphilum gen. nov., sp. nov., a haloalkaliphilic anaerobic chitinolytic bacterium representing a novel class in the phylum fibrobacteres

    NARCIS (Netherlands)

    Sorokin, Dimitry Y.; Rakitin, Andrey L.; Gumerov, Vadim M.; Beletsky, Alexey V.; Sinninghe Damsté, Jaap S.; Mardanov, Andrey V.; Ravin, Nikolai V.

    Anaerobic enrichment from sediments of hypersaline alkaline lakes in Wadi el Natrun (Egypt) with chitin resulted in the isolation of a fermentative haloalkaliphilic bacterium, strain ACht6-1, growing exclusively with insoluble chitin as the substrate in a sodium carbonate-based medium at pH 8.5-10.5

  19. Phenotypic and genomic properties of Chitinispirillum alkaliphilum gen. nov., sp. nov., a haloalkaliphilic anaerobic chitinolytic bacterium representing a novel class in the phylum fibrobacteres

    NARCIS (Netherlands)

    Sorokin, Dimitry Y.; Rakitin, Andrey L.; Gumerov, Vadim M.; Beletsky, Alexey V.; Sinninghe Damsté, Jaap S.; Mardanov, Andrey V.; Ravin, Nikolai V.

    2016-01-01

    Anaerobic enrichment from sediments of hypersaline alkaline lakes in Wadi el Natrun (Egypt) with chitin resulted in the isolation of a fermentative haloalkaliphilic bacterium, strain ACht6-1, growing exclusively with insoluble chitin as the substrate in a sodium carbonate-based medium at pH

  20. Desulfovibrio paquesii sp. nov., a hydrogenotrophic sulfate-reducing bacterium isolated from a synthesis-gas-fed bioreactor treating zinc- and sulfate-rich wastewater

    NARCIS (Netherlands)

    Houten, van B.H.G.W.; Meulepas, R.J.W.; Doesburg, van W.; Smidt, H.; Muyzer, G.; Stams, A.J.M.

    2009-01-01

    A hydrogenotrophic, sulfate-reducing bacterium, designated strain SB1(T), was isolated from sulfidogenic sludge of a full-scale synthesis-gas-fed bioreactor used to remediate wastewater from a zinc smelter. Strain SB1(T) was found to be an abundant micro-organism in the sludge at the time of

  1. Halomonas indalinina sp.nov., a moderately halophilic bacterium isolated from a solar saltern in Cabo de Gata, Al,eria, southern Spain

    NARCIS (Netherlands)

    Cabrera, A.; Aguilera, M.; Fuentes Enriquez de Salamanca, S.; Incerti, C.; Russell, N.J.; Ramos-Cormenzana, A.; Monteoliva-Sanchez, M.

    2007-01-01

    moderately halophilic bacterium, strain CG2.1T, isolated from a solar saltern at Cabo de Gata, a wildlife reserve located in the province of Almería, southern Spain, was subjected to a polyphasic taxonomic study. This organism was an aerobic, motile, Gram-negative rod that produced orange-pigmented

  2. Lysinibacillus louembei sp. nov., a spore-forming bacterium isolated from Ntoba Mbodi, alkaline fermented leaves of cassava from the Republic of the Congo

    DEFF Research Database (Denmark)

    Ouoba, Labia Irène I.; Mbozo, Alain B. Vouidibio; Thorsen, Line

    2015-01-01

    Investigation of the microbial diversity of Ntoba Mbodi, an African food made from the alkaline fermentation of cassava leaves, revealed the presence of a Gram-positive, catalase-positive, aerobic, motile and rod-shaped endospore-forming bacterium (NM73) with unusual phenotypic and genotypic...

  3. “Nigerium massiliense” gen. nov., sp. nov., a new bacterium isolated from the gut from a patient with acute malnutrition

    Directory of Open Access Journals (Sweden)

    Sory Ibrahima Traore

    2016-09-01

    Full Text Available We propose the main characteristics of a new bacterium named “Nigerium massiliense” strain SIT5 (CSURP1302 that was isolated from the stool of a 2-year-old Nigerian child suffering from kwashiorkor, a form of severe acute malnutrition. Keywords: Culturomics, Taxonomy, Genomics, Taxono-genomics, “Nigerium massiliense”

  4. A novel mcl PHA-producing bacterium, Pseudomonas guezennei sp. nov., isolated from a 'kopara' mat located in Rangiroa, an atoll of French Polynesia.

    Science.gov (United States)

    Simon-Colin, C; Alain, K; Colin, S; Cozien, J; Costa, B; Guezennec, J G; Raguénès, G H C

    2008-02-01

    The aim of the present study was to describe an aerobic, mesophilic and heterotrophic bacterium, designated RA26, able to produce a medium-chain-length polyhydroxyalkanoate (PHA). It was isolated from a French Polynesian bacterial mat located in the atoll of Rangiroa. This micro-organism, on the basis of the phenotypical features and genotypic investigations can be clearly assigned to the Pseudomonas genus and the name of Pseudomonas guezennei is proposed. Optimal growth occurs between 33 and 37 degrees C, at a pH between 6.4 and 7.1 and at ionic strength of 15 g l(-1) of sea salts. The G+C content of DNA is 63.2%. Under laboratory conditions, this bacterium produced a novel, medium-chain-length PHA, mainly composed of 3-hydroxydecanaote (64 mol.%) and 3-hydroxyoctanoate (24 mol.%) (GC-MS, NMR) from a single nonrelated carbon substrate, i.e. glucose. The bacterium P. guezennei produces a novel PHA mcl with elastomeric properties. PHAs share physical and material properties that recommend them for application in various areas, and are considered as an alternative to nonbiodegradable plastics produced from fossil oils. In this study, we describe a new bacteria with the capability to synthesize a novel PHA with promising biotechnological applications.

  5. A gold nanoparticle-linked glycoconjugate vaccine against Burkholderia mallei.

    Science.gov (United States)

    Gregory, Anthony E; Judy, Barbara M; Qazi, Omar; Blumentritt, Carla A; Brown, Katherine A; Shaw, Andrew M; Torres, Alfredo G; Titball, Richard W

    2015-02-01

    Burkholderia mallei are Gram-negative bacteria, responsible for the disease glanders. B. mallei has recently been classified as a Tier 1 agent owing to the fact that this bacterial species can be weaponised for aerosol release, has a high mortality rate and demonstrates multi-drug resistance. Furthermore, there is no licensed vaccine available against this pathogen. Lipopolysaccharide (LPS) has previously been identified as playing an important role in generating host protection against Burkholderia infection. In this study, we present gold nanoparticles (AuNPs) functionalised with a glycoconjugate vaccine against glanders. AuNPs were covalently coupled with one of three different protein carriers (TetHc, Hcp1 and FliC) followed by conjugation to LPS purified from a non-virulent clonal relative, B. thailandensis. Glycoconjugated LPS generated significantly higher antibody titres compared with LPS alone. Further, they improved protection against a lethal inhalation challenge of B. mallei in the murine model of infection. Burkholderia mallei is associated with multi-drug resistance, high mortality and potentials for weaponization through aerosol inhalation. The authors of this study present gold nanoparticles (AuNPs) functionalized with a glycoconjugate vaccine against this Gram negative bacterium demonstrating promising results in a murine model even with the aerosolized form of B. Mallei. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. An ensemble of structures of Burkholderia pseudomallei 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase

    Energy Technology Data Exchange (ETDEWEB)

    Davies, Douglas R.; Staker, Bart L.; Abendroth, Jan A.; Edwards, Thomas E.; Hartley, Robert; Leonard, Jess; Kim, Hidong; Rychel, Amanda L.; Hewitt, Stephen N.; Myler, Peter J.; Stewart, Lance J. (UWASH); (Emerald)

    2011-12-07

    Burkholderia pseudomallei is a soil-dwelling bacterium endemic to Southeast Asia and Northern Australia. Burkholderia is responsible for melioidosis, a serious infection of the skin. The enzyme 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (PGAM) catalyzes the interconversion of 3-phosphoglycerate and 2-phosphoglycerate, a key step in the glycolytic pathway. As such it is an extensively studied enzyme and X-ray crystal structures of PGAM enzymes from multiple species have been elucidated. Vanadate is a phosphate mimic that is a powerful tool for studying enzymatic mechanisms in phosphoryl-transfer enzymes such as phosphoglycerate mutase. However, to date no X-ray crystal structures of phosphoglycerate mutase have been solved with vanadate acting as a substrate mimic. Here, two vanadate complexes together with an ensemble of substrate and fragment-bound structures that provide a comprehensive picture of the function of the Burkholderia enzyme are reported.

  7. Burkholderia terrae BS001 migrates proficiently with diverse fungal hosts through soil and provides protection from antifungal agents

    NARCIS (Netherlands)

    Nazir, Rashid; Tazetdinova, Diana I.; van Elsas, Jan Dirk

    2014-01-01

    Soil bacteria can benefit from co-occurring soil fungi in respect of the acquisition of carbonaceous nutrients released by fungal hyphae and the access to novel territories in soil. Here, we investigated the capacity of the mycosphere-isolated bacterium Burkholderia terrae BS001 to comigrate through

  8. Complete Genome Sequence of the d-Amino Acid Catabolism Bacterium Phaeobacter sp. Strain JL2886, Isolated from Deep Seawater of the South China Sea

    Science.gov (United States)

    Fu, Yingnan; Wang, Rui

    2016-01-01

    Phaeobacter sp. strain JL2886, isolated from deep seawater of the South China Sea, can catabolize d-amino acids. Here, we report the complete genome sequence of Phaeobacter sp. JL2886. It comprises ~4.06 Mbp, with a G+C content of 61.52%. A total of 3,913 protein-coding genes and 10 genes related to d-amino acid catabolism were obtained. PMID:27587825

  9. Burkholderia pseudomallei Genotype Distribution in the Northern Territory, Australia.

    Science.gov (United States)

    Chapple, Stephanie N J; Price, Erin P; Sarovich, Derek S; McRobb, Evan; Mayo, Mark; Kaestli, Mirjam; Spratt, Brian G; Currie, Bart J

    2016-01-01

    Melioidosis is a tropical disease of high mortality caused by the environmental bacterium, Burkholderia pseudomallei. We have collected clinical isolates from the highly endemic Northern Territory of Australia routinely since 1989, and animal and environmental B. pseudomallei isolates since 1991. Here we provide a complete record of all B. pseudomallei multilocus sequence types (STs) found in the Northern Territory to date, and distribution maps of the eight most common environmental STs. We observed surprisingly restricted geographic distributions of STs, which is contrary to previous reports suggesting widespread environmental dissemination of this bacterium. Our data suggest that B. pseudomallei from soil and water does not frequently disperse long distances following severe weather events or by migration of infected animals. © The American Society of Tropical Medicine and Hygiene.

  10. A chitinase with high activity toward partially N-acetylated chitosan from a new, moderately thermophilic, chitin-degrading bacterium, Ralstonia sp. A-471.

    Science.gov (United States)

    Sutrisno, A; Ueda, M; Abe, Y; Nakazawa, M; Miyatake, K

    2004-01-01

    A moderately thermophilic bacterium, strain A-471, capable of degrading chitin was isolated from a composting system of chitin-containing waste. Analysis of the 16S rDNA sequence revealed that the bacterium belongs to the genus Ralstonia. A thermostable chitinase A ( Ra-ChiA) was purified from culture fluid of the bacterium grown in colloidal chitin medium. Purification of the enzyme was achieved mainly by exploiting its binding to the colloidal chitin. The molecular mass of the enzyme was estimated to be 70 kDa and the isoelectric point approximately 4.7. N-terminal amino acid sequencing revealed a sequence of ADPYLKVAYYP, which had high homology (66% identity) with that of chitinase A1 from Bacillus circulans WL-12. The pH and temperature optima were determined to be 5.0 and 70 degrees C, respectively. The enzyme was classified as a retaining glycosyl hydrolase and was most active against partially N-acetylated chitosans. Its activities towards the partially N-acetylated chitosans, i.e. chitosan 7B, chitosan 8B, and chitosan 9B, were about 11-fold, 9-fold, and 5-fold higher than towards colloidal chitin, respectively. Ra-ChiA cleaved (GlcNAc)6 almost exclusively into (GlcNAc)2. Activation of Ra-ChiA was observed by the addition of 1 mM Cu2+, Mn2+, Ca2+, or Mg2+. Degradation of the partially N-acetylated chitosan produced oligosaccharides with a degree of polymerization ranging from 1-8; these are products that offer potential application for functional oligosaccharide production.

  11. Molecular insights into Burkholderia pseudomallei and Burkholderia mallei pathogenesis.

    Science.gov (United States)

    Galyov, Edouard E; Brett, Paul J; DeShazer, David

    2010-01-01

    Burkholderia pseudomallei and Burkholderia mallei are closely related gram-negative bacteria that can cause serious diseases in humans and animals. This review summarizes the current and rapidly expanding knowledge on the specific virulence factors employed by these pathogens and their roles in the pathogenesis of melioidosis and glanders. In particular, the contributions of recently identified virulence factors are described in the context of the intracellular lifestyle of these pathogens. Throughout this review, unique and shared virulence features of B. pseudomallei and B. mallei are discussed.

  12. Genus-wide acid tolerance accounts for the biogeographical distribution of soil Burkholderia populations.

    Science.gov (United States)

    Stopnisek, Nejc; Bodenhausen, Natacha; Frey, Beat; Fierer, Noah; Eberl, Leo; Weisskopf, Laure

    2014-06-01

    Bacteria belonging to the genus Burkholderia are highly versatile with respect to their ecological niches and lifestyles, ranging from nodulating tropical plants to causing melioidosis and fatal infections in cystic fibrosis patients. Despite the clinical importance and agronomical relevance of Burkholderia species, information about the factors influencing their occurrence, abundance and diversity in the environment is scarce. Recent findings have demonstrated that pH is the main predictor of soil bacterial diversity and community structure, with the highest diversity observed in neutral pH soils. As many Burkholderia species have been isolated from low pH environments, we hypothesized that acid tolerance may be a general feature of this genus, and pH a good predictor of their occurrence in soils. Using a combination of environmental surveys at trans-continental and local scales, as well as in vitro assays, we show that, unlike most bacteria, Burkholderia species have a competitive advantage in acidic soils, but are outcompeted in alkaline soils. Physiological assays and diversity analysis based on 16S rRNA clone libraries demonstrate that pH tolerance is a general phenotypic trait of the genus Burkholderia. Our results provide a basis for building a predictive understanding of the biogeographical patterns exhibited by Burkholderia sp. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

  13. Effects of the tomato pathogen Fusarium oxysporum f. sp. radicis-lycopersici and of the biocontrol bacterium Pseudomonas fluorescens WCS365 on the composition of organic acids and sugars in tomato root exudate.

    Science.gov (United States)

    Kamilova, Faina; Kravchenko, Lev V; Shaposhnikov, Alexander I; Makarova, Nataliya; Lugtenberg, Ben

    2006-10-01

    The effects of the pathogenic fungus Fusarium oxysporum f. sp. radicis-lycopersici and of the bacterial biocontrol strain Pseudomonas fluorescens WCS365, and of both microbes, on the amounts and composition of root exudate components of tomato plants grown in a gnotobiotic stonewool substrate system were studied. Conditions were selected under which introduction of F. oxysporum f. sp. radicis-lycopersici caused severe foot and root rot, whereas inoculation of the seed with P. fluorescens WCS365 decreased the percentage of diseased plants from 96 to 7%. This is a much better disease control level than was observed in potting soil. Analysis of root exudate revealed that the presence of F. oxysporum f. sp. radicis-lycopersici did not alter the total amount of organic acids, but that the amount of citric acid decreased and that of succinic acid increased compared with the nontreated control. In contrast, in the presence of the P. fluorescens biocontrol strain WCS365, the total amount of organic acid increased, mainly due to a strong increase of the amount of citric acid, whereas the amount of succinic acid decreased dramatically. Under biocontrol conditions, when both microbes are present, the content of succinic acid decreased and the level of citric acid was similar to that in the nontreated control. The amount of sugar was approximately half that of the control sample when either one of the microbes was present alone or when both were present. Analysis of the interactions between the two microbes grown together in sterile tomato root exudate showed that WCS365 inhibited multiplication of F. oxysporum f. sp. radicis-lycopersici, whereas the fungus did not affect the number of CFU of the bacterium.

  14. Genome Sequence of Thermotoga sp Strain RQ2, a Hyperthermophilic Bacterium Isolated from a Geothermally Heated Region of the Seafloor near Ribeira Quente, the Azores

    Energy Technology Data Exchange (ETDEWEB)

    Swithers, Kristen S [University of Connecticut, Storrs; DiPippo, Jonathan L [University of Connecticut, Storrs; Bruce, David [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Pennacchio, Len [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Lykidis, A [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Stetter, Karl O [Universitat Regensburg, Regensburg, Germany; Nelson, Karen E [J. Craig Venter Institute; Gogarten, Peter [University of Connecticut, Storrs; Noll, Kenneth M [University of Connecticut, Storrs

    2011-01-01

    Thermotoga sp. strain RQ2 is probably a strain of Thermotoga maritima. Its complete genome sequence allows for an examination of the extent and consequences of gene flow within Thermotoga species and strains. Thermotoga sp. RQ2 differs from T. maritima in its genes involved in myo-inositol metabolism. Its genome also encodes an apparent fructose phosphotransferase system (PTS) sugar transporter. This operon is also found in Thermotoga naphthophila strain RKU-10 but no other Thermotogales. These are the first reported PTS transporters in the Thermotogales.

  15. The tomato rhizosphere, an environment rich in nitrogen-fixing Burkholderia species with capabilities of interest for agriculture and bioremediation.

    Science.gov (United States)

    Caballero-Mellado, Jesús; Onofre-Lemus, Janette; Estrada-de Los Santos, Paulina; Martínez-Aguilar, Lourdes

    2007-08-01

    Burkholderia strains are promising candidates for biotechnological applications. Unfortunately, most of these strains belong to species of the Burkholderia cepacia complex (Bcc) involved in human infections, hampering potential applications. Novel diazotrophic Burkholderia species, phylogenetically distant from the Bcc species, have been discovered recently, but their environmental distribution and relevant features for agro-biotechnological applications are little known. In this work, the occurrence of N2-fixing Burkholderia species in the rhizospheres and rhizoplanes of tomato plants field grown in Mexico was assessed. The results revealed a high level of diversity of diazotrophic Burkholderia species, including B. unamae, B. xenovorans, B. tropica, and two other unknown species, one of them phylogenetically closely related to B. kururiensis. These N2-fixing Burkholderia species exhibited activities involved in bioremediation, plant growth promotion, or biological control in vitro. Remarkably, B. unamae and B. kururiensis grew with aromatic compounds (phenol and benzene) as carbon sources, and the presence of aromatic oxygenase genes was confirmed in both species. The rhizospheric and endophyte nature of B. unamae and its ability to degrade aromatic compounds suggest that it could be used in rhizoremediation and for improvement of phytoremediation. B. kururiensis and other Burkholderia sp. strains grew with toluene. B. unamae and B. xenovorans exhibited ACC (1-aminocyclopropane-1-carboxylic acid) deaminase activity, and the occurrence of acdS genes encoding ACC deaminase was confirmed. Mineral phosphate solubilization through organic acid production appears to be the mechanism used by most diazotrophic Burkholderia species, but in B. tropica, there presumably exists an additional unknown mechanism. Most of the diazotrophic Burkholderia species produced hydroxamate-type siderophores. Certainly, the N2-fixing Burkholderia species associated with plants have great

  16. Genome Sequence of Lactobacillus saerimneri 30a (Formerly Lactobacillus sp. Strain 30a), a Reference Lactic Acid Bacterium Strain Producing Biogenic Amines

    NARCIS (Netherlands)

    Romano, Andrea; Trip, Hein; Campbell-Sills, Hugo; Bouchez, Olivier; Sherman, David; Lolkema, Juke S.; Lucas, Patrick M.

    2013-01-01

    Lactobacillus sp. strain 30a (Lactobacillus saerimneri) produces the biogenic amines histamine, putrescine, and cadaverine by decarboxylating their amino acid precursors. We report its draft genome sequence (1,634,278 bases, 42.6% G+C content) and the principal findings from its annotation, which

  17. Draft Genome Sequence of Clostridium sp. Strain Ade.TY, a New Biohydrogen- and Biochemical-Producing Bacterium Isolated from Landfill Leachate Sludge.

    Science.gov (United States)

    Wong, Y M; Juan, J C; Ting, Adeline; Wu, T Y; Gan, H M; Austin, C M

    2014-03-06

    Clostridium sp. strain Ade.TY is potentially a new biohydrogen-producing species isolated from landfill leachate sludge. Here we present the assembly and annotation of its genome, which may provide further insights into its gene interactions for efficient biohydrogen production.

  18. Draft Genome Sequence of Clostridium sp. Strain Ade.TY, a New Biohydrogen- and Biochemical-Producing Bacterium Isolated from Landfill Leachate Sludge

    Science.gov (United States)

    Wong, Y. M.; Ting, Adeline; Wu, T. Y.; Gan, H. M.; Austin, C. M.

    2014-01-01

    Clostridium sp. strain Ade.TY is potentially a new biohydrogen-producing species isolated from landfill leachate sludge. Here we present the assembly and annotation of its genome, which may provide further insights into its gene interactions for efficient biohydrogen production. PMID:24604640

  19. Draft Genome Sequence of Marinomonas sp. Strain D104, a Polycyclic Aromatic Hydrocarbon-Degrading Bacterium from the Deep-Sea Sediment of the Arctic Ocean.

    Science.gov (United States)

    Dong, Chunming; Bai, Xiuhua; Lai, Qiliang; Xie, Yanrong; Chen, Xin; Shao, Zongze

    2014-01-23

    Marinomonas sp. strain D104 was isolated from a polycyclic aromatic hydrocarbon-degrading consortium enriched from deep-sea sediment from the Arctic Ocean. The draft genome sequence of D104 (approximately 3.83 Mbp) contains 62 contigs and 3,576 protein-encoding genes, with a G+C content of 44.8%.

  20. Lactobacillus caviae sp nov., an obligately heterofermentative bacterium isolated from the oral cavity of a guinea pig (Cavia aperea f. porcellus)

    Czech Academy of Sciences Publication Activity Database

    Killer, Jiří; Pechar, R.; Švec, P.; Salmonová, H.; Švejstil, R.; Geigerová, M.; Rada, V.; Vlková, E.; Mekadim, Ch.

    2017-01-01

    Roč. 67, č. 7 (2017), s. 2903-2909 ISSN 1466-5026 R&D Projects: GA ČR GA13-08803S; GA MZe QJ1510338 Institutional support: RVO:67985904 Keywords : Lactobacillus sp. nov. * oral cavity * guinea pig Subject RIV: EE - Microbiology, Virology Impact factor: 2.134, year: 2016

  1. Draft Genome Sequence of Methylobacterium sp. Strain L2-4, a Leaf-Associated Endophytic N-Fixing Bacterium Isolated from Jatropha curcas L.

    OpenAIRE

    Madhaiyan, Munusamy; Chan, Kam Lock; Ji, Lianghui

    2014-01-01

    Methylobacterium sp. strain L2-4 is an efficient nitrogen-fixing leaf colonizer of biofuel crop Jatropha curcas. This strain is able to greatly improve the growth and seed yield of Jatropha curcas and is the second reported genome sequence of plant growth-promoting bacteria isolated from Jatropha curcas.

  2. 6-Hydroxymethyl-1-phenazine-carboxamide and 1,6-phenazinedimethanol from a marine bacterium, Brevibacterium sp. KMD 003, associated with marine purple vase sponge.

    Science.gov (United States)

    Choi, Eun Ju; Kwon, Hak Cheol; Ham, Jungyeob; Yang, Hyun Ok

    2009-11-01

    Two new antibacterial phenazines were isolated from the culture broth of Brevibacterium sp. KMD 003 obtained from a marine purple vase sponge of the genus Callyspongia, collected in Kyeongpo, Gangwondo, Korea. The structures of these compounds were determined to be 6-hydroxymethyl-1-phenazine-carboxamide (1) and 1,6-phenazinedimethanol (2) through analyses of HR-EI-MS and NMR data. Compounds 1 and 2 showed antibacterial activities against Enterococcus hirae and Micrococcus luteus with 5 microM MIC values.

  3. Draft Genome Sequence of Sphingobium sp. Strain C100, a Polycyclic Aromatic Hydrocarbon-Degrading Bacterium from the Deep-Sea Sediment of the Arctic Ocean.

    Science.gov (United States)

    Dong, Chunming; Bai, Xiuhua; Lai, Qiliang; Xie, Yanrong; Chen, Xin; Shao, Zongze

    2014-01-30

    Sphingobium sp. strain C100 was isolated from a polycyclic aromatic hydrocarbon (PAH)-degrading consortium from the deep-sea sediment of the Arctic Ocean. It can degrade two- to four-ring PAHs at 25°C. Here we present the draft genome sequence of this strain, which is 4,776,810 bp with a G+C content of 63.9%.

  4. PRODUCTION AND CHARACTERIZATION OF AN ALKALOTHERMOSTABLE, ORGANIC SOLVENT TOLERANT AND SURFACTANT TOLERANT ESTERASE PRODUCED BY A THERMOPHILIC BACTERIUM GEOBACILLUS SP. AGP-04, ISOLATED FROM BAKRESHWAR HOT SPRING, INDIA

    Directory of Open Access Journals (Sweden)

    Amit Ghati

    2013-10-01

    Full Text Available A thermophilic bacteria, Geobacillus sp. AGP-04, isolated from Surya Kund hot spring, Bakreshwar, West Bengal, India was studied in terms of capability of tributyrin hydrolysis and characterization of its thermostable esterase activity using p-nitrophenyl butyrate (PNPB as substrate. The extracellular crude preparation was characterized in terms of pH and temperature optima and stability, organic solvent tolerance capacity and stability, substrate specificity, surfactant tolerance capacity, kinetic parameters and activation/inhibition behavior towards some metal ions and chemicals. Tributyrin agar assay exhibited that Geobacillus sp. AGP-04 secretes an extracellular esterase. The Vmax and Km values of the esterase were found to be 5099 U/Land 103.5µM, respectively in the presence of PNPB as substrate. The optimum temperature and pH, for Geobacillus sp. AGP-04 esterase was 60oC and 8.0, respectively. Although the enzyme activity was not significantly altered by incubating crude extract solution at 20-70oC for 1 hour, the enzyme activity was fully lost at 90oC for same incubation period. The pH stability profile showed that original crude esterase activity is stable at a broad range (pH 5.0-10.0. Moreover, the enzyme was highly organic solvent and surfactant tolerant. The effect of some chemical on crude esterase activity indicated that Geobacillus sp. AGP-04 produce an esterase which contains a serine residue in active site and for its activity -SH groups are essential. Besides, enzyme production was highly induced if fermentation medium contain polysaccharides and oil as carbon source.

  5. CHROMOSOMAL MULTIPLICITY IN BURKHOLDERIA CEPACIA

    Science.gov (United States)

    We have used CHEF gel electrophoresis to screen preparations of large DNA from different Burkholderia cepacia isolates for the presence of DNA species corresponding to the linearized forms of the three chromosomes of 3.4,2.5, and 0.9 Mb identified in B. cepacia strain 17616. DNA ...

  6. Quorum Sensing Influences Burkholderia thailandensis Biofilm Development and Matrix Production.

    Science.gov (United States)

    Tseng, Boo Shan; Majerczyk, Charlotte D; Passos da Silva, Daniel; Chandler, Josephine R; Greenberg, E Peter; Parsek, Matthew R

    2016-10-01

    Members of the genus Burkholderia are known to be adept at biofilm formation, which presumably assists in the survival of these organisms in the environment and the host. Biofilm formation has been linked to quorum sensing (QS) in several bacterial species. In this study, we characterized Burkholderia thailandensis biofilm development under flow conditions and sought to determine whether QS contributes to this process. B. thailandensis biofilm formation exhibited an unusual pattern: the cells formed small aggregates and then proceeded to produce mature biofilms characterized by "dome" structures filled with biofilm matrix material. We showed that this process was dependent on QS. B. thailandensis has three acyl-homoserine lactone (AHL) QS systems (QS-1, QS-2, and QS-3). An AHL-negative strain produced biofilms consisting of cell aggregates but lacking the matrix-filled dome structures. This phenotype was rescued via exogenous addition of the three AHL signals. Of the three B. thailandensis QS systems, we show that QS-1 is required for proper biofilm development, since a btaR1 mutant, which is defective in QS-1 regulation, forms biofilms without these dome structures. Furthermore, our data show that the wild-type biofilm biomass, as well as the material inside the domes, stains with a fucose-binding lectin. The btaR1 mutant biofilms, however, are negative for fucose staining. This suggests that the QS-1 system regulates the production of a fucose-containing exopolysaccharide in wild-type biofilms. Finally, we present data showing that QS ability during biofilm development produces a biofilm that is resistant to dispersion under stress conditions. The saprophyte Burkholderia thailandensis is a close relative of the pathogenic bacterium Burkholderia pseudomallei, the causative agent of melioidosis, which is contracted from its environmental reservoir. Since most bacteria in the environment reside in biofilms, B. thailandensis is an ideal model organism for

  7. Differential expression of the seven rRNA operon promoters from the plant growth-promoting bacterium Pseudomonas sp. UW4.

    Science.gov (United States)

    Duan, Jin; Reimer, Lori; Heikkila, John J; Glick, Bernard R

    2014-12-01

    Bacteria often have multiple copies of ribosomal RNA (rrn) genes in their genomes. The presence of multiple rrn operons suggests an advantage to the organism, perhaps through adjustable control of protein expression in response to altered environmental conditions. In the work described here, the strengths of the seven rRNA promoters of Pseudomonas sp. UW4 were individually assessed by separately cloning each promoter region into an expression vector and monitoring the activity of the reporter protein, the Escherichia coli lacZ gene product. The lacZ expression was the highest for the rrnE promoter under all growth conditions, with the various promoters demonstrating a range of strengths. These findings indicate that these promoters are not functionally identical. This observation suggests that the differential expression of rrn operons under various physiological conditions and growth stages allows better regulation of rRNA, conferring an advantage to P. sp. UW4 through a more fine-tuned control of protein expression in a wide range of environmental situations. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  8. Catalytic hydrolysis of starch for biohydrogen production by using a newly identified amylase from a marine bacterium Catenovulum sp. X3.

    Science.gov (United States)

    Wu, Yi-Rui; Mao, Aihua; Sun, Chongran; Shanmugam, Sabarathinam; Li, Jin; Zhong, Mingqi; Hu, Zhong

    2017-11-01

    An identified cold-adaptive, organic solvents-tolerant alkaline α-amylase (HP664) from Catenovulum sp. strain X3 was heterologously expressed and characterized in E. coli, and it was further applied to starch saccharification for biohydrogen production. The recombinant HP664 belongs to a member of glycoside hydrolase family 13 (GH13), with a molecular weight of 69.6kDa without signal peptides, and also shares a relatively low similarity (49%) to other reported amylases. Biochemical characterization demonstrated that the maximal enzymatic activity of HP664 was observed at 35°C and pH 9.0. Most metal ions inhibited its activity; however, low polar organic solvents (e.g., benzene and n-hexane) could enhance the activity by 35-50%. Additionally, HP664 also exhibited the catalytic capability on various polysaccharides, including potato starch, amylopectin, dextrin and agar. In order to increase the bioavailability of starch for H2 production, HP664 was utilized to elevate fermentable oligosaccharide level, and the results revealed that the maximal hydrolytic percentage of starch was up to 44% with 12h of hydrolysis using 5.63U of HP664. Biohydrogen fermentation of the starch hydrolysate by Clostridium sp. strain G1 yielded 297.7mL of H2 after 84h of fermentation, which is 3.73-fold higher than the control without enzymatic treatment of HP664. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Impacts of Hydrogen Peroxide and Copper Sulfate on the Control of Microcystis aeruginosa and MC-LR and the Inhibition of MC-LR Degrading Bacterium Bacillus sp.

    Directory of Open Access Journals (Sweden)

    Michelline M. R. Kansole

    2017-04-01

    Full Text Available Laboratory batch experiments were carried out to evaluate the impacts of H2O2 and copper sulfate on M. aeruginosa PCC7820, microcystin-LR (MC-LR and its degrading bacteria Bacillus sp., previously isolated from Hulupi Lake in Taiwan. The study shows that 3 mg·L−1 hydrogen peroxide removed only 9% M. aeruginosa within seven days of exposure, from an initial cell concentration of 2 × 106 cells/mL. With copper sulfate, a concentration of 2 mg·L−1 removed 99% M. aeruginosa cells, but showed negligible efficacy in removing 0.05 mg·L−1 MC-LR. At a higher dosage, 20 mg·L−1 H2O2 led to 40% and 95% removal, respectively for MC-LR and M. aeruginosa cells. Copper sulfate and H2O2 were both lethal to Bacillus sp. population, with mortality rate constants of k = 0.04 h−1 and 0.03 h−1 under 1 mg·L−1 copper sulfate and 5 mg·L−1 H2O2, respectively. H2O2 is competitive in terms of cost, with a capability of degrading organic compounds with the assistance of ultraviolet (UV light, and it may be considered as an alternative algaecide to copper sulfate in reservoirs for algae growth control.

  10. Analysis of defence systems and a conjugative IncP-1 plasmid in the marine polyaromatic hydrocarbons-degrading bacterium Cycloclasticus sp. 78-ME.

    Science.gov (United States)

    Yakimov, Michail M; Crisafi, Francesca; Messina, Enzo; Smedile, Francesco; Lopatina, Anna; Denaro, Renata; Pieper, Dietmar H; Golyshin, Peter N; Giuliano, Laura

    2016-08-01

    Marine prokaryotes have evolved a broad repertoire of defence systems to protect their genomes from lateral gene transfer including innate or acquired immune systems and infection-induced programmed cell suicide and dormancy. Here we report on the analysis of multiple defence systems present in the genome of the strain Cycloclasticus sp. 78-ME isolated from petroleum deposits of the tanker 'Amoco Milford Haven'. Cycloclasticus are ubiquitous bacteria globally important in polyaromatic hydrocarbons degradation in marine environments. Two 'defence islands' were identified in 78-ME genome: the first harbouring CRISPR-Cas with toxin-antitoxin system, while the second was composed by an array of genes for toxin-antitoxin and restriction-modification proteins. Among all identified spacers of CRISPR-Cas system only seven spacers match sequences of phages and plasmids. Furthermore, a conjugative plasmid p7ME01, which belongs to a new IncP-1θ ancestral archetype without any accessory mobile elements was found in 78-ME. Our results provide the context to the co-occurrence of diverse defence mechanisms in the genome of Cycloclasticus sp. 78-ME, which protect the genome of this highly specialized PAH-degrader. This study contributes to the further understanding of complex networks established in petroleum-based microbial communities. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

  11. Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. NT-26.

    Science.gov (United States)

    Andres, Jérémy; Arsène-Ploetze, Florence; Barbe, Valérie; Brochier-Armanet, Céline; Cleiss-Arnold, Jessica; Coppée, Jean-Yves; Dillies, Marie-Agnès; Geist, Lucie; Joublin, Aurélie; Koechler, Sandrine; Lassalle, Florent; Marchal, Marie; Médigue, Claudine; Muller, Daniel; Nesme, Xavier; Plewniak, Frédéric; Proux, Caroline; Ramírez-Bahena, Martha Helena; Schenowitz, Chantal; Sismeiro, Odile; Vallenet, David; Santini, Joanne M; Bertin, Philippe N

    2013-01-01

    Arsenic is widespread in the environment and its presence is a result of natural or anthropogenic activities. Microbes have developed different mechanisms to deal with toxic compounds such as arsenic and this is to resist or metabolize the compound. Here, we present the first reference set of genomic, transcriptomic and proteomic data of an Alphaproteobacterium isolated from an arsenic-containing goldmine: Rhizobium sp. NT-26. Although phylogenetically related to the plant-associated bacteria, this organism has lost the major colonizing capabilities needed for symbiosis with legumes. In contrast, the genome of Rhizobium sp. NT-26 comprises a megaplasmid containing the various genes, which enable it to metabolize arsenite. Remarkably, although the genes required for arsenite oxidation and flagellar motility/biofilm formation are carried by the megaplasmid and the chromosome, respectively, a coordinate regulation of these two mechanisms was observed. Taken together, these processes illustrate the impact environmental pressure can have on the evolution of bacterial genomes, improving the fitness of bacterial strains by the acquisition of novel functions.

  12. Identification of a copper-responsive promoter and development of a copper biosensor in the soil bacterium Achromobacter sp. AO22.

    Science.gov (United States)

    Ng, Shee Ping; Palombo, Enzo A; Bhave, Mrinal

    2012-05-01

    A number of human activities result in environmental contamination with copper compounds that can cause severe detrimental effects on the ecosystem as well as human health. The physico-chemical methods of metal detection have limitations such as inability to distinguish between total versus bio-available metals and differences in metal uptake in different organisms. The heavy metal resistance-encoding genetic systems of certain bacteria provide critical tools for development of biosensors for these purposes. This study reports a copper biosensor utilizing the cop operon of the heavy metal resistant bacterial isolate, Achromobacter sp. AO22, isolated from a contaminated site in Australia. A section located between the divergently transcribed putative response regulator gene copR and multicopper oxidase gene copA that included a palindromic cop box was identified as a copper-responsive promoter using a lacZ reporter construct, pCOPRP, in E. coli. The expression was found to be enhanced by inclusion of copR. Another engineered strain, AO22(pCOPRP), showed stronger induction, and the lacZ expression in both backgrounds was enhanced significantly (250-400 fold) by copper but minimally by other metals. The construct in Achromobacter sp. AO22 thus has a high potential as biosensor for detecting copper bioavailability (hence potential toxicity) in a soil bacterial background, while the construct in E. coli is ideal for laboratory-based testing.

  13. Isolation and characterization of Desulfocurvus thunnarius sp. nov., a sulfate-reducing bacterium isolated from an anaerobic sequencing batch reactor treating cooking wastewater.

    Science.gov (United States)

    Hamdi, Olfa; Ben Hania, Wajdi; Postec, Anne; Bartoli, Manon; Hamdi, Moktar; Bouallagui, Hassib; Fauque, Guy; Ollivier, Bernard; Fardeau, Marie-Laure

    2013-11-01

    A novel anaerobic, chemo-organotrophic, sulfate-reducing bacterium, designated strain Olac 40(T), was isolated from a Tunisian wastewater digestor. Cells were curved, motile rods or vibrios (5.0-7.0×0.5 µm). Strain Olac 40(T) grew at temperatures between 15 and 50 °C (optimum 40 °C), and between pH 5.0 and 9.0 (optimum pH 7.1). It did not require NaCl for growth but tolerated it up to 50 g l(-1) (optimum 2 g l(-1)). In the presence of sulfate or thiosulfate, strain Olac 40(T) used lactate, pyruvate and formate as energy sources. Growth was observed on H2 only in the presence of acetate as carbon source. In the presence of sulfate or thiosulfate, the end products of lactate oxidation were acetate, sulfide and CO2. Sulfate, thiosulfate and sulfite were used as terminal electron acceptors, but not elemental sulfur, nitrate or nitrite. The genomic DNA G+C content of strain Olac 40(T) was 70 mol%. The profile of polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and four phospholipids. The main fatty acids were C16 : 0, anteiso-C15 : 0 and iso-C15 : 0. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain Olac 40(T) was affiliated with the family Desulfovibrionaceae within the class Deltaproteobacteria. On the basis of 16S rRNA gene sequence comparisons and physiological characteristics, strain Olac 40(T) is proposed to be assigned to a novel species of the genus Desulfocurvus, for which the name Desulfocurvus thunnarius is proposed. The type strain is Olac 40(T) ( = DSM 26129(T) = JCM 18546(T)).

  14. Identification of Burkholderia pseudomallei Near-Neighbor Species in the Northern Territory of Australia

    Science.gov (United States)

    Ginther, Jennifer L.; Mayo, Mark; Warrington, Stephanie D.; Kaestli, Mirjam; Mullins, Travis; Wagner, David M.; Currie, Bart J.; Tuanyok, Apichai; Keim, Paul

    2015-01-01

    Identification and characterization of near-neighbor species are critical to the development of robust molecular diagnostic tools for biothreat agents. One such agent, Burkholderia pseudomallei, a soil bacterium and the causative agent of melioidosis, is lacking in this area because of its genomic diversity and widespread geographic distribution. The Burkholderia genus contains over 60 species and occupies a large range of environments including soil, plants, rhizospheres, water, animals and humans. The identification of novel species in new locations necessitates the need to identify the true global distribution of Burkholderia species, especially the members that are closely related to B. pseudomallei. In our current study, we used the Burkholderia-specific recA sequencing assay to analyze environmental samples from the Darwin region in the Northern Territory of Australia where melioidosis is endemic. Burkholderia recA PCR negative samples were further characterized using 16s rRNA sequencing for species identification. Phylogenetic analysis demonstrated that over 70% of the bacterial isolates were identified as B. ubonensis indicating that this species is common in the soil where B. pseudomallei is endemic. Bayesian phylogenetic analysis reveals many novel branches within the B. cepacia complex, one novel B. oklahomensis-like species, and one novel branch containing one isolate that is distinct from all other samples on the phylogenetic tree. During the analysis with recA sequencing, we discovered 2 single nucleotide polymorphisms in the reverse priming region of B. oklahomensis. A degenerate primer was developed and is proposed for future use. We conclude that the recA sequencing technique is an effective tool to classify Burkholderia and identify soil organisms in a melioidosis endemic area. PMID:26121041

  15. Identification of Burkholderia pseudomallei Near-Neighbor Species in the Northern Territory of Australia.

    Directory of Open Access Journals (Sweden)

    Jennifer L Ginther

    Full Text Available Identification and characterization of near-neighbor species are critical to the development of robust molecular diagnostic tools for biothreat agents. One such agent, Burkholderia pseudomallei, a soil bacterium and the causative agent of melioidosis, is lacking in this area because of its genomic diversity and widespread geographic distribution. The Burkholderia genus contains over 60 species and occupies a large range of environments including soil, plants, rhizospheres, water, animals and humans. The identification of novel species in new locations necessitates the need to identify the true global distribution of Burkholderia species, especially the members that are closely related to B. pseudomallei. In our current study, we used the Burkholderia-specific recA sequencing assay to analyze environmental samples from the Darwin region in the Northern Territory of Australia where melioidosis is endemic. Burkholderia recA PCR negative samples were further characterized using 16s rRNA sequencing for species identification. Phylogenetic analysis demonstrated that over 70% of the bacterial isolates were identified as B. ubonensis indicating that this species is common in the soil where B. pseudomallei is endemic. Bayesian phylogenetic analysis reveals many novel branches within the B. cepacia complex, one novel B. oklahomensis-like species, and one novel branch containing one isolate that is distinct from all other samples on the phylogenetic tree. During the analysis with recA sequencing, we discovered 2 single nucleotide polymorphisms in the reverse priming region of B. oklahomensis. A degenerate primer was developed and is proposed for future use. We conclude that the recA sequencing technique is an effective tool to classify Burkholderia and identify soil organisms in a melioidosis endemic area.

  16. Nitrous oxide emission potentials of Burkholderia species isolated from the leaves of a boreal peat moss Sphagnum fuscum.

    Science.gov (United States)

    Nie, Yanxia; Li, Li; Wang, Mengcen; Tahvanainen, Teemu; Hashidoko, Yasuyuki

    2015-01-01

    Using a culture-based nitrous oxide (N2O) emission assay, three active N2O emitters were isolated from Sphagnum fuscum leaves and all identified as members of Burkholderia. These isolates showed N2O emission in the medium supplemented with [Formula: see text] but not with [Formula: see text], and Burkholderia sp. SF-E2 showed the most efficient N2O emission (0.20 μg·vial(-1)·day(-1)) at 1.0 mM KNO3. In Burkholderia sp. SF-E2, the optimum pH for N2O production was 5.0, close to that of the phyllosphere of Sphagnum mosses, while the optimum temperature was uniquely over 30 °C. The stimulating effect of additional 1.5 mM sucrose on N2O emission was ignorable, but Burkholderia sp. SF-E2 upon exposure to 100 mg·L(-1) E-caffeic acid showed uniquely 67-fold higher N2O emission. All of the three N2O emitters were negative in both acetylene inhibition assay and PCR assay for nosZ-detection, suggesting that N2O reductase or the gene itself is missing in the N2O-emitting Burkholderia.

  17. Divergent homologs of the predicted small RNA BpCand697 in Burkholderia spp.

    Science.gov (United States)

    Damiri, Nadzirah; Mohd-Padil, Hirzahida; Firdaus-Raih, Mohd

    2015-09-01

    The small RNA (sRNA) gene candidate, BpCand697 was previously reported to be unique to Burkholderia spp. and is encoded at 3' non-coding region of a putative AraC family transcription regulator gene. This study demonstrates the conservation of BpCand697 sequence across 32 Burkholderia spp. including B. pseudomallei, B. mallei, B. thailandensis and Burkholderia sp. by integrating both sequence homology and secondary structural analyses of BpCand697 within the dataset. The divergent sequence of BpCand697 was also used as a discriminatory power in clustering the dataset according to the potential virulence of Burkholderia spp., showing that B. thailandensis was clearly secluded from the virulent cluster of B. pseudomallei and B. mallei. Finally, the differential co-transcript expression of BpCand697 and its flanking gene, bpsl2391 was detected in Burkholderia pseudomallei D286 after grown under two different culture conditions using nutrient-rich and minimal media. It is hypothesized that the differential expression of BpCand697-bpsl2391 co-transcript between the two standard prepared media might correlate with nutrient availability in the culture media, suggesting that the physical co-localization of BpCand697 in B. pseudomallei D286 might be directly or indirectly involved with the transcript regulation of bpsl2391 under the selected in vitro culture conditions.

  18. Detection of the plant pathogenic bacterium Xanthomonas campestris pv. Campestris in seed extracts of Brassica sp. Applying fluorescent antibodies and flow cytometry.

    Science.gov (United States)

    Chitarra, L G; Langerak, C J; Bergervoet, J H W; van den Bulk, R W

    2002-02-01

    Xanthomonas campestris pv. campestris (Xcc) is a seed-transmitted plant pathogenic bacterium that causes black rot of crucifers. Seed lots and plants are screened for contamination with this pathogen using plating or serological assays. These methods, however, are time consuming and not very sensitive, respectively. Therefore, flow cytometry (FCM) was evaluated as a tool for the rapid detection and quantification of Xcc cells labeled with a mixture of specific fluorescein isothicyanate (FITC)-monoclonal antibodies (mAb) in pure culture, in mixed cultures of Xcc with either the common saprophyte Pseudomonas fluorescens (Psf) or a nonpathogenic X. campestris isolate (Xc), and in crude seed extracts. The mAb 18G12, conjugated with FITC, was tested at dilutions of 1:50, 1:100, 1:200, and 1:400. For mixed suspensions of Xcc and Psf, mAb 18G12 was used at a dilution of 1:100. The combination of mAbs 18G12, 2F4, and 20H6, all conjugated with FITC, was used at a dilution of 1:100 for the detection and quantification of Xcc cells in mixed suspensions containing Xcc and Xc and in crude seed extracts. The analyses were performed with a Coulter EPICS XL-MCL flow cytometer, at low flow rate during 2 min. Using FCM, Xcc cells labeled with FITC-conjugated mAbs (18G12, 2F4, and 20H6) were detected and quantified rapidly at low numbers, i.e., 10(3) colony-forming units per milliliter in pure and in mixed cultures with Psf. The presence of the nonpathogenic Xc in the seed extracts did not interfere with the FCM results. Xcc cells were distinguished from the cells of other organisms and from small particles present in the seed extract based on the high-intensity fluorescence of the labeled cells. The application of FCM in combination with FITC-conjugated mAbs appears to be a promising technique for the detection and quantification of Xcc cells in seed extracts of crucifers. Copyright 2002 Wiley-Liss, Inc.

  19. The effect of environmental conditions on biofilm formation of Burkholderia pseudomallei clinical isolates.

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    Nur Siti K Ramli

    Full Text Available Burkholderia pseudomallei, a Gram-negative saprophytic bacterium, is the causative agent of the potentially fatal melioidosis disease in humans. In this study, environmental parameters including temperature, nutrient content, pH and the presence of glucose were shown to play a role in in vitro biofilm formation by 28 B. pseudomallei clinical isolates, including four isolates with large colony variants (LCVs and small colony variants (SCVs morphotypes. Enhanced biofilm formation was observed when the isolates were tested in LB medium, at 30 °C, at pH 7.2, and in the presence of as little as 2 mM glucose respectively. It was also shown that all SVCs displayed significantly greater capacity to form biofilms than the corresponding LCVs when cultured in LB at 37 °C. In addition, octanoyl-homoserine lactone (C(8-HSL, a quorum sensing molecule, was identified by mass spectrometry analysis in bacterial isolates referred to as LCV CTH, LCV VIT, SCV TOM, SCV CTH, 1 and 3, and the presence of other AHL's with higher masses; decanoyl-homoserine lactone (C(10-HSL and dodecanoyl-homoserine lactone (C(12-HSL were also found in all tested strain in this study. Last but not least, we had successfully acquired two Bacillus sp. soil isolates, termed KW and SA respectively, which possessed strong AHLs degradation activity. Biofilm formation of B. pseudomallei isolates was significantly decreased after treated with culture supernatants of KW and SA strains, demonstrating that AHLs may play a role in B. pseudomallei biofilm formation.

  20. Phylogeographic, genomic, and meropenem susceptibility analysis of Burkholderia ubonensis.

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    Erin P Price

    2017-09-01

    Full Text Available The bacterium Burkholderia ubonensis is commonly co-isolated from environmental specimens harbouring the melioidosis pathogen, Burkholderia pseudomallei. B. ubonensis has been reported in northern Australia and Thailand but not North America, suggesting similar geographic distribution to B. pseudomallei. Unlike most other Burkholderia cepacia complex (Bcc species, B. ubonensis is considered non-pathogenic, although its virulence potential has not been tested. Antibiotic resistance in B. ubonensis, particularly towards drugs used to treat the most severe B. pseudomallei infections, has also been poorly characterised. This study examined the population biology of B. ubonensis, and includes the first reported isolates from the Caribbean. Phylogenomic analysis of 264 B. ubonensis genomes identified distinct clades that corresponded with geographic origin, similar to B. pseudomallei. A small proportion (4% of strains lacked the 920kb chromosome III replicon, with discordance of presence/absence amongst genetically highly related strains, demonstrating that the third chromosome of B. ubonensis, like other Bcc species, probably encodes for a nonessential pC3 megaplasmid. Multilocus sequence typing using the B. pseudomallei scheme revealed that one-third of strains lack the "housekeeping" narK locus. In comparison, all strains could be genotyped using the Bcc scheme. Several strains possessed high-level meropenem resistance (≥32 μg/mL, a concern due to potential transmission of this phenotype to B. pseudomallei. In silico analysis uncovered a high degree of heterogeneity among the lipopolysaccharide O-antigen cluster loci, with at least 35 different variants identified. Finally, we show that Asian B. ubonensis isolate RF23-BP41 is avirulent in the BALB/c mouse model via a subcutaneous route of infection. Our results provide several new insights into the biology of this understudied species.

  1. Phylogeographic, genomic, and meropenem susceptibility analysis of Burkholderia ubonensis.

    Science.gov (United States)

    Price, Erin P; Sarovich, Derek S; Webb, Jessica R; Hall, Carina M; Jaramillo, Sierra A; Sahl, Jason W; Kaestli, Mirjam; Mayo, Mark; Harrington, Glenda; Baker, Anthony L; Sidak-Loftis, Lindsay C; Settles, Erik W; Lummis, Madeline; Schupp, James M; Gillece, John D; Tuanyok, Apichai; Warner, Jeffrey; Busch, Joseph D; Keim, Paul; Currie, Bart J; Wagner, David M

    2017-09-01

    The bacterium Burkholderia ubonensis is commonly co-isolated from environmental specimens harbouring the melioidosis pathogen, Burkholderia pseudomallei. B. ubonensis has been reported in northern Australia and Thailand but not North America, suggesting similar geographic distribution to B. pseudomallei. Unlike most other Burkholderia cepacia complex (Bcc) species, B. ubonensis is considered non-pathogenic, although its virulence potential has not been tested. Antibiotic resistance in B. ubonensis, particularly towards drugs used to treat the most severe B. pseudomallei infections, has also been poorly characterised. This study examined the population biology of B. ubonensis, and includes the first reported isolates from the Caribbean. Phylogenomic analysis of 264 B. ubonensis genomes identified distinct clades that corresponded with geographic origin, similar to B. pseudomallei. A small proportion (4%) of strains lacked the 920kb chromosome III replicon, with discordance of presence/absence amongst genetically highly related strains, demonstrating that the third chromosome of B. ubonensis, like other Bcc species, probably encodes for a nonessential pC3 megaplasmid. Multilocus sequence typing using the B. pseudomallei scheme revealed that one-third of strains lack the "housekeeping" narK locus. In comparison, all strains could be genotyped using the Bcc scheme. Several strains possessed high-level meropenem resistance (≥32 μg/mL), a concern due to potential transmission of this phenotype to B. pseudomallei. In silico analysis uncovered a high degree of heterogeneity among the lipopolysaccharide O-antigen cluster loci, with at least 35 different variants identified. Finally, we show that Asian B. ubonensis isolate RF23-BP41 is avirulent in the BALB/c mouse model via a subcutaneous route of infection. Our results provide several new insights into the biology of this understudied species.

  2. Hugonella massiliensis gen. nov., sp. nov., genome sequence, and description of a new strictly anaerobic bacterium isolated from the human gut.

    Science.gov (United States)

    Elsawi, Ziena; Togo, Amadou Hamidou; Beye, Mamadou; Dubourg, Grégory; Andrieu, Claudia; Armsrtong, Nicholas; Richez, Magali; di Pinto, Fabrizio; Bittar, Fadi; Labas, Noémie; Fournier, Pierre-Edouard; Raoult, Didier; Khelaifia, Saber

    2017-08-01

    The human gut is composed of a large diversity of microorganisms, which have been poorly described. Here, using culturomics, a new concept based on the variation in culture conditions and MALDI-TOF MS identification, we proceed to explore the microbial diversity of the complex ecosystem of the human gut. Using this approach, we isolated strain AT8T (=CSUR P2118 =  DSM 101782) from stool specimens collected from a 51-year-old obese French woman. Strain AT8T is a strictly anaerobic, nonmotile, nonspore-forming gram-positive coccus that do not exhibit catalase and oxidase activities. 16S rDNA-based identification of strain AT8T demonstrated 92% gene sequence similarity with Eggerthella lenta DSM 2243, the phylogenetically closed validly named type species. Here, we present a set of features for the strain AT8T and the description of its complete genome sequence and annotation. The 2,091,845 bp long genome has a G+C content of 63.46% and encodes1,849 predicted genes; 1,781 were protein-coding genes, and 68 were RNAs. On the basis of the characteristics reported here, we propose the creation of a new bacterial genus Hugonella gen. nov., belonging to the Eggerthellaceae family and including Hugonella massiliensis gen. nov., sp. nov., strain AT8T as the type strain. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  3. Physical Map Location of the Multicopy Genes Coding for Ammonia Monooxygenase and Hydroxylamine Oxidoreductase in the Ammonia-Oxidizing Bacterium Nitrosomonas sp. Strain ENI-11

    Science.gov (United States)

    Hirota, Ryuichi; Yamagata, Akira; Kato, Junichi; Kuroda, Akio; Ikeda, Tsukasa; Takiguchi, Noboru; Ohtake, Hisao

    2000-01-01

    Pulsed-field gel electrophoresis of PmeI digests of the Nitrosomonas sp. strain ENI-11 chromosome produced four bands ranging from 1,200 to 480 kb in size. Southern hybridizations suggested that a 487-kb PmeI fragment contained two copies of the amoCAB genes, coding for ammonia monooxygenase (designated amoCAB1 and amoCAB2), and three copies of the hao gene, coding for hydroxylamine oxidoreductase (hao1, hao2, and hao3). In this DNA fragment, amoCAB1 and amoCAB2 were about 390 kb apart, while hao1, hao2, and hao3 were separated by at least about 100 kb from each other. Interestingly, hao1 and hao2 were located relatively close to amoCAB1 and amoCAB2, respectively. DNA sequence analysis revealed that hao1 and hao2 shared 160 identical nucleotides immediately upstream of each translation initiation codon. However, hao3 showed only 30% nucleotide identity in the 160-bp corresponding region. PMID:10633121

  4. Cloning and Characterization of a Novel Agarase from a Newly Isolated Bacterium Simiduia sp. Strain TM-2 Able to Degrade Various Seaweeds.

    Science.gov (United States)

    Tawara, Mika; Sakatoku, Akihiro; Tiodjio, Rosine E; Tanaka, Daisuke; Nakamura, Shogo

    2015-10-01

    A new bacterial strain capable of reducing thalli of various seaweeds (red, green, and brown algae) was isolated from marine sediments of Uozu in Toyama Prefecture, Japan. We designated the strain Simiduia sp. TM-2 based on analyses of the 16S rRNA gene and gyrB gene sequences and its biochemical and morphological characteristics. Zymography methods revealed numerous active bands of alginate lyases, cellulases, and agarases in the cells and culture supernatants of TM-2, showing that the strain possessed multiple polysaccharide lyases. A novel agarase gene (agaTM2) was cloned from TM-2 and expressed in Escherichia coli. The resulting DNA sequence contained an open reading frame of 1764 bp that encoded a protein of 587 amino acids with an estimated molecular mass of 64 kDa and pI of 4.62. The deduced amino acid sequence, AgaTM2, had a typical signal peptide followed by a glycoside hydrolase family 16 catalytic domain and two carbohydrate-binding modules 6. A BLAST search indicated that AgaTM2 shared 75.5 % amino acid sequence identity with agarase from Simiduia agarivorans SA1. The cloned and purified AgaTM2 protein showed optimal activity at 35 °C and pH 8.0, and its thermostability increased in the presence of calcium ions. AgaTM2 degraded agarose to tetraose and hexaose.

  5. Use of the phytopathogenic effect for studies of Burkholderia virulence.

    Science.gov (United States)

    Molchanova, E V; Ageeva, N P

    2015-02-01

    The phytopathogenic effect of the pseudomallei group Burkholderia is demonstrated on the Peireskia aculeata model. A method for evaluation of the effect is suggested. The effect correlates with the levels of Burkholderia pseudomallei, Burkholderia mallei, and Burkholderia thailandensis virulence for laboratory animals. P. aculeata can be used as a model for preliminary studies of the virulence of the above species.

  6. Structural insights into the multispecific recognition of dipeptides of deep-sea gram-negative bacterium Pseudoalteromonas sp. strain SM9913.

    Science.gov (United States)

    Li, Chun-Yang; Chen, Xiu-Lan; Qin, Qi-Long; Wang, Peng; Zhang, Wei-Xin; Xie, Bin-Bin; Su, Hai-Nan; Zhang, Xi-Ying; Zhou, Bai-Cheng; Zhang, Yu-Zhong

    2015-03-01

    Peptide uptake is important for nutrition supply for marine bacteria. It is also an important step in marine nitrogen cycling. However, how marine bacteria absorb peptides is still not fully understood. DppA is the periplasmic dipeptide binding protein of dipeptide permease (Dpp; an important peptide transporter in bacteria) and exclusively controls the substrate specificity of Dpp. Here, the substrate binding specificity of deep-sea Pseudoalteromonas sp. strain SM9913 DppA (PsDppA) was analyzed for 25 different dipeptides with various properties by using isothermal titration calorimetry measurements. PsDppA showed binding affinities for 8 dipeptides. To explain the multispecific substrate recognition mechanism of PsDppA, we solved the crystal structures of unliganded PsDppA and of PsDppA in complex with 4 different types of dipeptides (Ala-Phe, Met-Leu, Gly-Glu, and Val-Thr). PsDppA alternates between an "open" and a "closed" form during substrate binding. Structural analyses of the 4 PsDppA-substrate complexes combined with mutational assays indicate that PsDppA binds to different substrates through a precise mechanism: dipeptides are bound mainly by the interactions between their backbones and PsDppA, in particular by anchoring their N and C termini through ion-pair interactions; hydrophobic interactions are important in binding hydrophobic dipeptides; and Lys457 is necessary for the binding of dipeptides with a C-terminal glutamic acid or glutamine. Additionally, sequence alignment suggests that the substrate recognition mechanism of PsDppA may be common in Gram-negative bacteria. All together, our results provide structural insights into the multispecific substrate recognition mechanism of marine Gram-negative bacterial DppA, which provides a better understanding of the mechanisms of marine bacterial peptide uptake. Peptide uptake plays a significant role in nutrition supply for marine bacteria. It is also an important step in marine nitrogen cycling. However

  7. Advanced Microbial Taxonomy Combined with Genome-Based-Approaches Reveals that Vibrio astriarenae sp. nov., an Agarolytic Marine Bacterium, Forms a New Clade in Vibrionaceae.

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    Nurhidayu Al-Saari

    Full Text Available Advances in genomic microbial taxonomy have opened the way to create a more universal and transparent concept of species but is still in a transitional stage towards becoming a defining robust criteria for describing new microbial species with minimum features obtained using both genome and classical polyphasic taxonomies. Here we performed advanced microbial taxonomies combined with both genome-based and classical approaches for new agarolytic vibrio isolates to describe not only a novel Vibrio species but also a member of a new Vibrio clade. Two novel vibrio strains (Vibrio astriarenae sp. nov. C7T and C20 showing agarolytic, halophilic and fermentative metabolic activity were isolated from a seawater sample collected in a coral reef in Okinawa. Intraspecific similarities of the isolates were identical in both sequences on the 16S rRNA and pyrH genes, but the closest relatives on the molecular phylogenetic trees on the basis of 16S rRNA and pyrH gene sequences were V. hangzhouensis JCM 15146T (97.8% similarity and V. agarivorans CECT 5085T (97.3% similarity, respectively. Further multilocus sequence analysis (MLSA on the basis of 8 protein coding genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA, and topA obtained by the genome sequences clearly showed the V. astriarenae strain C7T and C20 formed a distinct new clade protruded next to V. agarivorans CECT 5085T. The singleton V. agarivorans has never been included in previous MLSA of Vibrionaceae due to the lack of some gene sequences. Now the gene sequences are completed and analysis of 100 taxa in total provided a clear picture describing the association of V. agarivorans into pre-existing concatenated network tree and concluded its relationship to our vibrio strains. Experimental DNA-DNA hybridization (DDH data showed that the strains C7T and C20 were conspecific but were separated from all of the other Vibrio species related on the basis of both 16S rRNA and pyrH gene phylogenies (e.g., V

  8. Global and regional dissemination and evolution of Burkholderia pseudomallei

    Science.gov (United States)

    Chewapreecha, Claire; Holden, Matthew T. G.; Vehkala, Minna; Välimäki, Niko; Yang, Zhirong; Harris, Simon R; Mather, Alison E.; Tuanyok, Apichai; De Smet, Birgit; Le Hello, Simon; Bizet, Chantal; Mayo, Mark; Wuthiekanun, Vanaporn; Limmathurotsakul, Direk; Phetsouvanh, Rattanaphone; Spratt, Brian G; Corander, Jukka; Keim, Paul; Dougan, Gordon; Dance, David A. B.; Currie, Bart J; Parkhill, Julian; Peacock, Sharon J.

    2017-01-01

    The environmental bacterium Burkholderia pseudomallei causes an estimated 165,000 cases of human melioidosis per year worldwide, and is also classified as a biothreat agent. We used whole genome sequences of 469 B. pseudomallei isolates from 30 countries collected over 79 years to explore its geographic transmission. Our data point to Australia as an early reservoir, with transmission to Southeast Asia followed by onward transmission to South Asia, and East Asia. Repeated reintroduction was observed within the Malay Peninsula, and between countries bordered by the Mekong river. Our data support an African origin of the Central and South American isolates with introduction of B. pseudomallei into the Americas between 1650 and 1850, providing a temporal link with the slave trade. We also identified geographically distinct genes/variants in Australasian or Southeast Asian isolates alone, with virulence-associated genes being among those overrepresented. This provides a potential explanation for clinical manifestations of melioidosis that are geographically restricted. PMID:28112723

  9. Glaciecola polaris sp. nov., a novel budding and prosthecate bacterium from the Arctic Ocean, and emended description of the genus Glaciecola.

    Science.gov (United States)

    Van Trappen, Stefanie; Tan, Tjhing-Lok; Yang, Jifang; Mergaert, Joris; Swings, Jean

    2004-09-01

    Four strains of cold-adapted, strictly aerobic and facultative oligotrophic bacteria were isolated from polar seas and investigated using a polyphasic taxonomic approach. Two strains (LMG 21857T and LMG 21854) derive from Arctic sea water whereas the other two strains (LMG 21855 and LMG 21858) were isolated from Antarctic sea water. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains belong to the gamma-subclass of the Proteobacteria and are related to the genus Glaciecola, with 98.0-99.7 % sequence similarity to Glaciecola mesophila and 94.2-95.3 % sequence similarity to Glaciecola punicea, their nearest phylogenetic neighbours. Two strains (LMG 21855 and LMG 21858) were identified as G. mesophila, whereas DNA-DNA hybridization results and differences in phenotypic characteristics showed that the other two strains (LMG 21857T and LMG 21854) constitute a novel species within the genus Glaciecola, with a DNA G + C content of 44.0 mol%. The isolates are Gram-negative, chemoheterotrophic, motile, rod-shaped cells that are psychrotolerant and moderately halophilic. Buds can be produced on mother cells and on prosthecae. Branch formation of prosthecae occurs. Whole-cell fatty acid profiles of the isolates are very similar and include C(16 : 0) and C(16 : 1)omega7c as the major fatty acid components. On the basis of genotypic and phenotypic properties, a novel species of the genus Glaciecola is described, for which the name Glaciecola polaris sp. nov. is proposed, with isolate LMG 21857T (= CIP 108324T = ARK 150T) as the type strain. An emended description of the genus Glaciecola is presented.

  10. Lentisphaera araneosa gen. nov., sp. nov, a transparent exopolymer producing marine bacterium, and the description of a novel bacterial phylum, Lentisphaerae.

    Science.gov (United States)

    Cho, Jang-Cheon; Vergin, Kevin L; Morris, Robert M; Giovannoni, Stephen J

    2004-06-01

    Two phylogenetically distinct marine strains producing transparent exopolymers (TEP), designated HTCC2155(T) and HTCC2160, were cultivated from Oregon coast seawater by dilution to extinction in a high throughput culturing format. When cultured in low-nutrient seawater media, these strains copiously produced Alcian Blue-stainable viscous TEP. Growing cells were attached to each other by the TEP in a three dimensional network. Polymerase chain reaction employing 16S rDNA primers specific for the novel isolates indicated that they are indigenous to the water column of the Atlantic and Pacific oceans. The abundance of the isolates as determined by 16S rRNA dot blots, however, indicated that they are less than 1% of the total bacterial community. In phylogenetic analyses, the strains consistently formed a new phylum-level lineage within the domain Bacteria, together with members of the candidate phylum VadinBE97, which consists of Victivallis, the first cultured genus in the candidate phylum, and 16S rRNA gene clones from DNA extracted from marine or anaerobic terrestrial habitats. Five putative subgroups were delineated within this phylum-level lineage, including a marine group and an anaerobic group. The isolates are Gram negative, strictly aerobic, chemoheterotrophic, and facultatively oligotrophic sphere-shaped bacteria. The DNA G+C content of strain HTCC2155(T) was 48.3 mol% and the genome size was 2.9 mb. It is proposed from these observations that the strains be placed into a new genus and a new species named Lentisphaera araneosa (type strain HTCC2155(T) = ATCC BAA-859(T) = KCTC 12141(T)) gen. nov., sp. nov., the cultured marine representative of the Lentisphaerae phyl. nov., and the phylum be divided into two novel orders named the Lentisphaerales ord. nov. and the Victivallales ord. nov.

  11. Isolation and Complete Genome Sequence of Algibacter alginolytica sp. nov., a Novel Seaweed-Degrading Bacteroidetes Bacterium with Diverse Putative Polysaccharide Utilization Loci.

    Science.gov (United States)

    Sun, Cong; Fu, Ge-Yi; Zhang, Chong-Ya; Hu, Jing; Xu, Lin; Wang, Rui-Jun; Su, Yue; Han, Shuai-Bo; Yu, Xiao-Yun; Cheng, Hong; Zhang, Xin-Qi; Huo, Ying-Yi; Xu, Xue-Wei; Wu, Min

    2016-05-15

    The members of the phylum Bacteroidetes are recognized as some of the most important specialists for the degradation of polysaccharides. However, in contrast to research on Bacteroidetes in the human gut, research on polysaccharide degradation by marine Bacteroidetes is still rare. The genus Algibacter belongs to the Flavobacteriaceae family of the Bacteroidetes, and most species in this genus are isolated from or near the habitat of algae, indicating a preference for the complex polysaccharides of algae. In this work, a novel brown-seaweed-degrading strain designated HZ22 was isolated from the surface of a brown seaweed (Laminaria japonica). On the basis of its physiological, chemotaxonomic, and genotypic characteristics, it is proposed that strain HZ22 represents a novel species in the genus Algibacter with the proposed name Algibacter alginolytica sp. nov. The genome of strain HZ22, the type strain of this species, harbors 3,371 coding sequences (CDSs) and 255 carbohydrate-active enzymes (CAZymes), including 104 glycoside hydrolases (GHs) and 18 polysaccharide lyases (PLs); this appears to be the highest proportion of CAZymes (∼7.5%) among the reported strains in the class Flavobacteria Seventeen polysaccharide utilization loci (PUL) are predicted to be specific for marine polysaccharides, especially algal polysaccharides from red, green, and brown seaweeds. In particular, PUL N is predicted to be specific for alginate. Taking these findings together with the results of assays of crude alginate lyases, we prove that strain HZ22(T) can completely degrade alginate. This work reveals that strain HZ22(T) has good potential for the degradation of algal polysaccharides and that the structure and related mechanism of PUL in strain HZ22(T) are worth further research. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  12. Haloferula rosicola sp. nov., an endophytic bacterium isolated from the root of a halophyte, Rosa rugosa, and emended description of the genus Haloferula.

    Science.gov (United States)

    Bibi, Fehmida; Aslam, Zubair; Song, Geun Cheol; Yoon, Hwan Sik; Jeon, Che Ok; Chung, Young Ryun

    2010-01-01

    A Gram-negative, non-spore forming endophytic bacterial strain YC6886T, was isolated from the root of a halophyte, Rosa rugosa, inhabiting coastal areas of Namhae island, located off southern end of Korea. The Cells were non-motile, obligately aerobic, and rod-shaped and formed colonies that were pale yellow in colour. The strain was able to grow at 4-32 degrees C (optimum at 25-28 degrees C) and at pH 6.5-9.5 (optimum at pH 7.5). It grew optimally in 2-3 % (w/v) NaCl, but NaCl was not an absolute requirement for growth. Strain YC6886T produced yellow carotenoid pigments. Comparison of 16S rRNA gene sequences showed that the strain was a member of the genus Haloferula, a member of phylum Verrucomicrobia, exhibiting highest similarity with Haloferula sargassicola MN1-1037T (97.4 %). Sequence similarities of the strain YC6886T to the other Haloferula type strains were 93.9-94.7 %. The DNA-DNA relatedness values of the strain YC6886T with H. sargassicola KCTC 22202T and H. rosea KCTC 22201T were 27 and 15 %, respectively. The predominant fatty acids were iso-C14:0, C16:0 and C16:1omega9c. The major respiratory quinone was menaquinone-9 and the DNA G+C content was 58.5 mol%. On the basis of phenotypic, chemotaxonomic, DNA-DNA hybridization data and phylogenetic analysis, strain YC6886T represents a novel species in the genus Haloferula, for which the name Haloferula rosicola sp. nov. is proposed. The type strain is YC6886T (= KCTC 22447T = DSM 21608T).

  13. The plant-growth-promoting bacterium Klebsiella sp. SBP-8 confers induced systemic tolerance in wheat (Triticum aestivum) under salt stress.

    Science.gov (United States)

    Singh, Rajnish Prakash; Jha, Prameela; Jha, Prabhat Nath

    2015-07-20

    Plant-growth-promoting bacteria (PGPB) with 1-aminocyclopropane-1-carboxylatedeaminase (ACCD) activity can protect plants from the deleterious effects of abioticstressors. An ACCD bacterial strain, SBP-8, identified as Klebsiella sp., also having other plant-growth-promoting activities, was isolated from Sorghum bicolor growing in the desertregion of Rajasthan, India. ACCD activity of SBP-8 was characterized at biochemical, physiological, and molecular levels. The presence of AcdS, a structural gene for ACCD, was confirmed by the polymerase chain reaction. Strain SBP-8 showed optimum growth and ACCD activity at increased salt (NaCl) concentrations of up to 6%, indicating its potential to survive and associate with plants growing in saline soil. Inoculation of wheat plants with SBP-8 when grow in the presence of salt (150-200 mM) and temperature (30-40 °C) stressors resulted inamelioration of stress conditions by increasing plant biomass and chlorophyll content, and are duction in plant growth inhibition (10-100%) occurred due to salt and temperature stressors. Moreover, strain SBP-8 also caused Na(+) exclusion (65%) and increased uptake of K(+) (84.21%) in the host plant. This property can protect plants from adverse effects of Na(+) on plant growth and physiology. Thus, SBP-8 improves growth of the host plant and protects from salt stressors through more than one mechanism including an effect of ACCD activity and on K(+)/Na(+) ratio in plants. The colonization efficiency of strain SBP-8 was confirmedby CFU (colony-forming unit) count, microscopy, and ERIC-PCR based DNA-finger-printing approach. Therefore, and the use of efficient colonizing plant-growth-promoting bacteria may provideinsights into possible biotechnological approaches to decrease the impact of salinity and other stressors. Copyright © 2015 Elsevier GmbH. All rights reserved.

  14. Methylocystis bryophila sp. nov., a facultatively methanotrophic bacterium from acidic Sphagnum peat, and emended description of the genus Methylocystis (ex Whittenbury et al. 1970) Bowman et al. 1993.

    Science.gov (United States)

    Belova, Svetlana E; Kulichevskaya, Irina S; Bodelier, Paul L E; Dedysh, Svetlana N

    2013-03-01

    A novel species is proposed for two facultatively methanotrophic representatives of the genus Methylocystis, strains H2s(T) and S284, which were isolated from an acidic (pH 4.3) Sphagnum peat-bog lake (Teufelssee, Germany) and an acidic (pH 3.8) peat bog (European North Russia), respectively. Cells of strains H2s(T) and S284 are aerobic, Gram-negative, non-motile, curved coccoids or short rods that contain an intracytoplasmic membrane system typical of type-II methanotrophs. They possess both a soluble and a particulate methane monooxygenase (MMO); the latter is represented by two isozymes, pMMO1 and pMMO2. The preferred growth substrates are methane and methanol. In the absence of C1 substrates, however, these methanotrophs are capable of slow growth on acetate. Atmospheric nitrogen is fixed by means of an aerotolerant nitrogenase. Strains H2s(T) and S284 grow between pH 4.2 and 7.6 (optimum pH 6.0-6.5) and at 8-37 °C (optimum 25-30 °C). The major fatty acids are C18 : 1ω8c, C18 : 1ω7c and C16 : 1ω7c; the major quinone is Q-8. The DNA G+C content is 62.0-62.3 mol%. Strains H2s(T) and S284 share identical 16S rRNA gene sequences, which displayed 96.6-97.3 % similarity to sequences of other taxonomically characterized members of the genus Methylocystis. Therefore, strains H2s(T) and S284 are classified as members of a novel species, for which the name Methylocystis bryophila sp. nov. is proposed; strain H2s(T) ( = DSM 21852(T)  = VKM B-2545(T)) is the type strain.

  15. Thermalkalibacillus uzonensis gen. nov. sp. nov, a novel aerobic alkali-tolerant thermophilic bacterium isolated from a hot spring in Uzon Caldera, Kamchatka.

    Science.gov (United States)

    Zhao, Weidong; Weber, Carolyn; Zhang, Chuanlun L; Romanek, Christopher S; King, Gary M; Mills, Gary; Sokolova, Tatyana; Wiegel, Juergen

    2006-08-01

    A novel thermophilic, alkali-tolerant, and CO-tolerant strain JW/WZ-YB58(T) was isolated from green mat samples obtained from the Zarvarzin II hot spring in the Uzon Caldera, Kamchatka (Far East Russia). Cells were Gram-type and Gram stain-positive, strictly aerobic, 0.7-0.8 mum in width and 5.5-12 mum in length and produced terminal spherical spores of 1.2-1.6 mum in diameter with the mother cell swelling around 2 mum in diameter (drumstick-type morphology). Cells grew optimally at pH(25 degrees C) 8.2-8.4 and temperature 50-52 degrees C and tolerated maximally 6% (w/v) NaCl. They were strict heterotrophs and could not use either CO or CO(2 )(both with or without H(2)) as sole carbon source, but tolerated up to 90% (v/v) CO in the headspace. The isolate grew on various complex substrates such as yeast extract, on carbohydrates, and organic acids, which included starch, D: -galactose, D: -mannose, glutamate, fumarate and acetate. Catalase reaction was negative. The membrane polar lipids were dominated by branched saturated fatty acids, which included iso-15:0 (24.5%), anteiso-15:0 (18.3%), iso-16:0 (9.9%), iso-17:0 (17.5%) and anteiso-17:0 (9.7%) as major constituents. The DNA G+C content of the strain is 45 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain JW/WZ-YB58(T) is distantly (<93% similarity) related to members of Bacillaceae. On the basis of 16S rRNA gene sequence, physiological and phenotypic characteristics, the isolate JW/WZ-YB58(T) (ATCC BAA-1258; DSM 17740) is proposed to be the type strain for the type species of the new taxa within the family Bacillaceae, Thermalkalibacillus uzoniensis gen. nov. sp. nov. The Genbank accession number for the 16S rRNA gene sequence is DQ221694.

  16. Diverse Burkholderia Species Isolated from Soils in the Southern United States with No Evidence of B. pseudomallei.

    Science.gov (United States)

    Hall, Carina M; Busch, Joseph D; Shippy, Kenzie; Allender, Christopher J; Kaestli, Mirjam; Mayo, Mark; Sahl, Jason W; Schupp, James M; Colman, Rebecca E; Keim, Paul; Currie, Bart J; Wagner, David M

    2015-01-01

    The global distribution of the soil-dwelling bacterium Burkholderia pseudomallei, causative agent of melioidosis, is poorly understood. We used established culturing methods developed for B. pseudomallei to isolate Burkholderia species from soil collected at 18 sampling sites in three states in the southern United States (Arizona (n = 4), Florida (n = 7), and Louisiana (n = 7)). Using multi-locus sequence typing (MLST) of seven genes, we identified 35 Burkholderia isolates from these soil samples. All species belonged to the B. cepacia complex (Bcc), including B. cenocepacia, B. cepacia, B. contaminans, B. diffusa, B. metallica, B. seminalis, B. vietnamiensis and two unnamed members of the Bcc. The MLST analysis provided a high level of resolution among and within these species. Despite previous clinical cases within the U.S. involving B. pseudomallei and its close phylogenetic relatives, we did not isolate any of these taxa. The Bcc contains a number of opportunistic pathogens that cause infections in cystic fibrosis patients. Interestingly, we found that B. vietnamiensis was present in soil from all three states, suggesting it may be a common component in southern U.S. soils. Most of the Burkholderia isolates collected in this study were from Florida (30/35; 86%), which may be due to the combination of relatively moist, sandy, and acidic soils found there compared to the other two states. We also investigated one MLST gene, recA, for its ability to identify species within Burkholderia. A 365bp fragment of recA recovered nearly the same species-level identification as MLST, thus demonstrating its cost effective utility when conducting environmental surveys for Burkholderia. Although we did not find B. pseudomallei, our findings document that other diverse Burkholderia species are present in soils in the southern United States.

  17. Thermoanaerobacter uzonensis sp. nov., an anaerobic thermophilic bacterium isolated from a hot spring within the Uzon Caldera, Kamchatka, Far East Russia.

    Science.gov (United States)

    Wagner, Isaac D; Zhao, Weidong; Zhang, Chuanlun L; Romanek, Christopher S; Rohde, Manfred; Wiegel, Juergen

    2008-11-01

    (T) was 64 %. Based on the physiological, phylogenetic and genotypic data, strain JW/IW010(T) represents a novel taxon, for which the name Thermoanaerobacter uzonensis sp. nov. is proposed. The type strain is JW/IW010(T) (=ATCC BAA-1464(T)=DSM 18761(T)). The effectively published strain, 1501/60, of 'Clostridium uzonii' [Krivenko, V. V., Vadachloriya, R. M., Chermykh, N. A., Mityushina, L. L. & Krasilnikova, E. N. (1990). Microbiology (English translation of Mikrobiologiia) 59, 741-748] had approximately 88.0 % DNA-DNA relatedness with strain JW/IW010(T) and was included in the novel taxon.

  18. Characterization of a new feather-degrading bacterium from Calotes ...

    African Journals Online (AJOL)

    A total of 842 spore-forming strains were isolated from 221 animal feces samples, in which a new feather-degrading bacterium identified as Bacillus sp. 50-3 based on morphological, biochemical and 16S rDNA tests was isolated from Calotes versicolor (an agamid lizard) feces. The bacterium can degrade native feather ...

  19. Distinct human antibody response to the biological warfare agent Burkholderia mallei.

    Science.gov (United States)

    Varga, John J; Vigil, Adam; DeShazer, David; Waag, David M; Felgner, Philip; Goldberg, Joanna B

    2012-10-01

    The genetic similarity between Burkholderia mallei (glanders) and Burkholderia pseudomallei (melioidosis) had led to the general assumption that pathogenesis of each bacterium would be similar. In 2000, the first human case of glanders in North America since 1945 was reported in a microbiology laboratory worker. Leveraging the availability of pre-exposure sera for this individual and employing the same well-characterized protein array platform that has been previously used to study a large cohort of melioidosis patients in southeast Asia, we describe the antibody response in a human with glanders. Analysis of 156 peptides present on the array revealed antibodies against 17 peptides with a > 2-fold increase in this infection. Unexpectedly, when the glanders data were compared with a previous data set from B. pseudomallei infections, there were only two highly increased antibodies shared between these two infections. These findings have implications in the diagnosis and treatment of B. mallei and B. pseudomallei infections.

  20. Thermoflexus hugenholtzii gen. nov., sp. nov., a thermophilic, microaerophilic, filamentous bacterium representing a novel class in the Chloroflexi, Thermoflexia classis nov., and description of Thermoflexaceae fam. nov. and Thermoflexales ord. nov.

    Energy Technology Data Exchange (ETDEWEB)

    Dodsworth, Jeremy A.; Gevorkian, Jonathan; Despujos, Fairuz; Cole, Jesse; Murugapiran, Senthil K.; Ming, Hong; Li, Wen J.; Zhang, Gengxin; Dohnalkova, Alice; Hedlund, Brian P.

    2014-06-06

    A thermophilic, filamentous, heterotrophic bacterium designated strain JAD2T was isolated from sediment of Great Boiling Spring in Nevada, USA. Cells had an average diameter of 0.3 µm and length of 4.0 µm, and formed filaments typically ranging in length from 20 µm to 200 µm. Filaments were negative for the Gram stain reaction, spores were not formed, and motility was not observed. The optimum temperature for growth was 75 °C with a range from 67.5-75 °C, and the optimum pH for growth was 6.75 with a range from 6.5-7.75. Peptone, tryptone or yeast extract were able to support growth when supplemented with a vitamin solution, but no growth was observed using a variety of defined organic substrates. Strain JAD2T was a facultative microaerophile, with optimal growth at 1% v/v O2 and an upper limit of 8% O2, and anaerobic growth was stimulated by fumarate but inhibited by sulfite and elemental sulfur. The major cellular fatty acids (>5%) were C16:0, C19:0, C18:0, C20:0, and C19:1. The genomic DNA G+C content was 69.3%. Phylogenetic and phylogenomic analyses using 16S rRNA gene sequences and other conserved genes placed JAD2T and other members of the yet-uncultivated GAL35 group within the phylum Chloroflexi, but not within any existing class in this phylum. These results indicate that strain JAD2T is the first cultivated representative of a new lineage within the phylum Chloroflexi, for which we propose the name Thermoflexus hugenholtzii gen. nov., sp. nov., type strain JAD2T, within Thermoflexia classis nov., Thermoflexales ord. nov., and Thermoflexaceae fam. nov.

  1. Crystal structures of Burkholderia cenocepacia dihydropteroate synthase in the apo-form and complexed with the product 7,8-dihydropteroate.

    Science.gov (United States)

    Morgan, Rachel E; Batot, Gaëlle O; Dement, Jennifer M; Rao, Vincenzo A; Eadsforth, Thomas C; Hunter, William N

    2011-05-09

    The enzyme dihydropteroate synthase (DHPS) participates in the de novo synthesis of folate cofactors by catalyzing the formation of 7,8-dihydropteroate from condensation of p-aminobenzoic acid with 6-hydroxymethyl-7,8-dihydropteroate pyrophosphate. DHPS is absent from humans, who acquire folates from diet, and has been validated as an antimicrobial therapeutic target by chemical and genetic means. The bacterium Burkholderia cenocepacia is an opportunistic pathogen and an infective agent of cystic fibrosis patients. The organism is highly resistant to antibiotics and there is a recognized need for the identification of new drugs against Burkholderia and related Gram-negative pathogens. Our characterization of the DHPS active site and interactions with the enzyme product are designed to underpin early stage drug discovery. An efficient recombinant protein expression system for DHPS from B. cenocepacia (BcDHPS) was prepared, the dimeric enzyme purified in high yield and crystallized. The structure of the apo-enzyme and the complex with the product 7,8-dihydropteroate have been determined to 2.35 Å and 1.95 Å resolution respectively in distinct orthorhombic crystal forms. The latter represents the first crystal structure of the DHPS-pterin product complex, reveals key interactions involved in ligand binding, and reinforces data generated by other structural studies. Comparisons with orthologues identify plasticity near the substrate-binding pocket and in particular a range of loop conformations that contribute to the architecture of the DHPS active site. These structural data provide a foundation for hit discovery. An intriguing observation, an artifact of the analysis, that of a potential sulfenamide bond within the ligand complex structure is mentioned. Structural similarities between BcDHPS and orthologues from other Gram-negative species are evident as expected on the basis of a high level of sequence identity. The presence of 7,8-dihydropteroate in the binding

  2. Crystal structures of Burkholderia cenocepacia dihydropteroate synthase in the apo-form and complexed with the product 7,8-dihydropteroate

    Directory of Open Access Journals (Sweden)

    Eadsforth Thomas C

    2011-05-01

    Full Text Available Abstract Background The enzyme dihydropteroate synthase (DHPS participates in the de novo synthesis of folate cofactors by catalyzing the formation of 7,8-dihydropteroate from condensation of p-aminobenzoic acid with 6-hydroxymethyl-7,8-dihydropteroate pyrophosphate. DHPS is absent from humans, who acquire folates from diet, and has been validated as an antimicrobial therapeutic target by chemical and genetic means. The bacterium Burkholderia cenocepacia is an opportunistic pathogen and an infective agent of cystic fibrosis patients. The organism is highly resistant to antibiotics and there is a recognized need for the identification of new drugs against Burkholderia and related Gram-negative pathogens. Our characterization of the DHPS active site and interactions with the enzyme product are designed to underpin early stage drug discovery. Results An efficient recombinant protein expression system for DHPS from B. cenocepacia (BcDHPS was prepared, the dimeric enzyme purified in high yield and crystallized. The structure of the apo-enzyme and the complex with the product 7,8-dihydropteroate have been determined to 2.35 Å and 1.95 Å resolution respectively in distinct orthorhombic crystal forms. The latter represents the first crystal structure of the DHPS-pterin product complex, reveals key interactions involved in ligand binding, and reinforces data generated by other structural studies. Comparisons with orthologues identify plasticity near the substrate-binding pocket and in particular a range of loop conformations that contribute to the architecture of the DHPS active site. These structural data provide a foundation for hit discovery. An intriguing observation, an artifact of the analysis, that of a potential sulfenamide bond within the ligand complex structure is mentioned. Conclusion Structural similarities between BcDHPS and orthologues from other Gram-negative species are evident as expected on the basis of a high level of sequence

  3. In Vitro Susceptibilities of Burkholderia mallei in Comparison to Those of Other Pathogenic Burkholderia spp.

    OpenAIRE

    Kenny, D. J.; Russell, P.; Rogers, D.; Eley, S M; Titball, R W

    1999-01-01

    The in vitro antimicrobial susceptibilities of isolates of Burkholderia mallei to 16 antibiotics were assessed and compared with the susceptibilities of Burkholderia pseudomallei and Burkholderia cepacia. The antibiotic susceptibility profile of B. mallei resembled that of B. pseudomallei more closely than that of B. cepacia, which corresponds to their similarities in terms of biochemistry, antigenicity, and pathogenicity. Ceftazidime, imipenem, doxycycline, and ciprofloxacin were active agai...

  4. Phylogenomic Study of Burkholderia glathei-like Organisms, Proposal of 13 Novel Burkholderia Species and Emended Descriptions of Burkholderia sordidicola, Burkholderia zhejiangensis, and Burkholderia grimmiae

    OpenAIRE

    Peeters, Charlotte; Meier-Kolthoff, Jan P.; Verheyde, Bart; De Brandt, Evie; Vaughn S Cooper; Vandamme, Peter

    2016-01-01

    Partial gyrB gene sequence analysis of 17 isolates from human and environmental sources revealed 13 clusters of strains and identified them as Burkholderia glathei Glade (BGC) bacteria. The taxonomic status of these clusters was examined by whole-genome sequence analysis, determination of the G+C content, whole-cell fatty acid analysis and biochemical characterization. The whole-genome sequence-based phylogeny was assessed using the Genome Blast Distance Phylogeny (GBDP) method and an extende...

  5. Degradación de Fenantreno por bacterias del género Burkholderia y Rhizobium aisladas de nódulos de mimosas

    Directory of Open Access Journals (Sweden)

    Arnoldo Wong-Villarreal

    2017-01-01

    Full Text Available El presente trabajo tuvo como objetivo identificar y evaluar la capacidad de degradación de microorganismos aislados de nódulos de mimosas, que puedan ser utilizados en procesos de biorremediación de suelos contaminados con fenantreno . Método . Se realizó el aislamiento de 122 cepas bacterianas de nódulos de mimosas; fueron crecidas en el medio de cultivo Maconkey para descartar enterobacterias. L as cepas bacterianas que dieron resultado negativo a esta prueba, fueron inoculadas en el medio de cultivo que contenía como úni ca fuente de carbono fenantreno; tres aislados tuvieron la capacidad de crecer en este medio. Las tres cepas fueron identificadas por secuencia del gen 1 6s ribosomal, se evaluó su capacidad de crecimiento en presencia de fenantreno mediante curvas de crecimiento microbiano; la capacidad para degradar fenantreno de las tres cepas fue cuantificada por cromatografía de gases acoplado a masas. Resultados . La s secuencias obtenidas del gen 16s ribosomal tienen relación genética con las especies de Burkholderia phenoliruptrix , Burkholderia phymatum y Rhizobium paknamense. El crecimiento microbiano de las tres cepas, suministradas con fenantreno, tuvieron un comp ortamiento similar al control , el cual contenía succinato como fuente de carbono. La cepa de Burkholderia sp. BB26 degradó 78.5 % , Burkholderia sp. BB24 68.5 % y Rhizobium sp. BY8 99%. Discusión . Los resultados de degradación de fenantreno por las cepas de Burkholderia sp. BB26 , Burkholderia sp. BB24 y Rhizobium sp. BY8 sugieren que las tres cepas tienen p otencial para utilizarse en procesos de biorremediación de suelos contaminados con fenantreno.

  6. Prevalence and Identification of Burkholderia pseudomallei and Near-Neighbor Species in the Malabar Coastal Region of India

    Science.gov (United States)

    Peddayelachagiri, Bhavani V.; Paul, Soumya; Nagaraj, Sowmya; Gogoi, Madhurjya; Sripathy, Murali H.; Batra, Harsh V.

    2016-01-01

    Accurate identification of pathogens with biowarfare importance requires detection tools that specifically differentiate them from near-neighbor species. Burkholderia pseudomallei, the causative agent of a fatal disease melioidosis, is one such biothreat agent whose differentiation from its near-neighbor species is always a challenge. This is because of its phenotypic similarity with other Burkholderia species which have a wide spread geographical distribution with shared environmental niches. Melioidosis is a major public health concern in endemic regions including Southeast Asia and northern Australia. In India, the disease is still considered to be emerging. Prevalence surveys of this saprophytic bacterium in environment are under-reported in the country. A major challenge in this case is the specific identification and differentiation of B. pseudomallei from the growing list of species of Burkholderia genus. The objectives of this study included examining the prevalence of B. pseudomallei and near-neighbor species in coastal region of South India and development of a novel detection tool for specific identification and differentiation of Burkholderia species. Briefly, we analyzed soil and water samples collected from Malabar coastal region of Kerala, South India for prevalence of B. pseudomallei. The presumptive Burkholderia isolates were identified using recA PCR assay. The recA PCR assay identified 22 of the total 40 presumptive isolates as Burkholderia strains (22.72% and 77.27% B. pseudomallei and non-pseudomallei Burkholderia respectively). In order to identify each isolate screened, we performed recA and 16S rDNA sequencing. This two genes sequencing revealed that the presumptive isolates included B. pseudomallei, non-pseudomallei Burkholderia as well as non-Burkholderia strains. Furthermore, a gene termed D-beta hydroxybutyrate dehydrogenase (bdha) was studied both in silico and in vitro for accurate detection of Burkholderia genus. The optimized bdha

  7. Prevalence and Identification of Burkholderia pseudomallei and Near-Neighbor Species in the Malabar Coastal Region of India.

    Directory of Open Access Journals (Sweden)

    Bhavani V Peddayelachagiri

    2016-09-01

    Full Text Available Accurate identification of pathogens with biowarfare importance requires detection tools that specifically differentiate them from near-neighbor species. Burkholderia pseudomallei, the causative agent of a fatal disease melioidosis, is one such biothreat agent whose differentiation from its near-neighbor species is always a challenge. This is because of its phenotypic similarity with other Burkholderia species which have a wide spread geographical distribution with shared environmental niches. Melioidosis is a major public health concern in endemic regions including Southeast Asia and northern Australia. In India, the disease is still considered to be emerging. Prevalence surveys of this saprophytic bacterium in environment are under-reported in the country. A major challenge in this case is the specific identification and differentiation of B. pseudomallei from the growing list of species of Burkholderia genus. The objectives of this study included examining the prevalence of B. pseudomallei and near-neighbor species in coastal region of South India and development of a novel detection tool for specific identification and differentiation of Burkholderia species. Briefly, we analyzed soil and water samples collected from Malabar coastal region of Kerala, South India for prevalence of B. pseudomallei. The presumptive Burkholderia isolates were identified using recA PCR assay. The recA PCR assay identified 22 of the total 40 presumptive isolates as Burkholderia strains (22.72% and 77.27% B. pseudomallei and non-pseudomallei Burkholderia respectively. In order to identify each isolate screened, we performed recA and 16S rDNA sequencing. This two genes sequencing revealed that the presumptive isolates included B. pseudomallei, non-pseudomallei Burkholderia as well as non-Burkholderia strains. Furthermore, a gene termed D-beta hydroxybutyrate dehydrogenase (bdha was studied both in silico and in vitro for accurate detection of Burkholderia genus. The

  8. PPO zoekt naar mogelijkheden aanpak Burkholderia

    NARCIS (Netherlands)

    Dwarswaard, A.; Dam, van M.F.N.

    2014-01-01

    In de bloemen- en knollenteelt van gladiool komt de afgelopen decennia met enige regelmaat de bacterieziekte Burkholderia voor. Vorig jaar startte PPO met een onderzoek naar de mogelijkheden om deze ziekte aan te pakken. Een tussenstand.

  9. Aquibacillus halophilus gen. nov., sp. nov., a moderately halophilic bacterium from a hypersaline lake, and reclassification of Virgibacillus koreensis as Aquibacillus koreensis comb. nov. and Virgibacillus albus as Aquibacillus albus comb. nov.

    Science.gov (United States)

    Amoozegar, Mohammad Ali; Bagheri, Maryam; Didari, Maryam; Mehrshad, Maliheh; Schumann, Peter; Spröer, Cathrin; Sánchez-Porro, Cristina; Ventosa, Antonio

    2014-11-01

    A novel Gram-stain-positive, moderately halophilic bacterium, designated strain B6B(T), was isolated from the water of an Iranian hypersaline lake, Aran-Bidgol, and characterized taxonomically using a polyphasic approach. Cells of strain B6B(T) were rod-shaped, motile and produced ellipsoidal endospores in terminal positions in non-swollen sporangia. Strain B6B(T) was a strictly aerobic bacterium and catalase- and oxidase-positive. The strain was able to grow at NaCl concentrations of 0.5-20.0% (w/v), with optimum growth occurring at 10.0% (w/v) NaCl. The optimum temperature and pH for growth were 35 °C and pH 7.0. On the basis of 16S rRNA gene sequence analysis, strain B6B(T) was shown to belong to the phylum Firmicutes and its closest phylogenetic similarities were with the species Virgibacillus koreensis BH30097(T) (97.5%), Virgibacillus albus YIM 93624(T) (97.4%), Sediminibacillus halophilus EN8d(T) (96.8%), Sediminibacillus albus NHBX5(T) (96.6%), Virgibacillus carmonensis LMG 20964(T) (96.3%) and Paraliobacillus quinghaiensis YIM-C158(T) (96.0%), respectively. Phylogenetic analysis revealed that strain B6B(T), along with V. koreensis BH30097(T) and V. albus YIM 93624(T), clustered in a separate clade in the family Bacillaceae. The DNA G+C content of the novel isolate was 35.8 mol%. DNA-DNA hybridization experiments revealed low levels of relatedness between strain B6B(T)and V. koreensis BH30097(T) (13%) and V. albus YIM 93624(T) (33%). The major cellular fatty acid of strain B6B(T) was anteiso-C15 : 0 (75.1%) and its polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol, an unknown phospholipid and an unknown glycolipid. The isoprenoid quinones were MK-7 (90%) and MK-6 (3%). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. All of these features support the placement of isolate B6B(T) within the phylum Firmicutes. It is closely related to V. koreensis and V. albus, but with features that clearly

  10. Molecular Procedure for Rapid Detection of Burkholderia mallei and Burkholderia pseudomallei

    OpenAIRE

    Bauernfeind, Adolf; Roller, Carsten; Meyer, Detlef; Jungwirth, Renate; Schneider, Ines

    1998-01-01

    A PCR procedure for the discrimination of Burkholderia mallei and Burkholderia pseudomallei was developed. It is based on the nucleotide difference T 2143 C (T versus C at position 2143) between B. mallei and B. pseudomallei detected in the 23S rDNA sequences. In comparison with conventional methods the procedure allows more rapid identification at reduced risk for infection of laboratory personnel.

  11. Revised structures for the predominant O-polysaccharides expressed by Burkholderia pseudomallei and Burkholderia mallei

    OpenAIRE

    Heiss, Christian; Burtnick, Mary N.; Rosemary A Roberts; Black, Ian; Azadi, Parastoo; Brett, Paul J

    2013-01-01

    O-Polysaccharides (OPS) were isolated from purified Burkholderia pseudomallei and Burkholderia mallei lipopolysaccharides by mild-acid hydrolysis and gel-permeation chromatography. 1-D and 2-D 1H and 13C NMR spectroscopy experiments revealed that the OPS antigens were unbranched heteropolymers with the following structures:

  12. Characterization of Burkholderia cepacia genomovar I as a potential ...

    African Journals Online (AJOL)

    USER

    2010-06-14

    Jun 14, 2010 ... Burkholderia cepacia complex (Bcc) consists of nine discrete genomic species ... evaluated by using dual culture and poison food tests. Genotype ..... population of Burkholderia cepacia: effect of seed treatment on disease ...

  13. PCR detection of Burkholderia multivorans in water and soil samples

    NARCIS (Netherlands)

    Peeters, C. (Charlotte); Daenekindt, S. (Stijn); A.M. Vandamme (Anne Mieke)

    2016-01-01

    textabstractBackground: Although semi-selective growth media have been developed for the isolation of Burkholderia cepacia complex bacteria from the environment, thus far Burkholderia multivorans has rarely been isolated from such samples. Because environmental B. multivorans isolates mainly

  14. Use of the common marmoset to study Burkholderia mallei infection.

    Directory of Open Access Journals (Sweden)

    Tomislav Jelesijevic

    Full Text Available Burkholderia mallei is a host-adapted bacterium that does not persist outside of its equine reservoir. The organism causes the zoonosis glanders, which is endemic in Asia, Africa, the Middle East and South America. Infection by B. mallei typically occurs via the respiratory or percutaneous route, and the most common manifestations are life-threatening pneumonia and bacteremia. Glanders is difficult to diagnose and requires prolonged antibiotic therapy with low success rates. There is no vaccine to protect against B. mallei and there is concern regarding its use as a biothreat agent. Thus, experiments were performed to establish a non-human primate model of intranasal infection to study the organism and develop countermeasures. Groups of marmosets (Callithrix jacchus were inoculated intranasally with B. mallei strain ATCC 23344 and monitored for clinical signs of illness for up to 13 days. We discovered that 83% of marmosets inoculated with doses of 2.5 X 10(4 to 2.5 X 10(5 bacteria developed acute lethal infection within 3-4 days. Signs of disease were severe and included lethargy, inappetence, conjunctivitis, mucopurulent and hemorrhagic nasal discharges, and increased respiratory effort with abdominal lifts. Burkholderia mallei was cultured from the lungs, spleen and liver of these animals, and pathologic examination of tissues revealed lesions characteristic of glanders. Challenge experiments also revealed that 91% of animals infected with doses ranging from 25 to 2.5 X 10(3 bacteria exhibited mild non-specific signs of illness and were culture negative. One marmoset inoculated with 2.5 X 10(3 organisms developed moderate signs of disease and reached humane end-points 8 days post-infection. The liver and spleen of this animal were colonized with the agent and pathological analysis of tissues showed nasal, splenic and hepatic lesions. Taken together, these data indicate that the marmoset is a suitable model to study respiratory infection by B

  15. Development of ceftazidime resistance in an acute Burkholderia pseudomallei infection

    Directory of Open Access Journals (Sweden)

    Sarovich DS

    2012-08-01

    Full Text Available Derek S Sarovich,1,2,* Erin P Price,1,2,* Direk Limmathurotsakul,3 James M Cook,1 Alex T Von Schulze,1 Spenser R Wolken,1 Paul Keim,1 Sharon J Peacock,3,4 Talima Pearson1 1Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA; 2Tropical and Emerging Infectious Diseases Division, Menzies School of Health Research, Darwin, Australia; 3Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; 4Department of Medicine, University of Cambridge, Cambridge, United Kingdom*These authors contributed equally to this workAbstract: Burkholderia pseudomallei, a bacterium that causes the disease melioidosis, is intrinsically resistant to many antibiotics. First-line antibiotic therapy for treating melioidosis is usually the synthetic β-lactam, ceftazidime (CAZ, as almost all B. pseudomallei strains are susceptible to this drug. However, acquired CAZ resistance can develop in vivo during treatment with CAZ, which can lead to mortality if therapy is not switched to a different drug in a timely manner. Serial B. pseudomallei isolates obtained from an acute Thai melioidosis patient infected by a CAZ susceptible strain, who ultimately succumbed to infection despite being on CAZ therapy for the duration of their infection, were analyzed. Isolates that developed CAZ resistance due to a proline to serine change at position 167 in the β-lactamase PenA were identified. Importantly, these CAZ resistant isolates remained sensitive to the alternative melioidosis treatments; namely, amoxicillin-clavulanate, imipenem, and meropenem. Lastly, real-time polymerase chain reaction-based assays capable of rapidly identifying CAZ resistance in B. pseudomallei isolates at the position 167 mutation site were developed. The ability to rapidly identify the emergence of CAZ resistant B. pseudomallei populations in melioidosis patients will allow timely alterations in treatment strategies

  16. Use of the common marmoset to study Burkholderia mallei infection.

    Science.gov (United States)

    Jelesijevic, Tomislav; Zimmerman, Shawn M; Harvey, Stephen B; Mead, Daniel G; Shaffer, Teresa L; Estes, D Mark; Michel, Frank; Quinn, Frederick D; Hogan, Robert J; Lafontaine, Eric R

    2015-01-01

    Burkholderia mallei is a host-adapted bacterium that does not persist outside of its equine reservoir. The organism causes the zoonosis glanders, which is endemic in Asia, Africa, the Middle East and South America. Infection by B. mallei typically occurs via the respiratory or percutaneous route, and the most common manifestations are life-threatening pneumonia and bacteremia. Glanders is difficult to diagnose and requires prolonged antibiotic therapy with low success rates. There is no vaccine to protect against B. mallei and there is concern regarding its use as a biothreat agent. Thus, experiments were performed to establish a non-human primate model of intranasal infection to study the organism and develop countermeasures. Groups of marmosets (Callithrix jacchus) were inoculated intranasally with B. mallei strain ATCC 23344 and monitored for clinical signs of illness for up to 13 days. We discovered that 83% of marmosets inoculated with doses of 2.5 X 10(4) to 2.5 X 10(5) bacteria developed acute lethal infection within 3-4 days. Signs of disease were severe and included lethargy, inappetence, conjunctivitis, mucopurulent and hemorrhagic nasal discharges, and increased respiratory effort with abdominal lifts. Burkholderia mallei was cultured from the lungs, spleen and liver of these animals, and pathologic examination of tissues revealed lesions characteristic of glanders. Challenge experiments also revealed that 91% of animals infected with doses ranging from 25 to 2.5 X 10(3) bacteria exhibited mild non-specific signs of illness and were culture negative. One marmoset inoculated with 2.5 X 10(3) organisms developed moderate signs of disease and reached humane end-points 8 days post-infection. The liver and spleen of this animal were colonized with the agent and pathological analysis of tissues showed nasal, splenic and hepatic lesions. Taken together, these data indicate that the marmoset is a suitable model to study respiratory infection by B. mallei.

  17. 40 CFR 725.1075 - Burkholderia cepacia complex.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Burkholderia cepacia complex. 725.1075... Specific Microorganisms § 725.1075 Burkholderia cepacia complex. (a) Microorganism and significant new uses subject to reporting. (1) The microorganisms identified as the Burkholderia cepacia complex defined as...

  18. Enhanced degradation of haloacid by heterologous expression in related Burkholderia species.

    Science.gov (United States)

    Su, Xianbin; Deng, Liyu; Kong, Ka Fai; Tsang, Jimmy S H

    2013-10-01

    Haloacids are environmental pollutant and can be transformed to non-toxic alkanoic acids by microbial dehalogenase. Bacterium Burkholderia species MBA4 was enriched from soil for its ability to bioremediate haloacids such as mono-chloroacetate (MCA), mono-bromoacetate (MBA), 2-mono-chloropropionate, and 2-mono-bromopropionate. MBA4 produces an inducible dehalogenase Deh4a that catalyzes the dehalogenation process. The growth of MBA4 on haloacid also relies on the presence of a haloacid-uptake system. Similar dehalogenase genes can be found in the genome of many related species. However, wildtype Burkholderia caribensis MWAP64, Burkholderia phymatum STM815, and Burkholderia xenovorans LB400 were not able to grow on MCA. When a plasmid containing the regulatory and structural gene of Deh4a was transformed to these species, they were able to grow on haloacid. The specific enzyme activities in these recombinants ranges from 2- to 30-fold that of MBA4 in similar condition. Reverse transcription-quantitative real-time PCR showed that the relative transcript levels in these recombinant strains ranges from 9 to over 1,600 times that of MBA4 in similar condition. A recombinant has produced nearly five times of dehalogenase that MBA4 could ever achieve. While the expressions of Deh4a were more relaxed in these phylogenetically related species, an MCA-uptake activity was found to be inducible. These metabolically engineered strains are better degraders than the haloacid-enriched MBA4. Copyright © 2013 Wiley Periodicals, Inc.

  19. Evaluation of a latex agglutination assay for the identification of Burkholderia pseudomallei and Burkholderia mallei.

    Science.gov (United States)

    Duval, Brea D; Elrod, Mindy G; Gee, Jay E; Chantratita, Narisara; Tandhavanant, Sarunporn; Limmathurotsakul, Direk; Hoffmaster, Alex R

    2014-06-01

    Cases of melioidosis and glanders are rare in the United States, but the etiologic agents of each disease (Burkholderia pseudomallei and Burkholderia mallei, respectively) are classified as Tier 1 select agents because of concerns about their potential use as bioterrorism agents. A rapid, highly sensitive, and portable assay for clinical laboratories and field use is required. Our laboratory has further evaluated a latex agglutination assay for its ability to identify B. pseudomallei and B. mallei isolates. This assay uses a monoclonal antibody that specifically recognizes the capsular polysaccharide produced by B. pseudomallei and B. mallei, but is absent in closely related Burkholderia species. A total of 110 B. pseudomallei and B. mallei were tested, and 36 closely related Burkholderia species. The latex agglutination assay was positive for 109 of 110 (99.1% sensitivity) B. pseudomallei and B. mallei isolates tested. © The American Society of Tropical Medicine and Hygiene.

  20. Comparison of four selective media for the isolation of Burkholderia mallei and Burkholderia pseudomallei.

    Science.gov (United States)

    Glass, Mindy B; Beesley, Cari A; Wilkins, Patricia P; Hoffmaster, Alex R

    2009-06-01

    Currently there are no commercially available selective media indicated for the isolation of Burkholderia mallei and Burkholderia pseudomallei. Ashdown's agar, a custom selective medium for isolation of B. pseudomallei, is well described in the literature but unavailable commercially. Three commercially available media, Burkholderia cepacia selective agar (BCSA), oxidative-fermentative-polymyxin B-bacitracin-lactose (OFPBL) agar, and Pseudomonas cepacia (PC) agar are recommended for isolation of B. cepacia from respiratory secretions of cystic fibrosis patients. We evaluated the sensitivity and selectivity of these four media using 20 B. mallei, 20 B. pseudomallei, 20 Burkholderia spp., and 15 diagnostically challenging organisms. Ashdown's agar was the most sensitive medium for the isolation of B. pseudomallei, but it was unable to support growth of B. mallei. Pseudomonas cepacia agar was highly sensitive and selective for both organisms. In non-endemic areas, we suggest the use of the commercially available PC agar for the isolation of B. mallei and B. pseudomallei.