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Sample records for anaerobic bacterium isolated

  1. Thermotoga lettingae sp. nov. : a novel thermophilic, methanol-degrading bacterium isolated from a thermophilic anaerobic reactor

    NARCIS (Netherlands)

    Balk, M.; Weijma, J.; Stams, A.J.M.

    2002-01-01

    A novel, anaerobic, non-spore-forming, mobile, Gram-negative, thermophilic bacterium, strain TMO(T), was isolated from a thermophilic sulfate-reducing bioreactor operated at 65 degrees C with methanol as the sole substrate. The G C content of the DNA of strain TMO(T) was 39.2 molÐThe optimum pH,

  2. Caldicoprobacter guelmensis sp. nov., a thermophilic, anaerobic, xylanolytic bacterium isolated from a hot spring.

    Science.gov (United States)

    Bouanane-Darenfed, Amel; Ben Hania, Wajdi; Hacene, Hocine; Cayol, Jean-Luc; Ollivier, Bernard; Fardeau, Marie-Laure

    2013-06-01

    A hyperthermophilic anaerobic bacterium, designated D2C22(T), was isolated from the hydrothermal hot spring of Guelma in north-east Algeria. The isolate was a Gram-stain-positive, non-sporulating, non-motile rod, appearing singly or in pairs (0.3-0.4 × 8.0-9.0 µm). Strain D2C22(T) grew anaerobically at 45-85 °C (optimum 65 °C), at pH 5-9 (optimum pH 6.8) and with 0-20 g NaCl l(-1). Strain D2C22(T) used glucose, galactose, lactose, fructose, ribose, xylose, arabinose, maltose, cellobiose, mannose, melibiose, sucrose, xylan and pyruvate (only in the presence of yeast extract or biotrypticase) as electron donors. The end products from glucose fermentation were acetate, lactate, CO2 and H2. Nitrate, nitrite, thiosulfate, elemental sulfur, sulfate and sulfite were not used as electron acceptors. The predominant cellular fatty acids were iso-C15:0 and iso-C17:0. The DNA G+C content was 41.6 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain D2C22(T) was most closely related to Caldicoprobacter oshimai JW/HY-331(T), Caldicoprobacter algeriensis TH7C1(T) and Acetomicrobium faecale DSM 20678(T) (95.5, 95.5 and 95.3% 16S rRNA gene sequence similarity, respectively). Based on phenotypic, phylogenetic and chemotaxonomic characteristics, strain D2C22(T) is proposed to be a representative of a novel species of the genus Caldicoprobacter within the order Clostridiales, for which the name Caldicoprobacter guelmensis sp. nov. is proposed. The type strain is D2C22(T) (=DSM 24605(T)=JCM 17646(T)).

  3. Mobilisporobacter senegalensis gen. nov., sp. nov., an anaerobic bacterium isolated from tropical shea cake.

    Science.gov (United States)

    Mbengue, Malick; Thioye, Abdoulaye; Labat, Marc; Casalot, Laurence; Joseph, Manon; Samb, Abdoulaye; Ben Ali Gam, Zouhaier

    2016-03-01

    A Gram-stain positive, endospore-forming, strictly anaerobic bacterium, designated strain Gal1 T , was isolated from shea cake, a waste material from the production of shea butter, originating from Saraya, Senegal. The cells were rod-shaped, slightly curved, and motile with peritrichous flagella. The strain was oxidase-negative and catalase-negative. Growth was observed at temperatures ranging from 15 to 45 °C (optimum 30 °C) and at pH 6.5-9.3 (optimum pH 7.8). The salinity range for growth was 0-3.5 % NaCl (optimum 1 %). Yeast extract was required for growth. Strain Gal1 T fermented various carbohydrates such as mannose, mannitol, arabinose, cellobiose, fructose, glucose, maltose, sucrose, trehalose and lactose and the major end-products were ethanol and acetate. The only major cellular fatty acid was C16 : 0 (19.6 %). The DNA base G+C content of strain Gal1 T was 33.8 mol%. Analysis of the 16S rRNA gene sequence of the isolate indicated that this strain was related to Mobilitalea sibirica DSM 26468 T with 94.27 % similarity, Clostridium populeti ATTC 35295 T with 93.94 % similarity, and Clostridium aminovalericum DSM 1283 T and Anaerosporobacter mobilis DSM 15930 T with 93.63 % similarity. On the basis of phenotypic characteristics, phylogenetic analysis and the results of biochemical and physiological tests, strain Gal1 T was clearly distinguished from closely related genera, and strain Gal1 T can be assigned to a novel species of a new genus for which the name Mobilisporobacter senegalensis gen. nov., sp. nov. is proposed. The type strain is Gal1 T ( = DSM 26537 T  = JCM 18753 T ).

  4. Caldicoprobacter algeriensis sp. nov. a new thermophilic anaerobic, xylanolytic bacterium isolated from an Algerian hot spring.

    Science.gov (United States)

    Bouanane-Darenfed, Amel; Fardeau, Marie-Laure; Grégoire, Patrick; Joseph, Manon; Kebbouche-Gana, Salima; Benayad, Tahar; Hacene, Hocine; Cayol, Jean-Luc; Ollivier, Bernard

    2011-03-01

    A thermophilic anaerobic bacterium (strain TH7C1(T)) was isolated from the hydrothermal hot spring of Guelma in the northeast of Algeria. Strain TH7C1(T) stained Gram-positive, was a non-motile rod appearing singly, in pairs, or as long chains (0.7-1 × 2-6 μm(2)). Spores were never observed. It grew at temperatures between 55 and 75°C (optimum 65°C) and at pH between 6.2 and 8.3 (optimum 6.9). It did not require NaCl for growth, but tolerated it up to 5 g l(-1). Strain TH7C1(T) is an obligatory heterotroph fermenting sugars including glucose, galactose, lactose, raffinose, fructose, ribose, xylose, arabinose, maltose, mannitol, cellobiose, mannose, melibiose, saccharose, but also xylan, and pyruvate. Fermentation of sugars only occurred in the presence of yeast extract (0.1%). The end-products from glucose fermentation were acetate, lactate, ethanol, CO(2), and H(2). Nitrate, nitrite, thiosulfate, elemental sulfur, sulfate, and sulfite were not used as electron acceptors. The G+C content of the genomic DNA was 44.7 mol% (HPLC techniques). Phylogenetic analysis of the small-subunit ribosomal RNA (rRNA) gene sequence indicated that strain TH7C1(T) was affiliated to Firmicutes, order Clostridiales, family Caldicoprobacteraceae, with Caldicoprobacter oshimai (98.5%) being its closest relative. Based on phenotypic, phylogenetic, and genetic characteristics, strain TH7C1(T) is proposed as a novel species of genus Caldicoprobacter, Caldicoprobacter algeriensis, sp. nov. (strain TH7C1(T) = DSM 22661(T) = JCM 16184(T)).

  5. 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).

  6. Isolation and characterization of Caldicellulosiruptor lactoaceticus sp. nov., an extremely thermophilic, cellulolytic, anaerobic bacterium

    DEFF Research Database (Denmark)

    Mladenovska, Zuzana; Mathrani, Indra M.; Ahring, Birgitte Kiær

    1995-01-01

    and ethanol occurred as minor fermentation products. Only a restricted number of carbon sources (cellulose, xylan, starch, pectin, cellobiose, xylose, maltose and lactose) were used as substrates. During growth on Avicel, the bacterium produced free cellulases with carboxymethylcellulase and avicelase...... activity. The G + C content of the cellular DNA of strain 6A was 35.2 +/- 0.8 mol%. Complete 16S rDNA sequence analysis showed that strain 6A was phylogenetically related to Caldicellulosiruptor saccharolyticus. It is proposed that the isolated bacterium be named Caldicellulosiruptor lactoaceticus sp. nov....

  7. Chitinolytic enzymes from bacterium inhabiting human gastrointestinal tract - critical parameters of protein isolation from anaerobic culture

    Czech Academy of Sciences Publication Activity Database

    Dušková, Jarmila; Tishchenko, Galina; Ponomareva, E.; Šimůnek, Jiří; Koppová, Ingrid; Skálová, Tereza; Štěpánková, Andrea; Hašek, Jindřich; Dohnálek, Jan

    2011-01-01

    Roč. 58, č. 2 (2011), s. 261-263 ISSN 0001-527X R&D Projects: GA ČR GA310/09/1407; GA ČR GA305/07/1073 Institutional research plan: CEZ:AV0Z40500505; CEZ:AV0Z50450515 Keywords : chitinolytic enzymes * anaerobic cultivation * protein isolation Subject RIV: EE - Microbiology, Virology Impact factor: 1.491, year: 2011 http://www.actabp.pl/pdf/2_2011/261.pdf

  8. Chitinolytic enzymes from bacterium inhabiting human gastrointestinal tract -- critical parameters of protein isolation from anaerobic culture.

    Science.gov (United States)

    Dušková, Jarmila; Tishchenko, Galina; Ponomareva, Evgenia; Šimůnek, Jiří; Koppová, Ingrid; Skálová, Tereza; Štěpánková, Andrea; Hašek, Jindřich; Dohnálek, Jan

    2011-01-01

    The object of this study are chitinolytic enzymes produced by bacterium Clostridium paraputrificum J4 isolated from the gastrointestinal tract of a healthy human. In particular, we focus on the development of purification protocols, determination of properties of the enzymes and their activity profiles. The process of bacteria cultivation and isolation of chitinolytic complex of enzymes showing specific activities of endo-, exo-chitinase and N-acetyl-β-glucosaminidase was optimized. A range of various purification procedures were used such as ultrafiltration, precipitation, chromatographic separations (ion-exchange, size exclusion, chromatofocusing) in altered combinations. The optimal purification protocol comprises two or three steps. Individual samples were analyzed by SDS/PAGE electrophoresis and after renaturation their activity could be detected using zymograms. Mass spectroscopy peptide fragment analysis and MALDI analysis of the purest samples indicate presence of endochitinase B (molecular mass about 85 kDa) and of 60-kDa endo- and exochitinases.

  9. Partial characterization of xylanase produced by Caldicoprobacter algeriensis, a new thermophilic anaerobic bacterium isolated from an Algerian hot spring.

    Science.gov (United States)

    Bouacem, Khelifa; Bouanane-Darenfed, Amel; Boucherba, Nawel; Joseph, Manon; Gagaoua, Mohammed; Ben Hania, Wajdi; Kecha, Mouloud; Benallaoua, Said; Hacène, Hocine; Ollivier, Bernard; Fardeau, Marie-Laure

    2014-11-01

    To date, xylanases have expanded their use in many processing industries, such as pulp, paper, food, and textile. This study aimed the production and partial characterization of a thermostable xylanase from a novel thermophilic anaerobic bacterium Caldicoprobacter algeriensis strain TH7C1(T) isolated from a northeast hot spring in Algeria. The obtained results showed that C. algeriensis xylanase seems not to be correlated with the biomass growth profile whereas the maximum enzyme production (140.0 U/ml) was recorded in stationary phase (18 h). The temperature and pH for optimal activities were 70 °C and 11.0, respectively. The enzyme was found to be stable at 50, 60, 70, and 80 °C, with a half-life of 10, 9, 8, and 4 h, respectively. Influence of metal ions on enzyme activity revealed that Ca(+2) enhances greatly the relative activity to 151.3 %; whereas Hg(2+) inhibited significantly the enzyme. At the best of our knowledge, this is the first report on the production of xylanase by the thermophilic bacterium C. algeriensis. This thermo- and alkaline-tolerant xylanase could be used in pulp bleaching process.

  10. Isolation and characterization of Desulfitobacterium dehalogenans gen. nov., sp. nov., an anaerobic bacterium which reductively dechlorinates chlorophenolic compounds.

    Science.gov (United States)

    Utkin, I; Woese, C; Wiegel, J

    1994-10-01

    An organism that is able to reductively ortho-dechlorinate 2,4-dichlorophenol and 3-chloro-4-hydroxyphenylacetate (3-Cl-4-OHPA) was isolated from a methanogenic lake sediment. This organism, an anaerobic, motile, Gram-type-positive, rod-shaped bacterium, grew in the presence of 0.1% yeast extract when pyruvate, lactate, formate, or hydrogen was used as the electron donor for reductive dehalogenation of 3-Cl-4-OHPA. Sulfite, thiosulfate, and sulfur were reduced to sulfide, nitrate was reduced to nitrite, and fumarate was reduced to succinate. Dissimilatory reduction of sulfate could not be demonstrated, and no adenylylsulfate reductase was detected with an immunoassay. The organism fermented two pyruvate molecules to one lactate molecule, one acetate molecule, and one carbon dioxide molecule. The pH and temperature optima for both growth and dechlorination of 3-Cl-4-OHPA were 7.5 and 38 degrees C, respectively. The doubling time under these conditions was approximately 3.5 h. On the basis of the results of a 16S rRNA analysis and the inability of the organism to use sulfate as an electron acceptor, strain JW/IU-DC1 is described as the type strain of the new taxon Desulfitobacterium dehalogenans gen. nov., sp. nov.

  11. 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...... was observed exclusively in the presence of a hydrogen sulfide scavenger, e.g., ferrihydrite. In the absence of a scavenger, sulfide and sulfate production were observed but no growth occurred. Strain SB164P1 grew also by disproportionation of thiosulfate and sulfite. With thiosulfate, the growth efficiency...... was higher in ferrihydrite-supplemented media than in media without ferrihydrite. Growth coupled to sulfate reduction was not observed. However, a slight sulfide production occurred in cultures incubated with formate and sulfate. Strain SB164P1 is the first bacterium described that grows...

  12. Thioarsenate Formation Coupled with Anaerobic Arsenite Oxidation by a Sulfate-Reducing Bacterium Isolated from a Hot Spring

    Directory of Open Access Journals (Sweden)

    Geng Wu

    2017-07-01

    Full Text Available Thioarsenates are common arsenic species in sulfidic geothermal waters, yet little is known about their biogeochemical traits. In the present study, a novel sulfate-reducing bacterial strain Desulfotomaculum TC-1 was isolated from a sulfidic hot spring in Tengchong geothermal area, Yunnan Province, China. The arxA gene, encoding anaerobic arsenite oxidase, was successfully amplified from the genome of strain TC-1, indicating it has a potential ability to oxidize arsenite under anaerobic condition. In anaerobic arsenite oxidation experiments inoculated with strain TC-1, a small amount of arsenate was detected in the beginning but became undetectable over longer time. Thioarsenates (AsO4-xSx2- with x = 1–4 formed with mono-, di- and tri-thioarsenates being dominant forms. Tetrathioarsenate was only detectable at the end of the experiment. These results suggest that thermophilic microbes might be involved in the formation of thioarsenates and provide a possible explanation for the widespread distribution of thioarsenates in terrestrial geothermal environments.

  13. 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).

  14. 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

    2018-04-01

    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 ).

  15. 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).

  16. 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.

  17. FERMENTATION OF INULIN BY CLOSTRIDIUM-THERMOSUCCINOGENES SP-NOV, A THERMOPHILIC ANAEROBIC BACTERIUM ISOLATED FROM VARIOUS HABITATS

    NARCIS (Netherlands)

    DRENT, WJ; LAHPOR, GA; WIEGANT, WM; GOTTSCHAL, JC

    Four closely related strains of thermophilic bacteria were isolated via enrichment in batch and continuous culture with inulin as the sole source of carbon and energy by using inoculations from various sources. These new strains were isolated from beet pulp from a sugar refinery, soil around a

  18. Thermoanaerobacter pentosaceus sp. nov., an anaerobic, extreme thermophilic, high ethanol-yielding bacterium isolated from household waste

    DEFF Research Database (Denmark)

    Tomás, Ana Faria; Karakashev, Dimitar Borisov; Angelidaki, Irini

    2013-01-01

    of approximately 0.5 µm. Optimal growth occurred at 70 °C and pH(25°C) 7, with a maximum growth rate of 0.1 h-1. DNA G+C content was 34.2 mol %. Strain DTU01(T) could ferment arabinose, cellobiose, fructose, galactose, glucose, inulin, lactose, mannose, melibiose, pectin, starch, sucrose, xylan, yeast extract...... and xylose, but not cellulose, Avicel®, mannitol, inositol, glycerol, acetate, lactate, ethanol, butanol or peptone. Ethanol was the major fermentation product and a maximum yield of 1.39 mol of ethanol per mol xylose was achieved when sulphite was added to the cultivation medium. Thiosulphite......, the physiological and phylogenetic differences (DNA G+C content, substrate utilization, electron acceptors, phylogenetic distance, isolation site) allow for the proposal of strain DTU01(T) as a new species within the genus Thermoanaerobacter, for which the name Thermoanaerobacter pentosaceus sp. nov. is proposed...

  19. Isolation and Cultivation of Anaerobes

    DEFF Research Database (Denmark)

    Aragao Börner, Rosa

    2016-01-01

    Anaerobic microorganisms play important roles in different biotechnological processes. Their complex metabolism and special cultivation requirements have led to less isolated representatives in comparison to their aerobic counterparts.In view of that, the isolation and cultivation of anaerobic...... microorganisms is still a promising venture, and conventional methodologies as well as considerations and modifications are presented here. An insight into new methodologies and devices as well as a discussion on future perspectives for the cultivation of anaerobes may open the prospects of the exploitation...... of these microorganisms as a source for biotechnology....

  20. Colwellia agarivorans sp. nov., an agar-digesting marine bacterium isolated from coastal seawater

    Science.gov (United States)

    A novel Gram-stain-negative, facultatively anaerobic, yellowish and agar-digesting marine bacterium, designated strain QM50**T, was isolated from coastal seawater in an aquaculture site near Qingdao, China. Phylogenetic analysis based on 16S rDNA sequences revealed that the novel isolate represented...

  1. Isolation, characterization, and U(VI)-reducing potential of a facultatively anaerobic, acid-resistant Bacterium from Low-pH, nitrate- and U(VI)-contaminated subsurface sediment and description of Salmonella subterranea sp. nov.

    Science.gov (United States)

    Shelobolina, Evgenya S; Sullivan, Sara A; O'Neill, Kathleen R; Nevin, Kelly P; Lovley, Derek R

    2004-05-01

    A facultatively anaerobic, acid-resistant bacterium, designated strain FRCl, was isolated from a low-pH, nitrate- and U(VI)-contaminated subsurface sediment at site FW-024 at the Natural and Accelerated Bioremediation Research Field Research Center in Oak Ridge, Tenn. Strain FRCl was enriched at pH 4.5 in minimal medium with nitrate as the electron acceptor, hydrogen as the electron donor, and acetate as the carbon source. Clones with 16S ribosomal DNA (rDNA) sequences identical to the sequence of strain FRCl were also detected in a U(VI)-reducing enrichment culture derived from the same sediment. Cells of strain FRCl were gram-negative motile regular rods 2.0 to 3.4 micro m long and 0.7 to 0.9 microm in diameter. Strain FRCl was positive for indole production, by the methyl red test, and for ornithine decarboxylase; it was negative by the Voges-Proskauer test (for acetylmethylcarbinol production), for urea hydrolysis, for arginine dihydrolase, for lysine decarboxylase, for phenylalanine deaminase, for H(2)S production, and for gelatin hydrolysis. Strain FRCl was capable of using O(2), NO(3)(-), S(2)O(3)(2-), fumarate, and malate as terminal electron acceptors and of reducing U(VI) in the cell suspension. Analysis of the 16S rDNA sequence of the isolate indicated that this strain was 96.4% similar to Salmonella bongori and 96.3% similar to Enterobacter cloacae. Physiological and phylogenetic analyses suggested that strain FRCl belongs to the genus Salmonella and represents a new species, Salmonella subterranea sp. nov.

  2. Characterization of Halanaerocella petrolearia gen. nov., sp. nov., a new anaerobic moderately halophilic fermentative bacterium isolated from a deep subsurface hypersaline oil reservoir : New taxa: Firmicutes (Class Clostridia, Order Halanaerobiales, Halobacteroidaceae, Halobacteroides).

    Science.gov (United States)

    Gales, G; Chehider, N; Joulian, C; Battaglia-Brunet, F; Cayol, J-L; Postec, A; Borgomano, J; Neria-Gonzalez, I; Lomans, B P; Ollivier, B; Alazard, D

    2011-09-01

    An anaerobic, halophilic, and fermentative bacterium, strain S200(T), was isolated from a core sample of a deep hypersaline oil reservoir. Cells were rod-shaped, non-motile, and stained Gram-positive. It grew at NaCl concentrations ranging from 6 to 26% (w/v), with optimal growth at 15% (w/v) NaCl, and at temperatures between 25 and 47°C with an optimum at 40-45°C. The optimum pH was 7.3 (range 6.2-8.8; no growth at pH 5.8 and pH 9). The doubling time in optimized growth conditions was 3.5 h. Strain S200(T) used exclusively carbohydrates as carbon and energy sources. The end products of glucose degradation were lactate, formate, ethanol, acetate, H(2), and CO(2). The predominant cellular fatty acids were non-branched fatty acids C(16:1), C(16:0), and C(14:0). The G + C mole% of the DNA was 32.7%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain S200(T) formed a distinct lineage within the family Halobacteroidaceae, order Halanaerobiales, and was most closely related to Halanaerobaculum tunisiense DSM 19997(T) and Halobacteroides halobius DSM 5150(T), with sequence similarity of 92.3 and 91.9%, respectively. On the basis of its physiological and genotypic properties, strain S200(T) is proposed to be assigned to a novel species of a novel genus, for which the name Halanaerocella petrolearia is proposed. The type strain of Halanaerocella petrolearia is strain S200(T) (=DSM 22693(T) = JCM 16358(T)).

  3. Moorella stamsii sp. nov., a new anaerobic thermophilic hydrogenogenic carboxydotroph isolated from digester sludge

    NARCIS (Netherlands)

    Alves, J.I.; Gelder, van A.H.; Alves, M.M.; Sousa, D.Z.; Plugge, C.M.

    2013-01-01

    A novel anaerobic, thermophilic, carbon monoxide-utilizing bacterium, strain E3-O, was isolated from anaerobic sludge of a municipal solid waste digester. Cells were straight rods, 0.6 to 1µm in diameter and 2 to 3 µm in length, growing as single cells or in pairs. Cells formed round terminal

  4. ISOLATION OF OBLIGATELY ANAEROBIC PSYCHROPHILIC BACTERIA.

    Science.gov (United States)

    SINCLAIR, N A; STOKES, J L

    1964-03-01

    Sinclair, N. A. (Washington State University, Pullman), and J. L. Stokes. Isolation of obligately anaerobic psychrophilic bacteria. J. Bacteriol. 87:562-565. 1964.-A total of 11 strains of strictly anaerobic psychrophilic bacteria have been isolated from soil, mud, and sewage. The organisms grow well at 0 C in liquid and on solid media, and grow only in the complete absence of oxygen. On the basis of shape, sporulation, flagellation, and strictly anaerobic growth, all of the organisms were classified as strains of Clostridium. Some of the biochemical properties of the strains and the effect of temperature on growth are described.

  5. 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

  6. 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

  7. Xylan degradation by the anaerobic bacterium Bacteroides xylanolyticus

    NARCIS (Netherlands)

    Schyns, P.J.Y.M.L.

    1997-01-01

    Plant cell walls are the major reservoir of fixed carbon in nature. The mineralization of the fiber material, the so called lignocellulosic complex, proceeds almost exclusively by microbial processes in both aerobic and anaerobic environments. In anaerobic microbial processes the energy of

  8. Isolation and characterization of a novel toluene-degrading, sulfate-reducing bacterium.

    OpenAIRE

    Beller, H R; Spormann, A M; Sharma, P K; Cole, J R; Reinhard, M

    1996-01-01

    A novel sulfate-reducing bacterium isolated from fuel-contaminated subsurface soil, strain PRTOL1, mineralizes toluene as the sole electron donor and carbon source under strictly anaerobic conditions. The mineralization of 80% of toluene carbon to CO2 was demonstrated in experiments with [ring-U-14C]toluene; 15% of toluene carbon was converted to biomass and nonvolatile metabolic by-products, primarily the former. The observed stoichiometric ratio of moles of sulfate consumed per mole of tolu...

  9. A novel electrophototrophic bacterium Rhodopseudomonas palustris strain RP2, exhibits hydrocarbonoclastic potential in anaerobic environments

    Directory of Open Access Journals (Sweden)

    Krishnaveni Venkidusamy

    2016-07-01

    Full Text Available An electrophototrophic, hydrocarbonoclastic bacterium Rhodopseudomonas palustris stain RP2 was isolated from the anodic biofilms of hydrocarbon fed microbial electrochemical remediation systems (MERS. Salient properties of the strain RP2 were direct electrode respiration, dissimilatory metal oxide reduction, spore formation, anaerobic nitrate reduction, free living diazotrophy and the ability to degrade n-alkane components of petroleum hydrocarbons in anoxic, photic environments. In acetate fed microbial electrochemical cells, a maximum current density of 305±10 mA/m2 (1000Ω was generated (power density 131.65±10 mW/m2 by strain RP2 with a coulombic efficiency of 46.7 ± 1.3%. Cyclic voltammetry studies showed that anaerobically grown cells of strain RP2 is electrochemically active and likely to transfer electrons extracellularly to solid electron acceptors through membrane bound compounds, however, aerobically grown cells lacked the electrochemical activity. The ability of strain RP2 to produce current (maximum current density 21±3 mA/m2; power density 720±7 µW/m2, 1000Ω using petroleum hydrocarbon (PH as a sole energy source was also examined using an initial concentration of 800 mg l-1 of diesel range hydrocarbons (C9- C36 with a concomitant removal of 47.4 ± 2.7% hydrocarbons in MERS. Here, we also report the first study that shows an initial evidence for the existence of a hydrocarbonoclastic behavior in the strain RP2 when grown in different electron accepting and illuminated conditions (anaerobic and MERS degradation. Such observations reveal the importance of photoorganotrophic growth in the utilization of hydrocarbons from contaminated environments. Identification of such novel petrochemical hydrocarbon degrading electricigens, not only expands the knowledge on the range of bacteria known for the hydrocarbon bioremediation but also shows a biotechnological potential that goes well beyond its applications to MERS.

  10. Energy transduction in the thermophilic anaerobic bacterium Clostridium fervidus is exclusively coupled to sodium ions

    NARCIS (Netherlands)

    SPEELMANS, G; POOLMAN, B; ABEE, T; KONINGS, WN

    1993-01-01

    The thermophilic, peptidolytic, anaerobic bacterium Clostridium fervidus is unable to generate a pH gradient in the range of 5.5-8.0, which limits growth of the organism to a narrow pH range (6.3-7.7). A significant membrane potential (DELTApsi almost-equal-to -60 mV) and chemical gradient of Na+

  11. 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

  12. Agathobaculum butyriciproducens gen. nov.  sp. nov., a strict anaerobic, butyrate-producing gut bacterium isolated from human faeces and reclassification of Eubacterium desmolans as Agathobaculum desmolans comb. nov.

    Science.gov (United States)

    Ahn, Sharon; Jin, Tae-Eun; Chang, Dong-Ho; Rhee, Moon-Soo; Kim, Hyun Ju; Lee, Sang Jun; Park, Doo-Sang; Kim, Byoung-Chan

    2016-09-01

    A novel bacterial strain, SR79T, was isolated from a Korean faecal sample and characterized using a polyphasic approach. SR79T was found to be a strictly anaerobic, Gram-stain-positive, non-spore-forming, non-motile, catalase- and oxidase-negative short rod with no flagella. SR79T grew optimally at 37 °C in the presence of 0.5 % (w/v) NaCl at pH 7. The NaCl range for growth was 0-1 % (w/v). The isolate produced butyric acid (>18  mM) as a major end product. A phylogenetic analysis based on 16S rRNA gene sequences revealed that the most closely related type strains were Eubacteriumdesmolans ATCC 43058T and Butyricicoccus pullicaecorum 25-3T (96.4 and 96.0 % similarity, respectively). The DNA G+C content was determined to be 52.9 mol%. The major cellular fatty acids (>10 %) were C16 : 0, C18 : 1cis-9, C19 : 1 cyc 9,10 and C14 : 0. Meso-diaminopimelic acid was present in the cell wall peptidoglycan and the cell wall hydrolysates contained ribose, glucose and galactose. The 16S rRNA gene sequence similarity, phylogenetic analysis, chemotaxonomic and phenotypic characteristics allowed differentiation of SR79T, which represents a novel species of a new genus within the family Ruminococcaceae, for which the name Agathobaculum butyriciproducens gen. nov. sp. nov. is proposed. The type strain is SR79T (=KCTC 15532T=DSM 100391T). Based on the results of this study, it is also proposed to transfer Eubacteriumdesmolans to this new genus, as Agathobaculum desmolans comb. nov. The type strain of Agathobaculum desmolans is ATCC 43058T (=CCUG 27818T).

  13. Involvement of a novel fermentative bacterium in acidification in a thermophilic anaerobic digester.

    Science.gov (United States)

    Hori, Tomoyuki; Akuzawa, Masateru; Haruta, Shin; Ueno, Yoshiyuki; Ogata, Atsushi; Ishii, Masaharu; Igarashi, Yasuo

    2014-12-01

    Acidification results from the excessive accumulation of volatile fatty acids and the breakthrough of buffering capacity in anaerobic digesters. However, little is known about the identity of the acidogenic bacteria involved. Here, we identified an active fermentative bacterium during acidification in a thermophilic anaerobic digester by sequencing and phylogenetic analysis of isotopically labeled rRNA. The digestion sludge retrieved from the beginning of pH drop in the laboratory-scale anaerobic digester was incubated anaerobically at 55 °C for 4 h during which 13 C-labeled glucose was supplemented repeatedly. 13 CH 4 and 13 CO 2 were produced after substrate addition. RNA extracts from the incubated sludge was density-separated by ultracentrifugation, and then bacterial communities in the density fractions were screened by terminal restriction fragment length polymorphism and clone library analyses based on 16S rRNA transcripts. Remarkably, a novel lineage within the genus Thermoanaerobacterium became abundant with increasing the buoyant density and predominated in the heaviest fraction of RNA. The results in this study indicate that a thermoacidophilic bacterium exclusively fermented the simple carbohydrate glucose, thereby playing key roles in acidification in the thermophilic anaerobic digester. © 2014 Federation of European Microbiological Societies.

  14. Clostridium acetireducens sp nov, a novel amino acid-oxidizing, acetate-reducing anaerobic bacterium

    NARCIS (Netherlands)

    Orlygsson, J; Krooneman, J; Collins, Matthew D.; Pascual, C; Gottschall, JC

    Strain 30A(T) (T = type strain), which was isolated from an anaerobic bioreactor fed on waste from a potato starch factory in De Krim, The Netherlands, is a nonmotile, gram-positive, anaerobic, rod-shaped organism that is able to degrade various amino acids, including alanine, leucine, isoleucine,

  15. Amylase activity of a yellow pigmented bacterium isolated from ...

    African Journals Online (AJOL)

    This study investigated the amylase activity of a yellow pigmented bacterium isolated from cassava wastes obtained from a dumpsite near a gari processing factory in Ibadan, Nigeria. Isolate was grown in nutrient broth containing 1% starch and then centrifuged at 5,000 rpm. Amylase activity was assayed using the DNSA ...

  16. Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota

    OpenAIRE

    Kublanov, Ilya V.; Sigalova, Olga M.; Gavrilov, Sergey N.; Lebedinsky, Alexander V.; Rinke, Christian; Kovaleva, Olga; Chernyh, Nikolai A.; Ivanova, Natalia; Daum, Chris; Reddy, T.B.K.; Klenk, Hans-Peter; Spring, Stefan; G?ker, Markus; Reva, Oleg N.; Miroshnichenko, Margarita L.

    2017-01-01

    © 2017 Kublanov, Sigalova, Gavrilov, Lebedinsky, Rinke, Kovaleva, Chernyh, Ivanova, Daum, Reddy, Klenk, Spring, Göker, Reva, Miroshnichenko, Kyrpides, Woyke, Gelfand, Bonch-Osmolovskaya. The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to impl...

  17. Anaerobic CO2 fixation by the acetogenic bacterium Moorella thermoacetica

    Energy Technology Data Exchange (ETDEWEB)

    Hu, P; Rismani-Yazdi, H; Stephanopoulos, G

    2013-05-16

    Anaerobic bacteria such as Moorella thermoacetica have the capacity of fixing carbon dioxide with carbon monoxide and hydrogen for the production of ethanol, acetic acid, and other useful chemicals. In this study, we evaluated the fixation of CO2 for the production of acetic acid, as a product in its own right but also as precursor for lipid synthesis by oleaginous organisms. We achieved maximum cell optical density of 11.3, acetic acid titer of 31 g/L, and productivity of 0.55 g/L-h at CO mass-transfer rate of 83 mM/h. We also showed electron availability by CO mass transfer limited the process at CO mass transfer rates lower than 30 mM/h. Further enhancement of mass-transfer rate removed such limitations in favor of biological kinetics as main limitation. This work underlines the potential of microbial processes for converting syngas to fuel and chemical products in processes suitable for distributed feedstock utilization. (c) 2013 American Institute of Chemical Engineers AIChE J, 59: 3176-3183, 2013

  18. Biodegradation of 2 - methoxyethanol by a new bacterium isolate ...

    African Journals Online (AJOL)

    Microbial biodegradation of 2-methoxyethanol also known as Methyl glycol (MG) under anaerobic conditions has received much attention during the past decade. However, not much is known about the aerobic degradation of 2-methoxyethanol. Samples from various environmental niches were enriched to isolate and ...

  19. Thermotoga subterranea sp. nov., a new thermophilic bacterium isolated from a continental oil reservoir.

    Science.gov (United States)

    Jeanthon, C; Reysenbach, A L; L'Haridon, S; Gambacorta, A; Pace, N R; Glénat, P; Prieur, D

    1995-08-01

    A thermophilic, strictly anaerobic bacterium, designated strain SL1, was isolated from a deep, continental oil reservoir in the East Paris Basin (France). This organism grew between 50 and 75 degrees C, with an optimum at 70 degrees C. It was inhibited by elemental sulfur and was able to reduce cystine and thiosulfate to hydrogen sulfide. The G+C content (40 mol%), the presence of a lipid structure unique to the genus Thermotoga, and the 16S rRNA sequence of strain SL1 indicated that the isolate belongs to the genus Thermotoga. Based on DNA-DNA hybridization, isolate SL1 does not show species-level similarity with the recognized species T. maritima, T. neapolitana, and T. thermarum. Based on this description of strain SL1, we propose the recognition of a new species: Thermotoga subterranea.

  20. Biological conversion of biogas to methanol using methanotrophs isolated from solid-state anaerobic digestate.

    Science.gov (United States)

    Sheets, Johnathon P; Ge, Xumeng; Li, Yueh-Fen; Yu, Zhongtang; Li, Yebo

    2016-02-01

    The aim of this work was to isolate methanotrophs (methane oxidizing bacteria) that can directly convert biogas produced at a commercial anaerobic digestion (AD) facility to methanol. A methanotrophic bacterium was isolated from solid-state anaerobic digestate. The isolate had characteristics comparable to obligate methanotrophs from the genus Methylocaldum. This newly isolated methanotroph grew on biogas or purified CH4 and successfully converted biogas from AD to methanol. Methanol production was achieved using several methanol dehydrogenase (MDH) inhibitors and formate as an electron donor. The isolate also produced methanol using phosphate with no electron donor or using formate with no MDH inhibitor. The maximum methanol concentration (0.43±0.00gL(-1)) and 48-h CH4 to methanol conversion (25.5±1.1%) were achieved using biogas as substrate and a growth medium containing 50mM phosphate and 80mM formate. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Enrichment and physiological characterization of an anaerobic ammonium-oxidizing bacterium ‘ Candidatus Brocadia sapporoensis’

    KAUST Repository

    Narita, Yuko

    2017-08-18

    Anaerobic ammonium-oxidation (anammox) is recognized as an important microbial process in the global nitrogen cycle and wastewater treatment. In this study, we successfully enriched a novel anammox bacterium affiliated with the genus ‘Candidatus Brocadia’ with high purity (>90%) in a membrane bioreactor (MBR). The enriched bacterium was distantly related to the hitherto characterized ‘Ca. Brocadia fulgida’ and ‘Ca. Brocadia sinica’ with 96% and 93% of 16S ribosomal RNA gene sequence identity, respectively. The bacterium exhibited the common structural features of anammox bacteria and the production of hydrazine in the presence of hydroxylamine under anoxic conditions. The temperature range of anammox activity was 20 − 45°C with a maximum activity at 37°C. The maximum specific growth rate (μmax) was determined to be 0.0082h−1 at 37°C, corresponding to a doubling time of 3.5 days. The half-saturation constant (KS) for nitrite was 5±2.5μM. The anammox activity was inhibited by nitrite with 11.6mM representing the 50% inhibitory concentration (IC50) but no significant inhibition was observed in the presence of formate and acetate. The major respiratory quinone was identified to be menaquinone-7 (MK-7). Comparative genome analysis revealed that the anammox bacterium enriched in present study shared nearly half of genes with ‘Ca. Brocadia sinica’ and ‘Ca. Brocadia fulgida’. The bacterium enriched in this study showed all known physiological characteristics of anammox bacteria and can be distinguished from the close relatives by its rRNA gene sequences. Therefore, we proposed the name ‘Ca. Brocadia sapporoensis’ sp. nov.

  2. Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments

    KAUST Repository

    Wang, Yong

    2016-07-01

    Aerophobetes (or CD12) is a recently defined bacterial phylum, of which the metabolic processes and ecological importance remain unclear. In the present study, we obtained the draft genome of an Aerophobetes bacterium TCS1 from saline sediment near the Thuwal cold seep in the Red Sea using a genome binning method. Analysis of 16S rRNA genes of TCS1 and close relatives revealed wide distribution of Aerophobetes in deep-sea sediments. Phylogenetic relationships showed affinity between Aerophobetes TCS1 and some thermophilic bacterial phyla. The genome of TCS1 (at least 1.27 Mbp) contains a full set of genes encoding core metabolic pathways, including glycolysis and pyruvate fermentation to produce acetyl-CoA and acetate. The identification of cross-membrane sugar transporter genes further indicates its potential ability to consume carbohydrates preserved in the sediment under the microbial mat. Aerophobetes bacterium TCS1 therefore probably carried out saccharolytic and fermentative metabolism. The genes responsible for autotrophic synthesis of acetyl-CoA via the Wood–Ljungdahl pathway were also found in the genome. Phylogenetic study of the essential genes for the Wood–Ljungdahl pathway implied relative independence of Aerophobetes bacterium from the known acetogens and methanogens. Compared with genomes of acetogenic bacteria, Aerophobetes bacterium TCS1 genome lacks the genes involved in nitrogen metabolism, sulfur metabolism, signal transduction and cell motility. The metabolic activities of TCS1 might depend on geochemical conditions such as supplies of CO2, hydrogen and sugars, and therefore the TCS1 might be a facultative bacterium in anaerobic saline sediments near cold seeps. © 2016, Science China Press and Springer-Verlag Berlin Heidelberg.

  3. Aerobic Reduction of Arsenate by a Bacterium Isolated From Activated Sludge

    Science.gov (United States)

    Kozai, N.; Ohnuki, T.; Hanada, S.; Nakamura, K.; Francis, A. J.

    2006-12-01

    Microlunatus phosphovorus strain NM-1 is a polyphosphate-accumulating bacterium isolated from activated sludge. This bacterium takes up a large amount of polyphosphate under aerobic conditions and release phosphate ions by hydrolysis of polyphosphate to orthophosphate under anaerobic conditions to derive energy for taking up substrates. To understand the nature of this strain, especially, influence of potential contaminants in sewage and wastewater on growth, we have been investigating behavior of this bacterium in media containing arsenic. The present paper mainly reports reduction of arsenate by this bacterium under aerobic conditions. The strain NM-1 (JCM 9379) was aerobically cultured at 30 °C in a nutrient medium containing 2.5 g/l peptone, 0.5 g/l glucose, 1.5 g/l yeast extract, and arsenic [Na2HAsO4 (As(V)) or Na3AsO3 (As(III))] at concentrations between 0 and 50 mM. The cells collected from arsenic-free media were dispersed in buffer solutions containing 2mM HEPES, 10mM NaCl, prescribed concentrations of As(V), and 0-0.2 percent glucose. Then, this cell suspension was kept at 20 °C under aerobic or anaerobic conditions. The speciation of arsenic was carried out by ion chromatography and ICP-MS. The growth of the strain under aerobic conditions was enhanced by the addition of As(V) at the concentration between 1 and 10 mM. The maximum optical density of the culture in the medium containing 5mM As(V) was 1.4 times greater than that of the control culture. Below the As(V) concentration of 10mM, most of the As(V) was reduced to As(III). The growth of the strain under anaerobic conditions has not been observed so far. The cells in the buffer solutions reduced As(V) under aerobic condition. The reduction was enhanced by the addition of glucose. However, the cell did not reduce As(V) under anaerobic conditions. The strain NM-1 showed high resistance to As(V) and As(III). The maximum optical density of the culture grown in a medium containing 50 mM As(V) was only

  4. Fervidicella metallireducens gen. nov., sp. nov., a thermophilic, anaerobic bacterium from geothermal waters.

    Science.gov (United States)

    Ogg, Christopher D; Patel, Bharat K C

    2010-06-01

    A strictly anaerobic, thermophilic bacterium, designated strain AeB(T), was isolated from microbial mats colonizing a run-off channel formed by free-flowing thermal water from a bore well (registered number 17263) of the Great Artesian Basin, Australia. Cells of strain AeB(T) were slightly curved rods (2.5-6.0x1.0 mum) that stained Gram-negative and formed spherical terminal to subterminal spores. The strain grew optimally in tryptone-yeast extract-Casamino acids medium at 50 degrees C (range 37-55 degrees C) and pH 7 (range pH 5-9). Strain AeB(T) grew poorly on yeast extract (0.2 %) and tryptone (0.2 %) as sole carbon sources, which were obligately required for growth on other energy sources. Growth of strain AeB(T) increased in the presence of various carbohydrates and amino acids, but not organic acids. End products detected from glucose fermentation were ethanol, acetate, CO2 and H2. In the presence of 0.2 % yeast extract, iron(III), manganese(IV), vanadium(V) and cobalt(III) were reduced, but not sulfate, thiosulfate, sulfite, elemental sulfur, nitrate or nitrite. Iron(III) was also reduced in the presence of tryptone, peptone, Casamino acids and amyl media (Research Achievement), but not starch, xylan, chitin, glycerol, ethanol, pyruvate, benzoate, lactate, acetate, propionate, succinate, glycine, serine, lysine, threonine, arginine, glutamate, valine, leucine, histidine, alanine, aspartate, isoleucine or methionine. Growth was inhibited by chloramphenicol, streptomycin, tetracycline, penicillin, ampicillin and NaCl concentrations >2 %. The DNA G+C content was 35.4+/-1 mol%, as determined by the thermal denaturation method. 16S rRNA gene sequence analysis indicated that strain AeB(T) is a member of the family Clostridiaceae, class Clostridia, phylum 'Firmicutes', and is positioned approximately equidistantly between the genera Sarcina, Anaerobacter, Caloramator and Clostridium (16S rRNA gene similarity values of 87.8-90.9 %). On the basis of 16S rRNA gene

  5. Complete Genome Sequence of Alkaliphilus metalliredigens Strain QYMF, an Alkaliphilic and Metal-Reducing Bacterium Isolated from Borax-Contaminated Leachate Ponds.

    Science.gov (United States)

    Hwang, C; Copeland, A; Lucas, S; Lapidus, A; Barry, K; Detter, J C; Glavina Del Rio, T; Hammon, N; Israni, S; Dalin, E; Tice, H; Pitluck, S; Chertkov, O; Brettin, T; Bruce, D; Han, C; Schmutz, J; Larimer, F; Land, M L; Hauser, L; Kyrpides, N; Mikhailova, N; Ye, Q; Zhou, J; Richardson, P; Fields, M W

    2016-11-03

    Alkaliphilus metalliredigens strain QYMF is an anaerobic, alkaliphilic, and metal-reducing bacterium associated with phylum Firmicutes QYMF was isolated from alkaline borax leachate ponds. The genome sequence will help elucidate the role of metal-reducing microorganisms under alkaline environments, a capability that is not commonly observed in metal respiring-microorganisms. Copyright © 2016 Hwang et al.

  6. Effects of an equol-producing bacterium isolated from human faeces on isoflavone and lignan metabolism in mice.

    Science.gov (United States)

    Tamura, Motoi; Hori, Sachiko; Nakagawa, Hiroyuki; Yamauchi, Satoshi; Sugahara, Takuya

    2016-07-01

    Equol is a metabolite of daidzein that is produced by intestinal microbiota. The oestrogenic activity of equol is stronger than daidzein. Equol-producing bacteria are believed to play an important role in the gut. The rod-shaped and Gram-positive anaerobic equol-producing intestinal bacterium Slackia TM-30 was isolated from healthy human faeces and its effects on urinary phyto-oestrogen, plasma and faecal lipids were assessed in adult mice. The urinary amounts of equol in urine were significantly higher in mice receiving the equol-producing bacterium TM-30 (BAC) group than in the control (CO) group (P mice. The equol-producing bacterium TM-30 likely influences the metabolism of phyto-oestrogen via changes in the gastrointestinal environment. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

  7. Bioethanol production from mannitol by a newly isolated bacterium, Enterobacter sp. JMP3.

    Science.gov (United States)

    Wang, Jing; Kim, Young Mi; Rhee, Hong Soon; Lee, Min Woo; Park, Jong Moon

    2013-05-01

    In this study a new bacterium capable of growing on brown seaweed Laminaria japonica, Enterobacter sp. JMP3 was isolated from the gut of turban shell, Batillus cornutus. In anaerobic condition, it produced high yields of ethanol (1.15 mol-EtOH mol-mannitol(-1)) as well as organic acids from mannitol, the major carbohydrate component of L. japonica. Based on carbon distribution and metabolic flux analysis, it was revealed that mannitol was more favorable than glucose for ethanol production due to their different redox states. This indicates that L. japonica is one of the promising feedstock for bioethanol production. Additionally, the mannitol dehydrogenation pathway in Enterobacter sp. JMP3 was examined and verified. Finally, an attempt was made to explore the possibility of controlling ethanol production by altering the redox potential via addition of external NADH in mannitol fermentation. Copyright © 2012 Elsevier Ltd. All rights reserved.

  8. Aerobic and Anaerobic Bacterial Isolates on the Surface and Core of Tonsils from Patients with Chronic Tonsillitis

    Directory of Open Access Journals (Sweden)

    Meera Niranjan Khadilkar

    2017-08-01

    Full Text Available Introduction Controversy regarding treatment of tonsillitis based on throat culture report still persists. If surface culture is a determinant of bacteriology of the core, then rational therapy could be aimed at organisms cultured by surface swab. Materials and Methods A Cross-sectional study was conducted on 100 patients of chronic tonsillitis who underwent tonsillectomy. Tonsil surface and core swabs were studied for aerobic and anaerobic growth. Result Eighty seven percent patients had aerobic growth on tonsil surface and ninety percent in tonsil core. Staphylococcus aureus was the commonest aerobic bacteria isolated. Anaerobic growth was present in 47% patients on tonsil surface, and 48% in core. Porphyromonas sp. was the commonest anaerobic bacterium isolated. Discussion There was no statistically significant difference between aerobic and anaerobic bacteria found in tonsil surface and core.  Conclusion Throat swabs adequately represent core pathogen, and are dependable in detecting bacteriology of chronic tonsillitis.

  9. Caloramator australicus sp. nov., a thermophilic, anaerobic bacterium from the Great Artesian Basin of Australia.

    Science.gov (United States)

    Ogg, Christopher D; Patel, Bharat K C

    2009-01-01

    A strictly anaerobic, thermophilic bacterium, designated strain RC3T, was isolated from microbial mats colonizing thermal waters of a run-off channel formed by free-flowing waters from a bore well (registered no. 17263) of the Great Artesian Basin, Australia. The slightly curved rods (2.5-4.2x0.8-1.0 microm) of strain RC3T stained Gram-positive and grew optimally in tryptone-yeast extract-glucose medium at 60 degrees C (range 45-70 degrees C) and pH 7 (range pH 5-9). Strain RC3T grew poorly on yeast extract (0.2 %) but did not grow on tryptone (0.2 %) as a sole carbon source; yeast extract was required for growth on other energy sources, which included glucose, fructose, galactose, xylose, maltose, sucrose, raffinose, mannose, cellobiose, cellulose, starch, amylopectin, xylan, peptone, amyl media (Research Achievement), threonine and pyruvate but did not include arabinose, ribose, lactose, CM-cellulose, myo-inositol, mannitol, chitin, casein, formate, acetate, succinate, propionate, lactate, benzoate, glycerol, ethanol, Casamino acids, arginine, alanine, serine, glycine, glutamine, leucine, isoleucine, methionine or aspartate. The end products of glucose fermentation were ethanol and acetate. In the presence of 0.2 % yeast extract, iron(III), manganese(IV) and elemental sulfur were reduced but not sulfate, sulfite, thiosulfate, nitrate or nitrite. Iron(III) was also reduced in the presence of peptone, tryptone, amyl media, threonine and glycerol but not chitin, xylan, pectin, starch, pyruvate, acetate, benzoate, lactate, propionate, succinate, inositol, ethanol, mannitol, arginine, glutamine or serine. Strain RC3T was not able to utilize molecular hydrogen and/or carbon dioxide in the presence or absence of iron(III). In the presence of iron(III) and glycerol, increased concentrations of Fe(II) corresponded to increased cell numbers, demonstrating that strain RC3(T) was able to conserve energy to support growth from the reduction of Fe(III) to Fe

  10. 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.

  11. 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.

  12. 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)).

  13. Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota.

    Science.gov (United States)

    Kublanov, Ilya V; Sigalova, Olga M; Gavrilov, Sergey N; Lebedinsky, Alexander V; Rinke, Christian; Kovaleva, Olga; Chernyh, Nikolai A; Ivanova, Natalia; Daum, Chris; Reddy, T B K; Klenk, Hans-Peter; Spring, Stefan; Göker, Markus; Reva, Oleg N; Miroshnichenko, Margarita L; Kyrpides, Nikos C; Woyke, Tanja; Gelfand, Mikhail S; Bonch-Osmolovskaya, Elizaveta A

    2017-01-01

    The genome of Caldithrix abyssi , the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H 2 during fermentation, and one is apparently bidirectional. The ability to reduce nitrate is determined by a nitrate reductase of the Nap family, while nitrite reduction to ammonia is presumably catalyzed by an octaheme cytochrome c nitrite reductase εHao. The genome contained genes of respiratory polysulfide/thiosulfate reductase, however, elemental sulfur and thiosulfate were not used as the electron acceptors for anaerobic respiration with acetate or H 2 , probably due to the lack of the gene of the maturation protein. Nevertheless, elemental sulfur and thiosulfate stimulated growth on fermentable substrates (peptides), being reduced to sulfide, most probably through the action of the cytoplasmic sulfide dehydrogenase and/or NAD(P)-dependent [NiFe]-hydrogenase (sulfhydrogenase) encoded by the genome. Surprisingly, the genome of this anaerobic microorganism encoded all genes for cytochrome c oxidase, however, its maturation machinery seems to be non-operational due to genomic rearrangements of supplementary genes. Despite the fact that sugars were not among the substrates reported when C. abyssi was first described, our genomic analysis revealed multiple genes of glycoside hydrolases, and some of them were predicted to be secreted. This finding aided in bringing out four carbohydrates that supported the growth of C. abyssi : starch, cellobiose, glucomannan and xyloglucan. The genomic analysis

  14. Genomic analysis of Melioribacter roseus, facultatively anaerobic organotrophic bacterium representing a novel deep lineage within Bacteriodetes/Chlorobi group.

    Directory of Open Access Journals (Sweden)

    Vitaly V Kadnikov

    Full Text Available Melioribacter roseus is a moderately thermophilic facultatively anaerobic organotrophic bacterium representing a novel deep branch within Bacteriodetes/Chlorobi group. To better understand the metabolic capabilities and possible ecological functions of M. roseus and get insights into the evolutionary history of this bacterial lineage, we sequenced the genome of the type strain P3M-2(T. A total of 2838 open reading frames was predicted from its 3.30 Mb genome. The whole proteome analysis supported phylum-level classification of M. roseus since most of the predicted proteins had closest matches in Bacteriodetes, Proteobacteria, Chlorobi, Firmicutes and deeply-branching bacterium Caldithrix abyssi, rather than in one particular phylum. Consistent with the ability of the bacterium to grow on complex carbohydrates, the genome analysis revealed more than one hundred glycoside hydrolases, glycoside transferases, polysaccharide lyases and carbohydrate esterases. The reconstructed central metabolism revealed pathways enabling the fermentation of complex organic substrates, as well as their complete oxidation through aerobic and anaerobic respiration. Genes encoding the photosynthetic and nitrogen-fixation machinery of green sulfur bacteria, as well as key enzymes of autotrophic carbon fixation pathways, were not identified. The M. roseus genome supports its affiliation to a novel phylum Ignavibateriae, representing the first step on the evolutionary pathway from heterotrophic ancestors of Bacteriodetes/Chlorobi group towards anaerobic photoautotrophic Chlorobi.

  15. Studies on fibrolytic bacterium Butyrivibrio fibrisolvens isolated from sheep rumen

    Directory of Open Access Journals (Sweden)

    Sawanon, S.

    2007-03-01

    Full Text Available Fibrolytic Butyrivibrio fibrisolvens was an attractive target for genetic engineering in rumen bacteria. The experiment was initiated in making culture collection of this species, some of which may be useful ascandidate strain in the future. Hay suspended in sheep rumen was used as the source of isolates. The source was enriched with filter paper degradation, diluted with an anaerobic solution and used for pure culturing bya roll tube technique. After colony forming, Gram-negative curved rods bacteria were selected and screened for further identification with volatile fatty acid (VFA profiling and 16S rDNA sequencing. Fibrolyticstrains were selected to find fibrolytic enzymes and attachment to and digestion of various fibers. Fortyseven strains of Gram-negative curved rods were isolated. After determining cellulase, xylanase activities and VFA profile, 2 strains were chosen and employed for 16S rDNA sequencing. Both strains producingbutyrate were B. fibrisolvens. Of these 2 strains, most fibrolytic S-28 was selected. The strain S-28 could degrade natural fibers but not cellulose and showed strong attachment to them. A strong xylanase activitywas detected and presence of cellulase, β-glucosidase, β-xylosidase, α-L-arabinofuranosidase and β- cellobiosidase were also demonstrated.

  16. ANAEROBIC RESISTANCE TO HIGH LEVELS OF CADMIUM AND OTHER TOXIC METALS IN A FACULTATIVE ANAEROBE ISOLATED FROM PRISTINE SALT MARSH SEDIMENTS

    Energy Technology Data Exchange (ETDEWEB)

    SHARMA,P.K.; VAIRAVAMURTHY,A.; KIELECZAWA,J.

    1999-06-20

    The authors have isolated many Cd (II) resistant bacterial strains from relatively pristine sediments collected from salt marshes in Shelter Island, New York. Detailed studies are being performed on one isolate, strain Cd-1. Strain Cd-1 is metabolically diverse, halotolerant, Gram-negative, facultative anaerobe. It can resist high amounts of Cd (II), Cr (VI), As (V), Se (IV), Co (II), Pb (II), or Zn (II) under defined anaerobic conditions. With pyruvate as the energy source, Cd-1 can grow well at examined Cd (II) concentrations ranging up to 15 mM. It can resist Cd (II) with or without marine level NaCl concentration, under acidic or neutral conditions. It can resist Cd (II) under aerobic conditions as well. These features are novel for a heavy metal resistant bacterium.

  17. 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.

  18. Thermophilic Anaerobic Degradation of Butyrate by a Butyrate-Utilizing Bacterium in Coculture and Triculture with Methanogenic Bacteria

    OpenAIRE

    Ahring, Birgitte K.; Westermann, Peter

    1987-01-01

    We studied syntrophic butyrate degradation in thermophilic mixed cultures containing a butyrate-degrading bacterium isolated in coculture with Methanobacterium thermoautotrophicum or in triculture with M. thermoautotrophicum and the TAM organism, a thermophilic acetate-utilizing methanogenic bacterium. Butyrate was β-oxidized to acetate with protons as the electron acceptors. Acetate was used concurrently with its production in the triculture. We found a higher butyrate degradation rate in th...

  19. Identification of ceramide phosphorylethanolamine and ceramide phosphorylglycerol in the lipids of an anaerobic bacterium.

    Science.gov (United States)

    LaBach, J P; White, D C

    1969-09-01

    Nearly half the phospholipids isolated from the anerobic bacterium Bacteroides melaninogenicus are phosphosphingolipids. The two major phosphosphingolipids have been characterized as ceramide phosphorylethanolamine and ceramide phosphorylglycerol. The long-chain bases of these phosphosphingolipids appear to have branched and normal saturated carbon chains of 17, 18, and 19 atoms; the phosphate is at the 1-position of the long-chain base. The composition of the amide-linked fatty acids of the phosphosphingolipids differs from that of the ester-linked fatty acids of the diacylphosphoglycerides in having a higher percentage of 14:0, 17:0, and 18:0 acids as well as containing nearly all the monoenoic fatty acids found in the bacterial lipids. The finding of phosphosphingolipids in bacteria is exceedingly rare and to our knowledge ceramide phosphorylglycerol has not been previously found in nature.

  20. 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 ).

  1. Isolation of a tannic acid-degrading Streptococcus sp. from an anaerobic shea cake digester.

    Science.gov (United States)

    Nitiema, L W; Dianou, D; Simpore, J; Karou, S D; Savadogo, P W; Traore, A S

    2010-01-01

    An anaerobic digester fed with shea cake rich in tannins and phenolic compounds rich-shea cake and previously inoculated with anaerobic sludge from the pit of a slaughterhouse, enabled six months acclimatization of the bacteria to aromatic compounds. Afterwards, digester waste water samples were subject to successive culture on media with 1 g L(-1) tannic acid allowing the isolation of a bacterial strain coded AB. Strain AB was facultatively anaerobic, mesophilic, non-motile, non-sporulating, catalase and oxidase negative bacterium, namely strain AB, was isolated from an anaerobic digester fed with shea cake rich in tannins and phenolic compounds, after inoculation with anaerobic sludge from the pit of a slaughterhouse and enrichment on tannic acid. The coccoid cells occurred in pair, short or long chains and stained Gram-positive. Strain AB fermented a wide range of carbohydrates including glucose, fructose, galactose, raffinose, arabinose, sucrose, maltose, lactose, starch and cellulose. Optimum growth occurred with glucose and tannic acid at 37 degrees C and pH 8. The pH, temperature and salt concentration for growth ranged from 5 to 9, 20 to 45 degrees C and 0 to 15 g L(-1), respectively. Strain AB converted tannic acid to gallic acid. These features were similar to those of the Streptococcus genus. The determination of tannic acid hydrolysis end products, ability to utilize various organic acids, alcohols and peptides, GC% of the DNA, the sequencing of 16S rRNA gene and DNA-DNA hybridization will permit to confirm this affiliation and to determine the species.

  2. Isolation and characterization of a novel toluene-degrading, sulfate-reducing bacterium.

    Science.gov (United States)

    Beller, H R; Spormann, A M; Sharma, P K; Cole, J R; Reinhard, M

    1996-01-01

    A novel sulfate-reducing bacterium isolated from fuel-contaminated subsurface soil, strain PRTOL1, mineralizes toluene as the sole electron donor and carbon source under strictly anaerobic conditions. The mineralization of 80% of toluene carbon to CO2 was demonstrated in experiments with [ring-U-14C]toluene; 15% of toluene carbon was converted to biomass and nonvolatile metabolic by-products, primarily the former. The observed stoichiometric ratio of moles of sulfate consumed per mole of toluene consumed was consistent with the theoretical ratio for mineralization of toluene coupled with the reduction of sulfate to hydrogen sulfide. Strain PRTOL1 also transforms o- and p-xylene to metabolic products when grown with toluene. However, xylene transformation by PRTOL1 is slow relative to toluene degradation and cannot be sustained over time. Stable isotope-labeled substrates were used in conjunction with gas chromatography-mass spectrometry to investigate the by-products of toluene and xylene metabolism. The predominant by-products from toluene, o-xylene, and p-xylene were benzylsuccinic acid, (2-methylbenzyl)succinic acid, and 4-methylbenzoic acid (or p-toluic acid), respectively. Metabolic by-products accounted for nearly all of the o-xylene consumed. Enzyme assays indicated that acetyl coenzyme A oxidation proceeded via the carbon monoxide dehydrogenase pathway. Compared with the only other reported toluene-degrading, sulfate-reducing bacterium, strain PRTOL1 is distinct in that it has a novel 16S rRNA gene sequence and was derived from a freshwater rather than marine environment. PMID:8919780

  3. 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.

  4. Enterobacter siamensis sp. nov., a transglutaminase-producing bacterium isolated from seafood processing wastewater in Thailand.

    Science.gov (United States)

    Khunthongpan, Suwannee; Bourneow, Chaiwut; H-Kittikun, Aran; Tanasupawat, Somboon; Benjakul, Soottawat; Sumpavapol, Punnanee

    2013-01-01

    A novel strain of Enterobacter, C2361(T), a Gram-negative, non-spore-forming, rod-shaped and facultative anaerobic bacterium with the capability to produce transglutaminase, was isolated from seafood processing wastewater collected from a treatment pond of a seafood factory in Songkhla Province, Thailand. Phylogenetic analyses and phenotypic characteristics, including chemotaxonomic characteristics, showed that the strain was a member of the genus Enterobacter. The 16S rRNA gene sequence similarities between strain C2361(T) and Enterobacter cloacae subsp. cloacae ATCC 13047(T) and Enterobacter cloacae subsp. dissolvens LMG 2683(T) were 97.5 and 97.5%, respectively. Strain C2361(T) showed a low DNA-DNA relatedness with the above-mentioned species. The major fatty acids were C16:0, C17:0cyclo and C14:0. The DNA G+C content was 53.0 mol%. On the basis of the polyphasic evidence gathered in this study, it should be classified as a novel species of the genus Enterobacter for which the name Enterobacter siamensis sp. nov. is proposed. The type strain is C2361(T) (= KCTC 23282(T) = NBRC 107138(T)).

  5. Isolation of Clostridium tetani from anaerobic empyema.

    Science.gov (United States)

    Mayall, B C; Snashall, E A; Peel, M M

    1998-11-01

    We report the isolation of Clostridium tetani (along with Fusobacterium mortiferum) from empyema pus. The patient, a 68 year old retired farmer from rural NSW, had recently undergone cholecystectomy, had heart failure and developed an empyema. He improved after drainage of the empyema and penicillin therapy, but died suddenly during convalescence.

  6. Fermentative degradation of polyethylene glycol by a strictly anaerobic, gram-negative, nonsporeforming bacterium, Pelobacter venetianus sp. nov.

    Science.gov (United States)

    Schink, B; Stieb, M

    1983-06-01

    The synthetic polyether polyethylene glycol (PEG) with a molecular weight of 20,000 was anaerobically degraded in enrichment cultures inoculated with mud of limnic and marine origins. Three strains (Gra PEG 1, Gra PEG 2, and Ko PEG 2) of rod-shaped, gram-negative, nonsporeforming, strictly anaerobic bacteria were isolated in mineral medium with PEG as the sole source of carbon and energy. All strains degraded dimers, oligomers, and polymers of PEG up to a molecular weight of 20,000 completely by fermentation to nearly equal amounts of acetate and ethanol. The monomer ethylene glycol was not degraded. An ethylene glycol-fermenting anaerobe (strain Gra EG 12) isolated from the same enrichments was identified as Acetobacterium woodii. The PEG-fermenting strains did not excrete extracellular depolymerizing enzymes and were inhibited by ethylene glycol, probably owing to a blocking of the cellular uptake system. PEG, some PEG-containing nonionic detergents, 1,2-propanediol, 1,2-butanediol, glycerol, and acetoin were the only growth substrates utilized of a broad variety of sugars, organic acids, and alcohols. The isolates did not reduce sulfate, sulfur, thiosulfate, or nitrate and were independent of growth factors. In coculture with A. woodii or Methanospirillum hungatei, PEGs and ethanol were completely fermented to acetate (and methane). A marine isolate is described as the type strain of a new species, Pelobacter venetianus sp. nov. Its physiology and ecological significance, as well as the importance and possible mechanism of anaerobic polyether degradation, are discussed.

  7. Fermentative Degradation of Polyethylene Glycol by a Strictly Anaerobic, Gram-Negative, Nonsporeforming Bacterium, Pelobacter venetianus sp. nov

    OpenAIRE

    1983-01-01

    The synthetic polyether polyethylene glycol (PEG) with a molecular weight of 20,000 was anaerobically degraded in enrichment cultures inoculated with mud of limnic and marine origins. Three strains (Gra PEG 1, Gra PEG 2, and Ko PEG 2) of rod-shaped, gram-negative, nonsporeforming, strictly anaerobic bacteria were isolated in mineral medium with PEG as the sole source of carbon and energy. All strains degraded dimers, oligomers, and polymers of PEG up to a molecular weight of 20,000 completely...

  8. Bacillus tamaricis sp. nov., an alkaliphilic bacterium isolated from a Tamarix cone soil.

    Science.gov (United States)

    Zhang, Yong-Guang; Zhou, Xing-Kui; Guo, Jian-Wei; Xiao, Min; Wang, Hong-Fei; Wang, Yun; Bobodzhanova, Khursheda; Li, Wen-Jun

    2018-02-01

    A Gram-stain-positive, alkaliphilic bacterium, designated EGI 80668 T , was isolated from a Tamarix cone soil in Xinjiang, north-west China. Cells were facultatively anaerobic, terminal endospore-forming and motile by means of peritrichous flagella. Colonies were yellowish and the cells showed oxidase-negative and catalase-positive reactions. Strain EGI 80668 T grew at pH 8.0-10.0 and with 0-10 % (w/v) NaCl (optimally at pH 9.0 and with 1-2 % NaCl) on marine agar 2216. The predominant menaquinone was MK-7. The major fatty acids were anteiso-C17 : 0 and anteiso-C15 : 0. The cellular polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unknown phospholipids and one unknown aminophospholipid. The G+C content of the genomic DNA was 38.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain EGI 80668 T was affiliated to the genus Bacillus. The highest 16S rRNA gene sequence similarity between strain EGI 80668 T and a member of the genus Bacillus was 96.83 % with Bacillus cellulosilyticus JCM 9156 T . A polyphasic taxonomic study based on morphological, physiological, biochemical and phylogenetic data indicated that strain EGI 80668 T represents a novel species of the genus Bacillus, for which the name Bacillus tamaricis sp. nov. (type strain EGI 80668 T =KCTC 33703 T =CGMCC 1.15917 T ) is proposed.

  9. Dehalogenimonas formicexedens sp. nov., a chlorinated alkane-respiring bacterium isolated from contaminated groundwater.

    Science.gov (United States)

    Key, Trent A; Bowman, Kimberly S; Lee, Imchang; Chun, Jongsik; Albuquerque, Luciana; da Costa, Milton S; Rainey, Fred A; Moe, William M

    2017-05-01

    A strictly anaerobic, Gram-stain-negative, non-spore-forming bacterium designated NSZ-14T, isolated from contaminated groundwater in Louisiana (USA), was characterized using a polyphasic approach. Strain NSZ-14T reductively dehalogenated a variety of polychlorinated aliphatic alkanes, producing ethene from 1,2-dichloroethane, propene from 1,2-dichloropropane, a mixture of cis- and trans-1,2-dichloroethene from 1,1,2,2-tetrachloroethane, vinyl chloride from 1,1,2-trichloroethane and allyl chloride (3-chloro-1-propene) from 1,2,3-trichloropropane. Formate or hydrogen could both serve as electron donors. Dechlorination occurred between pH 5.5 and 7.5 and over a temperature range of 20-37 °C. Major cellular fatty acids included C18 : 1ω9c, C14 : 0 and C16 : 0. 16S rRNA gene sequence-based phylogenetic analysis indicated that the strain clusters within the class Dehalococcoidia of the phylum Chloroflexi, most closely related to but distinct from type strains of the species Dehalogenimonas alkenigignens (97.63 % similarity) and Dehalogenimonas lykanthroporepellens (95.05 %). A complete genome sequence determined for strain NSZ-14T revealed a DNA G+C content of 53.96 mol%, which was corroborated by HPLC (54.1±0.2 mol% G+C). Genome-wide comparisons based on average nucleotide identity by orthology and estimated DNA-DNA hybridization values combined with phenotypic and chemotaxonomic traits and phylogenetic analysis indicate that strain NSZ-14T represents a novel species within the genus Dehalogenimonas, for which the name Dehalogenimonas formicexedens sp. nov. is proposed. The type strain is NSZ-14T (=HAMBI 3672T=JCM 19277T=VKM B-3058T). An emended description of Dehalogenimonas alkenigignens is also provided.

  10. Draft genome sequence of a denitrifying bacterium Paracoccus marcusii PAMC 22219 isolated from Arctic marine sediment.

    Science.gov (United States)

    Cha, In-Tae; Song, Eun-Ji; Seok, Yoon Ji; Lee, Hyunjin; Park, Inhye; Lee, Yoo Kyung; Roh, Seong Woon; Choi, Hak-Jong; Nam, Young-Do; Seo, Myung-Ji

    2015-06-01

    A denitrifying bacterium, Paracoccus marcusii PAMC 22219, was isolated from Arctic marine sediment in Svalbard, Norway. The obtained contigs were 265 with genome size of 4.0Mb and G+C content of 66.1%. This bacterial genome revealed that it had nitrate and nitrite ammonification genes involved in the denitrification process, suggesting that P. marcusii PAMC 22219 is a denitrifying bacterium. This is the first genome that has been sequenced in the genus Paracoccus, isolated from an Arctic environment. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Isolation and identification of antifungal peptides from Bacillus BH072, a novel bacterium isolated from honey.

    Science.gov (United States)

    Zhao, Xin; Zhou, Zhi-jiang; Han, Ye; Wang, Zhan-zhong; Fan, Jie; Xiao, Hua-zhi

    2013-11-07

    A bacterial strain BH072 isolated from a honey sample showed antifungal activity against mold. Based on morphological, biochemical, physiological tests, and analysis of 16S rDNA sequence, the strain was identified to be a new subspecies of Bacillus sp. It had a broad spectrum of antifungal activity against various mold, such as Aspergillus niger, Pythium, and Botrytis cinerea. Six pairs of antifungal genes primers were designed and synthesized, and ituA, hag, tasA genes were detected by PCR analysis. The remarkable antifungal activity could be associated with the co-production of these three peptides. One of them was purified by 30-40% ammonium sulfate precipitation, Sephadex G-75 gel filtration and anion exchange chromatography on D201 resin. The purified peptide was estimated to be 35.615 kDa and identified to be flagellin by micrOTOF-Q II. By using methanol extraction, another substance was isolated from fermentation liquor, and determined to be iturin with liquid chromatography-mass spectrometry (LC-MS) method. The third possible peptide encoded by tasA was not isolated in this study. The culture liquor displayed antifungal activity in a wide pH range (5.0-9.0) and at 40-100°C. The result of the present work suggested that Bacillus BH072 might be a bio-control bacterium of research value. Copyright © 2013 Elsevier GmbH. All rights reserved.

  12. Isotope effects associated with the anaerobic oxidation of sulfide by the purple photosynthetic bacterium, Chromatium vinosum

    International Nuclear Information System (INIS)

    Fry, B.; Gest, H.; Hayes, J.M.

    1984-01-01

    Small inverse isotope effects of 1-3 per thousand were consistently observed for the oxidation of sulfide to elemental sulfur during anaerobic photometabolism by Chromatium vinosum. The inverse fractionation can be accounted for by an equilibrium isotope effect between H 2 S and HS - , and may indicate that C. vinosum (and other photosynthetic bacteria) utilizes H 2 S rather than HS - as the substrate during sulfide oxidation. (Auth.)

  13. Thermaerobacter litoralis sp. nov., a strictly aerobic and thermophilic bacterium isolated from a coastal hydrothermal field

    DEFF Research Database (Denmark)

    Tanaka, Reiji; Kawaichi, Satoshi; Nishimura, Hiroshi

    2006-01-01

    A novel thermophilic bacterium, strain KW1T, was isolated from a coastal hydrothermal field on the Satsuma Peninsula, Kagoshima Prefecture, Japan. The variably Gram-stained cells were motile rods with flagella, did not form spores and proliferated at 52-78°C (optimum, 70°C), pH 5-8 (optimum, pH 7...

  14. Isolation and Structure Elucidation of a Novel Yellow Pigment from the Marine Bacterium Pseudoalteromonas tunicata

    Directory of Open Access Journals (Sweden)

    N. Kumar

    2005-10-01

    Full Text Available The marine environment is a major source for many novel natural compounds. A new yellow pigment has been isolated from the marine bacterium P. tunicata and identified as a new member of the tambjamine class of compounds. The structural identification was achieved by a combination of 1D and 2D-NMR spectroscopy and high resolution mass spectrometry data.

  15. Fervidicola ferrireducens gen. nov., sp. nov., a thermophilic anaerobic bacterium from geothermal waters of the Great Artesian Basin, Australia.

    Science.gov (United States)

    Ogg, Christopher D; Patel, Bharat K C

    2009-05-01

    A strictly anaerobic, thermophilic bacterium, designated strain Y170(T), was isolated from a microbial mat colonizing thermal waters of a run-off channel created by the free-flowing waters of a Great Artesian Basin (GAB) bore well (New Lorne bore; registered number 17263). Cells of strain Y170(T) were slightly curved rods (1.2-12x0.8-1.1 mum) and stained Gram-negative. The strain grew optimally in tryptone-yeast extract-glucose medium at 70 degrees C (temperature range for growth was 55-80 degrees C) and pH 7 (pH range for growth was 5-9). Strain Y170(T) grew poorly on yeast extract as a sole carbon source, but not on tryptone (0.2 %). Yeast extract could not be replaced by tryptone and was obligately required for growth on tryptone, peptone, glucose, fructose, galactose, cellobiose, mannose, sucrose, xylose, mannitol, formate, pyruvate, Casamino acids and threonine. No growth was observed on arabinose, lactose, maltose, raffinose, chitin, xylan, pectin, starch, acetate, benzoate, lactate, propionate, succinate, myo-inositol, ethanol, glycerol, amyl media, aspartate, leucine, glutamate, alanine, arginine, serine and glycine. End products detected from glucose fermentation were acetate, ethanol and presumably CO(2) and H(2). Iron(III), manganese(IV), thiosulfate and elemental sulfur, but not sulfate, sulfite, nitrate or nitrite, were used as electron acceptors in the presence of 0.2 % yeast extract. Iron(III) in the form of amorphous Fe(III) oxhydroxide and Fe(III) citrate was also reduced in the presence of tryptone, peptone and Casamino acids, but not with chitin, xylan, pectin, formate, starch, pyruvate, acetate, benzoate, threonine, lactate, propionate, succinate, inositol, ethanol, glycerol, mannitol, aspartate, leucine, glutamate, alanine, arginine, serine or glycine. Strain Y170(T) was not able to utilize molecular hydrogen and/or carbon dioxide in the presence or absence of iron(III). Chloramphenicol, streptomycin, tetracycline, penicillin and ampicillin and

  16. Isolation and Characterization of a Bacteriophage Preying an Antifungal Bacterium

    Directory of Open Access Journals (Sweden)

    Aryan Rahimi-Midani

    2016-12-01

    Full Text Available Several Bacillus species were isolated from rice field soils, and 16S rRNA gene sequence analysis showed that Bacillus cereus was the most abundant. A strain named BC1 showed antifungal activity against Rhizoctonia solani. Bacteriophages infecting strain BC1 were isolated from the same soil sample. The isolated phage PK16 had an icosahedral head of 100 ± 5 nm and tail of 200 ± 5 nm, indicating that it belonged to the family Myoviridae. Analysis of the complete linear dsDNA genome revealed a 158,127-bp genome with G + C content of 39.9% comprising 235 open reading frames as well as 19 tRNA genes (including 1 pseudogene. Blastp analysis showed that the proteins encoded by the PK16 genome had the closest hits to proteins of seven different bacteriophages. A neighbor-joining phylogenetic tree based on the major capsid protein showed a robust clustering of phage PK16 with phage JBP901 and BCP8-2 isolated from Korean fermented food.

  17. Studies on amylase activity of an amylolytic bacterium isolated from ...

    African Journals Online (AJOL)

    Enzyme activity gradually got reduced with the addition of increasing concentrations of ethylenediaminetetraacetic acid (EDTA), confirming the need for calcium for enzyme action. The amylase produced in the medium was isolated by centrifugation and partially purified by ammonium sulphate fractionation followed by ...

  18. A probiotic bacterium, Pediococcus pentosaceus OZF, isolated from ...

    African Journals Online (AJOL)

    Pediococcus pentosaceus OZF, originally isolated from healthy human breast milk, produces antimicrobial activities against many gram-positive bacterial species, including the food borne pathogen, Listeria monocytogenes. A bacteriocin was purified to homogeneity from the supernatant of exponentially growing cells using ...

  19. Azospirillum brasilense, a Beneficial Soil Bacterium: Isolation and Cultivation.

    Science.gov (United States)

    Alexandre, Gladys

    2017-11-09

    Bacteria of the genus Azospirillum comprise 15 species to date, with A. brasilense the best studied species in the genus. Azospirillum are soil bacteria able to promote the growth of plants from 113 species spanning 35 botanical families. These non-pathogenic and beneficial bacteria are ubiquitous in soils and inhabit the roots of diverse plants. These bacteria are microaerophilic, able to fix nitrogen under free-living conditions, motile, and able to navigate in gradients of various chemicals, including oxygen. These physiological traits are used to isolate these soil bacteria from soil and plant root samples, providing isolates that can be used for studying microbial physiology and plant growth promotion. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  20. Desulfosporosinus acididurans sp. nov.: an acidophilic sulfate-reducing bacterium isolated from acidic sediments

    NARCIS (Netherlands)

    Sanchez Andrea, I.; Stams, A.J.M.; Hedrich, S.; Nancucheo, I.; Johnson, D.B.

    2015-01-01

    Three strains of sulfate-reducing bacteria (M1T, D, and E) were isolated from acidic sediments (White river and Tinto river) and characterized phylogenetically and physiologically. All three strains were obligately anaerobic, mesophilic, spore-forming straight rods, stained Gram-negative and

  1. [Isolation of endophytic antagonistic bacterium from Amorphophallus konjac and research on its antibacterial metabolite].

    Science.gov (United States)

    Zhou, Ying; Chen, Lin; Chai, Xin-Li; Yu, Zi-Niu; Sun, Ming

    2007-12-01

    An endophytic antagonistic bacterium was isolated from Amorphophallus konjac calli. In order to identify this bacterium, 16S rDNA was amplified and partially sequenced. Sequence comparison showed that this sequence has the highest similarity to that in Bacillus subtilis, with 99.0% identities. That demonstrated this bacterium belongs to Bacillus subtili , named BSn5. The extracted extracellular protein from strain BSn5 had antibacterial activity against Erwinia carotovora subp. carotovora, which was unstable after heated, sensitive to proteinase K and resistant to trypsin. There was only a 31.6kDa protein component as by SDS-PAGE detection. Nondenaturing polyacrylaminde gel was used to purify this protein. The purified 31.6kDa protein exhibited inhibitory activity against Erwinia carotovora subp. carotovora. This protein is different from all known metabolites from Bacillus subtilis, suggesting that it may be a novel antibacterial protein.

  2. Antibiotic Susceptibility Pattern of Aerobic and Anaerobic Bacteria Isolated From Surgical Site Infection of Hospitalized Patients.

    Science.gov (United States)

    Akhi, Mohammad Taghi; Ghotaslou, Reza; Beheshtirouy, Samad; Asgharzadeh, Mohammad; Pirzadeh, Tahereh; Asghari, Babak; Alizadeh, Naser; Toloue Ostadgavahi, Ali; Sorayaei Somesaraei, Vida; Memar, Mohammad Yousef

    2015-07-01

    Surgical Site Infections (SSIs) are infections of incision or deep tissue at operation sites. These infections prolong hospitalization, delay wound healing, and increase the overall cost and morbidity. This study aimed to investigate anaerobic and aerobic bacteria prevalence in surgical site infections and determinate antibiotic susceptibility pattern in these isolates. One hundred SSIs specimens were obtained by needle aspiration from purulent material in depth of infected site. These specimens were cultured and incubated in both aerobic and anaerobic condition. For detection of antibiotic susceptibility pattern in aerobic and anaerobic bacteria, we used disk diffusion, agar dilution, and E-test methods. A total of 194 bacterial strains were isolated from 100 samples of surgical sites. Predominant aerobic and facultative anaerobic bacteria isolated from these specimens were the members of Enterobacteriaceae family (66, 34.03%) followed by Pseudomonas aeruginosa (26, 13.4%), Staphylococcus aureus (24, 12.37%), Acinetobacter spp. (18, 9.28%), Enterococcus spp. (16, 8.24%), coagulase negative Staphylococcus spp. (14, 7.22%) and nonhemolytic streptococci (2, 1.03%). Bacteroides fragilis (26, 13.4%), and Clostridium perfringens (2, 1.03%) were isolated as anaerobic bacteria. The most resistant bacteria among anaerobic isolates were B. fragilis. All Gram-positive isolates were susceptible to vancomycin and linezolid while most of Enterobacteriaceae showed sensitivity to imipenem. Most SSIs specimens were polymicrobial and predominant anaerobic isolate was B. fragilis. Isolated aerobic and anaerobic strains showed high level of resistance to antibiotics.

  3. Ethanol production from wet-exploded wheat straw hydrolysate by thermophilic anaerobic bacterium Thermoanaerobacter BG1L1 in a continuous immobilized reactor

    DEFF Research Database (Denmark)

    Georgieva, Tania I.; Mikkelsen, Marie Just; Ahring, Birgitte Kiær

    2008-01-01

    to sugar mixtures of glucose and xylose ranging from 12 to 41 g/l. The organism, thermophilic anaerobic bacterium Thermoanaerobacter BG1L1, exhibited significant resistance to high levels of acetic acid (up to 10 g/l) and other metabolic inhibitors present in the hydrolysate. Although the hydrolysate...... considerable potential to be a novel candidate for lignocellulose bioconversion into ethanol. The work reported here also demonstrates that the use of FBR configuration might be a viable approach for thermophilic anaerobic ethanol fermentation....

  4. Genome analysis of Chitinivibrio alkaliphilus gen. nov., sp. nov., a novel extremely haloalkaliphilic anaerobic chitinolytic bacterium from the candidate phylum Termite Group 3

    NARCIS (Netherlands)

    Sorokin, D.Y.; Gumerov, V.M.; Rakitin, A.L.; Beletsky, A.V.; Sinninghe Damsté, J.S.; Muyzer, G.; Mardanov, A.V.; Ravin, N.V.

    2014-01-01

    Anaerobic enrichments from hypersaline soda lakes with chitin as substrate yielded five closely related anaerobic haloalkaliphilic isolates growing on insoluble chitin by fermentation at pH10 and salinities up to 3.5M. The chitinolytic activity was exclusively cell associated. To better understand

  5. Genome analysis of Chitinivibrio alkaliphilus gen. nov., sp. nov., a novel extremely haloalkaliphilic anaerobic chitinolytic bacterium from the candidate phylum Termite Group 3

    NARCIS (Netherlands)

    Sorokin, D.Y.; Gumerov, V.M.; Rakitin, A.L.; Beletsky, A.V.; Sinninghe Damsté, J.S.; Muyzer, G.; Mardanov, A.V.; Ravin, N.V.

    2014-01-01

    Anaerobic enrichments from hypersaline soda lakes with chitin as substrate yielded five closely related anaerobic haloalkaliphilic isolates growing on insoluble chitin by fermentation at pH 10 and salinities up to 3.5 M. The chitinolytic activity was exclusively cell associated. To better understand

  6. Genome-enabled studies of anaerobic, nitrate-dependent iron oxidation in the chemolithoautotrophic bacterium Thiobacillus denitrificans

    Directory of Open Access Journals (Sweden)

    Harry R Beller

    2013-08-01

    Full Text Available Thiobacillus denitrificans is a chemolithoautotrophic bacterium capable of anaerobic, nitrate-dependent U(IV and Fe(II oxidation, both of which can strongly influence the long-term efficacy of in situ reductive immobilization of uranium in contaminated aquifers. We previously identified two c-type cytochromes involved in nitrate-dependent U(IV oxidation in T. denitrificans and hypothesized that c-type cytochromes would also catalyze Fe(II oxidation, as they have been found to play this role in anaerobic phototrophic Fe(II-oxidizing bacteria. Here we report on efforts to identify genes associated with nitrate-dependent Fe(II oxidation, namely (a whole-genome transcriptional studies [using FeCO3, Fe2+, and U(IV oxides as electron donors under denitrifying conditions], (b Fe(II oxidation assays performed with knockout mutants targeting primarily highly expressed or upregulated c-type cytochromes, and (c random transposon-mutagenesis studies with screening for Fe(II oxidation. Assays of mutants for 26 target genes, most of which were c-type cytochromes, indicated that none of the mutants tested were significantly defective in nitrate-dependent Fe(II oxidation. The non-defective mutants included the c1-cytochrome subunit of the cytochrome bc1 complex (complex III, which has relevance to a previously proposed role for this complex in nitrate-dependent Fe(II oxidation and to current concepts of reverse electron transfer. A transposon mutant with a disrupted gene associated with NADH:ubiquinone oxidoreductase (complex I was ~35% defective relative to the wild-type strain; this strain was similarly defective in nitrate reduction with thiosulfate as the electron donor. Overall, our results indicate that nitrate-dependent Fe(II oxidation in T. denitrificans is not catalyzed by the same c-type cytochromes involved in U(IV oxidation, nor have other c-type cytochromes yet been implicated in the process.

  7. Five new amicoumacins isolated from a marine-derived Bacterium bacillus subtilis

    KAUST Repository

    Li, Yongxin

    2012-02-03

    Four novel amicoumacins, namely lipoamicoumacins A-D (1-4), and one new bacilosarcin analog (5) were isolated from culture broth of a marine-derived bacterium Bacillus subtilis, together with six known amicoumacins. Their structures were elucidated on the basis of extensive spectroscopic (2D NNR, IR, CD and MS) analysis and in comparison with data in literature. 2012 by the authors; licensee MDPI.

  8. [Identification and antagonistic activities of an endophytic bacterium MGP3 isolated from papaya fruit].

    Science.gov (United States)

    Shi, Jingying; Liu, Aiyuan; Li, Xueping; Chen, Weixin

    2011-09-01

    Postharvest decay resulted from anthracnose caused by pathogens Colletotrichum gloeosporioides and blight diseases caused by Phytophthora nicotianae leads to significant loss of papaya fruits. In order to reduce such loss, we isolated endophytic bacteria that may possess powerful antagonistic activities toward these pathogens for effective biological control of anthracnose and blight diseases. The methods of dilution and inhibition circle were used for isolating and screening endophytic bacteria from papaya fruit. Based on morphological, physiological and biochemical characteristics, and homology analysis of the partial sequence of 16S rDNA, an endophytic bacterium was identified. The colonization of the antagonistic endophyte in papaya was detected by inoculating suspension of strains in caudices of papaya plant after Rifampicin-resistant mutants (rif(r)) induction. The effects on diseases caused by Colletotrichum gloeosporioides and Phytophthora nicotianae were tested by preharvest and postharvest experiments. One of the endophytic bacteria named MGP3 was selected from the papaya pericarp and identified as Pseudomonas aeruginosa (Accession No. JF708186). This bacterium was able to colonize in the laminae, leafstalk or pericarp of papaya, and strongly inhibit 10 phytopathogens. In the postharvest experiment, MGP3 inhibited 50% anthracnose and 71% blight of harvested papaya fruits. The application of MGP3 at five preharvest stages of papaya significantly reduced latent infection rate of Colletotrichum gloeosporioides and disease index of anthracnose. Antagonistic endophytic bacterium MGP3 isolated from papaya fruit had potential application value as a biological control agent.

  9. Anaerosporomusa subterranea gen. nov., sp. nov., a spore-forming anaerobe belonging to the class Negativicutes isolated from saprolite.

    Science.gov (United States)

    Choi, Jessica K; Shah, Madhavi; Yee, Nathan

    2016-10-01

    A Gram-stain-negative, spore-forming, anaerobic bacterium designated strain RU4T was isolated from a saprolite core collected from Oak Ridge, Tennessee, USA. Cells were slightly curved rods and exhibited an outer membrane exterior to a thin cell wall. Strain RU4T formed heat-resistant endospores in late-log phase and stationary phase cultures. Under anaerobic conditions, strain RU4T grew by fermenting fumarate and maleate, but did not grow on glucose, glycerol, pyruvate, lactate, succinate, citrate, formate, acetate, propionate, butyrate or valerate. Strain RU4T did not reduce sulfate or ferric iron. The main cellular fatty acids were C17 : 0 cyclo, C16 : 0 and C15 : 0. The DNA G+C content was 52 mol%. Analysis of the 16S rRNA, rpoB, recA, infB, gyrB and atpD gene sequences indicated that the isolate is related to members of the family Sporomusaceae. Based on 92 % sequence similarity of the 16S rRNA gene to its closest relatives in the family Sporomusaceae and divergent physiological traits, the newly-cultivated isolate was assigned to a novel species of a new genus, Anaerosporomusa subterranea gen. nov., sp. nov. The type strain of Anaerosporomusa subterranea is RU4T (=DSM 29728T=ATCC BAA-2723T).

  10. Chitinilyticum aquatile gen. nov., sp. nov., a chitinolytic bacterium isolated from a freshwater pond used for Pacific white shrimp culture.

    Science.gov (United States)

    Chang, Shu-Chen; Chen, Wen-Ming; Wang, Jih-Terng; Wu, Ming-Chang

    2007-12-01

    Strain c14(T), originally isolated from surface water of a freshwater pond located in Pingtung (southern Taiwan) used for culture of Pacific white shrimp (Litopenaeus vannamei), was subjected to a polyphasic taxonomic approach. The strain exhibited strong chitinolytic activity and was able to grow under aerobic and anaerobic conditions by utilizing chitin exclusively as the carbon, nitrogen and energy source. Phylogenetic analysis of the 16S rRNA gene sequence revealed a clear affiliation of the proposed bacterium to the Betaproteobacteria, most closely related to Chitinibacter tainanensis S1(T), Deefgea rivuli WB 3.4-79(T) and Silvimonas terrae KM-45(T), with 94.6, 93.6 and 92.9 % 16S rRNA gene sequence similarity, respectively. The predominant fatty acids detected in cells of strain c14(T) were C(16 : 0), C(18 : 1)omega7c and summed feature 3 (C(16 : 1)omega7c and/or C(15 : 0) iso 2-OH). The G+C content of the genomic DNA was 69.5 (+/-1.0) mol%. Biochemical, physiological, chemotaxonomic and phylogenetic analyses showed that strain c14(T) could not be assigned to any known genus of the Betaproteobacteria. Therefore, strain c14(T) is classified within a novel genus and species, for which the name Chitinilyticum aquatile gen. nov., sp. nov. is proposed. The type strain of Chitinilyticum aquatile is c14(T) (=LMG 23346(T) =BCRC 17533(T)).

  11. Frequency of resistance in obligate anaerobic bacteria isolated from dogs, cats, and horses to antimicrobial agents.

    Science.gov (United States)

    Lawhon, S D; Taylor, A; Fajt, V R

    2013-11-01

    Clinical specimens from dogs, cats, and horses were examined for the presence of obligate anaerobic bacteria. Of 4,018 specimens cultured, 368 yielded 606 isolates of obligate anaerobic bacteria (248 from dogs, 50 from cats, and 308 from horses). There were 100 specimens from 94 animals from which only anaerobes were isolated (25 dogs, 8 cats, and 61 horses). The most common sites tested were abdominal fluid (dogs and cats) and intestinal contents (horses). The most common microorganism isolated from dogs, cats, and horses was Clostridium perfringens (75, 13, and101 isolates, respectively). The MICs of amoxicillin with clavulanate, ampicillin, chloramphenicol, metronidazole, and penicillin were determined using a gradient endpoint method for anaerobes. Isolates collected at necropsy were not tested for antimicrobial susceptibility unless so requested by the clinician. There were 1/145 isolates tested that were resistant to amoxicillin-clavulanate (resistance breakpoint ≥ 16/8 μg/ml), 7/77 isolates tested were resistant to ampicillin (resistance breakpoint ≥ 2 μg/ml), 4/242 isolates tested were resistant to chloramphenicol (resistance breakpoint ≥ 32 μg/ml), 12/158 isolates tested were resistant to clindamycin (resistance breakpoint ≥ 8 μg/ml), 10/247 isolates tested were resistant to metronidazole (resistance breakpoint ≥ 32 μg/ml), and 54/243 isolates tested were resistant to penicillin (resistance breakpoint ≥ 2 μg/ml). These data suggest that anaerobes are generally susceptible to antimicrobial drugs in vitro.

  12. Isolation, identification, and biocontrol of antagonistic bacterium against Botrytis cinerea after tomato harvest

    Directory of Open Access Journals (Sweden)

    Jun-Feng Shi

    Full Text Available ABSTRACT Tomato is one of the most important vegetables in the world. Decay after harvest is a major issue in the development of tomato industry. Currently, the most effective method for controlling decay after harvest is storage of tomato at low temperature combined with usage of chemical bactericide; however, long-term usage of chemical bactericide not only causes pathogen resistance but also is harmful for human health and environment. Biocontrol method for the management of disease after tomato harvest has great practical significance. In this study, antagonistic bacterium B-6-1 strain was isolated from the surface of tomato and identified as Enterobacter cowanii based on morphological characteristics and physiological and biochemical features combined with sequence analysis of 16SrDNA and ropB gene and construction of dendrogram. Effects of different concentrations of antagonistic bacterium E. cowanii suspension on antifungal activity after tomato harvest were analyzed by mycelium growth rate method. Results revealed that antifungal activity was also enhanced with increasing concentrations of antagonistic bacterium; inhibitory rates of 1 × 105 colony-forming units (cfu/mL antagonistic bacterial solution on Fusarium verticillioides, Alternaria tenuissima, and Botrytis cinerea were 46.31%, 67.48%, and 75.67%, respectively. By using in vivo inoculation method, it was further confirmed that antagonistic bacterium could effectively inhibit the occurrence of B. cinerae after tomato harvest, biocontrol effect of 1 × 109 cfu/mL zymotic fluid reached up to 95.24%, and antagonistic bacterium E. cowanii has biocontrol potential against B. cinerea after harvest of fruits and vegetables.

  13. Characterization and high-quality draft genome sequence of Herbivorax saccincola A7, an anaerobic, alkaliphilic, thermophilic, cellulolytic, and xylanolytic bacterium.

    Science.gov (United States)

    Aikawa, Shimpei; Baramee, Sirilak; Sermsathanaswadi, Junjarus; Thianheng, Phakhinee; Tachaapaikoon, Chakrit; Shikata, Ayumi; Waeonukul, Rattiya; Pason, Patthra; Ratanakhanokchai, Khanok; Kosugi, Akihiko

    2018-02-11

    An anaerobic, cellulolytic-xylanolytic bacterium, designated strain A7, was isolated from a cellulose-degrading bacterial community inhabiting bovine manure compost on Ishigaki Island, Japan, by enrichment culture using unpretreated corn stover as the sole carbon source. The strain was Gram-positive, non-endospore forming, non-motile, and formed orange colonies on solid medium. Strain A7 was identified as Herbivorax saccincola by DNA-DNA hybridization, and phylogenetic analysis based on 16S rRNA gene sequences showed that it was closely related to H. saccincola GGR1 (= DSM 101079 T ). H. saccincola A7 (= JCM 31827=DSM 104321) had quite similar phenotypic characteristics to those of strain GGR1. However, the optimum growth of A7 was at alkaline pH (9.0) and 55°C, compared to pH 7.0 at 60°C for GGR1, and the fatty acid profile of A7 contained 1.7-times more C 17:0 iso than GGR1. The draft genome sequence revealed that H. saccincola A7 possessed a cellulosome-like extracellular macromolecular complex, which has also been found for Clostridium thermocellum and C. clariflavum. H. saccincola A7 contained more glycoside hydrolases (GHs) belonging to GH families-11 and -2, and more diversity of xylanolytic enzymes, than C. thermocellum and C. clariflavum. H. saccincola A7 could grow on xylan because it encoded essential genes for xylose metabolism, such as a xylose transporter, xylose isomerase, xylulokinase, and ribulose-phosphate 3-epimerase, which are absent from C. thermocellum. These results indicated that H. saccincola A7 has great potential as a microorganism that can effectively degrade lignocellulosic biomass. Copyright © 2018 Elsevier GmbH. All rights reserved.

  14. Antimicrobial resistance determinants among anaerobic bacteria isolated from footrot.

    Science.gov (United States)

    Lorenzo, María; García, Nuria; Ayala, Juan Alfonso; Vadillo, Santiago; Píriz, Segundo; Quesada, Alberto

    2012-05-25

    Antibiotic resistance has been evaluated among 36 Gram negative and anaerobic bacilli (10 Bacteroides, 11 Prevotella, 7 Porphyromonas and 8 Fusobacterium strains) isolated from clinical cases of caprine and ovine footrot (necrotic pododermatitis). The initial analysis on this bacterial consortium evaluates the relationships existing among antimicrobial resistance determinants, phenotype expression and mobilization potential. The Bacteroides strains were generally resistant to penicillins, first-generation cephalosporins, tetracycline and erythromycin, and expressed low level of β-lactamase activity. The main determinants found among the Bacteroides strains were cepA and tetQ genes, conferring resistance to β-lactams and tetracycline, respectively. A general susceptibility to β-lactams was shown for most Prevotella, Porphyromonas and Fusobacterium strains, where none of the β-lactamase genes described in Bacteroides was detected. Resistance to tetracycline and/or erythromycin was found among the three bacterial groups. Although tetQ genes were detected for several Prevotella and Porphyromonas strains, a unique ermF positive was revealed among Prevotella strains. The expression of resistance markers was not related with the polymorphism of their coding sequences. However, the finding of sequence signatures for conjugative transposons in the vicinities of tetQ and ermF suggests a mobilization potential that might have contributed to the spread of antimicrobial resistance genes. Copyright © 2011 Elsevier B.V. All rights reserved.

  15. Isolation, characterization, and optimization of an aerobic butanol-producing bacterium from Singapore.

    Science.gov (United States)

    Ng, Cheng Ying Chloe; Takahashi, Katsuyuki; Liu, Zhibin

    2016-01-01

    We aimed to isolate aerobic butanol-producing microorganisms from environmental samples as potential platform strains for butanol production. Soil samples collected were subjected to a semi-high-throughput screening strategy. A microorganism capable of producing butanol in high concentrations under aerobic conditions was isolated and identified as Bacillus species by 16S rDNA analysis. The growth and butanol production under both aerobic and anaerobic conditions of the isolated Bacillus sp. 15, together with a different composition of by-products, suggest different metabolic networks from the obligate anaerobes Clostridia. At 1 L scale fermentation with 0.2 L/Min of ariflow, butanol titer reached up to 10.38 g/L in a batch culture. The fermentation process of the isolate also occurred in two phases and the acidic condition is critical for butanol production. The butanol concentration was further improved to 12.3 g/L with minimized by-products using a microaerobic condition. With the above-mentioned distinct features, the isolated Bacillus sp. 15 is a suitable platform strain for further process development and metabolic engineering for butanol production. © 2015 International Union of Biochemistry and Molecular Biology, Inc.

  16. 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.

  17. IDENTIFICATION AND PATHOGENICITY OF ISOLATE OF BACTERIUM CAUSED LEAF BLIGHT DISEASE ON Maranta arundinacea

    Directory of Open Access Journals (Sweden)

    Supriadi Supriadi

    2018-01-01

    Full Text Available Arrowroot (Maranta arundinacea L is a multi-functional plant used as a source of medicinal, carbohydrate (especially the green leaf type and also as ornamental plant (the streaked white leaf type. A leaf blight disease is recently found on the streaked white type in Bogor. Preliminary observation indicated that the disease was associated with bacterial infection. The cause of the disease has not been studied. This study was aimed to identify the cause of bacterial leaf blight disease. Experiments were conducted in the laboratory of Research Institute for Spice and Medicinal Crops in Bogor. Suspected bacteria were isolated from diseased leaves. The results showed that the bacterium produced white to brownish colonies on rich agar media containing peptone or cassamino acid. 3-5 mm in diameter, circular, and did not yield fluorescent pigment on King’s B medium. The bacterium formed rod cells, Gram negative, accumulated poly β hydroxybutyrate, utilized glucose under aerobic condition, not hydrolyse arginine and starch, positive catalase, insensitive to tetrazolium salt (0.1%, and grew at 35oC. The bacterium neither producted xanthomonadin pigment nor reduced nitrate to nitrite. The pathogen was tolerant to penicillin and oxolinic acid, but sensitive to streptomycin and oxytetracycline at high concentration (1.000 ppm. These characteristics met to those of Pseudomonas cepacia. Pathogenicity test on detached leaves showed that the typical symptom of blight was similar to that of natural infection on arrowroot. This is the first report on occurrence of P cepacia on arrowroot plant.

  18. Cadmium resistance and uptake by bacterium, Salmonella enterica 43C, isolated from industrial effluent.

    Science.gov (United States)

    Khan, Zaman; Rehman, Abdul; Hussain, Syed Z; Nisar, Muhammad A; Zulfiqar, Soumble; Shakoori, Abdul R

    2016-12-01

    Cadmium resistant bacterium, isolated from industrial wastewater, was characterized as Salmonella enterica 43C on the basis of biochemical and 16S rRNA ribotyping. It is first ever reported S. enterica 43C bared extreme resistance against heavy metal consortia in order of Pb(2+)>Cd(2+)>As(3+)>Zn(2+)>Cr(6+)>Cu(2+)>Hg(2+). Cd(2+) stress altered growth pattern of the bacterium in time dependent manner. It could remove nearly 57 % Cd(2+) from the medium over a period of 8 days. Kinetic and thermodynamic studies based on various adsorption isotherm models (Langmuir and Freundlich) depicted the Cd(2+) biosorption as spontaneous, feasible and endothermic in nature. Interestingly, the bacterium followed pseudo first order kinetics, making it a good biosorbent for heavy metal ions. The S. enterica 43C Cd(2+) processivity was significantly influenced by temperature, pH, initial Cd(2+) concentration, biomass dosage and co-metal ions. FTIR analysis of the bacterium revealed the active participation of amide and carbonyl moieties in Cd(2+) adsorption confirmed by EDX analysis. Electron micrographs beckoned further surface adsorption and increased bacterial size due to intracellular Cd(2+) accumulation. An overwhelming increase in glutathione and other non-protein thiols levels played a significant role in thriving oxidative stress generated by metal cations. Presence of metallothionein clearly depicted the role of such proteins in bacterial metal resistance mechanism. The present study results clearly declare S. enterica 43C a suitable candidate for green chemistry to bioremediate environmental Cd(2+).

  19. Isolation of a soil bacterium capable of biodegradation and detoxification of endosulfan and endosulfan sulfate.

    Science.gov (United States)

    Lee, Jung-Bok; Sohn, Ho-Yong; Shin, Kee-Sun; Jo, Min-Sub; Kim, Jang-Eok; Lee, Se-Won; Shin, Ji-Won; Kum, Eun-Joo; Kwon, Gi-Seok

    2006-11-15

    Endosulfan, an endocrine disrupting chemical, is a widely used cyclodiene organochlorine pesticide worldwide, and it blocks neuronal GABA(A)-gated chloride channels in mammals and aquatic organisms. Endosulfan and its metabolites, such as endosulfan sulfate, are persistent in environments and are considered as toxic chemicals. For bioremediation of endosulfan, in this study, an attempt was made to isolate an endosulfan and endosulfan sulfate degrading bacterium from endosulfan-polluted agricultural soil. Through repetitive enrichment and successive subculture using endosulfan or endosulfan sulfate as the sole carbon source, a bacterium KS-2P was isolated. The KS-2P was identified as Pseudomonas sp. on the basis of the results of a 16S rDNA sequencing analysis and MIDI test. The degradation ratios for endosulfan or endosulfan sulfate in minimal medium containing endosulfan (23.5 microg mL(-1)) or endosulfan sulfate (21 microg mL(-1)) were 52% and 71%, respectively. Our results suggest that Pseudomonas sp. KS-2P has potential as a biocatalyst for endosulfan bioremediation.

  20. (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.

  1. Novel Poly[(R-3-Hydroxybutyrate]-Producing Bacterium Isolated from a Bolivian Hypersaline Lake

    Directory of Open Access Journals (Sweden)

    María Soledad Marqués-Calvo

    2013-01-01

    Full Text Available Poly[(R-3-hydroxybutyrate] (PHB constitutes a biopolymer synthesized from renewable resources by various microorganisms. This work focuses on finding a new PHB-producing bacterium capable of growing in conventional media used for industrial biopolymer production, its taxonomical identification, and characterization of its biopolymer. Thus, a bacterial isolation process was carried out from environmental samples of water and mud. Among the isolates, strain S29 was selected and used in a fed-batch fermentation to generate a biopolymer. This biopolymer was recovered and identified as PHB homopolymer. Surprisingly, it featured several fractions of different molecular masses, and thermal properties unusual for PHB. Hence, the microorganism S29, genetically identified as a new strain of Bacillus megaterium, proved to be interesting not only due to its growth and PHB accumulation kinetics under the investigated cultivation conditions, but also due to the thermal properties of the produced PHB.

  2. Vibrio oceanisediminis sp. nov., a nitrogen-fixing bacterium isolated from an artificial oil-spill marine sediment.

    Science.gov (United States)

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

    2015-10-01

    A Gram-staining-negative, halophilic, facultatively anaerobic, motile, rod-shaped and nitrogen-fixing bacterium, designated strain S37T, was isolated from an artificial oil-spill sediment sample from the coast of Taean, South Korea. Cells grew at 10-37 °C and pH 5.0-9.0, with optimal growth at 28 °C and pH 6.0-8.0. Growth was observed with 1-9 % (w/v) NaCl in marine broth, with optimal growth with 3-5 % NaCl, but no growth was observed in the absence of NaCl. According to the results of 16S rRNA gene sequence analysis, strain S37T represents a member of the genus Vibrio of the class Gammaproteobacteria and forms a clade with Vibrio plantisponsor MSSRF60T (97.38 %), Vibrio diazotrophicus ATCC 33466T (97.31 %), Vibrio aestuarianus ATCC 35048T (97.07 %) Vibrio areninigrae J74T (96.76 %) and Vibrio hispanicus LMG 13240T (96.76 %). The major fatty acids were C16 : 0, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c. The DNA G+C content was 41.9 %. The DNA-DNA hybridization analysis results showed a 30.2 % association value with the closely related type strain V. plantisponsor DSM 21026T. On the basis of phenotypic and chemotaxonomic characteristics, strain S37T represents a novel species of the genus Vibrio, for which the name Vibrio oceanisediminis sp. nov., is proposed with the type strain S37T ( = KEMB 2255-005T = JCM 30409T).

  3. Antimicrobial susceptibility of clinical isolates of anaerobic bacteria in Ontario, 2010-2011.

    Science.gov (United States)

    Marchand-Austin, Alex; Rawte, Prasad; Toye, Baldwin; Jamieson, Frances B; Farrell, David J; Patel, Samir N

    2014-08-01

    The local epidemiology of antimicrobial susceptibility patterns in anaerobic bacteria is important in guiding the empiric treatment of infections. However, susceptibility data are very limited on anaerobic organisms, particularly among non-Bacteroides organisms. To determine susceptibility profiles of clinically-significant anaerobic bacteria in Ontario Canada, anaerobic isolates from sterile sites submitted to Public Health Ontario Laboratory (PHOL) for identification and susceptibility testing were included in this study. Using the E-test method, isolates were tested for various antimicrobials including, penicillin, cefoxitin, clindamycin, meropenem, piperacillin-tazobactam and metronidazole. The MIC results were interpreted based on guidelines published by Clinical and Laboratory Standards Institute. Of 2527 anaerobic isolates submitted to PHOL, 1412 were either from sterile sites or bronchial lavage, and underwent susceptibility testing. Among Bacteroides fragilis, 98.2%, 24.7%, 1.6%, and 1.2% were resistant to penicillin, clindamycin, piperacillin-tazobactam, and metronidazole, respectively. Clostridium perfringens was universally susceptible to penicillin, piperacillin-tazobactam, and meropenem, whereas 14.2% of other Clostridium spp. were resistant to penicillin. Among Gram-positive anaerobes, Actinomyces spp., Parvimonas micra and Propionibacterium spp. were universally susceptible to β-lactams. Eggerthella spp., Collinsella spp., and Eubacterium spp. showed variable resistance to penicillin. Among Gram-negative anaerobes, Fusobacterium spp., Prevotella spp., and Veillonella spp. showed high resistance to penicillin but were universally susceptible to meropenem and piperacillin-tazobactam. The detection of metronidazole resistant B. fragilis is concerning as occurrence of these isolates is extremely rare. These data highlight the importance of ongoing surveillance to provide clinically relevant information to clinicians for empiric management of

  4. Alicyclobacillus vulcanalis sp. nov., a thermophilic, acidophilic bacterium isolated from Coso Hot Springs, California, USA.

    Science.gov (United States)

    Simbahan, Jessica; Drijber, Rhae; Blum, Paul

    2004-09-01

    A thermo-acidophilic Gram-positive bacterium, strain CsHg2T, which grows aerobically at 35-65 degrees C (optimum 55 degrees C) and at pH 2.0-6.0 (optimum 4.0), was isolated from a geothermal pool located in Coso Hot Springs in the Mojave Desert, California, USA. Phylogenetic analysis of 16S rRNA gene sequences showed that this bacterium was most closely related to the type strains of Alicyclobacillus acidocaldarius (97.8 % identity) and Alicyclobacillus sendaiensis (96.9 %), three Japanese strains denoted as UZ-1, KHA-31 and MIH 332 (96.1-96.5 %) and Alicyclobacillus genomic species FR-6 (96.3 %). Phenotypic characteristics including temperature and pH optima, G+C composition, acid production from a variety of carbon sources and sensitivity to different metal salts distinguished CsHg2T from A. acidocaldarius, A. sendaiensis and FR-6. The cell lipid membrane was composed mainly of omega-cyclohexyl fatty acid, consistent with membranes from other Alicyclobacillus species. Very low DNA-DNA hybridization values between CsHg2T and the type strains of Alicyclobacillus indicate that CsHg2T represents a distinct species. On the basis of these results, the name Alicyclobacillus vulcanalis sp. nov. is proposed for this organism. The type strain is CsHg2T (ATCC BAA-915T = DSM 16176T).

  5. Isolation, identification and characteristics of an endophytic quinclorac degrading bacterium Bacillus megaterium Q3.

    Directory of Open Access Journals (Sweden)

    Min Liu

    Full Text Available In this study, we isolated an endophytic quinclorac-degrading bacterium strain Q3 from the root of tobacco grown in quinclorac contaminated soil. Based on morphological characteristics, Biolog identification, and 16S rDNA sequence analysis, we identified strain Q3 as Bacillus megaterium. We investigated the effects of temperature, pH, inoculation size, and initial quinclorac concentration on growth and degrading efficiency of Q3. Under the optimal degrading condition, Q3 could degrade 93% of quinclorac from the initial concentration of 20 mg/L in seven days. We analyzed the degradation products of quinclorac using liquid chromatography-tandem mass spectrometry (LC-MS/MS. The major degradation products by Q3 were different from those of previously identified quinclorac degrading strains, which suggests that Q3 may employ new pathways for quinclorac degradation. Our indoor pot experiments demonstrated that Q3 can effectively alleviate the quinclorac phytotoxicity in tobacco. As the first endophytic microbial that is capable of degrading quinclorac, Q3 can be a good bioremediation bacterium for quinclorac phytotoxicity.

  6. Epidemiology and Antimicrobial Susceptibilities of Wound Isolates of Obligate Anaerobes from Combat Casualties

    Science.gov (United States)

    White, Brian K.; Mende, Katrin; Weintrob, Amy C.; Beckius, Miriam L.; Zera, Wendy C.; Lu, Dan; Bradley, William; Tribble, David R.; Schnaubelt, Elizabeth R.; Murray, Clinton K.

    2015-01-01

    Data from recent conflicts related to war wounds and obligate anaerobes are limited. We define the epidemiology and antimicrobial susceptibility of obligate anaerobes from Iraq and Afghanistan casualties (6/2009–12/2013), as well as their association with clinical outcomes. Susceptibility against eleven antibiotics (7 classes) was tested. Overall, 59 patients had 119 obligate anaerobes identified (83 were first isolates). Obligate anaerobes were isolated 7–13 days post-injury, primarily from lower extremity wounds (43%), and were largely Bacteroides spp. (42%) and Clostridium spp. (19%). Patients with pelvic wounds were more likely to have Bacteroides spp. and concomitant resistant gram-negative aerobes. Seventy-three percent of isolates were resistant to ≥1 antimicrobials. Bacteroides spp. demonstrated the most resistance (16% of first isolates). Patients with resistant isolates had similar outcomes to those with susceptible strains. Serial recovery of isolates occurred in 15% of patients and was significantly associated with isolation of Bacteroides spp., along with resistant gram-negative aerobes. PMID:26607420

  7. 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.

  8. Isolation and characterization of transducing bacteriophage BP1 for Bacterium anitratum (Achromobacter sp.).

    Science.gov (United States)

    Twarog, R; Blouse, L E

    1968-07-01

    A small transducing phage has been isolated against a strain of Bacterium anitratum. The particle has a head dimension of 450 A and a tail approximately 200 A long. The latent period is 16 min and the average burst size is 98. The intact particle has an absorption maximum and minimum at 260 and 237 mmu, respectively. The sedimentation coefficient (S(20)) is 460. The phage contains double-stranded DNA with an S degrees (20,w) of 32.8. Molecular weight estimates of the deoxyribonucleic acid ranged from 2.33 x 10(7) to 2.66 x 10(7) based on sedimentation velocity studies. The percentage guanine plus cytosine compositions of the deoxyribonucleic acid, determined by melting temperature and cesium chloride equilibrium centrifugation, were 40.7 and 42.0, respectively.

  9. Emergence of a New Population of Rathayibacter toxicus: An Ecologically Complex, Geographically Isolated Bacterium.

    Science.gov (United States)

    Arif, Mohammad; Busot, Grethel Y; Mann, Rachel; Rodoni, Brendan; Liu, Sanzhen; Stack, James P

    2016-01-01

    Rathayibacter toxicus is a gram-positive bacterium that infects the floral parts of several Poaceae species in Australia. Bacterial ooze is often produced on the surface of infected plants and bacterial galls are produced in place of seed. R. toxicus is a regulated plant pathogen in the U.S. yet reliable detection and diagnostic tools are lacking. To better understand this geographically-isolated plant pathogen, genetic variation as a function of geographic location, host species, and date of isolation was determined for isolates collected over a forty-year period. Discriminant analyses of recently collected and archived isolates using Multi-Locus Sequence Typing (MLST) and Inter-Simple Sequence Repeats (ISSR) identified three populations of R. toxicus; RT-I and RT-II from South Australia and RT-III from Western Australia. Population RT-I, detected in 2013 and 2014 from the Yorke Peninsula in South Australia, is a newly emerged population of R. toxicus not previously reported. Commonly used housekeeping genes failed to discriminate among the R. toxicus isolates. However, strategically selected and genome-dispersed MLST genes representing an array of cellular functions from chromosome replication, antibiotic resistance and biosynthetic pathways to bacterial acquired immunity were discriminative. Genetic variation among isolates within the RT-I population was less than the within-population variation for the previously reported RT-II and RT-III populations. The lower relative genetic variation within the RT-I population and its absence from sampling over the past 40 years suggest its recent emergence. RT-I was the dominant population on the Yorke Peninsula during the 2013-2014 sampling period perhaps indicating a competitive advantage over the previously detected RT-II population. The potential for introduction of this bacterial plant pathogen into new geographic areas provide a rationale for understanding the ecological and evolutionary trajectories of R. toxicus.

  10. Loktanella spp. Gb03 as an algicidal bacterium, isolated from the culture of Dinoflagellate Gambierdiscus belizeanus

    Directory of Open Access Journals (Sweden)

    Anmar Hameed Bloh

    2016-02-01

    Full Text Available Aim: Bacteria associated with harmful algal blooms can play a crucial role in regulating algal blooms in the environment. This study aimed at isolating and identifying algicidal bacteria in Dinoflagellate culture and to determine the optimum growth requirement of the algicidal bacteria, Loktanella sp. Gb-03. Materials and Methods: The Dinoflagellate culture used in this study was supplied by Professor Gires Usup’s Laboratory, School of Environmental and Natural Resources Sciences, Faculty of Science and Technology, University Kebangsaan Malaysia, Malaysia. The culture was used for the isolation of Loktanella sp., using biochemical tests, API 20 ONE kits. The fatty acid content of the isolates and the algicidal activity were further evaluated, and the phenotype was determined through the phylogenetic tree. Results: Gram-negative, non-motile, non-spore-forming, short rod-shaped, aerobic bacteria (Gb01, Gb02, Gb03, Gb04, Gb05, and Gb06 were isolated from the Dinoflagellate culture. The colonies were pink in color, convex with a smooth surface and entire edge. The optimum growth temperature for the Loktanella sp. Gb03 isolate was determined to be 30°C, in 1% of NaCl and pH7. Phylogenetic analysis based on 16S rRNA gene sequences showed that the bacterium belonged to the genus Loktanella of the class Alphaproteobacteria and formed a tight cluster with the type strain of Loktanella pyoseonensis (97.0% sequence similarity. Conclusion: On the basis of phenotypic, phylogenetic data and genetic distinctiveness, strain Gb-03, were placed in the genus Loktanella as the type strain of species. Moreover, it has algicidal activity against seven toxic Dinoflagellate. The algicidal property of the isolated Loktanella is vital, especially where biological control is needed to mitigate algal bloom or targeted Dinoflagellates.

  11. 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.

  12. Degradation of Reactive Black 5 dye by a newly isolated bacterium Pseudomonas entomophila BS1.

    Science.gov (United States)

    Khan, Sana; Malik, Abdul

    2016-03-01

    The textile and dye industries are considered as one of the major sources of environmental pollution. The present study was conducted to investigate the degradation of the azo dye Reactive Black 5 (RB 5) using a bacterium isolated from soil samples collected around a textile industry. The bacterial strain BS1 capable of degrading RB 5 was isolated and identified as Pseudomonas entomophila on the basis of 16S rDNA sequencing. The effects of different parameters on the degradation of RB 5 were studied to find out the optimal conditions required for maximum degradation, which was 93% after 120 h of incubation. Static conditions with pH in the range of 5-9 and a temperature of 37 °C were found to be optimum for degrading RB 5. Enzyme assays demonstrated that P. entomophila possessed azoreductase, which played an important role in degradation. The enzyme was dependent on flavin mononucleotide and NADH for its activity. Furthermore, a possible degradation pathway of the dye was proposed through gas chromatography - mass spectrometry analysis, which revealed that the metabolic products were naphthalene-1,2-diamine and 4-(methylsulfonyl) aniline. Thus the ability of this indigenous bacterial isolate for simultaneous decolorization and degradation of the azo dye signifies its potential application for treatment of industrial wastewaters containing azo dyes.

  13. Thymidine uptake, thymidine incorporation, and thymidine kinase activity in marine bacterium isolates

    International Nuclear Information System (INIS)

    Jeffrey, W.H.; Paul, J.H.

    1990-01-01

    One assumption made in bacterial production estimates from [ 3 H]thymidine incorporation is that all heterotrophic bacteria can incorporate exogenous thymidine into DNA. Heterotrophic marine bacterium isolates from Tampa Bay, Fla., Chesapeake Bay, Md., and a coral surface microlayer were examined for thymidine uptake (transport), thymidine incorporation, the presence of thymidine kinase genes, and thymidine kinase enzyme activity. Of the 41 isolates tested, 37 were capable of thymidine incorporation into DNA. The four organisms that could not incorporate thymidine also transported the thymidine poorly and lacked thymidine kinase activity. Attempts to detect thymidine kinase genes in the marine isolates by molecular probing with gene probes made from Escherichia coli and herpes simplex virus thymidine kinase genes proved unsuccessful. To determine if the inability to incorporate thymidine was due to the lack of thymidine kinase, one organism, Vibro sp. strain DI9, was transformed with a plasmid (pGQ3) that contained an E. coli thymidine kinase gene. Although enzyme assays indicated high levels of thymidine kinase activity in transformants, these cells still failed to incorporate exogenous thymidine into DNA or to transport thymidine into cells. These results indicate that the inability of certain marine bacteria to incorporate thymidine may not be solely due to the lack of thymidine kinase activity but may also be due to the absence of thymidine transport systems

  14. Study on bioremediation of Lead by exopolysaccharide producing metallophilic bacterium isolated from extreme habitat

    Directory of Open Access Journals (Sweden)

    Debajit Kalita

    2017-12-01

    Full Text Available Lead released from manufacturing factories, recycling plants, automobile company and landfill leachate is abundantly found in wastewater. An efficient bioremediating agent for lead removal from wastewater is expected to ease the ever increasing problem. The present study reports Pseudomonas sp. W6 isolated from extreme habitat of hot water spring of North–East India evaluated for its Lead biosorption property. The bacterium showed capacity to resist 1.0 mM lead in both solid and liquid minimal media. Epifluorescence microscopy reveal the viability of bacterial cells under metal stress condition. ICP-MS analysis revealed 65% and 61.2% removal of lead from the Synthetic Bangladesh Ground Water medium in batch culture and column study respectively which was higher when compared to biosorption capacity of P. aeruginosa MTCC2474, P. alcaligenes MJ7 from forest soil and P. ficuserectae PKRS11 from uranium rich soil. Exopolysaccharide released by the isolate which influenced biosorption revealed the presence of ligands assayed using microbial hydrophobicity and FTIR. The extremophilic isolate is proposed as a choice for efficient bioremediation of lead contaminated wastewater. Keywords: Extremophile, Pseudomonas, Lead bioremediation, Epifluorescence microscopy, ICP-MS, FTIR

  15. Study on bioremediation of Lead by exopolysaccharide producing metallophilic bacterium isolated from extreme habitat.

    Science.gov (United States)

    Kalita, Debajit; Joshi, S R

    2017-12-01

    Lead released from manufacturing factories, recycling plants, automobile company and landfill leachate is abundantly found in wastewater. An efficient bioremediating agent for lead removal from wastewater is expected to ease the ever increasing problem. The present study reports Pseudomonas sp. W6 isolated from extreme habitat of hot water spring of North-East India evaluated for its Lead biosorption property. The bacterium showed capacity to resist 1.0 mM lead in both solid and liquid minimal media. Epifluorescence microscopy reveal the viability of bacterial cells under metal stress condition. ICP-MS analysis revealed 65% and 61.2% removal of lead from the Synthetic Bangladesh Ground Water medium in batch culture and column study respectively which was higher when compared to biosorption capacity of P. aeruginosa MTCC 2474, P. alcaligenes MJ7 from forest soil and P. ficuserectae PKRS11 from uranium rich soil. Exopolysaccharide released by the isolate which influenced biosorption revealed the presence of ligands assayed using microbial hydrophobicity and FTIR. The extremophilic isolate is proposed as a choice for efficient bioremediation of lead contaminated wastewater.

  16. Electricity Generation in Microbial Fuel Cell (MFC) by Bacterium Isolated from Rice Paddy Field Soil

    Science.gov (United States)

    Fakhirruddin, Fakhriah; Amid, Azura; Salim, Wan Wardatul Amani Wan; Suhaida Azmi, Azlin

    2018-03-01

    Microbial fuel cell (MFC) is an alternative approach in generating renewable energy by utilising bacteria that will oxidize organic or inorganic substrates, producing electrons yielded as electrical energy. Different species of exoelectrogenic bacteria capable of generating significant amount of electricity in MFC has been identified, using various organic compounds for fuel. Soil sample taken from rice paddy field is proven to contain exoelectrogenic bacteria, thus electricity generation using mixed culture originally found in the soil, and pure culture isolated from the soil is studied. This research will isolate the exoelectrogenic bacterial species in the rice paddy field soil responsible for energy generation. Growth of bacteria isolated from the MFC is observed by measuring the optical density (OD), cell density weight (CDW) and viable cell count. Mixed bacterial species found in paddy field soil generates maximum power of 77.62 μW and 0.70 mA of current. In addition, the research also shows that the pure bacterium in rice paddy field soil can produce maximum power and current at 51.32 μW and 0.28 mA respectively.

  17. PCR-based detection of resistance genes in anaerobic bacteria isolated from intra-abdominal infections.

    Science.gov (United States)

    Tran, Chau Minh; Tanaka, Kaori; Watanabe, Kunitomo

    2013-04-01

    Little information is available on the distribution of antimicrobial resistance genes in anaerobes in Japan. To understand the background of antimicrobial resistance in anaerobes involved in intra-abdominal infections, we investigated the distribution of eight antimicrobial resistance genes (cepA, cfiA, cfxA, ermF, ermB, mefA, tetQ, and nim) and a mutation in the gyrA gene in a total of 152 organisms (Bacteroides spp., Prevotella spp., Fusobacterium spp., Porphyromonas spp., Bilophila wadsworthia, Desulfovibrio desulfuricans, Veillonella spp., gram-positive cocci, and non-spore-forming gram-positive bacilli) isolated between 2003 and 2004 in Japan. The cepA gene was distributed primarily in Bacteroides fragilis. Gene cfxA was detected in about 9 % of the Bacteroides isolates and 75 % of the Prevotella spp. isolates and did not appear to contribute to cephamycin resistance. Two strains of B. fragilis contained the metallo-β-lactamase gene cfiA, but they did not produce the protein product. Gene tetQ was detected in about 81, 44, and 63 % of B. fragilis isolates, other Bacteroides spp., and Prevotella spp. isolates, respectively. The ermF gene was detected in 25, 13, 56, 64, and 16 % of Bacteroides spp., Prevotella spp., Fusobacterium spp., B. wadsworthia, and anaerobic cocci, respectively. Gene mefA was found in only 10 % of the B. fragilis strains and 3 % of the non-B. fragilis strains. Genes nim and ermB were not detected in any isolate. Substitution at position 82 (Ser to Phe) in gyrA was detected in B. fragilis isolates that were less susceptible or resistant to moxifloxacin. This study is the first report on the distribution of resistance genes in anaerobes isolated from intra-abdominal infections in Japan. We expect that the results might help in understanding the resistance mechanisms of specific anaerobes.

  18. Isolation of a Campylobacter lanienae-like bacterium from laboratory chinchillas (Chinchilla laniger).

    Science.gov (United States)

    Turowski, E E; Shen, Z; Ducore, R M; Parry, N M A; Kirega, A; Dewhirst, F E; Fox, J G

    2014-12-01

    Routine necropsies of 27 asymptomatic juvenile chinchillas revealed a high prevalence of gastric ulcers with microscopic lymphoplasmacytic gastroenteritis and typhlocolitis. Polymerase chain reaction (PCR) analysis using Campylobacter genus-specific partial 16S rRNA primers revealed the presence of Campylobacter spp. DNA in the faeces of 12 of 27 animals (44.4%). Species-specific partial 16S rRNA PCR and sequencing confirmed that these animals were colonized with Campylobacter lanienae, a gram-negative, microaerophilic bacterium that was first identified on routine faecal screening of slaughterhouse employees and subsequently isolated from faeces of livestock. Campylobacter lanienae was isolated from the faeces of six PCR-positive animals and identified with species-specific PCR and full 16S rRNA sequencing. Phylogenetic analysis showed that these isolates clustered with C. lanienae strain NCTC 13004. PCR analysis of DNA extracted from gastrointestinal tissues revealed the presence of C. lanienae DNA in the caecum and colon of these chinchillas. Gastrointestinal lesions were scored and compared between C. lanienae-positive and C. lanienae-negative animals. There was no correlation between colonization status and lesion severity in the stomach, liver, duodenum, or colon. Possible routes of C. lanienae infection in chinchillas could include waterborne transmission and faecal-oral transmission from wild mice and rats or livestock. Based on these findings, the authors conclude that C. lanienae colonizes the lower bowel of chinchillas in the absence of clinical disease. This is the first report of C. lanienae in any rodent species. Campylobacter lanienae isolates from different mammalian species demonstrate heterogeneity by 16S rRNA sequence comparison. Analysis using rpoB suggests that isolates and clones currently identified as C. lanienae may represent multiple species or subspecies. © 2014 Blackwell Verlag GmbH.

  19. A Comparative biochemical study on two marine endophytes, Bacterium SRCnm and Bacillus sp. JS, Isolated from red sea algae.

    Science.gov (United States)

    Ahmed, Eman Fadl; Hassan, Hossam Mokhtar; Rateb, Mostafa Ezzat; Abdel-Wahab, Noha; Sameer, Somayah; Aly Taie, Hanan Anwar; Abdel-Hameed, Mohammed Sayed; Hammouda, Ola

    2016-01-01

    Two marine endophytic bacteria were isolated from the Red Sea algae; a red alga; Acanthophora dendroides and the brown alga Sargassum sabrepandum. The isolates were identified based on their 16SrRNA sequences as Bacterium SRCnm and Bacillus sp. JS. The objective of this study was to investigate the potential anti-microbial and antioxidant activities of the extracts of the isolated bacteria grown in different nutrient conditions. Compared to amoxicillin (25μg/disk) and erythromycin (15μg/disk), the extracts of Bacterium SRCn min media II, III, IV and V were potent inhibitors of the gram-positive bacterium Sarcina maxima even at low concentrations. Also, the multidrug resistant Staphylococcus aureus(MRSA) was more sensitive to the metabolites produced in medium (II) of the same endophyte than erythromycin (15μg/disk). A moderate activity of the Bacillus sp. JS extracts of media I and II was obtained against the same pathogen. The total compounds (500ug/ml) of both isolated endophytes showed moderate antioxidant activities (48.9% and 46.1%, respectively). LC/MS analysis of the bacterial extracts was carried out to investigate the likely natural products produced. Cyclo(D-cis-Hyp-L-Leu), dihydrosphingosine and 2-Amino-1,3-hexadecanediol were identified in the fermentation medium of Bacterium SRCnm, whereas cyclo (D-Pro-L-Tyr) and cyclo (L-Leu-L-Pro) were the suggested compounds of Bacillus sp. JS.

  20. Draft genome sequence of Enterobacter sp. Sa187, an endophytic bacterium isolated from the desert plant Indigofera argentea

    NARCIS (Netherlands)

    Lafi, Feras F.; Alam, Intikhab; Geurts, Rene; Bisseling, Ton; Bajic, Vladimir B.; Hirt, Heribert; Saad, Maged M.

    2017-01-01

    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

  1. First Insights into the Genome Sequence of Clostridium thermopalmarium DSM 5974, a Butyrate-Producing Bacterium Isolated from Palm Wine.

    Science.gov (United States)

    Poehlein, Anja; Hettwer, Eva; Mohnike, Lennart; Daniel, Rolf

    2018-04-26

    Clostridium thermopalmarium is a moderate thermophilic, rod-shaped, and endospore-forming bacterium, which was isolated from palm wine in Senegal. Butyrate is produced from a broad variety of sugar substrates. Here, we present the draft genome sequence of C. thermopalmarium DSM 5974 (2.822 Mb) containing 2,665 predicted protein-encoding genes. Copyright © 2018 Poehlein et al.

  2. Complete genome of Pandoraea pnomenusa RB-38, an oxalotrophic bacterium isolated from municipal solid waste landfill site.

    Science.gov (United States)

    Lim, Yan-Lue; Ee, Robson; Yong, Delicia; Tee, Kok-Keng; Yin, Wai-Fong; Chan, Kok-Gan

    2015-11-20

    Pandoraea pnomenusa RB-38 is a bacterium isolated from a former sanitary landfill site. Here, we present the complete genome of P. pnomenusa RB38 in which an oxalate utilization pathway was identified. The genome analysis suggested the potential of this strain as an effective biocontrol agent against oxalate-producing phytopathogens. Copyright © 2015 Elsevier B.V. All rights reserved.

  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. Isolation and characterization of a radiation resistant thermophilic bacterium from radon hot spring

    International Nuclear Information System (INIS)

    Liang Xinle; Yang Long; Zhang Hong; Zhang Lei

    2011-01-01

    A radiation resistant and thermophilic bacterium strain R4-33 was isolated from radon hot spring water samples, pretreated with 60 Co γ-rays and UV irradiation. Tests on morphological, physiological and biochemical characters, fatty acid compositions, (G + C) mol% contents, and 16S rDNA sequencing were conducted. The results showed that strain R4-33 was of rod-shape, Gram-negative, atrichous, and endospore-forming. The optimum growth temperature and pH were 60 ℃ and 7.5, respectively. The strain utilized glucose, maltose and trehalose as carbon sources, and hydrolyzed casein and starch. Its catalase positive. The strain was sensitive to penicillin, neomycin, erythromycin, vancomycin, streptomycin, gentamycin, amikacin and ampicillin. The major cellular fatty acids were C 14:1 (48.8%) and C 15:1 (15.2%). The (G + C) mol% content of DNA was 58.2%. Phylogenetic tree based on 16S rDNA sequence showed R4-33 shared highly similarity to those of species in genus Anoxybacillus, especially to that of Anoxybacillus gonensis (99.5%). Based on the above, the strain R4-33 was proposed to the evolution branch of Anoxybacillus and designated as Anoxybacillu sp. R4-33. The UV and γ-radiation tests showed that the strain R4-33 had an ability of resistance to UV of 396 J/m 2 and 60 Co γ-rays irradiation of 14.0 kGy, indicating that the strain was a radiation resistant and thermophilic bacterium. (authors)

  5. Tenacibaculum agarivorans sp. nov., an agar-degrading bacterium isolated from marine alga Porphyra yezoensis Ueda.

    Science.gov (United States)

    Xu, Zhen-Xing; Yu, Pei; Mu, Da-Shuai; Liu, Yan; Du, Zong-Jun

    2017-12-01

    A novel Gram-stain-negative, aerobic, rod-shaped, non-flagellated and agar-digesting marine bacterium, designated as HZ1 T , was isolated from the marine alga Porphyra yezoensis Ueda (AST58-103) collected from the coastal area of Weihai, PR China. Phylogenetic analysis based on 16S rRNA gene sequences placed HZ1 T in the genus Tenacibaculum, and it formed a distinct clade in the phylogenetic tree with the type strains of Tenacibaculum amylolyticum and Tenacibaculum skagerrakense, with 97.0 % and 96.7 % 16S rRNA gene sequence similarities, respectively. The DNA G+C content of the isolate was 31.8 mol%. HZ1 T contained MK-6 as the predominant menaquinone and iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH and iso-C15 : 1G as the major fatty acids. The major polar lipids were phosphatidylethanolamine, four unidentified lipids and five unidentified aminolipids. On the basis of the results of the phylogenetic analysis and phenotypic properties, it is concluded that HZ1 T represents a novel species of the genus Tenacibaculum, for which the name Tenacibaculumagarivorans sp. nov. is proposed. The type strain is HZ1 T (=MCCC 1H00174 T =KCTC 52476 T ).

  6. Isolation of Aureimonas altamirensis, a Brucella canis-like bacterium, from an edematous canine testicle.

    Science.gov (United States)

    Reilly, Thomas J; Calcutt, Michael J; Wennerdahl, Laura A; Williams, Fred; Evans, Tim J; Ganjam, Irene K; Bowman, Jesse W; Fales, William H

    2014-11-01

    Microbiological and histological analysis of a sample from a swollen testicle of a 2-year-old Border Collie dog revealed a mixed infection of the fungus Blastomyces dermatitidis and the Gram-negative bacterium Aureimonas altamirensis. When subjected to an automated microbial identification system, the latter isolate was provisionally identified as Psychrobacter phenylpyruvicus, but the organism shared several biochemical features with Brucella canis and exhibited agglutination, albeit weakly, with anti-B. canis antiserum. Unequivocal identification of the organism was only achieved by 16S ribosomal RNA gene sequencing, ultimately establishing the identity as A. altamirensis. Since its first description in 2006, this organism has been isolated infrequently from human clinical samples, but, to the authors' knowledge, has not been reported from a veterinary clinical sample. While of unknown clinical significance with respect to the pathology observed for the polymicrobial infection described herein, it highlights the critical importance to unambiguously identify the microbe for diagnostic, epidemiological, infection control, and public health purposes. © 2014 The Author(s).

  7. Isolation and characterization of acetate-utilizing anaerobes from a freshwater sediment

    NARCIS (Netherlands)

    Scholten, J.C.M.; Stams, A.J.M.

    2000-01-01

    Acetate-degrading anaerobic microorganisms in freshwater sediment were quantified by the most probable number technique. From the highest dilutions a methanogenic, a sulfate-reducing, and a nitrate-reducing microorganism were isolated with acetate as substrate. The methanogen (culture AMPB-Zg) was

  8. Isolation and characterization of mercuric reductase by newly isolated halophilic bacterium, Bacillus firmus MN8

    Directory of Open Access Journals (Sweden)

    M. Noroozi

    2017-12-01

    Full Text Available The current study was aimed at isolating and identifying the halophilic and halotolerant bacteria which can produce mercuric reductase in Gavkhuni wetland in Iran. Moreover, tracking and sequencing merA gene and kinetic properties of mercuric reductase in the selected strain were performed in this study. Soil samples were taken from Gavkhuni wetland and cultured in nutrient agar medium with 5% NaCl. To examine the tolerance of purified colonies to mercury, agar dilution method was administered. Similarly, the phylogenetic analysis based on 16SrRNA gene sequencing was conducted. To investigate enzyme activity of kinetic parameters, a spectrophotometer was used to measure the NADPH oxidation decrease at 340 n.m. The results showed that among the 21 halophilic and halotolerant strains isolated from Gavkhuni wetland, 4 were resistant to mercuric chloride. A strain designated MN8 was selected for further studies because it showed the highest resistance to mercury. According to phylogenetic sequencing of 16S rRNA gene and phenotypic characteristics, the strain was categorized in the Bacillus genus and nearly related to Bacillus firmus. This strain had merA gene. The mercuric reductase showed Vmax and Km values of 0.106 U/mg and 24.051 µM, respectively. Evaluation of different concentrations of NaCl at 37°C and pH=7.5 in mercuric reductase enzyme activity indicated that the enzyme shows 50% activity in concentration of 1.5 M. Optimum pH and temperature of  enzyme activity were 7.5 and 35 °C, respectively. The results suggested that MN8 strain could be a proper candidate for bioremediation of mercury-contaminated environments such as industrial wastewaters.

  9. Bacillus radicibacter sp. nov., a new bacterium isolated from root nodule of Oxytropis ochrocephala Bunge.

    Science.gov (United States)

    Wei, Xiu Li; Lin, Yan Bing; Xu, Lin; Han, Meng Sha; Dong, Dan Hong; Chen, Wei Min; Wang, Li; Wei, Ge Hong

    2015-10-01

    A Gram-positive, facultative anaerobic, rod-shaped, and endospore-forming strain, designated 53-2(T) was isolated from the root nodule of Oxytropis ochrocephala Bunge growing on Qilian mountain, China. The strain can grow at pH 7.0-8.0, 10-50 °C and tolerate up to 11% NaCl. Optimal growth occurred at pH 7.2 and 37 °C. The result of BLASTn search based on 16S rRNA gene sequence revealed that strain 53-2(T) , being closest related to Bacillus acidicola 105-2(T) , possessed remote similarity (less than 95.64%) to the species within genus Bacillus. The DNA G + C content was 37.8%. Chemotaxonomic data (major quinone is MK-7; major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, unknown phospholipid, and aminoglycophospholipid; fatty acids are anteiso-C15: 0 , iso-C15:0 and anteiso-C17: 0 ) supported the affiliation of the isolate to the genus Bacillus. On the basis of physiological, phylogenetic, and biochemical properties, strain 53-2(T) represents a novel species within genus Bacillus, for which the name Bacillus radicibacter is proposed. The type strain is 53-2(T) (=DSM27302(T) =ACCC06115(T) =CCNWQLS5(T) ). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Directory of Open Access Journals (Sweden)

    Tony Martin Callaghan

    2015-03-01

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

  11. Clostridium punense sp. nov., an obligate anaerobe isolated from healthy human faeces.

    Science.gov (United States)

    Lanjekar, Vikram Bholanath; Marathe, Nachiket Prakash; Shouche, Yogesh Shreepad; Ranade, Dilip Ramchandra

    2015-12-01

    An obligately anaerobic, rod-shaped (0.5-1.0 × 2.0-10.0 μm), Gram-stain-positive bacterium, occurring mainly singly or in pairs, and designated BLPYG-8T, was isolated from faeces of a healthy human volunteer aged 56 years. Cells were non-motile. Oval, terminal spores were formed that swell the cells. The strain was affiliated with the genus Clostridium sensu stricto (Clostridium rRNA cluster I) as revealed by 16S rRNA gene sequence analysis. Strain BLPYG-8T showed 97.3 to 97.4 % 16S rRNA gene sequence similarity with Clostridium sulfidigenes DSM 18982T, Clostridium subterminale DSM 6970T and Clostridium thiosulfatireducens DSM 13105T. DNA-DNA hybridization and phenotypic analysis showed that the strain was distinct from its closest relatives, C. sulfidigenes DSM 18982T, C. subterminale DSM 6970T, C. thiosulfatireducens DSM 13105T with 54.2, 53.9 and 53.3 % DNA-DNA relatedness, respectively. Strain BLPYG-8T grew in PYG broth at temperatures between 20 and 40 °C (optimum 37 °C). The strain utilized a range of amino acids as well as carbohydrates as a source of carbon and energy. Glucose fermentation resulted in the formation of volatile fatty acids mainly acetic acid, n-butyric acid and organic acids such as succinic and lactic acid. The DNA G+C content of strain BLPYG-8T was 44.1 mol%. The major fatty acids (>10 %) were C14 : 0, iso-C15 : 0, C16 : 1ω7c and C16 : 0. Phylogenetic analysis and specific phenotypic characteristics and/or DNA G+C content differentiated the strain from its closest relatives. On the basis of these data, strain BLPYG-8T represents a novel species of the genus Clostridium, for which the name Clostridium punense sp. nov. is proposed. The type strain is BLPYG-8T ( = DSM 28650T = CCUG 64195T = MCC 2737T).

  12. 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 ).

  13. 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).

  14. Isolation and characterization of a mesophilic heavy-metals-tolerant sulfate-reducing bacterium Desulfomicrobium sp. from an enrichment culture using phosphogypsum as a sulfate source

    International Nuclear Information System (INIS)

    Azabou, Samia; Mechichi, Tahar; Patel, Bharat K.C.; Sayadi, Sami

    2007-01-01

    A sulfate-reducing bacterium, was isolated from a 6 month trained enrichment culture in an anaerobic media containing phosphogypsum as a sulfate source, and, designated strain SA2. Cells of strain SA2 were rod-shaped, did not form spores and stained Gram-negative. Phylogenetic analysis of the 16S rRNA gene sequence of the isolate revealed that it was related to members of the genus Desulfomicrobium (average sequence similarity of 98%) with Desulfomicrobium baculatum being the most closely related (sequence similarity of 99%). Strain SA2 used thiosulfate, sulfate, sulfite and elemental sulfur as electron acceptors and produced sulfide. Strain SA2 reduced sulfate contained in 1-20 g/L phosphogypsum to sulfide with reduction of sulfate contained in 2 g/L phosphogypsum being the optimum concentration. Strain SA2 grew with metalloid, halogenated and non-metal ions present in phosphogypsum and with added high concentrations of heavy metals (125 ppm Zn and 100 ppm Ni, W, Li and Al). The relative order for the inhibitory metal concentrations, based on the IC 50 values, was Cu, Te > Cd > Fe, Co, Mn > F, Se > Ni, Al, Li > Zn

  15. Catenisphaera adipataccumulans gen. nov., sp. nov., a member of the family Erysipelotrichaceae isolated from an anaerobic digester.

    Science.gov (United States)

    Kanno, Manabu; Katayama, Taiki; Morita, Naoki; Tamaki, Hideyuki; Hanada, Satoshi; Kamagata, Yoichi

    2015-03-01

    An obligately anaerobic bacterium, designated strain GK12(T), was isolated from an anaerobic digester in Fukagawa, Hokkaido Prefecture, Japan. The cells of strain GK12(T) were non-motile, non-spore-forming cocci that commonly occurred in chains. 16S rRNA gene sequence analysis revealed that strain GK12(T) was affiliated with the family Erysipelotrichaceae in the phylum Firmicutes and showed 91.8 % sequence similarity to the most closely related species, Faecalicoccus acidiformans. The strain grew at 30-50 °C (optimally at 40 °C) and at pH 5.5-8.5 (optimally at pH 7.5). The main end product of glucose fermentation was lactate. Yeast extract was required for growth. The strain contained C14 : 0, C14 : 0 1,1-dimethoxyalkane (DMA), C16 : 0 DMA and C18 : 0 DMA as the major cellular fatty acids (>10 % of the total). The polar lipid profile was composed of phosphatidylglycerol, phosphatidylinositol and an unidentified phospholipid. The whole-cell sugars were galactose, rhamnose and ribose. The cell-wall murein contained alanine, glutamic acid, lysine, serine and threonine, but not diaminopimelic acid. The G+C content of the genomic DNA was 47.7 mol%. Based on phenotypic, phylogenetic and chemotaxonomic properties, a novel genus and species, Catenisphaera adipataccumulans gen. nov., sp. nov., is proposed to accommodate strain GK12(T) ( = NBRC 108915(T) = DSM 25799(T)). © 2015 IUMS.

  16. A lactic acid bacterium isolated from kimchi ameliorates intestinal inflammation in DSS-induced colitis.

    Science.gov (United States)

    Park, Jin-Soo; Joe, Inseong; Rhee, Paul Dong; Jeong, Choon-Soo; Jeong, Gajin

    2017-04-01

    Some species of lactic acid bacteria have been shown to be beneficial in inflammatory bowel disease (IBD). In the present study, a strain of lactic acid bacterium (Lactobacillus paracasei LS2) was isolated from the Korean food, kimchi, and was shown to inhibit the development of experimental colitis induced by dextran sulfate sodium (DSS). To investigate the role of LS2 in IBD, mice were fed DSS in drinking water for seven days along with LS2 bacteria which were administered intragastrically to some of the mice, while phosphate-buffered saline (PBS) was administered to others (the controls). The administration of LS2 reduced body weight loss and increased survival, and disease activity indexes (DAI) and histological scores indicated that the severity of colitis was significantly reduced. The production of inflammatory cytokines and myeloperoxidase (MPO) activity also decreased. Flow cytometry analysis showed that the number of Th1 (IFN-γ) population cells was significantly reduced in the LS2-administered mice compared with the controls. The administration of LS2 induced the increase of CD4 + FOXP3 + Treg cells, which are responsible for IL-10. Numbers of macrophages (CD11b + F4/80 + ), and neutrophils (CD11b + Gr-1 + ) among lamina propria lymphocytes (LPL) were also reduced. These results indicate that LS2 has an anti-inflammatory effect and ameliorates DSS-induced colitis.

  17. [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.

  18. 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.

  19. Jeotgalibacillus soli sp. nov., a Gram-stain-positive bacterium isolated from soil.

    Science.gov (United States)

    Cunha, Sofia; Tiago, Igor; Paiva, Gabriel; Nobre, Fernanda; da Costa, Milton S; Veríssimo, António

    2012-03-01

    A Gram-staining-positive, motile, rod-shaped, spore-forming bacterium, designated P9(T), was isolated from soil in Portugal. This organism was aerobic and catalase- and oxidase-positive. It had an optimum growth temperature of about 35 °C and an optimum growth pH of about 8.0-8.5, and grew in medium with 0-9% (w/v) NaCl. The cell-wall peptidoglycan was of the A1α type, with L-lysine as the diagnostic diamino acid. The major respiratory quinone was menaquinone 7 (MK-7) and the major fatty acids were anteiso-C(15:0) (45.4%), iso-C(15:0) (22.0%) and anteiso-C(17:0) (11.2%). The genomic DNA G+C content was about 39.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain P9(T) was most closely related to Jeotgalibacillus campisalis DSM 18983(T) (96.8%) and Jeotgalibacillus marinus DSM 1297(T) (96.5%). These two recognized species formed a coherent cluster with strain P9(T) that was supported by a bootstrap value of 99%. On the basis of the phylogenetic analysis and physiological and biochemical characteristics, strain P9(T) (=DSM 23228(T)=LMG 25523(T)) represents a novel species of the genus Jeotgalibacillus, for which the name Jeotgalibacillus soli sp. nov. is proposed.

  20. Pseudomonas aestus sp. nov., a plant growth-promoting bacterium isolated from mangrove sediments.

    Science.gov (United States)

    Vasconcellos, Rafael L F; Santos, Suikinai Nobre; Zucchi, Tiago Domingues; Silva, Fábio Sérgio Paulino; Souza, Danilo Tosta; Melo, Itamar Soares

    2017-10-01

    Strain CMAA 1215 T , a Gram-reaction-negative, aerobic, catalase positive, polarly flagellated, motile, rod-shaped (0.5-0.8 × 1.3-1.9 µm) bacterium, was isolated from mangrove sediments, Cananéia Island, Brazil. Analysis of the 16S rRNA gene sequences showed that strain CMAA 1215 T forms a distinct phyletic line within the Pseudomonas putida subclade, being closely related to P. plecoglossicida ATCC 700383 T , P. monteilii NBRC 103158 T , and P. taiwanensis BCRC 17751 T of sequence similarity of 98.86, 98.73, and 98.71%, respectively. Genomic comparisons of the strain CMAA 1215 T with its closest phylogenetic type strains using average nucleotide index (ANI) and DNA:DNA relatedness approaches revealed 84.3-85.3% and 56.0-63.0%, respectively. A multilocus sequence analysis (MLSA) performed concatenating 16S rRNA, gyrB and rpoB gene sequences from the novel species was related with Pseudomonas putida subcluster and formed a new phylogenetic lineage. The phenotypic, physiological, biochemical, and genetic characteristics support the assignment of CMAA 1215 T to the genus Pseudomonas, representing a novel species. The name Pseudomonas aestus sp.nov. is proposed, with CMAA 1215 T (=NRRL B-653100 T  = CBMAI 1962 T ) as the type strain.

  1. Pseudomonas kunmingensis sp. nov., an exopolysaccharide-producing bacterium isolated from a phosphate mine.

    Science.gov (United States)

    Xie, Fuhong; Ma, Huan; Quan, Shujing; Liu, Dehai; Chen, Guocan; Chao, Yapeng; Qian, Shijun

    2014-02-01

    A Gram-stain-negative, rod-shaped, exopolysaccharide-producing, strictly aerobic bacterium with a single polar flagellum, designated strain HL22-2(T), was isolated from a phosphate mine situated in a suburb of Kunmming in Yunnan province in south-western China. The taxonomic status of this strain was evaluated by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HL22-2(T) was related to members of the genus Pseudomonas. 16S rRNA gene sequence similarities between strain HL22-2(T) and Pseudomonas xanthomarina KMM 1447(T), Pseudomonas alcaliphila AL15-21(T) and Pseudomonas stutzeri ATCC 17588(T) were 98.9, 98.10% and 98.06%, respectively. The major cellular fatty acids were C(18 : 1)ω7c, C(16 : 0) and summed feature 3 (C(16 : 1)ω7c and/or C(16 : 1)ω6c). The DNA G+C content was 60.3 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness values, strain HL22-2(T) represents a novel species of the genus Pseudomonas, for which the name Pseudomonas kunmingensis sp. nov. is proposed. The type strain is HL22-2(T) ( = CGMCC 1.12273(T) = DSM 25974(T)).

  2. 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).

  3. [Isolation and identification of Mn oxidizing bacterium Aminobacter sp. H1 and its oxidation mechanism].

    Science.gov (United States)

    Yan, Ping; Jiang, Li-Ying; Chen, Jian-Meng; He, Zhi-Min; Xiao, Shao-Dan; Jiang, Yi-Feng

    2014-04-01

    A bacterium with high manganese oxidizing activity was isolated from a biological manganese removal filter and named as H1. Based on its characteristics and the analysis of 16S rDNA sequence, the strain H1 belonged to the genus Aminobacter sp. and its manganese oxidizing ability had never been reported. In this paper, the microbiologic properties of the strain H1, the manganese oxidation mechanisms and characteristics of biogenic manganese oxides were investigated. The results showed that the maximal tolerant Mn concentration of strain H1 was 50 mmol x L(-1), and Mn(II) could be completely removed by strain H1 when the concentration was lower than 10 mmol x L(-1). Strain H1 could oxidize Mn2+ by both the production of manganese oxidizing activity factor and alkaline metabolites during growth, which were synthesized in the cell and then secreted into extracellular culture medium. During the oxidation process, the intermediate of soluble Mn(III) was detected. SEM showed that the biogenic manganese oxides were amorphous and poorly-crystalline, and it closely combined with bacteria. The components of the biogenic manganese oxides produced by strain H1 were identified as MnCO3, MnOOH, Mn3O4 and MnO2 by XRD, XPS and SEM-EDX.

  4. Isolation and identification of anaerobic organisms from the male and female urogenital tracts.

    Science.gov (United States)

    Moss, S

    1983-06-01

    Since Bacteroides spp may play an important role together with Gardnerella vaginalis in the pathogenesis of non-specific vaginitis and balanoposthitis, anaerobic organisms were isolated and identified from 34 female and 20 male patients attending a department of genitourinary medicine, and the results compared with the clinical findings and the presence of other routinely isolated pathogens. Twenty-three different organisms were recovered from 13 of the 20 men; of these organisms, 20 were of the Bacteroides spp. Most isolates were of the B melaninogenicus/oralis group, which forms part of the commensal vaginal flora in women. A definite association between the presence of anaerobes and other pathogens needs to be firmly established, as this obviously causes important complications in treating these conditions.

  5. Genome analysis of Chitinivibrio alkaliphilus gen. nov., sp. nov., a novel extremely haloalkaliphilic anaerobic chitinolytic bacterium from the candidate phylum Termite Group 3.

    Science.gov (United States)

    Sorokin, Dimitry Y; Gumerov, Vadim M; Rakitin, Andrey L; Beletsky, Alexey V; Damsté, J S Sinninghe; Muyzer, Gerard; Mardanov, Andrey V; Ravin, Nikolai V

    2014-06-01

    Anaerobic enrichments from hypersaline soda lakes with chitin as substrate yielded five closely related anaerobic haloalkaliphilic isolates growing on insoluble chitin by fermentation at pH 10 and salinities up to 3.5 M. The chitinolytic activity was exclusively cell associated. To better understand the biology and evolutionary history of this novel bacterial lineage, the genome of the type strain ACht1 was sequenced. Analysis of the 2.6 Mb draft genome revealed enzymes of chitin-degradation pathways, including secreted cell-bound chitinases. The reconstructed central metabolism revealed pathways enabling the fermentation of polysaccharides, while it lacks the genes needed for aerobic or anaerobic respiration. The Rnf-type complex, oxaloacetate decarboxylase and sodium-transporting V-type adenosine triphosphatase were identified among putative membrane-bound ion pumps. According to 16S ribosomal RNA analysis, the isolates belong to the candidate phylum Termite Group 3, representing its first culturable members. Phylogenetic analysis using ribosomal proteins and taxonomic distribution analysis of the whole proteome supported a class-level classification of ACht1 most probably affiliated to the phylum Fibribacteres. Based on phylogenetic, phenotypic and genomic analyses, the novel bacteria are proposed to be classified as Chitinivibrio alkaliphilus gen. nov., sp. nov., within a novel class Chitinivibrione. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

  6. Chryseobacterium formosus sp. nov., a bacterium isolated from an ancient tree trunk.

    Science.gov (United States)

    Akter, Shahina; NGO, Hien T T; Du, Juan; Won, KyungHwa; Singh, Hina; Yin, Chang Shik; Kook, MooChang; Yi, Tae-Hoo

    2015-10-01

    A Gram-reaction-negative, non-motile and rod-shaped bacterium, designated as THG-DN3.6(T), was isolated from an ancient tree trunk from Republic of Korea. On the basis of 16S rRNA gene sequence analysis, strain THG-DN3.6(T) was shown to belong to the genus Chryseobacterium and the highest similarity to Chryseobacterium indoltheticum LMG 4025(T) (97.2%) and the closest phylogenetic relatives were Chryseobacterium scophthalmum (96.8%), Chryseobacterium piscium (96.7%) and Chryseobacterium balustinum KCTC 2903(T) (96.3%). The DNA G + C content of the isolate was 33.2 mol%. The predominant isoprenoid quinone was menaquinone-6. The major fatty acids were iso-C15:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω7t and/or iso-C15:0 2-OH), iso-C17:1 ω9c and iso-C17:0 3-OH. The major polar lipids of strain THG-DN3.6(T) were phosphatidylethanolamine. The mean DNA-DNA relatedness of strain THG-DN3.6(T) to C. indoltheticum LMG 4025(T) was 52 ± 0.5%. Based on the results of polyphasic characterization, strain THG-DN3.6(T) represented a novel species within the genus Chryseobacterium, for which the name Chryseobacterium formosus sp. nov. is proposed. The type strain is THG-DN3.6(T) (=KCTC 42606 = CCTCC AB 2015118). The NCBI GenBank accession number for the 16S rRNA gene sequence of strain THG-DN3.6(T) is KM035938.

  7. 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.

  8. 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.

  9. Intestinimonas butyriciproducens gen. nov., sp. nov., a novel butyrate-producing bacterium from the mouse intestine

    NARCIS (Netherlands)

    Kläring, K.; Hanske, L.; Bui, T.P.N.; Charrier, C.; Blaut, M.; Haller, D.; Plugge, C.M.; Clavel, T.

    2013-01-01

    Whilst creating a bacterial collection of strains from the mouse intestine, we isolated a Gram-negative, spore-forming, non-motile and strictly anaerobic rod-shaped bacterium from the caecal content of a TNFdeltaARE mouse. The isolate, referred to as strain SRB-521-5-IT, was originally cultured on a

  10. Tindallia californiensis sp. nov., a new anaerobic, haloalkaliphilic, spore-forming acetogen isolated from Mono Lake in California

    Science.gov (United States)

    Pikuta, E. V.; Hoover, R. B.; Bej, A. K.; Marsic, D.; Detkova, E. N.; Whitman, W. B.; Krader, P.

    2003-01-01

    A novel extremely haloalkaliphilic, strictly anaerobic, acetogenic bacterium strain APO was isolated from sediments of the athalassic, meromictic, alkaline Mono Lake in California. The Gram-positive, spore-forming, slightly curved rods with sizes 0.55- 0.7x1.7-3.0 microns were motile by a single laterally attached flagellum. Strain APO was mesophilic (range 10-48 C, optimum of 37 C); halophilic (NaCl range 1-20% (w/v) with optimum of 3-5% (w/v), and alkaliphilic (pH range 8.0-10.5, optimum 9.5). The novel isolate required sodium ions in the medium. Strain APO was an organotroph with a fermentative type of metabolism and used the substrates peptone, bacto-tryptone, casamino acid, yeast extract, L-serine, L-lysine, L-histidine, L-arginine, and pyruvate. The new isolate performed the Stickland reaction with the following amino acid pairs: proline + alanine, glycine + alanine, and tryptophan + valine. The main end product of growth was acetate. High activity of CO dehydrogenase and hydrogenase indicated the presence of a homoacetogenic, non-cycling acetyl-coA pathway. Strain APO was resistant to kanamycin but sensitive to chloramphenicol, tetracycline, and gentamycin. The G+C content of the genomic DNA was 44.4 mol% (by HPLC method). The sequence of the 16s rRNA gene of strain APO possessed 98.2% similarity with the sequence from Tindullia magadiensis Z-7934, but the DNA-DNA hybridization value between these organisms was only 55%. On the basis of these physiological and molecular properties, strain APO is proposed to be a novel species of the genus Tindallia with the name Tindallia californiensis sp. nov., (type strain APO = ATCC BAA-393 - DSM 14871).

  11. Isolation and identification of berberine and berberrubine metabolites by berberine-utilizing bacterium Rhodococcus sp. strain BD7100.

    Science.gov (United States)

    Ishikawa, Kazuki; Takeda, Hisashi; Wakana, Daigo; Sato, Fumihiko; Hosoe, Tomoo

    2016-05-01

    Based on the finding of a novel berberine (BBR)-utilizing bacterium, Rhodococcus sp. strain BD7100, we investigated the degradation of BBR and its analog berberrubine (BRU). Resting cells of BD7100 demethylenated BBR and BRU, yielding benzeneacetic acid analogs. Isolation of benzeneacetic acid analogs suggested that BD7100 degraded the isoquinoline ring of the protoberberine skeleton. This work represents the first report of cleavage of protoberberine skeleton by a microorganism.

  12. Draft Genome Sequence of Bacillus aryabhattai Strain PHB10, a Poly(3-Hydroxybutyrate)-Accumulating Bacterium Isolated from Domestic Sewerage.

    Science.gov (United States)

    Balakrishna Pillai, Aneesh; Jaya Kumar, Arjun; Thulasi, Kavitha; Reghunathan, Dinesh; Prasannakumar, Manoj; Kumarapillai, Harikrishnan

    2017-10-12

    Bacillus aryabhattai PHB10 is a poly(3-hydroxybutyrate) (PHB)-accumulating bacterium isolated from domestic sewerage. Here, we report the 4.19-Mb draft genome sequence, with 4,050 protein-coding genes and a G+C content of 37.5%. This sequence will be helpful in the study of the high-level PHB accumulation mechanism of the strain. Copyright © 2017 Balakrishna Pillai et al.

  13. Complete genome sequence of Agarivorans gilvus WH0801(T), an agarase-producing bacterium isolated from seaweed.

    Science.gov (United States)

    Zhang, Pujuan; Rui, Junpeng; Du, Zongjun; Xue, Changhu; Li, Xiangzhen; Mao, Xiangzhao

    2016-02-10

    Agarivorans gilvus WH0801(T), an agarase-producing bacterium, was isolated from the surface of seaweed. Here, we present the complete genome sequence, which consists of one circular chromosome of 4,416,600 bp with a GC content of 45.9%. This genetic information will provide insight into biotechnological applications of producing agar for food and industry. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. Halanaeroarchaeum sulfurireducens gen. nov., sp. nov., the first obligately anaerobic sulfur-respiring haloarchaeon, isolated from a hypersaline lake

    NARCIS (Netherlands)

    Sorokin, Dimitry Y.; Kublanov, Ilya V.; Yakimov, Mikhail M.; Rijpstra, W. Irene C; Sinninghe Damsté, Jaap S.

    2016-01-01

    Anaerobic enrichments with acetate as electron donor and carbon source, and elemental sulfur as electron acceptor at 4 M NaCl using anaerobic sediments and brines from several hypersaline lakes in Kulunda Steppe (Altai, Russia) resulted in isolation in pure culture of four strains of obligately

  15. Azospirillum humicireducens sp. nov., a nitrogen-fixing bacterium isolated from a microbial fuel cell.

    Science.gov (United States)

    Zhou, Shungui; Han, Luchao; Wang, Yueqiang; Yang, Guiqin; Zhuang, Li; Hu, Pei

    2013-07-01

    A Gram-negative, facultative anaerobic, motile, spiral, straight-to-slightly curved rod-shaped and nitrogen-fixing strain, designated SgZ-5(T), was isolated from a microbial fuel cell (MFC) and was characterized by means of a polyphasic approach. Growth occurred with 0-1 % (w/v) NaCl (optimum 1 %) and at pH 5.5-8.5 (optimum pH 7.2) and at 25-37 °C (optimum 30 °C) in nutrient broth (NB). The strain had the ability to grow under anaerobic conditions via the oxidation of various organic compounds coupled to the reduction of anthraquione-2,6-disulfonate (AQDS). Chemotaxonomic characteristics (main ubiquinone Q-10, major fatty acid C18 : 1ω7c/C18 : 1ω6c and DNA G+C content 67.7 mol%) were similar to those of members of the genus Azospirillum. According to the results of phylogenetic analyses, strain SgZ-5(T) belonged to the genus Azospirillum within the family Rhodospirillaceae of the class Alphaproteobacteria, and was related most closely to the type strains of Azospirillum lipoferum, Azospirillum thiophilum and Azospirillum oryzae (98.0, 97.6 and 97.1 % 16S rRNA gene sequence similarity, respectively). DNA-DNA pairing studies showed that the unidentified organism displayed reassociation values of 36.7 ± 3.7, 24.1 ± 2.2 and 22.3 ± 2.4 % to the type strains of A. lipoferum, A. thiophilum and A. oryzae, respectively. Similarities between nifH gene sequences of strain SgZ-5(T) and members of the genus Azospirillum ranged from 94.0 to 97.0 %. A combination of phenotypic, chemotaxonomic, phylogenetic and genotypic data clearly indicated that strain SgZ-5(T) represents a novel species, for which the name Azospirillum humicireducens sp. nov. is proposed. The type strain is SgZ-5(T) ( = CCTCC AB 2012021(T) = KACC 16605(T)).

  16. 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).

  17. Shewanella algicola sp. nov., a marine bacterium isolated from brown algae.

    Science.gov (United States)

    Kim, Ji-Young; Yoo, Han-Su; Lee, Dong-Heon; Park, So-Hyun; Kim, Young-Ju; Oh, Duck-Chul

    2016-06-01

    A Gram-stain-negative, aerobic, rod-shaped bacterium motile by means of a single polar flagella, strain ST-6T, was isolated from a brown alga (Sargassum thunbergii) collected in Jeju, Republic of Korea. Strain ST-6T was psychrotolerant, growing at 4-30 °C (optimum 20 °C). Phylogenetic analysis based on 16S rRNA and gyrB gene sequences revealed that strain ST-6T belonged to a distinct lineage in the genus Shewanella. Strain ST-6T was related most closely to Shewanella basaltis J83T, S. gaetbuli TF-27T, S. arctica IT12T, S. vesiculosa M7T and S. aestuarii SC18T, showing 96-97 % and 85-70 % 16S rRNA and gyrB gene sequences similarities, respectively. DNA-DNA relatedness values between strain ST-6T and the type strains of two species of the genus Shewanella were 5 %) were summed feature 3 (comprising C16:1ω7c and/ or iso-C15:0 2-OH), C16:0, iso-C13:0 and C17:1ω8c. The DNA G+C content of strain ST-6Twas 42.4 mol%, and the predominant isoprenoid quinones were menaquinone MK-7 and ubiquinones Q-7 and Q-8. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain ST-6T is considered to represent a novel species of the genus Shewanella, for which the name Shewanella algicola sp. nov. is proposed. The type strain is ST-6T (= KCTC 23253T = JCM 31091T).

  18. Paenibacillus mobilis sp. nov., a Gram-stain-negative bacterium isolated from soil.

    Science.gov (United States)

    Yang, Dahye; Cha, Seho; Choi, Jiwon; Seo, Taegun

    2018-04-01

    A novel Gram-stain-negative bacterium, designated strain S8 T , was isolated from a soil sample obtained in Gyeonggi Province, Republic of Korea. Cells of strain S8 T were endospore-forming, motile by means of peritrichous flagella, and rod-shaped. S8 T colonies were round, convex, wavy and white. Strain S8 T grew optimally at 37 °C, pH 6-8, and up to 2.0 % (w/v) NaCl. Based on 16S rRNA gene sequence similarity, strain S8 T was affiliated with the genus Paenibacillus in the family Paenibacillaceae and was most closely related to Paenibacillus yonginensis DCY84 T and Paenibacillus physcomitrellae XB T (98.8 and 97.1 % sequence similarity). The DNA G+C content of the novel strain was 53.1±0.3 mol%. Strain S8 T contained diphosphatidylglycerol, phosphatidylglycerol, two phospholipids, four aminophospholipids, an aminolipid and three unidentified lipids. The major fatty acid was anteiso-branched C15 : 0. The quinone was menaquinone MK-7. The peptidoglycan of strain S8 T contained meso-diaminopimelic acid. The DNA-DNA hybridization values of strain S8 T with P. yonginensis KCTC 33428 T and P. physcomitrellae DSM 29851 T were 44 % and 32 %, respectively. Data from the DNA-DNA hybridization, biochemical, phylogenetic and physiological analyses indicate that strain S8 T (=KCTC 33848 T =JCM 31672 T ) represents a novel species of the genus Paenibacillus, for which the name Paenibacillus mobilis sp. nov. is proposed.

  19. 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 ).

  20. Thermoactinomyces khenchelensis sp. nov., a filamentous bacterium isolated from soil sediment of a terrestrial hot spring.

    Science.gov (United States)

    Mokrane, Salim; Bouras, Noureddine; Meklat, Atika; Lahoum, Abdelhadi; Zitouni, Abdelghani; Verheecke, Carol; Mathieu, Florence; Schumann, Peter; Spröer, Cathrin; Sabaou, Nasserdine; Klenk, Hans-Peter

    2016-02-01

    A novel thermophilic filamentous bacterium, designated strain T36(T), was isolated from soil sediment sample from a hot spring source collected in Khenchela province, Algeria. Strain T36(T) was identified as a member of the genus Thermoactinomyces by a polyphasic approach. Strain T36(T) was observed to form white aerial mycelium and non-coloured to pale yellow substrate mycelium, both producing endospores, sessile or borne by short sporophores. The optimum growth temperature and pH were found to be 37-55 °C and 7.0-9.0, respectively and the optimum NaCl concentration for growth was found to be 0-7 % (w/v). The diagnostic diamino acid in the cell wall peptidoglycan was identified as meso-diaminopimelic acid. The predominant menaquinone of strain T36(T) was identified as MK-7 (H0). The major fatty acids were found to be iso-C15:0 and iso-C17:0. The phospholipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphoglycolipid. The chemotaxonomic properties of strain T36(T) are consistent with those shared by members of the genus Thermoactinomyces. 16S rRNA gene sequence analysis indicated that the sequence similarities between strain T36(T) and Thermoactinomyces species with validly published names were less than 98 %. Based on the combined genotypic and phenotypic evidence, it is proposed that strain T36(T) should be classified as representative of a novel species, for which the name Thermoactinomyces khenchelensis sp. nov. is proposed. The type strain is T36(T) (=DSM 45951(T) = CECT 8579(T)).

  1. Halomonas rifensis sp. nov., an exopolysaccharide-producing, halophilic bacterium isolated from a solar saltern.

    Science.gov (United States)

    Amjres, Hakima; Béjar, Victoria; Quesada, Emilia; Abrini, Jamal; Llamas, Inmaculada

    2011-11-01

    A polyphasic taxonomic study was conducted on strain HK31(T), a moderately halophilic bacterium isolated from a solar saltern in Chefchaouen, Morocco. The strain was a Gram-reaction-negative, oxidase-positive rod, which was motile by means of peritrichous flagella. The strain required NaCl for growth and grew in salt concentrations (mixture of sea salts) of 0.5-20 % (w/v) (optimum 5-7.5 %, w/v), at 25-45 °C (optimum 32 °C) and at pH 5-10 (optimum pH 6-9). Strain HK31(T) did not produce acids from sugars and its metabolism was respiratory, using oxygen as terminal electron acceptor. The strain was positive for the accumulation of poly-β-hydroxyalkanoate granules and formed mucoid colonies due to the excretion of an exopolysaccharide. The DNA G+C content was 61.5 mol%. 16S rRNA gene sequence analysis indicated that it belonged to the genus Halomonas in the class Gammaproteobacteria. The most phylogenetically related species was Halomonas anticariensis, with which strain HK31(T) showed a 16S rRNA gene sequence similarity of 96.48 %. Its major fatty acids were C(18 : 1)ω7c, C(16 : 0), C(19 : 0) cyclo ω8c, C(16 : 1)ω7c/iso-C(15 : 0) 2-OH and C(12 : 0) 3-OH and the predominant respiratory lipoquinone was ubiquinone with nine isoprene units (Q-9). Based on the evidence provided in this study, strain HK31(T) (= CECT 7698(T) = LMG 25695(T)) represents a novel species of the genus Halomonas, for which the name Halomonas rifensis is proposed.

  2. Pseudomonas sagittaria sp. nov., a siderophore-producing bacterium isolated from oil-contaminated soil.

    Science.gov (United States)

    Lin, Shih-Yao; Hameed, Asif; Liu, You-Cheng; Hsu, Yi-Han; Lai, Wei-An; Chen, Wen-Ming; Shen, Fo-Ting; Young, Chiu-Chung

    2013-07-01

    An aerobic, Gram-stain-negative, rod-shaped bacterium with a single polar flagellum, designated CC-OPY-1(T), was isolated from an oil-contaminated site in Taiwan. CC-OPY-1(T) produces siderophores, and can grow at temperatures of 25-37 °C and pH 5.0-9.0 and tolerate Pseudomonas alcaligenes BCRC 11893(T) (97.1 %), Pseudomonas. alcaliphila DSM 17744(T) (97.1 %), Pseudomonas tuomuerensis JCM 14085(T) (97.1 %), Pseudomonas toyotomiensis JCM 15604(T) (96.9 %) and lower sequence similarity to remaining species of the genus Pseudomonas. The phylogenetic trees reconstructed based on gyrB and rpoB gene sequences supported the classification of CC-OPY-1(T) as a novel member of the genus Pseudomonas. The predominant quinone system of strain CC-OPY-1T was ubiquinone (Q-9) and the DNA G+C content was 68.4 ± 0.3 mol%. The major fatty acids were C12 : 0, C16 : 0, C17 : 0 cyclo and summed features 3 and 8 consisting of C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c, respectively. The major polar lipids were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylcholine (PC) and two unknown phospholipids (PL1-2). Due to distinct phylogenetic, phenotypic and chemotaxonomic features, CC-OPY-1(T) is proposed to represent a novel species within the genus Pseudomonas for which the name Pseudomonas sagittaria sp. nov. is proposed. The type strain is CC-OPY-1(T) ( = BCRC 80399(T) = JCM 18195(T)).

  3. 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

  4. Dehalogenimonas alkenigignens sp. nov., a chlorinated-alkane-dehalogenating bacterium isolated from groundwater.

    Science.gov (United States)

    Bowman, Kimberly S; Nobre, M Fernanda; da Costa, Milton S; Rainey, Fred A; Moe, William M

    2013-04-01

    Two strictly anaerobic bacterial strains, designated IP3-3(T) and SBP-1, were isolated from groundwater contaminated by chlorinated alkanes and alkenes at a Superfund Site located near Baton Rouge, Louisiana (USA). Both strains reductively dehalogenate a variety of polychlorinated aliphatic alkanes, including 1,2-dichloroethane, 1,2-dichloropropane, 1,1,2,2-tetrachloroethane, 1,1,2-trichloroethane and 1,2,3-trichloropropane, when provided with hydrogen as the electron donor. To clarify their taxonomic position, strains IP3-3(T) and SBP-1 were characterized using a polyphasic approach. Both IP3-3(T) and SBP-1 are mesophilic, non-spore-forming, non-motile and Gram-stain-negative. Cells of both strains are irregular cocci with diameters of 0.4-1.1 µm. Both are resistant to ampicillin and vancomycin. The genomic DNA G+C contents of strains IP3-3(T) and SBP-1 are 55.5±0.4 and 56.2±0.2 mol% (HPLC), respectively. Major cellular fatty acids include C18 : 1ω9c, C16 : 0, C14 : 0 and C16 : 1ω9c. 16S rRNA gene sequence based phylogenetic analyses indicated that the strains cluster within the phylum Chloroflexi most closely related to but distinct from the species Dehalogenimonas lykanthroporepellens (96.2 % pairwise similarity) and Dehalococcoides mccartyi (90.6 % pairwise similarity). Physiological and chemotaxonomic traits as well as phylogenetic analysis support the conclusion that these strains represent a novel species within the genus Dehalogenimonas for which the name Dehalogenimonas alkenigignens sp. nov. is proposed. The type strain is IP3-3(T) ( = JCM 17062(T) = NRRL B-59545(T)).

  5. Biocorrosion of carbon steel alloys by an hydrogenotrophic sulfate-reducing bacterium Desulfovibrio capillatus isolated from a Mexican oil field separator

    Energy Technology Data Exchange (ETDEWEB)

    Miranda, E. [IRD, Institut de Recherche pour le Developement, Universites de Provence et de la Mediterranee, ESIL Case 925, 163 Avenue de Luminy, F-13288 Marseille, Cedex 09 (France); Bethencourt, M. [Departamento de Ciencia de los Materiales e Ingenieria Metalurgica y Quimica Inorganica, CASEM, Universidad de Cadiz, Poligono Rio San Pedro s/n, 11510 Puerto Real (Spain)]. E-mail: manuel.bethencourt@uca.es; Botana, F.J. [Departamento de Ciencia de los Materiales e Ingenieria Metalurgica y Quimica Inorganica, CASEM, Universidad de Cadiz, Poligono Rio San Pedro s/n, 11510 Puerto Real (Spain); Cano, M.J. [Departamento de Ciencia de los Materiales e Ingenieria Metalurgica y Quimica Inorganica, CASEM, Universidad de Cadiz, Poligono Rio San Pedro s/n, 11510 Puerto Real (Spain); Sanchez-Amaya, J.M. [Departamento de Ciencia de los Materiales e Ingenieria Metalurgica y Quimica Inorganica, CASEM, Universidad de Cadiz, Poligono Rio San Pedro s/n, 11510 Puerto Real (Spain); Corzo, A. [Departamento de Biologia, CASEM, Universidad de Cadiz, Poligono Rio San Pedro s/n, 11510 Puerto Real (Spain); Garcia de Lomas, J. [Departamento de Biologia, CASEM, Universidad de Cadiz, Poligono Rio San Pedro s/n, 11510 Puerto Real (Spain); Fardeau, M.L. [IRD, Institut de Recherche pour le Developement, Universites de Provence et de la Mediterranee, ESIL Case 925, 163 Avenue de Luminy, F-13288 Marseille, Cedex 09 (France); Ollivier, B. [IRD, Institut de Recherche pour le Developement, Universites de Provence et de la Mediterranee, ESIL Case 925, 163 Avenue de Luminy, F-13288 Marseille, Cedex 09 (France)

    2006-09-15

    The hydrogenotrophic sulfate-reducing bacterium (SRB) Desulfovibrio capillatus (DSM14982{sup T}) was isolated from an oil field separator with serious corrosion problems; this is the study of its role in the corrosion of carbon steels under anaerobic conditions. Immersion tests with two steel alloys, St-35.8 (typical carbon steel employed in European naval industry), and API-5XL52 (weathering alloy steel employed in Mexican oil industries) were performed. Total exposure was 45 days and different concentrations of thiosulfate as electron acceptor for bacterial growth were employed. The samples immersed in media with SRB undergo fast activation and numerous active sites form on the surface. Microscopic observations were made by environmental scanning electron microscopy (ESEM). Weight loss and electrochemical testing included open circuit potential (E {sub corr}), polarization resistance (R {sub p}), electrochemical impedance spectroscopy (EIS) and electrochemical noise (EN) were measured with and without bacteria in the culture medium in order to determine corrosion rates and mechanisms. All electrochemical techniques have shown that after the end of the exponential phase the corrosion activity notably increased due to the high concentration of bacterial metabolites. Finally, the corrosion behavior of API-5XL52 was worse than St-35.8.

  6. Antimicrobial susceptibility of clinically isolated anaerobic bacteria in a University Hospital Centre Split, Croatia in 2013.

    Science.gov (United States)

    Novak, Anita; Rubic, Zana; Dogas, Varja; Goic-Barisic, Ivana; Radic, Marina; Tonkic, Marija

    2015-02-01

    Anaerobic bacteria play a significant role in many endogenous polymicrobial infections. Since antimicrobial resistance among anaerobes has increased worldwide, it is useful to provide local susceptibility data to guide empirical therapy. The present study reports recent data on the susceptibility of clinically relevant anaerobes in a University Hospital Centre (UHC) Split, Croatia. A total of 63 Gram-negative and 59 Gram-positive anaerobic clinical isolates from various body sites were consecutively collected from January to December 2013. Antimicrobial susceptibility testing was performed using standardized methods and interpreted using EUCAST criteria. Patient's clinical and demographic data were recorded by clinical microbiologist. Among 35 isolates of Bacteroides spp., 97.1% were resistant to penicillin (PCN), 5.7% to amoxicillin/clavulanic acid (AMC), 8.6% to piperacillin/tazobactam (TZP), 29.0% to clindamycin (CLI) and 2.9% to metronidazole (MZ). Percentages of susceptible strains to imipenem (IPM), meropenem (MEM) and ertapenem (ETP) were 94.3. Resistance of other Gram-negative bacilli was 76.0% to PCN, 8.0% to AMC, 12.0% to TZP, 28.0% to CLI and 8% to MZ. All other Gram-negative strains were fully susceptible to MEM and ETP, while 96.0% were susceptible to IPM. Clostridium spp. isolates were 100% susceptible to all tested antibiotics except to CLI (two of four tested isolates were resistant). Propionibacterium spp. showed resistance to CLI in 4.3%, while 100% were resistant to MZ. Among other Gram-positive bacilli, 18.2% were resistant to PCN, 9.1% to CLI and 54.5% to MZ, while 81.8% of isolates were susceptible to carbapenems. Gram-positive cocci were 100% susceptible to all tested antimicrobials except to MZ, where 28.6% of resistant strains were recorded. Abdomen was the most common source of isolates (82.5%). The most prevalent types of infection were abscess (22.1%), sepsis (14.8%), appendicitis (13.9%) and peritonitis (6.6%). Twenty four patients (19

  7. Galliscardovia ingluviei gen. nov., sp. nov., a thermophilic bacterium of the family Bifidobacteriaceae isolated from the crop of a laying hen (Gallus gallus f. domestica).

    Science.gov (United States)

    Pechar, R; Killer, J; Švejstil, R; Salmonová, H; Geigerová, M; Bunešová, V; Rada, V; Benada, O

    2017-07-01

    Bacteria with potential probiotic applications are not yet sufficiently explored, even for animals with economic importance. Therefore, we decided to isolate and identify representatives of the family Bifidobacteriaceae, which inhabit the crop of laying hens. During the study, a fructose-6-phosphate phosphoketolase-positive strain, RP51T, with a regular/slightly irregular and sometimes an S-shaped slightly curved rod-like shape, was isolated from the crop of a 13 -month-old Hisex Brown hybrid laying hen. The best growth of the Gram-stain-positive bacterium, which was isolated using Bifidobacterium-selective mTPY agar, was found out to be under strictly anaerobic conditions, however an ability to grow under microaerophilic and aerobic conditions was also observed. Sequencing of the almost complete 16S rRNA gene (1444 bp) showed Alloscardovia omnicolens CCUG 31649T and Bombiscardovia coagulans BLAPIII/AGVT to be the most closely related species with similarities of 93.4 and 93.1 %, respectively. Lower sequence similarities were determined with other scardovial genera and other representatives of the genus Bifidobacterium. Taxonomic relationships with A. omnicolens and other members of the family Bifidobacteriaceaewere also demonstrated, based on the sequences of dnaK, fusA, hsp60 and rplB gene fragments. Low sequence similarities of phylogenetic markers to related scardovial genera and bifidobacteria along with unique features of the bacterial strain investigated within the family Bifidobacteriaceae(including the lowest DNA G+C value (44.3 mol%), a unique spectrum of cellular fatty acids and polar lipids, cellular morphology, the wide temperature range for growth (15-49 °C) and habitat) clearly indicate that strain RP51T is a representative of a novel genus within the family Bifidobacteriaceae for which the name Galliscardovia ingluviei gen. nov., sp. nov. (RP51T=DSM 100235T=LMG 28778T=CCM 8606T) is proposed.

  8. Klebsiella sp. FIRD 2, a TBT-resistant bacterium isolated from contaminated surface sediment along Strait of Johor Malaysia.

    Science.gov (United States)

    Abubakar, Abdussamad; Mustafa, Muskhazli B; Johari, Wan Lutfi Wan; Zulkifli, Syaizwan Zahmir; Ismail, Ahmad; Mohamat-Yusuff, Ferdaus Binti

    2015-12-15

    A possible tributyltin (TBT)-degrading bacterium isolated from contaminated surface sediment was successfully identified as Klebsiella sp. FIRD 2. It was found to be the best isolate capable of resisting TBT at a concentration of 1000 μg L(-1). This was a concentration above the reported contaminated level at the sampling station, 790 μg L(-1). Further studies revealed that the isolate was Gram negative and resisted TBT concentrations of up to 1500 μg L(-1) in a Minimal Salt Broth without the addition of any carbon source within the first 48 h of incubation. It is expected that additional work could be conducted to check the degradation activity of this new isolate and possibly improve the degradation capacity in order to contribute to finding a safe and sustainable remediation solution of TBT contamination. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. Anaerobic gut fungi: Advances in isolation, culture, and cellulolytic enzyme discovery for biofuel production.

    Science.gov (United States)

    Haitjema, Charles H; Solomon, Kevin V; Henske, John K; Theodorou, Michael K; O'Malley, Michelle A

    2014-08-01

    Anaerobic gut fungi are an early branching family of fungi that are commonly found in the digestive tract of ruminants and monogastric herbivores. It is becoming increasingly clear that they are the primary colonizers of ingested plant biomass, and that they significantly contribute to the decomposition of plant biomass into fermentable sugars. As such, anaerobic fungi harbor a rich reservoir of undiscovered cellulolytic enzymes and enzyme complexes that can potentially transform the conversion of lignocellulose into bioenergy products. Despite their unique evolutionary history and cellulolytic activity, few species have been isolated and studied in great detail. As a result, their life cycle, cellular physiology, genetics, and cellulolytic metabolism remain poorly understood compared to aerobic fungi. To help address this limitation, this review briefly summarizes the current body of knowledge pertaining to anaerobic fungal biology, and describes progress made in the isolation, cultivation, molecular characterization, and long-term preservation of these microbes. We also discuss recent cellulase- and cellulosome-discovery efforts from gut fungi, and how these interesting, non-model microbes could be further adapted for biotechnology applications. © 2014 Wiley Periodicals, Inc.

  10. 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

  11. Vibrio xiamenensis sp. nov., a cellulase-producing bacterium isolated from mangrove soil.

    Science.gov (United States)

    Gao, Zhao-Ming; Xiao, Jing; Wang, Xing-Na; Ruan, Ling-Wei; Chen, Xiu-Lan; Zhang, Yu-Zhong

    2012-08-01

    A taxonomic study was carried out on a cellulase-producing bacterium, strain G21(T), isolated from mangrove soil in Xiamen, Fujian province, China. Cells were Gram-negative, slightly curved rods, motile with a single polar flagellum. The strain grew at 15-40 °C and in 0.5-10% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain G21(T) belonged to the genus Vibrio and formed a clade with Vibrio furnissii ATCC 350116(T) (97.4% sequence similarity), V. fluvialis LMG 7894(T) (97.1%) and V. ponticus CECT 5869(T) (96.1%). However, multilocus sequence analysis (using rpoA, recA, mreB, gapA, gyrB and pyrH sequences) and DNA-DNA hybridization experiments indicated that the strain was distinct from the closest related Vibrio species. Additionally, strain G21(T) could be differentiated from them phenotypically by the ability to grow in 10% NaCl but not on TCBS plates, its enzyme activity spectrum, citrate utilization, oxidization of various carbon sources, hydrolysis of several substrates and its cellular fatty acid profile. The G+C content of the genomic DNA was 46.0 mol%. The major cellular fatty acids were summed feature 3 (C(16:1)ω7c and/or iso-C(15:0) 2-OH), C(16:0) and C(18:1)ω7c. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol, with trace amounts of diphosphatidylglycerol. The predominant quinones were Q-8 and Q-7. Based on phylogenetic, phenotypic and chemotaxonomic characteristics and DNA-DNA hybridization analysis, it is concluded that strain G21(T) represents a novel species of the genus Vibrio, for which the name Vibrio xiamenensis sp. nov. is proposed. The type strain is G21(T) ( = DSM 22851(T)  = CGMCC 1.10228(T)).

  12. Advenella alkanexedens sp. nov., an alkane-degrading bacterium isolated from biogas slurry samples.

    Science.gov (United States)

    Wang, Huimin; Zhou, Shan; Wang, Yanwei; Kong, Delong; Guo, Xiang; Zhu, Jie; Dong, Weiwei; Ruan, Zhiyong

    2016-02-01

    A novel aerobic bacterium, designated strain LAM0050 T , was isolated from a biogas slurry sample, which had been enriched with diesel oil for 30 days. Cells of strain LAM0050 T were gram-stain-negative, non-motile, non-spore-forming and coccoid-shaped. The optimal temperature and pH for growth were 30-35 °C and 8.5, respectively. The strain did not require NaCl for growth, but tolerated up to 5.3 % (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain LAM0050 T was a member of the genus Advenella , and was most closely related to Advenella faeciporci KCTC 23732 T , Advenella incenata CCUG 45225 T , Advenella kashmirensis DSM 17095 T and Advenella mimigardefordensis DSM 17166 T , with 98.1, 96.6, 96.6 and 96.3 % sequence similarity, respectively. The DNA-DNA hybridization relatedness between strain LAM0050 T and A. faeciporci KCTC 23732 T was 41.7 ± 2.4 %. The genomic DNA G+C content was 51.2 mol%, as determined by the T m method. The major fatty acids of strain LAM0050 T were C 16 : 0 , C 17 : 0 cyclo, summed feature 3 (C 16 : 1 ω7 c and/or C 16 : 1 ω6 c ) and summed feature 8 (C 18 : 1 ω7 c and/or C 18 : 1 ω6 c ). The predominant ubiquinone was Q-8. The main polar lipids were diphosphatidyglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine and four unidentified phospholipids. Based on the phenotypic and genotypic properties, strain LAM0050 T is suggested to represent a novel species of the genus Advenella , for which the name Advenella alkanexedens sp. nov., is proposed, the type strain is LAM0050 T ( = ACCC 06485 T  = JCM 30465 T ).

  13. Marinirhabdus citrea sp. nov., a marine bacterium isolated from a seaweed.

    Science.gov (United States)

    Yang, Sung-Hyun; Oh, Ji Hye; Seo, Hyun-Seok; Lee, Jung-Hyun; Kwon, Kae Kyoung

    2018-02-01

    A gram-stain-negative, aerobic, rod-shaped (1.3-1.9×0.3-0.5 µm) and non-motile marine bacterium, designated MEBiC09412 T , was isolated from seaweed collected at Yeonggwang County, South Korea. 16S rRNA gene sequence analysis demonstrated that strain MEBiC09412 T shared high sequence similarity with Marinirhabdus gelatinilytica NH83 T (95.4 %). Growth was observed at 17-38 °C (optimum 30 °C), at pH 4.0-8.5 (optimum pH 7.0) and with 0.5-6.0 % (w/v; optimum 2.5 %) NaCl. The predominant cellular fatty acids were iso-C15 : 0 (27.4 %), iso-C15 : 1 G (9.6 %), anteiso-C15 : 0 (14.6 %), iso-C16 : 0 (6.2 %), iso-C17 : 0 3OH (13.2 %) and summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c; 7.4 %). The DNA G+C content was determined to be 43.1 mol%, while the major respiratory quinone was menaquinone-6. Several phenotypic characteristics such as indole production, the oxidizing patterns of several carbohydrtaes (of glucose, fructose, sucrose, maltose, mannose etc.) and organic acids, and the enzyme activities of α-chymotrypsin and α-glucosidase differentiated strain MEBiC09412 T from M. gelatinilytica NH83 T . On the basis of this polyphasic taxonomic data, strain MEBiC09412 T should be classified as a novel species of the genus Marinirhabduswith the suggested name Marinirhabdus citrea sp. nov. The type strain is MEBiC09412 T (=KCCM 43216 T =JCM 31588 T ).

  14. Identification of a novel acetate-utilizing bacterium belonging to Synergistes group 4 in anaerobic digester sludge

    Science.gov (United States)

    Ito, Tsukasa; Yoshiguchi, Kazumi; Ariesyady, Herto Dwi; Okabe, Satoshi

    2011-01-01

    Major acetate-utilizing bacterial and archaeal populations in methanogenic anaerobic digester sludge were identified and quantified by radioisotope- and stable-isotope-based functional analyses, microautoradiography-fluorescence in situ hybridization (MAR-FISH) and stable-isotope probing of 16S rRNA (RNA-SIP) that can directly link 16S rRNA phylogeny with in situ metabolic function. First, MAR-FISH with 14C-acetate indicated the significant utilization of acetate by only two major groups, unidentified bacterial cells and Methanosaeta-like filamentous archaeal cells, in the digester sludge. To identify the acetate-utilizing unidentified bacteria, RNA-SIP was conducted with 13C6-glucose and 13C3-propionate as sole carbon source, which were followed by phylogenetic analysis of 16S rRNA. We found that bacteria belonging to Synergistes group 4 were commonly detected in both 16S rRNA clone libraries derived from the sludge incubated with 13C-glucose and 13C-propionate. To confirm that this bacterial group can utilize acetate, specific FISH probe targeting for Synergistes group 4 was newly designed and applied to the sludge incubated with 14C-acetate for MAR-FISH. The MAR-FISH result showed that bacteria belonging to Synergistes group 4 significantly took up acetate and their active population size was comparable to that of Methanosaeta in this sludge. In addition, as bacteria belonging to Synergistes group 4 had high Km for acetate and maximum utilization rate, they are more competitive for acetate over Methanosaeta at high acetate concentrations (2.5–10 m). To our knowledge, it is the first time to report the acetate-utilizing activity of uncultured bacteria belonging to Synergistes group 4 and its competitive significance to acetoclastic methanogen, Methanosaeta. PMID:21562600

  15. 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).

  16. Biofilm growth kinetics of a monomethylamine producing Alphaproteobacteria strain isolated from an anaerobic reactor.

    Science.gov (United States)

    Jopia, Paz; Ruiz-Tagle, Nathaly; Villagrán, Marcelo; Sossa, Katherine; Pantoja, Silvio; Rueda, Luis; Urrutia-Briones, Homero

    2010-02-01

    Industrial fishing effluents are characterized by high loads of protein and sulfate that stimulate the activity of proteolytic and sulfate reducing bacteria during anaerobic digestion. Their metabolic products (NH3 and H2S respectively) have a well-known detrimental effect on the activity of methanogens. Since methylamine is a carbon source used by methylaminotrophic methane producing archaea (mMPA) but not by sulfate reducing bacteria (SRB), enriched mMPA anaerobic biofilms have been developed on ceramics. We propose that methylated amines could be produced in the biofilm by using betaine, a known precursor of methylamine, as a carbon and energy source. We isolated an anaerobic betainotrophic methylaminogenic bacterial strain (bMB) from an anaerobic bioreactor, using betaine as the only carbon and energy source. This strain was identified by a standard biochemical test (API 20NE), cloning, and 16S rDNA sequencing. bMB biofilm structure and biofilm growth kinetic parameters were determined by means of scanning electron microscopy (SEM), and the Gompertz growth model, respectively. Monomethylamine production was determined by infrared spectroscopy and by high pressure liquid chromatography. The isolated bMB strain was determined as Stappia stellulata (Proteobacteria phylum). It was able to form biofilm on ceramics and its kinetic growth parameters resulted in: maximum biofilm bacterial count (A) of 6.25 x 10(8) UFC/cm(2) and maximum specific growth rate (mu(m)) of 0.0221/h. Production of monomethylamine was about 4.027 atogram/cell/day (at/cell/day) after 15 days of incubation in biofilms. This study confirms the adhesion capacity of this bMB strain on ceramic supports, assuring that monomethylamine production in biofilms could be enriched with mMPA that use monomethylamine. 2009 Elsevier Ltd. All rights reserved.

  17. Isolation and characterization of an algicidal bacterium indigenous to lake Taihu with a red pigment able to lyse microcystis aeruginosa.

    Science.gov (United States)

    Yang, Fei; Wei, Hai Yan; Li, Xiao Qin; Li, Yun Hui; Li, Xiao Bo; Yin, Li Hong; Pu, Yue Pu

    2013-02-01

    To isolate and characterize indigenous algicidal bacteria and their algae-lysing compounds active against Microcystis aeruginosa, strains TH1, TH2, and FACHB 905. The bacteria were identified using the Biolog automated microbial identification system and 16S rDNA sequence analysis. The algae-lysing compounds were isolated and purified by silica gel column chromatography and reverse-phase high performance liquid chromatography. Their structures were confirmed by Nuclear Magnetic Resonance (NMR) and Fourier Transform Infrared (FT-IR) spectroscopy. Algae-lysing activity was observed using microscopy. The algae-lysing bacterium LTH-2 isolated from Lake Taihu was identified as Serratia marcescens. Strain LTH-2 secreted a red pigment identified as prodigiosin (C20H25N3O), which showed strong lytic activity with algal strains M. aeruginosa TH1, TH2, and FACHB 905 in a concentration-dependent manner. The 50% inhibitory concentration (IC50) of prodigiosin with the algal strains was 4.8 (± 0.4)× 10⁻² μg/mL, 8.9 (± 1.1)× 10⁻² μg/mL, and 1.7 (± 0.1)× 10⁻¹ μg/mL in 24 h, respectively. The bacterium LTH-2 and its pigment had strong Microcystis-lysing activity probably related to damage of cell membranes. The bacterium LTH-2 and its red pigment are potentially useful for regulating blooms of harmful M. aeruginosa. Copyright © 2013 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

  18. Isolation of an indigenous imidacloprid-degrading bacterium and imidacloprid bioremediation under simulated in situ and ex situ conditions.

    Science.gov (United States)

    Hu, Guiping; Zhao, Yan; Liu, Bo; Song, Fengqing; You, Minsheng

    2013-11-28

    The Bacterial community structure and its complexity of the enrichment culture during the isolation and screening of imidacloprid-degrading strain were studied using denaturating gradient gel electrophoresis analysis. The dominant bacteria in the original tea rhizosphere soil were uncultured bacteria, Rhizobium sp., Sinorhizobium, Ochrobactrum sp., Alcaligenes, Bacillus sp., Bacterium, Klebsiella sp., and Ensifer adhaerens. The bacterial community structure was altered extensively and its complexity reduced during the enrichment process, and four culturable bacteria, Ochrobactrum sp., Rhizobium sp., Geobacillus stearothermophilus, and Alcaligenes faecalis, remained in the final enrichment. Only one indigenous strain, BCL-1, with imidacloprid-degrading potential, was isolated from the sixth enrichment culture. This isolate was a gram-negative rod-shaped bacterium and identified as the genus Ochrobactrum based on its morphological, physiological, and biochemical properties and its 16S rRNA gene sequence. The degradation test showed that approximately 67.67% of the imidacloprid (50 mg/l) was degraded within 48 h by strain BCL-1. The optimum conditions for degradation were a pH of 8 and 30°C. The simulation of imidacloprid bioremediation by strain BCL-1 in soil demonstrated that the best performance in situ (tea soil) resulted in the degradation of 92.44% of the imidacloprid (100 mg/g) within 20 days, which was better than those observed in the ex situ simulations that were 64.66% (cabbage soil), 41.15% (potato soil), and 54.15% (tomato soil).

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

    Directory of Open Access Journals (Sweden)

    E.H. Seck

    2016-03-01

    Full Text Available We propose the main phenotypic characteristics and the complete genome sequence and annotation of Planococcus massiliensis strain ES2T (= CSUR P1103 = DSM 28915, the type strain of P. massiliensis sp. nov., isolated from a faeces sample collected from a healthy Senegalese man. It is an aerobic, Gram-positive, moderately halophilic, motile and rod-shaped bacterium. The 3 357 017 bp long genome exhibits a G+C content of 46.0% and contains 3357 protein-coding genes and 48 RNA genes.

  20. Zymomonas mobilis: a bacterium for ethanol production

    Energy Technology Data Exchange (ETDEWEB)

    Baratti, J.C.; Bu' Lock, J.D.

    1986-01-01

    Zymomonas mobilis is a facultative anaerobic gram negative bacterium first isolated in tropical countries from alcoholic beverages like the African palm wine, the Mexican pulque and also as a contaminant of cider (cider sickness) or beer in the European countries. It is one of the few facultative anaerobic bacteria degrading glucose by the Entner-Doudoroff pathway usually found in strictly aerobic microorganisms. Some work was devoted to this bacterium in the 50s and 60s and was reviewed by Swings and De Ley in their classical paper published in 1977. During the 70s there was very little work on the bacterium until 1979 and the first report by the Australian group of P.L. Rogers on the great potentialities of Z. mobilis for ethanol production. At that time the petroleum crisis had led the developed countries to search for alternative fuel from renewable resources. The Australian group clearly demonstrated the advantages of the bacterium compared to the yeasts traditionally used for the alcoholic fermentation. As a result, there was a considerable burst in the Zymomonas literature which started from nearly zero in the late 70s to attain 70 papers published in the field in 1984. In this article, papers published from 1982 to 1986 are reviewed.

  1. Isolation and characterization of a prokaryotic cell organelle from the anammox bacterium

    NARCIS (Netherlands)

    Neumann, S.; Wessels, H.J.C.T.; Rijpstra, W.I.C.; Sinninghe Damsté, J.S.; Kartal, B.; Jetten, M.S.M.; van Niftrik, L.

    2014-01-01

    Anaerobic ammonium oxidizing (anammox) bacteria oxidize ammonium with nitrite to nitrogen gas in the absence of oxygen. These microorganisms form a significant sink for fixed nitrogen in the oceans and the anammox process is applied as a cost-effective and environment-friendly nitrogen removal

  2. Deletion of a gene cluster for [Ni-Fe] hydrogenase maturation in the anaerobic hyperthermophilic bacterium Caldicellulosiruptor bescii identifies its role in hydrogen metabolism.

    Science.gov (United States)

    Cha, Minseok; Chung, Daehwan; Westpheling, Janet

    2016-02-01

    The anaerobic, hyperthermophlic, cellulolytic bacterium Caldicellulosiruptor bescii grows optimally at ∼80 °C and effectively degrades plant biomass without conventional pretreatment. It utilizes a variety of carbohydrate carbon sources, including both C5 and C6 sugars, released from plant biomass and produces lactate, acetate, CO2, and H2 as primary fermentation products. The C. bescii genome encodes two hydrogenases, a bifurcating [Fe-Fe] hydrogenase and a [Ni-Fe] hydrogenase. The [Ni-Fe] hydrogenase is the most widely distributed in nature and is predicted to catalyze hydrogen production and to pump protons across the cellular membrane creating proton motive force. Hydrogenases are the key enzymes in hydrogen metabolism and their crystal structure reveals complexity in the organization of their prosthetic groups suggesting extensive maturation of the primary protein. Here, we report the deletion of a cluster of genes, hypABFCDE, required for maturation of the [Ni-Fe] hydrogenase. These proteins are specific for the hydrogenases they modify and are required for hydrogenase activity. The deletion strain grew more slowly than the wild type or the parent strain and produced slightly less hydrogen overall, but more hydrogen per mole of cellobiose. Acetate yield per mole of cellobiose was increased ∼67 % and ethanol yield per mole of cellobiose was decreased ∼39 %. These data suggest that the primary role of the [Ni-Fe] hydrogenase is to generate a proton gradient in the membrane driving ATP synthesis and is not the primary enzyme for hydrogen catalysis. In its absence, ATP is generated from increased acetate production resulting in more hydrogen produced per mole of cellobiose.

  3. [Isolation, Identification and Characteristic Analysis of an Oil-producing Chlorella sp. Tolerant to High-strength Anaerobic Digestion Effluent].

    Science.gov (United States)

    Yang, Chuang; Wang, Wen-guo; Ma, Dan-wei; Tang, Xiao-yu; Hu, Qi-chun

    2015-07-01

    A Chlorella strain tolerant to high-strength anaerobic digestion effluent was isolated from the anaerobic digestion effluent with a long-term exposure to air. The strain was identified as a Chlorella by morphological and molecular biological methods, and named Chlorella sp. BWY-1, The anaerobic digestion effluent used in this study was from a biogas plant with the raw materials of swine wastewater after solid-liquid separation. The Chlorella regularis (FACHB-729) was used as the control strain. The comparative study showed that Chlorella sp, BWY-Ihad relatively higher growth rate, biomass accumulation capacity and pollutants removal rate in BG11. and different concentrations of anaerobic digestion effluent. Chlorella sp. BWY-1 had the highest growth rate and biomass productivity (324.40 mg.L-1) in BG11, but its lipid productivity and lipid content increased with the increase of anaerobic digestion effluent concentration, In undiluted anaerobic digestion effluent, the lipid productivity and lipid content of Chlorella sp. BWY-1 were up to 44. 43% and 108. 70 mg.L-1, respectively. Those results showed that the isolated algal strain bad some potential applications in livestock wastewater treatment and bioenergy production, it could be combined with a solid-liquid separation, anaerobic fermentation and other techniques for processing livestock wastewater and producing biodiesel.

  4. Caldisericum exile gen. nov., sp. nov., an anaerobic, thermophilic, filamentous bacterium of a novel bacterial phylum, Caldiserica phyl. nov., originally called the candidate phylum OP5, and description of Caldisericaceae fam. nov., Caldisericales ord. nov. and Caldisericia classis nov.

    Science.gov (United States)

    Mori, Koji; Yamaguchi, Kaoru; Sakiyama, Yayoi; Urabe, Tetsuro; Suzuki, Ken-ichiro

    2009-11-01

    An anaerobic, thermophilic, thiosulfate-reducing bacterium, strain AZM16c01(T), isolated from a hot spring in Japan [Mori, K., Sunamura, M., Yanagawa, K., Ishibashi, J., Miyoshi, Y., Iino, T., Suzuki, K. & Urabe, T. (2008). Appl Environ Microbiol 74, 6223-6229] was characterized in detail. The 16S rRNA gene sequence analysis had revealed that strain AZM16c01(T) was the first cultivated representative of the candidate phylum OP5. The cells were multicellular filaments with a single polar flagellum. The strain contained iso-C(17 : 0) as the major fatty acid and menaquinone-8(H(6)), menaquinone-8(H(8)) and menaquinone-8(H(10)) as the respiratory quinones. The G+C content of the genomic DNA of strain AZM16c01(T) was 34.6 mol%. Optimum growth was obtained at 65 degrees C, pH 6.5 and in the absence of NaCl, with a doubling time of 10.6 h. On the basis of the results of phylogenetic analysis based on the 16S rRNA gene sequence and the characterization of the strain in this study, we propose the name Caldisericum exile gen. nov., sp. nov. for strain AZM16c01(T) (=NBRC 104410(T)=DSM 21853(T)). In addition, we propose the new phylum name Caldiserica phyl. nov. for the candidate phylum OP5 represented by C. exile gen. nov., sp. nov., and Caldisericaceae fam. nov., Caldisericales ord. nov. and Caldisericia classis nov.

  5. Isolation of a sulfate reducing bacterium and its application in sulfate ...

    African Journals Online (AJOL)

    The results show that the effect of C. freundii in removing sulfate was best when the temperature was 32°C, pH was 7.0, COD/SO42- was 5.0 and the initial SO42- concentration was 1500 mg/L. Also, the SRB was inoculated onto an up-flow anaerobic sludge bed (UASB) to remove sulfate in actual tannery wastewater.

  6. Going from Microbial Ecology to Genome Data and Back: Studies on a Haloalkaliphilic Bacterium Isolated from Soap Lake, Washington State

    Directory of Open Access Journals (Sweden)

    Melanie R. Mormile

    2014-11-01

    Full Text Available Soap Lake is a meromictic, alkaline (~pH 9.8 and saline (~14 to 140 g liter-1 lake located in the semiarid area of eastern Washington State. Of note is the length of time it has been meromictic (at least 2000 years and the extremely high sulfide level (~140 mM in its monimolimnion. As expected, the microbial ecology of this lake is greatly influenced by these conditions. A bacterium, Halanaerobium hydrogeniformans, was isolated from the mixolimnion region of this lake. H. hydrogeniformans is a haloalkaliphilic bacterium capable of forming hydrogen from 5- and 6-carbon sugars derived from hemicellulose and cellulose. Due to its ability to produce hydrogen under saline and alkaline conditions, in amounts that rival genetically modified organisms, its genome was sequenced. This sequence data provides an opportunity to explore the unique metabolic capabilities of this organism, including the mechanisms for tolerating the extreme conditions of both high salinity and alkalinity of its environment.

  7. First report of a lipopeptide biosurfactant from thermophilic bacterium Aneurinibacillus thermoaerophilus MK01 newly isolated from municipal landfill site.

    Science.gov (United States)

    Sharafi, Hakimeh; Abdoli, Mahya; Hajfarajollah, Hamidreza; Samie, Nima; Alidoust, Leila; Abbasi, Habib; Fooladi, Jamshid; Zahiri, Hossein Shahbani; Noghabi, Kambiz Akbari

    2014-07-01

    A biosurfactant-producing thermophile was isolated from the Kahrizak landfill of Tehran and identified as a bacterium belonging to the genus Aneurinibacillus. A thermostable lipopeptide-type biosurfactant was purified from the culture medium of this bacterium and showed stability in the temperature range of 20-90 °C and pH range of 5-10. The produced biosurfactant could reduce the surface tension of water from 72 to 43 mN/m with a CMC of 1.21 mg/mL. The strain growing at a temperature of 45 °C produces a substantial amount of 5 g/L of biosurfactant in the medium supplemented with sunflower oil as the sole carbon source. Response surface methodology was employed to optimize the biosurfactant production using sunflower oil, sodium nitrate, and yeast extract as variables. The optimization resulted in 6.75 g/L biosurfactant production, i.e., 35% improved as compared to the unoptimized condition. Thin-layer chromatography, FTIR spectroscopy, 1H-NMR spectroscopy, and biochemical composition analysis confirmed the lipopeptide structure of the biosurfactant.

  8. Gene function analysis in environmental isolates: The nif regulon of the strict iron oxidizing bacterium Leptospirillum ferrooxidans

    Science.gov (United States)

    Parro, Víctor; Moreno-Paz, Mercedes

    2003-01-01

    A random genomic library from an environmental isolate of the Gram-negative bacterium Leptospirillum ferrooxidans has been printed on a microarray. Gene expression analysis was carried out with total RNA extracted from L. ferrooxidans cultures in the presence or absence of ammonium as nitrogen source under aerobic conditions. Although practically nothing is known about the genome sequence of this bacterium, this approach allowed us the selection and sequencing of only those clones bearing genes that showed an altered expression pattern. By sequence comparison, we have identified most of the genes of nitrogen fixation regulon in L. ferrooxidans, like the nifHDKENX operon, encoding the structural components of Mo-Fe nitrogenase; nifSU-hesB-hscBA-fdx operon, for Fe-S cluster assembly; the amtB gene (ammonium transporter); modA (molybdenum ABC type transporter); some regulatory genes like ntrC, nifA (the specific activator of nif genes); or two glnB-like genes (encoding the PII regulatory protein). Our results show that shotgun DNA microarrays are very powerful tools to accomplish gene expression studies with environmental bacteria whose genome sequence is still unknown, avoiding the time and effort necessary for whole genome sequencing projects. PMID:12808145

  9. Genetic identification and antimicrobial susceptibility of clinically isolated anaerobic bacteria: A prospective multicenter surveillance study in Japan.

    Science.gov (United States)

    Yunoki, Tomoyuki; Matsumura, Yasufumi; Yamamoto, Masaki; Tanaka, Michio; Hamano, Kyoko; Nakano, Satoshi; Noguchi, Taro; Nagao, Miki; Ichiyama, Satoshi

    2017-12-01

    This prospective multicenter surveillance study was designed to provide antimicrobial susceptibility profiles of clinical anaerobic bacteria with genetic species identification in Japan. In 2014, a total of 526 non-duplicate clinical anaerobic isolates were collected from 11 acute-care hospitals in the Kyoto and Shiga regions of Japan. Genetic identification was performed using 16S rRNA sequencing. Minimum inhibitory concentrations were determined in the central laboratory and were interpreted using the CLSI criteria. Genetic analysis provided species-level identification for 496 isolates (83 species in 40 genera) and genus-level identification for 21 isolates (13 genera). Among these 517 isolates, the most frequent anaerobes were Bacteroides spp. (n = 207), Prevotella spp. (n = 43), Clostridium spp. (n = 40), and Peptoniphilus spp. (n = 40). B. fragilis was the most common species (n = 107) and showed 91.6%-97.2% susceptibility to β-lactam/β-lactamase inhibitor combinations (BLBLIs; ampicillin-sulbactam, amoxicillin-clavulanate, and piperacillin-tazobactam) and carbapenems (imipenem and meropenem) as well as 100% susceptibility to metronidazole. Gram-negative anaerobes were highly susceptible to metronidazole (99.0%) followed by BLBLIs and carbapenems (>90% each). BLBLIs or carbapenems also retained activity against Gram-positive anaerobes (99.5%-100%) except Clostridioides difficile. All isolates were susceptible to combinations of metronidazole with BLBLIs or carbapenems. Thus, BLBLIs or carbapenems are first choices for empirical therapy of anaerobic infections in Japan, and these antimicrobials in combination with metronidazole should be reserved for very severe infections and targeted therapy. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. 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.

  11. [Isolation and identification of aerobic and facultative anaerobic bacteria in the oral cavity].

    Science.gov (United States)

    Lu, Wenxin; Wu, Fanzi; Zhou, Xinxuan; Wu, Lan; Li, Mingyun; Ren, Biao; Guo, Qiang; Huang, Ruijie; Li, Jiyao; Xiao, Liying; Li, Yan

    2015-12-01

    To establish a systematic method for isolation and identification of aerobic and facultative anaerobic bacteria in the oral cavity. Samples of the saliva, dental plaque and periapical granulation tissue were collected from 20 subjects with healthy oral condition and from 8 patients with different oral diseases. The bacteria in the samples were identified by morphological identification, VITEK automatic microorganism identification and 16s rRNA gene sequencing. VITEK automatic microorganism identification and 16s rRNA gene sequencing showed an agreement rate of 22.39% in identifying the bacteria in the samples. We identified altogether 63 bacterial genus (175 species), among which Streptococcus, Actinomyces and Staphylococcus were the most common bacterial genus, and Streptococcus anginosus, Actinomyces oris, Streptococcus mutans and Streptococcus mitis were the most common species. Streptococcus anginosus was commonly found in patients with chronic periapical periodontitis. Streptococcus intermedius and Staphylococcus aureus were common in patients with radiation caries, and in patients with rampant caries, Streptococcus mutans was found at considerably higher rate than other species. Aerobic and facultative anaerobic bacteria are commonly found in the oral cavity, and most of them are gram-positive. 16s rRNA gene sequencing is more accurate than VITEK automatic microorganism identification in identifying the bacteria.

  12. Draft Genome Sequences of 17 Isolates of the Plant Pathogenic Bacterium Dickeya

    OpenAIRE

    Pritchard, Leighton; Humphris, Sonia; Saddler, Gerry S.; Elphinstone, John G.; Pirhonen, Minna; Toth, Ian K.

    2013-01-01

    Dickeya (formerly Erwinia chrysanthemi) species cause diseases on a wide range of crops and ornamental plants worldwide. Here we present the draft sequences of 17 Dickeya isolates spanning four Dickeya species, including five isolates that are currently unassigned to a species.

  13. Draft genome sequences of 17 isolates of the plant pathogenic bacterium dickeya.

    Science.gov (United States)

    Pritchard, Leighton; Humphris, Sonia; Saddler, Gerry S; Elphinstone, John G; Pirhonen, Minna; Toth, Ian K

    2013-11-21

    Dickeya (formerly Erwinia chrysanthemi) species cause diseases on a wide range of crops and ornamental plants worldwide. Here we present the draft sequences of 17 Dickeya isolates spanning four Dickeya species, including five isolates that are currently unassigned to a species.

  14. Taylorella asinigenitalis sp. nov., a bacterium isolated from the genital tract of male donkeys (Equus asinus).

    Science.gov (United States)

    Jang, S S; Donahue, J M; Arata, A B; Goris, J; Hansen, L M; Earley, D L; Vandamme, P A; Timoney, P J; Hirsh, D C

    2001-05-01

    Three bacterial isolates that were phenotypically indistinguishable from Taylorella equigenitalis were obtained from the urethral fossae of three male donkeys (Equus asinus), one located in the state of California and the other two in the state of Kentucky, USA. Based on results of pulsed-field gel electrophoresis, the isolate from California differed from the two Kentucky isolates, which were the same. Mares bred artificially (California) or naturally (Kentucky) did not show signs of disease, even though infection with the organism was established in those bred naturally. Mares and, uncharacteristically, all three jacks produced antibodies that reacted in the complement fixation test utilized to identify mares recently infected with T. equigenitalis. Sequence analysis of DNA encoding the 16S rRNA revealed that the gene sequences of these isolates were virtually identical to each other (>99.8% similarity), but different (97.6% similarity) from those of several confirmed isolates of T. equigenitalis. The 16S rDNA sequences of the latter were 100% identical. DNA-DNA hybridization studies revealed a mean hybridization level of 89% between the donkey isolate from California and the donkey isolate from Kentucky. On the other hand, the mean DNA-DNA hybridization level from the donkey isolates with DNA from a strain of T. equigenitalis was 23%. The DNA G+C composition was 37.8 mol% for the two donkey isolates, as well as the strain of T. equigenitalis used in the hybridization studies. These data support our opinion that micro-organisms isolated from the male donkeys are different from T. equigenitalis and it is proposed that they be considered a new species within the genus Taylorella and named Taylorella asinigenitalis sp. nov. The type strain is strain UCD-1T (= ATCC 700933T = LMG 19572T).

  15. 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).

  16. 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)).

  17. ‘Lactomassilus timonensis,’ a new anaerobic bacterial species isolated from the milk of a healthy African mother

    Directory of Open Access Journals (Sweden)

    A.H. Togo

    2018-01-01

    Full Text Available We here report the main characteristics of a new anaerobic bacterial genus and species ‘Lactomassilus timonensis,’ strain Marseille-P4641T (CSUR = P4641, isolated by microbial culturomics from the milk of a 35-year-old healthy lactating mother from Mali.

  18. 16S rRNA gene sequencing in routine identification of anaerobic bacteria isolated from blood cultures

    DEFF Research Database (Denmark)

    Justesen, Ulrik Stenz; Skov, Marianne Nielsine; Knudsen, Elisa

    2010-01-01

    A comparison between conventional identification and 16S rRNA gene sequencing of anaerobic bacteria isolated from blood cultures in a routine setting was performed (n = 127). With sequencing, 89% were identified to the species level, versus 52% with conventional identification. The times...

  19. Tellurite-, tellurate-, and selenite-based anaerobic respiration by strain CM-3 isolated from gold mine tailings.

    Science.gov (United States)

    Maltman, Chris; Piercey-Normore, Michele D; Yurkov, Vladimir

    2015-09-01

    The newly discovered strain CM-3, a Gram-negative, rod-shaped bacterium from gold mine tailings of the Central Mine in Nopiming Provincial Park, Canada, is capable of dissimilatory anaerobic reduction of tellurite, tellurate, and selenite. CM-3 possesses very high level resistance to these oxides, both aerobically and anaerobically. During aerobic growth, tellurite and tellurate resistance was up to 1500 and 1000 µg/ml, respectively. In the presence of selenite, growth occurred at the highest concentration tested, 7000 µg/ml. Under anaerobic conditions, resistance was decreased to 800 µg/ml for the Te oxides; however, much like under aerobic conditions, growth with selenite still took place at 7000 µg/ml. In the absence of oxygen, CM-3 couples oxide reduction to an increase in biomass. Following an initial drop in viable cells, due to switching from aerobic to anaerobic conditions, there was an increase in CFU/ml greater than one order of magnitude in the presence of tellurite (6.6 × 10(3)-8.6 × 10(4) CFU/ml), tellurate (4.6 × 10(3)-1.4 × 10(5) CFU/ml), and selenite (2.7 × 10(5)-5.6 × 10(6) CFU/ml). A control culture without metalloid oxides showed a steady decrease in CFU/ml with no recovery. ATP production was also increased in the presence of each oxide, further indicating anaerobic respiration. Partial 16S rRNA gene sequencing revealed a 99.0 % similarity of CM-3 to Pseudomonas reactans.

  20. Isolation and identification of intestinal bacteria from Japanese tree frog (Hlya japonica) with the special reference to anaerobic bacteria.

    Science.gov (United States)

    Benno, Y; Izumi-Kurotani, A; Yamashita, M

    1992-08-01

    The bacteria in the large intestines of eight Japanese tree frogs (Hlya japonica) were enumerated by using an anaerobic culture system. The microorganisms at approximately 3.1 x 10(9) bacteria per g (wet weight) of intestinal contents were present in the intestine of all the frogs tested. No difference of the total bacteria in the frog intestine was observed between two different incubation-temperatures (room temperature and 37 degrees C). Eleven genera and 16 species were isolated from the frog intestine. In most frogs, Bacteroides (B.) caccae and B. vulgatus were detected as the predominant organisms. Escherichia coli was also present in greater numbers in the intestine. Other bacteria isolated at high dilutions were strict anaerobes, including Fusobacterium and Clostridium. Enterococcus faecalis was frequently isolated from the frog intestine. However, four genera of Bifidobacterium, Eubacterium, Peptostreptococcus, and Lactobacillus were not isolated from the frog intestine.

  1. ‘Arcanobacterium urinimassiliense’ sp. nov., a new bacterium isolated from the urogenital tract

    Directory of Open Access Journals (Sweden)

    K. Diop

    2017-07-01

    Full Text Available Herein we report the main characteristics of ‘Arcanobacterium urinimassiliense’ strain Marseille-P3248T (=CSUR P3248 isolated from a urine sample of a 54-day-old girl with rotavirus gastroenteritis.

  2. 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.

    17679T) was isolated from a marine solar saltern sample collected from Kakinada, India. 8 Acknowledgements We thank Dr. J. Euzeby for his expert suggestion for the correct species epithet and Latin etymology. We also thank Council of Scientific...

  3. Geobacter daltonii sp. nov., an Fe(III)- and uranium(VI)-reducing bacterium isolated from a shallow subsurface exposed to mixed heavy metal and hydrocarbon contamination.

    Science.gov (United States)

    Prakash, Om; Gihring, Thomas M; Dalton, Dava D; Chin, Kuk-Jeong; Green, Stefan J; Akob, Denise M; Wanger, Greg; Kostka, Joel E

    2010-03-01

    An Fe(III)- and uranium(VI)-reducing bacterium, designated strain FRC-32(T), was isolated from a contaminated subsurface of the USA Department of Energy Oak Ridge Field Research Center (ORFRC) in Oak Ridge, Tennessee, where the sediments are exposed to mixed waste contamination of radionuclides and hydrocarbons. Analyses of both 16S rRNA gene and the Geobacteraceae-specific citrate synthase (gltA) mRNA gene sequences retrieved from ORFRC sediments indicated that this strain was abundant and active in ORFRC subsurface sediments undergoing uranium(VI) bioremediation. The organism belonged to the subsurface clade of the genus Geobacter and shared 92-98 % 16S rRNA gene and 75-81 % rpoB gene sequence similarities with other recognized species of the genus. In comparison to its closest relative, Geobacter uraniireducens Rf4(T), according to 16S rRNA gene sequence similarity, strain FRC-32(T) showed a DNA-DNA relatedness value of 21 %. Cells of strain FRC-32(T) were Gram-negative, non-spore-forming, curved rods, 1.0-1.5 microm long and 0.3-0.5 microm in diameter; the cells formed pink colonies in a semisolid cultivation medium, a characteristic feature of the genus Geobacter. The isolate was an obligate anaerobe, had temperature and pH optima for growth at 30 degrees C and pH 6.7-7.3, respectively, and could tolerate up to 0.7 % NaCl although growth was better in the absence of NaCl. Similar to other members of the Geobacter group, strain FRC-32(T) conserved energy for growth from the respiration of Fe(III)-oxyhydroxide coupled with the oxidation of acetate. Strain FRC-32(T) was metabolically versatile and, unlike its closest relative, G. uraniireducens, was capable of utilizing formate, butyrate and butanol as electron donors and soluble ferric iron (as ferric citrate) and elemental sulfur as electron acceptors. Growth on aromatic compounds including benzoate and toluene was predicted from preliminary genomic analyses and was confirmed through successive transfer with

  4. 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

  5. Draft Genome Sequence of Salinibacillus aidingensis Strain MSP4, an Obligate Halophilic Bacterium Isolated from a Salt Crystallizer of the Rann of Kutch, India

    Science.gov (United States)

    Dey, Rinku; Sherathia, Dharmesh; Dalsania, Trupti; Savsani, Kinjal; Patel, Ilaxi; Thomas, Manesh; Ghorai, Sucheta; Vanpariya, Sejal; Rupapara, Rupal; Acharya, Namrata; Rawal, Priya; Joshi, Pragnesh; Sukhadiya, Bhoomika; Mandaliya, Mona; Saxena, Anil Kumar

    2013-01-01

    We report the 7.42-Mbp draft whole genome sequence of Salinibacillus aidingensis strain MSP4, an obligate halophilic bacterium, isolated from a salt crystallizer of the Rann of Kutch in India. Analysis of the genome of this organism will lead to a better understanding of the genes and metabolic pathways involved in imparting osmotolerance. PMID:23833129

  6. Complete genome sequence of the caprolactam-degrading bacterium Pseudomonas mosselii SJ10 isolated from wastewater of a nylon 6 production plant.

    Science.gov (United States)

    Park, Gun-Seok; Chu, Ji-Hun; Hong, Sung-Jun; Kwak, Yunyoung; Khan, Abdur Rahim; Jung, Byung Kwon; Ullah, Ihsan; Shin, Jae-Ho

    2014-12-20

    Pseudomonas mosselii strain SJ10 is a caprolactam-degrading bacterium belonging to the class Gammaproteobacteria, which was isolated from wastewater of the nylon 6 producing Seongseo industrial complex in Daegu, Republic of Korea. Here, we report the complete genome sequence of the strain, providing genetic information for biodegradation of aromatic compounds.

  7. Draft Genome Sequence of the Phosphate-Solubilizing Bacterium Pseudomonas argentinensis Strain SA190 Isolated from the Desert Plant Indigofera argentea

    KAUST Repository

    Lafi, Feras Fawzi

    2016-12-23

    Pseudomonas argentinensis strain SA190 is a plant endophytic-inhabiting bacterium that was 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 SA190, highlighting several functional genes related to plant growth-promoting activity, environment adaption, and antifungal activity.

  8. Cecembia lonarensis gen. nov., sp. nov., a haloalkalitolerant bacterium of the family Cyclobacteriaceae, isolated from a haloalkaline lake and emended descriptions of the genera Indibacter, Nitritalea and Belliella

    Digital Repository Service at National Institute of Oceanography (India)

    AnilKumar, P.; Srinivas, T.N.R.; Madhu, S.; Sravan, R.; Singh, S.; Naqvi, S.W.A.; Mayilraj, S.; Shivaji, S.

    A novel Gram-staining-negative, rod-shaped, non-motile bacterium, designated strain LW9T, was isolated from a water sample collected from Lonar Lake of Buldhana district, Maharashtra, India. Colonies and broth cultures were reddish orange due...

  9. Draft Genome Sequence of Aeribacillus pallidus Strain 8m3, a Thermophilic Hydrocarbon-Oxidizing Bacterium Isolated from the Dagang Oil Field (China).

    Science.gov (United States)

    Poltaraus, Andrey B; Sokolova, Diyana S; Grouzdev, Denis S; Ivanov, Timophey M; Malakho, Sophia G; Korshunova, Alena V; Rozanov, Aleksey S; Tourova, Tatiyana P; Nazina, Tamara N

    2016-06-09

    The draft genome sequence of Aeribacillus pallidus strain 8m3, a thermophilic aerobic oil-oxidizing bacterium isolated from production water from the Dagang high-temperature oil field, China, is presented here. The genome is annotated to provide insights into the genomic and phenotypic diversity of the genus Aeribacillus. Copyright © 2016 Poltaraus et al.

  10. Draft Genome Sequence of Aeribacillus pallidus Strain 8m3, a Thermophilic Hydrocarbon-Oxidizing Bacterium Isolated from the Dagang Oil Field (China)

    OpenAIRE

    Poltaraus, Andrey B.; Sokolova, Diyana S.; Grouzdev, Denis S.; Ivanov, Timophey M.; Malakho, Sophia G.; Korshunova, Alena V.; Rozanov, Aleksey S.; Tourova, Tatiyana P.; Nazina, Tamara N.

    2016-01-01

    The draft genome sequence of Aeribacillus pallidus strain 8m3, a thermophilic aerobic oil-oxidizing bacterium isolated from production water from the Dagang high-temperature oil field, China, is presented here. The genome is annotated to provide insights into the genomic and phenotypic diversity of the genus Aeribacillus.

  11. “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”

  12. Draft Genome Sequence of the Hydrocarbon-Degrading Bacterium Alcanivorax dieselolei KS-293 Isolated from Surface Seawater in the Eastern Mediterranean Sea

    KAUST Repository

    Barbato, Marta

    2015-12-10

    We report here the draft genome sequence of Alcanivorax dieselolei KS-293, a hydrocarbonoclastic bacterium isolated from the Mediterranean Sea, by supplying diesel oil as the sole carbon source. This strain contains multiple putative genes associated with hydrocarbon degradation pathways and that are highly similar to those described in A. dieselolei type strain B5.

  13. Complete Genome Sequence of Bacillus velezensis CBMB205, a Phosphate-Solubilizing Bacterium Isolated from the Rhizoplane of Rice in the Republic of Korea

    OpenAIRE

    Hwangbo, Kyeong; Um, Yurry; Kim, Ki Yoon; Madhaiyan, Munusamy; Sa, Tong Min; Lee, Yi

    2016-01-01

    Bacillus velezensis CBMB205 (= KACC 13105T = NCCB 100236T) was isolated from the rhizoplane of rice (Oryza sativa L. cv. O-dae). According to previous studies, this bacterium has several genes that can promote plant growth, such as the phosphorus-solubilizing protein-coding gene. Here, we present the first complete genome of B.?velezensis CBMB205.

  14. Complete Genome Sequence of Spiroplasma floricola 23-6T (ATCC 29989), a Bacterium Isolated from a Tulip Tree (Liriodendron tulipifera L.).

    Science.gov (United States)

    Tsai, Yi-Ming; Wu, Pei-Shan; Lo, Wen-Sui; Kuo, Chih-Horng

    2018-04-19

    Spiroplasma floricola 23-6 T (ATCC 29989) was isolated from the flower surface of a tulip tree ( Liriodendron tulipifera L.). Here, we report the complete genome sequence of this bacterium to facilitate the investigation of its biology and the comparative genomics among Spiroplasma species. Copyright © 2018 Tsai et al.

  15. Bombella intestini gen. nov., sp. nov., an acetic acid bacterium isolated from bumble bee crop.

    Science.gov (United States)

    Li, Leilei; Praet, Jessy; Borremans, Wim; Nunes, Olga C; Manaia, Célia M; Cleenwerck, Ilse; Meeus, Ivan; Smagghe, Guy; De Vuyst, Luc; Vandamme, Peter

    2015-01-01

    In the frame of a bumble bee gut microbiota study, acetic acid bacteria (AAB) were isolated using a combination of direct isolation methods and enrichment procedures. MALDI-TOF MS profiling of the isolates and a comparison of these profiles with profiles of established AAB species identified most isolates as Asaia astilbis or as 'Commensalibacter intestini', except for two isolates (R-52486 and LMG 28161(T)) that showed an identical profile. A nearly complete 16S rRNA gene sequence of strain LMG 28161(T) was determined and showed the highest pairwise similarity to Saccharibacter floricola S-877(T) (96.5%), which corresponded with genus level divergence in the family Acetobacteraceae. Isolate LMG 28161(T) was subjected to whole-genome shotgun sequencing; a 16S-23S rRNA internal transcribed spacer (ITS) sequence as well as partial sequences of the housekeeping genes dnaK, groEL and rpoB were extracted for phylogenetic analyses. The obtained data confirmed that this isolate is best classified into a new genus in the family Acetobacteraceae. The DNA G+C content of strain LMG 28161(T) was 54.9 mol%. The fatty acid compositions of isolates R-52486 and LMG 28161(T) were similar to those of established AAB species [with C18:1ω7c (43.1%) as the major component], but the amounts of fatty acids such as C19:0 cyclo ω8c, C14:0 and C14:0 2-OH enabled to differentiate them. The major ubiquinone was Q-10. Both isolates could also be differentiated from the known genera of AAB by means of biochemical characteristics, such as their inability to oxidize ethanol to acetic acid, negligible acid production from melibiose, and notable acid production from d-fructose, sucrose and d-mannitol. In addition, they produced 2-keto-d-gluconate, but not 5-keto-d-gluconate from d-glucose. Therefore, the name Bombella intestini gen nov., sp. nov. is proposed for this new taxon, with LMG 28161(T) ( =DSM 28636(T) =R-52487(T)) as the type strain of the type species. © 2015 IUMS.

  16. A Desulfitobacterium strain isolated from human feces that does not dechlorinate chloroethenes or chlorophenols

    NARCIS (Netherlands)

    van de Pas, BA; Harmsen, HJM; Raangs, GC; de Vos, WM; Schraa, G; Stams, AJM

    An anaerobic bacterium, strain DP7, was isolated from human feces in mineral medium with formate and 0.02% yeast extract as energy and carbon source. This rod-shaped motile bacterium used pyruvate, lactate, formate, hydrogen, butyrate, and ethanol as electron donor for sulfite reduction. Other

  17. Effect of xylose and nutrients concentration on ethanol production by a newly isolated extreme thermophilic bacterium.

    Science.gov (United States)

    Tomas, Ana F; Karakashev, Dimitar; Angelidaki, Irini

    2011-01-01

    An extreme thermophilic ethanol-producing strain was isolated from an ethanol high-yielding mixed culture, originally isolated from a hydrogen producing reactor operated at 70 degrees C. Ethanol yields were assessed with increasing concentrations of xylose, up to 20 g/l. The ability of the strain to grow without nutrient addition (yeast extract, peptone and vitamins) was also assessed. The maximum ethanol yield achieved was 1.28 mol ethanol/mol xylose consumed (77% of the theoretical yield), at 2 g/l of initial xylose concentration. The isolate was able to grow and produce ethanol as the main fermentation product under most of the conditions tested, including in media lacking vitamins, peptone and yeast extract. The results indicate that this new organism is a promising candidate for the development of a second generation bio-ethanol production process.

  18. Agromyces ulmi sp. nov., a xylanolytic bacterium isolated from Ulmus nigra in Spain.

    Science.gov (United States)

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

    2004-11-01

    Two xylan-degrading bacterial strains were isolated from a decayed Ulmus nigra tree in Spain. The isolates were Gram-positive, non-motile, aerobic and formed substrate mycelium which fragmented into irregular rods. 16S rRNA gene sequence analysis indicated that the isolates form a separate branch within the genus Agromyces phylogenetic cluster, with Agromyces mediolanus DSM 20152(T) being their closest relative (97.7 and 97.6 % sequence similarity). Catalase, nitrate reduction and urease tests differentiated these strains from A. mediolanus. Cell-wall peptidoglycan composition, major menaquinone, predominant fatty acids and phospholipid pattern were typical of the genus Agromyces. The DNA G+C content determined for the type strain XIL01(T) was 72 mol%. Based on the data presented, a novel species Agromyces ulmi sp. nov. is proposed. The type strain is XIL01(T) (=LMG 21954(T)=DSM 15747(T)).

  19. Morganella psychrotolerans sp. nov., a histamine-producing bacterium isolated from various seafoods

    DEFF Research Database (Denmark)

    Emborg, Jette; Dalgaard, Paw; Ahrens, Peter

    2006-01-01

    Morganella morganii subsp. morganii (strain LMG 7874T) and Morganella morganii subsp. sibonii (strain DSM 14850T), respectively. Analysis of the 16S rRNA gene sequences showed a similarity of 98.6 % between mesophilic and psychrotolerant isolates. However, fragments of seven protein-encoding housekeeping...... genes (atpD, dnaN, gyrB, hdc, infB, rpoB and tuf) all showed less than 90.9 % sequence similarity between the two groups. The psychrotolerant isolates grew at 0-2 {degrees}C and also differed from the mesophilic M. morganii isolates with respect to growth at 37 {degrees}C and in 8.5 % (w/v) Na......Cl and fermentation of D-galactose. The psychrotolerant strains appear to represent a novel species, for which the name Morganella psychrotolerans sp. nov. is proposed. The type strain is U2/3T (=LMG 23374T=DSM 17886T)....

  20. Effect of xylose and nutrients concentration on ethanol production by a newly isolated extreme thermophilic bacterium

    DEFF Research Database (Denmark)

    Tomás, Ana Faria; Karakashev, Dimitar Borisov; Angelidaki, Irini

    2011-01-01

    An extreme thermophilic ethanol-producing strain was isolated from an ethanol high-yielding mixed culture, originally isolated from a hydrogen producing reactor operated at 70 °C. Ethanol yields were assessed with increasing concentrations of xylose, up to 20 g/l. The ability of the strain to gro...... product under most of the conditions tested, including in media lacking vitamins, peptone and yeast extract. The results indicate that this new organism is a promising candidate for the development of a second generation bio-ethanol production process. © IWA Publishing 2011....

  1. Tindallia Californiensis sp. nov.: A New Halo-Alkaliphilic Primary Anaerobe, Isolated from Meromictic soda Mono Lake in California and the Correction of Diagnosis for Genus Tindallia

    Science.gov (United States)

    Pikuta, Elena; Marsic, Damien; Hoover, Richard B.; Kevbrin, Vadim; Whitman, William B.; Krader, Paul; Cleland, Dave; Six, N. Frank (Technical Monitor)

    2002-01-01

    A novel extremely halo-alkaliphilic, bacterium strain APO (sup T) was isolated from sediments of the athalassic, meromictic, soda Mono Lake in California. Gram positive, spore-forming, slightly curved rods with sizes 0.6-0.7x 2.5-4.0 micrometers which occur singly, in pairs or short curved chains. Cells, are motile by singular subcentral flagellum. Strain APO (sup T) is mesophilic: growth was observed over the temperature range of +10 C to +48 C (optimum +37 C), NaCl concentration range 1-20 %, wt/vol (optimum 3-5%, wt/vol) and pH range 8.0-11.0 (optimum pH 9.5). The novel isolate is strictly halo-alkaliphilic, requires sodium chloride in medium, obligately anaerobic and catalase-negative. Strain APO (sup T) is organo-heterotroph with fermentative type of metabolism, and uses as substrates: peptone, badotryptone, casamino acids, yeast extract, L-serine, L-lysine, L-histidine, L-arginine, and pyruvate. The main end products of growth on peptone medium were: lactate, acetate, propionate, and ethanol. Strain APO (sup T) is resistant to kanamycin, but sensitive to chloramphenicol, tetracycline, and gentamycin. The sum of G+C in DNA is 44.4 mol% (by HPLC method). On the bait of physiological and molecular properties, the isolate was considered as novel species of genus Tindallia; and the name Tindallia californiensis sp. nov., is proposed for new isolate (type strain APO (sup T) - ATCC BAA_393(sup T) = DSMZ 14871 (sup T)).

  2. An efficient thermotolerant and halophilic biosurfactant-producing bacterium isolated from Dagang oil field for MEOR application

    Science.gov (United States)

    Wu, Langping; Richnow, Hans; Yao, Jun; Jain, Anil

    2014-05-01

    Dagang Oil field (Petro China Company Limited) is one of the most productive oil fields in China. In this study, 34 biosurfactant-producing strains were isolated and cultured from petroleum reservoir of Dagang oil field, using haemolytic assay and the qualitative oil-displacement test. On the basis of 16S rDNA analysis, the isolates were closely related to the species in genus Pseudomonas, Staphylococcus and Bacillus. One of the isolates identified as Bacillus subtilis BS2 were selected for further study. This bacterium was able to produce a type of biosurfactant with excessive foam-forming properties at 37ºC as well as at higher temperature of 55ºC. The biosurfactant produced by the strain BS2 could reduce the surface tension of the culture broth from 70.87 mN/m to 28.97 mN/m after 8 days of incubation at 37ºC and to 36.15 mN/m after 20 days of incubation at 55ºC, respectively. The biosurfactant showed stability at high temperature (up to 120ºC), a wide range of pH (2 to 12) and salt concentrations (up to 12%) offering potential for biotechnology. Fourier transform infrared (FT-IR) spectrum of extracted biosurfactant tentatively characterized the produced biosurfactant as glycolipid derivative. Elemental analysis of the biosurfactant by energy dispersive X-ray spectroscopy (EDS) reveals that the biosurfactant was anionic in nature. 15 days of biodegradation of crude oil suggested a preferential usage of n-alkane upon microbial metabolism of BS2 as a carbon substrate and consequently also for the synthesis of biosurfactants. Core flood studies for oil release indicated 9.6% of additional oil recovery over water flooding at 37ºC and 7.2% of additional oil recovery at 55 ºC. Strain BS2 was characterized as an efficient biosurfactant-producing, thermotolerant and halophillic bacterium and has the potential for application for microbial enhanced oil recovery (MEOR) through water flooding in China's oil fields even in situ as adapted to reservoir chemistry and

  3. Methylohalobius crimeensis gen. nov., sp. nov., a moderately halophilic, methanotrophic bacterium isolated from hypersaline lakes of Crimea.

    Science.gov (United States)

    Heyer, Jürgen; Berger, Ursula; Hardt, Martin; Dunfield, Peter F

    2005-09-01

    A novel genus and species are proposed for two strains of methanotrophic bacteria isolated from hypersaline lakes in the Crimean Peninsula of Ukraine. Strains 10Ki(T) and 4Kr are moderate halophiles that grow optimally at 1-1.5 M (5.8-8.7%, w/v) NaCl and tolerate NaCl concentrations from 0.2 M up to 2.5 M (1.2-15%). This optimum and upper limit are the highest for any methanotrophic bacterium known to date. The strains are Gram-negative, aerobic, non-pigmented, motile, coccoid to spindle-shaped bacteria that grow on methane or methanol only and utilize the ribulose monophosphate pathway for carbon assimilation. They are neutrophilic (growth occurs only in the range pH 6.5-7.5) and mesophilic (optimum growth occurs at 30 degrees C). On the basis of 16S rRNA gene sequence phylogeny, strains 10Ki(T) and 4Kr represent a type I methanotroph within the 'Gammaproteobacteria'. However, the 16S rRNA gene sequence displays <91.5 % identity to any public-domain sequence. The most closely related methanotrophic bacterium is the thermophilic strain HB. The DNA G+C content is 58.7 mol%. The major phospholipid fatty acids are 18:1omega7 (52-61%), 16:0 (22-23%) and 16:1omega7 (14-20%). The dominance of 18:1 over 16:0 and 16:1 fatty acids is unique among known type I methanotrophs. The data suggest that strains 10Ki(T) and 4Kr should be considered as belonging to a novel genus and species of type I methanotrophic bacteria, for which the name Methylohalobius crimeensis gen. nov., sp. nov. is proposed. Strain 10Ki(T) (=DSM 16011(T)=ATCC BAA-967(T)) is the type strain.

  4. Psychromonas boydii sp. nov., a gas-vacuolate, psychrophilic bacterium isolated from an Arctic sea-ice core.

    Science.gov (United States)

    Auman, Ann J; Breezee, Jennifer L; Gosink, John J; Schumann, Peter; Barnes, Carmen R; Kämpfer, Peter; Staley, James T

    2010-01-01

    A gas-vacuolate bacterium, strain 174(T), was isolated from a sea-ice core collected from Point Barrow, Alaska, USA. Comparative analysis of 16S rRNA gene sequences showed that this bacterium was most closely related to Psychromonas ingrahamii 37(T), with a similarity of >99 %. However, strain 174(T) could be clearly distinguished from closely related species by DNA-DNA hybridization; relatedness values determined by two different methods between strain 174(T) and P. ingrahamii 37(T) were 58.4 and 55.7 % and those between strain 174(T) and Psychromonas antarctica DSM 10704(T) were 46.1 and 33.1 %, which are well below the 70 % level used to define a distinct species. Phenotypic analysis, including cell size (strain 174(T) is the largest member of the genus Psychromonas, with rod-shaped cells, 8-18 microm long), further differentiated strain 174(T) from other members of the genus Psychromonas. Strain 174(T) could be distinguished from its closest relative, P. ingrahamii, by its utilization of D-mannose and D-xylose as sole carbon sources, its ability to ferment myo-inositol and its inability to use fumarate and glycerol as sole carbon sources. In addition, strain 174(T) contained gas vacuoles of two distinct morphologies and grew at temperatures ranging from below 0 to 10 degrees C and its optimal NaCl concentration for growth was 3.5 %. The DNA G+C content was 40 mol%. Whole-cell fatty acid analysis showed that 16 : 1omega7c and 16 : 0 comprised 44.9 and 26.4 % of the total fatty acid content, respectively. The name Psychromonas boydii sp. nov. is proposed for this novel species, with strain 174(T) (=DSM 17665(T) =CCM 7498(T)) as the type strain.

  5. Salinicola tamaricis sp. nov., a heavy-metal-tolerant, endophytic bacterium isolated from the halophyte Tamarix chinensis Lour.

    Science.gov (United States)

    Zhao, Guo-Yan; Zhao, Li-Ya; Xia, Zhi-Jie; Zhu, Jin-Lei; Liu, Di; Liu, Chun-Yue; Chen, Xiu-Lan; Zhang, Yu-Zhong; Zhang, Xi-Ying; Dai, Mei-Xue

    2017-06-01

    A Gram-stain-negative, rod-shaped bacterium, strain F01T, was isolated from leaves of Tamarix chinensis Lour. The isolate grew optimally at 30 °C, at pH 7.0 and with 5.0 % (w/v) NaCl, and showed a high tolerance to manganese, lead, nickel, ferrous ions and copper ions. The major fatty acids were C18 : 1ω7c and C16 : 0, and the predominant respiratory quinone was Q-9. Polar lipids were dominated by diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, unidentified aminoglycolipids and phospholipids. The DNA G+C content was 65.8 %. Based on multilocus phylogenetic analysis, strain F01T belonged to the genus Salinicola, with highest 16S rRNA gene sequence similarity to Salinicola peritrichatus CGMCC 1.12381T (97.7 %). The level of DNA-DNA hybridization between strain F01T and closely related Salinicola strains was well below 70 %. According to the phenotypic, genetic and chemotaxonomic data, strain F01T is considered to represent a novel species in the genus Salinicola, for which the name Salinicola tamaricis sp. nov. is proposed. The type strain is F01T (=CCTCC AB 2015304T=KCTC 42855T).

  6. Isolation and polyphasic characterization of a novel hyper catalase producing thermophilic bacterium for the degradation of hydrogen peroxide.

    Science.gov (United States)

    Sooch, Balwinder Singh; Kauldhar, Baljinder Singh; Puri, Munish

    2016-11-01

    A newly isolated microbial strain of thermophilic genus Geobacillus has been described with emphasis on polyphasic characterization and its application for degradation of hydrogen peroxide. The validation of this thermophilic strain of genus Geobacillus designated as BSS-7 has been demonstrated by polyphasic taxonomy approaches through its morphological, biochemical, fatty acid methyl ester profile and 16S rDNA sequencing. This thermophilic species of Geobacillus exhibited growth at broad pH and temperature ranges coupled with production of extraordinarily high quantities of intracellular catalase, the latter of which as yet not been reported in any member of this genus. The isolated thermophilic bacterial culture BSS-7 exhibited resistance against a variety of organic solvents. The immobilized whole cells of the bacterium successfully demonstrated the degradation of hydrogen peroxide (H2O2) in a packed bed reactor. This strain has potential application in various analytical and diagnostic methods in the form of biosensors and biomarkers in addition to applications in the textile, paper, food and pharmaceutical industries.

  7. Biosynthesis and characterization of polyhydroxyalkanoates produced by an extreme halophilic bacterium, Halomonas nitroreducens, isolated from hypersaline ponds.

    Science.gov (United States)

    Cervantes-Uc, J M; Catzin, J; Vargas, I; Herrera-Kao, W; Moguel, F; Ramirez, E; Rincón-Arriaga, S; Lizama-Uc, G

    2014-10-01

    Morphological, biochemical and genotypic characterization of a halophilic bacterium isolated from hypersaline ponds located at Las Coloradas (Río Lagartos, Yucatán, Mexico). Characterization of polymer produced by this strain was also performed. Twenty strains were isolated from water samples of salt ponds and selected based on both morphological features and their PHA storage capacity, which were determined by SEM and staining methods with Nile red and Nile blue, respectively; strains were also analysed by the fluorescence imaging technique. Among them, JCCOL25.8 strain showed the highest production of PHA's reason why phenotypic and genotypic characterization was performed; this strain was identified as Halomonas nitroreducens. Polymer produced by this strain was characterized by FTIR, DSC, GPC and EDX spectroscopy. Results indicated that the biosynthesized polymer was polyhydroxybutyrate (PHB) which had a melting peak at 170°C and a crystallinity percentage of about 36%. Based on phenotypic and genotypic aspects, JCCOL25.8 strain was identified as H. nitroreducens and it was capable to accumulate PHB. To our knowledge, there is only one study published on the biosynthesis of PHA's by H. nitroreducens strains, although the characterization of the obtained polymer was not reported. © 2014 The Society for Applied Microbiology.

  8. Selective inhibition of toxic cyanobacteria by β-carboline-containing bacterium Bacillus flexus isolated from Saudi freshwaters.

    Science.gov (United States)

    Alamri, Saad A; Mohamed, Zakaria A

    2013-10-01

    A bacterial strain SSZ01 isolated from a eutrophic lake in Saudi Arabia dominated by cyanobacterial blooms, showed an antialgal activity against cyanobacteria species. Based on the analysis of the 16S rDNA gene sequence, the isolated strain (SSZ01) most likely belonged to the genus Bacillus with a 99% similarity to Bacillus flexus strain EMGA5. The thin layer chromatography (TLC) analysis of the ethyl acetate extract of this bacterium revealed that this strain can produce harmine and norharmane compared to different β-carboline analog standards. Harmine and norharmane were also detected in considerable amounts in bacterial growth medium, indicating a potential excretion of these compounds into the aquatic environment. The crude extract of Bacillus flexus as well as pure materials of harmine and norharmane inhibited the growth of tested species of cyanobacteria. However, the bacterial crude extract has a higher toxicity against tested species of cyanobacteria than harmine and norharmane. In addition, harmine was more toxic to cyanobacteria than norharmane. On the other hand, neither pure compounds of harmine and norharmane nor crude bacterial extract showed any antialgal activity against tested species of green algae. The results of the present study suggest that B. flexus SSZ01 or its crude extract containing harmine and norharmane could be a candidate for the selective control of cyanobacterial blooms without affecting other algal species.

  9. Efficient isolation of total RNA from antibiotic-producing bacterium Amycolatopsis mediterranei.

    Science.gov (United States)

    Yao, Yufeng; Zhang, Weiwen; Jiao, Ruishen; Zhao, Guoping; Jiang, Weihong

    2002-10-01

    RNA extraction from antibiotic-producing actinomycetes can be a difficult and time-consuming process due to their special peptidoglycans cell wall composition and the short life of RNA. Hence, the rapidity of cellular lysis and complete inhibition of RNase are of particular importance for isolating intact RNA of high quality. The genus of Amycolatopsis mediterranei produces many clinically important antibiotics, such as rifamycin and vancomycin; however, the available methods for bacterial RNA isolation did not work very well with this genus. In this report, we described a new method for RNA isolation using the combination of LiCl, urea and guanidinium thiocyanate to disrupt the cell wall of Amycolatopsis. Compared with earlier published RNA isolation methods, the method gave higher yields of pure and intact RNA. About 1 microg total RNA free of DNA contamination can be obtained from 1 mg wet weight of A. mediterranei. The integrity of the RNA was demonstrated by formaldehyde agarose gel electrophoresis and Northern blot analyses.

  10. 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.

  11. 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.

    . Nogi, Y., Soda, K. & Oikawa, T. (2005). Flavobacterium frigidimaris sp. nov., isolated from Antarctic seawater. Syst Appl Microbiol 28, 310-315. Ryu, S. H., Park, J. H., Moon, J. C., Sung, Y., Lee, S. S. & Jeon, C. O. (2008). Flavobacterium...

  12. 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.

  13. Isolation and Characterization of a New KOR-1 from an Anaerobic Digester Using Pig Slurry

    Directory of Open Access Journals (Sweden)

    Urantulkhuur Battumur

    2016-04-01

    Full Text Available A new methanogen was isolated from an anaerobic digester using pig slurry in South Korea. Only one strain, designated KOR-1, was characterized in detail. Cells of KOR-1 were straight or crooked rods, non-motile, 5 to 15 μm long and 0.7 μm wide. They stained Gram-positive and produced methane from H2+CO2 and formate. Strain KOR-1 grew optimally at 38°C. The optimum pH for growth was 7.0. The strain grew at 0.5% to 3.0% NaCl, with optimum growth at 2.5% NaCl. The G+C content of genomic DNA of strain KOR-1 was 41 mol%. The strain tolerated ampicillin, penicillin G, kanamycin and streptomycin but tetracycline inhibited cell growth. A large fragment of the 16S rRNA gene (~1,350 bp was obtained from the isolate and sequenced. Comparison of 16S rRNA genes revealed that strain KOR–1 is related to Methanobacterium formicicum (98%, sequence similarity, Methanobacterium bryantii (95% and Methanobacterium ivanovii (93%. Phylogenetic analysis of the deduced mcrA gene sequences confirmed the closest relative as based on mcrA gene sequence analysis was Methanobacterium formicicum strain (97% nucleic acid sequence identity. On the basis of physiological and phylogenetic characteristics, strain KOR-1 is proposed as a new strain within the genus Methanobacterium, Methanobacterium formicicum KOR-1.

  14. A heavy metal tolerant novel bacterium, Bacillus malikii sp. nov., isolated from tannery effluent wastewater.

    Science.gov (United States)

    Abbas, Saira; Ahmed, Iftikhar; Kudo, Takuji; Iqbal, Muhammad; Lee, Yong-Jae; Fujiwara, Toru; Ohkuma, Moriya

    2015-12-01

    The taxonomic position of a Gram-stain positive and heavy metal tolerant bacterium, designated strain NCCP-662(T), was investigated by polyphasic characterisation. Cells of strain NCCP-662(T) were observed to be rod to filamentous shaped, motile and strictly aerobic, and to grow at 10-50 °C (optimum 30-37 °C) and at pH range of 6-10 (optimum pH 7-8). The strain was found to be able to tolerate 0-12 % NaCl (w/v) and heavy metals (Cr 1200 ppm, Pb 1800 ppm and Cu 1200 ppm) in tryptic soya agar medium. The phylogenetic analysis based on the 16S rRNA gene sequence of strain NCCP-662(T) showed that it belongs to the genus Bacillus and showed high sequence similarity (98.2 and 98.0 %, respectively) with the type strains of Bacillus niabensis 4T19(T) and Bacillus halosaccharovorans E33(T). The chemotaxonomic data showed that the major quinone is MK-7; the predominant cellular fatty acids are anteiso-C15 :0, iso-C14:0, iso-C16:0 and C16:0 and iso-C15:0; the major polar lipids are diphosphatidylglycerol, phosphatidylglycerol along with several unidentified glycolipids, phospholipids and polar lipids. The DNA G+C content was determined to be 36.9 mol%. These data also support the affiliation of strain NCCP-662(T) with the genus Bacillus. The level of DNA-DNA relatedness between strain NCCP-662(T) and B. niabensis JCM 16399(T) was 20.5 ± 0.5 %. On the basis of physiological and biochemical characteristics, phylogenetic analyses and DNA-DNA hybridization data, strain NCCP-662(T) can be clearly differentiated from the validly named Bacillus species and thus represents a new species, for which the name Bacillus malikii sp. nov. is proposed with the type strain NCCP-662(T) (= LMG 28369(T) = DSM 29005(T) = JCM 30192(T)).

  15. Biochemical identification and determination of antimicrobial resistance in clinical isolates of anaerobic bacteria obtained from the Hospital San Juan de Dios in the period 2009 to 2011

    International Nuclear Information System (INIS)

    Meza Pena, Maria Daniela

    2014-01-01

    Clinical isolates of 81 anaerobic bacteria isolated are identified to patients of the Hospital San Juan de Dios, between 2009 to 2011; by algorithms that have employed biochemical methods of reference chemical samples. Antimicrobial resistance is determined. The miniaturized methods and biochemical algorithms proposed were compared to identify differences between methods. The minimum inhibitory concentration of metronidazole, clindamycin, amoxicillin, tetracycline and cefotaxime are determined to 81 anaerobic bacteria isolated from the Hospital mentioned [es

  16. Genome Sequence ofVerrucomicrobiumsp. Strain GAS474, a Novel Bacterium Isolated from Soil.

    Science.gov (United States)

    Pold, Grace; Conlon, Erin M; Huntemann, Marcel; Pillay, Manoj; Mikhailova, Natalia; Stamatis, Dimitrios; Reddy, T B K; Daum, Chris; Shapiro, Nicole; Kyrpides, Nikos; Woyke, Tanja; DeAngelis, Kristen M

    2018-01-25

    Verrucomicrobium sp. strain GAS474 was isolated from the mineral soil of a temperate deciduous forest in central Massachusetts. Here, we present the complete genome sequence of this phylogenetically novel organism, which consists of a total of 3,763,444 bp on a single scaffold, with a 65.8% GC content and 3,273 predicted open reading frames. Copyright © 2018 Pold et al.

  17. Development of a PCR assay based on the 16S-23S rDNA internal transcribed spacer for identification of strictly anaerobic bacterium Zymophilus

    Czech Academy of Sciences Publication Activity Database

    Felsberg, Jürgen; Jelínková, Markéta; Kubizniaková, P.; Matoulková, D.

    2015-01-01

    Roč. 33, June (2015), s. 85-89 ISSN 1075-9964 Institutional support: RVO:61388971 Keywords : Brewing microbiology * Strictly anaerobic bacteria * Yeast contamination Subject RIV: GM - Food Processing Impact factor: 2.424, year: 2015

  18. Study of Growth Process and Phenol Biodegradation by a Bacterium Isolated from Wastewater (in vitro

    Directory of Open Access Journals (Sweden)

    Somayye Eskandary

    2011-07-01

    Full Text Available Phenol is a carbonic compound that is dangerous for humans at a concentration of 0.5 ppm in the environment. The best phenol removal from coal tar wastewaters is achieved by bioremediation. In this study, we isolated indigenous bacteria from phenolic wastewater and adapted it to a high concentration of phenol for its removal from wastewater. We also investigated the growth and removal curves of the bacteria in media with 2000 and 4000 ppm of phenol. It was observed that after lag phases of 24 and 48 hours, they grew and removed all of the phenol concentration over 264 and 312 hours. It was also found that this isolate was able to remove 2233 ppm of phenol in natural wastewater over a period of 120 hours. Identification tests showed that it is a gram-negative bactetium possibly belonging to the pseudomonas species. Phenol concentrations in wastewater can be reduced over a shorter period of time by using either this isolate alone or a group of them.

  19. Isolation of probiotics bacterium from coral reef for controlling vibriosis in tiger shrimp (Penaeus monodon larvae

    Directory of Open Access Journals (Sweden)

    Ade Dwi Sasanti

    2013-03-01

    Full Text Available Pathogenic Vibrio, especially luminous Vibrio harveyi, could cause mass mortality in tiger shrimp culture. One of the technique to work against luminous Vibrio is, using probiotic bacteria to inhibit the luminous Vibrio growth. This study was carried out to obtain bacteria isolates from coral reef which potentially inhibit V. harveyi growth. A total of 110 isolates were isolated from Acropora sp, Merulina sp, Hystrix sp., Poecillophora sp, Porites sp and Haliophora sp., and have probiotic activity against V. harveyi in in vitro and in vivo test.Of the total 110 isolates, 54 isolates show the inhibiting zone. Two isolates(8A and 1Cwere not pathogenic and have the most effective activity in inhibiting growth of V. harveyi and significantly reduced larval mortality in in vitro and in vivo test. Treatment using probiotics candidate have significant different survival rate (83.33% compared with positive control (61.67%. The growth rate of lenght of larvae treatment with isolate of 8A (5.25% and 1C (5.06% show the significant different compared with positive control (3.54%. The growth rate of weight of larvae treatment withisolate of 8A (17.51% and 1C (17.61% show significant different compared with negative (15.27% and positive control (14.69%.Key word: coral reef, probiotic, tiger shrimp, vibriosis, V. harveyi. ABSTRAKVibrio patogen, khususnya Vibrio harveyi berpendar, dapat menyebabkan kematian massal pada budidaya udang windu. Salah satu alternatif untuk menghambat Vibrio harveyi berpendar adalah dengan menggunakan bakteri probiotik yang dapat menekan pertumbuhan Vibrio tersebut. Penelitian ini bertujuan untuk mendapatkan isolat bakteri dari terumbu karang yang potensial menghambat pertumbuhan V. harveyi. Total 110 isolat diisolasi dari Acropora sp, Merulina sp., Hystrix sp., Poecillophora sp., Porites sp. dan Haliophora sp, dilakukan penapisan untuk melihat aktivitas kemampuannya melawan V. harveyi MR 5339 RfR dalam uji in vitro dan uji in vivo

  20. Azospirillum canadense sp. nov., a nitrogen-fixing bacterium isolated from corn rhizosphere.

    Science.gov (United States)

    Mehnaz, Samina; Weselowski, Brian; Lazarovits, George

    2007-03-01

    A free-living diazotrophic strain, DS2(T), was isolated from corn rhizosphere. Polyphasic taxonomy was performed including morphological characterization, Biolog analysis, and 16S rRNA, cpn60 and nifH gene sequence analyses. 16S rRNA gene sequence analysis indicated that strain DS2(T) was closely related to the genus Azospirillum (96 % similarity). Chemotaxonomic characteristics (DNA G+C content 67.9 mol%; Q-10 quinone system; major fatty acid 18 : 1omega7c) were also similar to those of the genus Azospirillum. In all the analyses, including phenotypic characterization using Biolog analysis and comparison of cellular fatty acids, this isolate was found to be different from the closely related species Azospirillum lipoferum, Azospirillum oryzae and Azospirillum brasilense. On the basis of these results, a novel species is proposed for this nitrogen-fixing strain. The name Azospirillum canadense sp. nov. is suggested with the type strain DS2(T) (=NCCB 100108(T)=LMG 23617(T)).

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

    Science.gov (United States)

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

    2016-04-01

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

  2. Isolation and identification of chemical constituents from the bacterium Bacillus sp. and their nematicidal activities.

    Science.gov (United States)

    Zeng, Liming; Jin, Hui; Lu, Dengxue; Yang, Xiaoyan; Pan, Le; Cui, Haiyan; He, Xiaofeng; Qiu, Hongdeng; Qin, Bo

    2015-10-01

    A strain SMrs28 was isolated from the rhizosphere soil of a toxic plant Stellera chamaejasme and identified as Bacillus sp. on the basis of morphological and partial 16S rRNA gene sequence analysis. The crude extract of SMrs28 fermentation broth showed strong nematocidal activities in preliminary test. To define the active nematocidal metabolites of SMrs28, a novel compound (1), 4-oxabicyclo[3.2.2]nona-1(7), 5,8-triene, along with five known compounds (2-6), were isolated from the strain by various column chromatographic techniques and characterized on the basis of spectroscopic analysis. Results of the in vitro nematicidal tests showed that the metabolites presented different levels of activity at certain exposure conditions. Compounds (1-3) displayed LC50 values of 904.12, 451.26, 232.98 µg/ml and 1594.0, 366.62, 206.38 µg/ml against Bursaphelenchus xylophilus and Ditylenchus destructor at 72 h, respectively. This is the first report of the nematicidal activity of the compounds as constituents of Bacillus sp.. Our findings help to find potential chemical structures to develop nematicides from microbial source for the management of nematode-infected plant diseases. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Complete genome sequence of a commensal bacterium, Hafnia alvei CBA7124, isolated from human feces.

    Science.gov (United States)

    Song, Hye Seon; Kim, Joon Yong; Kim, Yeon Bee; Jeong, Myeong Seon; Kang, Jisu; Rhee, Jin-Kyu; Kwon, Joseph; Kim, Ju Suk; Choi, Jong-Soon; Choi, Hak-Jong; Nam, Young-Do; Roh, Seong Woon

    2017-01-01

    Members of the genus Hafnia have been isolated from the feces of mammals, birds, reptiles, and fish, as well as from soil, water, sewage, and foods. Hafnia alvei is an opportunistic pathogen that has been implicated in intestinal and extraintestinal infections in humans. However, its pathogenicity is still unclear. In this study, we isolated H. alvei from human feces and performed sequencing as well as comparative genomic analysis to better understand its pathogenicity. The genome of H. alvei CBA7124 comprised a single circular chromosome with 4,585,298 bp and a GC content of 48.8%. The genome contained 25 rRNA genes (9 5S rRNA genes, 8 16S rRNA genes, and 8 23S rRNA genes), 88 tRNA genes, and 4043 protein-coding genes. Using comparative genomic analysis, the genome of this strain was found to have 72 strain-specific singletons. The genome also contained genes for antibiotic and antimicrobial resistance, as well as toxin-antitoxin systems. We revealed the complete genome sequence of the opportunistic gut pathogen, H. alvei CBA7124. We also performed comparative genomic analysis of the sequences in the genome of H. alvei CBA7124, and found that it contained strain-specific singletons, antibiotic resistance genes, and toxin-antitoxin systems. These results could improve our understanding of the pathogenicity and the mechanism behind the antibiotic resistance of H. alvei strains.

  4. Lactobacillus musae sp. nov., a novel lactic acid bacterium isolated from banana fruits.

    Science.gov (United States)

    Chen, Yi-Sheng; Wang, Li-Ting; Liao, Yu-Jou; Lan, Yi-Shan; Chang, Chi-Huan; Chang, Yu-Chung; Wu, Hui-Chung; Lo, Huei-Yin; Otoguro, Misa; Yanagida, Fujitoshi

    2017-12-01

    Two Gram-stain-positive, catalase-negative, rod-shaped, bacterial strains (313 T and 311) were isolated from banana fruits in Taiwan. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the highest similarity to both strains corresponded to the type strain of Lactobacillus nantensis (99.19 %), followed by Lactobacillus crustorum (98.99 %), Lactobacillus heilongjiangensis (98.59 %) and Lactobacillus farciminis (98.52 %). Phylogenetic analysis based on the sequences of two housekeeping genes, pheS and rpoA, revealed that these two strains were well separated from the Lactobacillus reference strains. DNA-DNA relatedness values revealed genotype separation of the two strains from the above four species. The DNA G+C content of strain 313 T was 35.5 mol%. The strains were homofermentative and mainly produced l-lactic acid from glucose. The major cellular fatty acids of strain 313 T were 18 : 1ω6c and/or 18 : 1ω7c, 16 : 0, and 19 : 1ω6c and/or 19 : 0 cyclo ω10c. Based on their physiological and genotypic characteristics, the isolates represent a novel species of the genus Lactobacillus, for which the name Lactobacillusmusae sp. nov. is proposed. The type strain is 313 T =NBRC 112868 T =BCRC 81020 T ).

  5. Description of Alicyclobacillus montanus sp. nov., a mixotrophic bacterium isolated from acidic hot springs.

    Science.gov (United States)

    López, G; Díaz-Cárdenas, C; David Alzate, J; Gonzalez, L N; Shapiro, N; Woyke, T; Kyrpides, N C; Restrepo, S; Baena, S

    2018-03-20

    Three morphologically similar thermo-acidophilic strains, USBA-GBX-501, USBA-GBX-502 and USBA-GBX-503 T , were isolated from acidic thermal springs at the National Natural Park Los Nevados (Colombia). All isolates were spore-forming, Gram-stain-positive and motile, growing aerobically at 25-55 °C (optimum ~45 °C) and at pH 1.5-4.5 (optimum pH ~3.0). Phylogenetic analysis of the 16S rRNA gene sequences of these isolates showed an almost identical sequence (99.0 % similarity) and they formed a robust cluster with the closest relative Alicyclobacillus tolerans DSM 16297 T with a sequence similarity of 99.0 %. Average similarity to other species of the genus Alicyclobacillus was 93.0 % and average similarity to species of the genus Effusibacillus was 90 %. In addition, the level of DNA-DNA hybridization between strain USBA-GBX-503 T and Alicyclobacillus tolerans DSM 16297 T was 31.7 %. The genomic DNA G+C content of strain USBA-GBX-503 T was 44.6 mol%. The only menaquinone was MK-7 (100.0 %). No ω-alicyclic fatty acids were detected in strain USBA-GBX-503 T , and the major cellular fatty acids were C18 : 1ω7c, anteiso-C17 : 0 and iso-C17 : 0. Based on phenotypic and chemotaxonomic characteristics, phylogenetic analysis and DNA-DNA relatedness values, along with low levels of identity at the whole genome level (ANIb and ANIm values of <67.0 and <91.0 %, respectively), it can be concluded that strain USBA-GBX-503 T represents a novel species of the genus Alicyclobacillus, for which the name Alicyclobacillus montanus sp. nov. is proposed. The type strain is USBA-GBX-503 T (=CMPUJ UGB U503 T =CBMAI1927 T ).

  6. Pseudomonas yamanorum sp. nov., a psychrotolerant bacterium isolated from a subantarctic environment.

    Science.gov (United States)

    Arnau, Víctor Gonzalo; Sánchez, Leandro Arturo; Delgado, Osvaldo Daniel

    2015-02-01

    A psychrotolerant strain, 8H1(T), was isolated from soil samples collected in Isla de los Estados, Ushuaia, Argentina. Cells were Gram-negative, aerobic, straight rods, occurring singly or in pairs, non-spore-forming and motile by means of two polar flagella. The isolate was able to grow in the range 4-35 °C, with optimum growth at 28 °C. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The polar lipid pattern of strain 8H1(T) comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unknown phospholipid. Ubiquinone 9 (Q-9) was the predominant lipoquinone. The DNA G+C content was 59.8 mol%. 16S rRNA gene sequence-based phylogeny suggested the affiliation of strain 8H1(T) to the 'Pseudomonas fluorescens group', displaying ≥98.5 % sequence similarity to 29 type strains. A multilocus sequence analysis (MLSA) study performed by concatenating 16S rRNA, gyrB, rpoD and rpoB gene sequences showed that isolate 8H1(T) could be discriminated from closely related species of the genus Pseudomonas and placed in the 'Pseudomonas gessardii subgroup', including the species with the highest MLSA sequence similarities: Pseudomonas brenneri (96.2 %), P. gessardii (96.1 %), P. proteolytica (96.0 %), P. meridiana (96.0 %) and P. mucidolens (95.4 %). DNA-DNA hybridization analysis between 8H1(T) and the type strains of these closely related species revealed relatedness values of 27.0, 8.8, 41.2, 39.7 and 46.1 %, respectively. These results, together with differences in several phenotypic features, support the classification of a novel species, for which the name Pseudomonas yamanorum sp. nov. is proposed. The type strain is 8H1(T) ( = DSM 26522(T) = CCUG 63249(T) = LMG 27247(T)). © 2015 IUMS.

  7. Biosurfactant-producing bacterium, Pseudomonas aeruginosa MA01 isolated from spoiled apples: physicochemical and structural characteristics of isolated biosurfactant.

    Science.gov (United States)

    Abbasi, Habib; Hamedi, Mir Manochehr; Lotfabad, Tayebe Bagheri; Zahiri, Hossein Shahbani; Sharafi, Hakimeh; Masoomi, Fatemeh; Moosavi-Movahedi, Ali Akbar; Ortiz, Antonio; Amanlou, Massoud; Noghabi, Kambiz Akbari

    2012-02-01

    An extensive investigation was conducted to isolate indigenous bacterial strains with outstanding performance for biosurfactant production from different types of spoiled fruits, food-related products and food processing industries. An isolate was selected from 800 by the highest biosurfactant yield in soybean oil medium and it was identified by 16S rRNA and the two most relevant hypervariable regions of this gene; V3 and V6 as Pseudomonas aeruginosa MA01. The isolate was able to produce 12 g/l of a glycolipid-type biosurfactant and generally less efficient to emulsify vegetable oils compared to hydrocarbons and could emulsify corn and coconut oils more than 50%. However, emulsification index (E(24)) of different hydrocarbons including hexane, toluene, xylene, brake oil, kerosene and hexadecane was between 55.8% and 100%. The surface tension of pure water decreased gradually with increasing biosurfactant concentration to 32.5 mNm(-1) with critical micelle concentration (CMC) value of 10.1mg/l. Among all carbon substrates examined, vegetable oils were the most effective on biosurfactant production. Two glycolipid fractions were purified from the biosurfactant crude extracts, and FTIR and ES-MS were used to determine the structure of these compounds. The analysis indicated the presence of three major monorhamnolipid species: R(1)C(10)C(10), R(1)C(10)C(12:1), and R(1)C(10)C(12); as well as another three major dirhamnolipid species: R(2)C(10)C(10), R(2)C(10)C(12:1), and R(2)C(10)C(12). The strain sweep experiment for measuring the linear viscoelastic of biosurfactant showed that typical behavior characteristics of a weak viscoelastic gel, with storage modulus greater than loss modulus at all frequencies examined, both showing some frequency dependence. Copyright © 2011 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  8. Bacillus catenulatus sp. nov., an alkalitolerant bacterium isolated from a soda lake.

    Science.gov (United States)

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

    2017-12-01

    Two novel (18C T and 6C) Gram-stain-positive, rod shaped, motile and endospore-forming bacterial strains were isolated from Lonar soda lake, India. Based on 16S rRNA gene sequence analysis, strains 18C T and 6C were identified as belonging to the class Firmibacteria, and were most closely related to Bacillus cohnii KCTC 3572 T (99.3 and 99.9%, respectively), Bacillus zhanjiangensis KCTC 13713 T (97.4 and 98.0%, respectively), Bacillus halmapalus LMG 17950 T (97.0 and 97.6%, respectively) and other members in the genus Bacillus (Bacillus, for which the name Bacillus catenulatus sp. nov. is proposed. The type strain is 18C T (=KCTC 33781 T  = CGMCC 1.15475 T ).

  9. Bacillus alcaliphilum sp. nov., a bacterium isolated from a soda lake.

    Science.gov (United States)

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

    2017-11-01

    Two novel (14B T and 7B) Gram-stain-positive, rod-shaped, motile and endospore-forming bacterial strains were isolated from Lonar soda lake, India. Based on 16S rRNA gene sequence analysis, the strains 14B T and 7B were identified as belonging to the class Firmibacteria and were most closely related to Bacillus halodurans LMG 7121 T (99.7 and 99.8%, respectively), Bacillus okuhidensis LMG 22468 T (99.1 and 99.2%, respectively) and other members in the genus Bacillus (Bacillus, for which the name Bacillus alcaliphilum sp. nov. is proposed. The type strain is 14B T (=KCTC 33777 T  = CGMCC 1.15474 T ).

  10. 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)).

  11. Ferrovibrio soli sp. nov., a novel cellulolytic bacterium isolated from stream bank soil.

    Science.gov (United States)

    Dahal, Ram Hari; Kim, Jaisoo

    2018-01-01

    Two isolates of bacterial strains A15 T and A17 were isolated from stream bank soil in Kyonggi University. Cells were aerobic, Gram-stain-negative, oxidase- and catalase-positive, motile, non-spore-forming, rod-shaped, opaque, and cream coloured. Both strains hydrolysed CM-cellulose. Strains were able to grow at 20-42 °C, pH 5.5-10.0 and at 1.5 % NaCl concentration (w/v). Indole test was positive. Analyses of phylogenetic trees based on its 16S rRNA gene sequences indicated that strain A15 T formed a lineage within the family Rhodospirillaceae of the phylum Proteobacteria which was distinct from Ferrovibrio denitrificans S3 T (98.4 % sequence similarity) and Ferrovibrio xuzhouensis LM-6 T (97.4 %). The sole detected respiratory quinone was Q-10. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminolipid. The major cellular fatty acids were C19 : 0 cycloω8c, C16 : 0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C18 : 0cyclo and C12 : 0. The DNA G+C contents of strains A15 T and A17 were 63.4 and 62.9 mol%, respectively. DNA-DNA relatedness between strain A15 T and other two members of the genus Ferrovibrioranged from 25 to 37 %. The polyphasic characterization revealed strains A15 T and A17 represent a novel species in the genus Ferrovibrio, for which the name Ferrovibriosoli sp. nov. is proposed. The type strain is A15 T (=KEMB 9005-522 T =KACC 19102 T =NBRC 112682 T ).

  12. Isolation and characterization of a novel gamma-hexachlorocyclohexane-degrading bacterium.

    Science.gov (United States)

    Thomas, J C; Berger, F; Jacquier, M; Bernillon, D; Baud-Grasset, F; Truffaut, N; Normand, P; Vogel, T M; Simonet, P

    1996-10-01

    The natural biotic capacity of soils to degrade gamma-hexachlorocyclohexane (gamma-HCH, lindane) was estimated using an enrichment technique based on the ability of soil bacteria to develop on synthetic media and degrade the xenobiotic compound, used as the sole source of carbon and energy. Bacterial inocula from relatively highly contaminated soils (from wood treatment factories) were found to promote efficiently the degradation of gamma-HCH, which subsequently permitted isolation of a competent gamma-HCH-degrading microorganism. The decrease of gamma-HCH concurrently with the release of chloride ions and the production of CO2 demonstrated the complete mineralization of gamma-HCH mediated by the isolate. This was confirmed by gas chromatography-mass spectrometry analyses showing that degradation subproducts of gamma-HCH included an unidentified tetrachlorinated compound and subsequently 1,2,4-trichlorobenzene and 2,5-dichlorophenol. The two linA- and linB-like genes coding, respectively, for a gamma-HCH dehydrochlorinase and a dehalogenase were characterized by using a PCR strategy based on sequence homologies with previously published sequences from Sphingomonas paucimobilis UT26. Nucleotide sequence analysis of the linA-like region revealed the presence of a 472-bp open reading frame exhibiting high homology with the linA gene from S. paucimobilis, while a preliminary study also indicated strong homology among the two linB genes. All enzymes involved in the gamma-HCH degradative pathway appear to be extracellular and encoded by genes located on the chromosome, although numerous cryptic plasmids have been detected.

  13. 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).

  14. Bacillus isabeliae sp. nov., a halophilic bacterium isolated from a sea salt evaporation pond.

    Science.gov (United States)

    Albuquerque, Luciana; Tiago, Igor; Taborda, Marco; Nobre, M Fernanda; Veríssimo, António; da Costa, Milton S

    2008-01-01

    A low-G+C, Gram-positive isolate, designated strain CVS-8(T), was isolated from a sea salt evaporation pond on the Island of Sal in the Cape Verde Archipelago. This organism was found to be a catalase- and oxidase-positive, non-motile, spore-forming, aerobic, curved rod-shaped organism with an optimum growth temperature of about 35-37 degrees C and an optimum pH between 7.5 and 8.0. Optimal growth occurred in media containing 4-6% (w/v) NaCl and no growth occurred in medium without NaCl. The cell-wall peptidoglycan was of the A1gamma type with meso-diaminopimelic acid, the major respiratory quinone was MK-7, the major fatty acids were iso-15:0, 16:0, anteiso-15:0 and iso-16:0 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified aminoglycophospholipid. The G+C content of the DNA was 37.9 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain CVS-8(T) represented a novel species of the genus Bacillus, the highest levels of sequence similarity (mean pairwise similarity values of approximately 97.5 %) being found with respect to the type strains of Bacillus shackletonii and Bacillus acidicola. On the basis of the phylogenetic, physiological and biochemical data, strain CVS-8(T) represents a novel species of the genus Bacillus, for which the name Bacillus isabeliae sp. nov. is proposed. The type strain is CVS-8(T) (=LMG 22838(T)=CIP 108578(T)).

  15. Fermentative hydrogen production from hydrolyzed cellulosic feedstock prepared with a thermophilic anaerobic bacterial isolate

    Energy Technology Data Exchange (ETDEWEB)

    Lo, Yung Chung [Department of Chemical Engineering, National Cheng Kung University, No. 1 University Road, Tainan 701 (China); Huang, Chi-Yu.; Fu, Tzu-Ning [Department of Environmental Engineering and Science, Tunghai University, Taichung 407 (China); Chen, Chun-Yen; Chang, Jo-Shu [Department of Chemical Engineering, National Cheng Kung University, No. 1 University Road, Tainan 701 (China); Sustainable Environment Research Center, National Cheng Kung University, Tainan (China)

    2009-08-15

    Hydrogen gas was produced via dark fermentation from natural cellulosic materials and {alpha}-cellulose via a two-step process, in which the cellulosic substrates were first hydrolyzed by an isolated cellulolytic bacterium Clostridium strain TCW1, and the resulting hydrolysates were then used as substrate for fermentative H{sub 2} production. The TCW1 strain was able to hydrolyze all the cellulosic materials examined to produce reducing sugars (RS), attaining the best reducing sugar production yield of 0.65 g reducing sugar/g substrate from hydrolysis of {alpha}-cellulose. The hydrolysates of those cellulosic materials were successfully converted to H{sub 2} via dark fermentation using seven H{sub 2}-producing bacterial isolates. The bioH{sub 2} production performance was highly dependent on the type of cellulosic feedstock used, the initial reducing sugar concentration (C{sub RS,o}) (ranging from 0.7 to 4.5 mg/l), as well as the composition of sugar and soluble metabolites present in the cellulosic hydrolysates. It was found that Clostridium butyricum CGS5 displayed the highest H{sub 2}-producing efficiency with a cumulative H{sub 2} production of 270 ml/l from {alpha}-cellulose hydrolysate (C{sub RS,o} = 4.52 mg/l) and a H{sub 2} yield of 7.40 mmol/g RS (or 6.66 mmol/g substrate) from napier grass hydrolysate (C{sub RS,o} = 1.22 g/l). (author)

  16. Identification and biological activity of potential probiotic bacterium isolated from the stomach mucus of breast-fed lamb

    Directory of Open Access Journals (Sweden)

    H. Kiňová Sepov��

    2011-09-01

    Full Text Available The lactic acid bacterium E isolated from the stomach mucus of breast-fed lamb was identified by sequencing of 16S rDNA fragment and species-specific PCR as Lactobacillus reuteri. Its potential antimicrobial activity and ability to modulate immune system in vitro and in vivo was determined. The growth inhibition of potential pathogens decreased from Staphylococcus aureus, Pseudomonas aeruginosa, Salmonella enterica ser. Minnesota to Escherichia coli. The lowest inhibition activity was observed in the case of Candida albicans. The ability of L. reuteri E to modulate biological activities of human and mouse mononuclear cells was estimated in vitro and in vivo, respectively. The production of IL-1β by monocytes in vitro was significantly induced by L. reuteri E (relative activity 2.47. The ability to modulate biological activities of mononuclear cells by living L. reuteri E cells in vitro in comparison to disintegrated L. reuteri E cells in vivo differed. For example lysozyme activity in vitro was inhibited while in vivo was stimulated (relative activities 0.30 and 1.83, respectively. The peroxidase activity in vitro was stimulated while in vivo was inhibited (relative activities 1.53 and 0.17, respectively. Obtained results indicate that L. reuteri E is potential candidate to be used in probiotic preparations for animals and/or human.

  17. Humitalea rosea gen. nov., sp. nov., an aerobic bacteriochlorophyll-containing bacterium of the family Acetobacteraceae isolated from soil.

    Science.gov (United States)

    Margesin, Rosa; Zhang, De-Chao

    2013-04-01

    A Gram-staining-negative, pale-pink-pigmented, non-motile, obligately aerobic and rod-shaped bacterium, designated strain W37(T), was isolated from soil and subjected to a taxonomic investigation using a polyphasic approach. The strain grew at 1-30 °C, oxidized thiosulfate and accumulated polyhydroxyalkanoates. Photosynthetic pigments were represented by bacteriochlorophyll a and carotenoids. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain W37(T) was most closely related to members of the genera Roseococcus and Rubritepida (with sequence similarities of Acetobacteraceae. The polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, three unidentified aminolipids and one other unidentified lipid. The predominant cellular fatty acids were C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The DNA G+C content of strain W37(T) was 68.2 mol%. On the basis of phenotypic characteristics and phylogenetic analysis, strain W37(T) represents a novel species of a new genus in the family Acetobacteraceae, for which the name Humitalea rosea gen. nov., sp. nov. is proposed. The type strain of the type species is W37(T) ( = CIP 110261(T) = LMG 26243(T)).

  18. Mitigation of Membrane Biofouling in MBR Using a Cellulolytic Bacterium, Undibacterium sp. DM-1, Isolated from Activated Sludge.

    Science.gov (United States)

    Nahm, Chang Hyun; Lee, Seonki; Lee, Sang Hyun; Lee, Kibaek; Lee, Jaewoo; Kwon, Hyeokpil; Choo, Kwang-Ho; Lee, Jung-Kee; Jang, Jae Young; Lee, Chung-Hak; Park, Pyung-Kyu

    2017-03-28

    Biofilm formation on the membrane surface results in the loss of permeability in membrane bioreactors (MBRs) for wastewater treatment. Studies have revealed that cellulose is not only produced by a number of bacterial species but also plays a key role during formation of their biofilm. Hence, in this study, cellulase was introduced to a MBR as a cellulose-induced biofilm control strategy. For practical application of cellulase to MBR, a cellulolytic ( i.e ., cellulase-producing) bacterium, Undibacterium sp. DM-1, was isolated from a lab-scale MBR for wastewater treatment. Prior to its application to MBR, it was confirmed that the cell-free supernatant of DM-1 was capable of inhibiting biofilm formation and of detaching the mature biofilm of activated sludge and cellulose-producing bacteria. This suggested that cellulase could be an effective anti-biofouling agent for MBRs used in wastewater treatment. Undibacterium sp. DM-1-entrapping beads ( i.e ., cellulolytic-beads) were applied to a continuous MBR to mitigate membrane biofouling 2.2-fold, compared with an MBR with vacant-beads as a control. Subsequent analysis of the cellulose content in the biofilm formed on the membrane surface revealed that this mitigation was associated with an approximately 30% reduction in cellulose by cellulolytic-beads in MBR.

  19. Purification and characterization of a novel alginate lyase from the marine bacterium Cobetia sp. NAP1 isolated from brown algae.

    Science.gov (United States)

    Yagi, Hisashi; Fujise, Asako; Itabashi, Narumi; Ohshiro, Takashi

    2016-12-01

    The application of marine resources, instead of fossil fuels, for biomass production is important for building a sustainable society. Seaweed is valuable as a source of marine biomass for producing biofuels such as ethanol, and can be used in various fields. Alginate is an anionic polysaccharide that forms the main component of brown algae. Various alginate lyases (e.g. exo- and endo-types and oligoalginate lyase) are generally used to degrade alginate. We herein describe a novel alginate lyase, AlgC-PL7, which belongs to the polysaccharide lyase 7 family. AlgC-PL7 was isolated from the halophilic Gram-negative bacterium Cobetia sp. NAP1 collected from the brown algae Padina arborescens Holmes. The optimal temperature and pH for AlgC-PL7 activity were 45 °C and 8, respectively. Additionally, AlgC-PL7 was thermostable and salt-tolerant, exhibited broad substrate specificity, and degraded alginate into monosaccharides. Therefore, AlgC-PL7 is a promising enzyme for the production of biofuels.

  20. Spongiimicrobium salis gen. nov., sp. nov., a bacterium of the family Flavobacteriaceae isolated from a marine sponge.

    Science.gov (United States)

    Yoon, Jaewoo; Adachi, Kyoko; Kasai, Hiroaki

    2016-09-01

    A Gram-stain-negative, strictly aerobic, pale-yellow pigmented, rod-shaped, chemoheterotrophic bacterium, designated A6F-11(T), was isolated from a marine sponge collected in Japan. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the novel marine strain was affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it shared the highest (92.9 %) sequence similarity with Arenibacter palladensis LMG 21972(T). The strain could be differentiated phenotypically from related members of the family Flavobacteriaceae. The major fatty acids of strain A6F-11(T) were iso-C15:1 G, iso-C15:0, C16:1 ω6c and/or C16:1 ω7c and iso-C17:0 3-OH. The polar lipid profile consisted of phosphatidylglycerol, two unidentified aminolipids and two unidentified lipids. The DNA G+C content was 34.7 mol%, and the major respiratory quinone was menaquinone 6 (MK-6). From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel taxon in the family Flavobacteriaceae, for which the name Spongiimicrobium salis gen. nov., sp. nov. is proposed. The type strain of S. salis gen. nov., sp. nov. is A6F-11(T) (= KCTC 42753(T) = NBRC 111401(T)).

  1. Genetic characterization, nickel tolerance, biosorption, kinetics, and uptake mechanism of a bacterium isolated from electroplating industrial effluent.

    Science.gov (United States)

    Nagarajan, N; Gunasekaran, P; Rajendran, P

    2015-04-01

    Electroplating industries in Madurai city produce approximately 49,000 L of wastewater and 1200 L of sludge every day revealing 687-5569 ppm of nickel (Ni) with other contaminants. Seventeen Ni-tolerant bacterial strains were isolated from nutrient-enriched effluents. Among them one hyper Ni accumulating strain was scored and identified as Bacillus cereus VP17 on the basis of morphology, biochemical tests, 16S rDNA gene sequencing, and phylogenetic analysis. Equilibrium data of Ni(II) ions using the bacterium as sorbent at isothermal conditions (37 °C) and pH 6 were best adjusted by Langmuir (R(2) = 0.6268) and Freundlich models (R(2) = 0.9505). Experimental validation reveals Ni sorption takes place on a heterogeneous surface of the biosorbent, and predicted metal sorption capacity is 434 ppm. The pseudo-second-order kinetic model fitted the biosorption kinetic data better than the pseudo-first-order kinetic model (R(2) = 0.9963 and 0.3625). Scanning electron microscopy, energy dispersive X-ray, and Fourier transform infrared spectroscopy studies of the bacterial strain with and without Ni(II) ion reveals the biosorption mechanism. The results conclude possibilities of using B. cereus VP17 for Ni bioremediation.

  2. Screening, identification and culture optimization of a newly isolated aromatic nitrilase-producing bacterium--Pseudomonas putida CGMCC3830.

    Science.gov (United States)

    Zhu, Xiaoyan; Gong, Jinsong; Li, Heng; Lu, Zhenming; Zhou, Zhemin; Shi, Jinsong; Xu, Zhenghong

    2014-03-01

    Microbial nitrilases have attracted increasing attention in nitrile hydrolysis for carboxylic acid production in recent years. A bacterium with nitrilase activity was isolated and identified as Pseudomonas putida CGMCC3830 based on its morphology, physiological and biochemical characteristics, as well as 16S rRNA gene sequence. The nitrilase production was optimized by varying culture conditions using the one-factor-at-a-time method and response surface methodology. Glycerol 13.54 g/L, tryptone 11.59 g/L, yeast extract 5.21 g/L, KH2PO4 1 g/L, NaCl 1 g/L, urea 1 g/L, initial pH 6.0 and culture temperature 30 degrees C were proved to be the optimal culture conditions. It resulted in the maximal nitrilase production of 36.12 U/mL from 2.02 U/mL. Investigations on substrate specificity demonstrate P. putida nitrilase preferentially hydrolyze aromatic nitriles. When applied in nicotinic acid synthesis, 2 mg/mL P. putida cells completely hydrolyzed 20.8 g/L 3-cyanopyridine into nicotinic acid in 90 min. The results indicated P. putida CGMCC3830 displayed potential for industrial production of nicotinic acid.

  3. 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...... is genomically distinct enough to be considered a novel species. The name Photobacterium galatheae is proposed and the type-strain is S2753T( = LMG 28894T = DSM 100496T)....

  4. Thermostable hemicellulases of a bacterium, Geobacillus sp. DC3, isolated from the former Homestake gold mine in Lead, South Dakota.

    Science.gov (United States)

    Bergdale, Terran E; Hughes, Stephen R; Bang, Sookie S

    2014-04-01

    A thermophilic strain, Geobacillus sp. DC3, capable of producing hemicellulolytic enzymes was isolated from the 1.5-km depth of the former Homestake gold mine in Lead, South Dakota. The DC3 strain expressed a high level of extracellular endoxylanase at 39.5 U/mg protein with additional hemicellulases including β-xylosidase (0.209 U/mg) and arabinofuranosidase (0.230 U/mg), after the bacterium was grown in xylan for 24 h. Partially purified DC3 endoxylanase exhibited a molecular mass of approximately 43 kDa according to zymography with an optimal pH of 7 and optimal temperature of 70 °C. The kinetic constants, K m and V max, were 13.8 mg/mL and 77.5 μmol xylose/min·mg xylan, respectively. The endoxylanase was highly stable and maintained 70 % of its original activity after 16 h incubation at 70 °C. The thermostable properties and presence of three different hemicellulases of Geobacillus sp. DC3 strain support its potential application for industrial hydrolysis of renewable biomass such as lignocelluloses.

  5. Cloning and biochemical characterization of a novel κ-carrageenase from newly isolated marine bacterium Pedobacter hainanensis NJ-02.

    Science.gov (United States)

    Zhu, Benwei; Ni, Fang; Ning, Limin; Yao, Zhong; Du, Yuguang

    2018-03-01

    Enzymatic preparation of carrageenan oligosaccharides has drawn increasing attention due to its advantages of mild reaction conditions and excellent product-specificity. A novel gene (CgkA) encoding a new κ-carrageenase was cloned, heterogeneously expressed and characterized from a newly isolated marine bacterium Pedobacter hainanensis NJ-02. It consisted of 1539bp and encoded 512 amino acid residues with a molecular weight of 57.12kDa. Multiple alignment analysis indicated that CgkA belongs to glycoside hydrolase (GH) family 16 and was most homologous to κ-carrageenase of Zobellia sp. M-2 with identity of 50%. The recombinant enzyme showed maximal activity of 3659.72U/mg at 40°C and pH 7.0. Additionally, it could retain more than 80% of its maximal activity after being incubated at pH of 5.0-9.0 below 40°C.K + and Na + with a wide range of concentration can activate the enzyme, while other divalent ions such as Cu 2+ , Zn 2+ showed inhibitory effect on the enzyme. The ESI-MS analysis of hydrolysates indicated that the enzyme can endolytically depolymerize the carrageenan into tetrasaccharides and hexasaccharides. The results suggest that it is an endo-type carrageenase and could be a valuable enzyme tool to produce carrageenan oligosaccharides with higher Dps. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Characterization of the plant growth promoting bacterium, Enterobacter cloacae MSR1, isolated from roots of non-nodulating Medicago sativa.

    Science.gov (United States)

    Khalifa, Ashraf Y Z; Alsyeeh, Abdel-Moneium; Almalki, Mohammed A; Saleh, Farag A

    2016-01-01

    The aim of the present study was to characterize the endophytic bacterial strain designated MSR1 that was isolated from inside the non-nodulating roots of Medicago sativa after surface-sterilization. MSR1 was identified as Enterobacter cloacae using both 16S rDNA gene sequence analysis and API20E biochemical identification system (Biomerieux, France). Furthermore, this bacterium was characterized using API50CH kit (Biomerieux, France) and tested for antibacterial activities against some food borne pathogens. The results showed that E. cloacae consumed certain carbohydrates such as glycerol, d-xylose, d-maltose and esculin melibiose as a sole carbon source and certain amino acids such as arginine, tryptophan ornithine as nitrogen source. Furthermore, MSR1 possessed multiple plant-growth promoting characteristics; phosphate solubility, production of phytohormones acetoin and bioactive compounds. Inoculation of Pisum sativum with MSR1 significantly improved the growth parameters (the length and dry weight) of this economically important grain legume compared to the non-treated plants. To our knowledge, this is the first report addressing E. cloacae which exist in roots of alfalfa growing in Al-Ahsaa region. The results confirmed that E. cloacae exhibited traits for plant growth promoting and could be developed as an eco-friendly biofertilizer for P. sativum and probably for other important plant species in future.

  7. Characterisation of the phenanthrene degradation-related genes and degrading ability of a newly isolated copper-tolerant bacterium.

    Science.gov (United States)

    Song, Mengke; Yang, Ying; Jiang, Longfei; Hong, Qing; Zhang, Dayi; Shen, Zhenguo; Yin, Hua; Luo, Chunling

    2017-01-01

    A copper-tolerant phenanthrene (PHE)-degrading bacterium, strain Sphingobium sp. PHE-1, was newly isolated from the activated sludge in a wastewater treatment plant. Two key genes, ahdA1b-1 encoding polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHDɑ) and xyLE encoding catechol-2,3-dioxygenase (C23O), involved in the PHE metabolism by strain PHE-1 were identified. The PAH-RHD gene cluster showed 96% identity with the same cluster of Sphingomonas sp. P2. Our results indicated the induced transcription of xylE and ahdA1b-1 genes by PHE, simultaneously promoted by Cu(II). For the first time, high concentration of Cu(II) is found to encourage the expression of PAH-RHDɑ and C23O genes during PHE degradation. Applying Sphingomonas PHE-1 in PHE-contaminated soils for bioaugmentation, the abundance of xylE gene was increased by the planting of ryegrass and the presence of Cu(II), which, in turn, benefited ryegrass growth. The best performance of PHE degradation and the highest abundance of xylE genes occurred in PHE-copper co-contaminated soils planted with ryegrass. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Characterization of a novel melamine-degrading bacterium isolated from a melamine-manufacturing factory in China.

    Science.gov (United States)

    Wang, Han; Geng, Chunnu; Li, Jiangwei; Hu, Anyi; Yu, Chang-Ping

    2014-04-01

    Melamine (2,4,6-triamino-1,3,5-triazine, C3H6N6), belonging to the s-triazine family, is an anthropogenic and versatile raw material for a large number of consumer products and its extensive use has resulted in the contamination of melamine in the environment. A novel melamine-degrading bacterium strain CY1 was isolated from a melamine-manufacturing factory in China. The strain is phylogenetically different from the known melamine-degrading bacteria. Approximately, 94 % melamine (initial melamine concentration 4.0 mM, initial cell OD 0.05) was degraded in 10 days without the addition of additional carbon source. High-performance liquid chromatography showed the production of degradation intermediates including ammeline, ammelide, cyanuric acid, biuret, and urea. Kinetic simulation analysis indicated that transformation of urea into ammonia was the rate-limiting step for the degradation process. The melamine-cyanurate complex was formed due to self-assembly of melamine and cyanuric acid during the degradation. The tracking experiment using CY1 cells and (13)C3-melamine showed that the CY1 could mineralize s-triazine ring carbon to CO2. The strain CY1 could also catalyze partial transformation of cyromazine, a cyclopropyl derivative of melamine, to 6-(cyclopropylamino)-[1,3,5]triazine-2,4-diol.

  9. Draft Genome Sequence of Falsirhodobacter sp. Strain alg1, an Alginate-Degrading Bacterium Isolated from Fermented Brown Algae.

    Science.gov (United States)

    Mori, Tetsushi; Takahashi, Mami; Tanaka, Reiji; Shibata, Toshiyuki; Kuroda, Kouichi; Ueda, Mitsuyoshi; Takeyama, Haruko

    2014-08-21

    Falsirhodobacter sp. alg1 is an alginate-degrading bacterium, the second species from the nonphototrophic bacterial genus Falsirhodobacter. We report the first draft genome of a bacterium from this genus and point out possible important features related to alginate assimilation and its evolutionary aspects. Copyright © 2014 Mori et al.

  10. 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)).

  11. 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.)

  12. 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.

  13. Veillonella rogosae sp. nov., an anaerobic, Gram-negative coccus isolated from dental plaque

    Science.gov (United States)

    Arif, Nausheen; Do, Thuy; Byun, Roy; Sheehy, Evelyn; Clark, Douglas; Gilbert, Steven C.; Beighton, David

    2008-01-01

    Strains of a novel anaerobic, Gram-negative coccus were isolated from the supra-gingival plaque of children. Independent strains from each of six subjects were shown, at a phenotypic level and based on 16S rRNA gene sequencing, to be members of the genus Veillonella. Analysis revealed that the six strains shared 99.7 % similarity in their 16S rRNA gene sequences and 99.0 % similarity in their rpoB gene sequences. The six novel strains formed a distinct group and could be clearly separated from recognized species of the genus Veillonella of human or animal origin. The novel strains exhibited 98 and 91 % similarity to partial 16S rRNA and rpoB gene sequences of Veillonella parvula ATCC 10790T, the most closely related member of the genus. The six novel strains could be differentiated from recognized species of the genus Veillonella based on partial 16S rRNA and rpoB gene sequencing. The six novel strains are thus considered to represent a single novel species of the genus Veillonella, for which the name Veillonella rogosae sp. nov. is proposed. The type strain is CF100T (=CCUG 54233T=DSM 18960T). PMID:18319459

  14. 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-6 T , 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-6 T 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-6 T 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-6 T (=KACC 17600 T =NBRC 109805 T =NCAIM B 02535 T ).

  15. Isolation and characterization of a novel bacterium, Sphingomonas bisphenolicum strain AO1, that degrades bisphenol A.

    Science.gov (United States)

    Oshiman, Ko-ichi; Tsutsumi, Yuji; Nishida, Tomoaki; Matsumura, Yoshinobu

    2007-04-01

    Bisphenol A (2,2-bis(4-hydroxyphenyl) propane, BPA), which is used as a synthetic resin material or a plasticizer, is a pollutant that possesses endocrine-disrupting activity. Bioremediation of BPA is used to decrease its polluting effects, and here we report a novel bacterial strain AO1, which is able to degrade BPA. This strain was isolated using enrichment cultivation from a soil sample from a vegetable-growing field; the sample was one of 500 soil samples collected across Japan. Strain AO1 degraded 100 mg/l BPA to an undetectable level within 6 h in MYPG medium (containing malt extract, yeast extract, peptone, and glucose) and within 48 h in minimum medium containing 1% glucose at 30 degrees C. Strain AO1 can utilize BPA as a sole source of carbon and as an energy source under aerobic conditions. The estrogenic activity of BPA in MYPG medium was ultimately reduced by strain AO1, although the activity initially increased. Taxonomical analysis showed that strain AO1 is closely related to Sphingomonas chlorophenolicum and S. herbicidovorans, neither of which have a capacity for BPA degradation. DNA-DNA hybridization showed that strain AO1 is a novel species of the Sphingomonas genus, and we designated AO1 as S. bisphenolicum.

  16. Characterization of a cold-active bacterium isolated from the South Pole “Ice Tunnel”

    Energy Technology Data Exchange (ETDEWEB)

    Madigan, Michael T.; Kempher, Megan L.; Bender, Kelly S.; Sullivan, Paul; Matthew Sattley, W.; Dohnalkova, Alice C.; Joye, Samantha B.

    2017-07-05

    Abstract Extremely cold microbial habitats on Earth (those below -30 °C) are rare and have not been surveyed for microbes as extensively as environments in the 0 to -20 °C range. Using cryoprotected growth media incubated at -5 °C, we enriched a cold-active Pseudomonas species from -50 °C ice collected from a utility tunnel for wastewater pipes under Amundsen–Scott South Pole Station, Antarctica. The isolate, strain UC-1, is related to other cold-active Pseudomonas species, most notably P. psychrophila, and grew at -5 °C to +34–37 °C; growth of UC-1 at +3 °C was significantly faster than at +34 °C. Strain UC-1 synthesized a surface exopolymer and high levels of unsaturated fatty acids under cold growth conditions. A 16S rRNA gene diversity screen of the ice sample that yielded strain UC-1 revealed over 1200 operational taxonomic units (OTUs) distributed across eight major classes of Bacteria. Many of the OTUs were Clostridia and Bacteriodia and some of these were probably of wastewater origin. However, a significant fraction of the OTUs were Proteobacteria and Actinobacteria of likely environmental origin. Our results shed light on the lower temperature limits to life and the possible existence of functional microbial communities in ultra-cold environments.

  17. Bacillus beringensis sp. nov., a psychrotolerant bacterium isolated from the Bering Sea.

    Science.gov (United States)

    Yu, Yong; Li, Hui-Rong; Zeng, Yin-Xin; Chen, Bo

    2011-03-01

    Psychrotolerant Bacillus-like strains BR035(T) and BR011 were isolated from seawater of the Bering Sea and were characterized by means of a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that these strains were related to the members of the genus Bacillus and had the highest 16S rRNA gene sequence similarity with Bacillus korlensis ZLC-26(T). DNA-DNA hybridization experiments confirmed that strains BR035(T) and BR011 belonged to the same species and were distinct from their closest relatives. The cells were Gram-positive, rods, motile, spore-forming and psychrotolerant. The temperature range for growth was 4-42°C. The main respiratory quinone was MK-7. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unknown aminolipid and two unknown phospholipids. The major cellular fatty acids were iso-C15:0, anteiso-C15:0, iso-C14:0 and C16:1ω7c alcohol. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The genomic DNA G + C content was 37.6-37.8 mol%. On the basis of the phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data, a novel species Bacillus beringensis is proposed and the type strain is BR035(T) (=CGMCC 1.9126(T)=DSM 22571(T)).

  18. Anoxybacillus kamchatkensis subsp. asaccharedens subsp. nov., a thermophilic bacterium isolated from a hot spring in Batman.

    Science.gov (United States)

    Gul-Guven, Reyhan; Guven, Kemal; Poli, Annarita; Nicolaus, Barbara

    2008-12-01

    A new thermophilic spore-forming strain KG8(T) was isolated from the mud of Taslidere hot spring in Batman. Strain KG8(T) was aerobe, Gram-positive, rod-shaped, motile, occurring in pairs or filamentous. Growth was observed from 35-65 degrees C (optimum 55 degrees C) and at pH 5.5-9.5 (optimum pH 7.5). It was capable of utilizing starch, growth was observed until 3% NaCl (w/v) and it was positive for nitrate reduction. On the basis of 16S rRNA gene sequence similarity, strain KG8(T) was shown to be related most closely to Anoxybacillus species. Chemotaxonomic data (major isoprenoid quinone-menaquinone-7; major fatty acid-iso-C15:0 and iso-C17:0) supported the affiliation of strain KG8(T) to the genus Anoxybacillus. The results of DNA-DNA hybridization, physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain KG8(T). Based on these results we propose assigning a novel subspecies of Anoxybacillus kamchatkensis, to be named Anoxybacillus kamchatkensis subsp. asaccharedens subsp. nov. with the type strain KG8(T) (DSM 18475(T)=CIP 109280(T)).

  19. Caldovatus sediminis gen. nov., sp. nov., a moderately thermophilic bacterium isolated from a hot spring.

    Science.gov (United States)

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

    2017-11-01

    A Gram-stain-negative, ovoid-shaped, aerobic, non-motile, catalase- and oxidase-positive, and moderately thermophilic bacterial strain, designated strain YIM 72346 T , was isolated from a sediment sample collected from a hot spring in Tengchong county, Yunnan province, south-west China. Growth occurred at 37-50 °C (optimum, 45 °C), at pH 6.0-9.0 (optimum, pH 6.5-7.0) and in the presence of 0.5-1.0 % (w/v) NaCl (optimum, 0.5 %). The major cellular fatty acids were C18 : 1ω7c, C16 : 0, C19 : 0cyclo ω8c,and C18 : 1 2-OH. The genomic DNA G+C content was determined to be 69.8 mol%. The predominant ubiquinone was Q-10. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified aminolipid and two unidentified phospholipids. Bacteriochlorophyll α and carotenoic acids were not detected. Strain YIM 72346 T was not observed for the accumulation of poly-β-hydroxybutyrate. The strain shared highest 16S rRNA gene sequence identities with Crenalkalicoccus roseus YIM 78023 T (93.3 %) and Craurococcus roseus NS130 T (92.7 %), but formed a distinct lineage within the family Acetobacteraceae in the phylogenetic trees. On the basis of genotypic, phenotypic, chemotaxonomic and phylogenetic analyses, strain YIM 72346 T is considered to represent a novel genus and species of the family Acetobacteraceae, for which the name Caldovatus sediminis gen. nov., sp. nov. is proposed. The type strain of Caldovatus sediminis is YIM 72346 T (=KCTC 52714 T =CGMCC 1.16330 T ).

  20. Azospirillum zeae sp. nov., a diazotrophic bacterium isolated from rhizosphere soil of Zea mays.

    Science.gov (United States)

    Mehnaz, Samina; Weselowski, Brian; Lazarovits, George

    2007-12-01

    Two free-living nitrogen-fixing bacterial strains, N6 and N7(T), were isolated from corn rhizosphere. A polyphasic taxonomic approach, including morphological characterization, Biolog analysis, DNA-DNA hybridization, and 16S rRNA, cpn60 and nifH gene sequence analysis, was taken to analyse the two strains. 16S rRNA gene sequence analysis indicated that strains N6 and N7(T) both belonged to the genus Azospirillum and were closely related to Azospirillum oryzae (98.7 and 98.8 % similarity, respectively) and Azospirillum lipoferum (97.5 and 97.6 % similarity, respectively). DNA-DNA hybridization of strains N6 and N7(T) showed reassociation values of 48 and 37 %, respectively, with A. oryzae and 43 % with A. lipoferum. Sequences of the nifH and cpn60 genes of both strains showed 99 and approximately 95 % similarity, respectively, with those of A. oryzae. Chemotaxonomic characteristics (Q-10 as quinone system, 18 : 1omega7c as major fatty acid) and G+C content of the DNA (67.6 mol%) were also similar to those of members of the genus Azospirillum. Gene sequences and Biolog and fatty acid analysis showed that strains N6 and N7(T) differed from the closely related species A. lipoferum and A. oryzae. On the basis of these results, it is proposed that these nitrogen-fixing strains represent a novel species. The name Azospirillum zeae sp. nov. is suggested, with N7(T) (=NCCB 100147(T)=LMG 23989(T)) as the type strain.

  1. Azospirillum thiophilum sp. nov., a diazotrophic bacterium isolated from a sulfide spring.

    Science.gov (United States)

    Lavrinenko, Ksenia; Chernousova, Elena; Gridneva, Elena; Dubinina, Galina; Akimov, Vladimir; Kuever, Jan; Lysenko, Anatoly; Grabovich, Margarita

    2010-12-01

    A novel nitrogen-fixing strain, designated BV-S(T), was isolated from a sulfur bacterial mat collected from a sulfide spring of the Stavropol Krai, North Caucasus, Russia. Strain BV-S(T) grew optimally at pH 7.5 and 37°C. According to the results of phylogenetic analysis, strain BV-S(T) belonged to the genus Azospirillum within the family Rhodospirillaceae of the class Alphaproteobacteria. Within the genus Azospirillum, strain BV-S(T) was most closely related to Azospirillum doebereinerae GSF71(T), A. picis IMMIB TAR-3(T) and A. lipoferum ATCC 29707(T) (97.7, 97.7 and 97.4 % 16S rRNA gene sequence similarity, respectively). DNA-DNA relatedness between strain BV-S(T) and A. doebereinerae DSM 13131(T), A. picis DSM 19922(T) and A. lipoferum ATCC 29707(T) was 38, 55 and 42 %, respectively. Similarities between nifH sequences of strain BV-S(T) and members of the genus Azospirillum ranged from 94.5 to 96.8 %. Chemotaxonomic characteristics (quinone Q-10, major fatty acid C(18 : 1)ω7c and G+C content 67 mol%) were similar to those of members of the genus Azospirillum. In contrast to known Azospirillum species, strain BV-S(T) was capable of mixotrophic growth under microaerobic conditions with simultaneous utilization of organic substrates and thiosulfate as electron donors for energy conservation. Oxidation of sulfide was accompanied by deposits of sulfur globules within the cells. Based on these observations, strain BV-S(T) is considered as a representative of a novel species of the genus Azospirillum, for which the name Azospirillum thiophilum sp. nov. is proposed. The type strain is BV-S(T) (=DSM 21654(T) =VKM B-2513(T)).

  2. 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)).

  3. 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.

  4. Rhizobium subbaraonis sp. nov., an endolithic bacterium isolated from beach sand.

    Science.gov (United States)

    Ramana, Ch V; Parag, B; Girija, K R; Ram, B Raghu; Ramana, V Venkata; Sasikala, Ch

    2013-02-01

    Two strains (JC85(T) and JC108) of Gram-stain-negative, motile bacteria were isolated from endolithic beach sand samples on an oligotrophic medium. Based on the 16S rRNA gene sequence analysis, both strains were identified as belonging to the genus Rhizobium. Strain JC108 had 16S rRNA gene sequence similarity of 100 % with Rhizobium pusense NRCPB10(T) and formed a cluster with this strain. Strain JC85(T) had 96.9 % 16S rRNA gene sequence similarity and was 18 % related (based on DNA-DNA hybridization) to Rhizobium borbori DN316(T). With other strains of the genus Rhizobium, the 16S rRNA gene sequence similarity was less than 96.3 %. Strain JC85(T) could tolerate up to 3 % salinity, fix N(2), was resistant to ampicillin (10 µg) and was positive for catalase and oxidase. The major fatty acid was C(18 : 1)ω7c (69 %) with minor amounts of C(19 : 0) cyclo ω8c (8.9 %), C(16 : 0) (6.9 %), C(12 : 0) (5.7 %) and C(19 : 1)ω7c/C(19 : 1)ω6c (2.2 %). Polar lipids of strain JC85(T) include two unidentified aminophospholipids (APL1,2), two unidentified phospholipids (PL1,2), phosphatidylcholine and four unidentified lipids (L1-4). Q-10 is the major quinone of strain JC85(T). Based on polyphasic taxonomic analysis, strain JC85(T) represents a novel species for which, the name Rhizobium subbaraonis JC85(T) is proposed. The type strain is JC85(T) ( = DSM 24765(T) = KCTC 23614(T)).

  5. Celeribacter persicus sp. nov., a polycyclic-aromatic-hydrocarbon-degrading bacterium isolated from mangrove soil.

    Science.gov (United States)

    Jami, Mansooreh; Lai, Qiliang; Ghanbari, Mahdi; Moghadam, Mohsen Shahriari; Kneifel, Wolfgang; Domig, Konrad J

    2016-04-01

    A Gram-stain-negative, mesophilic bacterial strain, designated SBU1T, which degrades polycyclic aromatic hydrocarbons was isolated from the sediments of the mangrove forests of Nayband Bay in the Iranian Persian Gulf during a bioremediation experiment. The 16S rRNA gene sequence of strain SBU1T exhibited highest similarities with Celeribacter indicus P73T (98.52%) and Celeribacter neptunius H 14T (97.05%). Phylogenetic analysis, based on 16S rRNA gene sequences, demonstrated that strain SBU1T fell within a cluster consisting of the type strains of species of the genus Celeribacter and formed a stable clade with C. indicus P73T in trees generated with three algorithms. The fatty acid profile of strain SBU1T consisted of the major fatty acids C18:1ω7c/ω6c and C18:1ω7c 11-methyl. The major compounds in the polar lipid profile were one phosphatidylglycerol and four unidentified phospholipids. The quinone system exclusively comprised ubiquinone (Q-10). The DNA G+C content was 60.4 mol%. A combination of phylogenetic analysis, DNA-DNA hybridization estimation, average nucleotide identity results and differential phenotypic and chemotaxonomic characteristics demonstrated that strain SBU1T could be distinguished from its close relatives. Therefore, strain SBU1T is considered to represent a novel species of the genus Celeribacter for which the name Celeribacter persicus sp. nov. is proposed. The type strain is SBU1T (=MCCC 1A00672T=DSM 100434T).

  6. Ornithinibacillus salinisoli sp. nov., a moderately halophilic bacterium isolated from a saline-alkali soil.

    Science.gov (United States)

    Gan, Longzhan; Zhang, Heming; Long, Xiufeng; Tian, Jiewei; Wang, Zhikuan; Zhang, Yuqin; Dai, Yumei; Tian, Yongqiang

    2018-03-01

    A taxonomic study was performed on strain LCB256 T , which was isolated from a saline-alkali soil sample taken from northwestern China. Cells of strain LCB256 T were Gram-stain-positive, aerobic, rod-shaped and grew at 3-17 % (w/v) NaCl (optimum 10-15 %), 10-52 °C (optimum 25-30 °C) and pH 7.0-9.0 (optimum 8.0). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LCB256 T was most closely related to the two genera of Ornithinibacillus and Oceanobacillus, showing highest sequence similarity to Oceanobacillus limi KCTC 13823 T (97.8 %) and Ornithinibacillus bavariensis WSBC 24001 T (97.2 %). The peptidoglycan amino acid type was found to be A4β and the major respiratory quinone was determined to be MK-7. The polar lipid profile of strain LCB256 T contained diphosphatidylglycerol, phosphatidylglycerol, one unidentified phospholipid and two unidentified aminolipids. The dominant cellular fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The G+C content of genomic DNA was 39.3 mol%. DNA-DNA relatedness values between strain LCB256 T and Ornithinibacillus halophilus KCTC 13822 T and Oceanobacillus limi KCTC 13823 T were 46.2 and 34.8 %, respectively. Based on this polyphasic taxonomic study, a novel species of the genus Ornithinibacillus, Ornithinibacillussalinisoli sp. nov. is proposed. The type strain is LCB256 T (=CGMCC 1.15809 T =KCTC 33862 T ).

  7. Intra-Genomic Heterogeneity in 16S rRNA Genes in Strictly Anaerobic Clinical Isolates from Periodontal Abscesses

    Science.gov (United States)

    Chen, Jiazhen; Miao, Xinyu; Xu, Meng; He, Junlin; Xie, Yi; Wu, Xingwen; Chen, Gang; Yu, Liying; Zhang, Wenhong

    2015-01-01

    Background Members of the genera Prevotella, Veillonella and Fusobacterium are the predominant culturable obligate anaerobic bacteria isolated from periodontal abscesses. When determining the cumulative number of clinical anaerobic isolates from periodontal abscesses, ambiguous or overlapping signals were frequently encountered in 16S rRNA gene sequencing chromatograms, resulting in ambiguous identifications. With the exception of the genus Veillonella, the high intra-chromosomal heterogeneity of rrs genes has not been reported. Methods The 16S rRNA genes of 138 clinical, strictly anaerobic isolates and one reference strain were directly sequenced, and the chromatograms were carefully examined. Gene cloning was performed for 22 typical isolates with doublet sequencing signals for the 16S rRNA genes, and four copies of the rrs-ITS genes of 9 Prevotella intermedia isolates were separately amplified by PCR, sequenced and compared. Five conserved housekeeping genes, hsp60, recA, dnaJ, gyrB1 and rpoB from 89 clinical isolates of Prevotella were also amplified by PCR and sequenced for identification and phylogenetic analysis along with 18 Prevotella reference strains. Results Heterogeneity of 16S rRNA genes was apparent in clinical, strictly anaerobic oral bacteria, particularly in the genera Prevotella and Veillonella. One hundred out of 138 anaerobic strains (72%) had intragenomic nucleotide polymorphisms (SNPs) in multiple locations, and 13 strains (9.4%) had intragenomic insertions or deletions in the 16S rRNA gene. In the genera Prevotella and Veillonella, 75% (67/89) and 100% (19/19) of the strains had SNPs in the 16S rRNA gene, respectively. Gene cloning and separate amplifications of four copies of the rrs-ITS genes confirmed that 2 to 4 heterogeneous 16S rRNA copies existed. Conclusion Sequence alignment of five housekeeping genes revealed that intra-species nucleotide similarities were very high in the genera Prevotella, ranging from 94.3–100%. However, the

  8. Physiological and genomic features of a novel violacein-producing bacterium isolated from surface seawater.

    Directory of Open Access Journals (Sweden)

    Yue-Hong Wu

    Full Text Available Strains JW1T and JW3, isolated from surface seawater of the Arabian Sea, were subjected to polyphasic taxonomic analysis. Cells of both strains were Gram-stain-negative, aerobic, and rod-shaped. They formed violet pigment and produced violacein. On the basis of 16S rRNA gene sequence analysis, strains JW1T and JW3 showed high 16S rRNA gene sequence similarity with Pseudoalteromonas byunsanensis JCM12483T (98.2%, P. shioyasakiensis SE3T (97.8%, P. arabiensis JCM 17292T (97.3%, and P. gelatinilytica NH153T (97.1%. The 16S rRNA gene sequence similarity between JW1T and JW3 was 100%. Phylogenetic analyses revealed that both strains fell within the cluster of the genus Pseudoalteromonas and represented an independent lineage. The average nucleotide identity and in silico DNA-DNA hybridization values between JW1T and type strains of the closely related Pseudoalteromonas species were 70.9-83.3% and 20.0-26.4%, respectively. The sole respiratory quinone in both strains is ubiquinone 8 (Q-8. The principal fatty acids are summed feature 3 (C16:1ω7c and/or iso-C15:0 2OH, C18:1ω7c, and C16:0. The major polar lipids are phosphatidylethanolamine, phosphatidylglycerol, one unidentified glycolipid, one unidentified aminolipid, and one unidentified phospholipid. The DNA G+C content was 43.3 mol%. Differential phylogenetic distinctiveness, chemotaxonomic differences, and phenotypic properties indicated that strains JW1T and JW3 could be differentiated from the Pseudoalteromonas species with validly published names. Therefore, it is proposed that strains JW1T and JW3 represent a novel species of the genus Pseudoalteromonas, for which the name Pseudoalteromonas amylolytica sp. nov. (type strain, JW1T = CGMCC 1.15681T = KCTC 52406T = MCCC 1K02162T is proposed.

  9. 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).

  10. Planococcus salinus sp. nov., a moderately halophilic bacterium isolated from a saline-alkali soil.

    Science.gov (United States)

    Gan, Longzhan; Zhang, Heming; Tian, Jiewei; Li, Xiaoguang; Long, Xiufeng; Zhang, Yuqin; Dai, Yumei; Tian, Yongqiang

    2018-02-01

    A novel aerobic, Gram-stain-positive, motile, moderately halophilic and coccoid bacterial strain, designated LCB217 T , was isolated from a saline-alkali soil in north-western China and identified using a polyphasic taxonomic approach. Growth occurred with 3-15 % (w/v) NaCl (optimum 3-5 %), at 10-45 °C (optimum 30 °C) and at pH 7.0-9.0 (optimum pH 9.0). Strain LCB217 T contained MK-7 and MK-8 as the predominant menaquinones and anteiso-C15 : 0, iso-C14 : 0 and iso-C16 : 0 as the major fatty acids. The polar lipids from strain LCB217 T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified phospholipid, one unidentified aminophospholipid and one unidentified lipid. The peptidoglycan type was A4α (l-Lys-d-Glu). Phylogenetic analysis of the 16S rRNA gene sequence showed that strain LCB217 T belonged to the genus Planococcus and was closely related to the type strains Planococcus plakortidis AS/ASP6 (II) T (98.2 % similarity), Planococcus maitriensis S1 T (97.7 %) and Planococcus salinarum ISL-16 T (97.2 %). The G+C content of the genomic DNA was 49.4 mol%. DNA-DNA relatedness values between strain LCB217 T andPlanococcusplakortidis AS/ASP6 (II) T , Planococcusmaitriensis S1 T andPlanococcussalinarum ISL-16 T were 29.5, 38.1 and 39.5 %, respectively. On the basis of the phenotypic, phylogenetic and genomic data, strain LCB217 T represents a novel species of the genus Planococcus, for which the name Planococcus salinus sp. nov. is proposed. The type strain is LCB217 T (=CGMCC 1.15685 T =KCTC 33861 T ).

  11. Complete Genome Sequence of Bacillus velezensis CBMB205, a Phosphate-Solubilizing Bacterium Isolated from the Rhizoplane of Rice in the Republic of Korea.

    Science.gov (United States)

    Hwangbo, Kyeong; Um, Yurry; Kim, Ki Yoon; Madhaiyan, Munusamy; Sa, Tong Min; Lee, Yi

    2016-07-14

    Bacillus velezensis CBMB205 (= KACC 13105(T) = NCCB 100236(T)) was isolated from the rhizoplane of rice (Oryza sativa L. cv. O-dae). According to previous studies, this bacterium has several genes that can promote plant growth, such as the phosphorus-solubilizing protein-coding gene. Here, we present the first complete genome of B. velezensis CBMB205. Copyright © 2016 Hwangbo et al.

  12. Megasphaera indica sp. nov., an obligate anaerobic bacteria isolated from human faeces.

    Science.gov (United States)

    Lanjekar, V B; Marathe, N P; Ramana, V Venkata; Shouche, Y S; Ranade, D R

    2014-07-01

    Two coccoid, non-motile, obligately anaerobic, Gram-stain-negative bacteria, occurring singly or in pairs, or as short chains, with a mean size of 1.4-2.5 µm were isolated from the faeces of two healthy human volunteers, aged 26 and 56 years, and were designated NMBHI-10(T) and BLPYG-7, respectively. Both the strains were affiliated to the sub-branch Sporomusa of the class Clostridia as revealed by 16S rRNA gene sequence analysis. The isolates NMBHI-10(T) and BLPYG-7 showed 99.1 and 99.2% 16S rRNA gene sequence similarity, respectively, with Megasphaera elsdenii JCM 1772(T). DNA-DNA hybridization and phenotypic analysis showed that both the strains were distinct from their closest relative, M. elsdenii JCM 1772(T) (42 and 53% DNA-DNA relatedness with NMBHI-10(T) and BLPYG-7, respectively), but belong to the same species (DNA-DNA relatedness of 80.9 % between the isolates). According to DNA-DNA hybridization results, the coccoid strains belong to the same genospecies, and neither is related to any of the recognized species of the genus Megasphaera. Strains NMBHI-10(T) and BLPYG-7 grew in PYG broth at temperatures of between 15 and 40 °C (optimum 37 °C), but not at 45 °C. The strains utilized a range of carbohydrates as sources of carbon and energy including glucose, lactose, cellobiose, rhamnose, galactose and sucrose. Glucose fermentation resulted in the formation of volatile fatty acids, mainly caproic acid and organic acids such as succinic acid. Phylogenetic analysis, specific phenotypic characteristics and/or DNA G+C content also differentiated the strains from each other and from their closest relatives. The DNA G+C contents of strains NMBHI-10(T) and BLPYG-7 are 57.7 and 54.9 mol%, respectively. The major fatty acids were 12 : 0 FAME and 17 : 0 CYC FAME. On the basis of these data, we conclude that strains NMBHI-10(T) and BLPYG-7 should be classified as representing a novel species of the genus Megasphaera, for which the name Megsphaera indica sp. nov

  13. Biomineralization by a Newly-Isolated Stalk-Forming Fe-oxidizing Bacterium: Towards Interpretation of Putative Fe Microfossils

    Science.gov (United States)

    Krepski, S. T.; Chan, C. S.

    2010-12-01

    Diverse aerobic, lithotrophic Fe-oxidizing bacteria (FeOB) produce distinctive extracellular Fe-rich filaments, which resemble putative Fe microfossils dating from recent to 1.7 Ga (Slack et al., 2007, EPSL: 243). The filament morphology, texture, and composition are promising biosignatures for these FeOB; however, somewhat similar morphologies have been shown to result from chemical precipitates. In order to accurately identify and interpret such biosignatures, morphology must described in detail and be linked to physiological function and growth conditions in extant organisms. Towards this goal, we aimed to isolate a novel, stalk-forming microaerophilic FeOB, since there exist few isolates. We successfully obtained a pure strain (named R-1) from a circumneutral, freshwater Fe seep in Christiana Creek, Newark, DE. This strain produces a twisted stalk, similar to Gallionella and Mariprofundus in morphology and in mineralogy. Our work shows that R-1 is a neutrophilic obligate FeOB, unable to oxidize other organic or inorganic substrates. It is a Beta-Proteobacterium in the Gallionellaceae family but is phylogenetically distinct from previously isolated Gallionella sp. and Sideroxydans sp. The closest cultured relative is S. lithotrophicus (97% similar) and the closest environmental clone is 98% similar. We have begun growing R-1 and the marine stalk-forming FeOB Mariprofundus ferrooxydans in microslide cultures, which allow direct microscope observation without disturbing growth. We are monitoring oxygen concentration gradients and FeOB response to oxygen levels. In order to link morphology to biological function and growth conditions, we will observe stalk formation under various conditions and document various morphological and textural parameter (e.g. branching and orientation) to establish criteria for biogenicity. No organisms are known to make stalks under anaerobic conditions, so if these structures are detected in the rock record, they could be used as

  14. Characterization of Desulfovibrio salinus sp. nov., a slightly halophilic sulfate-reducing bacterium isolated from a saline lake in Tunisia.

    Science.gov (United States)

    Ben Ali Gam, Zouhaier; Thioye, Abdoulaye; Cayol, Jean-Luc; Joseph, Manon; Fauque, Guy; Labat, Marc

    2018-03-01

    A novel slightly halophilic sulfate-reducing bacterium, designated strain P1BSR T , was isolated from water of a saline lake in Tunisia. Strain P1BSR T had motile (single polar flagellum), Gram-negative, rod-shaped, non-spore-forming cells, occurring singly or in pairs. Strain P1BSR T grew at temperatures between 15 and 45 °C (optimum 40 °C), and in a pH range between 6 and 8.5 (optimum pH 6.7). The strain required NaCl for growth (1 % w/v), and tolerated high NaCl concentration (up to 12 % w/v) with an optimum of 3 % (w/v). Sulfate, thiosulfate and sulfite served as terminal electron acceptors, but not elemental sulfur, fumarate, nitrate and nitrite. Strain P1BSR T utilized lactate, pyruvate, formate, d-fructose and glycerol as carbon and energy sources. The main cellular fatty acid was C16 : 0 (50.8 %). The genomic DNA G+C content was 47.7 mol%. Phylogenetic analysis of 16S rRNA gene sequence similarity indicated that strain P1BSR T was affiliated to the genus Desulfovibrio, with the type strains Desulfovibrio salexigens (96.51 %), Desulfovibrio zosterae (95.68 %), Desulfovibrio hydrothermalis (94.81 %) and Desulfovibrio ferrireducens (94.73 %) as its closest phylogenetic relatives. On the basis of genotypic, phenotypic and phylogenetic characteristics, it is proposed to assign strain P1BSR T to a novel species of the genus Desulfovibrio, Desulfovibrio salinus sp. nov. The type strain is P1BSR T (=DSM 101510 T =JCM 31065 T ).

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

    Science.gov (United States)

    Min, Jun; Chen, Weiwei; Wang, Jinpei; Hu, Xiaoke

    2017-01-01

    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.

  16. 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.

  17. Desulfotomaculum arcticum sp. nov., a novel spore-forming, moderately thermophilic, sulfate-reducing bacterium isolated from a permanently cold fjord sediment of Svalbard

    DEFF Research Database (Denmark)

    Vandieken, Verona; Knoblauch, Christian; Jørgensen, Bo Barker

    2006-01-01

    Strain 15T is a novel spore-forming, sulfate-reducing bacterium isolated from a permanently cold fjord sediment of Svalbard. Sulfate could be replaced by sulfite or thiosulfate. Hydrogen, formate, lactate, propionate, butyrate, hexanoate, methanol, ethanol, propanol, butanol, pyruvate, malate...... growth occurred at 44 degrees C. Therefore, strain 15T apparently cannot grow at in situ temperatures of Arctic sediments from where it was isolated, and it was proposed that it was present in the sediment in the form of spores. The DNA G+C content was 48.9 mol%. Strain 15T was most closely related...

  18. Desulfotomaculum arcticum sp nov., a novel spore-formin, moderately thermophilic, sulfate-reducing bacterium isolated from a permanently cold fjord sediment of Svalbard

    DEFF Research Database (Denmark)

    Vandieken, V.; Knoblauch, C.; Jørgensen, BB

    2006-01-01

    Strain 15 T is a novel spore-forming, sulfate-reducing bacterium isolated from a permanently cold fjord sediment of Svalbard. Sulfate could be replaced by sulfite or thiosulfate. Hydrogen, formate, lactate, propionate, butyrate, hexanoate, methanol, ethanol, propanol, butanol, pyruvate, malate...... and optimal growth occurred at 44 degrees C. Therefore, strain 15 T apparently cannot grow at in situ temperatures of Arctic sediments from where it was isolated, and it was proposed that it was present in the sediment in the form of spores. The DNA G+C content was 48(.)9 mol%. Strain 15 T was most closely...

  19. Umezawamides, new bioactive polycyclic tetramate macrolactams isolated from a combined-culture of Umezawaea sp. and mycolic acid-containing bacterium.

    Science.gov (United States)

    Hoshino, Shotaro; Wong, Chin Piow; Ozeki, Masahiro; Zhang, Huiping; Hayashi, Fumiaki; Awakawa, Takayoshi; Asamizu, Shumpei; Onaka, Hiroyasu; Abe, Ikuro

    2018-03-14

    New polycyclic tetramate macrolactams, Umezawamides A (1) and B (2) were isolated from a combined-culture of Umezawaea sp. RD066910 and mycolic-acid containing bacterium Tsukamurella pulmonis TP-B0596. Their planar structures and partial stereochemistries were determined based on the spectroscopic analysis, MMFF conformational search, and ECD calculations. Umezawamides are the first secondary metabolites isolated from the genus Umezawaea and they exhibited cytotoxicities to P388 murine leukemia cells. Furthermore, umezawamide A (1) showed growth inhibitory activity against Candida albicans.

  20. 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)).

  1. 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

  2. [Identification of anaerobic gram-negative bacilli isolated from various clinical specimens and determination of antibiotic resistance profiles with E-test methods].

    Science.gov (United States)

    Demir, Cengiz; Keşli, Recep

    2018-01-01

    The aim of this study was to identify gram-negative anaerobic bacilli isolated from various clinical specimens that were obtained from patients with suspected anaerobic infections and to determine the antibiotic resistance profiles by using the antibiotic concentration gradient method. The study was performed in Afyon Kocatepe University Ahmet Necdet Sezer Research and Practice Hospital, Medical Microbiology Laboratory between 1 November 2014 and 30 October 2015. Two hundred and seventyeight clinical specimens accepted for anaerobic culture were enrolled in the study. All the samples were cultivated anaerobically by using Schaedler agar with 5% defibrinated sheep blood and Schaedler broth. The isolated anaerobic gram-negative bacilli were identified by using both the conventional methods and automated identification system (VITEK 2, bioMerieux, France). Antibiotic susceptibility tests were performed with antibiotic concentration gradient method (E-test, bioMerieux, France); against penicillin G, clindamycin, cefoxitin, metronidazole, moxifloxacin, imipenem, meropenem, ertapenem and doripenem for each isolate. Of the 28 isolated anaerobic gram-negative bacilli; 14 were identified as Bacteroides fragilis group, 9 were Prevotella spp., and 5 were Fusobacterium spp. The highest resistance rate was found against penicillin (78.5%) and resistance rates against clindamycin and cefoxitin were found as 17.8% and 21.4%, respectively. No resistance was found against metronidazole, moxifloxacin, imipenem, meropenem, ertapenem and doripenem. As a result, isolation and identification of anaerobic bacteria are difficult, time-consuming and more expensive when compared with the cost of aerobic culture. The rate of anaerobic bacteria isolation may be increased by obtaining the appropriate clinical specimen and appropriate transportation of these specimens. We believe that the data obtained from the study in our center may offer benefits for the follow up and treatment of infections

  3. Lebetimonas natsushimae sp. nov., a novel strictly anaerobic, moderately thermophilic chemoautotroph isolated from a deep-sea hydrothermal vent polychaete nest in the Mid-Okinawa Trough.

    Science.gov (United States)

    Nagata, Ryousuke; Takaki, Yoshihiro; Tame, Akihiro; Nunoura, Takuro; Muto, Hisashi; Mino, Sayaka; Sawayama, Shigeki; Takai, Ken; Nakagawa, Satoshi

    2017-09-01

    A moderately thermophilic, strictly anaerobic, chemoautotrophic bacterium, designated strain HS1857 T , was isolated from a deep-sea hydrothermal vent at the Noho site in the Mid-Okinawa Trough. Strain HS1857 T grew between 35 and 63°C (optimum 55°C), in the presence of 10-55gl -1 NaCl (optimum 25gl -1 ), and pH 5.5-7.1 (optimum 6.4). Growth occurred with molecular hydrogen as the electron donor and elemental sulfur, nitrate, or selenate as the electron acceptors. Formate could serve as an alternative electron donor with nitrate as an electron acceptor. During growth with nitrate as the electron acceptor, strain HS1857 T produced ammonium and formed a biofilm. CO 2 was utilized as the sole carbon source. The G+C content of the genomic DNA was 33.2mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain HS1857 T is a member of the order Nautiliales, showing a sequence similarity of 95.0% with Lebetimonas acidiphila Pd55 T . The fatty acid composition was similar to that of L. acidiphila, which was dominated by C 18:0 (47.0%) and C 18:1 (23.7%). Based on the genomic, chemotaxonomic, phenotypic characteristics, the name Lebetimonas natsushimae sp. nov., is proposed. The type strain is HS1857 T (=NBRC 112478 T =DSM 104102 T ). Copyright © 2017 Elsevier GmbH. All rights reserved.

  4. Butyricimonas phoceensis sp. nov., a new anaerobic species isolated from the human gut microbiota of a French morbidly obese patient.

    Science.gov (United States)

    Togo, A H; Diop, A; Dubourg, G; Nguyen, T T; Andrieu, C; Caputo, A; Couderc, C; Fournier, P-E; Maraninchi, M; Valero, R; Raoult, D; Million, M

    2016-11-01

    Butyricimonas phoceensis strain AT9 (= CSUR 1981 = DSM 100664) was isolated from a stool sample from a morbidly obese French patient living in Marseille using the culturomics approach. The genome of this Gram-negative-staining, anaerobic and non-spore forming rod bacillus is 4 736 949 bp long and contains 3947 protein-coding genes. Genomic analysis identified 173 genes as ORFans (4.5%) and 1650 orthologous proteins (42%) not shared with the closest phylogenetic species, Butyricimonas virosa. Its major fatty acid was the branched acid iso-C15:0 (62.3%).

  5. Butyricimonas phoceensis sp. nov., a new anaerobic species isolated from the human gut microbiota of a French morbidly obese patient

    Directory of Open Access Journals (Sweden)

    A.H. Togo

    2016-11-01

    Full Text Available Butyricimonas phoceensis strain AT9 (= CSUR 2478 = DSM 100838 was isolated from a stool sample from a morbidly obese French patient living in Marseille using the culturomics approach. The genome of this Gram-negative-staining, anaerobic and non–spore forming rod bacillus is 4 736 949 bp long and contains 3947 protein-coding genes. Genomic analysis identified 173 genes as ORFans (4.5% and 1650 orthologous proteins (42% not shared with the closest phylogenetic species, Butyricimonas virosa. Its major fatty acid was the branched acid iso-C15:0 (62.3%.

  6. Culturable prokaryotic diversity of deep, gas hydrate sediments: first use of a continuous high-pressure, anaerobic, enrichment and isolation system for subseafloor sediments (DeepIsoBUG)

    OpenAIRE

    Parkes, R John; Sellek, Gerard; Webster, Gordon; Martin, Derek; Anders, Erik; Weightman, Andrew J; Sass, Henrik

    2009-01-01

    Deep subseafloor sediments may contain depressurization-sensitive, anaerobic, piezophilic prokaryotes. To test this we developed the DeepIsoBUG system, which when coupled with the HYACINTH pressure-retaining drilling and core storage system and the PRESS core cutting and processing system, enables deep sediments to be handled without depressurization (up to 25 MPa) and anaerobic prokaryotic enrichments and isolation to be conducted up to 100 MPa. Here, we describe the system and its first use...

  7. Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CFL1, a Lactic Acid Bacterium Isolated from French Handcrafted Fermented Milk

    OpenAIRE

    Meneghel, Julie; Dugat-Bony, Eric; Irlinger, Fran?oise; Loux, Valentin; Vidal, Marie; Passot, St?phanie; B?al, Catherine; Layec, S?verine; Fonseca, Fernanda

    2016-01-01

    Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) is a lactic acid bacterium widely used for the production of yogurt and cheeses. Here, we report the genome sequence of L. bulgaricus CFL1 to improve our knowledge on its stress-induced damages following production and end-use processes.

  8. 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

  9. High rate of non-susceptibility to metronidazole and clindamycin in anaerobic isolates: Data from a clinical laboratory from Karachi, Pakistan.

    Science.gov (United States)

    Sheikh, Sadia Omer; Jabeen, Kauser; Qaiser, Saba; Ahsan, Syed Tanwir; Khan, Erum; Zafar, Afia

    2015-06-01

    Due to increasing resistance amongst anaerobic pathogens periodic surveillance of resistance has been recommended in regional/local settings. Anaerobic antimicrobial susceptibility testing is not routinely performed in many laboratories in Pakistan, hence absence of local data may lead to inappropriate empirical therapy in serious cases. 121 clinically significant anaerobic strains (26/121; 21% bacteremic isolates) were isolated and saved from 2010 to 2011. Susceptibility testing against metronidazole, clindamycin, co-amoxiclav, meropenem, piperacillin/tazobactam, linezolid and gatifloxacin was performed by determining minimum inhibitory concentrations (MICs). A high proportion of non-susceptible strains to metronidazole (10% of 121 isolates) and clindamycin (12% of 121 isolates) was seen, most noticeable in Bacteroides fragilis. Three Bacteroides species strains were non-susceptible to both metronidazole and clindamycin. One strain of Clostridium species was fully resistant to metronidazole and had intermediate resistance to clindamycin. No resistance to any of the other tested antibiotics was seen. Resistance to metronidazole was higher in bacteremic vs. non bacteremic isolates (p = value 0.07). In our setting where there is a high usage of empirical metronidazole and clindamycin for the treatment of serious anaerobic infections clinicians should be aware of increased resistance to these agents. Periodic surveillance of resistance to anti-anaerobic drugs especially metronidazole and clindamycin should be performed to generate antibiogram and guide appropriate empiric therapy. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Evaluation of continuous ethanol fermentation of dilute-acid corn stover hydrolysate using thermophilic anaerobic bacterium Thermoanaerobacter BG1L1

    DEFF Research Database (Denmark)

    Georgieva, Tania I.; Ahring, Birgitte Kiær

    2007-01-01

    fermented yielding ethanol of 0.39–0.42 g/g-sugars consumed. Xylose was nearly completely utilized (89–98%) for PCS up to 10% TS, whereas at 15% TS, xylose conversion was lowered to 67%. The reactor was operated continuously for 135 days, and no contamination was seen without the use of any agent......Dilute sulfuric acid pretreated corn stover is potential feedstock of industrial interest for second generation fuel ethanol production. However, the toxicity of corn stover hydrolysate (PCS) has been a challenge for fermentation by recombinant xylose fermenting organisms. In this work...... for preventing bacterial infections. This study demonstrated that the use of immobilized thermophilic anaerobic bacteria for continuous ethanol fermentation could be promising in a commercial ethanol process in terms of system stability to process hardiness and reactor contamination. The tested microorganism has...

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

    OpenAIRE

    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...

  12. Complete genome sequence of Arthrobacter alpinus ERGS4:06, a yellow pigmented bacterium tolerant to cold and radiations isolated from Sikkim Himalaya.

    Science.gov (United States)

    Kumar, Rakshak; Singh, Dharam; Swarnkar, Mohit Kumar; Singh, Anil Kumar; Kumar, Sanjay

    2016-02-20

    Arthrobacter alpinus ERGS4:06, a yellow pigmented bacterium which exhibited tolerance to cold and UV radiations was isolated from the glacial stream of East Rathong glacier in Sikkim Himalaya. Here we report the 4.3Mb complete genome assembly that has provided the basis for potential role of pigments as a survival strategy to combat stressed environment of cold and high UV-radiation and additionally the ability to produce cold active industrial enzymes. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Prevalence and antimicrobial susceptibilities of anaerobic bacteria isolated from perforated corneal ulcers by culture and multiplex PCR: an evaluation in cases with keratitis and endophthalmitis.

    Science.gov (United States)

    Tokman, Hrisi Bahar; İskeleli, Güzin; Dalar, Zeynep Güngördü; Kangaba, Achille Aime; Demirci, Mehmet; Akay, Hatice K; Borsa, Bariş Ata; Algingil, Reyhan Çalişkan; Kocazeybek, Bekir S; Torun, Müzeyyen Mamal; Kiraz, Nuri

    2014-01-01

    Anaerobic bacteria play an important role in eye infections; however, there is limited epidemiologic data based on the the role of these bacteria in the etiology of keratitis and endophthalmitis. The aim of this re- search is to determine the prevalence of anaerobic bacteria in perforated corneal ulcers of patients with keratitis and endophthalmitis and to evaluate their antimicrobial susceptibilities. Corneal scrapings were taken by the ophthalmologist using sterile needles. For the isolation of anaerobic bacteria, samples were inoculated on specific media and were incubated under anaerobic conditions obtained with Anaero-Gen (Oxoid & Mitsubishi Gas Company) in anaerobic jars (Oxoid USA, Inc. Columbia, MD, USA). The molecular identification of anaerobic bacteria was performed by multiplex PCR and the susceptibilities of an- aerobic bacteria to penicillin, chloramphenicol, and clindamycin were determined with the E test (bioMerieux). 51 strains of anaerobic bacteria belonging to four different genuses were detected by multiplex PCR and only 46 strains were isolated by culture. All of them were found susceptible to chloramphenicol whereas penicillin resistance was found in 13.3% of P.anaerobius strains, clindamycin resistance was found in 34.8% of P.acnes and 13.3% of P. anaerobius strains. Additionnaly, one strain of P. granulosum was found resistant to clindamycin, one strain of B. fragilis and one strain of P.melaninogenica were found resistant to penicillin and clindamycin. Routine analyses of anaerobes in perforated corneal ulcers is inevitable and usage of appropriate molecular methods, for the detection of bacteria responsible from severe infections which might not be deter- mined by cultivation, may serve for the early decision of the appropriate treatment. Taking into account the in- creasing antimicrobial resistance of anaerobic bacteria, alternative eye specific antibiotics effective against anaer- obes are needed to achieve a successful treatment.

  14. Transcriptomic analysis of lignocellulosic biomass degradation by the anaerobic fungal isolate Orpinomyces sp. strain C1A.

    Science.gov (United States)

    Couger, M B; Youssef, Noha H; Struchtemeyer, Christopher G; Liggenstoffer, Audra S; Elshahed, Mostafa S

    2015-01-01

    Anaerobic fungi reside in the rumen and alimentary tract of herbivores where they play an important role in the digestion of ingested plant biomass. The anaerobic fungal isolate Orpinomyces sp. strain C1A is an efficient biomass degrader, capable of simultaneous saccharification and fermentation of the cellulosic and hemicellulosic fractions in multiple types of lignocellulosic biomass. To understand the mechanistic and regulatory basis of biomass deconstruction in anaerobic fungi, we analyzed the transcriptomic profiles of C1A when grown on four different types of lignocellulosic biomass (alfalfa, energy cane, corn stover, and sorghum) versus a soluble sugar monomer (glucose). A total of 468.2 million reads (70.2 Gb) were generated and assembled into 27,506 distinct transcripts. CAZyme transcripts identified included 385, 246, and 44 transcripts belonging to 44, 13, and 8 different glycoside hydrolases (GH), carbohydrate esterases, and polysaccharide lyases families, respectively. Examination of CAZyme transcriptional patterns indicates that strain C1A constitutively transcribes a high baseline level of CAZyme transcripts on glucose. Although growth on lignocellulosic biomass substrates was associated with a significant increase in transcriptional levels in few GH families, including the highly transcribed GH1 β-glucosidase, GH6 cellobiohydrolase, and GH9 endoglucanase, the transcriptional levels of the majority of CAZyme families and transcripts were not significantly altered in glucose-grown versus lignocellulosic biomass-grown cultures. Further, strain C1A co-transcribes multiple functionally redundant enzymes for cellulose and hemicellulose saccharification that are mechanistically and structurally distinct. Analysis of fungal dockerin domain-containing transcripts strongly suggests that anaerobic fungal cellulosomes represent distinct catalytic units capable of independently attacking and converting intact plant fibers to sugar monomers. Collectively, these

  15. Biotransformation of ginsenoside Rb1 to ginsenoside Rg3 by endophytic bacterium Burkholderia sp. GE 17-7 isolated from Panax ginseng.

    Science.gov (United States)

    Fu, Y; Yin, Z-H; Yin, C-Y

    2017-06-01

    To isolate a novel endophytic bacterium from Panax ginseng that could have excellent properties in converting ginsenoside Rb1 to ginsenoside Rg3. Based on a 16S rDNA gene sequence, the strain named GE 17-7 was identified as Burkholderia sp. This strain has shown the highest activity in converting ginsenoside Rb1 to 20(S)-ginsenoside Rg3. During the biotransformation of ginsenoside Rb1, the final metabolite was identified by nuclear magnetic resonance analysis and the transformation pathway of ginsenoside Rb1 was also identified by thin-layer chromatography and high performance liquid chromatography analysis in this study. We have successfully isolated a β-glucosidase-producing endophytic bacterium GE 17-7 from P. ginseng. Ginsenoside Rg3 was produced by strain GE 17-7 from ginsenoside Rb1 via ginsenoside Rd. This is the first report of the conversion of major ginsenoside Rb1 into minor ginsenoside Rg3 by fermentation with Burkholderia sp. endophytic bacteria in P. ginseng. These results suggest a new preparation method for ginsenoside Rg3 using strain GE 17-7 in the pharmaceutical industry. © 2017 The Society for Applied Microbiology.

  16. Pseudomonas sp. ZXY-1, a newly isolated and highly efficient atrazine-degrading bacterium, and optimization of biodegradation using response surface methodology.

    Science.gov (United States)

    Zhao, Xinyue; Wang, Li; Ma, Fang; Bai, Shunwen; Yang, Jixian; Qi, Shanshan

    2017-04-01

    Atrazine, a widely used herbicide, is increasing the agricultural production effectively, while also causing great environmental concern. Efficient atrazine-degrading bacterium is necessary to removal atrazine rapidly to keep a safe environment. In the present study, a new atrazine-degrading strain ZXY-1, identified as Pseudomonas, was isolated. This new isolated strain has a strong ability to biodegrade atrazine with a high efficiency of 9.09mg/L/hr. Temperature, pH, inoculum size and initial atrazine concentration were examined to further optimize the degradation of atrazine, and the synthetic effect of these factors were investigated by the response surface methodology. With a high quadratic polynomial mathematical model (R 2 =0.9821) being obtained, the highest biodegradation efficiency of 19.03mg/L/hr was reached compared to previous reports under the optimal conditions (30.71°C, pH7.14, 4.23% (V/V) inoculum size and 157.1mg/L initial atrazine concentration). Overall, this study provided an efficient bacterium and approach that could be potentially useful for the bioremediation of wastewater containing atrazine. Copyright © 2016. Published by Elsevier B.V.

  17. Alternative anaerobic enrichments to the bacteriological analytical manual culture method for isolation of Shigella sonnei from selected types of fresh produce.

    Science.gov (United States)

    Jacobson, Andrew P; Thunberg, Richard L; Johnson, Mildred L; Hammack, Thomas S; Andrews, Wallace H

    2004-01-01

    Alternative methods of reducing oxygen during anaerobic enrichment in the Bacteriological Analytical Manual (BAM) Shigella culture method were evaluated and compared to the current and less practical GasPak method. The alternative anaerobic methods included the use of reducing agents in Shigella broth and reducing culture container headspace volume to minimize atmospheric effects on oxygen concentration in Shigella broth during enrichment. The reducing agents evaluated were sodium thioglycollate, L-cystine, L-cysteine, titanium(III) citrate, and dithiothreitol, each at concentrations of 0.1, 0.05, and 0.01%. The use of Oxyrase for Broth with the enrichment medium (Shigella broth) was evaluated at concentrations of 10, 20 and 30 microL/mL. Recoveries of chill- and freeze-stressed S. sonnei strains 357 and 20143 were determined with each anaerobic method, including the GasPak method, using inoculation levels ranging from 10(0)to 10(3) cells. For each anaerobic method, strain, inoculation level, and stress type, 5 replicate enrichments were evaluated by streaking to MacConkey agar for isolation. The numbers of cultures with each method from which S. sonnei was isolated were used to compare the alternative anaerobic methods to the GasPak method. The alternative anaerobic method with which chill- and freeze-stressed S. sonnei strains 357 and 20143 were isolated most consistently was the use of Oxyrase for Broth in Shigella broth at a concentration of 20 microL/mL. This method was compared to the GasPak anaerobic method in evaluations on the recovery of S. sonnei strains 357 and 20143 from artificially contaminated test portions of parsley, cilantro, green onions, strawberries, carrots, and celery. A third anaerobic method included the use of 0.5 cm mineral oil overlay on cultures containing Oxyrase for Broth at concentrations of 20 microL/mL. Recovery rates of strain 357 were significantly greater (p cultures. The use of mineral oil overlay with Oxyrase for Broth also

  18. Microbial reduction of uranium(VI) by anaerobic microorganisms isolated from a former uranium mine

    Energy Technology Data Exchange (ETDEWEB)

    Gerber, Ulrike; Krawczyk-Baersch, Evelyn [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Biogeochemistry; Arnold, Thuro [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Inst. of Resource Ecology; Scheinost, Andreas C. [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Molecular Structures

    2017-06-01

    The former uranium mine Koenigstein (Germany) is currently in the process of controlled flooding by reason of remediation purposes. However, the flooding water still contains high concentrations of uranium and other heavy metals. For that reason the water has to be cleaned up by a conventional waste water treatment plant. The aim of this study was to investigate the interactions between anaerobic microorganisms and uranium for possible bioremediation approaches, which could be an great alternative for the intensive and expensive waste water treatment. EXAFS (extended X-ray absorption fine structure) and XANES (X-ray absorption near edge structure) measurements were performed and revealed a complete reduction of U(VI) to U(IV) only by adding 10 mM glycerol.

  19. Microbial reduction of uranium(VI) by anaerobic microorganisms isolated from a former uranium mine

    International Nuclear Information System (INIS)

    Gerber, Ulrike; Krawczyk-Baersch, Evelyn; Arnold, Thuro; Scheinost, Andreas C.

    2017-01-01

    The former uranium mine Koenigstein (Germany) is currently in the process of controlled flooding by reason of remediation purposes. However, the flooding water still contains high concentrations of uranium and other heavy metals. For that reason the water has to be cleaned up by a conventional waste water treatment plant. The aim of this study was to investigate the interactions between anaerobic microorganisms and uranium for possible bioremediation approaches, which could be an great alternative for the intensive and expensive waste water treatment. EXAFS (extended X-ray absorption fine structure) and XANES (X-ray absorption near edge structure) measurements were performed and revealed a complete reduction of U(VI) to U(IV) only by adding 10 mM glycerol.

  20. Selenite reduction by the obligate aerobic bacterium Comamonas testosteroni S44 isolated from a metal-contaminated soil

    DEFF Research Database (Denmark)

    Zheng, Shixue; Su, Jing; Wang, Liang

    2014-01-01

    ) and EDS Elemental Mapping showed no element Se and SeNPs were produced inside cells whereas Se(IV) was reduced to red-colored selenium in the cytoplasmic fraction in presence of NADPH. Tungstate inhibited Se(VI) but not Se(IV) reduction, indicating the Se(IV)-reducing determinant does not contain......Background: Selenium (Se) is an essential trace element in most organisms but has to be carefully handled since there is a thin line between beneficial and toxic concentrations. Many bacteria have the ability to reduce selenite (Se(IV)) and (or) selenate (Se(VI)) to red elemental selenium...... that is less toxic. Results: A strictly aerobic bacterium, Comamonas testosteroni S44, previously isolated from metal(loid)-contaminated soil in southern China, reduced Se(IV) to red selenium nanoparticles (SeNPs) with sizes ranging from 100 to 200 nm. Both energy dispersive X-ray Spectroscopy (EDX or EDS...

  1. Hemicellulases from anaerobic thermophiles. Progress report

    Energy Technology Data Exchange (ETDEWEB)

    Wiegel, J.

    1994-05-01

    The longterm goal of this research effort is to obtain an anaerobic thermophilic bacterium that efficiently converts various hemicellulose-containing biomass to ethanol over a broad pH range. The strategy is to modify the outfit and regulation of the rate-limiting xylanases, glycosidases and xylan esterases in the ethanologenic, anaerobic thermophile Thermoanaerobacter ethanolicus, which grows between pH 4.5 and 9.5. Although it utilizes xylans, the xylanase, acetyl(xylan) esterase and O-methylglucuronidase activities in T. ethanolicus are barely measurable and regarded as the rate limiting steps in its xylan utilization. Thus, and also due to the presently limited knowledge of hemicellulases in anaerobic thermophiles, we characterize the hemicellulolytic enzymes from this and other anaerobic thermophiles as enzyme donors. Beside the active xylosidase/arabinosidase from T. ethanolicus, exhibiting the two different activities, we characterized 2 xylosidases, two acetyl(xylan) esterases, and an O-methylglucuronidase from Thermoanaerobacterium spec. We will continue with the characterization of xylanases from novel isolated slightly acidophilic, neutrophilic and slightly alkalophilic thermophiles. We have cloned, subcloned and partially sequenced the 165,000 Da (2 x 85,000) xylosidase/arabinosidase from T. ethanolicus and started with the cloning of the esterases from Thermoanaerobacterium spec. Consequently, we will develop a shuttle vector and continue to apply electroporation of autoplasts as a method for cloning into T. ethanolicus.

  2. 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.

  3. Isolation, Free-Living Capacities, and Genome Structure of “Candidatus Glomeribacter gigasporarum,” the Endocellular Bacterium of the Mycorrhizal Fungus Gigaspora margarita

    Science.gov (United States)

    Jargeat, P.; Cosseau, C.; Ola'h, B.; Jauneau, A.; Bonfante, P.; Batut, J.; Bécard, G.

    2004-01-01

    “Candidatus Glomeribacter gigasporarum” is an endocellular β-proteobacterium present in the arbuscular mycorrhizal (AM) fungus Gigaspora margarita. We established a protocol to isolate “Ca. Glomeribacter gigasporarum” from its host which allowed us to carry out morphological, physiological, and genomic investigations on purified bacteria. They are rod shaped, with a cell wall typical of gram-negative bacteria and a cytoplasm rich in ribosomes, and they present no flagella or pili. Isolated bacteria could not be grown in any of the 19 culture media tested, but they could be kept alive for up to 4 weeks. PCR-based investigations of purified DNA from isolated bacteria did not confirm the presence of all genes previously assigned to “Ca. Glomeribacter gigasporarum.” In particular, the presence of nif genes could not be detected. Pulsed-field gel electrophoresis analyses allowed us to estimate the genome size of “Ca. Glomeribacter gigasporarum” to approximately 1.4 Mb with a ca. 750-kb chromosome and a 600- to 650-kb plasmid. This is the smallest genome known for a β-proteobacterium. Such small genome sizes are typically found in endocellular bacteria living permanently in their host. Altogether, our data suggest that “Ca. Glomeribacter gigasporarum” is an ancient obligate endocellular bacterium of the AM fungus G. margarita. PMID:15466041

  4. Isolation, free-living capacities, and genome structure of "Candidatus Glomeribacter gigasporarum," the endocellular bacterium of the mycorrhizal fungus Gigaspora margarita.

    Science.gov (United States)

    Jargeat, P; Cosseau, C; Ola'h, B; Jauneau, A; Bonfante, P; Batut, J; Bécard, G

    2004-10-01

    "Candidatus Glomeribacter gigasporarum" is an endocellular beta-proteobacterium present in the arbuscular mycorrhizal (AM) fungus Gigaspora margarita. We established a protocol to isolate "Ca. Glomeribacter gigasporarum" from its host which allowed us to carry out morphological, physiological, and genomic investigations on purified bacteria. They are rod shaped, with a cell wall typical of gram-negative bacteria and a cytoplasm rich in ribosomes, and they present no flagella or pili. Isolated bacteria could not be grown in any of the 19 culture media tested, but they could be kept alive for up to 4 weeks. PCR-based investigations of purified DNA from isolated bacteria did not confirm the presence of all genes previously assigned to "Ca. Glomeribacter gigasporarum." In particular, the presence of nif genes could not be detected. Pulsed-field gel electrophoresis analyses allowed us to estimate the genome size of "Ca. Glomeribacter gigasporarum" to approximately 1.4 Mb with a ca. 750-kb chromosome and a 600- to 650-kb plasmid. This is the smallest genome known for a beta-proteobacterium. Such small genome sizes are typically found in endocellular bacteria living permanently in their host. Altogether, our data suggest that "Ca. Glomeribacter gigasporarum" is an ancient obligate endocellular bacterium of the AM fungus G. margarita.

  5. Isolation and Characterization of a New Methanobacterium formicicum KOR-1 from an Anaerobic Digester Using Pig Slurry.

    Science.gov (United States)

    Battumur, Urantulkhuur; Yoon, Young-Man; Kim, Chang-Hyun

    2016-04-01

    A new methanogen was isolated from an anaerobic digester using pig slurry in South Korea. Only one strain, designated KOR-1, was characterized in detail. Cells of KOR-1 were straight or crooked rods, non-motile, 5 to 15 μm long and 0.7 μm wide. They stained Gram-positive and produced methane from H2+CO2 and formate. Strain KOR-1 grew optimally at 38°C. The optimum pH for growth was 7.0. The strain grew at 0.5% to 3.0% NaCl, with optimum growth at 2.5% NaCl. The G+C content of genomic DNA of strain KOR-1 was 41 mol%. The strain tolerated ampicillin, penicillin G, kanamycin and streptomycin but tetracycline inhibited cell growth. A large fragment of the 16S rRNA gene (~1,350 bp) was obtained from the isolate and sequenced. Comparison of 16S rRNA genes revealed that strain KOR-1 is related to Methanobacterium formicicum (98%, sequence similarity), Methanobacterium bryantii (95%) and Methanobacterium ivanovii (93%). Phylogenetic analysis of the deduced mcrA gene sequences confirmed the closest relative as based on mcrA gene sequence analysis was Methanobacterium formicicum strain (97% nucleic acid sequence identity). On the basis of physiological and phylogenetic characteristics, strain KOR-1 is proposed as a new strain within the genus Methanobacterium, Methanobacterium formicicum KOR-1.

  6. First Report of Clostridium lavalense Isolated in Human Blood Cultures

    Directory of Open Access Journals (Sweden)

    Richard Garceau

    2016-01-01

    Full Text Available An 88-year-old man was admitted to the hospital with worsening malaise, fever, and weakness. Anaerobic blood culture bottles revealed the presence of an anaerobic, Gram-positive sporulated bacillus. Empirical antibiotherapy with intravenous piperacillin-tazobactam was initiated. The patient defervesced after four days and was switched to oral amoxicillin on his 6th day of antibiotic therapy and later discharged from the hospital. Four months later, he had recovered. The bacterium was initially identified as Clostridium butyricum using anaerobic manual identification panel. 16S rRNA gene sequence and phylogenetic analysis showed the bacterium to be Clostridium lavalense, a recently described species with no previously published case of isolation in human diagnostic samples so far. This is the first report of Clostridium lavalense isolation from human blood cultures. Further studies are needed in order to elucidate the role of Clostridium lavalense in human disease and its virulence factors.

  7. Isolation and characterization of a novel biosurfactant produced by hydrocarbon-degrading bacterium Alcanivorax dieselolei B-5.

    Science.gov (United States)

    Qiao, N; Shao, Z

    2010-04-01

    Our goal was to identify a novel biosurfactant produced by a marine oil-degrading bacterium. Biosurfactants were produced by Alcanivorax dieselolei strain B-5(T) growing with diesel oil as the sole carbon and energy source. Culture supernatant was first extracted with chloroform/methanol (1:1, v/v), then further purified step by step with a normal phase silica gel column, a Sephadex LH20 gel column and a preparative thin layer plate. The main component was determined to be a lipopeptide; it was chemically characterized with nuclear magnetic resonance, liquid chromatography-quadrupole ion-trap mass spectrometry, amino acid analysis and GC-MS and was found to be a mixture of proline lipids. The monomers of the proline lipids were composed of a proline residue and a fatty acid (C(14:0), C(16:0) or C(18:0)). The critical micelle concentration of the mixed proline lipids was determined to be 40 mg l(-1). Moreover, activity variations in ranges of pH, temperature and salinity were also detected and showed reasonable stability. Alcanivorax dieselolei B-5 produced a novel linear lipoamino biosurfactant, characterized as a proline lipid. A proline lipid was characterized for the first time as a bacterial biosurfactant. This product has potential in both environmental and industrial applications.

  8. Isolation of a lactic acid bacterium and yeast consortium from a fermented material of Ulva spp. (Chlorophyta).

    Science.gov (United States)

    Uchida, M; Murata, M

    2004-01-01

    Microbiota in a fermented culture of Ulva spp. was examined with the objective to characterize the type of fermentation and to obtain starter microbes for performing seaweed fermentation. Fermented Ulva spp. cultures which were obtained and transferred in a laboratory were examined for their microbiota. With phenotypic characterization and phylogenetic analysis based on rRNA gene nucleotide sequences, the predominant micro-organisms were identified as Lactobacillus brevis, Debaryomyces hanseni var. hansenii, and a Candida zeylanoides-related specimen, suggesting that the observed fermentation can be categorized to lactic acid and ethanol fermentation. Inoculating the individually cultured cell suspensions of the three kinds of micro-organisms with cellulase induced the fermentation in various kinds of seaweed. A microbial consortium composed of a lactic acid bacterium, L. brevis, and yeasts, D. hansenii and a C. zeylanoides-related specimen, were predominant in a fermented culture of Ulva spp. Lactic acid and ethanol fermentation could be induced in various kinds of seaweed by adding this microbial consortium along with cellulase. This is the first report of lactic acid and ethanol fermentation in seaweed, which is expected to provide a new material for food and dietary applications.

  9. 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.

  10. Isolation and characterization of a new CO-utilizing strain, Thermoanaerobacter thermohydrosulfuricus subsp. carboxydovorans, isolated from a geothermal spring in Turkey

    NARCIS (Netherlands)

    Balk, M.; Heilig, G.H.J.; Eekert, van M.H.A.; Stams, A.J.M.; Rijpstra, W.I.C.; Sinninghe-Damsté, J.S.; Vos, de W.M.; Kengen, S.W.M.

    2009-01-01

    A novel anaerobic, thermophilic, Gram-positive, spore-forming, and sugar-fermenting bacterium (strain TLO) was isolated from a geothermal spring in Aya¿, Turkey. The cells were straight to curved rods, 0.4-0.6 mum in diameter and 3.5-10 mum in length. Spores were terminal and round. The temperature

  11. The fate of a nitrobenzene-degrading bacterium in pharmaceutical wastewater treatment sludge.

    Science.gov (United States)

    Ren, Yuan; Yang, Juan; Chen, Shaoyi

    2015-12-01

    This paper describes the fate of a nitrobenzene-degrading bacterium, Klebsiella oxytoca NBA-1, which was isolated from a pharmaceutical wastewater treatment facility. The 90-day survivability of strain NBA-1 after exposure to sludge under anaerobic and aerobic conditions was investigated. The bacterium was inoculated into sludge amended with glucose and p-chloronitrobenzene (p-CNB) to compare the bacterial community variations between the modified sludge and nitrobenzene amendment. The results showed that glucose had no obvious effect on nitrobenzene biodegradation in the co-metabolism process, regardless of the presence/absence of oxygen. When p-CNB was added under anaerobic conditions, the biodegradation rate of nitrobenzene remained unchanged although p-CNB inhibited the production of aniline. The diversity of the microbial community increased and NBA-1 continued to be one of the dominant strains. Under aerobic conditions, the degradation rate of both nitrobenzene and p-CNB was only 20% of that under anaerobic conditions. p-CNB had a toxic effect on the microorganisms in the sludge so that most of the DGGE (denaturing gradient gel electrophoresis) bands, including that of NBA-1, began to disappear under aerobic conditions after 90days of exposure. These data show that the bacterial community was stable under anaerobic conditions and the microorganisms, including NBA-1, were more resistant to the adverse environment. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Dehalogenimonas lykanthroporepellens gen. nov., sp. nov., a reductively dehalogenating bacterium isolated from chlorinated solvent-contaminated groundwater.

    Science.gov (United States)

    Moe, William M; Yan, Jun; Nobre, M Fernanda; da Costa, Milton S; Rainey, Fred A

    2009-11-01

    Two recently reported bacterial strains that are able to reductively dehalogenate polychlorinated aliphatic alkanes, including 1,2,3-trichloropropane, 1,2-dichloropropane, 1,1,2,2-tetrachloroethane, 1,1,2-trichloroethane and 1,2-dichloroethane, were further characterized to clarify their taxonomic position. The two strains, designated BL-DC-8 and BL-DC-9(T), were mesophilic, non-spore-forming, non-motile, Gram-negative staining and strictly anaerobic. Cells were irregular cocci, 0.3-0.6 mum in diameter. The two strains were resistant to ampicillin and vancomycin. Hydrogen was utilized as an electron donor. The genomic DNA G+C content of strains BL-DC-8 and BL-DC-9(T) was 54.0 and 53.8 mol%, respectively. The major cellular fatty acids were C(18 : 1)omega9c, C(16 : 1)omega9c, C(16 : 0) and C(14 : 0). Phylogenetic analyses based on 16S rRNA gene sequences indicated that the strains cluster within the phylum Chloroflexi, but are related only distantly to all recognized taxa in the phylum. Morphological, physiological and chemotaxonomic traits as well as phylogenetic analysis support the conclusion that these two strains represent a novel species of a new genus in the phylum Chloroflexi, for which the name Dehalogenimonas lykanthroporepellens gen. nov., sp. nov. is proposed. The type strain of Dehalogenimonas lykanthroporepellens is BL-DC-9(T) (=ATCC BAA-1523(T) =JCM 15061(T)).

  13. Helicobacter ganmani sp nov., a urease-negative anaerobe isolated from the intestines of laboratory mice

    DEFF Research Database (Denmark)

    Robertson, B.R.; O'Rourke, J.L.; Vandamme, P.

    2001-01-01

    and found to be identical to one another. H. rodentium was the most closely related species in terms of 16S rDNA sequence similarity (98.2%). Numerical analysis of whole-cell proteins by SDS-PAGE for nine isolates was carried out with a comparison to all known Helicobacter species, including newly...

  14. Antibiotic resistance genes in anaerobic bacteria isolated from primary dental root canal infections.

    Science.gov (United States)

    Rôças, Isabela N; Siqueira, José F

    2012-12-01

    Fourty-one bacterial strains isolated from infected dental root canals and identified by 16S rRNA gene sequence were screened for the presence of 14 genes encoding resistance to beta-lactams, tetracycline and macrolides. Thirteen isolates (32%) were positive for at least one of the target antibiotic resistance genes. These strains carrying at least one antibiotic resistance gene belonged to 11 of the 26 (42%) infected root canals sampled. Two of these positive cases had two strains carrying resistance genes. Six out of 7 Fusobacterium strains harbored at least one of the target resistance genes. One Dialister invisus strain was positive for 3 resistance genes, and 4 other strains carried two of the target genes. Of the 6 antibiotic resistance genes detected in root canal strains, the most prevalent were blaTEM (17% of the strains), tetW (10%), and ermC (10%). Some as-yet-uncharacterized Fusobacterium and Prevotella isolates were positive for blaTEM, cfxA and tetM. Findings demonstrated that an unexpectedly large proportion of dental root canal isolates, including as-yet-uncharacterized strains previously regarded as uncultivated phylotypes, can carry antibiotic resistance genes. Copyright © 2012 Elsevier Ltd. All rights reserved.

  15. Aeromonas veronii, a tributyltin (TBT)-degrading bacterium isolated from an estuarine environment, Ria de Aveiro in Portugal.

    Science.gov (United States)

    Cruz, Andreia; Caetano, Tânia; Suzuki, Satoru; Mendo, Sónia

    2007-12-01

    Organotin compounds are used in a variety of industrial processes therefore their subsequent discharge into the environment is widespread. Bacteria play an important role in biogeochemical transformations acting as natural decontamination agents. Therefore, screening for tributyltin (TBT)-resistant and -degrading bacteria is relevant for the selection of isolates with decontamination ability of these polluted areas. With this purpose, 50 strains were isolated from sediment and water from Ria de Aveiro and their tolerance to TBT, up to 3mM, was evaluated. Generally, occurrence of highly TBT-resistant bacteria was observed, and Gram negative bacteria exhibited more tolerance to TBT than Gram positive bacteria. A memory response was observed when bacteria were progressively exposed to increasingly higher TBT concentrations. One isolate, Aeromonas veronii Av27, highly resistant to TBT (3mM) uses this compound as carbon source and degrades it to less toxic compounds.

  16. Keratinase production and biodegradation of polluted secondary chicken feather wastes by a newly isolated multi heavy metal tolerant bacterium-Alcaligenes sp. AQ05-001.

    Science.gov (United States)

    Yusuf, Ibrahim; Ahmad, Siti Aqlima; Phang, Lai Yee; Syed, Mohd Arif; Shamaan, Nor Aripin; Abdul Khalil, Khalilah; Dahalan, Farrah Aini; Shukor, Mohd Yunus

    2016-12-01

    Biodegradation of agricultural wastes, generated annually from poultry farms and slaughterhouses, can solve the pollution problem and at the same time yield valuable degradation products. But these wastes also constitute environmental nuisance, especially in Malaysia where their illegal disposal on heavy metal contaminated soils poses a serious biodegradation issue as feather tends to accumulate heavy metals from the surrounding environment. Further, continuous use of feather wastes as cheap biosorbent material for the removal of heavy metals from effluents has contributed to the rising amount of polluted feathers, which has necessitated the search for heavy metal-tolerant feather degrading strains. Isolation, characterization and application of a novel heavy metal-tolerant feather-degrading bacterium, identified by 16S RNA sequencing as Alcaligenes sp. AQ05-001 in degradation of heavy metal polluted recalcitrant agricultural wastes, have been reported. Physico-cultural conditions influencing its activities were studied using one-factor-at-a-time and a statistical optimisation approach. Complete degradation of 5 g/L feather was achieved with pH 8, 2% inoculum at 27 °C and incubation period of 36 h. The medium optimisation after the response surface methodology (RSM) resulted in a 10-fold increase in keratinase production (88.4 U/mL) over the initial 8.85 U/mL when supplemented with 0.5% (w/v) sucrose, 0.15% (w/v) ammonium bicarbonate, 0.3% (w/v) skim milk, and 0.01% (w/v) urea. Under optimum conditions, the bacterium was able to degrade heavy metal polluted feathers completely and produced valuable keratinase and protein-rich hydrolysates. About 83% of the feathers polluted with a mixture of highly toxic metals were degraded with high keratinase activities. The heavy metal tolerance ability of this bacterium can be harnessed not only in keratinase production but also in the bioremediation of heavy metal-polluted feather wastes. Copyright © 2016. Published by

  17. Salirhabdus euzebyi gen. nov., sp. nov., a Gram-positive, halotolerant bacterium isolated from a sea salt evaporation pond.

    Science.gov (United States)

    Albuquerque, Luciana; Tiago, Igor; Rainey, Fred A; Taborda, Marco; Nobre, M Fernanda; Veríssimo, António; da Costa, Milton S

    2007-07-01

    A low-G+C, Gram-positive bacterium, designated CVS-14(T), was recovered from a sea salt evaporation pond on the island of Sal in the Cape Verde Archipelago. This organism was catalase- and oxidase-positive. Cells were motile, spore-forming aerobic rods, with an optimum growth temperature of about 35-40 degrees C and optimum pH between 7.0 and 8.5. Optimal growth occurred in media containing 4-6 % (w/v) NaCl, although the organism was able to grow in medium without added NaCl and in medium containing 16 % NaCl. The cell-wall peptidoglycan was of A1 gamma type and the major respiratory quinone was menaquinone 7 (MK-7). Major fatty acids were iso-15 : 0, anteiso-15 : 0, iso-17 : 0 and anteiso-17 : 0. The DNA G+C content was 37.0 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain CVS-14(T) formed a distinct new branch within the radiation of the moderately halophilic bacilli group, forming a separate lineage from species of the genera Salinibacillus, Paucisalibacillus, Oceanobacillus, Lentibacillus and Virgibacillus. Strain CVS-14(T) showed 16S rRNA gene pairwise similarity values of approximately 95 % with species of the genus Salinibacillus. On the basis of morphological, physiological, chemotaxonomic and phylogenetic characteristics, strain CVS-14(T) is considered to represent a novel species in a new genus, for which the name Salirhabdus euzebyi gen. nov., sp. nov. is proposed. The type strain is CVS-14(T) (=LMG 22839(T)=CIP 108577(T)).

  18. Savagea faecisuis gen. nov., sp. nov., a tylosin- and tetracycline-resistant bacterium isolated from a swine-manure storage pit.

    Science.gov (United States)

    Whitehead, Terence R; Johnson, Crystal N; Patel, Nisha B; Cotta, Michael A; Moore, Edward R B; Lawson, Paul A

    2015-07-01

    A polyphasic taxonomic study using morphological, biochemical, chemotaxonomic and molecular methods was performed on three strains of a Gram-stain positive, non-sporeforming, motile aerobic rod-shaped bacterium resistant to tylosin and tetracycline isolated from a swine-manure storage pit. On the basis of 16S rRNA gene sequence analyses, it was confirmed that these isolates are highly related to each other and form a hitherto unknown lineage within the Planococcaceae. In particular, pairwise analysis of the 16S rRNA gene sequence demonstrated that the novel organism is closely related to members of the genus Sporosarcina (92.8-94.5 %), Pyschrobacillus (93.5-93.9 %) and Paenisporosarcina (93.3-94.5 %). The predominant fatty acids were found to consist of iso-C15:0 and iso-C17:1 ω10c and the G+C mol% was determined to be 41.8. Based on biochemical, chemotaxonomic, and phylogenetic evidence, it is proposed that these novel strains be classified as a novel genus and species, Savagea faecisuis gen nov., sp. nov. The type strain is Con12(T) (=CCUG 63563(T) = NRRL B-59945(T) = NBRC 109956(T)).

  19. Desulfotignum toluenicum sp. nov., a novel toluene-degrading, sulphate-reducing bacterium isolated from an oil-reservoir model column.

    Science.gov (United States)

    Ommedal, Hege; Torsvik, Terje

    2007-12-01

    A Gram-negative, sulphate-reducing bacterium (strain H3(T)) was isolated from an oil-reservoir model column. The new isolate was able to oxidize toluene coupled to hydrogen sulphide production. For growth, the optimum salt concentration was 1.5 % (w/v), the optimum pH was 7.2 and the optimum temperature was 34 degrees C. The cells were straight to slightly curved rods, 0.6-1.0 microm in diameter and 1.4-2.5 microm in length. The predominant fatty acids were C(16 : 0), C(16 : 1)omega7c and C(17 : 0) cyclo, and the cells also contained dimethylacetals. Cloning and sequencing of a 1505 bp long fragment of the 16S rRNA gene showed that strain H3(T) is a member of the Deltaproteobacteria and is related closely to Desulfotignum balticum DSM 7044(T). The G+C content of the DNA was 52.0 mol% and the DNA-DNA similarity to D. balticum DSM 7044(T) was 56.1 %. Based on differences in DNA sequence and the unique property of toluene degradation, it is proposed that strain H3(T) should be designated a member of a novel species within the genus Desulfotignum, for which the name Desulfotignum toluenicum sp. nov. is proposed. The type strain is H3(T) (=DSM 18732(T)=ATCC BAA-1460(T)).

  20. Genome Sequence of Aeribacillus pallidus Strain GS3372, an Endospore-Forming Bacterium Isolated in a Deep Geothermal Reservoir

    OpenAIRE

    Sevasti Filippidou; Marion Jaussi; Thomas Junier; Tina Wunderlin; Nicole Jeanneret; Simona Regenspurg; Po-E Li; Chien-Chi Lo; Shannon Johnson; Kim McMurry; Cheryl D. Gleasner; Momchilo Vuyisich; Patrick S. Chain; Pilar Junier

    2015-01-01

    The genome of strain GS3372 is the first publicly available strain of Aeribacillus pallidus. This endospore-forming thermophilic strain was isolated from a deep geothermal reservoir. The availability of this genome can contribute to the clarification of the taxonomy of the closely related Anoxybacillus, Geobacillus, and Aeribacillus genera.

  1. Genome Sequence of Aeribacillus pallidus Strain GS3372, an Endospore-Forming Bacterium Isolated in a Deep Geothermal Reservoir.

    Science.gov (United States)

    Filippidou, Sevasti; Jaussi, Marion; Junier, Thomas; Wunderlin, Tina; Jeanneret, Nicole; Regenspurg, Simona; Li, Po-E; Lo, Chien-Chi; Johnson, Shannon; McMurry, Kim; Gleasner, Cheryl D; Vuyisich, Momchilo; Chain, Patrick S; Junier, Pilar

    2015-08-27

    The genome of strain GS3372 is the first publicly available strain of Aeribacillus pallidus. This endospore-forming thermophilic strain was isolated from a deep geothermal reservoir. The availability of this genome can contribute to the clarification of the taxonomy of the closely related Anoxybacillus, Geobacillus, and Aeribacillus genera. Copyright © 2015 Filippidou et al.

  2. Vibrio plantisponsor sp. nov., a diazotrophic bacterium isolated from a mangrove associated wild rice (Porteresia coarctata Tateoka)

    Digital Repository Service at National Institute of Oceanography (India)

    Rameshkumar, N.; Gomez-Gil, B.; Sproer, C.; Lang, E.; Kumar, N.D.; Krishnamurthi, S.; Nair, S.; Roque, A.

    similarity (Fig. 3), which indicates that these two isolates doesn’t belong to any strains of Diazotrophicus clade and further supporting the results of DNA-DNA relatedness. As it is has been previously shown that rep-PCR similarities around 65 % represent...

  3. Optimization of culturing conditions for isolated Arthrobacter sp. ZXY-2, an effective atrazine-degrading and salt-adaptive bacterium

    NARCIS (Netherlands)

    Zhao, X.; Wang, Li; Du, Linna; Yang, Jixian; Dong, Jing; Ma, Fang

    2017-01-01

    The increasing salinity in aquatic environments has had a negative impact on the biodegradation of atrazine, an extensively used herbicide which has been proven to pollute soil and water ecosystems. In the present study, a novel atrazine-degrading strain (ZXY-2) was isolated from industrial

  4. Draft Genome Sequence of Prevotella copri Isolated from the Gut of a Healthy Indian Adult

    OpenAIRE

    Bag, Satyabrata; Ghosh, Tarini Shankar; Das, Bhabatosh

    2017-01-01

    ABSTRACT Prevotella copri, a Gram-negative anaerobic rod-shaped bacterium, is frequently associated with the human gastrointestinal tract and influences host physiology, immunity, and metabolic pathways. In the present study, we report the draft genome sequence of P.?copri isolated from the gut of a healthy Indian adult.

  5. Draft Genome Sequence of Prevotella copri Isolated from the Gut of a Healthy Indian Adult

    Science.gov (United States)

    Bag, Satyabrata; Ghosh, Tarini Shankar

    2017-01-01

    ABSTRACT Prevotella copri, a Gram-negative anaerobic rod-shaped bacterium, is frequently associated with the human gastrointestinal tract and influences host physiology, immunity, and metabolic pathways. In the present study, we report the draft genome sequence of P. copri isolated from the gut of a healthy Indian adult. PMID:28912310

  6. Genome Sequence of Vibrio campbellii Strain UMTGB204, a Marine Bacterium Isolated from a Green Barrel Tunicate

    Science.gov (United States)

    Gan, Huan You; Noor, Mohd Ezhar Mohd; Saari, Nur Azna; Musa, Najiah; Mustapha, Baharim; Usup, Gires

    2015-01-01

    Vibrio campbellii strain UMTGB204 was isolated from a green barrel tunicate. The genome of this strain comprises 5,652,224 bp with 5,014 open reading frames, 9 rRNAs, and 116 tRNAs. It contains genes related to virulence and environmental tolerance. Gene clusters for the biosynthesis of nonribosomal peptides and bacteriocin were also identified. PMID:25814609

  7. Purification and characterization of a thermostable glutamate dehydrogenase from a thermophilic bacterium isolated from a sterilization drying oven

    Directory of Open Access Journals (Sweden)

    Maximiliano J. Amenábar

    2012-02-01

    Full Text Available Glutamate dehydrogenase from axenic bacterial cultures of anew microorganism, called GWE1, isolated from the interior ofa sterilization drying oven, was purified by anion-exchange andmolecular-exclusion liquid chromatography. The apparent molecularmass of the native enzyme was 250.5 kDa and wasshown to be an hexamer with similar subunits of molecularmass 40.5 kDa. For glutamate oxidation, the enzyme showedan optimal pH and temperature of 8.0 and 70oC, respectively.In contrast to other glutamate dehydrogenases isolated frombacteria, the enzyme isolated in this study can use both NAD+and NADP+ as electron acceptors, displaying more affinity forNADP+ than for NAD+. No activity was detected with NADHor NADPH, 2-oxoglutarate and ammonia. The enzyme was exceptionallythermostable, maintaining more than 70% of activityafter incubating at 100oC for more than five hours suggestingbeing one of the most thermoestable enzymes reported inthe family of dehydrogenases. [BMB reports 2012; 45(2: 91-95

  8. An efficient biosurfactant-producing bacterium Selenomonas ruminantium CT2, isolated from mangrove sediment in south of Thailand.

    Science.gov (United States)

    Saimmai, Atipan; Onlamool, Theerawat; Sobhon, Vorasan; Maneerat, Suppasil

    2013-01-01

    Biosurfactant-producing bacteria, isolate CT2, was isolated from mangrove sediment in the south of Thailand. The sequence of the 16S rRNA gene from isolate CT2 showed 100 % similarity with Selenomonas ruminantium. The highest biosurfactant production (5.02 g/l) was obtained when the cells were grown on minimal salt medium containing 15 g/l molasses and 1 g/l commercial monosodium glutamate supplemented with 1 g/l NaCl, 0.1 g/l leucine, 5 % (v/v) inoculum size at 30 °C and 150 rpm after 54 h of cultivation. The biosurfactant obtained by extraction with ethyl acetate showed high surface tension reduction (25.5 mN/m), a small CMC value (8 mg/l), thermal and pH stability with respect to surface tension reduction and emulsification activity and a high level of salt tolerance. The biosurfactant obtained was confirmed as a lipopeptide by using a biochemical test, FT-IR, MNR and mass spectrometry. The crude biosurfactant showed a broad spectrum of antimicrobial activity and also had the ability to emulsify oil and enhance PAHs solubility.

  9. Ruthenibacterium lactatiformans gen. nov., sp. nov., an anaerobic, lactate-producing member of the family Ruminococcaceae isolated from human faeces.

    Science.gov (United States)

    Shkoporov, Andrei N; Chaplin, Andrei V; Shcherbakova, Victoria A; Suzina, Natalia E; Kafarskaia, Lyudmila I; Bozhenko, Vladimir K; Efimov, Boris A

    2016-08-01

    Two novel strains of Gram-stain-negative, rod-shaped, obligately anaerobic, non-spore-forming, non-motile bacteria were isolated from the faeces of healthy human subjects. The strains, designated as 585-1T and 668, were characterized by mesophilic fermentative metabolism, production of d-lactic acid, succinic acid and acetic acid as end products of d-glucose fermentation, prevalence of C18 : 1ω9, C18 : 1ω9 aldehyde, C16 : 0 and C16 : 1ω7c fatty acids, presence of glycine, glutamic acid, lysine, alanine and aspartic acid in the petidoglycan peptide moiety and lack of respiratory quinones. Whole genome sequencing revealed the DNA G+C content was 56.4-56.6 mol%. The complete 16S rRNA gene sequences of the two strains shared 91.7/91.6 % similarity with Anaerofilum pentosovorans FaeT, 91.3/91.2 % with Gemmiger formicilis ATCC 27749T and 88.9/88.8 % with Faecalibacterium prausnitzii ATCC 27768T. On the basis of chemotaxonomic and genomic properties it was concluded that the strains represent a novel species in a new genus within the family Ruminococcaceae, for which the name Ruthenibacterium lactatiformans gen. nov., sp. nov. is proposed. The type strain of Ruthenibacterium lactatiformans is 585-1T (=DSM 100348T=VKM B-2901T).

  10. Efficient breaking of water/oil emulsions by a newly isolated de-emulsifying bacterium, Ochrobactrum anthropi strain RIPI5-1.

    Science.gov (United States)

    Mohebali, Ghasemali; Kaytash, Ashk; Etemadi, Narges

    2012-10-01

    Water-oil emulsions occur throughout oil production, transportation, and processing. The breaking of the water/oil emulsion improves oil quality and as a consequence chemically synthesized de-emulsifiers are commonly used in the petroleum industries. Microbial de-emulsifiers represent potential alternatives to the chemicals and may become important products for petroleum industries. The main goal of this work was isolation, identification, and characterization of an efficient de-emulsifying bacterium. Following a multi-step enrichment programme a de-emulsifying bacterium, Ochrobactrum anthropi strain RIPI5-1was isolated from the oil-polluted sandy bank of Siri Island, Iran. The presence of an oil phase in growth medium was found to be unnecessary for production of the de-emulsifier. The de-emulsifying activity of both the whole culture and the cells of this strain was examined using a model multiple water-crude oil (w/o/w) emulsion. This w/o/w emulsion was used for the first time in microbial de-emulsification research. Whole cells of strain RIPI5-1 exhibited high de-emulsifying activity during the late-exponential growth and stationary phases; de-emulsifying activity of the whole culture was highest during the early-exponential growth phase. The time course of de-emulsification by whole culture and whole cells of strain RIPI5-1 was investigated; the initial rate (DeI(1)) of breaking of the multiple water-crude oil emulsion by whole culture and whole cells was calculated as 11% and 54%, respectively. However, overall de-emulsification (DeI(8.5)) for whole culture and whole cells was calculated as 63% and 72%, respectively. A clear correlation was observed between cell surface hydrophobicity and the de-emulsifying activity of whole cells. With the water/kerosene emulsion, emulsion half-life (t(1/2)) was found to be oilfield emulsion. Copyright © 2012 Elsevier B.V. All rights reserved.

  11. Isolation and characterization of a bacterium which utilizes polyester polyurethane as a sole carbon and nitrogen source.

    Science.gov (United States)

    Nakajima-Kambe, T; Onuma, F; Kimpara, N; Nakahara, T

    1995-06-01

    Various soil samples were screened for the presence of microorganisms which have the ability to degrade polyurethane compounds. Two strains with good polyurethane degrading activity were isolated. The more active strain was tentatively identified as Comamonas acidovorans. This strain could utilize polyester-type polyurethanes but not the polyether-type polyurethanes as sole carbon and nitrogen sources. Adipic acid and diethylene glycol were probably the main degradation products when polyurethane was supplied as a sole carbon and nitrogen source. When ammonium nitrate was used as nitrogen source, only diethylene glycol was detected after growth on polyurethane.

  12. Isolation of a diphenylamine-degrading bacterium and characterization of its metabolic capacities, bioremediation and bioaugmentation potential.

    Science.gov (United States)

    Perruchon, Chiara; Batianis, Christos; Zouborlis, Stelios; Papadopoulou, Evangelia S; Ntougias, Spyridon; Vasileiadis, Sotirios; Karpouzas, Dimitrios G

    2015-12-01

    The antioxidant diphenylamine (DPA) is used in fruit-packaging plants for the control of the physiological disorder apple scald. Its use results in the production of DPA-contaminated wastewater which should be treated before finally discharged. Biological treatment systems using tailored-made microbial inocula with specific catabolic activities comprise an appealing and sustainable solution. This study aimed to isolate DPA-degrading bacteria, identify the metabolic pathway of DPA and evaluate their potential for future implementation in bioremediation and biodepuration applications. A Pseudomonas putida strain named DPA1 able to rapidly degrade and utilize DPA as the sole C and N source was enriched from a DPA-contaminated soil. The isolated strain degraded spillage-level concentrations of DPA in liquid culture (2000 mg L(-1)) and in contaminated soil (1000 mg kg(-1)) and metabolized DPA via the transient formation of aniline and catechol. Further evidence for the bioremediation and biodepuration potential of the P. putida strain DPA1 was provided by its capacity to degrade the post-harvest fungicide ortho-phenylphenol (OPP), concurrently used by the fruit-packaging plants, although at slower rates and DPA in a wide range of pH (4.5-9) and temperatures (15-37 °C). These findings revealed the high potential of the P. putida strain DPA1 for use in future soil bioremediation strategies and/or as start-up inocula in wastewater biodepuration systems.

  13. The potential of bacteria isolated from ruminal contents of seaweed-eating North Ronaldsay sheep to hydrolyse seaweed components and produce methane by anaerobic digestion in vitro.

    Science.gov (United States)

    Williams, Allan G; Withers, Susan; Sutherland, Alastair D

    2013-01-01

    The production of methane biofuel from seaweeds is limited by the hydrolysis of polysaccharides. The rumen microbiota of seaweed-eating North Ronaldsay sheep was studied for polysaccharidic bacterial isolates degrading brown-seaweed polysaccharides. Only nine isolates out of 65 utilized >90% of the polysaccharide they were isolated on. The nine isolates (eight Prevotella spp. and one Clostridium butyricum) utilized whole Laminaria hyperborea extract and a range of seaweed polysaccharides, including alginate (seven out of nine isolates), laminarin and carboxymethylcellulose (eight out of nine isolates); while two out of nine isolates additionally hydrolysed fucoidan to some extent. Crude enzyme extracts from three of the isolates studied further had diverse glycosidases and polysaccharidase activities; particularly against laminarin and alginate (two isolates were shown to have alginate lyase activity) and notably fucoidan and carageenan (one isolate). In serial culture rumen microbiota hydrolysed a range of seaweed polysaccharides (fucoidan to a notably lesser degree) and homogenates of L. hyperborea, mixed Fucus spp. and Ascophyllum nodosum to produce methane and acetate. The rumen microbiota and isolates represent potential adjunct organisms or enzymes which may improve hydrolysis of seaweed components and thus improve the efficiency of seaweed anaerobic digestion for methane biofuel production. © 2012 The Authors. Microbial Biotechnology © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

  14. In vitro efficacy of cefovecin against anaerobic bacteria isolated from subgingival plaque of dogs and cats with periodontal disease.

    Science.gov (United States)

    Khazandi, Manouchehr; Bird, Philip S; Owens, Jane; Wilson, Gary; Meyer, James N; Trott, Darren J

    2014-08-01

    Periodontal disease is a common disease of dogs and cats often requiring antimicrobial treatment as an adjunct to mechanical debridement. However, correct compliance with oral antimicrobial therapy in companion animals is often difficult. Cefovecin is a recently introduced veterinary cephalosporin that has demonstrated prolonged concentrations in extracellular fluid, allowing for dosing intervals of up to 14 days. Subgingival samples were collected from the oral cavity of 29 dogs and eight cats exhibiting grade 2 or grade 3 periodontal disease. Samples were cultivated on Wilkin Chalgrens agar and incubated in an anaerobic chamber for seven days. Selected anaerobic bacteria were isolated and identified to species level using 16S rRNA gene sequence analysis. Minimum inhibitory concentrations were determined for cefovecin and six additional antimicrobials using the agar dilution methodology recommended by the Clinical and Laboratory Standards Institute. The 65 clinical isolates were identified as Porphyromonas gulae (n = 45), Porphyromonas crevioricanis (n = 12), Porphyromonas macacae (n = 1), Porphyromonas cangingivalis (n = 1) Fusobacterium nucleatum (n = 2), Fusobacterium russii (n = 1) and Solobacterium moorei (n = 3). This is the first report of S. moorei being isolated from companion animals with periodontal disease. All isolates were highly susceptible to cefovecin, with a MIC90 of ≤0.125 μg/ml. Conversely, different resistance rates to ampicillin, amoxicillin and erythromycin between isolates were detected. Cefovecin is thus shown to be effective in vitro against anaerobic bacteria isolated from dogs and cats with periodontal disease. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. 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.

  16. Bacillus lindianensis sp. nov., a novel alkaliphilic and moderately halotolerant bacterium isolated from saline and alkaline soils.

    Science.gov (United States)

    Dou, Guiming; Liu, Hongcan; He, Wei; Ma, Yuchao

    2016-01-01

    Two alkaliphilic and halotolerant Gram-stain positive, rod-shaped and endospore-forming bacteria, designated strains 12-3(T) and 12-4, were isolated from saline and alkaline soils collected in Lindian county, Heilongjiang province, China. Both strains were observed to grow well at a wide range of temperature and pH values, 10-45 °C and pH 8-12, with optimal growth at 37 °C and pH 9.0, respectively. Growth of the two strains was found to occur at total salt concentrations of 0-12 % (w/v), with an optimum at 4 % (w/v). The G+C contents of the genomic DNA of strains 12-3(T) and 12-4 were determined to be 42.7 and 42.4 mol%, respectively, and the major cellular fatty acids were identified as anteiso-C15:0 and anteiso-C17:0. In isolate 12-3(T), meso-diaminopimelic acid was found to be the diagnostic diamino acid of the cell wall peptidoglycan; diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol were identified as the major cellular polar lipids; and menaquinone-7 was identified as the predominant isoprenoid quinone. Strains 12-3(T) and 12-4 share very close 16S rRNA gene sequence similarity (99.74 %) and their DNA-DNA relatedness was 95.3 ± 0.63 %, meaning that the two strains can be considered to belong to the same species. 16S rRNA gene sequence-based phylogenetic analysis revealed strains 12-3(T) and 12-4 exhibit high similarities to Bacillus pseudofirmus DSM 8715(T) (98.7 %), Bacillus marmarensis DSM 21297(T) (97.2 %) and Bacillus nanhaiisediminis CGMCC 1.10116(T) (97.1 and 97.0 %, respectively). DNA-DNA hybridization values between isolate 12-3(T) and the type strains of closely related Bacillus species were below 30 %. On the basis of the polyphasic evidence presented, strains 12-3(T) and 12-4 are considered to represent a novel species of the genus Bacillus, for which the name Bacillus lindianensis sp. nov. is proposed. The type strain is 12-3(T) (DSM 26864(T) = CGMCC 1.12717(T)).

  17. Assessment of Bioflocculant Production by Bacillus sp. Gilbert, a Marine Bacterium Isolated from the Bottom Sediment of Algoa Bay

    Directory of Open Access Journals (Sweden)

    Okoh I. Anthony

    2011-07-01

    Full Text Available The bioflocculant-producing potentials of a marine bacteria isolated from the bottom sediment of Algoa Bay was investigated using standard methods. The 16S rDNA sequence analysis revealed 98% similarity to that of Bacillus sp. HXG-C1 and the nucleotide sequence was deposited in GenBank as Bacillus sp. Gilbert with accession number HQ537128. Bioflocculant was optimally produced when sucrose (72% flocculating activity and ammonium chloride (91% flocculating activity were used as sole sources of carbon and nitrogen, respectively; an initial pH 6.2 of the production medium; and Mg2+ as cation. Chemical analysis of the purified bioflocculant revealed the compound to be a polysaccharide.

  18. Isolation and characterization of phenol degrading bacterium strain Bacillus thuringiensis J20 from olive waste in Palestine.

    Science.gov (United States)

    Ereqat, Suheir I; Abdelkader, Ahmad A; Nasereddin, Abedelmajeed F; Al-Jawabreh, Amer O; Zaid, Taher M; Letnik, Ilya; Abdeen, Ziad A

    2018-01-02

    This study aimed at isolation of phenol degrading bacteria from olive mill wastes in Palestine. The efficiency of phenol removal and factors affecting phenol degradation were investigated. A bacterial strain (J20) was isolated from solid olive mill waste and identified as Bacillus thuringiensis based on standard morphological, biochemical characteristics and 16SrRNA sequence analysis. The strain was able to grow in a phenol concentration of 700 mg/L as the sole carbon and energy source. The culture conditions showed a significant impact on the ability of these cells to remove phenol. This strain exhibited optimum phenol degradation performance at pH 6.57 and 30 °C . Under the optimized conditions, this strain could degrade 88.6% of phenol (700 mg/L) within 96 h when the initial cell density was OD 600 0.2. However, the degradation efficiency could be improved from about 88% to nearly 99% by increasing the cell density. Immobilization of J20 was carried out using 4% sodium alginate. Phenol degradation efficiency of the immobilized cells of J20 was higher than that of the free cells, 100% versus 88.6% of 700 mg/L of phenol in 120 h, indicating the improved tolerance of the immobilized cells toward phenol toxicity. The J20 was used in detoxifying crude OMWW, phenolic compounds levels were reduced by 61% compared to untreated OMWW after five days of treatment. Hence, B. thuringiensis-J20 can be effectively used for bioremediation of phenol-contaminated sites in Palestine. These findings may lead to new biotechnological applications for the degradation of phenol, related to olive oil production.

  19. 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 ).

  20. Decolorization of textile azo dye and Congo red by an isolated strain of the dissimilatory manganese-reducing bacterium Shewanella xiamenensis BC01.

    Science.gov (United States)

    Ng, I-Son; Chen, Tingting; Lin, Rong; Zhang, Xia; Ni, Chao; Sun, Dongzhe

    2014-03-01

    Shewanella xiamenensis BC01 (SXM) was isolated from sediment collected off Xiamen, China and was identified based on the phylogenetic tree of 16S rRNA sequences and the gyrB gene. This strain showed high activity in the decolorization of textile azo dyes, especially methyl orange, reactive red 198, and recalcitrant dye Congo red, decolorizing at rates of 96.2, 93.0, and 87.5%, respectively. SXM had the best performance for the specific decolorization rate (SDR) of azo dyes compared to Proteus hauseri ZMd44 and Aeromonas hydrophila NIU01 strains and had an SDR similar to Shewanella oneidensis MR-1 in Congo red decolorization. Luria-Bertani medium was the optimal culture medium for SXM, as it reached a density of 4.69 g-DCW L(-1) at 16 h. A mediator (manganese) significantly enhanced the biodegradation and flocculation of Congo red. Further analysis with UV-VIS, Fourier Transform Infrared spectroscopy, and Gas chromatography-mass spectrometry demonstrated that Congo red was cleaved at the azo bond, producing 4,4'-diamino-1,1'-biphenyl and 1,2'-diamino naphthalene 4-sulfonic acid. Finally, SEM results revealed that nanowires exist between the bacteria, indicating that SXM degradation of the azo dyes was coupled with electron transfer through the nanowires. The purpose of this work is to explore the utilization of a novel, dissimilatory manganese-reducing bacterium in the treatment of wastewater containing azo dyes.

  1. Insights into the extremotolerance of Acinetobacter radioresistens 50v1, a gram-negative bacterium isolated from the Mars Odyssey spacecraft.

    Science.gov (United States)

    McCoy, K B; Derecho, I; Wong, T; Tran, H M; Huynh, T D; La Duc, M T; Venkateswaran, K; Mogul, R

    2012-09-01

    The microbiology of the spacecraft assembly process is of paramount importance to planetary exploration, as the biological contamination that can result from remote-enabled spacecraft carries the potential to impact both life-detection experiments and extraterrestrial evolution. Accordingly, insights into the mechanisms and range of extremotolerance of Acinetobacter radioresistens 50v1, a Gram-negative bacterium isolated from the surface of the preflight Mars Odyssey orbiter, were gained by using a combination of microbiological, enzymatic, and proteomic methods. In summary, A. radioresistens 50v1 displayed a remarkable range of survival against hydrogen peroxide and the sequential exposures of desiccation, vapor and plasma phase hydrogen peroxide, and ultraviolet irradiation. The survival is among the highest reported for non-spore-forming and Gram-negative bacteria and is based upon contributions from the enzyme-based degradation of H(2)O(2) (catalase and alkyl hydroperoxide reductase), energy management (ATP synthase and alcohol dehydrogenase), and modulation of the membrane composition. Together, the biochemical and survival features of A. radioresistens 50v1 support a potential persistence on Mars (given an unintended or planned surface landing of the Mars Odyssey orbiter), which in turn may compromise the scientific integrity of future life-detection missions.

  2. 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).

  3. 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.

  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. Photosynthetic inhibition and oxidative stress to the toxic Phaeocystis globosa caused by a diketopiperazine isolated from products of algicidal bacterium metabolism.

    Science.gov (United States)

    Tan, Shuo; Hu, Xiaoli; Yin, Pinghe; Zhao, Ling

    2016-05-01

    Algicidal bacteria have been turned out to be available for inhibiting Phaeocystis globosa which frequently caused harmful algal blooms and threatened to economic development and ecological balance. A marine bacterium Bacillus sp. Ts-12 exhibited significant algicidal activity against P. globosa by indirect attack. In present study, an algicidal compound was isolated by silica gel column, Sephadex G-15 column and HPLC, further identified as hexahydropyrrolo[1,2-a]pyrazine-1,4-dione, cyclo-(Pro-Gly), by GC-MS and (1)H-NMR. Cyclo-(Pro-Gly) significantly increased the level of reactive oxygen species (ROS) within P. globosa cells, further activating the enzymatic and non-enzymatic antioxidant systems, including superoxide dismutase (SOD), catalase (CAT), glutathione (GSH) and ascorbic acid (AsA). The increase in methane dicarboxylic aldehyde (MDA) content showed that the surplus ROS induced lipid peroxidation on membrane system. Transmission electron microscope (TEM) and flow cytometry (FCM) analysis revealed that cyclo-(Pro-Gly) caused reduction of Chl-a content, destruction of cell membrane integrity, chloroplasts and nuclear structure. Real-time PCR assay showed that the transcriptions of photosynthesis related genes (psbA, psbD, rbcL) were significantly inhibited. This study indicated that cyclo-(Pro-Gly) from marine Bacillus sp. Ts-12 exerted photosynthetic inhibition and oxidative stress to P. globosa and eventually led to the algal cells lysis. This algicidal compound might be potential bio-agent for controlling P. globosa red tide.

  6. Isolation of Bioactive Phenazine-1-Carboxamide from the Soil Bacterium Pantoea agglomerans and Study of Its Anticancer Potency on Different Cancer Cell Lines.

    Science.gov (United States)

    Ali, Hayssam M; El-Shikh, Mohamed S; Salem, Mohamed Z M; M, Muzaheed

    2016-09-01

    The study was designed to investigate the anticancer effect of phenazine-1-carboxamide (PCN) isolated from the bacterium Pantoea agglomerans naturally present in soil. PCN showed cytotoxicity in a dose-dependent manner, and inhibitory concentrations on the cancer cell lines A549, HeLa, and SW480 were between 32 and 40 μM. Significantly increased concentrations of lactate dehydrogenase were found with increasing concentrations of PCN, which resulted in increased destruction of the cancer cell membrane. A significantly increased p53 level was accompanied by the increased production of cytochrome c protein in all cancer cell lines studied. This condition in cells leads to the overexpression of caspase 3 and Bcl-2 family proteins. Upregulation and downregulation of proapoptotic and antiproapoptotic proteins were analyzed for their messenger RNA and protein expression. The activation of caspases and their cleavage compounds paves the way for the complete apoptosis process in cancer cells. We conclude that P. agglomerans-derived PCN acts as an effective anticancer drug or compound.

  7. 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; Huang, Xiaoli; Du, Xue; Wang, Chang'an; Li, Jinnan; Wang, Liansheng

    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. PMID:27840823

  8. Characterization of Fe (III)-reducing enrichment culture and isolation of Fe (III)-reducing bacterium Enterobacter sp. L6 from marine sediment.

    Science.gov (United States)

    Liu, Hongyan; Wang, Hongyu

    2016-07-01

    To enrich the Fe (III)-reducing bacteria, sludge from marine sediment was inoculated into the medium using Fe (OH)3 as the sole electron acceptor. Efficiency of Fe (III) reduction and composition of Fe (III)-reducing enrichment culture were analyzed. The results indicated that the Fe (III)-reducing enrichment culture with the dominant bacteria relating to Clostridium and Enterobacter sp. had high Fe (III) reduction of (2.73 ± 0.13) mmol/L-Fe (II). A new Fe (III)-reducing bacterium was isolated from the Fe (III)-reducing enrichment culture and identified as Enterobacter sp. L6 by 16S rRNA gene sequence analysis. The Fe (III)-reducing ability of strain L6 under different culture conditions was investigated. The results indicated that strain L6 had high Fe (III)-reducing activity using glucose and pyruvate as carbon sources. Strain L6 could reduce Fe (III) at the range of NaCl concentrations tested and had the highest Fe (III) reduction of (4.63 ± 0.27) mmol/L Fe (II) at the NaCl concentration of 4 g/L. This strain L6 could reduce Fe (III) with unique properties in adaptability to salt variation, which indicated that it can be used as a model organism to study Fe (III)-reducing activity isolated from marine environment. Copyright © 2015 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  9. Isolation of genes coding for chitin-degrading enzymes in the novel chitinolytic bacterium, Chitiniphilus shinanonensis, and characterization of a gene coding for a family 19 chitinase.

    Science.gov (United States)

    Huang, Lanxiang; Garbulewska, Ewelina; Sato, Kazuaki; Kato, Yuichi; Nogawa, Masahiro; Taguchi, Goro; Shimosaka, Makoto

    2012-03-01

    Chitiniphilus shinanonensis type strain SAY3(T) is a strongly chitinolytic bacterium, originally isolated from the moat water in Ueda, Japan. To elucidate the chitinolytic activity of this strain, 15 genes (chiA-chiO) coding for putative chitin-degrading enzymes were isolated from a genomic library. Sequence analysis revealed the genes comprised 12 family 18 chitinases, a family 19 chitinase, a family 20 β-N-acetylglucosaminidase, and a polypeptide with a chitin-binding domain but devoid of a catalytic domain. Two operons were detected among the sequences: chiCDEFG and chiLM. The gene coding for the polypeptide (chiN) showed sequence similarity to family 19 chitinases and was successfully expressed in Escherichia coli. ChiN demonstrated a multi-domain structure, composed of the N-terminal, two chitin-binding domains connected by a Pro- and Thr-rich linker, and a family 19 catalytic domain located at the C-terminus. The recombinant protein rChiN catalyzed an endo-type cleavage of N-acetyl-d-glucosamine oligomers, and also degraded insoluble chitin and soluble chitosan (degree of deacetylation of 80%). rChiN exhibited an inhibitory effect on hyphal growth of the fungus Trichoderma reesei. The chitin-binding domains of ChiN likely play an important role in the degradation of insoluble chitin, and are responsible for a growth inhibitory effect on fungi. Copyright © 2011 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  10. Polyhydroxyalkanoate production by a novel bacterium Massilia sp. UMI-21 isolated from seaweed, and molecular cloning of its polyhydroxyalkanoate synthase gene.

    Science.gov (United States)

    Han, Xuerong; Satoh, Yasuharu; Kuriki, Yumi; Seino, Teruyuki; Fujita, Shinji; Suda, Takanori; Kobayashi, Takanori; Tajima, Kenji

    2014-11-01

    We successfully isolated one microorganism (UMI-21) from Ulva, a green algae that contains starch. The strain UMI-21 can produce polyhydroxyalkanoate (PHA) from starch, maltotriose, or maltose as a sole carbon source. Taxonomic studies and 16S rDNA sequence analysis revealed that strain UMI-21 was phylogenetically related to species of the genus Massilia. The PHA content under the cultivation condition using a 10-L jar fermentor was 45.5% (w/w). This value was higher than that obtained after cultivation in a flask, suggesting the possibility of large-scale PHA production by UMI-21 from starch. A major issue for the industrial production of microbial PHAs is the very high production cost. Starch is a relatively inexpensive substrate that is also found in abundant seaweeds such as Ulva. Therefore, the strain isolated in this study may be very useful for producing PHA from seaweeds containing polysaccharides such as starch. In addition, a 3.7-kbp DNA fragment containing the whole PHA synthase gene (phaC) was obtained from the strain UMI-21. The results of open reading frame (ORF) analysis suggested that the DNA fragment contained two ORFs, which were composed of 1740 (phaC) and 564 bp (phaR). The deduced amino acid sequence of PhaC from strain UMI-21 shared high similarity with PhaC from Ralstonia eutropha, which is a representative PHA-producing bacterium with a class I PHA synthase. This is the first report for the cloning of the PHA synthase gene from Massilia species. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  11. Isolation and Characterization of Novel Denitrifying Bacterium sp. SG-01 Strain from Wood Chips Composted with Swine Manure

    Directory of Open Access Journals (Sweden)

    Seung-Hak Yang

    2013-11-01

    Full Text Available Nitrate contamination in ground and surface water is an increasingly serious environmental problem and only a few bacterial strains have been identified that have the ability to remove nitrogen pollutants from wastewater under thermophilic conditions. We therefore isolated thermophilic facultative bacterial strains from wood chips that had been composted with swine manure under aerated high temperature conditions so as to identify strains with denitrifying ability. Nine different colonies were screened and 3 long rod-shaped bacterial strains designated as SG-01, SG-02, and SG-03 were selected. The strain SG-01 could be differentiated from SG-02 and SG-03 on the basis of the method that it used for sugar utilization. The 16S rRNA genes of this strain also had high sequence similarity with Geobacillus thermodenitrificans 465T (99.6%. The optimal growth temperatures (55°C, pH values (pH 7.0, and NaCl concentrations (1% required for the growth of strain SG-01 were established. This strain reduced 1.18 mM nitrate and 1.45 mM nitrite in LB broth after 48 h of incubation. These results suggest that the G. thermodenitrificans SG-01 strain may be useful in the removal of nitrates and nitrites from wastewater generated as a result of livestock farming.

  12. Complete genome of Phenylobacterium zucineum – a novel facultative intracellular bacterium isolated from human erythroleukemia cell line K562

    Directory of Open Access Journals (Sweden)

    Sun Jie

    2008-08-01

    Full Text Available Abstract Background Phenylobacterium zucineum is a recently identified facultative intracellular species isolated from the human leukemia cell line K562. Unlike the known intracellular pathogens, P. zucineum maintains a stable association with its host cell without affecting the growth and morphology of the latter. Results Here, we report the whole genome sequence of the type strain HLK1T. The genome consists of a circular chromosome (3,996,255 bp and a circular plasmid (382,976 bp. It encodes 3,861 putative proteins, 42 tRNAs, and a 16S-23S-5S rRNA operon. Comparative genomic analysis revealed that it is phylogenetically closest to Caulobacter crescentus, a model species for cell cycle research. Notably, P. zucineum has a gene that is strikingly similar, both structurally and functionally, to the cell cycle master regulator CtrA of C. crescentus, and most of the genes directly regulated by CtrA in the latter have orthologs in the former. Conclusion This work presents the first complete bacterial genome in the genus Phenylobacterium. Comparative genomic analysis indicated that the CtrA regulon is well conserved between C. crescentus and P. zucineum.

  13. 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)).

  14. Optimization of copper, lead and cadmium biosorption onto newly isolated bacterium using a Box-Behnken design.

    Science.gov (United States)

    Choińska-Pulit, Anna; Sobolczyk-Bednarek, Justyna; Łaba, Wojciech

    2018-03-01

    Due to the progressive development of industrial and technological activities, heavy metal contamination is increasing each year and it poses a serious health and environmental risk. Microorganisms are capable of removing heavy metals from a contaminated environment. In this work, 51 microbial strains were isolated from heavy metal contaminated water and soil. The JAW1 strain, identified as Pseudomonas azotoformans, was selected and applied in bioremediation of the specific mixture of metals (Cd, Cu, and Pb) in an aqueous medium. The Box-Behnken design was used to optimize the biosorption process, with three factors: pH, initial metal concentration, concentration of the biosorbent. For the strain P. azotoformans JAW1, the optimal conditions were pH = 6.0, 25mg/L of each metal and 2g/L, following removal levels were achieved: Cd 44,67%; Cu 63,32%; Pb 78,23%. The possible interactions of cell-metal ions were evaluated using FT-IR analysis. The study indicated the presence of groups, which may be responsible for bonding of metal ions. The studies conducted on bioremediation mechanisms indicated that metal accumulation could occur on the cell surface (biosorption) where the amount of adsorbed metals reached: Cd 98,57%, Cu 69,76%, Pb 88,58%. P. azotoformans JAW1 exhibited a potential for application in the bioremediation of mining wastewater with complex metal contaminations. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. Screening and characterizing a denitrifying phosphorus-accumulating bacterium isolated from a circular plug-flow reactor.

    Science.gov (United States)

    Xie, En; Ding, Aizhong; Zheng, Lei; Dou, Junfeng; Anderson, Bruce; Huang, Xiaolong; Jing, Ruoting

    2016-11-01

    Denitrifying phosphorus-accumulating organisms (DNPAO) are viewed as one of the most effective means to solve the removal contradiction of nitrogen and phosphorus in wastewater treatment. In this study, we isolated a DNPAO (C-17, accession number: KU745702) from activated sludge in a patented circular plug-flow reactor, physiologically to Pseudomonas sp. based on 16S rRNA sequence and phenotypic characteristics. The results of denitrifying phosphorus-accumulating experiment showed that Pseudomonas C-17 has high removal efficiencies for [Formula: see text] and NO3-N, 75% and 87%, respectively. The ratio of phosphorus release was 25.0 mg [Formula: see text] (with anabolism) and 26.8 mg [Formula: see text] (without anabolism), respectively. Our results indicated that Pseudomonas C-17 had strong capacity of phosphorus release, and its uptake is often imprecisely evaluated by ignoring the part of metabolic consumption. Pseudomonas C-17 is capable of utilizing oxygen, nitrate and nitrite as electron acceptors under experimental conditions.

  16. A low cost fermentation medium for potential fibrinolytic enzyme production by a newly isolated marine bacterium, Shewanella sp. IND20

    Directory of Open Access Journals (Sweden)

    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.

  17. The isolation and characterization of new C. thermocellum strains and the evaluation of multiple anaerobic digestion systems

    Science.gov (United States)

    Lv, Wen

    The overall objective of my research was to improve the efficiencies of bioconversions that produce renewable energy from lignocellulosic biomass. To this end, my studies addressed issues important to two promising strategies: consolidated bioprocessing (CBP) and anaerobic digestion (AD). CBP achieves saccharolytic enzyme production, hydrolysis, and fermentation in a single step and is considered to be the most cost-effective model. Anaerobic bacteria that can be used in CBP are highly desirable. To that end, two thermophilic and cellulolytic bacterial strains were isolated and characterized (Chapter 3). Based on 16S rRNA gene sequence analysis, both strains CS7 and CS8 are closely related to Clostridium thermocellum ATCC 27405. However, they had significantly higher specific cellulase activities and ethanol/acetate ratios than C. thermocellum ATCC 27405. As a result, CS7 and CS8 are two new highly cellulolytic and ethanologenic C. thermocellum strains, with application potentials in research and development of CBP. As some of the most promising AD processes, two temperature-phased AD (TPAD) systems, in comparison with a thermophilic single-stage AD (TSAD) system and a mesophilic two-stage AD (MTAD) system, were studied in treating high-strength dairy cattle manure. The TPAD systems, with the thermophilic digesters acidified (AT-TPAD, Chapter 4) or operated at neutral pH (NT-TPAD, Chapter 5), were optimized at the thermophilic temperature of 50°C and a volume ratio between the thermophilic and the mesophilic digesters of 1:2. Despite similar methane productions, the NT-TPAD system achieved significantly higher volatile solid (VS) removal than the AT-TPAD system and needed no external pH adjustments (Chapter 6). At the same overall OLR, the TSAD system achieved the highest performance, followed by the NT-TPAD and the MTAD systems (Chapter 7). Each digester harbored distinct yet dynamic microbial populations, some of which were significantly correlated or associated

  18. Draft Genome Sequence ofPrevotella copriIsolated from the Gut of a Healthy Indian Adult.

    Science.gov (United States)

    Bag, Satyabrata; Ghosh, Tarini Shankar; Das, Bhabatosh

    2017-09-14

    Prevotella copri , a Gram-negative anaerobic rod-shaped bacterium, is frequently associated with the human gastrointestinal tract and influences host physiology, immunity, and metabolic pathways. In the present study, we report the draft genome sequence of P. copri isolated from the gut of a healthy Indian adult. Copyright © 2017 Bag et al.

  19. 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.

  20. Isolation and characterization of an agaro-oligosaccharide (AO)-hydrolyzing bacterium from the gut microflora of Chinese individuals.

    Science.gov (United States)

    Li, Miaomiao; Li, Guangsheng; Zhu, Liying; Yin, Yeshi; Zhao, Xiaoliang; Xiang, Charlie; Yu, Guangli; Wang, Xin

    2014-01-01

    Agarose (AP) from red algae has a long history as food ingredients in East Asia. Agaro-oligosaccharides (AO) derived from AP have shown potential prebiotic effects. However, the human gut microbes responsible for the degradation of AO and AP have not yet been fully investigated. Here, we reported that AO and AP can be degraded and utilized at various rates by fecal microbiota obtained from different individuals. Bacteroides uniformis L8 isolated from human feces showed a pronounced ability to degrade AO and generate D-galactose as its final end product. PCR-DGGE analysis showed B. uniformis to be common in the fecal samples, but only B. uniformis L8 had the ability to degrade AO. A synergistic strain, here classified as Escherichia coli B2, was also identified because it could utilize the D-galactose as the growth substrate. The cross-feeding interaction between B. uniformis L8 and E. coli B2 led to exhaustion of the AO supply. Bifidobacterium infantis and Bifidobacterium adolescentis can utilize one of the intermediates of AO hydrolysis, agarotriose. Growth curves indicated that AO was the substrate that most favorably sustained the growth of B. uniformis L8. In contrast, κ-carrageenan oligosaccharides (KCO), guluronic acid oligosaccharides (GO), and mannuronic acid oligosaccharides (MO) were found to be unusable to B. uniformis L8. Current results indicate that B. uniformis L8 is a special degrader of AO in the gut microbiota. Because B. uniformis can mitigate high-fat-diet-induced metabolic disorders, further study is required to determine the potential applications of AO.

  1. Molecular identification of phosphate solubilizing bacterium ...

    African Journals Online (AJOL)

    A phosphate solubilizing bacterium was isolated from the rhizosphere soil of upland rice and identified by 16S rRNA gene sequencing. The gene sequence showed 99% homology with Alcaligenes faecalis. Based on the gene sequence homology, it was identified as A. faecalis. Interaction effect of this bacterium on growth ...

  2. 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

    2018-03-01

    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 LMG3413 T , 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

  3. 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.

  4. Genome analysis of the Anerobic Thermohalophilic bacterium Halothermothrix orenii

    Energy Technology Data Exchange (ETDEWEB)

    Mavromatis, Konstantinos; Ivanova, Natalia; Anderson, Iain; Lykidis, Athanasios; Hooper, Sean D.; Sun, Hui; Kunin, Victor; Lapidus, Alla; Hugenholtz, Philip; Patel, Bharat; Kyrpides, Nikos C.

    2008-11-03

    Halothermothirx orenii is a strictly anaerobic thermohalophilic bacterium isolated from sediment of a Tunisian salt lake. It belongs to the order Halanaerobiales in the phylum Firmicutes. The complete sequence revealed that the genome consists of one circular chromosome of 2578146 bps encoding 2451 predicted genes. This is the first genome sequence of an organism belonging to the Haloanaerobiales. Features of both Gram positive and Gram negative bacteria were identified with the presence of both a sporulating mechanism typical of Firmicutes and a characteristic Gram negative lipopolysaccharide being the most prominent. Protein sequence analyses and metabolic reconstruction reveal a unique combination of strategies for thermophilic and halophilic adaptation. H. orenii can serve as a model organism for the study of the evolution of the Gram negative phenotype as well as the adaptation under thermohalophilic conditions and the development of biotechnological applications under conditions that require high temperatures and high salt concentrations.

  5. Perchlorate reduction by a novel chemolithoautotrophic, hydrogen-oxidizing bacterium.

    Science.gov (United States)

    Zhang, Husen; Bruns, Mary Ann; Logan, Bruce E

    2002-10-01

    Water treatment technologies are needed that can remove perchlorate from drinking water without introducing organic chemicals that stimulate bacterial growth in water distribution systems. Hydrogen is an ideal energy source for bacterial degradation of perchlorate as it leaves no organic residue and is sparingly soluble. We describe here the isolation of a perchlorate-respiring, hydrogen-oxidizing bacterium (Dechloromonas sp. strain HZ) that grows with carbon dioxide as sole carbon source. Strain HZ is a Gram-negative, rod-shaped facultative anaerobe that was isolated from a gas-phase anaerobic packed-bed biofilm reactor treating perchlorate-contaminated groundwater. The ability of strain HZ to grow autotrophically with carbon dioxide as the sole carbon source was confirmed by demonstrating that biomass carbon (100.9%) was derived from CO2. Chemolithotrophic growth with hydrogen was coupled with complete reduction of perchlorate (10 mM) to chloride with a maximum doubling time of 8.9 h. Strain HZ also grew using acetate as the electron donor and chlorate, nitrate, or oxygen (but not sulphate) as an electron acceptor. Phylogenetic analysis of the 16S rRNA sequence placed strain HZ in the genus Dechloromonas within the beta subgroup of the Proteobacteria. The study of this and other novel perchlorate-reducing bacteria may lead to new, safe technologies for removing perchlorate and other chemical pollutants from drinking water.

  6. Genome Sequence and Mutational Analysis of Plant-Growth-Promoting Bacterium Agrobacterium tumefaciens CCNWGS0286 Isolated from a Zinc-Lead Mine Tailing

    Science.gov (United States)

    Hao, Xiuli; Xie, Pin; Johnstone, Laurel; Miller, Susan J.

    2012-01-01

    The plant-growth-promoting bacterium Agrobacterium tumefaciens CCNWGS0286, isolated from the nodules of Robinia pseudoacacia growing in zinc-lead mine tailings, both displayed high metal resistance and enhanced the growth of Robinia plants in a metal-contaminated environment. Our goal was to determine whether bacterial metal resistance or the capacity to produce phytohormones had a larger impact on the growth of host plants under zinc stress. Eight zinc-sensitive mutants and one zinc-sensitive mutant with reduced indole-3-acetic acid (IAA) production were obtained by transposon mutagenesis. Analysis of the genome sequence and of transcription via reverse transcriptase PCR (RT-PCR) combined with transposon gene disruptions revealed that ZntA-4200 and the transcriptional regulator ZntR1 played important roles in the zinc homeostasis of A. tumefaciens CCNWGS0286. In addition, interruption of a putative oligoketide cyclase/lipid transport protein reduced IAA synthesis and also showed reduced zinc and cadmium resistance but had no influence on copper resistance. In greenhouse studies, R. pseudoacacia inoculated with A. tumefaciens CCNWGS0286 displayed a significant increase in biomass production over that without inoculation, even in a zinc-contaminated environment. Interestingly, the differences in plant biomass improvement among A. tumefaciens CCNWGS0286, A. tumefaciens C58, and zinc-sensitive mutants 12-2 (zntA::Tn5) and 15-6 (low IAA production) revealed that phytohormones, rather than genes encoding zinc resistance determinants, were the dominant factor in enhancing plant growth in contaminated soil. PMID:22636006

  7. Vibrio panuliri sp. nov., a marine bacterium isolated from spiny lobster, Panulirus penicillatus and transfer of Vibrio ponticus from Scophthalmi clade to the newly proposed Ponticus clade.

    Science.gov (United States)

    Kumari, Prabla; Poddar, Abhijit; Schumann, Peter; Das, Subrata K

    2014-12-01

    A novel marine bacterium, strain LBS2(T) was isolated from eggs carried on pleopods of the spiny lobster collected from Andaman Sea. Heterotrophic growth occurred at 1-7% NaCl. 16S rRNA gene sequence similarity revealed the strain LBS2(T) belonged to the genus Vibrio and showed above 97% similarity with eight type strains of the genus Vibrio. Multilocus analysis based on ftsZ, gapA, gyrB, mreB, pyrH recA, rpoA, and topA revealed LBS2(T) formed a separate cluster with Vibrio ponticus DSM 16217(T) with 89.8% multilocus gene sequence similarity. However, strain LBS2(T) is distantly related with other members of the Scophthalmi clade in terms of 16S rRNA signatures, phenotypic variations and multilocus gene sequence similarity, for which we propose LBS2(T) belongs to a new clade i.e. Ponticus clade with V. ponticus DSM 16217(T) as the representative type strain of the clade. DNA-DNA homologies between strain LBS2(T) and closely related strains were well below 70%. DNA G + C content was 45.3 mol%. On the basis of our polyphasic study, strain LBS2(T) represents a novel species of the genus Vibrio, for which the name Vibrio panuliri sp. nov. is proposed. The type strain is LBS2(T) (= JCM 19500(T) = DSM 27724(T) = LMG 27902(T)). Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  8. Vibrio algivorus sp. nov., an alginate- and agarose-assimilating bacterium isolated from the gut flora of a turban shell marine snail.

    Science.gov (United States)

    Doi, Hidetaka; Chinen, Akito; Fukuda, Hiroo; Usuda, Yoshihiro

    2016-08-01

    An agarose- and alginate-assimilating, Gram-reaction-negative, non-motile, rod-shaped bacterium, designated strain SA2T, was isolated from the gut of a turban shell sea snail (Turbo cornutus) collected near Noto Peninsula, Ishikawa Prefecture, Japan. The 16S rRNA gene sequence of strain SA2T was 99.59 % identical to that of Vibrio rumoiensis DSM 19141T and 98.19 % identical to that of Vibrio litoralis DSM 17657T. This suggested that strain SA2T could be a subspecies of V. rumoiensis or V. litoralis. However, DNA-DNA hybridization results showed only 37.5 % relatedness to DSM 19141T and 44.7 % relatedness to DSM 17657T, which was far lower than the 70 % widely accepted to define common species. Strain SA2T could assimilate agarose as a sole carbon source, whereas strains DSM 19141T and DSM 17657T could not assimilate it at all. Furthermore, results using API 20NE and API ZYM kits indicated that their enzymic and physiological phenotypes were also different. These results suggested that strain SA2T represented a novel species within the genus Vibrio. The major isoprenoid quinone in SA2T was Q-8, and its major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The major fatty acids were summed feature 3, (comprising C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0, and summed feature 8 (comprising C18 : 1ω6c and/or C18 : 1ω7c). The DNA G+C content of SA2T was 40.7 mol%. The name proposed for this novel species of the genus Vibrio is Vibrio algivorus sp. nov., with the type strain designated SA2T (=DSM 29824T=NBRC 111146T).

  9. Cecembia lonarensis gen. nov., sp. nov., a haloalkalitolerant bacterium of the family Cyclobacteriaceae, isolated from a haloalkaline lake and emended descriptions of the genera Indibacter, Nitritalea and Belliella.

    Science.gov (United States)

    Anil Kumar, P; Srinivas, T N R; Madhu, S; Sravan, R; Singh, Shashi; Naqvi, S W A; Mayilraj, S; Shivaji, S

    2012-09-01

    A novel Gram-staining-negative, rod-shaped, non-motile bacterium, designated strain LW9(T), was isolated from a water sample collected from Lonar Lake of Buldhana district, Maharashtra, India. Colonies and broth cultures were reddish orange due to the presence of carotenoid pigments. Strain LW9(T) was positive for catalase, ornithine decarboxylase and lysine decarboxylase activities and negative for gelatinase, oxidase, urease and lipase activities. The predominant fatty acids were iso-C(15 : 0) (31.3 %), iso-C(16 : 0) (9.3 %), anteiso-C(15 : 0) (7.3 %), iso-C(16 : 1) H (6.1 %), summed feature 3 (comprising C(16 : 1)ω7c/C(16 : 1)ω6c; 5.9 %), iso-C(17 : 1)ω9c (5.4 %) and iso-C(17 : 0) 3-OH (5.0 %). Strain LW9(T) contained MK-7 as the major respiratory quinone. The polar lipids consisted of phosphatidylethanolamine, two unidentified aminolipids and seven unidentified lipids. The DNA G+C content of strain LW9(T) was 40.5 mol%. 16S rRNA gene sequence analysis indicated that the type strains of Indibacter alkaliphilus and Aquiflexum balticum, two members of the family Cyclobacteriaceae (phylum 'Bacteroidetes') were the most closely related strains with sequence similarities of 93.0 and 94.0 %, respectively. Other members of the family Cyclobacteriaceae showed sequence similarities <93.0 %. Based on these phenotypic characteristics and on phylogenetic inference, strain LW9(T) is proposed as the representative of novel species in a new genus, Cecembia lonarensis gen. nov., sp. nov. The type strain of the type species, Cecembia lonarensis, is LW9(T) (= CCUG 58316(T) = KCTC 22772(T)). Emended descriptions of the genera Indibacter, Nitritalea and Belliella are also proposed.

  10. De novo synthesis of fatty acids is regulated by FapR protein in Exiguobacterium antarcticum B7, a psychrotrophic bacterium isolated from Antarctica.

    Science.gov (United States)

    Baraúna, Rafael A; das Graças, Diego A; Nunes, Catarina I P; Schneider, Maria P C; Silva, Artur; Carepo, Marta S P

    2016-09-20

    FapR protein from the psychrotrophic species Exiguobacterium antarcticum B7 was expressed and purified, and subsequently evaluated for its capacity to bind to the promoter regions of the fabH1-fabF and fapR-plsX-fabD-fabG operons, using electrophoretic mobility shift assay. The genes that compose these operons encode for enzymes involved in the de novo synthesis of fatty acids molecules. In Bacillus subtilis, FapR regulates the expression of these operons, and consequently has influence in the synthesis of long or short-chain fatty acids. To analyze the bacterial cold adaptation, this is an important metabolic pathway because psychrotrophic microrganisms tend to synthesize short and branched-chain unsaturated fatty acids at cold to maintain cell membrane fluidity. In this work, it was observed that recombinant protein was able to bind to the promoter of the fully amplified fabH1-fabF and fapR-plsX-fabD-fabG operons. However, FapR was unable to bind to the promoter of fapR-plsX-fabD-fabG operon when synthesized only up to the protein-binding palindrome 5'-TTAGTACCAGATACTAA-3', thus showing the importance of the entire promoter sequence for the correct protein-DNA interaction. Through this observation, we demonstrate that the FapR protein possibly regulates the same operons as described for other species, which emphasizes its importance to cold adaptation process of E. antarcticum B7, a psychrotrophic bacterium isolated at Antarctica.

  11. Expression and partial characterization of an ice binding protein from a bacterium isolated at a depth of 3,519 meters in the Vostok ice core, Antarctica

    Directory of Open Access Journals (Sweden)

    Amanda Marie Achberger

    2011-12-01

    Full Text Available Cryopreservation of microorganisms in ancient glacial ice is possible if lethal levels of macromolecular damage are not incurred and cellular integrity is not compromised via intracellular ice formation or recrystallization. Previously, a bacterium (isolate 3519-10 recovered from a depth of 3,519 meters below the surface in the Vostok ice core was shown to secrete an IBP that inhibits the recrystallization of ice. To explore the advantage that IBPs confer to ice-entrapped cells, experiments were designed to examine the expression of 3519-10’s IBP gene and protein at different temperatures, assess the effect of the IBP on bacterial viability in ice, and determine how the IBP influences the physical structure of the ice. Total RNA isolated from cultures grown between 4 to 25⁰C and analyzed by reverse transcription-PCR indicated constitutive expression of the IBP gene. SDS-PAGE analysis of 3519-10’s extracellular proteins also revealed a polypeptide of the predicted size of the 54 kDa IBP at all temperatures tested. In the presence of 100 µg mL-1 of extracellular protein from 3519-10, the survival of Escherichia coli was increased by greater than 34-fold after freeze-thaw cycling. Microscopic analysis of ice formed in the presence of the IBP indicated that per mm2 field of view, there were ~5 times as many crystals as in ice formed in the presence of washed 3519-10 cells and non-IBP producing bacteria, and ~10 times as many crystals as in filtered deionized water. Presumably, the effect that the IBP has on bacterial viability and ice crystal structure is due to its activity as an inhibitor of ice recrystallization. A myriad of molecular adaptations are likely to play a role in bacterial persistence under frozen conditions, but the ability of 3519-10’s IBP to control ice crystal structure, and thus the liquid vein network within the ice, may provide one explanation for its successful survival deep within the Antarctic ice sheet for

  12. 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.

  13. Isolation and characterization of Magnetospirillum sp. strain 15-1 as a representative anaerobic toluene-degrader from a constructed wetland model.

    Directory of Open Access Journals (Sweden)

    Ingrid Meyer-Cifuentes

    Full Text Available Previously, Planted Fixed-Bed Reactors (PFRs have been used to investigate microbial toluene removal in the rhizosphere of constructed wetlands. Aerobic toluene degradation was predominant in these model systems although bulk redox conditions were hypoxic to anoxic. However, culture-independent approaches indicated also that microbes capable of anaerobic toluene degradation were abundant. Therefore, we aimed at isolating anaerobic-toluene degraders from one of these PFRs. From the obtained colonies which consisted of spirilli-shaped bacteria, a strain designated 15-1 was selected for further investigations. Analysis of its 16S rRNA gene revealed greatest similarity (99% with toluene-degrading Magnetospirillum sp. TS-6. Isolate 15-1 grew with up to 0.5 mM of toluene under nitrate-reducing conditions. Cells reacted to higher concentrations of toluene by an increase in the degree of saturation of their membrane fatty acids. Strain 15-1 contained key genes for the anaerobic degradation of toluene via benzylsuccinate and subsequently the benzoyl-CoA pathway, namely bssA, encoding for the alpha subunit of benzylsuccinate synthase, bcrC for subunit C of benzoyl-CoA reductase and bamA for 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase. Finally, most members of a clone library of bssA generated from the PFR had highest similarity to bssA from strain 15-1. Our study provides insights about the physiological capacities of a strain of Magnetospirillum isolated from a planted system where active rhizoremediation of toluene is taking place.

  14. Erratum to: two novel species Enterococcus lemanii sp. nov. and Enterococcus eurekensis sp. nov., isolated from a swine manure storage pit

    Science.gov (United States)

    A polyphasic taxonomic study using morphological, biochemical, chemotaxonomic, and molecular genetic methods was performed on six strains of an unknown Gram-positive, nonspore-forming, facultative anaerobic coccus-shaped bacterium isolated from a swine-manure storage pit. On the basis of 16S rRNA, R...

  15. Characterization of bacterium isolated from the sediment at coastal area of Omura Bay in Japan and several biological activities of pigment produced by this isolate.

    Science.gov (United States)

    Nakashima, Takuji; Kurachi, Maki; Kato, Yoko; Yamaguchi, Kenichi; Oda, Tatsuya

    2005-01-01

    Recently we discovered a bacterial strain (MS-02-063) that produces large amounts of red pigment from coastal area of Nagasaki Prefecture, Japan. Comparative 16S rDNA gene sequencing analysis revealed that strain MS-02-063 was phylogenetically closely related to gamma-proteobacterium Hahella sp. MBIC 3957 that produces prodigiosin. However, some physiological and biochemical differences between strain MS-02-063 and Hahella sp. MBIC 3957 were observed. The red pigment (RP-063) produced by this isolate was highly purified from the culture supernatant. It was speculated that RP-063 might be prodigiosin-like pigment in physical properties and biological activities such as antibacterial and cytotoxic activity. Antibacterial activity of RP-063 was examined by an agar dilution method. The results indicated that RP-063 showed antibacterial activity for specific for pathogenic gram-positive bacteria such as Staphylococcus aureus. The potency of antibacterial activity against S. aureus was nearly equal to those of tetracycline. Moreover, RP-063 showed inhibition of the superoxide generation by 12-O-tetradecanoylphorbol-13-acetate (TPA)-stimulated mouse macrophage RAW 264.7 cell line. Prodigiosin members have a wide variety of biological properties, including anticancer and antimalarial, etc. Especially, potent immunosuppressive properties have been reported for prodigiosin members with the mechanism of action different from that of the other well known immunosuppressors in atopic dermatitis therapy such as cyclosporin A, FK506 and rapamycin. It is suggested that RP-063 may be able to arrest the inflammation caused by superantigens secreted from S. aureus, which colonized skin on atopic dermatitis as well as suppression of activated lymphocyte proliferation and superoxide generation from leucocytes.

  16. Identification and growth conditions of purple non-sulfur photosynthetic bacteria isolated from palm oil mill effluent

    International Nuclear Information System (INIS)

    Radziah Ariffin

    2004-01-01

    An indigenous strain of the purple non-sulphur photosynthetic bacterium, isolated from palm oil mill effluent was presumably identified as species of Rhodopseudomonas palustris. Cultivation in synthetic medium under different conditions indicated that it gave maximum carotenoid and bacteriophyll synthesis under anaerobic conditions in the light with values of 12.6 and 108.1 mg/g dry cell weight respectively. These values were significantly higher than the pigment content obtained from aerobic cultivation. The specific growth rates in anaerobic was twice those in aerobic conditions in the light. Growth was not occurred in anaerobic or aerobic conditions in the dark. (Author)

  17. Isolation and characterization of newMethanosarcina mazeistrains KOR-3, -4, -5, and -6 from an anaerobic digester using pig slurry.

    Science.gov (United States)

    Battumur, Urantulkhuur; Yoon, Youngman; Bae, Gui Sek; Kim, Chang-Hyun

    2017-08-01

    An experiment was conducted to isolate and identify new methanogens in Korea from an anaerobic digester that uses pig slurry. An anaerobic digestate sample was collected from an anaerobic digester using pig slurry. Pre-reduced media were used for the growth and isolation of methanogens. Growth temperature range, pH range, NaCl concentration range, substrate utilization, and antibiotic tolerance were investigated to determine the physiological characteristics of isolated methanogens. The isolates were also examined microscopically for their morphology and Gram-stained. Polymerase chain reaction of 16S rRNA and mcrA gene-based amplicons was used for identification purpose. Four strains, designated KOR-3, -4, -5, and -6, were isolated and were non-motile, irregular coccoid, and 0.5 to 1.5 μm in diameter. Moreover, the cell walls of isolated strains were Gram-negative. KOR-3 and KOR-4 strains used acetate for methane production but did not use H 2 +CO 2 , formate, or methanol as a growth substrate KOR-5 and KOR-6 strains utilized acetate, methanol, and trimethylamine for methanogenesis but did not use H 2 +CO 2 or formate as a growth substrate. The optimum temperature and pH for growth of four strains were 39°C and 6.8 to 7.2, respectively. The optimum concentration of NaCl for growth of KOR-3, KOR-5, and KOR-6 were 1.0% (w/v). The optimum NaCl concentration for KOR-4 was 0.5% (w/v). All of the strains tolerated ampicillin, penicillin G, kanamycin, streptomycin, and tetracycline; however, chloramphenicol inhibited cell growth. Phylogenetic analysis of 16S rRNA and mcrA genes demonstrated that strains KOR-3, -4, -5, and -6 are related to Methanosarcina mazei ( M. mazei , 99% sequence similarity). On the basis of physiological and phylogenetic characteristics, strains KOR-3, -4, -5, and -6 are proposed to be new strains within the genus Methanosarcina , named M. mazei KOR-3, -4, -5, and -6.

  18. A comparative evaluation of antibacterial effectiveness of sodium hypochlorite, Curcuma longa, and Camellia sinensis as irrigating solutions on isolated anaerobic bacteria from infected primary teeth.

    Science.gov (United States)

    Dhariwal, Neha Shashikant; Hugar, Shivayogi M; Harakuni, Sheetal; Sogi, Suma; Assudani, Harsha G; Mistry, Laresh Naresh

    2016-01-01

    In endodontics, most of the commercial intra-canal medicaments have cytotoxic reactions and because of their inability to eliminate bacteria from dentinal tubules, recent medicine has turned its attention to the usage of biologic medication prepared from natural plants. The literature to testify the efficacy of natural alternatives in primary teeth is meagre and its effects as irrigating solutions need to be evaluated. To evaluate the antibacterial effectiveness of sodium hypochlorite, ethanolic extracts of Curcuma longa (turmeric) and Camellia sinensis (green tea) as irrigating solutions against the anaerobic bacteria isolated from the root canals of infected primary teeth. Thirty patients were selected based on the selected inclusion and exclusion criteria. Preoperative radiographs were taken. Rubber dam isolation and working length estimation were done, following which thirty samples were taken from the root canals of infected primary teeth using sterile absorbent paper points and transferred to tubes containing thioglycolate transport medium. The bacteria were then isolated using standard microbiological protocols and were subjected to antibiotic sensitivity testing using the three test irrigants. SPSS 18 software using Chi-square test was used for statistical analysis. The most commonly isolated bacteria included Porphyromonas sp., Bacteroides fragilis, Peptostreptococcus, and Staphylococcus aureus. Sodium hypochlorite and C. longa (turmeric) showed good antibacterial effect and were effective against most of the isolated bacteria. There was statistically significant difference in the antibacterial effect among the three tested groups (P < 0.001). The least effective was C. sinensis (green tea). The infected primary teeth almost always present with a polymicrobial structure with a wide variety of anaerobic bacteria. The chemo-mechanical preparation plays an important role in eradicating the population of predominant micro-organisms in treating these teeth with

  19. A comparative evaluation of antibacterial effectiveness of sodium hypochlorite, Curcuma longa, and Camellia sinensis as irrigating solutions on isolated anaerobic bacteria from infected primary teeth

    Directory of Open Access Journals (Sweden)

    Neha Shashikant Dhariwal

    2016-01-01

    Full Text Available Context: In endodontics, most of the commercial intra-canal medicaments have cytotoxic reactions and because of their inability to eliminate bacteria from dentinal tubules, recent medicine has turned its attention to the usage of biologic medication prepared from natural plants. The literature to testify the efficacy of natural alternatives in primary teeth is meagre and its effects as irrigating solutions need to be evaluated. Aim: To evaluate the antibacterial effectiveness of sodium hypochlorite, ethanolic extracts of Curcuma longa (turmeric and Camellia sinensis (green tea as irrigating solutions against the anaerobic bacteria isolated from the root canals of infected primary teeth. Materials and Methods: Thirty patients were selected based on the selected inclusion and exclusion criteria. Preoperative radiographs were taken. Rubber dam isolation and working length estimation were done, following which thirty samples were taken from the root canals of infected primary teeth using sterile absorbent paper points and transferred to tubes containing thioglycolate transport medium. The bacteria were then isolated using standard microbiological protocols and were subjected to antibiotic sensitivity testing using the three test irrigants. Statistical Analysis: SPSS 18 software using Chi-square test was used for statistical analysis. Results: The most commonly isolated bacteria included Porphyromonas sp., Bacteroides fragilis, Peptostreptococcus, and Staphylococcus aureus. Sodium hypochlorite and C. longa (turmeric showed good antibacterial effect and were effective against most of the isolated bacteria. There was statistically significant difference in the antibacterial effect among the three tested groups (P < 0.001. The least effective was C. sinensis (green tea. Conclusion: The infected primary teeth almost always present with a polymicrobial structure with a wide variety of anaerobic bacteria. The chemo-mechanical preparation plays an important

  20. Hydrogen as clean fuel via continuous fermentation by anaerobic ...

    African Journals Online (AJOL)

    free and oxidized to water as a combustion product. Bioconversion of synthesis gas to hydrogen was demonstrated in a continuous fermentation utilizing malate as a carbon source. Rhodospirillum rubrum, an anaerobic photosynthetic bacterium ...

  1. Improved dechlorinating performance of upflow anaerobic sludge blanket reactors by incorporation of Dehalospirillum multivorans into granular sludge

    DEFF Research Database (Denmark)

    Hörber, Christine; Christiansen, Nina; Arvin, Erik

    1998-01-01

    Dechlorination of tetrachloroethene, also known as perchloroethylene (PCE), was investigated in an upflow anaerobic sludge blanket (UASB) reactor after incorporation of the strictly anaerobic, reductively dechlorinating bacterium Dehalospirillum multivorans into granular sludge. This reactor...

  2. Draft Genome Sequence of Bacillus amyloliquefaciens EBL11, a New Strain of Plant Growth-Promoting Bacterium Isolated from Rice Rhizosphere

    Science.gov (United States)

    Wang, Yinghuan; Greenfield, Paul; Jin, Decai

    2014-01-01

    Bacillus amyloliquefaciens strain EBL11 is a bacterium that can promote plant growth by inhibiting the growth of fungi on plant surfaces and providing nutrients as a nonchemical biofertilizer. The estimated genome of this strain is 4.05 Mb in size and harbors 3,683 coding genes (CDSs). PMID:25059875

  3. 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...

  4. Complete Genome Sequence of Paenibacillus polymyxa CR1, a Plant Growth-Promoting Bacterium Isolated from the Corn Rhizosphere Exhibiting Potential for Biocontrol, Biomass Degradation, and Biofuel Production.

    Science.gov (United States)

    Eastman, Alexander W; Weselowski, Brian; Nathoo, Naeem; Yuan, Ze-Chun

    2014-01-23

    Here we report the complete genome sequence of the bacterium Paenibacillus polymyxa CR1 (accession no. CP006941), which consists of one circular chromosome of 6,024,666 bp with 5,283 coding sequences (CDS), 87 tRNAs, and 12 rRNA operons. Data presented will allow for further insights into the mechanisms underpinning agriculturally and industrially relevant processes.

  5. 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.

  6. Anaerobic Biotransformation and Mobility of Pu and of Pu-EDTA

    Energy Technology Data Exchange (ETDEWEB)

    Xun, Luying

    2009-11-20

    The enhanced mobility of radionuclides by co-disposed chelating agent, ethylenediaminetetraacetate (EDTA), is likely to occur only under anaerobic conditions. Our extensive effort to enrich and isolate anaerobic EDTA-degrading bacteria has failed. Others has tried and also failed. To explain the lack of anaerobic biodegradation of EDTA, we proposed that EDTA has to be transported into the cells for metabolism. A failure of uptake may contribute to the lack of EDTA degradation under anaerobic conditions. We demonstrated that an aerobic EDTA-degrading bacterium strain BNC1 uses an ABC-type transporter system to uptake EDTA. The system has a periplasmic binding protein that bind EDTA and then interacts with membrane proteins to transport EDTA into the cell at the expense of ATP. The bind protein EppA binds only free EDTA with a Kd of 25 nM. The low Kd value indicates high affinity. However, the Kd value of Ni-EDTA is 2.4 x 10^(-10) nM, indicating much stronger stability. Since Ni and other trace metals are essential for anaerobic respiration, we conclude that the added EDTA sequestrates all trace metals and making anaerobic respiration impossible. Thus, the data explain the lack of anaerobic enrichment cultures for EDTA degradation. Although we did not obtain an EDTA degrading culture under anaerobic conditions, our finding may promote the use of certain metals that forms more stable metal-EDTA complexes than Pu(III)-EDTA to prevent the enhanced mobility. Further, our data explain why EDTA is the most dominant organic pollutant in surface waters, due to the lack of degradation of certain metal-EDTA complexes.

  7. Anaerobic Biotransformation and Mobility of Pu and of Pu-EDTA

    International Nuclear Information System (INIS)

    Xun, Luying

    2009-01-01

    The enhanced mobility of radionuclides by co-disposed chelating agent, ethylenediaminetetraacetate (EDTA), is likely to occur only under anaerobic conditions. Our extensive effort to enrich and isolate anaerobic EDTA-degrading bacteria has failed. Others has tried and also failed. To explain the lack of anaerobic biodegradation of EDTA, we proposed that EDTA has to be transported into the cells for metabolism. A failure of uptake may contribute to the lack of EDTA degradation under anaerobic conditions. We demonstrated that an aerobic EDTA-degrading bacterium strain BNC1 uses an ABC-type transporter system to uptake EDTA. The system has a periplasmic binding protein that bind EDTA and then interacts with membrane proteins to transport EDTA into the cell at the expense of ATP. The bind protein EppA binds only free EDTA with a Kd of 25 nM. The low Kd value indicates high affinity. However, the Kd value of Ni-EDTA is 2.4 x 10 -10 nM, indicating much stronger stability. Since Ni and other trace metals are essential for anaerobic respiration, we conclude that the added EDTA sequestrates all trace metals and making anaerobic respiration impossible. Thus, the data explain the lack of anaerobic enrichment cultures for EDTA degradation. Although we did not obtain an EDTA degrading culture under anaerobic conditions, our finding may promote the use of certain metals that forms more stable metal-EDTA complexes than Pu(III)-EDTA to prevent the enhanced mobility. Further, our data explain why EDTA is the most dominant organic pollutant in surface waters, due to the lack of degradation of certain metal-EDTA complexes.

  8. Lactobacillus psittaci sp. nov., isolated from a hyacinth macaw (Anodorhynchus hyacinthinus).

    Science.gov (United States)

    Lawson, P A; Wacher, C; Hansson, I; Falsen, E; Collins, M D

    2001-05-01

    A Gram-positive, non-spore-forming, catalase-negative, facultatively anaerobic coccibacillus to rod-shaped bacterium isolated from a parrot was characterized using phenotypic and molecular taxonomic methods. The unknown bacterium phenotypically resembled lactobacilli and comparative 16S rRNA gene sequencing demonstrated that the organism represents a distinct subline within the Lactobacillus delbrueckii rRNA cluster of the genus. 16S rRNA sequence divergence values of > 6% with recognized Lactobacillus species clearly demonstrated the phylogenetic separateness of the parrot bacterium. On the basis of phylogenetic evidence and the phenotypic distinctiveness of the unknown bacterium, a new species, Lactobacillus psittaci sp. nov., is proposed. The type strain of Lactobacillus psittaci is CCUG 42378T (= CIP 106492T).

  9. Potential application of anaerobic extremophiles for hydrogen production

    Science.gov (United States)

    Pikuta, Elena V.; Hoover, Richard B.

    2004-11-01

    In processes of the substrate fermentation most anaerobes produce molecular hydrogen as a waste end product, which often controls the culture growth as an inhibitor. Usually in nature the hydrogen is easily removed from an ecosystem, due to its physical features, and an immediate consumption by the secondary anaerobes that sometimes behave as competitors for electron donors; a classical example of this kind of substrate competition in anaerobic microbial communities is the interaction between methanogens and sulfate- or sulfur-reducers. Previously, on the mixed cultures of anaerobes at neutral pH, it was demonstrated that bacterial hydrogen production could provide a good alternative energy source. At neutral pH the original cultures could easily contaminated by methanogens, and the most unpleasant side effect of these conditions is the development of pathogenic bacteria. In both cases the rate of hydrogen production was dramatically decreased since some part of the hydrogen was transformed to methane, and furthermore, the cultivation with pathogenic contaminants on an industrial scale would create an unsafe situation. In our laboratory the experiments with obligately alkaliphilic bacteria producing hydrogen as an end metabolic product were performed at different conditions. The mesophilic, haloalkaliphilic and obligately anaerobic bacterium Spirochaeta americana ASpG1T was studied and various cultivation regimes were compared for the most effective hydrogen production. In a highly mineralized media with pH 9.5-10.0 not many known methanogens are capable of growth, and the probability of developing pathogenic contaminants is theoretically is close to zero (in medicine carbonate- saturated solutions are applied as antiseptics). Therefore the cultivation of alkaliphilic hydrogen producing bacteria could be considered as a safe and economical process for large-scale industrial bio-hydrogen production in the future. Here we present and discuss the experimental data

  10. Degradation of Reactive Black 5 dye using anaerobic/aerobic membrane bioreactor (MBR) and photochemical membrane reactor

    International Nuclear Information System (INIS)

    You, Sheng-Jie; Damodar, Rahul A.; Hou, Sheng-Chon

    2010-01-01

    Three different types of advance treatment methods were evaluated for the degradation of Reactive Black 5 (RB5). The performance of two stage anaerobic SBR-aerobic MBR, anaerobic MBR with immobilized and suspended biocells and an integrated membrane photocatalytic reactor (MPR) using slurry UV/TiO 2 system were investigated. The results suggest that, nearly 99.9% color removal and 80-95% organic COD and TOC removal can be achieved using different reactor systems. Considering the Taiwan EPA effluent standard discharge criteria for COD/TOC, the degree of treatment achieved by combining the anaerobic-aerobic system was found to be acceptable. Anew, Bacilluscereus, high color removal bacterium was isolated from Anaerobic SBR. Furthermore, when this immobilized into PVA-calcium alginate pellets, and suspended in the anaerobic MBR was able to achieve high removal efficiencies, similar to the suspended biocells system. However, the immobilized cell Anaerobic MBR was found to be more advantageous, due to lower fouling rates in the membrane unit. Results from slurry type MPR system showed that this system was capable of mineralizing RB5 dyes with faster degradation rate as compared to other systems. The reactor was also able to separate the catalyst effectively and perform efficiently without much loss of catalyst activity.

  11. Desulfotomaculum thermobenzoicum subsp. thermosyntrophicum subsp. nov., a thermophilic, syntrophic, propionate-oxidizing, spore-forming bacterium

    NARCIS (Netherlands)

    Plugge, C.M.; Balk, M.; Stams, A.J.M.

    2002-01-01

    From granular sludge from a laboratory-scale upflow anaerobic sludge bed reactor operated at 55 degrees C with a mixture of volatile fatty acids as feed, a novel anaerobic, moderately thermophilic, syntrophic, spore-forming bacterium, strain TPO, was enriched on propionate in co-culture with

  12. Isolation and characterization of 14 additional genes specifying the anaerobic biosynthesis of cobalamin (vitamin B12) in Propionibacterium freudenreichii (P. shermanii).

    Science.gov (United States)

    Roessner, Charles A; Huang, Ke-Xue; Warren, Martin J; Raux, Evelyne; Scott, A Ian

    2002-06-01

    A search for genes encoding enzymes involved in cobalamin (vitamin B12) production in the commercially important organism Propionibacterium freudenreichii (P. shermanii) has resulted in the isolation of an additional 14 genes encoding enzymes responsible for 17 steps of the anaerobic B12 pathway in this organism. All of the genes believed to be necessary for the biosynthesis of adenosylcobinamide from uroporphyrinogen III have now been isolated except two (cbiA and an as yet unidentified gene encoding cobalt reductase). Most of the genes are contained in two divergent operons, one of which, in turn, is closely linked to the operon encoding the B12-dependent enzyme methylmalonyl-CoA mutase. The close linkage of the three genes encoding the subunits of transcarboxylase to the hemYHBXRL gene cluster is reported. The functions of the P. freudenreichii B12 pathway genes are discussed, and a mechanism for the regulation of cobalamin and propionic acid production by oxygen in this organism is proposed.

  13. 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.

  14. Isolation of a star-shaped uranium(V/VI) cluster from the anaerobic photochemical reduction of uranyl(VI)

    International Nuclear Information System (INIS)

    Chatelain, Lucile; White, Sarah; Scopelliti, Rosario; Mazzanti, Marinella

    2016-01-01

    Actinide oxo clusters are an important class of compounds due to their impact on actinide migration in the environment. The photolytic reduction of uranyl(VI) has potential application in catalysis and spent nuclear fuel reprocessing, but the intermediate species involved in this reduction have not yet been elucidated. Here we show that the photolysis of partially hydrated uranyl(VI) in anaerobic conditions leads to the reduction of uranyl(VI), and to the incorporation of the resulting U V species into the stable mixed-valent star-shaped U VI /U V oxo cluster [U(UO 2 ) 5 (μ 3 -O) 5 (PhCOO) 5 (Py) 7 ]. This cluster is only the second example of a U VI /U V cluster and the first one associating uranyl groups to a non-uranyl(V) center. The U V center in 1 is stable, while the reaction of uranyl(V) iodide with potassium benzoate leads to immediate disproportionation and formation of the U 12 IV U 4 V O 24 cluster {[K(Py) 2 ] 2 [K(Py)] 2 [U 16 O 24 (PhCOO) 24 (Py) 2 ]}.

  15. Isolation of a star-shaped uranium(V/VI) cluster from the anaerobic photochemical reduction of uranyl(VI)

    Energy Technology Data Exchange (ETDEWEB)

    Chatelain, Lucile; White, Sarah; Scopelliti, Rosario; Mazzanti, Marinella [Ecole Polytechnique Federale de Lausanne (EPFL) (Switzerland). Inst. de Sciences et Ingenierie Chimiques

    2016-11-07

    Actinide oxo clusters are an important class of compounds due to their impact on actinide migration in the environment. The photolytic reduction of uranyl(VI) has potential application in catalysis and spent nuclear fuel reprocessing, but the intermediate species involved in this reduction have not yet been elucidated. Here we show that the photolysis of partially hydrated uranyl(VI) in anaerobic conditions leads to the reduction of uranyl(VI), and to the incorporation of the resulting U{sup V} species into the stable mixed-valent star-shaped U{sup VI}/U{sup V} oxo cluster [U(UO{sub 2}){sub 5}(μ{sub 3}-O){sub 5}(PhCOO){sub 5}(Py){sub 7}]. This cluster is only the second example of a U{sup VI}/U{sup V} cluster and the first one associating uranyl groups to a non-uranyl(V) center. The U{sup V} center in 1 is stable, while the reaction of uranyl(V) iodide with potassium benzoate leads to immediate disproportionation and formation of the U{sub 12}{sup IV}U{sub 4}{sup V}O{sub 24} cluster {[K(Py)_2]_2[K(Py)]_2[U_1_6O_2_4(PhCOO)_2_4(Py)_2]}.

  16. Oxygen sensitivity of various anaerobic bacteria.

    Science.gov (United States)

    Loesche, W J

    1969-11-01

    Anaerobes differ in their sensitivity to oxygen, as two patterns were recognizable in the organisms included in this study. Strict anaerobes were species incapable of agar surface growth at pO(2) levels greater than 0.5%. Species that were found to be strict anaerobes were Treponema macrodentium, Treponema denticola, Treponema oralis n. sp., Clostridium haemolyticum, Selenomonas ruminatium, Butyrivibrio fibrisolvens, Succinivibrio dextrinosolvens, and Lachnospira multiparus. Moderate anaerobes would include those species capable of growth in the presence of oxygen levels as high as 2 to 8%. The moderate anaerobes could be exposed to room atmosphere for 60 to 90 min without appreciable loss of viability. Species considered as moderate anaerobes were Bacteroides fragilis, B. melaninogenicus, B. oralis, Fusobacteria nucleatum, Clostridium novyi type A, and Peptostreptococcus elsdenii. The recognition of at least two general types of anaerobes would seem to have practical import in regard to the primary isolation of anaerobes from source material.

  17. Anaerobic microbial associations degrading aminoaromatic acids

    NARCIS (Netherlands)

    Kotova, I.; Savelieva, O.; Dyakonova, A.T.; Sklyar, V.; Kalyushnyi, S.V.; Stams, A.J.M.; Netrusov, A.

    2005-01-01

    Anaerobic microbial associations have been isolated that degrade aminoaromatic acids to methane and carbon dioxide at high rates. Significant differences between the morphological, cytological, and physiological traits of cultures isolated from samples of adapted and unadapted sludge are shown. The

  18. Competition for L-lactate betweenDesulfovibrio, Veillonella, andAcetobacterium species isolated from anaerobic intertidal sediments.

    Science.gov (United States)

    Laanbroek, H J; Geerligs, H J; Peijnenburg, A A; Siesling, J

    1983-12-01

    Almost equal numbers ofDesulfovibrio, Veillonella, andAcetobacterium species were found in agar shake dilutions of anaerobic intertidal brackish sediments applying L-lactate as the only energy source and sulfate as electron acceptor. Pure cultures of these bacteria were studied in more detail in batch cultures as well as in L-lactate-limited chemostats. The maximal specific growth rates on L-lactate were determined in washout experiments and amounted to 0.16, 0.30, and 0.06 h(-1) forDesulfovibrio baculatus H.L21,Veillonella alcalescens NS.L49, andAcetobacterium NS.L40, respectively. Competition for L-lactate was studied in energy-limited chemostats at a dilution rate of 0.02 h(-1).D. baculatus H.L21 turned out to be the best competitor at low L-lactate concentrations provided that sufficient sulfate and iron were present.V. alcalescens NS.L49 was favored by the absence of sulfate and iron. Coexistence ofD. baculatus H.L21 andV. alcalescens NS.L49 was observed in a L-lactate-limited chemostat with additional sulfate and citrate. Syntrophic growth ofV. alcalescens NS.L49 andAcetobacterium NS.L40 occurred in a L-lactate-limited chemostat in the absence of sulfate. No coexistence betweenD. baculatus H.L21 andAcetobacterium NS.L40 was observed in a L-lactate-limited chemostat without sulfate. Addition of calcium-saturated illite to an energy-limited mixed culture ofV. alcalescens NS.L49 andAcetobacterium NS.L40 induced iron limitation and subsequent washout of theAcetobacterium species. Finally, the ecological niches of the 3 species in relation to the consumption of lactate were discussed.

  19. Survival of Anaerobic Fe2+ Stress Requires the ClpXP Protease.

    Science.gov (United States)

    Bennett, Brittany D; Redford, Kaitlyn E; Gralnick, Jeffrey A

    2018-04-15

    . Dissimilatory metal-reducing bacteria must therefore have mechanisms to tolerate anaerobic Fe 2+ stress, and studying resistance in these organisms may help elucidate the basis of toxicity. Shewanella oneidensis is a model dissimilatory metal-reducing bacterium isolated from metal-rich sediments. Here we demonstrate a role for ClpXP, a protease system widely conserved in bacteria, in anaerobic Fe 2+ resistance in both S. oneidensis and Escherichia coli . Copyright © 2018 American Society for Microbiology.

  20. Whole-Genome Sequence of Pseudomonas putida Strain UASWS0946, a Highly Ammonia-Tolerant Nitrifying Bacterium Isolated from Sewage Sludge Aerobic Granules

    OpenAIRE

    Crovadore, Julien; Calmin, Gautier; Cochard, Bastien; Chablais, Romain; Grizard, Damien; Berthon, Jean-Yves; Lefort, François

    2015-01-01

    We report here the genome of Pseudomonas putida strain UASWS0946, a highly ammonia-tolerant nitrifying strain isolated from sewage sludge aerobic granules, which displays adequate genetic equipment for soil depollution, sludge treatment, and biological fertilization in agriculture.

  1. Geovibrio ferrireducens, a phylogenetically distinct dissimilatory Fe(III)-reducing bacterium

    Science.gov (United States)

    Caccavo, F.; Coates, J.D.; Rossello-Mora, R. A.; Ludwig, W.; Schleifer, K.H.; Lovley, D.R.; McInerney, M.J.

    1996-01-01

    A new, phylogenetically distinct, dissimilatory, Fe(III)-reducing bacterium was isolated from surface sediment of a hydrocarbon-contaminated ditch. The isolate, designated strain PAL-1, was an obligately anaerobic, non-fermentative, motile, gram-negative vibrio. PAL-1 grew in a defined medium with acetate as electron donor and ferric pyrophosphate, ferric oxyhydroxide, ferric citrate, Co(III)-EDTA, or elemental sulfur as sole electron acceptor. PAL-1 also used proline, hydrogen, lactate, propionate, succinate, fumarate, pyruvate, or yeast extract as electron donors for Fe(III) reduction. It is the first bacterium known to couple the oxidation of an amino acid to Fe(III) reduction. PAI-1 did not reduce oxygen, Mn(IV), U(VI), Cr(VI), nitrate, sulfate, sulfite, or thiosulfate with acetate as the electron donor. Cell suspensions of PAL-1 exhibited dithionite-reduced minus air-oxidized difference spectra that were characteristic of c-type cytochromes. Analysis of the 16S rRNA gene sequence of PAL-1 showed that the strain is not related to any of the described metal-reducing bacteria in the Proteobacteria and, together with Flexistipes sinusarabici, forms a separate line of descent within the Bacteria. Phenotypically and phylogenetically, strain PAI-1 differs from all other described bacteria, and represents the type strain of a new genus and species. Geovibrio ferrireducens.

  2. Physiologically anaerobic microorganisms of the deep subsurface

    Energy Technology Data Exchange (ETDEWEB)

    Stevens, S.E. Jr.; Chung, K.T.

    1991-06-01

    This study seeks to determine numbers, diversity, and morphology of anaerobic microorganisms in 15 samples of subsurface material from the Idaho National Engineering Laboratory, in 18 samples from the Hanford Reservation and in 1 rock sample from the Nevada Test Site; set up long term experiments on the chemical activities of anaerobic microorganisms based on these same samples; work to improve methods for the micro-scale determination of in situ anaerobic microbial activity;and to begin to isolate anaerobes from these samples into axenic culture with identification of the axenic isolates.

  3. [Thiobacillus sajanensis sp. nov., a new obligately autotrophic sulfur-oxidizing bacterium isolated from Khoito-Gol hydrogen-sulfide springs, Buryatia].

    Science.gov (United States)

    Dul'tseva, N M; Turova, T P; Spiridonova, E M; Kolganova, T V; Osipov, G A; Gorlenko, V M

    2006-01-01

    Four strains of rod-shaped gram-negative sulfur-oxidizing bacteria were isolated from Khoito-Gol hydrogen-sulfide springs in the eastern Sayan Mountains (Buryatia). The cells of the new isolates were motile by means of a single polar flagellum. The strains were obligately chemolithoautotrophic aerobes that oxidized thiosulfate (with the production of sulfur and sulfates) and hydrogen sulfide. They grew in a pH range of 6.8-9.5, with an optimum at pH 9.3 and in a temperature range of 5-39 degrees C, with an optimum at 28-32 degrees C. The cells contained ubiquinone Q-8. The DNA G+C content of the new strains was 62.3-64.2 mol %. According to the results of analysis of their 16S rRNA genes, the isolates belong to the genus Thiobacillus within the subclass Betaproteobacteria. However, the similarity level of nucleotide sequences of the 16S rRNA genes was insufficient to assign the isolates to known species of this genus. The affiliation to the genus Thiobacillus was confirmed by DNA-DNA hybridization of the isolates with the type strain of the type species of the genus Thiobacillus, T. thioparus DSM 505T (= ATCC 8158T). Despite the phenotypic similarity, the hybridization level was as low as 21-29%. In addition, considerable differences were revealed in the structure of the genes encoding RuBPC, the key enzyme of autotrophic CO2 assimilation, between the known Thiobacillus species and the new isolates. Based on molecular-biological features and certain phenotypic distinctions, the new isolates were assigned to a new Thiobacillus species, T. sajanensis sp. nov., with the type strain 4HGT (= VKM B-2365T).

  4. Identification of antimicrobial resistance genes in multidrug-resistant clinical Bacteroides fragilis isolates by whole genome shotgun sequencing

    DEFF Research Database (Denmark)

    Sydenham, Thomas Vognbjerg; Sóki, József; Hasman, Henrik

    2015-01-01

    Bacteroides fragilis constitutes the most frequent anaerobic bacterium causing bacteremia in humans. The genetic background for antimicrobial resistance in B. fragilis is diverse with some genes requiring insertion sequence (IS) elements inserted upstream for increased expression. To evaluate whole...... genome shotgun sequencing as a method for predicting antimicrobial resistance properties, one meropenem resistant and five multidrug-resistant blood culture isolates were sequenced and antimicrobial resistance genes and IS elements identified using ResFinder 2.1 (http...

  5. Whole-Genome Sequence of Pseudomonas putida Strain UASWS0946, a Highly Ammonia-Tolerant Nitrifying Bacterium Isolated from Sewage Sludge Aerobic Granules.

    Science.gov (United States)

    Crovadore, Julien; Calmin, Gautier; Cochard, Bastien; Chablais, Romain; Grizard, Damien; Berthon, Jean-Yves; Lefort, François

    2015-10-08

    We report here the genome of Pseudomonas putida strain UASWS0946, a highly ammonia-tolerant nitrifying strain isolated from sewage sludge aerobic granules, which displays adequate genetic equipment for soil depollution, sludge treatment, and biological fertilization in agriculture. Copyright © 2015 Crovadore et al.

  6. Two novel alkane hydroxylase-rubredoxin fusion genes isolated from a Dietzia bacterium and the functions of fused rubredoxin domains in long-chain n-alkane degradation.

    Science.gov (United States)

    Nie, Yong; Liang, Jieliang; Fang, Hui; Tang, Yue-Qin; Wu, Xiao-Lei

    2011-10-01

    Two alkane hydroxylase-rubredoxin fusion gene homologs (alkW1 and alkW2) were cloned from a Dietzia strain, designated DQ12-45-1b, which can grow on crude oil and n-alkanes ranging in length from 6 to 40 carbon atoms as sole carbon sources. Both AlkW1 and AlkW2 have an integral-membrane alkane monooxygenase (AlkB) conserved domain and a rubredoxin (Rd) conserved domain which are fused together. Phylogenetic analysis showed that these two AlkB-fused Rd domains formed a novel third cluster with all the Rds from the alkane hydroxylase-rubredoxin fusion gene clusters in Gram-positive bacteria and that this third cluster was distant from the known AlkG1- and AlkG2-type Rds. Expression of the alkW1 gene in DQ12-45-1b was induced when cells were grown on C(8) to C(32) n-alkanes as sole carbon sources, but expression of the alkW2 gene was not detected. Functional heterologous expression in an alkB deletion mutant of Pseudomonas fluorescens KOB2Δ1 suggested the alkW1 could restore the growth of KOB2Δ1 on C(14) and C(16) n-alkanes and induce faster growth on C(18) to C(32) n-alkanes than alkW1ΔRd, the Rd domain deletion mutant gene of alkW1, which also caused faster growth than KOB2Δ1 itself. In addition, the artificial fusion of AlkB from the Gram-negative P. fluorescens CHA0 and the Rds from both Gram-negative P. fluorescens CHA0 and Gram-positive Dietzia sp. DQ12-45-1b significantly increased the degradation of C(32) alkane compared to that seen with AlkB itself. In conclusion, the alkW1 gene cloned from Dietzia species encoded an alkane hydroxylase which increased growth on and degradation of n-alkanes up to C(32) in length, with its fused rubredoxin domain being necessary to maintain the functions. In addition, the fusion of alkane hydroxylase and rubredoxin genes from both Gram-positive and -negative bacteria can increase the degradation of long-chain n-alkanes (such as C(32)) in the Gram-negative bacterium.

  7. Eubacterium rangiferina, a novel usnic acid-resistant bacterium from the reindeer rumen

    Science.gov (United States)

    Sundset, Monica A.; Kohn, Alexandra; Mathiesen, Svein D.; Præsteng, Kirsti E.

    2008-08-01

    Reindeer are able to eat and utilize lichens as an important source of energy and nutrients. In the current study, the activities of antibiotic secondary metabolites including usnic, antranoric, fumarprotocetraric, and lobaric acid commonly found in lichens were tested against a collection of 26 anaerobic rumen bacterial isolates from reindeer ( Rangifer tarandus tarandus) using the agar diffusion method. The isolates were identified based on their 16S ribosomal ribonucleic acid (rRNA) gene sequences. Usnic acid had a potent antimicrobial effect against 25 of the isolates, belonging to Clostridiales, Enterococci, and Streptococci. Isolates of Clostridia and Streptococci were also susceptible to atranoric and lobaric acid. However, one isolate (R3_91_1) was found to be resistant to usnic, antranoric, fumarprotocetraric, and lobaric acid. R3_91_1 was also seen invading and adhering to lichen particles when grown in a liquid anaerobic culture as demonstrated by transmission electron microscopy. This was a Gram-negative, nonmotile rod (0.2-0.7 × 2.0-3.5 μm) with a deoxyribonucleic acid G + C content of 47.0 mol% and main cellular fatty acids including 15:0 anteiso-dimethyl acetal (DMA), 16:0 iso-fatty acid methyl ester (FAME), 13:0 iso-3OH FAME, and 17:0 anteiso-FAME, not matching any of the presently known profiles in the MIDI database. Combined, the phenotypic and genotypic traits including the 16S rRNA gene sequence show that R3_91_1 is a novel species inside the order Clostridiales within the family Lachnospiraceae, for which we propose the name Eubacterium rangiferina. This is the first record of a rumen bacterium able to tolerate and grow in the presence of usnic acid, indicating that the rumen microorganisms in these animals have adapted mechanisms to deal with lichen secondary metabolites, well known for their antimicrobial and toxic effects.

  8. Ultrastructure and viral metagenome of bacteriophages from an anaerobic methane oxidizing methylomirabilis bioreactor enrichment culture

    NARCIS (Netherlands)

    Gambelli, Lavinia; Cremers, Geert; Mesman, Rob; Guerrero, Simon; Dutilh, Bas E.; Jetten, Mike S M; den Camp, Huub J M Op; van Niftrik, Laura

    2016-01-01

    With its capacity for anaerobic methane oxidation and denitrification, the bacterium Methylomirabilis oxyfera plays an important role in natural ecosystems. Its unique physiology can be exploited for more sustainable wastewater treatment technologies. However, operational stability of full-scale

  9. Ultrastructure and Viral Metagenome of Bacteriophages from an Anaerobic Methane Oxidizing Methylomirabilis Bioreactor Enrichment Culture

    NARCIS (Netherlands)

    Gambelli, L.; Cremers, G.; Mesman, R.; Guerrero, S.; Dutilh, B.E.; Jetten, M.S.; Camp, H.J. Op den; Niftrik, L. van

    2016-01-01

    With its capacity for anaerobic methane oxidation and denitrification, the bacterium Methylomirabilis oxyfera plays an important role in natural ecosystems. Its unique physiology can be exploited for more sustainable wastewater treatment technologies. However, operational stability of full-scale

  10. Biodegradation of endosulfan by a soil bacterium.

    Science.gov (United States)

    Shivaramaiah, H M; Kennedy, I R

    2006-01-01

    A bacterium capable of metabolizing endosulfan (6,7,8,9,10,10-hexachloro-1,5,5a,6,9,9a-hexahydro-6,9-methano-2,4,3-benzodioxathiepine3-oxide) was isolated from cotton-growing soil and effectively shown to degrade endosulfan into endosulfan sulfate. The bacterium degraded 50% of the compound within 3 days of incubation. Endosulfan sulfate was the only terminal product and no other metabolites were formed during the incubation. Endosulfan and its metabolites were analyzed by gas chromatography. The metabolites formed indicated that the organism follows an oxidative pathway for metabolism of this pesticide. Therefore, the present study, microbial degradation of endosulfan by a soil bacterium, may provide a basis for the development of bioremediation strategies to remediate the pollutants in the environment.

  11. Adaptive and cross-protective responses against cadmium and zinc toxicity in cadmium-resistant bacterium isolated from a zinc mine

    Directory of Open Access Journals (Sweden)

    Benjaphorn Prapagdee

    2009-12-01

    Full Text Available Cadmium (Cd is a major environmental hazard, which usually is detected in its ionic form of Cd2+. It also causes adverse toxic effects on human health and other living organisms. Cd-resistant bacteria were isolated from Cd-contaminated soils. One isolate, TAK1, was highly resistance level to Cd toxicity. TAK1 was isolated from soil contaminated with a high Cd concentration (204.1 mg.kg-1. The result of 16S rDNA sequence analysis found that the TAK1 showed the similarity to Ralstonia sp. Physiological adaptive and cross-protective responses to Cd and Zn killing were investigated in Ralstonia sp.TAK1. Exposure to a low concentration of Cd induced adaptive resistance to higher concentrations of Cd. In addition, pretreatment of Ralstonia sp.TAK1 with an inducing concentration of Cd conferred cross-protective response against subsequent exposure to the lethal concentrations of Zn. The induced adaptive and cross-protective response Ralstonia sp.TAK1 required newly synthesized protein(s. Cd-induced adaptive and cross-protective responses against Cd and Zn toxicity are the important mechanisms used by Ralstonia sp.TAK1 to survive in the heavy metal contaminated environments. These findings might lead to the use of Ralstonia sp.TAK1 for microbial based remediation in Cd and Zn-contaminated soils.

  12. Anaerobic Biotransformation and Mobility of Pu and Pu-EDTA

    Energy Technology Data Exchange (ETDEWEB)

    Bolton, H., Jr.; Rai, D.; Xun, L.

    2005-04-18

    The complexation of radionuclides (e.g., plutonium (Pu) and {sup 60}Co) by codisposed ethylenediaminetetraacetate (EDTA) has enhanced their transport in sediments at DOE sites. Our previous NABIR research investigated the aerobic biodegradation and biogeochemistry of Pu(IV)-EDTA. Plutonium(IV) forms stable complexes with EDTA under aerobic conditions and an aerobic EDTA degrading bacterium can degrade EDTA in the presence of Pu and decrease Pu mobility. However, our recent studies indicate that while Pu(IV)-EDTA is stable in simple aqueous systems, it is not stable in the presence of relatively soluble Fe(III) compounds (i.e., Fe(OH){sub 3}(s)--2-line ferrihydrite). Since most DOE sites have Fe(III) containing sediments, Pu(IV) in likely not the mobile form of Pu-EDTA in groundwater. The only other Pu-EDTA complex stable in groundwater relevant to DOE sites would be Pu(III)-EDTA, which only forms under anaerobic conditions. Research is therefore needed in this brand new project to investigate the biotransformation of Pu and Pu-EDTA under anaerobic conditions. The biotransformation of Pu and Pu-EDTA under various anaerobic regimes is poorly understood including the reduction kinetics of Pu(IV) to Pu(III) from soluble (Pu(IV)-EDTA) and insoluble Pu(IV) as PuO2(am) by metal reducing bacteria, the redox conditions required for this reduction, the strength of the Pu(III)-EDTA complex, how the Pu(III)-EDTA complex competes with other dominant anoxic soluble metals (e.g., Fe(II)), and the oxidation kinetics of Pu(III)-EDTA. Finally, the formation of a stable soluble Pu(III)-EDTA complex under anaerobic conditions would require degradation of the EDTA complex to limit Pu(III) transport in geologic environments. Anaerobic EDTA degrading microorganisms have not been isolated. These knowledge gaps preclude the development of a mechanistic understanding of how anaerobic conditions will influence Pu and Pu-EDTA fate and transport to assess, model, and design approaches to stop

  13. Anaerobic Biotransformation and Mobility of Pu and Pu-EDTA

    International Nuclear Information System (INIS)

    Bolton, H. Jr.; Rai, D.; Xun, L.

    2005-01-01

    The complexation of radionuclides (e.g., plutonium (Pu) and 60 Co) by codisposed ethylenediaminetetraacetate (EDTA) has enhanced their transport in sediments at DOE sites. Our previous NABIR research investigated the aerobic biodegradation and biogeochemistry of Pu(IV)-EDTA. Plutonium(IV) forms stable complexes with EDTA under aerobic conditions and an aerobic EDTA degrading bacterium can degrade EDTA in the presence of Pu and decrease Pu mobility. However, our recent studies indicate that while Pu(IV)-EDTA is stable in simple aqueous systems, it is not stable in the presence of relatively soluble Fe(III) compounds (i.e., Fe(OH) 3 (s)--2-line ferrihydrite). Since most DOE sites have Fe(III) containing sediments, Pu(IV) in likely not the mobile form of Pu-EDTA in groundwater. The only other Pu-EDTA complex stable in groundwater relevant to DOE sites would be Pu(III)-EDTA, which only forms under anaerobic conditions. Research is therefore needed in this brand new project to investigate the biotransformation of Pu and Pu-EDTA under anaerobic conditions. The biotransformation of Pu and Pu-EDTA under various anaerobic regimes is poorly understood including the reduction kinetics of Pu(IV) to Pu(III) from soluble (Pu(IV)-EDTA) and insoluble Pu(IV) as PuO2(am) by metal reducing bacteria, the redox conditions required for this reduction, the strength of the Pu(III)-EDTA complex, how the Pu(III)-EDTA complex competes with other dominant anoxic soluble metals (e.g., Fe(II)), and the oxidation kinetics of Pu(III)-EDTA. Finally, the formation of a stable soluble Pu(III)-EDTA complex under anaerobic conditions would require degradation of the EDTA complex to limit Pu(III) transport in geologic environments. Anaerobic EDTA degrading microorganisms have not been isolated. These knowledge gaps preclude the development of a mechanistic understanding of how anaerobic conditions will influence Pu and Pu-EDTA fate and transport to assess, model, and design approaches to stop Pu

  14. Taxonomic characterization of the cellulose-degrading bacterium NCIB 10462

    Energy Technology Data Exchange (ETDEWEB)

    Dees, C.; Ringleberg, D.; Scott, T.C. [Oak Ridge National Lab., TN (United States); Phelps, T. [Univ. of Tennessee, Knoxville, TN (United States)

    1994-06-01

    The gram negative cellulase-producing bacterium NCIB 10462 has been previously named Pseudomonas fluorescens subsp. or var. cellulosa. Since there is renewed interest in cellulose-degrading bacteria for use in bioconversion of cellulose to chemical feed stocks and fuels, we re-examined the characteristics of this microorganism to determine its proper taxonomic characterization and to further define it`s true metabolic potential. Metabolic and physical characterization of NCIB 10462 revealed that this was an alkalophilic, non-fermentative, gram negative, oxidase positive, motile, cellulose-degrading bacterium. The aerobic substrate utilization profile of this bacterium was found to have few characteristics consistent with a classification of P. fluorescens with a very low probability match with the genus Sphingomonas. Total lipid analysis did not reveal that any sphingolipid bases are produced by this bacterium. NCIB 10462 was found to grow best aerobically but also grows well in complex media under reducing conditions. NCIB 10462 grew slowly under full anaerobic conditions on complex media but growth on cellulosic media was found only under aerobic conditions. Total fatty acid analysis (MIDI) of NCIB 10462 failed to group this bacterium with a known pseudomonas species. However, fatty acid analysis of the bacteria when grown at temperatures below 37{degrees}C suggest that the organism is a pseudomonad. Since a predominant characteristic of this bacterium is it`s ability to degrade cellulose, we suggest it be called Pseudomonas cellulosa.

  15. High-quality draft genome sequence of Enterobacter sp. Bisph2, a glyphosate-degrading bacterium isolated from a sandy soil of Biskra, Algeria.

    Science.gov (United States)

    Benslama, Ouided; Boulahrouf, Abderrahmane

    2016-06-01

    Enterobacter sp. strain Bisph2 was isolated from a sandy soil from Biskra, Algeria and exhibits glyphosate-degrading activity. Multilocus sequence analysis of the 16S rRNA, rpoB, hsp60, gyrB and dnaJ genes demonstrated that Bisph2 might be a member of a new species of the genus Enterobacter. Genomic sequencing of Bisph2 was used to better clarify the relationships among Enterobacter species. Annotation and analysis of the genome sequence showed that the 5.535.656 bp genome of Enterobacter sp. Bisph2 consists in one chromosome and no detectable plasmid, has a 53.19% GC content and 78% of genes were assigned a putative function. The genome contains four prophages of which 3 regions are intact and no CRISPER was detected. The nucleotide sequence of this genome was deposited into DDBJ/EMBL/GenBank under the accession JXAF00000000.

  16. High-quality draft genome sequence of Enterobacter sp. Bisph2, a glyphosate-degrading bacterium isolated from a sandy soil of Biskra, Algeria

    Directory of Open Access Journals (Sweden)

    Ouided Benslama

    2016-06-01

    Full Text Available Enterobacter sp. strain Bisph2 was isolated from a sandy soil from Biskra, Algeria and exhibits glyphosate-degrading activity. Multilocus sequence analysis of the 16S rRNA, rpoB, hsp60, gyrB and dnaJ genes demonstrated that Bisph2 might be a member of a new species of the genus Enterobacter. Genomic sequencing of Bisph2 was used to better clarify the relationships among Enterobacter species. Annotation and analysis of the genome sequence showed that the 5.535.656 bp genome of Enterobacter sp. Bisph2 consists in one chromosome and no detectable plasmid, has a 53.19% GC content and 78% of genes were assigned a putative function. The genome contains four prophages of which 3 regions are intact and no CRISPER was detected. The nucleotide sequence of this genome was deposited into DDBJ/EMBL/GenBank under the accession JXAF00000000.

  17. 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.

  18. Isolation and characterization of Bacillus subtilis strain BY-3, a thermophilic and efficient cellulase-producing bacterium on untreated plant biomass.

    Science.gov (United States)

    Meng, F; Ma, L; Ji, S; Yang, W; Cao, B

    2014-09-01

    Bioconversion of biomass, particularly crop wastes, into biofuels is being developed as an alternative approach in meeting the high energy demand. In this study, a thermophilic bacterial strain BY-3 that exhibits cellulolytic potential was isolated from faecal samples of Tibetan pigs; this strain was identified as Bacillus subtilis. The strain can produce cellulase when grown on various substrates, including carboxymethyl cellulose, rice straw, corn stover, soluble starch and wheat bran. The maximum cellulase activity of the strain was up to 4·323 ± 0·065 U ml(-1) when cultivated in the medium containing corn stover (30 g l(-1) ) for 24 h. The results demonstrated that corn stover is the most suitable substrate for cellulase production by the strain BY-3. The crude cellulase of strain BY-3 was most active at pH 5·5 and 60°C, and the enzyme in acetate buffer (50 mmol l(-1) ) demonstrated a good stability at 60°C for at least 1 h. The crude cellulase exhibited a strong antibacterial activity against Staphylococcus aureus. The strain can be used in cost-efficient cellulase production for bioconversion of agricultural residual biomass into biofuels. The increased consumption of fossil fuels has caused serious energy crisis and environmental problem. Thus, an alternative energy source is necessary. Bioconversion of biomass, particularly agricultural residuals, into value-added bioproducts, such as biofuels and chemical solvents, has received considerable attention. In this study, the newly isolated thermophilic Bacillus subtilis strain BY-3 produces cellulase efficiently with the use of untreated corn stover as a sole carbon source. This strain possesses the thermostable cellulase that is active with diverse crop wastes with a broad pH range and is a highly promising candidate for agricultural waste management. © 2014 The Society for Applied Microbiology.

  19. Aquiflexum balticum gen. nov., sp. nov., a novel marine bacterium of the Cytophaga-Flavobacterium-Bacteroides group isolated from surface water of the central Baltic Sea.

    Science.gov (United States)

    Brettar, Ingrid; Christen, Richard; Höfle, Manfred G

    2004-11-01

    A bacterial isolate from the Baltic Sea, BA160(T), was characterized for its physiological and biochemical features, fatty acid profile, G+C content and phylogenetic position based on 16S rRNA gene sequences. The strain was isolated from the surface water of the central Baltic Sea during the decay of a plankton bloom. Phylogenetic analyses of the 16S rRNA gene sequence revealed a clear affiliation with the family 'Flexibacteraceae', and showed the closest phylogenetic relationship with the species Belliella baltica and Cyclobacterium marinum. The G+C content of the DNA was 38.4 mol%. The strain was red-coloured due to carotenoids, Gram-negative, rod-shaped, and catalase- and oxidase-positive. Growth was observed at salinities from 0 to 6 %, with an optimum around 1.5 %. Temperature for growth ranged from 4 to 40 degrees C, with an optimum around 30 degrees C. The fatty acids were dominated by branched-chain fatty acids (>87 %), with a high abundance of iso-C(15 : 0) (23 %) and anteiso-C(15 : 0) (19 %). According to its morphology, physiology, fatty acid composition, G+C content and 16S rRNA gene sequence, strain BA160(T) is considered to represent a new genus of the family 'Flexibacteraceae'. Due to its aquatic origin, the name Aquiflexum balticum gen. nov, sp. nov. is suggested for the type species (type strain, BA160(T)=DSM 16537(T)=LMG 22565(T)=CIP 108445(T)) of the new genus.

  20. Microbiological Hydrogen Production by Anaerobic Fermentation and Photosynthetic Process

    International Nuclear Information System (INIS)

    Asada, Y.; Ohsawa, M.; Nagai, Y.; Fukatsu, M.; Ishimi, K.; Ichi-ishi, S.

    2009-01-01

    Hydrogen gas is a clean and renewable energy carrier. Microbiological hydrogen production from glucose or starch by combination used of an anaerobic fermenter and a photosynthetic bacterium, Rhodobacter spheroides RV was studied. In 1984, the co-culture of Clostridium butyricum and RV strain to convert glucose to hydrogen was demonstrated by Miyake et al. Recently, we studied anaerobic fermentation of starch by a thermophilic archaea. (Author)

  1. pGIAK1, a heavy metal resistant plasmid from an obligate alkaliphilic and halotolerant bacterium isolated from the Antarctic Concordia station confined environment.

    Directory of Open Access Journals (Sweden)

    Suxia Guo

    Full Text Available pGIAK1 is a 38-kb plasmid originating from the obligate alkaliphilic and halotolerant Bacillaceae strain JMAK1. The strain was originally isolated from the confined environments of the Antarctic Concordia station. Analysis of the pGIAK1 38,362-bp sequence revealed that, in addition to its replication region, this plasmid contains the genetic determinants for cadmium and arsenic resistances, putative methyltransferase, tyrosine recombinase, spore coat protein and potassium transport protein, as well as several hypothetical proteins. Cloning the pGIAK1 cad operon in Bacillus cereus H3081.97 and its ars operon in Bacillus subtilis 1A280 conferred to these hosts cadmium and arsenic resistances, respectively, therefore confirming their bona fide activities. The pGIAK1 replicon region was also shown to be functional in Bacillus thuringiensis, Bacillus subtilis and Staphylococcus aureus, but was only stably maintained in B. subtilis. Finally, using an Escherichia coli - B. thuringiensis shuttle BAC vector, pGIAK1 was shown to display conjugative properties since it was able to transfer the BAC plasmid among B. thuringiensis strains.

  2. Nitrogen-removal efficiency of a novel aerobic denitrifying bacterium, Pseudomonas stutzeri strain ZF31, isolated from a drinking-water reservoir.

    Science.gov (United States)

    Huang, Tinglin; Guo, Lin; Zhang, Haihan; Su, Junfeng; Wen, Gang; Zhang, Kai

    2015-11-01

    An aerobic denitrifier, identified as Pseudomonas stutzeri strain ZF31, was isolated from the Zhoucun drinking-water reservoir. Strain ZF31 removed 97% of nitrate nitrogen after 16h, without nitrite accumulation. Sequence amplification indicated the presence of the denitrification genes napA, nirS, norB, and nosZ. Nitrogen balance analysis revealed that approximately 75% of the initial nitrogen was removed as gas products. Response surface methodology (RSM) experiments showed that maximum removal of total nitrogen (TN) occurred at pH 8.23, a C/N ratio of 6.68, temperature of 27.72°C, and with shaking at 54.15rpm. The TN removal rate at low C/N ratio (i.e., 3) and low temperature (i.e., 10°C) was 73.30% and 60.08%, respectively. These results suggest that strain ZF31 has potential applications for the bioremediation of slightly polluted drinking-water reservoirs. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Isolation and characterization of a cold-active, alkaline, detergent stable α-amylase from a novel bacterium Bacillus subtilis N8.

    Science.gov (United States)

    Arabacı, Nihan; Arıkan, Burhan

    2018-03-21

    A cold-active alkaline amylase producer Bacillus subtilis N8 was isolated from soil samples. Amylase synthesis optimally occurred at 15°C and pH 10.0 on agar plates containing starch. The molecular weight of the enzyme was found to be 205 kDa by performing SDS-PAGE. While the enzyme exhibited the highest activity at 25°C and pH 8.0, it was highly stable in alkaline media (pH 8.0-12.0) and retained 96% of its original activity at low temperatures (10-40°C) for 24 h. While the amylase activity increased in the presence of β-mercaptoethanol (103%); Ba 2+ , Ca 2+ , Na + , Zn 2+ , Mn 2+ , H 2 O 2 and TritonX-100 slightly inhibited the activity. The enzyme showed resistance to some denaturants: such as SDS, EDTA, and urea (52, 65 and 42%, respectively). N8 α -amylase displayed the maximum remaining activity of 56% with 3% NaCl. The major final products of starch were glucose, maltose, and maltose-derived oligosaccharides. This novel cold-active α -amylase has the potential to be used in the industries of detergent and food, bioremediation process and production of prebiotics.

  4. Bacillus velezensis sp. nov., a surfactant-producing bacterium isolated from the river Vélez in Málaga, southern Spain.

    Science.gov (United States)

    Ruiz-García, Cristina; Béjar, Victoria; Martínez-Checa, Fernando; Llamas, Inmaculada; Quesada, Emilia

    2005-01-01

    Two Gram-positive, endospore-forming bacterial strains, CR-502T and CR-14b, which produce surfactant molecules are described. Phenotypic tests and phylogenetic analyses showed these strains to be members of the genus Bacillus and related to the species Bacillus atrophaeus, Bacillus mojavensis, Bacillus subtilis, Bacillus vallismortis and Bacillus amyloliquefaciens, although they differ from these species in a number of phenotypic characteristics. DNA-DNA hybridization confirmed that they show less than 20 % hybridization with the above-mentioned species and therefore represent a novel species of Bacillus. The DNA G+C content is 46.4 mol% in strain CR-502T and 46.1 mol% in strain CR-14b. The main fatty acids in strain CR-502T are 15 : 0 anteiso (32.70 %), 15 : 0 iso (29.86 %) and 16 : 0 (13.41 %). The main quinone in strain CR-502T is MK-7 (96.6 %). In the light of the polyphasic evidence gathered in this study, it is proposed that these strains be classified as a novel species of the genus Bacillus, with the name Bacillus velezensis sp. nov. The type strain (CR-502T=CECT 5686T=LMG 22478T) was isolated from a brackish water sample taken from the river Vélez at Torredelmar in Málaga, southern Spain.

  5. Porphyromonas pogonae sp. nov., an anaerobic but low concentration oxygen adapted coccobacillus isolated from lizards (Pogona vitticeps) or human clinical specimens, and emended description of the genus Porphyromonas Shah and Collins 1988.

    Science.gov (United States)

    Kawamura, Yoshiaki; Kuwabara, Saki; Kania, Stephen A; Kato, Hisayuki; Hamagishi, Manami; Fujiwara, Nagatoshi; Sato, Takuichi; Tomida, Junko; Tanaka, Kaori; Bemis, David A

    2015-03-01

    During the process of identifying a Gram-negative coccobacillus isolated from a human clinical specimen, we found that the isolate's 16S rRNA gene had very close sequence identity with that of a variant Porphyromonas isolated from polymicrobial infections in the central bearded dragon, a species of lizard [2]. The 16S rRNA gene sequences of the human isolate and of six isolates from lizards were nearly identical (99.9-100%). Phylogenetic analysis placed all of these isolates in a single phylogenetic cluster well separated from other species in the genus Porphyromonas. The closest species was Porphyromonas catoniae with 90.7-90.9% sequence identity, although there was less than 6% DNA similarity between the P. catoniae type strain and our representative isolates from lizards (PAGU 1787(T)) and human (PAGU 1776). These isolates could grow under anaerobic or microaerobic conditions (6% O2 atmosphere). The isolates were positive for catalase and very strong β-hemolytic activity, but did not show black or brown pigmentation. Biochemically, the isolates could be differentiated from closely related species by pyroglutamic acid arylamidase and glycine arylamidase activity, and some others. The fermentation products mainly included succinic acid and propionic acid. The major fatty acids detected in cells of the isolates were iso-C15:0, anteiso-C15:0, and 3OH-iso-C17:0. The G+C content was 43.0 ± 0.62 mol%. The species name Porphyromonas pogonae sp. nov. is proposed for these isolates with the type strain of PAGU 1787(T) (=MI 10-1288(T)=JCM 19732(T)=ATCC BAA-2643(T)). Copyright © 2014 Elsevier GmbH. All rights reserved.

  6. 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.

  7. In vitro activity of mecillinam against anaerobic bacteria.

    OpenAIRE

    Steinkraus, G E; McCarthy, L R

    1980-01-01

    A microtiter broth dilution method was employed to determine the in vitro activity of mecillinam against 201 recent clinical isolates of anaerobic bacteria. Both the anerobic gram-positive and anaerobic gram-negative bacilli displayed a wide range of minimal inhibitory concentrations of mecillinam; most strains were resistant to the antibiotic. The anaerobic cocci exhibited a narrower range of minimal inhibitory concentrations than were observed with other anaerobes, but also exhibited mecill...

  8. 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

  9. Treatment of Alkaline Cr(VI)-Contaminated Leachate with an Alkaliphilic Metal-Reducing Bacterium.

    Science.gov (United States)

    Watts, Mathew P; Khijniak, Tatiana V; Boothman, Christopher; Lloyd, Jonathan R

    2015-08-15

    Chromium in its toxic Cr(VI) valence state is a common contaminant particularly associated with alkaline environments. A well-publicized case of this occurred in Glasgow, United Kingdom, where poorly controlled disposal of a cementitious industrial by-product, chromite ore processing residue (COPR), has resulted in extensive contamination by Cr(VI)-contaminated alkaline leachates. In the search for viable bioremediation treatments for Cr(VI), a variety of bacteria that are capable of reduction of the toxic and highly soluble Cr(VI) to the relatively nontoxic and less mobile Cr(III) oxidation state, predominantly under circumneutral pH conditions, have been isolated. Recently, however, alkaliphilic bacteria that have the potential to reduce Cr(VI) under alkaline conditions have been identified. This study focuses on the application of a metal-reducing bacterium to the remediation of alkaline Cr(VI)-contaminated leachates from COPR. This bacterium, belonging to the Halomonas genus, was found to exhibit growth concomitant to Cr(VI) reduction under alkaline conditions (pH 10). Bacterial cells were able to rapidly remove high concentrations of aqueous Cr(VI) (2.5 mM) under anaerobic conditions, up to a starting pH of 11. Cr(VI) reduction rates were controlled by pH, with slower removal observed at pH 11, compared to pH 10, while no removal was observed at pH 12. The reduction of aqueous Cr(VI) resulted in the precipitation of Cr(III) biominerals, which were characterized using transmission electron microscopy and energy-dispersive X-ray analysis (TEM-EDX) and X-ray photoelectron spectroscopy (XPS). The effectiveness of this haloalkaliphilic bacterium for Cr(VI) reduction at high pH suggests potential for its use as an in situ treatment of COPR and other alkaline Cr(VI)-contaminated environments. Copyright © 2015, Watts et al.

  10. Anaerobic biodegradability of macropollutants

    DEFF Research Database (Denmark)

    Angelidaki, Irini

    2002-01-01

    A variety of test procedures for determination of anaerobic biodegradability has been reported. This paper reviews the methods developed for determination of anaerobic biodegradability of macro-pollutants. Anaerobic biodegradability of micro-pollutants is not included. Furthermore, factors...

  11. Enrichment and characterization of an anaerobic cellulolytic microbial consortium SQD-1.1 from mangrove soil.

    Science.gov (United States)

    Gao, Zhao-Ming; Xu, Xun; Ruan, Ling-Wei

    2014-01-01

    Enrichment of microbial consortia provides an approach to simulate and investigate microbial communities in natural environments. In this study, a cellulolytic microbial consortium SQD-1.1 was enriched from mangrove soil of Qinglan port (Hainan, China) by 27 times continuous subcultivation under anaerobic static conditions. The consortium could completely degrade 0.2% (w/v) filter paper within 3 days and utilized it as the sole carbon source. PCR-denaturing gradient gel electrophoresis analysis revealed a stable microbial community structure in the incubation process of 10 days and in the procedure of subcultivation. Twenty-four operational taxonomic units belonging to seven phyla were obtained from the full-length 16S rRNA gene library. Five clones, closest related to the genera Alkaliflexus, Clostridium, Alistipes, Spirochaeta, and Trichococcus, were the predominant ones. Among them, M117, phylogeneticly showing high similarity (16S rRNA gene identity, 95.3%) with the cellulolytic anaerobic bacterium Clostridium straminisolvens CSK1(T), was the potential key cellulolytic bacterium. Using the plate cultivation method, 12 strains, including one potential new species and four potential new species of new genera, were isolated. The strain P2, corresponding to the most frequently detected clone (M05) in the 16S rRNA gene library, showed both CMCase and xylanase activity and may be another important cellulolytic bacterium. The findings of cellulase activity in cell pellet and cohesion and dockerin domains in metagenome data further suggested the potential of utilization of cellulosomes by the consortium to degrade cellulose. Consortium SQD-1.1 provides a candidate for investigating the mechanism of cellulose degradation under anoxic conditions in natural environments.

  12. Probing the redox metabolism in the strictly anaerobic, extremely thermophilic, hydrogen-producing Caldicellulosiruptor saccharolyticus using amperometry

    DEFF Research Database (Denmark)

    Kostesha, Natalie; Willquist, Karin; Emnéus, Jenny

    2011-01-01

    Changes in the redox metabolism in the anaerobic, extremely thermophilic, hydrogen-forming bacterium Caldicellulosiruptor saccharolyticus were probed for the first time in vivo using mediated amperometry with ferricyanide as a thermotolerant external mediator. Clear differences in the intracellul...

  13. [Achievement of Sulfate-Reducing Anaerobic Ammonium Oxidation Reactor Started with Nitrate-Reducting Anaerobic Ammonium Oxidation].

    Science.gov (United States)

    Liu, Zheng-chuan; Yuan, Lin-jiang; Zhou, Guo-biao; Li, Jing

    2015-09-01

    The transformation of nitrite-reducing anaerobic ammonium oxidation to sulfate-reducing anaerobic ammonium oxidation in an UASB was performed and the changes in microbial community were studied. The result showed that the sulfate reducing anaerobic ammonium oxidation process was successfully accomplished after 177 days' operation. The removal rate of ammonium nitrogen and sulfate were up to 58. 9% and 15. 7%, the removing load of ammonium nitrogen and sulfate were 74. 3 mg.(L.d)-1 and 77. 5 mg.(L.d)-1 while concentration of ammonium nitrogen and sulfate of influent were 130 mg.(L.d)-1 and 500 mg.(L.d)-1, respectively. The lost nitrogen and sulphur was around 2 in molar ratio. The pH value of the effluent was lower than that of the influent. Instead of Candidatus brocadia in nitrite reducing anaerobic ammonium oxidation granular sludge, Bacillus benzoevorans became the dominant species in sulfate reducing anaerobic ammonium oxidation sludge. The dominant bacterium in the two kinds of anaerobic ammonium oxidation process is different. Our results imply that the two anaerobic ammonium oxidation processes are carried out by different kind of bacterium.

  14. Anaerobic Bacteria in Clinical Specimens – Frequent, But a Neglected Lot: A Five Year Experience at a Tertiary Care Hospital

    Science.gov (United States)

    Shenoy, Padmaja Ananth; Gawda, Ashwini; Shetty, Seema; Anegundi, Renuka; Varma, Muralidhar; Mukhopadhyay, Chiranjay; Chawla, Kiran

    2017-01-01

    Introduction Anaerobic bacteria which constitute a significant proportion of the normal microbiota also cause variety of infections involving various anatomic sites. Considering the tedious culture techniques with longer turnaround time, anaerobic cultures are usually neglected by clinicians and microbiologists. Aim To study the frequency of isolation of different anaerobic bacteria from various clinical specimens. Materials and Methods A retrospective study to analyse the frequency of isolation of different anaerobic bacteria, was conducted over a period of five years from 2011 to 2015 including various clinical specimens submitted to anaerobic division of Microbiology laboratory. Anaerobic bacteria were isolated and identified following standard bacteriological techniques. Results Pathogenic anaerobes (n=336) were isolated from 278 (12.48%) of overall 2227 specimens processed with an average yield of 1.2 isolates. Anaerobes were isolated as polymicrobial flora with or without aerobic bacterial pathogens in 159 (57.2%) patients. Anaerobic Gram-negative bacilli (140, 41.7%) were the predominant isolates. B. fragilis group (67, 19.9%) were the most commonly isolated anaerobic pathogens. Anaerobes were predominantly isolated from deep seated abscess (23.9%). Conclusion Pathogenic anaerobes were isolated from various infection sites. Unless culture and susceptibility tests are performed as a routine, true magnitude of antimicrobial resistance among anaerobic pathogens will not be known. Knowledge of the distribution of these organisms may assist in the selection of appropriate empirical therapy for anaerobic infections. PMID:28892897

  15. Anaerobic Bacteria in Clinical Specimens - Frequent, But a Neglected Lot: A Five Year Experience at a Tertiary Care Hospital.

    Science.gov (United States)

    Shenoy, Padmaja Ananth; Vishwanath, Shashidhar; Gawda, Ashwini; Shetty, Seema; Anegundi, Renuka; Varma, Muralidhar; Mukhopadhyay, Chiranjay; Chawla, Kiran

    2017-07-01

    Anaerobic bacteria which constitute a significant proportion of the normal microbiota also cause variety of infections involving various anatomic sites. Considering the tedious culture techniques with longer turnaround time, anaerobic cultures are usually neglected by clinicians and microbiologists. To study the frequency of isolation of different anaerobic bacteria from various clinical specimens. A retrospective study to analyse the frequency of isolation of different anaerobic bacteria, was conducted over a period of five years from 2011 to 2015 including various clinical specimens submitted to anaerobic division of Microbiology laboratory. Anaerobic bacteria were isolated and identified following standard bacteriological techniques. Pathogenic anaerobes (n=336) were isolated from 278 (12.48%) of overall 2227 specimens processed with an average yield of 1.2 isolates. Anaerobes were isolated as polymicrobial flora with or without aerobic bacterial pathogens in 159 (57.2%) patients. Anaerobic Gram-negative bacilli (140, 41.7%) were the predominant isolates. B. fragilis group (67, 19.9%) were the most commonly isolated anaerobic pathogens. Anaerobes were predominantly isolated from deep seated abscess (23.9%). Pathogenic anaerobes were isolated from various infection sites. Unless culture and susceptibility tests are performed as a routine, true magnitude of antimicrobial resistance among anaerobic pathogens will not be known. Knowledge of the distribution of these organisms may assist in the selection of appropriate empirical therapy for anaerobic infections.

  16. Physiologically anaerobic microorganisms of the deep subsurface

    Energy Technology Data Exchange (ETDEWEB)

    Stevens, S.E. Jr.; Chung, K.T.

    1992-06-01

    A variety of different media were used to isolate facultatively (FAB) and obligately anaerobic bacteria (OAB). These bacteria were isolated from core subsamples obtained from boreholes at the Idaho National Engineering Lab. (INEL) or at the Hanford Lab. (Yakima). Core material was sampled at various depths to 600 feet below the surface. All core samples with culturable bacteria contained at least FAB making thisthe most common physiological type of anaerobic bacteria present in the deep subsurface at these two sites. INEL core samples are characterized by isolates of both FAB and OAB. No isolates of acetogenic, methanogenic, or sulfate reducing bacteria were obtained. Yakima core samples are characterized by a marked predominance of FAB in comparison to OAB. In addition, isolates of acetogenic, methanogenic, and sulfate reducing bacteria were obtained. The Yakima site has the potential for complete anaerobic mineralization of organic compounds whereas this potential appears to be lacking at INEL.

  17. Anaerobic Thermophiles

    Directory of Open Access Journals (Sweden)

    Francesco Canganella

    2014-02-01

    Full Text Available The term “extremophile” was introduced to describe any organism capable of living and growing under extreme conditions. With the further development of studies on microbial ecology and taxonomy, a variety of “extreme” environments have been found and an increasing number of extremophiles are being described. Extremophiles have also been investigated as far as regarding the search for life on other planets and even evaluating the hypothesis that life on Earth originally came from space. The first extreme environments to be largely investigated were those characterized by elevated temperatures. The naturally “hot environments” on Earth range from solar heated surface soils and water with temperatures up to 65 °C, subterranean sites such as oil reserves and terrestrial geothermal with temperatures ranging from slightly above ambient to above 100 °C, to submarine hydrothermal systems with temperatures exceeding 300 °C. There are also human-made environments with elevated temperatures such as compost piles, slag heaps, industrial processes and water heaters. Thermophilic anaerobic microorganisms have been known for a long time, but scientists have often resisted the belief that some organisms do not only survive at high temperatures, but actually thrive under those hot conditions. They are perhaps one of the most interesting varieties of extremophilic organisms. These microorganisms can thrive at temperatures over 50 °C and, based on their optimal temperature, anaerobic thermophiles can be subdivided into three main groups: thermophiles with an optimal temperature between 50 °C and 64 °C and a maximum at 70 °C, extreme thermophiles with an optimal temperature between 65 °C and 80 °C, and finally hyperthermophiles with an optimal temperature above 80 °C and a maximum above 90 °C. The finding of novel extremely thermophilic and hyperthermophilic anaerobic bacteria in recent years, and the fact that a large fraction of them belong

  18. Anaerobic benzene degradation by bacteria.

    Science.gov (United States)

    Vogt, Carsten; Kleinsteuber, Sabine; Richnow, Hans-Hermann

    2011-11-01

    Benzene is a widespread and toxic contaminant. The fate of benzene in contaminated aquifers seems to be primarily controlled by the abundance of oxygen: benzene is aerobically degraded at high rates by ubiquitous microorganisms, and the oxygen-dependent pathways for its breakdown were elucidated more than 50 years ago. In contrast, benzene was thought to be persistent under anoxic conditions until 25 years ago. Nevertheless, within the last 15 years, several benzene-degrading cultures have been enriched under varying electron acceptor conditions in laboratories around the world, and organisms involved in anaerobic benzene degradation have been identified, indicating that anaerobic benzene degradation is a relevant environmental process. However, only a few benzene degraders have been isolated in pure culture so far, and they all use nitrate as an electron acceptor. In some highly enriched strictly anaerobic cultures, benzene has been described to be mineralized cooperatively by two or more different organisms. Despite great efforts, the biochemical mechanism by which the aromatic ring of benzene is activated in the absence of oxygen is still not fully elucidated; methylation, hydroxylation and carboxylation are discussed as likely reactions. This review summarizes the current knowledge about the 'key players' of anaerobic benzene degradation under different electron acceptor conditions and the possible pathway(s) of anaerobic benzene degradation. © 2011 The Authors; Journal compilation © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

  19. Anaerobic benzene degradation by bacteria

    Science.gov (United States)

    Vogt, Carsten; Kleinsteuber, Sabine; Richnow, Hans‐Hermann

    2011-01-01

    Summary Benzene is a widespread and toxic contaminant. The fate of benzene in contaminated aquifers seems to be primarily controlled by the abundance of oxygen: benzene is aerobically degraded at high rates by ubiquitous microorganisms, and the oxygen‐dependent pathways for its breakdown were elucidated more than 50 years ago. In contrast, benzene was thought to be persistent under anoxic conditions until 25 years ago. Nevertheless, within the last 15 years, several benzene‐degrading cultures have been enriched under varying electron acceptor conditions in laboratories around the world, and organisms involved in anaerobic benzene degradation have been identified, indicating that anaerobic benzene degradation is a relevant environmental process. However, only a few benzene degraders have been isolated in pure culture so far, and they all use nitrate as an electron acceptor. In some highly enriched strictly anaerobic cultures, benzene has been described to be mineralized cooperatively by two or more different organisms. Despite great efforts, the biochemical mechanism by which the aromatic ring of benzene is activated in the absence of oxygen is still not fully elucidated; methylation, hydroxylation and carboxylation are discussed as likely reactions. This review summarizes the current knowledge about the ‘key players’ of anaerobic benzene degradation under different electron acceptor conditions and the possible pathway(s) of anaerobic benzene degradation. PMID:21450012

  20. Salt-inducible promoter derivable from a lactic acid bacterium, and its use in a lactic acid bacterium for production of a desired protein

    NARCIS (Netherlands)

    Sanders, Jan Willem; Kok, Jan; Venema, Gerard; Ledeboer, Adrianus Marinus

    1998-01-01

    The invention provides a salt-inducible promoter present in SEQ ID NO: 10 and derivable from a lactic acid bacterium in isolation from the coding sequence normally controlled by said promoter in a wild-type lactic acid bacterium, with modifications and important parts thereof. Also provided are a

  1. Infections Caused by Actinomyces neuii: A Case Series and Review of an Unusual Bacterium

    Directory of Open Access Journals (Sweden)

    Nathan Zelyas

    2016-01-01

    Full Text Available Background. Actinomyces neuii is a Gram-positive bacillus rarely implicated in human infections. However, its occurrence is being increasingly recognized with the use of improved identification systems. Objective. To analyse A. neuii infections in Alberta, Canada, and review the literature regarding this unusual pathogen. Methods. Cases of A. neuii were identified in 2013-2014 in Alberta. Samples were cultured aerobically and anaerobically. A predominant catalase positive Gram-positive coryneform bacillus with no branching was isolated in each case. Testing was initially done with API-CORYNE® (bioMérieux and isolates were sent to the Provincial Laboratory for Public Health for further testing. Isolates’ identities were confirmed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry microbial identification system (MALDI-TOF MS MIS; bioMérieux and/or DNA sequencing. Results. Six cases of A. neuii infection were identified. All patients had soft tissue infections; typically, incision and drainage were done followed by a course of antibiotics. Agents used included cephalexin, ertapenem, ciprofloxacin, and clindamycin. All had favourable outcomes. Conclusions. While A. neuii is infrequently recognized, it can cause a diverse array of infections. Increased use of MALDI-TOF MS MIS is leading to increased detection; thus, understanding the pathogenicity of this bacterium and its typical susceptibility profile will aid clinical decision-making.

  2. Anaerobic fungal populations

    International Nuclear Information System (INIS)

    Brookman, J.L.; Nicholson, M.J.

    2005-01-01

    The development of molecular techniques has greatly broadened our view of microbial diversity and enabled a more complete detection and description of microbial communities. The application of these techniques provides a simple means of following community changes, for example, Ishii et al. described transient and more stable inhabitants in another dynamic microbial system, compost. Our present knowledge of anaerobic gut fungal population diversity within the gastrointestinal tract is based upon isolation, cultivation and observations in vivo. It is likely that there are many species yet to be described, some of which may be non-culturable. We have observed a distinct difference in the ease of cultivation between the different genera, for example, Caecomyes isolates are especially difficult to isolate and maintain in vitro, a feature that is likely to result in the under representation of this genera in culture-based enumerations. The anaerobic gut fungi are the only known obligately anaerobic fungi. For the majority of their life cycles, they are found tightly associated with solid digesta in the rumen and/or hindgut. They produce potent fibrolytic enzymes and grow invasively on and into the plant material they are digesting making them important contributors to fibre digestion. This close association with intestinal digesta has made it difficult to accurately determine the amount of fungal biomass present in the rumen, with Orpin suggesting 8% contribution to the total microbial biomass, whereas Rezaeian et al. more recently gave a value of approximately 20%. It is clear that the rumen microbial complement is affected by dietary changes, and that the fungi are more important in digestion in the rumens of animals fed with high-fibre diets. It seems likely that the gut fungi play an important role within the rumen as primary colonizers of plant fibre, and so we are particularly interested in being able to measure the appearance and diversity of fungi on the plant

  3. Species identification of clinical isolates of anaerobic bacteria: a comparison of two matrix-assisted laser desorption ionization-time of flight mass spectrometry systems

    DEFF Research Database (Denmark)

    Justesen, Ulrik Stenz; Holm, Anette; Knudsen, Elisa

    2011-01-01

    We compared two matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems (Shimadzu/SARAMIS and Bruker) on a collection of consecutive clinically important anaerobic bacteria (n = 290). The Bruker system had more correct identifications to the species level...... (67.2% versus 49.0%), but also more incorrect identifications (7.9% versus 1.4%). The system databases need to be optimized to increase identification levels. However, MALDI-TOF MS in its present version seems to be a fast and inexpensive method for identification of most clinically important...

  4. Anaerobic bacterial meningitis in adults.

    Science.gov (United States)

    Lee, Jun-Jun; Lien, Chia-Yi; Chien, Chun-Chih; Huang, Chi-Ren; Tsai, Nai-Wen; Chang, Chiung-Chih; Lu, Cheng-Hsien; Chang, Wen-Neng

    2018-01-22

    Anaerobic infection is a very uncommon condition in adult bacterial meningitis (ABM), and its clinical characteristics have yet to be clarified. We enrolled 540 patients with culture-proven bacterial meningitis during a study period of 30 years (1986-2015), of whom 13 (2.4%) had anaerobic infections. These 13 patients were eight men and five women, aged 22-77 years. Among them, 53.8% (7/13) had a postneurosurgical state as the preceding event, and 79.6% (10/13) had underlying medical conditions including diabetes mellitus, malignancy, liver cirrhosis, cerebral infarct and alcoholism. Nosocomial and mixed infections were found in 15.5% (2/13) and 46.1% (6/13) of the patients, respectively. A total of 14 anaerobic strains were isolated from cerebrospinal fluid specimens, including nine Gram-negative (G(-)) strains: Fusobacterium nucleatum (3), Prevotella species (3) and Bacteroides fragilis (3), and five Gram-positive (G(+)) strains: Propionibacterium acnes (3) and Peptostreptococcus micros (also known as Parvimonas micra) (2). All of the implicated G(+) anaerobic bacteria were susceptible to penicillin, and no multiple drug-resistant strains were found among the implicated G(-) anaerobic bacteria. Despite treatment, 30.8% (4/13) of the patients died. Of the nine survivors, 22.2% (2/9) had a full recovery, while the other 77.8% (7/9) had varying degrees of neurological deficits. Compared with the good outcome group (n = 6, modified Rankin scale (mRS) scores: 0-2), the poor outcome group (n = 7, mRS scores ≧3) had higher incidence of seizure. These results may offer a preliminary view of the clinical characteristics of anaerobic ABM. Copyright © 2018 Elsevier Ltd. All rights reserved.

  5. Anaerobic Digestion: Process

    DEFF Research Database (Denmark)

    Angelidaki, Irini; Batstone, Damien J.

    2011-01-01

    Organic waste may degrade anaerobically in nature as well as in engineered systems. The latter is called anaerobic digestion or biogasification. Anaerobic digestion produces two main outputs: An energy-rich gas called biogas and an effluent. The effluent, which may be a solid as well as liquid...... with very little dry matter may also be called a digest. The digest should not be termed compost unless it specifically has been composted in an aerated step. This chapter describes the basic processes of anaerobic digestion. Chapter 9.5 describes the anaerobic treatment technologies, and Chapter 9.......6 addresses the mass balances and environmental aspects of anaerobic digestion....

  6. [Anaerobes analysis in 80 cases with ora maxillofacial infections

    Science.gov (United States)

    Huang, Y F

    1999-12-01

    OBJECTIVE:To define the infection types of 80 cases of ora-maxillofacial infection and investigate its anaerobes' distribution and the role of the anaerobes' metabolic products in their identification.METHODS:We isolated and cultured anaerobes from the purulent specimen and applied the gasliquid chromatograph (GLC) technique to analyze the anaerobes' metabolic products to define their genera and species in the meantime.RESULTS:Bacteria were isolated from all of the purulent specimen.Isolation rate of bacteria was 100.00% and isolation rate of anaerobes,which distributed in 8 genera,29 species,was 95.00%. The higher detectable rate of them were respectively peptostreptococcus,petococcus,bacteroides,fusobacterium,verillonella,eubacterium. The rate of mixed infection was 80.00%. The proportion ratio of aerobes and anaerobes was 1:1.08.CONCLUSION:Oral-maxillofacial infection mostly belongs to endogenous mixed infection in which anaerobes are preponderant bacteria. GLC technique is a effective,sensitive,selective and specific method for defining anaerobes' genera and species through analyzing their metabolic products. It is a promising and recommendable rapid anaerobes' identification method comparatively at present.

  7. Hemicellulases from the ethanologenic thermophile, Thermoanaerobacter ethanolicus and related anaerobic thermophiles. Final report, September 1992--June 1996

    Energy Technology Data Exchange (ETDEWEB)

    Wiegel, J.

    1998-09-01

    The short term goals of this application were to characterize hemicellulases from anaerobic thermophiles on the biochemical and molecular level to extend the presently limited knowledge of hemicellulases in anaerobic thermophilic bacteria. This objective includes the following tasks: (1) Traditional purification and biochemical/biophysical characterization of xylanases from the newly isolated, slightly alkalitolerant strain NDF190, and the slightly acid-tolerant strain YS485, both with high xylanolytic activities, and of the 4-O-methyl glucuronidase and arabinosidase from strain NDF190 and the acetyl (xylan) esterase from T. ethanolicus. This also includes determining the N-terminal sequences and obtaining gene probes. (2) Elucidation of the regulation of hemicellulolytic enzymes in anaerobic thermophiles. (3) To clone into E. coli and identify the multiplicity of the enzymes involved in hemicellulose degradation by T. ethanolicus and other suitable organisms. (4) To purify and characterize the recombinant enzymes with the goal of identifying the best enzymes for cloning into the ethanologenic T. ethanolicus to obtain an optimized hemicellulose utilization by this bacterium.

  8. Hemicellulases from the ethanologenic thermophile Thermoanaerobacter ethanolicus and related anaerobic thermophiles. Final report, September 1992--June 1996

    Energy Technology Data Exchange (ETDEWEB)

    Wiegel, J.

    1998-05-01

    The SHORT TERM GOALS of this application were to characterize hemicellulases from anaerobic thermophiles on the biochemical and molecular level to extend the presently limited knowledge of hemicellulases in anaerobic thermophilic bacteria. This objective includes the following TASKS: (1) Traditional purification and biochemical/biophysical characterization of xylanases from the newly isolated, slightly alkalitolerant strain NDF190, and the slightly acid-tolerant strain YS485, both with high xylanolytic activities, and of the 4-0-methyl glucuronidase and arabinosidase from strain NDF190 and the acetyl (xylan) esterase from T. ethanolicus. This also includes determining the N-terminal sequences and obtaining gene probes. (2) Elucidation of the regulation of hemicellulolytic enzymes in anaerobic thermophiles. (3) To clone into E. coli and identify the multiplicity of the enzymes involved in hemicellulose degradation by T. ethanolicus and other suitable organisms. (4) To purify and characterize the recombinant enzymes with the goal of identifying the best enzymes for cloning into the ethanologenic T. ethanolicus to obtain an optimized hemicellulose utilization by this bacterium (one of our long term goals).

  9. Livestock Anaerobic Digester Database

    Science.gov (United States)

    The Anaerobic Digester Database provides basic information about anaerobic digesters on livestock farms in the United States, organized in Excel spreadsheets. It includes projects that are under construction, operating, or shut down.

  10. [Application of anaerobic bacteria detection in oral and maxillofacial infection].

    Science.gov (United States)

    Bao, Zhen-ying; Lin, Qin; Meng, Yan-hong; He, Chun; Su, Jia-zeng; Peng, Xin

    2016-02-18

    To investigate the distribution and drug resistance of anaerobic bacteria in the patients with oral and maxillofacial infection. Aerobic and anaerobic bacteria cultures from 61 specimens of pus from the patients with oral and maxillofacial infection in the Department of Oral and Maxillofacial Surgery, Peking University School of Stomatology were identified. The culture type was evaluated by API 20A kit and drug resistance test was performed by Etest method. The clinical data and antibacterial agents for the treatment of the 61 cases were collected, and the final outcomes were recorded. The bacteria cultures were isolated from all the specimens, with aerobic bacteria only in 6 cases (9.8%), anaerobic bacteria only in 7 cases (11.5%), and both aerobic and anaerobic bacteria in 48 cases (78.7%). There were 55 infected cases (90.2%) with anaerobic bacteria, and 81 anaerobic bacteria stains were isolated. The highest bacteria isolation rate of Gram positive anaerobic bacteria could be found in Peptostreptococcus, Bifidobacterium and Pemphigus propionibacterium. No cefoxitin, amoxicillin/carat acid resistant strain was detected in the above three Gram positive anaerobic bacteria. The highest bacteria isolation rate of Gram negative anaerobic bacteria could be detected in Porphyromonas and Prevotella. No metronidazole, cefoxitin, amoxicillin/carat acid resistant strain was found in the two Gram negative anaerobic bacteria. In the study, 48 patients with oral and maxillofacial infection were treated according to the results of drug resistance testing, and the clinical cure rate was 81.3%. Mixed aerobic and anaerobic bacteria cultures are very common in most oral and maxillofacial infection patients. Anaerobic bacteria culture and drug resistance testing play an important role in clinical treatment.

  11. Screening and characterization of petroleum-degrading bacterium ...

    African Journals Online (AJOL)

    Petroleum-degrading bacterium JY6 was isolated from petroleum-contaminated soils in DaQing oil field. It was identified as Bacillus cereus based on its morphological, physiological and biochemical characteristics, and analysis of its 16SrRNA gene. Biodegradation function of petroleum and oil degradation rates were ...

  12. Isolation and purification of membrane-bound cytochrome c from ...

    African Journals Online (AJOL)

    Administrator

    2007-05-02

    ferrochrome and redox spectra showed the presence of heme-c. Key words: Cytochrome c, respiratory chain and Proteus mirabilis. INTRODUCTION. Proteus mirabilis is facultative anaerobic, rod-shaped, gram negative bacterium.

  13. Aerobic and facultative anaerobic bacteria from gut of red palm ...

    African Journals Online (AJOL)

    Pure cultures were obtained after incubating the plates at different atmospheric conditions (aerobic, and strictly anaerobic). The majority of isolated microbiota observed were aerobes and facultative anaerobes (Bacillus sp., Salmonella sp., Enterococcus sp., and Xanthomonas sp.). These qualitative differences of bacteria, ...

  14. Stable carbon isotopic fractionations associated with inorganic carbon fixation by anaerobic ammonium-oxidizing bacteria.

    Science.gov (United States)

    Schouten, Stefan; Strous, Marc; Kuypers, Marcel M M; Rijpstra, W Irene C; Baas, Marianne; Schubert, Carsten J; Jetten, Mike S M; Sinninghe Damsté, Jaap S

    2004-06-01

    Isotopic analyses of Candidatus "Brocadia anammoxidans," a chemolithoautotrophic bacterium that anaerobically oxidizes ammonium (anammox), show that it strongly fractionates against (13)C; i.e., lipids are depleted by up to 47 per thousand versus CO(2). Similar results were obtained for the anammox bacterium Candidatus "Scalindua sorokinii," which thrives in the anoxic water column of the Black Sea, suggesting that different anammox bacteria use identical carbon fixation pathways, which may be either the Calvin cycle or the acetyl coenzyme A pathway.

  15. Genotypic and antimicrobial characterisation of Propionibacterium acnes isolates from surgically excised lumbar disc herniations

    DEFF Research Database (Denmark)

    Rollason, Jess; McDowell, Andrew; Albert, Hanne B

    2013-01-01

    The anaerobic skin commensal Propionibacterium acnes is an underestimated cause of human infections and clinical conditions. Previous studies have suggested a role for the bacterium in lumbar disc herniation and infection. To further investigate this, five biopsy samples were surgically excised...... from each of 64 patients with lumbar disc herniation. P. acnes and other bacteria were detected by anaerobic culture, followed by biochemical and PCR-based identification. In total, 24/64 (38%) patients had evidence of P. acnes in their excised herniated disc tissue. Using recA and mAb typing methods...... isolate collection (63%) suggests that the role of P. acnes in lumbar disc herniation should not be readily dismissed....

  16. Isolation from a shea cake digester of a tannin-tolerant Escherichia coli strain decarboxylating p-hydroxybenzoic and vanillic acids.

    Science.gov (United States)

    Chamkha, Mohamed; Record, Eric; Garcia, Jean-Louis; Asther, Marcel; Labat, Marc

    2002-05-01

    A facultatively anaerobic, mesophilic, Gram-negative, non-motile, non-sporulated bacterium, designated strain C2, was isolated from an anaerobic digester fed with shea cake rich in tannins and aromatic compounds and previously inoculated with anaerobic sludge from the pit of a slaughterhouse, after enrichment on tannic acid. The straight rods occurred singly or in pairs. Strain C2 fermented numerous carbohydrates (fructose, galactose, glucose, lactose, mannose, maltose, melibiose, raffinose, rhamnose, ribose, saccharose, sorbitol, trehalose, and xylose) and peptides (Biotrypcase, Casamino acids, and yeast extract), producing acid and gas, and had a G + C content of 51.6 +/- 0.1 mol %. Strain C2 was very closely related to Escherichia coli (= DSM 30083(T)) phylogenetically (similarity of 99%), genotypically (DNA homology of 79%), and phenotypically. The isolate tolerated tannic acid (hydrolyzable tannin) and decarboxylated by non-oxidative decarboxylation only p-hydroxybenzoic and vanillic acids to their corresponding phenol and guaicol, under anaerobic and aerobic conditions without further degradation. Adding glucose increased growth and the rate of conversion. High concentrations of p-hydroxybenzoic acid or vanillic acid inhibited growth, and decarboxylation could not occur completely, suggesting phenol toxicity. In contrast, the type strain of E. coli cannot metabolize p-hydroxybenzoic and vanillic acids, anaerobically or aerobically, with or without glucose added.

  17. Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus

    Energy Technology Data Exchange (ETDEWEB)

    Saw, Jimmy H [Los Alamos National Laboratory; Mountain, Bruce W [NEW ZEALAND; Feng, Lu [NANKAI UNIV; Omelchenko, Marina V [NCBI/NLM/NIH; Hou, Shaobin [UNIV OF HAWAII; Saito, Jennifer A [UNIV OF HAWAII; Stott, Matthew B [NEW ZEALAND; Li, Dan [NANKAI UNIV; Zhao, Guang [NANKAI UNIV; Wu, Junli [NANKAI UNIV; Galperin, Michael Y [NCBI/NLM/NIH; Koonin, Eugene V [NCBI/NLM/NIH; Makarova, Kira S [NCBI/NLM/NIH; Wolf, Yuri I [NCBI/NLM/NIH; Rigden, Daniel J [UNIV OF LIVERPOOL; Dunfield, Peter F [UNIV OF CALGARY; Wang, Lei [NANKAI UNIV; Alam, Maqsudul [UNIV OF HAWAII

    2008-01-01

    Gram-positive bacteria of the genus Anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, and in processed foods such as gelatin and milk powder. Anoxybacillus flavithermus is a facultatively anaerobic bacterium found in super-saturated silica solutions and in opaline silica sinter. The ability of A. flavithermus to grow in super-saturated silica solutions makes it an ideal subject to study the processes of sinter formation, which might be similar to the biomineralization processes that occurred at the dawn of life. We report here the complete genome sequence of A. flavithermus strain WK1, isolated from the waste water drain at the Wairakei geothermal power station in New Zealand. It consists of a single chromosome of 2,846,746 base pairs and is predicted to encode 2,863 proteins. In silico genome analysis identified several enzymes that could be involved in silica adaptation and biofilm formation, and their predicted functions were experimentally validated in vitro. Proteomic analysis confirmed the regulation of biofilm-related proteins and crucial enzymes for the synthesis of long-chain polyamines as constituents of silica nanospheres. Microbial fossils preserved in silica and silica sinters are excellent objects for studying ancient life, a new paleobiological frontier. An integrated analysis of the A. flavithermus genome and proteome provides the first glimpse of metabolic adaptation during silicification and sinter formation. Comparative genome analysis suggests an extensive gene loss in the Anoxybacillus/Geobacillus branch after its divergence from other bacilli.

  18. Chitin Degradation Proteins Produced by the Marine Bacterium Vibrio harveyi Growing on Different Forms of Chitin

    OpenAIRE

    Svitil, A. L.; Chadhain, S.; Moore, J. A.; Kirchman, D. L.

    1997-01-01

    Relatively little is known about the number, diversity, and function of chitinases produced by bacteria, even though chitin is one of the most abundant polymers in nature. Because of the importance of chitin, especially in marine environments, we examined chitin-degrading proteins in the marine bacterium Vibrio harveyi. This bacterium had a higher growth rate and more chitinase activity when grown on (beta)-chitin (isolated from squid pen) than on (alpha)-chitin (isolated from snow crab), pro...

  19. Cell yields and fermentation responses of a Salmonella Typhimurium poultry isolate at different dilution rates in an anaerobic steady state continuous culture

    Science.gov (United States)

    The objectives of these studies were to determine cell yield and fermentation responses of a Salmonella enterica serovar Typhimurium poultry isolate using various dilution rates in steady state continuous culture incubations. S. enterica Typhimurium cells were propagated in continuous cultures with ...

  20. Draft Genome Sequence of the Cellulolytic Strain Clostridium sp. Bc-iso-3 Isolated from an Industrial-Scale Anaerobic Digester.

    Science.gov (United States)

    Sun, Li; Schnürer, Anna

    2016-10-27

    Clostridium sp. Bc-iso-3 is a cellulolytic strain isolated from a Swedish industrial-scale biogas digester. Here, we present the draft genome sequence of this strain, which consists of four contigs with a total length of 4,327,139 bp and an average coverage of 312.97×. Copyright © 2016 Sun and Schnürer.

  1. Anaerobe Reinigung von Abwasser

    OpenAIRE

    Sternad, W.; Mohr, M.; Spork, C.; Troesch, W.; Trick, I.; Krischke, W.

    2007-01-01

    WO 2007076953 A1 UPAB: 20070822 NOVELTY - The municipal wastewater purification comprises anaerobic biological purification of the wastewater by using a biomass (15-100 g/l) from psychrophilic microorganisms, concentrating the sludge by separating the wastewater and feeding back the sludge into the anaerobic biological purification. The psychrophilic microorganisms exhibit an optimum temperature of less than 25degreesC. The anaerobic purification takes place as single- or two-step methanizati...

  2. Halobacterium denitrificans sp. nov., an extremely halophilic denitrifying bacterium

    Science.gov (United States)

    Tomlinson, G. A.; Jahnke, L. L.; Hochstein, L. I.

    1986-01-01

    Halobacterium denitrificans was one of several carbohydrate-utilizing, denitrifying, extremely halophilic bacteria isolated by anaerobic enrichment in the presence of nitrate. Anaerobic growth took place only when nitrate (or nitrite) was present and was accompanied by the production of dinitrogen. In the presence of high concentrations of nitrate (i.e., 0.5 percent), nitrous oxide and nitrite were also detected. When grown aerobically in a mineral-salts medium containing 0.005 percent yeast extract, H. denitrificans utilized a variety of carbohydrates as sources of carbon and energy. In every case, carbohydrate utilization was accompanied by acid production.

  3. Halobacterium denitrificans sp. nov. - An extremely halophilic denitrifying bacterium

    Science.gov (United States)

    Tomlinson, G. A.; Jahnke, L. L.; Hochstein, L. I.

    1986-01-01

    Halobacterium denitrificans was one of several carbohydrate-utilizing, denitrifying, extremely halophilic bacteria isolated by anaerobic enrichment in the presence of nitrate. Anaerobic growth took place only when nitrate (or nitrite) was present and was accompanied by the production of dinitrogen. In the presence of high concentrations of nitrate (i.e., 0.5 percent), nitrous oxide and nitrite were also detected. When grown aerobically in a mineral-salts medium containing 0.005 percent yeast extract, H. denitrificans utilized a variety of carbohydrates as sources of carbon and energy. In every case, carbohydrate utilization was accompanied by acid production.

  4. Reclassification of Eubacterium desmolans as Butyricicoccus desmolans comb. nov., and description of Butyricicoccus faecihominis sp. nov., a butyrate-producing bacterium from human faeces.

    Science.gov (United States)

    Takada, Toshihiko; Watanabe, Koichi; Makino, Hiroshi; Kushiro, Akira

    2016-10-01

    A Gram-positive-staining, coccoid-shaped, non-motile, asporogenous, obligately anaerobic and butyrate-producing bacterium was recovered from a healthy human's faeces. The organism was isolated by the enrichment culture technique using yeast extract-casein hydrolysate-fatty acids broth supplemented with 0.5 % mucin. Phylogenetic analysis of 16S rRNA gene sequences demonstrated that the novel strain should be classified as a member of the Eubacterium desmolans-related cluster in the family Ruminococcaceae. Furthermore, this analysis demonstrated that the type strains of Butyricicoccus pullicaecorum (95.6 %) and Eubacterium desmolans (94.7 %) were the closest phylogenetic neighbours to strain YIT 12789T. However, DNA‒DNA reassociation values with these closest strains were less than 20 %. On the basis of the phenotypic, genotypic and chemotaxonomic features, the novel coccoid-shaped bacterium should be designated as a representative of a novel species of the genus Butyricicoccus, for which the name Butyricicoccus faecihominis sp. nov. is proposed. The type strain is YIT 12789T (=JCM 31056T=DSM 100989T). It is also proposed that Eubacterium desmolans be reclassified in the genus Butyricicoccus as Butyricicoccus desmolans comb. nov.

  5. My Lifelong Passion for Biochemistry and Anaerobic Microorganisms.

    Science.gov (United States)

    Thauer, Rudolf Kurt

    2015-01-01

    Early parental influence led me first to medical school, but after developing a passion for biochemistry and sensing the need for a deeper foundation, I changed to chemistry. During breaks between semesters, I worked in various biochemistry labs to acquire a feeling for the different areas of investigation. The scientific puzzle that fascinated me most was the metabolism of the anaerobic bacterium Clostridium kluyveri, which I took on in 1965 in Karl Decker's lab in Freiburg, Germany. I quickly realized that little was known about the biochemistry of strict anaerobes such as clostridia, methanogens, acetogens, and sulfate-reducing bacteria and that these were ideal model organisms to study fundamental questions of energy conservation, CO2 fixation, and the evolution of metabolic pathways. My passion for anaerobes was born then and is unabated even after 50 years of study.

  6. Isolation, characterization and toxicity of native Bacillus thuringiensis isolates from different hosts and habitats in Iran

    Directory of Open Access Journals (Sweden)

    Ghassemi-Kahrizeh Akbar

    2017-09-01

    Full Text Available Bacillus thuringiensis is a Gram-positive, aerobic, facultative anaerobic and endospore-forming bacterium. Different strains of this species have the ability to produce parasporal crystalline inclusions which are toxic to larvae of different insect orders and other invertebrates and cause rapid death of the host. To determine the importance of this species in microbial control, we collected native strains and studied their virulence on the diamondback moth, Plutella xylostella. More than 148 samples were collected from Alborz, Guilan and Mazandaran Provinces. Experimental samples, including soil samples from forests, fruit gardens, agricultural fields, diseased and dead larvae, were transferred to a laboratory in sterile plastic containers. For evaluating B. thuringiensis isolates virulence, a cabbage leaf dip method with 106 cell · ml−1 concentration of various Bt isolates was applied to diamondback moths. Larval mortality was recorded 72 h after treatment. Based on bioassay results, all isolates were classified into three high, medium and low virulence groups. Protein level characterization based on the SDS-PAGE gel analysis showed that two isolates from a high virulence group have proteins of high molecular masses of 121 and 109 kDa. Results revealed that there is a positive correlation between protein masses and virulence of isolates. In addition, this research introduced nine strains that are highly toxic to P. xylostella and would be valuable as insecticidal agents for controlling lepidopteran pests.

  7. Enrichment and isolation of Bacillus beveridgei sp. nov., a facultative anaerobic haloalkaliphile from Mono Lake, California, that respires oxyanions of tellurium, selenium, and arsenic

    Science.gov (United States)

    Baesman, S.M.; Stolz, J.F.; Kulp, T.R.; Oremland, R.S.

    2009-01-01

    Mono Lake sediment slurries incubated with lactate and tellurite [Te(IV)] turned progressively black with time because of the precipitation of elemental tellurium [Te(0)]. An enrichment culture was established from these slurries that demonstrated Te(IV)-dependent growth. The enrichment was purified by picking isolated black colonies from lactate/Te(IV) agar plates, followed by repeated streaking and picking. The isolate, strain MLTeJB, grew in aqueous Te(IV)-medium if provided with a small amount of sterile solid phase material (e.g., agar plug; glass beads). Strain MLTeJB grew at high concentrations of Te(IV) (~8 mM) by oxidizing lactate to acetate plus formate, while reducing Te(IV) to Te(0). Other electron acceptors that were found to sustain growth were tellurate, selenate, selenite, arsenate, nitrate, nitrite, fumarate and oxygen. Notably, growth on arsenate, nitrate, nitrite and fumarate did not result in the accumulation of formate, implying that in these cases lactate was oxidized to acetate plus CO2. Strain MLTeJB is a low G + C Gram positive motile rod with pH, sodium, and temperature growth optima at 8.5-9.0, 0.5-1.5 M, and 40??C, respectively. The epithet Bacillus beveridgei strain MLTeJBT is proposed. ?? 2009 Springer.

  8. Anaerobic sludge granulation

    NARCIS (Netherlands)

    Hulshoff Pol, L.W.; Castro Lopes, de S.I.; Lettinga, G.; Lens, P.N.L.

    2004-01-01

    This paper reviews different theories on anaerobic sludge granulation in UASB-reactors that have been proposed during the past two decades
    This paper reviews different theories on anaerobic sludge granulation in UASB-reactors that have been proposed during the past two decades. The initial

  9. Molecular ecology of anaerobic reactor systems

    DEFF Research Database (Denmark)

    Hofman-Bang, H. Jacob Peider; Zheng, D.; Westermann, Peter

    2003-01-01

    for these processes. Only a few percent of Bacteria and Archaea have so far been isolated, and almost nothing is known about the dynamics and interactions between these and other microorganisms. This lack of knowledge is most clearly exemplified by the sometimes unpredictable and unexplainable failures...... to the abundance of each microbe in anaerobic reactor systems by rRNA probing. This chapter focuses on various molecular techniques employed and problems encountered when elucidating the microbial ecology of anaerobic reactor systems. Methods such as quantitative dot blot/fluorescence in-situ probing using various...

  10. [Isolation and identification of electrochemically active microorganism from micro-aerobic environment].

    Science.gov (United States)

    Wu, Song; Xiao, Yong; Zheng, Zhi-Yong; Zheng, Yue; Yang, Zhao-Hui; Zhao, Feng

    2014-10-01

    Extracellular electron transfer of electrochemically active microorganism plays vital role in biogeochemical cycling of metals and carbon and in biosynthesis of bioenergy. Compared to anaerobic anode, micro-aerobic anode captures more energy from microbial fuel cell. However, most of previous researches focused on functioning bacteria in anaerobic anode, functioning bacteria in micro-aerobic anode was rarely studied. Herein, we used the traditional aerobic screening technology to isolate functioning bacteria from a micro-aerobic anode. Three pure cultures Aeromonas sp. WS-XY2, Citrobacter sp. WS-XY3 and Bacterium strain WS-XY4 were obtained. WS-XY2 and WS-XY3 were belonged to Proteobacteria, whereas WS-XY4 was possibly a new species. Cyclic voltammetry and chronoamperometry analysis demonstrated all of them showed the electrochemical activity by direct extracellular electron transfer, and micro-aerobic anode could select bacteria that have similar electrochemical activity to proliferate on the anode. We further conclude that functioning bacteria in micro-aerobic anode are more efficient than that of anaerobic anode may be the reason that micro-aerobic anode has better performance than anaerobic anode. Therefore, a thorough study of functioning bacteria in micro-aerobic anode will significantly promote the energy recovery from microbial fuel cell.

  11. Phenotypic, Genotypic, and Antimicrobial Characteristics of Streptococcus halichoeri Isolates from Humans, Proposal To Rename Streptococcus halichoeri as Streptococcus halichoeri subsp. halichoeri, and Description of Streptococcus halichoeri subsp. hominis subsp. nov., a Bacterium Associated with Human Clinical Infections.

    Science.gov (United States)

    Shewmaker, P L; Whitney, A M; Humrighouse, B W

    2016-03-01

    Phenotypic, genotypic, and antimicrobial characteristics of six phenotypically distinct human clinical isolates that most closely resembled the type strain of Streptococcus halichoeri isolated from a seal are presented. Sequencing of the 16S rRNA, rpoB, sodA, and recN genes; comparative whole-genome analysis; conventional biochemical and Rapid ID 32 Strep identification methods; and antimicrobial susceptibility testing were performed on the human isolates, the type strain of S. halichoeri, and type strains of closely related species. The six human clinical isolates were biochemically indistinguishable from each other and showed 100% 16S rRNA, rpoB, sodA, and recN gene sequence similarity. Comparative 16S rRNA gene sequencing analysis revealed 98.6% similarity to S. halichoeri CCUG 48324(T), 97.9% similarity to S. canis ATCC 43496(T), and 97.8% similarity to S. ictaluri ATCC BAA-1300(T). A 3,530-bp fragment of the rpoB gene was 98.8% similar to the S. halichoeri type strain, 84.6% to the S. canis type strain, and 83.8% to the S. ictaluri type strain. The S. halichoeri type strain and the human clinical isolates were susceptible to the antimicrobials tested based on CLSI guidelines for Streptococcus species viridans group with the exception of tetracycline and erythromycin. The human isolates were phenotypically distinct from the type strain isolated from a seal; comparative whole-genome sequence analysis confirmed that the human isolates were S. halichoeri. On the basis of these results, a novel subspecies, Streptococcus halichoeri subsp. hominis, is proposed for the human isolates and Streptococcus halichoeri subsp. halichoeri is proposed for the gray seal isolates. The type strain of the novel subspecies is SS1844(T) = CCUG 67100(T) = LMG 28801(T). Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  12. Amino Acid Transport in the Thermophilic Anaerobe Clostridium fervidus Is Driven by an Electrochemical Sodium Gradient

    NARCIS (Netherlands)

    SPEELMANS, G; POOLMAN, B; KONINGS, WN

    Amino acid transport was studied in membranes of the peptidolytic, thermophitic, anaerobic bacterium Clostridium fervidus. Uptake of the negatively charged amino acid L-glutamate, the neutral amino acid L-serine, and the positively charged amino acid L-arginine was examined in membrane vesicles

  13. Antimicrobial Susceptibility of Enteric Gram Negative Facultative Anaerobe Bacilli in Aerobic versus Anaerobic Conditions

    Science.gov (United States)

    Amachawadi, Raghavendra G.; Renter, David G.; Volkova, Victoriya V.

    2016-01-01

    Antimicrobial treatments result in the host’s enteric bacteria being exposed to the antimicrobials. Pharmacodynamic models can describe how this exposure affects the enteric bacteria and their antimicrobial resistance. The models utilize measurements of bacterial antimicrobial susceptibility traditionally obtained in vitro in aerobic conditions. However, in vivo enteric bacteria are exposed to antimicrobials in anaerobic conditions of the lower intestine. Some of enteric bacteria of food animals are potential foodborne pathogens, e.g., Gram-negative bacilli Escherichia coli and Salmonella enterica. These are facultative anaerobes; their physiology and growth rates change in anaerobic conditions. We hypothesized that their antimicrobial susceptibility also changes, and evaluated differences in the susceptibility in aerobic vs. anaerobic conditions of generic E. coli and Salmonella enterica of diverse serovars isolated from cattle feces. Susceptibility of an isolate was evaluated as its minimum inhibitory concentration (MIC) measured by E-Test® following 24 hours of adaptation to the conditions on Mueller-Hinton agar, and on a more complex tryptic soy agar with 5% sheep blood (BAP) media. We considered all major antimicrobial drug classes used in the U.S. to treat cattle: β-lactams (specifically, ampicillin and ceftriaxone E-Test®), aminoglycosides (gentamicin and kanamycin), fluoroquinolones (enrofloxacin), classical macrolides (erythromycin), azalides (azithromycin), sulfanomides (sulfamethoxazole/trimethoprim), and tetracyclines (tetracycline). Statistical analyses were conducted for the isolates (n≥30) interpreted as susceptible to the antimicrobials based on the clinical breakpoint interpretation for human infection. Bacterial susceptibility to every antimicrobial tested was statistically significantly different in anaerobic vs. aerobic conditions on both media, except for no difference in susceptibility to ceftriaxone on BAP agar. A satellite experiment

  14. Porphyromonas loveana sp. nov., isolated from the oral cavity of Australian marsupials.

    Science.gov (United States)

    Bird, Philip S; Trott, Darren J; Mikkelsen, Deirdre; Milinovich, Gabriel J; Hillman, Kristine M; Burrell, Paul C; Blackall, Linda L

    2016-10-01

    An obligatory anaerobic, Gram-stain-negative coccobacillus with black-pigmented colonies was isolated from the oral cavity of selected Australian marsupial species. Phenotypic and molecular criteria showed that this bacterium was a distinct species within the genus Porphyromonas, and was closely related to Porphyromonas gingivalis and Porphyromonas gulae. This putative novel species and P. gulae could be differentiated from P. gingivalis by catalase activity. Further characterization by multi-locus enzyme electrophoresis of glutamate dehydrogenase and malate dehydrogenase enzyme mobility and matrix-assisted laser desorption ionization time-of-flight MS showed that this putative novel species could be differentiated phenotypically from P. gingivalis and P. gulae. Definitive identification by 16S rRNA gene sequencing showed that this bacterium belonged to a unique monophyletic lineage, phylogenetically distinct from P. gingivalis (94.9 % similarity) and P. gulae (95.5 %). This also was supported by 16S-23S rRNA intergenic spacer region and glutamate dehydrogenase gene sequencing. A new species epithet, Porphyromonas loveana sp. nov., is proposed for this bacterium, with DSM 28520T (=NCTC 13658T=UQD444T=MRK101T), isolated from a musky rat kangaroo, as the type strain.

  15. Draft Genome Sequence of Blood Disease Bacterium A2 HR-MARDI, a Pathogen Causing Banana Bacterial Wilt.

    Science.gov (United States)

    Badrun, Rafidah; Abu Bakar, Norliza; Laboh, Rozeita; Redzuan, Rohaiza; Bala Jaganath, Indu

    2017-06-01

    Blood disease bacterium A2 HR-MARDI was isolated from banana plants infected with banana blood disease and which were planted in Kuala Kangsar, Malaysia. Here, we report a draft genome sequence of blood disease bacterium A2 HR-MARDI, which could provide important information on the virulence mechanism of this pathogen. Copyright © 2017 Badrun et al.

  16. Biosorption of heavy metals by a marine bacterium

    International Nuclear Information System (INIS)

    Iyer, Anita; Mody, Kalpana; Jha, Bhavanath

    2005-01-01

    Heavy metal chelation property of exopolysaccharide produced by Enterobacter cloaceae, a marine bacterium, isolated from the West Coast of India, is reported in this paper. The exopolysaccharide demonstrated excellent chelating properties with respect to cadmium (65%) followed by copper (20%) and cobalt (8%) at 100 mg/l heavy metal concentration. However, it could not chelate mercury. A comparative study of the percentage biosorption of the above mentioned metals is presented here

  17. Genome Sequence of the Milbemycin-Producing Bacterium Streptomyces bingchenggensis▿

    OpenAIRE

    Wang, Xiang-Jing; Yan, Yi-Jun; Zhang, Bo; An, Jing; Wang, Ji-Jia; Tian, Jun; Jiang, Ling; Chen, Yi-Hua; Huang, Sheng-Xiong; Yin, Min; Zhang, Ji; Gao, Ai-Li; Liu, Chong-Xi; Zhu, Zhao-Xiang; Xiang, Wen-Sheng

    2010-01-01

    Streptomyces bingchenggensis is a soil-dwelling bacterium producing the commercially important anthelmintic macrolide milbemycins. Besides milbemycins, the insecticidal polyether antibiotic nanchangmycin and some other antibiotics have also been isolated from this strain. Here we report the complete genome sequence of S. bingchenggensis. The availability of the genome sequence of S. bingchenggensis should enable us to understand the biosynthesis of these structurally intricate antibiotics bet...

  18. Inhibition experiments on anaerobic methane oxidation

    Energy Technology Data Exchange (ETDEWEB)

    Alperin, M.J.; Reeburgh, W.S.

    1985-10-01

    Anaerobic methane oxidation is a general process important in controlling fluxes of methane from anoxic marine sediments. The responsible organism has not been isolated, and little is known about the electron acceptors and substrates involved in the process. Laboratory evidence indicates that sulfate reducers and methanogens are able to oxidize small quantities of methane. Field evidence suggests anaerobic methane oxidation may be linked to sulfate reduction. Experiments with specific inhibitors for sulfate reduction (molybdate), methanogenesis (2-bromoethanesulfonic acid), and acetate utilization (fluoroacetate) were performed on marine sediments from the zone of methane oxidation to determine whether sulfate-reducing bacteria or methanogenic bacteria are responsible for methane oxidation. The inhibition experiment results suggest that methane oxidation in anoxic marine sediments is not directly mediated by sulfate-reducing bacteria or methanogenic bacteria. Our results are consistent with two possibilities: anaerobic methane oxidation may be mediated by an unknown organism or a consortium involving an unknown methane oxidizer and sulfate-reducing bacteria.

  19. Lactococcus lactis - a diploid bacterium

    DEFF Research Database (Denmark)

    Michelsen, Ole; Hansen, Flemming G.; Jensen, Peter Ruhdal

    the next division. Thus, the regions of the chromosome that are the last to be replicated are haploid even in fast-growing bacteria. In contrast to this general rule for bacteria, we found that Lactococcus lactis, a bacterium which has been exploited for thousands of years for the production of fermented...... milk products, is born with two complete non-replicating chromosomes. L. lactis therefore remain diploid throughout its entire life cycle....

  20. Anaerobic Digestion and its Applications

    Science.gov (United States)

    Anaerobic digestion is a natural biological process. The initials "AD" may refer to the process of anaerobic digestion, or the built systems of anaerobic digesters. While there are many kinds of digesters, the biology is basically the same for all. Anaerobic digesters are built...