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Sample records for bacterium pseudomonas sp

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

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

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    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. Pseudomonas glareae sp. nov., a marine sediment-derived bacterium with antagonistic activity.

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    Romanenko, Lyudmila A; Tanaka, Naoto; Svetashev, Vassilii I; Mikhailov, Valery V

    2015-06-01

    An aerobic, Gram-negative, motile, rod-shaped bacterium designated KMM 9500(T) was isolated from a sediment sample collected from the Sea of Japan seashore. Comparative 16S rRNA gene sequence analysis affiliated strain KMM 9500(T) to the genus Pseudomonas as a distinct subline clustered with Pseudomonas marincola KMM 3042(T) and Pseudomonas segetis KCTC 12331(T) sharing the highest similarities of 98 and 97.9 %, respectively. Strain KMM 9500(T) was characterized by mainly possessing ubiquinone Q-9, and by the predominance of C18:1 ω7c, C16:1 ω7c, and C16:0 followed by C12:0 in its fatty acid profile. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminophospholipid, and unknown phospholipids. Strain KMM 9500(T) was found to inhibit growth of Gram-negative and Gram-positive indicatory microorganisms. Based on the phylogenetic analysis and distinctive phenotypic characteristics, strain 9500(T) is concluded to represent a novel species of the genus Pseudomonas, for which the name Pseudomonas glareae sp. nov. is proposed. The type strain of the species is strain KMM 9500(T) (=NRIC 0939(T)).

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

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    Jin Duan

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

  5. The Complete Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas sp. UW4

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    Duan, Jin; Jiang, Wei; Cheng, Zhenyu; Heikkila, John J.; Glick, Bernard R.

    2013-01-01

    The plant growth-promoting bacterium (PGPB) Pseudomonas sp. UW4, previously isolated from the rhizosphere of common reeds growing on the campus of the University of Waterloo, promotes plant growth in the presence of different environmental stresses, such as flooding, high concentrations of salt, cold, heavy metals, drought and phytopathogens. In this work, the genome sequence of UW4 was obtained by pyrosequencing and the gaps between the contigs were closed by directed PCR. The P. sp. UW4 genome contains a single circular chromosome that is 6,183,388 bp with a 60.05% G+C content. The bacterial genome contains 5,423 predicted protein-coding sequences that occupy 87.2% of the genome. Nineteen genomic islands (GIs) were predicted and thirty one complete putative insertion sequences were identified. Genes potentially involved in plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, trehalose production, siderophore production, acetoin synthesis, and phosphate solubilization were determined. Moreover, genes that contribute to the environmental fitness of UW4 were also observed including genes responsible for heavy metal resistance such as nickel, copper, cadmium, zinc, molybdate, cobalt, arsenate, and chromate. Whole-genome comparison with other completely sequenced Pseudomonas strains and phylogeny of four concatenated “housekeeping” genes (16S rRNA, gyrB, rpoB and rpoD) of 128 Pseudomonas strains revealed that UW4 belongs to the fluorescens group, jessenii subgroup. PMID:23516524

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

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    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.

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

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

    1989-08-01

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

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

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

    2016-07-01

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

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

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    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.

  10. Crystal structures of complexes of NAD+-dependent formate dehydrogenase from methylotrophic bacterium Pseudomonas sp. 101 with formate

    International Nuclear Information System (INIS)

    Filippova, E. V.; Polyakov, K. M.; Tikhonova, T. V.; Stekhanova, T. N.; Boiko, K. M.; Sadykhov, I. G.; Tishkov, V. I.; Popov, V. O.; Labru, N.

    2006-01-01

    Formate dehydrogenase (FDH) from the methylotrophic bacterium Pseudomonas sp. 101 catalyzes oxidation of formate to NI 2 with the coupled reduction of nicotinamide adenine dinucleotide (NAD + ). The three-dimensional structures of the apo form (the free enzyme) and the holo form (the ternary FDH-NAD + -azide complex) of FDH have been established earlier. In the present study, the structures of FDH complexes with formate are solved at 2.19 and 2.28 A resolution by the molecular replacement method and refined to the R factors of 22.3 and 20.5%, respectively. Both crystal structures contain four protein molecules per asymmetric unit. These molecules form two dimers identical to the dimer of the apo form of FDH. Two possible formatebinding sites are found in the active site of the FDH structure. In the complexes the sulfur atom of residue Cys354 exists in the oxidized state

  11. Further characterization of o-nitrobenzaldehyde degrading bacterium Pseudomonas sp. ONBA-17 and deduction on its metabolic pathway.

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    Yu, Fang-Bo; Li, Xiao-Dan; Ali, Shinawar Waseem; Shan, Sheng-Dao; Luo, Lin-Ping; Guan, Li-Bo

    2014-01-01

    A previously reported o-nitrobenzaldehyde (ONBA) degrading bacterium Pseudomonas sp. ONBA-17 was further identified and characterized. Based on results of DNA base composition and DNA-DNA hybridization, the strain was identified as P. putida. Its degradation effect enhanced with increase of inoculum amount and no lag phase was observed. Higher removal rate was achieved under shaking conditions. All tested ONBA with different initial concentrations could be completely degraded within 5 d. In addition, degradative enzyme(s) involved was confirmed as intra-cellular distributed and constitutively expressed. Effects of different compounds on relative activity of degradative enzyme(s) within cell-free extract were also evaluated. Finally, 2-nitrobenzoic acid and 2, 3-dihydroxybenzoic acid were detected as metabolites of ONBA degradation by P. putida ONBA-17, and relevant metabolic pathway was preliminary proposed. This study might help with future research in better understanding of nitroaromatics biodegradation.

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

    Science.gov (United States)

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

    2015-12-01

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

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

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

    2015-02-01

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

  14. Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp. SH-C52 for antimicrobial compounds

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    Menno evan der Voort

    2015-07-01

    Full Text Available The plant microbiome represents an enormous untapped resource for discovering novel genes and bioactive compounds. Previously, we isolated Pseudomonas sp. SH-C52 from the rhizosphere of sugar beet plants grown in a soil suppressive to the fungal pathogen Rhizoctonia solani and showed that its antifungal activity is, in part, attributed to the production of the chlorinated 9-amino-acid lipopeptide thanamycin (Mendes et al. 2011. Science. To get more insight into its biosynthetic repertoire, the genome of Pseudomonas sp. SH-C52 was sequenced and subjected to in silico, mutational and functional analyses. The sequencing revealed a genome size of 6.3 Mb and 5,579 predicted ORFs. Phylogenetic analysis placed strain SH-C52 within the Pseudomonas corrugata clade. In silico analysis for secondary metabolites revealed a total of six nonribosomal peptide synthetase (NRPS gene clusters, including the two previously described NRPS clusters for thanamycin and the 2-amino acid antibacterial lipopeptide brabantamide. Here we show that thanamycin also has activity against an array of other fungi and that brabantamide A exhibits anti-oomycete activity and affects phospholipases of the late blight pathogen Phytophthora infestans. Most notably, mass spectrometry led to the discovery of a third LP, designated thanapeptin, with a 22-amino-acid peptide moiety. Seven structural variants of thanapeptin were found with varying degrees of activity against P. infestans. Of the remaining four NRPS clusters, one was predicted to encode for yet another and unknown lipopeptide with a predicted peptide moiety of 8-amino acids. Collectively, these results show an enormous metabolic potential for Pseudomonas sp. SH-C52, with at least three structurally diverse lipopeptides, each with a different antimicrobial activity spectrum.

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

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    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.

  16. Pseudomonas matsuisoli sp. nov., isolated from a soil sample.

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    Lin, Shih-Yao; Hameed, Asif; Hung, Mei-Hua; Liu, You-Cheng; Hsu, Yi-Han; Young, Li-Sen; Young, Chiu-Chung

    2015-03-01

    An aerobic, Gram-stain-negative, rod-shaped and polar-flagellated bacterium, designated strain CC-MHH0089(T), was isolated from a soil sample taken on Matsu Island (Taiwan). Strain CC-MHH0089(T) grew at 15-30 °C and pH 5.0-10.0 and tolerated ≤8 % (w/v) NaCl. 16S rRNA gene sequence analysis showed high pairwise sequence similarity to Pseudomonas azotifigens 6H33b(T) (97.3 %) and Pseudomonas balearica SP1402(T) (96.7 %) and lower sequence similarity to other strains (Pseudomonas, for which the name Pseudomonas matsuisoli sp. nov. is proposed. The type strain is CC-MHH0089(T) ( = BCRC 80771(T) = JCM 30078(T)). © 2015 IUMS.

  17. Pseudomonas soli sp. nov., a novel producer of xantholysin congeners.

    Science.gov (United States)

    Pascual, Javier; García-López, Marina; Carmona, Cristina; Sousa, Thiciana da S; de Pedro, Nuria; Cautain, Bastien; Martín, Jesús; Vicente, Francisca; Reyes, Fernando; Bills, Gerald F; Genilloud, Olga

    2014-09-01

    A chemoorganotrophic Gram-negative bacterium was isolated by means of a diffusion sandwich system from a soil sample from the Sierra Nevada National Park, Spain. Strain F-279,208(T) was oxidase and catalase positive, strictly aerobic, non-spore-forming and motile by single polar flagellum. Phylogenetic analysis of the 16S rRNA, gyrB, rpoB and rpoD genes revealed that strain F-279,208(T) belongs to the Pseudomonas putida group with Pseudomonas mosselii and Pseudomonas entomophila as its closest relatives. DNA-DNA hybridization assays and phenotypic traits confirmed that this strain belongs to a novel species of the genus Pseudomonas, for which the name Pseudomonas soli sp. nov. is proposed. The type strain is F-279,208(T) (=DSM 28043(T)=LMG 27941(T)), and during fermentation it produces xantholysins, a family of lipodepsipeptides. The major compound, xantholysin A, showed an interesting activity in a RCC4 kidney tumor cell line with inactivation of VHL linked with the HIF pathway, without any cytotoxic effects against other human tumor cell lines tested including, liver, pancreas and breast. Copyright © 2014 Elsevier GmbH. All rights reserved.

  18. Characterization of the epoxide hydrolase from an epichlorohydrin-degrading Pseudomonas sp.

    NARCIS (Netherlands)

    Jacobs, Mariken H.J.; van den Wijngaard, Abraham; Pentenga, Marjan; Janssen, Dick B.

    1991-01-01

    An epoxide hydrolase was purified to homogeneity from the epichlorohydrin-utilizing bacterium Pseudomonas sp. strain AD1. The enzyme was found to be a monomeric protein with a molecular mass of 35 kDa. With epichlorohydrin as the substrate, the enzyme followed Michaelis-Menten kinetics with a Km

  19. Factors Affecting Zebra Mussel Kill by the Bacterium Pseudomonas fluorescens

    Energy Technology Data Exchange (ETDEWEB)

    Daniel P. Molloy

    2004-02-24

    The specific purpose of this research project was to identify factors that affect zebra mussel kill by the bacterium Pseudomonas fluorescens. Test results obtained during this three-year project identified the following key variables as affecting mussel kill: treatment concentration, treatment duration, mussel siphoning activity, dissolved oxygen concentration, water temperature, and naturally suspended particle load. Using this latter information, the project culminated in a series of pipe tests which achieved high mussel kill inside power plants under once-through conditions using service water in artificial pipes.

  20. Bioactivities by a crude extract from the Greenlandic Pseudomonas sp. In5 involves the nonribosomal peptides, nunamycin and nunapeptin

    DEFF Research Database (Denmark)

    Frydenlund Michelsen, Charlotte; Jensen, Helle; Venditto, Vincent J.

    2015-01-01

    Bioactive microbial metabolites provide a successful source of novel compounds with pharmaceutical potentials. The bacterium Pseudomonas sp. In5 is a biocontrol strain isolated from a plant disease suppressive soil in Greenland, which produces two antimicrobial nonribosomal peptides (NRPs), nunap......), nunapeptin and nunamycin. In this study, we used in vitro antimicrobial and anticancer bioassays to evaluate the potential bioactivities of both a crude extract derived from Pseudomonas sp. In5 and NRPs purified from the crude extract....

  1. Pseudomonas yangmingensis sp. nov., an alkaliphilic denitrifying species isolated from a hot spring.

    Science.gov (United States)

    Wong, Biing-Teo; Lee, Duu-Jong

    2014-01-01

    This study isolated and identified a facultative, alkaliphilic, denitrifying Pseudomonas strain designed as CRS1 from a hot spring, Yang-Ming Mountain, Taiwan. The biochemical characterization, phenotypic characteristics and phylogenetic relationship of strain CRS1 were studied. On the basis of the 16S rRNA sequence similarity, phenotypic and genotypic characteristics and chemotaxonomic data, the strain CRS1 represents a novel species of the genus Pseudomonas, for which the name Pseudomonas yangmingensis sp. nov., is proposed. The strain CRS1 is a facultative autotrophic bacterium that has capability of mixotrophic and heterotrophic denitrification. Copyright © 2013 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

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

    2016-03-01

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

  3. Pseudomonas oceani sp. nov., isolated from deep seawater.

    Science.gov (United States)

    Wang, Ming-Qing; Sun, Li

    2016-10-01

    In this study, we identified a novel Gram-stain-negative, aerobic, motile, and rod-shaped bacterium, strain KX 20T, isolated from the deep seawater in Okinawa Trough, northwestern Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain KX 20T was related to members of the genus Pseudomonas and shares the highest sequence identities with Pseudomonas aestusnigri CECT 8317T (99.4 %) and Pseudomonas pachastrellae JCM 12285T (98.5 %). The 16S rRNA gene sequence identities between strain KX 20T and other members of the genus Pseudomonaswere below 96.6 %. The gyrB and rpoD genes of strain KX 20T shared 82.0 to 89.3 % sequence identity with the gyrB and rpoD genes of the closest phylogenetic neighbours of KX 20T. The predominant cellular fatty acids of strain KX 20T were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) (29.2 %), C16 : 0 (24.5 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) (21.5 %) and C12 : 0 (8.2 %). The major polar lipids of strain KX 20T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and unknown phospholipids. The genomic DNA G+C content of strain KX 20T was 62.9 mol%. On the basis of phylogenetic analysis and phenotypic characteristics, a novel species, Pseudomonas oceani sp. nov. is proposed. The type strain is KX 20T (=CGMCC 1.15195T=DSM 100277T).

  4. Pseudomonas lactis sp. nov. and Pseudomonas paralactis sp. nov., isolated from bovine raw milk.

    Science.gov (United States)

    von Neubeck, Mario; Huptas, Christopher; Glück, Claudia; Krewinkel, Manuel; Stoeckel, Marina; Stressler, Timo; Fischer, Lutz; Hinrichs, Jörg; Scherer, Siegfried; Wenning, Mareike

    2017-06-01

    Five strains, designated WS 4672T, WS 4998, WS 4992T, WS 4997 and WS 5000, isolated from bovine raw milk formed two individual groups in a phylogenetic analysis. The most similar species on the basis of 16S rRNA gene sequences were Pseudomonas azotoformans IAM 1603T, Pseudomonas gessardii CIP 105469T and Pseudomonas libanensis CIP 105460T showing 99.7-99.6 % similarity. Using rpoD gene sequences Pseudomonas veronii LMG 17761T (93.3 %) was most closely related to strain WS 4672T and Pseudomonas libanensis CIP 105460T to strain WS 4992T (93.3 %). The five strains could be differentiated from their closest relatives and from each other by phenotypic and chemotaxonomic characterization and ANIb values calculated from draft genome assemblies. ANIb values of strains WS 4992T and WS4671T to the closest relatives are lower than 90 %. The major cellular polar lipids of both strains are phosphatidylethanolamine, phosphatidylglycerol, a phospholipid and diphosphatidylglycerol, and their major quinone is Q-9. The DNA G+C content of strains WS 4992T and WS 4672T were 60.0  and 59.7  mol%, respectively. Based on these genotypic and phenotypic traits two novel species of the genus Pseudomonas are proposed: Pseudomonas lactis sp. nov. [with type strain WS 4992T (=DSM 29167T=LMG 28435T) and the additional strains WS 4997 and WS 5000], and Pseudomonasparalactis sp. nov. [with type strain WS 4672T (=DSM 29164T=LMG 28439T) and additional strain WS 4998].

  5. Anthranilate degradation by a cold-adapted Pseudomonas sp.

    Science.gov (United States)

    Kim, Dockyu; Yoo, Miyoun; Kim, Eungbin; Hong, Soon Gyu

    2015-03-01

    An alpine soil bacterium Pseudomonas sp. strain PAMC 25931 was characterized as eurypsychrophilic (both psychrophilic and mesotolerant) with a broad temperature range of 5-30 °C both for anthranilate (2-aminobenzoate) degradation and concomitant cell growth. Two degradative gene clusters (antABC and catBCA) were detected from a fosmid clone in the PAMC 25931 genomic library; each cluster was confirmed to be specifically induced by anthranilate. When expressed in Escherichia coli, the recombinant AntABC (anthranilate 1,2-dioxygenase, AntDO) converted anthranilate into catechol, exhibiting strict specificity toward anthranilate. Recombinant CatA (catechol 1,2-dioxygenase, C12O) from the organism was active over a broad temperature range (5-37 °C). However, CatA rapidly lost the enzyme activity when incubated at above 25 °C. For example, 1 h-preincubation at 37 °C resulted in 100% loss of enzyme activity, while a counterpart from mesophilic Pseudomonas putida mt-2 did not show any negative effect on the initial enzyme activity. These results suggest that CatA is a new cold-adapted thermolabile enzyme, which might be a product through the adaptation process of PAMC 25931 to naturally cold environments and contribute to its ability to grow on anthranilate there. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Complete genome of Pseudomonas sp. strain L10.10, a psychrotolerant biofertilizer that could promote plant growth.

    Science.gov (United States)

    See-Too, Wah Seng; Lim, Yan-Lue; Ee, Robson; Convey, Peter; Pearce, David A; Yin, Wai-Fong; Chan, Kok Gan

    2016-03-20

    Pseudomonas sp. strain L10.10 (=DSM 101070) is a psychrotolerant bacterium which was isolated from Lagoon Island, Antarctica. Analysis of its complete genome sequence indicates its possible role as a plant-growth promoting bacterium, including nitrogen-fixing ability and indole acetic acid (IAA)-producing trait, with additional suggestion of plant disease prevention attributes via hydrogen cyanide production. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Pseudomonas salina sp. nov., isolated from a salt lake.

    Science.gov (United States)

    Zhong, Zhi-Ping; Liu, Ying; Hou, Ting-Ting; Liu, Hong-Can; Zhou, Yu-Guang; Wang, Fang; Liu, Zhi-Pei

    2015-09-01

    A Gram-staining-negative, facultatively aerobic bacterium, strain XCD-X85(T), was isolated from Xiaochaidan Lake, a salt lake (salinity 9.9%, w/v) in Qaidam basin, Qinghai province, China. Its taxonomic position was determined by using a polyphasic approach. Cells of strain XCD-X85(T) were non-endospore-forming rods, 0.4-0.6 μm wide and 1.0-1.6 μm long, and motile by means of a single polar flagellum. Strain XCD-X85(T) was catalase- and oxidase-positive. Growth was observed in the presence of 0-12.0% (w/v) NaCl (optimum, 1.0-2.0%) and at 4-35 °C (optimum, 25-30 °C) and pH 6.5-10.5 (optimum, pH 8.0-8.5). Strain XCD-X85(T) contained (>10%) summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C12 : 0, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the predominant fatty acids. The major respiratory quinone was ubiquinone 9 (Q-9). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 57.4 mol%. Phylogenetic trees based on 16S rRNA gene sequences showed that strain XCD-X85(T) was associated with the genus Pseudomonas, and showed highest 16S rRNA gene sequence similarities to Pseudomonas pelagia CL-AP6(T) (99.0%) and Pseudomonas bauzanensis BZ93(T) (96.8%). DNA-DNA relatedness of strain XCD-X85T to P. pelagia JCM 15562(T) was 19 ± 1%. On the basis of the data presented above, it is concluded that strain XCD-X85(T) represents a novel species of the genus Pseudomonas, for which the name Pseudomonas salina sp. nov. is proposed. The type strain is XCD-X85(T) ( = CGMCC 1.12482(T) = JCM 19469(T)).

  8. Uranium and thorium uptake by live and dead cells of Pseudomonas Sp

    International Nuclear Information System (INIS)

    Siva Prasath, C.S.; Manikandan, N.; Prakash, S.

    2010-01-01

    This study presents uptake of uranium (U) and thorium (Th) by live and dead cells of Pseudomonas Sp. Increasing concentration of U and Tb showed decrease in absorption by Pseudomonas Sp. Dead cells of Pseudomonas Sp. exhibited same or more uptake of U and Th than living cells. Increasing temperature promotes uptake of U and Th by Pseudomonas Sp. (author)

  9. OXIDATION OF POLYCHLORINATED BIPHENYLS BY PSEUDOMONAS SP. STRAIN LB400 AND PSEUDOMONAS PSEUDOALCALIGENES KF707

    Science.gov (United States)

    Biphenyl-grown cells and cell extracts prepared from biphenyl-grown cells of Pseudomonas sp. strain LB400 oxidize a much wider range of chlorinated biphenyls than do analogous preparations from Pseudomonas pseudoalcaligenes KF707. These results are attributed to differences in th...

  10. Taxonomic study of bacteria isolated from natural mineral waters: proposal of Pseudomonas jessenii sp. nov. and Pseudomonas mandelii sp. nov.

    Science.gov (United States)

    Verhille, S; Baida, N; Dabboussi, F; Izard, D; Leclerc, H

    1999-02-01

    The taxonomic position of 23 strains isolated from mineral waters and previously grouped in the authentic pseudomonads on the basis of a phenotypic analysis (cluster IX, subclusters XIIIa and XIIIc of VERHILLE, S., ELOMARI, M., COROLER, L., IZARD, D., LECLERC, H. (Syst. Appl. Microbiol, 20, 137-149, 1997) has been genotypically further studied in the present work. On the basis of hybridization results, these strains were gathered into two new genomic groups for which we propose the names of Pseudomonas jessenii sp. nov. (Type strain CIP 105274) and Pseudomonas mandelii sp. nov. (Type strain CIP 105273). Deoxyribonucleic acid relatedness levels showed homologies ranging from 78 to 100% for Pseudomonas jessenii and from 77 to 100% for Pseudomonas mandelii. Furthermore, hybrization rates with 66 representative well characterized species or only partially characterized species of the genus Pseudomonas were below 53%, with delta Tm values of 7 degrees C and more. The mol% G + C content ranged from 57 to 58. The two new species presented basic morphological characteristics common to all pseudomonads. Various phenotypic features, such as denitrification, growth at 4 degrees C or 41 degrees C, trigonelline assimilation, alpha-L-glutamyl-L-histidine arylarmidase activity, growth on benzoate and meso-tartrate were found to differentiate Pseudomonas jessenii from Pseudomonas mandelii and from other Pseudomonas species. Pseudomonas jessenii encompassed a total of 9 strains from both phenotypic groups IX and XIIIa. Pseudomonas mandelii clustered a total of 13 strains from both phenotypic groups IX and XIIIc. Their clinical significance is unknown. The 16S rDNA of each type strain was sequenced and compared with the known sequences of the representative strains of the genus Pseudomonas. A phylogenetic tree was constructed to determine the intrageneric relationships within the genus Pseudomonas.

  11. Active efflux systems in the solvent-tolerant bacterium Pseudomonas putida S12

    NARCIS (Netherlands)

    Kieboom, J.

    2002-01-01

    The aim of the research presented in this thesis was to study the molecular mechanisms of organic solvent tolerance in Pseudomonas putida S12. This bacterium is capable of growth at saturated solvent concentrations, which are lethal to normal bacteria. Organic

  12. Engineering the Soil Bacterium Pseudomonas putida for Arsenic Methylation

    OpenAIRE

    Chen, Jian; Qin, Jie; Zhu, Yong-Guan; de Lorenzo, Víctor; Rosen, Barry P.

    2013-01-01

    Accumulation of arsenic has potential health risks through consumption of food. Here, we inserted the arsenite [As(III)] S-adenosylmethionine methyltransferase (ArsM) gene into the chromosome of Pseudomonas putida KT2440. Recombinant bacteria methylate inorganic arsenic into less toxic organoarsenicals. This has the potential for bioremediation of environmental arsenic and reducing arsenic contamination in food.

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

    Directory of Open Access Journals (Sweden)

    Przemieniecki Wojciech Sebastian

    2015-01-01

    Full Text Available The Pseudomonas sp. SP0113 strain from a partially closed aquatic environment was identified as a plant growth promoting bacterium (PGPB. Laboratory tests revealed that PS0113 has multiple plant growth promoting traits, including mineral phosphate solubilizing ability, ammonifying ability that increases nitrogen availability for plants via the root system, and phosphatase activity that plays an important role in organic phosphorus mineralization. Tricalcium phosphate (Ca3(PO42 solubilizing ability was described as average (2-3 mm after 7 days of incubation and as high (>3 mm after 14 days of incubation. The analyzed bacterium was an antagonist of major crop pathogenic fungi. A high degree of pathogen growth inhibition was reported with regard to Rhizoctonia solani (38%, whereas the tested strain's ability to inhibit the growth of fungi of the genera Fusarium and Microdochium nivalis was somewhat lower at 20-29%. The bacterium proliferated in Roundup 360 SL solutions with concentrations of 0.1, 1 and 10 mg•ml-1.

  14. PRODUCCIÓN DE BIOFERTILIZANTES UTILIZANDO Pseudomonas sp.

    OpenAIRE

    Santillana-Villanueva, Nery; Universidad Nacional Agraria La Molina (Perú).

    2006-01-01

    Con el objetivo de producir biofertilizantes utilizando 3 cepas de Pseudomonas sp., se realizaron tres experimentos: el primero, para encontrar un medio de cultivo apropiado para la multiplicación de las bacterias; el segundo, para determinar la sobrevivencia de las cepas de Pseudomonas sp en los biofertilizantes y el tercero para determinar la dosis eficiente de aplicación del biofertilizante en frijol, maíz, papa y tomate, en condiciones de invernadero. Al evaluar los resultados, se determi...

  15. New emulsifying and cryoprotective exopolysaccharide from Antarctic Pseudomonas sp. ID1.

    Science.gov (United States)

    Carrión, Ornella; Delgado, Lidia; Mercade, Elena

    2015-03-06

    Pseudomonas sp. ID1 is a cold-adapted bacterium isolated from a marine sediment sample collected from South Shetland Islands (Antarctica) that is noted for the highly mucous appearance of its colonies. In this work, we have characterized an exopolysaccharide (EPS) produced by this strain, which is mainly composed of glucose, galactose and fucose, and has a molecular mass higher than 2×10(6) Da. We have also studied its potential biotechnological applications as an emulsifier and cryoprotectant agent. The EPS emulsifying activity against different food and cosmetic oils was much higher than commercial gums such as xanthan gum and arabic gum, and surfarctants such as Span 20. It formed highly stable emulsions against the cosmetic oil cetiol V, exhibiting pseudoplastic flow behavior, low thixotrophy and yield stress. The EPS of Pseudomonas sp. ID1 conferred significant cryoprotection for the strain itself as well as for other bacteria, including Escherichia coli, suggesting a universal cryoprotectant role. The cryoprotective activity of the EPS showed a clear dose-response relation at -20 °C and -80 °C and was significantly higher than that observed for the membrane stabilizer fetal bovine serum (FBS). These properties make the EPS of Pseudomonas sp. ID1 a promising alternative to commercial polysaccharides as an emulsifier and cryoprotectant agent for food, pharmaceutical and cosmetic industries. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Pseudomonas tarimensis sp. nov., an endophytic bacteria isolated from Populus euphratica.

    Science.gov (United States)

    Anwar, Nusratgul; Rozahon, Manziram; Zayadan, Bolatkhan; Mamtimin, Hormathan; Abdurahman, Mehfuzem; Kurban, Marygul; Abdurusul, Mihribangul; Mamtimin, Tursunay; Abdukerim, Muhtar; Rahman, Erkin

    2017-11-01

    An endophytic bacterium, MA-69 T , was isolated from the storage liquid in the stems of Populuseuphratica trees at the ancient Ugan River in Xinjiang, PR China. Strain MA-69 T was found to be short rod-shaped, Gram-stain-negative, non-spore-forming, aerobic and motile by means of a monopolar flagellum. According to phylogenetic analysis based on 16S rRNA gene sequences, strain MA-69 T was assigned to the genus Pseudomonas with highest 16S rRNA gene sequence similarity of 97.5 % to Pseudomonas azotifigens JCM 12708 T , followed by Pseudomonas matsuisoli JCM 30078 T (97.5 %), Pseudomonas balearica DSM 6083 T (97.1 %), Azotobacter salinestris ATCC 49674 T (96.1 %) and Pseudomonas indica DSM 14015 T (95.9 %). Analysis of strain MA-69 T based on the three housekeeping genes, rpoB, rpoD and gyrB, further confirmed the isolate to be distinctly delineated from species of the genus Pseudomonas. The DNA G+C content of strain MA-69 T was 64.1 mol%. DNA-DNA hybridization with Pseudomonas azotifigens JCM 12708 T , Pseudomonas matsuisoli JCM 30078 T and Pseudomonas balearica DSM 6083 T revealed 62.9, 60.1 and 49.0 % relatedness, respectively. The major fatty acids in strain MA-69 T were summed feature 3 (25.7 %), summed feature 8 (24.0 %), C19 : 0cyclo ω8c (19.9 %), C16 : 0 (14.6 %) and C12 : 0 (6.3 %). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Q-9 was the major quinone in strain MA-69 T . Based on phenotypic, chemotaxonomic and phylogenetic properties, strain MA-69 T represents a novel species of the genus Pseudomonas, for which the name Pseudomonas tarimensis sp. nov. is proposed. The type strain is MA-69 T (=CCTCC AB 2013065 T =KCTC 42447 T ).

  17. 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)).

  18. 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 ).

  19. Copper homeostasis networks in the bacteriumPseudomonas aeruginosa.

    Science.gov (United States)

    Quintana, Julia; Novoa-Aponte, Lorena; Argüello, José M

    2017-09-22

    Bacterial copper (Cu + ) homeostasis enables both precise metallation of diverse cuproproteins and control of variable metal levels. To this end, protein networks mobilize Cu + to cellular targets with remarkable specificity. However, the understanding of these processes is rather fragmented. Here, we use genome-wide transcriptomic analysis by RNA-Seq to characterize the response of Pseudomonas aeruginosa to external 0.5 mm CuSO 4 , a condition that did not generate pleiotropic effects. Pre-steady-state (5-min) and steady-state (2-h) Cu + fluxes resulted in distinct transcriptome landscapes. Cells quickly responded to Cu 2+ stress by slowing down metabolism. This was restored once steady state was reached. Specific Cu + homeostasis genes were strongly regulated in both conditions. Our system-wide analysis revealed induction of three Cu + efflux systems (a P 1B -ATPase, a porin, and a resistance-nodulation-division (RND) system) and of a putative Cu + -binding periplasmic chaperone and the unusual presence of two cytoplasmic CopZ proteins. Both CopZ chaperones could bind Cu + with high affinity. Importantly, novel transmembrane transporters probably mediating Cu + influx were among those largely repressed upon Cu + stress. Compartmental Cu + levels appear independently controlled; the cytoplasmic Cu + sensor CueR controls cytoplasmic chaperones and plasma membrane transporters, whereas CopR/S responds to periplasmic Cu + Analysis of Δ copR and Δ cueR mutant strains revealed a CopR regulon composed of genes involved in periplasmic Cu + homeostasis and its putative DNA recognition sequence. In conclusion, our study establishes a system-wide model of a network of sensors/regulators, soluble chaperones, and influx/efflux transporters that control the Cu + levels in P. aeruginosa compartments. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  20. Transformation of 3-chlorodibenzofuran by Pseudomonas sp. HH69.

    Science.gov (United States)

    Harms, H; Wilkes, H; Sinnwell, V; Wittich, R M; Figge, K; Francke, W; Fortnagel, P

    1991-06-01

    The dibenzofuran-degrading bacterial strain Pseudomonas sp. HH69 showed high oxidative activity towards 3-chlorodibenzofuran (3CDF). During the co-metabolic turnover of 3CDF large amounts of 4-chlorosalicylate and temporarily small amounts of salicylate were excreted. Simultaneously a yellow colour appeared due to the excretion of two polar products. Conversion of 3CDF by a mutant, derived from Pseudomonas sp. HH69 and defective in 2,3-dihydroxybiphenyl-1,2-dioxygenase led to the formation of equal quantities of 4'-chloro-2,2',3-trihydroxybiphenyl (4'CTHBP) and 4-chloro-2,2',3-trihydroxybiphenyl (4CTHBP). Crude extracts of the wild type transformed 4'CTHBP to 4-chlorosalicylate, whilst 4CTHBP was transformed to salicylate. Hence, we propose a non-selective initial attack on both aromatic rings of 3CDF and a degradative pathway for the resulting chlorotrihydroxybiphenyls.

  1. 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.

  2. Pseudomonas sp. BUP6, a novel isolate from Malabari goat produces an efficient rhamnolipid type biosurfactant.

    Science.gov (United States)

    Priji, Prakasan; Sajith, Sreedharan; Unni, Kizhakkepowathial Nair; Anderson, Robin C; Benjamin, Sailas

    2017-01-01

    This study describes the characteristics of a biosurfactant produced by Pseudomonas sp. BUP6, a rumen bacterium, and optimization of parameters required for its production. Initial screening of five parameters (pH, temperature, agitation, incubation, and substrate concentration) was carried out employing Plackett-Burman design, which reduced the number of parameters to 3 (pH, temperature, and incubation) according to their significance on the yield of biosurfactant. A suitable statistical model for the production of biosurfactant by Pseudomonas sp. BUP6 was established according to Box-Behnken design, which resulted in 11% increase (at pH 7, 35 °C, incubation 75 h) in the yield (2070 mg L -1 ) of biosurfactant. The biosurfactant was found stable at a wide range of pH (3-9) with 48 mg L -1 critical micelle concentration; and maintained over 90% of its emulsification ability even after boiling and in presence of sodium chloride (0.5%). The highest cell hydrophobicity (37%) and emulsification (69%) indices were determined with groundnut oil and kerosene, respectively. The biosurfactant was found to inhibit the growth and adhesion of E. coli and S. aureus significantly. From the phytotoxicity studies, the biosurfactant did not show any adverse effect on the germinating seeds of rice and green gram. The structural characterization of biosurfactant employing orcinol method, thin layer chromatography and FT-IR indicated that it is a rhamnolipid (glycolipid). Thus, Pseudomonas sp. BUP6, a novel isolate from Malabari goat is demonstrated as a producer of an efficient rhamnolipid type biosurfactant suitable for application in various industries. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Science.gov (United States)

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

    2014-01-01

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

  4. Complete genome sequence of Pseudomonas azotoformans S4, a potential biocontrol bacterium

    Science.gov (United States)

    Fang, Yang; Wu, Lijuan; Chen, Guoqing; Feng, Guozhong

    2016-01-01

    Pseudomonas azotoformans is a Gram-negative bacterium and infects cereal grains, especially rice. P. azotoformans S4 from soil sample derived from Lijiang, Yunnan Province, China, appeared to be strong inhibitory activity against Fusarium fujikurio, a serious rice fungal pathogen. Here, we present the complete genome of P. azotoformans S4, which consists of 6,859,618 bp with a circle chromosome, 5991 coding DNA sequences, 70 tRNA and 19 rRNA. The genomic analysis revealed that 9 candidate gene clusters are involved in the biosynthesis of secondary metabolites. PMID:27080451

  5. Mutagenesis and reparation processes in the methylotrophic bacterium Pseudomonas methanolica after UV irradiation

    International Nuclear Information System (INIS)

    Naumov, G.N.; Bokhan, I.K.; Multykh, I.G.

    1986-01-01

    High resistance of cells of methylotrophic bacterium Pseudomonas methanolica to bactericidal and mutagenous effects of ultraviolet irradiation is shown as well as activity of reparation processes after UV irradiation. The presence of low photoreactivating activity in P. methanolica is shown as well. Observed recovery in innutritious medium and decrease of irradiated cells survival rates under effect of reparation inhibitors (coffeine and acriflavine) testify to activity of excision reparation and, perhaps, recombination branch of postreplicative reparation. No manifestation of inducible reparation system is discovered. It is concluded that increased resistance of P. methanolica cells to bactericidal and mutagenous effects of short-wave ultraviolet radiation is related to activity of exact reparation systems

  6. Rapid identification and quantitative validation of a caffeine-degrading pathway in Pseudomonas sp. CES.

    Science.gov (United States)

    Yu, Chi Li; Summers, Ryan M; Li, Yalan; Mohanty, Sujit Kumar; Subramanian, Mani; Pope, R Marshall

    2015-01-02

    Understanding the genes and enzymes involved in caffeine metabolism can lead to applications such as production of methylxanthines and environmental waste remediation. Pseudomonas sp. CES may provide insights into these applications, since this bacterium degrades caffeine and thrives in concentrations of caffeine that are three times higher (9.0 g L(-1)) than the maximum tolerable levels of other reported bacteria. We took a novel approach toward identifying the enzymatic pathways in Pseudomonas sp. CES that metabolize caffeine, which largely circumvented the need for exhaustive isolation of enzymes and the stepwise reconstitution of their activities. Here we describe an optimized, rapid alternative strategy based on multiplexed LC-MS/MS assays and show its application by discovering caffeine-degrading enzymes in the CES strain based on quantitative comparison of proteomes from bacteria grown in the absence and presence of caffeine, the latter condition of which was found to have a highly induced capacity for caffeine degradation. Comparisons were made using stable isotope dimethyl labeling, differences in the abundance of particular proteins were substantiated by reciprocal labeling experiments, and the role of the identified proteins in caffeine degradation was independently verified by genetic sequencing. Overall, multiple new components of a N-demethylase system were identified that resulted in rapid pathway validation and gene isolation using this new approach.

  7. Pseudomonas granadensis sp. nov., a new bacterial species isolated from the Tejeda, Almijara and Alhama Natural Park, Granada, Spain.

    Science.gov (United States)

    Pascual, Javier; García-López, Marina; Bills, Gerald F; Genilloud, Olga

    2015-02-01

    During the course of screening bacterial isolates as sources of as-yet unknown bioactive compounds with pharmaceutical applications, a chemo-organotrophic, Gram-negative bacterium was isolated from a soil sample taken from the Tejeda, Almijara and Alhama Natural Park, Granada, Spain. Strain F-278,770(T) was oxidase- and catalase-positive, aerobic, with a respiratory type of metabolism with oxygen as the terminal electron acceptor, non-spore-forming and motile by one polar flagellum, although some cells had two polar flagella. Phylogenetic analysis of the 16S rRNA, gyrB, rpoB and rpoD genes revealed that strain F-278,770(T) belongs to the Pseudomonas koreensis subgroup (Pseudomonas fluorescens lineage), with Pseudomonas moraviensis, P. koreensis, P. baetica and P. helmanticensis as its closest relatives. Chemotaxonomic traits such as polar lipid and fatty acid compositions and G+C content of genomic DNA corroborated the placement of strain F-278,770(T) in the genus Pseudomonas. DNA-DNA hybridization assays and phenotypic traits confirmed that this strain represents a novel species of the genus Pseudomonas, for which the name Pseudomonas granadensis sp. nov. is proposed. The type strain is F-278,770(T) ( = DSM 28040(T) = LMG 27940(T)). © 2015 Fundacion MEDINA, Centro de Excelencia en Investigacion de Medicamentos Innovadores en Andalucia.

  8. Light spectrum modifies the utilization pattern of energy sources in Pseudomonas sp. DR 5-09.

    Science.gov (United States)

    Gharaie, Samareh; Vaas, Lea A I; Rosberg, Anna Karin; Windstam, Sofia T; Karlsson, Maria E; Bergstrand, Karl-Johan; Khalil, Sammar; Wohanka, Walter; Alsanius, Beatrix W

    2017-01-01

    Despite the overruling impact of light in the phyllosphere, little is known regarding the influence of light spectra on non-phototrophic bacteria colonizing the leaf surface. We developed an in vitro method to study phenotypic profile responses of bacterial pure cultures to different bands of the visible light spectrum using monochromatic (blue: 460 nm; red: 660 nm) and polychromatic (white: 350-990 nm) LEDs, by modification and optimization of a protocol for the Phenotype MicroArray™ technique (Biolog Inc., CA, USA). The new protocol revealed high reproducibility of substrate utilization under all conditions tested. Challenging the non-phototrophic bacterium Pseudomonas sp. DR 5-09 with white, blue, and red light demonstrated that all light treatments affected the respiratory profile differently, with blue LED having the most decisive impact on substrate utilization by impairing respiration of 140 substrates. The respiratory activity was decreased on 23 and 42 substrates under red and white LEDs, respectively, while utilization of one, 16, and 20 substrates increased in the presence of red, blue, and white LEDs, respectively. Interestingly, on four substrates contrasting utilization patterns were found when the bacterium was exposed to different light spectra. Although non-phototrophic bacteria do not rely directly on light as an energy source, Pseudomonas sp. DR 5-09 changed its respiratory activity on various substrates differently when exposed to different lights. Thus, ability to sense and distinguish between different wavelengths even within the visible light spectrum must exist, and leads to differential regulation of substrate usage. With these results, we hypothesize that different light spectra might be a hitherto neglected key stimulus for changes in microbial lifestyle and habits of substrate usage by non-phototrophic phyllospheric microbiota, and thus might essentially stratify leaf microbiota composition and diversity.

  9. Light spectrum modifies the utilization pattern of energy sources in Pseudomonas sp. DR 5-09.

    Directory of Open Access Journals (Sweden)

    Samareh Gharaie

    Full Text Available Despite the overruling impact of light in the phyllosphere, little is known regarding the influence of light spectra on non-phototrophic bacteria colonizing the leaf surface. We developed an in vitro method to study phenotypic profile responses of bacterial pure cultures to different bands of the visible light spectrum using monochromatic (blue: 460 nm; red: 660 nm and polychromatic (white: 350-990 nm LEDs, by modification and optimization of a protocol for the Phenotype MicroArray™ technique (Biolog Inc., CA, USA. The new protocol revealed high reproducibility of substrate utilization under all conditions tested. Challenging the non-phototrophic bacterium Pseudomonas sp. DR 5-09 with white, blue, and red light demonstrated that all light treatments affected the respiratory profile differently, with blue LED having the most decisive impact on substrate utilization by impairing respiration of 140 substrates. The respiratory activity was decreased on 23 and 42 substrates under red and white LEDs, respectively, while utilization of one, 16, and 20 substrates increased in the presence of red, blue, and white LEDs, respectively. Interestingly, on four substrates contrasting utilization patterns were found when the bacterium was exposed to different light spectra. Although non-phototrophic bacteria do not rely directly on light as an energy source, Pseudomonas sp. DR 5-09 changed its respiratory activity on various substrates differently when exposed to different lights. Thus, ability to sense and distinguish between different wavelengths even within the visible light spectrum must exist, and leads to differential regulation of substrate usage. With these results, we hypothesize that different light spectra might be a hitherto neglected key stimulus for changes in microbial lifestyle and habits of substrate usage by non-phototrophic phyllospheric microbiota, and thus might essentially stratify leaf microbiota composition and diversity.

  10. Pseudomonas floridensis sp. nov., a bacterial pathogen isolated from tomato.

    Science.gov (United States)

    Timilsina, Sujan; Minsavage, Gerald V; Preston, James; Newberry, Eric A; Paret, Matthews L; Goss, Erica M; Jones, Jeffrey B; Vallad, Gary E

    2018-01-01

    An unusual fluorescent pseudomonad was isolated from tomato exhibiting leaf spot symptoms similar to bacterial speck. Strains were fluorescent, oxidase- and arginine-dihydrolase-negative, elicited a hypersensitive reaction on tobacco and produced a soft rot on potato slices. However, the strains produced an unusual yellow, mucoid growth on media containing 5 % sucrose that is not typical of levan. Based on multilocus sequence analysis using 16S rRNA, gap1, gltA, gyrB and rpoD, these strains formed a distinct phylogenetic group in the genus Pseudomonas and were most closely related to Pseudomonas viridiflava within the Pseudomonassyringae complex. Whole-genome comparisons, using average nucleotide identity based on blast, of representative strain GEV388 T and publicly available genomes representing the genus Pseudomonas revealed phylogroup 7 P. viridiflava strain UASW0038 and P. viridiflava type strain ICMP 2848 T as the closest relatives with 86.59 and 86.56 % nucleotide identity, respectively. In silico DNA-DNA hybridization using the genome-to-genome distance calculation method estimated 31.1 % DNA relatedness between GEV388 T and P. viridiflava ATCC 13223 T , strongly suggesting the strains are representatives of different species. These results together with Biolog GEN III tests, fatty acid methyl ester profiles and phylogenetic analysis using 16S rRNA and multiple housekeeping gene sequences demonstrated that this group represents a novel species member of the genus Pseudomonas. The name Pseudomonas floridensis sp. nov. is proposed with GEV388 T (=LMG 30013 T =ATCC TSD-90 T ) as the type strain.

  11. Gene cloning, identification, and characterization of the multicopper oxidase CumA from Pseudomonas sp. 593.

    Science.gov (United States)

    Yang, Sheng; Long, Yan; Yan, Hong; Cai, Huawan; Li, Yadong; Wang, Xingguo

    2017-05-01

    The cumA, a gene encoding a multicopper oxidase (MCO), was cloned from the soil-dwelling bacterium Pseudomonas sp. 593. Its corresponding product was overexpressed in Escherichia coli BL21 (DE3) pLysS and purified to homogeneity through Ni-affinity chromatography. The amino acid sequence of the CumA of Pseudomonas sp. 593 was strongly homologous to that of CumA as previously reported. The CumA was quite stable in neutral pH and had poor thermostability. Meanwhile, its optimum pH and temperature toward laccase substrates 2,6-dimethoxyphenol (DMP), syringaldazine (SGZ), and 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) were 5.0 and 55 °C, 7.5 and 60 °C, and 5.0 and 60 °C, respectively. Cu 2+ remarkably enhanced the activity of the CumA. By contrast, the activity of the CumA was inhibited by the addition of Fe 2+ . Kinetic studies gave the K m , k cat , and k cat /K m values of 0.438 mmol·L -1 , 0.056 Sec -1 , and 0.128 Sec -1 ·mmol -1 ·L for DMP; 0.017 mmol·L -1 , 0.031 Sec -1 , and 1.824 Sec -1 ·mmol -1 ·L for SGZ; and 0.101 mmol·L -1 , 0.393 Sec -1 , and 3.891 Sec -1 ·mmol -1 ·L for ABTS. To our knowledge, this is the first report of cloning, expressing in E. coli of the cumA from Pseudomonas and characterization of the CumA. © 2016 International Union of Biochemistry and Molecular Biology, Inc.

  12. Pseudomonas wadenswilerensis sp. nov. and Pseudomonas reidholzensis sp. nov., two novel species within the Pseudomonas putida group isolated from forest soil.

    Science.gov (United States)

    Frasson, David; Opoku, Michael; Picozzi, Tara; Torossi, Tanja; Balada, Stefanie; Smits, Theo H M; Hilber, Urs

    2017-08-01

    Within the frame of a biotechnological screening, we isolated two Pseudomonas strains from forest soil. 16S rRNA gene sequence analysis indicated that strain CCOS 864T shared 99.8 % similarity with Pseudomonas donghuensis HYST, while strain CCOS 865T shared 99.0 % similarity with Pseudomonas putida DSM 291T and lower similarity with other P. putida group type strains. Based on multilocus sequence analysis, the two strains were genotypically distinct from each other, each forming a separate clade. Strains CCOS 864T and CCOS 865T were Gram-stain-negative, motile and rod-shaped, growing at a temperature range of 4-37 °C. Strain CCOS 864T could be phenotypically distinguished from P. putida group species by the combination of gelatinase-positive reaction and positive growth on N-acetyl-d-glucosamine, p-hydroxyphenylacetic acid and inosine but lack of fluorescein production on King's B medium, while strain CCOS 865T could be distinguished from P. putida group species by the combination of positive growth with saccharic acid and negative growth with p-hydroxyphenylacetic acid and l-pyroglutamic acid. The major polar lipid for both strains was phosphatidylethanolamine; the major quinone was ubiquinone Q-9. DNA-DNA hybridization and average nucleotide identities confirmed the novel species status for the two strains. The DNA G+C contents of CCOS 864T and CCOS 865T were 62.1 and 63.8 mol%, respectively. The phenotypic, phylogenetic and DNA-DNA relatedness data support the suggestion that CCOS 864T and CCOS 865T represent two novel Pseudomonas species. The names Pseudomonas wadenswilerensis sp. nov. (type strain CCOS 864T=LMG 29327T) and Pseudomonas reidholzensis sp. nov. (type strain CCOS 865T=LMG 29328T) are proposed.

  13. Interaction between fish spoilage bacteria Pseudomonas sp and Shewanella putrefaciens in fish extracts and on fish tissue

    DEFF Research Database (Denmark)

    Gram, Lone; Melchiorsen, Jette

    1996-01-01

    , supernatant fluids from siderophore- negative Pseudomonas isolates did not inhibit growth of S. putrefaciens. The inhibitory effect was, except for one strain of Pseudomonas, not seen in supernatant fluids from iron- enriched cultures of Pseudomonas sp. Finally, siderophore- producing Pseudomonas sp. lowered...

  14. Pseudomonas versuta sp. nov., isolated from Antarctic soil.

    Science.gov (United States)

    See-Too, Wah Seng; Salazar, Sergio; Ee, Robson; Convey, Peter; Chan, Kok-Gan; Peix, Álvaro

    2017-06-01

    In this study we analysed three bacterial strains coded L10.10 T , A4R1.5 and A4R1.12, isolated in the course of a study of quorum-quenching bacteria occurring in Antarctic soil. The 16S rRNA gene sequence was identical in the three strains and showed 99.7% pairwise similarity with respect to the closest related species Pseudomonas weihenstephanensis WS4993 T . Therefore, the three strains were classified within the genus Pseudomonas. Analysis of housekeeping genes (rpoB, rpoD and gyrB) sequences showed similarities of 84-95% with respect to the closest related species of Pseudomonas, confirming its phylogenetic affiliation. The ANI values were less than 86% to the closest related species type strains. The respiratory quinone is Q9. The major fatty acids are C16:0, C16:1 ω7c/ C16:1 ω6c in summed feature 3 and C18:1 ω7c / C18:1 ω6c in summed feature 8. The strains are oxidase- and catalase-positive. Growth occurs at 4-30°C, and at pH 4.0-10. The DNA G+C content is 58.2-58.3mol %. The combined genotypic, phenotypic and chemotaxonomic data support the classification of strains L10.10 T , A4R1.5 and A4R1.12 into a novel species of Pseudomonas, for which the name P. versuta sp. nov. is proposed. The type strain is L10.10 T (LMG 29628 T , DSM 101070 T ). Copyright © 2017 Elsevier GmbH. All rights reserved.

  15. Bioreduction of Cu(II) by cell-free copper reductase from a copper resistant Pseudomonas sp. NA.

    Science.gov (United States)

    Andreazza, Robson; Okeke, Benedict C; Pieniz, Simone; Brandelli, Adriano; Lambais, Mácio R; Camargo, Flávio A O

    2011-11-01

    Environmental copper contamination is a serious human health problem. Copper reductase is produced by microorganisms to facilitate copper uptake by ATPases into the cells increasing copper biosorption. This study assessed the reduction of Cu(II) by cell-free extracts of a highly copper-resistant bacterium, Pseudomonas sp. strain NA, isolated from vineyard soil contaminated with copper. Both intact cells and cell-free extract of Pseudomonas sp. strain NA displayed substantial reduction of Cu(II). Intact cells reduced more then 80 mg L(-1) of Cu(II) from medium amended with 200 mg L(-1) of copper after 24 h of incubation. Cell-free extract of the isolate reduced more than 65% of the Cu(II) at initial copper concentration of 200 mg L(-1) after 24 h. Soluble protein production was high at 72 h of incubation at 100 mg L(-1) of copper, with more then 60 μg L(-1) of total soluble protein in cell-free extract recorded. Cu(II) reduction by isolate NA was increased when copper concentration increased for both intact cells and cell-free extract. Results indicate that Pseudomonas sp. strain NA produces copper reductase enzyme as the key mechanism of copper biotransformation.

  16. Evaluation of traditional plant extracts for innate immune mechanisms and disease resistance against fish bacterial Aeromonas hydrophila and Pseudomonas sp.

    Science.gov (United States)

    Hardi, E. H.; Saptiani, G.; Kusuma, I. W.; Suwinarti, W.; Nugroho, R. A.

    2018-03-01

    The purposes of this study were to evaluate effect of ethanol herbal extracts of Boesenbergia pandurata, Solanum ferox and Zingimber zerumbet on Tilapia (Oreochromis nilaticus) innate immune mechanisms and disease resistance against Aeromonas hydrophila and Pseudomonas sp. Fish were intramuscularly injected with 0.1 mL/fish (1010 CFU mL-1) of each bacterium on the day 6th of post treatment using extract by several methods (injection, oral administration and immersion). The doses of extract were 600 ppm of B. pandurata, 900 ppm S. ferox and 200 ppm of Z. zerumbet. The percentage mortality, Relative Percent Survival (RPS) and innate immune response were assessed on weeks 1, 2, 3 and 4. All the methods were effective to enhance the immune parameters after 2 weeks application and the RPS of treatment reached more than 90 %. The results showed that the injection method of extracts was the most effective method to control A. hydrophila and Pseudomonas sp. The result indicated that all the doses of extracts could be significantly influence the immune response and protect the health status of tilapia against A. hydrophila and Pseudomonas sp. infections.

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

    Directory of Open Access Journals (Sweden)

    Peng Jiang

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

  18. Biomineralization of a calcifying ureolytic bacterium Microbacterium sp. GM-1

    Directory of Open Access Journals (Sweden)

    Guojing Xu

    2017-01-01

    Conclusions: The results of this research provide evidence that Microbacterium sp. GM-1 can biologically induce calcification and suggest that strain GM-1 may play a potential role in the synthesis of new biominerals and in bioremediation or biorecovery.

  19. Carbazole degradation by Pseudomonas sp. LD2: metabolic characteristics and the identification of some metabolites

    Energy Technology Data Exchange (ETDEWEB)

    Gieg, L.M.; Otter, A.; Fedorak, P.M. [University of Alberta, Edmonton, AB (Canada). Depts. of Biological Sciences and Chemistry

    1996-02-01

    A carbazole-degrading bacterium was isolated by enrichment from a creosote-contaminated soil. This organism, designated Pseudomonas sp. LD2, utilized carbazole as a sole source of carbon, nitrogen, and energy. When isolate LD2 was grown in nitrogen-free mineral medium with {sup 14}C labeled carbazole, 43% was recovered as {sup 14}CO{sub 2} after 3 days of incubation. Numerous aromatic and heterocyclic compounds were tested as growth substrates for isolate LD2, but few supported the growth of this bacterium. Anthranilic acid and catechol served as growth substrates and were positively identified as intermediates of carbazole degradation by isolate LD2. In addition, 10 nitrogen-containing metabolites were observed in acidified extracts of LD2 culture supernatants, four of which were unequivocally identified. These included indole-3-acetic acid, 5-(2-aminophenyl)-5-oxopentanoic acid, and the cyclized products of 5-(2-aminophenyl)-5-oxopent-3-enoic acid and 6-(2-aminophenyl)-2-hydroxy-6-oxohexa-2,4-dienoic acid. 63refs., 6 figs., 1 tab.

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

    KAUST Repository

    Harjes, Janno

    2014-03-06

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

  1. Pseudomonas alkylphenolica sp. nov., a bacterial species able to form special aerial structures when grown on p-cresol.

    Science.gov (United States)

    Mulet, Magdalena; Sánchez, David; Lalucat, Jorge; Lee, Kyoung; García-Valdés, Elena

    2015-11-01

    Pseudomonas sp. KL28T is an aerobic, rod-shaped bacterium that was isolated from the soil of Changwon, South Korea, based on its ability to grow in the presence of linear alkylphenols (C1-C5). Despite several studies on strain KL28T, it could not be assigned to any known species in the genus Pseudomonas. The name 'Pseudomonas alkylphenolia' was proposed for KL28T, but the strain had not until now been characterized taxonomically and the name currently has no standing in the bacterial nomenclature. A 16S rRNA gene sequence based phylogenetic analysis suggested an affiliation of strain KL28T with the Pseudomonas putida group, with Pseudomonas vranovensis DSM 16006T as the most closely related type strain (99.1 % similarity). A multilocus phylogenetic sequence analysis performed by concatenating 16S rRNA, gyrB, rpoD and rpoB partial gene sequences showed that isolate KL28T could be differentiated from P. vranovensis DSM 16006T (sequence similarity 93.7 %). Genomic comparisons of strain KL28T with the type strains of the species in the P. putida group using average nucleotide index based on blast (ANIb) and genome-to genome distances (GGDC) revealed 87.06 % and 32.20 % similarities with P. vranovensis DSM 16006T, respectively, as the closest type strain. Both values are far from the thresholds established for species differentiation. These results, together with differences in phenotypic features and chemotaxonomic analyses [fatty acids and whole-cell matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS], support the proposal of strain KL28T ( = JCM 16553T = KCTC 22206T) as the type strain of a novel species, for which the formerly proposed name, 'P. alkylphenolia', is correctly latinized as Pseudomonas alkylphenolica sp. nov.

  2. Biodegradation of hexavalent chromium (Cr+6) in wastewater using Pseudomonas sp. and Bacillus sp. bacterial strains

    Energy Technology Data Exchange (ETDEWEB)

    Qasim, Muhammad [Department of Chemical Engineering, American University of Sharjah (United Arab Emirates)

    2013-07-01

    The recovery of toxic metal compounds is a deep concern in all industries. Hexavalent chromium is particularly worrying because of its toxic influence on human health. In this paper, biodegradation of hexavalent chromium (Cr+6) present in wastewater has been studied using two different bacterial strains; Pseudomonas sp. and Bacillus sp. A chemostat (with and without recycle of cells) with 10 L liquid culture volume was used to study the substrate and the biomass cell concentrations with time. Also, the degree of substrate conversion was studied by the varying the dilution rate as an independent parameter. The dilution rate (ratio of feed flow rate to the culture volume) was varied by varying the feed volumetric rate from 110-170 mL/h for inlet hexavalent chromium concentrations of 70 mg/dm3. The results show that a chemostat with recycle gives a better performance in terms of substrate conversion than a chemostat without a recycle. Moreover, the degree of substrate conversion decreases as the dilution rate is increased. Also, Bacillus sp. was found to give higher conversions compared to pseudomonas sp.

  3. Bidirectional gene sequences with similar homology to functional proteins of alkane degrading bacterium pseudomonas fredriksbergensis DNA

    International Nuclear Information System (INIS)

    Megeed, A.A.

    2011-01-01

    The potential for two overlapping fragments of DNA from a clone of newly isolated alkanes degrading bacterium Pseudomonas frederiksbergensis encoding sequences with similar homology to two parts of functional proteins is described. One strand contains a sequence with high homology to alkanes monooxygenase (alkB), a member of the alkanes hydroxylase family, and the other strand contains a sequence with some homology to alcohol dehydrogenase gene (alkJ). Overlapping of the genes on opposite strands has been reported in eukaryotic species, and is now reported in a bacterial species. The sequence comparisons and ORFS results revealed that the regulation and the genes organization involved in alkane oxidation represented in Pseudomonas frederiksberghensis varies among the different known alkane degrading bacteria. The alk gene cluster containing homologues to the known alkane monooxygenase (alkB), and rubredoxin (alkG) are oriented in the same direction, whereas alcohol dehydrogenase (alkJ) is oriented in the opposite direction. Such genomes encode messages on both strands of the DNA, or in an overlapping but different reading frames, of the same strand of DNA. The possibility of creating novel genes from pre-existing sequences, known as overprinting, which is a widespread phenomenon in small viruses. Here, the origin and evolution of the gene overlap to bacteriophages belonging to the family Microviridae have been investigated. Such a phenomenon is most widely described in extremely small genomes such as those of viruses or small plasmids, yet here is a unique phenomenon. (author)

  4. Production and characterization of biosurfactant produced by a novel Pseudomonas sp. 2B.

    Science.gov (United States)

    Aparna, A; Srinikethan, G; Smitha, H

    2012-06-15

    Biosurfactant-producing bacteria were isolated from terrestrial samples collected in areas contaminated with petroleum compounds. Isolates were screened for biosurfactant production using Cetyl Tri Ammonium Bromide (CTAB)-Methylene blue agar selection medium and the qualitative drop-collapse test. An efficient bacterial strain was selected based on rapid drop collapse activity and highest biosurfactant production. The biochemical characteristics and partial sequenced 16S rRNA gene of isolate, 2B, identified the bacterium as Pseudomonas sp. Five different low cost carbon substrates were evaluated for their effect on biosurfactant production. The maximum biosurfactant synthesis (4.97 g/L) occurred at 96 h when the cells were grown on modified PPGAS medium containing 1% (v/v) molasses at 30 °C and 150 rpm. The cell free broth containing the biosurfactant could reduce the surface tension to 30.14 mN/m. The surface active compound showed emulsifying activity against a variety of hydrocarbons and achieved a maximum emulsion index of 84% for sunflower oil. Compositional analysis of the biosurfactant reveals that the extracted biosurfactant was a glycolipid type, which was composed of high percentages of lipid (∼65%, w/w) and carbohydrate (∼32%, w/w). Fourier transform infrared (FT-IR) spectrum of extracted biosurfactant indicates the presence of carboxyl, hydroxyl and methoxyl functional groups. The mass spectra (MS) shows that dirhamnolipid (l-rhamnopyranosyl-l-rhamnopyranosyl-3-hydroxydecanoyl-3-hydroxydecanoate, Rha-Rha-C(10)-C(10)) was detected in abundance with the predominant congener monorhamnolipid (l-rhamnopyranosyl-β-hydroxydecanoyl-β-hydroxydecanoate, Rha-C(10)-C(10)). The crude oil recovery studies using the biosurfactant produced by Pseudomonas sp. 2B suggested its potential application in microbial enhanced oil recovery and bioremediation. Copyright © 2012 Elsevier B.V. All rights reserved.

  5. Engineering of a silica encapsulation platform for hydrocarbon degradation using Pseudomonas sp. NCIB 9816-4.

    Science.gov (United States)

    Sakkos, Jonathan K; Kieffer, Daniel P; Mutlu, Baris R; Wackett, Lawrence P; Aksan, Alptekin

    2016-03-01

    Industrial application of encapsulated bacteria for biodegradation of hydrocarbons in water requires mechanically stable materials. A silica gel encapsulation method was optimized for Pseudomonas sp. NCIB 9816-4, a bacterium that degrades more than 100 aromatic hydrocarbons. The design process focused on three aspects: (i) mechanical property enhancement; (ii) gel cytocompatibility; and (iii) reduction of the diffusion barrier in the gel. Mechanical testing indicated that the compressive strength at failure (σf ) and elastic modulus (E) changed linearly with the amount of silicon alkoxide used in the gel composition. Measurement of naphthalene biodegradation by encapsulated cells indicated that the gel maintained cytocompatibility at lower levels of alkoxide. However, significant loss in activity was observed due to methanol formation during hydrolysis at high alkoxide concentrations, as measured by FTIR spectroscopy. The silica gel with the highest amount of alkoxide (without toxicity from methanol) had a biodegradation rate of 285 ± 42 nmol/L-s, σf  = 652 ± 88 kPa, and E = 15.8 ± 2.0 MPa. Biodegradation was sustained for 1 month before it dropped below 20% of the initial rate. In order to improve the diffusion through the gel, polyvinyl alcohol (PVA) was used as a porogen and resulted in a 48 ± 19% enhancement in biodegradation, but it impacted the mechanical properties negatively. This is the first report studying how the silica composition affects biodegradation of naphthalene by Pseudomonas sp. NCIB 9816-4 and establishes a foundation for future studies of aromatic hydrocarbon biodegradation for industrial application. © 2015 Wiley Periodicals, Inc.

  6. Pseudomonas songnenensis sp. nov., isolated from saline and alkaline soils in Songnen Plain, China.

    Science.gov (United States)

    Zhang, Lei; Pan, Yuanyuan; Wang, Kaibiao; Zhang, Xiaoxia; Zhang, Shuang; Fu, Xiaowei; Zhang, Cheng; Jiang, Juquan

    2015-03-01

    The strain NEAU-ST5-5(T) was isolated from the saline and alkaline soil in Songnen Plain, North East of China. The bacterium was found to be aerobic, Gram-stain negative, rod-shaped and motile by means of several polar flagella. It forms yellow-orange colonies with a radial wrinkled surface. Phylogenetic analyses based on the separate 16S rRNA gene sequences and concatenated 16S rRNA, gyrB and rpoD gene sequences indicated that it belongs to the genus Pseudomonas in the class Gammaproteobacteria. Strain NEAU-ST5-5(T) shows gene sequence similarities of 98.8-97.1 % for 16S rRNA, 90.5-78.4 % for gyrB and 90.4-71.1 % for rpoD with type strains of the closely related species of the genus Pseudomonas, respectively. DNA-DNA hybridization relatedness between strain NEAU-ST5-5(T) and type strains of the most closely related species, Pseudomonas stutzeri DSM 5190(T), P. xanthomarina DSM 18231(T), P. kunmingensis CGMCC 1.12273(T), P. alcaliphila DSM 17744(T) and P. oleovorans subsp. lubricantis DSM 21016(T) were 43 ± 1 to 25 ± 2 %. The major fatty acids (>10 %) were determined to be C18:1 ω7c/C18:1 ω6c, C16:1 ω7c/C16:1 ω6c and C16:0, the predominant respiratory quinone was identified as ubiquinone 9 and polar lipids were found to consist of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unknown phospholipid, one unidentified aminophospholipid and one unknown lipid. The genotypic, chemotaxonomic and phenotypic analysis indicated that strain NEAU-ST5-5(T) represents a novel species of the genus Pseudomonas, for which the name Pseudomonas songnenensis sp. nov. is proposed. The type strain is NEAU-ST5-5(T) (=ACCC 06361(T) = DSM 27560(T)).

  7. Biosorpsi Logam Zn Pada Limbah Sintetik Menggunakan Biomassa Campuran Pseudomonas aeruginosa dan Pseudomonas sp

    Directory of Open Access Journals (Sweden)

    Hidayati Hidayati

    2013-12-01

    Full Text Available Zinc is one of the heavy metals that could be harmful for environment. This metal usually arises from industrial activities. Biosorption of zinc in synthetic waste was conducted using biomass mixture of Pseudomonas aeruginosa and Pseudomonas sp. This research aims to determine the zinc adsorption capacity of the biomass in synthetic waste water. Zinc biosorption was performed at pH 4, room temperature and stirring 800 rpm. Variation of contact time used was 30, 60 and 120 min; and the amount of biomass used was 0.01 g, 0.02 g, 0.03 g, 0.04 g and 0.05 g. The highest zinc biosorption capacity was obtained 25.43% at the time of 120 minutes and the amount of biomass used 0.01 g. The optimum condition for biomass biosorption and removal capacity based on the correlation between experimental data and mathematical models was obtained with the addition of 0.04 g of biomass with correlation coefficient (R 1 and 0,965 respectively.ABSTRAK Salah satu logam berat yang berbahaya dari hasil kegiatan industri adalah logam Zn (seng. Biosorpsi logam Zn pada limbah sintetik dilakukan dengan menggunakan biomassa campuran Pseudomonas aeruginosa dan Pseudomonas sp. Penelitian ini bertujuan untuk mengetahui kapasitas biomassa dalam mengadsorpsi logam Zn pada limbah sintetik. Biosorpsi logam Zn dilakukan pada kondisi pH 4, temperatur ruang dan pengadukan 800 rpm. Variasi waktu kontak dilakukan pada 30, 60 dan 120 menit  dan menggunakan jumlah biomassa 0,01 g, 0,02 g, 0,03 g, 0,04 g  dan 0,05 g. Kapasitas biosorpsi logam Zn tertinggi diperoleh sebesar 25,43% pada waktu 120 menit dengan jumlah biomassa 0,01 g. Kondisi optimum biosorpsi logam Zn berdasarkan korelasi antara data eksperimen dan model matematika diperoleh pada penambahan jumlah biomassa sebesar 0,04 g baik untuk kapasitas biosorpsi logam Zn maupun efisiensi removal logam Zn dengan nilai koefisien korelasi (R2 masing-masing adalah 1 dan 0,965.

  8. 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....

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

    Science.gov (United States)

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

    1978-01-01

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

  10. Phosphatidylcholine synthesis is essential for HrpZ harpin secretion in plant pathogenic Pseudomonas syringae and non-pathogenic Pseudomonas sp. 593.

    Science.gov (United States)

    Xiong, Min; Long, Deliang; He, Huoguang; Li, Yang; Li, Yadong; Wang, Xingguo

    2014-01-01

    Pseudomonas syringae pv. syringae van Hall is important phytopathogenic bacterium of stone fruit trees, and able to elicit hypersensitive response (HR) in nonhost plants. The HrpZ, secreted via type III secretion system (T3SS) to the extracellular space of the plant, is a T3SS-dependent protein and a sole T3SS effector able to induce the host defense response outside host cells. We deleted the phosphatidylcholine synthase gene (pcs) of P. syringae pv. syringae van Hall CFCC 1336, and found that the 1336 pcs(-) mutant was unable to synthesize phosphatidylcholine and elicit a typical HR in soybean. Further studies showed that the 1336 pcs(-) mutant was unable to secrete HrpZ harpin but could express HrpZ protein in cytoplasm as effectively as the wild type. To confirm if phosphatidylcholine affects HrpZ harpin secretion, we introduced the hrpZ gene into the soil-dwelling bacterium Pseudomonas sp. 593 and the 593 pcs(-) mutant, which were unable to express HrpZ harpin and elicit HR in tobacco or soybean. Western blotting and HR assay showed that the 593H not only secreted HrpZ harpin but also caused a strong HR in tobacco and soybean. In contrast, the 593 pcs(-)H only expressed HrpZ protein in its cytoplasm at the wild type level, but did not secrete HrpZ harpin or elicit HR reaction. Our results demonstrate that phosphatidylcholine is essential for the secretion of HrpZ harpin in P. syringae pv. syringae van Hall and other Pseudomonas strains. Copyright © 2013 Elsevier GmbH. All rights reserved.

  11. The chitinase C gene PsChiC from Pseudomonas sp. and its synergistic effects on larvicidal activity

    Directory of Open Access Journals (Sweden)

    Wanfang Zhong

    2015-09-01

    Full Text Available Pseudomonas sp. strain TXG6-1, a chitinolytic gram-negative bacterium, was isolated from a vegetable field in Taixing city, Jiangsu Province, China. In this study, a Pseudomonas chitinase C gene (PsChiC was isolated from the chromosomal DNA of this bacterium using a pair of specific primers. The PsChiC gene consisted of an open reading frame of 1443 nucleotides and encoded 480 amino acid residues with a calculated molecular mass of 51.66 kDa. The deduced PsChiC amino acid sequence lacked a signal sequence and consisted of a glycoside hydrolase family 18 catalytic domain responsible for chitinase activity, a fibronectin type III-like domain (FLD and a C-terminal chitin-binding domain (ChBD. The amino acid sequence of PsChiCshowed high sequence homology (> 95% with chitinase C from Serratia marcescens. SDS-PAGE showed that the molecular mass of chitinase PsChiC was 52 kDa. Chitinase assays revealed that the chitobiosidase and endochitinase activities of PsChiCwere 51.6- and 84.1-fold higher than those of pET30a, respectively. Although PsChiC showed little insecticidal activity towards Spodoptera litura larvae, an insecticidal assay indicated that PsChiC increased the insecticidal toxicity of SpltNPV by 1.78-fold at 192 h and hastened death. These results suggest that PsChiC from Pseudomonas sp. could be useful in improving the pathogenicity of baculoviruses.

  12. Pseudomonas donghuensis sp. nov., exhibiting high-yields of siderophore.

    Science.gov (United States)

    Gao, Jingwei; Xie, Guanfang; Peng, Fang; Xie, Zhixiong

    2015-01-01

    A strain giving high-yields of siderophores, designated HYS(T), was isolated from the water of East Lake (also called Donghu Lake) of Wuhan in China. Strain HYS(T) is Gram-stain negative, non-spore-forming and rod-shaped with polar flagella. Phylogenetic analysis based on 16S rRNA gene and the other three housekeeping genes (gyrB, rpoD and rpoB) indicated that strain HYS(T) belongs to the genus Pseudomonas. Genomic DNA comparison experiments including DNA-DNA hybridization and whole-genome sequence similarities were performed between HYS(T) and its phylogenetically most closely related type strains, all of the relatedness values are lower than the threshold to ascribe strain HYS(T) to a known species. The major cellular fatty acids of strain HYS(T) are C16:0, C17:0 cyclo, Summed feature 3 (C16:1 ω7c or/and C16:1 ω6c) and Summed feature 8 (C18:1 ω7c or C18:1 ω6c). Its predominant isoprenoid quinone was identified as Q-9, and the minor isoprenoid quinone was Q-8. Phylogenetic analysis together with genomic DNA comparison, phenotypic metabolic tests and chemotaxonomic analysis justified the proposal of strain HYS(T) as a representative of a novel species, for which the name Pseudomonas donghuensis sp. nov. is proposed. The type strain is HYS(T) ( = CCTCC AB 2012141(T) = NRRL B-59108(T)).

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

    Science.gov (United States)

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

    2015-02-01

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

  14. Working draft genome sequence of the mesophilic acetate oxidizing bacterium Syntrophaceticus schinkii strain Sp3

    OpenAIRE

    Manzoor, Shahid; M?ller, Bettina; Niazi, Adnan; Schn?rer, Anna; Bongcam-Rudloff, Erik

    2015-01-01

    Syntrophaceticus schinkii strain Sp3 is a mesophilic syntrophic acetate oxidizing bacterium, belonging to the Clostridia class within the phylum Firmicutes, originally isolated from a mesophilic methanogenic digester. It has been shown to oxidize acetate in co-cultivation with hydrogenotrophic methanogens forming methane. The draft genome shows a total size of 3,196,921?bp, encoding 3,688 open reading frames, which includes 3,445 predicted protein-encoding genes and 55 RNA genes. Here, we are...

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

    Science.gov (United States)

    Liu, Yang; Wang, Runping; Zeng, Runying

    2014-12-01

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

  16. 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.

  17. Three Alginate Lyases from Marine Bacterium Pseudomonas fluorescens HZJ216: Purification and Characterization

    Energy Technology Data Exchange (ETDEWEB)

    Liyan, Li [Ocean University of China, Qingdao, PRC; Jiang, Xiaolu [Ocean University of China, Qingdao, PRC; Wang, Peng [Ocean University of China, Qingdao, PRC; Guan, Huashi [Ocean University of China, Qingdao, PRC; Guo, Hong [ORNL

    2010-01-01

    Three alginate lyases (A, B, and C) from an alginate-degrading marine bacterium strain HZJ216 isolated from brown seaweed in the Yellow Sea of China and identified preliminarily as Pseudomonas fluorescens are purified, and their biochemical properties are described. Molecular masses of the three enzymes are determined by SDS-PAGE to be 60.25, 36, and 23 kDa with isoelectric points of 4, 4.36, and 4.59, respectively. Investigations of these enzymes at different pH and temperatures show that they are most active at pH 7.0 and 35 C. Alginate lyases A and B are stable in the pH range of 5.0 9.0, while alginate lyase C is stable in the pH range of 5.0 7.0. Among the metal ions tested, additions of Na+, K+, and Mg2+ ions can enhance the enzyme activities while Fe2+, Fe3+, Ba2+, and Zn2+ ions show inhibitory effects. The substrate specificity results demonstrate that alginate lyase C has the specificity for G block while alginate lyases A and B have the activities for both M and G blocks. It is the first report about extracellular alginate lyases with high alginate-degrading activity from P. fluorescens.

  18. Rhodococcus biphenylivorans sp. nov., a polychlorinated biphenyl-degrading bacterium.

    Science.gov (United States)

    Su, Xiaomei; Liu, Yindong; Hashmi, Muhammad Zaffar; Hu, Jinxing; Ding, Linxian; Wu, Min; Shen, Chaofeng

    2015-01-01

    A Gram-positive, aerobic, non-motile and rod-coccus shaped novel actinobacterial strain, designated as TG9(T), was isolated from a polychlorinated biphenyl (PCB)-contaminated sediment in Taizhou city, Zhejiang province, eastern China. The isolate was observed to grow at 10-45 °C (optimum 28-32 °C), pH 5.0-11.0 (optimum pH 7.0-8.0) and with 0-9.0 % (w/v) NaCl (optimum 0-3.0 %). Comparison of the 16S rRNA gene sequences of strain TG9(T) and other members of the genus Rhodococcus showed that strain TG9(T) shared highest similarities with Rhodococcus pyridinivorans DSM 44555(T) (99.4 %), R. rhodochrous DSM 43241(T) (99.2 %), R. gordoniae DSM 44689(T) (99.2 %) and R. artemisiae DSM 45380(T) (98.2 %). However, low levels of DNA-DNA relatedness (15-48 %), which are below the 70 % limit for prokaryotic species identification, were obtained by DNA-DNA hybridization. Strain TG9(T) was found to contain meso-diaminopimelic acid as the diagnostic diamino acid and arabinose and galactose in the whole-cell hydrolysate. Mycolic acids were found to be present. The major fatty acids were identified as C16:0, C16:1 ω7c and/or iso-C15:0 2-OH, 10-methyl C18:0 and C18:1 ω9c. The only menaquinone detected was MK-8 (H2). The major polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, glycolipid and traces of some unknown lipids. The genomic DNA G+C content of strain TG9(T) was determined to be 62.8 %. The combined phenotypic and genotypic data show that the strain represents a novel species of the genus Rhodococcus for which the name Rhodococcus biphenylivorans sp. nov. is proposed, with the type strain TG9(T) (=CGMCC 1.12975(T) = KCTC 29673(T) = MCCC 1K00286(T)).

  19. 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.

  20. Toksisitas Produk Ekstraseluler dan Intraseluler Bakteri Pseudomonas sp. pada Ikan Nila (Oreochromis niloticus (TOXICITY OF EXTRACELLULAR AND INTRACELLULAR PRODUCT OF PSEUDOMONAS SP IN TILAPIA (OREOCHROMIS NILOTICUS

    Directory of Open Access Journals (Sweden)

    Esti Handayani Hardi

    2014-10-01

    Full Text Available The aim of the research was to investigate the toxicity of extracellular product (ECP and intracellularproduct (ICP of Pseudomonas sp. on tilapia. A total of 40 tilapias weighing 15 grams were injected withECP and ICP. The ECP and ICP were harvested from Pseudomonas sp. culture on two kinds of culturemedia and different time of incubation. The Pseudomonas was cultured on trypticase soy agar (TSA andtrypticase soy broth (TSB and incubated at 24, 48 and 72 hours. The slurry of the bacteria was centrifugedat 10000 g, for 30 minutes on 4oC to get ECP and in room temperature to get ICP. The supernatant wasfiltered with 0.45 ?m paper mesh. A hundred percent mortality was found in tilapia six hours postinjection with ICP (72 hours whereas tilapias were injected with ECP caused 60% mortality in 12 hours.The tilapia showed whirling at 24 hour post injected with ECP of Pseudomonas sp which was cultured inTSA for 48 hours incubated. Opacity of the cornea and exopthalmia were occurred at 48 hours postinjection of ECP and ICP which were harvested from both media. Injection of ICP caused pathologychanges on internal organ of fish i.e. pale appearance of spleen and liver. In conclusion, the ECP and ICPwere a virulence factors of Pseudomonas sp. and the ICP seem more pathogenic and caused mortality thanECP. Both culture media and time of incubation influence of ECP and ICP production. The ECP and ICPwhich were harvested from Pseudomonas sp incubate for 24-48 hour more virulent than 72 hour.

  1. A specific antimicrobial protein CAP-1 from Pseudomonas sp. isolated from the jellyfish Cyanea capillata.

    Science.gov (United States)

    Yin, Manman; Liu, Dan; Xu, Feng; Xiao, Liang; Wang, Qianqian; Wang, Beilei; Chang, Yinlong; Zheng, Jiemin; Tao, Xia; Liu, Guoyan; Zhang, Liming

    2016-01-01

    A bacterium strain, designated as CMF-2, was isolated from the jellyfish Cyanea capillata and its culture supernatant exhibited a significant antimicrobial activity. The strain CMF-2 was identified as Pseudomonas sp. based on the morphological, biochemical and physiological characteristics as well as 16S rRNA sequence analysis. In this study, an antimicrobial protein, named as CAP-1, was isolated from the culture of CMF-2 through ammonium sulfate precipitation and gel filtration chromatography. According to the result of sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), a major band indicated that the antimicrobial protein had a molecular mass of about 15 kDa, and it was identified as a hypothetical protein by MALDI-TOF-MS analysis and Mascot searching. CAP-1 displayed a broad antimicrobial spectrum against the indicator bacteria and fungus, including Staphylococcus aureus, Escherichia coli, Bacillus subtilis and Candida albicans, especially some marine-derived microorganisms such as Vibrio vulnificus, Vibrio alginolyticus, Vibrio parahaemolyticus, Vibrio cholera, and Vibrio anguillarum, but showed little impact on tumor cells and normal human cells. The protein CAP-1 remained a stable antimicrobial activity in a wide range of temperature (20-80°C) and pH (2-10) conditions. These results suggested that CAP-1 might have a specific antimicrobial function not due to cytotoxicity. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. BIODEGRADATION OF PHENOL BY FREE AND IMMOBILIZED CELLS OF A NOVEL Pseudomonas sp. NBM11

    Directory of Open Access Journals (Sweden)

    Satya Sundar Mohanty

    Full Text Available Abstract In the present study, a pure culture of bacterium (Pseudomonas sp. Strain NBM11 was isolated from the soil sample from a site contaminated with medical wastes and wastewater. The isolated strain can degrade up to 1000 mg/L of phenol completely. It was observed that temperature, pH and initial concentration of phenol play key roles in determining the rate of phenol degradation. The isolated strain exhibited the maximal degradation of the substrate within a range of pH 6.8 to 7.2 and an incubation temperature between 30 ºC and 32 ºC. It was found that by increasing the concentration of phenol, the lag phase gets extended due to the inhibitory nature of phenol. The kinetic parameters such as µmax (maximum specific growth rate, Ks (half-saturation coefficient and Ki (substrate inhibition constant were estimated as 0.184 1/h, 7.79 mg/L and 319.24 mg/L, respectively, by fitting the growth kinetics data to the Haldane model of substrate inhibition. The bacterial strain was immobilized in alginate beads and its phenol degradation efficiency was observed to increase many fold. The immobilized cells were found to be used efficiently for seven cycles consecutively without any decrease in their efficiency.

  3. Isolation and characterization of Pseudomonas resistant to heavy ...

    African Journals Online (AJOL)

    represented high potential to grow in medium supplemented with copper and phenanthrene. Isolated bacterium was identified as Pseudomonas sp. by biochemical tests. Over 70% of copper sorbed on Pseudomonas sp. within 150 min. In addition, about 96.52% of initial concentration of phenanthrene was degraded during ...

  4. Isolation and characterization of a Pseudomonas sp. strain IITR01 capable of degrading α-endosulfan and endosulfan sulfate.

    Science.gov (United States)

    Bajaj, A; Pathak, A; Mudiam, M R; Mayilraj, S; Manickam, N

    2010-12-01

    To isolate bacteria capable of degrading endosulfan (ES) and the more toxic ES sulfate and to characterize their metabolites. A Pseudomonas sp. strain IITR01 capable of degrading α-ES and toxic ES sulfate was isolated using technical-ES through enrichment culture techniques. No growth and no degradation were observed using β-ES. Thin-layer chromatography and gas chromatography-mass spectrum analysis revealed the disappearance of both α-ES and ES sulfate and the formation of hydroxylated products ES diol, ether and lactone. We show here for the first time the formation of aforementioned metabolites in contrast to ES hemisulfate yielded by an Arthrobacter sp. Metabolism of α-ES and endosulfate was also observed using the crude cell extract of IITR01. The molecular mass of protein induced during the degradation of α-ES and sulfate as substrate was found to be approximately 150 kDa as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). We describe characterization of bacterium capable of degrading α-ES and ES sulfate but not β-ES. Genetic investigation suggests that a gene nonhomologous to the reported esd may be present in the strain IITR01. This study describes toxic ES degradation by a Pseudomonas species that may be utilized for the bioremediation of the industrial soils contaminated with ES residues. © 2010 The Authors. Journal of Applied Microbiology © 2010 The Society for Applied Microbiology.

  5. Coupled carbon, sulfur and nitrogen cycles of mixotrophic growth of Pseudomonas sp. C27 under denitrifying sulfide removal conditions.

    Science.gov (United States)

    Guo, Hongliang; Chen, Chuan; Lee, Duu-Jong; Wang, Aijie; Gao, Dawen; Ren, Nanqi

    2014-11-01

    Pseudomonas sp. C27 is a facultative autotrophic bacterium (FAB) that can effectively conduct mixotrophic denitrifying sulfide removal (DSR) reactions using organic matters and sulfide as electron donors. Quantitative proteomics analysis of C27 using isobaric tag for relative and absolute quantitation (iTRAQ) and bioinformatics techniques identified 1916 unique proteins, based on which a novel pathway utilizing couple carbon, sulfide and nitrogen cycles for mixotrophic growth of C27. DSR experiments at different C/N ratios confirmed the presence of the new pathway. This novel pathway may be of great significance for C27-alike strains to conduct sulfide and nitrate removals in biological treatments. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. Toxicity of Phenol and Salt on the Phenol-Degrading Pseudomonas aeruginosa Bacterium

    Directory of Open Access Journals (Sweden)

    Samaei

    2016-08-01

    Full Text Available Background Phenolic compounds, phenol and phenol derivatives are environmental contaminants in some industrial effluents. Entrance of such substances into the environment causes severe environmental pollution, especially pollution of water resources. Biological treatment is a method that uses the potential of microorganisms to clean up contaminated environments. Among microorganisms, bacteria play an important role in treating wastewater contaminated with phenol. Objectives This study aimed to examine the effects of Pseudomonas aeruginosa on degradation of phenol in wastewater contaminated with this pollutant. Methods In this method, the growth rate of P. aeruginosa bacteria was investigated using different concentrations of salt and phenol. This is an experimental study conducted as a pilot in a batch reactor with different concentrations of phenol (25, 50, 100, 150, 300 and 600 mg L-1 and salt (0%, 0.5%, 1%, 2.5% and 5% during 9, 12 and 15 hours. During three days, from 5 experimental and 3 control samples, 18 samples were taken a day forming a sample size of 54 samples for each phenol concentration. Given the number of phenol concentrations (n = 6, a total of 324 samples were analyzed using a spectrophotometer at a wavelength of 600 nm. Results The phenol concentration of 600 mg L-1 was toxic for P. aeruginosa. However, at a certain concentration, it acts as a carbon source for P. aeruginosa. During investigations, it was found that increasing the concentration of phenol increases the rate of bacteria growth. The highest bacteria growth rate occurred was at the salt concentration of zero and phenol concentration of 600 mg L-1. Conclusions The findings of the current study indicate that at high concentrations of salt, the growth of bacteria reduces so that it stops at a concentration of 50 mg L-1 (5%. Thus, the bacterium is halotolerant or halophilic. With an increase in phenol concentration, the growth rate increased. Phenol toxicity appears

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

    Directory of Open Access Journals (Sweden)

    Arora Pankaj

    2012-11-01

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

  8. Antibiofilm Activity of the Marine Bacterium Pseudoalteromonas sp. Strain 3J6▿

    Science.gov (United States)

    Dheilly, Alexandra; Soum-Soutéra, Emmanuelle; Klein, Géraldine L.; Bazire, Alexis; Compère, Chantal; Haras, Dominique; Dufour, Alain

    2010-01-01

    Biofilm formation results in medical threats or economic losses and is therefore a major concern in a variety of domains. In two-species biofilms of marine bacteria grown under dynamic conditions, Pseudoalteromonas sp. strain 3J6 formed mixed biofilms with Bacillus sp. strain 4J6 but was largely predominant over Paracoccus sp. strain 4M6 and Vibrio sp. strain D01. The supernatant of Pseudoalteromonas sp. 3J6 liquid culture (SN3J6) was devoid of antibacterial activity against free-living Paracoccus sp. 4M6 and Vibrio sp. D01 cells, but it impaired their ability to grow as single-species biofilms and led to higher percentages of nonviable cells in 48-h biofilms. Antibiofilm molecules of SN3J6 were able to coat the glass surfaces used to grow biofilms and reduced bacterial attachment about 2-fold, which might partly explain the biofilm formation defect but not the loss of cell viability. SN3J6 had a wide spectrum of activity since it affected all Gram-negative marine strains tested except other Pseudoalteromonas strains. Biofilm biovolumes of the sensitive strains were reduced 3- to 530-fold, and the percentages of nonviable cells were increased 3- to 225-fold. Interestingly, SN3J6 also impaired biofilm formation by three strains belonging to the human-pathogenic species Pseudomonas aeruginosa, Salmonella enterica, and Escherichia coli. Such an antibiofilm activity is original and opens up a variety of applications for Pseudoalteromonas sp. 3J6 and/or its active exoproducts in biofilm prevention strategies. PMID:20363799

  9. 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.

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

    Science.gov (United States)

    Taghavi, Safiyh; van der Lelie, Daniel; Hoffman, Adam; Zhang, Yian-Biao; Walla, Michael D.; Vangronsveld, Jaco; Newman, Lee; Monchy, Sébastien

    2010-01-01

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

  11. Transformation of carbon tetrachloride by Pseudomonas sp. strain KC under denitrification conditions

    International Nuclear Information System (INIS)

    Criddle, C.S.; DeWitt, J.T.; Grbic-Galic, D.; McCarty, P.L.

    1990-01-01

    A denitrifying Pseudomonas sp. (strain KC) capable of transforming carbon tetrachloride (CT) was isolated from groundwater aquifer solids. Major products of the transformation of 14 C-labeled CT by Pseudomonas strain KC under denitrification conditions were 14 CO 2 and an unidentified water-soluble fraction. Little or no chloroform was produced. Addition of dissolved trace metals, notably, ferrous iron and cobalt, to the growth medium appeared to enhance growth of Pseudomonas strain KC while inhibiting transformation of CT. It is hypothesized that transformation of CT by this organism is associated with the mechanism of trace-metal scavenging

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-05-13

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

  13. Gas Chromatography - Mass Spectrometry Analysis and Antibacterial Activity of Bluish-Green Pigment from Pseudomonas sp. JJTBVK (KF836502

    Directory of Open Access Journals (Sweden)

    Bala Verma

    2015-08-01

    Full Text Available The present study was conducted for the isolation of potential bacteria from the desert soil, their molecular identification and prediction of restriction sites of the potential isolate using the bioinformatics tools. Production of the metabolites was done by inoculating in nutrient broth of pH 8.6. Metabolite was bluish-green in color; it was extracted and dried by using methanol and used for partial characterization by using GC-MS spectroscopy. Antibacterial activity was performed with the clinical human pathogenic isolates. The bacterium was identified as Pseudomonas sp.JJTBVK on the basis of 16S rRNA sequencing. The sequence was analyzed for the restriction cleavage sites, which showed that the sequence had various restriction sites for different enzymes. Antibacterial activity (MIC of methanol extract of the bacterial culture broth showed antibacterial activity (MIC, which was 29, 30, 30 and 29 mm for Pseudomonas aeruginosa, Staphylococcus aureus, Bacillus subtilis and Salmonella typhi, respectively. GC-MS analysis of the methanol extract showed the presence of naphth [2,3-B] azet-2 (1H -one, 1-phenyl-, which was the characteristic compound showing the antibacterial activity.

  14. 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.

  15. [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.

  16. OXIDATION OF BIPHENYL BY A MULTICOMPONENT ENZYME SYSTEM FROM PSEUDOMONAS SP. STRAIN LB400

    Science.gov (United States)

    Pseudomonas sp. strain LB400 grows on biphenyl as the sole carbon and energy source. This organism also cooxidizes several chlorinated biphenyl congeners. Biphenyl dioxygenase activity in cell extract required addition of NAD(P)H as an electron donor for the conversion of bipheny...

  17. Improvement in solvent tolerance by exogenous glycerol in Pseudomonas sp. BCNU 106.

    Science.gov (United States)

    Choi, H J; Lim, B R; Park, Y J; Joo, W H

    2017-08-01

    Solvent hypertolerant Pseudomonas sp. BCNU 106 still has some underlying growth limitation in solvents. Therefore, efficient mass cultivation methods are needed to pursue its applications in biotechnology. Pseudomonas sp. BCNU 106 was cultured in a medium supplemented with 0·05 mol l -1 glycerol and cell survival was monitored during its cultivation in the presence of 1% (v/v) toluene. Exogenously supplemented glycerol provided more protection against damage caused by toluene stress and conferred higher solvent tolerance of Pseudomonas sp. BCNU 106 to toluene compared to control Pseudomonas sp. BCNU 106 without the supplementation of glycerol. This low-cost mass cultivation method can be used to efficiently apply solvent-tolerant bacteria in biotransformation and biodegradation. Protection against toluene and improvement in bacterial cell growth by supplementation of glycerol in the presence of toluene are demonstrated in this study. This result can be used to solve growth-related hindrances of solvent-tolerant bacteria and establish their low-cost mass cultivation, thereby broadening their industrial and environmental applications. © 2017 The Society for Applied Microbiology.

  18. Utilization of petroleum hydrocarbons by Pseudomonas sp. and ...

    African Journals Online (AJOL)

    pseudomonas isolated from a petroleum-contaminated soil was instable. In this work, t is shown that when the isolates are immobilized on Perlite, they are more stable for oil egradation. Although the isolate did not have any chemotaxis to ...

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

    OpenAIRE

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

    2013-01-01

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

  20. Engineering mediator-based electroactivity in the obligate aerobic bacterium Pseudomonas putida KT2440

    OpenAIRE

    Simone eSchmitz; Salome eNies; Nick eWierckx; Lars M Blank; Miriam A. Rosenbaum

    2015-01-01

    Pseudomonas putida strains are being developed as microbial production hosts for production of a range of amphiphilic and hydrophobic biochemicals. P. putida's obligate aerobic growth thereby can be an economical and technical challenge because it requires constant rigorous aeration and often causes reactor foaming. Here, we engineered a strain of P. putida KT2440 that can produce phenazine redox-mediators from Pseudomonas aeruginosa to allow partial redox balancing with an electrode under ox...

  1. Pseudomonas sesami sp. nov., a plant growth-promoting Gammaproteobacteria isolated from the rhizosphere of Sesamum indicum L.

    Science.gov (United States)

    Madhaiyan, Munusamy; Poonguzhali, Selvaraj; Saravanan, Venkatakrishnan Sivaraj; Selvapravin, Kumaran; Duraipandiyan, Veeramuthu; Al-Dhabi, Naif Abdullah

    2017-07-01

    A novel Gram-stain negative, aerobic, motile, rod-shaped bacterium was isolated from Sesame (Sesamum indicum L.) rhizosphere soil. Based on the 16S rRNA gene similarity value (99.4-98.6%) obtained with phylogenetically closely related strains and through analyses of their house keeping genes (atpD, infB and rpoB), the strain SI-P133 T was delineated among the species of the genus Pseudomonas and was subjected to polyphasic taxonomic analysis. It was a chemoorganotroph which grew at wide range of temperature (4-45 °C), pH (5.5-9.5) and NaCl concentrations (0-7% (w/v). DNA-DNA hybridization values with closely related type strains DSM 9751 T , DSM 19095 T , DSM 21509 T , ICMP 9151 T and DSM 6929 T ranged from 23.1 to 44.2%. The most abundant fatty acids were C 16:0 , C 10:0 3-OH, summed feature 3 (comprising C 16:1 ω7c and/or C 16:1 ω6c), C 17:0 cyclo and C 12:0 3-OH. The major isoprenoid quinone system was ubiquinone 9 (Q-9) and the G+C content was 61.3 mol%. The major polar lipids of the strain SI-P133 T were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. With regard to prospective use in agriculture, plant growth-promoting properties of the strain were tested and plant growth-promotion was demonstrated under in vitro conditions. Based on the various polyphasic taxonomic traits analysed, the strain SI-P-133 T was novel and placed within the genus Pseudomonas. Hence we propose a novel species named Pseudomonas sesami sp. nov., for which the type strain is SI-P133 T (=NCIMB 14519 T  = KCTC 22518 T ).

  2. 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.

  3. Granulibacter bethesdensis gen. nov., sp. nov., a distinctive pathogenic acetic acid bacterium in the family Acetobacteraceae.

    Science.gov (United States)

    Greenberg, David E; Porcella, Stephen F; Stock, Frida; Wong, Alexandra; Conville, Patricia S; Murray, Patrick R; Holland, Steven M; Zelazny, Adrian M

    2006-11-01

    A Gram-negative, aerobic, coccobacillus to rod-shaped bacterium was isolated from three patients with chronic granulomatous disease. The organism was subjected to a polyphasic taxonomic study. A multilocus phylogenetic analysis based on the 16S rRNA gene, the internal transcribed spacer (ITS) region and the RecA protein demonstrated that the organism belongs to a new sublineage within the acetic acid bacteria in the family Acetobacteraceae. Phenotypic features are summarized as follows: the organism grew at an optimum temperature of 35-37 degrees C and optimum pH of 5.0-6.5. It produced a yellow pigment, oxidized lactate and acetate, the latter weakly, produced little acetic acid from ethanol and could use methanol as a sole carbon source. The two major fatty acids were a straight-chain unsaturated acid (C18:1omega7c) and C16:0. The DNA base composition was 59.1 mol% G+C. The very weak production of acetic acid from ethanol, the ability to use methanol, the yellow pigmentation and high optimum temperature for growth distinguished this organism from other acetic acid bacteria. The unique phylogenetic and phenotypic characteristics suggest that the bacterium should be classified within a separate genus, for which the name Granulibacter bethesdensis gen. nov., sp. nov. is proposed. The type strain is CGDNIH1T (=ATCC BAA-1260T=DSM 17861T).

  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. 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.

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

    Directory of Open Access Journals (Sweden)

    Yajian Song

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

  7. 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

  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. 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.

  10. 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.

  11. 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.

  12. Pseudomonas fluvialis sp. nov., a novel member of the genus Pseudomonas isolated from the river Ganges, India.

    Science.gov (United States)

    Sudan, Sarabjeet Kour; Pal, Deepika; Bisht, Bhawana; Kumar, Narender; Chaudhry, Vasvi; Patil, Prabhu; Sahni, Girish; Mayilraj, Shanmugam; Krishnamurthi, Srinivasan

    2018-01-01

    A bacterial strain, designated ASS-1 T , was isolated and identified from a sediment sample of the river Ganges, Allahabad, India. The strain was Gram-stain-negative, formed straw-yellow pigmented colonies, was strictly aerobic, motile with a single polar flagellum, and positive for oxidase and catalase. The major fatty acids were C16 : 1ω7c/ 16 : 1 C16 : 1ω6c, C18 : 1ω7c and C16 : 0. Sequence analysis based on the 16S rRNA gene revealed that strain ASS-1 T showed high similarity to Pseudomonas guguanensis CC-G9A T (98.2 %), Pseudomonas alcaligenes ATCC 14909 T (98.2 %), Pseudomonas oleovorans DSM 1045 T (98.1 %), Pseudomonas indolxydans IPL-1 T (98.1 %) and Pseudomonas toyotomiensis HT-3 T (98.0 %). Analysis of its rpoB and rpoD housekeeping genes confirmed its phylogenetic affiliation and showed identities lower than 93 % with respect to the closest relatives. Phylogenetic analysis based on the 16S rRNA, rpoB, rpoD genes and the whole genome assigned it to the genus Pseudomonas. The results of digital DNA-DNA hybridization based on the genome-to-genome distance calculator and average nucleotide identity revealed low genome relatedness to its close phylogenetic neighbours (below the recommended thresholds of 70 and 95 %, respectively, for species delineation). Strain ASS-1 T also differed from the related strains by some phenotypic characteristics, i.e. growth at pH 5.0 and 42 °C, starch and casein hydrolysis, and citrate utilization. Therefore, based on data obtained from phenotypic and genotypic analysis, it is evident that strain ASS-1 T should be regarded as a novel species within the genus Pseudomonas, for which the name Pseudomonasfluvialis sp. nov. is proposed. The type strain is ASS-1 T (=KCTC 52437 T =CCM 8778 T ).

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

    Science.gov (United States)

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

    2007-01-01

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

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

    Science.gov (United States)

    Powell, Ryan J.

    2013-01-01

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

  15. Effect of Indigenous Pseudomonas sp. and Bacillus sp. Strains on Yield and Main Chemical Growth Parameters of Radicchio

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    Stanojković-Sebić Aleksandra

    2018-03-01

    Full Text Available Pseudomonas sp. and Bacillus sp. belong to plant growth promoting rhizobacteria which are able to colonize the plants roots and stimulate growth. In this study, the effect of two indigenous plant growth promoting rhizobacterial strains Pseudomonas sp. Q4 and Bacillus sp. Q10 and their mixture (mix Q4+Q10 on content of the main chemical growth parameters (nitrogen, phosphorus, potassium, calcium and magnesium and the yield of dry biomass of radicchio (Cichorium spp. var. rossa di treviso aerial parts and root, was investigated. The study was carried out with stagnosol type of soil in pot experiments under semi-controlled conditions in the Institute of Soil Science (Belgrade, in the period from July to October in 2013. Phosphorus was determined by spectrophotometer, potassium - by flame emission photometry and total nitrogen and carbon - using elemental CNS analyzer, while calcium and magnesium were determined by AAS. The data on yield of both aerial parts and root dry biomass of radicchio showed that its treatment with Q4 and Q10 strains, as well as with their mixture, caused noticeably increase in this parameter in relation to the control, whereby the strain Q4 was more effective for aerial parts, while mix Q4+Q10 - for roots. The obtained data on the studied chemical parameters of radicchio root and aerial parts were in total accordance with their yield. Concluding, studied strains have a potential in promoting the biomass yield and main chemical growth parameters of both aerial parts and root of radicchio.

  16. The efficiency of gamma irradiation on the bacterium pseudomonas fluorescence (Migh) against the mediterranean fruit fly ceratitis capitata (wiedemann)

    International Nuclear Information System (INIS)

    Fadel, A.M.

    2002-01-01

    The efficiency of the bacterium pseudomonas fluorescence against the mediterranean fruit fly ceratitis capitata (Wied.) was investigated. Adult emergence was significantly reduced by applying the wild and gamma irradiated strain (150 and 300 Gy). The highest reduction occurred by the mutant P1 and the highest concentration (10 8 ). The activity of this bacteria increased by gamma irradiation compared to that of the wild isolate. The reduction in adult survival of both males and females was highly significant by applying the irradiated bacteria with the two doses of gamma radiation and different concentration (10 8 , 10 6 and 10 4 ) of bacterial suspension. Applying the bacteria as a culture filtrate reduced adult survival of wild strain significantly, while the irradiated strain recorded a significant reduction in males and females with the highest concentration (100 %) and by applying the two doses of gamma radiation (150 and 300 Gy) and in females only at the concentration 50% by using the dose of 150 Gy

  17. Responses of a soil bacterium, Pseudomonas chlororaphis O6 to commercial metal oxide nanoparticles compared with responses to metal ions

    International Nuclear Information System (INIS)

    Dimkpa, Christian O.; Calder, Alyssa; Britt, David W.; McLean, Joan E.; Anderson, Anne J.

    2011-01-01

    The toxicity of commercially-available CuO and ZnO nanoparticles (NPs) to pathogenic bacteria was compared for a beneficial rhizosphere isolate, Pseudomonas chlororaphis O6. The NPs aggregated, released ions to different extents under the conditions used for bacterial exposure, and associated with bacterial cell surface. Bacterial surface charge was neutralized by NPs, dependent on pH. The CuO NPs were more toxic than the ZnO NPs. The negative surface charge on colloids of extracellular polymeric substances (EPS) was reduced by Cu ions but not by CuO NPs; the EPS protected cells from CuO NPs-toxicity. CuO NPs-toxicity was eliminated by a Cu ion chelator, suggesting that ion release was involved. Neither NPs released alkaline phosphatase from the cells' periplasm, indicating minimal outer membrane damage. Accumulation of intracellular reactive oxygen species was correlated with CuO NPs lethality. Environmental deposition of NPs could create niches for ion release, with impacts on susceptible soil microbes. - Highlights: → Toxicity of metallic nanoparticles (NPs) was evaluated in a beneficial bacterium, Pseudomonas chlororaphis O6 (PcO6). → Aggregated commercial CuO and ZnO NPs released Cu and Zn ions and changed bacterial surface charge, depending on pH. → The NPs were toxic to PcO6 through NP-specific, but also ion release mechanisms. → Reactive oxygen species were produced by CuO NP and Cu ion at lethal concentrations, but bacterial EPS protected against Cu. → The periplasmic marker, alkaline phosphate, activity was increased by the NPs and ions. - Aggregated CuO and ZnO nanoparticles release ions and cause different toxicities in a beneficial soil bacterium.

  18. Pseudomonas kribbensis sp. nov., isolated from garden soils in Daejeon, Korea.

    Science.gov (United States)

    Chang, Dong-Ho; Rhee, Moon-Soo; Kim, Ji-Sun; Lee, Yookyung; Park, Mi Young; Kim, Haseong; Lee, Seung-Goo; Kim, Byoung-Chan

    2016-11-01

    Two bacterial strains, 46-1 and 46-2 T , were isolated from garden soil. These strains were observed to be aerobic, Gram-stain negative, rod-shaped, non-spore-forming, motile and catalase and oxidase positive. Phylogenetic analysis based on 16S rRNA gene sequences showed that the two strains shared 100 % sequence similarity with each other and belong to the genus Pseudomonas in the class Gammaproteobacteria. The concatenated 16S rRNA, gyrB, rpoB and rpoD gene sequences further confirmed that the isolates belong to the Pseudomonas koreensis subgroup (SG), with P. koreensis Ps 9-14 T , Pseudomonas moraviensis 1B4 T and Pseudomonas granadensis F-278,770 T as their close relatives (>96 % pairwise similarity). DNA-DNA hybridization with the closely related type strain P. koreensis SG revealed a low level of relatedness (15 %) in the isolates but it was a minor component (Pseudomonas, for which the name Pseudomonas kribbensis sp. nov. is proposed; the type strain is 46-2 T (=KCTC 32541 T  = DSM 100278 T ).

  19. Physiological and biochemical characterization of a novel nicotine-degrading bacterium Pseudomonas geniculata N1.

    Directory of Open Access Journals (Sweden)

    Yanghui Liu

    Full Text Available Management of solid wastes with high nicotine content, such as those accumulated during tobacco manufacturing, poses a major challenge, which can be addressed by using bacteria such as Pseudomonas and Arthrobacter. In this study, a new species of Pseudomonas geniculata, namely strain N1, which is capable of efficiently degrading nicotine, was isolated and identified. The optimal growth conditions for strain N1 are a temperature of 30°C, and a pH 6.5, at a rotation rate of 120 rpm min(-1 with 1 g l(-1 nicotine as the sole source of carbon and nitrogen. Myosmine, cotinine, 6-hydroxynicotine, 6-hydroxy-N-methylmyosmine, and 6-hydroxy-pseudooxynicotine were detected as the five intermediates through gas chromatography-mass and liquid chromatography-mass analyses. The identified metabolites were different from those generated by Pseudomonas putida strains. The analysis also highlighted the bacterial metabolic diversity in relation to nicotine degradation by different Pseudomonas strains.

  20. Evolutionary history of the phl gene cluster in the plant-associated bacterium Pseudomonas fluorescens

    NARCIS (Netherlands)

    Moynihan, J.A.; Morrissey, J.P.; Coppoolse, E.; Stiekema, W.J.; O'Gara, F.; Boyd, E.F.

    2009-01-01

    Pseudomonas fluorescens is of agricultural and economic importance as a biological control agent largely because of its plant-association and production of secondary metabolites, in particular 2, 4-diacetylphloroglucinol (2, 4-DAPG). This polyketide, which is encoded by the eight gene phl cluster,

  1. 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.

  2. Survival Strategies of the Plant-Associated Bacterium Enterobacter sp. Strain EG16 under Cadmium Stress.

    Science.gov (United States)

    Chen, Yanmei; Chao, Yuanqing; Li, Yaying; Lin, Qingqi; Bai, Jun; Tang, Lu; Wang, Shizhong; Ying, Rongrong; Qiu, Rongliang

    2016-01-04

    Plant-associated bacteria are of great interest because of their potential use in phytoremediation. However, their ability to survive and promote plant growth in metal-polluted soils remains unclear. In this study, a soilborne Cd-resistant bacterium was isolated and identified as Enterobacter sp. strain EG16. It tolerates high external Cd concentrations (Cd(2+) MIC, >250 mg liter(-1)) and is able to produce siderophores and the plant hormone indole-3-acetic acid (IAA), both of which contribute to plant growth promotion. Surface biosorption in this strain accounted for 31% of the total Cd accumulated. The potential presence of cadmium sulfide, shown by energy-dispersive X-ray (EDX) analysis, suggested intracellular Cd binding as a Cd response mechanism of the isolate. Cd exposure resulted in global regulation at the transcriptomic level, with the bacterium switching to an energy-conserving mode by inhibiting energy-consuming processes while increasing the production of stress-related proteins. The stress response system included increased import of sulfur and iron, which become deficient under Cd stress, and the redirection of sulfur metabolism to the maintenance of intracellular glutathione levels in response to Cd toxicity. Increased production of siderophores, responding to Cd-induced Fe deficiency, not only is involved in the Cd stress response systems of EG16 but may also play an important role in promoting plant growth as well as alleviating the Cd-induced inhibition of IAA production. The newly isolated strain EG16 may be a suitable candidate for microbially assisted phytoremediation due to its high resistance to Cd and its Cd-induced siderophore production, which is likely to contribute to plant growth promotion. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  3. Alsobacter metallidurans gen. nov., sp. nov., a thallium-tolerant soil bacterium in the order Rhizobiales.

    Science.gov (United States)

    Bao, Zhihua; Sato, Yoshinori; Fujimura, Reiko; Ohta, Hiroyuki

    2014-03-01

    A thallium-tolerant, aerobic bacterium, designated strain SK200a-9(T), isolated from a garden soil sample was characterized using a polyphasic approach. Comparative analysis of 16S rRNA gene sequences revealed that strain SK200a-9(T) was affiliated with an uncultivated lineage within the Alphaproteobacteria and the nearest cultivated neighbours were bacteria in genera in the family Methylocystaceae (93.3-94.4% 16S rRNA gene sequence similarity) and the family Beijerinckiaceae (92.3-93.1%) in the order Rhizobiales. Cells of strain SK200a-9(T) were Gram-stain-negative, non-motile, non-spore-forming, poly-β-hydroxybutyrate-accumulating rods. The strain was a chemo-organotrophic bacterium, which was incapable of growth on C1 substrates. Catalase and oxidase were positive. Atmospheric nitrogen fixation and nitrate reduction were negative. The strain contained ubiquinone Q-10 and cellular fatty acids C18 : 1ω7c, C18 : 0, C16 : 1ω7c and C16 : 0 as predominant components. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was 64.8 mol%. On the basis of the information described above, strain SK200a-9(T) is considered to represent a novel species of a new genus in the order Rhizobiales, for which the name Alsobacter metallidurans gen. nov., sp. nov. is proposed. The type strain of Alsobacter metallidurans is SK200a-9(T) ( = NBRC 107718(T) = CGMCC 1.12214(T)).

  4. In vitro selective growth inhibition of breast adenocarcinoma cell lines by Pseudomonas sp. UW4 metabolites

    Directory of Open Access Journals (Sweden)

    Maedeh Pasiar

    2016-12-01

    Full Text Available Background: Breast cancer is a malignant proliferation of epithelial cells that lining the ducts or lobules of the breast. It is the second common cancer, after lung cancer in women. Since growth inhibition is an important strategy in cancer treatment, many attempts are in program to find new apoptotic inducer agents. Today there is some reports about effect of metabolites of Pseudomonas on cancer cells, hence, metabolites of Pseudomonas sp. UW4, were isolated and anti-cancer and anti-microbial activity of these metabolites was studied. Methods: This experimental study was performed in cellular and developmental biology of Shahrekord Islamic Azad University from April 2015 to August 2015. Anti-microbial activity of metabolites of Pseudomonas sp. UW4 was tested against a pathogenic bacteria, including Escherichia coli, Bacillus cereus and Staphylococcus aureus. For anti-cancer activity, in this study SKBR3 cells and normal fibroblast cells (HU-02 were cultured in DMEM medium with 10% fetal bovine serum (FBS. The cells were treated by various concentrations of these metabolites 5, 10, 15 and 20 mg/ml for 24, 48 and 72 h. Cell viability was assessed by MTS assay. Cells were seeded at 5×103 cells/ml in 96 well plates and incubated for 24 hr. Then metabolites of bacteria were added, after indicated times MTS (20 µl was added and the absorbance was measured at 492 nm using ELISA plate reader. Results: Pseudomonas sp. UW4 was able to produce antimicrobial metabolites against Staphylococcus aureus. Metabolites decreases the viability of SKBR3 cell line in a time and dose dependent manner, so that the most effective concentration of this substance was 20 mg/ml and 72 h after treatment (P< 0.01. While Pseudomonas sp. UW4 in various concentrations had no significant effect on normal fibroblast cells (P= 0.24. Conclusion: Bioactive compounds produced by of Pseudomonas sp. UW4 could be used for elimination of infections and treatment of breast cancer SK

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

    Directory of Open Access Journals (Sweden)

    Ana Cristina dos Reis Ferreira

    2015-06-01

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

  6. Indole acetic acid overproduction transformants of the rhizobacterium Pseudomonas sp. UW4.

    Science.gov (United States)

    Duca, Daiana R; Rose, David R; Glick, Bernard R

    2018-02-28

    The plant growth-promoting rhizobacterium Pseudomonas sp. UW4 was transformed to increase the biosynthesis of the auxin, indole-3-acetic acid (IAA). Four native IAA biosynthesis genes from strain UW4 were individually cloned into an expression vector and introduced back into the wild-type strain. Quantitative real-time polymerase chain reaction analysis revealed that the introduced genes ami, nit, nthAB and phe were all overexpressed in these transformants. A significant increase in the production of IAA was observed for all modified strains. Canola plants inoculated with the modified strains showed enhanced root elongation under gnotobiotic conditions. The growth rate and 1-aminocyclopropane-1-carboxylate deaminase activity of transformant strains was lower compared to the wild-type. The indoleacetic acid biosynthesis pathways and the role of this phytohormone in the mechanism of plant growth stimulation by Pseudomonas sp. UW4 is discussed.

  7. Degradation and metabolism of synthetic plastics and associated products by Pseudomonas sp.: capabilities and challenges.

    Science.gov (United States)

    Wilkes, R A; Aristilde, L

    2017-09-01

    Synthetic plastics, which are widely present in materials of everyday use, are ubiquitous and slowly-degrading polymers in environmental wastes. Of special interest are the capabilities of microorganisms to accelerate their degradation. Members of the metabolically diverse genus Pseudomonas are of particular interest due to their capabilities to degrade and metabolize synthetic plastics. Pseudomonas species isolated from environmental matrices have been identified to degrade polyethylene, polypropylene, polyvinyl chloride, polystyrene, polyurethane, polyethylene terephthalate, polyethylene succinate, polyethylene glycol and polyvinyl alcohol at varying degrees of efficiency. Here, we present a review of the current knowledge on the factors that control the ability of Pseudomonas sp. to process these different plastic polymers and their by-products. These factors include cell surface attachment within biofilms, catalytic enzymes involved in oxidation or hydrolysis of the plastic polymer, metabolic pathways responsible for uptake and assimilation of plastic fragments and chemical factors that are advantageous or inhibitory to the biodegradation process. We also highlight future research directions required in order to harness fully the capabilities of Pseudomonas sp. in bioremediation strategies towards eliminating plastic wastes. © 2017 The Society for Applied Microbiology.

  8. Characteristics of a Monoacylglycerol Lipase Isolated from Pseudomonas sp. LP7315 -Hydrolysis and Synthesis of Monoglycerides

    OpenAIRE

    Sakiyama, Takaharu; Yoshimi, Tsuyoshi; Miyake, Akira; Umeoka, Midori; Tanaka, Atsushi; Ozaki, Sho; Nakanishi, Kazuhiro

    2001-01-01

    A monoacylglycerol lipase (MGL) was purified from Pseudomonas sp. LP7315 by ammonium sulfate precipitation, anion-exchange chromatography, and preparative electrophoresis. The purified enzyme was homogeneous on an SDS-polyacrylamide gel with a molecular mass of 59 kDa. Itshydrolytic activity was confirmed to be specific for monoglycerides: the enzyme did not hydrolyze diandtriglycerides. MGL was found to be stable even after l-h incubation at 65℃. The hydrolytic activity depended not only on ...

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

    OpenAIRE

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

    2014-01-01

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

  10. Biodegradation of Methyl tert-Butyl Ether by Co-Metabolism with a Pseudomonas sp. Strain

    Directory of Open Access Journals (Sweden)

    Shanshan Li

    2016-09-01

    Full Text Available Co-metabolic bioremediation is supposed to be an impressive and promising approach in the elimination technology of methyl tert-butyl ether (MTBE, which was found to be a common pollutant worldwide in the ground or underground water in recent years. In this paper, bacterial strain DZ13 (which can co-metabolically degrade MTBE was isolated and named as Pseudomonas sp. DZ13 based on the result of 16S rRNA gene sequencing analysis. Strain DZ13 could grow on n-alkanes (C5-C8, accompanied with the co-metabolic degradation of MTBE. Diverse n-alkanes with different carbon number showed a significant influence on the degradation rate of MTBE and accumulation of tert-butyl alcohol (TBA. When Pseudomonas sp. DZ13 co-metabolically degraded MTBE with n-pentane as the growth substrate, a higher MTBE-degrading rate (Vmax = 38.1 nmol/min/mgprotein, Ks = 6.8 mmol/L and lower TBA-accumulation was observed. In the continuous degradation experiment, the removal efficiency of MTBE by Pseudomonas sp. Strain DZ13 did not show an obvious decrease after five times of continuous addition.

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

    Science.gov (United States)

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

    2013-07-01

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

  12. Soil components mitigate the antimicrobial effects of silver nanoparticles towards a beneficial soil bacterium, Pseudomonas chlororaphis O6

    International Nuclear Information System (INIS)

    Calder, Alyssa J.; Dimkpa, Christian O.; McLean, Joan E.; Britt, David W.; Johnson, William; Anderson, Anne J.

    2012-01-01

    Silver nanoparticles (Ag NPs) are widely used for their antimicrobial activity and consequently the particles will become environmental contaminants. This study evaluated in sand and soil matrices the toxicity of 10 nm spherical Ag NPs (1 and 3 mg Ag/L) toward a beneficial soil bacterium, Pseudomonas chlororaphis O6. In sand, both NP doses resulted in loss in bacterial culturability whereas in a loam soil, no cell death was observed. Amendments of sand with clays (30% v/v kaolinite or bentonite) did not protect the bacterium when challenged with Ag NPs. However, culturability of the bacterium was maintained when the Ag NP-amended sand was mixed with soil pore water or humic acid. Imaging by atomic force microscopy revealed aggregation of single nanoparticles in water, and their embedding into background material when suspended in pore water and humic acids. Zeta potential measurements supported aggregation and surface charge modifications with pore water and humic acids. Measurement of soluble Ag in the microcosms and geochemical modeling to deduce the free ion concentration revealed bacterial culturability was governed by the predicted free Ag ion concentrations. Our study confirmed the importance of Ag NPs as a source of ions and illustrated that processes accounting for protection in soil against Ag NPs involved distinct NP- and ion-effects. Processes affecting NP bioactivity involved surface charge changes due to sorption of Ca 2+ from the pore water leading to agglomeration and coating of the NPs with humic acid and other organic materials. Removal of bioactive ions included the formation of soluble Ag complexes with dissolved organic carbon and precipitation of Ag ions with chloride in pore water. We conclude that mitigation of toxicity of Ag NPs in soils towards a soil bacterium resides in several interactions that differentially involve protection from the Ag NPs or the ions they produce. - Highlights: ► Silver nanoparticles (Ag NPs) are widely used for

  13. Comparative study on the degradation of dibutyl phthalate by two newly isolated Pseudomonas sp. V21b and Comamonas sp. 51F

    Directory of Open Access Journals (Sweden)

    Vinay Kumar

    2017-09-01

    Full Text Available Dibutyl phthalate is (DBP the top priority toxicant responsible for carcinogenicity, teratogenicity and endocrine disruption. This study demonstrates the DBP degradation capability of the two newly isolated bacteria from municipal solid waste leachate samples. The isolated bacteria were designated as Pseudomonas sp. V21b and Comamonas sp. 51F after scanning electron microscopy, transmission electron microscopy, Gram-staining, antibiotic sensitivity tests, biochemical characterization, 16S-rRNA gene identification and phylogenetic studies. They were able to grow on DBP, benzyl butyl phthalate, monobutyl phthalate, diisodecyl phthalate, dioctyl phthalate, and protocatechuate. It was observed that Pseudomonas sp. V21b was more efficient in DBP degradation when compared with Comamonas sp. 51F. It degraded 57% and 76% of the initial DBP in minimal salt medium and in DBP contaminated samples respectively. Kinetics for the effects of DBP concentration on Pseudomonas sp. V21b and Comamonas sp. 51F growth was also evaluated. Stoichiometry for DBP degradation and biomass formation were compared for both the isolates. Two major metabolites diethyl phthalate and monobutyl phthalates were identified using GC–MS in the extracts. Key genes were amplified from the genomes of Pseudomonas sp. V21b and Comamonas sp. 51F. DBP degradation pathway was also proposed.

  14. Pseudomonas endophytica sp. nov., isolated from stem tissue of Solanum tuberosum L. in Spain.

    Science.gov (United States)

    Ramírez-Bahena, Martha-Helena; Cuesta, Maria José; Tejedor, Carmen; Igual, José Mariano; Fernández-Pascual, Mercedes; Peix, Álvaro

    2015-07-01

    A bacterial strain named BSTT44(T) was isolated in the course of a study of endophytic bacteria occurring in stems and roots of potato growing in a soil from Salamanca, Spain. The 16S rRNA gene sequence had 99.7% identity with respect to that of its closest relative, Pseudomonas psychrophila E-3T, and the next most closely related type strains were those of Pseudomonas fragi, with 99.6% similarity, Pseudomonas deceptionensis, with 99.2% similarity, and Pseudomonas lundensis, with 99.0% similarity; these results indicate that BSTT44(T) should be classified within the genus Pseudomonas. Analysis of the housekeeping genes rpoB, rpoD and gyrB confirmed its phylogenetic affiliation and showed identities lower than 92% in all cases with respect to the above-mentioned closest relatives. Cells of the strain bore one polar-subpolar flagellum. The respiratory quinone was Q-9.The major fatty acids were C16:0, C18:1ω7c and summed feature 3 (C16:1ω7c and/or C16:1ω6c). The strain was oxidase-, catalase- and urease-positive and the arginine dihydrolase system was present, but tests for nitrate reduction, β-galactosidase production and aesculin hydrolysis were negative. It could grow at 35 °C and at pH 5-9.The DNA G+C content was 60.2 mol%. DNA-DNA hybridization results showed less than 48% relatedness with respect to the type strains of the four most closely related species. Therefore, the combined results of genotypic, phenotypic and chemotaxonomic analyses support the classification of strain BSTT44 into a novel species of the genus Pseudomonas, for which the name Pseudomonas endophytica sp. nov. is proposed. The type strain is BSTT44(T) ( = LMG 28456(T) = CECT 8691(T)).

  15. 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 ).

  16. 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.

  17. 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)).

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

    Science.gov (United States)

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

    2016-06-01

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

  1. Genome sequence of Enterobacter sp. ST3, a quorum sensing bacterium associated with marine dinoflagellate

    Directory of Open Access Journals (Sweden)

    Jin Zhou

    2016-03-01

    Full Text Available Phycosphere environment is a typical marine niche, harbor diverse populations of microorganisms, which are thought to play a critical role in algae host and influence mutualistic and competitive interactions. Understanding quorum sensing-based acyl-homoserine lactone (AHL language may shed light on the interaction between algal-associated microbial communities in the native environment. In this work, we isolated an epidermal bacterium (was tentatively named Enterobacter sp. ST3, and deposited in SOA China, the number is MCCC1K02277-ST3 from the marine dinoflagellate Scrippsiella trochoidea, and found it has the ability to produce short-chain AHL signal. In order to better understand its communication information at molecular level, the genomic map was investigated. The genome size was determined to be 4.81 Mb with a G + C content of 55.59%, comprising 6 scaffolds of 75 contigs containing 4647 protein-coding genes. The functional proteins were predicted, and 3534 proteins were assigned to COG functional categories. An AHL-relating gene, LuxR, was found in upstream position at contig 1. This genome data may provide clues to increase understanding of the chemical characterization and ecological behavior of strain ST3 in the phycosphere microenvironment.

  2. A thermostable serralysin inhibitor from marine bacterium Flavobacterium sp. YS-80-122

    Science.gov (United States)

    Liang, Pengjuan; Li, Shangyong; Wang, Kun; Wang, Fang; Xing, Mengxin; Hao, Jianhua; Sun, Mi

    2017-06-01

    Serralysin inhibitors have been proposed as potent drugs against many diseases and may help to prevent further development of antibiotic-resistant pathogenic bacteria. In this study, a novel serralysin inhibitor gene, lupI, was cloned from the marine bacterium Flavobacterium sp. YS-80-122 and expressed in Escherichia coli. The deduced serralysin inhibitor, LupI, shows <40% amino acid identity to other reported serralysin inhibitors. Multiple sequence alignment and phylogenetic analysis of LupI with other serralysin inhibitors indicated that LupI was a novel type of serralysin inhibitor. The inhibitory constant for LupI towards its target metalloprotease was 0.64 μmol/L. LupI was thermostable at high temperature, in which 35.6%-90.7% of its inhibitory activity was recovered after treatment at 100°C for 1-60 min followed by incubation at 0°C. This novel inhibitor may represent a candidate drug for the treatment of serralysin-related infections.

  3. 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).

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

    Directory of Open Access Journals (Sweden)

    Xinhua Fu

    2014-01-01

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

  5. [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.

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

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    Ang eLiu

    2016-04-01

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

  7. Mammalian cell line-based bioassays for toxicological evaluation of landfill leachate treated by Pseudomonas sp. ISTDF1.

    Science.gov (United States)

    Ghosh, Pooja; Das, Mihir Tanay; Thakur, Indu Shekhar

    2014-01-01

    Landfill leachate has become a serious environmental concern because of the presence of many hazardous compounds which even at trace levels are a threat to human health and environment. Therefore, it is important to assess the toxicity of leachate generated and discharge it conforming to the safety standards. The present work examined the efficiency of an earlier reported Pseudomonas sp. strain ISTDF1 for detoxification of leachate collected from Okhla landfill site (New Delhi, India). GC-MS analysis performed after treatment showed the removal of compounds like alpha-limonene diepoxide, brominated dioxin-2-one, Bisphenol A, nitromusk, phthalate derivative, and nitrobenzene originally found in untreated leachate. ICP-AES analysis for heavy metals also showed reduction in concentrations of Zn, Cd, Cr, Fe, Ni, and Pb bringing them within the limit of safety discharge. Methyl tetrazolium (MTT) assay for cytotoxicity, alkaline comet assay for genotoxicity, and 7-ethoxyresorufin-O-deethylase (EROD) assay for dioxin-like behavior were carried out in human hepato-carcinoma cell line HepG2 to evaluate the toxic potential of treated and untreated leachates. The bacterium reduced toxicity as shown by 2.5-fold reduction of MTT EC50 value, 7-fold reduction in Olive Tail Moment, and 2.8-fold reduction in EROD induction after 240 h of bacterial treatment.

  8. Draft genome sequence of a caprolactam degrader bacterium: Pseudomonas taiwanensis strain SJ9.

    Science.gov (United States)

    Hong, Sung-Jun; Park, Gun-Seok; Khan, Abdur Rahim; Jung, Byung Kwon; Shin, Jae-Ho

    Pseudomonas taiwanensis strain SJ9 is a caprolactam degrader, isolated from industrial wastewater in South Korea and considered to have the potential for caprolactam bioremediation. The genome of this strain is approximately 6.2 Mb (G+C content, 61.75%) with 6,010 protein-coding sequences (CDS), of which 46% are assigned to recognized functional genes. This draft genome of strain SJ9 will provide insights into the genetic basis of its caprolactam-degradation ability. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

  9. Draft genome sequence of a caprolactam degrader bacterium: Pseudomonas taiwanensis strain SJ9

    Directory of Open Access Journals (Sweden)

    Sung-Jun Hong

    Full Text Available Abstract Pseudomonas taiwanensis strain SJ9 is a caprolactam degrader, isolated from industrial wastewater in South Korea and considered to have the potential for caprolactam bioremediation. The genome of this strain is approximately 6.2 Mb (G + C content, 61.75% with 6,010 protein-coding sequences (CDS, of which 46% are assigned to recognized functional genes. This draft genome of strain SJ9 will provide insights into the genetic basis of its caprolactam-degradation ability.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-03-01

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

  11. Pumilacidin-Like Lipopeptides Derived from Marine Bacterium Bacillus sp. Strain 176 Suppress the Motility of Vibrio alginolyticus.

    Science.gov (United States)

    Xiu, Pengyuan; Liu, Rui; Zhang, Dechao; Sun, Chaomin

    2017-06-15

    Bacterial motility is a crucial factor during the invasion and colonization processes of pathogens, which makes it an attractive therapeutic drug target. Here, we isolated a marine bacterium ( Vibrio alginolyticus strain 178) from a seamount in the tropical West Pacific that exhibits vigorous motility on agar plates and severe pathogenicity to zebrafish. We found that V. alginolyticus 178 motility was significantly suppressed by another marine bacterium, Bacillus sp. strain 176, isolated from the same niche. We isolated, purified, and characterized two different cyclic lipopeptides (CLPs) from Bacillus sp. 176 using high-performance liquid chromatography, mass spectrometry, and nuclear magnetic resonance spectroscopy. The two related CLPs have a pumilacidin-like structure and were both effective inhibitors of V. alginolyticus 178 motility. The CLPs differ by only one methylene group in their fatty acid chains. In addition to motility suppression, the CLPs also induced cell aggregation in the medium and reduced adherence of V. alginolyticus 178 to glass substrates. Notably, upon CLP treatment, the expression levels of two V. alginolyticus flagellar assembly genes ( flgA and flgP ) dropped dramatically. Moreover, the CLPs inhibited biofilm formation in several other strains of pathogenic bacteria without inducing cell death. This study indicates that CLPs from Bacillus sp. 176 show promise as antimicrobial lead compounds targeting bacterial motility and biofilm formation with a low potential for eliciting antibiotic resistance. IMPORTANCE Pathogenic bacteria often require motility to establish infections and subsequently spread within host organisms. Thus, motility is an attractive therapeutic target for the development of novel antibiotics. We found that cyclic lipopeptides (CLPs) produced by marine bacterium Bacillus sp. strain 176 dramatically suppress the motility of the pathogenic bacterium Vibrio alginolyticus strain 178, reduce biofilm formation, and promote

  12. 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.

  13. APPLICATION OF PSEUDOMONAS PUTIDA AND RHODOCOCCUS SP. BY BIODEGRADATION OF PAH(S, PCB(S AND NEL SOIL SAMPLES FROM THE HAZARDOUS WASTE DUMP IN POZĎÁTKY (CZECH REPUBLIC

    Directory of Open Access Journals (Sweden)

    Radmila Kucerova

    2006-12-01

    Full Text Available The objective of the project was a laboratory check of biodegradation of soil samples contaminated by PAH(s, PCB(s and NEL from the hazardous waste dump in the Pozďátky locality. For the laboratory check, pure bacterial cultures of Rhodococcus sp. and Pseudomonas putida have been used. It is apparent from the laboratory experiments results that after one-month bacterial leaching, applying the bacterium of Rhodococcus sp. there is a 83 % removal of NEL, a 79 % removal of PAH(s and a 14 % removal of PCB(s. Applying a pure culture of Pseudomonas putida there is a 87 % removal of NEL, a 81 % removal of PAH(s and a 14 % removal of PCB(s.

  14. Antibacterial activity of the Antarctic bacterium Janthinobacterium sp. SMN 33.6 against multi-resistant Gram-negative bacteria

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    Geraldine Asencio

    2014-01-01

    Conclusions: The ethanolic extract of Janthinobacterium sp. SMN 33.6 possesses antibacterial activity against a chromosomal AmpC beta-lactamase-producing strain of Serratia marcescens, an extended-spectrum beta-lactamase-producing Escherichia coli and also against carbapenemase-producing strains of Acinetobacter baumannii and Pseudomonas aeruginosa. This becomes a potential and interesting biotechnological tool for the control of bacteria with multi-resistance to commonly used antibiotics.

  15. Engineering mediator-based electroactivity in the obligate aerobic bacterium Pseudomonas putida KT2440

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    Simone eSchmitz

    2015-04-01

    Full Text Available Pseudomonas putida strains are being developed as microbial production hosts for production of a range of amphiphilic and hydrophobic biochemicals. P. putida’s obligate aerobic growth thereby can be an economical and technical challenge because it requires constant rigorous aeration and often causes reactor foaming. Here, we engineered a strain of P. putida KT2440 that can produce phenazine redox-mediators from Pseudomonas aeruginosa to allow partial redox balancing with an electrode under oxygen-limited conditions. P. aeruginosa is known to employ its phenazine-type redox mediators for electron exchange with an anode in bioelectrochemical systems. We transferred the seven core phenazine biosynthesis genes phzA-G and the two specific genes phzM and phzS required for pyocyanin synthesis from P. aeruginosa on two inducible plasmids into P. putida KT2440. The best clone, P. putida pPhz, produced 45 mg/ L pyocyanin over 25 h of growth, which was visible as blue color formation and is comparable to the pyocyanin production of P. aeruginosa. This new strain was then characterized under different oxygen-limited conditions with electrochemical redox control and changes in central energy metabolism were evaluated in comparison to the unmodified P. putida KT2440. In the new strain, phenazine synthesis with supernatant concentrations up to 33 µg/ mL correlated linearly with the ability to discharge electrons to an anode, whereby phenazine-1-carboxylic acid served as the dominating redox mediator. P. putida pPhz sustained strongly oxygen-limited metabolism for up to 2 weeks at up to 12 µA/ cm² anodic current density. Together, this work lays a foundation for future oxygen-limited biocatalysis with P. putida strains.

  16. Engineering mediator-based electroactivity in the obligate aerobic bacterium Pseudomonas putida KT2440

    Science.gov (United States)

    Schmitz, Simone; Nies, Salome; Wierckx, Nick; Blank, Lars M.; Rosenbaum, Miriam A.

    2015-01-01

    Pseudomonas putida strains are being developed as microbial production hosts for production of a range of amphiphilic and hydrophobic biochemicals. P. putida's obligate aerobic growth thereby can be an economical and technical challenge because it requires constant rigorous aeration and often causes reactor foaming. Here, we engineered a strain of P. putida KT2440 that can produce phenazine redox-mediators from Pseudomonas aeruginosa to allow partial redox balancing with an electrode under oxygen-limited conditions. P. aeruginosa is known to employ its phenazine-type redox mediators for electron exchange with an anode in bioelectrochemical systems (BES). We transferred the seven core phenazine biosynthesis genes phzA-G and the two specific genes phzM and phzS required for pyocyanin synthesis from P. aeruginosa on two inducible plasmids into P. putida KT2440. The best clone, P. putida pPhz, produced 45 mg/L pyocyanin over 25 h of growth, which was visible as blue color formation and is comparable to the pyocyanin production of P. aeruginosa. This new strain was then characterized under different oxygen-limited conditions with electrochemical redox control and changes in central energy metabolism were evaluated in comparison to the unmodified P. putida KT2440. In the new strain, phenazine synthesis with supernatant concentrations up to 33 μg/mL correlated linearly with the ability to discharge electrons to an anode, whereby phenazine-1-carboxylic acid served as the dominating redox mediator. P. putida pPhz sustained strongly oxygen-limited metabolism for up to 2 weeks at up to 12 μA/cm2 anodic current density. Together, this work lays a foundation for future oxygen-limited biocatalysis with P. putida strains. PMID:25914687

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

    Science.gov (United States)

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

    2017-01-01

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

  18. 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.

  19. 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).

  20. 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.

  1. 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.

  2. 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 ).

  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. 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.

  5. 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)).

  6. 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)).

  7. 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)).

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

    Science.gov (United States)

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

    2017-06-12

    Most marine bacteria can produce exopolysaccharides (EPS). However, very few structures of EPS produced by marine bacteria have been determined. The characterization of EPS structure is important for the elucidation of their biological functions and ecological roles. In this study, the structure of EPS produced by a marine bacterium, Alteromonas sp. JL2810, was characterized, and the biosorption of the EPS for heavy metals Cu 2+ , Ni 2+ , and Cr 6+ was also investigated. Nuclear magnetic resonance (NMR) analysis indicated that the JL2810 EPS have a novel structure consisting of the repeating unit of [-3)-α-Rha p -(1→3)-α-Man p -(1→4)-α-3OAc-GalA p -(1→]. The biosorption of the EPS for heavy metals was affected by a medium pH; the maximum biosorption capacities for Cu 2+ and Ni 2+ were 140.8 ± 8.2 mg/g and 226.3 ± 3.3 mg/g at pH 5.0; however, for Cr 6+ it was 215.2 ± 5.1 mg/g at pH 5.5. Infrared spectrometry analysis demonstrated that the groups of O-H, C=O, and C-O-C were the main function groups for the adsorption of JL2810 EPS with the heavy metals. The adsorption equilibrium of JL2810 EPS for Ni 2+ was further analyzed, and the equilibrium data could be better represented by the Langmuir isotherm model. The novel EPS could be potentially used in industrial applications as a novel bio-resource for the removal of heavy metals.

  9. 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).

  10. 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.

  11. Interaction of Pb(II) and biofilm associated extracellular polymeric substances of a marine bacterium Pseudomonas pseudoalcaligenes NP103

    Science.gov (United States)

    Kumari, Supriya; Mangwani, Neelam; Das, Surajit

    2017-02-01

    Three-dimensional excitation-emission matrix (3D EEM) fluorescence spectroscopy and attenuated total reflectance fourier-transformed infrared spectroscopy (ATR-FTIR) was used to evaluate the interaction of biofilm associated extracellular polymeric substances (EPS) of a marine bacterium Pseudomonas pseudoalcaligenes NP103 with lead [Pb(II)]. EEM fluorescence spectroscopic analysis revealed the presence of one protein-like fluorophore in the EPS of P. pseudoalcaligenes NP103. Stern-Volmer equation indicated the existence of only one binding site (n = 0.789) in the EPS of P. pseudoalcaligenes NP103. The interaction of Pb(II) with EPS was spontaneous at room temperature (Δ G = - 2.78 kJ/K/mol) having binding constant (Kb) of 2.59 M- 1. ATR-FTIR analysis asserted the involvement of various functional groups such as sulphydryl, phosphate and hydroxyl and amide groups of protein in Pb(II) binding. Scanning electron microscopy (SEM) and fluorescence microscopy analysis displayed reduced growth of biofilm with altered surface topology in Pb(II) supplemented medium. Energy dispersive X-ray spectroscopy (EDX) analysis revealed the entrapment of Pb in the EPS. Uronic acid, a characteristic functional group of biofilm, was observed in 1H NMR spectroscopy. The findings suggest that biofilm associated EPS are perfect organic ligands for Pb(II) complexation and may significantly augment the bioavailability of Pb(II) in the metal contaminated environment for subsequent sequestration.

  12. Biosynthesis of silver nanoparticles from deep sea bacterium Pseudomonas aeruginosa JQ989348 for antimicrobial, antibiofilm, and cytotoxic activity.

    Science.gov (United States)

    Ramalingam, V; Rajaram, R; PremKumar, C; Santhanam, P; Dhinesh, P; Vinothkumar, S; Kaleshkumar, K

    2014-09-01

    Pseudomonas aeruginosa (JQ989348) was isolated from deep sea water sample and used for synthesis of silver nanoparticles (AgNPs). AgNPs were confirmed by analyzing surface plasmon resonance using UV-visible spectrophotometer at 420 nm. Further scanning electron microscope analysis confirmed the range of particle size between 13 and 76 nm and XRD pattern authorizes the anisotropic crystalline nature of AgNPs. Fourier transform infrared spectrum endorsed the presence of high amount of proteins and other secondary metabolites in synthesized AgNPs influence the reduction process and stabilization of nanoparticles. The inhibitory activity of AgNPs was tested against human pathogens showed high activity against Eschericia coli, Vibrio cholerae, Aeromonas sp., and Cornebacterium sp. demonstrating its antimicrobial value against pathogenic diseases. Additionally, biologically synthesized AgNPs have notable anti-biofilm activity against primary biofilm forming bacteria P. aeruginosa and Staphylococcus aureus. The MTT assay method was evaluated using human cervical cancer cells exposed the AgNPs have excellent cytotoxic activity. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Conversion of the Pseudomonas aeruginosa Quinolone Signal and Related Alkylhydroxyquinolines by Rhodococcus sp. Strain BG43.

    Science.gov (United States)

    Müller, Christine; Birmes, Franziska S; Niewerth, Heiko; Fetzner, Susanne

    2014-12-01

    A bacterial strain, which based on the sequences of its 16S rRNA, gyrB, catA, and qsdA genes, was identified as a Rhodococcus sp. closely related to Rhodococcus erythropolis, was isolated from soil by enrichment on the Pseudomonas quinolone signal [PQS; 2-heptyl-3-hydroxy-4(1H)-quinolone], a quorum sensing signal employed by the opportunistic pathogen Pseudomonas aeruginosa. The isolate, termed Rhodococcus sp. strain BG43, cometabolically degraded PQS and its biosynthetic precursor 2-heptyl-4(1H)-quinolone (HHQ) to anthranilic acid. HHQ degradation was accompanied by transient formation of PQS, and HHQ hydroxylation by cell extracts required NADH, indicating that strain BG43 has a HHQ monooxygenase isofunctional to the biosynthetic enzyme PqsH of P. aeruginosa. The enzymes catalyzing HHQ hydroxylation and PQS degradation were inducible by PQS, suggesting a specific pathway. Remarkably, Rhodococcus sp. BG43 is also capable of transforming 2-heptyl-4-hydroxyquinoline-N-oxide to PQS. It thus converts an antibacterial secondary metabolite of P. aeruginosa to a quorum sensing signal molecule. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  14. Impact of a Recombinant Biocontrol Bacterium, Pseudomonas fluorescens pc78, on Microbial Community in Tomato Rhizosphere

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    Hyun Gi Kong

    2016-04-01

    Full Text Available Pseudomonas fluorescens pc78 is an effective biocontrol agent for soil-borne fungal diseases. We previously constructed a P43-gfp tagged biocontrol bacteria P. fluorescens pc78-48 to investigate bacterial traits in natural ecosystem and the environmental risk of genetically modified biocontrol bacteria in tomato rhizosphere. Fluctuation of culturable bacteria profile, microbial community structure, and potential horizontal gene transfer was investigated over time after the bacteria treatment to the tomato rhizosphere. Tagged gene transfer to other organisms such as tomato plants and bacteria cultured on various media was examined by polymerase chain reaction, using gene specific primers. Transfer of chromosomally integrated P43-gfp from pc78 to other organisms was not apparent. Population and colony types of culturable bacteria were not significantly affected by the introduction of P. fluorescens pc78 or pc78-48 into tomato rhizosphere. Additionally, terminal restriction fragment length polymorphism profiles were investigated to estimate the influence on the microbial community structure in tomato rhizosphere between non-treated and pc78-48-treated samples. Interestingly, rhizosphere soil treated with strain pc78-48 exhibited a significantly different bacterial community structure compared to that of non-treated rhizosphere soil. Our results suggest that biocontrol bacteria treatment influences microbial community in tomato rhizosphere, while the chromosomally modified biocontrol bacteria may not pose any specific environmental risk in terms of gene transfer.

  15. Impact of a Recombinant Biocontrol Bacterium, Pseudomonas fluorescens pc78, on Microbial Community in Tomato Rhizosphere.

    Science.gov (United States)

    Kong, Hyun Gi; Kim, Nam Hee; Lee, Seung Yeup; Lee, Seon-Woo

    2016-04-01

    Pseudomonas fluorescens pc78 is an effective biocontrol agent for soil-borne fungal diseases. We previously constructed a P43-gfp tagged biocontrol bacteria P. fluorescens pc78-48 to investigate bacterial traits in natural ecosystem and the environmental risk of genetically modified biocontrol bacteria in tomato rhizosphere. Fluctuation of culturable bacteria profile, microbial community structure, and potential horizontal gene transfer was investigated over time after the bacteria treatment to the tomato rhizosphere. Tagged gene transfer to other organisms such as tomato plants and bacteria cultured on various media was examined by polymerase chain reaction, using gene specific primers. Transfer of chromosomally integrated P43-gfp from pc78 to other organisms was not apparent. Population and colony types of culturable bacteria were not significantly affected by the introduction of P. fluorescens pc78 or pc78-48 into tomato rhizosphere. Additionally, terminal restriction fragment length polymorphism profiles were investigated to estimate the influence on the microbial community structure in tomato rhizosphere between non-treated and pc78-48-treated samples. Interestingly, rhizosphere soil treated with strain pc78-48 exhibited a significantly different bacterial community structure compared to that of non-treated rhizosphere soil. Our results suggest that biocontrol bacteria treatment influences microbial community in tomato rhizosphere, while the chromosomally modified biocontrol bacteria may not pose any specific environmental risk in terms of gene transfer.

  16. Getting the ecology into interactions between plants and the plant growth-promoting bacterium Pseudomonas fluorescens.

    Science.gov (United States)

    Hol, W H Gera; Bezemer, T Martijn; Biere, Arjen

    2013-01-01

    Plant growth-promoting rhizobacteria (PGPR) are increasingly appreciated for their contributions to primary productivity through promotion of growth and triggering of induced systemic resistance in plants. Here we focus on the beneficial effects of one particular species of PGPR (Pseudomonas fluorescens) on plants through induced plant defense. This model organism has provided much understanding of the underlying molecular mechanisms of PGPR-induced plant defense. However, this knowledge can only be appreciated at full value once we know to what extent these mechanisms also occur under more realistic, species-diverse conditions as are occurring in the plant rhizosphere. To provide the necessary ecological context, we review the literature to compare the effect of P. fluorescens on induced plant defense when it is present as a single species or in combination with other soil dwelling species. Specifically, we discuss combinations with other plant mutualists (bacterial or fungal), plant pathogens (bacterial or fungal), bacterivores (nematode or protozoa), and decomposers. Synergistic interactions between P. fluorescens and other plant mutualists are much more commonly reported than antagonistic interactions. Recent developments have enabled screenings of P. fluorescens genomes for defense traits and this could help with selection of strains with likely positive interactions on biocontrol. However, studies that examine the effects of multiple herbivores, pathogens, or herbivores and pathogens together on the effectiveness of PGPR to induce plant defenses are underrepresented and we are not aware of any study that has examined interactions between P. fluorescens and bacterivores or decomposers. As co-occurring soil organisms can enhance but also reduce the effectiveness of PGPR, a better understanding of the biotic factors modulating P. fluorescens-plant interactions will improve the effectiveness of introducing P. fluorescens to enhance plant production and defense.

  17. Beneficial Soil Bacterium Pseudomonas frederiksbergensis OS261 Augments Salt Tolerance and Promotes Red Pepper Plant Growth

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    Poulami Chatterjee

    2017-05-01

    Full Text Available Soil salinity, being a part of natural ecosystems, is an increasing problem in agricultural soils throughout the world. Pseudomonas frederiksbergensis OS261 has already been proved to be an effective bio-inoculant for enhancing cold stress tolerance in plants, however, its effect on salt stress tolerance is unknown. The main aim of the present study was to elucidate P. frederiksbergensis OS261 mediated salt stress tolerance in red pepper. The plants were exposed to a salt stress using NaCl at the concentrations of 50, 100, and 150 mM after 12 days of transplantation, while plant growth and enzyme activity were estimated 50 days after sowing. The height in P. frederiksbergensis OS261 inoculated plants was significantly increased by 19.05, 34.35, 57.25, and 61.07% compared to un-inoculated controls at 0, 50, 100, and 150 mM of NaCl concentrations, respectively, under greenhouse conditions. The dry biomass of the plants increased by 31.97, 37.47, 62.67, and 67.84% under 0, 50, 100, and 150 mM of NaCl concentrations, respectively. A high emission of ethylene was observed in un-inoculated red pepper plants under salinity stress. P. frederiksbergensis OS261 inoculation significantly reduced ethylene emission by 20.03, 18.01, and 20.07% at 50, 100, and 150 mM of NaCl concentrations, respectively. Furthermore, the activity of antioxidant enzymes (ascorbate peroxidase, superoxide dismutase, and catalase also varied in the inoculated red pepper plants. Salt stress resistance in the bacterized plants was evident from the improved antioxidant activity in leaf tissues and the decreased hydrogen ion concentration. Thus, we conclude that P. frederiksbergensis OS261 possesses stress mitigating property which can enhance plant growth under high soil salinity by reducing the emission of ethylene and regulating antioxidant enzymes.

  18. Antimicrobial activities of Rhizobium sp. strains against Pseudomonas savastanoi, the agent responsible for the olive knot disease in Algeria

    Energy Technology Data Exchange (ETDEWEB)

    Mourad, K.; Fadhila, K.; Chahinez, M.; Merien, R.; Philippe, L. de; Abdelkader, B.

    2009-07-01

    In the present investigation, six Rhizobium strains isolated from Algerian soil were checked for their antimicrobial activity against Pseudomonas savastanoi, the agent responsible for olive knot disease. Rhizobium sp. ORN 24 and ORN 83 were found to produce antimicrobial activities against Pseudomonas savastanoi. The antimicrobial activity produced by Rhizobium sp. ORN24 was precipitable with ammonium sulfate, between 1,000 and 10,000 KDa molecular weight, heat resistant but sensitive to proteases and detergents. These characteristics suggest the bacteriocin nature of the antimicrobial substance produced by Rhizobium sp. ORN24, named rhizobiocin 24. In contrast, the antimicrobial activity produced by Rhizobium sp. ORN83 was not precipitable with ammonium sulfate; it was smaller than 1,000 KDa molecular weight, heat labile, and protease and detergent resistant. These characteristics could indicate the relationship between the antimicrobial substance produced by Rhizobium sp. ORN 83 and the small bacteriocins described in other rhizobia. (Author) 51 refs.

  19. Accumulation of a Polyhydroxyalkanoate Containing Primarily 3-Hydroxydecanoate from Simple Carbohydrate Substrates by Pseudomonas sp. Strain NCIMB 40135

    OpenAIRE

    Haywood, Geoffrey W.; Anderson, Alistair J.; Ewing, David F.; Dawes, Edwin A.

    1990-01-01

    A number of Pseudomonas species have been identified which accumulate a polyhydroxyalkanoate containing mainly 3-hydroxydecanoate monomers from sodium gluconate as the sole carbon source. One of these, Pseudomonas sp. strain NCIMB 40135, was further investigated and shown to accumulate such a polyhydroxyalkanoate from a wide range of carbon sources (C2 to C6); however, when supplied with octanoic acid it produced a polyhydroxyalkanoate containing mainly 3-hydroxyoctanoate monomers. Polymer sy...

  20. The Role of Exopolymers in Protection of Ralstonia sp., a Cadmium-resistant Bacterium, from Cadmium Toxicity

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    Anchulee Watcharamusik

    2008-07-01

    Full Text Available Production of exopolymers is one of heavy metal resistance mechanisms in bacteria. Ralstonia sp. TAK1, a cadmium-resistant bacterium, was isolated from a high cadmium (Cd contaminated soil at the zinc mine, Tak province, Thailand. The bacterium was cultivated in LB broth and its growth was monitored. The yields of exopolymers were measured by the phenol-sulfuric method at different growth phases. The levels of Cd resistance were quantitatively determined by survival cell assay. The highest amount of exopolymers (0.69 mg glucose equivalent/ mg dry weight was found at the stationary phase and sharply decreased at the late-stationary phase. In addition to high production of exopolymers at the stationary phase, Ralstonia sp. TAK1 was more resistant to Cd than that of exponential phase cells. These results suggested that the resistance to Cd toxicity in Ralstonia sp. TAK1 at the stationary phase is mediated by exopolymer production. Contradictorily, there was no correlation between Cd resistance level and exopolymer production of cells at exponential phase indicating that other mechanism(s is responsible for Cd resistance of exponential phase cells. In addition, 0.4 mM CdCl2 was able to induce the increasing of exopolymers at the mid-exponential phases compared to uninduced cells. Exopolymer production of Cd-induced cells was constant from the mid-stationary to late-stationary phase. However, the highest exopolymers was found in uninduced cells at the stationary phase.

  1. Pyoverdine synthesis by the Mn(II-oxidizing bacterium Pseudomonas putida GB-1

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    Dorothy Lundquist Parker

    2014-05-01

    Full Text Available When iron-starved, the Mn(II-oxidizing bacteria Pseudomonas putida strains GB-1 and MnB1 produce pyoverdines (PVDGB-1 and PVDMnB1, siderophores that both influence iron uptake and inhibit manganese(II oxidation by these strains. To explore the properties and genetics of a PVD that can affect manganese oxidation, LC-MS/MS and various siderotyping techniques were used to identify the peptides of PVDGB-1 and PVDMnB1 as being (for both PVDs: chromophore-Asp-Lys-OHAsp-Ser-Gly-aThr-Lys-cOHOrn, resembling a structure previously reported for P. putida CFML 90-51, which does not oxidize Mn. All three strains also produced an azotobactin and a sulfonated PVD, each with the peptide sequence above, but with unknown regulatory or metabolic effects. Bioinformatic analysis of the sequenced genome of P. putida GB-1 suggested that a particular non-ribosomal peptide synthetase, coded by the operon PputGB1_4083-4086, could produce the peptide backbone of PVDGB-1. To verify this prediction, plasmid integration disruption of PputGB1_4083 was performed and the resulting mutant failed to produce detectable PVD. In silico analysis of the modules in PputGB1_4083-4086 predicted a peptide sequence of Asp-Lys-Asp-Ser-Ala-Thr-Lsy-Orn, which closely matches the peptide determined by MS/MS. To extend these studies to other organisms, various Mn(II-oxidizing and non-oxidizing isolates of P. putida, P. fluorescens, P. marincola, P. fluorescens-syringae group, P. mendocina-resinovorans group and P. stutzerii group were screened for PVD synthesis. The PVD producers (12 out of 16 tested strains were siderotyped and placed into four sets of differing PVD structures, some corresponding to previously characterized PVDs and some to novel PVDs. These results combined with previous studies suggested that the presence of OHAsp or the flexibility of the pyoverdine polypeptide may enable efficient binding of Mn(III.

  2. Pyoverdine synthesis by the Mn(II)-oxidizing bacterium Pseudomonas putida GB-1

    Science.gov (United States)

    Parker, Dorothy L.; Lee, Sung-Woo; Geszvain, Kati; Davis, Richard E.; Gruffaz, Christelle; Meyer, Jean-Marie; Torpey, Justin W.; Tebo, Bradley M.

    2014-01-01

    When iron-starved, the Mn(II)-oxidizing bacteria Pseudomonas putida strains GB-1 and MnB1 produce pyoverdines (PVDGB-1 and PVDMnB1), siderophores that both influence iron uptake and inhibit manganese(II) oxidation by these strains. To explore the properties and genetics of a PVD that can affect manganese oxidation, LC-MS/MS, and various siderotyping techniques were used to identify the peptides of PVDGB-1 and PVDMnB1 as being (for both PVDs): chromophore-Asp-Lys-OHAsp-Ser-Gly-aThr-Lys-cOHOrn, resembling a structure previously reported for P. putida CFML 90-51, which does not oxidize Mn. All three strains also produced an azotobactin and a sulfonated PVD, each with the peptide sequence above, but with unknown regulatory or metabolic effects. Bioinformatic analysis of the sequenced genome of P. putida GB-1 suggested that a particular non-ribosomal peptide synthetase (NRPS), coded by the operon PputGB1_4083-4086, could produce the peptide backbone of PVDGB-1. To verify this prediction, plasmid integration disruption of PputGB1_4083 was performed and the resulting mutant failed to produce detectable PVD. In silico analysis of the modules in PputGB1_4083-4086 predicted a peptide sequence of Asp-Lys-Asp-Ser-Ala-Thr-Lsy-Orn, which closely matches the peptide determined by MS/MS. To extend these studies to other organisms, various Mn(II)-oxidizing and non-oxidizing isolates of P. putida, P. fluorescens, P. marincola, P. fluorescens-syringae group, P. mendocina-resinovorans group, and P. stutzerii group were screened for PVD synthesis. The PVD producers (12 out of 16 tested strains) were siderotyped and placed into four sets of differing PVD structures, some corresponding to previously characterized PVDs and some to novel PVDs. These results combined with previous studies suggested that the presence of OHAsp or the flexibility of the pyoverdine polypeptide may enable efficient binding of Mn(III). PMID:24847318

  3. A Cyanide-Induced 3-Cyanoalanine Nitrilase in the Cyanide-Assimilating Bacterium Pseudomonas pseudoalcaligenes Strain CECT 5344.

    Science.gov (United States)

    Acera, Felipe; Carmona, María Isabel; Castillo, Francisco; Quesada, Alberto; Blasco, Rafael

    2017-05-01

    Pseudomonas pseudoalcaligenes CECT 5344 is a bacterium able to assimilate cyanide as a sole nitrogen source. Under this growth condition, a 3-cyanoalanine nitrilase enzymatic activity was induced. This activity was encoded by nit4 , one of the four nitrilase genes detected in the genome of this bacterium, and its expression in Escherichia coli enabled the recombinant strain to fully assimilate 3-cyanoalanine. P. pseudoalcaligenes CECT 5344 showed a weak growth level with 3-cyanoalanine as the N source, unless KCN was also added. Moreover, a nit4 knockout mutant of P. pseudoalcaligenes CECT 5344 became severely impaired in its ability to grow with 3-cyanoalanine and cyanide as nitrogen sources. The native enzyme expressed in E. coli was purified up to electrophoretic homogeneity and biochemically characterized. Nit4 seems to be specific for 3-cyanoalanine, and the amount of ammonium derived from the enzymatic activity doubled in the presence of exogenously added asparaginase activity, which demonstrated that the Nit4 enzyme had both 3-cyanoalanine nitrilase and hydratase activities. The nit4 gene is located downstream of the cyanide resistance transcriptional unit containing cio1 genes, whose expression levels are under the positive control of cyanide. Real-time PCR experiments revealed that nit4 expression was also positively regulated by cyanide in both minimal and LB media. These results suggest that this gene cluster including cio1 and nit4 could be involved both in cyanide resistance and in its assimilation by P. pseudoalcaligenes CECT 5344. IMPORTANCE Cyanide is a highly toxic molecule present in some industrial wastes due to its application in several manufacturing processes, such as gold mining and the electroplating industry. The biodegradation of cyanide from contaminated wastes could be an attractive alternative to physicochemical treatment. P. pseudoalcaligenes CECT 5344 is a bacterial strain able to assimilate cyanide under alkaline conditions, thus

  4. 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)).

  5. 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

  6. 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

  7. 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)).

  8. 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

  9. 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 ).

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

    KAUST Repository

    Zhang, Guishan

    2017-10-06

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

  11. 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 ).

  12. Methylphosphonate metabolism by Pseudomonas sp. populations contributes to the methane oversaturation paradox in an oxic freshwater lake.

    Science.gov (United States)

    Wang, Qian; Dore, John E; McDermott, Timothy R

    2017-06-01

    The 'CH 4 oversaturation paradox' has been observed in oxygen-rich marine and lake waters, and viewed to significantly contribute to biosphere cycling of methane, a potent greenhouse gas. Our study focused on the intriguing well-defined pelagic methane enriched zone (PMEZ) in freshwater lakes. Spiking Yellowstone Lake PMEZ samples with 13 C-labeled potential methanogenesis substrates found only 13 C-methylphosphonate (MPn) resulted in 13 CH 4 generation. In 16S rRNA gene Illumina libraries, four Pseudomonas sp. operational taxonomic units surprisingly accounted for ∼11% abundance in the PMEZ community. Pseudomonas sp. isolates were also obtained from MPn enrichments with PMEZ water; they were most aggressive in MPn metabolism and their 16S rRNA gene sequences matched 35% of the Illumina PMEZ Pseudomonas reads. Further, two key genes encoding C-P lyase (phnJL, an important enzyme for dealkylation of MPn), were only amplifiable from PMEZ DNA and all PCR generated phnJL clones matched those of the Pseudomonas sp. isolates. Notably, methanogen 16S rRNA signatures were absent in all Illumina libraries and mcrA was not detected via PCR. Collectively, these observations are consistent with the conclusion that MPn metabolism contributes significantly to CH 4 oversaturation in Yellowstone Lake and likely other oxic freshwater lake environments, and that Pseudomonas sp. populations are critical participants. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  13. Pseudomonas coleopterorum sp nov., a cellulase-producing bacterium isolated from the bark beetle Hylesinus fraxini

    Czech Academy of Sciences Publication Activity Database

    Menéndez, E.; Ramírez-Bahena, M.H.; Fabryová, Anna; Igual, J.M.; Benada, Oldřich; Mateos, P.; Peix, A.; Kolařík, Miroslav; García-Fraile, Paula

    2015-01-01

    Roč. 65, September (2015), s. 2852-2858 ISSN 1466-5026 R&D Projects: GA MŠk(CZ) EE2.3.30.0003 Institutional support: RVO:61388971 Keywords : CURCULIONIDAE SCOLYTINAE * NUCLEOTIDE-SEQUENCES * DENDROCTONUS-RHIZOPHAGUS Subject RIV: EE - Microbiology, Virology Impact factor: 2.439, year: 2015

  14. Pseudomonas coleopterorum sp nov., a cellulase-producing bacterium isolated from the bark beetle Hylesinus fraxini

    Czech Academy of Sciences Publication Activity Database

    Menéndez, E.; Ramírez-Bahena, M.H.; Fabryová, A.; Igual, J.M.; Benada, Oldřich

    2015-01-01

    Roč. 65, SEP 2015 (2015), s. 2852-2858 ISSN 1466-5026 R&D Projects: GA MŠk(CZ) EE2.3.30.0003 Institutional support: RVO:61388971 Keywords : CURCULIONIDAE SCOLYTINAE * NUCLEOTIDE-SEQUENCES * DENDROCTONUS-RHIZOPHAGUS Subject RIV: EE - Microbiology, Virology Impact factor: 2.439, year: 2015

  15. Hydrolytic potential of a psychrotrophic Pseudomonas isolated from refrigerated raw milk

    Directory of Open Access Journals (Sweden)

    Ana Paula F. Corrêa

    2011-12-01

    Full Text Available The production of extracellular hydrolases by a psychrotrophic bacterium isolated from refrigerated raw milk, and identified as a Pseudomonas sp. belonging to the Pseudomonas jenssenii group, was studied. This bacterium produced proteolytic and lipolytic enzymes in all media investigated (skim milk, cheese whey, casein broth, and tryptone soy broth. High levels of α-glucosidase were produced in skim milk broth. Hydrolytic enzymes detected in skim milk broth are of particular concern, indicating that these enzymes could be produced by Pseudomonas sp. during the cold storage of raw milk, contributing to the spoilage problem in milk and dairy products.

  16. The biocontrol endophytic bacterium Pseudomonas fluorescens PICF7 induces systemic defense responses in aerial tissues upon colonization of olive roots

    Directory of Open Access Journals (Sweden)

    Carmen eGómez-Lama Cabanás

    2014-09-01

    Full Text Available Pseudomonas fluorescens PICF7, a native olive root endophyte and effective biocontrol agent (BCA against Verticillium wilt of olive, is able to trigger a broad range of defense responses in root tissues of this woody plant. In order to elucidate whether strain PICF7 also induces systemic defense responses in above-ground organs, aerial tissues of olive plants grown under non-gnotobiotic conditions were collected at different time points after root bacterization with this endophytic BCA. A suppression subtractive hybridization (SSH cDNA library, enriched in up-regulated genes, was generated. This strategy enabled the identification of 376 ESTs (99 contigs and 277 singlets, many of them related to response to different stresses. Five ESTs, involved in defense responses, were selected to carry out time-course quantitative real-time PCR (qRT-PCR experiments aiming to: (i validate the induction of these genes, and (ii shed light on their expression pattern along time (from 1 to 15 days. Induction of olive genes potentially coding for lypoxigenase 2, catalase, 1-aminocyclopropane-1-carboxylate oxidase and phenylananine ammonia-lyase was thus confirmed at some time points. Computational analysis also revealed that different transcription factors were up-regulated in olive aerial tissues (i.e. jerf, bHLH, WRKYs, as previously reported for roots. Results confirmed that root colonization by this endophytic bacterium does not only trigger defense responses in this organ but also mount a wide array of systemic defense responses in distant tissues (stems, leaves. This sheds light on how olive plants respond to the ‘non-hostile’ colonization by a bacterial endophyte and how induced defense response can contribute to the biocontrol activity of strain PICF7.

  17. The biocontrol endophytic bacterium Pseudomonas fluorescens PICF7 induces systemic defense responses in aerial tissues upon colonization of olive roots.

    Science.gov (United States)

    Gómez-Lama Cabanás, Carmen; Schilirò, Elisabetta; Valverde-Corredor, Antonio; Mercado-Blanco, Jesús

    2014-01-01

    Pseudomonas fluorescens PICF7, a native olive root endophyte and effective biocontrol agent (BCA) against Verticillium wilt of olive, is able to trigger a broad range of defense responses in root tissues of this woody plant. In order to elucidate whether strain PICF7 also induces systemic defense responses in above-ground organs, aerial tissues of olive plants grown under non-gnotobiotic conditions were collected at different time points after root bacterization with this endophytic BCA. A suppression subtractive hybridization (SSH) cDNA library, enriched in up-regulated genes, was generated. This strategy enabled the identification of 376 ESTs (99 contigs and 277 singlets), many of them related to response to different stresses. Five ESTs, involved in defense responses, were selected to carry out time-course quantitative real-time PCR (qRT-PCR) experiments aiming to: (1) validate the induction of these genes, and (2) shed light on their expression pattern along time (from 1 to 15 days). Induction of olive genes potentially coding for lipoxygenase 2, catalase, 1-aminocyclopropane-1-carboxylate oxidase, and phenylananine ammonia-lyase was thus confirmed at some time points. Computational analysis also revealed that different transcription factors were up-regulated in olive aerial tissues (i.e., JERF, bHLH, WRKY), as previously reported for roots. Results confirmed that root colonization by this endophytic bacterium does not only trigger defense responses in this organ but also mounts a wide array of systemic defense responses in distant tissues (stems, leaves). This sheds light on how olive plants respond to the "non-hostile" colonization by a bacterial endophyte and how induced defense response can contribute to the biocontrol activity of strain PICF7.

  18. 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.

  19. Phospholipids and protein adaptation of Pseudomonas sp. to the xenoestrogen tributyltin chloride (TBT).

    Science.gov (United States)

    Bernat, Przemysław; Siewiera, Paulina; Soboń, Adrian; Długoński, Jerzy

    2014-09-01

    A tributyltin (TBT)-resistant strain of Pseudomonas sp. isolated from an overworked car filter was tested for its adaptation to TBT. The isolate was checked for organotin degradation ability, as well as membrane lipid and cellular protein composition in the presence of TBT. The phospholipid profiles of bacteria, grown with and without increased amounts of TBT, were characterized using liquid chromatography/electrospray ionization/mass spectrometry. The strain reacted to the biocide by changing the composition of its phospholipids. TBT induced a twofold decline in the amounts of many molecular species of phosphatidylglycerol and an increase in the levels of phosphatidic acid (by 58%) and phosphatidylethanolamine (by 70%). An increase in the degree of saturation of phospholipid fatty acids of TBT exposed Pseudomonas sp. was observed. These changes in the phospholipid composition and concentration reflect the mechanisms which support optimal lipid ordering in the presence of toxic xenobiotic. In the presence of TBT the abundances of 16 proteins, including TonB-dependent receptors, porins and peroxidases were modified, which could indicate a contribution of some enzymes to TBT resistance.

  20. Low-density polyethylene degradation by Pseudomonas sp. AKS2 biofilm.

    Science.gov (United States)

    Tribedi, Prosun; Sil, Alok K

    2013-06-01

    Polyethylene materials are a serious environmental concern as their nondegradable nature allows them to persist in the environment. Recent studies have shown that polyethylene can be degraded by microbes at a very slow rate, whereby detectable changes are evident after several years. In the present study, we report the degradation of low-density polyethylene by Pseudomonas sp. AKS2. Unlike the previous reports, degradation by Pseudomonas sp. AKS2 is relatively fast as it can degrade 5 ± 1 % of the starting material in 45 days without prior oxidation. This degradation can be altered by agents that modulate hydrophobic interaction between polythene and the microbe. As mineral oil promotes hydrophobic interactions, it enhances bacterial attachment to the polymer surface. This enhanced attachment results in increased biofilm formation and enhanced polymer degradation. In contrast, Tween 80 reduces bacterial attachment to the polymer surface by lowering hydrophobic interactions and thereby reduces polymer degradation. Thus, this study establishes a correlation between hydrophobic interaction and polymer degradation and also relates the biofilm formation ability of bacteria to polymer degrading potential.

  1. Isolation and amino acid sequence of a dehydratase acting on d-erythro-3-hydroxyaspartate from Pseudomonas sp. N99, and its application in the production of optically active 3-hydroxyaspartate.

    Science.gov (United States)

    Nagano, Hiroyuki; Shibano, Kana; Matsumoto, Yu; Yokota, Atsushi; Wada, Masaru

    2017-06-01

    An enzyme catalyzing the ammonia-lyase reaction for the conversion of d-erythro-3-hydroxyaspartate to oxaloacetate was purified from the cell-free extract of a soil-isolated bacterium Pseudomonas sp. N99. The enzyme exhibited ammonia-lyase activity toward l-threo-3-hydroxyaspartate and d-erythro-3-hydroxyaspartate, but not toward other 3-hydroxyaspartate isomers. The deduced amino acid sequence of the enzyme, which belongs to the serine/threonine dehydratase family, shows similarity to the sequence of l-threo-3-hydroxyaspartate ammonia-lyase (EC 4.3.1.16) from Pseudomonas sp. T62 (74%) and Saccharomyces cerevisiae (64%) and serine racemase from Schizosaccharomyces pombe (65%). These results suggest that the enzyme is similar to l-threo-3-hydroxyaspartate ammonia-lyase from Pseudomonas sp. T62, which does not act on d-erythro-3-hydroxyaspartate. We also then used the recombinant enzyme expressed in Escherichia coli to produce optically pure l-erythro-3-hydroxyaspartate and d-threo-3-hydroxyaspartate from the corresponding dl-racemic mixtures. The enzymatic resolution reported here is one of the simplest and the first enzymatic method that can be used for obtaining optically pure l-erythro-3-hydroxyaspartate.

  2. The nitrogen-fixation island insertion site is conserved in diazotrophic Pseudomonas stutzeri and Pseudomonas sp. isolated from distal and close geographical regions.

    Directory of Open Access Journals (Sweden)

    Anastasia Venieraki

    Full Text Available The presence of nitrogen fixers within the genus Pseudomonas has been established and so far most isolated strains are phylogenetically affiliated to Pseudomonas stutzeri. A gene ortholog neighborhood analysis of the nitrogen fixation island (NFI in four diazotrophic P. stutzeri strains and Pseudomonas azotifigens revealed that all are flanked by genes coding for cobalamin synthase (cobS and glutathione peroxidise (gshP. The putative NFIs lack all the features characterizing a mobilizable genomic island. Nevertheless, bioinformatic analysis P. stutzeri DSM 4166 NFI demonstrated the presence of short inverted and/or direct repeats within both flanking regions. The other P. stutzeri strains carry only one set of repeats. The genetic diversity of eleven diazotrophic Pseudomonas isolates was also investigated. Multilocus sequence typing grouped nine isolates along with P. stutzeri and two isolates are grouped in a separate clade. A Rep-PCR fingerprinting analysis grouped the eleven isolates into four distinct genotypes. We also provided evidence that the putative NFI in our diazotrophic Pseudomonas isolates is flanked by cobS and gshP genes. Furthermore, we demonstrated that the putative NFI of Pseudomonas sp. Gr65 is flanked by inverted repeats identical to those found in P. stutzeri DSM 4166 and while the other P. stutzeri isolates harbor the repeats located in the intergenic region between cobS and glutaredoxin genes as in the case of P. stutzeri A1501. Taken together these data suggest that all putative NFIs of diazotrophic Pseudomonas isolates are anchored in an intergenic region between cobS and gshP genes and their flanking regions are designated by distinct repeats patterns. Moreover, the presence of almost identical NFIs in diazotrophic Pseudomonas strains isolated from distal geographical locations around the world suggested that this horizontal gene transfer event may have taken place early in the evolution.

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

    Science.gov (United States)

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

    2013-11-01

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

  4. 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

  5. Methylocapsa acidiphila gen. nov., sp. nov., a novel methane-oxidizing and dinitrogen-fixing acidophilic bacterium from Sphagnum bog.

    Science.gov (United States)

    Dedysh, Svetlana N; Khmelenina, Valentina N; Suzina, Natalia E; Trotsenko, Yuri A; Semrau, Jeremy D; Liesack, Werner; Tiedje, James M

    2002-01-01

    A novel genus and species, Methylocapsa acidiphila gen. nov., sp. nov., are proposed for a methane-oxidizing bacterium isolated from an acidic Sphagnum peat bog. This bacterium, designated strain B2T, represents aerobic, gram-negative, colourless, non-motile, curved coccoids that form conglomerates covered by an extracellular polysaccharide matrix. The cells use methane and methanol as sole sources of carbon and energy and utilize the serine pathway for carbon assimilation. Strain B2T is a moderately acidophilic organism with growth between pH 4.2 and 7.2 and at temperatures from 10 to 30 degrees C. The cells possess a well-developed system of intracytoplasmic membranes (ICM) packed in parallel on only one side of the cell membrane. This type of ICM structure represents a novel arrangement, which was termed type III. The resting cells are Azotobacter-type cysts. Strain B2T is capable of atmospheric nitrogen fixation; it possesses particulate methane monooxygenase and does not express soluble methane monooxygenase. The major phospholipid fatty acid is 18:1omega7c and the major phospholipids are phosphatidylglycerols. The G+C content of the DNA is 63.1 mol%. This bacterium belongs to the alpha-subclass of the Proteobacteria and is most closely related to the acidophilic methanotroph Methylocella palustris KT (97.3% 16S rDNA sequence similarity). However, the DNA-DNA hybridization value between strain B2T and Methylocella palustris K(T) is only 7%. Thus, strain B2T is proposed to comprise a novel genus and species, Methylocapsa acidiphila gen. nov., sp. nov. Strain B2T (= DSM 13967T = NCIMB 13765T) is the type strain.

  6. Antimicrobial resistance in Pseudomonas sp. causing infections in trauma patients: A 6 year experience from a south asian country

    Directory of Open Access Journals (Sweden)

    Nonika Rajkumari

    2014-01-01

    Full Text Available Drug resistance to Pseudomonas sp. has spread to such a level irrespective of the type of patients, that its pattern of distribution and antibiotic resistance needs to be studied in detail, especially in trauma patients and hence the study. A 6 year study was carried out among trauma patients to see the trend and type of resistance prevalent in the apex hospital for trauma care in India among nonduplicate isolates where multidrug-resistance (MDR, cross-resistance and pan-drug resistance in Pseudomonas sp. were analyzed. Of the total 2,269 isolates obtained, the species, which was maximally isolated was Pseudomonas aeruginosa (2,224, 98%. The highest level of resistance was seen in tetracycline (2,166, 95.5%, P < 0.001 and chloramphenicol (2,160, 95.2%, P < 0.001 and least in meropenem (1,739, 76.7%, P < 0.003. Of the total, 1,692 (74.6% isolates were MDR in which P. aeruginosa (75% were maximum. MDR Pseudomonas is slowing increasing since the beginning of the study period. Of 1,797 imipenem-resistant P. aeruginosa isolated during the study period, 1,763 (98% showed resistance to ciprofloxacin or levofloxacin, suggesting that cross-resistance may have developed for imipenem due to prior use of fluoroquinolones. Antibiotic resistance in Pseudomonas sp. is fast becoming a problem in trauma patients, especially in those who requires prolong hospital stay, which calls for proper antimicrobial stewardship.

  7. Biosurfactant-producing microorganism Pseudomonas sp. SB assists the phytoremediation of DDT-contaminated soil by two grass species.

    Science.gov (United States)

    Wang, Beibei; Wang, Qingling; Liu, Wuxing; Liu, Xiaoyan; Hou, Jinyu; Teng, Ying; Luo, Yongming; Christie, Peter

    2017-09-01

    Phytoremediation together with microorganisms may confer the advantages of both phytoremediation and microbial remediation of soils containing organic contaminants. In this system biosurfactants produced by Pseudomonas sp. SB may effectively help to increase the bioavailability of organic pollutants and thereby enhance their microbial degradation in soil. Plants may enhance the rhizosphere environment for microorganisms and thus promote the bioremediation of contaminants. In the present pot experiment study, dichlorodiphenyltrichloroethane (DDT) residues underwent an apparent decline after soil bioremediation compared with the original soil. The removal efficiency of fertilizer + tall fescue, fertilizer + tall fescue + Pseudomonas, fertilizer + perennial ryegrass, and fertilizer + perennial ryegrass + Pseudomonas treatments were 59.4, 65.6, 69.0, and 65.9%, respectively, and were generally higher than that in the fertilizer control (40.3%). Principal coordinates analysis (PCoA) verifies that plant species greatly affected the soil bacterial community irrespective of inoculation with Pseudomonas sp. SB. Furthermore, community composition analysis shows that Proteobacteria, Acidobacteria and Actinobacteria were the three dominant phyla in all groups. In particular, the relative abundance of Pseudomonas for fertilizer + tall fescue + Pseudomonas (0.25%) was significantly greater than fertilizer + tall fescue and this was related to the DDT removal efficiency. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Inhibition of marine Vibrio sp. by pyoverdine from Pseudomonas aeruginosa PA1.

    Science.gov (United States)

    Zhang, Weiwei; Liang, Weikang; Li, Chenghua

    2016-01-25

    Siderophores are low-molecular-weight chemicals that are secreted by many microorganisms to chelate iron from the external environment in order to facilitate their growth and diverse metabolisms. In this study, a fluorescent siderophore, pyoverdine, secreted by Pseudomonas aeruginosa PA1 was purified by affinity chromatography using Cu-sepharose. Pyoverdine was determined to have a molecular mass of 1333.54 Da, as determined by MALDI-TOF/TOF, and belong to type I pyoverdine, as determined by PCR analysis of its corresponding outer membrane ferri-pyoverdine receptor. Pyoverdine showed different degrees of inhibitory effects on the growth of marine Vibrio sp. strains. It was also shown that the biofilm developed by Vibrio parahaemolyticus WzW1 and Wz2121 and Vibrio cyclitrophicus HS12 was significantly reduced, alone with the repressed growth in the presence of pyoverdine. Siderophore production was determined in the strains of Vibrio sp. in response to the pyoverdine-induced iron-limited conditions. The siderophore production of most Vibrio sp. was up-regulated, with the exception of the bacteria that produced little siderophore. Furthermore, Apostichopus japonicus cultured in pyoverdine pretreated seawater showed a relative percent of survival of 89% when they were challenged by Vibrio splendidus. Our results demonstrated that pyoverdine may be a promising agent that could be potentially applied to treat vibriosis. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Long-term induction of defense gene expression in potato by pseudomonas sp. LBUM223 and streptomyces scabies

    NARCIS (Netherlands)

    Arseneault, Tanya; Pieterse, Corné M J; Gérin-Ouellet, Maxime; Goyer, Claudia; Filion, Martin

    Streptomyces scabies is a causal agent of common scab of potato, which generates necrotic tuber lesions. We have previously demonstrated that inoculation of potato plants with phenazine-1-carboxylic acid (PCA)- producing Pseudomonas sp. LBUM223 could significantly reduce common scab symptoms. In the

  10. Long-Term induction of defense gene expression in potato by Pseudomonas sp. LBUM223 and Streptomyces scabies

    NARCIS (Netherlands)

    Arseneault, T.; Pieterse, C.M.J.; Gérin-Ouellet, M.; Goyer, C.; Filion, M.

    2014-01-01

    Streptomyces scabies is a causal agent of common scab of potato, which generates necrotic tuber lesions. We have previously demonstrated that inoculation of potato plants with phenazine-1-carboxylic acid (PCA)-producing Pseudomonas sp. LBUM223 could significantly reduce common scab symptoms. In the

  11. Membrane-aerated biofilm reactor for the removal of 1,2-dichloroethane by Pseudomonas sp strain DCA1

    NARCIS (Netherlands)

    Hage, J.C.; Houten, R.T.; Tramper, J.; Hartmans, S.

    2004-01-01

    A membrane-aerated biofilm reactor (MBR) with a biofilm of Pseudomonas sp. strain DCA1 was studied for the removal of 1,2-dichloroethane (DCA) from water. A hydrophobic membrane was used to create a barrier between the liquid and the gas phase. Inoculation of the MBR with cells of strain DCA1 grown

  12. Involvement of phenazines and biosurfactants in biocontrol of Pythium myriotylum root rot on cocoyam by Pseudomonas sp. CMR12A

    Science.gov (United States)

    Pseudomonas sp. CMR12a was isolated from the rhizosphere of the tropical tuber crop cocoyam and produces both phenazines and cyclic lipopeptide (CLP) biosurfactants. CMR12a was shown to be an efficient biocontrol agent of P. myriotylum on cocoyam. To assess the importance of phenazine and biosurfact...

  13. Two novel cyclic peptides are key components of the antimicrobial activity of the Greenlandic isolate Pseudomonas sp. In5

    DEFF Research Database (Denmark)

    Hennessy, Rosanna Catherine; Phippen, Christopher; Nielsen, Kristian F.

    suppressive soil, Pseudomonas sp. In5 is therefore a promising potential biocontrol agent with potent activity against plant pathogens. Studies to date have shown nunamycin and nunapeptin as key components underpinning this antimicrobial activity. Current research is focussed on unravelling the regulation...

  14. 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...

  15. 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

  16. 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...

  17. Ability of the marine bacterium Pseudomonas fluorescens BA3SM1 to counteract the toxicity of CdSe nanoparticles.

    Science.gov (United States)

    Poirier, Isabelle; Kuhn, Lauriane; Demortière, Arnaud; Mirvaux, Boris; Hammann, Philippe; Chicher, Johana; Caplat, Christelle; Pallud, Marie; Bertrand, Martine

    2016-10-04

    In the marine environment, bacteria from estuarine and coastal sediments are among the first targets of nanoparticle pollution; it is therefore relevant to improve the knowledge of interactions between bacteria and nanoparticles. In this work, the response of the marine bacterium Pseudomonas fluorescens BA3SM1 to CdSe nanocrystals (CdSe NPs) of 3nm (NP3) and 8nm (NP8) in diameter was evaluated through microscopic, physiological, biochemical and proteomic approaches. Transmission electron microscopy images showed that NP3 were able to penetrate the bacteria, while NP8 were highly concentrated around the cells, embedded in large exopolysaccharides. In our experimental conditions, both CdSe NP sizes induced a decrease in respiration during the stationary growth phase, while only NP8 caused growth retardation and a decrease in pyoverdine production. Proteomic analyses highlighted that the strain responded to CdSe NP toxicity by inducing various defence mechanisms such as cell aggregation, extracellular CdSe NP sequestration, effective protection against oxidative stress, modifications of envelope organization and properties, and cadmium export. In addition, BA3SM1 presented a biosorption capacity of 1.6×10(16)NP3/g dry weight and 1.7×10(15)NP8/g dry weight. This strain therefore appears as a promising agent for NP bioremediation processes. Proteomic data are available via ProteomeXchange with identifier PXD004012. To the best of our knowledge, this is the first report focussing on the effects of CdSe colloidal nanocrystals (CdSe NPs) on a marine strain of Pseudomonas fluorescens. CdSe NPs are extensively used in the industry of renewable energies and it is regrettably expected that these pollutants will sometime soon appear in the marine environment through surface runoff, urban effluents and rivers. Bacteria living in estuarine and coastal sediments will be among the first targets of these new pollutants. The pseudomonads are frequently found in these ecosystems

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

    DEFF Research Database (Denmark)

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

    2013-01-01

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

  19. Characterization of a nitrilase and a nitrile hydratase from Pseudomonas sp. strain UW4 that converts indole-3-acetonitrile to indole-3-acetic acid.

    Science.gov (United States)

    Duca, Daiana; Rose, David R; Glick, Bernard R

    2014-08-01

    Indole-3-acetic acid (IAA) is a fundamental phytohormone with the ability to control many aspects of plant growth and development. Pseudomonas sp. strain UW4 is a rhizospheric plant growth-promoting bacterium that produces and secretes IAA. While several putative IAA biosynthetic genes have been reported in this bacterium, the pathways leading to the production of IAA in strain UW4 are unclear. Here, the presence of the indole-3-acetamide (IAM) and indole-3-acetaldoxime/indole-3-acetonitrile (IAOx/IAN) pathways of IAA biosynthesis is described, and the specific role of two of the enzymes (nitrilase and nitrile hydratase) that mediate these pathways is assessed. The genes encoding these two enzymes were expressed in Escherichia coli, and the enzymes were isolated and characterized. Substrate-feeding assays indicate that the nitrilase produces both IAM and IAA from the IAN substrate, while the nitrile hydratase only produces IAM. The two nitrile-hydrolyzing enzymes have very different temperature and pH optimums. Nitrilase prefers a temperature of 50°C and a pH of 6, while nitrile hydratase prefers 4°C and a pH of 7.5. Based on multiple sequence alignments and motif analyses, physicochemical properties and enzyme assays, it is concluded that the UW4 nitrilase has an aromatic substrate specificity. The nitrile hydratase is identified as an iron-type metalloenzyme that does not require the help of a P47K activator protein to be active. These data are interpreted in terms of a preliminary model for the biosynthesis of IAA in this bacterium.

  20. The heterocyclic ring fission and dehydroxylation of catechins and related compounds by Eubacterium sp. strain SDG-2, a human intestinal bacterium.

    Science.gov (United States)

    Wang, L Q; Meselhy, M R; Li, Y; Nakamura, N; Min, B S; Qin, G W; Hattori, M

    2001-12-01

    A human intestinal bacterium, Eubacterium (E.) sp. strain SDG-2, was tested for its ability to metabolize various (3R)- and (3S)-flavan-3-ols and their 3-O-gallates. This bacterium cleaved the C-ring of (3R)- and (3S)-flavan-3-ols to give 1,3-diphenylpropan-2-ol derivatives, but not their 3-O-gallates. Furthermore, E. sp. strain SDG-2 had the ability of p-dehydroxylation in the B-ring of (3R)-flavan-3-ols, such as (-)-catechin, (-)-epicatechin, (-)-gallocatechin and (-)-epigallocatechin, but not of (3S)-flavan-3-ols, such as (+)-catechin and (+)-epicatechin.

  1. Pseudomonas cerasi sp. nov. (non Griffin, 1911) isolated from diseased tissue of cherry.

    Science.gov (United States)

    Kałużna, Monika; Willems, Anne; Pothier, Joël F; Ruinelli, Michela; Sobiczewski, Piotr; Puławska, Joanna

    2016-09-01

    Eight isolates of Gram-negative fluorescent bacteria (58(T), 122, 374, 791, 963, 966, 970a and 1021) were obtained from diseased tissue of cherry trees from different regions of Poland. The symptoms resembled those of bacterial canker. Based on an analysis of 16S rDNA sequences the isolates shared the highest over 99.9% similarity with Pseudomonas ficuserectae JCM 2400(T) and P. congelans DSM 14939(T). Phylogenetic analysis using housekeeping genes gyrB, rpoD and rpoB revealed that they form a separate cluster and confirmed their closest relation to P. syringae NCPPB 281(T) and P. congelans LMG 21466(T). DNA-DNA hybridization between the cherry isolate 58(T) and the type strains of these two closely related species revealed relatedness values of 58.2% and 41.9%, respectively. This was further supported by Average Nucleotide Identity (ANIb) and Genome-to-Genome Distance (GGDC) between the whole genome sequences of strain LMG 28609(T) and closely related Pseudomonas species. The major cellular fatty acids are 16:0 and summed feature 3 (16:1 ω7c/15:0 iso 2OH). Phenotypic characteristics differentiated the novel isolates from other closely related species. The G+C content of the genomic DNA of strain 58(T) was 59%. The diversity was proved by PCR MP and BOX PCR, eliminating the possibility that they constitute a clonal population. Based on the evidence of this polyphasic taxonomic study the eight strains are considered to represent a novel species of the genus Pseudomonas for which the name P. cerasi sp. nov. (non Griffin, 1911) is proposed. The type strain of this species is 58(T) (=LMG 28609(T)=CFBP 8305(T)). Copyright © 2016 Elsevier GmbH. All rights reserved.

  2. Ageing of atrazine in manure amended soils assessed by bioavailability to Pseudomonas sp. strain ADP

    DEFF Research Database (Denmark)

    Glæsner, Nadia; Bælum, Jacob; Strobel, Bjarne W.

    2014-01-01

    bacteria Pseudomonas sp. strain ADP. Throughout an ageing period of 90 days bioavailability was investigated at days 1, 10, 32, 60 and 90, where ~108 cells g−1 of the ADP strain was inoculated to the 14C-atrazine exposed soil and 14CO2 was collected over 7 days as a measure of mineralized atrazine. Even...... though the bioavailable residue decreased in all of the three soils as time proceeded, we found that ageing occurred faster in the topsoils rich in organic carbon than in subsoil. For one topsoil rich in organic carbon content, Simmelkær, we observed a higher degree of ageing when treated with manure....... Contrarily, sorption experiments showed less sorption to Simmelkær treated with manure than the untreated soil indicating that sorption processes are not the only mechanisms of ageing. The other topsoil low in organic carbon content, Ringe, showed no significant difference in ageing between the manure...

  3. Pseudomonas sp. xylanase for clarification of Mausambi and Orange fruit juice

    Science.gov (United States)

    Sharma, Pawan Kumar; Chand, Duni

    2012-07-01

    Xylanase can be usd for many Industrial applications and juice clarification is one of them. Pseudomonas sp. xylanase was used for fruit juice clarification in free State. Maximum amount of juice clarification was in case of Mausambi juice was observed at 40 C∞ and 52 hours, in case of free enzyme treated juice there is 46.9% increase in clarity and 1.7 fold increase in reducing sugars of the juice and enzyme dose was optimized as 8U with maximum flow rate of 6 ml/min at this dose. In case of orange juice in free enzyme treated juice maximum clarity was observed at 40 C∞ and 52 hours, juice was found to be 42.14 % clear with increase of 1.9 fold of reducing sugars, enzyme dose optimized was 8.06U with maximum flow rate of 0.86 ml/min.

  4. Influence of multiple bioprocess parameters on production of lipase from Pseudomonas sp. BWS-5

    Directory of Open Access Journals (Sweden)

    Balwinder Singh Sooch

    2013-10-01

    Full Text Available The aim of the present work was to study the influence of multiple bioprocess parameters for the maximum production of lipase from Pseudomonas sp. BWS-5. The culture reached the stationary phase of growth after 36h of incubation when the maximum lipase production was obtained at flask level. The different media components such as carbon sources, nitrogen sources, trace elements and process parameters such as the pH of the medium, temperature and time of incubation, agitation/stationary conditions, etc. were optimized at flask level and at bioreactor level. The maximum enzyme production of 298 IU/mL was obtained with the use of simple medium with pH 6.5 containing glucose (1 %, w/v, peptone (3 %, w/v and KCl (0.05 %, w/v after 30h of incubation at 37°C under agitation (200 rpm conditions with 0.75 vvm of air supply.

  5. Enhancement of the potential to utilize octopine in the nonfluorescent Pseudomonas sp. strain 92

    International Nuclear Information System (INIS)

    Gill, S.S.; Boivin, R.; Dion, P.

    1991-01-01

    The nonfluorescent Pseudomonas sp. strain 92 requires the presence of a supplementary carbon source for growth on octopine, whereas the spontaneous mutant RB100 has acquired the capacity to utilize this opine as the sole carbon and nitrogen source. Insertional mutagenesis of RB100 with transposon Tn5 generated mutants which were unable to grow on octopine and others which grew slowly on this substrate. Both types of mutants yielded revertants that had regained the ability to utilize octopine. Some of the revertants had lost the transposon, whereas in others the transposon was retained but with rearrangements of the insertion site. Genes of octopine catabolism from strain 92 were cloned on a cosmid vector to generate pK3. The clone pK3 conferred the ability to utilize octopine as the sole carbon and nitrogen source on the host Pseudomonas putida KT2440. Although they conferred an equivalent growth phenotype, the mutant genes carried by RB100 and the cloned genes on pK3 differed in their regulation. Utilization of [ 14 C]octopine was inducible by octopine in RB100 and was constitutive in KT2440(pK3)

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

    Science.gov (United States)

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

    2017-07-01

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

  7. Polycyclic aromatic hydrocarbon degradation by biosurfactant-producing Pseudomonas sp. IR1

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, M. [Unidad de Biotecnologia del Petroleo, Centro de Biotecnologia, Fundacion Inst. de Estudios Avanzados (IDEA), Caracas (Venezuela); Synthesis and Biotics Div., Indian Oil Corp., Research and Development Center, Haryana (India); Leon, V.; Materano, A.D.S.; Ilzins, O.A.; Galindo-Castro, I.; Fuenmayor, S.L. [Unidad de Biotecnologia del Petroleo, Centro de Biotecnologia, Fundacion Inst. de Estudios Avanzados (IDEA), Caracas (Venezuela)

    2006-03-15

    We characterized a newly isolated bacterium, designated as IR1, with respect to its ability to degrade polycyclic aromatic hydrocarbons (PAHs) and to produce biosurfactants. Isolated IR1 was identified as Pseudomonas putida by analysis of 16S rRNA sequences (99.6% homology). It was capable of utilizing two-, three- and four-ring PAHs but not hexadecane and octadecane as a sole carbon and energy source. PCR and DNA hybridization studies showed that enzymes involved in PAH metabolism were related to the naphthalene dioxygenase pathway. Observation of both tensio-active and emulsifying activities indicated that biosurfactants were produced by IR1 during growth on both water miscible and immiscible substrates. The biosurfactants lowered the surface tension of medium from 54.9 dN cm{sup -1} to 35.4 dN cm{sup -1} and formed a stable and compact emulsion with an emulsifying activity of 74% with diesel oil, when grown on dextrose. These findings indicate that this isolate may be useful for bioremediation of sites contaminated with aromatic hydrocarbons. (orig.)

  8. Deepening TOL and TOU catabolic pathways of Pseudomonas sp. OX1: cloning, sequencing and characterization of the lower pathways.

    Science.gov (United States)

    Bertini, Laura; Cafaro, Valeria; Proietti, Silvia; Caporale, Carlo; Capasso, Paola; Caruso, Carla; Di Donato, Alberto

    2013-02-01

    Pseudomonas sp. OX1 is able to metabolize toluene and o-xylene through the TOU catabolic pathway, whereas its mutant M1 strain was found to be able to use m- and p-xylene as carbon and energy source, using the TOL catabolic pathway. Here we report the complete nucleotide sequence of the phe lower operon of the TOU catabolic pathway, and the sequence of the last four genes of the xyl-like lower operon of the TOL catabolic pathway. DNA sequence analysis shows the gene order within the operons to be pheCDEFGHI (phe operon) and xyl-likeQKIH (xyl-like operon), identical to the order found for the isofunctional genes of meta operons in the toluene/xylene pathway of TOL plasmid pWW0 from Pseudomonas putida mt-2 and the phenol/methylphenol pathway of pVIl50 from Pseudomonas sp. CF600. The nucleotide and the deduced amino acid sequences are homologous to the equivalent gene and enzyme sequences from other Pseudomonas meta pathways. Recombinant 2-hydroxymuconic semialdehyde dehydrogenase (HMSD) and 2-hydroxymuconic semialdehyde hydrolase (HMSH), coded by pheCD genes, respectively, and ADA and HOA enzymes from both phe and xyl operons were expressed in E. coli and steady-state kinetic analysis was carried out. The analysis of the kinetic parameters of HMSD and HMSH showed that the enzymes from Pseudomonas sp. OX1 are more specialized to channel metabolites into the two branches of the lower pathway than homologous enzymes from other pseudomonads. The kinetics parameters of recombinant ADA from phe and xyl-like operon were found to be similar to those of homologous enzymes from other Pseudomonas strains. In addition, the enzyme from xyl-like operon showed a substrate affinity three times higher than the enzyme from phe operon. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

  9. Optimization of cold-active protease production by the psychrophilic bacterium Colwellia sp. NJ341 with response surface methodology.

    Science.gov (United States)

    Wang, Quanfu; Hou, Yanhua; Xu, Zhong; Miao, Jinlai; Li, Guangyou

    2008-04-01

    Culture conditions were optimized for an extracellular cold-active protease production by the psychrophilic bacterium Colwellia sp. NJ341. Response surface methodology was applied for the most significant fermentation parameters (casein, citrate sodium, temperature and Tween-80) identified earlier by one-factor-at-a-time approach. A 2(4) full factorial central composite design was employed to determine the maximum protease production. Using this methodology, the quadratic regression model of producing cold-active protease was built and the optimal combinations of media constituents for maximum protease production (183.21 U/mL) were determined as casein 5.18 g/L, citrate sodium 3.84 g/L, temperature 7.96 degrees C, Tween-80 0.23 g/L. Protease production obtained experimentally coincident with the predicted value and the model was proven to be adequate.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-06-15

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

  11. Fourier transform Raman spectroscopic characterisation of cells of the plant-associated soil bacterium Azospirillum brasilense Sp7

    Science.gov (United States)

    Kamnev, A. A.; Tarantilis, P. A.; Antonyuk, L. P.; Bespalova, L. A.; Polissiou, M. G.; Colina, M.; Gardiner, P. H. E.; Ignatov, V. V.

    2001-05-01

    Structural and compositional features of bacterial cell samples and of lipopolysaccharide-protein complex isolated from the cell surface of the plant-growth-promoting rhizobacterium Azospirillum brasilense (wild-type strain Sp7) were characterised using Fourier transform (FT) Raman spectroscopy. The structural spectroscopic information obtained is analysed and considered together with analytical data on the content of metal cations (Co 2+, Cu 2+ and Zn 2+) in the bacterial cells grown in a standard medium as well as in the presence of each of the cations (0.2 mM). The latter, being taken up by bacterial cells from the culture medium in significant amounts, were shown to induce certain metabolic changes in the bacterium revealed in FT-Raman spectra, which is discussed from the viewpoint of bacterial response to environmental stresses.

  12. 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.

  13. Purification and Characterization of a New κ-Carrageenase from the Marine Bacterium Vibrio sp. NJ-2.

    Science.gov (United States)

    Zhu, Benwei; Ning, Limin

    2016-02-01

    The carrageenan-degrading marine bacterium Vibrio sp. strain NJ-2 was isolated from rotten red algae, and κ-carrageenase with high activity was purified from the culture supernatant. The purified enzyme with molecular mass of 33 kDa showed the maximal activity of 937 U/mg at 40°C and pH 8.0. It maintained 80% of total activity below 40°C and between pH 6.0 and 10.0. The kinetics experiment showed the Km and Vmax values were 2.54 mg/ml and 138.89 mmol/min/mg, respectively. The thin layer chromatography and ESI-MS analysis of hydrolysates indicated that the enzyme can endolytically depolymerize the kappa-carrageenan into oligosaccharides with degrees of depolymerization of 2-8. Owing to its high activity, it could be a valuable tool to produce κ-carrageenan oligosaccharides with various biological activities.

  14. 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.

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

    Science.gov (United States)

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

    2013-12-11

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

  16. Complete genome sequencing of the luminescent bacterium, Vibrio qinghaiensis sp. Q67 using PacBio technology

    Science.gov (United States)

    Gong, Liang; Wu, Yu; Jian, Qijie; Yin, Chunxiao; Li, Taotao; Gupta, Vijai Kumar; Duan, Xuewu; Jiang, Yueming

    2018-01-01

    Vibrio qinghaiensis sp.-Q67 (Vqin-Q67) is a freshwater luminescent bacterium that continuously emits blue-green light (485 nm). The bacterium has been widely used for detecting toxic contaminants. Here, we report the complete genome sequence of Vqin-Q67, obtained using third-generation PacBio sequencing technology. Continuous long reads were attained from three PacBio sequencing runs and reads >500 bp with a quality value of >0.75 were merged together into a single dataset. This resultant highly-contiguous de novo assembly has no genome gaps, and comprises two chromosomes with substantial genetic information, including protein-coding genes, non-coding RNA, transposon and gene islands. Our dataset can be useful as a comparative genome for evolution and speciation studies, as well as for the analysis of protein-coding gene families, the pathogenicity of different Vibrio species in fish, the evolution of non-coding RNA and transposon, and the regulation of gene expression in relation to the bioluminescence of Vqin-Q67.

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

    KAUST Repository

    Andres-Barrao, Cristina

    2017-10-20

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

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

    Directory of Open Access Journals (Sweden)

    Seur Kee Park

    2015-09-01

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

  19. Dehydration of the off-flavor chemical 2-methylisoborneol by the R-limonene-degrading bacteria Pseudomonas sp. strain 19-rlim and Sphingomonas sp. strain BIR2-rlima.

    Science.gov (United States)

    Eaton, Richard W

    2012-04-01

    The terpene 2-methylisoborneol (MIB), a major cause of off-flavor in farm-raised catfish and drinking water, is transformed by various different terpene-degrading bacteria. Two of these, the R-limonene-degrading strains Pseudomonas sp. 19-rlim and Sphingomonas sp. BIR2-rlima, dehydrated MIB with the formation of odorless metabolites 2-methylenebornane and 4-methylcamphene. These metabolites which have a structural resemblance to camphor, could be further transformed by camphor-degrading bacteria to more oxidized products. The bacterial dehydrations demonstrated here may have application in removing MIB where it is a problem.

  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. Complete Genome Sequence of Dietzia sp. Strain WMMA184, a Marine Coral-Associated Bacterium

    OpenAIRE

    Braun, Doug R.; Chevrette, Marc G.; Acharya, Deepa; Currie, Cameron R.; Rajski, Scott R.; Ritchie, Kim B.; Bugni, Tim S.

    2018-01-01

    ABSTRACT Dietzia sp. strain WMMA184 was isolated from the marine coral Montastraea faveolata as part of ongoing drug discovery efforts. Analysis of the 4.16-Mb genome provides information regarding interspecies interactions as it pertains to the regulation of secondary metabolism and natural product biosynthesis potential.

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

    Digital Repository Service at National Institute of Oceanography (India)

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

    . 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...

  3. Genome sequence of the agar-degrading marine bacterium Alteromonadaceae sp. strain G7.

    Science.gov (United States)

    Kwak, Min-Jung; Song, Ju Yeon; Kim, Byung Kwon; Chi, Won-Jae; Kwon, Soon-Kyeong; Choi, Soobeom; Chang, Yong-Keun; Hong, Soon-Kwang; Kim, Jihyun F

    2012-12-01

    Here, we present the high-quality draft genome sequence of the agar-degrading marine gammaproteobacterium Alteromonadaceae sp. strain G7, which was isolated from coastal seawater to be utilized as a bioresource for production of agar-derived biofuels. The 3.91-Mb genome contains a number of genes encoding algal polysaccharide-degrading enzymes such as agarases and sulfatases.

  4. Genome Sequence of the Agar-Degrading Marine Bacterium Alteromonadaceae sp. Strain G7

    OpenAIRE

    Kwak, Min-Jung; Song, Ju Yeon; Kim, Byung Kwon; Chi, Won-Jae; Kwon, Soon-Kyeong; Choi, Soobeom; Chang, Yong-Keun; Hong, Soon-Kwang; Kim, Jihyun F.

    2012-01-01

    Here, we present the high-quality draft genome sequence of the agar-degrading marine gammaproteobacterium Alteromonadaceae sp. strain G7, which was isolated from coastal seawater to be utilized as a bioresource for production of agar-derived biofuels. The 3.91-Mb genome contains a number of genes encoding algal polysaccharide-degrading enzymes such as agarases and sulfatases.

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

    Science.gov (United States)

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

    2017-07-01

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

  6. 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.

  7. 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)).

  8. Expression and enzymatic characterization of a cold-adapted β-agarase from Antarctic bacterium Pseudoalteromonas sp. NJ21

    Science.gov (United States)

    Li, Jiang; Sha, Yujie

    2015-03-01

    An agar-degrading bacterium, designated as Pseudoalteromonas sp. NJ21, was isolated from an Antarctic sediment sample. The agarase gene aga1161 from Pseudoalteromonas sp. NJ21 consisting of a 2 382-bp coding region was cloned. The gene encodes a 793-amino acids protein and was found to possess characteristic features of the Glyco_hydro_42 family. The recombinant agarase (rAga1161) was overexpressed in Escherichia coli and purified as a fusion protein. Enzyme activity analysis revealed that the optimum temperature and pH for the purified recombinant agarase were 30-40°C and 8.0, respectively. rAga1161 was found to maintain as much as 80% of its maximum activity at 10°C, which is typical of a coldadapted enzyme. The pattern of agar hydrolysis demonstrated that the enzyme is an β-agarase, producing neoagarobiose (NA2) as the final main product. Furthermore, this work is the first proof of an agarolytic activity in Antarctic bacteria and these results indicate the potential for the Antarctic agarase as a catalyst in medicine, food and cosmetic industries.

  9. 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.

  10. 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...

  11. Analysis of Draft Genome Sequence of Pseudomonas sp. QTF5 Reveals Its Benzoic Acid Degradation Ability and Heavy Metal Tolerance

    Directory of Open Access Journals (Sweden)

    Yang Li

    2017-01-01

    Full Text Available Pseudomonas sp. QTF5 was isolated from the continuous permafrost near the bitumen layers in the Qiangtang basin of Qinghai-Tibetan Plateau in China (5,111 m above sea level. It is psychrotolerant and highly and widely tolerant to heavy metals and has the ability to metabolize benzoic acid and salicylic acid. To gain insight into the genetic basis for its adaptation, we performed whole genome sequencing and analyzed the resistant genes and metabolic pathways. Based on 120 published and annotated genomes representing 31 species in the genus Pseudomonas, in silico genomic DNA-DNA hybridization (<54% and average nucleotide identity calculation (<94% revealed that QTF5 is closest to Pseudomonas lini and should be classified into a novel species. This study provides the genetic basis to identify the genes linked to its specific mechanisms for adaptation to extreme environment and application of this microorganism in environmental conservation.

  12. 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.

  13. 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.

  14. Asaia lannaensis sp. nov., a new acetic acid bacterium in the Alphaproteobacteria.

    Science.gov (United States)

    Malimas, Taweesak; Yukphan, Pattaraporn; Takahashi, Mai; Kaneyasu, Mika; Potacharoen, Wanchern; Tanasupawat, Somboon; Nakagawa, Yasuyoshi; Tanticharoen, Morakot; Yamada, Yuzo

    2008-03-01

    Asaia lannaensis sp. nov. was described for two strains isolated from flowers of the spider lily collected in Chiang Mai, Thailand. The isolates produced acetic acid from ethanol on ethanol/calcium carbonate agar, differing from the type strains of Asaia bogorensis, Asaia siamensis, and Asaia krungthepensis, but did not grow in the presence of 0.35% acetic acid (v/v). The new species is the fourth of the genus Asaia, the family Acetobacteraceae.

  15. 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.)

  16. Production and characterization of a trehalolipid biosurfactant produced by the novel marine bacterium Rhodococcus sp., strain PML026.

    Science.gov (United States)

    White, D A; Hird, L C; Ali, S T

    2013-09-01

    The aim of this study was to evaluate biosurfactant production by a novel marine Rhodococcus sp., strain PML026 and characterize the chemical nature and properties of the biosurfactant. A novel marine bacterium (Rhodococcus species; strain PML026) was shown to produce biosurfactant in the presence of hydrophobic substrate (sunflower oil). Biosurfactant production (identified as a trehalolipid) was monitored in whole-batch cultures (oil layer and aqueous phase), aqueous phase (no oil layer) and filtered (0·2 μm) aqueous phase (no oil or cells; extracellular) and was shown to be closely associated with growth/biomass production. Extracellular trehalolipid levels increased postonset of stationary growth phase. Purified trehalolipid was able to reduce the surface tension of water to 29 mN m(-1) at Critical Micellar Concentration (CMC) of c. 250 mg l(-1) and produced emulsions that were stable to a wide range of conditions (pH 2-10, temperatures of 20-100°C and NaCl concentrations of 5-25% w/v). Separate chemical analyses of the intact trehalolipid and its constituents demonstrated the compound was in fact a mixture of homologues (>1180 MW) consisting of a trehalose moiety esterified to a series of straight chain and hydroxylated fatty acids. The trehalolipid biosurfactant produced by the novel marine strain Rhodococcus sp. PML026 was characterized and exhibited high surfactant activity under a wide range of conditions. Strain PML026 of Rhodococcus sp. is a potential candidate for bioremediation or biosurfactant production for various applications. © 2013 The Society for Applied Microbiology.

  17. Sequential interactions of silver-silica nanocomposite (Ag-SiO2NC) with cell wall, metabolism and genetic stability of Pseudomonas aeruginosa, a multiple antibiotic-resistant bacterium

    Digital Repository Service at National Institute of Oceanography (India)

    Anas, A.; Jiya, J.; Rameez, M.J.; Anand, P.B.; Anantharaman, M.R.; Nair, S.

    The study was carried out to understand the effect of silver-silica nanocomposite (Ag-SiO sub(2)NC) on the cell wall integrity, metabolism and genetic stability of Pseudomonas aeruginosa, a multiple drug-resistant bacterium Bacterial sensitivity...

  18. Sequential interactions of silver-silica nanocomposite (Ag-SiO2 NC) with cell wall, metabolism and genetic stability of Pseudomonas aeruginosa, a multiple antibiotic-resistant bacterium

    Digital Repository Service at National Institute of Oceanography (India)

    Anas, A.; Jiya, J.; Rameez, M.J.; Anand, P.B.; Anantharaman, M.R.; Nair, S.

    The study was carried out to understand the effect of silver–silica nanocomposite (Ag-SiO sub(2)NC) on the cell wall integrity, metabolism and genetic stability of Pseudomonas aeruginosa, a multiple drug-resistant bacterium. Bacterial sensitivity...

  19. Biodegradation of benzalkonium chlorides singly and in mixtures by a Pseudomonas sp. isolated from returned activated sludge

    Energy Technology Data Exchange (ETDEWEB)

    Khan, Adnan Hossain, E-mail: akhan462@uwo.ca [Department of Chemical and Biochemical Engineering, University of Western Ontario, London, ON N6A 5B9 (Canada); Topp, Edward, E-mail: Ed.Topp@AGR.GC.CA [Agriculture and Agri-Food Canada, London, ON N5V 4T3 (Canada); Department of Biology, University of Western Ontario, London, ON N6A 5B7 (Canada); Scott, Andrew, E-mail: Andrew.Scott@AGR.GC.CA [Agriculture and Agri-Food Canada, London, ON N5V 4T3 (Canada); Sumarah, Mark, E-mail: Mark.Sumarah@agr.gc.ca [Agriculture and Agri-Food Canada, London, ON N5V 4T3 (Canada); Macfie, Sheila M., E-mail: smacfie@uwo.ca [Department of Biology, University of Western Ontario, London, ON N6A 5B7 (Canada); Ray, Madhumita B., E-mail: mbhowmic@uwo.ca [Department of Chemical and Biochemical Engineering, University of Western Ontario, London, ON N6A 5B9 (Canada)

    2015-12-15

    Highlights: • Pseudomonas sp. degraded two benzalkonium chlorides: BDDA and BDTA. • Although BDTA biodegraded at low concentration, it inhibited the degradation of BDDA. • For BDDA, two transformation products indicate two sites of bacterial activity. • {sup 14}C-labelled BDDA was mineralized to {sup 14}CO{sub 2} within 300 h. - Abstract: Bactericidal cationic surfactants such as quaternary ammonium compounds (QACs) are widely detected in the environment, and found at mg kg{sup −1} concentrations in biosolids. Although individual QACs are amenable to biodegradation, it is possible that persistence is increased for mixtures of QACs with varying structure. The present study evaluated the biodegradation of benzyl dimethyl dodecyl ammonium chloride (BDDA) singly and in the presence of benzyl dimethyl tetradecyl ammonium chloride (BDTA) using Pseudomonas sp., isolated from returned activated sludge. Growth was evaluated, as was biodegradation using {sup 14}C and HPLC-MS methods. BDTA was more toxic to growth of Pseudomonas sp. compared to BDDA, and BDTA inhibited BDDA biodegradation. The benzyl ring of [U-{sup 14}C-benzyl] BDDA was readily and completely mineralized. The detection of the transformation products benzyl methyl amine and dodecyl dimethyl amine in spent culture liquid was consistent with literature. Overall, this study demonstrates the antagonistic effect of interactions on biodegradation of two widely used QACs suggesting further investigation on the degradation of mixture of QACs in wastewater effluents and biosolids.

  20. Biodegradation of benzalkonium chlorides singly and in mixtures by a Pseudomonas sp. isolated from returned activated sludge

    International Nuclear Information System (INIS)

    Khan, Adnan Hossain; Topp, Edward; Scott, Andrew; Sumarah, Mark; Macfie, Sheila M.; Ray, Madhumita B.

    2015-01-01

    Highlights: • Pseudomonas sp. degraded two benzalkonium chlorides: BDDA and BDTA. • Although BDTA biodegraded at low concentration, it inhibited the degradation of BDDA. • For BDDA, two transformation products indicate two sites of bacterial activity. • 14 C-labelled BDDA was mineralized to 14 CO 2 within 300 h. - Abstract: Bactericidal cationic surfactants such as quaternary ammonium compounds (QACs) are widely detected in the environment, and found at mg kg −1 concentrations in biosolids. Although individual QACs are amenable to biodegradation, it is possible that persistence is increased for mixtures of QACs with varying structure. The present study evaluated the biodegradation of benzyl dimethyl dodecyl ammonium chloride (BDDA) singly and in the presence of benzyl dimethyl tetradecyl ammonium chloride (BDTA) using Pseudomonas sp., isolated from returned activated sludge. Growth was evaluated, as was biodegradation using 14 C and HPLC-MS methods. BDTA was more toxic to growth of Pseudomonas sp. compared to BDDA, and BDTA inhibited BDDA biodegradation. The benzyl ring of [U- 14 C-benzyl] BDDA was readily and completely mineralized. The detection of the transformation products benzyl methyl amine and dodecyl dimethyl amine in spent culture liquid was consistent with literature. Overall, this study demonstrates the antagonistic effect of interactions on biodegradation of two widely used QACs suggesting further investigation on the degradation of mixture of QACs in wastewater effluents and biosolids.

  1. Microarray-mediated transcriptome analysis of the tributyltin (TBT)-resistant bacterium Pseudomonas aeruginosa 25W in the presence of TBT.

    Science.gov (United States)

    Dubey, Santosh K; Tokashiki, Tsutomu; Suzuki, Satoru

    2006-04-01

    The tributyltin (TBT)-resistant bacterium, Pseudomonas aeruginosa 25W, which was isolated in seawater from the Arabian Sea, was subjected to transcriptome analysis in the presence of high concentrations of TBT. Only slight effects were observed at TBT concentration of 50 microM, but exposure to 500 microM resulted in the upregulation of 6 genes and the downregulation of 75. Among the 75 downregulated genes, 53% (40 out of 75) were of hypothetical function, followed by 14 transcriptional regulation- and translation-associated genes. The results of this study indicated that although the 25W strain was highly resistant to TBT, high concentrations of TBT result in toxic effect on the transcriptional and translational levels. The target genes likely belong to a specific category of transcription- and translation-associated genes rather than to other gene categories.

  2. 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.

  3. 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.

  4. Degradation of ethyl mercaptan and its major intermediate diethyl disulfide by Pseudomonas sp. strain WL2.

    Science.gov (United States)

    Wang, Xiangqian; Wu, Chao; Liu, Nan; Li, Sujing; Li, Wei; Chen, Jianmeng; Chen, Dongzhi

    2015-04-01

    A Pseudomonas sp. strain WL2 that is able to efficiently metabolize ethyl mercaptan (EM) into diethyl disulfide (DEDS) through enzymatic oxidation was isolated from the activated sludge of a pharmaceutical wastewater plant. One hundred percent removal of 113.5 mg L(-1) EM and 110.3 mg L(-1) DEDS were obtained within 14 and 32 h, respectively. A putative EM degradation pathway that involved the catabolism via DEDS was proposed, which indicated DEDS were further mineralized into carbon dioxide (CO2), bacterial cells, and sulfate (SO4 (2-)) through the transformation of element sulfur and ethyl aldehyde. Degradation kinetics for EM and DEDS with different initial concentrations by strain WL2 were evaluated using Haldane-Andrews model with maximum specific degradation rates of 3.13 and 1.33 g g(-1) h(-1), respectively, and maximum degradation rate constants of 0.522 and 0.175 h(-1) using pseudo-first-order kinetic model were obtained. Results obtained that aerobic degradation of EM by strain WL2 was more efficient than those from previous studies. Substrate range studies of strain WL2 demonstrated its ability to degrade several mercaptans, disulfides, aldehydes, and methanol. All the results obtained highlight the potential of strain WL2 for the use in the biodegradation of volatile organic sulfur compounds (VOSCs).

  5. Metabolic Degradation of 1,4-dichloronaphthalene by Pseudomonas sp. HY

    Directory of Open Access Journals (Sweden)

    Jian Yu

    2015-08-01

    Full Text Available There is increasing concern regarding the adverse health effects of polychlorinated naphthalenes (PCNs. The metabolic degradation of 1,4-dichloronaphthalene (1,4-DCN as a model PCN, was studied using a strain of Pseudomonas sp. HY. The metabolites were analyzed by gas chromatography-mass spectrometry (GC-MS. A series of metabolites including dihydroxy-dichloro-naphthalene, epoxy-dichlorinated naphthalene, dichlorinated naphthol, and dichlorinated salicylic acid were identified. The time-concentration plots of the degradation curves of 1,4-DCN was also obtained from the experiments, which set the initial concentration of 1,4-DCN to 10 mg/L and 20 mg/L, respectively. The results showed that 98% removal could be achieved within 48 h at an initial 1,4-DCN concentration of 10 mg/L. Nevertheless, it took 144 h to reach the same degradation efficiency at an initial concentration of 20 mg/L. The degradation of 1,4-DCN may not remove the chloride ions during the processes and the metabolites may not benefit the bacterial growth. The research suggests a metabolic pathway of 1,4-DCN, which is critical for the treatment of this compound through biological processes.

  6. A study on metabolic prowess of Pseudomonas sp. RPT 52 to degrade imidacloprid, endosulfan and coragen.

    Science.gov (United States)

    Gupta, Manasi; Mathur, Samarth; Sharma, Tarun K; Rana, Manish; Gairola, Ajay; Navani, Naveen K; Pathania, Ranjana

    2016-01-15

    A bacterial strain identified as Pseudomonas sp. RPT 52, was isolated from an agricultural field by soil enrichment technique. The bacterial strain was able to metabolize three different chlorinated pesticides; imidacloprid, endosulfan and coragen (belonging to neonicotinoid, organochlorine and anthranillic diamide categories, respectively). RPT 52 was able to degrade 46.5%, 96.6%, 92.7% and 80.16% of 0.5 mM of imidacloprid, endosulfan α, endosulfan β and coragen, respectively, in minimal medium over a period of 40 h, when provided as sole source of carbon and energy. Degradation kinetics showed that imidacloprid, endosulfan α and endosulfan β followed first order kinetics whereas coragen followed zero order kinetics. Toxicity studies show reduction in toxicity of the parent compound when degraded by RPT 52. Laboratory scale, soil microcosm studies showed that strain RPT 52 is a suitable candidate for bioremediation of endosulfan and coragen contaminated sites. Thus, RPT 52 holds potential for toxicity reduction in the affected environment. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Biosurfactant production by Pseudomonas sp. and its role in aqueous phase partitioning and biodegradation of chlorpyrifos.

    Science.gov (United States)

    Singh, P B; Sharma, S; Saini, H S; Chadha, B S

    2009-09-01

    To study the effect of biosurfactant on aqueous phase solubility and biodegradation of chlorpyrifos. A Pseudomonas sp. (ChlD), isolated from agricultural soil by enrichment culture technique in the presence of chlorpyrifos, was capable of producing biosurfactant (rhamnolipids) and degrading chlorpyrifos (0.01 g l(-1)). The partially purified rhamnolipid biosurfactant preparation, having a CMC of 0.2 g l(-1), was evaluated for its ability to enhance aqueous phase partitioning and degradation of chlorpyrifos (0.01 g l(-1)) by ChlD strain. The best degradation efficiency was observed at 0.1 g l(-1) supplement of biosurfactant, as validated by GC and HPLC studies. The addition of biosurfactant at 0.1 g l(-1) resulted in more than 98% degradation of chlorpyrifos when compared to 84% in the absence of biosurfactant after 120-h incubation. This first report, to the best of our knowledge, on enhanced degradation of chlorpyrifos in the presence of biosurfactant(s), would help in developing bioremediation protocols to counter accumulation of organophosphates to toxic/carcinogenic levels in environment.

  8. Rhizobacteria Pseudomonas fluorescens and Azospirillum sp. association enhances growth of Lactuca sativa L. under tropical conditions

    Directory of Open Access Journals (Sweden)

    Amael APONTE

    2017-06-01

    Full Text Available The selection of microorganisms that enhance plant growth and confer biotic and abiotic tolerance to crops constitutes a biotechnology currently gaining importance on a global scale. The aim of this investigation was to evaluate the effects of inoculating rhizobacteria to lettuce (Lactuca sativa L. on seed germination and vegetative development in order to use isolates as potential biofertilizers under tropical conditions. Five isolates of Pseudomonas fluorescens (Pf and one of Azospirillum sp. (Az were inoculated to seeds using a bacterial suspension of 1.5*108 CFU*mL-1. In vitro, none of the isolates promoted germination. In vivo, isolates promoted growth and acted as stress alleviators by conferring tolerance to high temperatures (≥ 30 °C. The highest seedling emergence percentages were induced by the association of P.fluorescens with Azospirillum. This association also promoted the highest leaf-area in 25 d seedlings and exhibited a significantly higher dry-weight in 40 d plants compared to the control (P≤0.05 supporting the advantages of bio-consortiums over individual strains. The strains were able to produce dependent L-tryptophan indole-3-acetic acid (IAA, to solubilize phosphorous in vitro and tolerated at least 5%-salt stress. The results indicate that isolate Pf (26 and Az possess plant growth promoting rhizobacteria (PGPR traits and should be further assessed. This study suggests that P. fluorescens and Azospirillum act synergically and are able to trigger an induced-tolerance mechanism in lettuce under abiotic stress.

  9. Insights into metabolism and sodium chloride adaptability of carbaryl degrading halotolerant Pseudomonas sp. strain C7.

    Science.gov (United States)

    Trivedi, Vikas D; Bharadwaj, Anahita; Varunjikar, Madhushri S; Singha, Arminder K; Upadhyay, Priya; Gautam, Kamini; Phale, Prashant S

    2017-08-01

    Pseudomonas sp. strain C7 isolated from sediment of Thane creek near Mumbai, India, showed the ability to grow on glucose and carbaryl in the presence of 7.5 and 3.5% of NaCl, respectively. It also showed good growth in the absence of NaCl indicating the strain to be halotolerant. Increasing salt concentration impacted the growth on carbaryl; however, the specific activity of various enzymes involved in the metabolism remained unaffected. Among various enzymes, 1-naphthol 2-hydroxylase was found to be sensitive to chloride as compared to carbaryl hydrolase and gentisate 1,2-dioxygenase. The intracellular concentration of Cl - ions remained constant (6-8 mM) for cells grown on carbaryl either in the presence or absence of NaCl. Thus the ability to adapt to the increasing concentration of NaCl is probably by employing chloride efflux pump and/or increase in the concentration of osmolytes as mechanism for halotolerance. The halotolerant nature of the strain will be beneficial to remediate carbaryl from saline agriculture fields, ecosystems and wastewaters.

  10. Statistical media design for efficient polyhydroxyalkanoate production in Pseudomonas sp. MNNG-S.

    Science.gov (United States)

    Saranya, V; Rajeswari, V; Abirami, P; Poornimakkani, K; Suguna, P; Shenbagarathai, R

    2016-07-03

    Polyhydroxyalkanoate (PHA) is a promising polymer for various biomedical applications. There is a high need to improve the production rate to achieve end use. When a cost-effective production was carried out with cheaper agricultural residues like molasses, traces of toxins were incorporated into the polymer, which makes it unfit for biomedical applications. On the other hand, there is an increase in the popularity of using chemically defined media for the production of compounds with biomedical applications. However, these media do not exhibit favorable characteristics such as efficient utilization at large scale compared to complex media. This article aims to determine the specific nutritional requirement of Pseudomonas sp. MNNG-S for efficient production of polyhydroxyalkanoate. Response surface methodology (RSM) was used in this study to statistically design for PHA production based on the interactive effect of five significant variables (sucrose; potassium dihydrogen phosphate; ammonium sulfate; magnesium sulfate; trace elements). The interactive effects of sucrose with ammonium sulfate, ammonium sulfate with combined potassium phosphate, and trace element with magnesium sulfate were found to be significant (p < .001). The optimization approach adapted in this study increased the PHA production more than fourfold (from 0.85 g L(-1) to 4.56 g L(-1)).

  11. Sorption of ferrous iron by EPS from the acidophilic bacterium Acidiphilium Sp.: A mechanism proposal

    International Nuclear Information System (INIS)

    Tapia, J.M.; MuNoz, J.; Gonzlez, F.; Blazquez, M.L.; Ballester, A.

    2016-01-01

    The aim of this work was to assess the uptake of Fe(II) by extracellular polymeric substances (EPS) from the acidophilic bacterium Acidiphillium 3.2Sup(5). These EPS were extracted using EDTA. EPS of A. 3.2Sup(5) loaded in sorption tests with Fe(II), were characterized using the following experimental techniques: scanning electron microscopy (SEM) with energy dispersive X-ray microanalysis (EDX), X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR). The experimental results indicate that EPS adsorb ferrous iron according to Freundlich model with a metal sorption uptake of K = 1.14 mg1−1/n L1/n g−1 and a sorption intensity of 1/n = 1.26. In addition, ferrous iron sorption by EPS took place by preferential interaction with the carboxyl group which promotes the formation of ferrous iron oxalates (FeC2O4). Since the interaction reaction was reversible (Log K = 0.77 ± 0.33), that means that the cation sorption can be reversed at convenience. (Author)

  12. Sorption of ferrous iron by EPS from the acidophilic bacterium Acidiphilium Sp.: A mechanism proposal

    Energy Technology Data Exchange (ETDEWEB)

    Tapia, J.M.; MuNoz, J.; Gonzlez, F.; Blazquez, M.L.; Ballester, A.

    2016-07-01

    The aim of this work was to assess the uptake of Fe(II) by extracellular polymeric substances (EPS) from the acidophilic bacterium Acidiphillium 3.2Sup(5). These EPS were extracted using EDTA. EPS of A. 3.2Sup(5) loaded in sorption tests with Fe(II), were characterized using the following experimental techniques: scanning electron microscopy (SEM) with energy dispersive X-ray microanalysis (EDX), X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR). The experimental results indicate that EPS adsorb ferrous iron according to Freundlich model with a metal sorption uptake of K = 1.14 mg1−1/n L1/n g−1 and a sorption intensity of 1/n = 1.26. In addition, ferrous iron sorption by EPS took place by preferential interaction with the carboxyl group which promotes the formation of ferrous iron oxalates (FeC2O4). Since the interaction reaction was reversible (Log K = 0.77 ± 0.33), that means that the cation sorption can be reversed at convenience. (Author)

  13. A polysaccharide-degrading marine bacterium Flammeovirga sp. MY04 and its extracellular agarase system

    Science.gov (United States)

    Han, Wenjun; Gu, Jingyan; Yan, Qiujie; Li, Jungang; Wu, Zhihong; Gu, Qianqun; Li, Yuezhong

    2012-09-01

    Bacteria of the genus Flammeovirga can digest complex polysaccharides (CPs), but no details have been reported regarding the CP depolymerases of these bacteria. MY04, an agarolytic marine bacterium isolated from coastal sediments, has been identified as a new member of the genus Flammeovirga. The MY04 strain is able to utilize multiple CPs as a sole carbon source and grows well on agarose, mannan, or xylan. This strain produces high concentrations of extracellular proteins (490 mg L-1 ± 18.2 mg L-1 liquid culture) that exhibit efficient and extensive degradation activities on various polysaccharides, especially agarose. These proteins have an activity of 310 U mg-1 ± 9.6 U mg-1 proteins. The extracellular agarase system (EAS) in the crude extracellular enzymes contains at least four agarose depolymerases, which are with molecular masses of approximately 30-70 kDa. The EAS is stable at a wide range of pH values (6.0-11.0), temperatures (0-50°C), and sodium chloride (NaCl) concentrations (0-0.9 mol L-1). Two major degradation products generated from agarose by the EAS are identified to be neoagarotetraose and neoagarohexaose, suggesting that β-agarases are the major constituents of the MY04 EAS. These results suggest that the Flammeovirga strain MY04 and its polysaccharide-degradation system hold great promise in industrial applications.

  14. Adenosine deaminase production by an endophytic bacterium (Lysinibacillus sp.) from Avicennia marina.

    Science.gov (United States)

    Kathiresan, Kandasamy; Saravanakumar, Kandasamy; Sahu, Sunil Kumar; Sivasankaran, Muthu

    2014-06-01

    The present study was carried out with the following objectives: (1) to isolate the endophytic bacilli strains from the leaves of mangrove plant Avicennia marina, (2) to screen the potential strains for the production of adenosine deaminase, (3) to statistically optimize the factors that influence the enzyme activity in the potent strain, and (4) to identify the potent strain using 16S rRNA sequence and construct its phylogenetic tree. The bacterial strains isolated from the fresh leaves of a mangrove A. marina were assessed for adenosine deaminase activity by plating method. Optimization of reaction process was carried out using response surface methodology of central composite design. The potent strain was identified based on 16S rRNA sequencing and phylogeny. Of five endophytic strains, EMLK1 showed a significant deaminase activity over other four strains. The conditions for maximum activity of the isolated adenosine deaminase are described. The potent strain EMLK1 was identified as Lysinibacillus sp. (JQ710723) being the first report as a mangrove endophyte. Mangrove-derived endophytic bacillus strain Lysinibacillus sp. EMLK1 is proved to be a promising source for the production of adenosine deaminase and this enzyme deserves further studies for purification and its application in disease diagnosis.

  15. 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.

  16. Getting the ecology into the interactions between plants and the plant-growth promoting bacterium Pseudomonas fluorescens

    NARCIS (Netherlands)

    Hol, W.H.G.; Bezemer, T.M.; Biere, A.

    2013-01-01

    Plant growth-promoting rhizobacteria (PGPR) are increasingly appreciated for their contributions to primary productivity through promotion of growth and triggering of induced systemic resistance in plants. Here we focus on the beneficial effects of one particular species of PGPR (Pseudomonas

  17. Molecular stress responses to nano-sized zero-valent iron (nZVI) particles in the soil bacterium Pseudomonas stutzeri.

    Science.gov (United States)

    Saccà, Maria Ludovica; Fajardo, Carmen; Martinez-Gomariz, Montserrat; Costa, Gonzalo; Nande, Mar; Martin, Margarita

    2014-01-01

    Nanotoxicological studies were performed in vitro using the common soil bacterium Pseudomonas stutzeri to assess the potentially toxic impact of commercial nano-sized zero-valent iron (nZVI) particles, which are currently used for environmental remediation projects. The phenotypic response of P. stutzeri to nZVI toxicity includes an initial insult to the cell wall, as evidenced by TEM micrographs. Transcriptional analyses using genes of particular relevance in cellular activity revealed that no significant changes occurred among the relative expression ratios of narG, nirS, pykA or gyrA following nZVI exposure; however, a significant increase in katB expression was indicative of nZVI-induced oxidative stress in P. stutzeri. A proteomic approach identified two major defence mechanisms that occurred in response to nZVI exposure: a downregulation of membrane proteins and an upregulation of proteins involved in reducing intracellular oxidative stress. These biomarkers served as early indicators of nZVI response in this soil bacterium, and may provide relevant information for environmental hazard assessment.

  18. 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.

  19. 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)).

  20. Thalassospiramide G, a New γ-Amino-Acid-Bearing Peptide from the Marine Bacterium Thalassospira sp.

    Directory of Open Access Journals (Sweden)

    Sang Kook Lee

    2013-02-01

    Full Text Available In the chemical investigation of marine unicellular bacteria, a new peptide, thalassospiramide G (1, along with thalassospiramides A and D (2–3, was discovered from a large culture of Thalassospira sp. The structure of thalassospiramide G, bearing γ-amino acids, such as 4-amino-5-hydroxy-penta-2-enoic acid (AHPEA, 4-amino-3,5-dihydroxy-pentanoic acid (ADPA, and unique 2-amino-1-(1H-indol-3-yl ethanone (AIEN, was determined via extensive spectroscopic analysis. The absolute configuration of thalassospiramide D (3, including 4-amino-3-hydroxy-5-phenylpentanoic acid (AHPPA, was rigorously determined by 1H–1H coupling constant analysis and chemical derivatization. Thalassospiramides A and D (2–3 inhibited nitric oxide (NO production in lipopolysaccharide (LPS-stimulated mouse macrophage RAW 264.7 cells, with IC50 values of 16.4 and 4.8 μM, respectively.

  1. 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 ).

  2. 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 ).

  3. 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)....

  4. Display of a thermostable lipase on the surface of a solvent-resistant bacterium, Pseudomonas putida GM730, and its applications in whole-cell biocatalysis

    Directory of Open Access Journals (Sweden)

    Kwon Seok-Joon

    2006-04-01

    Full Text Available Abstract Background Whole-cell biocatalysis in organic solvents has been widely applied to industrial bioprocesses. In two-phase water-solvent processes, substrate conversion yields and volumetric productivities can be limited by the toxicity of solvents to host cells and by the low mass transfer rates of the substrates from the solvent phase to the whole-cell biocatalysts in water. Results To solve the problem of solvent toxicity, we immobilized a thermostable lipase (TliA from Pseudomonas fluorescens on the cell surface of a solvent-resistant bacterium, Pseudomonas putida GM730. Surface immobilization of enzymes eliminates the mass-transfer limitation imposed by the cell wall and membranes. TliA was successfully immobilized on the surface of P. putida cells using the ice-nucleation protein (INP anchoring motif from Pseudomonas syrinage. The surface location was confirmed by flow cytometry, protease accessibility and whole-cell enzyme activity using a membrane-impermeable substrate. Three hundred and fifty units of whole-cell hydrolytic activity per gram dry cell mass were obtained when the enzyme was immobilized with a shorter INP anchoring motif (INPNC. The surface-immobilized TliA retained full enzyme activity in a two-phase water-isooctane reaction system after incubation at 37°C for 12 h, while the activity of the free form enzyme decreased to 65% of its initial value. Whole cells presenting immobilized TliA were shown to catalyze three representative lipase reactions: hydrolysis of olive oil, synthesis of triacylglycerol and chiral resolution. Conclusion In vivo surface immobilization of enzymes on solvent-resistant bacteria was demonstrated, and appears to be useful for a variety of whole-cell bioconversions in the presence of organic solvents.

  5. Display of a thermostable lipase on the surface of a solvent-resistant bacterium, Pseudomonas putida GM730, and its applications in whole-cell biocatalysis

    Science.gov (United States)

    Jung, Heung-Chae; Kwon, Seok-Joon; Pan, Jae-Gu

    2006-01-01

    Background Whole-cell biocatalysis in organic solvents has been widely applied to industrial bioprocesses. In two-phase water-solvent processes, substrate conversion yields and volumetric productivities can be limited by the toxicity of solvents to host cells and by the low mass transfer rates of the substrates from the solvent phase to the whole-cell biocatalysts in water. Results To solve the problem of solvent toxicity, we immobilized a thermostable lipase (TliA) from Pseudomonas fluorescens on the cell surface of a solvent-resistant bacterium, Pseudomonas putida GM730. Surface immobilization of enzymes eliminates the mass-transfer limitation imposed by the cell wall and membranes. TliA was successfully immobilized on the surface of P. putida cells using the ice-nucleation protein (INP) anchoring motif from Pseudomonas syrinage. The surface location was confirmed by flow cytometry, protease accessibility and whole-cell enzyme activity using a membrane-impermeable substrate. Three hundred and fifty units of whole-cell hydrolytic activity per gram dry cell mass were obtained when the enzyme was immobilized with a shorter INP anchoring motif (INPNC). The surface-immobilized TliA retained full enzyme activity in a two-phase water-isooctane reaction system after incubation at 37°C for 12 h, while the activity of the free form enzyme decreased to 65% of its initial value. Whole cells presenting immobilized TliA were shown to catalyze three representative lipase reactions: hydrolysis of olive oil, synthesis of triacylglycerol and chiral resolution. Conclusion In vivo surface immobilization of enzymes on solvent-resistant bacteria was demonstrated, and appears to be useful for a variety of whole-cell bioconversions in the presence of organic solvents. PMID:16620394

  6. 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.

  7. 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)).

  8. 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).

  9. 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.

  10. Sulfonamide inhibition studies of the β-carbonic anhydrase from the newly discovered bacterium Enterobacter sp. B13.

    Science.gov (United States)

    Eminoğlu, Ayşenur; Vullo, Daniela; Aşık, Aycan; Çolak, Dilşat Nigar; Çanakçı, Sabriye; Beldüz, Ali Osman; Supuran, Claudiu T

    2016-04-01

    The genome of the newly identified bacterium Enterobacter sp. B13 encodes for a β-class carbonic anhydrases (CAs, EC 4.2.1.1), EspCA. This enzyme was recently cloned, and characterized kinetically by this group (J. Enzyme Inhib. Med. Chem. 2016, 31). Here we report an inhibition study with sulfonamides and sulfamates of this enzyme. The best EspCA inhibitors were some sulfanylated sulfonamides with elongated molecules, metanilamide, 4-aminoalkyl-benzenesulfonamides, acetazolamide, and deacetylated methazolamide (KIs in the range of 58.7-96.5nM). Clinically used agents such as methazolamide, ethoxzolamide, dorzolamide, brinzolamide, benzolamide, zonisamide, sulthiame, sulpiride, topiramate and valdecoxib were slightly less effective inhibitors (KIs in the range of 103-138nM). Saccharin, celecoxib, dichlorophenamide and many simple benzenesulfonamides were even less effective as EspCA inhibitors, with KIs in the range of 384-938nM. Identification of effective inhibitors of this bacterial enzyme may lead to pharmacological tools useful for understanding the physiological role(s) of the β-class CAs in bacterial pathogenicity/virulence. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Cloning, expression and biochemical characterization of a β-carbonic anhydrase from the soil bacterium Enterobacter sp. B13.

    Science.gov (United States)

    Eminoğlu, Ayşenur; Vullo, Daniela; Aşık, Aycan; Çolak, Dilşat Nigar; Supuran, Claudiu T; Çanakçı, Sabriye; Osman Beldüz, Ali

    2016-12-01

    A recombinant carbonic anhydrase (CA, EC 4.2.1.1) from the soil-dwelling bacterium Enterobacter sp. B13 was cloned and purified by Co(2+) affinity chromatography. Bioinformatic analysis showed that the new enzyme (denominated here B13-CA) belongs to the β-class CAs and to possess 95% homology with the ortholog enzyme from Escherichia coli encoded by the can gene, whereas its sequence homology with the other such enzyme from E. coli (encoded by the cynT gene) was of 33%. B13-CA was characterized kinetically as a catalyst for carbon dioxide hydration to bicarbonate and protons. The enzyme shows a significant catalytic activity, with the following kinetic parameters at 20 °C and pH of 8.3: kcat of 4.8 × 10(5) s(-1) and kcat/Km of 5.6 × 10(7) M(-1) × s(-1). This activity was potently inhibited by acetazolamide which showed a KI of 78.9 nM. Although only this compound was investigated for the moment as B13-CA inhibitor, further studies may reveal new classes of inhibitors/activators of this enzyme which may show biomedical or environmental applications, considering the posssible role of this enzyme in CaCO3 biomineralization processes.

  12. Disruption and characterization of the excision repair pathway in the extremely radioresistant bacterium Deinococcus SP. BR501

    International Nuclear Information System (INIS)

    Liu Xiumin; Lin Min; Wu Jing; Zhang Wei; Lu Wei; Ping Shuzhen; Chen Ming

    2007-01-01

    Deinococcus sp. BR501, an extremely radioresistant bacterium may contain two nucleotide excision repair pathways: the UV damage endonuclease β (UvsE)-dependent excision repair pathway and the UvrABC-dependent pathway. And the UvsE (coded by dr1819) and UvrABC(Unit A coded by dr1771) are their key enzymes respectively. PCR primers were designed and homologous genes were cloned and disrupted in vitro according to the completely nucleotide sequence of Deinococcus radiodurans R1 genome. Then PCR production was transformed to BR501, and the disrupted mutants (triangle open dr1771, triangle open dr1819 and triangle open dr1771dr1819) were checked and confirmed by homologous recombination. These mutants and the wild type were irradiated by UV light and exposed to the DNA-damaging agents MMC and H 2 O 2 . The results showed that these pathways were existed in BR501 and only the two pathway losses could result in increased sensitivity to UV and MMC. (authors)

  13. 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)).

  14. 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.

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

    Directory of Open Access Journals (Sweden)

    Quanfu Wang

    2014-01-01

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

  16. 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.

  17. 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).

  18. 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)).

  19. 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)).

  20. 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 ).

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

    Science.gov (United States)

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

    2012-05-01

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

  3. Description of a novel marine bacterium, Vibrio hyugaensis sp. nov., based on genomic and phenotypic characterization.

    Science.gov (United States)

    Urbanczyk, Yoshiko; Ogura, Yoshitoshi; Hayashi, Tetsuya; Urbanczyk, Henryk

    2015-07-01

    Three luminous bacteria strains have been isolated from seawater samples collected in the coastal regions of the Miyazaki prefecture in Japan. Analysis of the 16S rRNA gene sequences identified the three strains as members of the genus Vibrio (Vibrionaceae, Gammaproteobacteria), closely related to bacteria in the so-called 'Harveyi clade.' The genomes of the three strains were estimated to be between 5.49Mbp and 5.95Mbp, with average G+C of 43.91%. The genome sequence data was used to estimate relatedness of the three strains to related Vibrio bacteria, including estimation of frequency of recombination events, calculation of average nucleotide identity (ANI), and a phylogenetic analysis based on concatenated alignment of nucleotide sequences of 135 protein coding genes. Results of these analyses in all cases showed the three strains forming a group clearly separate from previously described Vibrio species. A phenotypic analysis revealed that the three strains have character similar to Vibrio bacteria in the 'Harveyi clade', but can be differentiated from previously described species by testing for hydrolysis of esculin. Based on results of genomic, phylogenetic and phenotypic analyses presented in this study, it can be concluded that the three strains represent a novel species, for which the name Vibrio hyugaensis sp. nov. is proposed. The type strain is 090810a(T) (=LMG 28466(T)=NBRC 110633(T)). Copyright © 2015 Elsevier GmbH. All rights reserved.

  4. 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.

  5. Methylocella tundrae sp. nov., a novel methanotrophic bacterium from acidic tundra peatlands.

    Science.gov (United States)

    Dedysh, Svetlana N; Berestovskaya, Yulia Y; Vasylieva, Lina V; Belova, Svetlana E; Khmelenina, Valentina N; Suzina, Natalia E; Trotsenko, Yuri A; Liesack, Werner; Zavarzin, George A

    2004-01-01

    A novel species, Methylocella tundrae, is proposed for three methanotrophic strains (T4T, TCh1 and TY1) isolated from acidic Sphagnum tundra peatlands. These strains are aerobic, Gram-negative, non-motile, dinitrogen-fixing rods that possess a soluble methane monooxygenase and utilize the serine pathway for carbon assimilation. Strains T4T, TCh1 and TY1 are moderately acidophilic organisms capable of growth between pH 4.2 and 7.5 (optimum 5.5-6.0) and between 5 and 30 degrees C (optimum 15 degrees C). The major phospholipid fatty acid is 18:1omega7c. The DNA G+C content of strain T4T is 63.3 mol%. The three strains possess almost identical 16S rRNA gene sequences and are most closely related to two previously identified species of Methylocella, Methylocella palustris (97% similarity) and Methylocella silvestris (97.5% similarity). DNA-DNA hybridization values of strain T4T with Methylocella palustris KT and Methylocella silvestris BL2T were respectively 27 and 36%. Thus, the tundra strains represent a novel species, for which the name Methylocella tundrae sp. nov. is proposed. Strain T4T (=DSM 15673T=NCIMB 13949T) is the type strain.

  6. 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 ).

  7. Isolation of plant growth-promoting Pseudomonas sp. PPR8 from the rhizosphere of Phaseolus vulgaris L.

    Directory of Open Access Journals (Sweden)

    Kumar Pankaj

    2016-01-01

    Full Text Available In vitro screening of plant growth-promoting (PGP traits was carried out using eight Pseudomonas spp., PPR1 to PPR8, isolated from the rhizosphere of Phaseolus vulgaris growing on the Uttarakhand Himalayan range in India. All the isolates were fast growers, positive for catalase, oxidase and urease activities, and utilized lactose and some amino acids. All the isolates were indole acetic acid (IAA positive, however PPR8 solubilized potassium and zinc along with various other types of inorganic (tricalcium, dicalcium and zinc phosphate and organic (calcium phytate phosphates, as well as producing siderophore and ACC deaminase. PPR8 also produced cyanogens, extracellular chitinase, β-1,3-glucanase, β-1,4-glucanase and oxalate oxidase. Based on the PGP traits of all isolates, PPR8 was found to be the most potent plant growth-promoting rhizobacteria (PGPR. Further, PPR8 was identified as Pseudomonas sp. PPR8, based on 16S rRNA gene sequencing analysis. Moreover, the PGP activities of PPR8 confirmed it to be a potent biocontrol agent, inhibiting the growth of various plant pathogenic fungi. This study reveals the potential of Pseudomonas sp. PPR8 to be used as a good bioinoculant for growth promotion of common bean and for the protection of important legume crops from various deleterious phytopathogens.

  8. Ecofriendly biodegradation and detoxification of Reactive Red 2 textile dye by newly isolated Pseudomonas sp. SUK1

    International Nuclear Information System (INIS)

    Kalyani, D.C.; Telke, A.A.; Dhanve, R.S.; Jadhav, J.P.

    2009-01-01

    The aim of this work is to evaluate textile dyes degradation by novel bacterial strain isolated from the waste disposal sites of local textile industries. Detailed taxonomic studies identified the organisms as Pseudomonas species and designated as strain Pseudomonas sp. SUK1. The isolate was able to decolorize sulfonated azo dye (Reactive Red 2) in a wide range (up to 5 g l -1 ), at temperature 30 deg. C, and pH range 6.2-7.5 in static condition. This isolate also showed decolorization of the media containing a mixture of dyes. Measurements of COD were done at regular intervals to have an idea of mineralization, showing 52% reduction in the COD within 24 h. Induction in the activity of lignin peroxidase and azoreductase was observed during decolorization of Reactive Red 2 in the batch culture, which represented their role in degradation. The biodegradation was monitored by UV-vis, IR spectroscopy, HPLC. The final product, 2-naphthol was characterized by GC-mass spectroscopy. The phytotoxicity study revealed the degradation of Reactive Red 2 into non-toxic product by Pseudomonas sp. SUK1

  9. Ecofriendly biodegradation and detoxification of Reactive Red 2 textile dye by newly isolated Pseudomonas sp. SUK1

    Energy Technology Data Exchange (ETDEWEB)

    Kalyani, D.C.; Telke, A.A.; Dhanve, R.S. [Department of Biochemistry, Shivaji University, Kolhapur 416004 (India); Jadhav, J.P. [Department of Biochemistry, Shivaji University, Kolhapur 416004 (India)], E-mail: jpj_biochem@unishivaji.ac.in

    2009-04-30

    The aim of this work is to evaluate textile dyes degradation by novel bacterial strain isolated from the waste disposal sites of local textile industries. Detailed taxonomic studies identified the organisms as Pseudomonas species and designated as strain Pseudomonas sp. SUK1. The isolate was able to decolorize sulfonated azo dye (Reactive Red 2) in a wide range (up to 5 g l{sup -1}), at temperature 30 deg. C, and pH range 6.2-7.5 in static condition. This isolate also showed decolorization of the media containing a mixture of dyes. Measurements of COD were done at regular intervals to have an idea of mineralization, showing 52% reduction in the COD within 24 h. Induction in the activity of lignin peroxidase and azoreductase was observed during decolorization of Reactive Red 2 in the batch culture, which represented their role in degradation. The biodegradation was monitored by UV-vis, IR spectroscopy, HPLC. The final product, 2-naphthol was characterized by GC-mass spectroscopy. The phytotoxicity study revealed the degradation of Reactive Red 2 into non-toxic product by Pseudomonas sp. SUK1.

  10. Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds.

    Science.gov (United States)

    Miyazaki, Ryo; Bertelli, Claire; Benaglio, Paola; Canton, Jonas; De Coi, Nicoló; Gharib, Walid H; Gjoksi, Bebeka; Goesmann, Alexander; Greub, Gilbert; Harshman, Keith; Linke, Burkhard; Mikulic, Josip; Mueller, Linda; Nicolas, Damien; Robinson-Rechavi, Marc; Rivolta, Carlo; Roggo, Clémence; Roy, Shantanu; Sentchilo, Vladimir; Siebenthal, Alexandra Von; Falquet, Laurent; van der Meer, Jan Roelof

    2015-01-01

    Pseudomonas knackmussii B13 was the first strain to be isolated in 1974 that could degrade chlorinated aromatic hydrocarbons. This discovery was the prologue for subsequent characterization of numerous bacterial metabolic pathways, for genetic and biochemical studies, and which spurred ideas for pollutant bioremediation. In this study, we determined the complete genome sequence of B13 using next generation sequencing technologies and optical mapping. Genome annotation indicated that B13 has a variety of metabolic pathways for degrading monoaromatic hydrocarbons including chlorobenzoate, aminophenol, anthranilate and hydroxyquinol, but not polyaromatic compounds. Comparative genome analysis revealed that B13 is closest to Pseudomonas denitrificans and Pseudomonas aeruginosa. The B13 genome contains at least eight genomic islands [prophages and integrative conjugative elements (ICEs)], which were absent in closely related pseudomonads. We confirm that two ICEs are identical copies of the 103 kb self-transmissible element ICEclc that carries the genes for chlorocatechol metabolism. Comparison of ICEclc showed that it is composed of a variable and a 'core' region, which is very conserved among proteobacterial genomes, suggesting a widely distributed family of so far uncharacterized ICE. Resequencing of two spontaneous B13 mutants revealed a number of single nucleotide substitutions, as well as excision of a large 220 kb region and a prophage that drastically change the host metabolic capacity and survivability. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  11. A Leaf-Inhabiting Endophytic Bacterium, Rhodococcus sp. KB6, Enhances Sweet Potato Resistance to Black Rot Disease Caused by Ceratocystis fimbriata.

    Science.gov (United States)

    Hong, Chi Eun; Jeong, Haeyoung; Jo, Sung Hee; Jeong, Jae Cheol; Kwon, Suk Yoon; An, Donghwan; Park, Jeong Mee

    2016-03-01

    Rhodococcus species have become increasingly important owing to their ability to degrade a wide range of toxic chemicals and produce bioactive compounds. Here, we report isolation of the Rhodococcus sp. KB6, which is a new leaf-inhabiting endophytic bacterium that suppresses black rot disease in sweet potato leaves. We determined the 7.0 Mb draft genome sequence of KB6 and have predicted 19 biosynthetic gene clusters for secondary metabolites, including heterobactins, which are a new class of siderophores. Notably, we showed the first internal colonization of host plants with Rhodococcus sp. KB6 and discuss its potential as a biocontrol agent for sustainable agriculture.

  12. Inhibition of Steptococcus mutans biofilm formation by extracts of Tenacibaculum sp. 20J, a bacterium with wide-spectrum quorum quenching activity

    OpenAIRE

    Muras, Andrea; Mayer, Celia; Romero, Manuel; Camino, Tamara; Ferrer, Maria D.; Mira, Alex; Otero, Ana

    2018-01-01

    ABSTRACT Background: Previous studies have suggested the quorum sensing signal AI-2 as a potential target to prevent the biofilm formation by Streptococcus mutans, a pathogen involved in tooth decay. Objective: To obtain inhibition of biofilm formation by S. mutans by extracts obtained from the marine bacterium Tenacibaculum sp. 20J interfering with the AI-2 quorum sensing system. Design: The AI-2 inhibitory activity was tested with the biosensors Vibrio harveyi BB170 and JMH597. S. mutans AT...

  13. Penapisan Limbah Pertanian (Sabut Kelapa Dan Arang Sekam) Dalam Peningkatan Ketahanan Bibit Pisang Barangan Bermikoriza Terhadap Blood Disease Bacterium Dan Fusarium Oxysporum F.sp. Cubense

    OpenAIRE

    Suswati; Indrawati, Asmah; Putra, Deddi Prima

    2015-01-01

    Agricultural waste screening (coconut fibre and chaff charcoal) in improving the resistance of Mychorrizae Barangan seedling to Blood diseases bacterium and Fusarium oxysporum f. sp. cubense. The application of soil and compost are very general in Barangan banana seedling. However, those media always contaminated by BDB and Foc propagul. This research was intended to examine the influence of planting media composition (soil, coconut fibre and chuff charcoal) in improving the resistance of Myc...

  14. 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.

  15. Characterization of a cold-adapted esterase and mutants from a psychotolerant Pseudomonas sp. strain.

    Science.gov (United States)

    Dong, Juan; Gasmalla, Mohammed A A; Zhao, Wei; Sun, Jingtao; Liu, Wenyu; Wang, Mingming; Han, Liang; Yang, Ruijin

    2017-09-01

    A cold-adapted esterase-producing strain named T1-39 was isolated from Glacier No. 1, Tianshan, People's Republic of China and identified as Pseudomonas sp. from 16S rRNA sequence analysis. The esterase (EstT1-39) secreted by this strain preferentially hydrolyzed esters of glycerol with short- and medium-chain fatty acids. Mutants of T1-39 were generated by the atmospheric and room temperature plasma method and screened for enhanced esterase activity. Among all the mutants, strain TB11 had 4.45-fold higher esterase productivity than T1-39, with high genetic stability over 10 generations of continuous cultivation. Maximum activity of EstT1-39 and EstTB11 was observed at 30 ℃, pH 9.0 and 25 ℃, pH 8.5, respectively. EstTB11 was thermally more stable (50 ℃ for 1 H) and active over a broader pH range than EstT1-39. EstTB11 also retained 38% of its maximal activity at 0 ℃ and was found to be able to hydrolyze milk fats into short- and medium-chain fatty acids at 4 ℃. The characteristics of EstT1-39 made it a cold-adapted enzyme and the EstTB11 from the mutant, with its higher activity at lower temperatures, may be suitable for the production of aromas and flavors in the dairy industry. © 2016 International Union of Biochemistry and Molecular Biology, Inc.

  16. 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)).

  17. 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 ).

  18. 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.

  19. 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)).

  20. 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).

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

    Science.gov (United States)

    Yu, Xiumei; Cloutier, Sylvie; Tambong, James T; Bromfield, Eden S P

    2014-09-01

    Sixteen strains of symbiotic bacteria from root nodules of Glycine max grown in Ottawa, Canada, were previously characterized and placed in a novel group within the genus Bradyrhizobium. To verify their taxonomic status, these strains were further characterized using a polyphasic approach. All strains possessed identical 16S rRNA gene sequences that were 99.79 % similar to the closest relative, Bradyrhizobium liaoningense LMG 18230(T). Phylogenetic analysis of concatenated atpD, glnII, recA, gyrB, rpoB and dnaK genes divided the 16 strains into three multilocus sequence types that were placed in a highly supported lineage distinct from named species of the genus Bradyrhizobium consistent with results of DNA-DNA hybridization. Based on analysis of symbiosis gene sequences (nodC and nifH), all novel strains were placed in a phylogenetic group with five species of the genus Bradyrhizobium that nodulate soybeans. The combination of phenotypic characteristics from several tests including carbon and nitrogen source utilization and antibiotic resistance could be used to differentiate representative strains from recognized species of the genus Bradyrhizobium. Novel strain OO99(T) elicits effective nodules on Glycine max, Glycine soja and Macroptilium atropurpureum, partially effective nodules on Desmodium canadense and Vigna unguiculata, and ineffective nodules on Amphicarpaea bracteata and Phaseolus vulgaris. Based on the data presented, we conclude that our strains represent a novel species for which the name Bradyrhizobium ottawaense sp. nov. is proposed, with OO99(T) ( = LMG 26739(T) = HAMBI 3284(T)) as the type strain. The DNA G+C content is 62.6 mol%. © 2014 Her Majesty the Queen in right of Canada as represented by the Minister of AAFC.

  2. Defluviitalea phaphyphila sp. nov., a Novel Thermophilic Bacterium That Degrades Brown Algae.

    Science.gov (United States)

    Ji, Shi-Qi; Wang, Bing; Lu, Ming; Li, Fu-Li

    2016-02-01

    Brown algae are one of the largest groups of oceanic primary producers for CO2 removal and carbon sinks for coastal regions. However, the mechanism for brown alga assimilation remains largely unknown in thermophilic microorganisms. In this work, a thermophilic alginolytic community was enriched from coastal sediment, from which an obligate anaerobic and thermophilic bacterial strain, designated Alg1, was isolated. Alg1 shared a 16S rRNA gene identity of 94.6% with Defluviitalea saccharophila LIND6LT2(T). Phenotypic, chemotaxonomic, and phylogenetic studies suggested strain Alg1 represented a novel species of the genus Defluviitalea, for which the name Defluviitalea phaphyphila sp. nov. is proposed. Alg1 exhibited an intriguing ability to convert carbohydrates of brown algae, including alginate, laminarin, and mannitol, to ethanol and acetic acid. Three gene clusters participating in this process were predicted to be in the genome, and candidate enzymes were successfully expressed, purified, and characterized. Six alginate lyases were demonstrated to synergistically deconstruct alginate into unsaturated monosaccharide, followed by one uronic acid reductase and two 2-keto-3-deoxy-d-gluconate (KDG) kinases to produce pyruvate. A nonclassical mannitol 1-phosphate dehydrogenase, catalyzing D-mannitol 1-phosphate to fructose 1-phosphate in the presence of NAD(+), and one laminarase also were disclosed. This work revealed that a thermophilic brown alga-decomposing system containing numerous novel thermophilic alginate lyases and a unique mannitol 1-phosphate dehydrogenase was adopted by the natural ethanologenic strain Alg1 during the process of evolution in hostile habitats. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  3. 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)).

  4. 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.

  5. 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 ).

  6. 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).

  7. 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)).

  8. 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.

  9. 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).

  10. 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).

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

    Science.gov (United States)

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

    2014-01-01

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

  12. Bradyrhizobium subterraneum sp. nov., a symbiotic nitrogen-fixing bacterium from root nodules of groundnuts.

    Science.gov (United States)

    Grönemeyer, Jann Lasse; Chimwamurombe, Percy; Reinhold-Hurek, Barbara

    2015-10-01

    Seven strains of symbiotic bacteria from root nodules of local races of Bambara groundnut (Vigna subterranea) and peanuts (Arachis hypogaea) grown on subsistence farmers' fields in the Kavango region, Namibia, were previously characterized and identified as a novel group within the genus Bradyrhizobium. To corroborate their taxonomic status, these strains were further characterized using a polyphasic approach. All strains possessed identical 16S rRNA gene sequences with Bradyrhizobium yuanmingense CCBAU 10071T being the most closely related type strain in the 16S rRNA gene phylogenetic analysis, and Bradyrhizobium daqingense CCBAU 15774T in the ITS sequence analysis. Phylogenetic analysis of concatenated glnII-recA-rpoB-dnaK placed the strains in a highly supported lineage distinct from named species of the genus Bradyrhizobium, most closely related to Bradyrhizobium yuanmingense CCBAU 10071T. The species status was validated by results of DNA–DNA hybridization. Phylogenetic analysis of nifH genes placed the novel strains in a group with nifH of ‘Bradyrhizobium arachidis’ CCBAU 051107 that also nodulates peanuts. The combination of phenotypic characteristics from several tests including carbon source utilization and antibiotic resistance could be used to differentiate representative strains from recognized species of the genus Bradyrhizobium. Novel strain 58 2-1T induced effective nodules on V. subterranea, Vigna unguiculata and A. hypogaea, and some strains on Lablab purpureus. Based on the data presented, we conclude that our strains represent a novel species for which the name Bradyrhizobium subterraneum sp. nov. is proposed, with 58 2-1T [ = DSM 100298T = LMG 28792T = NTCCM0016T (Windhoek)] as the type strain. The DNA G+C content of strain 58 2-1T was 64.7 mol% (T m).

  13. 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)).

  14. 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 ).

  15. Accumulation of a Polyhydroxyalkanoate Containing Primarily 3-Hydroxydecanoate from Simple Carbohydrate Substrates by Pseudomonas sp. Strain NCIMB 40135.

    Science.gov (United States)

    Haywood, G W; Anderson, A J; Ewing, D F; Dawes, E A

    1990-11-01

    A number of Pseudomonas species have been identified which accumulate a polyhydroxyalkanoate containing mainly 3-hydroxydecanoate monomers from sodium gluconate as the sole carbon source. One of these, Pseudomonas sp. strain NCIMB 40135, was further investigated and shown to accumulate such a polyhydroxyalkanoate from a wide range of carbon sources (C(2) to C(6)); however, when supplied with octanoic acid it produced a polyhydroxyalkanoate containing mainly 3-hydroxyoctanoate monomers. Polymer synthesis occurred in batch culture after cessation of growth due to exhaustion of nitrogen. In continuous culture under nitrogen limitation up to 16.9% (wt/wt) polyhydroxyalkanoate was synthesized from glucose as the carbon source. The monomer units are mainly of the R-(-) configuration. Nuclear magnetic resonance studies confirmed the composition of the polymer. Differential scanning calorimetry suggested that the solvent-extracted polymer contained a significant proportion of crystalline material. The weight-average molecular weight of the polymer from glucose-grown cells was 143,000.

  16. 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).

  17. 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.

  18. 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)).

  19. 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 ).

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

    Science.gov (United States)

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

    2011-09-01

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

  1. 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).

  2. 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 ).

  3. Novel Essential Role of Ethanol Oxidation Genes at Low Temperature Revealed by Transcriptome Analysis in the Antarctic Bacterium Pseudomonas extremaustralis

    DEFF Research Database (Denmark)

    Tribelli, Paula Maria; Solar Venero, Esmeralda C.; Ricardi, Martiniano M

    2015-01-01

    up-regulated genes, those coding for transcriptional regulatory and signal transduction proteins were over-represented at cold conditions. Remarkably, we found that genes involved in ethanol oxidation, exaA, exaB and exaC, encoding a pyrroloquinoline quinone (PQQ)-dependent ethanol dehydrogenase...... grown at 8°C support the conclusion that this pathway is important under cold conditions. The obtained results have led to the identification of novel components involved in cold adaptation mechanisms in this bacterium, suggesting for the first time a role of the ethanol oxidation pathway for bacterial...

  4. [Cloning, expression and characterization of a gamma-butyrobetaine hydroxylase gene bbh from Pseudomonas sp. L-1].

    Science.gov (United States)

    Lu, Xiangfeng; Zhang, Pengcheng; Li, Qianyan; Liu, Hui; Lin, Xiaoqing; Ma, Xiaohang

    2012-05-04

    Gamma-butyrobetaine hydroxylase is an enzyme that catalyzes the last step in the biosynthesis of L-carnitine. We cloned, expressed and characterized a gamma-butyrobetaine hydroxylase gene bbh from Pseudomonas sp. L-1, to facilitate the production of L-carnitine using microorganisms. We cloned bbh gene by PCR, and then cloned the open reading frame of bbh into pET-15b vector and expressed by Isopropyl beta-D-1-thiogalactopyranoside (IPTG) induction. After His-Bind Resin purification, the characteristics of BBH were studied. The three-dimensional structure of BBH monomer was modeled by SWISS-MODEL Workspace and resting cells were used for L-carnitine transformation. We cloned a gamma-butyrobetaine hydroxylase gene bbh (GenBank: JQ250036) from Pseudomonas sp. L-1 and expressed the gene in Escherichia coli BL21(DE3). BBH fusion protein was a homodimer, and the molecular weight of subunit was about 46.5kDa. The optimal temperature and pH was 30 degrees C and pH 7.5. The enzyme was stable below 45 degrees C. The enzyme was most stable at pH 6.0. We used resting cells of recombinant E. coli for L-carnitine biotransformation, after incubated at 30 degrees C and pH 7.0 for 31 h, the concentration of L-carnitine reached 12.7 mmol/L. The bbh gene from Pseudomonas sp. L-1 strain is remarkably different from that of reported one. The gamma-butyrobetaine hydroxylase expressed by this gene could effectively transform gamma-butyrobetaine for L-carnitine production. Beside by reporting of a bbh gene from bacteria, this research also provided a new process for biotransformation of L-carnitine.

  5. Medium Optimization for Enzymatic Production of L-Cysteine by Pseudomonas sp. Zjwp-14 Using Response Surface Methodology

    Directory of Open Access Journals (Sweden)

    Guo-Ying Lv

    2008-01-01

    Full Text Available Response surface methodology was applied to optimize medium constituents for enzymatic production of L-cysteine from DL-2-amino-Δ^2-thiazoline-4-carboxylic acid (DL-ATC by a novel Pseudomonas sp. Zjwp-14. With the Plackett-Burman design experiment, glycerol, DL-ATC, yeast extract, and pH were found to be the most powerful factors among the eight tested variables that influence intracellular enzyme activity for biotransformation of DL-ATC to L-cysteine. In order to investigate the quantitative effects for four variables selected from Plackett-Burman design on enzyme activity, a central composite design was subsequently employed for further optimization. The determination coefficient (R^2 was 0.9817, and the results show that the regression models adequately explain the data variation and represent the actual relationships between the parameters and responses. The optimal medium for Pseudomonas sp. Zjwp-14 was composed of (in g/L: glycerol 16.94, DL-ATC 4.59, yeast extract 6.99, NaCl 5.0, peptone 5.0, beef extract 5.0, MgSO4·7H2O 0.4, and pH=7.94. Under the optimal conditions, the maximum intracellular enzyme activity of 918.7 U/mL in theory and 903.6 U/mL in the experiment were obtained, with an increase of 15.6 % compared to the original medium components. In a 5-litre fermentor, cultivation time for Pseudomonas sp. Zjwp-14 was cut down for 6 h and the maximum enzyme activity reached 929.6 U/mL.

  6. Genetic responses induced in olive roots upon colonization by the biocontrol endophytic bacterium Pseudomonas fluorescens PICF7.

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    Elisabetta Schilirò

    Full Text Available Knowledge on the genetic basis underlying interactions between beneficial bacteria and woody plants is still very limited, and totally absent in the case of olive. We aimed to elucidate genetic responses taking place during the colonization of olive roots by the native endophyte Pseudomonas fluorescens PICF7, an effective biocontrol agent against Verticillium wilt of olive. Roots of olive plants grown under non-gnotobiotic conditions were collected at different time points after PICF7 inoculation. A Suppression Subtractive Hybridization cDNA library enriched in induced genes was generated. Quantitative real time PCR (qRT-PCR analysis validated the induction of selected olive genes. Computational analysis of 445 olive ESTs showed that plant defence and response to different stresses represented nearly 45% of genes induced in PICF7-colonized olive roots. Moreover, quantitative real-time PCR (qRT-PCR analysis confirmed induction of lipoxygenase, phenylpropanoid, terpenoids and plant hormones biosynthesis transcripts. Different classes of transcription factors (i.e., bHLH, WRKYs, GRAS1 were also induced. This work highlights for the first time the ability of an endophytic Pseudomonas spp. strain to mount a wide array of defence responses in an economically-relevant woody crop such as olive, helping to explain its biocontrol activity.

  7. Selection of a new Pseudomonas chlororaphis strain for the biological control of Fusarium oxysporum f. sp. radicis-lycopersici

    Directory of Open Access Journals (Sweden)

    Gerardo PUOPOLO

    2011-09-01

    Full Text Available Fluorescent pseudomonads possess several physiological characteristics exploitable for the biological control of phytopathogenic fungi. A group of 11 pseudomonads able to inhibit tomato pathogenic fungi in vitro were identified using the Biolog test and the phylogenetic analysis of recA. Strain M71 of Pseudomonas chlororaphis was selected as a new potential biocontrol agent. This strain drastically reduced Fusarium oxysporum f. sp. radicis-lycopersici pathogenicity on tomato plantlets in seed assays and greenhouse trials. Moreover, the strain produced several important secondary metabolites, including proteases, siderophores and antibiotics. The presence of a region involved in phenazine production and the biosynthesis of N-acyl homoserine lactones were also assessed.

  8. Pyrroloquinoline Quinone-Dependent Cytochrome Reduction in Polyvinyl Alcohol-Degrading Pseudomonas sp. Strain VM15C

    OpenAIRE

    Shimao, Masayuki; Onishi, Syuji; Kato, Nobuo; Sakazawa, Chikahiro

    1989-01-01

    A polyvinyl alcohol (PVA) oxidase-deficient mutant of Pseudomonas sp. strain VM15C, strain ND1, was shown to possess PVA dehydrogenase, in which pyrroloquinoline quinone (PQQ) functions as a coenzyme. The mutant grew on PVA and required PQQ for utilization of PVA as an essential growth factor. Incubation of the membrane fraction of the mutant with PVA caused cytochrome reduction of the fraction. Furthermore, it was found that in spite of the presence of PVA oxidase, the membrane fraction of s...

  9. 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)).

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

    Science.gov (United States)

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

    2012-04-01

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

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

    Science.gov (United States)

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

    2013-09-01

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

  12. 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 ).

  13. 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.

  14. 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).

  15. 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.

  16. 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)).

  17. ‘Cand. Actinochlamydia clariae’ gen. nov., sp. nov., a Unique Intracellular Bacterium Causing Epitheliocystis in Catfish (Clarias gariepinus) in Uganda

    Science.gov (United States)

    Steigen, Andreas; Nylund, Are; Karlsbakk, Egil; Akoll, Peter; Fiksdal, Ingrid U.; Nylund, Stian; Odong, Robinson; Plarre, Heidrun; Semyalo, Ronald; Skår, Cecilie; Watanabe, Kuninori

    2013-01-01

    Background and Objectives Epitheliocystis, caused by bacteria infecting gill epithelial cells in fish, is common among a large range of fish species in both fresh- and seawater. The aquaculture industry considers epitheliocystis an important problem. It affects the welfare of the fish and the resulting gill disease may lead to mortalities. In a culture facility in Kampala, Uganda, juveniles of the African sharptooth catfish (Clarias gariepinus) was observed swimming in the surface, sometimes belly up, showing signs of respiratory problems. Histological examination of gill tissues from this fish revealed large amounts of epitheliocysts, and also presence of a few Ichthyobodo sp. and Trichodina sp. Methods and Results Sequencing of the epitheliocystis bacterium 16S rRNA gene shows 86.3% similarity with Candidatus Piscichlamydia salmonis causing epitheliocystis in Atlantic salmon (Salmo salar). Transmission electron microscopy showed that the morphology of the developmental stages of the bacterium is similar to that of members of the family Chlamydiaceae. The similarity of the bacterium rRNA gene sequences compared with other chlamydia-like bacteria ranged between 80.5% and 86.3%. Inclusions containing this new bacterium have tubules/channels (termed actinae) that are radiating from the inclusion membrane and opening on the cell surface or in neighbouring cells. Conclusions Radiation of tubules/channels (actinae) from the inclusion membrane has never been described in any of the other members of Chlamydiales. It seems to be a completely new character and an apomorphy. We propose the name Candidatus Actinochlamydia clariae gen. nov., sp. nov. (Actinochlamydiaceae fam. nov., order Chlamydiales, phylum Chlamydiae) for this new agent causing epitheliocystis in African sharptooth catfish. PMID:23826156

  18. Purification and Characterization of Allophanate Hydrolase (AtzF) from Pseudomonas sp. Strain ADP

    Science.gov (United States)

    Shapir, Nir; Sadowsky, Michael J.; Wackett, Lawrence P.

    2005-01-01

    AtzF, allophanate hydrolase, is a recently discovered member of the amidase signature family that catalyzes the terminal reaction during metabolism of s-triazine ring compounds by bacteria. In the present study, the atzF gene from Pseudomonas sp. strain ADP was cloned and expressed as a His-tagged protein, and the protein was purified and characterized. AtzF had a deduced subunit molecular mass of 66,223, based on the gene sequence, and an estimated holoenzyme molecular mass of 260,000. The active protein did not contain detectable metals or organic cofactors. Purified AtzF hydrolyzed allophanate with a kcat/Km of 1.1 × 104 s−1 M−1, and 2 mol of ammonia was released per mol allophanate. The substrate range of AtzF was very narrow. Urea, biuret, hydroxyurea, methylcarbamate, and other structurally analogous compounds were not substrates for AtzF. Only malonamate, which strongly inhibited allophanate hydrolysis, was an alternative substrate, with a greatly reduced kcat/Km of 21 s−1 M−1. Data suggested that the AtzF catalytic cycle proceeds through a covalent substrate-enzyme intermediate. AtzF reacts with malonamate and hydroxylamine to generate malonohydroxamate, potentially derived from hydroxylamine capture of an enzyme-tethered acyl group. Three putative catalytically important residues, one lysine and two serines, were altered by site-directed mutagenesis, each with complete loss of enzyme activity. The identity of a putative serine nucleophile was probed using phenyl phosphorodiamidate that was shown to be a time-dependent inhibitor of AtzF. Inhibition was due to phosphoroamidation of Ser189 as shown by liquid chromatography/matrix-assisted laser desorption ionization mass spectrometry. The modified residue corresponds in sequence alignments to the nucleophilic serine previously identified in other members of the amidase signature family. Thus, AtzF affects the cleavage of three carbon-to-nitrogen bonds via a mechanism similar to that of enzymes

  19. Analysis of the phylogenetic relationships of strains of Burkholderia solanacearum, Pseudomonas syzygii, and the blood disease bacterium of banana based on 16S rRNA gene sequences.

    Science.gov (United States)

    Taghavi, M; Hayward, C; Sly, L I; Fegan, M

    1996-01-01

    We determined nearly complete 16S rRNA gene sequences for 19 isolates of Burkholderia solanacearum, three isolates of the blood disease bacterium of bananas, and two isolates of Pseudomonas syzygii, the cause of Sumatra disease of cloves. The dendrogram produced by comparing all of these sequences revealed that there were two divisions, which corresponded to the results obtained previously in a restriction fragment length polymorphism analysis (D. Cook, E. Barlow, and L. Sequeira, Mol. Plant Microbe Interact. 2:113-121, 1989) and a total 16S ribosomal DNA (rDNA) sequence analysis of four isolates representing four biovars of B. solanacearum (X. Li, M. Dorsch, T. Del Dot, L. I. Sly, E. Stackebrandt, and A. C. Hayward, J. Appl. Bacteriol. 74:324-329, 1993). Division 1 comprised biovars 3, 4, and 5 and an aberrant biovar 2 isolate (strain ACH0732), and division 2 included biovars 1, 2, and N2, the blood disease bacterium, and P. syzygii. Specific nucleotides at positions 458 to 460 (UUC) and 474 (A) characterized division 2, whereas in division 1 the nucleotides at these positions were ACU and U, respectively. However, strain ACH0732 had a U at position 458, as did division 2 isolates, and G instead of U at position 474. Division 2 consisted of two subdivisions; one subdivision contained two B. solanacearum isolates that originated from Indonesia, P. syzygii strains, and blood disease bacterium strains, and the other subdivision contained all of the other division 2 isolates. Within division 1, the level of 16S rDNA sequence similarity ranged from 99.8 to 100%, and within division 2, the levels of 16S rDNA sequence similarity ranged from 99.1 to 100%. The division 1 isolates exhibited an average level of 16S rDNA sequence similarity to division 2 isolates of 99.3% (range, 99.1 to 99.5%). The occurrence of consistent polymorphisms in the 16S rDNA sequences of B. solanacearum strains, in particular unique 16S rDNA sequence differences in aberrant biovar 2 isolate ACH

  20. Chemical Structure of the Lipid A component of Pseudomonas sp. strain PAMC 28618 from Thawing Permafrost in Relation to Pathogenicity.

    Science.gov (United States)

    Park, Han-Gyu; Sathiyanarayanan, Ganesan; Hwang, Cheol-Hwan; Ann, Da-Hee; Kim, Jung-Ho; Bang, Geul; Jang, Kyoung-Soon; Ryu, Hee Wook; Lee, Yoo Kyung; Yang, Yung-Hun; Kim, Yun-Gon

    2017-05-19

    Climate change causes permafrost thawing, and we are confronted with the unpredictable risk of newly discovered permafrost microbes that have disease-causing capabilities. Here, we first characterized the detailed chemical structure of the lipid A moiety from a Pseudomonas species that was isolated from thawing arctic permafrost using MALDI-based mass spectrometric approaches (i.e., MALDI-TOF MS and MALDI-QIT-TOF MS n ). The MALDI multi-stage mass spectrometry (MS) analysis of lipid A extracted from the Pseudomonas sp. strain PAMC 28618 demonstrated that the hexaacyl lipid A ([M-H] - at m/z 1616.5) contains a glucosamine (GlcN) disaccharide backbone, two phosphates, four main acyl chains and two branched acyl chains. Moreover, the lipid A molecule-based structural activity relationship with other terrestrial Gram-negative bacteria indicated that strain PAMC 28618 has an identical lipid A structure with the mesophilic Pseudomonas cichorii which can cause rot disease in endive (Cichorium endivia) and that their bacterial toxicities were equivalent. Therefore, the overall lipid A validation process provides a general strategy for characterizing bacteria that have been isolated from arctic permafrost and analyzing their respective pathogenicities.

  1. Molecular characterization of genes of Pseudomonas sp. strain HR199 involved in bioconversion of vanillin to protocatechuate.

    Science.gov (United States)

    Priefert, H; Rabenhorst, J; Steinbüchel, A

    1997-01-01

    The gene loci vdh, vanA, and vanB, which are involved in the bioconversion of vanillin to protocatechuate by Pseudomonas sp. strain HR199 (DSM 7063), were identified as the structural genes of a novel vanillin dehydrogenase (vdh) and the two subunits of a vanillate demethylase (vanA and vanB), respectively. These genes were localized on an EcoRI fragment (E230), which was cloned from a Pseudomonas sp. strain HR199 genomic library in the cosmid pVK100. The vdh gene was identified on a subfragment (HE35) of E230, and the vanA and vanB genes were localized on a different subfragment (H110) of E230. The nucleotide sequences of fragment HE35 and part of fragment H110 were determined, revealing open reading frames of 1062, 951, and 1446 bp, representing vanA, vanB, and vdh, respectively. The vdh gene was organized in one operon together with a fourth open reading frame (ORF2), of 735 bp, which was located upstream of vdh. The deduced amino acid sequences of vanA and vanB exhibited 78.8 and 62.1% amino acid identity, respectively, to the corresponding gene products from Pseudomonas sp. strain ATCC 19151 (F. Brunel and J. Davison, J. Bacteriol. 170:4924-4930, 1988). The deduced amino acid sequence of the vdh gene exhibited up to 35.3% amino acid identity to aldehyde dehydrogenases from different sources. The deduced amino acid sequence of ORF2 exhibited up to 28.4% amino acid identity to those of enoyl coenzyme A hydratases. Escherichia coli strains harboring fragment E230 cloned in pBluescript SK- converted vanillin to protocatechuate via vanillate, indicating the functional expression of vdh, vanA, and vanB in E. coli. High expression of vdh in E. coli was achieved with HE35 cloned in pBluescript SK-. The resulting recombinant strains converted vanillin to vanillate at a rate of up to 0.3 micromol per min per ml of culture. Transfer of vanA, vanB, and vdh to Alcaligenes eutrophus and to different Pseudomonas strains, which were unable to utilize vanillin or vanillate as

  2. Molecular Cloning and Functional Expression of a Δ9- Fatty Acid Desaturase from an Antarctic Pseudomonas sp. A3

    Science.gov (United States)

    Garba, Lawal; Mohamad Ali, Mohd Shukuri; Oslan, Siti Nurbaya; Rahman, Raja Noor Zaliha Raja Abd

    2016-01-01

    Fatty acid desaturase enzymes play an essential role in the synthesis of unsaturated fatty acids. Pseudomonas sp. A3 was found to produce a large amount of palmitoleic and oleic acids after incubation at low temperatures. Using polymerase Chain Reaction (PCR), a novel Δ9- fatty acid desaturase gene was isolated, cloned, and successfully expressed in Escherichia coli. The gene was designated as PA3FAD9 and has an open reading frame of 1,185 bp which codes for 394 amino acids with a predicted molecular weight of 45 kDa. The activity of the gene product was confirmed via GCMS, which showed a functional putative Δ9-fatty acid desaturase capable of increasing the total amount of cellular unsaturated fatty acids of the E. coli cells expressing the gene. The results demonstrate that the cellular palmitoleic acids have increased two-fold upon expression at 15°C using only 0.1 mM IPTG. Therefore, PA3FAD9 from Pseudomonas sp.A3 codes for a Δ9-fatty acid desaturase-like protein which was actively expressed in E. coli. PMID:27494717

  3. Pesticide tolerant and phosphorus solubilizing Pseudomonas sp. strain SGRAJ09 isolated from pesticides treated Achillea clavennae rhizosphere soil.

    Science.gov (United States)

    Rajasankar, R; Manju Gayathry, G; Sathiavelu, A; Ramalingam, C; Saravanan, V S

    2013-05-01

    In this study, an attempt was made to identify an effective phosphate solubilizing bacteria from pesticide polluted field soil. Based on the formation of solubilization halo on Pikovskaya's agar, six isolates were selected and screened for pesticide tolerance and phosphate (P) solubilization ability through liquid assay. The results showed that only one strain (SGRAJ09) obtained from Achillea clavennae was found to tolerate maximum level of the pesticides tested and it was phylogenetically identified as Pseudomonas sp. It possessed a wide range of pesticide tolerance, ranging from 117 μg mL(-1) for alphamethrin to 2,600 μg mL(-1) for endosulfan. The available P concentrations increased with the maximum and double the maximum dose of monocrotophos and imidacloprid, respectively. On subjected to FT-IR and HPLC analysis, the presence of organic acids functional group in the culture broth and the production of gluconic acid as dominant acid aiding the P solubilization were identified. On comparison with control broth, monocrotophos and imidacloprid added culture broth showed quantitatively high organic acids production. In addition to gluconic acid production, citric and acetic acids were also observed in the pesticide amended broth. Furthermore, the Pseudomonas sp. strain SGRAJ09 possessed all the plant growth promoting traits tested. In presence of monocrotophos and imidacloprid, its plant growth promoting activities were lower than that of the pesticides unamended treatment.

  4. EVALUACIÓN DE LA RESISTENCIA DE UN AISLADO BACTERIANO NATIVO COMPATIBLE CON PSEUDOMONA SP. AL INSECTICIDA LORSBAN 4 EC

    Directory of Open Access Journals (Sweden)

    Adriana María Quinchía

    Full Text Available Se evaluó la resistencia de un aislado bacteriano compatible con Pseudomona sp. frente al insecticida Lorsban 4EC (ingrediente activo Chlorpyrifos a escala de laboratorio. El aislado bacteriano se obtuvo a partir de un suelo del Oriente Antioqueño sometido a la aplicación del insecticida para el cultivo de pastos. Al suelo se le analizaron los principales factores que afectan la movilidad y adsorción del insecticida en él, se obtuvieron como resultados un porcentaje alto de materia orgánica, elementos mayores y menores así como media a alta capacidad de intercambio catiónico, lo que facilita la adsorción del plaguicida en su fracción coloidal de la micela orgánica e inorgánica. La textura franco arenosa del suelo genera buena aireación, que favorece los procesos de volatilización y degradación del plaguicida. El aislado bacteriano se expuso a diferentes concentraciones del insecticida (480 ppm, 4.800 ppm, 24.000 ppm y 48.000 ppm, evaluando de esta manera el efecto del agente sobre la población bacteriana. Según los resultados de los ensayos, la bacteria nativa compatible con Pseudomona sp. es resistente al insecticida con las concentraciones estudiadas y puede poseer la capacidad de degradar el insecticida.

  5. Pseudomonas canadensis sp. nov., a biological control agent isolated from a field plot under long-term mineral fertilization.

    Science.gov (United States)

    Tambong, James T; Xu, Renlin; Bromfield, Eden S P

    2017-04-01

    The bacterial strain 2-92T, isolated from a field plot under long-term (>40 years) mineral fertilization, exhibited in vitro antagonistic properties against fungal pathogens. A polyphasic approach was undertaken to verify its taxonomic status. Strain 2-92T was Gram-reaction-negative, aerobic, non-spore-forming, motile by one or more flagella, and oxidase-, catalase- and urease-positive. The optimal growth temperature of strain 2-92T was 30 °C. 16S rRNA gene sequence analysis demonstrated that the strain is related to species of the genus Pseudomonas. Phylogenetic analysis of six housekeeping genes (dnaA, gyrB, recA, recF, rpoB and rpoD) revealed that strain 2-92T clustered as a distinct and well separated lineage with Pseudomonassimiae as the most closely related species. Polar lipid and fatty acid compositions corroborated the taxonomic position of strain 2-92T in the genus Pseudomonas. Phenotypic characteristics from carbon utilization tests could be used to differentiate strain 2-92T from closely related species of the genus Pseudomonas. DNA-DNA hybridization values (wet laboratory and genome-based) and average nucleotide identity data confirmed that this strain represents a novel species. On the basis of phenotypic and genotypic characteristics, it is concluded that this strain represents a separate novel species for which the name Pseudomonas canadensis sp. nov. is proposed, with type strain 2-92T (=LMG 28499T=DOAB 798T). The DNA G+C content is 60.30 mol%.

  6. The Sensor Kinase GacS Negatively Regulates Flagellar Formation and Motility in a Biocontrol Bacterium, Pseudomonas chlororaphis O6

    Directory of Open Access Journals (Sweden)

    Ji Soo Kim

    2014-06-01

    Full Text Available The GacS/GacA two component system regulates various traits related to the biocontrol potential of plant-associated pseudomonads. The role of the sensor kinase, GacS, differs between strains in regulation of motility. In this study, we determined how a gacS mutation changed cell morphology and motility in Pseudomonas chlororaphis O6. The gacS mutant cells were elongated in stationary-phase compared to the wild type and the complemented gacS mutant, but cells did not differ in length in logarithmic phase. The gacS mutant had a two-fold increase in the number of flagella compared with the wild type strain; flagella number was restored to that of the wild type in the complemented gacS mutant. The more highly flagellated gacS mutant cells had greater swimming motilities than that of the wild type strain. Enhanced flagella formation in the gacS mutant correlated with increased expression of three genes, fleQ, fliQ and flhF, involved in flagellar formation. Expression of these genes in the complemented gacS mutant was similar to that of the wild type. These findings show that this root-colonizing pseudomonad adjusts flagella formation and cell morphology in stationary-phase using GacS as a major regulator.

  7. Potential application of aerobic denitrifying bacterium Pseudomonas aeruginosa PCN-2 in nitrogen oxides (NOx) removal from flue gas.

    Science.gov (United States)

    Zheng, Maosheng; Li, Can; Liu, Shufeng; Gui, Mengyao; Ni, Jinren

    2016-11-15

    Conventional biological removal of nitrogen oxides (NOx) from flue gas has been severely restricted by the presence of oxygen. This paper presents an efficient alternative for NOx removal at varying oxygen levels using the newly isolated bacterial strain Pseudomonas aeruginosa PCN-2 which was capable of aerobic and anoxic denitrification. Interestingly, nitric oxide (NO), as the obligatory intermediate, was negligibly accumulated during nitrate and nitrite reduction. Moreover, normal nitrate reduction with decreasing NO accumulation was realized under O2 concentration ranging from 0 to 100%. Reverse transcription and real-time quantitative polymerase chain reaction (RT-qPCR) analysis revealed that high efficient NO removal was attributed to the coordinate regulation of gene expressions including napA (for periplasmic nitrate reductase), nirS (for cytochrome cd1 nitrite reductase) and cnorB (for NO reductase). Further batch experiments demonstrated the immobilized strain PCN-2 possessed high capability of removing NO and nitrogen dioxide (NO2) at O2 concentration of 0-10%. A biotrickling filter established with present strain achieved high NOx removal efficiencies of 91.94-96.74% at inlet NO concentration of 100-500ppm and O2 concentration of 0-10%, which implied promising potential applications in purifying NOx contaminated flue gas. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. 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 ).

  9. 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

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

    Science.gov (United States)

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

    2005-10-01

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

  11. Two Inducible Prophages of an Antarctic Pseudomonas sp. ANT_H14 Use the Same Capsid for Packaging Their Genomes – Characterization of a Novel Phage Helper-Satellite System

    Science.gov (United States)

    Dziewit, Lukasz; Radlinska, Monika

    2016-01-01

    Two novel prophages ФAH14a and ФAH14b of a psychrotolerant Antarctic bacterium Pseudomonas sp. ANT_H14 have been characterized. They were simultaneously induced with mitomycin C and packed into capsids of the same size and protein composition. The genome sequences of ФAH14a and ФAH14b have been determined. ФAH14b, the phage with a smaller genome (16,812 bp) seems to parasitize ФAH14a (55,060 bp) and utilizes its capsids, as only the latter encodes a complete set of structural proteins. Both viruses probably constitute a phage helper-satellite system, analogous to the P2-P4 duo. This study describes the architecture and function of the ФAH14a and ФAH14b genomes. Moreover, a functional analysis of a ФAH14a-encoded lytic enzyme and a DNA methyltransferase was performed. In silico analysis revealed the presence of the homologs of ФAH14a and ФAH14b in other Pseudomonas genomes, which may suggest that helper-satellite systems related to the one described in this work are common in pseudomonads. PMID:27387973

  12. The ppuI-rsaL-ppuR quorum-sensing system regulates cellular motility, pectate lyase activity, and virulence in potato opportunistic pathogen Pseudomonas sp. StFLB209.

    Science.gov (United States)

    Kato, Taro; Morohoshi, Tomohiro; Someya, Nobutaka; Ikeda, Tsukasa

    2015-01-01

    Pseudomonas sp. StFLB209 was isolated from potato leaf as an N-acylhomoserine lactone (AHL)-producing bacterium and showed a close phylogenetic relationship with P. cichorii, a known plant pathogen. Although there are no reports of potato disease caused by pseudomonads in Japan, StFLB209 was pathogenic to potato leaf. In this study, we reveal the complete genome sequence of StFLB209, and show that the strain possesses a ppuI-rsaL-ppuR quorum-sensing system, the sequence of which shares a high similarity with that of Pseudomonas putida. Disruption of ppuI results in a loss of AHL production as well as remarkable reduction in motility. StFLB209 possesses strong pectate lyase activity and causes maceration on potato tuber and leaf, which was slightly reduced in the ppuI mutant. These results suggest that the quorum-sensing system is well conserved between StFLB209 and P. putida and that the system is essential for motility, full pectate lyase activity, and virulence in StFLB209.

  13. Two Inducible Prophages of an Antarctic Pseudomonas sp. ANT_H14 Use the Same Capsid for Packaging Their Genomes - Characterization of a Novel Phage Helper-Satellite System.

    Directory of Open Access Journals (Sweden)

    Lukasz Dziewit

    Full Text Available Two novel prophages ФAH14a and ФAH14b of a psychrotolerant Antarctic bacterium Pseudomonas sp. ANT_H14 have been characterized. They were simultaneously induced with mitomycin C and packed into capsids of the same size and protein composition. The genome sequences of ФAH14a and ФAH14b have been determined. ФAH14b, the phage with a smaller genome (16,812 bp seems to parasitize ФAH14a (55,060 bp and utilizes its capsids, as only the latter encodes a complete set of structural proteins. Both viruses probably constitute a phage helper-satellite system, analogous to the P2-P4 duo. This study describes the architecture and function of the ФAH14a and ФAH14b genomes. Moreover, a functional analysis of a ФAH14a-encoded lytic enzyme and a DNA methyltransferase was performed. In silico analysis revealed the presence of the homologs of ФAH14a and ФAH14b in other Pseudomonas genomes, which may suggest that helper-satellite systems related to the one described in this work are common in pseudomonads.

  14. 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.

  15. 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.

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

    DEFF Research Database (Denmark)

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

    2004-01-01

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

  17. Genome Sequence of Pseudomonas sp. Strain Chol1, a Model Organism for the Degradation of Bile Salts and Other Steroid Compounds

    KAUST Repository

    Holert, Johannes

    2013-01-15

    Bacterial degradation of steroid compounds is of high ecological and biotechnological relevance. Pseudomonas sp. strain Chol1 is a model organism for studying the degradation of the steroid compound cholate. Its draft genome sequence is presented and reveals one gene cluster responsible for the metabolism of steroid compounds.

  18. Draft Genome Sequence of Pseudomonas i>sp. Strain In5 Isolated from a Greenlandic Disease Suppressive Soil with Potent Antimicrobial Activity

    DEFF Research Database (Denmark)

    Hennessy, Rosanna C.; Glaring, Mikkel Andreas; Frydenlund Michelsen, Charlotte

    2015-01-01

    Pseudomonas sp. In5 is an isolate of disease suppressive soil with potent activity against pathogens. Its antifungal activity has been linked to a gene cluster encoding nonribosomal peptide synthetases producing the peptides nunamycin and nunapeptin. The genome sequence will provide insight into ...

  19. Equilibrium, thermodynamic and kinetic studies on biosorption of Mn(II) from aqueous solution by Pseudomonas sp., Staphylococcus xylosus and Blakeslea trispora cells

    International Nuclear Information System (INIS)

    Gialamouidis, D.; Mitrakas, M.; Liakopoulou-Kyriakides, M.

    2010-01-01

    Biosorption of Mn(II) from aqueous solutions using Pseudomonas sp., Staphylococcus xylosus and Blakeslea trispora cells was investigated under various experimental conditions of pH, biomass concentration, contact time and temperature. The optimum pH value was determined to 6.0 and the optimum biomass concentration to 1.0 g L -1 for all types of cells. Mn(II) biosorption was found to fit better to the Langmuir model for Pseudomonas sp. and B. trispora and to Freundlich model for S. xylosus. Langmuir model gave maximum Mn(II) uptake capacity 109 mg g -1 for Pseudomonas sp. and much lower, 59 mg g -1 and 40 mg g -1 for S. xylosus and B. trispora, respectively. Pseudo-second-order kinetic model was also found to be in good agreement with the experimental results. Thermodynamic parameters of the adsorption confirmed the endothermic nature of sorption process with positive heat of enthalpy, accompanied by a positive value of entropy change. Interestingly, desorption experiments by treating biomass with 0.1 M HNO 3 solution resulted to more than 88% recovery of the adsorbed Mn(II) from Pseudomonas sp. and almost 95% and 99% from S. xylosus and B. trispora cells respectively, thus indicating that Mn(II) can be easily and quantitatively recovered from biomass.

  20. Metabolism of 2,2'-dihydroxybiphenyl by Pseudomonas sp. strain HBP1 : production and consumption of 2,2',3-trihydroxybiphenyl

    NARCIS (Netherlands)

    Kohler, Hans-Peter E.; Schmid, Andreas; Maarel, Marc van der

    Cells of Pseudomonas sp. strain HBP1 grown on 2-hydroxy- or 2,2'-dihydroxybiphenyl contain NADH-dependent monooxygenase activity that hydroxylates 2,2'-dihydroxybiphenyl. The product of this reaction was identified as 2,2',3-trihydroxybiphenyl by 1H nuclear magnetic resonance and mass spectrometry.

  1. Heterotrophic bacterium Pseudomonas saponiphila and sunlight as impact factors on organo-mineral colloids transformations in boreal humic waters

    Science.gov (United States)

    Oleinikova, Olga; Drozdova, Olga; Shirokova, Liudmila; Lapitskiy, Sergey; Bychkov, Andrew; Pokrovsky, Oleg

    2017-04-01

    Two of the main factors of carbon balance in high latitudes, known to govern the CO2 flux from the lakes and rivers to the atmosphere, are bacterial mineralization (respiration) of allochthonous dissolved organic matter (DOM) and photochemical degradation of DOM. Yet, in contrast to large numbers of experimental and field studies on these factors impact on the utilization of DOM of different origin, the fate of metals bound to colloids during bacterial processing of DOM and behavior of trace element (TE) during photodegradation of DOM remains poorly constrained. This is especially important in view of essentially organic and organo-mineral colloidal status of TE in most boreal waters. To answer this questions, a monoculture of Pseudomonas saponiphila from a boreal creek in NW Karelia (Russia) was separated and allowed to interact with boreal peat leachate in nutrient-free media. We quantified colloidal transformation of the peat leachate during 5-days activity of live bacteria using 3 kDa, 50 kDa Amicon® centrifugal filtration and 0.45 µm syringe filtration. The total net decrease of the concentration of Dissolved Organic Carbon (DOC) over 93 h of exposure was within 5% of the initial value for all fractions except low molecular weight one (bio-uptake or coagulation. Elements most affected by bacterial presence were Al, Mn, (Ni), Cu, Ga, REEs, Y, U which exhibited essentially the adsorption at the cell surface over first hrs of reaction, and Fe, Ti, (Zr), and Nb showing short-term adsorption and long-term assimilation. Towards a better understanding of concentration, size fractionation and speciation change of TE in boreal waters subjected to solar radiation, we conducted on-site photo-degradation experiments in stream and bog water from pristine zone of Northern Karelia (Russian subarctic). After 5 days of exposure, the DOM in stream photodegraded in a much smaller degree than that in the bog water with 25 and 60% removal of initial DOC, respectively. Specific

  2. Endophytic Bacterium Pseudomonas fluorescens RG11 May Transform Tryptophan to Melatonin and Promote Endogenous Melatonin Levels in the Roots of Four Grape Cultivars.

    Science.gov (United States)

    Ma, Yaner; Jiao, Jian; Fan, Xiucai; Sun, Haisheng; Zhang, Ying; Jiang, Jianfu; Liu, Chonghuai

    2016-01-01

    Endophytes have been verified to synthesize melatonin in vitro and promote abiotic stress-induced production of endogenous melatonin in grape ( Vitis vinifera L.) roots. This study aimed to further characterize the biotransformation of tryptophan to melatonin in the endophytic bacterium Pseudomonas fluorescens RG11 and to investigate its capacity for enhancing endogenous melatonin levels in the roots of different grape cultivars. Using ultra performance liquid chromatography-tandem mass spectrometry combined with 15N double-labeled L -tryptophan as the precursor for melatonin, we detected isotope-labeled 5-hydroxytryptophan, serotonin, N -acetylserotonin, and melatonin, but tryptamine was not detected during the in vitro incubation of P. fluorescens RG11. Furthermore, the production capacity of these four compounds peaked during the exponential growth phase. RG11 colonization increased the endogenous levels of 5-hydroxytryptophan, N -acetylserotonin, and melatonin, but reduced those of tryptamine and serotonin, in the roots of the Red Globe grape cultivar under salt stress conditions. Quantitative real-time PCR revealed that RG11 reduced the transcription of grapevine tryptophan decarboxylase and serotonin N -acetyltransferase genes when compared to the un-inoculated control. These results correlated with decreased reactive oxygen species bursts and cell damage, which were alleviated by RG11 colonization under salt stress conditions. Additionally, RG11 promoted plant growth and enhanced the levels of endogenous melatonin in different grape cultivars. Intraspecific variation in the levels of melatonin precursors was found among four grape cultivars, and the associated root crude extracts appeared to significantly induce RG11 melatonin biosynthesis in vitro . Overall, this study provides useful information that enhances the existing knowledge of a potential melatonin synthesis pathway in rhizobacteria, and it reveals plant-rhizobacterium interactions that affect

  3. Characterization of a Pseudomonas putida rough variant evolved in a mixed species biofilm with Acinetobacter sp. strain C6

    DEFF Research Database (Denmark)

    Hansen, Susse Kirkelund; Haagensen, Janus Anders Juul; Gjermansen, Morten

    2007-01-01

    Genetic differentiation by natural selection is readily observed among microbial populations, but a more comprehensive understanding of evolutionary forces, genetic causes, and resulting phenotypic advantages is not often sought. Recently, a surface population of Pseudomonas putida bacteria...... biosynthesis. Here we investigate further the biofilm physiology and the phenotypic characteristics of the selected P. putida rough colony variants. The coexistence of the P. putida population in a mixed-species biofilm with Acinetobacter sp. strain C6 is dependent on the benzoate excreted from Acinetobacter....... putida wild-type cells, which readily dispersed from the mixed-species biofilm in response to oxygen starvation, the rough variant cells displayed a nondispersal phenotype. However, in monospecies biofilms proliferating on benzoate, the rough variant (like the wild-type population) dispersed in response...

  4. 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.

  5. Cell surface hydrophobicity: a key component in the degradation of polyethylene succinate by Pseudomonas sp. AKS2.

    Science.gov (United States)

    Tribedi, P; Sil, A K

    2014-02-01

    Polyethylene succinate (PES) contains hydrolysable ester bonds that make it a potential substitute for polyethylene (PE) and polypropylene (PP). Towards bioremediation of PES, we have already reported that a new strain of Pseudomonas, Pseudomonas sp. AKS2, can efficiently degrade PES and hypothesized that cell surface hydrophobicity plays an important role in this degradation process. In this study, our efforts were targeted towards establishing a correlation between cell surface hydrophobicity and PES degradation. We have manipulated cell surface hydrophobicity of AKS2 by varying concentrations of glucose and ammonium sulphate in the growth medium and subsequently examined the extent of PES degradation. We observed an increase in PES degradation by AKS2 with an increase in cell surface hydrophobicity. The increased surface hydrophobicity caused an enhanced biofilm formation on PES surface that resulted in better polymer degradation. The current study establishes a direct correlation between cell surface hydrophobicity of an organism and its potential to degrade a nonpolar polymer like PES. Cell surface hydrophobicity manipulation can be used as an important strategy to increase bioremediation of nonpolar polymer like PES. © 2013 The Society for Applied Microbiology.

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

    Directory of Open Access Journals (Sweden)

    Amira M. Embaby

    2014-01-01

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

  7. 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.

  8. 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.

  9. 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

  10. 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

  11. Borneol Dehydrogenase from Pseudomonas sp. Strain TCU-HL1 Catalyzes the Oxidation of (+)-Borneol and Its Isomers to Camphor.

    Science.gov (United States)

    Tsang, Hoi-Lung; Huang, Jui-Lin; Lin, Yu-Hsuan; Huang, Kai-Fa; Lu, Pei-Luen; Lin, Guang-Huey; Khine, Aye Aye; Hu, Anren; Chen, Hao-Ping

    2016-11-01

    Most plant-produced monoterpenes can be degraded by soil microorganisms. Borneol is a plant terpene that is widely used in traditional Chinese medicine. Neither microbial borneol dehydrogenase (BDH) nor a microbial borneol degradation pathway has been reported previously. One borneol-degrading strain, Pseudomonas sp. strain TCU-HL1, was isolated by our group. Its genome was sequenced and annotated. The genome of TCU-HL1 consists of a 6.2-Mbp circular chromosome and one circular plasmid, pTHL1 (12.6 kbp). Our results suggest that borneol is first converted into camphor by BDH in TCU-HL1 and is further decomposed through a camphor degradation pathway. The recombinant BDH was produced in the form of inclusion bodies. The apparent K m values of refolded recombinant BDH for (+)-borneol and (-)-borneol were 0.20 ± 0.01 and 0.16 ± 0.01 mM, respectively, and the k cat values for (+)-borneol and (-)-borneol were 0.75 ± 0.01 and 0.53 ± 0.01 s -1 , respectively. Two plant BDH genes have been reported previously. The k cat and k cat /K m values of lavender BDH are about 1,800-fold and 500-fold lower, respectively, than those of TCU-HL1 BDH. The degradation of borneol in a soil microorganism through a camphor degradation pathway is reported in this study. We also report a microbial borneol dehydrogenase. The k cat and k cat /K m values of lavender BDH are about 1,800-fold and 500-fold lower, respectively, than those of TCU-HL1 BDH. The indigenous borneol- and camphor-degrading strain isolated, Pseudomonas sp. strain TCU-HL1, reminds us of the time 100 years ago when Taiwan was the major producer of natural camphor in the world. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  12. 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

  13. 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,

  14. Complete Nucleotide Sequence and Organization of the Atrazine Catabolic Plasmid pADP-1 from Pseudomonas sp. Strain ADP

    Science.gov (United States)

    Martinez, Betsy; Tomkins, Jeffrey; Wackett, Lawrence P.; Wing, Rod; Sadowsky, Michael J.

    2001-01-01

    The complete 108,845-nucleotide sequence of catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP was determined. Plasmid pADP-1 was previously shown to encode AtzA, AtzB, and AtzC, which catalyze the sequential hydrolytic removal of s-triazine ring substituents from the herbicide atrazine to yield cyanuric acid. Computational analyses indicated that pADP-1 encodes 104 putative open reading frames (ORFs), which are predicted to function in catabolism, transposition, and plasmid maintenance, transfer, and replication. Regions encoding transfer and replication functions of pADP-1 had 80 to 100% amino acid sequence identity to pR751, an IncPβ plasmid previously isolated from Enterobacter aerogenes. pADP-1 was shown to contain a functional mercury resistance operon with 99% identity to Tn5053. Complete copies of transposases with 99% amino acid sequence identity to TnpA from IS1071 and TnpA from Pseudomonas pseudoalcaligenes were identified and flank each of the atzA, atzB, and atzC genes, forming structures resembling nested catabolic transposons. Functional analyses identified three new catabolic genes, atzD, atzE, and atzF, which participate in atrazine catabolism. Crude extracts from Escherichia coli expressing AtzD hydrolyzed cyanuric acid to biuret. AtzD showed 58% amino acid sequence identity to TrzD, a cyanuric acid amidohydrolase, from Pseudomonas sp. strain NRRLB-12227. Two other genes encoding the further catabolism of cyanuric acid, atzE and atzF, reside in a contiguous cluster adjacent to a potential LysR-type transcriptional regulator. E. coli strains bearing atzE and atzF were shown to encode a biuret hydrolase and allophanate hydrolase, respectively. atzDEF are cotranscribed. AtzE and AtzF are members of a common amidase protein family. These data reveal the complete structure of a catabolic plasmid and show that the atrazine catabolic genes are dispersed on three disparate regions of the plasmid. These results begin to provide insight into how

  15. Pesquisa de Acinetobacter sp e Pseudomonas aeruginosa produtores de metalo-β-lactamase em hospital de emergência de Porto Alegre, Estado do Rio Grande do Sul, Brasil Investigation of metallo-β-lactamase-producing Acinetobacter sp and Pseudomonas aeruginosa at an emergency hospital in Porto Alegre, State of Rio Grande do Sul, Brazil

    Directory of Open Access Journals (Sweden)

    Vani Dos Santos Laranjeira

    2010-08-01

    Full Text Available INTRODUÇÃO: O aparecimento de Pseudomonas aeruginosa e Acinetobacter sp produtores de metalo-β-lactamases (MBLs é um desafio para os hospitais. MÉTODOS: Verificou-se a produção de MBL em cepas clínicas de Pseudomonas aeruginosa e Acinetobacter sp de um hospital de emergência de Porto Alegre pelo método de aproximação de disco e E-test MBL. Os genes bla foram pesquisados pela PCR. RESULTADOS: Duas cepas de Pseudomonas aeruginosa e oito Acinetobacter sp demonstraram fenótipo de MBLs. A amplificação do gene blaSPM-1 confirmou a enzima em P. aeruginosa.. CONCLUSÕES: Deve-se ter cautela ao avaliar testes fenotípicos utilizados na detecção rotineira de metalo-enzima.INTRODUCTION: The appearance of metallo-β-lactamase (MBL-producing Pseudomonas aeruginosa and Acinetobacter sp. is a challenge for hospitals. METHODS: The production of MBL in clinical isolates of Pseudomonas aeruginosa and Acinetobacter sp. From an emergency hospital in Porto Alegre was investigated using the disk approximation test and MBL E-test. The bla genes were determined using PCR. RESULTS: Two strains of Pseudomonas aeruginosa and eight of Acinetobacter sp were shown to be MBL phenotypes. Amplification of the blaSPM-1 gene confirmed the presence of the enzyme in P. aeruginosa. CONCLUSIONS: Caution is needed in evaluating phenotype tests used for routine detection of metallo-β-lactamases.

  16. Studies of antibacterial effects of synthesized silver nanoparticles using a novel thermotolerant Isoptericola variabilis sp. IRSH1 against Staphylococcus aureus and Pseudomonas aeruginosa

    Directory of Open Access Journals (Sweden)

    F. Hajmohammadi

    2017-08-01

    Full Text Available Background: Silver nanoparticles can consider as an alternative source for some antibiotic usages due to those effective antibacterial activity and eco-friendly characteristics. Objective: This in vitro study was done to evaluate the inhibitory effect of extracellular synthesized of silver nanoparticles using inexpensive cellulosic materials and supernatant culture of Isoptericola variabilis sp. IRSH1 against Staphylococcus aureus and Pseudomonas aeruginosa. Methods: Silver nanoparticles were produced by extracellular biosynthesis using supernatant culture of a novel thermotolerant Isoptericola variabilis sp.IRSH1 and characterized. The antibacterial activities of the synthesized silver nanoparticles were examined by the standard KirbyBauer disc diffusion method against Staphylococcus aureus and Pseudomonas aeruginosa on Muller-Hinton agar plates. Findings: The silver nanoparticles were produced with an average size of 77 nm and 0.29 polydispersity index (PDI. The inhibition zones of AgNPs (1000 µg/ml were 10 mm and 11 mm against Staphylococcus aureus and Pseudomonas aeruginosa respectively. Conclusion: The biosynthesized AgNPs has good antibacterial activity against Staphylococcus aureus and Pseudomonas aeruginosa. The results indicate Pseudomonas aeruginosa is more sensitive to silver nanoparticles.

  17. Isolation and evaluation of potent Pseudomonas species for bioremediation of phorate in amended soil.

    Science.gov (United States)

    Jariyal, Monu; Gupta, V K; Jindal, Vikas; Mandal, Kousik

    2015-12-01

    Use of phorate as a broad spectrum pesticide in agricultural crops is finding disfavor due to persistence of both the principal compound as well as its toxic residues in soil. Three phorate utilizing bacterial species (Pseudomonas sp. strain Imbl 4.3, Pseudomonas sp. strain Imbl 5.1, Pseudomonas sp. strain Imbl 5.2) were isolated from field soils. Comparative phorate degradation analysis of these species in liquid cultures identified Pseudomonas sp. strain Imbl 5.1 to cause complete metabolization of phorate during seven days as compared to the other two species in 13 days. In soils amended with phorate at different levels (100, 200, 300 mg kg(-1) soil), Pseudomonas sp. strain Imbl 5.1 resulted in active metabolization of phorate by between 94.66% and 95.62% establishing the same to be a potent bacterium for significantly relieving soil from phorate residues. Metabolization of phorate to these phorate residues did not follow the first order kinetics. This study proves that Pseudomonas sp. strain Imbl 5.1 has huge potential for active bioremediation of phorate both in liquid cultures and agricultural soils. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Lunatimonas lonarensis gen. nov., sp. nov., a haloalkaline bacterium of the family Cyclobacteriaceae with nitrate reducing activity

    Digital Repository Service at National Institute of Oceanography (India)

    Srinivas, T.N.R.; Aditya, S.; Bhumika, V.; AnilKumar, P.

    parsimony methods using the MEGA5 package [32] and the resultant tree topologies were evaluated based on 1000 resamplings. The bacterium was subjected to Matrix-assisted laser-desorption/ionization time- of flight (MALDI-TOF) assay (Bruker Daltonics.... Acknowledgements We thank Council of Scientific and Industrial Research (CSIR), Directors of IMTECH, Chandigarh and NIO, Goa and Department of Biotechnology, Government of India for financial assistance and encouragement. We would like to thank Mr. Deepak...

  19. Protection of Tomato Seedlings against Infection by Pseudomonas syringae pv. Tomato by Using the Plant Growth-Promoting Bacterium Azospirillum brasilense†

    Science.gov (United States)

    Bashan, Yoav; de-Bashan, Luz E.

    2002-01-01

    Pseudomonas syringae pv. tomato, the causal agent of bacterial speck of tomato, and the plant growth-promoting bacterium Azospirillum brasilense were inoculated onto tomato plants, either alone, as a mixed culture, or consecutively. The population dynamics in the rhizosphere and foliage, the development of bacterial speck disease, and their effects on plant growth were monitored. When inoculated onto separate plants, the A. brasilense population in the rhizosphere of tomato plants was 2 orders of magnitude greater than the population of P. syringae pv. tomato (107 versus 105 CFU/g [dry weight] of root). Under mist chamber conditions, the leaf population of P. syringae pv. tomato was 1 order of magnitude greater than that of A. brasilense (107 versus 106 CFU/g [dry weight] of leaf). Inoculation of seeds with a mixed culture of the two bacterial strains resulted in a reduction of the pathogen population in the rhizosphere, an increase in the A. brasilense population, the prevention of bacterial speck disease development, and improved plant growth. Inoculation of leaves with the mixed bacterial culture under mist conditions significantly reduced the P. syringae pv. tomato population and significantly decreased disease severity. Challenge with P. syringae pv. tomato after A. brasilense was established in the leaves further reduced both the population of P. syringae pv. tomato and disease severity and significantly enhanced plant development. Both bacteria maintained a large population in the rhizosphere for 45 days when each was inoculated separately onto tomato seeds (105 to 106 CFU/g [dry weight] of root). However, P. syringae pv. tomato did not survive in the rhizosphere in the presence of A. brasilense. Foliar inoculation of A. brasilense after P. syringae pv. tomato was established on the leaves did not alleviate bacterial speck disease, and A. brasilense did not survive well in the phyllosphere under these conditions, even in a mist chamber. Several applications

  20. Draft genome sequence of Agrobacterium sp. strain R89-1, a morphine alkaloid-biotransforming bacterium

    Czech Academy of Sciences Publication Activity Database

    Zahradník, Jiří; Kyslíková, Eva; Kyslík, Pavel

    2016-01-01

    Roč. 4, č. 2 (2016), e00196-16 ISSN 2169-8287 Institutional support: RVO:61388971 Keywords : Agrobacterium sp. strain R89-1 * codeine/morphine * phylogenetic lineage Subject RIV: EE - Microbiology, Virology

  1. Inoculation of hybrid poplar with the endophytic bacterium Enterobacter sp. 638 increases biomass but does not impact leaf level physiology

    Energy Technology Data Exchange (ETDEWEB)

    Rogers, A.; McDonald, K.; Muehlbauer, M. F.; Hoffman, A.; Koenig, K.; Newman, L.; Taghavi, S.; Van Der Lelie, D.

    2011-01-01

    Endophytic bacteria have been shown to provide several advantages to their host, including enhanced growth. Inoculating biofuel species with endophytic bacteria is therefore an attractive option to increase the productivity of biofuel feedstocks. Here, we investigated the effect of inoculating hard wood cuttings of Populus deltoides Bartr. x Populus. nigra L. clone OP367 with Enterobacter sp. 638. After 17 weeks, plants inoculated with Enterobacter sp. 638 had 55% greater total biomass than un-inoculated control plants. Study of gas exchange and fluorescence in developing and mature leaves over a diurnal cycle and over a 5 week measurement campaign revealed no effects of inoculation on photosynthesis, stomatal conductance, photosynthetic water use efficiency or the maximum and operating efficiency of photosystem II. However, plants inoculated with Enterobacter sp. 638 had a canopy that was 39% larger than control plants indicating that the enhanced growth was fueled by increased leaf area, not by improved physiology. Leaf nitrogen content was determined at two stages over the 5 week measurement period. No effect of Enterobacter sp. 638 on leaf nitrogen content was found indicating that the larger plants were acquiring sufficient nitrogen. Enterobacter sp. 638 lacks the genes for N{sub 2} fixation, therefore the increased availability of nitrogen likely resulted from enhanced nitrogen acquisition by the 84% larger root system. These data show that Enterobacter sp. 638 has the potential to dramatically increase productivity in poplar. If fully realized in the production environment, these results indicate that an increase in the environmental and economic viability of poplar as a biofuel feedstock is possible when inoculated with endophytic bacteria like Enterobacter sp. 638.

  2. 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.

  3. 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.

  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. PENAPISAN LIMBAH PERTANIAN (SABUT KELAPA DAN ARANG SEKAM DALAM PENINGKATAN KETAHANAN BIBIT PISANG BARANGAN BERMIKORIZA TERHADAP BLOOD DISEASE BACTERIUM DAN FUSARIUM OXYSPORUM F.SP. CUBENSE

    Directory of Open Access Journals (Sweden)

    Suswati .

    2015-03-01

    Full Text Available Agricultural waste screening (coconut fibre and chaff charcoal in improving the resistance of Mychorrizae Barangan seedling to Blood diseases bacterium and Fusarium oxysporum f. sp. cubense. The application of soil and compost are very general in Barangan banana seedling. However, those media always contaminated by BDB and Foc propagul. This research was intended to examine the influence of planting media composition (soil, coconut fibre and chuff charcoal in improving the resistance of Mychorrizae Barangan banana seedling to blood diseases bacterium dan Fusarium oxysporum f sp.cubense. Some experiments conducted in wirehouse using a randomized complete block design application of two subtracts for soil substitution included to either coconut fibre (A or chuff charcoal (B (v:v completed by 6 treatments of each: A0 = 100% soil media, A1 = 50% soil + 50% chuff charcoal, A2 = 50% soil + 25% chuff charcoal + 25% sand, A3 = 25% soil + 50% chuff charcoal + 25% sand; A4 = 75% chuff charcoal + 25% sand, A5 = 100% chuff charcoal, B0 = 100% soil, B1 = 50% soil + 50 % chuff charcoal; B2 = 50% soil + 25 % coconut fiber + 25% sand, B3 = 25% soil +50% coconut fiber +25% sand; B4 = 75% coconut fiber + 25% sand, B5 = 100% coconut fiber. The soil generated from banana seedling area of Sempakata village that seriously infected BDB and Foc. The observation variables encompassed percentage of disease attack, density of BDB and Foc. population, period of pathogen incubation and measurement of Barangan seed and AMF colonization resistance development. The results indicated the planting of Mychorrizae Barangan banana seeds applied diminishing soil media as much as 25–100% substituted by chuff charcoal or coconut fiber increased the seed resistance of BDB and Foc.

  6. Isolation of a novel Pseudomonas sp from soil that can efficiently degrade polyethylene succinate.

    Science.gov (United States)

    Tribedi, Prosun; Sarkar, Subhasis; Mukherjee, Koushik; Sil, Alok K

    2012-07-01

    Polyethylene succinate (PES) is a biodegradable synthetic polymer and therefore widely used as a base material in plastic industry to circumvent the environmental problems related with the non-biodegradability of other polymers like polyethylene. Till date only few organisms have been reported to have the ability to degrade PES. Therefore for better management of PES-related environmental waste, the present study is targeted towards isolating mesophilic organism(s) capable of more efficient degradation of PES. Strain AKS2 was isolated from soil based on survival on a selection plate wherein PES was used as sole carbon source. Ribotyping and biochemical tests revealed that AKS2 is a new strain of Pseudomonas. Scanning electron and atomic force microscopic analysis of the PES films obtained after incubation with AKS2 confirmed PES-degradation ability of AKS2, wherein an alteration in surface topology was observed. The kinetics of PES weight loss showed that AKS2 degrades PES maximally during its logarithmic growth phase at a rate of 1.65 mg/day. This degradation is mediated by esterase activity and may also involve cell-surface hydrophobicity. It has also been observed that AKS2 is able to degrade PES considerably even in the presence of glucose, which is likely to increase the bioremediation potential of this isolate. A new strain of Pseudomonas has been isolated from soil that is able to adhere to PES and degrade this polymer efficiently. This organism has the potential to be implemented as a useful tool for bioremediation of PES-derived materials.

  7. 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.

  8. Characterization of a marine-isolated mercury-resistant Pseudomonas putida strain SP1 and its potential application in marine mercury reduction

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Weiwei; Chen, Lingxin; Liu, Dongyan [Chinese Academy of Sciences, Yantai, SD (China). Yantai Inst. of Coastal Zone Research (YICCAS); Chinese Academy of Sciences, Yantai, SD (China). Shandong Provincial Key Lab. of Coastal Zone Environmental Processes

    2012-02-15

    The Pseudomonas putida strain SP1 was isolated from marine environment and was found to be resistant to 280 {mu}M HgCl{sub 2}. SP1 was also highly resistant to other metals, including CdCl{sub 2}, CoCl{sub 2}, CrCl{sub 3}, CuCl{sub 2}, PbCl{sub 2}, and ZnSO{sub 4}, and the antibiotics ampicillin (Ap), kanamycin (Kn), chloramphenicol (Cm), and tetracycline (Tc). mer operon, possessed by most mercury-resistant bacteria, and other diverse types of resistant determinants were all located on the bacterial chromosome. Cold vapor atomic absorption spectrometry and a volatilization test indicated that the isolated P. putida SP1 was able to volatilize almost 100% of the total mercury it was exposed to and could potentially be used for bioremediation in marine environments. The optimal pH for the growth of P. putida SP1 in the presence of HgCl{sub 2} and the removal of HgCl{sub 2} by P. putida SP1 was between 8.0 and 9.0, whereas the optimal pH for the expression of merA, the mercuric reductase enzyme in mer operon that reduces reactive Hg{sup 2+} to volatile and relatively inert monoatomic Hg{sup 0} vapor, was around 5.0. LD50 of P. putida SP1 to flounder and turbot was 1.5 x 10{sup 9} CFU. Biofilm developed by P. putida SP1 was 1- to 3-fold lower than biofilm developed by an aquatic pathogen Pseudomonas fluorescens TSS. The results of this study indicate that P. putida SP1 is a low virulence strain that can potentially be applied in the bioremediation of HgCl{sub 2} contamination over a broad range of pH. (orig.)

  9. Biosynthesis of indigo dye by newly isolated naphthalene-degrading strain Pseudomonas sp. HOB1 and its application in dyeing cotton fabric.

    Science.gov (United States)

    Pathak, Hilor; Madamwar, Datta

    2010-03-01

    Indigo is one of the oldest dyes manufactured chemically and is mostly used in textile, food, and pharmaceutical industries. However, owing to the environmental hazards posed by the chemical production, the present scenario in the field stipulates a biosynthesis alternative for indigo production. The present study describes an indigenously isolated naphthalene-degrading strain Pseudomonas sp. HOB1 producing a blue pigment when indole was added in the growth medium. This blue pigment was analyzed by high-pressure thin-layer chromatography and other spectroscopic techniques which revealed it to be the indigo dye. Pseudomonas sp. HOB1 showed ability to produce 246 mg indigo liter(-1) of the medium. The K (m) for the enzyme naphthalene dioxygenase which is involved in indigo formation is 0.3 mM, and V (max) was as high as 50 nmol min(-1) mg dry biomass(-1). The bacterial indigo dye was further successfully applied for dyeing cotton fabrics. The high indigo productivity of Pseudomonas sp. HOB1 using naphthalene as growth substrate and its applicability on cotton fabrics, therefore, stems the probability of using this culture for commercial indigo production.

  10. Bioprospecting of marine Streptomycetes sp. for its antagonistic activity on MDR Pseudomonas aeruginosa and Acinetobacter baumannii isolates

    Directory of Open Access Journals (Sweden)

    Shanthi John

    2014-02-01

    Full Text Available Objective: To assess the antimicrobial activity of the Actinobacteria bioactive secondary metabolite and characterize the drug resistance mechanisms of Pseudomonas aeruginosa (P. aeruginosa and Acinetobacter baumannii (A. baumannii. Methods: Potential marine Actinobacteria were isolated and the crude extract was purified using thin layer chromatography, the fractions were tested for antimicrobial activity and phylogeny of the selected strain was analyzed. Isolated pathogenic strains were screened for extended spectrum beta-lactamase, mannan-binding lectin, AmpC production, efflux mechanism and polymerase chain reaction. The cephalosporin and carbapenem antibiotics were synergistically tested along with Streptomyces sp. PM49 fraction by combination disc test and double-disc synergy test. Heterogeneous susceptibility assay, minimum inhibitory concentration and expression of DnaK (Hsp70 were determined. Results: Streptomyces sp. PM49 active fraction of Rfvalue 0.69 showed antimicrobial activity and an inhibitory zone of 15 to 7 mm obtained. About 34.1% of P. aeruginosa and 4.8% of A. baumannii were multiple drug resistant. AmpC β-lactamase was found in 12% of A. baumannii, efflux mechanism was putatively positive in 8/23 of P. aeruginosa and 3/20 of A. baumannii. Combination disc test and double-disc synergy test with both PM49 compound and antibiotics showed an increase in the inhibitory zone of <3 mm to 4 mm, three P. aeruginosa isolates expressed blaIMP. Heteroresistant subcolonies grew at a frequency of 3 ×10-5 to 1 ×10-5. Stress induction analysis showed increase of DnaK during heat shock at 52 °C, the levels of protein doubled after exposure to the antibiotics. Conclusions: Novel unexplored Streptomyces spp. antimicrobial constituents can be developed as an inhibitor and can be substituted along with the available antibiotics to combat the drug resistant pathogens.

  11. Chlorpyrifos pollution: its effect on brain acetylcholinesterase activity in rat and treatment of polluted soil by indigenous Pseudomonas sp.

    Science.gov (United States)

    Sharma, Shelly; Singh, Partap Bir; Chadha, Pooja; Saini, Harvinder Singh

    2017-01-01

    The study was aimed to evaluate the levels of chlorpyrifos (CPF) pollution in agricultural soil of Punjab, India, its detrimental effects on acetylcholinesterase (AChE) activity in rat brain and bioremediation of soils polluted with CPF using indigenous and adapted bacterial lab isolate. The analysis revealed that soil samples of Bathinda and Amritsar regions are highly contaminated with chlorpyrifos showing 19 to 175 mg/kg concentrations of CPF. The non-targeted animals may get poisoned with CPF by its indirect dermal absorption, inhalation of toxic fumes and regular consumption of soiled food grains. The study indicated that even the lowermost concentrations of CPF, 19 and 76 mg/kg of soil found in the Amritsar and Bathinda regions respectively can significantly inhibit the AChE activity in rat brain within 24 h of its treatment. This represents the antagonistic effect of CPF on AChE which is a prime neurotransmitter present in all living beings including humans. In light of this, an attempt was made to remediate the polluted soil, a major reservoir of CPF, using Pseudomonas sp. (ChlD), an indigenous bacterial isolate. The culture efficiently degraded 10 to 100 mg/kg chlorpyrifos supplemented in the soil and utilized it as sole source of carbon and energy for its growth. Thus, this study provides a detailed insight regarding the level of CPF pollution in Punjab, its detrimental effects on mammals and bio-based solution to remediate the sites polluted with CPF.

  12. Gene Sequence and Properties of an s-Triazine Ring-Cleavage Enzyme from Pseudomonas sp. Strain NRRLB-12227

    Science.gov (United States)

    Karns, Jeffrey S.

    1999-01-01

    Pesticides based on the s-triazine ring structure are widely used in cultivation of food crops. Cleavage of the s-triazine ring is an important step in the mineralization of s-triazine compounds and hence in their complete removal from the environment. Cyanuric acid amidohydrolase cleaves cyanuric acid (2,4,6-trihydroxy-s-triazine), which yields carbon dioxide and biuret; the biuret is subject to further metabolism, which yields CO2 and ammonia. The trzD gene encoding cyanuric acid amidohydrolase was cloned into pMMB277 from Pseudomonas sp. strain NRRLB-12227, a strain that is capable of utilizing s-triazines as nitrogen sources. Hydrolysis of cyanuric acid was detected in crude extracts of Escherichia coli containing the cloned gene by monitoring the disappearance of cyanuric acid and the appearance of biuret by high-performance liquid chromatography (HPLC). DEAE and hydrophobic interaction HPLC were used to purify cyanuric acid amidohydrolase to homogeneity, and a spectrophotometric assay for the purified enzyme was developed. The purified enzyme had an apparent Km of 0.05 mM for cyanuric acid at pH 8.0. The enzyme did not cleave any other s-triazine or hydroxypyrimidine compound, although barbituric acid (2,4,6-trihydroxypyrimidine) was found to be a strong competitive inhibitor. Neither the nucleotide sequence of trzD nor the amino acid sequence of the gene product exhibited a significant level of similarity to any known gene or protein. PMID:10427042

  13. Polyhydroxyalkanoates from Pseudomonas sp. using synthetic and olive mill wastewater under limiting conditions.

    Science.gov (United States)

    Kourmentza, C; Ntaikou, I; Lyberatos, G; Kornaros, M

    2015-03-01

    The present study aimed at investigating the ability of bacteria isolated from an enriched mixed culture to produce polyhydroxyalkanoates (PHAs) and examining the effect of nitrogen and dual nitrogen-oxygen limitation on PHAs production, by using both synthetic and olive mill wastewater (OMW). PHAs production was performed through batch experiments using both the enriched culture and the isolated strains (belonging to the genus of Pseudomonas) aiming to compare PHAs accumulation capacity, yields and rates. The use of enriched culture and synthetic wastewater under nitrogen limitation resulted in the highest PHA accumulation, i.e. 64.4%gPHAs/g of cell dry mass (CDM). However, when OMW was used, PHAs accumulation significantly decreased, i.e. 8.8%gPHAs/g CDM. The same trend was followed by the isolated strains, nevertheless, their ability to synthesize PHAs was lower. Although, dual nitrogen-oxygen limitation generally slowed down PHAs biosynthesis, in certain strains PHAs production was positively affected. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. Structural characterization of pyoverdines produced by Pseudomonas putida KT2440 and Pseudomonas taiwanensis VLB120.

    Science.gov (United States)

    Baune, Matthias; Qi, Yulin; Scholz, Karen; Volmer, Dietrich A; Hayen, Heiko

    2017-08-01

    The previously unknown sequences of several pyoverdines (PVD) produced by a biotechnologically-relevant bacterium, namely, Pseudomonas taiwanensis VLB120, were characterized by high performance liquid chromatography (HPLC)-high resolution mass spectrometry (HRMS). The same structural characterization scheme was checked before by analysis of Pseudomonas sp. putida KT2440 samples with known PVDs. A new sample preparation strategy based on solid-phase extraction was developed, requiring significantly reduced sample material as compared to existing methods. Chromatographic separation was performed using hydrophilic interaction liquid chromatography with gradient elution. Interestingly, no signals for apoPVDs were detected in these analyses, only the corresponding aluminum(III) and iron(III) complexes were seen. The chromatographic separation readily enabled separation of PVD complexes according to their individual structures. HPLC-HRMS and complementary fragmentation data from collision-induced dissociation and electron capture dissociation enabled the structural characterization of the investigated pyoverdines. In Pseudomonas sp. putida KT2240 samples, the known pyoverdines G4R and G4R A were readily confirmed. No PVDs have been previously described for Pseudomonas sp. taiwanensis VLB120. In our study, we identified three new PVDs, which only differed in their acyl side chains (succinic acid, succinic amide and malic acid). Peptide sequencing by MS/MS provided the sequence Orn-Asp-OHAsn-Thr-AcOHOrn-Ser-cOHOrn. Of particular interest is the presence of OHAsn, which has not been reported as PVD constituent before.

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

    Science.gov (United States)

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

    2004-10-15

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

  16. 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.

  17. Flux coupling and transcriptional regulation within the metabolic network of the photosynthetic bacterium Synechocystis sp. PCC6803

    DEFF Research Database (Denmark)

    Montagud, Arnau; Zelezniak, Aleksej; Navarro, Emilio

    2011-01-01

    Synechocystis sp. PCC6803 is a model cyanobacterium capable of producing biofuels with CO2 as carbon source and with its metabolism fueled by light, for which it stands as a potential production platform of socio-economic importance. Compilation and characterization of Synechocystis genome...... networks, surrounded by a stable core of pathways leading to biomass building blocks. This analysis identified potential bottlenecks for hydrogen and ethanol production. Integration of transcriptomic data with the Synechocystis flux coupling networks lead to identification of reporter flux coupling pairs...... and reporter flux coupling groups - regulatory hot spots during metabolic shifts triggered by the availability of light. Overall, flux coupling analysis provided insight into the structural organization of Synechocystis sp. PCC6803 metabolic network toward designing of a photosynthesis-based production...

  18. A novel goose-type lysozyme gene with chitinolytic activity from the moderately thermophilic bacterium Ralstonia sp. A-471: cloning, sequencing, and expression.

    Science.gov (United States)

    Ueda, Mitsuhiro; Ohata, Konomi; Konishi, Toshiaki; Sutrisno, Aji; Okada, Hitomi; Nakazawa, Masami; Miyatake, Kazutaka

    2009-01-01

    In this study, we cloned the gene encoding goose-type (G-type) lysozyme with chitinase (Ra-ChiC) activity from Ralstonia sp. A-471 genomic DNA library. This is the first report of another type of chitinase after the previously reported chitinases ChiA (Ra-ChiA) and ChiB (Ra-ChiB) in the chitinase system of the moderately thermophilic bacterium, Ralstonia sp. A-471 and also the first such data in Ralstonia sp. G-type lysozyme gene. It consisted of 753 bp nucleotides, which encodes 251 amino acids including a putative signal peptide. This ORF was modular enzyme composed of a signal sequence, chitin-binding domain, linker, and catalytic domain. The catalytic domain of Ra-ChiC showed homologies to those of G-type lysozyme (glycoside hydrolases (GH) family 23, 16.8%) and lysozyme-like enzyme from Clostridium beijerincki (76.1%). Ra-ChiC had activities against ethylene glycol chitin, carboxyl methyl chitin, and soluble chitin but not against the cell wall of Micrococcus lysodeikticus. The enzyme produced alpha-anomer by hydrolyzing beta-1,4-glycosidic linkage of the substrate, indicating that the enzyme catalyzes the hydrolysis through an inverting mechanism. When N-acetylglucosamine hexasaccharide [(GlcNAc)6] was hydrolyzed by the enzyme, the second and third glycosidic linkage from the non-reducing end were split producing (GlcNAc)2 + (GlcNAc)4 and (GlcNAc)3 + (GlcNAc)3 of almost the same concentration in the early stage of the reaction. The G-type lysozyme hydrolyzed (GlcNAc)6 in an endo-splitting manner, which produced (GlcNAc)3 + (GlcNAc)3 predominating over that to (GlcNAc)2 + (GlcNAc)4. Thus, Ra-ChiC was found to be a novel enzyme in its structural and functional properties.

  19. D-xylose isomerase from a marine bacterium, Vibrio sp. strain XY-214, and D-xylulose production from β-1,3-xylan.

    Science.gov (United States)

    Umemoto, Yoshiaki; Shibata, Toshiyuki; Araki, Toshiyoshi

    2012-02-01

    The xylA gene from a marine bacterium, Vibrio sp. strain XY-214, encoding D-xylose isomerase (XylA) was cloned and expressed in Escherichia coli. The xylA gene consisted of 1,320-bp nucleotides encoding a protein of 439 amino acids with a predicted molecular weight of 49,264. XylA was classified into group II xylose isomerases. The native XylA was estimated to be a homotetramer with a molecular mass of 190 kDa. The purified recombinant XylA exhibited maximal activity at 60°C and pH 7.5. Its apparent K (m) values for D-xylose and D-glucose were 7.93 and 187 mM, respectively. Furthermore, we carried out D-xylulose production from β-1,3-xylan, a major cell wall polysaccharide component of the killer alga Caulerpa taxifolia. The synergistic action of β-1,3-xylanase (TxyA) and β-1,3-xylosidase (XloA) from Vibrio sp. strain XY-214 enabled efficient saccharification of β-1,3-xylan to D-xylose. D-xylose was then converted to D-xylulose by using XylA from the strain XY-214. The conversion rate of D-xylose to D-xylulose by XylA was found to be approximately 40% in the presence of 4 mM sodium tetraborate after 2 h of incubation. These results demonstrated that TxyA, XloA, and XylA from Vibrio sp. strain XY-214 are useful tools for D-xylulose production from β-1,3-xylan. Because D-xylulose can be used as a source for ethanol fermentation by yeast Saccharomyces cerevisiae, the present study will provide a basis for ethanol production from β-1,3-xylan.

  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. Enhanced toxicity of Bacillus thuringiensis subspecies kurstaki and aizawai to black cutworm larvae (Lepidoptera: Noctuidae) with Bacillus sp. NFD2 and Pseudomonas sp. FNFD1.

    Science.gov (United States)

    Mashtoly, Tamer A; Abolmaaty, Assem; El-Zemaity, Mohamed El-said; Hussien, Mohamed I; Alm, Steven R

    2011-02-01

    Bacillus thuringiensis subspecies kurstaki and aizawai are important control agents for lepidopteran pests. Bioassays were designed to test B. t. kurstaki and aizawai against second- and-fourth instar black cutworm larvae with and without Bacillus sp. NFD2 and Pseudomonas sp. FNFD1 bacteria. B. thuringiensis subsp. aizawai (XenTari) was more toxic to both second- and fourth-instar black cutworm, Agrotis ipsilon (Hufnagel) (Lepidoptera: Noctuidae), larvae than B. t. kurstaki (DiPel) at 7 d after treatment (DAT). When DiPel was combined with NFD2 or FNFD1 versus second instars, the LC50s were 5.0X and 4.7X lower, respectively, than with DiPel alone. DiPel combined with both NFD2 and FNFD1 versus second instars resulted in an LC50 value 7.7X lower than with DiPel alone. When XenTari was combined with NFD2 or FNFD1 versus second instars, the LC50s were 5.2X and 3.8X lower, respectively, than with XenTari alone. XenTari combined with both NFD2 and FNFD1 versus second instars resulted in an LC50 9.7X lower than with XenTari alone. When DiPel was combined with NFD2 or FNFD1 versus fourth instars, the LC50s were 4.4X and 3.4X lower, respectively, than with DiPel alone. DiPel combined with both NFD2 and FNFD1 versus fourth instars resulted in an LC50 5.0X lower than with DiPel alone. When XenTari was combined with NFD2 or FNFD1 versus fourth instars, the LC50s were 5.7X and 3.3X lower, respectively, than with XenTari alone. XenTari combined with both NFD2 and FNFD1 versus fourth instars resulted in an LC50 6.7X lower than with XenTari alone.

  2. Characterization and Genomic Analysis of a Highly Efficient Dibutyl Phthalate-Degrading Bacterium Gordonia sp. Strain QH-12

    Directory of Open Access Journals (Sweden)

    Decai Jin

    2016-06-01

    Full Text Available A bacterial strain QH-12 isolated from activated sludge was identified as Gordonia sp. based on analysis of 16S rRNA gene sequence and was found to be capable of utilizing dibutyl phthalate (DBP and other common phthalate esters (PAEs as the sole carbon and energy source. The degradation kinetics of DBP under different concentrations by the strain QH-12 fit well with the modified Gompertz model (R2 > 0.98. However, strain QH-12 could not utilize the major intermediate product phthalate (phthalic acid; PA as the sole carbon and energy source, and only a little amount of PA was detected. The QH-12 genome analysis revealed the presence of putative hydrolase/esterase genes involved in PAEs-degradation but no phthalic acid catabolic gene cluster was found, suggesting that a novel degradation pathway of PAEs was present in Gordonia sp. QH-12. This information will be valuable for obtaining a more holistic understanding on diverse genetic mechanisms of PAEs-degrading Gordonia sp. strains.

  3. Biosorption of Lead by Pseudomonas sp Isolated from Oil-Contaminated Wastewaters in Khuzestan

    Directory of Open Access Journals (Sweden)

    Seyed Mansour Meybodi

    2015-05-01

    Full Text Available Biosorption is a most effective technology for the removal of such toxic substances as heavy metals. The objective of this study was four-fold: 1 to isolate lead resistant Pseudomonas strains, 2 to determine the optimal conditions of their growth, 3 to obtain the minimum inhibitory concentration of lead, and 4 to evaluate the bioremoval of lead from culture solutions. For the purposes of this study, oil-contaminated wastewater samples were collected from Khuzestan region and transferred to laboratory where they were homogenized and serially diluted up to 10-10 with sterile saline before they were cultured in Luria Bertani agar medium containing 5ppm of lead nitrate. Resistant strains were then isolated at 37°C for 24h. The samples were subsequently cultured in Macconkey agar for isolation of appropriate gram negative strains. Biochemical tests were used to identify the bacteria, 10 strains of which were screened as lead resistant ones from all the 24 isolates. The bacterial colonies were selected and tested with different concentrations (100- 2100 ppm of lead for their resistance. The plates were then incubated at 37ºC for 24h and Mso1 was chosen from among the lead resistant colonies for further experiments. This strain showed resistance to chloramphenicol (30µg and erythromycin (15µg when subjected to the antimicrobial susceptibility test. Optimal growth conditions included a temperature of 40°C at 100 rpm and a pH level of 6 in the presence of lead by spectrophotometry at 600nm. Absorption tests showed that the Mso1 strain had a metal removal efficiency of 38.45% from an aqueous solution containing 100 ppm of lead over 24h. The results confirmed the capability of Pseudomonassp in the bioremediation of Pb-contaminated wastewaters.

  4. Ageloline A, new antioxidant and antichlamydial quinolone from the marine sponge-derived bacterium Streptomyces sp. SBT345

    OpenAIRE

    Cheng, Cheng; Othman, Eman M.; Reimer, Anastasija; Grüne, Matthias; Kozjak-Pavlovic, Vera; Stopper, Helga; Hentschel, Ute; Abdelmohsen, Usama R.

    2016-01-01

    A new chlorinated quinolone, ageloline A, was isolated from the broth culture of Streptomyces sp. SBT345 that was cultivated from the Mediterranean sponge Agelas oroides. The structure of this compound was determined by spectroscopic analysis including 1D and 2D NMR as well as HR-ESI-MS experiments. Ageloline A exhibited antioxidant potential using cell-free and cell-based assays and was further able to reduce oxidative stress and genomic damage induced by the oxidative stress inducer 4-nitro...

  5. Draft genome sequence of Halomonas sp. strain KM-1, a moderately halophilic bacterium that produces the bioplastic poly(3-hydroxybutyrate).

    Science.gov (United States)

    Kawata, Yoshikazu; Kawasaki, Kazunori; Shigeri, Yasushi

    2012-05-01

    We report the draft genome sequence of Halomonas sp. strain KM-1, which was isolated in Ikeda City, Osaka, Japan, and which produces the bioplastic poly(3-hydroxybutyrate). The total length of the assembled genome is 4,992,811 bp, and 4,220 coding sequences were predicted within the genome. Genes encoding proteins that are involved in the production and depolymerization of poly(3-hydroxybutyrate) were identified. The identification of these genes might be of use in the production of the bioplastic poly(3-hydroxybutyrate) and its monomer 3-hydroxybutyrate.

  6. 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)....

  7. 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

  8. Enzymatic characterization and gene identification of aconitate isomerase, an enzyme involved in assimilation of trans-aconitic acid, from Pseudomonas sp. WU-0701.

    Science.gov (United States)

    Yuhara, Kahori; Yonehara, Hiromi; Hattori, Takasumi; Kobayashi, Keiichi; Kirimura, Kohtaro

    2015-11-01

    trans-Aconitic acid is an unsaturated organic acid that is present in some plants such as soybean and wheat; however, it remains unclear how trans-aconitic acid is degraded and/or assimilated by living cells in nature. From soil, we isolated Pseudomonas sp. WU-0701 assimilating trans-aconitic acid as a sole carbon source. In the cell-free extract of Pseudomonas sp. WU-0701, aconitate isomerase (AI; EC 5.3.3.7) activity was detected. Therefore, it seems likely that strain Pseudomonas sp. WU-0701 converts trans-aconitic acid to cis-aconitic acid with AI, and assimilates this via the tricarboxylic acid cycle. For the characterization of AI from Pseudomonas sp. WU-0701, we performed purification, determination of enzymatic properties and gene identification of AI. The molecular mass of AI purified from cell-free extract was estimated to be ~ 25 kDa by both SDS/PAGE and gel filtration analyses, indicating that AI is a monomeric enzyme. The optimal pH and temperature of purified AI for the reaction were 6.0 °C and 37 °C, respectively. The gene ais encoding AI was cloned on the basis of the N-terminal amino acid sequence of the protein, and Southern blot analysis revealed that only one copy of ais is located on the bacterial genome. The gene ais contains an ORF of 786 bp, encoding a polypeptide of 262 amino acids, including the N-terminal 22 amino acids as a putative periplasm-targeting signal peptide. It is noteworthy that the amino acid sequence of AI shows 90% and 74% identity with molybdenum ABC transporter substrate-binding proteins of Pseudomonas psychrotolerans and Xanthomonas albilineans, respectively. This is the first report on purification to homogeneity, characterization and gene identification of AI. The nucleotide sequence of ais described in this article is available in the DDBJ/EMBL/GenBank nucleotide sequence databases under the Accession No. LC010980. © 2015 FEBS.

  9. 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.

  10. Identification of a 4-Deoxy-l-erythro-5-hexoseulose Uronic Acid Reductase, FlRed, in an Alginolytic Bacterium Flavobacterium sp. Strain UMI-01

    Directory of Open Access Journals (Sweden)

    Akira Inoue

    2015-01-01

    Full Text Available In alginate-assimilating bacteria, alginate is depolymerized to unsaturated monosaccharide by the actions of endolytic and exolytic alginate lyases (EC 4.2.2.3 and EC 4.2.2.11. The monosaccharide is non-enzymatically converted to 4-deoxy-l-ery thro-5-hexoseulose uronic acid (DEH, then reduced to 2-keto-3-deoxy-d-gluconate (KDG by a specific reductase, and metabolized through the Entner–Doudoroff pathway. Recently, the NADPH-dependent reductase A1-R that belongs to short-chain dehydrogenases/reductases (SDR superfamily was identified as the DEH-reductase in Sphingomonas sp. A1. We have subsequently noticed that an SDR-like enzyme gene, flred, occurred in the genome of an alginolytic bacterium Flavobacterium sp. strain UMI-01. In the present study, we report on the deduced amino-acid sequence of flred and DEH-reducing activity of recombinant FlRed. The deduced amino-acid sequence of flred comprised 254 residues and showed 34% amino-acid identities to that of A1-R from Sphingomonas sp. A1 and 80%–88% to those of SDR-like enzymes from several alginolytic bacteria. Common sequence motifs of SDR-superfamily enzymes, e.g., the catalytic tetrad Asn-Lys-Tyr-Ser and the cofactor-binding sequence Thr-Gly-x-x-x-Gly-x-Gly in Rossmann fold, were completely conserved in FlRed. On the other hand, an Arg residue that determined the NADPH-specificity of Sphingomonas A1-R was replaced by Glu in FlRed. Thus, we investigated cofactor-preference of FlRed using a recombinant enzyme. As a result, the recombinant FlRed (recFlRed was found to show high specificity to NADH. recFlRed exhibited practically no activity toward variety of aldehyde, ketone, keto ester, keto acid and aldose substrates except for DEH. On the basis of these results, we conclude that FlRed is the NADH-dependent DEH-specific SDR of Flavobacterium sp. strain UMI-01.

  11. Control of pore geometry in soil microcosms and its effect on the growth and spread of Pseudomonas and Bacillus sp.

    Science.gov (United States)

    Otten, Wilfred; Juyal, Archana; Eickhorst, Thilo; Falconer, Ruth; Spiers, Andrew; Baveye, Philippe

    2017-04-01

    The way micro-organisms access C and interact with each other in heterogeneous environments is key to our understanding of soil processes. Growth and mobility of bacteria is crucial aspect of these processes in particular how this is affected by complicated pathways of water and air-filled pores. Simplified experimental systems, often referred to with the term microcosms, have played a central role in the development of modern ecological thinking ranging from competitive exclusion to examination of spatial resources and competitive mechanisms, with important model driven insights to the field. However, in the majority of cases these do not include detailed description of the soil physical conditions and hence there is still little insight in how soil structure affects these processes. Recent advances in the use of Xray CT now allow for a different approach to this as we can obtain quantitative insight in to the pathways of interaction and how these are controlled in microcosms. In the current presentation we therefor ask the following questions: - To what extent can we control the pore geometry in microcosm studies through manipulation of common variables such as density and aggregate size? Are replicated microcosms really replicated at the microscale? - What is the effect of pore geometry on the growth dynamics of bacteria following introduction into soil? - What is the effect of pore geometry on the rate and extent of spread of bacteria in soil? We focus on Pseudomonas sp. and Bacillus sp. Both species are abundantly present in the rhizosphere and bulk-soil, frequently studied for their growth promoting ability, yet there is still very little knowledge available on how the growth and spread is affected by soil physical conditions such as pore geometry and wetness. We show how pore geometry, connectivity and interface areas are affected by the way soil is packed into microcosms and how this affects growth and spread of both species. We emphasize that microscopic

  12. Ligand complex structures of l-amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 and its conformational change.

    Science.gov (United States)

    Im, Dohyun; Matsui, Daisuke; Arakawa, Takatoshi; Isobe, Kimiyasu; Asano, Yasuhisa; Fushinobu, Shinya

    2018-03-01

    l-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 (l-AAO/MOG) catalyzes both the oxidative deamination and oxidative decarboxylation of the α-group of l-Lys to produce a keto acid and amide, respectively. l-AAO/MOG exhibits limited specificity for l-amino acid substrates with a basic side chain. We previously determined its ligand-free crystal structure and identified a key residue for maintaining the dual activities. Here, we determined the structures of l-AAO/MOG complexed with l-Lys, l-ornithine, and l-Arg and revealed its substrate recognition. Asp238 is located at the ceiling of a long hydrophobic pocket and forms a strong interaction with the terminal, positively charged group of the substrates. A mutational analysis on the D238A mutant indicated that the interaction is critical for substrate binding but not for catalytic control between the oxidase/monooxygenase activities. The catalytic activities of the D238E mutant unexpectedly increased, while the D238F mutant exhibited altered substrate specificity to long hydrophobic substrates. In the ligand-free structure, there are two channels connecting the active site and solvent, and a short region located at the dimer interface is disordered. In the l-Lys complex structure, a loop region is displaced to plug the channels. Moreover, the disordered region in the ligand-free structure forms a short helix in the substrate complex structures and creates the second binding site for the substrate. It is assumed that the amino acid substrate enters the active site of l-AAO/MOG through this route. The atomic coordinates and structure factors (codes 5YB6, 5YB7, and 5YB8) have been deposited in the Protein Data Bank (http://wwpdb.org/). 1.4.3.2 (l-amino acid oxidase), 1.13.12.2 (lysine 2-monooxygenase).

  13. 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...

  14. 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.

  15. Enhancement of DNaseI Salt Tolerance by Mimicking the Domain Structure of DNase from an Extremely Halotolerant Bacterium Thioalkalivibrio sp. K90mix.

    Directory of Open Access Journals (Sweden)

    Gediminas Alzbutas

    Full Text Available In our previous work we showed that DNaseI-like protein from an extremely halotolerant bacterium Thioalkalivibrio sp. K90mix retained its activity at salt concentrations as high as 4 M NaCl and the key factor allowing this was the C-terminal DNA-binding domain, which comprised two HhH (helix-hairpin-helix motifs. The further investigations revealed that this domain originated from proteins related to bacterial competence ComEA/ComE proteins. It is likely that in the course of evolution the DNA-binding domain from these proteins was fused to a metallo-β-lactamase superfamily domain. Very likely such domain organization having proteins subsequently "donated" the DNA-binding domain to bacterial DNases. In this study we have mimicked this evolutionary step by fusing bovine DNaseI and DNA-binding domains. We have created two fusions: one harboring the DNA-binding domain of DNaseI-like protein from Thioalkalivibrio sp. K90mix and the second one harboring the DNA-binding domain of bacterial competence protein ComEA from Bacillus subtilis. Both domains enhanced salt tolerance of DNaseI, albeit to different extent. Molecular modeling revealed the essential differences between their interaction with DNA shedding some light on the differences in salt tolerance. In this study we have enhanced salt tolerance of bovine DNaseI; thus, we successfully mimicked the Nature's evolutionary engineering that created the extremely halotolerant bacterial DNase. We have demonstrated that the newly engineered DNaseI variants can be successfully used in applications where activity of the wild type bovine DNaseI is impeded by buffers used.

  16. Enhancement of DNaseI Salt Tolerance by Mimicking the Domain Structure of DNase from an Extremely Halotolerant Bacterium Thioalkalivibrio sp. K90mix.

    Science.gov (United States)

    Alzbutas, Gediminas; Kaniusaite, Milda; Lagunavicius, Arunas

    2016-01-01

    In our previous work we showed that DNaseI-like protein from an extremely halotolerant bacterium Thioalkalivibrio sp. K90mix retained its activity at salt concentrations as high as 4 M NaCl and the key factor allowing this was the C-terminal DNA-binding domain, which comprised two HhH (helix-hairpin-helix) motifs. The further investigations revealed that this domain originated from proteins related to bacterial competence ComEA/ComE proteins. It is likely that in the course of evolution the DNA-binding domain from these proteins was fused to a metallo-β-lactamase superfamily domain. Very likely such domain organization having proteins subsequently "donated" the DNA-binding domain to bacterial DNases. In this study we have mimicked this evolutionary step by fusing bovine DNaseI and DNA-binding domains. We have created two fusions: one harboring the DNA-binding domain of DNaseI-like protein from Thioalkalivibrio sp. K90mix and the second one harboring the DNA-binding domain of bacterial competence protein ComEA from Bacillus subtilis. Both domains enhanced salt tolerance of DNaseI, albeit to different extent. Molecular modeling revealed the essential differences between their interaction with DNA shedding some light on the differences in salt tolerance. In this study we have enhanced salt tolerance of bovine DNaseI; thus, we successfully mimicked the Nature's evolutionary engineering that created the extremely halotolerant bacterial DNase. We have demonstrated that the newly engineered DNaseI variants can be successfully used in applications where activity of the wild type bovine DNaseI is impeded by buffers used.

  17. Pseudomonas silesiensis sp. nov. strain A3Tisolated from a biological pesticide sewage treatment plant and analysis of the complete genome sequence.

    Science.gov (United States)

    Kaminski, Michał A; Furmanczyk, Ewa M; Sobczak, Adam; Dziembowski, Andrzej; Lipinski, Leszek

    2018-01-01

    Microorganisms classified in to the Pseudomonas genus are a ubiquitous bacteria inhabiting variety of environmental niches and have been isolated from soil, sediment, water and different parts of higher organisms (plants and animals). Members of this genus are known for their metabolic versatility and are able to utilize different chemical compounds as a source of carbon, nitrogen or phosphorus, which makes them an interesting microorganism for bioremediation or bio-transformation. Moreover, Pseudomonas sp. has been described as a microorganism that can easily adapt to new environmental conditions due to its resistance to the presence of high concentrations of heavy metals or chemical pollution. Here we present the isolation and analysis of Pseudomonas silesiensis sp. nov. strain A3 T isolated from peaty soil used in a biological wastewater treatment plant exploited by a pesticide packaging company. Phylogenetic MLSA analysis of 4 housekeeping genes (16S rRNA, gyrB, rpoD and rpoB), complete genome sequence comparison (ANIb, Tetranucleotide identity, digital DDH), FAME analysis, and other biochemical tests indicate the A3 T strain (type strain PCM 2856 T =DSM 103370 T ) differs significantly from the closest relative species and therefore represents a new species within the Pseudomonas genus. Moreover, bioinformatic analysis of the complete sequenced genome showed that it consists of 6,823,539bp with a 59.58mol% G+C content and does not contain any additional plasmids. Genome annotation predicted the presence of 6066 genes, of which 5875 are coding proteins and 96 are RNA genes. Copyright © 2017 Elsevier GmbH. All rights reserved.

  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. Fourier transform infrared spectroscopic characterisation of heavy metal-induced metabolic changes in the plant-associated soil bacterium Azospirillum brasilense Sp7

    Science.gov (United States)

    Kamnev, A. A.; Antonyuk, L. P.; Tugarova, A. V.; Tarantilis, P. A.; Polissiou, M. G.; Gardiner, P. H. E.

    2002-06-01

    Structural and compositional features of whole cells of the plant-growth-promoting rhizobacterium Azospirillum brasilense Sp7 under standard and heavy metal-stressed conditions are analysed using Fourier transform infrared (FTIR) spectroscopy and compared with the FT-Raman spectroscopic data obtained previously [J. Mol. Struct. 563-564 (2001) 199]. The structural spectroscopic information is considered together with inductively coupled plasma-mass spectrometric (ICP-MS) analytical data on the content of the heavy metal cations (Co2+, Cu2+ and Zn2+) in the bacterial cells. As a bacterial response to heavy metal stress, all the three metals, being taken up by bacterial cells from the culture medium (0.2 mM) in significant amounts (ca. 0.12, 0.48 and 4.2 mg per gram of dry biomass for Co, Cu and Zn, respectively), are shown to induce essential metabolic changes in the bacterium revealed in the spectra, including the accumulation of polyester compounds in bacterial cells and their enhanced hydration affecting certain IR vibrational modes of functional groups involved.

  20. 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.

  1. Stopping AI-2 chatter by means of an indigenous bacterium ( Acinetobacter sp. DKY-1): A new anti-biofouling strategy in an MBR for wastewater treatment.

    Science.gov (United States)

    Lee, Kibaek; Kim, Yea-Won; Lee, Seonki; Lee, Sang Hyun; Nahm, Chang Hyun; Kwon, Hyeokpil; Park, Pyung-Kyu; Choo, Kwang-Ho; Koyuncu, Ismail; Drews, Anja; Lee, Chung-Hak; Lee, Jung-Kee

    2018-05-01

    Bacterial quorum quenching (QQ) by means of degrading signaling molecules has been applied to anti-biofouling strategy in a membrane bioreactor (MBR) for wastewater treatment. However, the target signaling molecules have been limited to N-acyl homoserine lactones participating in intra-species quorum sensing. Here, an approach to disrupt autoinducer-2 (AI-2) signaling molecules participating in inter-species quorum sensing, was pursued as a next-generation anti-biofouling strategy in an MBR for wastewater treatment. We isolated an indigenous QQ bacterium ( Acinetobacter sp. DKY-1) that can attenuate the expression of quorum sensing (QS) response through inactivation of autoinducer-2 signaling molecule, 4,5-dihydroxy-2,3-pentanedione (DPD) among four kinds of autoinducer-2 QS bacteria. DKY-1 released AI-2 QQ compound(s), which was verified to be hydrophilic with a molecular weight biofouling. This new approach, combining molecular biology with wastewater engineering, could enlarge the range of QQ-MBR for anti-biofouling and energy savings in the field of wastewater treatment.

  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. A novel marine bacterium Isoptericola sp. JS-C42 with the ability to saccharifying the plant biomasses for the aid in cellulosic ethanol production

    Directory of Open Access Journals (Sweden)

    Velayudhan Satheeja Santhi

    2014-06-01

    Full Text Available The ever growing demands for food products such as starch and sugar produces; there is a need to find the sources for saccharification for cellulosic bioethanol production. This study provides the first evidence of the lignocellulolytic and saccharifying ability of a marine bacterium namely Isoptericola sp. JS-C42, a Gram positive actinobacterium with the cocci cells embedded on mycelia isolated from the Arabian Sea, India. It exhibited highest filter paper unit effect, endoglucanase, exoglucanase, cellobiohydrolase, β-glucosidase, xylanase and ligninase effect. The hydrolytic potential of the enzymes displayed the efficient saccharification capability of steam pretreated biomass. It was also found to degrade the paddy, sorghum, Acacia mangium and Ficus religiosa into simple reducing sugars by its efficient lignocellulose enzyme complex with limited consumption of sugars. Production of ethanol was also achieved with the Saccharomyces cerevisiae. Overall, it offers a great potential for the cellulosic ethanol production in an economically reliable and eco-friendly point-of-care.

  4. 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)).

  5. Pilot-Scale Production and Thermostability Improvement of the M23 Protease Pseudoalterin from the Deep Sea Bacterium Pseudoalteromonas sp. CF6-2

    Directory of Open Access Journals (Sweden)

    Jie Yang

    2016-11-01

    Full Text Available Pseudoalterin is the most abundant protease secreted by the marine sedimental bacterium Pseudoalteromonas sp. CF6-2 and is a novel cold-adapted metalloprotease of the M23 family. Proteases of the M23 family have high activity towards peptidoglycan and elastin, suggesting their promising biomedical and biotechnological potentials. To lower the fermentive cost and improve the pseudoalterin production of CF6-2, we optimized the fermentation medium by using single factor experiments, added 0.5% sucrose as a carbon source, and lowered the usage of artery powder from 1.2% to 0.6%. In the optimized medium, pseudoalterin production reached 161.15 ± 3.08 U/mL, 61% greater than that before optimization. We further conducted a small-scale fermentation experiment in a 5-L fermenter and a pilot-scale fermentation experiment in a 50-L fermenter. Pseudoalterin production during pilot-scale fermentation reached 103.48 ± 8.64 U/mL, 77% greater than that before the medium was optimized. In addition, through single factor experiments and orthogonal tests, we developed a compound stabilizer for pseudoalterin, using medically safe sugars and polyols. This stabilizer showed a significant protective effect for pseudoalterin against enzymatic thermal denaturation. These results lay a solid foundation for the industrial production of pseudoalterin and the development of its biomedical and biotechnological potentials.

  6. Antimicrobial activity of PVP from an Antarctic bacterium, Janthinobacterium sp. Ant5-2, on multi-drug and methicillin resistant Staphylococcus aureus

    KAUST Repository

    Huang, Jonathan P.

    2012-04-11

    Multiple drug resistant (MDR) and methicillin-resistant Staphylococcus aureus (MRSA) have become increasingly prevalent as a community acquired infection. As a result limited treatment options are available with conventional synthetic antibiotics. Bioprospecting natural products with potent antimicrobial activity show promise for developing new drugs against this pathogen. In this study, we have investigated the antimicrobial activity of a purple violet pigment (PVP) from an Antarctic bacterium, Janthinobacterium sp. Ant5-2 on 15 clinical MDR and MRSA strains. The colorimetric resazurin assay was employed to determine the minimum inhibitory concentration (MIC90) of PVP against MDR and MRSA. The MIC90 ranged between 1.57 µg/mL and 3.13 µg/mL, which are significantly lower than many antimicrobials tested from natural sources against this pathogen. The spectrophotometrically determined growth analysis and total microscopic counts using Live/dead® BacLight™ fluorescent stain exhibited a steady decrease in viability of both MDR and MRSA cultures following treatment with PVP at the MIC levels. In silico predictive molecular docking study revealed that PVP could be a DNA-targeting minor groove binding antimicrobial compound. The continued development of novel antimicrobials derived from natural sources with the combination of a suite of conventional antibiotics could stem the rising pandemic of MDR and MRSA along with other deadly microbial pathogens.

  7. Oxidation of thiosulfate by a new bacterium, Bosea thiooxidans (strain BI-42) gen. nov., sp. nov.: analysis of phylogeny based on chemotaxonomy and 16S ribosomal DNA sequencing.

    Science.gov (United States)

    Das, S K; Mishra, A K; Tindall, B J; Rainey, F A; Stackebrandt, E

    1996-10-01

    A gram-negative bacterium which was capable of oxidizing reduced inorganic sulfur compounds was isolated from agricultural soil and designated BI-42. This new isolate grew on a wide range of organic substrates but was not able to grow autotrophically and lacked ribulose 1,5-bisphosphate carboxylase, a key enzyme of carbon dioxide fixation. These results suggested that strain BI-42 was a chemolithoheterotroph. Ammonia and nitrate were not used as sole nitrogen sources for growth, and strain BI-42 lacked glutamate synthase activity, which resulted in glutamate auxotrophy. The glutamate dehydrogenase activity of this organism was apparently insufficient for ammonia assimilation. On the basis of the results of additional biochemical tests, the G + C content of the DNA, the results of a respiratory ubiquinone analysis, the results of a 16S ribosomal DNA sequence analysis, the fatty acid composition, and the results of a membrane lipid analysis, strain BI-42 was identified as a phylogenetically and physiologically distinct taxon belonging to the alpha subclass of the Proteobacteria. Bosea thiooxidans gen. nov., sp. nov. is the name proposed for this taxon.

  8. 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.

  9. Methylomusa anaerophila gen. nov., sp. nov., an anaerobic methanol-utilizing bacterium isolated from a microbial fuel cell.

    Science.gov (United States)

    Amano, Nanako; Yamamuro, Ayaka; Miyahara, Morio; Kouzuma, Atsushi; Abe, Takashi; Watanabe, Kazuya

    2018-04-01

    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 ).

  10. 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)).

  11. 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.

  12. Identification and Characterization of a New Alkaline SGNH Hydrolase from a Thermophilic Bacterium Bacillus sp. K91.

    Science.gov (United States)

    Yu, Tingting; Ding, Junmei; Zheng, Qingxia; Han, Nanyu; Yu, Jialin; Yang, Yunjuan; Li, Junjun; Mu, Yuelin; Wu, Qian; Huang, Zunxi

    2016-04-28

    est19 is a gene from Bacillus sp. K91 that encodes a new esterase. A comparison of the amino acid sequence showed that Est19 has typical Ser-Gly-Asn-His (SGNH) family motifs and could be grouped into the SGNH hydrolase family. The Est19 protein was functionally cloned, and expressed and purified from Escherichia coli BL21(DE3). The enzyme activity was optimal at 60°C and pH 9.0, and displayed esterase activity towards esters with short-chain acyl esters (C₂-C₆). A structural model of Est19 was constructed using phospholipase A1 from Streptomyces albidoflavus NA297 as a template. The structure showed an α/β-hydrolase fold and indicated the presence of the typical catalytic triad Ser49-Asp227-His230, which were further investigated by site-directed mutagenesis. To the best of our knowledge, Est19 is a new member of the SGNH hydrolase family identified from thermophiles, which may be applicable in the industrial production of semisynthetic β-lactam antibiotics after modification.

  13. The role of exochitinase type A1 in the fungistatic activity of the rhizosphere bacterium Paenibacillus sp. M4

    Directory of Open Access Journals (Sweden)

    Jankiewicz Urszula

    2016-01-01

    Full Text Available The aim of the study was to detect the activity and characterize potentially fungistatic chitinases synthesized by rhizosphere bacteria identified as Paenibacillus sp. M4. Maximum chitinolytic activity was achieved on the fifth day of culturing bacteria in a growth medium with 1% colloidal chitin. Analysis of a zymogram uncovered the presence of four activity bands in the crude bacterial extract. The used three-stage protein purification procedure resulted in a single band of chitinase activity on the zymogram. The purified enzyme exhibited maximum activity at pH 6.5 and temperature 45oC, and thermal stability at 40oC for 4 h. In terms of substrate specificity, it is an exochitinase (chitobiose. The amino acid sequence obtained after mass spectrometry showed similarity to chitinase A1 synthesized by Bacillus circulans. The M4 isolate demonstrated the highest growth inhibiting activity against plant pathogens belonging to the genera Fusarium, Rhizoctonia and Alternaria. Fungistatic activity, although to a somewhat lesser degree, was also demonstrated by purified chitinase. The obtained results confirm the participation of the studied exochitinase in antagonism towards pathogenic molds. However, the lower fungistatic effectiveness of the chitinases points to the synergistic action of different metabolites in biocontrol by these bacteria.

  14. Pandoraea thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soils of sesame (Sesamum indicum L.).

    Science.gov (United States)

    Anandham, Rangasamy; Indiragandhi, Pandiyan; Kwon, Soon Wo; Sa, Tong Min; Jeon, Che Ok; Kim, Yong Ki; Jee, Hyeong Jin

    2010-01-01

    A facultatively chemolithoautotrophic, thiosulfate-oxidizing, Gram-negative, aerobic, motile, rod-shaped bacterial strain, designated ATSB16(T), was isolated from rhizosphere soils of sesame (Sesamum indicum L.). 16S rRNA gene sequence analysis demonstrated that this strain was closely related to Pandoraea pnomenusa LMG 18087(T) (96.7 % similarity), P. pulmonicola LMG 18016(T) (96.5 %), P. apista LMG 16407(T) (96.2 %), P. norimbergensis LMG 18379(T) (96.1 %) and P. sputorum LMG 18819(T) (96.0 %). Strain ATSB16(T) shared 96.0-96.4 % sequence similarity with four unnamed genomospecies of Pandoraea. The major cellular fatty acids of the strain ATSB16(T) were C(17 : 0) cyclo (33.0 %) and C(16 : 0) (30.6 %). Q-8 was the predominant respiratory quinone. The major polar lipids were phosphatidylmethylethanolamine, diphosphatidylglycerol, phosphatidylethanolamine and two unidentified aminophospholipids. Hydroxyputrescine and putrescine were the predominant polyamines. The genomic DNA G+C content of the strain was 64.0 mol%. On the basis of the results obtained from this study, strain ATSB16(T) represents a novel species of the genus Pandoraea, for which the name Pandoraea thiooxydans sp. nov. is proposed. The type strain is ATSB16(T) (=KACC 12757(T) =LMG 24779(T)).

  15. 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.

  16. Identification of the para-nitrophenol catabolic pathway, and characterization of three enzymes involved in the hydroquinone pathway, in pseudomonas sp. 1-7

    Directory of Open Access Journals (Sweden)

    Zhang Shuangyu

    2012-03-01

    Full Text Available Abstract Background para-Nitrophenol (PNP, a priority environmental pollutant, is hazardous to humans and animals. However, the information relating to the PNP degradation pathways and their enzymes remain limited. Results Pseudomonas sp.1-7 was isolated from methyl parathion (MP-polluted activated sludge and was shown to degrade PNP. Two different intermediates, hydroquinone (HQ and 4-nitrocatechol (4-NC were detected in the catabolism of PNP. This indicated that Pseudomonas sp.1-7 degraded PNP by two different pathways, namely the HQ pathway, and the hydroxyquinol (BT pathway (also referred to as the 4-NC pathway. A gene cluster (pdcEDGFCBA was identified in a 10.6 kb DNA fragment of a fosmid library, which cluster encoded the following enzymes involved in PNP degradation: PNP 4-monooxygenase (PdcA, p-benzoquinone (BQ reductase (PdcB, hydroxyquinol (BT 1,2-dioxygenase (PdcC, maleylacetate (MA reductase (PdcF, 4-hydroxymuconic semialdehyde (4-HS dehydrogenase (PdcG, and hydroquinone (HQ 1,2-dioxygenase (PdcDE. Four genes (pdcDEFG were expressed in E. coli and the purified pdcDE, pdcG and pdcF gene products were shown to convert HQ to 4-HS, 4-HS to MA and MA to β-ketoadipate respectively by in vitro activity assays. Conclusions The cloning, sequencing, and characterization of these genes along with the functional PNP degradation studies identified 4-NC, HQ, 4-HS, and MA as intermediates in the degradation pathway of PNP by Pseudomonas sp.1-7. This is the first conclusive report for both 4-NC and HQ- mediated degradation of PNP by one microorganism.

  17. Surface motility in Pseudomonas sp DSS73 is required for efficient biological containment of the root-pathogenic microfungi Rhizoctonia solani and Pythium ultimum

    DEFF Research Database (Denmark)

    Andersen, Jens Bo; Koch, Birgit; Nielsen, T.H.

    2003-01-01

    Pseudomonas sp. DSS73 was isolated from the rhizoplane of sugar beet seedlings. This strain exhibits antagonism towards the root-pathogenic microfungi Pythium ultimum and Rhizoctonia solani. Production of the cyclic lipopeptide amphisin in combination with expression of flagella enables the growi...... bacterial culture to move readily over the surface of laboratory media. Amphisin is a new member of a group of dual-functioning compounds such as tensin, viscosin and viscosinamid that display both biosurfactant and antifungal properties. The ability of DSS73 to efficiently contain root...

  18. 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)).

  19. 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).

  20. 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 ).

  1. 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.

  2. Bradyrhizobium namibiense sp. nov., a symbiotic nitrogen-fixing bacterium from root nodules of Lablab purpureus, hyacinth bean, in Namibia.

    Science.gov (United States)

    Grönemeyer, Jann Lasse; Bünger, Wiebke; Reinhold-Hurek, Barbara

    2017-10-16

    Four strains of symbiotic bacteria from root nodules of hyacinth bean (Lablab purpureus (L.) Sweet) from Namibia were previously identified as a novel group within the genus Bradyrhizobium. To confirm their taxonomic status, these strains were further characterized by taking a polyphasic approach. The type strain possessed 16S rRNA gene sequences identical to Bradyrhizobium paxllaeri LMTR 21 T and Bradyrhizobiumicense LMTR 13 T , the full-length sequences were identical to those retrieved from SAMN05230119 and SAMN05230120, respectively. However, the intergenic spacer sequences of the novel group showed identities of less than 93.1 % to described Bradyrhizobium species and were placed in a well-supported separate lineage in the phylogenetic tree. Phylogenetic analyses of six concatenated housekeeping genes, recA, glnII, gyrB, dnaK, atpD and rpoB, corroborated that the novel strains belonged to a lineage distinct from named species of the genus Bradyrhizobium, with highest sequence identities to Bradyrhizobiumjicamae and B. paxllaeri (below 93 %). The species status was validated by results of DNA-DNA hybridization and average nucleotide identity values of genome sequences. The combination of phenotypic characteristics from several tests, including carbon source utilization and antibiotic resistance, could be used to differentiate representative strains from recognized species of the genus Bradyrhizobium. Phylogenetic analysis of nodC and nifH genes placed the novel strains in a group with B. paxllaeri and B.lablabi. Novel strain 5-10 T induces effective nodules on Lablab purpureus, Vigna subterranea, Vigna unguiculata and Arachis hypogaea. Based on our results, we conclude that our strains represent a novel species for which the name Bradyrhizobium namibiense sp. nov. is proposed, with type strain 5-10 T [LMG 28789, DSM 100300, NTCCM0017 (Windhoek)].

  3. Bradyrhizobium kavangense sp. nov., a symbiotic nitrogen-fixing bacterium from root nodules of traditional Namibian pulses.

    Science.gov (United States)

    Lasse Grönemeyer, Jann; Hurek, T; Reinhold-Hurek, Barbara

    2015-12-01

    Eight strains of symbiotic bacteria from root nodules of local races of cowpea (Vigna unguiculata) and Bambara groundnut (Vigna subterranea) grown on subsistence farmers' fields in the Kavango region, Namibia, were previously characterized and identified as a novel group within the genus Bradyrhizobium. To clarify their taxonomic status, these strains were further characterized using a polyphasic approach. In phylogenetic analysis of the 16S rRNA gene sequence the novel group was most closely related to Bradyrhizobium iriomotense EK05T and Bradyrhizobium ingae BR 10250T, and to 'Bradyrhizobium arachidis' CCBAU 051107 in the ITS sequence analysis. Phylogenetic analysis of concatenated glnII-recA-rpoB-dnaK sequences placed the strains in a lineage distinct from named species of the genus Bradyrhizobium. The species status was validated by results of DNA-DNA hybridization. Phylogenetic analysis of nifH and nodC genes placed the novel strains in a group with 'B. arachidis' CCBAU 051107. The combination of phenotypic characteristics from several tests including carbon source utilization and antibiotic resistance could be used to differentiate representative strains from recognized species of the genus Bradyrhizobium. Novel strain 14-3T induces effective nodules on Vigna subterranea, Vigna unguiculata, Arachis hypogaea and Lablab purpureus. Based on the data presented, it is concluded that the strains represent a novel species of the genus Bradyrhizobium, for which the name Bradyrhizobium kavangense sp. nov. is proposed. The type strain is 14-3T [ = DSM 100299T = LMG 28790T = NTCCM 0012T (Windhoek)]. The DNA G+C content of strain 14-3T is 63.8 mol% (Tm).

  4. Pseudomonas aestusnigri sp. nov., isolated from crude oil-contaminated intertidal sand samples after the Prestige oil spill.

    Science.gov (United States)

    Sánchez, David; Mulet, Magdalena; Rodríguez, Ana C; David, Zoyla; Lalucat, Jorge; García-Valdés, Elena

    2014-03-01

    Strains VGXO14(T) and Vi1 were isolated from the Atlantic intertidal shore from Galicia, Spain, after the Prestige oil spill. Both strains were Gram-negative rod-shaped bacteria with one polar inserted flagellum, strictly aerobic, and able to grow at 18-37°C, pH 6-10 and 2-10% NaCl. A preliminary analysis of the 16S rRNA and the partial rpoD gene sequences indicated that these strains belonged to the Pseudomonas genus but were distinct from any known Pseudomonas species. A polyphasic taxonomic approach including phylogenetic, chemotaxonomic, phenotypic and genotypic data confirmed that the strains belonged to the Pseudomonas pertucinogena group. In a multilocus sequence analysis, the similarity of VGXO14(T) and Vi1 to the closest type strain of the group, Pseudomonas pachastrellae, was 90.4%, which was lower than the threshold of 97% established to discriminate species in the Pseudomonas genus. The DNA-DNA hybridisation similarity between strains VGXO14(T) and Vi1 was 79.6%, but below 70% with the type strains in the P. pertucinogena group. Therefore, the strains should be classified within the genus Pseudomonas as a novel species, for which the name Pseudomonas aestusnigri is proposed. The type strain is VGXO14(T) (=CCUG 64165(T)=CECT 8317(T)). Copyright © 2013 Elsevier GmbH. All rights reserved.

  5. Draft genome sequence analysis of a Pseudomonas putida W15Oct28 strain with antagonistic activity to Gram-positive and Pseudomonas sp. pathogens.

    Science.gov (United States)

    Ye, Lumeng; Hildebrand, Falk; Dingemans, Jozef; Ballet, Steven; Laus, George; Matthijs, Sandra; Berendsen, Roeland; Cornelis, Pierre

    2014-01-01

    Pseudomonas putida is a member of the fluorescent pseudomonads known to produce the yellow-green fluorescent pyoverdine siderophore. P. putida W15Oct28, isolated from a stream in Brussels, was found to produce compound(s) with antimicrobial activity against the opportunistic pathogens Staphylococcus aureus, Pseudomonas aeruginosa, and the plant pathogen Pseudomonas syringae, an unusual characteristic for P. putida. The active compound production only occurred in media with low iron content and without organic nitrogen sources. Transposon mutants which lost their antimicrobial activity had the majority of insertions in genes involved in the biosynthesis of pyoverdine, although purified pyoverdine was not responsible for the antagonism. Separation of compounds present in culture supernatants revealed the presence of two fractions containing highly hydrophobic molecules active against P. aeruginosa. Analysis of the draft genome confirmed the presence of putisolvin biosynthesis genes and the corresponding lipopeptides were found to contribute to the antimicrobial activity. One cluster of ten genes was detected, comprising a NAD-dependent epimerase, an acetylornithine aminotransferase, an acyl CoA dehydrogenase, a short chain dehydrogenase, a fatty acid desaturase and three genes for a RND efflux pump. P. putida W15Oct28 genome also contains 56 genes encoding TonB-dependent receptors, conferring a high capacity to utilize pyoverdines from other pseudomonads. One unique feature of W15Oct28 is also the presence of different secretion systems including a full set of genes for type IV secretion, and several genes for type VI secretion and their VgrG effectors.

  6. 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.

  7. 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

  8. 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.

  9. 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)).

  10. Methyloferula stellata gen. nov., sp. nov., an acidophilic, obligately methanotrophic bacterium that possesses only a soluble methane monooxygenase.

    Science.gov (United States)

    Vorobev, Alexey V; Baani, Mohamed; Doronina, Nina V; Brady, Allyson L; Liesack, Werner; Dunfield, Peter F; Dedysh, Svetlana N

    2011-10-01

    genus and species, Methyloferula stellata gen. nov., sp. nov., to accommodate strains AR4(T), SOP9 and LAY. Strain AR4(T) ( = DSM 22108(T)  = LMG 25277(T)  = VKM B-2543(T)) is the type strain of Methyloferula stellata.

  11. High quality draft genome sequence of the type strain of Pseudomonas lutea OK2(T), a phosphate-solubilizing rhizospheric bacterium.

    Science.gov (United States)

    Kwak, Yunyoung; Park, Gun-Seok; Shin, Jae-Ho

    2016-01-01

    Pseudomonas lutea OK2(T) (=LMG 21974(T), CECT 5822(T)) is the type strain of the species and was isolated from the rhizosphere of grass growing in Spain in 2003 based on its phosphate-solubilizing capacity. In order to identify the functional significance of phosphate solubilization in Pseudomonas Plant growth promoting rhizobacteria, we describe here the phenotypic characteristics of strain OK2(T) along with its high-quality draft genome sequence, its annotation, and analysis. The genome is comprised of 5,647,497 bp with 60.15 % G + C content. The sequence includes 4,846 protein-coding genes and 95 RNA genes.

  12. Lunatimonas lonarensis gen. nov., sp. nov., a haloalkaline bacterium of the family Cyclobacteriaceae with nitrate reducing activity.

    Science.gov (United States)

    Srinivas, T N R; Aditya, S; Bhumika, V; Kumar, P Anil

    2014-02-01

    . DNA-DNA hybridization between strains AK24(T) and AK26 showed a relatedness of 82% and their rep-PCR banding patterns were very similar. Based on data from the current polyphasic study, it is proposed that the isolates be placed in a new genus and species with the name Lunatimonas lonarensis gen. nov., sp. nov. The type strain of Lunatimonas lonarensis is AK24(T) (=JCM 18822(T)=MTCC 11627(T)). Copyright © 2013 Elsevier GmbH. All rights reserved.

  13. Characterization of a metal resistant Pseudomonas sp. isolated from uranium mine for its potential in heavy metal (Ni2+, Co2+, Cu2+, and Cd2+) sequestration.

    Science.gov (United States)

    Choudhary, Sangeeta; Sar, Pinaki

    2009-05-01

    Heavy metal sequestration by a multimetal resistant Pseudomonas strain isolated from a uranium mine was characterized for its potential application in metal bioremediation. 16S rRNA gene analysis revealed phylogenetic relatedness of this isolate to Pseudomonas fluorescens. Metal uptake by this bacterium was monophasic, fast saturating, concentration and pH dependent with maximum loading of 1048 nmol Ni(2+) followed by 845 nmol Co(2+), 828 nmol Cu(2+) and 700 nmol Cd(2+)mg(-1) dry wt. Preferential metal deposition in cell envelope was confirmed by TEM and cell fractionation. FTIR spectroscopy and EDX analysis revealed a major role of carboxyl and phosphoryl groups along with a possible ion exchange mechanism in cation binding. Binary system demonstrated selective metal binding affinity in the order of Cu(2+)>Ni(2+)>Co(2+)>Cd(2+). A comparison with similar metal uptake reports considering live bacteria strongly indicated the superiority of this strain in metal sequestration, which could be useful for developing efficient metal removal system.

  14. Biodegradation of malachite green by strain Pseudomonas sp. K9 and cloning of the tmr2 gene associated with an ISPpu12.

    Science.gov (United States)

    Huan-Mei; Lian-Tai, Li; Cai-Fang, Yan; Jin-Jin, Sun; Yuan-Gao; Hong, Qing; Shun-Peng, Li

    2011-06-01

    A bacterial strain K9 capable of degrading malachite green was isolated from the sludge of the wastewater treatment system of a chemical plant. It was identified preliminarily as Pseudomonas sp. Strain K9 was also able to degrade other triphenylmethane dyes, such as Crystal Violet and Basic Fuchsin. The gene tmr2, encoding the triphenylmethane reductase, was cloned from strain K9, and functionally expressed in E. coli. A 5946-bp DNA fragment including the tmr2 gene was cloned from the genomic DNA of strain K9 by chromosome walking. Its sequence analysis showed that tmr2 was associated with a typical mobile element ISPpu12 consisting of tnpA (encoding a transposase), lspA (encoding a lipoprotein signal peptidase) and orf1 (encoding a putative MerR family regulator), orf2 (encoding a CDF family heavy metal/H(+) antiporter). This association was also found in another malachite green-degrading strain Pseudomonas sp. MDB-1, which indicated that the tmr2 gene might be a horizontally transferable gene.

  15. ABILITY OF BACTERIAL CONSORTIUM: Bacillus coagulans, Bacilus licheniformis, Bacillus pumilus, Bacillus subtilis, Nitrosomonas sp. and Pseudomonas putida IN BIOREMEDIATION OF WASTE WATER IN CISIRUNG WASTE WATER TREATMENT PLANT

    Directory of Open Access Journals (Sweden)

    Ratu SAFITRI

    2015-10-01

    Full Text Available This study was conducted in order to determine the ability of bacterial consortium: Bacillus coagulans, Bacilus licheniformis, Bacillus pumilus, Bacillus subtilis, Nitrosomonas sp., and Pseudomonas putida in bioremediation of wastewater origin Cisirung WWTP. This study uses an experimental method completely randomized design (CRD, which consists of two treatment factors (8x8 factorial design. The first factor is a consortium of bacteria (K, consisting of 8 level factors (k1, k2, k3, k4, k5, k6, k7, and k8. The second factor is the time (T, consisting of a 7 level factors (t0, t1, t2, t3, t4, t5, t6, and t7. Test parameters consist of BOD (Biochemical Oxygen Demand, COD (Chemical Oxygen Demand, TSS (Total Suspended Solid, Ammonia and Population of Microbes during bioremediation. Data were analyzed by ANOVA, followed by Duncan test. The results of this study showed that the consortium of Bacillus pumilus, Bacillus subtilis, Bacillus coagulans, Nitrosomonas sp., and Pseudomonas putida with inoculum concentration of 5% (k6 is a consortium of the most effective in reducing BOD 71.93%, 64.30% COD, TSS 94.85%, and 88.58% of ammonia.

  16. Draft Genome Sequence Analysis of a Pseudomonas putida W15Oct28 Strain with Antagonistic Activity to Gram-Positive and Pseudomonas sp. Pathogens

    Science.gov (United States)

    Ye, Lumeng; Hildebrand, Falk; Dingemans, Jozef; Ballet, Steven; Laus, George; Matthijs, Sandra; Berendsen, Roeland; Cornelis, Pierre

    2014-01-01

    Pseudomonas putida is a member of the fluorescent pseudomonads known to produce the yellow-green fluorescent pyoverdine siderophore. P. putida W15Oct28, isolated from a stream in Brussels, was found to produce compound(s) with antimicrobial activity against the opportunistic pathogens Staphylococcus aureus, Pseudomonas aeruginosa, and the plant pathogen Pseudomonas syringae, an unusual characteristic for P. putida. The active compound production only occurred in media with low iron content and without organic nitrogen sources. Transposon mutants which lost their antimicrobial activity had the majority of insertions in genes involved in the biosynthesis of pyoverdine, although purified pyoverdine was not responsible for the antagonism. Separation of compounds present in culture supernatants revealed the presence of two fractions containing highly hydrophobic molecules active against P. aeruginosa. Analysis of the draft genome confirmed the presence of putisolvin biosynthesis genes and the corresponding lipopeptides were found to contribute to the antimicrobial activity. One cluster of ten genes was detected, comprising a NAD-dependent epimerase, an acetylornithine aminotransferase, an acyl CoA dehydrogenase, a short chain dehydrogenase, a fatty acid desaturase and three genes for a RND efflux pump. P. putida W15Oct28 genome also contains 56 genes encoding TonB-dependent receptors, conferring a high capacity to utilize pyoverdines from other pseudomonads. One unique feature of W15Oct28 is also the presence of different secretion systems including a full set of genes for type IV secretion, and several genes for type VI secretion and their VgrG effectors. PMID:25369289

  17. 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).

  18. 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.

  19. 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.

  20. 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).

  1. 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.

  2. Expression and characterization of a new heat-stable endo-type alginate lyase from deep-sea bacterium Flammeovirga sp. NJ-04.

    Science.gov (United States)

    Zhu, Benwei; Ni, Fang; Sun, Yun; Yao, Zhong

    2017-11-01

    Alginate lyases play an essential role in the production of oligosaccharides by degrading alginate polysaccharide. Although many alginate lyases from various microorganisms have been characterized, reports on alginate lyases with special characteristics and commercial potential are still rather rare. In this study, a new alginate lyase, FsAlgA, was cloned from the deep-sea marine bacterium Flammeovirga sp. NJ-04. The recombinant enzyme was purified on Ni-NTA sepharose and then characterized in detail. It exhibited the highest activity (3343.7 U/mg) at pH 7.0 and 50 °C. Notably, the FsAlgA retained more than 80% of its maximum activity after incubation at 50 °C for 30 min, suggesting that FsAlgA was a heat-stable alginate lyase. Additionally, FsAlgA possessed broad substrate specificity, showing high activities toward both poly β-D-mannuronate (polyM) and poly α-L-guluronate (polyG). Furthermore, the K m values of FsAlgA toward sodium alginate (0.48 mM) and polyG (0.94 mM) were lower than that toward polyM (1.42 mM). The TLC and ESI-MS analyses indicated that FsAlgA endolytically degraded alginate polysaccharide and released oligosaccharides with degree of polymerization (DP) of 2-5. Therefore, it may be a potent tool to produce alginate oligosaccharides with low DPs.

  3. 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.

  4. Molecular and biochemical characteristics of β-propeller phytase from marine Pseudomonas sp. BS10-3 and its potential application for animal feed additives.

    Science.gov (United States)

    Nam, Seung-Jeung; Kim, Young-Ok; Ko, Tae-Kyung; Kang, Jin-Ku; Chun, Kwang-Hoon; Auh, Joong-Hyuck; Lee, Chul-Soon; Lee, In-Kyu; Park, Sunghoon; Oh, Byung-Chul

    2014-10-01

    Phytate is an antinutritional factor that impacts the bioavailability of essential minerals such as Ca(2+), Mg(2+), Mn(2+), Zn(2+), and Fe(2+) by forming insoluble mineral-phytate salts. These insoluble mineral-phytate salts are hydrolyzed rarely by monogastric animals, because they lack the hydrolyzing phytases and thus excrete the majority of them. The β-propeller phytases (BPPs) hydrolyze these insoluble mineral-phytate salts efficiently. In this study, we cloned a novel BPP gene from a marine Pseudomonas sp. This Pseudomonas BPP gene (PsBPP) had low sequence identity with other known phytases and contained an extra internal repeat domain (residues 24-279) and a typical BPP domain (residues 280-634) at the C-terminus. Structurebased sequence alignment suggested that the N-terminal repeat domain did not possess the active-site residues, whereas the C-terminal BPP domain contained multiple calcium-binding sites, which provide a favorable electrostatic environment for substrate binding and catalytic activity. Thus, we overexpressed the BPP domain from Pseudomonas sp. to potentially hydrolyze insoluble mineral-phytate salts. Purified recombinant PsBPP required Ca(2+) or Fe(2+) for phytase activity, indicating that PsBPP hydrolyzes insoluble Fe(2+)-phytate or Ca2+-phytate salts. The optimal temperature and pH for the hydrolysis of Ca(2+)-phytate by PsBPP were 50°C and 6.0, respectively. Biochemical and kinetic studies clearly showed that PsBPP efficiently hydrolyzed Ca(2+)-phytate salts and yielded myo-inositol 2,4,6-trisphosphate and three phosphate groups as final products. Finally, we showed that PsBPP was hi