Draft Genome Sequence of Limnobacter sp. Strain CACIAM 66H1, a Heterotrophic Bacterium Associated with Cyanobacteria.

Science.gov (United States)

da Silva, Fábio Daniel Florêncio; Lima, Alex Ranieri Jerônimo; Moraes, Pablo Henrique Gonçalves; Siqueira, Andrei Santos; Dall'Agnol, Leonardo Teixeira; Baraúna, Anna Rafaella Ferreira; Martins, Luisa Carício; Oliveira, Karol Guimarães; de Lima, Clayton Pereira Silva; Nunes, Márcio Roberto Teixeira; Vianez-Júnior, João Lídio Silva Gonçalves; Gonçalves, Evonnildo Costa

2016-05-19

Ecological interactions between cyanobacteria and heterotrophic prokaryotes are poorly known. To improve the genomic studies of heterotrophic bacterium-cyanobacterium associations, the draft genome sequence (3.2 Mbp) of Limnobacter sp. strain CACIAM 66H1, found in a nonaxenic culture of Synechococcus sp. (cyanobacteria), is presented here. Copyright © 2016 da Silva et al.

Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T.

Directory of Open Access Journals (Sweden)

Ronald M Weiner

2008-05-01

Full Text Available The marine bacterium Saccharophagus degradans strain 2-40 (Sde 2-40 is emerging as a vanguard of a recently discovered group of marine and estuarine bacteria that recycles complex polysaccharides. We report its complete genome sequence, analysis of which identifies an unusually large number of enzymes that degrade >10 complex polysaccharides. Not only is this an extraordinary range of catabolic capability, many of the enzymes exhibit unusual architecture including novel combinations of catalytic and substrate-binding modules. We hypothesize that many of these features are adaptations that facilitate depolymerization of complex polysaccharides in the marine environment. This is the first sequenced genome of a marine bacterium that can degrade plant cell walls, an important component of the carbon cycle that is not well-characterized in the marine environment.

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

KAUST Repository

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

2016-01-01

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 SA

Genome Sequence of the Enterobacter mori Type Strain, LMG 25706, a Pathogenic Bacterium of Morus alba L. ▿

Science.gov (United States)

Zhu, Bo; Zhang, Guo-Qing; Lou, Miao-Miao; Tian, Wen-Xiao; Li, Bin; Zhou, Xue-Ping; Wang, Guo-Feng; Liu, He; Xie, Guan-Lin; Jin, Gu-Lei

2011-01-01

Enterobacter mori is a plant-pathogenic enterobacterium responsible for the bacterial wilt of Morus alba L. Here we present the draft genome sequence of the type strain, LMG 25706. To the best of our knowledge, this is the first genome sequence of a plant-pathogenic bacterium in the genus Enterobacter. PMID:21602328

Growth characteristics of a strain of iron-oxidizing bacterium and its application in bioleaching of uranium ores

International Nuclear Information System (INIS)

Zhang Rui; Liu Yajie; Gao Feng; Xu Lingling

2008-01-01

05B is a strain of iron-oxidizing bacterium which separated from a uranium ore. The effect of temperature, initial pH, inoculation amount and initial total iron concentration on the strain's growth and activities in bioleaching of uranium ores are studied. The results show that the optimum growth temperature is 40-45 degree C, the optimum inoculation pH value being 1.5-1.7, the optimum initial inoculation amount being 10%-20%, and the initial total iron concentration being not more than 5 g/L. 05B is fit for leaching of low grade uranium ores. (authors)

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.

Degradation of Phenol via Phenylphosphate and Carboxylation to 4-Hydroxybenzoate by a Newly Isolated Strain of the Sulfate-Reducing Bacterium Desulfobacterium anilini▿ †

OpenAIRE

Ahn, Young-Beom; Chae, Jong-Chan; Zylstra, Gerben J.; Häggblom, Max M.

2009-01-01

A sulfate-reducing phenol-degrading bacterium, strain AK1, was isolated from a 2-bromophenol-utilizing sulfidogenic estuarine sediment enrichment culture. On the basis of phylogenetic analysis of the 16S rRNA gene and DNA homology, strain AK1 is most closely related to Desulfobacterium anilini strain Ani1 (= DSM 4660T). In addition to phenol, this organism degrades a variety of other aromatic compounds, including benzoate, 2-hydroxybenzoate, 4-hydroxybenzoate, 4-hydroxyphenylacetate, 2-aminob...

Ralstonia syzygii, the Blood Disease Bacterium and Some Asian R. solanacearum Strains Form a Single Genomic Species Despite Divergent Lifestyles

Science.gov (United States)

Cellier, Gilles; Jacobs, Jonathan M.; Mangenot, Sophie; Barbe, Valérie; Lajus, Aurélie; Vallenet, David; Medigue, Claudine; Fegan, Mark; Allen, Caitilyn; Prior, Philippe

2011-01-01

The Ralstonia solanacearum species complex includes R. solanacearum, R. syzygii, and the Blood Disease Bacterium (BDB). All colonize plant xylem vessels and cause wilt diseases, but with significant biological differences. R. solanacearum is a soilborne bacterium that infects the roots of a broad range of plants. R. syzygii causes Sumatra disease of clove trees and is actively transmitted by cercopoid insects. BDB is also pathogenic to a single host, banana, and is transmitted by pollinating insects. Sequencing and DNA-DNA hybridization studies indicated that despite their phenotypic differences, these three plant pathogens are actually very closely related, falling into the Phylotype IV subgroup of the R. solanacearum species complex. To better understand the relationships among these bacteria, we sequenced and annotated the genomes of R. syzygii strain R24 and BDB strain R229. These genomes were compared to strain PSI07, a closely related Phylotype IV tomato isolate of R. solanacearum, and to five additional R. solanacearum genomes. Whole-genome comparisons confirmed previous phylogenetic results: the three phylotype IV strains share more and larger syntenic regions with each other than with other R. solanacearum strains. Furthermore, the genetic distances between strains, assessed by an in-silico equivalent of DNA-DNA hybridization, unambiguously showed that phylotype IV strains of BDB, R. syzygii and R. solanacearum form one genomic species. Based on these comprehensive data we propose a revision of the taxonomy of the R. solanacearum species complex. The BDB and R. syzygii genomes encoded no obvious unique metabolic capacities and contained no evidence of horizontal gene transfer from bacteria occupying similar niches. Genes specific to R. syzygii and BDB were almost all of unknown function or extrachromosomal origin. Thus, the pathogenic life-styles of these organisms are more probably due to ecological adaptation and genomic convergence during vertical

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.

Degradative capacities and bioaugmentation potential of an anaerobic benzene-degrading bacterium strain DN11

Energy Technology Data Exchange (ETDEWEB)

Yuki Kasai; Yumiko Kodama; Yoh Takahata; Toshihiro Hoaki; Kazuya Watanabe [Marine Biotechnology Institute, Kamaishi (Japan)

2007-09-15

Azoarcus sp. strain DN11 is a denitrifying bacterium capable of benzene degradation under anaerobic conditions. The present study evaluated strain DN11 for its application to bioaugmentation of benzene-contaminated underground aquifers. Strain DN11 could grow on benzene, toluene, m-xylene, and benzoate as the sole carbon and energy sources under nitrate-reducing conditions, although o- and p-xylenes were transformed in the presence of toluene. Phenol was not utilized under anaerobic conditions. Kinetic analysis of anaerobic benzene degradation estimated its apparent affinity and inhibition constants to be 0.82 and 11 {mu}M, respectively. Benzene-contaminated groundwater taken from a former coal-distillation plant site in Aichi, Japan was anaerobically incubated in laboratory bottles and supplemented with either inorganic nutrients (nitrogen, phosphorus, and nitrate) alone, or the nutrients plus strain DN11, showing that benzene was significantly degraded only when DN11 was introduced. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments, and quantitative PCR revealed that DN11 decreased after benzene was degraded. Following the decrease in DN11 16S rRNA gene fragments corresponding to bacteria related to Owenweeksia hongkongensis and Pelotomaculum isophthalicum, appeared as strong bands, suggesting possible metabolic interactions in anaerobic benzene degradation. Results suggest that DN11 is potentially useful for degrading benzene that contaminates underground aquifers at relatively low concentrations. 50 refs., 6 figs., 1 tab.

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.

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

Science.gov (United States)

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

2016-11-03

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

Bacterial vaginosis diagnosed by analysis of first-void-urine specimens

DEFF Research Database (Denmark)

Datcu, Raluca; Gesink, Dionne; Mulvad, Gert

2014-01-01

Bacterial vaginosis (BV) is traditionally diagnosed using vaginal samples. The aim of this study was to investigate whether BV can be diagnosed from first-void urine (FVU). Self-collected vaginal smears, vaginal swabs, and FVU were obtained from 176 women. BV was diagnosed by Nugent's criteria....... The FVU and vaginal swabs were analyzed by quantitative PCRs (qPCRs) for selected vaginal bacteria (Atopobium vaginae, Prevotella spp., Gardnerella vaginalis, bacterial vaginosis-associated bacterium 2, Eggerthella-like bacterium, "Leptotrichia amnionii," Megasphaera type 1), and all had an area under...

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

Science.gov (United States)

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

2017-10-12

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

Draft Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum copahuensis Strain CINDEFI1 Isolated from the Geothermal Copahue System, Neuqu?n, Argentina

OpenAIRE

Willis Poratti, Graciana; Yaakop, Amira Suriaty; Chan, Chia Sing; Urbieta, M. Sof?a; Chan, Kok-Gan; Ee, Robson; Tan-Guan-Sheng, Adrian; Goh, Kian Mau; Donati, Edgardo R.

2016-01-01

Desulfotomaculum copahuensis strain CINDEFI1 is a novel spore-forming sulfate-reducing bacterium isolated from the Copahue volcano area, Argentina. Here, we present its draft genome in which we found genes related with the anaerobic respiration of sulfur compounds similar to those present in the Copahue environment.

Extracellular proteases of Halobacillus blutaparonensis strain M9, a new moderately halophilic bacterium.

Science.gov (United States)

Santos, Anderson F; Valle, Roberta S; Pacheco, Clarissa A; Alvarez, Vanessa M; Seldin, Lucy; Santos, André L S

2013-12-01

Halophilic microorganisms are source of potential hydrolytic enzymes to be used in industrial and/or biotechnological processes. In the present study, we have investigated the ability of the moderately halophilic bacterium Halobacillus blutaparonensis (strain M9), a novel species described by our group, to release proteolytic enzymes. This bacterial strain abundantly proliferated in Luria-Bertani broth supplemented with 2.5% NaCl as well as secreted proteases to the extracellular environment. The production of proteases occurred in bacterial cells grown under different concentration of salt, ranging from 0.5% to 10% NaCl, in a similar way. The proteases secreted by H. blutaparonensis presented the following properties: (i) molecular masses ranging from 30 to 80 kDa, (ii) better hydrolytic activities under neutral-alkaline pH range, (iii) expression modulated according to the culture age, (iv) susceptibility to phenylmethylsulphonyl fluoride, classifying them as serine-type proteases, (v) specific cleavage over the chymotrypsin substrate, and (vi) enzymatic stability in the presence of salt (up to 20% NaCl) and organic solvents (e.g., ether, isooctane and cyclohexane). The proteases described herein are promising for industrial practices due to its haloalkaline properties.

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.

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

OpenAIRE

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

2016-01-01

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

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

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

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

Science.gov (United States)

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

2016-06-09

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

Formation of Highly Twisted Ribbons in a Carboxymethylcellulase Gene-Disrupted Strain of a Cellulose-Producing Bacterium

Science.gov (United States)

Sugano, Yasushi; Shoda, Makoto; Sakakibara, Hitoshi; Oiwa, Kazuhiro; Tuzi, Satoru; Imai, Tomoya; Sugiyama, Junji; Takeuchi, Miyuki; Yamauchi, Daisuke

2013-01-01

Cellulases are enzymes that normally digest cellulose; however, some are known to play essential roles in cellulose biosynthesis. Although some endogenous cellulases of plants and cellulose-producing bacteria are reportedly involved in cellulose production, their functions in cellulose production are unknown. In this study, we demonstrated that disruption of the cellulase (carboxymethylcellulase) gene causes irregular packing of de novo-synthesized fibrils in Gluconacetobacter xylinus, a cellulose-producing bacterium. Cellulose production was remarkably reduced and small amounts of particulate material were accumulated in the culture of a cmcax-disrupted G. xylinus strain (F2-2). The particulate material was shown to contain cellulose by both solid-state 13C nuclear magnetic resonance analysis and Fourier transform infrared spectroscopy analysis. Electron microscopy revealed that the cellulose fibrils produced by the F2-2 cells were highly twisted compared with those produced by control cells. This hypertwisting of the fibrils may reduce cellulose synthesis in the F2-2 strains. PMID:23243308

Draft Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum copahuensis Strain CINDEFI1 Isolated from the Geothermal Copahue System, Neuquén, Argentina.

Science.gov (United States)

Willis Poratti, Graciana; Yaakop, Amira Suriaty; Chan, Chia Sing; Urbieta, M Sofía; Chan, Kok-Gan; Ee, Robson; Tan-Guan-Sheng, Adrian; Goh, Kian Mau; Donati, Edgardo R

2016-08-18

Desulfotomaculum copahuensis strain CINDEFI1 is a novel spore-forming sulfate-reducing bacterium isolated from the Copahue volcano area, Argentina. Here, we present its draft genome in which we found genes related with the anaerobic respiration of sulfur compounds similar to those present in the Copahue environment. Copyright © 2016 Willis Poratti et al.

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

Directory of Open Access Journals (Sweden)

Krishnaveni Venkidusamy

2016-07-01

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

Clostridium scatologenes strain SL1 isolated as an acetogenic bacterium from acidic sediments.

Science.gov (United States)

Küsel, K; Dorsch, T; Acker, G; Stackebrandt, E; Drake, H L

2000-03-01

A strictly anaerobic, H2-utilizing bacterium, strain SL1, was isolated from the sediment of an acidic coal mine pond. Cells of strain SL1 were sporulating, motile, long rods with a multilayer cell wall. Growth was observed at 5-35 degrees C and pH 3.9-7.0. Acetate was the sole end product of H2 utilization and was produced in stoichiometries indicative of an acetyl-CoA-pathway-dependent metabolism. Growth and substrate utilization also occurred with CO/CO2, vanillate, syringate, ferulate, ethanol, propanol, 1-butanol, glycerine, cellobiose, glucose, fructose, mannose, xylose, formate, lactate, pyruvate and gluconate. With most substrates, acetate was the main or sole product formed. Growth in the presence of H2/CO2 or CO/CO2 was difficult to maintain in laboratory cultures. Methoxyl, carboxyl and acrylate groups of various aromatic compounds were O-demethylated, decarboxylated and reduced, respectively. Small amounts of butyrate were produced during the fermentation of sugars. The acrylate group of ferulate was reduced. Nitrate, sulfate, thiosulfate, dimethylsulfoxide and Fe(III) were not utilized as electron acceptors. Analysis of the 16S rRNA gene sequence of strain SL1 demonstrated that it is closely related to Clostridium scatologenes (99.6% sequence similarity), an organism characterized as a fermentative anaerobe but not previously shown to be capable of acetogenic growth. Comparative experiments with C. scatologenes DSM 757T demonstrated that it utilized H2/CO2 (negligible growth), CO/CO2 (negligible growth), formate, ethanol and aromatic compounds according to stoichiometries indicative of the acetyl-CoA pathway. CO dehydrogenase, formate dehydrogenase and hydrogenase activities were present in both strain SL1 and C. scatologenes DSM 757T. These results indicate that (i) sediments of acidic coal mine ponds harbour acetogens and (ii) C. scatologenes is an acetogen that tends to lose its capacity to grow acetogenically under H2/CO2 or CO/CO2 after prolonged

Denitrifying metabolism of the methylotrophic marine bacterium Methylophaga nitratireducenticrescens strain JAM1.

Science.gov (United States)

Mauffrey, Florian; Cucaita, Alexandra; Constant, Philippe; Villemur, Richard

2017-01-01

Methylophaga nitratireducenticrescens strain JAM1 is a methylotrophic, marine bacterium that was isolated from a denitrification reactor treating a closed-circuit seawater aquarium. It can sustain growth under anoxic conditions by reducing nitrate ([Formula: see text]) to nitrite ([Formula: see text]). These physiological traits are attributed to gene clusters that encode two dissimilatory nitrate reductases (Nar). Strain JAM1 also contains gene clusters encoding two nitric oxide (NO) reductases and one nitrous oxide (N 2 O) reductase, suggesting that NO and N 2 O can be reduced by strain JAM1. Here we characterized further the denitrifying activities of M. nitratireducenticrescens JAM1. Series of oxic and anoxic cultures of strain JAM1 were performed with N 2 O, [Formula: see text] or sodium nitroprusside, and growth and N 2 O, [Formula: see text], [Formula: see text] and N 2 concentrations were measured. Ammonium ([Formula: see text])-free cultures were also tested to assess the dynamics of N 2 O, [Formula: see text] and [Formula: see text]. Isotopic labeling of N 2 O was performed in 15 NH 4 + -amended cultures. Cultures with the JAM1Δ narG1narG2 double mutant were performed to assess the involvement of the Nar systems on N 2 O production. Finally, RT-qPCR was used to measure the gene expression levels of the denitrification genes cytochrome bc -type nitric oxide reductase ( cnorB1 and cnorB2 ) and nitrous oxide reductase ( nosZ ), and also nnrS and norR that encode NO-sensitive regulators. Strain JAM1 can reduce NO to N 2 O and N 2 O to N 2 and can sustain growth under anoxic conditions by reducing N 2 O as the sole electron acceptor. Although strain JAM1 lacks a gene encoding a dissimilatory [Formula: see text] reductase, [Formula: see text]-amended cultures produce N 2 O, representing up to 6% of the N-input. [Formula: see text] was shown to be the key intermediate of this production process. Upregulation in the expression of c norB1 , cnorB2, nnrS and nor

Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium Xylella fastidiosa

Directory of Open Access Journals (Sweden)

Walker M Andrew

2006-09-01

Full Text Available Abstract Background The Gram-negative, xylem-limited phytopathogenic bacterium Xylella fastidiosa is responsible for causing economically important diseases in grapevine, citrus and many other plant species. Despite its economic impact, relatively little is known about the genomic variations among strains isolated from different hosts and their influence on the population genetics of this pathogen. With the availability of genome sequence information for four strains, it is now possible to perform genome-wide analyses to identify and categorize such DNA variations and to understand their influence on strain functional divergence. Results There are 1,579 genes and 194 non-coding homologous sequences present in the genomes of all four strains, representing a 76. 2% conservation of the sequenced genome. About 60% of the X. fastidiosa unique sequences exist as tandem gene clusters of 6 or more genes. Multiple alignments identified 12,754 SNPs and 14,449 INDELs in the 1528 common genes and 20,779 SNPs and 10,075 INDELs in the 194 non-coding sequences. The average SNP frequency was 1.08 × 10-2 per base pair of DNA and the average INDEL frequency was 2.06 × 10-2 per base pair of DNA. On an average, 60.33% of the SNPs were synonymous type while 39.67% were non-synonymous type. The mutation frequency, primarily in the form of external INDELs was the main type of sequence variation. The relative similarity between the strains was discussed according to the INDEL and SNP differences. The number of genes unique to each strain were 60 (9a5c, 54 (Dixon, 83 (Ann1 and 9 (Temecula-1. A sub-set of the strain specific genes showed significant differences in terms of their codon usage and GC composition from the native genes suggesting their xenologous origin. Tandem repeat analysis of the genomic sequences of the four strains identified associations of repeat sequences with hypothetical and phage related functions. Conclusion INDELs and strain specific genes

[Identification and function test of an alkali-tolerant denitrifying bacterium].

Science.gov (United States)

Wang, Ru; Zheng, Ping; Li, Wei; Chen, Hui; Chen, Tingting; Ghulam, Abbas

2013-04-04

We obtained an alkali-tolerant denitrifying bacterium, and determined its denitrifying activity and alkali-tolerance. An alkali-tolerant denitrifying bacterial strain was obtained by isolation and purification. We identified the bacterial strain by morphological observation, physiological test and 16S rRNA analysis. We determined the denitrifying activity and alkali-tolerance by effects of initial nitrate concentration and initial pH on denitrification. An alkali-tolerant denitrifier strain R9 was isolated from the lab-scale high-rate denitrifying reactor, and it was identified as Diaphorobater nitroreducens. The strain R9 grew heterotrophically with methanol as the electron donor and nitrate as the electron acceptor. The nitrate conversion was 93.25% when strain R9 was cultivated for 288 h with initial nitrate concentration 50 mg/L and initial pH 9.0. The denitrification activity could be inhibited at high nitrate concentration with a half inhibition constant of 202.73 mg N/L. Strain R9 showed a good alkali tolerance with the nitrate removal rate at pH 11.0 remained 86% of that at pH 9.0. Strain R9 was identified as Diaphorobater nitroreducens, and it was an alkali-tolerant denitrifying bacterium with optimum pH value of 9.0.

Denitrifying metabolism of the methylotrophic marine bacterium Methylophaga nitratireducenticrescens strain JAM1

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Florian Mauffrey

2017-11-01

Full Text Available Background Methylophaga nitratireducenticrescens strain JAM1 is a methylotrophic, marine bacterium that was isolated from a denitrification reactor treating a closed-circuit seawater aquarium. It can sustain growth under anoxic conditions by reducing nitrate ( ${\\mathrm{NO}}_{3}^{-}$ NO 3 − to nitrite ( ${\\mathrm{NO}}_{2}^{-}$ NO 2 − . These physiological traits are attributed to gene clusters that encode two dissimilatory nitrate reductases (Nar. Strain JAM1 also contains gene clusters encoding two nitric oxide (NO reductases and one nitrous oxide (N2O reductase, suggesting that NO and N2O can be reduced by strain JAM1. Here we characterized further the denitrifying activities of M. nitratireducenticrescens JAM1. Methods Series of oxic and anoxic cultures of strain JAM1 were performed with N2O, ${\\mathrm{NO}}_{3}^{-}$ NO 3 − or sodium nitroprusside, and growth and N2O, ${\\mathrm{NO}}_{3}^{-}$ NO 3 − , ${\\mathrm{NO}}_{2}^{-}$ NO 2 − and N2 concentrations were measured. Ammonium ( ${\\mathrm{NH}}_{4}^{+}$ NH 4 + -free cultures were also tested to assess the dynamics of N2O, ${\\mathrm{NO}}_{3}^{-}$ NO 3 − and ${\\mathrm{NO}}_{2}^{-}$ NO 2 − . Isotopic labeling of N2O was performed in 15NH4+-amended cultures. Cultures with the JAM1ΔnarG1narG2 double mutant were performed to assess the involvement of the Nar systems on N2O production. Finally, RT-qPCR was used to measure the gene expression levels of the denitrification genes cytochrome bc-type nitric oxide reductase (cnorB1 and cnorB2 and nitrous oxide reductase (nosZ, and also nnrS and norR that encode NO-sensitive regulators. Results Strain JAM1 can reduce NO to N2O and N2O to N2 and can sustain growth under anoxic conditions by reducing N2O as the sole electron acceptor. Although strain JAM1 lacks a gene encoding a dissimilatory ${\\mathrm{NO}}_{2}^{-}$ NO 2 − reductase, ${\\mathrm{NO}}_{3}^{-}$ NO 3 − -amended cultures produce N2O, representing up to 6% of the N

Complete genome of Martelella sp. AD-3, a moderately halophilic polycyclic aromatic hydrocarbons-degrading bacterium.

Science.gov (United States)

Cui, Changzheng; Li, Zhijie; Qian, Jiangchao; Shi, Jie; Huang, Ling; Tang, Hongzhi; Chen, Xin; Lin, Kuangfei; Xu, Ping; Liu, Yongdi

2016-05-10

Martelella sp. strain AD-3, a moderate halophilic bacterium, was isolated from a petroleum-contaminated soil with high salinity in China. Here, we report the complete genome of strain AD-3, which contains one circular chromosome and two circular plasmids. An array of genes related to metabolism of polycyclic aromatic hydrocarbons and halophilic mechanism in this bacterium was identified by the whole genome analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

Marine Bacteria from Danish Coastal Waters Show Antifouling Activity against the Marine Fouling Bacterium Pseudoalteromonas sp. Strain S91 and Zoospores of the Green Alga Ulva australis Independent of Bacteriocidal Activity

DEFF Research Database (Denmark)

Bernbom, Nete; Ng, Yoke Yin; Kjelleberg, Staffan

2011-01-01

, representing the major taxonomic groups, different seasons, and isolation strategies, were tested for antiadhesive effect against the marine biofilm-forming bacterium Pseudoalteromonas sp. strain S91 and zoospores of the green alga Ulva australis. The antiadhesive effects were assessed by quantifying...... the number of strain S91 or Ulva spores attaching to a preformed biofilm of each of the 22 strains. The strongest antifouling activity was found in Pseudoalteromonas strains. Biofilms of Pseudoalteromonas piscicida, Pseudoalteromonas tunicata, and Pseudoalteromonas ulvae prevented Pseudoalteromonas S91 from...

Genome sequence of the pink-pigmented marine bacterium Loktanella hongkongensis type strain (UST950701-009P(T)), a representative of the Roseobacter group.

Science.gov (United States)

Lau, Stanley Ck; Riedel, Thomas; Fiebig, Anne; Han, James; Huntemann, Marcel; Petersen, Jörn; Ivanova, Natalia N; Markowitz, Victor; Woyke, Tanja; Göker, Markus; Kyrpides, Nikos C; Klenk, Hans-Peter; Qian, Pei-Yuan

2015-01-01

Loktanella hongkongensis UST950701-009P(T) is a Gram-negative, non-motile and rod-shaped bacterium isolated from a marine biofilm in the subtropical seawater of Hong Kong. When growing as a monospecies biofilm on polystyrene surfaces, this bacterium is able to induce larval settlement and metamorphosis of a ubiquitous polychaete tubeworm Hydroides elegans. The inductive cues are low-molecular weight compounds bound to the exopolymeric matrix of the bacterial cells. In the present study we describe the features of L. hongkongensis strain DSM 17492(T) together with its genome sequence and annotation and novel aspects of its phenotype. The 3,198,444 bp long genome sequence encodes 3104 protein-coding genes and 57 RNA genes. The two unambiguously identified extrachromosomal replicons contain replication modules of the RepB and the Rhodobacteraceae-specific DnaA-like type, respectively.

Isolation and characterization of Halomonas sp. strain C2SS100, a hydrocarbon-degrading bacterium under hypersaline conditions.

Science.gov (United States)

Mnif, S; Chamkha, M; Sayadi, S

2009-09-01

To isolate and characterize an efficient hydrocarbon-degrading bacterium under hypersaline conditions, from a Tunisian off-shore oil field. Production water collected from 'Sercina' petroleum reservoir, located near the Kerkennah island, Tunisia, was used for the screening of halotolerant or halophilic bacteria able to degrade crude oil. Bacterial strain C2SS100 was isolated after enrichment on crude oil, in the presence of 100 g l(-1) NaCl and at 37 degrees C. This strain was aerobic, Gram-negative, rod-shaped, motile, oxidase + and catalase +. Phenotypic characters and phylogenetic analysis based on the 16S rRNA gene of the isolate C2SS100 showed that it was related to members of the Halomonas genus. The degradation of several compounds present in crude oil was confirmed by GC-MS analysis. The use of refined petroleum products such as diesel fuel and lubricating oil as sole carbon source, under the same conditions of temperature and salinity, showed that significant amounts of these heterogenic compounds could be degraded. Strain C2SS100 was able to degrade hexadecane (C16). During growth on hexadecane, cells surface hydrophobicity and emulsifying activity increased indicating the production of biosurfactant by strain C2SS100. A halotolerant bacterial strain Halomonas sp. C2SS100 was isolated from production water of an oil field, after enrichment on crude oil. This strain is able to degrade hydrocarbons efficiently. The mode of hydrocarbon uptake is realized by the production of a biosurfactant which enhances the solubility of hydrocarbons and renders them more accessible for biodegradation. The biodegradation potential of the Halomonas sp. strain C2SS100 gives it an advantage for possibly application on bioremediation of water, hydrocarbon-contaminated sites under high-salinity level.

Evaluation of Arthrobacter aurescens Strain TC1 as Bioaugmentation Bacterium in Soils Contaminated with the Herbicidal Substance Terbuthylazine.

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Vera P Silva

Full Text Available In the last years the chloro-s-triazine active substance terbuthylazine has been increasingly used as an herbicide and may leave residues in the environment which can be of concern. The present study aimed at developing a bioaugmentation tool based on the soil bacterium Arthrobacter aurescens strain TC1 for the remediation of terbuthylazine contaminated soils and at examining its efficacy for both soil and aquatic compartments. First, the feasibility of growing the bioaugmentation bacterium inocula on simple sole nitrogen sources (ammonium and nitrate instead of atrazine, while still maintaining its efficiency to biodegrade terbuthylazine was shown. In sequence, the successful and quick (3 days bioremediation efficacy of ammonium-grown A. aurescens TC1 cells was proven in a natural soil freshly spiked or four-months aged with commercial terbuthylazine at a dose 10× higher than the recommended in corn cultivation, to mimic spill situations. Ecotoxicity assessment of the soil eluates towards a freshwater microalga supported the effectiveness of the bioaugmentation tool. Obtained results highlight the potential to decontaminate soil while minimizing terbuthylazine from reaching aquatic compartments via the soil-water pathway. The usefulness of this bioaugmentation tool to provide rapid environment decontamination is particularly relevant in the event of accidental high herbicide contamination. Its limitations and advantages are discussed.

Evaluation of Arthrobacter aurescens Strain TC1 as Bioaugmentation Bacterium in Soils Contaminated with the Herbicidal Substance Terbuthylazine

Science.gov (United States)

Silva, Vera P.; Moreira-Santos, Matilde; Mateus, Carla; Teixeira, Tânia; Ribeiro, Rui; Viegas, Cristina A.

2015-01-01

In the last years the chloro-s-triazine active substance terbuthylazine has been increasingly used as an herbicide and may leave residues in the environment which can be of concern. The present study aimed at developing a bioaugmentation tool based on the soil bacterium Arthrobacter aurescens strain TC1 for the remediation of terbuthylazine contaminated soils and at examining its efficacy for both soil and aquatic compartments. First, the feasibility of growing the bioaugmentation bacterium inocula on simple sole nitrogen sources (ammonium and nitrate) instead of atrazine, while still maintaining its efficiency to biodegrade terbuthylazine was shown. In sequence, the successful and quick (3 days) bioremediation efficacy of ammonium-grown A. aurescens TC1 cells was proven in a natural soil freshly spiked or four-months aged with commercial terbuthylazine at a dose 10× higher than the recommended in corn cultivation, to mimic spill situations. Ecotoxicity assessment of the soil eluates towards a freshwater microalga supported the effectiveness of the bioaugmentation tool. Obtained results highlight the potential to decontaminate soil while minimizing terbuthylazine from reaching aquatic compartments via the soil-water pathway. The usefulness of this bioaugmentation tool to provide rapid environment decontamination is particularly relevant in the event of accidental high herbicide contamination. Its limitations and advantages are discussed. PMID:26662024

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

An anaerobic, extremely thermophilic, cellulolytic, non-spore-forming bacterium, strain 6A, was isolated from an alkaline hot spring in Hverageroi, Iceland. The bacterium was non-motile, rod-shaped (1.5-3.5 x 0.7 mu m) and occurred singly, in pairs or in chains and stained gram-negative. The growth...

Nitrous Oxide Reduction by an Obligate Aerobic Bacterium, Gemmatimonas aurantiaca Strain T-27.

Science.gov (United States)

Park, Doyoung; Kim, Hayeon; Yoon, Sukhwan

2017-06-15

,000 parts per million by volume [ppmv]). Although a large fraction of nosZ genes recovered from soil is affiliated with nosZ found in the genomes of the obligate aerobic phylum Gemmatimonadetes , N 2 O reduction has not yet been confirmed in any of these organisms. This study demonstrates that N 2 O is reduced by an obligate aerobic bacterium, Gemmatimonas aurantiaca strain T-27, and suggests a novel regulation mechanism for N 2 O reduction in this organism, which may also be applicable to other obligate aerobic organisms possessing nosZ genes. We expect that these findings will significantly advance the understanding of N 2 O dynamics in environments with frequent transitions between oxic and anoxic conditions. Copyright © 2017 American Society for Microbiology.

Antagonistic bioactivity of an endophytic bacterium isolated from ...

African Journals Online (AJOL)

Antagonistic bioactivity of an endophytic bacterium isolated from Epimedium brevicornu Maxim. R He, G Wang, X Liu, C Zhang, F Lin. Abstract. Endophytic bacteria are one of the most potential biological control agents in plant disease protection. The aim of this work was to evaluate the antimicrobial activities of a strain of ...

Degradation of phenol via phenylphosphate and carboxylation to 4-hydroxybenzoate by a newly isolated strain of the sulfate-reducing bacterium Desulfobacterium anilini.

Science.gov (United States)

Ahn, Young-Beom; Chae, Jong-Chan; Zylstra, Gerben J; Häggblom, Max M

2009-07-01

A sulfate-reducing phenol-degrading bacterium, strain AK1, was isolated from a 2-bromophenol-utilizing sulfidogenic estuarine sediment enrichment culture. On the basis of phylogenetic analysis of the 16S rRNA gene and DNA homology, strain AK1 is most closely related to Desulfobacterium anilini strain Ani1 (= DSM 4660(T)). In addition to phenol, this organism degrades a variety of other aromatic compounds, including benzoate, 2-hydroxybenzoate, 4-hydroxybenzoate, 4-hydroxyphenylacetate, 2-aminobenzoate, 2-fluorophenol, and 2-fluorobenzoate, but it does not degrade aniline, 3-hydroxybenzoate, 4-cyanophenol, 2,4-dihydroxybenzoate, monohalogenated phenols, or monohalogenated benzoates. Growth with sulfate as an electron acceptor occurred with acetate and pyruvate but not with citrate, propionate, butyrate, lactate, glucose, or succinate. Strain AK1 is able to use sulfate, sulfite, and thiosulfate as electron acceptors. A putative phenylphosphate synthase gene responsible for anaerobic phenol degradation was identified in strain AK1. In phenol-grown cultures inducible expression of the ppsA gene was verified by reverse transcriptase PCR, and 4-hydroxybenzoate was detected as an intermediate. These results suggest that the pathway for anaerobic degradation of phenol in D. anilini strain AK1 proceeds via phosphorylation of phenol to phenylphosphate, followed by carboxylation to 4-hydroxybenzoate. The details concerning such reaction pathways in sulfidogenic bacteria have not been characterized previously.

Marinobacter nitratireducens sp. nov., a halophilic and lipolytic bacterium isolated from coastal surface sea water

Digital Repository Service at National Institute of Oceanography (India)

Bhumika, V.; Ravinder, K.; Korpole, S.; Srinivas, T.N.R.; AnilKumar, P.

A novel Gram-stain-negative, rod-shaped, motile bacterium, designated strain AK21^T , was isolated from coastal surface sea water at Visakhapatnam, India. The strain was positive for oxidase, catalase, lipase, L-proline arylamidase...

Genetic Engineering of a Radiation-Resistant Bacterium for Biodegradation of Mixed Wastes. Final Report

International Nuclear Information System (INIS)

Lidstrom, Mary E.

2003-01-01

Aqueous mixed low level wastes (MLLW) containing radionuclides, solvents, and/or heavy metals represent a serious current and future problem for DOE environmental management and cleanup. In order to provide low-cost treatment alternatives under mild conditions for such contained wastes, we have proposed to use the radiation-resistant bacterium, Deinococcus radiodurans. This project has focused on developing D. radiodurans strains for dual purpose processes: cometabolic treatment of haloorganics and other solvents and removal of heavy metals from waste streams in an above-ground reactor system. The characteristics of effective treatment strains that must be attained are: (a) high biodegradative and metal binding activity; (b) stable treatment characteristics in the absence of selection and in the presence of physiological stress; (c) survival and activity under harsh chemical conditions, including radiation. The result of this project has been a suite of strains with high biodegradative capabilities that are candidates for pilot stage treatment systems. In addition, we have determined how to create conditions to precipitate heavy metals on the surface of the bacterium, as the first step towards creating dual-use treatment strains for contained mixed wastes of importance to the DOE. Finally, we have analyzed stress response in this bacterium, to create the foundation for developing treatment processes that maximize degradation while optimizing survival under high stress conditions

Echinicola shivajiensis sp. nov., a novel bacterium of the family "Cyclobacteriaceae" isolated from brackish water pond

Digital Repository Service at National Institute of Oceanography (India)

Srinivas, T.N.R.; Tryambak, B.K.; AnilKumar, P.

Strain AK12 sup(T), an orange pigmented Gramnegative, rod shaped, non-motile bacterium, was isolated fromamud sample collected froma brackishwater pond at Rampur of West Bengal, India. The strain was positive for oxidase, catalase and phosphatase...

Oceanospirillum nioense sp. nov., a marine bacterium isolated from sediment sample of Palk bay, India

Digital Repository Service at National Institute of Oceanography (India)

Krishna, K.K.; Bhumika, V.; Thomas, M.; AnilKumar, P.; Srinivas, T.N.R.

A novel Gram-negative, spiral shaped, motile bacterium, designated strain NIO-S6T, was isolated from a sediment sample collected from Offshore Rameswaram, Tamilnadu, India. Strain NIO-S6 sup(T) was found to be positive for oxidase, DNase and lysine...

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

The atherogenic bacterium Porphyromonas gingivalis evades circulating phagocytes by adhering to erythrocytes

DEFF Research Database (Denmark)

Belstrøm, Daniel; Holmstrup, Palle; Damgaard, Christian

2011-01-01

A relationship between periodontitis and coronary heart disease has been investigated intensively. A pathogenic role for the oral bacterium Porphyromonas gingivalis has been suggested for both diseases. We examined whether complement activation by P. gingivalis strain ATCC 33277 allows...... the bacterium to adhere to human red blood cells (RBCs) and thereby evade attack by circulating phagocytes. On incubation with normal human serum, the P. gingivalis strain efficiently fixed complement component 3 (C3). Incubation of bacteria with washed whole blood cells suspended in autologous serum resulted...... in a dose- and time-dependent adherence to RBCs. The adherence required functionally intact complement receptor 1 (CR1; also called CD35) on the RBCs and significantly inhibited the uptake of P. gingivalis by neutrophils and B cells within 1 min of incubation (by 64% and 51%, respectively...

Genomic Analysis of a Marine Bacterium: Bioinformatics for Comparison, Evaluation, and Interpretation of DNA Sequences

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Bhagwan N. Rekadwad

2016-01-01

Full Text Available A total of five highly related strains of an unidentified marine bacterium were analyzed through their short genome sequences (AM260709–AM260713. Genome-to-Genome Distance (GGDC showed high similarity to Pseudoalteromonas haloplanktis (X67024. The generated unique Quick Response (QR codes indicated no identity to other microbial species or gene sequences. Chaos Game Representation (CGR showed the number of bases concentrated in the area. Guanine residues were highest in number followed by cytosine. Frequency of Chaos Game Representation (FCGR indicated that CC and GG blocks have higher frequency in the sequence from the evaluated marine bacterium strains. Maximum GC content for the marine bacterium strains ranged 53-54%. The use of QR codes, CGR, FCGR, and GC dataset helped in identifying and interpreting short genome sequences from specific isolates. A phylogenetic tree was constructed with the bootstrap test (1000 replicates using MEGA6 software. Principal Component Analysis (PCA was carried out using EMBL-EBI MUSCLE program. Thus, generated genomic data are of great assistance for hierarchical classification in Bacterial Systematics which combined with phenotypic features represents a basic procedure for a polyphasic approach on unambiguous bacterial isolate taxonomic classification.

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

Digital Repository Service at National Institute of Oceanography (India)

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

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

Isolation and characterization of two cryptic plasmids in the ammonia-oxidizing bacterium Nitrosomonas sp. strain ENI-11.

Science.gov (United States)

Yamagata, A; Kato, J; Hirota, R; Kuroda, A; Ikeda, T; Takiguchi, N; Ohtake, H

1999-06-01

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

Effect of cell immobilization on the treatment of olive mill wastewater by a total phenols, acetic acid and formic acid degrading bacterium strain

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Errami, Mohamed

2005-06-01

Full Text Available Olive mill wastewater (OMW is a pure vegetative by-product, containing a high organic and polyphenol content and is resistant to biodegradation. Its disposal lead to major environmental pollution problems in the Mediterranean basin. An aerobic bacterium was isolated from OMW. During three consecutive diluted and supplemented OMW treatment cycles, significant abatement of its phytotoxic substances was observed. In fact, total phenols, acetic and formic acids were reduced between 33 and 64 % when cells of the isolated bacterium were grown free; and between 62 and 78 % when cells of the same isolated bacterium were grown immobilized in a polyurethane sponge. These results suggest that the bacterium culture of the new isolate would decrease the OMW phytotoxicity. Phylogenetic analysis of 16S ribosomal DNA showed that all the related sequences are members of the Enterobacteriaceae family and revealed that the isolated bacterium was characterized as a Klebsiella oxytoca strain.El alpechín (OMW es un residuo puro de la extracción del aceite de oliva, que contiene una elevada carga orgánica y de polifenoles por lo que es resistente a la degradación. Su descarga produce graves problemas de contaminación medioambiental en toda el área mediterránea. Se ha aislado una bacteria anaerobia del OMW, que , durante tres ciclos consecutivos de tratamiento del OMW diluido y suplementado, produjo una disminución significativa de las sustancias fitotóxicas del residuo. De hecho, la concentración en fenoles totales, ácido acético y ácido fórmico se redujeron entre 33 y 64 % cuando las células no estaban inmovilizadas y entre el 62 y 78 % cuando las células bacterianas se inmovilizaron en una esponja de poliuretano. Estos resultados indican que el cultivo de la nueva bacteria aislada puede disminuir la fototoxicidad del alpechín. Análisis filogenético del ribosoma 16S de DNA demostró que todas las secuencias eran miembros de la familia

Genome Sequence of Lactobacillus delbrueckii subsp. lactis CNRZ327, a Dairy Bacterium with Anti-Inflammatory Properties.

Science.gov (United States)

El Kafsi, Hela; Binesse, Johan; Loux, Valentin; Buratti, Julien; Boudebbouze, Samira; Dervyn, Rozenn; Hammani, Amal; Maguin, Emmanuelle; van de Guchte, Maarten

2014-07-17

Lactobacillus delbrueckii subsp. lactis CNRZ327 is a dairy bacterium with anti-inflammatory properties both in vitro and in vivo. Here, we report the genome sequence of this bacterium, which appears to contain no less than 215 insertion sequence (IS) elements, an exceptionally high number regarding the small genome size of the strain. Copyright © 2014 El Kafsi et al.

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

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Cristina A Viegas

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

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

Aliidiomarina haloalkalitolerans sp. nov., a marine bacterium isolated from coastal surface seawater

Digital Repository Service at National Institute of Oceanography (India)

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

A novel Gram-negative, rod shaped, motile, non-sporing strictly aerobic bacterium, designated strain AK5 sup(T), was isolated from a sea water sample collected near Visakhapatnam coast, Bay of Bengal, India. Colonies on marine agar were circular, 3...

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

International Nuclear Information System (INIS)

Liang Xinle; Yang Long; Zhang Hong; Zhang Lei

2011-01-01

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

Whole-Genome Sequence of the Purple Photosynthetic Bacterium Rhodovulum sulfidophilum Strain W4

OpenAIRE

Masuda, Shinji; Hori, Koichi; Maruyama, Fumito; Ren, Shukun; Sugimoto, Saori; Yamamoto, Nozomi; Mori, Hiroshi; Yamada, Takuji; Sato, Shusei; Tabata, Satoshi; Ohta, Hiroyuki; Kurokawa, Ken

2013-01-01

We report the draft genome sequence of the purple photosynthetic bacterium Rhodovulum sulfidophilum. The photosynthesis gene cluster comprises two segments?a unique feature among photosynthesis gene clusters of purple bacteria. The genome information will be useful for further analysis of bacterial photosynthesis.

Optimization of liquid media and biosafety assessment for algae-lysing bacterium NP23.

Science.gov (United States)

Liao, Chunli; Liu, Xiaobo; Shan, Linna

2014-09-01

To control algal bloom caused by nutrient pollution, a wild-type algae-lysing bacterium was isolated from the Baiguishan reservoir in Henan province of China and identified as Enterobacter sp. strain NP23. Algal culture medium was optimized by applying a Placket-Burman design to obtain a high cell concentration of NP23. Three minerals (i.e., 0.6% KNO3, 0.001% MnSO4·H2O, and 0.3% K2HPO4) were found to be independent factors critical for obtaining the highest cell concentration of 10(13) CFU/mL, which was 10(4) times that of the control. In the algae-lysing experiment, the strain exhibited a high lysis rate for the 4 algae test species, namely, Chlorella vulgari, Scenedesmus, Microcystis wesenbergii, and Chlorella pyrenoidosa. Acute toxicity and mutagenicity tests showed that the bacterium NP23 had no toxic and mutagenic effects on fish, even in large doses such as 10(7) or 10(9) CFU/mL. Thus, Enterobacter sp. strain NP23 has strong potential application in the microbial algae-lysing project.

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,

(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.

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

KAUST Repository

Balk, Melike; Mehboob, Farrakh; van Gelder, Antonie H; Rijpstra, W Irene C; Damsté , Jaap S Sinninghe; Stams, Alfons J M

2010-01-01

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

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.

Clostridium geopurificans strain MJ1 sp. nov., a strictly anaerobic bacterium that grows via fermentation and reduces the cyclic nitramine explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX).

Science.gov (United States)

Kwon, Man Jae; Wei, Na; Millerick, Kayleigh; Popovic, Jovan; Finneran, Kevin

2014-06-01

A fermentative, non-spore forming, motile, rod-shaped bacterium, designated strain MJ1(T), was isolated from an RDX contaminated aquifer at a live-fire training site in Northwest NJ, United States. On the basis of 16S rRNA gene sequencing and DNA base composition, strain MJ1(T) was assigned to the Firmicutes. The DNA G+C content was 42.8 mol%. Fermentative growth was supported by glucose and citrate in a defined basal medium. The bacterium is a strict anaerobe that grows between at pH 6.0 and pH 8.0 and 18 and 37 °C. The culture did not grow with hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) as the electron acceptor or mineralize RDX under these conditions. However, MJ1(T) transformed RDX into MNX, methylenedinitramine, formaldehyde, formate, ammonium, nitrous oxide, and nitrate. The nearest phylogenetic relative with a validly published name was Desulfotomaculum guttoideum (95 % similarity). However, MJ1(T) was also related to Clostridium celerecrescens DSM 5628 (95 %), Clostridium indolis DSM 755 (94 %), and Clostridium sphenoides DSM 632 (94 %). DNA:DNA hybridization with these strains was between 6.7 and 58.7 percent. The dominant cellular fatty acids (greater than 5 % of the total, which was 99.0 % recovery) were 16:0 fatty acid methyl ester (FAME) (32.12 %), 18:1cis 11 dimethyl acetal (DMA) (16.47 %), 16:1cis 9 DMA (10.28 %), 16:1cis 9 FAME (8.10 %), and 18:1cis 9 DMA (5.36 %). On the basis of morphological, physiological, and phylogenetic data, Clostridium geopurificans is proposed as a new species in genus Clostridium, with strain MJ1(T) as the type strain.

Studies on the pathogenic bacterium of ulcer disease in Epinephelus awoara

Institute of Scientific and Technical Information of China (English)

无

2006-01-01

Studies were conducted to determine the cause of the acute mortality of cage-cultured Epinephelus awoara in the Tong'an Bay of Xiamen, China during the summer of 2002. Predominant bacteria strain TS-628 was isolated from the diseased grouper. The virulence test confirmed that TS-628 was the pathogenic bacterium. Biochemical characteristics of the isolates were determined using the automatic bacterial identification system and standard tube tests. To further confirm the identification, a 1 121 bp 16S rRNA gene sequence of the isolate was amplified by PCR, which had been deposited into Genbank (accession number: AY747308). According to the biochemical characteristics and by comparing the 16S rRNA gene homology of the isolate, the pathogenic bacterium was identified as Vibrio harveyi. Drug sensitivity tests showed that this pathogenic bacterium was sensitive to 16 antibacterials, especially to chloramphenicol and actinospectacin, but completely resistant to antibacterials likes vancomycin, penicillin, lincomycin, and so on.

Organic metabolites produced by Vibrio parahaemolyticus strain ...

African Journals Online (AJOL)

Identification and action of several antibacterial metabolites produced by a fish pathogen Vibrio parahaemolyticus strain An3 from marine ecosystem of Goa has been demonstrated. Antibacterial activity of the crude cell extract of the test bacterium has been evaluated against indicator pathogenic bacterial strains such as ...

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...

Photoproduction of hydrogen by a non-sulphur bacterium isolated from root zones of water fern Azolla pinnata

Energy Technology Data Exchange (ETDEWEB)

Singh, S.P.; Srivastava, S.C.; Pandey, K.D. (Banaras Hindu Univ., Varanasi (IN). Centre of Advanced Study in Botany)

1990-01-01

A photosynthetic bacterium Rhodopseudomonas sp. BHU strain 1 was isolated from the root zone of water fern Azolla pinnata. The bacterium was found to produce hydrogen with potato starch under phototrophic conditions. The immobilized bacterial cells showed sustained hydrogen production with a more than 4-fold difference over free cell suspensions. The data have been discussed in the light of possible utilization of relatively cheaper raw materials by non-sulphur bacteria to evolve hydrogen. (author).

Antifouling Activity towards Mussel by Small-Molecule Compounds from a Strain of Vibrio alginolyticus Bacterium Associated with Sea Anemone Haliplanella sp.

Science.gov (United States)

Wang, Xiang; Huang, Yanqiu; Sheng, Yanqing; Su, Pei; Qiu, Yan; Ke, Caihuan; Feng, Danqing

2017-03-28

Mussels are major fouling organisms causing serious technical and economic problems. In this study, antifouling activity towards mussel was found in three compounds isolated from a marine bacterium associated with the sea anemone Haliplanella sp. This bacterial strain, called PE2, was identified as Vibrio alginolyticus using morphology, biochemical tests, and phylogenetic analysis based on sequences of 16S rRNA and four housekeeping genes ( rpoD, gyrB, rctB, and toxR ). Three small-molecule compounds (indole, 3-formylindole, and cyclo (Pro-Leu)) were purified from the ethyl acetate extract of V. alginolyticus PE2 using column chromatography techniques. They all significantly inhibited byssal thread production of the green mussel Perna viridis , with EC 50 values of 24.45 μg/ml for indole, 50.07 μg/ml for 3-formylindole, and 49.24 μg/ml for cyclo (Pro-Leu). Previous research on the antifouling activity of metabolites from marine bacteria towards mussels is scarce. Indole, 3-formylindole and cyclo (Pro-Leu) also exhibited antifouling activity against settlement of the barnacle Balanus albicostatus (EC 50 values of 8.84, 0.43, and 11.35 μg/ml, respectively) and the marine bacterium Pseudomonas sp. (EC 50 values of 42.68, 69.68, and 39.05 μg/ml, respectively). These results suggested that the three compounds are potentially useful for environmentally friendly mussel control and/or the development of new antifouling additives that are effective against several biofoulers.

High genetic diversity among strains of the unindustrialized lactic acid bacterium Carnobacterium maltaromaticum in dairy products as revealed by multilocus sequence typing.

Science.gov (United States)

Rahman, Abdur; Cailliez-Grimal, Catherine; Bontemps, Cyril; Payot, Sophie; Chaillou, Stéphane; Revol-Junelles, Anne-Marie; Borges, Frédéric

2014-07-01

Dairy products are colonized with three main classes of lactic acid bacteria (LAB): opportunistic bacteria, traditional starters, and industrial starters. Most of the population structure studies were previously performed with LAB species belonging to these three classes and give interesting knowledge about the population structure of LAB at the stage where they are already industrialized. However, these studies give little information about the population structure of LAB prior their use as an industrial starter. Carnobacterium maltaromaticum is a LAB colonizing diverse environments, including dairy products. Since this bacterium was discovered relatively recently, it is not yet commercialized as an industrial starter, which makes C. maltaromaticum an interesting model for the study of unindustrialized LAB population structure in dairy products. A multilocus sequence typing scheme based on an analysis of fragments of the genes dapE, ddlA, glpQ, ilvE, pyc, pyrE, and leuS was applied to a collection of 47 strains, including 28 strains isolated from dairy products. The scheme allowed detecting 36 sequence types with a discriminatory index of 0.98. The whole population was clustered in four deeply branched lineages, in which the dairy strains were spread. Moreover, the dairy strains could exhibit a high diversity within these lineages, leading to an overall dairy population with a diversity level as high as that of the nondairy population. These results are in agreement with the hypothesis according to which the industrialization of LAB leads to a diversity reduction in dairy products. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Cellulosic ethanol production via consolidated bioprocessing by a novel thermophilic anaerobic bacterium isolated from a Himalayan hot spring.

Science.gov (United States)

Singh, Nisha; Mathur, Anshu S; Tuli, Deepak K; Gupta, Ravi P; Barrow, Colin J; Puri, Munish

2017-01-01

Cellulose-degrading thermophilic anaerobic bacterium as a suitable host for consolidated bioprocessing (CBP) has been proposed as an economically suited platform for the production of second-generation biofuels. To recognize the overall objective of CBP, fermentation using co-culture of different cellulolytic and sugar-fermenting thermophilic anaerobic bacteria has been widely studied as an approach to achieving improved ethanol production. We assessed monoculture and co-culture fermentation of novel thermophilic anaerobic bacterium for ethanol production from real substrates under controlled conditions. In this study, Clostridium sp. DBT-IOC-C19, a cellulose-degrading thermophilic anaerobic bacterium, was isolated from the cellulolytic enrichment cultures obtained from a Himalayan hot spring. Strain DBT-IOC-C19 exhibited a broad substrate spectrum and presented single-step conversion of various cellulosic and hemicellulosic substrates to ethanol, acetate, and lactate with ethanol being the major fermentation product. Additionally, the effect of varying cellulose concentrations on the fermentation performance of the strain was studied, indicating a maximum cellulose utilization ability of 10 g L -1 cellulose. Avicel degradation kinetics of the strain DBT-IOC-C19 displayed 94.6% degradation at 5 g L -1 and 82.74% degradation at 10 g L -1 avicel concentration within 96 h of fermentation. In a comparative study with Clostridium thermocellum DSM 1313, the ethanol and total product concentrations were higher by the newly isolated strain on pretreated rice straw at an equivalent substrate loading. Three different co-culture combinations were used on various substrates that presented two-fold yield improvement than the monoculture during batch fermentation. This study demonstrated the direct fermentation ability of the novel thermophilic anaerobic bacteria on various cellulosic and hemicellulosic substrates into ethanol without the aid of any exogenous enzymes

Phosphate enhances levan production in the endophytic bacterium Gluconacetobacter diazotrophicus Pal5

Science.gov (United States)

Idogawa, Nao; Amamoto, Ryuta; Murata, Kousaku; Kawai, Shigeyuki

2014-01-01

Gluconacetobacter diazotrophicus is a gram-negative and endophytic nitrogen-fixing bacterium that has several beneficial effects in host plants; thus, utilization of this bacterium as a biofertilizer in agriculture may be possible. G. diazotrophicus synthesizes levan, a D-fructofuranosyl polymer with β-(2→6) linkages, as an exopolysaccharide and the synthesized levan improves the stress tolerance of the bacterium. In this study, we found that phosphate enhances levan production by G. diazotrophicus Pal5, a wild type strain that showed a stronger mucous phenotype on solid medium containing 28 mM phosphate than on solid medium containing 7 mM phosphate. A G. diazotrophicus Pal5 levansucrase disruptant showed only a weak mucous phenotype regardless of the phosphate concentration, indicating that the mucous phenotype observed on 28 mM phosphate medium was caused by levan. To our knowledge, this is the first report of the effect of a high concentration of phosphate on exopolysaccharide production. PMID:24717418

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

OpenAIRE

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

2015-01-01

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

Genome Sequence of Campylobacter jejuni strain 327, a strain isolated from a turkey slaughterhouse

DEFF Research Database (Denmark)

Takamiya, Monica; Özen, Asli Ismihan; Rasmussen, Morten

2011-01-01

, catalase positive bacterium obtains energy from the metabolism of amino acids and Krebs cycle intermediates. Strain 327 was isolated from a turkey slaughter production line and is considered environmentally sensitive to food processing (cold, heat, drying) and storage conditions. The 327 whole genome...

Complete genome sequence of Klebsiella pneumoniae J1, a protein-based microbial flocculant-producing bacterium.

Science.gov (United States)

Pang, Changlong; Li, Ang; Cui, Di; Yang, Jixian; Ma, Fang; Guo, Haijuan

2016-02-20

Klebsiella pneumoniae J1 is a Gram-negative strain, which belongs to a protein-based microbial flocculant-producing bacterium. However, little genetic information is known about this species. Here we carried out a whole-genome sequence analysis of this strain and report the complete genome sequence of this organism and its genetic basis for carbohydrate metabolism, capsule biosynthesis and transport system. Copyright © 2016 Elsevier B.V. All rights reserved.

[Development of a liquid fermentation system and encystment for a nitrogen-fixing bacterium strain having biofertilizer potential].

Science.gov (United States)

Camelo-Rusinque, Mauricio; Moreno-Galván, Andrés; Romero-Perdomo, Felipe; Bonilla-Buitrago, Ruth

The indiscriminate use of chemical fertilizers has contributed to the deterioration of the biological, physical and chemical properties of the soil, resulting in the loss of its productive capacity. For this reason, the use of biofertilizers has emerged as a technological alternative. The objective of this research was to develop a suitable liquid fermentation system and encystment for the multiplication of Azotobacter chroococcum AC1 strain, a bacterium employed in a biofertilizer formulation produced at present by CARPOICA, Colombia. Sequential statistical designs were used to determine the conditions in the fermentation system. The interaction between agitation, aeration and pH was evaluated on the viable biomass (CFU/ml) of AC1. In addition, the encystment ability of the strain was evaluated using two encystment agents and the potential plant growth-promoting rhizobacteria (PGPR) activity was assessed by different techniques, such as nitrogen fixation by ARA, phosphate solubilization by the phospho-molybdenum-blue reaction and indolic compound production by colorimetric reaction using the Salkowski reagent. Results showed significant effects (p<0.05) on the viable biomass in the three conditions (pH, aeration and agitation) tested individually, in one dual interaction and one tripartite interaction, were demonstrated to have a positive effect on the response variable aeration and agitation. The addition of the two encystment agents evaluated, AE01 and AE02, demonstrated the ability of AC1 to form cysts under stress conditions. Likewise, fermentation and encystment conditions did not affect the biological activities tested. Copyright © 2017 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

Alteration of the Canine Small-Intestinal Lactic Acid Bacterium Microbiota by Feeding of Potential Probiotics

OpenAIRE

Manninen, Titta J. K.; Rinkinen, Minna L.; Beasley, Shea S.; Saris, Per E. J.

2006-01-01

Five potentially probiotic canine fecal lactic acid bacterium (LAB) strains, Lactobacillus fermentum LAB8, Lactobacillus salivarius LAB9, Weissella confusa LAB10, Lactobacillus rhamnosus LAB11, and Lactobacillus mucosae LAB12, were fed to five permanently fistulated beagles for 7 days. The survival of the strains and their potential effects on the indigenous intestinal LAB microbiota were monitored for 17 days. Denaturing gradient gel electrophoresis (DGGE) demonstrated that the five fed LAB ...

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.

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

Science.gov (United States)

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

2015-04-02

Lysobacter sp. strain A03 is a protease-producing bacterium isolated from decomposing-penguin feathers collected in the Antarctic environment. This strain has the ability to degrade keratin at low temperatures. The A03 genome sequence provides the possibility of finding new genes with biotechnological potential to better understand its cold-adaptation mechanism and survival in cold environments. Copyright © 2015 Pereira et al.

[Isolation and identification of a lactate-utilizing, butyrate-producing bacterium and its primary metabolic characteristics].

Science.gov (United States)

Liu, Wei; Zhu, Wei-yun; Yao, Wen; Mao, Sheng-yong

2007-06-01

The distal mammalian gut harbors prodigiously abundant microbes, which provide unique metabolic traits to host. A lactate-utilizing, butyrate-producing bacterium, strain LB01, was isolated from adult swine feces by utilizing modified Hungate technique with rumen liquid-independent YCFA medium supplemented with lactate as the single carbon source. It was an obligate anaerobic, Gram positive bacterium, and could utilize glucose, fructose, maltose and lactate with a large amount of gas products. 16S rRNA sequence analysis revealed that it had the high similarity with members of the genus Megasphaera. The metabolic characteristics of strain LB01 was investigated by using in vitro fermentation system. Lactate at the concentration of 65 mmol/L in YCFA medium was rapidly consumed within 9 hours and was mainly converted to propionate and butyrate after 24h. As the level of acetate declined, the concentration of butyrate rose only in the presence of glucose, suggesting that butyrate could possibly be synthesized by the acetyl CoA: butyryl CoA transferase. When co-cultured with lactic acid bacteria strain K9, strain LB01 evidently reduced the concentration of lactate produced by strain K9 and decelerated the rapid pH drop, finally producing 12.11 mmol/L butyrate and 4.06 mmol/L propionate. The metabolic characteristics that strain LB01 efficiently converts toxic lactate and excessive acetate to butyrate can prevent lactate and acetate accumulation in the large intestine and maintain the slightly acidic environment of the large intestine, consequently revealing that stain LB01 could act as a potential probiotics.

Draft Genome Sequence of Lactobacillus paracasei DmW181, a Bacterium Isolated from Wild Drosophila

OpenAIRE

Hammer, Austin J.; Walters, Amber; Carroll, Courtney; Newell, Peter D.; Chaston, John M.

2017-01-01

ABSTRACT The draft genome sequence of Lactobacillus paracasei DmW181, an anaerobic bacterium isolate from wild Drosophila flies, is reported here. Strain DmW181 possesses genes for sialic acid and mannose metabolism. The assembled genome is 3,201,429?bp, with 3,454 predicted genes.

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.

Cesiribacter roseus sp. nov., a pink-pigmented bacterium isolated from desert sand.

Science.gov (United States)

Liu, Ming; Qi, Huan; Luo, Xuesong; Dai, Jun; Peng, Fang; Fang, Chengxiang

2012-01-01

A pink-pigmented, Gram-negative, rod-shaped, motile, strictly aerobic bacterium, designated strain 311(T), was isolated from desert sand in Xinjiang, China. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain 311(T) was related closely to Cesiribacter andamanensis AMV16(T) (94.6% similarity). The DNA G+C content of strain 311(T) was 47.1 mol% and the major respiratory quinone was menaquinone 7 (MK-7). The main cellular fatty acids were C(16:1)ω5c (29.9%), iso-C(15:0) (21.9%), iso-C(17:0) 3-OH (13.3%) and summed feature 4 (iso-C(17:1) I and/or anteiso-C(17:1) B; 13.0%). Based on phenotypic and chemotaxonomic data and phylogenetic analysis, strain 311(T) is considered to represent a novel species of the genus Cesiribacter, for which the name Cesiribacter roseus sp. nov. is proposed. The type strain is 311(T) (=CCTCC AB 207142(T) =KACC 15456(T)).

Deferribacter thermophilus gen. nov., sp. nov., a novel thermophilic manganese- and iron-reducing bacterium isolated from a petroleum reservoir.

Science.gov (United States)

Greene, A C; Patel, B K; Sheehy, A J

1997-04-01

A thermophilic anaerobic bacterium, designated strain BMAT (T = type strain), was isolated from the production water of Beatrice oil field in the North Sea (United Kingdom). The cells were straight to bent rods (1 to 5 by 0.3 to 0.5 microns) which stained gram negative. Strain BMAT obtained energy from the reduction of manganese (IV), iron(III), and nitrate in the presence of yeast extract, peptone, Casamino Acids, tryptone, hydrogen, malate, acetate, citrate, pyruvate, lactate, succinate, and valerate. The isolate grew optimally at 60 degrees C (temperature range for growth, 50 to 65 degrees C) and in the presence of 2% (wt/vol) NaCl (NaCl range for growth, 0 to 5% [wt/vol]). The DNA base composition was 34 mol% G + C. Phylogenetic analyses of the 16S rRNA gene indicated that strain BMAT is a member of the domain Bacteria. The closest known bacterium is the moderate thermophile Flexistipes sinusarabici (similarity value, 88%). Strain BMAT possesses phenotypic and phylogenetic traits that do not allow its classification as a member of any previously described genus; therefore, we propose that this isolate should be described as a member of a novel species of a new genus, Deferribacter thermophilus gen. nov., sp. nov.

Draft Genome Sequence of Pontibacter sp. nov. BAB1700, a Halotolerant, Industrially Important Bacterium

Science.gov (United States)

Joshi, M. N.; Sharma, A. C.; Pandya, R. V.; Patel, R. P.; Saiyed, Z. M.; Saxena, A. K.

2012-01-01

Pontibacter sp. nov. BAB1700 is a halotolerant, Gram-negative, rod-shaped, pink-pigmented, menaquinone-7-producing bacterium isolated from sediments of a drilling well. The draft genome sequence of the strain, consisting of one chromosome of 4.5 Mb, revealed vital gene clusters involved in vitamin biosynthesis and resistance against various metals and antibiotics. PMID:23105068

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

KAUST Repository

Barbato, Marta

2015-12-10

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

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

KAUST Repository

Barbato, Marta; Mapelli, Francesca; Chouaia, Bessem; Crotti, Elena; Daffonchio, Daniele; Borin, Sara

2015-01-01

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

Draft Genome Sequence of Lactobacillus paracasei DmW181, a Bacterium Isolated from Wild Drosophila.

Science.gov (United States)

Hammer, Austin J; Walters, Amber; Carroll, Courtney; Newell, Peter D; Chaston, John M

2017-07-06

The draft genome sequence of Lactobacillus paracasei DmW181, an anaerobic bacterium isolate from wild Drosophila flies, is reported here. Strain DmW181 possesses genes for sialic acid and mannose metabolism. The assembled genome is 3,201,429 bp, with 3,454 predicted genes. Copyright © 2017 Hammer et al.

Reduction of molybdate to molybdenum blue by Klebsiella sp. strain hkeem.

Science.gov (United States)

Lim, H K; Syed, M A; Shukor, M Y

2012-06-01

A novel molybdate-reducing bacterium, tentatively identified as Klebsiella sp. strain hkeem and based on partial 16s rDNA gene sequencing and phylogenetic analysis, has been isolated. Strain hkeem produced 3 times more molybdenum blue than Serratia sp. strain Dr.Y8; the most potent Mo-reducing bacterium isolated to date. Molybdate was optimally reduced to molybdenum blue using 4.5 mM phosphate, 80 mM molybdate and using 1% (w/v) fructose as a carbon source. Molybdate reduction was optimum at 30 °C and at pH 7.3. The molybdenum blue produced from cellular reduction exhibited absorption spectrum with a maximum peak at 865 nm and a shoulder at 700 nm. Inhibitors of electron transport system such as antimycin A, rotenone, sodium azide, and potassium cyanide did not inhibit the molybdenum-reducing enzyme. Mercury, silver, and copper at 1 ppm inhibited molybdenum blue formation in whole cells of strain hkeem. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

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Jun-Feng Shi

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

Isolation and characterization of a novel hydrocarbon-degrading bacterium Achromobacter sp. HZ01 from the crude oil-contaminated seawater at the Daya Bay, southern China

International Nuclear Information System (INIS)

Deng, Mao-Cheng; Li, Jing; Liang, Fu-Rui; Yi, Meisheng; Xu, Xiao-Ming; Yuan, Jian-Ping; Peng, Juan; Wu, Chou-Fei; Wang, Jiang-Hai

2014-01-01

Graphical abstract: Morphological properties of the colonies and cells of strain HZ01. (A) Colonies of strain HZ01 on the LB solid plate; (B) Gram-negative bacterium of strain HZ01 (20 × 100); (C) Scanning electron microscopy (SEM) photograph of strain HZ01 (×15,000); and (D) Transmission electronic microscopy (TEM) photograph of strain HZ01 (×5000). - Highlights: • A novel petroleum degrading bacterium HZ01 was obtained from the crude oil-contaminated seawater. • Strain HZ01 had been identified as Achromobacter sp. • Strain HZ01 could degrade the evaporated diesel oil with the degradability of 96.6%. • Strain HZ01 could effectively degrade anthracene, phenanthrene and pyrence. • Strain HZ01 may be employed to remove hydrocarbon contaminants. - Abstract: Microorganisms play an important role in the biodegradation of petroleum contaminants, which have attracted great concern due to their persistent toxicity and difficult biodegradation. In this paper, a novel hydrocarbon-degrading bacterium HZ01 was isolated from the crude oil-contaminated seawater at the Daya Bay, South China Sea, and identified as Achromobacter sp. Under the conditions of pH 7.0, NaCl 3% (w/v), temperature 28 °C and rotary speed 150 rpm, its degradability of the total n-alkanes reached up to 96.6% after 10 days of incubation for the evaporated diesel oil. Furthermore, Achromobacter sp. HZ01 could effectively utilize polycyclic aromatic hydrocarbons (PAHs) as its sole carbon source, and could remove anthracene, phenanthrene and pyrence about 29.8%, 50.6% and 38.4% respectively after 30 days of incubation. Therefore, Achromobacter sp. HZ01 may employed as an excellent degrader to develop one cost-effective and eco-friendly method for the bioremediation of marine environments polluted by crude oil

Extracellular Pectinase from a Novel Bacterium Chryseobacterium indologenes Strain SD and Its Application in Fruit Juice Clarification

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Karabi Roy

2018-01-01

Full Text Available Pectinase is one of the important enzymes of industrial sectors. Presently, most of the pectinases are of plant origin but there are only a few reports on bacterial pectinases. The aim of the present study was to isolate a novel and potential pectinase producing bacterium as well as optimization of its various parameters for maximum enzyme production. A total of forty bacterial isolates were isolated from vegetable dump waste soil using standard plate count methods. Primary screening was done by hydrolysis of pectin. Pectinase activity was determined by measuring the increase in reducing sugar formed by the enzymatic hydrolysis of pectin. Among the bacterial isolates, the isolate K6 exhibited higher pectinase activity in broth medium and was selected for further studies. The selected bacterial isolate K6 was identified as Chryseobacterium indologenes strain SD. The isolate was found to produce maximum pectinase at 37°C with pH 7.5 upon incubation for 72 hours, while cultured in production medium containing citrus pectin and yeast extract as C and N sources, respectively. During enzyme-substrate reaction phase, the enzyme exhibited its best activity at pH of 8.0 and temperature of 40°C using citrus pectin as substrate. The pectinase of the isolate showed potentiality on different types of fruit juice clarification.

Two New Cholic Acid Derivatives from the Marine Ascidian-Associated Bacterium Hasllibacter halocynthiae

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Sung Hun Kim

2012-10-01

Full Text Available The investigation of secondary metabolites in liquid cultures of a recently discovered marine bacterium, Hasllibacter halocynthiae strain KME 002T, led to the isolation of two new cholic acid derivatives. The structures of these compounds were determined to be 3,3,12-trihydroxy-7-ketocholanic acid (1 and 3,3,12-trihydroxy-7-deoxycholanic acid (2 through HRFABMS and NMR data analyses.

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

Science.gov (United States)

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

1997-07-01

A mesophilic, acetate-oxidizing, sulfur-reducing bacterium, strain NZ27T, was isolated from anoxic mud from a freshwater sulfur spring. The cells were ovoid, motile, and gram negative. In addition to acetate, the strain oxidized pyruvate, succinate, and fumarate. Sulfur flower could be replaced by polysulfide as an electron acceptor. Ferric nitrilotriacetic acid was reduced in the presence of pyruvate; however, this reduction did not sustain growth. These phenotypic characteristics suggested that strain NZ27T is affiliated with the genus Desulfuromonas. A phylogenetic analysis based on the results of comparative 16S ribosomal DNA sequencing confirmed that strain NZ27T belongs to the Desulfuromonas cluster in the recently proposed family "Geobacteracea" in the delta subgroup of the Proteobacteria. In addition, the results of DNA-DNA hybridization studies confirmed that strain NZ27T represents a novel species. Desulfuromonas thiophila, a name tentatively used in previous publication, is the name proposed for strain NZ27T in this paper.

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).

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.

Examination of the Anaerobic Growth of Campylobacter concisus Strains

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Hoyul Lee

2014-01-01

Full Text Available Campylobacter concisus is an oral bacterium that is associated with intestinal diseases. C. concisus was previously described as a bacterium that requires H2-enriched microaerobic conditions for growth. The level of H2 in the oral cavity is extremely low, suggesting that C. concisus is unlikely to have a microaerobic growth there. In this study, the anaerobic growth of C. concisus was investigated. The growth of fifty-seven oral C. concisus strains and six enteric C. concisus strains under various atmospheric conditions including anaerobic conditions with and without H2 was examined. The atmospheric conditions were generated using commercially available gas-generation systems. C. concisus putative virulence proteins were identified using mass spectrometry analysis. Under anaerobic conditions, 92% of the oral C. concisus strains (52/57 and all six enteric strains grew without the presence of H2 and the presence of H2 greatly increased C. concisus growth. An oral C. concisus strain was found to express a number of putative virulence proteins and the expression levels of these proteins were not affected by H2. The levels of H2 appeared to affect the optimal growth of C. concisus. This study provides useful information in understanding the natural colonization site and pathogenicity of C. concisus.

Draft genome sequence of Therminicola potens strain JR

Energy Technology Data Exchange (ETDEWEB)

Byrne-Bailey, K.G.; Wrighton, K.C.; Melnyk, R.A.; Agbo, P.; Hazen, T.C.; Coates, J.D.

2010-07-01

'Thermincola potens' strain JR is one of the first Gram-positive dissimilatory metal-reducing bacteria (DMRB) for which there is a complete genome sequence. Consistent with the physiology of this organism, preliminary annotation revealed an abundance of multiheme c-type cytochromes that are putatively associated with the periplasm and cell surface in a Gram-positive bacterium. Here we report the complete genome sequence of strain JR.

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

DEFF Research Database (Denmark)

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

2002-01-01

The biocontrol bacterium Burkholderia cepacia is known to suppress a broad range of root pathogenic fungi, while its impact on other beneficial non-target organisms such as arbuscular mycorrhizal (AM) fungi is unknown. Direct interactions between five B. cepacia strains and the AM fungus, Glomus ...

Elemental sulfur and thiosulfate disproportionation by Desulfocapsa sulfoexigens sp. nov., a new anaerobic bacterium isolated from marine surface sediment.

Science.gov (United States)

Finster, K; Liesack, W; Thamdrup, B

1998-01-01

A mesophilic, anaerobic, gram-negative bacterium, strain SB164P1, was enriched and isolated from oxidized marine surface sediment with elemental sulfur as the sole energy substrate in the presence of ferrihydrite. Elemental sulfur was disproportionated to hydrogen sulfide and sulfate. Growth was observed exclusively in the presence of a hydrogen sulfide scavenger, e.g., ferrihydrite. In the absence of a scavenger, sulfide and sulfate production were observed but no growth occurred. Strain SB164P1 grew also by disproportionation of thiosulfate and sulfite. With thiosulfate, the growth efficiency was higher in ferrihydrite-supplemented media than in media without ferrihydrite. Growth coupled to sulfate reduction was not observed. However, a slight sulfide production occurred in cultures incubated with formate and sulfate. Strain SB164P1 is the first bacterium described that grows chemolithoautotrophically exclusively by the disproportionation of inorganic sulfur compounds. Comparative 16S rDNA sequencing analysis placed strain SB164P1 into the delta subclass of the class Proteobacteria. Its closest relative is Desulfocapsa thiozymogenes, and slightly more distantly related are Desulfofustis glycolicus and Desulforhopalus vacuolatus. This phylogenetic cluster of organisms, together with members of the genus Desulfobulbus, forms one of the main lines of descent within the delta subclass of the Proteobacteria. Due to the common phenotypic characteristics and the phylogenetic relatedness to Desulfocapsa thiozymogenes, we propose that strain SB164P1 be designated the type strain of Desulfocapsa sulfoexigens sp. nov.

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

DEFF Research Database (Denmark)

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

2006-01-01

Strain 15 T is a novel spore-forming, sulfate-reducing bacterium isolated from a permanently cold fjord sediment of Svalbard. Sulfate could be replaced by sulfite or thiosulfate. Hydrogen, formate, lactate, propionate, butyrate, hexanoate, methanol, ethanol, propanol, butanol, pyruvate, malate, s...... related to Desulfotomaculum thermosapovorans MLF(T) (93-5% 16S rRNA gene sequence similarity). Strain 15 T represents a novel species, for which the name Desulfotomaculurn arcticum sp. nov. is proposed. The type strain is strain 15 T (=DSM 17038(T)=jCM 12923(T))....

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...

Gold nanoparticles synthesized by Geobacillus sp. strain ID17 a thermophilic bacterium isolated from Deception Island, Antarctica

Science.gov (United States)

2013-01-01

Background The use of microorganisms in the synthesis of nanoparticles emerges as an eco-friendly and exciting approach, for production of nanoparticles due to its low energy requirement, environmental compatibility, reduced costs of manufacture, scalability, and nanoparticle stabilization compared with the chemical synthesis. Results The production of gold nanoparticles by the thermophilic bacterium Geobacillus sp. strain ID17 is reported in this study. Cells exposed to Au3+ turned from colourless into an intense purple colour. This change of colour indicates the accumulation of intracellular gold nanoparticles. Elemental analysis of particles composition was verified using TEM and EDX analysis. The intracellular localization and particles size were verified by TEM showing two different types of particles of predominant quasi-hexagonal shape with size ranging from 5–50 nm. The mayority of them were between 10‒20 nm in size. FT-IR was utilized to characterize the chemical surface of gold nanoparticles. This assay supports the idea of a protein type of compound on the surface of biosynthesized gold nanoparticles. Reductase activity involved in the synthesis of gold nanoparticles has been previously reported to be present in others microorganisms. This reduction using NADH as substrate was tested in ID17. Crude extracts of the microorganism could catalyze the NADH-dependent Au3+ reduction. Conclusions Our results strongly suggest that the biosynthesis of gold nanoparticles by ID17 is mediated by enzymes and NADH as a cofactor for this biological transformation. PMID:23919572

Draft Genome Sequence of Ochrobactrum intermedium Strain SA148, a Plant Growth-Promoting Desert Rhizobacterium

KAUST Repository

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

2017-01-01

Ochrobactrum intermedium strain SA148 is a plant growth-promoting bacterium isolated from sandy soil in the Jizan area of Saudi Arabia. Here, we report the 4.9-Mb draft genome sequence of this strain, highlighting different pathways characteristic

DNA type analysis to differentiate strains of Xylophilus ampelinus from Europe and Hokkaido, Japan

OpenAIRE

Komatsu, Tsutomu; Shinmura, Akinori; Kondo, Norio

2016-01-01

Strains of the bacterium Xylophilus ampelinus were collected from Europe and Hokkaido, Japan. Genomic fingerprints generated from 43 strains revealed four DNA types (A-D) using the combined results of Rep-, ERIC-, and Box-PCR. Genetic variation was found among the strains examined; strains collected from Europe belonged to DNA types A or B, and strains collected from Hokkaido belonged to DNA types C or D. However, strains belonging to each DNA type showed the same pathogenicity to grapevines ...

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

Science.gov (United States)

Ren, Yuan; Yang, Juan; Chen, Shaoyi

2015-12-01

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

Anaerostipes caccae gen. nov., sp. nov., a new saccharolytic, acetate-utilising, butyrate-producing bacterium from human faeces.

Science.gov (United States)

Schwiertz, Andreas; Hold, Georgina L; Duncan, Sylvia H; Gruhl, Barbel; Collins, Matthew D; Lawson, Paul A; Flint, Harry J; Blaut, Michael

2002-04-01

Two strains of a previously undescribed Eubacterium-like bacterium were isolated from human faeces. The strains are Gram-variable, obligately anaerobic, catalase negative, asporogenous rod-shaped cells which produced acetate, butyrate and lactate as the end products of glucose metabolism. The two isolates displayed 99.9% 16S rRNA gene sequence similarity to each other and treeing analysis demonstrated the faecal isolates are far removed from Eubacterium sensu stricto and that they represent a new subline within the Clostridium coccoides group of organisms. Based on phenotypic and phylogenetic criteria, it is proposed that the two strains from faeces be classified as a new genus and species, Anaerostipes caccae. The type strain of Anaerostipes caccae is NCIMB 13811T (= DSM 14662T).

Crassaminicella profunda gen. nov., sp. nov., an anaerobic marine bacterium isolated from deep-sea sediments.

Science.gov (United States)

Lakhal, Raja; Pradel, Nathalie; Postec, Anne; Ollivier, Bernard; Cayol, Jean-Luc; Godfroy, Anne; Fardeau, Marie-Laure; Galés, Grégoire

2015-09-01

A novel, anaerobic, chemo-organotrophic bacterium, designated strain Ra1766H(T), was isolated from sediments of the Guaymas basin (Gulf of California, Mexico) taken from a depth of 2002  m. Cells were thin, motile, Gram-stain-positive, flexible rods forming terminal endospores. Strain Ra1766H(T) grew at temperatures of 25-45 °C (optimum 30 °C), pH 6.7-8.1 (optimum 7.5) and in a salinity of 5-60 g l(-1) NaCl (optimum 30 g l(-1)). It was an obligate heterotrophic bacterium fermenting carbohydrates (glucose and mannose) and organic acids (pyruvate and succinate). Casamino acids and amino acids (glutamate, aspartate and glycine) were also fermented. The main end products from glucose fermentation were acetate, butyrate, ethanol, H2 and CO2. Sulfate, sulfite, thiosulfate, elemental sulfur, fumarate, nitrate, nitrite and Fe(III) were not used as terminal electron acceptors. The predominant cellular fatty acids were C14  : 0, C16 : 1ω7, C16 : 1ω7 DMA and C16 : 0. The main polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phospholipids. The G+C content of the genomic DNA was 33.7 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain Ra1766H(T) was affiliated to cluster XI of the order Clostridiales, phylum Firmicutes. The closest phylogenetic relative of Ra1766H(T) was Geosporobacter subterraneus (94.2% 16S rRNA gene sequence similarity). On the basis of phylogenetic inference and phenotypic properties, strain Ra1766H(T) ( = DSM 27501(T) = JCM 19377(T)) is proposed to be the type strain of a novel species of a novel genus, named Crassaminicella profunda.

Partial genome sequence of Thioalkalivibrio thiocyanodenitrificans ARhD 1T, a chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium capable of complete denitrification

NARCIS (Netherlands)

Berben, T.; Sorokin, D.Y.; Ivanova, N.; Pati, A.; Kyrpides, N.; Goodwin, L.A; Woyke, T.; Muyzer, G.

2015-01-01

Thioalkalivibrio thiocyanodenitrificans strain ARhD 1 T is a motile, Gram-negative bacterium isolated from soda lakes that belongs to the Gammaproteobacteria. It derives energy for growth and carbon fixation from the oxidation of sulfur compounds, most notably thiocyanate, and so is a

Draft genome sequence of Bacillus okhensis Kh10-101T, a halo-alkali tolerant bacterium from Indian saltpan

Directory of Open Access Journals (Sweden)

Pilla Sankara Krishna

2015-12-01

Full Text Available We report the 4.86-Mb draft genome sequence of Bacillus okhensis strain Kh10-101T, a halo-alkali tolerant rod shaped bacterium isolated from a salt pan near port of Okha, India. This bacterium is a potential model to study the molecular response of bacteria to salt as well as alkaline stress, as it thrives under both high salt and high pH conditions. The draft genome consist of 4,865,284 bp with 38.2% G + C, 4952 predicted CDS, 157 tRNAs and 8 rRNAs. Sequence was deposited at DDBJ/EMBL/GenBank under the project accession JRJU00000000.

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

DEFF Research Database (Denmark)

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

2015-01-01

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

Complete genome sequence of Paenibacillus sp. strain JDR-2

Science.gov (United States)

Virginia Chow; Guang Nong; Franz J. St. John; John D. Rice; Ellen Dickstein; Olga Chertkov; David Bruce; Chris Detter; Thomas Brettin; James Han; Tanja Woyke; Sam Pitluck; Matt Nolan; Amrita Pati; Joel Martin; Alex Copeland; Miriam L. Land; Lynne Goodwin; Jeffrey B. Jones; Lonnie O. Ingram; Keelnathan T. Shanmugam; James F. Preston

2012-01-01

Paenibacillus sp. strain JDR-2, an aggressively xylanolytic bacterium isolated from sweetgum (Liquidambar styraciflua) wood, is able to efficiently depolymerize, assimilate and metabolize 4-O-methylglucuronoxylan, the predominant structural component of hardwood hemicelluloses. A basis for this capability was first supported by...

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.

‘Lactobacillus raoultii’ sp. nov., a new bacterium isolated from the vaginal flora of a woman with bacterial vaginosis

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B. Nicaise

2018-01-01

Full Text Available We report the isolation of a new bacterium species, ‘Lactobacillus raoultii’ strain Marseille P4006 (CSUR P4006, isolated from a vaginal sample of a 45-year-old woman with bacterial vaginosis. Keywords: Bacterial vaginosis, culturomics, emerging bacteria, human microbiota, Lactobacillus raoultii, vaginal microbiota

Draft genome sequence of Xylella fastidiosa pear leaf scorch strain in Taiwan

Science.gov (United States)

The draft genome sequence of Xylella fastidiosa pear leaf scorch strain (PLS229) isolated from pear cultivar Hengshan (Pyrus pyrifolia) in Taiwan is reported. The bacterium has a genome size of 2,733,013 bp with a G+C content of 53.1%. The PLS229 strain genome was annotated to have 3,259 open readin...

Isolation and characterization of Alicycliphilus denitrificans strain BC, which grows on benzene with chlorate as the electron acceptor

NARCIS (Netherlands)

Weelink, S.A.B.; Tan, N.C.G.; Broeke, H. ten; Kieboom, C. van den; Doesburg, W. van; Langenhoff, A.A.M.; Gerritse, J.; Junca, H.; Stams, A.J.M.

2008-01-01

A bacterium, strain BC, was isolated from a benzene-degrading chlorate-reducing enrichment culture. Strain BC degrades benzene in conjunction with chlorate reduction. Cells of strain BC are short rods that are 0.6 μm wide and 1 to 2 μm long, are motile, and stain gram negative. Strain BC grows on

Behavior of the meat-borne bacterium Lactobacillus sakei during its transit through the gastrointestinal tracts of axenic and conventional mice.

Science.gov (United States)

Chiaramonte, Fabrizio; Blugeon, Sébastien; Chaillou, Stéphane; Langella, Philippe; Zagorec, Monique

2009-07-01

A Lactobacillus sakei strain named FLEC01 was isolated from human feces and characterized genotypically. Comparison of the genetic features of this strain with those of both the meat-borne L. sakei strain 23K and another human isolate, LTH5590, showed that they belong to different but closely related clusters. The three L. sakei strains did not persist and only transited through the gastrointestinal tracts (GITs) of conventional C3H/HeN mice. In contrast, they all colonized the GITs of axenic mice and rapidly reached a population of 10(9) CFU/g of feces, which remained stable until day 51. Five days after mice were fed, a first subpopulation, characterized by small colonies, appeared and reached 50% of the total L. sakei population in mice. Fifteen to 21 days after feeding, a second subpopulation, characterized by rough colonies, appeared. It coexisted with the two other populations until day 51, and its cell shapes were also affected, suggesting a dysfunction of the cell division or cell wall. No clear difference between the behaviors of the meat-borne strain and the two human isolates in both conventional and axenic mice was observed, suggesting that L. sakei is a food-borne bacterium rather than a commensal one and that its presence in human feces originates from diet. Previous observations of Escherichia coli strains suggest that the mouse GIT environment could induce mutations to increase their survival and colonization capacities. Here, we observed similar mutations concerning a food-grade gram-positive bacterium for the first time.

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

Noncontiguous finished genome sequence and description of Paenibacillus antibioticophila sp. nov. GD11T, the type strain of Paenibacillus antibioticophila

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G. Dubourg

2015-11-01

Full Text Available Paenibacillus antibioticophila strain GD11T sp. nov. is the type strain of a new species within the genus Paenibacillus. This strain, whose genome is described here, was isolated from human faeces of a 63-year-old woman with multidrug-resistant tuberculosis who was receiving numerous antibiotics at the time of stool collection. P. antibioticophila is a Gram-positive aerobic bacterium. We describe here the features of this bacterium, together with the complete genome sequence and annotation. The 5 562 631 bp long genome contains 5084 protein-coding and 71 RNA genes.

Albibacter methylovorans gen. nov., sp. nov., a novel aerobic, facultatively autotrophic and methylotrophic bacterium that utilizes dichloromethane.

Science.gov (United States)

Doronina, N V; Trotsenko, Y A; Tourova, T P; Kuznetsov, B B; Leisinger, T

2001-05-01

A novel genus, Albibacter, with one species, Albibacter methylovorans sp. nov., is proposed for a facultatively chemolithotrophic and methylotrophic bacterium (strain DM10T) with the ribulose bisphosphate (RuBP) pathway of C1 assimilation. The bacterium is a Gram-negative, aerobic, asporogenous, nonmotile, colourless rod that multiplies by binary fission. The organism utilizes dichloromethane, methanol, methylamine, formate and CO2/H2, as well as a variety of polycarbon compounds, as carbon and energy sources. It is neutrophilic and mesophilic. The major cellular fatty acids are straight-chain unsaturated C18:1, saturated C16:0 and cyclopropane C19:0 acids. The main ubiquinone is Q-10. The dominant phospholipids are phosphatidyl ethanolamine, phosphatidyl glycerol, phosphatidyl choline and cardiolipin. The DNA G+C content is 66.7 mol%. Strain DM10T has a very low degree of DNA-DNA hybridization (4-7%) with the type species of the genera Paracoccus, Xanthobacter, Blastobacter, Angulomicrobium, Ancylobacter and Ralstonia of RuBP pathway methylobacteria. Another approach, involving comparative 16S rDNA analysis, has shown that the novel isolate represents a separate branch within the alpha-2 subgroup of the Proteobacteria. The type species of the new genus is Albibacter methylovorans sp. nov.; the type strain is DM10T (= VKM B-2236T = DSM 13819T).

Kocuria polaris sp. nov., an orange-pigmented psychrophilic bacterium isolated from an Antarctic cyanobacterial mat sample.

Science.gov (United States)

Reddy, Gundlapally S N; Prakash, Jogadhenu S S; Prabahar, Vadivel; Matsumoto, Genki I; Stackebrandt, Erko; Shivaji, Sisinthy

2003-01-01

Strain CMS 76orT, an orange-pigmented bacterium, was isolated from a cyanobacterial mat sample from a pond located in McMurdo Dry Valley, Antarctica. On the basis of chemotaxonomic and phylogenetic properties, strain CMS 76orT was identified as a member of the genus Kocuria. It exhibited a 16S rDNA similarity of 99.8% and DNA-DNA similarity of 71% with Kocuria rosea (ATCC 186T). Phenotypic traits confirmed that strain CMS 78orT and K. rosea were well differentiated. Furthermore, strain CMS 76orT could be differentiated from the other reported species of Kocuria, namely Kocuria kristinae (ATCC 27570T), Kocuria varians (ATCC 15306T), Kocuria rhizophila (DSM 11926T) and Kocuria palustris (DSM 11025T), on the basis of a number of phenotypic features. Therefore, it is proposed that strain CMS 76orT (= MTCC 3702T = DSM 14382T) be assigned to a novel species of the genus Kocuria, as Kocuria polaris.

Elemental sulfur and thiosulfate disproportionation by Desulfocapsa sulfoexigens sp. nov., a new anaerobic bacterium isolated from marine surface sediment

DEFF Research Database (Denmark)

Finster, Kai; Liesack, Werner; Thamdrup, Bo

1998-01-01

A mesophilic, anaerobic, gram-negative bacterium, strain SB164P1, was enriched and isolated from oxidized marine surface sediment with elemental sulfur as the sole energy substrate in the presence of ferrihydrite. Elemental sulfur was disproportionated to hydrogen sulfide and sulfate. Growth was ...

Biochemical and genetical analysis reveal a new clade of biovar 3 Dickeya spp. strains isolated from potato in Europe

NARCIS (Netherlands)

Slawiak, M.; Beckhoven, van J.R.C.M.; Speksnijder, A.G.C.L.; Czajkowski, R.L.; Grabe, G.; Wolf, van der J.M.

2009-01-01

Sixty-five potato strains of the soft rot-causing plant pathogenic bacterium Dickeya spp., and two strains from hyacinth, were characterised using biochemical assays, REP-PCR genomic finger printing, 16S rDNA and dnaX sequence analysis. These methods were compared with nineteen strains representing

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

DEFF Research Database (Denmark)

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

2012-01-01

Burkholderia terrae BS001 is a soil bacterium which was originally isolated from the mycosphere of the ectomycorrhizal fungus Laccaria proxima. It exhibits a range of fungus-interacting traits which reveal its propensity to actively interact at fungal interfaces. Here, we present the approximately...

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

Science.gov (United States)

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

2015-11-20

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

UV-induced variability of the amylolytic thermophilic bacterium Bacillus diastaticus

International Nuclear Information System (INIS)

Murygina, V.P.

1978-01-01

UV-induced variability of a thermophilic bacterium Bacillus diastaticus 13 by amylase formation has been studied. It has been shown, that variability limits in amylase biosynthesis vary from 2.2 to 158.7% under UV irradiation. At 41.8x10 2 erg/mm 2 UV dose a ''plus-variant'' designated as the UV1 mutant has been prepared. Its subsequent selection without using mutagene permitted to select the UV 1-25 variant, exceeding the initial strain in amylase biosynthesis by 43.3%. Under UV irradiation two low-active in biosynthesis amylases of the mutant were prepared. Demands for growth factors of some mutant have been studied as well

UV-induced variability of the amylolytic thermophilic bacterium Bacillus diastaticus

Energy Technology Data Exchange (ETDEWEB)

Murygina, V P

1978-03-01

Ultroviolet-radioinduced variability in analyase biosynthesis of a thermophilic bacterium Bacillus diastaticus 13, has been studied. It has been shown that amylase biosynthesis varies from 2.2 to 158.7% under UV irradiation. At 41.8x10/sup 2/ erg/mm/sup 2/ UV dose, a ''plus-variant'' designated as the UV1 mutant has been prepared. Its subsequent selection without using mutagene permitted to select the UV 1-25 variant, exceeding the initial strain in amylase biosynthesis by 43.3%. Under UV irradiation, two mutants with reduced amylose biosynthesis activity were prepared. Demands for growth factors by some mutants have been studied as well.

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

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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.

Amerindian Helicobacter pylori strains go extinct, as european strains expand their host range.

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Maria G Domínguez-Bello

Full Text Available We studied the diversity of bacteria and host in the H. pylori-human model. The human indigenous bacterium H. pylori diverged along with humans, into African, European, Asian and Amerindian groups. Of these, Amerindians have the least genetic diversity. Since niche diversity widens the sets of resources for colonizing species, we predicted that the Amerindian H. pylori strains would be the least diverse. We analyzed the multilocus sequence (7 housekeeping genes of 131 strains: 19 cultured from Africans, 36 from Spanish, 11 from Koreans, 43 from Amerindians and 22 from South American Mestizos. We found that all strains that had been cultured from Africans were African strains (hpAfrica1, all from Spanish were European (hpEurope and all from Koreans were hspEAsia but that Amerindians and Mestizos carried mixed strains: hspAmerind and hpEurope strains had been cultured from Amerindians and hpEurope and hpAfrica1 were cultured from Mestizos. The least genetically diverse H. pylori strains were hspAmerind. Strains hpEurope were the most diverse and showed remarkable multilocus sequence mosaicism (indicating recombination. The lower genetic structure in hpEurope strains is consistent with colonization of a diversity of hosts. If diversity is important for the success of H. pylori, then the low diversity of Amerindian strains might be linked to their apparent tendency to disappear. This suggests that Amerindian strains may lack the needed diversity to survive the diversity brought by non-Amerindian hosts.

Marine Bacteria from Danish Coastal Waters Show Antifouling Activity against the Marine Fouling Bacterium Pseudoalteromonas sp. Strain S91 and Zoospores of the Green Alga Ulva australis Independent of Bacteriocidal Activity▿†

Science.gov (United States)

Bernbom, Nete; Ng, Yoke Yin; Kjelleberg, Staffan; Harder, Tilmann; Gram, Lone

2011-01-01

The aims of this study were to determine if marine bacteria from Danish coastal waters produce antifouling compounds and if antifouling bacteria could be ascribed to specific niches or seasons. We further assess if antibacterial effect is a good proxy for antifouling activity. We isolated 110 bacteria with anti-Vibrio activity from different sample types and locations during a 1-year sampling from Danish coastal waters. The strains were identified as Pseudoalteromonas, Phaeobacter, and Vibrionaceae based on phenotypic tests and partial 16S rRNA gene sequence similarity. The numbers of bioactive bacteria were significantly higher in warmer than in colder months. While some species were isolated at all sampling locations, others were niche specific. We repeatedly isolated Phaeobacter gallaeciensis at surfaces from one site and Pseudoalteromonas tunicata at two others. Twenty-two strains, representing the major taxonomic groups, different seasons, and isolation strategies, were tested for antiadhesive effect against the marine biofilm-forming bacterium Pseudoalteromonas sp. strain S91 and zoospores of the green alga Ulva australis. The antiadhesive effects were assessed by quantifying the number of strain S91 or Ulva spores attaching to a preformed biofilm of each of the 22 strains. The strongest antifouling activity was found in Pseudoalteromonas strains. Biofilms of Pseudoalteromonas piscicida, Pseudoalteromonas tunicata, and Pseudoalteromonas ulvae prevented Pseudoalteromonas S91 from attaching to steel surfaces. P. piscicida killed S91 bacteria in the suspension cultures, whereas P. tunicata and P. ulvae did not; however, they did prevent adhesion by nonbactericidal mechanism(s). Seven Pseudoalteromonas species, including P. piscicida and P. tunicata, reduced the number of settling Ulva zoospores to less than 10% of the number settling on control surfaces. The antifouling alpP gene was detected only in P. tunicata strains (with purple and yellow pigmentation), so

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

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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.

Draft Genome Sequence of Ochrobactrum intermedium Strain SA148, a Plant Growth-Promoting Desert Rhizobacterium

KAUST Repository

Lafi, Feras Fawzi

2017-03-03

Ochrobactrum intermedium strain SA148 is a plant growth-promoting bacterium isolated from sandy soil in the Jizan area of Saudi Arabia. Here, we report the 4.9-Mb draft genome sequence of this strain, highlighting different pathways characteristic of plant growth promotion activity and environmental adaptation of SA148.

Complete genome sequence of the aerobically denitrifying thermophilic bacterium Chelatococcus daeguensis TAD1

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Yunlong Yang

Full Text Available ABSTRACT Chelatococcus daeguensis TAD1 is a themophilic bacterium isolated from a biotrickling filter used to treat NOx in Ruiming Power Plant, located in Guangzhou, China, which shows an excellent aerobic denitrification activity at high temperature. The complete genome sequence of this strain was reported in the present study. Genes related to the aerobic denitrification were identified through whole genome analysis. This work will facilitate the mechanism of aerobic denitrification and provide evidence for its potential application in the nitrogen removal.

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

Science.gov (United States)

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

2014-09-01

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

Xenophilus arseniciresistens sp. nov., an arsenite-resistant bacterium isolated from soil.

Science.gov (United States)

Li, Qin-Fen; Sun, Li-Na; Kwon, Soon-Wo; Chen, Qing; He, Jian; Li, Shun-Peng; Zhang, Jun

2014-06-01

A Gram-reaction-negative, aerobic, motile, rod-shaped, arsenite [As(III)]-resistant bacterium, designated strain YW8(T), was isolated from agricultural soil. 16S rRNA gene sequence analysis showed over 97% sequence similarity to strains of the environmental species Xenophilus azovorans, Xenophilus aerolatus, Simplicispira metamorpha, Variovorax soli, and Xylophilus ampelinus. However, the phylogenetic tree indicated that strain YW8(T) formed a separate clade from Xenophilus azovorans. DNA-DNA hybridization experiments showed that the DNA-DNA relatedness values between strain YW8(T) and its closest phylogenetic neighbours were below 24.2-35.5%, which clearly separated the strain from these closely related species. The major cellular fatty acids of strain YW8(T) were C(16 : 0), C(17 : 0) cyclo, C(18 : 1)ω7c, and summed feature 3(C(16 : 1)ω6c and/or C(16 : 1)ω7c). The genomic DNA G+C content was 69.3 mol%, and the major respiratory quinone was ubiquinone-8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown phospholipids, an unknown polar lipid and phosphatidylserine. The major polyamines were 2-hydroxyputrescine and putrescine. On the basis of morphological, physiological and biochemical characteristics, phylogenetic position, DNA-DNA hybridization and chemotaxonomic data, strain YW8(T) is considered to represent a novel species of the genus Xenophilus, for which the name Xenophilus arseniciresistens sp. nov. is proposed; the type strain is YW8(T) ( = CCTCC AB2012103(T) = KACC 16853(T)). © 2014 IUMS.

Draft genome sequence of Bradyrhizobium sp. strain BR 3267, an elite strain recommended for cowpea inoculation in Brazil

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Jean Luiz Simões-Araújo

Full Text Available Abstract The strain BR 3267 is a nitrogen-fixing symbiotic bacteria isolated from soil of semi-arid area of Brazilian Northeast using cowpea as the trap plant. This strain is used as commercial inoculant for cowpea and presents high efficient in nitrogen fixation as consequence of its adaptation potential to semi-arid conditions. We report here the draft genome sequence of Bradyrhizobium sp. strain BR 3267, an elite bacterium used as inoculant for cowpea. Whole genome sequencing of BR 3267 using Illumina MiSeq sequencing technology has 55 scaffolds with a total genome size of 7,904,309 bp and C+G 63%. Annotation was added by the RAST prokaryotic genome annotation service and has shown 7314 coding sequences and 52 RNA genes.

Draft Genome Sequence of the Antagonistic Rhizosphere Bacterium Serratia plymuthica Strain PRI-2C

NARCIS (Netherlands)

Garbeva, P.; van Elsas, J.D.; de Boer, W.

Serratia plymuthica strain PRI-2C is a rhizosphere bacterial strain with antagonistic activity against different plant pathogens. Here we present the 5.39-Mb (G+C content, 55.67%) draft genome sequence of S. plymuthica strain PRI-2C with the aim of providing insight into the genomic basis of its

Molecular identification of phosphate solubilizing bacterium ...

African Journals Online (AJOL)

A phosphate solubilizing bacterium was isolated from the rhizosphere soil of upland rice and identified by 16S rRNA gene sequencing. The gene sequence showed 99% homology with Alcaligenes faecalis. Based on the gene sequence homology, it was identified as A. faecalis. Interaction effect of this bacterium on growth ...

“Nigerium massiliense” gen. nov., sp. nov., a new bacterium isolated from the gut from a patient with acute malnutrition

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Sory Ibrahima Traore

2016-09-01

Full Text Available We propose the main characteristics of a new bacterium named “Nigerium massiliense” strain SIT5 (CSURP1302 that was isolated from the stool of a 2-year-old Nigerian child suffering from kwashiorkor, a form of severe acute malnutrition. Keywords: Culturomics, Taxonomy, Genomics, Taxono-genomics, “Nigerium massiliense”

Extreme furfural tolerance of a soil bacterium Enterobacter cloacae GGT036.

Science.gov (United States)

Choi, Sun Young; Gong, Gyeongtaek; Park, Hong-Sil; Um, Youngsoon; Sim, Sang Jun; Woo, Han Min

2015-01-10

Detoxification process of cellular inhibitors including furfural is essential for production of bio-based chemicals from lignocellulosic biomass. Here we isolated an extreme furfural-tolerant bacterium Enterobacter cloacae GGT036 from soil sample collected in Mt. Gwanak, Republic of Korea. Among isolated bacteria, only E. cloacae GGT036 showed cell growth with 35 mM furfural under aerobic culture. Compared to the maximal half inhibitory concentration (IC50) of well-known industrial strains Escherichia coli (24.9 mM furfural) and Corynebacterium glutamicum (10 mM furfural) based on the cell density, IC50 of E. cloacae GGT036 (47.7 mM) was significantly higher after 24 h, compared to E. coli and C. glutamicum. Since bacterial cell growth was exponentially inhibited depending on linearly increased furfural concentrations in the medium, we concluded that E. cloacae GGT036 is an extreme furfural-tolerant bacterium. Recently, the complete genome sequence of E. cloacae GGT036 was announced and this could provide an insight for engineering of E. cloacae GGT036 itself or other industrially relevant bacteria. Copyright © 2014 Elsevier B.V. All rights reserved.

High quality draft genome sequence of the moderately halophilic bacterium Pontibacillus yanchengensis Y32(T) and comparison among Pontibacillus genomes.

Science.gov (United States)

Huang, Jing; Qiao, Zi Xu; Tang, Jing Wei; Wang, Gejiao

2015-01-01

Pontibacillus yanchengensis Y32(T) is an aerobic, motile, Gram-positive, endospore-forming, and moderately halophilic bacterium isolated from a salt field. In this study, we describe the features of P. yanchengensis strain Y32(T) together with a comparison with other four Pontibacillus genomes. The 4,281,464 bp high-quality-draft genome of strain Y32(T) is arranged into 153 contigs containing 3,965 protein-coding genes and 77 RNA encoding genes. The genome of strain Y32(T) possesses many genes related to its halophilic character, flagellar assembly and chemotaxis to support its survival in a salt-rich environment.

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).

Economic Game Theory to Model the Attenuation of Virulence of an Obligate Intracellular Bacterium.

Science.gov (United States)

Tago, Damian; Meyer, Damien F

2016-01-01

Diseases induced by obligate intracellular pathogens have a large burden on global human and animal health. Understanding the factors involved in the virulence and fitness of these pathogens contributes to the development of control strategies against these diseases. Based on biological observations, a theoretical model using game theory is proposed to explain how obligate intracellular bacteria interact with their host. The equilibrium in such a game shows that the virulence and fitness of the bacterium is host-triggered and by changing the host's defense system to which the bacterium is confronted, an evolutionary process leads to an attenuated strain. Although, the attenuation procedure has already been conducted in practice in order to develop an attenuated vaccine (e.g., with Ehrlichia ruminantium), there was a lack of understanding of the theoretical basis behind this process. Our work provides a model to better comprehend the existence of different phenotypes and some underlying evolutionary mechanisms for the virulence of obligate intracellular bacteria.

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

DEFF Research Database (Denmark)

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

2006-01-01

Strain 15T is a novel spore-forming, sulfate-reducing bacterium isolated from a permanently cold fjord sediment of Svalbard. Sulfate could be replaced by sulfite or thiosulfate. Hydrogen, formate, lactate, propionate, butyrate, hexanoate, methanol, ethanol, propanol, butanol, pyruvate, malate...

Sulfurospirillum arcachonense sp. nov., a new microaerophilic sulfur-reducing bacterium.

Science.gov (United States)

Finster, K; Liesack, W; Tindall, B J

1997-10-01

The isolation of a new motile, gram-negative, heterotrophic, sulfur-reducing, microaerophilic, vibrioid bacterium, strain F1F6, from oxidized marine surface sediment (Arcachon Bay, French Atlantic coast) is described. Hydrogen (with acetate as the carbon source), formate (with acetate as the carbon source), pyruvate, lactate, alpha-ketoglutarate, glutarate, glutamate, and yeast extract supported growth with elemental sulfur under anaerobic conditions. Apart from H2 and formate, the oxidation of the substrates was incomplete. Microaerophilic growth was supported with hydrogen (acetate as the carbon source), formate (acetate as the carbon source), acetate, propionate, pyruvate, lactate, alpha-ketoglutarate, glutamate, yeast extract, fumarate, succinate, malate, citrate, and alanine. The isolate grew fermentatively with fumarate, succinate being the only organic product. Elemental sulfur and oxygen were the only electron acceptors used. Vitamins or amino acids were not required. The isolate was oxidase, catalase, and urease positive. Comparative 16S rDNA sequence analysis revealed a tight cluster consisting of the validly described species Sulfurospirillum deleyianum and the strains SES-3 and CCUG 13942 as the closest relatives of strain F1F6 (level of sequence similarity, 91.7 to 92.4%). Together with strain F1F6, these organisms form a novel lineage within the epsilon subclass of proteobacteria clearly separated from the described species of the genera Arcobacter, Campylobacter, Wolinella, and Helicobacter. Due to the phenotypic characteristics shared by strain F1F6 and S. deleyianum and considering their phylogenetic relationship, we propose the inclusion of strain F1F6 in the genus Sulfurospirillum, namely, as S. arcachonense sp. nov. Based on the results of this study, an emended description of the genus Sulfurospirillum is given.

[Isolation, identification and characterization of a diethylstilbestrol-degrading bacterial strain Serratia sp].

Science.gov (United States)

Xu, Ran-Fang; Sun, Min-Xia; Liu, Juan; Wang, Hong; Li, Xin; Zhu, Xue-Zhu; Ling, Wan-Ting

2014-08-01

Utilizing the diethylstilbestrol (DES)-degrading bacteria to biodegrade DES is a most reliable technique for cleanup of DES pollutants from the environment. However, little information is available heretofore on the isolation of DES-degrading bacteria and their DES removal performance in the environment. A novel bacterium capable of degrading DES was isolated from the activated sludge of a wastewater treatment plant. According to its morphology, physiochemical characteristics, and 16S rDNA sequence analysis, this strain was identified as Serratia sp.. The strain was an aerobic bacterium, and it could degrade 68.3% of DES (50 mg x L(-1)) after culturing for 7 days at 30 degrees C, 150 r x min(-1) in shaking flasks. The optimal conditions for DES biodegradation by the obtained strain were 30 degrees C, 40-60 mg x L(-1) DES, pH 7.0, 5% of inoculation volume, 0 g x L(-1) of added NaCl, and 10 mL of liquid medium volume in 100 mL flask.

Large-scale bioreactor production of the herbicide-degrading Aminobacter sp. strain MSH1

DEFF Research Database (Denmark)

Schultz-Jensen, Nadja; Knudsen, Berith Elkær; Frkova, Zuzana

2014-01-01

The Aminobacter sp. strain MSH1 has potential for pesticide bioremediation because it degrades the herbicide metabolite 2,6-dichlorobenzamide (BAM). Production of the BAM-degrading bacterium using aerobic bioreactor fermentation was investigated. A mineral salt medium limited for carbon and with ......The Aminobacter sp. strain MSH1 has potential for pesticide bioremediation because it degrades the herbicide metabolite 2,6-dichlorobenzamide (BAM). Production of the BAM-degrading bacterium using aerobic bioreactor fermentation was investigated. A mineral salt medium limited for carbon...... and with an element composition similar to the strain was generated. The optimal pH and temperature for strain growth were determined using shaker flasks and verified in bioreactors. Glucose, fructose, and glycerol were suitable carbon sources for MSH1 (μ =0.1 h−1); slower growth was observed on succinate and acetic...... acid (μ =0.01 h−1). Standard conditions for growth of theMSH1 strain were defined at pH 7 and 25 °C, with glucose as the carbon source. In bioreactors (1 and 5 L), the specific growth rate of MSH1 increased from μ =0.1 h−1 on traditional mineral salt medium to μ =0.18 h−1 on the optimized mineral salt...

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.

Isolation of a human intestinal anaerobe, Bifidobacterium sp. strain SEN, capable of hydrolyzing sennosides to sennidins.

OpenAIRE

Akao, T; Che, Q M; Kobashi, K; Yang, L; Hattori, M; Namba, T

1994-01-01

A strictly anaerobic bacterium capable of metabolizing sennosides was isolated from human feces and identified as Bifidobacterium sp., named strain SEN. The bacterium hydrolyzed sennosides A and B to sennidins A and B via sennidin A and B 8-monoglucosides, respectively. Among nine species of Bifidobacterium having beta-glucosidase activity, only Bifidobacterium dentium and B. adolescentis metabolized sennoside B to sennidin B, suggesting that the sennoside-metabolizing bacteria produce a nove...

Halomonas indalinina sp.nov., a moderately halophilic bacterium isolated from a solar saltern in Cabo de Gata, Al,eria, southern Spain

NARCIS (Netherlands)

Cabrera, A.; Aguilera, M.; Fuentes Enriquez de Salamanca, S.; Incerti, C.; Russell, N.J.; Ramos-Cormenzana, A.; Monteoliva-Sanchez, M.

2007-01-01

moderately halophilic bacterium, strain CG2.1T, isolated from a solar saltern at Cabo de Gata, a wildlife reserve located in the province of Almería, southern Spain, was subjected to a polyphasic taxonomic study. This organism was an aerobic, motile, Gram-negative rod that produced orange-pigmented

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

Science.gov (United States)

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

2017-10-01

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

Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1T), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta

Energy Technology Data Exchange (ETDEWEB)

Abt, Birte; Han, Cliff; Scheuner, Carmen; Lu, Megan; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxane; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Huntemann, Marcel; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Brambilla, Evelyne-Marie; Rohde, Manfred; Spring, Stefan; Gronow, Sabine; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Detter, John C.

2012-05-25

Spirochaeta coccoides Dröge et al. 2006 is a member of the genus Spirochaeta Ehrenberg 1835, one of the oldest named genera within the Bacteria. S. coccoides is an obligately anaerobic, Gram-negative, non-motile, spherical bacterium that was isolated from the hindgut contents of the termite Neotermes castaneus. The species is of interest because it may play an important role in the digestion of breakdown products from cellulose and hemicellulose in the termite gut. Here we provide a taxonomic re-evaluation for strain SPN1T, and based on physiological and genomic characteristics, we propose its reclassification as a novel species in the genus Sphaerochaeta, a recently published sister group of the Spirochaeta. The 2,227,296 bp long genome of strain SPN1T with its 1,866 protein-coding and 58 RNA genes is a part of the GenomicEncyclopedia of Bacteria and Archaea project.

Growth of a Strictly Anaerobic Bacterium on Furfural (2-Furaldehyde)

Science.gov (United States)

Brune, Gerhard; Schoberth, Siegfried M.; Sahm, Hermann

1983-01-01

A strictly anaerobic bacterium was isolated from a continuous fermentor culture which converted the organic constituents of sulfite evaporator condensate to methane and carbon dioxide. Furfural is one of the major components of this condensate. This furfural isolate could degrade furfural as the sole source of carbon and energy in a defined mineral-vitamin-sulfate medium. Acetic acid was the major fermentation product. This organism could also use ethanol, lactate, pyruvate, or fumarate and contained cytochrome c3 and desulfoviridin. Except for furfural degradation, the characteristics of the furfural isolate were remarkably similar to those of the sulfate reducer Desulfovibrio gigas. The furfural isolate has been tentatively identified as Desulfovibrio sp. strain F-1. Images PMID:16346423

A bacterium that can grow by using arsenic instead of phosphorus

Energy Technology Data Exchange (ETDEWEB)

Wolfe-Simon, F; Blum, J S; Kulp, T R; Gordon, G W; Hoeft, S E; Pett-Ridge, J; Stolz, J F; Webb, S M; Weber, P K; Davies, P W; Anbar, A D; Oremland, R S

2010-11-01

Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur and phosphorus. Although these six elements make up nucleic acids, proteins and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, CA, which substitutes arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical significance.

A bacterium that can grow by using arsenic instead of phosphorus.

Science.gov (United States)

Wolfe-Simon, Felisa; Switzer Blum, Jodi; Kulp, Thomas R; Gordon, Gwyneth W; Hoeft, Shelley E; Pett-Ridge, Jennifer; Stolz, John F; Webb, Samuel M; Weber, Peter K; Davies, Paul C W; Anbar, Ariel D; Oremland, Ronald S

2011-06-03

Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. Although these six elements make up nucleic acids, proteins, and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here, we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, California, that is able to substitute arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical importance.

Aggregation of the rhizospheric bacterium Azospirillum brasilense in response to oxygen

Science.gov (United States)

Abdoun, Hamid; McMillan, Mary; Pereg, Lily

2016-04-01

Azospirillum brasilense spp. have ecological, scientific and agricultural importance. As model plant growth promoting rhizobacteria they interact with a large variety of plants, including important food and cash crops. Azospirillum strains are known for their production of plant growth hormones that enhance root systems and for their ability to fix nitrogen. Azospirillum cells transform in response to environmental cues. The production of exopolysaccharides and cell aggregation during cellular transformation are important steps in the attachment of Azospirillum to roots. We investigate signals that induce cellular transformation and aggregation in the Azospirillum and report on the importance of oxygen to the process of aggregation in this rhizospheric bacterium.

Echinicola rosea sp. nov., a marine bacterium isolated from surface seawater.

Science.gov (United States)

Liang, Pan; Sun, Jia; Li, Hao; Liu, Minyuan; Xue, Zhaocheng; Zhang, Yao

2016-09-01

A novel Gram-stain-negative, rod-shaped, gliding, halotolerant, aerobic, light-pink-pigmented bacterium, strain JL3085T, was isolated from surface water of the South China Sea (16° 49' 4″ N 112° 20' 24″ E; temperature: 28.3 °C, salinity: 34.5%). The major respiratory quinone was menaquinone 7 (MK-7). The polar lipids of strain JL3085T comprised phosphatidylethanolamine, four unidentified phospholipids and three unidentified lipids. The major fatty acids were iso-C15 : 0, summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C17 : 0 3-OH, iso-C17 : 1ω9c, C17 : 1ω6c, anteiso-C15 : 0 and C16 : 1ω5c. The DNA G+C content of strain JL3085T was 43.8 mol%. 16S rRNA gene sequence analysis indicated that strain JL3085T was affiliated with the genus Echinicola, a member of the phylum Bacteroidetes, and was related most closely to Echinicola vietnamensis KMM 6221T (96.8 % similarity). DNA-DNA relatedness between strain JL3085T and E. vietnamensis KMM 6221T was 27.5 %. Based on the evidence presented here, strain JL3085T is regarded as representing a novel species of the genus Echinicola, for which the name Echinicola rosea sp. nov. is proposed. The type strain is JL3085T (=NBRC 111782T=CGMCC 1.15407T).

Complete Genome Sequence of the Pigmented Streptococcus thermophilus Strain JIM8232

Science.gov (United States)

Delorme, Christine; Bartholini, Claire; Luraschi, Mélanie; Pons, Nicolas; Loux, Valentin; Almeida, Mathieu; Guédon, Eric; Gibrat, Jean-François; Renault, Pierre

2011-01-01

Streptococcus thermophilus is a dairy species commonly used in the manufacture of cheese and yogurt. Here, we report the complete sequence of S. thermophilus strain JIM8232, isolated from milk and which produces a yellow pigment, an atypical trait for this bacterium. PMID:21914889

Culture conditions of Roseobacter strain 27-4 affect its attachment and biofilm formation as quantified by real-time PCR

DEFF Research Database (Denmark)

Bruhn, Jesper Bartholin; Haagensen, Janus Anders Juul; Bagge-Ravn, D.

2006-01-01

The fish probiotic bacterium Roseobacter strain 27-4 grows only as rosettes and produces its antibacterial compound under static growth conditions. It forms three-dimensional biofilms when precultured under static conditions. We quantified attachment of Roseobacter strain 27-4 using a direct real...

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.

Bacterium oxidizing carbon monoxide

Energy Technology Data Exchange (ETDEWEB)

Kistner, A

1953-01-01

Present-day knowledge of the microbiological oxidation of carbon monoxide is based on doubtful observations and imperfect experimental procedures. By making use of shake cultures in contact with gas mixtures containing high concentrations of CO and by employing liquid enrichment media with a low content of organic matter and solid media of the same composition with not more than 1.2% agar, it proved possible to isolate a co-oxidizing bacterium of the genus hydrogenomonas from sewage sludge. For the first time irrefutable proof has been given of the oxidation of carbon monoxide by a pure culture of a bacterium, both in growing cultures and in resting cell suspensions. 12 references.

Draft Genome Sequence of Komagataeibacter intermedius Strain AF2, a Producer of Cellulose, Isolated from Kombucha Tea.

Science.gov (United States)

Dos Santos, Renato Augusto Corrêa; Berretta, Andresa Aparecida; Barud, Hernane da Silva; Ribeiro, Sidney José Lima; González-García, Laura Natalia; Zucchi, Tiago Domingues; Goldman, Gustavo H; Riaño-Pachón, Diego M

2015-12-03

Here, we present the draft genome sequence of Komagataeibacter intermedius strain AF2, which was isolated from Kombucha tea and is capable of producing cellulose, although at lower levels compared to another bacterium from the same environment, K. rhaeticus strain AF1. Copyright © 2015 dos Santos et al.

Biodegradation pathway of L-glutamatediacetate by Rhizobium radiobacter strain BG-1

NARCIS (Netherlands)

Ginkel, van C.G.; Geerts, R.; Nguyen, P.D.; Plugge, C.M.

2008-01-01

An aerobic bacterium was isolated from activated sludge in a medium containing l-glutamate-N,N-diacetate (l-GLDA) as sole carbon and energy source. The isolate was identified as a Rhizobium radiobacter species. Besides l-GLDA, the strain utilized nitrilotriacetate (NTA) and proposed intermediates in

Complete genome sequence of Vibrio anguillarum strain NB10, a virulent isolate from the Gulf of Bothnia.

Science.gov (United States)

Holm, Kåre Olav; Nilsson, Kristina; Hjerde, Erik; Willassen, Nils-Peder; Milton, Debra L

2015-01-01

Vibrio anguillarum causes a fatal hemorrhagic septicemia in marine fish that leads to great economical losses in aquaculture world-wide. Vibrio anguillarum strain NB10 serotype O1 is a Gram-negative, motile, curved rod-shaped bacterium, isolated from a diseased fish on the Swedish coast of the Gulf of Bothnia, and is slightly halophilic. Strain NB10 is a virulent isolate that readily colonizes fish skin and intestinal tissues. Here, the features of this bacterium are described and the annotation and analysis of its complete genome sequence is presented. The genome is 4,373,835 bp in size, consists of two circular chromosomes and one plasmid, and contains 3,783 protein-coding genes and 129 RNA genes.

Strain Dependent Genetic Networks for Antibiotic-Sensitivity in a Bacterial Pathogen with a Large Pan-Genome.

Directory of Open Access Journals (Sweden)

Tim van Opijnen

2016-09-01

Full Text Available The interaction between an antibiotic and bacterium is not merely restricted to the drug and its direct target, rather antibiotic induced stress seems to resonate through the bacterium, creating selective pressures that drive the emergence of adaptive mutations not only in the direct target, but in genes involved in many different fundamental processes as well. Surprisingly, it has been shown that adaptive mutations do not necessarily have the same effect in all species, indicating that the genetic background influences how phenotypes are manifested. However, to what extent the genetic background affects the manner in which a bacterium experiences antibiotic stress, and how this stress is processed is unclear. Here we employ the genome-wide tool Tn-Seq to construct daptomycin-sensitivity profiles for two strains of the bacterial pathogen Streptococcus pneumoniae. Remarkably, over half of the genes that are important for dealing with antibiotic-induced stress in one strain are dispensable in another. By confirming over 100 genotype-phenotype relationships, probing potassium-loss, employing genetic interaction mapping as well as temporal gene-expression experiments we reveal genome-wide conditionally important/essential genes, we discover roles for genes with unknown function, and uncover parts of the antibiotic's mode-of-action. Moreover, by mapping the underlying genomic network for two query genes we encounter little conservation in network connectivity between strains as well as profound differences in regulatory relationships. Our approach uniquely enables genome-wide fitness comparisons across strains, facilitating the discovery that antibiotic responses are complex events that can vary widely between strains, which suggests that in some cases the emergence of resistance could be strain specific and at least for species with a large pan-genome less predictable.

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)).

Isolation of a strain of Acidithiobacillus caldus and its role in bioleaching of chalcopyrite

Energy Technology Data Exchange (ETDEWEB)

Zhou, Q.G.; Bo, F.; Bo, Z.H.; Xi, L.; Jian, G.; Fei, L.F.; Hua, C.X. [Central South University of Technology, Changsha (China)

2007-09-15

A moderately thermophilic and acidophilic sulfur-oxidizing bacterium named S-2, was isolated from coal heap drainage. The bacterium was motile, Gramnegative, rod-shaped, measured 0.4 to 0.6 by 1 to 2 gm, and grew optimally at 42-45{sup o}C and an initial pH of 2.5. The strain S-2 grew autotrophically by using elemental sulfur, sodium thiosulfate and potassium tetrathionate as energy sources. The strain did not use organic matter and inorganic minerals including ferrous sulfate, pyrite and chalcopyrite as energy sources. The morphological, biochemical, physiological characterization and analysis based on 16S rRNA gene sequence indicated that the strain S2 is most closely related to Acidithiobacillus caldus (> 99% similarity in gene sequence). The combination of the strain S-2 with Leptospirillum ferriphilum or Acidithiobacillus ferrooxidans in chalcopyrite bioleaching improved the copper-leaching efficiency. Scanning electron microscope (SEM) analysis revealed that the chalcopyrite surface in a mixed culture of Leptospirillum ferriphilum and Acidithiobacillus caldus was heavily etched. The energy dispersive X-ray (EDX) analysis indicated that Acidithiobacillus caldus has the potential role to enhance the recovery of copper from chalcopyrite by oxidizing the sulfur formed during the bioleaching progress.

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.

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.

Draft genome sequence of Bradyrhizobium sp. strain BR 3262, an effective microsymbiont recommended for cowpea inoculation in Brazil.

Science.gov (United States)

Simões-Araújo, Jean Luiz; Leite, Jakson; Marie Rouws, Luc Felicianus; Passos, Samuel Ribeiro; Xavier, Gustavo Ribeiro; Rumjanek, Norma Gouvêa; Zilli, Jerri Édson

The strain BR 3262 was isolated from nodule of cowpea (Vigna unguiculata L. Walp) growing in soil of the Atlantic Forest area in Brazil and it is reported as an efficient nitrogen fixing bacterium associated to cowpea. Firstly, this strain was assigned as Bradyrhizobium elkanii, however, recently a more detailed genetic and molecular characterization has indicated it could be a Bradyrhizobium pachyrhizi species. We report here the draft genome sequence of B. pachyrhizi strain BR 3262, an elite bacterium used as inoculant for cowpea. The whole genome with 116 scaffolds, 8,965,178bp and 63.8% of C+G content for BR 3262 was obtained using Illumina MiSeq sequencing technology. Annotation was added by the RAST prokaryotic genome annotation service and shown 8369 coding sequences, 52 RNAs genes, classified in 504 subsystems. Published by Elsevier Editora Ltda.

Draft genome sequence of Bradyrhizobium sp. strain BR 3262, an effective microsymbiont recommended for cowpea inoculation in Brazil

Directory of Open Access Journals (Sweden)

Jean Luiz Simões-Araújo

Full Text Available Abstract The strain BR 3262 was isolated from nodule of cowpea (Vigna unguiculata L. Walp growing in soil of the Atlantic Forest area in Brazil and it is reported as an efficient nitrogen fixing bacterium associated to cowpea. Firstly, this strain was assigned as Bradyrhizobium elkanii, however, recently a more detailed genetic and molecular characterization has indicated it could be a Bradyrhizobium pachyrhizi species. We report here the draft genome sequence of B. pachyrhizi strain BR 3262, an elite bacterium used as inoculant for cowpea. The whole genome with 116 scaffolds, 8,965,178 bp and 63.8% of C+G content for BR 3262 was obtained using Illumina MiSeq sequencing technology. Annotation was added by the RAST prokaryotic genome annotation service and shown 8369 coding sequences, 52 RNAs genes, classified in 504 subsystems.

Intraspecies diversity of Lactobacillus sakei response to oxidative stress and variability of strain performance in mixed strains challenges.

Science.gov (United States)

Guilbaud, Morgan; Zagorec, Monique; Chaillou, Stéphane; Champomier-Vergès, Marie-Christine

2012-04-01

Lactobacillus sakei is a meat-borne lactic acid bacterium species exhibiting a wide genomic diversity. We have investigated the diversity of response to various oxidative compounds, between L. sakei strains, among a collection representing the genomic diversity. We observed various responses to the different compounds as well as a diversity of response depending on the aeration conditions used for cell growth. A principal component analysis revealed two main phenotypic groups, partially correlating with previously described genomic clusters. We designed strains mixes composed of three different strains, in order to examine the behavior of each strain, when cultured alone or in the presence of other strains. The strains composing the mixtures were chosen as diverse as possible, i.e. exhibiting diverse responses to oxidative stress and belonging to different genomic clusters. Growth and survival rates of each strain were monitored under various aeration conditions, with or without heme supplementation. The results obtained suggest that some strains may act as "helper" or "burden" strains depending on the oxidative conditions encountered during incubation. This study confirms that resistance to oxidative stress is extremely variable within the L. sakei species and that this property should be considered when investigating starter performance in the complex meat bacterial ecosystems. Copyright © 2011 Elsevier Ltd. All rights reserved.

[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.

Genome sequences of two Leuconostoc pseudomesenteroides strains isolated from Danish dairy starter cultures

DEFF Research Database (Denmark)

Pedersen, Thomas Bæk; Kot, Witold Piotr; Hansen, L.H.

2014-01-01

The lactic acid bacterium Leuconostoc pseudomesenteroides can be found in mesophilic cheese starters, where it produces aromatic compounds from, e.g., citrate. Here, we present the draft genome sequences of two L. pseudomesenteroides strains isolated from traditional Danish cheese starters....

The Lipid A from the Haloalkaliphilic Bacterium Salinivibrio sharmensis Strain BAGT

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Maria Michela Corsaro

2013-01-01

Full Text Available Lipid A is a major constituent of the lipopolysaccharides (or endotoxins, which are complex amphiphilic macromolecules anchored in the outer membrane of Gram-negative bacteria. The glycolipid lipid A is known to possess the minimal chemical structure for LPSs endotoxic activity, able to cause septic shock. Lipid A isolated from extremophiles is interesting, since very few cases of pathogenic bacteria have been found among these microorganisms. In some cases their lipid A has shown to have an antagonist activity, i.e., it is able to interact with the immune system of the host without triggering a proinflammatory response by blocking binding of substances that could elicit such a response. However, the relationship between the structure and the activity of these molecules is far from being completely clear. A deeper knowledge of the lipid A chemical structure can help the understanding of these mechanisms. In this manuscript, we present our work on the complete structural characterization of the lipid A obtained from the lipopolysaccharides (LPS of the haloalkaliphilic bacterium Salinivibrio sharmensis. Lipid A was obtained from the purified LPS by mild acid hydrolysis. The lipid A, which contains different number of fatty acids residues, and its partially deacylated derivatives were completely characterized by means of electrospray ionization Fourier transform ion cyclotron (ESI FT-ICR mass spectrometry and chemical analysis.

Phenotypical and molecular responses of Arabidopsis thaliana roots as a result of inoculation with the auxin-producing bacterium Azospirillum brasilense.

Science.gov (United States)

Spaepen, Stijn; Bossuyt, Stijn; Engelen, Kristof; Marchal, Kathleen; Vanderleyden, Jos

2014-02-01

The auxin-producing bacterium Azospirillum brasilense Sp245 can promote the growth of several plant species. The model plant Arabidopsis thaliana was chosen as host plant to gain an insight into the molecular mechanisms that govern this interaction. The determination of differential gene expression in Arabidopsis roots after inoculation with either A. brasilense wild-type or an auxin biosynthesis mutant was achieved by microarray analysis. Arabidopsis thaliana inoculation with A. brasilense wild-type increases the number of lateral roots and root hairs, and elevates the internal auxin concentration in the plant. The A. thaliana root transcriptome undergoes extensive changes on A. brasilense inoculation, and the effects are more pronounced at later time points. The wild-type bacterial strain induces changes in hormone- and defense-related genes, as well as in plant cell wall-related genes. The A. brasilense mutant, however, does not elicit these transcriptional changes to the same extent. There are qualitative and quantitative differences between A. thaliana responses to the wild-type A. brasilense strain and the auxin biosynthesis mutant strain, based on both phenotypic and transcriptomic data. This illustrates the major role played by auxin in the Azospirillum-Arabidopsis interaction, and possibly also in other bacterium-plant interactions. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Analysis of the genetic variation in Mycobacterium tuberculosis strains by multiple genome alignments

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Morales Juan

2008-11-01

Full Text Available Abstract Background The recent determination of the complete nucleotide sequence of several Mycobacterium tuberculosis (MTB genomes allows the use of comparative genomics as a tool for dissecting the nature and consequence of genetic variability within this species. The multiple alignment of the genomes of clinical strains (CDC1551, F11, Haarlem and C, along with the genomes of laboratory strains (H37Rv and H37Ra, provides new insights on the mechanisms of adaptation of this bacterium to the human host. Findings The genetic variation found in six M. tuberculosis strains does not involve significant genomic rearrangements. Most of the variation results from deletion and transposition events preferentially associated with insertion sequences and genes of the PE/PPE family but not with genes implicated in virulence. Using a Perl-based software islandsanalyser, which creates a representation of the genetic variation in the genome, we identified differences in the patterns of distribution and frequency of the polymorphisms across the genome. The identification of genes displaying strain-specific polymorphisms and the extrapolation of the number of strain-specific polymorphisms to an unlimited number of genomes indicates that the different strains contain a limited number of unique polymorphisms. Conclusion The comparison of multiple genomes demonstrates that the M. tuberculosis genome is currently undergoing an active process of gene decay, analogous to the adaptation process of obligate bacterial symbionts. This observation opens new perspectives into the evolution and the understanding of the pathogenesis of this bacterium.

Gracilibacillus aidingensis sp. nov., a novel moderately halophilic bacterium isolated from Aiding salt lake.

Science.gov (United States)

Guan, Tong-Wei; Tian, Lei; Li, En-Yuan; Tang, Shu-Kun; Zhang, Xiao-Ping

2017-11-01

A novel Gram-positive, aerobe, moderately halophilic bacterium was isolated from saline soil of Aiding lake in Xinjiang, north-west of China, designated strain YIM 98001 T . Cells were rod-shaped, motile and grew at 5-20% (w/v) NaCl (optimum 10%), pH 6-10 (optimum pH 7.0) and 4-45 °C (optimum 37 °C). The major cellular fatty acids were anteiso C 15:0 , anteiso C 17:0 , iso C 15:0 . The predominant respiratory quinone was MK-7. Diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid were the major polar lipids. Meso-diaminopimelic acid was the diagnostic diamino acid of the cell-wall peptidoglycan. The G+C content was 36.46 mol%. 16S rRNA gene sequence analysis showed that the strain belongs to the family Bacillaceae, with the highest sequence similarity to the type strain Gracilibacillus thailandensis TP2-8 T (96.84%), followed by Gracilibacillus saliphilus YIM 91119 T (96.78%) and Gracilibacillus ureilyticus MF38 T (96.57%), thus confirming the affiliation of strain YIM 98001 T to the genus Gracilibacillus. The polyphasic approach indicates that strain YIM 98001 T represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus aidingensis is proposed. The type strain is YIM 98001 T (=KCTC 42683 T  = DSMZ 104330 T ).

Thermincola carboxydiphila gen. nov., sp. nov., a novel anaerobic, carboxydotrophic, hydrogenogenic bacterium from a hot spring of the Lake Baikal area.

Science.gov (United States)

Sokolova, Tatyana G; Kostrikina, Nadezhda A; Chernyh, Nikolai A; Kolganova, Tatjana V; Tourova, Tatjana P; Bonch-Osmolovskaya, Elizaveta A

2005-09-01

A novel anaerobic, thermophilic, alkalitolerant bacterium, strain 2204(T), was isolated from a hot spring of the Baikal Lake region. The cells of strain 2204(T) were straight rods of variable length, Gram-positive with an S-layer, motile with one to two lateral flagella, and often formed aggregates of 3-15 cells. The isolate was shown to be an obligate anaerobe oxidizing CO and producing equimolar quantities of H(2) and CO(2) according to the equation CO+H(2)O-->CO(2)+H(2). No organic substrates were used as energy sources. For lithotrophic growth on CO, 0.2 g acetate or yeast extract l(-1) was required but did not support growth in the absence of CO. Growth was observed in the temperature range 37-68 degrees C, the optimum being 55 degrees C. The pH range for growth was 6.7-9.5, the optimum pH being 8.0. The generation time under optimal conditions was 1.3 h. The DNA G+C content was 45 mol%. Penicillin, erythromycin, streptomycin, rifampicin, vancomycin and tetracycline completely inhibited both growth and CO utilization by strain 2204(T). Thus, isolate 2204(T) was found to be the first known moderately thermophilic and alkalitolerant H(2)-producing anaerobic carboxydotroph. The novel bacterium fell within the cluster of the family Peptococcaceae within the low-G+C-content Gram-positive bacteria, where it formed a separate branch. On the basis of morphological, physiological and phylogenetic features, strain 2204(T) should be assigned to a novel genus and species, for which the name Thermincola carboxydiphila gen. nov., sp. nov. is proposed. The type strain is strain 2204(T) (=DSM 17129(T)=VKM B-2283(T)=JCM 13258(T)).

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

Science.gov (United States)

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

2014-10-01

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

Screening and Molecular Identification of New Microbial Strains for Production of Enzymes of Biotechnological Interest

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Imen Ghazala

Full Text Available ABSTRACT: This research focused on isolation, identification and characterization of new strains of fungi and bacteria, which were able to produce extracellular xylanase, mannanase, pectinase and α-amylase. Fungi isolates were identified on the basis of analyses of 18S gene sequencing and internal transcribed spacer region. The closest phylogenetic neighbors according to 18S gene sequence and ITS region data for the two isolates M1 and SE were Aspergillus fumigatus and Aspergillus sydowii, respectively. I4 was identified as Bacillus mojavensis on the basis of the 16S rRNA gene sequencing and biochemical properties. The enzyme production was evaluated by cultivating the isolated microorganisms in liquid-state bioprocess using wheat bran as carbon source. Two fungi (M1, and SE and one bacterium (I4 strains were found to be xylanase producer, and several were proven to be outstanding producers of microbial xylanase. The strains producing xylanase secreted variable amounts of starch-debranching enzymes and produced low level β-mannan-degrading enzyme systems. The bacterium strain was found to be capable of producing pectinolytic enzymes on wheat bran at high level. Some of the strains have good potential for use as sources of important industrial enzymes.

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

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María Soledad Marqués-Calvo

2013-01-01

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

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

Science.gov (United States)

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

2015-03-01

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

Methylobacterium oryzae sp. nov., an aerobic, pink-pigmented, facultatively methylotrophic, 1-aminocyclopropane-1-carboxylate deaminase-producing bacterium isolated from rice.

Science.gov (United States)

Madhaiyan, Munusamy; Kim, Byung-Yong; Poonguzhali, Selvaraj; Kwon, Soon-Wo; Song, Myung-Hee; Ryu, Jeoung-Hyun; Go, Seung-Joo; Koo, Bon-Sung; Sa, Tong-Min

2007-02-01

A pink-pigmented, facultatively methylotrophic bacterium, strain CBMB20T, isolated from stem tissues of rice, was analysed by a polyphasic approach. Strain CBMB20T utilized 1-aminocyclopropane 1-carboxylate (ACC) as a nitrogen source and produced ACC deaminase. It was related phylogenetically to members of the genus Methylobacterium. 16S rRNA gene sequence analysis indicated that strain CBMB20T was most closely related to Methylobacterium fujisawaense, Methylobacterium radiotolerans and Methylobacterium mesophilicum; however, DNA-DNA hybridization values were less than 70 % with the type strains of these species. The DNA G+C content of strain CBMB20T was 70.6 mol%. The study presents a detailed phenotypic characterization of strain CBMB20T that allows its differentiation from other Methylobacterium species. In addition, strain CBMB20T is the only known member of the genus Methylobacterium to be described from the phyllosphere of rice. Based on the data presented, strain CBMB20T represents a novel species in the genus Methylobacterium, for which the name Methylobacterium oryzae sp. nov. is proposed, with strain CBMB20T (=DSM 18207T=LMG 23582T=KACC 11585T) as the type strain.

Complete genome sequence of Kytococcus sedentarius type strain (strain 541T)

Energy Technology Data Exchange (ETDEWEB)

Sims, David; Brettin, Thomas; Detter, John C.; Han, Cliff; Lapidus, Alla; Copeland, Alex; Glavina Del Rio, Tijana; Nolan, Matt; Chen, Feng; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ovchinnikova, Galina; Pati, Amrita; Ivanova, Natalia; Mavrommatis, Konstantinos; Chen, Amy; Palaniappan, Krishna; D' haeseleer, Patrick; Chain, Patrick; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Schneider, Susanne; Goker, Markus; Pukall, Rudiger; Kyrpides, Nikos C.; Klenk, Hans-Peter

2009-05-20

Kytococcus sedentarius (ZoBell and Upham 1944) Stackebrandt et al. 1995 is the type strain of the species, and is of phylogenetic interest because of its location in the Dermacoccaceae, a poorly studied family within the actinobacterial suborder Micrococcineae. K. sedentarius is known for the production of oligoketide antibiotics as well as for its role as an opportunistic pathogen causing valve endocarditis, hemorrhagic pneumonia, and pitted keratolysis. It is strictly aerobic and can only grow when several amino acids are provided in the medium. The strain described in this report is a free-living, nonmotile, Gram-positive bacterium, originally isolated from a marine environment. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family Dermacoccaceae and the 2,785,024 bp long single replicon genome with its 2639 protein-coding and 64 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

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

KAUST Repository

Balk, Melike

2009-08-23

A novel anaerobic, thermophilic, Gram-positive, spore-forming, and sugar-fermenting bacterium (strain TLO) was isolated from a geothermal spring in Ayaş, Turkey. The cells were straight to curved rods, 0.4-0.6 microm in diameter and 3.5-10 microm in length. Spores were terminal and round. The temperature range for growth was 40-80 degrees C, with an optimum at 70 degrees C. The pH optimum was between 6.3 and 6.8. Strain TLO has the capability to ferment a wide variety of mono-, di-, and polysaccharides and proteinaceous substrates, producing mainly lactate, next to acetate, ethanol, alanine, H(2), and CO(2). Remarkably, the bacterium was able to grow in an atmosphere of up to 25% of CO as sole electron donor. CO oxidation was coupled to H(2) and CO(2) formation. The G + C content of the genomic DNA was 35.1 mol%. Based on 16S rRNA gene sequence analysis and the DNA-DNA hybridization data, this bacterium is most closely related to Thermoanaerobacter thermohydrosulfuricus and Thermoanaerobacter siderophilus (99% similarity for both). However, strain TLO differs from Thermoanaerobacter thermohydrosulfuricus in important aspects, such as CO-utilization and lipid composition. These differences led us to propose that strain TLO represents a subspecies of Thermoanaerobacter thermohydrosulfuricus, and we therefore name it Thermoanaerobacter thermohydrosulfuricus subsp. carboxydovorans.

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

KAUST Repository

Balk, Melike; Heilig, Hans G H J; van Eekert, Miriam H A; Stams, Alfons J M; Rijpstra, Irene C; Sinninghe-Damsté , Jaap S; de Vos, Willem M; Kengen, Servé W M

2009-01-01

A novel anaerobic, thermophilic, Gram-positive, spore-forming, and sugar-fermenting bacterium (strain TLO) was isolated from a geothermal spring in Ayaş, Turkey. The cells were straight to curved rods, 0.4-0.6 microm in diameter and 3.5-10 microm in length. Spores were terminal and round. The temperature range for growth was 40-80 degrees C, with an optimum at 70 degrees C. The pH optimum was between 6.3 and 6.8. Strain TLO has the capability to ferment a wide variety of mono-, di-, and polysaccharides and proteinaceous substrates, producing mainly lactate, next to acetate, ethanol, alanine, H(2), and CO(2). Remarkably, the bacterium was able to grow in an atmosphere of up to 25% of CO as sole electron donor. CO oxidation was coupled to H(2) and CO(2) formation. The G + C content of the genomic DNA was 35.1 mol%. Based on 16S rRNA gene sequence analysis and the DNA-DNA hybridization data, this bacterium is most closely related to Thermoanaerobacter thermohydrosulfuricus and Thermoanaerobacter siderophilus (99% similarity for both). However, strain TLO differs from Thermoanaerobacter thermohydrosulfuricus in important aspects, such as CO-utilization and lipid composition. These differences led us to propose that strain TLO represents a subspecies of Thermoanaerobacter thermohydrosulfuricus, and we therefore name it Thermoanaerobacter thermohydrosulfuricus subsp. carboxydovorans.

Ultrastructure and Development of Pasteuria sp. (S-1 strain), an Obligate Endoparasite of Belonolaimus longicaudatus (Nemata: Tylenchida).

Science.gov (United States)

Giblin-Davis, R M; Williams, D S; Wergin, W P; Dickson, D W; Hewlett, T E; Bekal, S; Becker, J O

2001-12-01

Pasteuria sp., strain S-1, is a gram-positive, obligate endoparasitic bacterium that uses the phytoparasitic sting nematode, Belonolaimus longicaudatus, as its host in Florida. The host attachment of S-1 appears to be specific to the genus Belonolaimus with development occurring only in juveniles and adults of B. longicaudatus. This bacterium is characterized from other described species of Pasteuria using ultrastructure of the mature endospore. Penetration, development, and sporogenesis were elucidated with TEM, LTSEM, and SEM and are similar to other nematode-specific Pasteuria. Recent analysis of 16S rDNA sequence homology confirms its congeneric ranking with other Pasteuria species and strains from nematodes and cladocerans, and corroborates ultrastructural, morphological, morphometric, and host-range evidence suggesting separate species status.

Competitive Interactions Between Incompatible Mutants of the Social Bacterium Myxococcus xanthus DK1622

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Ya Gong

2018-06-01

Full Text Available Due to the high similarity in their requirements for space and food, close bacterial relatives may be each other's strongest competitors. Close bacterial relatives often form visible boundaries to separate their swarming colonies, a phenomenon termed colony-merger incompatibility. While bacterial species are known to have many incompatible strains, it is largely unclear which traits lead to multiple incompatibilities and the interactions between multiple incompatible siblings. To investigate the competitive interactions of closely related incompatible strains, we mutated Myxococcus xanthus DK1622, a predatory bacterium with complex social behavior. From 3392 random transposon mutations, we obtained 11 self-identification (SI deficient mutants that formed unmerged colony boundaries with the ancestral strain. The mutations were at nine loci with unknown functions and formed nine independent SI mutants. Compared with their ancestral strain, most of the SI mutants showed reduced growth, swarming and development abilities, but some remained unchanged from their monocultures. When pairwise mixed with their ancestral strain for co-cultivation, these mutants exhibited improved, reduced or unchanged competitive abilities compared with the ancestral strain. The sporulation efficiencies were affected by the DK1622 partner, ranging from almost complete inhibition to 360% stimulation. The differences in competitive growth between the SI mutants and DK1622 were highly correlated with the differences in their sporulation efficiencies. However, the competitive efficiencies of the mutants in mixture were inconsistent with their growth or sporulation abilities in monocultures. We propose that the colony-merger incompatibility in M. xanthus is associated with multiple independent genetic loci, and the incompatible strains hold competitive interaction abilities, which probably determine the complex relationships between multiple incompatible M. xanthus strains and

Genome Sequence of Carbon Dioxide-Sequestering Serratia sp. Strain ISTD04 Isolated from Marble Mining Rocks

OpenAIRE

Kumar, Manish; Gazara, Rajesh Kumar; Verma, Sandhya; Kumar, Madan; Verma, Praveen Kumar; Thakur, Indu Shekhar

2016-01-01

The Serratia sp. strain ISTD04 has been identified as a carbon dioxide (CO2)-sequestering bacterium isolated from marble mining rocks in the Umra area, Rajasthan, India. This strain grows chemolithotrophically on media that contain sodium bicarbonate (NaHCO3) as the sole carbon source. Here, we report the genome sequence of 5.07?Mb Serratia sp. ISTD04.

Isolation of a human intestinal anaerobe, Bifidobacterium sp. strain SEN, capable of hydrolyzing sennosides to sennidins.

Science.gov (United States)

Akao, T; Che, Q M; Kobashi, K; Yang, L; Hattori, M; Namba, T

1994-01-01

A strictly anaerobic bacterium capable of metabolizing sennosides was isolated from human feces and identified as Bifidobacterium sp., named strain SEN. The bacterium hydrolyzed sennosides A and B to sennidins A and B via sennidin A and B 8-monoglucosides, respectively. Among nine species of Bifidobacterium having beta-glucosidase activity, only Bifidobacterium dentium and B. adolescentis metabolized sennoside B to sennidin B, suggesting that the sennoside-metabolizing bacteria produce a novel type of beta-glucosidase capable of hydrolyzing sennosides to sennidins. PMID:8161172

Insights into Brevibacillus borstelensis AK1 through Whole Genome Sequencing: A Thermophilic Bacterium Isolated from a Hot Spring in Saudi Arabia

KAUST Repository

Khalil, Amjad B.

2018-05-24

Brevibacillus borstelensis AK1 is a thermophile which grows between the temperatures of 45°C and 70°C. The present study is an extended genome report of B. borstelensis AK1 along with the morphological characterization. The strain is isolated from a hot spring in Saudi Arabia (southeast of the city Gazan). It is observed that the strain AK1 is rod-shaped, motile, and strictly aerobic bacterium. The whole genome sequence resulted in 29 contigs with a total length of 5,155,092 bp. In total, 3,946 protein-coding genes and 139 RNA genes were identified. Comparison with the previously submitted strains of B. borstelensis strains illustrates that strain AK1 has a small genome size but high GC content. The strain possesses putative genes for degradation of a wide range of substrates including polyethylene (plastic) and long-chain hydrocarbons. These genomic features may be useful for future environmental/biotechnological applications.

Insights into Brevibacillus borstelensis AK1 through Whole Genome Sequencing: A Thermophilic Bacterium Isolated from a Hot Spring in Saudi Arabia

KAUST Repository

Khalil, Amjad B.; Neelamegam, Sivakumar; Arslan, Muhammad; Saleem, Hamna; Alqarawi, Sami

2018-01-01

Brevibacillus borstelensis AK1 is a thermophile which grows between the temperatures of 45°C and 70°C. The present study is an extended genome report of B. borstelensis AK1 along with the morphological characterization. The strain is isolated from a hot spring in Saudi Arabia (southeast of the city Gazan). It is observed that the strain AK1 is rod-shaped, motile, and strictly aerobic bacterium. The whole genome sequence resulted in 29 contigs with a total length of 5,155,092 bp. In total, 3,946 protein-coding genes and 139 RNA genes were identified. Comparison with the previously submitted strains of B. borstelensis strains illustrates that strain AK1 has a small genome size but high GC content. The strain possesses putative genes for degradation of a wide range of substrates including polyethylene (plastic) and long-chain hydrocarbons. These genomic features may be useful for future environmental/biotechnological applications.

Closed Genome Sequence of Phytopathogen Biocontrol Agent Bacillus velezensis Strain AGVL-005, Isolated from Soybean.

Science.gov (United States)

Pylro, Victor Satler; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini; Morais, Daniel Kumazawa; Varani, Alessandro de Mello; Andreote, Cristiane Cipolla Fasanella; Bernardo, Eduardo Roberto de Almeida; Zucchi, Tiago

2018-02-15

We report here the closed and near-complete genome sequence and annotation of Bacillus velezensis strain AGVL-005, a bacterium isolated from soybean seeds in Brazil and used for phytopathogen biocontrol. Copyright © 2018 Pylro et al.

Nitrate-Dependent Degradation of Acetone by Alicycliphilus and Paracoccus Strains and Comparison of Acetone Carboxylase Enzymes ▿

Science.gov (United States)

Dullius, Carlos Henrique; Chen, Ching-Yuan; Schink, Bernhard

2011-01-01

A novel acetone-degrading, nitrate-reducing bacterium, strain KN Bun08, was isolated from an enrichment culture with butanone and nitrate as the sole sources of carbon and energy. The cells were motile short rods, 0.5 to 1 by 1 to 2 μm in size, which gave Gram-positive staining results in the exponential growth phase and Gram-negative staining results in the stationary-growth phase. Based on 16S rRNA gene sequence analysis, the isolate was assigned to the genus Alicycliphilus. Besides butanone and acetone, the strain used numerous fatty acids as substrates. An ATP-dependent acetone-carboxylating enzyme was enriched from cell extracts of this bacterium and of Alicycliphilus denitrificans K601T by two subsequent DEAE Sepharose column procedures. For comparison, acetone carboxylases were enriched from two additional nitrate-reducing bacterial species, Paracoccus denitrificans and P. pantotrophus. The products of the carboxylase reaction were acetoacetate and AMP rather than ADP. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis of cell extracts and of the various enzyme preparations revealed bands corresponding to molecular masses of 85, 78, and 20 kDa, suggesting similarities to the acetone carboxylase enzymes described in detail for the aerobic bacterium Xanthobacter autotrophicus strain Py2 (85.3, 78.3, and 19.6 kDa) and the phototrophic bacterium Rhodobacter capsulatus. Protein bands were excised and compared by mass spectrometry with those of acetone carboxylases of aerobic bacteria. The results document the finding that the nitrate-reducing bacteria studied here use acetone-carboxylating enzymes similar to those of aerobic and phototrophic bacteria. PMID:21841031

Genome Sequence of Lactococcus lactis subsp. lactis NCDO 2118, a GABA-Producing Strain

DEFF Research Database (Denmark)

Oliveira, Letícia C; Saraiva, Tessália D L; Soares, Siomar C

2014-01-01

Lactococcus lactis subsp. lactis NCDO 2118 is a nondairy lactic acid bacterium, a xylose fermenter, and a gamma-aminobutyric acid (GABA) producer isolated from frozen peas. Here, we report the complete genome sequence of L. lactis NCDO 2118, a strain with probiotic potential activity....

A bacterium that degrades and assimilates poly(ethylene terephthalate).

Science.gov (United States)

Yoshida, Shosuke; Hiraga, Kazumi; Takehana, Toshihiko; Taniguchi, Ikuo; Yamaji, Hironao; Maeda, Yasuhito; Toyohara, Kiyotsuna; Miyamoto, Kenji; Kimura, Yoshiharu; Oda, Kohei

2016-03-11

Poly(ethylene terephthalate) (PET) is used extensively worldwide in plastic products, and its accumulation in the environment has become a global concern. Because the ability to enzymatically degrade PET has been thought to be limited to a few fungal species, biodegradation is not yet a viable remediation or recycling strategy. By screening natural microbial communities exposed to PET in the environment, we isolated a novel bacterium, Ideonella sakaiensis 201-F6, that is able to use PET as its major energy and carbon source. When grown on PET, this strain produces two enzymes capable of hydrolyzing PET and the reaction intermediate, mono(2-hydroxyethyl) terephthalic acid. Both enzymes are required to enzymatically convert PET efficiently into its two environmentally benign monomers, terephthalic acid and ethylene glycol. Copyright © 2016, American Association for the Advancement of Science.

Complete Genome Sequence of Bacillus vallismortis NBIF-001, a Novel Strain from Shangri-La, China, That Has High Activity against Fusarium oxysporum.

Science.gov (United States)

Liu, Xiaoyan; Min, Yong; Huang, Daye; Zhou, Ronghua; Fang, Wei; Liu, Cuijun; Rao, Ben; Zhang, Guangyang; Wang, Kaimei; Yang, Ziwen

2017-11-30

Bacillus vallismortis NBIF-001, a Gram-positive bacterium, was isolated from soil in Shangri-La, China. Here, we provide the complete genome sequence of this bacterium, which has a 3,929,787-bp-long genome, including 4,030 protein-coding genes and 195 RNA genes. This strain possesses a number of genes encoding virulence factors of pathogens. Copyright © 2017 Liu et al.

Draft Genome Sequence of Plant Growth–Promoting Micrococcus luteus Strain K39 Isolated from Cyperus conglomeratus in Saudi Arabia

KAUST Repository

Lafi, Feras Fawzi; Ramirez Prado, Juan Sebastian; Alam, Intikhab; Bajic, Vladimir B.; Hirt, Heribert; Saad, Maged

2017-01-01

Micrococcus luteus strain K39 is an endophyte bacterium isolated from roots of the desert plant Cyperus conglomeratus collected from the Red Sea shore, Thuwal, Saudi Arabia. The draft genome sequence of strain K39 revealed a number of enzymes involved in salinity and oxidative stress tolerance or having herbicide-resistance activity.

Draft Genome Sequence of Plant Growth–Promoting Micrococcus luteus Strain K39 Isolated from Cyperus conglomeratus in Saudi Arabia

KAUST Repository

Lafi, Feras Fawzi

2017-01-27

Micrococcus luteus strain K39 is an endophyte bacterium isolated from roots of the desert plant Cyperus conglomeratus collected from the Red Sea shore, Thuwal, Saudi Arabia. The draft genome sequence of strain K39 revealed a number of enzymes involved in salinity and oxidative stress tolerance or having herbicide-resistance activity.

MODELING OF MIXED CHEMOSTAT CULTURES OF AN AEROBIC BACTERIUM, COMAMONAS-TESTOSTERONI, AND AN ANAEROBIC BACTERIUM, VEILLONELLA-ALCALESCENS - COMPARISON WITH EXPERIMENTAL-DATA

NARCIS (Netherlands)

GERRITSE, J; SCHUT, F; GOTTSCHAL, JC

A mathematical model of mixed chemostat cultures of the obligately aerobic bacterium Comamonas testosteroni and the anaerobic bacterium Veillonella alcalescens grown under dual limitation Of L-lactate and oxygen was constructed. The model was based on Michaelis-Menten-type kinetics for the

Competitive Dominance by a Bacteriocin-Producing Vibrio harveyi Strain.

Science.gov (United States)

Hoyt, P R; Sizemore, R K

1982-09-01

Vibrio (Beneckea) harveyi, a bioluminescent marine bacterium, has been shown to produce a bacteriocin-like substance the production of which is mediated by a plasmid. This substance is assumed to be proteinaceous because of its sensitivity to certain proteolytic enzymes. It is stable at low temperatures and can be concentrated by ammonium sulfate precipitation or negative-pressure dialysis. The molecular weight of the bacteriocin was determined to be 2.4 x 10 by molecular exclusion chromatography. Competition experiments indicated that bacteriocin-producing strains predominated over cured variants of the same strain in broth culture experiments. We studied several environmental parameters (pH, salinity, temperature, nutrient concentration) to determine their effects on the competitive advantage bestowed on a bacteriocin-producing strain. Under simulated free-living conditions, no competitive advantage attributable to bacteriocin production was observed. In a simulated enteric habitat, a bacteriocin-producing strain showed dramatic (>90%) inhibition of the sensitive strain within 24 h.

Quorum sensing activity of Citrobacter amalonaticus L8A, a bacterium isolated from dental plaque.

Science.gov (United States)

Goh, Share-Yuan; Khan, Saad Ahmed; Tee, Kok Keng; Abu Kasim, Noor Hayaty; Yin, Wai-Fong; Chan, Kok-Gan

2016-02-10

Cell-cell communication is also known as quorum sensing (QS) that happens in the bacterial cells with the aim to regulate their genes expression in response to increased cell density. In this study, a bacterium (L8A) isolated from dental plaque biofilm was identified as Citrobacter amalonaticus by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). Its N-acylhomoserine-lactone (AHL) production was screened by using two types of AHL biosensors namely Chromobacterium violaceum CV026 and Escherichia coli [pSB401]. Citrobacter amalonaticus strain L8A was identified and confirmed producing numerous types of AHL namely N-butyryl-L-homoserine lactone (C4-HSL), N-hexanoyl-L-homoserine lactone (C6-HSL), N-octanoyl-L-homoserine lactone (C8-HSL) and N-hexadecanoyl-L-homoserine lactone (C16-HSL). We performed the whole genome sequence analysis of this oral isolate where its genome sequence reveals the presence of QS signal synthase gene and our work will pave the ways to study the function of the related QS genes in this bacterium.

Nocardioides daejeonensis sp. nov., a denitrifying bacterium isolated from sludge in a sewage-disposal plant.

Science.gov (United States)

Woo, Sung-Geun; Srinivasan, Sathiyaraj; Yang, Jihoon; Jung, Yong-An; Kim, Myung Kyum; Lee, Myungjin

2012-05-01

Strain MJ31(T), a gram-reaction-positive, aerobic, rod-shaped, non-motile bacterium, was isolated from a sludge sample collected at the Daejeon sewage-disposal plant, in South Korea, and characterized in order to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MJ31(T) belonged to the genus Nocardioides, appearing most closely related to Nocardioides dubius KSL-104(T) (98.6 % sequence similarity), Nocardioides jensenii DSM 20641(T) (97.6 %), Nocardioides daedukensis MDN22(T) (97.2 %) and Nocardioides mesophilus MSL-22(T) (97.0 %). The chemotaxonomic properties of strain MJ31(T) were consistent with those of the genus Nocardioides: MK-8(H(4)) was the predominant menaquinone, iso-C(16 : 0), iso-C(17 : 0) and C(18 : 1)ω9c were the predominant cellular fatty acids, and the cell-wall peptidoglycan was based on LL-2,6-diaminopimelic acid. The genomic DNA G+C content of strain MJ31(T) was 71.2 mol%. Some differential phenotypic properties and low DNA-DNA relatedness values (<28 %) with the type strains of closely related species indicated that strain MJ31(T) represents a novel species, for which the name Nocardioides daejeonensis sp. nov. is proposed. The type strain is MJ31(T) ( = KCTC 19772(T) = JCM 16922(T)).

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.

Genome Sequence of Carbon Dioxide-Sequestering Serratia sp. Strain ISTD04 Isolated from Marble Mining Rocks.

Science.gov (United States)

Kumar, Manish; Gazara, Rajesh Kumar; Verma, Sandhya; Kumar, Madan; Verma, Praveen Kumar; Thakur, Indu Shekhar

2016-10-20

The Serratia sp. strain ISTD04 has been identified as a carbon dioxide (CO 2 )-sequestering bacterium isolated from marble mining rocks in the Umra area, Rajasthan, India. This strain grows chemolithotrophically on media that contain sodium bicarbonate (NaHCO 3 ) as the sole carbon source. Here, we report the genome sequence of 5.07 Mb Serratia sp. ISTD04. Copyright © 2016 Kumar et al.

Draft genome sequence of Pseudomonas sp. strain M47T1, carried by Bursaphelenchus xylophilus isolated from Pinus pinaster.

Science.gov (United States)

Proença, Diogo Neves; Espírito Santo, Christophe; Grass, Gregor; Morais, Paula V

2012-09-01

The draft genome sequence of Pseudomonas sp. strain M47T1, carried by the Bursaphelenchus xylophilus pinewood nematode, the causative agent of pine wilt disease, is presented. In Pseudomonas sp. strain M47T1, genes that make this a plant growth-promoting bacterium, as well as genes potentially involved in nematotoxicity, were identified.

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 ).

Isolation and characterization of a furfural-degrading bacterium Bacillus cereus sp. strain DS1.

Science.gov (United States)

Zheng, Dan; Bao, Jianguo; Lu, Jueming; Gao, Chunlei

2015-02-01

Furfural was found to be the main organic pollutant in the wastewater coming from the Diosgenin factory. This substance is derived from acidic pentosan in Dioscorea zingiberensis and is also found in a variety of agricultural byproducts, including corncobs, oat, wheat bran, and sawdust. It is regarded as a toxicant and an inhibitor to the growth of microorganism in both sewage disposal and biological fermentation. A furfural-degrading strain (DS1) was isolated from activated sludge of wastewater treatment plant in a diosgenin factory by continuous enrichment culture. The strain was identified as Bacillus cereus based on morphological, physiological tests, as well as on 16S rDNA sequence and Biolog analyses. The capacity of this strain to grow on a mineral salt medium, utilizing furfural as the sole carbon and energy source to degrade furfural, was investigated in this study. Under the condition of pH 9.0, temperature 35 °C, with rotating speed of 150 rpm, and an inoculum of 6 %, the strain showed that the furfural degradation capacity reaches 35 % in 7 days, as measured by high-performance liquid chromatography. The addition of inorganic carbon sources could bring down the biodegradation efficiency of the furfural. The strain DS1 showed better furfural removal capacity, as compared to other inorganic carbon sources in the media. Furthermore, a furfural concentration of as high as 4,000 mg L(-1) was tolerated by the culture. The capacity to degrade furfural was demonstrated for the first time by using the genus B. cereus. This study suggests the possible application in biodegradation strategies.

Draft genome sequence of the arsenite-oxidizing strain Aliihoeflea sp. 2WW, isolated from arsenic-contaminated groundwater

NARCIS (Netherlands)

Cavalca, L.; Corsini, A.; Andreoni, V.; Muyzer, G.

2013-01-01

Here, we report the draft genome sequence of the arsenite-oxidizing bacterium Aliihoeflea sp. strain 2WW, which consists of a 4.15-Mb chromosome and contains different genes that are involved in arsenic transformations.

Natural Competence of Xylella fastidiosa Occurs at a High Frequency Inside Microfluidic Chambers Mimicking the Bacterium's Natural Habitats.

Science.gov (United States)

Kandel, Prem P; Lopez, Samantha M; Almeida, Rodrigo P P; De La Fuente, Leonardo

2016-09-01

Xylella fastidiosa is a xylem-limited bacterium that is the causal agent of emerging diseases in a number of economically important crops. Genetic diversity studies have demonstrated homologous recombination occurring among X. fastidiosa strains, which has been proposed to contribute to host plant shifts. Moreover, experimental evidence confirmed that X. fastidiosa is naturally competent for recombination in vitro Here, as an approximation of natural habitats (plant xylem vessels and insect mouthparts), recombination was studied in microfluidic chambers (MCs) filled with media amended with grapevine xylem sap. First, different media were screened for recombination in solid agar plates using a pair of X. fastidiosa strains that were previously reported to recombine in coculture. The highest frequency of recombination was obtained with PD3 medium, compared to those with the other two media (X. fastidiosa medium [XFM] and periwinkle wilt [PW] medium) used in previous studies. Dissection of the media components led to the identification of bovine serum albumin as an inhibitor of recombination that was correlated to its previously known effect on inhibition of twitching motility. When recombination was performed in liquid culture, the frequencies were significantly higher under flow conditions (MCs) than under batch conditions (test tubes). The recombination frequencies in MCs and agar plates were not significantly different from each other. Grapevine xylem sap from both susceptible and tolerant varieties allowed high recombination frequency in MCs when mixed with PD3. These results suggest that X. fastidiosa has the ability to be naturally competent in the natural growth environment of liquid flow, and this phenomenon could have implications in X. fastidiosa environmental adaptation. Xylella fastidiosa is a plant pathogen that lives inside xylem vessels (where water and nutrients are transported inside the plant) and the mouthparts of insect vectors. This bacterium

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

Science.gov (United States)

Madhaiyan, Munusamy; Poonguzhali, Selvaraj

2014-02-01

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

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).

Engineering a wild fast-growing Mycoplasma bacterium to generate ...

International Development Research Centre (IDRC) Digital Library (Canada)

2018-01-12

Jan 12, 2018 ... The CCPP bacterium causes sick animals to experience severe symptoms ... because antibiotic treatment does not eliminate the responsible bacterium. ... To develop a fast growing CCPP vaccine for cheaper production and ...

Draft Genome Sequence of the Plant Growth–Promoting Rhizobacterium Acinetobacter radioresistens Strain SA188 Isolated from the Desert Plant Indigofera argentea

KAUST Repository

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

2017-01-01

Acinetobacter radioresistens strain SA188 is a plant endophytic bacterium, isolated from root nodules of the desert plants Indigofera spp., collected in Jizan, Saudi Arabia. Here, we report the 3.2-Mb draft genome sequence of strain SA188, highlighting characteristic pathways for plant growth–promoting activity and environmental adaptation.

Draft Genome Sequence of the Plant Growth–Promoting Rhizobacterium Acinetobacter radioresistens Strain SA188 Isolated from the Desert Plant Indigofera argentea

KAUST Repository

Lafi, Feras Fawzi

2017-03-03

Acinetobacter radioresistens strain SA188 is a plant endophytic bacterium, isolated from root nodules of the desert plants Indigofera spp., collected in Jizan, Saudi Arabia. Here, we report the 3.2-Mb draft genome sequence of strain SA188, highlighting characteristic pathways for plant growth–promoting activity and environmental adaptation.

Helicobacter Catalase Devoid of Catalytic Activity Protects the Bacterium against Oxidative Stress.

Science.gov (United States)

Benoit, Stéphane L; Maier, Robert J

2016-11-04

Catalase, a conserved and abundant enzyme found in all domains of life, dissipates the oxidant hydrogen peroxide (H 2 O 2 ). The gastric pathogen Helicobacter pylori undergoes host-mediated oxidant stress exposure, and its catalase contains oxidizable methionine (Met) residues. We hypothesized catalase may play a large stress-combating role independent of its classical catalytic one, namely quenching harmful oxidants through its recyclable Met residues, resulting in oxidant protection to the bacterium. Two Helicobacter mutant strains ( katA H56A and katA Y339A ) containing catalase without enzyme activity but that retain all Met residues were created. These strains were much more resistant to oxidants than a catalase-deletion mutant strain. The quenching ability of the altered versions was shown, whereby oxidant-stressed (HOCl-exposed) Helicobacter retained viability even upon extracellular addition of the inactive versions of catalase, in contrast to cells receiving HOCl alone. The importance of the methionine-mediated quenching to the pathogen residing in the oxidant-rich gastric mucus was studied. In contrast to a catalase-null strain, both site-change mutants proficiently colonized the murine gastric mucosa, suggesting that the amino acid composition-dependent oxidant-quenching role of catalase is more important than the well described H 2 O 2 -dissipating catalytic role. Over 100 years after the discovery of catalase, these findings reveal a new non-enzymatic protective mechanism of action for the ubiquitous enzyme. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Fermentation of glycolate by a pure culture of a strictly anaerobic gram-positive bacterium belonging to the family Lachnospiraceae.

Science.gov (United States)

Janssen, Peter H; Hugenholtz, Philip

2003-05-01

The component bacteria of a three-membered mixed culture able to ferment glycolate to acetate, propionate and CO(2) were isolated in pure culture. All three strains were strict anaerobes that, on the basis of comparative 16S rRNA gene sequence analysis, belonged to the order Clostridiales in the phylum Firmicutes (low G+C gram-positive bacteria). Two of the strains were not involved in glycolate metabolism. The third, the glycolate-fermenting strain 19gly4 (DSM 11261), was related to members of the family Lachnospiraceae. The cells of strain 19gly4 were oval- to lemon-shaped, 0.85 microm long and 0.65 microm in diameter, occurring singly, in pairs, or in chains of up to 30 cells. Strain 19gly4 fermented glycolate or fumarate to acetate, succinate, and CO(2). Hydrogen was not formed, and strain 19gly4 was able to grow on glycolate in pure culture without any syntrophic hydrogen transfer and without the use of an external electron acceptor. There was no evidence for homoacetogenic metabolism. This bacterium therefore differs in metabolism from previously reported glycolate-utilising anaerobes.

Zymomonas mobilis: a bacterium for ethanol production

Energy Technology Data Exchange (ETDEWEB)

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

1986-01-01

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

Taxonomic characterization of the cellulose-degrading bacterium NCIB 10462

Energy Technology Data Exchange (ETDEWEB)

Dees, C.; Ringleberg, D.; Scott, T.C. [Oak Ridge National Lab., TN (United States); Phelps, T. [Univ. of Tennessee, Knoxville, TN (United States)

1994-06-01

The gram negative cellulase-producing bacterium NCIB 10462 has been previously named Pseudomonas fluorescens subsp. or var. cellulosa. Since there is renewed interest in cellulose-degrading bacteria for use in bioconversion of cellulose to chemical feed stocks and fuels, we re-examined the characteristics of this microorganism to determine its proper taxonomic characterization and to further define it`s true metabolic potential. Metabolic and physical characterization of NCIB 10462 revealed that this was an alkalophilic, non-fermentative, gram negative, oxidase positive, motile, cellulose-degrading bacterium. The aerobic substrate utilization profile of this bacterium was found to have few characteristics consistent with a classification of P. fluorescens with a very low probability match with the genus Sphingomonas. Total lipid analysis did not reveal that any sphingolipid bases are produced by this bacterium. NCIB 10462 was found to grow best aerobically but also grows well in complex media under reducing conditions. NCIB 10462 grew slowly under full anaerobic conditions on complex media but growth on cellulosic media was found only under aerobic conditions. Total fatty acid analysis (MIDI) of NCIB 10462 failed to group this bacterium with a known pseudomonas species. However, fatty acid analysis of the bacteria when grown at temperatures below 37{degrees}C suggest that the organism is a pseudomonad. Since a predominant characteristic of this bacterium is it`s ability to degrade cellulose, we suggest it be called Pseudomonas cellulosa.

Lipid transfer proteins and protease inhibitors as key factors in the priming of barley responses to Fusarium head blight disease by a biocontrol strain of Pseudomonas fluorescens.

Science.gov (United States)

Petti, Carloalberto; Khan, Mojibur; Doohan, Fiona

2010-11-01

Strains of non-pathogenic pseudomonad bacteria, can elicit host defence responses against pathogenic microorganisms. Pseudomonas fluorescens strain MKB158 can protect cereals from pathogenesis by Fusarium fungi, including Fusarium head blight which is an economically important disease due to its association with both yield loss and mycotoxin contamination of grain. Using the 22 K barley Affymetrix chip, trancriptome studies were undertaken to determine the local effect of P. fluorescens strain MKB158 on the transcriptome of barley head tissue, and to discriminate transcripts primed by the bacterium to respond to challenge by Fusarium culmorum, a causal agent of the economically important Fusarium head blight disease of cereals. The bacterium significantly affected the accumulation of 1203 transcripts and primed 74 to positively, and 14 to negatively, respond to the pathogen (P = 0.05). This is the first study to give insights into bacterium priming in the Triticeae tribe of grasses and associated transcripts were classified into 13 functional classes, associated with diverse functions, including detoxification, cell wall biosynthesis and the amplification of host defence responses. In silico analysis of Arabidopsis homologs of bacterium-primed barley genes indicated that, as is the case in dicots, jasmonic acid plays a role in pseudomonad priming of host responses. Additionally, the transcriptome studies described herein also reveal new insights into bacterium-mediated priming of host defences against necrotrophs, including the positive effects on grain filling, lignin deposition, oxidative stress responses, and the inhibition of protease inhibitors and proteins that play a key role in programmed cell death.

Sepsis and Hemocyte Loss in Honey Bees (Apis mellifera) Infected with Serratia marcescens Strain Sicaria.

Science.gov (United States)

Burritt, Nancy L; Foss, Nicole J; Neeno-Eckwall, Eric C; Church, James O; Hilger, Anna M; Hildebrand, Jacob A; Warshauer, David M; Perna, Nicole T; Burritt, James B

2016-01-01

Global loss of honey bee colonies is threatening the human food supply. Diverse pathogens reduce honey bee hardiness needed to sustain colonies, especially in winter. We isolated a free-living Gram negative bacillus from hemolymph of worker honey bees (Apis mellifera) found separated from winter clusters. In some hives, greater than 90% of the dying bees detached from the winter cluster were found to contain this bacterium in their hemolymph. Throughout the year, the same organism was rarely found in bees engaged in normal hive activities, but was detected in about half of Varroa destructor mites obtained from colonies that housed the septic bees. Flow cytometry of hemolymph from septic bees showed a significant reduction of plasmatocytes and other types of hemocytes. Interpretation of the16S rRNA sequence of the bacterium indicated that it belongs to the Serratia genus of Gram-negative Gammaproteobacteria, which has not previously been implicated as a pathogen of adult honey bees. Complete genome sequence analysis of the bacterium supported its classification as a novel strain of Serratia marcescens, which was designated as S. marcescens strain sicaria (Ss1). When compared with other strains of S. marcescens, Ss1 demonstrated several phenotypic and genetic differences, including 65 genes not previously found in other Serratia genomes. Some of the unique genes we identified in Ss1 were related to those from bacterial insect pathogens and commensals. Recovery of this organism extends a complex pathosphere of agents which may contribute to failure of honey bee colonies.

Sepsis and Hemocyte Loss in Honey Bees (Apis mellifera) Infected with Serratia marcescens Strain Sicaria

Science.gov (United States)

Burritt, Nancy L.; Foss, Nicole J.; Neeno-Eckwall, Eric C.; Church, James O.; Hildebrand, Jacob A.; Warshauer, David M.; Perna, Nicole T.; Burritt, James B.

2016-01-01

Global loss of honey bee colonies is threatening the human food supply. Diverse pathogens reduce honey bee hardiness needed to sustain colonies, especially in winter. We isolated a free-living Gram negative bacillus from hemolymph of worker honey bees (Apis mellifera) found separated from winter clusters. In some hives, greater than 90% of the dying bees detached from the winter cluster were found to contain this bacterium in their hemolymph. Throughout the year, the same organism was rarely found in bees engaged in normal hive activities, but was detected in about half of Varroa destructor mites obtained from colonies that housed the septic bees. Flow cytometry of hemolymph from septic bees showed a significant reduction of plasmatocytes and other types of hemocytes. Interpretation of the16S rRNA sequence of the bacterium indicated that it belongs to the Serratia genus of Gram-negative Gammaproteobacteria, which has not previously been implicated as a pathogen of adult honey bees. Complete genome sequence analysis of the bacterium supported its classification as a novel strain of Serratia marcescens, which was designated as S. marcescens strain sicaria (Ss1). When compared with other strains of S. marcescens, Ss1 demonstrated several phenotypic and genetic differences, including 65 genes not previously found in other Serratia genomes. Some of the unique genes we identified in Ss1 were related to those from bacterial insect pathogens and commensals. Recovery of this organism extends a complex pathosphere of agents which may contribute to failure of honey bee colonies. PMID:28002470

Microflora of urogenital tract in pregnancy with asymptomatic bacterium

International Nuclear Information System (INIS)

Abdullaeva, R.A.

2006-01-01

The article contains results of research interrelationship from colonization of vagina and urinary tract diseases. E.coli one of the main factors in development asymptomatic bacterium. Presented high effects of penicillin medicaments and nitrofurans in treatment of asymptomatic bacterium

The Ssr protein (T1E_1405) from Pseudomonas putida DOT-T1E enables oligonucleotide-based recombineering in platform strain P. putida EM42

DEFF Research Database (Denmark)

Aparicio, Tomás; Ingemann Jensen, Sheila; Nielsen, Alex Toftgaard

2016-01-01

Some strains of the soil bacterium Pseudomonas putida have become in recent years platforms of choice for hosting biotransformations of industrial interest. Despite availability of many genetic tools for this microorganism, genomic editing of the cell factory P. putida EM42 (a derivative of refer......Some strains of the soil bacterium Pseudomonas putida have become in recent years platforms of choice for hosting biotransformations of industrial interest. Despite availability of many genetic tools for this microorganism, genomic editing of the cell factory P. putida EM42 (a derivative...

First report of a cross-kingdom pathogenic bacterium, Achromobacter xylosoxidans isolated from stipe-rot Coprinus comatus.

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Ye, Luona; Guo, Mengpei; Ren, Pengfei; Wang, Gangzheng; Bian, Yinbing; Xiao, Yang; Zhou, Yan

2018-03-01

Coprinus comatus is an edible mushroom widely cultivated in China as a delicious food. Various diseases have occurred on C. comatus with the cultivated area increasing. In this study, the pathogenic bacterium JTG-B1, identified as Achromobacter xylosoxidans by 16S rDNA and nrdA gene sequencing, was isolated from edible mushroom Coprinus comatus with serious rot disease on its stipe. A. xylosoxidans has been confirmed as an important opportunistic human pathogenic bacterium and has been isolated from respiratory samples from cystic fibrosis. It is widely distributed in the environment. Here, we first report that fungi can also serve as a host for A. xylosoxidans. We confirmed that it can cross-kingdom infect between animals (mice) and fungi (C. comatus). The results of pathogenicity tests, physiological, biochemical and genotyping analysis of A. xylosoxidans from different hosts suggested that different strain of A. xylosoxidans may have pathogenicity differentiation. A. xylosoxidans not only is pathogenic to C. comatus but also may threaten human health. Copyright © 2017 Elsevier GmbH. All rights reserved.

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

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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.

Low nitrogen stress stimulating the indole-3-acetic acid biosynthesis of Serratia sp. ZM is vital for the survival of the bacterium and its plant growth-promoting characteristic.

Science.gov (United States)

Ouyang, Liming; Pei, Haiyan; Xu, Zhaohui

2017-04-01

Serratia sp. ZM is a plant growth-promoting (PGP) bacterial strain isolated from the rhizospheric soil of Populus euphratica in northwestern China. In this study, low nitrogen supply significantly stimulated the production of indole-3-acetic acid (IAA) in Serratia sp.ZM. The inoculation of the bacterium to wheat seedlings improved plant growth compared with the uninoculated group, and the stimulating effect was more prominent under low nitrogen stress. Inactivation of the predicted key gene in the IAA biosynthesis pathway impaired IAA production and significantly hampered mutant growth in poor medium. Furthermore, the IAA-deficient mutant lost the PGP effect under either normal or low nitrogen conditions in plant experiments. This study revealed the significant impact of environmental nitrogen levels on IAA production in the PGP strain and the vital effect of IAA on resistance physiology of both the bacterium and host plant. The characteristics of Serratia sp. ZM also indicated its application potential as a biofertilizer for plants, especially those suffering from poor nitrogen soil.

[Isolation and characterization of Thermopirellula anaerolimosa gen. nov., sp. nov., an obligate anaerobic hydrogen-producing bacterium of the phylum Planctomycetes].

Science.gov (United States)

Liu, Dongying; Liu, Yi; Men, Xuehui; Guo, Qunqun; Guo, Rongbo; Qiu, Yanling

2012-08-04

To cultivate various yet-to-be cultured heterotrophs from anaerobic granule sludge, we used a selective culture medium with low concentrations of substrates supplemented a variety of antibiotics. An obligate anaerobic, thermophilic, hydrogen-producing bacterium, strain VM20-7(T), was isolated from an upflow anaerobic sludge blanket (UASB) reactor treating high-strength organic wastewater from isomerized sugar production processes. Cells of strain VM20-7(T) are non-motile, spherical, pear or teardrop shaped, occurring singly(o)r as aggregates (0.7 - 2.0 microm x 0.7 - 2.0 microm). Spore formation was not observed. Growth temperature ranges from 35 - 50 degrees C (optimum 45 degrees C), pH ranges from 6.0 - 8.3 (optimum 7.0 - 7.5) , NaCl tolerant concentration ranges from 0% - 0.5% (w/v, optimum 0% ). Nitrate, sulfate, thiosulfate, sulfite, elemental sulfur and Fe (III)-NTA were not used as terminal electron acceptors. Strain VM20-7(T) utilizes a wide range of carbohydrates, including glucose, maltose, ribose, xylose, sucrose, galactose, mannose, raffinose, pectin, yeast extract and xylan. Acetate and H2 are the main end products of glucose fermentation. The G + C content of the genomic DNA was 60.9 mol%. 16S rRNA gene sequence analysis revealed that it is related to the Pirellula-Rhodopirellula-Blastopirellula (PRB) clade within the order Planctomycetales (82.7 - 84.3% similarity with 16S rRNA genes of other known related species). The first obligate anaerobic bacterium within the phylum Planctomycetes was isolated with low concentration of carbohydrates and antibiotics. On the basis of the physiological and phylogenetic data, the name Thermopirellula anaerolimosa gen. nov. , sp. nov. is proposed for strain VM20-7(T) (= CGMCC 1.5169(T) = JCM 17478(T) = DSM 24165(T)).

Hydrogen production by recombinant Escherichia coli strains

Science.gov (United States)

Maeda, Toshinari; Sanchez‐Torres, Viviana; Wood, Thomas K.

2012-01-01

Summary The production of hydrogen via microbial biotechnology is an active field of research. Given its ease of manipulation, the best‐studied bacterium Escherichia coli has become a workhorse for enhanced hydrogen production through metabolic engineering, heterologous gene expression, adaptive evolution, and protein engineering. Herein, the utility of E. coli strains to produce hydrogen, via native hydrogenases or heterologous ones, is reviewed. In addition, potential strategies for increasing hydrogen production are outlined and whole‐cell systems and cell‐free systems are compared. PMID:21895995

Reduction of nitric oxide catalyzed by hydroxylamine oxidoreductase from an anammox bacterium.

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Irisa, Tatsuya; Hira, Daisuke; Furukawa, Kenji; Fujii, Takao

2014-12-01

The hydroxylamine oxidoreductase (HAO) from the anammox bacterium, Candidatus Kuenenia stuttgartiensis has been reported to catalyze the oxidation of hydroxylamine (NH2OH) to nitric oxide (NO) by using bovine cytochrome c as an oxidant. In contrast, we investigated whether the HAO from anammox bacterium strain KSU-1 could catalyze the reduction of NO with reduced benzyl viologen (BVred) and the NO-releasing reagent, NOC 7. The reduction proceeded, resulting in the formation of NH2OH as a product. The oxidation rate of BVred was proportional to the concentration of BVred itself for a short period in each experiment, a situation that was termed quasi-steady state. The analyses of the states at various concentrations of HAO allowed us to determine the rate constant for the catalytic reaction, (2.85 ± 0.19) × 10(5) M(-1) s(-1), governing NO reduction by BVred and HAO, which was comparable to that reported for the HAO from the ammonium oxidizer, Nitrosomonas with reduced methyl viologen. These results suggest that the anammox HAO functions to adjust anammox by inter-conversion of NO and NH2OH depending on the redox potential of the physiological electron transfer protein in anammox bacteria. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Mechanisms of tolerance and high degradation capacity of the herbicide mesotrione by Escherichia coli strain DH5-α.

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Luiz R Olchanheski

Full Text Available The intensive use of agrochemicals has played an important role in increasing agricultural production. One of the impacts of agrochemical use has been changes in population structure of soil microbiota. The aim of this work was to analyze the adaptive strategies that bacteria use to overcome oxidative stress caused by mesotrione, which inhibits 4-hydroxyphenylpyruvate dioxygenase. We also examined antioxidative stress systems, saturation changes of lipid membranes, and the capacity of bacteria to degrade mesotrione. Escherichia coli DH5-á was chosen as a non-environmental strain, which is already a model bacterium for studying metabolism and adaptation. The results showed that this bacterium was able to tolerate high doses of the herbicide (10× field rate, and completely degraded mesotrione after 3 h of exposure, as determined by a High Performance Liquid Chromatography. Growth rates in the presence of mesotrione were lower than in the control, prior to the period of degradation, showing toxic effects of this herbicide on bacterial cells. Changes in the saturation of the membrane lipids reduced the damage caused by reactive oxygen species and possibly hindered the entry of xenobiotics in the cell, while activating glutathione-S-transferase enzyme in the antioxidant system and in the metabolizing process of the herbicide. Considering that E. coli DH5-α is a non-environmental strain and it had no previous contact with mesotrione, the defense system found in this strain could be considered non-specific. This bacterium system response may be a general adaptation mechanism by which bacterial strains resist to damage from the presence of herbicides in agricultural soils.

A novel radio-tolerant astaxanthin-producing bacterium reveals a new astaxanthin derivative: astaxanthin dirhamnoside.

Science.gov (United States)

Asker, Dalal; Awad, Tarek S; Beppu, Teruhiko; Ueda, Kenji

2012-01-01

Astaxanthin is a red ketocarotenoid that exhibits extraordinary health-promoting activities such as antioxidant, anti-inflammatory, antitumor, and immune booster. The recent discovery of the beneficial roles of astaxanthin against many degenerative diseases such as cancers, heart diseases, and exercise-induced fatigue has raised its market demand as a nutraceutical and medicinal ingredient in aquaculture, food, and pharmaceutical industries. To satisfy the growing demand for this high-value nutraceuticals ingredient and consumer interest in natural products, many research efforts are being made to discover novel microbial producers with effective biotechnological production of astaxanthin. Using a rapid screening method based on 16S rRNA gene, and effective HPLC-Diodearray-MS methods for carotenoids analysis, we succeeded to isolate a unique astaxanthin-producing bacterium (strain TDMA-17(T)) that belongs to the family Sphingomonadaceae (Asker et al., Appl Microbiol Biotechnol 77: 383-392, 2007). In this chapter, we provide a detailed description of effective HPLC-Diodearray-MS methods for rapid analysis and identification of the carotenoids produced by strain TDMA-17(T). We also describe the methods of isolation and identification for a novel bacterial carotenoid (astaxanthin derivative), a major carotenoid that is produced by strain TDMA-17(T). Finally, we describe the polyphasic taxonomic analysis of strain TDMA-17(T) and the description of a novel species belonging to genus Sphingomonas.

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

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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.

Plant growth-promoting bacterium Acinetobacter calcoaceticus P23 increases the chlorophyll content of the monocot Lemna minor (duckweed) and the dicot Lactuca sativa (lettuce).

Science.gov (United States)

Suzuki, Wakako; Sugawara, Masayuki; Miwa, Kyoko; Morikawa, Masaaki

2014-07-01

Acinetobacter calcoaceticus P23 is a plant growth-promoting bacterium that was isolated from the surface of duckweed (Lemna aoukikusa). The bacterium was observed to colonize on the plant surfaces and increase the chlorophyll content of not only the monocotyledon Lemna minor but also the dicotyledon Lactuca sativa in a hydroponic culture. This effect on the Lactuca sativa was significant in nutrient-poor (×1/100 dilution of H2 medium) and not nutrient-rich (×1 or ×1/10 dilutions of H2 medium) conditions. Strain P23 has the potential to play a part in the future development of fertilizers and energy-saving hydroponic agricultural technologies. Copyright © 2013 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

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.

Draft Genome Sequence of Sphingopyxis sp. Strain MWB1, a Crude-Oil-Degrading Marine Bacterium

Science.gov (United States)

Kim, Jonghyun; Kim, Soo Jung; Kim, Seon Hee; Kim, Seung Il; Moon, Yoon-Jung; Park, Sung-Joon

2014-01-01

Sphingopyxis sp. strain MWB1, which is capable of degrading crude oil, diesel, and kerosene, was isolated from crude oil–contaminated seashore in Tae-an, South Korea. Here, we report the draft genome sequence of this strain, which comprises 3,118,428 bp with a G+C content of 62.85 mol%. PMID:25477411

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

Science.gov (United States)

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

2011-04-01

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

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

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Vitaly V Kadnikov

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

Helicobacter Catalase Devoid of Catalytic Activity Protects the Bacterium against Oxidative Stress*♦

Science.gov (United States)

Benoit, Stéphane L.; Maier, Robert J.

2016-01-01

Catalase, a conserved and abundant enzyme found in all domains of life, dissipates the oxidant hydrogen peroxide (H2O2). The gastric pathogen Helicobacter pylori undergoes host-mediated oxidant stress exposure, and its catalase contains oxidizable methionine (Met) residues. We hypothesized catalase may play a large stress-combating role independent of its classical catalytic one, namely quenching harmful oxidants through its recyclable Met residues, resulting in oxidant protection to the bacterium. Two Helicobacter mutant strains (katAH56A and katAY339A) containing catalase without enzyme activity but that retain all Met residues were created. These strains were much more resistant to oxidants than a catalase-deletion mutant strain. The quenching ability of the altered versions was shown, whereby oxidant-stressed (HOCl-exposed) Helicobacter retained viability even upon extracellular addition of the inactive versions of catalase, in contrast to cells receiving HOCl alone. The importance of the methionine-mediated quenching to the pathogen residing in the oxidant-rich gastric mucus was studied. In contrast to a catalase-null strain, both site-change mutants proficiently colonized the murine gastric mucosa, suggesting that the amino acid composition-dependent oxidant-quenching role of catalase is more important than the well described H2O2-dissipating catalytic role. Over 100 years after the discovery of catalase, these findings reveal a new non-enzymatic protective mechanism of action for the ubiquitous enzyme. PMID:27605666

Survival of diverse bacillus thuringiensis strains in gypsy moth (Lepidotera: Lymantriidae) is correlated with urease production

Science.gov (United States)

Bacillus thuringiensis is an entomopathogenic bacterium that can kill a variety of pest insects, but seldom causes epizootics because it replicates poorly in insects. By attempting to repeatedly pass lepidopteran-active B. thuringiensis strains through gypsy moth larvae, we found that only those str...

Rhodoluna lacicola gen. nov., sp. nov., a planktonic freshwater bacterium with stream-lined genome.

Science.gov (United States)

Hahn, Martin W; Schmidt, Johanna; Taipale, Sami J; Doolittle, W Ford; Koll, Ulrike

2014-09-01

A pure culture of an actinobacterium previously described as 'Candidatus Rhodoluna lacicola' strain MWH-Ta8 was established and deposited in two public culture collections. Strain MWH-Ta8(T) represents a free-living planktonic freshwater bacterium obtained from hypertrophic Meiliang Bay, Lake Taihu, PR China. The strain was characterized by phylogenetic and taxonomic investigations, as well as by determination of its complete genome sequence. Strain MWH-Ta8(T) is noticeable due to its unusually low values of cell size (0.05 µm(3)), genome size (1.43 Mbp), and DNA G+C content (51.5 mol%). Phylogenetic analyses based on 16S rRNA gene and RpoB sequences suggested that strain MWH-Ta8(T) is affiliated with the family Microbacteriaceae with Pontimonas salivibrio being its closest relative among the currently described species within this family. Strain MWH-Ta8(T) and the type strain of Pontimonas salivibrio shared a 16S rRNA gene sequence similarity of 94.3 %. The cell-wall peptidoglycan of strain MWH-Ta8(T) was of type B2β (B10), containing 2,4-diaminobutyric acid as the diamino acid. The predominant cellular fatty acids were anteiso-C15 : 0 (36.5 %), iso-C16 : 0 (16.5 %), iso-C15 : 0 (15.6 %) and iso-C14 : 0 (8.9 %), and the major (>10 %) menaquinones were MK-11 and MK-12. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The combined phylogenetic, phenotypic and chemotaxonomic data clearly suggest that strain MWH-Ta8(T) represents a novel species of a new genus in the family Microbacteriaceae, for which the name Rhodoluna lacicola gen. nov., sp. nov. is proposed. The type strain of the type species is MWH-Ta8(T) ( = DSM 23834(T) = LMG 26932(T)). © 2014 IUMS.

Salt-inducible promoter derivable from a lactic acid bacterium, and its use in a lactic acid bacterium for production of a desired protein

NARCIS (Netherlands)

Sanders, Jan Willem; Kok, Jan; Venema, Gerard; Ledeboer, Adrianus Marinus

1998-01-01

The invention provides a salt-inducible promoter present in SEQ ID NO: 10 and derivable from a lactic acid bacterium in isolation from the coding sequence normally controlled by said promoter in a wild-type lactic acid bacterium, with modifications and important parts thereof. Also provided are a

Characterization of the arsenite oxidizer Aliihoeflea sp. strain 2WW and its potential application in the removal of arsenic from groundwater in combination with Pf-ferritin

NARCIS (Netherlands)

Corsini, A.; Colombo, M.; Muyzer, G.; Cavalca, L.

2015-01-01

A heterotrophic arsenite-oxidizing bacterium, strain 2WW, was isolated from a biofilter treating arsenic-rich groundwater. Comparative analysis of 16S rRNA gene sequences showed that it was closely related (98.7 %) to the alphaproteobacterium Aliihoeflea aesturari strain N8T. However, it was

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.

Screening of Mutation High-Yielding Biocontrol Bacterium BJ1 by Ion Beam Irradiation and Effect of Controlling Fusarium oxysporum cucunerinum Disease

International Nuclear Information System (INIS)

Ma Shuang; Dong Xicun; Li Wenjian; Wang Jufang; Yu Lixia; Liu Jing

2010-01-01

BJ1 of Bacillus subtilis is an important biocontrol factor in control of fungus disease. In order to improve the antagonistic ability of the strain,and obtain high-efficiency strains, 12 C 6+ of different doses and linear energy transfer (LET) was used to irradiate the biocontrol bacterium BJ1. The optimum dose and LET of ion beam irradiation for the BJ1 are 200-400 Gy and 60 keV/μm,respectively. The antagonistic ability is increased by 2%-21%. The control effect of mutation to Fusarium oxysporum f. sp. cucunerinum is increased by 17.48% over that of BJ1, and mutation also has better plant growth-promoting effect. (authors)

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 ).

Metabolic Engineering of the Actinomycete Amycolatopsis sp. Strain ATCC 39116 towards Enhanced Production of Natural Vanillin

OpenAIRE

Fleige, Christian; Meyer, Florian; Steinbüchel, Alexander

2016-01-01

The Gram-positive bacterium Amycolatopsis sp. ATCC 39116 is used for the fermentative production of natural vanillin from ferulic acid on an industrial scale. The strain is known for its outstanding tolerance to this toxic product. In order to improve the productivity of the fermentation process, the strain's metabolism was engineered for higher final concentrations and molar yields. Degradation of vanillin could be decreased by more than 90% through deletion of the vdh gene, which codes for ...

Natranaerobaculum magadiense gen. nov., sp. nov., an anaerobic, alkalithermophilic bacterium from soda lake sediment.

Science.gov (United States)

Zavarzina, Daria G; Zhilina, Tatyana N; Kuznetsov, Boris B; Kolganova, Tatyana V; Osipov, Georgy A; Kotelev, Mikhail S; Zavarzin, Georgy A

2013-12-01

An obligately alkaliphilic, anaerobic, thermo- and halotolerant, spore-forming bacterium was isolated from sediments of soda lake Magadi (Kenya) and designated strain Z-1001(T). Cells of strain Z-1001(T) were straight, Gram-positive rods, slowly motile. Strain Z-1001(T) was found to be an obligate anaerobe. It grew within a pH range from 7.5 to 10.7 with an optimum at 9.25-9.5 (at 40 °C), a temperature range from 20 to 57 °C with an optimum at 45-50 °C, and a NaCl concentration range from 0 to 1.55 M with an optimum at 1.2-1.4 M. Peptides, such as meat and yeast extracts, peptone and tryptone, were fermented by Z-1001(T). Carbohydrates did not support growth. With yeast extract as an electron donor, strain Z-1001(T) reduced S(2)O(3)(2-), NO(-)(3), AsO(3-)(4), Fe(III) citrate and anthraquinone-2,6-disulfonate (AQDS) as electron acceptors. The isolate was able to grow oligotrophically with a very small amount of yeast extract: 0.03 g l(-1). The main fatty acids were C16 : 0, C16 : 1ω7c, C18 : 0 and C18 : 1ω9. The DNA G+C content of the isolate was 35.6 mol%. 16S rRNA gene sequence analysis showed that strain Z-1001(T) is a member of family Natranaerobiaceae, clustering with the type strain of Natranaerobius thermophilus (95.8-96.0 % sequence similarity). On the basis of physiological and phylogenetic data it is proposed that strain Z-1001(T) ( = DSM 24923(T) = VKM B-2666(T)) represents a novel genus and species, Natranaerobaculum magadiense gen. nov., sp. nov.

Characterization of a halophilic heterotrophic nitrification-aerobic denitrification bacterium and its application on treatment of saline wastewater.

Science.gov (United States)

Duan, Jinming; Fang, Hongda; Su, Bing; Chen, Jinfang; Lin, Jinmei

2015-03-01

A novel halophilic bacterium capable of heterotrophic nitrification-aerobic denitrification was isolated from marine sediments and identified as Vibrio diabolicus SF16. It had ability to remove 91.82% of NH4(+)-N (119.77 mg/L) and 99.71% of NO3(-)-N (136.43 mg/L). The nitrogen balance showed that 35.83% of initial NH4(+)-N (119.77 mg/L) was changed to intracellular nitrogen, and 53.98% of the initial NH4(+)-N was converted to gaseous denitrification products. The existence of napA gene further proved the aerobic denitrification ability of strain SF16. The optimum culture conditions were salinity 1-5%, sodium acetate as carbon source, C/N 10, and pH 7.5-9.5. When an aerated biological filter system inoculated with strain SF16 was employed to treat saline wastewater, the average removal efficiency of NH4(+)-N and TN reached 97.14% and 73.92%, respectively, indicating great potential of strain SF16 for future full-scale applications. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

Characterization and Potential Applications of a Selenium Nanoparticle Producing and Nitrate Reducing Bacterium Bacillus oryziterrae sp. nov.

Science.gov (United States)

Bao, Peng; Xiao, Ke-Qing; Wang, Hui-Jiao; Xu, Hao; Xu, Peng-Peng; Jia, Yan; Häggblom, Max M.; Zhu, Yong-Guan

2016-09-01

A novel nitrate- and selenite reducing bacterium strain ZYKT was isolated from a rice paddy soil in Dehong, Yunnan, China. Strain ZYKT is a facultative anaerobe and grows in up to 150, 000 ppm O2. The comparative genomics analysis of strain ZYKT implies that it shares more orthologues with B. subtilis subsp. subtilis NCIB 3610T (ANIm values, 85.4-86.7%) than with B. azotoformans NBRC 15712T (ANIm values, 84.4-84.7%), although B. azotoformans NBRC 15712T (96.3% 16S rRNA gene sequence similarity) is the closest Bacillus species according to 16S rRNA gene comparison. The major cellular fatty acids of strain ZYKT were iso-C14:0 (17.8%), iso-C15:0 (17.8%), and C16:0 (32.0%). The polar lipid profile consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unidentified aminophospholipid. Based on physiological, biochemical and genotypic properties, the strain was considered to represent a novel species of the genus Bacillus, for which the name Bacillus oryziterrae sp. nov. is proposed. The type strain is ZYKT (=DSM 26460T =CGMCC 1.5179T). Strain ZYKT can reduce nitrate to nitrite and ammonium and possesses metabolic genes for nitrate reduction including nar, nap and nrf. Biogenic selenium nanoparticles of strain ZYKT show a narrow size distribution and agree with the gaussian distribution. These selenium nanoparticles show significant dose-dependent inhibition of the lung cancer cell line H157, which suggests potential for application in cancer therapy.

Draft Genome Sequence of the Biocontrol Strain Serratia plymuthica A30, Isolated from Rotting Potato Tuber Tissue

NARCIS (Netherlands)

Czajkowski, R.L.; Wolf, van der J.M.

2012-01-01

Serratia plymuthica A30 is a Gram-negative bacterium expressing antagonistic activity toward blackleg- and soft rot-causing Dickeya sp. biovar 3 (“Dickeya solani”). Here, we present the draft genome sequence of strain A30, which has been isolated from rotten potato tuber tissue

Methylobacterium populi sp. nov., a novel aerobic, pink-pigmented, facultatively methylotrophic, methane-utilizing bacterium isolated from poplar trees (Populus deltoides x nigra DN34).

Science.gov (United States)

Van Aken, Benoit; Peres, Caroline M; Doty, Sharon Lafferty; Yoon, Jong Moon; Schnoor, Jerald L

2004-07-01

A pink-pigmented, aerobic, facultatively methylotrophic bacterium, strain BJ001T, was isolated from internal poplar tissues (Populus deltoidesxnigra DN34) and identified as a member of the genus Methylobacterium. Phylogenetic analyses showed that strain BJ001T is related to Methylobacterium thiocyanatum, Methylobacterium extorquens, Methylobacterium zatmanii and Methylobacterium rhodesianum. However, strain BJ001T differed from these species in its carbon-source utilization pattern, particularly its use of methane as the sole source of carbon and energy, an ability that is shared with only one other member of the genus, Methylobacterium organophilum. In addition, strain BJ001T is the only member of the genus Methylobacterium to be described as an endophyte of poplar trees. On the basis of its physiological, genotypic and ecological properties, the isolate is proposed as a member of a novel species of the genus Methylobacterium, Methylobacterium populi sp. nov. (type strain, BJ001T=ATCC BAA-705T=NCIMB 13946T).

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

Science.gov (United States)

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

2014-05-01

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

Differential gene expression in Xylella fastidiosa 9a5c during co-cultivation with the endophytic bacterium Methylobacterium mesophilicum SR1.6/6.

Science.gov (United States)

Dourado, Manuella Nóbrega; Santos, Daiene Souza; Nunes, Luiz Roberto; Costa de Oliveira, Regina Lúcia Batista da; de Oliveira, Marcus Vinicius; Araújo, Welington Luiz

2015-12-01

Xylella fastidiosa, the causal agent of citrus variegated chlorosis (CVC), colonizes plant xylem, reducing sap flow, and inducing internerval chlorosis, leaf size reduction, necrosis, and harder and smaller fruits. This bacterium may be transmitted from plant to plant by sharpshooter insects, including Bucephalogonia xanthopis. The citrus endophytic bacterium Methylobacterium mesophilicum SR1.6/6 colonizes citrus xylem and previous studies showed that this strain is also transferred from plant to plant by B. xanthopis (Insecta), suggesting that this endophytic bacterium may interact with X. fastidiosa in planta and inside the insect vector during co-transmission by the same insect vector. To better understand the X. fastidiosa behavior in the presence of M. mesophilicum, we evaluated the X. fastidiosa transcriptional profile during in vitro interaction with M. mesophilicum SR1.6/6. The results showed that during co-cultivation, X. fastidiosa down-regulated genes related to growth and up-regulated genes related to energy production, stress, transport, and motility, suggesting the existence of a specific adaptive response to the presence of M. mesophilicum in the culture medium. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Noncontiguous finished genome sequence and description of Paenibacillus ihumii sp. nov. strain AT5

Directory of Open Access Journals (Sweden)

A.H. Togo

2016-03-01

Full Text Available Paenibacillus ihumii sp. nov. strain AT5 (= CSUR 1981 = DSM 100664 is the type strain of P. ihumii. This bacterium was isolated from a stool sample from a morbidly obese French patient using the culturomics approach. The genome of this Gram-negative, facultative anaerobic, motile and spore-forming bacillus is 5 924 686 bp long. Genomic analysis identified 253 (5% of 3812 genes as ORFans and at least 2599 (50.03% of 5194 orthologous proteins not shared with the closest phylogenetic species.

Primary Isolation Strain Determines Both Phage Type and Receptors Recognised by Campylobacter jejuni Bacteriophages

DEFF Research Database (Denmark)

Sørensen, Martine C. Holst; Gencay, Yilmaz Emre; Birk, Tina

2015-01-01

were identified based on host range analysis and genome restriction profiles. Most phages were isolated using C. jejuni strains NCTC12662 and RM1221 and interestingly phage genome size (140 kb vs. 190 kb), host range and morphological appearance correlated with the isolation strain. Thus, according......In this study we isolated novel bacteriophages, infecting the zoonotic bacterium Campylobacter jejuni. These phages may be used in phage therapy of C. jejuni colonized poultry to prevent spreading of the bacteria to meat products causing disease in humans. Many C. jejuni phages have been isolated...... therefore chose seven C. jejuni strains each expressing different CPS structures as indicator strains in a large screening for phages in samples collected from free-range poultry farms. Forty-three phages were isolated using C. jejuni NCTC12658, NCTC12662 and RM1221 as host strains and 20 distinct phages...

Caldanaerobacter uzonensis sp. nov., an anaerobic, thermophilic, heterotrophic bacterium isolated from a hot spring.

Science.gov (United States)

Kozina, Irina V; Kublanov, Ilya V; Kolganova, Tatyana V; Chernyh, Nikolai A; Bonch-Osmolovskaya, Elizaveta A

2010-06-01

An anaerobic thermophilic bacterium, strain K67(T), was isolated from a terrestrial hot spring of Uzon Caldera, Kamchatka Peninsula. Analysis of the 16S rRNA gene sequence revealed that the novel isolate belongs to the genus Caldanaerobacter, with 95 % 16S rRNA gene sequence similarity to Caldanaerobacter subterraneus subsp. subterraneus SEBR 7858(T), suggesting that it represents a novel species of the genus Caldanaerobacter. Strain K67(T) was characterized as an obligate anaerobe, a thermophile (growth at 50-75 degrees capital ES, Cyrillic; optimum 68-70 degrees C), a neutrophile (growth at pH(25 degrees C) 4.8-8.0; optimum pH(25 degrees C) 6.8) and an obligate organotroph (growth by fermentation of various sugars, peptides and polysaccharides). Major fermentation products were acetate, H2 and CO2; ethanol, lactate and l-alanine were formed in smaller amounts. Thiosulfate stimulated growth and was reduced to hydrogen sulfide. Nitrate, sulfate, sulfite and elemental sulfur were not reduced and did not stimulate growth. Thus, according to the strain's phylogenetic position and phenotypic novelties (lower upper limit of temperature range for growth, the ability to grow on arabinose, the inability to reduce elemental sulfur and the formation of alanine as a minor fermentation product), the novel species Caldanaerobacter uzonensis sp. nov. is proposed, with the type strain K67(T) (=DSM 18923(T) =VKM capital VE, Cyrillic-2408(T)).

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

Science.gov (United States)

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

2012-01-01

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

Draft Genome Sequence of the Biocontrol Strain Serratia plymuthica A30, Isolated from Rotting Potato Tuber Tissue

NARCIS (Netherlands)

Czajkowski, R.L.; Van der Wolf, J.M.

2012-01-01

Serratia plymuthica A30 is a Gram-negative bacterium expressing antagonistic activity toward blackleg- and soft rot-causing Dickeya sp. biovar 3 ("Dickeya solani"). Here, we present the draft genome sequence of strain A30, which has been isolated from rotten potato tuber tissue. [KEYWORDS: biovar 3

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

Science.gov (United States)

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

2015-07-01

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

Genome Sequence of Anoxybacillus geothermalis Strain GSsed3, a Novel Thermophilic Endospore-Forming Species

Science.gov (United States)

Filippidou, Sevasti; Jaussi, Marion; Junier, Thomas; Wunderlin, Tina; Roussel-Delif, Ludovic; Jeanneret, Nicole; Vieth-Hillebrand, Andrea; Vetter, Alexandra; Regenspurg, Simona; McMurry, Kim; Gleasner, Cheryl D.; Lo, Chien-Chi; Li, Paul; Vuyisich, Momchilo; Chain, Patrick S.

2015-01-01

Anoxybacillus geothermalis strain GSsed3 is an endospore-forming thermophilic bacterium isolated from filter deposits in a geothermal site. This novel species has a larger genome size (7.2 Mb) than that of any other Anoxybacillus species, and it possesses genes that support its phenotypic metabolic characterization and suggest an intriguing link to metals. PMID:26067952

Degradation of pyrene in soil and in vitro by a Bacillus lentus strain ...

African Journals Online (AJOL)

A bacterium isolated from an asphalt plant soil and identified as a strain of Bacillus lentus was tested in vitro and in sterilized and native soils for ability to survive and sustain pyrene degradation over a period of 63 days. The exponential growth rate in vitro was 0.049 d-1 and the doubling time 2.65 d. In the control flask ...

Curiously modern DNA for a "250 million-year-old" bacterium.

Science.gov (United States)

Nickle, David C; Learn, Gerald H; Rain, Matthew W; Mullins, James I; Mittler, John E

2002-01-01

Studies of ancient DNA have attracted considerable attention in scientific journals and the popular press. Several of the more extreme claims for ancient DNA have been questioned on biochemical grounds (i.e., DNA surviving longer than expected) and evolutionary grounds (i.e., nucleotide substitution patterns not matching theoretical expectations for ancient DNA). A recent letter to Nature from Vreeland et al. (2000), however, tops all others with respect to age and condition of the specimen. These researchers extracted and cultured a bacterium from an inclusion body from what they claim is a 250 million-year (Myr)-old salt crystal. If substantiated, this observation could fundamentally alter views about bacterial physiology, ecology and evolution. Here we report on molecular evolutionary analyses of the 16S rDNA from this specimen. We find that 2-9-3 differs from a modern halophile, Salibacillus marismortui, by just 3 unambiguous bp in 16S rDNA, versus the approximately 59 bp that would be expected if these bacteria evolved at the same rate as other bacteria. We show, using a Poisson distribution, that unless it can be shown that S. marismortui evolves 5 to 10 times more slowly than other bacteria for which 16S rDNA substitution rates have been established, Vreeland et al.'s claim would be rejected at the 0.05 level. Also, a molecular clock test and a relative rates test fail to substantiate Vreeland et al.'s claim that strain 2-9-3 is a 250-Myr-old bacterium. The report of Vreeland et al. thus falls into a long series of suspect ancient DNA studies.

Lethal Effect on Bacterium of Decay of Incorporated Radioactive Atoms (3H, 14C, 32P)

International Nuclear Information System (INIS)

Apelgot, Sonia

1968-01-01

The biological effect of decay of 3 H, 14 C and 32 P incorporated into a bacterium depends on the nature of the organic molecule labelled, on the position of the isotope within it and on the isotope itself. In sum, results obtained to date show that: The decay of 3 H atoms incorporated into certain macromolecules of a bacterium causes sterilization through ionization by the ß - particle emitted; transmutation is of negligible importance. This self-irradiation is comparable in effect with X-rays and is affected in a similar manner by the same factors: temperature, presence of a radioprotector, radiosensitivity of the strain. Decay of 14 C or 32 P atoms incorporated into bacterial DNA is lethal because of the transmutation effect; ionizations produced by emitted ß - particles may be disregarded. Survival curves for 32 P transmutations depend on the experimental conditions. Some of the results obtained with 32 P are similar to those obtained with X-rays, e.g. effects of temperature, radical capture and oxygen, while others are similar to those of u.v. light, e.g., effect of growth conditions. Comparative tests made with 32 P indicate that the recoil energy of transmutation is not the phenomenon responsible for the lethal effect observed. Comparison of the results obtained after X-irradiation or decay of 3 H or 32 P incorporated into the DNA of bacteria of the same strain of E. coli shows that the efficiency of a 32 P transmutation is about four times greater than that of an ionization produced at random within the same DNA. (author) [fr

ISOLATION AND CHARACTERIZATION OF A MOLYBDENUM-REDUCING AND AZO-DYE DECOLORIZING SERRATIA MARCESCENS STRAIN NENI-1 FROM INDONESIAN SOIL

Directory of Open Access Journals (Sweden)

Neni Gusmanizar

2016-01-01

Full Text Available Heavy metals and organic xenobiotics including dyes are important industrial components with their usage amounting to the millions of tonnes yearly. Their presence in the environment is a serious pollution issue globally. Bioremediation of these pollutants using microbes with multiple detoxification capacity is constantly being sought. In this work we screen the ability of a molybdenum-reducing bacterium isolated from contaminated soil to decolorize various azo and triphenyl methane dyes. The bacterium reduces molybdate to molybdenum blue (Mo-blue optimally at pH 6.0, and temperatures of between 25 and 40oC. Glucose was the best electron donor for supporting molybdate reduction followed by sucrose, trehalose, maltose, d-sorbitol, dmannitol, d-mannose, myo-inositol, glycerol and salicin in descending order. Other requirements include a phosphate concentration of between 5.0 and 7.5 mM and a molybdate concentration between 10 and 20 mM. The absorption spectrum of the Moblue produced was similar to previous Mo-reducing bacterium, and closely resembles a reduced phosphomolybdate. Molybdenum reduction was inhibited by copper, silver and mercury at 2 ppm by 43.8%, 42.3% and 41.7%, respectively. We screen for the ability of the bacterium to decolorize various dyes. The bacterium was able to decolorize the dye Congo Red. Biochemical analysis resulted in a tentative identification of the bacterium as Serratia marcescens strain Neni-1. The ability of this bacterium to detoxify molybdenum and decolorize azo dye makes this bacterium an important tool for bioremediation.

Isolation and characterization of Ethanologenbacterium HitB49 gen. nov. sp. nov., an anaerobic, high hydrogen-producing bacterium with a special ethanol-type-fermentation

Energy Technology Data Exchange (ETDEWEB)

Lin, M. [Harbin Inst. of Technology, Harbin, HL (China). School of Municipal and Environmental Engineering]|[Nanyang Technological Univ., Singapore (Singapore). Inst. of Environmental Science and Engineering; Ren, N.Q.; Wang, A.J. [Harbin Inst. of Technology, Harbin, HL (China). School of Municipal and Environmental Engineering; Liang, D.T.; Tay, J.H. [Nanyang Technological Univ., Singapore (Singapore). Inst. of Environmental Science and Engineering

2004-07-01

Hydrogen, an important future energy source, can be produced by several fermentative microorganisms. The factor that prevents widespread biohydrogen production is the difficulty in isolating the ideal high hydrogen-producing bacterium (HPB). In this study, the Hungate technology was used to isolate and cultivate 210 strains of dominant fermentative bacteria. They were isolated from 6 sludges with ethanol-type fermentation (ETF) bioreactors. The study examined the production of hydrogen in pH 4, very low pH in ETF. The maximum rate in the biohydrogen-producing reactor was promising under continuous flow condition. The novel genus of HPB was Ethanologenbacterium Hit, of which strain B49 belonged to the ETF bacteria.

Atomic force microscopy study of the structure function relationships of the biofilm-forming bacterium Streptococcus mutans

Science.gov (United States)

Cross, Sarah E.; Kreth, Jens; Zhu, Lin; Qi, Fengxia; Pelling, Andrew E.; Shi, Wenyuan; Gimzewski, James K.

2006-02-01

Atomic force microscopy (AFM) has garnered much interest in recent years for its ability to probe the structure, function and cellular nanomechanics inherent to specific biological cells. In particular, we have used AFM to probe the important structure-function relationships of the bacterium Streptococcus mutans. S. mutans is the primary aetiological agent in human dental caries (tooth decay), and is of medical importance due to the virulence properties of these cells in biofilm initiation and formation, leading to increased tolerance to antibiotics. We have used AFM to characterize the unique surface structures of distinct mutants of S. mutans. These mutations are located in specific genes that encode surface proteins, thus using AFM we have resolved characteristic surface features for mutant strains compared to the wild type. Ultimately, our characterization of surface morphology has shown distinct differences in the local properties displayed by various S. mutans strains on the nanoscale, which is imperative for understanding the collective properties of these cells in biofilm formation.

Anoxybacillus vitaminiphilus sp. nov., a strictly aerobic and moderately thermophilic bacterium isolated from a hot spring.

Science.gov (United States)

Zhang, Xin-Qi; Zhang, Zhen-Li; Wu, Nan; Zhu, Xu-Fen; Wu, Min

2013-11-01

A strictly aerobic, Gram-stain-positive, motile and spore-forming bacterium, strain 3nP4(T), was isolated from the Puge hot spring located in the south-western geothermal area of China. Strain 3nP4(T) grew at 38-66 °C (optimum 57-60 °C), at pH 6.0-9.3 (optimum 7.0-7.5) and with 0-4 % (w/v) NaCl (optimum 0-0.5 %). Phylogenetic analysis of 16S rRNA gene sequences, as well as DNA-DNA relatedness values, indicated that the isolate represents a novel species of the genus Anoxybacillus, related most closely to Anoxybacillus voinovskiensis DSM 12111(T). Strain 3nP4(T) had diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and one unidentified phospholipid as major polar lipids and iso-C15 : 0 and iso-C17 : 0 as major fatty acids, which are both typical chemotaxonomic characteristics of the genus Anoxybacillus. The mean DNA G+C content of strain 3nP4(T) was 39.2±0.95 mol% (HPLC). A distinctive characteristic of the novel isolate was its extreme reliance on vitamin mixture or yeast extract for growth. Based on data from this taxonomic study using a polyphasic approach, strain 3nP4(T) is considered to represent a novel species of the genus Anoxybacillus, for which the name Anoxybacillus vitaminiphilus sp. nov. is proposed. The type strain is 3nP4(T) ( = CGMCC 1.8979(T) = JCM 16594(T)).

Lactic acid production from xylose by Geobacillus stearothermophilus strain 15

Science.gov (United States)

Kunasundari, B.; Naresh, S.; Chu, J. E.

2017-09-01

Lactic acid is an important compound with a wide range of industrial applications. The present study tested the efficiency of xylose, as a sole carbon source to be converted to lactic acid by Geobacillus stearothermophilus strain 15. To the best of our knowledge, limited information is available on the directed fermentation of xylose to lactic acid by this bacterium. The effects of different parameters such as temperature, pH, incubation time, agitation speed, concentrations of nitrogen and carbon sources on the lactic acid production were investigated statistically. It was found that the bacterium exhibited poor assimilation of xylose to lactic acid. Temperature, agitation rate and incubation time were determined to improve the lactic acid production slightly. The highest lactic acid yield obtained was 8.9% at 45°C, 300 RPM, 96 h, pH of 6.0 with carbon and nitrogen source concentrations were fixed at 5% w/v.

Brockia lithotrophica gen. nov., sp. nov., an anaerobic thermophilic bacterium from a terrestrial hot spring.

Science.gov (United States)

Perevalova, Anna A; Kublanov, Ilya V; Baslerov, R V; Zhang, Gengxin; Bonch-Osmolovskaya, Elizaveta A

2013-02-01

A novel thermophilic bacterium, strain Kam1851(T), was isolated from a terrestrial hot spring of the Uzon Caldera, Kamchatka Peninsula, Russia. Cells of strain Kam1851(T) were spore-forming rods with a gram-positive type of cell wall. Growth was observed between 46 and 78 °C, and pH 5.5-8.5. The optimal growth (doubling time, 6.0 h) was at 60-65 °C and pH 6.5. The isolate was an obligate anaerobe growing in pre-reduced medium only. It grew on mineral medium with molecular hydrogen or formate as electron donors, and elemental sulfur, thiosulfate or polysulfide as electron acceptors. The main cellular fatty acids were C(16 : 0) (34.2 %), iso-C(16 : 0) (18 %), C(18 : 0) (12.8 %) and iso-C(17 : 0) (11.1 %). The G+C content of the genomic DNA of strain Kam1851(T) was 63 mol%. 16S rRNA gene sequence analysis showed that strain Kam1851(T) belonged to the order Thermoanaerobacterales, but it was not closely related to representatives of any genera with validly published names. The most closely related strains, which had no more than 89.2 % sequence similarity, were members of the genera Ammonifex and Caldanaerobacter. On the basis of its phylogenetic position and novel phenotypic features, isolate Kam1851(T) is proposed to represent a novel species in a new genus, Brockia lithotrophica gen. nov., sp. nov.; the type strain of Brockia lithotrophica is Kam1851(T) ( = DSM 22653(T) = VKM B-2685(T)).

Metabolic engineering of a diazotrophic bacterium improves ammonium release and biofertilization of plants and microalgae.

Science.gov (United States)

Ambrosio, Rafael; Ortiz-Marquez, Juan Cesar Federico; Curatti, Leonardo

2017-03-01

The biological nitrogen fixation carried out by some Bacteria and Archaea is one of the most attractive alternatives to synthetic nitrogen fertilizers. However, with the exception of the symbiotic rhizobia-legumes system, progress towards a more extensive realization of this goal has been slow. In this study we manipulated the endogenous regulation of both nitrogen fixation and assimilation in the aerobic bacterium Azotobacter vinelandii. Substituting an exogenously inducible promoter for the native promoter of glutamine synthetase produced conditional lethal mutant strains unable to grow diazotrophically in the absence of the inducer. This mutant phenotype could be reverted in a double mutant strain bearing a deletion in the nifL gene that resulted in constitutive expression of nif genes and increased production of ammonium. Under GS non-inducing conditions both the single and the double mutant strains consistently released very high levels of ammonium (>20mM) into the growth medium. The double mutant strain grew and excreted high levels of ammonium under a wider range of concentrations of the inducer than the single mutant strain. Induced mutant cells could be loaded with glutamine synthetase at different levels, which resulted in different patterns of extracellular ammonium accumulation afterwards. Inoculation of the engineered bacteria into a microalgal culture in the absence of sources of C and N other than N 2 and CO 2 from the air, resulted in a strong proliferation of microalgae that was suppressed upon addition of the inducer. Both single and double mutant strains also promoted growth of cucumber plants in the absence of added N-fertilizer, while this property was only marginal in the parental strain. This study provides a simple synthetic genetic circuit that might inspire engineering of optimized inoculants that efficiently channel N 2 from the air into crops. Copyright © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All

Production and characterization of bioemulsifier from a marine bacterium, Acinetobacter calcoaceticus subsp. anitratus SM7

Directory of Open Access Journals (Sweden)

Kulnaree Phetrong

2008-05-01

Full Text Available Marine bacterium strain SM7 was isolated as a bioemulsifier-producing bacterium from oil-spilled seawater in Songkhla lagoon, Thailand. It was identified as Acinetobacter calcoaceticus subsp. anitratus based on morphology, biochemicalcharacteristics and 16S rRNA sequence. A. calcoaceticus subsp. anitratus SM7 produced an extracellular emulsifying agent when grown in a minimal salt medium (pH 7.0 containing 0.3% (v/v n-heptadecane and 0.1% (w/v ammoniumhydrogen carbonate as carbon source and nitrogen source, respectively, at 30oC with agitation rate of 200 rpm. Crude bioemulsifier was recovered from the culture supernatant by ethanol precipitation with a yield of 2.94 g/l and had a criticalemulsifier concentration of 0.04 g/ml. The crude bioemulsifier was capable of emulsifying n-hexadecane in a broad pH range (6-12, temperatures (30-121oC and in the presence of NaCl up to 12% (w/v. The bioemulsifier was stable in saltsolution ranging from 0 to 0.1% (w/v of MgCl2 and CaCl2. The broad range of pH stability, thermostability and salt tolerance suggested that the bioemulsifier from A. calcoaceticus subsp. anitratus SM7 could be useful in environmentalapplication, especially bioremediation of oil-polluted seawater.

Prior Inoculation with Type B Strains of Francisella tularensis Provides Partial Protection against Virulent Type A Strains in Cottontail Rabbits.

Directory of Open Access Journals (Sweden)

Vienna R Brown

Full Text Available Francisella tularensis is a highly virulent bacterium that is capable of causing severe disease (tularemia in a wide range of species. This organism is characterized into two distinct subspecies: tularensis (type A and holarctica (type B which vary in several crucial ways, with some type A strains having been found to be considerably more virulent in humans and laboratory animals. Cottontail rabbits have been widely implicated as a reservoir species for this subspecies; however, experimental inoculation in our laboratory revealed type A organisms to be highly virulent, resulting in 100% mortality following challenge with 50-100 organisms. Inoculation of cottontail rabbits with the same number of organisms from type B strains of bacteria was found to be rarely lethal and to result in a robust humoral immune response. The objective of this study was to characterize the protection afforded by a prior challenge with type B strains against a later inoculation with a type A strain in North American cottontail rabbits (Sylvilagus spp. Previous infection with a type B strain of organism was found to lengthen survival time and in some cases prevent death following inoculation with a type A2 strain of F. tularensis. In contrast, inoculation of a type A1b strain was uniformly lethal in cottontail rabbits irrespective of a prior type B inoculation. These findings provide important insight about the role cottontail rabbits may play in environmental maintenance and transmission of this organism.

[Screening and optimization of cholesterol conversion strain].

Science.gov (United States)

Fan, Dan; Xiong, Bingjian; Pang, Cuiping; Zhu, Xiangdong

2014-10-04

Bacterial strain SE-1 capable of transforming cholesterol was isolated from soil and characterized. The transformation products were identified. Fermentation conditions were optimized for conversion. Cholesterol was used as sole carbon source to isolate strain SE-1. Morphology, physiological and biochemical characteristics of strain SE-1 were studied. 16S rRNA gene was sequenced and subjected to phylogenetic analysis. Fermentation supernatants were extracted with chloroform, the transformation products were analyzed by silica gel thin layer chromatography and Sephadex LH20. Their structures were identified by 1H-NMR and 13C-NMR. Fermentation medium including carbon and nitrogen, methods of adding substrates and fermentation conditions for Strain SE-1 were optimized. Strain SE-1 was a Gram-negative bacterium, exhibiting the highest homologs to Burkholderia cepacia based on the physiological analysis. The sequence analysis of 16S rRNA gene of SE-1 strain and comparison with related Burkholderia show that SE-1 strain was very close to B. cepacia (Genbank No. U96927). The similarity was 99%. The result of silica gel thin layer chromatography shows that strain SE-1 transformed cholesterol to two products, 7beta-hydroxycholesterol and the minor product was 7-oxocholesterol. The optimum culture conditions were: molasses 5%, (NH4 )2SO4 0.3%, 4% of inoculation, pH 7.5 and 36 degrees C. Under the optimum culture condition, the conversion rate reached 34.4% when concentration of cholesterol-Tween 80 was 1 g/L. Cholesterol 7beta-hydroxylation conversion rate under optimal conditions was improved by 20.8%. Strain SE-1 isolated from soil is capable of converting cholesterol at lab-scale.

Gellertiella hungarica gen. nov., sp. nov., a novel bacterium of the family Rhizobiaceae isolated from a spa in Budapest.

Science.gov (United States)

Tóth, Erika; Szuróczki, Sára; Kéki, Zsuzsa; Bóka, Károly; Szili-Kovács, Tibor; Schumann, Peter

2017-11-01

A novel alphaproteobacterium, strain RAM11 T , belonging to the family Rhizobiaceae was isolated from the pool water of a thermal bath in Budapest, Hungary. Based on the 16S rRNA gene sequence strain RAM11 T shows the highest sequence similarity values to Ensifer adhaerens Casida A (97.44 %), to Ensifer (syn. Sinorhizobium) americanus CFNEI 156 T (96.87 %) and to Rhizobium azooxidifex Po 20/26 T (96.76 %). The new bacterium is strictly aerobic, its optimum growth occurs at 20-37 °C, between pH 7 and 9 and without NaCl. It is motile due to a single polar flagellum, capable of budding and forms rosettes in liquid culture. The major isoprenoid quinone of strain RAM11 T is Q-10, the major cellular fatty acids are C18 : 1ω7c and 11-MeC18 : 1ω7c. The polar lipid profile contains phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, an unidentified aminolipid and an unidentified phospholipid. The G+C content of DNA of the type strain is 62.9 mol%. Strain RAM11 T (=DSM 29853 T =NCAIM B.02618 T ) is proposed as type strain of a new genus and species with the proposed name Gellertiella hungarica gen. nov., sp. nov.

Limnobacter litoralis sp. nov., a thiosulfate-oxidizing, heterotrophic bacterium isolated from a volcanic deposit, and emended description of the genus Limnobacter.

Science.gov (United States)

Lu, Hongsheng; Sato, Yoshinori; Fujimura, Reiko; Nishizawa, Tomoyasu; Kamijo, Takashi; Ohta, Hiroyuki

2011-02-01

A Gram-negative, aerobic, heterotrophic bacterium, designated KP1-19(T), was isolated from a 22-year-old volcanic deposit at a site lacking vegetation on the island of Miyake, Japan. Strain KP1-19(T) was able to use thiosulfate (optimum concentration 10 mM) as an additional energy source. 16S rRNA gene sequence analysis indicated that strain KP1-19(T) was closely related to Limnobacter thiooxidans CS-K2(T) within the class Betaproteobacteria (97.7 % 16S rRNA gene sequence similarity). The cellular fatty acid profile was characteristic of the genus Limnobacter: the major fatty acids (>5 %) were C(16 : 0), C(16 : 1)ω7c and C(18 : 1)ω7c and minor amounts of C(10 : 0) 3-OH were also found. DNA-DNA relatedness between strain KP1-19(T) and L. thiooxidans LMG 19593(T) was 18 %. Therefore, strain KP1-19(T) represents a novel species, for which the name Limnobacter litoralis sp. nov. is proposed. The type strain is KP1-19(T) (=LMG 24869(T) =NBRC 105857(T) =CIP 109929(T)).

Rhodonellum psychrophilum gen. nov., sp. nov., a novel psychrophilic and alkaliphilic bacterium of the phylum Bacteroidetes isolated from Greenland.

Science.gov (United States)

Schmidt, Mariane; Priemé, Anders; Stougaard, Peter

2006-12-01

A novel alkaliphilic and psychrophilic bacterium was isolated from the cold and alkaline ikaite tufa columns of the Ikka Fjord in south-west Greenland. According to 16S rRNA gene sequence analysis, strain GCM71(T) belonged to the family 'Flexibacteraceae' in the phylum Bacteroidetes. Strain GCM71(T), together with five related isolates from ikaite columns, formed a separate cluster with 86-93 % gene sequence similarity to their closest relative, Belliella baltica. The G+C content of the DNA from strain GCM71(T) was 43.1 mol%, whereas that of B. baltica was reported to be 35 mol%. DNA-DNA hybridization between strain GCM71(T) and B. baltica was 9.5 %. The strain was red pigmented, Gram-negative, strictly aerobic with non-motile, rod-shaped cells. The optimal growth conditions for strain GCM71(T) were pH 9.2-10.0, 5 degrees C and 0.6 % NaCl. The fatty acid profile of the novel strain was dominated by branched and unsaturated fatty acids (90-97 %), with a high abundance of iso-C(17 : 1)omega9c (17.5 %), iso-C(17 : 0) 3-OH (17.5 %) and summed feature 3, comprising iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c (12.6 %). Phylogenetic, chemotaxonomic and physiological characteristics showed that the novel strain could not be affiliated to any known genus. A new genus, Rhodonellum gen. nov., is proposed to accommodate the novel strain. Strain GCM71(T) (=DSM 17998(T)=LMG 23454(T)) is proposed as the type strain of the type species, Rhodonellum psychrophilum sp. nov.

Draft Genome Sequence of a Kale (Brassica oleracea L.) Root Endophyte, Pseudomonas sp. Strain C9.

Science.gov (United States)

Laugraud, Aurelie; Young, Sandra; Gerard, Emily; O'Callaghan, Maureen; Wakelin, Steven

2017-04-13

Pseudomonas sp. strain C9 is a plant growth-promoting bacterium isolated from the root tissue of Brassica oleracea L. grown in soil from Marlborough, New Zealand. Its draft genome of 6,350,161 bp contains genes associated with plant growth promotion and biological control. Copyright © 2017 Laugraud et al.

Haloalkane-utilizing Rhodococcus strains isolated from geographically distinct locations possess a highly conserved gene cluster encoding haloalkane catabolism

NARCIS (Netherlands)

Poelarends, GJ; Bosma, T; Kulakov, LA; Larkin, MJ; Marchesi, [No Value; Weightman, AJ; Janssen, DB; Kulakov, Leonid A.; Larkin, Michael J.; Marchesi, Julian R.; Weightman, Andrew J.

The sequences of the 16S rRNA and haloalkane dehalogenase (dhaA) genes of five gram-positive haloalkane-utilizing bacteria isolated from contaminated sites in Europe, Japan, and the United States and of the archetypal haloalkane-degrading bacterium Rhodococcus sp. strain NCIMB13064 were compared.

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

OpenAIRE

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

2015-01-01

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

Genome Sequence of Streptomyces viridosporus Strain T7A ATCC 39115, a Lignin-Degrading Actinomycete

Energy Technology Data Exchange (ETDEWEB)

Davis, Jennifer R. [Brown University; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Teshima, Hazuki [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Wei, Chia-Lin [Los Alamos National Laboratory (LANL); Han, James [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Szeto, Ernest [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Peters, Lin [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Sello, Jason K. [Brown University

2013-01-01

We announce the availability of the genome sequence of Streptomyces viridosporus strain T7A ATCC 39115, a plant biomass- degrading actinomycete. This bacterium is of special interest because of its capacity to degrade lignin, an underutilized compo- nent of plants in the context of bioenergy. It has a full complement of genes for plant biomass catabolism.

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.

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.

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

Science.gov (United States)

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

2014-07-01

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

The impact of strain-specific immunity on Lyme disease incidence is spatially heterogeneous.

Science.gov (United States)

Khatchikian, Camilo E; Nadelman, Robert B; Nowakowski, John; Schwartz, Ira; Wormser, Gary P; Brisson, Dustin

2017-12-01

Lyme disease, caused by the bacterium Borrelia burgdorferi, is the most common tick-borne infection in the US. Recent studies have demonstrated that the incidence of human Lyme disease would have been even greater were it not for the presence of strain-specific immunity, which protects previously infected patients against subsequent infections by the same B. burgdorferi strain. Here, spatial heterogeneity is incorporated into epidemiological models to accurately estimate the impact of strain-specific immunity on human Lyme disease incidence. The estimated reduction in the number of Lyme disease cases is greater in epidemiologic models that explicitly include the spatial distribution of Lyme disease cases reported at the county level than those that utilize nationwide data. strain-specific immunity has the greatest epidemiologic impact in geographic areas with the highest Lyme disease incidence due to the greater proportion of people that have been previously infected and have developed strain-specific immunity. Copyright © 2017 Elsevier Inc. All rights reserved.

Whole-Genome Sequence of Chlamydia abortus Strain GN6 Isolated from Aborted Yak Fetus

OpenAIRE

Li, Zhaocai; Cai, Jinshan; Cao, Xiaoan; Lou, Zhongzi; Chao, Yilin; Kan, Wei; Zhou, Jizhang

2017-01-01

ABSTRACT The obligate intracellular Gram-negative bacterium Chlamydia abortus is one of the causative agents of abortion and fetal loss in sheep, goats, and cattle in many countries. It also affects the reproductivity of yaks (Bos grunniens). This study reports the whole-genome sequence of Chlamydia abortus strain GN6, which was isolated from aborted yak fetus in Qinghai-Tibetan Plateau, China.

Draft Genome Sequences of Two Propionibacterium acnes Strains Isolated from Progressive Macular Hypomelanosis Lesions of Human Skin

DEFF Research Database (Denmark)

Petersen, Rolf; Lomholt, Hans B.; Scholz, Christian F. P.

2015-01-01

Propionibacterium acnes is a Gram-positive bacterium that is prevalent on human skin. It has been associated with skin disorders such as acne vulgaris and progressive macular hypomelanosis (PMH). Here, we report draft genome sequences of two type III P. acnes strains, PMH5 and PMH7, isolated from...

Draft Genome Sequence of Cupriavidus pauculus Strain KF709, a Biphenyl-Utilizing Bacterium Isolated from Biphenyl-Contaminated Soil

OpenAIRE

Watanabe, Takahito; Yamazoe, Atsushi; Hosoyama, Akira; Fujihara, Hidehiko; Suenaga, Hikaru; Hirose, Jun; Futagami, Taiki; Goto, Masatoshi; Kimura, Nobutada; Furukawa, Kensuke

2015-01-01

We report the draft genome sequence of Cupriavidus pauculus strain KF709, which comprises 6,826,799 bp with 6,272 coding sequences. The strain KF709 utilizes biphenyl and degrades low-chlorinated biphenyls; however, it possesses fewer coding sequences involved in the degradation of aromatic compounds than other strains belonging to the Betaproteobacteria.

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

Science.gov (United States)

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

2015-08-27

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

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

Science.gov (United States)

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

2007-09-01

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

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).

ANALYSIS OF IMMUNE RESPONSES ON TRANSGENIC TIGER SHRIMP (Penaeus monodon AGAINST PATHOGENIC BACTERIUM Vibrio harveyi

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Andi Parenrengi

2014-06-01

Full Text Available Vibriosis is one of main diseases of the black tiger shrimp Penaeus monodon infected by pathogenic bioluminous bacterium Vibrio harveyi that can cause mass mortalities in shrimp culture. The bacteria can also trigger the disease white spot syndrome virus (WSSV. An effort to produce shrimp disease-resistant strains has been done through transgenesis technology with antiviral gene transfection. By this technology, it is expected an increase in the immune response of shrimp in a variety of diseasecausing pathogens. This study aimed to determine the immune responses (total haemocytes, haemocyte differentiation, and phenoloxydase activity of transgenic tiger shrimp against pathogenic bacterium V. harveyi. Research using completely randomized design, which consists of two treatments and three replications. Test animals being used were transgenic and non-transgenic shrimp with size, weight 3.93±1.25 g and a total length of 7.59±0.87 cm. Treatments being tested were the injection of bacterium V. harveyi (density of 5x106 cfu/mL of 0.1 mL/individual on transgenic (A and non-transgenic shrimp (B. Immune response parameters such as total haemocytes, haemocyte differentiation, and phenoloxydase activity were observed on day 1, 3, and 6 days after challenging. Data were analyzed using t-test by SPSS software. The results showed that the total haemocyte of transgenic shrimp was not significantly different (P>0.05 from non-transgenic shrimp, but haemocyte differentiation and phenoloxydase activity were significantly different (P<0.05 especially on sixth days after being exposed to the bioluminescent bacteria. The study results implied that transgenic shrimp has a better immune response compared than non-transgenic shrimp.

Development of plasmid vector and electroporation condition for gene transfer in sporogenic lactic acid bacterium, Bacillus coagulans.

Science.gov (United States)

Rhee, Mun Su; Kim, Jin-Woo; Qian, Yilei; Ingram, L O; Shanmugam, K T

2007-07-01

Bacillus coagulans is a sporogenic lactic acid bacterium that ferments glucose and xylose, major components of plant biomass, a potential feedstock for cellulosic ethanol. The temperature and pH for optimum rate of growth of B. coagulans (50 to 55 degrees C, pH 5.0) are very similar to that of commercially developed fungal cellulases (50 degrees C; pH 4.8). Due to this match, simultaneous saccharification and fermentation (SSF) of cellulose to products by B. coagulans is expected to require less cellulase than needed if the SSF is conducted at a sub-optimal temperature, such as 30 degrees C, the optimum for yeast, the main biocatalyst used by the ethanol industry. To fully exploit B. coagulans as a platform organism, we have developed an electroporation method to transfer plasmid DNA into this genetically recalcitrant bacterium. We also constructed a B. coagulans/E. coli shuttle vector, plasmid pMSR10 that contains the rep region from a native plasmid (pMSR0) present in B. coagulans strain P4-102B. The native plasmid, pMSR0 (6823bp), has 9 ORFs, and replicates by rolling-circle mode of replication. Plasmid pNW33N, developed for Geobacillus stearothermophilus, was also transformed into this host and stably maintained while several other Bacillus/Escherichia coli shuttle vector plasmids were not transformed into B. coagulans. The transformation efficiency of B. coagulans strain P4-102B using the plasmids pNW33N or pMSR10 was about 1.5x10(16) per mole of DNA. The availability of shuttle vectors and an electroporation method is expected to aid in genetic and metabolic engineering of B. coagulans.

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

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Nagarajan, N; Gunasekaran, P; Rajendran, P

2015-04-01

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

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)....

Isolation and Antibiotic Sensitivity of Bacillus thuringinesis Strain From Dump Soil

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Sarker, D.

2010-01-01

Full Text Available Bacillus thuringiensis (or Bt is a commonly used as a pesticide. B. thuringiensis is a naturally-occurring soil bacterium, also occurs naturally in the gut of caterpillars of various types of moths and butterflies, as well as on the dark surface of plants. The xylanase producing bacterial strains were isolated from dump soil. The strains were isolated on xylan agar media and screening was carried out by xylanolysis method. To test the sensitivity of the isolates, ten different antibiotics were used. The strains were tested for resistance to doxycyclin, erythromycin, chloramphenical, cephallaxin, kanamycin, ampicillin, steptomycin, vancomycin, amoxycillin and neomycin. The strains showed sensitive to doxycyclin, erythromycin, chloramphenical, cephallaxin, kanamycin, ampicillin, steptomycin and vancomycin and also showed resistance to amoxycillin and neomycin, when tested by disc diffusion method on nutrient agar plate confirmed by antibiotic spread plate method. The inhibitory effect of B. thuringiensis strains against the test bacteria Bacillus subtilis, Sarcina lutca, Shigella dysenteriae, Shigella sonnei and Pseudomonus aeruginosa examined. It was found that, B. thuringiensis S1, B. thuringiensis S2 and B. thuringiensis S3 strains showed an inhibitory effect on all of the test bacteria.

Aerobic degradation of 4-nitroaniline (4-NA) via novel degradation intermediates by Rhodococcus sp. strain FK48

Energy Technology Data Exchange (ETDEWEB)

Khan, Fazlurrahman; Pandey, Janmejay; Vikram, Surendra; Pal, Deepika; Cameotra, Swaranjit Singh, E-mail: ssc@imtech.res.in

2013-06-15

Highlights: • This study reports isolation of a novel bacterium capable of mineralizing 4-nitroaniline (4-NA). • This bacterium has been identified as Rhodococcus sp. strain FK48. • Strain FK48 degrades 4-NA via a novel aerobic degradation pathway that involves 4-AP and 1,2,4-BT. • Subsequent degradation proceeds via ring fission and formation of maleylacetate. • This is the first report showing elucidation of catabolic pathway for microbial degradation 4-NA. -- Abstract: An aerobic strain, Rhodococcus sp. strain FK48, capable of growing on 4-nitroaniline (4-NA) as the sole source of carbon, nitrogen, and energy has been isolated from enrichment cultures originating from contaminated soil samples. During growth studies with non- induced cells of FK48 catalyzed sequential denitrification (release of NO{sub 2} substituent) and deamination (release of NH{sub 2} substituent) of 4-NA. However, none of the degradation intermediates could be identified with growth studies. During resting cell studies, 4-NA-induced cells of strain FK48 transformed 4-NA via a previously unknown pathway which involved oxidative hydroxylation leading to formation of 4-aminophenol (4-AP). Subsequent degradation involved oxidated deamination of 4-AP and formation of 1,2,4-benzenetriol (BT) as the major identified terminal aromatic intermediate. Identification of these intermediates was ascertained by HPLC, and GC–MS analyses of the culture supernatants. 4-NA-induced cells of strain FK48 showed positive activity for 1,2,4-benzenetriol dioxygenase in spectrophotometric assay. This is the first conclusive study on aerobic microbial degradation of 4-NA and elucidation of corresponding metabolic pathway.

Aerobic degradation of 4-nitroaniline (4-NA) via novel degradation intermediates by Rhodococcus sp. strain FK48

International Nuclear Information System (INIS)

Khan, Fazlurrahman; Pandey, Janmejay; Vikram, Surendra; Pal, Deepika; Cameotra, Swaranjit Singh

2013-01-01

Highlights: • This study reports isolation of a novel bacterium capable of mineralizing 4-nitroaniline (4-NA). • This bacterium has been identified as Rhodococcus sp. strain FK48. • Strain FK48 degrades 4-NA via a novel aerobic degradation pathway that involves 4-AP and 1,2,4-BT. • Subsequent degradation proceeds via ring fission and formation of maleylacetate. • This is the first report showing elucidation of catabolic pathway for microbial degradation 4-NA. -- Abstract: An aerobic strain, Rhodococcus sp. strain FK48, capable of growing on 4-nitroaniline (4-NA) as the sole source of carbon, nitrogen, and energy has been isolated from enrichment cultures originating from contaminated soil samples. During growth studies with non- induced cells of FK48 catalyzed sequential denitrification (release of NO 2 substituent) and deamination (release of NH 2 substituent) of 4-NA. However, none of the degradation intermediates could be identified with growth studies. During resting cell studies, 4-NA-induced cells of strain FK48 transformed 4-NA via a previously unknown pathway which involved oxidative hydroxylation leading to formation of 4-aminophenol (4-AP). Subsequent degradation involved oxidated deamination of 4-AP and formation of 1,2,4-benzenetriol (BT) as the major identified terminal aromatic intermediate. Identification of these intermediates was ascertained by HPLC, and GC–MS analyses of the culture supernatants. 4-NA-induced cells of strain FK48 showed positive activity for 1,2,4-benzenetriol dioxygenase in spectrophotometric assay. This is the first conclusive study on aerobic microbial degradation of 4-NA and elucidation of corresponding metabolic pathway

Involvement of an ATP-dependent carboxylase in a CO2-dependent pathway of acetone metabolism by Xanthobacter strain Py2.

OpenAIRE

Sluis, M K; Small, F J; Allen, J R; Ensign, S A

1996-01-01

The metabolism of acetone by the aerobic bacterium Xanthobacter strain Py2 was investigated. Cell suspensions of Xanthobacter strain Py2 grown with propylene or glucose as carbon sources were unable to metabolize acetone. The addition of acetone to cultures grown with propylene or glucose resulted in a time-dependent increase in acetone-degrading activity. The degradation of acetone by these cultures was prevented by the addition of rifampin and chloramphenicol, demonstrating that new protein...

Draft genome sequence of Paraburkholderia tropica Ppe8 strain, a sugarcane endophytic diazotrophic bacterium.

Science.gov (United States)

Silva, Paula Renata Alves da; Simões-Araújo, Jean Luiz; Vidal, Márcia Soares; Cruz, Leonardo Magalhães; Souza, Emanuel Maltempi de; Baldani, José Ivo

Paraburkholderia tropica (syn Burkholderia tropica) are nitrogen-fixing bacteria commonly found in sugarcane. The Paraburkholderia tropica strain Ppe8 is part of the sugarcane inoculant consortium that has a beneficial effect on yield. Here, we report a draft genome sequence of this strain elucidating the mechanisms involved in its interaction mainly with Poaceae. A genome size of approximately 8.75Mb containing 7844 protein coding genes distributed in 526 subsystems was de novo assembled with ABySS and annotated by RAST. Genes related to the nitrogen fixation process, the secretion systems (I, II, III, IV, and VI), and related to a variety of metabolic traits, such as metabolism of carbohydrates, amino acids, vitamins, and proteins, were detected, suggesting a broad metabolic capacity and possible adaptation to plant association. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Draft Genome Sequence of Cupriavidus pauculus Strain KF709, a Biphenyl-Utilizing Bacterium Isolated from Biphenyl-Contaminated Soil.

Science.gov (United States)

Watanabe, Takahito; Yamazoe, Atsushi; Hosoyama, Akira; Fujihara, Hidehiko; Suenaga, Hikaru; Hirose, Jun; Futagami, Taiki; Goto, Masatoshi; Kimura, Nobutada; Furukawa, Kensuke

2015-03-26

We report the draft genome sequence of Cupriavidus pauculus strain KF709, which comprises 6,826,799 bp with 6,272 coding sequences. The strain KF709 utilizes biphenyl and degrades low-chlorinated biphenyls; however, it possesses fewer coding sequences involved in the degradation of aromatic compounds than other strains belonging to the Betaproteobacteria. Copyright © 2015 Watanabe et al.

ISOLATION AND CHARACTERIZATION OF A MOLYBDENUM-REDUCING AND GLYPHOSATE-DEGRADING Klebsiella oxytoca STRAIN SAW-5 IN SOILS FROM SARAWAK

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M.K. Sabullah

2016-02-01

Full Text Available Bioremediation of pollutants including heavy metals and xenobiotics is an economic and environmentally friendly process. A novel molybdenum-reducing bacterium with the ability to utilize the pesticide glyphosate as a carbon source is reported. The characterization works were carried out utilizing bacterial resting cells in a microplate format. The bacterium reduces molybdate to Mo-blue optimally between pH 6.3 and 6.8 and at 34oC. Glucose was the best electron donor for supporting molybdate reduction followed by lactose, maltose, melibiose, raffinose, d-mannitol, d-xylose, l-rhamnose, l-arabinose, dulcitol, myo-inositol and glycerol in descending order. Other requirements include a phosphate concentration at 5.0 mM and a molybdate concentration between 20 and 30 mM. The molybdenum blue exhibited an absorption spectrum resembling a reduced phosphomolybdate. Molybdenum reduction was inhibited by mercury, silver, cadmium and copper at 2 ppm by 45.5, 26.0, 18.5 and 16.3%, respectively. Biochemical analysis identified the bacterium as Klebsiella oxytoca strain Saw-5. To conclude, the capacity of this bacterium to reduce molybdenum into a less toxic form and to grow on glyphosate is novel and makes the bacterium an important instrument for bioremediation of these pollutants.

Isolation and initial characterization of the tellurite reducing moderately halophilic bacterium, Salinicoccus sp. strain QW6.

Science.gov (United States)

Amoozegar, Mohammad Ali; Ashengroph, Morahem; Malekzadeh, Feridon; Reza Razavi, Mohamad; Naddaf, Saied; Kabiri, Mahboubeh

2008-01-01

Among the 49 strains of moderately halophilic bacteria isolated from the salty environments of Iran, a Gram-positive coccus designated as strain QW6 showed high capacity in the removal of toxic oxyanions of tellurium in a wide range of culture medium factors including pH (5.5-10.5), temperature (25-45 degrees C), various salts including NaCl, KCl, and Na(2)SO(4) (0.5-4 M), selenooxyanions (2-10 mM), and at different concentrations of potassium tellurite (0.5-1 mM) under aerobic condition. Phenotypic characterization and phylogenetic analyses based on 16S rDNA sequence comparisons indicated that this strain was a member of the genus Salinicoccus. The maximum tellurite removal was exhibited in 1.5M NaCl at 35 degrees C, while the activity reduced by 53% and 47% at 25 and 45 degrees C, respectively. The optimum pH for removal activity was shown to be 7.5, with 90% and 83% reduced removal capacities at the two extreme values of 5.5 and 10, respectively. The impact of different concentrations of selenooxyanions (2-10 mM) on tellurite removal by strain QW6 was evaluated. The ability of strain QW6 in the removal of tellurite in the presence of 6mM selenite increased by 25%. The concentration of toxic potassium tellurite in the supernatant of the bacterial culture medium decreased by 99% (from 0.5 to 0.005 mM) after 6 days and the color of the medium changed to black due to the formation of less toxic elemental tellurium.

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

2018-07-01

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).

Study on screening of anti-predator rhizosphere bacterium against Caenorhabditis elegans and its anti predation mechanism

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HE Qingling

2016-08-01

Full Text Available Althoughmicrobial fertilizer is multi-effect,environmental friendly and long-term efficient,its practical application effect is but decreased for being prey by the other creators living in soil frequently.Many bacterium have developed their mechanisms that expel or kill worms to defend themselves from predators.Screening of anti-predator rhizosphere bacterium helps us to find out competitive plant growth promoting rhizobacteria(PGPR.Using Caenorhabditis elegans as sample,this study roughly observed two strains of biocontrol:Pseudomonas aurantiaca JD37 and Pseudomonas fluorescens P13.Using Escherichia coli OP50 as control group,we find the preference order of worms,from highest to lowest,is P13,OP50 and JD37.In slow killing assay,the death rate of worms for JD37 and P13 are 26.12% and 18.66% respectively.The activity and reproduction rate of C.elegans decrease when it is fed on JD37.The results of chemical and micro-biological study show that JD37 cannot produce any currently studied second metabolites which kill worms,while P13 can produce Hydrogen cyanide (HCN.All these results show that JD37 has the ability of anti-predator,and is more competitive under predation pressure,which suggests its broad application prospect as microbial fertilizer.

Spectroscopic characterization of cell membranes and their constituents of the plant-associated soil bacterium Azospirillum brasilense

Science.gov (United States)

Kamnev, A. A.; Antonyuk, L. P.; Matora, L. Yu.; Serebrennikova, O. B.; Sumaroka, M. V.; Colina, M.; Renou-Gonnord, M.-F.; Ignatov, V. V.

1999-05-01

Structural and compositional features of bacterial membranes and some of their isolated constituents (cell surface lipopolysaccharide, phospholipids) of the plant-growth-promoting diazotrophic rhizobacterium Azospirillum brasilense (wild-type strain Sp245) were characterized using Fourier transform infrared (FTIR) spectroscopy and some other techniques. FTIR spectra of the cell membranes were shown to comprise the main vibration modes of the relevant lipopolysaccharide and protein components which are believed to be involved in associative plant-bacterium interactions, as well as of phospholipid constituents. The role and functions of metal cations in the structural organization and physicochemical properties of bacterial cell membranes are also discussed considering their accumulation in the membranes from the culture medium.

Characterization of Burkholderia pseudomallei Strains Using a Murine Intraperitoneal Infection Model and In Vitro Macrophage Assays.

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Susan L Welkos

Full Text Available Burkholderia pseudomallei, the etiologic agent of melioidosis, is a gram-negative facultative intracellular bacterium. This bacterium is endemic in Southeast Asia and Northern Australia and can infect humans and animals by several routes. It has also been estimated to present a considerable risk as a potential biothreat agent. There are currently no effective vaccines for B. pseudomallei, and antibiotic treatment can be hampered by nonspecific symptomology, the high incidence of naturally occurring antibiotic resistant strains, and disease chronicity. Accordingly, there is a concerted effort to better characterize B. pseudomallei and its associated disease. Before novel vaccines and therapeutics can be tested in vivo, a well characterized animal model is essential. Previous work has indicated that mice may be a useful animal model. In order to develop standardized animal models of melioidosis, different strains of bacteria must be isolated, propagated, and characterized. Using a murine intraperitoneal (IP infection model, we tested the virulence of 11 B. pseudomallei strains. The IP route offers a reproducible way to rank virulence that can be readily reproduced by other laboratories. This infection route is also useful in distinguishing significant differences in strain virulence that may be masked by the exquisite susceptibility associated with other routes of infection (e.g., inhalational. Additionally, there were several pathologic lesions observed in mice following IP infection. These included varisized abscesses in the spleen, liver, and haired skin. This model indicated that commonly used laboratory strains of B. pseudomallei (i.e., K96243 and 1026b were significantly less virulent as compared to more recently acquired clinical isolates. Additionally, we characterized in vitro strain-associated differences in virulence for macrophages and described a potential inverse relationship between virulence in the IP mouse model of some strains

Characterization of Burkholderia pseudomallei Strains Using a Murine Intraperitoneal Infection Model and In Vitro Macrophage Assays.

Science.gov (United States)

Welkos, Susan L; Klimko, Christopher P; Kern, Steven J; Bearss, Jeremy J; Bozue, Joel A; Bernhards, Robert C; Trevino, Sylvia R; Waag, David M; Amemiya, Kei; Worsham, Patricia L; Cote, Christopher K

2015-01-01

Burkholderia pseudomallei, the etiologic agent of melioidosis, is a gram-negative facultative intracellular bacterium. This bacterium is endemic in Southeast Asia and Northern Australia and can infect humans and animals by several routes. It has also been estimated to present a considerable risk as a potential biothreat agent. There are currently no effective vaccines for B. pseudomallei, and antibiotic treatment can be hampered by nonspecific symptomology, the high incidence of naturally occurring antibiotic resistant strains, and disease chronicity. Accordingly, there is a concerted effort to better characterize B. pseudomallei and its associated disease. Before novel vaccines and therapeutics can be tested in vivo, a well characterized animal model is essential. Previous work has indicated that mice may be a useful animal model. In order to develop standardized animal models of melioidosis, different strains of bacteria must be isolated, propagated, and characterized. Using a murine intraperitoneal (IP) infection model, we tested the virulence of 11 B. pseudomallei strains. The IP route offers a reproducible way to rank virulence that can be readily reproduced by other laboratories. This infection route is also useful in distinguishing significant differences in strain virulence that may be masked by the exquisite susceptibility associated with other routes of infection (e.g., inhalational). Additionally, there were several pathologic lesions observed in mice following IP infection. These included varisized abscesses in the spleen, liver, and haired skin. This model indicated that commonly used laboratory strains of B. pseudomallei (i.e., K96243 and 1026b) were significantly less virulent as compared to more recently acquired clinical isolates. Additionally, we characterized in vitro strain-associated differences in virulence for macrophages and described a potential inverse relationship between virulence in the IP mouse model of some strains and in the

Whole-Genome Sequence of Chlamydia abortus Strain GN6 Isolated from Aborted Yak Fetus.

Science.gov (United States)

Li, Zhaocai; Cai, Jinshan; Cao, Xiaoan; Lou, Zhongzi; Chao, Yilin; Kan, Wei; Zhou, Jizhang

2017-08-31

The obligate intracellular Gram-negative bacterium Chlamydia abortus is one of the causative agents of abortion and fetal loss in sheep, goats, and cattle in many countries. It also affects the reproductivity of yaks ( Bos grunniens ). This study reports the whole-genome sequence of Chlamydia abortus strain GN6, which was isolated from aborted yak fetus in Qinghai-Tibetan Plateau, China. Copyright © 2017 Li et al.

Metabolomic response of a marine bacterium to 3,6-anhydro-l-galactose, the rare sugar from red macroalgae, as the sole carbon source.

Science.gov (United States)

Yun, Eun Ju; Yu, Sora; Kim, Sooah; Kim, Kyoung Heon

2018-03-20

Marine red macroalgae have received much attention as sustainable resources for producing bio-based products. Therefore, understanding the metabolic pathways of carbohydrates from red macroalgae, in fermentative microorganisms, is crucial for efficient bioconversion of the carbohydrates into bio-based products. Recently, the novel catabolic pathway of 3,6-anhydro-l-galactose (AHG), the main component of red macroalgae, was discovered in a marine bacterium, Vibrio sp. strain EJY3. However, the global metabolic network in response to AHG remains unclear. Here, the intracellular metabolites of EJY3 grown on AHG, glucose, or galactose were comparatively profiled using gas chromatography/time-of-flight mass spectrometry. The global metabolite profiling results revealed that the metabolic profile for AHG significantly differed from those for other common sugars. Specifically, the metabolic intermediate of the AHG pathway, 3,6-anhydrogalactonate, was detected during growth only in the presence of AHG; thus, the recently discovered key steps in AHG catabolism was found not to occur in the catabolism of other common sugars. Moreover, the levels of metabolic intermediates related to glycerolipid metabolism and valine biosynthesis were higher with AHG than those with other sugars. These comprehensive metabolomic analytical results for AHG in this marine bacterium can be used as the basis for having fermentative microbial strains to engineered to efficiently utilize AHG from macroalgal biomass. Copyright © 2018 Elsevier B.V. All rights reserved.

Complete Genome Sequence of Rhodococcus sp. Strain WMMA185, a Marine Sponge-Associated Bacterium

OpenAIRE

Adnani, Navid; Braun, Doug R.; McDonald, Bradon R.; Chevrette, Marc G.; Currie, Cameron R.; Bugni, Tim S.

2016-01-01

The Rhodococcus strain WMMA185 was isolated from the marine sponge Chondrilla nucula as part of ongoing drug discovery efforts. Analysis of the 4.44-Mb genome provides information regarding interspecies interactions as pertains to regulation of secondary metabolism and natural product biosynthetic potentials.

Dense populations of a giant sulfur bacterium in Namibian shelf sediments

DEFF Research Database (Denmark)

Schulz, HN; Brinkhoff, T.; Ferdelman, TG

1999-01-01

A previously unknown giant sulfur bacterium is abundant in sediments underlying the oxygen minimum zone of the Benguela Current upwelling system. The bacterium has a spherical cell that exceeds by up to 100-fold the biovolume of the largest known prokaryotes. On the basis of 16S ribosomal DNA...

Characterization of the Metabolically Modified Heavy Metal-Resistant Cupriavidus metallidurans Strain MSR33 Generated for Mercury Bioremediation

Science.gov (United States)

Rojas, Luis A.; Yáñez, Carolina; González, Myriam; Lobos, Soledad; Smalla, Kornelia; Seeger, Michael

2011-01-01

Background Mercury-polluted environments are often contaminated with other heavy metals. Therefore, bacteria with resistance to several heavy metals may be useful for bioremediation. Cupriavidus metallidurans CH34 is a model heavy metal-resistant bacterium, but possesses a low resistance to mercury compounds. Methodology/Principal Findings To improve inorganic and organic mercury resistance of strain CH34, the IncP-1β plasmid pTP6 that provides novel merB, merG genes and additional other mer genes was introduced into the bacterium by biparental mating. The transconjugant Cupriavidus metallidurans strain MSR33 was genetically and biochemically characterized. Strain MSR33 maintained stably the plasmid pTP6 over 70 generations under non-selective conditions. The organomercurial lyase protein MerB and the mercuric reductase MerA of strain MSR33 were synthesized in presence of Hg2+. The minimum inhibitory concentrations (mM) for strain MSR33 were: Hg2+, 0.12 and CH3Hg+, 0.08. The addition of Hg2+ (0.04 mM) at exponential phase had not an effect on the growth rate of strain MSR33. In contrast, after Hg2+ addition at exponential phase the parental strain CH34 showed an immediate cessation of cell growth. During exposure to Hg2+ no effects in the morphology of MSR33 cells were observed, whereas CH34 cells exposed to Hg2+ showed a fuzzy outer membrane. Bioremediation with strain MSR33 of two mercury-contaminated aqueous solutions was evaluated. Hg2+ (0.10 and 0.15 mM) was completely volatilized by strain MSR33 from the polluted waters in presence of thioglycolate (5 mM) after 2 h. Conclusions/Significance A broad-spectrum mercury-resistant strain MSR33 was generated by incorporation of plasmid pTP6 that was directly isolated from the environment into C. metallidurans CH34. Strain MSR33 is capable to remove mercury from polluted waters. This is the first study to use an IncP-1β plasmid directly isolated from the environment, to generate a novel and stable bacterial strain

Characterization of the metabolically modified heavy metal-resistant Cupriavidus metallidurans strain MSR33 generated for mercury bioremediation.

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Luis A Rojas

Full Text Available BACKGROUND: Mercury-polluted environments are often contaminated with other heavy metals. Therefore, bacteria with resistance to several heavy metals may be useful for bioremediation. Cupriavidus metallidurans CH34 is a model heavy metal-resistant bacterium, but possesses a low resistance to mercury compounds. METHODOLOGY/PRINCIPAL FINDINGS: To improve inorganic and organic mercury resistance of strain CH34, the IncP-1β plasmid pTP6 that provides novel merB, merG genes and additional other mer genes was introduced into the bacterium by biparental mating. The transconjugant Cupriavidus metallidurans strain MSR33 was genetically and biochemically characterized. Strain MSR33 maintained stably the plasmid pTP6 over 70 generations under non-selective conditions. The organomercurial lyase protein MerB and the mercuric reductase MerA of strain MSR33 were synthesized in presence of Hg(2+. The minimum inhibitory concentrations (mM for strain MSR33 were: Hg(2+, 0.12 and CH(3Hg(+, 0.08. The addition of Hg(2+ (0.04 mM at exponential phase had not an effect on the growth rate of strain MSR33. In contrast, after Hg(2+ addition at exponential phase the parental strain CH34 showed an immediate cessation of cell growth. During exposure to Hg(2+ no effects in the morphology of MSR33 cells were observed, whereas CH34 cells exposed to Hg(2+ showed a fuzzy outer membrane. Bioremediation with strain MSR33 of two mercury-contaminated aqueous solutions was evaluated. Hg(2+ (0.10 and 0.15 mM was completely volatilized by strain MSR33 from the polluted waters in presence of thioglycolate (5 mM after 2 h. CONCLUSIONS/SIGNIFICANCE: A broad-spectrum mercury-resistant strain MSR33 was generated by incorporation of plasmid pTP6 that was directly isolated from the environment into C. metallidurans CH34. Strain MSR33 is capable to remove mercury from polluted waters. This is the first study to use an IncP-1β plasmid directly isolated from the environment, to generate a novel

Neutropenia restores virulence to an attenuated Cu,Zn superoxide dismutase-deficient Haemophilus ducreyi strain in the swine model of chancroid.

Science.gov (United States)

San Mateo, L R; Toffer, K L; Orndorff, P E; Kawula, T H

1999-10-01

Haemophilus ducreyi causes chancroid, a sexually transmitted cutaneous genital ulcer disease associated with increased heterosexual transmission of human immunodeficiency virus. H. ducreyi expresses a periplasmic copper-zinc superoxide dismutase (Cu, Zn SOD) that protects the bacterium from killing by exogenous superoxide in vitro. We hypothesized that the Cu,Zn SOD would protect H. ducreyi from immune cell killing, enhance survival, and affect ulcer development in vivo. In order to test this hypothesis and study the role of the Cu,Zn SOD in H. ducreyi pathogenesis, we compared a Cu,Zn SOD-deficient H. ducreyi strain to its isogenic wild-type parent with respect to survival and ulcer development in immunocompetent and immunosuppressed pigs. The Cu,Zn SOD-deficient strain was recovered from significantly fewer inoculated sites and in significantly lower numbers than the wild-type parent strain or a merodiploid (sodC+ sodC) strain after infection of immunocompetent pigs. In contrast, survival of the wild-type and Cu,Zn SOD-deficient strains was not significantly different in pigs that were rendered neutropenic by treatment with cyclophosphamide. Ulcer severity in pigs was not significantly different between sites inoculated with wild type and sites inoculated with Cu,Zn SOD-deficient H. ducreyi. Our data suggest that the periplasmic Cu,Zn SOD is an important virulence determinant in H. ducreyi, protecting the bacterium from host immune cell killing and contributing to survival and persistence in the host.

Host-adaptation of Francisella tularensis alters the bacterium's surface-carbohydrates to hinder effectors of innate and adaptive immunity.

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Tiffany M Zarrella

Full Text Available The gram-negative bacterium Francisella tularensis survives in arthropods, fresh water amoeba, and mammals with both intracellular and extracellular phases and could reasonably be expected to express distinct phenotypes in these environments. The presence of a capsule on this bacterium has been controversial with some groups finding such a structure while other groups report that no capsule could be identified. Previously we reported in vitro culture conditions for this bacterium which, in contrast to typical methods, yielded a bacterial phenotype that mimics that of the bacterium's mammalian, extracellular phase.SDS-PAGE and carbohydrate analysis of differentially-cultivated F. tularensis LVS revealed that bacteria displaying the host-adapted phenotype produce both longer polymers of LPS O-antigen (OAg and additional HMW carbohydrates/glycoproteins that are reduced/absent in non-host-adapted bacteria. Analysis of wildtype and OAg-mutant bacteria indicated that the induced changes in surface carbohydrates involved both OAg and non-OAg species. To assess the impact of these HMW carbohydrates on the access of outer membrane constituents to antibody we used differentially-cultivated bacteria in vitro to immunoprecipitate antibodies directed against outer membrane moieties. We observed that the surface-carbohydrates induced during host-adaptation shield many outer membrane antigens from binding by antibody. Similar assays with normal mouse serum indicate that the induced HMW carbohydrates also impede complement deposition. Using an in vitro macrophage infection assay, we find that the bacterial HMW carbohydrate impedes TLR2-dependent, pro-inflammatory cytokine production by macrophages. Lastly we show that upon host-adaptation, the human-virulent strain, F. tularensis SchuS4 also induces capsule production with the effect of reducing macrophage-activation and accelerating tularemia pathogenesis in mice.F. tularensis undergoes host-adaptation which

ISOLATION AND CHARACTERIZATION OF A MOLYBDENUM-REDUCING, PHENOL- AND CATECHOL-DEGRADING PSEUDOMONAS PUTIDA STRAIN AMR-12 IN SOILS FROM EGYPT

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M. Abd. AbdEl-Mongy

2016-02-01

Full Text Available Sites contaminated with both heavy metals and organic xenobiotic pollutants warrants the effective use of either a multitude of bacterial degraders or bacteria having the capacity to detoxify numerous toxicants simultaneously. A molybdenum-reducing bacterium with the capacity to degrade phenolics is reported. Molybdenum (sodium molybdate reduction was optimum between pH 6.0 and 7.0 and between 20 and 30 °C. The most suitable electron donor was glucose. A narrow range of phosphate concentrations between 5.0 and 7.5 mM was required for optimal reduction, while molybdate between 20 and 30 mM were needed for optimal reduction. The scanning absorption spectrum of the molybdenum blue produced indicated that Mo-blue is a reduced phosphomolybdate. Molybdenum reduction was inhibited by the heavy metals mercury, silver and chromium. Biochemical analysis identified the bacterium as Pseudomonas putida strain Amr-12. Phenol and phenolics cannot support molybdenum reduction. However, the bacterium was able to grow on the phenolic compounds (phenol and catechol with observable lag periods. Maximum growth on phenol and catechol occurred around the concentrations of 600 mg∙L-1. The ability of this bacterium to detoxify molybdenum and grown on toxic phenolic makes this bacterium an important tool for bioremediation.

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.

Moritella viscosa, a pathogenic bacterium affecting the fillet quality in fish

DEFF Research Database (Denmark)

Ingerslev, Hans-Christian; Nielsen, Michael Engelbrecht

2011-01-01

Moritella viscosa is a bacterium belonging to the family Moritellaceae and was formerly known as Vibrio viscosus. The name ‘viscosa’ originates from the slimy nature of the bacterium. M. viscosa is considered to be the main causative agent of the phenomenon ‘winter ulcer’ or ‘cold-water ulcer......’ which affects various fish species in seawater during cold periods (Lunder et al. 1995). The bacterium is mainly a problem for farmed salmonid species, such as Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss), but has also been isolated from other fish species, including Atlantic...... market price because of a quality downgrade caused by textural changes in the fillet....

Description of Paralactobacillus selangorensis gen. nov., sp. nov., a new lactic acid bacterium isolated from chili bo, a Malaysian food ingredient.

Science.gov (United States)

Leisner, J J; Vancanneyt, M; Goris, J; Christensen, H; Rusul, G

2000-01-01

Paralactobacillus selangorensis gen. nov., sp. nov. is described. This organism, isolated from a Malaysian food ingredient called chili bo, is an obligatory homofermentative, rod-shaped lactic acid bacterium. The G+C content is 46.1-46.2+/-0.3 mol%. Earlier 16S rRNA studies showed that this organism constitutes a new taxon distantly related to the Lactobacillus casei-Pediococcus group. A phenotypic description that distinguishes Paralactobacillus selangorensis from other genera of lactic acid bacteria is presented. The type strain of Paralactobacillus selangorensis is LMG 17710T.

Detection of misidentifications of species from the Burkholderia cepacia complex and description of a new member, the soil bacterium Burkholderia catarinensis sp. nov.

Science.gov (United States)

Bach, Evelise; Sant'Anna, Fernando Hayashi; Magrich Dos Passos, João Frederico; Balsanelli, Eduardo; de Baura, Valter Antonio; Pedrosa, Fábio de Oliveira; de Souza, Emanuel Maltempi; Passaglia, Luciane Maria Pereira

2017-08-31

The correct identification of bacteria from the Burkholderia cepacia complex (Bcc) is crucial for epidemiological studies and treatment of cystic fibrosis infections. However, genome-based identification tools are revealing many controversial Bcc species assignments. The aim of this work is to re-examine the taxonomic position of the soil bacterium B. cepacia 89 through polyphasic and genomic approaches. recA and 16S rRNA gene sequence analysis positioned strain 89 inside the Bcc group. However, based on the divergence score of seven concatenated allele sequences, and values of average nucleotide identity, and digital DNA:DNA hybridization, our results suggest that strain 89 is different from other Bcc species formerly described. Thus, we propose to classify Burkholderia sp. 89 as the novel species Burkholderia catarinensis sp. nov. with strain 89T (=DSM 103188T = BR 10601T) as the type strain. Moreover, our results call the attention to some probable misidentifications of Bcc genomes at the National Center for Biotechnology Information database. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Remediation of contaminated subsurface materials by a metal-reducing bacterium

International Nuclear Information System (INIS)

Gorby, Y.A.; Amonette, J.E.; Fruchter, J.S.

1994-11-01

A biotic approach for remediating subsurface sediments and groundwater contaminated with carbon tetrachloride (CT) and chromium was evaluated. Cells of the Fe(iii)-reducing bacterium strain BrY were added to sealed, anoxic flasks containing Hanford groundwater, natural subsurface sediments, and either carbon tetrachloride, CT, or oxidized chromium, Cr(VI). With lactate as the electron donor, BrY transformed CT to chloroform (CF), which accumulated to about 1 0 % of the initial concentration of CT. The remainder of the CT was transformed to unidentified, nonvolatile compounds. Transformation of CT by BrY was an indirect process Cells reduced solid phase Fe(ill) to chemically reactive FE(II) that chemically transformed the chlorinated contaminant. Cr(VI), in contrast, was reduced by a direct enzymatic reaction in the presence or absence of Fe(III)-bearing sediments. These results demonstrate that Fe(ill)-reducing bacteria provide potential for transforming CT and for reducing CR(VI) to less toxic Cr(III). Technologies for stimulating indigenous populations of metal-reducing bacteria or for introducing specific metal-reducing bacteria to the subsurface are being investigated

Comparative Phenotype and Genome Analysis of Cellvibrio sp. PR1, a Xylanolytic and Agarolytic Bacterium from the Pearl River

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Zhangzhang Xie

2017-01-01

Full Text Available Cellvibrio sp. PR1 is a xylanolytic and agarolytic bacterium isolated from the Pearl River. Strain PR1 is closely related to Cellvibrio fibrivorans and C. ostraviensis (identity > 98%. The xylanase and agarase contents of strain PR1 reach up to 15.4 and 25.9 U/mL, respectively. The major cellular fatty acids consisted of C16:0 (36.7%, C18:0 (8.8%, C20:0 (6.8%, C15:0 iso 2-OH or/and C16:1ω7c (17.4%, and C18:1ω7c or/and C18:1ω6c (6.7%. A total of 251 CAZyme modules (63 CBMs, 20 CEs, 128 GHs, 38 GTs, and 2 PLs were identified from 3,730 predicted proteins. Genomic analysis suggested that strain PR1 has a complete xylan-hydrolyzing (5 β-xylanases, 16 β-xylosidases, 17 α-arabinofuranosidases, 9 acetyl xylan esterases, 4 α-glucuronidases, and 2 ferulic acid esterases and agar-hydrolyzing enzyme system (2 β-agarases and 2 α-neoagarooligosaccharide hydrolases. In addition, the main metabolic pathways of xylose, arabinose, and galactose are established in the genome-wide analysis. This study shows that strain PR1 contains a large number of glycoside hydrolases.

Polyphasic analysis of Acidovorax citrulli strains from northeastern Brazil

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Kirley Michele Marques Silva

2016-06-01

Full Text Available ABSTRACT Bacterial fruit blotch (BFB of cucurbit plants is caused by Acidovorax citrulli and represents a serious concern to melon (Cucumis melo L. growers worldwide, including those in Brazil. Thirty-four A. citrulli strains from different melon production areas of northeastern Brazil were characterized for their virulence on melon fruits and their substrate utilization and molecular profiles. Based on the analysis of BFB severity on melon fruits, the A. citrulli strains were divided into three groups, classified as mildly, moderately or highly virulent. Although host-related groups were not observed, the watermelon and ‘melão-pepino’ strains exhibited only low or moderate virulence on melon fruit. Substrate utilization profiles revealed that 94 % of the 95 tested compounds were used by A. citrulli strains as a carbon source. Overall, based on substrate utilization, low variability was observed with no relationship to host of origin. The formation of one group of A. citrulli strains based on Repetitive Sequence-based PCR (rep-PCR analysis confirmed the low variability observed in the substrate utilization analyses. Bayesian inference based on the analysis of 23S rDNA partial sequence data resulted in one well-supported clade and clustered the strains with the A. citrulli-type species with high posterior probability support. Based on the markers used, the Brazilian A. citrulli strains belong to a single group, which corresponds to the previously described Group I for this bacterium in the United States.

Different transcriptional responses from slow and fast growth rate strains of Listeria monocytogenes adapted to low temperature

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Ninoska eCordero

2016-03-01

Full Text Available Listeria monocytogenes has become one of the principal foodborne pathogens worldwide. The capacity of this bacterium to grow at low temperatures has opened an interesting field of study in terms of the identification and classification of new strains of L. monocytogenes with different growth capacities at low temperatures. We determined the growth rate at 8 ºC of 110 strains of L. monocytogenes isolated from different food matrices. We identified a group of slow and fast strains according to their growth rate at 8 °C and performed a global transcriptomic assay in strains previously adapted to low temperature. We then identified shared and specific transcriptional mechanisms, metabolic and cellular processes of both groups; bacterial motility was the principal process capable of differentiating the adaptation capacity of L. monocytogenes strains with different ranges of tolerance to low temperatures. Strains belonging to the fast group were less motile, which may allow these strains to achieve a greater rate of proliferation at low temperature.

Descriptions of Roseiarcus fermentans gen. nov., sp. nov., a bacteriochlorophyll a-containing fermentative bacterium related phylogenetically to alphaproteobacterial methanotrophs, and of the family Roseiarcaceae fam. nov.

Science.gov (United States)

Kulichevskaya, Irina S; Danilova, Olga V; Tereshina, Vera M; Kevbrin, Vadim V; Dedysh, Svetlana N

2014-08-01

A light-pink-pigmented, microaerophilic bacterium was obtained from a methanotrophic consortium enriched from acidic Sphagnum peat and designated strain Pf56(T). Cells of this bacterium were Gram-negative, non-motile, thick curved rods that contained a vesicular intracytoplasmic membrane system characteristic of some purple non-sulfur alphaproteobacteria. The absorption spectrum of acetone/methanol extracts of cells grown in the light showed maxima at 363, 475, 505, 601 and 770 nm; the peaks at 363 and 770 nm are characteristic of bacteriochlorophyll a. However, in contrast to purple non-sulfur bacteria, strain Pf56(T) was unable to grow phototrophically under anoxic conditions in the light. Best growth occurred on some sugars and organic acids under micro-oxic conditions by means of fermentation. The fermentation products were propionate, acetate and hydrogen. Slow chemo-organotrophic growth was also observed under fully oxic conditions. Light stimulated growth. C1 substrates were not utilized. Strain Pf56(T) grew at pH 4.0-7.0 (optimum pH 5.5-6.5) and at 15-30 °C (optimum 22-28 °C). The major cellular fatty acids were 19 : 0 cyclo ω8c and 18 : 1ω7c; quinones were represented by ubiquinone Q-10. The G+C content of the DNA was 70.0 mol%. Strain Pf56 displays 93.6-94.7 and 92.7-93.7% 16S rRNA gene sequence similarity to members of the families Methylocystaceae and Beijerinckiaceae, respectively, and belongs to a large cluster of environmental sequences retrieved from various wetlands and forest soils in cultivation-independent studies. Phenotypic, genotypic and chemotaxonomic characteristics of strain Pf56(T) suggest that it represents a novel genus and species of bacteriochlorophyll a-containing fermentative bacteria, for which the name Roseiarcus fermentans gen. nov., sp. nov. is proposed. Strain Pf56(T) ( = DSM 24875(T) = VKM B-2876(T)) is the type strain of Roseiarcus fermentans, and is also the first characterized member of a novel family

An evaluation of the wilt-causing bacterium Ralstonia solanacearum as a potential biological control agent for the alien Kahili ginger (Hedychium gardnerianum) in Hawaiian forests

Science.gov (United States)

1999-01-01

Kahili ginger (Hedychium gardnerianum) is an invasive weed in tropical forests in Hawaii and elsewhere. Bacterial wilt caused by the ginger strain of Ralstonia(=Pseudomonas) solanacearum systemically infects edible ginger (Zingiber officinale) and ornamental gingers (Hedychium spp.), causing wilt in infected plants. The suitability of R. solanacearum as a biological control agent for kahili ginger was investigated by inoculating seedlings and rooted cuttings of native forest plants, ornamental ginger, and solanaceous species to confirm host specificity. Inoculation via stem injection or root wounding with a bacterial–water suspension was followed by observation for 8 weeks. Inoculations on H. gardnerianum were then carried out in ohia-lehua (Metrosideros polymorpha) wet forests of Hawaii Volcanoes National Park to determine the bacterium's efficacy in the field. No native forest or solanaceous species developed wilt or other symptoms during the study. The bacterium caused limited infection near the inoculation site on H. coronarium, Z. zerumbet, Heliconia latispatha, and Musa sapientum. However, infection did not become systemic in any of these species, and normal growth resumed following appearance of initial symptoms. All inoculated H. gardnerianum plants developed irreversible chlorosis and severe wilting 3–4 weeks following inoculation. Systemic infection also caused death and decay of rhizomes. Most plants were completely dead 16–20 weeks following inoculation. The destructiveness of the ginger strain of R. solanacearum to edible ginger has raised questions regarding its use for biological control. However, because locations of kahili ginger infestations are often remote, the risk of contaminating edible ginger plantings is unlikely. The ability of this bacterium to cause severe disease in H. gardnerianum in the field, together with its lack of virulence in other ginger species, contributes to its potential as a biological control agent.

Draft Genome Sequence of Halomonas elongata Strain K4, an Endophytic Growth-Promoting Bacterium Enhancing Salinity Tolerance In Planta

KAUST Repository

Lafi, Feras Fawzi; Ramirez Prado, Juan Sebastian; Alam, Intikhab; Bajic, Vladimir B.; Hirt, Heribert; Saad, Maged

2016-01-01

Halomonas elongata strain K4 is an endophytic bacterial strain that was isolated from roots of Cyperus conglomeratus collected at the Red Sea coast in Thuwal, Saudi Arabia. Here, we present a draft genome sequence of this strain, highlighting a number of pathways involved in plant growth promotion under salt stress.

Draft Genome Sequence of Halomonas elongata Strain K4, an Endophytic Growth-Promoting Bacterium Enhancing Salinity Tolerance In Planta

KAUST Repository

Lafi, Feras Fawzi

2016-11-04

Halomonas elongata strain K4 is an endophytic bacterial strain that was isolated from roots of Cyperus conglomeratus collected at the Red Sea coast in Thuwal, Saudi Arabia. Here, we present a draft genome sequence of this strain, highlighting a number of pathways involved in plant growth promotion under salt stress.

Genetic Techniques for Manipulation of the Phytosterol Biotransformation Strain Mycobacterium neoaurum NRRL B-3805.

Science.gov (United States)

Loraine, Jessica K; Smith, Margaret C M

2017-01-01

Mycobacterium neoaurum is a saprophytic, soil-dwelling bacterium. The strain NRRL B-3805 converts phytosterols to androst-4-ene-3,17-dione (androstenedione; AD), a precursor of multiple C19 steroids of importance to industry. NRRL B-3805 itself is able to convert AD to other steroid products, including testosterone (Ts) and androst-1,4-diene-3,17-dione (androstadienedione; ADD). However to improve this strain for industrial use, genetic modification is a priority. In this chapter, we describe a range of genetic techniques that can be used for M. neoaurum NRRL B-3805. Methods for transformation, expression, and gene knockouts are presented as well as plasmid maintenance and stability.

Rhizoxin analogs, orfamide A and chitinase production contribute to the toxicity of Pseudomonas protegens strain Pf-5 to Drosophila melanogaster

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Pseudomonas protegens strain Pf-5 is a soil bacterium that was first described for its activity in biological control of plant diseases and has since been shown to be lethal to certain insects. Among these is the fruit fly Drosophila melanogaster, a well-established model organism for studies evalu...

Isolation and characterization of a phosphate solubilizing heavy metal tolerant bacterium from River Ganga, West Bengal, India

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Dipak Paul

2015-12-01

Full Text Available Phosphates solubilizing bacterial (PSB strains were isolated from the jute mill effluent discharge area of the Ganga river water at Bansberia, West Bengal, India. Experimental studies found that the strain KUPSB16 was effective in solubilization of phosphate with phosphate solubilization index (SI = 3.14 in Pikovskaya’s agar plates along with maximum solubilized phosphate production of 208.18 g mL-1 in broth culture. Highest drop in pH value was associated with maximum amount of phosphate solubilization by the PSB strain KUPSB16 where pH decreased to 3.53 from initial value of 7.0±0.2. The isolated PSB strains were tested for tolerance against four heavy metals such as cadmium (Cd, chromium (Cr, lead (Pb and zinc (Zn at concentrations 1-15 mM. The results showed that most of the PSB isolates grew well at low concentrations of heavy metals and their number gradually decreased as the concentration increased. Isolated PSB strain KUPSB16 was tested for its multiple metal resistances. Minimal inhibitory concentrations (MIC for Cd2+, Cr6+, Pb2+ and Zn2+ in tris-minimal broth medium were 4.2, 5.5, 3.6 and 9.5 mM respectively. The MIC values for the metals studied on agar medium was higher than in broth medium and ranged from 4.8-11.0 mM. The isolated bacterial strain KUPSB16 was subjected to morphological, physiological and biochemical characterization and identified as the species of the genus Bacillus. The phosphate solubilizing bacterium possessing the properties of multiple heavy metal tolerance in heavy metal contaminated areas might be exploited for bioremediation studies in future.

Genome Sequence of Acidovorax avenae Strain T10_61 Associated with Sugarcane Red Stripe in Argentina

Science.gov (United States)

Fontana, Cecilia A.; Bassi, Daniela; Puglisi, Edoardo; Salazar, Sergio M.; Vignolo, Graciela M.; Coccocelli, Pier S.

2016-01-01

Red stripe of sugarcane in Argentina is a bacterial disease caused by Acidovorax avenae. The genome sequence from the first isolate of this bacterium in Argentina is presented here. The draft genome of the A. avenae T10_61 strain contains 5,646,552 bp and has a G+C content of 68.6 mol%. PMID:26847889

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

Science.gov (United States)

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

2015-01-01

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

Paraburkholderia aromaticivorans sp. nov., an aromatic hydrocarbon-degrading bacterium, isolated from gasoline-contaminated soil.

Science.gov (United States)

Lee, Yunho; Jeon, Che Ok

2018-04-01

A Gram-stain-negative, facultatively aerobic, aromatic hydrocarbon-degrading bacterium, designated strain BN5 T , was isolated from gasoline-contaminated soil. Cells were motile and slightly curved rods with a single flagellum showing catalase and oxidase activities. Growth was observed at 20-37 °C (optimum, 25-30 °C), pH 3-7 (optimum, pH 5-6) and 0-2 % NaCl (optimum, 0 %). Ubiquinone-8 was the predominant respiratory quinone. The major fatty acids were C16 : 0, cyclo-C19 : 0ω8c and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phosphoamino lipid, three unidentified amino lipids and eight unidentified lipids were the identified polar lipids. The DNA G+C content was 62.93 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BN5 T formed a phylogenic lineage with members of the genus Paraburkholderia and showed the highest 16S rRNA gene sequence similarities to Paraburkholderia phytofirmans PsJN T (99.4 %), Paraburkholderia dipogonis DL7 T (98.8 %) and Paraburkholderia insulsa PNG-April T (98.8 %). The average nucleotide identity and in silico DNA-DNA hybridization (DDH) values between strain BN5 T and P. phytofirmans PsJN T were 88.5 and 36.5 %, respectively. The DDH values for strain BN5 T with P. dipogonis LMG 28415 T and P. insulsa DSM 28142 T were 41.0±4.9 % (reciprocal, 33.0±4.3 %) and 47.1±6.6 % (reciprocal, 51.7±5.4 %), respectively. Based on its physiological, chemotaxonomic and phylogenetic features, we conclude that strain BN5 T is a novel species of the genus Paraburkholderia, for which the name Paraburkholderia aromaticivorans sp. nov. is proposed. The type strain is BN5 T (=KACC 19419 T =JCM 32303 T ).

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

Characteristics of cesium accumulation in the filamentous soil bacterium Streptomyces sp. K202

International Nuclear Information System (INIS)

Kuwahara, Chikako; Fukumoto, Atsushi; Nishina, Masami; Sugiyama, Hideo; Anzai, Yojiro; Kato, Fumio

2011-01-01

A filamentous soil bacterium, strain K202, was isolated from soil where an edible mushroom (Boletopsis leucomelas) was growing and identified as belonging to the genus Streptomyces on the basis of its morphological characteristics and the presence of LL-2, 6-diaminopimelic acid. We studied the existence states of Cs and its migration from extracellular to intracellular fluid in the mycelia of Streptomyces sp. K202. The results indicated that Cs accumulated in the cells through at least 2 steps: in the first step, Cs + was immediately and non-specifically adsorbed on the negatively charged cell surface, and in the second step, this adsorbed Cs + was taken up into the cytoplasm, and a part of the Cs entering the cytoplasm was taken up by an energy-dependent transport system(s). Further, we confirmed that a part of the Cs + was taken up into the mycelia competitively with K + , because K + uptake into the intact mycelia of the strain was significantly inhibited by the presence of Cs + in the culture media. This suggested that part of the Cs is transported by the potassium transport system. Moreover, 133 Cs-NMR spectra and SEM-EDX spectra of the mycelia that accumulated Cs showed the presence of at least 2 intracellular Cs states: Cs + trapped by intercellular materials such as polyphosphate and Cs + present in a cytoplasmic pool. - Research highlights: → Cs was taken up into the cells of Streptomyces sp. K202 via 2 steps. → The existence states of Cs accumulated in strain K202 were at least 2 types. → The localized Cs in the cells would be trapped by granules such as polyphosphate. → The localized Cs in the cells might involve in Cs detoxification of strain K202.

Investigation of Antibiotic Susceptibility Pattern of Staphylococcus aureus Strains Isolated from Patients Referring to Some Treatment Centers of Qom City, Iran

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Sara Mosaei

2017-07-01

Full Text Available Background and Objectives: Staphylococcus aureus is one of the important causes of nosocomial infections. Resistance to various antibiotics, such as beta-lactams, aminoglycosides, and macrolides is one of the major problems in treatment and prevention of infections caused by this bacterium. Therefore, accurate determination of antibiotic susceptibility pattern of organisms isolated from patients can be beneficial in treatment and prevention of dangerous infections. The objective of this study was to isolate S. aureus bacterium and to determine the antibiotic susceptibility pattern of the isolated strains in patients referred to some treatment centers of Qom city. Methods: In this descriptive cross-sectional study, 340 clinical samples, were collected from September 2016 to July 2017. After isolation and primary identification of S. aureus isolates (using standard bacteriology methods, the isolated strains were confirmed by PCR technique and amplification of femA gene as a molecular diagnostic marker of S. aureus. Finally, antibiotic susceptibility pattern of the strains, was determined by disk diffusion method according to CLSI guideline. Results: Out of 340 clinical samples, 86 S. aureus strains were isolated and identified based on phenotypic characteristics. The femA gene was observed only in 45 strains (52.32% based on molecular analysis. The results of the antibiotic susceptibility test showed that the highest resistance was to penicillin (86.04% and the lowest resistance was to chloramphenicol (0%. Conclusion: The results of this study indicated that femA gene cannot by itself identify all the S. aureus strains. Also, with regard to the results of antibiogram test, it seems that antibiotic susceptibility test is necessary for S. aureus strains isolated from patients.

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

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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)).

Roseomonas chloroacetimidivorans sp. nov., a chloroacetamide herbicide-degrading bacterium isolated from activated sludge.

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Chu, Cui-Wei; Chen, Qing; Wang, Cheng-Hong; Wang, Hong-Mei; Sun, Zhong-Guan; He, Qin; He, Jian; Gu, Jin-Gang

2016-05-01

A Gram-negative, aerobic, short rod-shaped, pink-pigmented, non-motile bacterium, designated BUT-13(T), was isolated from activated sludge of an herbicide-manufacturing wastewater treatment facility in Jiangsu province, China. Growth was observed at 0-5.5 % NaCl, pH 6.0-9.0 and 12-37 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BUT-13(T) is a member of the genus Roseomonas, and shows high sequence similarities to R. pecuniae N75(T) (98.0 %) and R. rosea 173-96(T) (97.5 %), and lower (<97 %) sequence similarities to all other Roseomonas species. Chemotaxonomic analysis revealed that strain BUT-13(T) possesses Q-10 as the predominant ubiquinone; summed feature 8 (C18:1 w7c and/or C18:1 w6c; 38.8 %), C18:0 (16.6 %), C16:0 (15.2 %), summed feature 3 (C16:1 ω6c and/or C16:1 ω7; 7.9 %) and C18:1 w9c (4.7 %) as the major fatty acids. The polar lipids were found to consist of two aminolipids, a glycolipid, a phospholipid, a phosphoglycolipid, phosphatidylcholine, phosphatidylethanolamine and diphosphatidylglycerol. Strain BUT-13(T) showed low DNA-DNA relatedness with R. pecuniae N75(T) (45.2 %) and R. rosea 173-96(T) (51.2 %). The DNA G+C content was determined to be 67.6 mol%. Based on the phylogenetic analysis, DNA-DNA hybridization and chemotaxonomic analysis, as well as biochemical characteristics, strain BUT-13(T) can be clearly distinguished from all currently recognised Roseomonas species and should be classified as a novel species of the genus Roseomonas, for which the name Roseomonas chloroacetimidivorans sp. nov. is proposed. The type strain is BUT-13(T) (CCTCC AB 2015299(T) = JCM 31050(T)).

Isolation of endosulfan sulfate-degrading Rhodococcus koreensis strain S1-1 from endosulfan contaminated soil and identification of a novel metabolite, endosulfan diol monosulfate

International Nuclear Information System (INIS)

Ito, Koji; Kawashima, Fujimasa; Takagi, Kazuhiro; Kataoka, Ryota; Kotake, Masaaki; Kiyota, Hiromasa; Yamazaki, Kenichi; Sakakibara, Futa; Okada, Sanae

2016-01-01

An aerobic endosulfan sulfate-degrading bacterium, Rhodococcus koreensis strain S1-1, was isolated from soil to which endosulfan had been applied annually for more than 10 years until 2008. The strain isolated in this work reduced the concentration of endosulfan sulfate (2) from 12.25 μM to 2.11 μM during 14 d at 30 °C. Using ultra performance liquid chromatography-electrospray ionization-mass spectroscopy (UPLC-ESI-MS), a new highly water-soluble metabolite possessing six chlorine atoms was found to be endosulfan diol monosulfate (6), derived from 2 by hydrolysis of the cyclic sulfate ester ring. The structure of 6 was elucidated by chemical synthesis of the candidate derivatives and by HR-MS and UPLC-MS analyses. Therefore, it was suggested that the strain S1-1 has a new metabolic pathway of 2. In addition, 6 was expected to be less toxic among the metabolites of 1 because of its higher water-solubility. -- Highlights: •A novel endosulfan sulfate-degrading bacterium was isolated and named strain S1-1. •Strain S1-1 degraded endosulfan sulfate into a novel metabolite endosulfan diol monosulfate. •Endosulfan diol monosulfate showed higher polarity than other known metabolites of endosulfan. •We proposed the plausible metabolic pathway of endosulfan in terms of organic chemistry.

Isolation of endosulfan sulfate-degrading Rhodococcus koreensis strain S1-1 from endosulfan contaminated soil and identification of a novel metabolite, endosulfan diol monosulfate

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Ito, Koji; Kawashima, Fujimasa [Department of Applied Biology and Chemistry, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502 (Japan); Organochemicals Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604 (Japan); Takagi, Kazuhiro, E-mail: ktakagi@affrc.go.jp [Department of Applied Biology and Chemistry, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502 (Japan); Organochemicals Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604 (Japan); Kataoka, Ryota [Department of Environmental Science, University of Yamanashi, 41-4-37 Takeda, Kofu, Yamanashi (Japan); Kotake, Masaaki [Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 981-8555 (Japan); Kiyota, Hiromasa [Graduate School of Environmental & Life Science, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530 (Japan); Yamazaki, Kenichi [Organochemicals Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604 (Japan); Sakakibara, Futa [Organochemicals Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604 (Japan); The Japan Society for the Promotion of Science(JSPS), 1-8 Chiyoda-ku, Tokyo (Japan); Okada, Sanae [Department of Applied Biology and Chemistry, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502 (Japan)

2016-05-13

An aerobic endosulfan sulfate-degrading bacterium, Rhodococcus koreensis strain S1-1, was isolated from soil to which endosulfan had been applied annually for more than 10 years until 2008. The strain isolated in this work reduced the concentration of endosulfan sulfate (2) from 12.25 μM to 2.11 μM during 14 d at 30 °C. Using ultra performance liquid chromatography-electrospray ionization-mass spectroscopy (UPLC-ESI-MS), a new highly water-soluble metabolite possessing six chlorine atoms was found to be endosulfan diol monosulfate (6), derived from 2 by hydrolysis of the cyclic sulfate ester ring. The structure of 6 was elucidated by chemical synthesis of the candidate derivatives and by HR-MS and UPLC-MS analyses. Therefore, it was suggested that the strain S1-1 has a new metabolic pathway of 2. In addition, 6 was expected to be less toxic among the metabolites of 1 because of its higher water-solubility. -- Highlights: •A novel endosulfan sulfate-degrading bacterium was isolated and named strain S1-1. •Strain S1-1 degraded endosulfan sulfate into a novel metabolite endosulfan diol monosulfate. •Endosulfan diol monosulfate showed higher polarity than other known metabolites of endosulfan. •We proposed the plausible metabolic pathway of endosulfan in terms of organic chemistry.

Biodegradation of malathion by Bacillus licheniformis strain ML-1

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Khan Sara

2016-01-01

Full Text Available Malathion, a well-known organophosphate pesticide, has been used in agriculture over the last two decades for controlling pests of economically important crops. In the present study, a single bacterium, ML-1, was isolated by soil-enrichment technique and identified as Bacillus licheniformis on the basis of the 16S rRNA technique. The bacterium was grown in carbon-free minimal salt medium (MSM and was found to be very efficient in utilizing malathion as the sole source of carbon. Biodegradation experiments were performed in MSM without carbon source to determine the malathion degradation by the selected strain, and the residues of malathion were determined quantitatively using HPLC techniques. Bacillus licheniformis showed very promising results and efficiently consumed malathion as the sole carbon source via malathion carboxylesterase (MCE, and about 78% malathion was degraded within 5 days. The carboxylesterase activity was determined by using crude extract while using malathion as substrate, and the residues were determined by HPLC. It has been found that the MCE hydrolyzed 87% malathion within 96 h of incubation. Characterization of crude MCE revealed that the enzyme is robust in nature in terms of organic solvents, as it was found to be stable in various concentrations of ethanol and acetonitrile. Similarly, and it can work in a wide pH and temperature range. The results of this study highlighted the potential of Bacillus licheniformis strain ML-1 as a biodegrader that can be used for the bioremediation of malathion-contaminated soil.

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

International Nuclear Information System (INIS)

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

2007-01-01

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

A Pseudomonas putida strain genetically engineered for 1,2,3-trichloropropane bioremediation.

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Samin, Ghufrana; Pavlova, Martina; Arif, M Irfan; Postema, Christiaan P; Damborsky, Jiri; Janssen, Dick B

2014-09-01

1,2,3-Trichloropropane (TCP) is a toxic compound that is recalcitrant to biodegradation in the environment. Attempts to isolate TCP-degrading organisms using enrichment cultivation have failed. A potential biodegradation pathway starts with hydrolytic dehalogenation to 2,3-dichloro-1-propanol (DCP), followed by oxidative metabolism. To obtain a practically applicable TCP-degrading organism, we introduced an engineered haloalkane dehalogenase with improved TCP degradation activity into the DCP-degrading bacterium Pseudomonas putida MC4. For this purpose, the dehalogenase gene (dhaA31) was cloned behind the constitutive dhlA promoter and was introduced into the genome of strain MC4 using a transposon delivery system. The transposon-located antibiotic resistance marker was subsequently removed using a resolvase step. Growth of the resulting engineered bacterium, P. putida MC4-5222, on TCP was indeed observed, and all organic chlorine was released as chloride. A packed-bed reactor with immobilized cells of strain MC4-5222 degraded >95% of influent TCP (0.33 mM) under continuous-flow conditions, with stoichiometric release of inorganic chloride. The results demonstrate the successful use of a laboratory-evolved dehalogenase and genetic engineering to produce an effective, plasmid-free, and stable whole-cell biocatalyst for the aerobic bioremediation of a recalcitrant chlorinated hydrocarbon. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Construction of a stable GFP-tagged Vibrio harveyi strain for bacterial dynamics analysis of abalone infection.

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Travers, Marie-Agnès; Barbou, Annaïck; Le Goïc, Nelly; Huchette, Sylvain; Paillard, Christine; Koken, Marcel

2008-12-01

Vibrio harveyi is a bacterial marine pathogen that can cause fatal disease in a large range of vertebrates and invertebrates, including the commercially important marine gastropod, Haliotis tuberculata. Since 1997, strains of this bacterium have regularly been causing high mortalities in farmed and wild abalone populations. The way in which the pathogen enters into abalone and the disease transmission mechanisms are thus far unknown. Therefore, a pathogenic strain, ORM4, was green fluorescent protein-tagged and validated both for its growth characteristics and for its virulence as a genuine model for abalone disease. The strain allows V. harveyi quantification by flow cytometry in seawater and in abalone haemolymph as well as the in situ detection of the parasite inside abalone tissues.

Selection of the N-acylhomoserine lactone-degrading bacterium Alteromonas stellipolaris PQQ-42 and of its potential for biocontrol in aquaculture

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Marta eTorres

2016-05-01

Full Text Available The production of virulence factors by many pathogenic microorganisms depends on the intercellular communication system called quorum sensing (QS, which involves the production and release of signal molecules known as autoinducers. Based on this, new-therapeutic strategies have emerged for the treatment of a variety of infections, such as the enzymatic degradation of signalling molecules, known as quorum quenching (QQ. In this study, we present the screening of QQ activity amongst 450 strains isolated from a bivalve hatchery in Granada (Spain, and the selection of the strain PQQ-42, which degrades a wide range of N-acylhomoserine lactones (AHLs. The selected strain, identified as Alteromonas stellipolaris, degraded the accumulation of AHLs and reduced the production of protease and chitinase and swimming motility of a Vibrio species in co-cultivation experiments in vitro. In the bio-control experiment, strain PQQ-42 significantly reduced the pathogenicity of V. mediterranei VibC-Oc-097 upon the coral Oculina patagonica showing a lower degree of tissue damage (29.25±14.63 % in its presence, compared to when the coral was infected with V. mediterranei VibC-Oc-097 alone (77.53±13.22 %. Our results suggest that this AHL-degrading bacterium may have biotechnological applications in aquaculture.

Uranium biomineralization by a metal resistant Pseudomonas aeruginosa strain isolated from contaminated mine waste

Energy Technology Data Exchange (ETDEWEB)

Choudhary, Sangeeta [Department of Biotechnology, Indian Institute of Technology, Kharagpur 721302 (India); Sar, Pinaki, E-mail: sarpinaki@yahoo.com [Department of Biotechnology, Indian Institute of Technology, Kharagpur 721302 (India)

2011-02-15

Uranium biomineralization by a metal-resistant Pseudomonas aeruginosa strain isolated from uranium mine waste was characterized for its potential in bioremediation. Uranium resistance, its cellular localization and chemical nature of uranium-bacteria interaction were elucidated. Survival and uranium biomineralization from mine water were investigated using microcosm experiments. The selected bacterium showed U resistance and accumulation (maximum of 275 mg U g{sup -1} cell dry wt.) following incubation in 100 mg U L{sup -1}, pH 4.0, for 6 h. Transmission electron microscopy and X-ray diffraction analyses revealed that bioaccumulated uranium was deposited within the cell envelope as needle shaped U-phosphate compounds that attain crystallinity only at pH 4.0. A synergistic involvement of deprotonated phosphate and carboxyl moieties in facilitating bioprecipitation of uranium was evident from FTIR analysis. Based on these findings we attribute the localized U sequestration by this bacterium as innocuous complex to its possible mechanism of uranium resistance. Microcosm data confirmed that the strain can remove soluble uranium (99%) and sequester it as U oxide and phosphate minerals while maintaining its viability. The study showed that indigenous bacteria from contaminated site that can survive uranium and other heavy metal toxicity and sequester soluble uranium as biominerals could play important role in uranium bioremediation.

Nanostructural point-contact sensors for diagnostics of carcinogenic strains of Helicobacter pylori

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Г. В. Камарчук

2017-12-01

Full Text Available Background: The problem of detecting the different strains of H. pylori has gained great importance today due to the worldwide prevalence of this bacterium and its role in the pathogenesis of a number of serious gastric and extragastric diseases. However, not all H. pylori strains are aggressive and require antibiotic treatment. Thus, the question arises about the necessity of differentiating these bacterium strains with respect to their virulence factors. In accordance with the IV Maastricht Consensus Report, among the variety of ways to diagnose H. pylori infection, non-invasive methods should be given preference. Most of them are based on the analysis of gas which is exhaled by a human. Mass spectrometry, gas chromatography, and IR spectroscopy are currently the mostly used ones. However, despite the obvious advantages, these techniques have a number of disadvantages that make them difficult to use in everyday medical practice. Modern sensor devices can become an inexpensive and easy to access alternative to these technologies. Objectives: The aim of the work is to develop a new type of sensor device for selective recognition of H. pylori strains which is based on analysis of a mixture of gases exhaled by human. Such a kind of device can be designed on the basis of a point-contact gas sensor. Materials and methods: Anion-radical salts of the organic conductor TCNQ were chosen as the sensitive material for point-contact sensors. The fundamental properties of point contacts which are used in the Yanson point-contact spectroscopy make it possible to create a point-contact mesoscopic matrix on the basis of this material, which is sensitive to small concentrations of components in complex gas media. The sensors were obtained by electrochemical deposition of salts from a solvent characterized by a high vapor pressure on a textolite substrate. Gas exhaled by a human served as the substance to be analyzed. The measurements were carried out following

Desulfomusa hansenii gen. nov., sp. nov., a novel marine propionate-degrading, sulfate-reducing bacterium isolated from Zostera marina roots.

Science.gov (United States)

Finster, K; Thomsen, T R; Ramsing, N B

2001-11-01

The physiology and phylogeny of a novel sulfate-reducing bacterium, isolated from surface-sterilized roots of the marine macrophyte Zostera marina, are presented. The strain, designated P1T, was enriched and isolated in defined oxygen-free, bicarbonate-buffered, iron-reduced seawater medium with propionate as sole carbon source and electron donor and sulfate as electron acceptor. Strain P1T had a rod-shaped, slightly curved cell morphology and was motile by means of a single polar flagellum. Cells generally aggregated in clumps throughout the growth phase. High CaCl2 (10 mM) and MgCl2 (50 mM) concentrations were required for optimum growth. In addition to propionate, strain P1T utilized fumarate, succinate, pyruvate, ethanol, butanol and alanine. Oxidation of propionate was incomplete and acetate was formed in stoichiometric amounts. Strain P1T thus resembles members of the sulfate-reducing genera Desulfobulbus and Desulforhopalus, which both oxidize propionate incompletely and form acetate in addition to CO2. However, sequence analysis of the small-subunit rDNA and the dissimilatory sulfite reductase gene revealed that strain P1T was unrelated to the incomplete oxidizers Desulfobulbus and Desulforhopalus and that it constitutes a novel lineage affiliated with the genera Desulfococcus, Desulfosarcina, Desulfonema and 'Desulfobotulus'. Members of this branch, with the exception of 'Desulfobotulus sapovorans', oxidize a variety of substrates completely to CO2. Strain P1T (= DSM 12642T = ATCC 700811T) is therefore proposed as Desulfomusa hansenii gen. nov., sp. nov. Strain p1T thus illustrates the difficulty of extrapolating rRNA similarities to physiology and/or ecological function.

Comparative Genomic and Functional Analysis of 100 Lactobacillus rhamnosus Strains and Their Comparison with Strain GG

Science.gov (United States)

Pietilä, Taija E.; Järvinen, Hanna M.; Messing, Marcel; Randazzo, Cinzia L.; Paulin, Lars; Laine, Pia; Ritari, Jarmo; Caggia, Cinzia; Lähteinen, Tanja; Brouns, Stan J. J.; Satokari, Reetta; von Ossowski, Ingemar; Reunanen, Justus; Palva, Airi; de Vos, Willem M.

2013-01-01

Lactobacillus rhamnosus is a lactic acid bacterium that is found in a large variety of ecological habitats, including artisanal and industrial dairy products, the oral cavity, intestinal tract or vagina. To gain insights into the genetic complexity and ecological versatility of the species L. rhamnosus, we examined the genomes and phenotypes of 100 L. rhamnosus strains isolated from diverse sources. The genomes of 100 L. rhamnosus strains were mapped onto the L. rhamnosus GG reference genome. These strains were phenotypically characterized for a wide range of metabolic, antagonistic, signalling and functional properties. Phylogenomic analysis showed multiple groupings of the species that could partly be associated with their ecological niches. We identified 17 highly variable regions that encode functions related to lifestyle, i.e. carbohydrate transport and metabolism, production of mucus-binding pili, bile salt resistance, prophages and CRISPR adaptive immunity. Integration of the phenotypic and genomic data revealed that some L. rhamnosus strains possibly resided in multiple niches, illustrating the dynamics of bacterial habitats. The present study showed two distinctive geno-phenotypes in the L. rhamnosus species. The geno-phenotype A suggests an adaptation to stable nutrient-rich niches, i.e. milk-derivative products, reflected by the alteration or loss of biological functions associated with antimicrobial activity spectrum, stress resistance, adaptability and fitness to a distinctive range of habitats. In contrast, the geno-phenotype B displays adequate traits to a variable environment, such as the intestinal tract, in terms of nutrient resources, bacterial population density and host effects. PMID:23966868

Comparative genomic and functional analysis of 100 Lactobacillus rhamnosus strains and their comparison with strain GG.

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François P Douillard

Full Text Available Lactobacillus rhamnosus is a lactic acid bacterium that is found in a large variety of ecological habitats, including artisanal and industrial dairy products, the oral cavity, intestinal tract or vagina. To gain insights into the genetic complexity and ecological versatility of the species L. rhamnosus, we examined the genomes and phenotypes of 100 L. rhamnosus strains isolated from diverse sources. The genomes of 100 L. rhamnosus strains were mapped onto the L. rhamnosus GG reference genome. These strains were phenotypically characterized for a wide range of metabolic, antagonistic, signalling and functional properties. Phylogenomic analysis showed multiple groupings of the species that could partly be associated with their ecological niches. We identified 17 highly variable regions that encode functions related to lifestyle, i.e. carbohydrate transport and metabolism, production of mucus-binding pili, bile salt resistance, prophages and CRISPR adaptive immunity. Integration of the phenotypic and genomic data revealed that some L. rhamnosus strains possibly resided in multiple niches, illustrating the dynamics of bacterial habitats. The present study showed two distinctive geno-phenotypes in the L. rhamnosus species. The geno-phenotype A suggests an adaptation to stable nutrient-rich niches, i.e. milk-derivative products, reflected by the alteration or loss of biological functions associated with antimicrobial activity spectrum, stress resistance, adaptability and fitness to a distinctive range of habitats. In contrast, the geno-phenotype B displays adequate traits to a variable environment, such as the intestinal tract, in terms of nutrient resources, bacterial population density and host effects.

Draft Genome Sequence of the Plant Growth-Promoting Cupriavidus gilardii Strain JZ4 Isolated from the Desert Plant Tribulus terrestris

KAUST Repository

Lafi, Feras Fawzi; Bokhari, Ameerah; Alam, Intikhab; Bajic, Vladimir B.; Hirt, Heribert; Saad, Maged

2016-01-01

We isolated the plant endophytic bacterium Cupriavidus gilardii strain JZ4 from the roots of the desert plant Tribulus terrestris, collected from the Jizan region, Saudi Arabia. We report here the draft genome sequence of JZ4, together with several enzymes related to plant growth-promoting activity, environmental adaption, and antifungal activity.

Draft Genome Sequence of the Plant Growth-Promoting Cupriavidus gilardii Strain JZ4 Isolated from the Desert Plant Tribulus terrestris

KAUST Repository

Lafi, Feras Fawzi

2016-07-28

We isolated the plant endophytic bacterium Cupriavidus gilardii strain JZ4 from the roots of the desert plant Tribulus terrestris, collected from the Jizan region, Saudi Arabia. We report here the draft genome sequence of JZ4, together with several enzymes related to plant growth-promoting activity, environmental adaption, and antifungal activity.

Selection and evaluation of reference genes for RT-qPCR expression studies on Burkholderia tropica strain Ppe8, a sugarcane-associated diazotrophic bacterium grown with different carbon sources or sugarcane juice.

Science.gov (United States)

da Silva, Paula Renata Alves; Vidal, Marcia Soares; de Paula Soares, Cleiton; Polese, Valéria; Simões-Araújo, Jean Luís; Baldani, José Ivo

2016-11-01

Among the members of the genus Burkholderia, Burkholderia tropica has the ability to fix nitrogen and promote sugarcane plant growth as well as act as a biological control agent. There is little information about how this bacterium metabolizes carbohydrates as well as those carbon sources found in the sugarcane juice that accumulates in stems during plant growth. Reverse transcription quantitative PCR (RT-qPCR) can be used to evaluate changes in gene expression during bacterial growth on different carbon sources. Here we tested the expression of six reference genes, lpxC, gyrB, recA, rpoA, rpoB, and rpoD, when cells were grown with glucose, fructose, sucrose, mannitol, aconitic acid, and sugarcane juice as carbon sources. The lpxC, gyrB, and recA were selected as the most stable reference genes based on geNorm and NormFinder software analyses. Validation of these three reference genes during strain Ppe8 growth on the same carbon sources showed that genes involved in glycogen biosynthesis (glgA, glgB, glgC) and trehalose biosynthesis (treY and treZ) were highly expressed when Ppe8 was grown in aconitic acid relative to other carbon sources, while otsA expression (trehalose biosynthesis) was reduced with all carbon sources. In addition, the expression level of the ORF_6066 (gluconolactonase) gene was reduced on sugarcane juice. The results confirmed the stability of the three selected reference genes (lpxC, gyrB, and recA) during the RT-qPCR and also their robustness by evaluating the relative expression of genes involved in glycogen and trehalose biosynthesis when strain Ppe8 was grown on different carbon sources and sugarcane juice.

Genetic characterization of type A enterotoxigenic Clostridium perfringens strains.

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Agi Deguchi

2009-05-01

Full Text Available Clostridium perfringens type A, is both a ubiquitous environmental bacterium and a major cause of human gastrointestinal disease, which usually involves strains producing C. perfringens enterotoxin (CPE. The gene (cpe encoding this toxin can be carried on the chromosome or a large plasmid. Interestingly, strains carrying cpe on the chromosome and strains carrying cpe on a plasmid often exhibit different biological characteristics, such as resistance properties against heat. In this study, we investigated the genetic properties of C. perfringens by PCR-surveying 21 housekeeping genes and genes on representative plasmids and then confirmed those results by Southern blot assay (SB of five genes. Furthermore, sequencing analysis of eight housekeeping genes and multilocus sequence typing (MLST analysis were also performed. Fifty-eight C. perfringens strains were examined, including isolates from: food poisoning cases, human gastrointestinal disease cases, foods in Japan or the USA, or feces of healthy humans. In the PCR survey, eight of eleven housekeeping genes amplified positive reactions in all strains tested. However, by PCR survey and SB assay, one representative virulence gene, pfoA, was not detected in any strains carrying cpe on the chromosome. Genes involved in conjugative transfer of the cpe plasmid were also absent from almost all chromosomal cpe strains. MLST showed that, regardless of their geographic origin, date of isolation, or isolation source, chromosomal cpe isolates, i assemble into one definitive cluster ii lack pfoA and iii lack a plasmid related to the cpe plasmid. Similarly, independent of their origin, strains carrying a cpe plasmid also appear to be related, but are more variable than chromosomal cpe strains, possibly because of the instability of cpe-borne plasmid(s and/or the conjugative transfer of cpe-plasmid(s into unrelated C. perfringens strains.

Genome Sequence of the 1,4-Dioxane-Degrading Pseudonocardia dioxanivoransStrain CB1190▿

Science.gov (United States)

Sales, Christopher M.; Mahendra, Shaily; Grostern, Ariel; Parales, Rebecca E.; Goodwin, Lynne A.; Woyke, Tanja; Nolan, Matt; Lapidus, Alla; Chertkov, Olga; Ovchinnikova, Galina; Sczyrba, Alexander; Alvarez-Cohen, Lisa

2011-01-01

Pseudonocardia dioxanivoransCB1190 is the first bacterium reported to be capable of growth on the environmental contaminant 1,4-dioxane and the first member of the genus Pseudonocardiafor which there is an annotated genome sequence. Preliminary analysis of the genome (chromosome and three plasmids) indicates that strain CB1190 possesses several multicomponent monooxygenases that could be involved in the aerobic degradation of 1,4-dioxane and other environmental contaminants. PMID:21725009

Sporosalibacterium faouarense gen. nov., sp. nov., a moderately halophilic bacterium isolated from oil-contaminated soil.

Science.gov (United States)

Rezgui, Raja; Ben Ali Gam, Zouhaier; Ben Hamed, Said; Fardeau, Marie-Laure; Cayol, Jean-Luc; Maaroufi, Abderrazak; Labat, Marc

2011-01-01

A novel strictly anaerobic, moderately halophilic and mesophilic bacterium, designated strain SOL3f37(T), was isolated from a hydrocarbon-polluted soil surrounding a deep petroleum environment located in south Tunisia. Cells of strain SOL3f37(T) stained Gram-positive and were motile, straight and spore-forming. Strain SOL3f37(T) had a typical Gram-positive-type cell-wall structure, unlike the thick, multilayered cell wall of its closest relative Clostridiisalibacter paucivorans. The major fatty acids were iso-C(15 : 0) (41 %), iso-C(14 : 0) 3-OH and/or iso-C(15 : 0) dimethyl acetal (21.6 %), iso-C(13 : 0) (4.4 %), anteiso-C(15 : 0) (3.9 %) and iso-C(15 : 1) (2.8 %). Strain SOL3f37(T) grew between 20 and 48 °C (optimum 40 °C) and at pH 6.2-8.1 (optimum pH 6.9). Strain SOL3f37(T) required at least 0.5 NaCl l(-1) and grew in the presence of NaCl concentrations up to 150 g l(-1) (optimum 40 g l(-1)). Yeast extract (2 g l(-1)) was required for degradation of pyruvate, fumarate, fructose, glucose and mannitol. Also, strain SOL3f37(T) grew heterotrophically on yeast extract, peptone and bio-Trypticase, but was unable to grow on Casamino acids. Sulfate, thiosulfate, sulfite, elemental sulfur, fumarate, nitrate and nitrite were not reduced. The DNA G+C content was 30.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SOL3f37(T) was a member of the family Clostridiaceae in the order Clostridiales; strain SOL3f37(T) was related to members of various genera of the family Clostridiaceae. It exhibited highest 16S rRNA gene sequence similarity (93.4 %) with Clostridiisalibacter paucivorans 37HS60(T), 91.8 % with Thermohalobacter berrensis CTT3(T) and 91.7 % with Caloranaerobacter azorensis MV1087(T). On the basis of genotypic, phenotypic and phylogenetic data, it is suggested that strain SOL3f37(T) represents a novel species in a new genus. The name Sporosalibacterium faouarense gen. nov., sp. nov. is

Molecular phylogenetic analysis of non-sexually transmitted strains of Haemophilus ducreyi.

Science.gov (United States)

Gaston, Jordan R; Roberts, Sally A; Humphreys, Tricia L

2015-01-01

Haemophilus ducreyi, the etiologic agent of chancroid, has been previously reported to show genetic variance in several key virulence factors, placing strains of the bacterium into two genetically distinct classes. Recent studies done in yaws-endemic areas of the South Pacific have shown that H. ducreyi is also a major cause of cutaneous limb ulcers (CLU) that are not sexually transmitted. To genetically assess CLU strains relative to the previously described class I, class II phylogenetic hierarchy, we examined nucleotide sequence diversity at 11 H. ducreyi loci, including virulence and housekeeping genes, which encompass approximately 1% of the H. ducreyi genome. Sequences for all 11 loci indicated that strains collected from leg ulcers exhibit DNA sequences homologous to class I strains of H. ducreyi. However, sequences for 3 loci, including a hemoglobin receptor (hgbA), serum resistance protein (dsrA), and a collagen adhesin (ncaA) contained informative amounts of variation. Phylogenetic analyses suggest that these non-sexually transmitted strains of H. ducreyi comprise a sub-clonal population within class I strains of H. ducreyi. Molecular dating suggests that CLU strains are the most recently developed, having diverged approximately 0.355 million years ago, fourteen times more recently than the class I/class II divergence. The CLU strains' divergence falls after the divergence of humans from chimpanzees, making it the first known H. ducreyi divergence event directly influenced by the selective pressures accompanying human hosts.

Molecular phylogenetic analysis of non-sexually transmitted strains of Haemophilus ducreyi.

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Jordan R Gaston

Full Text Available Haemophilus ducreyi, the etiologic agent of chancroid, has been previously reported to show genetic variance in several key virulence factors, placing strains of the bacterium into two genetically distinct classes. Recent studies done in yaws-endemic areas of the South Pacific have shown that H. ducreyi is also a major cause of cutaneous limb ulcers (CLU that are not sexually transmitted. To genetically assess CLU strains relative to the previously described class I, class II phylogenetic hierarchy, we examined nucleotide sequence diversity at 11 H. ducreyi loci, including virulence and housekeeping genes, which encompass approximately 1% of the H. ducreyi genome. Sequences for all 11 loci indicated that strains collected from leg ulcers exhibit DNA sequences homologous to class I strains of H. ducreyi. However, sequences for 3 loci, including a hemoglobin receptor (hgbA, serum resistance protein (dsrA, and a collagen adhesin (ncaA contained informative amounts of variation. Phylogenetic analyses suggest that these non-sexually transmitted strains of H. ducreyi comprise a sub-clonal population within class I strains of H. ducreyi. Molecular dating suggests that CLU strains are the most recently developed, having diverged approximately 0.355 million years ago, fourteen times more recently than the class I/class II divergence. The CLU strains' divergence falls after the divergence of humans from chimpanzees, making it the first known H. ducreyi divergence event directly influenced by the selective pressures accompanying human hosts.

Lactococcus lactis - a diploid bacterium

DEFF Research Database (Denmark)

Michelsen, Ole; Hansen, Flemming G.; Jensen, Peter Ruhdal

the next division. Thus, the regions of the chromosome that are the last to be replicated are haploid even in fast-growing bacteria. In contrast to this general rule for bacteria, we found that Lactococcus lactis, a bacterium which has been exploited for thousands of years for the production of fermented...... milk products, is born with two complete non-replicating chromosomes. L. lactis therefore remain diploid throughout its entire life cycle....

Growth of hydroxyapatite on the cellular membrane of the bacterium Bacillus thuringiensis for the preparation of hybrid biomaterials

Energy Technology Data Exchange (ETDEWEB)

Cervantes, Eric Reyes, E-mail: onomaeric@hotmail.com [Centro de Investigación en Ciencias Microbiológicas, Benemérita Universidad Autónoma de Puebla, Prolongación de la 24 Sur y Ave San Claudio, Ciudad Universitaria, Col San Manuel, C.P. 72570 Puebla, Pue (Mexico); Torres, Maykel González, E-mail: mikegcu@fata.unam.mx [Centro de Física Aplicada y Tecnología Avanzada, Universidad Nacional Autónoma de México, Campus Juriquilla, Boulevard Juriquilla 3001, Santiago de Querétaro, Querétaro C.P. 76230 (Mexico); Muñoz, Susana Vargas, E-mail: vmsu@unam.mx [Centro de Física Aplicada y Tecnología Avanzada, Universidad Nacional Autónoma de México, Campus Juriquilla, Boulevard Juriquilla 3001, Santiago de Querétaro, Querétaro C.P. 76230 (Mexico); Rosas, Efraín Rubio, E-mail: efrainrubio@yahoo.com [Centro de Investigación en Ciencias Microbiológicas, Benemérita Universidad Autónoma de Puebla, Prolongación de la 24 Sur y Ave San Claudio, Ciudad Universitaria, Col San Manuel, C.P. 72570 Puebla, Pue (Mexico); and others

2016-01-01

This study aimed to grow hydroxyapatite (HAp) crystals on the cellular wall of the Gram-positive bacterium Bacillus thuringiensis using a bio-mimetic method. Several strains were phenotypically and genotypically characterized using multilocus sequence typing (MLST) gene markers to differentiate the strains and confirm the identity of the isolated species to guarantee that the selected species was not harmful to human health or the environment. Three of the analyzed strains were selected because they exhibited the best nucleation and growth of HAp on the bacterial surface. This innovative method to grow HAp crystals on a cellular membrane helps to elucidate the mechanisms by which osseous tissue is formed in nature. The optimum concentration for the simulated physiological fluid (SPF) was 1.5 ×. The hybrid materials were characterized by optical microscopy, atomic force microscopy (AFM), scanning electron microscopy (SEM), X-ray powder diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR). - Highlights: • HAp crystals are grown on the cellular wall of a GP bacteria Bacillus thuringiensis. • The growing was carried out by using a bio-mimetic method. • Hybrid materials were characterized with morphological and spectroscopic techniques. • The reported method allows understanding the mechanisms to produce osseous tissue. • The membrane of Bacillus thuringiensis can grow more HAp than Bacillus halodurans.

Phenotypic and Genotypic Characterization of Staphylococcus aureus Strains from Italian Dairy Products

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Stefano Morandi

2009-01-01

Full Text Available Staphylococcus aureus is a known major cause of foodborne illnesses, and milk and dairy products are often contaminated by enterotoxigenic strains of this bacterium. In the present study, 122 S. aureus isolates collected from different dairy products were characterised by phenotypic properties, by the distribution of genes encoding staphylococcal enterotoxins (sea, sec, sed, seg, seh, sei, sej, and sel and by randomly amplified polymorphic DNA PCR (RAPD-PCR. Moreover, strain resistance to vancomycin and methicillin (oxacillin was studied. The differences in the RAPD-PCR profiles obtained with the primers M13 and AP4 revealed the presence of a great genetic heterogeneity among the different S. aureus strains. Using the primer AP4 and M13, eight groups were distinguished by RAPD-PCR cluster analysis, although, except in few cases, it was not possible to correlate the isolates of different animal species (cow or ovine with the presence of se genes. None of the isolates showed resistance to vancomycin or methicillin.

Mineralization of PCBs by the genetically modified strain Cupriavidus necator JMS34 and its application for bioremediation of PCBs in soil

Energy Technology Data Exchange (ETDEWEB)

Saavedra, Juan Matias; Acevedo, Francisca; Gonzalez, Myriam; Seeger, Michael [Universidad Tecnica Federico Santa Maria, Valparaiso (Chile). Lab. de Microbiologia Molecular y Biotecnologia

2010-07-15

Polychlorobiphenyls (PCBs) are classified as ''high-priority pollutants''. Diverse microorganisms are able to degrade PCBs. However, bacterial degradation of PCBs is generally incomplete, leading to the accumulation of chlorobenzoates (CBAs) as dead-end metabolites. To obtain a microorganism able to mineralize PCB congeners, the bph locus of Burkholderia xenovorans LB400, which encodes one of the most effective PCB degradation pathways, was incorporated into the genome of the CBA-degrading bacterium Cupriavidus necator JMP134-X3. The bph genes were transferred into strain JMP134-X3, using the mini-Tn5 transposon system and biparental mating. The genetically modified derivative, C. necator strain JMS34, had only one chromosomal insertion of bph locus, which was stable under nonselective conditions. This modified bacterium was able to grow on biphenyl, 3-CBA and 4-CBA, and degraded 3,5-CBA in the presence of m-toluate. The strain JMS34 mineralized 3-CB, 4-CB, 2,4{sup '}-CB, and 3,5-CB, without accumulation of CBAs. Bioaugmentation of PCB-polluted soils with C. necator strain JMS34 and with the native B. xenovorans LB400 was monitored. It is noteworthy that strain JMS34 degraded, in 1 week, 99% of 3-CB and 4-CB and approximately 80% of 2,4{sup '}-CB in nonsterile soil, as well as in sterile soil. Additionally, the bacterial count of strain JMS34 increased by almost two orders of magnitude in PCB-polluted nonsterile soil. In contrast, the presence of native microflora reduced the degradation of these PCBs by strain LB400 from 73% (sterile soil) to approximately 50% (nonsterile soil). This study contributes to the development of improved biocatalysts for remediation of PCB-contaminated environments. (orig.)

Marinobacter lacisalsi sp. nov., a moderately halophilic bacterium isolated from the saline-wetland wildfowl reserve Fuente de Piedra in southern Spain.

Science.gov (United States)

Aguilera, Margarita; Jiménez-Pranteda, Maria L; Kharroub, Karima; González-Paredes, Ana; Durban, Juan J; Russell, Nick J; Ramos-Cormenzana, Alberto; Monteoliva-Sánchez, Mercedes

2009-07-01

A Gram-negative, non-spore-forming, motile, moderately halophilic, aerobic, rod-shaped bacterium, designated strain FP2.5(T), was isolated from the inland hypersaline lake Fuente de Piedra, a saline-wetland wildfowl reserve located in the province of Málaga in southern Spain. Strain FP2.5(T) was subjected to a polyphasic taxonomic study. It produced colonies with a light-yellow pigment. Strain FP2.5(T) grew at salinities of 3-15 % (w/v) and at temperatures of 20-40 degrees C. The pH range for growth was 5-9. Strain FP2.5(T) was able to utilize various organic acids as sole carbon and energy source. Its major fatty acids were C(16 : 0), C(18 : 1)omega9c and C(16 : 1)omega9c. The DNA G+C content was 58.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain FP2.5(T) appeared to be a member of the genus Marinobacter and clustered closely with the type strains of Marinobacter segnicrescens, Marinobacter bryozoorum and Marinobacter gudaonensis (levels of 16S rRNA gene sequence similarity of 98.1, 97.4 and 97.2 %, respectively). However, DNA-DNA relatedness between the new isolate and the type strains of its closest related Marinobacter species was low; levels of DNA-DNA relatedness between strain FP2.5(T) and M. segnicrescens LMG 23928(T), M. bryozoorum DSM 15401(T) and M. gudaonensis DSM 18066(T) were 36.3, 32.1 and 24.9 %, respectively. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data, strain FP2.5(T) is considered to represent a novel species of the genus Marinobacter, for which the name Marinobacter lacisalsi sp. nov. is proposed. The type strain is FP2.5(T) (=CECT 7297(T)=LMG 24237(T)).

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.

Canthaxanthin production with modified Mucor circinelloides strains.

Science.gov (United States)

Papp, Tamás; Csernetics, Arpád; Nagy, Gábor; Bencsik, Ottó; Iturriaga, Enrique A; Eslava, Arturo P; Vágvölgyi, Csaba

2013-06-01

Canthaxanthin is a natural diketo derivative of β-carotene primarily used by the food and feed industries. Mucor circinelloides is a β-carotene-accumulating zygomycete fungus and one of the model organisms to study the carotenoid biosynthesis in fungi. In this study, the β-carotene ketolase gene (crtW) of the marine bacterium Paracoccus sp. N81106 fused with fungal promoter and terminator regions was integrated into the M. circinelloides genome to construct stable canthaxanthin-producing strains. Different transformation methods including polyethylene glycol-mediated transformation with linear DNA fragments, restriction enzyme-mediated integration and Agrobacterium tumefaciens-mediated transformation were tested to integrate the crtW gene into the Mucor genome. Mitotic stability, site of integration and copy number of the transferred genes were analysed in the transformants, and several stable strains containing the crtW gene in high copy number were isolated. Carotenoid composition of selected transformants and effect of culturing conditions, such as temperature, carbon sources and application of certain additives in the culturing media, on their carotenoid content were analysed. Canthaxanthin-producing transformants were able to survive at higher growth temperature than the untransformed strain, maybe due to the effect of canthaxanthin on the membrane fluidity and integrity. With the application of glucose, trehalose, dihydroxyacetone and L-aspartic acid as sole carbon sources in minimal medium, the crtW-expressing M. circinelloides strain, MS12+pCA8lf/1, produced more than 200 μg/g (dry mass) of canthaxanthin.

Bacillus halodurans Strain C125 Encodes and Synthesizes Enzymes from Both Known Pathways To Form dUMP Directly from Cytosine Deoxyribonucleotides

DEFF Research Database (Denmark)

Oehlenschlæger, Christian Berg; Løvgreen, Monika Nøhr; Reinauer, Eva

2015-01-01

Analysis of the genome of Bacillus halodurans strain C125 indicated that two pathways leading from a cytosine deoxyribonucleotide to dUMP, used for dTMP synthesis, were encoded by the genome of the bacterium. The genes that were responsible, the comEB gene and the dcdB gene, encoding dCMP deaminase...

Endohyphal bacterium enhances production of indole-3-acetic acid by a foliar fungal endophyte.

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Michele T Hoffman

Full Text Available Numerous plant pathogens, rhizosphere symbionts, and endophytic bacteria and yeasts produce the important phytohormone indole-3-acetic acid (IAA, often with profound effects on host plants. However, to date IAA production has not been documented among foliar endophytes -- the diverse guild of primarily filamentous Ascomycota that live within healthy, above-ground tissues of all plant species studied thus far. Recently bacteria that live within hyphae of endophytes (endohyphal bacteria have been detected, but their effects have not been studied previously. Here we show not only that IAA is produced in vitro by a foliar endophyte (here identified as Pestalotiopsis aff. neglecta, Xylariales, but that IAA production is enhanced significantly when the endophyte hosts an endohyphal bacterium (here identified as Luteibacter sp., Xanthomonadales. Both the endophyte and the endophyte/bacterium complex appear to rely on an L-tryptophan dependent pathway for IAA synthesis. The bacterium can be isolated from the fungus when the symbiotic complex is cultivated at 36°C. In pure culture the bacterium does not produce IAA. Culture filtrate from the endophyte-bacterium complex significantly enhances growth of tomato in vitro relative to controls and to filtrate from the endophyte alone. Together these results speak to a facultative symbiosis between an endophyte and endohyphal bacterium that strongly influences IAA production, providing a new framework in which to explore endophyte-plant interactions.

Removal of Chlorpyrifos by Water Hyacinth (Eichhornia crassipes) and the Role of a Plant-Associated Bacterium.

Science.gov (United States)

Anudechakul, Choochai; Vangnai, Alisa S; Ariyakanon, Naiyanan

2015-01-01

The objective of this research was to study the efficiency of water hyacinth (Eichhornia crassipes) and the role of any plant-associated bacteria in removing chlorpyrifos from water. The relative growth rate (RGR) of E. crassipes in the presence of 0.1 mg/L chlorpyrifos was not significantly different from that in its absence and only slightly decreased at concentrations of 0.5 and 1.0 mg/L by ∼1.1- and ∼1.2-fold, respectively, with an observed dry weight based RGRDW for E. crassipes of 0.036-0.041 mg/g/d. The removal rate constants of chlorpyrifos in the absence of plants were low at 3.52, 2.29 and 1.84 h(-1) for concentrations of 0.1, 0.5 and 1.0 mg/L, respectively, but were some 3.89- to 4.87-fold higher in the presence of E. crassipes. Chlorpyrifos removal was markedly facilitated by the presence of a root-associated bacterium, preliminarily identified as Acinetobacter sp. strain WHA. The interaction of E. crassipes and Acinetobacter sp. strain WHA provide an efficient and ecological alternative to accelerate the removal and degradation of chlorpyrifos pollution from aquatic systems including wastewater.

Genome Sequence of Lactobacillus saerimneri 30a (Formerly Lactobacillus sp. Strain 30a), a Reference Lactic Acid Bacterium Strain Producing Biogenic Amines

NARCIS (Netherlands)

Romano, Andrea; Trip, Hein; Campbell-Sills, Hugo; Bouchez, Olivier; Sherman, David; Lolkema, Juke S.; Lucas, Patrick M.

2013-01-01

Lactobacillus sp. strain 30a (Lactobacillus saerimneri) produces the biogenic amines histamine, putrescine, and cadaverine by decarboxylating their amino acid precursors. We report its draft genome sequence (1,634,278 bases, 42.6% G+C content) and the principal findings from its annotation, which

Isolation and identification of a bacterium from marine shrimp digestive tract: A new degrader of starch and protein

Science.gov (United States)

Li, Jiqiu; Tan, Beiping; Mai, Kangsen

2011-09-01

It is a practical approach to select candidate probiotic bacterial stains on the basis of their special traits. Production of digestive enzyme was used as a trait to select a candidate probiotic bacterial strain in this study. In order to select a bacterium with the ability to degrade both starch and protein, an ideal bacterial strain STE was isolated from marine shrimp ( Litopenaeus vannamei) intestines by using multiple selective media. The selected isolate STE was identified on the basis of its morphological, physiological, and biochemical characteristics as well as molecular analyses. Results of degradation experiments confirmed the ability of the selected isolate to degrade both starch and casein. The isolate STE was aerobic, Gram-negative, rod-shaped, motile and non-spore-forming, and had catalase and oxidase activities but no glucose fermentation activity. Among the tested carbon/nitrogen sources, only Tween40, alanyl-glycine, aspartyl-glycine, and glycyl-l-glutamic acid were utilized by the isolate STE. Results of homology comparison analyses of the 16S rDNA sequences showed that the isolate STE had a high similarity to several Pseudoalteromonas species and, in the phylogenetic tree, grouped with P. ruthenica with maximum bootstrap support (100%). In conclusion, the isolate STE was characterized as a novel strain belonging to the genus Pseudoalteromonas. This study provides a further example of a probiotic bacterial strain with specific characteristics isolated from the host gastrointestinal tract.

Genome sequence of Ochrobactrum anthropi strain SUBG007, a plant pathogen and potential xenobiotic compounds degradation bacterium

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Kiran S. Chudasama

2017-03-01

Full Text Available Ochrobactrum anthropi SUBG007 was isolated from the fruit of Prunus dulcis in Rajkot (22.30°N, 70.78°E, Gujarat, India. Here we present the 4.37 Mb genome sequence strain SUBG007, which may provide the genetic information for the application in environment pollution degradation and agriculture field. The strain also posses many genes cluster which involved in production of important secondary metabolites. The nucleotide sequence of this genome was deposited into NCBI GenBank under the accession LUAY00000000.

Complete genome sequence of 'Thermobaculum terrenum' type strain (YNP1).

Science.gov (United States)

Kiss, Hajnalka; Cleland, David; Lapidus, Alla; Lucas, Susan; Del Rio, Tijana Glavina; Nolan, Matt; Tice, Hope; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D; Lu, Megan; Brettin, Thomas; Detter, John C; Göker, Markus; Tindall, Brian J; Beck, Brian; McDermott, Timothy R; Woyke, Tanja; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Cheng, Jan-Fang

2010-10-27

'Thermobaculum terrenum' Botero et al. 2004 is the sole species within the proposed genus 'Thermobaculum'. Strain YNP1(T) is the only cultivated member of an acid tolerant, extremely thermophilic species belonging to a phylogenetically isolated environmental clone group within the phylum Chloroflexi. At present, the name 'Thermobaculum terrenum' is not yet validly published as it contravenes Rule 30 (3a) of the Bacteriological Code. The bacterium was isolated from a slightly acidic extreme thermal soil in Yellowstone National Park, Wyoming (USA). Depending on its final taxonomic allocation, this is likely to be the third completed genome sequence of a member of the class Thermomicrobia and the seventh type strain genome from the phylum Chloroflexi. The 3,101,581 bp long genome with its 2,872 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Pseudomonas pseudoalcaligenes CECT5344, a cyanide-degrading bacterium with by-product (polyhydroxyalkanoates) formation capacity.

Science.gov (United States)

Manso Cobos, Isabel; Ibáñez García, María Isabel; de la Peña Moreno, Fernando; Sáez Melero, Lara Paloma; Luque-Almagro, Víctor Manuel; Castillo Rodríguez, Francisco; Roldán Ruiz, María Dolores; Prieto Jiménez, María Auxiliadora; Moreno Vivián, Conrado

2015-06-10

Cyanide is one of the most toxic chemicals produced by anthropogenic activities like mining and jewelry industries, which generate wastewater residues with high concentrations of this compound. Pseudomonas pseudoalcaligenes CECT5344 is a model microorganism to be used in detoxification of industrial wastewaters containing not only free cyanide (CN(-)) but also cyano-derivatives, such as cyanate, nitriles and metal-cyanide complexes. Previous in silico analyses suggested the existence of genes putatively involved in metabolism of short chain length (scl-) and medium chain length (mcl-) polyhydroxyalkanoates (PHAs) located in three different clusters in the genome of this bacterium. PHAs are polyesters considered as an alternative of petroleum-based plastics. Strategies to optimize the bioremediation process in terms of reducing the cost of the production medium are required. In this work, a biological treatment of the jewelry industry cyanide-rich wastewater coupled to PHAs production as by-product has been considered. The functionality of the pha genes from P. pseudoalcaligenes CECT5344 has been demonstrated. Mutant strains defective in each proposed PHA synthases coding genes (Mpha(-), deleted in putative mcl-PHA synthases; Spha(-), deleted in the putative scl-PHA synthase) were generated. The accumulation and monomer composition of scl- or mcl-PHAs in wild type and mutant strains were confirmed by gas chromatography-mass spectrometry (GC-MS). The production of PHAs as by-product while degrading cyanide from the jewelry industry wastewater was analyzed in batch reactor in each strain. The wild type and the mutant strains grew at similar rates when using octanoate as the carbon source and cyanide as the sole nitrogen source. When cyanide was depleted from the medium, both scl-PHAs and mcl-PHAs were detected in the wild-type strain, whereas scl-PHAs or mcl-PHAs were accumulated in Mpha(-) and Spha(-), respectively. The scl-PHAs were identified as homopolymers of 3

Efficacy of the Non-Pathogenic Agrobacterium Strains K84 and K1026 against Crown Gall in Tunisia

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A. Rhouma

2004-08-01

Full Text Available The non-pathogenic Agrobacterium radiobacter strain K84 and its genetically modified (GEM strain K1026 were tested for their effectiveness against local Tunisian strains and two reference strains (C58 and B6 of the crown gall bacterium Agrobacterium tumefaciens. Tests in planta were carried out on herbaceous plants (tomato and tagetes and on some sensitive rootstocks (bitter almond, peach almond hybrid GF677 and quince BA29. In vitro tests showed that both K84 and K1026 were effective and that the difference between these strains was not statistically significant. On tomato and tagetes, strain K84 was effective against all crown gall isolates with the exception of the A. tumefaciens reference strain B6. GEM strain K1026 was very effective against all isolates from Tunisia and against the reference strains. Both antagonistic strains significantly reduced the percentage of galled plants as well as the number of galls per plant. Under field conditions, both antagonists controlled crown gall effectively. Best results were obtained on the bitter almond-tree rootstock. Antagonist effectiveness was less evident on quince BA29 and peach almond GF677 rootstocks. The genetically modified strain K1026 is of interest in controlling crown gall disease in Tunisia.

Isolation of Dickeya dadantii strains from potato disease and biocontrol by their bacteriophages

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Abbas Soleimani-Delfan

2015-09-01

Full Text Available One of the most economically important bacterial pathogens of plants and plant products is Dickeya dadantii. This bacterium causes soft rot disease in tubers and other parts of the potato and other plants of the Solanaceae family. The application of restricted host range bacteriophages as biocontrol agents has recently gained widespread interest. This study purposed to isolate the infectious agent of the potato and evaluate its biocontrol by bacteriophages. Two phytopathogenic strains were isolated from infected potatoes, identified based on biochemical and 16S rRNA gene sequencing, and submitted to GenBank as D. dadantii strain pis3 (accession no. HQ423668 and D. dadantii strain sip4 (accession no. HQ423669. Their bacteriophages were isolated from Caspian Sea water by enriching the water filtrate with D. dadantii strains as hosts using spot or overlay methods. On the basis of morphotypes, the isolated bacteriophages were identified as members of the Myoviridae and Siphoviridae families and could inhibit the growth of antibiotic resistant D. dadantii strains in culture medium. Moreover, in Dickeya infected plants treated with bacteriophage, no disease progression was detected. No significant difference was seen between phage-treated and control plants. Thus, isolated bacteriophages can be suggested for the biocontrol of plant disease caused by Dickeya strains.

Carboxydobrachium pacificum gen. nov., sp. nov., a new anaerobic, thermophilic, CO-utilizing marine bacterium from Okinawa Trough.

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Sokolova, T G; González, J M; Kostrikina, N A; Chernyh, N A; Tourova, T P; Kato, C; Bonch-Osmolovskaya, E A; Robb, F T

2001-01-01

A new anaerobic, thermophilic, CO-utilizing marine bacterium, strain JMT, was isolated from a submarine hot vent in Okinawa Trough. Cells of strain JMT were non-motile thin straight rods, sometimes branching, with a cell wall of the Gram-positive type, surrounded with an S-layer. Chains of three to five cells were often observed. The isolate grew chemolithotrophically on CO, producing equimolar quantities of H2 and CO2 (according to the equation CO+H2O-->CO2+H2) and organotrophically on peptone, yeast extract, starch, cellobiose, glucose, galactose, fructose and pyruvate, producing H2, acetate and CO2. Growth was observed from 50 to 80 degrees C with an optimum at 70 degrees C. The optimum pH was 6.8-7.1. The optimum concentration of sea salts in the medium was 20.5-25.5 g l(-1). The generation time under optimal conditions was 7.1 h. The DNA G+C content was 33 mol %. Growth of isolate JMT was not inhibited by penicillin, but ampicillin, streptomycin, kanamycin and neomycin completely inhibited growth. The results of 16S rDNA sequence analysis revealed that strain JMT belongs to the Thermoanaerobacter phylogenetic group within the Bacillus-Clostridium subphylum of Gram-positive bacteria but represents a separate branch of this group. On the basis of morphological and physiological features and phylogenetic data, this isolate should be assigned to a new genus, for which the name Carboxydobrachium is proposed. The type species is Carboxydobrachium pacificum; the type strain is JMT (= DSM 12653T).

Influence of Environmental Parameters on Trichoderma Strains with Biocontrol Potential

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Zsuzsanna Antal

2003-01-01

Full Text Available Several mycoparasitic strains belonging to the filamentous fungal genus Trichoderma are promising candidates for the biological control of plant pathogenic fungi. When planning the application of antagonistic Trichoderma strains for the purposes of biological control, it is very important to consider the environmental parameters affecting the biocontrol agents in the soil. A series of abiotic and biotic environmental parameters has an influence on the biocontrol efficacy of Trichoderma. Some important parameters to be considered are the effects of temperature, water potential and pH, and the presence of pesticides, metal ions and antagonistic bacteria in the soil. Most of the Trichoderma strains are mesophilic. Low temperatures in winter may cause a problem during biological control by influencing the activity of the biocontrol agents. Another problem emerging during the application of Trichoderma strains as biocontrol agents is that they cannot tolerate dry conditions, however, we may need biocontrol agents against plant pathogenic fungi which are able to grow and cause disease even in dry soils. The pH characteristics of the soil also belong to the most important environmental parameters affecting the activities of mycoparasitic Trichoderma strains. Within the frames of a complex integrated plant protection strategy, we may have to combine Trichoderma strains with chemical pesticides or metal compounds, therefore it is important to collect information about the effects of pesticides and metal ions on the biocontrol strains. Antagonistic soil bacteria may also have negative effects on the biocontrol abilities of Trichoderma strains, therefore it may be advantageous if a biocontrol strain possesses bacterium- degrading abilities as well. This review will discuss the literature about the influence of temperature, water potential, pH, pesticides, metal ions and antagonistic bacteria on mycoparasitic Trichoderma strains including the results of our

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

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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 ).

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

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Abd Rahman, Raja Noor Zaliha Raja; Leow, Thean Chor; Salleh, Abu Bakar; Basri, Mahiran

2007-08-10

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 degrees 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. 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 degrees C and was also stable up to 60 degrees 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). Strain T1T was able to secrete extracellular thermostable lipase into culture

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

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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

Draft Genome Sequence of Streptomyces sp. Strain Wb2n-11, a Desert Isolate with Broad-Spectrum Antagonism against Soilborne Phytopathogens

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Köberl, Martina; White, Richard A.; Erschen, Sabine; El-Arabi, Tarek F.; Jansson, Janet K.; Berg, Gabriele

2015-08-06

Streptomyces sp. strain Wb2n-11, isolated from native desert soil, exhibited broad-spectrum antagonism against plant pathogenic fungi, bacteria and nematodes. The 8.2 Mb draft genome reveals genes putatively responsible for its promising biocontrol activity and genes which enable the soil bacterium to directly interact beneficially with plants.

Genome sequence of the moderately halophilic bacterium Salinicoccus carnicancri type strain Crm(T) (= DSM 23852(T)).

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Hyun, Dong-Wook; Whon, Tae Woong; Cho, Yong-Joon; Chun, Jongsik; Kim, Min-Soo; Jung, Mi-Ja; Shin, Na-Ri; Kim, Joon-Yong; Kim, Pil Soo; Yun, Ji-Hyun; Lee, Jina; Oh, Sei Joon; Bae, Jin-Woo

2013-01-01

Salinicoccus carnicancri Jung et al. 2010 belongs to the genus Salinicoccus in the family Staphylococcaceae. Members of the Salinicoccus are moderately halophilic and originate from various salty environments. The halophilic features of the Salinicoccus suggest their possible uses in biotechnological applications, such as biodegradation and fermented food production. However, the genus Salinicoccus is poorly characterized at the genome level, despite its potential importance. This study presents the draft genome sequence of S. carnicancri strain Crm(T) and its annotation. The 2,673,309 base pair genome contained 2,700 protein-coding genes and 78 RNA genes with an average G+C content of 47.93 mol%. It was notable that the strain carried 72 predicted genes associated with osmoregulation, which suggests the presence of beneficial functions that facilitate growth in high-salt environments.

Preparation of genomic DNA from a single species of uncultured magnetotactic bacterium by multiple-displacement amplification.

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Arakaki, Atsushi; Shibusawa, Mie; Hosokawa, Masahito; Matsunaga, Tadashi

2010-03-01

Magnetotactic bacteria comprise a phylogenetically diverse group that is capable of synthesizing intracellular magnetic particles. Although various morphotypes of magnetotactic bacteria have been observed in the environment, bacterial strains available in pure culture are currently limited to a few genera due to difficulties in their enrichment and cultivation. In order to obtain genetic information from uncultured magnetotactic bacteria, a genome preparation method that involves magnetic separation of cells, flow cytometry, and multiple displacement amplification (MDA) using phi29 polymerase was used in this study. The conditions for the MDA reaction using samples containing 1 to 100 cells were evaluated using a pure-culture magnetotactic bacterium, "Magnetospirillum magneticum AMB-1," whose complete genome sequence is available. Uniform gene amplification was confirmed by quantitative PCR (Q-PCR) when 100 cells were used as a template. This method was then applied for genome preparation of uncultured magnetotactic bacteria from complex bacterial communities in an aquatic environment. A sample containing 100 cells of the uncultured magnetotactic coccus was prepared by magnetic cell separation and flow cytometry and used as an MDA template. 16S rRNA sequence analysis of the MDA product from these 100 cells revealed that the amplified genomic DNA was from a single species of magnetotactic bacterium that was phylogenetically affiliated with magnetotactic cocci in the Alphaproteobacteria. The combined use of magnetic separation, flow cytometry, and MDA provides a new strategy to access individual genetic information from magnetotactic bacteria in environmental samples.

Uranium biomineralization by a metal resistant Pseudomonas aeruginosa strain isolated from contaminated mine waste.

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Choudhary, Sangeeta; Sar, Pinaki

2011-02-15

Uranium biomineralization by a metal-resistant Pseudomonas aeruginosa strain isolated from uranium mine waste was characterized for its potential in bioremediation. Uranium resistance, its cellular localization and chemical nature of uranium-bacteria interaction were elucidated. Survival and uranium biomineralization from mine water were investigated using microcosm experiments. The selected bacterium showed U resistance and accumulation (maximum of 275 mg U g(-1)cell dry wt.) following incubation in 100 mg U L(-1), pH 4.0, for 6 h. Transmission electron microscopy and X-ray diffraction analyses revealed that bioaccumulated uranium was deposited within the cell envelope as needle shaped U-phosphate compounds that attain crystallinity only at pH 4.0. A synergistic involvement of deprotonated phosphate and carboxyl moieties in facilitating bioprecipitation of uranium was evident from FTIR analysis. Based on these findings we attribute the localized U sequestration by this bacterium as innocuous complex to its possible mechanism of uranium resistance. Microcosm data confirmed that the strain can remove soluble uranium (99%) and sequester it as U oxide and phosphate minerals while maintaining its viability. The study showed that indigenous bacteria from contaminated site that can survive uranium and other heavy metal toxicity and sequester soluble uranium as biominerals could play important role in uranium bioremediation. Copyright © 2010 Elsevier B.V. All rights reserved.

Comparative proteomic analysis of pathogenic and non-pathogenic strains from the swine pathogen Mycoplasma hyopneumoniae

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Klein Cátia S

2009-12-01

Full Text Available Abstract Background Mycoplasma hyopneumoniae is a highly infectious swine pathogen and is the causative agent of enzootic pneumonia (EP. Following the previous report of a proteomic survey of the pathogenic 7448 strain of swine pathogen, Mycoplasma hyopneumoniae, we performed comparative protein profiling of three M. hyopneumoniae strains, namely the non-pathogenic J strain and the two pathogenic strains 7448 and 7422. Results In 2DE comparisons, we were able to identify differences in expression levels for 67 proteins, including the overexpression of some cytoadherence-related proteins only in the pathogenic strains. 2DE immunoblot analyses allowed the identification of differential proteolytic cleavage patterns of the P97 adhesin in the three strains. For more comprehensive protein profiling, an LC-MS/MS strategy was used. Overall, 35% of the M. hyopneumoniae genome coding capacity was covered. Partially overlapping profiles of identified proteins were observed in the strains with 81 proteins identified only in one strain and 54 proteins identified in two strains. Abundance analysis of proteins detected in more than one strain demonstrates the relative overexpression of 64 proteins, including the P97 adhesin in the pathogenic strains. Conclusions Our results indicate the physiological differences between the non-pathogenic strain, with its non-infective proliferate lifestyle, and the pathogenic strains, with its constitutive expression of adhesins, which would render the bacterium competent for adhesion and infection prior to host contact.

Complete Genome Sequence of Lactobacillus salivarius CECT 5713, a Probiotic Strain Isolated from Human Milk and Infant Feces▿

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Jiménez, Esther; Martín, Rocío; Maldonado, Antonio; Martín, Virginia; Gómez de Segura, Aranzazu; Fernández, Leonides; Rodríguez, Juan M.

2010-01-01

Lactobacillus salivarius is a homofermentative lactic acid bacterium and is frequently isolated from mucosal surfaces of healthy humans. L. salivarius CECT 5713, a strain isolated simultaneously from breast milk and infant feces of a healthy mother-infant pair, has immunomodulatory, anti-inflammatory, and anti-infectious properties, as revealed by several in vitro and in vivo assays. Here, we report its complete and annotated genome sequence. PMID:20675488

Stable transformation of the gram-positive phytopathogenic bacterium Clavibacter michiganensis subsp. sepedonicus with several cloning vectors.

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Laine, M J; Nakhei, H; Dreier, J; Lehtilä, K; Meletzus, D; Eichenlaub, R; Metzler, M C

1996-05-01

In this paper we describe transformation of Clavibacter michiganensis subsp. sepedonicus, the potato ring rot bacterium, with plasmid vectors. Three of the plasmids used, pDM100, pDM302, and pDM306, contain the origin of replication from pCM1, a native plasmid of C. michiganensis subsp. michiganensis. We constructed two new cloning vectors, pHN205 and pHN216, by using the origin of replication of pCM2, another native plasmid of C. michiganensis subsp. michiganensis. Plasmids pDM302, pHN205, and pHN216 were stably maintained without antibiotic selection in various strains of C. michiganensis subsp. sepedonicus. We observed that for a single plasmid, different strains of C. michiganensis subsp. sepedonicus showed significantly different transformation efficiencies. We also found unexplained strain-to-strain differences in stability with various plasmid constructions containing different arrangements of antibiotic resistance genes and origins of replication. We examined the effect of a number of factors on transformation efficiency. The best transformation efficiencies were obtained when C. michiganensis subsp. sepedonicus cells were grown on DM agar plates, harvested during the early exponential growth phase, and used fresh (without freezing) for electroporation. The maximal transformation efficiency obtained was 4.6 x 10(4) CFU/microgram of pHN216 plasmid DNA. To demonstrate the utility of this transformation system, we cloned a beta-1,4-endoglucanase-encoding gene from C. michiganensis subsp. sepedonicus into pHN216. When this construction, pHN216:C8, was electroporated into competent cells of a cellulase-deficient mutant, it restored cellulase production to almost wild-type levels.

Initiation of chromosomal replication in predatory bacterium Bdellovibrio bacteriovorus

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Lukasz Makowski

2016-11-01

Full Text Available Bdellovibrio bacteriovorus is a small Gram-negative predatory bacterium that attacks other Gram-negative bacteria, including many animal, human, and plant pathogens. This bacterium exhibits a peculiar biphasic life cycle during which two different types of cells are produced: non-replicating highly motile cells (the free-living phase and replicating cells (the intracellular-growth phase. The process of chromosomal replication in B. bacteriovorus must therefore be temporally and spatially regulated to ensure that it is coordinated with cell differentiation and cell cycle progression. Recently, B. bacteriovorus has received considerable research interest due to its intriguing life cycle and great potential as a prospective antimicrobial agent. Although we know that chromosomal replication in bacteria is mainly regulated at the initiation step, no data exists about this process in B. bacteriovorus. We report the first characterization of key elements of initiation of chromosomal replication – DnaA protein and oriC region from the predatory bacterium, B. bacteriovorus. In vitro studies using different approaches demonstrate that the B. bacteriovorus oriC (BdoriC is specifically bound and unwound by the DnaA protein. Sequence comparison of the DnaA-binding sites enabled us to propose a consensus sequence for the B. bacteriovorus DnaA box (5’-NN(A/TTCCACA-3’. Surprisingly, in vitro analysis revealed that BdoriC is also bound and unwound by the host DnaA proteins (relatively distantly related from B. bacteriovorus. We compared the architecture of the DnaA–oriC complexes (orisomes in homologous (oriC and DnaA from B. bacteriovorus and heterologous (BdoriC and DnaA from prey, E. coli or P. aeruginosa systems. This work provides important new entry points toward improving our understanding of the initiation of chromosomal replication in this predatory bacterium.

Metabolism of isoeugenol via isoeugenol-diol by a newly isolated strain of Bacillus subtilis HS8.

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Zhang, Yongmei; Xu, Ping; Han, Shuai; Yan, Haiqin; Ma, Cuiqing

2006-12-01

A bacterium designated as HS8 was newly isolated from soil based on its ability to degrade isoeugenol. The strain was identified as Bacillus subtilis according to its 16S rDNA sequence analysis and biochemical characteristics. The metabolic pathway for the degradation of isoeugenol was examined. Isoeugenol-diol, for the first time, was detected as an intermediate from isoeugenol to vanillin by a bacterial strain. Isoeugenol was converted to vanillin via isoeugenol-diol, and vanillin was then metabolized via vanillic acid to guaiacol by strain HS8. These metabolites, vanillin, vanillic acid, and guaiacol, are all valuable aromatic compounds in flavor production. At the same time, the bipolymerization of isoeugenol was observed, which produced dehydrodiisoeugenol and decreased the vanillin yield. High level of vanillic acid decarboxylase activity was detected in cell-free extract. These findings provided a detailed profile of isoeugenol metabolism by a B. subtilis strain for the first time, which would improve the production of valuable aromatic compounds by biotechnology.

Hsp90 Is Essential under Heat Stress in the Bacterium Shewanella oneidensis

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Flora Ambre Honoré

2017-04-01

Full Text Available The Hsp90 chaperone is essential in eukaryotes and activates a large array of client proteins. In contrast, its role is still elusive in bacteria, and only a few Hsp90 bacterial clients are known. Here, we found that Hsp90 is essential in the model bacterium Shewanella oneidensis under heat stress. A genetic screen for Hsp90 client proteins identified TilS, an essential protein involved in tRNA maturation. Overexpression of TilS rescued the growth defect of the hsp90 deletion strain under heat stress. In vivo, the activity and the amount of TilS were significantly reduced in the absence of Hsp90 at high temperature. Furthermore, we showed that Hsp90 interacts with TilS, and Hsp90 prevents TilS aggregation in vitro at high temperature. Together, our results indicate that TilS is a client of Hsp90 in S. oneidensis. Therefore, our study links the essentiality of bacterial Hsp90 at high temperature with the identification of a client.

Kinetics of molybdenum reduction to molybdenum blue by Bacillus sp. strain A.rzi.

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Othman, A R; Bakar, N A; Halmi, M I E; Johari, W L W; Ahmad, S A; Jirangon, H; Syed, M A; Shukor, M Y

2013-01-01

Molybdenum is very toxic to agricultural animals. Mo-reducing bacterium can be used to immobilize soluble molybdenum to insoluble forms, reducing its toxicity in the process. In this work the isolation of a novel molybdate-reducing Gram positive bacterium tentatively identified as Bacillus sp. strain A.rzi from a metal-contaminated soil is reported. The cellular reduction of molybdate to molybdenum blue occurred optimally at 4 mM phosphate, using 1% (w/v) glucose, 50 mM molybdate, between 28 and 30 °C and at pH 7.3. The spectrum of the Mo-blue product showed a maximum peak at 865 nm and a shoulder at 700 nm. Inhibitors of bacterial electron transport system (ETS) such as rotenone, sodium azide, antimycin A, and potassium cyanide could not inhibit the molybdenum-reducing activity. At 0.1 mM, mercury, copper, cadmium, arsenic, lead, chromium, cobalt, and zinc showed strong inhibition on molybdate reduction by crude enzyme. The best model that fitted the experimental data well was Luong followed by Haldane and Monod. The calculated value for Luong's constants p max, K(s), S(m), and n was 5.88 μmole Mo-blue hr(-1), 70.36 mM, 108.22 mM, and 0.74, respectively. The characteristics of this bacterium make it an ideal tool for bioremediation of molybdenum pollution.

Production of an extracellular thermohalophilic lipase from a moderately halophilic bacterium, Salinivibrio sp. strain SA-2.

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Amoozegar, Mohammad Ali; Salehghamari, Ensieh; Khajeh, Khosro; Kabiri, Mahbube; Naddaf, Saied

2008-06-01

Fifty strains of moderately halophilic bacteria were isolated from various salty environments in Iran. A strain designated as SA-2 was shown to be the best producer of extracellular lipase and was selected for further studies. Biochemical and physiological characterization along with 16S rDNA sequence analysis placed SA-2 in the genus Salinivibrio. The optimum salt, pH, temperature and aeration for enzyme production were 0.1 M KCl, pH 8, 35 degrees C and 150 rpm, respectively. The enzyme production was synchronized bacterial growth and reached a maximum level during the early-stationary phase in the basal medium containing 1 M NaCl. Triacylglycerols enhanced lipase production, while carbohydrates had inhibitory effects on it. The maximum lipase activity was obtained at pH 7.5, 50 degrees C and CaCl(2) concentration of 0.01 M. The enzyme was stable at pH range of 7.5-8 and retained 90% of its activity at 80 degrees C for 30 min. Different concentrations of NaNO(3), Na(2)SO(4), KCl and NaCl had no affect on lipase stability for 3 h. These results suggest that the lipase secreted by Salinivibrio sp. strain SA-2 is industrially important from the perspective of its tolerance to a broad temperature range, its moderate thermoactivity and its high tolerance to a wide range of salt concentrations (0-3 M NaCl).

A putative marker for human pathogenic strains of Anaplasma phagocytophilum correlates with geography and host, but not human tropism.

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Foley, Janet; Stephenson, Nicole; Cubilla, Michelle Pires; Qurollo, Barbara; Breitschwerdt, Edward B

2016-03-01

Anaplasma phagocytophilum is an Ixodes species tick-transmitted bacterium that is capable of infecting a variety of host species, although there is a diversity of bacterial strains with differing host tropism. Recent analysis of A. phagocytophilum strains suggested that "drhm", a gene locus designated "distantly related to human marker" (drhm), which was predicted to be an integral membrane protein with possible transporter functions was not present in available canine and human isolates. By assessing 117 strains from 14 host species from across the US, we extended this analysis. Phylogenetic clades were associated with geography, but not host species. Additionally, a virulent clade that lacks drhm and infects dogs, horses, and humans in northeastern US was identified. Copyright © 2015 Elsevier GmbH. All rights reserved.

[Clinical significance of infection with cag A and vac A positive Helicobacter pylori strains].

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Sokić-Milutinović, Aleksandra; Todorović, Vera; Milosavljević, Tomica

2004-01-01

Clinical relevance of infection with different Helicobacter pylori strains was reviewed in this paper. Helicobacter pylori (H. pylori) infection plays a role in pathogenesis of chronic gastritis, peptic ulcer disease, gastric adenocarcinoma and MALT lymphoma. Extragastric manifestations of H. pylori infection most probably include acne rosacea and chronic urticaria, while the importance of H. pylori infection for pathogenesis of growth retardation in children, iron deficiency anemia, coronary heart disease, stroke and idiopathic thrombocytopenic purpura remains vague. The expression of two H. pylori proteins, cytotoxin associated protein (cag A) and vacuolization cytotoxin (vac A) is considered to be related with pathogenicity of the bacterium. It is clear that presence of cag A+ strains is important for development of peptic ulcer; nevertheless, it is also protective against esophageal reflux disease. On the other hand, cag A+ strains are common in gastric adenocarcinoma and MALT lymphoma patients, but it seems that certain subtypes of vac A cytotoxin are more important risk factors. Infection with cag A+ strains is more common in patients with acne rosacea, stroke and coronary heart disease.

Clinical significance of infection with cag A and vac A positive helicobacter pylori strains

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Sokić-Milutinović Aleksandra

2004-01-01

Full Text Available Clinical relevance of infection with different Helicobacter pylori strains was reviewed in this paper. Helicobacter pylori (H. pylori infection plays a role in pathogenesis of chronic gastritis, peptic ulcer disease, gastric adenocarcinoma and MALT lymphoma. Extragastric manifestations of H. pylori infection most probably include acne rosacea and chronic urticaria, while the importance of H. pylori infection for pathogenesis of growth retardation in children, iron deficiency anemia, coronary heart disease, stroke and idiopathic thrombocytopenic purpura remains vague. The expression of two H. pylori proteins, cytotoxin associated protein (cag A and vacuolization cytotoxin (vac A is considered to be related with pathogenicity of the bacterium. It is clear that presence of cag A+ strains is important for development of peptic ulcer; nevertheless, it is also protective against esophageal reflux disease. On the other hand, cag A+ strains are common in gastric adenocarcinoma and MALT lymphoma patients, but it seems that certain subtypes of vac A cytotoxin are more important risk factors. Infection with cag A+ strains is more common in patients with acne rosacea, stroke and coronary heart disease.

Serpentine endophytic bacterium Pseudomonas azotoformans ASS1 accelerates phytoremediation of soil metals under drought stress.

Science.gov (United States)

Ma, Ying; Rajkumar, Mani; Moreno, António; Zhang, Chang; Freitas, Helena

2017-10-01

This study evaluates the potential of serpentine endophytic bacterium to foster phytoremediation efficiency of Trifolium arvense grown on multi-metal (Cu, Zn and Ni) contaminated soils under drought stress. A drought resistant endophytic bacterial strain ASS1 isolated from the leaves of Alyssum serpyllifolium grown in serpentine soils was identified as Pseudomonas azotoformans based on biochemical tests and partial 16S rRNA gene sequencing. P. azotoformans ASS1 possessed abiotic stress resistance (heavy metals, drought, salinity, antibiotics and extreme temperature) and plant growth promoting (PGP) properties (phosphate solubilization, nitrogen fixation, production of 1-aminocyclopropane-1-carboxylate deaminase, siderophore and ammonia). Inoculation of T. arvense with ASS1 considerably increased the plant biomass and leaf relative water content in both roll towel assay and pot experiments in the absence and presence of drought stress (DS). In the pot experiments, ASS1 greatly enhanced chlorophyll content, catalase, peroxidase, superoxide dismutase activities, and proline content (only in the absence of drought) in plant leaves, whereas they decreased the concentrations of malondialdehyde. Irrespective of water stress, ASS1 significantly improved accumulation, total removal, bio-concentration factor and biological accumulation coefficient of metals (Cu, Zn and Ni), while decreased translocation factors of Cu. The effective colonization and survival in the rhizosphere and tissue interior assured improved plant growth and successful metal phytoremediation under DS. These results demonstrate the potential of serpentine endophytic bacterium ASS1 for protecting plants against abiotic stresses and helping plants to thrive in semiarid ecosystems and accelerate phytoremediation process in metal polluted soils. Copyright © 2017 Elsevier Ltd. All rights reserved.

Benz[a]anthracene Biotransformation and Production of Ring Fission Products by Sphingobium sp. Strain KK22

Science.gov (United States)

Kunihiro, Marie; Ozeki, Yasuhiro; Nogi, Yuichi; Hamamura, Natsuko

2013-01-01

A soil bacterium, designated strain KK22, was isolated from a phenanthrene enrichment culture of a bacterial consortium that grew on diesel fuel, and it was found to biotransform the persistent environmental pollutant and high-molecular-weight polycyclic aromatic hydrocarbon (PAH) benz[a]anthracene. Nearly complete sequencing of the 16S rRNA gene of strain KK22 and phylogenetic analysis revealed that this organism is a new member of the genus Sphingobium. An 8-day time course study that consisted of whole-culture extractions followed by high-performance liquid chromatography (HPLC) analyses with fluorescence detection showed that 80 to 90% biodegradation of 2.5 mg liter−1 benz[a]anthracene had occurred. Biodegradation assays where benz[a]anthracene was supplied in crystalline form (100 mg liter−1) confirmed biodegradation and showed that strain KK22 cells precultured on glucose were equally capable of benz[a]anthracene biotransformation when precultured on glucose plus phenanthrene. Analyses of organic extracts from benz[a]anthracene biodegradation by liquid chromatography negative electrospray ionization tandem mass spectrometry [LC/ESI(−)-MS/MS] revealed 10 products, including two o-hydroxypolyaromatic acids and two hydroxy-naphthoic acids. 1-Hydroxy-2- and 2-hydroxy-3-naphthoic acids were unambiguously identified, and this indicated that oxidation of the benz[a]anthracene molecule occurred via both the linear kata and angular kata ends of the molecule. Other two- and single-aromatic-ring metabolites were also documented, including 3-(2-carboxyvinyl)naphthalene-2-carboxylic acid and salicylic acid, and the proposed pathways for benz[a]anthracene biotransformation by a bacterium were extended. PMID:23686261

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.

Natural plasmid transformation in a high-frequency-of transformation marine Vibrio strain

International Nuclear Information System (INIS)

Frischer, M.E.; Thurmond, J.M.; Paul, J.H.

1990-01-01

The estuarine bacterium Vibrio strain DI-9 has been shown to be naturally transformable with both broad host range plasmid multimers and homologous chromosomal DNA at average frequencies of 3.5 x 10 -9 and 3.4 x 10 -7 transformants per recipient, respectively. Growth of plasmid transformants in nonselective medium resulted in cured strains that transformed 6 to 42,857 times more frequently than the parental strain, depending on the type of transforming DNA. These high-frequency-of-transformation (HfT) strains were transformed at frequencies ranging from 1.1 x 10 -8 to 1.3 x 10 -4 transformants per recipient with plasmid DNA and at an average frequency of 8.3 x 10 -5 transformants per recipient with homologous chromosomal DNA. The highest transformation frequencies were observed by using multimers of an R1162 derivative carrying the transposon Tn5 (pQSR50). Probing of total DNA preparations from one of the cured strains demonstrated that no plasmid DNA remained in the cured strains which may have provided homology to the transforming DNA. All transformants and cured strains could be differentiated from the parental strains by colony morphology. DNA binding studies indicated that late-log-phase HfT strains bound [ 3 H]bacteriophage lambda DNA 2.1 times more rapidly than the parental strain. These results suggest that the original plasmid transformation event of strain DI-9 was the result of uptake and expression of plasmid DNA by a competent mutant (HfT strain). Additionally, it was found that a strain of Vibrio parahaemolyticus, USFS 3420, could be naturally transformed with plasmid DNA. Natural plasmid transformation by high-transforming mutants may be a means of plasmid acquisition by natural aquatic bacterial populations

Clostridium difficile infection: Early history, diagnosis and molecular strain typing methods.

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Rodriguez, C; Van Broeck, J; Taminiau, B; Delmée, M; Daube, G

2016-08-01

Recognised as the leading cause of nosocomial antibiotic-associated diarrhoea, the incidence of Clostridium difficile infection (CDI) remains high despite efforts to improve prevention and reduce the spread of the bacterium in healthcare settings. In the last decade, many studies have focused on the epidemiology and rapid diagnosis of CDI. In addition, different typing methods have been developed for epidemiological studies. This review explores the history of C. difficile and the current scope of the infection. The variety of available laboratory tests for CDI diagnosis and strain typing methods are also examined. Copyright © 2016 Elsevier Ltd. All rights reserved.

Isolation of perchlorate-reducing Azospira suillum strain JB524 from tidal flats of the Yellow Sea

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Nirmala Bardiya

2016-11-01

Full Text Available Objective: To isolate and identify perchlorate-reducing bacterium from an enriched consortium from tidal flats of the Yellow Sea. Methods: A perchlorate-enriched consortium from tidal flats of the Yellow Sea was used to isolate Azospira suillum (A. suillum strain JB524. The strain was identified based on partial 16S rDNA sequencing. Perchlorate reduction by the strain was tested with acetate as the e - donor in the presence of NaCl, nitrate and at different growth temperatures using standard anaerobic techniques. The complete enzymatic destruction of perchlorate was confirmed as evolution of O2 by chlorite dismutase in the absence of acetate. Results: Strain JB524 shared 100% 16S rDNA sequence similarity with the type strain A. suillum PST isolated from a swine waste treatment lagoon. Perchlorate reduction coincided with concomitant increase in cell density. Although, acclimatization of the strain PST at suboptimal temperature for perchlorate reduction is not reported, the newly isolated strain could rapidly reduce perchlorate at 22 °C after brief acclimatization. Conclusions: Reduction of perchlorate by A. suillum strain JB524 was negatively affected in the presence of NaCl, suboptimal temperature, presence of nitrate, and limiting amount of acetate as the e-donor.

Thermosyntropha lipolytica gen. nov., sp. nov., a lipolytic, anaerobic, alkalitolerant, thermophilic bacterium utilizing short- and long-chain fatty acids in syntrophic coculture with a methanogenic archaeum.

Science.gov (United States)

Svetlitshnyi, V; Rainey, F; Wiegel, J

1996-10-01

Three strains of an anaerobic thermophilic organoheterotrophic lipolytic alkalitolerant bacterium, Thermosyntropha lipolytica gen. nov., sp. nov. (type strain JW/VS-265T; DSM 11003), were isolated from alkaline hot springs of Lake Bogoria (Kenya). The cells were nonmotile, non-spore forming, straight or slightly curved rods. At 60 degrees C the pH range for growth determined at 25 degrees C [pH25 degrees C] was 7.15 to 9.5, with an optimum between 8.1 and 8.9 (pH60 degrees C of 7.6 and 8.1). At a pH25 degrees C of 8.5 the temperature range for growth was from 52 to 70 degrees C, with an optimum between 60 and 66 degrees C. The shortest doubling time was around 1 h. In pure culture the bacterium grew in a mineral base medium supplemented with yeast extract, tryptone, Casamino Acids, betaine, and crotonate as carbon sources, producing acetate as a major product and constitutively a lipase. During growth in the presence of olive oil, free long-chain fatty acids were accumulated in the medium but the pure culture could not utilize olive oil, triacylglycerols, short- and long-chain fatty acids, and glycerol for growth. In syntrophic coculture (Methanobacterium strain JW/VS-M29) the lipolytic bacteria grew on triacylglycerols and linear saturated and unsaturated fatty acids with 4 to 18 carbon atoms, but glycerol was not utilized. Fatty acids with even numbers of carbon atoms were degraded to acetate and methane, while from odd-numbered fatty acids 1 mol of propionate per mol of fatty acid was additionally formed. 16S rDNA sequence analysis identified Syntrophospora and Syntrophomonas spp. as closest phylogenetic neighbors.

Rapid detection of human fecal Eubacterium species and related genera by nested PCR method.

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Kageyama, A; Benno, Y

2001-01-01

PCR procedures based on 16S rDNA gene sequence specific for seven Eubacterium spp. and Eggerthella lenta that predominate in the human intestinal tract were developed, and used for direct detection of these species in seven human feces samples. Three species of Eggerthella lenta, Eubacterium rectale, and Eubacterium eligens were detected from seven fecal samples. Eubacterium biforme was detected from six samples. It was reported that E. rectale, E. eligens, and E. biforme were difficult to detect by traditional culture method, but the nested PCR method is available for the detection of these species. This result shows that the nested PCR method utilizing a universal primer pair, followed by amplification with species-specific primers, would allow rapid detection of Eubacterium species in human feces.

Polycyclovorans algicola gen. nov., sp. nov., an aromatic-hydrocarbon-degrading marine bacterium found associated with laboratory cultures of marine phytoplankton.

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Gutierrez, Tony; Green, David H; Nichols, Peter D; Whitman, William B; Semple, Kirk T; Aitken, Michael D

2013-01-01

A strictly aerobic, halotolerant, rod-shaped bacterium, designated strain TG408, was isolated from a laboratory culture of the marine diatom Skeletonema costatum (CCAP1077/1C) by enrichment with polycyclic aromatic hydrocarbons (PAHs) as the sole carbon source. 16S rRNA gene sequence analysis placed this organism within the order Xanthomonadales of the class Gammaproteobacteria. Its closest relatives included representatives of the Hydrocarboniphaga-Nevskia-Sinobacter clade (compounds and small organic acids. Notably, it displayed versatility in degrading two- and three-ring PAHs. Moreover, catechol 2,3-dioxygenase activity was detected in lysates, indicating that this strain utilizes the meta-cleavage pathway for aromatic compound degradation. Cells produced surface blebs and contained a single polar flagellum. The predominant isoprenoid quinone of strain TG408 was Q-8, and the dominant fatty acids were C(16:0), C(16:1) ω7c, and C(18:1) ω7c. The G+C content of the isolate's DNA was 64.3 mol% ± 0.34 mol%. On the basis of distinct phenotypic and genotypic characteristics, strain TG408 represents a novel genus and species in the class Gammaproteobacteria for which the name Polycyclovorans algicola gen. nov., sp. nov., is proposed. Quantitative PCR primers targeting the 16S rRNA gene of this strain were developed and used to show that this organism is found associated with other species of marine phytoplankton. Phytoplankton may be a natural biotope in the ocean where new species of hydrocarbon-degrading bacteria await discovery and which contribute significantly to natural remediation processes.

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

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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)).

Microbial culturomics to isolate halophilic bacteria from table salt: genome sequence and description of the moderately halophilic bacterium Bacillus salis sp. nov.

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Seck, E H; Diop, A; Armstrong, N; Delerce, J; Fournier, P-E; Raoult, D; Khelaifia, S

2018-05-01

Bacillus salis strain ES3 T (= CSUR P1478 = DSM 100598) is the type strain of B. salis sp. nov. It is an aerobic, Gram-positive, moderately halophilic, motile and spore-forming bacterium. It was isolated from commercial table salt as part of a broad culturomics study aiming to maximize the culture conditions for the in-depth exploration of halophilic bacteria in salty food. Here we describe the phenotypic characteristics of this isolate, its complete genome sequence and annotation, together with a comparison with closely related bacteria. Phylogenetic analysis based on 16S rRNA gene sequences indicated 97.5% similarity with Bacillus aquimaris, the closest species. The 8 329 771 bp long genome (one chromosome, no plasmids) exhibits a G+C content of 39.19%. It is composed of 18 scaffolds with 29 contigs. Of the 8303 predicted genes, 8109 were protein-coding genes and 194 were RNAs. A total of 5778 genes (71.25%) were assigned a putative function.

Draft Genome Sequence of Paenibacillus sp. Strain DMB20, Isolated from Alang Ship-Breaking Yard, Which Harbors Genes for Xenobiotic Degradation.

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Shah, Binal; Jain, Kunal; Patel, Namrata; Pandit, Ramesh; Patel, Anand; Joshi, Chaitanya G; Madamwar, Datta

2015-06-11

Paenibacillus sp. strain DMB20, in cometabolism with other Proteobacteria and Firmicutes, exhibits azoreduction of textile dyes. Here, we report the draft genome sequence of this bacterium, consisting of 6,647,181 bp with 7,668 coding sequences (CDSs). The data presented highlight multiple sets of functional genes associated with xenobiotic compound degradation. Copyright © 2015 Shah et al.

The physiology of the filamentous bacterium Microthrix parvicella

NARCIS (Netherlands)

Slijkhuis, H.

1983-01-01

A study has been made of the physiology of Microthrix parvicella. This filamentous bacterium often causes poor settleability of activated sludge in oxidation ditches supplied with domestic sewage. The organism was found to utilize only long chain fatty acids (preferably in

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

Science.gov (United States)

Zhang, Kundi; Li, Fuli

2011-05-01

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(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(-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(-1) h(-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.

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.)

Meningococcal genetic variation mechanisms viewed through comparative analysis of serogroup C strain FAM18.

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Stephen D Bentley

2007-02-01

Full Text Available The bacterium Neisseria meningitidis is commonly found harmlessly colonising the mucosal surfaces of the human nasopharynx. Occasionally strains can invade host tissues causing septicaemia and meningitis, making the bacterium a major cause of morbidity and mortality in both the developed and developing world. The species is known to be diverse in many ways, as a product of its natural transformability and of a range of recombination and mutation-based systems. Previous work on pathogenic Neisseria has identified several mechanisms for the generation of diversity of surface structures, including phase variation based on slippage-like mechanisms and sequence conversion of expressed genes using information from silent loci. Comparison of the genome sequences of two N. meningitidis strains, serogroup B MC58 and serogroup A Z2491, suggested further mechanisms of variation, including C-terminal exchange in specific genes and enhanced localised recombination and variation related to repeat arrays. We have sequenced the genome of N. meningitidis strain FAM18, a representative of the ST-11/ET-37 complex, providing the first genome sequence for the disease-causing serogroup C meningococci; it has 1,976 predicted genes, of which 60 do not have orthologues in the previously sequenced serogroup A or B strains. Through genome comparison with Z2491 and MC58 we have further characterised specific mechanisms of genetic variation in N. meningitidis, describing specialised loci for generation of cell surface protein variants and measuring the association between noncoding repeat arrays and sequence variation in flanking genes. Here we provide a detailed view of novel genetic diversification mechanisms in N. meningitidis. Our analysis provides evidence for the hypothesis that the noncoding repeat arrays in neisserial genomes (neisserial intergenic mosaic elements provide a crucial mechanism for the generation of surface antigen variants. Such variation will have an

Potato seed dressing with Pseudomonas aeruginosa strain RZ9 enhances yield and reduces black scurf

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Moncef MRABET

2015-09-01

Full Text Available A rhizospheric strain RZ9 of Pseudomonas aeruginosa was assessed for in-vitro growth inhibition of Rhizoctonia solani and effectiveness to control black scurf on potatoes (Solanum tuberosum L. of the cultivars Spunta and Nicola, in greenhouse and field experiments. The strain RZ9 inhibited R. solani mycelial growth by more than 60% and completely inhibited the germination of sclerotia from infested potato tubers in in-vitro tests. In greenhouse assays, seed potato treatment with RZ9 cell suspension increased stem length, decreased the relative weight of infected potato tubers (by 67%, and increased the potato yield (by 16% compared to pathogen-inoculated plants for both potato cultivars. In field trials conducted on sandy soils during 2012 and 2013, strain RZ9 reduced black scurf incidence and increased potato yield by an average of 5.3 t ha-1 for ′Spunta′ and 5 t ha-1 for ′Nicola′. This study showed that the selected strain of P. aeruginosa is an efficient bacterium for enhancing yield and reducing black scurf of field-grown potatoes.

Biodegradation of nicotine by a novel nicotine-degrading bacterium, Pseudomonas plecoglossicida TND35 and its new biotransformation intermediates.

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Raman, Gurusamy; Mohan, KasiNadar; Manohar, Venkat; Sakthivel, Natarajan

2014-02-01

Tobacco wastes that contain nicotine alkaloids are harmful to human health and the environment. In the investigation, a novel nicotine-biodegrading bacterium TND35 was isolated and identified as Pseudomonas plecoglossicida on the basis of phenotypic, biochemical characteristics and 16S rRNA sequence homology. We have studied the nicotine biodegradation potential of strain TND35 by detecting the intermediate metabolites using an array of approaches such as HPLC, GC-MS, NMR and FT-IR. Biotransformation metabolites, N-methylmyosmine, 4-hydroxy-1-(3-pyridyl)-1-butanone (HPB) and other three new intermediate metabolites namely, 3,5-bis (1-methylpyrrolidin-2-yl) pyridine, 2,3-dihydro-1-methyl-5-(pyridin-3-yl)-1H-pyrrol-2-ol and 5-(pyridin-3-yl)-1H-pyrrol-2(3H)-one have been identified. Interestingly, these intermediate metabolites suggest that the strain TND35 employs a novel nicotine biodegradation pathway, which is different from the reported pathways of Aspergillus oryzae 112822, Arthrobacter nicotinovorans pAO1, Agrobacterium tumefaciens S33 and other species of Pseudomonas. The metabolite, HPB reported in this study can also be used as biochemical marker for tobacco related cancer studies.

Comparative genomic characterization of citrus-associated Xylella fastidiosa strains

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Nunes Luiz R

2007-12-01

Full Text Available Abstract Background The xylem-inhabiting bacterium Xylella fastidiosa (Xf is the causal agent of Pierce's disease (PD in vineyards and citrus variegated chlorosis (CVC in orange trees. Both of these economically-devastating diseases are caused by distinct strains of this complex group of microorganisms, which has motivated researchers to conduct extensive genomic sequencing projects with Xf strains. This sequence information, along with other molecular tools, have been used to estimate the evolutionary history of the group and provide clues to understand the capacity of Xf to infect different hosts, causing a variety of symptoms. Nonetheless, although significant amounts of information have been generated from Xf strains, a large proportion of these efforts has concentrated on the study of North American strains, limiting our understanding about the genomic composition of South American strains – which is particularly important for CVC-associated strains. Results This paper describes the first genome-wide comparison among South American Xf strains, involving 6 distinct citrus-associated bacteria. Comparative analyses performed through a microarray-based approach allowed identification and characterization of large mobile genetic elements that seem to be exclusive to South American strains. Moreover, a large-scale sequencing effort, based on Suppressive Subtraction Hybridization (SSH, identified 290 new ORFs, distributed in 135 Groups of Orthologous Elements, throughout the genomes of these bacteria. Conclusion Results from microarray-based comparisons provide further evidence concerning activity of horizontally transferred elements, reinforcing their importance as major mediators in the evolution of Xf. Moreover, the microarray-based genomic profiles showed similarity between Xf strains 9a5c and Fb7, which is unexpected, given the geographical and chronological differences associated with the isolation of these microorganisms. The newly

Comparative genome analysis of the high pathogenicity Salmonella Typhimurium strain UK-1.

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Yingqin Luo

Full Text Available Salmonella enterica serovar Typhimurium, a gram-negative facultative rod-shaped bacterium causing salmonellosis and foodborne disease, is one of the most common isolated Salmonella serovars in both developed and developing nations. Several S. Typhimurium genomes have been completed and many more genome-sequencing projects are underway. Comparative genome analysis of the multiple strains leads to a better understanding of the evolution of S. Typhimurium and its pathogenesis. S. Typhimurium strain UK-1 (belongs to phage type 1 is highly virulent when orally administered to mice and chickens and efficiently colonizes lymphoid tissues of these species. These characteristics make this strain a good choice for use in vaccine development. In fact, UK-1 has been used as the parent strain for a number of nonrecombinant and recombinant vaccine strains, including several commercial vaccines for poultry. In this study, we conducted a thorough comparative genome analysis of the UK-1 strain with other S. Typhimurium strains and examined the phenotypic impact of several genomic differences. Whole genomic comparison highlights an extremely close relationship between the UK-1 strain and other S. Typhimurium strains; however, many interesting genetic and genomic variations specific to UK-1 were explored. In particular, the deletion of a UK-1-specific gene that is highly similar to the gene encoding the T3SS effector protein NleC exhibited a significant decrease in oral virulence in BALB/c mice. The complete genetic complements in UK-1, especially those elements that contribute to virulence or aid in determining the diversity within bacterial species, provide key information in evaluating the functional characterization of important genetic determinants and for development of vaccines.

Metabolism of nitrodiphenyl ether herbicides by dioxin-degrading bacterium Sphingomonas wittichii RW1.

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Keum, Young Soo; Lee, Young Ju; Kim, Jeong-Han

2008-10-08

Nitrodiphenyl ether herbicides, including chlomethoxyfen, nitrofen, and oxyfluorfen are potent herbicides. Some metabolites and parent compounds are considered as possible mutagens and endocrine disruptors. Both properties pose serious hygienic and environmental risks. Sphingomonas wittichii RW1 is a well-known degrader of polychlorinated dibenzo- p-dioxins, dibenzofurans, and diphenyl ethers. However, no detailed research of its metabolic activity has been performed against pesticides with a diphenyl ether scaffold. In this study, we report S. wittichii RW1 as a very potent diphenyl ether herbicide-metabolizing bacterium with broad substrate specificity. The structures of metabolites were determined by instrumental analysis and synthetic standards. Most pesticides were rapidly removed from the culture medium in the order of nitrofen > oxyfluorfen > chlomethoxyfen. In general, herbicides were degraded through the initial reduction and N-acetylation of nitro groups, followed by ether bond cleavage. Relatively low concentrations of phenolic and catecholic metabolites throughout the study suggested that these metabolites were rapidly metabolized and incorporated into primary metabolism. These results indicate that strain RW1 has very versatile metabolic activities over a wide range of environmental contaminants.

Anaerobic oxidation of 2-chloroethanol under denitrifying conditions by Pseudomonas stutzeri strain JJ.

Science.gov (United States)

Dijk, J A; Stams, A J M; Schraa, G; Ballerstedt, H; de Bont, J A M; Gerritse, J

2003-11-01

A bacterium that uses 2-chloroethanol as sole energy and carbon source coupled to denitrification was isolated from 1,2-dichloroethane-contaminated soil. Its 16 S rDNA sequence showed 98% similarity with the type strain of Pseudomonas stutzeri (DSM 5190) and the isolate was tentatively identified as Pseudomonas stutzeri strain JJ. Strain JJ oxidized 2-chloroethanol completely to CO(2) with NO(3)(- )or O(2) as electron acceptor, with a preference for O(2) if supplied in combination. Optimum growth on 2-chloroethanol with nitrate occurred at 30 degrees C with a mu(max) of 0.14 h(-1) and a yield of 4.4 g protein per mol 2-chloroethanol metabolized. Under aerobic conditions, the mu(max) was 0.31 h(-1). NO(2)(-) also served as electron acceptor, but reduction of Fe(OH)(3), MnO(2), SO(4)(2-), fumarate or ClO(3)(-) was not observed. Another chlorinated compound used as sole energy and carbon source under aerobic and denitrifying conditions was chloroacetate. Various different bacterial strains, including some closely related Pseudomonas stutzeri strains, were tested for their ability to grow on 2-chloroethanol as sole energy and carbon source under aerobic and denitrifying conditions, respectively. Only three strains, Pseudomonas stutzeri strain LMD 76.42, Pseudomonas putida US2 and Xanthobacter autotrophicus GJ10, grew aerobically on 2-chloroethanol. This is the first report of oxidation of 2-chloroethanol under denitrifying conditions by a pure bacterial culture.

Complete genome sequence of Halanaerobium praevalens type strain (GSLT)

Energy Technology Data Exchange (ETDEWEB)

Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Chertkov, Olga [Los Alamos National Laboratory (LANL); Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Kannan, K. Palani [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Tindall, Brian [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute

2011-01-01

Halanaerobium praevalens Zeikus et al. 1984 is the type species of the genus Halanaero- bium, which in turn is the type genus of the family Halanaerobiaceae. The species is of inter- est because it is able to reduce a variety of nitro-substituted aromatic compounds at a high rate, and because of its ability to degrade organic pollutants. The strain is also of interest be- cause it functions as a hydrolytic bacterium, fermenting complex organic matter and produc- ing intermediary metabolites for other trophic groups such as sulfate-reducing and methano- genic bacteria. It is further reported as being involved in carbon removal in the Great Salt Lake, its source of isolation. This is the first completed genome sequence of a representative of the genus Halanaerobium and the second genome sequence from a type strain of the fami- ly Halanaerobiaceae. The 2,309,262 bp long genome with its 2,110 protein-coding and 70 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Monitoring of a novel bacterium, Lactobacillus thermotolerans , in ...

African Journals Online (AJOL)

Abstract. We successfully established fluorescence in situ hybridization (FISH) method for specific detection and enumeration of a novel bacterium, Lactobacillus thermotolerans, in chicken feces. The specific FISH probes were designed based on the L. thermotolerans 16S rRNA gene sequences, and these sequences were ...

Kinetics of Molybdenum Reduction to Molybdenum Blue by Bacillus sp. Strain A.rzi

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A. R. Othman

2013-01-01

Full Text Available Molybdenum is very toxic to agricultural animals. Mo-reducing bacterium can be used to immobilize soluble molybdenum to insoluble forms, reducing its toxicity in the process. In this work the isolation of a novel molybdate-reducing Gram positive bacterium tentatively identified as Bacillus sp. strain A.rzi from a metal-contaminated soil is reported. The cellular reduction of molybdate to molybdenum blue occurred optimally at 4 mM phosphate, using 1% (w/v glucose, 50 mM molybdate, between 28 and 30°C and at pH 7.3. The spectrum of the Mo-blue product showed a maximum peak at 865 nm and a shoulder at 700 nm. Inhibitors of bacterial electron transport system (ETS such as rotenone, sodium azide, antimycin A, and potassium cyanide could not inhibit the molybdenum-reducing activity. At 0.1 mM, mercury, copper, cadmium, arsenic, lead, chromium, cobalt, and zinc showed strong inhibition on molybdate reduction by crude enzyme. The best model that fitted the experimental data well was Luong followed by Haldane and Monod. The calculated value for Luong’s constants pmax, Ks, Sm, and n was 5.88 μmole Mo-blue hr−1, 70.36 mM, 108.22 mM, and 0.74, respectively. The characteristics of this bacterium make it an ideal tool for bioremediation of molybdenum pollution.

Bioaugmentation-assisted phytoextraction of Co, Pb and Zn: an assessment with a phosphate-solubilizing bacterium isolated from metal-contaminated mines of Boryeong Area in South Korea

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Arunakumara, KKIU.

2015-01-01

Full Text Available Description of the subject. Make use of microbes having remarkable metal tolerance and plant growth-promoting abilities to remediate metal-contaminated soils. Objectives. The objectives were to isolate phosphate solubilizing bacterial strain, assess metal (Co, Pb and Zn mobilization potential of the strain and to evaluate the effects of the strain on growth and uptake of metals by Helianthus annuus. Method. A phosphate solubilizing bacterium was isolated from metal-contaminated soils. Heavy metal (Co, Pb and Zn tolerance of the strain was assessed using the agar dilution method. Bacterial-assisted growth promotion and metal uptake by H. annuus was evaluated in a pot experiment. The impact of bacterial inoculation on the mobility of metals in soil was investigated in a batch experiment. Results. The strain showed close proximity with Klebsiella oxytoca JCM1665, according to 16S rRNA sequence analysis. The strain was efficient in solubilizing phosphate, both in the presence and absence of metals. Inoculation of the strain enhanced the growth of H. annuus (49, 22 and 39% respectively in Co, Pb and Zn contaminated soils compared to non-inoculated plants. Accumulation and translocation of Co, Pb and Zn from roots to shoots were also enhanced by the strain. Water soluble fraction of Co, Pb and Zn in soil was increased by 51, 24 and 76% respectively in inoculated soils with regard to those of non-inoculated soils. Conclusions. Taking the plant growth promotion and metal mobilizing potential of the strain into account, practical application of the strain in enhancing phytoextraction of Co, Pb and Zn from contaminated soils could be recommended.

Desulfobacter psychrotolerans sp. nov., a new psychrotolerant sulfate-reducing bacterium and descriptions of its physiological response to temperature changes.

Science.gov (United States)

Tarpgaard, Irene H; Boetius, Antje; Finster, Kai

2006-01-01

A psychrotrolerant acetate-oxidizing sulfate-reducing bacterium (strain akvb(T)) was isolated from sediment from the northern part of The North Sea with annual temperature fluctuations between 8 and 14 degrees C. Of the various substrates tested, strain akvb(T) grew exclusively by the oxidation of acetate coupled to the reduction of sulfate. The cells were motile, thick rods with round ends and grew in dense aggregates. Strain akvb(T) grew at temperatures ranging from -3.6 to 26.3 degrees C. Optimal growth was observed at 20 degrees C. The highest cell specific sulfate reduction rate of 6.2 fmol cell(-1) d(-1) determined by the (35)SO(2-)(40) method was measured at 26 degrees C. The temperature range of short-term sulfate reduction rates exceeded the temperature range of growth by 5 degrees C. The Arrhenius relationship for the temperature dependence of growth and sulfate reduction was linear, with two distinct slopes below the optimum temperatures of both processes. The critical temperature was 6.4 degrees C. The highest growth yield (4.3-4.5 g dry weight mol(-1) acetate) was determined at temperatures between 5 and 15 degrees C. The cellular fatty acid composition was determined with cultures grown at 4 and 20 degrees C, respectively. The relative proportion of cellular unsaturated fatty acids (e.g. 16:1omega7c) was higher in cells grown at 4 degrees C than in cells grown at 20 degrees C. The physiological responses to temperature changes showed that strain akvb(T) was well adapted to the temperature regime of the environment from which it was isolated. Phylogenetic analysis showed that strain akvb(T) is closest related to Desulfobacter hydrogenophilus, with a 16S rRNA gene sequence similarity of 98.6%. DNA-DNA-hybridization showed a similarity of 32% between D. hydrogenophilus and strain akvb(T). Based on phenotypic and DNA-based characteristics we propose that strain akvb(T) is a member of a new species, Desulfobacter psychrotolerans sp. nov.

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

A Genetic System for the Thermophilic Acetogenic Bacterium Thermoanaerobacter kivui.

Science.gov (United States)

Basen, Mirko; Geiger, Irina; Henke, Laura; Müller, Volker

2018-02-01

Thermoanaerobacter kivui is one of the very few thermophilic acetogenic microorganisms. It grows optimally at 66°C on sugars but also lithotrophically with H 2 + CO 2 or with CO, producing acetate as the major product. While a genome-derived model of acetogenesis has been developed, only a few physiological or biochemical experiments regarding the function of important enzymes in carbon and energy metabolism have been carried out. To address this issue, we developed a method for targeted markerless gene deletions and for integration of genes into the genome of T. kivui The strain naturally took up plasmid DNA in the exponential growth phase, with a transformation frequency of up to 3.9 × 10 -6 A nonreplicating plasmid and selection with 5-fluoroorotate was used to delete the gene encoding the orotate phosphoribosyltransferase ( pyrE ), resulting in a Δ pyrE uracil-auxotrophic strain, TKV002. Reintroduction of pyrE on a plasmid or insertion of pyrE into different loci within the genome restored growth without uracil. We subsequently studied fructose metabolism in T. kivui The gene fruK (TKV_c23150) encoding 1-phosphofructosekinase (1-PFK) was deleted, using pyrE as a selective marker via two single homologous recombination events. The resulting Δ fruK strain, TKV003, did not grow on fructose; however, growth on glucose (or on mannose) was unaffected. The combination of pyrE as a selective marker and the natural competence of the strain for DNA uptake will be the basis for future studies on CO 2 reduction and energy conservation and their regulation in this thermophilic acetogenic bacterium. IMPORTANCE Acetogenic bacteria are currently the focus of research toward biotechnological applications due to their potential for de novo synthesis of carbon compounds such as acetate, butyrate, or ethanol from H 2 + CO 2 or from synthesis gas. Based on available genome sequences and on biochemical experiments, acetogens differ in their energy metabolism. Thus, there is an

The temperature--dependent expression of GST of Schistosoma japonicum (Philippine strain).

Science.gov (United States)

Cai, Z H; Song, G C; Xu, Y X; Liu, S X

1993-03-01

Obtained from pSj5, the cDNA gene encoding GST antigen of Schistosoma japonicum (Philippine strain) was ligated with efficient temperature-dependent PBV220 vector which was constructed in CAPM, and then introduced into host bacterium-DH5 alpha (E. coli) by transformation. Transformants were selected by ampicillin and recombinant clones were identified by restriction mapping. The result showed that recombinant clone 43 was the one carrying recombinant plasmid PBV 220 with the correct insertion of the gene fragment. The GST expression ability of clone 43 was investigated by GST enzymic activity assay and SDS-PAGE. A relatively high level of GST enzymic activity was expressed by this clone under the temperature-dependent condition, that is, cultured at 30 degrees C and expressed at 42 degrees C. A more strongly stained 26 kDa protein band was identified by SDS-PAGE. The result indicated that GST of S. japonicum (Philippine strain) could be expressed not only by IPTG induction, but also by the temperature-dependent method.

Hydrogen production by co-cultures of Lactobacillus and a photosynthetic bacterium, Rhodobacter sphaeroides RV

Energy Technology Data Exchange (ETDEWEB)

Asada, Yasuo; Ishimi, Katsuhiro [Department of General Education, College of Science and Technology, Nihon University, Narashinodai, Chiba 274-8501 (Japan); Tokumoto, Masaru; Aihara, Yasuyuki; Oku, Masayo; Kohno, Hideki [Department of Applied Molecular Chemistry, College of Industrial Technology, Nihon University, Izumi-cho, Chiba 275-8575 (Japan); Wakayama, Tatsuki; Miyake, Jun [Research Institute for Cell Engineering, National Institute of Advanced Industrial Science and Technology, Nakoji, Amagasaki, Hyogo 661-0974 (Japan); Tomiyama, Masamitsu [Genetic Diversity Department, National Institute of Agrobiological Science, Tsukuba, Ibaraki 305-8602 (Japan)

2006-09-15

Hydrogen production with glucose by using co-immobilized cultures of a lactic acid bacterium, Lactobacillus delbrueckii NBRC13953, and a photosynthetic bacterium, Rhodobacter sphaeroides RV, in agar gels was studied. Glucose was converted to hydrogen gas in a yield of 7.1mol of hydrogen per mole of glucose at a maximum under illuminated conditions. (author)

High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies.

Directory of Open Access Journals (Sweden)

Anjana Srivatsan

2008-08-01

Full Text Available Whole-genome sequencing is a powerful technique for obtaining the reference sequence information of multiple organisms. Its use can be dramatically expanded to rapidly identify genomic variations, which can be linked with phenotypes to obtain biological insights. We explored these potential applications using the emerging next-generation sequencing platform Solexa Genome Analyzer, and the well-characterized model bacterium Bacillus subtilis. Combining sequencing with experimental verification, we first improved the accuracy of the published sequence of the B. subtilis reference strain 168, then obtained sequences of multiple related laboratory strains and different isolates of each strain. This provides a framework for comparing the divergence between different laboratory strains and between their individual isolates. We also demonstrated the power of Solexa sequencing by using its results to predict a defect in the citrate signal transduction pathway of a common laboratory strain, which we verified experimentally. Finally, we examined the molecular nature of spontaneously generated mutations that suppress the growth defect caused by deletion of the stringent response mediator relA. Using whole-genome sequencing, we rapidly mapped these suppressor mutations to two small homologs of relA. Interestingly, stable suppressor strains had mutations in both genes, with each mutation alone partially relieving the relA growth defect. This supports an intriguing three-locus interaction module that is not easily identifiable through traditional suppressor mapping. We conclude that whole-genome sequencing can drastically accelerate the identification of suppressor mutations and complex genetic interactions, and it can be applied as a standard tool to investigate the genetic traits of model organisms.

Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1(T)).

Science.gov (United States)

Schleheck, David; Weiss, Michael; Pitluck, Sam; Bruce, David; Land, Miriam L; Han, Shunsheng; Saunders, Elizabeth; Tapia, Roxanne; Detter, Chris; Brettin, Thomas; Han, James; Woyke, Tanja; Goodwin, Lynne; Pennacchio, Len; Nolan, Matt; Cook, Alasdair M; Kjelleberg, Staffan; Thomas, Torsten

2011-12-31

Parvibaculum lavamentivorans DS-1(T) is the type species of the novel genus Parvibaculum in the novel family Rhodobiaceae (formerly Phyllobacteriaceae) of the order Rhizobiales of Alphaproteobacteria. Strain DS-1(T) is a non-pigmented, aerobic, heterotrophic bacterium and represents the first tier member of environmentally important bacterial communities that catalyze the complete degradation of synthetic laundry surfactants. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,914,745 bp long genome with its predicted 3,654 protein coding genes is the first completed genome sequence of the genus Parvibaculum, and the first genome sequence of a representative of the family Rhodobiaceae.

Antibacterial Property of a Coral-Associated Bacterium Pseudoalteromonas luteoviolacea Against Shrimp Pathogenic Vibrio harveyi (In Vitro Study)

OpenAIRE

OCKY KARNA RADJASA; TORBEN MARTENS; HANS-PETER GROSSART; AGUS SABDONO; MEINHARD SIMON; TONNY BACHTIAR

2005-01-01

A coral-associated bacterium was successfully screened for secondary metabolites production based on PCR amplification of the nonribosomal peptide synthetase gene and was identified as closely related to Pseudoalteromonas luteoviolacea based on its 16S rDNA. The bacterium was found to inhibit the growth of shrimp pathogenic bacterium tested, Vibrio harveyi. To characterize the inhibiting metabolite, a 279 bp long DNA fragment was obtained and the deduced amino acid sequence showed conserved s...

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

Directory of Open Access Journals (Sweden)

Jin Duan

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

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

Science.gov (United States)

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

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.

A two-dimensional electrophoretic profile of the proteins secreted by Herbaspirillum seropedicae strain Z78.

Science.gov (United States)

Chaves, Daniela Fojo Seixas; de Souza, Emanuel Maltempi; Monteiro, Rose Adele; de Oliveira Pedrosa, Fábio

2009-11-02

Herbaspirillum seropedicae is an endophytic bacterium that associates with rice, sugarcane and other economically important crops. Secreted proteins play a key role in the plant-bacterial interaction. Using 2D electrophoresis and peptide mass fingerprint mass spectrometry, 63 protein spots representing 41 different secreted proteins were identified during growth of H. seropedicae under nitrogen-sufficient conditions. In silico analysis showed that 25.4% of the proteins had signal peptides and 15.9% were predicted to be non-classically secreted. Among the most abundant were flagellar components and ABC-type transport system proteins. Nine secreted proteins had also been identified in the cellular proteome, suggesting that they also play a role in the extracellular environment. No type III secreted proteins were detected by comparison of the wild type strain with an hrcN mutant strain.

Biological consequences of ancient gene acquisition and duplication in the large genome soil bacterium, ""solibacter usitatus"" strain Ellin6076

Energy Technology Data Exchange (ETDEWEB)

Challacombe, Jean F [Los Alamos National Laboratory; Eichorst, Stephanie A [Los Alamos National Laboratory; Xie, Gary [Los Alamos National Laboratory; Kuske, Cheryl R [Los Alamos National Laboratory; Hauser, Loren [ORNL; Land, Miriam [ORNL

2009-01-01

Bacterial genome sizes range from ca. 0.5 to 10Mb and are influenced by gene duplication, horizontal gene transfer, gene loss and other evolutionary processes. Sequenced genomes of strains in the phylum Acidobacteria revealed that 'Solibacter usistatus' strain Ellin6076 harbors a 9.9 Mb genome. This large genome appears to have arisen by horizontal gene transfer via ancient bacteriophage and plasmid-mediated transduction, as well as widespread small-scale gene duplications. This has resulted in an increased number of paralogs that are potentially ecologically important (ecoparalogs). Low amino acid sequence identities among functional group members and lack of conserved gene order and orientation in the regions containing similar groups of paralogs suggest that most of the paralogs were not the result of recent duplication events. The genome sizes of cultured subdivision 1 and 3 strains in the phylum Acidobacteria were estimated using pulsed-field gel electrophoresis to determine the prevalence of the large genome trait within the phylum. Members of subdivision 1 were estimated to have smaller genome sizes ranging from ca. 2.0 to 4.8 Mb, whereas members of subdivision 3 had slightly larger genomes, from ca. 5.8 to 9.9 Mb. It is hypothesized that the large genome of strain Ellin6076 encodes traits that provide a selective metabolic, defensive and regulatory advantage in the variable soil environment.

New insights into virulence mechanisms of rice pathogen Acidovorax avenae subsp. avenae strain RS-1 following exposure to ?-lactam antibiotics

OpenAIRE

Li, Bin; Ge, Mengyu; Zhang, Yang; Wang, Li; Ibrahim, Muhammad; Wang, Yanli; Sun, Guochang; Chen, Gongyou

2016-01-01

Recent research has shown that pathogen virulence can be altered by exposure to antibiotics, even when the growth rate is unaffected. Investigating this phenomenon provides new insights into understanding the virulence mechanisms of bacterial pathogens. This study investigates the phenotypic and transcriptomic responses of the rice pathogenic bacterium Acidovorax avenae subsp. avenae (Aaa) strain RS-1 to ?-lactam antibiotics especially Ampicillin (Amp). Our results indicate that exposure to A...

Virgibacillus ainsalahensis sp. nov., a Moderately Halophilic Bacterium Isolated from Sediment of a Saline Lake in South of Algeria.

Science.gov (United States)

Amziane, Meriam; Darenfed-Bouanane, Amel; Abderrahmani, Ahmed; Selama, Okba; Jouadi, Lydia; Cayol, Jean-Luc; Nateche, Farida; Fardeau, Marie-Laure

2017-02-01

A Gram-positive, moderately halophilic, endospore-forming bacterium, designated MerV T , was isolated from a sediment sample of a saline lake located in Ain Salah, south of Algeria. The cells were rod shaped and motile. Isolate MerV T grew at salinity interval of 0.5-25% NaCl (optimum, 5-10%), pH 6.0-12.0 (optimum, 8.0), and temperature between 10 and 40 °C (optimum, 30 °C).The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, a glycolipid, a phospholipid, and two lipids, and MK-7 is the predominant menaquinone. The predominant cellular fatty acids were anteiso C 15:0 and anteiso C 17:0 . The DNA G+C content was 45.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain MerV T was most closely related to Virgibacillus halodenitrificans (gene sequence similarity of 97.0%). On the basis of phenotypic, chemotaxonomic properties, and phylogenetic analyses, strain MerV T (=DSM = 28944 T ) should be placed in the genus Virgibacillus as a novel species, for which the name Virgibacillus ainsalahensis is proposed.

Growth in coculture stimulates metabolism of the phenylurea herbicide isoproturon by Sphingomonas sp. strain SRS2.

Science.gov (United States)

Sørensen, Sebastian R; Ronen, Zeev; Aamand, Jens

2002-07-01

Metabolism of the phenylurea herbicide isoproturon by Sphingomonas sp. strain SRS2 was significantly enhanced when the strain was grown in coculture with a soil bacterium (designated strain SRS1). Both members of this consortium were isolated from a highly enriched isoproturon-degrading culture derived from an agricultural soil previously treated regularly with the herbicide. Based on analysis of the 16S rRNA gene, strain SRS1 was assigned to the beta-subdivision of the proteobacteria and probably represents a new genus. Strain SRS1 was unable to degrade either isoproturon or its known metabolites 3-(4-isopropylphenyl)-1-methylurea, 3-(4-isopropylphenyl)-urea, or 4-isopropyl-aniline. Pure culture studies indicate that Sphingomonas sp. SRS2 is auxotrophic and requires components supplied by association with other soil bacteria. A specific mixture of amino acids appeared to meet these requirements, and it was shown that methionine was essential for Sphingomonas sp. SRS2. This suggests that strain SRS1 supplies amino acids to Sphingomonas sp. SRS2, thereby leading to rapid metabolism of (14)C-labeled isoproturon to (14)CO(2) and corresponding growth of strain SRS2. Proliferation of strain SRS1 suggests that isoproturon metabolism by Sphingomonas sp. SRS2 provides unknown metabolites or cell debris that supports growth of strain SRS1. The role of strain SRS1 in the consortium was not ubiquitous among soil bacteria; however, the indigenous soil microflora and some strains from culture collections also stimulate isoproturon metabolism by Sphingomonas sp. strain SRS2 to a similar extent.

Lentibacillus amyloliquefaciens sp. nov., a halophilic bacterium isolated from saline sediment sample.

Science.gov (United States)

Wang, Jing-Li; Ma, Ke-Dong; Wang, Yan-Wei; Wang, Hui-Min; Li, Yan-Bin; Zhou, Shan; Chen, Xiao-Rong; Kong, De-Long; Guo, Xiang; He, Ming-Xiong; Ruan, Zhi-Yong

2016-02-01

A Gram-stain positive, non-motile, non-sporogenous, aerobic, rod-shaped and halophilic bacterium, designated LAM0015(T), was isolated from a saline sediment sample collected from Yantai City in China. The isolate was found to be able to grow at NaCl concentrations of 5-25 % (w/v) (optimum: 7-12 %), 15-45 °C (optimum: 35 °C) and pH 5.0-9.0 (optimum: 7.0). The major fatty acids were determined to be anteiso-C15:0 and anteiso-C17:0. The predominant respiratory quinone was identified as MK-7. The cell wall peptidoglycan was determined to contain meso-diaminopimelic acid. The polar lipids were found to be diphosphatidyglycerol, phosphatidylglycerol, five phospholipids and one glycolipid. The DNA G+C content was 43.1 mol% as determined by the T m method. Analysis of the 16S rRNA gene sequence indicated that the isolate belongs within the genus Lentibacillus and is closely related to Lentibacillus persicus DSM 22530(T), Lentibacillus salicampi JCM 11462(T) and Lentibacillus jeotgali JCM 15795(T) with 97.3, 96.7 and 96.4 % sequence similarity, respectively. The DNA-DNA hybridization value between LAM0015(T) and L. persicus DSM 22530(T) was 51.2 ± 1.4 %. Based on its phenotypic, phylogenetic and chemotaxonomic characteristics, strain LAM0015(T) is concluded to represent a novel species of the genus Lentibacillus, for which the name Lentibacillus amyloliquefaciens sp. nov. is proposed. The type strain is LAM0015(T) (=ACCC 06401(T) = JCM 19838(T)).

Purification and molecular characterization of subtilisin-like alkaline protease BPP-A from Bacillus pumilus strain MS-1.

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Miyaji, T; Otta, Y; Nakagawa, T; Watanabe, T; Niimura, Y; Tomizuka, N

2006-03-01

The present study was conducted by screening zein-degrading bacteria in an attempt to obtain zein-degrading protease. Soil bacteria were screened by formation of a clear zone on zein plates. Characterization of a zein-degrading bacterium indicated a taxonomic affiliation to Bacillus pumilus, and was named MS-1 strain. The strain produced two different types of extracellular proteases, BPP-A and BPP-B. In this study, we purified and characterized BPP-A because it exhibited a higher ability to hydrolyze zein than BPP-B. When casein was used as the substrate, the optimal pH for BPP-A was 11.0. In BPP-A, zein was better substrate than casein at pH 13.0, whereas casein was better one than zein at pH 11.0. The bppA gene encoded a 383-amino acid pre-pro form of BPP-A, and mature BPP-A contained 275 amino acid residues. It was concluded that BPP-A belonged to the subtilisin family. A zein-degrading bacterium assigned to B. pumilus produced two different types of extracellular proteases, BPP-A and BPP-B. BPP-A exhibited an ability to hydrolyze zein in an extreme alkaline condition. This is a first report on screening for zein-degrading micro-organisms. The subtilisin-like protease BPP-A is possible to utilize as an industrial enzyme for the production of zein hydrolysates.

Microbial survival of space vacuum and extreme ultraviolet irradiation: strain isolation and analysis during a rocket flight.

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Saffary, Roya; Nandakumar, Renu; Spencer, Dennis; Robb, Frank T; Davila, Joseph M; Swartz, Marvin; Ofman, Leon; Thomas, Roger J; DiRuggiero, Jocelyne

2002-09-24

We have recovered new isolates from hot springs, in Yellowstone National Park and the Kamchatka Peninsula, after gamma-irradiation and exposure to high vacuum (10(-6) Pa) of the water and sediment samples. The resistance to desiccation and ionizing radiation of one of the isolates, Bacillus sp. strain PS3D, was compared to that of the mesophilic bacterium, Deinococcus radiodurans, a species well known for its extraordinary resistance to desiccation and high doses of ionizing radiation. Survival of these two microorganisms was determined in real and simulated space conditions, including exposure to extreme UV radiation (10-100 nm) during a rocket flight. We found that up to 15 days of desiccation alone had little effect on the viability of either bacterium. In contrast, exposure to space vacuum ( approximately 10(-6) Pa) decreased cell survival by two and four orders of magnitude for Bacillus sp. strain PS3D and D. radiodurans, respectively. Simultaneous exposure to space vacuum and extreme UV radiation further decreased the survival of both organisms, compared to unirradiated controls. This is the first report on the isolated effect of extreme UV at 30 nm on cell survival. Extreme UV can only be transmitted through high vacuum, therefore its penetration into the cells may only be superficial, suggesting that in contrast to near UV, membrane proteins rather than DNA were damaged by the radiation.

Isolation of a halophilic bacterium, Bacillus sp. strain NY-6 for organic contaminants removal in saline wastewater on ship

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Gao, Jie; Yu, Zhenjiang; Zhang, Xiaohui; Zhao, Dan; Zhao, Fangbo

2013-06-01

The objective of this research was to examine if certain strains of Bacillus bacteria, could survive in dry powder products and if so, could the bacteria degrade organic contaminants in saline wastewater on a ship. As part of the study, we isolated 7 domesticated strains named NY1, NY2,..., and NY7, the strain NY6 showed to have the best performance for organic matter degradation and could survive in dry powder more than 3 months. NY6 was identified as Bacillus aerius, based on the morphological and physic-chemical properties. Its optimal growth conditions were as follows: salinity was 2%; temperature was 37°C; pH was in 6.5-7.0; best ratio of C: N: P was 100:5:1. The capability of its dry powder for Chemical Oxygen Demand (COD) removal was 800mg COD/g in synthesized marine wastewater with 2% salinity. The spores in the dry powder were 1.972×108 g -1.

Biodegradation of Benzene, Toluene, Ethylbenzene, and o-, m-, and p-Xylenes by the Newly Isolated Bacterium Comamonas sp. JB.

Science.gov (United States)

Jiang, Bei; Zhou, Zunchun; Dong, Ying; Tao, Wei; Wang, Bai; Jiang, Jingwei; Guan, Xiaoyan

2015-07-01

A bacterium designated strain JB, able to degrade six benzene, toluene, ethylbenzene, and o-, m-, and p-xylene (BTEX) compounds, was isolated from petroleum-contaminated soil. Taxonomic analyses showed that the isolate belonged to Comamonas, and until now, the genus Comamonas has not included any known BTEX degraders. The BTEX biodegradation rate was slightly low on the mineral salt medium (MSM), but adding a small amount of yeast extract greatly enhanced the biodegradation. The relationship between specific degradation rate and individual BTEX was described well by Michaelis-Menten kinetics. The treatment of petrochemical wastewater containing BTEX mixture and phenol was shown to be highly efficient by BTEX-grown JB. In addition, toxicity assessment indicated the treatment of the petrochemical wastewater by BTEX-grown JB led to less toxicity than untreated wastewater.

New recombinant bacterium comprises a heterologous gene encoding glycerol dehydrogenase and/or an up-regulated native gene encoding glycerol dehydrogenase, useful for producing ethanol

DEFF Research Database (Denmark)

2010-01-01

dehydrogenase encoding region of the bacterium, or is inserted into a phosphotransacetylase encoding region of the bacterium, or is inserted into an acetate kinase encoding region of the bacterium. It is operably linked to an inducible, a regulated or a constitutive promoter. The up-regulated glycerol......TECHNOLOGY FOCUS - BIOTECHNOLOGY - Preparation (claimed): Producing recombinant bacterium having enhanced ethanol production characteristics when cultivated in growth medium comprising glycerol comprises: (a) transforming a parental bacterium by (i) the insertion of a heterologous gene encoding...... glycerol dehydrogenase; and/or (ii) up-regulating a native gene encoding glycerol dehydrogenase; and (b) obtaining the recombinant bacterium. Preferred Bacterium: In the recombinant bacterium above, the inserted heterologous gene and/or the up-regulated native gene is encoding a glycerol dehydrogenase...

Genome Sequence of Rhodoferax antarcticus ANT.BRT; A Psychrophilic Purple Nonsulfur Bacterium from an Antarctic Microbial Mat

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Jennifer M. Baker

2017-02-01

Full Text Available Rhodoferax antarcticus is an Antarctic purple nonsulfur bacterium and the only characterized anoxygenic phototroph that grows best below 20 °C. We present here a high-quality draft genome of Rfx. antarcticus strain ANT.BRT, isolated from an Antarctic microbial mat. The circular chromosome (3.8 Mbp of Rfx. antarcticus has a 59.1% guanine + cytosine (GC content and contains 4036 open reading frames. In addition, the bacterium contains a sizable plasmid (198.6 kbp, 48.4% GC with 226 open reading frames that comprises about 5% of the total genetic content. Surprisingly, genes encoding light-harvesting complexes 1 and 3 (LH1 and LH3, but not light-harvesting complex 2 (LH2, were identified in the photosynthesis gene cluster of the Rfx. antarcticus genome, a feature that is unique among purple phototrophs. Consistent with physiological studies that showed a strong capacity for nitrogen fixation in Rfx. antarcticus, a nitrogen fixation gene cluster encoding a molybdenum-type nitrogenase was present, but no alternative nitrogenases were identified despite the cold-active phenotype of this phototroph. Genes encoding two forms of ribulose 1,5-bisphosphate carboxylase/oxygenase were present in the Rfx. antarcticus genome, a feature that likely provides autotrophic flexibility under varying environmental conditions. Lastly, genes for assembly of both type IV pili and flagella are present, with the latter showing an unusual degree of clustering. This report represents the first genomic analysis of a psychrophilic anoxygenic phototroph and provides a glimpse of the genetic basis for maintaining a phototrophic lifestyle in a permanently cold, yet highly variable, environment.

Draft genome sequence of an endophytic bacterium, Paenibacillus tyrfis strain SUK123, isolated from Santiria apiculata stem

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Emmanuel Haruna

2017-12-01

Full Text Available Here we report the draft genome sequence of an endophytic Paenibacillus tyrfis strain isolated from the Universiti Kebangsaan Malaysia reserve forest, Malaysia. The genome size was approximately 8.04 Mb, and the assembly consisted of 107 scaffolds with 168 contigs, and had a G + C content of 53%. Phylogenetic analysis of strain SUK123 using the 16S rRNA gene revealed that it belonged to the family Paenibacillaceae with the highest similarity to Paenibacillus elgii SDT (99%. Whole genome comparison of SUK123 with related species using average nucleotide identity (ANI analysis revealed a similarity of 98% to Paenibacillus tyrfis Mst1T, 94% to Paenibacillus elgii B69T, 91% to Paenibacillus ehimensis A2T, 68% to Paenibacillus polymyxa SC2T and 69% to Paenibacillus alvei DMS29T. The draft genome was deposited at the European Nucleotide Archive (PRJEB21373.

Characterization of rumen bacterial strains isolated from enrichments of rumen content in the presence of propolis.

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de Aguiar, Sílvia Cristina; Zeoula, Lucia Maria; do Prado, Odimari Pricila Pires; Arcuri, Pedro Braga; Forano, Evelyne

2014-11-01

Propolis presents many biological properties, including antibacterial activities, and has been proposed as an additive in ruminant nutrition. Twenty bacterial strains, previously isolated from enrichments of Brazilian cow rumen contents in the presence of different propolis extracts (LLOS), were characterized using phenotyping and 16S rRNA identification. Seven strains were assigned to Streptococcus sp., most likely S. bovis, and were all degrading starch. One amylolytic lactate-utilizing strain of Selenomonas ruminantium was also found. Two strains of Clostridium bifermentans were identified and showed proteolytic activity. Two strains were assigned to Mitsuokella jalaludinii and were saccharolytic. One strain belonged to a Bacillus species and seven strains were affiliated with Escherichia coli. All of the 20 strains were able to use many sugars, but none of them were able to degrade the polysaccharides carboxymethylcellulose and xylans. The effect of three propolis extracts (LLOS B1, C1 and C3) was tested on the in vitro growth of four representative isolates of S. bovis, E. coli, M. jalaludinii and C. bifermentans. The growth of S. bovis, E. coli and M. jalaludinii was not affected by the three propolis extracts at 1 mg ml(-1). C. bifermentans growth was completely inhibited at this LLOS concentration, but this bacterium was partially resistant at lower concentrations. LLOS C3, with the lower concentration of phenolic compounds, was a little less inhibitory than B1 and C1 on this strain.

Cloning of a two-component signal transduction system of Xanthomonas campestris pv. phaseoli var. fuscans strain BXPF65

DEFF Research Database (Denmark)

Chan, JWYF; Maynard, Scott; Goodwin, PH

1998-01-01

A putative two-component signal transduction system was amplified and cloned from the plant pathogenic bacterium Xanthomonas campestris pv. phaseoli var. fuscans isolate BXPF65. The 620 bp amplified fragment was sequenced and analyzed with the BLAST Enhanced Alignment Utility (BEAUTY). BEAUTY...... that the putative histidine kinase has homology with conserved “transmitter” domains of sensor proteins in two-component signal transduction systems. RFLP analysis using the putative signal transduction system showed polymorphisms among the strains....

Biodiversity among Lactobacillus helveticus Strains Isolated from Different Natural Whey Starter Cultures as Revealed by Classification Trees

Science.gov (United States)

Gatti, Monica; Trivisano, Carlo; Fabrizi, Enrico; Neviani, Erasmo; Gardini, Fausto

2004-01-01

Lactobacillus helveticus is a homofermentative thermophilic lactic acid bacterium used extensively for manufacturing Swiss type and aged Italian cheese. In this study, the phenotypic and genotypic diversity of strains isolated from different natural dairy starter cultures used for Grana Padano, Parmigiano Reggiano, and Provolone cheeses was investigated by a classification tree technique. A data set was used that consists of 119 L. helveticus strains, each of which was studied for its physiological characters, as well as surface protein profiles and hybridization with a species-specific DNA probe. The methodology employed in this work allowed the strains to be grouped into terminal nodes without difficult and subjective interpretation. In particular, good discrimination was obtained between L. helveticus strains isolated, respectively, from Grana Padano and from Provolone natural whey starter cultures. The method used in this work allowed identification of the main characteristics that permit discrimination of biotypes. In order to understand what kind of genes could code for phenotypes of technological relevance, evidence that specific DNA sequences are present only in particular biotypes may be of great interest. PMID:14711641

Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal

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Vreeland, Russell H.; Rosenzweig, William D.; Powers, Dennis W.

2000-10-01

Bacteria have been found associated with a variety of ancient samples, however few studies are generally accepted due to questions about sample quality and contamination. When Cano and Borucki isolated a strain of Bacillus sphaericus from an extinct bee trapped in 25-30 million-year-old amber, careful sample selection and stringent sterilization techniques were the keys to acceptance. Here we report the isolation and growth of a previously unrecognized spore-forming bacterium (Bacillus species, designated 2-9-3) from a brine inclusion within a 250million-year-old salt crystal from the Permian Salado Formation. Complete gene sequences of the 16S ribosomal DNA show that the organism is part of the lineage of Bacillus marismortui and Virgibacillus pantothenticus. Delicate crystal structures and sedimentary features indicate the salt has not recrystallized since formation. Samples were rejected if brine inclusions showed physical signs of possible contamination. Surfaces of salt crystal samples were sterilized with strong alkali and acid before extracting brines from inclusions. Sterilization procedures reduce the probability of contamination to less than 1 in 10 9.

Unexpected diversity in the mobilome of a Pseudomonas aeruginosa strain isolated from a dental unit waterline revealed by SMRT Sequencing.

Science.gov (United States)

Vincent, Antony T; Charette, Steve J; Barbeau, Jean

2018-05-01

The Gram-negative bacterium Pseudomonas aeruginosa is found in several habitats, both natural and human-made, and is particularly known for its recurrent presence as a pathogen in the lungs of patients suffering from cystic fibrosis, a genetic disease. Given its clinical importance, several major studies have investigated the genomic adaptation of P. aeruginosa in lungs and its transition as acute infections become chronic. However, our knowledge about the diversity and adaptation of the P. aeruginosa genome to non-clinical environments is still fragmentary, in part due to the lack of accurate reference genomes of strains from the numerous environments colonized by the bacterium. Here, we used PacBio long-read technology to sequence the genome of PPF-1, a strain of P. aeruginosa isolated from a dental unit waterline. Generating this closed genome was an opportunity to investigate genomic features that are difficult to accurately study in a draft genome (contigs state). It was possible to shed light on putative genomic islands, some shared with other reference genomes, new prophages, and the complete content of insertion sequences. In addition, four different group II introns were also found, including two characterized here and not listed in the specialized group II intron database.

Biodegradation of buprofezin by Rhodococcus sp. strain YL-1 isolated from rice field soil.

Science.gov (United States)

Li, Chao; Zhang, Ji; Wu, Zhi-Guo; Cao, Li; Yan, Xin; Li, Shun-Peng

2012-03-14

A buprofezin-degrading bacterium, YL-1, was isolated from rice field soil. YL-1 was identified as Rhodococcus sp. on the basis of the comparative analysis of 16S rDNA sequences. The strain could use buprofezin as the sole source of carbon and nitrogen for growth and was able to degrade 92.4% of 50 mg L(-1) buprofezin within 48 h in liquid culture. During the degradation of buprofezin, four possible metabolites, 2-tert-butylimino-3-isopropyl-1,3,5-thiadiazinan-4-one, N-tert-butyl-thioformimidic acid formylaminomethyl ester, 2-isothiocyanato-2-methyl-propane, and 2-isothiocyanato-propane, were identified using gas chromatography-mass spectrometry (GC-MS) analysis. The catechol 2,3-dioxygenase activity was strongly induced during the degradation of buprofezin. A novel microbial biodegradation pathway for buprofezin was proposed on the basis of these metabolites. The inoculation of soils treated with buprofezin with strain YL-1 resulted in a higher degradation rate than that observed in noninoculated soils, indicating that strain YL-1 has the potential to be used in the bioremediation of buprofezin-contaminated environments.

Polyhydroxyalkanoate production by a novel bacterium Massilia sp. UMI-21 isolated from seaweed, and molecular cloning of its polyhydroxyalkanoate synthase gene.

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Han, Xuerong; Satoh, Yasuharu; Kuriki, Yumi; Seino, Teruyuki; Fujita, Shinji; Suda, Takanori; Kobayashi, Takanori; Tajima, Kenji

2014-11-01

We successfully isolated one microorganism (UMI-21) from Ulva, a green algae that contains starch. The strain UMI-21 can produce polyhydroxyalkanoate (PHA) from starch, maltotriose, or maltose as a sole carbon source. Taxonomic studies and 16S rDNA sequence analysis revealed that strain UMI-21 was phylogenetically related to species of the genus Massilia. The PHA content under the cultivation condition using a 10-L jar fermentor was 45.5% (w/w). This value was higher than that obtained after cultivation in a flask, suggesting the possibility of large-scale PHA production by UMI-21 from starch. A major issue for the industrial production of microbial PHAs is the very high production cost. Starch is a relatively inexpensive substrate that is also found in abundant seaweeds such as Ulva. Therefore, the strain isolated in this study may be very useful for producing PHA from seaweeds containing polysaccharides such as starch. In addition, a 3.7-kbp DNA fragment containing the whole PHA synthase gene (phaC) was obtained from the strain UMI-21. The results of open reading frame (ORF) analysis suggested that the DNA fragment contained two ORFs, which were composed of 1740 (phaC) and 564 bp (phaR). The deduced amino acid sequence of PhaC from strain UMI-21 shared high similarity with PhaC from Ralstonia eutropha, which is a representative PHA-producing bacterium with a class I PHA synthase. This is the first report for the cloning of the PHA synthase gene from Massilia species. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Genome Sequence Analysis of the Naphthenic Acid Degrading and Metal Resistant Bacterium Cupriavidus gilardii CR3.

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Xiaoyu Wang

Full Text Available Cupriavidus sp. are generally heavy metal tolerant bacteria with the ability to degrade a variety of aromatic hydrocarbon compounds, although the degradation pathways and substrate versatilities remain largely unknown. Here we studied the bacterium Cupriavidus gilardii strain CR3, which was isolated from a natural asphalt deposit, and which was shown to utilize naphthenic acids as a sole carbon source. Genome sequencing of C. gilardii CR3 was carried out to elucidate possible mechanisms for the naphthenic acid biodegradation. The genome of C. gilardii CR3 was composed of two circular chromosomes chr1 and chr2 of respectively 3,539,530 bp and 2,039,213 bp in size. The genome for strain CR3 encoded 4,502 putative protein-coding genes, 59 tRNA genes, and many other non-coding genes. Many genes were associated with xenobiotic biodegradation and metal resistance functions. Pathway prediction for degradation of cyclohexanecarboxylic acid, a representative naphthenic acid, suggested that naphthenic acid undergoes initial ring-cleavage, after which the ring fission products can be degraded via several plausible degradation pathways including a mechanism similar to that used for fatty acid oxidation. The final metabolic products of these pathways are unstable or volatile compounds that were not toxic to CR3. Strain CR3 was also shown to have tolerance to at least 10 heavy metals, which was mainly achieved by self-detoxification through ion efflux, metal-complexation and metal-reduction, and a powerful DNA self-repair mechanism. Our genomic analysis suggests that CR3 is well adapted to survive the harsh environment in natural asphalts containing naphthenic acids and high concentrations of heavy metals.

Microbial culturomics to isolate halophilic bacteria from table salt: genome sequence and description of the moderately halophilic bacterium Bacillus salis sp. nov.

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E.H. Seck

2018-05-01

Full Text Available Bacillus salis strain ES3T (= CSUR P1478 = DSM 100598 is the type strain of B. salis sp. nov. It is an aerobic, Gram-positive, moderately halophilic, motile and spore-forming bacterium. It was isolated from commercial table salt as part of a broad culturomics study aiming to maximize the culture conditions for the in-depth exploration of halophilic bacteria in salty food. Here we describe the phenotypic characteristics of this isolate, its complete genome sequence and annotation, together with a comparison with closely related bacteria. Phylogenetic analysis based on 16S rRNA gene sequences indicated 97.5% similarity with Bacillus aquimaris, the closest species. The 8 329 771 bp long genome (one chromosome, no plasmids exhibits a G+C content of 39.19%. It is composed of 18 scaffolds with 29 contigs. Of the 8303 predicted genes, 8109 were protein-coding genes and 194 were RNAs. A total of 5778 genes (71.25% were assigned a putative function. Keywords: Bacillus salis, culturomics, genome, halophilic bacteria, human gut, taxonogenomics

Species attribution and strain typing of Oenococcus oeni (formerly Leuconostoc oenos) with restriction endonuclease fingerprints.

Science.gov (United States)

Viti, C; Giovannetti, L; Granchi, L; Ventura, S

1996-10-01

In several wines, malolactic fermentation is required to improve the organoleptic characters and to stabilize the final product. In order to establish a controlled malolactic fermentation in wine, easy identification and sensitive typing of strains of Oenococcus oeni (new name of the malolactic bacterium Leuconostoc oenos) used as starter cultures are necessary. To accomplish these tasks, several strains of Oenococcus oeni isolated from wines of the Chianti region (Italy), along with reference strains and strains of L. mesenteroides subsp. mesenteroides, L. carnosum, L. fallax, L. pseudomesenteroides, L. lactis and Weisella paramesenteroides, were studied with RFLP of ribosomal genes and ultrasensitive total DNA restriction pattern analysis performed on polyacrylamide gel. With each of four restriction endonucleases used, identical restriction profiles of ribosomal genes were obtained for all strains of O. oeni. These ribopatterns, being strongly dissimilar to profiles of the other lactic acid bacteria tested, appear to be well suited for the attribution of wine lactic acid bacteria to the species O. oeni. Cluster analysis performed on two total DNA restriction profile data sets showed that the species O. oeni possesses a good degree of genomic homogeneity. Very sensitive typing of strains of O. oeni was obtained with total DNA restriction profiles. The potential of an integrated approach using restriction profiles for species assignment and typing of selected malolactic bacteria is demonstrated.