Science.gov

Sample records for bacterium magnetospirillum magnetotacticum

  1. Adverse effects of microgravity on the magnetotactic bacterium Magnetospirillum magnetotacticum.

    PubMed

    Urban, J E

    2000-11-01

    Bacteria that contain magnetosomes display magnetotaxis and align themselves to the earth's magnetic field. When magnetotactic bacteria were first isolated several decades ago it was presumed that geomagnetic orientation allowed magnetotactic bacteria to orient themselves downward towards sediments where the habitat is favorable to their growth and metabolism. As more species of magnetotactic bacteria have been isolated and studied, differences in magnetotactic responses have been observed which suggested that the primary role of magnetosomes might simply be to enhance a microorganism's response to gravity. To resolve if gravity influences magnetotactic behavior in bacteria, Magnetospirillum magnetotacticum was used to examine magnetotaxis in the absence of gravity. Experiments to compare the orientation of bacteria to north- or south-pole magnets were conducted in normal gravity and in the microgravity environments aboard the Space Shuttle and Space Station MIR. In each of the microgravity situations studied, bacteria were impaired in their ability to orient to magnets and the failure to exhibit magnetotaxis appeared to be a function of the loss of magnetosomes. The disappearance of aggregated magnetosomes seemed to correlate with a general loss of cellular integrity in microgravity. PMID:11543576

  2. Effect of Polyethylene Glycol on the Formation of Magnetic Nanoparticles Synthesized by Magnetospirillum magnetotacticum MS-1.

    PubMed

    Shimoshige, Hirokazu; Kobayashi, Hideki; Mizuki, Toru; Nagaoka, Yutaka; Inoue, Akira; Maekawa, Toru

    2015-01-01

    Magnetotactic bacteria (MTB) synthesize intracellular magnetic nanocrystals called magnetosomes, which are composed of either magnetite (Fe3O4) or greigite (Fe3S4) and covered with lipid membranes. The production of magnetosomes is achieved by the biomineralization process with strict control over the formation of magnetosome membrane vesicles, uptake and transport of iron ions, and synthesis of mature crystals. These magnetosomes have high potential for both biotechnological and nanotechnological applications, but it is still extremely difficult to grow MTB and produce a large amount of magnetosomes under the conventional cultural conditions. Here, we investigate as a first attempt the effect of polyethylene glycol (PEG) added to the culture medium on the increase in the yield of magnetosomes formed in Magnetospirillum magnetotacticum MS-1. We find that the yield of the formation of magnetosomes can be increased up to approximately 130 % by adding PEG200 to the culture medium. We also measure the magnetization of the magnetosomes and find that the magnetosomes possess soft ferromagnetic characteristics and the saturation mass magnetization is increased by 7 %. PMID:25993286

  3. Effect of Polyethylene Glycol on the Formation of Magnetic Nanoparticles Synthesized by Magnetospirillum magnetotacticum MS-1

    PubMed Central

    Shimoshige, Hirokazu; Kobayashi, Hideki; Mizuki, Toru; Nagaoka, Yutaka; Inoue, Akira; Maekawa, Toru

    2015-01-01

    Magnetotactic bacteria (MTB) synthesize intracellular magnetic nanocrystals called magnetosomes, which are composed of either magnetite (Fe3O4) or greigite (Fe3S4) and covered with lipid membranes. The production of magnetosomes is achieved by the biomineralization process with strict control over the formation of magnetosome membrane vesicles, uptake and transport of iron ions, and synthesis of mature crystals. These magnetosomes have high potential for both biotechnological and nanotechnological applications, but it is still extremely difficult to grow MTB and produce a large amount of magnetosomes under the conventional cultural conditions. Here, we investigate as a first attempt the effect of polyethylene glycol (PEG) added to the culture medium on the increase in the yield of magnetosomes formed in Magnetospirillum magnetotacticum MS-1. We find that the yield of the formation of magnetosomes can be increased up to approximately 130 % by adding PEG200 to the culture medium. We also measure the magnetization of the magnetosomes and find that the magnetosomes possess soft ferromagnetic characteristics and the saturation mass magnetization is increased by 7 %. PMID:25993286

  4. Magnetic guidance of the magnetotactic bacterium Magnetospirillum gryphiswaldense.

    PubMed

    Loehr, Johannes; Pfeiffer, Daniel; Schüler, Dirk; Fischer, Thomas M

    2016-04-21

    Magnetospirillum gryphiswaldense is a magnetotactic bacterium with a permanent magnetic moment capable of swimming using two bipolarly located flagella. In their natural environment these bacteria swim along the field lines of the homogeneous geomagnetic field in a typical run and reversal pattern and thereby create non-differentiable trajectories with sharp edges. In the current work we nevertheless achieve stable guidance along curved lines of mechanical instability by using a heterogeneous magnetic field of a garnet film. The successful guidance of the bacteria depends on the right balance between motility and the magnetic moment of the magnetosome chain. PMID:26972517

  5. Magnetospirillum caucaseum sp. nov., Magnetospirillum marisnigri sp. nov. and Magnetospirillum moscoviense sp. nov., freshwater magnetotactic bacteria isolated from three distinct geographical locations in European Russia.

    PubMed

    Dziuba, Marina; Koziaeva, Veronika; Grouzdev, Denis; Burganskaya, Ekaterina; Baslerov, Roman; Kolganova, Tatjana; Chernyadyev, Alexander; Osipov, Georgy; Andrianova, Ekaterina; Gorlenko, Vladimir; Kuznetsov, Boris

    2016-05-01

    Three strains of helical, magnetotactic bacteria, SO-1T, SP-1T and BB-1T, were isolated from freshwater sediments collected from three distinct locations in European Russia. Phylogenetic analysis showed that the strains belong to the genus Magnetospirillum. Strains SO-1T and SP-1T showed the highest 16S rRNA gene sequence similarity to Magnetospirillum magnetotacticum MS-1T (99.3 and 98.1 %, respectively), and strain BB-1T with Magnetospirillum gryphiswaldense MSR-1T (97.3 %). The tree based on concatenated deduced amino acid sequences of the MamA, B, K, M, O, P, Q and T proteins, which are involved in magnetosome formation, was congruent with the tree based on 16S rRNA gene sequences. The genomic DNA G+C contents of strains SO-1T, SP-1T and BB-1T were 65.9, 63.0 and 65.2 mol%, respectively. As major fatty acids, C18 : 1ω9, C16 : 1ω7c, C16 : 0 and C18 : 0 were detected. DNA-DNA hybridization values between the novel strains and their closest relatives in the genus Magnetospirillum were less than 51.7 ± 2.3 %. In contrast to M. magnetotacticum MS-1T, the strains could utilize butyrate and propionate; strains SO-1T and BB-1T could also utilize glycerol. Strain SP-1T showed strictly microaerophilic growth, whereas strains SO-1T and BB-1T were more tolerant of oxygen. The results of DNA-DNA hybridization and physiological tests allowed genotypic and phenotypic differentiation of the strains from each other as well as from the two species of Magnetospirillum with validly published names. Therefore, the strains represent novel species, for which we propose the names Magnetospirillum caucaseum sp. nov. (type strain SO-1T = DSM 28995T = VKM B-2936T), Magnetospirillum marisnigri sp. nov. (type strain SP-1T = DSM 29006T = VKM B-2938T) and Magnetospirillum moscoviense sp. nov. (type strain BB-1T = DSM 29455T = VKM B-2939T). PMID:26921147

  6. Studying the Transfer of Optical Orbital Angular Momentum to a Helical Bacterium

    NASA Astrophysics Data System (ADS)

    Davis, Dana; Horton, Timothy; Reichman, Steven; Link, Justin; Schmitzer, Heidrun; Robbins, Jennifer; Engle, Dorothy

    2014-03-01

    The purpose of this research is to study how the angular momentum of an optical vortex created by a 1064 nm laser is transferred to a helical shaped bacterium. When under the influence of a laser in optical tweezers, the helical shape of the bacteria causes it to spin in the trap. A spatial light modulator reshapes the beam and is twisted either into a left handed or right handed helix. This results in an optical vortex with a diameter which can be adjusted from roughly half a micron to three microns. The rotational speed of a helical bacterium in this type of optical trap should depend on the handedness of the vortex and the handedness of the bacterium being tweezed. When both the tweezing beam and the bacterium have the same handedness, a slight reduction in rotational speed should be observed; when the tweezing beam has the opposite handedness of the bacterium, a slight increase in rotational speed should be expected. We present our first experiments with magnetospirillum magnetotacticum and rhodospirillum rubrum.

  7. Magnetospirillum bellicus sp. nov., a Novel Dissimilatory Perchlorate-Reducing Alphaproteobacterium Isolated from a Bioelectrical Reactor ▿

    PubMed Central

    Thrash, J. Cameron; Ahmadi, Sarir; Torok, Tamas; Coates, John D.

    2010-01-01

    Previously isolated dissimilatory perchlorate-reducing bacteria (DPRB) have been primarily affiliated with the Betaproteobacteria. Enrichments from the cathodic chamber of a bioelectrical reactor (BER) inoculated from creek water in Berkeley, CA, yielded a novel organism most closely related to a previously described strain, WD (99% 16S rRNA gene identity). Strain VDYT has 96% 16S rRNA gene identity to both Magnetospirillum gryphiswaldense and Magnetospirillum magnetotacticum, and along with strain WD, distinguishes a clade of perchlorate-reducing Magnetospirillum species in the Alphaproteobacteria. In spite of the phylogenetic location of VDYT, attempted PCR for the key magnetosome formation genes mamI and mamL was negative. Strain VDYT was motile, non-spore forming, and, in addition to perchlorate, could use oxygen, chlorate, nitrate, nitrite, and nitrous oxide as alternative electron acceptors with acetate as the electron donor. Transient chlorate accumulation occurred during respiration of perchlorate. The organism made use of fermentation end products, such as acetate and ethanol, as carbon sources and electron donors for heterotrophic growth, and in addition, strain VDYT could grow chemolithotrophically with hydrogen serving as the electron donor. VDYT contains a copy of the RuBisCo cbbM gene, which was expressed under autotrophic but not heterotrophic conditions. DNA-DNA hybridization with strain WD confirmed VDYT as a separate species (46.2% identity), and the name Magnetospirillum bellicus sp. nov. (DSM 21662, ATCC BAA-1730) is proposed. PMID:20495050

  8. Magnetospirillum bellicus sp. nov., a novel dissimilatory perchlorate-reducing alphaproteobacterium isolated from a bioelectrical reactor.

    PubMed

    Thrash, J Cameron; Ahmadi, Sarir; Torok, Tamas; Coates, John D

    2010-07-01

    Previously isolated dissimilatory perchlorate-reducing bacteria (DPRB) have been primarily affiliated with the Betaproteobacteria. Enrichments from the cathodic chamber of a bioelectrical reactor (BER) inoculated from creek water in Berkeley, CA, yielded a novel organism most closely related to a previously described strain, WD (99% 16S rRNA gene identity). Strain VDY(T) has 96% 16S rRNA gene identity to both Magnetospirillum gryphiswaldense and Magnetospirillum magnetotacticum, and along with strain WD, distinguishes a clade of perchlorate-reducing Magnetospirillum species in the Alphaproteobacteria. In spite of the phylogenetic location of VDY(T), attempted PCR for the key magnetosome formation genes mamI and mamL was negative. Strain VDY(T) was motile, non-spore forming, and, in addition to perchlorate, could use oxygen, chlorate, nitrate, nitrite, and nitrous oxide as alternative electron acceptors with acetate as the electron donor. Transient chlorate accumulation occurred during respiration of perchlorate. The organism made use of fermentation end products, such as acetate and ethanol, as carbon sources and electron donors for heterotrophic growth, and in addition, strain VDY(T) could grow chemolithotrophically with hydrogen serving as the electron donor. VDY(T) contains a copy of the RuBisCo cbbM gene, which was expressed under autotrophic but not heterotrophic conditions. DNA-DNA hybridization with strain WD confirmed VDY(T) as a separate species (46.2% identity), and the name Magnetospirillum bellicus sp. nov. (DSM 21662, ATCC BAA-1730) is proposed. PMID:20495050

  9. Photoemission electron microscopy and scanning electron microscopy of Magnetospirillum magnetotacticum’s magnetosome chains

    SciTech Connect

    Keutner, Christoph; von Bohlen, Alex; Berges, Ulf; Espeter, Philipp; Schneider, Claus M.; Westphal, Carsten

    2014-10-07

    Magnetotactic bacteria are of great interdisciplinary interest, since a vast field of applications from magnetic recording media to medical nanorobots is conceivable. A key feature for a further understanding is the detailed knowledge about the magnetosome chain within the bacteria. We report on two preparation procedures suitable for UHV experiments in reflective geometry. Further, we present the results of scanning electron microscopy, as well as the first photoemission electron microscopy experiments, both accessing the magnetosomes within intact magnetotactic bacteria and compare these to scanning electron microscopy data from the literature. From the images, we can clearly identify individual magnetosomes within their chains.

  10. Identification of Promoters for Efficient Gene Expression in Magnetospirillum gryphiswaldense▿ †

    PubMed Central

    Lang, Claus; Pollithy, Anna; Schüler, Dirk

    2009-01-01

    To develop an expression system for the magnetotactic bacterium Magnetospirillum gryphiswaldense, we compared gene expression from the widely used Escherichia coli Plac promoter with that from known and predicted genuine M. gryphiswaldense promoters. With the use of green fluorescent protein as a reporter, the highest expression level was observed with the magnetosomal PmamDC promoter. We demonstrate that this promoter can be used for the expression of modified magnetosome proteins to generate “antibody-binding” magnetosomes. PMID:19395573

  11. Draft Genome Sequences of Two Magnetotactic Bacteria, Magnetospirillum moscoviense BB-1 and Magnetospirillum marisnigri SP-1.

    PubMed

    Koziaeva, Veronika V; Dziuba, Marina V; Ivanov, Timophey M; Kuznetsov, Boris B; Skryabin, Konstantin G; Grouzdev, Denis S

    2016-01-01

    We report here the draft genome sequences of two recently isolated magnetotactic species, Magnetospirillum moscoviense BB-1 and Magnetospirillum marisnigri SP-1. The genome of M. moscoviense BB-1 has 4,164,497 bp, 65.2% G+C content, and comprises 207 contigs. The genome of M. marisnigri SP-1 consists of 131 contigs and has a length of 4,619,819 bp and 64.7% G+C content. PMID:27516508

  12. Draft Genome Sequences of Two Magnetotactic Bacteria, Magnetospirillum moscoviense BB-1 and Magnetospirillum marisnigri SP-1

    PubMed Central

    Koziaeva, Veronika V.; Dziuba, Marina V.; Ivanov, Timophey M.; Kuznetsov, Boris B.; Skryabin, Konstantin G.

    2016-01-01

    We report here the draft genome sequences of two recently isolated magnetotactic species, Magnetospirillum moscoviense BB-1 and Magnetospirillum marisnigri SP-1. The genome of M. moscoviense BB-1 has 4,164,497 bp, 65.2% G+C content, and comprises 207 contigs. The genome of M. marisnigri SP-1 consists of 131 contigs and has a length of 4,619,819 bp and 64.7% G+C content. PMID:27516508

  13. The homopentameric chlorite dismutase from Magnetospirillum sp.

    PubMed

    Freire, Diana M; Rivas, Maria G; Dias, André M; Lopes, Ana T; Costa, Cristina; Santos-Silva, Teresa; Van Doorslaer, Sabine; González, Pablo J

    2015-10-01

    Chlorite dismutase (Cld) is a b-type heme containing enzyme that catalyzes the reduction of chlorite into chloride plus dioxygen. This enzyme has gained attention because it can be used in the development of bioremediation processes, biosensors, and controlled dioxygen production. In the present work, Cld was purified from Magnetospirillum sp. cells cultured anaerobically with acetate/perchlorate until stationary phase. Biochemical, spectroscopic and X-ray crystallography methods showed that Cld from Magnetospirillum sp. is a ~140 kDa homopentamer comprising ~27.8 kDa monomers. Preliminary X-ray crystallography studies confirmed the quaternary structure and the presence of one b-type heme per monomer. The EPR spectroscopic signature of the as-purified Cld samples is affected by the buffer composition used during the purification. Potassium phosphate buffer is the only buffer that affected neither the spectral nor the kinetic properties of Cld. Kinetic studies in solution revealed that Cld from Magnetospirillum sp. decomposes chlorite at high turnover rates with optimal pH6.0. A temperature below 10 °C is required to avoid enzyme inactivation due to cofactor bleaching during turnover, and to achieve full substrate consumption. Cld kinetic parameters were not affected when kinetic assays were performed in the presence of air or under argon atmosphere, but chloride is a weak mixed inhibitor that modifies the EPR signal of as-prepared samples. PMID:26218477

  14. Alteration of the Magnetic Properties of Aquaspirillum magnetotacticum by a Pulse Magnetization Technique †

    PubMed Central

    Ricci, Juan C. Diaz; Woodford, Barbara J.; Kirschvink, Joseph L.; Hoffmann, Michael R.

    1991-01-01

    The presence of a narrow shape and size distribution for magnetite crystals within magnetotactic organisms suggests strongly that there are species-specific mechanisms that control the process of biomineralization. In order to explore the extent of this control, cultures of Aquaspirillum magnetotacticum in the exponential growth phase were exposed to increasing magnetic pulses with the aim of separating cell populations on the basis of their magnetic coercivities. Isothermal remanent magnetization and anhysteretic remanent magnetization studies were performed with freeze-dried magnetic cells after the remagnetization treatment. Subpopulations of A. magnetotacticum that showed an increase in coercivity correlated with the intensity of the magnetic pulses were isolated. After successive subcultures of the remaining north-seeking cells, a maximum bulk coercivity (Hbmax) of 40 mT was obtained after treatment with a 55-mT pulse. Although we obtained A. magnetotacticum variants displaying higher coercivities than the wild-type strain, changes in crystal size or shape of the magnetite crystals were below reliable detection limits with transmission electron microscopy. Attempts to shift the coercivity towards higher values caused it to decrease, a change which was accompanied by an increase in magnetostatic interactions of the magnetosome chains as well as an increase in the cell population displaying an abnormal distribution of the magnetosome chains. Ultrastructural analyses of cells and magnetosomes revealed the appearance of cystlike bodies which occasionally contained magnetosomes. The increase in cystlike cells and abnormal magnetosome chains when higher magnetic pulses were used suggested that magnetosomes were collapsing because of stronger interparticle magnetostatic forces. Images PMID:16348587

  15. Isolation and characterization of Magnetospirillum from saline lagoon.

    PubMed

    Revathy, T; Jacob, Jobin John; Jayasri, M A; Suthindhiran, K

    2016-07-01

    Magnetotactic bacteria (MTB) are aquatic prokaryotes that orient themselves to earth's magnetic field with the help of intracellular organelle magnetosomes. Although many species of MTB have been identified, the isolation of MTB is a challenging task due to the lack of systematic isolation procedure and/or commercial media. In this study, we are reporting the isolation of magnetotactic spirillum from the Pulicat lagoon, India using a systematic and selective procedure. Sampling site was chosen on the basis of physicochemical properties of the ecosystem and the catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH) analysis of sediment samples. In the current study, a combination of techniques including 'capillary racetrack' Purification and gradient cultivation resulted in the isolation of magnetotactic spirilla from aquatic sediments. Based on the 16S rRNA gene sequence analysis, the strain was identified as Magnetospirillum and was designated as Magnetospirillum sp. VITRJS1. The genes responsible for magnetosome formation (mamA, B, E, F, K, M, O, P, Q, T) were successfully detected using PCR amplification. The presence of cbbM gene confirmed that the isolate is chemolithoautotroph and utilises reduced sulphur as an electron source. Furthermore, magnetosomes extracted from VITRJS1 found to be cubo-octahedral in shape and 45 nm in size. Our results indicate that the systematic procedure using sediment analysis, CARD-FISH, and a combination of isolation methods enables the selective and rapid isolation of MTB from aquatic sediment sample. PMID:27263004

  16. Insight into the Evolution of Magnetotaxis in Magnetospirillum spp., Based on mam Gene Phylogeny

    PubMed Central

    Lefèvre, Christopher T.; Schmidt, Marian L.; Viloria, Nathan; Trubitsyn, Denis; Schüler, Dirk

    2012-01-01

    Vibrioid- to helical-shaped magnetotactic bacteria phylogenetically related to the genus Magnetospirillum were isolated in axenic cultures from a number of freshwater and brackish environments located in the southwestern United States. Based on 16S rRNA gene sequences, most of the new isolates represent new Magnetospirillum species or new strains of known Magnetospirillum species, while one isolate appears to represent a new genus basal to Magnetospirillum. Partial sequences of conserved mam genes, genes reported to be involved in the magnetosome and magnetosome chain formation, and form II of the ribulose-1,5-bisphosphate carboxylase/oxygenase gene (cbbM) were determined in the new isolates and compared. The cbbM gene was chosen for comparison because it is not involved in magnetosome synthesis; it is highly conserved and is present in all but possibly one of the genomes of the magnetospirilla and the new isolates. Phylogenies based on 16S rRNA, cbbM, and mam gene sequences were reasonably congruent, indicating that the genes involved in magnetotaxis were acquired by a common ancestor of the Magnetospirillum clade. However, in one case, magnetosome genes might have been acquired through horizontal gene transfer. Our results also extend the known diversity of the Magnetospirillum group and show that they are widespread in freshwater environments. PMID:22865076

  17. Ligand Binding to Chlorite Dismutase from Magnetospirillum sp.

    PubMed

    De Schutter, Amy; Correia, Hugo D; Freire, Diana M; Rivas, María G; Rizzi, Alberto; Santos-Silva, Teresa; González, Pablo J; Van Doorslaer, Sabine

    2015-10-29

    Chlorite dismutase (Cld) catalyzes the reduction of chlorite to chloride and dioxygen. Here, the ligand binding to Cld of Magnetospirillum sp. (MaCld) is investigated with X-ray crystallography and electron paramagnetic resonance (EPR). EPR reveals a large heterogeneity in the structure of wild-type MaCld, showing a variety of low- and high-spin ferric heme forms. Addition of an axial ligand, such as azide or imidazole, removes this heterogeneity almost entirely. This is in line with the two high resolution crystal structures of MaCld obtained in the presence of azide and thiocyanate that show the coordination of the ligands to the heme iron. The crystal structure of the MaCld-azide complex reveals a single well-defined orientation of the azide molecule in the heme pocket. EPR shows, however, a pH-dependent heme structure, probably due to acid-base transitions of the surrounding amino-acid residues stabilizing azide. For the azide and imidazole complex of MaCld, the hyperfine and nuclear quadrupole interactions with the close-by (14)N and (1)H nuclei are determined using pulsed EPR. These values are compared to the corresponding data for the low-spin forms observed in the ferric wild-type MaCld and to existing EPR data on azide and imidazole complexes of other heme proteins. PMID:26287794

  18. Characterization of a Spontaneous Nonmagnetic Mutant of Magnetospirillum gryphiswaldense Reveals a Large Deletion Comprising a Putative Magnetosome Island

    PubMed Central

    Schübbe, Sabrina; Kube, Michael; Scheffel, André; Wawer, Cathrin; Heyen, Udo; Meyerdierks, Anke; Madkour, Mohamed H.; Mayer, Frank; Reinhardt, Richard; Schüler, Dirk

    2003-01-01

    Frequent spontaneous loss of the magnetic phenotype was observed in stationary-phase cultures of the magnetotactic bacterium Magnetospirillum gryphiswaldense MSR-1. A nonmagnetic mutant, designated strain MSR-1B, was isolated and characterized. The mutant lacked any structures resembling magnetosome crystals as well as internal membrane vesicles. The growth of strain MSR-1B was impaired under all growth conditions tested, and the uptake and accumulation of iron were drastically reduced under iron-replete conditions. A large chromosomal deletion of approximately 80 kb was identified in strain MSR-1B, which comprised both the entire mamAB and mamDC clusters as well as further putative operons encoding a number of magnetosome-associated proteins. A bacterial artificial chromosome clone partially covering the deleted region was isolated from the genomic library of wild-type M. gryphiswaldense. Sequence analysis of this fragment revealed that all previously identified mam genes were closely linked with genes encoding other magnetosome-associated proteins within less than 35 kb. In addition, this region was remarkably rich in insertion elements and harbored a considerable number of unknown gene families which appeared to be specific for magnetotactic bacteria. Overall, these findings suggest the existence of a putative large magnetosome island in M. gryphiswaldense and other magnetotactic bacteria. PMID:13129949

  19. Angle sensing in magnetotaxis of Magnetospirillum magneticum AMB-1.

    PubMed

    Zhu, Xuejun; Ge, Xin; Li, Ning; Wu, Long-Fei; Luo, Chunxiong; Ouyang, Qi; Tu, Yuhai; Chen, Guanjun

    2014-07-24

    The mechanism of how magnetotactic bacteria navigate along the magnetic field has been a puzzle. Two main models disagree on whether the magnetotactic behavior results from passive alignment with the magnetic field or active sensing of the magnetic force. Here, we quantitatively studied the swimming patterns of Magnetospirillum magneticum AMB-1 cells to understand the origin of their magnetotactic behaviors. Single-cell tracking and swimming pattern analysis showed that the cells follow a mixed run-reverse-tumble pattern. The average run time decreased with the angle between the cell's moving velocity and the external magnetic field. For mutant cells without the methyl-accepting chemotaxis protein (MCP) Amb0994, such dependence disappeared and bacteria failed to align with magnetic field lines. This dysfunction was recovered by complementary Amb0994 on a plasmid. At high magnetic field (>5 mT), all strains with intact magnetosome chains (including the Δamb0994-0995 strains) showed alignment with the external magnetic field. These results suggested that the mechanism for magnetotaxis is magnetic field dependent. Due to the magnetic dipole moment of the cell, the external magnetic field exerts a torque on the cell. In high magnetic fields, this torque is large enough to overcome the random re-orientation of the cell, and the cells align passively with the external magnetic field, much like a compass. In smaller (and biologically more relevant) external fields, the external force alone is not strong enough to align the cell mechanically. However, magnetotactic behaviors persist due to an active sensing mechanism in which the cell senses the torque by Amb0994 and actively regulates the flagella bias accordingly to align its orientation with the external magnetic field. Our results reconciled the two putative models for magnetotaxis and revealed a key molecular component in the underlying magneto-sensing pathway. PMID:24877161

  20. Angle Sensing in Magnetotaxis of Magnetospirillum magneticum AMB-1

    PubMed Central

    Zhu, Xuejun; Ge, Xin; Li, Ning; Wu, Long-Fei; Luo, Chunxiong; Ouyang, Qi; Tu, Yuhai; Chen, Guanjun

    2014-01-01

    The mechanism of how magnetotactic bacteria navigate along magnetic field has been a puzzle. Two main models disagree on whether the magnetotactic behavior results from passive alignment to the magnetic field or active sensing of the magnetic force. Here, we quantitatively studied the swimming patterns of Magnetospirillum magneticum AMB-1 cells to understand the origin of their magnetotaxis behaviors. Single-cell tracking and swimming pattern analysis showed that the cells follow a mixed run/reverse/tumble pattern. The average run time decreased with the angle between the cell’s moving velocity and the external magnetic field. For mutant cells without the methyl-accepting chemotaxis protein (MCP) Amb0994, such dependence disappeared and bacteria failed to align to magnetic field lines. This dysfunction was recovered by complementary amb0994 on plasmid. At high magnetic field (>5mT), all strains with intact magnetosome chains (including the Δamb0994-0995 strain) showed alignment with the external magnetic field. These results suggested that the mechanism for magnetotaxis is magnetic field dependent. Due to the magnetic dipole moment of the cell, the external magnetic field exerts a torque on the cell. In high magnetic fields, this torque is large enough to overcome the random re-orientation of the cell, and the cells align passively with the external magnetic field, much like a compass. In smaller (and biologically more relevant) external fields, the external force alone is not strong enough to align the cell mechanically. However, magnetotactic behaviors persist due to an active sensing mechanism in which the cell senses the torque by Amb0994 and actively regulate the flagella bias accordingly to align its orientation with the external magnetic field. Our results reconciled the two putative models for magnetotaxis and revealed a key molecular component in the underlying magneto-sensing pathway. PMID:24877161

  1. Redox control of iron biomineralization in Magnetospirillum magneticum AMB-1

    NASA Astrophysics Data System (ADS)

    Jones, Stephanie Rhianon

    Magnetotactic bacteria have evolved complex subcellular machinery to construct linear chains of magnetite nanocrystals that allow the host cell to sense direction. Each mixed-valent iron nanoparticle is mineralized from soluble iron within a membrane-encapsulated vesicle termed the magnetosome, which serves as a specialized compartment that regulates the iron, redox, and pH environment of the growing mineral. In order to dissect the biological components that control this process, we have carried out genetic and biochemical studies of proteins proposed to function in iron mineralization in Magnetospirillum magneticum AMB-1. As iron biomineralization by magnetotactic bacteria represents a particularly interesting case for understanding how the production of nanomaterials can be programmed at the genetic level, we also apply synthetic biology techniques towards the production of new cellular materials and new cellular functions. As the production of magnetite requires both the formation of Fe(II) and Fe(III), the redox components of the magnetosome play an essential role in this process. Using genetic complementation studies, we show that the redox cofactors or heme sites of the two putative redox partners, MamP and MamT, are required for magnetite biomineralization in vivo and that removal of one or both sites leads to defects in mineralization. We develop and optimize a heterologous expression method in the E. coli periplasm to cleanly isolate fully heme-loaded MamP for biochemical studies. Spectrochemical redox titrations show that the reduction potential of MamP lies in a different range than other c-type cytochrome involved in either Fe(III) reduction or Fe(II) oxidation. Nonetheless, in vitro mineralization studies with MamP and Fe(II) show that it is able to catalyze the formation of mixed-valent Fe(II)/Fe(III) oxides such as green rust. Biomineralization also requires lattice-templating proteins that guide the growth of the functional crystalline material. We

  2. Characterizing and optimizing magnetosome production of Magnetospirillum sp. XM-1 isolated from Xi'an City Moat, China.

    PubMed

    Wang, Yinzhao; Lin, Wei; Li, Jinhua; Zhang, Tongwei; Li, Ying; Tian, Jiesheng; Gu, Lixin; Heyden, Yvan Vander; Pan, Yongxin

    2015-11-01

    Pure culture of magnetotactic bacteria is desirable to understand their physiology, evolution and biomineralization. Here, we report a new strain Magnetospirillum sp. XM-1 that was recently isolated and cultivated from the eutrophic city moat of Xi'an, China. Magnetosome biomineralization, crystallographic and magnetic properties of XM-1 were characterized by using a combination of transmission electron microscopy and rock magnetic methods. Cell growth and magnetite production was optimized by response surface methodology. We found that the Magnetospirillum strain XM-1 is different from the model strain Magnetospirillum magneticum AMB-1 in terms of magnetite magnetosomes, optimal growth temperature and nutrient requirements. Sodium succinate, sodium nitrate and ferric citrate are the three most significant factors associated with the optimization of cell growth and magnetosome production for XM-1. PMID:26376913

  3. Magnetite Biomineralization in Magnetospirillum magneticum Is Regulated by a Switch-like Behavior in the HtrA Protease MamE.

    PubMed

    Hershey, David M; Browne, Patrick J; Iavarone, Anthony T; Teyra, Joan; Lee, Eun H; Sidhu, Sachdev S; Komeili, Arash

    2016-08-19

    Magnetotactic bacteria are aquatic organisms that produce subcellular magnetic particles in order to orient in the earth's geomagnetic field. MamE, a predicted HtrA protease required to produce magnetite crystals in the magnetotactic bacterium Magnetospirillum magneticum AMB-1, was recently shown to promote the proteolytic processing of itself and two other biomineralization factors in vivo Here, we have analyzed the in vivo processing patterns of three proteolytic targets and used this information to reconstitute proteolysis with a purified form of MamE. MamE cleaves a custom peptide substrate with positive cooperativity, and its autoproteolysis can be stimulated with exogenous substrates or peptides that bind to either of its PDZ domains. A misregulated form of the protease that circumvents specific genetic requirements for proteolysis causes biomineralization defects, showing that proper regulation of its activity is required during magnetite biosynthesis in vivo Our results represent the first reconstitution of the proteolytic activity of MamE and show that its behavior is consistent with the previously proposed checkpoint model for biomineralization. PMID:27302060

  4. Synthesis of bacterial magnetic particles during cell cycle of Magnetospirillum magneticum AMB-1.

    PubMed

    Yang, C D; Takeyama, H; Tanaka, T; Hasegawa, A; Matsunaga, T

    2001-01-01

    We investigated the relationship between the synthesis of bacterial magnetic particles (BMPs) and the transcription of magA gene-encoding iron transport protein using synchronous culture of Magnetospirillum magneticum AMB-1. Synchronously cultured cells were subjected to transmission electron microscopic observation and fluorescence in situ hybridization. The average number of BMPs slowly increased in the cell with increasing cell size. A sharp increase in BMPs occurred just before cell division and resulted in maximum BMP production of 30 particles/cell. The transcription of magA was regulated immediately before and after cell division. PMID:11963844

  5. Isolation of Magnetospirillum magneticum AMB-1 mutants defective in bacterial magnetic particle synthesis by transposon mutagenesis.

    PubMed

    Wahyudi, A T; Takeyama, H; Matsunaga, T

    2001-01-01

    Nonmagnetic mutants of Magnetospirillum magneticum AMB-1 were recovered following mini-Tn5 transposon mutagenesis. Transconjugants with kanamycin resistance were obtained at a frequency of 2.7 x 10(-7) per recipient. Of 3327 transconjugants, 62 were defective for bacterial magnetic particle (BMP) synthesis. The frequency of independent transposition events for nonmagnetic mutants was about 1.4% in transconjugants. Further analysis of DNA sequences flanking transposon by inverted polymerase chain reaction allowed isolation of at least 10 genes or DNA sequences involved in BMP synthesis in M. magneticum AMB-1. PMID:11963843

  6. The chemical formula of a magnetotactic bacterium.

    PubMed

    Naresh, Mohit; Das, Sayoni; Mishra, Prashant; Mittal, Aditya

    2012-05-01

    Elucidation of the chemical logic of life is one of the grand challenges in biology, and essential to the progress of the upcoming field of synthetic biology. Treatment of microbial cells explicitly as a "chemical" species in controlled reaction (growth) environments has allowed fascinating discoveries of elemental formulae of a few species that have guided the modern views on compositions of a living cell. Application of mass and energy balances on living cells has proved to be useful in modeling of bioengineering systems, particularly in deriving optimized media compositions for growing microorganisms to maximize yields of desired bio-derived products by regulating intra-cellular metabolic networks. In this work, application of elemental mass balance during growth of Magnetospirillum gryphiswaldense in bioreactors has resulted in the discovery of the chemical formula of the magnetotactic bacterium. By developing a stoichiometric equation characterizing the formation of a magnetotactic bacterial cell, coupled with rigorous experimental measurements and robust calculations, we report the elemental formula of M. gryphiswaldense cell as CH(2.06)O(0.13)N(0.28)Fe(1.74×10(-3)). Remarkably, we find that iron metabolism during growth of this magnetotactic bacterium is much more correlated individually with carbon and nitrogen, compared to carbon and nitrogen with each other, indicating that iron serves more as a nutrient during bacterial growth rather than just a mineral. Magnetotactic bacteria have not only invoked some interest in the field of astrobiology for the last two decades, but are also prokaryotes having the unique ability of synthesizing membrane bound intracellular organelles. Our findings on these unique prokaryotes are a strong addition to the limited repertoire, of elemental compositions of living cells, aimed at exploring the chemical logic of life. PMID:22170293

  7. A mutation upstream of an ATPase gene significantly increases magnetosome production in Magnetospirillum gryphiswaldense.

    PubMed

    Liu, Jiangning; Ding, Yao; Jiang, Wei; Tian, Jiesheng; Li, Ying; Li, Jilun

    2008-12-01

    A mutant of Magnetospirillum gryphiswaldense, NPHB, was obtained from a conjugation experiment. An aberrant recombination occurred between a putative elongation factor-G gene (fus-like) of the bacterial chromosome and the chloramphenicol resistant gene (cat) of a suicide vector, pSUP202. Complementary experiments and transcription analysis of genes around the recombinant site showed that the cat promoter enhanced the expression of adenosine triphosphatase gene downstream. Adenosine triphosphate hydrolyzing activity in NPHB was 35% higher than in the wild-type strain (M. gryphiswaldense MSR-1). NPHB accumulated 71% less poly-beta-hydroxybutyrate and consumed 56% more oxygen and 40% more lactate than MSR-1. The magnetosome content of NPHB was 69% higher than MSR-1 in flask culture. NPHB cultured in a 7.5-L bioreactor gave a maximum yield of 58.4 +/- 6.4 mg magnetosomes per liter. PMID:18800186

  8. A novel role for Crp in controlling magnetosome biosynthesis in Magnetospirillum gryphiswaldense MSR-1

    PubMed Central

    Wen, Tong; Guo, Fangfang; Zhang, Yunpeng; Tian, Jiesheng; Li, Ying; Li, Jilun; Jiang, Wei

    2016-01-01

    Magnetotactic bacteria (MTB) are specialized microorganisms that synthesize intracellular magnetite particles called magnetosomes. Although many studies have focused on the mechanism of magnetosome synthesis, it remains unclear how these structures are formed. Recent reports have suggested that magnetosome formation is energy dependent. To investigate the relationship between magnetosome formation and energy metabolism, a global regulator, named Crp, which mainly controls energy and carbon metabolism in most microorganisms, was genetically disrupted in Magnetospirillum gryphiswaldense MSR-1. Compared with the wild-type or complemented strains, the growth, ferromagnetism and intracellular iron content of crp-deficient mutant cells were dramatically decreased. Transmission electron microscopy (TEM) showed that magnetosome synthesis was strongly impaired by the disruption of crp. Further gene expression profile analysis showed that the disruption of crp not only influenced genes related to energy and carbon metabolism, but a series of crucial magnetosome island (MAI) genes were also down regulated. These results indicate that Crp is essential for magnetosome formation in MSR-1. This is the first time to demonstrate that Crp plays an important role in controlling magnetosome biomineralization and provides reliable expression profile data that elucidate the mechanism of Crp regulation of magnetosome formation in MSR-1. PMID:26879571

  9. Transcriptome analysis reveals physiological characteristics required for magnetosome formation in Magnetospirillum gryphiswaldense MSR-1.

    PubMed

    Wang, Xu; Wang, Qing; Zhang, Yang; Wang, Yinjia; Zhou, Yuan; Zhang, Weijia; Wen, Tong; Li, Li; Zuo, Meiqing; Zhang, Ziding; Tian, Jiesheng; Jiang, Wei; Li, Ying; Wang, Lei; Li, Jilun

    2016-06-01

    Magnetosome synthesis ability of Magnetospirillum gryphiswaldense MSR-1 in an autofermentor can be precisely controlled through strict control of dissolved oxygen concentration. In this study, using transcriptome data we discovered gene transcriptional differences and compared physiological characteristics of MSR-1 cells cultured under aerobic (high-oxygen) and micro-aerobic (low-oxygen) conditions. The results showed that 77 genes were up-regulated and 95 genes were down-regulated significantly under micro-aerobic situation. These genes were involved primarily in the categories of cell metabolism, transport, regulation and unknown-function proteins. The nutrient transport and physiological metabolism were slowed down under micro-aerobic condition, whereas dissimilatory denitrification pathways were activated and it may supplemental energy was made available for magnetosome synthesis. The result suggested that the genes of magnetosome membrane proteins (Mam and Mms) are not directly regulated by oxygen level, or are constitutively expressed. A proposed regulatory network of differentially expressed genes reflects the complexity of physiological metabolism in MSR-1, and suggests that some yet-unknown functional proteins play important roles such as ferric iron uptake and transport during magnetosome synthesis. The transcriptome data provides a holistic view of the responses of MSR-1 cells to differing oxygen levels. This approach will give new insights into general principles of magnetosome formation. PMID:27043321

  10. mamO and mamE genes are essential for magnetosome crystal biomineralization in Magnetospirillum gryphiswaldense MSR-1.

    PubMed

    Yang, Wei; Li, Ruiguo; Peng, Tao; Zhang, Yang; Jiang, Wei; Li, Ying; Li, Jilun

    2010-10-01

    Four non-magnetic mutants of Magnetospirillum gryphiswaldense strain MSR-1 were isolated by transposon mutagenesis and found to contain interruption of either the mamO or mamE gene within the mamAB operon. Studies indicated that mamO and mamE genes are essential for magnetosome crystal biomineralization in MSR-1. This is the first report of a single gene (mamO or mamE) whose mutation affects crystal biomineralization in MSR-1. PMID:20674739

  11. Sudden motility reversal indicates sensing of magnetic field gradients in Magnetospirillum magneticum AMB-1 strain

    PubMed Central

    González, Lina M; Ruder, Warren C; Mitchell, Aaron P; Messner, William C; LeDuc, Philip R

    2015-01-01

    Many motile unicellular organisms have evolved specialized behaviors for detecting and responding to environmental cues such as chemical gradients (chemotaxis) and oxygen gradients (aerotaxis). Magnetotaxis is found in magnetotactic bacteria and it is defined as the passive alignment of these cells to the geomagnetic field along with active swimming. Herein we show that Magnetospirillum magneticum (AMB-1) show a unique set of responses that indicates they sense and respond not only to the direction of magnetic fields by aligning and swimming, but also to changes in the magnetic field or magnetic field gradients. We present data showing that AMB-1 cells exhibit sudden motility reversals when we impose them to local magnetic field gradients. Our system employs permalloy (Ni80Fe20) islands to curve and diverge the magnetic field lines emanating from our custom-designed Helmholtz coils in the vicinity of the islands (creating a drop in the field across the islands). The three distinct movements we have observed as they approach the permalloy islands are: unidirectional, single reverse and double reverse. Our findings indicate that these reverse movements occur in response to magnetic field gradients. In addition, using a permanent magnet we found further evidence that supports this claim. Motile AMB-1 cells swim away from the north and south poles of a permanent magnet when the magnet is positioned less than ∼30 mm from the droplet of cells. All together, these results indicate previously unknown response capabilities arising from the magnetic sensing systems of AMB-1 cells. These responses could enable them to cope with magnetic disturbances that could in turn potentially inhibit their efficient search for nutrients. PMID:25478682

  12. Sudden motility reversal indicates sensing of magnetic field gradients in Magnetospirillum magneticum AMB-1 strain.

    PubMed

    González, Lina M; Ruder, Warren C; Mitchell, Aaron P; Messner, William C; LeDuc, Philip R

    2015-06-01

    Many motile unicellular organisms have evolved specialized behaviors for detecting and responding to environmental cues such as chemical gradients (chemotaxis) and oxygen gradients (aerotaxis). Magnetotaxis is found in magnetotactic bacteria and it is defined as the passive alignment of these cells to the geomagnetic field along with active swimming. Herein we show that Magnetospirillum magneticum (AMB-1) show a unique set of responses that indicates they sense and respond not only to the direction of magnetic fields by aligning and swimming, but also to changes in the magnetic field or magnetic field gradients. We present data showing that AMB-1 cells exhibit sudden motility reversals when we impose them to local magnetic field gradients. Our system employs permalloy (Ni(80)Fe(20)) islands to curve and diverge the magnetic field lines emanating from our custom-designed Helmholtz coils in the vicinity of the islands (creating a drop in the field across the islands). The three distinct movements we have observed as they approach the permalloy islands are: unidirectional, single reverse and double reverse. Our findings indicate that these reverse movements occur in response to magnetic field gradients. In addition, using a permanent magnet we found further evidence that supports this claim. Motile AMB-1 cells swim away from the north and south poles of a permanent magnet when the magnet is positioned less than ∼30 mm from the droplet of cells. All together, these results indicate previously unknown response capabilities arising from the magnetic sensing systems of AMB-1 cells. These responses could enable them to cope with magnetic disturbances that could in turn potentially inhibit their efficient search for nutrients. PMID:25478682

  13. Changes of cell growth and magnetosome biomineralization in Magnetospirillum magneticum AMB-1 after ultraviolet-B irradiation

    PubMed Central

    Wang, Yinzhao; Lin, Wei; Li, Jinhua; Pan, Yongxin

    2013-01-01

    Effects of ultraviolet radiation on microorganisms are of great interest in field of microbiology and planetary sciences. In the present study, we used Magnetospirillum magneticum AMB-1 as a model organism to examine the influence of ultraviolet-B (UV-B) radiation on cell growth and magnetite biomineralization of magnetotactic bacteria (MTB). Live AMB-1 cells were exposed to UV-B radiation for 60, 300 and 900 s, which correspond to radiation doses of 120 J/m2, 600 J/m2, and 1800 J/m2, respectively. After irradiation, the amounts of cyclobutane pyrimidine dimers (CPD) and reactive oxygen species (ROS) of the cells were increased, and cell growth was stunted up to ~170 h, depending on the UV-B radiation doses. The UV-B irradiated cells also produced on average more magnetite crystals with larger grain sizes and longer chains, which results in changes of their magnetic properties. PMID:24391631

  14. Changes of cell growth and magnetosome biomineralization in Magnetospirillum magneticum AMB-1 after ultraviolet-B irradiation.

    PubMed

    Wang, Yinzhao; Lin, Wei; Li, Jinhua; Pan, Yongxin

    2013-01-01

    Effects of ultraviolet radiation on microorganisms are of great interest in field of microbiology and planetary sciences. In the present study, we used Magnetospirillum magneticum AMB-1 as a model organism to examine the influence of ultraviolet-B (UV-B) radiation on cell growth and magnetite biomineralization of magnetotactic bacteria (MTB). Live AMB-1 cells were exposed to UV-B radiation for 60, 300 and 900 s, which correspond to radiation doses of 120 J/m(2), 600 J/m(2), and 1800 J/m(2), respectively. After irradiation, the amounts of cyclobutane pyrimidine dimers (CPD) and reactive oxygen species (ROS) of the cells were increased, and cell growth was stunted up to ~170 h, depending on the UV-B radiation doses. The UV-B irradiated cells also produced on average more magnetite crystals with larger grain sizes and longer chains, which results in changes of their magnetic properties. PMID:24391631

  15. Deletion of the ftsZ-like gene results in the production of superparamagnetic magnetite magnetosomes in Magnetospirillum gryphiswaldense.

    PubMed

    Ding, Yao; Li, Jinhua; Liu, Jiangning; Yang, Jing; Jiang, Wei; Tian, Jiesheng; Li, Ying; Pan, Yongxin; Li, Jilun

    2010-02-01

    Magnetotactic bacteria (MTB) synthesize unique organelles termed "magnetosomes," which are membrane-enclosed structures containing crystals of magnetite or greigite. Magnetosomes form a chain around MamK cytoskeletal filaments and provide the basis for the ability of MTB to navigate along geomagnetic field lines in order to find optimal microaerobic habitats. Genomes of species of the MTB genus Magnetospirillum, in addition to a gene encoding the tubulin-like FtsZ protein (involved in cell division), contain a second gene termed "ftsZ-like," whose function is unknown. In the present study, we found that the ftsZ-like gene of Magnetospirillum gryphiswaldense strain MSR-1 belongs to a 4.9-kb mamXY polycistronic transcription unit. We then purified the recombinant FtsZ-like protein to homogeneity. The FtsZ-like protein efficiently hydrolyzed ATP and GTP, with ATPase and GTPase activity levels of 2.17 and 5.56 mumol phosphorus per mol protein per min, respectively. The FtsZ-like protein underwent GTP-dependent polymerization into long filamentous bundles in vitro. To determine the role of the ftsZ-like gene, we constructed a ftsZ-like mutant (DeltaftsZ-like mutant) and its complementation strain (DeltaftsZ-like_C strain). Growth of DeltaftsZ-like cells was similar to that of the wild type, indicating that the DeltaftsZ-like gene is not involved in cell division. Transmission electron microscopic observations indicated that the DeltaftsZ-like cells, in comparison to wild-type cells, produced smaller magnetosomes, with poorly defined morphology and irregular alignment, including large gaps. Magnetic analyses showed that DeltaftsZ-like produced mainly superparamagnetic (SP) magnetite particles, whereas wild-type and DeltaftsZ-like_C cells produced mainly single-domain (SD) particles. Our findings suggest that the FtsZ-like protein is required for synthesis of SD particles and magnetosomes in M. gryphiswaldense. PMID:20023033

  16. Deletion of the ftsZ-Like Gene Results in the Production of Superparamagnetic Magnetite Magnetosomes in Magnetospirillum gryphiswaldense▿ †

    PubMed Central

    Ding, Yao; Li, Jinhua; Liu, Jiangning; Yang, Jing; Jiang, Wei; Tian, Jiesheng; Li, Ying; Pan, Yongxin; Li, Jilun

    2010-01-01

    Magnetotactic bacteria (MTB) synthesize unique organelles termed “magnetosomes,” which are membrane-enclosed structures containing crystals of magnetite or greigite. Magnetosomes form a chain around MamK cytoskeletal filaments and provide the basis for the ability of MTB to navigate along geomagnetic field lines in order to find optimal microaerobic habitats. Genomes of species of the MTB genus Magnetospirillum, in addition to a gene encoding the tubulin-like FtsZ protein (involved in cell division), contain a second gene termed “ftsZ-like,” whose function is unknown. In the present study, we found that the ftsZ-like gene of Magnetospirillum gryphiswaldense strain MSR-1 belongs to a 4.9-kb mamXY polycistronic transcription unit. We then purified the recombinant FtsZ-like protein to homogeneity. The FtsZ-like protein efficiently hydrolyzed ATP and GTP, with ATPase and GTPase activity levels of 2.17 and 5.56 μmol phosphorus per mol protein per min, respectively. The FtsZ-like protein underwent GTP-dependent polymerization into long filamentous bundles in vitro. To determine the role of the ftsZ-like gene, we constructed a ftsZ-like mutant (ΔftsZ-like mutant) and its complementation strain (ΔftsZ-like_C strain). Growth of ΔftsZ-like cells was similar to that of the wild type, indicating that the ΔftsZ-like gene is not involved in cell division. Transmission electron microscopic observations indicated that the ΔftsZ-like cells, in comparison to wild-type cells, produced smaller magnetosomes, with poorly defined morphology and irregular alignment, including large gaps. Magnetic analyses showed that ΔftsZ-like produced mainly superparamagnetic (SP) magnetite particles, whereas wild-type and ΔftsZ-like_C cells produced mainly single-domain (SD) particles. Our findings suggest that the FtsZ-like protein is required for synthesis of SD particles and magnetosomes in M. gryphiswaldense. PMID:20023033

  17. The magnetosome membrane protein, MmsF, is a major regulator of magnetite biomineralization in Magnetospirillum magneticum AMB-1.

    PubMed

    Murat, Dorothée; Falahati, Veesta; Bertinetti, Luca; Csencsits, Roseann; Körnig, André; Downing, Kenneth; Faivre, Damien; Komeili, Arash

    2012-08-01

    Magnetotactic bacteria (MTB) use magnetosomes, membrane-bound crystals of magnetite or greigite, for navigation along geomagnetic fields. In Magnetospirillum magneticum sp. AMB-1, and other MTB, a magnetosome gene island (MAI) is essential for every step of magnetosome formation. An 8-gene region of the MAI encodes several factors implicated in control of crystal size and morphology in previous genetic and proteomic studies. We show that these factors play a minor role in magnetite biomineralization in vivo. In contrast, MmsF, a previously uncharacterized magnetosome membrane protein encoded within the same region plays a dominant role in defining crystal size and morphology and is sufficient for restoring magnetite synthesis in the absence of the other major biomineralization candidates. In addition, we show that the 18 genes of the mamAB gene cluster of the MAI are sufficient for the formation of an immature magnetosome organelle. Addition of MmsF to these 18 genes leads to a significant enhancement of magnetite biomineralization and an increase in the cellular magnetic response. These results define a new biomineralization protein and lay down the foundation for the design of autonomous gene cassettes for the transfer of the magnetic phenotype in other bacteria. PMID:22716969

  18. The magnetosome membrane protein, MmsF, is a major regulator of magnetite biomineralization in Magnetospirillum magneticum AMB-1

    PubMed Central

    Murat, Dorothée; Falahati, Veesta; Bertinetti, Luca; Csencsits, Roseann; Körnig, André; Downing, Kenneth; Faivre, Damien; Komeili, Arash

    2013-01-01

    Summary Magnetotactic bacteria (MTB) use magnetosomes, membrane bound crystals of magnetite or greigite, for navigation along geomagnetic fields. In Magnetospirillum magneticum sp. AMB-1, and other MTB, a magnetosome gene island (MAI) is essential for every step of magnetosome formation. An 8-gene region of the MAI encodes several factors implicated in control of crystal size and morphology in previous genetic and proteomic studies. We show that these factors play a minor role in magnetite biomineralization in vivo. In contrast, MmsF, a previously uncharacterized magnetosome membrane protein encoded within the same region plays a dominant role in defining crystal size and morphology and is sufficient for restoring magnetite synthesis in the absence of the other major biomineralization candidates. In addition, we show that the 18 genes of the mamAB gene cluster of the MAI are sufficient for the formation of an immature magnetosome organelle. Addition of MmsF to these 18 genes leads to a significant enhancement of magnetite biomineralization and an increase in the cellular magnetic response. These results define a new biomineralization protein and lay down the foundation for the design of autonomous gene cassettes for the transfer of the magnetic phenotype in other bacteria. PMID:22716969

  19. Genetic and biochemical investigations of the role of MamP in redox control of iron biomineralization in Magnetospirillum magneticum

    PubMed Central

    Jones, Stephanie R.; Wilson, Tiffany D.; Brown, Margaret E.; Rahn-Lee, Lilah; Yu, Yi; Fredriksen, Laura L.; Ozyamak, Ertan; Komeili, Arash; Chang, Michelle C. Y.

    2015-01-01

    Magnetotactic bacteria have evolved complex subcellular machinery to construct linear chains of magnetite nanocrystals that allow the host cell to sense direction. Each mixed-valent iron nanoparticle is mineralized from soluble iron within a membrane-encapsulated vesicle termed the magnetosome, which serves as a specialized compartment that regulates the iron, redox, and pH environment of the growing mineral. To dissect the biological components that control this process, we have carried out a genetic and biochemical study of proteins proposed to function in iron mineralization. In this study, we show that the redox sites of c-type cytochromes of the Magnetospirillum magneticum AMB-1 magnetosome island, MamP and MamT, are essential to their physiological function and that ablation of one or both heme motifs leads to loss of function, suggesting that their ability to carry out redox chemistry in vivo is important. We also develop a method to heterologously express fully heme-loaded MamP from AMB-1 for in vitro biochemical studies, which show that its Fe(III)–Fe(II) redox couple is set at an unusual potential (−89 ± 11 mV) compared with other related cytochromes involved in iron reduction or oxidation. Despite its low reduction potential, it remains competent to oxidize Fe(II) to Fe(III) and mineralize iron to produce mixed-valent iron oxides. Finally, in vitro mineralization experiments suggest that Mms mineral-templating peptides from AMB-1 can modulate the iron redox chemistry of MamP. PMID:25775527

  20. Light scattering and birefrigence by magnetic bacteria

    SciTech Connect

    Johnston, R.G.; Jacobson, P.L.

    1990-01-01

    The bacterium Aquaspirillum magnetotacticum grows its own internal single domain magnets. For a number of reasons, these magnets make the bacterium an extremely interesting scattering particle. We are engaging in light scattering and birefringence studies on Aquaspirillum magnetotacticum. 9 refs., 4 figs.

  1. Magnetite magnetosome and fragmental chain formation of Magnetospirillum magneticum AMB-1: transmission electron microscopy and magnetic observations

    NASA Astrophysics Data System (ADS)

    Li, Jinhua; Pan, Yongxin; Chen, Guanjun; Liu, Qingsong; Tian, Lanxiang; Lin, Wei

    2009-04-01

    Stable single-domain (SD) magnetite formed intracellularly by magnetotactic bacteria is of fundamental interest in sedimentary and environmental magnetism. In this study, we studied the time course of magnetosome growth and magnetosome chain formation (0-96 hr) in Magnetospirillum magneticum AMB-1 by transmission electron microscopy (TEM) observation and rock magnetism. The initial non-magnetic cells were microaerobically batch cultured at 26 °C in a modified magnetic spirillum growth medium. TEM observations indicated that between 20 and 24 hr magnetosome crystals began to mineralize simultaneously at multiple sites within the cell body, followed by a phase of rapid growth lasting up to 48 hr cultivation. The synthesized magnetosomes were found to be assembled into 3-5 subchains, which were linearly aligned along the long axis of the cell, supporting the idea that magnetosome vesicles were linearly anchored to the inner membrane of cell. By 96 hr cultivation, 14 cubo-octahedral magnetosome crystals in average with a mean grain size of ~44.5 nm were formed in a cell. Low-temperature (10-300 K) thermal demagnetization, room-temperature hysteresis loops and first-order reversal curves (FORCs) were conducted on whole cell samples. Both coercivity (4.7-18.1 mT) and Verwey transition temperature (100-106 K) increase with increasing cultivation time length, which can be explained by increasing grain size and decreasing non-stoichiometry of magnetite, respectively. Shapes of hysteresis loops and FORCs indicated each subchain behaving as an `ideal' uniaxial SD particle and extremely weak magnetostatic interaction fields between subchains. Low-temperature thermal demagnetization of remanence demonstrated that the Moskowitz test is valid for such linear subchain configurations (e.g. δFC/δZFC > 2.0), implying that the test is applicable to ancient sediments where magnetosome chains might have been broken up into short chains due to disintegration of the organic scaffold

  2. Crystallization and preliminary crystallographic analysis of the C-terminal domain of MamM, a magnetosome-associated protein from Magnetospirillum gryphiswaldense MSR-1

    PubMed Central

    Zeytuni, Natalie; Offer, Tal; Davidov, Geula; Zarivach, Raz

    2012-01-01

    MamM is a unique magnetosome-associated protein that shares substantial homology with cation diffusion facilitator (CDF) proteins, a group of heavy-metal-ion efflux transporters that participate in metal-ion homeostasis in all domains of life. Magnetotactic bacteria utilize CDF proteins in iron-oxide biomineralization and in magnetosome formation. Here, the crystallization and preliminary X-ray analysis of recombinant Magnetospirillum gryphiswaldense MamM is reported. The C-terminal domain of MamM was crystallized in the orthorhombic space group C2221, with unit-cell parameters a = 37.1, b = 94.0, c = 53.3 Å. X-ray diffraction data were collected to a resolution of 2.0 Å. PMID:22869124

  3. Single Bacterium Detection Using Sers

    NASA Astrophysics Data System (ADS)

    Gonchukov, S. A.; Baikova, T. V.; Alushin, M. V.; Svistunova, T. S.; Minaeva, S. A.; Ionin, A. A.; Kudryashov, S. I.; Saraeva, I. N.; Zayarny, D. A.

    2016-02-01

    This work is devoted to the study of a single Staphylococcus aureus bacterium detection using surface-enhanced Raman spectroscopy (SERS) and resonant Raman spectroscopy (RS). It was shown that SERS allows increasing sensitivity of predominantly low frequency lines connected with the vibrations of Amide, Proteins and DNA. At the same time the lines of carotenoids inherent to this kind of bacterium are well-detected due to the resonance Raman scattering mechanism. The reproducibility and stability of Raman spectra strongly depend on the characteristics of nanostructured substrate, and molecular structure and size of the tested biological object.

  4. The FtsZ-Like Protein FtsZm of Magnetospirillum gryphiswaldense Likely Interacts with Its Generic Homolog and Is Required for Biomineralization under Nitrate Deprivation

    PubMed Central

    Müller, Frank D.; Raschdorf, Oliver; Nudelman, Hila; Messerer, Maxim; Katzmann, Emanuel; Plitzko, Jürgen M.; Zarivach, Raz

    2014-01-01

    Midcell selection, septum formation, and cytokinesis in most bacteria are orchestrated by the eukaryotic tubulin homolog FtsZ. The alphaproteobacterium Magnetospirillum gryphiswaldense (MSR-1) septates asymmetrically, and cytokinesis is linked to splitting and segregation of an intracellular chain of membrane-enveloped magnetite crystals (magnetosomes). In addition to a generic, full-length ftsZ gene, MSR-1 contains a truncated ftsZ homolog (ftsZm) which is located adjacent to genes controlling biomineralization and magnetosome chain formation. We analyzed the role of FtsZm in cell division and biomineralization together with the full-length MSR-1 FtsZ protein. Our results indicate that loss of FtsZm has a strong effect on microoxic magnetite biomineralization which, however, could be rescued by the presence of nitrate in the medium. Fluorescence microscopy revealed that FtsZm-mCherry does not colocalize with the magnetosome-related proteins MamC and MamK but is confined to asymmetric spots at midcell and at the cell pole, coinciding with the FtsZ protein position. In Escherichia coli, both FtsZ homologs form distinct structures but colocalize when coexpressed, suggesting an FtsZ-dependent recruitment of FtsZm. In vitro analyses indicate that FtsZm is able to interact with the FtsZ protein. Together, our data suggest that FtsZm shares key features with its full-length homolog but is involved in redox control for magnetite crystallization. PMID:24272781

  5. Preparation and anti-tumor efficiency evaluation of doxorubicin-loaded bacterial magnetosomes: magnetic nanoparticles as drug carriers isolated from Magnetospirillum gryphiswaldense.

    PubMed

    Sun, Jian-Bo; Duan, Jin-Hong; Dai, Shun-Ling; Ren, Jun; Guo, Lin; Jiang, Wei; Li, Ying

    2008-12-15

    Bacterial magnetosomes (BMs) are commonly used as vehicles for certain enzymes, nucleic acids and antibodies, although they have never been considered drug carriers. To evaluate the clinical potential of BMs extracted from Magnetospirillum gryphiswaldense in cancer therapy, doxorubicin (DOX) was loaded onto the purified BMs at a ratio of 0.87 +/- 0.08 mg/mg using glutaraldehyde. The DOX-coupled BMs (DBMs) and BMs exhibited uniform sizes and morphology evaluated by TEM. The diameters of DBMs and BMs obtained by AFM were 71.02 +/- 6.73 and 34.93 +/- 8.24 nm, respectively. The DBMs released DOX slowly into serum and maintained at least 80% stability following 48 h of incubation. In vitro cytotoxic tests showed that the DBMs were cytotoxic to HL60 and EMT-6 cells, manifested as inhibition of cell proliferation and suppression in c-myc expression, consistent with DOX. These observations depicted in vitro antitumor property of DBMs similar to DOX. The approach of coupling DOX to magnetosomes may have clinical potential in anti-tumor drug delivery. PMID:18980188

  6. Iron Response Regulator Protein IrrB in Magnetospirillum gryphiswaldense MSR-1 Helps Control the Iron/Oxygen Balance, Oxidative Stress Tolerance, and Magnetosome Formation

    PubMed Central

    Wang, Qing; Wang, Meiwen; Wang, Xu; Guan, Guohua; Peng, Youliang; Li, Jilun

    2015-01-01

    Magnetotactic bacteria are capable of forming nanosized, membrane-enclosed magnetosomes under iron-rich and oxygen-limited conditions. The complete genomic sequence of Magnetospirillum gryphiswaldense strain MSR-1 has been analyzed and found to contain five fur homologue genes whose protein products are predicted to be involved in iron homeostasis and the response to oxidative stress. Of these, only the MGMSRv2_3149 gene (irrB) was significantly downregulated under high-iron and low-oxygen conditions, during the transition of cell growth from the logarithmic to the stationary phase. The encoded protein, IrrB, containing the conserved HHH motif, was identified as an iron response regulator (Irr) protein belonging to the Fur superfamily. To investigate the function of IrrB, we constructed an irrB deletion mutant (ΔirrB). The levels of cell growth and magnetosome formation were lower in the ΔirrB strain than in the wild type (WT) under both high-iron and low-iron conditions. The ΔirrB strain also showed lower levels of iron uptake and H2O2 tolerance than the WT. Quantitative real-time reverse transcription-PCR analysis indicated that the irrB mutation reduced the expression of numerous genes involved in iron transport, iron storage, heme biosynthesis, and Fe-S cluster assembly. Transcription studies of the other fur homologue genes in the ΔirrB strain indicated complementary functions of the Fur proteins in MSR-1. IrrB appears to be directly responsible for iron metabolism and homeostasis and to be indirectly involved in magnetosome formation. We propose two IrrB-regulated networks (under high- and low-iron conditions) in MSR-1 cells that control the balance of iron and oxygen metabolism and account for the coexistence of five Fur homologues. PMID:26386052

  7. A key time point for cell growth and magnetosome synthesis of Magnetospirillum gryphiswaldense based on real-time analysis of physiological factors

    PubMed Central

    Yang, Jing; Li, Shuqi; Huang, Xiuliang; Tang, Tao; Jiang, Weizhong; Zhang, Tongwei; Li, Ying

    2013-01-01

    Pure culture of magnetotactic bacteria with high magnetosome yield has been achieved for only a few strains. The major obstacles involve the nutritional requirements and culture conditions of the cells. To increase cell density and magnetosome production, it is necessary to elucidate the physiological characteristics of a particular strain during cell growth and develop an appropriate artificial control strategy. Large-scale culture of Magnetospirillum gryphiswaldense strain MSR-1 was successfully performed for 48 h in a 42-L autofermentor, and several key physiological parameters were measured in real time. Maximal values of cell density (OD565) (19.4) and cell yield (dry weight) (4.76 g/L) were attained at 40 h. The key time point for cell growth and magnetosome formation was found to be 18–20 h. At this point, cells entered the log phase of growth, the maximal values of Cmag (1.78), iron content (0.47%), and magnetosome number (26 ± 3 per cell) were observed, superoxide dismutase (SOD) activity began to decrease more rapidly, ATP content dropped to an extremely low level (0.17 fmol), and reducing power (NADH/NAD+ ratio) began to increase very rapidly. Excessive levels of dissolved oxygen (≥20 ppb) and lactic acid in the medium caused notable cytotoxic effects after 20 h. Artificial control measures for fermentation must be based on realistic cell physiological conditions. At the key time point (18–20 h), cell density is high and magnetosomes have matured. The process of magnetosome synthesis involves a high consumption of ATP and reducing power, and the cells require replenishment of nutrients prior to the 18–20 h time point. Culture conditions that effectively minimize dissolved oxygen accumulation, lactic acid content, and reducing power at this point will enhance magnetosome yield without obvious inhibition of cell growth. PMID:23898327

  8. MamX encoded by the mamXY operon is involved in control of magnetosome maturation in Magnetospirillum gryphiswaldense MSR-1

    PubMed Central

    2013-01-01

    Background Magnetotactic bacteria produce membrane-enveloped magnetite crystals (magnetosomes) whose formation is controlled primarily by a gene island termed the magnetosome island (MAI). Characterization of single gene and operon function in MAI has elucidated in part the genetic basis of magnetosome formation. The mamX gene, located in the mamXY operon, is highly conserved in the MAI of all Magnetospirillum strains studied to date. Little is known regarding the function of mamX in the process of biomineralization. Results A mamX deletion mutant (∆mamX) and its complemented strain (CmamX) by conjugation in M. gryphiswaldense strain MSR-1 were constructed. There were no striking differences in cell growth among ∆mamX, CmamX, and wild-type strain (WT). ∆mamX displayed a much weaker magnetic response than WT. Transmission electron microscopy revealed the presence of irregular, superparamagnetic magnetite particles in ∆mamX, in contrast to regular, single-domain particles in WT and CmamX. The phenotype of ∆mamX was similar to that of an ftsZ-like deleted mutant and mamXY operon deleted mutant reported previously. Quantitative real-time RT-PCR (qPCR) results indicated that the deletion of mamX had differential effects on the transcription levels of the other three genes in the operon. Conclusions The MamX protein plays an important role in controlling magnetosome size, maturation, and crystal form. The four MamXY proteins appear to have redundant functions involved in magnetosome formation. Our findings provide new insights into the coordinated function of MAI genes and operons in magnetosome formation. PMID:24020498

  9. Interplay between Two Bacterial Actin Homologs, MamK and MamK-Like, Is Required for the Alignment of Magnetosome Organelles in Magnetospirillum magneticum AMB-1

    PubMed Central

    Abreu, Nicole; Mannoubi, Soumaya; Ozyamak, Ertan; Pignol, David; Ginet, Nicolas

    2014-01-01

    Many bacterial species contain multiple actin-like proteins tasked with the execution of crucial cell biological functions. MamK, an actin-like protein found in magnetotactic bacteria, is important in organizing magnetosome organelles into chains that are used for navigation along geomagnetic fields. MamK and numerous other magnetosome formation factors are encoded by a genetic island termed the magnetosome island. Unlike most magnetotactic bacteria, Magnetospirillum magneticum AMB-1 (AMB-1) contains a second island of magnetosome-related genes that was named the magnetosome islet. A homologous copy of mamK, mamK-like, resides within this islet and encodes a protein capable of filament formation in vitro. Previous work had shown that mamK-like is expressed in vivo, but its function, if any, had remained unknown. Though MamK-like is highly similar to MamK, it contains a mutation that in MamK and other actins blocks ATPase activity in vitro and filament dynamics in vivo. Here, using genetic analysis, we demonstrate that mamK-like has an in vivo role in assisting organelle alignment. In addition, MamK-like forms filaments in vivo in a manner that is dependent on the presence of MamK and the two proteins interact in a yeast two-hybrid assay. Surprisingly, despite the ATPase active-site mutation, MamK-like is capable of ATP hydrolysis in vitro and promotes MamK filament turnover in vivo. Taken together, these experiments suggest that direct interactions between MamK and MamK-like contribute to magnetosome alignment in AMB-1. PMID:24957623

  10. The Periplasmic Nitrate Reductase Nap Is Required for Anaerobic Growth and Involved in Redox Control of Magnetite Biomineralization in Magnetospirillum gryphiswaldense

    PubMed Central

    Li, Yingjie; Katzmann, Emanuel; Borg, Sarah

    2012-01-01

    The magnetosomes of many magnetotactic bacteria consist of membrane-enveloped magnetite crystals, whose synthesis is favored by a low redox potential. However, the cellular redox processes governing the biomineralization of the mixed-valence iron oxide have remained unknown. Here, we show that in the alphaproteobacterium Magnetospirillum gryphiswaldense, magnetite biomineralization is linked to dissimilatory nitrate reduction. A complete denitrification pathway, including gene functions for nitrate (nap), nitrite (nir), nitric oxide (nor), and nitrous oxide reduction (nos), was identified. Transcriptional gusA fusions as reporters revealed that except for nap, the highest expression of the denitrification genes coincided with conditions permitting maximum magnetite synthesis. Whereas microaerobic denitrification overlapped with oxygen respiration, nitrate was the only electron acceptor supporting growth in the entire absence of oxygen, and only the deletion of nap genes, encoding a periplasmic nitrate reductase, and not deletion of nor or nos genes, abolished anaerobic growth and also delayed aerobic growth in both nitrate and ammonium media. While loss of nosZ or norCB had no or relatively weak effects on magnetosome synthesis, deletion of nap severely impaired magnetite biomineralization and resulted in fewer, smaller, and irregular crystals during denitrification and also microaerobic respiration, probably by disturbing the proper redox balance required for magnetite synthesis. In contrast to the case for the wild type, biomineralization in Δnap cells was independent of the oxidation state of carbon substrates. Altogether, our data demonstrate that in addition to its essential role in anaerobic respiration, the periplasmic nitrate reductase Nap has a further key function by participating in redox reactions required for magnetite biomineralization. PMID:22730130

  11. Iron response regulator protein IrrB in Magnetospirillum gryphiswaldense MSR-1 helps control the iron/oxygen balance, oxidative stress tolerance, and magnetosome formation.

    PubMed

    Wang, Qing; Wang, Meiwen; Wang, Xu; Guan, Guohua; Li, Ying; Peng, Youliang; Li, Jilun

    2015-12-01

    Magnetotactic bacteria are capable of forming nanosized, membrane-enclosed magnetosomes under iron-rich and oxygen-limited conditions. The complete genomic sequence of Magnetospirillum gryphiswaldense strain MSR-1 has been analyzed and found to contain five fur homologue genes whose protein products are predicted to be involved in iron homeostasis and the response to oxidative stress. Of these, only the MGMSRv2_3149 gene (irrB) was significantly downregulated under high-iron and low-oxygen conditions, during the transition of cell growth from the logarithmic to the stationary phase. The encoded protein, IrrB, containing the conserved HHH motif, was identified as an iron response regulator (Irr) protein belonging to the Fur superfamily. To investigate the function of IrrB, we constructed an irrB deletion mutant (ΔirrB). The levels of cell growth and magnetosome formation were lower in the ΔirrB strain than in the wild type (WT) under both high-iron and low-iron conditions. The ΔirrB strain also showed lower levels of iron uptake and H2O2 tolerance than the WT. Quantitative real-time reverse transcription-PCR analysis indicated that the irrB mutation reduced the expression of numerous genes involved in iron transport, iron storage, heme biosynthesis, and Fe-S cluster assembly. Transcription studies of the other fur homologue genes in the ΔirrB strain indicated complementary functions of the Fur proteins in MSR-1. IrrB appears to be directly responsible for iron metabolism and homeostasis and to be indirectly involved in magnetosome formation. We propose two IrrB-regulated networks (under high- and low-iron conditions) in MSR-1 cells that control the balance of iron and oxygen metabolism and account for the coexistence of five Fur homologues. PMID:26386052

  12. Interplay between two bacterial actin homologs, MamK and MamK-Like, is required for the alignment of magnetosome organelles in Magnetospirillum magneticum AMB-1.

    PubMed

    Abreu, Nicole; Mannoubi, Soumaya; Ozyamak, Ertan; Pignol, David; Ginet, Nicolas; Komeili, Arash

    2014-09-01

    Many bacterial species contain multiple actin-like proteins tasked with the execution of crucial cell biological functions. MamK, an actin-like protein found in magnetotactic bacteria, is important in organizing magnetosome organelles into chains that are used for navigation along geomagnetic fields. MamK and numerous other magnetosome formation factors are encoded by a genetic island termed the magnetosome island. Unlike most magnetotactic bacteria, Magnetospirillum magneticum AMB-1 (AMB-1) contains a second island of magnetosome-related genes that was named the magnetosome islet. A homologous copy of mamK, mamK-like, resides within this islet and encodes a protein capable of filament formation in vitro. Previous work had shown that mamK-like is expressed in vivo, but its function, if any, had remained unknown. Though MamK-like is highly similar to MamK, it contains a mutation that in MamK and other actins blocks ATPase activity in vitro and filament dynamics in vivo. Here, using genetic analysis, we demonstrate that mamK-like has an in vivo role in assisting organelle alignment. In addition, MamK-like forms filaments in vivo in a manner that is dependent on the presence of MamK and the two proteins interact in a yeast two-hybrid assay. Surprisingly, despite the ATPase active-site mutation, MamK-like is capable of ATP hydrolysis in vitro and promotes MamK filament turnover in vivo. Taken together, these experiments suggest that direct interactions between MamK and MamK-like contribute to magnetosome alignment in AMB-1. PMID:24957623

  13. Genetic Dissection of the mamAB and mms6 Operons Reveals a Gene Set Essential for Magnetosome Biogenesis in Magnetospirillum gryphiswaldense

    PubMed Central

    Lohße, Anna; Borg, Sarah; Raschdorf, Oliver; Kolinko, Isabel; Tompa, Éva; Pósfai, Mihály; Faivre, Damien; Baumgartner, Jens

    2014-01-01

    Biosynthesis of bacterial magnetosomes, which are intracellular membrane-enclosed, nanosized magnetic crystals, is controlled by a set of >30 specific genes. In Magnetospirillum gryphiswaldense, these are clustered mostly within a large conserved genomic magnetosome island (MAI) comprising the mms6, mamGFDC, mamAB, and mamXY operons. Here, we demonstrate that the five previously uncharacterized genes of the mms6 operon have crucial functions in the regulation of magnetosome biomineralization that partially overlap MamF and other proteins encoded by the adjacent mamGFDC operon. While all other deletions resulted in size reduction, elimination of either mms36 or mms48 caused the synthesis of magnetite crystals larger than those in the wild type (WT). Whereas the mms6 operon encodes accessory factors for crystal maturation, the large mamAB operon contains several essential and nonessential genes involved in various other steps of magnetosome biosynthesis, as shown by single deletions of all mamAB genes. While single deletions of mamL, -P, -Q, -R, -B, -S, -T, and -U showed phenotypes similar to those of their orthologs in a previous study in the related M. magneticum, we found mamI and mamN to be not required for at least rudimentary iron biomineralization in M. gryphiswaldense. Thus, only mamE, -L, -M, -O, -Q, and -B were essential for formation of magnetite, whereas a mamI mutant still biomineralized tiny particles which, however, consisted of the nonmagnetic iron oxide hematite, as shown by high-resolution transmission electron microscopy (HRTEM) and the X-ray absorption near-edge structure (XANES). Based on this and previous studies, we propose an extended model for magnetosome biosynthesis in M. gryphiswaldense. PMID:24816605

  14. A Large Gene Cluster Encoding Several Magnetosome Proteins Is Conserved in Different Species of Magnetotactic Bacteria

    PubMed Central

    Grünberg, Karen; Wawer, Cathrin; Tebo, Bradley M.; Schüler, Dirk

    2001-01-01

    In magnetotactic bacteria, a number of specific proteins are associated with the magnetosome membrane (MM) and may have a crucial role in magnetite biomineralization. We have cloned and sequenced the genes of several of these polypeptides in the magnetotactic bacterium Magnetospirillum gryphiswaldense that could be assigned to two different genomic regions. Except for mamA, none of these genes have been previously reported to be related to magnetosome formation. Homologous genes were found in the genome sequences of M. magnetotacticum and magnetic coccus strain MC-1. The MM proteins identified display homology to tetratricopeptide repeat proteins (MamA), cation diffusion facilitators (MamB), and HtrA-like serine proteases (MamE) or bear no similarity to known proteins (MamC and MamD). A major gene cluster containing several magnetosome genes (including mamA and mamB) was found to be conserved in all three of the strains investigated. The mamAB cluster also contains additional genes that have no known homologs in any nonmagnetic organism, suggesting a specific role in magnetosome formation. PMID:11571158

  15. Novel Waddlia Intracellular Bacterium in Artibeus intermedius Fruit Bats, Mexico

    PubMed Central

    Pierlé, Sebastián Aguilar; Morales, Cirani Obregón; Martínez, Leonardo Perea; Ceballos, Nidia Aréchiga; Rivero, Juan José Pérez; Díaz, Osvaldo López; Brayton, Kelly A.

    2015-01-01

    An intracellular bacterium was isolated from fruit bats (Artibeus intermedius) in Cocoyoc, Mexico. The bacterium caused severe lesions in the lungs and spleens of bats and intracytoplasmic vacuoles in cell cultures. Sequence analyses showed it is related to Waddlia spp. (order Chlamydiales). We propose to call this bacterium Waddlia cocoyoc. PMID:26583968

  16. Novel Waddlia Intracellular Bacterium in Artibeus intermedius Fruit Bats, Mexico.

    PubMed

    Pierlé, Sebastián Aguilar; Morales, Cirani Obregón; Martínez, Leonardo Perea; Ceballos, Nidia Aréchiga; Rivero, Juan José Pérez; Díaz, Osvaldo López; Brayton, Kelly A; Setién, Alvaro Aguilar

    2015-12-01

    An intracellular bacterium was isolated from fruit bats (Artibeus intermedius) in Cocoyoc, Mexico. The bacterium caused severe lesions in the lungs and spleens of bats and intracytoplasmic vacuoles in cell cultures. Sequence analyses showed it is related to Waddlia spp. (order Chlamydiales). We propose to call this bacterium Waddlia cocoyoc. PMID:26583968

  17. Ratoon stunting disease of sugarcane: isolation of the causal bacterium.

    PubMed

    Davis, M J; Gillaspie, A G; Harris, R W; Lawson, R H

    1980-12-19

    A small coryneform bacterium was consistently isolated from sugarcane with ratoon stunting disease and shown to be the causal agent. A similar bacterium was isolated from Bermuda grass. Both strains multiplied in sugarcane and Bermuda grass, but the Bermuda grass strain did not incite the symptoms of ratoon stunting disease in sugarcane. Shoot growth in Bermuda grass was retarded by both strains. PMID:17817853

  18. Agrobacterium tumefaciens is a diazotrophic bacterium

    SciTech Connect

    Kanvinde, L.; Sastry, G.R.K. )

    1990-07-01

    This is the first report that Agrobacterium tumefaciens can fix nitrogen in a free-living condition as shown by its abilities to grown on nitrogen-free medium, reduce acetylene to ethylene, and incorporate {sup 15}N supplied as {sup 15}N{sub 2}. As with most other well-characterized diazotrophic bacteria, the presence of NH{sub 4}{sup +} in the medium and aerobic conditions repress nitrogen fixation by A. tumefaciens. The system requires molybdenum. No evidence for nodulation was found with pea, peanut, or soybean plants. Further understanding of the nitrogen-fixing ability of this bacterium, which has always been considered a pathogen, should cast new light on the evolution of a pathogenic versus symbiotic relationship.

  19. Characterizations of intracellular arsenic in a bacterium

    NASA Astrophysics Data System (ADS)

    Wolfe-Simon, F.; Yannone, S. M.; Tainer, J. A.

    2011-12-01

    Life requires a key set of chemical elements to sustain growth. Yet, a growing body of literature suggests that microbes can alter their nutritional requirements based on the availability of these chemical elements. Under limiting conditions for one element microbes have been shown to utilize a variety of other elements to serve similar functions often (but not always) in similar molecular structures. Well-characterized elemental exchanges include manganese for iron, tungsten for molybdenum and sulfur for phosphorus or oxygen. These exchanges can be found in a wide variety of biomolecules ranging from protein to lipids and DNA. Recent evidence suggested that arsenic, as arsenate or As(V), was taken up and incorporated into the cellular material of the bacterium GFAJ-1. The evidence was interpreted to support As(V) acting in an analogous role to phosphate. We will therefore discuss our ongoing efforts to characterize intracellular arsenate and how it may partition among the cellular fractions of the microbial isolate GFAJ-1 when exposed to As(V) in the presence of various levels of phosphate. Under high As(V) conditions, cells express a dramatically different proteome than when grown given only phosphate. Ongoing studies on the diversity and potential role of proteins and metabolites produced in the presence of As(V) will be reported. These investigations promise to inform the role and additional metabolic potential for As in biology. Arsenic assimilation into biomolecules contributes to the expanding set of chemical elements utilized by microbes in unusual environmental niches.

  20. Genome Sequence of the Soil Bacterium Janthinobacterium sp. KBS0711.

    PubMed

    Shoemaker, William R; Muscarella, Mario E; Lennon, Jay T

    2015-01-01

    We present a draft genome of Janthinobacterium sp. KBS0711 that was isolated from agricultural soil. The genome provides insight into the ecological strategies of this bacterium in free-living and host-associated environments. PMID:26089434

  1. Genome Sequence of the Soil Bacterium Janthinobacterium sp. KBS0711

    PubMed Central

    Shoemaker, William R.; Muscarella, Mario E.

    2015-01-01

    We present a draft genome of Janthinobacterium sp. KBS0711 that was isolated from agricultural soil. The genome provides insight into the ecological strategies of this bacterium in free-living and host-associated environments. PMID:26089434

  2. Detection of Salmonella bacterium in drinking water using microring resonator.

    PubMed

    Bahadoran, Mahdi; Noorden, Ahmad Fakhrurrazi Ahmad; Mohajer, Faeze Sadat; Abd Mubin, Mohamad Helmi; Chaudhary, Kashif; Jalil, Muhammad Arif; Ali, Jalil; Yupapin, Preecha

    2016-01-01

    A new microring resonator system is proposed for the detection of the Salmonella bacterium in drinking water, which is made up of SiO2-TiO2 waveguide embedded inside thin film layer of the flagellin. The change in refractive index due to the binding of the Salmonella bacterium with flagellin layer causes a shift in the output signal wavelength and the variation in through and drop port's intensities, which leads to the detection of Salmonella bacterium in drinking water. The sensitivity of proposed sensor for detecting of Salmonella bacterium in water solution is 149 nm/RIU and the limit of detection is 7 × 10(-4)RIU. PMID:25133457

  3. Taxonomic characterization of the cellulose-degrading bacterium NCIB 10462

    SciTech Connect

    Dees, C.; Ringleberg, D.; Scott, T.C.; Phelps, T.

    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.

  4. Pangenome Evolution in the Marine Bacterium Alteromonas

    PubMed Central

    López-Pérez, Mario; Rodriguez-Valera, Francisco

    2016-01-01

    We have examined a collection of the free-living marine bacterium Alteromonas genomes with cores diverging in average nucleotide identities ranging from 99.98% to 73.35%, i.e., from microbes that can be considered members of a natural clone (like in a clinical epidemiological outbreak) to borderline genus level. The genomes were largely syntenic allowing a precise delimitation of the core and flexible regions in each. The core was 1.4 Mb (ca. 30% of the typical strain genome size). Recombination rates along the core were high among strains belonging to the same species (37.7–83.7% of all nucleotide polymorphisms) but they decreased sharply between species (18.9–5.1%). Regarding the flexible genome, its main expansion occurred within the boundaries of the species, i.e., strains of the same species already have a large and diverse flexible genome. Flexible regions occupy mostly fixed genomic locations. Four large genomic islands are involved in the synthesis of strain-specific glycosydic receptors that we have called glycotypes. These genomic regions are exchanged by homologous recombination within and between species and there is evidence for their import from distant taxonomic units (other genera within the family). In addition, several hotspots for integration of gene cassettes by illegitimate recombination are distributed throughout the genome. They code for features that give each clone specific properties to interact with their ecological niche and must flow fast throughout the whole genus as they are found, with nearly identical sequences, in different species. Models for the generation of this genomic diversity involving phage predation are discussed. PMID:27189983

  5. Pangenome Evolution in the Marine Bacterium Alteromonas.

    PubMed

    López-Pérez, Mario; Rodriguez-Valera, Francisco

    2016-01-01

    We have examined a collection of the free-living marine bacterium Alteromonas genomes with cores diverging in average nucleotide identities ranging from 99.98% to 73.35%, i.e., from microbes that can be considered members of a natural clone (like in a clinical epidemiological outbreak) to borderline genus level. The genomes were largely syntenic allowing a precise delimitation of the core and flexible regions in each. The core was 1.4 Mb (ca. 30% of the typical strain genome size). Recombination rates along the core were high among strains belonging to the same species (37.7-83.7% of all nucleotide polymorphisms) but they decreased sharply between species (18.9-5.1%). Regarding the flexible genome, its main expansion occurred within the boundaries of the species, i.e., strains of the same species already have a large and diverse flexible genome. Flexible regions occupy mostly fixed genomic locations. Four large genomic islands are involved in the synthesis of strain-specific glycosydic receptors that we have called glycotypes. These genomic regions are exchanged by homologous recombination within and between species and there is evidence for their import from distant taxonomic units (other genera within the family). In addition, several hotspots for integration of gene cassettes by illegitimate recombination are distributed throughout the genome. They code for features that give each clone specific properties to interact with their ecological niche and must flow fast throughout the whole genus as they are found, with nearly identical sequences, in different species. Models for the generation of this genomic diversity involving phage predation are discussed. PMID:27189983

  6. Hydrogen Production by the Thermophilic Bacterium Thermotoga neapolitana.

    PubMed

    Pradhan, Nirakar; Dipasquale, Laura; d'Ippolito, Giuliana; Panico, Antonio; Lens, Piet N L; Esposito, Giovanni; Fontana, Angelo

    2015-01-01

    As the only fuel that is not chemically bound to carbon, hydrogen has gained interest as an energy carrier to face the current environmental issues of greenhouse gas emissions and to substitute the depleting non-renewable reserves. In the last years, there has been a significant increase in the number of publications about the bacterium Thermotoga neapolitana that is responsible for production yields of H2 that are among the highest achievements reported in the literature. Here we present an extensive overview of the most recent studies on this hyperthermophilic bacterium together with a critical discussion of the potential of fermentative production by this bacterium. The review article is organized into sections focused on biochemical, microbiological and technical issues, including the effect of substrate, reactor type, gas sparging, temperature, pH, hydraulic retention time and organic loading parameters on rate and yield of gas production. PMID:26053393

  7. Hydrogen Production by the Thermophilic Bacterium Thermotoga neapolitana

    PubMed Central

    Pradhan, Nirakar; Dipasquale, Laura; d’Ippolito, Giuliana; Panico, Antonio; Lens, Piet N. L.; Esposito, Giovanni; Fontana, Angelo

    2015-01-01

    As the only fuel that is not chemically bound to carbon, hydrogen has gained interest as an energy carrier to face the current environmental issues of greenhouse gas emissions and to substitute the depleting non-renewable reserves. In the last years, there has been a significant increase in the number of publications about the bacterium Thermotoga neapolitana that is responsible for production yields of H2 that are among the highest achievements reported in the literature. Here we present an extensive overview of the most recent studies on this hyperthermophilic bacterium together with a critical discussion of the potential of fermentative production by this bacterium. The review article is organized into sections focused on biochemical, microbiological and technical issues, including the effect of substrate, reactor type, gas sparging, temperature, pH, hydraulic retention time and organic loading parameters on rate and yield of gas production. PMID:26053393

  8. Extreme Ionizing-Radiation-Resistant Bacterium

    NASA Technical Reports Server (NTRS)

    Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.; Schwendner, Petra

    2013-01-01

    potential for transfer, and subsequent proliferation, on another solar body such as Mars and Europa. These organisms are more likely to escape planetary protection assays, which only take into account presence of spores. Hence, presences of extreme radiation-resistant Deinococcus in the cleanroom facility where spacecraft are assembled pose a serious risk for integrity of life-detection missions. The microorganism described herein was isolated from the surfaces of the cleanroom facility in which the Phoenix Lander was assembled. The isolated bacterial strain was subjected to a comprehensive polyphasic analysis to characterize its taxonomic position. This bacterium exhibits very low 16SrRNA similarity with any other environmental isolate reported to date. Both phenotypic and phylogenetic analyses clearly indicate that this isolate belongs to the genus Deinococcus and represents a novel species. The name Deinococcus phoenicis was proposed after the Phoenix spacecraft, which was undergoing assembly, testing, and launch operations in the spacecraft assembly facility at the time of isolation. D. phoenicis cells exhibited higher resistance to ionizing radiation (cobalt-60; 14 kGy) than the cells of the D. radiodurans (5 kGy). Thus, it is in the best interest of NASA to thoroughly characterize this organism, which will further assess in determining the potential for forward contamination. Upon the completion of genetic and physiological characteristics of D. phoenicis, it will be added to a planetary protection database to be able to further model and predict the probability of forward contamination.

  9. Extreme Ionizing-Radiation-Resistant Bacterium

    NASA Technical Reports Server (NTRS)

    Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.; Schwendner, Petra

    2012-01-01

    potential for transfer, and subsequent proliferation, on another solar body such as Mars and Europa. These organisms are more likely to escape planetary protection assays, which only take into account presence of spores. Hence, presences of extreme radiation-resistant Deinococcus in the cleanroom facility where spacecraft are assembled pose a serious risk for integrity of life-detection missions. The microorganism described herein was isolated from the surfaces of the cleanroom facility in which the Phoenix Lander was assembled. The isolated bacterial strain was subjected to a comprehensive polyphasic analysis to characterize its taxonomic position. This bacterium exhibits very low 16SrRNA similarity with any other environmental isolate reported to date. Both phenotypic and phylogenetic analyses clearly indicate that this isolate belongs to the genus Deinococcus and represents a novel species. The name Deinococcus phoenicis was proposed after the Phoenix spacecraft, which was undergoing assembly, testing, and launch operations in the spacecraft assembly facility at the time of isolation. D. phoenicis cells exhibited higher resistance to ionizing radiation (cobalt-60; 14 kGy) than the cells of the D. radiodurans (5 kGy). Thus, it is in the best interest of NASA to thoroughly characterize this organism, which will further assess in determining the potential for forward contamination. Upon the completion of genetic and physiological characteristics of D. phoenicis, it will be added to a planetary protection database to be able to further model and predict the probability of forward contamination.

  10. Microcalorimetric Measurements of Glucose Metabolism by Marine Bacterium Vibrio alginolyticus

    PubMed Central

    Gordon, Andrew S.; Millero, Frank J.; Gerchakov, Sol M.

    1982-01-01

    Microcalorimetric measurements of heat production from glucose by Vibrio alginolyticus were made to assess the viability of calorimetry as a technique for studying the metabolism of marine bacteria at organic nutrient concentrations found in marine waters. The results show that the metabolism of glucose by this bacterium can be measured by calorimetry at submicromolar concentrations. A linear correlation between glucose concentration and total heat production was observed over a concentration range of 8 mM to 0.35 μM. It is suggested that these data indicate a constant efficiency of metabolism for this bacterium over the wide range of glucose concentrations studied. PMID:16346131

  11. Biological colloid engineering: Self-assembly of dipolar ferromagnetic chains in a functionalized biogenic ferrofluid

    NASA Astrophysics Data System (ADS)

    Ruder, Warren C.; Hsu, Chia-Pei D.; Edelman, Brent D.; Schwartz, Russell; LeDuc, Philip R.

    2012-08-01

    We have studied the dynamic behavior of nanoparticles in ferrofluids consisting of single-domain, biogenic magnetite (Fe3O4) isolated from Magnetospirillum magnetotacticum (MS-1). Although dipolar chains form in magnetic colloids in zero applied field, when dried upon substrates, the solvent front disorders nanoparticle aggregation. Using avidin-biotin functionalization of the particles and substrate, we generated self-assembled, linear chain motifs that resist solvent front disruption in zero-field. The engineered self-assembly process we describe here provides an approach for the creation of ordered magnetic structures that could impact fields ranging from micro-electro-mechanical systems development to magnetic imaging of biological structures.

  12. Complete Genome of the Cellulolytic Ruminal Bacterium Ruminococcus albus 7

    SciTech Connect

    Suen, Garret; Stevenson, David M; Bruce, David; Chertkov, Olga; Copeland, A; Cheng, Jan-Fang; Detter, J. Chris; Goodwin, Lynne A.; Han, Cliff; Hauser, Loren John; Ivanova, N; Kyrpides, Nikos C; Land, Miriam L; Lapidus, Alla L.; Lucas, Susan; Ovchinnikova, Galina; Pitluck, Sam; Tapia, Roxanne; Woyke, Tanja; Boyum, Julie; Mead, David; Weimer, Paul J

    2011-01-01

    Ruminococcus albus 7 is a highly cellulolytic ruminal bacterium that is a member of the phylum Firmicutes. Here, we describe the complete genome of this microbe. This genome will be useful for rumen microbiology and cellulosome biology and in biofuel production, as one of its major fermentation products is ethanol.

  13. Complete genome of the cellulolytic ruminal bacterium Ruminococcus albus 7

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ruminococcus albus 7 is a highly cellulolytic rumen bacterium that is a member of the phylum Firmicutes. Here, we describe the complete genome for this microbe. This genome will be useful for rumen microbiology, cellulosome biology, and in biofuel production, as one of its major fermentation product...

  14. Draft Genome Sequence of Oral Bacterium Streptococcus mutans JH1140.

    PubMed

    Escano, Jerome; Deng, Peng; Lu, Shi-En; Smith, Lief

    2016-01-01

    Streptococcus mutans JH1140 is an oral bacterium known to produce the bacteriocin mutacin 1140, and the strain has been genetically engineered to combat dental caries. Here, we report the 2.0-Mb draft genome of S. mutans JH1140. This genome provides new insights into the strain's superior colonization properties and its utility in replacement therapy. PMID:27257196

  15. Draft Genome Sequence of Oral Bacterium Streptococcus mutans JH1140

    PubMed Central

    Escano, Jerome; Deng, Peng; Lu, Shi-En

    2016-01-01

    Streptococcus mutans JH1140 is an oral bacterium known to produce the bacteriocin mutacin 1140, and the strain has been genetically engineered to combat dental caries. Here, we report the 2.0-Mb draft genome of S. mutans JH1140. This genome provides new insights into the strain’s superior colonization properties and its utility in replacement therapy. PMID:27257196

  16. Isolation of a bacterium capable of degrading peanut hull lignin

    SciTech Connect

    Kerr, T.A.; Kerr, R.D.; Benner, R.

    1983-11-01

    Thirty-seven bacterial strains capable of degrading peanut hull lignin were isolated by using four types of lignin preparations and hot-water-extracted peanut hulls. One of the isolates, tentatively identified as Arthrobacter species, was capable of utilizing all four lignin preparations as well as extracted peanut hulls as a sole source of carbon. The bacterium was also capable of degrading specifically labeled (/sup 14/C) lignin-labeled lignocellulose and (/sup 14/C)cellulose-labeled lignocellulose from the cordgrass Spartina alterniflora and could also degrade (/sup 14/C) Kraft lignin from slash pine. After 10 days of incubation with (/sup 14/C) cellulose-labeled lignocellulose or (/sup 14/C) lignin-labeled lignocellulose from S. alterniflora, the bacterium mineralized 6.5% of the polysaccharide component and 2.9% of the lignin component. (Refs. 24).

  17. A Streamlined Strategy for Biohydrogen Production with an Alkaliphilic Bacterium

    SciTech Connect

    Elias, Dwayne A; Wall, Judy D.; Mormile, Dr. Melanie R.; Begemann, Matthew B

    2012-01-01

    Biofuels are anticipated to enable a shift from fossil fuels for renewable transportation and manufacturing fuels, with biohydrogen considered attractive since it could offer the largest reduction of global carbon budgets. Currently, biohydrogen production remains inefficient and heavily fossil fuel-dependent. However, bacteria using alkali-treated biomass could streamline biofuel production while reducing costs and fossil fuel needs. An alkaliphilic bacterium, Halanaerobium strain sapolanicus, is described that is capable of biohydrogen production at levels rivaling neutrophilic strains, but at pH 11 and hypersaline conditions. H. sapolanicus ferments a variety of 5- and 6- carbon sugars derived from hemicellulose and cellulose including cellobiose, and forms the end products hydrogen and acetate. Further, it can also produce biohydrogen from switchgrass and straw pretreated at temperatures far lower than any previously reported and in solutions compatible with growth. Hence, this bacterium can potentially increase the efficiency and efficacy of biohydrogen production from renewable biomass resources.

  18. Thermostable purified endoglucanase from thermophilic bacterium acidothermus cellulolyticus

    DOEpatents

    Tucker, Melvin P.; Grohmann, Karel; Himmel, Michael E.; Mohagheghi, Ali

    1992-01-01

    A substantially purified high molecular weight cellulase enzyme having a molecular weight of between about 156,000 to about 203,400 daltons isolated from the bacterium Acidothermus cellulolyticus (ATCC 43068) and a method of producing it are disclosed. The enzyme is water soluble, possesses both C.sub.1 and C.sub.x types of enzymatic activity, has a high degree of stability toward heat and exhibits both a high optimum temperature activity and high inactivation characteristics.

  19. Delta8(14)-steroids in the bacterium Methylococcus capsulatus.

    PubMed Central

    Bouvier, P; Rohmer, M; Benveniste, P; Ourisson, G

    1976-01-01

    The 4,4-dimethyl and 4alpha-methyl sterols of the bacterium Methylococcus capsulatus were identified as 4,4-dimethyl- and 4alpha-methyl-5alpha-cholest-8(14)-en-3beta-ol and 4,4-dimethyl- and 4alpha-methyl-5alpha-cholesta-8(14),24-dien-3beta-ol. Sterol biosynthesis is blocked at the level of 4alpha-methyl delta8(14)-sterols. PMID:999649

  20. Isolation and Characterization of a Chlorinated-Pyridinol-Degrading Bacterium

    PubMed Central

    Feng, Y.; Racke, K. D.; Bollag, J.

    1997-01-01

    The isolation of a pure culture of bacteria able to use 3,5,6-trichloro-2-pyridinol (TCP) as a sole source of carbon and energy under aerobic conditions was achieved for the first time. The bacterium was identified as a Pseudomonas sp. and designated ATCC 700113. [2,6-(sup14)C]TCP degradation yielded (sup14)CO(inf2), chloride, and unidentified polar metabolites. PMID:16535719

  1. An on-bacterium flow cytometric immunoassay for protein quantification.

    PubMed

    Lan, Wen-Jun; Lan, Wei; Wang, Hai-Yan; Yan, Lei; Wang, Zhe-Li

    2013-09-01

    The polystyrene bead-based flow cytometric immunoassay has been widely reported. However, the preparation of functional polystyrene bead is still inconvenient. This study describes a simple and easy on-bacterium flow cytometric immunoassay for protein quantification, in which Staphylococcus aureus (SAC) is used as an antibody-antigen carrier to replace the polystyrene bead. The SAC beads were prepared by carboxyfluorescein diacetate succinimidyl ester (CFSE) labeling, paraformaldehyde fixation and antibody binding. Carcinoembryonic antigen (CEA) and cytokeratin-19 fragment (CYFRA 21-1) proteins were used as models in the test system. Using prepared SAC beads, biotinylated proteins, and streptavidin-phycoerythrin (SA-PE), the on-bacterium flow cytometric immunoassay was validated by quantifying CEA and CYFRA 21-1 in sample. Obtained data demonstrated a concordant result between the logarithm of the protein concentration and the logarithm of the PE mean fluorescence intensity (MFI). The limit of detection (LOD) in this immunoassay was at least 0.25 ng/ml. Precision and accuracy assessments appeared that either the relative standard deviation (R.S.D.) or the relative error (R.E.) was <10%. The comparison between this immunoassay and a polystyrene bead-based flow cytometric immunoassay showed a correlation coefficient of 0.998 for serum CEA or 0.996 for serum CYFRA 21-1. In conclusion, the on-bacterium flow cytometric immunoassay may be of use in the quantification of serum protein. PMID:23739299

  2. Influence of plaque-forming bacterium, Rhodobacteraceae sp. on the growth of Chlorella vulgaris.

    PubMed

    Chen, Zhangran; Zhang, Jingyan; Lei, Xueqian; Zhang, Bangzhou; Cai, Guanjing; Zhang, Huajun; Li, Yi; Zheng, Wei; Tian, Yun; Xu, Hong; Zheng, Tianling

    2014-10-01

    Experiments were conducted to find out the molecular features, infection process of a special alga plaque-forming microorganism and its potential influence on the biomass of Chlorella vulgaris during the infection process. Direct contact between the algal cell and the bacterium may be the primary steps needed for the bacterium to lyse the alga. Addition of C. vulgaris cells into f/2 medium allowed us obtain the object bacterium. The 16S rRNA gene sequence comparisons results showed that the plaque-forming bacterium kept the closest relationship with Labrenzia aggregata IAM 12614(T) at 98.90%. The existence of the bacterium could influence both the dry weight and lipid content of C. vulgaris. This study demonstrated that direct cell wall disruption of C. vulgaris by the bacterium would be a potentially effective method to utilize the biomass of microalgae. PMID:25086475

  3. Fast Neutron Irradiation of the Highly Radioresistant Bacterium Deinococcus Radiodurans

    NASA Astrophysics Data System (ADS)

    Case, Diane Louise

    Fast neutron dose survival curves were generated for the bacterium Deinococcus radiodurans, which is renowned for its unusually high resistance to gamma, x-ray, and ultraviolet radiation, but for which fast neutron response was unknown. The fast neutrons were produced by the University of Massachusetts Lowell 5.5-MV, type CN Van de Graaff accelerator through the ^7Li(p,n)^7 Be reaction by bombarding a thick metallic lithium target with a 4-MeV proton beam. The bacteria were uniformly distributed on 150-mm agar plates and were exposed to the fast neutron beam under conditions of charged particle equilibrium. The plates were subdivided into concentric rings of increasing diameter from the center to the periphery of the plate, within which the average neutron dose was calculated as the product of the precisely known neutron fluence at the average radius of the ring and the neutron energy dependent kerma factor. The neutron fluence and dose ranged from approximately 3 times 1013 n cm^ {-2} to 1 times 1012 n cm^ {-2}, and 200 kilorad to 5 kilorad, respectively, from the center to the periphery of the plate. Percent survival for Deinococcus radiodurans as a function of fast neutron dose was derived from the ability of the irradiated cells to produce visible colonies within each ring compared to that of a nonirradiated control population. The bacterium Escherichia coli B/r (CSH) was irradiated under identical conditions for comparative purposes. The survival response of Deinococcus radiodurans as a result of cumulative fast neutron exposures was also investigated. The quantification of the ability of Deinococcus radiodurans to survive cellular insult from secondary charged particles, which are produced by fast neutron interactions in biological materials, will provide valuable information about damage and repair mechanisms under extreme cellular stress, and may provide new insight into the origin of this bacterium's unprecedented radiation resistance.

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

    SciTech Connect

    Daniel P. Molloy

    2004-02-24

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

  5. Intracellular iron minerals in a dissimilatory iron-reducing bacterium.

    PubMed

    Glasauer, Susan; Langley, Sean; Beveridge, Terry J

    2002-01-01

    Among prokaryotes, there are few examples of controlled mineral formation; the formation of crystalline iron oxides and sulfides [magnetite (Fe3O4) or greigite (Fe3S4)] by magnetotactic bacteria is an exception. Shewanella putrefaciens CN32, a Gram-negative, facultative anaerobic bacterium that is capable of dissimilatory iron reduction, produced microscopic intracellular grains of iron oxide minerals during growth on two-line ferrihydrite in a hydrogen-argon atmosphere. The minerals, formed at iron concentrations found in the soil and sedimentary environments where these bacteria are active, could represent an unexplored pathway for the cycling of iron by bacteria. PMID:11778045

  6. The terminal oxidase in the marine bacterium Pseudomonas nautica 617.

    PubMed

    Simpson, H; Denis, M; Malatesta, F

    1997-06-01

    The molecular properties of a novel membrane quinol oxidase from the marine bacterium Pseudomonas nautica 617 are presented. The protein contains 2b hemes/mole which may be distinguished by EPR spectroscopy but not by optical spectroscopy and electrochemistry. Respiration, though being cyanide insensitive, is not inhibited by carbon monoxide and oxygen reduction is carried out only half-way with production of hydrogen peroxide. The terminal oxidase represents, therefore, a unique example in the large family of terminal oxidases known up to date. PMID:9337488

  7. Triazine herbicide resistance in the photosynthetic bacterium Rhodopseudomonas sphaeroides

    SciTech Connect

    Brown, A.E.; Gilbert, C.W.; Guy, R.; Arntzen, C.J.

    1984-10-01

    The photoaffinity herbicide azidoatrazine (2-azido-4-ethylamino-6-isopropylamino-s-triazine) selectively labels the L subunit of the reaction center of the photosynthetic bacterium Rhodopseudomonas sphaeroides. Herbicide-resistant mutants retain the L subunit and have altered binding properties for methylthio- and chloro-substituted triazines as well as altered equilibrium constants for electron transfer between primary and secondary electron acceptors. We suggest that a subtle alteration in the L subunit is responsible for herbicide resistance and that the L subunit is the functional analog of the 32-kDa Q/sub B/ protein of chloroplast membranes. 42 references, 6 figures, 1 table.

  8. Molybdate Reduction to Molybdenum Blue by an Antarctic Bacterium

    PubMed Central

    Ahmad, S. A.; Shukor, M. Y.; Shamaan, N. A.; Mac Cormack, W. P.; Syed, M. A.

    2013-01-01

    A molybdenum-reducing bacterium from Antarctica has been isolated. The bacterium converts sodium molybdate or Mo6+ to molybdenum blue (Mo-blue). Electron donors such as glucose, sucrose, fructose, and lactose supported molybdate reduction. Ammonium sulphate was the best nitrogen source for molybdate reduction. Optimal conditions for molybdate reduction were between 30 and 50 mM molybdate, between 15 and 20°C, and initial pH between 6.5 and 7.5. The Mo-blue produced had a unique absorption spectrum with a peak maximum at 865 nm and a shoulder at 710 nm. Respiratory inhibitors such as antimycin A, sodium azide, potassium cyanide, and rotenone failed to inhibit the reducing activity. The Mo-reducing enzyme was partially purified using ion exchange and gel filtration chromatography. The partially purified enzyme showed optimal pH and temperature for activity at 6.0 and 20°C, respectively. Metal ions such as cadmium, chromium, copper, silver, lead, and mercury caused more than 95% inhibition of the molybdenum-reducing activity at 0.1 mM. The isolate was tentatively identified as Pseudomonas sp. strain DRY1 based on partial 16s rDNA molecular phylogenetic assessment and the Biolog microbial identification system. The characteristics of this strain would make it very useful in bioremediation works in the polar and temperate countries. PMID:24381945

  9. Molybdate reduction to molybdenum blue by an Antarctic bacterium.

    PubMed

    Ahmad, S A; Shukor, M Y; Shamaan, N A; Mac Cormack, W P; Syed, M A

    2013-01-01

    A molybdenum-reducing bacterium from Antarctica has been isolated. The bacterium converts sodium molybdate or Mo⁶⁺ to molybdenum blue (Mo-blue). Electron donors such as glucose, sucrose, fructose, and lactose supported molybdate reduction. Ammonium sulphate was the best nitrogen source for molybdate reduction. Optimal conditions for molybdate reduction were between 30 and 50 mM molybdate, between 15 and 20°C, and initial pH between 6.5 and 7.5. The Mo-blue produced had a unique absorption spectrum with a peak maximum at 865 nm and a shoulder at 710 nm. Respiratory inhibitors such as antimycin A, sodium azide, potassium cyanide, and rotenone failed to inhibit the reducing activity. The Mo-reducing enzyme was partially purified using ion exchange and gel filtration chromatography. The partially purified enzyme showed optimal pH and temperature for activity at 6.0 and 20°C, respectively. Metal ions such as cadmium, chromium, copper, silver, lead, and mercury caused more than 95% inhibition of the molybdenum-reducing activity at 0.1 mM. The isolate was tentatively identified as Pseudomonas sp. strain DRY1 based on partial 16s rDNA molecular phylogenetic assessment and the Biolog microbial identification system. The characteristics of this strain would make it very useful in bioremediation works in the polar and temperate countries. PMID:24381945

  10. Biological Control of Meloidogyne hapla Using an Antagonistic Bacterium

    PubMed Central

    Park, Jiyeong; Seo, Yunhee; Kim, Young Ho

    2014-01-01

    We examined the efficacy of a bacterium for biocontrol of the root-knot nematode (RKN) Meloidogyne hapla in carrot (Daucus carota subsp. sativus) and tomato (Solanum lycopersicum). Among 542 bacterial isolates from various soils and plants, the highest nematode mortality was observed for treatments with isolate C1-7, which was identified as Bacillus cereus based on cultural and morphological characteristics, the Biolog program, and 16S rRNA sequencing analyses. The population density and the nematicidal activity of B. cereus C1-7 remained high until the end of culture in brain heart infusion broth, suggesting that it may have sustainable biocontrol potential. In pot experiments, the biocontrol efficacy of B. cereus C1-7 was high, showing complete inhibition of root gall or egg mass formation by RKN in carrot and tomato plants, and subsequently reducing RKN damage and suppressing nematode population growth, respectively. Light microscopy of RKN-infected carrot root tissues treated with C1-7 showed reduced formation of gall cells and fully developed giant cells, while extensive gall cells and fully mature giant cells with prominent cell wall ingrowths formed in the untreated control plants infected with RKNs. These histopathological characteristics may be the result of residual or systemic biocontrol activity of the bacterium, which may coincide with the biocontrol efficacies of nematodes in pots. These results suggest that B. cereus C1-7 can be used as a biocontrol agent for M. hapla. PMID:25289015

  11. Radiation response mechanisms of the extremely radioresistant bacterium Deinococcus radiodurans.

    PubMed

    Kobayashi, Yasuhiko; Narumi, Issay; Satoh, Katsuya; Funayama, Tomoo; Kikuchi, Masahiro; Kitayama, Shigeru; Watanabe, Hiroshi

    2004-11-01

    Effect of microgravity on recovery of bacterial cells from radiation damage was examined in IML-2, S/MM-4 and S/MM-9 experiments using the extremely radioresistant bacterium Deinococcus radiodurans. The cells were irradiated with gamma rays before the space flight and incubated on board the Space Shuttle. The survival of the wild type cells incubated in space increased compared with the ground controls, suggesting that the recovery of this bacterium from radiation damage was enhanced under the space environment. No difference was observed between the survivals of radiosensitive mutant rec30 cells incubated in space and on the ground. The amount of DNA-repair related RecA protein induced under microgravity was similar to those of ground controls, however, induction of PprA protein, product of a unique radiation-inducible gene (designated pprA) responsible for loss of radiation resistance in repair-deficient mutant, KH311, was enhanced under microgravity compared with ground controls. Recent investigation in vitro showed that PprA preferentially bound to double-stranded DNA carrying strand breaks, inhibited Escherichia coli exonuclease III activity, and stimulated the DNA end-joining reaction catalyzed by DNA ligases. These results suggest that D. radiodurans has a radiation-induced non-homologous end-joining (NHEJ) repair mechanism in which PprA plays a critical role. PMID:15858357

  12. Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus.

    PubMed

    Gardner, Jeffrey G

    2016-07-01

    Study of recalcitrant polysaccharide degradation by bacterial systems is critical for understanding biological processes such as global carbon cycling, nutritional contributions of the human gut microbiome, and the production of renewable fuels and chemicals. One bacterium that has a robust ability to degrade polysaccharides is the Gram-negative saprophyte Cellvibrio japonicus. A bacterium with a circuitous history, C. japonicus underwent several taxonomy changes from an initially described Pseudomonas sp. Most of the enzymes described in the pre-genomics era have also been renamed. This review aims to consolidate the biochemical, structural, and genetic data published on C. japonicus and its remarkable ability to degrade cellulose, xylan, and pectin substrates. Initially, C. japonicus carbohydrate-active enzymes were studied biochemically and structurally for their novel polysaccharide binding and degradation characteristics, while more recent systems biology approaches have begun to unravel the complex regulation required for lignocellulose degradation in an environmental context. Also included is a discussion for the future of C. japonicus as a model system, with emphasis on current areas unexplored in terms of polysaccharide degradation and emerging directions for C. japonicus in both environmental and biotechnological applications. PMID:27263016

  13. Metabolism of threo-beta-methylmalate by a soil bacterium.

    PubMed

    Suzuki, S; Takeuchi, Y; Sasaki, K; Katsuki, H

    1976-10-01

    Studies on threo-beta-methylmalate metabolism in a soil bacterium of the genus Bacillus which can utilize threo-beta-methylmalate as a sole carbon source were carried out. When DL-threo-beta-methylmalate was incubated with a cell-free extract of the bacterium, citramalate was found to be formed. Similarly, formation of threo-beta-methylmalate from DL-citramalate was confirmed. These dicarbosylic acids were identified by gas chromatography-mass spectrometry. Examination of inducibility, substrate specificity, and cofactor requirement of the enzymes involved in the reactions showed the existence of two interconversion reactions between the threo-beta-methylmalate and citramalate. One was an interconversion reaction between L-threo-beta-methylmalate and L-citramalate via mesaconate and the other was an interconversion reaction between D-threo-beta-methylmalate and D-citramalate via citraconate. These reactions were both reversible and were catalyzed by distinct and inducible enzymes. It is suggested that the two reactions participate in the catabolism of threo-beta-methylmalate. PMID:1010849

  14. Isolation and characterization of luminescent bacterium for sludge biodegradation.

    PubMed

    Zahaba, Maryam; Halmi, Mohd Izuan Effendi; Ahmad, Siti Aqlima; Shukor, Mohd Yunus; Syed, Mohd Arif

    2015-11-01

    Microtox is based on the inhibition of luminescence of the bacterium Vibrio fischeri by the toxicants. This technique has been accepted by the USEPA (United States Environmental Protection Agency) as a biomonitoring tool for remediation of toxicants such as hydrocarbon sludge. In the present study, a luminescent bacterium was isolated from yellow striped scad (Selaroides leptolepis) and was tentatively identified as Vibrio sp. isolate MZ. This aerobic isolate showed high luminescence activity in a broad range of temperature from 25 to 35 °C. In addition, optimal conditions for high bioluminescence activity in range of pH 7.5 to 8.5 and 10 gl(-1) of sodium chloride, 10 gl(-1) of peptone and 10 gl(-1) of sucrose as carbon source. Bench scale biodegradation 1% sludge (w/v) was set up and degradation was determined using gas chromatography with flame ionised detector (GC-FID). In this study, Rhodococcus sp. strain AQ5NOL2 was used to degrade the sludge. Based on the preliminary results obtained, Vibrio sp. isolate MZwas able to monitor the biodegradation of sludge. Therefore, Vibrio sp. isolate MZ has the potential to be used as a biomonitoring agent for biomonitoring of sludge biodegradation particularly in the tropical ranged environment. PMID:26688958

  15. Hydrogenomics of the Extremely Thermophilic Bacterium Caldicellulosiruptor saccharolyticus▿ †

    PubMed Central

    van de Werken, Harmen J. G.; Verhaart, Marcel R. A.; VanFossen, Amy L.; Willquist, Karin; Lewis, Derrick L.; Nichols, Jason D.; Goorissen, Heleen P.; Mongodin, Emmanuel F.; Nelson, Karen E.; van Niel, Ed W. J.; Stams, Alfons J. M.; Ward, Donald E.; de Vos, Willem M.; van der Oost, John; Kelly, Robert M.; Kengen, Servé W. M.

    2008-01-01

    Caldicellulosiruptor saccharolyticus is an extremely thermophilic, gram-positive anaerobe which ferments cellulose-, hemicellulose- and pectin-containing biomass to acetate, CO2, and hydrogen. Its broad substrate range, high hydrogen-producing capacity, and ability to coutilize glucose and xylose make this bacterium an attractive candidate for microbial bioenergy production. Here, the complete genome sequence of C. saccharolyticus, consisting of a 2,970,275-bp circular chromosome encoding 2,679 predicted proteins, is described. Analysis of the genome revealed that C. saccharolyticus has an extensive polysaccharide-hydrolyzing capacity for cellulose, hemicellulose, pectin, and starch, coupled to a large number of ABC transporters for monomeric and oligomeric sugar uptake. The components of the Embden-Meyerhof and nonoxidative pentose phosphate pathways are all present; however, there is no evidence that an Entner-Doudoroff pathway is present. Catabolic pathways for a range of sugars, including rhamnose, fucose, arabinose, glucuronate, fructose, and galactose, were identified. These pathways lead to the production of NADH and reduced ferredoxin. NADH and reduced ferredoxin are subsequently used by two distinct hydrogenases to generate hydrogen. Whole-genome transcriptome analysis revealed that there is significant upregulation of the glycolytic pathway and an ABC-type sugar transporter during growth on glucose and xylose, indicating that C. saccharolyticus coferments these sugars unimpeded by glucose-based catabolite repression. The capacity to simultaneously process and utilize a range of carbohydrates associated with biomass feedstocks is a highly desirable feature of this lignocellulose-utilizing, biofuel-producing bacterium. PMID:18776029

  16. Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus

    DOE PAGESBeta

    Gardner, Jeffrey G.

    2016-06-04

    Study of recalcitrant polysaccharide degradation by bacterial systems is critical for understanding biological processes such as global carbon cycling, nutritional contributions of the human gut microbiome, and the production of renewable fuels and chemicals. One bacterium that has a robust ability to degrade polysaccharides is the Gram-negative saprophyte Cellvibrio japonicus. A bacterium with a circuitous history, C. japonicus underwent several taxonomy changes from an initially described Pseudomonas sp. Most of the enzymes described in the pre-genomics era have also been renamed. Furthermore, this review aims to consolidate the biochemical, structural, and genetic data published on C. japonicus and its remarkablemore » ability to degrade cellulose, xylan, and pectin substrates. Initially, C. japonicus carbohydrate-active enzymes were studied biochemically and structurally for their novel polysaccharide binding and degradation characteristics, while more recent systems biology approaches have begun to unravel the complex regulation required for lignocellulose degradation in an environmental context. Also included is a discussion for the future of C. japonicus as a model system, with emphasis on current areas unexplored in terms of polysaccharide degradation and emerging directions for C. japonicus in both environmental and biotechnological applications.« less

  17. Structure and morphology of magnetite anaerobically-produced by a marine magnetotactic bacterium and a dissimilatory iron-reducing bacterium

    USGS Publications Warehouse

    Sparks, N.H.C.; Mann, S.; Bazylinski, D.A.; Lovley, D.R.; Jannasch, H.W.; Frankel, R.B.

    1990-01-01

    Intracellular crystals of magnetite synthesized by cells of the magnetotactic vibroid organism, MV-1, and extracellular crystals of magnetite produced by the non-magnetotactic dissimilatory iron-reducing bacterium strain GS-15, were examined using high-resolution transmission electron microscopy, electron diffraction and 57Fe Mo??ssbauer spectroscopy. The magnetotactic bacterium contained a single chain of approximately 10 crystals aligned along the long axis of the cell. The crystals were essentially pure stoichiometric magnetite. When viewed along the crystal long axis the particles had a hexagonal cross-section whereas side-on they appeared as rectangules or truncated rectangles of average dimension, 53 ?? 35 nm. These findings are explained in terms of a three-dimensional morphology comprising a hexagonal prism of {110} faces which are capped and truncated by {111} end faces. Electron diffraction and lattice imaging studies indicated that the particles were structurally well-defined single crystals. In contrast, magnetite particles produced by the strain, GS-15 were irregular in shape and had smaller mean dimensions (14 nm). Single crystals were imaged but these were not of high structural perfection. These results highlight the influence of intracellular control on the crystallochemical specificity of bacterial magnetites. The characterization of these crystals is important in aiding the identification of biogenic magnetic materials in paleomagnetism and in studies of sediment magnetization. ?? 1990.

  18. Genome Sequence of the Antarctic Psychrophile Bacterium Planococcus antarcticus DSM 14505

    PubMed Central

    Margolles, Abelardo; Gueimonde, Miguel

    2012-01-01

    Planococcus antarcticus DSM 14505 is a psychrophile bacterium that was isolated from cyanobacterial mat samples, originally collected from ponds in McMurdo, Antarctica. This orange-pigmented bacterium grows at 4°C and may possess interesting enzymatic activities at low temperatures. Here we report the first genomic sequence of P. antarcticus DSM 14505. PMID:22843594

  19. Draft Genome Sequence of Ensifer adhaerens M78, a Mineral-Weathering Bacterium Isolated from Soil.

    PubMed

    Wang, Yuanli; Chen, Wei; He, Linyan; Wang, Qi; Sheng, Xia-Fang

    2016-01-01

    Ensifer adhaerens M78, a bacterium isolated from soil, can weather potash feldspar and release Fe, Si, and Al from rock under nutrient-poor conditions. Here, we report the draft genome sequence of strain M78, which may facilitate a better understanding of the molecular mechanism involved in mineral weathering by the bacterium. PMID:27609930

  20. Kinetic study of trichloroethylene and toluene degradation by a bioluminescent reporter bacterium

    SciTech Connect

    Kelly, C.J.; Sanseverino, J.; Bienkowski, P.R.; Sayler, G.S.

    1995-12-31

    A constructed bioluminescent reporter bacterium, Pseudomonas putida B2, is very briefly described in this paper. The bacterium degrades toluene and trichloroethylene (TCE), and produces light in the presence of toluene. The light response is an indication of cellular viability and expression of the genes encoding toluene and TCE degrading enzymes.

  1. Near-complete genome sequence of the cellulolytic Bacterium Bacteroides (Pseudobacteroides) cellulosolvens ATCC 35603

    DOE PAGESBeta

    Dassa, Bareket; Utturkar, Sagar M.; Hurt, Richard A.; Klingeman, Dawn Marie; Keller, Martin; Xu, Jian; Reddy, Harish Kumar; Borovok, Ilya; Grinberg, Inna Rozman; Lamed, Raphael; et al

    2015-09-24

    We report the single-contig genome sequence of the anaerobic, mesophilic, cellulolytic bacterium, Bacteroides cellulosolvens. The bacterium produces a particularly elaborate cellulosome system, whereas the types of cohesin-dockerin interactions are opposite of other known cellulosome systems: cell-surface attachment is thus mediated via type-I interactions whereas enzymes are integrated via type-II interactions.

  2. FEEDING EXPERIMENTS WITH BACTERIUM PULLORUM. THE TOXICITY OF INFECTED EGGS.

    PubMed

    Rettger, L F; Hull, T G; Sturges, W S

    1916-04-01

    The problem of eradicating ovarian infection in the domestic fowl assumes still greater importance than heretofore, in the light of data recently acquired. Not only is it of great significance to eliminate the permanent carriers of Bacterium pullorum from all flocks of fowls from the standpoint of successful poultry breeding, but also because they constitute a possible source of danger to man. Eggs which harbor Bacterium pullorum in the yolk in large numbers may produce abnormal conditions, when fed, not only in young chicks, but in adult fowls, young rabbits, guinea pigs, and kittens. The toxicity for young rabbits is most pronounced, the infection usually resulting in the death of the animals. In kittens the most prominent symptoms are those of severe food-poisoning with members of the paratyphoid group of bacteria. The possibility of infected eggs causing serious disturbances in young children and in the sick and convalescent of all ages must therefore receive serious consideration. Ovarian infection of fowls is very common throughout this country. Hence, a large proportion of the marketed eggs are infected with Bacterium pullorum. When such eggs are allowed to remain in nests under broody hens, or in warm storage places, for comparatively few hours, they contain large numbers of the organism. Soft boiling, coddling, and frying on one side only do not necessarily render the yolks free from viable bacteria; therefore, eggs which have gone through these processes may, like raw eggs, be the cause of serious disturbances in persons who are particularly susceptible to such influences, and especially to infants. That no well authenticated instances of egg-poisoning of this kind are on record does not warrant the assumption that there have been no cases. The etiology of infantile stomach and intestinal disturbances is as yet too little understood; in fact, it may be said that many of these disorders have no known cause, and almost as much may be said regarding gastro

  3. Fungal lysis by a soil bacterium fermenting cellulose.

    PubMed

    Tolonen, Andrew C; Cerisy, Tristan; El-Sayyed, Hafez; Boutard, Magali; Salanoubat, Marcel; Church, George M

    2015-08-01

    Recycling of plant biomass by a community of bacteria and fungi is fundamental to carbon flow in terrestrial ecosystems. Here we report how the plant fermenting, soil bacterium Clostridium phytofermentans enhances growth on cellulose by simultaneously lysing and consuming model fungi from soil. We investigate the mechanism of fungal lysis to show that among the dozens of different glycoside hydrolases C. phytofermentans secretes on cellulose, the most highly expressed enzymes degrade fungi rather than plant substrates. These enzymes, the GH18 Cphy1799 and Cphy1800, synergize to hydrolyse chitin, a main component of the fungal cell wall. Purified enzymes inhibit fungal growth and mutants lacking either GH18 grow normally on cellulose and other plant substrates, but have a reduced ability to hydrolyse chitinous substrates and fungal hyphae. Thus, C. phytofermentans boosts growth on cellulose by lysing fungi with its most highly expressed hydrolases, highlighting the importance of fungal interactions to the ecology of cellulolytic bacteria. PMID:24798076

  4. Characterization of the quinones in purple sulfur bacterium Thermochromatium tepidum.

    PubMed

    Kimura, Yuuka; Kawakami, Tomoaki; Yu, Long-Jiang; Yoshimura, Miku; Kobayashi, Masayuki; Wang-Otomo, Zheng-Yu

    2015-07-01

    Quinone distributions in the thermophilic purple sulfur bacterium Thermochromatium tepidum have been investigated at different levels of the photosynthetic apparatus. Here we show that, on average, the intracytoplasmic membrane contains 18 ubiquinones (UQ) and 4 menaquinones (MQ) per reaction center (RC). About one-third of the quinones are retained in the light-harvesting-reaction center core complex (LH1-RC) with a similar ratio of UQ to MQ. The numbers of quinones essentially remains unchanged during crystallization of the LH1-RC. There are 1-2 UQ and 1 MQ associated with the RC-only complex in the purified solution sample. Our results suggest that a large proportion of the quinones are confined to the core complex and at least five UQs remain invisible in the current LH1-RC crystal structure. PMID:26048701

  5. Mechanism of anaerobic degradation of triethanolamine by a homoacetogenic bacterium

    SciTech Connect

    Speranza, Giovanna . E-mail: giovanna.speranza@unimi.it; Morelli, Carlo F.; Cairoli, Paola; Mueller, Britta; Schink, Bernhard

    2006-10-20

    Triethanolamine (TEA) is converted into acetate and ammonia by a strictly anaerobic, gram-positive Acetobacterium strain LuTria3. Fermentation experiments with resting cell suspensions and specifically deuterated substrates indicate that in the acetate molecule the carboxylate and the methyl groups correspond to the alcoholic function and to its adjacent methylene group, respectively, of the 2-hydroxyethyl unit of TEA. A 1,2 shift of a hydrogen (deuterium) atom from -CH{sub 2} -O- to =N-CH{sub 2} - without exchange with the medium was observed. This fact gives evidence that a radical mechanism occurs involving the enzyme and/or coenzyme molecule as a hydrogen carrier. Such a biodegradation appears analogous to the conversion of 2-phenoxyethanol into acetate mediated by another strain of the anaerobic homoacetogenic bacterium Acetobacterium.

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

    PubMed

    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. PMID:26965627

  7. Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene

    SciTech Connect

    Maymo-Gatell, X.; Chien, Yueh-tyng; Zinder, S.H.

    1997-06-06

    Tetrachloroethene is a prominent groundwater pollutant that can be reductively dechlorinated by mixed anaerobic microbial populations to the nontoxic product ethene. Strain 195, a coccoid bacterium that dechlorinates tetrachlorethene to ethene, was isolated and characterized. Growth of strain 195 with H{sub 2} and tetrachloroethene as the electron donor and acceptor pair required extracts from mixed microbial cultures. Growth of strain 195 was resistant to ampicillin and vancomycin; its cell wall did not react with a peptidoglycan-specific lectin and its ultrastructure resembled S-layers of Archaea. Analysis of the 16S ribosomal DNA sequence of strain 195 indicated that it is a eubacterium without close affiliation to any known groups. 24 refs., 4 figs., 1 tab.

  8. The domestication of the probiotic bacterium Lactobacillus acidophilus

    PubMed Central

    Bull, Matthew J.; Jolley, Keith A.; Bray, James E.; Aerts, Maarten; Vandamme, Peter; Maiden, Martin C. J.; Marchesi, Julian R.; Mahenthiralingam, Eshwar

    2014-01-01

    Lactobacillus acidophilus is a Gram-positive lactic acid bacterium that has had widespread historical use in the dairy industry and more recently as a probiotic. Although L. acidophilus has been designated as safe for human consumption, increasing commercial regulation and clinical demands for probiotic validation has resulted in a need to understand its genetic diversity. By drawing on large, well-characterised collections of lactic acid bacteria, we examined L. acidophilus isolates spanning 92 years and including multiple strains in current commercial use. Analysis of the whole genome sequence data set (34 isolate genomes) demonstrated L. acidophilus was a low diversity, monophyletic species with commercial isolates essentially identical at the sequence level. Our results indicate that commercial use has domesticated L. acidophilus with genetically stable, invariant strains being consumed globally by the human population. PMID:25425319

  9. The capacity of phototrophic sulfur bacterium Thiocapsa roseopersicina for chemosynthesis.

    PubMed

    Kondratieva, E N; Zhukov, V G; Ivanovsky, R N; Petushkova, U P; Monosov, E Z

    1976-07-01

    Purple sulfur bacterium Thiocapsa roseopersicina strain BBS requiring vitamin B12 may grow in the dark in media containing no other organic compounds. Under such conditions the cells oxidize sulfide and thiosulfate with the use of O2 and assimilate carbon dioxide. After 10--30s assimilation of NaH14CO3 about 60% of radioactivity is found in phosphorylated compounds characteristic for the reductive pentose phosphate cycle. The possibility of the function of this cycle in the dark in the presence of O2 is confirmed by the capacity of cells grown under such conditions to synthesize ribulose-1,5-diphosphate carboxylase. All this evidence suggests the ability of T. roseopersicina to change from phototrophy to aerobic chemolithoautotrophy. PMID:942280

  10. Metabolic characterisation of a novel vanillylmandelate-degrading bacterium.

    PubMed

    Turner, J E; Allison, N; Fewson, C A

    1996-10-01

    A newly isolated gram-negative bacterium, possibly Brevundimonas diminuta, utilised D,L-vanillylmandelate (D,L-VMA) as a sole carbon and energy source. The organism converted D,L-VMA to vanillylglyoxylate using a soluble NAD-dependent dehydrogenase specific for D-VMA and a dye-linked, membrane-associated L-VMA dehydrogenase. Vanillylglyoxylate was further metabolised by decarboxylation, dehydrogenation and demethylation to protocatechuate. A 4,5-dioxygenase cleaved protocatechuate to 2-hydroxy-4-carboxymuconic semialdehyde. Partially purified d-VMA dehydrogenase exhibited optimal activity at 30 degrees C and pH 9.5 and had an apparent Km for D-VMA of 470 microM. Although induced by several substituted mandelates, the enzyme had a narrow substrate specificity range with virtually no activity towards D-mandelate. Such properties render the enzyme of potential use in both diagnostic and biosynthetic applications. PMID:8824148

  11. Genome analysis of the Anerobic Thermohalophilic bacterium Halothermothrix orenii

    SciTech Connect

    Mavromatis, Konstantinos; Ivanova, Natalia; Anderson, Iain; Lykidis, Athanasios; Hooper, Sean D.; Sun, Hui; Kunin, Victor; Lapidus, Alla; Hugenholtz, Philip; Patel, Bharat; Kyrpides, Nikos C.

    2008-11-03

    Halothermothirx orenii is a strictly anaerobic thermohalophilic bacterium isolated from sediment of a Tunisian salt lake. It belongs to the order Halanaerobiales in the phylum Firmicutes. The complete sequence revealed that the genome consists of one circular chromosome of 2578146 bps encoding 2451 predicted genes. This is the first genome sequence of an organism belonging to the Haloanaerobiales. Features of both Gram positive and Gram negative bacteria were identified with the presence of both a sporulating mechanism typical of Firmicutes and a characteristic Gram negative lipopolysaccharide being the most prominent. Protein sequence analyses and metabolic reconstruction reveal a unique combination of strategies for thermophilic and halophilic adaptation. H. orenii can serve as a model organism for the study of the evolution of the Gram negative phenotype as well as the adaptation under thermohalophilic conditions and the development of biotechnological applications under conditions that require high temperatures and high salt concentrations.

  12. Ecology and metabolism of the beneficial intestinal commensal bacterium Faecalibacterium prausnitzii.

    PubMed

    Miquel, Sylvie; Martín, Rebeca; Bridonneau, Chantal; Robert, Véronique; Sokol, Harry; Bermúdez-Humarán, Luis G; Thomas, Muriel; Langella, Philippe

    2014-01-01

    Faecalibacterium prausnitzii is a major commensal bacterium, and its prevalence is often decreased in conditions of intestinal dysbiosis. The phylogenic identity of this bacterium was described only recently. It is still poorly characterized, and its specific growth requirements in the human gastrointestinal tract are not known. In this review, we consider F. prausnitzii metabolism, its ecophysiology in both humans and animals, and the effects of drugs and nutrition on its population. We list important questions about this beneficial and ubiquitous commensal bacterium that it would be valuable to answer. PMID:24637606

  13. Anaerobic degradation of toluene by a denitrifying bacterium.

    PubMed Central

    Evans, P J; Mang, D T; Kim, K S; Young, L Y

    1991-01-01

    A denitrifying bacterium, designated strain T1, that grew with toluene as the sole source of carbon under anaerobic conditions was isolated. The type of agar used in solid media and the toxicity of toluene were determinative factors in the successful isolation of strain T1. Greater than 50% of the toluene carbon was oxidized to CO2, and 29% was assimilated into biomass. The oxidation of toluene to CO2 was stoichiometrically coupled to nitrate reduction and denitrification. Strain T1 was tolerant of and grew on 3 mM toluene after a lag phase. The rate of toluene degradation was 1.8 mumol min-1 liter-1 (56 nmol min-1 mg of protein-1) in a cell suspension. Strain T1 was distinct from other bacteria that oxidize toluene anaerobically, but it may utilize a similar biochemical pathway of oxidation. In addition, o-xylene was transformed to a metabolite in the presence of toluene but did not serve as the sole source of carbon for growth of strain T1. This transformation was dependent on the degradation of toluene. Images PMID:2059037

  14. Denitrification characteristics of a marine origin psychrophilic aerobic denitrifying bacterium.

    PubMed

    Zheng, Haiyan; Liu, Ying; Sun, Guangdong; Gao, Xiyan; Zhang, Qingling; Liu, Zhipei

    2011-01-01

    A psychrophilic aerobic denitrifying bacterium, strain S1-1, was isolated from a biological aerated filter conducted for treatment of recirculating water in a marine aquaculture system. Strain S1-1 was preliminarily identified as Psychrobacter sp. based on the analysis of its 16S rRNA gene sequence, which showed 100% sequence similarity to that of Psychrobacter sp. TSBY-70. Strain S1-1 grew well either in high nitrate or high nitrite conditions with a removal of 100% nitrate or 63.50% nitrite, and the total nitrogen removal rates could reach to 46.48% and 31.89%, respectively. The results indicated that nitrate was mainly reduced in its logarithmic growth phase with a very low level accumulation of nitrite, suggesting that the aerobic denitrification process of strain S1-1 occurred mainly in this phase. The GC-MS results showed that N2O was formed as the major intermediate during the aerobic denitrifying process of strain S1-1. Finally, factors affecting the growth of strain S1-1 and its aerobic denitrifying ability were also investigated. Results showed that the optimum aerobic denitrification conditions for strain S1-1 were sodium succinate as carbon source, C/N ratio15, salinity 10 g/L NaCl, incubation temperature 20 degrees C and initial pH 6.5. PMID:22432315

  15. Mechanisms of gold biomineralization in the bacterium Cupriavidus metallidurans.

    PubMed

    Reith, Frank; Etschmann, Barbara; Grosse, Cornelia; Moors, Hugo; Benotmane, Mohammed A; Monsieurs, Pieter; Grass, Gregor; Doonan, Christian; Vogt, Stefan; Lai, Barry; Martinez-Criado, Gema; George, Graham N; Nies, Dietrich H; Mergeay, Max; Pring, Allan; Southam, Gordon; Brugger, Joël

    2009-10-20

    While the role of microorganisms as main drivers of metal mobility and mineral formation under Earth surface conditions is now widely accepted, the formation of secondary gold (Au) is commonly attributed to abiotic processes. Here we report that the biomineralization of Au nanoparticles in the metallophillic bacterium Cupriavidus metallidurans CH34 is the result of Au-regulated gene expression leading to the energy-dependent reductive precipitation of toxic Au(III)-complexes. C. metallidurans, which forms biofilms on Au grains, rapidly accumulates Au(III)-complexes from solution. Bulk and microbeam synchrotron X-ray analyses revealed that cellular Au accumulation is coupled to the formation of Au(I)-S complexes. This process promotes Au toxicity and C. metallidurans reacts by inducing oxidative stress and metal resistances gene clusters (including a Au-specific operon) to promote cellular defense. As a result, Au detoxification is mediated by a combination of efflux, reduction, and possibly methylation of Au-complexes, leading to the formation of Au(I)-C-compounds and nanoparticulate Au(0). Similar particles were observed in bacterial biofilms on Au grains, suggesting that bacteria actively contribute to the formation of Au grains in surface environments. The recognition of specific genetic responses to Au opens the way for the development of bioexploration and bioprocessing tools. PMID:19815503

  16. Heavy Metal Induced Antibiotic Resistance in Bacterium LSJC7

    PubMed Central

    Chen, Songcan; Li, Xiaomin; Sun, Guoxin; Zhang, Yingjiao; Su, Jianqiang; Ye, Jun

    2015-01-01

    Co-contamination of antibiotics and heavy metals prevails in the environment, and may play an important role in disseminating bacterial antibiotic resistance, but the selective effects of heavy metals on bacterial antibiotic resistance is largely unclear. To investigate this, the effects of heavy metals on antibiotic resistance were studied in a genome-sequenced bacterium, LSJC7. The results showed that the presence of arsenate, copper, and zinc were implicated in fortifying the resistance of LSJC7 towards tetracycline. The concentrations of heavy metals required to induce antibiotic resistance, i.e., the minimum heavy metal concentrations (MHCs), were far below (up to 64-fold) the minimum inhibition concentrations (MIC) of LSJC7. This finding indicates that the relatively low heavy metal levels in polluted environments and in treated humans and animals might be sufficient to induce bacterial antibiotic resistance. In addition, heavy metal induced antibiotic resistance was also observed for a combination of arsenate and chloramphenicol in LSJC7, and copper/zinc and tetracycline in antibiotic susceptible strain Escherichia coli DH5α. Overall, this study implies that heavy metal induced antibiotic resistance might be ubiquitous among various microbial species and suggests that it might play a role in the emergence and spread of antibiotic resistance in metal and antibiotic co-contaminated environments. PMID:26426011

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

    USGS Publications Warehouse

    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.

  18. Novel Rickettsiella Bacterium in the Leafhopper Orosius albicinctus (Hemiptera: Cicadellidae)

    PubMed Central

    Iasur-Kruh, Lilach; Weintraub, Phyllis G.; Mozes-Daube, Netta; Robinson, Wyatt E.; Perlman, Steve J.

    2013-01-01

    Bacteria in the genus Rickettsiella (Coxiellaceae), which are mainly known as arthropod pathogens, are emerging as excellent models to study transitions between mutualism and pathogenicity. The current report characterizes a novel Rickettsiella found in the leafhopper Orosius albicinctus (Hemiptera: Cicadellidae), a major vector of phytoplasma diseases in Europe and Asia. Denaturing gradient gel electrophoresis (DGGE) and pyrosequencing were used to survey the main symbionts of O. albicinctus, revealing the obligate symbionts Sulcia and Nasuia, and the facultative symbionts Arsenophonus and Wolbachia, in addition to Rickettsiella. The leafhopper Rickettsiella is allied with bacteria found in ticks. Screening O. albicinctus from the field showed that Rickettsiella is highly prevalent, with over 60% of individuals infected. A stable Rickettsiella infection was maintained in a leafhopper laboratory colony for at least 10 generations, and fluorescence microscopy localized bacteria to accessory glands of the female reproductive tract, suggesting that the bacterium is vertically transmitted. Future studies will be needed to examine how Rickettsiella affects host fitess and its ability to vector phytopathogens. PMID:23645190

  19. High cell density cultivation of the chemolithoautotrophic bacterium Nitrosomonas europaea.

    PubMed

    Papp, Benedek; Török, Tibor; Sándor, Erzsébet; Fekete, Erzsébet; Flipphi, Michel; Karaffa, Levente

    2016-05-01

    Nitrosomonas europaea is a chemolithoautotrophic nitrifier, a gram-negative bacterium that can obtain all energy required for growth from the oxidation of ammonia to nitrite, and this may be beneficial for various biotechnological and environmental applications. However, compared to other bacteria, growth of ammonia oxidizing bacteria is very slow. A prerequisite to produce high cell density N. europaea cultures is to minimize the concentrations of inhibitory metabolic by-products. During growth on ammonia nitrite accumulates, as a consequence, N. europaea cannot grow to high cell concentrations under conventional batch conditions. Here, we show that single-vessel dialysis membrane bioreactors can be used to obtain substantially increased N. europaea biomasses and substantially reduced nitrite levels in media initially containing high amounts of the substrate. Dialysis membrane bioreactor fermentations were run in batch as well as in continuous mode. Growth was monitored with cell concentration determinations, by assessing dry cell mass and by monitoring ammonium consumption as well as nitrite formation. In addition, metabolic activity was probed with in vivo acridine orange staining. Under continuous substrate feed, the maximal cell concentration (2.79 × 10(12)/L) and maximal dry cell mass (0.895 g/L) achieved more than doubled the highest values reported for N. europaea cultivations to date. PMID:26358065

  20. Bacterium organizes hierarchical amorphous structure in microbial cellulose

    NASA Astrophysics Data System (ADS)

    Koizumi, S.; Yue, Z.; Tomita, Y.; Kondo, T.; Iwase, H.; Yamaguchi, D.; Hashimoto, T.

    2008-05-01

    A pellicle, a gel film of microbial cellulose, is a supermolecular system containing 99% of water by weight, which is closely related to an amorphous structure in it. Using ultra-small-angle neutron scattering, in order to cover over a wide range of length scales from nm to 10μm, we examined the hierarchical amorphous structure in the microbial cellulose, which is synthesized by a bacterium (Acetobacter xylinum). The microbial cellulose swollen by water shows small-angle scattering that obeys a power law q -behavior according to q-α as a function of the magnitude of the scattering vector q . The power law, determined by scattering, is attributed to a mass fractal due to the distribution of the center of mass for the crystallite (microfibril) in amorphous cellulose swollen by water. As q increases, α takes the values of 2.5, 1, and 2.35, corresponding, respectively, to a gel network composed of bundles, a bundle composed of cellulose ribbons, and concentration fluctuations in a bundle. From the mass fractal q -behavior and its length scale limits, we evaluated a volume fraction of crystallite in microbial cellulose. It was found that 90% of the cellulose bundle is occupied by amorphous cellulose containing water.

  1. Fitness correlates with the extent of cheating in a bacterium.

    PubMed

    Jiricny, N; Diggle, S P; West, S A; Evans, B A; Ballantyne, G; Ross-Gillespie, A; Griffin, A S

    2010-04-01

    There is growing awareness of the importance of cooperative behaviours in microbial communities. Empirical support for this insight comes from experiments using mutant strains, termed 'cheats', which exploit the cooperative behaviour of wild-type strains. However, little detailed work has gone into characterising the competitive dynamics of cooperative and cheating strains. We test three specific predictions about the fitness consequences of cheating to different extents by examining the production of the iron-scavenging siderophore molecule, pyoverdin, in the bacterium Pseudomonas aeruginosa. We create a collection of mutants that differ in the amount of pyoverdin that they produce (from 1% to 96% of the production of paired wild types) and demonstrate that these production levels correlate with both gene activity and the ability to bind iron. Across these mutants, we found that (1) when grown in a mixed culture with a cooperative wild-type strain, the relative fitness of a mutant is negatively correlated with the amount of pyoverdin that it produces; (2) the absolute and relative fitness of the wild-type strain in the mixed culture is positively correlated with the amount of pyoverdin that the mutant produces; and (3) when grown in a monoculture, the absolute fitness of the mutant is positively correlated with the amount of pyoverdin that it produces. Overall, we demonstrate that cooperative pyoverdin production is exploitable and illustrate how variation in a social behaviour determines fitness differently, depending on the social environment. PMID:20210835

  2. P450 enzymes from the bacterium Novosphingobium aromaticivorans.

    PubMed

    Bell, Stephen G; Wong, Luet-Lok

    2007-08-31

    Twelve of the fifteen potential P450 enzymes from the bacterium Novosphingobium aromaticivorans, which is known to degrade a wide range of aromatic hydrocarbons, have been produced via heterologous expression in Escherichia coli. The enzymes were tested for their ability to bind a range of substrates including polyaromatic hydrocarbons. While two of the enzymes were found to bind aromatic compounds (CYP108D1 and CYP203A2), the others show binding with a variety of compounds including linear alkanes (CYP153C1) and mono- and sesqui-terpenoid compounds (CYP101B1, CYP101C1, CYP101D1, CYP101D2, CYP111A1, and CYP219A1). A 2Fe-2S ferredoxin (Arx-A), which is associated with CYP101D2, was also produced. The activity of five of the P450 enzymes (CYP101B1, CYP101C1, CYP101D1, CYP101D2, and CYP111A2) was reconstituted with Arx-A and putidaredoxin reductase (of the P450cam system from Pseudomonas putida) in a Class I type electron transfer system. Preliminary characterisation of the majority of the substrate oxidation products is reported. PMID:17618912

  3. Bioconversion of methane to lactate by an obligate methanotrophic bacterium

    PubMed Central

    Henard, Calvin A.; Smith, Holly; Dowe, Nancy; Kalyuzhnaya, Marina G.; Pienkos, Philip T.; Guarnieri, Michael T.

    2016-01-01

    Methane is the second most abundant greenhouse gas (GHG), with nearly 60% of emissions derived from anthropogenic sources. Microbial conversion of methane to fuels and value-added chemicals offers a means to reduce GHG emissions, while also valorizing this otherwise squandered high-volume, high-energy gas. However, to date, advances in methane biocatalysis have been constrained by the low-productivity and limited genetic tractability of natural methane-consuming microbes. Here, leveraging recent identification of a novel, tractable methanotrophic bacterium, Methylomicrobium buryatense, we demonstrate microbial biocatalysis of methane to lactate, an industrial platform chemical. Heterologous overexpression of a Lactobacillus helveticus L-lactate dehydrogenase in M. buryatense resulted in an initial titer of 0.06 g lactate/L from methane. Cultivation in a 5 L continuously stirred tank bioreactor enabled production of 0.8 g lactate/L, representing a 13-fold improvement compared to the initial titer. The yields (0.05 g lactate/g methane) and productivity (0.008 g lactate/L/h) indicate the need and opportunity for future strain improvement. Additionally, real-time analysis of methane utilization implicated gas-to-liquid transfer and/or microbial methane consumption as process limitations. This work opens the door to develop an array of methanotrophic bacterial strain-engineering strategies currently employed for biocatalytic sugar upgrading to “green” chemicals and fuels. PMID:26902345

  4. A serine sensor for multicellularity in a bacterium

    PubMed Central

    Subramaniam, Arvind R; DeLoughery, Aaron; Bradshaw, Niels; Chen, Yun; O’Shea, Erin; Losick, Richard; Chai, Yunrong

    2013-01-01

    We report the discovery of a simple environmental sensing mechanism for biofilm formation in the bacterium Bacillus subtilis that operates without the involvement of a dedicated RNA or protein. Certain serine codons, the four TCN codons, in the gene for the biofilm repressor SinR caused a lowering of SinR levels under biofilm-inducing conditions. Synonymous substitutions of these TCN codons with AGC or AGT impaired biofilm formation and gene expression. Conversely, switching AGC or AGT to TCN codons upregulated biofilm formation. Genome-wide ribosome profiling showed that ribosome density was higher at UCN codons than at AGC or AGU during biofilm formation. Serine starvation recapitulated the effect of biofilm-inducing conditions on ribosome occupancy and SinR production. As serine is one of the first amino acids to be exhausted at the end of exponential phase growth, reduced translation speed at serine codons may be exploited by other microbes in adapting to stationary phase. DOI: http://dx.doi.org/10.7554/eLife.01501.001 PMID:24347549

  5. P450 enzymes from the bacterium Novosphingobium aromaticivorans

    SciTech Connect

    Bell, Stephen G. . E-mail: stephen.bell@chem.ox.ac.uk; Wong, Luet-Lok

    2007-08-31

    Twelve of the fifteen potential P450 enzymes from the bacterium Novosphingobium aromaticivorans, which is known to degrade a wide range of aromatic hydrocarbons, have been produced via heterologous expression in Escherichia coli. The enzymes were tested for their ability to bind a range of substrates including polyaromatic hydrocarbons. While two of the enzymes were found to bind aromatic compounds (CYP108D1 and CYP203A2), the others show binding with a variety of compounds including linear alkanes (CYP153C1) and mono- and sesqui-terpenoid compounds (CYP101B1, CYP101C1, CYP101D1, CYP101D2, CYP111A1, and CYP219A1). A 2Fe-2S ferredoxin (Arx-A), which is associated with CYP101D2, was also produced. The activity of five of the P450 enzymes (CYP101B1, CYP101C1, CYP101D1, CYP101D2, and CYP111A2) was reconstituted with Arx-A and putidaredoxin reductase (of the P450cam system from Pseudomonas putida) in a Class I type electron transfer system. Preliminary characterisation of the majority of the substrate oxidation products is reported.

  6. The acetylproteome of Gram-positive model bacterium Bacillus subtilis.

    PubMed

    Kim, Dooil; Yu, Byung Jo; Kim, Jung Ae; Lee, Yong-Jik; Choi, Soo-Geun; Kang, Sunghyun; Pan, Jae-Gu

    2013-05-01

    N(ε) -lysine acetylation, a reversible and highly regulated PTM, has been shown to occur in the model Gram-negative bacteria Escherichia coli and Salmonella enterica. Here, we extend this acetylproteome analysis to Bacillus subtilis, a model Gram-positive bacterium. Through anti-acetyllysine antibody-based immunoseparation of acetylpeptides followed by nano-HPLC/MS/MS analysis, we identified 332 unique lysine-acetylated sites on 185 proteins. These proteins are mainly involved in cellular housekeeping functions such as central metabolism and protein synthesis. Fifity-nine of the lysine-acetylated proteins showed homology with lysine-acetylated proteins previously identified in E. coli, suggesting that acetylated proteins are more conserved. Notably, acetylation was found at or near the active sites predicted by Prosite signature, including SdhA, RocA, Kbl, YwjH, and YfmT, indicating that lysine acetylation may affect their activities. In 2-amino-3-ketobutyrate CoA ligase Kbl, a class II aminotransferase, a lysine residue involved in pyridoxal phosphate attachment was found to be acetylated. This data set provides evidence for the generality of lysine acetylation in eubacteria and opens opportunities to explore the consequences of acetylation modification on the molecular physiology of B. subtilis. PMID:23468065

  7. Heavy Metal Induced Antibiotic Resistance in Bacterium LSJC7.

    PubMed

    Chen, Songcan; Li, Xiaomin; Sun, Guoxin; Zhang, Yingjiao; Su, Jianqiang; Ye, Jun

    2015-01-01

    Co-contamination of antibiotics and heavy metals prevails in the environment, and may play an important role in disseminating bacterial antibiotic resistance, but the selective effects of heavy metals on bacterial antibiotic resistance is largely unclear. To investigate this, the effects of heavy metals on antibiotic resistance were studied in a genome-sequenced bacterium, LSJC7. The results showed that the presence of arsenate, copper, and zinc were implicated in fortifying the resistance of LSJC7 towards tetracycline. The concentrations of heavy metals required to induce antibiotic resistance, i.e., the minimum heavy metal concentrations (MHCs), were far below (up to 64-fold) the minimum inhibition concentrations (MIC) of LSJC7. This finding indicates that the relatively low heavy metal levels in polluted environments and in treated humans and animals might be sufficient to induce bacterial antibiotic resistance. In addition, heavy metal induced antibiotic resistance was also observed for a combination of arsenate and chloramphenicol in LSJC7, and copper/zinc and tetracycline in antibiotic susceptible strain Escherichia coli DH5α. Overall, this study implies that heavy metal induced antibiotic resistance might be ubiquitous among various microbial species and suggests that it might play a role in the emergence and spread of antibiotic resistance in metal and antibiotic co-contaminated environments. PMID:26426011

  8. Hydrodynamics and collective behavior of the tethered bacterium Thiovulum majus

    PubMed Central

    Petroff, Alexander; Libchaber, Albert

    2014-01-01

    The ecology and dynamics of many microbial systems, particularly in mats and soils, are shaped by how bacteria respond to evolving nutrient gradients and microenvironments. Here we show how the response of the sulfur-oxidizing bacterium Thiovulum majus to changing oxygen gradients causes cells to organize into large-scale fronts. To study this phenomenon, we develop a technique to isolate and enrich these bacteria from the environment. Using this enrichment culture, we observe the formation and dynamics of T. majus fronts in oxygen gradients. We show that these dynamics can be understood as occurring in two steps. First, chemotactic cells moving up the oxygen gradient form a front that propagates with constant velocity. We then show, through observation and mathematical analysis, that this front becomes unstable to changes in cell density. Random perturbations in cell density create oxygen gradients. The response of cells magnifies these gradients and leads to the formation of millimeter-scale fluid flows that actively pull oxygenated water through the front. We argue that this flow results from a nonlinear instability excited by stochastic fluctuations in the density of cells. Finally, we show that the dynamics by which these modes interact can be understood from the chemotactic response of cells. These results provide a mathematically tractable example of how collective phenomena in ecological systems can arise from the individual response of cells to a shared resource. PMID:24459183

  9. Molecular study on cloned endoglucanase gene from rumen bacterium.

    PubMed

    Ozkose, Emin; Akyol, Ismail; Ekinci, Mehmet Sait

    2004-01-01

    An endoglucanase gene was subcloned from anaerobic rumen bacterium Ruminococcus flavefaciens strain 17. To express endoglucanase gene in Escherichia coli and Streptococcus bovis JB1, an endoglucanase gene fragment was inserted into pVA838-based shuttle vectors. Removal of endoglucanase gene promoter and expression of endoglucanase by promoter of S. bovis JB1 alpha-amylase gene (pACMCS) was also achieved. Survival of constructs pVACMCI, pTACMC and pACMCS, which carry endoglucanase gene, and stability of endoglucanase gene in S. bovis JB1, were observed. Maximal endoglucanase activities from S. bovis JB1/pVACMCI were 2- to 3-fold higher than from E. coli/pVACMCI. Specific cell activity of E. coli/pACMCS was found to be approximately 2- to -3 fold higher than the both E. coli/pVACMCI and E. coli/pTACMC. Specific cell activity of S. bovis JB1/pACMCS was also found to be approximately 2-fold higher than the both S. bovis/pVACMCI and S. bovis JB1/pTACMC. PMID:15925902

  10. Bioconversion of methane to lactate by an obligate methanotrophic bacterium.

    PubMed

    Henard, Calvin A; Smith, Holly; Dowe, Nancy; Kalyuzhnaya, Marina G; Pienkos, Philip T; Guarnieri, Michael T

    2016-01-01

    Methane is the second most abundant greenhouse gas (GHG), with nearly 60% of emissions derived from anthropogenic sources. Microbial conversion of methane to fuels and value-added chemicals offers a means to reduce GHG emissions, while also valorizing this otherwise squandered high-volume, high-energy gas. However, to date, advances in methane biocatalysis have been constrained by the low-productivity and limited genetic tractability of natural methane-consuming microbes. Here, leveraging recent identification of a novel, tractable methanotrophic bacterium, Methylomicrobium buryatense, we demonstrate microbial biocatalysis of methane to lactate, an industrial platform chemical. Heterologous overexpression of a Lactobacillus helveticus L-lactate dehydrogenase in M. buryatense resulted in an initial titer of 0.06 g lactate/L from methane. Cultivation in a 5 L continuously stirred tank bioreactor enabled production of 0.8 g lactate/L, representing a 13-fold improvement compared to the initial titer. The yields (0.05 g lactate/g methane) and productivity (0.008 g lactate/L/h) indicate the need and opportunity for future strain improvement. Additionally, real-time analysis of methane utilization implicated gas-to-liquid transfer and/or microbial methane consumption as process limitations. This work opens the door to develop an array of methanotrophic bacterial strain-engineering strategies currently employed for biocatalytic sugar upgrading to "green" chemicals and fuels. PMID:26902345

  11. Mutation of bacterium Vibrio gazogenes for selective preparation of colorants.

    PubMed

    Alihosseini, Farzaneh; Lango, Jozsef; Ju, Kou-San; Hammock, Bruce D; Sun, Gang

    2010-01-01

    A novel marine bacterium strain effectively produced prodiginine type pigments. These colorants could dye wool, silk and synthetic fabrics such as polyester and polyacrylic and also show antibacterial properties against Escherichia coli and Staphylococcus aureus bacteria on the dyed products. Methyl nitrosoguanidine was used as a mutation agent to increase the genetic diversity and the production yield of the bacteria of the family of Vibrio gazogenes. The analysis of the mutated samples showed that two new main colorants as well as three previously found ones were produced. Liquid chromatography electro spray ionization mass spectrometry (LC-ESI-MS) and nuclear magnetic resonance (NMR) spectroscopic techniques were used to elucidate the structures of the newly produced colorants. Mass measurements revealed that the colorants C1, C2, C3, C4 have molecular masses of 321, 323, 351, and 295 Da. One unstable colorant C5 with molecular mass of 309 Da was detected as well. The mutated bacteria strains increased the yield of pigment production by about 81% and produced prodigiosin in 97% purity. The antibiotic activities of pure colorants are discussed as well. Based on their bio-activity and excellent dyeing capabilities, these colorants could be employed in cosmetic and textile industries. PMID:19902486

  12. Mechanisms of gold biomineralization in the bacterium Cupriavidus metallidurans

    PubMed Central

    Reith, Frank; Etschmann, Barbara; Grosse, Cornelia; Moors, Hugo; Benotmane, Mohammed A.; Monsieurs, Pieter; Grass, Gregor; Doonan, Christian; Vogt, Stefan; Lai, Barry; Martinez-Criado, Gema; George, Graham N.; Nies, Dietrich H.; Mergeay, Max; Pring, Allan; Southam, Gordon; Brugger, Joël

    2009-01-01

    While the role of microorganisms as main drivers of metal mobility and mineral formation under Earth surface conditions is now widely accepted, the formation of secondary gold (Au) is commonly attributed to abiotic processes. Here we report that the biomineralization of Au nanoparticles in the metallophillic bacterium Cupriavidus metallidurans CH34 is the result of Au-regulated gene expression leading to the energy-dependent reductive precipitation of toxic Au(III)-complexes. C. metallidurans, which forms biofilms on Au grains, rapidly accumulates Au(III)-complexes from solution. Bulk and microbeam synchrotron X-ray analyses revealed that cellular Au accumulation is coupled to the formation of Au(I)-S complexes. This process promotes Au toxicity and C. metallidurans reacts by inducing oxidative stress and metal resistances gene clusters (including a Au-specific operon) to promote cellular defense. As a result, Au detoxification is mediated by a combination of efflux, reduction, and possibly methylation of Au-complexes, leading to the formation of Au(I)-C-compounds and nanoparticulate Au0. Similar particles were observed in bacterial biofilms on Au grains, suggesting that bacteria actively contribute to the formation of Au grains in surface environments. The recognition of specific genetic responses to Au opens the way for the development of bioexploration and bioprocessing tools. PMID:19815503

  13. Novel Trypanosomatid-Bacterium Association: Evolution of Endosymbiosis in Action

    PubMed Central

    Kostygov, Alexei Y.; Dobáková, Eva; Grybchuk-Ieremenko, Anastasiia; Váhala, Dalibor; Maslov, Dmitri A.; Votýpka, Jan

    2016-01-01

    ABSTRACT We describe a novel symbiotic association between a kinetoplastid protist, Novymonas esmeraldas gen. nov., sp. nov., and an intracytoplasmic bacterium, “Candidatus Pandoraea novymonadis” sp. nov., discovered as a result of a broad-scale survey of insect trypanosomatid biodiversity in Ecuador. We characterize this association by describing the morphology of both organisms, as well as their interactions, and by establishing their phylogenetic affinities. Importantly, neither partner is closely related to other known organisms previously implicated in eukaryote-bacterial symbiosis. This symbiotic association seems to be relatively recent, as the host does not exert a stringent control over the number of bacteria harbored in its cytoplasm. We argue that this unique relationship may represent a suitable model for studying the initial stages of establishment of endosymbiosis between a single-cellular eukaryote and a prokaryote. Based on phylogenetic analyses, Novymonas could be considered a proxy for the insect-only ancestor of the dixenous genus Leishmania and shed light on the origin of the two-host life cycle within the subfamily Leishmaniinae. PMID:26980834

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

    PubMed

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

    2016-09-01

    A novel halophilic bacterium, strain K7(T), was isolated from kimchi, a traditional Korean fermented food. The strain is Gram-positive, motile, and produces terminal endospores. The isolate is facultative aerobic and grows at salinities of 0.0-25.0% (w/v) NaCl (optimum 10-15% NaCl), pH 5.5-8.5 (optimum pH 7.0-7.5), and 15-42°C (optimum 37°C). The predominant isoprenoid quinone in the strain is menaquinone-7 and the peptidoglycan of the strain is meso-diaminopimelic acid. The major fatty acids of the strain are anteisio-C15:0, iso-C15:0, and, C16:0 (other components were < 10.0%), while the major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and three unidentified lipids. A phylogenetic analysis of 16S rRNA gene sequence similarity showed that the isolated strain was a cluster of the genus Gracilibacillus. High levels of gene sequence similarity were observed between strain K7(T) and Gracilibacillus orientalis XH-63(T) (96.5%), and between the present strain and Gracilibacillus xinjiangensis (96.5%). The DNA G+C content of this strain is 37.7 mol%. Based on these findings, strain K7(T) is proposed as a novel species: Gracilibacillus kimchii sp. nov. The type strain is K7(T) (KACC 18669(T); JCM 31344(T)). PMID:27572507

  15. Bioconversion of methane to lactate by an obligate methanotrophic bacterium

    DOE PAGESBeta

    Henard, Calvin A.; Smith, Holly; Dowe, Nancy; Kalyuzhnaya, Marina G.; Pienkos, Philip T.; Guarnieri, Michael T.

    2016-02-23

    Methane is the second most abundant greenhouse gas (GHG), with nearly 60% of emissions derived from anthropogenic sources. Microbial conversion of methane to fuels and value-added chemicals offers a means to reduce GHG emissions, while also valorizing this otherwise squandered high-volume, high-energy gas. However, to date, advances in methane biocatalysis have been constrained by the low-productivity and limited genetic tractability of natural methane-consuming microbes. Here, leveraging recent identification of a novel, tractable methanotrophic bacterium, Methylomicrobium buryatense, we demonstrate microbial biocatalysis of methane to lactate, an industrial platform chemical. Heterologous overexpression of a Lactobacillus helveticus L-lactate dehydrogenase in M. buryatense resultedmore » in an initial titer of 0.06 g lactate/L from methane. Cultivation in a 5 L continuously stirred tank bioreactor enabled production of 0.8 g lactate/L, representing a 13-fold improvement compared to the initial titer. The yields (0.05 g lactate/g methane) and productivity (0.008 g lactate/L/h) indicate the need and opportunity for future strain improvement. Additionally, real-time analysis of methane utilization implicated gas-to-liquid transfer and/or microbial methane consumption as process limitations. This work opens the door to develop an array of methanotrophic bacterial strain-engineering strategies currently employed for biocatalytic sugar upgrading to “green” chemicals and fuels.« less

  16. A new isolation method for labyrinthulids using a bacterium, Psychrobacter phenylpyruvicus.

    PubMed

    Yokochi, T; Nakahara, T; Higashihara, T; Yamaoka, M; Kurane, R

    2001-01-01

    A new isolation method for labyrinthulids, marine microbes with spindle-shaped vegetative cells and gliding movement, is presented. The method for isolating labyrinthulids has been found to be more difficult and less reproducible than that for thraustochytrids, classified in the same order. So far serum seawater agar fortified with antibiotics has been proposed to be the best for isolation of labyrinthulids. The method presented here involves placing plant samples on an agar medium on which a marine bacterium, Psychrobacter phenylpyruvicus, has been grown. The new method, which utilizes fallen mangrove leaves as source material, was more than twice as effective as isolation agar medium without the bacterium. The increased effectiveness appears to derive partly from the bacterial colonies' delaying extension of fungal mycelium. The bacterium was more effective for the isolation of labyrinthulids than either the bacterium Shewanella sp. or the yeast Rhodotorula rubra. PMID:14961392

  17. IN SITU RT-PCR WITH A SULFATE-REDUCING BACTERIUM ISOLATED FROM SEAGRASS ROOTS

    EPA Science Inventory

    Bacteria considered to be obligate anaerobes internally colonize roots of the submerged macrophyte Halodule wrightii. A sulfate reducing bacterium, Summer lac 1, was isolated on lactate from H. wrightii roots. The isolate has physiological characteristics typical of Desulfovibri...

  18. Characterization of a Neochlamydia-like bacterium associated with epitheliocystis in cultured Arctic charr Salvelinus alpinus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Infections of branchial epithelium by intracellular gram-negative bacteria, termed epitheliocystis, have limited culture of Arctic char (Salvelinus alpinus). To characterize a bacterium associated with epitheliocystis in cultured char, gills were sampled for histopathologic examination, conventiona...

  19. Extracellular electron transfer of a highly adhesive and metabolically versatile bacterium.

    PubMed

    Liu, Huan; Ishikawa, Masahito; Matsuda, Shoichi; Kimoto, Yuki; Hori, Katsutoshi; Hashimoto, Kazuhito; Nakanishi, Shuji

    2013-08-01

    Bacterial adhesion to a solid plays a predominant role in mediating the extracellular electron transfer for genus Acinetobactor, a metabolically versatile bacterium that can couple toluene degradation and electricity generation. PMID:23813865

  20. Draft Genome Sequence of the Versatile Alkane-Degrading Bacterium Aquabacterium sp. Strain NJ1

    PubMed Central

    Shiwa, Yuh; Yoshikawa, Hirofumi; Zylstra, Gerben J.

    2014-01-01

    The draft genome sequence of a soil bacterium, Aquabacterium sp. strain NJ1, capable of utilizing both liquid and solid alkanes, was deciphered. This is the first report of an Aquabacterium genome sequence. PMID:25477416

  1. Characterization of a Neochlamydia-like Bacterium Associated with Epitheliocystis in Cultured Artic Char Salvelinus alpinus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Infections of branchial epithelium by intracellular gram-negative bacteria, termed epitheliocystis, have limited culture of Arctic char (Salvelinus alpinus). To characterize a bacterium associated with epitheliocystis in cultured char, gills were sampled for histopathologic examination, conventional...

  2. Enhancement of xylose utilization from corn stover by a recombinant bacterium for ethanol production

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recombinant ethanologenic Escherichia coli ferments glucose, xylose and arabinose to ethanol. However, the bacterium preferentially utilizes glucose first, then arabinose and finally xylose (sequential utilization of sugars) during fermentation of lignocellulosic hydrolyzates to ethanol making the p...

  3. Draft Genome Sequence of Erythrobacter vulgaris Strain O1, a Glycosyl Hydrolase-Producing Bacterium

    PubMed Central

    Yaakop, Amira Suriaty; Chan, Chia Sing; Kahar, Ummirul Mukminin; Ee, Robson

    2015-01-01

    Erythrobacter vulgaris strain O1, a moderate halophile, was isolated from a beach in Johor, Malaysia. Here, we present the draft genome and suggest potential applications of this bacterium. PMID:25977433

  4. Draft Genome Sequence of DLB, a Dyella-Like Bacterium from the Planthopper Hyalesthes obsoletus

    PubMed Central

    Lahav, Tamar; Zchori-Fein, Einat; Naor, Vered; Freilich, Shiri

    2016-01-01

    We report here the draft genome sequence of a Dyella-like bacterium (DLB) isolated from Hyalesthes obsoletus, the insect vector of the uncultivable mollicute bacterium “Candidatus Phytoplasma.” This isolate inhibits Spiroplasma melliferum, a cultivable mollicute. The draft genome of DLB consists of 4,196,214 bp, with a 68.6% G+C content, and 3,757 genes were predicted. PMID:27445378

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

    PubMed

    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. PMID:26988395

  6. Endohyphal Bacterium Enhances Production of Indole-3-Acetic Acid by a Foliar Fungal Endophyte

    PubMed Central

    Hoffman, Michele T.; Gunatilaka, Malkanthi K.; Wijeratne, Kithsiri; Gunatilaka, Leslie; Arnold, A. Elizabeth

    2013-01-01

    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. PMID:24086270

  7. Metabolomics evaluation of the impact of smokeless tobacco exposure on the oral bacterium Capnocytophaga sputigena.

    PubMed

    Sun, Jinchun; Jin, Jinshan; Beger, Richard D; Cerniglia, Carl E; Yang, Maocheng; Chen, Huizhong

    2016-10-01

    The association between exposure to smokeless tobacco products (STP) and oral diseases is partially due to the physiological and pathological changes in the composition of the oral microbiome and its metabolic profile. However, it is not clear how STPs affect the physiology and ecology of oral microbiota. A UPLC/QTof-MS-based metabolomics study was employed to analyze metabolic alterations in oral bacterium, Capnocytophaga sputigena as a result of smokeless tobacco exposure and to assess the capability of the bacterium to metabolize nicotine. Pathway analysis of the metabolome profiles indicated that smokeless tobacco extracts caused oxidative stress in the bacterium. The metabolomics data also showed that the arginine-nitric oxide pathway was perturbed by the smokeless tobacco treatment. Results also showed that LC/MS was useful in identifying STP constituents and additives, including caffeine and many flavoring compounds. No significant changes in levels of nicotine and its major metabolites were found when C. sputigena was cultured in a nutrient rich medium, although hydroxylnicotine and cotinine N-oxide were detected in the bacterial metabolites suggesting that nicotine metabolism might be present as a minor degradation pathway in the bacterium. Study results provide new insights regarding the physiological and toxicological effects of smokeless tobacco on oral bacterium C. sputigena and associated oral health as well as measuring the ability of the oral bacterium to metabolize nicotine. PMID:27480511

  8. Metabolic Evolution of a Deep-Branching Hyperthermophilic Chemoautotrophic Bacterium

    PubMed Central

    Braakman, Rogier; Smith, Eric

    2014-01-01

    Aquifex aeolicus is a deep-branching hyperthermophilic chemoautotrophic bacterium restricted to hydrothermal vents and hot springs. These characteristics make it an excellent model system for studying the early evolution of metabolism. Here we present the whole-genome metabolic network of this organism and examine in detail the driving forces that have shaped it. We make extensive use of phylometabolic analysis, a method we recently introduced that generates trees of metabolic phenotypes by integrating phylogenetic and metabolic constraints. We reconstruct the evolution of a range of metabolic sub-systems, including the reductive citric acid (rTCA) cycle, as well as the biosynthesis and functional roles of several amino acids and cofactors. We show that A. aeolicus uses the reconstructed ancestral pathways within many of these sub-systems, and highlight how the evolutionary interconnections between sub-systems facilitated several key innovations. Our analyses further highlight three general classes of driving forces in metabolic evolution. One is the duplication and divergence of genes for enzymes as these progress from lower to higher substrate specificity, improving the kinetics of certain sub-systems. A second is the kinetic optimization of established pathways through fusion of enzymes, or their organization into larger complexes. The third is the minimization of the ATP unit cost to synthesize biomass, improving thermodynamic efficiency. Quantifying the distribution of these classes of innovations across metabolic sub-systems and across the tree of life will allow us to assess how a tradeoff between maximizing growth rate and growth efficiency has shaped the long-term metabolic evolution of the biosphere. PMID:24516572

  9. Paenibacillus xylanilyticus sp. nov., an airborne xylanolytic bacterium.

    PubMed

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

    2005-01-01

    During a search for xylan-degrading micro-organisms, a sporulating bacterium was recovered from xylan-containing agar plates exposed to air in a research laboratory (Salamanca University, Spain). The airborne isolate (designated strain XIL14T) was identified by 16S rRNA gene sequencing as representing a Paenibacillus species most closely related to Paenibacillus illinoisensis JCM 9907T (99.3 % sequence similarity) and Paenibacillus pabuli DSM 3036T (98 % sequence similarity). Phenotypic, chemotaxonomic and DNA-DNA hybridization data indicated that the isolate belongs to a novel species of the genus Paenibacillus. Cells of strain XIL14T were motile, sporulating, rod-shaped, Gram-positive and facultatively anaerobic. The predominant cellular fatty acids were anteiso-C(15 : 0) and C(16 : 0). The DNA G+C content of strain XIL14T was 50.5 mol%. Growth was observed with many carbohydrates, including xylan, as the only carbon source and gas production was not observed from glucose. Catalase was positive and oxidase was negative. The airborne isolate produced a variety of hydrolytic enzymes, including xylanases, amylases, gelatinase and beta-galactosidase. DNA-DNA hybridization levels between strain XIL14T and P. illinoisensis DSM 11733T and P. pabuli DSM 3036T were 43.3 and 36.3 %, respectively. According to the data obtained, strain XIL14T is considered to represent a novel species for which the name Paenibacillus xylanilyticus sp. nov. is proposed (=LMG 21957T=CECT 5839T). PMID:15653909

  10. Metabolic evolution of a deep-branching hyperthermophilic chemoautotrophic bacterium.

    PubMed

    Braakman, Rogier; Smith, Eric

    2014-01-01

    Aquifex aeolicus is a deep-branching hyperthermophilic chemoautotrophic bacterium restricted to hydrothermal vents and hot springs. These characteristics make it an excellent model system for studying the early evolution of metabolism. Here we present the whole-genome metabolic network of this organism and examine in detail the driving forces that have shaped it. We make extensive use of phylometabolic analysis, a method we recently introduced that generates trees of metabolic phenotypes by integrating phylogenetic and metabolic constraints. We reconstruct the evolution of a range of metabolic sub-systems, including the reductive citric acid (rTCA) cycle, as well as the biosynthesis and functional roles of several amino acids and cofactors. We show that A. aeolicus uses the reconstructed ancestral pathways within many of these sub-systems, and highlight how the evolutionary interconnections between sub-systems facilitated several key innovations. Our analyses further highlight three general classes of driving forces in metabolic evolution. One is the duplication and divergence of genes for enzymes as these progress from lower to higher substrate specificity, improving the kinetics of certain sub-systems. A second is the kinetic optimization of established pathways through fusion of enzymes, or their organization into larger complexes. The third is the minimization of the ATP unit cost to synthesize biomass, improving thermodynamic efficiency. Quantifying the distribution of these classes of innovations across metabolic sub-systems and across the tree of life will allow us to assess how a tradeoff between maximizing growth rate and growth efficiency has shaped the long-term metabolic evolution of the biosphere. PMID:24516572

  11. Jeongeupia chitinilytica sp. nov., a chitinolytic bacterium isolated from soil.

    PubMed

    Chen, Wen-Ming; Chang, Rey-Chang; Cheng, Chih-Yu; Shiau, Yu-Wen; Sheu, Shih-Yi

    2013-03-01

    A novel bacterium, designated strain Jchi(T), was isolated from soil in Taiwan and characterized using a polyphasic approach. Cells of strain Jchi(T) were aerobic, Gram-stain-negative, motile and rod-shaped. They contained poly-β-hydroxybutyrate granules and formed dark-yellow colonies. Growth occurred at 20-37 °C (optimum between 25 and 30 °C), at pH 6.0-8.0 (optimum between pH 7.0 and pH 8.0) and with 0-2 % NaCl (optimum between 0 and 1 %). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain Jchi(T) belonged to the genus Jeongeupia and that its closest neighbour was Jeongeupia naejangsanensis BIO-TAS4-2(T) (98.0 % sequence similarity). The major fatty acids (>10 %) of strain Jchi(T) were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The major cellular hydroxy fatty acid was C12 : 0 3-OH. The isoprenoid quinone was Q-8 and the genomic DNA G+C content was 66.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylserine and two unidentified phospholipids. The DNA-DNA relatedness value between strain Jchi(T) and J. naejangsanensis BIO-TAS4-2(T) was about 41.0 %. On the basis of the genotypic and phenotypic data, strain Jchi(T) represents a novel species in the genus Jeongeupia, for which the name Jeongeupia chitinilytica sp. nov. is proposed. The type strain is Jchi(T) ( = BCRC 80367(T)  = KCTC 23701(T)). PMID:22659500

  12. Characterization of a rhodanese from the cyanogenic bacterium Pseudomonas aeruginosa.

    PubMed

    Cipollone, Rita; Bigotti, Maria Giulia; Frangipani, Emanuela; Ascenzi, Paolo; Visca, Paolo

    2004-12-01

    Pseudomonas aeruginosa, the rRNA group I type species of genus Pseudomonas, is a Gram-negative, aerobic bacterium responsible for serious infection in humans. P. aeruginosa pathogenicity has been associated with the production of several virulence factors, including cyanide. Here, the biochemical characterization of recombinant P. aeruginosa rhodanese (Pa RhdA), catalyzing the sulfur transfer from thiosulfate to a thiophilic acceptor, e.g., cyanide, is reported. Sequence homology analysis of Pa RhdA predicts the sulfur-transfer reaction to occur through persulfuration of the conserved catalytic Cys230 residue. Accordingly, the titration of active Pa RhdA with cyanide indicates the presence of one extra sulfur bound to the Cys230 Sgamma atom per active enzyme molecule. Values of K(m) for thiosulfate binding to Pa RhdA are 1.0 and 7.4mM at pH 7.3 and 8.6, respectively, and 25 degrees C. However, the value of K(m) for cyanide binding to Pa RhdA (=14 mM, at 25 degrees C) and the value of V(max) (=750 micromol min(-1)mg(-1), at 25 degrees C) for the Pa RhdA-catalyzed sulfur-transfer reaction are essentially pH- and substrate-independent. Therefore, the thiosulfate-dependent Pa RhdA persulfuration is favored at pH 7.3 (i.e., the cytosolic pH of the bacterial cell) rather than pH 8.6 (i.e., the standard pH for rhodanese activity assay). Within this pH range, conformational change(s) occur at the Pa RhdA active site during the catalytic cycle. As a whole, rhodanese may participate in multiple detoxification mechanisms protecting P. aeruginosa from endogenous and environmental cyanide. PMID:15522204

  13. Carbonate biomineralization induced by soil bacterium Bacillus megaterium

    NASA Astrophysics Data System (ADS)

    Lian, Bin; Hu, Qiaona; Chen, Jun; Ji, Junfeng; Teng, H. Henry

    2006-11-01

    Biogenic carbonates spawned from microbial activities are common occurrences in soils. Here, we investigate the carbonate biomineralization mediated by the bacterium Bacillus megaterium, a dominant strain separated from a loess profile in China. Upon completing bacterial cultivation, the ensuring products are centrifuged, and the resultant supernatant and the concentrated bacterial sludge as well as the un-separated culture are added separately into a Ca-CO 3 containing solution for crystallization experiments. Results of XRD and SEM analysis indicate that calcite is the dominant mineral phase formed when the bacteria are present. When the supernatant alone is used, however, a significant portion of vaterite is also precipitated. Experimental results further reveal that the bacteria have a strong tendency to colonize the center area of the calcite {1 0 1¯ 4} faces. Observed crystal morphology suggests that the bacterial colony may promote the growth normal to each individual {1 0 1¯ 4} face of calcite when the cell concentration is high, but may retard it or even cause dissolution of the immediate substrate surfaces when the concentration is low. SEM images taken at earlier stages of the crystallization experiments demonstrate the nucleation of calcite on the bacterial cell walls but do not show obvious morphological changes on the nanometer- to submicron-sized nuclei. δ 13C measurements unveil that the crystals grown in the presence of bacteria are further enriched in the heavy carbon isotope, implying that the bacterial metabolism may not be the carbon sources for the mineralization. Based upon these findings, we propose a mechanism for the B. megaterium mediated calcite mineralization and conclude that the whole process involves epi- and inter-cellular growth in the local microenvironments whose conditions may be controlled by cell sequestration and proton pumping during bacterial respiration.

  14. Bacterium-Mimicking Nanoparticle Surface Functionalization with Targeting Motifs

    PubMed Central

    Lai, Mei-Hsiu; Clay, Nicholas E.; Kim, Dong Hyun; Kong, Hyunjoon

    2015-01-01

    In recent years, surface modification of nanocarriers with targeting motifs has been explored to modulate delivery of various diagnostic, sensing and therapeutic molecular cargos to desired sites of interest in in vitro bioengineering platforms and in vivo pathologic tissue. However, most surface functionalization approaches are often plagued by complex chemical modifications and effortful purifications. To resolve such challenges, this study demonstrates a unique method to immobilize antibodies that can act as targeting motifs on the surfaces of nanocarriers, inspired by a process that bacteria use for immobilization of the host’s antibodies. We hypothesized that alkylated Staphylococcus aureus protein A (SpA) would self-assemble with micelles and subsequently induce stable coupling of antibodies to the micelles. We examined this hypothesis by using poly(2-hydroxyethyl-co-octadecyl aspartamide) (PHEA-g-C18) as a model polymer to form micelles. The self-assembly between micelles and alkylated SpA became more thermodynamically favorable by increasing the degree of substitution of octadecyl chains to PHEA-g-C18, due to a positive entropy change. Lastly, the simple mixing of SpA-PA-coupled micelles with antibodies resulted in the micelles coated by antibodies, as confirmed with a fluorescence resonance energy transfer (FRET) assay. The micelles coated by antibodies to VCAM-1 or integrin αv displayed higher binding affinity to a substrate coated by VCAM-1 and integrin αvβ3, respectively, than other controls, as evaluated with surface plasmon resonance (SPR) spectroscopy and a circulation-simulating flow chamber. We envisage this bacterium-inspired protein immobilization approach will be useful to improving the quality of targeted delivery of nanoparticles, and can be extended to modify the surface of a wide array of nanocarriers. PMID:25804130

  15. Interaction of Cadmium With the Aerobic Bacterium Pseudomonas Mendocina

    NASA Astrophysics Data System (ADS)

    Schramm, P. J.; Haack, E. A.; Maurice, P. A.

    2006-05-01

    The fate of toxic metals in the environment can be heavily influenced by interaction with bacteria in the vadose zone. This research focuses on the interactions of cadmium with the strict aerobe Pseudomonas mendocina. P. mendocina is a gram-negative bacterium that has shown potential in the bioremediation of recalcitrant organic compounds. Cadmium is a common environmental contaminant of wide-spread ecological consequence. In batch experiments P. mendocina shows typical bacterial growth curves, with an initial lag phase followed by an exponential phase and a stationary to death phase; concomitant with growth was an increase in pH from initial values of 7 to final values at 96 hours of 8.8. Cd both delays the onset of the exponential phase and decreases the maximum population size, as quantified by optical density and microscopic cell counts (DAPI). The total amount of Cd removed from solution increases over time, as does the amount of Cd removed from solution normalized per bacterial cell. Images obtained with transmission electron microscopy (TEM) showed the production of a cadmium, phosphorus, and iron containing precipitate that was similar in form and composition to precipitates formed abiotically at elevated pH. However, by late stationary phase, the precipitate had been re-dissolved, perhaps by biotic processes in order to obtain Fe. Stressed conditions are suggested by TEM images showing the formation of pili, or nanowires, when 20ppm Cd was present and a marked decrease in exopolysaccharide and biofilm material in comparison to control cells (no cadmium added).

  16. Regulation of caffeate respiration in the acetogenic bacterium Acetobacterium woodii.

    PubMed

    Dilling, Sabrina; Imkamp, Frank; Schmidt, Silke; Müller, Volker

    2007-06-01

    The anaerobic acetogenic bacterium Acetobacterium woodii can conserve energy by oxidation of various substrates coupled to either carbonate or caffeate respiration. We used a cell suspension system to study the regulation and kinetics of induction of caffeate respiration. After addition of caffeate to suspensions of fructose-grown cells, there was a lag phase of about 90 min before caffeate reduction commenced. However, in the presence of tetracycline caffeate was not reduced, indicating that de novo protein synthesis is required for the ability to respire caffeate. Induction also took place in the presence of CO(2), and once a culture was induced, caffeate and CO(2) were used simultaneously as electron acceptors. Induction of caffeate reduction was also observed with H(2) plus CO(2) as the substrate, but the lag phase was much longer. Again, caffeate and CO(2) were used simultaneously as electron acceptors. In contrast, during oxidation of methyl groups derived from methanol or betaine, acetogenesis was the preferred energy-conserving pathway, and caffeate reduction started only after acetogenesis was completed. The differential flow of reductants was also observed with suspensions of resting cells in which caffeate reduction was induced prior to harvest of the cells. These cell suspensions utilized caffeate and CO(2) simultaneously with fructose or hydrogen as electron donors, but CO(2) was preferred over caffeate during methyl group oxidation. Caffeate-induced resting cells could reduce caffeate and also p-coumarate or ferulate with hydrogen as the electron donor. p-Coumarate or ferulate also served as an inducer for caffeate reduction. Interestingly, caffeate-induced cells reduced ferulate in the absence of an external reductant, indicating that caffeate also induces the enzymes required for oxidation of the methyl group of ferulate. PMID:17416687

  17. Competitive PCR for Quantitation of a Cytophaga-Flexibacter-Bacteroides Phylum Bacterium Associated with the Tuber borchii Vittad. Mycelium

    PubMed Central

    Barbieri, Elena; Riccioni, Giulia; Pisano, Anna; Sisti, Davide; Zeppa, Sabrina; Agostini, Deborah; Stocchi, Vilberto

    2002-01-01

    An uncultured bacterium associated with the ectomycorrhizal fungus Tuber borchii Vittad. was identified as a novel member of the Cytophaga-Flexibacter-Bacteroides group. Utilizing a quantitative PCR targeting the 16S rRNA gene, we relatively quantified this bacterium in the host. The estimated number of bacteria was found to be approximately 106 cells per 30-day-old T. borchii mycelium culture. This represents the first molecular attempt to enumerate an uncultured bacterium associated with a mycorrhizal fungus. PMID:12450871

  18. Regulation of Polyhydroxybutyrate Synthesis in the Soil Bacterium Bradyrhizobium diazoefficiens.

    PubMed

    Quelas, J I; Mesa, S; Mongiardini, E J; Jendrossek, D; Lodeiro, A R

    2016-07-15

    Polyhydroxybutyrate (PHB) is a carbon and energy reserve polymer in various prokaryotic species. We determined that, when grown with mannitol as the sole carbon source, Bradyrhizobium diazoefficiens produces a homopolymer composed only of 3-hydroxybutyrate units (PHB). Conditions of oxygen limitation (such as microoxia, oxic stationary phase, and bacteroids inside legume nodules) were permissive for the synthesis of PHB, which was observed as cytoplasmic granules. To study the regulation of PHB synthesis, we generated mutations in the regulator gene phaR and the phasin genes phaP1 and phaP4 Under permissive conditions, mutation of phaR impaired PHB accumulation, and a phaP1 phaP4 double mutant produced more PHB than the wild type, which was accumulated in a single, large cytoplasmic granule. Moreover, PhaR negatively regulated the expression of phaP1 and phaP4 as well as the expression of phaA1 and phaA2 (encoding a 3-ketoacyl coenzyme A [CoA] thiolases), phaC1 and phaC2 (encoding PHB synthases), and fixK2 (encoding a cyclic AMP receptor protein [CRP]/fumarate and nitrate reductase regulator [FNR]-type transcription factor of genes for microoxic lifestyle). In addition to the depressed PHB cycling, phaR mutants accumulated more extracellular polysaccharides and promoted higher plant shoot dry weight and competitiveness for nodulation than the wild type, in contrast to the phaC1 mutant strain, which is defective in PHB synthesis. These results suggest that phaR not only regulates PHB granule formation by controlling the expression of phasins and biosynthetic enzymes but also acts as a global regulator of excess carbon allocation and symbiosis by controlling fixK2 IMPORTANCE: In this work, we investigated the regulation of polyhydroxybutyrate synthesis in the soybean-nodulating bacterium Bradyrhizobium diazoefficiens and its influence in bacterial free-living and symbiotic lifestyles. We uncovered a new interplay between the synthesis of this carbon reserve polymer

  19. Photoactive yellow protein from the halophilic bacterium Salinibacter ruber.

    PubMed

    Memmi, Samy; Kyndt, John; Meyer, Terry; Devreese, Bart; Cusanovich, Michael; Van Beeumen, Jozef

    2008-02-19

    A gene for photoactive yellow protein (PYP) was identified from the genome sequence of the extremely halophilic aerobic bacterium Salinibacter ruber (Sr). The sequence is distantly related to the prototypic PYP from Halorhodospira halophila (Hh) (37% identity) and contains most of the amino acid residues identified as necessary for function. However, the Sr pyp gene is not flanked by its two biosynthetic genes as in other species. To determine as to whether the Sr pyp gene encodes a functional protein, we cloned and expressed it in Escherichia coli, along with the genes for chromophore biosynthesis from Rhodobacter capsulatus. The Sr PYP has a 31-residue N-terminal extension as compared to other PYPs that appears to be important for dimerization; however, truncation of these extra residues did not change the spectral and photokinetic properties. Sr PYP has an absorption maximum at 431 nm, which is at shorter wavelengths than the prototypical Hh PYP (at 446 nm). It is also photoactive, being reversibly bleached by either blue or white light. The kinetics of dark recovery is slower than any of the PYPs reported to date (4.27 x 10(-4) s(-1) at pH 7.5). Sr PYP appears to have a normal photocycle with the I1 and I2 intermediates. The presence of the I2' intermediate is also inferred on the basis of the effects of temperature and alchohol on recovery. Sr PYP has an intermediate spectral form in equilibrium with the 431 nm form, similar to R. capsulatus PYP and the Y42F mutant of Hh PYP. Increasing ionic strength stabilizes the 431 nm form at the expense of the intermediate spectral form, and the kinetics of recovery is accelerated 6.4-fold between 0 and 3.5 M salt. This is observed with ions from both the chaotropic and the kosmotropic series. Ionic strength also stabilizes PYP against thermal denaturation, as the melting temperature is increased from 74 degrees C in buffer alone to 92 degrees C in 2 M KCl. Sr accumulates KCl in the cytoplasm, like Halobacterium, to

  20. Further studies on a human intestinal bacterium Ruminococcus sp. END-1 for transformation of plant lignans to mammalian lignans.

    PubMed

    Jin, Jong-Sik; Hattori, Masao

    2009-08-26

    A human intestinal bacterium Ruminococcus (R.) sp. END-1 capable of oxidizing (-)-enterodiol to (-)-enterolactone, enantioselectively, was further investigated from the perspective of transformation of plant lignans to mammalian lignans; A cell-free extract of the bacterium transformed (-)-enterodiol to (-)-enterolactone through an intermediate, enterolactol. The bacterium showed not only oxidation but also demethylation and deglucosylation activities for plant lignans. Arctiin and secoisolariciresinol diglucoside were converted to (-)-dihydroxyenterolactone and (+)-dihydroxyenterodiol, respectively. Moreover, by coincubation with Eggerthella sp. SDG-2, the bacterium transformed arctiin and secoisolariciresinol diglucoside to (-)-enterolactone and (+)-enterodiol, respectively. PMID:19630415

  1. Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

    PubMed Central

    Rhee, Mun Su; Moritz, Brélan E.; Xie, Gary; Glavina del Rio, T.; Dalin, E.; Tice, H.; Bruce, D.; Goodwin, L.; Chertkov, O.; Brettin, T.; Han, C.; Detter, C.; Pitluck, S.; Land, Miriam L.; Patel, Milind; Ou, Mark; Harbrucker, Roberta; Ingram, Lonnie O.; Shanmugam, K. T.

    2011-01-01

    Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 °C and pH 5.0 and ferments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 °C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemicellulose. This bacterium is also considered as a potential probiotic. Complete genome sequence of a representative strain, B. coagulans strain 36D1, is presented and discussed. PMID:22675583

  2. Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

    SciTech Connect

    Xie, Gary; Dalin, Eileen; Tice, Hope; Chertkov, Olga; Land, Miriam L

    2011-01-01

    Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 C and pH 5.0 and fer-ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemi-cellulose. This bacterium is also considered as a potential probiotic. Complete genome squence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

  3. Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

    SciTech Connect

    Rhee, Mun Su; Moritz, Brelan E.; Xie, Gary; Glavina Del Rio, Tijana; Dalin, Eileen; Tice, Hope; Bruce, David; Goodwin, Lynne A.; Chertkov, Olga; Brettin, Thomas S; Han, Cliff; Detter, J. Chris; Pitluck, Sam; Land, Miriam L; Patel, Milind; Ou, Mark; Harbrucker, Roberta; Ingram, Lonnie O.; Shanmugam, Keelnathan T.

    2011-01-01

    Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 C and pH 5.0 and fer- ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this spo- rogenic lactic acid bacterium to grow at 50-55 C and pH 5.0 makes this organism an attrac- tive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemi- cellulose. This bacterium is also considered as a potential probiotic. Complete genome se- quence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

  4. Investigations of Iron Minerals Formed by Dissimilatory Alkaliphilic Bacterium with {sup 57}Fe Moessbauer Spectroscopy

    SciTech Connect

    Chistyakova, N. I.; Rusakov, V. S.; Shapkin, A. A.; Zhilina, T. N.; Zavarzina, D. G.; Kohout, J.

    2010-07-13

    Anaerobic alkaliphilic bacterium of Geoalkalibacter ferrihydriticus type (strain Z-0531), isolated from a bottom sediment sample from the weakly mineralized soda Lake Khadyn, have been analyzed. The strain uses the amorphous Fe(III)-hydroxide (AFH) as an electron acceptor and acetate CH{sub 3}COO{sup -} as an electron donor. Moessbauer investigations of solid phase samples obtained during the process of the bacterium growth were carried out at room temperature, 77.8 K, 4.2 K without and with the presence of an external magnetic field (6 T) applied perpendicular to the {gamma}-bebam.

  5. Ammonificins C and D, Hydroxyethylamine Chromene Derivatives from a Cultured Marine Hydrothermal Vent Bacterium, Thermovibrio ammonificans

    PubMed Central

    Andrianasolo, Eric H.; Haramaty, Liti; Rosario-Passapera, Richard; Vetriani, Costantino; Falkowski, Paul; White, Eileen; Lutz, Richard

    2012-01-01

    Chemical and biological investigation of the cultured marine hydrothermal vent bacterium, Thermovibrio ammonifican led to the isolation of two hydroxyethylamine chromene derivatives, ammonificins C and D. Their structures were elucidated using combination of NMR and mass spectrometry. Absolute stereochemistry was ascertained by comparison of experimental and calculated CD spectra. Biological evaluation and assessment were determined using the patented ApopScreen cell-based screen for apoptosis-induction. Ammonificins C and D induce apoptosis in micromolar concentrations. To our knowledge, this finding is the first report of chemical compounds that induce apoptosis from the cultured deep-sea marine organism, hydrothermal vent bacterium, Thermovibrio ammonificans. PMID:23170085

  6. From Genome to Function: Systematic Analysis of the Soil Bacterium Bacillus Subtilis

    PubMed Central

    Crawshaw, Samuel G.; Wipat, Anil

    2001-01-01

    Bacillus subtilis is a sporulating Gram-positive bacterium that lives primarily in the soil and associated water sources. Whilst this bacterium has been studied extensively in the laboratory, relatively few studies have been undertaken to study its activity in natural environments. The publication of the B. subtilis genome sequence and subsequent systematic functional analysis programme have provided an opportunity to develop tools for analysing the role and expression of Bacillus genes in situ. In this paper we discuss analytical approaches that are being developed to relate genes to function in environments such as the rhizosphere. PMID:18628943

  7. Description of a bacterium associated with redmouth disease of rainbow trout (Salmo gairdneri)

    USGS Publications Warehouse

    1966-01-01

    A description was given of a gram-negative, peritrichously flagellated, fermentative bacterium that was isolated on numerous occasions from kidney tissues of rainbow trout (Salmo gairdneri) afflicted with redmouth disease. Although the bacteria apparently were members of the family Enterobacteriaceae, it was impossible to determine their taxonomic position within the family with certainty. Hence it was recommended that their taxonomic position remain sub judice for the present. As a temporary designation RM bacterium was used. Redmouth disease was transmitted from infected to normal fish through the medium of water.

  8. Cadherin Domains in the Polysaccharide-Degrading Marine Bacterium Saccharophagus degradans 2-40 Are Carbohydrate-Binding Modules▿

    PubMed Central

    Fraiberg, Milana; Borovok, Ilya; Bayer, Edward A.; Weiner, Ronald M.; Lamed, Raphael

    2011-01-01

    The complex polysaccharide-degrading marine bacterium Saccharophagus degradans strain 2-40 produces putative proteins that contain numerous cadherin and cadherin-like domains involved in intercellular contact interactions. The current study reveals that both domain types exhibit reversible calcium-dependent binding to different complex polysaccharides which serve as growth substrates for the bacterium. PMID:21036994

  9. Draft Genome Sequence of an Anaerobic and Extremophilic Bacterium, Caldanaerobacter yonseiensis, Isolated from a Geothermal Hot Stream

    PubMed Central

    Lee, Sang-Jae; Lee, Yong-Jik; Park, Gun-Seok; Kim, Byoung-Chan; Lee, Sang Jun; Shin, Jae-Ho

    2013-01-01

    Caldanaerobacter yonseiensis is a strictly anaerobic, thermophilic, spore-forming bacterium, which was isolated from a geothermal hot stream in Indonesia. This bacterium utilizes xylose and produces a variety of proteases. Here, we report the draft genome sequence of C. yonseiensis, which reveals insights into the pentose phosphate pathway and protein degradation metabolism in thermophilic microorganisms. PMID:24201201

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

    PubMed Central

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

    2014-01-01

    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. PMID:25035318

  11. Draft Genome Sequence of Arthrobacter sp. Strain SPG23, a Hydrocarbon-Degrading and Plant Growth-Promoting Soil Bacterium

    PubMed Central

    Gkorezis, Panagiotis; Bottos, Eric M.; Van Hamme, Jonathan D.; Thijs, Sofie; Rineau, Francois; Balseiro-Romero, Maria; Weyens, Nele

    2015-01-01

    We report here the 4.7-Mb draft genome of Arthrobacter sp. SPG23, a hydrocarbonoclastic Gram-positive bacterium belonging to the Actinobacteria, isolated from diesel-contaminated soil at the Ford Motor Company site in Genk, Belgium. Strain SPG23 is a potent plant growth promoter useful for diesel fuel remediation applications based on plant-bacterium associations. PMID:26701084

  12. Response to comments on "A bacterium that can grow using arsenic instead of phosphorus"

    USGS Publications Warehouse

    Wolfe-Simon, Felisa; Blum, Jodi Switzer; 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.

    2011-01-01

    Concerns have been raised about our recent study suggesting that arsenic (As) substitutes for phosphorus in major biomolecules of a bacterium that tolerates extreme As concentrations. We welcome the opportunity to better explain our methods and results and to consider alternative interpretations. We maintain that our interpretation of As substitution, based on multiple congruent lines of evidence, is viable.

  13. Complete genome sequence of the bioleaching bacterium Leptospirillum sp. group II strain CF-1.

    PubMed

    Ferrer, Alonso; Bunk, Boyke; Spröer, Cathrin; Biedendieck, Rebekka; Valdés, Natalia; Jahn, Martina; Jahn, Dieter; Orellana, Omar; Levicán, Gloria

    2016-03-20

    We describe the complete genome sequence of Leptospirillum sp. group II strain CF-1, an acidophilic bioleaching bacterium isolated from an acid mine drainage (AMD). This work provides data to gain insights about adaptive response of Leptospirillum spp. to the extreme conditions of bioleaching environments. PMID:26853478

  14. Draft Genome Sequence of Sphingobium yanoikuyae TJ, a Halotolerant Di-n-Butyl-Phthalate-Degrading Bacterium

    PubMed Central

    Jin, Decai; Zhu, Ying; Wang, Xinxin; Kong, Xiao; Liu, Huijun; Wang, Yafeng

    2016-01-01

    Sphingobium yanoikuyae TJ is a halotolerant di-n-butyl-phthalate-degrading bacterium, isolated from the Haihe estuary in Bohai Bay, Tianjin, China. Here, we report the 5.1-Mb draft genome sequence of this strain, which will provide insights into the diversity of Sphingobium spp. and the mechanism of phthalate ester degradation in the estuary. PMID:27313307

  15. Draft Genome Sequence and Annotation of the Entomopathogenic Bacterium Xenorhabdus nematophila Strain F1

    PubMed Central

    Lanois, Anne; Ogier, Jean-Claude; Gouzy, Jérome; Laroui, Christine; Rouy, Zoé; Givaudan, Alain

    2013-01-01

    We report the 4.3-Mb genome sequence of Xenorhabdus nematophila strain F1, a Gram-negative bacterium that is a symbiont of the entomopathogenic nematode Steinernema carpocapsae and pathogenic by direct injection for a wide variety of insects. PMID:23788541

  16. Draft Genome Sequence of Photorhabdus luminescens subsp. laumondii HP88, an Entomopathogenic Bacterium Isolated from Nematodes.

    PubMed

    Ghazal, Shimaa; Oshone, Rediet; Simpson, Stephen; Morris, Krystalynne; Abebe-Akele, Feseha; Thomas, W Kelley; Khalil, Kamal M; Tisa, Louis S

    2016-01-01

    Photorhabdus luminescens subsp. laumondii HP88 is an entomopathogenic bacterium that forms a symbiotic association with Heterorhabditis nematodes. We report here a 5.27-Mbp draft genome sequence for P. luminescens subsp. laumondii HP88, with a G+C content of 42.4% and containing 4,243 candidate protein-coding genes. PMID:26988056

  17. Draft Genome Sequence of Photorhabdus luminescens subsp. laumondii HP88, an Entomopathogenic Bacterium Isolated from Nematodes

    PubMed Central

    Ghazal, Shimaa; Oshone, Rediet; Simpson, Stephen; Morris, Krystalynne; Abebe-Akele, Feseha; Thomas, W. Kelley; Khalil, Kamal M.

    2016-01-01

    Photorhabdus luminescens subsp. laumondii HP88 is an entomopathogenic bacterium that forms a symbiotic association with Heterorhabditis nematodes. We report here a 5.27-Mbp draft genome sequence for P. luminescens subsp. laumondii HP88, with a G+C content of 42.4% and containing 4,243 candidate protein-coding genes. PMID:26988056

  18. Genome Sequence of Marichromatium gracile YL-28, a Purple Sulfur Bacterium with Bioremediation Potential

    PubMed Central

    Zhang, Xiaobo; Zhao, Chungui; Hong, Xuan

    2016-01-01

    The draft genome sequence of Marichromatium gracile YL-28 contains 3,840,251 bp, with a G+C content of 68.84%. The annotated genome sequence provides the genetic basis for revealing its role as a purple sulfur bacterium in the harvesting of energy and the development of bioremediation applications. PMID:27151789

  19. Aerobic mineralization of vinyl chlorides by a bacterium of the order Actinomycetales

    SciTech Connect

    Phelps, T.J.; Malachowsky, K.; Schram, R.M. ); White, D.C. Oak Ridge National Lab., TN )

    1991-04-01

    A gram-positive branched bacterium isolated from a trichloroethylene-degrading consortium mineralized vinyl chloride in growing cultures and cell suspensions. Greater than 67% of the (1,2-{sup 14}C)vinyl chloride was mineralized to carbon dioxide, with approximately 10% of the radioactivity appearing in {sup 14}C-aqueous-phase products.

  20. Complete Genome Sequence of Enterobacter cloacae B2-DHA, a Chromium-Resistant Bacterium

    PubMed Central

    Rahman, Aminur; Nahar, Noor; Olsson, Björn

    2016-01-01

    Previously, we reported a chromium-resistant bacterium, Enterobacter cloacae B2-DHA, isolated from the landfills of tannery industries in Bangladesh. Here, we investigated its genetic composition using massively parallel sequencing and comparative analysis with other known Enterobacter genomes. Assembly of the sequencing reads revealed a genome of ~4.21 Mb in size. PMID:27257201

  1. Comment on "A bacterium that degrades and assimilates poly(ethylene terephthalate)".

    PubMed

    Yang, Yu; Yang, Jun; Jiang, Lei

    2016-08-19

    Yoshida et al (Report, 11 March 2016, p. 1196) reported that the bacterium Ideonella sakaiensis 201-F6 can degrade and assimilate poly(ethylene terephthalate) (PET). However, the authors exaggerated degradation efficiency using a low-crystallinity PET and presented no straightforward experiments to verify depolymerization and assimilation of PET. Thus, the authors' conclusions are rather misleading. PMID:27540159

  2. Draft Genome Sequence of Alcaligenes faecalis Strain IITR89, an Indole-Oxidizing Bacterium.

    PubMed

    Regar, Raj Kumar; Gaur, Vivek Kumar; Mishra, Gayatri; Jadhao, Sudhir; Kamthan, Mohan; Manickam, Natesan

    2016-01-01

    We report the draft genome sequence of Alcaligenes faecalis strain IITR89, a bacterium able to form indigo by utilizing indole as the sole carbon source. The Alcaligenes species is increasingly reported for biodegradation of diverse toxicants and thus complete sequencing may provide insight into biodegradation capabilities and other phenotypes. PMID:26941148

  3. Draft Genome Sequence of Alcaligenes faecalis Strain IITR89, an Indole-Oxidizing Bacterium

    PubMed Central

    Regar, Raj Kumar; Gaur, Vivek Kumar; Mishra, Gayatri; Jadhao, Sudhir; Kamthan, Mohan

    2016-01-01

    We report the draft genome sequence of Alcaligenes faecalis strain IITR89, a bacterium able to form indigo by utilizing indole as the sole carbon source. The Alcaligenes species is increasingly reported for biodegradation of diverse toxicants and thus complete sequencing may provide insight into biodegradation capabilities and other phenotypes. PMID:26941148

  4. Complete Genome Sequence of Lysinibacillus sphaericus B1-CDA, a Bacterium That Accumulates Arsenic

    PubMed Central

    Rahman, Aminur; Nahar, Noor; Jass, Jana; Olsson, Björn

    2016-01-01

    Here, we report the genomic sequence and genetic composition of an arsenic-resistant bacterium, Lysinibacillus sphaericus B1-CDA. Assembly of the sequencing reads revealed that the genome size is ~4.5 Mb, encompassing ~80% of the chromosomal DNA. PMID:26798084

  5. Draft Genome Sequence of an Anaerobic Ammonium-Oxidizing Bacterium, “Candidatus Brocadia sinica”

    PubMed Central

    Oshiki, Mamoru; Shinyako-Hata, Kaori; Satoh, Hisashi

    2015-01-01

    A draft genome sequence of an anaerobic ammonium-oxidizing (anammox) bacterium, “Candidatus Brocadia sinica,” was determined by pyrosequencing and by screening a fosmid library. A 4.07-Mb genome sequence comprising 3 contigs was assembled, in which 3,912 gene-coding regions, 47 tRNAs, and a single rrn operon were annotated. PMID:25883286

  6. Draft Genome Sequence of the Obligately Alkaliphilic Sulfate-Reducing Bacterium Desulfonatronum thiodismutans Strain MLF1

    PubMed Central

    Trubitsyn, Denis; Geurink, Corey; Pikuta, Elena; Lefèvre, Christopher T.; McShan, W. Michael; Gillaspy, Allison F.

    2014-01-01

    Desulfonatronum thiodismutans strain MLF1, an alkaliphilic bacterium capable of sulfate reduction, was isolated from Mono Lake, California. Here we report the 3.92-Mb draft genome sequence comprising 34 contigs and some results of its automated annotation. These data will improve our knowledge of mechanisms by which bacteria withstand extreme environments. PMID:25081260

  7. Draft Genome Sequence of a Thermophilic Desulfurization Bacterium, Geobacillus thermoglucosidasius Strain W-2

    PubMed Central

    Zhu, Lin; Li, Mingchang; Guo, Shuyi

    2016-01-01

    Geobacillus thermoglucosidasius strain W-2 is a thermophilic bacterium isolated from a deep-subsurface oil reservoir in northern China, which is capable of degrading organosulfur compounds. Here, we report the draft genome sequence of G. thermoglucosidasius strain W-2, which may help to elucidate the genetic basis of biodegradation of organosulfur pollutants under heated conditions. PMID:27491977

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

    PubMed Central

    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

  9. Draft Genome Sequence of the Halophilic Bacterium Halobacillus sp. Strain BAB-2008

    PubMed Central

    Joshi, M. N.; Pandit, A. S.; Sharma, A.; Pandya, R. V.; Saxena, A. K.

    2013-01-01

    The Halobacillus sp. strain BAB-2008 is a moderately halophilic, rod-shaped, Gram-positive, orange-pigmented, carotenoid-producing bacterium isolated from saline soil near Zazam-Solar Park Road, Gujarat, India. Here we present the 3.7-Mb genome sequence to provide insights into its functional genomics and potential applications for carotenoid and enzyme production. PMID:23469348

  10. Draft genome sequence of Pontibacter sp. nov. BAB1700, a halotolerant, industrially important bacterium.

    PubMed

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

    2012-11-01

    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

  11. Draft Genome Sequence of the Halophilic Bacterium Halobacillus sp. Strain BAB-2008.

    PubMed

    Joshi, M N; Pandit, A S; Sharma, A; Pandya, R V; Saxena, A K; Bagatharia, S B

    2013-01-01

    The Halobacillus sp. strain BAB-2008 is a moderately halophilic, rod-shaped, Gram-positive, orange-pigmented, carotenoid-producing bacterium isolated from saline soil near Zazam-Solar Park Road, Gujarat, India. Here we present the 3.7-Mb genome sequence to provide insights into its functional genomics and potential applications for carotenoid and enzyme production. PMID:23469348

  12. Complete genome sequence of the xylan-degrading subseafloor bacterium Microcella alkaliphila JAM-AC0309.

    PubMed

    Kurata, Atsushi; Hirose, Yuu; Misawa, Naomi; Wakazuki, Sachiko; Kishimoto, Noriaki; Kobayashi, Tohru

    2016-03-10

    Here we report the complete genome sequence of Microcella alkaliphila JAM-AC0309, which was newly isolated from the deep subseafloor core sediment from offshore of the Shimokita Peninsula of Japan. An array of genes related to utilization of xylan in this bacterium was identified by whole genome analysis. PMID:26808869

  13. Genome Sequence of Marichromatium gracile YL-28, a Purple Sulfur Bacterium with Bioremediation Potential.

    PubMed

    Zhang, Xiaobo; Zhao, Chungui; Hong, Xuan; Chen, Shicheng; Yang, Suping

    2016-01-01

    The draft genome sequence of Marichromatium gracile YL-28 contains 3,840,251 bp, with a G+C content of 68.84%. The annotated genome sequence provides the genetic basis for revealing its role as a purple sulfur bacterium in the harvesting of energy and the development of bioremediation applications. PMID:27151789

  14. Genome Sequence of the Spinosyns-Producing Bacterium Saccharopolyspora spinosa NRRL 18395 ▿

    PubMed Central

    Pan, Yuanlong; Yang, Xi; Li, Jing; Zhang, Ruifen; Hu, Yongfei; Zhou, Yuguang; Wang, Jun; Zhu, Baoli

    2011-01-01

    Saccharopolyspora spinosa is a Gram-positive bacterium that produces spinosad, a well-known biodegradable insecticide that is used for agricultural pest control and has an excellent environmental and mammalian toxicological profile. Here, we present the first draft genome sequence of the type strain Saccharopolyspora spinosa NRRL 18395, which consists of 22 scaffolds. PMID:21478350

  15. Draft Genome Sequence of Burkholderia cenocepacia Strain 869T2, a Plant-Beneficial Endophytic Bacterium.

    PubMed

    Ho, Ying-Ning; Huang, Chieh-Chen

    2015-01-01

    An endophytic bacterium, Burkholderia cenocepacia 869T2, isolated from vetiver grass, has shown its abilities for both in planta biocontrol and plant growth promotion. Its draft genome sequence was determined to provide insights into those metabolic pathways involved in plant-beneficial activity. This is the first genome report for endophytic B. cenocepacia. PMID:26564046

  16. Draft Genome Sequence and Gene Annotation of the Uropathogenic Bacterium Proteus mirabilis Pr2921

    PubMed Central

    Giorello, F. M.; Romero, V.; Farias, J.; Scavone, P.; Umpiérrez, A.; Zunino, P.

    2016-01-01

    Here, we report the genome sequence of Proteus mirabilis Pr2921, a uropathogenic bacterium that can cause severe complicated urinary tract infections. After gene annotation, we identified two additional copies of ucaA, one of the most studied fimbrial protein genes, and other fimbriae related-proteins that are not present in P. mirabilis HI4320. PMID:27340058

  17. Complete Genome Sequence of the Cellulose-Degrading Bacterium Cellulosilyticum lentocellum

    SciTech Connect

    Miller, David A; Suen, Garret; Bruce, David; Copeland, A; Cheng, Jan-Fang; Detter, J. Chris; Goodwin, Lynne A.; Han, Cliff; Hauser, Loren John; Land, Miriam L; Lapidus, Alla L.; Lucas, Susan; Meincke, Linda; Pitluck, Sam; Tapia, Roxanne; Teshima, Hazuki; Woyke, Tanja; Fox, Brian G.; Angert, Esther R.; Currie, Cameron

    2011-01-01

    Cellulosilyticum lentocellum DSM 5427 is an anaerobic, endospore-forming member of the Firmicutes. We describe the complete genome sequence of this cellulose-degrading bacterium; originally isolated from estuarine sediment of a river that received both domestic and paper mill waste. Comparative genomics of cellulolytic clostridia will provide insight into factors that influence degradation rates.

  18. Effect of tannic acid on the transcriptome of the soil bacterium Pseudomonas protegens Pf-5

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tannins are plant-produced organic compounds that are found in soils, are able to sequester iron, and have antimicrobial properties. We studied the effect of tannic acid on the molecular physiology of the soil-inhabiting biocontrol bacterium Pseudomonas protegens Pf-5 (formerly Pseudomonas fluoresce...

  19. Draft Genome Sequence of a Bacillus Bacterium from the Atacama Desert Wetlands Metagenome.

    PubMed

    Vilo, Claudia; Galetovic, Alexandra; Araya, Jorge E; Gómez-Silva, Benito; Dong, Qunfeng

    2015-01-01

    We report here the draft genome sequence of a Bacillus bacterium isolated from the microflora of Nostoc colonies grown at the Andean wetlands in northern Chile. We consider this genome sequence to be a molecular tool for exploring microbial relationships and adaptation strategies to the prevailing extreme conditions at the Atacama Desert. PMID:26294639

  20. Genome sequence of the mycorrhizal helper bacterium Pseudomonas fluorescens BBc6R8

    SciTech Connect

    Deveau, Aurelie; Grob, Harald; Morin, Emmanuelle; Karpinets, Tatiana V; Utturkar, Sagar M; Mehnaz, Samina; Kurz, Sven; Martin, Francis; Frey-Klett, Pascale; Labbe, Jessy L

    2014-01-01

    We report the draft genome sequence of the mycorrhiza helper bacterium Pseudomonas fluorescens strain BBc6R8 . Several traits which could be involved in the mycorrhiza helper ability of the bacterial strain such as multiple secretion systems, auxin metabolism and phosphate mobilization were evidenced in the genome.

  1. Draft Genome Sequence of “Candidatus Phytoplasma pruni” Strain CX, a Plant-Pathogenic Bacterium

    PubMed Central

    Shao, J.; Bottner-Parker, K. D.; Gundersen-Rindal, D. E.; Zhao, Y.; Davis, R. E.

    2015-01-01

    “Candidatus Phytoplasma pruni” strain CX, belonging to subgroup 16SrIII-A, is a plant-pathogenic bacterium causing economically important diseases in many fruit crops. Here, we report the draft genome sequence, which consists of 598,508 bases, with a G+C content of 27.21 mol%. PMID:26472824

  2. The construction of an engineered bacterium to remove cadmium from wastewater.

    PubMed

    Chang, S; Shu, H

    2014-01-01

    The removal of cadmium (Cd) from wastewater before it is released from factories is important for protecting human health. Although some researchers have developed engineered bacteria, the resistance of these engineered bacteria to Cd have not been improved. In this study, two key genes involved in glutathione synthesis (gshA and gshB), a serine acetyltransferase gene (cysE), a Thlaspi caerulescens phytochelatin synthase gene (TcPCS1), and a heavy metal ATPase gene (TcHMA3) were transformed into Escherichia coli BL21. The resistance of the engineered bacterium to Cd was significantly greater than that of the initial bacterium and the Cd accumulation in the engineered bacterium was much higher than in the initial bacterium. In addition, the Cd resistance of the bacteria harboring gshB, gshA, cysE, and TcPCS1 was higher than that of the bacteria harboring gshA, cysE, and TcPCS1. This finding demonstrated that gshB played an important role in glutathione synthesis and that the reaction catalyzed by glutathione synthase was the limiting step for producing phytochelatins. Furthermore, TcPCS1 had a greater specificity and a higher capacity for removing Cd than SpPCS1, and TcHMA3 not only played a role in T. caerulescens but also functioned in E. coli. PMID:25521138

  3. Five New Amicoumacins Isolated from a Marine-Derived Bacterium Bacillus subtilis

    PubMed Central

    Li, Yongxin; Xu, Ying; Liu, Lingli; Han, Zhuang; Lai, Pok Yui; Guo, Xiangrong; Zhang, Xixiang; Lin, Wenhan; Qian, Pei-Yuan

    2012-01-01

    Four novel amicoumacins, namely lipoamicoumacins A–D (1–4), and one new bacilosarcin analog (5) were isolated from culture broth of a marine-derived bacterium Bacillus subtilis, together with six known amicoumacins. Their structures were elucidated on the basis of extensive spectroscopic (2D NNR, IR, CD and MS) analysis and in comparison with data in literature. PMID:22412803

  4. Draft Genome Sequence of the Deinococcus-Thermus Bacterium Meiothermus ruber Strain A

    DOE PAGESBeta

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

    2015-03-26

    The draft genome sequence of the Deinococcus-Thermus group bacterium Meiothermus ruber strain A, isolated from a cyanobacterial enrichment culture obtained from Octopus Spring (Yellowstone National Park, WY), comprises 2,968,099 bp in 170 contigs. It is predicted to contain 2,895 protein-coding genes, 44 tRNA-coding genes, and 2 rRNA operons.

  5. Genome Sequence of Bacillus mycoides B38V, a Growth-Promoting Bacterium of Sunflower.

    PubMed

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

    2015-01-01

    Bacillus mycoides B38V is a bacterium isolated from the sunflower rhizosphere that is able to promote plant growth and N uptake. The genome of the isolate has approximately 5.80 Mb and presents sequence codifiers for plant growth-promoting characteristics, such as nitrate reduction and ammonification and iron-siderophore uptake. PMID:25838494

  6. Genome Sequence of Bacillus mycoides B38V, a Growth-Promoting Bacterium of Sunflower

    PubMed Central

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

    2015-01-01

    Bacillus mycoides B38V is a bacterium isolated from the sunflower rhizosphere that is able to promote plant growth and N uptake. The genome of the isolate has approximately 5.80 Mb and presents sequence codifiers for plant growth-promoting characteristics, such as nitrate reduction and ammonification and iron-siderophore uptake. PMID:25838494

  7. Draft Genome Sequence of the Syntrophic Lactate-Degrading Bacterium Tepidanaerobacter syntrophicus JLT

    PubMed Central

    Matsuura, Norihisa; Ohashi, Akiko; Tourlousse, Dieter M.

    2016-01-01

    We report here a high-quality draft genome sequence of the type strain (JL) of Tepidanaerobacter syntrophicus, an obligately anaerobic and moderately thermophilic bacterium, which is able to perform syntrophic lactate degradation with hydrogenotrophic methanogens. The genome comprises 2.43 Mb in 9 scaffolds, with a G+C content of 38.6%. PMID:26868399

  8. Draft Genome Sequence of the Moderately Halophilic Bacterium Marinobacter lipolyticus Strain SM19

    PubMed Central

    Papke, R. Thane; de la Haba, Rafael R.; Infante-Domínguez, Carmen; Pérez, Dolores; Sánchez-Porro, Cristina; Lapierre, Pascal

    2013-01-01

    Marinobacter lipolyticus strain SM19, isolated from saline soil in Spain, is a moderately halophilic bacterium belonging to the class Gammaproteobacteria. Here, we report the draft genome sequence of this strain, which consists of a 4.0-Mb chromosome and which is able to produce the halophilic enzyme lipase LipBL. PMID:23814106

  9. First Insights into the Genome of the Moderately Thermophilic Bacterium Clostridium tepidiprofundi SG 508T.

    PubMed

    Poehlein, Anja; Friedrich, Ines; Krüger, Larissa; Daniel, Rolf

    2016-01-01

    The moderately thermophilic bacterium Clostridium tepidiprofundi is Gram-positive and belongs to clostridial cluster I. It was isolated from a hydrothermal vent chimney. Substrates utilized by C. tepidiprofundi include casein, peptone, tryptone, yeast extract, beef extract, starch, maltose, and glucose. The genome consists of one replicon (3.06 Mb). PMID:27174286

  10. Draft Genome Sequence of Potato ‘Zebra Chip’ Associated Bacterium ‘Candidatus Liberibacter solanacearum’

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A new species of Candidatus Liberibacter, ‘Ca. L. solanacearum’ (Lso) was recently confirmed to be associated with potato zebra chip (ZC) disease. The bacterium belongs to gram negative, phloem-limited, a-Proteobacteria. Because Koch’s postulates have not been fulfilled, information regarding the et...

  11. Robinsoniella peoriensis: A model anaerobic commensal bacterium for acquisition of antibiotic resistance?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: R. peoriensis was characterized in our laboratories from swine manure and feces as a Gram-positive, anaerobic bacterium. Since then strains of this species have been identified from a variety of mammalian and other gastrointestinal (GI) tracts, suggesting it is a member of the commensal ...

  12. First Insights into the Genome of the Moderately Thermophilic Bacterium Clostridium tepidiprofundi SG 508T

    PubMed Central

    Poehlein, Anja; Friedrich, Ines; Krüger, Larissa

    2016-01-01

    The moderately thermophilic bacterium Clostridium tepidiprofundi is Gram-positive and belongs to clostridial cluster I. It was isolated from a hydrothermal vent chimney. Substrates utilized by C. tepidiprofundi include casein, peptone, tryptone, yeast extract, beef extract, starch, maltose, and glucose. The genome consists of one replicon (3.06 Mb). PMID:27174286

  13. Rapid detection of Flavobacterium columnare, the bacterium causing Columnaris Disease in fish

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Flavobacterium columnare is a ubiquitous bacterium that causes columnaris disease in a wide variety of fish resulting in devastating losses particularly in the commercial aquaculture industry worldwide. Timely diagnosis of disease is imperative for prevention of spread and to reduce the economic los...

  14. Genome Sequence of the Acetogenic Bacterium Moorella mulderi DSM 14980T

    PubMed Central

    Castillo Villamizar, Genis Andrés

    2016-01-01

    Here, we report the draft genome sequence of Moorella mulderi DSM 14980T, a thermophilic acetogenic bacterium, which is able to grow autotrophically on H2 plus CO2 using the Wood-Ljungdahl pathway. The genome consists of a circular chromosome (2.99 Mb). PMID:27231372

  15. Complete Genome Sequence of the Haloalkaliphilic, Hydrogen-Producing Bacterium Halanaerobium hydrogeniformans▿

    PubMed Central

    Brown, Steven D.; Begemann, Matthew B.; Mormile, Melanie R.; Wall, Judy D.; Han, Cliff S.; Goodwin, Lynne A.; Pitluck, Samuel; Land, Miriam L.; Hauser, Loren J.; Elias, Dwayne A.

    2011-01-01

    Halanaerobium hydrogenoformans is an alkaliphilic bacterium capable of biohydrogen production at pH 11 and 7% (wt/vol) salt. We present the 2.6-Mb genome sequence to provide insights into its physiology and potential for bioenergy applications. PMID:21602336

  16. Complete Genome Sequence of a γ-Hexachlorocyclohexane-Degrading Bacterium, Sphingobium sp. Strain MI1205

    PubMed Central

    Tabata, Michiro; Ohhata, Satoshi; Nikawadori, Yuki; Sato, Takuya; Kishida, Kouhei; Ohtsubo, Yoshiyuki; Tsuda, Masataka

    2016-01-01

    Here, we report the complete genome sequence of a γ-hexachlorocyclohexane (γ-HCH)-degrading bacterium, Sphingobium sp. strain MI1205. The genome of MI1205 consists of two chromosomes and four plasmids with sizes of 33 to 292 kb. All the lin genes for γ-HCH metabolism are dispersed on the four plasmids. PMID:27056230

  17. Complete Genome Sequence of the Type Strain of the Acetogenic Bacterium Moorella thermoacetica DSM 521T

    PubMed Central

    Poehlein, Anja; Bengelsdorf, Frank R.; Esser, Carola; Schiel-Bengelsdorf, Bettina; Daniel, Rolf

    2015-01-01

    Here we report the closed genome sequence of the type strain Moorella thermoacetica DSM 521T, an acetogenic bacterium, which is able to grow autotrophically on H2 + CO2 and/or CO, using the Wood-Ljungdahl pathway. The genome consists of a circular chromosome (2.53 Mb). PMID:26450731

  18. Draft Genome Sequence of the Ionic Liquid-Tolerant Bacterium Bacillus amyloliquefaciens CMW1

    PubMed Central

    Hirose, Yuu; Misawa, Naomi; Hurunaka, Kohei; Kishimoto, Noriaki

    2014-01-01

    Here, we report the draft genome sequence of an ionic liquid-tolerant bacterium, Bacillus amyloliquefaciens CMW1, which is newly isolated from a Japanese fermented soybean paste. The genome sequence will allow for a characterization of the molecular mechanism of its ionic liquid tolerance. PMID:25323721

  19. Complete Genome Sequence of Sphingomonas sp. Strain NIC1, an Efficient Nicotine-Degrading Bacterium

    PubMed Central

    Zhu, Xiongyu; Wang, Weiwei; Xu, Ping

    2016-01-01

    Sphingomonas sp. strain NIC1, an efficient nicotine-degrading bacterium, was isolated from tobacco leaves. Here, we present the complete genome sequence of strain NIC1, which contains one circular chromosome and two circular plasmids. The genomic information will provide insights into its molecular mechanism for nicotine degradation. PMID:27417841

  20. Complete Genome Sequence of Enterobacter cloacae B2-DHA, a Chromium-Resistant Bacterium.

    PubMed

    Rahman, Aminur; Nahar, Noor; Olsson, Björn; Mandal, Abul

    2016-01-01

    Previously, we reported a chromium-resistant bacterium, Enterobacter cloacae B2-DHA, isolated from the landfills of tannery industries in Bangladesh. Here, we investigated its genetic composition using massively parallel sequencing and comparative analysis with other known Enterobacter genomes. Assembly of the sequencing reads revealed a genome of ~4.21 Mb in size. PMID:27257201

  1. Draft Genome Sequence of a Bacillus Bacterium from the Atacama Desert Wetlands Metagenome

    PubMed Central

    Vilo, Claudia; Galetovic, Alexandra; Araya, Jorge E.; Dong, Qunfeng

    2015-01-01

    We report here the draft genome sequence of a Bacillus bacterium isolated from the microflora of Nostoc colonies grown at the Andean wetlands in northern Chile. We consider this genome sequence to be a molecular tool for exploring microbial relationships and adaptation strategies to the prevailing extreme conditions at the Atacama Desert. PMID:26294639

  2. Draft Genome Sequence of Jeotgalibacillus soli DSM 23228, a Bacterium Isolated from Alkaline Sandy Soil

    PubMed Central

    Chan, Kok-Gan; Yaakop, Amira Suriaty; Chan, Chia Sing; Ee, Robson; Tan, Wen-Si; Gan, Han Ming

    2015-01-01

    Jeotgalibacillus soli, a bacterium capable of degrading N-acyl homoserine lactone, was isolated from a soil sample in Portugal. J. soli constitutes the only Jeotgalibacillus species isolated from a non-marine source. Here, the draft genome, several interesting glycosyl hydrolases, and its putative N-acyl homoserine lactonases are presented. PMID:25999554

  3. Draft Genome Sequence of the Radioresistant Bacterium Deinococcus grandis, Isolated from Freshwater Fish in Japan

    PubMed Central

    Onodera, Takefumi; Omoso, Kota; Takeda-Yano, Kiyoko; Katayama, Takeshi; Oono, Yutaka; Narumi, Issay

    2016-01-01

    Deinococcus grandis is a radioresistant bacterium isolated from freshwater fish in Japan. Here we reported the draft genome sequence of D. grandis (4.1 Mb), which will be useful for elucidating the common principles of radioresistance in Deinococcus species through the comparative analysis of genomic sequences. PMID:26868384

  4. Draft Genome Sequence of Burkholderia cenocepacia Strain 869T2, a Plant-Beneficial Endophytic Bacterium

    PubMed Central

    Ho, Ying-Ning

    2015-01-01

    An endophytic bacterium, Burkholderia cenocepacia 869T2, isolated from vetiver grass, has shown its abilities for both in planta biocontrol and plant growth promotion. Its draft genome sequence was determined to provide insights into those metabolic pathways involved in plant-beneficial activity. This is the first genome report for endophytic B. cenocepacia. PMID:26564046

  5. Draft Genome Sequence of a Benzo[a]pyrene-Degrading Bacterium, Olleya sp. Strain ITB9

    PubMed Central

    Okai, Masahiko; Watanabe, Akihiro; Ishida, Masami

    2015-01-01

    Olleya sp. ITB9 is a benzo[a]pyrene-degrading bacterium, isolated from surface water near a waste treatment plant at Tokyo Bay, Japan. Here, we present the draft genome sequence of this strain, which consists of 58 contigs corresponding to 3.4 Mb and a G+C content of 31.2%. PMID:26564047

  6. Draft Genome Sequence of Perfluorooctane Acid-Degrading Bacterium Pseudomonas parafulva YAB-1

    PubMed Central

    Tang, Chongjian; Peng, Qingjing; Peng, Qingzhong

    2015-01-01

    Pseudomonas parafulva YAB-1, isolated from perfluorinated compound-contaminated soil, has the ability to degrade perfluorooctane acid (PFOA) compound. Here, we report the draft genome sequence and annotation of the PFOA-degrading bacterium P. parafulva YAB-1. The data provide the basis to investigate the molecular mechanism of PFOA metabolism. PMID:26337877

  7. Distribution, abundance and diversity of the extremely halophilic bacterium Salinibacter ruber

    PubMed Central

    Antón, Josefa; Peña, Arantxa; Santos, Fernando; Martínez-García, Manuel; Schmitt-Kopplin, Philippe; Rosselló-Mora, Ramon

    2008-01-01

    Since its discovery in 1998, representatives of the extremely halophilic bacterium Salinibacter ruber have been found in many hypersaline environments across the world, including coastal and solar salterns and solar lakes. Here, we review the available information about the distribution, abundance and diversity of this member of the Bacteroidetes. PMID:18957079

  8. Preliminary evaluation of nanoscale biogenic magnetite-based ferromagnetic transduction mechanisms for mobile phone bioeffects.

    PubMed

    Cranfield, Charles; Wieser, Heinz Gregor; Al Madan, Jaffar; Dobson, Jon

    2003-03-01

    Ferromagnetic transduction models have been proposed as a potential mechanism for mobile phone bioeffects. These models are based on the coupling of RF and pulsed electromagnetic emissions to biogenic magnetite (Fe3O4) present in the human brain via either ferromagnetic resonance or mechanical activation of cellular ion channels. We have tested these models experimentally for the first time using a bacterial analogue (Magnetospirillum magnetotacticum) which produces intracellular biogenic magnetite similar to that present in the human brain. Experimental evaluation revealed that exposure to mobile phone emissions resulted in a consistent and significantly higher proportion of cell death in exposed cultures versus sham exposure (p = 0.037). Though there appears to be a repeatable trend toward higher cell mortality in magnetite-producing bacteria exposed to mobile phone emissions, it is not yet clear that this would extrapolate to a deleterious health effect in humans. PMID:15382422

  9. Biological colloid engineering: Self-assembly of dipolar ferromagnetic chains in a functionalized biogenic ferrofluid.

    PubMed

    Ruder, Warren C; Hsu, Chia-Pei D; Edelman, Brent D; Schwartz, Russell; Leduc, Philip R

    2012-08-01

    We have studied the dynamic behavior of nanoparticles in ferrofluids consisting of single-domain, biogenic magnetite (Fe(3)O(4)) isolated from Magnetospirillum magnetotacticum (MS-1). Although dipolar chains form in magnetic colloids in zero applied field, when dried upon substrates, the solvent front disorders nanoparticle aggregation. Using avidin-biotin functionalization of the particles and substrate, we generated self-assembled, linear chain motifs that resist solvent front disruption in zero-field. The engineered self-assembly process we describe here provides an approach for the creation of ordered magnetic structures that could impact fields ranging from micro-electro-mechanical systems development to magnetic imaging of biological structures. PMID:22952408

  10. Competitive PCR for quantitation of a Cytophaga-Flexibacter-Bacteroides phylum bacterium associated with the Tuber borchii Vittad. mycelium.

    PubMed

    Barbieri, Elena; Riccioni, Giulia; Pisano, Anna; Sisti, Davide; Zeppa, Sabrina; Agostini, Deborah; Stocchi, Vilberto

    2002-12-01

    An uncultured bacterium associated with the ectomycorrhizal fungus Tuber borchii Vittad. was identified as a novel member of the Cytophaga-Flexibacter-Bacteroides group. Utilizing a quantitative PCR targeting the 16S rRNA gene, we relatively quantified this bacterium in the host. The estimated number of bacteria was found to be approximately 10(6) cells per 30-day-old T. borchii mycelium culture. This represents the first molecular attempt to enumerate an uncultured bacterium associated with a mycorrhizal fungus. PMID:12450871

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

    PubMed Central

    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. PMID:27610355

  12. Gene function analysis in extremophiles: the "nif" regulon of the strict iron oxidizing bacterium "Leptospirillum ferrooxidans"

    NASA Astrophysics Data System (ADS)

    Parro, Victor; Moreno-Paz, Mercedes

    2004-03-01

    In Centro de Astrobiologia it has been considered the Tinto river as a model ecosystem to study life based on iron. The final goal is to study the biological and metabolic diversity in microorganisms living there, following a genomic approach, to get insights to the mechanisms of adaptation to this environment. The Gram-negative bacterium Leptospirillum ferrooxidans is one of the most abundant microorganisms in the river, and it is one of the main responsible in maintenance of pH balance and, as a consequence, the physico-chemical properties of the exosystem. We have constructed a Shotgun DNA microarrays from this bacterium and we have used it to studied its genetic capacity for nitrogen fixation. With this approach we have identified most of the genes necessary for dinitrogen (N2) reduction, confirming the capacity of L. ferrooxidans as a free diazotrophic (nitrogen fixer) microorganism.

  13. Single-bacterium nanomechanics in biomedicine: unravelling the dynamics of bacterial cells

    NASA Astrophysics Data System (ADS)

    Aguayo, S.; Donos, N.; Spratt, D.; Bozec, L.

    2015-02-01

    The use of the atomic force microscope (AFM) in microbiology has progressed significantly throughout the years since its first application as a high-resolution imaging instrument. Modern AFM setups are capable of characterizing the nanomechanical behaviour of bacterial cells at both the cellular and molecular levels, where elastic properties and adhesion forces of single bacterium cells can be examined under different experimental conditions. Considering that bacterial and biofilm-mediated infections continue to challenge the biomedical field, it is important to understand the biophysical events leading towards bacterial adhesion and colonization on both biological and non-biological substrates. The purpose of this review is to present the latest findings concerning the field of single-bacterium nanomechanics, and discuss future trends and applications of nanoindentation and single-cell force spectroscopy techniques in biomedicine.

  14. Isolation and biological characteristics of aerobic marine magnetotactic bacterium YSC-1

    NASA Astrophysics Data System (ADS)

    Gao, Jun; Pan, Hongmiao; Yue, Haidong; Song, Tao; Zhao, Yong; Chen, Guanjun; Wu, Longfei; Xiao, Tian

    2006-12-01

    Magnetotactic bacteria have become a hot spot of research in microbiology attracting intensive interest of researchers in multiple disciplinary fields. However, the studies were limited in few fastidious bacteria. The objective of this study aims at isolating new marine magnetic bacteria and better comprehension of magnetotactic bacteria. In this study, an aerobic magnetotactic bacterium YSC-1 was isolated from sediments in the Yellow Sea Cold Water Mass (YSCWM). In TEM, magnetic cells have one or several circular magnetosomes in diameter of 100nm, and consist of Fe and Co shown on energy dispersive X-ray spectrum. The biological and physiological characteristics of this bacterium were also described. The colour of YSC-1 colony is white in small rod. The gram stain is negative. Results showed that Strain YSC-1 differs from microaerophile magnetotactic bacteria MS-1 and WD-1 in biology.

  15. Crystal structure of ribosomal protein L1 from the bacterium Aquifex aeolicus

    NASA Astrophysics Data System (ADS)

    Nikonova, E. Yu.; Tishchenko, S. V.; Gabdulkhakov, A. G.; Shklyaeva, A. A.; Garber, M. B.; Nikonov, S. V.; Nevskaya, N. A.

    2011-07-01

    The crystal structure of ribosomal protein L1 from the bacterium Aquifex aeolicus was solved by the molecular-replacement method and refined to R cryst = 19.4% and R free = 25.1% at 2.1 Å protein consists of two domains linked together by a flexible hinge region. In the structure under consideration, the domains are in close proximity and adopt a closed conformation. Earlier, this conformation has been found in the structure of protein L1 from the bacterium Thermus thermophilus, whereas the structures of archaeal L1 proteins and the structures of all L1 proteins in the RNA-bound form have an open conformation. The fact that a closed conformation was found in the structures of two L1 proteins which crystallize in different space groups and belong to different bacteria suggests that this conformation is a characteristic feature of L1 bacterial proteins in the free form.

  16. Methanogenesis from acetate: a nonmethanogenic bacterium from an anaerobic acetate enrichment.

    PubMed

    Ward, D M; Mah, R A; Kaplan, I R

    1978-06-01

    A methanogenic acetate enrichment was initiated by inoculation of an acetate-mineral salts medium with domestic anaerobic digestor sludge and maintained by weekly transfer for 2 years. The enrichment culture contained a Methanosarcina and several obligately anaerobic nonmethanogenic bacteria. These latter organisms formed varying degrees of association with the Methanosarcina, ranging from the nutritionally fastidious gram-negative rod called the satellite bacterium to the nutritionally nonfastidious Eubacterium limosum. The satellite bacterium had growth requirements for amino acids, a peptide, a purine base, vitamin B12, and other B vitamins. Glucose, mannitol, starch, pyruvate, cysteine, lysine, leucine, isoleucine, arginine, and asparagine stimulated growth and hydrogen production. Acetate was neither incorporated nor metabolized by the satellite organism. Since acetate was the sole organic carbon source in the enrichment culture, organism(s) which metabolize acetate (such as the Methanosarcina) must produce substrates and growth factors for associated organisms which do not metabolize acetate. PMID:677881

  17. Comparative genome analysis of Lysinibacillus B1-CDA, a bacterium that accumulates arsenics.

    PubMed

    Rahman, Aminur; Nahar, Noor; Nawani, Neelu N; Jass, Jana; Ghosh, Sibdas; Olsson, Björn; Mandal, Abul

    2015-12-01

    Previously, we reported an arsenic resistant bacterium Lysinibacillus sphaericus B1-CDA, isolated from an arsenic contaminated lands. Here, we have investigated its genetic composition and evolutionary history by using massively parallel sequencing and comparative analysis with other known Lysinibacillus genomes. Assembly of the sequencing reads revealed a genome of ~4.5 Mb in size encompassing ~80% of the chromosomal DNA. We found that the set of ordered contigs contains abundant regions of similarity with other Lysinibacillus genomes and clearly identifiable genome rearrangements. Furthermore, all genes of B1-CDA that were predicted be involved in its resistance to arsenic and/or other heavy metals were annotated. The presence of arsenic responsive genes was verified by PCR in vitro conditions. The findings of this study highlight the significance of this bacterium in removing arsenics and other toxic metals from the contaminated sources. The genetic mechanisms of the isolate could be used to cope with arsenic toxicity. PMID:26387925

  18. A Streamlined Strategy for Biohydrogen Production with Halanaerobium hydrogeniformans, an Alkaliphilic Bacterium

    PubMed Central

    Begemann, Matthew B.; Mormile, Melanie R.; Sitton, Oliver C.; Wall, Judy D.; Elias, Dwayne A.

    2012-01-01

    Biofuels are anticipated to enable a shift from fossil fuels for renewable transportation and manufacturing fuels, with biohydrogen considered attractive since it could offer the largest reduction of global carbon budgets. Currently, lignocellulosic biohydrogen production remains inefficient with pretreatments that are heavily fossil fuel-dependent. However, bacteria using alkali-treated biomass could streamline biofuel production while reducing costs and fossil fuel needs. An alkaliphilic bacterium, Halanaerobium hydrogeniformans, is described that is capable of biohydrogen production at levels rivaling neutrophilic strains, but at pH 11 and hypersaline conditions. H. hydrogeniformans ferments a variety of 5- and 6-carbon sugars derived from hemicellulose and cellulose including cellobiose, and forms the end products hydrogen, acetate, and formate. Further, it can also produce biohydrogen from switchgrass and straw pretreated at temperatures far lower than any previously reported and in solutions compatible with growth. Hence, this bacterium can potentially increase the efficiency and efficacy of biohydrogen production from renewable biomass resources. PMID:22509174

  19. Copper-binding characteristics of exopolymers from a freshwater-sediment bacterium

    SciTech Connect

    Mittelman, M.W.; Geesey, G.G.

    1985-04-01

    Copper-binding activity by exopolymers from adherent cells of freshwater-sediment bacterium was demonstrated by a combination of equilibrium dialysis and flameless atomic absorption spectrometry. Crude, cell-free exopolymer preparations containing protein and polysaccharide components bound up to 37 nmol of Cu per mg (dry weight). A highly purified exopolysaccharide preparation bound up to 253 nmol of Cu per mg of carbohydrate. The conditional stability constant for the crude exopolymer-Cu complex was 7.3 x 10/sup 8/. This value was similar to those obtained for Cu complexes formed with humic acids and xanthan, an exopolysaccharide produced by Xanthomonas campestris. Studies conducted at copper concentrations, pHs, and temperatures found in sediments from which the bacterium was isolated indicated that the exopolymers were capable of binding copper under natural conditions.

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

    PubMed

    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. PMID:27610355

  1. N-Acyl Dehydrotyrosines, Tyrosinase Inhibitors from the Marine Bacterium Thalassotalea sp. PP2-459.

    PubMed

    Deering, Robert W; Chen, Jianwei; Sun, Jiadong; Ma, Hang; Dubert, Javier; Barja, Juan L; Seeram, Navindra P; Wang, Hong; Rowley, David C

    2016-02-26

    Thalassotalic acids A-C and thalassotalamides A and B are new N-acyl dehydrotyrosine derivatives produced by Thalassotalea sp. PP2-459, a Gram-negative bacterium isolated from a marine bivalve aquaculture facility. The structures were elucidated via a combination of spectroscopic analyses emphasizing two-dimensional NMR and high-resolution mass spectrometric data. Thalassotalic acid A (1) displays in vitro inhibition of the enzyme tyrosinase with an IC50 value (130 μM) that compares favorably to the commercially used control compounds kojic acid (46 μM) and arbutin (100 μM). These are the first natural products reported from a bacterium belonging to the genus Thalassotalea. PMID:26824128

  2. Draft Genome Sequence of a Strictly Anaerobic Dichloromethane-Degrading Bacterium.

    PubMed

    Kleindienst, Sara; Higgins, Steven A; Tsementzi, Despina; Konstantinidis, Konstantinos T; Mack, E Erin; Löffler, Frank E

    2016-01-01

    An anaerobic, dichloromethane-degrading bacterium affiliated with novel Peptococcaceae was maintained in a microbial consortium. The organism originated from pristine freshwater sediment collected from Rio Mameyes in Luquillo, Puerto Rico, in October 2009 (latitude 18°21'43.9″, longitude -65°46'8.4″). The draft genome sequence is 2.1 Mb and has a G+C content of 43.5%. PMID:26941136

  3. The F- or V-type Na(+)-ATPase of the thermophilic bacterium Clostridium fervidus.

    PubMed Central

    Speelmans, G; Poolman, B; Abee, T; Konings, W N

    1994-01-01

    Clostridium fervidus is a thermophilic, anaerobic bacterium which uses solely Na+ as a coupling ion for energy transduction. Important features of the primary Na+ pump (ATPase) that generates the sodium motive force are presented. The advantage of using a sodium rather than a proton motive force at high temperatures becomes apparent from the effect of temperature on H+ and Na+ permeation in liposomes. PMID:8051034

  4. Draft Genome Sequence of Uncultured SAR324 Bacterium lautmerah10, Binned from a Red Sea Metagenome

    PubMed Central

    Thompson, Luke R.

    2016-01-01

    A draft genome of SAR324 bacterium lautmerah10 was assembled from a metagenome of a surface water sample from the Red Sea, Saudi Arabia. The genome is more complete and has a higher G+C content than that of previously sequenced SAR324 representatives. Its genomic information shows a versatile metabolism that confers an advantage to SAR324, which is reflected in its distribution throughout different depths of the marine water column. PMID:26868398

  5. Massilia sp. BS-1, a novel violacein-producing bacterium isolated from soil.

    PubMed

    Agematu, Hitosi; Suzuki, Kazuya; Tsuya, Hiroaki

    2011-01-01

    A novel bacterium, Massilia sp. BS-1, producing violacein and deoxyviolacein was isolated from a soil sample collected from Akita Prefecture, Japan. The 16S ribosomal DNA of strain BS-1 displayed 93% homology with its nearest violacein-producing neighbor, Janthinobacterium lividum. Strain BS-1 grew well in a synthetic medium, but required both L-tryptophan and a small amount of L-histidine to produce violacein. PMID:21979084

  6. Fourier transform infrared spectroscopic study of intact cells of the nitrogen-fixing bacterium Azospirillum brasilense

    NASA Astrophysics Data System (ADS)

    Kamnev, A. A.; Ristić, M.; Antonyuk, L. P.; Chernyshev, A. V.; Ignatov, V. V.

    1997-06-01

    The data of Fourier transform infrared (FTIR) spectroscopic measurements performed on intact cells of the soil nitrogen-fixing bacterium Azospirillum brasilense grown in a standard medium and under the conditions of an increased metal uptake are compared and discussed. The structural FTIR information obtained is considered together with atomic absorption spectrometry (AAS) data on the content of metal cations in the bacterial cells. Some methodological aspects concerning preparation of bacterial cell samples for FTIR measurements are also discussed.

  7. Halobacterium saccharovorum sp. nov., a carbohydrate-metabolizing, extremely halophilic bacterium

    NASA Technical Reports Server (NTRS)

    Tomlinson, G. A.; Hochstein, L. I.

    1976-01-01

    The previously described extremely halophilic bacterium, strain M6, metabolizes a variety of carbohydrates with the production of acid. In addition, the organism produces nitrite (but no gas) from nitrate, is motile, and grows most rapidly at about 50 C. These characteristics distinguish it from all previously described halophilic bacteria in the genus Halobacterium. It is suggested that it be designated as a new species, Halobacterium saccharovorum.

  8. Complete Genome Sequence of the Thermophilic, Piezophilic, Heterotrophic Bacterium Marinitoga piezophila KA3

    SciTech Connect

    Lucas, Susan; Han, James; Lapidus, Alla L.; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Sam; Peters, Lin; Mikhailova, Natalia; Teshima, Hazuki; Detter, J. Chris; Han, Cliff; Tapia, Roxanne; Land, Miriam L; Hauser, Loren John; Kyrpides, Nikos C; Ivanova, N; Pagani, Ioanna; Vannier, Pauline; Oger, Phil; Bartlett, Douglas; Noll, Kenneth M; Woyke, Tanja; Jebbar, Mohamed

    2012-01-01

    Marinitoga piezophila KA3 is a thermophilic, anaerobic, chemoorganotrophic, sulfur-reducing bacterium isolated from the Grandbonum deep-sea hydrothermal vent site at the East Pacific Rise (13 degrees N, 2,630-m depth). The genome of M. piezophila KA3 comprises a 2,231,407-bp circular chromosome and a 13,386-bp circular plasmid. This genome was sequenced within Department of Energy Joint Genome Institute CSP 2010.

  9. Draft Genome Sequence of the Extremely Halophilic Phototrophic Purple Sulfur Bacterium Halorhodospira halochloris

    PubMed Central

    Singh, Kumar Saurabh; Kirksey, Jared; Hoff, Wouter D.; Deole, Ratnakar

    2014-01-01

    Halorhodospira halochloris is an extremely halophilic bacterium isolated from hypersaline Wadi Nantrun lakes in Egypt. Here we report the draft genome sequence of this gammaproteobacteria (GI number: 589289709, GenBank Accession number: CP007268). The 3.5-Mb genome encodes for photosynthesis and biosynthesis of organic osmoprotectants. Comparison with the genome of H.halophila promises to yield insights into the evolution of halophilic adaptations. PMID:25057327

  10. Draft Genome Sequence of the Deinococcus-Thermus Bacterium Meiothermus ruber Strain A

    PubMed Central

    Thiel, Vera; Tomsho, Lynn P.; Burhans, Richard; Gay, Scott E.; Schuster, Stephan C.; Ward, David M.

    2015-01-01

    The draft genome sequence of the Deinococcus-Thermus group bacterium Meiothermus ruber strain A, isolated from a cyanobacterial enrichment culture obtained from Octopus Spring (Yellowstone National Park, WY), comprises 2,968,099 bp in 170 contigs. It is predicted to contain 2,895 protein-coding genes, 44 tRNA-coding genes, and 2 rRNA operons. PMID:25814606

  11. Draft Genome Sequence of the Deinococcus-Thermus Bacterium Meiothermus ruber Strain A.

    PubMed

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

    2015-01-01

    The draft genome sequence of the Deinococcus-Thermus group bacterium Meiothermus ruber strain A, isolated from a cyanobacterial enrichment culture obtained from Octopus Spring (Yellowstone National Park, WY), comprises 2,968,099 bp in 170 contigs. It is predicted to contain 2,895 protein-coding genes, 44 tRNA-coding genes, and 2 rRNA operons. PMID:25814606

  12. Draft Genome Sequence of the Moderately Thermophilic Bacterium Schleiferia thermophila Strain Yellowstone (Bacteroidetes).

    PubMed

    Thiel, Vera; Hamilton, Trinity L; Tomsho, Lynn P; Burhans, Richard; Gay, Scott E; Ramaley, Robert F; Schuster, Stephan C; Steinke, Laurey; Bryant, Donald A

    2014-01-01

    The draft genome sequence of the moderately thermophilic bacterium Schleiferia thermophila strain Yellowstone (Bacteroidetes), isolated from Octopus Spring (Yellowstone National Park, WY, USA) was sequenced and comprises 2,617,694 bp in 35 contigs. The draft genome is predicted to encode 2,457 protein coding genes and 37 tRNA encoding genes and two rRNA operons. PMID:25169864

  13. Expression of Heterogenous Arsenic Resistance Genes in the Obligately Autotrophic Biomining Bacterium Thiobacillus ferrooxidans.

    PubMed

    Peng, J B; Yan, W M; Bao, X Z

    1994-07-01

    Two arsenic-resistant plasmids were constructed and introduced into Thiobacillus ferrooxidans strains by conjugation. The plasmids with the replicon of wide-host-range plasmid RSF1010 were stable in T. ferrooxidans. The arsenic resistance genes originating from the heterotroph were expressed in this obligately autotrophic bacterium, but the promoter derived from T. ferrooxidans showed no special function in its original host. PMID:16349341

  14. PSEUDOMONAS NATRIEGENS, A MARINE BACTERIUM WITH A GENERATION TIME OF LESS THAN 10 MINUTES

    PubMed Central

    Eagon, R. G.

    1962-01-01

    Eagon, R. G. (University of Georgia, Athens). Pseudomonas natriegens, a marine bacterium with a generation time of less than 10 minutes. J. Bacteriol. 83:736–737. 1962.—Pseudomonas natriegens, a marine microorganism, was demonstrated to have a generation time of 9.8 min. This is the shortest generation time reported to date. Optimal growth occurred at 37 C in brain heart infusion broth supplemented with 1.5% sea salt. PMID:13888946

  15. Sexual Transmission of a Plant Pathogenic Bacterium, Candidatus Liberibacter asiaticus, between Conspecific Insect Vectors during Mating

    PubMed Central

    Mann, Rajinder S.; Pelz-Stelinski, Kirsten; Hermann, Sara L.; Tiwari, Siddharth; Stelinski, Lukasz L.

    2011-01-01

    Candidatus Liberibacter asiaticus is a fastidious, phloem-inhabiting, gram-negative bacterium transmitted by Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae). The bacterium is the presumed causal agent of huanglongbing (HLB), one of the most destructive and economically important diseases of citrus. We investigated whether Las is transmitted between infected and uninfected D. citri adults during courtship. Our results indicate that Las was sexually transmitted from Las-infected male D. citri to uninfected females at a low rate (<4%) during mating. Sexual transmission was not observed following mating of infected females and uninfected males or among adult pairs of the same sex. Las was detected in genitalia of both sexes and also in eggs of infected females. A latent period of 7 days or more was required to detect the bacterium in recipient females. Rod shaped as well as spherical structures resembling Las were observed in ovaries of Las-infected females with transmission electron microscopy, but were absent in ovaries from uninfected D. citri females. The size of the rod shaped structures varied from 0.39 to 0.67 µm in length and 0.19 to 0.39 µm in width. The spherical structures measured from 0.61 to 0.80 µm in diameter. This investigation provides convincing evidence that a plant pathogenic bacterium is sexually transmitted from male to female insects during courtship and established evidence that bacteria persist in reproductive organs. Moreover, these findings provide an alternative sexually horizontal mechanism for the spread of Las within populations of D. citri, even in the absence of infected host trees. PMID:22216209

  16. Draft Genome Sequence of the Moderately Thermophilic Bacterium Schleiferia thermophila Strain Yellowstone (Bacteroidetes)

    PubMed Central

    Thiel, Vera; Hamilton, Trinity L.; Tomsho, Lynn P.; Burhans, Richard; Gay, Scott E.; Ramaley, Robert F.; Schuster, Stephan C.; Steinke, Laurey

    2014-01-01

    The draft genome sequence of the moderately thermophilic bacterium Schleiferia thermophila strain Yellowstone (Bacteroidetes), isolated from Octopus Spring (Yellowstone National Park, WY, USA) was sequenced and comprises 2,617,694 bp in 35 contigs. The draft genome is predicted to encode 2,457 protein coding genes and 37 tRNA encoding genes and two rRNA operons. PMID:25169864

  17. Draft Genome Sequence of Gordonia sihwensis Strain 9, a Branched Alkane-Degrading Bacterium

    PubMed Central

    Brown, Lisa M.; Gunasekera, Thusitha S.; Striebich, Richard C.

    2016-01-01

    Gordonia sihwensis strain 9 is a Gram-positive bacterium capable of efficient aerobic degradation of branched and normal alkanes. The draft genome of G. sihwensis S9 is 4.16 Mb in size, with 3,686 coding sequences and 68.1% G+C content. Alkane monooxygenase and P-450 cytochrome genes required for alkane degradation are predicted in G. sihwensis S9. PMID:27340079

  18. Draft Genome Sequence of Pseudomonas frederiksbergensis SI8, a Psychrotrophic Aromatic-Degrading Bacterium

    PubMed Central

    Brown, Lisa M.; Striebich, Richard C.; Mueller, Susan S.; Gunasekera, Thusitha S.

    2015-01-01

    Pseudomonas frederiksbergensis strain SI8 is a psychrotrophic bacterium capable of efficient aerobic degradation of aromatic hydrocarbons. The draft genome of P. frederiksbergensis SI8 is 6.57 Mb in size, with 5,904 coding sequences and 60.5% G+C content. The isopropylbenzene (cumene) degradation pathway is predicted to be present in P. frederiksbergensis SI8. PMID:26184950

  19. Draft Genome Sequence of a Strictly Anaerobic Dichloromethane-Degrading Bacterium

    PubMed Central

    Higgins, Steven A.; Tsementzi, Despina; Konstantinidis, Konstantinos T.; Mack, E. Erin

    2016-01-01

    An anaerobic, dichloromethane-degrading bacterium affiliated with novel Peptococcaceae was maintained in a microbial consortium. The organism originated from pristine freshwater sediment collected from Rio Mameyes in Luquillo, Puerto Rico, in October 2009 (latitude 18°21′43.9″, longitude −65°46′8.4″). The draft genome sequence is 2.1 Mb and has a G+C content of 43.5%. PMID:26941136

  20. Effect of Tannic Acid on the Transcriptome of the Soil Bacterium Pseudomonas protegens Pf-5

    PubMed Central

    Lim, Chee Kent; Penesyan, Anahit; Hassan, Karl A.

    2013-01-01

    Tannins are a diverse group of plant-produced, polyphenolic compounds with metal-chelating and antimicrobial properties that are prevalent in many soils. Using transcriptomics, we determined that tannic acid, a form of hydrolysable tannin, broadly affects the expression of genes involved in iron and zinc homeostases, sulfur metabolism, biofilm formation, motility, and secondary metabolite biosynthesis in the soil- and rhizosphere-inhabiting bacterium Pseudomonas protegens Pf-5. PMID:23435890

  1. Isolation and Characterization of Strain MMB-1 (CECT 4803), a Novel Melanogenic Marine Bacterium.

    PubMed

    Solano, F; Garcia, E; Perez, D; Sanchez-Amat, A

    1997-09-01

    A novel marine melanogenic bacterium, strain MMB-1, was isolated from the Mediterranean Sea. The taxonomic characterization of this strain indicated that it belongs to the genus Alteromonas. Under in vivo conditions, L-tyrosine was the specific monophenolic precursor for melanin synthesis. This bacterium contained all types of activities associated with polyphenol oxidases (PPOs), cresolase (EC 1.18.14.1), catecholase (EC 1.10.3.1), and laccase (EC 1.10.3.2). These activities were due to the presence of two different PPOs. The first one showed all the enzymatic activities, but it was not involved in melanogenesis in vivo, since amelanogenic mutant strains obtained by nitrosoguanidine treatment contained levels of this PPO similar to that of the wild-type MMB-1 strain. The second PPO showed cresolase and catecholase activities but no laccase, and it was involved in melanogenesis, since this enzyme was lost in amelanogenic mutant strains. This PPO was strongly activated by sodium dodecyl sulfate below the critical micelle concentration, and it is a tyrosinase-like enzyme showing a lag period in its tyrosine hydroxylase activity that could be avoided by small amounts of L-dopa. This is the first report of a bacterium that contains two PPOs and also the first report of a pluripotent PPO showing all types of oxidase activities. The bacterium and the pluripotent PPO may be useful models for exploring the roles of PPOs in cellular physiology, aside from melanin formation. On the other hand, the high oxidizing capacity of the PPO for a wide range of substrates could make possible its application in phenolic biotransformations, food processing, or the cosmetic industry, where fungal and plant PPOs are being used. PMID:16535688

  2. Isolation and Characterization of Strain MMB-1 (CECT 4803), a Novel Melanogenic Marine Bacterium

    PubMed Central

    Solano, F.; Garcia, E.; Perez, De; Sanchez-Amat, A.

    1997-01-01

    A novel marine melanogenic bacterium, strain MMB-1, was isolated from the Mediterranean Sea. The taxonomic characterization of this strain indicated that it belongs to the genus Alteromonas. Under in vivo conditions, L-tyrosine was the specific monophenolic precursor for melanin synthesis. This bacterium contained all types of activities associated with polyphenol oxidases (PPOs), cresolase (EC 1.18.14.1), catecholase (EC 1.10.3.1), and laccase (EC 1.10.3.2). These activities were due to the presence of two different PPOs. The first one showed all the enzymatic activities, but it was not involved in melanogenesis in vivo, since amelanogenic mutant strains obtained by nitrosoguanidine treatment contained levels of this PPO similar to that of the wild-type MMB-1 strain. The second PPO showed cresolase and catecholase activities but no laccase, and it was involved in melanogenesis, since this enzyme was lost in amelanogenic mutant strains. This PPO was strongly activated by sodium dodecyl sulfate below the critical micelle concentration, and it is a tyrosinase-like enzyme showing a lag period in its tyrosine hydroxylase activity that could be avoided by small amounts of L-dopa. This is the first report of a bacterium that contains two PPOs and also the first report of a pluripotent PPO showing all types of oxidase activities. The bacterium and the pluripotent PPO may be useful models for exploring the roles of PPOs in cellular physiology, aside from melanin formation. On the other hand, the high oxidizing capacity of the PPO for a wide range of substrates could make possible its application in phenolic biotransformations, food processing, or the cosmetic industry, where fungal and plant PPOs are being used. PMID:16535688

  3. Complete genome sequence of Lactobacillus helveticus MB2-1, a probiotic bacterium producing exopolysaccharides.

    PubMed

    Li, Wei; Xia, Xiudong; Chen, Xiaohong; Rui, Xin; Jiang, Mei; Zhang, Qiuqin; Zhou, Jianzhong; Dong, Mingsheng

    2015-09-10

    Lactobacillus helveticus MB2-1 is a probiotic bacterium producing exopolysaccharides (EPS), which was isolated from traditional Sayram ropy fermented milk in southern Xinjiang, China. The genome consists of a circular 2,084,058bp chromosome with no plasmid. The genome sequence indicated that this strain includes a 15.20kb gene cluster involved in EPS biosynthesis. Genome sequencing information has provided the basis for understanding the potential molecular mechanism behind the EPS production. PMID:26065338

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

    PubMed

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

    2016-12-01

    Cadmium resistant bacterium, isolated from industrial wastewater, was characterized as Salmonella enterica 43C on the basis of biochemical and 16S rRNA ribotyping. It is first ever reported S. enterica 43C bared extreme resistance against heavy metal consortia in order of Pb(2+)>Cd(2+)>As(3+)>Zn(2+)>Cr(6+)>Cu(2+)>Hg(2+). Cd(2+) stress altered growth pattern of the bacterium in time dependent manner. It could remove nearly 57 % Cd(2+) from the medium over a period of 8 days. Kinetic and thermodynamic studies based on various adsorption isotherm models (Langmuir and Freundlich) depicted the Cd(2+) biosorption as spontaneous, feasible and endothermic in nature. Interestingly, the bacterium followed pseudo first order kinetics, making it a good biosorbent for heavy metal ions. The S. enterica 43C Cd(2+) processivity was significantly influenced by temperature, pH, initial Cd(2+) concentration, biomass dosage and co-metal ions. FTIR analysis of the bacterium revealed the active participation of amide and carbonyl moieties in Cd(2+) adsorption confirmed by EDX analysis. Electron micrographs beckoned further surface adsorption and increased bacterial size due to intracellular Cd(2+) accumulation. An overwhelming increase in glutathione and other non-protein thiols levels played a significant role in thriving oxidative stress generated by metal cations. Presence of metallothionein clearly depicted the role of such proteins in bacterial metal resistance mechanism. The present study results clearly declare S. enterica 43C a suitable candidate for green chemistry to bioremediate environmental Cd(2+). PMID:27491862

  5. Catalytic Biomineralization of Fluorescent Calcite by the Thermophilic Bacterium Geobacillus thermoglucosidasius▿

    PubMed Central

    Yoshida, Naoto; Higashimura, Eiji; Saeki, Yuichi

    2010-01-01

    The thermophilic Geobacillus bacterium catalyzed the formation of 100-μm hexagonal crystals at 60°C in a hydrogel containing sodium acetate, calcium chloride, and magnesium sulfate. Under fluorescence microscopy, crystals fluoresced upon excitation at 365 ± 5, 480 ± 20, or 545 ± 15 nm. X-ray diffraction indicated that the crystals were magnesium-calcite in calcite-type calcium carbonate. PMID:20851984

  6. Draft Genome Sequence of Staphylococcus succinus Strain CSM-77, a Moderately Halophilic Bacterium Isolated from a Triassic Salt Mine.

    PubMed

    Megaw, Julianne; Gilmore, Brendan F

    2016-01-01

    Here, we report the draft genome sequence of Staphylococcus succinus strain CSM-77. This moderately halophilic bacterium was isolated from the surface of a halite sample obtained from a Triassic salt mine. PMID:27284152

  7. Draft Genome Sequence of Staphylococcus succinus Strain CSM-77, a Moderately Halophilic Bacterium Isolated from a Triassic Salt Mine

    PubMed Central

    Gilmore, Brendan F.

    2016-01-01

    Here, we report the draft genome sequence of Staphylococcus succinus strain CSM-77. This moderately halophilic bacterium was isolated from the surface of a halite sample obtained from a Triassic salt mine. PMID:27284152

  8. Genome Sequence of the Endophytic Bacterium Bacillus thuringiensis Strain KB1, a Potential Biocontrol Agent against Phytopathogens.

    PubMed

    Jeong, Haeyoung; Jo, Sung Hee; Hong, Chi Eun; Park, Jeong Mee

    2016-01-01

    ITALIC! Bacillus thuringiensisis the most widely known microbial pesticide used in agricultural applications. Herein, we report a draft genome sequence of the endophytic bacterium ITALIC! Bacillus thuringiensisstrain KB1, which exhibits antagonism against phytopathogens. PMID:27103716

  9. Genome Sequence of the Endophytic Bacterium Bacillus thuringiensis Strain KB1, a Potential Biocontrol Agent against Phytopathogens

    PubMed Central

    Jo, Sung Hee; Hong, Chi Eun

    2016-01-01

    Bacillus thuringiensis is the most widely known microbial pesticide used in agricultural applications. Herein, we report a draft genome sequence of the endophytic bacterium Bacillus thuringiensis strain KB1, which exhibits antagonism against phytopathogens. PMID:27103716

  10. Phosphate enhances levan production in the endophytic bacterium Gluconacetobacter diazotrophicus Pal5.

    PubMed

    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

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

    SciTech Connect

    Mary E. Lidstrom

    2003-12-26

    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.

  12. Deinococcus mumbaiensis sp. nov., a radiation-resistant pleomorphic bacterium isolated from Mumbai, India.

    PubMed

    Shashidhar, Ravindranath; Bandekar, Jayant R

    2006-01-01

    A radiation-resistant, Gram-negative and pleomorphic bacterium (CON-1) was isolated from a contaminated tryptone glucose yeast extract agar plate in the laboratory. It was red pigmented, nonmotile, nonsporulating, and aerobic, and contained MK-8 as respiratory quinone. The cell wall of this bacterium contained ornithine. The major fatty acids were C16:0, C16:1, C17:0, C18:1 and iso C18:0. The DNA of CON-1 had a G+C content of 70 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that CON-1 exhibited a maximum similarity (94.72%) with Deinococcus grandis. Based on the genotypic, phenotypic and chemotaxonomic characteristics, the bacterium CON-1 was identified as a new species of the genus Deinococcus, for which the name Deinococcus mumbaiensis sp. nov. is proposed. The type strain of D. mumbaiensis is CON-1 (MTCC 7297(T)=DSM 17424(T)). PMID:16445756

  13. [Mechanisms of Forespore Formation during Polysporogenesis of an Anaerobic Bacterium Anaerobacter polyendosporus PST(T)].

    PubMed

    Duda, V I; Suzina, N E

    2015-01-01

    Forespore formation in the anaerobic bacterium Anaerobacterpolyendosporus PS-1(T) was studied by phase contrast, fluorescence, and electron microscopy. It is concluded that in this bacterium the formation of all forespores in multispore sporangia occurs via the same mechanism as that operating in all known bacilli and clostridia during the single-spore variant of endogenous sporogenesis. Its cytological indicators are as follows: (1) formation of the forespore septum, (2) engulfment of the smaller prespore cell by the larger mother cell, (3) cortex synthesis, (4) assembly of the spore coats, (5) exosporium formation, and (6) lysis of the mother cell. Polysporogenesis in strain PS-1(T) is characterized by synchronous formation of all spores (siblings) in a given sporangium and by the absence of any indication of forespore division within the mother cell. These data suggest that multiple spores within a single PS-1(T) cell result not from division of the first forespores developing at one or two cell poles, as it was reported for another polysporogenic bacterium, "Metabacterium polyspora", but rather from simultaneous independent formation of several prespores in a single mother cell in the course of modified cell division. PMID:27169242

  14. Chitin Degradation Proteins Produced by the Marine Bacterium Vibrio harveyi Growing on Different Forms of Chitin

    PubMed Central

    Svitil, A. L.; Chadhain, S.; Moore, J. A.; Kirchman, D. L.

    1997-01-01

    Relatively little is known about the number, diversity, and function of chitinases produced by bacteria, even though chitin is one of the most abundant polymers in nature. Because of the importance of chitin, especially in marine environments, we examined chitin-degrading proteins in the marine bacterium Vibrio harveyi. This bacterium had a higher growth rate and more chitinase activity when grown on (beta)-chitin (isolated from squid pen) than on (alpha)-chitin (isolated from snow crab), probably because of the more open structure of (beta)-chitin. When exposed to different types of chitin, V. harveyi excreted several chitin-degrading proteins into the culture media. Some chitinases were present with all of the tested chitins, while others were unique to a particular chitin. We cloned and identified six separate chitinase genes from V. harveyi. These chitinases appear to be unique based on DNA restriction patterns, immunological data, and enzyme activity. This marine bacterium and probably others appear to synthesize separate chitinases for efficient utilization of different forms of chitin and chitin by-products. PMID:16535505

  15. Development of a markerless deletion system for the fish-pathogenic bacterium Flavobacterium psychrophilum.

    PubMed

    Gómez, Esther; Álvarez, Beatriz; Duchaud, Eric; Guijarro, José A

    2015-01-01

    Flavobacterium psychrophilum is a Gram-negative fish pathogen that causes important economic losses in aquaculture worldwide. Although the genome of this bacterium has been determined, the function and relative importance of genes in relation to virulence remain to be established. To investigate their respective contribution to the bacterial pathogenesis, effective tools for gene inactivation are required. In the present study, a markerless gene deletion system has been successfully developed for the first time in this bacterium. Using this method, the F. psychrophilum fcpB gene, encoding a predicted cysteine protease homologous to Streptococcus pyogenes streptopain, was deleted. The developed system involved the construction of a conjugative plasmid that harbors the flanking sequences of the fcpB gene and an I-SceI meganuclease restriction site. Once this plasmid was integrated in the genome by homologous recombination, the merodiploid was resolved by the introduction of a plasmid expressing I-SceI under the control of the fpp2 F. psychrophilum inducible promoter. The resulting deleted fcpB mutant presented a decrease in extracellular proteolytic activity compared to the parental strain. However, there were not significant differences between their LD50 in an intramuscularly challenged rainbow trout infection model. The mutagenesis approach developed in this work represents an improvement over the gene inactivation tools existing hitherto for this "fastidious" bacterium. Unlike transposon mutagenesis and gene disruption, gene markerless deletion has less potential for polar effects and allows the mutation of virtually any non-essential gene or gene clusters. PMID:25692569

  16. Anomalous Magnetic Orientations of Magnetosome Chains in a Magnetotactic Bacterium: Magnetovibrio blakemorei Strain MV-1

    PubMed Central

    Kalirai, Samanbir S.; Bazylinski, Dennis A.; Hitchcock, Adam P.

    2013-01-01

    There is a good deal of published evidence that indicates that all magnetosomes within a single cell of a magnetotactic bacterium are magnetically oriented in the same direction so that they form a single magnetic dipole believed to assist navigation of the cell to optimal environments for their growth and survival. Some cells of the cultured magnetotactic bacterium Magnetovibrio blakemorei strain MV-1 are known to have relatively wide gaps between groups of magnetosomes that do not seem to interfere with the larger, overall linear arrangement of the magnetosomes along the long axis of the cell. We determined the magnetic orientation of the magnetosomes in individual cells of this bacterium using Fe 2p X-ray magnetic circular dichroism (XMCD) spectra measured with scanning transmission X-ray microscopy (STXM). We observed a significant number of cases in which there are sub-chains in a single cell, with spatial gaps between them, in which one or more sub-chains are magnetically polarized opposite to other sub-chains in the same cell. These occur with an estimated frequency of 4.0±0.2%, based on a sample size of 150 cells. We propose possible explanations for these anomalous cases which shed insight into the mechanisms of chain formation and magnetic alignment. PMID:23308202

  17. Purification and Characterization of Haloalkaline, Organic Solvent Stable Xylanase from Newly Isolated Halophilic Bacterium-OKH

    PubMed Central

    Sanghvi, Gaurav; Jivrajani, Mehul; Patel, Nirav; Jivrajani, Heta; Bhaskara, Govinal Badiger; Patel, Shivani

    2014-01-01

    A novel, alkali-tolerant halophilic bacterium-OKH with an ability to produce extracellular halophilic, alkali-tolerant, organic solvent stable, and moderately thermostable xylanase was isolated from salt salterns of Mithapur region, Gujarat, India. Identification of the bacterium was done based upon biochemical tests and 16S rRNA sequence. Maximum xylanase production was achieved at pH 9.0 and 37°C temperature in the medium containing 15% NaCl and 1% (w/v) corn cobs. Sugarcane bagasse and wheat straw also induce xylanase production when used as carbon source. The enzyme was active over a range of 0–25% sodium chloride examined in culture broth. The optimum xylanase activity was observed at 5% sodium chloride. Xylanase was purified with 25.81%-fold purification and 17.1% yield. Kinetic properties such as Km and Vmax were 4.2 mg/mL and 0.31 μmol/min/mL, respectively. The enzyme was stable at pH 6.0 and 50°C with 60% activity after 8 hours of incubation. Enzyme activity was enhanced by Ca2+, Mn2+, and Mg2+ but strongly inhibited by heavy metals such as Hg2+, Fe3+, Ni2+, and Zn2+. Xylanase was found to be stable in organic solvents like glutaraldehyde and isopropanol. The purified enzyme hydrolysed lignocellulosic substrates. Xylanase, purified from the halophilic bacterium-OKH, has potential biotechnological applications. PMID:27350996

  18. Phosphate enhances levan production in the endophytic bacterium Gluconacetobacter diazotrophicus Pal5

    PubMed Central

    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

  19. Anaerobic, Nitrate-Dependent Oxidation of U(IV) Oxide Minerals by the Chemolithoautotrophic Bacterium Thiobacillus denitrificans

    PubMed Central

    Beller, Harry R.

    2005-01-01

    Under anaerobic conditions and at circumneutral pH, cells of the widely distributed, obligate chemolithoautotrophic bacterium Thiobacillus denitrificans oxidatively dissolved synthetic and biogenic U(IV) oxides (uraninite) in nitrate-dependent fashion: U(IV) oxidation required the presence of nitrate and was strongly correlated with nitrate consumption. This is the first report of anaerobic U(IV) oxidation by an autotrophic bacterium. PMID:15812053

  20. Draft Genome Sequence of Bacillus murimartini LMG 21005T, an Alkalitolerant Bacterium Isolated from a Church Wall Mural in Germany

    PubMed Central

    Wang, Jie-ping; Liu, Guo-hong; Xiao, Rong-feng; Zheng, Xue-fang; Shi, Huai; Ge, Ci-bin

    2015-01-01

    Bacillus murimartini LMG 21005T is a Gram-positive, spore-forming, and alkalitolerant bacterium isolated from a church wall mural. Here, we report the 4.17-Mb genome sequence of B. murimartini LMG 21005T, which will accelerate the application of this alkalitolerant bacterium and provide useful information for genomic taxonomy and phylogenomics of Bacillus-like bacteria. PMID:26494676

  1. Alcanivorax dieselolei, an alkane-degrading bacterium associated with the mucus of the zoanthid Palythoa caribaeorum (Cnidaria, Anthozoa).

    PubMed

    Campos, F F; Garcia, J E; Luna-Finkler, C L; Davolos, C C; Lemos, M V F; Pérez, C D

    2015-05-01

    Analyses of 16S rDNA genes were used to identify the microbiota isolated from the mucus of the zoanthid Palythoa caribaeorum at Porto de Galinhas on the coast of Pernambuco State, Brazil. This study is important as the first report of this association, because of the potential biotechnological applications of the bacterium Alcanivorax dieselolei, and as evidence for the presence of a hydrocarbon degrading bacterium in a reef ecosystem such as Porto de Galinhas. PMID:26132028

  2. Draft Genome Sequence of Bacillus licheniformis Strain GB2, a Hydrocarbon-Degrading and Plant Growth-Promoting Soil Bacterium

    PubMed Central

    Gkorezis, Panagiotis; Van Hamme, Jonathan; Bottos, Eric; Thijs, Sofie; Balseiro-Romero, Maria; Monterroso, Carmela; Kidd, Petra Suzan; Rineau, Francois; Weyens, Nele; Sillen, Wouter

    2016-01-01

    We report the 4.39 Mb draft genome of Bacillus licheniformis GB2, a hydrocarbonoclastic Gram-positive bacterium of the family Bacillaceae, isolated from diesel-contaminated soil at the Ford Motor Company site in Genk, Belgium. Strain GB2 is an effective plant-growth promoter useful for diesel fuel remediation applications based on plant-bacterium associations. PMID:27340073

  3. Anaerobic, Nitrate-Dependent Oxidation of U(IV) Oxide Minerals by the Chemolithoautotrophic Bacterium Thiobacillus denitrificans

    SciTech Connect

    Beller, H R

    2004-06-25

    Under anaerobic conditions and at circumneutral pH, cells of the widely-distributed, obligate chemolithoautotrophic bacterium Thiobacillus denitrificans oxidatively dissolved synthetic and biogenic U(IV) oxides (uraninite) in nitrate-dependent fashion: U(IV) oxidation required the presence of nitrate and was strongly correlated to nitrate consumption. This is the first report of anaerobic U(IV) oxidation by an autotrophic bacterium.

  4. Draft Genome Sequence of Bacillus licheniformis Strain GB2, a Hydrocarbon-Degrading and Plant Growth-Promoting Soil Bacterium.

    PubMed

    Gkorezis, Panagiotis; Van Hamme, Jonathan; Bottos, Eric; Thijs, Sofie; Balseiro-Romero, Maria; Monterroso, Carmela; Kidd, Petra Suzan; Rineau, Francois; Weyens, Nele; Sillen, Wouter; Vangronsveld, Jaco

    2016-01-01

    We report the 4.39 Mb draft genome of Bacillus licheniformis GB2, a hydrocarbonoclastic Gram-positive bacterium of the family Bacillaceae, isolated from diesel-contaminated soil at the Ford Motor Company site in Genk, Belgium. Strain GB2 is an effective plant-growth promoter useful for diesel fuel remediation applications based on plant-bacterium associations. PMID:27340073

  5. Effect of arsenite-oxidizing bacterium B. laterosporus on arsenite toxicity and arsenic translocation in rice seedlings.

    PubMed

    Yang, Gui-Di; Xie, Wan-Ying; Zhu, Xi; Huang, Yi; Yang, Xiao-Jun; Qiu, Zong-Qing; Lv, Zhen-Mao; Wang, Wen-Na; Lin, Wen-Xiong

    2015-10-01

    Arsenite [As (III)] oxidation can be accelerated by bacterial catalysis, but the effects of the accelerated oxidation on arsenic toxicity and translocation in rice plants are poorly understood. Herein we investigated how an arsenite-oxidizing bacterium, namely Brevibacillus laterosporus, influences As (III) toxicity and translocation in rice plants. Rice seedlings of four cultivars, namely Guangyou Ming 118 (GM), Teyou Hang II (TH), Shanyou 63 (SY) and Minghui 63 (MH), inoculated with or without the bacterium were grown hydroponically with As (III) to investigate its effects on arsenic toxicity and translocation in the plants. Percentages of As (III) oxidation in the solutions with the bacterium (100%) were all significantly higher than those without (30-72%). The addition of the bacterium significantly decreased As (III) concentrations in SY root, GM root and shoot, while increased the As (III) concentrations in the shoot of SY, MH and TH and in the root of MH. Furthermore, the As (III) concentrations in the root and shoot of SY were both the lowest among the treatments with the bacterium. On the other hand, its addition significantly alleviated the As (III) toxicity on four rice cultivars. Among the treatments amended with B. laterosporus, the bacterium showed the best remediation on SY seedlings, with respect to the subdued As (III) toxicity and decreased As (III) concentration in its roots. These results indicated that As (III) oxidation accelerated by B. laterosporus could be an effective method to alleviate As (III) toxicity on rice seedlings. PMID:26024808

  6. Treatment of Alkaline Cr(VI)-Contaminated Leachate with an Alkaliphilic Metal-Reducing Bacterium

    PubMed Central

    Watts, Mathew P.; Khijniak, Tatiana V.; Boothman, Christopher

    2015-01-01

    Chromium in its toxic Cr(VI) valence state is a common contaminant particularly associated with alkaline environments. A well-publicized case of this occurred in Glasgow, United Kingdom, where poorly controlled disposal of a cementitious industrial by-product, chromite ore processing residue (COPR), has resulted in extensive contamination by Cr(VI)-contaminated alkaline leachates. In the search for viable bioremediation treatments for Cr(VI), a variety of bacteria that are capable of reduction of the toxic and highly soluble Cr(VI) to the relatively nontoxic and less mobile Cr(III) oxidation state, predominantly under circumneutral pH conditions, have been isolated. Recently, however, alkaliphilic bacteria that have the potential to reduce Cr(VI) under alkaline conditions have been identified. This study focuses on the application of a metal-reducing bacterium to the remediation of alkaline Cr(VI)-contaminated leachates from COPR. This bacterium, belonging to the Halomonas genus, was found to exhibit growth concomitant to Cr(VI) reduction under alkaline conditions (pH 10). Bacterial cells were able to rapidly remove high concentrations of aqueous Cr(VI) (2.5 mM) under anaerobic conditions, up to a starting pH of 11. Cr(VI) reduction rates were controlled by pH, with slower removal observed at pH 11, compared to pH 10, while no removal was observed at pH 12. The reduction of aqueous Cr(VI) resulted in the precipitation of Cr(III) biominerals, which were characterized using transmission electron microscopy and energy-dispersive X-ray analysis (TEM-EDX) and X-ray photoelectron spectroscopy (XPS). The effectiveness of this haloalkaliphilic bacterium for Cr(VI) reduction at high pH suggests potential for its use as an in situ treatment of COPR and other alkaline Cr(VI)-contaminated environments. PMID:26048926

  7. Studies of the extracellular glycocalyx of the anaerobic cellulolytic bacterium Ruminococcus albus 7.

    PubMed

    Weimer, Paul J; Price, Neil P J; Kroukamp, Otini; Joubert, Lydia-Marie; Wolfaardt, Gideon M; Van Zyl, Willem H

    2006-12-01

    Anaerobic cellulolytic bacteria are thought to adhere to cellulose via several mechanisms, including production of a glycocalyx containing extracellular polymeric substances (EPS). As the compositions and structures of these glycocalyces have not been elucidated, variable-pressure scanning electron microscopy (VP-SEM) and chemical analysis were used to characterize the glycocalyx of the ruminal bacterium Ruminococcus albus strain 7. VP-SEM revealed that growth of this strain was accompanied by the formation of thin cellular extensions that allowed the bacterium to adhere to cellulose, followed by formation of a ramifying network that interconnected individual cells to one another and to the unraveling cellulose microfibrils. Extraction of 48-h-old whole-culture pellets (bacterial cells plus glycocalyx [G] plus residual cellulose [C]) with 0.1 N NaOH released carbohydrate and protein in a ratio of 1:5. Boiling of the cellulose fermentation residue in a neutral detergent solution removed almost all of the adherent cells and protein while retaining a residual network of adhering noncellular material. Trifluoroacetic acid hydrolysis of this residue (G plus C) released primarily glucose, along with substantial amounts of xylose and mannose, but only traces of galactose, the most abundant sugar in most characterized bacterial exopolysaccharides. Linkage analysis and characterization by nuclear magnetic resonance suggested that most of the glucosyl units were not present as partially degraded cellulose. Calculations suggested that the energy demand for synthesis of the nonprotein fraction of EPS by this organism represents only a small fraction (<4%) of the anabolic ATP expenditure of the bacterium. PMID:17028224

  8. Treatment of Alkaline Cr(VI)-Contaminated Leachate with an Alkaliphilic Metal-Reducing Bacterium.

    PubMed

    Watts, Mathew P; Khijniak, Tatiana V; Boothman, Christopher; Lloyd, Jonathan R

    2015-08-15

    Chromium in its toxic Cr(VI) valence state is a common contaminant particularly associated with alkaline environments. A well-publicized case of this occurred in Glasgow, United Kingdom, where poorly controlled disposal of a cementitious industrial by-product, chromite ore processing residue (COPR), has resulted in extensive contamination by Cr(VI)-contaminated alkaline leachates. In the search for viable bioremediation treatments for Cr(VI), a variety of bacteria that are capable of reduction of the toxic and highly soluble Cr(VI) to the relatively nontoxic and less mobile Cr(III) oxidation state, predominantly under circumneutral pH conditions, have been isolated. Recently, however, alkaliphilic bacteria that have the potential to reduce Cr(VI) under alkaline conditions have been identified. This study focuses on the application of a metal-reducing bacterium to the remediation of alkaline Cr(VI)-contaminated leachates from COPR. This bacterium, belonging to the Halomonas genus, was found to exhibit growth concomitant to Cr(VI) reduction under alkaline conditions (pH 10). Bacterial cells were able to rapidly remove high concentrations of aqueous Cr(VI) (2.5 mM) under anaerobic conditions, up to a starting pH of 11. Cr(VI) reduction rates were controlled by pH, with slower removal observed at pH 11, compared to pH 10, while no removal was observed at pH 12. The reduction of aqueous Cr(VI) resulted in the precipitation of Cr(III) biominerals, which were characterized using transmission electron microscopy and energy-dispersive X-ray analysis (TEM-EDX) and X-ray photoelectron spectroscopy (XPS). The effectiveness of this haloalkaliphilic bacterium for Cr(VI) reduction at high pH suggests potential for its use as an in situ treatment of COPR and other alkaline Cr(VI)-contaminated environments. PMID:26048926

  9. NH4+ transport system of a psychrophilic marine bacterium, Vibrio sp. strain ABE-1.

    PubMed

    Chou, M; Matsunaga, T; Takada, Y; Fukunaga, N

    1999-05-01

    NH4(+) transport system of a psychrophilic marine bacterium Vibrio sp. strain ABE-1 (Vibrio ABE-1) was examined by measuring the uptake of [14C]methylammonium ion (14CH3NH3+) into the intact cells. 14CH3NH3+ uptake was detected in cells grown in medium containing glutamate as the sole nitrogen source, but not in those grown in medium containing NH4Cl instead of glutamate. Vibrio ABE-1 did not utilize CH3NH3+ as a carbon or nitrogen source. NH4Cl and nonradiolabeled CH3NH3+ completely inhibited 14CH3NH3+ uptake. These results indicate that 14CH3NH3+ uptake in this bacterium is mediated via an NH4+ transport system and not by a specific carrier for CH3NH3+. The respiratory substrate succinate was required to drive 14CH3NH3+ uptake and the uptake was completely inhibited by KCN, indicating that the uptake was energy dependent. The electrochemical potentials of H+ and/or Na+ across membranes were suggested to be the driving forces for the transport system because the ionophores carbonylcyanide m-chlorophenylhydrazone and monensin strongly inhibited uptake activities at pH 6.5 and 8.5, respectively. Furthermore, KCl activated 14CH3NH3+ uptake. The 14CH3NH3+ uptake activity of Vibrio ABE-1 was markedly high at temperatures between 0 degrees and 15 degrees C, and the apparent Km value for CH3NH3+ of the uptake did not change significantly over the temperature range from 0 degrees to 25 degrees C. Thus, the NH4+ transport system of this bacterium was highly active at low temperatures. PMID:10356994

  10. Measurement of soil bacterial colony temperatures and isolation of a high heat-producing bacterium

    PubMed Central

    2013-01-01

    Background The cellular temperatures of microorganisms are considered to be the same as those of their surroundings because the cellular volume is too small to maintain a cellular temperature that is different from the ambient temperature. However, by forming a colony or a biofilm, microorganisms may be able to maintain a cellular temperature that is different from the ambient temperature. In this study, we measured the temperatures of bacterial colonies isolated from soils using an infrared imager and investigated the thermogenesis by a bacterium that increases its colony temperature. Results The temperatures of some colonies were higher or lower than that of the surrounding medium. A bacterial isolate with the highest colony temperature was identified as Pseudomonas putida. This bacterial isolate had an increased colony temperature when it grew at a temperature suboptimal for its growth. Measurements of heat production using a microcalorimeter showed that the temperature of this extraordinary, microcalorimetrically determined thermogenesis corresponded with the thermographically observed increase in bacterial colony temperature. When investigating the effects of the energy source on this thermal behavior, we found that heat production by this bacterium increased without additional biomass production at a temperature suboptimal for its growth. Conclusions We found that heat production by bacteria affected the bacterial colony temperature and that a bacterium identified as Pseudomonas putida could maintain a cellular temperature different from the ambient temperature, particularly at a sub-optimal growth temperature. The bacterial isolate P. putida KT1401 increased its colony temperature by an energy-spilling reaction when the incubation temperature limited its growth. PMID:23497132

  11. Haloanaerobium salsugo sp. nov., a moderately halophilic, anaerobic bacterium from a subterranean brine

    SciTech Connect

    Bhupathiraju, V.K.; Sharma, P.K.; Tanner, R.S.; McInerney, M.J.; Oren, A.; Woese, C.R.

    1994-07-01

    A strictly anaerobic, moderately halophilic, gram-negative bacterium was isolated from a highly saline oil field brine. The bacterium was a non-spore-forming, nonmotile rod, appearing singly, in pairs, or occasionally as long chains, and measured 0.3 to 0.4 by 2.6 to 4 {micro}m. The bacterium had a specific requirement for NaCl and grew at NaCl concentrations of between 6 and 24%, with optimal growth at 9% NaCl. The isolate grew at temperatures of between 22 and 51 C and pH values of between 5.6 and 8.0. The doubling time in a complex medium containing 10% NaCl was 9 h. Growth was inhibited by chloramphenicol, tetracycline, and penicillin but not by cycloheximide or azide. Fermentable substrates were predominantly carbohydrates. The end products of glucose fermentation were acetate, ethanol, CO{sub 2}, and H{sub 2}. The major components of the cellular fatty acids were C{sub 14:0}, C{sub 16:0}, C{sub 16:1}, and C{sub 17:0 cyc} acids. The DNA base composition of the isolate was 34 mol% G+C. Oligonucleotide catalog and sequence analyses of the 16S rRNA showed that strain VS-752{sup T} was most closely related to Haloanaerobium praevalens GSL{sup T} (ATCC 33744), the sole member of the genus Haloanaerobium. The authors propose that strain VS-752 (ATCC 51327) by established as the type strain of a new species, Haloanaerobium salsugo, in the genus Haloanaerobium. 40 refs., 3 figs, 5 tabs.

  12. Development of a Markerless Deletion System for the Fish-Pathogenic Bacterium Flavobacterium psychrophilum

    PubMed Central

    Gómez, Esther; Álvarez, Beatriz; Duchaud, Eric; Guijarro, José A.

    2015-01-01

    Flavobacterium psychrophilum is a Gram-negative fish pathogen that causes important economic losses in aquaculture worldwide. Although the genome of this bacterium has been determined, the function and relative importance of genes in relation to virulence remain to be established. To investigate their respective contribution to the bacterial pathogenesis, effective tools for gene inactivation are required. In the present study, a markerless gene deletion system has been successfully developed for the first time in this bacterium. Using this method, the F. psychrophilum fcpB gene, encoding a predicted cysteine protease homologous to Streptococcus pyogenes streptopain, was deleted. The developed system involved the construction of a conjugative plasmid that harbors the flanking sequences of the fcpB gene and an I-SceI meganuclease restriction site. Once this plasmid was integrated in the genome by homologous recombination, the merodiploid was resolved by the introduction of a plasmid expressing I-SceI under the control of the fpp2 F. psychrophilum inducible promoter. The resulting deleted fcpB mutant presented a decrease in extracellular proteolytic activity compared to the parental strain. However, there were not significant differences between their LD50 in an intramuscularly challenged rainbow trout infection model. The mutagenesis approach developed in this work represents an improvement over the gene inactivation tools existing hitherto for this “fastidious” bacterium. Unlike transposon mutagenesis and gene disruption, gene markerless deletion has less potential for polar effects and allows the mutation of virtually any non-essential gene or gene clusters. PMID:25692569

  13. Pontibacter diazotrophicus sp. nov., a Novel Nitrogen-Fixing Bacterium of the Family Cytophagaceae

    PubMed Central

    Xu, Linghua; Zeng, Xian-Chun; Nie, Yao; Luo, Xuesong; Zhou, Enmin; Zhou, Lingli; Pan, Yunfan; Li, Wenjun

    2014-01-01

    Few diazotrophs have been found to belong to the family Cytophagaceae so far. In the present study, a Gram-negative, rod-shaped bacterium that forms red colonies, was isolated from sands of the Takalamakan desert. It was designated H4XT. Phylogenetic and biochemical analysis indicated that the isolate is a new species of the genus Pontibacter. The 16S rRNA gene of H4XT displays 94.2–96.8% sequence similarities to those of other strains in Pontibacter. The major respiratory quinone is menaquinone-7 (MK-7). The DNA G+C content is 46.6 mol%. The major cellular fatty acids are iso-C15∶0, C16∶1ω5c, summed feature 3 (containing C16∶1ω6c and/or C16∶1ω7c) and summed feature 4 (comprising anteiso-C17∶1B and/or iso-C17∶1I). The major polar lipids are phosphatidylethanolamine (PE), one aminophospholipid (APL) and some unknown phospholipids (PLs). It is interesting to see that this bacterium can grow very well in a nitrogen-free medium. PCR amplification suggested that the bacterium possesses at least one type of nitrogenase gene. Acetylene reduction assay showed that H4XT actually possesses nitrogen-fixing activity. Therefore, it can be concluded that H4XT is a new diazotroph. We thus referred it to as Pontibacter diazotrophicus sp. nov. The type strain is H4XT ( = CCTCC AB 2013049T = NRRL B-59974T). PMID:24647674

  14. Draft Genome Sequence of the Endophytic Strain Rhodococcus kyotonensis KB10, a Potential Biodegrading and Antibacterial Bacterium Isolated from Arabidopsis thaliana

    PubMed Central

    Hong, Chi Eun; Jo, Sung Hee

    2016-01-01

    Rhodococcus kyotonensis KB10 is an endophytic bacterium isolated from Arabidopsis thaliana. The organism showed mild antibacterial activity against the phytopathogen Pseudomonas syringae pv. tomato DC3000. This study reports the genome sequence of R. kyotonensis KB10. This bacterium contains an ectoine biosynthesis gene cluster and has the potential to degrade nitroaromatic compounds. The identified bacterium may be a suitable biocontrol agent and degrader of environmental pollutants. PMID:27389269

  15. Draft Genome Sequence of the Endophytic Strain Rhodococcus kyotonensis KB10, a Potential Biodegrading and Antibacterial Bacterium Isolated from Arabidopsis thaliana.

    PubMed

    Hong, Chi Eun; Jo, Sung Hee; Jeong, Haeyoung; Park, Jeong Mee

    2016-01-01

    Rhodococcus kyotonensis KB10 is an endophytic bacterium isolated from Arabidopsis thaliana The organism showed mild antibacterial activity against the phytopathogen Pseudomonas syringae pv. tomato DC3000. This study reports the genome sequence of R. kyotonensis KB10. This bacterium contains an ectoine biosynthesis gene cluster and has the potential to degrade nitroaromatic compounds. The identified bacterium may be a suitable biocontrol agent and degrader of environmental pollutants. PMID:27389269

  16. Complete genome of a coastal marine bacterium Muricauda lutaonensis KCTC 22339(T).

    PubMed

    Oh, Jeongsu; Choe, Hanna; Kim, Byung Kwon; Kim, Kyung Mo

    2015-10-01

    Muricauda lutaonensis KCTC 22339(T) is a yellow-pigmented, gram-negative, rod-shaped bacterium that was isolated from a coastal hot spring of a volcanic island in the Pacific Ocean, off the eastern coast of Taiwan. We here report the complete genome of M. lutaonensis KCTC 22339(T), which consists of 3,274,259bp with the G+C content of 44.97%. The completion of the M. lutaonensis genome sequence is expected to provide a valuable resource for understanding the secondary metabolic pathways related to bacterial pigmentation. PMID:25986927

  17. Genome sequence of Xanthomonas sacchari R1, a biocontrol bacterium isolated from the rice seed.

    PubMed

    Fang, Yunxia; Lin, Haiyan; Wu, Liwen; Ren, Deyong; Ye, Weijun; Dong, Guojun; Zhu, Li; Guo, Longbiao

    2015-07-20

    Xanthomonas sacchari, was first identified as a pathogenic bacterium isolated from diseased sugarcane in Guadeloupe. In this study, R1 was first isolated from rice seed samples from Philippines in 2002. The antagonistic ability against several rice pathogens raises our attention. The genomic feature of this strain was described in this paper. The total genome size of X. sacchari R1 is 5,000,479 bp with 4315 coding sequences (CDS), 59 tRNAs, 2rRNAs and one plasmid. PMID:25931193

  18. Aggregation of the rhizospheric bacterium Azospirillum brasilense in response to oxygen

    NASA Astrophysics Data System (ADS)

    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.

  19. Cadmium-nickel toxicity interactions towards a bacterium, filamentous fungi, and a cultured mammalian cell line

    SciTech Connect

    Babich, H.; Shopsis, C.; Borenfreund, E.

    1986-10-01

    The response of the biota to exposure to individual metals may differ from its response to multiple metals, as mixtures of metals may interact antagonistically or synergistically in their resultant toxicity. The present study evaluated the effects of a combination of Cd and Ni on the freshwater bacterium, Aeromonas hydrophila, the terrestrial fungi, Trichodema viride and Aspergillus niger, and the mammalian cell line, BALB/c mouse 3T3 fibroblasts. This particular spectrum of target cells was selected because studies in the literature show a wide variety of possible interactions between Cd and Ni in their combined toxicities towards bacteria cyanobacteria, slime molds, isolated rat hepatocytes, and rats.

  20. An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3

    PubMed Central

    2014-01-01

    When the genome of Ruegeria pomeroyi DSS-3 was published in 2004, it represented the first sequence from a heterotrophic marine bacterium. Over the last ten years, the strain has become a valuable model for understanding the cycling of sulfur and carbon in the ocean. To ensure that this genome remains useful, we have updated 69 genes to incorporate functional annotations based on new experimental data, and improved the identification of 120 protein-coding regions based on proteomic and transcriptomic data. We review the progress made in understanding the biology of R. pomeroyi DSS-3 and list the changes made to the genome. PMID:25780504

  1. Complete genome sequence of Enterobacter cloacae GGT036: a furfural tolerant soil bacterium.

    PubMed

    Gong, Gyeongtaek; Um, Youngsoon; Park, Tai Hyun; Woo, Han Min

    2015-01-10

    Enterobacter cloacae is a facultative anaerobic bacterium to be an important cause of nosocomial infection. However, the isolated E. cloacae GGT036 showed higher furfural-tolerant cellular growth, compared to industrial relevant strains such as Escherichia coli and Corynebacterium glutamicum. Here, we report the complete genome sequence of E. cloacae GGT036 isolated from Mt. Gwanak, Seoul, Republic of Korea. The genomic DNA sequence of E. cloacae GGT036 will provide valuable genetic resources for engineering of industrially relevant strains being tolerant to cellular inhibitors present in lignocellulosic hydrolysates. PMID:25444880

  2. Illuminating the landscape of host–pathogen interactions with the bacterium Listeria monocytogenes

    PubMed Central

    Cossart, Pascale

    2011-01-01

    Listeria monocytogenes has, in 25 y, become a model in infection biology. Through the analysis of both its saprophytic life and infectious process, new concepts in microbiology, cell biology, and pathogenesis have been discovered. This review will update our knowledge on this intracellular pathogen and highlight the most recent breakthroughs. Promising areas of investigation such as the increasingly recognized relevance for the infectious process, of RNA-mediated regulations in the bacterium, and the role of bacterially controlled posttranslational and epigenetic modifications in the host will also be discussed. PMID:22114192

  3. Dissolution of Fe(III)(hydr)oxides by an Aerobic Bacterium

    SciTech Connect

    Maurice, P.

    2004-12-13

    This project investigated the effects of an aerobic Pseudomonas mendocina bacterium on the dissolution of Fe(III)(hydr)oxides. The research is important because metals and radionuclides that adsorb to Fe(III)(hydr)oxides could potentially be remobilized by dissolving bacteria. We showed that P. mendocina is capable of dissolving Fe-bearing minerals by a variety of mechanisms, including production of siderophores, pH changes, and formation of reductants. The production of siderophores by P. mendocina was quantified under a variety of growth conditions. Finally, we demonstrated that microbial siderophores may adsorb to and enhance dissolution of clay minerals.

  4. Complete genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344.

    PubMed

    Wibberg, Daniel; Luque-Almagro, Víctor M; Igeño, Ma Isabel; Bremges, Andreas; Roldán, Ma Dolores; Merchán, Faustino; Sáez, Lara P; Guijo, Ma Isabel; Manso, Ma Isabel; Macías, Daniel; Cabello, Purificación; Becerra, Gracia; Ibáñez, Ma Isabel; Carmona, Ma Isabel; Escribano, Ma María Paz; Castillo, Francisco; Sczyrba, Alexander; Moreno-Vivián, Conrado; Blasco, Rafael; Pühler, Alfred; Schlüter, Andreas

    2014-04-10

    Pseudomonas pseudoalcaligenes CECT5344, a Gram-negative bacterium isolated from the Guadalquir River (Córdoba, Spain), is able to utilize different cyano-derivatives. Here, the complete genome sequence of P. pseudoalcaligenes CECT5344 harboring a 4,686,340bp circular chromosome encoding 4513 genes and featuring a GC-content of 62.34% is reported. Necessarily, remaining gaps in the genome had to be closed by assembly of few long reads obtained from PacBio single molecule real-time sequencing. Here, the first complete genome sequence for the species P. pseudoalcaligenes is presented. PMID:24553071

  5. Coarse grained simulation reveals antifreeze properties of hyperactive antifreeze protein from Antarctic bacterium Colwellia sp.

    NASA Astrophysics Data System (ADS)

    Nguyen, Hung; Van, Thanh Dac; Le, Ly

    2015-10-01

    The novel hyperactive antifreeze protein (AFP) of Antarctic sea ice bacterium Colwellia sp. provides a target for studying the protection of psychrophilic microgoranisms against freezing environment. Interestingly, the Colwellia sp. hyperactive antifreeze protein (ColAFP) was crystallized without the structural dynamic characteristics. Here, the result indicated, through coarse grained simulation of ColAFP under various subfreezing temperature, that ColAFP remains active at temperature of equal and greater than 275 K (∼2 °C). Extensive simulation analyses also revealed the adaptive mechanism of ColAFP in subfreezing environment. Our result provides a structural dynamic understanding of the ColAFP.

  6. Chronic granulomatous disease: fatal septicemia caused by an unnamed gram-negative bacterium.

    PubMed Central

    Seger, R A; Hollis, D G; Weaver, R E; Hitzig, W H

    1982-01-01

    A 2-year-old boy with proven X-linked chronic granulomatous disease was placed under continuous co-trimoxazole prophylaxis. He remained free of infection for 4 years. At age 6.25 years, he suddenly developed a fever with no localizing signs and died 16 days later in septic shock. A gram-negative, catalase-positive, halophilic, aerobic bacterium was cultured from blood, bone marrow, and ascitic fluid. This organism could not be identified in microbiological laboratories in Europe and the United States. Its biochemical features indicate that it may belong to a species which has not previously been described. PMID:7153335

  7. Complete Genome Sequence of the Filamentous Anoxygenic Phototrophic Bacterium Chloroflexus aurantiacus

    SciTech Connect

    Tang, Kuo-Hsiang; Barry, Kerrie; Chertkov, Olga; Dalin, Eileen; Han, Cliff; Hauser, Loren John; Honchak, Barbara M; Karbach, Lauren E; Land, Miriam L; Lapidus, Alla L.; Larimer, Frank W; Mikhailova, Natalia; Pitluck, Sam; Pierson, Beverly K

    2011-01-01

    Chloroflexus aurantiacus is a thermophilic filamentous anoxygenic phototrophic (FAP) bacterium, and can grow phototrophically under anaerobic conditions or chemotrophically under aerobic and dark conditions. According to 16S rRNA analysis, Chloroflexi species are the earliest branching bacteria capable of photosynthesis, and Cfl. aurantiacus has been long regarded as a key organism to resolve the obscurity of the origin and early evolution of photosynthesis. Cfl. aurantiacus contains a chimeric photosystem that comprises some characters of green sulfur bacteria and purple photosynthetic bacteria, and also has some unique electron transport proteins compared to other photosynthetic bacteria.

  8. Numerical Simulation of the Twitching Motility of Bacterium Crawling on a Solid Surface

    NASA Astrophysics Data System (ADS)

    Morikawa, Ryota; Tamakoshi, Masatada; Miyakawa, Takeshi; Takasu, Masako

    A dynamics model of bacterial twitching motility is devised. A bacterial body is bound on a plane surface and driven by multiple type IV pili (TFP) which are appendages of the bacterium. The drag force following Stokes' law also applies to the bacterial body in the viscous fluid. By using the individual model, the numerical simulations are performed and the velocities and the rotational velocity of the bacterial body are investigated. From the results of the simulations, a rapid motion with rotationcalled slingshot, which was found in P. aeruginosa, is reproduced. There is a possibility that the slingshot motion may be carried out widely in many species of bacteria having TFP.

  9. Bisucaberin B, a linear hydroxamate class siderophore from the marine bacterium Tenacibaculum mesophilum.

    PubMed

    Fujita, Masaki J; Nakano, Koji; Sakai, Ryuichi

    2013-01-01

    A siderophore, named bisucaberin B, was isolated from Tenacibaculum mesophilum bacteria separated from a marine sponge collected in the Republic of Palau. Using spectroscopic and chemical methods, the structure of bisucaberin B (1) was clearly determined to be a linear dimeric hydroxamate class siderophore. Although compound 1 is an open form of the known macrocyclic dimer bisucaberin (2), and was previously described as a bacterial degradation product of desferrioxamine B (4), the present report is the first description of the de novo biosynthesis of 1. To the best of our knowledge, compound 1 is the first chemically characterized siderophore isolated from a bacterium belonging to the phylum Bacteroidetes. PMID:23549298

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

    PubMed

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

    2016-06-10

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

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

    USGS Publications Warehouse

    Wolfe-Simon, Felisa; 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.C.W.; Anbar, A.D.; Oremland, R.S.

    2011-01-01

    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, 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.

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

    NASA Astrophysics Data System (ADS)

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

    2006-12-01

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

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

    SciTech Connect

    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.

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

    PubMed Central

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

    2016-01-01

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

  15. Response to Comments on "A Bacterium That Can Grow Using Arsenic Instead of Phosphorus"

    SciTech Connect

    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

    2011-03-07

    Concerns have been raised about our recent study describing a bacterium that can grow using arsenic (As) instead of phosphorus (P). Our data suggested that As could act as a substitute for P in major biomolecules in this organism. Although the issues raised are of investigative interest, we contend that they do not invalidate our conclusions. We argue that while no single line of evidence we presented was sufficient to support our interpretation of the data, taken as an entire dataset we find no plausible alternative to our conclusions. Here we reply to the critiques and provide additional arguments supporting the assessment of the data we reported.

  16. Clostridium perfringens: a flesh-eating bacterium living in your garden.

    PubMed

    Rothwell, Ann

    2010-10-01

    Gas gangrene is a painful, rapidly developing and potentially fatal infection despite antibiotic treatment. During the First World War thousands of soldiers died from this disease. Dr Alexis Carrel pioneered a controversial method of irrigating wounds with Dakin's solution to destroy Clostridium perfringens, a bacterium found in heavily fertilised soils that causes gas gangrene. Although this method is no longer used due to the discovery of antibiotics, many of his other ideas, such as scientifically determining the type and number of bacteria and delaying the closure of a wound until the bacteria had been eradicated, are still used today. PMID:21049805

  17. Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2T

    DOE PAGESBeta

    Berben, Tom; Sorokin, Dimitry Y.; Ivanova, Natalia; Pati, Amrita; Kyrpides, Nikos; Goodwin, Lynne A.; Woyke, Tanja; Muyzer, Gerard

    2015-10-26

    Thioalkalivibrio thiocyanoxidans strain ARh 2T is a sulfur-oxidizing bacterium isolated from haloalkaline soda lakes. It is a motile, Gram-negative member of the Gammaproteobacteria. Remarkable properties include the ability to grow on thiocyanate as the sole energy, sulfur and nitrogen source, and the capability of growth at salinities of up to 4.3 M total Na+. This draft genome sequence consists of 61 scaffolds comprising 2,765,337 bp, and contains 2616 protein-coding and 61 RNA-coding genes. In conclusion, this organism was sequenced as part of the Community Science Program of the DOE Joint Genome Institute.

  18. An O2-sensing stressosome from a Gram-negative bacterium

    PubMed Central

    Jia, Xin; Wang, Jian-bo; Rivera, Shannon; Duong, Duc; Weinert, Emily E.

    2016-01-01

    Bacteria have evolved numerous pathways to sense and respond to changing environmental conditions, including, within Gram-positive bacteria, the stressosome complex that regulates transcription of general stress response genes. However, the signalling molecules recognized by Gram-positive stressosomes have yet to be identified, hindering our understanding of the signal transduction mechanism within the complex. Furthermore, an analogous pathway has yet to be described in Gram-negative bacteria. Here we characterize a putative stressosome from the Gram-negative bacterium Vibrio brasiliensis. The sensor protein RsbR binds haem and exhibits ligand-dependent control of the stressosome complex activity. Oxygen binding to the haem decreases activity, while ferrous RsbR results in increased activity, suggesting that the V. brasiliensis stressosome may be activated when the bacterium enters anaerobic growth conditions. The findings provide a model system for investigating ligand-dependent signalling within stressosome complexes, as well as insights into potential pathways controlled by oxygen-dependent signalling within Vibrio species. PMID:27488264

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

    PubMed

    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. PMID:26086561

  20. A highly infective plant-associated bacterium influences reproductive rates in pea aphids

    PubMed Central

    Hendry, Tory A.; Clark, Kelley J.; Baltrus, David A.

    2016-01-01

    Pea aphids, Acyrthosiphon pisum, have the potential to increase reproduction as a defence against pathogens, though how frequently this occurs or how infection with live pathogens influences this response is not well understood. Here we determine the minimum infective dose of an environmentally common bacterium and possible aphid pathogen, Pseudomonas syringae, to determine the likelihood of pathogenic effects to pea aphids. Additionally, we used P. syringae infection to investigate how live pathogens may alter reproductive rates. We found that oral bacterial exposure decreased subsequent survival of aphids in a dose-dependent manner and we estimate that ingestion of less than 10 bacterial cells is sufficient to increase aphid mortality. Pathogen dose was positively related to aphid reproduction. Aphids exposed to low bacterial doses showed decreased, although statistically indistinguishable, fecundity compared to controls. Aphids exposed to high doses reproduced significantly more than low dose treatments and also more, but not significantly so, than controls. These results are consistent with previous studies suggesting that pea aphids may use fecundity compensation as a response to pathogens. Consequently, even low levels of exposure to a common plant-associated bacterium may therefore have significant effects on pea aphid survival and reproduction. PMID:26998321

  1. Application of DNA adductomics to soil bacterium Sphingobium sp. strain KK22.

    PubMed

    Kanaly, Robert A; Micheletto, Ruggero; Matsuda, Tomonari; Utsuno, Youko; Ozeki, Yasuhiro; Hamamura, Natsuko

    2015-10-01

    Toward the development of ecotoxicology methods to investigate microbial markers of impacts of hydrocarbon processing activities, DNA adductomic analyses were conducted on a sphingomonad soil bacterium. From growing cells that were exposed or unexposed to acrolein, a commonly used biocide in hydraulic fracturing processes, DNA was extracted, digested to 2'-deoxynucleosides and analyzed by liquid chromatography-positive ionization electrospray-tandem mass spectrometry in selected reaction monitoring mode transmitting the [M + H](+) > [M + H - 116](+) transition over 100 transitions. Overall data shown as DNA adductome maps revealed numerous putative DNA adducts under both conditions with some occurring specifically for each condition. Adductomic analyses of triplicate samples indicated that elevated levels of some targeted putative adducts occurred in exposed cells. Two exposure-specific adducts were identified in exposed cells as 3-(2'-deoxyribosyl)-5,6,7,8-tetrahydro-6-hydroxy-(and 8-hydroxy-)pyrimido[1,2-a]- purine-(3H)-one (6- and 8-hydroxy-PdG) following synthesis of authentic standards of these compounds and subsequent analyses. A time course experiment showed that 6- and 8-hydroxy-PdG were detected in bacterial DNA within 30 min of acrolein exposure but were not detected in unexposed cells. This work demonstrated the first application of DNA adductomics to examine DNA damage in a bacterium and sets a foundation for future work. PMID:26305056

  2. Melanin from the Nitrogen-Fixing Bacterium Azotobacter chroococcum: A Spectroscopic Characterization

    PubMed Central

    Banerjee, Raja

    2014-01-01

    Melanins, the ubiquitous hetero-polymer pigments found widely dispersed among various life forms, are usually dark brown/black in colour. Although melanins have variety of biological functions, including protection against ultraviolet radiation of sunlight and are used in medicine, cosmetics, extraction of melanin from the animal and plant kingdoms is not an easy task. Using complementary physicochemical techniques (i.e. MALDI-TOF, FTIR absorption and cross-polarization magic angle spinning solid-state 13C NMR), we report here the characterization of melanins extracted from the nitrogen-fixing non-virulent bacterium Azotobacter chroococcum, a safe viable source. Moreover, considering dihydroxyindole moiety as the main constituent, an effort is made to propose the putative molecular structure of the melanin hetero-polymer extracted from the bacterium. Characterization of the melanin obtained from Azotobacter chroococcum would provide an inspiration in extending research activities on these hetero-polymers and their use as protective agent against UV radiation. PMID:24416247

  3. The effect of low pH on protein expression by the probiotic bacterium Lactobacillus reuteri.

    PubMed

    Lee, KiBeom; Lee, Hong-Gu; Pi, KyungBae; Choi, Yun-Jaie

    2008-04-01

    The ability of a lactic acid bacterium to survive passage through the gastrointestinal tract is a key point in its function as a probiotic. In this study, protein synthesis by the probiotic bacterium, Lactobacillus reuteri, was analyzed under transiently decreased pH conditions. L. reuteri cells grown to the midexponential growth phase at 37 degrees C were exposed to transient (1 h) low-pH stresses from pH 6.8 to pH 5.0, 4.5, or 4.0. 2-DE allowed us to identify 40 common proteins that were consistently and significantly altered under all three low-pH conditions. PMF was used to identify these 40 proteins, and functional annotation allowed them to be distributed to six major classes: (i) transport and binding proteins; (ii) transcription-translation; (iii) nucleotide metabolism and amino acid biosynthesis; (iv) carbon energy metabolism; (v) pH homeostasis and stress; and (vi) unassigned. These findings provide new insight into the inducible mechanisms underlying the capacity of gastrointestinal L. reuteri to tolerate acid stress. PMID:18351691

  4. Accurate Cell Division in Bacteria: How Does a Bacterium Know Where its Middle Is?

    NASA Astrophysics Data System (ADS)

    Howard, Martin; Rutenberg, Andrew

    2004-03-01

    I will discuss the physical principles lying behind the acquisition of accurate positional information in bacteria. A good application of these ideas is to the rod-shaped bacterium E. coli which divides precisely at its cellular midplane. This positioning is controlled by the Min system of proteins. These proteins coherently oscillate from end to end of the bacterium. I will present a reaction-diffusion model that describes the diffusion of the Min proteins, and their binding/unbinding from the cell membrane. The system possesses an instability that spontaneously generates the Min oscillations, which control accurate placement of the midcell division site. I will then discuss the role of fluctuations in protein dynamics, and investigate whether fluctuations set optimal protein concentration levels. Finally I will examine cell division in a different bacteria, B. subtilis. where different physical principles are used to regulate accurate cell division. See: Howard, Rutenberg, de Vet: Dynamic compartmentalization of bacteria: accurate division in E. coli. Phys. Rev. Lett. 87 278102 (2001). Howard, Rutenberg: Pattern formation inside bacteria: fluctuations due to the low copy number of proteins. Phys. Rev. Lett. 90 128102 (2003). Howard: A mechanism for polar protein localization in bacteria. J. Mol. Biol. 335 655-663 (2004).

  5. Extreme furfural tolerance of a soil bacterium Enterobacter cloacae GGT036.

    PubMed

    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. PMID:25444876

  6. Novel detoxification of the trichothecene mycotoxin deoxynivalenol by a soil bacterium isolated by enrichment culture.

    PubMed Central

    Shima, J; Takase, S; Takahashi, Y; Iwai, Y; Fujimoto, H; Yamazaki, M; Ochi, K

    1997-01-01

    A mixed microbial culture capable of metabolizing deoxynivalenol was obtained from soil samples by an enrichment culture procedure. A bacterium (strain E3-39) isolated from the enrichment culture completely removed exogenously supplied deoxynivalenol from culture medium after incubation for 1 day. On the basis of morphological, physiological, and phylogenetic studies, strain E3-39 was classified as a bacterium belonging to the Agrobacterium-Rhizobium group. Thin-layer chromatographic analysis indicated the presence of one major and two minor metabolites of deoxynivalenol in ethyl acetate extracts of the E3-39 culture filtrates. The main metabolite was identified as 3-keto-4-deoxynivalenol by mass spectroscopy and 1H and 13C nuclear magnetic resonance analysis. The immunosuppressive toxicity of 3-keto-4-deoxynivalenol was evaluated by means of a bioassay based on the mitogen-induced and mitogen-free proliferations of mouse spleen lymphocytes. This compound exhibited a remarkably decreased (to less than one tenth) immunosuppressive toxicity relative to deoxynivalenol, indicating that the 3-OH group in deoxynivalenol is likely to be involved in exerting its immunosuppressive toxicity. Strain E3-39 was also capable of transforming 3-acetyldeoxynivalenol but not nivalenol and fusarenon-X. PMID:9327545

  7. Inflammasomes Coordinate Pyroptosis and Natural Killer Cell Cytotoxicity to Clear Infection by a Ubiquitous Environmental Bacterium.

    PubMed

    Maltez, Vivien I; Tubbs, Alan L; Cook, Kevin D; Aachoui, Youssef; Falcone, E Liana; Holland, Steven M; Whitmire, Jason K; Miao, Edward A

    2015-11-17

    Defective neutrophils in patients with chronic granulomatous disease (CGD) cause susceptibility to extracellular and intracellular infections. Microbes must first be ejected from intracellular niches to expose them to neutrophil attack, so we hypothesized that inflammasomes detect certain CGD pathogens upstream of neutrophil killing. Here, we identified one such ubiquitous environmental bacterium, Chromobacterium violaceum, whose extreme virulence was fully counteracted by the NLRC4 inflammasome. Caspase-1 protected via two parallel pathways that eliminated intracellular replication niches. Pyroptosis was the primary bacterial clearance mechanism in the spleen, but both pyroptosis and interleukin-18 (IL-18)-driven natural killer (NK) cell responses were required for liver defense. NK cells cleared hepatocyte replication niches via perforin-dependent cytotoxicity, whereas interferon-γ was not required. These insights suggested a therapeutic approach: exogenous IL-18 restored perforin-dependent cytotoxicity during infection by the inflammasome-evasive bacterium Listeria monocytogenes. Therefore, inflammasomes can trigger complementary programmed cell death mechanisms, directing sterilizing immunity against intracellular bacterial pathogens. PMID:26572063

  8. Non-specific immune response of bullfrog Rana catesbeiana to intraperitoneal injection of bacterium Aeromonas hydrophila

    NASA Astrophysics Data System (ADS)

    Zhang, Junjie; Zou, Wenzheng; Yan, Qingpi

    2008-08-01

    Non-specific immune response of bullfrog Rana catesbeiana to pathogenic Aeromonas hydrophila was studied to 60 individuals in two groups. Each bullfrog in bacterium-injected group was injected intraperitoneally (i.p.) with 0.2 ml bacterial suspension at a density of 5.2 × 106 CFU/ml, while each one in control group injected i.p. with 0.2 ml sterile saline solution (0.85%, w/v). Three bullfrogs in both groups were sampled at 0, 1, 3, 7, 11, 15 and 20 days post-injection (dpi) for the evaluation of non-specific immune parameters. It was observed that intraperitoneal injection of A. hydrophila significantly increased the number of leucocytes and that of NBT-positive cells in peripheral blood. Significant increases in serum bactericidal activity and serum acid phosphatase activity were also observed in the bacterium-injected frogs when compared with those in the control group. However, a significant reduction was detected in vitro in phagocytosis activity of peripheral blood phagocytes. No significant difference in changes in the number of peripheral erythrocytes, serum superoxide dismutase (SOD) activity, and lysozyme activity was detected between the two groups. It is suggested that bullfrogs may produce a series of non-specific immune reactions in response to the A. hydrophila infection.

  9. Root-to-Root Travel of the Beneficial Bacterium Azospirillum brasilense†

    PubMed Central

    Bashan, Yoav; Holguin, Gina

    1994-01-01

    The root-to-root travel of the beneficial bacterium Azospirillum brasilense on wheat and soybean roots in agar, sand, and light-textured soil was monitored. We used a motile wild-type (Mot+) strain and a motility-deficient (Mot-) strain which was derived from the wild-type strain. The colonization levels of inoculated roots were similar for the two strains. Mot+ cells moved from inoculated roots (either natural or artificial roots in agar, sand, or light-textured soil) to noninoculated roots, where they formed a band-type colonization composed of bacterial aggregates encircling a limited part of the root, regardless of the plant species. The Mot- strain did not move toward noninoculated roots of either plant species and usually stayed at the inoculation site and root tips. The effect of attractants and repellents was the primary factor governing the motility of Mot+ cells in the presence of adequate water. We propose that interroot travel of A. brasilense is an essential preliminary step in the root-bacterium recognition mechanism. Bacterial motility might have a general role in getting Azospirillum cells to the site where firmer attachment favors colonization of the root system. Azospirillum travel toward plants is a nonspecific active process which is not directly dependent on nutrient deficiency but is a consequence of a nonspecific bacterial chemotaxis, influenced by the balance between attractants and possibly repellents leaked by the root. PMID:16349297

  10. A cambialistic superoxide dismutase in the thermophilic photosynthetic bacterium Chloroflexus aurantiacus.

    PubMed

    Lancaster, Vanessa L; LoBrutto, Russell; Selvaraj, Fabiyola M; Blankenship, Robert E

    2004-06-01

    Superoxide dismutase from the thermophilic anoxygenic photosynthetic bacterium Chloroflexus aurantiacus was cloned, purified, and characterized. This protein is in the manganese- and iron-containing family of superoxide dismutases and is able to use both manganese and iron catalytically. This appears to be the only soluble superoxide dismutase in C. aurantiacus. Iron and manganese cofactors were identified by using electron paramagnetic resonance spectroscopy and were quantified by atomic absorption spectroscopy. By metal enrichment of growth media and by performing metal fidelity studies, the enzyme was found to be most efficient with manganese incorporated, yet up to 30% of the activity was retained with iron. Assimilation of iron or manganese ions into superoxide dismutase was also found to be affected by the growth conditions. This enzyme was also found to be remarkably thermostable and was resistant to H2O2 at concentrations up to 80 mM. Reactive oxygen defense mechanisms have not been previously characterized in the organisms belonging to the phylum Chloroflexi. These systems are of interest in C. aurantiacus since this bacterium lives in a hyperoxic environment and is subject to high UV radiation fluxes. PMID:15150226

  11. Roseovarius aquimarinus sp. nov., a slightly halophilic bacterium isolated from seawater.

    PubMed

    Kang, Hyeonji; Kim, Jong-Hwa; Jeon, Che Ok; Yoon, Jung-Hoon; Kim, Wonyong

    2015-12-01

    A Gram-stain-negative, non-spore-forming, rod-shaped, motile, facultatively anaerobic bacterium, designated CAU 1059T, was isolated from a seawater sample from Jeju Island, Republic of Korea. The bacterium grew optimally at 37 °C, at pH 7.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CAU 1059T belonged to the genus Roseovarius. It exhibited only 91.5-96.9 % sequence similarity to the type strains of recognized Roseovarius species. Similar to other species of the genus Roseovarius, strain CAU 1059T had ubiquinone-10 (Q-10) as the predominant ubiquinone and C16 : 0 and summed feature 8 (C18 : 1ω7c/ω6c) as the major fatty acids. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine; three unidentified phospholipids, two aminolipids, an aminophospholipid and nine other lipids were also found. The G+C content of the genomic DNA was 61.9 mol%. On the basis of the data provided, strain CAU 1059T should be classified as representing a novel species of the genus Roseovarius, for which the name Roseovarius aquimarinus sp. nov. is proposed. The type strain is CAU 1059T ( = KCTC 32014T = CCUG 64792T). PMID:26374629

  12. Isolation, cloning and characterization of an azoreductase from the halophilic bacterium Halomonas elongata.

    PubMed

    Eslami, Maryam; Amoozegar, Mohammad Ali; Asad, Sedigheh

    2016-04-01

    Azo dyes are a major class of colorants used in various industries including textile, paper and food. These dyes are regarded as pollutant since they are not readily reduced under aerobic conditions. Halomonas elongata, a halophilic bacterium, has the ability to decolorize different mono and di-azo dyes in anoxic conditions. In this study the putative azoreductase gene of H. elongata, formerly annotated as acp, was isolated, heterologously expressed in Escherichia coli, purified and characterized. The gene product, AzoH, was found to have a molecular mass of 22 kDa. The enzyme requires NADH, as an electron donor for its activity. The apparent Km was 63 μM for NADH and 12 μM for methyl red as a mono-azo dye substrate. The specific activity for methyl red was 0.27 μmol min(-1)mg(-1). The optimum enzyme activity was achieved in 50mM sodium phosphate buffer at pH 6. Although increased salinity resulted in reduced activity, AzoH could decolorize azo dye at NaCl concentrations up to 15% (w/v). The enzyme was also shown to be able to decolorize remazol black B as a representative of di-azo dyes. This is the first report describing the sequence and activity of an azo-reducing enzyme from a halophilic bacterium. PMID:26724685

  13. Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Produces N-Acyl-Homoserine Lactone Autoinducers

    PubMed Central

    Bottomley, Peter J.

    2015-01-01

    Nitrobacter winogradskyi is a chemolithotrophic bacterium that plays a role in the nitrogen cycle by oxidizing nitrite to nitrate. Here, we demonstrate a functional N-acyl-homoserine lactone (acyl-HSL) synthase in this bacterium. The N. winogradskyi genome contains genes encoding a putative acyl-HSL autoinducer synthase (nwi0626, nwiI) and a putative acyl-HSL autoinducer receptor (nwi0627, nwiR) with amino acid sequences 38 to 78% identical to those in Rhodopseudomonas palustris and other Rhizobiales. Expression of nwiI and nwiR correlated with acyl-HSL production during culture. N. winogradskyi produces two distinct acyl-HSLs, N-decanoyl-l-homoserine lactone (C10-HSL) and a monounsaturated acyl-HSL (C10:1-HSL), in a cell-density- and growth phase-dependent manner, during batch and chemostat culture. The acyl-HSLs were detected by bioassay and identified by ultraperformance liquid chromatography with information-dependent acquisition mass spectrometry (UPLC-IDA-MS). The C=C bond in C10:1-HSL was confirmed by conversion into bromohydrin and detection by UPLC-IDA-MS. PMID:26092466

  14. Evaluation of nitrate removal by continuous culturing of an aerobic denitrifying bacterium, Paracoccus pantotrophus.

    PubMed

    Hasegawa-Kurisu, K; Otani, Y; Hanaki, K

    2006-01-01

    Nitrate removal under aerobic conditions was investigated using pure cultures of Paracoccus pantotrophus, which is a well-known aerobic-denitrifying (AD) bacterium. When a high concentration of cultures with a high carbon/nitrogen (C/N) ratio was preserved at the beginning of batch experiments, subsequently added nitrate was completely removed. When continuous culturing was perpetuated, a high nitrate removal rate (66.5%) was observed on day 4 post-culture, although gradual decreases in AD ability with time were observed. The attenuation in AD ability was probably caused by carbon limitation, because when carbon concentration of inflow water was doubled, nitrate removal efficiency improved from 18.1% to 59.6%. Bacterial community analysis using the polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) method showed that P. pantotrophus disappeared in the suspended medium on day 8 post-culture, whereas other bacterial communities dominated by Acidovorax sp. appeared. Interestingly, this replaced bacterial community also showed AD ability. As P. pantotrophus was detected as attached colonies around the membrane and bottom of the reactor, this bacterium can therefore be introduced in a fixed form for treatment of wastewater containing nitrate with a high C/N ratio. PMID:17163031

  15. Removal of arsenic from groundwater by using a native isolated arsenite-oxidizing bacterium.

    PubMed

    Kao, An-Chieh; Chu, Yu-Ju; Hsu, Fu-Lan; Liao, Vivian Hsiu-Chuan

    2013-12-01

    Arsenic (As) contamination of groundwater is a significant public health concern. In this study, the removal of arsenic from groundwater using biological processes was investigated. The efficiency of arsenite (As(III)) bacterial oxidation and subsequent arsenate (As(V)) removal from contaminated groundwater using bacterial biomass was examined. A novel As(III)-oxidizing bacterium (As7325) was isolated from the aquifer in the blackfoot disease (BFD) endemic area in Taiwan. As7325 oxidized 2300μg/l As(III) using in situ As(III)-contaminated groundwater under aerobic conditions within 1d. After the oxidation of As(III) to As(V), As(V) removal was further examined using As7325 cell pellets. The results showed that As(V) could be adsorbed efficiently by lyophilized As7325 cell pellets, the efficiency of which was related to lyophilized cell pellet concentration. Our study conducted the examination of an alternative technology for the removal of As(III) and As(V) from groundwater, indicating that the oxidation of As(III)-contaminated groundwater by native isolated bacterium, followed by As(V) removal using bacterial biomass is a potentially effective technology for the treatment of As(III)-contaminated groundwater. PMID:24096199

  16. Development of a gene cloning system for the hydrogen-producing marine photosynthetic bacterium Rhodopseudomonas sp.

    PubMed Central

    Matsunaga, T; Matsunaga, N; Tsubaki, K; Tanaka, T

    1986-01-01

    Seventy-six strains of marine photosynthetic bacteria were analyzed by agarose gel electrophoresis for plasmid DNA content. Among these strains, 12 carried two to four different plasmids with sizes ranging from 3.1 to 11.0 megadaltons. The marine photosynthetic bacterium Rhodopseudomonas sp. NKPB002106 had two plasmids, pRD06S and pRD06L. The smaller plasmid, pRD06S, had a molecular weight of 3.8 megadaltons and was cut at a single site by restriction endonucleases SalI, SmaI, PstI, XhoI, and BglII. Moreover, the marine photosynthetic bacterium Rhodopseudomonas sp. NKPB002106 containing plasmid pRD06 had a satisfactory growth rate (doubling time, 7.5 h), a hydrogen-producing rate of 0.96 mumol/mg (dry weight) of cells per h, and nitrogen fixation capability. Plasmid pRD06S, however, had neither drug resistance nor heavy-metal resistance, and its copy number was less than 10. Therefore, a recombinant plasmid consisting of pRD06S and Escherichia coli cloning vector pUC13 was constructed and cloned in E. coli. The recombinant plasmid was transformed into Rhodopseudomonas sp. NKPB002106. As a result, Rhodopseudomonas sp. NKPB002106 developed ampicillin resistance. Thus, a shuttle vector for gene transfer was constructed for marine photosynthetic bacteria. PMID:3020006

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

    PubMed

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

    2016-01-01

    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. PMID:26860259

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

    PubMed Central

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

    2016-01-01

    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. PMID:26860259

  19. Biogenesis of antibacterial silver nanoparticles using the endophytic bacterium Bacillus cereus isolated from Garcinia xanthochymus

    PubMed Central

    Sunkar, Swetha; Nachiyar, C Valli

    2012-01-01

    Objective To synthesize the ecofriendly nanoparticles, which is viewed as an alternative to the chemical method which initiated the use of microbes like bacteria and fungi in their synthesis. Methods The current study uses the endophytic bacterium Bacillus cereus isolated from the Garcinia xanthochymus to synthesize the silver nanoparticles (AgNPs). The AgNPs were synthesized by reduction of silver nitrate solution by the endophytic bacterium after incubation for 3-5 d at room temperature. The synthesis was initially observed by colour change from pale white to brown which was confirmed by UV-Vis spectroscopy. The AgNPs were further characterized using FTIR, SEM-EDX and TEM analyses. Results The synthesized nanoparticles were found to be spherical with the size in the range of 20-40 nm which showed a slight aggregation. The energy-dispersive spectra of the nanoparticle dispersion confirmed the presence of elemental silver. The AgNPs were found to have antibacterial activity against a few pathogenic bacteria like Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Salmonella typhi and Klebsiella pneumoniae. Conclusions The endophytic bacteria identified as Bacillus cereus was able to synthesize silver nanoparticles with potential antibacterial activity. PMID:23593575

  20. Structural characterization of the lipid A from the LPS of the haloalkaliphilic bacterium Halomonas pantelleriensis.

    PubMed

    Carillo, Sara; Pieretti, Giuseppina; Casillo, Angela; Lindner, Buko; Romano, Ida; Nicolaus, Barbara; Parrilli, Michelangelo; Giuliano, Mariateresa; Cammarota, Marcella; Lanzetta, Rosa; Corsaro, Maria Michela

    2016-09-01

    Halomonas pantelleriensis DSM9661(Τ) is a Gram-negative haloalkaliphilic bacterium isolated from the sand of the volcanic Venus mirror lake, closed to seashore in the Pantelleria Island in the south of Italy. It is able to optimally grow in media containing 3-15 % (w/v) total salt and at pH between 9 and 10. To survive in these harsh conditions, the bacterium has developed several strategies that probably concern the bacteria outer membrane, a barrier regulating the exchange with the environment. In such a context, the lipopolysaccharides (LPSs), which are among the major constituent of the Gram-negative outer membrane, are thought to contribute to the restrictive membrane permeability properties. The structure of the lipid A family derived from the LPS of Halomonas pantelleriensis DSM 9661(T) is reported herein. The lipid A was obtained from the purified LPS by mild acid hydrolysis. The lipid A, which contains different numbers of fatty acids residues, and its partially deacylated derivatives were completely characterized by means of ESI FT-ICR mass spectrometry and chemical analysis. Preliminary immunological assays were performed, and a comparison with the lipid A structure of the phylogenetic proximal Halomonas magadiensis is also reported. PMID:27329160

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

    PubMed

    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. PMID:25188453

  2. Application of DNA adductomics to soil bacterium Sphingobium sp. strain KK22

    PubMed Central

    Kanaly, Robert A; Micheletto, Ruggero; Matsuda, Tomonari; Utsuno, Youko; Ozeki, Yasuhiro; Hamamura, Natsuko

    2015-01-01

    Toward the development of ecotoxicology methods to investigate microbial markers of impacts of hydrocarbon processing activities, DNA adductomic analyses were conducted on a sphingomonad soil bacterium. From growing cells that were exposed or unexposed to acrolein, a commonly used biocide in hydraulic fracturing processes, DNA was extracted, digested to 2′-deoxynucleosides and analyzed by liquid chromatography-positive ionization electrospray-tandem mass spectrometry in selected reaction monitoring mode transmitting the [M + H]+ > [M + H − 116]+ transition over 100 transitions. Overall data shown as DNA adductome maps revealed numerous putative DNA adducts under both conditions with some occurring specifically for each condition. Adductomic analyses of triplicate samples indicated that elevated levels of some targeted putative adducts occurred in exposed cells. Two exposure-specific adducts were identified in exposed cells as 3-(2′-deoxyribosyl)-5,6,7,8-tetrahydro-6-hydroxy-(and 8-hydroxy-)pyrimido[1,2-a]- purine-(3H)-one (6- and 8-hydroxy-PdG) following synthesis of authentic standards of these compounds and subsequent analyses. A time course experiment showed that 6- and 8-hydroxy-PdG were detected in bacterial DNA within 30 min of acrolein exposure but were not detected in unexposed cells. This work demonstrated the first application of DNA adductomics to examine DNA damage in a bacterium and sets a foundation for future work. PMID:26305056

  3. Biodegradation of Ethylene Glycol by a Salt-Requiring Bacterium1

    PubMed Central

    Gonzalez, Carlos F.; Taber, Willard A.; Zeitoun, M. A.

    1972-01-01

    A gram-negative nonmotile rod which was capable of using 1,2-14C-ethylene glycol as a sole carbon source for growth was isolated from a brine pond, Great Salt Lake, Utah. The bacterium (ATCC 27042) required at least 0.85% NaCl for growth and, although the chloride ion was replaceable by sulfate ion, the sodium ion was not replaceable by potassium ion. The maximal concentration of salt tolerated for growth was approximately 12%. The bacterium was oxidase-negative when N,N-dimethyl-p-phenylenediamine was used and weakly positive when N,N,N′,N′-tetramethyl-p-phenylenediamine was used. It grows on many sugars but does not ferment them, it does not have an exogenous vitamin requirement, and it possesses a guanine plus cytosine ratio of 64.3%. Incorporation of ethylene glycol carbon into cell and respired CO2 was quantitated by use of radioactive ethylene glycol and a force-aerated fermentor. Glucose suppressed ethylene glycol metabolism. Cells grown on ethylene and propylene glycol respired ethylene glycol in a Warburg respirometer more rapidly than cells grown on glucose. Spectrophotometric evidence was obtained for oxidation of glycolate to glyoxylate by a dialyzed cell extract. PMID:4568254

  4. Enrichment and physiological characterization of a novel Nitrospira-like bacterium obtained from a marine sponge.

    PubMed

    Off, Sandra; Alawi, Mashal; Spieck, Eva

    2010-07-01

    Members of the nitrite-oxidizing genus Nitrospira are most likely responsible for the second step of nitrification, the conversion of nitrite (NO(2)(-)) to nitrate (NO(3)(-)), within various sponges. We succeeded in obtaining an enrichment culture of Nitrospira derived from the mesohyl of the marine sponge Aplysina aerophoba using a traditional cultivation approach. Electron microscopy gave first evidence of the shape and ultrastructure of this novel marine Nitrospira-like bacterium (culture Aa01). We characterized these bacteria physiologically with regard to optimal incubation conditions, especially the temperature and substrate range in comparison to other Nitrospira cultures. Best growth was obtained at temperatures between 28 degrees C and 30 degrees C in mineral medium with 70% North Sea water and a substrate concentration of 0.5 mM nitrite under microaerophilic conditions. The Nitrospira culture Aa01 is very sensitive against nitrite, because concentrations higher than 1.5 mM resulted in a complete inhibition of growth. Sequence analyses of the 16S rRNA gene revealed that the novel Nitrospira-like bacterium is separated from the sponge-specific subcluster and falls together with an environmental clone from Mediterranean sediments (98.6% similarity). The next taxonomically described species Nitrospira marina is only distantly related, with 94.6% sequence similarity, and therefore the culture Aa01 represents a novel species of nitrite-oxidizing bacteria. PMID:20511427

  5. A symbiotic bacterium differentially influences arsenate absorption and transformation in Dunaliella salina under different phosphate regimes.

    PubMed

    Wang, Ya; Zhang, Chun Hua; Lin, Man Man; Ge, Ying

    2016-11-15

    In this study, we investigated the effects of a symbiotic bacterium and phosphate (PO4(3-)) nutrition on the toxicity and metabolism of arsenate (As(V)) in Dunaliella salina. The bacterium was identified as Alteromonas macleodii based on analysis of its 16S rRNA gene sequence. When no As(V) was added, A. macleodii significantly enhanced the growth of D. salina, irrespective of PO4(3-) nutrition levels, but this effect was reversed after As(V)+PO4(3-) treatment (1.12mgL(-1)) for 3 days. Arsenic (As) absorption by the non-axenic D. salina was significantly higher than that by its axenic counterpart during incubation with 1.12mgL(-1) PO4(3-). However, when the culture was treated with 0.112mgL(-1) PO4(3-), As(V) reduction and its subsequent arsenite (As(III)) excretion by non-axenic D. salina were remarkably enhanced, which, in turn, contributed to lower As absorption in non-axenic algal cells from days 7 to 9. Moreover, dimethylarsinic acid was synthesized by D. salina alone, and the rates of its production and excretion were accelerated when the PO4(3-) concentration was 0.112mgL(-1). Our data demonstrate that A. macleodii strongly affected As toxicity, uptake, and speciation in D. salina, and these impacts were mediated by PO4(3-) in the cultures. PMID:27450336

  6. The Complete Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis ssp. lactis IL1403

    PubMed Central

    Bolotin, Alexander; Wincker, Patrick; Mauger, Stéphane; Jaillon, Olivier; Malarme, Karine; Weissenbach, Jean; Ehrlich, S. Dusko; Sorokin, Alexei

    2001-01-01

    Lactococcus lactis is a nonpathogenic AT-rich gram-positive bacterium closely related to the genus Streptococcus and is the most commonly used cheese starter. It is also the best-characterized lactic acid bacterium. We sequenced the genome of the laboratory strain IL1403, using a novel two-step strategy that comprises diagnostic sequencing of the entire genome and a shotgun polishing step. The genome contains 2,365,589 base pairs and encodes 2310 proteins, including 293 protein-coding genes belonging to six prophages and 43 insertion sequence (IS) elements. Nonrandom distribution of IS elements indicates that the chromosome of the sequenced strain may be a product of recent recombination between two closely related genomes. A complete set of late competence genes is present, indicating the ability of L. lactis to undergo DNA transformation. Genomic sequence revealed new possibilities for fermentation pathways and for aerobic respiration. It also indicated a horizontal transfer of genetic information from Lactococcus to gram-negative enteric bacteria of Salmonella-Escherichia group. [The sequence data described in this paper has been submitted to the GenBank data library under accession no. AE005176.] PMID:11337471

  7. A highly infective plant-associated bacterium influences reproductive rates in pea aphids.

    PubMed

    Hendry, Tory A; Clark, Kelley J; Baltrus, David A

    2016-02-01

    Pea aphids, Acyrthosiphon pisum, have the potential to increase reproduction as a defence against pathogens, though how frequently this occurs or how infection with live pathogens influences this response is not well understood. Here we determine the minimum infective dose of an environmentally common bacterium and possible aphid pathogen, Pseudomonas syringae, to determine the likelihood of pathogenic effects to pea aphids. Additionally, we used P. syringae infection to investigate how live pathogens may alter reproductive rates. We found that oral bacterial exposure decreased subsequent survival of aphids in a dose-dependent manner and we estimate that ingestion of less than 10 bacterial cells is sufficient to increase aphid mortality. Pathogen dose was positively related to aphid reproduction. Aphids exposed to low bacterial doses showed decreased, although statistically indistinguishable, fecundity compared to controls. Aphids exposed to high doses reproduced significantly more than low dose treatments and also more, but not significantly so, than controls. These results are consistent with previous studies suggesting that pea aphids may use fecundity compensation as a response to pathogens. Consequently, even low levels of exposure to a common plant-associated bacterium may therefore have significant effects on pea aphid survival and reproduction. PMID:26998321

  8. A model of insect—pathogen dynamics in which a pathogenic bacterium can also reproduce saprophytically

    PubMed Central

    Godfray, H. C. J.; Briggs, C. J.; Barlow, N. D.; O'Callaghan, M.; Glare, T. R.; Jackson, T. A.

    1999-01-01

    We developed a model of the population dynamic interaction between an insect and a pathogenic bacterium motivated by study of Serratia entomophila, a commercially exploited pathogen of the New Zealand grass grub (Costelytra zealandica). The bacterium is able to reproduce saprophytically, though it competes for saprophytic substrates with non-pathogenic strains, which appear to be superior competitors, probably because they lack a plasmid that carries genes required for pathogenicity. The effect of saprophytism and competition on the invasion criterion (R0), short-term dynamics and long-term dynamics are described. Saprophytism can reduce (possibly to zero) the host threshold at which the pathogen can invade, though this reduction is less when there is competition with non-pathogenic strains. In a model of short-term population dynamics designed to mimic the application of bacteria to a host epizootic, saprophytism enhances the reduction in host density, though again this is tempered by competition with non-pathogens. In the long term, a pathogen that can develop saprophytically can drive its host to extinction in the absence of competition with non-pathogens. When the latter are present, host extinction is prevented. The addition of saprophytic reproduction can stabilize an otherwise unstable host–pathogen model, but we were unable to find a stable equilibrium given the further addition of a wholly saprophytic bacterial strain. The model suggests that enhancing or selecting for saprophytic ability could be a way of improving biological control.

  9. Pseudomonas sp. strain 273, and aerobic {alpha},{omega}-dichloroalkane-degrading bacterium

    SciTech Connect

    Wischnak, C.; Mueller, R.; Loeffler, F.E. |; Li, J.; Urbance, J.W.

    1998-09-01

    A gram-negative, aerobic bacterium was isolated from soil; this bacterium grew in 50% (vol/vol) suspensions of 1,10-dichlorodecane (1,10-DCD) as the sole source of carbon and energy. Phenotypic and small-subunit ribosomal RNA characterizations identified the organism, designated strain 273, as a member of the genus Pseudomonas. After induction with 1,10-DCD, Pseudomonas sp. strain 273 released stoichiometric amounts of chloride from C{sub 5} to C{sub 12} {alpha},{omega}-dichloroalkanes in the presence of oxygen. No dehalogenation occurred under anaerobic conditions. The best substrates for dehalogenation and growth were C{sub 9} to C{sub 12} chloroalkanes. The isolate also grew with nonhalogenated aliphatic compounds, and decane-grown cells dechlorinated 1,10-DCD without a lag phase. In addition, cells grown on decane dechlorinated 1,10-DCD in the presence of chloramphenicol, indicating that the 1,10-DCD-dechlorinating enzyme system was also induced by decane. Other known alkane-degrading Pseudomonas species did not grow with 1,10-DCD as a carbon source. Dechlorination of 1,10-DCD was demonstrated in cell extracts of Pseudomonas sp. strain 273. Cell-free activity was strictly oxygen dependent, and NADH stimulated dechlorination, whereas EDTA had an inhibitory effect.

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

    PubMed

    Simbahan, Jessica; Drijber, Rhae; Blum, Paul

    2004-09-01

    A thermo-acidophilic Gram-positive bacterium, strain CsHg2T, which grows aerobically at 35-65 degrees C (optimum 55 degrees C) and at pH 2.0-6.0 (optimum 4.0), was isolated from a geothermal pool located in Coso Hot Springs in the Mojave Desert, California, USA. Phylogenetic analysis of 16S rRNA gene sequences showed that this bacterium was most closely related to the type strains of Alicyclobacillus acidocaldarius (97.8 % identity) and Alicyclobacillus sendaiensis (96.9 %), three Japanese strains denoted as UZ-1, KHA-31 and MIH 332 (96.1-96.5 %) and Alicyclobacillus genomic species FR-6 (96.3 %). Phenotypic characteristics including temperature and pH optima, G+C composition, acid production from a variety of carbon sources and sensitivity to different metal salts distinguished CsHg2T from A. acidocaldarius, A. sendaiensis and FR-6. The cell lipid membrane was composed mainly of omega-cyclohexyl fatty acid, consistent with membranes from other Alicyclobacillus species. Very low DNA-DNA hybridization values between CsHg2T and the type strains of Alicyclobacillus indicate that CsHg2T represents a distinct species. On the basis of these results, the name Alicyclobacillus vulcanalis sp. nov. is proposed for this organism. The type strain is CsHg2T (ATCC BAA-915T = DSM 16176T). PMID:15388732

  11. Isolation, Identification and Characteristics of an Endophytic Quinclorac Degrading Bacterium Bacillus megaterium Q3

    PubMed Central

    Wang, Yunsheng; Zeng, Aiping; Zhou, Xiaomao; Luo, Feng; Bai, Lianyang

    2014-01-01

    In this study, we isolated an endophytic quinclorac-degrading bacterium strain Q3 from the root of tobacco grown in quinclorac contaminated soil. Based on morphological characteristics, Biolog identification, and 16S rDNA sequence analysis, we identified strain Q3 as Bacillus megaterium. We investigated the effects of temperature, pH, inoculation size, and initial quinclorac concentration on growth and degrading efficiency of Q3. Under the optimal degrading condition, Q3 could degrade 93% of quinclorac from the initial concentration of 20 mg/L in seven days. We analyzed the degradation products of quinclorac using liquid chromatography–tandem mass spectrometry (LC-MS/MS). The major degradation products by Q3 were different from those of previously identified quinclorac degrading strains, which suggests that Q3 may employ new pathways for quinclorac degradation. Our indoor pot experiments demonstrated that Q3 can effectively alleviate the quinclorac phytotoxicity in tobacco. As the first endophytic microbial that is capable of degrading quinclorac, Q3 can be a good bioremediation bacterium for quinclorac phytotoxicity. PMID:25244184

  12. Inhibitory effect of the natural product betulin and its derivatives against the intracellular bacterium Chlamydia pneumoniae.

    PubMed

    Salin, Olli; Alakurtti, Sami; Pohjala, Leena; Siiskonen, Antti; Maass, Viola; Maass, Matthias; Yli-Kauhaluoma, Jari; Vuorela, Pia

    2010-10-15

    Chlamydia pneumoniae is a universal pathogen that has been indicated to play a part in the development of asthma, atherosclerosis and lung cancer. The complete eradication of this intracellular bacterium is in practice impossible with the antibiotics that are currently in use and studies on new antichlamydial compounds is challenging because Chlamydia research lacks the tools required for the genetic modification of this bacterium. Betulin is a natural lupane-class triterpene derived from plants with a wide variety of biological activities. This compound group thus has wide medical potentials, and in fact has been shown to be active against intracellular pathogens. For this reason, betulin and its derivatives were selected to be assayed against C. pneumoniae in the present study. Thirty-two betulin derivatives were assayed against C. pneumoniae using an acute infection model in vitro. Five promising compounds with potential lead compound characteristics were identified. Compound 24 (betulin dioxime) gave a minimal inhibitory concentration (MIC) of 1 microM against strain CWL-029 and showed activity in nanomolar concentrations, as 50% inhibition was achieved at 290 nM. The antichlamydial effect of 24 was confirmed with a clinical isolate CV-6, showing a MIC of 2.2 microM. Previous research on betulin and its derivatives has not identified such a remarkable inhibition of Gram-negative bacterial growth. Furthermore, we also demonstrated that this antichlamydial activity was not due to PLA(2) (EC 3.1.1.4) inhibition caused by the betulin derivatives. PMID:20615390

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

    PubMed Central

    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 μm in diameter, and 2–8 μm in length, growing as single cells or in pairs. The cells grew optimally at 37°C, and the pH optimum was around 7. Strain An4 converted various alcohols, organic acids, fructose, acetoin, and H2/CO2 to acetate, usually as the only product. Succinate was decarboxylated to propionate. The isolate was able to respire with (per)chlorate, nitrate, and CO2. 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. PMID:20680263

  14. A Commensal Bacterium Promotes Virulence of an Opportunistic Pathogen via Cross-Respiration

    PubMed Central

    Stacy, Apollo; Fleming, Derek; Lamont, Richard J.; Rumbaugh, Kendra P.

    2016-01-01

    ABSTRACT Bacteria rarely inhabit infection sites alone, instead residing in diverse, multispecies communities. Despite this fact, bacterial pathogenesis studies primarily focus on monoculture infections, overlooking how community interactions influence the course of disease. In this study, we used global mutant fitness profiling (transposon sequencing [Tn-seq]) to determine the genetic requirements for the pathogenic bacterium Aggregatibacter actinomycetemcomitans to cause disease when coinfecting with the commensal bacterium Streptococcus gordonii. Our results show that S. gordonii extensively alters A. actinomycetemcomitans requirements for virulence factors and biosynthetic pathways during infection. In addition, we discovered that the presence of S. gordonii enhances the bioavailability of oxygen during infection, allowing A. actinomycetemcomitans to shift from a primarily fermentative to a respiratory metabolism that enhances its growth yields and persistence. Mechanistically, respiratory metabolism enhances the fitness of A. actinomycetemcomitans in vivo by increasing ATP yields via central metabolism and creating a proton motive force. Our results reveal that, similar to cross-feeding, where one species provides another species with a nutrient, commensal bacteria can also provide electron acceptors that promote the respiratory growth and fitness of pathogens in vivo, an interaction that we term cross-respiration. PMID:27353758

  15. Enzymatic properties of chitinase-producing antagonistic bacterium Paenibacillus chitinolyticus with various substrates.

    PubMed

    Song, Yong-Su; Seo, Dong-Jun; Ju, Wan-Taek; Lee, Yong-Seong; Jung, Woo-Jin

    2015-12-01

    Various chitin substrates were used to investigate the properties of enzymes produced from the chitinase-producing bacterium Paenibacillus chitinolyticus MP-306 against phytopathogens. The MP-306 bacterium was incubated in nine culture media [crab shell powder chitin (CRS), chitin-protein complex powder (CPC), carboxymethyl-chitin powder (CMC), yeast extract only (YE), LB (Trypton, NaCl, and yeast extract), GT (Trypton, NaCl, and glucose), crab shell colloidal chitin (CSC), squid pen powder chitin (SPC), and cicada slough powder chitin (CSP)] at 30 °C for 3 days. Chitinase isozymes in CPC medium were expressed strongly as CN1, CN2, CN3, CN4, CN5, and CN6 bands on native-PAGE gels. Chitinase isozymes in CPC and CMC medium were expressed as 13 bands (CS1-CS13) on SDS-PAGE gels. Chitinase isozymes were expressed strongly on SDS-PAGE gels as two bands (CS6 and CS8) on YE and LB medium and 13 bands (CS1-CS13) on SPC medium. In crude enzyme, chitinase isozymes at pH 7 and pH 9 in chitin media appeared strongly on SDS-PAGE gels. Partial purified enzyme indicated high stability of enzyme activity at various temperatures and pHs in chitin medium, while these enzymes indicated low activity staining of enzyme on electrophoresis gels at various temperatures and pHs condition of chitin medium. PMID:26546718

  16. Characterization of outer membrane vesicles released by the psychrotolerant bacterium Pseudoalteromonas antarctica NF3

    PubMed Central

    Nevot, Maria; Deroncelé, Víctor; Messner, Paul; Guinea, Jesús; Mercadé, Elena

    2015-01-01

    Summary Pseudoalteromonas antarctica NF3 is an Antarctic psychrotolerant Gram-negative bacterium that accumulates large amounts of an extracellular polymeric substance (EPS) with high protein content. Transmission electron microscopy analysis after high-pressure freezing and freeze substitution (HPF-FS) shows that the EPS is composed of a capsular polymer and large numbers of outer membrane vesicles (OMVs). These vesicles are bilayered structures and predominantly spherical in shape, with an average diameter of 25–70 nm, which is similar to what has been observed in OMVs from other Gram-negative bacteria. Analyses of lipopolysaccharide (LPS), phospholipids and protein profiles of OMVs are consistent with the bacterial outer membrane origin of these vesicles. In an initial attempt to elucidate the functions of OMVs proteins, we conducted a proteomic analysis on 1D SDS-PAGE bands. Those proteins putatively identified match with outer membrane proteins and proteins related to nutrient processing and transport in Gram-negative bacteria. This approach suggests that OMVs present in the EPS from P. antarctica NF3, might function to deliver proteins to the external media, and therefore play an important role in the survival of the bacterium in the extreme Antarctic environment. PMID:16913913

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

    PubMed

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

    2012-01-01

    A Gram-positive marine bacterium, Exiguobacterium sp. SBH81, was isolated as a hydrophilic organic-solvent tolerant bacterium, and exhibited high tolerance to various types of toxic hydrophilic organic solvents, including acetonitrile, at relatively high concentrations (up to 6% [v/v]) under the growing conditions. Investigation of its tolerance mechanisms illustrated that it does not rely on solvent inactivation processes or modification of cell surface characteristics, but rather, increase of the cell size lowers solvent partitioning into cells and the extrusion of solvents through the efflux system. A test using efflux pump inhibitors suggested that secondary transporters, i.e. resistance nodulation cell division (RND) and the multidrug and toxic compound extrusion (MATE) family, are involved in acetonitrile tolerance in this strain. In addition, its acetonitrile tolerance ability could be stably and significantly enhanced by repetitive growth in the presence of toxic acetonitrile. The marked acetonitrile tolerance of Exiguobacterium sp. SBH81 indicates its potential use as a host for biotechnological fermentation processes as well as bioremediation. PMID:21971080

  18. Genome Analysis of Thermosulfurimonas dismutans, the First Thermophilic Sulfur-Disproportionating Bacterium of the Phylum Thermodesulfobacteria.

    PubMed

    Mardanov, Andrey V; Beletsky, Alexey V; Kadnikov, Vitaly V; Slobodkin, Alexander I; Ravin, Nikolai V

    2016-01-01

    Thermosulfurimonas dismutans S95(T), isolated from a deep-sea hydrothermal vent is the first bacterium of the phylum Thermodesulfobacteria reported to grow by the disproportionation of elemental sulfur, sulfite, or thiosulfate with carbon dioxide as the sole carbon source. In contrast to its phylogenetically close relatives, which are dissimilatory sulfate-reducers, T. dismutans is unable to grow by sulfate respiration. The features of this organism and its 2,1 Mb draft genome sequence are described in this report. Genome analysis revealed that the T. dismutans genome contains the set of genes for dissimilatory sulfate reduction including ATP sulfurylase, the AprA and B subunits of adenosine-5'-phosphosulfate reductase, and dissimilatory sulfite reductase. The oxidation of elemental sulfur to sulfite could be enabled by APS reductase-associated electron transfer complex QmoABC and heterodisulfide reductase. The genome also contains several membrane-linked molybdopterin oxidoreductases that are thought to be involved in sulfur metabolism as subunits of thiosulfate, polysulfide, or tetrathionate reductases. Nitrate could be used as an electron acceptor and reduced to ammonium, as indicated by the presence of periplasmic nitrate and nitrite reductases. Autotrophic carbon fixation is enabled by the Wood-Ljungdahl pathway, and the complete set of genes that is required for nitrogen fixation is also present in T. dismutans. Overall, our results provide genomic insights into energy and carbon metabolism of chemolithoautotrophic sulfur-disproportionating bacterium that could be important primary producer in microbial communities of deep-sea hydrothermal vents. PMID:27379079

  19. Marinobacter hydrocarbonoclasticus NY-4, a novel denitrifying, moderately halophilic marine bacterium.

    PubMed

    Li, Rongpeng; Zi, Xiaoli; Wang, Xinfeng; Zhang, Xia; Gao, Haofeng; Hu, Nan

    2013-01-01

    The isolation and characterization of a novel halophilic denitrifying marine bacterium is described. The halophilic bacterium, designated as NY-4, was isolated from soil in Yancheng City, China, and identified as Marinobacter hydrocarbonoclasticus by 16S rRNA gene sequence phylogenetic analysis. This organism can grow in NaCl concentrations ranging from 20 to 120 g/L. Optimum growth occurs at 80 g/L NaCl and pH 8.0. The organism can grow on a broad range of carbon sources and demonstrated efficient denitrifying ability (94.2% of nitrate removal and 80.9% of total nitrogen removal in 48 h). During denitrification by NY-4, no NO2 (-)-N was accumulated, N2 was the only gaseous product and no harmful N2O was produced. Because of its rapid denitrification ability, broad carbon use range and ability to grow under high salinity and pH conditions, NY-4 holds promise for the treatment of saline waste waters. PMID:25538872

  20. Microfabrication of patterns of adherent marine bacterium Phaeobacter inhibens using soft lithography and scanning probe lithography.

    PubMed

    Zhao, Chuan; Burchardt, Malte; Brinkhoff, Thorsten; Beardsley, Christine; Simon, Meinhard; Wittstock, Gunther

    2010-06-01

    Two lithographic approaches have been explored for the microfabrication of cellular patterns based on the attachment of marine bacterium Phaeobacter inhibens strain T5. Strain T5 produces a new antibiotic that makes this bacterium potentially interesting for the pharmaceutical market and as a probiotic organism in aquacultures and in controlling biofouling. The microcontact printing (microCP) method is based on the micropatterning of self-assembled monolayers (SAMs) terminated with adhesive end groups such as CH(3) and COOH and nonadhesive groups (e.g., short oligomers of ethylene glycol (OEG)) to form micropatterned substrates for the adhesion of strain T5. The scanning probe lithographic method is based on the surface modification of OEG SAM by using a microelectrode, the probe of a scanning electrochemical microscope (SECM). Oxidizing agents (e.g., Br(2)) were electrogenerated in situ at the microelectrodes from Br(-) in aqueous solution to remove OEG SAMs locally, which allows the subsequent adsorption of bacteria. Various micropatterns of bacteria could be formed in situ on the substrate without a prefabricated template. The fabricated cellular patterns may be applied to a variety of marine biological studies that require the analysis of biofilm formation, cell-cell and cell-surface interactions, and cell-based biosensors and bioelectronics. PMID:20397716

  1. INDISIM-Paracoccus, an individual-based and thermodynamic model for a denitrifying bacterium.

    PubMed

    Araujo Granda, Pablo; Gras, Anna; Ginovart, Marta; Moulton, Vincent

    2016-08-21

    We have developed an individual-based model for denitrifying bacteria. The model, called INDISIM-Paracoccus, embeds a thermodynamic model for bacterial yield prediction inside the individual-based model INDISIM, and is designed to simulate the bacterial cell population behavior and the product dynamics within the culture. The INDISIM-Paracoccus model assumes a culture medium containing succinate as a carbon source, ammonium as a nitrogen source and various electron acceptors such as oxygen, nitrate, nitrite, nitric oxide and nitrous oxide to simulate in continuous or batch culture the different nutrient-dependent cell growth kinetics of the bacterium Paracoccus denitrificans. The individuals in the model represent microbes and the individual-based model INDISIM gives the behavior-rules that they use for their nutrient uptake and reproduction cycle. Three previously described metabolic pathways for P. denitrificans were selected and translated into balanced chemical equations using a thermodynamic model. These stoichiometric reactions are an intracellular model for the individual behavior-rules for metabolic maintenance and biomass synthesis and result in the release of different nitrogen oxides to the medium. The model was implemented using the NetLogo platform and it provides an interactive tool to investigate the different steps of denitrification carried out by a denitrifying bacterium. The simulator can be obtained from the authors on request. PMID:27179457

  2. Enrichment, isolation and characterization of pentachlorophenol degrading bacterium Acinetobacter sp. ISTPCP-3 from effluent discharge site.

    PubMed

    Sharma, Ashwani; Thakur, Indu Shekhar; Dureja, Prem

    2009-09-01

    Three pentachlorophenol (PCP) degrading bacterial strains were isolated from sediment core of pulp and paper mill effluent discharge site. The strains were continuously enriched in mineral salts medium supplemented with PCP as sole source of carbon and energy. One of the acclimated strains with relatively high PCP degradation capability was selected and characterized in this study. Based on morphology, biochemical tests, 16S rDNA sequence analysis and phylogenetic characteristics, the strains showed greatest similarity with Acinetobacter spp. The strain was identified as Acinetobacter sp. ISTPCP-3. The physiological characteristics and optimum growth conditions of the bacterial strain were investigated. The results of optimum growth temperature revealed that it was a mesophile. The optimum growth temperature for the strain was 30 degrees C. The preferential initial pH for the strain was ranging at 6.5-7.5, the optimum pH was 7. The bacterium was able to tolerate and degrade PCP up to a concentration of 200 mg/l. Increase in PCP concentration had a negative effect on biodegradation rate and PCP concentration above 250 mg/l was inhibitory to its growth. Acinetobacter sp. ISTPCP-3 was able to utilize PCP through an oxidative route with ortho ring-cleavage with the formation of 2,3,5,6-tetrachlorohydroquinone and 2-chloro-1,4-benzenediol, identified using gas chromatograph-mass spectrometric (GC-MS) analysis. The degradation pathway followed by isolated bacterium is different from previously characterized pathway. PMID:19214760

  3. Marine bacterium strain screening and pyrethroid insecticide-degrading efficiency analysis

    NASA Astrophysics Data System (ADS)

    Sun, Aili; Liu, Jinghua; Shi, Xizhi; Li, Dexiang; Chen, Jiong; Tang, Daojun

    2014-09-01

    A pyrethroid insecticide-degrading bacterium, strain HS-24, was isolated from an offshore seawater environment. The strain, which can degrade cypermethrin (CYP) and deltamethrin (DEL), was identified as Methylophaga sp. The optimal culture and degradation conditions for CYP and DEL by strain HS-24 is pH 7 at 28°C. Under optimum culture conditions, strain HS-24 exhibited a broad degradation concentration range of 100, 200, 400, 600, and 800 mg/L for CYP and DEL. The metabolic intermediates were analyzed by NMR, which provided strong evidence that CYP and DEL removal occurred mainly because of a biological process. The toxicity of the degradation products of strain HS-24 was studied simultaneously by measuring the light output of the luminescence bacterium. This demonstrated that the biodegradation ability of strain HS-24 significantly decreased the toxicity of CYP- and DEL-contaminated aquaculture seawater. Finally, the findings of this paper indicate that strain HS-24 is thus revealed as a biological agent for the remediation of marine aquatic environments.

  4. Geovibrio ferrireducens, a phylogenetically distinct dissimilatory Fe(III)-reducing bacterium

    USGS Publications Warehouse

    Caccavo, F., Jr.; Coates, J.D.; Rossello-Mora, R. A.; Ludwig, W.; Schleifer, K.H.; Lovley, D.R.; McInerney, M.J.

    1996-01-01

    A new, phylogenetically distinct, dissimilatory, Fe(III)-reducing bacterium was isolated from surface sediment of a hydrocarbon-contaminated ditch. The isolate, designated strain PAL-1, was an obligately anaerobic, non-fermentative, motile, gram-negative vibrio. PAL-1 grew in a defined medium with acetate as electron donor and ferric pyrophosphate, ferric oxyhydroxide, ferric citrate, Co(III)-EDTA, or elemental sulfur as sole electron acceptor. PAL-1 also used proline, hydrogen, lactate, propionate, succinate, fumarate, pyruvate, or yeast extract as electron donors for Fe(III) reduction. It is the first bacterium known to couple the oxidation of an amino acid to Fe(III) reduction. PAI-1 did not reduce oxygen, Mn(IV), U(VI), Cr(VI), nitrate, sulfate, sulfite, or thiosulfate with acetate as the electron donor. Cell suspensions of PAL-1 exhibited dithionite-reduced minus air-oxidized difference spectra that were characteristic of c-type cytochromes. Analysis of the 16S rRNA gene sequence of PAL-1 showed that the strain is not related to any of the described metal-reducing bacteria in the Proteobacteria and, together with Flexistipes sinusarabici, forms a separate line of descent within the Bacteria. Phenotypically and phylogenetically, strain PAI-1 differs from all other described bacteria, and represents the type strain of a new genus and species. Geovibrio ferrireducens.

  5. Complete genome and comparative analysis of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5

    PubMed Central

    2010-01-01

    Background Oligotropha carboxidovorans OM5 T. (DSM 1227, ATCC 49405) is a chemolithoautotrophic bacterium capable of utilizing CO (carbon monoxide) and fixing CO2 (carbon dioxide). We previously published the draft genome of this organism and recently submitted the complete genome sequence to GenBank. Results The genome sequence of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5 consists of a 3.74-Mb chromosome and a 133-kb megaplasmid that contains the genes responsible for utilization of carbon monoxide, carbon dioxide, and hydrogen. To our knowledge, this strain is the first one to be sequenced in the genus Oligotropha, the closest fully sequenced relatives being Bradyrhizobium sp. BTAi and USDA110 and Nitrobacter hamburgiensis X14. Analysis of the O. carboxidovorans genome reveals potential links between plasmid-encoded chemolithoautotrophy and chromosomally-encoded lipid metabolism. Comparative analysis of O. carboxidovorans with closely related species revealed differences in metabolic pathways, particularly in carbohydrate and lipid metabolism, as well as transport pathways. Conclusion Oligotropha, Bradyrhizobium sp and Nitrobacter hamburgiensis X14 are phylogenetically proximal. Although there is significant conservation of genome organization between the species, there are major differences in many metabolic pathways that reflect the adaptive strategies unique to each species. PMID:20863402

  6. Photobacterium damselae subsp. damselae, a bacterium pathogenic for marine animals and humans.

    PubMed

    Rivas, Amable J; Lemos, Manuel L; Osorio, Carlos R

    2013-01-01

    Photobacterium damselae subsp. damselae (formerly Vibrio damsela) is a pathogen of a variety of marine animals including fish, crustaceans, molluscs, and cetaceans. In humans, it can cause opportunistic infections that may evolve into necrotizing fasciitis with fatal outcome. Although the genetic basis of virulence in this bacterium is not completely elucidated, recent findings demonstrate that the phospholipase-D Dly (damselysin) and the pore-forming toxins HlyApl and HlyAch play a main role in virulence for homeotherms and poikilotherms. The acquisition of the virulence plasmid pPHDD1 that encodes Dly and HlyApl has likely constituted a main driving force in the evolution of a highly hemolytic lineage within the subspecies. Interestingly, strains that naturally lack pPHDD1 show a strong pathogenic potential for a variety of fish species, indicating the existence of yet uncharacterized virulence factors. Future and deep analysis of the complete genome sequence of Photobacterium damselae subsp. damselae will surely provide a clearer picture of the virulence factors employed by this bacterium to cause disease in such a varied range of hosts. PMID:24093021

  7. Physiological and taxonomic description of the novel autotrophic, metal oxidizing bacterium, Pseudogulbenkiania sp. strain 2002.

    PubMed

    Weber, Karrie A; Hedrick, David B; Peacock, Aaron D; Thrash, J Cameron; White, David C; Achenbach, Laurie A; Coates, John D

    2009-06-01

    A lithoautotrophic, Fe(II) oxidizing, nitrate-reducing bacterium, strain 2002 (ATCC BAA-1479; =DSM 18807), was isolated as part of a study on nitrate-dependent Fe(II) oxidation in freshwater lake sediments. Here we provide an in-depth phenotypic and phylogenetic description of the isolate. Strain 2002 is a gram-negative, non-spore forming, motile, rod-shaped bacterium which tested positive for oxidase, catalase, and urease. Analysis of the complete 16S rRNA gene sequence placed strain 2002 in a clade within the family Neisseriaceae in the order Nessieriales of the Betaproteobacteria 99.3% similar to Pseudogulbenkiania subflava. Similar to P. sublfava, predominant whole cell fatty acids were identified as 16:17c, 42.4%, and 16:0, 34.1%. Whole cell difference spectra of the Fe(II) reduced minus nitrate oxidized cyctochrome content revealed a possible role of c-type cytochromes in nitrate-dependent Fe(II) oxidation. Strain 2002 was unable to oxidize aqueous or solid-phase Mn(II) with nitrate as the electron acceptor. In addition to lithotrophic growth with Fe(II), strain 2002 could alternatively grow heterotrophically with long-chain fatty acids, simple organic acids, carbohydrates, yeast extract, or casamino acids. Nitrate, nitrite, nitrous oxide, and oxygen also served as terminal electron acceptors with acetate as the electron donor. PMID:19333599

  8. Data supporting functional diversity of the marine bacterium Cobetia amphilecti KMM 296.

    PubMed

    Balabanova, Larissa; Nedashkovskaya, Olga; Podvolotskaya, Anna; Slepchenko, Lubov; Golotin, Vasily; Belik, Alexey; Shevchenko, Ludmila; Son, Oksana; Rasskazov, Valery

    2016-09-01

    Data is presented in support of functionality of hyper-diverse protein families encoded by the Cobetia amphilecti KMM 296 (formerly Cobetia marina KMM 296) genome ("The genome of the marine bacterium Cobetia marina KMM 296 isolated from the mussel Crenomytilus grayanus (Dunker, 1853)" [1]) providing its nutritional versatility, adaptability and biocontrol that could be the basis of the marine bacterium evolutionary and application potential. Presented data include the information of growth and biofilm-forming properties of the food-associated isolates of Pseudomonas, Bacillus, Listeria, Salmonella and Staphylococcus under the conditions of their co-culturing with C. amphilecti KMM 296 to confirm its high inter-species communication and anti-microbial activity. Also included are the experiments on the crude petroleum consumption by C. amphilecti KMM 296 as the sole source of carbon in the presence of sulfate or nitrate to ensure its bioremediation capacity. The multifunctional C. amphilecti KMM 296 genome is a promising source for the beneficial psychrophilic enzymes and essential secondary metabolites. PMID:27508225

  9. Cloning of the cnr operon into a strain of Bacillaceae bacterium for the development of a suitable biosorbent.

    PubMed

    Fosso-Kankeu, Elvis; Mulaba-Bafubiandi, Antoine F; Piater, Lizelle A; Tlou, Matsobane G

    2016-07-01

    In this study, a potential microbial biosorbent was engineered to improve its capacity to remediate heavy metal contaminated water resources. A Bacillaceae bacterium isolated from a mining area was transformed with a plasmid carrying the (pECD312)-based cnr operon that encodes nickel and cobalt resistance. The bioadsorption ability of the transformed strain was evaluated for removal of nickel from metallurgical water relative to the wildtype strain. Results showed that transformation improved the adsorption capacity of the bacterium by 37 % at nickel concentrations equivalent to 150 mg/L. Furthermore it was possible to apply prediction modelling to study the bioadsorption behaviour of the transformed strain. As such, this work may be extended to the design of a nickel bioremediation plant utilising the newly developed Bacillaceae bacterium as a biosorbent. PMID:27263009

  10. A novel strategy for the construction of genomic mutants of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125.

    PubMed

    Giuliani, Maria; Parrilli, Ermenegilda; Pezzella, Cinzia; Rippa, Valentina; Duilio, Angela; Marino, Gennaro; Tutino, Maria Luisa

    2012-01-01

    The sequencing and the annotation of the marine Antarctic Pseudoalteromonas haloplanktis TAC125 genome has paved the way to investigate on the molecular mechanisms involved in adaptation to cold conditions. The growing interest in this unique bacterium prompted the developing of several genetic tools for studying it at the molecular level. To allow a deeper understanding of the PhTAC125 physiology a genetic system for the reverse genetics in this bacterium was developed. In the present work, we describe a practical technique for allelic exchange and/or gene inactivation by in-frame deletion and the use of a counterselectable marker in P. haloplanktis. The construction of suitable non-replicating plasmid and methods used to carry out a two-step integration-segregation strategy in this bacterium are reported in detail.Furthermore two examples, in which the developed methodology was applied to find out gene function or to construct genetically engineered bacterial strains, were described. PMID:22160901

  11. Therapeutic value of a Lactobacillus gasseri and Bifidobacterium longum fixed bacterium combination in acute diarrhea: a randomized, double-blind, controlled clinical trial.

    PubMed

    Margreiter, M; Ludl, K; Phleps, W; Kaehler, S T

    2006-05-01

    A multicenter, parallel-group, randomized, double-blind, active-controlled clinical trial, involving 169 outpatients at 9 centers, was conducted to assess the efficacy of a fixed bacterium combination of Lactobacillus gasseri and Bifidobacterium longum in the therapy of acute diarrhea. In particular, this clinical trial was designed to prove equivalent therapeutic efficacy of a fixed bacterium combination versus an exhaustive investigated mono-bacterium medicinal product. All patients, free to carry on usual daily activities, received 1 capsule 3 times a day of either a fixed bacterium combination of Lactobacillus gasseri and Bifidobacterium longum or Enterococcus faecium mono-bacterium. All treatments were continued for a maximum of 6 days in line with the normal course of acute diarrhea. Primary efficacy criterion was the severity and duration of diarrhea assessed by the ensemble of stool frequency as change from baseline and stool consistency at trial Day 2, 3 and 4, and time in days until normal bowel function (recovery). The median duration of diarrhea was 2.70 days versus 2.67 days (fixed bacterium combination of Lactobacillus gasseri and Bifidobacterium longum versus mono-bacterium Enterococcus feacium). The total mean difference of duration of diarrhea was 0.072 days. This result can be considered equivalent. However, the proportion of patients with complete recovery tended to be higher in the fixed bacterium combination group (92.6% versus 87.1%) resulting in a number needed to treat (NNT) of 18.1. The fixed bacterium combination reduced the number of unformed stools by 80% and the mono-bacterium by 75% during the first 2 days of treatment. Both treatments were well tolerated. Oral therapy with a fixed combination of Lactobacillus gasseri and Bifidobacterium longum shortens the duration and decreases the severity of acute self-limiting diarrhea in adults comparable to an effective mono-bacterium medicinal product. It therefore appears to be a useful and

  12. Bacterium-Like Particles for Efficient Immune Stimulation of Existing Vaccines and New Subunit Vaccines in Mucosal Applications

    PubMed Central

    Van Braeckel-Budimir, Natalija; Haijema, Bert Jan; Leenhouts, Kees

    2013-01-01

    The successful development of a mucosal vaccine depends critically on the use of a safe and effective immunostimulant and/or carrier system. This review describes the effectiveness and mode of action of an immunostimulating particle, derived from bacteria, used in mucosal subunit vaccines. The non-living particles, designated bacterium-like particles are based on the food-grade bacterium Lactococcus lactis. The focus of the overview is on the development of intranasal BLP-based vaccines to prevent diseases caused by influenza and respiratory syncytial virus, and includes a selection of Phase I clinical data for the intranasal FluGEM vaccine. PMID:24062748

  13. Whole-Genome Sequence of Filimonas lacunae, a Bacterium of the Family Chitinophagaceae Characterized by Marked Colony Growth under a High-CO2 Atmosphere.

    PubMed

    Shiratori-Takano, Hatsumi; Takano, Hideaki; Ueda, Kenji

    2016-01-01

    We report here the genome sequence of Filimonas lacunae, a bacterium of the family Chitinophagaceae characterized by high-CO2-dependent growth. The 7.81-Mb circular genome harbors many genes involved in carbohydrate degradation and related genetic regulation, suggesting the role of the bacterium as a carbohydrate degrader in diverse environments. PMID:27417842

  14. Genome Assembly of Chryseobacterium polytrichastri ERMR1:04, a Psychrotolerant Bacterium with Cold Active Proteases, Isolated from East Rathong Glacier in India.

    PubMed

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

    2015-01-01

    We report here the genome assembly of a psychrotolerant bacterium, Chryseobacterium polytrichastri ERMR1:04, which secretes cold-active proteases. The bacterium was isolated from a pristine location, the East Rathong Glacier in the Sikkim Himalaya. The 5.53-Mb genome provides insight into the cold-active industrial enzyme and adaptation in the cold environment. PMID:26543128

  15. Genome Assembly of Chryseobacterium polytrichastri ERMR1:04, a Psychrotolerant Bacterium with Cold Active Proteases, Isolated from East Rathong Glacier in India

    PubMed Central

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

    2015-01-01

    We report here the genome assembly of a psychrotolerant bacterium, Chryseobacterium polytrichastri ERMR1:04, which secretes cold-active proteases. The bacterium was isolated from a pristine location, the East Rathong Glacier in the Sikkim Himalaya. The 5.53-Mb genome provides insight into the cold-active industrial enzyme and adaptation in the cold environment. PMID:26543128

  16. Whole-Genome Sequence of Filimonas lacunae, a Bacterium of the Family Chitinophagaceae Characterized by Marked Colony Growth under a High-CO2 Atmosphere

    PubMed Central

    Shiratori-Takano, Hatsumi; Takano, Hideaki

    2016-01-01

    We report here the genome sequence of Filimonas lacunae, a bacterium of the family Chitinophagaceae characterized by high-CO2-dependent growth. The 7.81-Mb circular genome harbors many genes involved in carbohydrate degradation and related genetic regulation, suggesting the role of the bacterium as a carbohydrate degrader in diverse environments. PMID:27417842

  17. Isolation and characterization of Leu[7]-Surfactin from the endophytic bacterium Bacillus mojavensis RRC 101, a biocontrol agent for Fusarium verticillioides

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bacillus mojavensis is an endophytic bacterium patented for control of fungal diseases in maize and other plants. Culture extracts and filtrates from this bacterium were antagonistic to the pathogenic and mycotoxic fungus Fusarium verticillioides. However, the identity of the inhibitory substance ...

  18. Near-complete genome sequence of the cellulolytic Bacterium Bacteroides (Pseudobacteroides) cellulosolvens ATCC 35603

    SciTech Connect

    Dassa, Bareket; Utturkar, Sagar M.; Hurt, Richard A.; Klingeman, Dawn Marie; Keller, Martin; Xu, Jian; Reddy, Harish Kumar; Borovok, Ilya; Grinberg, Inna Rozman; Lamed, Raphael; Zhivin, Olga; Bayer, Edward A.; Brown, Steven D.

    2015-09-24

    We report the single-contig genome sequence of the anaerobic, mesophilic, cellulolytic bacterium, Bacteroides cellulosolvens. The bacterium produces a particularly elaborate cellulosome system, whereas the types of cohesin-dockerin interactions are opposite of other known cellulosome systems: cell-surface attachment is thus mediated via type-I interactions whereas enzymes are integrated via type-II interactions.

  19. Complete Genome Sequence of the Unclassified Iron-Oxidizing, Chemolithoautotrophic Burkholderiales Bacterium GJ-E10, Isolated from an Acidic River

    PubMed Central

    Tojo, Fuyumi; Asano, Ryoki; Kobayashi, Yayoi; Shimura, Yoichiro; Okano, Kunihiro; Miyata, Naoyuki

    2015-01-01

    Burkholderiales bacterium GJ-E10, isolated from the Tamagawa River in Akita Prefecture, Japan, is an unclassified, iron-oxidizing chemolithoautotrophic bacterium. Its single circular genome, consisting of 3,276,549 bp, was sequenced by using three types of next-generation sequencers and the sequences were then confirmed by PCR-based Sanger sequencing. PMID:25657271

  20. A Pathway Closely Related to the d-Tagatose Pathway of Gram-Negative Enterobacteria Identified in the Gram-Positive Bacterium Bacillus licheniformis

    PubMed Central

    Van der Heiden, Edwige; Lebrun, Sarah; Freichels, Régine; Brans, Alain; Vastenavond, Christian M.; Galleni, Moreno; Joris, Bernard

    2013-01-01

    We report the first identification of a gene cluster involved in d-tagatose catabolism in Bacillus licheniformis. The pathway is closely related to the d-tagatose pathway of the Gram-negative bacterium Klebsiella oxytoca, in contrast to the d-tagatose 6-phosphate pathway described in the Gram-positive bacterium Staphylococcus aureus. PMID:23524682

  1. Enhanced bactericidal potency of nanoliposomes by modification of the fusion activity between liposomes and bacterium

    PubMed Central

    Ma, Yufan; Wang, Zhao; Zhao, Wen; Lu, Tingli; Wang, Rutao; Mei, Qibing; Chen, Tao

    2013-01-01

    Background Pseudomonas aeruginosa represents a good model of antibiotic resistance. These organisms have an outer membrane with a low level of permeability to drugs that is often combined with multidrug efflux pumps, enzymatic inactivation of the drug, or alteration of its molecular target. The acute and growing problem of antibiotic resistance of Pseudomonas to conventional antibiotics made it imperative to develop new liposome formulations to overcome these mechanisms, and investigate the fusion between liposome and bacterium. Methods The rigidity, stability and charge properties of phospholipid vesicles were modified by varying the cholesterol, 1,2-dioleoyl-sn-glycero-3-phosphatidylethanolamine (DOPE), and negatively charged lipids 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol sodium salt (DMPG), 1,2-dimyristoyl-sn-glycero-3-phopho-L-serine sodium salt (DMPS), 1,2-dimyristoyl-sn-glycero-3-phosphate monosodium salt (DMPA), nature phosphatidylserine sodium salt from brain and nature phosphatidylinositol sodium salt from soybean concentrations in liposomes. Liposomal fusion with intact bacteria was monitored using a lipid-mixing assay. Results It was discovered that the fluid liposomes-bacterium fusion is not dependent on liposomal size and lamellarity. A similar degree of fusion was observed for liposomes with a particle size from 100 to 800 nm. The fluidity of liposomes is an essential pre-request for liposomes fusion with bacteria. Fusion was almost completely inhibited by incorporation of cholesterol into fluid liposomes. The increase in the amount of negative charges in fluid liposomes reduces fluid liposomes-bacteria fusion when tested without calcium cations due to electric repulsion, but addition of calcium cations brings the fusion level of fluid liposomes to similar or higher levels. Among the negative phospholipids examined, DMPA gave the highest degree of fusion, DMPS and DMPG had intermediate fusion levels, and PI resulted in the lowest degree of fusion

  2. The impact of a pathogenic bacterium on a social carnivore population.

    PubMed

    Höner, Oliver P; Wachter, Bettina; Goller, Katja V; Hofer, Heribert; Runyoro, Victor; Thierer, Dagmar; Fyumagwa, Robert D; Müller, Thomas; East, Marion L

    2012-01-01

    1. The long-term ecological impact of pathogens on group-living, large mammal populations is largely unknown. We evaluated the impact of a pathogenic bacterium, Streptococcus equi ruminatorum, and other key ecological factors on the dynamics of the spotted hyena Crocuta crocuta population in the Ngorongoro Crater, Tanzania. 2. We compared key demographic parameters during two years when external signs of bacterial infection were prevalent ('outbreak') and periods of five years before and after the outbreak when such signs were absent or rare. We also tested for density dependence and calculated the basic reproductive rate R(0) of the bacterium. 3. During the five pre-outbreak years, the mean annual hyena mortality rate was 0.088, and annual population growth was relatively high (13.6%). During the outbreak, mortality increased by 78% to a rate of 0.156, resulting in an annual population decline of 4.3%. After the outbreak, population size increased moderately (5.1%) during the first three post-outbreak years before resuming a growth similar to pre-outbreak levels (13.9%). We found no evidence that these demographic changes were driven by density dependence or other ecological factors. 4. Most hyenas showed signs of infection when prey abundance in their territory was low. During the outbreak, mortality increased among adult males and yearlings, but not among adult females - the socially dominant group members. These results suggest that infection and mortality were modulated by factors linked to low social status and poor nutrition. During the outbreak, we estimated R(0) for the bacterium to be 2.7, indicating relatively fast transmission. 5. Our results suggest that the short-term 'top-down' impact of S. equi ruminatorum during the outbreak was driven by 'bottom-up' effects on nutritionally disadvantaged age-sex classes, whereas the longer-term post-outbreak reduction in population growth was caused by poor survival of juveniles during the outbreak and subsequent

  3. High Prevalence of Antibodies against the Bacterium Treponema pallidum in Senegalese Guinea Baboons (Papio papio)

    PubMed Central

    Knauf, Sascha; Barnett, Ulrike; Maciej, Peter; Klapproth, Matthias; Ndao, Ibrahima; Frischmann, Sieghard; Fischer, Julia; Zinner, Dietmar; Liu, Hsi

    2015-01-01

    The bacterium Treponema pallidum is known to cause syphilis (ssp. pallidum), yaws (ssp. pertenue), and endemic syphilis (ssp. endemicum) in humans. Nonhuman primates have also been reported to be infected with the bacterium with equally versatile clinical manifestations, from severe skin ulcerations to asymptomatic. At present all simian strains are closely related to human yaws-causing strains, an important consideration for yaws eradication. We tested clinically healthy Guinea baboons (Papio papio) at Parc National Niokolo Koba in south eastern Senegal for the presence of anti-T. pallidum antibodies. Since T. pallidum infection in this species was identified 50 years ago, and there has been no attempt to treat non-human primates for infection, it was hypothesized that a large number of West African baboons are still infected with simian strains of the yaws-bacterium. All animals were without clinical signs of treponematoses, but 18 of 20 (90%) baboons tested positive for antibodies against T. pallidum based on treponemal tests. Yet, Guinea baboons seem to develop no clinical symptoms, though it must be assumed that infection is chronic or comparable to the latent stage in human yaws infection. The non-active character is supported by the low anti-T. pallidum serum titers in Guinea baboons (median = 1:2,560) versus serum titers that are found in genital-ulcerated olive baboons with active infection in Tanzania (range of medians among the groups of initial, moderate, and severe infected animals = 1:15,360 to 1:2.097e+7). Our findings provide evidence for simian infection with T. pallidum in wild Senegalese baboons. Potentially, Guinea baboons in West Africa serve as a natural reservoir for human infection, as the West African simian strain has been shown to cause sustainable yaws infection when inoculated into humans. The present study pinpoints an area where further research is needed to support the currently on-going second WHO led yaws eradication campaign with

  4. High Prevalence of Antibodies against the Bacterium Treponema pallidum in Senegalese Guinea Baboons (Papio papio).

    PubMed

    Knauf, Sascha; Barnett, Ulrike; Maciej, Peter; Klapproth, Matthias; Ndao, Ibrahima; Frischmann, Sieghard; Fischer, Julia; Zinner, Dietmar; Liu, Hsi

    2015-01-01

    The bacterium Treponema pallidum is known to cause syphilis (ssp. pallidum), yaws (ssp. pertenue), and endemic syphilis (ssp. endemicum) in humans. Nonhuman primates have also been reported to be infected with the bacterium with equally versatile clinical manifestations, from severe skin ulcerations to asymptomatic. At present all simian strains are closely related to human yaws-causing strains, an important consideration for yaws eradication. We tested clinically healthy Guinea baboons (Papio papio) at Parc National Niokolo Koba in south eastern Senegal for the presence of anti-T. pallidum antibodies. Since T. pallidum infection in this species was identified 50 years ago, and there has been no attempt to treat non-human primates for infection, it was hypothesized that a large number of West African baboons are still infected with simian strains of the yaws-bacterium. All animals were without clinical signs of treponematoses, but 18 of 20 (90%) baboons tested positive for antibodies against T. pallidum based on treponemal tests. Yet, Guinea baboons seem to develop no clinical symptoms, though it must be assumed that infection is chronic or comparable to the latent stage in human yaws infection. The non-active character is supported by the low anti-T. pallidum serum titers in Guinea baboons (median = 1:2,560) versus serum titers that are found in genital-ulcerated olive baboons with active infection in Tanzania (range of medians among the groups of initial, moderate, and severe infected animals = 1:15,360 to 1:2.097e+7). Our findings provide evidence for simian infection with T. pallidum in wild Senegalese baboons. Potentially, Guinea baboons in West Africa serve as a natural reservoir for human infection, as the West African simian strain has been shown to cause sustainable yaws infection when inoculated into humans. The present study pinpoints an area where further research is needed to support the currently on-going second WHO led yaws eradication campaign with

  5. Thermally Induced Leakage from Vibrio marinus, an Obligately Psychrophilic Marine Bacterium1

    PubMed Central

    Haight, Roger D.; Morita, Richard Y.

    1966-01-01

    Haight, Rodger D. (Oregon State University, Corvallis), and Richard Y. Morita. Thermally induced leakage from Vibrio marinus, an obligately psychrophilic bacterium. J. Bacteriol. 92:1388–1393. 1966.—Leakage of various cellular components into the surrounding menstruum occurred when Vibrio marinus was subjected to temperatures above 20 C (organism's maximal growth temperature). These materials, listed in decreasing rates of leakage, were identified as protein, deoxyribonucleic acid, ribonucleic acid, and amino acids. The amount of polar amino acids increased as the time and temperature of heat treatment were increased, whereas the nonpolar amino acids decreased. The ribonucleic acid in the supernatant fluid resulting from heat treatment was both polymeric and nonpolymeric. Leakage of cellular components may be one of the reasons that V. marinus MP-1 loses viability when exposed to temperatures above its maximal temperature for growth. PMID:5924270

  6. Tyrosine binding and promiscuity in the arginine repressor from the pathogenic bacterium Corynebacterium pseudotuberculosis.

    PubMed

    Mariutti, Ricardo Barros; Ullah, Anwar; Araujo, Gabriela Campos; Murakami, Mario Tyago; Arni, Raghuvir Krishnaswamy

    2016-07-01

    The arginine repressor (ArgR) regulates arginine biosynthesis in a number of microorganisms and consists of two domains interlinked by a short peptide; the N-terminal domain is involved in DNA binding and the C-terminal domain binds arginine and forms a hexamer made-up of a dimer of trimers. The crystal structure of the C-terminal domain of ArgR from the pathogenic Corynebacterium pseudotuberculosis determined at 1.9 Å resolution contains a tightly bound tyrosine at the arginine-binding site indicating hitherto unobserved promiscuity. Structural analysis of the binding pocket displays clear molecular adaptations to accommodate tyrosine binding suggesting the possible existence of an alternative regulatory process in this pathogenic bacterium. PMID:27233609

  7. A cultured greigite-producing magnetotactic bacterium in a novel group of sulfate-reducing bacteria.

    PubMed

    Lefèvre, Christopher T; Menguy, Nicolas; Abreu, Fernanda; Lins, Ulysses; Pósfai, Mihály; Prozorov, Tanya; Pignol, David; Frankel, Richard B; Bazylinski, Dennis A

    2011-12-23

    Magnetotactic bacteria contain magnetosomes--intracellular, membrane-bounded, magnetic nanocrystals of magnetite (Fe(3)O(4)) or greigite (Fe(3)S(4))--that cause the bacteria to swim along geomagnetic field lines. We isolated a greigite-producing magnetotactic bacterium from a brackish spring in Death Valley National Park, California, USA, strain BW-1, that is able to biomineralize greigite and magnetite depending on culture conditions. A phylogenetic comparison of BW-1 and similar uncultured greigite- and/or magnetite-producing magnetotactic bacteria from freshwater to hypersaline habitats shows that these organisms represent a previously unknown group of sulfate-reducing bacteria in the Deltaproteobacteria. Genomic analysis of BW-1 reveals the presence of two different magnetosome gene clusters, suggesting that one may be responsible for greigite biomineralization and the other for magnetite. PMID:22194580

  8. Glutathione-mediated response to acid stress in the probiotic bacterium, Lactobacillus salivarius.

    PubMed

    Lee, Kibeom; Pi, Kyungbae; Kim, Eun Bae; Rho, Beom-Seop; Kang, Sang-Kee; Lee, Hong Gu; Choi, Yun-Jaie

    2010-07-01

    Lactobacillus salivarius, a probiotic bacterium, encounters acidic conditions in its passage through the gastrointestinal tract of human and animal hosts. We studied the effect of a rapid downshift in extracellular pH from 6.5 to 4 on cell growth. The maximum growth rate was higher in low pH medium with glutathione supplementation than without. Cells developed a GSH-mediated acid-tolerance response and, when grown with 0.5 mM GSH, reached a higher final density than with other conditions. These findings suggest that the increased growth rate is caused by uptake of GSH which acts as a nutrient source as well as having protective functions, allowing for continued growth. PMID:20349113

  9. Decoherence dynamics of coherent electronic excited states in the photosynthetic purple bacterium Rhodobacter sphaeroides

    NASA Astrophysics Data System (ADS)

    Liang, Xian-Ting; Zhang, Wei-Min; Zhuo, Yi-Zhong

    2010-01-01

    In this paper, we present a theoretical description to the quantum coherence and decoherence phenomena of energy transfer in photosynthesis observed in a recent experiment [Science 316, 1462 (2007)]. As a successive two-color laser pulses with selected frequencies cast on a sample of the photosynthetic purple bacterium Rb. sphaeroides two resonant excitations of electrons in chromophores can be generated. However, this effective two-level subsystem will interact with its protein environment and decoherence is inevitable. We describe this subsystem coupled with its environment as a dynamical spin-boson model. The non-Markovian decoherence dynamics is described using a quasiadiabatic propagator path integral (QUAPI) approach. With the photon-induced effective time-dependent level splitting energy and level flip coupling coefficient between the two excited states and the environment-induced non-Markovian decoherence dynamics, our theoretical result is in good agreement with the experimental data.

  10. The glucose transport system of the hyperthermophilic anaerobic bacterium Thermotoga neapolitana

    SciTech Connect

    Galperin, M.Y.; Noll, K.M.; Romano, A.H.

    1996-08-01

    The glucose transport system of the extremely thermophilic anaerobic bacterium Thermotoga neapolitana was studied with the nonmetabolizable glucose analog 2-deoxy-D-glucose (2-DOG). T. neapolitana accumulated 2-DOG against a concentration gradient in an intracellular free sugar pool that was exchangeable with external D-glucose. This active transport of 2-DOG was dependent upon the presence of sodium ion and an external source of energy, such as pyruvate, and was inhibited by arsenate and gramicidin D. There was no phosphoenolpyruvate-dependent phosphorylation of glucose, 2-DOG, or fructose by cell extracts or toluene-treated cells, indicating the absence of a phosphoenolpyruvate:sugar phosphotransferase system. These data indicate that D-glucose is taken up by T.neapolitana via an active transport system that is energized by an ion gradient generated by ATP, derived from substrate-level phosphorylation. 33 refs., 3 figs., 1 tab.

  11. Novel Pathway of Toluene Catabolism in the Trichloroethylene-Degrading Bacterium G4

    PubMed Central

    Shields, Malcolm S.; Montgomery, Stacy O.; Chapman, Peter J.; Cuskey, Stephen M.; Pritchard, P. H.

    1989-01-01

    o-Cresol and 3-methylcatechol were identified as successive transitory intermediates of toluene catabolism by the trichloroethylene-degrading bacterium G4. The absence of a toluene dihydrodiol intermediate or toluene dioxygenase and toluene dihydrodiol dehydrogenase activities suggested that G4 catabolizes toluene by a unique pathway. Formation of a hybrid species of 18O- and 16O-labeled 3-methylcatechol from toluene in an atmosphere of 18O2 and 16O2 established that G4 catabolizes toluene by successive monooxygenations at the ortho and meta positions. Detection of trace amounts of 4-methylcatechol from toluene catabolism suggested that the initial hydroxylation of toluene was not exclusively at the ortho position. Further catabolism of 3-methylcatechol was found to proceed via catechol-2,3-dioxygenase and hydroxymuconic semialdehyde hydrolase activities. PMID:16347956

  12. Expression and secretion of an Arthrobacter dextranase in the oral bacterium Streptococcus gordonii.

    PubMed Central

    Kubo, S; Kubota, H; Ohnishi, Y; Morita, T; Matsuya, T; Matsushiro, A

    1993-01-01

    We have constructed a plasmid to express and secrete dextranase in the oral bacterium Streptococcus gordonii. The dextranase gene from Arthrobacter sp. strain CB-8 was linked to a promoter and a DNA sequence encoding the signal peptide of Streptococcus downei glucosyltransferase I (gtfI) followed by the Escherichia coli rrnBt1t2 terminator and inserted in the shuttle vector pVA838. S. gordonii transformed with this plasmid (pMNK-4) expressed and secreted mature Arthrobacter dextranase. The transformant was found to repress the firm adherence of water-insoluble glucan in a coculture experiment with cariogenic bacteria, Streptococcus sobrinus, in the presence of sucrose. Such genetically engineered oral bacteria could provide a therapy to prevent dental caries. Images PMID:8406828

  13. Identification of an anaerobic bacterium which reduces perchlorate and chlorate as Wolinella succinogenes

    SciTech Connect

    Wallace, W.; Attaway, H. |

    1995-12-31

    Perchlorate and chlorate salts are widely used by the chemical, aerospace and defense industries as oxidizers in propellant, explosives and pyrotechnics. The authors have isolated a anaerobic bacterium which is capable of the dissimilatory reduction of both perchlorate and chlorate for energy and growth. Strain HAP-1 is a gram negative, thin rod, non-sporeforming, highly motile strict anaerobe. Antibiotic resistance profiles, utilization of carbon substrates and electron acceptors demonstrated similar physiological characteristics to Wolinella succinogenes. Pairwise comparisons of 16S RNA sequences showed only a 0.75% divergence between strain HAP-1 and W. succinogenes. Physiological, morphological and 16S RRNA sequence data indicate strain HAP-1 is a subspecies of W. succinogenes that can utilize perchlorate and chlorate as terminal electron acceptors.

  14. New crystal forms of NTPDase1 from the bacterium Legionella pneumophila

    PubMed Central

    Zebisch, Matthias; Schäfer, Petra; Lauble, Peter; Sträter, Norbert

    2013-01-01

    Nucleoside triphosphate diphosphohydrolases (NTPDases) are a large class of nucleotidases that hydrolyze the (γ/β)- and (β/α)-anhydride bonds of nucleoside triphosphates and diphosphates, respectively. NTPDases are found throughout the eukaryotic domain. In addition, a very small number of members can be found in bacteria, most of which live as parasites of eukaryotic hosts. NTPDases of intracellular and extracellular parasites are emerging as important regulators for the survival of the parasite. To deepen the knowledge of the structure and function of this enzyme class, recombinant production of the NTPDase1 from the bacterium Legionella pneumophila has been established. The protein could be crystallized in six crystal forms, of which one has been described previously. The crystals diffracted to resolutions of between 1.4 and 2.5 Å. Experimental phases determined by a sulfur SAD experiment using an orthorhombic crystal form produced an interpretable electron-density map. PMID:23519799

  15. Isolation and characterization of bacterium producing lipid from short-chain fatty acids.

    PubMed

    Okamura, Yoshiko; Nakai, Shota; Ohkawachi, Masahiko; Suemitsu, Masahiro; Takahashi, Hirokazu; Aki, Tsunehiro; Matsumura, Yukihiko; Tajima, Takahisa; Nakashimada, Yutaka; Matsumoto, Mitsufumi

    2016-02-01

    Anaerobic fermentation generates propionic acid, which inhibits microbial growth and accumulates in wastewater containing increased amounts of organic matter. We therefore isolated a propionic acid-assimilating bacterium that could produce triacylglycerol, for use in wastewater treatment. Nitratireductor sp. strain OM-1 can proliferate in medium containing propionic, acetic, butyric, and valeric acids as well as glycerol, and produces triacylglycerol when both propionic and acetic acids or glycerol are present. In composite model wastewater containing acetic acid, propionic acid and glycerol, this strain shows an even higher conversion rate, suggesting that it is suitable for wastewater treatment. Further, nitrogen depletion in medium containing an acetic-propionic acid mixture resulted in the production of the light oil 2-butenoic acid 1-methylethyl ester, but not triacylglycerol. Collectively, our data indicate that strain OM-1 has the potential to reduce accumulation of activated sludge in wastewater treatment and may contribute to the production of biodiesel. PMID:26649900

  16. Plague bacterium as a transformer species in prairie dogs and the grasslands of western North America.

    PubMed

    Eads, David A; Biggins, Dean E

    2015-08-01

    Invasive transformer species change the character, condition, form, or nature of ecosystems and deserve considerable attention from conservation scientists. We applied the transformer species concept to the plague bacterium Yersinia pestis in western North America, where the pathogen was introduced around 1900. Y. pestis transforms grassland ecosystems by severely depleting the abundance of prairie dogs (Cynomys spp.) and thereby causing declines in native species abundance and diversity, including threatened and endangered species; altering food web connections; altering the import and export of nutrients; causing a loss of ecosystem resilience to encroaching invasive plants; and modifying prairie dog burrows. Y. pestis poses an important challenge to conservation biologists because it causes trophic-level perturbations that affect the stability of ecosystems. Unfortunately, understanding of the effects of Y. pestis on ecosystems is rudimentary, highlighting an acute need for continued research. PMID:25817984

  17. Genome sequence of the marine bacterium Corynebacterium maris type strain Coryn-1(T) (= DSM 45190(T)).

    PubMed

    Schaffert, Lena; Albersmeier, Andreas; Bednarz, Hanna; Niehaus, Karsten; Kalinowski, Jörn; Rückert, Christian

    2013-07-30

    Corynebacterium maris Coryn-1(T) Ben-Dov et al. 2009 is a member of the genus Corynebacterium which contains Gram-positive, non-spore forming bacteria with a high G+C content. C. maris was isolated from the mucus of the Scleractinian coral Fungia granulosa and belongs to the aerobic and non-haemolytic corynebacteria. It displays tolerance to salts (up to 10%) and is related to the soil bacterium Corynebacterium halotolerans. As this is a type strain in a subgroup of Corynebacterium without complete genome sequences, this project, describing the 2.78 Mbp long chromosome and the 45.97 kbp plasmid pCmaris1, with their 2,584 protein-coding and 67 RNA genes, will aid the G enomic E ncyclopedia of Bacteria and Archaea project. PMID:24501635

  18. Shigella infection of Henle intestinal epithelial cells: role of the bacterium.

    PubMed Central

    Hale, T L; Bonventre, P F

    1979-01-01

    Epithelial cell infection by Shigella flexneri 2a was studied in an in vitro model system. Using the Henle 407 human intestinal epithelial cell line as host cells, a standardized experimental protocol which allowed quantitative measurement of infection was developed. Intravellular residence of infecting organisms was confirmed by indirect fluorescent-antibody staining of unfixed and methanol-fixed (Henle 407) cells and by quantitative bacteriological culture of disrupted host cells after infection. The process of shigella entry into cells was evaluated by chemical or physical modulation of the bacterium under controlled experimental conditions. Shigella were subjected to mild heat, ultraviolet radiation aminoglycoside antibiotics, and immunoglobulins raised against S. flexneri 2a. The data show that heat-stable antigens on the bacterial surface are not solely responsible for infectivity of S. flexneri 2a. Furthermore, it was shown that physiological and synthetic functions of shigellae are required for entry into host cells. PMID:381204

  19. An outbreak in 1965 of severe respiratory illness caused by the Legionnaires' disease bacterium.

    PubMed

    Thacker, S B; Bennett, J V; Tsai, T F; Fraser, D W; McDade, J E; Shepard, C C; Williams, K H; Stuart, W H; Dull, H B; Eickhoff, T C

    1978-10-01

    In January 1977 an unsolved outbreak of infection at St. Elizabeth's Hospital (Washington, D.C.) that occurred in 1965 was linked with Legionnaires' disease. The link was made by fluorescent antibody testing with the bacterium isolated from tissues of persons with Legionnaires' disease in the 1976 outbreak in Philadelphia. In July and August 1965, an epidemic of severe respiratory disease characterized by abrupt onset of high fever, weakness, malaise, and nonproductive cough, frequently accompanied by radiographic evidence of pneumonia, affected at least 81 patients at St. Elizabeth's Hospital, a general psychiatric hospital. Fourteen (17%) of the affected patients died. Intensive epidemiologic and laboratory investigations in 1965 did not determine the etiology. The etiologic organism may have become airborne from sites of soil excavation. PMID:361897

  20. Initial reactions in anaerobic ethylbenzene oxidation by a denitrifying bacterium, strain EB1.

    PubMed Central

    Ball, H A; Johnson, H A; Reinhard, M; Spormann, A M

    1996-01-01

    Initial reactions in anaerobic oxidation of ethylbenzene were investigated in a denitrifying bacterium, strain EB1. Cells of strain EB1 mineralized ethylbenzene to CO2 under denitrifying conditions, as demonstrated by conversion of 69% of [14C]ethylbenzene to 14CO2. In anaerobic suspensions of strain EB1 cells metabolizing ethylbenzene, the transient formation and consumption of 1-phenylethanol, acetophenone, and an as yet unidentified compound were observed. On the basis of growth experiments and spectroscopic data, the unknown compound is proposed to be benzoyl acetate. Cell suspension experiments using H2(18)O demonstrated that the hydroxyl group of the first product of anoxic ethylbenzene oxidation, 1-phenylethanol, is derived from water. A tentative pathway for anaerobic ethylbenzene mineralization by strain EB1 is proposed. PMID:8824622

  1. Columnaris disease in fish: a review with emphasis on bacterium-host interactions

    PubMed Central

    2013-01-01

    Flavobacterium columnare (F. columnare) is the causative agent of columnaris disease. This bacterium affects both cultured and wild freshwater fish including many susceptible commercially important fish species. F. columnare infections may result in skin lesions, fin erosion and gill necrosis, with a high degree of mortality, leading to severe economic losses. Especially in the last decade, various research groups have performed studies aimed at elucidating the pathogenesis of columnaris disease, leading to significant progress in defining the complex interactions between the organism and its host. Despite these efforts, the pathogenesis of columnaris disease hitherto largely remains unclear, compromising the further development of efficient curative and preventive measures to combat this disease. Besides elaborating on the agent and the disease it causes, this review aims to summarize these pathogenesis data emphasizing the areas meriting further investigation. PMID:23617544

  2. Heterotrophic ammonium removal characteristics of an aerobic heterotrophic nitrifying-denitrifying bacterium, Providencia rettgeri YL.

    PubMed

    Taylor, Shauna M; He, Yiliang; Zhao, Bin; Huang, Jue

    2009-01-01

    Bacterium Providencia rettgeri YL was found to exhibit an unusual ability to heterotrophically nitrify and aerobically denitrify various concentrations of ammonium (NH4+-N). In order to further understand its removal ability, several experiments were conducted to identify the growth and ammonium removal response at different carbon to nitrogen (C/N) mass ratios, shaking speeds, temperatures, ammonium concentrations and to qualitatively verify the production of nitrogen gas using gas chromatography techniques. Results showed that under optimum conditions (C/N 10, 30 degrees C, 120 r/min), YL can significantly remove low and high concentrations of ammonium within 12 to 48 h of growth, respectively. The nitrification products hydroxylamine (NH2OH), nitrite (NO2(-)) and nitrate (NO3(-)) as well as the denitrification product, nitrogen gas (N2), were detected under completely aerobic conditions. PMID:19999986

  3. The structure of ferricytochrome c552 from the psychrophilic marine bacterium Colwellia psychrerythraea 34H

    PubMed Central

    Harvilla, Paul B.; Wolcott, Holly N.

    2014-01-01

    Approximately 40% of all proteins are metalloproteins, and approximately 80% of Earth’s ecosystems are at temperatures ≤ 5 °C, including 90% of the global ocean. Thus, an essential aspect of marine metallobiochemistry is an understanding of the structure, dynamics, and mechanisms of cold adaptation of metalloproteins from marine microorganisms. Here, the molecular structure of the electron-transfer protein cytochrome c552 from the psychrophilic marine bacterium Colwellia psychrerythraea 34H has been determined by X-ray crystallography (PDB: 4O1W). The structure is highly superimposable with that of the homologous cytochrome from the mesophile Marinobacter hydrocarbonoclasticus. Based on structural analysis and comparison of psychrophilic, psychrotolerant, and mesophilic sequences, a methionine-based ligand-substitution mechanism for psychrophilic protein stabilization is proposed. PMID:24727932

  4. Nanomechanical properties of the sea-water bacterium Paracoccus seriniphilus--a scanning force microscopy approach.

    PubMed

    Davoudi, Neda; Müller-Renno, Christine; Ziegler, Christiane; Raid, Indek; Seewig, Jörg; Schlegel, Christin; Muffler, Kai; Ulber, Roland

    2015-01-01

    The measurement of force-distance curves on a single bacterium provides a unique opportunity to detect properties such as the turgor pressure under various environmental conditions. Marine bacteria are very interesting candidates for the production of pharmaceuticals, but are only little studied so far. Therefore, the elastic behavior of Paracoccus seriniphilus, an enzyme producing marine organism, is presented in this study. After a careful evaluation of the optimal measurement conditions, the spring constant and the turgor pressure are determined as a function of ionic strength and pH. Whereas the ionic strength changes the turgor pressure passively, the results give a hint that the change to acidic pH increases the turgor pressure by an active mechanism. Furthermore, it could be shown, that P. seriniphilus has adhesive protrusions outside its cell wall. PMID:25708634

  5. Continuous synthesis and excretion of the compatible solute ectoine by a transgenic, nonhalophilic bacterium.

    PubMed

    Schubert, Torsten; Maskow, Thomas; Benndorf, Dirk; Harms, Hauke; Breuer, Uta

    2007-05-01

    The compatible solute 1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid (ectoine) acts in microorganisms as an osmotic counterweight against halostress and has attracted commercial attention as a protecting agent. Its production and application are restricted by the drawbacks of the discontinuous harvesting procedure involving salt shocks, which reduces volumetric yield, increases reactor corrosion, and complicates downstream processing. In order to synthesize ectoine continuously in less-aggressive media, we introduced the ectoine genes ectABC of the halophilic bacterium Chromohalobacter salexigens into an Escherichia coli strain using the expression vector pASK-IBA7. Under the control of a tet promoter, the transgenic E. coli synthesized 6 g liter-1 ectoine with a space-time yield of 40 mg liter-1 h-1, with the vast majority of the ectoine being excreted. PMID:17369334

  6. Swimming patterns of a polarly flagellated bacterium in environments of increasing complexity

    NASA Astrophysics Data System (ADS)

    Raatz, M.; Hintsche, M.; Bahrs, M.; Theves, M.; Beta, C.

    2015-07-01

    The natural habitat of many bacterial swimmers is dominated by interfaces and narrow interstitial spacings where they frequently interact with the fluid boundaries in their vicinity. To quantify these interactions, we investigated the swimming behavior of the soil bacterium Pseudomonas putida in a variety of confined environments. Using microfluidic techniques, we fabricated structured microchannels with different configurations of cylindrical obstacles. In these environments, we analyzed the swimming trajectories for different obstacle densities and arrangements. Although the overall swimming pattern remained similar to movement in the bulk fluid, we observed a change in the turning angle distribution that could be attributed to collisions with the cylindrical obstacles. Furthermore, a comparison of the mean run length of the bacteria to the mean free path of a billiard particle in the same geometry indicated that, inside a densely packed environment, the trajectories of the bacterial swimmers are efficiently guided along the open spacings.

  7. Cytochrome P450 enzymes from the metabolically diverse bacterium Rhodopseudomonas palustris

    SciTech Connect

    Bell, Stephen G. . E-mail: stephen.bell@chem.ox.ac.uk; Hoskins, Nicola; Xu Feng; Caprotti, Domenico; Rao Zihe; Wong, L.-L. . E-mail: luet.wong@chem.ox.ac.uk

    2006-03-31

    Four (CYP195A2, CYP199A2, CYP203A1, and CYP153A5) of the seven P450 enzymes, and palustrisredoxin A, a ferredoxin associated with CYP199A2, from the metabolically diverse bacterium Rhodopseudomonas palustris have been expressed and purified. A range of substituted benzenes, phenols, benzaldehydes, and benzoic acids was shown to bind to the four P450 enzymes. Monooxygenase activity of CYP199A2 was reconstituted with palustrisredoxin A and putidaredoxin reductase of the P450cam system from Pseudomonas putida. We found that 4-ethylbenzoate and 4-methoxybenzoate were oxidized to single products, and 4-methoxybenzoate was demethylated to form 4-hydroxybenzoate. Crystals of substrate-free CYP199A2 which diffracted to {approx}2.0 A have been obtained.

  8. Nobel lecture. The photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis.

    PubMed Central

    Deisenhofer, J; Michel, H

    1989-01-01

    In our lectures we first describe the history and methods of membrane protein crystallization, before we show how the structure of the photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis was solved. Then the structure of this membrane protein complex is correlated with its function as a light-driven electron pump across the photosynthetic membrane. Finally we draw conclusions on the structure of the photosystem II reaction centre from plants and discuss the aspects of membrane protein structure. Sections 1 (crystallization), 4 (conclusions on the structure of photosystem II reaction centre and evolutionary aspects) and 5 (aspects of membrane protein structure) were presented and written by H.M., Sections 2 (determination of the structure) and 3 (structure and function) by J.D. We have arranged the paper in this way in order to facilitate continuous reading. Images PMID:2676514

  9. Detoxification of vinyl chloride to ethene coupled to growth of an anaerobic bacterium.

    PubMed

    He, Jianzhong; Ritalahti, Kirsti M; Yang, Kun-Lin; Koenigsberg, Stephen S; Löffler, Frank E

    2003-07-01

    Tetrachloroethene (PCE) and trichloroethene (TCE) are ideal solvents for numerous applications, and their widespread use makes them prominent groundwater pollutants. Even more troubling, natural biotic and abiotic processes acting on these solvents lead to the accumulation of toxic intermediates (such as dichloroethenes) and carcinogenic intermediates (such as vinyl chloride). Vinyl chloride was found in at least 496 of the 1,430 National Priorities List sites identified by the US Environmental Protection Agency, and its precursors PCE and TCE are present in at least 771 and 852 of these sites, respectively. Here we describe an unusual, strictly anaerobic bacterium that destroys dichloroethenes and vinyl chloride as part of its energy metabolism, generating environmentally benign products (biomass, ethene and inorganic chloride). This organism might be useful for cleaning contaminated subsurface environments and restoring drinking-water reservoirs. PMID:12840758

  10. New evidence for 250 Ma age of halotolerant bacterium from a Permian salt crystal

    NASA Astrophysics Data System (ADS)

    Satterfield, Cindy L.; Lowenstein, Tim K.; Vreeland, Russell H.; Rosenzweig, William D.; Powers, Dennis W.

    2005-04-01

    The purported oldest living organism, the spore-forming bacterium Virgibacillus sp. Permian strain 2 9-3, was recently cultured from a brine inclusion in halite of the 250 Ma Permian Salado Formation. However, the antiquity of Virgibacillus sp. 2 9-3 has been challenged; it has been argued that the halite crystal and the fluid inclusion from which the bacterial spores were extracted may be younger than the Permian Salado salts. Here we report that brine inclusions from the same layer of salt that housed Virgibacillus sp. 2 9-3 are composed of evaporated Late Permian seawater that was trapped in halite cement crystals precipitated syndepositionally from shallow groundwater brines at temperatures of 17 37 °C. These results support the 250 Ma age of the fluid inclusions, and by inference, the long-term survivability of microorganisms such as Virgibacillus sp. 2 9-3.

  11. Characterization of a halotolerant-psychroloterant bacterium from dry valley Antarctic soil

    NASA Astrophysics Data System (ADS)

    Miller, K. J.; Leschine, S. B.; Huguenin, R. L.

    The saline soils of the ice free dry valleys of Victoria Land, Antarctica may provide the closest analog on Earth to Martian conditions. We have initiated a study aimed at examining microbial adaptations to the harsh environment of these dry valley soils. In this report we describe the characterization of one bacterium, strain A4a, isolated from Taylor Valley soil. Strain A4a was an obligately aerobic, orange-pigmented, Gram-positive coccus that grew over wide ranges of both temperature (0° C - 40° C) and sodium chloride concentration (0 - 2.0M). The optimal temperature for growth at all NaCl concentrations was 25° C. Phospholipid composition and guanine plus cytosine content of the DNA of the isolate indicate a close relation to the genus Planococcus.

  12. Uncoupling effect of fatty acids in halo- and alkalotolerant bacterium Bacillus pseudofirmus FTU.

    PubMed

    Popova, I V; Bodrova, M E; Mokhova, E N; Muntyan, M S

    2004-10-01

    Natural uncouplers of oxidative phosphorylation, long-chain non-esterified fatty acids, cause uncoupling in the alkalo- and halotolerant bacterium Bacillus pseudofirmus FTU. The uncoupling effect in the bacterial cells was manifested as decrease of membrane potential and increase of respiratory activity. The membrane potential decrease was detected only in bacterial cells exhausted by their endogenous substrates. In proteoliposomes containing reconstituted bacterial cytochrome c oxidase, fatty acids caused a "mild" uncoupling effect by reducing membrane potential only at low rate of membrane potential generation. "Free respiration" induced by the "mild" uncouplers, the fatty acids, can be considered as possible mechanism responsible for adaptation of the bacteria to a constantly changed environment. PMID:15527418

  13. A Mutant Strain of a Surfactant-Producing Bacterium with Increased Emulsification Activity

    NASA Astrophysics Data System (ADS)

    Liu, Qingmei; Yao, Jianming; Pan, Renrui; Yu, Zengliang

    2005-06-01

    As reported in this paper, a strain of oil-degrading bacterium Sp-5-3 was determined to belong to Enterobacteriaceae, which would be useful for microbial enhanced oil recovery (MEOR). The aim of our study was to generate a mutant using low energy N+ beam implantation. With 10 keV of energy and 5.2 × 1014 N+/cm2 of dose - the optimum condition, a mutant, S-34, was obtained, which had nearly a 5-fold higher surface and a 13-fold higher of emulsification activity than the wild type. The surface activity was measured by two methods, namely, a surface tension measuring instrument and a recording of the repulsive circle of the oil film; the emulsification activity was scaled through measuring the separating time of the oil-fermentation mixture. The metabolic acid was determined as methane by means of gas chromatography.

  14. Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil.

    PubMed

    Rice, Marlen C; Norton, Jeanette M; Valois, Frederica; Bollmann, Annette; Bottomley, Peter J; Klotz, Martin G; Laanbroek, Hendrikus J; Suwa, Yuichi; Stein, Lisa Y; Sayavedra-Soto, Luis; Woyke, Tanja; Shapiro, Nicole; Goodwin, Lynne A; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Kyrpides, Nikos; Varghese, Neha; Mikhailova, Natalia; Markowitz, Victor; Palaniappan, Krishna; Ivanova, Natalia; Stamatis, Dimitrios; Reddy, T B K; Ngan, Chew Yee; Daum, Chris

    2016-01-01

    Nitrosospira briensis C-128 is an ammonia-oxidizing bacterium isolated from an acid agricultural soil. N. briensis C-128 was sequenced with PacBio RS technologies at the DOE-Joint Genome Institute through their Community Science Program (2010). The high-quality finished genome contains one chromosome of 3.21 Mb and no plasmids. We identified 3073 gene models, 3018 of which are protein coding. The two-way average nucleotide identity between the chromosomes of Nitrosospira multiformis ATCC 25196 and Nitrosospira briensis C-128 was found to be 77.2 %. Multiple copies of modules encoding chemolithotrophic metabolism were identified in their genomic context. The gene inventory supports chemolithotrophic metabolism with implications for function in soil environments. PMID:27471578

  15. Two-dimensional gel-based alkaline proteome of the probiotic bacterium Lactobacillus acidophilus NCFM.

    PubMed

    Majumder, Avishek; Cai, Liyang; Ejby, Morten; Schmidt, Bjarne G; Lahtinen, Sampo J; Jacobsen, Susanne; Svensson, Birte

    2012-04-01

    Lactobacillus acidophilus NCFM (NCFM) is a well-documented probiotic bacterium isolated from human gut. Detailed 2D gel-based NCFM proteomics addressed the so-called alkaline range, i.e., pH 6-11. Proteins were identified in 150 of the 202 spots picked from the Coomassie Brilliant Blue stained 2D gel using MALDI-TOF-MS. The 102 unique gene products among the 150 protein identifications were assigned to different functional categories, and evaluated by considering a calculated distribution of abundance as well as grand average of hydrophobicity values. None of the very few available lactic acid bacteria proteome reference maps included the range of pI >7.0. The present report of such data on the proteome of NCFM fundamentally complements current knowledge on protein profiles limited to the acid and neutral pH range. PMID:22522807

  16. Acetylcholinesterase-Inhibiting Activity of Pyrrole Derivatives from a Novel Marine Gliding Bacterium, Rapidithrix thailandica

    PubMed Central

    Sangnoi, Yutthapong; Sakulkeo, Oraphan; Yuenyongsawad, Supreeya; Kanjana-opas, Akkharawit; Ingkaninan, Kornkanok; Plubrukarn, Anuchit; Suwanborirux, Khanit

    2008-01-01

    Acetylcholinesterase-inhibiting activity of marinoquinoline A (1), a new pyrroloquinoline from a novel species of a marine gliding bacterium Rapidithrix thailandica, was assessed (IC50 4.9 μM). Two related pyrrole derivatives, 3-(2′-aminophenyl)-pyrrole (3) and 2,2-dimethyl-pyrrolo-1,2-dihydroquinoline (4), were also isolated from two other strains of R. thailandica. The isolation of 3 from a natural source is reported here for the first time. Compound 4 was proposed to be an isolation artifact derived from 3. The two isolated compounds were virtually inactive in the acetylcholinesterase-inhibitory assay (enzyme inhibition < 30% at 0.1 g L−1). PMID:19172195

  17. Triplet excited state spectra and dynamics of carotenoids from the thermophilic purple photosynthetic bacterium Thermochromatium tepidum

    SciTech Connect

    Niedzwiedzki, Dariusz; Kobayashi, Masayuki; Blankenship, R. E.

    2011-01-13

    Light-harvesting complex 2 from the anoxygenic phototrophic purple bacterium Thermochromatium tepidum was purified and studied by steady-state absorption, fluorescence and flash photolysis spectroscopy. Steady-state absorption and fluorescence measurements show that carotenoids play a negligible role as supportive energy donors and transfer excitation to bacteriochlorophyll-a with low energy transfer efficiency of ~30%. HPLC analysis determined that the dominant carotenoids in the complex are rhodopin and spirilloxanthin. Carotenoid excited triplet state formation upon direct (carotenoid) or indirect (bacteriochlorophyll-a Q{sub x} band) excitation shows that carotenoid triplets are mostly localized on spirilloxanthin. In addition, no triplet excitation transfer between carotenoids was observed. Such specific carotenoid composition and spectroscopic results strongly suggest that this organism optimized carotenoid composition in the light-harvesting complex 2 in order to maximize photoprotective capabilities of carotenoids but subsequently drastically suppressed their supporting role in light-harvesting process.

  18. Purification and characterization of the alternative nitrogenase from the photosynthetic bacterium Rhodospirillum rubrum.

    PubMed Central

    Davis, R; Lehman, L; Petrovich, R; Shah, V K; Roberts, G P; Ludden, P W

    1996-01-01

    The alternative nitrogenase from a nifH mutant of the photosynthetic bacterium Rhodospirillum rubrum has been purified and characterized. The dinitrogenase protein (ANF1) contains three subunits in an apparent alpha2beta2gamma2 structure and contains Fe but no Mo or V. A factor capable of activating apo-dinitrogenase (lacking the FeMo cofactor) from Azotobacter vinelandii was extracted from the alternative dinitrogenase protein with N-methylformamide. The electron paramagnetic resonance (EPR) signal of the dinitrogenase protein is not characteristic of the EPR signals of molybdenum- or vanadium-containing dinitrogenases. The alternative dinitrogenase reductase (ANF2) was purified as an alpha2 dimer containing an Fe4S4 cluster and exhibited an EPR spectrum characteristic of dinitrogenase reductases. The enzyme complex reduces protons to H2 very well but reduces N2 to ammonium poorly. Acetylene is reduced to a mixture of ethylene and ethane. PMID:8631723

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

    PubMed

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

    2013-05-01

    In this study a new bacterium capable of growing on brown seaweed Laminaria japonica, Enterobacter sp. JMP3 was isolated from the gut of turban shell, Batillus cornutus. In anaerobic condition, it produced high yields of ethanol (1.15 mol-EtOH mol-mannitol(-1)) as well as organic acids from mannitol, the major carbohydrate component of L. japonica. Based on carbon distribution and metabolic flux analysis, it was revealed that mannitol was more favorable than glucose for ethanol production due to their different redox states. This indicates that L. japonica is one of the promising feedstock for bioethanol production. Additionally, the mannitol dehydrogenation pathway in Enterobacter sp. JMP3 was examined and verified. Finally, an attempt was made to explore the possibility of controlling ethanol production by altering the redox potential via addition of external NADH in mannitol fermentation. PMID:23186687

  20. Strain IMB-1, a novel bacterium for the removal of methyl bromide in fumigated agricultural soils

    USGS Publications Warehouse

    Connell, Hancock T.L.; Costello, A.M.; Lidstrom, M.E.; Oremland, R.S.

    1998-01-01

    A facultatively methylotrophic bacterium, strain IMB-1, that has been isolated from agricultural soil grows on methyl bromide (MeBr), methyl iodide, methyl chloride, and methylated amines, as well as on glucose, pyruvate, or acetate. Phylogenetic analysis of its 16S rRNA gene sequence indicates that strain IMB-1 classes in the alpha subgroup of the class Proteobacteria and is closely related to members of the genus Rhizobium. The ability of strain IMB-1 to oxidize MeBr to CO2 is constitutive in cells regardless of the growth substrate. Addition of cell suspensions of strain IMB-1 to soils greatly accelerates the oxidation of MeBr, as does pretreatment of soils with low concentrations of methyl iodide. These results suggest that soil treatment strategies can be devised whereby bacteria can effectively consume MeBr during field fumigations, which would diminish or eliminate the outward flux of MeBr to the atmosphere.

  1. Regulation of arylsulfate sulfotransferase from a human intestinal bacterium by nucleotides and magnesium ion.

    PubMed

    Konishi-Imamura, L; Kim, D H; Koizumi, M; Kobashi, K

    1995-01-01

    Arylsulfate sulfotransferase (ASST) from a human intestinal bacterium stoichiometrically catalyzed the transfer of a sulfate group from phenylsulfate esters to phenolic compounds. Pentachlorophenol, one of the selective inhibitors of phenol sulfoconjugation in mammalian tissues, inhibited both phenol and tyramine sulfation by ASST. Nucleotide triphosphates such as ATP, GTP, UTP and CTP, and pyrophosphate inhibited the ASST activity, whereas Mg2+ and Mn2+ activated the enzyme and prevented its inhibition by ATP and pyrophosphate. Equimolar binding of [alpha-] and [gamma-32P]ATP to the enzyme showed that the enzyme protein was not phosphorylated, but bound ATP. These results suggest that nucleotide triphosphates and divalent cations are important modulators in the control of ASST activity. PMID:7542320

  2. Prediction for the mixture toxicity of six organophosphorus pesticides to the luminescent bacterium Q67.

    PubMed

    Zhang, Ya-Hui; Liu, Shu-Shen; Song, Xiao-Qing; Ge, Hui-Lin

    2008-11-01

    Organophosphorus (OP) pesticides are ubiquitous in the surface water as mixtures. To examine the mixture toxicity in the multi-component space, the uniform design (UD) which can explore the concentration changes with few experimental efforts was employed to design the mixtures. On the other hand, the fixed concentration ratio ray was applied into six UD mixtures and two equivalent-effect concentration mixtures to build the whole concentration-response curves to overcome the demerit of the classical "point-to-point" method. The experimental toxicities of six pesticides and their mixtures to the luminescent bacterium Q67 were determined. The mixture toxicities were predicted by two models, concentration addition (CA) and independent action (IA). The results showed that all the mixture toxicities observed had no significant differences from the ones predicted by CA. However, the mixture toxicities were also well predicted by IA especially at the low-concentration section. PMID:18308393

  3. Electron microscopic investigation of the hydrogen-oxidizing acetate-forming anaerobic bacterium Acetobacterium woodii.

    PubMed

    Mayer, F; Lurz, R; Schoberth, S

    1977-11-18

    Acetobacterium woodii is a Gram-positive anaerobic nonsporeforming bacterium able to grow on H2 and CO2 as sole sources of energy. The product of fermentation is acetic acid. Fine structural analysis showed rod-shaped flagellated cells, and coccoid cells without flagella arranged predominantly in pairs and chains. The cell wall was found to be composed of three layers. The cell surface exhibited a periodic array of particles consisting of subunits. The cytoplasmic membrane showed particles either in random distribution or in a hexagonal pattern. Intracytoplasmic membranes were rarely observed, whereas inclusion bodies of varying shapes, predominantly in an uncommon disc-shape, could frequently be observed. Their content was dissolved in ultrathin sections indicating hydrophobic nature. PMID:596994

  4. Bioluminescent reporter bacterium for toxicity monitoring in biological wastewater treatment systems

    SciTech Connect

    Kelly, C.J.; Lajoie, C.A.; Layton, A.C.; Sayler, G.S.

    1999-01-01

    Toxic shock due to certain chemical loads in biological wastewater treatment systems can result in death of microorganisms and loss of floc structure. To overcome the limitations of existing approaches to toxicity monitoring, genes encoding enzymes for light production were inserted to a bacterium (Shk 1) isolated from activated sludge. The Shk 1 bioreporter indicated a toxic response to concentrations of cadmium, 2,4-dinitrophenol, and hydroquinone by reductions in initial levels of bioluminescence on exposure to the toxicant. The decrease in bioluminescence was more severe with increasing toxicant concentration. Bioluminescence did not decrease in response to ethanol concentrations up to 1,000 mg/L or to pH conditions between 6.1 and 7.9. A continuous toxicity monitoring system using this bioreporter was developed for influent wastewater and tested with hydroquinone. The reporter exhibited a rapid and proportional decrease in bioluminescence in response to increasing hydroquinone concentrations.

  5. The nucleotide sequence of Beneckea harveyi 5S rRNA. [bioluminescent marine bacterium

    NASA Technical Reports Server (NTRS)

    Luehrsen, K. R.; Fox, G. E.

    1981-01-01

    The primary sequence of the 5S ribosomal RNA isolated from the free-living bioluminescent marine bacterium Beneckea harveyi is reported and discussed in regard to indications of phylogenetic relationships with the bacteria Escherichia coli and Photobacterium phosphoreum. Sequences were determined for oligonucleotide products generated by digestion with ribonuclease T1, pancreatic ribonuclease and ribonuclease T2. The presence of heterogeneity is indicated for two sites. The B. harveyi sequence can be arranged into the same four helix secondary structures as E. coli and other prokaryotic 5S rRNAs. Examination of the 5S-RNS sequences of the three bacteria indicates that B. harveyi and P. phosphoreum are specifically related and share a common ancestor which diverged from an ancestor of E. coli at a somewhat earlier time, consistent with previous studies.

  6. Molecular Mechanisms of Adaptation of the Moderately Halophilic Bacterium Halobacillis halophilus to Its Environment

    PubMed Central

    Hänelt, Inga; Müller, Volker

    2013-01-01

    The capability of osmoadaptation is a prerequisite of organisms that live in an environment with changing salinities. Halobacillus halophilus is a moderately halophilic bacterium that grows between 0.4 and 3 M NaCl by accumulating both chloride and compatible solutes as osmolytes. Chloride is absolutely essential for growth and, moreover, was shown to modulate gene expression and activity of enzymes involved in osmoadaptation. The synthesis of different compatible solutes is strictly salinity- and growth phase-dependent. This unique hybrid strategy of H. halophilus will be reviewed here taking into account the recently published genome sequence. Based on identified genes we will speculate about possible scenarios of the synthesis of compatible solutes and the uptake of potassium ion which would complete our knowledge of the fine-tuned osmoregulation and intracellular osmolyte balance in H. halophilus. PMID:25371341

  7. Isolation and characterization of an anaerobic ruminal bacterium capable of degrading hydrolyzable tannins.

    PubMed Central

    Nelson, K E; Pell, A N; Schofield, P; Zinder, S

    1995-01-01

    An anaerobic diplococcoid bacterium able to degrade hydrolyzable tannins was isolated from the ruminal fluid of a goat fed desmodium (Desmodium ovalifolium), a tropical legume which contains levels as high as 17% condensed tannins. This strain grew under anaerobic conditions in the presence of up to 30 g of tannic acid per liter and tolerated a range of phenolic monomers, including gallic, ferulic, and p-coumaric acids. The predominant fermentation product from tannic acid breakdown was pyrogallol, as detected by high-performance liquid chromatography and mass spectrometry. Tannic acid degradation was dependent on the presence of a sugar such as glucose, fructose, arabinose, sucrose, galactose, cellobiose, or soluble starch as an added carbon and energy source. The strain also demonstrated resistance to condensed tannins up to a level of 4 g/liter. PMID:7574640

  8. The structure of ferricytochrome c552 from the psychrophilic marine bacterium Colwellia psychrerythraea 34H.

    PubMed

    Harvilla, Paul B; Wolcott, Holly N; Magyar, John S

    2014-06-01

    Approximately 40% of all proteins are metalloproteins, and approximately 80% of Earth's ecosystems are at temperatures ≤5 °C, including 90% of the global ocean. Thus, an essential aspect of marine metallobiochemistry is an understanding of the structure, dynamics, and mechanisms of cold adaptation of metalloproteins from marine microorganisms. Here, the molecular structure of the electron-transfer protein cytochrome c552 from the psychrophilic marine bacterium Colwellia psychrerythraea 34H has been determined by X-ray crystallography (PDB: ). The structure is highly superimposable with that of the homologous cytochrome from the mesophile Marinobacter hydrocarbonoclasticus. Based on structural analysis and comparison of psychrophilic, psychrotolerant, and mesophilic sequences, a methionine-based ligand-substitution mechanism for psychrophilic protein stabilization is proposed. PMID:24727932

  9. Comparative phylogenomics and multi-gene cluster analyses of the CitrusHuanglongbing (HLB)-associated bacterium Candidatus Liberibacter

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Huanglongbing (HLB, previously known as citrus greening), is associated with Candidatus Liberibacter species and is a serious threat to citrus production world-wide. The pathogen is a Gram negative, unculturable, phloem-limited bacterium with limited known genomic information. Expanding the genetic ...

  10. Comparative Genomics and Phylogenetic Analyses of Newly Cloned Genomic Regions From the Citrus Huanglongbing (HLB)-associated Bacterium Candidatus Liberibacter

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Huanglongbing (HLB), or citrus greening disease, caused by Candidatus Liberibacter species, is a serious threat to citrus production worldwide. The pathogen is a gram negative, unculturable, phloem-limited bacterium, with little known genomic information. Here, we report cloning and characterizatio...

  11. Rhizobium sp. strain BN4 (a selenium oxyanion-reducing bacterium) 16S rRNA gene complete sequence

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study used 1482 base pair 16S rRNA gene sequence methods in conjunction with other biochemical and morphological studies to confirm the identification of a bacterium (refer to as the BN4 strain) as a Rhizobium sp. The 16S rRNA gene sequence places it with the Rhizobium clade that includes R. d...

  12. Draft Genome Sequence of Photorhabdus temperata Strain Meg1, an Entomopathogenic Bacterium Isolated from Heterorhabditis megidis Nematodes

    PubMed Central

    Hurst, Sheldon G.; Ghazal, Shimaa; Morris, Krystalynne; Abebe-Akele, Feseha; Thomas, W. Kelley; Badr, Usama M.; Hussein, Mona A.; AbouZaied, Mohamed A.; Khalil, Kamal M.

    2014-01-01

    Photorhabdus temperata strain Meg1 is an entomopathogenic bacterium that forms a symbiotic association with Heterorhabditis nematodes. We report here a 4.9-Mbp draft genome sequence for P. temperata strain Meg1, with a G+C content of 43.18% and containing 4,340 candidate protein-coding genes. PMID:25502670

  13. Draft Genome Sequence of Photorhabdus luminescens Strain BA1, an Entomopathogenic Bacterium Isolated from Nematodes Found in Egypt.

    PubMed

    Ghazal, Shimaa; Hurst, Sheldon G; Morris, Krystalynne; Abebe-Akele, Feseha; Thomas, W Kelley; Badr, Usama M; Hussein, Mona A; Abouzaied, Mohamed A; Khalil, Kamal M; Tisa, Louis S

    2014-01-01

    Photorhabdus luminescens strain BA1 is an entomopathogenic bacterium that forms a symbiotic association with Heterorhabditis nematodes. We report here a 5.0-Mbp draft genome sequence for P. luminscens strain BA1, with a G+C content of 42.46% and 4,250 candidate protein-coding genes. PMID:24786955

  14. Draft Genome Sequence of Photorhabdus luminescens Strain BA1, an Entomopathogenic Bacterium Isolated from Nematodes Found in Egypt

    PubMed Central

    Ghazal, Shimaa; Hurst, Sheldon G.; Morris, Krystalynne; Abebe-Akele, Feseha; Thomas, W. Kelley; Badr, Usama M.; Hussein, Mona A.; AbouZaied, Mohamed A.; Khalil, Kamal M.

    2014-01-01

    Photorhabdus luminescens strain BA1 is an entomopathogenic bacterium that forms a symbiotic association with Heterorhabditis nematodes. We report here a 5.0-Mbp draft genome sequence for P. luminscens strain BA1, with a G+C content of 42.46% and 4,250 candidate protein-coding genes. PMID:24786955

  15. Draft Genome Sequence of Photorhabdus temperata Strain Meg1, an Entomopathogenic Bacterium Isolated from Heterorhabditis megidis Nematodes.

    PubMed

    Hurst, Sheldon G; Ghazal, Shimaa; Morris, Krystalynne; Abebe-Akele, Feseha; Thomas, W Kelley; Badr, Usama M; Hussein, Mona A; AbouZaied, Mohamed A; Khalil, Kamal M; Tisa, Louis S

    2014-01-01

    Photorhabdus temperata strain Meg1 is an entomopathogenic bacterium that forms a symbiotic association with Heterorhabditis nematodes. We report here a 4.9-Mbp draft genome sequence for P. temperata strain Meg1, with a G+C content of 43.18% and containing 4,340 candidate protein-coding genes. PMID:25502670

  16. Draft genome sequence of Enterobacter cloacae subsp. cloacae strain 08XA1, a fecal bacterium of giant pandas.

    PubMed

    Yan, Yue; Zhao, Chuan-Wu; Zhang, Yi-Zheng; Zhang, Zhi-He; Pan, Guang-Lin; Liu, Wen-Wang; Ma, Qing-Yi; Hou, Rong; Tan, Xue-Mei

    2012-12-01

    Enterobacter cloacae, a common pathogenic bacterium, is a Gram-negative bacillus. We analyzed the draft genome of Enterobacter cloacae subsp. cloacae strain 08XA1 from the feces of a giant panda in China. Genes encoding a β-lactamase and efflux pumps, as well as other factors, have been found in the genome. PMID:23209197

  17. Complete Genome Sequence of a Marine Bacterium, Pseudomonas pseudoalcaligenes Strain S1, with High Mercury Resistance and Bioaccumulation Capacity.

    PubMed

    Liu, Bing; Bian, Chao; Huang, Huiwei; Yin, Zhiwei; Shi, Qiong; Deng, Xu

    2016-01-01

    Pseudomonas pseudoalcaligenes S1, a marine bacterium, exhibited strong resistance to a high concentration of Hg(2+) and remarkable Hg(2+) bioaccumulation capacity. Here, we report the 6.9-Mb genome sequence of P. pseudoalcaligenes S1, which may help clarify its phylogenetic status and provide further understanding of the mechanisms of mercury bioremediation in a marine environment. PMID:27198018

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

    PubMed

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

    2016-02-10

    Agarivorans gilvus WH0801(T), an agarase-producing bacterium, was isolated from the surface of seaweed. Here, we present the complete genome sequence, which consists of one circular chromosome of 4,416,600 bp with a GC content of 45.9%. This genetic information will provide insight into biotechnological applications of producing agar for food and industry. PMID:26689482

  19. Complete Genome Sequence of the Sugar Beet Endophyte Pseudomonas poae RE*1-1-14, a Disease-Suppressive Bacterium

    PubMed Central

    Zachow, Christin; Alavi, Mohammadali; Tilcher, Ralf; Krempl, Peter Mauritius; Thallinger, Gerhard Günther; Berg, Gabriele

    2013-01-01

    The endophytic bacterium Pseudomonas poae RE*1-1-14 shows broad antagonistic activity and is applied to seeds as a biocontrol agent to suppress late root rot in the sugar beet. The completely sequenced 5.5-Mb genome reveals genes that putatively contribute to this antagonistic activity and the intimate plant-microbe interaction. PMID:23516179

  20. Draft Genome Sequence of Bacillus humi LMG 22167T (DSM 16318), an Endospore-Forming Bacterium Isolated from Soil

    PubMed Central

    Wang, Jie-ping; Liu, Guo-hong; Pan, Zhizhen; Xiao, Rong-feng; Chen, Meichun; Chen, De-ju

    2016-01-01

    Bacillus humi LMG 22167T is a Gram-positive, aerobic, and spore-forming bacterium Here, we report the 4.80-Mb draft genome sequence of B. humi LMG 22167T, which is the first genome sequence of this species and will promote its fundamental research. PMID:26847898

  1. Draft Genome Sequence of Bacillus plakortidis P203T (DSM 19153), an Alkali- and Salt-Tolerant Marine Bacterium

    PubMed Central

    Wang, Jie-ping; Liu, Guo-hong; Ge, Ci-bin; Xiao, Rong-feng; Zheng, Xue-fang; Shi, Huai

    2016-01-01

    Bacillus plakortidis P203T is a Gram-positive, spore-forming, and alkali- and salt-tolerant marine bacterium. Here, we report the 3.97-Mb draft genome sequence of B. plakortidis P203T, which will promote its fundamental research and provide useful information for genomic taxonomy and phylogenomics of Bacillus-like bacteria. PMID:26847896

  2. Draft Genome of Shewanella frigidimarina Ag06-30, a Marine Bacterium Isolated from Potter Peninsula, King George Island, Antarctica

    PubMed Central

    Parmeciano Di Noto, Gisela; Vázquez, Susana C.; MacCormack, Walter P.; Iriarte, Andrés

    2016-01-01

    We present the draft genome of Shewanella frigidimarina Ag06-30, a marine bacterium from King George Island, Antarctica, which encodes the carbapenemase SFP-1. The assembly contains 4,799,218 bp (G+C content 41.24%). This strain harbors several mobile genetic elements that provide insight into lateral gene transfer and bacterial plasticity and evolution. PMID:27151790

  3. Draft Genome of Shewanella frigidimarina Ag06-30, a Marine Bacterium Isolated from Potter Peninsula, King George Island, Antarctica.

    PubMed

    Parmeciano Di Noto, Gisela; Vázquez, Susana C; MacCormack, Walter P; Iriarte, Andrés; Quiroga, Cecilia

    2016-01-01

    We present the draft genome of Shewanella frigidimarina Ag06-30, a marine bacterium from King George Island, Antarctica, which encodes the carbapenemase SFP-1. The assembly contains 4,799,218 bp (G+C content 41.24%). This strain harbors several mobile genetic elements that provide insight into lateral gene transfer and bacterial plasticity and evolution. PMID:27151790

  4. Genome Sequence of Klebsiella oxytoca SA2, an Endophytic Nitrogen-Fixing Bacterium Isolated from the Pioneer Grass Psammochloa villosa

    PubMed Central

    Chen, Mingyue; Lin, Li; Zhang, Yanming; Sun, Li

    2013-01-01

    Klebsiella oxytoca strain SA2 is an endophytic nitrogen-fixing bacterium isolated from the pioneer grass Psammochloa villosa, which grows in the moving sand dunes of Ordos Plateau, China. The SA2 genome sequence provides the genetic background for understanding its endophytic lifestyle and survival in association with grass in nitrogen-poor environments. PMID:23950120

  5. Genome Sequence of Klebsiella oxytoca SA2, an Endophytic Nitrogen-Fixing Bacterium Isolated from the Pioneer Grass Psammochloa villosa.

    PubMed

    Chen, Mingyue; Lin, Li; Zhang, Yanming; Sun, Li; An, Qianli

    2013-01-01

    Klebsiella oxytoca strain SA2 is an endophytic nitrogen-fixing bacterium isolated from the pioneer grass Psammochloa villosa, which grows in the moving sand dunes of Ordos Plateau, China. The SA2 genome sequence provides the genetic background for understanding its endophytic lifestyle and survival in association with grass in nitrogen-poor environments. PMID:23950120

  6. Complete genome sequence of a keratin-degrading bacterium Chryseobacterium gallinarum strain DSM 27622(T) isolated from chicken.

    PubMed

    Park, Gun-Seok; Hong, Sung-Jun; Jung, Byung Kwon; Khan, Abdur Rahim; Park, Yeong-Jun; Park, Chang Eon; Lee, Ara; Kwak, Yunyoung; Lee, Yong-Jik; Lee, Dong-Woo; Lee, Changhee; Park, Choi Kyu; Shin, Jae-Ho

    2015-10-10

    Chryseobacterium gallinarum strain DSM 27622(T) is a keratin-degrading bacterium belonging to the class Flavobacteriia, which was isolated from chicken. Here, we report the 4633,632bp complete genome sequence of the strain DSM 27622(T) with 4161 genes. PMID:26209507

  7. Draft Genome Sequence of Chryseobacterium sp. Strain P1-3, a Keratinolytic Bacterium Isolated from Poultry Waste.

    PubMed

    Park, Gun-Seok; Hong, Sung-Jun; Lee, Chang-Hyun; Khan, Abdur Rahim; Ullah, Ihsan; Jung, Byung Kwon; Choi, JungBae; Kwak, Yunyoung; Back, Chang-Gi; Jung, Hee-Young; Shin, Jae-Ho

    2014-01-01

    Chryseobacterium sp. strain P1-3, harboring keratin degrading activity, has recently been isolated from poultry waste. Here, we report the 4.6-Mbp draft genome sequence of the keratinolytic bacterium with a G+C content of 37.0% and 4,087 protein-coding genes. PMID:25428979

  8. Draft Genome Sequence for Microbacterium laevaniformans Strain OR221, a Bacterium Tolerant to Metals, Nitrate, and Low pH

    PubMed Central

    Brown, Steven D.; Palumbo, Anthony V.; Panikov, Nicolai; Ariyawansa, Thilini; Klingeman, Dawn M.; Johnson, Courtney M.; Land, Miriam L.; Utturkar, Sagar M.

    2012-01-01

    Microbacterium laevaniformans strain OR221 was isolated from subsurface sediments obtained from the Field Research Center (FRC) in Oak Ridge, TN. It was characterized as a bacterium tolerant to heavy metals, such as uranium, nickel, cobalt, and cadmium, as well as nitrate and low pH. We present its draft genome sequence. PMID:22628508

  9. Draft Genome Sequence of Acinetobacter calcoaceticus Strain P23, a Plant Growth-Promoting Bacterium of Duckweed

    PubMed Central

    Hosoyama, Akira; Yamazoe, Atsushi; Morikawa, Masaaki

    2015-01-01

    Acinetobacter calcoaceticus strain P23 is a plant growth-promoting bacterium, which was isolated from the surface of duckweed. We report here the draft genome sequence of strain P23. The genome data will serve as a valuable reference for understanding the molecular mechanism of plant growth promotion in aquatic plants. PMID:25720680

  10. Draft Genome Sequence of Acinetobacter calcoaceticus Strain P23, a Plant Growth-Promoting Bacterium of Duckweed.

    PubMed

    Sugawara, Masayuki; Hosoyama, Akira; Yamazoe, Atsushi; Morikawa, Masaaki

    2015-01-01

    Acinetobacter calcoaceticus strain P23 is a plant growth-promoting bacterium, which was isolated from the surface of duckweed. We report here the draft genome sequence of strain P23. The genome data will serve as a valuable reference for understanding the molecular mechanism of plant growth promotion in aquatic plants. PMID:25720680

  11. Friend and foe: factors influencing the movement of the bacterium Helicobacter pylori along the parasitism–mutualism continuum

    PubMed Central

    Lin, Derek; Koskella, Britt

    2015-01-01

    Understanding the transition of bacterial species from commensal to pathogen, or vice versa, is a key application of evolutionary theory to preventative medicine. This requires working knowledge of the molecular interaction between hosts and bacteria, ecological interactions among microbes, spatial variation in bacterial prevalence or host life history, and evolution in response to these factors. However, there are very few systems for which such broad datasets are available. One exception is the gram-negative bacterium, Helicobacter pylori, which infects upwards of 50% of the global human population. This bacterium is associated with a wide breadth of human gastrointestinal disease, including numerous cancers, inflammatory disorders, and pathogenic infections, but is also known to confer fitness benefits to its host both indirectly, through interactions with other pathogens, and directly. Outstanding questions are therefore why, when, and how this bacterium transitions along the parasitism–mutualism continuum. We examine known virulence factors, genetic predispositions of the host, and environmental contributors that impact progression of clinical disease and help define geographical trends in disease incidence. We also highlight the complexity of the interaction and discuss future therapeutic strategies for disease management and public health in light of the longstanding evolutionary history between the bacterium and its human host. PMID:25667600

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

    PubMed

    Meneghel, Julie; Dugat-Bony, Eric; Irlinger, Françoise; Loux, Valentin; Vidal, Marie; Passot, Stéphanie; Béal, Catherine; Layec, Séverine; Fonseca, Fernanda

    2016-01-01

    Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) is a lactic acid bacterium widely used for the production of yogurt and cheeses. Here, we report the genome sequence of L. bulgaricus CFL1 to improve our knowledge on its stress-induced damages following production and end-use processes. PMID:26941141

  13. Boron nitride nanotube-based biosensing of various bacterium/viruses: continuum modelling-based simulation approach.

    PubMed

    Panchal, Mitesh B; Upadhyay, Sanjay H

    2014-09-01

    In this study, the feasibility of single walled boron nitride nanotube (SWBNNT)-based biosensors has been ensured considering the continuum modelling-based simulation approach, for mass-based detection of various bacterium/viruses. Various types of bacterium or viruses have been taken into consideration at the free-end of the cantilevered configuration of the SWBNNT, as a biosensor. Resonant frequency shift-based analysis has been performed with the adsorption of various bacterium/viruses considered as additional mass to the SWBNNT-based sensor system. The continuum mechanics-based analytical approach, considering effective wall thickness has been considered to validate the finite element method (FEM)-based simulation results, based on continuum volume-based modelling of the SWBNNT. As a systematic analysis approach, the FEM-based simulation results are found in excellent agreement with the analytical results, to analyse the SWBNNTs for their wide range of applications such as nanoresonators, biosensors, gas-sensors, transducers and so on. The obtained results suggest that by using the SWBNNT of smaller size the sensitivity of the sensor system can be enhanced and detection of the bacterium/virus having mass of 4.28 × 10⁻²⁴ kg can be effectively performed. PMID:25082222

  14. Isolation and characterization of a novel poly(vinyl alcohol)-degrading bacterium, Sphingopyxis sp. PVA3.

    PubMed

    Yamatsu, Atsushi; Matsumi, Rie; Atomi, Haruyuki; Imanaka, Tadayuki

    2006-10-01

    We have isolated a poly(vinyl alcohol) (PVA)-degrading bacterium from an activated sludge sample obtained from the drainage of a dyeing factory. Enrichment cultures were performed in media containing PVA as the sole or major carbon source. After several rounds of cultivation on liquid and solid media, we were able to isolate a single colony with PVA-degrading ability (strain PVA3). The bacterium could degrade PVA in the absence of symbionts or cofactors such as pyrroloquinoline quinone (PQQ). Over 90% of PVA, at an initial concentration of 0.1%, was degraded within a 6-day cultivation. Degradation was confirmed by both iodometric methods and gel permeation chromatography. Examination of the PVA attached to the cells revealed a large increase in carbonyl groups, suggesting the oxidation of hydroxyl groups of the polymer on the surfaces of cells. Addition of PQQ to the culture medium did not enhance the growth and the PVA-degrading rates of strain PVA3. Furthermore, we found that cells grown on PVA generated hydrogen peroxide upon the addition of PVA. The results strongly suggest that the initial oxidation of PVA is mediated via a PVA oxidase, and not a PQQ-dependent dehydrogenase. A biochemical and phylogenetic characterization of the bacterium was performed. The sequence of the 16S ribosomal RNA gene of the bacterium indicated a phylogenetic position of the strain within the genus Sphingopyxis, and the strain was therefore designated Sphingopyxis sp. PVA3. PMID:16583228

  15. Draft Genome Sequence and Description of Janthinobacterium sp. Strain CG3, a Psychrotolerant Antarctic Supraglacial Stream Bacterium.

    PubMed

    Smith, Heidi; Akiyama, Tatsuya; Foreman, Christine; Franklin, Michael; Woyke, Tanja; Teshima, Hazuki; Davenport, Karen; Daligault, Hajnalka; Erkkila, Tracy; Goodwin, Lynne; Gu, Wei; Xu, Yan; Chain, Patrick

    2013-01-01

    Here we present the draft genome sequence of Janthinobacterium sp. strain CG3, a psychrotolerant non-violacein-producing bacterium that was isolated from the Cotton Glacier supraglacial stream. The genome sequence of this organism will provide insight as to the mechanisms necessary for bacteria to survive in UV-stressed icy environments. PMID:24265494

  16. Isolation and characterization of an Enterococcus-like bacterium causing muscle necrosis and mortality in Macrobrachium rosenbergii in Taiwan.

    PubMed

    Cheng, W; Chen, J C

    1998-10-01

    A Gram-positive, ovoid, diplococoid bacterium tentatively identified as Enterococcus-like was isolated from diseased Macrobrachium rosenbergii in Taiwanese aquaculture ponds. The diseased prawns displayed poor growth, anorexia, inactivity, opaque and whitish musculature, and mortality. In histological preparations, melanized hemocytic granulomas were seen in the connective tissue around hemal sinuses together with hemocytic aggregation in necrotic musculature. Five isolates of diplococci were collected from diseased prawns at 4 farms and these were evaluated for 93 characteristics including morphology, physiology, biochemistry and sensitivity to antibiotics. The results indicated that the isolates belonged to a single species. They grew in 0.5 to 6.0% NaCl, at 10 to 40 degrees C, at pH 9.6 and on bile esculin medium, gave positive pyrrolidonylarylamidase, arginine dehydrolase and Voges-Proskauer tests, were resistant to bacitracin and SXT, and were CAMP-negative and non-hemolytic on sheep blood agar. These findings indicated an Enterococcus-like bacterium closely related to Enterococcus seriolicida (recently reduced to synonymy with Lactococcus garvieae). Experimental injection of 3 x 10(5) cells of strain KM002 of this Enterococcus-like bacterium into the ventral sinus of the prawn cephalothorax caused 100% mortality in 11 d, and induced muscular necrosis and hepatopancreatitis, gross signs and histopathology similar to those observed in the naturally infected prawns. It was concluded that this Enterococcus-like bacterium was the etiological agent associated with mortality of the farmed, diseased prawns. PMID:9828405

  17. Draft Genome Sequence for Microbacterium laevaniformans Strain OR221, a Bacterium Tolerant to Metals, Nitrate, and Low pH

    SciTech Connect

    Brown, Steven D; Palumbo, Anthony Vito; Panikov, Nikolai; Ariyawansa, Thilini; Klingeman, Dawn Marie; Johnson, Courtney M; Land, Miriam L; Utturkar, Sagar M; Epstein, Slava

    2012-01-01

    Microbacterium laevaniformans strain OR221 was isolated from subsurface sediments obtained from the Field Research Center (FRC) in Oak Ridge, TN. It was characterized as a bacterium tolerant to heavy metals such as uranium, nickel, cobalt, cadmium, as well as nitrate and low pH. We present its draft genome sequence.

  18. Complete Genome Sequence of Streptococcus salivarius HSISS4, a Human Commensal Bacterium Highly Prevalent in the Digestive Tract.

    PubMed

    Mignolet, Johann; Fontaine, Laetitia; Kleerebezem, Michiel; Hols, Pascal

    2016-01-01

    The human commensal bacterium Streptococcus salivarius plays a major role in the equilibrium of microbial communities of the digestive tract. Here, we report the first complete genome sequence of a Streptococcus salivarius strain isolated from the small intestine, namely, HSISS4. Its circular chromosome comprises 1,903 coding sequences and 2,100,988 nucleotides. PMID:26847886

  19. Complete Genome Sequence of Streptococcus salivarius HSISS4, a Human Commensal Bacterium Highly Prevalent in the Digestive Tract

    PubMed Central

    Fontaine, Laetitia; Kleerebezem, Michiel

    2016-01-01

    The human commensal bacterium Streptococcus salivarius plays a major role in the equilibrium of microbial communities of the digestive tract. Here, we report the first complete genome sequence of a Streptococcus salivarius strain isolated from the small intestine, namely, HSISS4. Its circular chromosome comprises 1,903 coding sequences and 2,100,988 nucleotides. PMID:26847886

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

    PubMed

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

    2015-01-01

    Here, we report a draft genome sequence of Anaeromyxobacter sp. strain PSR-1, an arsenate-respiring bacterium isolated from arsenic-contaminated soil. It contained three distinct arsenic resistance gene clusters (ars operons), while no respiratory arsenate reductase gene (arr) was identified. PMID:25977440

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

    PubMed Central

    Tonomura, Mimori; Ehara, Ayaka; Suzuki, Haruo

    2015-01-01

    Here, we report a draft genome sequence of Anaeromyxobacter sp. strain PSR-1, an arsenate-respiring bacterium isolated from arsenic-contaminated soil. It contained three distinct arsenic resistance gene clusters (ars operons), while no respiratory arsenate reductase gene (arr) was identified. PMID:25977440

  2. Draft genome sequence for Microbacterium laevaniformans strain OR221, a bacterium tolerant to metals, nitrate, and low pH.

    PubMed

    Brown, Steven D; Palumbo, Anthony V; Panikov, Nicolai; Ariyawansa, Thilini; Klingeman, Dawn M; Johnson, Courtney M; Land, Miriam L; Utturkar, Sagar M; Epstein, Slava S

    2012-06-01

    Microbacterium laevaniformans strain OR221 was isolated from subsurface sediments obtained from the Field Research Center (FRC) in Oak Ridge, TN. It was characterized as a bacterium tolerant to heavy metals, such as uranium, nickel, cobalt, and cadmium, as well as nitrate and low pH. We present its draft genome sequence. PMID:22628508

  3. Complete Genome Sequence of Enterococcus hirae R17, a Daptomycin-Resistant Bacterium Isolated from Retail Pork in China.

    PubMed

    Peng, Zixin; Wang, Wei; Hu, Yujie; Li, Fengqin

    2016-01-01

    Daptomycin-resistant Enterococcus hirae R17 was isolated from retail pork sold at a free-trade market in Beijing, China. The complete genome sequence of R17 contains a circular 2,886,481-bp chromosome and a circular 73,574-bp plasmid. Genes involved in cell envelope homeostasis of this bacterium were identified by whole-genome analysis. PMID:27340071

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

    PubMed

    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

    2016-01-01

    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. PMID:27198027

  5. ["Candidatus contubernalis alkalaceticum," an obligately syntrophic alkaliphilic bacterium capable of anaerobic acetate oxidation in a coculture with Desulfonatronum cooperativum].

    PubMed

    Zhilina, T N; Zavarzina, D G; Kolganova, T V; Turova, T P; Zavarzin, G A

    2005-01-01

    From the silty sediments of the Khadyn soda lake (Tuva), a binary sulfidogenic bacterial association capable of syntrophic acetate oxidation at pH 10.0 was isolated. An obligately syntrophic, gram-positive, spore-forming alkaliphilic rod-shaped bacterium performs acetate oxidation in a syntrophic association with a hydrogenotrophic, alkaliphilic sulfate-reducing bacterium; the latter organism was previously isolated and characterized as the new species Desulfonatronum cooperativum. Other sulfate-reducing bacteria of the genera Desulfonatronum and Desulfonatronovibrio can also act as the hydrogenotrophic partner. Apart from acetate, the syntrophic culture can oxidize ethanol, propanol, isopropanol, serine, fructose, and isobutyric acid. Selective amplification of 16S rRNA gene fragments of the acetate-utilizing syntrophic component of the binary culture was performed; it was found to cluster with clones of uncultured gram-positive bacteria within the family Syntrophomonadaceae. The acetate-oxidizing bacterium is thus the first representative of this cluster obtained in a laboratory culture. Based on its phylogenetic position, the new acetate-oxidizing syntrophic bacterium is proposed to be assigned, in a Candidate status, to a new genus and species: "Candidatus Contubernalis alkalaceticum." PMID:16400991

  6. Draft Genome Sequence of Vibrio sp. Strain Evh12, a Bacterium Retrieved from the Gorgonian Coral Eunicella verrucosa

    PubMed Central

    Franco, Telma; Califano, Gianmaria; Gonçalves, Ana C. S.; Cúcio, Catarina

    2016-01-01

    To shed light on the associations established between Vibrio species and soft corals in coastal ecosystems, we report here the draft genome sequence of Vibrio sp. strain Evh12, a bacterium that has been isolated from the gorgonian coral Eunicella verrucosa and that shows antagonistic activity against Escherichia coli. PMID:26868405

  7. Thermoregulation of N-Acyl Homoserine Lactone-Based Quorum Sensing in the Soft Rot Bacterium Pectobacterium atrosepticum▿

    PubMed Central

    Latour, Xavier; Diallo, Stéphanie; Chevalier, Sylvie; Morin, Danièle; Smadja, Bruno; Burini, Jean-François; Haras, Dominique; Orange, Nicole

    2007-01-01

    The psychrotolerant bacterium Pectobacterium atrosepticum produces four N-acyl homoserine lactones under a wide range of temperatures. Their thermoregulation differs from that of the exoenzyme production, described as being under quorum-sensing control. A mechanism involved in this thermoregulation consists of controlling N-acyl homoserine lactones synthase production at a transcriptional level. PMID:17468275

  8. Draft Genome Sequence and Description of Janthinobacterium sp. Strain CG3, a Psychrotolerant Antarctic Supraglacial Stream Bacterium

    PubMed Central

    Smith, Heidi; Akiyama, Tatsuya; Franklin, Michael; Woyke, Tanja; Teshima, Hazuki; Davenport, Karen; Daligault, Hajnalka; Erkkila, Tracy; Goodwin, Lynne; Gu, Wei; Xu, Yan; Chain, Patrick

    2013-01-01

    Here we present the draft genome sequence of Janthinobacterium sp. strain CG3, a psychrotolerant non-violacein-producing bacterium that was isolated from the Cotton Glacier supraglacial stream. The genome sequence of this organism will provide insight as to the mechanisms necessary for bacteria to survive in UV-stressed icy environments. PMID:24265494

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

    PubMed

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

    2016-01-01

    Two marine endophytic bacteria were isolated from the Red Sea algae; a red alga; Acanthophora dendroides and the brown alga Sargassum sabrepandum. The isolates were identified based on their 16SrRNA sequences as Bacterium SRCnm and Bacillus sp. JS. The objective of this study was to investigate the potential anti-microbial and antioxidant activities of the extracts of the isolated bacteria grown in different nutrient conditions. Compared to amoxicillin (25μg/disk) and erythromycin (15μg/disk), the extracts of Bacterium SRCn min media II, III, IV and V were potent inhibitors of the gram-positive bacterium Sarcina maxima even at low concentrations. Also, the multidrug resistant Staphylococcus aureus(MRSA) was more sensitive to the metabolites produced in medium (II) of the same endophyte than erythromycin (15μg/disk). A moderate activity of the Bacillus sp. JS extracts of media I and II was obtained against the same pathogen. The total compounds (500ug/ml) of both isolated endophytes showed moderate antioxidant activities (48.9% and 46.1%, respectively). LC/MS analysis of the bacterial extracts was carried out to investigate the likely natural products produced. Cyclo(D-cis-Hyp-L-Leu), dihydrosphingosine and 2-Amino-1,3-hexadecanediol were identified in the fermentation medium of Bacterium SRCnm, whereas cyclo (D-Pro-L-Tyr) and cyclo (L-Leu-L-Pro) were the suggested compounds of Bacillus sp. JS. PMID:26826831

  10. Complete Genome Sequence of Dyella thiooxydans ATSB10, a Thiosulfate-Oxidizing Bacterium Isolated from Sunflower Fields in South Korea.

    PubMed

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

    2016-01-01

    Dyella thiooxydans ATSB10 (KACC 12756(T) = LMG 24673(T)) is a thiosulfate-oxidizing bacterium isolated from rhizosphere soils of sunflower plants. In this study, we completely sequenced the genome of D. thiooxydans ATSB10 and identified the genes involved in thiosulfate oxidation and the metabolism of aromatic intermediates. PMID:27340060

  11. Draft Genome Sequence of a Potential Nitrate-Dependent Fe(II)-Oxidizing Bacterium, Aquabacterium parvum B6

    PubMed Central

    Zhang, Xiaoxin

    2016-01-01

    Aquabacterium parvum B6 is a potential nitrate-dependent Fe(II)-oxidizing bacterium. The genes related to its denitrifying mechanism and iron metabolisms were unknown. We present the draft genome of Aquabacterium parvum B6, which could provide further insight into the nitrate-dependent Fe(II)-oxidizing mechanism of strain B6. PMID:26823591

  12. Draft Genome Sequence of a Potential Nitrate-Dependent Fe(II)-Oxidizing Bacterium, Aquabacterium parvum B6.

    PubMed

    Zhang, Xiaoxin; Ma, Fang; Szewzyk, Ulrich

    2016-01-01

    Aquabacterium parvum B6 is a potential nitrate-dependent Fe(II)-oxidizing bacterium. The genes related to its denitrifying mechanism and iron metabolisms were unknown. We present the draft genome of Aquabacterium parvum B6, which could provide further insight into the nitrate-dependent Fe(II)-oxidizing mechanism of strain B6. PMID:26823591

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

    PubMed

    Jeong, Jin-Ju; Park, Byeong Hyeok; Park, Hongjae; Choi, In-Geol; Kim, Ki Deok

    2016-01-01

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

  14. Genomic Sequence of Burkholderia multivorans NKI379, a Soil Bacterium That Inhibits the Growth of Burkholderia pseudomallei

    PubMed Central

    Hsueh, Pei-Tan; Liu, Jong-Kang; Chen, Ya-Lei; Liu, Pei-Ju; Ni, Wen-Fan; Chen, Yao-Shen; Wu, Keh-Ming

    2015-01-01

    Burkholderia multivorans NKI379 is a soil bacterium that exhibits an antagonistic effect against the growth of Burkholderia pseudomallei, the causative agent of the infectious disease melioidosis. We report the draft genomic sequence of B. multivorans NKI379, which has a G+C content of 67% and 5,203 candidate protein-encoding genes. PMID:26586873

  15. Genomic Sequence of Burkholderia multivorans NKI379, a Soil Bacterium That Inhibits the Growth of Burkholderia pseudomallei.

    PubMed

    Hsueh, Pei-Tan; Liu, Jong-Kang; Chen, Ya-Lei; Liu, Pei-Ju; Ni, Wen-Fan; Chen, Yao-Shen; Wu, Keh-Ming; Lin, Hsi-Hsun

    2015-01-01

    Burkholderia multivorans NKI379 is a soil bacterium that exhibits an antagonistic effect against the growth of Burkholderia pseudomallei, the causative agent of the infectious disease melioidosis. We report the draft genomic sequence of B. multivorans NKI379, which has a G+C content of 67% and 5,203 candidate protein-encoding genes. PMID:26586873

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  18. Complete Genome Sequence of Dyella thiooxydans ATSB10, a Thiosulfate-Oxidizing Bacterium Isolated from Sunflower Fields in South Korea

    PubMed Central

    Hwangbo, Kyeong; Um, Yurry; Chung, Hee; Yoo, Jemin; Kim, Ki Yoon; Madhaiyan, Munusamy; Sa, Tong Min

    2016-01-01

    Dyella thiooxydans ATSB10 (KACC 12756T = LMG 24673T) is a thiosulfate-oxidizing bacterium isolated from rhizosphere soils of sunflower plants. In this study, we completely sequenced the genome of D. thiooxydans ATSB10 and identified the genes involved in thiosulfate oxidation and the metabolism of aromatic intermediates. PMID:27340060

  19. Draft Genome Sequence of Bacillus pseudalcaliphilus PN-137T (DSM 8725), an Alkaliphilic Halotolerant Bacterium Isolated from Garden Soils.

    PubMed

    Wang, Jie-Ping; Liu, Bo; Liu, Guo-Hong; Xiao, Rong-Feng; Zheng, Xue-Fang; Shi, Huai; Ge, Ci-Bin

    2015-01-01

    Bacillus pseudalcaliphilus PN-137(T) (DSM 8725) is a Gram-positive, spore-forming, alkaliphilic, and halotolerant bacterium. Here, we report the 4.49-Mb genome sequence of B. pseudalcaliphilus PN-137(T), which will accelerate the application of this alkaliphile and provide useful information for genomic taxonomy and phylogenomics of Bacillus-like bacteria. PMID:26272579

  20. Complete Genome Sequence of Raoultella ornithinolytica Strain S12, a Lignin-Degrading Bacterium Isolated from Forest Soil.

    PubMed

    Bao, Wenying; Zhou, Yun; Jiang, Jingwei; Xu, Zhihui; Hou, Liyuan; Leung, Frederick Chi-Ching

    2015-01-01

    We report the complete genome sequence of Raoultella ornithinolytica strain S12, isolated from a soil sample collected from areas bordering rotten wood and wet soil on Mt. Zijin, Nanjing. The complete genome of this bacterium may contribute toward the discovery of efficient lignin-degrading pathways. PMID:25792045

  1. Draft Genome Sequence of Sporosarcina globispora W 25T (DSM 4), a Psychrophilic Bacterium Isolated from Soil and River Water

    PubMed Central

    Wang, Jie-ping; Liu, Guo-hong; Xiao, Rong-feng; Zheng, Xue-fang; Shi, Huai; Ge, Ci-bin

    2015-01-01

    Sporosarcina globispora W 25T (DSM 4) is a Gram-positive, round-spore-forming, and psychrophilic bacterium. Here, we report the 5.66-Mb genome sequence of S. globispora W 25T, which will accelerate the application of this psychrophile and provide useful information for genomic taxonomy and phylogenomics of Bacillus-like bacteria. PMID:26494677

  2. Extraction of DNA from orange juice and detection of bacterium Candidatus Liberibacter asiaticus by real-time PCR

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Orange juice processed from Huanglongbing (HLB) affected fruit is often associated with bitter taste and/or off-flavor. HLB disease in Florida is associated with Candidatus Liberibacter asiaticus (CLas), a phloem limited bacterium. The current standard to confirm CLas for citrus trees is to take sam...

  3. Draft Genome Sequence of the Piezotolerant and Crude Oil-Degrading Bacterium Rhodococcus qingshengii Strain TUHH-12

    PubMed Central

    Hamilton, Trinity L.; Valladares Juárez, Ana Gabriela; Schedler, Martina; Macalady, Jennifer L.; Müller, Rudolf; Freeman, Katherine H.

    2015-01-01

    We report here the draft genome sequence of Rhodococcus qingshengii strain TUHH-12. The ability of this piezotolerant bacterium to grow on crude oil and tetracosane as sole carbon sources at 150 × 105 Pa makes it useful in studies of hydrocarbon degradation under simulated deep-sea conditions. PMID:25858843

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

    PubMed

    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. PMID:26393955

  5. Quantitative analysis of growth and volatile fatty acid production by the anaerobic ruminal bacterium Megasphaera elsdenii T81

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Megaspheara elsdenii T81 grew on either DL-lactate or D-glucose at similar rates (0.85 per h), but displayed major differences in the fermentation of these substrates. Lactate was fermented at up to 210-mM concentration to yield acetic, propionic, butyric, and valeric acids. The bacterium was able t...

  6. Draft Genome Sequence of the Polyhydroxyalkanoate-Producing Bacterium Burkholderia sacchari LMG 19450 Isolated from Brazilian Sugarcane Plantation Soil

    PubMed Central

    Alexandrino, Paulo Moises Raduan; Mendonça, Thatiane Teixeira; Guamán Bautista, Linda Priscila; Cherix, Juliano; Lozano-Sakalauskas, Gabriela Cazonato; Fujita, André; Ramos Filho, Edmar; Long, Paul; Padilla, Gabriel; Taciro, Marilda Keico; Gomez, José Gregório Cabrera

    2015-01-01

    Burkholderia sacchari LMG 19450, isolated from the soil of a sugarcane plantation in Brazil, accumulates large amounts of polyhydroxyalkanoates from sucrose, xylose, other carbohydrates, and organic acids. We present the draft genome sequence of this industrially relevant bacterium, which is 7.2 Mb in size and has a G+C content of 64%. PMID:25953171

  7. Draft Genome Sequence of Bacillus farraginis R-6540T (DSM 16013), a Spore-Forming Bacterium Isolated at Dairy Farms

    PubMed Central

    Wang, Jie-ping; Liu, Guo-hong; Ge, Ci-bin; Xiao, Rong-feng; Zheng, Xue-fang; Shi, Huai

    2016-01-01

    Bacillus farraginis R-6540T is a Gram-positive, aerobic, and spore-forming bacterium with very high intrinsic heat resistance. Here, we report the 5.32-Mb draft genome sequence of B. farraginis R-6540T, which is the first genome sequence of this species and will promote its fundamental research. PMID:27313303

  8. Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis subsp. lactis TOMSC161, Isolated from a Nonscalded Curd Pressed Cheese

    PubMed Central

    Velly, H.; Abraham, A.-L.; Loux, V.; Delacroix-Buchet, A.; Fonseca, F.; Bouix, M.

    2014-01-01

    Lactococcus lactis is a lactic acid bacterium used in the production of many fermented foods, such as dairy products. Here, we report the genome sequence of L. lactis subsp. lactis TOMSC161, isolated from nonscalded curd pressed cheese. This genome sequence provides information in relation to dairy environment adaptation. PMID:25377704

  9. THE ENDOPHYTE CURTOBACTERIUM FLACCUMFACIENS REDUCES SYMPTOMS CAUSED BY XYLELLA FASTIDIOSA IN CATHARANTHUS ROSEUSAN ENDOPHYTIC BACTERIUM FROM CITRUS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Citrus variegated chlorosis (CVC) is a disease of sweet orange (Citrus sinensis (L.)) caused by Xylella fastidiosa subsp. pauca, a phytopathogenic bacterium that can infect all sweet orange cultivars. Sweet orange trees are sometimes observed to be infected by Xylella fastidiosa without showing seve...

  10. Complete Genome Sequence of Enterococcus hirae R17, a Daptomycin-Resistant Bacterium Isolated from Retail Pork in China

    PubMed Central

    Peng, Zixin; Wang, Wei; Hu, Yujie

    2016-01-01

    Daptomycin-resistant Enterococcus hirae R17 was isolated from retail pork sold at a free-trade market in Beijing, China. The complete genome sequence of R17 contains a circular 2,886,481-bp chromosome and a circular 73,574-bp plasmid. Genes involved in cell envelope homeostasis of this bacterium were identified by whole-genome analysis. PMID:27340071

  11. Draft Genome Sequence of Pannonibacter phragmitetus Strain CGMCC9175, a Halotolerant Polycyclic Aromatic Hydrocarbon-Degrading Bacterium

    PubMed Central

    Jin, Decai; Zhou, Lisha; Zhang, Zhuo

    2016-01-01

    Pannonibacter phragmitetus CGMCC9175 is a halotolerant polycyclic aromatic hydrocarbon (PAH)-degrading bacterium isolated from PAH-contaminated intertidal zone sediment. Here, we report the 5.7-Mb draft genome sequence of this strain, which will provide insights into the diversity of Pannonibacter and the mechanism of PAH degradation in sediments. PMID:26823598

  12. Draft Genome Sequence of Pseudoalteromonas tetraodonis Strain MQS005, a Bacterium with Potential Quorum-Sensing Regulation.

    PubMed

    Pan, Yonglong; Wang, Yanbo; Yan, Xiaoqing; Mazumder, Asit; Liang, Yan

    2016-01-01

    We present here the draft genome sequence of Pseudoalteromonas tetraodonis strain MQS005, a bacterium possessing potential quorum-sensing regulatory activity. This strain was isolated from water from the South China Sea, People's Republic of China. The assembly consists of 4,252,538 bp and contains 144 contigs, with a G+C content of 41.85%. PMID:27491986

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

    Meneghel, Julie; Irlinger, Françoise; Loux, Valentin; Vidal, Marie; Passot, Stéphanie; Béal, Catherine; Layec, Séverine

    2016-01-01

    Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) is a lactic acid bacterium widely used for the production of yogurt and cheeses. Here, we report the genome sequence of L. bulgaricus CFL1 to improve our knowledge on its stress-induced damages following production and end-use processes. PMID:26941141

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

    PubMed Central

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

    2016-01-01

    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 (Cd2+ 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. PMID:26729719

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

    PubMed

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

    2016-01-01

    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. PMID:26729719

  17. Metabolism of Kaempferia parviflora polymethoxyflavones by human intestinal bacterium Bautia sp. MRG-PMF1.

    PubMed

    Kim, Mihyang; Kim, Nayoung; Han, Jaehong

    2014-12-24

    Poylmethoxyflavones (PMFs) are major bioactive flavonoids, which exhibit various biological activities, such as anticancer effects. The biotransformation of PMFs and characterization of a PMF-metabolizing human intestinal bacterium were studied herein for the first time. Hydrolysis of aryl methyl ether functional groups by human fecal samples was observed from the bioconversion of various PMFs. Activity-guided screening for PMF-metabolizing intestinal bacteria under anaerobic conditions resulted in the isolation of a strict anaerobic bacterium, which was identified as Blautia sp. MRG-PMF1. The isolated MRG-PMF1 was able to metabolize various PMFs to the corresponding demethylated flavones. The microbial conversion of bioactive 5,7-dimethoxyflavone (5,7-DMF) and 5,7,4'-trimethoxyflavone (5,7,4'-TMF) was studied in detail. 5,7-DMF and 5,7,4'-TMF were completely metabolized to 5,7-dihydroxyflavone (chrysin) and 5,7,4'-trihydroxyflavone (apigenin), respectively. From a kinetics study, the methoxy group on the flavone C-7 position was found to be preferentially hydrolyzed. 5-Methoxychrysin, the intermediate of 5,7-DMF metabolism by Blautia sp. MRG-PMF1, was isolated and characterized by nuclear magnetic resonance spectroscopy. Apigenin was produced from the sequential demethylation of 5,7,4'-TMF, via 5,4'-dimethoxy-7-hydroxyflavone and 7,4'-dihydroxy-5-methoxyflavone (thevetiaflavone). Not only demethylation activity but also deglycosylation activity was exhibited by Blautia sp. MRG-PMF1, and various flavonoids, including isoflavones, flavones, and flavanones, were found to be metabolized to the corresponding aglycones. The unprecedented PMF demethylation activity of Blautia sp. MRG-PMF1 will expand our understanding of flavonoid metabolism in the human intestine and lead to novel bioactive compounds. PMID:25437273

  18. Computational prediction of essential genes in an unculturable endosymbiotic bacterium, Wolbachia of Brugia malayi

    PubMed Central

    2009-01-01

    Background Wolbachia (wBm) is an obligate endosymbiotic bacterium of Brugia malayi, a parasitic filarial nematode of humans and one of the causative agents of lymphatic filariasis. There is a pressing need for new drugs against filarial parasites, such as B. malayi. As wBm is required for B. malayi development and fertility, targeting wBm is a promising approach. However, the lifecycle of neither B. malayi nor wBm can be maintained in vitro. To facilitate selection of potential drug targets we computationally ranked the wBm genome based on confidence that a particular gene is essential for the survival of the bacterium. Results wBm protein sequences were aligned using BLAST to the Database of Essential Genes (DEG) version 5.2, a collection of 5,260 experimentally identified essential genes in 15 bacterial strains. A confidence score, the Multiple Hit Score (MHS), was developed to predict each wBm gene's essentiality based on the top alignments to essential genes in each bacterial strain. This method was validated using a jackknife methodology to test the ability to recover known essential genes in a control genome. A second estimation of essentiality, the Gene Conservation Score (GCS), was calculated on the basis of phyletic conservation of genes across Wolbachia's parent order Rickettsiales. Clusters of orthologous genes were predicted within the 27 currently available complete genomes. Druggability of wBm proteins was predicted by alignment to a database of protein targets of known compounds. Conclusion Ranking wBm genes by either MHS or GCS predicts and prioritizes potentially essential genes. Comparison of the MHS to GCS produces quadrants representing four types of predictions: those with high confidence of essentiality by both methods (245 genes), those highly conserved across Rickettsiales (299 genes), those similar to distant essential genes (8 genes), and those with low confidence of essentiality (253 genes). These data facilitate selection of wBm genes

  19. Upregulation of Intestinal Mucin Expression by the Probiotic Bacterium E. coli Nissle 1917.

    PubMed

    Hafez, Mohamed M

    2012-06-01

    The probiotic E. coli Nissle 1917 (EcN) has been reported to have various health benefits; however, very little is known about their underlying mechanisms. In this regard, the present study aimed to elucidate the effect of the bacterium on mucin production by intestinal epithelial cells. Incubation of HT-29 cells with EcN lead to a contact time-dependent rise in mRNA levels of the MUC2, MUC3, MUC5AC, and MUC5A. The expression was markedly higher with MUC5AC gene. In most cases, MUC genes expression was more pronounced in polarized cells compared to non-polarized ones. In contrast to MUC3, the basal stimulation of polarized cells brought about markedly higher levels of other tested mucins. Similar but milder results were observed when living EcN was replaced by inactivated bacteria. With exception of MUC3, the conditioned media showed no significant effect on the mRNA level of the tested mucins. The above-mentioned mRNA results were confirmed on protein level using enzyme-linked lectin assay (ELLA) and enzyme-linked immunosorbant assay (ELISA). In contrast to other treatments, basal stimulation of polarized cells showed a growth phase-dependent MUC induction with more prominent effect by stationary-phase bacteria. In contrast to MUC 2 and MUC3, the induction of MUC5AC and MUC5B showed a bacterial count-dependent pattern. In conclusion, EcN was found to stimulate MUC gene expression in HT-29 intestinal cells. This stimulation was more distinct with polarized cells. Such observation may partially interpret some health benefits of the probiotic bacterium including antagonizing pathogen adhesion and protection of the intestinal mucosa. PMID:26781849

  20. Genome Analysis of Thermosulfurimonas dismutans, the First Thermophilic Sulfur-Disproportionating Bacterium of the Phylum Thermodesulfobacteria

    PubMed Central

    Mardanov, Andrey V.; Beletsky, Alexey V.; Kadnikov, Vitaly V.; Slobodkin, Alexander I.; Ravin, Nikolai V.

    2016-01-01

    Thermosulfurimonas dismutans S95T, isolated from a deep-sea hydrothermal vent is the first bacterium of the phylum Thermodesulfobacteria reported to grow by the disproportionation of elemental sulfur, sulfite, or thiosulfate with carbon dioxide as the sole carbon source. In contrast to its phylogenetically close relatives, which are dissimilatory sulfate-reducers, T. dismutans is unable to grow by sulfate respiration. The features of this organism and its 2,1 Mb draft genome sequence are described in this report. Genome analysis revealed that the T. dismutans genome contains the set of genes for dissimilatory sulfate reduction including ATP sulfurylase, the AprA and B subunits of adenosine-5′-phosphosulfate reductase, and dissimilatory sulfite reductase. The oxidation of elemental sulfur to sulfite could be enabled by APS reductase-associated electron transfer complex QmoABC and heterodisulfide reductase. The genome also contains several membrane-linked molybdopterin oxidoreductases that are thought to be involved in sulfur metabolism as subunits of thiosulfate, polysulfide, or tetrathionate reductases. Nitrate could be used as an electron acceptor and reduced to ammonium, as indicated by the presence of periplasmic nitrate and nitrite reductases. Autotrophic carbon fixation is enabled by the Wood–Ljungdahl pathway, and the complete set of genes that is required for nitrogen fixation is also present in T. dismutans. Overall, our results provide genomic insights into energy and carbon metabolism of chemolithoautotrophic sulfur-disproportionating bacterium that could be important primary producer in microbial communities of deep-sea hydrothermal vents. PMID:27379079