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Sample records for bacterium myxococcus xanthus

  1. Cell division resets polarity and motility for the bacterium Myxococcus xanthus.

    PubMed

    Harvey, Cameron W; Madukoma, Chinedu S; Mahserejian, Shant; Alber, Mark S; Shrout, Joshua D

    2014-11-01

    Links between cell division and other cellular processes are poorly understood. It is difficult to simultaneously examine division and function in most cell types. Most of the research probing aspects of cell division has experimented with stationary or immobilized cells or distinctly asymmetrical cells. Here we took an alternative approach by examining cell division events within motile groups of cells growing on solid medium by time-lapse microscopy. A total of 558 cell divisions were identified among approximately 12,000 cells. We found an interconnection of division, motility, and polarity in the bacterium Myxococcus xanthus. For every division event, motile cells stop moving to divide. Progeny cells of binary fission subsequently move in opposing directions. This behavior involves M. xanthus Frz proteins that regulate M. xanthus motility reversals but is independent of type IV pilus "S motility." The inheritance of opposing polarity is correlated with the distribution of the G protein RomR within these dividing cells. The constriction at the point of division limits the intracellular distribution of RomR. Thus, the asymmetric distribution of RomR at the parent cell poles becomes mirrored at new poles initiated at the site of division. PMID:25157084

  2. Role for Vitamin B12 in Light Induction of Gene Expression in the Bacterium Myxococcus xanthus

    PubMed Central

    Cervantes, María; Murillo, Francisco J.

    2002-01-01

    A light-inducible promoter (PB) drives the carB operon (carotenoid genes) of the bacterium Myxococcus xanthus. A gene encoding a regulator of carotenoid biosynthesis was identified by studying mutant strains carrying a transcriptional fusion to PB and deletions in three candidate genes. Our results prove that the identified gene, named carA, codes for a repressor of the PB promoter in the dark. They also show that the carA gene product does not participate in the light activation of two other promoters connected with carotenoid synthesis or its regulation in M. xanthus. CarA is a novel protein consisting of a DNA-binding domain of the family of MerR helix-turn-helix transcriptional regulators, directly joined to a cobalamin-binding domain. In support of this, we report here that the presence of vitamin B12 or some other cobalamin derivatives is absolutely required for activation of the PB promoter by light. PMID:11914353

  3. A barrier to homologous recombination between sympatric strains of the cooperative soil bacterium Myxococcus xanthus

    PubMed Central

    Wielgoss, Sébastien; Didelot, Xavier; Chaudhuri, Roy R; Liu, Xuan; Weedall, Gareth D; Velicer, Gregory J; Vos, Michiel

    2016-01-01

    The bacterium Myxococcus xanthus glides through soil in search of prey microbes, but when food sources run out, cells cooperatively construct and sporulate within multicellular fruiting bodies. M. xanthus strains isolated from a 16 × 16-cm-scale patch of soil were previously shown to have diversified into many distinct compatibility types that are distinguished by the failure of swarming colonies to merge upon encounter. We sequenced the genomes of 22 isolates from this population belonging to the two most frequently occurring multilocus sequence type (MLST) clades to trace patterns of incipient genomic divergence, specifically related to social divergence. Although homologous recombination occurs frequently within the two MLST clades, we find an almost complete absence of recombination events between them. As the two clades are very closely related and live in sympatry, either ecological or genetic barriers must reduce genetic exchange between them. We find that the rate of change in the accessory genome is greater than the rate of amino-acid substitution in the core genome. We identify a large genomic tract that consistently differs between isolates that do not freely merge and therefore is a candidate region for harbouring gene(s) responsible for self/non-self discrimination. PMID:27046334

  4. Active matter model of Myxococcus xanthus aggregation

    NASA Astrophysics Data System (ADS)

    Patch, Adam; Bahar, Fatmagul; Liu, Guannan; Thutupalli, Shashi; Welch, Roy; Yllanes, David; Shaevitz, Joshua; Marchetti, M. Cristina

    Myxococcus xanthus is a soil-dwelling bacterium that exhibits several fascinating collective behaviors including streaming, swarming, and generation of fruiting bodies. A striking feature of M. xanthus is that it periodically reverses its motility direction. The first stage of fruiting body formation is characterized by the aggregation of cells on a surface into round mesoscopic structures. Experiments have shown that this aggregation relies heavily on regulation of the reversal rate and local mechanical interactions, suggesting motility-induced phase separation may play an important role. We have adapted self-propelled particle models to include cell reversal and motility suppression resulting from sporulation observed in aggregates. Using 2D molecular dynamics simulations, we map the phase behavior in the space of Péclet number and local density and examine the kinetics of aggregation for comparison to experiments.

  5. Accordion waves in Myxococcus xanthus

    PubMed Central

    Sliusarenko, Oleksii; Neu, John; Zusman, David R.; Oster, George

    2006-01-01

    Myxococcus xanthus are Gram-negative bacteria that glide on solid surfaces, periodically reversing their direction of movement. When starved, M. xanthus cells organize their movements into waves of cell density that sweep over the colony surface. These waves are unique: Although they appear to interpenetrate, they actually reflect off one another when they collide, so that each wave crest oscillates back and forth with no net displacement. Because the waves reflect the coordinated back and forth oscillations of the individual bacteria, we call them “accordion” waves. The spatial oscillations of individuals are a manifestation of an internal biochemical oscillator, probably involving the Frz chemosensory system. These internal “clocks,” each of which is quite variable, are synchronized by collisions between individual cells using a contact-mediated signal-transduction system. The result of collision signaling is that the collective spatial behavior is much less variable than the individual oscillators. In this work, we present experimental observations in which individual cells marked with GFP can be followed in groups of unlabeled cells in monolayer cultures. These data, together with an agent-based computational model demonstrate that the only properties required to explain the ripple patterns are an asymmetric biochemical limit cycle that controls direction reversals and asymmetric contact-induced signaling between cells: Head-to-head signaling is stronger than head-to-tail signaling. Together, the experimental and computational data provide new insights into how populations of interacting oscillators can synchronize and organize spatially to produce morphogenetic patterns that may have parallels in higher organisms. PMID:16432222

  6. Crystal Structure of the HMG-CoA Synthase MvaS from the Gram-Negative Bacterium Myxococcus xanthus.

    PubMed

    Bock, Tobias; Kasten, Janin; Müller, Rolf; Blankenfeldt, Wulf

    2016-07-01

    A critical step in bacterial isoprenoid production is the synthesis of 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) catalyzed by HMG-CoA synthase (HMGCS). In myxobacteria, this enzyme is also involved in a recently discovered alternative and acetyl-CoA-dependent isovaleryl CoA biosynthesis pathway. Here we present crystal structures of MvaS, the HMGCS from Myxococcus xanthus, in complex with CoA and acetylated active site Cys115, with the second substrate acetoacetyl CoA and with the product of the condensation reaction, 3-hydroxy-3-methylglutaryl CoA. With these structures, we show that MvaS uses the common HMGCS enzymatic mechanism and provide evidence that dimerization plays a role in the formation and stability of the active site. Overall, MvaS shows features typical of the eukaryotic HMGCS and exhibits differences from homologues from Gram-positive bacteria. This study provides insights into myxobacterial alternative isovaleryl CoA biosynthesis and thereby extends the toolbox for the biotechnological production of renewable fuel and chemicals. PMID:27124816

  7. Molecular Mechanisms of Signaling in Myxococcus xanthus Development.

    PubMed

    Bretl, Daniel J; Kirby, John R

    2016-09-25

    Myxococcus xanthus is an environmental bacterium that displays a complex life cycle that includes motility, predation, multicellular fruiting body development, and sporulation. Given the elaborate fruiting body development of this bacterial species, M. xanthus has served as a model organism for the study of multicellular development of bacteria, and a remarkable number of genes have been identified that contribute to the regulation of this highly dynamic process. Included among these developmental factors is a robust repertoire of signaling proteins, which have arisen from extensive gene duplication in M. xanthus and related species. In this review, we explore several aspects of the molecular mechanisms of signaling in M. xanthus development. This includes mechanisms of kin selection, single-cell sensing of nutrient depletion and the stringent response, the production of and response to extracellular population cues, and the contribution of several two-component signaling systems regulating developmental transcriptional programs. Collectively, these signaling mechanisms function to tightly regulate the sensing of nutrient depletion, the aggregation of populations of cells, and the temporal and spatial formation of complex fruiting bodies and sporulation of M. xanthus. PMID:27430596

  8. Phase separation dynamics during Myxococcus xanthus fruiting body formation

    NASA Astrophysics Data System (ADS)

    Liu, Guannan; Bahar, Fatmagul; Patch, Adam; Thutupalli, Shashi; Yllanes, David; Marchetti, M. Cristina; Welch, Roy; Shaevitz, Joshua

    Many living systems take advantage of collective behavior for group survival. We use the soil-dwelling bacterium Myxococcus xanthus as a model to study out-of-equilibrium phase separation during fruiting body formation. M. xanthus cells have the ability to glide on solid surfaces and reverse their direction periodically. When starved, M. xanthus cells aggregate together and form structures called fruiting bodies, inside of which cells sporulate to survive stressful conditions. We show that at high cell density the formation of fruiting bodies is a phase separation process. From experimental data that combines single-cell tracking, population-scale imaging, mutants, and drug applications, we construct the phase diagram of M. xanthus in the space of Péclet number and cell density. When wild type cells are starved, we find that they actively increase their Péclet number by modulating gliding speed and reversal frequency which induces a phase separation from a gas-like state to an aggregated fruiting body state.

  9. Myxococcus xanthus Growth, Development, and Isolation.

    PubMed

    Vaksman, Zalman; Kaplan, Heidi B

    2015-11-03

    Myxobacteria are a highly social group among the delta proteobacteria that display unique multicellular behaviors during their complex life cycle and provide a rare opportunity to study the boundary between single cells and multicellularity. These organisms are also unusual as their entire life cycle is surface associated and includes a number of social behaviors: social gliding and rippling motility, 'wolf-pack'-like predation, and self-organizing complex biostructures, termed fruiting bodies, which are filled with differentiated environmentally resistant spores. Here we present methods for the growth, maintenance, and storage of Myxococcus xanthus, the most commonly studied of the myxobacteria. We also include methods to examine various developmental and social behaviors (fruiting body and spore formation, predation, and rippling motility). As the myxobacteria, similar to the streptomycetes, are excellent sources of many characterized and uncharacterized antibiotics and other natural products, we have provided a protocol for obtaining natural isolates from a variety of environmental sources.

  10. Dual Biochemical Oscillators May Control Cellular Reversals in Myxococcus xanthus

    PubMed Central

    Eckhert, Erik; Rangamani, Padmini; Davis, Annie E.; Oster, George; Berleman, James E.

    2014-01-01

    Myxococcus xanthus is a Gram-negative, soil-dwelling bacterium that glides on surfaces, reversing direction approximately once every 6 min. Motility in M. xanthus is governed by the Che-like Frz pathway and the Ras-like Mgl pathway, which together cause the cell to oscillate back and forth. Previously, Igoshin et al. (2004) suggested that the cellular oscillations are caused by cyclic changes in concentration of active Frz proteins that govern motility. In this study, we present a computational model that integrates both the Frz and Mgl pathways, and whose downstream components can be read as motor activity governing cellular reversals. This model faithfully reproduces wildtype and mutant behaviors by simulating individual protein knockouts. In addition, the model can be used to examine the impact of contact stimuli on cellular reversals. The basic model construction relies on the presence of two nested feedback circuits, which prompted us to reexamine the behavior of M. xanthus cells. We performed experiments to test the model, and this cell analysis challenges previous assumptions of 30 to 60 min reversal periods in frzCD, frzF, frzE, and frzZ mutants. We demonstrate that this average reversal period is an artifact of the method employed to record reversal data, and that in the absence of signal from the Frz pathway, Mgl components can occasionally reverse the cell near wildtype periodicity, but frz- cells are otherwise in a long nonoscillating state. PMID:25468349

  11. Earthquake-like dynamics in Myxococcus xanthus social motility

    PubMed Central

    Gibiansky, Maxsim L.; Hu, Wei; Dahmen, Karin A.; Shi, Wenyuan; Wong, Gerard C. L.

    2013-01-01

    Myxococcus xanthus is a bacterium capable of complex social organization. Its characteristic social (“S”)-motility mechanism is mediated by type IV pili (TFP), linear actuator appendages that propel the bacterium along a surface. TFP are known to bind to secreted exopolysaccharides (EPS), but it is unclear how M. xanthus manages to use the TFP-EPS technology common to many bacteria to achieve its unique coordinated multicellular movements. We examine M. xanthus S-motility, using high-resolution particle-tracking algorithms, and observe aperiodic stick–slip movements. We show that they are not due to chemotaxis, but are instead consistent with a constant TFP-generated force interacting with EPS, which functions both as a glue and as a lubricant. These movements are quantitatively homologous to the dynamics of earthquakes and other crackling noise systems. These systems exhibit critical behavior, which is characterized by a statistical hierarchy of discrete “avalanche” motions described by a power law distribution. The measured critical exponents from M. xanthus are consistent with mean field theoretical models and with other crackling noise systems, and the measured Lyapunov exponent suggests the existence of highly branched EPS. Such molecular architectures, which are common for efficient lubricants but rare in bacterial EPS, may be necessary for S-motility: We show that the TFP of leading “locomotive” cells initiate the collective motion of follower cells, indicating that lubricating EPS may alleviate the force generation requirements on the lead cell and thus make S-motility possible. PMID:23341622

  12. Gliding motility in bacteria: insights from studies of Myxococcus xanthus.

    PubMed

    Spormann, A M

    1999-09-01

    Gliding motility is observed in a large variety of phylogenetically unrelated bacteria. Gliding provides a means for microbes to travel in environments with a low water content, such as might be found in biofilms, microbial mats, and soil. Gliding is defined as the movement of a cell on a surface in the direction of the long axis of the cell. Because this definition is operational and not mechanistic, the underlying molecular motor(s) may be quite different in diverse microbes. In fact, studies on the gliding bacterium Myxococcus xanthus suggest that two independent gliding machineries, encoded by two multigene systems, operate in this microorganism. One machinery, which allows individual cells to glide on a surface, independent of whether the cells are moving alone or in groups, requires the function of the genes of the A-motility system. More than 37 A-motility genes are known to be required for this form of movement. Depending on an additional phenotype, these genes are divided into two subclasses, the agl and cgl genes. Videomicroscopic studies on gliding movement, as well as ultrastructural observations of two myxobacteria, suggest that the A-system motor may consist of multiple single motor elements that are arrayed along the entire cell body. Each motor element is proposed to be localized to the periplasmic space and to be anchored to the peptidoglycan layer. The force to glide which may be generated here is coupled to adhesion sites that move freely in the outer membrane. These adhesion sites provide a specific contact with the substratum. Based on single-cell observations, similar models have been proposed to operate in the unrelated gliding bacteria Flavobacterium johnsoniae (formerly Cytophaga johnsonae), Cytophaga strain U67, and Flexibacter polymorphus (a filamentous glider). Although this model has not been verified experimentally, M. xanthus seems to be the ideal organism with which to test it, given the genetic tools available. The second gliding

  13. Gliding Motility in Bacteria: Insights from Studies of Myxococcus xanthus

    PubMed Central

    Spormann, Alfred M.

    1999-01-01

    Gliding motility is observed in a large variety of phylogenetically unrelated bacteria. Gliding provides a means for microbes to travel in environments with a low water content, such as might be found in biofilms, microbial mats, and soil. Gliding is defined as the movement of a cell on a surface in the direction of the long axis of the cell. Because this definition is operational and not mechanistic, the underlying molecular motor(s) may be quite different in diverse microbes. In fact, studies on the gliding bacterium Myxococcus xanthus suggest that two independent gliding machineries, encoded by two multigene systems, operate in this microorganism. One machinery, which allows individual cells to glide on a surface, independent of whether the cells are moving alone or in groups, requires the function of the genes of the A-motility system. More than 37 A-motility genes are known to be required for this form of movement. Depending on an additional phenotype, these genes are divided into two subclasses, the agl and cgl genes. Videomicroscopic studies on gliding movement, as well as ultrastructural observations of two myxobacteria, suggest that the A-system motor may consist of multiple single motor elements that are arrayed along the entire cell body. Each motor element is proposed to be localized to the periplasmic space and to be anchored to the peptidoglycan layer. The force to glide which may be generated here is coupled to adhesion sites that move freely in the outer membrane. These adhesion sites provide a specific contact with the substratum. Based on single-cell observations, similar models have been proposed to operate in the unrelated gliding bacteria Flavobacterium johnsoniae (formerly Cytophaga johnsonae), Cytophaga strain U67, and Flexibacter polymorphus (a filamentous glider). Although this model has not been verified experimentally, M. xanthus seems to be the ideal organism with which to test it, given the genetic tools available. The second gliding

  14. The high-mobility group A-type protein CarD of the bacterium Myxococcus xanthus as a transcription factor for several distinct vegetative genes.

    PubMed Central

    Galbis-Martínez, Marisa; Fontes, Marta; Murillo, Francisco J

    2004-01-01

    CarD is the only reported prokaryotic protein showing structural and functional features typical of eukaryotic high-mobility group A transcription factors. In prokaryotes, proteins similar to CarD appear to be confined primarily to myxobacteria. In Myxococcus xanthus, CarD has been previously shown to act as a positive element in two different regulatory networks: one for light-induced synthesis of carotenoids and the other for starvation-induced fruiting body formation. We have now tested the effect of a loss-of-function mutation in the carD gene (carD1) on the expression of a random collection of lacZ-tagged genes, which are normally expressed in the dark during vegetative growth in rich medium. Our results indicate that CarD plays a significant role in the transcriptional regulation of various indicated genes. The carD1 mutation downregulates some genes and upregulates others. Also reported here is the isolation of several mutations that suppress the strong effect of carD1 on the expression of a particular vegetative gene. One of them (sud-2) also suppresses the effect of carD1 on other vegetative genes and on fruiting-body formation. Thus, CarD and the sud-2 gene product appear to participate in a single mechanism, which underlies various apparently diverse regulatory phenomena ascribed to CarD. PMID:15342500

  15. Growth of Myxococcus xanthus in continuous-flow-cell bioreactors as a method for studying development.

    PubMed

    Smaldone, Gregory T; Jin, Yujie; Whitfield, Damion L; Mu, Andrew Y; Wong, Edward C; Wuertz, Stefan; Singer, Mitchell

    2014-04-01

    Nutrient sensors and developmental timers are two classes of genes vital to the establishment of early development in the social soil bacterium Myxococcus xanthus. The products of these genes trigger and regulate the earliest events that drive the colony from a vegetative state to aggregates, which ultimately leads to the formation of fruiting bodies and the cellular differentiation of the individual cells. In order to more accurately identify the genes and pathways involved in the initiation of this multicellular developmental program in M. xanthus, we adapted a method of growing vegetative populations within a constant controllable environment by using flow cell bioreactors, or flow cells. By establishing an M. xanthus community within a flow cell, we are able to test developmental responses to changes in the environment with fewer concerns for effects due to nutrient depletion or bacterial waste production. This approach allows for greater sensitivity in investigating communal environmental responses, such as nutrient sensing. To demonstrate the versatility of our growth environment, we carried out time-lapse confocal laser scanning microscopy to visualize M. xanthus biofilm growth and fruiting body development, as well as fluorescence staining of exopolysaccharides deposited by biofilms. We also employed the flow cells in a nutrient titration to determine the minimum concentration required to sustain vegetative growth. Our data show that by using a flow cell, M. xanthus can be held in a vegetative growth state at low nutrient concentrations for long periods, and then, by slightly decreasing the nutrient concentration, cells can be allowed to initiate the developmental program.

  16. Stigmergy co-ordinates multicellular collective behaviours during Myxococcus xanthus surface migration.

    PubMed

    Gloag, Erin S; Turnbull, Lynne; Javed, Muhammad A; Wang, Huabin; Gee, Michelle L; Wade, Scott A; Whitchurch, Cynthia B

    2016-01-01

    Surface translocation by the soil bacterium Myxococcus xanthus is a complex multicellular phenomenon that entails two motility systems. However, the mechanisms by which the activities of individual cells are coordinated to manifest this collective behaviour are currently unclear. Here we have developed a novel assay that enables detailed microscopic examination of M. xanthus motility at the interstitial interface between solidified nutrient medium and a glass coverslip. Under these conditions, M. xanthus motility is characterised by extensive micro-morphological patterning that is considerably more elaborate than occurs at an air-surface interface. We have found that during motility on solidified nutrient medium, M. xanthus forges an interconnected furrow network that is lined with an extracellular matrix comprised of exopolysaccharides, extracellular lipids, membrane vesicles and an unidentified slime. Our observations have revealed that M. xanthus motility on solidified nutrient medium is a stigmergic phenomenon in which multi-cellular collective behaviours are co-ordinated through trail-following that is guided by physical furrows and extracellular matrix materials. PMID:27225967

  17. Stigmergy co-ordinates multicellular collective behaviours during Myxococcus xanthus surface migration

    PubMed Central

    Gloag, Erin S.; Turnbull, Lynne; Javed, Muhammad A.; Wang, Huabin; Gee, Michelle L.; Wade, Scott A.; Whitchurch, Cynthia B.

    2016-01-01

    Surface translocation by the soil bacterium Myxococcus xanthus is a complex multicellular phenomenon that entails two motility systems. However, the mechanisms by which the activities of individual cells are coordinated to manifest this collective behaviour are currently unclear. Here we have developed a novel assay that enables detailed microscopic examination of M. xanthus motility at the interstitial interface between solidified nutrient medium and a glass coverslip. Under these conditions, M. xanthus motility is characterised by extensive micro-morphological patterning that is considerably more elaborate than occurs at an air-surface interface. We have found that during motility on solidified nutrient medium, M. xanthus forges an interconnected furrow network that is lined with an extracellular matrix comprised of exopolysaccharides, extracellular lipids, membrane vesicles and an unidentified slime. Our observations have revealed that M. xanthus motility on solidified nutrient medium is a stigmergic phenomenon in which multi-cellular collective behaviours are co-ordinated through trail-following that is guided by physical furrows and extracellular matrix materials. PMID:27225967

  18. The lethal cargo of Myxococcus xanthus outer membrane vesicles.

    PubMed

    Berleman, James E; Allen, Simon; Danielewicz, Megan A; Remis, Jonathan P; Gorur, Amita; Cunha, Jack; Hadi, Masood Z; Zusman, David R; Northen, Trent R; Witkowska, H Ewa; Auer, Manfred

    2014-01-01

    Myxococcus xanthus is a bacterial micro-predator known for hunting other microbes in a wolf pack-like manner. Outer membrane vesicles (OMVs) are produced in large quantities by M. xanthus and have a highly organized structure in the extracellular milieu, sometimes occurring in chains that link neighboring cells within a biofilm. OMVs may be a vehicle for mediating wolf pack activity by delivering hydrolytic enzymes and antibiotics aimed at killing prey microbes. Here, both the protein and small molecule cargo of the OMV and membrane fractions of M. xanthus were characterized and compared. Our analysis indicates a number of proteins that are OMV-specific or OMV-enriched, including several with putative hydrolytic function. Secondary metabolite profiling of OMVs identifies 16 molecules, many associated with antibiotic activities. Several hydrolytic enzyme homologs were identified, including the protein encoded by MXAN_3564 (mepA), an M36 protease homolog. Genetic disruption of mepA leads to a significant reduction in extracellular protease activity suggesting MepA is part of the long-predicted (yet to date undetermined) extracellular protease suite of M. xanthus. PMID:25250022

  19. Mechanism for Collective Cell Alignment in Myxococcus xanthus Bacteria

    PubMed Central

    Balagam, Rajesh; Igoshin, Oleg A.

    2015-01-01

    Myxococcus xanthus cells self-organize into aligned groups, clusters, at various stages of their lifecycle. Formation of these clusters is crucial for the complex dynamic multi-cellular behavior of these bacteria. However, the mechanism underlying the cell alignment and clustering is not fully understood. Motivated by studies of clustering in self-propelled rods, we hypothesized that M. xanthus cells can align and form clusters through pure mechanical interactions among cells and between cells and substrate. We test this hypothesis using an agent-based simulation framework in which each agent is based on the biophysical model of an individual M. xanthus cell. We show that model agents, under realistic cell flexibility values, can align and form cell clusters but only when periodic reversals of cell directions are suppressed. However, by extending our model to introduce the observed ability of cells to deposit and follow slime trails, we show that effective trail-following leads to clusters in reversing cells. Furthermore, we conclude that mechanical cell alignment combined with slime-trail-following is sufficient to explain the distinct clustering behaviors observed for wild-type and non-reversing M. xanthus mutants in recent experiments. Our results are robust to variation in model parameters, match the experimentally observed trends and can be applied to understand surface motility patterns of other bacterial species. PMID:26308508

  20. The lethal cargo of Myxococcus xanthus outer membrane vesicles

    PubMed Central

    Berleman, James E.; Allen, Simon; Danielewicz, Megan A.; Remis, Jonathan P.; Gorur, Amita; Cunha, Jack; Hadi, Masood Z.; Zusman, David R.; Northen, Trent R.; Witkowska, H. Ewa; Auer, Manfred

    2014-01-01

    Myxococcus xanthus is a bacterial micro-predator known for hunting other microbes in a wolf pack-like manner. Outer membrane vesicles (OMVs) are produced in large quantities by M. xanthus and have a highly organized structure in the extracellular milieu, sometimes occurring in chains that link neighboring cells within a biofilm. OMVs may be a vehicle for mediating wolf pack activity by delivering hydrolytic enzymes and antibiotics aimed at killing prey microbes. Here, both the protein and small molecule cargo of the OMV and membrane fractions of M. xanthus were characterized and compared. Our analysis indicates a number of proteins that are OMV-specific or OMV-enriched, including several with putative hydrolytic function. Secondary metabolite profiling of OMVs identifies 16 molecules, many associated with antibiotic activities. Several hydrolytic enzyme homologs were identified, including the protein encoded by MXAN_3564 (mepA), an M36 protease homolog. Genetic disruption of mepA leads to a significant reduction in extracellular protease activity suggesting MepA is part of the long-predicted (yet to date undetermined) extracellular protease suite of M. xanthus. PMID:25250022

  1. Mechanism of cell alignment in groups of Myxococcus xanthus bacteria

    NASA Astrophysics Data System (ADS)

    Balgam, Rajesh; Igoshin, Oleg

    2015-03-01

    Myxococcus xanthus is a model for studying self-organization in bacteria. These flexible cylindrical bacteria move along. In groups, M. xanthus cells align themselves into dynamic cell clusters but the mechanism underlying their formation is unknown. It has been shown that steric interactions can cause alignment in self-propelled hard rods but it is not clear how flexibility and reversals affect the alignment and cluster formation. We have investigated cell alignment process using our biophysical model of M. xanthus cell in an agent-based simulation framework under realistic cell flexibility values. We observed that flexible model cells can form aligned cell clusters when reversals are suppressed but these clusters disappeared when reversals frequency becomes similar to the observed value. However, M. xanthus cells follow slime (polysaccharide gel like material) trails left by other cells and we show that implementing this into our model rescues cell clustering for reversing cells. Our results show that slime following along with periodic cell reversals act as positive feedback to reinforce existing slime trails and recruit more cells. Furthermore, we have observed that mechanical cell alignment combined with slime following is sufficient to explain the distinct clustering patterns of reversing and non-reversing cells as observed in recent experiments. This work is supported by NSF MCB 0845919 and 1411780.

  2. Mechanism for Collective Cell Alignment in Myxococcus xanthus Bacteria.

    PubMed

    Balagam, Rajesh; Igoshin, Oleg A

    2015-08-01

    Myxococcus xanthus cells self-organize into aligned groups, clusters, at various stages of their lifecycle. Formation of these clusters is crucial for the complex dynamic multi-cellular behavior of these bacteria. However, the mechanism underlying the cell alignment and clustering is not fully understood. Motivated by studies of clustering in self-propelled rods, we hypothesized that M. xanthus cells can align and form clusters through pure mechanical interactions among cells and between cells and substrate. We test this hypothesis using an agent-based simulation framework in which each agent is based on the biophysical model of an individual M. xanthus cell. We show that model agents, under realistic cell flexibility values, can align and form cell clusters but only when periodic reversals of cell directions are suppressed. However, by extending our model to introduce the observed ability of cells to deposit and follow slime trails, we show that effective trail-following leads to clusters in reversing cells. Furthermore, we conclude that mechanical cell alignment combined with slime-trail-following is sufficient to explain the distinct clustering behaviors observed for wild-type and non-reversing M. xanthus mutants in recent experiments. Our results are robust to variation in model parameters, match the experimentally observed trends and can be applied to understand surface motility patterns of other bacterial species. PMID:26308508

  3. Light induction of gene expression in Myxococcus xanthus

    PubMed Central

    Balsalobre, Josefa M.; Ruiz-Vazquez, Rosa M.; Murillo, Francisco J.

    1987-01-01

    The synthesis of carotenoids by Myxococcus xanthus requires illumination with blue light. Mutations at two loci (carA and carR) remove the blue-light requirement and cause constitutive production of carotenoids. Mutations at a different locus (carB) prevent carotenogenesis in both wild-type and constitutive mutant strains. We describe here three independent car mutations induced by insertion of Tn5 lac, a transposon that carries a transcriptional probe for exogenous promoters. All three transposon insertions block carotenogenesis even in constitutive mutant strains. One insertion is in a previously unknown car gene and the other two are in the carB locus. One of the carB insertions expresses β-galactosidase at very low levels in the dark but is strongly activated by light. When this Tn5 lac insertion is introduced in carA or carR mutants it expresses β-galactosidase in dark- as well as light-grown cells. We conclude that carotenogenesis in M. xanthus is activated at the level of transcription by a light-induced mechanism in which the carA and the carR loci (or their gene products) take part. The potential usefulness of M. xanthus as a simple and sensitive tool for studies in photobiology is discussed. PMID:16593825

  4. Growth of Myxococcus xanthus in Continuous-Flow-Cell Bioreactors as a Method for Studying Development

    PubMed Central

    Smaldone, Gregory T.; Jin, Yujie; Whitfield, Damion L.; Mu, Andrew Y.; Wong, Edward C.; Wuertz, Stefan

    2014-01-01

    Nutrient sensors and developmental timers are two classes of genes vital to the establishment of early development in the social soil bacterium Myxococcus xanthus. The products of these genes trigger and regulate the earliest events that drive the colony from a vegetative state to aggregates, which ultimately leads to the formation of fruiting bodies and the cellular differentiation of the individual cells. In order to more accurately identify the genes and pathways involved in the initiation of this multicellular developmental program in M. xanthus, we adapted a method of growing vegetative populations within a constant controllable environment by using flow cell bioreactors, or flow cells. By establishing an M. xanthus community within a flow cell, we are able to test developmental responses to changes in the environment with fewer concerns for effects due to nutrient depletion or bacterial waste production. This approach allows for greater sensitivity in investigating communal environmental responses, such as nutrient sensing. To demonstrate the versatility of our growth environment, we carried out time-lapse confocal laser scanning microscopy to visualize M. xanthus biofilm growth and fruiting body development, as well as fluorescence staining of exopolysaccharides deposited by biofilms. We also employed the flow cells in a nutrient titration to determine the minimum concentration required to sustain vegetative growth. Our data show that by using a flow cell, M. xanthus can be held in a vegetative growth state at low nutrient concentrations for long periods, and then, by slightly decreasing the nutrient concentration, cells can be allowed to initiate the developmental program. PMID:24509931

  5. Bacterial social networks: structure and composition of Myxococcus xanthus outer membrane vesicle chains.

    PubMed

    Remis, Jonathan P; Wei, Dongguang; Gorur, Amita; Zemla, Marcin; Haraga, Jessica; Allen, Simon; Witkowska, H Ewa; Costerton, J William; Berleman, James E; Auer, Manfred

    2014-02-01

    The social soil bacterium, Myxococcus xanthus, displays a variety of complex and highly coordinated behaviours, including social motility, predatory rippling and fruiting body formation. Here we show that M. xanthus cells produce a network of outer membrane extensions in the form of outer membrane vesicle chains and membrane tubes that interconnect cells. We observed peritrichous display of vesicles and vesicle chains, and increased abundance in biofilms compared with planktonic cultures. By applying a range of imaging techniques, including three-dimensional (3D) focused ion beam scanning electron microscopy, we determined these structures to range between 30 and 60 nm in width and up to 5 μm in length. Purified vesicle chains consist of typical M. xanthus lipids, fucose, mannose, N-acetylglucosamine and N-acetylgalactoseamine carbohydrates and a small set of cargo protein. The protein content includes CglB and Tgl outer membrane proteins known to be transferable between cells in a contact-dependent manner. Most significantly, the 3D organization of cells within biofilms indicates that cells are connected via an extensive network of membrane extensions that may connect cells at the level of the periplasmic space. Such a network would allow the transfer of membrane proteins and other molecules between cells, and therefore could provide a mechanism for the coordination of social activities.

  6. Bacterial Social Networks: Structure and composition of Myxococcus xanthus outer membrane vesicle chains

    PubMed Central

    Remis, Jonathan P.; Wei, Doug; Gorur, Amita; Zemla, Marcin; Haraga, Jessica; Allen, Simon; Witkowska, H. Ewa; Costerton, J. William; Berleman, James E.; Auer, Manfred

    2014-01-01

    Summary The social soil bacterium, Myxococcus xanthus, displays a variety of complex and highly coordinated behaviors, including social motility, predatory rippling and fruiting body formation. Here we show that M. xanthus cells produce a network of outer membrane extensions in the form of vesicles and vesicle chains that interconnect cells. We observed peritrichous display of vesicles and vesicle chains and increased abundance in biofilms compared to planktonic cultures. By applying a range of imaging techniques, including 3D Focused Ion Beam Scanning Electron Microscopy (FIB/SEM), we determined these structures to range between 30-60 nm in width and up to 5 μm in length. Purified vesicle chains consist of typical M. xanthus lipids, fucose, mannose, N-acetylglucosamine (GlcNAc) and N-acetylgalactoseamine (GalNAc) carbohydrates and a small set of cargo protein. The protein content includes CglB and Tgl membrane proteins transferred in a contact-dependent manner. Most significantly, the 3D organization of cells within biofilms indicates that cells are connected via an extensive network of membrane extensions that may connect cells at the level of the periplasmic space. Such a network would allow the transfer of membrane proteins and other molecules between cells, and likely provides a mechanism for the coordination of social activities. PMID:23848955

  7. Biofilm formation protects Escherichia coli against killing by Caenorhabditis elegans and Myxococcus xanthus.

    PubMed

    DePas, William H; Syed, Adnan K; Sifuentes, Margarita; Lee, John S; Warshaw, David; Saggar, Vinay; Csankovszki, Györgyi; Boles, Blaise R; Chapman, Matthew R

    2014-11-01

    Enteric bacteria, such as Escherichia coli, are exposed to a variety of stresses in the nonhost environment. The development of biofilms provides E. coli with resistance to environmental insults, such as desiccation and bleach. We found that biofilm formation, specifically production of the matrix components curli and cellulose, protected E. coli against killing by the soil-dwelling nematode Caenorhabditis elegans and the predatory bacterium Myxococcus xanthus. Additionally, matrix-encased bacteria at the air-biofilm interface exhibited ∼40-fold-increased survival after C. elegans and M. xanthus killing compared to the non-matrix-encased cells that populate the interior of the biofilm. To determine if nonhost Enterobacteriaceae reservoirs supported biofilm formation, we grew E. coli on media composed of pig dung or commonly contaminated foods, such as beef, chicken, and spinach. Each of these medium types provided a nutritional environment that supported matrix production and biofilm formation. Altogether, we showed that common, nonhost reservoirs of E. coli supported the formation of biofilms that subsequently protected E. coli against predation.

  8. Biofilm Formation Protects Escherichia coli against Killing by Caenorhabditis elegans and Myxococcus xanthus

    PubMed Central

    DePas, William H.; Syed, Adnan K.; Sifuentes, Margarita; Lee, John S.; Warshaw, David; Saggar, Vinay; Csankovszki, Györgyi; Boles, Blaise R.

    2014-01-01

    Enteric bacteria, such as Escherichia coli, are exposed to a variety of stresses in the nonhost environment. The development of biofilms provides E. coli with resistance to environmental insults, such as desiccation and bleach. We found that biofilm formation, specifically production of the matrix components curli and cellulose, protected E. coli against killing by the soil-dwelling nematode Caenorhabditis elegans and the predatory bacterium Myxococcus xanthus. Additionally, matrix-encased bacteria at the air-biofilm interface exhibited ∼40-fold-increased survival after C. elegans and M. xanthus killing compared to the non-matrix-encased cells that populate the interior of the biofilm. To determine if nonhost Enterobacteriaceae reservoirs supported biofilm formation, we grew E. coli on media composed of pig dung or commonly contaminated foods, such as beef, chicken, and spinach. Each of these medium types provided a nutritional environment that supported matrix production and biofilm formation. Altogether, we showed that common, nonhost reservoirs of E. coli supported the formation of biofilms that subsequently protected E. coli against predation. PMID:25192998

  9. Genic and Allelic Interactions in the Carotenogenic Response of Myxococcus Xanthus to Blue Light

    PubMed Central

    Martinez-Laborda, A.; Murillo, F. J.

    1989-01-01

    In the bacterium Myxococcus xanthus, the synthesis of carotenoids requires illumination with blue light. This stimulates transcription of the carB locus, which is positively required for carotenogenesis. Mutations at the carR locus and the only mutation known at carA cause constitutive expression of carB and thus remove the light requirement for carotenoid accumulation (Car(c) phenotype). The carR locus is unlinked, and carA is linked, to carB. We have now identified a novel class of car mutation, closely linked to carR, that block accumulation of carotenoids and transcription of carB, and are epistatic over the Car(c) mutations at carR but not over the Car(c) mutation at carA. We also report here the cloning of a 16-kb DNA fragment that contains the entire carA gene in a shuttle vector for DNA transfer between Escherichia coli and M. xanthus. The study of allelic interactions at this gene strongly indicate that carA is a cis-acting element for the control of carB expression. A regulatory model that satisfies all the indicated data is presented. PMID:17246505

  10. Identification and Characterization of a Putative Arginine Kinase Homolog from Myxococcus xanthus Required for Fruiting Body Formation and Cell Differentiation

    PubMed Central

    Bragg, Jonathan; Rajkovic, Andrei; Anderson, Chance; Curtis, Rachael; Van Houten, Jason; Begres, Brittany; Naples, Colin; Snider, Mark; Fraga, Dean

    2012-01-01

    Arginine kinases catalyze the reversible transfer of a high-energy phosphoryl group from ATP to l-arginine to form phosphoarginine, which is used as an energy buffer in insects, crustaceans, and some unicellular organisms. It plays an analogous role to that of phosphocreatine in vertebrates. Recently, putative arginine kinases were identified in several bacterial species, including the social Gram-negative soil bacterium Myxococcus xanthus. It is still unclear what role these proteins play in bacteria and whether they have evolved to acquire novel functions in the species in which they are found. In this study, we biochemically purified and characterized a putative M. xanthus arginine kinase, Ark, and demonstrated that it has retained the ability to catalyze the phosphorylation of arginine by using ATP. We also constructed a null mutation in the ark gene and demonstrated its role in both certain stress responses and development. PMID:22389486

  11. Triple mutants uncover three new genes required for social motility in Myxococcus xanthus.

    PubMed

    Youderian, Philip; Hartzell, Patricia L

    2007-09-01

    The bacterium Myxococcus xanthus glides over surfaces using two different locomotive mechanisms, called S (social) and A (adventurous) motility that enable cells to move both as groups and as individuals. Neither mechanism involves flagella. The functions of these two motors are coordinated by the activity of a small Ras-like protein, encoded by the mglA gene. The results of previous studies of a second-site suppressor of the mglA-8 missense mutation masK-815 indicate that MglA interacts with a protein tyrosine kinase, MasK, to control social motility. Sequence analysis of the sites of 12 independent insertions of the transposon magellan-4 that result in the loss of motility in an M. xanthus mglA-8 masK-815 double mutant shows that nine of these 12 insertions are in genes known to be required for S gliding motility. This result confirms that the masK-815 suppressor restores S but not A motility. Three of the 12 insertions define three new genes required for S motility and show that the attachment of heptose to the lipopolysaccharide inner core, an ortholog of the CheR methyltransferase, and a large protein with YD repeat motifs, are required for S motility. When these three insertions are backcrossed into an otherwise wild-type genetic background, their recombinants are found to have defects in S, but not, A motility. The spectrum of magellan-4 insertions that lead to the loss of S motility in the mglA-8 masK-815 double mutant background is different than that resulting from a previous mutant hunt starting with a different (A mutant) genetic background, suggesting that the number of genes required for S motility in M. xanthus is quite large.

  12. The mechanistic basis of Myxococcus xanthus rippling behavior and its physiological role during predation.

    PubMed

    Zhang, Haiyang; Vaksman, Zalman; Litwin, Douglas B; Shi, Peng; Kaplan, Heidi B; Igoshin, Oleg A

    2012-01-01

    Myxococcus xanthus cells self-organize into periodic bands of traveling waves, termed ripples, during multicellular fruiting body development and predation on other bacteria. To investigate the mechanistic basis of rippling behavior and its physiological role during predation by this Gram-negative soil bacterium, we have used an approach that combines mathematical modeling with experimental observations. Specifically, we developed an agent-based model (ABM) to simulate rippling behavior that employs a new signaling mechanism to trigger cellular reversals. The ABM has demonstrated that three ingredients are sufficient to generate rippling behavior: (i) side-to-side signaling between two cells that causes one of the cells to reverse, (ii) a minimal refractory time period after each reversal during which cells cannot reverse again, and (iii) physical interactions that cause the cells to locally align. To explain why rippling behavior appears as a consequence of the presence of prey, we postulate that prey-associated macromolecules indirectly induce ripples by stimulating side-to-side contact-mediated signaling. In parallel to the simulations, M. xanthus predatory rippling behavior was experimentally observed and analyzed using time-lapse microscopy. A formalized relationship between the wavelength, reversal time, and cell velocity has been predicted by the simulations and confirmed by the experimental data. Furthermore, the results suggest that the physiological role of rippling behavior during M. xanthus predation is to increase the rate of spreading over prey cells due to increased side-to-side contact-mediated signaling and to allow predatory cells to remain on the prey longer as a result of more periodic cell motility.

  13. Cyclic Di-GMP Regulates Type IV Pilus-Dependent Motility in Myxococcus xanthus

    PubMed Central

    Skotnicka, Dorota; Petters, Tobias; Heering, Jan; Hoppert, Michael; Kaever, Volkhard

    2015-01-01

    ABSTRACT The nucleotide-based second messenger bis-(3′-5′)-cyclic dimeric GMP (c-di-GMP) is involved in regulating a plethora of processes in bacteria that are typically associated with lifestyle changes. Myxococcus xanthus undergoes major lifestyle changes in response to nutrient availability, with the formation of spreading colonies in the presence of nutrients and spore-filled fruiting bodies in the absence of nutrients. Here, we investigated the function of c-di-GMP in M. xanthus and show that this bacterium synthesizes c-di-GMP during growth. Manipulation of the c-di-GMP level by expression of either an active, heterologous diguanylate cyclase or an active, heterologous phosphodiesterase correlated with defects in type IV pilus (T4P)-dependent motility, whereas gliding motility was unaffected. An increased level of c-di-GMP correlated with reduced transcription of the pilA gene (which encodes the major pilin of T4P), reduced the assembly of T4P, and altered cell agglutination, whereas a decreased c-di-GMP level correlated with altered cell agglutination. The systematic inactivation of the 24 genes in M. xanthus encoding proteins containing GGDEF, EAL, or HD-GYP domains, which are associated with c-di-GMP synthesis, degradation, or binding, identified three genes encoding proteins important for T4P-dependent motility, whereas all mutants had normal gliding motility. Purified DmxA had diguanylate cyclase activity, whereas the hybrid histidine protein kinases TmoK and SgmT, each of which contains a GGDEF domain, did not have diguanylate cyclase activity. These results demonstrate that c-di-GMP is important for T4P-dependent motility in M. xanthus. IMPORTANCE We provide the first direct evidence that M. xanthus synthesizes c-di-GMP and demonstrate that c-di-GMP is important for T4P-dependent motility, whereas we did not obtain evidence that c-di-GMP regulates gliding motility. The data presented uncovered a novel mechanism for regulation of T4P

  14. Bacterial Community Dynamics During the Application of a Myxococcus xanthus-Inoculated Culture Medium Used for Consolidation of Ornamental Limestone

    PubMed Central

    Jimenez-Lopez, Concepcion; Sterflinger, Katja; Ettenauer, Jörg; Jroundi, Fadwa; Fernandez-Vivas, Antonia; Gonzalez-Muñoz, Maria Teresa

    2010-01-01

    In this study, we investigated under laboratory conditions the bacterial communities inhabiting quarry and decayed ornamental carbonate stones before and after the application of a Myxococcus xanthus-inoculated culture medium used for consolidation of the stones. The dynamics of the community structure and the prevalence of the inoculated bacterium, M. xanthus, were monitored during the time course of the consolidation treatment (30 days). For this purpose, we selected a molecular strategy combining fingerprinting by denaturing gradient gel electrophoresis (DGGE) with the screening of eubacterial 16S rDNA clone libraries by DGGE and sequencing. Quantification of the inoculated strain was performed by quantitative real-time PCR (qPCR) using M. xanthus-specific primers designed in this work. Results derived from DGGE and sequencing analysis showed that, irrespective of the origin of the stone, the same carbonatogenic microorganisms were activated by the application of a M. xanthus culture. Those microorganisms were Pseudomonas sp., Bacillus sp., and Brevibacillus sp. The monitoring of M. xanthus in the culture media of treated stones during the time course experiment showed disparate results depending on the applied technique. By culture-dependent methods, the detection of this bacterium was only possible in the first day of the treatment, showing the limitation of these conventional techniques. By PCR-DGGE analysis, M. xanthus was detected during the first 3–6 days of the experiment. At this time, the population of this bacterium in the culture media varied between 108–106 cells ml−1, as showed by qPCR analyses. Thereafter, DGGE analyses showed to be not suitable for the detection of M. xanthus in a mixed culture. Nevertheless, qPCR analysis using specific primers for M. xanthus showed to be a more sensitive technique for the detection of this bacterium, revealing a population of 104 cells ml−1 in the culture media of both treated stones at the end of

  15. Role of phase variation in the resistance of Myxococcus xanthus fruiting bodies to Caenorhabditis elegans predation.

    PubMed

    Dahl, John L; Ulrich, Christina H; Kroft, Tim L

    2011-10-01

    The phenomenon of phase variation between yellow and tan forms of Myxococcus xanthus has been recognized for several decades, but it is not known what role this variation may play in the ecology of myxobacteria. We confirm an earlier report that tan variants are disproportionately more numerous in the resulting spore population of a M. xanthus fruiting body than the tan vegetative cells that contributed to fruiting body formation. However, we found that tan cells may not require yellow cells for fruiting body formation or starvation-induced sporulation of tan cells. Here we report three differences between the yellow and tan variants that may play important roles in the soil ecology of M. xanthus. Specifically, the yellow variant is more capable of forming biofilms, is more sensitive to lysozyme, and is more resistant to ingestion by bacteriophagous nematodes. We also show that the myxobacterial fruiting body is more resistant to predation by worms than are dispersed M. xanthus cells. PMID:21821771

  16. Chemosensory Regulation of a HEAT-Repeat Protein Couples Aggregation and Sporulation in Myxococcus xanthus

    PubMed Central

    Darnell, Cynthia L.; Wilson, Janet M.; Tiwari, Nitija; Fuentes, Ernesto J.

    2014-01-01

    Chemosensory systems are complex, highly modified two-component systems (TCS) used by bacteria to control various biological functions ranging from motility to sporulation. Chemosensory systems and TCS both modulate phosphorelays comprised of histidine kinases and response regulators, some of which are single-domain response regulators (SD-RRs) such as CheY. In this study, we have identified and characterized the Che7 chemosensory system of Myxococcus xanthus, a common soil bacterium which displays multicellular development in response to stress. Both genetic and biochemical analyses indicate that the Che7 system regulates development via a direct interaction between the SD-RR CheY7 and a HEAT repeat domain-containing protein, Cpc7. Phosphorylation of the SD-RR affects the interaction with its target, and residues within the α4-β5-α5 fold of the REC domain govern this interaction. The identification of the Cpc7 interaction with CheY7 extends the diversity of known targets for SD-RRs in biological systems. PMID:24957622

  17. Lipid body formation plays a central role in cell fate determination during developmental differentiation of Myxococcus xanthus.

    PubMed

    Hoiczyk, Egbert; Ring, Michael W; McHugh, Colleen A; Schwär, Gertrud; Bode, Edna; Krug, Daniel; Altmeyer, Matthias O; Lu, Jeff Zhiqiang; Bode, Helge B

    2009-10-01

    Cell differentiation is widespread during the development of multicellular organisms, but rarely observed in prokaryotes. One example of prokaryotic differentiation is the gram-negative bacterium Myxococcus xanthus. In response to starvation, this gliding bacterium initiates a complex developmental programme that results in the formation of spore-filled fruiting bodies. How the cells metabolically support the necessary complex cellular differentiation from rod-shaped vegetative cells into spherical spores is unknown. Here, we present evidence that intracellular lipid bodies provide the necessary metabolic fuel for the development of spores. Formed at the onset of starvation, these lipid bodies gradually disappear until they are completely used up by the time the cells have become mature spores. Moreover, it appears that lipid body formation in M. xanthus is an important initial step indicating cell fate during differentiation. Upon starvation, two subpopulations of cells occur: cells that form lipid bodies invariably develop into spores, while cells that do not form lipid bodies end up becoming peripheral rods, which are cells that lack signs of morphological differentiation and stay in a vegetative-like state. These data indicate that lipid bodies not only fuel cellular differentiation but that their formation represents the first known morphological sign indicating cell fate during differentiation. PMID:19788540

  18. Lipid body formation plays a central role in cell fate determination during developmental differentiation of Myxococcus xanthus

    PubMed Central

    Ring, Michael W.; McHugh, Colleen A.; Schwär, Gertrud; Bode, Edna; Krug, Daniel; Altmeyer, Matthias O.; Lu, Jeff Zhiqiang

    2010-01-01

    Summary Cell differentiation is widespread during the development of multicellular organisms, but rarely observed in prokaryotes. One example of prokaryotic differentiation is the Gramnegative bacterium Myxococcus xanthus. In response to starvation, this gliding bacterium initiates a complex developmental program that results in the formation of spore-filled fruiting bodies. How the cells metabolically support the necessary complex cellular differentiation from rod-shaped vegetative cells into spherical spores is unknown. Here, we present evidence that intra-cellular lipid bodies provide the necessary metabolic fuel for the development of spores. Formed at the onset of starvation, these lipid bodies gradually disappear until they are completely used up by the time the cells have become mature spores. Moreover, it appears that lipid body formation in M. xanthus is an important initial step indicating cell fate during differentiation. Upon starvation, two subpopulations of cells occur: cells that form lipid bodies invariably develop into spores, while cells that do not form lipid bodies end up becoming peripheral rods, which are cells that lack signs of morphological differentiation and stay in a vegetative-like state. These data indicate that lipid bodies not only fuel cellular differentiation but that their formation represents the first known morphological sign indicating cell fate during differentiation. PMID:19788540

  19. Directional reversals enable Myxococcus xanthus cells to produce collective one-dimensional streams during fruiting-body formation

    PubMed Central

    Thutupalli, Shashi; Sun, Mingzhai; Bunyak, Filiz; Palaniappan, Kannappan; Shaevitz, Joshua W.

    2015-01-01

    The formation of a collectively moving group benefits individuals within a population in a variety of ways. The surface-dwelling bacterium Myxococcus xanthus forms dynamic collective groups both to feed on prey and to aggregate during times of starvation. The latter behaviour, termed fruiting-body formation, involves a complex, coordinated series of density changes that ultimately lead to three-dimensional aggregates comprising hundreds of thousands of cells and spores. How a loose, two-dimensional sheet of motile cells produces a fixed aggregate has remained a mystery as current models of aggregation are either inconsistent with experimental data or ultimately predict unstable structures that do not remain fixed in space. Here, we use high-resolution microscopy and computer vision software to spatio-temporally track the motion of thousands of individuals during the initial stages of fruiting-body formation. We find that cells undergo a phase transition from exploratory flocking, in which unstable cell groups move rapidly and coherently over long distances, to a reversal-mediated localization into one-dimensional growing streams that are inherently stable in space. These observations identify a new phase of active collective behaviour and answer a long-standing open question in Myxococcus development by describing how motile cell groups can remain statistically fixed in a spatial location. PMID:26246416

  20. A Minimal Threshold of c-di-GMP Is Essential for Fruiting Body Formation and Sporulation in Myxococcus xanthus

    PubMed Central

    Skotnicka, Dorota; Trampari, Eleftheria; Liang, Jennifer; Kaever, Volkhard; Malone, Jacob G.; Singer, Mitchell; Søgaard-Andersen, Lotte

    2016-01-01

    Generally, the second messenger bis-(3’-5’)-cyclic dimeric GMP (c-di-GMP) regulates the switch between motile and sessile lifestyles in bacteria. Here, we show that c-di-GMP is an essential regulator of multicellular development in the social bacterium Myxococcus xanthus. In response to starvation, M. xanthus initiates a developmental program that culminates in formation of spore-filled fruiting bodies. We show that c-di-GMP accumulates at elevated levels during development and that this increase is essential for completion of development whereas excess c-di-GMP does not interfere with development. MXAN3735 (renamed DmxB) is identified as a diguanylate cyclase that only functions during development and is responsible for this increased c-di-GMP accumulation. DmxB synthesis is induced in response to starvation, thereby restricting DmxB activity to development. DmxB is essential for development and functions downstream of the Dif chemosensory system to stimulate exopolysaccharide accumulation by inducing transcription of a subset of the genes encoding proteins involved in exopolysaccharide synthesis. The developmental defects in the dmxB mutant are non-cell autonomous and rescued by co-development with a strain proficient in exopolysaccharide synthesis, suggesting reduced exopolysaccharide accumulation as the causative defect in this mutant. The NtrC-like transcriptional regulator EpsI/Nla24, which is required for exopolysaccharide accumulation, is identified as a c-di-GMP receptor, and thus a putative target for DmxB generated c-di-GMP. Because DmxB can be—at least partially—functionally replaced by a heterologous diguanylate cyclase, these results altogether suggest a model in which a minimum threshold level of c-di-GMP is essential for the successful completion of multicellular development in M. xanthus. PMID:27214040

  1. The mysterious nature of bacterial surface (gliding) motility: A focal adhesion-based mechanism in Myxococcus xanthus.

    PubMed

    Islam, Salim T; Mignot, Tâm

    2015-10-01

    Motility of bacterial cells promotes a range of important physiological phenomena such as nutrient detection, harm avoidance, biofilm formation, and pathogenesis. While much research has been devoted to the mechanism of bacterial swimming in liquid via rotation of flagellar filaments, the mechanisms of bacterial translocation across solid surfaces are poorly understood, particularly when cells lack external appendages such as rotary flagella and/or retractile type IV pili. Under such limitations, diverse bacteria at the single-cell level are still able to "glide" across solid surfaces, exhibiting smooth translocation of the cell along its long axis. Though multiple gliding mechanisms have evolved in different bacterial classes, most remain poorly characterized. One exception is the gliding motility mechanism used by the Gram-negative social predatory bacterium Myxococcus xanthus. The available body of research suggests that M. xanthus gliding motility is mediated by trafficked multi-protein (Glt) cell envelope complexes, powered by proton-driven flagellar stator homologues (Agl). Through coupling to the substratum via polysaccharide slime, Agl-Glt assemblies can become fixed relative to the substratum, forming a focal adhesion site. Continued directional transport of slime-associated substratum-fixed Agl-Glt complexes would result in smooth forward movement of the cell. In this review, we have provided a comprehensive synthesis of the latest mechanistic and structural data for focal adhesion-mediated gliding motility in M. xanthus, with emphasis on the role of each Agl and Glt protein. Finally, we have also highlighted the possible connection between the motility complex and a new type of spore coat assembly system, suggesting that gliding and cell envelope synthetic complexes are evolutionarily linked. PMID:26520023

  2. A Minimal Threshold of c-di-GMP Is Essential for Fruiting Body Formation and Sporulation in Myxococcus xanthus.

    PubMed

    Skotnicka, Dorota; Smaldone, Gregory T; Petters, Tobias; Trampari, Eleftheria; Liang, Jennifer; Kaever, Volkhard; Malone, Jacob G; Singer, Mitchell; Søgaard-Andersen, Lotte

    2016-05-01

    Generally, the second messenger bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) regulates the switch between motile and sessile lifestyles in bacteria. Here, we show that c-di-GMP is an essential regulator of multicellular development in the social bacterium Myxococcus xanthus. In response to starvation, M. xanthus initiates a developmental program that culminates in formation of spore-filled fruiting bodies. We show that c-di-GMP accumulates at elevated levels during development and that this increase is essential for completion of development whereas excess c-di-GMP does not interfere with development. MXAN3735 (renamed DmxB) is identified as a diguanylate cyclase that only functions during development and is responsible for this increased c-di-GMP accumulation. DmxB synthesis is induced in response to starvation, thereby restricting DmxB activity to development. DmxB is essential for development and functions downstream of the Dif chemosensory system to stimulate exopolysaccharide accumulation by inducing transcription of a subset of the genes encoding proteins involved in exopolysaccharide synthesis. The developmental defects in the dmxB mutant are non-cell autonomous and rescued by co-development with a strain proficient in exopolysaccharide synthesis, suggesting reduced exopolysaccharide accumulation as the causative defect in this mutant. The NtrC-like transcriptional regulator EpsI/Nla24, which is required for exopolysaccharide accumulation, is identified as a c-di-GMP receptor, and thus a putative target for DmxB generated c-di-GMP. Because DmxB can be-at least partially-functionally replaced by a heterologous diguanylate cyclase, these results altogether suggest a model in which a minimum threshold level of c-di-GMP is essential for the successful completion of multicellular development in M. xanthus.

  3. Genome Evolution and the Emergence of Fruiting Body Development in Myxococcus xanthus

    PubMed Central

    Goldman, Barry; Bhat, Swapna; Shimkets, Lawrence J.

    2007-01-01

    Background Lateral gene transfer (LGT) is thought to promote speciation in bacteria, though well-defined examples have not been put forward. Methodology/Principle Findings We examined the evolutionary history of the genes essential for a trait that defines a phylogenetic order, namely fruiting body development of the Myxococcales. Seventy-eight genes that are essential for Myxococcus xanthus development were examined for LGT. About 73% of the genes exhibit a phylogeny similar to that of the 16S rDNA gene and a codon bias consistent with other M. xanthus genes suggesting vertical transmission. About 22% have an altered codon bias and/or phylogeny suggestive of LGT. The remaining 5% are unique. Genes encoding signal production and sensory transduction were more likely to be transmitted vertically with clear examples of duplication and divergence into multigene families. Genes encoding metabolic enzymes were frequently acquired by LGT. Myxobacteria exhibit aerobic respiration unlike most of the δ Proteobacteria. M. xanthus contains a unique electron transport pathway shaped by LGT of genes for succinate dehydrogenase and three cytochrome oxidase complexes. Conclusions/Significance Fruiting body development depends on genes acquired by LGT, particularly those involved in polysaccharide production. We suggest that aerobic growth fostered innovation necessary for development by allowing myxobacteria access to a different gene pool from anaerobic members of the δ Proteobacteria. Habitat destruction and loss of species diversity could restrict the evolution of new bacterial groups by limiting the size of the prospective gene pool. PMID:18159227

  4. Describing Myxococcus xanthus Aggregation Using Ostwald Ripening Equations for Thin Liquid Films

    PubMed Central

    Bahar, Fatmagül; Pratt-Szeliga, Philip C.; Angus, Stuart; Guo, Jiaye; Welch, Roy D.

    2014-01-01

    When starved, a swarm of millions of Myxococcus xanthus cells coordinate their movement from outward swarming to inward coalescence. The cells then execute a synchronous program of multicellular development, arranging themselves into dome shaped aggregates. Over the course of development, about half of the initial aggregates disappear, while others persist and mature into fruiting bodies. This work seeks to develop a quantitative model for aggregation that accurately simulates which will disappear and which will persist. We analyzed time-lapse movies of M. xanthus development, modeled aggregation using the equations that describe Ostwald ripening of droplets in thin liquid films, and predicted the disappearance and persistence of aggregates with an average accuracy of 85%. We then experimentally validated a prediction that is fundamental to this model by tracking individual fluorescent cells as they moved between aggregates and demonstrating that cell movement towards and away from aggregates correlates with aggregate disappearance. Describing development through this model may limit the number and type of molecular genetic signals needed to complete M. xanthus development, and it provides numerous additional testable predictions. PMID:25231319

  5. Alkaline, acid, and neutral phosphatase activities are induced during development in Myxococcus xanthus.

    PubMed Central

    Weinberg, R A; Zusman, D R

    1990-01-01

    One of the signals that has been reported to be important in stimulating fruiting body formation of Myxococcus xanthus is starvation for phosphate. We therefore chose to study phosphatase activity during M. xanthus development. Many phosphatases can cleave the substrate p-nitrophenol phosphate. Using this substrate in buffers at various pHs, we obtained a profile of phosphatase activities during development and germination of M. xanthus. These experiments indicated that there are five patterns of phosphatase activity in M. xanthus: two vegetative and three developmental. The two uniquely vegetative activities have pH optima at 7.2 and 8.5. Both require magnesium and both are inhibited by the reducing agent dithiothreitol. The developmental (spores) patterns of activity have pH optima of 5.2, 7.2, and 8.5. All three activities are Mg independent. Only the alkaline phosphatase activity is inhibited by dithiothreitol. The acid phosphatase activity is induced very early in development, within the first 2 to 4 h. Both the neutral and alkaline phosphatase Mg-independent activities are induced much later, about the time that myxospores become evident (24 to 30 h). The three activities are greatly diminished upon germination; however, the kinetics of loss differ for all three. The acid phosphatase activity declines very rapidly, the neutral activity begins to decline only after spores begin to convert to rods, and the alkaline phosphatase activity remains high until the time the cells begin to divide. All three developmental activities were measured in the developmental signalling mutants carrying asg, csg, and dsg. The pattern of expression obtained in the mutants was consistent with that of other developmentally regulated genes which exhibit similar patterns of expression during development. The ease with which phosphatases can be assayed should make the activities described in this report useful biochemical markers of stages of both fruiting body formation and

  6. Ribonucleic acid synthesis during fruiting body formation in Myxococcus xanthus.

    PubMed

    Smith, B A; Dworkin, M

    1981-04-01

    A method has been devised that allowed us, for the first time, to pulse-label M. xanthus cells with precursors for ribonucleic acid biosynthesis while they were undergoing fruiting body formation. Using this method, we examined patterns of ribonucleic acid (RNA) accumulation throughout the process of fruiting body formation. As development proceeded, the rate of RNA accumulation increased at two periods of the developmental cycle: once just before aggregation and once late in the cycle, when sporulation was essentially completed. In contrast to vegetatively growing cells, in which only stable RNA species are labeled during a 30-min pulse, the majority of radioactivity found in RNA from 30-min pulse-labeled developing cells was found in an unstable heterodisperse fraction that migrated to the 5S to 16S region of sucrose density gradients and sodium dodecyl sulfate-polyacrylamide gels. This pattern of incorporation could not be induced (i) by a shift down of vegetatively growing cells to a nutritionally poor medium, in which the generation time was increased to that of developing cells during the growth phase, or (ii) by plating of vegetative cells onto the same solid-surface environment as that of developing cells, but which surface supported vegetative growth rather than fruiting body formation. Thus, the RNA synthesis pattern observed appeared to be related to development per se rather than to nutritional depletion or growth on a solid surface alone. The radioactivity incorporated into the unstable 5S to 16S RNA fraction accumulated as the pulse length was increased from 10 to 30 min; in contrast, an analogous unstable fraction from vegetative cells decreased as pulse length was increased. This suggested that developmental 5S to 16S RNA was more stable than vegetative cell 5S to 16S RNA (presumptive messenger RNA). However, during a 45-min chase period, radioactivity in 30-min-pulse-labeled developmental 5S to 16S RNA decayed to an extent twice that of

  7. Transposon insertions of magellan-4 that impair social gliding motility in Myxococcus xanthus.

    PubMed

    Youderian, Philip; Hartzell, Patricia L

    2006-03-01

    Myxococcus xanthus has two different mechanisms of motility, adventurous (A) motility, which permits individual cells to glide over solid surfaces, and social (S) motility, which permits groups of cells to glide. To identify the genes involved in S-gliding motility, we mutagenized a delta aglU (A-) strain with the defective transposon, magellan-4, and screened for S- mutants that form nonmotile colonies. Sequence analysis of the sites of the magellan-4 insertions in these mutants and the alignment of these sites with the M. xanthus genome sequence show that two-thirds of these insertions lie within 27 of the 37 nonessential genes known to be required for social motility, including those necessary for the biogenesis of type IV pili, exopolysaccharide, and lipopolysaccharide. The remaining insertions also identify 31 new, nonessential genes predicted to encode both structural and regulatory determinants of S motility. These include three tetratricopeptide repeat proteins, several regulators of transcription that may control the expression of genes involved in pilus extension and retraction, and additional enzymes involved in polysaccharide metabolism. Three insertions that abolish S motility lie within genes predicted to encode glycolytic enzymes, suggesting that the signal for pilus retraction may be a simple product of exopolysaccharide catabolism.

  8. A Clp/Hsp100 Chaperone Functions in Myxococcus xanthus Sporulation and Self-Organization

    PubMed Central

    Yan, Jinyuan; Garza, Anthony G.; Bradley, Michael D.

    2012-01-01

    The Clp/Hsp100 proteins are chaperones that play a role in protein degradation and reactivation. In bacteria, they exhibit a high degree of pleiotropy, affecting both individual and multicellular phenotypes. In this article, we present the first characterization of a Clp/Hsp100 homolog in Myxococcus xanthus (MXAN_4832 gene locus). Deletion of MXAN_4832 causes defects in both swarming and aggregation related to cell motility and the production of fibrils, which are an important component of the extracellular matrix of a swarm. The deletion also affects the formation of myxospores during development, causing them to become sensitive to heat. The protein product of MXAN_4832 can act as a chaperone in vitro, providing biochemical evidence in support of our hypothesis that MXAN_4832 is a functional Clp/Hsp100 homolog. There are a total of 12 Clp/Hsp100 homologs in M. xanthus, including MXAN_4832, and, based on its mutational and biochemical characterization, they may well represent an important group. PMID:22287524

  9. From individual cell motility to collective behaviors: insights from a prokaryote, Myxococcus xanthus.

    PubMed

    Zhang, Yong; Ducret, Adrien; Shaevitz, Joshua; Mignot, Tâm

    2012-01-01

    In bird flocks, fish schools, and many other living organisms, regrouping among individuals of the same kin is frequently an advantageous strategy to survive, forage, and face predators. However, these behaviors are costly because the community must develop regulatory mechanisms to coordinate and adapt its response to rapid environmental changes. In principle, these regulatory mechanisms, involving communication between individuals, may also apply to cellular systems which must respond collectively during multicellular development. Dissecting the mechanisms at work requires amenable experimental systems, for example, developing bacteria. Myxococcus xanthus, a Gram-negative delatproteobacterium, is able to coordinate its motility in space and time to swarm, predate, and grow millimeter-size spore-filled fruiting bodies. A thorough understanding of the regulatory mechanisms first requires studying how individual cells move across solid surfaces and control their direction of movement, which was recently boosted by new cell biology techniques. In this review, we describe current molecular knowledge of the motility mechanism and its regulation as a lead-in to discuss how multicellular cooperation may have emerged from several layers of regulation: chemotaxis, cell-cell signaling, and the extracellular matrix. We suggest that Myxococcus is a powerful system to investigate collective principles that may also be relevant to other cellular systems.

  10. Structural Insights into RNA Polymerase Recognition and Essential Function of Myxococcus xanthus CdnL

    PubMed Central

    Gallego-García, Aránzazu; Mirassou, Yasmina; García-Moreno, Diana; Elías-Arnanz, Montserrat; Jiménez, María Angeles; Padmanabhan, S.

    2014-01-01

    CdnL and CarD are two functionally distinct members of the CarD_CdnL_TRCF family of bacterial RNA polymerase (RNAP)-interacting proteins, which co-exist in Myxococcus xanthus. While CarD, found exclusively in myxobacteria, has been implicated in the activity of various extracytoplasmic function (ECF) σ-factors, the function and mode of action of the essential CdnL, whose homologs are widespread among bacteria, remain to be elucidated in M. xanthus. Here, we report the NMR solution structure of CdnL and present a structure-based mutational analysis of its function. An N-terminal five-stranded β-sheet Tudor-like module in the two-domain CdnL mediates binding to RNAP-β, and mutations that disrupt this interaction impair cell growth. The compact CdnL C-terminal domain consists of five α-helices folded as in some tetratricopeptide repeat-like protein-protein interaction domains, and contains a patch of solvent-exposed nonpolar and basic residues, among which a set of basic residues is shown to be crucial for CdnL function. We show that CdnL, but not its loss-of-function mutants, stabilizes formation of transcriptionally competent, open complexes by the primary σA-RNAP holoenzyme at an rRNA promoter in vitro. Consistent with this, CdnL is present at rRNA promoters in vivo. Implication of CdnL in RNAP-σA activity and of CarD in ECF-σ function in M. xanthus exemplifies how two related members within a widespread bacterial protein family have evolved to enable distinct σ-dependent promoter activity. PMID:25272012

  11. Sibling Rivalry in Myxococcus xanthus Is Mediated by Kin Recognition and a Polyploid Prophage

    PubMed Central

    Dey, Arup; Vassallo, Christopher N.; Conklin, Austin C.; Pathak, Darshankumar T.; Troselj, Vera

    2016-01-01

    ABSTRACT Myxobacteria form complex social communities that elicit multicellular behaviors. One such behavior is kin recognition, in which cells identify siblings via their polymorphic TraA cell surface receptor, to transiently fuse outer membranes and exchange their contents. In addition, outer membrane exchange (OME) regulates behaviors, such as inhibition of wild-type Myxococcus xanthus (DK1622) from swarming. Here we monitored the fate of motile cells and surprisingly found they were killed by nonmotile siblings. The kill phenotype required OME (i.e., was TraA dependent). The genetic basis of killing was traced to ancestral strains used to construct DK1622. Specifically, the kill phenotype mapped to a large “polyploid prophage,” Mx alpha. Sensitive strains contained a 200-kb deletion that removed two of three Mx alpha units. To explain these results, we suggest that Mx alpha expresses a toxin-antitoxin cassette that uses the OME machinery of M. xanthus to transfer a toxin that makes the population “addicted” to Mx alpha. Thus, siblings that lost Mx alpha units (no immunity) are killed by cells that harbor the element. To test this, an Mx alpha-harboring laboratory strain was engineered (by traA allele swap) to recognize a closely related species, Myxococcus fulvus. As a result, M. fulvus, which lacks Mx alpha, was killed. These TraA-mediated antagonisms provide an explanation for how kin recognition specificity might have evolved in myxobacteria. That is, recognition specificity is determined by polymorphisms in traA, which we hypothesize were selected for because OME with non-kin leads to lethal outcomes. IMPORTANCE The transition from single cell to multicellular life is considered a major evolutionary event. Myxobacteria have successfully made this transition. For example, in response to starvation, individual cells aggregate into multicellular fruiting bodies wherein cells differentiate into spores. To build fruits, cells need to recognize their

  12. Regulation of a Protein Acetyltransferase in Myxococcus xanthus by the Coenzyme NADP+

    PubMed Central

    Liu, Xin-Xin

    2015-01-01

    ABSTRACT NADP+ is a vital cofactor involved in a wide variety of activities, such as redox potential and cell death. Here, we show that NADP+ negatively regulates an acetyltransferase from Myxococcus xanthus, Mxan_3215 (MxKat), at physiologic concentrations. MxKat possesses an NAD(P)-binding domain fused to the Gcn5-type N-acetyltransferase (GNAT) domain. We used isothermal titration calorimetry (ITC) and a coupled enzyme assay to show that NADP+ bound to MxKat and that the binding had strong effects on enzyme activity. The Gly11 residue of MxKat was confirmed to play an important role in NADP+ binding using site-directed mutagenesis and circular dichroism spectrometry. In addition, using mass spectrometry, site-directed mutagenesis, and a coupling enzymatic assay, we demonstrated that MxKat acetylates acetyl coenzyme A (acetyl-CoA) synthetase (Mxan_2570) at Lys622 in response to changes in NADP+ concentration. Collectively, our results uncovered a mechanism of protein acetyltransferase regulation by the coenzyme NADP+ at physiological concentrations, suggesting a novel signaling pathway for the regulation of cellular protein acetylation. IMPORTANCE Microorganisms have developed various protein posttranslational modifications (PTMs), which enable cells to respond quickly to changes in the intracellular and extracellular milieus. This work provides the first biochemical characterization of a protein acetyltransferase (MxKat) that contains a fusion between a GNAT domain and NADP+-binding domain with Rossmann folds, and it demonstrates a novel signaling pathway for regulating cellular protein acetylation in M. xanthus. We found that NADP+ specifically binds to the Rossmann fold of MxKat and negatively regulates its acetyltransferase activity. This finding provides novel insight for connecting cellular metabolic status (NADP+ metabolism) with levels of protein acetylation, and it extends our understanding of the regulatory mechanisms underlying PTMs. PMID:26598367

  13. Transmission of a signal that synchronizes cell movements in swarms of Myxococcus xanthus

    PubMed Central

    Kaiser, Dale; Warrick, Hans

    2014-01-01

    We offer evidence for a signal that synchronizes the behavior of hundreds of Myxococcus xanthus cells in a growing swarm. Swarms are driven to expand by the periodic reversing of direction by members. By using time-lapse photomicroscopy, two organized multicellular elements of the swarm were analyzed: single-layered, rectangular rafts and round, multilayered mounds. Rafts of hundreds of cells with their long axes aligned in parallel enlarge as individual cells from the neighborhood join them from either side. Rafts can also add a second layer piece by piece. By repeating layer additions to a raft and rounding each layer, a regular multilayered mound can be formed. About an hour after a five-layered mound had formed, all of the cells from its top layer descended to the periphery of the fourth layer, both rapidly and synchronously. Following the first synchronized descent and spaced at constant time intervals, a new fifth layer was (re)constructed from fourth-layer cells, in very close proximity to its old position and with a number of cells similar to that before the “explosive” descent. This unexpected series of changes in mound structure can be explained by the spread of a signal that synchronizes the reversals of large groups of individual cells. PMID:25149859

  14. A repressor-antirepressor pair links two loci controlling light-induced carotenogenesis in Myxococcus xanthus.

    PubMed

    López-Rubio, José Juan; Elías-Arnanz, Montserrat; Padmanabhan, S; Murillo, Francisco José

    2002-03-01

    The light-inducible carB operon encodes all but one of the structural genes for carotenogenesis in Myxococcus xanthus. It is transcriptionally controlled by two proteins expressed from two unlinked genetic loci: CarS from the light-inducible carQRS operon, and CarA from the light-independent carA operon. CarA represses transcription from the carB promoter (P(B)) in the dark, and CarS counteracts this on illumination. The CarA sequence revealed a helix-turn-helix DNA-binding motif of the type found in bacterial MerR transcriptional factors, whereas CarS contains no known DNA-binding motif. Here, we examine the molecular interplay between CarA and CarS. We demonstrate the following. (i) Whereas CarS exhibits no DNA binding in vitro, CarA binds specifically to a region encompassing P(B) to form at least two distinct complexes. (ii) A palindrome located between positions -46 and -63 relative to the transcription start point is essential but not sufficient for the formation of the two CarA-DNA complexes observed. (iii) CarS abrogates the specific DNA binding of CarA. CarA is therefore a repressor and CarS an antirepressor. (iv) CarS physically interacts with CarA; thus, the functional interaction between them is mediated by protein-protein interactions.

  15. Pattern formation by a cell surface-associated morphogen in Myxococcus xanthus

    PubMed Central

    Jelsbak, Lars; Søgaard-Andersen, Lotte

    2002-01-01

    In response to starvation, an unstructured population of identical Myxococcus xanthus cells rearranges into an asymmetric, stable pattern of multicellular fruiting bodies. Central to this pattern formation process are changes in organized cell movements from swarming to aggregation. Aggregation is induced by the cell surface-associated C-signal. To understand how aggregation is accomplished, we have analyzed how C-signal modulates cell behavior. We show that C-signal induces a motility response that includes increases in transient gliding speeds and in the duration of gliding intervals and decreases in stop and reversal frequencies. This response results in a switch in cell behavior from an oscillatory to a unidirectional type of behavior in which the net-distance traveled by a cell per minute is increased. We propose that the C-signal-dependent regulation of the reversal frequency is essential for aggregation and that the remaining C-signal-dependent changes in motility parameters contribute to aggregation by increasing the net-distance traveled by starving cells per minute. In our model for symmetry-breaking and aggregation, C-signal transmission is a local event involving direct contacts between cells that results in a global organization of cells. This pattern formation mechanism does not require a diffusible substance or other actions at a distance. Rather it depends on contact-induced changes in motility behavior to direct cells appropriately PMID:11842199

  16. Synthesis of several membrane proteins during developmental aggregation in Myxococcus xanthus.

    PubMed

    Orndorff, P E; Dworkin, M

    1982-01-01

    We have examined the pattern of synthesis of several membrane proteins during the aggregation phase of development in Myxococcus xanthus. Development was initiated by plating vegetative cells on polycarbonate filters placed on top of an agar medium that supported fruiting body formation. At various times during aggregation a filter was removed, the cells were pulse-labeled with [35S]methionine, and the membrane proteins were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The rate of synthesis of numerous individual proteins changed during aggregation; we concentrated on six whose pattern of synthesis was greatly altered during aggregation. The rate of synthesis of five of the six proteins increased considerably during aggregation; that of the remaining protein was curtailed and appeared to be regulated by nutrient conditions. Three of the five major membrane proteins that increased during aggregation had a unique pattern of synthesis that was displayed only under conditions that are are required for development - high cell density, nutrient depletion, and a solid (agar) surface. The remaining two proteins were not unique to development; the appearance of one protein could be induced under conditions of high cell density, whereas the other could be induced by placing the cells on a solid agar surface. All of the five major proteins that appeared during development did so during the preaggregation stage, and the synthesis of four of the five proteins appeared to be curtailed late in aggregation. The synthesis of the remaining protein continued throughout aggregation. PMID:6798022

  17. Conservation of ornamental stone by Myxococcus xanthus-induced carbonate biomineralization.

    PubMed

    Rodriguez-Navarro, Carlos; Rodriguez-Gallego, Manuel; Ben Chekroun, Koutar; Gonzalez-Muñoz, Maria Teresa

    2003-04-01

    Increasing environmental pollution in urban areas has been endangering the survival of carbonate stones in monuments and statuary for many decades. Numerous conservation treatments have been applied for the protection and consolidation of these works of art. Most of them, however, either release dangerous gases during curing or show very little efficacy. Bacterially induced carbonate mineralization has been proposed as a novel and environmentally friendly strategy for the conservation of deteriorated ornamental stone. However, the method appeared to display insufficient consolidation and plugging of pores. Here we report that Myxococcus xanthus-induced calcium carbonate precipitation efficiently protects and consolidates porous ornamental limestone. The newly formed carbonate cements calcite grains by depositing on the walls of the pores without plugging them. Sonication tests demonstrate that these new carbonate crystals are strongly attached to the substratum, mostly due to epitaxial growth on preexisting calcite grains. The new crystals are more stress resistant than the calcite grains of the original stone because they are organic-inorganic composites. Variations in the phosphate concentrations of the culture medium lead to changes in local pH and bacterial productivity. These affect the structure of the new cement and the type of precipitated CaCO(3) polymorph (vaterite or calcite). The manipulation of culture medium composition creates new ways of controlling bacterial biomineralization that in the future could be applied to the conservation of ornamental stone.

  18. MasABK Proteins Interact with Proteins of the Type IV Pilin System to Affect Social Motility of Myxococcus xanthus

    PubMed Central

    Fremgen, Sarah; Williams, Amanda; Furusawa, Gou; Dziewanowska, Katarzyna; Settles, Matthew; Hartzell, Patricia

    2013-01-01

    Gliding motility is critical for normal development of spore-filled fruiting bodies in the soil bacterium Myxococcus xanthus. Mutations in mgl block motility and development but one mgl allele can be suppressed by a mutation in masK, the last gene in an operon adjacent to the mgl operon. Deletion of the entire 5.5 kb masABK operon crippled gliding and fruiting body development and decreased sporulation. Expression of pilAGHI, which encodes type IV pili (TFP) components essential for social (S) gliding, several cryptic pil genes, and a LuxR family protein were reduced significantly in the Δmas mutant while expression of the myxalamide operon was increased significantly. Localization and two-hybrid analysis suggest that the three Mas proteins form a membrane complex. MasA-PhoA fusions confirmed that MasA is an integral cytoplasmic membrane protein with a ≈100 amino acid periplasmic domain. Results from yeast two-hybrid assays showed that MasA interacts with the lipoprotein MasB and MasK, a protein kinase and that MasB and MasK interact with one another. Additionally, yeast two-hybrid analysis revealed a physical interaction between two gene products of the mas operon, MasA and MasB, and PilA. Deletion of mas may be accompanied by compensatory mutations since complementation of the Δmas social gliding and developmental defects required addition of both pilA and masABK. PMID:23342171

  19. Coliphage P1-mediated transduction of cloned DNA from Escherichia coli to Myxococcus xanthus: use for complementation and recombinational analyses.

    PubMed Central

    O'Connor, K A; Zusman, D R

    1983-01-01

    We have found that coliphage P1 can be used to transduce cloned DNA from Escherichia coli to Myxococcus xanthus. Transduction occurred at a high efficiency, and no evidence for DNA restriction was observed. The analysis of the transductants showed that they fall into three general categories: (i) haploid cells which contain portions of the cloned DNA substituted for homologous chromosomal DNA; (ii) heterozygous merodiploids which contain the recombinant plasmid integrated into the chromosome at a region of homology; and (iii) homozygous merodiploids which contain two copies of a portion of the cloned DNA with the loss of the chromosomal copy of the genes. The merodiploids, once formed, are relatively stable. They were used to analyze two genes necessary for aggregation and thus fruiting body formation. P1 transduction also permits the reintroduction and substitution of mutated regions of cloned DNA into M. xanthus for the analysis of the role of the DNA in cellular physiology and development. Images PMID:6305916

  20. Myxococcus xanthus mokA Encodes a Histidine Kinase-Response Regulator Hybrid Sensor Required for Development and Osmotic Tolerance

    PubMed Central

    Kimura, Yoshio; Nakano, Hiromi; Terasaka, Hideaki; Takegawa, Kaoru

    2001-01-01

    A gene, mokA, encoding a protein with similarities to histidine kinase-response regulator hybrid sensor, was cloned from a Myxococcus xanthus genomic library. The predicted mokA gene product was found to contain three domains: an amino-terminal input domain, a central transmitter domain, and a carboxy-terminal receiver domain. mokA mutants placed under starvation conditions exhibited reduced sporulation. Mutation of mokA also caused marked growth retardation at high osmolarity. These results indicated that M. xanthus MokA is likely a transmembrane sensor that is required for development and osmotic tolerance. The putative function of MokA is similar to that of the hybrid histidine kinase, DokA, of the eukaryotic slime mold Dictyostelium discoideum. PMID:11157925

  1. Myxococcus xanthus Pph2 Is a Manganese-dependent Protein Phosphatase Involved in Energy Metabolism*

    PubMed Central

    García-Hernández, Raquel; Moraleda-Muñoz, Aurelio; Castañeda-García, Alfredo; Pérez, Juana; Muñoz-Dorado, José

    2009-01-01

    The multicellular behavior of the myxobacterium Myxococcus xanthus requires the participation of an elevated number of signal-transduction mechanisms to coordinate the cell movements and the sequential changes in gene expression patterns that lead to the morphogenetic and differentiation events. These signal-transduction mechanisms are mainly based on two-component systems and on the reversible phosphorylation of protein targets mediated by eukaryotic-like protein kinases and phosphatases. Among all these factors, protein phosphatases are the elements that remain less characterized. Hence, we have studied in this work the physiological role and biochemical activity of the protein phosphatase of the family PPP (phosphoprotein phosphatases) designated as Pph2, which is forming part of the same operon as the two-component system phoPR1. We have demonstrated that this operon is induced upon starvation in response to the depletion of the cell energy levels. The increase in the expression of the operon contributes to an efficient use of the scarce energy resources available for developing cells to ensure the completion of the life cycle. In fact, a Δpph2 mutant is defective in aggregation, sporulation yield, morphology of the myxospores, and germination efficiency. The yeast two-hybrid technology has shown that Pph2 interacts with the gene products of MXAN_1875 and 5630, which encode a hypothetical protein and a glutamine synthetase, respectively. Because Pph2 exhibits Ser/Thr, and to some extent Tyr, Mn2+-dependent protein phosphatase activity, it is expected that this function is accomplished by dephosphorylation of the specific protein substrates. PMID:19706604

  2. Colony Expansion of Socially Motile Myxococcus xanthus Cells Is Driven by Growth, Motility, and Exopolysaccharide Production

    PubMed Central

    Patra, Pintu; Kissoon, Kimberley; Cornejo, Isabel; Kaplan, Heidi B.; Igoshin, Oleg A.

    2016-01-01

    Myxococcus xanthus, a model organism for studies of multicellular behavior in bacteria, moves exclusively on solid surfaces using two distinct but coordinated motility mechanisms. One of these, social (S) motility is powered by the extension and retraction of type IV pili and requires the presence of exopolysaccharides (EPS) produced by neighboring cells. As a result, S motility requires close cell-to-cell proximity and isolated cells do not translocate. Previous studies measuring S motility by observing the colony expansion of cells deposited on agar have shown that the expansion rate increases with initial cell density, but the biophysical mechanisms involved remain largely unknown. To understand the dynamics of S motility-driven colony expansion, we developed a reaction-diffusion model describing the effects of cell density, EPS deposition and nutrient exposure on the expansion rate. Our results show that at steady state the population expands as a traveling wave with a speed determined by the interplay of cell motility and growth, a well-known characteristic of Fisher’s equation. The model explains the density-dependence of the colony expansion by demonstrating the presence of a lag phase–a transient period of very slow expansion with a duration dependent on the initial cell density. We propose that at a low initial density, more time is required for the cells to accumulate enough EPS to activate S-motility resulting in a longer lag period. Furthermore, our model makes the novel prediction that following the lag phase the population expands at a constant rate independent of the cell density. These predictions were confirmed by S motility experiments capturing long-term expansion dynamics. PMID:27362260

  3. Comparative genomics of transport proteins in developmental bacteria: Myxococcus xanthus and Streptomyces coelicolor

    PubMed Central

    2013-01-01

    Background Two of the largest fully sequenced prokaryotic genomes are those of the actinobacterium, Streptomyces coelicolor (Sco), and the δ-proteobacterium, Myxococcus xanthus (Mxa), both differentiating, sporulating, antibiotic producing, soil microbes. Although the genomes of Sco and Mxa are the same size (~9 Mbp), Sco has 10% more genes that are on average 10% smaller than those in Mxa. Results Surprisingly, Sco has 93% more identifiable transport proteins than Mxa. This is because Sco has amplified several specific types of its transport protein genes, while Mxa has done so to a much lesser extent. Amplification is substrate- and family-specific. For example, Sco but not Mxa has amplified its voltage-gated ion channels but not its aquaporins and mechano-sensitive channels. Sco but not Mxa has also amplified drug efflux pumps of the DHA2 Family of the Major Facilitator Superfamily (MFS) (49 versus 6), amino acid transporters of the APC Family (17 versus 2), ABC-type sugar transport proteins (85 versus 6), and organic anion transporters of several families. Sco has not amplified most other types of transporters. Mxa has selectively amplified one family of macrolid exporters relative to Sco (16 versus 1), consistent with the observation that Mxa makes more macrolids than does Sco. Conclusions Except for electron transport carriers, there is a poor correlation between the types of transporters found in these two organisms, suggesting that their solutions to differentiative and metabolic needs evolved independently. A number of unexpected and surprising observations are presented, and predictions are made regarding the physiological functions of recognizable transporters as well as the existence of yet to be discovered transport systems in these two important model organisms and their relatives. The results provide insight into the evolutionary processes by which two dissimilar prokaryotes evolved complexity, particularly through selective chromosomal gene

  4. Synthesis and Assembly of a Novel Glycan Layer in Myxococcus xanthus Spores*

    PubMed Central

    Holkenbrink, Carina; Hoiczyk, Egbert; Kahnt, Jörg; Higgs, Penelope I.

    2014-01-01

    Myxococcus xanthus is a Gram-negative deltaproteobacterium that has evolved the ability to differentiate into metabolically quiescent spores that are resistant to heat and desiccation. An essential feature of the differentiation processes is the assembly of a rigid, cell wall-like spore coat on the surface of the outer membrane. In this study, we characterize the spore coat composition and describe the machinery necessary for secretion of spore coat material and its subsequent assembly into a stress-bearing matrix. Chemical analyses of isolated spore coat material indicate that the spore coat consists primarily of short 1–4- and 1–3-linked GalNAc polymers that lack significant glycosidic branching and may be connected by glycine peptides. We show that 1–4-linked glucose (Glc) is likely a minor component of the spore coat with the majority of the Glc arising from contamination with extracellular polysaccharides, O-antigen, or storage compounds. Neither of these structures is required for the formation of resistant spores. Our analyses indicate the GalNAc/Glc polymer and glycine are exported by the ExoA-I system, a Wzy-like polysaccharide synthesis and export machinery. Arrangement of the capsular-like polysaccharides into a rigid spore coat requires the NfsA–H proteins, members of which reside in either the cytoplasmic membrane (NfsD, -E, and -G) or outer membrane (NfsA, -B, and -C). The Nfs proteins function together to modulate the chain length of the surface polysaccharides, which is apparently necessary for their assembly into a stress-bearing matrix. PMID:25271164

  5. Colony Expansion of Socially Motile Myxococcus xanthus Cells Is Driven by Growth, Motility, and Exopolysaccharide Production.

    PubMed

    Patra, Pintu; Kissoon, Kimberley; Cornejo, Isabel; Kaplan, Heidi B; Igoshin, Oleg A

    2016-06-01

    Myxococcus xanthus, a model organism for studies of multicellular behavior in bacteria, moves exclusively on solid surfaces using two distinct but coordinated motility mechanisms. One of these, social (S) motility is powered by the extension and retraction of type IV pili and requires the presence of exopolysaccharides (EPS) produced by neighboring cells. As a result, S motility requires close cell-to-cell proximity and isolated cells do not translocate. Previous studies measuring S motility by observing the colony expansion of cells deposited on agar have shown that the expansion rate increases with initial cell density, but the biophysical mechanisms involved remain largely unknown. To understand the dynamics of S motility-driven colony expansion, we developed a reaction-diffusion model describing the effects of cell density, EPS deposition and nutrient exposure on the expansion rate. Our results show that at steady state the population expands as a traveling wave with a speed determined by the interplay of cell motility and growth, a well-known characteristic of Fisher's equation. The model explains the density-dependence of the colony expansion by demonstrating the presence of a lag phase-a transient period of very slow expansion with a duration dependent on the initial cell density. We propose that at a low initial density, more time is required for the cells to accumulate enough EPS to activate S-motility resulting in a longer lag period. Furthermore, our model makes the novel prediction that following the lag phase the population expands at a constant rate independent of the cell density. These predictions were confirmed by S motility experiments capturing long-term expansion dynamics.

  6. Identification and Characterization of Genes Required for Early Myxococcus xanthus Developmental Gene Expression

    PubMed Central

    Guo, Dongchuan; Wu, Yun; Kaplan, Heidi B.

    2000-01-01

    Starvation and cell density regulate the developmental expression of Myxococcus xanthus gene 4521. Three classes of mutants allow expression of this developmental gene during growth on nutrient agar, such that colonies of strains containing a Tn5 lac Ω4521 fusion are Lac+. One class of these mutants inactivates SasN, a negative regulator of 4521 expression; another class activates SasS, a sensor kinase-positive regulator of 4521 expression; and a third class blocks lipopolysaccharide (LPS) O-antigen biosynthesis. To identify additional positive regulators of 4521 expression, 11 Lac− TnV.AS transposon insertion mutants were isolated from a screen of 18,000 Lac+ LPS O-antigen mutants containing Tn5 lac Ω4521 (Tcr). Ten mutations identified genes that could encode positive regulators of 4521 developmental expression based on their ability to abolish 4521 expression during development in the absence of LPS O antigen and in an otherwise wild-type background. Eight of these mutations mapped to the sasB locus, which encodes the known 4521 regulators SasS and SasN. One mapped to sasS, whereas seven identified new genes. Three mutations mapped to a gene encoding an NtrC-like response regulator homologue, designated sasR, and four others mapped to a gene designated sasP. One mutation, designated ssp10, specifically suppressed the LPS O-antigen defect; the ssp10 mutation had no effect on 4521 expression in an otherwise wild-type background but reduced 4521 developmental expression in the absence of LPS O antigen to a level close to that of the parent strain. All of the mutations except those in sasP conferred defects during growth and development. These data indicate that a number of elements are required for 4521 developmental expression and that most of these are necessary for normal growth and fruiting body development. PMID:10913090

  7. Characterization of Four Type IV Pilin Homologues in Stigmatella aurantiaca DSM17044 by Heterologous Expression in Myxococcus xanthus

    PubMed Central

    Pan, Hongwei; Zhou, Xiuwen; Liu, Xin; Luo, Ningning; Hu, Wei; Li, Yuezhong

    2013-01-01

    As prokaryotic models for multicellular development, Stigmatellaaurantiaca and Myxococcus xanthus share many similarities in terms of social behaviors, such as gliding motility. Our current understanding of myxobacterial grouped-cell motilities comes mainly from the research on M. xanthus, which shows that filamentous type IV pili (TFP), composed of type IV pilin (also called PilA protein) subunits, are the key apparatus for social motility (S-motility). However, little is known about the pilin protein in S. aurantiaca. We cloned and sequenced four genes (pilASa1~4) from S. aurantiaca DSM17044 that are homologous to pilAMx (pilA gene in M. xanthus DK1622). The homology and similarities among PilASa proteins and other myxobacterial homologues were systematically analyzed. To determine their potential biological functions, the four pilASa genes were expressed in M. xanthus DK10410 (ΔpilAMx), which did not restore S-motility on soft agar or EPS production to host cells. After further analysis of the motile behaviors in a methylcellulose solution, the M. xanthus strains were categorized into three types. YL6101, carrying pilASa1, and YL6104, carrying pilASa4, produced stable but unretractable surface pili; YL6102, carrying pilASa2, produced stable surface pili and exhibited reduced TFP-dependent motility in methylcellulose; YL6103, carrying pilASa3, produced unstable surface pili. Based on these findings, we propose that pilASa2 might be responsible for the type IV pilin production involved in group motility in S. aurantiaca DSM17044. After examining the developmental processes, it was suggested that the expression of PilASa4 protein might have positive effects on the fruiting body formation of M. xanthus DK10410 cells. Moreover, the formation of fruiting body in M. xanthus cells with stable exogenous TFPSa were compensated by mixing them with S. aurantiaca DSM17044 cells. Our results shed some light on the features and functions of type IV pilin homologues in S

  8. Myxococcus xanthus Gliding Motors Are Elastically Coupled to the Substrate as Predicted by the Focal Adhesion Model of Gliding Motility

    PubMed Central

    Balagam, Rajesh; Litwin, Douglas B.; Czerwinski, Fabian; Sun, Mingzhai; Kaplan, Heidi B.; Shaevitz, Joshua W.; Igoshin, Oleg A.

    2014-01-01

    Myxococcus xanthus is a model organism for studying bacterial social behaviors due to its ability to form complex multi-cellular structures. Knowledge of M. xanthus surface gliding motility and the mechanisms that coordinated it are critically important to our understanding of collective cell behaviors. Although the mechanism of gliding motility is still under investigation, recent experiments suggest that there are two possible mechanisms underlying force production for cell motility: the focal adhesion mechanism and the helical rotor mechanism, which differ in the biophysics of the cell–substrate interactions. Whereas the focal adhesion model predicts an elastic coupling, the helical rotor model predicts a viscous coupling. Using a combination of computational modeling, imaging, and force microscopy, we find evidence for elastic coupling in support of the focal adhesion model. Using a biophysical model of the M. xanthus cell, we investigated how the mechanical interactions between cells are affected by interactions with the substrate. Comparison of modeling results with experimental data for cell-cell collision events pointed to a strong, elastic attachment between the cell and substrate. These results are robust to variations in the mechanical and geometrical parameters of the model. We then directly measured the motor-substrate coupling by monitoring the motion of optically trapped beads and find that motor velocity decreases exponentially with opposing load. At high loads, motor velocity approaches zero velocity asymptotically and motors remain bound to beads indicating a strong, elastic attachment. PMID:24810164

  9. Expression and physiological role of three Myxococcus xanthus copper-dependent P1B-type ATPases during bacterial growth and development.

    PubMed

    Moraleda-Muñoz, Aurelio; Pérez, Juana; Extremera, Antonio Luis; Muñoz-Dorado, José

    2010-09-01

    Myxococcus xanthus is a soil-dwelling bacterium that exhibits a complex life cycle comprising social behavior, morphogenesis, and differentiation. In order to successfully complete this life cycle, cells have to cope with changes in their environment, among which the presence of copper is remarkable. Copper is an essential transition metal for life, but an excess of copper provokes cellular damage by oxidative stress. This dual effect forces the cells to maintain a tight homeostasis. M. xanthus encodes a large number of genes with similarities to others reported previously to be involved in copper homeostasis, most of which are redundant. We have identified three genes that encode copper-translocating P(1B)-ATPases (designated copA, copB, and copC) that exhibit the sequence motifs and modular organizations of those that extrude Cu(+). The expression of the ATPase copC has not been detected, but copA and copB are differentially regulated by the addition of external copper. However, while copB expression peaks at 2 h, copA is expressed at higher levels, and the maximum is reached much later. The fact that these expression profiles are nearly identical to those exhibited by the multicopper oxidases cuoA and cuoB suggests that the pairs CuoB-CopB and CuoA-CopA sequentially function to detoxify the cell. The deletion of any ATPase alters the expression profiles of other genes involved in copper homeostasis, such as the remaining ATPases or the Cus systems, yielding cells that are more resistant to the metal.

  10. The Bactofilin Cytoskeleton Protein BacM of Myxococcus xanthus Forms an Extended β-Sheet Structure Likely Mediated by Hydrophobic Interactions

    PubMed Central

    Xie, Kefang; Engelhardt, Harald; Bosch, Jürgen; Hoiczyk, Egbert

    2015-01-01

    Bactofilins are novel cytoskeleton proteins that are widespread in Gram-negative bacteria. Myxococcus xanthus, an important predatory soil bacterium, possesses four bactofilins of which one, BacM (Mxan_7475) plays an important role in cell shape maintenance. Electron and fluorescence light microscopy, as well as studies using over-expressed, purified BacM, indicate that this protein polymerizes in vivo and in vitro into ~3 nm wide filaments that further associate into higher ordered fibers of about 10 nm. Here we use a multipronged approach combining secondary structure determination, molecular modeling, biochemistry, and genetics to identify and characterize critical molecular elements that enable BacM to polymerize. Our results indicate that the bactofilin-determining domain DUF583 folds into an extended β-sheet structure, and we hypothesize a left-handed β-helix with polymerization into 3 nm filaments primarily via patches of hydrophobic amino acid residues. These patches form the interface allowing head-to-tail polymerization during filament formation. Biochemical analyses of these processes show that folding and polymerization occur across a wide variety of conditions and even in the presence of chaotropic agents such as one molar urea. Together, these data suggest that bactofilins are comprised of a structure unique to cytoskeleton proteins, which enables robust polymerization. PMID:25803609

  11. Light-induced carotenogenesis in Myxococcus xanthus: evidence that CarS acts as an anti-repressor of CarA.

    PubMed

    Whitworth, D E; Hodgson, D A

    2001-11-01

    In the bacterium Myxococcus xanthus, carotenoids are produced in response to illumination, as a result of expression of the crt carotenoid biosynthesis genes. The majority of crt genes are clustered in the crtEBDC operon, which is repressed in the dark by CarA. Genetic data suggest that, in the light, CarS is synthesized and achieves activation of the crtEBDC operon by removing the repressive action of CarA. As CarS contains no known DNA-binding motif, the relief of CarA-mediated repression was postulated to result from a direct interaction between these two proteins. Use of the yeast two-hybrid system demonstrated direct interaction between CarA and CarS. The two-hybrid system also implied that CarA and, possibly, CarS are capable of homodimerization. Direct evidence for CarS anti-repressor action was provided in vitro. A glutathione S-transferase (GST)-CarA protein fusion was shown to bind specifically to a palindromic operator sequence within the crtEBDC promoter. CarA was prevented from binding to its operator, and prebound CarA was removed by the addition of purified CarS. CarS is therefore an anti-repressor.

  12. Interplay between type IV pili activity and exopolysaccharides secretion controls motility patterns in single cells of Myxococcus xanthus

    PubMed Central

    Hu, Wei; Gibiansky, Maxsim L.; Wang, Jing; Wang, Chuandong; Lux, Renate; Li, Yuezhong; Wong, Gerard C. L.; Shi, Wenyuan

    2016-01-01

    Myxococcus xanthus performs coordinated social motility of cell groups through the extension and retraction of type IV pili (TFP) on solid surfaces, which requires both TFP and exopolysaccharides (EPS). By submerging cells in a liquid medium containing 1% methylcellulose, M. xanthus TFP-driven motility was induced in isolated cells and independently of EPS. We measured and analyzed the movements of cells using community tracking algorithms, which combine single-cell resolution with statistics from large sample populations. Cells without significant multi-cellular social interactions have surprisingly complex behaviors: EPS− cells exhibited a pronounced increase in the tendency to stand vertically and moved with qualitatively different characteristics than other cells. A decrease in the EPS secretion of cells correlates with a higher instantaneous velocity, but with lower directional persistence in trajectories. Moreover, EPS− cells do not adhere to the surface as strongly as wild-type and EPS overproducing cells, and display a greater tendency to have large deviations between the direction of movement and the cell axis, with cell velocity showing only minimal dependence on the direction of movement. The emerging picture is that EPS does not simply provide rheological resistance to a single mechanism but rather that the availability of EPS impacts motility pattern. PMID:26821939

  13. Two-Component Signal Transduction Systems That Regulate the Temporal and Spatial Expression of Myxococcus xanthus Sporulation Genes

    PubMed Central

    Sarwar, Zaara

    2015-01-01

    When starved for nutrients, Myxococcus xanthus produces a biofilm that contains a mat of rod-shaped cells, known as peripheral rods, and aerial structures called fruiting bodies, which house thousands of dormant and stress-resistant spherical spores. Because rod-shaped cells differentiate into spherical, stress-resistant spores and spore differentiation occurs only in nascent fruiting bodies, many genes and multiple levels of regulation are required. Over the past 2 decades, many regulators of the temporal and spatial expression of M. xanthus sporulation genes have been uncovered. Of these sporulation gene regulators, two-component signal transduction circuits, which typically contain a histidine kinase sensor protein and a transcriptional regulator known as response regulator, are among the best characterized. In this review, we discuss prototypical two-component systems (Nla6S/Nla6 and Nla28S/Nla28) that regulate an early, preaggregation phase of sporulation gene expression during fruiting body development. We also discuss orphan response regulators (ActB and FruA) that regulate a later phase of sporulation gene expression, which begins during the aggregation stage of fruiting body development. In addition, we summarize the research on a complex two-component system (Esp) that is important for the spatial regulation of sporulation. PMID:26369581

  14. Numerical simulations on active rod like particles as a model for the collective behavior of Myxococcus xanthus

    NASA Astrophysics Data System (ADS)

    Wigbers, Manon; Thutupalli, Shashi; Shaevitz, Joshua

    2015-03-01

    We study collective behavior of Myxococcus xanthus using numerical simulations. Under starvation conditions, these social bacteria organize into multi-cellular structures, called ``fruiting bodies,'' within which cells sporulate. During the process of fruiting body formation, cells show various collective motion patterns. One of the most striking of these patterns is the so called rippling motility, characterized by standing density waves of reversing bacteria. Similar rippling behaviour is also observed during predatory feeding of the bacteria. Until now, the principles underlying this rippling behavior are not fully elucidated. Analogous to the well studied liquid crystalline phases in condensed matter physics, the ordering of the baceria within these rippling waves resembles a smectic like layered structure. In contrast to active nematic liquid crystalline phases widely studied in recent times, this represents the first known empirical example of an active smectic phase. Inspired by single-cell resolution experimental data of the bacteria, we develop a modelof active rod like particles and use numerical simulations to study the organizing principles that drive the transitions between the various active liquid crystalline phases in the myxobacterial collective behavior.

  15. The Myxococcus xanthus two-component system CorSR regulates expression of a gene cluster involved in maintaining copper tolerance during growth and development.

    PubMed

    Sánchez-Sutil, María Celestina; Pérez, Juana; Gómez-Santos, Nuria; Shimkets, Lawrence J; Moraleda-Muñoz, Aurelio; Muñoz-Dorado, José

    2013-01-01

    Myxococcus xanthus is a soil-dwelling member of the δ-Proteobacteria that exhibits a complex developmental cycle upon starvation. Development comprises aggregation and differentiation into environmentally resistant myxospores in an environment that includes fluctuations in metal ion concentrations. While copper is essential for M. xanthus cells because several housekeeping enzymes use it as a cofactor, high copper concentrations are toxic. These opposing effects force cells to maintain a tight copper homeostasis. A plethora of paralogous genes involved in copper detoxification, all of which are differentially regulated, have been reported in M. xanthus. The use of in-frame deletion mutants and fusions with the reporter gene lacZ has allowed the identification of a two-component system, CorSR, that modulates the expression of an operon termed curA consisting of nine genes whose expression slowly increases after metal addition, reaching a plateau. Transcriptional regulation of this operon is complex because transcription can be initiated at different promoters and by different types of regulators. These genes confer copper tolerance during growth and development. Copper induces carotenoid production in a ΔcorSR mutant at lower concentrations than with the wild-type strain due to lack of expression of a gene product resembling subunit III of cbb3-type cytochrome c oxidase. This data may explain why copper induces carotenoid biosynthesis at suboptimal rather than optimal growth conditions in wild-type strains.

  16. Identification of the Ω4406 Regulatory Region, a Developmental Promoter of Myxococcus xanthus, and a DNA Segment Responsible for Chromosomal Position-Dependent Inhibition of Gene Expression

    PubMed Central

    Loconto, Jennifer; Viswanathan, Poorna; Nowak, Scott J.; Gloudemans, Monica; Kroos, Lee

    2005-01-01

    When starved, Myxococcus xanthus cells send signals to each other that coordinate their movements, gene expression, and differentiation. C-signaling requires cell-cell contact, and increasing contact brought about by cell alignment in aggregates is thought to increase C-signaling, which induces expression of many genes, causing rod-shaped cells to differentiate into spherical spores. C-signaling involves the product of the csgA gene. A csgA mutant fails to express many genes that are normally induced after about 6 h into the developmental process. One such gene was identified by insertion of Tn5 lac at site Ω4406 in the M. xanthus chromosome. Tn5 lac fused transcription of lacZ to the upstream Ω4406 promoter. In this study, the Ω4406 promoter region was identified by analyzing mRNA and by testing different upstream DNA segments for the ability to drive developmental lacZ expression in M. xanthus. The 5′ end of Ω4406 mRNA mapped to approximately 1.3 kb upstream of the Tn5 lac insertion. A 1.0-kb DNA segment from 0.8 to 1.8 kb upstream of the Tn5 lac insertion, when fused to lacZ and integrated at a phage attachment site in the M. xanthus chromosome, showed a similar pattern of developmental expression as Tn5 lac Ω4406. The DNA sequence upstream of the putative transcriptional start site was strikingly similar to promoter regions of other C-signal-dependent genes. Developmental lacZ expression from the 1.0-kb segment was abolished in a csgA mutant but was restored upon codevelopment of the csgA mutant with wild-type cells, which supply C-signal, demonstrating that the Ω4406 promoter responds to extracellular C-signaling. Interestingly, the 0.8-kb DNA segment immediately upstream of Tn5 lac Ω4406 inhibited expression of a downstream lacZ reporter in transcriptional fusions integrated at a phage attachment site in the chromosome but not at the normal Ω4406 location. To our knowledge, this is the first example in M. xanthus of a chromosomal position

  17. Light-induced carotenogenesis in Myxococcus xanthus: functional characterization of the ECF sigma factor CarQ and antisigma factor CarR.

    PubMed

    Browning, Douglas F; Whitworth, David E; Hodgson, David A

    2003-04-01

    Illumination of dark-grown Myxococcus xanthus with blue light leads to the induction of carotenoid synthesis. Central to this response is the activation of the light-inducible promoter, PcarQRS, and the transcription of three downstream genes, carQ, carR and carS. Sequence analysis predicted that CarQ is a member of the ECF (extracytoplasmic function) subfamily of RNA polymerase sigma factors, and that CarR is an inner membrane protein. Genetic analysis strongly implied that CarR is an antisigma factor that sequesters CarQ in a transcriptionally inactive complex. Using in vitro transcription run-off assays, we present biochemical evidence that CarQ functions as a bacterial sigma factor and is responsible for transcription initiation at PcarQRS. Similar experiments using the crtI promoter failed to implicate CarQ in direct transcription of the crtI gene. Experiments using the yeast two-hybrid system demonstrated a protein-protein interaction between CarQ and CarR, providing evidence of a CarQ-CarR complex. The yeast two-hybrid system data also indicated that CarR is capable of oligomerization. Fractionation of M. xanthus membranes with the detergent sarkosyl showed that CarR was associated with the inner membrane. Furthermore, CarR was found to be unstable in illuminated stationary phase cells, providing a possible mechanism by which the CarR-CarQ complex is disrupted.

  18. Alanine 32 in PilA is important for PilA stability and type IV pili function in Myxococcus xanthus

    PubMed Central

    Yang, Zhe; Hu, Wei; Chen, Kevin; Wang, Jing; Lux, Renate; Zhou, Z. Hong

    2011-01-01

    Type IV pili (TFP) are membrane-anchored filaments with a number of important biological functions. In the model organism Myxococcus xanthus, TFP act as molecular engines that power social (S) motility through cycles of extension and retraction. TFP filaments consist of several thousand copies of a protein called PilA or pilin. PilA contains an N-terminal α-helix essential for TFP assembly and a C-terminal globular domain important for its activity. The role of the PilA sequence and its structure–function relationship in TFP-dependent S motility remain active areas of research. In this study, we identified an M. xanthus PilA mutant carrying an alanine to valine substitution at position 32 in the α-helix, which produced structurally intact but retraction-defective TFP. Characterization of this mutant and additional single-residue variants at this position in PilA demonstrated the critical role of alanine 32 in PilA stability, TFP assembly and retraction. PMID:21493683

  19. The CarD/CarG regulatory complex is required for the action of several members of the large set of Myxococcus xanthus extracytoplasmic function σ factors.

    PubMed

    Abellón-Ruiz, Javier; Bernal-Bernal, Diego; Abellán, María; Fontes, Marta; Padmanabhan, S; Murillo, Francisco J; Elías-Arnanz, Montserrat

    2014-08-01

    Extracytoplasmic function (ECF) σ factors are critical players in signal transduction networks involved in bacterial response to environmental changes. The Myxococcus xanthus genome reveals ∼45 putative ECF-σ factors, but for the overwhelming majority, the specific signals or mechanisms for selective activation and regulation remain unknown. One well-studied ECF-σ, CarQ, binds to its anti-σ, CarR, and is inactive in the dark but drives its own expression from promoter P(QRS) on illumination. This requires the CarD/CarG complex, the integration host factor (IHF) and a specific CarD-binding site upstream of P(QRS). Here, we show that DdvS, a previously uncharacterized ECF-σ, activates its own expression in a CarD/CarG-dependent manner but is inhibited when specifically bound to the N-terminal zinc-binding anti-σ domain of its cognate anti-σ, DdvA. Interestingly, we find that the autoregulatory action of 11 other ECF-σ factors studied here depends totally or partially on CarD/CarG but not IHF. In silico analysis revealed possible CarD-binding sites that may be involved in direct regulation by CarD/CarG of target promoter activity. CarD/CarG-linked ECF-σ regulation likely recurs in other myxobacteria with CarD/CarG orthologous pairs and could underlie, at least in part, the global regulatory effect of the complex on M. xanthus gene expression.

  20. Identification of a gene involved in polysaccharide export as a transcription target of FruA, an essential factor for Myxococcus xanthus development.

    PubMed

    Ueki, Toshiyuki; Inouye, Sumiko

    2005-09-16

    Fruiting body development in Myxococcus xanthus is a multicellular event that is coordinated by exchanging intercellular signals. FruA is a transcription factor essential for fruiting body development and is thought to play a key role in the C-signal pathway. Here we present the first identification of a gene regulated by FruA. The gene was isolated from a genomic library via in vitro selection in a DNA binding assay by using the DNA-binding domain of FruA tagged with His(8) at the C-terminal end (FruA-DBD-H(8)). The gene, named fdgA (FruA-dependent gene A), encodes a protein homologous to the outer-membrane auxiliary family protein involved in the polysaccharide export system. FruA-DBD-H(8) bound the upstream promoter region of the fdgA gene from nucleotide -89 to nucleotide -64 with respect to the transcription initiation site, which was required for the induction of fdgA expression during development. fdgA mRNA induced during development was absent in a fruA deletion strain. The deletion of fdgA resulted in defective fruiting body formation and reduced sporulation efficiency (1% that of the parent strain). Moreover, FruA was required for the developmental expression of sasA, which is also involved in the biosynthesis of the lipopolysaccharide O-antigen and is required for fruiting body development. Furthermore, the expression of both fdgA and sasA was partially dependent on the C-signal. These findings expand our understanding of the signal transduction pathway mediated by FruA during development in M. xanthus. PMID:16040607

  1. Enzymatic characteristics of an ApaH-like phosphatase, PrpA, and a diadenosine tetraphosphate hydrolase, ApaH, from Myxococcus xanthus.

    PubMed

    Sasaki, Masashi; Takegawa, Kaoru; Kimura, Yoshio

    2014-09-17

    We characterized the activities of the Myxococcus xanthus ApaH-like phosphatases PrpA and ApaH, which share homologies with both phosphoprotein phosphatases and diadenosine tetraphosphate (Ap4A) hydrolases. PrpA exhibited a phosphatase activity towards p-nitrophenyl phosphate (pNPP), tyrosine phosphopeptide and tyrosine-phosphorylated protein, and a weak hydrolase activity towards ApnA and ATP. In the presence of Mn(2+), PrpA hydrolyzed Ap4A into AMP and ATP, whereas in the presence of Co(2+) PrpA hydrolyzed Ap4A into two molecules of ADP. ApaH exhibited high phosphatase activity towards pNPP, and hydrolase activity towards ApnA and ATP. Mn(2+) was required for ApaH-mediated pNPP dephosphorylation and ATP hydrolysis, whereas Co(2+) was required for ApnA hydrolysis. Thus, PrpA and ApaH may function mainly as a tyrosine protein phosphatase and an ApnA hydrolase, respectively. PMID:25107648

  2. The groEL2 gene, but not groEL1, is required for biosynthesis of the secondary metabolite myxovirescin in Myxococcus xanthus DK1622.

    PubMed

    Wang, Yan; Li, Xi; Zhang, Wenyan; Zhou, Xiuwen; Li, Yue-zhong

    2014-03-01

    Myxococcus xanthus DK1622 possesses two copies of the groEL gene: groEL1, which participates in development, and groEL2, which is involved in the predatory ability of cells. In this study, we determined that the groEL2 gene is required for the biosynthesis of the secondary metabolite myxovirescin (TA), which plays essential roles in predation. The groEL2-knockout mutant strain was defective in producing a zone of inhibition and displayed decreased killing ability against Escherichia coli, while the groEL1-knockout mutant strain exhibited little difference from the wild-type strain DK1622. HPLC revealed that deletion of the groEL2 gene blocked the production of TA, which was present in the groEL1-knockout mutant. The addition of exogenous TA rescued the inhibition and killing abilities of the groEL2-knockout mutant against E. coli. Analysis of GroEL domain-swapping mutants indicated that the C-terminal equatorial domain of GroEL2 was essential for TA production, while the N-terminal equatorial or apical domains of GroEL2 were not sufficient to rescue TA production of the groEL2 knockout.

  3. Cloning and sequencing of two genes, prtA and prtB, from Myxococcus xanthus, encoding PrtA and PrtB proteases, both of which are required for the protease activity.

    PubMed

    Quillet, L; Bensmail, L; Barray, S; Guespin-Michel, J

    1997-10-01

    The sequence of a 1955-bp TaqI DNA fragment from Myxococcus xanthus was determined. This fragment contains two complete genes, designated prtA and prtB. The prtA and prtB ORFs extend over 828 and 798 bp, respectively. They are separated only by 3 nt and appear to be present in a polycistronic transcriptional unit. A typical lipoprotein signal sequence is present at the N terminus of the two deduced polypeptides. The aa sequence of PrtA shows a high degree of identity to the region adjacent to the Ser residue belonging to the catalytic triad of serine proteases from Staphylococcus aureus and Enterococcus faecalis. It also exhibits features characteristic of trypsin-like serine proteases in that it contains the same pattern of variable and conserved regions. The deduced aa sequence of PrtB reveals a signature zinc-binding consensus motif (HEXXHXXGXXH/Met-turn) characteristic of the class of metalloproteases called metzincins. Plasmids containing prtA, prtB, or both were constructed. Protease activity studies of Escherichia coli clones containing these plasmids showed that both genes are necessary for this activity, whatever their cis or trans position. As prtB produces a putative membrane-bound lipoprotein of 266 aa, the protease activation must occur at the membrane level.

  4. The Type IV Pilus Assembly ATPase PilB of Myxococcus xanthus Interacts with the Inner Membrane Platform Protein PilC and the Nucleotide-binding Protein PilM.

    PubMed

    Bischof, Lisa Franziska; Friedrich, Carmen; Harms, Andrea; Søgaard-Andersen, Lotte; van der Does, Chris

    2016-03-25

    Type IV pili (T4P) are ubiquitous bacterial cell surface structures, involved in processes such as twitching motility, biofilm formation, bacteriophage infection, surface attachment, virulence, and natural transformation. T4P are assembled by machinery that can be divided into the outer membrane pore complex, the alignment complex that connects components in the inner and outer membrane, and the motor complex in the inner membrane and cytoplasm. Here, we characterize the inner membrane platform protein PilC, the cytosolic assembly ATPase PilB of the motor complex, and the cytosolic nucleotide-binding protein PilM of the alignment complex of the T4P machinery ofMyxococcus xanthus PilC was purified as a dimer and reconstituted into liposomes. PilB was isolated as a monomer and bound ATP in a non-cooperative manner, but PilB fused to Hcp1 ofPseudomonas aeruginosaformed a hexamer and bound ATP in a cooperative manner. Hexameric but not monomeric PilB bound to PilC reconstituted in liposomes, and this binding stimulated PilB ATPase activity. PilM could only be purified when it was stabilized by a fusion with a peptide corresponding to the first 16 amino acids of PilN, supporting an interaction between PilM and PilN(1-16). PilM-N(1-16) was isolated as a monomer that bound but did not hydrolyze ATP. PilM interacted directly with PilB, but only with PilC in the presence of PilB, suggesting an indirect interaction. We propose that PilB interacts with PilC and with PilM, thus establishing the connection between the alignment and the motor complex. PMID:26851283

  5. Structure-function dissection of Myxococcus xanthus CarD N-terminal domain, a defining member of the CarD_CdnL_TRCF family of RNA polymerase interacting proteins.

    PubMed

    Bernal-Bernal, Diego; Gallego-García, Aránzazu; García-Martínez, Gema; García-Heras, Francisco; Jiménez, María Angeles; Padmanabhan, S; Elías-Arnanz, Montserrat

    2015-01-01

    Two prototypes of the large CarD_CdnL_TRCF family of bacterial RNA polymerase (RNAP)-binding proteins, Myxococcus xanthus CarD and CdnL, have distinct functions whose molecular basis remain elusive. CarD, a global regulator linked to the action of several extracytoplasmic function (ECF) σ-factors, binds to the RNAP β subunit (RNAP-β) and to protein CarG via an N-terminal domain, CarDNt, and to DNA via an intrinsically unfolded C-terminal domain resembling eukaryotic high-mobility-group A (HMGA) proteins. CdnL, a CarDNt-like protein that is essential for cell viability, is implicated in σA-dependent rRNA promoter activation and interacts with RNAP-β but not with CarG. While the HMGA-like domain of CarD by itself is inactive, we find that CarDNt has low but observable ability to activate ECF σ-dependent promoters in vivo, indicating that the C-terminal DNA-binding domain is required to maximize activity. Our structure-function dissection of CarDNt reveals an N-terminal, five-stranded β -sheet Tudor-like domain, CarD1-72, whose structure and contacts with RNAP-β mimic those of CdnL. Intriguingly, and in marked contrast to CdnL, CarD mutations that disrupt its interaction with RNAP-β did not annul activity. Our data suggest that the CarDNt C-terminal segment, CarD61-179, may be structurally distinct from its CdnL counterpart, and that it houses at least two distinct and crucial function determinants: (a) CarG-binding, which is specific to CarD; and (b) a basic residue stretch, which is also conserved and functionally required in CdnL. This study highlights the evolution of shared and divergent interactions in similar protein modules that enable the distinct activities of two related members of a functionally important and widespread bacterial protein family.

  6. Structure-Function Dissection of Myxococcus xanthus CarD N-Terminal Domain, a Defining Member of the CarD_CdnL_TRCF Family of RNA Polymerase Interacting Proteins

    PubMed Central

    Bernal-Bernal, Diego; Gallego-García, Aránzazu; García-Martínez, Gema; García-Heras, Francisco; Jiménez, María Angeles; Padmanabhan, S.; Elías-Arnanz, Montserrat

    2015-01-01

    Two prototypes of the large CarD_CdnL_TRCF family of bacterial RNA polymerase (RNAP)-binding proteins, Myxococcus xanthus CarD and CdnL, have distinct functions whose molecular basis remain elusive. CarD, a global regulator linked to the action of several extracytoplasmic function (ECF) σ-factors, binds to the RNAP β subunit (RNAP-β) and to protein CarG via an N-terminal domain, CarDNt, and to DNA via an intrinsically unfolded C-terminal domain resembling eukaryotic high-mobility-group A (HMGA) proteins. CdnL, a CarDNt-like protein that is essential for cell viability, is implicated in σA-dependent rRNA promoter activation and interacts with RNAP-β but not with CarG. While the HMGA-like domain of CarD by itself is inactive, we find that CarDNt has low but observable ability to activate ECF σ-dependent promoters in vivo, indicating that the C-terminal DNA-binding domain is required to maximize activity. Our structure-function dissection of CarDNt reveals an N-terminal, five-stranded β -sheet Tudor-like domain, CarD1–72, whose structure and contacts with RNAP-β mimic those of CdnL. Intriguingly, and in marked contrast to CdnL, CarD mutations that disrupt its interaction with RNAP-β did not annul activity. Our data suggest that the CarDNt C-terminal segment, CarD61–179, may be structurally distinct from its CdnL counterpart, and that it houses at least two distinct and crucial function determinants: (a) CarG-binding, which is specific to CarD; and (b) a basic residue stretch, which is also conserved and functionally required in CdnL. This study highlights the evolution of shared and divergent interactions in similar protein modules that enable the distinct activities of two related members of a functionally important and widespread bacterial protein family. PMID:25811865

  7. C-factor has distinct aggregation and sporulation thresholds during Myxococcus development.

    PubMed Central

    Kim, S K; Kaiser, D

    1991-01-01

    C-factor, the protein product of the csgA gene, acts as a short-range morphogenetic signal. It is required for fruiting body development of the gram-negative bacterium Myxococcus xanthus. Aggregation, sporulation, and expression of a set of genes that are C-factor dependent, all of which fail in csgA mutant cells, are completely restored by addition of purified C-factor. We report here that, depending on its concentration, C-factor can elicit two distinct morphogenetic and transcriptional responses from csgA cells. Low levels of C-factor bring about aggregation and expression of an early C-dependent gene, whereas higher levels lead to the same effects plus expression of a late C-dependent gene and spore formation. C-factor positively regulates its own transcription. An approximately fourfold net increase in csgA transcription and C-factor levels during development was measured. We propose that autoregulation and the two distinct activity thresholds allow C-factor to act as a timer, first triggering aggregation, then sporulation, thereby producing the appropriate developmental order. Images PMID:1847908

  8. A New Mechanism for Collective Migration in Myxococcus xanthus

    NASA Astrophysics Data System (ADS)

    Starruß, J.; Bley, Th.; Søgaard-Andersen, L.; Deutsch, A.

    2007-07-01

    Myxobacteria exhibit a complex life cycle characterized by a sequence of cell patterns that culminate in the formation of three-dimensional fruiting bodies. This paper provides indications that the specific cell shape of myxobacteria might play an important role in the different morphogenetic processes during the life cycle. We introduce a new mechanism for collective migration that can explain the formation of aligned cell clusters in myxobacteria. This mechanism does not depend on cell cooperation, and in particular it does not depend on diffusive signals guiding cell motion. A Cellular Potts Model (CPM) that captures the rod cell shape, cell stiffness and active motion of myxobacteria is presented. By means of numerical simulations of model cell populations where cells interact via volume exclusion, we provide evidence of a purely mechanical mechanism for collective migration, which is controlled by the cells' length-to-width aspect ratio.

  9. Autolytic effect of the antibiotic produced by Myxococcus coralloides D.

    PubMed

    Montoya, M D; Gálvez, A; Arias, J M; Montoya, E

    1994-12-01

    Myxococcus coralloides D secretes an antibiotic, named corallolysin, when grown on a rich medium. When a critical concentration is reached, this antibiotic lyses the producer bacterium either during vegetative growth or during morphogenesis. Corallolysin has not effect on resting cells nor on myxospores. The autolytic effect is caused by the early inhibition of RNA synthesis.

  10. Decomposing predation: testing for parameters that correlate with predatory performance by a social bacterium.

    PubMed

    Mendes-Soares, Helena; Velicer, Gregory J

    2013-02-01

    Predator-prey interactions presumably play major roles in shaping the composition and dynamics of microbial communities. However, little is understood about the population biology of such interactions or how predation-related parameters vary or correlate across prey environments. Myxococcus xanthus is a motile soil bacterium that feeds on a broad range of other soil microbes that vary greatly in the degree to which they support M. xanthus growth. In order to decompose predator-prey interactions at the population level, we quantified five predation-related parameters during M. xanthus growth on nine phylogenetically diverse bacterial prey species. The horizontal expansion rate of swarming predator colonies fueled by prey lawns served as our measure of overall predatory performance, as it incorporates both the searching (motility) and handling (killing and consumption of prey) components of predation. Four other parameters-predator population growth rate, maximum predator yield, maximum prey kill, and overall rate of prey death-were measured from homogeneously mixed predator-prey lawns from which predator populations were not allowed to expand horizontally by swarming motility. All prey species fueled predator population growth. For some prey, predator-specific prey death was detected contemporaneously with predator population growth, whereas killing of other prey species was detected only after cessation of predator growth. All four of the alternative parameters were found to correlate significantly with predator swarm expansion rate to varying degrees, suggesting causal interrelationships among these diverse predation measures. More broadly, our results highlight the importance of examining multiple parameters for thoroughly understanding the population biology of microbial predation.

  11. Generation of food-grade recombinant Lactobacillus casei delivering Myxococcus xanthus prolyl endopeptidase

    PubMed Central

    Alvarez-Sieiro, Patricia; Martin, Maria Cruz; Redruello, Begoña; del Rio, Beatriz; Ladero, Victor; Palanski, Brad A.; Khosla, Chaitan; Fernandez, Maria; Alvarez, Miguel A.

    2015-01-01

    Prolyl endopeptidases (PEP), a family of serine proteases with the ability to hydrolyze the peptide bond on the carboxyl side of an internal proline residue, are able to degrade immunotoxic peptides responsible for celiac disease (CD), such as a 33-residue gluten peptide (33-mer). Oral administration of PEP has been suggested as a potential therapeutic approach for CD, although delivery of the enzyme to the small intestine requires intrinsic gastric stability or advanced formulation technologies. We have engineered two food-grade Lactobacillus casei strains to deliver PEP in an in vitro model of small intestine environment. One strain secretes PEP into the extracellular medium, whereas the other retains PEP in the intracellular environment. The strain that secretes PEP into the extracellular medium is the most effective to degrade the 33-mer and is resistant to simulated gastrointestinal stress. Our results suggest that in a future, after more studies and clinical trials, an engineered food-grade Lactobacillus strain may be useful as a vector for in situ production of PEP in the upper small intestine of CD patients. PMID:24752841

  12. Myxococcus CsgA, Drosophila Sniffer, and human HSD10 are cardiolipin phospholipases

    PubMed Central

    Boynton, Tye O'Hara; Shimkets, Lawrence Joseph

    2015-01-01

    Myxococcus xanthus development requires CsgA, a member of the short-chain alcohol dehydrogenase (SCAD) family of proteins. We show that CsgA and SocA, a protein that can replace CsgA function in vivo, oxidize the 2′-OH glycerol moiety on cardiolipin and phosphatidylglycerol to produce diacylglycerol (DAG), dihydroxyacetone, and orthophosphate. A lipid extract enriched in DAGs from wild-type cells initiates development and lipid body production in a csgA mutant to bypass the mutational block. This novel phospholipase C-like reaction is widespread. SCADs that prevent neurodegenerative disorders, such as Drosophila Sniffer and human HSD10, oxidize cardiolipin with similar kinetic parameters. HSD10 exhibits a strong preference for cardiolipin with oxidized fatty acids. This activity is inhibited in the presence of the amyloid β peptide. Three HSD10 variants associated with neurodegenerative disorders are inactive with cardiolipin. We suggest that HSD10 protects humans from reactive oxygen species by removing damaged cardiolipin before it induces apoptosis. PMID:26338420

  13. Role of cell bending and slime navigation in swarms of M. xanthus

    NASA Astrophysics Data System (ADS)

    Harvey, Cameron; Kaiser, Dale; Alber, Mark

    2012-02-01

    Many bacteria use motility described as swarming to colonize surfaces that allows them to optimize their access to nutrients. The swarming of the bacterium M. xanthus on surfaces is a remarkable interplay between motility mechanisms, cell flexibility, cell-cell adhesive interactions and directional reversals. The properties of individual cells from different mutant strains and density regimes will be demonstrated in this talk. Then, a computational model based on subcellular elements for cell representation and implemented on graphical processing units (GPUs) will be presented. High-quality high magnification movies of bacterial motility together with biologically justified computational simulations will be used for investigation of collective motion and order in swarming populations of bacteria. Collective motion will be shown to include the dynamical formation of cell clusters as well as streams of cells moving over networks of cell-generated slime tracks.

  14. Advanced mutasynthesis studies on the natural α-pyrone antibiotic myxopyronin from Myxococcus fulvus.

    PubMed

    Sahner, J Henning; Sucipto, Hilda; Wenzel, Silke C; Groh, Matthias; Hartmann, Rolf W; Müller, Rolf

    2015-04-13

    Myxopyronin is a natural α-pyrone antibiotic from the soil bacterium Myxococcus fulvus Mx f50. Myxopyronin inhibits bacterial RNA polymerase (RNAP) by binding to a part of the enzyme not targeted by the clinically used rifamycins. This mode of action makes myxopyronins promising molecules for the development of novel broad-spectrum antibacterials. We describe the derivatization of myxopyronins by an advanced mutasynthesis approach as a first step towards this goal. Site-directed mutagenesis of the biosynthetic machinery was used to block myxopyronin biosynthesis at different stages. The resulting mutants were fed with diverse precursors that mimic the biosynthetic intermediates to restore production. Mutasynthon incorporation and production of novel myxopyronin derivatives were analyzed by HPLC-MS/MS. This work sets the stage for accessing numerous myxopyronin derivatives, thus significantly expanding the chemical space of f α-pyrone antibiotics. PMID:25757034

  15. The Orphan Response Regulator DigR Is Required for Synthesis of Extracellular Matrix Fibrils in Myxococcus xanthus†

    PubMed Central

    Overgaard, Martin; Wegener-Feldbrügge, Sigrun; Søgaard-Andersen, Lotte

    2006-01-01

    In Myxococcus xanthus, two-component systems have crucial roles in regulating motility behavior and development. Here we describe an orphan response regulator, consisting of an N-terminal receiver domain and a C-terminal DNA binding domain, which is required for A and type IV pilus-dependent gliding motility. Genetic evidence suggests that phosphorylation of the conserved, phosphorylatable aspartate residue in the receiver domain is required for DigR activity. Consistent with the defect in type IV pilus-dependent motility, a digR mutant is slightly reduced in type IV pilus biosynthesis, and the composition of the extracellular matrix fibrils is abnormal, with an increased content of polysaccharides and decreased accumulation of the FibA metalloprotease. By using genome-wide transcriptional profiling, 118 genes were identified that are directly or indirectly regulated by DigR. These 118 genes include only 2, agmQ and cheY4, previously implicated in A and type IV pilus-dependent motility, respectively. In silico analyses showed that 36% of the differentially expressed genes are likely to encode exported proteins. Moreover, four genes encoding homologs of extracytoplasmic function (ECF) sigma factors, which typically control aspects of cell envelope homeostasis, are differentially expressed in a digR mutant. We suggest that the DigR response regulator has an important function in cell envelope homeostasis and that the motility defects in a digR mutant are instigated by the abnormal cell envelope and abnormal expression of agmQ and cheY4. PMID:16740945

  16. Complete Genome Sequence and Comparative Genomics of a Novel Myxobacterium Myxococcus hansupus

    PubMed Central

    Sharma, Gaurav; Narwani, Tarun; Subramanian, Srikrishna

    2016-01-01

    Myxobacteria, a group of Gram-negative aerobes, belong to the class δ-proteobacteria and order Myxococcales. Unlike anaerobic δ-proteobacteria, they exhibit several unusual physiogenomic properties like gliding motility, desiccation-resistant myxospores and large genomes with high coding density. Here we report a 9.5 Mbp complete genome of Myxococcus hansupus that encodes 7,753 proteins. Phylogenomic and genome-genome distance based analysis suggest that Myxococcus hansupus is a novel member of the genus Myxococcus. Comparative genome analysis with other members of the genus Myxococcus was performed to explore their genome diversity. The variation in number of unique proteins observed across different species is suggestive of diversity at the genus level while the overrepresentation of several Pfam families indicates the extent and mode of genome expansion as compared to non-Myxococcales δ-proteobacteria. PMID:26900859

  17. Myxothiazol, an antibiotic from Myxococcus fulvus (myxobacterales). I. Cultivation, isolation, physico-chemical and biological properties.

    PubMed

    Gerth, K; Irschik, H; Reichenbach, H; Trowitzsch, W

    1980-12-01

    Myxothiazol (AB-Mx f16-1), a new antifungal antibiotic, is produced by the myxobacterium Myxococcus fulvus strain Mx f16. It is active against many filamentous fungi, and completely inhibits growth of Mucor hiemalis at a concentration of 2 micrograms/ml. The molecular formula of myxothiazol was determined to e C25H33N3O3S2. PMID:6788741

  18. Gliding Motility Revisited: How Do the Myxobacteria Move without Flagella?

    PubMed Central

    Mauriello, Emilia M. F.; Mignot, Tâm; Yang, Zhaomin; Zusman, David R.

    2010-01-01

    Summary: In bacteria, motility is important for a wide variety of biological functions such as virulence, fruiting body formation, and biofilm formation. While most bacteria move by using specialized appendages, usually external or periplasmic flagella, some bacteria use other mechanisms for their movements that are less well characterized. These mechanisms do not always exhibit obvious motility structures. Myxococcus xanthus is a motile bacterium that does not produce flagella but glides slowly over solid surfaces. How M. xanthus moves has remained a puzzle that has challenged microbiologists for over 50 years. Fortunately, recent advances in the analysis of motility mutants, bioinformatics, and protein localization have revealed likely mechanisms for the two M. xanthus motility systems. These results are summarized in this review. PMID:20508248

  19. Improving cellular properties for genetic manipulation by dispersed growing mutagenesis in Myxococcus fulvus HW-1.

    PubMed

    Zhang, Cui-ying; Cai, Ke; Wu, Zhi-hong; Li, Yue-zhong

    2010-06-01

    One of the key limitations to genetic manipulation in myxobacteria is that the cells grow in clumps in liquid. A salt-tolerant strain HW-1 of Myxococcus fulvus was treated with UV irradiation and produced a completely dispersedly growing mutant UV684. There were no significant differences between the parent HW-1 and the mutant UV684 in terms of salt-tolerant growth. The mutant UV684 and the parent strain had the similar abilities of the fruiting body formation and S motility. Interestingly, the mutant exhibited high transformation/transposition efficiency with 10(5)-10(6) colony-forming units per microg DNA, which was about 10(3)-10(5) fold higher than HW-1. The results indicate that the mutation that led to dispersed growth in the UV684 mutant strain had a few impacts on social behavior, but greatly facilitated molecular genetic manipulation.

  20. The Structure of LiuC, a 3-Hydroxy-3-Methylglutaconyl CoA Dehydratase Involved in Isovaleryl-CoA Biosynthesis in Myxococcus xanthus, Reveals Insights into Specificity and Catalysis.

    PubMed

    Bock, Tobias; Reichelt, Joachim; Müller, Rolf; Blankenfeldt, Wulf

    2016-09-01

    Myxobacteria are able to produce the important metabolite isovaleryl coenzyme A by a route other than leucine degradation. The first step into this pathway is mediated by LiuC, a member of the 3-methylglutaconyl CoA hydratases (MGCH). Here we present crystal structures refined to 2.05 and 1.1 Å of LiuC in the apo form and bound to coenzyme A, respectively. By using simulated annealing we modeled the enzyme substrate complex and identified residues potentially involved in substrate binding, specificity, and catalysis. The dehydration of 3-hydroxy-3-methylglutaconyl CoA to 3-methylglutaconyl CoA catalyzed by LiuC involves Glu112 and Glu132 and likely employs the typical crotonase acid-base mechanism. In this, Tyr231 and Arg69 are key players in positioning the substrate to enable catalysis. Surprisingly, LiuC shows higher sequence and structural similarity to human MGCH than to bacterial forms, although they convert the same substrate. This study provides structural insights into the alternative isovaleryl coenzyme A biosynthesis pathway and might open a path for biofuel research, as isovaleryl-CoA is a source for isobutene, a precursor for renewable fuels and chemicals. PMID:27271456

  1. Project EAGLE (Early Academic Gifted Learning Experience): A Program for Gifted and Talented Students (Grades K-3)--Kindergarten Activity Booklets: Xanthus; Zhack; and Activity Pages H-Z.

    ERIC Educational Resources Information Center

    Merkoski, Kay

    Three activity booklets are presented for implementing Project EAGLE, an enrichment program for gifted and talented kindergarten children. The first activity booklet contains a poem by J. D. Evans titled "In Search of the Xanthus," which describes the search for an imaginary beast that leaves an "X" on the spot where it used to be. The second…

  2. Xanthusbase after five years expands to become Openmods

    PubMed Central

    Pratt-Szeliga, Philip C.; Skewes, Aaron D.; Yan, Jinyuan; Welch, Laura G.; Welch, Roy D.

    2012-01-01

    Xanthusbase (http://www.xanthusbase.org), a model organism database for the bacterium Myxococcus xanthus, functions as a collaborative information repository based on Wikipedia principles. It was created more than 5 years ago to serve as a cost-effective reference database for M. xanthus researchers, an education tool for undergraduate students to learn about genome annotation, and a means for the community of researchers to collaboratively improve their organism’s annotation. We have achieved several goals and are seeking creative solutions to ongoing challenges. Along the way we have made several important improvements to Xanthusbase related to stability, security and usability. Most importantly, we have designed and implemented an installer that enables other microbial model organism communities to use it as a MOD. This version, called Openmods, has already been used to create Xenorhabdusbase (http://xenorhabdusbase.bact.wisc.edu), Caulobacterbase (http://caulobacterbase.bsd.uchicago.edu) and soon Bdellovibriobase. PMID:22116063

  3. Xanthusbase after five years expands to become Openmods.

    PubMed

    Pratt-Szeliga, Philip C; Skewes, Aaron D; Yan, Jinyuan; Welch, Laura G; Welch, Roy D

    2012-01-01

    Xanthusbase (http://www.xanthusbase.org), a model organism database for the bacterium Myxococcus xanthus, functions as a collaborative information repository based on Wikipedia principles. It was created more than 5 years ago to serve as a cost-effective reference database for M. xanthus researchers, an education tool for undergraduate students to learn about genome annotation, and a means for the community of researchers to collaboratively improve their organism's annotation. We have achieved several goals and are seeking creative solutions to ongoing challenges. Along the way we have made several important improvements to Xanthusbase related to stability, security and usability. Most importantly, we have designed and implemented an installer that enables other microbial model organism communities to use it as a MOD. This version, called Openmods, has already been used to create Xenorhabdusbase (http://xenorhabdusbase.bact.wisc.edu), Caulobacterbase (http://caulobacterbase.bsd.uchicago.edu) and soon Bdellovibriobase. PMID:22116063

  4. 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.

  5. Diffusion through agar blocks of finite dimensions: a theoretical analysis of three systems of practical significance in microbiology.

    PubMed

    Koch, A L

    1999-03-01

    A number of experimental methods in biology depend on the kinetics of diffusion of a substance through a gel. This paper reviews the diffusion equations, gives the experimental limitations for some useful cases, and presents computer simulations for cases that cannot be treated analytically. While double diffusion is not considered, three single-diffusion situations are treated. (1) Systems for the study of chemotaxis in the gliding bacterium Myxococcus xanthus. Experimental designs used for this in many cases in the literature were inappropriate and mathematical analysis of these is presented. (2) The development of gradient plates. The time necessary for vertical diffusion to become substantially complete and before diffusion in the direction of the original slant has proceeded significantly is calculated. (3) The application to antimicrobial disk susceptibility tests. The basis of the measurement of antibiotic sensitivities with disks containing antimicrobial agents, as routinely used in clinical microbiological and testing laboratories, is analysed and the limitations are assessed and improvements suggested. PMID:10217498

  6. A shift from magnitude to sign epistasis during adaptive evolution of a bacterial social trait.

    PubMed

    Zee, Peter C; Mendes-Soares, Helena; Yu, Yuen-Tsu N; Kraemer, Susanne A; Keller, Heike; Ossowski, Stephan; Schneeberger, Korbinian; Velicer, Gregory J

    2014-09-01

    Although the importance of epistasis in evolution has long been recognized, remarkably little is known about the processes by which epistatic interactions evolve in real time in specific biological systems. Here, we have characterized how the epistatic fitness relationship between a social gene and an adapting genome changes radically over a short evolutionary time frame in the social bacterium Myxococcus xanthus. We show that a highly beneficial effect of this social gene in the ancestral genome is gradually reduced--and ultimately reversed into a deleterious effect--over the course of an experimental adaptive trajectory in which a primitive form of novel cooperation evolved. This reduction and reversal of a positive social allelic effect is driven solely by changes in the genetic context in which the gene is expressed as new mutations are sequentially fixed during adaptive evolution, and explicitly demonstrates a significant evolutionary change in the genetic architecture of an ecologically important social trait.

  7. Positively Frequency-Dependent Interference Competition Maintains Diversity and Pervades a Natural Population of Cooperative Microbes.

    PubMed

    Rendueles, Olaya; Amherd, Michaela; Velicer, Gregory J

    2015-06-29

    Positively frequency-dependent selection is predicted from theory to promote diversity in patchily structured populations and communities, but empirical support for this prediction has been lacking. Here, we investigate frequency-dependent selection among isolates from a local natural population of the highly social bacterium Myxococcus xanthus. Upon starvation, closely related cells of M. xanthus cooperate to construct multicellular fruiting bodies, yet recently diverged genotypes co-residing in a local soil population often antagonize one another during fruiting-body development in mixed groups. In the experiments reported here, both fitness per se and strong forms of interference competition exhibit pervasive and strong positive frequency dependence (PFD) among many isolates from a centimeter-scale soil population of M. xanthus. All strains that compete poorly at intermediate frequency are shown to be competitively dominant at high frequency in most genotype pairings during both growth and development, and strongly so. Interference competition is often lethal and appears to be contact dependent rather than mediated by diffusible compounds. Finally, we experimentally demonstrate that positively frequency-dependent selection maintains diversity when genotype frequencies vary patchily in structured populations. These results suggest that PFD contributes to the high levels of local diversity found among M. xanthus social groups in natural soil populations by reinforcing social barriers to cross-territory invasion and thereby also promotes high within-group relatedness. More broadly, our results suggest that potential roles of PFD in maintaining patchily distributed diversity should be investigated more extensively in other species. PMID:26051889

  8. Bacteria that glide with helical tracks

    PubMed Central

    Nan, Beiyan; McBride, Mark J.; Chen, Jing; Zusman, David R.; Oster, George

    2014-01-01

    Many bacteria glide smoothly on surfaces, but with no discernable propulsive organelles on their surface. Recent experiments with Myxococcus xanthus and Flavobacterium johnsoniae show that both distantly related bacterial species glide utilizing proteins that move in helical tracks, albeit with significantly different motility mechanisms. Both species utilize proton motive force for movement. However, the motors that power gliding in M. xanthus have been identified, while the F. johnsoniae motors remain to be discovered. PMID:24556443

  9. 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

  10. 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.

  11. Characterization of a novel extremely alkalophilic bacterium

    NASA Technical Reports Server (NTRS)

    Souza, K. A.; Deal, P. H.

    1977-01-01

    A new alkalophilic bacterium, isolated from a natural spring of high pH is characterized. It is a Gram-positive, non-sporulating, motile rod requiring aerobic and alkaline conditions for growth. The characteristics of this organism resemble those of the coryneform group of bacteria; however, there are no accepted genera within this group with which this organism can be closely matched. Therefore, a new genus may be warranted.

  12. 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.

  13. Agrobacterium tumefaciens Is a Diazotrophic Bacterium

    PubMed Central

    Kanvinde, Lalita; Sastry, G. R. K.

    1990-01-01

    This is the first report that Agrobacterium tumefaciens can fix nitrogen in a free-living condition as shown by its abilities to grow on nitrogen-free medium, reduce acetylene to ethylene, and incorporate 15N supplied as 15N2. As with most other well-characterized diazotrophic bacteria, the presence of NH4+ 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. Images PMID:16348237

  14. 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.

  15. Immobilization of the Methanogenic bacterium methanosarcina barkeri

    SciTech Connect

    Scherer, P.; Kluge, M.; Klein, J.; Sahm, H.

    1981-05-01

    Whole cells of the methanogen Methanosarcina barkeri were immobilized in an alginate network which was crosslinked with Ca/sup 2+/ calcium ions. The rates of methanol conversion to methane of entrapped cells were found to be in the same range as the corresponding rates of free cells. Furthermore, immobilized cells were active for a longer period than free cells. The particle size of the spherical alginate beads and thus diffusion has no obvious influence on the turnover of methanol. The half-value period for methanol conversion activity determined in a buffer medium was approximately 4 days at 37/degree/C for entrapped cells. The high rates of methanol degradation indicated that the immobilization technique preserved the cellular functions of this methanogenic bacterium. 24 refs.

  16. 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.

  17. Myxobacteria: Moving, Killing, Feeding, and Surviving Together

    PubMed Central

    Muñoz-Dorado, José; Marcos-Torres, Francisco J.; García-Bravo, Elena; Moraleda-Muñoz, Aurelio; Pérez, Juana

    2016-01-01

    Myxococcus xanthus, like other myxobacteria, is a social bacterium that moves and feeds cooperatively in predatory groups. On surfaces, rod-shaped vegetative cells move in search of the prey in a coordinated manner, forming dynamic multicellular groups referred to as swarms. Within the swarms, cells interact with one another and use two separate locomotion systems. Adventurous motility, which drives the movement of individual cells, is associated with the secretion of slime that forms trails at the leading edge of the swarms. It has been proposed that cellular traffic along these trails contributes to M. xanthus social behavior via stigmergic regulation. However, most of the cells travel in groups by using social motility, which is cell contact-dependent and requires a large number of individuals. Exopolysaccharides and the retraction of type IV pili at alternate poles of the cells are the engines associated with social motility. When the swarms encounter prey, the population of M. xanthus lyses and takes up nutrients from nearby cells. This cooperative and highly density-dependent feeding behavior has the advantage that the pool of hydrolytic enzymes and other secondary metabolites secreted by the entire group is shared by the community to optimize the use of the degradation products. This multicellular behavior is especially observed in the absence of nutrients. In this condition, M. xanthus swarms have the ability to organize the gliding movements of 1000s of rods, synchronizing rippling waves of oscillating cells, to form macroscopic fruiting bodies, with three subpopulations of cells showing division of labor. A small fraction of cells either develop into resistant myxospores or remain as peripheral rods, while the majority of cells die, probably to provide nutrients to allow aggregation and spore differentiation. Sporulation within multicellular fruiting bodies has the benefit of enabling survival in hostile environments, and increases germination and growth

  18. Myxobacteria: Moving, Killing, Feeding, and Surviving Together.

    PubMed

    Muñoz-Dorado, José; Marcos-Torres, Francisco J; García-Bravo, Elena; Moraleda-Muñoz, Aurelio; Pérez, Juana

    2016-01-01

    Myxococcus xanthus, like other myxobacteria, is a social bacterium that moves and feeds cooperatively in predatory groups. On surfaces, rod-shaped vegetative cells move in search of the prey in a coordinated manner, forming dynamic multicellular groups referred to as swarms. Within the swarms, cells interact with one another and use two separate locomotion systems. Adventurous motility, which drives the movement of individual cells, is associated with the secretion of slime that forms trails at the leading edge of the swarms. It has been proposed that cellular traffic along these trails contributes to M. xanthus social behavior via stigmergic regulation. However, most of the cells travel in groups by using social motility, which is cell contact-dependent and requires a large number of individuals. Exopolysaccharides and the retraction of type IV pili at alternate poles of the cells are the engines associated with social motility. When the swarms encounter prey, the population of M. xanthus lyses and takes up nutrients from nearby cells. This cooperative and highly density-dependent feeding behavior has the advantage that the pool of hydrolytic enzymes and other secondary metabolites secreted by the entire group is shared by the community to optimize the use of the degradation products. This multicellular behavior is especially observed in the absence of nutrients. In this condition, M. xanthus swarms have the ability to organize the gliding movements of 1000s of rods, synchronizing rippling waves of oscillating cells, to form macroscopic fruiting bodies, with three subpopulations of cells showing division of labor. A small fraction of cells either develop into resistant myxospores or remain as peripheral rods, while the majority of cells die, probably to provide nutrients to allow aggregation and spore differentiation. Sporulation within multicellular fruiting bodies has the benefit of enabling survival in hostile environments, and increases germination and growth

  19. Bacterially mediated mineralization of vaterite

    NASA Astrophysics Data System (ADS)

    Rodriguez-Navarro, Carlos; Jimenez-Lopez, Concepcion; Rodriguez-Navarro, Alejandro; Gonzalez-Muñoz, Maria Teresa; Rodriguez-Gallego, Manuel

    2007-03-01

    Myxococcus xanthus, a common soil bacterium, plays an active role in the formation of spheroidal vaterite. Bacterial production of CO 2 and NH 3 and the transformation of the NH 3 to NH4+ and OH -, thus increasing solution pH and carbonate alkalinity, set the physicochemical conditions (high supersaturation) leading to vaterite precipitation in the microenvironment around cells, and directly onto the surface of bacterial cells. In the latter case, fossilization of bacteria occurs. Vaterite crystals formed by aggregation of oriented nanocrystals with c-axis normal to the bacterial cell-wall, or to the core of the spherulite when bacteria were not encapsulated. While preferred orientation of vaterite c-axis appears to be determined by electrostatic affinity (ionotropic effect) between vaterite crystal (0001) planes and the negatively charged functional groups of organic molecules on the bacterium cell-wall or on extracellular polymeric substances (EPS), analysis of the changes in the culture medium chemistry as well as high resolution transmission electron microscopy (HRTEM) observations point to polymorph selection by physicochemical (kinetic) factors (high supersaturation) and stabilization by organics, both connected with bacterial activity. The latter is in agreement with inorganic precipitation of vaterite induced by NH 3 and CO 2 addition in the protein-rich sterile culture medium. Our results as well as recent studies on vaterite precipitation in the presence of different types of bacteria suggest that bacterially mediated vaterite precipitation is not strain-specific, and could be more common than previously thought.

  20. Chitoporin from the Marine Bacterium Vibrio harveyi

    PubMed Central

    Chumjan, Watcharin; Winterhalter, Mathias; Schulte, Albert; Benz, Roland; Suginta, Wipa

    2015-01-01

    VhChiP is a sugar-specific porin present in the outer membrane of the marine bacterium Vibrio harveyi. VhChiP is responsible for the uptake of chitin oligosaccharides, with particular selectivity for chitohexaose. In this study, we employed electrophysiological and biochemical approaches to demonstrate that Trp136, located at the mouth of the VhChiP pore, plays an essential role in controlling the channel's ion conductivity, chitin affinity, and permeability. Kinetic analysis of sugar translocation obtained from single channel recordings indicated that the Trp136 mutations W136A, W136D, W136R, and W136F considerably reduce the binding affinity of the protein channel for its best substrate, chitohexaose. Liposome swelling assays confirmed that the Trp136 mutations decreased the rate of bulk chitohexaose permeation through the VhChiP channel. Notably, all of the mutants show increases in the off-rate for chitohexaose of up to 20-fold compared with that of the native channel. Furthermore, the cation/anion permeability ratio Pc/Pa is decreased in the W136R mutant and increased in the W136D mutant. This demonstrates that the negatively charged surface at the interior of the protein lumen preferentially attracts cationic species, leading to the cation selectivity of this trimeric channel. PMID:26082491

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. The biogeography of kin discrimination across microbial neighbourhoods.

    PubMed

    Kraemer, Susanne A; Wielgoss, Sébastien; Fiegna, Francesca; Velicer, Gregory J

    2016-10-01

    The spatial distribution of potential interactants is critical to social evolution in all cooperative organisms. Yet the biogeography of microbial kin discrimination at the scales most relevant to social interactions is poorly understood. Here we resolve the microbiogeography of social identity and genetic relatedness in local populations of the model cooperative bacterium Myxococcus xanthus at small spatial scales, across which the potential for dispersal is high. Using two criteria of relatedness-colony-merger compatibility during cooperative motility and DNA-sequence similarity at highly polymorphic loci-we find that relatedness decreases greatly with spatial distance even across the smallest scale transition. Both social relatedness and genetic relatedness are maximal within individual fruiting bodies at the micrometre scale but are much lower already across adjacent fruiting bodies at the millimetre scale. Genetic relatedness was found to be yet lower among centimetre-scale samples, whereas social allotype relatedness decreased further only at the metre scale, at and beyond which the probability of social or genetic identity among randomly sampled isolates is effectively zero. Thus, in M. xanthus, high-relatedness patches form a rich mosaic of diverse social allotypes across fruiting body neighbourhoods at the millimetre scale and beyond. Individuals that migrate even short distances across adjacent groups will frequently encounter allotypic conspecifics and territorial kin discrimination may profoundly influence the spatial dynamics of local migration. Finally, we also found that the phylogenetic scope of intraspecific biogeographic analysis can affect the detection of spatial structure, as some patterns evident in clade-specific analysis were masked by simultaneous analysis of all strains. PMID:27540705

  6. The Mosaic Genome of Anaeromyxobacter dehalogenans Strain 2CP-C Suggests an Aerobic Common Ancestor to the Delta-Proteobacteria

    PubMed Central

    Thomas, Sara H.; Wagner, Ryan D.; Arakaki, Adrian K.; Skolnick, Jeffrey; Kirby, John R.; Shimkets, Lawrence J.; Sanford, Robert A.; Löffler, Frank E.

    2008-01-01

    Anaeromyxobacter dehalogenans strain 2CP-C is a versaphilic delta-Proteobacterium distributed throughout many diverse soil and sediment environments. 16S rRNA gene phylogenetic analysis groups A. dehalogenans together with the myxobacteria, which have distinguishing characteristics including strictly aerobic metabolism, sporulation, fruiting body formation, and surface motility. Analysis of the 5.01 Mb strain 2CP-C genome substantiated that this organism is a myxobacterium but shares genotypic traits with the anaerobic majority of the delta-Proteobacteria (i.e., the Desulfuromonadales). Reflective of its respiratory versatility, strain 2CP-C possesses 68 genes coding for putative c-type cytochromes, including one gene with 40 heme binding motifs. Consistent with its relatedness to the myxobacteria, surface motility was observed in strain 2CP-C and multiple types of motility genes are present, including 28 genes for gliding, adventurous (A-) motility and 17 genes for type IV pilus-based motility (i.e., social (S-) motility) that all have homologs in Myxococcus xanthus. Although A. dehalogenans shares many metabolic traits with the anaerobic majority of the delta-Proteobacteria, strain 2CP-C grows under microaerophilic conditions and possesses detoxification systems for reactive oxygen species. Accordingly, two gene clusters coding for NADH dehydrogenase subunits and two cytochrome oxidase gene clusters in strain 2CP-C are similar to those in M. xanthus. Remarkably, strain 2CP-C possesses a third NADH dehydrogenase gene cluster and a cytochrome cbb3 oxidase gene cluster, apparently acquired through ancient horizontal gene transfer from a strictly anaerobic green sulfur bacterium. The mosaic nature of the A. dehalogenans strain 2CP-C genome suggests that the metabolically versatile, anaerobic members of the delta-Proteobacteria may have descended from aerobic ancestors with complex lifestyles. PMID:18461135

  7. Coiled to diffuse: Brownian motion of a helical bacterium.

    PubMed

    Butenko, Alexander V; Mogilko, Emma; Amitai, Lee; Pokroy, Boaz; Sloutskin, Eli

    2012-09-11

    We employ real-time three-dimensional confocal microscopy to follow the Brownian motion of a fixed helically shaped Leptospira interrogans (LI) bacterium. We extract from our measurements the translational and the rotational diffusion coefficients of this bacterium. A simple theoretical model is suggested, perfectly reproducing the experimental diffusion coefficients, with no tunable parameters. An older theoretical model, where edge effects are neglected, dramatically underestimates the observed rates of translation. Interestingly, the coiling of LI increases its rotational diffusion coefficient by a factor of 5, compared to a (hypothetical) rectified bacterium of the same contour length. Moreover, the translational diffusion coefficients would have decreased by a factor of ~1.5, if LI were rectified. This suggests that the spiral shape of the spirochaete bacteria, in addition to being employed for their active twisting motion, may also increase the ability of these bacteria to explore the surrounding fluid by passive Brownian diffusion.

  8. 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

  9. 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

    2015-06-04

    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.

  10. Understanding the detailed motion of a model bacterium

    NASA Astrophysics Data System (ADS)

    Thawani, Akanksha; Tirumkudulu, Mahesh

    2014-11-01

    Inspired by the motion of flagellated bacteria such as Escherichia coli and Bacillus subtilis, we have built a macroscopic model bacterium, in order to investigate the intricate aspects of their motion which cannot be visualized under a microscope. The flagellated rod shaped cells were approximated with a spherical head attached to a rigid metal helix, via a plastic hook. The motion of model bacterium was observed in a high viscosity silicone oil to replicate the low Reynolds number flow conditions. A significant wobble was observed even in the absence of an off-axis flagellum. We suspect that the flexibility in the hook connecting the head and flagellum is the cause for wobble, since wobble was observed to increase significantly with hook-flexibility. The motion of the model bacterium was predicted using the Slender Body theory of Lighthill, and was compared with the measured trajectories.

  11. 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.

  12. 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.

  13. 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

  14. Gut bacterium of Dendrobaena veneta (Annelida: Oligochaeta) possesses antimycobacterial activity.

    PubMed

    Fiołka, Marta J; Zagaja, Mirosław P; Piersiak, Tomasz D; Wróbel, Marek; Pawelec, Jarosław

    2010-09-01

    The new bacterial strain with antimycobacterial activity has been isolated from the midgut of Dendrobaena veneta (Annelida). Biochemical and molecular characterization of isolates from 18 individuals identified all as Raoultella ornithinolytica genus with 99% similarity. The bacterium is a possible symbiont of the earthworm D. veneta. The isolated microorganism has shown the activity against four strains of fast-growing mycobacteria: Mycobacterium butiricum, Mycobacterium jucho, Mycobacterium smegmatis and Mycobacterium phlei. The multiplication of the gut bacterium on plates with Sauton medium containing mycobacteria has caused a lytic effect. After the incubation of the cell free extract prepared from the gut bacterium with four strains of mycobacteria in liquid Sauton medium, the cells of all tested strains were deformed and divided to small oval forms and sometimes created long filaments. The effect was observed by the use of light, transmission and scanning microscopy. Viability of all examined species of mycobacteria was significantly decreased. The antimycobacterial effect was probably the result of the antibiotic action produced by the gut bacterium of the earthworm. The application of ultrafiltration procedure allowed to demonstrate that antimicrobial substance with strong antimycobacterial activity from bacterial culture supernatant, is a protein with the molecular mass above 100 kDa.

  15. 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.

  16. Revised Genome Sequence of the Purple Photosynthetic Bacterium Blastochloris viridis

    PubMed Central

    Faulkner, Matthew; Liu, Xuan; Huang, Fang; Darby, Alistair C.; Hall, Neil

    2016-01-01

    Blastochloris viridis is a unique anaerobic, phototrophic purple bacterium that produces bacteriochlorophyll b. Here we report an improved genome sequence of Blastochloris viridis DSM133, which is instrumental to the studies of photosynthesis, metabolic versatility, and genetic engineering of this microorganism. PMID:26798090

  17. Rapid and widespread de novo evolution of kin discrimination

    PubMed Central

    Rendueles, Olaya; Zee, Peter C.; Dinkelacker, Iris; Amherd, Michaela; Wielgoss, Sébastien; Velicer, Gregory J.

    2015-01-01

    Diverse forms of kin discrimination, broadly defined as alteration of social behavior as a function of genetic relatedness among interactants, are common among social organisms from microbes to humans. However, the evolutionary origins and causes of kin-discriminatory behavior remain largely obscure. One form of kin discrimination observed in microbes is the failure of genetically distinct colonies to merge freely upon encounter. Here, we first use natural isolates of the highly social bacterium Myxococcus xanthus to show that colony-merger incompatibilities can be strong barriers to social interaction, particularly by reducing chimerism in multicellular fruiting bodies that develop near colony-territory borders. We then use experimental laboratory populations to test hypotheses regarding the evolutionary origins of kin discrimination. We show that the generic process of adaptation, irrespective of selective environment, is sufficient to repeatedly generate kin-discriminatory behaviors between evolved populations and their common ancestor. Further, we find that kin discrimination pervasively evolves indirectly between allopatric replicate populations that adapt to the same ecological habitat and that this occurs generically in many distinct habitats. Patterns of interpopulation discrimination imply that kin discrimination phenotypes evolved via many diverse genetic mechanisms and mutation-accumulation patterns support this inference. Strong incompatibility phenotypes emerged abruptly in some populations but strengthened gradually in others. The indirect evolution of kin discrimination in an asexual microbe is analogous to the indirect evolution of reproductive incompatibility in sexual eukaryotes and linguistic incompatibility among human cultures, the commonality being indirect, noncoordinated divergence of complex systems evolving in isolation. PMID:26150498

  18. Wet-surface-enhanced ellipsometric contrast microscopy identifies slime as a major adhesion factor during bacterial surface motility.

    PubMed

    Ducret, Adrien; Valignat, Marie-Pierre; Mouhamar, Fabrice; Mignot, Tâm; Theodoly, Olivier

    2012-06-19

    In biology, the extracellular matrix (ECM) promotes both cell adhesion and specific recognition, which is essential for central developmental processes in both eukaryotes and prokaryotes. However, live studies of the dynamic interactions between cells and the ECM, for example during motility, have been greatly impaired by imaging limitations: mostly the ability to observe the ECM at high resolution in absence of specific staining by live microscopy. To solve this problem, we developed a unique technique, wet-surface enhanced ellipsometry contrast (Wet-SEEC), which magnifies the contrast of transparent organic materials deposited on a substrate (called Wet-surf) with exquisite sensitivity. We show that Wet-SEEC allows both the observation of unprocessed nanofilms as low as 0.2 nm thick and their accurate 3D topographic reconstructions, directly by standard light microscopy. We next used Wet-SEEC to image slime secretion, a poorly defined property of many prokaryotic and eukaryotic organisms that move across solid surfaces in absence of obvious extracellular appendages (gliding). Using combined Wet-SEEC and fluorescent-staining experiments, we observed slime deposition by gliding Myxococcus xanthus cells at unprecedented resolution. Altogether, the results revealed that in this bacterium, slime associates preferentially with the outermost components of the motility machinery and promotes its adhesion to the substrate on the ventral side of the cell. Strikingly, analogous roles have been proposed for the extracellular proteoglycans of gliding diatoms and apicomplexa, suggesting that slime deposition is a general means for gliding organisms to adhere and move over surfaces.

  19. Isolation of a Bacterium Capable of Degrading Peanut Hull Lignin

    PubMed Central

    Kerr, Thomas J.; Kerr, Robert D.; Benner, Ronald

    1983-01-01

    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 sp., 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 [14C]lignin-labeled lignocellulose and [14C]cellulose-labeled lignocellulose from the cordgrass Spartina alterniflora and could also degrade [14C]Kraft lignin from slash pine. After 10 days of incubation with [14C]cellulose-labeled lignocellulose or [14C]lignin-labeled lignocellulose from S. alterniflora, the bacterium mineralized 6.5% of the polysaccharide component and 2.9% of the lignin component. Images PMID:16346424

  20. 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.

  1. Isolation of the Legionnaires' disease bacterium from environmental samples.

    PubMed

    Morris, G K; Patton, C M; Feeley, J C; Johnson, S E; Gorman, G; Martin, W T; Skaliy, P; Mallison, G F; Politi, B D; Mackel, D C

    1979-04-01

    We analyzed 24 environmental samples collected in or near the Indiana Memorial Union, where an epidemic of Legionnaires' disease occurred in early 1978. We conducted fluorescent antibody analyses and culture on F-G and charcoal yeast extract agars of each sample directly; splenic tissue of guinea pigs inoculated with the sample; and yolk sacs from embryonated eggs inoculated with splenic tissue of guinea pigs injected with the sample. Legionnaires' disease (LD) bacterium was isolated from seven of the 24 samples: one water sample from the air-conditioner cooling tower of the Union; three water samples from a stream near the Union; and three mud samples from the same stream. The LD bacterium strains were of three different serotypes. These findings indicate that LD bacteria may be widespread in nature. PMID:373549

  2. 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).

  3. Trichloroethylene Biodegradation by a Methane-Oxidizing Bacterium

    PubMed Central

    Little, C. Deane; Palumbo, Anthony V.; Herbes, Stephen E.; Lidstrom, Mary E.; Tyndall, Richard L.; Gilmer, Penny J.

    1988-01-01

    Trichloroethylene (TCE), a common groundwater contaminant, is a suspected carcinogen that is highly resistant to aerobic biodegradation. An aerobic, methane-oxidizing bacterium was isolated that degrades TCE in pure culture at concentrations commonly observed in contaminated groundwater. Strain 46-1, a type I methanotrophic bacterium, degraded TCE if grown on methane or methanol, producing CO2 and water-soluble products. Gas chromatography and 14C radiotracer techniques were used to determine the rate, methane dependence, and mechanism of TCE biodegradation. TCE biodegradation by strain 46-1 appears to be a cometabolic process that occurs when the organism is actively metabolizing a suitable growth substrate such as methane or methanol. It is proposed that TCE biodegradation by methanotrophs occurs by formation of TCE epoxide, which breaks down spontaneously in water to form dichloroacetic and glyoxylic acids and one-carbon products. Images PMID:16347616

  4. 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.

  5. 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

  6. Efficient Multiple Object Tracking Using Mutually Repulsive Active Membranes

    PubMed Central

    Deng, Yi; Coen, Philip; Sun, Mingzhai; Shaevitz, Joshua W.

    2013-01-01

    Studies of social and group behavior in interacting organisms require high-throughput analysis of the motion of a large number of individual subjects. Computer vision techniques offer solutions to specific tracking problems, and allow automated and efficient tracking with minimal human intervention. In this work, we adopt the open active contour model to track the trajectories of moving objects at high density. We add repulsive interactions between open contours to the original model, treat the trajectories as an extrusion in the temporal dimension, and show applications to two tracking problems. The walking behavior of Drosophila is studied at different population density and gender composition. We demonstrate that individual male flies have distinct walking signatures, and that the social interaction between flies in a mixed gender arena is gender specific. We also apply our model to studies of trajectories of gliding Myxococcus xanthus bacteria at high density. We examine the individual gliding behavioral statistics in terms of the gliding speed distribution. Using these two examples at very distinctive spatial scales, we illustrate the use of our algorithm on tracking both short rigid bodies (Drosophila) and long flexible objects (Myxococcus xanthus). Our repulsive active membrane model reaches error rates better than per fly per second for Drosophila tracking and comparable results for Myxococcus xanthus. PMID:23799046

  7. Identification and comparative analysis of microRNAs in barnyardgrass (Echinochloa crus-galli) in response to rice allelopathy.

    PubMed

    Fang, Changxun; Li, Yingzhe; Li, Chengxun; Li, Biliang; Ren, Yongjie; Zheng, Haiping; Zeng, Xiaomei; Shen, Lihua; Lin, Wenxiong

    2015-07-01

    Rice allelopathy is a hot topic in the field of allelopathy, and behaviour of donor allelopathic rice has been well documented. However, few study addresses response of receiver barnyardgrass (BYG). We found that expression of miRNAs relevant to plant hormone signal transduction, nucleotide excision repair and the peroxisome proliferator-activated receptor and p53 signalling pathways was enhanced in BYG co-cultured with the allelopathic rice cultivar PI312777, the expression levels of these miRNAs in BYG plants were positively correlated with allelopathic potential of the co-cultured rice varieties. Treatment of BYG plants with rice-produced phenolic acids also increased miRNA expression in BYG, while treatment with rice-produced terpenoids had no obvious effect on miRNA expression. In the hydroponic system, the largest number of Myxococcus sp. was found in the growth medium containing rice with the highest allelopathic potential. The addition of phenolic acids in the hydroponic medium also increased the number of Myxococcus sp. More interestingly, inoculation with Myxococcus xanthus significantly increased miRNA expression in the treated BYG. Jointed treatments of ferulic acid and M. xanthus led to strongest growth inhibition of BYG. The results suggest that there exist involvement of Myxococcus sp. and mediation of miRNA expression in rice allelopathy against BYG. PMID:25438645

  8. 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.

  9. 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.

  10. 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.

  11. CORNEAL REACTIONS TO BACTERIUM GRANULOSIS AND OTHER MICROORGANISMS

    PubMed Central

    Olitsky, Peter K.; Knutti, Ralph E.; Tyler, Joseph R.

    1932-01-01

    The conclusions which may be drawn from the results of the experiments here presented are: 1. The cornea of the rabbit is highly sensitive to the action of various injected bacteria. The lesions vary from insignificant, transient changes to severe, destructive panophthalmitis, with fine gradations from the mildest to the violent form of inflammation. Moreover, animals that receive the same organisms show like changes. 2. The varying degree of inflammatory reaction is related to the pathogenicity of the special culture employed; as, for example, is shown by the reactions to Type I pneumococci and to Bacterium granulosis. It is evident that when a microorganism having a certain degree of virulence is used, a lesion of localized vasculonebulous keratitis resembling pannus tenuis or vasculosus of human trachoma can be induced. Thus Bacterium granulosis, Bacillus xerosis, Hemophilus influenzae, Pneumococcus Type II, Streptococcus viridans, and gonococcus can cause the pannus-like corneal changes in the rabbit. Of these organisms, however, only Bacterium granulosis induces early, uncomplicated and enduring keratitic lesions; the others cause first, diffuse keratitis with suppurative lesions; then, as a residual effect, transient, localized, vasculonebulous changes in the cornea. These changes, in contradistinction to the granulosis lesions, are, therefore delayed, complicated, and transient. When, on the other hand, the invasiveness and infecting power of the organisms are low, as is the case with the filtrable, Gram-negative bacillus and the small, Gram-negative bacilli ultimately derived from cases of folliculosis, no marked effect is produced by their intracorneal inoculation. If the pathogenicity of bacteria is high (as shown by Pneumococcus Type I, hemolytic streptococcus, and the remaining bacteria), intracorneal inoculation of the microorganisms leads to serious suppurative or destructive changes. 3. The results of experiments with monkeys indicate that while

  12. 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

  13. Vector potential of houseflies for the bacterium Aeromonas caviae.

    PubMed

    Nayduch, D; Noblet, G Pittman; Stutzenberger, F J

    2002-06-01

    Houseflies, Musca domestica Linnaeus (Diptera: Muscidae), have been implicated as vectors or transporters of numerous gastrointestinal pathogens encountered during feeding and ovipositing on faeces. The putative enteropathogen Aeromonas caviae (Proteobacteria: Aeromonadaceae) may be present in faeces of humans and livestock. Recently A. caviae was detected in houseflies by PCR and isolated by culture methods. In this study, we assessed the vector potential of houseflies for A. caviae relative to multiplication and persistence of the bacterium in the fly and to contamination of other flies and food materials. In experimentally fed houseflies, the number of bacteria increased up to 2 days post-ingestion (d PI) and then decreased significantly 3 d PI. A large number of bacteria was detected in the vomitus and faeces of infected flies at 2-3 d PI. The bacteria persisted in flies for up to 8 d PI, but numbers were low. Experimentally infected flies transmitted A. caviae to chicken meat, and transmissibility was directly correlated with exposure time. Flies contaminated the meat for up to 7 d PI; however, a significant decrease in contamination was observed 2-3 d PI. In the fly-to-fly transmission experiments, the transmission of A. caviae was observed and was apparently mediated by flies sharing food. These results support houseflies as potential vectors for A. caviae because the bacterium multiplied, persisted in flies for up to 8 d PI, and could be transmitted to human food items.

  14. Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus

    DOE PAGES

    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

  15. 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

  16. 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

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

    NASA Astrophysics Data System (ADS)

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

    1990-04-01

    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.

  18. 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.

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

    PubMed Central

    Wang, Yuanli; Chen, Wei; He, Linyan; Wang, Qi

    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. Genome Sequence of the Mycorrhizal Helper Bacterium Pseudomonas fluorescens BBc6R8

    PubMed Central

    Gross, H.; Morin, E.; Karpinets, T.; Utturkar, S.; Mehnaz, S.; Martin, F.; Frey-Klett, P.; Labbé, J.

    2014-01-01

    We report the draft genome sequence of the mycorrhizal helper bacterium Pseudomonas fluorescens strain BBc6R8. This is the first genome of a mycorrhizal helper bacterium. The draft genome contains 6,952,353 bp and is predicted to encode 6,317 open reading frames. Comparative genomic analyses will help to identify helper traits. PMID:24407649

  1. 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

  2. Draft Genome Sequence of Pseudomonas aeruginosa Strain RB, a Bacterium Capable of Synthesizing Cadmium Selenide Nanoparticles.

    PubMed

    Ayano, Hiroyuki; Kuroda, Masashi; Soda, Satoshi; Ike, Michihiko

    2014-01-01

    Pseudomonas aeruginosa strain RB is a bacterium capable of synthesizing cadmium selenide (CdSe) nanoparticles and was isolated from a soil sample. Here, we present the draft genome sequence of P. aeruginosa strain RB. To the best of our knowledge, this is the first report of a draft genome of a CdSe-synthesizing bacterium.

  3. 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.

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

    DOE PAGES

    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.

  5. 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.

  6. 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

  7. 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.

  8. Characterisation of an unusual bacterium isolated from genital ulcers.

    PubMed

    Ursi, J P; van Dyck, E; Ballard, R C; Jacob, W; Piot, P; Meheus, A Z

    1982-02-01

    The preliminary characterisation of an unusual gram-negative bacillus isolated from genital ulcers in Swaziland is reported. Like Haemophilus ducreyi, it is an oxidase positive, nitrate-reductase-positive gram-negative rod that forms streptobacillary chains in some circumstances; it was therefore called the "ducreyi-like bacterium" (DLB). Distinguishing features of DLB are production of alpha-haemolysis on horse-blood agar, stimulation of growth by a microaerophilic atmosphere and by a factor produced by Staphylococcus aureus, a strongly positive porphyrin test, and a remarkable ability to undergo autolysis. DLB had a guanine + cytosine value of c. 50 mole% but it cannot be classified, even at the genus level, until more taxonomic data are obtained.

  9. 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.

  10. 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

  11. 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.

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

    PubMed

    Speranza, Giovanna; Morelli, Carlo F; Cairoli, Paola; Müller, 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 -CH2-O- to =N-CH2- 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.

  13. Genome Sequence of the Haloalkaliphilic Methanotrophic Bacterium Methylomicrobium alcaliphilum 20Z

    PubMed Central

    Vuilleumier, Stéphane; Khmelenina, Valentina N.; Bringel, Françoise; Reshetnikov, Alexandr S.; Lajus, Aurélie; Mangenot, Sophie; Rouy, Zoé; Op den Camp, Huub J. M.; Jetten, Mike S. M.; Dispirito, Alan A.; Dunfield, Peter; Klotz, Martin G.; Semrau, Jeremy D.; Stein, Lisa Y.; Barbe, Valérie; Médigue, Claudine; Trotsenko, Yuri A.

    2012-01-01

    Methylomicrobium strains are widespread in saline environments. Here, we report the complete genome sequence of Methylomicrobium alcaliphilum 20Z, a haloalkaliphilic methanotrophic bacterium, which will provide the basis for detailed characterization of the core pathways of both single-carbon metabolism and responses to osmotic and high-pH stresses. Final assembly of the genome sequence revealed that this bacterium contains a 128-kb plasmid, making M. alcaliphilum 20Z the first methanotrophic bacterium of known genome sequence for which a plasmid has been reported. PMID:22207753

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

    PubMed Central

    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

  15. 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.

  16. 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

  17. Tracing the run-flip motion of an individual bacterium

    NASA Astrophysics Data System (ADS)

    Liu, Bin; Morse, Michael; Tang, Jay; Powers, Thomas; Breuer, Kenneth S.

    2012-11-01

    We have developed a digital 3D tracking microscope in which the microscope stage follows the motion of an individual motile microorganism so that the target remains focused at the center of the view-field. The tracking mechanism is achieved by a high-speed feedback control through real-time image analysis and the trace of the microorganism is recorded with submicron accuracy. We apply this tracking microscope to a study of the motion of an individual Caulobacter crescentus, a bacterium that moves up to 100 microns (or 50 body lengths) per second and reverses its direction of motion occasionally by switching the rotation direction of its single helical flagellum. By tracking the motion of a single cell over many seconds, we show how a flip event occurs with submicron resolution and how the speed of a single cell varies over time and with the rotational rate of the flagellum. We also present statistics for the run-reverse dynamics of an ensemble of cells.

  18. Presence of an Unusual Methanogenic Bacterium in Coal Gasification Waste

    PubMed Central

    Tomei, Francisco A.; Rouse, Dwight; Maki, James S.; Mitchell, Ralph

    1988-01-01

    Methanogenic bacteria growing on a pilot-scale, anaerobic filter processing coal gasification waste were enriched in a mineral salts medium containing hydrogen and acetate as potential energy sources. Transfer of the enrichments to methanol medium resulted in the initial growth of a strain of Methanosarcina barkeri, but eventually small cocci became dominant. The cocci growing on methanol produced methane and exhibited the typical fluorescence of methanogenic bacteria. They grew in the presence of the cell wall synthesis-inhibiting antibiotics d-cycloserine, fosfomycin, penicillin G, and vancomycin as well as in the presence of kanamycin, an inhibitor of protein synthesis in eubacteria. The optimal growth temperature was 37°C, and the doubling time was 7.5 h. The strain lysed after reaching stationary phase. The bacterium grew poorly with hydrogen as the energy source and failed to grow on acetate. Morphologically, the coccus shared similarities with Methanosarcina sp. Cells were 1 μm wide, exhibited the typical thick cell wall and cross-wall formation, and formed tetrads. Packets and cysts were not formed. Images PMID:16347791

  19. 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

  20. Biophysical basis for cooperation among the bacterium Thiovulum majus

    NASA Astrophysics Data System (ADS)

    Petroff, A.; Libchaber, A.

    2013-12-01

    The organization of microorganisms into communities plays a vital role in determining how nutrients flow through an ecosystem. Here we investigate the basis of a mathematically simple form of community formation displayed by the bacterium Thiovulum majus. T. majus cells attach to surfaces using a tether. As a tethered cell beats its flagella, it creates a flow that pulls nutrients to the cell. At high cell densities, variations in the density of cells drive large-scale convective flows that stir the environment. Here we use a combination of experimental observations and mathematical analysis to investigate how the macroscopic dynamics of a community arise from the behavior of individual cells. We begin by considering the flow of water around a single tethered cell and the resulting cell motion. We then show how the behavior of cells responding to the flow of nutrients through the community gives rise to soliton-like collective modes that efficiently stir the environment. Finally, we present new techniques for visualizing the flow of nutrients through these communities and the resulting collective phenomena. Because these dynamics arise from hydrodynamic coupling between cells and their environment, this system can be understood using classical techniques of fluid mechanics. In this way, T. majus communities provide a tractable example of the general phenomenon of community formation in response to nutrient flow.

  1. 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)).

  2. 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

  3. New Type of Bacterium Expands Possibilities of Life, Scientists Indicate

    NASA Astrophysics Data System (ADS)

    Showstack, Randy

    2010-12-01

    Leading up to NASA's 2 December news briefing about a new astrobiology finding, segments of the blogosphere had run wild with speculation that the agency would announce that it has found life elsewhere. Although some bloggers and readers may have been disappointed in the actual announcement, scientists at the briefing at NASA headquarters in Washington, D. C., said the finding of a bacterium that can grow by using arsenic instead of phosphorus is “phenomenal,” with broad implications for searching for life on Earth and elsewhere and for other areas of research on Earth. Felisa Wolfe-Simon, a NASA Astrobiology Research Fellow in residence at the U.S. Geological Survey in Menlo Park, Calif., led a team that discovered and experimented on the microbe, known as strain GFAJ-1 of the common bacteria group Gammaproteobacteria. Noting that life is mostly composed of carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus, she said, “If there is an organism on Earth doing something different, we've cracked open the door to what is possible for life elsewhere.”

  4. 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

  5. Aerobic biodegradation of 4-methylquinoline by a soil bacterium.

    PubMed Central

    Sutton, S D; Pfaller, S L; Shann, J R; Warshawsky, D; Kinkle, B K; Vestal, J R

    1996-01-01

    Methylquinolines and related N-heterocyclic aromatic compounds are common contaminants associated with the use of hydrocarbons in both coal gasification and wood treatment processes. These compounds have been found in groundwater, and many are known mutagens. A stable, five-member bacterial consortium able to degrade 4-methylquinoline was established by selective enrichment using soil collected from an abandoned coal gasification site. The consortium was maintained for 5 years by serial transfer in a medium containing 4-methylquinoline. A gram-negative soil bacterium, strain Lep1, was isolated from the consortium and shown to utilize 4-methylquinoline as a source of carbon and energy during growth in liquid medium. A time course experiment demonstrated that both the isolate Lep1 and the consortium containing Lep1 were able to degrade 4-methylquinoline under aerobic conditions. Complete degradation of 4-methylquinoline by either strain Lep1 alone or the consortium was characterized by the production and eventual disappearance of 2-hydroxy-4-methylquinoline, followed by the appearance and persistence of a second metabolite tentatively identified as a hydroxy-4-methylcoumarin. Currently, there is no indication that 4-methylquinoline degradation proceeds differently in the consortium culture compared with Lep1 alone. This is the first report of 4-methylquinoline biodegradation under aerobic conditions. PMID:8702284

  6. 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.

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

    DOE PAGES

    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

  8. Perchlorate reduction by a novel chemolithoautotrophic, hydrogen-oxidizing bacterium.

    PubMed

    Zhang, Husen; Bruns, Mary Ann; Logan, Bruce E

    2002-10-01

    Water treatment technologies are needed that can remove perchlorate from drinking water without introducing organic chemicals that stimulate bacterial growth in water distribution systems. Hydrogen is an ideal energy source for bacterial degradation of perchlorate as it leaves no organic residue and is sparingly soluble. We describe here the isolation of a perchlorate-respiring, hydrogen-oxidizing bacterium (Dechloromonas sp. strain HZ) that grows with carbon dioxide as sole carbon source. Strain HZ is a Gram-negative, rod-shaped facultative anaerobe that was isolated from a gas-phase anaerobic packed-bed biofilm reactor treating perchlorate-contaminated groundwater. The ability of strain HZ to grow autotrophically with carbon dioxide as the sole carbon source was confirmed by demonstrating that biomass carbon (100.9%) was derived from CO2. Chemolithotrophic growth with hydrogen was coupled with complete reduction of perchlorate (10 mM) to chloride with a maximum doubling time of 8.9 h. Strain HZ also grew using acetate as the electron donor and chlorate, nitrate, or oxygen (but not sulphate) as an electron acceptor. Phylogenetic analysis of the 16S rRNA sequence placed strain HZ in the genus Dechloromonas within the beta subgroup of the Proteobacteria. The study of this and other novel perchlorate-reducing bacteria may lead to new, safe technologies for removing perchlorate and other chemical pollutants from drinking water.

  9. Biodegradation of nicosulfuron by the bacterium Serratia marcescens N80.

    PubMed

    Zhang, Hao; Mu, Wenhui; Hou, Zhiguang; Wu, Xian; Zhao, Weiwei; Zhang, Xianghui; Pan, Hongyu; Zhang, Shihong

    2012-01-01

    By enrichment culturing of the sludge collected from the industrial wastewater treatment pond, we isolated a highly efficient nicosulfuron degrading bacterium Serratia marcescens N80. In liquid medium, Serratia marcescens N80 grows using nicosulfuron as the sole nitrogen source, and the optimal temperature, pH values, and inoculation for degradation are 30-35°C, 6.0-7.0, and 3.0% (v/v), respectively. With the initial concentration of 10 mg L⁻¹, the degradation rate is 93.6% in 96 hours; as the initial concentrations are higher than 10 mg L⁻¹, the biodegradation rates decrease as the nicosulfuron concentrations increase; when the concentration is 400 mg L⁻¹, the degradation rate is only 53.1%. Degradation follows the pesticide degradation kinetic equation at concentrations between 5 mg L⁻¹ and 50 mg L⁻¹. Identification of the metabolites by the liquid chromatography/mass spectrometry (LC/MS) indicates that the degradation of nicosulfuron is achieved by breaking the sulfonylurea bridge. The strain N80 also degraded some other sulfonylurea herbicides, including ethametsulfuron, tribenuron-methyl, metsulfuron-methyl, chlorimuron-ethyl,and rimsulfuron.

  10. 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

  11. 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

  12. Acquisition of polyamines by the obligate intracytoplasmic bacterium Rickettsia prowazekii.

    PubMed Central

    Speed, R R; Winkler, H H

    1990-01-01

    Both the polyamine content and the route of acquisition of polyamines by Rickettsia prowazekii, an obligate intracellular parasitic bacterium, were determined. The rickettsiae grew normally in an ornithine decarboxylase mutant of the Chinese hamster ovary (C55.7) cell line whether or not putrescine, which this host cell required in order to grow, was present. The rickettsiae contained approximately 6 mM putrescine, 5 mM spermidine, and 3 mM spermine when cultured in the presence or absence of putrescine. Neither the transport of putrescine and spermidine by the rickettsiae nor a measurable rickettsial ornithine decarboxylase activity could be demonstrated. However, we demonstrated the de novo synthesis of polyamines from arginine by the rickettsiae. Arginine decarboxylase activity (29 pmol of 14CO2 released per h per 10(8) rickettsiae) was measured in the rickettsiae growing within their host cell. A markedly lower level of this enzymatic activity was observed in cell extracts of R. prowazekii and could be completely inhibited with 1 mM difluoromethylarginine, an irreversible inhibitor of the enzyme. R. prowazekii failed to grow in C55.7 cells that had been cultured in the presence of 1 mM difluoromethylarginine. After rickettsiae were grown in C55.7 in the presence of labeled arginine, the specific activities of arginine in the host cell cytoplasm and polyamines in the rickettsiae were measured; these measurements indicated that 100% of the total polyamine content of R. prowazekii was derived from arginine. PMID:2120188

  13. 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

  14. 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

  15. Heavy Metal Induced Antibiotic Resistance in Bacterium LSJC7.

    PubMed

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

    2015-09-29

    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.

  16. 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...

  17. O-allyl decoration on alpha-glucan isolated from the haloalkaliphilic Halomonas pantelleriensis bacterium.

    PubMed

    Corsaro, Maria Michela; Gambacorta, Agata; Lanzetta, Rosa; Nicolaus, Barbara; Pieretti, Giuseppina; Romano, Ida; Parrilli, Michelangelo

    2007-07-01

    An alpha-glucan containing the unprecedented peculiar O-allyl substituent was isolated from the haloalkaliphilic Gram-negative Halomonas pantelleriensis bacterium. Its dextran-like structure was deduced from chemical degradative and spectroscopic methods.

  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. 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

  20. 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...

  1. 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...

  2. Complete Genome Sequence of the p-Nitrophenol-Degrading Bacterium Pseudomonas putida DLL-E4

    PubMed Central

    Hu, Xiaojun; Wang, Jue; Wang, Fei; Chen, Qiongzhen; Huang, Yan

    2014-01-01

    The first complete genome sequence of a p-nitrophenol (PNP)-degrading bacterium is reported here. Pseudomonas putida DLL-E4, a Gram-negative bacterium isolated from methyl-parathion-polluted soil, can utilize PNP as the sole carbon and nitrogen source. P. putida DLL-E4 has a 6,484,062 bp circular chromosome that contains 5,894 genes, with a G+C content of 62.46%. PMID:24948765

  3. Draft Genome Sequence of a Dyella-Like Bacterium from the Planthopper Hyalesthes obsoletus.

    PubMed

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

    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

  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. Effect of alginic acid decomposing bacterium on the growth of Laminaria japonica (Phaeophyceae).

    PubMed

    Wang, You; Tang, Xue-Xi; Yang, Zhen; Yu, Zhi-Ming

    2006-01-01

    We collected the diseased blades of Laminaria japonica from Yantai Sea Farm from October to December 2002, and the alginic acid decomposing bacterium on the diseased blade was isolated and purified, and was identified as Alteromonas espejiana. This bacterium was applied as the causative pathogen to infect the blades of L. japonica under laboratory conditions. The aim of the present study was to identify the effects of the bacterium on the growth of L. japonica, and to find the possibly effective mechanism. Results showed that: (1) The blades of L. japonica exhibited symptoms of lesion, bleaching and deterioration when infected by the bacterium, and their growth and photosynthesis were dramatically suppressed. At the same time, the reactive oxygen species (ROS) generation enhanced obviously, and the relative membrane permeability increased significantly. The contents of malonaldehyde (MDA) and free fatty acid in the microsomol membrane greatly elevated, but the phospholipid content decreased. Result suggested an obvious peroxidation and deesterrification in the blades of L. japonica when infected by the bacterium. (2) The simultaneous assay on the antioxidant enzyme activities demonstrated that superoxide dismutase (SOD) and catalase (CAT) increased greatly when infected by the bacterium, but glutathione peroxidase (Gpx) and ascorbate peroxidase (APX) did not exhibit active responses to the bacterium throughout the experiment. (3) The histomorphological observations gave a distinctive evidence of the severity of the lesions as well as the relative abundance in the bacterial population on the blades after infection. The bacterium firstly invaded into the endodermis of L. japonica and gathered around there, and then resulted in the membrane damage, cells corruption and ultimately, the death of L. japonica.

  6. 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.

  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. Respiratory-driven Na+ electrical potential in the bacterium Vitreoscilla.

    PubMed

    Efiok, B J; Webster, D A

    1990-05-15

    Vitreoscilla is a Gram-negative bacterium with unique respiratory physiology in which Na+ was implicated as a coupling cation for the generation of a transmembrane electrical gradient (delta psi). Thus, cells respiring in the presence of 110 mM Na+ generated a delta psi of -142 mV compared to only -42 and -56 mV for Li+ and choline, respectively, and even the -42 and -56 mV were insensitive to the protonophore 3,5-di-tert-butyl-4-hydroxybenzaldehyde (DTHB). The kinetics of delta psi formation and collapse correlated well with the kinetics of Na+ fluxes but not with those of H+ fluxes. Cyanide inhibited respiration, Na+ extrusion, and delta psi formation 81% or more, indicating that delta psi formation and Na+ extrusion were coupled to respiration. Experiments were performed to distinguish among three possible transport systems for this coupling: (1) a Na(+)-transporting ATPase; (2) an electrogenic Na+/H+ antiport system; (3) a primary Na+ pump directly driven by the free energy of electron transport. DCCD and arsenate decreased cellular ATP up to 86% but had no effect on delta psi, evidence against a Na(+)-transporting ATPase. Low concentrations of DTHB had no effect on delta psi; high concentrations transiently collapsed delta psi, but led to a stimulation of Na+ extrusion, the opposite of that expected for a Na+/H+ antiport system. Potassium ion, which collapses delta psi, also stimulated Na+ extrusion. The experimental evidence is against Na+ extrusion by mechanisms 1 and 2 and supports the existence of a respiratory-driven primary Na+ pump for generating delta psi in Vitreoscilla. PMID:2372555

  9. Sulfobacillus thermotolerans sp. nov., a thermotolerant, chemolithotrophic bacterium.

    PubMed

    Bogdanova, Tat'yana I; Tsaplina, Iraida A; Kondrat'eva, Tamara F; Duda, Vitalii I; Suzina, Natalya E; Melamud, Vitalii S; Tourova, Tat'yana P; Karavaiko, Grigorii I

    2006-05-01

    A thermotolerant, Gram-positive, aerobic, endospore-forming, acidophilic bacterium (strain Kr1T) was isolated from the pulp of a gold-containing sulfide concentrate processed at 40 degrees C in a gold-recovery plant (Siberia). Cells of strain Kr1(T) were straight to slightly curved rods, 0.8-1.2 microm in diameter and 1.5-4.5 microm in length. Strain Kr1T formed spherical and oval, refractile, subterminally located endospores. The temperature range for growth was 20-60 degrees C, with an optimum at 40 degrees C. The pH range for growth on medium containing ferrous iron was 1.2-2.4, with an optimum at pH 2.0; the pH range for growth on medium containing S0 was 2.0-5.0, with an optimum at pH 2.5. Strain Kr1T was mixotrophic, oxidizing ferrous iron, S0, tetrathionate or sulfide minerals as energy sources in the presence of 0.02 % yeast extract or other organic substrates. The G+C content of the DNA of strain Kr1T was 48.2+/-0.5 mol%. Strain Kr1T showed a low level of DNA-DNA reassociation with the known Sulfobacillus species (11-44 %). 16S rRNA gene sequence analysis revealed that Kr1T formed a separate phylogenetic group with a high degree of similarity between the nucleotide sequences (98.3-99.6 %) and 100 % bootstrap support within the phylogenetic Sulfobacillus cluster. On the basis of its physiological properties and the results of phylogenetic analyses, strain Kr1T can be affiliated to a novel species of the genus Sulfobacillus, for which the name Sulfobacillus thermotolerans sp. nov. is proposed. The type strain is Kr1T (=VKM B-2339T=DSM 17362T).

  10. Energy coupling to K+ transport in a marine bacterium.

    PubMed

    Sedgwick, E G; MacLeod, R A

    1980-10-01

    Cells of the marine bacterium Alteromonas haloplanktis 214 ATCC 19855 (previously referred to as marine pseudomonad B-16) were depleted of K+ by washing with 0.1 M MgSO4. Washing with 0.05 M MgSO4 lowered the Vmax for K+ transport compared with washing with 0.1 M with 0.05 but did not change the Km, while washing with lower concentrations of MgSO4 caused loss of ultraviolet-absorbing material from the cells. K+ uptake was a strictly aerobic process and was accompanied by proton release. When an anaerobic suspension of cells was added to incubation mixtures containing increasing amounts of O2, intracellular ATP concentrations increased as the O2 concentration increased and reached near maximum values before K+ transport began. The O2 concentration initiating K+ transport caused transport to proceed at its maximum rate. For these experiments A. haloplanktis was depleted of ATP by incubating under anaerobic conditions. Incubating with either N,N'-dicyclohexyl carbodiimide (DCCD) or arsenate failed to deplete intact cells of ATP or prevent K+ transport. The inhibitory activity of DCCD for ATPase in membrane preparations was higher at 5 mM than at other MgSO4 concentrations and increased with time. Cyanide and the uncoupling agents tetrachloro-salicylanide (TCS) and carbonylcyanide p-trifluoromethoxyphenylhydrazone (FCCP) prevented K+ uptake while TSC and FCCP though not cyanide caused K+ to be released from K+-containing cells. It is concluded that the driving force for K+ transport in these cells is likely to be the membrane potential and that K+ transport may be gated.

  11. 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

  12. Trace Metal Sequestration by the Manganese Oxidizing Bacterium Pseudomonas putida

    NASA Astrophysics Data System (ADS)

    Toner, B.; Manceau, A.; Marcus, M. A.; Sposito, G.

    2002-12-01

    Bacterial cells are an important source of chemically reactive surfaces in freshwater and soil environments. Pseudomonas putida strain MnB1 cells, like many gram negative bacteria, present an outer membrane studded with phosphate groups and carbohydrates as well as a billowing biofilm of extracellular polysaccharides to the surrounding microenvironment. The cell outer membrane and the biofilm possess functional groups that complex trace metals. During certain growth phases P. putida is also a manganese oxidizing bacterium, causing the cells to coat themselves in Mn(IV) oxide. Therefore, in addition to the cell outer membrane and associated biofilm, trace metals may sorb to the biogenic Mn oxide. To explore the relative contributions to trace metal sorption by the bacterial cells and biogenic Mn oxide, zinc and nickel were added to suspensions of bacterial cells with three different conditions: cells in the absence of Mn, cells in the process of Mn oxidation and cells with preformed biogenic Mn oxide. Adsorption isotherms were measured to quantify Zn and Ni sorption to P. putida in the presence and absence of biogenic Mn oxide. Zinc and Ni K-edge EXAFS spectra were measured to determine how and where the metals were binding to the bacterial cells and biogenic Mn oxide. The Zn and Ni adsorption isotherms exhibited two plateaus. The metal complexation was dependent on concentration with Zn having a higher affinity for phosphate and Ni for carboxyl functional groups. The preformed biogenic Mn oxide has high affinity for Zn and Ni and the bacterial surface contributed little to metal removal from solution under these conditions. However, if the metal is present in solution while Mn oxidation is occurring the bacterial cell surface influences greatly the overall removal of metal. Manganese oxidizing bacteria such as P. putida contribute to environmental metal sequestration by catalyzing the production of Mn oxide minerals, and the bacterial cells are themselves reactive

  13. 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).

  14. Phenotypic Variation in the Plant Pathogenic Bacterium Acidovorax citrulli

    PubMed Central

    Shrestha, Ram Kumar; Rosenberg, Tally; Makarovsky, Daria; Eckshtain-Levi, Noam; Zelinger, Einat; Kopelowitz, June; Sikorski, Johannes; Burdman, Saul

    2013-01-01

    Acidovorax citrulli causes bacterial fruit blotch (BFB) of cucurbits, a disease that threatens the cucurbit industry worldwide. Despite the economic importance of BFB, little is known about pathogenicity and fitness strategies of the bacterium. We have observed the phenomenon of phenotypic variation in A. citrulli. Here we report the characterization of phenotypic variants (PVs) of two strains, M6 and 7a1, isolated from melon and watermelon, respectively. Phenotypic variation was observed following growth in rich medium, as well as upon isolation of bacteria from inoculated plants or exposure to several stresses, including heat, salt and acidic conditions. When grown on nutrient agar, all PV colonies possessed a translucent appearance, in contrast to parental strain colonies that were opaque. After 72 h, PV colonies were bigger than parental colonies, and had a fuzzy appearance relative to parental strain colonies that are relatively smooth. A. citrulli colonies are generally surrounded by haloes detectable by the naked eye. These haloes are formed by type IV pilus (T4P)-mediated twitching motility that occurs at the edge of the colony. No twitching haloes could be detected around colonies of both M6 and 7a1 PVs, and microscopy observations confirmed that indeed the PVs did not perform twitching motility. In agreement with these results, transmission electron microscopy revealed that M6 and 7a1 PVs do not produce T4P under tested conditions. PVs also differed from their parental strain in swimming motility and biofilm formation, and interestingly, all assessed variants were less virulent than their corresponding parental strains in seed transmission assays. Slight alterations could be detected in some DNA fingerprinting profiles of 7a1 variants relative to the parental strain, while no differences at all could be seen among M6 variants and parental strain, suggesting that, at least in the latter, phenotypic variation is mediated by slight genetic and/or epigenetic

  15. Idiomarina maris sp. nov., a marine bacterium isolated from sediment.

    PubMed

    Zhang, Yan-Jiao; Zhang, Xi-Ying; Zhao, Hui-Lin; Zhou, Ming-Yang; Li, Hui-Juan; Gao, Zhao-Ming; Chen, Xiu-Lan; Dang, Hong-Yue; Zhang, Yu-Zhong

    2012-02-01

    A protease-producing marine bacterium, designated CF12-14(T), was isolated from sediment of the South China Sea. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain CF12-14(T) formed a separate lineage within the genus Idiomarina (Gammaproteobacteria). The isolate showed the highest 16S rRNA gene sequence similarity with Idiomarina salinarum ISL-52(T) (94.7 %), Idiomarina seosinensis CL-SP19(T) (94.6 %) and other members of the genus Idiomarina (91.9-94.6 %). Cells were gram-negative, aerobic, flagellated, straight or slightly curved, and often formed buds and prosthecae. Strain CF12-14(T) grew at 4-42 °C (optimum 30-35 °C) and with 0.1-15 % (w/v) NaCl (optimum 2-3 %). The isolate reduced nitrate to nitrite and hydrolysed DNA, but did not produce acids from sugars. The predominant cellular fatty acids were iso-C(15 : 0) (27.4 %), iso-C(17 : 0) (16.0 %) and iso-C(17 : 1)ω9c (15.8 %). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major respiratory quinone was ubiquinone 8. The DNA G+C content was 50.4 mol%. The phylogenetic, phenotypic and chemotaxonomic data supported the conclusion that CF12-14(T) represents a novel species of the genus Idiomarina, for which the name Idiomarina maris sp. nov. is proposed. The type strain is CF12-14(T) ( = CCTCC AB 208166(T) = KACC 13974(T)).

  16. Bioconservation of deteriorated monumental calcarenite stone and identification of bacteria with carbonatogenic activity.

    PubMed

    Jroundi, Fadwa; Fernández-Vivas, Antonia; Rodriguez-Navarro, Carlos; Bedmar, Eulogio J; González-Muñoz, María Teresa

    2010-07-01

    The deterioration of the stone built and sculptural heritage has prompted the search and development of novel consolidation/protection treatments that can overcome the limitations of traditional ones. Attention has been drawn to bioconservation, particularly bacterial carbonatogenesis (i.e. bacterially induced calcium carbonate precipitation), as a new environmentally friendly effective conservation strategy, especially suitable for carbonate stones. Here, we study the effects of an in situ bacterial bioconsolidation treatment applied on porous limestone (calcarenite) in the sixteenth century San Jeronimo Monastery in Granada, Spain. The treatment consisted in the application of a nutritional solution (with and without Myxococcus xanthus inoculation) on decayed calcarenite stone blocks. The treatment promoted the development of heterotrophic bacteria able to induce carbonatogenesis. Both the consolidation effect of the treatment and the response of the culturable bacterial community present in the decayed stone were evaluated. A significant surface strengthening (consolidation) of the stone, without altering its surface appearance or inducing any detrimental side effect, was achieved upon application of the nutritional solution. The treatment efficacy was independent of the presence of M. xanthus (which is known as an effective carbonatogenic bacterium). The genetic diversity of 116 bacterial strains isolated from the stone, of which 113 strains showed carbonatogenic activity, was analysed by repetitive extragenic palindromic-polymerase chain reaction (REP-PCR) and 16S rRNA gene sequencing. The strains were distributed into 31 groups on the basis of their REP-PCR patterns, and a representative strain of each group was subjected to 16S rRNA gene sequencing. Analysis of these sequences showed that isolates belong to a wide variety of phylogenetic groups being closely related to species of 15 genera within the Proteobacteria, Firmicutes and the Actinobacteria. This

  17. Contrasts between subsurface microbial communities and their metabolic adaptation to polycyclic aromatic hydrocarbons at a forested and an urban coal-tar disposal site.

    PubMed

    Madsen, E L; Winding, A; Malachowsky, K; Thomas, C T; Ghiorse, W C

    1992-09-01

    The abundance and distribution of microorganisms and their potential for mineralizing polycyclic aromatic hydrocarbons (PAHs) were measured in subsurface sediment samples at two geographically separate buried coal-tar sites. At a relatively undisturbed forested site in the northeastern United States, metabolic adaptation to the PAHs was evident: Radiolabeled naphthalene and phenanthrene were converted to (14)CO2 in core material from inside but not outside a plume of groundwater contamination. However, at the urban site in the midwestern United States these PAHs were mineralized in sediments from both contaminated and uncontaminated boreholes. Thus, clear qualitative evidence showing an adaptational response by the subsurface microbial community was not obtained at the urban site. Instead, subtler clues suggesting metabolic adaptation by subsurface microorganisms from the urban site were discerned by comparing lag periods and extents of (14)CO2 production from radiolabeled PAHs added to samples from contaminated and uncontaminated boreholes. Despite slightly higher PAH mineralization activity in contaminated borehole samples, p-hydroxybenzoate was mineralized equally in all samples from the urban site regardless of location. No striking trends in the abundances of actinomycetes, fungi, and either viable or total bacteria were encountered. However, colonies of the soil bacterium, Bacillus mycoides, were detected on enumeration plates of several samples from unsaturated and saturated zones in both urban boreholes. Furthermore, other common soil bacteria, Myxococcus xanthus and Chromobacterium violaceum, were identified in samples from the uncontaminated urban borehole. The occurrence of bacteria usually restricted to surface soil, combined with the observation of fragments of building materials in many of the core samples, suggested that past excavation and backfilling operations may have caused mixing of surface soil with subsurface materials at the urban site. We

  18. Strict specificity for high-mannose type N-glycans and primary structure of a red alga Eucheuma serra lectin.

    PubMed

    Hori, Kanji; Sato, Yuichiro; Ito, Kaori; Fujiwara, Yoshifumi; Iwamoto, Yasumasa; Makino, Hiroyuki; Kawakubo, Akihiro

    2007-05-01

    We have elucidated the carbohydrate-binding profile of a non-monosaccharide-binding lectin named Eucheuma serra lectin (ESA)-2 from the red alga Eucheuma serra using a lectin-immobilized column and a centrifugal ultrafiltration-high performance liquid chromatography method with a variety of fluorescence-labeled oligosaccharides. In both methods, ESA-2 exclusively bound with high-mannose type (HM) N-glycans, but not with any of other N-glycans including complex type, hybrid type and core pentasaccharides, and oligosaccharides from glycolipids. These findings indicate that ESA-2 recognizes the branched oligomannosides of the N-glycans. However, ESA-2 did not bind with any of the free oligomannoses examined that are constituents of the branched oligomannosides implying that the portion of the core N-acetyl-D-glucosamine (GlcNAc) residue(s) of the N-glycans is also essential for binding. Thus, the algal lectin was strictly specific for HM N-glycans and recognized the extended carbohydrate structure with a minimum size of the pentasaccharide, Man(alpha1-3)Man(alpha1-6)Man(beta1-4)GlcNAc(beta1-4) GlcNAc. Kinetic analysis of binding with a HM heptasaccharide (M5) showed that ESA-2 has four carbohydrate-binding sites per polypeptide with a high association constant of 1.6x10(8) M-1. Sequence analysis, by a combination of Edman degradation and mass analyses of the intact protein and of peptides produced by its enzymic digestions, showed that ESA-2 is composed of 268 amino acids (molecular weight 27950) with four tandemly repeated domains of 67 amino acids. The number of repeats coincided with the number of carbohydrate-binding sites in the monomeric molecule. Surprisingly, the marine algal lectin was homologous to hemagglutinin from the soil bacterium Myxococcus xanthus. PMID:17259190

  19. Sodium-coupled ATP synthesis in the bacterium Vitreoscilla.

    PubMed

    Efiok, B J; Webster, D A

    1992-01-01

    The bacterium Vitreoscilla generates an electrical potential gradient due to sodium ion (delta psi Na+) across its membrane via respiratory-driven primary Na+ pump(s). The role of the delta psi Na+ as a driving force for ATP synthesis was, therefore, investigated. In respiring starved cells pulsed with 100 mM external Na+ [( Na+]o) there was a 167% net increase in cellular ATP concentration over basal levels compared with 0, 56, 78, and 78% for no addition, choline, Li+, and K+ controls, respectively. Doubling the [Na+]o to 200 mM boosted the net increase to 244% but a similar doubling of the choline caused only an increase to 78%. When the initial condition was intracellular Na+ ([Na+]i) = [Na+]o = 100 mM, there was a 94% net increase in cellular ATP compared with only 18 and 11% for Li+ and K+ controls, respectively, indicating that Nai+ may be the only cation tested that the cells extruded to generate the electrochemical gradient required to drive ATP synthesis. The Na(+)-dependent ATP synthesis was inhibited completely by monensin (12 microM), but only transiently by the protonophore 3,5-di-tert-butyl-4-hydroxybenzaldehyde (100 microM), further evidence that the Na+ gradient and not a H+ gradient was driving the ATP synthesis. ATP synthesis in response to an artificially imposed H+ gradient (delta pH approximately 3) in the absence of an added cation, or in the presence of Li+, K+, or choline, yielded similar delta ATP/delta pH ratios of 0.98-1.22. In the presence of Na+, however, this ratio dropped to 0.23, indicating that Na+ inhibited H(+)-coupling to ATP synthesis and possibly that H+ and Na+ coupling to ATP synthesis share a common catalyst. The above evidence adds to previous findings that under normal growth conditions Na+ is probably the main coupling cation for ATP synthesis in Vitreoscilla. PMID:1309288

  20. A plant growth-promoting bacterium that decreases nickel toxicity in seedlings

    SciTech Connect

    Burd, G.I.; Dixon, D.G.; Glick, B.R.

    1998-10-01

    A plant growth-promoting bacterium, Kluyvera ascorbata SUD165, that contained high levels of heavy metals was isolated from soil collected near Sudbury, Ontario, Canada. The bacterium was resistant to the toxic effects of Ni{sup 2+}, Pb{sup 2+}, Zn{sup 2+}, and CrO{sub 4}{sup {minus}}, produced a siderophore(s), and displayed 1-aminocyclopropane-1-carboxylic acid deaminase activity. Canola seeds inoculated with this bacterium and then grown under gnotobiotic conditions in the presence of high concentrations of nickel chloride were partially protected against nickel toxicity. In addition, protection by the bacterium against nickel toxicity was evident in pot experiments with canola and tomato seeds. The presence of K. ascorbata SUD165 had no measurable influence on the amount of nickel accumulated per milligram (dry weight) of either roots or shoots of canola plants. Therefore, the bacterial plant growth-promoting effect in the presence of nickel was probably not attributable to the reduction of nickel uptake by seedlings. Rather, it may reflect the ability of the bacterium to lower the level of stress ethylene induced by the nickel.

  1. 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.

  2. 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.

  3. 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

  4. Investigations of Iron Minerals Formed by Dissimilatory Alkaliphilic Bacterium with 57Fe Mössbauer Spectroscopy

    NASA Astrophysics Data System (ADS)

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

    2010-07-01

    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 CH3COO- as an electron donor. Mössbauer 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 γ-bebam.

  5. 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.

  6. 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.

  7. Isolation from the Sorghum bicolor Mycorrhizosphere of a Bacterium Compatible with Arbuscular Mycorrhiza Development and Antagonistic towards Soilborne Fungal Pathogens

    PubMed Central

    Budi, S. W.; van Tuinen, D.; Martinotti, G.; Gianinazzi, S.

    1999-01-01

    A gram-positive bacterium with antagonistic activity towards soilborne fungal pathogens has been isolated from the mycorrhizosphere of Sorghum bicolor inoculated with Glomus mosseae. It has been identified as Paenibacillus sp. strain B2 based on its analytical profile index and on 16S ribosomal DNA analysis. Besides having antagonistic activity, this bacterium stimulates mycorrhization. PMID:10543835

  8. 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

  9. 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

  10. 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

  11. Classification of the Legionnaires' disease bacterium: Legionella pneumophila, genus novum, species nova, of the family Legionellaceae, familia nova.

    PubMed

    Brenner, D J; Steigerwalt, A G; McDade, J E

    1979-04-01

    Deoxyribonucleic acid (DNA) relatedness was used to classify strains of the Legionnaires' disease (LD) bacterium. These DNA comparisons showed that all strains of the LD bacterium were members of the same species. Included were strains isolated from the environment and strains with three different O-antigens. The DNA from the LD bacterium was not significantly related to DNA from any other group of bacteria that was tested. Biochemical data, growth characteristics, and guanine-plus-cytosine ratios were used to rule out the possibility that the LD bacterium was significantly related to members of genera whose DNA was not tested. In view of these data we propose that the LD bacterium be named Legionella pneumophila species nova, the type species of Legionella, genus novum. The type strain of L. pneumophila is Philadelphia 1.

  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

    2014-08-28

    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.

  13. 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.

  14. 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

  15. 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

  16. Draft Genome Sequence of the Algicidal Bacterium Mangrovimonas yunxiaonensis Strain LY01

    PubMed Central

    Li, Yi; Zhu, Hong; Li, Chongping; Zhang, Huajun; Chen, Zhangran; Zheng, Wei

    2014-01-01

    Mangrovimonas yunxiaonensis LY01, a novel bacterium isolated from mangrove sediment, showed high algicidal effects on harmful algal blooms of Alexandrium tamarense. Here, we present the first draft genome sequence of this strain to further understanding of the functional genes related to algicidal activity. PMID:25428978

  17. 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.

  18. 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 ...

  19. 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

  20. 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

  1. 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

  2. Complete genome sequence of the cellulase-producing bacterium Clavibacter michiganensis PF008.

    PubMed

    Bae, Chungyun; Oh, Eom-Ji; Lee, Han-Beoyl; Kim, Byung-Yong; Oh, Chang-Sik

    2015-11-20

    The Gram-positive Actinobacterium Clavibacter michiganensis strain PF008 produces a cellulase of biotechnological interest, which is used for degradation of cellulose, a major component of plant cell walls. Here we report the complete genome sequence of this bacterium for better understanding of cellulase production and its virulence mechanism.

  3. 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.

  4. 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...

  5. 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

  6. 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

  7. 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

  8. 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.

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

    SciTech Connect

    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.

  10. Draft Genome Sequence of the Novel Agar-Digesting Marine Bacterium HQM9▿

    PubMed Central

    Du, Zongjun; Zhang, Zhewen; Miao, Tingting; Wu, Jiayan; Lü, Guoqiang; Yu, Jun; Xiao, Jingfa; Chen, Guanjun

    2011-01-01

    Strain HQM9, an aerobic, rod-shaped marine bacterium from red algae, can produce agarases and liquefy solid plating media efficiently when agar is used as a coagulant. Here we report the draft genome sequence and the initial findings from a preliminary analysis of strain HQM9, which should be a novel species of Flavobacteriaceae. PMID:21725015

  11. Bacterium induces cryptic meroterpenoid pathway in the pathogenic fungus Aspergillus fumigatus.

    PubMed

    König, Claudia C; Scherlach, Kirstin; Schroeckh, Volker; Horn, Fabian; Nietzsche, Sandor; Brakhage, Axel A; Hertweck, Christian

    2013-05-27

    Stimulating encounter: The intimate, physical interaction between the soil-derived bacterium Streptomyces rapamycinicus and the human pathogenic fungus Aspergillus fumigatus led to the activation of an otherwise silent polyketide synthase (PKS) gene cluster coding for an unusual prenylated polyphenol (fumicycline A). The meroterpenoid pathway is regulated by a pathway-specific activator gene as well as by epigenetic factors.

  12. Complete Genome Sequence of the Acetogenic Bacterium Moorella thermoacetica DSM 2955T

    PubMed Central

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

    2015-01-01

    Here, we report the complete genome sequence of Moorella thermoacetica DSM 2955T, an acetogenic bacterium, which uses the Wood–Ljungdahl pathway for reduction of H2 + CO2 or CO. The genome consists of a single circular chromosome (2.62 Mb). PMID:26450730

  13. Draft Genome Sequence of the Moderately Halophilic Bacterium Pseudoalteromonas ruthenica Strain CP76.

    PubMed

    de la Haba, Rafael R; Sánchez-Porro, Cristina; León, María José; Papke, R Thane; Ventosa, Antonio

    2013-05-23

    Pseudoalteromonas ruthenica strain CP76, isolated from a saltern in Spain, is a moderately halophilic bacterium belonging to the Gammaproteobacteria. Here we report the draft genome sequence, which consists of a 4.0-Mb chromosome, of this strain, which is able to produce the extracellular enzyme haloprotease CPI.

  14. 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

  15. 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

  16. 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

  17. 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

  18. Transcriptome analysis of the rhizosphere bacterium Azospirillum brasilense reveals an extensive auxin response.

    PubMed

    Van Puyvelde, Sandra; Cloots, Lore; Engelen, Kristof; Das, Frederik; Marchal, Kathleen; Vanderleyden, Jos; Spaepen, Stijn

    2011-05-01

    The rhizosphere bacterium Azospirillum brasilense produces the auxin indole-3-acetic acid (IAA) through the indole-3-pyruvate pathway. As we previously demonstrated that transcription of the indole-3-pyruvate decarboxylase (ipdC) gene is positively regulated by IAA, produced by A. brasilense itself or added exogenously, we performed a microarray analysis to study the overall effects of IAA on the transcriptome of A. brasilense. The transcriptomes of A. brasilense wild-type and the ipdC knockout mutant, both cultured in the absence and presence of exogenously added IAA, were compared.Interfering with the IAA biosynthesis/homeostasis in A. brasilense through inactivation of the ipdC gene or IAA addition results in much broader transcriptional changes than anticipated. Based on the multitude of changes observed by comparing the different transcriptomes, we can conclude that IAA is a signaling molecule in A. brasilense. It appears that the bacterium, when exposed to IAA, adapts itself to the plant rhizosphere, by changing its arsenal of transport proteins and cell surface proteins. A striking example of adaptation to IAA exposure, as happens in the rhizosphere, is the upregulation of a type VI secretion system (T6SS) in the presence of IAA. The T6SS is described as specifically involved in bacterium-eukaryotic host interactions. Additionally, many transcription factors show an altered regulation as well, indicating that the regulatory machinery of the bacterium is changing.

  19. 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.

  20. Mechanisms of Stress Resistance and Gene Regulation in the Radioresistant Bacterium Deinococcus radiodurans.

    PubMed

    Agapov, A A; Kulbachinskiy, A V

    2015-10-01

    The bacterium Deinococcus radiodurans reveals extraordinary resistance to ionizing radiation, oxidative stress, desiccation, and other damaging conditions. In this review, we consider the main molecular mechanisms underlying such resistance, including the action of specific DNA repair and antioxidation systems, and transcription regulation during the anti-stress response.

  1. 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

  2. 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

  3. 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

  4. Complete genome sequence of Pandoraea thiooxydans DSM 25325(T), a thiosulfate-oxidizing bacterium.

    PubMed

    Yong, Delicia; Ee, Robson; Lim, Yan-Lue; Yu, Choo-Yee; Ang, Geik-Yong; How, Kah-Yan; Tee, Kok-Keng; Yin, Wai-Fong; Chan, Kok-Gan

    2016-01-10

    Pandoraea thiooxydans DSM 25325(T) is a thiosulfate-oxidizing bacterium isolated from rhizosphere soils of a sesame plant. Here, we present the first complete genome of P. thiooxydans DSM 25325(T). Several genes involved in thiosulfate oxidation and biodegradation of aromatic compounds were identified.

  5. Isolation of Laribacter hongkongensis, a novel bacterium associated with gastroenteritis, from Chinese tiger frog.

    PubMed

    Lau, Susanna K P; Lee, Leo C K; Fan, Rachel Y Y; Teng, Jade L L; Tse, Cindy W S; Woo, Patrick C Y; Yuen, Kwok-Yung

    2009-01-31

    Laribacter hongkongensis is a recently discovered novel bacterium associated with community-acquired gastroenteritis. Although the bacterium has been isolated from freshwater fish and natural freshwater environments, it is not known if other freshwater animals could also be a source of L. hongkongensis. In a surveillance study on freshwater food animals (other than fish) in Hong Kong, L. hongkongensis was isolated from eight of 10 Chinese tiger frogs (Hoplobatrachus chinensis), a widespread frog species commonly consumed in China and southeast Asia. The large intestine was the site with the highest recovery rate, followed by the small intestine and stomach. None of the 30 Malaysian prawns, 20 pieces of sand shrimp, 20 Chinese mystery snails or 10 Chinese soft-shelled turtles was found to harbor the bacterium. Among the eight positive frogs, a total of 26 isolates of L. hongkongensis, confirmed by phenotypic tests and PCR, were obtained. As with human, freshwater fish and natural water isolates, a heterogeneous population of L. hongkongensis in frogs was identified by pulsed-field gel electrophoresis, with 6 different patterns among the 26 isolates and a single frog often carrying different strains. The present report represents the first to describe the isolation of L. hongkongensis from amphibians. The high isolation rate and genetic heterogeneity of L. hongkongensis among the Chinese tiger frogs suggested that these animals are also natural reservoir for the bacterium. Caution should be exercised in handling and cooking these frogs. PMID:19033083

  6. 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

  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. Genome sequence of Citrobacter sp. strain A1, a dye-degrading bacterium.

    PubMed

    Chan, Giek Far; Gan, Han Ming; Rashid, Noor Aini Abdul

    2012-10-01

    Citrobacter sp. strain A1, isolated from a sewage oxidation pond, is a facultative aerobe and mesophilic dye-degrading bacterium. This organism degrades azo dyes efficiently via azo reduction and desulfonation, followed by the successive biotransformation of dye intermediates under an aerobic environment. Here we report the draft genome sequence of Citrobacter sp. A1.

  9. Genome sequence of Pedobacter arcticus sp. nov., a sea ice bacterium isolated from tundra soil.

    PubMed

    Yin, Ye; Yue, Guidong; Gao, Qiang; Wang, Zhiyong; Peng, Fang; Fang, Chengxiang; Yang, Xu; Pan, Li

    2012-12-01

    Pedobacter arcticus sp. nov. was originally isolated from tundra soil collected from Ny-Ålesund, in the Arctic region of Norway. It is a Gram-negative bacterium which shows bleb-shaped appendages on the cell surface. Here, we report the draft annotated genome sequence of Pedobacter arcticus sp. nov., which belongs to the genus Pedobacter.

  10. Periodic reversal of direction allows Myxobacteria to swarm

    PubMed Central

    Wu, Yilin; Kaiser, A. Dale; Jiang, Yi; Alber, Mark S.

    2009-01-01

    Many bacteria can rapidly traverse surfaces from which they are extracting nutrient for growth. They generate flat, spreading colonies, called swarms because they resemble swarms of insects. We seek to understand how members of any dense swarm spread efficiently while being able to perceive and interfere minimally with the motion of others. To this end, we investigate swarms of the myxobacterium, Myxococcus xanthus. Individual M. xanthus cells are elongated; they always move in the direction of their long axis; and they are in constant motion, repeatedly touching each other. Remarkably, they regularly reverse their gliding directions. We have constructed a detailed cell- and behavior-based computational model of M. xanthus swarming that allows the organization of cells to be computed. By using the model, we are able to show that reversals of gliding direction are essential for swarming and that reversals increase the outflow of cells across the edge of the swarm. Cells at the swarm edge gain maximum exposure to nutrient and oxygen. We also find that the reversal period predicted to maximize the outflow of cells is the same (within the errors of measurement) as the period observed in experiments with normal M. xanthus cells. This coincidence suggests that the circuit regulating reversals evolved to its current sensitivity under selection for growth achieved by swarming. Finally, we observe that, with time, reversals increase the cell alignment, and generate clusters of parallel cells. PMID:19164578

  11. The social behavior of myxobacteria.

    PubMed

    Muñoz-Dorado, J; Arias, J M

    1995-12-01

    Myxobacteria are social microorganisms that undergo a spectacular cell cycle. Under starvation conditions, cells aggregate to certain points originating macroscopic fruiting bodies, inside which cells differentiate into myxospores. To accomplish this developmental cycle, cells must communicate. The signals that cells exchange during development as well as the signal transduction systems used by myxobacteria have been intensively studied during the last years. A family of eukaryotic-like protein serine/threonine kinases has been identified in Myxococcus xanthus, indicating that signal transduction systems similar to those used by eukaryotic cells may also function in myxobacteria.

  12. Correlated cryogenic photoactivated localization microscopy and cryo-electron tomography.

    PubMed

    Chang, Yi-Wei; Chen, Songye; Tocheva, Elitza I; Treuner-Lange, Anke; Löbach, Stephanie; Søgaard-Andersen, Lotte; Jensen, Grant J

    2014-07-01

    Cryo-electron tomography (CET) produces three-dimensional images of cells in a near-native state at macromolecular resolution, but identifying structures of interest can be challenging. Here we describe a correlated cryo-PALM (photoactivated localization microscopy)-CET method for localizing objects within cryo-tomograms to beyond the diffraction limit of the light microscope. Using cryo-PALM-CET, we identified multiple and new conformations of the dynamic type VI secretion system in the crowded interior of Myxococcus xanthus.

  13. Continuum modeling of clustering of myxobacteria

    PubMed Central

    Harvey, Cameron W.; Alber, Mark; Tsimring, Lev S.; Aranson, Igor S.

    2013-01-01

    In this paper we develop a continuum theory of clustering in ensembles of self-propelled inelastically colliding rods with applications to collective dynamics of common gliding bacteria Myxococcus Xanthus. A multiphase hydrodynamic model that couples densities of oriented and isotropic phases is described. This model is used for the analysis of an instability that leads to spontaneous formation of directionally moving dense clusters within initially dilute isotropic “gas” of myxobacteria. Numerical simulations of this model confirm the existence of stationary dense moving clusters and also elucidate the properties of their collisions. The results are shown to be in a qualitative agreement with experiments. PMID:23712128

  14. Melanin from the nitrogen-fixing bacterium Azotobacter chroococcum: a spectroscopic characterization.

    PubMed

    Banerjee, Aulie; Supakar, Subhrangshu; 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 (13)C 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.

  15. 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

  16. Helicobacter hepaticus sp. nov., a microaerophilic bacterium isolated from livers and intestinal mucosal scrapings from mice.

    PubMed Central

    Fox, J G; Dewhirst, F E; Tully, J G; Paster, B J; Yan, L; Taylor, N S; Collins, M J; Gorelick, P L; Ward, J M

    1994-01-01

    A bacterium with a spiral shape and bipolar, single, sheathed flagella was isolated from the livers of mice with active, chronic hepatitis. The bacteria also colonized the cecal and colonic mucosae of mice. The bacterium grew at 37 degrees C under microaerophilic and anaerobic conditions, rapidly hydrolyzed urea, was catalase and oxidase positive, reduced nitrate to nitrite, and was resistant to cephalothin metronidazole. On the basis of 16S rRNA gene sequence analysis, the organism was classified as a novel helicobacter, Helicobacter hepaticus. This new helicobacter, like two other murine Helicobacter species, H. muridarum and "H. rappini," is an efficient colonizer of the gastrointestinal tract, but in addition, it has the pathogenic potential to elicit persistent hepatitis in mice. Images PMID:8051250

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

    PubMed

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

    2015-02-13

    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.

  18. 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.

  19. The bacterium Xenorhabdus nematophila inhibits phospholipases A2 from insect, prokaryote, and vertebrate sources

    NASA Astrophysics Data System (ADS)

    Park, Youngjin; Kim, Yonggyun; Stanley, David

    The bacterium, Xenorhabdus nematophila, is a virulent insect pathogen. Part of its pathogenicity is due to impairing cellular immunity by blocking biosynthesis of eicosanoids, the major recognized signal transduction system in insect cellular immunity. X. nematophila inhibits the first step in eicosanoid biosynthesis, phospholipase A2 (PLA2). Here we report that the bacterium inhibits PLA2 from two insect immune tissues, hemocytes and fat body, as well as PLA2s selected to represent a wide range of organisms, including prokaryotes, insects, reptiles, and mammals. Our finding on a bacterial inhibitor of PLA2 activity contributes new insight into the chemical ecology of microbe-host interactions, which usually involve actions rather than inhibitors of PLA2s.

  20. 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

  1. 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.

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

    PubMed

    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, Halanaerobiumhydrogeniformans, 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.

  3. 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

  4. 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.

  5. A partial proteome reference map of the wine lactic acid bacterium Oenococcus oeni ATCC BAA-1163.

    PubMed

    Mohedano, María de la Luz; Russo, Pasquale; de Los Ríos, Vivian; Capozzi, Vittorio; Fernández de Palencia, Pilar; Spano, Giuseppe; López, Paloma

    2014-02-26

    Oenococcus oeni is the main lactic acid bacterium that carries out the malolactic fermentation in virtually all red wines and in some white and sparkling wines. Oenococcus oeni possesses an array of metabolic activities that can modify the taste and aromatic properties of wine. There is, therefore, industrial interest in the proteins involved in these metabolic pathways and related transport systems of this bacterium. In this work, we report the characterization of the O. oeni ATCC BAA-1163 proteome. Total and membrane protein preparations from O. oeni were standardized and analysed by two-dimensional gel electrophoresis. Using tandem mass spectrometry, we identified 224 different spots corresponding to 152 unique proteins, which have been classified by their putative function and subjected to bioinformatics analysis.

  6. 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.

  7. 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

  8. 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

  9. 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+).

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

    PubMed

    Lim, Chee Kent; Penesyan, Anahit; Hassan, Karl A; Loper, Joyce E; Paulsen, Ian T

    2013-05-01

    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.

  11. Insights in Nanoparticle-Bacterium Interactions: New Frontiers to Bypass Bacterial Resistance to Antibiotics.

    PubMed

    Diab, Roudayna; Khameneh, Bahman; Joubert, Olivier; Duval, Raphael

    2015-01-01

    Nanotechnology has been revealed as a fundamental approach for antibiotics delivery. In this paper, recent findings demonstrating the superiority of nanocarried-antibiotics over "naked" ones and the ways by which nanoparticles can help to overwhelm bacterial drug resistance are reviewed. The second part of this paper sheds light on nanoparticle-bacterium interaction patterns. Finally, key factors affecting the effectiveness of nanoparticles interactions with bacteria are discussed.

  12. Permanent draft genome of acetaldehyde degradation bacterium, Shewanella sp. YQH10.

    PubMed

    Liu, Yang; Shang, Xiexie; Zeng, Runying

    2015-02-01

    Shewanella sp. YQH10 isolated from mangrove sediment, was a novel species of Shewanella, which has the ability to degrade acetaldehyde. Here, we present an annotated draft genome sequence of Shewanella sp. YQH10, which contains 4,215,794 bp with a G + C content of 48.1%. This information regarding the genetic basis of this bacterium can greatly advance our understanding of the physiology of this species.

  13. 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

  14. 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

  15. 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

  16. 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

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

    PubMed

    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

  18. 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

  19. 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.

  20. Degradation of p-nitrophenol by the phototrophic bacterium Rhodobacter capsulatus.

    PubMed

    Roldán, M D; Blasco, R; Caballero, F J; Castillo, F

    1998-01-01

    The phototrophic bacterium Rhodobacter capsulatus detoxified p-nitrophenol and 4-nitrocatechol. The bacterium tolerated moderate concentrations of p-nitrophenol (up to 0.5 mM) and degraded it under light at an optimal O2 pressure of 20 kPa. The bacterium did not metabolize the xenobiotic in the dark or under strictly anoxic conditions or high O2 pressure. Bacterial growth with acetate in the presence of p-nitrophenol took place with the simultaneous release of nonstoichiometric amounts of 4-nitrocatechol, which can also be degraded by the bacterium. Crude extracts from R. capsulatus produced 4-nitrocatechol from p-nitrophenol upon the addition of NAD(P)H, although at a very low rate. A constitutive catechol 1, 2-dioxygenase activity yielding cis,cis-muconate was also detected in crude extracts of R. capsulatus. Further degradation of 4-nitrocatechol included both nitrite- and CO2-releasing steps since: (1) a strain of R. capsulatus (B10) unable to assimilate nitrate and nitrite released nitrite into the medium when grown with p-nitrophenol or 4-nitrocatechol, and the nitrite concentration was stoichiometric with the 4-nitrocatechol degraded, and (2) cultures of R. capsulatus growing microaerobically produced low amounts of 14CO2 from radiolabeled p-nitrophenol. The radioactivity was also incorporated into cellular compounds from cells grown with uniformly labeled 14C-p-nitrophenol. From these results we concluded that the xenobiotic is used as a carbon source by R. capsulatus, but that only the strain able to assimilate nitrite (E1F1) can use p-nitrophenol as a nitrogen source.

  1. 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.

  2. 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

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

    PubMed

    Liu, Yang; Wang, Runping; Zeng, Runying

    2014-12-01

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

  4. 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

  5. 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

  6. 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.

  7. Identification of insertion sequence from a gamma-hexachlorocyclohexane degrading bacterium, Sphingomonas paucimobilis UT26.

    PubMed

    Miyauchi, Keisuke; Fukuda, Masao; Tsuda, Masataka; Takagi, Masamichi; Nagata, Yuji

    2005-01-01

    Tn5-derived mutants of the gamma-hexachlorocyclohexane-degrading bacterium Sphingomonas paucimobilis UT26 were genetically characterized, and an endogenous insertion sequence (IS) which belongs to the IS1380 family was identified. The IS, named ISsp1, existed as multi copies in UT26, and its transposition appeared to be activated during the process of Tn5-mutagenesis. It was found that transposon mutagenesis can cause endogenous mutations.

  8. 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

  9. Draft genome sequence of a strictly anaerobic dichloromethane-degrading bacterium

    DOE PAGES

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

    2016-03-03

    Here, 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%.

  10. 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

  11. 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

  12. Hydrolysis of fenamiphos and its oxidation products by a soil bacterium in pure culture, soil and water.

    PubMed

    Megharaj, M; Singh, N; Kookana, R S; Naidu, R; Sethunathan, N

    2003-05-01

    A bacterium, identified as Brevibacterium sp. MM1, readily hydrolysed fenamiphos, a widely used organophosphorus insecticide and its toxic oxides (fenamiphos sulfoxide, fenamiphos sulfone), which all contain a common P-O-C bond, in a mineral salts medium. The bacterium also hydrolysed fenamiphos and its oxides in soil and groundwater. Interestingly, fenamiphos phenol, fenamiphos sulfoxide phenol and fenamiphos sulfone phenol, formed during bacterial hydrolysis of fenamiphos and its oxides, persisted in the mineral salts medium, but were transitory in soil and groundwater due to their further metabolism by indigenous micro-organisms. The cell-free preparation (crude enzyme) of this bacterium was very effective in hydrolysing fenamiphos. This is the first report on exceptionally rapid hydrolysis of fenamiphos by a bacterium in pure cultures, soil and groundwater.

  13. Microbial metabolism of polycyclic aromatic hydrocarbons: isolation and characterization of a pyrene-degrading bacterium.

    PubMed Central

    Heitkamp, M A; Franklin, W; Cerniglia, C E

    1988-01-01

    Microbiological analyses of sediments located near a point source for petrogenic chemicals resulted in the isolation of a pyrene-mineralizing bacterium. This isolate was identified as a Mycobacterium sp. on the basis of its cellular and colony morphology, gram-positive and strong acid-fast reactions, diagnostic biochemical tests, 66.6% G + C content of the DNA, and high-molecular-weight mycolic acids (C58 to C64). The mycobacterium mineralized pyrene when grown in a mineral salts medium supplemented with nutrients but was unable to utilize pyrene as a sole source of carbon and energy. The mycobacterium grew well at 24 and 30 degrees C and minimally at 35 degrees C. No growth was observed at 5 or 42 degrees C. The mycobacterium grew well at salt concentrations up to 4%. Pyrene-induced Mycobacterium cultures mineralized 5% of the pyrene after 6 h and reached a maximum of 48% mineralization within 72 h. Treatment of induced and noninduced cultures with chloramphenicol showed that pyrene-degrading enzymes were inducible in this Mycobacterium sp. This bacterium could also mineralize other polycyclic aromatic hydrocarbons and alkyl- and nitro-substituted polycyclic aromatic hydrocarbons including naphthalene, phenanthrene, fluoranthene, 3-methylcholanthrene, 1-nitropyrene, and 6-nitrochrysene. This is the first report of a bacterium able to extensively mineralize pyrene and other polycyclic aromatic hydrocarbons containing four aromatic rings. Images PMID:3202633

  14. Multiple cellobiohydrolases and cellobiose phosphorylases cooperate in the ruminal bacterium Ruminococcus albus 8 to degrade cellooligosaccharides

    PubMed Central

    Devendran, Saravanan; Abdel-Hamid, Ahmed M.; Evans, Anton F.; Iakiviak, Michael; Kwon, In Hyuk; Mackie, Roderick I.; Cann, Isaac

    2016-01-01

    Digestion of plant cell wall polysaccharides is important in energy capture in the gastrointestinal tract of many herbivorous and omnivorous mammals, including humans and ruminants. The members of the genus Ruminococcus are found in both the ruminant and human gastrointestinal tract, where they show versatility in degrading both hemicellulose and cellulose. The available genome sequence of Ruminococcus albus 8, a common inhabitant of the cow rumen, alludes to a bacterium well-endowed with genes that target degradation of various plant cell wall components. The mechanisms by which R. albus 8 employs to degrade these recalcitrant materials are, however, not clearly understood. In this report, we demonstrate that R. albus 8 elaborates multiple cellobiohydrolases with multi-modular architectures that overall enhance the catalytic activity and versatility of the enzymes. Furthermore, our analyses show that two cellobiose phosphorylases encoded by R. albus 8 can function synergistically with a cognate cellobiohydrolase and endoglucanase to completely release, from a cellulosic substrate, glucose which can then be fermented by the bacterium for production of energy and cellular building blocks. We further use transcriptomic analysis to confirm the over-expression of the biochemically characterized enzymes during growth of the bacterium on cellulosic substrates compared to cellobiose. PMID:27748409

  15. 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

  16. Bioremediation of hexavalent chromium (VI) by a soil-borne bacterium, Enterobacter cloacae B2-DHA.

    PubMed

    Rahman, Aminur; Nahar, Noor; Nawani, Neelu N; Jass, Jana; Hossain, Khaled; Saud, Zahangir Alam; Saha, Ananda K; Ghosh, Sibdas; Olsson, Björn; Mandal, Abul

    2015-01-01

    Chromium and chromium containing compounds are discharged into the nature as waste from anthropogenic activities, such as industries, agriculture, forest farming, mining and metallurgy. Continued disposal of these compounds to the environment leads to development of various lethal diseases in both humans and animals. In this paper, we report a soil borne bacterium, B2-DHA that can be used as a vehicle to effectively remove chromium from the contaminated sources. B2-DHA is resistant to chromium with a MIC value of 1000 µg mL(-1) potassium chromate. The bacterium has been identified as a Gram negative, Enterobacter cloacae based on biochemical characteristics and 16S rRNA gene analysis. TOF-SIMS and ICP-MS analyses confirmed intracellular accumulation of chromium and thus its removal from the contaminated liquid medium. Chromium accumulation in cells was 320 µg/g of cells dry biomass after 120-h exposure, and thus it reduced the chromium concentration in the liquid medium by as much as 81%. Environmental scanning electron micrograph revealed the effect of metals on cellular morphology of the isolates. Altogether, our results indicate that B2-DHA has the potential to reduce chromium significantly to safe levels from the contaminated environments and suggest the potential use of this bacterium in reducing human exposure to chromium, hence avoiding poisoning.

  17. Multiple cellobiohydrolases and cellobiose phosphorylases cooperate in the ruminal bacterium Ruminococcus albus 8 to degrade cellooligosaccharides

    NASA Astrophysics Data System (ADS)

    Devendran, Saravanan; Abdel-Hamid, Ahmed M.; Evans, Anton F.; Iakiviak, Michael; Kwon, In Hyuk; Mackie, Roderick I.; Cann, Isaac

    2016-10-01

    Digestion of plant cell wall polysaccharides is important in energy capture in the gastrointestinal tract of many herbivorous and omnivorous mammals, including humans and ruminants. The members of the genus Ruminococcus are found in both the ruminant and human gastrointestinal tract, where they show versatility in degrading both hemicellulose and cellulose. The available genome sequence of Ruminococcus albus 8, a common inhabitant of the cow rumen, alludes to a bacterium well-endowed with genes that target degradation of various plant cell wall components. The mechanisms by which R. albus 8 employs to degrade these recalcitrant materials are, however, not clearly understood. In this report, we demonstrate that R. albus 8 elaborates multiple cellobiohydrolases with multi-modular architectures that overall enhance the catalytic activity and versatility of the enzymes. Furthermore, our analyses show that two cellobiose phosphorylases encoded by R. albus 8 can function synergistically with a cognate cellobiohydrolase and endoglucanase to completely release, from a cellulosic substrate, glucose which can then be fermented by the bacterium for production of energy and cellular building blocks. We further use transcriptomic analysis to confirm the over-expression of the biochemically characterized enzymes during growth of the bacterium on cellulosic substrates compared to cellobiose.

  18. [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

  19. In Search of an Uncultured Human-Associated TM7 Bacterium in the Environment

    PubMed Central

    Dinis, Jorge M.; Barton, David E.; Ghadiri, Jamsheed; Surendar, Deepa; Reddy, Kavitha; Velasquez, Fernando; Chaffee, Carol L.; Lee, Mei-Chong Wendy; Gavrilova, Helen; Ozuna, Hazel; Smits, Samuel A.; Ouverney, Cleber C.

    2011-01-01

    We have identified an environmental bacterium in the Candidate Division TM7 with ≥98.5% 16S rDNA gene homology to a group of TM7 bacteria associated with the human oral cavity and skin. The environmental TM7 bacterium (referred to as TM7a-like) was readily detectable in wastewater with molecular techniques over two years of sampling. We present the first images of TM7a-like cells through FISH technique and the first images of any TM7 as viable cells through the STARFISH technique. In situ quantification showed TM7 concentration in wastewater up to five times greater than in human oral sites. We speculate that upon further characterization of the physiology and genetics of the TM7a-like bacterium from environmental sources and confirmation of its genomic identity to human-associated counterparts it will serve as model organisms to better understand its role in human health. The approach proposed circumvents difficulties imposed by sampling humans, provides an alternative strategy to characterizing some diseases of unknown etiology, and renders a much needed understanding of the ecophysiological role hundreds of unique Bacteria and Archaea strains play in mixed microbial communities. PMID:21701585

  20. 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

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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

  7. [Diversity analysis of desulfuration bacterium from the oxidation ditch of city sewage treatment plant with SO2 gas].

    PubMed

    Huang, Bing; Zhang, Shi-Ling; Zhang, Jiang-Hong; Ao, Yong; Shi, Zhe

    2011-07-01

    A group of removing SO2 bacterium was obtained from the oxidation ditch of city sewage treatment plant by inductive domestication over 6 d with low concentration SO2 gas, and they have an ability with biodegradation rate of 888 mg x (L x h)(-1) and a degradation efficiency of 85% during 1.5 h for SO2 dissolved in water with their synergy. The clone library and two phylogenetic trees of the removing SO2 bacterium communities were obtained based on 16S rRNA DNA comparison by DNA extraction of the sample and in situ polymerase chain reaction (PCR). The phylogenetic analysis showed that 8 dominant desulfuration bacterium occupy about 69% of all removing SO2 bacterium, and some of them have a kindred with discovered desulfuration bacterium but not homogeneity, and there are four belong to alpha-Proteobacteria, another four belong to beta-Proteobacteria in them. The gene information about 16S rRNA sequence of the dominant desulfuration bacteria and domestication method provide a basic of looking for or domesticating removing SO2 bacterium for development microbial desulfurization technology of contained SO2 tail gas.

  8. 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.

  9. Bacterial signaling and motility: Sure bets

    SciTech Connect

    Zhulin, Igor B

    2008-01-01

    cytoplasmic membrane. The interaction causes the supramembrane and cytoplasmic rings to rotate along with the flagellar filaments. The energy for flagellar rotation comes from proton motive force or other ions, especially sodium in marine bacteria, which generate an electrochemical gradient across the cell membrane. Three proteins, FliM, FliN, and FliG, located at the base of the motor act as switches that control the direction of flagellar rotation. As exemplified by the enteric bacteria Escherichia coli and Salmonella enterica serovar Typhimurium, changes in the direction of flagellar rotation affect the swimming behavior of the bacterial cell. Counterclockwise (CCW) rotation of the flagella causes the flagellar filaments to form a bundle that pushes the cell forward in a 'run.' In contrast, clockwise (CW) rotation causes the flagellar bundle to fly apart, and the cell tumbles to reorient to a new direction for the ensuing run upon the return of CCW rotation. The interchanging pattern of CCW and CW rotations produces a random walk, composed of relatively long runs with occasional direction changes or turns. By modulating the lengths of the runs or the frequency of tumbling, bacteria can regulate their motile behavior to move in a desirable direction. Many bacteria can also move on surfaces. Except for flagellum-driven swarming motility, all the other forms of known bacterial surface movement involve no flagella. The flagellum-independent surface motility, known as gliding, is observed in cyanobacteria, Mycoplasma species, Cytophaga-Flexibacterium species, and Myxococcus species. Without a doubt, the most thoroughly studied model gliding bacterium is Myxococcus xanthus, which also serves as a prokaryotic model for developmental biology due to its ability to develop multicellular fruiting bodies. M. xanthus cells use gliding motility both to hunt for food during vegetative growth and to aggregate during fruiting body formation. When nutrients are present, groups of cells or

  10. Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium.

    PubMed

    Derrien, Muriel; Vaughan, Elaine E; Plugge, Caroline M; de Vos, Willem M

    2004-09-01

    The diversity of mucin-degrading bacteria in the human intestine was investigated by combining culture and 16S rRNA-dependent approaches. A dominant bacterium, strain MucT, was isolated by dilution to extinction of faeces in anaerobic medium containing gastric mucin as the sole carbon and nitrogen source. A pure culture was obtained using the anaerobic soft agar technique. Strain MucT was a Gram-negative, strictly anaerobic, non-motile, non-spore-forming, oval-shaped bacterium that could grow singly and in pairs. When grown on mucin medium, cells produced a capsule and were found to aggregate. Strain MucT could grow on a limited number of sugars, including N-acetylglucosamine, N-acetylgalactosamine and glucose, but only when a protein source was provided and with a lower growth rate and final density than on mucin. The G + C content of DNA from strain MucT was 47.6 mol%. 16S rRNA gene sequence analysis revealed that the isolate was part of the division Verrucomicrobia. The closest described relative of strain MucT was Verrucomicrobium spinosum (92 % sequence similarity). Remarkably, the 16S rRNA gene sequence of strain MucT showed 99 % similarity to three uncultured colonic bacteria. According to the data obtained in this work, strain MucT represents a novel bacterium belonging to a new genus in subdivision 1 of the Verrucomicrobia; the name Akkermansia muciniphila gen. nov., sp. nov. is proposed; the type strain is MucT (= ATCC BAA-835T = CIP 107961T).

  11. An Oleaginous Bacterium That Intrinsically Accumulates Long-Chain Free Fatty Acids in its Cytoplasm

    PubMed Central

    Katayama, Taiki; Kanno, Manabu; Morita, Naoki; Hori, Tomoyuki; Narihiro, Takashi; Mitani, Yasuo

    2014-01-01

    Medium- and long-chain fatty acids are present in organisms in esterified forms that serve as cell membrane constituents and storage compounds. A large number of organisms are known to accumulate lipophilic materials as a source of energy and carbon. We found a bacterium, designated GK12, that intrinsically accumulates free fatty acids (FFAs) as intracellular droplets without exhibiting cytotoxicity. GK12 is an obligatory anaerobic, mesophilic lactic acid bacterium that was isolated from a methanogenic reactor. Phylogenetic analysis based on 16S rRNA gene sequences showed that GK12 is affiliated with the family Erysipelotrichaceae in the phylum Firmicutes but is distantly related to type species in this family (less than 92% similarity in 16S rRNA gene sequence). Saturated fatty acids with carbon chain lengths of 14, 16, 18, and 20 were produced from glucose under stress conditions, including higher-than-optimum temperatures and the presence of organic solvents that affect cell membrane integrity. FFAs were produced at levels corresponding to up to 25% (wt/wt) of the dry cell mass. Our data suggest that FFA accumulation is a result of an imbalance between excess membrane fatty acid biosynthesis due to homeoviscous adaptation and limited β-oxidation activity due to anaerobic growth involving lactic acid fermentation. FFA droplets were not further utilized as an energy and carbon source, even under conditions of starvation. A naturally occurring bacterium that accumulates significant amounts of long-chain FFAs with noncytotoxicity would provide useful strategies for microbial biodiesel production. PMID:24296497

  12. 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

  13. 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.

  14. Cloning and characterization of nif structural and regulatory genes in the purple sulfur bacterium, Halorhodospira halophila.

    PubMed

    Tsuihiji, Hisayoshi; Yamazaki, Yoichi; Kamikubo, Hironari; Imamoto, Yasushi; Kataoka, Mikio

    2006-03-01

    Halorhodospira halophila is a halophilic photosynthetic bacterium classified as a purple sulfur bacterium. We found that H. halophila generates hydrogen gas during photoautotrophic growth as a byproduct of a nitrogenase reaction. In order to consider the applied possibilities of this photobiological hydrogen generation, we cloned and characterized the structural and regulatory genes encoding the nitrogenase, nifH, nifD and nifA, from H. halophila. This is the first description of the nif genes for a purple sulfur bacterium. The amino-acid sequences of NifH and NifD indicated that these proteins are an Fe protein and a part of a MoFe protein, respectively. The important residues are conserved completely. The sequence upstream from the nifH region and sequence similarities of nifH and nifD with those of the other organisms suggest that the regulatory system might be a NifL-NifA system; however, H. halophila lacks nifL. The amino-acid sequence of H. halophila NifA is closer to that of the NifA of the NifL-NifA system than to that of NifA without NifL. H. halophila NifA does not conserve either the residue that interacts with NifL or the important residues involved in NifL-independent regulation. These results suggest the existence of yet another regulatory system, and that the development of functional systems and their molecular counterparts are not necessarily correlated throughout evolution. All of these Nif proteins of H. halophila possess an excess of acidic residues, which acts as a salt-resistant mechanism.

  15. Influence of Mn Ion on the Iron Biomineralization by an Iron-reducing Bacterium

    NASA Astrophysics Data System (ADS)

    Lee, S.; Roh, Y.; Lee, I.; Phelps, T. J.

    2003-12-01

    Manganese ion is known to be easily sorbed to iron oxide surface or co-precipitated into iron oxides structure, but the effect of manganese ion on iron biomineralization is not sufficiently understood. The objectives of this study were to examine the influence of Mn substitution and sorption on iron biomineralization and to identify biogeochemical factors determining phase distribution of Mn ion during iron biomineralization. The reductive biomineralization of Mn-substituted (Fe1-xMnxOOH) or Mn-sorbed (FeOOH plus MnCl2) akaganeite by an iron-reducing bacterium (Shewanella alga, PV-4) was investigated under ananerobic conditions at circumneutral pH (pH = 7 - 8) and at 25 deg.C. The influence of Mn ion on the iron biomineralization was explored along with effects of bicarbonate (30 - 210 mM) on biomineralization using lactate (10 mM) as an electron donor. No exogenous electron carrier substance (i.e., anthraquinone disulfonate) or reducing agent (i.e., cysteine) was added to the anaerobic medium. Solid phases and aqueous chemistry were characterized after incubations with both of the iron-reducing bacterium and Mn-substituted or Mn-sorbed akaganeite for 30 days. The iron reducing bacterium, S. alga, mainly formed siderite (FeCO3), green rust [Fe2+Fe3+(OH)16CO3 4H2O], and magnetite (Fe3O4) using Mn-substituted akaganeite, while rhodochrosite (MnCO3), siderite, and magnetite were dominant phases using Mn-sorbed akaganeite in the bicarbonate buffered medium. Scanning electron microscopy and transmission electron microscopy with energy dispersive X-ray analysis of iron minerals formed by S. alga showed that Mn was preferentially concentrated in the siderite and green rust. This research indicates that microorganisms may affect the cyclings of Fe, Mn and C and the fate of metal contaminants in subsurface environments.

  16. 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

  17. 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

  18. Studies of the Extracellular Glycocalyx of the Anaerobic Cellulolytic Bacterium Ruminococcus albus 7▿

    PubMed Central

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

    2006-01-01

    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

  19. Adhesive properties of a symbolic bacterium from a wood-boreing marine shipworm

    SciTech Connect

    Imam, S.H.; Greene, R.V.; Griffin, H.L. )

    1990-05-01

    Adhesive properties of cellulolytic, nitrogen-fixing bacterium isolated from a marine shipworm are described. {sup 35}S-labeled cells of the shipworm bacterium bound preferentially Whatman no.1 cellulose filter paper, compared with its binding to other cellulose substrata or substrata lacking cellulose. The ability of the bacteria to bind to Whatman no. 1 filter paper was significantly reduced by glutaraldehyde or heat treatment of cells. Pretreatment of cells with azide, valinomycin, gramicidin-D, bis-hexafluoroacetylacetone (1799), or carbonyl cyanide-p-trifluoromethoxyphenylhydrazone inhibited adhesion activity. Cells pretreated with pronase or trypsin also exhibited reduced binding activity, but chymotrypsin and peptidase had no effect on adhesion activity. Cellodextrins and methyl cellulose 15 inhibited the adhesion of the shipworm bacteria to filter paper, whereas glucose, cellobiose, and soluble carboxymethyl cellulose had no significant effect. The divalent cation chelators EDTA and EGTA (ethylene hlycol-bis({beta}-aminoethyl ether)-N,N,N{prime}N{prime}-tetraacetic acid) had little or no effect on adhesive properties of shipworm bacteria. Also, preabsorbing the substratum with extracellular endoglucanase isolated from the ship worm bacterium or 1% bovine serum albumin had no apparent effect on bacterial binding. Low concentration (0.01%) of sodium dodecyl sulfate solubilized a fraction from whole cells, which appeared to be involved in cellular binding activity. After removal of sodium dodecyl, sulfate, several proteins in this fraction associated with intact cells. These cells exhibited up to 50% enhanced binding to filter paper in comparison to cells which had not been exposed to the sodium dodecyl sulfate-solubilized fraction.

  20. 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

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

    PubMed

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

    2011-06-01

    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.

  2. 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

  3. 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

  4. Genome Sequence of the Boron-Tolerant and -Requiring Bacterium Bacillus boroniphilus

    PubMed Central

    Çöl, Bekir; Özkeserli, Zeynep; Kumar, Dibyendu; Özdağ, Hilal

    2014-01-01

    Bacillus boroniphilus is a highly boron-tolerant bacterium that also requires this element for its growth. The complete genome sequence of B. boroniphilus was determined by a combination of shotgun sequencing and paired-end sequencing using 454 pyrosequencing technology. A total of 84,872,624 reads from shotgun sequencing and a total of 194,092,510 reads from paired-end sequencing were assembled using Newbler 2.3. The estimated size of the draft genome is 5.2 Mb. PMID:24385571

  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. 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.

  7. 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

  8. [Isolation and characterization of a facultative anaerobic aniline-degrading bacterium].

    PubMed

    Zeng, Guo-Qu; Ren, Sui-Zhou; Cao, Wei; Hu, Jin-Cai; Lin, Lu-Jing; Sun, Guo-Ping

    2006-08-01

    An aniline-degrading bacterium (designated strain AN29) was isolated from dyeing wastewater process (anaerobic baffled reactor, ABR) with the capability of utilizing aniline as sole carbon source and nitrogen source. It was identified as Pseudomonas sp. based upon the phenotypic properties and a partial analysis of the 16S rDNA. The strain could degrade aniline under the aerobic and anaerobic conditions, the optimal initial pH 6.5 - 8.0, a temperature of 37 degrees C, and initial aniline concentrations of 500 - 2 000 mg/L with maximum concentration of 4 000 mg/L respectively.

  9. 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.

  10. 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.

  11. News & notes: paper digestion by the cellulolytic ruminal bacterium Fibrobacter succinogenes.

    PubMed

    Martin, S A; Martin, J A

    1998-12-01

    The objective of this study was to evaluate the ability of the predominant cellulolytic ruminal bacterium Fibrobacter succinogenes S85 to digest filter paper, office paper, newspaper, and magazine paper. When F. succinogenes S85 was incubated with all four paper sources, little digestion of any paper occurred between 0 and 48 h. However, digestion of filter paper increased from 12% at 48 h to 80% at 120 h. No significant digestion of office paper, newspaper, or magazine paper occurred between 48 and 120 h. These results suggest that F. succinogenes S85 is unable to digest office paper, newspaper, or magazine paper.

  12. 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.

  13. Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2T

    DOE PAGES

    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.

  14. 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

  15. 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

  16. 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.

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

    PubMed

    Rivers, Adam R; Smith, Christa B; Moran, Mary Ann

    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.

  18. 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.

  19. Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2(T).

    PubMed

    Berben, Tom; Sorokin, Dimitry Y; Ivanova, Natalia; Pati, Amrita; Kyrpides, Nikos; Goodwin, Lynne A; Woyke, Tanja; Muyzer, Gerard

    2015-01-01

    Thioalkalivibrio thiocyanoxidans strain ARh 2(T) 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. This organism was sequenced as part of the Community Science Program of the DOE Joint Genome Institute.

  20. Whole genome shotgun sequence of Bacillus amyloliquefaciens TF28, a biocontrol entophytic bacterium.

    PubMed

    Zhang, Shumei; Jiang, Wei; Li, Jing; Meng, Liqiang; Cao, Xu; Hu, Jihua; Liu, Yushuai; Chen, Jingyu; Sha, Changqing

    2016-01-01

    Bacillus amyloliquefaciens TF28 is a biocontrol endophytic bacterium that is capable of inhibition of a broad range of plant pathogenic fungi. The strain has the potential to be developed into a biocontrol agent for use in agriculture. Here we report the whole-genome shotgun sequence of the strain. The genome size of B. amyloliquefaciens TF28 is 3,987,635 bp which consists of 3754 protein-coding genes, 65 tandem repeat sequences, 47 minisatellite DNA, 2 microsatellite DNA, 63 tRNA, 7rRNA, 6 sRNA, 3 prophage and CRISPR domains. PMID:27688836

  1. 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

  2. FACTORS LIMITING BACTERIAL GROWTH : III. CELL SIZE AND "PHYSIOLOGIC YOUTH" IN BACTERIUM COLI CULTURES.

    PubMed

    Hershey, A D; Bronfenbrenner, J

    1938-07-20

    1. Measurements of the rate of oxygen uptake per cell in transplants of Bacterium coli from cultures of this organism in different phases of growth have given results in essential agreement with the observations of others. 2. Correlations of viable count, centrifugable nitrogen, and turbidity, with oxygen consumption, indicate that the increased metabolism during the early portion of the growth period is quantitatively referable to increased average size of cells. 3. Indirect evidence has suggested that the initial rate of growth of transplants is not related to the phase of growth of the parent culture.

  3. 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.

  4. 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.

  5. Exoelectrogenic bacterium phylogenetically related to Citrobacter freundii, isolated from anodic biofilm of a microbial fuel cell.

    PubMed

    Huang, Jianjian; Zhu, Nengwu; Cao, Yanlan; Peng, Yue; Wu, Pingxiao; Dong, Wenhao

    2015-02-01

    An electrogenic bacterium, named Citrobacter freundii Z7, was isolated from the anodic biofilm of microbial fuel cell (MFC) inoculated with aerobic sewage sludge. Cyclic voltammetry (CV) analysis exhibited that the strain Z7 had relatively high electrochemical activity. When the strain Z7 was inoculated into MFC, the maximum power density can reach 204.5 mW/m(2) using citrate as electron donor. Series of substrates including glucose, glycerol, lactose, sucrose, and rhammose could be utilized to generate power. CV tests and the addition of anode solution as well as AQDS experiments indicated that the strain Z7 might transfer electrons indirectly via secreted mediators.

  6. Draft genome sequence of algal polysaccharides degradation bacterium, Flammeovirga sp. OC4.

    PubMed

    Liu, Yang; Yi, Zhiwei; Cai, Yaping; Zeng, Runying

    2015-06-01

    Flammeovirga sp. OC4 was isolated from seawater sample of the South China Sea using the method of in-situ-enrichment, which has the ability to degrade algal polysaccharides. Colonies are reddish orange in the exponential growth phase and turn white in the late stationary growth phase, which is the indicator of the bacterial death. Here, we present an annotated draft genome sequence of Flammeovirga sp. OC4, which contains 8,069,312bp with a G+C content of 34.8%. This information regarding the genetic basis of this bacterium can greatly advance our understanding of algal polysaccharides-degrading mechanism and the physiology of this species.

  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. 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

  9. Complete genome sequence of Hymenobacter swuensis, an ionizing-radiation resistant bacterium isolated from mountain soil.

    PubMed

    Jung, Jong-Hyun; Yang, Ho-Yeon; Jeong, Sunwook; Joe, Min-Ho; Cho, Yong-Joon; Kim, Myung-Kyum; Lim, Sangyong

    2014-05-20

    Hymenobacter swuensis is a gamma-radiation resistant bacterium isolated from mountain soil in South Korea (N 35°51'38″, E 127°44'47″; altitude 1500m). The complete genome of H. swuensis consists of one chromosome (4,904,241bp) with three plasmids. The genomic sequence indicated that H. swuensis includes a series of genes involved in 2'-hydroxy-carotenoid biosynthesis. This is the first report describing the Hymenobacter genome and key enzymes in the 2'-hydroxy-carotenoid biosynthesis pathway. These data may provide opportunities for genetic engineering and antioxidant 2'-hydroxy-carotenoid production. PMID:24637374

  10. Francisella Inflammasomes: Integrated Responses to a Cytosolic Stealth Bacterium.

    PubMed

    Wallet, Pierre; Lagrange, Brice; Henry, Thomas

    2016-01-01

    Francisella tularensis is a facultative intracellular bacterium causing tularemia, a zoonotic disease. Francisella replicates in the macrophage cytosol and eventually triggers cytosolic immune responses. In murine macrophages, Francisella novicida and Francisella tularensis live vaccine strain lyse in the host cytosol and activate the cytosolic DNA receptor Aim2. Here, we review the mechanisms leading or contributing to Aim2 inflammasome activation, including the role of TLRs and of IFN signaling and the implication of the guanylate-binding proteins 2 and 5 in triggering cytosolic bacteriolysis. Furthermore, we present how this cytosolic Gram-negative bacterium escapes recognition by caspase-11 but can trigger a non-canonical caspase-8 inflammasome. In addition, we highlight the differences in inflammasome activation in murine and human cells with pyrin, NLRP3, and AIM2 involved in sensing Francisella in human phagocytes. From a bacterial prospective, we describe the hiding strategy of Francisella to escape recognition by innate sensors and to resist to bacteriolysis in the host cytosol. Finally, we discuss the inability of the inflammasome sensors to detect F. tularensis subspecies tularensis strains, making them highly pathogenic stealth microbes.

  11. Development of a gene cloning system for the hydrogen-producing marine photosynthetic bacterium Rhodopseudomonas sp

    SciTech Connect

    Matsunaga, T.; Matsunaga, N.; Tsubaki, K.; Tanaka, T.

    1986-10-01

    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 ..mu..mol/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.

  12. Detection of a novel bacterium associated with spores of the arbuscular mycorrhizal fungus Gigaspora margarita.

    PubMed

    Long, Liangkun; Yao, Qing; Ai, Yuncan; Deng, Mingrong; Zhu, Honghui

    2009-06-01

    With PCR-denaturing gradient gel electrophoresis analysis, two bacterial 16S rRNA gene V3 region sequences, 7A and 7B, were detected in association with the crushed spores of the arbuscular mycorrhizal fungus Gigaspora margarita W.N. Becker & I.R. Hall 1976 MAFF520054. DNA sequencing and phylogenetic analysis revealed that 7B was mostly related to the documented cytoplasm endosymbiotic bacterium Candidatus Glomeribacter gigasporarum of G. margarita, but 7A could not be confidently assigned to a known taxon. Further characterization of 7A was conducted by obtaining its almost complete 16S rRNA gene sequence via PCR amplification and sequencing. BLAST search indicates that the 16S rRNA gene sequence did not match any identified species sequences in the GenBank database. Further detection revealed that 7A was also associated with the clean G. margarita MAFF520054 spores that were obtained by the surface-sterilized method or dual culture with Ri T-DNA transformed carrot roots. Many ellipse-shaped or egg-shaped bacterium-like organisms were clustered in layer 3 of the fungal spore wall by transmission electron microscopy observation. Our results indicate that 7A represents a novel bacterial population associated with G. margarita MAFF520054 spores, and its doubtless location (wall or cytoplasm) remains unclear based on the present data.

  13. Expression and surface display of Cellulomonas endoglucanase in the ethanologenic bacterium Zymobacter palmae.

    PubMed

    Kojima, Motoki; Akahoshi, Tomohiro; Okamoto, Kenji; Yanase, Hideshi

    2012-11-01

    In order to reduce the cost of bioethanol production from lignocellulosic biomass, we developed a tool for cell surface display of cellulolytic enzymes on the ethanologenic bacterium Zymobacter palmae. Z. palmae is a novel ethanol-fermenting bacterium capable of utilizing a broad range of sugar substrates, but not cellulose. Therefore, to express and display heterologous cellulolytic enzymes on the Z. palmae cell surface, we utilized the cell-surface display motif of the Pseudomonas ice nucleation protein Ina. The gene encoding Ina from Pseudomonas syringae IFO3310 was cloned, and its product was comprised of three functional domains: an N-terminal domain, a central domain with repeated amino acid residues, and a C-terminal domain. The N-terminal domain of Ina was shown to function as the anchoring motif for a green fluorescence protein fusion protein in Escherichia coli. To express a heterologous cellulolytic enzyme extracellularly in Z. palmae, we fused the N-terminal coding sequence of Ina to the coding sequence of an N-terminal-truncated Cellulomonas endoglucanase. Z. palmae cells carrying the fusion endoglucanase gene were shown to degrade carboxymethyl cellulose. Although a portion of the expressed fusion endoglucanase was released from Z. palmae cells into the culture broth, we confirmed the display of the protein on the cell surface by immunofluorescence microscopy. The results indicate that the N-terminal anchoring motif of Ina from P. syringae enabled the translocation and display of the heterologous cellulase on the cell surface of Z. palmae.

  14. 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

  15. 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.

  16. Psychromonas ingrahamii sp. nov., a novel gas vacuolate, psychrophilic bacterium isolated from Arctic polar sea ice.

    PubMed

    Auman, Ann J; Breezee, Jennifer L; Gosink, John J; Kämpfer, Peter; Staley, James T

    2006-05-01

    A gas vacuolate bacterium, designated strain 37T, was isolated from a sea ice core collected from Point Barrow, Alaska, USA. Cells of strain 37T were large (6-14 microm in length), rod-shaped, contained gas vacuoles of two distinct morphologies, and grew well at NaCl concentrations of 1-10 % and at temperatures of -12 to 10 degrees C. The DNA G+C content was 40 mol%. Whole-cell fatty acid analysis showed that 16 : 1omega7c comprised 67 % of the total fatty acid content. Phylogenetic analysis of 16S rRNA gene sequences indicated that this bacterium was closely related to members of the genus Psychromonas, with highest sequence similarity (96.8 %) to Psychromonas antarctica. Phenotypic analysis differentiated strain 37T from P. antarctica on the basis of several characteristics, including cell morphology, growth temperature range and the ability to hydrolyse polymers. DNA-DNA hybridization experiments revealed a level of relatedness of 37 % between strain 37T and P. antarctica, providing further support that it represents a distinct species. The name Psychromonas ingrahamii sp. nov. is proposed for this novel species. The type strain is 37T (=CCUG 51855T=CIP 108865T).

  17. 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

  18. 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

  19. 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.

  20. Functional diversity of carbohydrate-active enzymes enabling a bacterium to ferment plant biomass.

    PubMed

    Boutard, Magali; Cerisy, Tristan; Nogue, Pierre-Yves; Alberti, Adriana; Weissenbach, Jean; Salanoubat, Marcel; Tolonen, Andrew C

    2014-11-01

    Microbial metabolism of plant polysaccharides is an important part of environmental carbon cycling, human nutrition, and industrial processes based on cellulosic bioconversion. Here we demonstrate a broadly applicable method to analyze how microbes catabolize plant polysaccharides that integrates carbohydrate-active enzyme (CAZyme) assays, RNA sequencing (RNA-seq), and anaerobic growth screening. We apply this method to study how the bacterium Clostridium phytofermentans ferments plant biomass components including glucans, mannans, xylans, galactans, pectins, and arabinans. These polysaccharides are fermented with variable efficiencies, and diauxies prioritize metabolism of preferred substrates. Strand-specific RNA-seq reveals how this bacterium responds to polysaccharides by up-regulating specific groups of CAZymes, transporters, and enzymes to metabolize the constituent sugars. Fifty-six up-regulated CAZymes were purified, and their activities show most polysaccharides are degraded by multiple enzymes, often from the same family, but with divergent rates, specificities, and cellular localizations. CAZymes were then tested in combination to identify synergies between enzymes acting on the same substrate with different catalytic mechanisms. We discuss how these results advance our understanding of how microbes degrade and metabolize plant biomass.

  1. 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

  2. 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

  3. Isolation and Characterization of an Anaerobic, Cellulolytic Bacterium, Clostridium cellulovorans sp. nov

    PubMed Central

    Sleat, Robert; Mah, Robert A.; Robinson, Ralph

    1984-01-01

    A new anaerobic, mesophilic, spore-forming cellulolytic bacterium is described. Cellulose is cleared within 24 to 48 h around colonies formed in cellulose agar roll tubes. Cells stain gram negative and are nonmotile rods which form oblong spores either centrally or subterminally in a clostridial swelling. Colonies are irregular with an opaque edge and a center devoid of both vegetative cells and spores. Cellulose, xylan, pectin, cellobiose, glucose, maltose, galactose, sucrose, lactose, and mannose serve as substrates for growth. H2, CO2, acetate, butyrate, formate, and lactate are produced during fermentation of cellulose or cellobiose. The temperature and pH for optimum growth are 37°C and 7.0, respectively. The DNA composition is 26 to 27 mol% guanine plus cytosine. This bacterium resembles “Clostridium lochheadii” in morphological and some biochemical characteristics but is not identical to it. The name Clostridium cellulovorans sp. nov. is proposed. The type strain is 743B (ATCC 35296). Images PMID:16346602

  4. Polaribacter butkevichii sp. nov., a novel marine mesophilic bacterium of the family Flavobacteriaceae.

    PubMed

    Nedashkovskaya, Olga I; Kim, Seung Bum; Lysenko, Anatoly M; Kalinovskaya, Nataliya I; Mikhailov, Valery V; Kim, In Seop; Bae, Kyung Sook

    2005-12-01

    A novel heterotrophic, yellow pigmented, aerobic, Gram-negative, nonmotile, oxidase- and catalase-positive bacterium KMM 3,938(T) was isolated from sea water collected in the Sea of Japan, Russia. The strain grew at mesophilic temperature range, and required the presence of NaCl for growth. 16S rRNA gene sequence analysis revealed that strain KMM 3,938(T) is a member of the family Flavobacteriaceae. The predominant fatty acids were C13:0 iso, C14:0 iso, C15:0 iso, C15:0, C15:1Delta6, 3OH-C15:0:3 iso, and 3OH-C15:0. The G + C content of the DNA of KMM 3938(T) was 32.4 mol%. On the basis of phenotypic, chemotaxonomic, genotypic, and phylogenetic characteristics, the novel bacterium was assigned to the genus Polaribacter as Polaribacter butkevichii sp. nov. The type strain is KMM 3938(T )(= KCTC 12100(T) = CCUG 48005(T)).

  5. 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.

  6. Nematode-Bacterium Symbioses - Cooperation and Conflict Revealed in the 'Omics' Age

    PubMed Central

    Murfin, Kristen E.; Dillman, Adler R.; Foster, Jeremy M.; Bulgheresi, Silvia; Slatko, Barton E.; Sternberg, Paul W.; Goodrich-Blair, Heidi

    2012-01-01

    Nematodes are ubiquitous organisms that have a significant global impact on ecosystems, economies, agriculture, and human health. The applied importance of nematodes and the experimental tractability of many species have promoted their use as models in various research areas, including developmental biology, evolutionary biology, ecology, and animal-bacterium interactions. Nematodes are particularly well suited for investigating host associations with bacteria because all nematodes have interacted with bacteria during their evolutionary history and engage in a diversity of association types. Interactions between nematodes and bacteria can be positive (mutualistic) or negative (pathogenic/parasitic) and may be transient or stably maintained (symbiotic). Furthermore, since many mechanistic aspects of nematode-bacterium interactions are conserved their study can provide broader insights into other types of associations, including those relevant to human diseases. Recently, genome-scale studies have been applied to diverse nematode-bacterial interactions, and have helped reveal mechanisms of communication and exchange between the associated partners. In addition to providing specific information about the system under investigation, these studies also have helped inform our understanding of genome evolution, mutualism, and innate immunity. In this review we will discuss the importance and diversity of nematodes, 'omics' studies in nematode-bacterial systems, and the wider implications of the findings. PMID:22983035

  7. 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

  8. 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.

  9. 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

  10. 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

  11. 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.

  12. (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

  13. 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.

  14. Photobacterium damselae subsp. damselae, a bacterium pathogenic for marine animals and humans

    PubMed Central

    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

  15. 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

  16. 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

  17. Proteomic analysis of membrane proteins from a radioresistant and moderate thermophilic bacterium Deinococcus geothermalis.

    PubMed

    Tian, Bing; Wang, Hu; Ma, Xiaoqiong; Hu, Yaping; Sun, Zongtao; Shen, Shaochuan; Wang, Fei; Hua, Yuejin

    2010-10-01

    Deinococcus geothermalis is a radioresistant and moderate thermophilic bacterium. Little was known about the membrane or membrane associated proteins of this bacterium. This study established the membrane subproteome profile of D. geothermalis, using 1-D PAGE and LC-MS/MS analysis following Triton X-114 detergent extraction. A total of 552 proteins from the membrane preparations were identified from two independent trials. In the total identified proteins, 117 were membrane subproteomic proteins, and 89 of them were described for the first time in D. geothermalis including fimbrial pilin (Dgeo_2038), cytochrome bd ubiquinol oxidase (Dgeo_2705) and multi-sensor (Dgeo_2096). The major membrane subproteomic proteins were distributed into 18 functional groups including nutrient transport and metabolism, energy production and conversion, cell wall/membrane biogenesis and a poorly characterized subclass. The identifications of Deinococcus-specific proteins, such as cell surface receptor IPT/TIG (Dgeo_1119) and four hypothetical proteins, demonstrated the special protein composition and functions in the cell membrane of Deinococcus. The results provide a basis for quantitative proteomic analysis, which will facilitate the understanding of the adaptation of this organism to different environmental stresses and the development of strategies for bioremediation of environmental waste.

  18. Geovibrio ferrireducens, a phylogenetically distinct dissimilatory Fe(III)-reducing bacterium

    USGS Publications Warehouse

    Caccavo, F.; Coates, J.D.; Rossello-Mora, R. A.; Ludwig, W.; Schleifer, K.H.; Lovley, D.R.; McInerney, M.J.

    1996-01-01

    A new, phylogenetically distinct, dissimilatory, Fe(III)-reducing bacterium was isolated from surface sediment of a hydrocarbon-contaminated ditch. The isolate, designated strain PAL-1, was an obligately anaerobic, non-fermentative, motile, gram-negative vibrio. PAL-1 grew in a defined medium with acetate as electron donor and ferric pyrophosphate, ferric oxyhydroxide, ferric citrate, Co(III)-EDTA, or elemental sulfur as sole electron acceptor. PAL-1 also used proline, hydrogen, lactate, propionate, succinate, fumarate, pyruvate, or yeast extract as electron donors for Fe(III) reduction. It is the first bacterium known to couple the oxidation of an amino acid to Fe(III) reduction. PAI-1 did not reduce oxygen, Mn(IV), U(VI), Cr(VI), nitrate, sulfate, sulfite, or thiosulfate with acetate as the electron donor. Cell suspensions of PAL-1 exhibited dithionite-reduced minus air-oxidized difference spectra that were characteristic of c-type cytochromes. Analysis of the 16S rRNA gene sequence of PAL-1 showed that the strain is not related to any of the described metal-reducing bacteria in the Proteobacteria and, together with Flexistipes sinusarabici, forms a separate line of descent within the Bacteria. Phenotypically and phylogenetically, strain PAI-1 differs from all other described bacteria, and represents the type strain of a new genus and species. Geovibrio ferrireducens.

  19. Biochemical and Structural Insights into Xylan Utilization by the Thermophilic Bacterium Caldanaerobius polysaccharolyticus*

    PubMed Central

    Han, Yejun; Agarwal, Vinayak; Dodd, Dylan; Kim, Jason; Bae, Brian; Mackie, Roderick I.; Nair, Satish K.; Cann, Isaac K. O.

    2012-01-01

    Hemicellulose is the next most abundant plant cell wall component after cellulose. The abundance of hemicellulose such as xylan suggests that their hydrolysis and conversion to biofuels can improve the economics of bioenergy production. In an effort to understand xylan hydrolysis at high temperatures, we sequenced the genome of the thermophilic bacterium Caldanaerobius polysaccharolyticus. Analysis of the partial genome sequence revealed a gene cluster that contained both hydrolytic enzymes and also enzymes key to the pentose-phosphate pathway. The hydrolytic enzymes in the gene cluster were demonstrated to convert products from a large endoxylanase (Xyn10A) predicted to anchor to the surface of the bacterium. We further use structural and calorimetric studies to demonstrate that the end products of Xyn10A hydrolysis of xylan are recognized and bound by XBP1, a putative solute-binding protein, likely for transport into the cell. The XBP1 protein showed preference for xylo-oligosaccharides as follows: xylotriose > xylobiose > xylotetraose. To elucidate the structural basis for the oligosaccharide preference, we solved the co-crystal structure of XBP1 complexed with xylotriose to a 1.8-Å resolution. Analysis of the biochemical data in the context of the co-crystal structure reveals the molecular underpinnings of oligosaccharide length specificity. PMID:22918832

  20. Conversion of Daidzein and Genistein by an Anaerobic Bacterium Newly Isolated from the Mouse Intestine▿

    PubMed Central

    Matthies, Anastasia; Clavel, Thomas; Gütschow, Michael; Engst, Wolfram; Haller, Dirk; Blaut, Michael; Braune, Annett

    2008-01-01

    The metabolism of isoflavones by gut bacteria plays a key role in the availability and bioactivation of these compounds in the intestine. Daidzein and genistein are the most common dietary soy isoflavones. While daidzein conversion yielding equol has been known for some time, the corresponding formation of 5-hydroxy-equol from genistein has not been reported previously. We isolated a strictly anaerobic bacterium (Mt1B8) from the mouse intestine which converted daidzein via dihydrodaidzein to equol as well as genistein via dihydrogenistein to 5-hydroxy-equol. Strain Mt1B8 was a gram-positive, rod-shaped bacterium identified as a member of the Coriobacteriaceae. Strain Mt1B8 also transformed dihydrodaidzein and dihydrogenistein to equol and 5-hydroxy-equol, respectively. The conversion of daidzein, genistein, dihydrodaidzein, and dihydrogenistein in the stationary growth phase depended on preincubation with the corresponding isoflavonoid, indicating enzyme induction. Moreover, dihydrogenistein was transformed even more rapidly in the stationary phase when strain Mt1B8 was grown on either genistein or daidzein. Growing the cells on daidzein also enabled conversion of genistein. This suggests that the same enzymes are involved in the conversion of the two isoflavones. PMID:18539813

  1. 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

  2. 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

  3. Chemical compounds effective against the citrus Huanglongbing bacterium 'Candidatus Liberibacter asiaticus' in planta.

    PubMed

    Zhang, Muqing; Powell, Charles A; Zhou, Lijuan; He, Zhenli; Stover, Ed; Duan, Yongping

    2011-09-01

    Citrus Huanglongbing (HLB) is one of the most destructive diseases of citrus worldwide and is threatening the survival of the Floridian citrus industry. Currently, there is no established cure for this century-old and emerging disease. As a possible control strategy for citrus HLB, therapeutic compounds were screened using a propagation test system with 'Candidatus Liberibacter asiaticus'-infected periwinkle and citrus plants. The results demonstrated that the combination of penicillin and streptomycin (PS) was effective in eliminating or suppressing the 'Ca. L. asiaticus' bacterium and provided a therapeutically effective level of control for a much longer period of time than when administering either antibiotic separately. When treated with the PS, 'Ca. L. asiaticus'-infected periwinkle cuttings achieved 70% of regeneration rates versus <50% by other treatments. The 'Ca. L. asiaticus' bacterial titers in the infected periwinkle plants, as measured by quantitative real-time polymerase chain reaction, decreased significantly following root soaking or foliar spraying with PS. Application of the PS via trunk injection or root soaking also eliminated or suppressed the 'Ca. L. asiaticus' bacterium in the HLB-affected citrus plants. This may provide a useful tool for the management of citrus HLB and other Liberibacter-associated diseases.

  4. 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

  5. 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).

  6. 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

  7. Biomass yield efficiency of the marine anammox bacterium, "Candidatus Scalindua sp.," is affected by salinity.

    PubMed

    Awata, Takanori; Kindaichi, Tomonori; Ozaki, Noriatsu; Ohashi, Akiyoshi

    2015-01-01

    The growth rate and biomass yield efficiency of anaerobic ammonium oxidation (anammox) bacteria are markedly lower than those of most other autotrophic bacteria. Among the anammox bacterial genera, the growth rate and biomass yield of the marine anammox bacterium "Candidatus Scalindua sp." is still lower than those of other anammox bacteria enriched from freshwater environments. The activity and growth of marine anammox bacteria are generally considered to be affected by the presence of salinity and organic compounds. Therefore, in the present study, the effects of salinity and volatile fatty acids (VFAs) on the anammox activity, inorganic carbon uptake, and biomass yield efficiency of "Ca. Scalindua sp." enriched from the marine sediments of Hiroshima Bay, Japan, were investigated in batch experiments. Differences in VFA concentrations (0-10 mM) were observed under varying salinities (0.5%-4%). Anammox activity was high at 0.5%-3.5% salinity, but was 30% lower at 4% salinity. In addition, carbon uptake was higher at 1.5%-3.5% salinity. The results of the present study clearly demonstrated that the biomass yield efficiency of the marine anammox bacterium "Ca. Scalindua sp." was significantly affected by salinity. On the other hand, the presence of VFAs up to 10 mM did not affect anammox activity, carbon uptake, or biomass yield efficiency.

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. 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

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

    PubMed

    Liu, Min; Luo, Kun; 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.

  14. 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.

  15. Engineering of a psychrophilic bacterium for the bioremediation of aromatic compounds.

    PubMed

    Parrilli, Ermengilda; Papa, Rosanna; Tutino, Maria Luisa; Sannia, Giovanni

    2010-01-01

    Microbial degradation of aromatic hydrocarbons has been studied with the aim of developing applications for the removal of toxic compounds. Efforts have been directed toward the genetic manipulation of mesophilic bacteria to improve their ability to degrade pollutants, even though many pollution problems occur in sea waters and in effluents of industrial processes which are characterized by low temperatures. From these considerations the idea of engineering a psychrophilic microorganism for the oxidation of aromatic compounds was developed.In a previous paper it was demonstrated that the recombinant Antarctic Pseudoalteromonas haloplanktis TAC125 (PhTAC/tou) expressing a toluene-o-xylene monooxygenase (ToMO) is able to convert several aromatic compounds into corresponding catechols. In our work we improved the metabolic capability of PhTAC/tou cells by combining action of recombinant ToMO enzyme with that of the endogenous P. haloplanktis TAC125 laccase-like protein. This strategy allowed conferring new and specific degradative capabilities to a bacterium isolated from an unpolluted environment; indeed engineered PhTAC/tou cells are able to grow on aromatic compounds as sole carbon and energy sources. Our approach demonstrates the possibility to use the engineered psychrophilic bacterium for the bioremediation of chemically contaminated marine environments and/or cold effluents.

  16. Characterization of a Marine Bacterium Associated with Crassostrea virginica (the Eastern Oyster)

    PubMed Central

    Weiner, Ronald M.; Segall, Anca M.; Colwell, Rita R.

    1985-01-01

    A gram-negative bacterium found to be closely associated with oysters has been isolated and characterized. The organism, designated LST, has a generation time of 106 min in Marine broth under optimal growth conditions at 25°C. During the decline phase of growth, it exhibits a morphological transition from a motile rod (ca. 1 μm in length) to an elongated, 3- to 40-μm, nonmotile, tightly coiled helix. LST synthesizes and releases a pigment in the stationary and decline phases of growth. Identified as melanin on the basis of chemical properties and UV absorbance maxima, the pigment comprises polymers of heterogeneous molecular weights, ranging from 12,000 to 120,000. The guanosine-plus-cytosine content of the LST DNA is 46%, and results of phenetic analysis and DNA-DNA hybridization indicate that this bacterium represents a new species. LST adheres to a variety of surfaces, including glass, plastics, and oyster shell, and has been shown to promote the settlement of oyster larvae. Images PMID:16346712

  17. Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Produces N-Acyl-Homoserine Lactone Autoinducers.

    PubMed

    Mellbye, Brett L; Bottomley, Peter J; Sayavedra-Soto, Luis A

    2015-09-01

    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.

  18. 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

  19. Cold adaptation in the marine bacterium, Sphingopyxis alaskensis, assessed using quantitative proteomics.

    PubMed

    Ting, Lily; Williams, Timothy J; Cowley, Mark J; Lauro, Federico M; Guilhaus, Michael; Raftery, Mark J; Cavicchioli, Ricardo

    2010-10-01

    The cold marine environment constitutes a large proportion of the Earth's biosphere. Sphingopyxis alaskensis was isolated as a numerically abundant bacterium from several cold marine locations, and has been extensively studied as a model marine bacterium. Recently, a metabolic labelling platform was developed to comprehensively identify and quantify proteins from S. alaskensis. The approach incorporated data normalization and statistical validation for the purpose of generating highly confident quantitative proteomics data. Using this approach, we determined quantitative differences between cells grown at 10°C (low temperature) and 30°C (high temperature). Cold adaptation was linked to specific aspects of gene expression: a dedicated protein-folding system using GroESL, DnaK, DnaJ, GrpE, SecB, ClpB and PPIase; polyhydroxyalkanoate-associated storage materials; a link between enzymes in fatty acid metabolism and energy generation; de novo synthesis of polyunsaturated fatty acids in the membrane and cell wall; inorganic phosphate ion transport by a phosphate import PstB homologue; TonB-dependent receptor and bacterioferritin in iron homeostasis; histidine, tryptophan and proline amino acid metabolism; and a large number of proteins without annotated functions. This study provides a new level of understanding on how important marine bacteria can adapt to compete effectively in cold marine environments. This study is also a benchmark for comparative proteomic analyses with other important marine bacteria and other cold-adapted organisms. PMID:20482592

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

    PubMed

    Liu, Min; Luo, Kun; 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

  1. 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

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. "Candidatus Paraholospora nucleivisitans", an intracellular bacterium in Paramecium sexaurelia shuttles between the cytoplasm and the nucleus of its host.

    PubMed

    Eschbach, Erik; Pfannkuchen, Martin; Schweikert, Michael; Drutschmann, Denja; Brümmer, Franz; Fokin, Sergei; Ludwig, Wolfgang; Görtz, Hans-Dieter

    2009-10-01

    An intracellular bacterium was discovered in two isolates of Paramecium sexaurelia from an aquarium with tropical fish in Münster (Germany) and from a pond in the Wilhelma zoological-botanical garden, Stuttgart (Germany). The bacteria were regularly observed in the cytoplasm of the host, but on some occasions they were found in the macronucleus of the host cell. In these cases, only a few, if any, bacteria were observed remaining in the cytoplasm. The bacterium was not infectious to P. sexaurelia or other species of Paramecium and appeared to be an obligate intracellular bacterium, while bacteria-free host cells were completely viable. The fluorescence in situ hybridisation (FISH) and comparative 16SrDNA sequence analyses showed that the bacterium belonged to a new genus, and was most closely, yet quite distantly, related to Holospora obtusa. In spite of this relationship, the new bacteria differed from Holospora by at least two biological features. Whereas all Holospora species reside exclusively in the nuclei of various species of Paramecium and show a life cycle with a morphologically distinct infectious form, for the new bacterium no infectious form and no life cycle have been observed. For the new bacterium, the name Candidatus Paraholospora nucleivisitans is suggested. The host P. sexaurelia is usually known from tropical and subtropical areas and is not a species typically found in Germany and central Europe. Possibly, it had been taken to Germany with fish or plants from tropical or subtropical waters. Candidatus Paraholospora nucleivisitans may therefore be regarded as an intracellular neobacterium for Germany.

  7. Helicobacter pylori infection and chronic immune thrombocytopenic purpura: long-term results of bacterium eradication and association with bacterium virulence profiles.

    PubMed

    Emilia, Giovanni; Luppi, Mario; Zucchini, Patrizia; Morselli, Monica; Potenza, Leonardo; Forghieri, Fabio; Volzone, Francesco; Jovic, Gordana; Leonardi, Giovanna; Donelli, Amedea; Torelli, Giuseppe

    2007-12-01

    Eradication of Helicobacter pylori may lead to improvement of chronic immune thrombocytopenic purpura (ITP), although its efficacy over time is uncertain. We report the results of H pylori screening and eradication in 75 consecutive adult patients with ITP. We also used molecular methods to investigate lymphocyte clonality and H pylori genotypes in the gastric biopsies from 10 H pylori-positive patients with ITP and 19 H pylori-positive patients without ITP with chronic gastritis. Active H pylori infection was documented in 38 (51%) patients and successfully eradicated in 34 (89%) patients. After a median follow-up of 60 months, a persistent platelet response in 23 (68%) of patients with eradicated infection was observed; 1 relapse occurred. No differences in mucosal B- or T-cell clonalities were observed between patients with ITP and control participants. Of note, the frequency of the H pylori cagA gene (P = .02) and the frequency of concomitant H pylori cagA, vacAs1, and iceA genes (triple-positive strains; P = .015) resulted statistically higher in patients with ITP than in control participants. All asymptomatic H pylori-positive patients with ITP were suffering from chronic gastritis. Our data suggest a sustained platelet recovery in a proportion of patients with ITP by H pylori eradication alone. Overrepresentation of specific H pylori genotypes in ITP suggests a possible role for bacterium-related factors in the disease pathogenesis. PMID:17652264

  8. 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

  9. Cloacibacillus porcorum sp. nov., a mucin-degrading bacterium from the swine intestinal tract and emended description of the genus Cloacibacillus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A novel anaerobic, mesophilic, amino-acid-fermenting bacterium, designated strain CL-84T, was isolated from the swine intestinal tract on mucin-based media. The bacterium had curved-rod cells (0.8-1.2 µm x 3.5-5.0 µm), stained Gram negative, and was non-motile with no evidence of spores. CL-84T pro...

  10. 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.

  11. 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

  12. 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

  13. Localization of propionibacterium acnes in granulomas supports a possible etiologic link between sarcoidosis and the bacterium.

    PubMed

    Negi, Mariko; Takemura, Tamiko; Guzman, Josune; Uchida, Keisuke; Furukawa, Asuka; Suzuki, Yoshimi; Iida, Tadatsune; Ishige, Ikuo; Minami, Junko; Yamada, Tetsuo; Kawachi, Hiroshi; Costabel, Ulrich; Eishi, Yoshinobu

    2012-09-01

    Sarcoidosis likely results from the exposure of a genetically susceptible subject to an environmental agent, possibly an infectious one. Mycobacterial and propionibacterial organisms are the most commonly implicated potential etiologic agents. Propionibacterium acnes is the only microorganism, however, found in sarcoid lesions by bacterial culture. To evaluate the pathogenic role of this indigenous bacterium, we screened for the bacterium in sarcoid and non-sarcoid tissues using immunohistochemical methods with novel P. acnes-specific monoclonal antibodies that react with cell-membrane-bound lipoteichoic acid (PAB antibody) and ribosome-bound trigger-factor protein (TIG antibody). We examined formalin-fixed and paraffin-embedded samples of lungs and lymph nodes from 196 patients with sarcoidosis, and corresponding control samples from 275 patients with non-sarcoidosis diseases. The samples were mostly from Japanese patients, with 64 lymph node samples from German patients. Immunohistochemistry with PAB antibody revealed small round bodies within sarcoid granulomas in 20/27 (74%) video-assisted thoracic surgery lung samples, 24/50 (48%) transbronchial lung biopsy samples, 71/81 (88%) Japanese lymph node samples, and 34/38 (89%) German lymph node samples. PAB antibody did not react with non-sarcoid granulomas in any of the 45 tuberculosis samples or the 34 samples with sarcoid reaction. In nongranulomatous areas, small round bodies detected by PAB antibody were found in alveolar macrophages of lungs and paracortical macrophages of lymph nodes from many sarcoid and some non-sarcoid patients. Large-spheroidal acid-fast bodies, Hamazaki-Wesenberg bodies, which were found in 50% of sarcoid and 15% of non-sarcoid lymph node samples, reacted with both PAB and TIG antibodies. Electron microscopy revealed that these Hamazaki-Wesenberg bodies had a single bacterial structure and lacked a cell wall with occasional protrusions from the body. The high frequency and specificity

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

    PubMed Central

    2012-01-01

    Background Chloronitrophenols (CNPs) are widely used in the synthesis of dyes, drugs and pesticides, and constitute a major group of environmental pollutants. 4-Chloro-2-nitrophenol (4C2NP) is an isomer of CNPs that has been detected in various industrial effluents. A number of physicochemical methods have been used for treatment of wastewater containing 4C2NP. These methods are not as effective as microbial degradation, however. Results A 4C2NP-degrading bacterium, Exiguobacterium sp. PMA, which uses 4C2NP as the sole carbon and energy source was isolated from a chemically-contaminated site in India. Exiguobacterium sp. PMA degraded 4C2NP with the release of stoichiometeric amounts of chloride and ammonium ions. The effects of different substrate concentrations and various inoculum sizes on degradation of 4C2NP were investigated. Exiguobacterium sp. PMA degraded 4C2NP up to a concentration of 0.6 mM. High performance liquid chromatography and gas chromatography–mass spectrometry identified 4-chloro-2-aminophenol (4C2AP) and 2-aminophenol (2AP) as possible metabolites of the 4C2NP degradation pathway. The crude extract of 4C2NP-induced PMA cells contained enzymatic activity for 4C2NP reductase and 4C2AP dehalogenase, suggesting the involvement of these enzymes in the degradation of 4C2NP. Microcosm studies using sterile and non-sterile soils spiked with 4C2NP were carried out to monitor the bioremediation potential of Exiguobacterium sp. PMA. The bioremediation of 4C2NP by Exiguobacterium sp. PMA was faster in non-sterilized soil than sterilized soil. Conclusions Our studies indicate that Exiguobacterium sp. PMA may be useful for the bioremediation of 4C2NP-contaminated sites. This is the first report of (i) the formation of 2AP in the 4C2NP degradation pathway by any bacterium and (iii) the bioremediation of 4C2NP by any bacterium. PMID:23171039

  15. 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

  16. 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

  17. 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

  18. 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

  19. Modular construction of a functional artificial epothilone polyketide pathway.

    PubMed

    Osswald, Corina; Zipf, Gregor; Schmidt, Gisela; Maier, Josef; Bernauer, Hubert S; Müller, Rolf; Wenzel, Silke C

    2014-10-17

    Natural products of microbial origin continue to be an important source of pharmaceuticals and agrochemicals exhibiting potent activities and often novel modes of action. Due to their inherent structural complexity chemical synthesis is often hardly possible, leaving fermentation as the only viable production route. In addition, the pharmaceutical properties of natural products often need to be optimized for application by sophisticated medicinal chemistry and/or biosynthetic engineering. The latter requires a detailed understanding of the biosynthetic process and genetic tools to modify the producing organism that are often unavailable. Consequently, heterologous expression of complex natural product pathways has been in the focus of development over recent years. However, piecing together existing DNA cloned from natural sources and achieving efficient expression in heterologous circuits represent several limitations that can be addressed by synthetic biology. In this work we have redesigned and reassembled the 56 kb epothilone biosynthetic gene cluster from Sorangium cellulosum for expression in the high GC host Myxococcus xanthus. The codon composition was adapted to a modified codon table for M. xanthus, and unique restriction sites were simultaneously introduced and others eliminated from the sequence in order to permit pathway assembly and future interchangeability of modular building blocks from the epothilone megasynthetase. The functionality of the artificial pathway was demonstrated by successful heterologous epothilone production in M. xanthus at significant yields that have to be improved in upcoming work. Our study sets the stage for future engineering of epothilone biosynthesis and production optimization using a highly flexible assembly strategy. PMID:23654254

  20. Genome sequence of the bioplastic-producing "Knallgas" bacterium Ralstonia eutropha H16.

    PubMed

    Pohlmann, Anne; Fricke, Wolfgang Florian; Reinecke, Frank; Kusian, Bernhard; Liesegang, Heiko; Cramm, Rainer; Eitinger, Thomas; Ewering, Christian; Pötter, Markus; Schwartz, Edward; Strittmatter, Axel; Voss, Ingo; Gottschalk, Gerhard; Steinbüchel, Alexander; Friedrich, Bärbel; Bowien, Botho

    2006-10-01

    The H(2)-oxidizing lithoautotrophic bacterium Ralstonia eutropha H16 is a metabolically versatile organism capable of subsisting, in the absence of organic growth substrates, on H(2) and CO(2) as its sole sources of energy and carbon. R. eutropha H16 first attracted biotechnological interest nearly 50 years ago with the realization that the organism's ability to produce and store large amounts of poly[R-(-)-3-hydroxybutyrate] and other polyesters could be harnessed to make biodegradable plastics. Here we report the complete genome sequence of the two chromosomes of R. eutropha H16. Together, chromosome 1 (4,052,032 base pairs (bp)) and chromosome 2 (2,912,490 bp) encode 6,116 putative genes. Analysis of the genome sequence offers the genetic basis for exploiting the biotechnological potential of this organism and provides insights into its remarkable metabolic versatility.

  1. Sulfonamide inhibition studies of the γ-carbonic anhydrase from the Antarctic bacterium Pseudoalteromonas haloplanktis.

    PubMed

    Vullo, Daniela; De Luca, Viviana; Del Prete, Sonia; Carginale, Vincenzo; Scozzafava, Andrea; Capasso, Clemente; Supuran, Claudiu T

    2015-09-01

    The Antarctic bacterium Pseudoalteromonas haloplanktis encodes for a γ-class carbonic anhydrase (CA, EC 4.2.1.1), which was cloned, purified and characterized. The enzyme (PhaCAγ) has a good catalytic activity for the physiologic reaction of CO2 hydration to bicarbonate and protons, with a k(cat) of 1.4×10(5) s(-1) and a k(cat)/K(m) of 1.9×10(6) M(-1)×s(-1). A series of sulfonamides and a sulfamate were investigated as inhibitors of the new enzyme. Methazolamide and indisulam showed the best inhibitory properties (K(I)s of 86.7-94.7 nM). This contribution shed new light on γ-CAs inhibition profiles with a relevant class of pharmacologic agents.

  2. Indole-based alkaloids from deep-sea bacterium Shewanella piezotolerans with antitumor activities.

    PubMed

    Wang, Yao; Tang, Xixiang; Shao, Zhongzhe; Ren, Jinwei; Liu, Dong; Proksch, Peter; Lin, Wenhan

    2014-05-01

    Chromatographic separation of a crude extract obtained from a fermentation broth of a chemically unknown bacterium Shewanella piezotolerans WP3 collected in deep-sea yielded three new indole alkaloids namely shewanellines A (1a), B (1b) and C (2), together with 12 known indole alkaloids. The structures were unambiguously elucidated on the basis of 1D and 2D NMR ((1)H, (13)C, COSY, HMBC, HSQC and NOESY) in association with MS and CD data. Compounds 1-4, 7, 9 and 11-14 were selected for the evaluation of their cytotoxic activities against human tumor cell lines HL-60 and BEL-7402, whereas compounds 2, 4 and 9 exhibited significant inhibition toward HL-60.

  3. 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

  4. Anaerobic metabolism of phthalate and other aromatic compounds by a denitrifying bacterium. [Pseudomonas sp

    SciTech Connect

    Nozawa, T.; Maruyama, Y. )

    1988-12-01

    The anaerobic metabolism of phthalate and other aromatic compounds by the denitrifying bacterium Pseudomonas sp. strain P136 was studied. Benzoate, cyclohex-1-ene-carboxylate, 2-hydroxycyclohexanecarboxylate, and pimelate were detected as predominant metabolic intermediates during the metabolism of three isomers of phthalate, m-hydroxybenzoate, p-hydroxybenzoate, and cyclohex-3-ene-carboxylate. Inducible acyl-coeznyme A synthetase activities for phthalates, benzoate, cyclohex-1-ene-carboxylate, and cyclohex-3-ene-carboxylate were detected in the cells grown on aromatic compounds. Simultaneous adaptation to these aromatic compounds also occurred. A similar phenomenon was observed in the aerobic metabolism of aromatic compounds by this strain. A new pathway for the anaerobic metabolism of phthalate and a series of other aromatic compounds by this strain was proposed. Some properties of the regulation of this pathway were also discussed.

  5. 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

    2015-03-02

    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.

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

    PubMed

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

    2004-03-01

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

  7. [Expression of phosphofructokinase gene from Escherichia coli K-12 in obligately autotrophic bacterium Acidithiobacillus thiooxidans].

    PubMed

    Tian, Keli; Lin, Jianqun; Liu, Xiangmei; Liu, Ying; Zhang, Changkai

    2003-10-01

    A plasmid pSDK-1 containing the Escherichia coli phosphofructokinase-1 (EC 2.7.1. 11) gene (pfkA) was constructed and transferred into Acidithiobacillus thiooxidans Tt-Z2 by conjugation. The transfer frequency of plasmid from E. coli to Tt-Z2 was 2.6 x 10(-6). More than 68% of Tt-Z2 cells carried the recombinant plasmids after being cultured for 50 generations without selective pressure, which showed that pSDK-1 was maintained consistently in Tt-Z2. The pfkA gene from E. coli could be expressed in this obligately autotrophic bacterium but the enzyme activity (14 U/g was lower than that in E. coli (K-12: 86 U/g; DF1010 carrying plasmid pSDK-1: 97 U/g). In th presence of glucose, the Tt-Z2 transconjugant consumed glucose leading to a better growth yield.

  8. 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

  9. 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.

  10. 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

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

    PubMed Central

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

    2015-01-01

    A strictly anaerobic Gram-stain positive, spore-forming, rod-shaped bacterium designated NE08VT, was isolated from a fecal sample of an individual residing in a remote Amazonian community in Peru. Phylogenetic analysis based on the 16S rRNA gene sequence showed the organism belonged to the genus Clostridium and is most closely related to Clostridium vulturis (97.4% sequence similarity) and was further characterized using biochemical and chemotaxonomic methods. The major cellular fatty acids were anteiso C13:0 and C16:0 with a genomic DNA G + C content of 31.6 mol%. Fermentation products during growth on glucose were acetate and butyrate. Based on phylogenetic, phenotypic and chemotaxonomic information, strain NE08V was identified as representing a novel species of the genus Clostridium, for which the name Clostridium amazonense sp. nov. is proposed. The type strain is NE08VT (DSM 23598T = CCUG 59712T). PMID:26123611

  12. Characterization and a point mutational approach of a psychrophilic lipase from an arctic bacterium, Bacillus pumilus.

    PubMed

    Wi, Ah Ram; Jeon, Sung-Jong; Kim, Sunghui; Park, Ha Ju; Kim, Dockyu; Han, Se Jong; Yim, Joung Han; Kim, Han-Woo

    2014-06-01

    A bacterium with lipolytic activity was isolated from the Chukchi Sea within the Arctic Ocean. The lipase BpL5 from the isolate, Bacillus pumilus ArcL5, belongs to subfamily 4 of lipase family I. The optimum pH and temperature of the recombinant enzyme BpL5, as expressed in Escherichia coli, were 9.0 and 20 °C, respectively. The enzyme retained 85 % of its activity at 5 °C. There was a significant difference between temperatures for maximal activity (20 °C) and for protein denaturation (approx. 45 °C). The enzyme preferred middle-chain (C8) p-nitrophenyl substrates. Two mutants, S139A and S139Y, were rationally designed based on the 3D-structure model, and their activities were compared with that of the wild type. The both mutants showed significantly improved activity against tricaprylin.

  13. 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.

  14. 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.

  15. 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.

  16. Biotransformation of luteoloside by a newly isolated human intestinal bacterium using UHPLC-Q-TOF/MS.

    PubMed

    Tao, Jin-hua; Wang, Dong-geng; Yang, Chi; Huang, Jin-hua; Qiu, Wen-qian; Zhao, Xi

    2015-06-01

    To explore the metabolic pathways and metabolites of luteoloside yielded by the isolated human intestinal bacteria from healthy human feces and characterize the β-d-glucosidase activity of the specific strain which catalyzed the breakdown of luteoloside, a preculture bacterial GAM broth and luteoloside were mixed incubated together for 48h. UHPLC-Q-TOF/MS was used for analysis of the metabolites of luteoloside in the corresponding supernatant fractions from fermentation. Aliquots of the reactive solutions were collected at different times and were measured with a microplate reader at 405nm to evaluate the enzymatic activity. Three metabolites (acetylated luteoloside, luteolin and deoxygenated luteolin) were detected in the fractions isolated from the bacterial samples. The variation of β-d-glucosidase activity inside the bacterium was in coincidence with the changes in luteolin generation or luteoloside degradation in different time periods.

  17. 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.

  18. 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

  19. Proteomic Profiling of the Dioxin-Degrading Bacterium Sphingomonas wittichii RW1

    PubMed Central

    Colquhoun, David R.; Hartmann, Erica M.; Halden, Rolf U.

    2012-01-01

    Sphingomonas wittichii RW1 is a bacterium of interest due to its ability to degrade polychlorinated dioxins, which represent priority pollutants in the USA and worldwide. Although its genome has been fully sequenced, many questions exist regarding changes in protein expression of S. wittichii RW1 in response to dioxin metabolism. We used difference gel electrophoresis (DIGE) and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) to identify proteomic changes induced by growth on dibenzofuran, a surrogate for dioxin, as compared to acetate. Approximately 10% of the entire putative proteome of RW1 could be observed. Several components of the dioxin and dibenzofuran degradation pathway were shown to be upregulated, thereby highlighting the utility of using proteomic analyses for studying bioremediation agents. This is the first global protein analysis of a microorganism capable of utilizing the carbon backbone of both polychlorinated dioxins and dibenzofurans as the sole source for carbon and energy. PMID:23091346

  20. 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

  1. Draft whole genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344.

    PubMed

    Luque-Almagro, Víctor M; Acera, Felipe; Igeño, Ma Isabel; Wibberg, Daniel; Roldán, Ma Dolores; Sáez, Lara P; Hennig, Magdalena; Quesada, Alberto; Huertas, Ma José; Blom, Jochen; Merchán, Faustino; Escribano, Ma Paz; Jaenicke, Sebastian; Estepa, Jessica; Guijo, Ma Isabel; Martínez-Luque, Manuel; Macías, Daniel; Szczepanowski, Rafael; Becerra, Gracia; Ramirez, Silvia; Carmona, Ma Isabel; Gutiérrez, Oscar; Manso, Isabel; Pühler, Alfred; Castillo, Francisco; Moreno-Vivián, Conrado; Schlüter, Andreas; Blasco, Rafael

    2013-01-01

    Pseudomonas pseudoalcaligenes CECT5344 is a Gram-negative bacterium able to tolerate cyanide and to use it as the sole nitrogen source. We report here the first draft of the whole genome sequence of a P. pseudoalcaligenes strain that assimilates cyanide. Three aspects are specially emphasized in this manuscript. First, some generalities of the genome are shown and discussed in the context of other Pseudomonadaceae genomes, including genome size, G + C content, core genome and singletons among other features. Second, the genome is analysed in the context of cyanide metabolism, describing genes probably involved in cyanide assimilation, like those encoding nitrilases, and genes related to cyanide resistance, like the cio genes encoding the cyanide insensitive oxidases. Finally, the presence of genes probably involved in other processes with a great biotechnological potential like production of bioplastics and biodegradation of pollutants also is discussed. PMID:22998548

  2. Phylogeny of the filamentous bacterium 'Nostocoida limicola' III from activated sludge.

    PubMed

    Liu, J R; McKenzie, C A; Seviour, E M; Webb, R I; Blackall, L L; Saint, C P; Seviour, R J

    2001-01-01

    Five strains of the filamentous bacterium 'Nostocoida limicola' III were successfully isolated into pure culture from samples of activated sludge biomass from five plants in Australia. 16S rRNA gene sequence analyses showed that all isolates were members of the Planctomycetales, most closely related to Isosphaera pallida, but they differed phenotypically from this species in that they did not glide and were not thermotolerant. The ultrastructure of these 'N. limicola' III isolates was also consistent with them being Planctomycetales, in that they possessed complex intracellular membrane systems compartmentalizing the cells. However, the arrangements of these intracellular membranes differed between isolates. These data confirm that 'N. limicola' III is phylogenetically unrelated to both 'N. limicola' I and 'N. limicola' II, activated sludge filamentous bacteria which share morphological features in common with 'N. limicola' III and which have been presumed historically to be the same or very similar bacteria. PMID:11211260

  3. [Electrooptical properties of soil nitrogen-fixing bacterium Azospirillum brasilense: effect of copper ions].

    PubMed

    Ignatov, O V; Kamnev, A A; Markina, L N; Antoniuk, L P; Kolina, M; Ignatov, V V

    2001-01-01

    The effects of copper ions on the uptake of some essential metals in the biomass and the electrooptical properties of cell suspensions of the nitrogen-fixing soil bacterium Azospirillum brasilense sp. 245 were studied. Copper cations were shown to be effectively taken up by the cell biomass from the culture medium. The addition of copper ions increased the rate of uptake of some other metals present in the culture medium. This was accompanied by changes in the electrooptical characteristics of cell suspension as measured within the orienting electric field frequency range of 10 to 10,000 kHz. The effects observed during short-term incubation of A. brasilense in the presence of copper cations were less significant than during long-term incubation. These results can be used for rapid screening of microbial cultures for enhanced efficiency of sorption and uptake of metals.

  4. Isolation of pigmentation mutants of the green filamentous photosynthetic bacterium Chloroflexus aurantiacus.

    PubMed

    Pierson, B K; Keith, L M; Leovy, J G

    1984-07-01

    Mutants deficient in the production of bacteriochlorophyll c (Bchl c) and one mutant lacking colored carotenoids were isolated from the filamentous gliding bacterium Chloroflexus aurantiacus. Mutagenesis was achieved by using UV radiation or N-methyl-N'-nitro-N-nitrosoguanidine. Several clones were isolated that were deficient in Bchl c synthesis. All reverted. One double mutant deficient both in Bchl c synthesis and in the synthesis of colored carotenoids under anaerobic conditions was isolated. Isolation of a revertant in Bchl c synthesis from this double mutant produced a mutant strain of Chloroflexus that grew photosynthetically under anaerobic conditions and lacked colored carotenoids. Analysis of pigment contents and growth rates of the mutants revealed a positive association between growth rate and content of Bchl c under light-limiting conditions.

  5. Identification of bisphosphatidic acid and its plasmalogen analogues in the phospholipids of a marine bacterium.

    PubMed

    McAllister, D J; De Siervo, A J

    1975-07-01

    A relatively nonpolar unidentified phospholipid (phospholipid X) , isolated from the gram-negative marine bacterium MB 45, was characterized both chromatographically and by chemical analysis. Phospholipid X was shown to be an acidic phospholipid without vicinal hydroxyl, free-amino, or amide groups. The presence of O-alkenyl groups was indicated by a positive reaction for plasmalogen. Mild alkaline methanolysis of phospholipid X yielded only glycerophosphoryglycerol as the derivative. Acetolysis produced only diacyl-glycerol monoacetate. Clevage of O-alkenyl chains by methanolic hydrochloride resulted in the formation of three lyso derivatives. It was estimated that 18.2% of phospholipid X was plasmalogen. From these data, together with chromatographic comparisons with standards, infrared spectra, a molecular weight estimation, and the determination of the glycerol-phosphate-acyl ester ratio, it was concluded that phospholipid X was bisphosphatidic acid mixed with its plasmalogen analogues. PMID:1141198

  6. 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

  7. 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

  8. Biodegradation of nitrobenzene in a lysogeny broth medium by a novel halophilic bacterium Bacillus licheniformis.

    PubMed

    Li, Tian; Deng, Xinping; Wang, Jinjun; Chen, Yucheng; He, Lin; Sun, Yuchuan; Song, Caixia; Zhou, Zhifeng

    2014-12-15

    The Bacillus licheniformis strain YX2, a novel nitrobenzene-degrading halophilic bacterium, was isolated from active sludge obtained from a pesticide factory. Strain YX2 can withstand highly acidic and alkaline conditions and high temperatures. Degradation of nitrobenzene (200mgL(-1)) by YX2 exceeded 70% after 72h in lysogeny broth medium (pH 4-9). Under optimal degradation conditions (33°C, pH 7 in LB medium) YX2 degraded 50, 100, 200, and 600mgL(-1) nitrobenzene within 36, 36, 72, and 156h, respectively. Even in the presence of benzene, phenol or aniline, strain YX2 efficiently degraded nitrobenzene. Furthermore, strain YX2 completely degraded 600mgL(-1) nitrobenzene in 7% NaCl (w/w). Thus, our data show that strain YX2 may have promise for removing nitrobenzene from complex wastewaters with high salinity and variable pH.

  9. 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.

  10. Microbial metabolism of haloaromatics: isolation and properties of a chlorobenzene-degrading bacterium

    SciTech Connect

    Reineke, W.; Knackmuss, H.J.

    1984-02-01

    A chlorobenzene-degrading bacterium was isolated by continuous enrichment from a mixture of soil and sewage samples. This organism, strain WR1306, was grown in a chemostat on a mineral medium with chlorobenzene being supplied through the vapor phase with a critical D/sub c/ value at a dilution rate of 0.55 h/sup -1/. Maximum growth rates in batch culture were accomplished at substrate concentrations of less than or equal to 0.5 mM in the culture medium. During growth on chlorobenzene, stoichiometric amounts of chloride were released. Respiration data and enzyme activities in cell extracts as well as the isolation of 3-chlorocatechol from the culture fluid are consistent with the degradation of chlorobenzene via 3-chloro-cis-1,2-dihydroxycyclohexa-3,5-diene, 3-chlorocatechol, 2-chloro-cis, cis-muconate, trans-4-carboxymethylenebut-2-en-4-olide, maleylacetate, and 3-oxoadipate. 55 references.

  11. Capnocytophaga ochracea-related Bacterium Bacteremia in a Hypertrophic Cardiomyopathy Patient without Neutropenia.

    PubMed

    Ito, Shimpei; Hagiya, Hideharu; Kimura, Keigo; Nishi, Isao; Yoshida, Hisao; Kioka, Hidetaka; Ohtani, Tomohito; Yamaguchi, Osamu; Tanabe, Kazuaki; Tomono, Kazunori; Sakata, Yasushi

    2016-01-01

    Gram-negative fusiform rods were detected in a blood culture obtained from a 63-year-old man who had been hospitalized for a long duration for severe heart failure. Although the organism could not be identified using a conventional method, it was finally identified as a bacterium of the Capnocytophaga ochracea group based on the results of biochemical testing, 16S rRNA sequencing and a matrix-assisted laser desorption ionization time-of-flight mass spectrometry analysis. Although neutropenic patients with poor oral hygiene are exclusively vulnerable to Capnocytophaga bacteremia, this case was unique because such predisposing conditions were not noted. A multi-centered investigation is warranted for a better understanding of this clinically rare, but potentially pathogenic organism. PMID:27629977

  12. 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

  13. Decoherence dynamics of coherent electronic excited states in the photosynthetic purple bacterium Rhodobacter sphaeroides.

    PubMed

    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.

  14. 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.

  15. 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.

  16. 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.

  17. Complete genome sequencing and analysis of Saprospira grandis str. Lewin, a predatory marine bacterium.

    PubMed

    Saw, Jimmy H W; Yuryev, Anton; Kanbe, Masaomi; Hou, Shaobin; Young, Aaron G; Aizawa, Shin-Ichi; Alam, Maqsudul

    2012-03-19

    Saprospira grandis is a coastal marine bacterium that can capture and prey upon other marine bacteria using a mechanism known as 'ixotrophy'. Here, we present the complete genome sequence of Saprospira grandis str. Lewin isolated from La Jolla beach in San Diego, California. The complete genome sequence comprises a chromosome of 4.35 Mbp and a plasmid of 54.9 Kbp. Genome analysis revealed incomplete pathways for the biosynthesis of nine essential amino acids but presence of a large number of peptidases. The genome encodes multiple copies of sensor globin-coupled rsbR genes thought to be essential for stress response and the presence of such sensor globins in Bacteroidetes is unprecedented. A total of 429 spacer sequences within the three CRISPR repeat regions were identified in the genome and this number is the largest among all the Bacteroidetes sequenced to date.

  18. [Isolation and characteristic of a moderately halophilic bacterium accumulated ectoine as main compatible solute].

    PubMed

    He, Jian; Wang, Ting; Sun, Ji-Quan; Gu, Li-Feng; Li, Shun-Peng

    2005-12-01

    A moderately halophilic bacterium(designated strain I15) was isolated from lawn soil. Based on the analysis of 16S rDNA (GenBank accession number DQ010162), morphology, physiological and biochemical characteristics, strain I15 was identified as Virgibacillus marismortuii. This strain was capable of growing under 0% approximately 25% NaCl, and exhibited an optimum NaCl concentration of 10% and an optimum temperature of 30 degrees C and an optimum pH of 7.5 - 8.0 for its growth, respectively. Under hyperosmotic stress, strain 115 accumulated ectoine as the main compatible solute. Under 15% NaCl conditions the intracellar ectoine can reach to 1.608 mmol/(g x cdw), accounted for 89.6% of the total compatible solutes. The biosynthesis of ectoine was under the control of osmotic, and the accumulated ectoine synthesized intraceilularly can released under hypoosmotic shocks and resynthesis under hyperosmotic shock rapidly. PMID:16496700

  19. 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.

  20. Sulfonamide inhibition studies of the γ-carbonic anhydrase from the Antarctic bacterium Pseudoalteromonas haloplanktis.

    PubMed

    Vullo, Daniela; De Luca, Viviana; Del Prete, Sonia; Carginale, Vincenzo; Scozzafava, Andrea; Capasso, Clemente; Supuran, Claudiu T

    2015-09-01

    The Antarctic bacterium Pseudoalteromonas haloplanktis encodes for a γ-class carbonic anhydrase (CA, EC 4.2.1.1), which was cloned, purified and characterized. The enzyme (PhaCAγ) has a good catalytic activity for the physiologic reaction of CO2 hydration to bicarbonate and protons, with a k(cat) of 1.4×10(5) s(-1) and a k(cat)/K(m) of 1.9×10(6) M(-1)×s(-1). A series of sulfonamides and a sulfamate were investigated as inhibitors of the new enzyme. Methazolamide and indisulam showed the best inhibitory properties (K(I)s of 86.7-94.7 nM). This contribution shed new light on γ-CAs inhibition profiles with a relevant class of pharmacologic agents. PMID:26174556

  1. 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.

  2. Proteolysin, a Novel Highly Thermostable and Cosolvent-Compatible Protease from the Thermophilic Bacterium Coprothermobacter proteolyticus

    PubMed Central

    Toplak, Ana; Wu, Bian; Fusetti, Fabrizia; Quaedflieg, Peter J. L. M.

    2013-01-01

    Through genome mining, we identified a gene encoding a putative serine protease of the thermitase subgroup of subtilases (EC 3.4.21.66) in the thermophilic bacterium Coprothermobacter proteolyticus. The gene was functionally expressed in Escherichia coli, and the enzyme, which we called proteolysin, was purified to near homogeneity from crude cell lysate by a single heat treatment step. Proteolysin has a broad pH tolerance and is active at temperatures of up to 80°C. In addition, the enzyme shows good activity and stability in the presence of organic solvents, detergents, and dithiothreitol, and it remains active in 6 M guanidinium hydrochloride. Based on its stability and activity profile, proteolysin can be an excellent candidate for applications where resistance to harsh process conditions is required. PMID:23851086

  3. New features of the cell wall of the radio-resistant bacterium Deinococcus radiodurans.

    PubMed

    Farci, Domenica; Bowler, Matthew W; Kirkpatrick, Joanna; McSweeney, Sean; Tramontano, Enzo; Piano, Dario

    2014-07-01

    We have analyzed the cell wall of the radio-resistant bacterium Deinococcus radiodurans. Unexpectedly, the bacterial envelope appears to be organized in different complexes of high molecular weight. Each complex is composed of several proteins, most of which are coded by genes of unknown function and the majority are constituents of the inner/outer membrane system. One of the most abundant complexes is constituted by the gene DR_0774. This protein is a type of secretin which is a known subunit of the homo-oligomeric channel that represents the main bulk of the type IV piliation family. Finally, a minor component of the pink envelope consists of several inner-membrane proteins. The implications of these findings are discussed.

  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.

  5. 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.

  6. Multiple, stochastic factors can determine acquisition success of the foregut-borne bacterium, Xylella fastidiosa, by a sharpshooter vector

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Xylella fastidiosa is a phytopathogenic foregut-borne bacterium whose vectors are sharpshooter leafhoppers. Despite several decades of study, the mechanisms of transmission (acquisition and inoculation) of X. fastidiosa still are not fully understood. Studies of the inoculation mechanism depend upon...

  7. 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

  8. Whole-Genome Sequence of Marine Bacterium Phaeodactylibacter xiamenensis Strain KD52, Isolated from the Phycosphere of Microalga Phacodactylum tricornutum

    PubMed Central

    Chen, Zhangran; Lei, Xueqian; Li, Yi; Zhang, Jingyan; Zhang, Huajun; Yang, Luxi; Zheng, Wei

    2014-01-01

    Phaeodactylibacter xiamenensis KD52 is a novel bacterium isolated from a culture of the alga Phaeodactylum tricornutum in Xiamen, Fujian Province, China. Here, we present the first draft genome sequence of this strain, which will provide an opportunity to further understand the functional genes related to signing for nutrition from the host algae and the molecular mechanisms underlying its beneficial properties. PMID:25502677

  9. 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

  10. 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

  11. 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

    2015-03-19

    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.

  12. Complete Genome Sequence of Spiroplasma turonicum Tab4cT, a Bacterium Isolated from Horse Flies (Haematopota sp.).

    PubMed

    Lo, Wen-Sui; Gasparich, Gail E; Kuo, Chih-Horng

    2016-09-22

    Spiroplasma turonicum Tab4c(T) was isolated from a horse fly (Haematopota sp.; probably Haematopota pluvialis) collected at Champchevrier, Indre-et-Loire, Touraine, France, in 1991. Here, we report the complete genome sequence of this bacterium to facilitate the investigation of its biology and the comparative genomics among Spiroplasma spp.

  13. 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

  14. 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

  15. 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

    2016-05-05

    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.

  16. Draft Genome Sequence of the Boron-Tolerant and Moderately Halotolerant Bacterium Gracilibacillus boraciitolerans JCM 21714T

    PubMed Central

    Oshima, Kenshiro; Suda, Wataru; Kitamura, Keiko; Iida, Toshiya; Ohmori, Yoshihiro; Fujiwara, Toru; Hattori, Masahira

    2014-01-01

    Gracilibacillus boraciitolerans JCM 21714T has been characterized as a highly boron-tolerant and moderately halotolerant bacterium. Here, we report the draft genome sequence of this strain. The genome sequence facilitates an understanding of the biochemical functions of boron and provides a base to identify the gene(s) involved in the boron tolerance mechanism of the strain. PMID:24558242

  17. Complete Genome Sequence of the Bacterium Aalborg_AAW-1, Representing a Novel Family within the Candidate Phylum SR1.

    PubMed

    Dueholm, Morten Simonsen; Albertsen, Mads; Stokholm-Bjerregaard, Mikkel; McIlroy, Simon J; Karst, Søren M; Nielsen, Per Halkjær

    2015-01-01

    Here, we present the complete genome sequence of the candidate phylum SR1 bacterium Aalborg_AAW-1. Its 16S rRNA gene is only 85.5% similar to that of the closest relative, RAAC1_SR1, and the genome of Aalborg_AAW-1 consequently represents the first of a novel family within the candidate phylum SR1.

  18. 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

  19. 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

  20. 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