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Sample records for bacterial populations co-existing

  1. Co-existence of periodic bursts and death of cycles in a population dynamics system

    NASA Astrophysics Data System (ADS)

    Iyengar, Sudharsana V.; Balakrishnan, Janaki; Kurths, Jürgen

    2016-09-01

    We study the dynamics of a discrete-time tritrophic model which mimics the observed periodicity in the population cycles of the larch budmoth insect which causes widespread defoliation of larch forests at high altitudes periodically. Our model employs q-deformation of numbers to model the system comprising the budmoth, one or more parasitoid species, and larch trees. Incorporating climate parameters, we introduce additional parasitoid species and show that their introduction increases the periodicity of the budmoth cycles as observed experimentally. The presence of these additional species also produces other interesting dynamical effects such as periodic bursting and oscillation quenching via oscillation death, amplitude death, and partial oscillation death which are also seen in nature. We suggest that introducing additional parasitoid species provides an alternative explanation for the collapse of the nine year budmoth outbreak cycles observed in the Swiss Alps after 1981. A detailed exploration of the parameter space of the system is performed with movies of bifurcation diagrams which enable variation of two parameters at a time. Limit cycles emerge through a Neimark-Sacker bifurcation with respect to all parameters in all the five and higher dimensional models we have studied.

  2. Bacterial computing with engineered populations.

    PubMed

    Amos, Martyn; Axmann, Ilka Maria; Blüthgen, Nils; de la Cruz, Fernando; Jaramillo, Alfonso; Rodriguez-Paton, Alfonso; Simmel, Friedrich

    2015-07-28

    We describe strategies for the construction of bacterial computing platforms by describing a number of results from the recently completed bacterial computing with engineered populations project. In general, the implementation of such systems requires a framework containing various components such as intracellular circuits, single cell input/output and cell-cell interfacing, as well as extensive analysis. In this overview paper, we describe our approach to each of these, and suggest possible areas for future research. PMID:26078340

  3. Bacterial computing with engineered populations.

    PubMed

    Amos, Martyn; Axmann, Ilka Maria; Blüthgen, Nils; de la Cruz, Fernando; Jaramillo, Alfonso; Rodriguez-Paton, Alfonso; Simmel, Friedrich

    2015-07-28

    We describe strategies for the construction of bacterial computing platforms by describing a number of results from the recently completed bacterial computing with engineered populations project. In general, the implementation of such systems requires a framework containing various components such as intracellular circuits, single cell input/output and cell-cell interfacing, as well as extensive analysis. In this overview paper, we describe our approach to each of these, and suggest possible areas for future research.

  4. Co-existence of zebra mussels and freshwater unionids: Population dynamics of Leptodea fragilis in a coastal wetland infested with zebra mussels

    USGS Publications Warehouse

    Nichols, S. Jerrine; Amberg, Jon

    1999-01-01

    In 1996, thousands of live Leptodea fragilis were collected from a marsh located in the western basin of Lake Erie that was infested with zebra mussels (Dreissena polymorpha). Despite the presence of zebra mussels at this site for a number of years, this L. fragilis population showed no signs of competition-induced changes in population dynamics. Biofouling was limited: fewer than 1% of the L. fragilis showed evidence of recent or past zebra mussel colonization. Successful recruitment occurred yearly, with multiple year classes collected that ranged in age from 1 to 12 years. However, age and shell length were not well correlated. Seventy-one percent of the individuals collected were 51-80 mm long, but ranged in age from 2 to 4.5 years. Three different patterns of growth or shell deposition were found. Some individuals grew rapidly, reaching 105 mm in 3.5 years, while others grew only 4.5 mm over the same time period. A few grew poorly during some years but very rapidly in others. Individuals with a shell length of 41 mm or more were sexually mature and females were more common than males. The strong recruitment and steady growth of this population showed no change between the years before and after the zebra mussel invasion, indicating that this marsh is functioning as a natural refugium from potential problems caused by zebra mussels.

  5. Bacterial population genetics, evolution and epidemiology.

    PubMed Central

    Spratt, B G; Maiden, M C

    1999-01-01

    Asexual bacterial populations inevitably consist of an assemblage of distinct clonal lineages. However, bacterial populations are not entirely asexual since recombinational exchanges occur, mobilizing small genome segments among lineages and species. The relative contribution of recombination, as opposed to de novo mutation, in the generation of new bacterial genotypes varies among bacterial populations and, as this contribution increases, the clonality of a given population decreases. In consequence, a spectrum of possible population structures exists, with few bacterial species occupying the extremes of highly clonal and completely non-clonal, most containing both clonal and non-clonal elements. The analysis of collections of bacterial isolates, which accurately represent the natural population, by nucleotide sequence determination of multiple housekeeping loci provides data that can be used both to investigate the population structure of bacterial pathogens and for the molecular characterization of bacterial isolates. Understanding the population structure of a given pathogen is important since it impacts on the questions that can be addressed by, and the methods and samples required for, effective molecular epidemiological studies. PMID:10365396

  6. Dynamics of adaptive immunity against phage in bacterial populations

    NASA Astrophysics Data System (ADS)

    Bradde, Serena; Vucelja, Marija; Tesileanu, Tiberiu; Balasubramanian, Vijay

    The CRISPR (clustered regularly interspaced short palindromic repeats) mechanism allows bacteria to adaptively defend against phages by acquiring short genomic sequences (spacers) that target specific sequences in the viral genome. We propose a population dynamical model where immunity can be both acquired and lost. The model predicts regimes where bacterial and phage populations can co-exist, others where the populations oscillate, and still others where one population is driven to extinction. Our model considers two key parameters: (1) ease of acquisition and (2) spacer effectiveness in conferring immunity. Analytical calculations and numerical simulations show that if spacers differ mainly in ease of acquisition, or if the probability of acquiring them is sufficiently high, bacteria develop a diverse population of spacers. On the other hand, if spacers differ mainly in their effectiveness, their final distribution will be highly peaked, akin to a ``winner-take-all'' scenario, leading to a specialized spacer distribution. Bacteria can interpolate between these limiting behaviors by actively tuning their overall acquisition rate.

  7. Co-existence of agricultural production systems.

    PubMed

    Jank, Bernhard; Rath, Johannes; Gaugitsch, Helmut

    2006-05-01

    Strategies and best practices for the co-existence of GM and non-GM crops need to be developed and implemented with the participation of farmers and other stakeholders. According to the principle of 'subsidiarity', decisions should be made by the lowest authority possible. When applying this concept to the case of GM crops, the affected society should determine their use and management in a regional decision-making process. Public participation is better accomplished at a lower level, and democratic deficits in decision-making on GMOs are better resolved, enabling farmers to manage or avoid GM crops. Ultimately, voluntary GMO-free zones might be a tool for sustainable co-existence and GM-free production and GMO-free zones might create a specific image for marketing regional products and services, such as tourism. PMID:16545877

  8. Co-existence of agricultural production systems.

    PubMed

    Jank, Bernhard; Rath, Johannes; Gaugitsch, Helmut

    2006-05-01

    Strategies and best practices for the co-existence of GM and non-GM crops need to be developed and implemented with the participation of farmers and other stakeholders. According to the principle of 'subsidiarity', decisions should be made by the lowest authority possible. When applying this concept to the case of GM crops, the affected society should determine their use and management in a regional decision-making process. Public participation is better accomplished at a lower level, and democratic deficits in decision-making on GMOs are better resolved, enabling farmers to manage or avoid GM crops. Ultimately, voluntary GMO-free zones might be a tool for sustainable co-existence and GM-free production and GMO-free zones might create a specific image for marketing regional products and services, such as tourism.

  9. Bacterial Landlines: Contact-dependent Signaling in Bacterial Populations

    PubMed Central

    Blango, Matthew G.; Mulvey, Matthew A.

    2009-01-01

    Summary Bacterial populations utilize a variety of signaling strategies to exchange information, including the secretion of quorum-sensing molecules and contact-dependent signaling cascades. Although quorum sensing has received the bulk of attention for many years, contact-dependent signaling is forging a niche in the research world with the identification of novel systems and the emergence of more mechanistic data. Contact-dependent signaling is likely a common strategy by which bacteria in close contact, such as within biofilms, can modulate the growth and behavior of both siblings and competitors. Ongoing work with diverse bacterial systems, including Myxococcus xanthus, pathogenic Escherichia coli strains, Bacillus subtilis, and dissimilatory metal-reducing soil bacteria, is providing increasingly detailed insight into the dynamic mechanisms and potential of contact-dependent signaling processes. PMID:19246237

  10. Population dynamics on heterogeneous bacterial substrates

    NASA Astrophysics Data System (ADS)

    Mobius, Wolfram; Murray, Andrew W.; Nelson, David R.

    2012-02-01

    How species invade new territories and how these range expansions influence the population's genotypes are important questions in the field of population genetics. The majority of work addressing these questions focuses on homogeneous environments. Much less is known about the population dynamics and population genetics when the environmental conditions are heterogeneous in space. To better understand range expansions in two-dimensional heterogeneous environments, we employ a system of bacteria and bacteriophage, the viruses of bacteria. Thereby, the bacteria constitute the environment in which a population of bacteriophages expands. The spread of phage constitutes itself in lysis of bacteria and thus formation of clear regions on bacterial lawns, called plaques. We study the population dynamics and genetics of the expanding page for various patterns of environments.

  11. Bacterial Population Genetics in a Forensic Context

    SciTech Connect

    Velsko, S P

    2009-11-02

    This report addresses the recent Department of Homeland Security (DHS) call for a Phase I study to (1) assess gaps in the forensically relevant knowledge about the population genetics of eight bacterial agents of concern, (2) formulate a technical roadmap to address those gaps, and (3) identify new bioinformatics tools that would be necessary to analyze and interpret population genetic data in a forensic context. The eight organisms that were studied are B. anthracis, Y. pestis, F. tularensis, Brucella spp., E. coli O157/H7, Burkholderia mallei, Burkholderia pseudomallei, and C. botulinum. Our study focused on the use of bacterial population genetics by forensic investigators to test hypotheses about the possible provenance of an agent that was used in a crime or act of terrorism. Just as human population genetics underpins the calculations of match probabilities for human DNA evidence, bacterial population genetics determines the level of support that microbial DNA evidence provides for or against certain well-defined hypotheses about the origins of an infecting strain. Our key findings are: (1) Bacterial population genetics is critical for answering certain types of questions in a probabilistic manner, akin (but not identical) to 'match probabilities' in DNA forensics. (2) A basic theoretical framework for calculating likelihood ratios or posterior probabilities for forensic hypotheses based on microbial genetic comparisons has been formulated. This 'inference-on-networks' framework has deep but simple connections to the population genetics of mtDNA and Y-STRs in human DNA forensics. (3) The 'phylogeographic' approach to identifying microbial sources is not an adequate basis for understanding bacterial population genetics in a forensic context, and has limited utility, even for generating 'leads' with respect to strain origin. (4) A collection of genotyped isolates obtained opportunistically from international locations augmented by phylogenetic representations

  12. Neurotransmitters co-existing with VIP or PACAP.

    PubMed

    Fahrenkrug, Jan; Hannibal, Jens

    2004-03-01

    It is now recognized that a neuron can produce, store and release more than one transmitter substance, and a number of examples of co-existing transmitters, particularly a neuropeptide together with a classical transmitter, have been reported. The present paper deals with transmitter substances, peptides or classical transmitters, co-existing with the two structurally related peptides VIP and PACAP and the possible functional implications of this co-existence.

  13. Dynamics of genome rearrangement in bacterial populations.

    PubMed

    Darling, Aaron E; Miklós, István; Ragan, Mark A

    2008-01-01

    characterization of genome arrangement evolution in a bacterial population evolving outside laboratory conditions. Insight into the process of genomic rearrangement may further the understanding of pathogen population dynamics and selection on the architecture of circular bacterial chromosomes. PMID:18650965

  14. Dynamics of Genome Rearrangement in Bacterial Populations

    PubMed Central

    Darling, Aaron E.; Miklós, István; Ragan, Mark A.

    2008-01-01

    first characterization of genome arrangement evolution in a bacterial population evolving outside laboratory conditions. Insight into the process of genomic rearrangement may further the understanding of pathogen population dynamics and selection on the architecture of circular bacterial chromosomes. PMID:18650965

  15. Optimal control methods for controlling bacterial populations with persister dynamics

    NASA Astrophysics Data System (ADS)

    Cogan, N. G.

    2016-06-01

    Bacterial tolerance to antibiotics is a well-known phenomena; however, only recent studies of bacterial biofilms have shown how multifaceted tolerance really is. By joining into a structured community and offering shared protection and gene transfer, bacterial populations can protect themselves genotypically, phenotypically and physically. In this study, we collect a line of research that focuses on phenotypic (or plastic) tolerance. The dynamics of persister formation are becoming better understood, even though there are major questions that remain. The thrust of our results indicate that even without detailed description of the biological mechanisms, theoretical studies can offer strategies that can eradicate bacterial populations with existing drugs.

  16. Molecular population genetic analysis of emerged bacterial pathogens: selected insights.

    PubMed Central

    Musser, J. M.

    1996-01-01

    Research in bacterial population genetics has increased in the last 10 years. Population genetic theory and tools and related strategies have been used to investigate bacterial pathogens that have contributed to recent episodes of temporal variation in disease frequency and severity. A common theme demonstrated by these analyses is that distinct bacterial clones are responsible for disease outbreaks and increases in infection frequency. Many of these clones are characterized by unique combinations of virulence genes or alleles of virulence genes. Because substantial interclonal variance exists in relative virulence, molecular population genetic studies have led to the concept that the unit of bacterial pathogenicity is the clone or cell line. Continued new insights into host parasite interactions at the molecular level will be achieved by combining clonal analysis of bacterial pathogens with large-scale comparative sequencing of virulence genes. PMID:8903193

  17. Bacterial associations reveal spatial population dynamics in Anopheles gambiae mosquitoes

    PubMed Central

    Buck, Moritz; Nilsson, Louise K. J.; Brunius, Carl; Dabiré, Roch K.; Hopkins, Richard; Terenius, Olle

    2016-01-01

    The intolerable burden of malaria has for too long plagued humanity and the prospect of eradicating malaria is an optimistic, but reachable, target in the 21st century. However, extensive knowledge is needed about the spatial structure of mosquito populations in order to develop effective interventions against malaria transmission. We hypothesized that the microbiota associated with a mosquito reflects acquisition of bacteria in different environments. By analyzing the whole-body bacterial flora of An. gambiae mosquitoes from Burkina Faso by 16 S amplicon sequencing, we found that the different environments gave each mosquito a specific bacterial profile. In addition, the bacterial profiles provided precise and predicting information on the spatial dynamics of the mosquito population as a whole and showed that the mosquitoes formed clear local populations within a meta-population network. We believe that using microbiotas as proxies for population structures will greatly aid improving the performance of vector interventions around the world. PMID:26960555

  18. Defining heterogeneity within bacterial populations via single cell approaches.

    PubMed

    Davis, Kimberly M; Isberg, Ralph R

    2016-08-01

    Bacterial populations are heterogeneous, which in many cases can provide a selective advantage during changes in environmental conditions. In some instances, heterogeneity exists at the genetic level, in which significant allelic variation occurs within a population seeded by a single cell. In other cases, heterogeneity exists due to phenotypic differences within a clonal, genetically identical population. A variety of mechanisms can drive this latter strategy. Stochastic fluctuations can drive differential gene expression, but heterogeneity in gene expression can also be driven by environmental changes sensed by individual cells residing in distinct locales. Utilizing multiple single cell approaches, workers have started to uncover the extent of heterogeneity within bacterial populations. This review will first describe several examples of phenotypic and genetic heterogeneity, and then discuss many single cell approaches that have recently been applied to define heterogeneity within bacterial populations. PMID:27273675

  19. Raw cow milk bacterial population shifts attributable to refrigeration.

    PubMed

    Lafarge, Véronique; Ogier, Jean-Claude; Girard, Victoria; Maladen, Véronique; Leveau, Jean-Yves; Gruss, Alexandra; Delacroix-Buchet, Agnès

    2004-09-01

    We monitored the dynamic changes in the bacterial population in milk associated with refrigeration. Direct analyses of DNA by using temporal temperature gel electrophoresis (TTGE) and denaturing gradient gel electrophoresis (DGGE) allowed us to make accurate species assignments for bacteria with low-GC-content (low-GC%) (<55%) and medium- or high-GC% (>55%) genomes, respectively. We examined raw milk samples before and after 24-h conservation at 4 degrees C. Bacterial identification was facilitated by comparison with an extensive bacterial reference database ( approximately 150 species) that we established with DNA fragments of pure bacterial strains. Cloning and sequencing of fragments missing from the database were used to achieve complete species identification. Considerable evolution of bacterial populations occurred during conservation at 4 degrees C. TTGE and DGGE are shown to be a powerful tool for identifying the main bacterial species of the raw milk samples and for monitoring changes in bacterial populations during conservation at 4 degrees C. The emergence of psychrotrophic bacteria such as Listeria spp. or Aeromonas hydrophila is demonstrated.

  20. Measurement of Behavioral Evolution in Bacterial Populations

    NASA Astrophysics Data System (ADS)

    Austin, Robert

    2013-03-01

    A curious aspect of bacterial behavior under stress is the induction of filamentation: the anomalous growth of certain bacteria in which cells continue to elongate but do not divide into progeny. We show that E.coli under the influence of the genotoxic antibiotic ciprofloxacin have robust filamentous growth, which provides individual bacteria a mesoscopic niche for evolution until resistant progeny can bud off and propagate. Hence, filamentation is a form of genomic amplification where even a single, isolated bacteria can have access to multiple genomes. We propose a model that predicts that the first arrival time of the normal sized progeny should follow a Gompertz distribution with the mean first arrival time proportional to the elongation rate of filament. These predictions agree with our experimental measurements. Finally, we suggest bacterial filament growth and budding has many similarities to tumor growth and metastasis and can serve as a simpler model to study those complicated processes. Sponsored by the NCI/NIH Physical Sciences Oncology Centers

  1. Dynamics of Sequence -Discrete Bacterial Populations Inferred Using Metagenomes

    SciTech Connect

    Stevens, Sarah; Bendall, Matthew; Kang, Dongwan; Froula, Jeff; Egan, Rob; Chan, Leong-Keat; Tringe, Susannah; McMahon, Katherine; Malmstrom, Rex

    2014-03-14

    From a multi-year metagenomic time series of two dissimilar Wisconsin lakes we have assembled dozens of genomes using a novel approach that bins contigs into distinct genome based on sequence composition, e.g. kmer frequencies, and contig coverage patterns at various times points. Next, we investigated how these genomes, which represent sequence-discrete bacterial populations, evolved over time and used the time series to discover the population dynamics. For example, we explored changes in single nucleotide polymorphism (SNP) frequencies as well as patterns of gene gain and loss in multiple populations. Interestingly, SNP diversity was purged at nearly every genome position in some populations during the course of this study, suggesting these populations may have experienced genome-wide selective sweeps. This represents the first direct, time-resolved observations of periodic selection in natural populations, a key process predicted by the ecotype model of bacterial diversification.

  2. Which games are growing bacterial populations playing?

    PubMed Central

    Li, Xiang-Yi; Pietschke, Cleo; Fraune, Sebastian; Altrock, Philipp M.; Bosch, Thomas C. G.; Traulsen, Arne

    2015-01-01

    Microbial communities display complex population dynamics, both in frequency and absolute density. Evolutionary game theory provides a natural approach to analyse and model this complexity by studying the detailed interactions among players, including competition and conflict, cooperation and coexistence. Classic evolutionary game theory models typically assume constant population size, which often does not hold for microbial populations. Here, we explicitly take into account population growth with frequency-dependent growth parameters, as observed in our experimental system. We study the in vitro population dynamics of the two commensal bacteria (Curvibacter sp. (AEP1.3) and Duganella sp. (C1.2)) that synergistically protect the metazoan host Hydra vulgaris (AEP) from fungal infection. The frequency-dependent, nonlinear growth rates observed in our experiments indicate that the interactions among bacteria in co-culture are beyond the simple case of direct competition or, equivalently, pairwise games. This is in agreement with the synergistic effect of anti-fungal activity observed in vivo. Our analysis provides new insight into the minimal degree of complexity needed to appropriately understand and predict coexistence or extinction events in this kind of microbial community dynamics. Our approach extends the understanding of microbial communities and points to novel experiments. PMID:26236827

  3. Dynamic control and quantification of bacterial population dynamics in droplets

    PubMed Central

    Huang, Shuqiang; Srimani, Jaydeep K.; Lee, Anna J.; Zhang, Ying; Lopatkin, Allison J.; Leong, Kam W.; You, Lingchong

    2015-01-01

    Culturing and measuring bacterial population dynamics are critical to develop insights into gene regulation or bacterial physiology. Traditional methods, based on bulk culture to obtain such quantification, have the limitations of higher cost/volume of reagents, non-amendable to small size of population and more laborious manipulation. To this end, droplet-based microfluidics represents a promising alternative that is cost-effective and high-throughput. However, difficulties in manipulating the droplet environment and monitoring encapsulated bacterial population for long-term experiments limit its utilization. To overcome these limitations, we used an electrode-free injection technology to modulate the chemical environment in droplets. This ability is critical for precise control of bacterial dynamics in droplets. Moreover, we developed a trapping device for long-term monitoring of population dynamics in individual droplets for at least 240 h. We demonstrated the utility of this new microfluidic system by quantifying population dynamics of natural and engineered bacteria. Our approach can further improve the analysis for systems and synthetic biology in terms of manipulability and high temporal resolution. PMID:26005763

  4. Co-existence of Functionally Different Vesicular Neurotransmitter Transporters

    PubMed Central

    Münster-Wandowski, Agnieszka; Zander, Johannes-Friedrich; Richter, Karin; Ahnert-Hilger, Gudrun

    2016-01-01

    The vesicular transmitter transporters VGLUT, VGAT, VMAT2 and VAChT, define phenotype and physiological properties of neuronal subtypes. VGLUTs concentrate the excitatory amino acid glutamate, VGAT the inhibitory amino acid GABA, VMAT2 monoamines, and VAChT acetylcholine (ACh) into synaptic vesicle (SV). Following membrane depolarization SV release their content into the synaptic cleft. A strict segregation of vesicular transporters is mandatory for the precise functioning of synaptic communication and of neuronal circuits. In the last years, evidence accumulates that subsets of neurons express more than one of these transporters leading to synaptic co-release of different and functionally opposing transmitters and modulation of synaptic plasticity. Synaptic co-existence of transporters may change during pathological scenarios in order to ameliorate misbalances in neuronal activity. In addition, evidence increases that transporters also co-exist on the same vesicle providing another layer of regulation. Generally, vesicular transmitter loading relies on an electrochemical gradient ΔμH+ driven by the proton ATPase rendering the lumen of the vesicle with respect to the cytosol positive (Δψ) and acidic (ΔpH). While the activity of VGLUT mainly depends on the Δψ component, VMAT, VGAT and VAChT work best at a high ΔpH. Thus, a vesicular synergy of transporters depending on the combination may increase or decrease the filling of SV with the principal transmitter. We provide an overview on synaptic co-existence of vesicular transmitter transporters including changes in the excitatory/inhibitory balance under pathological conditions. Additionally, we discuss functional aspects of vesicular synergy of transmitter transporters. PMID:26909036

  5. Electrical signaling and photosynthesis: can they co-exist together?

    PubMed

    Pavlovič, Andrej; Mancuso, Stefano

    2011-06-01

    Mechanical irritation of trigger hairs and subsequent generation of action potentials have significant impact on photosynthesis and respiration in carnivorous Venus flytrap (Dionaea muscipula). Action potential-mediated inhibition of photosynthesis and stimulation of respiration is confined only to the trap and was not recorded in adjacent photosynthetic lamina. We showed that the main primary target of electrical signals on assimilation is in the dark enzymatic reaction of photosynthesis. Without doubt, the electrical signaling is costly, and the possible co-existence of such type of signals and photosynthesis in plant cell is discussed.

  6. Coal and climate regulations can co-exist

    SciTech Connect

    Rogers, J.

    2006-07-15

    Jim Rogers, president and chief executive officer of Duke Energy Corporation, examines how coal and climate change regulations can co-exist. He addresses the need for economically sound choices for future energy needs, which is complicated by what he refers to as 'the elephant in the room'climate change. He observes that new CO{sub 2} regulations would increase the USA's cost of generating electricity over time and result in higher prices for customers, and he advocates that a gradual, economy-wide, market-based U.S. climate policy is the best option. 1 ref., 1 fig.

  7. Phage selection for bacterial cheats leads to population decline.

    PubMed

    Vasse, Marie; Torres-Barceló, Clara; Hochberg, Michael E

    2015-11-01

    While predators and parasites are known for their effects on bacterial population biology, their impact on the dynamics of bacterial social evolution remains largely unclear. Siderophores are iron-chelating molecules that are key to the survival of certain bacterial species in iron-limited environments, but their production can be subject to cheating by non-producing genotypes. In a selection experiment conducted over approximately 20 bacterial generations and involving 140 populations of the pathogenic bacterium Pseudomonas aeruginosa PAO1, we assessed the impact of a lytic phage on competition between siderophore producers and non-producers. We show that the presence of lytic phages favours the non-producing genotype in competition, regardless of whether iron use relies on siderophores. Interestingly, phage pressure resulted in higher siderophore production, which constitutes a cost to the producers and may explain why they were outcompeted by non-producers. By the end of the experiment, however, cheating load reduced the fitness of mixed populations relative to producer monocultures, and only monocultures of producers managed to grow in the presence of phage in situations where siderophores were necessary to access iron. These results suggest that public goods production may be modulated in the presence of natural enemies with consequences for the evolution of social strategies. PMID:26538598

  8. In Situ Hydrocarbon Degradation by Indigenous Nearshore Bacterial Populations

    SciTech Connect

    Cherrier, J.

    2005-05-16

    Potential episodic hydrocarbon inputs associated with oil mining and transportation together with chronic introduction of hydrocarbons via urban runoff into the relatively pristine coastal Florida waters poses a significant threat to Florida's fragile marine environment. It is therefore important to understand the extent to which indigenous bacterial populations are able to degrade hydrocarbon compounds and also determine factors that could potentially control and promote the rate at which these compounds are broken down in situ. Previous controlled laboratory experiments carried out by our research group demonstrated that separately both photo-oxidation and cometabolism stimulate bacterial hydrocarbon degradation by natural bacterial assemblages collected from a chronically petroleum contaminated site in Bayboro Bay, Florida. Additionally, we also demonstrated that stable carbon and radiocarbon abundances of respired CO{sub 2} could be used to trace in situ hydrocarbon degradation by indigenous bacterial populations at this same site. This current proposal had two main objectives: (a) to evaluate the cumulative impact of cometabolism and photo-oxidation on hydrocarbon degradation by natural bacterial assemblages collected the same site in Bayboro Bay, Florida and (b) to determine if in situ hydrocarbon degradation by indigenous bacterial populations this site could be traced using natural radiocarbon and stable carbon abundances of assimilated bacterial carbon. Funds were used for 2 years of full support for one ESI Ph.D. student, April Croxton. To address our first objective a series of closed system bacterial incubations were carried out using photo-oxidized petroleum and pinfish (i.e. cometabolite). Bacterial production of CO{sub 2} was used as the indicator of hydrocarbon degradation and {delta}{sup 13}C analysis of the resultant CO{sub 2} was used to evaluate the source of the respired CO{sub 2} (i.e. petroleum hydrocarbons or the pinfish cometabolite

  9. Differential resistance of drinking water bacterial populations to monochloramine disinfection.

    PubMed

    Chiao, Tzu-Hsin; Clancy, Tara M; Pinto, Ameet; Xi, Chuanwu; Raskin, Lutgarde

    2014-04-01

    The impact of monochloramine disinfection on the complex bacterial community structure in drinking water systems was investigated using culture-dependent and culture-independent methods. Changes in viable bacterial diversity were monitored using culture-independent methods that distinguish between live and dead cells based on membrane integrity, providing a highly conservative measure of viability. Samples were collected from lab-scale and full-scale drinking water filters exposed to monochloramine for a range of contact times. Culture-independent detection of live cells was based on propidium monoazide (PMA) treatment to selectively remove DNA from membrane-compromised cells. Quantitative PCR (qPCR) and pyrosequencing of 16S rRNA genes was used to quantify the DNA of live bacteria and characterize the bacterial communities, respectively. The inactivation rate determined by the culture-independent PMA-qPCR method (1.5-log removal at 664 mg·min/L) was lower than the inactivation rate measured by the culture-based methods (4-log removal at 66 mg·min/L). Moreover, drastic changes in the live bacterial community structure were detected during monochloramine disinfection using PMA-pyrosequencing, while the community structure appeared to remain stable when pyrosequencing was performed on samples that were not subject to PMA treatment. Genera that increased in relative abundance during monochloramine treatment include Legionella, Escherichia, and Geobacter in the lab-scale system and Mycobacterium, Sphingomonas, and Coxiella in the full-scale system. These results demonstrate that bacterial populations in drinking water exhibit differential resistance to monochloramine, and that the disinfection process selects for resistant bacterial populations.

  10. Development of polyvinyl chloride biofilms for succession of selected marine bacterial populations.

    PubMed

    Balasubramanian, V; Palanichamy, S; Subramanian, G; Rajaram, R

    2012-01-01

    Present investigation was made to bring out the pattern of biofilm formation by heterotrophic bacteria on nontoxic material, polyvinyl chloride (PVC) sheet fitted wooden rack that was immersed in seawater and the study was conducted in Tuticorin coast. Samplings were made over a period of 7 days with the following time period intervals: 30 min, 1, 2, 4, 24, 48, 72, 96, 120 and 144 hr. Bacterial enumeration was made by spread plate method on nutrient agar medium and characterization of bacterial isolates up to generic level was done. Gram-negative bacteria like Pseudomonas sp., Enterobacter sp., Aeromonas sp., Cytophaga sp. and Flavobacterium sp. were found to be the pioneer in colonizing the surface within 30 min and seven genera were represented in the biofilm. Among them two genera were found belonging to Gram-positive groups which included Micrococcus and Bacillus sp. The early stage biofilm i.e. up to 24th hr was wholly constituted by Gram-negative groups. However, the population density of Pseudomonas sp. was found to be higher (315 CFU) when compared to other Gram-negative forms. Occurrence of Gram-positive group was noted only at 48th hr old biofilm (28 to 150 CFU). The period between 48 and 96th hr was the transition where both the Gram-negative and Gram-positive groups co- existed. After 96th hr, the biofilm was found constituted only by Gram-positive groups. The isolates of early stage biofilm were found to produce allelopathic substance like bacteriocin.

  11. Bacterial populations and the volatilome associated to meat spoilage.

    PubMed

    Casaburi, Annalisa; Piombino, Paola; Nychas, George-John; Villani, Francesco; Ercolini, Danilo

    2015-02-01

    Microbial spoilage of meat is a complex event to which many different bacterial populations can contribute depending on the temperature of storage and packaging conditions. The spoilage can derive from microbial development and consumption of meat nutrients by bacteria with a consequent release of undesired metabolites. The volatile organic compounds (VOCs) that are generated during meat storage can have an olfactory impact and can lead to rejection of the product when their concentration increase significantly as a result of microbial development. The VOCs most commonly identified in meat during storage include alcohols, aldehydes, ketones, fatty acids, esters and sulfur compounds. In this review, the VOCs found in fresh meat during storage in specific conditions are described together with the possible bacterial populations responsible of their production. In addition, on the basis of the data available in the literature, the sensory impact of the VOCs and their dynamics during storage is discussed to highlight their possible contribution to the spoilage of meat.

  12. Detecting rare gene transfer events in bacterial populations

    PubMed Central

    Nielsen, Kaare M.; Bøhn, Thomas; Townsend, Jeffrey P.

    2014-01-01

    Horizontal gene transfer (HGT) enables bacteria to access, share, and recombine genetic variation, resulting in genetic diversity that cannot be obtained through mutational processes alone. In most cases, the observation of evolutionary successful HGT events relies on the outcome of initially rare events that lead to novel functions in the new host, and that exhibit a positive effect on host fitness. Conversely, the large majority of HGT events occurring in bacterial populations will go undetected due to lack of replication success of transformants. Moreover, other HGT events that would be highly beneficial to new hosts can fail to ensue due to lack of physical proximity to the donor organism, lack of a suitable gene transfer mechanism, genetic compatibility, and stochasticity in tempo-spatial occurrence. Experimental attempts to detect HGT events in bacterial populations have typically focused on the transformed cells or their immediate offspring. However, rare HGT events occurring in large and structured populations are unlikely to reach relative population sizes that will allow their immediate identification; the exception being the unusually strong positive selection conferred by antibiotics. Most HGT events are not expected to alter the likelihood of host survival to such an extreme extent, and will confer only minor changes in host fitness. Due to the large population sizes of bacteria and the time scales involved, the process and outcome of HGT are often not amenable to experimental investigation. Population genetic modeling of the growth dynamics of bacteria with differing HGT rates and resulting fitness changes is therefore necessary to guide sampling design and predict realistic time frames for detection of HGT, as it occurs in laboratory or natural settings. Here we review the key population genetic parameters, consider their complexity and highlight knowledge gaps for further research. PMID:24432015

  13. Modeling bacterial population growth from stochastic single-cell dynamics.

    PubMed

    Alonso, Antonio A; Molina, Ignacio; Theodoropoulos, Constantinos

    2014-09-01

    A few bacterial cells may be sufficient to produce a food-borne illness outbreak, provided that they are capable of adapting and proliferating on a food matrix. This is why any quantitative health risk assessment policy must incorporate methods to accurately predict the growth of bacterial populations from a small number of pathogens. In this aim, mathematical models have become a powerful tool. Unfortunately, at low cell concentrations, standard deterministic models fail to predict the fate of the population, essentially because the heterogeneity between individuals becomes relevant. In this work, a stochastic differential equation (SDE) model is proposed to describe variability within single-cell growth and division and to simulate population growth from a given initial number of individuals. We provide evidence of the model ability to explain the observed distributions of times to division, including the lag time produced by the adaptation to the environment, by comparing model predictions with experiments from the literature for Escherichia coli, Listeria innocua, and Salmonella enterica. The model is shown to accurately predict experimental growth population dynamics for both small and large microbial populations. The use of stochastic models for the estimation of parameters to successfully fit experimental data is a particularly challenging problem. For instance, if Monte Carlo methods are employed to model the required distributions of times to division, the parameter estimation problem can become numerically intractable. We overcame this limitation by converting the stochastic description to a partial differential equation (backward Kolmogorov) instead, which relates to the distribution of division times. Contrary to previous stochastic formulations based on random parameters, the present model is capable of explaining the variability observed in populations that result from the growth of a small number of initial cells as well as the lack of it compared to

  14. Detecting rare gene transfer events in bacterial populations.

    PubMed

    Nielsen, Kaare M; Bøhn, Thomas; Townsend, Jeffrey P

    2014-01-01

    Horizontal gene transfer (HGT) enables bacteria to access, share, and recombine genetic variation, resulting in genetic diversity that cannot be obtained through mutational processes alone. In most cases, the observation of evolutionary successful HGT events relies on the outcome of initially rare events that lead to novel functions in the new host, and that exhibit a positive effect on host fitness. Conversely, the large majority of HGT events occurring in bacterial populations will go undetected due to lack of replication success of transformants. Moreover, other HGT events that would be highly beneficial to new hosts can fail to ensue due to lack of physical proximity to the donor organism, lack of a suitable gene transfer mechanism, genetic compatibility, and stochasticity in tempo-spatial occurrence. Experimental attempts to detect HGT events in bacterial populations have typically focused on the transformed cells or their immediate offspring. However, rare HGT events occurring in large and structured populations are unlikely to reach relative population sizes that will allow their immediate identification; the exception being the unusually strong positive selection conferred by antibiotics. Most HGT events are not expected to alter the likelihood of host survival to such an extreme extent, and will confer only minor changes in host fitness. Due to the large population sizes of bacteria and the time scales involved, the process and outcome of HGT are often not amenable to experimental investigation. Population genetic modeling of the growth dynamics of bacteria with differing HGT rates and resulting fitness changes is therefore necessary to guide sampling design and predict realistic time frames for detection of HGT, as it occurs in laboratory or natural settings. Here we review the key population genetic parameters, consider their complexity and highlight knowledge gaps for further research.

  15. Bacteriocin-Mediated Competitive Interactions of Bacterial Populations and Communities

    NASA Astrophysics Data System (ADS)

    Riley, Margaret A.

    Explaining the coexistence of competing species is a major challenge in community ecology. In bacterial systems, competition is often driven by the production of bacteriocins; narrow spectrum proteinaceous toxins that serve to kill closely related species providing the producer better access to limited resources. Bacteriocin producers have been shown to competitively exclude sensitive, nonproducing strains. However, the interaction dynamics between bacteriocin producers, each lethal to its competitor, are largely unknown. Several recent studies have revealed some of the complexity of these interactions, employing a suite of in vitro, in vivo, and in silico bacterial model systems. This chapter describes the current state of knowledge regarding the population and community ecology of this potent family of toxins.

  16. Genes and processed paralogs co-exist in plant mitochondria.

    PubMed

    Cuenca, Argelia; Petersen, Gitte; Seberg, Ole; Jahren, Anne Hoppe

    2012-04-01

    RNA-mediated gene duplication has been proposed to create processed paralogs in the plant mitochondrial genome. A processed paralog may retain signatures left by the maturation process of its RNA precursor, such as intron removal and no need of RNA editing. Whereas it is well documented that an RNA intermediary is involved in the transfer of mitochondrial genes to the nucleus, no direct evidence exists for insertion of processed paralogs in the mitochondria (i.e., processed and un-processed genes have never been found simultaneously in the mitochondrial genome). In this study, we sequenced a region of the mitochondrial gene nad1, and identified a number of taxa were two different copies of the region co-occur in the mitochondria. The two nad1 paralogs differed in their (a) presence or absence of a group II intron, and (b) number of edited sites. Thus, this work provides the first evidence of co-existence of processed paralogs and their precursors within the plant mitochondrial genome. In addition, mapping the presence/absence of the paralogs provides indirect evidence of RNA-mediated gene duplication as an essential process shaping the mitochondrial genome in plants.

  17. Staphylococcus aureus SrrAB Affects Susceptibility to Hydrogen Peroxide and Co-Existence with Streptococcus sanguinis

    PubMed Central

    Oogai, Yuichi; Kawada-Matsuo, Miki; Komatsuzawa, Hitoshi

    2016-01-01

    Staphylococcus aureus is a pathogen and a commensal bacterial species that is found in humans. Bacterial two-component systems (TCSs) sense and respond to environmental stresses, which include antimicrobial agents produced by other bacteria. In this study, we analyzed the relation between the TCS SrrAB and susceptibility to the hydrogen peroxide (H2O2) that is produced by Streptococcus sanguinis, which is a commensal oral streptococcus. An srrA-inactivated S. aureus mutant demonstrated low susceptibility to the H2O2 produced by S. sanguinis. We investigated the expression of anti-oxidant factors in the mutant. The expression of katA in the mutant was significantly higher than in the wild-type (WT) in the presence or absence of 0.4 mM H2O2. The expression of dps in the mutant was significantly increased compared with the WT in the presence of H2O2 but not in the absence of H2O2. A katA or a dps-inactivated mutant had high susceptibility to H2O2 compared with WT. In addition, we found that the nitric oxide detoxification protein (flavohemoglobin: Hmp), which is regulated by SrrAB, was related to H2O2 susceptibility. The hmp-inactivated mutant had slightly lower susceptibility to the H2O2 produced by S. sanguinis than did WT. When a srrA-inactivated mutant or the WT were co-cultured with S. sanguinis, the population percentage of the mutant was significantly higher than the WT. In conclusion, SrrAB regulates katA, dps and hmp expression and affects H2O2 susceptibility. Our findings suggest that SrrAB is related in vivo to the co-existence of S. aureus with S. sanguinis. PMID:27441894

  18. Staphylococcus aureus SrrAB Affects Susceptibility to Hydrogen Peroxide and Co-Existence with Streptococcus sanguinis.

    PubMed

    Oogai, Yuichi; Kawada-Matsuo, Miki; Komatsuzawa, Hitoshi

    2016-01-01

    Staphylococcus aureus is a pathogen and a commensal bacterial species that is found in humans. Bacterial two-component systems (TCSs) sense and respond to environmental stresses, which include antimicrobial agents produced by other bacteria. In this study, we analyzed the relation between the TCS SrrAB and susceptibility to the hydrogen peroxide (H2O2) that is produced by Streptococcus sanguinis, which is a commensal oral streptococcus. An srrA-inactivated S. aureus mutant demonstrated low susceptibility to the H2O2 produced by S. sanguinis. We investigated the expression of anti-oxidant factors in the mutant. The expression of katA in the mutant was significantly higher than in the wild-type (WT) in the presence or absence of 0.4 mM H2O2. The expression of dps in the mutant was significantly increased compared with the WT in the presence of H2O2 but not in the absence of H2O2. A katA or a dps-inactivated mutant had high susceptibility to H2O2 compared with WT. In addition, we found that the nitric oxide detoxification protein (flavohemoglobin: Hmp), which is regulated by SrrAB, was related to H2O2 susceptibility. The hmp-inactivated mutant had slightly lower susceptibility to the H2O2 produced by S. sanguinis than did WT. When a srrA-inactivated mutant or the WT were co-cultured with S. sanguinis, the population percentage of the mutant was significantly higher than the WT. In conclusion, SrrAB regulates katA, dps and hmp expression and affects H2O2 susceptibility. Our findings suggest that SrrAB is related in vivo to the co-existence of S. aureus with S. sanguinis. PMID:27441894

  19. Spatiotemporal Co-existence of Female Thyroid and Breast Cancers in Hangzhou, China

    PubMed Central

    Fei, Xufeng; Christakos, George; Lou, Zhaohan; Ren, Yanjun; Liu, Qingmin; Wu, Jiaping

    2016-01-01

    Thyroid and breast cancers (TC, BC) are common female malignant tumors worldwide. Studies suggest that TC patients have a higher BC risk, and vice versa. However, it has not been investigated quantitatively if there is an association between the space-time TC and BC incidence distributions at the population level. This work aims to answer this question. 5358 TC and 8784 BC (female) cases were diagnosed in Hangzhou (China, 2008–2012). Pearson and Spearman rank correlation coefficients of the TC and BC incidences were high, and their patterns were geographically similar. The spatiotemporal co-existence of TC and BC distributions was investigated using the integrative disease predictability (IDP) criterion: if TC-BC association is part of the disease mapping knowledge bases, it should yield improved space-time incidence predictions. Improved TC (BC) incidence predictions were generated when integrating both TC and BC data than when using only TC (BC) data. IDP consistently demonstrated the spatiotemporal co-existence of TC and BC distributions throughout Hangzhou (2008–2012), which means that when the population experiences high incidences of one kind of cancer attention should be paid to the other kind of cancer too. The strength of TC-BC association was measured by the IDP coefficients and incidence prediction accuracy. PMID:27341638

  20. Spatiotemporal Co-existence of Female Thyroid and Breast Cancers in Hangzhou, China

    NASA Astrophysics Data System (ADS)

    Fei, Xufeng; Christakos, George; Lou, Zhaohan; Ren, Yanjun; Liu, Qingmin; Wu, Jiaping

    2016-06-01

    Thyroid and breast cancers (TC, BC) are common female malignant tumors worldwide. Studies suggest that TC patients have a higher BC risk, and vice versa. However, it has not been investigated quantitatively if there is an association between the space-time TC and BC incidence distributions at the population level. This work aims to answer this question. 5358 TC and 8784 BC (female) cases were diagnosed in Hangzhou (China, 2008–2012). Pearson and Spearman rank correlation coefficients of the TC and BC incidences were high, and their patterns were geographically similar. The spatiotemporal co-existence of TC and BC distributions was investigated using the integrative disease predictability (IDP) criterion: if TC-BC association is part of the disease mapping knowledge bases, it should yield improved space-time incidence predictions. Improved TC (BC) incidence predictions were generated when integrating both TC and BC data than when using only TC (BC) data. IDP consistently demonstrated the spatiotemporal co-existence of TC and BC distributions throughout Hangzhou (2008–2012), which means that when the population experiences high incidences of one kind of cancer attention should be paid to the other kind of cancer too. The strength of TC-BC association was measured by the IDP coefficients and incidence prediction accuracy.

  1. Attached bacterial populations shared by four species of aquatic angiosperms.

    PubMed

    Crump, Byron C; Koch, Evamaria W

    2008-10-01

    Symbiotic relationships between microbes and plants are common and well studied in terrestrial ecosystems, but little is known about such relationships in aquatic environments. We compared the phylogenetic diversities of leaf- and root-attached bacteria from four species of aquatic angiosperms using denaturing gradient gel electrophoresis (DGGE) and DNA sequencing of PCR-amplified 16S rRNA genes. Plants were collected from three beds in Chesapeake Bay at sites characterized as freshwater (Vallisneria americana), brackish (Potomogeton perfoliatus and Stuckenia pectinata), and marine (Zostera marina). DGGE analyses showed that bacterial communities were very similar for replicate samples of leaves from canopy-forming plants S. pectinata and P. perfoliatus and less similar for replicate samples of leaves from meadow-forming plants Z. marina and V. americana and of roots of all species. In contrast, bacterial communities differed greatly among plant species and between leaves and roots. DNA sequencing identified 154 bacterial phylotypes, most of which were restricted to single plant species. However, 12 phylotypes were found on more than one plant species, and several of these phylotypes were abundant in clone libraries and represented the darkest bands in DGGE banding patterns. Root-attached phylotypes included relatives of sulfur-oxidizing Gammaproteobacteria and sulfate-reducing Deltaproteobacteria. Leaf-attached phylotypes included relatives of polymer-degrading Bacteroidetes and phototrophic Alphaproteobacteria. Also, leaves and roots of three plant species hosted relatives of methylotrophic Betaproteobacteria belonging to the family Methylophilaceae. These results suggest that aquatic angiosperms host specialized communities of bacteria on their surfaces, including several broadly distributed and potentially mutualistic bacterial populations.

  2. Metagenomic reconstructions of bacterial CRISPR loci constrain population histories.

    PubMed

    Sun, Christine L; Thomas, Brian C; Barrangou, Rodolphe; Banfield, Jillian F

    2016-04-01

    Bacterial CRISPR-Cas systems provide insight into recent population history because they rapidly incorporate, in a unidirectional manner, short fragments (spacers) from coexisting infective virus populations into host chromosomes. Immunity is achieved by sequence identity between transcripts of spacers and their targets. Here, we used metagenomics to study the stability and dynamics of the type I-E CRISPR-Cas locus of Leptospirillum group II bacteria in biofilms sampled over 5 years from an acid mine drainage (AMD) system. Despite recovery of 452,686 spacers from CRISPR amplicons and metagenomic data, rarefaction curves of spacers show no saturation. The vast repertoire of spacers is attributed to phage/plasmid population diversity and retention of old spacers, despite rapid evolution of the targeted phage/plasmid genome regions (proto-spacers). The oldest spacers (spacers found at the trailer end) are conserved for at least 5 years, and 12% of these retain perfect or near-perfect matches to proto-spacer targets. The majority of proto-spacer regions contain an AAG proto-spacer adjacent motif (PAM). Spacers throughout the locus target the same phage population (AMDV1), but there are blocks of consecutive spacers without AMDV1 target sequences. Results suggest long-term coexistence of Leptospirillum with AMDV1 and periods when AMDV1 was less dominant. Metagenomics can be applied to millions of cells in a single sample to provide an extremely large spacer inventory, allow identification of phage/plasmids and enable analysis of previous phage/plasmid exposure. Thus, this approach can provide insights into prior bacterial environment and genetic interplay between hosts and their viruses. PMID:26394009

  3. Metagenomic reconstructions of bacterial CRISPR loci constrain population histories.

    PubMed

    Sun, Christine L; Thomas, Brian C; Barrangou, Rodolphe; Banfield, Jillian F

    2016-04-01

    Bacterial CRISPR-Cas systems provide insight into recent population history because they rapidly incorporate, in a unidirectional manner, short fragments (spacers) from coexisting infective virus populations into host chromosomes. Immunity is achieved by sequence identity between transcripts of spacers and their targets. Here, we used metagenomics to study the stability and dynamics of the type I-E CRISPR-Cas locus of Leptospirillum group II bacteria in biofilms sampled over 5 years from an acid mine drainage (AMD) system. Despite recovery of 452,686 spacers from CRISPR amplicons and metagenomic data, rarefaction curves of spacers show no saturation. The vast repertoire of spacers is attributed to phage/plasmid population diversity and retention of old spacers, despite rapid evolution of the targeted phage/plasmid genome regions (proto-spacers). The oldest spacers (spacers found at the trailer end) are conserved for at least 5 years, and 12% of these retain perfect or near-perfect matches to proto-spacer targets. The majority of proto-spacer regions contain an AAG proto-spacer adjacent motif (PAM). Spacers throughout the locus target the same phage population (AMDV1), but there are blocks of consecutive spacers without AMDV1 target sequences. Results suggest long-term coexistence of Leptospirillum with AMDV1 and periods when AMDV1 was less dominant. Metagenomics can be applied to millions of cells in a single sample to provide an extremely large spacer inventory, allow identification of phage/plasmids and enable analysis of previous phage/plasmid exposure. Thus, this approach can provide insights into prior bacterial environment and genetic interplay between hosts and their viruses.

  4. Plasmids foster diversification and adaptation of bacterial populations in soil.

    PubMed

    Heuer, Holger; Smalla, Kornelia

    2012-11-01

    It is increasingly being recognized that the transfer of conjugative plasmids across species boundaries plays a vital role in the adaptability of bacterial populations in soil. There are specific driving forces and constraints of plasmid transfer within bacterial communities in soils. Plasmid-mediated genetic variation allows bacteria to respond rapidly with adaptive responses to challenges such as irregular antibiotic or metal concentrations, or opportunities such as the utilization of xenobiotic compounds. Cultivation-independent detection and capture of plasmids from soil bacteria, and complete sequencing have provided new insights into the role and ecology of plasmids. Broad host range plasmids such as those belonging to IncP-1 transfer a wealth of accessory functions which are carried by similar plasmid backbones. Plasmids with a narrower host range can be more specifically adapted to particular species and often transfer genes which complement chromosomally encoded functions. Plasmids seem to be an ancient and successful strategy to ensure survival of a soil population in spatial and temporal heterogeneous conditions with various environmental stresses or opportunities that occur irregularly or as a novel challenge in soil.

  5. A rare case of breast carcinoma co-existing with axillary mantle cell lymphoma

    PubMed Central

    Dutta Roy, Subhajit; Stafford, Joanna A; Scally, John; Selvachandran, S N

    2003-01-01

    Background Mantle cell lymphoma (MCL) is a rare variety of non-Hodgkin's lymphoma which originates from CD5+ B-cell population in the mantle zones of lymphoid follicles. Coexistence of such tumours in the axillary lymph nodes with invasive breast cancers without prior history of adjuvant chemotherapy or radiotherapy has not been previously reported in literature. Case report We report a rare case of breast cancer co-existing with stage I mantle cell lymphoma of the ipsilateral axillary lymph node detected fortuitously by population screening. Conclusion Though some studies have tried to prove breast carcinomas and lymphomas to share a common molecular or viral link, more research needs to be done to establish whether such a link truly exists. PMID:14664721

  6. Population Dynamics of Patients with Bacterial Resistance in Hospital Environment.

    PubMed

    Qu, Leilei; Pan, Qiuhui; Gao, Xubin; He, Mingfeng

    2016-01-01

    During the past decades, the increase of antibiotic resistance has become a major concern worldwide. The researchers found that superbugs with new type of resistance genes (NDM-1) have two aspects of transmission characteristics; the first is that the antibiotic resistance genes can horizontally transfer among bacteria, and the other is that the superbugs can spread between humans through direct contact. Based on these two transmission mechanisms, we study the dynamics of population in hospital environment where superbugs exist. In this paper, we build three mathematic models to illustrate the dynamics of patients with bacterial resistance in hospital environment. The models are analyzed using stability theory of differential equations. Positive equilibrium points of the system are investigated and their stability analysis is carried out. Moreover, the numerical simulation of the proposed model is also performed which supports the theoretical findings.

  7. Population Dynamics of Patients with Bacterial Resistance in Hospital Environment

    PubMed Central

    Qu, Leilei; Pan, Qiuhui; Gao, Xubin; He, Mingfeng

    2016-01-01

    During the past decades, the increase of antibiotic resistance has become a major concern worldwide. The researchers found that superbugs with new type of resistance genes (NDM-1) have two aspects of transmission characteristics; the first is that the antibiotic resistance genes can horizontally transfer among bacteria, and the other is that the superbugs can spread between humans through direct contact. Based on these two transmission mechanisms, we study the dynamics of population in hospital environment where superbugs exist. In this paper, we build three mathematic models to illustrate the dynamics of patients with bacterial resistance in hospital environment. The models are analyzed using stability theory of differential equations. Positive equilibrium points of the system are investigated and their stability analysis is carried out. Moreover, the numerical simulation of the proposed model is also performed which supports the theoretical findings. PMID:26904150

  8. Population Dynamics of Patients with Bacterial Resistance in Hospital Environment.

    PubMed

    Qu, Leilei; Pan, Qiuhui; Gao, Xubin; He, Mingfeng

    2016-01-01

    During the past decades, the increase of antibiotic resistance has become a major concern worldwide. The researchers found that superbugs with new type of resistance genes (NDM-1) have two aspects of transmission characteristics; the first is that the antibiotic resistance genes can horizontally transfer among bacteria, and the other is that the superbugs can spread between humans through direct contact. Based on these two transmission mechanisms, we study the dynamics of population in hospital environment where superbugs exist. In this paper, we build three mathematic models to illustrate the dynamics of patients with bacterial resistance in hospital environment. The models are analyzed using stability theory of differential equations. Positive equilibrium points of the system are investigated and their stability analysis is carried out. Moreover, the numerical simulation of the proposed model is also performed which supports the theoretical findings. PMID:26904150

  9. Anaesthetic management of the child with co-existing pulmonary disease.

    PubMed

    Lauer, R; Vadi, M; Mason, L

    2012-12-01

    Children with co-existing pulmonary disease have a wide range of clinical manifestations with significant implications for anaesthetists. Although there are a number of pulmonary diseases in children, this review focuses on two of the most common pulmonary disorders, asthma and bronchopulmonary dysplasia (BPD). These diseases share the physiology of bronchoconstriction and variably decreased flow in the airways, but also have unique physiological consequences. The anaesthetist can make a difference in outcomes with proper preoperative evaluation and appropriate preparation for surgery in the context of a team approach to perioperative care with implementation of a stepwise approach to disease management. An understanding of the importance of minimizing the risk for bronchoconstriction and having the tools at hand to treat it when necessary is paramount in the care of these patients. Unique challenges exist in the management of pulmonary hypertension in BPD patients. This review covers medical treatment, intraoperative management, and postoperative care for both patient populations. PMID:23242751

  10. DNA profiling of complex bacterial populations: toxic cyanobacterial blooms.

    PubMed

    Saker, Martin; Moreira, Cristiana; Martins, Joana; Neilan, Brett; Vasconcelos, Vitor Manuel

    2009-11-01

    Cyanobacteria are prokaryotic photosynthetic living organisms that inhabit our planet for over three billion years. With a worldwide distribution, they can be found in all types of environments: fresh, brackish and saltwater as well as terrestrial. Though beneficial in the development of life on earth, they also constitute a serious risk to our ecosystems since they can biologically produce harmful secondary metabolites named cyanotoxins. When studying cyanobacteria and their cyanotoxins, several methodologies have been applied with an increasing relevance to molecular methods. Therefore, the aim of this review is to describe alternative molecular methods that can be used as alternative methods for the identification of cyanobacteria. More traditional chemotaxonomic methods are discussed briefly as are the standard and somewhat dated techniques for assessing genome content for taxonomic classification schemes. The use of DNA amplification technology has been applied to the systematics and phylogeny of many bacterial groups, and the optimisation of methods for rapid identification and classification of cyanobacteria are presented. Together with novel methods developed for these photosynthetic microorganisms, the generated DNA profiles have been utilised to study cyanobacterial bloom population diversity and prediction of strain toxigenicity. Finally, the genotypes found were applied to a variety of phylogenetic analyses; trees were reconstructed and compared to the current morphological system of classification. The ecology and diversity of the cyanobacteria is discussed with respect to the derived molecular phylogenies and systematics.

  11. Pyoverdin cheats fail to invade bacterial populations in stationary phase.

    PubMed

    Ghoul, M; West, S A; McCorkell, F A; Lee, Z-B; Bruce, J B; Griffin, A S

    2016-09-01

    Microbes engage in cooperative behaviours by producing and secreting public goods, the benefits of which are shared among cells, and are therefore susceptible to exploitation by nonproducing cheats. In nature, bacteria are not typically colonizing sterile, rich environments in contrast to laboratory experiments, which involve inoculating sterile culture with few bacterial cells that then race to fill the available niche. Here, we study the potential implications of this difference, using the production of pyoverdin, an iron-scavenging siderophore that acts as a public good in the bacteria Pseudomonas aeruginosa. We show that (1) nonproducers are able to invade cultures of producers when added at the start of growth or during early exponential growth phase, but not during late exponential or stationary phase; (2) the producer strain does not produce pyoverdin in the late exponential and stationary phases and so is not paying the cost of cooperating during those phases. These results suggest that whether a nonproducing mutant can invade will depend upon when the mutation arises, as well as the population structure, and raise a potential difficulty with the use of antimicrobial treatment strategies that propose to exploit the invasive abilities of cheats. PMID:27223690

  12. Metatranscriptomic Analysis of Groundwater Reveals an Active Anammox Bacterial Population

    NASA Astrophysics Data System (ADS)

    Jewell, T. N. M.; Karaoz, U.; Thomas, B. C.; Banfield, J. F.; Brodie, E.; Williams, K. H.; Beller, H. R.

    2014-12-01

    Groundwater is a major natural resource, yet little is known about the contribution of microbial anaerobic ammonium oxidation (anammox) activity to subsurface nitrogen cycling. During anammox, energy is generated as ammonium is oxidized under anaerobic conditions to dinitrogen gas, using nitrite as the final electron acceptor. This process is a global sink for fixed nitrogen. Only a narrow range of monophyletic bacteria within the Planctomycetes carries out anammox, and the full extent of their metabolism, and subsequent impact on nitrogen cycling and microbial community structure, is still unknown. Here, we employ a metatranscriptomic analysis on enriched mRNA to identify the abundance and activity of a population of anammox bacteria within an aquifer at Rifle, CO. Planktonic biomass was collected over a two-month period after injection of up to 1.5 mM nitrate. Illumina-generated sequences were mapped to a phylogenetically binned Rifle metagenome database. We identified transcripts for genes with high protein sequence identities (81-98%) to those of anammox strain KSU-1 and to two of the five anammox bacteria genera, Brocadia and Kuenenia, suggesting an active, if not diverse, anammox population. Many of the most abundant anammox transcripts mapped to a single scaffold, indicative of a single dominant anammox species. Transcripts of the genes necessary for the anammox pathway were present, including an ammonium transporter (amtB), nitrite/formate transporter, nitrite reductase (nirK), and hydrazine oxidoreductase (hzoB). The form of nitrite reductase encoded by anammox is species-dependent, and we only identified nirK, with no evidence of anammox nirS. In addition to the anammox pathway we saw evidence of the anammox bacterial dissimilatory nitrate reduction to ammonium pathway (narH, putative nrfA, and nrfB), which provides an alternate means of generating substrates for anammox from nitrate, rather than relying on an external pool. Transcripts for hydroxylamine

  13. Mathematical Modelling of Bacterial Populations in Bio-remediation Processes

    NASA Astrophysics Data System (ADS)

    Vasiliadou, Ioanna A.; Vayenas, Dimitris V.; Chrysikopoulos, Constantinos V.

    2011-09-01

    An understanding of bacterial behaviour concerns many field applications, such as the enhancement of water, wastewater and subsurface bio-remediation, the prevention of environmental pollution and the protection of human health. Numerous microorganisms have been identified to be able to degrade chemical pollutants, thus, a variety of bacteria are known that can be used in bio-remediation processes. In this study the development of mathematical models capable of describing bacterial behaviour considered in bio-augmentation plans, such as bacterial growth, consumption of nutrients, removal of pollutants, bacterial transport and attachment in porous media, is presented. The mathematical models may be used as a guide in designing and assessing the conditions under which areas contaminated with pollutants can be better remediated.

  14. Patchiness and Co-Existence of Indigenous and Invasive Mussels at Small Spatial Scales: The Interaction of Facilitation and Competition

    PubMed Central

    Erlandsson, Johan; McQuaid, Christopher D.; Sköld, Martin

    2011-01-01

    Ecological theory predicts that two species with similar requirements will fail to show long-term co-existence in situations where shared resources are limiting, especially at spatial scales that are small relative to the size of the organisms. Two species of intertidal mussels, the indigenous Perna perna and the invasive Mytilus galloprovincialis, form mixed beds on the south coast of South Africa in a situation that has been stable for several generations of these species, even though these populations are often limited by the availability of space. We examined the spatial structure of these species where they co-exist at small spatial scales in the absence of apparent environmental heterogeneity at two sites, testing: whether conspecific aggregation of mussels can occur (using spatial Monte-Carlo tests); the degree of patchiness (using Korcak B patchiness exponent), and whether there was a relationship between percent cover and patchiness. We found that under certain circumstances there is non-random conspecific aggregation, but that in other circumstances there may be random distribution (i.e. the two species are mixed), so that spatial patterns are context-dependent. The relative cover of the species differed between sites, and within each site, the species with higher cover showed low Korcak B values (indicating low patchiness, i.e. the existence of fewer, larger patches), while the less abundant species showed the reverse, i.e. high patchiness. This relationship did not hold for either species within sites. We conclude that co-existence between these mussels is possible, even at small spatial scales because each species is an ecological engineer and, while they have been shown to compete for space, this is preceded by initial facilitation. We suggest that a patchy pattern of co-existence is possible because of a balance between direct (competitive) and indirect (facilitative) interactions. PMID:22132084

  15. On a Mathematical Model with Noncompact Boundary Conditions Describing Bacterial Population

    NASA Astrophysics Data System (ADS)

    Boulanouar, Mohamed

    2013-04-01

    In this work, we are concerned with the well-posedness of a mathematical model describing a maturation-velocity structured bacterial population. Each bacterium is distinguished by its degree of maturity and its maturation velocity. The bacterial mitosis is mathematically described by noncompact boundary conditions. We show that the mathematical model is governed by a positive strongly continuous semigroup.

  16. Influence of immigration on epiphytic bacterial populations on navel orange leaves.

    PubMed

    Lindow, S E; Andersen, G L

    1996-08-01

    Factors that influenced the increase in epiphytic bacterial population size on navel orange leaves during winter months were investigated to test the assumption that such populations were the result of multiplication on orange leaves. The population sizes of bacteria of different kinds, including ice nucleation-active (Ice(sup+)) bacteria, were from 6- to 30-fold larger on leaves of navel orange trees adjacent to other plant species than on trees growing near other citrus species. Total and Ice(sup+) bacterial population sizes on other plant species growing near navel orange trees were from 18- to 60-fold and 2- to 18,000-fold larger, respectively, than on navel orange trees. About twice the number of bacterial cells of a given type were deposited onto petri dishes opened simultaneously in navel orange orchards with other plant species nearby as in orchards surrounded by citrus trees. Epiphytic bacteria and airborne bacteria were more numerous near the upwind edge of orchards bordering on other plant species, but not in orchards adjacent to other citrus trees, and decreased with distance from other plant species. Navel orange leaves also exhibited progressive increases in the ability to supercool as a function of increasing distance from the upwind edge of orchards adjacent to other plant species but not in orchards adjacent to other citrus trees. While the population size of three different bacterial strains remained nearly constant for 60 days after inoculation, total bacterial populations increased more than 50-fold during this period. These results suggest that immigration of bacteria from plants having high epiphytic bacterial populations could account for most, if not all, of the seasonal increase in bacterial populations on navel orange leaves and have important implications for procedures to modify bacterial communities on leaves. PMID:16535384

  17. Worldwide populations of APHIS CRACCIVORA have diverse facultative bacterial symbionts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Facultative bacterial endosymbionts can play an important role in the evolutionary trajectory of their hosts. Aphids are infected with a wide variety of facultative endosymbionts that can confer ecologically relevant traits, which in turn may drive microevolution in a dynamic selective environment....

  18. Impact of spontaneous prophage induction on the fitness of bacterial populations and host-microbe interactions.

    PubMed

    Nanda, Arun M; Thormann, Kai; Frunzke, Julia

    2015-02-01

    Bacteriophages and genetic elements, such as prophage-like elements, pathogenicity islands, and phage morons, make up a considerable amount of bacterial genomes. Their transfer and subsequent activity within the host's genetic circuitry have had a significant impact on bacterial evolution. In this review, we consider what underlying mechanisms might cause the spontaneous activity of lysogenic phages in single bacterial cells and how the spontaneous induction of prophages can lead to competitive advantages for and influence the lifestyle of bacterial populations or the virulence of pathogenic strains. PMID:25404701

  19. Impact of Spontaneous Prophage Induction on the Fitness of Bacterial Populations and Host-Microbe Interactions

    PubMed Central

    Nanda, Arun M.; Thormann, Kai

    2014-01-01

    Bacteriophages and genetic elements, such as prophage-like elements, pathogenicity islands, and phage morons, make up a considerable amount of bacterial genomes. Their transfer and subsequent activity within the host's genetic circuitry have had a significant impact on bacterial evolution. In this review, we consider what underlying mechanisms might cause the spontaneous activity of lysogenic phages in single bacterial cells and how the spontaneous induction of prophages can lead to competitive advantages for and influence the lifestyle of bacterial populations or the virulence of pathogenic strains. PMID:25404701

  20. Magnesium aminoclay enhances lipid production of mixotrophic Chlorella sp. KR-1 while reducing bacterial populations.

    PubMed

    Kim, Bohwa; Praveenkumar, Ramasamy; Lee, Jiye; Nam, Bora; Kim, Dong-Myung; Lee, Kyubock; Lee, Young-Chul; Oh, You-Kwan

    2016-11-01

    Improving lipid productivity and preventing overgrowth of contaminating bacteria are critical issues relevant to the commercialization of the mixotrophic microalgae cultivation process. In this paper, we report the use of magnesium aminoclay (MgAC) nanoparticles for enhanced lipid production from oleaginous Chlorella sp. KR-1 with simultaneous control of KR-1-associated bacterial growth in mixotrophic cultures with glucose as the model substrate. Addition of 0.01-0.1g/L MgAC promoted microalgal biomass production better than the MgAC-less control, via differential biocidal effects on microalgal and bacterial cells (the latter being more sensitive to MgAC's bio-toxicity than the former). The inhibition effect of MgAC on co-existing bacteria was, as based on density-gradient-gel-electrophoresis (DGGE) analysis, largely dosage-dependent and species-specific. MgAC also, by inducing an oxidative stress environment, increased both the cell size and lipid content of KR-1, resulting in a considerable, ∼25% improvement of mixotrophic algal lipid productivity (to ∼410mgFAME/L/d) compared with the untreated control. PMID:27543952

  1. Magnesium aminoclay enhances lipid production of mixotrophic Chlorella sp. KR-1 while reducing bacterial populations.

    PubMed

    Kim, Bohwa; Praveenkumar, Ramasamy; Lee, Jiye; Nam, Bora; Kim, Dong-Myung; Lee, Kyubock; Lee, Young-Chul; Oh, You-Kwan

    2016-11-01

    Improving lipid productivity and preventing overgrowth of contaminating bacteria are critical issues relevant to the commercialization of the mixotrophic microalgae cultivation process. In this paper, we report the use of magnesium aminoclay (MgAC) nanoparticles for enhanced lipid production from oleaginous Chlorella sp. KR-1 with simultaneous control of KR-1-associated bacterial growth in mixotrophic cultures with glucose as the model substrate. Addition of 0.01-0.1g/L MgAC promoted microalgal biomass production better than the MgAC-less control, via differential biocidal effects on microalgal and bacterial cells (the latter being more sensitive to MgAC's bio-toxicity than the former). The inhibition effect of MgAC on co-existing bacteria was, as based on density-gradient-gel-electrophoresis (DGGE) analysis, largely dosage-dependent and species-specific. MgAC also, by inducing an oxidative stress environment, increased both the cell size and lipid content of KR-1, resulting in a considerable, ∼25% improvement of mixotrophic algal lipid productivity (to ∼410mgFAME/L/d) compared with the untreated control.

  2. Bacterial population structure of the jute-retting environment.

    PubMed

    Munshi, Tulika K; Chattoo, Bharat B

    2008-08-01

    Jute is one of the most versatile bast fibers obtained through the process of retting, which is a result of decomposition of stalks by the indigenous microflora. However, bacterial communities associated with the retting of jute are not well characterized. To investigate the presence of microorganisms during the process of jute retting, full-cycle rRNA approach was followed, and two 16S rRNA gene libraries, from jute-retting locations of Krishnanagar and Barrackpore, were constructed. Phylotypes affiliating to seven bacterial divisions were identified in both libraries. The bulk of clones came from Proteobacteria ( approximately 37, 41%) and a comparatively smaller proportion of clones from the divisions-Firmicutes ( approximately 11, 12%), Cytophaga-Flexibacter-Bacteroidetes group (CFB; approximately 9, 7%), Verrucomicrobia ( approximately 6, 5%), Acidobacteria ( approximately 4, 5%), Chlorobiales ( approximately 5, 5%), and Actinobacteria ( approximately 4, 2%) were identified. Percent coverage value and diversity estimations of phylotype richness, Shannon-Weiner index, and evenness confirmed the diverse nature of both the libraries. Evaluation of the retting waters by whole cell rRNA-targeted flourescent in situ hybridization, as detected by domain- and group-specific probes, we observed a considerable dominance of the beta-Proteobacteria (25.9%) along with the CFB group (24.4%). In addition, 32 bacterial species were isolated on culture media from the two retting environments and identified by 16S rDNA analysis, confirming the presence of phyla, Proteobacteria ( approximately 47%), Firmicutes ( approximately 22%), CFB group ( approximately 19%), and Actinobacteria ( approximately 13%) in the retting niche. Thus, our study presents the first quantification of the dominant and diverse bacterial phylotypes in the retting ponds, which will further help in improving the retting efficiency, and hence the fiber quality.

  3. Instability in bacterial populations and the curvature tensor

    NASA Astrophysics Data System (ADS)

    Melgarejo, Augusto; Langoni, Laura; Ruscitti, Claudia

    2016-09-01

    In the geometry associated with equilibrium thermodynamics the scalar curvature Rs is a measure of the volume of correlation, and therefore the singularities of Rs indicates the system instabilities. We explore the use of a similar approach to study instabilities in non-equilibrium systems and we choose as a test example, a colony of bacteria. In this regard we follow the proposal made by Obata et al. of using the curvature tensor for studying system instabilities. Bacterial colonies are often found in nature in concentrated biofilms, or other colony types, which can grow into spectacular patterns visible under the microscope. For instance, it is known that a decrease of bacterial motility with density can promote separation into bulk phases of two coexisting densities; this is opposed to the logistic law for birth and death that allows only a single uniform density to be stable. Although this homogeneous configuration is stable in the absence of bacterial interactions, without logistic growth, a density-dependent swim speed v(ρ) leads to phase separation via a spinodal instability. Thus we relate the singularities in the curvature tensor R to the spinodal instability, that is the appearance of regions of different densities of bacteria.

  4. Population expansions shared among coexisting bacterial lineages are revealed by genetic evidence

    PubMed Central

    Avitia, Morena; Escalante, Ana E.; Rebollar, Eria A.; Moreno-Letelier, Alejandra; Eguiarte, Luis E.

    2014-01-01

    Comparative population studies can help elucidate the influence of historical events upon current patterns of biodiversity among taxa that coexist in a given geographic area. In particular, comparative assessments derived from population genetics and coalescent theory have been used to investigate population dynamics of bacterial pathogens in order to understand disease epidemics. In contrast, and despite the ecological relevance of non-host associated and naturally occurring bacteria, there is little understanding of the processes determining their diversity. Here we analyzed the patterns of genetic diversity in coexisting populations of three genera of bacteria (Bacillus, Exiguobacterium, and Pseudomonas) that are abundant in the aquatic systems of the Cuatro Cienegas Basin, Mexico. We tested the hypothesis that a common habitat leaves a signature upon the genetic variation present in bacterial populations, independent of phylogenetic relationships. We used multilocus markers to assess genetic diversity and (1) performed comparative phylogenetic analyses, (2) described the genetic structure of bacterial populations, (3) calculated descriptive parameters of genetic diversity, (4) performed neutrality tests, and (5) conducted coalescent-based historical reconstructions. Our results show a trend of synchronic expansions across most populations independent of both lineage and sampling site. Thus, we provide empirical evidence supporting the analysis of coexisting bacterial lineages in natural environments to advance our understanding of bacterial evolution beyond medical or health-related microbes. PMID:25548732

  5. Population expansions shared among coexisting bacterial lineages are revealed by genetic evidence.

    PubMed

    Avitia, Morena; Escalante, Ana E; Rebollar, Eria A; Moreno-Letelier, Alejandra; Eguiarte, Luis E; Souza, Valeria

    2014-01-01

    Comparative population studies can help elucidate the influence of historical events upon current patterns of biodiversity among taxa that coexist in a given geographic area. In particular, comparative assessments derived from population genetics and coalescent theory have been used to investigate population dynamics of bacterial pathogens in order to understand disease epidemics. In contrast, and despite the ecological relevance of non-host associated and naturally occurring bacteria, there is little understanding of the processes determining their diversity. Here we analyzed the patterns of genetic diversity in coexisting populations of three genera of bacteria (Bacillus, Exiguobacterium, and Pseudomonas) that are abundant in the aquatic systems of the Cuatro Cienegas Basin, Mexico. We tested the hypothesis that a common habitat leaves a signature upon the genetic variation present in bacterial populations, independent of phylogenetic relationships. We used multilocus markers to assess genetic diversity and (1) performed comparative phylogenetic analyses, (2) described the genetic structure of bacterial populations, (3) calculated descriptive parameters of genetic diversity, (4) performed neutrality tests, and (5) conducted coalescent-based historical reconstructions. Our results show a trend of synchronic expansions across most populations independent of both lineage and sampling site. Thus, we provide empirical evidence supporting the analysis of coexisting bacterial lineages in natural environments to advance our understanding of bacterial evolution beyond medical or health-related microbes. PMID:25548732

  6. Influence of Multiple Bacterial Populations on Phenanthrene Degradation, Bacterial Cell Elution, and Species Distribution

    NASA Astrophysics Data System (ADS)

    Patterson, B. M.; Brusseau, M. L.; Maier, R. M.; Frye, R.

    2001-05-01

    A single set of degradation coefficients is typically used when representing biodegradation in contaminant transport models. Implicit to this approach is the assumption that only a single degrading isolate exists, or that the entire community of degraders more typically present in natural systems has a uniform, constant growth rate and affinity for the contaminant. This assumption was evaluated through a miscible displacement experiment conducted using a column packed with a soil containing an indigenous microbial community comprised of 24 identified phenanthrene-degrading isolates. Results produced oscillating phenanthrene concentrations in the column effluent, indicating potential competitive interactions among the isolates. A second series of experiments, conducted in a simplified system comprised of sand and 1,2, or 3 indigenous isolates, examined the effects of species interactions on phenanthrene degradation and bacterial cell elution. Bacterial growth rates, density of cells within the column, and bacterial distribution were also evaluated. Results show single bacterial species produced relatively stable cell elution and phenanthrene concentrations in the effluent. Conversely, the behavior in the multiple species systems indicated synergistic and antagonistic interactions occurred among the species. These results illustrate that the dynamics of heterogeneous microbial communities should be considered when evaluating contaminant biodegradation and transport in subsurface systems.

  7. GM crop co-existence: a question of choice, not prejudice.

    PubMed

    Pearsall, Daniel

    2013-01-01

    The rapid uptake of biotech crops around the world demonstrates not only strong producer and consumer demand for the technology and its products, but also that where regulatory regimes function effectively and markets are allowed to operate as normal, co-existence between genetically modified (GM) and non-GM supply chains is readily achievable. However, the polarized debate over GMOs within the European Union over the past 15 years has resulted in a highly politicized and progressively impractical approach to the issue of GM crop co-existence, which in itself has become a further barrier to the technology's development. This article argues that co-existence should not be treated as a pro- or anti-GM issue, and that the aim of co-existence measures should be to permit consumer choice and freedom to operate whatever the production method involved. It suggests that supply chain-based solutions to co-existence, rather than Government prescription, offer the most pragmatic and flexible response to the commercial realities of servicing differentiated market demands. PMID:23988874

  8. Populations of Stored Product Mite Tyrophagus putrescentiae Differ in Their Bacterial Communities

    PubMed Central

    Erban, Tomas; Klimov, Pavel B.; Smrz, Jaroslav; Phillips, Thomas W.; Nesvorna, Marta; Kopecky, Jan; Hubert, Jan

    2016-01-01

    Background: Tyrophagus putrescentiae colonizes different human-related habitats and feeds on various post-harvest foods. The microbiota acquired by these mites can influence the nutritional plasticity in different populations. We compared the bacterial communities of five populations of T. putrescentiae and one mixed population of T. putrescentiae and T. fanetzhangorum collected from different habitats. Material: The bacterial communities of the six mite populations from different habitats and diets were compared by Sanger sequencing of cloned 16S rRNA obtained from amplification with universal eubacterial primers and using bacterial taxon-specific primers on the samples of adults/juveniles or eggs. Microscopic techniques were used to localize bacteria in food boli and mite bodies. The morphological determination of the mite populations was confirmed by analyses of CO1 and ITS fragment genes. Results: The following symbiotic bacteria were found in compared mite populations: Wolbachia (two populations), Cardinium (five populations), Bartonella-like (five populations), Blattabacterium-like symbiont (three populations), and Solitalea-like (six populations). From 35 identified OTUs97, only Solitalea was identified in all populations. The next most frequent and abundant sequences were Bacillus, Moraxella, Staphylococcus, Kocuria, and Microbacterium. We suggest that some bacterial species may occasionally be ingested with food. The bacteriocytes were observed in some individuals in all mite populations. Bacteria were not visualized in food boli by staining, but bacteria were found by histological means in ovaria of Wolbachia-infested populations. Conclusion: The presence of Blattabacterium-like, Cardinium, Wolbachia, and Solitalea-like in the eggs of T. putrescentiae indicates mother to offspring (vertical) transmission. Results of this study indicate that diet and habitats influence not only the ingested bacteria but also the symbiotic bacteria of T. putrescentiae. PMID

  9. Experimental Investigation on the Validity of Population Dynamics Approach to Bacterial Colony Formation

    NASA Astrophysics Data System (ADS)

    Wakita, Jun-ichi; Komatsu, Kenji; Nakahara, Akio; Matsuyama, Tohey; Matsushita, Mitsugu

    1994-03-01

    We have investigated the dynamics of a two-dimensional spreading of a bacterial population in a surface environment. After point inoculation of flagellated bacteria ( Bacillus subtilis) on nutrient-rich semi-solid medium, the bacterial population grew up by multiplication and translocation of cells, and developed a homogeneous round colony. By comparing experimental results with those of numerical simulations of the model equation, we found that this homogeneous population growth of bacteria is an actual manifestation of growth dynamics described by the Fisher's equation.

  10. Squamous cell carcinoma of kidney co-existing with renal calculi: a rare tumour.

    PubMed

    Verma, Nidhi; Yadav, Gulabdhar; Dhawan, Nishi; Kumar, Awanish

    2011-03-01

    Squamous cell carcinoma (SCC) of urinary tract is a very rare tumour known to be associated with chronic renal calculi and infection. This tumour is highly aggressive and often detected at advanced stage with poor outcome. The authors describe a case report of a 62-year-old male patient who was diagnosed with right nephrolithiasis with non-functioning kidney. Histopathology revealed an unexpected co-existing SCC in renal pelvis. The present case highlights the careful search and use of newer imaging modalities in cases of long-standing renal calculi as they may have co-existing hidden malignancy which may change the treatment plan and prognosis.

  11. Co-existence of Sarcina Organisms and Helicobacter pylori Gastritis/Duodenitis in Pediatric Siblings

    PubMed Central

    Sauter, Jennifer L.; Nayar, Suresh K.; Anders, Paige D.; D’Amico, Michael; Butnor, Kelly J.; Wilcox, Rebecca L.

    2015-01-01

    Sarcina are gram-positive anaerobic bacteria found to be associated with delayed gastric emptying and gastric outlet obstruction. We describe two cases of Sarcina co-existing with Helicobacter pylori organisms in pediatric siblings presenting within four months of each other with pyloric obstruction secondary to severe gastritis/duodenitis. The co-existence of Sarcina and Helicobacter pylori has not, to our knowledge, been previously reported. Its characteristic tetrad packeted morphology permits Sarcina to be readily identified on routine sections. Detection of these organisms in gastric biopsies should prompt consideration of gastric outlet obstruction and/or delayed gastric emptying as a possible etiologic factor. PMID:25664331

  12. Bacterial populations and processes in sediments containing gas hydrates (ODP Leg 146: Cascadia Margin)

    NASA Astrophysics Data System (ADS)

    Cragg, B. A.; Parkes, R. J.; Fry, J. C.; Weightman, A. J.; Rochelle, P. A.; Maxwell, J. R.

    1996-04-01

    Bacterial populations and activity were quantified at three sites in the Cascadia Margin accretionary wedge, off the West Canadian/American coast (ODP Leg 146). At two sites sediments contained gas hydrates, Site 889/890 had a discrete zone of hydrate approximately 10 m above a bottom simulating reflector (BSR) at 225 m below sea floor (mbsf) and Site 892 had disseminated hydrate in the upper 20 mbsf and a BSR at 74 mbsf. Site 888 was a control site without gas hydrates. The control site (888) and top approximately 90 mbsf of Site 889/890 had bacterial distributions similar to previous Pacific Ocean sites. In the upper approximately 30 m of Site 892, however, bacterial populations were much lower, suggesting inhibition by the high concentrations of H 2S within the hydrate zone. Below this depth bacterial populations rose to concentrations consistent with other sites. The control site was dominated by SO 4 reduction and rates of CH 4 oxidation in the top 90 m were low (0.002-0.033 nmol cm -3 d -1). At Site 889/890 bacterial populations and activity were stimulated in the discrete hydrate zone. CH 4 oxidation rates increased in the middle of this zone to 134.5 nmol cm -3 d -1 (ca. 9 times the average rate at other depths), resulting in a significant (× 10) increase in the total bacterial population. The anaerobic process(es) responsible for this oxidation remain unclear, despite SO 4-reducing bacteria, previously associated with CH 4 oxidation, also being stimulated in this zone. Fluid flux into accretionary wedge sediments may be an important process in providing electron acceptors to maintain these relatively high rates of CH 4 oxidation. This first microbiological study of gas hydrates indicates that bacterial processes are influenced by gas and fluid venting, and they play a major role in geochemical changes within these deep (> 200 mbsf) sediments.

  13. Bewitchment, Biology, or Both: The Co-Existence of Natural and Supernatural Explanatory Frameworks across Development

    ERIC Educational Resources Information Center

    Legare, Cristine H.; Gelman, Susan A.

    2008-01-01

    Three studies examined the co-existence of natural and supernatural explanations for illness and disease transmission, from a developmental perspective. The participants (5-, 7-, 11-, and 15-year-olds and adults; N = 366) were drawn from 2 Sesotho-speaking South African communities, where Western biomedical and traditional healing frameworks were…

  14. Carbon and oxygen isotopes in apatite CO/sub 2/ and co-existing calcite

    SciTech Connect

    Kolodny, Y.; Kaplan, I. R.

    1981-04-01

    Carbon and oxygen isotopes were analyzed in carbonate apatite CO/sub 2/ and in co-existing calcite. Both C and O in apatite CO/sub 2/ are enriched in the respective light isotopes relative to calcite. These results confirm the proposition that carbonate is part of the apatite structure.

  15. Bacterial populations associated with rice seed in the tropical environment.

    PubMed

    Cottyn, B; Regalado, E; Lanoot, B; De Cleene, M; Mew, T W; Swings, J

    2001-03-01

    ABSTRACT During the 1995 wet season, harvested rice seed was collected from farmers' fields at different locations in Iloilo, Philippines. Bacterial isolations from crushed seed yielded 428 isolates. The isolates were characterized by BOX-polymerase chain reaction fingerprinting of total genomic DNA and represented 151 fingerprint types (FPT). Most FPTs were found on a single occasion, although matching fingerprints for isolates from different samples also were found. Identifications were made by cellular fatty acid methyl ester analysis and additional use of Biolog GN/GP MicroPlates and API 20E/50CHE systems. The predominant bacteria were Enterobacteriaceae (25%), Bacillus spp. (22%), and Pseu-domonas spp. (14%). Other bacteria regularly present were identified as Xanthomonas spp., Cellulomonas flavigena, and Clavibacter michiganense. Of the total number of isolated bacteria, 4% exhibited in vitro antifungal activity against Rhizoctonia solani or Pyricularia grisea. Two percent of isolates were pathogens identified as Burkholderia glumae and Burkholderia gladioli. Five percent of isolates induced sheath necrosis on only 50 to 90% of inoculated plants and were related to Bacillus pumilus, Paenibacillus spp., Pseudomonas spp., and Pantoea spp.

  16. Bacterial Diversity in a Nonsaline Alkaline Environment: Heterotrophic Aerobic Populations

    PubMed Central

    Tiago, Igor; Chung, Ana Paula; Veríssimo, António

    2004-01-01

    Heterotrophic populations were isolated and characterized from an alkaline groundwater environment generated by active serpentinization, which results in a Ca(OH)2-enriched, extremely diluted groundwater with pH 11.4. One hundred eighty-five strains were isolated in different media at different pH values during two sampling periods. To assess the degree of diversity present in the environment and to select representative strains for further characterization of the populations, we screened the isolates by using random amplified polymorphic DNA-PCR profiles and grouped them based on similarities determined by fatty acid methyl ester analysis. Phenotypic characterization, determinations of G+C content, phylogenetic analyses by direct sequencing of 16S rRNA genes, and determinations of pH tolerance were performed with the selected isolates. Although 38 different populations were identified and characterized, the vast majority of the isolates were gram positive with high G+C contents and were affiliated with three distinct groups, namely, strains closely related to the species Dietzia natrolimnae (32% of the isolates), to Frigoribacterium/Clavibacter lineages (29% of the isolates), and to the type strain of Microbacterium kitamiense (20% of the isolates). Other isolates were phylogenetically related to strains of the genera Agrococcus, Leifsonia, Kytococcus, Janibacter, Kocuria, Rothia, Nesterenkonia, Citrococcus, Micrococcus, Actinomyces, Rhodococcus, Bacillus, and Staphylococcus. Only five isolates were gram negative: one was related to the Sphingobacteria lineage and the other four were related to the α-Proteobacteria lineage. Despite the pH of the environment, the vast majority of the populations were alkali tolerant, and only two strains were able to grow at pH 11. PMID:15574939

  17. Socioeconomic Disparities in the Presentation of Acute Bacterial Sinusitis Complications in the Pediatric Population.

    PubMed

    Mehta, Viraj J; Ling, Jeanie D; Mawn, Louise A

    2016-01-01

    Acute bacterial sinusitis is a common disease in the pediatric population that typically resolves without significant complications. Children who do suffer from complications involving the orbit or the brain often experience significant morbidity and potential mortality, typically requiring hospitalization for management. Numerous studies have demonstrated that children from low-income families with public or no insurance are less likely to receive adequate preventative care, are more likely to present with later disease stages, and ultimately endure worse health outcomes. We review the literature to examine if there are socioeconomic disparities in the presentation of complications of acute bacterial sinusitis in the pediatric population.

  18. Interactions of Bacterial and Amoebal Populations in Soil Microcosms with Fluctuating Moisture Content

    PubMed Central

    Bryant, R. J.; Woods, L. E.; Coleman, D. C.; Fairbanks, B. C.; McClellan, J. F.; Cole, C. V.

    1982-01-01

    Sterilized soil samples (20 g of soil per 50-ml flask), amended with 600 μg of glucose-carbon and 60 μg of NH4-N · g of dry soil−1, were inoculated with bacteria (Pseudomonas paucimobilis) alone or with bacteria and amoebae (Acanthamoeba polyphaga). We used wet-dry treatments, which involved air drying the samples to a moisture content of approximately 2% and remoistening the samples three times during the 83-day experiment. Control treatments were kept moist. In the absence of amoebae, bacterial populations were reduced by the first drying to about 60% of the moist control populations, but the third drying had no such effect. With amoebae present, bacterial numbers were not significantly affected by the dryings. Amoebal grazing reduced bacterial populations to 20 to 25% of the ungrazed bacterial populations in both moisture treatments. Encystment was an efficient survival mechanism for amoebae subjected to wet-dry cycles. The amoebal population was entirely encysted in dry soil, but the total number of amoebae was not affected by the three dryings. Growth efficiencies for amoebae feeding on bacteria were 0.33 and 0.39 for wet-dry and constantly moist treatments, respectively, results that compared well with those previously reported for Acanthamoeba spp. PMID:16345984

  19. Comparing the anterior nare bacterial community of two discrete human populations using Illumina amplicon sequencing.

    PubMed

    Camarinha-Silva, Amélia; Jáuregui, Ruy; Chaves-Moreno, Diego; Oxley, Andrew P A; Schaumburg, Frieder; Becker, Karsten; Wos-Oxley, Melissa L; Pieper, Dietmar H

    2014-09-01

    The anterior nares are an important reservoir for opportunistic pathogens and commensal microorganisms. A barcoded Illumina paired-end sequencing method targeting the 16S ribosomal RNA V1-2 hypervariable region was developed to compare the bacterial diversity of the anterior nares across distinct human populations (volunteers from Germany vs a Babongo Pygmy tribe, Africa). Of the 251 phylotypes detected, 231 could be classified to the genus level and 109 to the species level, including the unambiguous identification of the ubiquitous Staphylococcus aureus and Moraxella catarrhalis. The global bacterial community of both adult populations revealed that they shared 85% of the phylotypes, suggesting that our global bacterial communities have likely been with us for thousands of years. Of the 34 phylotypes unique to the non-westernized population, most were related to members within the suborder Micrococcineae. There was an even more overwelming distinction between children and adults of the same population, suggesting a progression of a childhood community of high-diversity comprising species of Moraxellaceae and Streptococcaceae to an adult community of lower diversity comprising species of Propionibacteriaceae, Clostridiales Incertae Sedis XI, Corynebacteriaceae and Staphylococcaceae. Thus, age was a stronger factor for accounting for differing bacterial assemblages than the origin of the human population sampled.

  20. Extinction of Bacterial Populations: A Change of Paradigm?

    NASA Astrophysics Data System (ADS)

    Lohmar, Ingo; Meerson, Baruch

    2012-02-01

    It is now well-established that individual bacteria of many types switch stochastically between two phenotypes: fast-growing ``normals'' susceptible to antibiotics, and slowly-growing ``persisters'' hardly affected by the drug. In the competition of species during exponential growth, persisters are a burden, but they may become beneficial when introducing ``stress'' phases like drug treatment. We suggest to shift the focus to the persistence of an established population. Due to fluctuations, the population will (after a long time) eventually go extinct; persisters act as a life insurance against this. We study a simple stochastic model of these processes. Using a WKB approximation, we find the most likely path to extinction and quantify the extinction risk under both favorable and adverse conditions. Analytical results are obtained both in the biologically relevant regime when the switching is rare compared with the birth and death processes, and in the opposite regime of frequent switching. We explain how persisters strongly reduce the extinction risk and show that rare switches are most beneficial to this end. [I. Lohmar and B. Meerson, Phys. Rev. E 84 051901 (2011)

  1. Detection of Only Viable Bacterial Spores Using a Live/Dead Indicator in Mixed Populations

    NASA Technical Reports Server (NTRS)

    Behar, Alberto E.; Stam, Christina N.; Smiley, Ronald

    2013-01-01

    This method uses a photoaffinity label that recognizes DNA and can be used to distinguish populations of bacterial cells from bacterial spores without the use of heat shocking during conventional culture, and live from dead bacterial spores using molecular-based methods. Biological validation of commercial sterility using traditional and alternative technologies remains challenging. Recovery of viable spores is cumbersome, as the process requires substantial incubation time, and the extended time to results limits the ability to quickly evaluate the efficacy of existing technologies. Nucleic acid amplification approaches such as PCR (polymerase chain reaction) have shown promise for improving time to detection for a wide range of applications. Recent real-time PCR methods are particularly promising, as these methods can be made at least semi-quantitative by correspondence to a standard curve. Nonetheless, PCR-based methods are rarely used for process validation, largely because the DNA from dead bacterial cells is highly stable and hence, DNA-based amplification methods fail to discriminate between live and inactivated microorganisms. Currently, no published method has been shown to effectively distinguish between live and dead bacterial spores. This technology uses a DNA binding photoaffinity label that can be used to distinguish between live and dead bacterial spores with detection limits ranging from 109 to 102 spores/mL. An environmental sample suspected of containing a mixture of live and dead vegetative cells and bacterial endospores is treated with a photoaffinity label. This step will eliminate any vegetative cells (live or dead) and dead endospores present in the sample. To further determine the bacterial spore viability, DNA is extracted from the spores and total population is quantified by real-time PCR. The current NASA standard assay takes 72 hours for results. Part of this procedure requires a heat shock step at 80 degC for 15 minutes before the

  2. Quantitation of free-living amoebae and bacterial populations in eyewash stations relative to flushing frequency.

    PubMed

    Bowman, E K; Vass, A A; Mackowski, R; Owen, B A; Tyndall, R L

    1996-07-01

    This study investigated the concentration of amoebic and bacterial populations in eyewash station water relative to various flushing regimens. Amoebae concentrations averaged approximately 200 amoebae/100 mL in 13 of 15 stations positive for amoebae and consisted of Hartmannella and Acanthamoeba. Bacterial concentrations ranged from 10(0) to more than 10(5) colony forming units per mL. Amoebic concentrations differed notably between stations located in Buildings X and Y (p < 0.0001). Further study indicated that removal of diffusing screens did not substantially change (p > 0.05) the concentration of amoeba. Amoebic and bacterial concentrations temporarily decreased with the various flushing regimens tested. Lower amoebic concentrations were not sustained by a weekly 3-minute or a monthly 1-minute flushing regimen. However, weekly 3-minute flushes appeared to be more effective in maintaining lowered bacterial concentrations (p < 0.0001). PMID:8686659

  3. Population-based surveillance for bacterial meningitis in the Dominican Republic: implications for control by vaccination.

    PubMed

    Gomez, E; Peguero, M; Sanchez, J; Castellanos, P L; Feris, J; Peña, C; Brudzinski-LaClaire, L; Levine, O S

    2000-12-01

    Quantifying the local burden of disease is an important step towards the introduction of new vaccines, such as Haemophilus influenzae type b (Hib) conjugate vaccine. We adapted a generic protocol developed by the World Health Organization for population-based surveillance of bacterial meningitis. All hospitals that admit paediatric patients with meningitis in the National District, Dominican Republic were included in the system and standard laboratory methods were used. The system identified 111 cases of confirmed bacterial meningitis. Hib was the leading cause of bacterial meningitis, followed by group B streptococcus, S. pneumoniae, and N. meningitidis. Unlike hospital-based case series, this population-based system was able to calculate incidence rates. The incidence of Hib meningitis was 13 cases per 100,000 children < 5 years old. The data from this study were used by the Ministry of Health to support the introduction of routine Hib vaccination and will be used to monitor its effectiveness.

  4. Humpback Whale Populations Share a Core Skin Bacterial Community: Towards a Health Index for Marine Mammals?

    PubMed Central

    Apprill, Amy; Robbins, Jooke; Eren, A. Murat; Pack, Adam A.; Reveillaud, Julie; Mattila, David; Moore, Michael; Niemeyer, Misty; Moore, Kathleen M. T.; Mincer, Tracy J.

    2014-01-01

    Microbes are now well regarded for their important role in mammalian health. The microbiology of skin – a unique interface between the host and environment - is a major research focus in human health and skin disorders, but is less explored in other mammals. Here, we report on a cross-population study of the skin-associated bacterial community of humpback whales (Megaptera novaeangliae), and examine the potential for a core bacterial community and its variability with host (endogenous) or geographic/environmental (exogenous) specific factors. Skin biopsies or freshly sloughed skin from 56 individuals were sampled from populations in the North Atlantic, North Pacific and South Pacific oceans and bacteria were characterized using 454 pyrosequencing of SSU rRNA genes. Phylogenetic and statistical analyses revealed the ubiquity and abundance of bacteria belonging to the Flavobacteria genus Tenacibaculum and the Gammaproteobacteria genus Psychrobacter across the whale populations. Scanning electron microscopy of skin indicated that microbial cells colonize the skin surface. Despite the ubiquity of Tenacibaculum and Psychrobater spp., the relative composition of the skin-bacterial community differed significantly by geographic area as well as metabolic state of the animals (feeding versus starving during migration and breeding), suggesting that both exogenous and endogenous factors may play a role in influencing the skin-bacteria. Further, characteristics of the skin bacterial community from these free-swimming individuals were assembled and compared to two entangled and three dead individuals, revealing a decrease in the central or core bacterial community members (Tenacibaculum and Psychrobater spp.), as well as the emergence of potential pathogens in the latter cases. This is the first discovery of a cross-population, shared skin bacterial community. This research suggests that the skin bacteria may be connected to humpback health and immunity and could possibly

  5. BSim: An Agent-Based Tool for Modeling Bacterial Populations in Systems and Synthetic Biology

    PubMed Central

    Gorochowski, Thomas E.; Matyjaszkiewicz, Antoni; Todd, Thomas; Oak, Neeraj; Kowalska, Kira; Reid, Stephen; Tsaneva-Atanasova, Krasimira T.

    2012-01-01

    Large-scale collective behaviors such as synchronization and coordination spontaneously arise in many bacterial populations. With systems biology attempting to understand these phenomena, and synthetic biology opening up the possibility of engineering them for our own benefit, there is growing interest in how bacterial populations are best modeled. Here we introduce BSim, a highly flexible agent-based computational tool for analyzing the relationships between single-cell dynamics and population level features. BSim includes reference implementations of many bacterial traits to enable the quick development of new models partially built from existing ones. Unlike existing modeling tools, BSim fully considers spatial aspects of a model allowing for the description of intricate micro-scale structures, enabling the modeling of bacterial behavior in more realistic three-dimensional, complex environments. The new opportunities that BSim opens are illustrated through several diverse examples covering: spatial multicellular computing, modeling complex environments, population dynamics of the lac operon, and the synchronization of genetic oscillators. BSim is open source software that is freely available from http://bsim-bccs.sf.net and distributed under the Open Source Initiative (OSI) recognized MIT license. Developer documentation and a wide range of example simulations are also available from the website. BSim requires Java version 1.6 or higher. PMID:22936991

  6. BSim: an agent-based tool for modeling bacterial populations in systems and synthetic biology.

    PubMed

    Gorochowski, Thomas E; Matyjaszkiewicz, Antoni; Todd, Thomas; Oak, Neeraj; Kowalska, Kira; Reid, Stephen; Tsaneva-Atanasova, Krasimira T; Savery, Nigel J; Grierson, Claire S; di Bernardo, Mario

    2012-01-01

    Large-scale collective behaviors such as synchronization and coordination spontaneously arise in many bacterial populations. With systems biology attempting to understand these phenomena, and synthetic biology opening up the possibility of engineering them for our own benefit, there is growing interest in how bacterial populations are best modeled. Here we introduce BSim, a highly flexible agent-based computational tool for analyzing the relationships between single-cell dynamics and population level features. BSim includes reference implementations of many bacterial traits to enable the quick development of new models partially built from existing ones. Unlike existing modeling tools, BSim fully considers spatial aspects of a model allowing for the description of intricate micro-scale structures, enabling the modeling of bacterial behavior in more realistic three-dimensional, complex environments. The new opportunities that BSim opens are illustrated through several diverse examples covering: spatial multicellular computing, modeling complex environments, population dynamics of the lac operon, and the synchronization of genetic oscillators. BSim is open source software that is freely available from http://bsim-bccs.sf.net and distributed under the Open Source Initiative (OSI) recognized MIT license. Developer documentation and a wide range of example simulations are also available from the website. BSim requires Java version 1.6 or higher. PMID:22936991

  7. Bacterial populations on the surfaces of organic and conventionally grown almond drupes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aims: To compare the bacterial populations on organically and conventionally grown almond drupes before and after hull split. Methods and Results: We constructed 16S rRNA gene libraries containing approximately 3,000 sequences each from the bacteria from organically and conventionally grown drupes b...

  8. The Population Biology of Bacterial Plasmids: A PRIORI Conditions for the Existence of Conjugationally Transmitted Factors

    PubMed Central

    Stewart, Frank M.; Levin, Bruce R.

    1977-01-01

    A mathematical model for the population dynamics of conjugationally transmitted plasmids in bacterial populations is presented and its properties analyzed. Consideration is given to nonbacteriocinogenic factors that are incapable of incorporation into the chromosome of their host cells, and to bacterial populations maintained in either continuous (chemostat) or discrete (serial transfer) culture. The conditions for the establishment and maintenance of these infectious extrachromosomal elements and equilibrium frequencies of cells carrying them are presented for different values of the biological parameters: population growth functions, conjugational transfer and segregation rate constants. With these parameters in a biologically realistic range, the theory predicts a broad set of physical conditions, resource concentrations and dilution rates, where conjugationally transmitted plasmids can become established and where cells carrying them will maintain high frequencies in bacterial populations. This can occur even when plasmid-bearing cells are much less fit (i.e., have substantially lower growth rates) than cells free of these factors. The implications of these results and the reality and limitations of the model are discussed and the values of its parameters in natural populations speculated upon. PMID:17248761

  9. Co-Existence of Various Clinical and Histopathological Features of Mycosis Fungoides in a Young Female

    PubMed Central

    Naeini, Farahnaz Fatemi; Soghrati, Mehrnaz; Abtahi-Naeini, Bahareh; Najafian, Jamshid; Rajabi, Parvin

    2015-01-01

    Mycosis fungoides is the most common type of cutaneous T-cell lymphoma (CTCL) and a rare disorder that typically affects older adults with erythematous scaling patches and plaques. Hypopigmented patches are a rare clinical variant of the disease. Granulomatous mycosis fungoides (GMF) is also a rare type of CTCL. No particular clinical criteria are available for the diagnosis of GMF, because of its variable presentations, and so the detection of GMF is primarily considered as a histopathological diagnosis. Rarely, a co-existence of more than one clinical or histopathological feature of mycosis fungoides may be present. To the best of our knowledge this is the first report of MF that shows the simultaneous co-existence of more than one clinical and histopathological variant of MF. We present a 29-year-old female with clinical presentations of both classic and hypopigmented mycosis fungoides (MF), and also the histopathological features of the classic and granulomatous types of the disease. PMID:25814741

  10. Co-existence of various clinical and histopathological features of mycosis fungoides in a young female.

    PubMed

    Naeini, Farahnaz Fatemi; Soghrati, Mehrnaz; Abtahi-Naeini, Bahareh; Najafian, Jamshid; Rajabi, Parvin

    2015-01-01

    Mycosis fungoides is the most common type of cutaneous T-cell lymphoma (CTCL) and a rare disorder that typically affects older adults with erythematous scaling patches and plaques. Hypopigmented patches are a rare clinical variant of the disease. Granulomatous mycosis fungoides (GMF) is also a rare type of CTCL. No particular clinical criteria are available for the diagnosis of GMF, because of its variable presentations, and so the detection of GMF is primarily considered as a histopathological diagnosis. Rarely, a co-existence of more than one clinical or histopathological feature of mycosis fungoides may be present. To the best of our knowledge this is the first report of MF that shows the simultaneous co-existence of more than one clinical and histopathological variant of MF. We present a 29-year-old female with clinical presentations of both classic and hypopigmented mycosis fungoides (MF), and also the histopathological features of the classic and granulomatous types of the disease.

  11. Sinobronchial allergic aspergillosis with allergic bronchopulmonary aspergillosis: a less common co-existence

    PubMed Central

    Upadhyay, Rashmi; Kant, Surya; Prakash, Ved; Saheer, S

    2014-01-01

    Allergic bronchopulmonary aspergillosis (ABPA) is an immunological pulmonary disorder that is characterised by a hyper-responsiveness of the airways to Aspergillus fumigatus. Although several other fungi may also present with similar clinical conditions, Aspergillus remains the most common fungal pathogen causing airway infections. Co-existence of ABPA with allergic Aspergillus sinusitis (AAS) is an uncommon presentation. The concept of one airway/one disease justifies the co-existence of ABPA with AAS, but it does not always hold true. We report a case of a 35-year-old woman who presented with symptoms suggestive of bronchial asthma. On further investigation, the radiological pattern showed fleeting shadows and CT scan showed central cystic bronchiectatic changes characteristic of ABPA. The nasal secretions were investigated for the presence of Aspergillus and were found to be positive. Hence a diagnosis of ABPA with AAS was established. The patient was treated with oral steroids and antifungal drugs. PMID:25371437

  12. Evaluation of in vitro gas production and rumen bacterial populations fermenting corn milling (co)products.

    PubMed

    Williams, W L; Tedeschi, L O; Kononoff, P J; Callaway, T R; Dowd, S E; Karges, K; Gibson, M L

    2010-10-01

    The objective of this study was to evaluate the fermentation dynamics of 2 commonly fed corn (co)products in their intact and defatted forms, using the in vitro gas production (IVGP) technique, and to investigate the shifts of the predominant rumen bacterial populations using the 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) technique. The bTEFAP technique was used to determine the bacterial profile of each fermentation time at 24 and 48 h. Bacterial populations were identified at the species level. Species were grouped by substrate affinities (guilds) for cellulose, hemicellulose, pectin, starch, sugars, protein, lipids, and lactate. The 2 (co)products were a dried distillers grain (DDG) plus solubles produced from a low-heat drying process (BPX) and a high-protein DDG without solubles (HP). Chemical analysis revealed that BPX contained about 11.4% ether extract, whereas HP contained only 3.88%. Previous studies have indicated that processing methods, as well as fat content, of corn (co)products directly affect fermentation rate and substrate availability, but little information is available regarding changes in rumen bacterial populations. Fermentation profiles of intact and defatted BPX and HP were compared with alfalfa hay as a standard profile. Defatting before incubation had no effect on total gas production in BPX or HP, but reduced lag time and the fractional rate of fermentation of BPX by at least half, whereas there was no effect for HP. The HP feed supported a greater percentage of fibrolytic and proteolytic bacteria than did BPX. Defatting both DDG increased the fibrolytic (26.8 to 38.7%) and proteolytic (26.1 to 37.2%) bacterial guild populations and decreased the lactate-utilizing bacterial guild (3.06 to 1.44%). Information regarding the fermentation kinetics and bacterial population shifts when feeding corn (co)products may lead to more innovative processing methods that improve feed quality (e.g., deoiling) and consequently

  13. Co-existence of Gel and Fluid Lipid Domains in Single-component Phospholipid Membranes

    SciTech Connect

    Armstrong, Clare L; Barrett, M; Toppozini, L; Yamani, Zahra; Kucerka, Norbert; Katsaras, John; Fragneto, Giovanna; Rheinstadter, Maikel C

    2012-01-01

    Lateral nanostructures in membranes, so-called rafts, are believed to strongly influence membrane properties and functions. The experimental observation of rafts has proven difficult as they are thought to be dynamic structures that likely fluctuate on nano- to microsecond time scales. Using neutron diffraction we present direct experimental evidence for the co-existence of gel and fluid lipid domains in a single-component phospholipid membrane made of DPPC as it undergoes its main phase transition. The coherence length of the neutron beam sets a lower limit for the size of structures that can be observed. Neutron coherence lengths between 30 and 242A used in this study were obtained by varying the incident neutron energy and the resolution of the neutron spectrometer. We observe Bragg peaks corresponding to co-existing nanometer sized structures, both in out-of-plane and in-plane scans, by tuning the neutron coherence length. During the main phase transition, instead of a continuous transition that shows a pseudo-critical behavior, we observe the co-existence of gel and fluid domains.

  14. Nutrient reduction induced stringent responses promote bacterial quorum-sensing divergence for population fitness

    PubMed Central

    Zhao, Kelei; Zhou, Xikun; Li, Wujiao; Zhang, Xiuyue; Yue, Bisong

    2016-01-01

    Bacteria use a cell-cell communication system termed quorum-sensing (QS) to adjust population size by coordinating the costly but beneficial cooperative behaviors. It has long been suggested that bacterial social conflict for expensive extracellular products may drive QS divergence and cause the “tragedy of the commons”. However, the underlying molecular mechanism of social divergence and its evolutionary consequences for the bacterial ecology still remain largely unknown. By using the model bacterium Pseudomonas aeruginosa PAO1, here we show that nutrient reduction can promote QS divergence for population fitness during evolution but requiring adequate cell density. Mechanically, decreased nutrient supplies can induce RpoS-directed stringent response and enhance the selection pressure on lasR gene, and lasR mutants are evolved in association with the DNA mismatch repair “switch-off”. The lasR mutants have higher relative fitness than QS-intact individuals due to their energy-saving characteristic under nutrient decreased condition. Furthermore an optimal incorporation of lasR mutants is capable of maximizing the fitness of entire population during in vitro culture and the colonization in mouse lung. Consequently, rather than worsen the population health, QS-coordinated social divergence is an elaborate evolutionary strategy that renders the entire bacterial population more fit in tough times. PMID:27713502

  15. Identification of Population Bottlenecks and Colonization Factors during Assembly of Bacterial Communities within the Zebrafish Intestine

    PubMed Central

    Stephens, W. Zac; Wiles, Travis J.; Martinez, Emily S.; Jemielita, Matthew; Burns, Adam R.; Parthasarathy, Raghuveer; Bohannan, Brendan J. M.

    2015-01-01

    ABSTRACT The zebrafish, Danio rerio, is a powerful model for studying bacterial colonization of the vertebrate intestine, but the genes required by commensal bacteria to colonize the zebrafish gut have not yet been interrogated on a genome-wide level. Here we apply a high-throughput transposon mutagenesis screen to Aeromonas veronii Hm21 and Vibrio sp. strain ZWU0020 during their colonization of the zebrafish intestine alone and in competition with each other, as well as in different colonization orders. We use these transposon-tagged libraries to track bacterial population sizes in different colonization regimes and to identify gene functions required during these processes. We show that intraspecific, but not interspecific, competition with a previously established bacterial population greatly reduces the ability of these two bacterial species to colonize. Further, using a simple binomial sampling model, we show that under conditions of interspecific competition, genes required for colonization cannot be identified because of the population bottleneck experienced by the second colonizer. When bacteria colonize the intestine alone or at the same time as the other species, we find shared suites of functional requirements for colonization by the two species, including a prominent role for chemotaxis and motility, regardless of the presence of another species. PMID:26507229

  16. Novel, Deep-Branching Heterotrophic Bacterial Populations Recovered from Thermal Spring Metagenomes

    PubMed Central

    Colman, Daniel R.; Jay, Zackary J.; Inskeep, William P.; Jennings, Ryan deM.; Maas, Kendra R.; Rusch, Douglas B.; Takacs-Vesbach, Cristina D.

    2016-01-01

    Thermal spring ecosystems are a valuable resource for the discovery of novel hyperthermophilic Bacteria and Archaea, and harbor deeply-branching lineages that provide insight regarding the nature of early microbial life. We characterized bacterial populations in two circumneutral (pH ~8) Yellowstone National Park thermal (T ~80°C) spring filamentous “streamer” communities using random metagenomic DNA sequence to investigate the metabolic potential of these novel populations. Four de novo assemblies representing three abundant, deeply-branching bacterial phylotypes were recovered. Analysis of conserved phylogenetic marker genes indicated that two of the phylotypes represent separate groups of an uncharacterized phylum (for which we propose the candidate phylum name “Pyropristinus”). The third new phylotype falls within the proposed Calescamantes phylum. Metabolic reconstructions of the “Pyropristinus” and Calescamantes populations showed that these organisms appear to be chemoorganoheterotrophs and have the genomic potential for aerobic respiration and oxidative phosphorylation via archaeal-like V-type, and bacterial F-type ATPases, respectively. A survey of similar phylotypes (>97% nt identity) within 16S rRNA gene datasets suggest that the newly described organisms are restricted to terrestrial thermal springs ranging from 70 to 90°C and pH values of ~7–9. The characterization of these lineages is important for understanding the diversity of deeply-branching bacterial phyla, and their functional role in high-temperature circumneutral “streamer” communities. PMID:27014227

  17. Novel, Deep-Branching Heterotrophic Bacterial Populations Recovered from Thermal Spring Metagenomes.

    PubMed

    Colman, Daniel R; Jay, Zackary J; Inskeep, William P; Jennings, Ryan deM; Maas, Kendra R; Rusch, Douglas B; Takacs-Vesbach, Cristina D

    2016-01-01

    Thermal spring ecosystems are a valuable resource for the discovery of novel hyperthermophilic Bacteria and Archaea, and harbor deeply-branching lineages that provide insight regarding the nature of early microbial life. We characterized bacterial populations in two circumneutral (pH ~8) Yellowstone National Park thermal (T ~80°C) spring filamentous "streamer" communities using random metagenomic DNA sequence to investigate the metabolic potential of these novel populations. Four de novo assemblies representing three abundant, deeply-branching bacterial phylotypes were recovered. Analysis of conserved phylogenetic marker genes indicated that two of the phylotypes represent separate groups of an uncharacterized phylum (for which we propose the candidate phylum name "Pyropristinus"). The third new phylotype falls within the proposed Calescamantes phylum. Metabolic reconstructions of the "Pyropristinus" and Calescamantes populations showed that these organisms appear to be chemoorganoheterotrophs and have the genomic potential for aerobic respiration and oxidative phosphorylation via archaeal-like V-type, and bacterial F-type ATPases, respectively. A survey of similar phylotypes (>97% nt identity) within 16S rRNA gene datasets suggest that the newly described organisms are restricted to terrestrial thermal springs ranging from 70 to 90°C and pH values of ~7-9. The characterization of these lineages is important for understanding the diversity of deeply-branching bacterial phyla, and their functional role in high-temperature circumneutral "streamer" communities.

  18. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

    PubMed Central

    Bendall, Matthew L; Stevens, Sarah LR; Chan, Leong-Keat; Malfatti, Stephanie; Schwientek, Patrick; Tremblay, Julien; Schackwitz, Wendy; Martin, Joel; Pati, Amrita; Bushnell, Brian; Froula, Jeff; Kang, Dongwan; Tringe, Susannah G; Bertilsson, Stefan; Moran, Mary A; Shade, Ashley; Newton, Ryan J; McMahon, Katherine D; Malmstrom, Rex R

    2016-01-01

    Multiple models describe the formation and evolution of distinct microbial phylogenetic groups. These evolutionary models make different predictions regarding how adaptive alleles spread through populations and how genetic diversity is maintained. Processes predicted by competing evolutionary models, for example, genome-wide selective sweeps vs gene-specific sweeps, could be captured in natural populations using time-series metagenomics if the approach were applied over a sufficiently long time frame. Direct observations of either process would help resolve how distinct microbial groups evolve. Here, from a 9-year metagenomic study of a freshwater lake (2005–2013), we explore changes in single-nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in 30 bacterial populations. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied by >1000-fold among populations. SNP allele frequencies also changed dramatically over time within some populations. Interestingly, nearly all SNP variants were slowly purged over several years from one population of green sulfur bacteria, while at the same time multiple genes either swept through or were lost from this population. These patterns were consistent with a genome-wide selective sweep in progress, a process predicted by the ‘ecotype model' of speciation but not previously observed in nature. In contrast, other populations contained large, SNP-free genomic regions that appear to have swept independently through the populations prior to the study without purging diversity elsewhere in the genome. Evidence for both genome-wide and gene-specific sweeps suggests that different models of bacterial speciation may apply to different populations coexisting in the same environment. PMID:26744812

  19. Assessing the Probability of Detection of Horizontal Gene Transfer Events in Bacterial Populations

    PubMed Central

    Townsend, Jeffrey P.; Bøhn, Thomas; Nielsen, Kaare Magne

    2012-01-01

    Experimental approaches to identify horizontal gene transfer (HGT) events of non-mobile DNA in bacteria have typically relied on detection of the initial transformants or their immediate offspring. However, rare HGT events occurring in large and structured populations are unlikely to be detected in a short time frame. Population genetic modeling of the growth dynamics of bacterial genotypes is therefore necessary to account for natural selection and genetic drift during the time lag and to predict realistic time frames for detection with a given sampling design. Here we draw on statistical approaches to population genetic theory to construct a cohesive probabilistic framework for investigation of HGT of exogenous DNA into bacteria. In particular, the stochastic timing of rare HGT events is accounted for. Integrating over all possible event timings, we provide an equation for the probability of detection, given that HGT actually occurred. Furthermore, we identify the key variables determining the probability of detecting HGT events in four different case scenarios that are representative of bacterial populations in various environments. Our theoretical analysis provides insight into the temporal aspects of dissemination of genetic material, such as antibiotic resistance genes or transgenes present in genetically modified organisms. Due to the long time scales involved and the exponential growth of bacteria with differing fitness, quantitative analyses incorporating bacterial generation time, and levels of selection, such as the one presented here, will be a necessary component of any future experimental design and analysis of HGT as it occurs in natural settings. PMID:22363321

  20. Assessing the probability of detection of horizontal gene transfer events in bacterial populations.

    PubMed

    Townsend, Jeffrey P; Bøhn, Thomas; Nielsen, Kaare Magne

    2012-01-01

    Experimental approaches to identify horizontal gene transfer (HGT) events of non-mobile DNA in bacteria have typically relied on detection of the initial transformants or their immediate offspring. However, rare HGT events occurring in large and structured populations are unlikely to be detected in a short time frame. Population genetic modeling of the growth dynamics of bacterial genotypes is therefore necessary to account for natural selection and genetic drift during the time lag and to predict realistic time frames for detection with a given sampling design. Here we draw on statistical approaches to population genetic theory to construct a cohesive probabilistic framework for investigation of HGT of exogenous DNA into bacteria. In particular, the stochastic timing of rare HGT events is accounted for. Integrating over all possible event timings, we provide an equation for the probability of detection, given that HGT actually occurred. Furthermore, we identify the key variables determining the probability of detecting HGT events in four different case scenarios that are representative of bacterial populations in various environments. Our theoretical analysis provides insight into the temporal aspects of dissemination of genetic material, such as antibiotic resistance genes or transgenes present in genetically modified organisms. Due to the long time scales involved and the exponential growth of bacteria with differing fitness, quantitative analyses incorporating bacterial generation time, and levels of selection, such as the one presented here, will be a necessary component of any future experimental design and analysis of HGT as it occurs in natural settings.

  1. Changes in Bacterial Population of Gastrointestinal Tract of Weaned Pigs Fed with Different Additives

    PubMed Central

    Roca, Mercè; Nofrarías, Miquel; Majó, Natàlia; Pérez de Rozas, Ana María; Castillo, Marisol; Martín-Orúe, Susana María; Espinal, Anna; Pujols, Joan; Badiola, Ignacio

    2014-01-01

    This study aimed to provide novel insights into the gastrointestinal microbial diversity from different gastrointestinal locations in weaning piglets using PCR-restriction fragment length polymorphism (PCR-RFLP). Additionally, the effect of different feed additives was analyzed. Thirty-two piglets were fed with four different diets: a control group and three enriched diets, with avilamycin, sodium butyrate, and a plant extract mixture. Digesta samples were collected from eight different gastrointestinal segments of each animal and the bacterial population was analysed by a PCR-RFLP technique that uses 16S rDNA gene sequences. Bacterial diversity was assessed by calculating the number of bands and the Shannon-Weaver index. Dendrograms were constructed to estimate the similarity of bacterial populations. A higher bacterial diversity was detected in large intestine compared to small intestine. Among diets, the most relevant microbial diversity differences were found between sodium butyrate and plant extract mixture. Proximal jejunum, ileum, and proximal colon were identified as those segments that could be representative of microbial diversity in pig gut. Results indicate that PCR-RFLP technique allowed detecting modifications on the gastrointestinal microbial ecology in pigs fed with different additives, such as increased biodiversity by sodium butyrate in feed. PMID:24575403

  2. Possibility of Non Fermi Liquid Like States Co-exists With Superconductivity in Doubly Filled Skutterudites

    NASA Astrophysics Data System (ADS)

    Venkateshwarlu, D.; Shanmukhrao, S.; Pandya, Swati; Chandra, L. S. Sharath; Vishwakarma, P. N.; Jain, Deepti; Gangrade, Mohan; Ganesan, V.

    2011-07-01

    Skutterudites is known to have fascinating ground states depending upon the void filling. Heat capacity of partially filled Pr0.8Pt4Ge12 and doubly filled Pr0.8Nd0.2Pt4Ge12 skutterudites has been investigated. Superconducting gaps have been quantified through heat capacity in the presence of magnetic fields. C/T versus T2 plot of Pr0.8Nd0.2Pt4Ge12 shows an upturn at low temperatures and this tendency increases with magnetic field, suggesting the possibility of a field induced NFL like states due to magnetic correlations co-existing with superconductivity.

  3. Co-existing heat currents in opposite directions in graphene nanoribbons

    NASA Astrophysics Data System (ADS)

    Zhang, Jingchao; Wang, Xinwei; Xie, Huaqing

    2013-12-01

    Using molecular dynamics simulations, we create an unprecedented scenario in graphene nanoribbons: co-existence of two heat currents in opposite directions at the same location. One heat current is carried by flexural mode phonons, and the other one by transverse/longitudinal modes phonons in the opposite direction. The local apparent thermal conductivity (κapp) varies in a very large range: -468 to 1434 W/m K. The negative κapp does not violate the second law of thermodynamics. It is a combined effect of the much higher thermal conductivity of flexural mode phonons and the weak coupling between them and transverse/longitudinal modes phonons.

  4. Embryonal Hepatoblastoma with Co-existent Glycogen Storage Disease in a Seven-month-old Child

    PubMed Central

    Kalra, Brahma Prakash; Bhat, Nowneet Kumar; Wasim, Sanobar

    2016-01-01

    Hepatoblastoma is an uncommon malignant liver tumour diagnosed usually during the first three years of life. It presents as abdominal mass with elevated alpha fetoprotein levels. The definite diagnosis requires histopathological confirmation. Although conditions like Familial Adenomatous Polyposis (FAP) or Beckwith-Wiedman Syndrome may be associated with hepatoblastomas, storage disorders are uncommonly documented. We describe a rare case of hepatoblastoma with co-existent glycogen storage disease in an infant male who presented with a progressively increasing mass in abdomen along with failure to thrive. PMID:27042474

  5. Distribution and Life Strategies of Two Bacterial Populations in a Eutrophic Lake

    PubMed Central

    Weinbauer, Markus G.; Höfle, Manfred G.

    1998-01-01

    Monoclonal antibodies and epifluorescence microscopy were used to determine the depth distribution of two indigenous bacterial populations in the stratified Lake Plußsee and characterize their life strategies. Populations of Comamonas acidovorans PX54 showed a depth distribution with maximum abundances in the oxic epilimnion, whereas Aeromonas hydrophila PU7718 showed a depth distribution with maximum abundances in the anoxic thermocline layer (metalimnion), i.e., in the water layer with the highest microbial activity. Resistance of PX54 to protist grazing and high metabolic versatility and growth rate of PU7718 were the most important life strategy traits for explaining the depth distribution of the two bacterial populations. Maximum abundance of PX54 was 16,000 cells per ml, and maximum abundance of PU7718 was 20,000 cells per ml. Determination of bacterial productivity in dilution cultures with different-size fractions of dissolved organic matter (DOM) from lake water indicates that low-molecular-weight (LMW) DOM is less bioreactive than total DOM (TDOM). The abundance and growth rate of PU7718 were highest in the TDOM fractions, whereas those of PX54 were highest in the LMW DOM fraction, demonstrating that PX54 can grow well on the less bioreactive DOM fraction. We estimated that 13 to 24% of the entire bacterial community and 14% of PU7718 were removed by viral lysis, whereas no significant effect of viral lysis on PX54 could be detected. Growth rates of PX54 (0.11 to 0.13 h−1) were higher than those of the entire bacterial community (0.04 to 0.08 h−1) but lower than those of PU7718 (0.26 to 0.31 h−1). In undiluted cultures, the growth rates were significantly lower, pointing to density effects such as resource limitation or antibiosis, and the effects were stronger for PU7718 and the entire bacterial community than for PX54. Life strategy characterizations based on data from literature and this study revealed that the fast-growing and metabolically

  6. Flow cytometric determination of bacterial populations in bottled natural mineral waters

    NASA Astrophysics Data System (ADS)

    Beisker, Wolfgang; Meier, H.

    1998-04-01

    In order to enhance the quality and safety of bottled natural mineral waters, new methodologies besides classical bacteriology have been evaluated. Multi laser flow cytometry has been used to identify bacterial populations based on their DNA content, physiological activity and phylogeny from in situ hybridization with rRNA targeted DNA probes. Due to the low content of organic material in these waters, the bacterial population are under conditions (low ribosome content, low activity, etc.) which makes it hard to detect them flow cytometrically. The numbers of bacteria are in the range between 1000 and 100,000 per ml (for uncarbonated waters). Filtration techniques to enrich the bacterial population have been developed in combination with specific staining and hybridization protocols. First results on some selected brands show, that most bacteria belong to the beta subclass of proteobacteria. If the DNA containing cells (DAPI staining) are counted as 100%, 84% could be stained with a eubacteria probe. From these 84% 68% belong to the beta subclass, 8.2% to the alpha and 0.3% to the gamma subclass of roteobacteria. 8.5% could be identified as cytophaga flexibacter. By optimizing DNA staining with cyanine dyes and enhancing the sensitivity of light scatter detection, the detection limit could be considerably lowered.

  7. Supplemental dietary inulin of variable chain lengths alters intestinal bacterial populations in young pigs.

    PubMed

    Patterson, Jannine K; Yasuda, Koji; Welch, Ross M; Miller, Dennis D; Lei, Xin Gen

    2010-12-01

    Previously, we showed that supplementation of diets with short-chain inulin (P95), long-chain inulin (HP), and a 50:50 mixture of both (Synergy 1) improved body iron status and altered expression of the genes involved in iron homeostasis and inflammation in young pigs. However, the effects of these 3 types of inulin on intestinal bacteria remain unknown. Applying terminal restriction fragment length polymorphism analysis, we determined the abundances of luminal and adherent bacterial populations from 6 segments of the small and large intestines of pigs (n = 4 for each group) fed an iron-deficient basal diet (BD) or the BD supplemented with 4% of P95, Synergy 1, or HP for 5 wk. Compared with BD, all 3 types of inulin enhanced (P < 0.05) the abundance of beneficial bifidobacteria and lactobacilli in the microbiota adherent to intestinal mucus of various gut segments of pigs. These changes were seen as proximal as in the jejunum with P95 but did not appear until the distal ileum or cecum with HP. Similar effects of inulin on bacterial populations in the lumen contents were found. Meanwhile, all 3 types of inulin suppressed the less desirable bacteria Clostridium spp. and members of the Enterobacteriaceae in the lumen and mucosa of various gut segments. Our findings suggest that the ability of dietary inulin to alter intestinal bacterial populations may partially account for its iron bioavailability-promoting effect and possibly other health benefits.

  8. Supplemental Dietary Inulin of Variable Chain Lengths Alters Intestinal Bacterial Populations in Young Pigs123

    PubMed Central

    Patterson, Jannine K.; Yasuda, Koji; Welch, Ross M.; Miller, Dennis D.; Lei, Xin Gen

    2010-01-01

    Previously, we showed that supplementation of diets with short-chain inulin (P95), long-chain inulin (HP), and a 50:50 mixture of both (Synergy 1) improved body iron status and altered expression of the genes involved in iron homeostasis and inflammation in young pigs. However, the effects of these 3 types of inulin on intestinal bacteria remain unknown. Applying terminal restriction fragment length polymorphism analysis, we determined the abundances of luminal and adherent bacterial populations from 6 segments of the small and large intestines of pigs (n = 4 for each group) fed an iron-deficient basal diet (BD) or the BD supplemented with 4% of P95, Synergy 1, or HP for 5 wk. Compared with BD, all 3 types of inulin enhanced (P < 0.05) the abundance of beneficial bifidobacteria and lactobacilli in the microbiota adherent to intestinal mucus of various gut segments of pigs. These changes were seen as proximal as in the jejunum with P95 but did not appear until the distal ileum or cecum with HP. Similar effects of inulin on bacterial populations in the lumen contents were found. Meanwhile, all 3 types of inulin suppressed the less desirable bacteria Clostridium spp. and members of the Enterobacteriaceae in the lumen and mucosa of various gut segments. Our findings suggest that the ability of dietary inulin to alter intestinal bacterial populations may partially account for its iron bioavailability-promoting effect and possibly other health benefits. PMID:20980641

  9. Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum

    PubMed Central

    Kumar, Nitin; Lad, Ganesh; Giuntini, Elisa; Kaye, Maria E.; Udomwong, Piyachat; Shamsani, N. Jannah; Young, J. Peter W.; Bailly, Xavier

    2015-01-01

    Biological species may remain distinct because of genetic isolation or ecological adaptation, but these two aspects do not always coincide. To establish the nature of the species boundary within a local bacterial population, we characterized a sympatric population of the bacterium Rhizobium leguminosarum by genomic sequencing of 72 isolates. Although all strains have 16S rRNA typical of R. leguminosarum, they fall into five genospecies by the criterion of average nucleotide identity (ANI). Many genes, on plasmids as well as the chromosome, support this division: recombination of core genes has been largely within genospecies. Nevertheless, variation in ecological properties, including symbiotic host range and carbon-source utilization, cuts across these genospecies, so that none of these phenotypes is diagnostic of genospecies. This phenotypic variation is conferred by mobile genes. The genospecies meet the Mayr criteria for biological species in respect of their core genes, but do not correspond to coherent ecological groups, so periodic selection may not be effective in purging variation within them. The population structure is incompatible with traditional ‘polyphasic taxonomy′ that requires bacterial species to have both phylogenetic coherence and distinctive phenotypes. More generally, genomics has revealed that many bacterial species share adaptive modules by horizontal gene transfer, and we envisage a more consistent taxonomic framework that explicitly recognizes this. Significant phenotypes should be recognized as ‘biovars' within species that are defined by core gene phylogeny. PMID:25589577

  10. Development of an Experimental Model of Diabetes Co-Existing with Metabolic Syndrome in Rats

    PubMed Central

    Suman, Rajesh Kumar; Ray Mohanty, Ipseeta; Borde, Manjusha K.; Maheshwari, Ujwala; Deshmukh, Y. A.

    2016-01-01

    Background. The incidence of metabolic syndrome co-existing with diabetes mellitus is on the rise globally. Objective. The present study was designed to develop a unique animal model that will mimic the pathological features seen in individuals with diabetes and metabolic syndrome, suitable for pharmacological screening of drugs. Materials and Methods. A combination of High-Fat Diet (HFD) and low dose of streptozotocin (STZ) at 30, 35, and 40 mg/kg was used to induce metabolic syndrome in the setting of diabetes mellitus in Wistar rats. Results. The 40 mg/kg STZ produced sustained hyperglycemia and the dose was thus selected for the study to induce diabetes mellitus. Various components of metabolic syndrome such as dyslipidemia {(increased triglyceride, total cholesterol, LDL cholesterol, and decreased HDL cholesterol)}, diabetes mellitus (blood glucose, HbA1c, serum insulin, and C-peptide), and hypertension {systolic blood pressure} were mimicked in the developed model of metabolic syndrome co-existing with diabetes mellitus. In addition to significant cardiac injury, atherogenic index, inflammation (hs-CRP), decline in hepatic and renal function were observed in the HF-DC group when compared to NC group rats. The histopathological assessment confirmed presence of edema, necrosis, and inflammation in heart, pancreas, liver, and kidney of HF-DC group as compared to NC. Conclusion. The present study has developed a unique rodent model of metabolic syndrome, with diabetes as an essential component. PMID:26880906

  11. Gene Expression Variability Underlies Adaptive Resistance in Phenotypically Heterogeneous Bacterial Populations.

    PubMed

    Erickson, Keesha E; Otoupal, Peter B; Chatterjee, Anushree

    2015-11-13

    The root cause of the antibiotic resistance crisis is the ability of bacteria to evolve resistance to a multitude of antibiotics and other environmental toxins. The regulation of adaptation is difficult to pinpoint due to extensive phenotypic heterogeneity arising during evolution. Here, we investigate the mechanisms underlying general bacterial adaptation by evolving wild-type Escherichia coli populations to dissimilar chemical toxins. We demonstrate the presence of extensive inter- and intrapopulation phenotypic heterogeneity across adapted populations in multiple traits, including minimum inhibitory concentration, growth rate, and lag time. To search for a common response across the heterogeneous adapted populations, we measured gene expression in three stress-response networks: the mar regulon, the general stress response, and the SOS response. While few genes were differentially expressed, clustering revealed that interpopulation gene expression variability in adapted populations was distinct from that of unadapted populations. Notably, we observed both increases and decreases in gene expression variability upon adaptation. Sequencing select genes revealed that the observed gene expression trends are not necessarily attributable to genetic changes. To further explore the connection between gene expression variability and adaptation, we propagated single-gene knockout and CRISPR (clustered regularly interspaced short palindromic repeats) interference strains and quantified impact on adaptation to antibiotics. We identified significant correlations that suggest genes with low expression variability have greater impact on adaptation. This study provides evidence that gene expression variability can be used as an indicator of bacterial adaptive resistance, even in the face of the pervasive phenotypic heterogeneity underlying adaptation. PMID:27623410

  12. Changes in gut bacterial populations and their translocation into liver and ascites in alcoholic liver cirrhotics

    PubMed Central

    2014-01-01

    Background The liver is the first line of defence against continuously occurring influx of microbial-derived products and bacteria from the gut. Intestinal bacteria have been implicated in the pathogenesis of alcoholic liver cirrhosis. Escape of intestinal bacteria into the ascites is involved in the pathogenesis of spontaneous bacterial peritonitis, which is a common complication of liver cirrhosis. The association between faecal bacterial populations and alcoholic liver cirrhosis has not been resolved. Methods Relative ratios of major commensal bacterial communities (Bacteroides spp., Bifidobacterium spp., Clostridium leptum group, Enterobactericaea and Lactobacillus spp.) were determined in faecal samples from post mortem examinations performed on 42 males, including cirrhotic alcoholics (n = 13), non-cirrhotic alcoholics (n = 15), non-alcoholic controls (n = 14) and in 7 healthy male volunteers using real-time quantitative PCR (RT-qPCR). Translocation of bacteria into liver in the autopsy cases and into the ascites of 12 volunteers with liver cirrhosis was also studied with RT-qPCR. CD14 immunostaining was performed for the autopsy liver samples. Results Relative ratios of faecal bacteria in autopsy controls were comparable to those of healthy volunteers. Cirrhotics had in median 27 times more bacterial DNA of Enterobactericaea in faeces compared to the healthy volunteers (p = 0.011). Enterobactericaea were also the most common bacteria translocated into cirrhotic liver, although there were no statistically significant differences between the study groups. Of the ascites samples from the volunteers with liver cirrhosis, 50% contained bacterial DNA from Enterobactericaea, Clostridium leptum group or Lactobacillus spp.. The total bacterial DNA in autopsy liver was associated with the percentage of CD14 expression (p = 0.045). CD14 expression percentage in cirrhotics was significantly higher than in the autopsy controls (p = 0

  13. The population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens.

    PubMed

    Wilson, Benjamin A; Garud, Nandita R; Feder, Alison F; Assaf, Zoe J; Pennings, Pleuni S

    2016-01-01

    Drug resistance is a costly consequence of pathogen evolution and a major concern in public health. In this review, we show how population genetics can be used to study the evolution of drug resistance and also how drug resistance evolution is informative as an evolutionary model system. We highlight five examples from diverse organisms with particular focus on: (i) identifying drug resistance loci in the malaria parasite Plasmodium falciparum using the genomic signatures of selective sweeps, (ii) determining the role of epistasis in drug resistance evolution in influenza, (iii) quantifying the role of standing genetic variation in the evolution of drug resistance in HIV, (iv) using drug resistance mutations to study clonal interference dynamics in tuberculosis and (v) analysing the population structure of the core and accessory genome of Staphylococcus aureus to understand the spread of methicillin resistance. Throughout this review, we discuss the uses of sequence data and population genetic theory in studying the evolution of drug resistance.

  14. Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics

    SciTech Connect

    Chan, Leong-Keat; Bendall, Matthew L.; Malfatti, Stephanie; Schwientek, Patrick; Tremblay, Julien; Schackwitz, Wendy; Martin, Joel; Pati, Amrita; Bushnell, Brian; Foster, Brian; Kang, Dongwan; Tringe, Susannah G.; Bertilsson, Stefan; Moran, Mary Ann; Shade, Ashley; Newton, Ryan J.; Stevens, Sarah; McMahon, Katherine D.; Malmstrom, Rex R.

    2014-06-18

    Multiple evolutionary models have been proposed to explain the formation of genetically and ecologically distinct bacterial groups. Time-series metagenomics enables direct observation of evolutionary processes in natural populations, and if applied over a sufficiently long time frame, this approach could capture events such as gene-specific or genome-wide selective sweeps. Direct observations of either process could help resolve how distinct groups form in natural microbial assemblages. Here, from a three-year metagenomic study of a freshwater lake, we explore changes in single nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in populations of Chlorobiaceae and Methylophilaceae. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied considerably among closely related, co-occurring Methylophilaceae populations. SNP allele frequencies, as well as the relative abundance of certain genes, changed dramatically over time in each population. Interestingly, SNP diversity was purged at nearly every genome position in one of the Chlorobiaceae populations over the course of three years, while at the same time multiple genes either swept through or were swept from this population. These patterns were consistent with a genome-wide selective sweep, a process predicted by the ‘ecotype model’ of diversification, but not previously observed in natural populations.

  15. Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics

    SciTech Connect

    Chan, Leong-Keat; Bendall, Matthew L.; Malfatti, Stephanie; Schwientek, Patrick; Tremblay, Julien; Schackwitz, Wendy; Martin, Joel; Pati, Amrita; Bushnell, Brian; Foster, Brian; Kang, Dongwan; Tringe, Susannah G.; Bertilsson, Stefan; Moran, Mary Ann; Shade, Ashley; Newton, Ryan J.; Stevens, Sarah; McMcahon, Katherine D.; Mamlstrom, Rex R.

    2014-05-12

    Multiple evolutionary models have been proposed to explain the formation of genetically and ecologically distinct bacterial groups. Time-series metagenomics enables direct observation of evolutionary processes in natural populations, and if applied over a sufficiently long time frame, this approach could capture events such as gene-specific or genome-wide selective sweeps. Direct observations of either process could help resolve how distinct groups form in natural microbial assemblages. Here, from a three-year metagenomic study of a freshwater lake, we explore changes in single nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in populations of Chlorobiaceae and Methylophilaceae. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied considerably among closely related, co-occurring Methylophilaceae populations. SNP allele frequencies, as well as the relative abundance of certain genes, changed dramatically over time in each population. Interestingly, SNP diversity was purged at nearly every genome position in one of the Chlorobiaceae populations over the course of three years, while at the same time multiple genes either swept through or were swept from this population. These patterns were consistent with a genome-wide selective sweep, a process predicted by the ecotype model? of diversification, but not previously observed in natural populations.

  16. Identifying currents in the gene pool for bacterial populations using an integrative approach.

    PubMed

    Tang, Jing; Hanage, William P; Fraser, Christophe; Corander, Jukka

    2009-08-01

    The evolution of bacterial populations has recently become considerably better understood due to large-scale sequencing of population samples. It has become clear that DNA sequences from a multitude of genes, as well as a broad sample coverage of a target population, are needed to obtain a relatively unbiased view of its genetic structure and the patterns of ancestry connected to the strains. However, the traditional statistical methods for evolutionary inference, such as phylogenetic analysis, are associated with several difficulties under such an extensive sampling scenario, in particular when a considerable amount of recombination is anticipated to have taken place. To meet the needs of large-scale analyses of population structure for bacteria, we introduce here several statistical tools for the detection and representation of recombination between populations. Also, we introduce a model-based description of the shape of a population in sequence space, in terms of its molecular variability and affinity towards other populations. Extensive real data from the genus Neisseria are utilized to demonstrate the potential of an approach where these population genetic tools are combined with an phylogenetic analysis. The statistical tools introduced here are freely available in BAPS 5.2 software, which can be downloaded from http://web.abo.fi/fak/mnf/mate/jc/software/baps.html.

  17. Fast, high-throughput measurement of collective behaviour in a bacterial population.

    PubMed

    Colin, R; Zhang, R; Wilson, L G

    2014-09-01

    Swimming bacteria explore their environment by performing a random walk, which is biased in response to, for example, chemical stimuli, resulting in a collective drift of bacterial populations towards 'a better life'. This phenomenon, called chemotaxis, is one of the best known forms of collective behaviour in bacteria, crucial for bacterial survival and virulence. Both single-cell and macroscopic assays have investigated bacterial behaviours. However, theories that relate the two scales have previously been difficult to test directly. We present an image analysis method, inspired by light scattering, which measures the average collective motion of thousands of bacteria simultaneously. Using this method, a time-varying collective drift as small as 50 nm s(-1) can be measured. The method, validated using simulations, was applied to chemotactic Escherichia coli bacteria in linear gradients of the attractant α-methylaspartate. This enabled us to test a coarse-grained minimal model of chemotaxis. Our results clearly map the onset of receptor methylation, and the transition from linear to logarithmic sensing in the bacterial response to an external chemoeffector. Our method is broadly applicable to problems involving the measurement of collective drift with high time resolution, such as cell migration and fluid flows measurements, and enables fast screening of tactic behaviours.

  18. Papillary thyroid microcarcinoma co-exists with Hashimoto's thyroiditis: Is strain elastography still useful?

    PubMed

    Li, Yi; Wang, Yan; Wu, Qiong; Hu, Bing

    2016-05-01

    To study the performance of strain elastography in differentiating papillary thyroid microcarcinoma (PTMC) combined with Hashimoto's thyroiditis (HT), conventional ultrasound scan (US) and strain elastography (SE) were performed on 558 nodules smaller than 10 mm by one examiner before surgeries. Serum concentrations of thyroid peroxidase antibody (TPO-Ab) (normal range: 0-60 U/ml) were measured. Continuous variables were analyzed by independent t test. Receiver operating characteristics (ROC) curve analysis was applied to calculate the cut-off values of strain ratio (SR) and elastography score (ES). The comparison of AUCs is performed by Z test. 482 nodules were diagnosed as PTMC and there were 181 nodules co-existed with HT. SR measurements were lower in PTMC co-existed with HT when comparing to those without HT. (7.292±6.581 vs 11.319±13.155, p<0.000). Taking the data from all of the 558 nodules, the best cut-off of diagnosing PTMC was SR>2.58. When taking the data from 181 PTMC with HT, the best cut-off was SR>2.10. The diagnostic value of SR>2.1 were higher than ES>3, conventional US and combining US and SE (z=3.595, 4.876, 4.420, p<0.001), but cut-off of SR>2.1 did not show significant enhancement of diagnostic value compared to SR>2.58 (z=0.439, p=0.8903>0.001) in PTMC with HT. There is a negative relation between SR and titer of TPO-Ab (r=-0.650, p<0.0001). PTMC with high TPO-Ab (>1000) titer presented lower SR (5.972±4.118 vs 8.379±9.172, p=0.009). Although SR measurements were lower in nodules co-existed with HT when comparing those without HT, using a regular ES and cut-off of SR measurement would not influence the diagnosing performance. SE is still very useful for diagnosing PTMC with HT. PTMC with high TPO-Ab titer might require a lower cut-off of SR. PMID:26945905

  19. Familiality of Co-existing ADHD and Tic Disorders: Evidence from a Large Sibling Study

    PubMed Central

    Roessner, Veit; Banaschewski, Tobias; Becker, Andreas; Buse, Judith; Wanderer, Sina; Buitelaar, Jan K.; Sergeant, Joseph A.; Sonuga-Barke, Edmund J.; Gill, Michael; Manor, Iris; Miranda, Ana; Mulas, Fernando; Oades, Robert D.; Roeyers, Herbert; Steinhausen, Hans-Christoph; Faraone, Steven V.; Asherson, Philip; Rothenberger, Aribert

    2016-01-01

    Background: The association of attention-deficit/hyperactivity disorder (ADHD) and tic disorder (TD) is frequent and clinically important. Very few and inconclusive attempts have been made to clarify if and how the combination of ADHD+TD runs in families. Aim: To determine the first time in a large-scale ADHD sample whether ADHD+TD increases the risk of ADHD+TD in siblings and, also the first time, if this is independent of their psychopathological vulnerability in general. Methods: The study is based on the International Multicenter ADHD Genetics (IMAGE) study. The present sub-sample of 2815 individuals included ADHD-index patients with co-existing TD (ADHD+TD, n = 262) and without TD (ADHD–TD, n = 947) as well as their 1606 full siblings (n = 358 of the ADHD+TD index patients and n = 1248 of the ADHD-TD index patients). We assessed psychopathological symptoms in index patients and siblings by using the Strength and Difficulties Questionnaire (SDQ) and the parent and teacher Conners' long version Rating Scales (CRS). For disorder classification the Parental Account of Childhood Symptoms (PACS-Interview) was applied in n = 271 children. Odds ratio with the GENMOD procedure (PROCGENMOD) was used to test if the risk for ADHD, TD, and ADHD+TD in siblings was associated with the related index patients' diagnoses. In order to get an estimate for specificity we compared the four groups for general psychopathological symptoms. Results: Co-existing ADHD+TD in index patients increased the risk of both comorbid ADHD+TD and TD in the siblings of these index patients. These effects did not extend to general psychopathology. Interpretation: Co-existence of ADHD+TD may segregate in families. The same holds true for TD (without ADHD). Hence, the segregation of TD (included in both groups) seems to be the determining factor, independent of further behavioral problems. This close relationship between ADHD and TD supports the clinical approach to carefully assess ADHD in any case

  20. Obligate bacterial mutualists evolving from environmental bacteria in natural insect populations.

    PubMed

    Hosokawa, Takahiro; Ishii, Yoshiko; Nikoh, Naruo; Fujie, Manabu; Satoh, Nori; Fukatsu, Takema

    2016-01-01

    Diverse organisms are associated with obligate microbial mutualists. How such essential symbionts have originated from free-living ancestors is of evolutionary interest. Here we report that, in natural populations of the stinkbug Plautia stali, obligate bacterial mutualists are evolving from environmental bacteria. Of six distinct bacterial lineages associated with insect populations, two are uncultivable with reduced genomes, four are cultivable with non-reduced genomes, one uncultivable symbiont is fixed in temperate populations, and the other uncultivable symbiont coexists with four cultivable symbionts in subtropical populations. Symbiont elimination resulted in host mortality for all symbionts, while re-infection with any of the symbionts restored normal host growth, indicating that all the symbionts are indispensable and almost equivalent functionally. Some aseptic newborns incubated with environmental soils acquired the cultivable symbionts and normal growth was restored, identifying them as environmental Pantoea spp. Our finding uncovers an evolutionary transition from a free-living lifestyle to obligate mutualism that is currently ongoing in nature. PMID:27571756

  1. Evaluation of the airborne bacterial population in the periodically confined Antarctic base Concordia.

    PubMed

    Van Houdt, Rob; De Boever, Patrick; Coninx, Ilse; Le Calvez, Claire; Dicasillati, Roberto; Mahillon, Jacques; Mergeay, Max; Leys, Natalie

    2009-05-01

    The environmental airborne bacterial population in relation to human confinement was investigated over a period of 1 year in the Concordia Research Station, which is located on the Eastern Antarctic plateau. The unique location of the station makes it suitable for different research domains such as glaciology, atmospheric sciences, astronomy, etc. Furthermore, it is used as a test bed for long-duration spaceflights to study the physiologic and psychological adaptation to isolated environments. A total of 96 samples were collected at eight different locations in the station at regular intervals. The airborne bacterial contamination was for 90% of the samples lower than 10.0 x 10(2) colony-forming units per cubic meter of air (CFU/m(3)) and the total bacterial contamination increased over time during confinement but diminished after re-opening of the base. Viable airborne bacteria with different morphology were identified by biochemical analyses. The predominant microflora was identified as Staphylococcus sp. (24.9% of total) and Bacillus sp. (11.6% of total) and was associated with human activity, but also environmental species such as Sphingomonas paucimobilis (belonging to the alpha-Proteobacteria) could establish themselves in the airborne population. A few opportunistic pathogens (6%) were also identified.

  2. Rare Co-existence of Squamous Cell Carcinoma with Infiltration of Renal Vein and Xanthogranulomatous Pyelonephritis

    PubMed Central

    Vanikar, A.V.; Patel, R.D.; Nigam, L. K.; Trivedi, H. L.

    2015-01-01

    Primary renal squamous cell carcinoma is a very rare malignancy of the upper urinary tract. Most patients have history of chronic urolithiasis, analgesics abuse, radiotherapy or infection. Co-existence of SCC with xanthogranulomatous pyelonephritis is exceedingly rare with only few reports in the literature. We report a case of a 60-year-old male presented with right flank pain and mild tenderness of abdomen. Computed tomography of the abdomen revealed gross hydronephrosis with parenchymal thinning and irregular thick enhancing wall of pelvicalyceal system with multiple calculi in right kidney. Right renal vein appeared distended, filled with hypo dense material. Right nephrectomy was performed and sent for pathological examination. Histological evaluation revealed keratinizing squamous cell carcinoma with infiltration of renal vein and xanthogranulomatous pyelonephritis. PMID:26816904

  3. Observations of co-existing double disks around Pleione with NAYUTA telescope

    NASA Astrophysics Data System (ADS)

    Tanaka, Ken'ichi; Sadakane, Kozo; Narusawa, Shin-Ya; Sakamoto, Makoto; Naito, Hiroyuki

    2007-11-01

    Spectroscopic and B, V bands photometric observations of Pleione have been carried out at Nishi-Harima Astronomical Observatory and at Osaka Kyoiku University during the period between November 2005 and April 2007. Both B and V magnitudes of Pleione had declined by 0.35 mag during the period. Spectroscopic observations carried out using the MALLS spectrograph of the 2-m NAYUTA telescope at Nishi-Harima Astronomical Observatory showed remarkable changes in profiles and strengths of the Balmer lines as well as in metallic lines. Analyses of spectral data revealed a formation and growth of a new disk around the star's equator in the latter half of 2005 and, at the same time, a rapid declining process of the long-existing old disk which was formed in 1972. The authors discovered the co-existence of two axially tilted disks around a Be star for the first time in Pleione.

  4. Daily variations in pathogenic bacterial populations in a monsoon influenced tropical environment.

    PubMed

    Khandeparker, Lidita; Anil, Arga Chandrashekar; Naik, Sneha D; Gaonkar, Chetan C

    2015-07-15

    Changing climatic conditions have influenced the monsoon pattern in recent years. Variations in bacterial population in one such tropical environment were observed everyday over two years and point out intra and inter annual changes driven by the intensity of rainfall. Vibrio spp. were abundant during the monsoon and so were faecal coliforms. Vibrio alginolyticus were negatively influenced by nitrate, whereas, silicate and rainfall positively influenced Vibrio parahaemolyticus numbers. It is also known that pathogenic bacteria are associated with the plankton. Changes in the abundance of plankton, which are governed mainly by environmental changes, could be responsible for variation in pathogenic bacterial abundance during monsoon, other than the land runoff due to precipitation and influx of fresh water.

  5. Horizontal Gene Transfer and the Evolution of Bacterial and Archaeal Population Structure

    PubMed Central

    Alm, Eric J.; Hanage, William P.

    2013-01-01

    Many bacterial and archaeal lineages have a history of extensive and ongoing horizontal gene transfer and loss, as evidenced by the large differences in genome content even among otherwise closely related isolates. How ecologically cohesive populations might evolve and be maintained under such conditions of rapid gene turnover has remained controversial. Here we synthesize recent literature demonstrating the importance of habitat and niche in structuring horizontal gene transfer. This leads to a model of ecological speciation via gradual genetic isolation triggered by differential habitat association of nascent populations. Further, we hypothesize that subpopulations can evolve through local gene exchange networks by tapping into a gene pool that is adaptive towards local, continuously changing organismic interactions and is, to a large degree, responsible for the observed rapid gene turnover. Overall, these insights help explain how bacteria and archaea form populations that display both ecological cohesion and high genomic diversity. PMID:23332119

  6. Magnetic polarity fractions in magnetotactic bacterial populations near the geomagnetic equator.

    PubMed

    de Araujo, F F; Germano, F A; Gonçalves, L L; Pires, M A; Frankel, R B

    1990-08-01

    The relative numbers of North-seeking and South-seeking polarity types in natural populations of magnetotactic bacteria were determined at sites on the coast of Brazil. These sites were South of the geomagnetic equator and had upward geomagnetic inclinations of 1-12 degrees . For upward inclinations >6 degrees , South-seeking cells predominated over North-seeking cells by more than a factor of 10. For upward inclinations <6 degrees , the fraction of North-seeking cells in the population increased with decreasing geomagnetic inclination, approaching 0.5 at the geomagnetic equator. We present a simple statistical model of a stochastic process that qualitatively accounts for the dynamics of the two polarity types in a magnetotactic bacterial population as a function of the geomagnetic field inclination.

  7. Bacterial population in intestines of the black tiger shrimp (Penaeus monodon) under different growth stages.

    PubMed

    Rungrassamee, Wanilada; Klanchui, Amornpan; Chaiyapechara, Sage; Maibunkaew, Sawarot; Tangphatsornruang, Sithichoke; Jiravanichpaisal, Pikul; Karoonuthaisiri, Nitsara

    2013-01-01

    Intestinal bacterial communities in aquaculture have been drawn to attention due to potential benefit to their hosts. To identify core intestinal bacteria in the black tiger shrimp (Penaeus monodon), bacterial populations of disease-free shrimp were characterized from intestines of four developmental stages (15-day-old post larvae (PL15), 1- (J1), 2- (J2), and 3-month-old (J3) juveniles) using pyrosequencing, real-time PCR and denaturing gradient gel electrophoresis (DGGE) approaches. A total of 25,121 pyrosequencing reads (reading length = 442±24 bases) were obtained, which were categorized by barcode for PL15 (7,045 sequences), J1 (3,055 sequences), J2 (13,130 sequences) and J3 (1,890 sequences). Bacteria in the phyla Bacteroides, Firmicutes and Proteobacteria were found in intestines at all four growth stages. There were 88, 14, 27, and 20 bacterial genera associated with the intestinal tract of PL15, J1, J2 and J3, respectively. Pyrosequencing analysis revealed that Proteobacteria (class Gammaproteobacteria) was a dominant bacteria group with a relative abundance of 89% for PL15 and 99% for J1, J2 and J3. Real-time PCR assay also confirmed that Gammaproteobacteria had the highest relative abundance in intestines from all growth stages. Intestinal bacterial communities from the three juvenile stages were more similar to each other than that of the PL shrimp based on PCA analyses of pyrosequencing results and their DGGE profiles. This study provides descriptive bacterial communities associated to the black tiger shrimp intestines during these growth development stages in rearing facilities.

  8. Quick discrimination of heavy metal resistant bacterial populations using infrared spectroscopy coupled with chemometrics.

    PubMed

    Gurbanov, Rafig; Simsek Ozek, Nihal; Gozen, Ayse Gul; Severcan, Feride

    2015-10-01

    Lead and cadmium are frequently encountered heavy metals in industrially polluted areas. Many heavy metal resistant bacterial strains have a high biosorption capacity and thus are good candidates for the removal of toxic metals from the environment. However, as of yet there is no accurate method for discrimination of highly adaptive bacterial strains among the populations present in a given habitat. In this study, we aimed to find distinguishing molecular features of lead and cadmium resistant bacteria using Attenuated Total Reflectance-Fourier Transformed Infrared (ATR-FT-IR) spectroscopy and chemometric approaches. Our results demonstrated that both control and metal exposed E. coli and S. aureus strains could be successfully discriminated from each other using hierarchical cluster and principal component analysis methods. Moreover, we found that lead exposed bacterial strains could be successfully discriminated from cadmium exposed ones with a high heterogeneity value. These clear discriminations can be described by the ability of a bacterium to change its metabolism in terms of the content and structure of cellular macromolecules under heavy metal stress. In our case, cadmium and lead-induced genetic response systems in bacteria caused remarkable alterations in overall cellular metabolism. Bacteria deal with a heavy metal stress by altering nucleic acid methylations and lipid and protein synthesis. Heavy metal burden led to the development of relevant metabolic changes in proteins, lipids, and nucleic acids of the resistant bacteria described in this study. Our approach showed that infrared spectra obtained via ATR-FT-IR spectroscopy coupled with chemometric analysis can be utilized for rapid, low-cost, informative, reliable, and operator-independent discrimination of resistant bacterial populations.

  9. Positive epistasis between co-infecting plasmids promotes plasmid survival in bacterial populations.

    PubMed

    San Millan, Alvaro; Heilbron, Karl; MacLean, R Craig

    2014-03-01

    Plasmids have a key role in the horizontal transfer of genes among bacteria. Although plasmids are catalysts for bacterial evolution, it is challenging to understand how they can persist in bacterial populations over the long term because of the burden they impose on their hosts (the 'plasmid paradox'). This paradox is especially perplexing in the case of 'small' plasmids, which are unable to self-transfer by conjugation. Here, for the first time, we investigate how interactions between co-infecting plasmids influence plasmid persistence. Using an experimental model system based on interactions between a diverse assemblage of 'large' plasmids and a single small plasmid, pNI105, in the pathogenic bacterium Pseudomonas aeruginosa, we demonstrate that positive epistasis minimizes the cost associated with carrying multiple plasmids over the short term and increases the stability of the small plasmid over a longer time scale. In support of these experimental data, bioinformatic analysis showed that associations between small and large plasmids are more common than would be expected owing to chance alone across a range of families of bacteria; more generally, we find that co-infection with multiple plasmids is more common than would be expected owing to chance across a wide range of bacterial phyla. Collectively, these results suggest that positive epistasis promotes plasmid stability in bacterial populations. These findings pave the way for future mechanistic studies aimed at elucidating the molecular mechanisms of plasmid-plasmid interaction, and evolutionary studies aimed at understanding how the coevolution of plasmids drives the spread of plasmid-encoded traits.

  10. Molecular analysis of bacterial population structure and dynamics during cold storage of untreated and treated milk.

    PubMed

    Rasolofo, Eric Andriamahery; St-Gelais, Daniel; LaPointe, Gisele; Roy, Denis

    2010-03-31

    Spoilage bacteria in milk are controlled by treatments such as thermization, microfiltration and addition of carbon dioxide. However, little information is known about the changes in microbial communities during subsequent cold storage of treated milk. Culture-dependent methods and a direct molecular approach combining 16S rRNA gene clone libraries and quantitative PCR (Q-PCR) were applied to obtain a better overview of the structure and the dynamics of milk microbiota. Raw milk samples were treated by the addition of carbon dioxide (CO(2)), thermization (TH) or microfiltration (MF) and stored at 4 degrees C or 8 degrees C up to 7d. Untreated milk (UT) was used as a control. Psychrotrophic and staphylococci bacteria were enumerated in the milk samples by culture methods. For the molecular approach, DNA was extracted from milk samples and 16S rRNA gene was amplified by PCR with universal primers prior to cloning. The Q-PCR method was used to evaluate the dynamics of dominant bacterial species revealed by clone library analysis of 16S rRNA gene. Comparison of the 16S rRNA gene sequence indicated that the two most abundant operational taxonomic units (OTU), determined at 97% identity, belonged to the class Gammaproteobacteria (40.3% of the 1415 sequences) and Bacilli (40%). Dominant bacterial species in UT, CO(2) and TH milk samples at day 3 were affiliated with Staphylococcus, Streptococcus, Clostridia, Aerococcus, Facklamia, Corynebacterium, Acinetobacter and Trichococcus. Dominant bacterial species detected in MF milk were Stenotrophomonas, Pseudomonas and Delftia, while Pseudomonas species dominated the bacterial population of UT, CO(2) and MF milk samples at day 7. Staphylococcus and Delftia were the dominant bacterial species in thermized milk. Q-PCR results showed that populations of S. aureus, A. viridans, A. calcoaceticus, C. variabile and S. uberis were stable during 7d of storage at 4 degrees C. Populations of P. fluorescens, S. uberis and total bacteria

  11. Changes in sulfate-reducing bacterial populations during the onset of black band disease.

    PubMed

    Bourne, David G; Muirhead, Andrew; Sato, Yui

    2011-03-01

    Factors that facilitate the onset of black band disease (BBD) of corals remain elusive, though anoxic conditions under the complex microbial mat and production of sulfide are implicated in necrosis of underlying coral tissues. This study investigated the diversity and quantitative shifts of sulfate-reducing bacterial (SRB) populations during the onset of BBD using real-time PCR (RT-PCR) and cloning approaches targeting the dissimilatory (bi)sulfite reductase (dsrA) gene. A quantitative-PCR (qPCR) assay targeting the 16S rRNA gene also provided an estimate of total bacteria, and allowed the relative percentage of SRB within the lesions to be determined. Three Montipora sp. coral colonies identified with lesions previously termed cyanobacterial patches (CPs) (comprising microbial communities unlike those of BBD lesions), were tagged and followed through time as CP developed into BBD. The dsrA-targeted qPCR detected few copies of the gene in the CP samples (<65 per ng DNA), though copy numbers increased in BBD lesions (>2500 per ng DNA). SRB in CP samples were less than 1% of the bacterial population, though represented up to 7.5% of the BBD population. Clone libraries also demonstrated a shift in the dominant dsrA sequences as lesions shifted from CP into BBD. Results from this study confirm that SRB increase during the onset of BBD, likely increasing sulfide concentrations at the base of the microbial mat and facilitating the pathogenesis of BBD. PMID:20811471

  12. Characterisation of the bacterial populations in a saline heat storage aquifer in the North German Basin

    NASA Astrophysics Data System (ADS)

    Alawi, M.; Lerm, S.; Vetter, A.; Vieth, A.; Mangelsdorf, K.; Seibt, A.; Wolfgramm, M.; Würdemann, H.

    2009-04-01

    The colonization and the ecology of microorganisms in the deep biosphere arouse increasing interest of scientists because of utilizing the subsurface for e.g. energy storage and recovery. The research project AquiScreen investigates the operational reliability of eight geothermally used groundwater systems in Germany under microbial, geochemical, mineralogical, and petrological aspects. This study shows the results of the heat storage in Neubrandenburg (depth: 1250 m), a typical site for saline fluids in the North German Basin. The seasonal alternation in charge and discharge mode enabled sampling the warm (75˚ C) and the cold (45˚ C) side of the geothermal doublet. The analyses focus on microbially induced corrosion on plant components and scaling resulting in filter and/or formation clogging. Microbiological analyses were carried out with fluid and solid phase samples by 16S rDNA based Single Strand Conformation Polymorphism (SSCP) fingerprinting. The analyses are utilized to evaluate the impact of microbial populations on such systems. The genetic fingerprinting revealed significant differences in the bacterial community structure between the warm and cold side of the heat storage. Since the geochemical analyses revealed no remarkable differences, the temperature might be crucial for the different community structures. At the warm side of the aquifer the identified bacteria are closely related to Variovorax and Sphingomonas. At the cold side of the heat storage sulphate reducing and fermentative bacteria were detected. These results correspond with locally observed iron sulphide precipitation and corrosion processes on plant components. Particularly the bacterial population of the cold side was studied over a period of two years. Thereby seasonal changes in the abundance of the identified bacteria, depending on the operational mode of the geothermal plant, were observed. After a malfunction in the pump system of the cold side of the heat storage changes in

  13. Imaging the Population Dynamics of Bacterial Communities in the Zebrafish Gut

    NASA Astrophysics Data System (ADS)

    Jemielita, Matthew; Taormina, Michael; Burns, Adam; Zac Stephens, W.; Hampton, Jennifer; Guillemin, Karen; Parthasarathy, Raghuveer

    2013-03-01

    The vertebrate gut is home to a diverse microbial ecosystem whose composition has a strong influence on the development and health of the host organism. While researchers are increasingly able to identify the constituent members of the microbiome, very little is known about the spatial and temporal dynamics of commensal microbial communities, including the mechanisms by which communities nucleate, grow, and interact. We address these issues using a model organism: the larval zebrafish (Danio rerio) prepared microbe-free and inoculated with controlled compositions of fluorophore-expressing bacteria. Live imaging with light sheet fluorescence microscopy enables visualization of individual bacterial cells as well as growing colonies over the entire volume of the gut over periods up to 24 hours. We analyze the structure and dynamics of imaged bacterial communities, uncovering correlations between population size, growth rates, and the timing of inoculations that suggest the existence of active changes in the host environment induced by early bacterial exposure. Our data provide the first visualizations of gut microbiota development over an extended period of time in a vertebrate.

  14. Video processing analysis for the determination and evaluation of the chemotactic response in bacterial populations.

    PubMed

    Nisenbaum, Melina; Maldonado, Emilio; Martínez Arca, Jorge; González, Jorge F; Passoni, Lucía I; Murialdo, Silvia E

    2016-08-01

    The aim of the present work was to design a methodology based on video processing to obtain indicators of bacterial population motility that allow the quantitative and qualitative analysis and comparison of the chemotactic phenomenon with different attractants in the agarose-in plug bridge method. Video image sequences were processed applying Shannon's entropy to the intensity time series of each pixel, which conducted to a final pseudo colored image resembling a map of the dynamic bacterial clusters. Processed images could discriminate perfectly between positive and negative attractant responses at different periods of time from the beginning of the assay. An index of spatial and temporal motility was proposed to quantify the bacterial response. With this index, this video processing method allowed obtaining quantitative information of the dynamic changes in space and time from a traditional qualitative assay. We conclude that this computational technique, applied to the traditional agarose-in plug assay, has demonstrated good sensitivity for identifying chemotactic regions with a broad range of motility. PMID:27291715

  15. Video processing analysis for the determination and evaluation of the chemotactic response in bacterial populations.

    PubMed

    Nisenbaum, Melina; Maldonado, Emilio; Martínez Arca, Jorge; González, Jorge F; Passoni, Lucía I; Murialdo, Silvia E

    2016-08-01

    The aim of the present work was to design a methodology based on video processing to obtain indicators of bacterial population motility that allow the quantitative and qualitative analysis and comparison of the chemotactic phenomenon with different attractants in the agarose-in plug bridge method. Video image sequences were processed applying Shannon's entropy to the intensity time series of each pixel, which conducted to a final pseudo colored image resembling a map of the dynamic bacterial clusters. Processed images could discriminate perfectly between positive and negative attractant responses at different periods of time from the beginning of the assay. An index of spatial and temporal motility was proposed to quantify the bacterial response. With this index, this video processing method allowed obtaining quantitative information of the dynamic changes in space and time from a traditional qualitative assay. We conclude that this computational technique, applied to the traditional agarose-in plug assay, has demonstrated good sensitivity for identifying chemotactic regions with a broad range of motility.

  16. Biogeochemical controls on the bacterial population in the eastern Atlantic Ocean

    NASA Astrophysics Data System (ADS)

    Neogi, S. B.; Koch, B. P.; Schmitt-Kopplin, P.; Pohl, C.; Kattner, G.; Yamasaki, S.; Lara, R. J.

    2011-08-01

    Little is known about bacterial dynamics in the oligotrophic ocean, particularly about its cultivable population. We examined the abundance of total and cultivable bacteria in relation to changes in biogeochemical conditions in the eastern Atlantic Ocean with special regard to Vibrio spp., a group of bacteria that can cause diseases in human and aquatic organisms. Surface, deep water and plankton samples (<20 μm, 20-55 μm and >55 μm) were collected between 50° N and 24° S. Chlorophyll-a was very low (<0.3 μg l-1) in most areas of the nutrient-poor Atlantic, except at a few locations near upwelling regions. In surface water, dissolved organic carbon (DOC) and nitrogen (DON) concentrations were 64-95 μM C and 2-10 μM N accounting for ≥90 % and ≥76 % of total organic C and N, respectively. DOC and DON gradually decreased to ~45 μM C and <5 μM N in the bottom water while dissolved inorganic nutrients (Si, P, N) increased with depth. In the surface layer, culture independent total bacteria, represented by 4´-6-diamidino-2-phenylindole (DAPI) counts, ranged mostly between 107 and 108 cells l-1, while cultivable bacterial counts (CBC) and Vibrio spp. were found at concentrations of 104-107 and 102-105 colony forming units (CFU) l-1, respectively. Most bacteria (>99 %) were found in the nanoplankton fraction (<20 μm), however, bacterial abundance did not correlate with suspended particulates (chlorophyll-a, particulate organic C and N). Instead, we found a highly significant correlation between bacterial abundance and temperature (p < 0.001) and a significant correlation with DOC and DON. Among the cultivable bacteria, the abundance of Vibrio was also highly significantly correlated with DOC and DON (p < 0.0005 and p < 0.005, respectively). In cold waters of the mid-pelagic and abyssal zones, CBC was 50 to 100-times lower than in the surface layer; however, cultivable Vibrio spp. could be isolated from the bathypelagic zone and even near the seafloor

  17. What is Growth? Concurrent determination of a bacterial population's many shades of growth

    NASA Astrophysics Data System (ADS)

    Lambert, Guillaume; Kussell, Edo

    2013-03-01

    One of the most exciting developments in the study of the physics of microbial life is the ability to precisely monitor stochastic variations of gene expression in individual cells. A fundamental question is whether these variations improve the long-term ability of a population to adapt to new environments. While variations in gene expression in bacteria are easily measured through the use of reporter systems such as green fluorescent proteins and its variants, precise determination of a cell's growth rate, and how it is influenced by its immediate environment, remains challenging. Here, we show that many conflicting and ambiguous definitions of bacterial growth can actually be used interchangeably in E. coli. Indeed, by monitoring small populations of E. coli bacteria inside a microfluidic device, we show that seemingly independent measurements of growth (elongation rate and the average division time, for instance) agree very precisely with one another. We combine these definitions with the population's length and age distribution to very precisely quantify the influence of temperature variations on a population's growth rate. We conclude by using coalescence theory to describe the evolution of a population's genetic structure over time.

  18. Active Marine Subsurface Bacterial Population Composition in Low Organic Carbon Environments from IODP Expedition 320

    NASA Astrophysics Data System (ADS)

    Shepard, A.; Reese, B. K.; Mills, H. J.; IODP Expedition 320 Shipboard Science Party

    2011-12-01

    The marine subsurface environment contains abundant and active microorganisms. These microbial populations are considered integral players in the marine subsurface biogeochemical system with significance in global geochemical cycles and reservoirs. However, variations in microbial community structure, activity and function associated with the wide-ranging sedimentary and geochemical environments found globally have not been fully resolved. Integrated Ocean Drilling Program Expedition 320 recovered sediments from site U1332. Two sampling depths were selected for analysis that spanned differing lithological units in the sediment core. Sediments were composed of mostly clay with zeolite minerals at 8 meters below sea floor (mbsf). At 27 mbsf, sediments were composed of alternating clayey radiolarian ooze and nannofossil ooze. The concentration of SO42- had little variability throughout the core and the concentration of Fe2+ remained close to, or below, detection limits (0.4 μM). Total organic carbon content ranged from a low of 0.03 wt% to a high of 0.07 wt% between 6 and 30 mbsf providing an opportunity to evaluate marine subsurface microbial communities under extreme electron donor limiting conditions. The metabolically active fraction of the bacterial population was isolated by the extraction and amplification of 16S ribosomal RNA. Pyrosequencing of 16S rRNA transcripts and subsequent bioinformatic analyses provided a robust data set (15,931 total classified sequences) to characterize the community at a high resolution. As observed in other subsurface environments, the overall diversity of active bacterial populations decreased with depth. The population shifted from a diverse but evenly distributed community at approximately 8 mbsf to a Firmicutes dominated population at 27 mbsf (80% of sequences). A total of 95% of the sequences at 27 mbsf were grouped into three genera: Lactobacillus (phylum Firmicutes) at 80% of the total sequences, Marinobacter (phylum

  19. Optimal control strategies for disinfection of bacterial populations with persister and susceptible dynamics.

    PubMed

    Cogan, N G; Brown, Jason; Darres, Kyle; Petty, Katherine

    2012-09-01

    It is increasingly clear that bacteria manage to evade killing by antibiotics and antimicrobials in a variety of ways, including mutation, phenotypic variations, and formation of biofilms. With recent advances in understanding the dynamics of the tolerance mechanisms, there have been subsequent advances in understanding how to manipulate the bacterial environments to eradicate the bacteria. This study focuses on using mathematical techniques to find the optimal disinfection strategy to eliminate the bacteria while managing the load of antibiotic that is applied. In this model, the bacterial population is separated into those that are tolerant to the antibiotic and those that are susceptible to disinfection. There are transitions between the two populations whose rates depend on the chemical environment. Our results extend previous mathematical studies to include more realistic methods of applying the disinfectant. The goal is to provide experimentally testable predictions that have been lacking in previous mathematical studies. In particular, we provide the optimal disinfection protocol under a variety of assumptions within the model that can be used to validate or invalidate our simplifying assumptions and the experimental hypotheses that we used to develop the model. We find that constant dosing is not the optimal method for disinfection. Rather, cycling between application and withdrawal of the antibiotic yields the fastest killing of the bacteria.

  20. EFFECT OF SITE ON BACTERIAL POPULATIONS IN THE SAPWOOD OF COARSE WOODY DEBRIS.

    SciTech Connect

    Porter, Emma, G.,; Waldrop, Thomas, A.; McElreath, Susan, D.; Tainter, Frank, H.

    1998-01-01

    Porter, Emma G., T.A. Waldrop, Susan D. McElreath, and Frank H. Tainter. 1998. Effect of site on bacterial populations in the sapwood of coarse woody debris. Pp. 480-484. In: Proc. 9th Bienn. South. Silv. Res. Conf. T.A. Waldrop (ed). USDA Forest Service, Southern Research Station. Gen. Tech. Rep. SRS-20. Abstract: Coarse woody debris (CWD) is an important structural component of southeastern forest ecosystems, yet little is known about its dynamics in these systems. This project identified bacterial populations associated with CWD and their dynamics across landscape ecosystem classification (LEC) units. Bolts of red oak and loblolly pine were placed on plots at each of three hydric, mesic, and xeric sites at the Savannah River Station. After the controls were processed, samples were taken at four intervals over a 16-week period. Samples were ground within an anaerobe chamber using nonselective media. Aerobic and facultative anaerobic bacteria were identified using the Biolog system and the anaerobes were identified using the API 20A system. Major genera isolated were: Bacillus, Buttiauxella, Cedecea, Enterobacter, Erwinia, Escherichia, Klebsiella, Pantoea, Pseudomonas, Serratia, and Xanthomonas. The mean total isolates were determined by LEC units and sample intervals. Differences occurred between the sample intervals with total isolates of 6.67, 13.33, 10.17, and 9.50 at 3, 6, 10, and 16 weeks, respectively. No significant differences in the numbers of bacteria isolated were found between LEC units.

  1. Co-existence of multiple attractors in the PWM controlled DC drives

    NASA Astrophysics Data System (ADS)

    Kundu, Susmita; Kar, Urmila; Chakrabarty, K.

    2013-07-01

    DC shunt and series drives are extensively used in the industry. The occurrence of bifurcation and chaos in dc shunt and permanent magnet drives are well known. It is observed that the behavior of the drives not only depends on the value of system parameters but also on the value of initial conditions. Multiple attractors can exist for same parameter value. Different choice of initial conditions gives different periodic behavior of the system. The drive is intended to operate in a parameter range to give period-1 behavior. We report the existence of sub- harmonic oscillations in the period-1 region of the bifurcation diagram along with co-existing attractor with fractal basin boundaries in PWM controlled dc series drives. The series drive is extensively used in electric traction and other applications. The dc drives are run with dc input voltage. This dc voltage may be derived from a dc source or an ac source with a rectifier. The dc series drive shows different bifurcation behavior when different types of input voltage and switching elements are used. The existence of period-1, period-2 and period-4 orbits are observed with different initial conditions in the desired period-1 region of the bifurcation diagram. The dependence of system's behavior on initial condition may render the system's behavior unpredictable. These phenomena may have serious implication in performance.

  2. Design and Evaluation of PCR Primers for Analysis of Bacterial Populations in Wine by Denaturing Gradient Gel Electrophoresis

    PubMed Central

    Lopez, Isabel; Ruiz-Larrea, Fernanda; Cocolin, Luca; Orr, Erica; Phister, Trevor; Marshall, Megan; VanderGheynst, Jean; Mills, David A.

    2003-01-01

    Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified ribosomal DNA (rDNA) is routinely used to compare levels of diversity of microbial communities and to monitor population dynamics. While using PCR-DGGE to examine the bacteria in wine fermentations, we noted that several commonly used PCR primers for amplifying bacterial 16S rDNA also coamplified yeast, fungal, or plant DNA present in samples. Unfortunately, amplification of nonbacterial DNA can result in a masking of bacterial populations in DGGE profiles. To surmount this problem, we developed two new primer sets for specific amplification of bacterial 16S rDNA in wine fermentation samples without amplification of eukaryotic DNA. One primer set, termed WLAB1 and WLAB2, amplified lactic acid bacteria, while another, termed WBAC1 and WBAC2, amplified both lactic acid bacterial and acetic acid bacterial populations found in wine. Primer specificity and efficacy were examined with DNA isolated from numerous bacterial, yeast, and fungal species commonly found in wine and must samples. Importantly, both primer sets effectively distinguished bacterial species in wine containing mixtures of yeast and bacteria. PMID:14602643

  3. Population-Dynamic Modeling of Bacterial Horizontal Gene Transfer by Natural Transformation.

    PubMed

    Mao, Junwen; Lu, Ting

    2016-01-01

    Natural transformation is a major mechanism of horizontal gene transfer (HGT) and plays an essential role in bacterial adaptation, evolution, and speciation. Although its molecular underpinnings have been increasingly revealed, natural transformation is not well characterized in terms of its quantitative ecological roles. Here, by using Neisseria gonorrhoeae as an example, we developed a population-dynamic model for natural transformation and analyzed its dynamic characteristics with nonlinear tools and simulations. Our study showed that bacteria capable of natural transformation can display distinct population behaviors ranging from extinction to coexistence and to bistability, depending on their HGT rate and selection coefficient. With the model, we also illustrated the roles of environmental DNA sources-active secretion and passive release-in impacting population dynamics. Additionally, by constructing and utilizing a stochastic version of the model, we examined how noise shapes the steady and dynamic behaviors of the system. Notably, we found that distinct waiting time statistics for HGT events, namely a power-law distribution, an exponential distribution, and a mix of the both, are associated with the dynamics in the regimes of extinction, coexistence, and bistability accordingly. This work offers a quantitative illustration of natural transformation by revealing its complex population dynamics and associated characteristics, therefore advancing our ecological understanding of natural transformation as well as HGT in general.

  4. Population-Dynamic Modeling of Bacterial Horizontal Gene Transfer by Natural Transformation.

    PubMed

    Mao, Junwen; Lu, Ting

    2016-01-01

    Natural transformation is a major mechanism of horizontal gene transfer (HGT) and plays an essential role in bacterial adaptation, evolution, and speciation. Although its molecular underpinnings have been increasingly revealed, natural transformation is not well characterized in terms of its quantitative ecological roles. Here, by using Neisseria gonorrhoeae as an example, we developed a population-dynamic model for natural transformation and analyzed its dynamic characteristics with nonlinear tools and simulations. Our study showed that bacteria capable of natural transformation can display distinct population behaviors ranging from extinction to coexistence and to bistability, depending on their HGT rate and selection coefficient. With the model, we also illustrated the roles of environmental DNA sources-active secretion and passive release-in impacting population dynamics. Additionally, by constructing and utilizing a stochastic version of the model, we examined how noise shapes the steady and dynamic behaviors of the system. Notably, we found that distinct waiting time statistics for HGT events, namely a power-law distribution, an exponential distribution, and a mix of the both, are associated with the dynamics in the regimes of extinction, coexistence, and bistability accordingly. This work offers a quantitative illustration of natural transformation by revealing its complex population dynamics and associated characteristics, therefore advancing our ecological understanding of natural transformation as well as HGT in general. PMID:26745428

  5. Structural instability and phase co-existence driven non-Gaussian resistance fluctuations in metal nanowires at low temperatures

    NASA Astrophysics Data System (ADS)

    Bid, Aveek; Raychaudhuri, A. K.

    2016-11-01

    We report a detailed experimental study of the resistance fluctuations measured at low temperatures in high quality metal nanowires ranging in diameter from 15–200 nm. The wires exhibit co-existing face-centered-cubic and 4H hcp phases of varying degrees as determined from the x-ray diffraction data. We observe the appearance of a large non-Gaussian noise for nanowires of diameter smaller than 50 nm over a certain temperature range around ≈30 K. The diameter range ∼30 nm, where the noise has maxima coincides with the maximum volume fraction of the co-existing 4H hcp phase thus establishing a strong link between the fluctuation and the phase co-existence. The resistance fluctuation in the same temperature range also shows a deviation of 1/f behavior at low frequency with appearance of single frequency Lorentzian type contribution in the spectral power density. The fluctuations are thermally activated with an activation energy {E}{{a}}∼ 35 meV, which is of same order as the activation energy of creation of stacking fault in FCC metals that leads to the co-existing crystallographic phases. Combining the results of crystallographic studies of the nanowires and analysis of the resistance fluctuations we could establish the correlation between the appearance of the large resistance noise and the onset of phase co-existence in these nanowires.

  6. Transovarial Transmission of Co-Existing Orientia tsutsugamushi Genotypes in Laboratory-Reared Leptotrombidium imphalum.

    PubMed

    Takhampunya, Ratree; Tippayachai, Bousaraporn; Korkusol, Achareeya; Promsathaporn, Sommai; Leepitakrat, Surachai; Sinwat, Warattaya; Schuster, Anthony L; Richards, Allen L

    2016-01-01

    The co-evolution of Orientia tsutsugamushi and its vector/host Leptotrombidium mites is important for this bacterium to survive and exist in its environment. The data in this study demonstrated that O. tsutsugamushi has adapted to take advantage of the parasitic nature of the host's larval stage and thus increase its chance of transmission to a vertebrate host and potentially to other vector mites by increasing its density at the time of transmission. Our data demonstrated that during the larval stage the density of O. tsutsugamushi was at its highest level compared to other life stages (Kruskal-Wallis, p < 0.0001). We further revealed that the different O. tsutsugamushi 56-kDa type-specific antigen (TSA) genotypes within the mite were maintained and preserved during transovarial transmission from the Leptotrombidium imphalum, lines Li-3 and Li-5. No sequence difference of 56-kDa TSA gene (variable domain I-III, 765 bp) was observed between the UT302-like genotype found in mothers and their offspring (100% identity). However, one or two nonsynonymous mutations in the 56-kDa TSA gene were observed in the Karp-like genotypes found in the F1 offspring with a percent difference ranging from 0.13 to 0.26 for nucleotide sequences and from 0.39 to 0.78 for amino acid sequences. Additionally, the composition of co-existing O. tsutsugamushi genotypes was maintained in L. imphalum lines through transsovarial and transstadial transmission processes; however, the proportion of these genotypes in each stage varied (larva, nymph, adult). These results show some of the key characteristics of O. tsutsugamushi maintenance within and transmission among its vector/host L. imphalum.

  7. Children with burns referred for child abuse evaluation: Burn characteristics and co-existent injuries.

    PubMed

    Pawlik, Marie-Christin; Kemp, Alison; Maguire, Sabine; Nuttall, Diane; Feldman, Kenneth W; Lindberg, Daniel M

    2016-05-01

    Intentional burns represent a serious form of physical abuse that must be identified to protect children from further harm. This study is a retrospectively planned secondary analysis of the Examining Siblings To Recognize Abuse (ExSTRA) network data. Our objective was to describe the characteristics of burns injuries in children referred to Child Abuse Pediatricians (CAPs) in relation to the perceived likelihood of abuse. We furthermore compare the extent of diagnostic investigations undertaken in children referred to CAPs for burn injuries with those referred for other reasons. Within this dataset, 7% (215/2890) of children had burns. Children with burns were older than children with other injuries (median age 20 months vs. 10 months). Physical abuse was perceived as likely in 40.9% (88) and unlikely in 59.1% (127). Scalds accounted for 52.6% (113) and contact burns for 27.6% (60). Several characteristics of the history and burn injury were associated with a significantly higher perceived likelihood of abuse, including children with reported inflicted injury, absent or inadequate explanation, hot water as agent, immersion scald, a bilateral/symmetric burn pattern, total body surface area ≥10%, full thickness burns, and co-existent injuries. The rates of diagnostic testing were significantly lower in children with burns than other injuries, yet the yield of skeletal survey and hepatic transaminases testing were comparable between the two groups. This would imply that children referred to CAPs for burns warrant the same level of comprehensive investigations as those referred for other reasons. PMID:27088728

  8. Co-existing autosomal dominant polycystic kidney disease and nephrotic syndrome in a Nigerian patient with lupus nephritis.

    PubMed

    Akinbodewa, A A; Adejumo, O A; Ogunsemoyin, A O; Osasan, S A; Adefolalu, O A

    2016-01-01

    A little over 30 cases on co-existing nephrotic syndrome and autosomal dominant polycystic kidney disease (ADPKD) have been reported from different regions of the world since 1957. We present a case report on co-existence of nephrotic syndrome (secondary to lupus nephritis) with ADPKD in a 24-year-old woman from Nigeria. She was positive for anti-double stranded DNA. Renal histology showed International Society of Nephrology/Renal Pathology Society Class II lupus nephritis. The co-existence of nephrotic syndrome and ADPKD may have been overlooked in Africa in the past. There is a need to screen for nephrotic syndrome in patients with ADPKD among clinicians in the African setting. PMID:27044732

  9. Selective labelling and eradication of antibiotic-tolerant bacterial populations in Pseudomonas aeruginosa biofilms.

    PubMed

    Chua, Song Lin; Yam, Joey Kuok Hoong; Hao, Piliang; Adav, Sunil S; Salido, May Margarette; Liu, Yang; Givskov, Michael; Sze, Siu Kwan; Tolker-Nielsen, Tim; Yang, Liang

    2016-01-01

    Drug resistance and tolerance greatly diminish the therapeutic potential of antibiotics against pathogens. Antibiotic tolerance by bacterial biofilms often leads to persistent infections, but its mechanisms are unclear. Here we use a proteomics approach, pulsed stable isotope labelling with amino acids (pulsed-SILAC), to quantify newly expressed proteins in colistin-tolerant subpopulations of Pseudomonas aeruginosa biofilms (colistin is a 'last-resort' antibiotic against multidrug-resistant Gram-negative pathogens). Migration is essential for the formation of colistin-tolerant biofilm subpopulations, with colistin-tolerant cells using type IV pili to migrate onto the top of the colistin-killed biofilm. The colistin-tolerant cells employ quorum sensing (QS) to initiate the formation of new colistin-tolerant subpopulations, highlighting multicellular behaviour in antibiotic tolerance development. The macrolide erythromycin, which has been previously shown to inhibit the motility and QS of P. aeruginosa, boosts biofilm eradication by colistin. Our work provides insights on the mechanisms underlying the formation of antibiotic-tolerant populations in bacterial biofilms and indicates research avenues for designing more efficient treatments against biofilm-associated infections. PMID:26892159

  10. Structural and functional dynamics of sulfate-reducing populations in bacterial biofilms

    SciTech Connect

    Santegoeds, C.M.; Ferdelman, T.G.; Muyzer, G.; Beer, D. de

    1998-10-01

    The authors describe the combined application of microsensors and molecular techniques to investigate the development of sulfate reduction and of sulfate-reducing bacterial populations in an aerobic bacterial biofilm. Microsensor measurements for oxygen showed that anaerobic zones developed in the biofilm within 1 week and that oxygen was depleted in the top 200 to 400 {micro}m during all stages of biofilm development. Sulfate reduction was first detected after 6 weeks of growth, although favorable conditions for growth of sulfate-reducing bacteria (SRB) were present from the first week. In situ hybridization with a 16S rRNA probe for SRB revealed that sulfate reducers were present in high numbers in all stages of development, both in the oxic and anoxic zones of the biofilm. Denaturing gradient gel electrophoresis (DGGE) showed that the genetic diversity of the microbial community increased during the development of the biofilm. Hybridization analysis of the DGGE profiles with taxon-specific oligonucleotide probes showed that Desulfobulbus and Desulfovibrio were the main sulfate-reducing bacteria in all biofilm samples as well as in the bulk activated sludge. However, different Desulfobulbus and Desulfovibrio species were found in the 6th and 8th weeks of incubation, respectively, coinciding with the development of sulfate reduction. Their data indicate that not all SRB detected by molecular analysis were sulfidogenically active in the biofilm.

  11. Selective labelling and eradication of antibiotic-tolerant bacterial populations in Pseudomonas aeruginosa biofilms

    PubMed Central

    Chua, Song Lin; Yam, Joey Kuok Hoong; Hao, Piliang; Adav, Sunil S.; Salido, May Margarette; Liu, Yang; Givskov, Michael; Sze, Siu Kwan; Tolker-Nielsen, Tim; Yang, Liang

    2016-01-01

    Drug resistance and tolerance greatly diminish the therapeutic potential of antibiotics against pathogens. Antibiotic tolerance by bacterial biofilms often leads to persistent infections, but its mechanisms are unclear. Here we use a proteomics approach, pulsed stable isotope labelling with amino acids (pulsed-SILAC), to quantify newly expressed proteins in colistin-tolerant subpopulations of Pseudomonas aeruginosa biofilms (colistin is a ‘last-resort' antibiotic against multidrug-resistant Gram-negative pathogens). Migration is essential for the formation of colistin-tolerant biofilm subpopulations, with colistin-tolerant cells using type IV pili to migrate onto the top of the colistin-killed biofilm. The colistin-tolerant cells employ quorum sensing (QS) to initiate the formation of new colistin-tolerant subpopulations, highlighting multicellular behaviour in antibiotic tolerance development. The macrolide erythromycin, which has been previously shown to inhibit the motility and QS of P. aeruginosa, boosts biofilm eradication by colistin. Our work provides insights on the mechanisms underlying the formation of antibiotic-tolerant populations in bacterial biofilms and indicates research avenues for designing more efficient treatments against biofilm-associated infections. PMID:26892159

  12. Live cell imaging of SOS and prophage dynamics in isogenic bacterial populations.

    PubMed

    Helfrich, Stefan; Pfeifer, Eugen; Krämer, Christina; Sachs, Christian Carsten; Wiechert, Wolfgang; Kohlheyer, Dietrich; Nöh, Katharina; Frunzke, Julia

    2015-11-01

    Almost all bacterial genomes contain DNA of viral origin, including functional prophages or degenerated phage elements. A frequent but often unnoted phenomenon is the spontaneous induction of prophage elements (SPI) even in the absence of an external stimulus. In this study, we have analyzed SPI of the large, degenerated prophage CGP3 (187 kbp), which is integrated into the genome of the Gram-positive Corynebacterium glutamicum ATCC 13032. Time-lapse fluorescence microscopy of fluorescent reporter strains grown in microfluidic chips revealed the sporadic induction of the SOS response as a prominent trigger of CGP3 SPI but also displayed a considerable fraction (∼30%) of RecA-independent SPI. Whereas approx. 20% of SOS-induced cells recovered from this stress and resumed growth, the spontaneous induction of CGP3 always led to a stop of growth and likely cell death. A carbon source starvation experiment clearly emphasized that SPI only occurs in actively proliferating cells, whereas sporadic SOS induction was still observed in resting cells. These data highlight the impact of sporadic DNA damage on the activity of prophage elements and provide a time-resolved, quantitative description of SPI as general phenomenon of bacterial populations.

  13. Effect of bacterial population density on germination wheat seeds and dynamics of simple artificial ecosystems

    NASA Astrophysics Data System (ADS)

    Somova, L. A.; Pechurkin, N. S.; Sarangova, A. B.; Pisman, T. I.

    Effect of the size of rhizospheric bacterial populations on germination of seeds and development of simple terrestrial "wheat plants - rhizospheric microorganisms - artificial soil" and "wheat plants - artificial soil" systems has been studied. Experiments demonstrated that within specify ranges in the inoculate, the rhizospheric bacteria are capable of increasing the yield of germinated seeds and stimulate the growth of plantlets. Germination of seeds inoculated with bacteria was either stimulated, or inhibited or remained at control levels depending on the amount of bacteria. Plant biomass growth and total photoassimilation has been found to depend on the amount of bacteria on the plant roots: the higher the amount of bacteria on plant roots, the smaller is the biomass of plants but the total photoassimilation is, higher. Thus, depending on the amount of bacteria on the roots of plants the system either increases the biomass of plants or increases the total photoassimilation, i.e. "pumps" carbon through itself involving bacteria.

  14. Critical dynamics of self-gravitating Langevin particles and bacterial populations.

    PubMed

    Sire, Clément; Chavanis, Pierre-Henri

    2008-12-01

    We study the critical dynamics of the generalized Smoluchowski-Poisson system (for self-gravitating Langevin particles) or generalized Keller-Segel model (for the chemotaxis of bacterial populations). These models [P. H. Chavanis and C. Sire, Phys. Rev. E 69, 016116 (2004)] are based on generalized stochastic processes leading to the Tsallis statistics. The equilibrium states correspond to polytropic configurations with index n similar to polytropic stars in astrophysics. At the critical index n_{3}=d(d-2) (where d>or=2 is the dimension of space), there exists a critical temperature Theta_{c} (for a given mass) or a critical mass M_{c} (for a given temperature). For Theta>Theta_{c} or MM_{c} the system collapses and forms, in a finite time, a Dirac peak containing a finite fraction M_{c} of the total mass surrounded by a halo. We study these regimes numerically and, when possible, analytically by looking for self-similar or pseudo-self-similar solutions. This study extends the critical dynamics of the ordinary Smoluchowski-Poisson system and Keller-Segel model in d=2 corresponding to isothermal configurations with n_{3}-->+infinity . We also stress the analogy between the limiting mass of white dwarf stars (Chandrasekhar's limit) and the critical mass of bacterial populations in the generalized Keller-Segel model of chemotaxis. PMID:19256806

  15. Distribution and Biogeochemical Importance of Bacterial Populations in a Thick Clay-Rich Aquitard System.

    PubMed

    Lawrence, J.R.; Hendry, M.J.; Wassenaar, L.I.; Germida, J.J.; Wolfaardt, G.M.; Fortin, N.; Greer, C.W.

    2000-12-01

    To investigate the distribution of microbial biomass, populations and activities within a clay-rich, low hydraulic conductivity (10-11 to 10-12 m s-1) aquitard complex, cores were aseptically obtained from a series of overlying clayey deposits; a fractured till, unfractured till (20-30 ka BP), a disturbed interfacial zone (20-30 ka BP), and a Cretaceous clay aquitard (71-72 Ma BP). The results of confocal microscopy studies, culture methods, molecular approaches, and extractive fatty acid analyses all indicated low bacterial numbers that were non-homogeneously distributed within the sediments. Various primers for catabolic genes were used to amplify extracted DNA. Results indicated the presence of eubacterial 23S rDNA, and the narH gene for nitrate reductase and ribulose-1,5-biphosphate carboxylase (RuBP carboxylase). Although there was no evidence of limitation by electron acceptors or donors, sulfate-reducing bacteria were not detected below the fractured till zone, using PCR, enrichment, or culture techniques. Denaturing gradient gel electrophoresis (DGGE) analyses indicated differences in community composition and abundance between the various geologic units. Results of FAME analyses of sediments yielded detectable extractable fatty acids throughout the aquitard complex. Bacterial activities were demonstrated by measuring mineralization of (14C) glucose. Porewater chemistry and stable isotope data were in keeping with an environment in which extremely slow growing, low populations of bacteria exert little impact. The observations also support the contention that in low permeability sediments bacteria may survive for geologic time periods. PMID:12035086

  16. Critical dynamics of self-gravitating Langevin particles and bacterial populations.

    PubMed

    Sire, Clément; Chavanis, Pierre-Henri

    2008-12-01

    We study the critical dynamics of the generalized Smoluchowski-Poisson system (for self-gravitating Langevin particles) or generalized Keller-Segel model (for the chemotaxis of bacterial populations). These models [P. H. Chavanis and C. Sire, Phys. Rev. E 69, 016116 (2004)] are based on generalized stochastic processes leading to the Tsallis statistics. The equilibrium states correspond to polytropic configurations with index n similar to polytropic stars in astrophysics. At the critical index n_{3}=d(d-2) (where d>or=2 is the dimension of space), there exists a critical temperature Theta_{c} (for a given mass) or a critical mass M_{c} (for a given temperature). For Theta>Theta_{c} or MM_{c} the system collapses and forms, in a finite time, a Dirac peak containing a finite fraction M_{c} of the total mass surrounded by a halo. We study these regimes numerically and, when possible, analytically by looking for self-similar or pseudo-self-similar solutions. This study extends the critical dynamics of the ordinary Smoluchowski-Poisson system and Keller-Segel model in d=2 corresponding to isothermal configurations with n_{3}-->+infinity . We also stress the analogy between the limiting mass of white dwarf stars (Chandrasekhar's limit) and the critical mass of bacterial populations in the generalized Keller-Segel model of chemotaxis.

  17. French invasive Asian tiger mosquito populations harbor reduced bacterial microbiota and genetic diversity compared to Vietnamese autochthonous relatives

    PubMed Central

    Minard, G.; Tran, F. H.; Van, Van Tran; Goubert, C.; Bellet, C.; Lambert, G.; Kim, Khanh Ly Huynh; Thuy, Trang Huynh Thi; Mavingui, P.; Valiente Moro, C.

    2015-01-01

    The Asian tiger mosquito Aedes albopictus is one of the most significant pathogen vectors of the twenty-first century. Originating from Asia, it has invaded a wide range of eco-climatic regions worldwide. The insect-associated microbiota is now recognized to play a significant role in host biology. While genetic diversity bottlenecks are known to result from biological invasions, the resulting shifts in host-associated microbiota diversity has not been thoroughly investigated. To address this subject, we compared four autochthonous Ae. albopictus populations in Vietnam, the native area of Ae. albopictus, and three populations recently introduced to Metropolitan France, with the aim of documenting whether these populations display differences in host genotype and bacterial microbiota. Population-level genetic diversity (microsatellite markers and COI haplotype) and bacterial diversity (16S rDNA metabarcoding) were compared between field-caught mosquitoes. Bacterial microbiota from the whole insect bodies were largely dominated by Wolbachia pipientis. Targeted analysis of the gut microbiota revealed a greater bacterial diversity in which a fraction was common between French and Vietnamese populations. The genus Dysgonomonas was the most prevalent and abundant across all studied populations. Overall genetic diversities of both hosts and bacterial microbiota were significantly reduced in recently established populations of France compared to the autochthonous populations of Vietnam. These results open up many important avenues of investigation in order to link the process of geographical invasion to shifts in commensal and symbiotic microbiome communities, as such shifts may have dramatic impacts on the biology and/or vector competence of invading hematophagous insects. PMID:26441903

  18. Negotiating Co-Existence in Divided Societies: Teachers, Students and Parents' Perspectives at a Shared School in Cyprus

    ERIC Educational Resources Information Center

    Zembylas, Michalinos

    2010-01-01

    This article describes a study conducted at a shared secondary school in Cyprus - that is, a school which co-educates children coming from two conflicting ethnic communities on the island. The study focuses on teachers', students' and parents' perspectives about the struggles to negotiate co-existence in this school. Drawing on a three-month…

  19. Measuring the Rate of Conjugal Plasmid Transfer in a Bacterial Population Using Quantitative PCR

    PubMed Central

    Wan, Zhenmao; Varshavsky, Joseph; Teegala, Sushma; McLawrence, Jamille; Goddard, Noel L.

    2011-01-01

    Horizontal transfer of genes between species is an important mechanism for bacterial genome evolution. In Escherichia coli, conjugation is the transfer from a donor (F+) to a recipient (F−) cell through cell-to-cell contact. We demonstrate what we believe to be a novel qPCR method for quantifying the transfer kinetics of the F plasmid in a population by enumerating the relative abundance of genetic loci unique to the plasmid and the chromosome. This approach allows us to query the plasmid transfer rate without the need for selective culturing with unprecedented single locus resolution. We fit the results to a mass action model where the rate of plasmid growth includes the lag time of newly formed F+ transconjugants and the recovery time between successive conjugation events of the F+ donors. By assaying defined mixtures of genotypically identical donor and recipient cells at constant inoculation densities, we extract an F plasmid transfer rate of 5 × 10−10 (cells/mL · min)−1. We confirm a plasmid/chromosome ratio of 1:1 in homogenous F+ populations throughout batch growth. Surprisingly, in some mixture experiments we observe an excess of F plasmid in the early saturation phase that equilibrates to a final ratio of one plasmid per chromosome. PMID:21723834

  20. Trends of Antibiotic Resistance in Mesophilic and Psychrotrophic Bacterial Populations during Cold Storage of Raw Milk

    PubMed Central

    Munsch-Alatossava, Patricia; Gauchi, Jean-Pierre; Chamlagain, Bhawani; Alatossava, Tapani

    2012-01-01

    Psychrotrophic bacteria in raw milk are most well known for their spoilage potential and cause significant economic losses in the dairy industry. Despite their ability to produce several exoenzyme types at low temperatures, psychrotrophs that dominate the microflora at the time of spoilage are generally considered benign bacteria. It was recently reported that raw milk-spoiling Gram-negative-psychrotrophs frequently carried antibiotic resistance (AR) features. The present study evaluated AR to four antibiotics (ABs) (gentamicin, ceftazidime, levofloxacin, and trimethoprim-sulfamethoxazole) in mesophilic and psychrotrophic bacterial populations recovered from 18 raw milk samples, after four days storage at 4°C or 6°C. Robust analysis of variance and non parametric statistics (e.g., REGW and NPS) revealed that AR prevalence among psychrotrophs, for milk samples stored at 4°C, often equalled the initial levels and equalled or increased during the cold storage at 6°C, depending on the AB. The study performed at 4°C with an intermediate sampling point at day 2 suggested that (1) different psychrotrophic communities with varying AR levels dominate over time and (2) that AR (determined from relative amounts) was most prevalent, transiently, after 2-day storage in psychrotrophic or mesophilic populations, most importantly at a stage where total counts were below or around 105 CFU/mL, at levels at which the milk is acceptable for industrial dairy industrial processes. PMID:23724333

  1. Life history correlates of fecal bacterial species richness in a wild population of the blue tit Cyanistes caeruleus.

    PubMed

    Benskin, Clare McW H; Rhodes, Glenn; Pickup, Roger W; Mainwaring, Mark C; Wilson, Kenneth; Hartley, Ian R

    2015-02-01

    Very little is known about the normal gastrointestinal flora of wild birds, or how it might affect or reflect the host's life-history traits. The aim of this study was to survey the species richness of bacteria in the feces of a wild population of blue tits Cyanistes caeruleus and to explore the relationships between bacterial species richness and various life-history traits, such as age, sex, and reproductive success. Using PCR-TGGE, 55 operational taxonomic units (OTUs) were identified in blue tit feces. DNA sequencing revealed that the 16S rRNA gene was amplified from a diverse range of bacteria, including those that shared closest homology with Bacillus licheniformis, Campylobacter lari, Pseudomonas spp., and Salmonella spp. For adults, there was a significant negative relationship between bacterial species richness and the likelihood of being detected alive the following breeding season; bacterial richness was consistent across years but declined through the breeding season; and breeding pairs had significantly more similar bacterial richness than expected by chance alone. Reduced adult survival was correlated with the presence of an OTU most closely resembling C. lari; enhanced adult survival was associated with an OTU most similar to Arthrobacter spp. For nestlings, there was no significant change in bacterial species richness between the first and second week after hatching, and nestlings sharing the same nest had significantly more similar bacterial richness. Collectively, these results provide compelling evidence that bacterial species richness was associated with several aspects of the life history of their hosts.

  2. Dandruff is associated with disequilibrium in the proportion of the major bacterial and fungal populations colonizing the scalp.

    PubMed

    Clavaud, Cécile; Jourdain, Roland; Bar-Hen, Avner; Tichit, Magali; Bouchier, Christiane; Pouradier, Florence; El Rawadi, Charles; Guillot, Jacques; Ménard-Szczebara, Florence; Breton, Lionel; Latgé, Jean-Paul; Mouyna, Isabelle

    2013-01-01

    The bacterial and fungal communities associated with dandruff were investigated using culture-independent methodologies in the French subjects. The major bacterial and fungal species inhabiting the scalp subject's were identified by cloning and sequencing of the conserved ribosomal unit regions (16S for bacterial and 28S-ITS for fungal) and were further quantified by quantitative PCR. The two main bacterial species found on the scalp surface were Propionibacterium acnes and Staphylococcus epidermidis, while Malassezia restricta was the main fungal inhabitant. Dandruff was correlated with a higher incidence of M. restricta and S. epidermidis and a lower incidence of P. acnes compared to the control population (p<0.05). These results suggested for the first time using molecular methods, that dandruff is linked to the balance between bacteria and fungi of the host scalp surface. PMID:23483996

  3. Similarity of Bacterial Populations in Saliva from African-American Mother-Child Dyads▿

    PubMed Central

    Li, Yihong; Ismail, Amid I.; Ge, Yao; Tellez, Marisol; Sohn, Woosung

    2007-01-01

    Using PCR-based denaturing gradient gel electrophoresis analyses of oral bacterial samples in 20 mother-child dyads, this study demonstrated a high degree of similarity of bacterial compositions between the mothers and their children; the two may share as much as 94% of their oral bacterial spectra, including cariogenic species. PMID:17634300

  4. Identification of 16S Ribosomal DNA-Defined Bacterial Populations at a Shallow Submarine Hydrothermal Vent near Milos Island (Greece)

    PubMed Central

    Sievert, Stefan M.; Kuever, Jan; Muyzer, Gerard

    2000-01-01

    In a recent publication (S. M. Sievert, T. Brinkhoff, G. Muyzer, W. Ziebis, and J. Kuever, Appl. Environ. Microbiol. 65:3834–3842, 1999) we described spatiotemporal changes in the bacterial community structure at a shallow-water hydrothermal vent in the Aegean Sea near the isle of Milos (Greece). Here we describe identification and phylogenetic analysis of the predominant bacterial populations at the vent site and their distribution at the vent site as determined by sequencing of DNA molecules (bands) excised from denaturing gradient gels. A total of 36 bands could be sequenced, and there were representatives of eight major lineages of the domain Bacteria. Cytophaga-Flavobacterium and Acidobacterium were the most frequently retrieved bacterial groups. Less than 33% of the sequences exhibited 90% or more identity with cultivated organisms. The predominance of putative heterotrophic populations in the sequences retrieved is explained by the input of allochthonous organic matter at the vent site. PMID:10877814

  5. Prophage-mediated dynamics of 'Candidatus Liberibacter asiaticus' populations, the destructive bacterial pathogens of citrus huanglongbing.

    PubMed

    Zhou, Lijuan; Powell, Charles A; Li, Wenbin; Irey, Mike; Duan, Yongping

    2013-01-01

    Prophages are highly dynamic components in the bacterial genome and play an important role in intraspecies variations. There are at least two prophages in the chromosomes of Candidatus Liberibacter asiaticus' (Las) Floridian isolates. Las is both unculturable and the most prevalent species of Liberibacter pathogens that cause huanglongbing (HLB), a worldwide destructive disease of citrus. In this study, seven new prophage variants resulting from two hyper-variable regions were identified by screening clone libraries of infected citrus, periwinkle and psyllids. Among them, Types A and B share highly conserved sequences and localize within the two prophages, FP1 and FP2, respectively. Although Types B and C were abundant in all three libraries, Type A was much more abundant in the libraries from the Las-infected psyllids than from the Las-infected plants, and Type D was only identified in libraries from the infected host plants but not from the infected psyllids. Sequence analysis of these variants revealed that the variations may result from recombination and rearrangement events. Conventional PCR results using type-specific molecular markers indicated that A, B, C and D are the four most abundant types in Las-infected citrus and periwinkle. However, only three types, A, B and C are abundant in Las-infected psyllids. Typing results for Las-infected citrus field samples indicated that mixed populations of Las bacteria present in Floridian isolates, but only the Type D population was correlated with the blotchy mottle symptom. Extended cloning and sequencing of the Type D region revealed a third prophage/phage in the Las genome, which may derive from the recombination of FP1 and FP2. Dramatic variations in these prophage regions were also found among the global Las isolates. These results are the first to demonstrate the prophage/phage-mediated dynamics of Las populations in plant and insect hosts, and their correlation with insect transmission and disease development.

  6. Arsenic oxidation capabilities of a chemoautotrophic bacterial population: Use for the treatment of an arsenic contaminated wastewater

    NASA Astrophysics Data System (ADS)

    Dictor, M.-C.; Battaglia-Brunet, F.; Garrido, F.; Baranger, P.

    2003-05-01

    An autotrophic bacterial population, named CAsOl, able to oxidise arsenic has been isolated from a former gold mine (Saint-Yrieix, France). This bacterial population was composed of two microorganisms: a bacterial strain close to Ralstonia picketii and the second one related to Thiomonas genus (identification by 16S rDNA sequencing). This microbial consortium was able to oxidise arsenic with CO2 as the carbon source, arsenite as electron donor and oxygen as electron accepter. A significant oxidising activity was observed in a pH range comprised between 3 to 8 (pH optimum 5 7). A laboratory experiment for the biological treatment of a synthetic effluent containing 100 mg.L^{-1} of arsenic has been carried out. A mineral support, pouzzolana, has been colonised by the population CAsOl and the column was fed continuously with a synthetic medium in order to determine the maximal arsenic oxidation rate and the optimal residence time. In our experimental conditions, the maximum arsenic oxidation rate was 3,9 g As(Ill). L^{-1}.day^{-1} with a residence time of 1 hour after 55 days of continuous running. The performance of our bacterial population for arsenite oxidation in arsenic contaminated wastewater are especially important in the case of a treatment of arsenious wastewater as it presents advantages compared to physico-chemical treatments (consumption and cost of chemicals, potential toxic by-products generation...).

  7. Impact of Bioreactor Environment and Recovery Method on the Profile of Bacterial Populations from Water Distribution Systems

    PubMed Central

    Luo, Xia; Jellison, Kristen L.; Huynh, Kevin; Widmer, Giovanni

    2015-01-01

    Multiple rotating annular reactors were seeded with biofilms flushed from water distribution systems to assess (1) whether biofilms grown in bioreactors are representative of biofilms flushed from the water distribution system in terms of bacterial composition and diversity, and (2) whether the biofilm sampling method affects the population profile of the attached bacterial community. Biofilms were grown in bioreactors until thickness stabilized (9 to 11 weeks) and harvested from reactor coupons by sonication, stomaching, bead-beating, and manual scraping. High-throughput sequencing of 16S rRNA amplicons was used to profile bacterial populations from flushed biofilms seeded into bioreactors as well as biofilms recovered from bioreactor coupons by different methods. β diversity between flushed and reactor biofilms was compared to β diversity between (i) biofilms harvested from different reactors and (ii) biofilms harvested by different methods from the same reactor. These analyses showed that average diversity between flushed and bioreactor biofilms was double the diversity between biofilms from different reactors operated in parallel. The diversity between bioreactors was larger than the diversity associated with different biofilm recovery methods. Compared to other experimental variables, the method used to recover biofilms had a negligible impact on the outcome of water biofilm analyses based on 16S amplicon sequencing. Results from this study show that biofilms grown in reactors over 9 to 11 weeks are not representative models of the microbial populations flushed from a distribution system. Furthermore, the bacterial population profile of biofilms grown in replicate reactors from the same flushed water are likely to diverge. However, four common sampling protocols, which differ with respect to disruption of bacterial cells, provide similar information with respect to the 16S rRNA population profile of the biofilm community. PMID:26196282

  8. Impact of Bioreactor Environment and Recovery Method on the Profile of Bacterial Populations from Water Distribution Systems.

    PubMed

    Luo, Xia; Jellison, Kristen L; Huynh, Kevin; Widmer, Giovanni

    2015-01-01

    Multiple rotating annular reactors were seeded with biofilms flushed from water distribution systems to assess (1) whether biofilms grown in bioreactors are representative of biofilms flushed from the water distribution system in terms of bacterial composition and diversity, and (2) whether the biofilm sampling method affects the population profile of the attached bacterial community. Biofilms were grown in bioreactors until thickness stabilized (9 to 11 weeks) and harvested from reactor coupons by sonication, stomaching, bead-beating, and manual scraping. High-throughput sequencing of 16S rRNA amplicons was used to profile bacterial populations from flushed biofilms seeded into bioreactors as well as biofilms recovered from bioreactor coupons by different methods. β diversity between flushed and reactor biofilms was compared to β diversity between (i) biofilms harvested from different reactors and (ii) biofilms harvested by different methods from the same reactor. These analyses showed that average diversity between flushed and bioreactor biofilms was double the diversity between biofilms from different reactors operated in parallel. The diversity between bioreactors was larger than the diversity associated with different biofilm recovery methods. Compared to other experimental variables, the method used to recover biofilms had a negligible impact on the outcome of water biofilm analyses based on 16S amplicon sequencing. Results from this study show that biofilms grown in reactors over 9 to 11 weeks are not representative models of the microbial populations flushed from a distribution system. Furthermore, the bacterial population profile of biofilms grown in replicate reactors from the same flushed water are likely to diverge. However, four common sampling protocols, which differ with respect to disruption of bacterial cells, provide similar information with respect to the 16S rRNA population profile of the biofilm community.

  9. Mechanisms Leading to Co-Existence of Gas Hydrate in Ocean Sediments [Part 1 of 2

    SciTech Connect

    Bryant, Steven; Juanes, Ruben

    2011-12-31

    In this project we have sought to explain the co-existence of gas and hydrate phases in sediments within the gas hydrate stability zone. We have focused on the gas/brine interface at the scale of individual grains in the sediment. The capillary forces associated with a gas/brine interface play a dominant role in many processes that occur in the pores of sediments and sedimentary rocks. The mechanical forces associated with the same interface can lead to fracture initiation and propagation in hydrate-bearing sediments. Thus the unifying theme of the research reported here is that pore scale phenomena are key to understanding large scale phenomena in hydrate-bearing sediments whenever a free gas phase is present. Our analysis of pore-scale phenomena in this project has delineated three regimes that govern processes in which the gas phase pressure is increasing: fracturing, capillary fingering and viscous fingering. These regimes are characterized by different morphology of the region invaded by the gas. On the other hand when the gas phase pressure is decreasing, the corresponding regimes are capillary fingering and compaction. In this project, we studied all these regimes except compaction. Many processes of interest in hydrate-bearing sediments can be better understood when placed in the context of the appropriate regime. For example, hydrate formation in sub-permafrost sediments falls in the capillary fingering regime, whereas gas invasion into ocean sediments is likely to fall into the fracturing regime. Our research provides insight into the mechanisms by which gas reservoirs are converted to hydrate as the base of the gas hydrate stability zone descends through the reservoir. If the reservoir was no longer being charged, then variation in grain size distribution within the reservoir explain hydrate saturation profiles such as that at Mt. Elbert, where sand-rich intervals containing little hydrate are interspersed between intervals containing large hydrate

  10. Mechanisms Leading to Co-Existence of Gas Hydrate in Ocean Sediments [Part 2 of 2

    SciTech Connect

    Bryant, Steven; Juanes, Ruben

    2011-12-31

    In this project we have sought to explain the co-existence of gas and hydrate phases in sediments within the gas hydrate stability zone. We have focused on the gas/brine interface at the scale of individual grains in the sediment. The capillary forces associated with a gas/brine interface play a dominant role in many processes that occur in the pores of sediments and sedimentary rocks. The mechanical forces associated with the same interface can lead to fracture initiation and propagation in hydrate-bearing sediments. Thus the unifying theme of the research reported here is that pore scale phenomena are key to understanding large scale phenomena in hydrate-bearing sediments whenever a free gas phase is present. Our analysis of pore-scale phenomena in this project has delineated three regimes that govern processes in which the gas phase pressure is increasing: fracturing, capillary fingering and viscous fingering. These regimes are characterized by different morphology of the region invaded by the gas. On the other hand when the gas phase pressure is decreasing, the corresponding regimes are capillary fingering and compaction. In this project, we studied all these regimes except compaction. Many processes of interest in hydrate-bearing sediments can be better understood when placed in the context of the appropriate regime. For example, hydrate formation in sub-permafrost sediments falls in the capillary fingering regime, whereas gas invasion into ocean sediments is likely to fall into the fracturing regime. Our research provides insight into the mechanisms by which gas reservoirs are converted to hydrate as the base of the gas hydrate stability zone descends through the reservoir. If the reservoir was no longer being charged, then variation in grain size distribution within the reservoir explain hydrate saturation profiles such as that at Mt. Elbert, where sand-rich intervals containing little hydrate are interspersed between intervals containing large hydrate

  11. Morphological peculiarities of Calanus finmarchicus and Calanus glacialis in the areas of the co-existence of their populations

    NASA Astrophysics Data System (ADS)

    Berchenko, I. V.; Stupnikova, A. N.

    2014-07-01

    Morphological studies of the females of Calanus finmarchicus, C. glacialis, and C. hyperboreus were performed for specimens sampled in different areas of the Greenland, Barents, Kara, and Laptev seas. Intraspecific variability was found for the ratio of the specimens characterized by different types of setae patterns on the endopodites of C. glacialis and C. finmarchicus. The variability of this parameter did not relate to the environmental peculiarities of the sampling sites and did not depend on the temperature regime. We assume that such differences may be the result of the hybridization of C. glacialis and C. finmarchicus due to the similarity of their reproduction systems and the overlapping of the body size ranges.

  12. Foolish Dreams in a Fabled Land: Living Co-Existence in an Israeli Arab School

    ERIC Educational Resources Information Center

    Court, Deborah

    2006-01-01

    This article presents the results of an ethnographic case study of an Israeli Arab middle school whose staff and students are Arab Israelis from the Moslem, Druze, and Christian population sectors. Against the Israeli backdrop of multiculturalism, political tensions, and terrorism, this school has created a multi-faceted curriculum for teaching…

  13. Integrated Kinetic and Probabilistic Modeling of the Growth Potential of Bacterial Populations

    PubMed Central

    George, S. M.; Métris, A.

    2015-01-01

    When bacteria are exposed to osmotic stress, some cells recover and grow, while others die or are unculturable. This leads to a viable count growth curve where the cell number decreases before the onset of the exponential growth phase. From such curves, it is impossible to estimate what proportion of the initial cells generates the growth because it leads to an ill-conditioned numerical problem. Here, we applied a combination of experimental and statistical methods, based on optical density measurements, to infer both the probability of growth and the maximum specific growth rate of the culture. We quantified the growth potential of a bacterial population as a quantity composed from the probability of growth and the “suitability” of the growing subpopulation to the new environment. We found that, for all three laboratory media studied, the probability of growth decreased while the “work to be done” by the growing subpopulation (defined as the negative logarithm of their suitability parameter) increased with NaCl concentration. The results suggest that the effect of medium on the probability of growth could be described by a simple shift parameter, a differential NaCl concentration that can be accounted for by the change in the medium composition. Finally, we highlighted the need for further understanding of the effect of the osmoprotectant glycine betaine on metabolism. PMID:25747002

  14. Integrated kinetic and probabilistic modeling of the growth potential of bacterial populations.

    PubMed

    George, S M; Métris, A; Baranyi, J

    2015-05-01

    When bacteria are exposed to osmotic stress, some cells recover and grow, while others die or are unculturable. This leads to a viable count growth curve where the cell number decreases before the onset of the exponential growth phase. From such curves, it is impossible to estimate what proportion of the initial cells generates the growth because it leads to an ill-conditioned numerical problem. Here, we applied a combination of experimental and statistical methods, based on optical density measurements, to infer both the probability of growth and the maximum specific growth rate of the culture. We quantified the growth potential of a bacterial population as a quantity composed from the probability of growth and the "suitability" of the growing subpopulation to the new environment. We found that, for all three laboratory media studied, the probability of growth decreased while the "work to be done" by the growing subpopulation (defined as the negative logarithm of their suitability parameter) increased with NaCl concentration. The results suggest that the effect of medium on the probability of growth could be described by a simple shift parameter, a differential NaCl concentration that can be accounted for by the change in the medium composition. Finally, we highlighted the need for further understanding of the effect of the osmoprotectant glycine betaine on metabolism.

  15. Airborne bacterial populations above desert soils of the McMurdo Dry Valleys, Antarctica.

    PubMed

    Bottos, Eric M; Woo, Anthony C; Zawar-Reza, Peyman; Pointing, Stephen B; Cary, Stephen C

    2014-01-01

    Bacteria are assumed to disperse widely via aerosolized transport due to their small size and resilience. The question of microbial endemicity in isolated populations is directly related to the level of airborne exogenous inputs, yet this has proven hard to identify. The ice-free terrestrial ecosystem of Antarctica, a geographically and climatically isolated continent, was used to interrogate microbial bio-aerosols in relation to the surrounding ecology and climate. High-throughput sequencing of bacterial ribosomal RNA (rRNA) genes was combined with analyses of climate patterns during an austral summer. In general terms, the aerosols were dominated by Firmicutes, whereas surrounding soils supported Actinobacteria-dominated communities. The most abundant taxa were also common to aerosols from other continents, suggesting that a distinct bio-aerosol community is widely dispersed. No evidence for significant marine input to bioaerosols was found at this maritime valley site, instead local influence was largely from nearby volcanic sources. Back trajectory analysis revealed transport of incoming regional air masses across the Antarctic Plateau, and this is envisaged as a strong selective force. It is postulated that local soil microbial dispersal occurs largely via stochastic mobilization of mineral soil particulates. PMID:24121801

  16. Interlinkages between bacterial populations dynamics and the operational parameters in a moving bed membrane bioreactor treating urban sewage.

    PubMed

    Reboleiro-Rivas, P; Martín-Pascual, J; Morillo, J A; Juárez-Jiménez, B; Poyatos, J M; Rodelas, B; González-López, J

    2016-01-01

    Bacteria are key players in biological wastewater treatments (WWTs), thus a firm knowledge of the bacterial population dynamics is crucial to understand environmental/operational factors affecting the efficiency and stability of the biological depuration process. Unfortunately, little is known about the microbial ecology of the advanced biological WWTs combining suspended biomass (SB) and attached biofilms (AB). This study explored in depth the bacterial community structure and population dynamics in each biomass fraction from a pilot-scale moving bed membrane bioreactor (MBMBR) treating municipal sewage, by means of temperature-gradient gel electrophoresis (TGGE) and 454-pyrosequencing. Eight experimental phases were conducted, combining different carrier filling ratios, hydraulic retention times and concentrations of mixed liquor total suspended solids. The bacterial community, dominated by Proteobacteria (20.9-53.8%) and Actinobacteria (20.6-57.6%), was very similar in both biomass fractions and able to maintain its functional stability under all the operating conditions, ensuring a successful and steady depuration process. Multivariate statistical analysis demonstrated that solids concentration, carrier filling ratio, temperature and organic matter concentration in the influent were the significant factors explaining population dynamics. Bacterial diversity increased as carrier filling ratio increased (from 20% to 35%, v/v), and solids concentration was the main factor triggering the shifts of the community structure. These findings provide new insights on the influence of operational parameters on the biology of the innovative MBMBRs.

  17. Interlinkages between bacterial populations dynamics and the operational parameters in a moving bed membrane bioreactor treating urban sewage.

    PubMed

    Reboleiro-Rivas, P; Martín-Pascual, J; Morillo, J A; Juárez-Jiménez, B; Poyatos, J M; Rodelas, B; González-López, J

    2016-01-01

    Bacteria are key players in biological wastewater treatments (WWTs), thus a firm knowledge of the bacterial population dynamics is crucial to understand environmental/operational factors affecting the efficiency and stability of the biological depuration process. Unfortunately, little is known about the microbial ecology of the advanced biological WWTs combining suspended biomass (SB) and attached biofilms (AB). This study explored in depth the bacterial community structure and population dynamics in each biomass fraction from a pilot-scale moving bed membrane bioreactor (MBMBR) treating municipal sewage, by means of temperature-gradient gel electrophoresis (TGGE) and 454-pyrosequencing. Eight experimental phases were conducted, combining different carrier filling ratios, hydraulic retention times and concentrations of mixed liquor total suspended solids. The bacterial community, dominated by Proteobacteria (20.9-53.8%) and Actinobacteria (20.6-57.6%), was very similar in both biomass fractions and able to maintain its functional stability under all the operating conditions, ensuring a successful and steady depuration process. Multivariate statistical analysis demonstrated that solids concentration, carrier filling ratio, temperature and organic matter concentration in the influent were the significant factors explaining population dynamics. Bacterial diversity increased as carrier filling ratio increased (from 20% to 35%, v/v), and solids concentration was the main factor triggering the shifts of the community structure. These findings provide new insights on the influence of operational parameters on the biology of the innovative MBMBRs. PMID:26599433

  18. Co-existence of anammox and denitrification for simultaneous nitrogen and carbon removal--Strategies and issues.

    PubMed

    Kumar, Mathava; Lin, Jih-Gaw

    2010-06-15

    The discovery of anaerobic ammonium oxidation (anammox) has greatly improved the understanding of the nitrogen cycle. Anammox provides great promise for the removal of nitrogen from wastewater, containing high concentration of ammonium. However, the presence of organic carbon is considered as unfavorable to this autotrophic process, i.e. anammox. Most of the real wastewaters contain both organic carbon and nitrogen. Under this circumstance, several processes have been established primarily for the complete removal of organic carbon. Subsequently, the wastewater containing no or low organic carbon and nitrogen is treated via a variety of nitrogen removal processes. The co-existence of anammox and denitrification could be useful for the simultaneous removal of nitrogen and organic carbon in a single system rather than a sequential chain of treatment. This review addresses the microbiology, strategies, consequences and the future research challenges in the co-existence of anammox and denitrification.

  19. Contrasting genomic patterns and infection strategies of two co-existing Bacteroidetes podovirus genera.

    PubMed

    Holmfeldt, Karin; Howard-Varona, Cristina; Solonenko, Natalie; Sullivan, Matthew B

    2014-08-01

    Bacterial viruses (phages) are abundant, ecologically important biological entities. However, our understanding of their impact is limited by model systems that are primarily not well represented in nature, e.g. Enterophages and their hosts. Here, we investigate genomic characteristics and infection strategies among six aquatic Bacteroidetes phages that represent two genera of exceptionally large (∼70-75 kb genome) podoviruses, which were isolated from the same seawater sample using Cellulophaga baltica as host. Quantitative host range studies reveal that these genera have contrasting narrow (specialist) and broad (generalist) host ranges, with one-step growth curves revealing reduced burst sizes for the generalist phages. Genomic comparisons suggest candidate genes in each genus that might explain this host range variation, as well as provide hypotheses about receptors in the hosts. One generalist phage, φ38:1, was more deeply characterized, as its infection strategy switched from lytic on its original host to either inefficient lytic or lysogenic on an alternative host. If lysogenic, this phage was maintained extrachromosomally in the alternative host and could not be induced by mitomycin C. This work provides fundamental knowledge regarding phage-host ranges and their genomic drivers while also exploring the 'host environment' as a driver for switching phage replication mode. PMID:24428166

  20. Characterization of the Rate and Temperature Sensitivities of Bacterial Remineralization of Dissolved Organic Phosphorus Compounds by Natural Populations

    PubMed Central

    White, Angelicque E.; Watkins-Brandt, Katie S.; Engle, Morgan A.; Burkhardt, Brian; Paytan, Adina

    2012-01-01

    Production, transformation, and degradation are the principal components of the cycling of dissolved organic matter (DOM) in marine systems. Heterotrophic Bacteria (and Archaea) play a large part in this cycling via enzymatic decomposition and intracellular transformations of organic material to inorganic carbon (C), nitrogen (N), and phosphorus (P). The rate and magnitude of inorganic nutrient regeneration from DOM is related to the elemental composition and lability of DOM substrates as well as the nutritional needs of the mediating organisms. While many previous efforts have focused on C and N cycling of DOM, less is known in regards to the controls of organic P utilization and remineralization by natural populations of bacteria. In order to constrain the relative time scales and degradation of select dissolved organic P (DOP) compounds we have conducted a series of experiments focused on (1) assessment of the short-term lability of a range of DOP compounds, (2) characterization of labile DOP remineralization rates, and (3) examination of temperature sensitivities of labile DOP remineralization for varying bacterial populations. Results reinforce previous findings of monoester and polyphosphate lability and the relative recalcitrance of a model phosphonate: 2-aminoethylphosphonate. High resolution time-series of P-monoester remineralization indicates decay constants on the order of 0.67–7.04 day−1 for bacterial populations isolated from coastal and open ocean surface waters. The variability of these rates is predictably related to incubation temperature and initial concentrations of heterotrophic bacteria. Additional controls on DOP hydrolysis included seasonal shifts in bacterial populations and the physiological state of bacteria at the initiation of DOP addition experiments. Composite results indicate that bacterial hydrolysis of P-monoesters exceeds bacterial P demand and thus DOP remineralization efficiency may control P availability to autotrophs

  1. Co-existence of non-alcoholic fatty liver disease and inflammatory bowel disease: A review article.

    PubMed

    Chao, Che-Yung; Battat, Robert; Al Khoury, Alex; Restellini, Sophie; Sebastiani, Giada; Bessissow, Talat

    2016-09-14

    Emerging data have highlighted the co-existence of non-alcoholic fatty liver disease (NAFLD) and inflammatory bowel disease; both of which are increasingly prevalent disorders with significant complications and impact on future health burden. Cross-section observational studies have shown widely variable prevalence rates of co-existing disease, largely due to differences in disease definition and diagnostic tools utilised in the studies. Age, obesity, insulin resistance and other metabolic conditions are common risks factors in observational studies. However, other studies have also suggested a more dominant role of inflammatory bowel disease related factors such as disease activity, duration, steroid use and prior surgical intervention, in the development of NAFLD. This suggests a potentially more complex pathogenesis and relationship between the two diseases which may be contributed by factors including altered intestinal permeability, gut dysbiosis and chronic inflammatory response. Commonly used immunomodulation agents pose potential hepatic toxicity, however no definitive evidence exist linking them to the development of hepatic steatosis, nor are there any data on the impact of therapy and prognosis in patient with co-existent diseases. Further studies are required to assess the impact and establish appropriate screening and management strategies in order to allow early identification, intervention and improve patient outcomes. PMID:27678354

  2. Co-existence of non-alcoholic fatty liver disease and inflammatory bowel disease: A review article.

    PubMed

    Chao, Che-Yung; Battat, Robert; Al Khoury, Alex; Restellini, Sophie; Sebastiani, Giada; Bessissow, Talat

    2016-09-14

    Emerging data have highlighted the co-existence of non-alcoholic fatty liver disease (NAFLD) and inflammatory bowel disease; both of which are increasingly prevalent disorders with significant complications and impact on future health burden. Cross-section observational studies have shown widely variable prevalence rates of co-existing disease, largely due to differences in disease definition and diagnostic tools utilised in the studies. Age, obesity, insulin resistance and other metabolic conditions are common risks factors in observational studies. However, other studies have also suggested a more dominant role of inflammatory bowel disease related factors such as disease activity, duration, steroid use and prior surgical intervention, in the development of NAFLD. This suggests a potentially more complex pathogenesis and relationship between the two diseases which may be contributed by factors including altered intestinal permeability, gut dysbiosis and chronic inflammatory response. Commonly used immunomodulation agents pose potential hepatic toxicity, however no definitive evidence exist linking them to the development of hepatic steatosis, nor are there any data on the impact of therapy and prognosis in patient with co-existent diseases. Further studies are required to assess the impact and establish appropriate screening and management strategies in order to allow early identification, intervention and improve patient outcomes.

  3. Co-existence of non-alcoholic fatty liver disease and inflammatory bowel disease: A review article

    PubMed Central

    Chao, Che-Yung; Battat, Robert; Al Khoury, Alex; Restellini, Sophie; Sebastiani, Giada; Bessissow, Talat

    2016-01-01

    Emerging data have highlighted the co-existence of non-alcoholic fatty liver disease (NAFLD) and inflammatory bowel disease; both of which are increasingly prevalent disorders with significant complications and impact on future health burden. Cross-section observational studies have shown widely variable prevalence rates of co-existing disease, largely due to differences in disease definition and diagnostic tools utilised in the studies. Age, obesity, insulin resistance and other metabolic conditions are common risks factors in observational studies. However, other studies have also suggested a more dominant role of inflammatory bowel disease related factors such as disease activity, duration, steroid use and prior surgical intervention, in the development of NAFLD. This suggests a potentially more complex pathogenesis and relationship between the two diseases which may be contributed by factors including altered intestinal permeability, gut dysbiosis and chronic inflammatory response. Commonly used immunomodulation agents pose potential hepatic toxicity, however no definitive evidence exist linking them to the development of hepatic steatosis, nor are there any data on the impact of therapy and prognosis in patient with co-existent diseases. Further studies are required to assess the impact and establish appropriate screening and management strategies in order to allow early identification, intervention and improve patient outcomes. PMID:27678354

  4. Co-existence of non-alcoholic fatty liver disease and inflammatory bowel disease: A review article

    PubMed Central

    Chao, Che-Yung; Battat, Robert; Al Khoury, Alex; Restellini, Sophie; Sebastiani, Giada; Bessissow, Talat

    2016-01-01

    Emerging data have highlighted the co-existence of non-alcoholic fatty liver disease (NAFLD) and inflammatory bowel disease; both of which are increasingly prevalent disorders with significant complications and impact on future health burden. Cross-section observational studies have shown widely variable prevalence rates of co-existing disease, largely due to differences in disease definition and diagnostic tools utilised in the studies. Age, obesity, insulin resistance and other metabolic conditions are common risks factors in observational studies. However, other studies have also suggested a more dominant role of inflammatory bowel disease related factors such as disease activity, duration, steroid use and prior surgical intervention, in the development of NAFLD. This suggests a potentially more complex pathogenesis and relationship between the two diseases which may be contributed by factors including altered intestinal permeability, gut dysbiosis and chronic inflammatory response. Commonly used immunomodulation agents pose potential hepatic toxicity, however no definitive evidence exist linking them to the development of hepatic steatosis, nor are there any data on the impact of therapy and prognosis in patient with co-existent diseases. Further studies are required to assess the impact and establish appropriate screening and management strategies in order to allow early identification, intervention and improve patient outcomes.

  5. Bacterial population and biodegradation potential in chronically crude oil-contaminated marine sediments are strongly linked to temperature.

    PubMed

    Bargiela, Rafael; Mapelli, Francesca; Rojo, David; Chouaia, Bessem; Tornés, Jesús; Borin, Sara; Richter, Michael; Del Pozo, Mercedes V; Cappello, Simone; Gertler, Christoph; Genovese, María; Denaro, Renata; Martínez-Martínez, Mónica; Fodelianakis, Stilianos; Amer, Ranya A; Bigazzi, David; Han, Xifang; Chen, Jianwei; Chernikova, Tatyana N; Golyshina, Olga V; Mahjoubi, Mouna; Jaouanil, Atef; Benzha, Fatima; Magagnini, Mirko; Hussein, Emad; Al-Horani, Fuad; Cherif, Ameur; Blaghen, Mohamed; Abdel-Fattah, Yasser R; Kalogerakis, Nicolas; Barbas, Coral; Malkawi, Hanan I; Golyshin, Peter N; Yakimov, Michail M; Daffonchio, Daniele; Ferrer, Manuel

    2015-01-01

    Two of the largest crude oil-polluted areas in the world are the semi-enclosed Mediterranean and Red Seas, but the effect of chronic pollution remains incompletely understood on a large scale. We compared the influence of environmental and geographical constraints and anthropogenic forces (hydrocarbon input) on bacterial communities in eight geographically separated oil-polluted sites along the coastlines of the Mediterranean and Red Seas. The differences in community compositions and their biodegradation potential were primarily associated (P < 0.05) with both temperature and chemical diversity. Furthermore, we observed a link between temperature and chemical and biological diversity that was stronger in chronically polluted sites than in pristine ones where accidental oil spills occurred. We propose that low temperature increases bacterial richness while decreasing catabolic diversity and that chronic pollution promotes catabolic diversification. Our results further suggest that the bacterial populations in chronically polluted sites may respond more promptly in degrading petroleum after accidental oil spills. PMID:26119183

  6. Bacterial population and biodegradation potential in chronically crude oil-contaminated marine sediments are strongly linked to temperature.

    PubMed

    Bargiela, Rafael; Mapelli, Francesca; Rojo, David; Chouaia, Bessem; Tornés, Jesús; Borin, Sara; Richter, Michael; Del Pozo, Mercedes V; Cappello, Simone; Gertler, Christoph; Genovese, María; Denaro, Renata; Martínez-Martínez, Mónica; Fodelianakis, Stilianos; Amer, Ranya A; Bigazzi, David; Han, Xifang; Chen, Jianwei; Chernikova, Tatyana N; Golyshina, Olga V; Mahjoubi, Mouna; Jaouanil, Atef; Benzha, Fatima; Magagnini, Mirko; Hussein, Emad; Al-Horani, Fuad; Cherif, Ameur; Blaghen, Mohamed; Abdel-Fattah, Yasser R; Kalogerakis, Nicolas; Barbas, Coral; Malkawi, Hanan I; Golyshin, Peter N; Yakimov, Michail M; Daffonchio, Daniele; Ferrer, Manuel

    2015-06-29

    Two of the largest crude oil-polluted areas in the world are the semi-enclosed Mediterranean and Red Seas, but the effect of chronic pollution remains incompletely understood on a large scale. We compared the influence of environmental and geographical constraints and anthropogenic forces (hydrocarbon input) on bacterial communities in eight geographically separated oil-polluted sites along the coastlines of the Mediterranean and Red Seas. The differences in community compositions and their biodegradation potential were primarily associated (P < 0.05) with both temperature and chemical diversity. Furthermore, we observed a link between temperature and chemical and biological diversity that was stronger in chronically polluted sites than in pristine ones where accidental oil spills occurred. We propose that low temperature increases bacterial richness while decreasing catabolic diversity and that chronic pollution promotes catabolic diversification. Our results further suggest that the bacterial populations in chronically polluted sites may respond more promptly in degrading petroleum after accidental oil spills.

  7. Co-habiting amphibian species harbor unique skin bacterial communities in wild populations

    PubMed Central

    McKenzie, Valerie J; Bowers, Robert M; Fierer, Noah; Knight, Rob; Lauber, Christian L

    2012-01-01

    Although all plant and animal species harbor microbial symbionts, we know surprisingly little about the specificity of microbial communities to their hosts. Few studies have compared the microbiomes of different species of animals, and fewer still have examined animals in the wild. We sampled four pond habitats in Colorado, USA, where multiple amphibian species were present. In total, 32 amphibian individuals were sampled from three different species including northern leopard frogs (Lithobates pipiens), western chorus frogs (Pseudacris triseriata) and tiger salamanders (Ambystoma tigrinum). We compared the diversity and composition of the bacterial communities on the skin of the collected individuals via barcoded pyrosequencing of the 16S rRNA gene. Dominant bacterial phyla included Acidobacteria, Actinobacteria, Bacteriodetes, Cyanobacteria, Firmicutes and Proteobacteria. In total, we found members of 18 bacterial phyla, comparable to the taxonomic diversity typically found on human skin. Levels of bacterial diversity varied strongly across species: L. pipiens had the highest diversity; A. tigrinum the lowest. Host species was a highly significant predictor of bacterial community similarity, and co-habitation within the same pond was not significant, highlighting that the skin-associated bacterial communities do not simply reflect those bacterial communities found in their surrounding environments. Innate species differences thus appear to regulate the structure of skin bacterial communities on amphibians. In light of recent discoveries that some bacteria on amphibian skin have antifungal activity, our finding suggests that host-specific bacteria may have a role in the species-specific resistance to fungal pathogens. PMID:21955991

  8. Life history correlates of fecal bacterial species richness in a wild population of the blue tit Cyanistes caeruleus

    PubMed Central

    Benskin, Clare McW H; Rhodes, Glenn; Pickup, Roger W; Mainwaring, Mark C; Wilson, Kenneth; Hartley, Ian R

    2015-01-01

    Very little is known about the normal gastrointestinal flora of wild birds, or how it might affect or reflect the host's life-history traits. The aim of this study was to survey the species richness of bacteria in the feces of a wild population of blue tits Cyanistes caeruleus and to explore the relationships between bacterial species richness and various life-history traits, such as age, sex, and reproductive success. Using PCR-TGGE, 55 operational taxonomic units (OTUs) were identified in blue tit feces. DNA sequencing revealed that the 16S rRNA gene was amplified from a diverse range of bacteria, including those that shared closest homology with Bacillus licheniformis, Campylobacter lari, Pseudomonas spp., and Salmonella spp. For adults, there was a significant negative relationship between bacterial species richness and the likelihood of being detected alive the following breeding season; bacterial richness was consistent across years but declined through the breeding season; and breeding pairs had significantly more similar bacterial richness than expected by chance alone. Reduced adult survival was correlated with the presence of an OTU most closely resembling C. lari; enhanced adult survival was associated with an OTU most similar to Arthrobacter spp. For nestlings, there was no significant change in bacterial species richness between the first and second week after hatching, and nestlings sharing the same nest had significantly more similar bacterial richness. Collectively, these results provide compelling evidence that bacterial species richness was associated with several aspects of the life history of their hosts. PMID:25750710

  9. Culturable bacterial populations associated with ectomycorrhizae of Norway spruce stands with different degrees of decline in the Czech Republic.

    PubMed

    Avidano, Lorena; Rinaldi, Maurizio; Gindro, Roberto; Cudlín, Pavel; Martinotti, Maria Giovanna; Fracchia, Letizia

    2010-01-01

    The aim of this study was to determine which species of culturable bacteria are associated with ectomycorrhizae (ECM) of Norway spruce (Picea abies (L.) Karst) in the Sudety Mountains, exposed for years to atmospheric pollutants, acid rain, and climatic stress, and to identify particular species that have adapted to those conditions. Biolog identification was performed on bacterial species from ECM of adult spruce trees and seedlings of stands with low, intermediate, and high forest decline. Bacterial diversity in ECM associated with adult spruce trees, seedlings, and seedlings grown on monoliths was calculated; although the expected values appeared to vary widely, no significant differences among sites were observed. Dendrograms based on the identified bacterial species showed that stands with low forest decline clustered separately from the others. Principal component analysis of the normalized data for ECM-associated species showed a clear separation between stands with high forest decline and stands with low forest decline for seedlings and a less evident separation for adult spruce trees. In conclusion, shifts in ECM-associated culturable bacterial populations seem to be associated with forest decline in Norway spruce stands. Some bacterial species were preferentially associated with mycorrhizal roots depending on the degree of forest decline; this was more evident in seedlings where the species Burkholderia cepacia and Pseudomonas fluorescens were associated with, respectively, ECM of the most damaged stands and those with low forest decline.

  10. Management Practices Affect Soil Nutrients and Bacterial Populations in Backgrounding Beef Feedlot.

    PubMed

    Netthisinghe, A M P; Cook, K L; Gilfillen, R A; Sistani, K R; Woosley, P B

    2015-11-01

    Contaminants associated with manure in animal production sites are of significant concern. Unless properly managed, manure-derived soil nutrients in livestock production sites can deteriorate soil and water quality. This 3-yr study evaluated a soil nutrient management strategy with four sequentially imposed management practices: 12-mo backgrounding (BG), manure removal from the feeder area (FD), 12-mo destocking (DS), and 12-mo grass hay harvesting (H) in a small backgrounding feedlot. Resulting soil nutrient levels, total (), and N cycling bacterial ( and ) populations after each management practice in feedlot feeder and grazing (GR) areas and in crop grown at the control location (CT) were measured. Irrespective of management practice, FD contained greater soil nutrient concentrations than the GR and CT. Regardless of management practice, total bacteria cells (1.4 × 10 cells g soil) and nitrate reducers (5.2 × 10 cells g soil) were an order of magnitude higher in the FD than in the GR and CT, whereas nitrifying bacteria concentrations (1.4 × 10 cells g soil) were higher in the GR. Manure removal from the feeder area reduced M3-P (39%), total C (21%), total N (23%), NH-N (47%), and NO-N (93%) levels established in the FD during BG. Destocking lowered total C and N (45%) in the FD and NH-N (47%), NO-N (76%), and Zn (16%) in the GR. Hay harvesting reduced all soil nutrients in the FD and GR marginally. The management strategy has potential to lower soil nutrient concentrations, control soil nutrient buildup, and limit nutrient spread within the feedlot. PMID:26641341

  11. Management Practices Affect Soil Nutrients and Bacterial Populations in Backgrounding Beef Feedlot.

    PubMed

    Netthisinghe, A M P; Cook, K L; Gilfillen, R A; Sistani, K R; Woosley, P B

    2015-11-01

    Contaminants associated with manure in animal production sites are of significant concern. Unless properly managed, manure-derived soil nutrients in livestock production sites can deteriorate soil and water quality. This 3-yr study evaluated a soil nutrient management strategy with four sequentially imposed management practices: 12-mo backgrounding (BG), manure removal from the feeder area (FD), 12-mo destocking (DS), and 12-mo grass hay harvesting (H) in a small backgrounding feedlot. Resulting soil nutrient levels, total (), and N cycling bacterial ( and ) populations after each management practice in feedlot feeder and grazing (GR) areas and in crop grown at the control location (CT) were measured. Irrespective of management practice, FD contained greater soil nutrient concentrations than the GR and CT. Regardless of management practice, total bacteria cells (1.4 × 10 cells g soil) and nitrate reducers (5.2 × 10 cells g soil) were an order of magnitude higher in the FD than in the GR and CT, whereas nitrifying bacteria concentrations (1.4 × 10 cells g soil) were higher in the GR. Manure removal from the feeder area reduced M3-P (39%), total C (21%), total N (23%), NH-N (47%), and NO-N (93%) levels established in the FD during BG. Destocking lowered total C and N (45%) in the FD and NH-N (47%), NO-N (76%), and Zn (16%) in the GR. Hay harvesting reduced all soil nutrients in the FD and GR marginally. The management strategy has potential to lower soil nutrient concentrations, control soil nutrient buildup, and limit nutrient spread within the feedlot.

  12. The role of indigenous bacterial and fungal soil populations in the biodegradation of crude oil in a desert soil.

    PubMed

    Embar, Keren; Forgacs, Chaim; Sivan, Alex

    2006-08-01

    The biodegradation capacity of indigenous microbial populations was examined in a desert soil contaminated with crude oil. To evaluate biodegradation, soil samples supplemented with 5, 10 or 20% (w/w) of crude oil were incubated for 90 days at 30 degrees C. The effect of augmentation of the soil with vermiculite (50% v/v) as a bulking agent providing increased surface/volume ratio and improved soil aeration was also tested. Maximal biodegradation (91%) was obtained in soil containing the highest concentration of crude oil (20%) and supplemented with vermiculite; only 74% of the oil was degraded in samples containing the same level of crude oil but lacking vermiculite. Gas chromatograms of distilled fractions of crude oil extracted from the soil before and after incubation demonstrated that most of the light and part of the intermediate weight fractions initially present in the oil extracts could not be detected after incubation. Monitoring of microbial population densities revealed an initial decline in bacterial viable counts after exposure to oil, presumably as a result of the crude oil's toxicity. This decline was followed by a steep recovery in microbial population density, then by a moderate increase that persisted until the end of incubation. By contrast, the inhibitory effect of crude oil on the fungal population was minimal. Furthermore, the overall increased growth response of the fungal population, at all three levels of contamination, was about one order of magnitude higher than that of the bacterial population. PMID:16570229

  13. Short-term effects of South Louisiana and Kuwait crude oils on glucose utilization by marine bacterial populations

    SciTech Connect

    Alexander, S.K.; Schwarz, J.R.

    1980-08-01

    Two crude oils, South Louisiana and Kuwait, were examined for their impact on glucose utilization by bacterial populations from the Gulf of Mexico. The uptake and mineralization of (U-/sup 14/C)glucose was assayed after a 4- to 23-h exposure to various concentrations of added crude oil (0, 0.001, 0.01, and 0.1% (vol/vol)). The effects of oil were determined in a total of 15 sediment and 13 water samples collected from offshore, open-bay, and salt marsh environments. The utilization of glucose by bacterial populations usually was not affected by added oil; in 10 sediment and 11 water samples, oil had no significant effect on either glucose uptake or mineralization. Stimulation by oil was recorded in four sediment samples. Oil inhibition occurred in one sediment and two water samples, but only in the presence of the highest concentration of added oil, i.e., 0.1%. Our data suggest that short-term exposure to either South Louisiana or Kuwait crude oil, even at 0.1%, usually has no toxic effect on glucose utilization by marine bacterial populations.

  14. Population Dynamics of a Salmonella Lytic Phage and Its Host: Implications of the Host Bacterial Growth Rate in Modelling

    PubMed Central

    Santos, Sílvio B.; Carvalho, Carla; Azeredo, Joana; Ferreira, Eugénio C.

    2014-01-01

    The prevalence and impact of bacteriophages in the ecology of bacterial communities coupled with their ability to control pathogens turn essential to understand and predict the dynamics between phage and bacteria populations. To achieve this knowledge it is essential to develop mathematical models able to explain and simulate the population dynamics of phage and bacteria. We have developed an unstructured mathematical model using delay-differential equations to predict the interactions between a broad-host-range Salmonella phage and its pathogenic host. The model takes into consideration the main biological parameters that rule phage-bacteria interactions likewise the adsorption rate, latent period, burst size, bacterial growth rate, and substrate uptake rate, among others. The experimental validation of the model was performed with data from phage-interaction studies in a 5 L bioreactor. The key and innovative aspect of the model was the introduction of variations in the latent period and adsorption rate values that are considered as constants in previous developed models. By modelling the latent period as a normal distribution of values and the adsorption rate as a function of the bacterial growth rate it was possible to accurately predict the behaviour of the phage-bacteria population. The model was shown to predict simulated data with a good agreement with the experimental observations and explains how a lytic phage and its host bacteria are able to coexist. PMID:25051248

  15. Bacterial populations on brewery filling hall surfaces as revealed by next-generation sequencing.

    PubMed

    Priha, Outi; Raulio, Mari; Maukonen, Johanna; Vehviläinen, Anna-Kaisa; Storgårds, Erna

    2016-01-01

    Due to the presence of moisture and nutrients, brewery filling line surfaces are susceptible to unwanted microbial attachment. Knowledge of the attaching microbes will aid in designing hygienic control of the process. In this study the bacterial diversity present on brewery filling line surfaces was revealed by next generation sequencing. The two filling lines studied maintained their characteristic bacterial community throughout three sampling times (13-163 days). On the glass bottle line, γ-proteobacteria dominated (35-82% of all OTUs), whereas on the canning line α-, β- and γ-proteobacteria and actinobacteria were most common. The most frequently detected genera were Acinetobacter, Propinobacterium and Pseudomonas. The halophilic genus Halomonas was commonly detected, which might be due to its tolerance to alkaline foam cleaners. This study has revealed a detailed overall picture of the bacterial groups present on filling line surfaces. Further effort should be given to determine the efficacy of washing procedures on different bacterial groups. PMID:27064426

  16. Periodic mesoporous organosilicas with co-existence of diurea and sulfanilamide as an effective drug delivery carrier

    SciTech Connect

    Parambadath, Surendran; Rana, Vijay Kumar; Moorthy, Santha; Chu, Sang-Wook; Park, Shin-Kyu; Lee, Daewoo; Sung, Giju; Ha, Chang-Sik

    2011-05-15

    In this article we report the synthesis of new periodic mesoporous organosilicas (PMOs) with the co-existence of diurea and sulfanilamide-bridged organosilica that are potentially useful for controlled drug release system. The materials possess hexagonal pores with a high degree of uniformity and show long-range order as confirmed by the measurements of small-angle X-ray scattering (SAXS), N{sub 2} adsorption isotherms, and transmission electron microscopy(TEM). FT-IR and solid state {sup 29}Si MAS and {sup 13}C CP MAS NMR spectroscopic analyses proved that the bridging groups in the framework are not cleaved and covalently attached in the walls of the PMOs. It was found that the organic functionality could be introduced in a maximum of 10 mol% with respect to the total silicon content and be thermally stable up to 230 {sup o}C. The synthesized materials were shown to be particularly suitable for adsorption and desorption of hydrophilic/hydrophobic drugs from a phosphate buffer solution at pH 7.4. -- Graphical Abstract: We report the synthesis of new periodic mesoporous organosilicas (PMOs) with the co-existence of diurea and sulfanilamide-bridged organosilica that are potentially useful for controlled drug release system. Display Omitted Highlights: {yields} Synthesis of new periodic mesoporous organosilicas (PMOs) with the co-existence of diurea and sulfanilamide-bridged organosilica that are potentially useful for controlled drug release system. {yields} The organic functionality could be introduced in a maximum of 10 mol% with respect to the total silicon content and be thermally stable up to 230 {sup o}C. {yields} The synthesized materials were shown to be particularly suitable for adsorption and desorption of hydrophilic/hydrophobic drugs from a phosphate buffer solution at pH 7.4.

  17. Bacterial populations in the groundwater on the US-Mexico border in El Paso County, Texas.

    PubMed

    Mroz, R C; Pillai, S D

    1994-12-01

    In El Paso County, Texas, 73 domestic wells were sampled using a variety of selective media to determine the extent of bacterial contamination of the groundwater on the US side of the United States-Mexico border. Thirteen wells were contaminated by fecal coliforms, whereas other wells contained a variety of bacterial genera including some potential pathogens that normally would not be detected by standard methods of water testing.

  18. Acute promyelocytic leukemia co-existing with JAK2 V617F positive myeloproliferative neoplasm: a case report

    PubMed Central

    Mamorska-Dyga, Aleksandra; Wu, Jingjing; Khattar, Pallavi; Ronny, Faisal M. H.; Islam, Humayun; Seiter, Karen

    2016-01-01

    The V617F mutation of Janus-associated kinase 2 (JAK2) is commonly seen in myeloproliferative neoplasms (MPN). Transformation of JAK2 positive MPNs to acute leukemia has been reported. We here report a case of acute promyelocytic leukemia which was later confirmed to have a co-existing JAK2 V617F positive MPN. In addition, the patient was found to have FLT3-TKD mutation, which, together with PML/RARa, could play a role in the MPN transformation to APL. PMID:27358900

  19. ADHD in girls and boys – gender differences in co-existing symptoms and executive function measures

    PubMed Central

    2013-01-01

    Background ADHD is diagnosed and treated more often in males than in females. Research on gender differences suggests that girls may be consistently underidentified and underdiagnosed because of differences in the expression of the disorder among boys and girls. One aim of the present study was to assess in a clinical sample of medication naïve boys and girls with ADHD, whether there were significant gender x diagnosis interactions in co-existing symptom severity and executive function (EF) impairment. The second aim was to delineate specific symptom ratings and measures of EF that were most important in distinguishing ADHD from healthy controls (HC) of the same gender. Methods Thirty-seven females with ADHD, 43 males with ADHD, 18 HC females and 32 HC males between 8 and 17 years were included. Co-existing symptoms were assessed with self-report scales and parent ratings. EF was assessed with parent ratings of executive skills in everyday situations (BRIEF), and neuropsychological tests. The three measurement domains (co-existing symptoms, BRIEF, neuropsychological EF tests) were investigated using analysis of variance (ANOVA) and random forest classification. Results ANOVAs revealed only one significant diagnosis x gender interaction, with higher rates of self-reported anxiety symptoms in females with ADHD. Random forest classification indicated that co-existing symptom ratings was substantially better in distinguishing subjects with ADHD from HC in females (93% accuracy) than in males (86% accuracy). The most important distinguishing variable was self-reported anxiety in females, and parent ratings of rule breaking in males. Parent ratings of EF skills were better in distinguishing subjects with ADHD from HC in males (96% accuracy) than in females (92% accuracy). Neuropsychological EF tests had only a modest ability to categorize subjects as ADHD or HC in males (73% accuracy) and females (79% accuracy). Conclusions Our findings emphasize the combination of

  20. Detailed analyses of the bacterial populations in processed cocoa beans of different geographic origin, subject to varied fermentation conditions.

    PubMed

    Bortolini, Cristian; Patrone, Vania; Puglisi, Edoardo; Morelli, Lorenzo

    2016-11-01

    The quality of chocolate is influenced by several parameters, one of which is bacterial diversity during fermentation and drying; a crucial factor for the generation of the optimal cocoa flavor precursors. Our understanding of the bacterial populations involved in chocolate fermentation can be improved by the use of high-throughput sequencing technologies (HTS), combined with PCR amplification of the 16S rRNA subunit. Here, we have conducted a high-throughput assessment of bacterial diversity in four processed samples of cocoa beans from different geographic origins. As part of this study, we also assessed whether different DNA extraction methods could affect the quality of our data. The dynamics of microbial populations were analyzed postharvest (fermentation and sun drying) and shipment, before entry to the industrial process. A total of 691,867 high quality sequences were obtained by Illumina MiSeq sequencing of the two bacterial 16S rRNA hypervariable regions, V3 and V4, following paired-read assembly of the raw reads. Manual curation of the 16S database allowed us to assign the correct taxonomic classifications, at species level, for 83.8% of those reads. This approach revealed a limited biodiversity and population dynamics for both the lactic acid bacteria (LAB) and acetic acid bacteria (AAB), both of which are key players during the acetification and lactic acid fermentation phases. Among the LAB, the most abundant species were Lactobacillus fermentum, Enterococcus casseliflavus, Weissella paramesenteroides, and Lactobacillus plantarum/paraplantarum. Among the AAB, Acetobacter syzygii, was most abundant, then Acetobacter senegalensis and Acetobacter pasteriuanus. Our results indicate that HTS approach has the ability to provide a comprehensive view of the cocoa bean microbiota at the species level.

  1. Detailed analyses of the bacterial populations in processed cocoa beans of different geographic origin, subject to varied fermentation conditions.

    PubMed

    Bortolini, Cristian; Patrone, Vania; Puglisi, Edoardo; Morelli, Lorenzo

    2016-11-01

    The quality of chocolate is influenced by several parameters, one of which is bacterial diversity during fermentation and drying; a crucial factor for the generation of the optimal cocoa flavor precursors. Our understanding of the bacterial populations involved in chocolate fermentation can be improved by the use of high-throughput sequencing technologies (HTS), combined with PCR amplification of the 16S rRNA subunit. Here, we have conducted a high-throughput assessment of bacterial diversity in four processed samples of cocoa beans from different geographic origins. As part of this study, we also assessed whether different DNA extraction methods could affect the quality of our data. The dynamics of microbial populations were analyzed postharvest (fermentation and sun drying) and shipment, before entry to the industrial process. A total of 691,867 high quality sequences were obtained by Illumina MiSeq sequencing of the two bacterial 16S rRNA hypervariable regions, V3 and V4, following paired-read assembly of the raw reads. Manual curation of the 16S database allowed us to assign the correct taxonomic classifications, at species level, for 83.8% of those reads. This approach revealed a limited biodiversity and population dynamics for both the lactic acid bacteria (LAB) and acetic acid bacteria (AAB), both of which are key players during the acetification and lactic acid fermentation phases. Among the LAB, the most abundant species were Lactobacillus fermentum, Enterococcus casseliflavus, Weissella paramesenteroides, and Lactobacillus plantarum/paraplantarum. Among the AAB, Acetobacter syzygii, was most abundant, then Acetobacter senegalensis and Acetobacter pasteriuanus. Our results indicate that HTS approach has the ability to provide a comprehensive view of the cocoa bean microbiota at the species level. PMID:27458718

  2. Hydrogeochemistry and coal-associated bacterial populations from a methanogenic coal bed

    USGS Publications Warehouse

    Barnhart, Elliott P.; Weeks, Edwin P.; Jones, Elizabeth J.P.; Ritter, Daniel J.; McIntosh, Jennifer C.; Clark, Arthur C.; Ruppert, Leslie F.; Cunningham, Alfred B.; Vinson, David S.; Orem, William H.; Fields, Matthew W.

    2016-01-01

    Biogenic coalbed methane (CBM), a microbially-generated source of natural gas trapped within coal beds, is an important energy resource in many countries. Specific bacterial populations and enzymes involved in coal degradation, the potential rate-limiting step of CBM formation, are relatively unknown. The U.S. Geological Survey (USGS) has established a field site, (Birney test site), in an undeveloped area of the Powder River Basin (PRB), with four wells completed in the Flowers-Goodale coal bed, one in the overlying sandstone formation, and four in overlying and underlying coal beds (Knoblach, Nance, and Terret). The nine wells were positioned to characterize the hydraulic conductivity of the Flowers-Goodale coal bed and were selectively cored to investigate the hydrogeochemistry and microbiology associated with CBM production at the Birney test site. Aquifer-test results indicated the Flowers-Goodale coal bed, in a zone from about 112 to 120 m below land surface at the test site, had very low hydraulic conductivity (0.005 m/d) compared to other PRB coal beds examined. Consistent with microbial methanogenesis, groundwater in the coal bed and overlying sandstone contain dissolved methane (46 mg/L average) with low δ13C values (−67‰ average), high alkalinity values (22 meq/kg average), relatively positive δ13C-DIC values (4‰ average), and no detectable higher chain hydrocarbons, NO3−, or SO42−. Bioassay methane production was greatest at the upper interface of the Flowers-Goodale coal bed near the overlying sandstone. Pyrotag analysis identified Aeribacillus as a dominant in situbacterial community member in the coal near the sandstone and statistical analysis indicated Actinobacteria predominated coal core samples compared to claystone or sandstone cores. These bacteria, which previously have been correlated with hydrocarbon-containing environments such as oil reservoirs, have demonstrated the ability to produce biosurfactants to break down

  3. Comparative modifications in bacterial gill-endosymbiotic populations of the two bivalves Codakia orbiculata and Lucina pensylvanica during bacterial loss and reacquisition.

    PubMed

    Elisabeth, Nathalie H; Caro, Audrey; Césaire, Thierry; Mansot, Jean-Louis; Escalas, Arthur; Sylvestre, Marie-Noëlle; Jean-Louis, Patrick; Gros, Olivier

    2014-09-01

    Until now, the culture of sulphur-oxidizing bacterial symbionts associated with marine invertebrates remains impossible. Therefore, few studies focused on symbiont's physiology under stress conditions. In this study, we carried out a comparative experiment based on two different species of lucinid bivalves (Codakia orbiculata and Lucina pensylvanica) under comparable stress factors. The bivalves were starved for 6 months in sulphide-free filtered seawater. For C. orbiculata only, starved individuals were then put back to the field, in natural sediment. We used in situ hybridization, flow cytometry and X-ray fluorescence to characterize the symbiont population hosted in the gills of both species. In L. pensylvanica, no decrease in symbiont abundance was observed throughout the starvation experiment, whereas elemental sulphur slowly decreased to zero after 3 months of starvation. Conversely, in C. orbiculata, symbiont abundance within bacteriocytes decreased rapidly and sulphur from symbionts disappeared during the first weeks of the experiment. The modifications of the cellular characteristics (SSC--relative cell size and FL1--genomic content) of the symbiotic populations along starvation were not comparable between species. Return to the sediment of starved C. orbiculata individuals led to a rapid (2-4 weeks) recovery of symbiotic cellular characteristics, comparable with unstressed symbionts. These results suggest that endosymbiotic population regulation is host-species-dependent in lucinids. PMID:24939560

  4. Comparative modifications in bacterial gill-endosymbiotic populations of the two bivalves Codakia orbiculata and Lucina pensylvanica during bacterial loss and reacquisition.

    PubMed

    Elisabeth, Nathalie H; Caro, Audrey; Césaire, Thierry; Mansot, Jean-Louis; Escalas, Arthur; Sylvestre, Marie-Noëlle; Jean-Louis, Patrick; Gros, Olivier

    2014-09-01

    Until now, the culture of sulphur-oxidizing bacterial symbionts associated with marine invertebrates remains impossible. Therefore, few studies focused on symbiont's physiology under stress conditions. In this study, we carried out a comparative experiment based on two different species of lucinid bivalves (Codakia orbiculata and Lucina pensylvanica) under comparable stress factors. The bivalves were starved for 6 months in sulphide-free filtered seawater. For C. orbiculata only, starved individuals were then put back to the field, in natural sediment. We used in situ hybridization, flow cytometry and X-ray fluorescence to characterize the symbiont population hosted in the gills of both species. In L. pensylvanica, no decrease in symbiont abundance was observed throughout the starvation experiment, whereas elemental sulphur slowly decreased to zero after 3 months of starvation. Conversely, in C. orbiculata, symbiont abundance within bacteriocytes decreased rapidly and sulphur from symbionts disappeared during the first weeks of the experiment. The modifications of the cellular characteristics (SSC--relative cell size and FL1--genomic content) of the symbiotic populations along starvation were not comparable between species. Return to the sediment of starved C. orbiculata individuals led to a rapid (2-4 weeks) recovery of symbiotic cellular characteristics, comparable with unstressed symbionts. These results suggest that endosymbiotic population regulation is host-species-dependent in lucinids.

  5. Drastic changes in aquatic bacterial populations from the Cuatro Cienegas Basin (Mexico) in response to long-term environmental stress.

    PubMed

    Pajares, Silvia; Eguiarte, Luis E; Bonilla-Rosso, German; Souza, Valeria

    2013-12-01

    Understanding the changes of aquatic microbial community composition in response to changes in temperature and ultraviolet irradiation is relevant for predicting biogeochemical modifications in the functioning of natural microbial communities under global climate change scenarios. Herein we investigate shifts in the bacterioplankton composition in response to long-term changes in temperature and UV radiation. For this purpose, 15 mesocosms were seeded with composite aquatic microbial communities from natural pools within the Cuatro Cienegas Basin (Mexican Chihuahuan desert) and were subject to different temperatures and UV conditions. 16S rRNA gene clone libraries were obtained from water samples at the mid-point (4 months) and the end of the experiment (8 months). An increase in bacterial diversity over time was found in the treatment of constant temperature and UV protection, which suggests that stable environments promote the establishment of complex and diverse bacterial community. Drastic changes in the phylogenetic bacterioplankton composition and structure were observed in response to fluctuating temperature and increasing UV radiation and temperature. Fluctuating temperature induced the largest decrease of bacterial richness during the experiment, indicating that frequent temperature changes drive the reduction in abundance of several species, most notably autotrophs. The long-term impact of these environmental stresses reduced diversity and selected for generalist aquatic bacterial populations, such as Porphyrobacter. These changes at the community level occur at an ecological time scale, suggesting that under global warming scenarios cascade effects on the food web are possible if the microbial diversity is modified.

  6. Changes in the bacterial populations of the highly alkaline saline soil of the former lake Texcoco (Mexico) following flooding.

    PubMed

    Valenzuela-Encinas, César; Neria-González, Isabel; Alcántara-Hernández, Rocio J; Estrada-Alvarado, Isabel; Zavala-Díaz de la Serna, Francisco Javier; Dendooven, Luc; Marsch, Rodolfo

    2009-07-01

    Flooding an extreme alkaline-saline soil decreased alkalinity and salinity, which will change the bacterial populations. Bacterial 16S rDNA libraries were generated of three soils with different electrolytic conductivity (EC), i.e. soil with EC 1.7 dS m(-1) and pH 7.80 (LOW soil), with EC 56 dS m(-1) and pH 10.11 (MEDIUM soil) and with EC 159 dS m(-1) and pH 10.02 (HIGH soil), using universal bacterial oligonucleotide primers, and 463 clone 16S rDNA sequences were analyzed phylogenetically. Library proportions and clone identification of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Cyanobacteria, Bacteroidetes, Firmicutes and Cloroflexi showed that the bacterial communities were different. Species and genera of the Rhizobiales, Rhodobacterales and Xanthomonadales orders of the alpha- and gamma-subdivision of Proteobacteria were found at the three sites. Species and genera of the Rhodospirillales, Sphingobacteriales, Clostridiales, Oscillatoriales and Caldilineales were found only in the HIGH soil, Sphingomonadales, Burkholderiales and Pseudomonadales in the MEDIUM soil, Myxococcales in the LOW soil, and Actinomycetales in the MEDIUM and LOW soils. It was found that the largest diversity at the order and species level was found in the MEDIUM soil as bacteria of both the HIGH and LOW soils were found in it.

  7. Developmental dyslexia is characterized by the co-existence of visuospatial and phonological disorders in Chinese children.

    PubMed

    Siok, Wai Ting; Spinks, John A; Jin, Zhen; Tan, Li Hai

    2009-10-13

    Developmental dyslexia is a neurological condition that is characterized by severe impairment in reading skill acquisition in people with adequate intelligence and typical schooling. For English readers, reading impairment is critically associated with a phonological processing disorder, which may co-occur with an orthographic (visual word form) processing deficit, but not with a general visual processing dysfunction in most dyslexics. The pathophysiology of dyslexia varies across languages: for instance, unlike English, written Chinese maps visually intricate graphic forms (characters) onto meanings; pronunciation of Chinese characters must be rote memorized. This suggests that, in Chinese, a fine-grained visuospatial analysis must be performed to activate characters' phonology and meaning; consequently, disordered phonological processing may commonly co-exist with abnormal visuospatial processing in Chinese dyslexia. To test this hypothesis, we conducted an fMRI experiment in which 12 Chinese dyslexics, shown previously to exhibit a phonological disorder, performed a physical size judgment measuring visuospatial dimensions. Compared with 12 control subjects, the dyslexics showed weaker activations in left intraparietal sulcus (IPS) mediating visuospatial processing. Analyses of individual dyslexics' performances further suggest that developmental dyslexia in Chinese is commonly associated with the co-existence of a visuospatial deficit and a phonological disorder.

  8. Estimate of blow-up and relaxation time for self-gravitating Brownian particles and bacterial populations.

    PubMed

    Chavanis, P-H; Sire, C

    2004-08-01

    We determine an exact asymptotic expression of the blow-up time t(coll) for self-gravitating Brownian particles or bacterial populations (chemotaxis) close to the critical point in d=3. We show that t(coll) = t(*) (eta- eta(c) )(-1/2) with t(*) =0.917 677 02..., where eta represents the inverse temperature (for Brownian particles) or the mass (for bacterial colonies), and eta(c) is the critical value of eta above which the system blows up. This result is in perfect agreement with the numerical solution of the Smoluchowski-Poisson system. We also determine the exact asymptotic expression of the relaxation time close to but above the critical temperature and derive a large time asymptotic expansion for the density profile exactly at the critical point.

  9. Interspecific Relationships in Benthic Assemblages of a Large Lowland River : Co-existence or Competition as a Result of Habitat Characteristics

    NASA Astrophysics Data System (ADS)

    Akopian, M.; Usseglio-Polatera, P.

    2005-05-01

    Macrobenthic assemblages of the lower, regulated and canalized Marne River (France) are dominated by several "exotic", recently introduced species. Arrival, installation and spread of such alien species were certainly promoted by (1) the close connection between French and other European river systems (Rhine, Danube), (2) the modification of natural river flow and benthic habitats. Both habitat characteristics (e.g. granulometric composition, organic content) and corresponding benthic assemblage structure were analysed to identify the substrate affinity of major taxa in the lower Marne River. The main aim of the study was to evaluate the possible biotic interactions (i.e. competition for food and/or space) among dominant taxa as function of habitat features and to predict the future development of newly established species, already known as potential invaders: Corbicula fluminea (Bivalvia), Hypania invalida (Polychaeta), Chelicorophium curvispinum (Amphipoda), etc. Most of the newly established species, coming from the same biogeographical area ("invasional meltdown" hypothesis?), are eurytopic, with high fecundity and large food spectrum. First results demonstrated the co-existence of such species in the Marne River. But the future ecological importance of these organisms in benthic assemblages of the river depends on their present population size, population dynamics, and ability to colonize bottom substrates.

  10. Identification of Bacterial Populations in Drinking Water Using 16S rRNA-Based Sequence Analyses

    EPA Science Inventory

    Intracellular RNA is rapidly degraded in stressed cells and is more unstable outside of the cell than DNA. As a result, RNA-based methods have been suggested to study the active microbial fraction in environmental matrices. The aim of this study was to identify bacterial populati...

  11. Prevalence of gastrointestinal bacterial pathogens in a population of zoo animals.

    PubMed

    Stirling, J; Griffith, M; Blair, I; Cormican, M; Dooley, J S G; Goldsmith, C E; Glover, S G; Loughrey, A; Lowery, C J; Matsuda, M; McClurg, R; McCorry, K; McDowell, D; McMahon, A; Cherie Millar, B; Nagano, Y; Rao, J R; Rooney, P J; Smyth, M; Snelling, W J; Xu, J; Moore, J E

    2008-04-01

    Faecal prevalence of gastrointestinal bacterial pathogens, including Campylobacter, Escherichia coli O157:H7, Salmonella, Shigella, Yersinia, as well as Arcobacter, were examined in 317 faecal specimens from 44 animal species in Belfast Zoological Gardens, during July-September 2006. Thermophilic campylobacters including Campylobacter jejuni, Campylobacter coli and Campylobacter lari, were the most frequently isolated pathogens, where members of this genus were isolated from 11 animal species (11 of 44; 25%). Yersinia spp. were isolated from seven animal species (seven of 44; 15.9%) and included, Yersinia enterocolitica (five of seven isolates; 71.4%) and one isolate each of Yersinia frederiksenii and Yersinia kristensenii. Only one isolate of Salmonella was obtained throughout the entire study, which was an isolate of Salmonella dublin (O 1,9,12: H g, p), originating from tiger faeces after enrichment. None of the animal species found in public contact areas of the zoo were positive for any gastrointestinal bacterial pathogens. Also, water from the lake in the centre of the grounds, was examined for the same bacterial pathogens and was found to contain C. jejuni. This study is the first report on the isolation of a number of important bacterial pathogens from a variety of novel host species, C. jejuni from the red kangaroo (Macropus rufus), C. lari from a maned wolf (Chrysocyon brachyurus), Y. kristensenii from a vicugna (Vicugna vicugna) and Y. enterocolitica from a maned wolf and red panda (Ailurus fulgens). In conclusion, this study demonstrated that the faeces of animals in public contact areas of the zoo were not positive for the bacterial gastrointestinal pathogens examined. This is reassuring for the public health of visitors, particularly children, who enjoy this educational and recreational resource.

  12. Characterization of methanotrophic bacterial populations in natural and agricultural aerobic soils of the European Russia

    NASA Astrophysics Data System (ADS)

    Kravchenko, Irina; Sukhacheva, Marina; Kizilova, Anna

    2014-05-01

    Atmospheric methane contributes to about 20% of the total radiative forcing by long-lived greenhouse gases, and microbial methane oxidation in upland soils is the only biological sink of methane. Microbial methane oxidation in aerated upland soils is estimated as 15 - 45 Tg yr-1 or 3-9% of the annual sink. Therefore there is need of extensive research to characterize methanotrophic activity in various ecosystems for possible application to reduce atmospheric methane fluxes and to minimize global climate change. The vast majority of known aerobic methanotrophs belongs to the Proteobacteria and placed in the families Methylococcaceae in the Gammaproteobacteria, and Methylocystaceae and Beijerinckiaceae in the Alphaproteobacteria. Known exceptions include the phylum Verrucomicrobia and uncultured methanotrophs such as Candidatus 'Methylomirabilis oxyfera' affiliated with the 'NC10' phylum. Plenty of studies of aerobic methane oxidation and key players of the process have been performed on various types of soils, and it was found that Methylocystis spp and uncultivated methanotrophs are abundant in upland soils. Two of the uncultured groups are upland soil cluster alphaproteobacteria (USCa) and gammaproteobacteria (USCg), as revealed by cultivation-independent surveys of pmoA diversity. Russia is extremely rich in soil types due to its vast territories, and most of these soils have never been investigated from the aspect of methanotrophy. This study addresses methane oxidation activity and diversity of aerobic methanotrophic bacteria in eight types of natural aerobic soils, four of which also had been under agricultural use. Methane fluxes have been measured by in situ static chamber method and methane oxidation rates in soil samples - by radioisotope tracer (14CH4) technique. Changes in methanotroph diversity and abundance were assessed by cloning and Sanger sequencing, and quantitative real-time PCR of pmoA genes. Methanotrophic population of unmanaged soils turned

  13. Effect of dietary supplementation of bacteriophage on performance, egg quality and caecal bacterial populations in laying hens.

    PubMed

    Kim, J H; Kim, J W; Shin, H S; Kim, M C; Lee, J H; Kim, G-B; Kil, D Y

    2015-01-01

    1. Bacteriophages (BP) have gained increasing attention as a treatment of bacterial infection for animals. However, the data pertaining to dietary application of BP for laying hens have been limited. 2. This study aimed to investigate the effect of dietary BP on laying performance, egg quality and caecal bacterial populations in laying hens. 3. The dietary BP used in this experiment was a mixture of individual BP targeting Salmonella gallinarum, Salmonella pullorum, Salmonella typhimurium, Salmonella enteritidis, Salmonella derby and Staphylococcus aureus. 4. A total of 360 Hy-Line Brown laying hens of 32 weeks of age were allotted to one of three dietary treatments with 6 replicates in a completely randomised design. The basal diet was prepared, and 0.4 or 0.8 g/kg BP mixture was supplemented to the basal diet. Diets were fed to hens for 8 weeks. 5. Laying performance and egg quality were not affected by dietary treatments. As inclusion levels of BP mixture in diets were increased, the DNA copy numbers for Salmonella spp. in the caecal contents decreased linearly, whereas the DNA copy numbers for Escherichia coli in the caecal contents increased linearly. 6. Results indicate that dietary supplementation of BP mixture decreases the target Salmonella spp. populations but increases Escherichia coli populations in the gastrointestinal tract of laying hens with little impact on laying performance and egg quality.

  14. Effect of dietary probiotic, prebiotic and synbiotic supplementation on performance, immune responses, intestinal morphology and bacterial populations in broilers.

    PubMed

    Salehimanesh, A; Mohammadi, M; Roostaei-Ali Mehr, M

    2016-08-01

    This study was conducted to investigate the effects of probiotic (Primalac), prebiotic (TechnoMos) and synbiotic (Primalac + TechnoMos) supplementation on performance, immune responses, intestinal morphology and bacterial populations of ileum in broilers. A total of 240 one-day-old broiler chicks were randomly divided into four treatment groups which included 60 birds. Control group did not receive any treatment. The chicks in the second, third and fourth groups were fed probiotic (0.9 g/kg), prebiotic (0.9 g/kg) and probiotic (0.9 g/kg) plus probiotic (0.9 g/kg; synbiotic), respectively, at entire period. Daily feed intake, daily weight gain and feed conversion ratio were evaluated. The birds were immunized by sheep red blood cell (SRBC) on days 12 and 29 of age and serum antibody titres were measured on days 28, 35 and 42. Newcastle vaccines administered on days 9, 18 and 27 to chicks and blood samples were collected on day 42. Intestinal morphometric assessment and enumeration of intestinal bacterial populations were performed on day 42. The results indicated that consumption of probiotic, prebiotic and synbiotic had no significant effect on daily feed intake, daily body weight gain, feed conversion ratio, carcass traits, intestinal morphology and bacterial populations of ileum (p > 0.05). Consumption of prebiotic increased total and IgM anti-SRBC titres on days 28 and 42 and antibody titre against Newcastle virus disease on day 42 (p < 0.05). Synbiotic increased only total anti-SRBC on day 28 (p < 0.05). It is concluded that consumption of prebiotic increased humoral immunity in broilers. Therefore, supplementation of diet with prebiotic for improvement of humoral immune responses is superior to synbiotic supplementation. PMID:26847817

  15. Bacterial antibiotic resistance studies using in vitro dynamic models: Population analysis vs. susceptibility testing as endpoints of mutant enrichment.

    PubMed

    Firsov, Alexander A; Strukova, Elena N; Portnoy, Yury A; Shlykova, Darya S; Zinner, Stephen H

    2015-09-01

    Emergence of bacterial antibiotic resistance is usually characterised either by population analysis or susceptibility testing. To compare these endpoints in their ability to demonstrate clear relationships with the ratio of 24-h area under the concentration-time curve (AUC24) to the minimum inhibitory concentration (MIC), enrichment of ciprofloxacin-resistant mutants of four clinical isolates of Pseudomonas aeruginosa was studied in an in vitro dynamic model that simulates mono-exponential pharmacokinetics of ciprofloxacin over a wide range of the AUC24/MIC ratios. Each organism was exposed to twice-daily ciprofloxacin for 3 days. Amplification of resistant mutants was monitored by plating on media with 2×, 4×, 8× and 16× MIC of ciprofloxacin. Population analysis data were expressed by the area under the bacterial mutant concentration-time curve (AUBCM). Changes in P. aeruginosa susceptibility were examined by daily MIC determinations. To account for the different susceptibilities of P. aeruginosa strains, post-exposure MICs (MICfinal) were related to the MICs determined with the starting inoculum (MICinitial). For each organism, AUC24/MIC relationships both with AUBCM and MICfinal/MICinitial were bell-shaped, but the latter were more strain-specific than the former. Using combined data on all four isolates, AUBCM showed a better correlation than MICfinal/MICinitial (r(2)=0.75 vs. r(2)=0.53). The shift of MICfinal/MICinitial relative to AUBCM vs. AUC24/MIC curves resulted in a weak correlation between AUBCM and MICfinal/MICinitial (r(2)=0.41). These data suggest that population analysis is preferable to susceptibility testing in bacterial resistance studies and that these endpoints should not be considered interchangeable.

  16. Transperitoneal repair of a juxtarenal abdominal aortic aneurysm and co-existent horseshoe kidney with division of the renal isthmus.

    PubMed

    Hajibandeh, Shahin; Hajibandeh, Shahab; Johnpulle, Michelle; Perricone, Vittorio

    2015-01-01

    The co-existence of abdominal aortic aneurysm (AAA) and horseshoe kidney (HSK) is rare. We report a 67-year-old man with an expanding juxtarenal AAA associated with a HSK. The aneurysm had a severely angulated neck and contained a significant amount of mural thrombus. The isthmus of HSK closely lied over the aneurysm, making its exposure extremely difficult. The aneurysm was successfully repaired using transperitoneal approach with division of the renal isthmus and without any need for the renal artery reconstruction. Despite the potential complications, particularly renal insufficiency, associated with division of the renal isthmus and suprarenal cross-clamping of the abdominal aorta, in our case, post-operative period was uneventful and the patient's recovery was satisfactory. PMID:26511935

  17. Effect of co-existing copper and calcium on the removal of As(V) by reused aluminum oxides.

    PubMed

    Yang, J K; Park, Y J; Kim, K H; Lee, H Y; Min, K C; Lee, S M

    2013-01-01

    Among the various heavy metals, arsenic is frequently found in abandoned mine drainage and the environmental fate of arsenic in real aqueous solutions can be highly dependent on the presence of co-existing ions. In this study, removal of arsenate through adsorption on the reused aluminum oxide or through precipitation was investigated in a single and in a binary system as a function of pH and concentration. Different removal behaviors of arsenate were observed in the presence of different cations as well as a variation of the molar ratios of arsenate to cations. Co-operative effects on arsenate removal by precipitation in solution occurred with an increase of copper concentration, while a decrease of arsenate removal resulted in increasing calcium concentration. It was observed that the arsenate removal in the presence of calcium would be highly dependent on the molar ratios of both elements. PMID:23128638

  18. In-situ synthesis of Au nano particles of co-existing morphologies in liquid crystalline matrix

    NASA Astrophysics Data System (ADS)

    Dan, Kaustabh; Datta, Alokmay

    2015-06-01

    The present study describes the in-situ synthesis of Au nano particles (Au-NP) in the room temperature nematic liquid crystalline (LC) substance MBBA (N-4 methoxybenzylidene 4 butylaniline) without any external reducing or stabilizing agents. UV-Visible absorption and fluorescence spectroscopy clearly show formation of Au-NP within the LC matrix through the plasmon resonance peak for the NPs and EDAX measurements confirm this formation. Transmission electron Microscopy shows co-existence of spherical and prismatic NPs. FTIR spectroscopy shows a considerable shift in the C=N stretch band pointing to the location of the growth centre of the NPs. Polarization microscopy data indicates a definite phase ordering and texture transformation from Nematic to highly ordered smectic mesophase.

  19. In-situ synthesis of Au nano particles of co-existing morphologies in liquid crystalline matrix

    SciTech Connect

    Dan, Kaustabh Datta, Alokmay

    2015-06-24

    The present study describes the in-situ synthesis of Au nano particles (Au-NP) in the room temperature nematic liquid crystalline (LC) substance MBBA (N-4 methoxybenzylidene 4 butylaniline) without any external reducing or stabilizing agents. UV-Visible absorption and fluorescence spectroscopy clearly show formation of Au-NP within the LC matrix through the plasmon resonance peak for the NPs and EDAX measurements confirm this formation. Transmission electron Microscopy shows co-existence of spherical and prismatic NPs. FTIR spectroscopy shows a considerable shift in the C=N stretch band pointing to the location of the growth centre of the NPs. Polarization microscopy data indicates a definite phase ordering and texture transformation from Nematic to highly ordered smectic mesophase.

  20. Bayesian risk maps for Schistosoma mansoni and hookworm mono-infections in a setting where both parasites co-exist.

    PubMed

    Raso, Giovanna; Vounatsou, Penelope; McManus, Donald P; Utzinger, Jürg

    2007-11-01

    There is growing interest in the use of Bayesian geostatistical models for predicting the spatial distribution of parasitic infections, including hookworm, Schistosoma mansoni and co-infections with both parasites. The aim of this study was to predict the spatial distribution of mono-infections with either hookworm or S. mansoni in a setting where both parasites co-exist. School-based cross-sectional parasitological and questionnaire surveys were carried out in 57 rural schools in the Man region, western Côte d'Ivoire. A single stool specimen was obtained from each schoolchild attending grades 3-5. Stool specimens were processed by the Kato-Katz technique and an ether concentration method and examined for the presence of hookworm and S. mansoni eggs. The combined results from the two diagnostic approaches were considered for the infection status of each child. Demographic data (i.e. age and sex) were obtained from readily available school registries. Each child's socio-economic status was estimated, using the questionnaire data following a household-based asset approach. Environmental data were extracted from satellite imagery. The different data sources were incorporated into a geographical information system. Finally, a Bayesian spatial multinomial regression model was constructed and the spatial patterns of S. mansoni and hookworm mono-infections were investigated using Bayesian kriging. Our approach facilitated the production of smooth risk maps for hookworm and S. mansoni mono-infections that can be utilized for targeting control interventions. We argue that in settings where S. mansoni and hookworm co-exist and control efforts are under way, there is a need for both mono- and co-infection risk maps to enhance the cost-effectiveness of control programmes.

  1. Assessment of co-existence of Helicobacter pylori and Candida fungi in diseases of the upper gastrointestinal tract.

    PubMed

    Karczewska, E; Wojtas, I; Sito, E; Trojanowska, D; Budak, A; Zwolinska-Wcislo, M; Wilk, A

    2009-12-01

    Candida spp. were found in the gastric mucosa of 27 (17%) patients, out of whom 18 (11%) showed co-existence of the fungi with H. pylori. Analysis of relationship between selected disorders of the upper gastrointestinal tract (non ulcer dyspepsia NUD, gastric ulcer, duodenal ulcer) and infection with H. pylori and/or Candida revealed a link between co-existence of H. pylori with Candida and gastric ulcers suggesting synergism of those microorganism in pathogenesis of the disease. On the contrary, according to quantitative studies performed, the fungi alone do not play a significant role in pathogenesis of the above mentioned disorders as they colonize only epithelium to the extent that is not pathologically significant (<10(3) CFU/ml). Genetical study was carried out on 57 Helicobacter pylori strains isolated from bioptates of the gastric mucosa. The genotypes of the strains (gene cagA and alleles of gene vacA - m1, m2, s1, s2) were determined using the PCR technique. As it was shown, the patients infected with H. pylori strains of genotype cagA+, vacA s1 are exposed to higher risk of peptic ulcer disease (PUD) as compared to the patients infected with cagA-, vacA s2 strains. In the case of the NUD patients a correlation with allele m2 was found only (p<0.001). This may suggest that in future some of the NUD patients infected with cagA+, vacA s1 strains will fall into the group at higher risk for PUD.

  2. The effect of wheat prebiotics on the gut bacterial population and iron status of iron deficient broiler chickens

    PubMed Central

    2014-01-01

    Background Currently, there is a lot of interest in improving gut health, and consequently increasing Fe absorption, by managing the colonic microbial population. This is traditionally done by the consumption of probiotics, live microbial food supplements. However, an alternative, and often very effective approach, is the consumption of food ingredients known as prebiotics. Fructans and arabinoxylans are naturally occurring non-digestible oligosaccharides in wheat that exhibit prebiotic properties and may enhance intestinal iron (Fe) absorption. The aim of this study was to assess the effect of prebiotics from wheat on Fe bioavailability in vitro (Caco-2 cells) and in vivo (broiler chickens, Gallus gallus). Methods In the current study, the effect of intra-amniotic administration of wheat samples extracts at 17 d of embryonic incubation on the Fe status and possible changes in the bacterial population in intestinal content of broiler hatchlings were investigated. A group of 144 eggs were injected with the specified solution (1 ml per egg) into the amniotic fluid. Immediately after hatch (21 d) and from each treatment group, 10 chicks were euthanized and their small intestine, liver and cecum were removed for relative mRNA abundance of intestinal Fe related transporters, relative liver ferritin amounts and bacterial analysis of cecal content, respectively. Results The in vivo results are in agreement with the in vitro observations, showing no differences in the hatchling Fe status between the treatment groups, as Fe bioavailability was not increased in vitro and no significant differences were measured in the intestinal expression of DMT1, Ferroportin and DcytB in vivo. However, there was significant variation in relative amounts of bifidobacteria and lactobacilli in the intestinal content between the treatments groups, with generally more bifidobacteria being produced with increased prebiotic content. Conclusions In this study we showed that prebiotics naturally

  3. Population Density Modulates Drug Inhibition and Gives Rise to Potential Bistability of Treatment Outcomes for Bacterial Infections

    PubMed Central

    Maltas, Jeff; Brumm, Peter; Wood, Kevin B.

    2016-01-01

    The inoculum effect (IE) is an increase in the minimum inhibitory concentration (MIC) of an antibiotic as a function of the initial size of a microbial population. The IE has been observed in a wide range of bacteria, implying that antibiotic efficacy may depend on population density. Such density dependence could have dramatic effects on bacterial population dynamics and potential treatment strategies, but explicit measures of per capita growth as a function of density are generally not available. Instead, the IE measures MIC as a function of initial population size, and population density changes by many orders of magnitude on the timescale of the experiment. Therefore, the functional relationship between population density and antibiotic inhibition is generally not known, leaving many questions about the impact of the IE on different treatment strategies unanswered. To address these questions, here we directly measured real-time per capita growth of Enterococcus faecalis populations exposed to antibiotic at fixed population densities using multiplexed computer-automated culture devices. We show that density-dependent growth inhibition is pervasive for commonly used antibiotics, with some drugs showing increased inhibition and others decreased inhibition at high densities. For several drugs, the density dependence is mediated by changes in extracellular pH, a community-level phenomenon not previously linked with the IE. Using a simple mathematical model, we demonstrate how this density dependence can modulate population dynamics in constant drug environments. Then, we illustrate how time-dependent dosing strategies can mitigate the negative effects of density-dependence. Finally, we show that these density effects lead to bistable treatment outcomes for a wide range of antibiotic concentrations in a pharmacological model of antibiotic treatment. As a result, infections exceeding a critical density often survive otherwise effective treatments. PMID:27764095

  4. Characterization of the major bacterial-fungal populations colonizing dandruff scalps in Shanghai, China, shows microbial disequilibrium.

    PubMed

    Wang, Lili; Clavaud, Cécile; Bar-Hen, Avner; Cui, Meng; Gao, Jun; Liu, Yuanyuan; Liu, Chen; Shibagaki, Nakako; Guéniche, Audrey; Jourdain, Roland; Lan, Ke; Zhang, Chiyu; Altmeyer, Ralf; Breton, Lionel

    2015-05-01

    Dandruff is a scalp disorder characterized by the formation of flaky white-yellowish scales due to an altered proliferation and differentiation status; a disrupted barrier function; a decrease in the level of hydration and of natural moisturizing factors (NMF) in the scalp, with a persistent and relapsing inflammatory condition. It was recently reported that an imbalance between bacterial and fungal species colonizing the scalp of French volunteers was associated with dandruff condition. The purpose of the present study was to analyze the major bacterial and fungal species present on the scalp surface of Chinese volunteers and to investigate possible region-related variation in the microbiota linked to dandruff condition. The data obtained from the Chinese populations were highly similar to those obtained in France, confirming that dandruff scalps are associated with a higher incidence of Malassezia restricta and Staphylococcal sp. The ratios of Malassezia to Propionibacterium and Propionibacterium to Staphylococcus were also significantly higher in the dandruff volunteers as compared to normal volunteers, suggesting that equilibrium between the major bacterial and fungal taxa found on the normal scalps is perturbed in the dandruff scalps. The main difference between the French and Shanghai subjects was in their Staphylococcal biota. The results obtained in China and in France suggest that targeting one particular Malassezia sp. by antifungals instead of using large spectrum antifungals and rebalancing the dandruff scalp microbiota could be common approach to improve dandruff condition in the two countries. PMID:25739873

  5. Bacterial population and biodegradation potential in chronically crude oil-contaminated marine sediments are strongly linked to temperature

    PubMed Central

    Bargiela, Rafael; Mapelli, Francesca; Rojo, David; Chouaia, Bessem; Tornés, Jesús; Borin, Sara; Richter, Michael; Del Pozo, Mercedes V.; Cappello, Simone; Gertler, Christoph; Genovese, María; Denaro, Renata; Martínez-Martínez, Mónica; Fodelianakis, Stilianos; Amer, Ranya A.; Bigazzi, David; Han, Xifang; Chen, Jianwei; Chernikova, Tatyana N.; Golyshina, Olga V.; Mahjoubi, Mouna; Jaouanil, Atef; Benzha, Fatima; Magagnini, Mirko; Hussein, Emad; Al-Horani, Fuad; Cherif, Ameur; Blaghen, Mohamed; Abdel-Fattah, Yasser R.; Kalogerakis, Nicolas; Barbas, Coral; Malkawi, Hanan I.; Golyshin, Peter N.; Yakimov, Michail M.; Daffonchio, Daniele; Ferrer, Manuel

    2015-01-01

    Two of the largest crude oil-polluted areas in the world are the semi-enclosed Mediterranean and Red Seas, but the effect of chronic pollution remains incompletely understood on a large scale. We compared the influence of environmental and geographical constraints and anthropogenic forces (hydrocarbon input) on bacterial communities in eight geographically separated oil-polluted sites along the coastlines of the Mediterranean and Red Seas. The differences in community compositions and their biodegradation potential were primarily associated (P < 0.05) with both temperature and chemical diversity. Furthermore, we observed a link between temperature and chemical and biological diversity that was stronger in chronically polluted sites than in pristine ones where accidental oil spills occurred. We propose that low temperature increases bacterial richness while decreasing catabolic diversity and that chronic pollution promotes catabolic diversification. Our results further suggest that the bacterial populations in chronically polluted sites may respond more promptly in degrading petroleum after accidental oil spills. PMID:26119183

  6. Effects of premilking udder preparation on bacterial population, sediment, and iodine residue in milk.

    PubMed

    Galton, D M; Petersson, L G; Merrill, W G; Bandler, D K; Shuster, D E

    1984-11-01

    Udder preparations that wet both udder surfaces and teats had the highest standard plate count in milk compared with methods that wet teats only. Physical action of cleaning teats with a dry towel lowered bacterial count compared with preparations wetting both udder surfaces and teats. Methods resulting in lowest bacterial counts were the use of water hose, wet towel, or premilking disinfectant teat dip followed by drying with paper towels. Counts of coliform and Staphylococcus sp. followed similar trends. In most comparisons, addition of udder wash sanitizer was of marginal or no benefit. Standard plate count of teat rinses after udder preparation confirmed the benefit of cleaning and drying teats. Physical manipulation of teats during cleaning was essential for lowering sediment in milk. Drying of teats with a paper towel for at least 10 s after dipping with a 1% iodophor disinfectant dip was essential for reducing iodine residue. Both premilking and postmilking disinfectant teat dipping with a 1% iodophor teat dip caused higher iodine residue in milk than premilking disinfectant dip with subsequent drying. A .5% iodophor teat dip contributed less iodine in milk than a 1% iodophor teat dip. Premilking udder preparation affects bacterial count, sediment, and iodine residue in milk. PMID:6520268

  7. Phylogenetic analysis of bacterial populations in waters of the former Texcoco Lake, Mexico.

    PubMed

    Jan-Roblero, Janet; Magos, Xochitl; Fernández, Luis; Hernández-Rodríguez, César; Le Borgne, Sylvie

    2004-12-01

    Molecular techniques were used to compare the compositions of the bacterial communities of the 2 following lagoons from the former soda Texcoco Lake, Mexico: the restored Facultativa lagoon and the Nabor Carrillo lagoon. Ribosomal intergenic spacer analysis (RISA) revealed that bacterial communities of the 2 lagoons were different and presented a relatively low diversity. Clone libraries of 16S rDNA genes were constructed, and significant phylotypes were distinguished by restriction fragment length polymorphism (RFLP). A representative clone from each phylotype was partially sequenced. Molecular identification and phylogenetic analyses based on ribosomal sequences revealed that the Facultativa lagoon harbored mainly gamma- and beta-Proteobacteria, low G+C Gram-positive bacteria, and several members of the Halobacteriaceae family of archaea. The Nabor Carrillo lagoon mainly included typical halophilic and alkaliphilic low G+C Gram-positive bacteria, gamma-Proteobacteria, and beta-Proteobacteria similar to those found in other soda lakes. Several probably noncultured new bacterial species were detected. Three strains were isolated from the Nabor Carrillo lagoon, their partial 16S rDNA sequences were obtained. On this basis, they were identified as Halomonas magadiensis (H1), Halomonas eurihalina (H2), and Staphylococcus sciuri (H3). This is the first study that uses molecular techniques to investigate potential genetic diversity in the Texcoco lakes. In this preliminary evaluation, we infer the presence of alkalophilic, halophilic, or haloalkaliphilic bacteria potentially useful for biotechnology.

  8. Usefulness of inflammatory biomarkers in discriminating between bacterial and aseptic meningitis in hospitalized children from a population with low vaccination coverage

    PubMed Central

    Wysocki, Jacek; Avonts, Dirk; Januszkiewicz-Lewandowska, Danuta; Michalak, Michal

    2016-01-01

    Introduction Neisseria meningitidis and Streptococcus pneumoniae are the most frequent pathogens responsible for meningitis beyond the neonatal period. Aseptic meningitis is a disabling condition, but bacterial meningitis if left untreated is 100% fatal. The aim of the study was to analyze the usefulness of biochemical and hematological parameters in distinguishing between bacterial and non-bacterial meningitis in children with meningitis from a population with low rates of vaccination against S. pneumoniae and N. meningitidis. Material and methods This study is a retrospective chart review of children hospitalized with meningitis. In patients with aseptic and bacterial meningitis the following parameters were compared: C-reactive protein, D-dimers, fibrinogen, glucose level, and leukocyte level, and in cerebrospinal fluid, protein, glucose, and leukocyte concentrations were analyzed. Number of points in the Bacterial Meningitis Score (BMS) was calculated. The predictive value of each parameter to distinguish between bacterial and aseptic meningitis was evaluated. Results In total, 129 patients were included in the study: 65 diagnosed with bacterial meningitis and 64 with aseptic meningitis. Bacterial and aseptic meningitis were statistically significantly different based on each analyzed parameter (p < 0.000001). Among children with aseptic meningitis 42 (66%) scored 0 points in the BMS, while all the children with bacterial meningitis had at least one point. Conclusions In children with meningitis inflammatory biomarkers differ statistically significantly depending on the etiology – bacterial or aseptic. Serum concentration of C-reactive protein higher than 80 mg/dl is a useful marker of bacterial etiology of meningitis. A high Bacterial Meningitis Score is indicative for bacterial meningitis. PMID:27186188

  9. Evolution in an Afternoon: Rapid Natural Selection and Adaptation of Bacterial Populations

    ERIC Educational Resources Information Center

    Delpech, Roger

    2009-01-01

    This paper describes a simple, rapid and low-cost technique for growing bacteria (or other microbes) in an environmental gradient, in order to determine the tolerance of the microbial population to varying concentrations of sodium chloride ions, and suggests how the evolutionary response of a microbial population to the selection pressure of the…

  10. Correlations between bacterial populations and process parameters in four full-scale anaerobic digesters treating sewage sludge.

    PubMed

    Shin, Seung Gu; Koo, Taewoan; Lee, Joonyeob; Han, Gyuseong; Cho, Kyungjin; Kim, Woong; Hwang, Seokhwan

    2016-08-01

    Process parameters and bacterial populations were investigated in four full-scale anaerobic digesters treating sewage sludge. Although the four digesters were operated under similar conditions, digesters A and B had higher pH (7.2-7.4) and lipid removal efficiencies (>50%) than C and D (pH 6.1-6.4; average lipid removal <16%). Bacterial richness, diversity, and evenness were higher in digesters C and D. Among the top-populated genera, ten (group I) were more abundant in digesters A and/or B; they were putative syntrophic fatty acid or protein/amino acid-utilizers. In contrast, fifteen others (group II) were less abundant in A and/or B and included potentially dormant/dead cells originated from activated sludge. Despite the overall richness trend, the presence of the 25 genera in groups I/II was greater in digesters A and B (24) than in C and D (17); this observation suggests that group I bacteria might be essential in AD of sewage sludge.

  11. Seasonal effects of heat shock on bacterial populations, including artificial Vibrio parahaemolyticus exposure, in the Pacific oyster, Crassostrea gigas.

    PubMed

    Aagesen, Alisha M; Häse, Claudia C

    2014-04-01

    During the warmer summer months, oysters are conditioned to spawn, resulting in massive physiological efforts for gamete production. Moreover, the higher temperatures during the summer typically result in increased bacteria populations in oysters. We hypothesized that these animals are under multiple stresses that lead to possible immune system impairments during the summer months that can possibly lead to death. Here we show that in the summer and the fall animals exposed to a short heat stress respond similarly, resulting in a general trend of more bacteria being found in heat shocked animals than their non-heat shocked counterparts. We also show that naturally occurring bacterial populations are effected by a heat shock. In addition, oysters artificially contaminated with Vibrio parahaemolyticus were also affected by a heat shock. Heat shocked animals contained higher concentrations of V. parahaemolyticus in their tissues and hemolymph than control animals and this was consistent for animals examined during summer and fall. Finally, oyster hemocyte interactions with V. parahaemolyticus differed based on the time of the year. Overall, these findings demonstrate that seasonal changes and/or a short heat shock is sufficient to impact bacterial retention, particularly V. parahaemolyticus, in oysters and this line of research might lead to important considerations for animal harvesting procedures.

  12. Frequency of genes in aromatic and aliphatic hydrocarbon biodegradation pathways within bacterial populations from Alaskan sediments.

    PubMed

    Sotsky, J B; Greer, C W; Atlas, R M

    1994-11-01

    A significant proportion of the naturally occurring hydrocarbon-degrading populations within Alaskan sediments affected by the Exxon Valdez oil spill had both the xylE and alkB genes and could convert hexadecane and naphthalene to carbon dioxide; a greater proportion of the population had xylE than had alkB, reflecting the composition of the residual oil at the time of sampling; nearly equal populations with xylE alone, alkB alone, and xylE + alkB genes together were found after exposure to fresh crude oil; populations with xylE lacking alkB increased after enrichment on naphthalene. Thus, the genotypes of hydrocarbon-degrading populations reflected the composition of the hydrocarbons to which they were exposed. PMID:7804909

  13. Improved Statistical Analysis of Low Abundance Phenomena in Bimodal Bacterial Populations

    PubMed Central

    Reinhard, Friedrich; van der Meer, Jan Roelof

    2013-01-01

    Accurate detection of subpopulation size determinations in bimodal populations remains problematic yet it represents a powerful way by which cellular heterogeneity under different environmental conditions can be compared. So far, most studies have relied on qualitative descriptions of population distribution patterns, on population-independent descriptors, or on arbitrary placement of thresholds distinguishing biological ON from OFF states. We found that all these methods fall short of accurately describing small population sizes in bimodal populations. Here we propose a simple, statistics-based method for the analysis of small subpopulation sizes for use in the free software environment R and test this method on real as well as simulated data. Four so-called population splitting methods were designed with different algorithms that can estimate subpopulation sizes from bimodal populations. All four methods proved more precise than previously used methods when analyzing subpopulation sizes of transfer competent cells arising in populations of the bacterium Pseudomonas knackmussii B13. The methods’ resolving powers were further explored by bootstrapping and simulations. Two of the methods were not severely limited by the proportions of subpopulations they could estimate correctly, but the two others only allowed accurate subpopulation quantification when this amounted to less than 25% of the total population. In contrast, only one method was still sufficiently accurate with subpopulations smaller than 1% of the total population. This study proposes a number of rational approximations to quantifying small subpopulations and offers an easy-to-use protocol for their implementation in the open source statistical software environment R. PMID:24205184

  14. Bacterial populations as perfect gases: genomic integrity and diversification tensions in Helicobacter pylori.

    PubMed

    Kang, Josephine; Blaser, Martin J

    2006-11-01

    Microorganisms that persist in single hosts face particular challenges. Helicobacter pylori, an obligate bacterial parasite of the human stomach, has evolved a lifestyle that features interstrain competition and intraspecies cooperation, both of which involve horizontal gene transfer. Microbial species must maintain genomic integrity, yet H. pylori has evolved a complex nonlinear system for diversification that exists in dynamic tension with the mechanisms for ensuring fidelity. Here, we review these tensions and propose that they create a dynamic pool of genetic variants that is sufficiently genetically diverse to allow H. pylori to occupy all of the potential niches in the stomach. PMID:17041630

  15. Studies of bacterial populations in the kitchens of the University of Papua New Guinea.

    PubMed

    Price, T V

    1979-12-01

    Washed cups, plates, forks, knives, spoons, utensils and table surfaces in the kitchens of the University of Papua New Guinea were assayed for total and coliform bacteria in 1976 and 1977. The total bacterial count per item for crockery and cutlery exceeded the desired limit by five to 6400 times, whilst the count for utensils was also exceeded by over 100 times in both years. Coliform and E. coli. were detected in all samples. Improper hygiene by kitchen staff and a lack of sufficient hot water were mainly responsible for the high counts. Recommendations are given for catering establishments.

  16. Biogeochemical controls on the bacterial populations in the eastern Atlantic Ocean

    NASA Astrophysics Data System (ADS)

    Neogi, S. B.; Koch, B. P.; Schmitt-Kopplin, P.; Pohl, C.; Kattner, G.; Yamasaki, S.; Lara, R. J.

    2011-12-01

    Little is known about bacterial dynamics in the oligotrophic ocean, particularly about cultivable bacteria. We examined the abundance of total and cultivable bacteria in relation to changes in biogeochemical conditions in the eastern Atlantic Ocean with special regard to Vibrio spp., a group of bacteria that can cause diseases in human and aquatic organisms. Surface, deep water and plankton (<20 μm, 20-55 μm and >55 μm) samples were collected between 50° N and 24° S. Chlorophyll-a was very low (<0.3 μg l-1) in most areas of the nutrient-poor Atlantic, except at a few locations near upwelling regions. In surface water, dissolved organic carbon (DOC) and nitrogen (DON) concentrations were 64-95 μM C and 2-10 μM N accounting for ≥90 % and ≥76 % of total organic C and N, respectively. DOC and DON gradually decreased to ~45 μM C and <5 μM N in the bottom water. In the surface layer, culture independent total bacteria and other prokaryotes represented by 4´-6-diamidino-2-phenylindole (DAPI) counts, ranged mostly between 107 and 108 cells l-1, while cultivable bacterial counts (CBC) and Vibrio spp. were found at concentrations of 104-107 and 102-105 colony forming units (CFU) l-1, respectively. Most bacteria (>99 %) were found in the nanoplankton fraction (<20 μm), however, bacterial abundance did not correlate with suspended particulates (chlorophyll-a, particulate organic C [POC] and N [PON]). Instead, we found a highly significant correlation between bacterial abundance and temperature (p < 0.001) and a significant correlation with DOC and DON (p < 0.005 and <0.01, respectively). In comparison to CBC and DAPI-stained prokaryotes, cultivable Vibrio showed a stronger and highly significant correlation with DOC and DON (p < 0.0005 and p < 0.005, respectively). In cold waters of the mesopelagic and abyssal zones, CBC was 50 to 100-times lower than in the surface layer; however, cultivable Vibrio spp. could be isolated from the bathypelagic zone and even

  17. Co-existence of PHF6 and NOTCH1 mutations in adult T-cell acute lymphoblastic leukemia

    PubMed Central

    LI, MIN; XIAO, LICHAN; XU, JINGYAN; ZHANG, RUN; GUO, JINGJING; OLSON, JUSTIN; WU, YUJIE; LI, JIANYONG; SONG, CHUNHUA; GE, ZHENG

    2016-01-01

    T-cell acute lymphoblastic leukemia (T-ALL) results from the collaboration of multiple genetic abnormalities in the transformation of T-cell progenitors. Plant homeodomain finger protein 6 (PHF6) has recently been established as a key tumor suppressor, which is mutated in T-ALL; however, the clinical significance of PHF6 mutations has not been fully determined in adult T-ALL. In the present study, amplification of the PHF6 exons was performed, followed by DNA sequencing to identify the genomic mutations and examine the expression of PHF6 in adult patients with T-ALL. The correlation between PHF6 mutations and clinical features was also analyzed using a χ2 test, and between PHF6 mutations and survival curve using the Kaplan-Meier methods. PHF6 mutations were detected in 27.1% of the Chinese adults with T-ALL (16/59), 10 of which were found to be novel mutations. A significantly lower expression level of PHF6 was observed in T-ALL patients with PHF6 mutations compared with those without mutations. Of the observed mutations in PHF6, 6/16 were frame-shift mutations, indicating a PHF6 dysfunction in those patients. Of note, PHF6 mutations were found to be significantly associated with older age, lower hemoglobin levels, higher frequency of CD13 positivity and higher incidence of splenomegaly or lymphadenopathy. Furthermore, PHF6 mutations were found to be significantly correlated with Notch homolog 1, translocation-associated (Drosophila) (NOTCH1) mutations. The patients with T-ALL with co-existence of the two mutations had a significantly shorter event-free survival and a poor prognosis. The present results indicated that PHF6 is inactivated in adult T-ALL, due to its low expression and mutations. The present data indicated the synergistic effect of PHF6 and NOTCH1 mutations, as well as their co-existence, on the oncogenesis of adult T-ALL, and their potential as a prognostic marker for the disease. PMID:27347093

  18. Bacterial and archaeal populations at two shallow hydrothermal vents off Panarea Island (Eolian Islands, Italy).

    PubMed

    Maugeri, Teresa Luciana; Lentini, Valeria; Gugliandolo, Concetta; Italiano, Francesco; Cousin, Sylvie; Stackebrandt, Erko

    2009-01-01

    The aim of this study was to investigate the microbial community thriving at two shallow hydrothermal vents off Panarea Island (Italy). Physico-chemical characteristics of thermal waters were examined in order to establish the effect of the vents on biodiversity of both Bacteria and Archaea. Water and adjacent sediment samples were collected at different times from two vents, characterised by different depth and temperature, and analysed to evaluate total microbial abundances, sulphur-oxidising and thermophilic aerobic bacteria. Total microbial abundances were on average of the order of 10(5) cells ml(-1), expressed as picoplanktonic size fraction. Picophytoplanktonic cells accounted for 0.77-3.83% of the total picoplanktonic cells. The contribution of bacterial and archaeal taxa to prokaryotic community diversity was investigated by PCR-DGGE fingerprinting method. The number of bands derived from bacterial DNA was highest in the DGGE profiles of water sample from the warmest and deepest site (site 2). In contrast, archaeal richness was highest in the water of the coldest and shallowest site (site 1). Sulphur-oxidising bacteria were detected by both culture-dependent and -independent methods. The primary production at the shallow hydrothermal system of Panarea is supported by a complex microbial community composed by phototrophs and chemolithotrophs. PMID:19050821

  19. Phylogenetic analysis of a biofilm bacterial population in a water pipeline in the Gulf of Mexico.

    PubMed

    López, Miguel A; Zavala-Díaz de la Serna, F Javier; Jan-Roblero, Janet; Romero, Juan M; Hernández-Rodríguez, César

    2006-10-01

    The aim of this study was to assess the bacterial diversity associated with a corrosive biofilm in a steel pipeline from the Gulf of Mexico used to inject marine water into the oil reservoir. Several aerobic and heterotrophic bacteria were isolated and identified by 16S rRNA gene sequence analysis. Metagenomic DNA was also extracted to perform a denaturing gradient gel electrophoresis analysis of ribosomal genes and to construct a 16S rRNA gene metagenomic library. Denaturing gradient gel electrophoresis profiles and ribosomal libraries exhibited a limited bacterial diversity. Most of the species detected in the ribosomal library or isolated from the pipeline were assigned to Proteobacteria (Halomonas spp., Idiomarina spp., Marinobacter aquaeolei, Thalassospira sp., Silicibacter sp. and Chromohalobacter sp.) and Bacilli (Bacillus spp. and Exiguobacterium spp.). This is the first report that associates some of these bacteria with a corrosive biofilm. It is relevant that no sulfate-reducing bacteria were isolated or detected by a PCR-based method. The diversity and relative abundance of bacteria from water pipeline biofilms may contribute to an understanding of the complexity and mechanisms of metal corrosion during marine water injection in oil secondary recovery.

  20. Population structure of the bacterial pathogen Xylella fastidiosa among street trees in Washington D.C.

    PubMed

    Harris, Jordan Lee; Balci, Yilmaz

    2015-01-01

    Bacterial leaf scorch, associated with the bacterial pathogen Xylella fastidiosa, is a widely established and problematic disease of landscape ornamentals in Washington D.C. A multi-locus sequence typing analysis was performed using 10 housekeeping loci for X. fastidiosa strains in order to better understand the epidemiology of leaf scorch disease in this municipal environment. Samples were collected from 7 different tree species located throughout the District of Columbia, consisting of 101 samples of symptomatic and asymptomatic foliage from 84 different trees. Five strains of the bacteria were identified. Consistent with prior data, these strains were host specific, with only one strain associated with members of the red oak family, one strain associated with American elm, one strain associated with American sycamore, and two strains associated with mulberry. Strains found for asymptomatic foliage were the same as strains from the symptomatic foliage on individual trees. Cross transmission of the strains was not observed at sites with multiple species of infected trees within an approx. 25 m radius of one another. X. fastidiosa strain specificity observed for each genus of tree suggests a highly specialized host-pathogen relationship. PMID:25815838

  1. Population dynamics of an algal bacterial cenosis in closed ecological system

    NASA Astrophysics Data System (ADS)

    Pisman, T. I.; Galayda, Ya. V.; Loginova, N. S.

    The paper deals with microalgae-bacteria interrelationships in the "autotroph-heterotroph" aquatic biotic cycle. Explanations of why and how algal-bacterial ecosystems are formed still remain controversial. The paper presents results of experimental and theoretical investigations of the functioning of the algal-bacterial cenosis (the microalga Chlorella vulgaris and concomitant microflora). The Chlorella microbial community is dominated by representatives of the genus Pseudomonas. Experiments with non-sterile batch cultures of Chlorella on Tamiya medium showed that the biomass of microorganisms increases simultaneously with the increase in microalgal biomass. The microflora of Chlorella can grow on organic substances released by photosynthesizing Chlorella. Microorganisms can also use dying Chlorella cells, i.e. form a "producer-reducer" biocycle. To get a better insight into the cenosis-forming role of microalgae, a mathematical model of the "autotroph-heterotroph" aquatic biotic cycle has been constructed, taking into account the utilization of Chlorella photosynthates and dead cells by microorganisms and the contribution of the components to the nitrogen cycle. A theoretical study showed that the biomass of concomitant bacteria grown on glucose and detritus is larger than the biomass of bacteria utilizing only microalgal photosynthates, which agrees well with the experimental data.

  2. Population dynamics of an algal-bacterial cenosis in closed ecological system.

    PubMed

    Pisman, T I; Galayda, Ya V; Loginova, N S

    2005-01-01

    The paper deals with microalgae-bacteria interrelationships in the "autotroph-heterotroph" aquatic biotic cycle. Explanations of why and how algal-bacterial ecosystems are formed still remain controversial. The paper presents results of experimental and theoretical investigations of the functioning of the algal-bacterial cenosis (the microalga Chlorella vulgaris and concomitant microflora). The Chlorella microbial community is dominated by representatives of the genus Pseudomonas. Experiments with non-sterile batch cultures of Chlorella on Tamiya medium showed that the biomass of microorganisms increases simultaneously with the increase in microalgal biomass. The microflora of Chlorella can grow on organic substances released by photosynthesizing Chlorella. Microorganisms can also use dying Chlorella cells, i.e. form a "producer-reducer" biocycle. To get a better insight into the cenosis-forming role of microalgae, a mathematical model of the "autotroph-heterotroph" aquatic biotic cycle has been constructed, taking into account the utilization of Chlorella photosynthates and dead cells by microorganisms and the contribution of the components to the nitrogen cycle. A theoretical study showed that the biomass of concomitant bacteria grown on glucose and detritus is larger than the biomass of bacteria utilizing only microalgal photosynthates, which agrees well with the experimental data. PMID:16175685

  3. Population structure of the bacterial pathogen Xylella fastidiosa among street trees in Washington D.C.

    PubMed

    Harris, Jordan Lee; Balci, Yilmaz

    2015-01-01

    Bacterial leaf scorch, associated with the bacterial pathogen Xylella fastidiosa, is a widely established and problematic disease of landscape ornamentals in Washington D.C. A multi-locus sequence typing analysis was performed using 10 housekeeping loci for X. fastidiosa strains in order to better understand the epidemiology of leaf scorch disease in this municipal environment. Samples were collected from 7 different tree species located throughout the District of Columbia, consisting of 101 samples of symptomatic and asymptomatic foliage from 84 different trees. Five strains of the bacteria were identified. Consistent with prior data, these strains were host specific, with only one strain associated with members of the red oak family, one strain associated with American elm, one strain associated with American sycamore, and two strains associated with mulberry. Strains found for asymptomatic foliage were the same as strains from the symptomatic foliage on individual trees. Cross transmission of the strains was not observed at sites with multiple species of infected trees within an approx. 25 m radius of one another. X. fastidiosa strain specificity observed for each genus of tree suggests a highly specialized host-pathogen relationship.

  4. DIFFERENTIAL RESPONSE TO BACTERIAL CHALLENGE IN POPULATIONS OF FUNDULUS HETERCLITUS FROM CLEAN AND POLLUTED SITES

    EPA Science Inventory

    Mummichogs (Fundulus heteroclitus) indigenous to an urban estuarine Superfund site in New Bedford Harbor (NBH, MA, USA) contain extremely high concentrations of the local contaminants, polychlorinated biphenyls (PCBs). These fish populations apparently persist due to an inherited...

  5. An obligatory bacterial mutualism in a multi-drug environment exhibits strong oscillatory population dynamics

    NASA Astrophysics Data System (ADS)

    Conwill, Arolyn; Yurtsev, Eugene; Gore, Jeff

    2014-03-01

    A common mechanism of antibiotic resistance in bacteria involves the production of an enzyme that inactivates the antibiotic. By inactivating the antibiotic, resistant cells can protect other cells in the population that would otherwise be sensitive to the drug. In a multidrug environment, an obligatory mutualism arises because populations of different strains rely on each other to breakdown antibiotics in the environment. Here, we experimentally track the population dynamics of two E. coli strains in the presence of two different antibiotics: ampicillin and chloramphenicol. Together the strains are able to grow in antibiotic concentrations that inhibit growth of either one of the strains alone. Although mutualisms are often thought to stabilize population dynamics, we observe strong oscillatory dynamics even when there is long-term coexistence between the two strains. We expect that our results will provide insight into the evolution of antibiotic resistance and, more generally, the evolutionary origin of phenotypic diversity, cooperation, and ecological stability.

  6. Response of single bacterial cells to stress gives rise to complex history dependence at the population level

    PubMed Central

    Mathis, Roland; Ackermann, Martin

    2016-01-01

    Most bacteria live in ever-changing environments where periods of stress are common. One fundamental question is whether individual bacterial cells have an increased tolerance to stress if they recently have been exposed to lower levels of the same stressor. To address this question, we worked with the bacterium Caulobacter crescentus and asked whether exposure to a moderate concentration of sodium chloride would affect survival during later exposure to a higher concentration. We found that the effects measured at the population level depended in a surprising and complex way on the time interval between the two exposure events: The effect of the first exposure on survival of the second exposure was positive for some time intervals but negative for others. We hypothesized that the complex pattern of history dependence at the population level was a consequence of the responses of individual cells to sodium chloride that we observed: (i) exposure to moderate concentrations of sodium chloride caused delays in cell division and led to cell-cycle synchronization, and (ii) whether a bacterium would survive subsequent exposure to higher concentrations was dependent on the cell-cycle state. Using computational modeling, we demonstrated that indeed the combination of these two effects could explain the complex patterns of history dependence observed at the population level. Our insight into how the behavior of single cells scales up to processes at the population level provides a perspective on how organisms operate in dynamic environments with fluctuating stress exposure. PMID:26960998

  7. In vitro bacterial growth and in vivo ruminal microbiota populations associated with bloat in steers grazing wheat forage.

    PubMed

    Min, B R; Pinchak, W E; Anderson, R C; Hume, M E

    2006-10-01

    on d 50 for bloated than for nonbloated steers when grazing wheat forage. The molecular analysis of the 16S rDNA showed that 2 different ruminal microbiota populations developed between bloated and nonbloated animals grazing wheat forage. Bloat in cattle grazing wheat pastures may be caused by increased production of biofilm, resulting from a diet-influenced switch in the rumen bacterial population. PMID:16971591

  8. Light Suppresses Bacterial Population through the Accumulation of Hydrogen Peroxide in Tobacco Leaves Infected with Pseudomonas syringae pv. tabaci.

    PubMed

    Cheng, Dan-Dan; Liu, Mei-Jun; Sun, Xing-Bin; Zhao, Min; Chow, Wah S; Sun, Guang-Yu; Zhang, Zi-Shan; Hu, Yan-Bo

    2016-01-01

    Pseudomonas syringae pv. tabaci (Pst) is a hemibiotrophic bacterial pathogen responsible for tobacco wildfire disease. Although considerable research has been conducted on the tobacco plant's tolerance to Pst, the role of light in the responses of the photosystems to Pst infection is poorly understood. This study aimed to elucidate the underlying mechanisms of the reduced photosystem damage in tobacco leaves due to Pst infection under light conditions. Compared to dark conditions, Pst infection under light conditions resulted in less chlorophyll degradation and a smaller decline in photosynthetic function. Although the maximal quantum yield of photosystem II (PSII) and the activity of the photosystem I (PSI) complex decreased as Pst infection progressed, damage to PSI and PSII after infection was reduced under light conditions compared to dark conditions. Pst was 17-fold more abundant in tobacco leaves under dark compared to light conditions at 3 days post inoculation (dpi). Additionally, H2O2 accumulated to a high level in tobacco leaves after Pst infection under light conditions; although to a lesser extent, H2O2 accumulation was also significant under dark conditions. Pretreatment with H2O2 alleviated chlorotic lesions and decreased Pst abundance in tobacco leaves at 3 dpi under dark conditions. MV pretreatment had the same effects under light conditions, whereas 3-(3,4-dichlorophenyl)-1,1-dimethylurea pretreatment aggravated chlorotic lesions and increased the Pst population. These results indicate that chlorotic symptoms and the size of the bacterial population are each negatively correlated with H2O2 accumulation. In other words, light appears to suppress the Pst population in tobacco leaves through the accumulation of H2O2 during infection. PMID:27148334

  9. [Effect of Inherent Immunity Factors of Development of Antibiotic Tolerance and Survival of Bacterial Populations under Antibiotic Attack].

    PubMed

    Demkina, E V; Loiko, N G; Mulyukin, A L; Smirnova, T A; Gaponov, A M; Pisarev, V M; Tutel'yan, A V; Nikolaev, Yu A; El'-Registan, G I

    2015-01-01

    Effect of human inherent immunity factors of, a gene-encoded antibacterial peptide indolicidin (Ind) and a cytokine interleukin 1 (IL1) on formation of antibiotic-tolerant persister cells surviving in the presence of ciprofloxacin (Cpf, 100 μg/mL) and ampicillin (Amp, 100 μg/mL) in submerged bacterial cultures (Staphylococcus aureus FGA 209P, Escherichia coli K12, and Pseudomonas aeruginosa PAO1) was studied. While Ind in physiological concentrations (0.3 and 3.0 μg/mL) introduced to the lag- or exponential-phase cultures of test organisms exhibited no reliable effect on population growth, the number of persisters increased at 3.0 μg/mL. Bactericidal Ind concentrations (9 μg/mL) suppressed S. aureus growth (-0.1% of surviving cells) with subsequent recovery due to development of the more antibiotic-tolerant white variant. Treatment with Cpf after Ind addition resulted in mutual potentiation of their antimicrobial activity, with the number of S. aureus persisters 2 to 3 orders of magnitude lower than in the case of the antibiotic alone. IL1, another immunity factor, when introduced (0.1-1 ng/mL) to the exponentially growing S. aureus culture (but not to the lag phase culture) had a temporary growth-static effect, with the number of persisters surviving Cpf treatment (100 μg/mL) increasing by 1 to 2 orders of magnitude. Electron microscopy revealed significant alterations in the outer cell envelope layer of surviving S. aureus cells, which should be associated with their changed antigenic properties. Thus, the factors of human inherent immunity have a dose-dependent effect on the growth of bacterial populations. In combination with antibiotics, they exhibit synergism of antimicrobial action (indolicidin) and minimize (indolicidin) or increase (interleukin 1) the frequency of formation of persister cells responsible for survival of a population subjected to an antibiotic attack.

  10. Light Suppresses Bacterial Population through the Accumulation of Hydrogen Peroxide in Tobacco Leaves Infected with Pseudomonas syringae pv. tabaci

    PubMed Central

    Cheng, Dan-Dan; Liu, Mei-Jun; Sun, Xing-Bin; Zhao, Min; Chow, Wah S.; Sun, Guang-Yu; Zhang, Zi-Shan; Hu, Yan-Bo

    2016-01-01

    Pseudomonas syringae pv. tabaci (Pst) is a hemibiotrophic bacterial pathogen responsible for tobacco wildfire disease. Although considerable research has been conducted on the tobacco plant’s tolerance to Pst, the role of light in the responses of the photosystems to Pst infection is poorly understood. This study aimed to elucidate the underlying mechanisms of the reduced photosystem damage in tobacco leaves due to Pst infection under light conditions. Compared to dark conditions, Pst infection under light conditions resulted in less chlorophyll degradation and a smaller decline in photosynthetic function. Although the maximal quantum yield of photosystem II (PSII) and the activity of the photosystem I (PSI) complex decreased as Pst infection progressed, damage to PSI and PSII after infection was reduced under light conditions compared to dark conditions. Pst was 17-fold more abundant in tobacco leaves under dark compared to light conditions at 3 days post inoculation (dpi). Additionally, H2O2 accumulated to a high level in tobacco leaves after Pst infection under light conditions; although to a lesser extent, H2O2 accumulation was also significant under dark conditions. Pretreatment with H2O2 alleviated chlorotic lesions and decreased Pst abundance in tobacco leaves at 3 dpi under dark conditions. MV pretreatment had the same effects under light conditions, whereas 3-(3,4-dichlorophenyl)-1,1-dimethylurea pretreatment aggravated chlorotic lesions and increased the Pst population. These results indicate that chlorotic symptoms and the size of the bacterial population are each negatively correlated with H2O2 accumulation. In other words, light appears to suppress the Pst population in tobacco leaves through the accumulation of H2O2 during infection. PMID:27148334

  11. Homozygous p.G61E mutation in a consanguineous Pakistani family with co-existence of juvenile-onset open angle glaucoma and primary congenital glaucoma.

    PubMed

    Bashir, Rasheeda; Tahir, Hafsa; Yousaf, Khazeema; Naz, Shagufta; Naz, Sadaf

    2015-10-10

    Glaucoma is one of the primary causes of visual impairment and blindness in the world. It is characterized by the damage to the optic nerve head and visual field loss. Variants in CYP1B1 are the most common cause of glaucoma in different world populations. We studied a consanguineous Pakistani family in which three affected individuals had a severe form of glaucoma with members in one generation diagnosed with juvenile-onset open angle glaucoma at 27 years of age, while the members of the next generation were affected with primary congenital glaucoma with onset at birth. Sequencing of CYP1B1 revealed a homozygous transition variant, c.182G>A, p.G61E which co-segregated with the disease phenotype. This variant has been previously reported to cause both recessively and dominantly inherited PCG and JOAG in different populations. However, this reported for the first time in Pakistani PCG and JOAG patients in a homozygous state. This is also the first ever report of a CYP1B1 variant segregating in a consanguineous family with co-existence of JOAG and PCG in two subsequent generations. This observation of different phenotypes due to an identical mutation suggests that primary congenital glaucoma and juvenile-onset open angle glaucoma can both be caused by homozygosity for the same mutation. It also indicates the reduced penetrance of the variant in those affected due to p.G61E mutation and further implies that modifiers have a role in controlling the time of onset of the disorder.

  12. The population structure of antibiotic-producing bacterial symbionts of Apterostigma dentigerum ants: impacts of coevolution and multipartite symbiosis.

    PubMed

    Caldera, Eric J; Currie, Cameron R

    2012-11-01

    Fungus-growing ants (Attini) are part of a complex symbiosis with Basidiomycetous fungi, which the ants cultivate for food, Ascomycetous fungal pathogens (Escovopsis), which parasitize cultivars, and Actinobacteria, which produce antibiotic compounds that suppress pathogen growth. Earlier studies that have characterized the association between attine ants and their bacterial symbionts have employed broad phylogenetic approaches, with conclusions ranging from a diffuse coevolved mutualism to no specificity being reported. However, the geographic mosaic theory of coevolution proposes that coevolved interactions likely occur at a level above local populations but within species. Moreover, the scale of population subdivision is likely to impact coevolutionary dynamics. Here, we describe the population structure of bacteria associated with the attine Apterostigma dentigerum across Central America using multilocus sequence typing (MLST) of six housekeeping genes. The majority (90%) of bacteria that were isolated grouped into a single clade within the genus Pseudonocardia. In contrast to studies that have suggested that Pseudonocardia dispersal is high and therefore unconstrained by ant associations, we found highly structured ([Formula: see text]) and dispersal-limited (i.e., significant isolation by distance; [Formula: see text], [Formula: see text]) populations over even a relatively small scale (e.g., within the Panama Canal Zone). Estimates of recombination versus mutation were uncharacteristically low compared with estimates for free-living Actinobacteria (e.g., [Formula: see text] in La Selva, Costa Rica), which suggests that recombination is constrained by association with ant hosts. Furthermore, Pseudonocardia population structure was correlated with that of Escovopsis species ([Formula: see text], [Formula: see text]), supporting the bacteria's role in disease suppression. Overall, the population dynamics of symbiotic Pseudonocardia are more consistent with a

  13. The population structure of antibiotic-producing bacterial symbionts of Apterostigma dentigerum ants: impacts of coevolution and multipartite symbiosis.

    PubMed

    Caldera, Eric J; Currie, Cameron R

    2012-11-01

    Fungus-growing ants (Attini) are part of a complex symbiosis with Basidiomycetous fungi, which the ants cultivate for food, Ascomycetous fungal pathogens (Escovopsis), which parasitize cultivars, and Actinobacteria, which produce antibiotic compounds that suppress pathogen growth. Earlier studies that have characterized the association between attine ants and their bacterial symbionts have employed broad phylogenetic approaches, with conclusions ranging from a diffuse coevolved mutualism to no specificity being reported. However, the geographic mosaic theory of coevolution proposes that coevolved interactions likely occur at a level above local populations but within species. Moreover, the scale of population subdivision is likely to impact coevolutionary dynamics. Here, we describe the population structure of bacteria associated with the attine Apterostigma dentigerum across Central America using multilocus sequence typing (MLST) of six housekeeping genes. The majority (90%) of bacteria that were isolated grouped into a single clade within the genus Pseudonocardia. In contrast to studies that have suggested that Pseudonocardia dispersal is high and therefore unconstrained by ant associations, we found highly structured ([Formula: see text]) and dispersal-limited (i.e., significant isolation by distance; [Formula: see text], [Formula: see text]) populations over even a relatively small scale (e.g., within the Panama Canal Zone). Estimates of recombination versus mutation were uncharacteristically low compared with estimates for free-living Actinobacteria (e.g., [Formula: see text] in La Selva, Costa Rica), which suggests that recombination is constrained by association with ant hosts. Furthermore, Pseudonocardia population structure was correlated with that of Escovopsis species ([Formula: see text], [Formula: see text]), supporting the bacteria's role in disease suppression. Overall, the population dynamics of symbiotic Pseudonocardia are more consistent with a

  14. Heterogeneous water supply affects growth and benefits of clonal integration between co-existing invasive and native Hydrocotyle species.

    PubMed

    Wang, Yong-Jian; Bai, Yun-Fei; Zeng, Shi-Qi; Yao, Bin; Wang, Wen; Luo, Fang-Li

    2016-07-21

    Spatial patchiness and temporal variability in water availability are common in nature under global climate change, which can remarkably influence adaptive responses of clonal plants, i.e. clonal integration (translocating resources between connected ramets). However, little is known about the effects of spatial patchiness and temporal heterogeneity in water on growth and clonal integration between congeneric invasive and native Hydrocotyle species. In a greenhouse experiment, we subjected severed or no severed (intact) fragments of Hydrocotyle vulgaris, a highly invasive species in China, and its co-existing, native congener H. sibthorpioides to different spatial patchiness (homogeneous and patchy) and temporal interval (low and high interval) in water supply. Clonal integration had significant positive effects on growth of both species. In the homogeneous water conditions, clonal integration greatly improved the growth in fragments of both species under low interval in water. However, in the patchy water conditions, clonal integration significantly increased growth in both ramets and fragments of H. vulgaris under high interval in water. Therefore, spatial patchiness and temporal interval in water altered the effects of clonal integration of both species, especially for H. vulgaris. The adaptation of H. vulgaris might lead to invasive growth and potential spread under the global water variability.

  15. Successful Outcome of Twin Gestation with Partial Mole and Co-Existing Live Fetus: A Case Report

    PubMed Central

    Rathod, Setu; Rani, Reddi; John, Lopamudra B.

    2015-01-01

    Sad fetus syndrome comprising of a live twin gestation with a hydatidiform mole is a rare entity. The condition is even rarer when the co-existing live fetus is associated with a partial mole than a complete mole. We report the case of a 24-year-old G2P1L1 at 28 weeks gestation who presented to our casualty in the second stage of labour. She had a previous ultrasound scan at 13 weeks which showed a live fetus with a focal area of multicystic placenta. She delivered an alive preterm male fetus weighing 1.32 kg vaginally. Following expulsion of normal placenta of the live fetus, partial mole was expelled. The fetus was admitted to neonatal ICU and discharged after two weeks. Soon after delivery, β-hCG (human chorionic gonadotropin) was 1,21,993 mIU/ml which decreased to 30mIU/ml within two weeks. The patient was discharged with advice of regular follow up of β-hCG reports. PMID:26436001

  16. Periodic mesoporous organosilicas with co-existence of diurea and sulfanilamide as an effective drug delivery carrier

    NASA Astrophysics Data System (ADS)

    Parambadath, Surendran; Rana, Vijay Kumar; Moorthy, Santha; Chu, Sang-Wook; Park, Shin-Kyu; Lee, Daewoo; Sung, Giju; Ha, Chang-Sik

    2011-05-01

    In this article we report the synthesis of new periodic mesoporous organosilicas (PMOs) with the co-existence of diurea and sulfanilamide-bridged organosilica that are potentially useful for controlled drug release system. The materials possess hexagonal pores with a high degree of uniformity and show long-range order as confirmed by the measurements of small-angle X-ray scattering (SAXS), N 2 adsorption isotherms, and transmission electron microscopy(TEM). FT-IR and solid state 29Si MAS and 13C CP MAS NMR spectroscopic analyses proved that the bridging groups in the framework are not cleaved and covalently attached in the walls of the PMOs. It was found that the organic functionality could be introduced in a maximum of 10 mol% with respect to the total silicon content and be thermally stable up to 230 °C. The synthesized materials were shown to be particularly suitable for adsorption and desorption of hydrophilic/hydrophobic drugs from a phosphate buffer solution at pH 7.4.

  17. Heterogeneous water supply affects growth and benefits of clonal integration between co-existing invasive and native Hydrocotyle species

    PubMed Central

    Wang, Yong-Jian; Bai, Yun-Fei; Zeng, Shi-Qi; Yao, Bin; Wang, Wen; Luo, Fang-Li

    2016-01-01

    Spatial patchiness and temporal variability in water availability are common in nature under global climate change, which can remarkably influence adaptive responses of clonal plants, i.e. clonal integration (translocating resources between connected ramets). However, little is known about the effects of spatial patchiness and temporal heterogeneity in water on growth and clonal integration between congeneric invasive and native Hydrocotyle species. In a greenhouse experiment, we subjected severed or no severed (intact) fragments of Hydrocotyle vulgaris, a highly invasive species in China, and its co-existing, native congener H. sibthorpioides to different spatial patchiness (homogeneous and patchy) and temporal interval (low and high interval) in water supply. Clonal integration had significant positive effects on growth of both species. In the homogeneous water conditions, clonal integration greatly improved the growth in fragments of both species under low interval in water. However, in the patchy water conditions, clonal integration significantly increased growth in both ramets and fragments of H. vulgaris under high interval in water. Therefore, spatial patchiness and temporal interval in water altered the effects of clonal integration of both species, especially for H. vulgaris. The adaptation of H. vulgaris might lead to invasive growth and potential spread under the global water variability. PMID:27439691

  18. Co-existence of Echinococcus granulosus infection and cancer metastasis in the liver correlates with reduced Th1 immune responses.

    PubMed

    Turhan, N; Esendagli, G; Ozkayar, O; Tunali, G; Sokmensuer, C; Abbasoglu, O

    2015-01-01

    A possible relationship between cancer and Echinococcus granulosus infection has been postulated. As T cells are critical players in immune responses against both infections and malignancies, in an experimental model of secondary echinococcosis and breast cancer, this study aims to observe the progression of cancer and to determine the characters of T-cell responses. 4T1 breast tumour cells were subcutaneously injected into mammary region, whereas protoscoleces were intraperitoneally inoculated into the mice. Hydatid cysts, tumours and metastases were determined with macroscopic and histopathological evaluation. T cells found in spleen, liver and tumour were characterised by flow cytometric analysis of CD3, CD4, CD8, CD25, CCR5, CCR3, IL-4 and IFN-γ. In the mice inoculated both with protoscoleces and with breast tumour cells, increased frequency of cancer metastasis was observed in the liver. The amount of CD4(+) T cells was increased in the liver and in the spleen of mice infected with E. granulosus. However, co-existence of echinococcosis and metastatic lesions in the liver was associated with significant reduction in the IFN-γ(+) and CCR5(+) Th1 cells and increase in the CD25(+) T cells. Our results may indicate an immunological link between cystic echinococcosis and cancer that allows tumour metastasis to flourish in the liver.

  19. Anti-cardiolipin/beta-2 glycoprotein activities co-exist on human anti-DNA antibody light chains.

    PubMed

    Kumar, Sanjeev; Nagl, Sylvia; Kalsi, J K; Ravirajan, C T; Athwal, Dee; Latchman, David S; Pearl, Laurence H; Isenberg, David A

    2003-12-01

    We have recently shown that the human anti-DNA antibodies B3 and 33H11 also bind cardiolipin and that the anti-autoantigen activity resides predominantly on their lambda light chains. We now show that the two auto-antibodies possess strong reactivity to the plasma-protein 2-Glycoprotein I (beta2-GPI) also. Utilizing chain shuffling experiments involving an unrelated anti-p185 antibody 4D5 with insignificant reactivity to cardiolipin or to beta2-GPI, we now demonstrate that hybrid Fabs with constituent light chain, but not the heavy chain, of B3 or 33H11, exhibit anti-cardiolipin activity. Furthermore, the constructs possessing the auto-antibody-derived light chain also exhibited significant reactivity to beta2-GPI. The results suggest that anti-DNA, anti-cardiolipin and anti-beta2-GPI activities co-exist on the light chains of the antibodies studied and, importantly, these activities could be transferred to antibody constructs by their light chains alone. Computer-generated models of the three-dimensional structures of the auto-antibodies and their hybrids, suggest predominant interaction of their light chains with domain IV of beta2-GPI.

  20. Heterogeneous water supply affects growth and benefits of clonal integration between co-existing invasive and native Hydrocotyle species.

    PubMed

    Wang, Yong-Jian; Bai, Yun-Fei; Zeng, Shi-Qi; Yao, Bin; Wang, Wen; Luo, Fang-Li

    2016-01-01

    Spatial patchiness and temporal variability in water availability are common in nature under global climate change, which can remarkably influence adaptive responses of clonal plants, i.e. clonal integration (translocating resources between connected ramets). However, little is known about the effects of spatial patchiness and temporal heterogeneity in water on growth and clonal integration between congeneric invasive and native Hydrocotyle species. In a greenhouse experiment, we subjected severed or no severed (intact) fragments of Hydrocotyle vulgaris, a highly invasive species in China, and its co-existing, native congener H. sibthorpioides to different spatial patchiness (homogeneous and patchy) and temporal interval (low and high interval) in water supply. Clonal integration had significant positive effects on growth of both species. In the homogeneous water conditions, clonal integration greatly improved the growth in fragments of both species under low interval in water. However, in the patchy water conditions, clonal integration significantly increased growth in both ramets and fragments of H. vulgaris under high interval in water. Therefore, spatial patchiness and temporal interval in water altered the effects of clonal integration of both species, especially for H. vulgaris. The adaptation of H. vulgaris might lead to invasive growth and potential spread under the global water variability. PMID:27439691

  1. The ecological proportion of indigenous bacterial populations in saliva is correlated with oral health status.

    PubMed

    Takeshita, Toru; Nakano, Yoshio; Kumagai, Takashi; Yasui, Masaki; Kamio, Noriaki; Shibata, Yukie; Shiota, Susumu; Yamashita, Yoshihisa

    2009-01-01

    To obtain deeper insights into the etiology of oral disease, an understanding of the composition of the surrounding bacterial environments that lead to health or disease is required, which is attracting increasing attention. In this study, the bacterial compositions in the saliva of 200 subjects aged 15-40 years were depicted as peak patterns by terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes. The subjects were classified into three clusters by partitioning around medoids clustering based on their T-RFLP profiles, and the clinical oral health parameters of the clusters were compared. The clustering of the T-RFLP profiles in this study was mainly based on differences in the abundance distribution of the dominant terminal restriction fragments (TRFs) detected in most of the subjects. Predicted from the sizes of the TRFs, the characteristically more predominant members of each were Prevotella and Veillonella species in cluster I; Streptococcus species in cluster II and Neisseria, Haemophilus or Aggregatibacter species and Porphyromonas species in cluster III. The parameters associated with periodontal disease were significantly different among the clusters. Clusters I and II had a higher percentage of sites of periodontal pockets greater than 4 mm than cluster III, and cluster I contained sites exhibiting bleeding on probing more often than cluster II or III; no significant differences were observed in other parameters. These results suggest that the abundance distribution of commensal bacteria in saliva is correlated with periodontal health, and might be involved in the susceptibility of an individual to periodontal disease. PMID:18830275

  2. Investigating bacterial populations in styrene-degrading biofilters by 16S rDNA tag pyrosequencing.

    PubMed

    Portune, Kevin J; Pérez, M Carmen; Álvarez-Hornos, F Javier; Gabaldón, Carmen

    2015-01-01

    Microbial biofilms are essential components in the elimination of pollutants within biofilters, yet still little is known regarding the complex relationships between microbial community structure and biodegradation function within these engineered ecosystems. To further explore this relationship, 16S rDNA tag pyrosequencing was applied to samples taken at four time points from a styrene-degrading biofilter undergoing variable operating conditions. Changes in microbial structure were observed between different stages of biofilter operation, and the level of styrene concentration was revealed to be a critical factor affecting these changes. Bacterial genera Azoarcus and Pseudomonas were among the dominant classified genera in the biofilter. Canonical correspondence analysis (CCA) and correlation analysis revealed that the genera Brevundimonas, Hydrogenophaga, and Achromobacter may play important roles in styrene degradation under increasing styrene concentrations. No significant correlations (P > 0.05) could be detected between biofilter operational/functional parameters and biodiversity measurements, although biological heterogeneity within biofilms and/or technical variability within pyrosequencing may have considerably affected these results. Percentages of selected bacterial taxonomic groups detected by fluorescence in situ hybridization (FISH) were compared to results from pyrosequencing in order to assess the effectiveness and limitations of each method for identifying each microbial taxon. Comparison of results revealed discrepancies between the two methods in the detected percentages of numerous taxonomic groups. Biases and technical limitations of both FISH and pyrosequencing, such as the binding of FISH probes to non-target microbial groups and lack of classification of sequences for defined taxonomic groups from pyrosequencing, may partially explain some differences between the two methods.

  3. Effects of fomesafen on soil enzyme activity, microbial population, and bacterial community composition.

    PubMed

    Zhang, Qingming; Zhu, Lusheng; Wang, Jun; Xie, Hui; Wang, Jinhua; Wang, Fenghua; Sun, Fengxia

    2014-05-01

    Fomesafen is a diphenyl ether herbicide that has an important role in the removal of broadleaf weeds in bean and fruit tree fields. However, very little information is known about the effects of this herbicide on soil microbial community structure and activities. In the present study, laboratory experiments were conducted to examine the effects of different concentrations of fomesafen (0, 10, 100, and 500 μg/kg) on microbial community structure and activities during an exposure period of 60 days, using soil enzyme assays, plate counting, and denaturing gradient gel electrophoresis (DGGE). The results of enzymatic activity experiments showed that fomesafen had different stimulating effects on the activities of acid phosphatase, alkaline phosphatase, and dehydrogenase, with dehydrogenase being most sensitive to fomesafen. On the tenth day, urease activity was inhibited significantly after treatment of different concentrations of fomesafen; this inhibiting effect then gradually disappeared and returned to the control level after 30 days. Plate counting experiments indicated that the number of bacteria and actinomycetes increased in fomesafen-spiked soil relative to the control after 30 days of incubation, while fungal number decreased significantly after only 10 days. The DGGE results revealed that the bacterial community varied in response to the addition of fomesafen, and the intensity of these six bands was greater on day 10. Sequencing and phylogenetic analyses indicated that the six excised DGGE bands were closely related to Emticicia, Bacillus, and uncultured bacteria. After 10 days, the bacterial community exhibited no obvious change compared with the control. Throughout the experiment, we concluded that 0-500 μg/kg of fomesafen could not produce significant toxic effects on soil microbial community structure and activities.

  4. Phage mutations in response to CRISPR diversification in a bacterial population.

    PubMed

    Sun, Christine L; Barrangou, Rodolphe; Thomas, Brian C; Horvath, Philippe; Fremaux, Christophe; Banfield, Jillian F

    2013-02-01

    Interactions between bacteria and their coexisting phage populations impact evolution and can strongly influence biogeochemical processes in natural ecosystems. Periodically, mutation or migration results in exposure of a host to a phage to which it has no immunity; alternatively, a phage may be exposed to a host it cannot infect. To explore the processes by which coexisting, co-evolving hosts and phage populations establish, we cultured Streptococcus thermophilus DGCC7710 with phage 2972 and tracked CRISPR (clustered regularly interspaced short palindromic repeats) diversification and host-phage co-evolution in a population derived from a colony that acquired initial CRISPR-encoded immunity. After 1 week of co-culturing, the coexisting host-phage populations were metagenomically characterized using 454 FLX Titanium sequencing. The evolved genomes were compared with reference genomes to identify newly incorporated spacers in S. thermophilus DGCC7710 and recently acquired single-nucleotide polymorphisms (SNPs) in phage 2972. Following phage exposure, acquisition of immune elements (spacers) led to a genetically diverse population with multiple subdominant strain lineages. Phage mutations that circumvented three early immunization events were localized in the proto-spacer adjacent motif (PAM) or near the PAM end of the proto-spacer, suggesting a strong selective advantage for the phage that mutated in this region. The sequential fixation or near fixation of these single mutations indicates selection events so severe that single phage genotypes ultimately gave rise to all surviving lineages and potentially carried traits unrelated to immunity to fixation.

  5. Phage mutations in response to CRISPR diversification in a bacterial population.

    PubMed

    Sun, Christine L; Barrangou, Rodolphe; Thomas, Brian C; Horvath, Philippe; Fremaux, Christophe; Banfield, Jillian F

    2013-02-01

    Interactions between bacteria and their coexisting phage populations impact evolution and can strongly influence biogeochemical processes in natural ecosystems. Periodically, mutation or migration results in exposure of a host to a phage to which it has no immunity; alternatively, a phage may be exposed to a host it cannot infect. To explore the processes by which coexisting, co-evolving hosts and phage populations establish, we cultured Streptococcus thermophilus DGCC7710 with phage 2972 and tracked CRISPR (clustered regularly interspaced short palindromic repeats) diversification and host-phage co-evolution in a population derived from a colony that acquired initial CRISPR-encoded immunity. After 1 week of co-culturing, the coexisting host-phage populations were metagenomically characterized using 454 FLX Titanium sequencing. The evolved genomes were compared with reference genomes to identify newly incorporated spacers in S. thermophilus DGCC7710 and recently acquired single-nucleotide polymorphisms (SNPs) in phage 2972. Following phage exposure, acquisition of immune elements (spacers) led to a genetically diverse population with multiple subdominant strain lineages. Phage mutations that circumvented three early immunization events were localized in the proto-spacer adjacent motif (PAM) or near the PAM end of the proto-spacer, suggesting a strong selective advantage for the phage that mutated in this region. The sequential fixation or near fixation of these single mutations indicates selection events so severe that single phage genotypes ultimately gave rise to all surviving lineages and potentially carried traits unrelated to immunity to fixation. PMID:23057534

  6. Identification and characterization of metabolic properties of bacterial populations recovered from arsenic contaminated ground water of North East India (Assam).

    PubMed

    Ghosh, Soma; Sar, Pinaki

    2013-12-01

    Diversity of culturable bacterial populations within the Arsenic (As) contaminated groundwater of North Eastern state (Assam) of India is studied. From nine As contaminated samples 89 bacterial strains are isolated. 16S rRNA gene sequence analysis reveals predominance of Brevundimonas (35%) and Acidovorax (23%) along with Acinetobacter (10%), Pseudomonas (9%) and relatively less abundant (<5%) Undibacterium, Herbaspirillum, Rhodococcus, Staphylococcus, Bosea, Bacillus, Ralstonia, Caulobacter and Rhizobiales members. High As(III) resistance (MTC 10-50 mM) is observed for the isolates obtained from As(III) enrichment, particularly for 3 isolates of genus Brevundimonas (MTC 50 mM). In contrast, high resistance to As(V) (MTC as high as 550 mM) is present as a ubiquitous property, irrespective of isolates' enrichment condition. Bacterial genera affiliated to other groups showed relatively lower degree of As resistance [MTCs of 15-20 mM As(III) and 250-350 mM As(V)]. As(V) reductase activity is detected in strains with high As(V) as well as As(III) resistance. A strong correlation could be established among isolates capable of reductase activity and siderophore production as well as As(III) tolerance. A large number of isolates (nearly 50%) is capable of anaerobic respiration using alternate inorganic electron acceptors [As(V), Se(VI), Fe(III), [NO(3)(2), SO(4)(2), S(2)O(3)(2). Ability to utilize different carbon sources ranging from C2-C6 compounds along with some complex sugars is also observed. Particularly, a number of strains is found to possess ability to grow chemolithotrophically using As(III) as the electron donor. The study reports for the first time the identity and metabolic abilities of bacteria in As contaminated ground water of North East India, useful to elucidate the microbial role in influencing mobilization of As in the region.

  7. Identification and characterization of metabolic properties of bacterial populations recovered from arsenic contaminated ground water of North East India (Assam).

    PubMed

    Ghosh, Soma; Sar, Pinaki

    2013-12-01

    Diversity of culturable bacterial populations within the Arsenic (As) contaminated groundwater of North Eastern state (Assam) of India is studied. From nine As contaminated samples 89 bacterial strains are isolated. 16S rRNA gene sequence analysis reveals predominance of Brevundimonas (35%) and Acidovorax (23%) along with Acinetobacter (10%), Pseudomonas (9%) and relatively less abundant (<5%) Undibacterium, Herbaspirillum, Rhodococcus, Staphylococcus, Bosea, Bacillus, Ralstonia, Caulobacter and Rhizobiales members. High As(III) resistance (MTC 10-50 mM) is observed for the isolates obtained from As(III) enrichment, particularly for 3 isolates of genus Brevundimonas (MTC 50 mM). In contrast, high resistance to As(V) (MTC as high as 550 mM) is present as a ubiquitous property, irrespective of isolates' enrichment condition. Bacterial genera affiliated to other groups showed relatively lower degree of As resistance [MTCs of 15-20 mM As(III) and 250-350 mM As(V)]. As(V) reductase activity is detected in strains with high As(V) as well as As(III) resistance. A strong correlation could be established among isolates capable of reductase activity and siderophore production as well as As(III) tolerance. A large number of isolates (nearly 50%) is capable of anaerobic respiration using alternate inorganic electron acceptors [As(V), Se(VI), Fe(III), [NO(3)(2), SO(4)(2), S(2)O(3)(2). Ability to utilize different carbon sources ranging from C2-C6 compounds along with some complex sugars is also observed. Particularly, a number of strains is found to possess ability to grow chemolithotrophically using As(III) as the electron donor. The study reports for the first time the identity and metabolic abilities of bacteria in As contaminated ground water of North East India, useful to elucidate the microbial role in influencing mobilization of As in the region. PMID:24210546

  8. Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations.

    PubMed Central

    Lenski, R E; Travisano, M

    1994-01-01

    We followed evolutionary change in 12 populations of Escherichia coli propagated for 10,000 generations in identical environments. Both morphology (cell size) and fitness (measured in competition with the ancestor) evolved rapidly for the first 2000 generations or so after the populations were introduced into the experimental environment, but both were nearly static for the last 5000 generations. Although evolving in identical environments, the replicate populations diverged significantly from one another in both morphology and mean fitness. The divergence in mean fitness was sustained and implies that the populations have approached different fitness peaks of unequal height in the adaptive landscape. Although the experimental time scale and environment were microevolutionary in scope, our experiments were designed to address questions concerning the origin as well as the fate of genetic and phenotypic novelties, the repeatability of adaptation, the diversification of lineages, and thus the causes and consequences of the uniqueness of evolutionary history. In fact, we observed several hallmarks of macroevolutionary dynamics, including periods of rapid evolution and stasis, altered functional relationships between traits, and concordance of anagenetic and cladogenetic trends. Our results support a Wrightian interpretation, in which chance events (mutation and drift) play an important role in adaptive evolution, as do the complex genetic interactions that underlie the structure of organisms. PMID:8041701

  9. BACTERIAL POPULATION SHIFTS IN THE RUMEN OF LACTATING DAIRY COWS WITHIN AND ACROSS FEEDING CYCLES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    While species composition of the ruminal microflora is thought to change during the feeding cycle due to variations in feed intake and ruminal environmental conditions, no studies have systematically characterized these purported population shifts. We used PCR amplification and automated ribosomal ...

  10. Bacterial populations within copper mine tailings: long-term effects of amendment with Class A biosolids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study evaluates the effect of surface application of dried Class A biosolids on microbial populations within copper mine tailings. Methods and Results: Mine tailing sites were established at ASARCO Mission Mine close to Sahuarita, Arizona. Site 1 (Dec. 1998) was amended with 248 tons ha-1 of C...

  11. Diversity in ATP concentrations in a single bacterial cell population revealed by quantitative single-cell imaging

    PubMed Central

    Yaginuma, Hideyuki; Kawai, Shinnosuke; Tabata, Kazuhito V.; Tomiyama, Keisuke; Kakizuka, Akira; Komatsuzaki, Tamiki; Noji, Hiroyuki; Imamura, Hiromi

    2014-01-01

    Recent advances in quantitative single-cell analysis revealed large diversity in gene expression levels between individual cells, which could affect the physiology and/or fate of each cell. In contrast, for most metabolites, the concentrations were only measureable as ensemble averages of many cells. In living cells, adenosine triphosphate (ATP) is a critically important metabolite that powers many intracellular reactions. Quantitative measurement of the absolute ATP concentration in individual cells has not been achieved because of the lack of reliable methods. In this study, we developed a new genetically-encoded ratiometric fluorescent ATP indicator “QUEEN”, which is composed of a single circularly-permuted fluorescent protein and a bacterial ATP binding protein. Unlike previous FRET-based indicators, QUEEN was apparently insensitive to bacteria growth rate changes. Importantly, intracellular ATP concentrations of numbers of bacterial cells calculated from QUEEN fluorescence were almost equal to those from firefly luciferase assay. Thus, QUEEN is suitable for quantifying the absolute ATP concentration inside bacteria cells. Finally, we found that, even for a genetically-identical Escherichia coli cell population, absolute concentrations of intracellular ATP were significantly diverse between individual cells from the same culture, by imaging QUEEN signals from single cells. PMID:25283467

  12. Measuring the Rate of Conjugal Plasmid Transfer and Phage Infection in a Bacterial Population Using Quantitative PCR

    NASA Astrophysics Data System (ADS)

    Wan, Zhenmao; Goddard, Noel

    2012-02-01

    Horizontal gene transfer between species is an important mechanism for bacterial genome evolution. In Escherichia coli, conjugation is the transfer from a donor(F^+) to a recipient(F^-) cell through cell-to-cell contact. We demonstrate a novel qPCR method for quantifying the transfer kinetics of the F plasmid in a population by enumerating the relative abundance of genetic loci unique to the plasmid and the chromosome. This approach allows us to query the plasmid transfer rate without the need for selective culturing with unprecedented single locus resolution. It also allows us to investigate the inhibition of conjugation in the presence of filamentous bacteriophages M13. Experimental data is then compared with numerical simulation using a mass action, resource limited model.

  13. Application of a High-Density Oligonucleotide Microarray Approach To Study Bacterial Population Dynamics during Uranium Reduction and Reoxidation†

    PubMed Central

    Brodie, Eoin L.; DeSantis, Todd Z.; Joyner, Dominique C.; Baek, Seung M.; Larsen, Joern T.; Andersen, Gary L.; Hazen, Terry C.; Richardson, Paul M.; Herman, Donald J.; Tokunaga, Tetsu K.; Wan, Jiamin M.; Firestone, Mary K.

    2006-01-01

    Reduction of soluble uranium U(VI) to less-soluble uranium U(IV) is a promising approach to minimize migration from contaminated aquifers. It is generally assumed that, under constant reducing conditions, U(IV) is stable and immobile; however, in a previous study, we documented reoxidation of U(IV) under continuous reducing conditions (Wan et al., Environ. Sci. Technol. 2005, 39:6162-6169). To determine if changes in microbial community composition were a factor in U(IV) reoxidation, we employed a high-density phylogenetic DNA microarray (16S microarray) containing 500,000 probes to monitor changes in bacterial populations during this remediation process. Comparison of the 16S microarray with clone libraries demonstrated successful detection and classification of most clone groups. Analysis of the most dynamic groups of 16S rRNA gene amplicons detected by the 16S microarray identified five clusters of bacterial subfamilies responding in a similar manner. This approach demonstrated that amplicons of known metal-reducing bacteria such as Geothrix fermentans (confirmed by quantitative PCR) and those within the Geobacteraceae were abundant during U(VI) reduction and did not decline during the U(IV) reoxidation phase. Significantly, it appears that the observed reoxidation of uranium under reducing conditions occurred despite elevated microbial activity and the consistent presence of metal-reducing bacteria. High-density phylogenetic microarrays constitute a powerful tool, enabling the detection and monitoring of a substantial portion of the microbial population in a routine, accurate, and reproducible manner. PMID:16957256

  14. Different bacterial populations associated with the roots and rhizosphere of rice incorporate plant-derived carbon.

    PubMed

    Hernández, Marcela; Dumont, Marc G; Yuan, Quan; Conrad, Ralf

    2015-03-01

    Microorganisms associated with the roots of plants have an important function in plant growth and in soil carbon sequestration. Rice cultivation is the second largest anthropogenic source of atmospheric CH4, which is a significant greenhouse gas. Up to 60% of fixed carbon formed by photosynthesis in plants is transported below ground, much of it as root exudates that are consumed by microorganisms. A stable isotope probing (SIP) approach was used to identify microorganisms using plant carbon in association with the roots and rhizosphere of rice plants. Rice plants grown in Italian paddy soil were labeled with (13)CO2 for 10 days. RNA was extracted from root material and rhizosphere soil and subjected to cesium gradient centrifugation followed by 16S rRNA amplicon pyrosequencing to identify microorganisms enriched with (13)C. Thirty operational taxonomic units (OTUs) were labeled and mostly corresponded to Proteobacteria (13 OTUs) and Verrucomicrobia (8 OTUs). These OTUs were affiliated with the Alphaproteobacteria, Betaproteobacteria, and Deltaproteobacteria classes of Proteobacteria and the "Spartobacteria" and Opitutae classes of Verrucomicrobia. In general, different bacterial groups were labeled in the root and rhizosphere, reflecting different physicochemical characteristics of these locations. The labeled OTUs in the root compartment corresponded to a greater proportion of the 16S rRNA sequences (∼20%) than did those in the rhizosphere (∼4%), indicating that a proportion of the active microbial community on the roots greater than that in the rhizosphere incorporated plant-derived carbon within the time frame of the experiment. PMID:25616793

  15. Uncovering potential 'herbal probiotics' in Juzen-taiho-to through the study of associated bacterial populations.

    PubMed

    Montenegro, Diego; Kalpana, Kriti; Chrissian, Christine; Sharma, Ashutosh; Takaoka, Anna; Iacovidou, Maria; Soll, Clifford E; Aminova, Olga; Heguy, Adriana; Cohen, Lisa; Shen, Steven; Kawamura, Akira

    2015-02-01

    Juzen-taiho-to (JTT) is an immune-boosting formulation of ten medicinal herbs. It is used clinically in East Asia to boost the human immune functions. The active factors in JTT have not been clarified. But, existing evidence suggests that lipopolysaccharide (LPS)-like factors contribute to the activity. To examine this possibility, JTT was subjected to a series of analyses, including high resolution mass spectrometry, which suggested the presence of structural variants of LPS. This finding opened a possibility that JTT contains immune-boosting bacteria. As the first step to characterize the bacteria in JTT, 16S ribosomal RNA sequencing was carried out for Angelica sinensis (dried root), one of the most potent immunostimulatory herbs in JTT. The sequencing revealed a total of 519 bacteria genera in A. sinensis. The most abundant genus was Rahnella, which is widely distributed in water and plants. The abundance of Rahnella appeared to correlate with the immunostimulatory activity of A. sinensis. In conclusion, the current study provided new pieces of evidence supporting the emerging theory of bacterial contribution in immune-boosting herbs. PMID:25547935

  16. Different Bacterial Populations Associated with the Roots and Rhizosphere of Rice Incorporate Plant-Derived Carbon

    PubMed Central

    Hernández, Marcela; Yuan, Quan; Conrad, Ralf

    2015-01-01

    Microorganisms associated with the roots of plants have an important function in plant growth and in soil carbon sequestration. Rice cultivation is the second largest anthropogenic source of atmospheric CH4, which is a significant greenhouse gas. Up to 60% of fixed carbon formed by photosynthesis in plants is transported below ground, much of it as root exudates that are consumed by microorganisms. A stable isotope probing (SIP) approach was used to identify microorganisms using plant carbon in association with the roots and rhizosphere of rice plants. Rice plants grown in Italian paddy soil were labeled with 13CO2 for 10 days. RNA was extracted from root material and rhizosphere soil and subjected to cesium gradient centrifugation followed by 16S rRNA amplicon pyrosequencing to identify microorganisms enriched with 13C. Thirty operational taxonomic units (OTUs) were labeled and mostly corresponded to Proteobacteria (13 OTUs) and Verrucomicrobia (8 OTUs). These OTUs were affiliated with the Alphaproteobacteria, Betaproteobacteria, and Deltaproteobacteria classes of Proteobacteria and the “Spartobacteria” and Opitutae classes of Verrucomicrobia. In general, different bacterial groups were labeled in the root and rhizosphere, reflecting different physicochemical characteristics of these locations. The labeled OTUs in the root compartment corresponded to a greater proportion of the 16S rRNA sequences (∼20%) than did those in the rhizosphere (∼4%), indicating that a proportion of the active microbial community on the roots greater than that in the rhizosphere incorporated plant-derived carbon within the time frame of the experiment. PMID:25616793

  17. Use of oleic acid to reduce the population of the bacterial flora of poultry skin.

    PubMed

    Hinton, A; Ingram, K D

    2000-09-01

    The effect of oleic acid on native bacterial flora of poultry skin was examined. Skin from commercial broiler carcasses was washed once or twice in solutions of 0, 2, 4, 6, 8, or 10% (wt/vol) oleic acid and rinsed in peptone water. Aerobic bacteria, Enterobacteriaceae, Campylobacter, and enterococci in the rinsates were enumerated. Significantly fewer aerobic bacteria, Enterobacteriaceae, Campylobacter, and enterococci were recovered from rinsates of skin washed in oleic acid than from control samples. Additionally, fewer bacteria were recovered from rinsates of skin washed in higher concentrations of oleic acid than from skin washed in lower concentrations of the fatty acid. In most cases, there was no significant difference in the number of bacteria recovered from rinsates of skin washed once or twice in solutions of oleic acid. Washing skin samples twice in 10% solutions of oleic acid significantly reduced the number of aerobic bacteria, Enterobacteriaceae, Campylobacter, and enterococci that remained attached to the skin. Campylobacter sp., Enterococcus faecalis, and Listeria monocytogenes isolates possessed the least resistance to the antibacterial activity of oleic acid in vitro, while Escherichia coli and Pseudomonas aeruginosa showed higher resistance. Enterobacter cloacae, Staphylococcus lentus, and Salmonella Typhimurium had the greatest resistance to the antibacterial activity of oleic acid. Findings indicate that oleic acid reduces the number of bacteria on the skin of processed broilers and that the fatty acid is bactericidal to several spoilage and pathogenic bacteria associated with poultry.

  18. Microbial Diversity Analysis of the Bacterial and Archaeal Population in Present Day Stromatolites

    NASA Technical Reports Server (NTRS)

    Ortega, Maya C.

    2011-01-01

    Stromatolites are layered sedimentary structures resulting from microbial mat communities that remove carbon dioxide from their environment and biomineralize it as calcium carbonate. Although prevalent in the fossil record, stromatolites are rare in the modem world and are only found in a few locations including Highbome Cay in the Bahamas. The stromatolites found at this shallow marine site are analogs to ancient microbial mat ecosystems abundant in the Precambrian period on ancient Earth. To understand how stromatolites form and develop, it is important to identify what microorganisms are present in these mats, and how these microbes contribute to geological structure. These results will provide insight into the molecular and geochemical processes of microbial communities that prevailed on ancient Earth. Since stromatolites are formed by lithifying microbial mats that are able to mineralize calcium carbonate, understanding the biological mechanisms involved may lead to the development of carbon sequestration technologies that will be applicable in human spaceflight, as well as improve our understanding of global climate and its sustainability. The objective of my project was to analyze the archaeal and bacterial dIversity in stromatolites from Highborn Cay in the Bahamas. The first step in studying the molecular processes that the microorganisms carry out is to ascertain the microbial complexity within the mats, which includes identifying and estimating the numbers of different microbes that comprise these mats.

  19. Bacterial populations and metabolites in the feces of free roaming and captive grizzly bears.

    PubMed

    Schwab, Clarissa; Cristescu, Bogdan; Boyce, Mark S; Stenhouse, Gordon B; Gänzle, Michael

    2009-12-01

    Gut physiology, host phylogeny, and diet determine the composition of the intestinal microbiota. Grizzly bears (Ursus arctos horribilis) belong to the Order Carnivora, yet feed on an omnivorous diet. The role of intestinal microflora in grizzly bear digestion has not been investigated. Microbiota and microbial activity were analysed from the feces of wild and captive grizzly bears. Bacterial composition was determined using culture-dependent and culture-independent methods. The feces of wild and captive grizzly bears contained log 9.1 +/- 0.5 and log 9.2 +/- 0.3 gene copies x g(-1), respectively. Facultative anaerobes Enterobacteriaceae and enterococci were dominant in wild bear feces. Among the strict anaerobes, the Bacteroides-Prevotella-Porphyromonas group was most prominent. Enterobacteriaceae were predominant in the feces of captive grizzly bears, at log 8.9 +/- 0.5 gene copies x g(-1). Strict anaerobes of the Bacteroides-Prevotella-Porphyromonas group and the Clostridium coccoides cluster were present at log 6.7 +/- 0.9 and log 6.8 +/- 0.8 gene copies x g(-1), respectively. The presence of lactate and short-chain fatty acids (SCFAs) verified microbial activity. Total SCFA content and composition was affected by diet. SCFA composition in the feces of captive grizzly bears resembled the SCFA composition of prey-consuming wild animals. A consistent data set was obtained that associated fecal microbiota and metabolites with the distinctive gut physiology and diet of grizzly bears.

  20. Bacterial populations and metabolites in the feces of free roaming and captive grizzly bears.

    PubMed

    Schwab, Clarissa; Cristescu, Bogdan; Boyce, Mark S; Stenhouse, Gordon B; Gänzle, Michael

    2009-12-01

    Gut physiology, host phylogeny, and diet determine the composition of the intestinal microbiota. Grizzly bears (Ursus arctos horribilis) belong to the Order Carnivora, yet feed on an omnivorous diet. The role of intestinal microflora in grizzly bear digestion has not been investigated. Microbiota and microbial activity were analysed from the feces of wild and captive grizzly bears. Bacterial composition was determined using culture-dependent and culture-independent methods. The feces of wild and captive grizzly bears contained log 9.1 +/- 0.5 and log 9.2 +/- 0.3 gene copies x g(-1), respectively. Facultative anaerobes Enterobacteriaceae and enterococci were dominant in wild bear feces. Among the strict anaerobes, the Bacteroides-Prevotella-Porphyromonas group was most prominent. Enterobacteriaceae were predominant in the feces of captive grizzly bears, at log 8.9 +/- 0.5 gene copies x g(-1). Strict anaerobes of the Bacteroides-Prevotella-Porphyromonas group and the Clostridium coccoides cluster were present at log 6.7 +/- 0.9 and log 6.8 +/- 0.8 gene copies x g(-1), respectively. The presence of lactate and short-chain fatty acids (SCFAs) verified microbial activity. Total SCFA content and composition was affected by diet. SCFA composition in the feces of captive grizzly bears resembled the SCFA composition of prey-consuming wild animals. A consistent data set was obtained that associated fecal microbiota and metabolites with the distinctive gut physiology and diet of grizzly bears. PMID:20029525

  1. Collective Bacterial Dynamics Revealed Using a Three-Dimensional Population-Scale Defocused Particle Tracking Technique

    PubMed Central

    Wu, Mingming; Roberts, John W.; Kim, Sue; Koch, Donald L.; DeLisa, Matthew P.

    2006-01-01

    An ability to monitor bacterial locomotion and collective dynamics is crucial to our understanding of a number of well-characterized phenotypes including biofilm formation, chemotaxis, and virulence. Here, we report the tracking of multiple swimming Escherichia coli cells in three spatial dimensions and at single-cell resolution using a novel three-dimensional (3D) defocused particle tracking (DPT) method. The 3D trajectories were generated for wild-type Escherichia coli strain RP437 as well as for isogenic derivatives that display smooth swimming due to a cheA deletion (strain RP9535) or incessant tumbling behavior due to a cheZ deletion (strain RP1616). The 3D DPT method successfully differentiated these three modes of locomotion and allowed direct calculation of the diffusion coefficient for each strain. As expected, we found that the smooth swimmer diffused more readily than the wild type, and both the smooth swimmer and the wild-type cells exhibited diffusion coefficients that were at least two orders of magnitude larger than that of the tumbler. Finally, we found that the diffusion coefficient increased with increasing cell density, a phenomenon that can be attributed to the hydrodynamic disturbances caused by neighboring bacteria. PMID:16820497

  2. Uncovering potential 'herbal probiotics' in Juzen-taiho-to through the study of associated bacterial populations.

    PubMed

    Montenegro, Diego; Kalpana, Kriti; Chrissian, Christine; Sharma, Ashutosh; Takaoka, Anna; Iacovidou, Maria; Soll, Clifford E; Aminova, Olga; Heguy, Adriana; Cohen, Lisa; Shen, Steven; Kawamura, Akira

    2015-02-01

    Juzen-taiho-to (JTT) is an immune-boosting formulation of ten medicinal herbs. It is used clinically in East Asia to boost the human immune functions. The active factors in JTT have not been clarified. But, existing evidence suggests that lipopolysaccharide (LPS)-like factors contribute to the activity. To examine this possibility, JTT was subjected to a series of analyses, including high resolution mass spectrometry, which suggested the presence of structural variants of LPS. This finding opened a possibility that JTT contains immune-boosting bacteria. As the first step to characterize the bacteria in JTT, 16S ribosomal RNA sequencing was carried out for Angelica sinensis (dried root), one of the most potent immunostimulatory herbs in JTT. The sequencing revealed a total of 519 bacteria genera in A. sinensis. The most abundant genus was Rahnella, which is widely distributed in water and plants. The abundance of Rahnella appeared to correlate with the immunostimulatory activity of A. sinensis. In conclusion, the current study provided new pieces of evidence supporting the emerging theory of bacterial contribution in immune-boosting herbs.

  3. Effect of co-existing kaolinite and goethite on the aggregation of graphene oxide in the aquatic environment.

    PubMed

    Huang, Guanxing; Guo, Huiyuan; Zhao, Jian; Liu, Yonghong; Xing, Baoshan

    2016-10-01

    Broad applications of graphene oxide (GO) will result in the release of GO into aquatic environments, where clay minerals and metal (hydr)oxides are commonly present. Thereby the interactions between GO and a binary system containing clay minerals and metal (hydr)oxides can occur. We investigated the aggregation of GO with kaolinite and kaolinite-goethite associations (KGAs) in aquatic systems under different pHs, ionic strengths, and GO concentrations. GO suspension was unstable at low pHs, and the aggregation of GO occurred in the presence of KGA-4% and KGA-10% until pH 5 and 6, respectively. Kaolinite decreased the critical coagulation concentration (CCC) of GO at pH 5.5 from around 50 to 20 mM NaCl due to the reduced energy barrier. Heteroaggregation of GO with KGAs was extremely sensitive to ionic strength at pH 5.5, and the CCC of GO in the presence of KGA-10% increased from less than 1 mM NaCl to 5 mM NaCl with the increase of pH from 5.5 to 9. The heteroaggregation extent of GO with KGAs was enhanced firstly, then reduced with the increase of GO concentrations at pH 5.0, which is likely because KGA plates were more efficiently wrapped by large-size GO sheets with increasing GO concentrations. These findings are useful for understanding and predicting the fate of GO in the relatively complicated aquatic and soil environments where binary minerals co-exist.

  4. Effect of co-existing kaolinite and goethite on the aggregation of graphene oxide in the aquatic environment.

    PubMed

    Huang, Guanxing; Guo, Huiyuan; Zhao, Jian; Liu, Yonghong; Xing, Baoshan

    2016-10-01

    Broad applications of graphene oxide (GO) will result in the release of GO into aquatic environments, where clay minerals and metal (hydr)oxides are commonly present. Thereby the interactions between GO and a binary system containing clay minerals and metal (hydr)oxides can occur. We investigated the aggregation of GO with kaolinite and kaolinite-goethite associations (KGAs) in aquatic systems under different pHs, ionic strengths, and GO concentrations. GO suspension was unstable at low pHs, and the aggregation of GO occurred in the presence of KGA-4% and KGA-10% until pH 5 and 6, respectively. Kaolinite decreased the critical coagulation concentration (CCC) of GO at pH 5.5 from around 50 to 20 mM NaCl due to the reduced energy barrier. Heteroaggregation of GO with KGAs was extremely sensitive to ionic strength at pH 5.5, and the CCC of GO in the presence of KGA-10% increased from less than 1 mM NaCl to 5 mM NaCl with the increase of pH from 5.5 to 9. The heteroaggregation extent of GO with KGAs was enhanced firstly, then reduced with the increase of GO concentrations at pH 5.0, which is likely because KGA plates were more efficiently wrapped by large-size GO sheets with increasing GO concentrations. These findings are useful for understanding and predicting the fate of GO in the relatively complicated aquatic and soil environments where binary minerals co-exist. PMID:27379727

  5. Experimental model considerations for the study of protein-energy malnutrition co-existing with ischemic brain injury.

    PubMed

    Prosser-Loose, Erin J; Smith, Shari E; Paterson, Phyllis G

    2011-05-01

    Protein-energy malnutrition (PEM) affects ~16% of patients at admission for stroke. We previously modeled this in a gerbil global cerebral ischemia model and found that PEM impairs functional outcome and influences mechanisms of ischemic brain injury and recovery. Since this model is no longer reliable, we investigated the utility of the rat 2-vessel occlusion (2-VO) with hypotension model of global ischemia for further study of this clinical problem. Male, Sprague-Dawley rats were exposed to either control diet (18% protein) or PEM induced by feeding a low protein diet (2% protein) for 7d prior to either global ischemia or sham surgery. PEM did not significantly alter the hippocampal CA1 neuron death (p = 0.195 by 2-factor ANOVA) or the increase in dendritic injury caused by exposure to global ischemia. Unexpectedly, however, a strong trend was evident for PEM to decrease the consistency of hippocampal damage, as shown by an increased incidence of unilateral or no hippocampal damage (p=0.069 by chi-square analysis). Although PEM caused significant changes to baseline arterial blood pH, pO(2), pCO(2), and fasting glucose (p<0.05), none of these variables (nor hematocrit) correlated significantly with CA1 cell counts in the malnourished group exposed to 2-VO (p>0.269). Intra-ischemic tympanic temperature and blood pressure were strictly and equally controlled between ischemic groups. We conclude that co-existing PEM confounded the consistency of hippocampal injury in the 2-VO model. Although the mechanisms responsible were not identified, this model of brain ischemia should not be used for studying this co-morbidity factor.

  6. Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem.

    PubMed

    Johnston, Eric R; Rodriguez-R, Luis M; Luo, Chengwei; Yuan, Mengting M; Wu, Liyou; He, Zhili; Schuur, Edward A G; Luo, Yiqi; Tiedje, James M; Zhou, Jizhong; Konstantinidis, Konstantinos T

    2016-01-01

    How soil microbial communities contrast with respect to taxonomic and functional composition within and between ecosystems remains an unresolved question that is central to predicting how global anthropogenic change will affect soil functioning and services. In particular, it remains unclear how small-scale observations of soil communities based on the typical volume sampled (1-2 g) are generalizable to ecosystem-scale responses and processes. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared to temperate soils. Here, we employed well-replicated shotgun metagenome and 16S rRNA gene amplicon sequencing to characterize community composition and metabolic potential in Alaskan tundra soils, combining our own datasets with those publically available from distant tundra and temperate grassland and agriculture habitats. We found that the abundance of many taxa and metabolic functions differed substantially between tundra soil metagenomes relative to those from temperate soils, and that a high degree of OTU-sharing exists between tundra locations. Tundra soils were an order of magnitude less complex than their temperate counterparts, allowing for near-complete coverage of microbial community richness (~92% breadth) by sequencing, and the recovery of 27 high-quality, almost complete (>80% completeness) population bins. These population bins, collectively, made up to ~10% of the metagenomic datasets, and represented diverse taxonomic groups and metabolic lifestyles tuned toward sulfur cycling, hydrogen metabolism, methanotrophy, and organic matter oxidation. Several population bins, including members of Acidobacteria, Actinobacteria, and Proteobacteria, were also present in geographically distant (~100-530 km apart) tundra habitats (full genome representation and up to 99.6% genome-derived average nucleotide identity). Collectively, our results revealed that

  7. Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations

    SciTech Connect

    Xue, Hong; Cordero, Otto X.; Camas, Francisco M.; Trimble, William; Meyer, Folker; Guglielmini, Julien; Rocha, Eduardo P. C.; Polz, Martin F.

    2015-05-05

    Although plasmids and other episomes are recognized as key players in horizontal gene transfer among microbes, their diversity and dynamics among ecologically structured host populations in the wild remain poorly understood. Here, we show that natural populations of marine Vibrionaceae bacteria host large numbers of families of episomes, consisting of plasmids and a surprisingly high fraction of plasmid-like temperate phages. Episomes are unevenly distributed among host populations, and contrary to the notion that high-density communities in biofilms act as hot spots of gene transfer, we identified a strong bias for episomes to occur in free-living as opposed to particle-attached cells. Mapping of episomal families onto host phylogeny shows that, with the exception of all phage and a few plasmid families, most are of recent evolutionary origin and appear to have spread rapidly by horizontal transfer. Such high eco-evolutionary turnover is particularly surprising for plasmids that are, based on previously suggested categorization, putatively nontransmissible, indicating that this type of plasmid is indeed frequently transferred by currently unknown mechanisms. Finally, analysis of recent gene transfer among plasmids reveals a network of extensive exchange connecting nearly all episomes. Genes functioning in plasmid transfer and maintenance are frequently exchanged, suggesting that plasmids can be rapidly transformed from one category to another. The broad distribution of episomes among distantly related hosts and the observed promiscuous recombination patterns show how episomes can offer their hosts rapid assembly and dissemination of novel functions.

  8. Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations

    DOE PAGES

    Xue, Hong; Cordero, Otto X.; Camas, Francisco M.; Trimble, William; Meyer, Folker; Guglielmini, Julien; Rocha, Eduardo P. C.; Polz, Martin F.

    2015-05-05

    Although plasmids and other episomes are recognized as key players in horizontal gene transfer among microbes, their diversity and dynamics among ecologically structured host populations in the wild remain poorly understood. Here, we show that natural populations of marine Vibrionaceae bacteria host large numbers of families of episomes, consisting of plasmids and a surprisingly high fraction of plasmid-like temperate phages. Episomes are unevenly distributed among host populations, and contrary to the notion that high-density communities in biofilms act as hot spots of gene transfer, we identified a strong bias for episomes to occur in free-living as opposed to particle-attached cells.more » Mapping of episomal families onto host phylogeny shows that, with the exception of all phage and a few plasmid families, most are of recent evolutionary origin and appear to have spread rapidly by horizontal transfer. Such high eco-evolutionary turnover is particularly surprising for plasmids that are, based on previously suggested categorization, putatively nontransmissible, indicating that this type of plasmid is indeed frequently transferred by currently unknown mechanisms. Finally, analysis of recent gene transfer among plasmids reveals a network of extensive exchange connecting nearly all episomes. Genes functioning in plasmid transfer and maintenance are frequently exchanged, suggesting that plasmids can be rapidly transformed from one category to another. The broad distribution of episomes among distantly related hosts and the observed promiscuous recombination patterns show how episomes can offer their hosts rapid assembly and dissemination of novel functions.« less

  9. Greenhouse gas, animal performance, and bacterial population structure responses to dietary monensin fed to dairy cows.

    PubMed

    Hamilton, Scott W; DePeters, Edward J; McGarvey, Jeffery A; Lathrop, Jeremy; Mitloehner, Frank M

    2010-01-01

    The present study investigated the effects of a feed additive and rumen microbial modifier, monensin sodium (monensin), on selected variables in lactating dairy cows. Monensin fed cows (MON, 600 mg d(-1)) were compared with untreated control cows (CON, 0 mg d(-1)) with respect to the effects of monensin on the production of three greenhouse gases (GHG), methane (CH(4)), nitrous oxide (N(2)O), and carbon dioxide (CO(2)), along with animal performance (dry matter intake; DMI), milk production, milk components, plasma urea nitrogen (PUN), milk urea nitrogen (MUN), and the microbial population structure of fresh feces. Measurements of GHG were collected at Days 14 and 60 in an environmental chamber simulating commercial dairy freestall housing conditions. Milk production and DMI measurements were collected twice daily over the 60-d experimental period; milk components, PUN, and MUN were measured on Days 14 and 60. The microbial population structure of feces from 6 MON and 6 CON cows was examined on three different occasions (Days 14, 30, and 60). Monensin did not affect emissions of methane (CH(4)), nitrous oxide (N(2)O), and carbon dioxide (CO(2)). Over a 24-h period, emissions of CH(4), N(2)O, and CO(2) decreased in both MON and CON groups. Animal performance and the microbial population structure of the animal fresh waste were also unaffected for MON vs. CON cows.

  10. Generality of the growth kinetics of the average individual cell in different bacterial populations.

    PubMed Central

    Trueba, F J; Neijssel, O M; Woldringh, C L

    1982-01-01

    The kinetics of growth of all the cells in a population is reflected in the shape of the size distribution of the population. To ascertain whether the kinetics of growth of the average individual cell is similar for different strains or growth conditions, we compared the shape of normalized size distributions obtained from steady-state populations. Significant differences in the size distributions were found, but these could be ascribed either to the precision achieved at division or to a constriction period which is long relative to the total cell cycle time. The remaining difference is quite small. Thus, without establishing the pattern itself, it is concluded that the basic course of growth is very similar for the various Escherichia coli strains examined and probably also for other rod-shaped bacteria. The effects of differences in culture technique (batch or chemostat culture), growth rate, and differences among strains were not found to influence the shape of the size distributions and hence the growth kinetics in a direct manner; small differences were found, but only when the precision at division or the fraction of constricted cells (long constriction period) were different as well. PMID:6804435

  11. Greenhouse gas, animal performance, and bacterial population structure responses to dietary monensin fed to dairy cows.

    PubMed

    Hamilton, Scott W; DePeters, Edward J; McGarvey, Jeffery A; Lathrop, Jeremy; Mitloehner, Frank M

    2010-01-01

    The present study investigated the effects of a feed additive and rumen microbial modifier, monensin sodium (monensin), on selected variables in lactating dairy cows. Monensin fed cows (MON, 600 mg d(-1)) were compared with untreated control cows (CON, 0 mg d(-1)) with respect to the effects of monensin on the production of three greenhouse gases (GHG), methane (CH(4)), nitrous oxide (N(2)O), and carbon dioxide (CO(2)), along with animal performance (dry matter intake; DMI), milk production, milk components, plasma urea nitrogen (PUN), milk urea nitrogen (MUN), and the microbial population structure of fresh feces. Measurements of GHG were collected at Days 14 and 60 in an environmental chamber simulating commercial dairy freestall housing conditions. Milk production and DMI measurements were collected twice daily over the 60-d experimental period; milk components, PUN, and MUN were measured on Days 14 and 60. The microbial population structure of feces from 6 MON and 6 CON cows was examined on three different occasions (Days 14, 30, and 60). Monensin did not affect emissions of methane (CH(4)), nitrous oxide (N(2)O), and carbon dioxide (CO(2)). Over a 24-h period, emissions of CH(4), N(2)O, and CO(2) decreased in both MON and CON groups. Animal performance and the microbial population structure of the animal fresh waste were also unaffected for MON vs. CON cows. PMID:20048298

  12. Divergent evolution peaks under intermediate population bottlenecks during bacterial experimental evolution

    PubMed Central

    Phillips, Robyn L.; Gifford, Danna R.; MacLean, R. Craig

    2016-01-01

    There is growing evidence that parallel molecular evolution is common, but its causes remain poorly understood. Demographic parameters such as population bottlenecks are predicted to be major determinants of parallelism. Here, we test the hypothesis that bottleneck intensity shapes parallel evolution by elucidating the genomic basis of adaptation to antibiotic-supplemented media in hundreds of populations of the bacterium Pseudomonas fluorescens Pf0-1. As expected, bottlenecking decreased the rate of phenotypic and molecular adaptation. Surprisingly, bottlenecking had no impact on the likelihood of parallel adaptive molecular evolution at a genome-wide scale. However, bottlenecking had a profound impact on the genes involved in antibiotic resistance. Specifically, under either intense or weak bottlenecking, resistance predominantly evolved by strongly beneficial mutations which provide high levels of antibiotic resistance. In contrast with intermediate bottlenecking regimes, resistance evolved by a greater diversity of genetic mechanisms, significantly reducing the observed levels of parallel genetic evolution. Our results demonstrate that population bottlenecking can be a major predictor of parallel evolution, but precisely how may be more complex than many simple theoretical predictions. PMID:27466449

  13. Further evidence for the regulation of bacterial populations in soil by protozoa.

    PubMed

    Habte, M; Alexander, M

    1977-06-20

    After the addition to soil of large numbers of a cowpea Rhizobium strain, the population declined steadily until the numbers reached about 10(7)/g, and the protozoa rose to about 10(4)/g. When indigenous protozoa were suppressed by the addition of actidione to the soil, the density of the test rhizobium did not fall initially, but its abundance declined to about 10(7)/g when actidione-resistant protozoa arose in significant numbers. The addition to actidione-treated soil of an antibiotic-resistant strain of Paramecium led to a rapid decrease in the population of the rhizobium, the density reaching essentially the same value as in soil receiving neither the drug nor the paramecia. The same changes occurred with Xanthomonas campestris as test prey except that its numbers fell to about 10(5)/g of soil. These data provide further evidence for the key role of protozoa in controlling the abundance of populations of certain bacteria introduced into soil. PMID:879960

  14. In situ spatial patterns of soil bacterial populations, mapped at multiple scales, in an arable soil.

    PubMed

    Nunan, N; Wu, K; Young, I M; Crawford, J W; Ritz, K

    2002-11-01

    Very little is known about the spatial organization of soil microbes across scales that are relevant both to microbial function and to field-based processes. The spatial distributions of microbes and microbially mediated activity have a high intrinsic variability. This can present problems when trying to quantify the effects of disturbance, management practices, or climate change on soil microbial systems and attendant function. A spatial sampling regime was implemented in an arable field. Cores of undisturbed soil were sampled from a 3 x 3 x 0.9 m volume of soil (topsoil and subsoil) and a biological thin section, in which the in situ distribution of bacteria could be quantified, prepared from each core. Geostatistical analysis was used to quantify the nature of spatial structure from micrometers to meters and spatial point pattern analysis to test for deviations from complete spatial randomness of mapped bacteria. Spatial structure in the topsoil was only found at the microscale (micrometers), whereas evidence for nested scales of spatial structure was found in the subsoil (at the microscale, and at the centimeter to meter scale). Geostatistical ranges of spatial structure at the micro scale were greater in the topsoil and tended to decrease with depth in the subsoil. Evidence for spatial aggregation in bacteria was stronger in the topsoil and also decreased with depth in the subsoil, though extremely high degrees of aggregation were found at very short distances in the deep subsoil. The data suggest that factors that regulate the distribution of bacteria in the subsoil operate at two scales, in contrast to one scale in the topsoil, and that bacterial patches are larger and more prevalent in the topsoil.

  15. Housefly Larva Vermicomposting Efficiently Attenuates Antibiotic Resistance Genes in Swine Manure, with Concomitant Bacterial Population Changes

    PubMed Central

    Wang, Hang; Li, Hongyi; Gilbert, Jack A.; Li, Haibo; Wu, Longhua; Liu, Meng; Wang, Liling; Zhou, Qiansheng; Yuan, Junxiang

    2015-01-01

    Manure from swine treated with antimicrobials as feed additives is a major source for the expansion of the antibiotic resistance gene (ARG) reservoir in the environment. Vermicomposting via housefly larvae (Musca domestica) can be efficiently used to treat manure and regenerate biofertilizer, but few studies have investigated its effect on ARG attenuation. Here, we tracked the abundances of 9 ARGs and the composition and structure of the bacterial communities in manure samples across 6 days of full-scale manure vermicomposting. On day 6, the abundances of genes encoding tetracycline resistance [tet(M), tet(O), tet(Q), and tet(W)] were reduced (P < 0.05), while those of genes encoding sulfonamide resistance (sul1 and sul2) were increased (P < 0.05) when normalized to 16S rRNA. The abundances of tetracycline resistance genes were correlated (P < 0.05) with the changing concentrations of tetracyclines in the manure. The overall diversity and richness of the bacteria significantly decreased during vermicomposting, accompanied by a 100 times increase in the relative abundance of Flavobacteriaceae spp. Variations in the abundances of ARGs were correlated with the changing microbial community structure and the relative abundances of the family Ruminococcaceae, class Bacilli, or phylum Proteobacteria. Vermicomposting, as a waste management practice, can reduce the overall abundance of ARGs. More research is warranted to assess the use of this waste management practice as a measure to attenuate the dissemination of antimicrobial residues and ARGs from livestock production before vermicompost can be safely used as biofertilizer in agroecosystems. PMID:26296728

  16. Housefly Larva Vermicomposting Efficiently Attenuates Antibiotic Resistance Genes in Swine Manure, with Concomitant Bacterial Population Changes.

    PubMed

    Wang, Hang; Li, Hongyi; Gilbert, Jack A; Li, Haibo; Wu, Longhua; Liu, Meng; Wang, Liling; Zhou, Qiansheng; Yuan, Junxiang; Zhang, Zhijian

    2015-11-01

    Manure from swine treated with antimicrobials as feed additives is a major source for the expansion of the antibiotic resistance gene (ARG) reservoir in the environment. Vermicomposting via housefly larvae (Musca domestica) can be efficiently used to treat manure and regenerate biofertilizer, but few studies have investigated its effect on ARG attenuation. Here, we tracked the abundances of 9 ARGs and the composition and structure of the bacterial communities in manure samples across 6 days of full-scale manure vermicomposting. On day 6, the abundances of genes encoding tetracycline resistance [tet(M), tet(O), tet(Q), and tet(W)] were reduced (P < 0.05), while those of genes encoding sulfonamide resistance (sul1 and sul2) were increased (P < 0.05) when normalized to 16S rRNA. The abundances of tetracycline resistance genes were correlated (P < 0.05) with the changing concentrations of tetracyclines in the manure. The overall diversity and richness of the bacteria significantly decreased during vermicomposting, accompanied by a 100 times increase in the relative abundance of Flavobacteriaceae spp. Variations in the abundances of ARGs were correlated with the changing microbial community structure and the relative abundances of the family Ruminococcaceae, class Bacilli, or phylum Proteobacteria. Vermicomposting, as a waste management practice, can reduce the overall abundance of ARGs. More research is warranted to assess the use of this waste management practice as a measure to attenuate the dissemination of antimicrobial residues and ARGs from livestock production before vermicompost can be safely used as biofertilizer in agroecosystems. PMID:26296728

  17. Housefly Larva Vermicomposting Efficiently Attenuates Antibiotic Resistance Genes in Swine Manure, with Concomitant Bacterial Population Changes.

    PubMed

    Wang, Hang; Li, Hongyi; Gilbert, Jack A; Li, Haibo; Wu, Longhua; Liu, Meng; Wang, Liling; Zhou, Qiansheng; Yuan, Junxiang; Zhang, Zhijian

    2015-11-01

    Manure from swine treated with antimicrobials as feed additives is a major source for the expansion of the antibiotic resistance gene (ARG) reservoir in the environment. Vermicomposting via housefly larvae (Musca domestica) can be efficiently used to treat manure and regenerate biofertilizer, but few studies have investigated its effect on ARG attenuation. Here, we tracked the abundances of 9 ARGs and the composition and structure of the bacterial communities in manure samples across 6 days of full-scale manure vermicomposting. On day 6, the abundances of genes encoding tetracycline resistance [tet(M), tet(O), tet(Q), and tet(W)] were reduced (P < 0.05), while those of genes encoding sulfonamide resistance (sul1 and sul2) were increased (P < 0.05) when normalized to 16S rRNA. The abundances of tetracycline resistance genes were correlated (P < 0.05) with the changing concentrations of tetracyclines in the manure. The overall diversity and richness of the bacteria significantly decreased during vermicomposting, accompanied by a 100 times increase in the relative abundance of Flavobacteriaceae spp. Variations in the abundances of ARGs were correlated with the changing microbial community structure and the relative abundances of the family Ruminococcaceae, class Bacilli, or phylum Proteobacteria. Vermicomposting, as a waste management practice, can reduce the overall abundance of ARGs. More research is warranted to assess the use of this waste management practice as a measure to attenuate the dissemination of antimicrobial residues and ARGs from livestock production before vermicompost can be safely used as biofertilizer in agroecosystems.

  18. Experimental approach for bacteriophage susceptibility testing of planktonic and sessile bacterial populations – Study protocol

    PubMed Central

    Neguţ, Alina Cristina; Săndulescu, Oana; Popa, Marcela; Streinu-Cercel, Anca; Alavidze, Zemphira; Berciu, Ioana; Bleotu, Coralia; Popa, Mircea Ioan; Chifiriuc, Mariana Carmen; Streinu-Cercel, Adrian

    2014-01-01

    Introduction Antimicrobial resistance is a growing threat for all clinical branches. This phenomenon poses important challenges in controlling infectious diseases. However, multidrug resistance is not the only issue, as bacteria that are otherwise susceptible to common antibiotics express other patterns for evading antibiotherapy, for example they can aggregate within a self-produced matrix to form biofilm. Methods We intend to perform a prospective laboratory study of the germs isolated from different samples collected from patients admitted with infectious pathology in reference hospitals in Romania. We will perform antibiotic resistance testing as well as phage testing, both on solid and liquid growth medium, for Staphylococcus spp., Enterococcus spp., and Pseudomonas spp. We intend to collect data for 150 patients with different infections with these identified pathogens. Phage susceptibility testing will be performed using 5 types of strain-specific bacteriophage mixtures: PYO, INTESTI, STAPHYLOCOCCAL (Eliava BioPreparations, Tbilisi, Georgia), PHAGYO, PHAGESTI (JSC “Biochimpharm”, Tbilisi, Georgia). For phage-susceptible strains, we will evaluate biofilm formation in the presence of phages, as well as phage effect on already formed biofilm. Expected results Through this study, we intend to provide the first set of results on bacteriophage-susceptibility of bacteria isolated from patients with hard to treat infections, from reference hospitals in Romania. By evaluating a large number of bacterial strains we aim to predict and project biofilm kinetics, while adding binary phage dilutions at key timepoints during biofilm formation. Acknowledgments POSDRU/159/1.5/S/141531; Carol Davila University of Medicine and Pharmacy, Young Researchers Grant no. 28341/2013. PMID:25505742

  19. Paths and patterns: the biology and physics of swimming bacterial populations

    NASA Technical Reports Server (NTRS)

    Kessler, J. O.; Strittmatter, R. P.; Swartz, D. L.; Wiseley, D. A.; Wojciechowski, M. F.

    1995-01-01

    The velocity distribution of swimming micro-organisms depends on directional cues supplied by the environment. Directional swimming within a bounded space results in the accumulation of organisms near one or more surfaces. Gravity, gradients of chemical concentration and illumination affect the motile behaviour of individual swimmers. Concentrated populations of organisms scatter and absorb light or consume molecules, such as oxygen. When supply is one-sided, consumption creates gradients; the presence of the population alters the intensity and the symmetry of the environmental cues. Patterns of cues interact dynamically with patterns of the consumer population. In suspensions, spatial variations in the concentration of organisms are equivalent to variations of mean mass density of the fluid. When organisms accumulate in one region whilst moving away from another region, the force of gravity causes convection that translocates both organisms and dissolved substances. The geometry of the resulting concentration-convection patterns has features that are remarkably reproducible. Of interest for biology are (1) the long-range organisation achieved by organisms that do not communicate, and (2) that the entire system, consisting of fluid, cells, directional supply of consumables, boundaries and gravity, generates a dynamic that improves the organisms' habitat by enhancing transport and mixing. Velocity distributions of the bacterium Bacillus subtilis have been measured within the milieu of the spatially and temporally varying oxygen concentration which they themselves create. These distributions of swimming speed and direction are the fundamental ingredients required for a quantitative mathematical treatment of the patterns. The quantitative measurement of swimming behaviour also contributes to our understanding of aerotaxis of individual cells.

  20. Composition of Bacterial Communities Associated with Aurelia aurita Changes with Compartment, Life Stage, and Population

    PubMed Central

    Weiland-Bräuer, Nancy; Neulinger, Sven C.; Pinnow, Nicole; Künzel, Sven; Baines, John F.

    2015-01-01

    The scyphozoan Aurelia aurita is recognized as a key player in marine ecosystems and a driver of ecosystem change. It is thus intensely studied to address ecological questions, although its associations with microorganisms remain so far undescribed. In the present study, the microbiota associated with A. aurita was visualized with fluorescence in situ hybridization (FISH) analysis, and community structure was analyzed with respect to different life stages, compartments, and populations of A. aurita by 16S rRNA gene amplicon sequencing. We demonstrate that the composition of the A. aurita microbiota is generally highly distinct from the composition of communities present in ambient water. Comparison of microbial communities from different developmental stages reveals evidence for life stage-specific community patterns. Significant restructuring of the microbiota during strobilation from benthic polyp to planktonic life stages is present, arguing for a restructuring during the course of metamorphosis. Furthermore, the microbiota present in different compartments of the adult medusa (exumbrella mucus and gastric cavity) display significant differences, indicating body part-specific colonization. A novel Mycoplasma strain was identified in both compartment-specific microbiota and is most likely present inside the epithelium as indicated by FISH analysis of polyps, indicating potential endosymbiosis. Finally, comparison of polyps of different populations kept under the same controlled laboratory conditions in the same ambient water showed population-specific community patterns, most likely due the genetic background of the host. In conclusion, the presented data indicate that the associated microbiota of A. aurita may play important functional roles, e.g., during the life cycle. PMID:26116680

  1. Bacterial population development and chemical characteristics of refuse decomposition in a simulated sanitary landfill

    SciTech Connect

    Barlaz, M.A.; Schaefer, D.M.; Ham, R.K. )

    1989-01-01

    Population development of key groups of bacteria involved in municipal refuse conversion to methane was measured from the time of initial incubation through the onset of methane production. Hemicellulolytic bacteria, cellulolytic bacteria, hydrogen-producing acetogens, and acetate-and H{sub 2}-plus-CO{sub 2}-utilizing methanogens were enumerated by the most-probable-number technique with media containing oat spelt xylan, ball-milled cellulose, butyrate, acetate, and H{sub 2} plus CO{sub 2}, respectively. The methane concentration of the sampled containers increased to 64% by day 69, at which time the maximum methane production rate, 929 liters of CH{sub 4} per day kg-year, was measured. Population increases of 2, 4, 5, 5, and 6 orders of magnitude were measured between fresh refuse and the methane production phase for the hemicellulolytic bacteria, cellulolytic bacteria, butyrate-catabolizing acetogens, and acetate- and H{sub 2}-CO{sub 2}-utilizing methanogens, respectively. The cellulolytic bacteria and acetogens increased more slowly than the methanogens and only after the onset of methane production. The initial decrease in the pH of the refuse ecosystem from 7.5 to 5.7 was attributed to the accumulation of acidic end products of sugar fermentation, to the low acid-consuming activity of the acetogenic and methanogenic bacteria, and to levels of oxygen and nitrate in the fresh refuse sufficient for oxidation of only 8% of the sugars to carbon dioxide and water. Cellulose and hemicellulose decomposition was most rapid after establishment of the methanogenic and acetogenic populations and a reduction in the initial accumulation of carboxylic acids. Initially acetate utilization, but ultimately polymer hydrolysis, limited the rate of refuse conversion to methane.

  2. Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem

    PubMed Central

    Johnston, Eric R.; Rodriguez-R, Luis M.; Luo, Chengwei; Yuan, Mengting M.; Wu, Liyou; He, Zhili; Schuur, Edward A. G.; Luo, Yiqi; Tiedje, James M.; Zhou, Jizhong; Konstantinidis, Konstantinos T.

    2016-01-01

    How soil microbial communities contrast with respect to taxonomic and functional composition within and between ecosystems remains an unresolved question that is central to predicting how global anthropogenic change will affect soil functioning and services. In particular, it remains unclear how small-scale observations of soil communities based on the typical volume sampled (1–2 g) are generalizable to ecosystem-scale responses and processes. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared to temperate soils. Here, we employed well-replicated shotgun metagenome and 16S rRNA gene amplicon sequencing to characterize community composition and metabolic potential in Alaskan tundra soils, combining our own datasets with those publically available from distant tundra and temperate grassland and agriculture habitats. We found that the abundance of many taxa and metabolic functions differed substantially between tundra soil metagenomes relative to those from temperate soils, and that a high degree of OTU-sharing exists between tundra locations. Tundra soils were an order of magnitude less complex than their temperate counterparts, allowing for near-complete coverage of microbial community richness (~92% breadth) by sequencing, and the recovery of 27 high-quality, almost complete (>80% completeness) population bins. These population bins, collectively, made up to ~10% of the metagenomic datasets, and represented diverse taxonomic groups and metabolic lifestyles tuned toward sulfur cycling, hydrogen metabolism, methanotrophy, and organic matter oxidation. Several population bins, including members of Acidobacteria, Actinobacteria, and Proteobacteria, were also present in geographically distant (~100–530 km apart) tundra habitats (full genome representation and up to 99.6% genome-derived average nucleotide identity). Collectively, our results revealed

  3. Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem.

    PubMed

    Johnston, Eric R; Rodriguez-R, Luis M; Luo, Chengwei; Yuan, Mengting M; Wu, Liyou; He, Zhili; Schuur, Edward A G; Luo, Yiqi; Tiedje, James M; Zhou, Jizhong; Konstantinidis, Konstantinos T

    2016-01-01

    How soil microbial communities contrast with respect to taxonomic and functional composition within and between ecosystems remains an unresolved question that is central to predicting how global anthropogenic change will affect soil functioning and services. In particular, it remains unclear how small-scale observations of soil communities based on the typical volume sampled (1-2 g) are generalizable to ecosystem-scale responses and processes. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared to temperate soils. Here, we employed well-replicated shotgun metagenome and 16S rRNA gene amplicon sequencing to characterize community composition and metabolic potential in Alaskan tundra soils, combining our own datasets with those publically available from distant tundra and temperate grassland and agriculture habitats. We found that the abundance of many taxa and metabolic functions differed substantially between tundra soil metagenomes relative to those from temperate soils, and that a high degree of OTU-sharing exists between tundra locations. Tundra soils were an order of magnitude less complex than their temperate counterparts, allowing for near-complete coverage of microbial community richness (~92% breadth) by sequencing, and the recovery of 27 high-quality, almost complete (>80% completeness) population bins. These population bins, collectively, made up to ~10% of the metagenomic datasets, and represented diverse taxonomic groups and metabolic lifestyles tuned toward sulfur cycling, hydrogen metabolism, methanotrophy, and organic matter oxidation. Several population bins, including members of Acidobacteria, Actinobacteria, and Proteobacteria, were also present in geographically distant (~100-530 km apart) tundra habitats (full genome representation and up to 99.6% genome-derived average nucleotide identity). Collectively, our results revealed that

  4. Artificially Constructed Quorum-Sensing Circuits Are Used for Subtle Control of Bacterial Population Density

    PubMed Central

    Wang, Zhaoshou; Wu, Xin; Peng, Jianghai; Hu, Yidan; Fang, Baishan; Huang, Shiyang

    2014-01-01

    Vibrio fischeri is a typical quorum-sensing bacterium for which lux box, luxR, and luxI have been identified as the key elements involved in quorum sensing. To decode the quorum-sensing mechanism, an artificially constructed cell–cell communication system has been built. In brief, the system expresses several programmed cell-death BioBricks and quorum-sensing genes driven by the promoters lux pR and PlacO-1 in Escherichia coli cells. Their transformation and expression was confirmed by gel electrophoresis and sequencing. To evaluate its performance, viable cell numbers at various time periods were investigated. Our results showed that bacteria expressing killer proteins corresponding to ribosome binding site efficiency of 0.07, 0.3, 0.6, or 1.0 successfully sensed each other in a population-dependent manner and communicated with each other to subtly control their population density. This was also validated using a proposed simple mathematical model. PMID:25119347

  5. Niche differentiation among sulfur-oxidizing bacterial populations in cave waters.

    PubMed

    Macalady, Jennifer L; Dattagupta, Sharmishtha; Schaperdoth, Irene; Jones, Daniel S; Druschel, Greg K; Eastman, Danielle

    2008-06-01

    The sulfidic Frasassi cave system affords a unique opportunity to investigate niche relationships among sulfur-oxidizing bacteria, including epsilonproteobacterial clades with no cultivated representatives. Oxygen and sulfide concentrations in the cave waters range over more than two orders of magnitude as a result of seasonally and spatially variable dilution of the sulfidic groundwater. A full-cycle rRNA approach was used to quantify dominant populations in biofilms collected in both diluted and undiluted zones. Sulfide concentration profiles within biofilms were obtained in situ using microelectrode voltammetry. Populations in rock-attached streamers depended on the sulfide/oxygen supply ratio of bulk water (r=0.97; P<0.0001). Filamentous epsilonproteobacteria dominated at high sulfide to oxygen ratios (>150), whereas Thiothrix dominated at low ratios (<75). In contrast, Beggiatoa was the dominant group in biofilms at the sediment-water interface regardless of sulfide and oxygen concentrations or supply ratio. Our results highlight the versatility and ecological success of Beggiatoa in diffusion-controlled niches, and demonstrate that high sulfide/oxygen ratios in turbulent water are important for the growth of filamentous epsilonproteobacteria.

  6. Bacterial reduction of highly concentrated perchlorate: Kinetics and influence of co-existing electron acceptors, temperature, pH and electron donors.

    PubMed

    Zhu, Yanping; Gao, Naiyun; Chu, Wenhai; Wang, Shuaifeng; Xu, Jianhong

    2016-04-01

    Perchlorate reduction kinetics and effects of various environmental conditions on removal of perchlorate from synthetic water were investigated to seek high-strength perchlorate removal using mixed perchlorate reducing bacteria. Results demonstrated that perchlorate (50-1500 mg L(-1)) could be degraded rapidly within 28 h under the optimal conditions. The maximum specific perchlorate reduction rate (qmax) and half saturation constant (Ks) were 0.92 mg-perchlorate (mg-dry weight)(-1) h(-1) and 157.7 mg L(-1), respectively. In the ClO4(-)-NO3(-) systems obvious but recoverable lags were caused in perchlorate reduction and the lag time increased with the ratio of nitrate to perchlorate concentration increasing from 0.5 to 3. While in the ClO4(-)-SO4(2-) systems inhibitions didn't occur until the ratio of sulfate to perchlorate concentration exceeded 10. The optimum temperature and pH value were 35 °C and 6.85, respectively. The optimal acetate-to-perchlorate ratio that could consume all perchlorate and acetate simultaneously was about 2. Dechloromonas, one of the most prominent perchlorate reducing bacteria, was identified as the dominant bacterium in the acclimated culture (69.33% of the whole clones). The study demonstrated that the perchlorate-acclimated mixed microorganisms can readily and efficiently realize reduction of highly concentrated perchlorate in wastewater.

  7. Both Leaf Properties and Microbe-Microbe Interactions Influence Within-Species Variation in Bacterial Population Diversity and Structure in the Lettuce (Lactuca Species) Phyllosphere▿

    PubMed Central

    Hunter, Paul J.; Hand, Paul; Pink, David; Whipps, John M.; Bending, Gary D.

    2010-01-01

    Morphological and chemical differences between plant genera influence phyllosphere microbial populations, but the factors driving within-species variation in phyllosphere populations are poorly understood. Twenty-six lettuce accessions were used to investigate factors controlling within-species variation in phyllosphere bacterial populations. Morphological and physiochemical characteristics of the plants were compared, and bacterial community structure and diversity were investigated using terminal restriction fragment length polymorphism (T-RFLP) profiling and 16S rRNA gene clone libraries. Plant morphology and levels of soluble carbohydrates, calcium, and phenolic compounds (which have long been associated with plant responses to biotic stress) were found to significantly influence bacterial community structure. Clone libraries from three representative accessions were found to be significantly different in terms of both sequence differences and the bacterial genera represented. All three libraries were dominated by Pseudomonas species and the Enterobacteriaceae family. Significant differences in the relative proportions of genera in the Enterobacteriaceae were detected between lettuce accessions. Two such genera (Erwinia and Enterobacter) showed significant variation between the accessions and revealed microbe-microbe interactions. We conclude that both leaf surface properties and microbial interactions are important in determining the structure and diversity of the phyllosphere bacterial community. PMID:20952648

  8. Climate change affects key nitrogen-fixing bacterial populations on coral reefs.

    PubMed

    Santos, Henrique F; Carmo, Flávia L; Duarte, Gustavo; Dini-Andreote, Francisco; Castro, Clovis B; Rosado, Alexandre S; van Elsas, Jan Dirk; Peixoto, Raquel S

    2014-11-01

    Coral reefs are at serious risk due to events associated with global climate change. Elevated ocean temperatures have unpredictable consequences for the ocean's biogeochemical cycles. The nitrogen cycle is driven by complex microbial transformations, including nitrogen fixation. This study investigated the effects of increased seawater temperature on bacteria able to fix nitrogen (diazotrophs) that live in association with the mussid coral Mussismilia harttii. Consistent increases in diazotroph abundances and diversities were found at increased temperatures. Moreover, gradual shifts in the dominance of particular diazotroph populations occurred as temperature increased, indicating a potential future scenario of climate change. The temperature-sensitive diazotrophs may provide useful bioindicators of the effects of thermal stress on coral reef health, allowing the impact of thermal anomalies to be monitored. In addition, our findings support the development of research on different strategies to improve the fitness of corals during events of thermal stress, such as augmentation with specific diazotrophs.

  9. Understanding anti-tuberculosis drug efficacy: rethinking bacterial populations and how we model them.

    PubMed

    Evangelopoulos, Dimitrios; da Fonseca, Joana Diniz; Waddell, Simon J

    2015-03-01

    Tuberculosis still remains a global health emergency, claiming 1.5 million lives in 2013. The bacterium responsible for this disease, Mycobacterium tuberculosis (M.tb), has successfully survived within hostile host environments, adapting to immune defence mechanisms, for centuries. This has resulted in a disease that is challenging to treat, requiring lengthy chemotherapy with multi-drug regimens. One explanation for this difficulty in eliminating M.tb bacilli in vivo is the disparate action of antimicrobials on heterogeneous populations of M.tb, where mycobacterial physiological state may influence drug efficacy. In order to develop improved drug combinations that effectively target diverse mycobacterial phenotypes, it is important to understand how such subpopulations of M.tb are formed during human infection. We review here the in vitro and in vivo systems used to model M.tb subpopulations that may persist during drug therapy, and offer aspirations for future research in this field. PMID:25809760

  10. A Gene-By-Gene Approach to Bacterial Population Genomics: Whole Genome MLST of Campylobacter.

    PubMed

    Sheppard, Samuel K; Jolley, Keith A; Maiden, Martin C J

    2012-01-01

    Campylobacteriosis remains a major human public health problem world-wide. Genetic analyses of Campylobacter isolates, and particularly molecular epidemiology, have been central to the study of this disease, particularly the characterization of Campylobacter genotypes isolated from human infection, farm animals, and retail food. These studies have demonstrated that Campylobacter populations are highly structured, with distinct genotypes associated with particular wild or domestic animal sources, and that chicken meat is the most likely source of most human infection in countries such as the UK. The availability of multiple whole genome sequences from Campylobacter isolates presents the prospect of identifying those genes or allelic variants responsible for host-association and increased human disease risk, but the diversity of Campylobacter genomes present challenges for such analyses. We present a gene-by-gene approach for investigating the genetic basis of phenotypes in diverse bacteria such as Campylobacter, implemented with the BIGSdb software on the pubMLST.org/campylobacter website. PMID:24704917

  11. Culturable and VBNC Vibrio cholerae: interactions with chironomid egg masses and their bacterial population.

    PubMed

    Halpern, Malka; Landsberg, Ori; Raats, Dina; Rosenberg, Eugene

    2007-02-01

    Vibrio cholerae, the etiologic agent of cholera, is autochthonous to various aquatic environments. Recently, it was found that chironomid (nonbiting midges) egg masses serve as a reservoir for the cholera bacterium and that flying chironomid adults are possible windborne carriers of V. cholerae non-O1 non-O139. Chironomids are the most widely distributed insect in freshwater. Females deposit egg masses at the water's edge, and each egg mass contains eggs embedded in a gelatinous matrix. Hemagglutinin/protease, an extracellular enzyme of V. cholerae, was found to degrade chironomid egg masses and to prevent them from hatching. In a yearly survey, chironomid populations and the V. cholerae in their egg masses followed phenological succession and interaction of host-pathogen population dynamics. In this report, it is shown via FISH technique that most of the V. cholerae inhabiting the egg mass are in the viable but nonculturable (VBNC) state. The diversity of culturable bacteria from chironomid egg masses collected from two freshwater habitats was determined. In addition to V. cholerae, representatives of the following genera were isolated: Acinetobacter, Aeromonas, Klebsiella, Shewanella, Pseudomonas, Paracoccus, Exiguobacterium, and unidentified bacteria. Three important human pathogens, Aeromonas veronii, A. caviae, and A. hydrophila, were isolated from chironomid egg masses, indicating that chironomid egg masses may be a natural reservoir for pathogenic Aeromonas species in addition to V. cholerae. All isolates of V. cholerae were capable of degrading chironomid egg masses. This may help explain their host-pathogen relationship with chironomids. In contrast, almost none of the other bacteria that were isolated from the egg masses possessed this ability. Studying the interaction between chironomid egg masses, the bacteria inhabiting them, and V. cholerae could contribute to our understanding of the nature of the V. cholerae-egg mass interactions. PMID:17186156

  12. High level multiple antibiotic resistance among fish surface associated bacterial populations in non-aquaculture freshwater environment.

    PubMed

    Ozaktas, Tugba; Taskin, Bilgin; Gozen, Ayse G

    2012-12-01

    Freshwater fish, Alburnus alburnus (bleak), were captured from Lake Mogan, situated in Ankara, during spring. The surface mucus of the fish was collected and associated bacteria were cultured and isolated. By sequencing PCR-amplified 16S RNA encoding genes, the isolates were identified as members of 12 different genera: Acinetobacter, Aeromonas, Bacillus, Brevundimonas, Gordonia, Kocuria, Microbacterium, Mycobacterium, Pseudomonas, Rhodococcus, and Staphylococcus, in addition to one strain that was unidentified. The mucus-dwelling bacterial isolates were tested for resistance against ampicillin, kanamycin, streptomycin and chloramphenicol. About 95% of the isolates were found to be resistant to ampicillin, 93% to chloramphenicol, and 88% to kanamycin and streptomycin. A Microbacterium oxydans and the unidentified environmental isolate were resistant to all four antibiotics tested at very high levels (>1600 μg/ml ampicillin and streptomycin; >1120 μg/ml kanamycin; >960 μg/ml chloramphenicol). Only a Kocuria sp. was sensitive to all four antibiotics at the lowest concentrations tested (3.10 μg/ml ampicillin and streptomycin; 2.15 μg/ml kanamycin; 1.85 μg/ml chloramphenicol). The rest of the isolates showed different resistance levels. Plasmid isolations were carried out to determine if the multiple antibiotic resistance could be attributed to the presence of plasmids. However, no plasmid was detected in any of the isolates. The resistance appeared to be mediated by chromosome-associated functions. This study indicated that multiple antibiotic resistance at moderate to high levels is common among the current phenotypes of the fish mucus-dwelling bacterial populations in this temperate, shallow lake which has not been subjected to any aquaculturing so far but under anthropogenic effect being in a recreational area. PMID:23039919

  13. Comparison of lysogeny (prophage induction) in heterotrophic bacterial and Synechococcus populations in the Gulf of Mexico and Mississippi River plume.

    PubMed

    Long, Amy; McDaniel, Lauren D; Mobberley, Jennifer; Paul, John H

    2008-02-01

    Lysogeny has been documented as a fundamental process occurring in natural marine communities of heterotrophic and autotrophic bacteria. Prophage induction has been observed to be prevalent during conditions of low host abundance, but factors controlling the process are poorly understood. A research cruise was undertaken to the Gulf of Mexico during July 2005 to explore environmental factors associated with lysogeny. Ambient physical and microbial parameters were measured and prophage induction experiments were performed in contrasting oligotrophic Gulf and eutrophic Mississippi plume areas. Three of 11 prophage induction experiments in heterotrophic bacteria (27%) demonstrated significant induction in response to Mitomycin C. In contrast, there was significant Synechococcus cyanophage induction in seven of nine experiments (77.8%). A strong negative correlation was observed between lysogeny and log-transformed activity measurements for both heterotrophic and autotrophic populations (r=-0.876, P=0.002 and r=-0.815, P=0.025, respectively), indicating that bacterioplankton with low host growth favor lysogeny. Multivariate statistical analyses indicated that ambient level of viral abundance and productivity were inversely related to heterotrophic prophage induction and both factors combined were most predictive of lysogeny (rho=0.899, P=0.001). For Synechococcus, low ambient cyanophage abundance was most predictive of lysogeny (rho=0.862, P=0.005). Abundance and productivity of heterotrophic bacteria was strongly inversely correlated with salinity, while Synechococcus was not. This indicated that heterotrophic bacterial populations were well adapted to the river plume environments, thus providing a possible explanation for differences in prevalence of lysogeny observed between the two populations. PMID:18049460

  14. Prophage-Mediated Dynamics of ‘Candidatus Liberibacter asiaticus’ Populations, the Destructive Bacterial Pathogens of Citrus Huanglongbing

    PubMed Central

    Zhou, Lijuan; Powell, Charles A.; Li, Wenbin; Irey, Mike; Duan, Yongping

    2013-01-01

    Prophages are highly dynamic components in the bacterial genome and play an important role in intraspecies variations. There are at least two prophages in the chromosomes of Candidatus Liberibacter asiaticus’ (Las) Floridian isolates. Las is both unculturable and the most prevalent species of Liberibacter pathogens that cause huanglongbing (HLB), a worldwide destructive disease of citrus. In this study, seven new prophage variants resulting from two hyper-variable regions were identified by screening clone libraries of infected citrus, periwinkle and psyllids. Among them, Types A and B share highly conserved sequences and localize within the two prophages, FP1 and FP2, respectively. Although Types B and C were abundant in all three libraries, Type A was much more abundant in the libraries from the Las-infected psyllids than from the Las-infected plants, and Type D was only identified in libraries from the infected host plants but not from the infected psyllids. Sequence analysis of these variants revealed that the variations may result from recombination and rearrangement events. Conventional PCR results using type-specific molecular markers indicated that A, B, C and D are the four most abundant types in Las-infected citrus and periwinkle. However, only three types, A, B and C are abundant in Las-infected psyllids. Typing results for Las-infected citrus field samples indicated that mixed populations of Las bacteria present in Floridian isolates, but only the Type D population was correlated with the blotchy mottle symptom. Extended cloning and sequencing of the Type D region revealed a third prophage/phage in the Las genome, which may derive from the recombination of FP1 and FP2. Dramatic variations in these prophage regions were also found among the global Las isolates. These results are the first to demonstrate the prophage/phage-mediated dynamics of Las populations in plant and insect hosts, and their correlation with insect transmission and disease

  15. Effect of bacterial association on the phenotype and genotype of an Entamoeba histolytica clonal population.

    PubMed

    De Menezes, L F; Rodríguez, M A; Vargas, M A; Salgado, L M; Orozco, E

    1997-01-01

    A several-times-cloned population of Entamoeba histolytica trophozoites (clone MAVIII) was cultured under axenic (MAVIIIax), monoxenic (MAVIIImx) and polyxenic (MAVIIIpx) conditions. Clones MAVIIIax and MAVIIImx presented similar virulence in vitro, but differed in their virulence in vivo, whereas MAVIIIpx trophozoites were neither virulent in vitro or in vivo. The MAVIII clones maintained their zymodeme and exhibited three unusual glucose phosphate isomerase bands, absent in other E. histolytica strains studied. Similar patterns were shown by the three MAVIII clones in the signature of a 482-bp DNA fragment from the M17 gene (which encodes for a variable immunodominant antigen), obtained by low stringency single specific primer PCR technique. However, MAVIII clones displayed genotypic variability in the patterns obtained by the random amplified polymorphic DNA technique using total DNA as template. Results suggest that monomorphism is kept in certain regions of the genome, mainly in those carrying protein encoding genes, but a high polymorphism is present in total DNA of cloned trophozoites cultured under different conditions, confirming the plasticity of the E. histolytica genome.

  16. Sulfur-oxidizing bacterial populations within cyanobacterial dominated coral disease lesions.

    PubMed

    Bourne, David G; van der Zee, Marc J J; Botté, Emmanuelle S; Sato, Yui

    2013-08-01

    This study investigated the diversity and quantitative shifts of sulfur-oxidizing bacteria (SOB) during the onset of black band disease (BBD) in corals using quantitative PCR (qPCR) and cloning approaches targeting the soxB gene, involved in sulfur oxidation. Four Montipora sp. coral colonies identified with lesions previously termed cyanobacterial patches (CP) (comprising microbial communities different from those of BBD lesions), was monitored in situ as CP developed into BBD. The overall abundance of SOB in both CP and BBD lesions were very low and near the detection limit of the qPCR assay, although consistently indicated that SOB populations decreased as the lesions transitioned from CP to BBD. Phylogenetic assessment of retrieved soxB genes showed that SOB in both CP and BBD lesions were dominated by one sequence type, representing > 70% of all soxB gene sequences and affiliated with members of the Rhodobacteraceae within the α-Proteobacteria. This study represents the first assessment targeting SOB within BBD lesions and clearly shows that SOB are not highly diverse or abundant in this complex microbial mat. The lack of oxidation of reduced sulfur compounds by SOB likely aids the accumulation of high levels of sulfide at the base of the BBD mat, a compound contributing to the pathogenicity of BBD lesions.

  17. Sulfur-oxidizing bacterial populations within cyanobacterial dominated coral disease lesions.

    PubMed

    Bourne, David G; van der Zee, Marc J J; Botté, Emmanuelle S; Sato, Yui

    2013-08-01

    This study investigated the diversity and quantitative shifts of sulfur-oxidizing bacteria (SOB) during the onset of black band disease (BBD) in corals using quantitative PCR (qPCR) and cloning approaches targeting the soxB gene, involved in sulfur oxidation. Four Montipora sp. coral colonies identified with lesions previously termed cyanobacterial patches (CP) (comprising microbial communities different from those of BBD lesions), was monitored in situ as CP developed into BBD. The overall abundance of SOB in both CP and BBD lesions were very low and near the detection limit of the qPCR assay, although consistently indicated that SOB populations decreased as the lesions transitioned from CP to BBD. Phylogenetic assessment of retrieved soxB genes showed that SOB in both CP and BBD lesions were dominated by one sequence type, representing > 70% of all soxB gene sequences and affiliated with members of the Rhodobacteraceae within the α-Proteobacteria. This study represents the first assessment targeting SOB within BBD lesions and clearly shows that SOB are not highly diverse or abundant in this complex microbial mat. The lack of oxidation of reduced sulfur compounds by SOB likely aids the accumulation of high levels of sulfide at the base of the BBD mat, a compound contributing to the pathogenicity of BBD lesions. PMID:23864565

  18. Interactions Between QTL SAP6 and SU91 on Resistance to Common Bacterial Blight in Red Kidney Bean and Pinto Bean Populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Resistance to common bacterial blight in common bean is a complex trait that is quantitatively inherited. We examined the interaction between two independent QTL, SAP6 and SU91, which condition resistance to CBB.The QTL were studied in a pinto bean F2 population a cross between Othello (sap6 sap6 //...

  19. Parental Choice of Schools and Parents' Perceptions of Multicultural and Co-Existence Education: The Case of the Israeli Palestinian-Jewish Bilingual Primary Schools

    ERIC Educational Resources Information Center

    Bekerman, Zvi; Tatar, Moshe

    2009-01-01

    The present research effort aims to better understand parental choice of the Israeli Palestinian-Jewish bilingual primary schools and its implications in contributing (or not) to fostering multicultural and co-existence educational efforts in conflict-ridden societies. The manuscript offers a short description of the educational initiative under…

  20. Characterization of Metabolically Active Bacterial Populations in Subseafloor Nankai Trough Sediments above, within, and below the Sulfate–Methane Transition Zone

    PubMed Central

    Mills, Heath J.; Reese, Brandi Kiel; Shepard, Alicia K.; Riedinger, Natascha; Dowd, Scot E.; Morono, Yuki; Inagaki, Fumio

    2012-01-01

    A remarkable number of microbial cells have been enumerated within subseafloor sediments, suggesting a biological impact on geochemical processes in the subseafloor habitat. However, the metabolically active fraction of these populations is largely uncharacterized. In this study, an RNA-based molecular approach was used to determine the diversity and community structure of metabolically active bacterial populations in the upper sedimentary formation of the Nankai Trough seismogenic zone. Samples used in this study were collected from the slope apron sediment overlying the accretionary prism at Site C0004 during the Integrated Ocean Drilling Program Expedition 316. The sediments represented microbial habitats above, within, and below the sulfate–methane transition zone (SMTZ), which was observed approximately 20 m below the seafloor (mbsf). Small subunit ribosomal RNA were extracted, quantified, amplified, and sequenced using high-throughput 454 pyrosequencing, indicating the occurrence of metabolically active bacterial populations to a depth of 57 mbsf. Transcript abundance and bacterial diversity decreased with increasing depth. The two communities below the SMTZ were similar at the phylum level, however only a 24% overlap was observed at the genus level. Active bacterial community composition was not confined to geochemically predicted redox stratification despite the deepest sample being more than 50 m below the oxic/anoxic interface. Genus-level classification suggested that the metabolically active subseafloor bacterial populations had similarities to previously cultured organisms. This allowed predictions of physiological potential, expanding understanding of the subseafloor microbial ecosystem. Unique community structures suggest very diverse active populations compared to previous DNA-based diversity estimates, providing more support for enhancing community characterizations using more advanced sequencing techniques. PMID:22485111

  1. Automated image analysis and in situ hybridization as tools to study bacterial populations in food resources, gut and cast of Lumbricus terrestris L.

    PubMed

    Schönholzer, Frank; Hahn, Dittmar; Zarda, Boris; Zeyer, Josef

    2002-01-01

    An image analysis procedure was developed for bacterial cells after staining with the DNA-intercalating dye 4'-6-diamidino-2-phenylindole (DAPI), and after in situ hybridization with Cy3-labeled, rRNA-targeted oligonucleotide probes. DAPI- and Cy3-images were captured separately from the same scenery with a cooled digital video camera with three CCD chips for the basic colors red (R), green (G) and blue (B). Using the appropriate filter sets, images of DAPI-stained cells were captured with the red channel shut down, while Cy3-stained cells were captured with the green and blue channels shut down. DAPI images and Cy3 images were subsequently merged to produce virtual color (RGB)-images. Processing of all color channels allowed to specifically enumerate DAPI-stained and hybridized bacteria, to measure their cell sizes, to subsequently calculate their biovolumes and to estimate their biomass. Using this procedure, significant differences were detected in bacterial populations in food resources, digestive tract and cast of the earthworm L. terrestris L. In leaves, bacteria were on average ten times more abundant and two times larger than in soil. In the digestive tract of L. terrestris, however, numbers and volumes of bacteria were comparable to those in soil indicating the disruption of cells originating from leaves before arriving in the foregut. Passage through the digestive tract of L. terrestris significantly reduced bacterial populations belonging to the alpha-, beta- and gamma-subdivisions of Proteobacteria. While these populations did not recover during incubation of cast, populations of the delta-subdivision of Proteobacteria and the Cytophaga-Flavobacterium cluster of the CFB phylum increased in cast. These results suggest a large impact of passage through the digestive tract of L. terrestris on bacterial community structure and demonstrate the usefulness of our image analysis procedure for the determination of cell sizes and biovolumes and thus biomass of

  2. Molecular analysis and conventional cytology: association between HPV and bacterial vaginosis in the cervical abnormalities of a Brazilian population.

    PubMed

    Peres, A L; Camarotti, J R S L; Cartaxo, M; Alencar, N; Stocco, R C; Beçak, W; Pontes-Filho, N T; Araújo, R F F; Lima-Filho, J L; Martins, D B G

    2015-01-01

    We investigated the association between bacterial vaginosis (BV) and human papillomavirus (HPV) infection in Papanicolaou smears in a Brazilian population. Cross-sectional analysis was performed on 673 samples collected from women attending public health centers in Olinda (PE, Brazil) by conventional cytology methodology and molecular analysis, PCR tests (GP5+/6+ and MY09/11). Cytological abnormalities, BV, and HPV-DNA were detected in 23 (3.4%) samples, 189 samples (28.1%), and 210 samples (31.2%), respectively. GP5+/6+ primers resulted in higher detection performance than MY09/11 primers, with 81% concordance between both primers (P < 0.0001). The occurrence of HPV-DNA and BV had ORs of 8.59 (P < 0.0001) and 2.91 (P = 0.0089) for abnormal cytology, respectively, whereas the concomitant presence of both infections showed an OR equal to 3.82 (P = 0.0054). Therefore, we observed an association between abnormal cervical cytology and HPV infection, BV, or both HPV infection and BV. These results highlight the necessity of monitoring patients presenting not only HPV, but also BV, as risk factors for cervical lesion development. PMID:26345883

  3. Effect of autochthonous bacteriocin-producing Lactococcus lactis on bacterial population dynamics and growth of halotolerant bacteria in Brazilian charqui.

    PubMed

    Biscola, Vanessa; Abriouel, Hikmate; Todorov, Svetoslav Dimitrov; Capuano, Verena Sant'Anna Cabral; Gálvez, Antonio; Franco, Bernadette Dora Gombossy de Melo

    2014-12-01

    Charqui is a fermented, salted and sun-dried meat product, widely consumed in Brazil and exported to several countries. Growth of microorganisms in this product is unlikely due to reduced Aw, but halophilic and halotolerant bacteria may grow and cause spoilage. Charqui is a good source of lactic acid bacteria able to produce antimicrobial bacteriocins. In this study, an autochthonous bacteriocinogenic strain (Lactococcus lactis subsp. lactis 69), isolated from charqui, was added to the meat used for charqui manufacture and evaluated for its capability to prevent the growth of spoilage bacteria during storage up to 45 days. The influence of L. lactis 69 on the bacterial diversity during the manufacturing of the product was also studied, using denaturing gradient gel electrophoresis (DGGE). L. lactis 69 did not affect the counts and diversity of lactic acid bacteria during manufacturing and storage, but influenced negatively the populations of halotolerant microorganisms, reducing the spoilage potential. The majority of tested virulence genes was absent, evidencing the safety and potential technological application of this strain as an additional hurdle to inhibit undesirable microbial growth in this and similar fermented meat products.

  4. Xylo-oligosaccharides and inulin affect genotoxicity and bacterial populations differently in a human colonic simulator challenged with soy protein.

    PubMed

    Christophersen, Claus T; Petersen, Anne; Licht, Tine R; Conlon, Michael A

    2013-09-23

    High dietary intakes of some protein sources, including soy protein, can increase colonic DNA damage in animals, whereas some carbohydrates attenuate this. We investigated whether inulin and xylo-oligosaccharides (XOS) could be protective against DNA strand breaks by adding them to a human colonic simulator consisting of a proximal vessel (PV) (pH 5.5) and a distal vessel (DV) (pH 6.8) inoculated with human faeces and media containing soy protein. Genotoxicity of the liquid phase and microbial population changes in the vessels were measured. Soy protein (3%) was fermented with 1% low amylose cornstarch for 10 day followed by soy protein with 1% XOS or 1% inulin for 10 day. Inulin did not alter genotoxicity but XOS significantly reduced PV genotoxicity and increased DV genotoxicity. Inulin and XOS significantly increased butyrate concentration in the DV but not PV. Numbers of the key butyrate-producing bacterium Faecalibacterium prausnitzii were significantly increased in the PV and DV by inulin but significantly decreased by XOS in both vessels. Other bacteria examined were also significantly impacted by the carbohydrate treatments or by the vessel (i.e., pH). There was a significant overall inverse correlation between levels of damage induced by the ferments and levels of sulphate-reducing bacteria, Bacteroides fragilis, and acetate. In conclusion, dietary XOS can potentially modulate the genotoxicity of the colonic environment and specific bacterial groups and short chain fatty acids may mediate this.

  5. Response of the rumen archaeal and bacterial populations to anti-methanogenic organosulphur compounds in continuous-culture fermenters.

    PubMed

    Martínez-Fernández, Gonzalo; Abecia, Leticia; Martín-García, A Ignacio; Ramos-Morales, Eva; Denman, Stuart E; Newbold, Charles J; Molina-Alcaide, Eduarda; Yáñez-Ruiz, David R

    2015-08-01

    Study of the efficacy of methanogenesis inhibitors in the rumen has given inconsistent results, mainly due to poorly understood effects on the key microbial groups involved in pathways for methane (CH4) synthesis. The experiment described in this report was designed to assess the effect of propyl propane thiosulfinate (PTS), diallyl disulfide (DDS) and bromochloromethane (BCM) on rumen fermentation, methane production and microbial populations in continuous culture fermenters. No effects on total volatile fatty acids (VFA) were observed with PTS or DDS, but VFA were decreased with BCM. Amylase activity increased with BCM as compared with the other treatments. A decrease in methane production was observed with PTS (48%) and BCM (94%) as compared with control values. The concentration of methanogenic archaea decreased with BCM from day 4 onward and with PTS on days 4 and 8. Pyrosequencing analysis revealed that PTS and BCM decreased the relative abundance of Methanomicrobiales and increased that of Methanobrevibacter and Methanosphaera. The total concentration of bacteria was not modified by any treatment, although treatment with BCM increased the relative abundance of Prevotella and decreased that of Ruminococcus. These results suggest that the inhibition of methane production in the rumen by PTS and BCM is associated with a shift in archaeal biodiversity and changes in the bacterial community with BCM. PMID:26183917

  6. Global analysis of saliva as a source of bacterial genes for insights into human population structure and migration studies

    PubMed Central

    2014-01-01

    Background The genetic diversity of the human microbiome holds great potential for shedding light on the history of our ancestors. Helicobacter pylori is the most prominent example as its analysis allowed a fine-scale resolution of past migration patterns including some that could not be distinguished using human genetic markers. However studies of H. pylori require stomach biopsies, which severely limits the number of samples that can be analysed. By focussing on the house-keeping gene gdh (coding for the glucose-6-phosphate dehydrogenase), on the virulence gene gtf (coding for the glucosyltransferase) of mitis-streptococci and on the 16S-23S rRNA internal transcribed spacer (ITS) region of the Fusobacterium nucleatum/periodonticum-group we here tested the hypothesis that bacterial genes from human saliva have the potential for distinguishing human populations. Results Analysis of 10 individuals from each of seven geographic regions, encompassing Africa, Asia and Europe, revealed that the genes gdh and ITS exhibited the highest number of polymorphic sites (59% and 79%, respectively) and most OTUs (defined at 99% identity) were unique to a given country. In contrast, the gene gtf had the lowest number of polymorphic sites (21%), and most OTUs were shared among countries. Most of the variation in the gdh and ITS genes was explained by the high clonal diversity within individuals (around 80%) followed by inter-individual variation of around 20%, leaving the geographic region as providing virtually no source of sequence variation. Conversely, for gtf the variation within individuals accounted for 32%, between individuals for 57% and among geographic regions for 11%. This geographic signature persisted upon extension of the analysis to four additional locations from the American continent. Pearson correlation analysis, pairwise Fst-cluster analysis as well as UniFrac analyses consistently supported a tree structure in which the European countries clustered tightly

  7. Population typing of the causal agent of cassava bacterial blight in the Eastern Plains of Colombia using two types of molecular markers

    PubMed Central

    2014-01-01

    Background Molecular typing of pathogen populations is an important tool for the development of effective strategies for disease control. Diverse molecular markers have been used to characterize populations of Xanthomonas axonopodis pv. manihotis (Xam), the main bacterial pathogen of cassava. Recently, diversity and population dynamics of Xam in the Colombian Caribbean coast were estimated using AFLPs, where populations were found to be dynamic, diverse and with haplotypes unstable across time. Aiming to examine the current state of pathogen populations located in the Colombian Eastern Plains, we also used AFLP markers and we evaluated the usefulness of Variable Number Tandem Repeats (VNTRs) as new molecular markers for the study of Xam populations. Results The population analyses showed that AFLP and VNTR provide a detailed and congruent description of Xam populations from the Colombian Eastern Plains. These two typing strategies clearly separated strains from the Colombian Eastern Plains into distinct populations probably because of geographical distance. Although the majority of analyses were congruent between typing markers, fewer VNTRs were needed to detect a higher number of genetic populations of the pathogen as well as a higher genetic flow among sampled locations than those detected by AFLPs. Conclusions This study shows the advantages of VNTRs over AFLPs in the surveillance of pathogen populations and suggests the implementation of VNTRs in studies that involve large numbers of Xam isolates in order to obtain a more detailed overview of the pathogen to improve the strategies for disease control. PMID:24946775

  8. Two novel temperate bacteriophages co-existing in Aeromonas sp. ARM81 - characterization of their genomes, proteomes and DNA methyltransferases.

    PubMed

    Dziewit, Lukasz; Radlinska, Monika

    2016-08-01

    Aeromonas species are causative agents of a wide spectrum of diseases in animals and humans. Although these bacteria are commonly found in various environments, little is known about their phages. Thus far, only one temperate Aeromonas phage has been characterized. Whole-genome sequencing of an Aeromonas sp. strain ARM81 revealed the presence of two prophage clusters. One of them is integrated into the chromosome and the other was maintained as an extrachromosomal, linear plasmid-like prophage encoding a protelomerase. Both prophages were artificially and spontaneously inducible. We separately isolated both phages and compared their genomes with other known viruses. The novel phages show no similarity to the previously characterized Aeromonas phages and might represent new evolutionary lineages of viruses infecting Aeromonadaceae. Apart from the comparative genomic analyses of these phages, complemented with their structural and molecular characterization, a functional analysis of four DNA methyltransferases encoded by these viruses was conducted. One of the investigated N6-adenine-modifying enzymes shares sequence specificity with a Dam-like methyltransferase of its bacterial host, while another one is non-specific, as it catalyzes adenine methylation in various sequence contexts. The presented results shed new light on the diversity of Aeromonas temperate phages.

  9. Smoking and smoking cessation in relation to the development of co-existing non-small cell lung cancer with chronic obstructive pulmonary disease.

    PubMed

    Zhai, Rihong; Yu, Xiaojin; Wei, Yongyue; Su, Li; Christiani, David C

    2014-02-15

    Previous studies have identified a mixed-phenotype of non-small cell lung cancer (NSCLC) with co-existing chronic obstructive pulmonary disease (COPD). Although NSCLC and COPD share a common risk factor in smoking, whether and how smoking may contribute to the coexistence of NSCLC with COPD (NSCLC-COPD) is unclear. Our study suggests that cigarette smoking is the major risk factor for the development of NSCLC-COPD, especially in females and among patients with squamous cell carcinoma subtype.

  10. Increased frequency of co-existing JAK2 exon-12 or MPL exon-10 mutations in patients with low JAK2(V617F) allelic burden.

    PubMed

    Nussenzveig, Roberto H; Pham, Ha T; Perkins, Sherrie L; Prchal, Josef T; Agarwal, Archana M; Salama, Mohamed E

    2016-01-01

    The frequency of co-existing JAK2(V617F)/MPL and JAK2(V617F)/JAK2 exon-12 mutations has not been previously investigated in MPNs. Poor survival was reported in primary myelofibrosis with low JAK2(V617F) allelic burden. However, mutational status of JAK2 exon-12 or MPL were not reported in these patients. This study developed a cost-effective multiplex high resolution melt assay that screens for mutations in JAK2 gene exons-12 and -14 ((V617F)) and MPL gene exon-10. Co-existing mutations with JAK2(V617F) were detected in 2.9% (6/208; two JAK2 exon-12 and four MPL exon-10) patient specimens with known JAK2(V617F) (allelic-burden range: 0.1-96.8%). Co-existing mutations were detected in specimens with < 12% JAK2(V617F) allelic burden. Current WHO guidelines do not recommend further testing once JAK2(V617F) mutation is detected in MPNs. The findings, however, indicate that quantification of JAK2(V617F) allele burden may be clinically relevant in MPNs and in those with low allelic burden additional testing for JAK2 exon-12 and MPL exon-10 mutation should be pursued.

  11. Effect of Lactobacillus johnsonii CRL1647 on different parameters of honeybee colonies and bacterial populations of the bee gut.

    PubMed

    Audisio, M C; Sabaté, D C; Benítez-Ahrendts, M R

    2015-01-01

    Lactobacillus johnsonii CRL1647, isolated from the intestinal tract of a worker-bee in Salta, Argentina, was delivered to Apis mellifera L. honey bee colonies according to two different administration schedules: 1×10(5) cfu/ml every 15 days (2011) or monthly (2012). The effect of each treatment on the bee-colony performance was monitored by measuring honey production, and the prevalence of varroasis and nosemosis. Worker bees from each assay were randomly captured 3 days after administration and assayed for the following intestinal culturable and defined bacterial populations: total aerobic microorganisms, Bacillus spp. spores, Lactobacillus spp., Enterococcus spp. and enterobacteria. Interestingly, both treatments generated a similar increase in honey production in treated colonies compared to controls: 36.8% (every 15 days) and 36.3% (monthly). Nosema index always exhibited a reduction when lactobacilli were administered; in turn, Varroa incidence was lower when the lactobacilli were administered once a month. Moreover, the administration of L. johnsonii CRL1647 every 15 days produced an increase in the total number of aerobic microorganisms and in bacteria belonging to the genera Lactobacillus and Enterococcus; at the same time, a decrease was observed in the number of total spores at the end of the treatment. The number of enterobacteria was constant and remained below that of control hives at the end of the assay. On the other hand, the delivery of lactobacilli once a month only showed an increase in the number of bacteria belonging to the genus Lactobacillus; meanwhile, viable counts of the remaining microorganisms assayed were reduced. Even though it seems that both treatments were similar, those bee colonies that received L. johnsonii CRL1647 every 15 days became so strong that they swarmed.

  12. Response of Ammonia-oxidizing Bacterial and Archaeal Populations to Organic Nitrogen Amendments in Low-Nutrient Groundwater

    SciTech Connect

    David W. Reed; Yoshiko Fujita; Jason M. Smith; Christopher A. Francis

    2010-02-01

    To better understand the fate of ammonia introduced into low-nutrient groundwater as a result of the application of a novel remediation approach for trace metal contaminants, the diversity and abundance of ammonia-oxidizing bacteria and archaea (AOB and AOA, respectively) were examined in samples collected during a field trial of the approach. The ammonia is derived from microbial urea hydrolysis, which has the potential to induce the formation of calcite and remove contaminants by coprecipitation in the calcite. The in situ oxidation of the ammonia by AOB and AOA could, however, potentially destabilize the calcite and lead to elevated nitrate levels in the groundwater. To evaluate the potential for stimulating ammonia oxidation by addition of urea, samples were collected from the Eastern Snake River Plain Aquifer in Idaho before, during, and after the addition of molasses and urea, and subjected to PCR analysis of ammonia monooxygenase subunit A (amoA) genes. AOB and AOA were present in all of the samples tested, with the AOA amoA genes more numerous in all of the samples except those collected following urea addition, when AOB genes were slightly more abundant. Following urea addition, nitrate levels rose and ammonia-oxidizing microorganisms (AOB + AOA) increased relative to the total microbial population, evidence that nitrification was stimulated by urea hydrolysis. Bacterial amoA diversity was limited to two sequence types, whereas the archaeal amoA analyses revealed 20 unique operational taxonomic units (OTUs), including several that were significantly different from any reported previously from other environments. In view of the results from this study, the potential for stimulation of ammonia-oxidizing communities should be considered in field-scale engineering activities involving microbial urea hydrolysis in groundwater.

  13. Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations.

    PubMed

    McNally, Alan; Oren, Yaara; Kelly, Darren; Pascoe, Ben; Dunn, Steven; Sreecharan, Tristan; Vehkala, Minna; Välimäki, Niko; Prentice, Michael B; Ashour, Amgad; Avram, Oren; Pupko, Tal; Dobrindt, Ulrich; Literak, Ivan; Guenther, Sebastian; Schaufler, Katharina; Wieler, Lothar H; Zhiyong, Zong; Sheppard, Samuel K; McInerney, James O; Corander, Jukka

    2016-09-01

    The use of whole-genome phylogenetic analysis has revolutionized our understanding of the evolution and spread of many important bacterial pathogens due to the high resolution view it provides. However, the majority of such analyses do not consider the potential role of accessory genes when inferring evolutionary trajectories. Moreover, the recently discovered importance of the switching of gene regulatory elements suggests that an exhaustive analysis, combining information from core and accessory genes with regulatory elements could provide unparalleled detail of the evolution of a bacterial population. Here we demonstrate this principle by applying it to a worldwide multi-host sample of the important pathogenic E. coli lineage ST131. Our approach reveals the existence of multiple circulating subtypes of the major drug-resistant clade of ST131 and provides the first ever population level evidence of core genome substitutions in gene regulatory regions associated with the acquisition and maintenance of different accessory genome elements. PMID:27618184

  14. Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations

    PubMed Central

    McNally, Alan; Oren, Yaara; Kelly, Darren; Sreecharan, Tristan; Vehkala, Minna; Välimäki, Niko; Prentice, Michael B.; Ashour, Amgad; Avram, Oren; Pupko, Tal; Literak, Ivan; Guenther, Sebastian; Schaufler, Katharina; Wieler, Lothar H.; Zhiyong, Zong; Sheppard, Samuel K.; Corander, Jukka

    2016-01-01

    The use of whole-genome phylogenetic analysis has revolutionized our understanding of the evolution and spread of many important bacterial pathogens due to the high resolution view it provides. However, the majority of such analyses do not consider the potential role of accessory genes when inferring evolutionary trajectories. Moreover, the recently discovered importance of the switching of gene regulatory elements suggests that an exhaustive analysis, combining information from core and accessory genes with regulatory elements could provide unparalleled detail of the evolution of a bacterial population. Here we demonstrate this principle by applying it to a worldwide multi-host sample of the important pathogenic E. coli lineage ST131. Our approach reveals the existence of multiple circulating subtypes of the major drug–resistant clade of ST131 and provides the first ever population level evidence of core genome substitutions in gene regulatory regions associated with the acquisition and maintenance of different accessory genome elements. PMID:27618184

  15. Massive Access Control Aided by Knowledge-Extraction for Co-Existing Periodic and Random Services over Wireless Clinical Networks.

    PubMed

    Du, Qinghe; Zhao, Weidong; Li, Weimin; Zhang, Xuelin; Sun, Bo; Song, Houbing; Ren, Pinyi; Sun, Li; Wang, Yichen

    2016-07-01

    The prosperity of e-health is boosted by fast development of medical devices with wireless communications capability such as wearable devices, tiny sensors, monitoring equipments, etc., which are randomly distributed in clinic environments. The drastically-increasing population of such devices imposes new challenges on the limited wireless resources. To relieve this problem, key knowledge needs to be extracted from massive connection attempts dispersed in the air towards efficient access control. In this paper, a hybrid periodic-random massive access (HPRMA) scheme for wireless clinical networks employing ultra-narrow band (UNB) techniques is proposed. In particular, the proposed scheme towards accommodating a large population of devices include the following new features. On one hand, it can dynamically adjust the resource allocated for coexisting periodic and random services based on the traffic load learned from signal collision status. On the other hand, the resource allocation within periodic services is thoroughly designed to simultaneously align with the timing requests of differentiated services. Abundant simulation results are also presented to demonstrate the superiority of the proposed HPRMA scheme over baseline schemes including time-division multiple access (TDMA) and random access approach, in terms of channel utilization efficiency, packet drop ratio, etc., for the support of massive devices' services.

  16. Characterization of Growing Bacterial Populations in McMurdo Dry Valley Soils through Stable Isotope Probing with 18O-water

    PubMed Central

    Schwartz, Egbert; Buelow, Heather N.; Gooseff, Michael N.; Barrett, John E.; Okie, Jordan G.; Takacs-Vesbach, Cristina D.; Van Horn, David J.

    2014-01-01

    Soil microbial communities of the McMurdo Dry Valleys, Antarctica (MDV) contain representatives from at least fourteen bacterial phyla. However, given low rates of microbial activity, it is unclear whether this richness represents functioning rather than dormant members of the community. We used stable isotope probing (SIP) with 18O-water to determine if microbial populations grow in MDV soils. Changes in the microbial community were characterized in soils amended with H2 18O and H2 18O-organic matter. Sequencing the 16S rRNA genes of the heavy and light fractions of the bacterial community DNA show that DNA of microbial populations was labeled with 18O-water, indicating these microorganisms grew in the MDV soils. Significant differences existed in the community composition of the heavy and light fractions of the H2 18O and H2 18O-organic matter amended samples (Anosim P<0.05 of weighted Unifrac distance). Control samples and the light DNA fraction of the H2 18O amended samples were dominated by representatives of the phyla Deinococcus-Thermus, Proteobacteria, Planctomyces, Gemmatimonadetes, Actinobacteria and Acidobacteria, whereas Proteobacteria were more prevalent in the heavy DNA fractions from the H2 18O-water and the H2 18O-water-organic matter treatments. Our results indicate that SIP with H2 18O can be used to distinguish active bacterial populations even in this low organic matter environment. PMID:24785369

  17. Bacterial communities associated with host-adapted populations of pea aphids revealed by deep sequencing of 16S ribosomal DNA.

    PubMed

    Gauthier, Jean-Pierre; Outreman, Yannick; Mieuzet, Lucie; Simon, Jean-Christophe

    2015-01-01

    Associations between microbes and animals are ubiquitous and hosts may benefit from harbouring microbial communities through improved resource exploitation or resistance to environmental stress. The pea aphid, Acyrthosiphon pisum, is the host of heritable bacterial symbionts, including the obligate endosymbiont Buchnera aphidicola and several facultative symbionts. While obligate symbionts supply aphids with key nutrients, facultative symbionts influence their hosts in many ways such as protection against natural enemies, heat tolerance, color change and reproduction alteration. The pea aphid also encompasses multiple plant-specialized biotypes, each adapted to one or a few legume species. Facultative symbiont communities differ strongly between biotypes, although bacterial involvement in plant specialization is uncertain. Here, we analyse the diversity of bacterial communities associated with nine biotypes of the pea aphid complex using amplicon pyrosequencing of 16S rRNA genes. Combined clustering and phylogenetic analyses of 16S sequences allowed identifying 21 bacterial OTUs (Operational Taxonomic Unit). More than 98% of the sequencing reads were assigned to known pea aphid symbionts. The presence of Wolbachia was confirmed in A. pisum while Erwinia and Pantoea, two gut associates, were detected in multiple samples. The diversity of bacterial communities harboured by pea aphid biotypes was very low, ranging from 3 to 11 OTUs across samples. Bacterial communities differed more between than within biotypes but this difference did not correlate with the genetic divergence between biotypes. Altogether, these results confirm that the aphid microbiota is dominated by a few heritable symbionts and that plant specialization is an important structuring factor of bacterial communities associated with the pea aphid complex. However, since we examined the microbiota of aphid samples kept a few generations in controlled conditions, it may be that bacterial diversity was

  18. Bacterial communities associated with host-adapted populations of pea aphids revealed by deep sequencing of 16S ribosomal DNA.

    PubMed

    Gauthier, Jean-Pierre; Outreman, Yannick; Mieuzet, Lucie; Simon, Jean-Christophe

    2015-01-01

    Associations between microbes and animals are ubiquitous and hosts may benefit from harbouring microbial communities through improved resource exploitation or resistance to environmental stress. The pea aphid, Acyrthosiphon pisum, is the host of heritable bacterial symbionts, including the obligate endosymbiont Buchnera aphidicola and several facultative symbionts. While obligate symbionts supply aphids with key nutrients, facultative symbionts influence their hosts in many ways such as protection against natural enemies, heat tolerance, color change and reproduction alteration. The pea aphid also encompasses multiple plant-specialized biotypes, each adapted to one or a few legume species. Facultative symbiont communities differ strongly between biotypes, although bacterial involvement in plant specialization is uncertain. Here, we analyse the diversity of bacterial communities associated with nine biotypes of the pea aphid complex using amplicon pyrosequencing of 16S rRNA genes. Combined clustering and phylogenetic analyses of 16S sequences allowed identifying 21 bacterial OTUs (Operational Taxonomic Unit). More than 98% of the sequencing reads were assigned to known pea aphid symbionts. The presence of Wolbachia was confirmed in A. pisum while Erwinia and Pantoea, two gut associates, were detected in multiple samples. The diversity of bacterial communities harboured by pea aphid biotypes was very low, ranging from 3 to 11 OTUs across samples. Bacterial communities differed more between than within biotypes but this difference did not correlate with the genetic divergence between biotypes. Altogether, these results confirm that the aphid microbiota is dominated by a few heritable symbionts and that plant specialization is an important structuring factor of bacterial communities associated with the pea aphid complex. However, since we examined the microbiota of aphid samples kept a few generations in controlled conditions, it may be that bacterial diversity was

  19. Studies on salinization in Haryana soils on free-living nitrogen-fixing bacterial populations and their activity.

    PubMed

    Kayasth, Monika; Gera, Rajesh; Dudeja, Surjit Singh; Sharma, Parveen Kumar; Kumar, Varun

    2014-03-01

    A total of 26 soil samples from saline soils of Haryana were collected. Based on their electrical conductivity (EC) values, which varied from 1.04 to 21.00 dS m(-1), the soils were categorized into non-saline soils (EC 0-2 dS m(-1)), weakly saline soils (EC 2-4 dS m(-1)), saline soils (EC 4-8 dS m(-1)), strongly saline soils (EC 8-16 dS m(-1)), and very strongly saline soils (EC >16 dS m(-1)). The pH values of these soil samples ranged from 6.03 to 8.62, while organic C, total N, and available P were in the range of 0.06-0.94%, 0.07-0.15%, and 0.11-0.29 μg g(-1) soil, respectively. As a measure of the impact of salinity on free-living N(2) fixers and their activity, the total bacterial populations on four media (Jensen's nitrogen-free medium, malate medium, Burk's medium, and soil extract agar medium) decreased from 6.12 to 3.70 log CFU g(-1) soil with increasing salinity level. PCR amplification of the nifH region of the DNA from 234 selected morphotypes from all the media showed the presence of nifH in 71 isolates. Out of these, 37% of the isolates were obtained using Jensen's medium; 35, 28, and 21% of the isolates were obtained using soil extract medium, Burk's medium, and malate medium, respectively. The majority of the free-living N(2) fixers (67%) were Gram negative. Apart from the acetylene reduction assay (ARA) activity in these isolates, other beneficial traits like ammonia excretion and indole acetic acid (IAA) production were also present. A decreasing trend in the activities was observed with increasing salinity levels. Isolates JN6, BP8, and MJ4 showed the highest ARA activity, ammonia excretion, and IAA production. The performance of isolates like BNC2 with good ARA activity, ammonia excretion, and IAA production and isolated from a very strongly saline soil should be further evaluated under high-saline conditions. PMID:23553356

  20. Studies on salinization in Haryana soils on free-living nitrogen-fixing bacterial populations and their activity.

    PubMed

    Kayasth, Monika; Gera, Rajesh; Dudeja, Surjit Singh; Sharma, Parveen Kumar; Kumar, Varun

    2014-03-01

    A total of 26 soil samples from saline soils of Haryana were collected. Based on their electrical conductivity (EC) values, which varied from 1.04 to 21.00 dS m(-1), the soils were categorized into non-saline soils (EC 0-2 dS m(-1)), weakly saline soils (EC 2-4 dS m(-1)), saline soils (EC 4-8 dS m(-1)), strongly saline soils (EC 8-16 dS m(-1)), and very strongly saline soils (EC >16 dS m(-1)). The pH values of these soil samples ranged from 6.03 to 8.62, while organic C, total N, and available P were in the range of 0.06-0.94%, 0.07-0.15%, and 0.11-0.29 μg g(-1) soil, respectively. As a measure of the impact of salinity on free-living N(2) fixers and their activity, the total bacterial populations on four media (Jensen's nitrogen-free medium, malate medium, Burk's medium, and soil extract agar medium) decreased from 6.12 to 3.70 log CFU g(-1) soil with increasing salinity level. PCR amplification of the nifH region of the DNA from 234 selected morphotypes from all the media showed the presence of nifH in 71 isolates. Out of these, 37% of the isolates were obtained using Jensen's medium; 35, 28, and 21% of the isolates were obtained using soil extract medium, Burk's medium, and malate medium, respectively. The majority of the free-living N(2) fixers (67%) were Gram negative. Apart from the acetylene reduction assay (ARA) activity in these isolates, other beneficial traits like ammonia excretion and indole acetic acid (IAA) production were also present. A decreasing trend in the activities was observed with increasing salinity levels. Isolates JN6, BP8, and MJ4 showed the highest ARA activity, ammonia excretion, and IAA production. The performance of isolates like BNC2 with good ARA activity, ammonia excretion, and IAA production and isolated from a very strongly saline soil should be further evaluated under high-saline conditions.

  1. Effects of adding a concentrated pomegranate-residue extract to the ration of lactating cows on in vivo digestibility and profile of rumen bacterial population.

    PubMed

    Jami, E; Shabtay, A; Nikbachat, M; Yosef, E; Miron, J; Mizrahi, I

    2012-10-01

    This study characterizes the effects of concentrated pomegranate-peel extract (CPE) addition to the TMR at levels of 1, 2, or 4% on voluntary intake, in vivo digestibility, milk yield and composition, and profile of rumen bacterial and archaeal populations in lactating Holstein cows. Supplementation of CPE significantly affected the abundance of methanogenic archaea and specific ruminal bacterial species related to cellulolytic activities and soluble sugar and lactic acid fermentation, as revealed by real-time PCR quantification. Furthermore, CPE supplementation had a significant dose-dependent effect on the whole ruminal bacterial community, as determined by automated ribosomal intergenic spacer analysis. These changes were accompanied by a significant increase in digestibility of dry matter, crude protein, and neutral detergent fiber, as well as milk and energy-corrected milk yields in cows fed the 4% CPE supplement. These results suggest that CPE supplementation significantly affects the rumen bacterial communities, which in turn may be related to a beneficial effect on dairy cow performance. PMID:22863105

  2. Occurrence and co-existence of localized musculoskeletal symptoms and findings in work-attending orchestra musicians - an exploratory cross-sectional study

    PubMed Central

    2012-01-01

    Background Due to ergonomic exposure musicians are at risk of work-related musculoskeletal disorders in the neck, back, and upper extremities. The literature confirms musculoskeletal problems in these anatomic regions among orchestra musicians. Methods An explorative cross-sectional study among 441 musicians from six Danish symphony orchestras; 216 underwent a clinical examination constructed for the purpose. Prior to the examination the musicians rated their maximally perceived trouble within the last week on a scheme blinded to the examiner. Accessibility to the clinical examination differed between orchestras. The aims were to assess the prevalence of 1) perceived symptoms within the previous week in the neck, back and limbs and of 2) clinical findings in the neck, back, and upper extremities, and 3) to investigate the co-existence of the perceived symptoms and clinical findings. Results Symptoms and findings were most common in the neck, back, and shoulders. Due to a poor co-existence between self-reported symptoms and clinical findings musicians experiencing bodily trouble could not be identified through this clinical examination. Free accessibility to the examination was of major importance to participation. Conclusions In compliance with the purpose, perceived symptoms within the previous week and present clinical findings were assessed. Although both symptoms and findings were most frequent in the neck, back, and shoulders the co-existence of anatomically localized symptoms and findings was generally quite poor in this study. Discrepancy between symptoms and findings might be caused by the participants currently attending work and therefore being relatively healthy, and the fluctuating nature of musculoskeletal problems. Furthermore from a comparison of different measuring units - self-reported symptoms being period prevalence rates and clinical findings point prevalence rates; a bias which may also be inherent in similar studies combining self

  3. [Qualitative and quantitative determination of bacterial populations in an aquatic environment. 7. Development of bacterial growth on raw materials exposed to potable water].

    PubMed

    Dott, W; Schoenen, D

    1985-05-01

    Refined steel plates coated with different materials that contained available organic compounds led to a microbial growth on the surface. Even plastics and bitumen which were used in the sphere of drinking water showed after an exposure time of three months up to 192 ml slime per square meter. The number of viable bacteria within the Aufwuchs was in the range of 10(7) cfu/ml. The production of slime increased with time. The relation of carbohydrate and protein content significantly changed from 2 at the beginning to 30 after 12 months of incubation the bitumen coating test plates. This indicates an increase synthesis of carbohydrate containing extracellular polymeric substances during the late phase of growth. The bacteria isolated from the Aufwuchs mainly belonged to the genera Pseudomonas, Flavobacterium, Acinetobacter, Caulobacter, sheated bacteria and other gramnegative physiologically nonreactiv roads. During exposure of the plates the relation changed within the bacterial communities of the main groups. Comparing the bacteria communities of inlet and outflow water it became evident that the later one was influenced by bacteria of the Aufwuchs. PMID:4024773

  4. Co-existence of Endometriotic Cyst of the Ovary and Arias-Stella Reaction in a Non-Pregnant Woman: Report of a Rare Case.

    PubMed

    Harikrishnan, Volga; Esaki, Muthuvel; Srinivasan, Chitra; Arockiasamy, Parimala; Ethirajan, Shanthi

    2016-03-01

    Endometriosis is defined as presence of endometrial tissue outside the uterus. It can occur anywhere in the ovary. In the ovary it is usually presented as cyst, termed as endometriotic cyst or Chocolate cyst. Arias-Stella reaction is usually seen in gestational endometrium or in ectopic gestation site and rarely in non-pregnant uterus with hormonal intake. Co-existence of endometriosis and Arias-Stella reaction is very rare. We present a very rare case of endometriotic cyst of the ovary exhibiting Arias -Stella reaction which was seen in of non pregnant patient without any history of hormonal intake. PMID:27134880

  5. Clinical Value of Assessing Cytokine Levels for the Differential Diagnosis of Bacterial Meningitis in a Pediatric Population

    PubMed Central

    Ye, Qing; Shao, Wen-Xia; Shang, Shi-Qiang; Shen, Hong-Qiang; Chen, Xue-Jun; Tang, Yong-Min; Yu, Yong-Lin; Mao, Jian-Hua

    2016-01-01

    Abstract We performed a prospective observational study to evaluate the utility of measuring inflammatory cytokine levels to discriminate bacterial meningitis from similar common pediatric diseases. Inflammatory cytokine levels and other cerebrospinal fluid (CSF) physicochemical indicators were evaluated in 140 patients who were diagnosed with bacterial meningitis via microbiological culture or PCR assay. The CSF concentrations of interleukin (IL)-6 and IL-10, CSF/blood IL-6 and IL-10 ratios, CSF white blood cell count, and CSF micro total protein were significantly elevated in bacterial meningitis patients compared with healthy children or patients with viral encephalitis, epilepsy, or febrile convulsions (P < 0.001). The area under the curve values for CSF concentrations of IL-6 and IL-10, CSF/blood IL-6 and IL-10 ratios, CSF white blood cell count, and CSF micro total protein to identify bacterial meningitis episodes by receiver-operating characteristic analysis were 0.988, 0.949, 0.995, 0.924, 0.945, and 0.928, respectively. The area under the curve for the combination of CSF IL-6 and CSF/blood IL-6 ratio was larger than that for either parameter alone, and the combination exhibited enhanced specificity and positive predictive value. After effective meningitis treatment, CSF IL-6 levels dropped significantly. These results suggest that CSF IL-6 and CSF/blood IL-6 ratio are good biomarkers in discriminating bacterial meningitis. Evaluating CSF IL-6 and CSF/blood IL-6 ratio in combination can improve diagnostic efficiency. Additionally, CSF IL-6 levels can be used to monitor the effects of bacterial meningitis treatment. PMID:27043692

  6. Antibiotic resistance genes in bacterial and bacteriophage fractions of Tunisian and Spanish wastewaters as markers to compare the antibiotic resistance patterns in each population.

    PubMed

    Colomer-Lluch, Marta; Calero-Cáceres, William; Jebri, Sihem; Hmaied, Fatma; Muniesa, Maite; Jofre, Juan

    2014-12-01

    The emergence and increased prevalence of antibiotic resistance genes (ARGs) in the environment may pose a serious global health concern. This study evaluates the abundance of several ARGs in bacterial and bacteriophage DNA via real-time qPCR in samples from five different sampling points in Tunisia; three wastewater treatment plants (WWTP 1, 2 and 3) and wastewater from two abattoirs slaughtering different animals. Results are compared with those obtained in the Barcelona area, in northeast Spain. Eight ARGs were quantified by qPCR from total and phage DNA fraction from the samples. Three β-lactamases (bla(TEM), bla(CTX-M) cluster 1 and bla(CTX-M) cluster 9), two quinolone resistance genes (qnrA and qnrS), the mecA gene that confers resistance to methicillin in Staphylococcus aureus, the emerging armA gene, conferring resistance to aminoglycosides and sul1, the most extended gene conferring resistance to sulfonamides, were evaluated. Sul1 and bla(TEM) were the most prevalent ARGs detected at all five Tunisian sampling points, similarly with the observations in Barcelona. bla(CTX-M-9) was more prevalent than bla(CTX-M-1) both in bacterial and DNA within phage particles in all samples analysed. mecA and armA were almost absent in Tunisian waters from human or animal origin in contrast with Barcelona that showed a medium prevalence. qnrA was more prevalent than qnrS in bacterial and phage DNA from all sampling points. In conclusion, our study shows that ARGs are found in the bacterial and is reflected in the phage DNA fraction of human and animal wastewaters. The densities of each ARGs vary depending on the ARGs shed by each population and is determined by the characteristics of each area. Thus, the evaluation of ARGs in wastewaters seems to be suitable as marker reflecting the antibiotic resistance patterns of a population.

  7. Global Co-Existence of Two Evolutionary Lineages of Parvovirus B19 1a, Different in Genome-Wide Synonymous Positions

    PubMed Central

    van Binnendijk, Rob S.; Boot, Hein J.; Zaaijer, Hans L.

    2012-01-01

    Parvovirus B19 (B19V) can cause infection in humans. To date, three genotypes of B19V, with subtypes, are known, of which genotype 1a is the most prevalent genotype in the Western world. We sequenced the genome of B19V strains of 65 asymptomatic, recently infected Dutch blood donors, to investigate the spatio-temporal distribution of B19V strains, in the years 2003–2009. The sequences were compared to B19V sequences from Dutch patients with fifth disease, and to global B19V sequences as available from GenBank. All Dutch B19V strains belonged to genotype 1a. Phylogenetic analysis of the strains from Dutch blood donors showed that two groups of genotype 1a co-exist. A clear-cut division into the two groups was also found among the B19V strains from Dutch patients, and among the B19V sequences in GenBank. The two groups of genotype 1a co-exist around the world and do not appear to differ in their ability to cause disease. Strikingly, the two groups of B19V predominantly differ in synonymous mutations, distributed throughout the entire genome of B19V. We propose to call the two groups of B19V genotype 1a respectively subtype 1a1 and 1a2. PMID:22912828

  8. The co-existence between transgenic and non-transgenic maize in the European Union: a focus on pollen flow and cross-fertilization.

    PubMed

    Devos, Yann; Reheul, Dirk; De Schrijver, Adinda

    2005-01-01

    The ongoing discussion on the co-existence between genetically modified (GM) and non-GM crops becomes more important in the European Union (EU). With the recent inscription of 17 GM maize varieties in the common EU catalogue of varieties of agricultural plant species, the acreage of transgenic maize for market purposes is expected to increase in some European countries. In the EU, specific tolerance thresholds have been established for the adventitious and technically unavoidable presence of GM material in non-GM produce, and member states are elaborating legal frames to cope with co-existence. As maize is a cross-pollinated crop relying on wind for the dispersal of its pollen, technical management measures will be imposed to reduce cross-fertilization between transgenic and non-transgenic maize. Various biological, physical and analytical parameters have been identified to play a role in the study of cross-fertilization in maize. This variability may hamper the comparison between research results and may complicate the definition of appropriate isolation distances and/or pollen barriers in order to limit out-crossing. The present review addresses these parameters and proposes containment measures in order to not exceed the legal labeling thresholds in maize. PMID:16402663

  9. [Dynamic effects of commonly co-existing anions on the removal of selenite from groundwater by nanoscale zero-valent iron].

    PubMed

    Yang, Wen-Jun; Guo, Ying-Qing; Du, Er-Deng

    2014-05-01

    Batch experiments are used to research selenite removal from groundwater by nanoscale zero-valent iron (nZVI) , and dynamic effects of commonly co-existing anions on the removal of selenite are also investigated. The results showed that under anoxic conditions,when nZVI dose was 0.1 g.L-1 , the concentration of Se( IV)/sodium chloride was 100 micromol.L-1/0. 01 mol L-1 , pH = 7.0, T = 25 degrees C +/- 1 degrees C, auto-adding 1 mmol.L -1 CO(2-)(3) or SO(2-)(4) , 5 mg. L -1 humic acid (HA), the removals of Se( IV ) were obviously inhibited. The weak effect on the removal of Se( IV) was observed when added 0. 5 mmol L- Ca2+ or Mg2 ,while concentrations of Ca2+ and Mg2+ were 3 mmol L-1 and 3 mmol L-1 respectively, removal efficiency of Se( IV) were evidently decreased. Without coexisting ions, Se( IV) were totally removed in 20 min, while with co-existing ions, removal efficiency of Se( NV) were achieved 100% in 30 min. Bivalent iron tended to stationary with the remove of Se( WV) in reaction processes. ORP rapidly decreased from positive to negative in the process of reaction, which illustrated the process of remove Se( IV) by nZVI was the reduction reaction.

  10. Genetic variation in bacterial kidney disease (BKD) susceptibility in Lake Michigan Chinook Salmon and its progenitor population from the Puget Sound

    USGS Publications Warehouse

    Purcell, Maureen K.; Hard, Jeffrey J.; Neely, Kathleen G.; Park, Linda K.; Winton, James R.; Elliott, Diane G.

    2014-01-01

    Mass mortality events in wild fish due to infectious diseases are troubling, especially given the potential for long-term, population-level consequences. Evolutionary theory predicts that populations with sufficient genetic variation will adapt in response to pathogen pressure. Chinook Salmon Oncorhynchus tshawytscha were introduced into Lake Michigan in the late 1960s from a Washington State hatchery population. In the late 1980s, collapse of the forage base and nutritional stress in Lake Michigan were thought to contribute to die-offs of Chinook Salmon due to bacterial kidney disease (BKD). Previously, we demonstrated that Lake Michigan Chinook Salmon from a Wisconsin hatchery have greater survival following BKD challenge relative to their progenitor population. Here, we evaluated whether the phenotypic divergence of these populations in BKD susceptibility was due to selection rather than genetic drift. Comparison of the overall magnitude of quantitative trait to neutral marker divergence between the populations suggested selection had occurred but a direct test of quantitative trait divergence was not significant, preventing the rejection of the null hypothesis of differentiation through genetic drift. Estimates of phenotypic variation (VP), additive genetic variation (VA) and narrow-sense heritability (h2) were consistently higher in the Wisconsin relative to the Washington population. If selection had acted on the Wisconsin population there was no evidence of a concomitant loss of genetic variation in BKD susceptibility. The Renibacterium salmoninarum exposures were conducted at both 14°C and 9°C; the warmer temperature accelerated time to death in both populations and there was no evidence of phenotypic plasticity or a genotype-by-environment (G × E) interaction. High h2 estimates for BKD susceptibility in the Wisconsin population, combined with a lack of phenotypic plasticity, predicts that future adaptive gains in BKD resistance are still possible and

  11. Bacterial β-(1,3)-glucan prevents DSS-induced IBD by restoring the reduced population of regulatory T cells.

    PubMed

    Lee, Kwang-Ho; Park, Min; Ji, Kon-Young; Lee, Hwa-Youn; Jang, Ji-Hun; Yoon, Il-Joo; Oh, Seung-Su; Kim, Su-Man; Jeong, Yun-Hwa; Yun, Chul-Ho; Kim, Mi-Kyoung; Lee, In-Young; Choi, Ha-Rim; Ko, Ki-sung; Kang, Hyung-Sik

    2014-10-01

    Bacterial β-(1,3)-glucan has more advantages in terms of cost, yield and efficiency than that derived from mushrooms, plants, yeasts and fungi. We have previously developed a novel and high-yield β-(1,3)-glucan produced by Agrobacterium sp. R259. This study aimed to elucidate the functional mechanism and therapeutic efficacy of bacterial β-(1,3)-glucan in dextran sulfate sodium (DSS)-induced inflammatory bowel disease (IBD).Mice were orally pretreated with bacterial β-(1,3)-glucan at daily doses of 2.5 or 5mg/kg for 2 weeks. After 6 days of DSS treatment, clinical assessment of IBD severity and expression of pro-inflammatory cytokines were evaluated. In vivo cell proliferation was examined by immunohistochemistry using Ki-67 and ER-TR7 antibodies. The frequency of regulatory T cells (Tregs) was analyzed by flow cytometry. Natural killer (NK) activity and IgA level were evaluated using NK cytotoxicity assay and ELISA.The deterioration of body weight gain, colonic architecture, disease score and histological score was recovered in DSS-induced IBD mice when pretreated with bacterial β-(1,3)-glucan. The recruitment of macrophages and the gene expression of proinflammatory cytokines, such as IL-1β, IL-6 and IL-17A/F, were markedly decreased in the colon of β-(1,3)-glucan-pretreated mice. β-(1,3)-Glucan induced the recovery of Tregs in terms of their frequency in DSS-induced IBD mice. Intriguingly, β-(1,3)-glucan reversed the functional defects of NK cells and excessive IgA production in DSS-induced IBD mice.We conclude that bacterial β-(1,3)-glucan prevented the progression of DSS-induced IBD by recovering the reduction of Tregs, functional defect of NK cells and excessive IgA production.

  12. Dynamics of bacterial populations during bench-scale bioremediation of oily seawater and desert soil bioaugmented with coastal microbial mats.

    PubMed

    Ali, Nidaa; Dashti, Narjes; Salamah, Samar; Sorkhoh, Naser; Al-Awadhi, Husain; Radwan, Samir

    2016-03-01

    This study describes a bench-scale attempt to bioremediate Kuwaiti, oily water and soil samples through bioaugmentation with coastal microbial mats rich in hydrocarbonoclastic bacterioflora. Seawater and desert soil samples were artificially polluted with 1% weathered oil, and bioaugmented with microbial mat suspensions. Oil removal and microbial community dynamics were monitored. In batch cultures, oil removal was more effective in soil than in seawater. Hydrocarbonoclastic bacteria associated with mat samples colonized soil more readily than seawater. The predominant oil degrading bacterium in seawater batches was the autochthonous seawater species Marinobacter hydrocarbonoclasticus. The main oil degraders in the inoculated soil samples, on the other hand, were a mixture of the autochthonous mat and desert soil bacteria; Xanthobacter tagetidis, Pseudomonas geniculata, Olivibacter ginsengisoli and others. More bacterial diversity prevailed in seawater during continuous than batch bioremediation. Out of seven hydrocarbonoclastic bacterial species isolated from those cultures, only one, Mycobacterium chlorophenolicum, was of mat origin. This result too confirms that most of the autochthonous mat bacteria failed to colonize seawater. Also culture-independent analysis of seawater from continuous cultures revealed high-bacterial diversity. Many of the bacteria belonged to the Alphaproteobacteria, Flavobacteria and Gammaproteobacteria, and were hydrocarbonoclastic. Optimal biostimulation practices for continuous culture bioremediation of seawater via mat bioaugmentation were adding the highest possible oil concentration as one lot in the beginning of bioremediation, addition of vitamins, and slowing down the seawater flow rate. PMID:26751253

  13. Influence of co-existed benzo[a]pyrene and copper on the cellular characteristics of Stenotrophomonas maltophilia during biodegradation and transformation.

    PubMed

    Chen, Shuona; Yin, Hua; Ye, Jinshao; Peng, Hui; Liu, Zehua; Dang, Zhi; Chang, Jingjing

    2014-04-01

    Microbial remediation has been proposed as a promising technique to remove pollutions, however, its application has been hindered by the lack of understanding the mechanisms involved in contaminants conversion and the influence of pollutants on cellular characteristics. To address this problem, biodegradation and transformation of BaP-Cu(II) by Stenotrophomonas maltophilia, along with interactions of these pollutants with microbial cells through FCM assay were investigated. The results indicated that BaP and Cu(II) were rapidly removed by S. maltophilia on the 1st d, but only less than 10% BaP was broken down due to temporary store in cells, instead of being decomposed immediately. The key ATP enzymes in cells were then activated by BaP to promote bacteria to further decompose BaP. Stimulation of co-existed contaminants strengthened cell membrane permeability and altered cell structure, but a higher esterase activity and DNA in cells of S. maltophilia were still retained.

  14. Co-existence generation of XG-PON and single carrier XLG-PON for ultra-high definition TV transmission with entirely passive optical plant

    NASA Astrophysics Data System (ADS)

    Niazi, Shahab Ahmad; Zhang, Xiao-guang; Xi, Li-xia; Munir, Abid; Idress, Muhammad

    2013-05-01

    International telecommunication union (ITU) recently has standardized ultra-high definition television (UHD-TV) with a resolution which is 16 times more than that of current high definition TV. Increasing the efficiency of video source coding or the capacity of transmission channels will be needed to deliver such programs by passive optical network (PON). In this paper, a complete passive co-existence of 10 Gbit-PON (XG-PON) and single carrier 40 Gbit-PON (XLG-PON) for overlay of UHD-TV distribution to 32 optical network units (ONUs) on broadcast basis is presented. The results show error free transmission performance with negligible power penalty over a 20 km bidirectional fiber.

  15. The roles of a pillared bentonite on enhancing Se(VI) removal by ZVI and the influence of co-existing solutes in groundwater.

    PubMed

    Dong, Huaping; Chen, Ya; Sheng, Guodong; Li, Jianfa; Cao, Jie; Li, Zhanfeng; Li, Yimin

    2016-03-01

    The zero-valent iron permeable reactive barrier (ZVI-PRB) is a promising technology for in-situ groundwater remediation. However, its long-term performance often declined due to the blocked reactive sites by corrosion products and by interference of co-existing solutes. In order to address these issues, a pillared bentonite (Al-bent) was homogeneously mixed with ZVI for removing selenate (Se(VI)) from simulated groundwater in column experiments. The Se(VI) removal was enhanced because first Al-bent could facilitate the mass transfer of Se(VI) from solution to iron surface and accelerate Se(VI) reduction. XANES analysis indicated that Se(VI) was almost completely reduced to Se(0) and Se(-II) of less toxicity and solubility by the ZVI/Al-bent mixture, and the buffering effect of Al-bent could maintain the pH at a lower level that favored the Se(VI) removal. Besides, Al-bent could transfer the corrosion products away from iron surface, leading to the enhanced reactivity and longevity of ZVI. The inhibition on reactivity towards Se(VI) in both the single ZVI and the ZVI/Al-bent systems increased in the order of Cl(-)co-existing solutes in groundwater.

  16. Effects of water temperature and backwashing on bacterial population and community in a biological activated carbon process at a water treatment plant.

    PubMed

    Kim, Tae Gwan; Yun, Jeonghee; Hong, Sung-Ho; Cho, Kyung-Suk

    2014-02-01

    Bacterial community dynamics was examined in an actual biological activated carbon (BAC) process for four consecutive seasons, using quantitative polymerase chain reaction and pyrosequencing. The BAC stably removed organic carbons for the period, although the water temperature substantially varied over the study period. Neither the population density nor community organization was correlated with time and temperature. However, the similarity degree between communities significantly reduced with time and temperature differences. Community analyses indicated that the community evolved over time, resulting in four distinct groups, and that the abundances of particular bacteria were significantly correlated with time and temperature, as well as their interaction. Additionally, backwashing did not affect the BAC bacterial population, community organization (diversity, evenness, and richness), or composition, although backwashing dislodged a large number of bacteria from the BAC (≈10(15) · m(-3)). These results suggest that water temperature is an important factor driving community dynamics and that backwashing is a harmless management option for biomass control.

  17. RNA-stable-isotope probing shows utilization of carbon from inulin by specific bacterial populations in the rat large bowel.

    PubMed

    Tannock, Gerald W; Lawley, Blair; Munro, Karen; Sims, Ian M; Lee, Julian; Butts, Christine A; Roy, Nicole

    2014-04-01

    Knowledge of the trophisms that underpin bowel microbiota composition is required in order to understand its complex phylogeny and function. Stable-isotope ((13)C)-labeled inulin was added to the diet of rats on a single occasion in order to detect utilization of inulin-derived substrates by particular members of the cecal microbiota. Cecal digesta from Fibruline-inulin-fed rats was collected prior to (0 h) and at 6, 12, 18 and 24 h following provision of the [(13)C]inulin diet. RNA was extracted from these cecal specimens and fractionated in isopycnic buoyant density gradients in order to detect (13)C-labeled nucleic acid originating in bacterial cells that had metabolized the labeled dietary constituent. RNA extracted from specimens collected after provision of the labeled diet was more dense than 0-h RNA. Sequencing of 16S rRNA genes amplified from cDNA obtained from these fractions showed that Bacteroides uniformis, Blautia glucerasea, Clostridium indolis, and Bifidobacterium animalis were the main users of the (13)C-labeled substrate. Culture-based studies of strains of these bacterial species enabled trophisms associated with inulin and its hydrolysis products to be identified. B. uniformis utilized Fibruline-inulin for growth, whereas the other species used fructo-oligosaccharide and monosaccharides. Thus, RNA-stable-isotope probing (RNA-SIP) provided new information about the use of carbon from inulin in microbiota metabolism.

  18. Responses of Ammonia-Oxidizing Bacterial and Archaeal Populations to Organic Nitrogen Amendments in Low-Nutrient Groundwater ▿

    PubMed Central

    Reed, David W.; Smith, Jason M.; Francis, Christopher A.; Fujita, Yoshiko

    2010-01-01

    To evaluate the potential for organic nitrogen addition to stimulate the in situ growth of ammonia oxidizers during a field scale bioremediation trial, samples collected from the Eastern Snake River Plain Aquifer in Idaho before, during, and after the addition of molasses and urea were subjected to PCR analysis of ammonia monooxygenase subunit A (amoA) genes. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) were present in all of the samples tested, with AOA amoA genes outnumbering AOB amoA genes in all of the samples. Following urea addition, nitrate levels rose and bacterial amoA copy numbers increased dramatically, suggesting that urea hydrolysis stimulated nitrification. Bacterial amoA diversity was limited to two Nitrosomonas phylotypes, whereas archaeal amoA analyses revealed 20 distinct operational taxonomic units, including several that were markedly different from all previously reported sequences. Results from this study demonstrate the likelihood of stimulating ammonia-oxidizing communities during field scale manipulation of groundwater conditions to promote urea hydrolysis. PMID:20190081

  19. Responses of ammonia-oxidizing bacterial and archaeal populations to organic nitrogen amendments in low-nutrient groundwater.

    PubMed

    Reed, David W; Smith, Jason M; Francis, Christopher A; Fujita, Yoshiko

    2010-04-01

    To evaluate the potential for organic nitrogen addition to stimulate the in situ growth of ammonia oxidizers during a field scale bioremediation trial, samples collected from the Eastern Snake River Plain Aquifer in Idaho before, during, and after the addition of molasses and urea were subjected to PCR analysis of ammonia monooxygenase subunit A (amoA) genes. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) were present in all of the samples tested, with AOA amoA genes outnumbering AOB amoA genes in all of the samples. Following urea addition, nitrate levels rose and bacterial amoA copy numbers increased dramatically, suggesting that urea hydrolysis stimulated nitrification. Bacterial amoA diversity was limited to two Nitrosomonas phylotypes, whereas archaeal amoA analyses revealed 20 distinct operational taxonomic units, including several that were markedly different from all previously reported sequences. Results from this study demonstrate the likelihood of stimulating ammonia-oxidizing communities during field scale manipulation of groundwater conditions to promote urea hydrolysis.

  20. RNA–Stable-Isotope Probing Shows Utilization of Carbon from Inulin by Specific Bacterial Populations in the Rat Large Bowel

    PubMed Central

    Lawley, Blair; Munro, Karen; Sims, Ian M.; Lee, Julian; Butts, Christine A.; Roy, Nicole

    2014-01-01

    Knowledge of the trophisms that underpin bowel microbiota composition is required in order to understand its complex phylogeny and function. Stable-isotope (13C)-labeled inulin was added to the diet of rats on a single occasion in order to detect utilization of inulin-derived substrates by particular members of the cecal microbiota. Cecal digesta from Fibruline-inulin-fed rats was collected prior to (0 h) and at 6, 12, 18 and 24 h following provision of the [13C]inulin diet. RNA was extracted from these cecal specimens and fractionated in isopycnic buoyant density gradients in order to detect 13C-labeled nucleic acid originating in bacterial cells that had metabolized the labeled dietary constituent. RNA extracted from specimens collected after provision of the labeled diet was more dense than 0-h RNA. Sequencing of 16S rRNA genes amplified from cDNA obtained from these fractions showed that Bacteroides uniformis, Blautia glucerasea, Clostridium indolis, and Bifidobacterium animalis were the main users of the 13C-labeled substrate. Culture-based studies of strains of these bacterial species enabled trophisms associated with inulin and its hydrolysis products to be identified. B. uniformis utilized Fibruline-inulin for growth, whereas the other species used fructo-oligosaccharide and monosaccharides. Thus, RNA–stable-isotope probing (RNA-SIP) provided new information about the use of carbon from inulin in microbiota metabolism. PMID:24487527

  1. [Population].

    PubMed

    1979-01-01

    Data on the population of Venezuela between 1975 and 1977 are presented in descriptive tables and graphs. Information is included on the employed population according to category, sex, and type of economic activity, and by sex, age, and area on the employment rate and the total, the economically active, and the unemployed population.

  2. Modulation of population density and size of silver nanoparticles embedded in bacterial cellulose via ammonia exposure: visual detection of volatile compounds in a piece of plasmonic nanopaper

    NASA Astrophysics Data System (ADS)

    Heli, B.; Morales-Narváez, E.; Golmohammadi, H.; Ajji, A.; Merkoçi, A.

    2016-04-01

    The localized surface plasmon resonance exhibited by noble metal nanoparticles can be sensitively tuned by varying their size and interparticle distances. We report that corrosive vapour (ammonia) exposure dramatically reduces the population density of silver nanoparticles (AgNPs) embedded within bacterial cellulose, leading to a larger distance between the remaining nanoparticles and a decrease in the UV-Vis absorbance associated with the AgNP plasmonic properties. We also found that the size distribution of AgNPs embedded in bacterial cellulose undergoes a reduction in the presence of volatile compounds released during food spoilage, modulating the studied nanoplasmonic properties. In fact, such a plasmonic nanopaper exhibits a change in colour from amber to light amber upon the explored corrosive vapour exposure and from amber to a grey or taupe colour upon fish or meat spoilage exposure. These phenomena are proposed as a simple visual detection of volatile compounds in a flexible, transparent, permeable and stable single-use nanoplasmonic membrane, which opens the way to innovative approaches and capabilities in gas sensing and smart packaging.The localized surface plasmon resonance exhibited by noble metal nanoparticles can be sensitively tuned by varying their size and interparticle distances. We report that corrosive vapour (ammonia) exposure dramatically reduces the population density of silver nanoparticles (AgNPs) embedded within bacterial cellulose, leading to a larger distance between the remaining nanoparticles and a decrease in the UV-Vis absorbance associated with the AgNP plasmonic properties. We also found that the size distribution of AgNPs embedded in bacterial cellulose undergoes a reduction in the presence of volatile compounds released during food spoilage, modulating the studied nanoplasmonic properties. In fact, such a plasmonic nanopaper exhibits a change in colour from amber to light amber upon the explored corrosive vapour exposure and

  3. Effect of non-starch-polysaccharide-degrading enzymes as feed additive on the rumen bacterial population in non-lactating cows quantified by real-time PCR.

    PubMed

    Zeitz, J O; Guertler, P; Pfaffl, M W; Eisenreich, R; Wiedemann, S; Schwarz, F J

    2013-12-01

    The effects of non-starch-polysaccharide-degrading enzymes, added to a maize silage- and grass silage-based total mixed ration (TMR) at least 14 h before feeding, on the rumen bacterial population were investigated. Six non-lactating Holstein Friesian cows were allocated to three treatment groups using a duplicate 3 × 3 Latin square design with three 31-day periods (29 days of adaptation and 2 days of sampling). Treatments were control TMR [69% forage and 31% concentrates on a dry matter (DM) basis] or TMR with 13.8 or 27.7 ml/kg of feed DM of Roxazyme G2 liquid with activities (U/ml enzyme preparation) of xylanase 260 000, β-glucanase 180 000 and cellulase 8000 (DSM Nutritional Products, Basel, Switzerland). The concentrations of 16S rDNA of Anaerovibrio lipolytica, Fibrobacter succinogenes, Prevotella ruminicola, Ruminococcus flavefaciens, Selenomonas ruminantium and Treponema bryantii, and their relative percentage of total bacteria in rumen samples obtained before feeding and 3 and 7 h after feeding and from two rumen fractions were determined using real-time PCR. Sampling time had only little influence, but bacterial numbers and the composition of the population differed between the transition layer between rumen fluid and the fibre mat (fraction A) and the rumen fluid (fraction B) highlighting the importance to standardize sampling. The 16S rDNA copies of total bacteria and the six bacterial species as well as the population composition were mainly unaffected by the high levels of exogenous enzymes supplemented at all sampling times and in both rumen fractions. Occasionally, the percentages of the non-fibrolytic species P. ruminicola and A. lipolytica changed in response to enzyme supplementation. Some increases in the potential degradability of the diet and decreases in lag time which occurred collaterally indicate that other factors than changes in numbers of non-particle-associated bacteria are mainly responsible for the effects of

  4. Entrainment and Control of Bacterial Populations: An in Silico Study over a Spatially Extended Agent Based Model.

    PubMed

    Mina, Petros; Tsaneva-Atanasova, Krasimira; Bernardo, Mario di

    2016-07-15

    We extend a spatially explicit agent based model (ABM) developed previously to investigate entrainment and control of the emergent behavior of a population of synchronized oscillating cells in a microfluidic chamber. Unlike most of the work in models of control of cellular systems which focus on temporal changes, we model individual cells with spatial dependencies which may contribute to certain behavioral responses. We use the model to investigate the response of both open loop and closed loop strategies, such as proportional control (P-control), proportional-integral control (PI-control) and proportional-integral-derivative control (PID-control), to heterogeinities and growth in the cell population, variations of the control parameters and spatial effects such as diffusion in the spatially explicit setting of a microfluidic chamber setup. We show that, as expected from the theory of phase locking in dynamical systems, open loop control can only entrain the cell population in a subset of forcing periods, with a wide variety of dynamical behaviors obtained outside these regions of entrainment. Closed-loop control is shown instead to guarantee entrainment in a much wider region of control parameter space although presenting limitations when the population size increases over a certain threshold. In silico tracking experiments are also performed to validate the ability of classical control approaches to achieve other reference behaviors such as a desired constant output or a linearly varying one. All simulations are carried out in BSim, an advanced agent-based simulator of microbial population which is here extended ad hoc to include the effects of control strategies acting onto the population. PMID:27110835

  5. Bacterial fitness shapes the population dynamics of antibiotic-resistant and -susceptible bacteria in a model of combined antibiotic and anti-virulence treatment

    PubMed Central

    Ternent, Lucy; Dyson, Rosemary J.; Krachler, Anne-Marie; Jabbari, Sara

    2015-01-01

    Bacterial resistance to antibiotic treatment is a huge concern: introduction of any new antibiotic is shortly followed by the emergence of resistant bacterial isolates in the clinic. This issue is compounded by a severe lack of new antibiotics reaching the market. The significant rise in clinical resistance to antibiotics is especially problematic in nosocomial infections, where already vulnerable patients may fail to respond to treatment, causing even greater health concern. A recent focus has been on the development of anti-virulence drugs as a second line of defence in the treatment of antibiotic-resistant infections. This treatment, which weakens bacteria by reducing their virulence rather than killing them, should allow infections to be cleared through the body׳s natural defence mechanisms. In this way there should be little to no selective pressure exerted on the organism and, as such, a predominantly resistant population should be less likely to emerge. However, before the likelihood of resistance to these novel drugs emerging can be predicted, we must first establish whether such drugs can actually be effective. Many believe that anti-virulence drugs would not be powerful enough to clear existing infections, restricting their potential application to prophylaxis. We have developed a mathematical model that provides a theoretical framework to reveal the circumstances under which anti-virulence drugs may or may not be successful. We demonstrate that by harnessing and combining the advantages of antibiotics with those provided by anti-virulence drugs, given infection-specific parameters, it is possible to identify treatment strategies that would efficiently clear bacterial infections, while preventing the emergence of antibiotic-resistant subpopulations. Our findings strongly support the continuation of research into anti-virulence drugs and demonstrate that their applicability may reach beyond infection prevention. PMID:25701634

  6. Bacterial fitness shapes the population dynamics of antibiotic-resistant and -susceptible bacteria in a model of combined antibiotic and anti-virulence treatment.

    PubMed

    Ternent, Lucy; Dyson, Rosemary J; Krachler, Anne-Marie; Jabbari, Sara

    2015-05-01

    Bacterial resistance to antibiotic treatment is a huge concern: introduction of any new antibiotic is shortly followed by the emergence of resistant bacterial isolates in the clinic. This issue is compounded by a severe lack of new antibiotics reaching the market. The significant rise in clinical resistance to antibiotics is especially problematic in nosocomial infections, where already vulnerable patients may fail to respond to treatment, causing even greater health concern. A recent focus has been on the development of anti-virulence drugs as a second line of defence in the treatment of antibiotic-resistant infections. This treatment, which weakens bacteria by reducing their virulence rather than killing them, should allow infections to be cleared through the body׳s natural defence mechanisms. In this way there should be little to no selective pressure exerted on the organism and, as such, a predominantly resistant population should be less likely to emerge. However, before the likelihood of resistance to these novel drugs emerging can be predicted, we must first establish whether such drugs can actually be effective. Many believe that anti-virulence drugs would not be powerful enough to clear existing infections, restricting their potential application to prophylaxis. We have developed a mathematical model that provides a theoretical framework to reveal the circumstances under which anti-virulence drugs may or may not be successful. We demonstrate that by harnessing and combining the advantages of antibiotics with those provided by anti-virulence drugs, given infection-specific parameters, it is possible to identify treatment strategies that would efficiently clear bacterial infections, while preventing the emergence of antibiotic-resistant subpopulations. Our findings strongly support the continuation of research into anti-virulence drugs and demonstrate that their applicability may reach beyond infection prevention.

  7. The effect of wheat prebiotics on the gut bacterial population and iron status of iron deficient broiler chickens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In recent years, there is a lot of interest in improving the intestinal health, and consequently increasing minerals as iron absorption, by managing the intestinal microbial population. This is traditionally done by the consumption of probiotics, which are live microbial food supplements. However, a...

  8. Antimicrobial-resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study compared the populations of antimicrobial-resistant bacteria and the repertoire of antimicrobial resistance genes in four environments: effluent of three municipal waste water treatment facilities, three cattle feedlot runoff catchment ponds, three swine waste lagoons, and two "low impact...

  9. Modulation of population density and size of silver nanoparticles embedded in bacterial cellulose via ammonia exposure: visual detection of volatile compounds in a piece of plasmonic nanopaper.

    PubMed

    Heli, B; Morales-Narváez, E; Golmohammadi, H; Ajji, A; Merkoçi, A

    2016-04-21

    The localized surface plasmon resonance exhibited by noble metal nanoparticles can be sensitively tuned by varying their size and interparticle distances. We report that corrosive vapour (ammonia) exposure dramatically reduces the population density of silver nanoparticles (AgNPs) embedded within bacterial cellulose, leading to a larger distance between the remaining nanoparticles and a decrease in the UV-Vis absorbance associated with the AgNP plasmonic properties. We also found that the size distribution of AgNPs embedded in bacterial cellulose undergoes a reduction in the presence of volatile compounds released during food spoilage, modulating the studied nanoplasmonic properties. In fact, such a plasmonic nanopaper exhibits a change in colour from amber to light amber upon the explored corrosive vapour exposure and from amber to a grey or taupe colour upon fish or meat spoilage exposure. These phenomena are proposed as a simple visual detection of volatile compounds in a flexible, transparent, permeable and stable single-use nanoplasmonic membrane, which opens the way to innovative approaches and capabilities in gas sensing and smart packaging.

  10. Modulation of population density and size of silver nanoparticles embedded in bacterial cellulose via ammonia exposure: visual detection of volatile compounds in a piece of plasmonic nanopaper.

    PubMed

    Heli, B; Morales-Narváez, E; Golmohammadi, H; Ajji, A; Merkoçi, A

    2016-04-21

    The localized surface plasmon resonance exhibited by noble metal nanoparticles can be sensitively tuned by varying their size and interparticle distances. We report that corrosive vapour (ammonia) exposure dramatically reduces the population density of silver nanoparticles (AgNPs) embedded within bacterial cellulose, leading to a larger distance between the remaining nanoparticles and a decrease in the UV-Vis absorbance associated with the AgNP plasmonic properties. We also found that the size distribution of AgNPs embedded in bacterial cellulose undergoes a reduction in the presence of volatile compounds released during food spoilage, modulating the studied nanoplasmonic properties. In fact, such a plasmonic nanopaper exhibits a change in colour from amber to light amber upon the explored corrosive vapour exposure and from amber to a grey or taupe colour upon fish or meat spoilage exposure. These phenomena are proposed as a simple visual detection of volatile compounds in a flexible, transparent, permeable and stable single-use nanoplasmonic membrane, which opens the way to innovative approaches and capabilities in gas sensing and smart packaging. PMID:27009781

  11. Generation of acid mine drainage around the Karaerik copper mine (Espiye, Giresun, NE Turkey): implications from the bacterial population in the Acısu effluent.

    PubMed

    Sağlam, Emine Selva; Akçay, Miğraç; Çolak, Dilşat Nigar; İnan Bektaş, Kadriye; Beldüz, Ali Osman

    2016-09-01

    The Karaerik Cu mine is a worked-out deposit with large volumes of tailings and slags which were left around the mine site without any protection. Natural feeding of these material and run-off water from the mineralised zones into the Acısu effluent causes a serious environmental degradation and creation of acid mine drainage (AMD) along its entire length. This research aims at modelling the formation of AMD with a specific attempt on the characterisation of the bacterial population in association with AMD and their role on its occurrence. Based on 16SrRNA analyses of the clones obtained from a composite water sample, the bacterial community was determined to consist of Acidithiobacillus ferrivorans, Ferrovum myxofaciens, Leptospirillum ferrooxidans and Acidithiobacillus ferrooxidans as iron-oxidising bacteria, Acidocella facilis, Acidocella aluminiidurans, Acidiphilium cryptum and Acidiphilium multivorum as iron-reducing bacteria, and Acidithiobacillus ferrivorans, Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans and Acidiphilium cryptum as sulphur-oxidising bacteria. This association of bacteria with varying roles was interpreted as evidence of a concomitant occurrence of sulphur and iron cycles during the generation of AMD along the Acısu effluent draining the Karaerik mine. PMID:27338270

  12. Isolate PM1 populations are dominant and novel methyl tert-butyl ether-degrading bacterial in compost biofilter enrichments.

    PubMed

    Bruns, M A; Hanson, J R; Mefford, J; Scow, K M

    2001-03-01

    The gasoline additive MTBE, methyl tert-butyl ether, is a widespread and persistent groundwater contaminant. MTBE undergoes rapid mineralization as the sole carbon and energy source of bacterial strain PM1, isolated from an enrichment culture of compost biofilter material. In this report, we describe the results of microbial community DNA profiling to assess the relative dominance of isolate PM1 and other bacterial strains cultured from the compost enrichment. Three polymerase chain reaction (PCR)-based profiling approaches were evaluated: denaturing gradient gel electrophoresis (DGGE) analysis of 230 bp 16S rDNA fragments; thermal gradient gel electrophoresis (TGGE) analysis of 575 bp 16S rDNA fragments; and non-denaturing polyacrylamide gel electrophoresis of 300-1,500 bp fragments containing 16S/23S ribosomal intergenic transcribed spacer (ITS) regions. Whereas all three DNA profiling approaches indicated that PM1-like bands predominated in mixtures from MTBE-grown enrichments, ITS profiling provided the most abundant and specific sequence data to confirm strain PM1's presence in the enrichment. Moreover, ITS profiling did not produce non-specific PCR products that were observed with T/DGGE. A further advantage of ITS community profiling over other methods requiring restriction digestion (e.g. terminal restriction fragment length polymorphisms) was that it did not require an additional digestion step or the use of automated sequencing equipment. ITS bands, excised from similar locations in profiles of the enrichment and PM1 pure culture, were 99.9% identical across 750 16S rDNA positions and 100% identical across 691 spacer positions. BLAST comparisons of nearly full-length 16S rDNA sequences showed 96% similarity between isolate PM1 and representatives of at least four different genera in the Leptothrix subgroup of the beta-Proteobacteria (Aquabacterium, Leptothrix, Rubrivivax and Ideonella). Maximum likelihood and parsimony analyses of 1,249 nucleotide

  13. Population.

    ERIC Educational Resources Information Center

    International Planned Parenthood Federation, London (England).

    In an effort to help meet the growing interest and concern about the problems created by the rapid growth of population, The International Planned Parenthood Federation has prepared this booklet with the aim of assisting the study of the history and future trends of population growth and its impact on individual and family welfare, national,…

  14. β-Thalassaemia and its Co-existence with Haemoglobin E and Haemoglobin S in Upper Assam Region of North Eastern India: A Hospital Based Study

    PubMed Central

    Deori, Rumi; Saikia, Sidhartha Protim; Pathak, Kalyani; Panyang, Rita; Rajkakati, Rashmi

    2016-01-01

    Introduction β-Thalassaemias are common genetic disorders in the Indian subcontinent and its status has not been well studied in the Upper Assam region of North Eastern India. Aim The aim of the study was to show the prevalence of β- thalassaemias and its co-existence with Haemoglobin E and Haemoglobin S in the Upper Assam region of North Eastern India. Materials and Methods A total of 1200 anaemic patients were investigated for β- thalassaemias. Complete Blood Count (CBC) and High Performance Liquid Chromatography (HPLC) were done for screening. Results Out of 1200 patients screened, 5.83% β-thalassaemia trait, 2.33% compound Hb E/β-Thalassaemia, 1.33% β-thalassaemia major and 0.42% compound Hb S/β- thalassaemia were detected. A high incidence of thalassaemia is found among the people of Upper Assam region of North Eastern India. Conclusion The only way to prevent the disease is carrier detection and awareness among the people about it. PMID:27190829

  15. Co-existence of diamagnetism and ferromagnetism and possible superconductivity in Y{sub 8}Ba{sub 5}Zn{sub 4}O{sub 21}

    SciTech Connect

    Topal, Ugur

    2011-02-15

    In the present study, we investigate structural and magnetic properties of the Y{sub 8}Ba{sub 5}Zn{sub 4}O{sub 21} structure, which was recently included in the catalog of the International Centre for Diffraction Data (ICDD) as a prototype structure. It was found that the Y{sub 8}Ba{sub 5}Zn{sub 4}O{sub 21} bulk sample seems to be electrically insulating at temperatures of liquid nitrogen and the room temperature. On the other hand, it has quite interesting magnetic properties. Diamagnetic phase transition was observed at {approx} 90 K, which resembles that of the superconducting materials. The studied composition repels permanent magnets at the liquid nitrogen temperature. Ferromagnetism also co-exists with diamagnetism in the temperature range between 50 K and 90 K. Possible reasons for these behaviors are discussed. - Research Highlights: {yields}Y{sub 8}Ba{sub 5}Zn{sub 4}O{sub 21} possesses both ferromagnetic and diamagnetic properties. {yields}A superconducting-like diamagnetic transition takes place at {approx} 90 K. {yields}Ferromagnetism and diamagnetism coexist between temperatures of 50 K and 90 K. {yields}At 10 K, only ferromagnetism exists and no traces of diamagnetism are detected. {yields}The studied samples repel permanent magnets in liquid nitrogen.

  16. Bacterial and archaeal symbionts in the South China Sea sponge Phakellia fusca: community structure, relative abundance, and ammonia-oxidizing populations.

    PubMed

    Han, Minqi; Liu, Fang; Zhang, Fengli; Li, Zhiyong; Lin, Houwen

    2012-12-01

    Many biologically active natural products have been isolated from Phakellia fusca, an indigenous sponge in the South China Sea; however, the microbial symbionts of Phakellia fusca remain unknown. The present investigations on sponge microbial community are mainly based on qualitative analysis, while quantitative analysis, e.g., relative abundance, is rarely carried out, and little is known about the roles of microbial symbionts. In this study, the community structure and relative abundance of bacteria, actinobacteria, and archaea associated with Phakellia fusca were revealed by 16S rRNA gene library-based sequencing and quantitative real time PCR (qRT-PCR). The ammonia-oxidizing populations were investigated based on amoA gene and anammox-specific 16S rRNA gene libraries. As a result, it was found that bacterial symbionts of sponge Phakellia fusca consist of Proteobacteria including Gamma-, Alpha-, and Delta-proteobacteria, Cyanobacteria with Gamma-proteobacteria as the predominant components. In particular, the diversity of actinobacterial symbionts in Phakellia fusca is high, which is composed of Corynebacterineae, Acidimicrobidae, Frankineae, Micrococcineae, and Streptosporangineae. All the observed archaea in sponge Phakellia fusca belong to Crenarchaeota, and the detected ammonia-oxidizing populations are ammonia-oxidizing archaea, suggesting the nitrification function of sponge archaeal symbionts. According to qRT-PCR analysis, bacterial symbionts dominated the microbial community, while archaea represented the second predominant symbionts, followed by actinobacteria. The revealed diverse prokaryotic symbionts of Phakellia fusca are valuable for the understanding and in-depth utilization of Phakellia fusca microbial symbionts. This study extends our knowledge of the community, especially the relative abundance of microbial symbionts in sponges.

  17. [Bacterial vaginosis].

    PubMed

    Romero Herrero, Daniel; Andreu Domingo, Antonia

    2016-07-01

    Bacterial vaginosis (BV) is the main cause of vaginal dysbacteriosis in the women during the reproductive age. It is an entity in which many studies have focused for years and which is still open for discussion topics. This is due to the diversity of microorganisms that cause it and therefore, its difficult treatment. Bacterial vaginosis is probably the result of vaginal colonization by complex bacterial communities, many of them non-cultivable and with interdependent metabolism where anaerobic populations most likely play an important role in its pathogenesis. The main symptoms are an increase of vaginal discharge and the unpleasant smell of it. It can lead to serious consequences for women, such as an increased risk of contracting sexually transmitted infections including human immunodeficiency virus and upper genital tract and pregnancy complications. Gram stain is the gold standard for microbiological diagnosis of BV, but can also be diagnosed using the Amsel clinical criteria. It should not be considered a sexually transmitted disease but it is highly related to sex. Recurrence is the main problem of medical treatment. Apart from BV, there are other dysbacteriosis less characterized like aerobic vaginitis of which further studies are coming slowly but are achieving more attention and consensus among specialists. PMID:27474242

  18. Decay of Fecal Indicator Bacterial Populations and Bovine-Associated Source-Tracking Markers in Freshly Deposited Cow Pats

    PubMed Central

    Oladeinde, Adelumola; Bohrmann, Thomas; Wong, Kelvin; Purucker, S. T.; Bradshaw, Ken; Brown, Reid; Snyder, Blake

    2014-01-01

    Understanding the survival of fecal indicator bacteria (FIB) and microbial source-tracking (MST) markers is critical to developing pathogen fate and transport models. Although pathogen survival in water microcosms and manure-amended soils is well documented, little is known about their survival in intact cow pats deposited on pastures. We conducted a study to determine decay rates of fecal indicator bacteria (Escherichia coli and enterococci) and bovine-associated MST markers (CowM3, Rum-2-bac, and GenBac) in 18 freshly deposited cattle feces from three farms in northern Georgia. Samples were randomly assigned to shaded or unshaded treatment in order to determine the effects of sunlight, moisture, and temperature on decay rates. A general linear model (GLM) framework was used to determine decay rates. Shading significantly decreased the decay rate of the E. coli population (P < 0.0001), with a rate of −0.176 day−1 for the shaded treatment and −0.297 day−1 for the unshaded treatment. Shading had no significant effect on decay rates of enterococci, CowM3, Rum-2-bac, and GenBac (P > 0.05). In addition, E. coli populations showed a significant growth rate (0.881 day−1) in the unshaded samples during the first 5 days after deposition. UV-B was the most important parameter explaining the decay rate of E. coli populations. A comparison of the decay behaviors among all markers indicated that enterococcus concentrations exhibit a better correlation with the MST markers than E. coli concentrations. Our results indicate that bovine-associated MST markers can survive in cow pats for at least 1 month after excretion, and although their decay dynamic differs from the decay dynamic of E. coli populations, they seem to be reliable markers to use in combination with enterococci to monitor fecal pollution from pasture lands. PMID:24141130

  19. Linking specific heterotrophic bacterial populations to bioreduction of uranium and nitrate using stable isotope probing in contaminated subsurface sediments

    SciTech Connect

    Akob, Denise M.; Kerkhof, Lee; Kusel, Kirsten; Watson, David B; Palumbo, Anthony Vito; Kostka, Joel

    2011-01-01

    Shifts in terminal electron-accepting processes during biostimulation of uranium-contaminated sediments were linked to the composition of stimulated microbial populations using DNA-based stable isotope probing. Nitrate reduction preceded U(VI) and Fe(III) reduction in [{sup 13}C]ethanol-amended microcosms. The predominant, active denitrifying microbial groups were identified as members of the Betaproteobacteria, whereas Actinobacteria dominated under metal-reducing conditions.

  20. Decay of fecal indicator bacterial populations and bovine-associated source-tracking markers in freshly deposited cow pats.

    PubMed

    Oladeinde, Adelumola; Bohrmann, Thomas; Wong, Kelvin; Purucker, S T; Bradshaw, Ken; Brown, Reid; Snyder, Blake; Molina, Marirosa

    2014-01-01

    Understanding the survival of fecal indicator bacteria (FIB) and microbial source-tracking (MST) markers is critical to developing pathogen fate and transport models. Although pathogen survival in water microcosms and manure-amended soils is well documented, little is known about their survival in intact cow pats deposited on pastures. We conducted a study to determine decay rates of fecal indicator bacteria (Escherichia coli and enterococci) and bovine-associated MST markers (CowM3, Rum-2-bac, and GenBac) in 18 freshly deposited cattle feces from three farms in northern Georgia. Samples were randomly assigned to shaded or unshaded treatment in order to determine the effects of sunlight, moisture, and temperature on decay rates. A general linear model (GLM) framework was used to determine decay rates. Shading significantly decreased the decay rate of the E. coli population (P < 0.0001), with a rate of -0.176 day(-1) for the shaded treatment and -0.297 day(-1) for the unshaded treatment. Shading had no significant effect on decay rates of enterococci, CowM3, Rum-2-bac, and GenBac (P > 0.05). In addition, E. coli populations showed a significant growth rate (0.881 day(-1)) in the unshaded samples during the first 5 days after deposition. UV-B was the most important parameter explaining the decay rate of E. coli populations. A comparison of the decay behaviors among all markers indicated that enterococcus concentrations exhibit a better correlation with the MST markers than E. coli concentrations. Our results indicate that bovine-associated MST markers can survive in cow pats for at least 1 month after excretion, and although their decay dynamic differs from the decay dynamic of E. coli populations, they seem to be reliable markers to use in combination with enterococci to monitor fecal pollution from pasture lands.

  1. Seasonal breeding drives the incidence of a chronic bacterial infection in a free-living herbivore population.

    PubMed

    Pathak, A K; Boag, B; Poss, M; Harvill, E T; Cattadori, I M

    2011-08-01

    Understanding seasonal changes in age-related incidence of infections can be revealing for disentangling how host heterogeneities affect transmission and how to control the spread of infections between social groups. Seasonal forcing has been well documented in human childhood diseases but the mechanisms responsible for age-related transmission in free-living and socially structured animal populations are still poorly known. Here we studied the seasonal dynamics of Bordetella bronchiseptica in a free-living rabbit population over 5 years and discuss the possible mechanisms of infection. This bacterium has been isolated in livestock and wildlife where it causes respiratory infections that rapidly spread between individuals and persist as subclinical infections. Sera were collected from rabbits sampled monthly and examined using an ELISA. Findings revealed that B. bronchiseptica circulates in the rabbit population with annual prevalence ranging between 88% and 97%. Both seroprevalence and antibody optical density index exhibited 1-year cycles, indicating that disease outbreaks were seasonal and suggesting that long-lasting antibody protection was transient. Intra-annual dynamics showed a strong seasonal signature associated with the recruitment of naive offspring during the breeding period. Infection appeared to be mainly driven by mother-to-litter contacts rather than by interactions with other members of the community. By age 2 months, 65% of the kittens were seropositive.

  2. Effect of Hydrogen Peroxide in Combination with Minimal Thermal Treatment for Reducing Bacterial Populations on Cantaloupe Rind Surfaces and Transfer to Fresh-Cut Pieces.

    PubMed

    Ukuku, Dike O; Mukhopadhyay, Sudarsan; Geveke, David; Olanya, Modesto; Niemira, Brendan

    2016-08-01

    Surface structure and biochemical characteristics of bacteria and produce play a major role in how and where bacteria attach, complicating decontamination treatments. Whole cantaloupe rind surfaces were inoculated with Salmonella, Escherichia coli O157:H7, and Listeria monocytogenes at 10(7) CFU/ml. Average population size of Salmonella, Escherichia coli O157:H7, and L. monocytogenes recovered after surface inoculation was 4.8 ± 0.12, 5.1 ± 0.14, and 3.6 ± 0.13 log CFU/cm(2), respectively. Inoculated melons were stored at 5 and 22°C for 7 days before washing treatment interventions. Intervention treatments used were (i) water (H2O) at 22°C, (ii) H2O at 80°C, (iii) 3% hydrogen peroxide (H2O2) at 22°C, and (iv) a combination of 3% H2O2 and H2O at 80°C for 300 s. The strength of pathogen attachment (SR value) at days 0, 3, and 7 of storage was determined, and then the efficacy of the intervention treatments to detach, kill, and reduce transfer of bacteria to fresh-cut pieces during fresh-cut preparation was investigated. Populations of E. coli O157:H7 attached to the rind surface at significantly higher levels (P < 0.05) than Salmonella and L. monocytogenes, but Salmonella exhibited the strongest attachment (SR value) at all days tested. Washing with 3% H2O2 alone led to significant reduction (P < 0.05) of bacteria and caused some changes in bacterial cell morphology. A combination treatment with H2O and 3% H2O2 at 8°C led to an average 4-log reduction of bacterial pathogens, and no bacterial pathogens were detected in fresh-cut pieces prepared from this combination treatment, including enriched fresh-cut samples. The results of this study indicate that the microbial safety of fresh-cut pieces from treated cantaloupes was improved at day 6 of storage at 5°C and day 3 of storage at 10°C.

  3. Effect of Hydrogen Peroxide in Combination with Minimal Thermal Treatment for Reducing Bacterial Populations on Cantaloupe Rind Surfaces and Transfer to Fresh-Cut Pieces.

    PubMed

    Ukuku, Dike O; Mukhopadhyay, Sudarsan; Geveke, David; Olanya, Modesto; Niemira, Brendan

    2016-08-01

    Surface structure and biochemical characteristics of bacteria and produce play a major role in how and where bacteria attach, complicating decontamination treatments. Whole cantaloupe rind surfaces were inoculated with Salmonella, Escherichia coli O157:H7, and Listeria monocytogenes at 10(7) CFU/ml. Average population size of Salmonella, Escherichia coli O157:H7, and L. monocytogenes recovered after surface inoculation was 4.8 ± 0.12, 5.1 ± 0.14, and 3.6 ± 0.13 log CFU/cm(2), respectively. Inoculated melons were stored at 5 and 22°C for 7 days before washing treatment interventions. Intervention treatments used were (i) water (H2O) at 22°C, (ii) H2O at 80°C, (iii) 3% hydrogen peroxide (H2O2) at 22°C, and (iv) a combination of 3% H2O2 and H2O at 80°C for 300 s. The strength of pathogen attachment (SR value) at days 0, 3, and 7 of storage was determined, and then the efficacy of the intervention treatments to detach, kill, and reduce transfer of bacteria to fresh-cut pieces during fresh-cut preparation was investigated. Populations of E. coli O157:H7 attached to the rind surface at significantly higher levels (P < 0.05) than Salmonella and L. monocytogenes, but Salmonella exhibited the strongest attachment (SR value) at all days tested. Washing with 3% H2O2 alone led to significant reduction (P < 0.05) of bacteria and caused some changes in bacterial cell morphology. A combination treatment with H2O and 3% H2O2 at 8°C led to an average 4-log reduction of bacterial pathogens, and no bacterial pathogens were detected in fresh-cut pieces prepared from this combination treatment, including enriched fresh-cut samples. The results of this study indicate that the microbial safety of fresh-cut pieces from treated cantaloupes was improved at day 6 of storage at 5°C and day 3 of storage at 10°C. PMID:27497118

  4. Molecular ecology of bacterial populations in environmental hazardous-chemical control. Final report, 1 Dec 88-30 Nov 91

    SciTech Connect

    Sayler, G.S.

    1991-11-30

    Basic research was conducted to develop and explore the use of modern molecular biology techniques in understanding the dynamics of microbial populations engaged in biodegradation of environmental pollutants. The research focused on (1) the use of environmental DNA extraction and gene probing techniques to quantify the presence and distribution of degradative genes in the environment, (2) characterizing new-degradative organisms and plasmids for eventual development of new catabolic gene probes for environmental use, and (3) construction of novel bioluminescent reporter bacteria to act as biosensors of catabolic activity in the environment.

  5. Can a safety-in-numbers effect and a hazard-in-numbers effect co-exist in the same data?

    PubMed

    Elvik, Rune

    2013-11-01

    Safety-in-numbers denotes a non-linear relationship between exposure (traffic volume) and the number of accidents, characterised by declining risk as traffic volume increases. There is safety-in-numbers when the number of accidents increases less than proportional to traffic volume, e.g. a doubling of traffic volume is associated with less than a doubling of the number of accidents. Hazard-in-numbers, a less-used concept, refers to the opposite effect: the number of accidents increases more than in proportion to traffic volume, e.g. is more than doubled when traffic volume is doubled. This paper discusses whether a safety-in-numbers effect and a hazard-in-numbers effect can co-exist in the same data. It is concluded that both effects can exist in a given data set. The paper proposes to make a distinction between partial safety-in-numbers and complete safety-in-numbers. Another issue that has been raised in discussions about the safety-in-numbers effect is whether the effect found in some studies is an artefact created by the way exposure was measured. The paper discusses whether measuring exposure as a rate or a share, e.g. kilometres travelled per inhabitant per year, will generate a safety-in-numbers effect as a statistical artefact. It is concluded that this is the case. The preferred measure of exposure is a count of the number of road users. The count should not be converted to a rate or to the share any group of road user contribute to total traffic volume.

  6. GH-3PAD - a new numerical solver for multiphase transport in porous media - new insights on gas hydrate and free gas co-existence

    NASA Astrophysics Data System (ADS)

    Burwicz, E.; Rupke, L.; Wallmann, K.

    2013-12-01

    Gas Hydrate-3 Phase Advanced Dynamics (GH-3PAD) code has been developed to study the geophysical and biochemical processes associated with gas hydrate as well as free methane gas formation and dissolution in marine sediments. Biochemical processes influencing in-situ organic carbon decay and, therefore, gas hydrate formation, such as Anaerobic Oxidation of Methane (AOM), sulfate reduction, and methanogenesis have been considered. The new model assumes a Lagrangian reference frame that is attached to the deposited sedimentary layers, which compact according to their individual lithological properties. Differential motion of the pore fluids and free gas is modeled as Darcy flow. Gas hydrate and free gas formation is either controlled by 1) instant gas hydrate crystallization assuming local thermodynamical equilibrium or by a 2) kinetically controlled rate of gas hydrate growth. The thermal evolution is computed from an energy equation that includes contributions from all phases present in the model (sediment grains, saline pore fluids, gas hydrate, and free gas). A first application of the GH-3PAD model has been the Blake Ridge Site, offshore South Carolina. Here seismic and well data points to the out-of-equilibrium co-existence of gas hydrate and free gas. It has been reported that these two distinct phases appear within sediment column with a gaseous phase tending to migrate upwards throughout the Gas Hydrate Stability Zone (GHSZ) until it reaches the seafloor despite relatively low gas hydrate content (4 - 7 vol. % after Paull et al., 1996). With the GH-3PAD model we quantify the complex transport- reaction processes that control three phase (gas hydrate, free gas, and dissolved CH4) out-of-equilibrium state. References: Paull C. K., Matsumoto R., Wallace P. J., 1996. 9. Site 997, Shipboard Scientific Party. Proceeding of the Ocean Drilling Program, Initial Reports, Vol. 164.

  7. Relationship between N2O Fluxes from an Almond Soil and Denitrifying Bacterial Populations Estimated by Quantitative PCR

    NASA Astrophysics Data System (ADS)

    Matiasek, M.; Suddick, E. C.; Smart, D. R.; Scow, K. M.

    2008-12-01

    Cultivated soils emit substantial quantities of nitrous oxide (N2O), a greenhouse gas with almost 300 times the radiative forcing potential of CO2. Agriculture-related activities generate from 6 to 35 Tg N2O-N per year, or about 60 to 70% of global production. The microbial processes of nitrification, denitrification and nitrifier denitrification are major biogenic sources of N2O to the atmosphere from soils. Denitrification is considered the major source of N2O especially when soils are wet. The microbial N transformations that produce N2O depend primarily on nitrogen (N) fertilizer, with water content, available carbon and soil temperature being secondary controllers. Despite the fact that microbial processes are responsible for N2O emissions, very little is known about the numbers or types of populations involved. The objective of this study was to relate changes in denitrifying population densities, using quantitative PCR (qPCR) of functional genes, to N2O emissions in a fertilized almond orchard. Quantitative PCR targeted three specific genes involved in denitrification: nirS, nirK and nosZ. Copy numbers of the genes were related back to population densities and the portion of organisms likely to produce nitrous oxide. The study site, a 21.7 acre almond orchard fitted with micro-sprinklers, was fertigated (irrigated and fertilized simultaneously) with 50 lbs/acre sodium nitrate in late March 2008, then irrigated weekly. Immediately after the initial fertigation, fluxes of N2O and CO2, moisture content, inorganic N and denitrification gene copy numbers were measured 6 times over 24 days. Despite the fact that N2O emissions increased following fertigation, there was no consistent increase in any of the targeted genes. The genes nirK and nirS ranged from 0.4-1.4 × 107 and 0.4-1.4 × 108, whereas nosZ ranged from 2-8 × 106 copy numbers per g soil, respectively. Considerable variation, compounded by the small sample sizes used for DNA analysis, made it difficult

  8. Modelling the effects of cell-to-cell variability on the output of interconnected gene networks in bacterial populations

    PubMed Central

    2015-01-01

    Background The interconnection of quantitatively characterized biological devices may lead to composite systems with apparently unpredictable behaviour. Context-dependent variability of biological parts has been investigated in several studies, measuring its entity and identifying the factors contributing to variability. Such studies rely on the experimental analysis of model systems, by quantifying reporter genes via population or single-cell approaches. However, cell-to-cell variability is not commonly included in predictability analyses, thus relying on predictive models trained and tested on central tendency values. This work aims to study in silico the effects of cell-to-cell variability on the population-averaged output of interconnected biological circuits. Methods The steady-state deterministic transfer function of individual devices was described by Hill equations and lognormal synthetic noise was applied to their output. Two- and three-module networks were studied, where individual devices implemented inducible/repressible functions. The single-cell output of such networks was simulated as a function of noise entity; their population-averaged output was computed and used to investigate the expected variability in transfer function identification. The study was extended by testing different noise models, module logic, intrinsic/extrinsic noise proportions and network configurations. Results First, the transfer function of an individual module was identified from simulated data of a two-module network. The estimated parameter variability among different noise entities was limited (14%), while a larger difference was observed (up to 62%) when estimated and true parameters were compared. Thus, low-variability parameter estimates can be obtained for different noise entities, although deviating from the true parameters, whose measurement requires noise knowledge. Second, the black-box input-output function of a two/three-module network was predicted from the

  9. Arthromitus (Bacillus cereus) symbionts in the cockroach Blaberus giganteus: dietary influences on bacterial development and population density.

    PubMed

    Feinberg, L; Jorgensen, J; Haselton, A; Pitt, A; Rudner, R; Margulis, L

    1999-01-01

    The filamentous spore-forming bacterium Arthromitus, discovered in termites, millipedes, sow bugs and other soil-dwelling arthropods by Leidy (1850), is the intestinal stage of Bacillus cereus. We extend the range of Arthromitus habitats to include the hindgut of Blaberus giganteus, the large tropical American cockroach. The occurrence and morphology of the intestinal form of the bacillus were compared in individual cockroaches (n=24) placed on four different diet regimes: diurnally maintained insects fed (1) dog food, (2) soy protein only, (3)purified cellulose only, and (4) a dog food-fed group maintained in continuous darkness. Food quality exerted strong influence on population densities and developmental stages of the filamentous bacterium and on fecal pellet composition. The most dramatic rise in Arthromitus populations, defined as the spore-forming filament intestinal stage, occurred in adult cockroaches kept in the dark on a dog food diet. Limited intake of cellulose or protein alone reduced both the frequency of Arthromitus filaments and the rate of weight gain of the insects. Spores isolated from termites, sow bugs, cockroaches and moths, grown on various hard surfaces display a branching mobility and resistance to antibiotics characteristic to group I Bacilli whose members include B. cereus, B. circulans, B. alvei and B. macerans. DNA isolated from pure cultures of these bacilli taken from the guts of Blaberus giganteus (cockroach), Junonia coenia (moth), Porcellio scaber (sow bug) and Cryptotermes brevis (termite) and subjected to Southern hybridization with a 23S-5S B. subtilis ribosomal sequence probe verified that they are indistinguishable from laboratory strains of Bacillus cereus.

  10. Arthromitus (Bacillus cereus) symbionts in the cockroach Blaberus giganteus: dietary influences on bacterial development and population density

    NASA Technical Reports Server (NTRS)

    Feinberg, L.; Jorgensen, J.; Haselton, A.; Pitt, A.; Rudner, R.; Margulis, L.

    1999-01-01

    The filamentous spore-forming bacterium Arthromitus, discovered in termites, millipedes, sow bugs and other soil-dwelling arthropods by Leidy (1850), is the intestinal stage of Bacillus cereus. We extend the range of Arthromitus habitats to include the hindgut of Blaberus giganteus, the large tropical American cockroach. The occurrence and morphology of the intestinal form of the bacillus were compared in individual cockroaches (n=24) placed on four different diet regimes: diurnally maintained insects fed (1) dog food, (2) soy protein only, (3)purified cellulose only, and (4) a dog food-fed group maintained in continuous darkness. Food quality exerted strong influence on population densities and developmental stages of the filamentous bacterium and on fecal pellet composition. The most dramatic rise in Arthromitus populations, defined as the spore-forming filament intestinal stage, occurred in adult cockroaches kept in the dark on a dog food diet. Limited intake of cellulose or protein alone reduced both the frequency of Arthromitus filaments and the rate of weight gain of the insects. Spores isolated from termites, sow bugs, cockroaches and moths, grown on various hard surfaces display a branching mobility and resistance to antibiotics characteristic to group I Bacilli whose members include B. cereus, B. circulans, B. alvei and B. macerans. DNA isolated from pure cultures of these bacilli taken from the guts of Blaberus giganteus (cockroach), Junonia coenia (moth), Porcellio scaber (sow bug) and Cryptotermes brevis (termite) and subjected to Southern hybridization with a 23S-5S B. subtilis ribosomal sequence probe verified that they are indistinguishable from laboratory strains of Bacillus cereus.

  11. Arthromitus (Bacillus cereus) symbionts in the cockroach Blaberus giganteus: dietary influences on bacterial development and population density.

    PubMed

    Feinberg, L; Jorgensen, J; Haselton, A; Pitt, A; Rudner, R; Margulis, L

    1999-01-01

    The filamentous spore-forming bacterium Arthromitus, discovered in termites, millipedes, sow bugs and other soil-dwelling arthropods by Leidy (1850), is the intestinal stage of Bacillus cereus. We extend the range of Arthromitus habitats to include the hindgut of Blaberus giganteus, the large tropical American cockroach. The occurrence and morphology of the intestinal form of the bacillus were compared in individual cockroaches (n=24) placed on four different diet regimes: diurnally maintained insects fed (1) dog food, (2) soy protein only, (3)purified cellulose only, and (4) a dog food-fed group maintained in continuous darkness. Food quality exerted strong influence on population densities and developmental stages of the filamentous bacterium and on fecal pellet composition. The most dramatic rise in Arthromitus populations, defined as the spore-forming filament intestinal stage, occurred in adult cockroaches kept in the dark on a dog food diet. Limited intake of cellulose or protein alone reduced both the frequency of Arthromitus filaments and the rate of weight gain of the insects. Spores isolated from termites, sow bugs, cockroaches and moths, grown on various hard surfaces display a branching mobility and resistance to antibiotics characteristic to group I Bacilli whose members include B. cereus, B. circulans, B. alvei and B. macerans. DNA isolated from pure cultures of these bacilli taken from the guts of Blaberus giganteus (cockroach), Junonia coenia (moth), Porcellio scaber (sow bug) and Cryptotermes brevis (termite) and subjected to Southern hybridization with a 23S-5S B. subtilis ribosomal sequence probe verified that they are indistinguishable from laboratory strains of Bacillus cereus. PMID:11762374

  12. Sexually transmitted infections, bacterial vaginosis, and candidiasis in women of reproductive age in rural Northeast Brazil: a population-based study.

    PubMed

    Oliveira, Fabíola Araújo; Pfleger, Viola; Lang, Katrin; Heukelbach, Jörg; Miralles, Iracema; Fraga, Francisco; Sousa, Anastácio Queiroz; Stoffler-Meilicke, Marina; Ignatius, Ralf; Kerr, Ligia Franco Sansigolo; Feldmeier, Hermann

    2007-09-01

    Population-based data on sexually transmitted infections (STI), bacterial vaginosis (BV), and candidiasis reflect the epidemiological situation more accurately than studies performed in specific populations, but such data are scarce. To determine the prevalence of STI, BV, and candidiasis among women of reproductive age from a resource-poor community in Northeast Brazil, a population-based cross sectional study was undertaken. All women from seven hamlets and the centre of Pacoti municipality in the state of Ceará, aged 12 to 49 years, were invited to participate. The women were asked about socio-demographic characteristics and genital symptoms, and thereafter examined gynaecologically. Laboratory testing included polymerase chain reaction (PCR) for human papillomavirus (HPV), ligase chain reaction (LCR) for Chlamydia trachomatis and Neisseria gonorrhoeae, ELISA for human immunodeficiency virus (HIV), venereal disease research laboratory (VDRL) and fluorescent treponema antibody absorption test (FTA-ABS) for syphilis, and analysis of wet mounts, gram stains and Pap smears for trichomoniasis, candidiasis, and BV. Only women who had initiated sexual life were included in the analysis (n = 592). The prevalences of STI were: HPV 11.7% (95% confidence interval: 9.3-14.7), chlamydia 4.5% (3.0-6.6), trichomoniasis 4.1% (2.7-6.1), gonorrhoea 1.2% (0.5-2.6), syphilis 0.2% (0.0-1.1), and HIV 0%. The prevalence of BV and candidiasis was 20% (16.9-23.6) and 12.5% (10.0-15.5), respectively. The most common gynaecological complaint was lower abdominal pain. STI are common in women in rural Brazil and represent an important health threat in view of the HIV pandemic.

  13. Antimicrobial-Resistant Bacterial Populations and Antimicrobial Resistance Genes Obtained from Environments Impacted by Livestock and Municipal Waste.

    PubMed

    Agga, Getahun E; Arthur, Terrance M; Durso, Lisa M; Harhay, Dayna M; Schmidt, John W

    2015-01-01

    This study compared the populations of antimicrobial-resistant bacteria and the repertoire of antimicrobial resistance genes in four environments: effluent of three municipal wastewater treatment facilities, three cattle feedlot runoff catchment ponds, three swine waste lagoons, and two "low impact" environments (an urban lake and a relict prairie). Multiple liquid and solid samples were collected from each environment. The prevalences and concentrations of antimicrobial-resistant (AMR) Gram-negative (Escherichia coli and Salmonella enterica) and Gram-positive (enterococci) bacteria were determined from individual samples (n = 174). The prevalences of 84 antimicrobial resistance genes in metagenomic DNA isolated from samples pooled (n = 44) by collection date, location, and sample type were determined. The prevalences and concentrations of AMR E. coli and Salmonella were similar among the livestock and municipal sample sources. The levels of erythromycin-resistant enterococci were significantly higher in liquid samples from cattle catchment ponds and swine waste lagoons than in liquid samples from municipal wastewater treatment facilities, but solid samples from these environments did not differ significantly. Similarly, trimethoprim/sulfamethoxazole-resistant E. coli concentrations were significantly higher in swine liquid than in municipal liquid samples, but there was no difference in solid samples. Multivariate analysis of the distribution of antimicrobial resistance genes using principal coordinate analysis showed distinct clustering of samples with livestock (cattle and swine), low impact environment and municipal samples forming three separate clusters. The numbers of class A beta-lactamase, class C beta-lactamase, and fluoroquinolone resistance genes detected were significantly higher (P < 0.05) in municipal samples than in cattle runoff or swine lagoon samples. In conclusion, we report that AMR is a very widespread phenomenon and that similar prevalences

  14. Mass and density measurements of live and dead Gram-negative and Gram-positive bacterial populations.

    PubMed

    Lewis, Christina L; Craig, Caelli C; Senecal, Andre G

    2014-06-01

    Monitoring cell growth and measuring physical features of food-borne pathogenic bacteria are important for better understanding the conditions under which these organisms survive and proliferate. To address this challenge, buoyant masses of live and dead Escherichia coli O157:H7 and Listeria innocua were measured using Archimedes, a commercially available suspended microchannel resonator (SMR). Cell growth was monitored with Archimedes by observing increased cell concentration and buoyant mass values of live growing bacteria. These growth data were compared to optical density measurements obtained with a Bioscreen system. We observed buoyant mass measurements with Archimedes at cell concentrations between 10(5) and 10(8) cells/ml, while growth was not observed with optical density measurements until the concentration was 10(7) cells/ml. Buoyant mass measurements of live and dead cells with and without exposure to hydrogen peroxide stress were also compared; live cells generally had a larger buoyant mass than dead cells. Additionally, buoyant mass measurements were used to determine cell density and total mass for both live and dead cells. Dead E. coli cells were found to have a larger density and smaller total mass than live E. coli cells. In contrast, density was the same for both live and dead L. innocua cells, while the total mass was greater for live than for dead cells. These results contribute to the ongoing challenge to further develop existing technologies used to observe cell populations at low concentrations and to measure unique physical features of cells that may be useful for developing future diagnostics. PMID:24705320

  15. Antimicrobial-Resistant Bacterial Populations and Antimicrobial Resistance Genes Obtained from Environments Impacted by Livestock and Municipal Waste.

    PubMed

    Agga, Getahun E; Arthur, Terrance M; Durso, Lisa M; Harhay, Dayna M; Schmidt, John W

    2015-01-01

    This study compared the populations of antimicrobial-resistant bacteria and the repertoire of antimicrobial resistance genes in four environments: effluent of three municipal wastewater treatment facilities, three cattle feedlot runoff catchment ponds, three swine waste lagoons, and two "low impact" environments (an urban lake and a relict prairie). Multiple liquid and solid samples were collected from each environment. The prevalences and concentrations of antimicrobial-resistant (AMR) Gram-negative (Escherichia coli and Salmonella enterica) and Gram-positive (enterococci) bacteria were determined from individual samples (n = 174). The prevalences of 84 antimicrobial resistance genes in metagenomic DNA isolated from samples pooled (n = 44) by collection date, location, and sample type were determined. The prevalences and concentrations of AMR E. coli and Salmonella were similar among the livestock and municipal sample sources. The levels of erythromycin-resistant enterococci were significantly higher in liquid samples from cattle catchment ponds and swine waste lagoons than in liquid samples from municipal wastewater treatment facilities, but solid samples from these environments did not differ significantly. Similarly, trimethoprim/sulfamethoxazole-resistant E. coli concentrations were significantly higher in swine liquid than in municipal liquid samples, but there was no difference in solid samples. Multivariate analysis of the distribution of antimicrobial resistance genes using principal coordinate analysis showed distinct clustering of samples with livestock (cattle and swine), low impact environment and municipal samples forming three separate clusters. The numbers of class A beta-lactamase, class C beta-lactamase, and fluoroquinolone resistance genes detected were significantly higher (P < 0.05) in municipal samples than in cattle runoff or swine lagoon samples. In conclusion, we report that AMR is a very widespread phenomenon and that similar prevalences

  16. Mass and density measurements of live and dead Gram-negative and Gram-positive bacterial populations.

    PubMed

    Lewis, Christina L; Craig, Caelli C; Senecal, Andre G

    2014-06-01

    Monitoring cell growth and measuring physical features of food-borne pathogenic bacteria are important for better understanding the conditions under which these organisms survive and proliferate. To address this challenge, buoyant masses of live and dead Escherichia coli O157:H7 and Listeria innocua were measured using Archimedes, a commercially available suspended microchannel resonator (SMR). Cell growth was monitored with Archimedes by observing increased cell concentration and buoyant mass values of live growing bacteria. These growth data were compared to optical density measurements obtained with a Bioscreen system. We observed buoyant mass measurements with Archimedes at cell concentrations between 10(5) and 10(8) cells/ml, while growth was not observed with optical density measurements until the concentration was 10(7) cells/ml. Buoyant mass measurements of live and dead cells with and without exposure to hydrogen peroxide stress were also compared; live cells generally had a larger buoyant mass than dead cells. Additionally, buoyant mass measurements were used to determine cell density and total mass for both live and dead cells. Dead E. coli cells were found to have a larger density and smaller total mass than live E. coli cells. In contrast, density was the same for both live and dead L. innocua cells, while the total mass was greater for live than for dead cells. These results contribute to the ongoing challenge to further develop existing technologies used to observe cell populations at low concentrations and to measure unique physical features of cells that may be useful for developing future diagnostics.

  17. Antimicrobial-Resistant Bacterial Populations and Antimicrobial Resistance Genes Obtained from Environments Impacted by Livestock and Municipal Waste

    PubMed Central

    Durso, Lisa M.; Harhay, Dayna M.; Schmidt, John W.

    2015-01-01

    This study compared the populations of antimicrobial-resistant bacteria and the repertoire of antimicrobial resistance genes in four environments: effluent of three municipal wastewater treatment facilities, three cattle feedlot runoff catchment ponds, three swine waste lagoons, and two “low impact” environments (an urban lake and a relict prairie). Multiple liquid and solid samples were collected from each environment. The prevalences and concentrations of antimicrobial-resistant (AMR) Gram-negative (Escherichia coli and Salmonella enterica) and Gram-positive (enterococci) bacteria were determined from individual samples (n = 174). The prevalences of 84 antimicrobial resistance genes in metagenomic DNA isolated from samples pooled (n = 44) by collection date, location, and sample type were determined. The prevalences and concentrations of AMR E. coli and Salmonella were similar among the livestock and municipal sample sources. The levels of erythromycin-resistant enterococci were significantly higher in liquid samples from cattle catchment ponds and swine waste lagoons than in liquid samples from municipal wastewater treatment facilities, but solid samples from these environments did not differ significantly. Similarly, trimethoprim/sulfamethoxazole-resistant E. coli concentrations were significantly higher in swine liquid than in municipal liquid samples, but there was no difference in solid samples. Multivariate analysis of the distribution of antimicrobial resistance genes using principal coordinate analysis showed distinct clustering of samples with livestock (cattle and swine), low impact environment and municipal samples forming three separate clusters. The numbers of class A beta-lactamase, class C beta-lactamase, and fluoroquinolone resistance genes detected were significantly higher (P < 0.05) in municipal samples than in cattle runoff or swine lagoon samples. In conclusion, we report that AMR is a very widespread phenomenon and that similar

  18. Photosynthesis of co-existing Phragmites haplotypes in their non-native range: are characteristics determined by adaptations derived from their native origin?

    PubMed Central

    Nguyen, Loc Xuan; Lambertini, Carla; Sorrell, Brian K.; Eller, Franziska; Achenbach, Luciana; Brix, Hans

    2013-01-01

    The Gulf Coast of North America (GC) is a ‘hot spot’ of Phragmites diversity as several lineages (defined according to the haplotypes of their chloroplast DNA) differing in origin, genetic traits and phenotype co-exist and interbreed in this area. We analysed differences in photosynthetic characteristics among and within four haplotypes to understand if differences in gas exchange can be attributed to adaptations acquired in their native ranges. We collected rhizomes of four GC haplotypes (I2, M1, M and AI; including the phenotypes ‘Land-type’, ‘Delta-type’, ‘EU-type’ and ‘Greeny-type’) and propagated them in a common controlled environment to compare photosynthesis–irradiance responses, CO2 responses, chlorophyll fluorescence, the activity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), specific leaf area (SLA), pigment contents, stomatal density and guard cell length. The maximum light-saturated photosynthetic rate, Amax, in the haplotype I2 (Land-type) and haplotype M1 (Delta-type) (34.3–36.1 µmol CO2 m−2 s−1) was higher than that in the invasive Eurasian haplotype M (22.4 ± 2.3 µmol CO2 m−2 s−1). The Amax of haplotype AI (Greeny3-type) was 29.1 ± 4.0 µmol CO2 m−2 s−1 and did not differ from the Amax of the other haplotypes. The carboxylation rate (Vcmax) and electron transport rate (Jmax) followed the same pattern as Amax. The haplotypes also differed in SLA (17.0–24.3 m2 kg−1 dry mass) and pigment content, whereas stomatal density and guard cell length, Rubisco activity and chlorophyll fluorescence did not differ significantly among haplotypes. The high photosynthetic activity and gas-exchange capacity of the two haplotypes originating in tropical Africa and the Mediterranean area (haplotypes I2 and M1) are apparently adaptations derived from their native ranges. Hence, the haplotypes can be regarded as ecotypes. However, it remains unclear how these differences relate to plant competitiveness and

  19. Modelling Niche Differentiation of Co-Existing, Elusive and Morphologically Similar Species: A Case Study of Four Macaque Species in Nakai-Nam Theun National Protected Area, Laos

    PubMed Central

    Coudrat, Camille N. Z.; Nekaris, K. Anne-Isola

    2013-01-01

    Simple Summary We investigated the niche separation of four macaque species (Macaca arctoides, M. assamensis, M. leonina, M. mulatta) occurring within Nakai-Nam Theun National Protected Area, central-eastern Laos using the environmental niche modelling software MaxEnt. The respective suitable habitat predicted for each species reveals niche segregation between the four species with a gradual geographical distribution following an environmental gradient of, notably, temperature, precipitation, elevation and slope within the study area. This means that the four species seem adapted to different ecological conditions within the area. This information has implications for future research on these species and for their management and conservation. Abstract Species misidentification often occurs when dealing with co-existing and morphologically similar species such as macaques, making the study of their ecology challenging. To overcome this issue, we use reliable occurrence data from camera-trap images and transect survey data to model their respective ecological niche and potential distribution locally in Nakai-Nam Theun National Protected Area (NNT NPA), central-Eastern Laos. We investigate niche differentiation of morphologically similar species using four sympatric macaque species in NNT NPA, as our model species: rhesus Macaca mulatta (Taxonomic Serial Number, TSN 180099), Northern pig-tailed M. leonina (TSN not listed); Assamese M. assamensis (TSN 573018) and stump-tailed M. arctoides (TSN 573017). We examine the implications for their conservation. We obtained occurrence data of macaque species from systematic 2006–2011 camera-trapping surveys and 2011–2012 transect surveys and model their niche and potential distribution with MaxEnt software using 25 environmental and topographic variables. The respective suitable habitat predicted for each species reveals niche segregation between the four species with a gradual geographical distribution following an

  20. Improvement of the piezoelectric properties in (K,Na)NbO{sub 3}-based lead-free piezoelectric ceramic with two-phase co-existing state

    SciTech Connect

    Yamada, H. Matsuoka, T.; Kozuka, H.; Yamazaki, M.; Ohbayashi, K.; Ida, T.

    2015-06-07

    Two phases of (K,Na)NbO{sub 3} (KNN) co-exist in a KNN-based composite lead-free piezoelectric ceramic 0.910(K{sub 1−x}Na{sub x}){sub 0.86}Ca{sub 0.04}Li{sub 0.02}Nb{sub 0.85}O{sub 3−δ}–0.042K{sub 0.85}Ti{sub 0.85}Nb{sub 1.15}O{sub 5} –0.036BaZrO{sub 3}–0.0016Co{sub 3}O{sub 4}– 0.0025Fe{sub 2}O{sub 3}–0.0069ZnO system, over a wide range of Na fractions, where 0.56 ≤ x ≤ 0.75. The crystal systems of the two KNN phases are identified to tetragonal and orthorhombic by analyzing the synchrotron powder X-ray diffraction (XRD) data, high-resolution transmission electron microscopy (HR-TEM), and selected-area electron diffraction (SAD). In the range 0.33 ≤ x ≤ 0.50, the main component of the composite system is found to be single-phase KNN with a tetragonal structure. Granular nanodomains of the orthorhombic phase dispersed in the tetragonal matrix have been identified by HR-TEM and SAD for 0.56 ≤ x ≤ 0.75. Only a trace amount of the orthorhombic phase has been found in the SAD patterns at the composition x = 0.56. However, the number of orthorhombic nanodomains gradually increases with increasing Na content up to x < 0.75, as observed from the HR-TEM images. An abrupt increase and agglomeration of the nanodomains are observed at x = 0.75, where weak diffraction peaks of the orthorhombic phase have also become detectable from the XRD data. The maximum value of the electromechanical coupling coefficient, k{sub p} = 0.56, has been observed at the composition x = 0.56.

  1. A study of pharmacokinetic interactions among co-existing ingredients in Viscum coloratum after intravenous administration of three different preparations to rats

    PubMed Central

    Ma, Yuying; Fan, Ronghua; Duan, Mengmeng; Yu, Zhiguo; Zhao, Yunli

    2015-01-01

    Background: Viscum coloratum (Komar) Nakai, known as Hujisheng in china, has been widely used as a herb medicine to treat a variety of diseases, including cardiovascular diseases, cancer, hypertension, hepatitis and hemorrhage. Objective: The aim was to investigate pharmacokinetic interactions among co-existing ingredients in V. coloratum after intravenous administration of three different preparations (four monomer solutions, the mixture of them and Viscum coloratum extracts) to rats. Materials and Methods: After protein precipitation pretreatment with plasma samples, high performance liquid chromatographic methods were developed and applied to quantitatively determinate the four components [syringin (Syri), homoeriodictyol-7-O-β-D-glycoside (Hedt-III), homoeriodictyol-7-O-β-D-apiose (1 → 2)-β-D-glycoside (Hedt-II) and homoeriodictyol-7-O-β-D-apiosiyl-(1 → 5)-β-D-apiosyl-(1 → 2)-β-D-glycoside (Hedt-I)]. The pharmacokinetic parameters (Area under the curve [AUC(0-t)], AUC(0-∞), t1/2) were calculated using DAS 2.1 software (Chinese Pharmacological Society, Shanghai, China) and compared statistically by One-way analysis of variance using SPSS software (18.0, Chicago, IL, USA) with P < 0.05 considered statistically significant. Results: Good linearities were achieved in the measured concentration range with R2 it0.9920. Precision, accuracy and extraction recovery were all within the acceptable range. For Syri, there was a significant difference only on t1/2 among three treatment groups. For Hedt-I, Hedt II and Hedt-III, three flavonoid glycosides, the change of AUC(0-t), AUC(0-∞) and t1/2 were markedly distinctive and even converse. Conclusion: Complex, extensive pharmacokinetic interactions were observed among these components in V. coloratum. They were mutually influenced by the in vivo absorption, distribution, metabolism and elimination. The result suggested traditional Chinese medicine was a complicated system, and we should take a scientific and

  2. Effects of fatty acid oxidation products (green odor) on rumen bacterial populations and lipid metabolism in vitro.

    PubMed

    Lee, M R F; Huws, S A; Scollan, N D; Dewhurst, R J

    2007-08-01

    addition, though microbial biomass remained similar. These preliminary studies have shown that FAOP can alter fatty acid biohydrogenation in the rumen. This change was associated with changes in the microbial population that were detected through DNA and branched- and odd-chain fatty acid profiling approaches. PMID:17638998

  3. Distribution of bacterial populations in a stratified fjord (Mariager Fjord, Denmark) quantified by in situ hybridization and related to chemical gradients in the water column.

    PubMed

    Ramsing, N B; Fossing, H; Ferdelman, T G; Andersen, F; Thamdrup, B

    1996-04-01

    The vertical distribution of major and intermediate electron acceptors and donors was measured in a shallow stratified fjord. Peaks of zero valence sulfur, Mn(IV), and Fe(III) were observed in the chemocline separating oxic surface waters from sulfidic and anoxic bottom waters. The vertical fluxes of electron acceptors and donors (principally O2 and H2S) balanced within 5%; however, the zones of oxygen reduction and sulfide oxidation were clearly separated. The pathway of electron transfer between O2 and H2S was not apparent from the distribution of sulfur, nitrogen, or metal compounds investigated. The chemical zonation was related to bacterial populations as detected by ethidium bromide (EtBr) staining and by in situ hybridization with fluorescent oligonucleotide probes of increasing specificity. About half of all EtBr-stained cells were detectable with a general oligonucleotide probe for all eubacteria when digital image analysis algorithms were used to improve sensitivity. Both EtBr staining and hybridization indicated a surprisingly uniform distribution of bacteria throughout the water column. However, the average cell size and staining intensity as well as the abundance of different morphotypes changed markedly within the chemocline. The constant overall cell counts thus concealed pronounced population shifts within the water column. Cells stained with a delta 385 probe (presumably sulfate-reducing bacteria) were detected at the chemocline at about 5 x 10(4) cells per ml, and this concentration increased to 2 x 10(5) cells per ml beneath the chemocline. A long slim rod-shaped bacterium was found in large numbers in the oxic part of the chemocline, whereas large ellipsoid cells dominated at greater depth. Application of selective probes for known genera of sulfate-reducing bacteria gave only low cell counts, and thus it was not possible to identify the dominant morphotypes of the sulfate-reducing community.

  4. High efficient removal of molybdenum from water by Fe2(SO4)3: Effects of pH and affecting factors in the presence of co-existing background constituents.

    PubMed

    Zhang, Xiang; Ma, Jun; Lu, Xixin; Huangfu, Xiaoliu; Zou, Jing

    2015-12-30

    Comparatively investigated the different effects of Fe2(SO4)3 coagulation-filtration and FeCl3 coagulation-filtration on the removal of Mo (VI). And the influence of calcium, sulfate, silicate, phosphate and humic acid (HA) were also studied. The following conclusions can be obtained: (1) compared with the case of FeCl3, Fe2(SO4)3 showed a higher Mo (VI) removal efficiency at pH 4.00-5.00, but an equal removal efficiency at pH 6.00-9.00. (2) The optimum Mo (VI) removal by Fe2(SO4)3 was achieved at pH 5.00-6.00; (3) The presence of calcium can reduce the removal of Mo (VI) over the entire pH range in the present study; (4) The effect of co-existing background anions (including HA) was dominated by three factors: Firstly the influence of co-existing background anions on the content of Fe intercepted from water (intercepted Fe). Secondly the competition of co-existing anions with Mo (VI) for adsorption sites. Thirdly the influence of co-existing background anions on the Zeta potential of the iron flocs. PMID:26340549

  5. Bacterial challenges in food

    PubMed Central

    Collee, J. G.

    1974-01-01

    Qualitative and quantitative aspects of bacterial challenges that might be encountered in food are discussed with reference to recognized and relatively unrecognized hazards. Mechanisms of pathogenicity are reviewed and the populations at risk are noted. The bacterial content of food as it is served at table merits more study. The challenge of prevention by education is discussed. Indirect bacterial challenges in our food are considered. The real challenge of diagnosis depends upon an awareness of a complex range of conditions; the importance of effective communication with efficient laboratory and epidemiological services is stressed. There is an increasing need for care in the preparation and distribution of food. PMID:4467860

  6. Bacterial Larvicide, Bacillus thuringiensis israelensis Strain AM 65-52 Water Dispersible Granule Formulation Impacts Both Dengue Vector, Aedes aegypti (L.) Population Density and Disease Transmission in Cambodia.

    PubMed

    Setha, To; Chantha, Ngan; Benjamin, Seleena; Socheat, Doung

    2016-09-01

    A multi-phased study was conducted in Cambodia from 2005-2011 to measure the impact of larviciding with the bacterial larvicide, Bacillus thuringiensis israelensis (Bti), a water dispersible granule (WG) formulation on the vector, Aedes aegypti (L.) and the epidemiology. In our studies, all in-use containers were treated at 8 g/1000 L, including smaller containers and animal feeders which were found to contribute 23% of Ae aegypti pupae. The treated waters were subjected to routine water exchange activities. Pupal production was suppressed by an average 91% for 8 weeks. Pupal numbers continued to remain significantly lower than the untreated commune (UTC) for 13 weeks post treatment in the peak dengue vector season (p<0.05). Suppression of pupal production was supported by very low adult numbers in the treated commune. An average 70% of the household harbored 0-5 Ae aegypti mosquitoes per home for 8 weeks post treatment, but in the same period of time >50% of the household in the UTC harbored ≥11 mosquitoes per home. The adult population continued to remain at significantly much lower numbers in the Bti treated commune than in the UTC for 10-12 weeks post treatment (p<0.05). In 2011, a pilot operational program was evaluated in Kandal Province, a temephos resistant site. It was concluded that 2 cycles of Bti treatment in the 6 months monsoon season with complete coverage of the target districts achieved an overall dengue case reduction of 48% in the 6 treated districts compared to the previous year, 2010. Five untreated districts in the same province had an overwhelming increase of 352% of dengue cases during the same period of time. The larvicide efficacy, treatment of all in-use containers at the start of the monsoon season, together with treatment coverage of entire districts interrupted disease transmission in the temephos resistant province. PMID:27627758

  7. Bacterial Larvicide, Bacillus thuringiensis israelensis Strain AM 65-52 Water Dispersible Granule Formulation Impacts Both Dengue Vector, Aedes aegypti (L.) Population Density and Disease Transmission in Cambodia

    PubMed Central

    Socheat, Doung

    2016-01-01

    A multi-phased study was conducted in Cambodia from 2005–2011 to measure the impact of larviciding with the bacterial larvicide, Bacillus thuringiensis israelensis (Bti), a water dispersible granule (WG) formulation on the vector, Aedes aegypti (L.) and the epidemiology. In our studies, all in-use containers were treated at 8 g/1000 L, including smaller containers and animal feeders which were found to contribute 23% of Ae aegypti pupae. The treated waters were subjected to routine water exchange activities. Pupal production was suppressed by an average 91% for 8 weeks. Pupal numbers continued to remain significantly lower than the untreated commune (UTC) for 13 weeks post treatment in the peak dengue vector season (p<0.05). Suppression of pupal production was supported by very low adult numbers in the treated commune. An average 70% of the household harbored 0–5 Ae aegypti mosquitoes per home for 8 weeks post treatment, but in the same period of time >50% of the household in the UTC harbored ≥11 mosquitoes per home. The adult population continued to remain at significantly much lower numbers in the Bti treated commune than in the UTC for 10–12 weeks post treatment (p<0.05). In 2011, a pilot operational program was evaluated in Kandal Province, a temephos resistant site. It was concluded that 2 cycles of Bti treatment in the 6 months monsoon season with complete coverage of the target districts achieved an overall dengue case reduction of 48% in the 6 treated districts compared to the previous year, 2010. Five untreated districts in the same province had an overwhelming increase of 352% of dengue cases during the same period of time. The larvicide efficacy, treatment of all in-use containers at the start of the monsoon season, together with treatment coverage of entire districts interrupted disease transmission in the temephos resistant province. PMID:27627758

  8. Baseline susceptibility to bacterial insecticides in populations of Culex pipiens complex (Diptera: Culicidae) from California and from the Mediterranean Island of Cyprus.

    PubMed

    Wirth, M C; Ferrari, J A; Georghiou, G P

    2001-08-01

    Bacterial insecticides play an increasingly important role in mosquito control. To establish guidelines for detecting resistance at an early stage, information on natural variation in susceptibility of insect populations to these insecticides is needed. Between 1990 and 1993, the susceptibility of Culex pipiens L. complex to Bacillus thuringiensis subsp. israelensis de Barjac and/or Bacillus sphaericus Neide was determined in 31 collections from California. These collections were undertaken before the widespread use of B. thuringiensis subsp. israelensis and before the registration of B. sphaericus in California. Seven collections from the Mediterranean island of Cyprus, where no microbial insecticides have been used, also were tested. The 1990-1991 California collections exhibited limited variation in susceptibility to B. thuringiensis subsp. israelensis. LC50 and LC95 values spanned about a three-fold and four-fold range, respectively. The 1993 Cyprus collections exhibited both higher mean LC values, and greater variability in those values, than the California collections. The LC50s for the Cyprus collections varied over a 10-fold range, whereas the LC50s varied over a 12.5-fold range. Variation in susceptibility to B. sphaericus among the 1991 California collections was about five-fold at the LC50 and LC95. No significant geographic variation in susceptibility to B. thuringiensis subsp. israelensis was observed among regions within California. Although variation in susceptibility was limited among California collections, the greater variability observed among the Cyprus collections and between the Cyprus and California collections illustrates the importance of establishing regional baselines to monitor accurately for changes in susceptibility.

  9. Bacterial Larvicide, Bacillus thuringiensis israelensis Strain AM 65-52 Water Dispersible Granule Formulation Impacts Both Dengue Vector, Aedes aegypti (L.) Population Density and Disease Transmission in Cambodia.

    PubMed

    Setha, To; Chantha, Ngan; Benjamin, Seleena; Socheat, Doung

    2016-09-01

    A multi-phased study was conducted in Cambodia from 2005-2011 to measure the impact of larviciding with the bacterial larvicide, Bacillus thuringiensis israelensis (Bti), a water dispersible granule (WG) formulation on the vector, Aedes aegypti (L.) and the epidemiology. In our studies, all in-use containers were treated at 8 g/1000 L, including smaller containers and animal feeders which were found to contribute 23% of Ae aegypti pupae. The treated waters were subjected to routine water exchange activities. Pupal production was suppressed by an average 91% for 8 weeks. Pupal numbers continued to remain significantly lower than the untreated commune (UTC) for 13 weeks post treatment in the peak dengue vector season (p<0.05). Suppression of pupal production was supported by very low adult numbers in the treated commune. An average 70% of the household harbored 0-5 Ae aegypti mosquitoes per home for 8 weeks post treatment, but in the same period of time >50% of the household in the UTC harbored ≥11 mosquitoes per home. The adult population continued to remain at significantly much lower numbers in the Bti treated commune than in the UTC for 10-12 weeks post treatment (p<0.05). In 2011, a pilot operational program was evaluated in Kandal Province, a temephos resistant site. It was concluded that 2 cycles of Bti treatment in the 6 months monsoon season with complete coverage of the target districts achieved an overall dengue case reduction of 48% in the 6 treated districts compared to the previous year, 2010. Five untreated districts in the same province had an overwhelming increase of 352% of dengue cases during the same period of time. The larvicide efficacy, treatment of all in-use containers at the start of the monsoon season, together with treatment coverage of entire districts interrupted disease transmission in the temephos resistant province.

  10. Bacterial genome remodeling through bacteriophage recombination.

    PubMed

    Menouni, Rachid; Hutinet, Geoffrey; Petit, Marie-Agnès; Ansaldi, Mireille

    2015-01-01

    Bacteriophages co-exist and co-evolve with their hosts in natural environments. Virulent phages lyse infected cells through lytic cycles, whereas temperate phages often remain dormant and can undergo lysogenic or lytic cycles. In their lysogenic state, prophages are actually part of the host genome and replicate passively in rhythm with host division. However, prophages are far from being passive residents: they can modify or bring new properties to their host. In this review, we focus on two important phage-encoded recombination mechanisms, i.e. site-specific recombination and homologous recombination, and how they remodel bacterial genomes. PMID:25790500

  11. Bacterial genome remodeling through bacteriophage recombination.

    PubMed

    Menouni, Rachid; Hutinet, Geoffrey; Petit, Marie-Agnès; Ansaldi, Mireille

    2015-01-01

    Bacteriophages co-exist and co-evolve with their hosts in natural environments. Virulent phages lyse infected cells through lytic cycles, whereas temperate phages often remain dormant and can undergo lysogenic or lytic cycles. In their lysogenic state, prophages are actually part of the host genome and replicate passively in rhythm with host division. However, prophages are far from being passive residents: they can modify or bring new properties to their host. In this review, we focus on two important phage-encoded recombination mechanisms, i.e. site-specific recombination and homologous recombination, and how they remodel bacterial genomes.

  12. Bacterial Sialidase

    NASA Technical Reports Server (NTRS)

    2004-01-01

    Data shows that elevated sialidase in bacterial vaginosis patients correlates to premature births in women. Bacterial sialidase also plays a significant role in the unusual colonization of Pseudomonas aeruginosa in cystic fibrosis patients. Crystals of Salmonella sialidase have been reproduced and are used for studying the inhibitor-enzyme complexes. These inhibitors may also be used to inhibit a trans-sialidase of Trypanosome cruzi, a very similar enzyme to bacterial sialidase, therefore preventing T. cruzi infection, the causitive agent of Chagas' disease. The Center for Macromolecular Crystallography suggests that inhibitors of bacterial sialidases can be used as prophylactic drugs to prevent bacterial infections in these critical cases.

  13. SIMPLAS: A Simulation of Bacterial Plasmid Maintenance.

    ERIC Educational Resources Information Center

    Dunn, A.; And Others

    1988-01-01

    This article describes a computer simulation of bacterial physiology during growth in a chemostat. The program was designed to help students to appreciate and understand the related effects of parameters which influence plasmid persistence in bacterial populations. (CW)

  14. Antimicrobials for bacterial bioterrorism agents.

    PubMed

    Sarkar-Tyson, Mitali; Atkins, Helen S

    2011-06-01

    The limitations of current antimicrobials for highly virulent pathogens considered as potential bioterrorism agents drives the requirement for new antimicrobials that are suitable for use in populations in the event of a deliberate release. Strategies targeting bacterial virulence offer the potential for new countermeasures to combat bacterial bioterrorism agents, including those active against a broad spectrum of pathogens. Although early in the development of antivirulence approaches, inhibitors of bacterial type III secretion systems and cell division mechanisms show promise for the future.

  15. Bacterial Proteasomes

    PubMed Central

    Jastrab, Jordan B.; Darwin, K. Heran

    2015-01-01

    Interest in bacterial proteasomes was sparked by the discovery that proteasomal degradation is required for the pathogenesis of Mycobacterium tuberculosis, one of the world's deadliest pathogens. Although bacterial proteasomes are structurally similar to their eukaryotic and archaeal homologs, there are key differences in their mechanisms of assembly, activation, and substrate targeting for degradation. In this article, we compare and contrast bacterial proteasomes with their archaeal and eukaryotic counterparts, and we discuss recent advances in our understanding of how bacterial proteasomes function to influence microbial physiology. PMID:26488274

  16. Cultural consonance, constructions of science and co-existence: a review of the integration of traditional, complementary and alternative medicine in low- and middle-income countries.

    PubMed

    Lakshmi, Josyula K; Nambiar, Devaki; Narayan, Venkatesh; Sathyanarayana, Tamysetty N; Porter, John; Sheikh, Kabir

    2015-10-01

    This review examined the determinants, patterns and imports of official recognition, and incorporation of different traditional, complementary and alternative systems of medicine (TCAM) in the public health establishment of low- and middle-income countries, with a particular focus on India. Public health systems in most countries have tended to establish health facilities centred on allopathy, and then to recognize or derecognize different TCAM based on evidence or judgement, to arrive at health-care configurations that include several systems of medicine with disparate levels of authority, jurisdiction and government support. The rationale for the inclusion of TCAM providers in the public health workforce ranges from the need for personnel to address the disease burden borne by the public health system, to the desirability of providing patients with a choice of therapeutic modalities, and the nurturing of local culture. Integration, mostly described as a juxtaposition of different systems of medical practice, is often implemented as a system of establishing personnel with certification in different medical systems, in predominantly allopathic health-care facilities, to practise allopathic medicine. A hierarchy of systems of medicine, often unacknowledged, is exercised in most societies, with allopathy at the top, certain TCAM systems next and local healing traditions last. The tools employed by TCAM practitioners in diagnosis, research, pharmacy, marketing and education and training, which are seen to increasingly emulate those of allopathy, are sometimes inappropriate for use in therapeutic systems with widely divergent epistemologies, which call for distinct research paradigms. The coexistence of numerous systems of medicine, while offering the population greater choice, and presumably enhancing geographical access to health care as well, is often fraught with tensions related to the coexistence of philosophically disparate, even opposed, disciplines, with

  17. Cultural consonance, constructions of science and co-existence: a review of the integration of traditional, complementary and alternative medicine in low- and middle-income countries

    PubMed Central

    Lakshmi, Josyula K; Nambiar, Devaki; Narayan, Venkatesh; Sathyanarayana, Tamysetty N; Porter, John; Sheikh, Kabir

    2015-01-01

    This review examined the determinants, patterns and imports of official recognition, and incorporation of different traditional, complementary and alternative systems of medicine (TCAM) in the public health establishment of low- and middle-income countries, with a particular focus on India. Public health systems in most countries have tended to establish health facilities centred on allopathy, and then to recognize or derecognize different TCAM based on evidence or judgement, to arrive at health-care configurations that include several systems of medicine with disparate levels of authority, jurisdiction and government support. The rationale for the inclusion of TCAM providers in the public health workforce ranges from the need for personnel to address the disease burden borne by the public health system, to the desirability of providing patients with a choice of therapeutic modalities, and the nurturing of local culture. Integration, mostly described as a juxtaposition of different systems of medical practice, is often implemented as a system of establishing personnel with certification in different medical systems, in predominantly allopathic health-care facilities, to practise allopathic medicine. A hierarchy of systems of medicine, often unacknowledged, is exercised in most societies, with allopathy at the top, certain TCAM systems next and local healing traditions last. The tools employed by TCAM practitioners in diagnosis, research, pharmacy, marketing and education and training, which are seen to increasingly emulate those of allopathy, are sometimes inappropriate for use in therapeutic systems with widely divergent epistemologies, which call for distinct research paradigms. The coexistence of numerous systems of medicine, while offering the population greater choice, and presumably enhancing geographical access to health care as well, is often fraught with tensions related to the coexistence of philosophically disparate, even opposed, disciplines, with

  18. Germination sensitivities to water potential among co-existing C3 and C4 grasses of cool semi-arid prairie grasslands.

    PubMed

    Mollard, F P O; Naeth, M A

    2015-03-01

    An untested theory states that C4 grass seeds could germinate under lower water potentials (Ψ) than C3 grass seeds. We used hydrotime modelling to study seed water relations of C4 and C3 Canadian prairie grasses to address Ψ divergent sensitivities and germination strategies along a risk-spreading continuum of responses to limited water. C4 grasses were Bouteloua gracilis, Calamovilfa longifolia and Schizachyrium scoparium; C3 grasses were Bromus carinatus, Elymus trachycaulus, Festuca hallii and Koeleria macrantha. Hydrotime parameters were obtained after incubation of non-dormant seeds under different Ψ PEG 6000 solutions. A t-test between C3 and C4 grasses did not find statistical differences in population mean base Ψ (Ψb (50)). We found idiosyncratic responses of C4 grasses along the risk-spreading continuum. B. gracilis showed a risk-taker strategy of a species able to quickly germinate in a dry soil due to its low Ψb (50) and hydrotime (θH ). The high Ψb (50) of S. scoparium indicates it follows the risk-averse strategy so it can only germinate in wet soils. C. longifolia showed an intermediate strategy: the lowest Ψb (50) yet the highest θH . K. macrantha, a C3 grass which thrives in dry habitats, had the highest Ψb (50), suggesting a risk-averse strategy for a C3 species. Other C3 species showed intermediate germination patterns in response to Ψ relative to C4 species. Our results indicate that grasses display germination sensitivities to Ψ across the risk-spreading continuum of responses. Thus seed water relations may be poor predictors to explain differential recruitment and distribution of C3 and C4 grasses in the Canadian prairies.

  19. Cultural consonance, constructions of science and co-existence: a review of the integration of traditional, complementary and alternative medicine in low- and middle-income countries.

    PubMed

    Lakshmi, Josyula K; Nambiar, Devaki; Narayan, Venkatesh; Sathyanarayana, Tamysetty N; Porter, John; Sheikh, Kabir

    2015-10-01

    This review examined the determinants, patterns and imports of official recognition, and incorporation of different traditional, complementary and alternative systems of medicine (TCAM) in the public health establishment of low- and middle-income countries, with a particular focus on India. Public health systems in most countries have tended to establish health facilities centred on allopathy, and then to recognize or derecognize different TCAM based on evidence or judgement, to arrive at health-care configurations that include several systems of medicine with disparate levels of authority, jurisdiction and government support. The rationale for the inclusion of TCAM providers in the public health workforce ranges from the need for personnel to address the disease burden borne by the public health system, to the desirability of providing patients with a choice of therapeutic modalities, and the nurturing of local culture. Integration, mostly described as a juxtaposition of different systems of medical practice, is often implemented as a system of establishing personnel with certification in different medical systems, in predominantly allopathic health-care facilities, to practise allopathic medicine. A hierarchy of systems of medicine, often unacknowledged, is exercised in most societies, with allopathy at the top, certain TCAM systems next and local healing traditions last. The tools employed by TCAM practitioners in diagnosis, research, pharmacy, marketing and education and training, which are seen to increasingly emulate those of allopathy, are sometimes inappropriate for use in therapeutic systems with widely divergent epistemologies, which call for distinct research paradigms. The coexistence of numerous systems of medicine, while offering the population greater choice, and presumably enhancing geographical access to health care as well, is often fraught with tensions related to the coexistence of philosophically disparate, even opposed, disciplines, with

  20. Bistability and Bacterial Infections

    PubMed Central

    Malka, Roy; Shochat, Eliezer; Rom-Kedar, Vered

    2010-01-01

    Bacterial infections occur when the natural host defenses are overwhelmed by invading bacteria. The main component of the host defense is impaired when neutrophil count or function is too low, putting the host at great risk of developing an acute infection. In people with intact immune systems, neutrophil count increases during bacterial infection. However, there are two important clinical cases in which they remain constant: a) in patients with neutropenic-associated conditions, such as those undergoing chemotherapy at the nadir (the minimum clinically observable neutrophil level); b) in ex vivo examination of the patient's neutrophil bactericidal activity. Here we study bacterial population dynamics under fixed neutrophil levels by mathematical modelling. We show that under reasonable biological assumptions, there are only two possible scenarios: 1) Bacterial behavior is monostable: it always converges to a stable equilibrium of bacterial concentration which only depends, in a gradual manner, on the neutrophil level (and not on the initial bacterial level). We call such a behavior type I dynamics. 2) The bacterial dynamics is bistable for some range of neutrophil levels. We call such a behavior type II dynamics. In the bistable case (type II), one equilibrium corresponds to a healthy state whereas the other corresponds to a fulminant bacterial infection. We demonstrate that published data of in vitro Staphylococcus epidermidis bactericidal experiments are inconsistent with both the type I dynamics and the commonly used linear model and are consistent with type II dynamics. We argue that type II dynamics is a plausible mechanism for the development of a fulminant infection. PMID:20463954

  1. Arsenic(III, V) adsorption on a goethite-based adsorbent in the presence of major co-existing ions: Modeling competitive adsorption consistent with spectroscopic and molecular evidence

    NASA Astrophysics Data System (ADS)

    Kanematsu, Masakazu; Young, Thomas M.; Fukushi, Keisuke; Green, Peter G.; Darby, Jeannie L.

    2013-04-01

    Adsorption of the two oxyanions, arsenate (As(V)) and arsenite (As(III)), on a common goethite-based granular porous adsorbent is studied in the presence of major co-existing ions in groundwater (i.e., phosphate, silicic acid, sulfate, carbonate, magnesium, and calcium) and predicted using the extended triple layer model (ETLM), a dipole modified single-site triple layer surface complexation model consistent with spectroscopic and molecular evidence. Surface species of all ions were selected according to the previous ETLM studies and published experimental spectroscopic/theoretical molecular information. The adsorption equilibrium constants for all ions were determined using adsorption data obtained in single-solute systems. The adsorption equilibrium constants referenced to the site-occupancy standard state (indicated by Kθ) were compared with those for goethite in the literature if available. The values of these constants for the goethite-based adsorbent are found to be close to the values for goethite previously studied. These "constrained" adsorption equilibrium constants determined in single-solute systems were used in the ETLM to predict the competitive interactions of As(III, V) with the co-existing ions in binary-solute systems. The ETLM is capable of predicting As(III, V) adsorption in the presence of oxyanions (phosphate, silicic acid, sulfate, and carbonate). This study presents the first successful and systematic prediction of the competitive interactions of As(III, V) with these oxyanions using the ETLM. The ETLM prediction of surface (and aqueous) speciation also provides insights into the distinct adsorption behavior of As(III, V) in the presence of the oxyanions. Magnesium and calcium significantly enhanced As(V) adsorption at higher pH values, while they had little effect on As(III) adsorption. The enhanced adsorption of As(V), however, could not be predicted by the ETLM using the surface species proposed in previous ETLM studies. Further studies

  2. Co-existence of P2Y-and PPADS-insensitive P2U-purinoceptors in endothelial cells from adrenal medulla.

    PubMed Central

    Mateo, J.; Miras-Portugal, M. T.; Castro, E.

    1996-01-01

    1. We have studied the effects of purinoceptor stimulation on Ca2+ signals in bovine adrenomedullary endothelial cells. [Ca2+]i was determined with the fluorescent probe fura-2 both in population samples and in single, isolated, endothelial cells in primary culture and after subculturing. 2. In endothelial cells, maintained in culture for more than one passage, several purinoceptor agonists elicited clear [Ca2+]i transient peaks that remained in the absence of extracellular Ca2+. Adenosine 5'-triphosphate (ATP) and uridine 5'-triphosphate (UTP) were equipotently active, with EC50 values of 8.5 +/- 0.9 microM and 6.9 +/- 1.5 microM, respectively, whereas 2-methylthioadenosine 5'-triphosphate (2MeSATP), adenosine 5'-(alpha, beta-methylene)triphosphate (alpha, beta-MeATP) and adenosine(5')tetraphospho(5')adenosine (Ap4A) were basically inactive. Adenosine 5'-O-(2-thiodiphosphate) (ADP beta S) was a weak agonist. The apparent potency order was UTP = ATP > ADP beta S >> 2MeSATP > alpha, beta-MeATP. 3. Cross-desensitization experiments revealed that UTP or ATP, added sequentially at concentrations of maximal effect, could completely abolish the [Ca2+]i response to the second agonist. ADP beta S exerted only a partial desensitization of the response to maximal ATP, in accordance with its lower potency in raising [Ca2+]i. 4. The effect on [Ca2+]i of 100 microM ATP in subcultured cells was reduced by only 25% with 100 microM suramin pretreatment and was negligibly affected by exposure to 10 microM pyridoxalphosphate-6-azophenyl-2', 4'-disulphonic acid (PPADS). The concentration-effect curve for ATP was not significantly affected by PPADS, but was displaced to the right by a factor of 6.5 by 100 microM suramin. 5. In primary cultures, clear [Ca2+]i responses were elicited by 2MeSATP. Suramin totally and selectively blocked 2MeSATP responses, whereas UTP-evoked [Ca2+]i transients were mainly unaffected by suramin or PPADS. Over 80% of cells tested showed responses to both 2Me

  3. Bacterial Keratitis

    MedlinePlus

    ... very quickly, and if left untreated, can cause blindness. The bacteria usually responsible for this type of ... to intense ultraviolet radiation exposure, e.g. snow blindness or welder's arc eye). Next Bacterial Keratitis Symptoms ...

  4. Population density profiles of nasopharyngeal carriage of 5 bacterial species in pre-school children measured using quantitative PCR offer potential insights into the dynamics of transmission

    PubMed Central

    Thors, Valtyr; Morales-Aza, Begonia; Pidwill, Grace; Vipond, Ian; Muir, Peter; Finn, Adam

    2016-01-01

    Bacterial vaccines can reduce carriage rates. Colonization is usually a binary endpoint. Real time quantitative PCR (qPCR) can quantify bacterial DNA in mucosal samples over a wide range. Using culture and single-gene species-specific qPCRs for Streptococcus pneumoniae (lytA), Streptococcus pyogenes (ntpC), Moraxella catarrhalis (ompJ), Haemophilus influenzae (hdp) and Staphylococcus aureus (nuc) and standard curves against log-phase reference strain broth cultures we described frequency and peak density distributions of carriage in nasopharyngeal swabs from 161 healthy 2–4 y old children collected into STGG broth. In general, detection by qPCR and culture was consistent. Discordance mostly occurred at lower detection thresholds of both methods, although PCR assays for S. pyogenes and S. aureus were less sensitive. Density varied across 5-7 orders of magnitude for the 5 species with the abundant species skewed toward high values (modes: S. pneumoniae log3-4, M. catarrhalis & H. influenzae log4-5 CFU/ml broth). Wide ranges of bacterial DNA concentrations in healthy children carrying these bacteria could mean that different individuals at different times vary greatly in infectiousness. Understanding the host, microbial and environmental determinants of colonization density will permit more accurate prediction of vaccine effectiveness. PMID:26367344

  5. Population density profiles of nasopharyngeal carriage of 5 bacterial species in pre-school children measured using quantitative PCR offer potential insights into the dynamics of transmission.

    PubMed

    Thors, Valtyr; Morales-Aza, Begonia; Pidwill, Grace; Vipond, Ian; Muir, Peter; Finn, Adam

    2016-01-01

    Bacterial vaccines can reduce carriage rates. Colonization is usually a binary endpoint. Real time quantitative PCR (qPCR) can quantify bacterial DNA in mucosal samples over a wide range. Using culture and single-gene species-specific qPCRs for Streptococcus pneumoniae (lytA), Streptococcus pyogenes (ntpC), Moraxella catarrhalis (ompJ), Haemophilus influenzae (hdp) and Staphylococcus aureus (nuc) and standard curves against log-phase reference strain broth cultures we described frequency and peak density distributions of carriage in nasopharyngeal swabs from 161 healthy 2-4 y old children collected into STGG broth. In general, detection by qPCR and culture was consistent. Discordance mostly occurred at lower detection thresholds of both methods, although PCR assays for S. pyogenes and S. aureus were less sensitive. Density varied across 5-7 orders of magnitude for the 5 species with the abundant species skewed toward high values (modes: S. pneumoniae log3-4, M. catarrhalis & H. influenzae log4-5 CFU/ml broth). Wide ranges of bacterial DNA concentrations in healthy children carrying these bacteria could mean that different individuals at different times vary greatly in infectiousness. Understanding the host, microbial and environmental determinants of colonization density will permit more accurate prediction of vaccine effectiveness.

  6. Denaturing gradient gel electrophoresis analysis of 16S ribosomal DNA amplicons to monitor changes in fecal bacterial populations of weaning pigs after introduction of Lactobacillus reuteri strain MM53.

    PubMed

    Simpson, J M; McCracken, V J; Gaskins, H R; Mackie, R I

    2000-11-01

    The diversity and stability of the fecal bacterial microbiota in weaning pigs was studied after introduction of an exogenous Lactobacillus reuteri strain, MM53, using a combination of cultivation and techniques based on genes encoding 16S rRNA (16S rDNA). Piglets (n = 9) were assigned to three treatment groups (control, daily dosed, and 4th-day dosed), and fresh fecal samples were collected daily. Dosed animals received 2.5 x 10(10) CFU of antibiotic-resistant L. reuteri MM53 daily or every 4th day. Mean Lactobacillus counts for the three groups ranged from 1 x 10(9) to 4 x 10(9) CFU/g of feces. Enumeration of strain L. reuteri MM53 on MRS agar (Difco) plates containing streptomycin and rifampin showed that the introduced strain fluctuated between 8 x 10(3) and 5 x 10(6) CFU/g of feces in the two dosed groups. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA fragments, with primers specific for variable regions 1 and 3 (V1 and V3), was used to profile complexity of fecal bacterial populations. Analysis of DGGE banding profiles indicated that each individual maintained a unique fecal bacterial population that was stable over time, suggesting a strong host influence. In addition, individual DGGE patterns could be separated into distinct time-dependent clusters. Primers designed specifically to restrict DGGE analysis to a select group of lactobacilli allowed examination of interspecies relationships and abundance. Based on relative band migration distance and sequence determination, L. reuteri was distinguishable within the V1 region 16S rDNA gene patterns. Daily fluctuations in specific bands within these profiles were observed, which revealed an antagonistic relationship between L. reuteri MM53 (band V1-3) and another indigenous Lactobacillus assemblage (band V1-6).

  7. Space Center Co-Exists With Nature

    NASA Video Gallery

    As part of Kennedy Space Center’s first Innovation Expo on Sept. 6, aquatic biologists with Inomedic Health Applications took employees on a field-guided boat tour of the unique estuarine ecosyst...

  8. Bacterial rheotaxis

    PubMed Central

    Marcos; Fu, Henry C.; Powers, Thomas R.; Stocker, Roman

    2012-01-01

    The motility of organisms is often directed in response to environmental stimuli. Rheotaxis is the directed movement resulting from fluid velocity gradients, long studied in fish, aquatic invertebrates, and spermatozoa. Using carefully controlled microfluidic flows, we show that rheotaxis also occurs in bacteria. Excellent quantitative agreement between experiments with Bacillus subtilis and a mathematical model reveals that bacterial rheotaxis is a purely physical phenomenon, in contrast to fish rheotaxis but in the same way as sperm rheotaxis. This previously unrecognized bacterial taxis results from a subtle interplay between velocity gradients and the helical shape of flagella, which together generate a torque that alters a bacterium's swimming direction. Because this torque is independent of the presence of a nearby surface, bacterial rheotaxis is not limited to the immediate neighborhood of liquid–solid interfaces, but also takes place in the bulk fluid. We predict that rheotaxis occurs in a wide range of bacterial habitats, from the natural environment to the human body, and can interfere with chemotaxis, suggesting that the fitness benefit conferred by bacterial motility may be sharply reduced in some hydrodynamic conditions. PMID:22411815

  9. Community Composition and Abundance of Bacterial, Archaeal and Nitrifying Populations in Savanna Soils on Contrasting Bedrock Material in Kruger National Park, South Africa

    PubMed Central

    Rughöft, Saskia; Herrmann, Martina; Lazar, Cassandre S.; Cesarz, Simone; Levick, Shaun R.; Trumbore, Susan E.; Küsel, Kirsten

    2016-01-01

    Savannas cover at least 13% of the global terrestrial surface and are often nutrient limited, especially by nitrogen. To gain a better understanding of their microbial diversity and the microbial nitrogen cycling in savanna soils, soil samples were collected along a granitic and a basaltic catena in Kruger National Park (South Africa) to characterize their bacterial and archaeal composition and the genetic potential for nitrification. Although the basaltic soils were on average 5 times more nutrient rich than the granitic soils, all investigated savanna soil samples showed typically low nutrient availabilities, i.e., up to 38 times lower soil N or C contents than temperate grasslands. Illumina MiSeq amplicon sequencing revealed a unique soil bacterial community dominated by Actinobacteria (20–66%), Chloroflexi (9–29%), and Firmicutes (7–42%) and an increase in the relative abundance of Actinobacteria with increasing soil nutrient content. The archaeal community reached up to 14% of the total soil microbial community and was dominated by the thaumarchaeal Soil Crenarchaeotic Group (43–99.8%), with a high fraction of sequences related to the ammonia-oxidizing genus Nitrosopshaera sp. Quantitative PCR targeting amoA genes encoding the alpha subunit of ammonia monooxygenase also revealed a high genetic potential for ammonia oxidation dominated by archaea (~5 × 107 archaeal amoA gene copies g−1 soil vs. mostly < 7 × 104 bacterial amoA gene copies g−1 soil). Abundances of archaeal 16S rRNA and amoA genes were positively correlated with soil nitrate, N and C contents. Nitrospira sp. was detected as the most abundant group of nitrite oxidizing bacteria. The specific geochemical conditions and particle transport dynamics at the granitic catena were found to affect soil microbial communities through clay and nutrient relocation along the hill slope, causing a shift to different, less diverse bacterial and archaeal communities at the footslope. Overall, our

  10. Bacterial differentiation.

    PubMed

    Shapiro, L; Agabian-Keshishian, N; Bendis, I

    1971-09-01

    The foregoing studies are intended to define a differentiation process and to permit genetic access to the mechanisms that control this process. In order to elucidate the basic mechanisms whereby a cell dictates its own defined morphogenic changes, we have found it helpful to study an organism that can be manipulated both biochemically and genetically. We have attempted to develop the studies initiated by Poindexter,Stove and Stanier, and Schmidt and Stanier (16, 17, 20) with the Caulobacter genus so that these bacteria can serve as a model system for prokaryotic differentiation. The Caulobacter life cycle, defined in synchronously growing cultures, includes a sequential series of morphological changes that occur at specific times in the cycle and at specific locations in the cell. Six distinct cellular characteristics, which are peculiar to these bacteria, have been defined and include (i) the synthesis of a polar organelle which may be membranous (21-23), (ii) a satellite DNA in the stalked cell (26), (iii) pili to which RNA bacteriophage specifically adsorb (16, 33), (iv) a single polar flagellum(17), (v) a lipopolysaccharide phage receptor site (27), and (vi) new cell wall material at the flagellated pole of the cell giving rise to a stalk (19, 20). Cell division, essential for the viability of the organism, is dependent on the irreversible differentiation of a flagellated swarmer cell to a mature stalked cell. The specific features of the Caulobacter system which make it a system of choice for studies of the control of sequential events resulting in cellular differentiation can be summarized as follows. 1) Cell populations can be synchronized, and homogeneous populations at each stage in the differentiation cycle can thus be obtained. 2) A specific technique has been developed whereby the progress of the differentiation cycle can be accurately measured by adsorption of labeled RNA phage or penetration of labeled phage DNA into specific cell forms. This

  11. Characterization of the cultivable bacterial populations associated with field grown Brassica napus L.: an evaluation of sampling and isolation protocols.

    PubMed

    Croes, Sarah; Weyens, Nele; Colpaert, Jan; Vangronsveld, Jaco

    2015-07-01

    Plant-associated bacteria are intensively investigated concerning their characteristics for plant growth promotion, biocontrol mechanisms and enhanced phytoremediation efficiency. To obtain endophytes, different sampling and isolation protocols are used although their representativeness is not always clearly demonstrated. The objective of this study was to acquire representative pictures of the cultivable bacterial root, stem and leaf communities for all Brassica napus L. individuals growing on the same field. For each plant organ, genotypic identifications of the endophytic communities were performed using three replicates. Root replicates were composed of three total root systems, whereas stem and leaf replicates needed to consist of six independent plant parts in order to be representative. Greater variations between replicates were found when considering phenotypic characteristics. Correspondence analysis revealed reliable phenotypic results for roots and even shoots, but less reliable ones for leaves. Additionally, realistic Shannon-Wiener biodiversity indices were calculated for all three organs and showed similar Evenness factors. Furthermore, it was striking that all replicates and thus the whole plant contained Pseudomonas and Bacillus strains although aboveground and belowground plant tissues differed in most dominant bacterial genera and characteristics. PMID:25367683

  12. Subcutaneous Adipose Fatty Acid Profiles and Related Rumen Bacterial Populations of Steers Fed Red Clover or Grass Hay Diets Containing Flax or Sunflower-Seed

    PubMed Central

    Dugan, Mike E. R.; McAllister, Tim A.

    2014-01-01

    Steers were fed 70∶30 forage∶concentrate diets for 205 days, with either grass hay (GH) or red clover silage (RC), and either sunflower-seed (SS) or flaxseed (FS), providing 5.4% oil in the diets. Compared to diets containing SS, FS diets had elevated (P<0.05) subcutaneous trans (t)-18:1 isomers, conjugated linoleic acids and n-6 polyunsaturated fatty acid (PUFA). Forage and oilseed type influenced total n-3 PUFA, especially α-linolenic acid (ALA) and total non-conjugated diene biohydrogenation (BH) in subcutaneous fat with proportions being greater (P<0.05) for FS or GH as compared to SS or RC. Of the 25 bacterial genera impacted by diet, 19 correlated with fatty acids (FA) profile. Clostridium were most abundant when levels of conjugated linolenic acids, and n-3 PUFA's were found to be the lowest in subcutaneous fat, suggestive of their role in BH. Anerophaga, Fibrobacter, Guggenheimella, Paludibacter and Pseudozobellia were more abundant in the rumen when the levels of VA in subcutaneous fat were low. This study clearly shows the impact of oilseeds and forage source on the deposition of subcutaneous FA in beef cattle. Significant correlations between rumen bacterial genera and the levels of specific FA in subcutaneous fat maybe indicative of their role in determining the FA profile of adipose tissue. However, despite numerous correlations, the dynamics of rumen bacteria in the BH of unsaturated fatty acid and synthesis of PUFA and FA tissue profiles require further experimentation to determine if these correlations are consistent over a range of diets of differing composition. Present results demonstrate that in order to achieve targeted FA profiles in beef, a multifactorial approach will be required that takes into consideration not only the PUFA profile of the diet, but also the non-oil fraction of the diet, type and level of feed processing, and the role of rumen microbes in the BH of unsaturated fatty acid. PMID:25093808

  13. Microheterogeneity in 16S Ribosomal DNA-Defined Bacterial Populations from a Stratified Planktonic Environment Is Related to Temporal Changes and to Ecological Adaptations

    PubMed Central

    Casamayor, Emilio O.; Pedrós-Alió, Carlos; Muyzer, Gerard; Amann, Rudolf

    2002-01-01

    Temporal changes of the bacterioplankton from a meromictic lake (Lake Vilar, Banyoles, Spain) were analyzed with four culture-independent techniques: epifluorescence microscopy, PCR-denaturing gradient gel electrophoresis (DGGE) fingerprinting, fluorescence in situ whole-cell hybridization and flow cytometry sorting. Microscopically, blooms of one cyanobacterium (Synechococcus sp.-like), one green sulfur bacterium (Chlorobium phaeobacteroides-like), and one purple sulfur bacterium (Thiocystis minor-like) were observed at different depths and times. DGGE retrieved these populations and, additionally, populations related to the Cytophaga-Flavobacterium-Bacteroides phylum as predominant community members. The analyses of partial 16S ribosomal DNA sequences from the DGGE fingerprints (550 bp analyzed) revealed higher genetic diversity than expected from microscopic observation for most of these groups. Thus, the sequences of two Synechococcus spp. (both had a similarity of 97% to Synechococcus sp. strain PCC6307 in 16S rRNA), two Thiocystis spp. (similarities to Thiocystis minor of 93 and 94%, respectively), and three Cytophaga spp. (similarities to Cytophaga fermentans of 88 and 89% and to Cytophaga sp. of 93%, respectively) were obtained. The two populations of Synechococcus exhibited different pigment compositions and temporal distributions and their 16S rRNA sequences were 97.3% similar. The two Thiocystis populations differed neither in pigment composition nor in morphology, but their 16S rRNA sequences were only 92.3% similar and they also showed different distributions over time. Finally, two of the Cytophaga spp. showed 96.2% similarity between the 16S rRNA sequences, but one of them was found to be mostly attached to particles and only in winter. Thus, the identity of the main populations changed over time, but the function of the microbial guilds was maintained. Our data showed that temporal shifts in the identity of the predominant population is a new

  14. Linking Specific Heterotrophic Bacterial Populations to Bioreduction of Uranium and Nitrate in Contaminated Subsurface Sediments by Using Stable Isotope Probing▿†

    PubMed Central

    Akob, Denise M.; Kerkhof, Lee; Küsel, Kirsten; Watson, David B.; Palumbo, Anthony V.; Kostka, Joel E.

    2011-01-01

    Shifts in terminal electron-accepting processes during biostimulation of uranium-contaminated sediments were linked to the composition of stimulated microbial populations using DNA-based stable isotope probing. Nitrate reduction preceded U(VI) and Fe(III) reduction in [13C]ethanol-amended microcosms. The predominant, active denitrifying microbial groups were identified as members of the Betaproteobacteria, whereas Actinobacteria dominated under metal-reducing conditions. PMID:21948831

  15. Prevalence and Correlates of Bacterial Vaginosis in Different Sub-Populations of Women in Sub-Saharan Africa: A Cross-Sectional Study

    PubMed Central

    Jespers, Vicky; Crucitti, Tania; Menten, Joris; Verhelst, Rita; Mwaura, Mary; Mandaliya, Kishor; Ndayisaba, Gilles F.; Delany-Moretlwe, Sinead; Verstraelen, Hans; Hardy, Liselotte; Buvé, Anne; van de Wijgert, Janneke

    2014-01-01

    Background Clinical development of vaginally applied products aimed at reducing the transmission of HIV and other sexually transmitted infections, has highlighted the need for a better characterisation of the vaginal environment. We set out to characterise the vaginal environment in women in different settings in sub-Saharan Africa. Methods A longitudinal study was conducted in Kenya, Rwanda and South-Africa. Women were recruited into pre-defined study groups including adult, non-pregnant, HIV-negative women; pregnant women; adolescent girls; HIV-negative women engaging in vaginal practices; female sex workers; and HIV-positive women. Consenting women were interviewed and underwent a pelvic exam. Samples of vaginal fluid and a blood sample were taken and tested for bacterial vaginosis (BV), HIV and other reproductive tract infections (RTIs). This paper presents the cross-sectional analyses of BV Nugent scores and RTI prevalence and correlates at the screening and the enrolment visit. Results At the screening visit 38% of women had BV defined as a Nugent score of 7–10, and 64% had more than one RTI (N. gonorrhoea, C. trachomatis, T. vaginalis, syphilis) and/or Candida. At screening the likelihood of BV was lower in women using progestin-only contraception and higher in women with more than one RTI. At enrolment, BV scores were significantly associated with the presence of prostate specific antigen (PSA) in the vaginal fluid and with being a self-acknowledged sex worker. Further, sex workers were more likely to have incident BV by Nugent score at enrolment. Conclusions Our study confirmed some of the correlates of BV that have been previously reported but the most salient finding was the association between BV and the presence of PSA in the vaginal fluid which is suggestive of recent unprotected sexual intercourse. PMID:25289640

  16. The Effect of the First Spontaneous Bacterial Peritonitis Event on the Mortality of Cirrhotic Patients with Ascites: A Nationwide Population-Based Study in Taiwan

    PubMed Central

    Hung, Tsung-Hsing; Tsai, Chen-Chi; Hsieh, Yu-Hsi; Tsai, Chih-Chun; Tseng, Chih-Wei; Tseng, Kuo-Chih

    2016-01-01

    Background/Aims Spontaneous bacterial peritonitis (SBP) contributes to poorer short-term mortality in cirrhotic patients with ascites. However, it is unknown how long the effect of the first SBP event persists in these patients. Methods The National Health Insurance Database, derived from the Taiwan National Health Insurance Program, was used to identify and enroll 7,892 cirrhotic patients with ascites who were hospitalized between January 1 and December 31, 2007. All patients were free from episodes of SBP from 1996 to 2006. Results The study included 1,176 patients with SBP. The overall 30-day, 90-day, 1-year, and 3-year mortality rates in this group were 21.8%, 38.9%, 57.5%, and 73.4%, respectively. The overall 30-day, 90-day, 1-year, and 3-year mortality rates in the non-SBP group were 15.7%, 32.5%, 53.3%, and 72.5%, respectively. After adjusting for gender, age, and other medical comorbidities, the adjusted hazard ratios of SBP for 30-day, 30- to 90-day, 90-day to 1-year, and 1- to 3-year mortality were 1.49 (95% confidence interval [CI], 1.30 to 1.71), 1.19 (95% CI, 1.02 to 1.38), 1.04 (95% CI, 0.90 to 1.20), and 0.90 (95% CI, 0.77 to 1.05), respectively, compared with the non-SBP group. Conclusions The effect of SBP on the mortality of cirrhotic patients with ascites disappeared in those surviving more than 90 days after the first SBP event. PMID:27563023

  17. Structure and chemistry of bacterially populated acidic microenvironments found on naturally colonized and weathered circumneutral pH unsaturated waste rock from the Antamina Mine, Peru

    NASA Astrophysics Data System (ADS)

    Dockrey, J. W.; Mayer, K. U.; Beckie, R. D.; Southam, G.

    2009-12-01

    The microbial community present in geochemically well characterized field cells and experimental waste rock piles at the Antamina Mine, were examined using electron microscopy, culture dependent, and culture independent techniques. Relatively large populations of up to 10^8 bacteria per gram were found, despite the young age of the waste rock (1.5 years). Most samples were at alkaline pH and dominated by bacteria capable of neutral pH thiosulfate oxidation. One sample from a field cell producing drainage at a pH of 6.5 was dominated by acidophilic bacteria capable of Fe^2+ and S^0 oxidation. A weathered massive sulfide from this sample was thoroughly examined using a field emission gun scanning electron microscope equipped with a focused ion beam (FE-SEM-FIB). Bacteria were abundant as monolayer and agglomerate biofilms upon and within a porous schwertmannite precipitate, while no bacteria were found directly attached to clean sulfide surfaces. Pitting of pyrrhotite was observed beneath the microbially inhabited schwertmannite, while no pitting was observed in adjacent clean pyrrhotite surfaces indicating greater oxidation of the pyrrhotite surface beneath the schwertmannite. Some waste rock that has been exposed to natural surface weathering conditions for more than twice the amount of time, possessed larger total populations of bacteria, but did not support significant populations of acidophiles, suggesting a succession from neutrophiles to acidophiles takes place prior to the development of acid mine drainage. The development of the porous iron oxide film may be prerequisite for acidophilic bacteria to flourish, creating acidic microenvironments within a neutral bulk, ambient pH mine waste.

  18. Microstructural and compositional change of NaOH-activated high calcium fly ash by incorporating Na-aluminate and co-existence of geopolymeric gel and C-S-H(I)

    SciTech Connect

    Oh, Jae Eun; Moon, Juhyuk; Oh, Sang-Gyun; Clark, Simon M.; Monteiro, Paulo J.M.

    2012-05-15

    This study explores the reaction products of alkali-activated Class C fly ash-based aluminosilicate samples by means of high-resolution synchrotron X-ray diffraction (HSXRD), scanning electron microscope (SEM), and compressive strength tests to investigate how the readily available aluminum affects the reaction. Class C fly ash-based aluminosilicate raw materials were prepared by incorporating Na-aluminate into the original fly ashes, then alkali-activated by 10 M NaOH solution. Incorporating Na-aluminate reduced the compressive strength of samples, with the reduction magnitude relatively constant regardless of length of curing period. The HSXRD provides evidence of the co-existence of C-S-H with geopolymeric gels and strongly suggests that the C-S-H formed in the current system is C-S-H(I). The back-scattered electron images suggest that the C-S-H(I) phase exists as small grains in a finely intermixed form with geopolymeric gels. Despite providing extra source of aluminum, adding Na-aluminate to the mixes did not decrease the Si/Al ratio of the geopolymeric gel.

  19. Assessment of genetic correlation between bacterial cold water disease resistance and spleen index in a domesticated population of rainbow trout: identification of QTL on chromosome Omy19.

    PubMed

    Wiens, Gregory D; Vallejo, Roger L; Leeds, Timothy D; Palti, Yniv; Hadidi, Sima; Liu, Sixin; Evenhuis, Jason P; Welch, Timothy J; Rexroad, Caird E

    2013-01-01

    Selective breeding of animals for increased disease resistance is an effective strategy to reduce mortality in aquaculture. However, implementation of selective breeding programs is limited by an incomplete understanding of host resistance traits. We previously reported results of a rainbow trout selection program that demonstrated increased survival following challenge with Flavobacterium psychrophilum, the causative agent of bacterial cold water disease (BCWD). Mechanistic study of disease resistance identified a positive phenotypic correlation between post-challenge survival and spleen somatic-index (SI). Herein, we investigated the hypothesis of a genetic correlation between the two traits influenced by colocalizing QTL. We evaluated the inheritance and calculated the genetic correlation in five year-classes of odd- and even-year breeding lines. A total of 322 pedigreed families (n = 25,369 fish) were measured for disease resistance, and 251 families (n = 5,645 fish) were evaluated for SI. Spleen index was moderately heritable in both even-year (h(2)  = 0.56±0.18) and odd-year (h(2)  = 0.60±0.15) lines. A significant genetic correlation between SI and BCWD resistance was observed in the even-year line (rg  = 0.45±0.20, P = 0.03) but not in the odd-year line (rg  = 0.16±0.12, P = 0.19). Complex segregation analyses of the even-year line provided evidence of genes with major effect on SI, and a genome scan of a single family, 2008132, detected three significant QTL on chromosomes Omy19, 16 and 5, in addition to ten suggestive QTL. A separate chromosome scan for disease resistance in family 2008132 identified a significant BCWD QTL on Omy19 that was associated with time to death and percent survival. In family 2008132, Omy19 microsatellite alleles that associated with higher disease resistance also associated with increased spleen size raising the hypothesis that closely linked QTL contribute to the correlation between these

  20. Assessment of genetic correlation between bacterial cold water disease resistance and spleen index in a domesticated population of rainbow trout: identification of QTL on chromosome Omy19.

    PubMed

    Wiens, Gregory D; Vallejo, Roger L; Leeds, Timothy D; Palti, Yniv; Hadidi, Sima; Liu, Sixin; Evenhuis, Jason P; Welch, Timothy J; Rexroad, Caird E

    2013-01-01

    Selective breeding of animals for increased disease resistance is an effective strategy to reduce mortality in aquaculture. However, implementation of selective breeding programs is limited by an incomplete understanding of host resistance traits. We previously reported results of a rainbow trout selection program that demonstrated increased survival following challenge with Flavobacterium psychrophilum, the causative agent of bacterial cold water disease (BCWD). Mechanistic study of disease resistance identified a positive phenotypic correlation between post-challenge survival and spleen somatic-index (SI). Herein, we investigated the hypothesis of a genetic correlation between the two traits influenced by colocalizing QTL. We evaluated the inheritance and calculated the genetic correlation in five year-classes of odd- and even-year breeding lines. A total of 322 pedigreed families (n = 25,369 fish) were measured for disease resistance, and 251 families (n = 5,645 fish) were evaluated for SI. Spleen index was moderately heritable in both even-year (h(2)  = 0.56±0.18) and odd-year (h(2)  = 0.60±0.15) lines. A significant genetic correlation between SI and BCWD resistance was observed in the even-year line (rg  = 0.45±0.20, P = 0.03) but not in the odd-year line (rg  = 0.16±0.12, P = 0.19). Complex segregation analyses of the even-year line provided evidence of genes with major effect on SI, and a genome scan of a single family, 2008132, detected three significant QTL on chromosomes Omy19, 16 and 5, in addition to ten suggestive QTL. A separate chromosome scan for disease resistance in family 2008132 identified a significant BCWD QTL on Omy19 that was associated with time to death and percent survival. In family 2008132, Omy19 microsatellite alleles that associated with higher disease resistance also associated with increased spleen size raising the hypothesis that closely linked QTL contribute to the correlation between these

  1. Assessment of Genetic Correlation between Bacterial Cold Water Disease Resistance and Spleen Index in a Domesticated Population of Rainbow Trout: Identification of QTL on Chromosome Omy19

    PubMed Central

    Hadidi, Sima; Liu, Sixin; Evenhuis, Jason P.; Welch, Timothy J.; Rexroad, Caird E.

    2013-01-01

    Selective breeding of animals for increased disease resistance is an effective strategy to reduce mortality in aquaculture. However, implementation of selective breeding programs is limited by an incomplete understanding of host resistance traits. We previously reported results of a rainbow trout selection program that demonstrated increased survival following challenge with Flavobacterium psychrophilum, the causative agent of bacterial cold water disease (BCWD). Mechanistic study of disease resistance identified a positive phenotypic correlation between post-challenge survival and spleen somatic-index (SI). Herein, we investigated the hypothesis of a genetic correlation between the two traits influenced by colocalizing QTL. We evaluated the inheritance and calculated the genetic correlation in five year-classes of odd- and even-year breeding lines. A total of 322 pedigreed families (n = 25,369 fish) were measured for disease resistance, and 251 families (n = 5,645 fish) were evaluated for SI. Spleen index was moderately heritable in both even-year (h2 = 0.56±0.18) and odd-year (h2 = 0.60±0.15) lines. A significant genetic correlation between SI and BCWD resistance was observed in the even-year line (rg = 0.45±0.20, P = 0.03) but not in the odd-year line (rg = 0.16±0.12, P = 0.19). Complex segregation analyses of the even-year line provided evidence of genes with major effect on SI, and a genome scan of a single family, 2008132, detected three significant QTL on chromosomes Omy19, 16 and 5, in addition to ten suggestive QTL. A separate chromosome scan for disease resistance in family 2008132 identified a significant BCWD QTL on Omy19 that was associated with time to death and percent survival. In family 2008132, Omy19 microsatellite alleles that associated with higher disease resistance also associated with increased spleen size raising the hypothesis that closely linked QTL contribute to the correlation between these traits. To

  2. How to Show the Real Microbial Biodiversity? A Comparison of Seven DNA Extraction Methods for Bacterial Population Analyses in Matrices Containing Highly Charged Natural Nanoparticles

    PubMed Central

    Kaden, Rene; Krolla-Sidenstein, Peter

    2015-01-01

    A DNA extraction that comprises the DNA of all available taxa in an ecosystem is an essential step in population analysis, especially for next generation sequencing applications. Many nanoparticles as well as naturally occurring clay minerals contain charged surfaces or edges that capture negatively charged DNA molecules after cell lysis within DNA extraction. Depending on the methodology of DNA extraction, this phenomenon causes a shift in detection of microbial taxa in ecosystems and a possible misinterpretation of microbial interactions. With the aim to describe microbial interactions and the bio-geo-chemical reactions during a clay alteration experiment, several methods for the detection of a high number of microbial taxa were examined in this study. Altogether, 13 different methods of commercially available DNA extraction kits provided by seven companies as well as the classical phenol-chloroform DNA extraction were compared. The amount and the quality of nucleic acid extracts were determined and compared to the amplifiable amount of DNA. The 16S rRNA gene fragments of several taxa were separated using denaturing gradient gel electrophoresis (DGGE) to determine the number of different species and sequenced to get the information about what kind of species the microbial population consists of. A total number of 13 species was detected in the system. Up to nine taxa could be detected with commercially available DNA extraction kits while phenol-chloroform extraction lead to three detected species. In this paper, we describe how to combine several DNA extraction methods for the investigation of microbial community structures in clay. PMID:27682112

  3. How to Show the Real Microbial Biodiversity? A Comparison of Seven DNA Extraction Methods for Bacterial Population Analyses in Matrices Containing Highly Charged Natural Nanoparticles

    PubMed Central

    Kaden, Rene; Krolla-Sidenstein, Peter

    2015-01-01

    A DNA extraction that comprises the DNA of all available taxa in an ecosystem is an essential step in population analysis, especially for next generation sequencing applications. Many nanoparticles as well as naturally occurring clay minerals contain charged surfaces or edges that capture negatively charged DNA molecules after cell lysis within DNA extraction. Depending on the methodology of DNA extraction, this phenomenon causes a shift in detection of microbial taxa in ecosystems and a possible misinterpretation of microbial interactions. With the aim to describe microbial interactions and the bio-geo-chemical reactions during a clay alteration experiment, several methods for the detection of a high number of microbial taxa were examined in this study. Altogether, 13 different methods of commercially available DNA extraction kits provided by seven companies as well as the classical phenol-chloroform DNA extraction were compared. The amount and the quality of nucleic acid extracts were determined and compared to the amplifiable amount of DNA. The 16S rRNA gene fragments of several taxa were separated using denaturing gradient gel electrophoresis (DGGE) to determine the number of different species and sequenced to get the information about what kind of species the microbial population consists of. A total number of 13 species was detected in the system. Up to nine taxa could be detected with commercially available DNA extraction kits while phenol-chloroform extraction lead to three detected species. In this paper, we describe how to combine several DNA extraction methods for the investigation of microbial community structures in clay.

  4. ICOS is required for the generation of both central and effector CD4(+) memory T-cell populations following acute bacterial infection.

    PubMed

    Marriott, Clare L; Carlesso, Gianluca; Herbst, Ronald; Withers, David R

    2015-06-01

    Interactions between ICOS and ICOS ligand (ICOSL) are essential for the development of T follicular helper (Tfh) cells and thus the formation and maintenance of GC reactions. Given the conflicting reports on the requirement of other CD4(+) T-cell populations for ICOS signals, we have employed a range of in vivo approaches to dissect requirements for ICOS signals in mice during an endogenous CD4(+) T-cell response and contrasted this with CD28 signals. Genetic absence of ICOSL only modestly reduced the total number of antigen-specific CD4(+) T cells at the peak of the primary response, but resulted in a severely diminished number of both T central memory and T effector memory cells. Treatment with blocking anti-ICOS mAb during the primary response recapitulated these effects and caused a more substantial reduction than blocking CD28 signals with CTLA4Ig. During the memory phase of the response further signals through ICOS or CD28 were not required for survival. However, upon secondary challenge only Tfh cell expansion remained heavily ICOS-dependent, while CD28 signals were required for optimal expansion of all subsets. These data demonstrate the importance of ICOS signals specifically for memory CD4(+) T-cell formation, while highlighting the potential of therapeutically targeting this pathway.

  5. ICOS is required for the generation of both central and effector CD4+ memory T‐cell populations following acute bacterial infection

    PubMed Central

    Marriott, Clare L.; Carlesso, Gianluca; Herbst, Ronald

    2015-01-01

    Interactions between ICOS and ICOS ligand (ICOSL) are essential for the development of T follicular helper (Tfh) cells and thus the formation and maintenance of GC reactions. Given the conflicting reports on the requirement of other CD4+ T‐cell populations for ICOS signals, we have employed a range of in vivo approaches to dissect requirements for ICOS signals in mice during an endogenous CD4+ T‐cell response and contrasted this with CD28 signals. Genetic absence of ICOSL only modestly reduced the total number of antigen‐specific CD4+ T cells at the peak of the primary response, but resulted in a severely diminished number of both T central memory and T effector memory cells. Treatment with blocking anti‐ICOS mAb during the primary response recapitulated these effects and caused a more substantial reduction than blocking CD28 signals with CTLA4Ig. During the memory phase of the response further signals through ICOS or CD28 were not required for survival. However, upon secondary challenge only Tfh cell expansion remained heavily ICOS‐dependent, while CD28 signals were required for optimal expansion of all subsets. These data demonstrate the importance of ICOS signals specifically for memory CD4+ T‐cell formation, while highlighting the potential of therapeutically targeting this pathway. PMID:25754933

  6. Transfer, composition and technological characterization of the lactic acid bacterial populations of the wooden vats used to produce traditional stretched cheeses.

    PubMed

    Scatassa, Maria Luisa; Gaglio, Raimondo; Macaluso, Giusi; Francesca, Nicola; Randazzo, Walter; Cardamone, Cinzia; Di Grigoli, Antonino; Moschetti, Giancarlo; Settanni, Luca

    2015-12-01

    The biofilms of 12 wooden vats used for the production of the traditional stretched cheeses Caciocavallo Palermitano and PDO Vastedda della valle del Belìce were investigated. Salmonella spp. and Listeria monocytogenes were never detected. Total coliforms were at low numbers with Escherichia coli found only in three vats. Coagulase-positive staphylococci (CPS) were below the enumeration limit, whereas lactic acid bacteria (LAB) dominated the surfaces of all vats. In general, the dominance was showed by coccus LAB. Enterococci were estimated at high numbers, but usually between 1 and 2 Log cycles lower than other LAB. LAB populations were investigated at species and strain level and for their technological properties relevant in cheese production. Eighty-five strains were analysed by a polyphasic genetic approach and allotted into 16 species within the genera Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Pediococcus and Streptococcus. Enterococcus faecium was found in all wooden vats and the species most frequently isolated were Enterococcus faecalis, Lactococcus lactis, Leuconostoc mesenteroides, Pediococcus acidilactici and Streptococcus thermophilus. The study of the quantitative data on acidification rate, autolysis kinetics, diacetyl production, antibacterial compound generation and proteolysis by cluster and principal component analysis led to the identification of some strains with promising dairy characteristics. Interestingly, a consistent percentage of LAB was bacteriocin-like inhibitory substances (BLIS) producer. Thus, the microbial biofilms of the wooden vats analysed in this study might contribute actively to the stability of the final cheeses.

  7. Transfer, composition and technological characterization of the lactic acid bacterial populations of the wooden vats used to produce traditional stretched cheeses.

    PubMed

    Scatassa, Maria Luisa; Gaglio, Raimondo; Macaluso, Giusi; Francesca, Nicola; Randazzo, Walter; Cardamone, Cinzia; Di Grigoli, Antonino; Moschetti, Giancarlo; Settanni, Luca

    2015-12-01

    The biofilms of 12 wooden vats used for the production of the traditional stretched cheeses Caciocavallo Palermitano and PDO Vastedda della valle del Belìce were investigated. Salmonella spp. and Listeria monocytogenes were never detected. Total coliforms were at low numbers with Escherichia coli found only in three vats. Coagulase-positive staphylococci (CPS) were below the enumeration limit, whereas lactic acid bacteria (LAB) dominated the surfaces of all vats. In general, the dominance was showed by coccus LAB. Enterococci were estimated at high numbers, but usually between 1 and 2 Log cycles lower than other LAB. LAB populations were investigated at species and strain level and for their technological properties relevant in cheese production. Eighty-five strains were analysed by a polyphasic genetic approach and allotted into 16 species within the genera Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Pediococcus and Streptococcus. Enterococcus faecium was found in all wooden vats and the species most frequently isolated were Enterococcus faecalis, Lactococcus lactis, Leuconostoc mesenteroides, Pediococcus acidilactici and Streptococcus thermophilus. The study of the quantitative data on acidification rate, autolysis kinetics, diacetyl production, antibacterial compound generation and proteolysis by cluster and principal component analysis led to the identification of some strains with promising dairy characteristics. Interestingly, a consistent percentage of LAB was bacteriocin-like inhibitory substances (BLIS) producer. Thus, the microbial biofilms of the wooden vats analysed in this study might contribute actively to the stability of the final cheeses. PMID:26338114

  8. Bacterial Hydrodynamics

    NASA Astrophysics Data System (ADS)

    Lauga, Eric

    2016-01-01

    Bacteria predate plants and animals by billions of years. Today, they are the world's smallest cells, yet they represent the bulk of the world's biomass and the main reservoir of nutrients for higher organisms. Most bacteria can move on their own, and the majority of motile bacteria are able to swim in viscous fluids using slender helical appendages called flagella. Low-Reynolds number hydrodynamics is at the heart of the ability of flagella to generate propulsion at the micrometer scale. In fact, fluid dynamic forces impact many aspects of bacteriology, ranging from the ability of cells to reorient and search their surroundings to their interactions within mechanically and chemically complex environments. Using hydrodynamics as an organizing framework, I review the biomechanics of bacterial motility and look ahead to future challenges.

  9. Bacterial arthritis.

    PubMed

    Ho, G

    2001-07-01

    The septic arthritis literature of 2000 revisited several topics previously examined in some detail. These include septic arthritis in rheumatoid arthritis, rheumatic manifestations of bacterial endocarditis, and infectious complications of prosthetic joints. The trend in antibiotic prophylaxis to prevent late infections in total joint replacement is to narrow the targeted hosts to those most at risk, to define the procedures associated with the greatest risk of bacteremia, and to simplify the antibiotic regimen. The diagnoses of septic arthritis of the lumbar facet joint and septic arthritis caused by direct inoculation of bacteria by a foreign object penetrating the joint are facilitated by noninvasive imaging technologies. Septic arthritis caused by uncommon microorganisms and septic arthritis in immunocompromised hosts are other noteworthy topics in this year's literature. PMID:11555734

  10. Bacterial vaginosis.

    PubMed Central

    Spiegel, C A

    1991-01-01

    Bacterial vaginosis (BV) is the most common of the vaginitides affecting women of reproductive age. It appears to be due to an alteration in the vaginal ecology by which Lactobacillus spp., the predominant organisms in the healthy vagina, are replaced by a mixed flora including Prevotella bivia, Prevotella disiens, Porphyromonas spp., Mobiluncus spp., and Peptostreptococcus spp. All of these organisms except Mobiluncus spp. are also members of the endogenous vaginal flora. While evidence from treatment trials does not support the notion that BV is sexually transmitted, recent studies have shown an increased risk associated with multiple sexual partners. It has also been suggested that the pathogenesis of BV may be similar to that of urinary tract infections, with the rectum serving as a reservoir for some BV-associated flora. The organisms associated with BV have also been recognized as agents of female upper genital tract infection, including pelvic inflammatory disease, and the syndrome BV has been associated with adverse outcome of pregnancy, including premature rupture of membranes, chorioamnionitis, and fetal loss; postpartum endometritis; cuff cellulitis; and urinary tract infections. The mechanisms by which the BV-associated flora causes the signs of BV are not well understood, but a role for H2O2-producing Lactobacillus spp. in protecting against colonization by catalase-negative anaerobic bacteria has been recognized. These and other aspects of BV are reviewed. PMID:1747864

  11. Bacterial concrete

    NASA Astrophysics Data System (ADS)

    Ramakrishnan, Venkataswamy; Ramesh, K. P.; Bang, S. S.

    2001-04-01

    Cracks in concrete are inevitable and are one of the inherent weaknesses of concrete. Water and other salts seep through these cracks, corrosion initiates, and thus reduces the life of concrete. So there was a need to develop an inherent biomaterial, a self-repairing material which can remediate the cracks and fissures in concrete. Bacterial concrete is a material, which can successfully remediate cracks in concrete. This technique is highly desirable because the mineral precipitation induced as a result of microbial activities is pollution free and natural. As the cell wall of bacteria is anionic, metal accumulation (calcite) on the surface of the wall is substantial, thus the entire cell becomes crystalline and they eventually plug the pores and cracks in concrete. This paper discusses the plugging of artificially cracked cement mortar using Bacillus Pasteurii and Sporosarcina bacteria combined with sand as a filling material in artificially made cuts in cement mortar which was cured in urea and CaCl2 medium. The effect on the compressive strength and stiffness of the cement mortar cubes due to the mixing of bacteria is also discussed in this paper. It was found that use of bacteria improves the stiffness and compressive strength of concrete. Scanning electron microscope (SEM) is used to document the role of bacteria in microbiologically induced mineral precipitation. Rod like impressions were found on the face of calcite crystals indicating the presence of bacteria in those places. Energy- dispersive X-ray (EDX) spectra of the microbial precipitation on the surface of the crack indicated the abundance of calcium and the precipitation was inferred to be calcite (CaCO3).

  12. Interfering with Bacterial Quorum Sensing

    PubMed Central

    Reuter, Kerstin; Steinbach, Anke; Helms, Volkhard

    2016-01-01

    Quorum sensing (QS) describes the exchange of chemical signals in bacterial populations to adjust the bacterial phenotypes according to the density of bacterial cells. This serves to express phenotypes that are advantageous for the group and ensure bacterial survival. To do so, bacterial cells synthesize autoinducer (AI) molecules, release them to the environment, and take them up. Thereby, the AI concentration reflects the cell density. When the AI concentration exceeds a critical threshold in the cells, the AI may activate the expression of virulence-associated genes or of luminescent proteins. It has been argued that targeting the QS system puts less selective pressure on these pathogens and should avoid the development of resistant bacteria. Therefore, the molecular components of QS systems have been suggested as promising targets for developing new anti-infective compounds. Here, we review the QS systems of selected gram-negative and gram-positive bacteria, namely, Vibrio fischeri, Pseudomonas aeruginosa, and Staphylococcus aureus, and discuss various antivirulence strategies based on blocking different components of the QS machinery. PMID:26819549

  13. Bacterial cheating limits antibiotic resistance

    NASA Astrophysics Data System (ADS)

    Xiao Chao, Hui; Yurtsev, Eugene; Datta, Manoshi; Artemova, Tanya; Gore, Jeff

    2012-02-01

    The widespread use of antibiotics has led to the evolution of resistance in bacteria. Bacteria can gain resistance to the antibiotic ampicillin by acquiring a plasmid carrying the gene beta-lactamase, which inactivates the antibiotic. This inactivation may represent a cooperative behavior, as the entire bacterial population benefits from removing the antibiotic. The cooperative nature of this growth suggests that a cheater strain---which does not contribute to breaking down the antibiotic---may be able to take advantage of cells cooperatively inactivating the antibiotic. Here we find experimentally that a ``sensitive'' bacterial strain lacking the plasmid conferring resistance can invade a population of resistant bacteria, even in antibiotic concentrations that should kill the sensitive strain. We observe stable coexistence between the two strains and find that a simple model successfully explains the behavior as a function of antibiotic concentration and cell density. We anticipate that our results will provide insight into the evolutionary origin of phenotypic diversity and cooperative behaviors.

  14. Spatial distribution of marine airborne bacterial communities

    PubMed Central

    Seifried, Jasmin S; Wichels, Antje; Gerdts, Gunnar

    2015-01-01

    The spatial distribution of bacterial populations in marine bioaerosol samples was investigated during a cruise from the North Sea to the Baltic Sea via Skagerrak and Kattegat. The analysis of the sampled bacterial communities with a pyrosequencing approach revealed that the most abundant phyla were represented by the Proteobacteria (49.3%), Bacteroidetes (22.9%), Actinobacteria (16.3%), and Firmicutes (8.3%). Cyanobacteria were assigned to 1.5% of all bacterial reads. A core of 37 bacterial OTUs made up more than 75% of all bacterial sequences. The most abundant OTU was Sphingomonas sp. which comprised 17% of all bacterial sequences. The most abundant bacterial genera were attributed to distinctly different areas of origin, suggesting highly heterogeneous sources for bioaerosols of marine and coastal environments. Furthermore, the bacterial community was clearly affected by two environmental parameters – temperature as a function of wind direction and the sampling location itself. However, a comparison of the wind directions during the sampling and calculated backward trajectories underlined the need for more detailed information on environmental parameters for bioaerosol investigations. The current findings support the assumption of a bacterial core community in the atmosphere. They may be emitted from strong aerosolizing sources, probably being mixed and dispersed over long distances. PMID:25800495

  15. Impermanence of bacterial clones

    PubMed Central

    Bobay, Louis-Marie; Traverse, Charles C.; Ochman, Howard

    2015-01-01

    Bacteria reproduce asexually and pass on a single genome copied from the parent, a reproductive mode that assures the clonal descent of progeny; however, a truly clonal bacterial species is extremely rare. The signal of clonality can be interrupted by gene uptake and exchange, initiating homologous recombination that results in the unique sequence of one clone being incorporated into another. Because recombination occurs sporadically and on local scales, these events are often difficult to recognize, even when considering large samples of completely sequenced genomes. Moreover, several processes can produce the appearance of clonality in populations that undergo frequent recombination. The rates and consequences of recombination have been studied in Escherichia coli for over 40 y, and, during this time, there have been several shifting views of its clonal status, population structure, and rates of gene exchange. We reexamine the studies and retrace the evolution of the methods that have assessed the extent of DNA flux, largely focusing on its impact on the E. coli genome. PMID:26195749

  16. Small bowel bacterial overgrowth

    MedlinePlus

    Overgrowth - intestinal bacteria; Bacterial overgrowth - intestine; Small intestinal bacterial overgrowth; SIBO ... Most of the time, the small intestine does not have a high number ... in the small intestine may use up the nutrients needed by the ...

  17. Specific Gene Repression by CRISPRi System Transferred through Bacterial Conjugation

    PubMed Central

    2014-01-01

    In microbial communities, bacterial populations are commonly controlled using indiscriminate, broad range antibiotics. There are few ways to target specific strains effectively without disrupting the entire microbiome and local environment. Here, we use conjugation, a natural DNA horizontal transfer process among bacterial species, to deliver an engineered CRISPR interference (CRISPRi) system for targeting specific genes in recipient Escherichia coli cells. We show that delivery of the CRISPRi system is successful and can specifically repress a reporter gene in recipient cells, thereby establishing a new tool for gene regulation across bacterial cells and potentially for bacterial population control. PMID:25409531

  18. Functional Taxonomy of Bacterial Hyperstructures

    PubMed Central

    Norris, Vic; den Blaauwen, Tanneke; Cabin-Flaman, Armelle; Doi, Roy H.; Harshey, Rasika; Janniere, Laurent; Jimenez-Sanchez, Alfonso; Jin, Ding Jun; Levin, Petra Anne; Mileykovskaya, Eugenia; Minsky, Abraham; Saier, Milton; Skarstad, Kirsten

    2007-01-01

    The levels of organization that exist in bacteria extend from macromolecules to populations. Evidence that there is also a level of organization intermediate between the macromolecule and the bacterial cell is accumulating. This is the level of hyperstructures. Here, we review a variety of spatially extended structures, complexes, and assemblies that might be termed hyperstructures. These include ribosomal or “nucleolar” hyperstructures; transertion hyperstructures; putative phosphotransferase system and glycolytic hyperstructures; chemosignaling and flagellar hyperstructures; DNA repair hyperstructures; cytoskeletal hyperstructures based on EF-Tu, FtsZ, and MreB; and cell cycle hyperstructures responsible for DNA replication, sequestration of newly replicated origins, segregation, compaction, and division. We propose principles for classifying these hyperstructures and finally illustrate how thinking in terms of hyperstructures may lead to a different vision of the bacterial cell. PMID:17347523

  19. Collective Functionality through Bacterial Individuality

    NASA Astrophysics Data System (ADS)

    Ackermann, Martin

    According to the conventional view, the properties of an organism are a product of nature and nurture - of its genes and the environment it lives in. Recent experiments with unicellular organisms have challenged this view: several molecular mechanisms generate phenotypic variation independently of environmental signals, leading to variation in clonal groups. My presentation will focus on the causes and consequences of this microbial individuality. Using examples from bacterial genetic model systems, I will first discuss different molecular and cellular mechanisms that give rise to bacterial individuality. Then, I will discuss the consequences of individuality, and focus on how phenotypic variation in clonal populations of bacteria can promote interactions between individuals, lead to the division of labor, and allow clonal groups of bacteria to cope with environmental uncertainty. Variation between individuals thus provides clonal groups with collective functionality.

  20. Jellyfish Modulate Bacterial Dynamic and Community Structure

    PubMed Central

    Tinta, Tinkara; Kogovšek, Tjaša; Malej, Alenka; Turk, Valentina

    2012-01-01

    Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom - forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish - enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to ‘jellyfish - associated’ and ‘free - living’ bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into

  1. Demonstrating Bacterial Flagella.

    ERIC Educational Resources Information Center

    Porter, John R.; And Others

    1992-01-01

    Describes an effective laboratory method for demonstrating bacterial flagella that utilizes the Proteus mirabilis organism and a special harvesting technique. Includes safety considerations for the laboratory exercise. (MDH)

  2. Characterization of bacterial community structure on a weathered pegmatitic granite.

    PubMed

    Gleeson, Deirdre B; Kennedy, Nabla M; Clipson, Nicholas; Melville, Karrie; Gadd, Geoffrey M; McDermott, Frank P

    2006-05-01

    This study exploited the contrasting major element chemistry of a pegmatitic granite to investigate mineralogical influences on bacterial community structure. Intact crystals of variably weathered muscovite, plagioclase, K-feldspar, and quartz were extracted, together with whole-rock granite. Environmental scanning electron microscopy revealed a diversity of bacterial structures, with rods and cocci clearly visible on surfaces of all mineral types. Bacterial automated ribosomal intergenic spacer analysis was used to generate a ribotype profile for each mineral. A randomization test revealed that community fingerprints differed between different mineral types, whereas canonical correspondence analysis (CCA) showed that mineral chemistry affected individual bacterial ribotypes. CCA also revealed that Al, Si, and Ca had a significant impact on bacterial community structure within the system, which contrasts with the finding within fungal communities that although Al and Si also had a significant impact, K rather than Ca was important. The bacterial populations associated with different minerals were different. Members of each of these populations were found almost exclusively on a single mineral type, as was previously reported for fungal populations. These results show that bacterial community structure was driven by the chemical composition of minerals, indicating selective pressure by individual chemical elements on bacterial populations in situ.

  3. Factors contributing to bacterial bulb rots of onion

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The incidence of bacterial rots of onion bulbs is increasing and has become a serious problem for growers. This increase is likely due to a combination of factors, such as high bacterial populations in soils and irrigation water, heavy rains flooding production fields, higher temperatures, etc. It m...

  4. Stochastic modelling of bacterial lag phase.

    PubMed

    Baranyi, József

    2002-03-01

    In order to study the lag distribution of the individual cells in a bacterial population, a stochastic birth model is used in this study. An integral formula is applied to transform the assumed lag distribution into a growth function describing the transition between lag and exponential phase of the cell population. By means of this formula, it is pointed out that traditional viable count curves are not suitable to identify the distribution of individual cells' lag time.

  5. Evidence of two lineages of the symbiont 'Candidatus Erwinia dacicola' in Italian populations of Bactrocera oleae (Rossi) based on 16S rRNA gene sequences.

    PubMed

    Savio, Claudia; Mazzon, Luca; Martinez-Sañudo, Isabel; Simonato, Mauro; Squartini, Andrea; Girolami, Vincenzo

    2012-01-01

    The close association between the olive fly Bactrocera oleae (Rossi) (Diptera: Tephritidae) and bacteria has been known for more than a century. Recently, the presence of a host-specific, hereditary, unculturable symbiotic bacterium, designated 'Candidatus Erwinia dacicola', has been described inside the cephalic organ of the fly, called the oesophageal bulb. In the present study, the 16S rRNA gene sequence variability of 'Ca. E. dacicola' was examined within and between 26 Italian olive fly populations sampled across areas where olive trees occur in the wild and areas where cultivated olive trees have been introduced through history. The bacterial contents of the oesophageal bulbs of 314 olive flies were analysed and a minimum of 781 bp of the 16S rRNA gene was sequenced. The corresponding host fly genotype was assessed by sequencing a 776 bp portion of the mitochondrial genome. Two 'Ca. E. dacicola' haplotypes were found (htA and htB), one being slightly more prevalent than the other (57%). The two haplotypes did not co-exist in the same individuals, as confirmed by cloning. Interestingly, the olive fly populations of the two main Italian islands, Sicily and Sardinia, appeared to be represented exclusively by the htB and htA haplotypes, respectively, while peninsular populations showed both bacterial haplotypes in different proportions. No significant correlation emerged between the two symbiont haplotypes and the 16 host fly haplotypes observed, suggesting evidence for a mixed model of vertical and horizontal transmission of the symbiont during the fly life cycle.

  6. Vimentin in Bacterial Infections

    PubMed Central

    Mak, Tim N.; Brüggemann, Holger

    2016-01-01

    Despite well-studied bacterial strategies to target actin to subvert the host cell cytoskeleton, thus promoting bacterial survival, replication, and dissemination, relatively little is known about the bacterial interaction with other components of the host cell cytoskeleton, including intermediate filaments (IFs). IFs have not only roles in maintaining the structural integrity of the cell, but they are also involved in many cellular processes including cell adhesion, immune signaling, and autophagy, processes that are important in the context of bacterial infections. Here, we summarize the knowledge about the role of IFs in bacterial infections, focusing on the type III IF protein vimentin. Recent studies have revealed the involvement of vimentin in host cell defenses, acting as ligand for several pattern recognition receptors of the innate immune system. Two main aspects of bacteria-vimentin interactions are presented in this review: the role of vimentin in pathogen-binding on the cell surface and subsequent bacterial invasion and the interaction of cytosolic vimentin and intracellular pathogens with regards to innate immune signaling. Mechanistic insight is presented involving distinct bacterial virulence factors that target vimentin to subvert its function in order to change the host cell fate in the course of a bacterial infection. PMID:27096872

  7. Gene-environment and protein-degradation signatures characterize genomic and phenotypic diversity in wild Caenorhabditis elegans populations

    PubMed Central

    2013-01-01

    Background Analyzing and understanding the relationship between genotypes and phenotypes is at the heart of genetics. Research on the nematode Caenorhabditis elegans has been instrumental for unraveling genotype-phenotype relations, and has important implications for understanding the biology of mammals, but almost all studies, including forward and reverse genetic screens, are limited by investigations in only one canonical genotype. This hampers the detection and functional analysis of allelic variants, which play a key role in controlling many complex traits. It is therefore essential to explore the full potential of the natural ge