Science.gov

Sample records for access microbial populations

  1. Microbial populations in contaminant plumes

    USGS Publications Warehouse

    Haack, S.K.; Bekins, B.A.

    2000-01-01

    Efficient biodegradation of subsurface contaminants requires two elements: (1) microbial populations with the necessary degradative capabilities, and (2) favorable subsurface geochemical and hydrological conditions. Practical constraints on experimental design and interpretation in both the hydrogeological and microbiological sciences have resulted in limited knowledge of the interaction between hydrogeological and microbiological features of subsurface environments. These practical constraints include: (1) inconsistencies between the scales of investigation in the hydrogeological and microbiological sciences, and (2) practical limitations on the ability to accurately define microbial populations in environmental samples. However, advances in application of small-scale sampling methods and interdisciplinary approaches to site investigations are beginning to significantly improve understanding of hydrogeological and microbiological interactions. Likewise, culture-based and molecular analyses of microbial populations in subsurface contaminant plumes have revealed significant adaptation of microbial populations to plume environmental conditions. Results of recent studies suggest that variability in subsurface geochemical and hydrological conditions significantly influences subsurface microbial-community structure. Combined investigations of site conditions and microbial-community structure provide the knowledge needed to understand interactions between subsurface microbial populations, plume geochemistry, and contaminant biodegradation.

  2. Microbial populations in contaminant plumes

    NASA Astrophysics Data System (ADS)

    Haack, Sheridan K.; Bekins, Barbara A.

    Efficient biodegradation of subsurface contaminants requires two elements: (1) microbial populations with the necessary degradative capabilities, and (2) favorable subsurface geochemical and hydrological conditions. Practical constraints on experimental design and interpretation in both the hydrogeological and microbiological sciences have resulted in limited knowledge of the interaction between hydrogeological and microbiological features of subsurface environments. These practical constraints include: (1) inconsistencies between the scales of investigation in the hydrogeological and microbiological sciences, and (2) practical limitations on the ability to accurately define microbial populations in environmental samples. However, advances in application of small-scale sampling methods and interdisciplinary approaches to site investigations are beginning to significantly improve understanding of hydrogeological and microbiological interactions. Likewise, culture-based and molecular analyses of microbial populations in subsurface contaminant plumes have revealed significant adaptation of microbial populations to plume environmental conditions. Results of recent studies suggest that variability in subsurface geochemical and hydrological conditions significantly influences subsurface microbial-community structure. Combined investigations of site conditions and microbial-community structure provide the knowledge needed to understand interactions between subsurface microbial populations, plume geochemistry, and contaminant biodegradation. La biodégradation efficace des polluants souterrains requiert deux éléments: des populations microbiennes possédant les aptitudes nécessaires à la dégradation, et des conditions géochimiques et hydrologiques souterraines favorables. Des contraintes pratiques sur la conception et l'interprétation des expériences à la fois en microbiologie et en hydrogéologie ont conduit à une connaissance limitée des interactions entre les

  3. Access to bird population data

    USGS Publications Warehouse

    Martin, E.; Peterjohn, B.G.; Koneff, M.D.

    2001-01-01

    Access to bird population data is critical for effective conservation planning and implementation. Although a tremendous volume of baseline data exists, it is often diffusely distributed and inaccessible to the resource manager and decision maker. A mechanism that facilitates assembly, documentation and delivery of avian data in a user-friendly manner is needed in order to integrate bird-related information resources across agencies and organizations. To address this fundamental need, the National Biological Information Infrastructure (NBII), in partnership with the U.S. Geological Survey's Patuxent Wildlife Research Center and the U.S. Fish and Wildlife Service, is developing a web-based interactive system that will focus on access to bird population and habitat data used in bird management and conservation. This system, known as the NBII Bird Conservation Node, will support planning and evaluation of bird conservation activities within the context of the North American Bird Conservation Initiative (NABCI), a framework for collaboration among organizations interested in bird conservation across North America. Initial development of the NBII Bird Conservation Node will focus on creating a prototype mapping application that will provide interactive access to data from the North American Breeding Bird Survey, the Colonial Waterbird Survey, the Breeding Waterfowl Population and Habitat Survey, and the Atlantic Flyway Mid-winter Waterfowl Survey. This prototype mapping application, to be available on-line at http://www.nbii.gov by Sep 2001, will lay the foundation for establishment of a Migratory Bird Data Center at Patuxent Wildlife Research Center, and will provide an opportunity for linking to and establishing partnerships with other sources of bird population and habitat data available over the Internet.

  4. Interval scanning photomicrography of microbial cell populations.

    NASA Technical Reports Server (NTRS)

    Casida, L. E., Jr.

    1972-01-01

    A single reproducible area of the preparation in a fixed focal plane is photographically scanned at intervals during incubation. The procedure can be used for evaluating the aerobic or anaerobic growth of many microbial cells simultaneously within a population. In addition, the microscope is not restricted to the viewing of any one microculture preparation, since the slide cultures are incubated separately from the microscope.

  5. Rapid quantitative profiling of complex microbial populations

    PubMed Central

    Palmer, Chana; Bik, Elisabeth M.; Eisen, Michael B.; Eckburg, Paul B.; Sana, Theodore R.; Wolber, Paul K.; Relman, David A.; Brown, Patrick O.

    2006-01-01

    Diverse and complex microbial ecosystems are found in virtually every environment on earth, yet we know very little about their composition and ecology. Comprehensive identification and quantification of the constituents of these microbial communities—a ‘census’—is an essential foundation for understanding their biology. To address this problem, we developed, tested and optimized a DNA oligonucleotide microarray composed of 10 462 small subunit (SSU) ribosomal DNA (rDNA) probes (7167 unique sequences) selected to provide quantitative information on the taxonomic composition of diverse microbial populations. Using our optimized experimental approach, this microarray enabled detection and quantification of individual bacterial species present at fractional abundances of <0.1% in complex synthetic mixtures. The estimates of bacterial species abundance obtained using this microarray are similar to those obtained by phylogenetic analysis of SSU rDNA sequences from the same samples—the current ‘gold standard’ method for profiling microbial communities. Furthermore, probes designed to represent higher order taxonomic groups of bacterial species reliably detected microbes for which there were no species-specific probes. This simple, rapid microarray procedure can be used to explore and systematically characterize complex microbial communities, such as those found within the human body. PMID:16407321

  6. Environmental Disturbances Decrease the Variability of Microbial Populations within Periphyton

    PubMed Central

    Webert, Kyle C.; McMahon, Katherine D.

    2016-01-01

    ABSTRACT A central pursuit of microbial ecology is to accurately model changes in microbial community composition in response to environmental factors. This goal requires a thorough understanding of the drivers of variability in microbial populations. However, most microbial ecology studies focus on the effects of environmental factors on mean population abundances, rather than on population variability. Here, we imposed several experimental disturbances upon periphyton communities and analyzed the variability of populations within disturbed communities compared with those in undisturbed communities. We analyzed both the bacterial and the diatom communities in the periphyton under nine different disturbance regimes, including regimes that contained multiple disturbances. We found several similarities in the responses of the two communities to disturbance; all significant treatment effects showed that populations became less variable as the result of environmental disturbances. Furthermore, multiple disturbances to these communities were often interactive, meaning that the effects of two disturbances could not have been predicted from studying single disturbances in isolation. These results suggest that environmental factors had repeatable effects on populations within microbial communities, thereby creating communities that were more similar as a result of disturbances. These experiments add to the predictive framework of microbial ecology by quantifying variability in microbial populations and by demonstrating that disturbances can place consistent constraints on the abundance of microbial populations. Although models will never be fully predictive due to stochastic forces, these results indicate that environmental stressors may increase the ability of models to capture microbial community dynamics because of their consistent effects on microbial populations. IMPORTANCE There are many reasons why microbial community composition is difficult to model. For example

  7. Detecting differential growth of microbial populations with Gaussian process regression

    PubMed Central

    Tonner, Peter D.; Darnell, Cynthia L.; Engelhardt, Barbara E.; Schmid, Amy K.

    2017-01-01

    Microbial growth curves are used to study differential effects of media, genetics, and stress on microbial population growth. Consequently, many modeling frameworks exist to capture microbial population growth measurements. However, current models are designed to quantify growth under conditions for which growth has a specific functional form. Extensions to these models are required to quantify the effects of perturbations, which often exhibit nonstandard growth curves. Rather than assume specific functional forms for experimental perturbations, we developed a general and robust model of microbial population growth curves using Gaussian process (GP) regression. GP regression modeling of high-resolution time-series growth data enables accurate quantification of population growth and allows explicit control of effects from other covariates such as genetic background. This framework substantially outperforms commonly used microbial population growth models, particularly when modeling growth data from environmentally stressed populations. We apply the GP growth model and develop statistical tests to quantify the differential effects of environmental perturbations on microbial growth across a large compendium of genotypes in archaea and yeast. This method accurately identifies known transcriptional regulators and implicates novel regulators of growth under standard and stress conditions in the model archaeal organism Halobacterium salinarum. For yeast, our method correctly identifies known phenotypes for a diversity of genetic backgrounds under cyclohexamide stress and also detects previously unidentified oxidative stress sensitivity across a subset of strains. Together, these results demonstrate that the GP models are interpretable, recapitulating biological knowledge of growth response while providing new insights into the relevant parameters affecting microbial population growth. PMID:27864351

  8. Cellulose accessibility and microbial community in solid state anaerobic digestion of rape straw.

    PubMed

    Tian, Jiang-Hao; Pourcher, Anne-Marie; Bureau, Chrystelle; Peu, Pascal

    2017-01-01

    Solid state anaerobic digestion (SSAD) with leachate recirculation is an appropriate method for the valorization of agriculture residues. Rape straw is a massively produced residue with considerable biochemical methane potential, but its degradation in SSAD remains poorly understood. A thorough study was conducted to understand the performance of rape straw as feedstock for laboratory solid state anaerobic digesters. We investigated the methane production kinetics of rape straw in relation to cellulose accessibility to cellulase and the microbial community. Improving cellulose accessibility through milling had a positive influence on both the methane production rate and methane yield. The SSAD of rape straw reached 60% of its BMP in a 40-day pilot-scale test. Distinct bacterial communities were observed in digested rape straw and leachate, with Bacteroidales and Sphingobacteriales as the most abundant orders, respectively. Archaeal populations showed no phase preference and increased chronologically.

  9. Cooperation, cheating, and collapse in microbial populations

    NASA Astrophysics Data System (ADS)

    Gore, Jeff

    2012-02-01

    Natural populations can suffer catastrophic collapse in response to small changes in environmental conditions, and recovery after such a collapse can be exceedingly difficult. We have used laboratory yeast populations to study proposed early warning signals of impending extinction. Yeast cooperatively breakdown the sugar sucrose, meaning that there is a minimum number of cells required to sustain the population. We have demonstrated experimentally that the fluctuations in the population size increase in magnitude and become slower as the population approaches collapse. The cooperative nature of yeast growth on sucrose suggests that the population may be susceptible to cheater cells, which do not contribute to the public good and instead merely take advantage of the cooperative cells. We have confirmed this possibility experimentally by using a cheater yeast strain that lacks the gene encoding the cooperative behavior [1]. However, recent results in the lab demonstrate that the presence of a bacterial competitor may drive cooperation within the yeast population.[4pt] [1] Gore et al, Nature 459, 253 -- 256 (2009)

  10. Temporal variation in airborne microbial populations and microbially-derived allergens in a tropical urban landscape

    NASA Astrophysics Data System (ADS)

    Woo, Anthony C.; Brar, Manreetpal S.; Chan, Yuki; Lau, Maggie C. Y.; Leung, Frederick C. C.; Scott, James A.; Vrijmoed, Lilian L. P.; Zawar-Reza, Peyman; Pointing, Stephen B.

    2013-08-01

    The microbial component of outdoor aerosols was assessed along a gradient of urban development from inner-city to rural in the seasonal-tropical metropolis of Hong Kong. Sampling over a continuous one-year period was conducted, with molecular analyses to characterize bacterial and eukaryal microbial populations, immuno-assays to detect microbially-derived allergens and extensive environmental and meteorological observations. The data revealed bio-aerosol populations were not significantly impacted by the level of urban development as measured by anthropogenic pollutants and human population levels, but instead exhibited a strong seasonal trend related to general climatic variables. We applied back-trajectory analysis to establish sources of air masses and this allowed further explanation of urban bio-aerosols largely in terms of summer-marine and winter-continental origins. We also evaluated bio-aerosols for the potential to detect human health threats. Many samples supported bacterial and fungal phylotypes indicative of known pathogenic taxa, together with common indicators of human presence. The occurrence of allergenic endotoxins and beta-glucans generally tracked trends in microbial populations, with levels known to induce symptoms detected during summer months when microbial loading was higher. This strengthens calls for bio-aerosols to be considered in future risk assessments and surveillance of air quality, along with existing chemical and particulate indices.

  11. 2007 Microbial Population Biology (July 22-26, 2007)

    SciTech Connect

    Anthony M. Dean Nancy Ryan Gray

    2008-04-01

    Microbial Population Biology covers a diverse range of cutting edge issues in the microbial sciences and beyond. Firmly founded in evolutionary biology and with a strongly integrative approach, past meetings have covered topics ranging from the dynamics and genetics of adaptation to the evolution of mutation rate, community ecology, evolutionary genomics, altruism, and epidemiology. This meeting is never dull: some of the most significant and contentious issues in biology have been thrashed out here. We anticipate the 2007 meeting being no exception. The final form of the 2007 meeting is yet to be decided, but the following topics are likely to be included: evolutionary emergence of infectious disease and antibiotic resistance, genetic architecture and implications for the evolution of microbial populations, ageing in bacteria, biogeography, evolution of symbioses, the role of microbes in ecosystem function, and ecological genomics.

  12. MICROBIAL POPULATION ANALYSIS AS A MEASURE OF ECOSYSTEM RESTORATION

    EPA Science Inventory

    During a controlled oil spill study in a freshwater wetland, four methods were used to track changes in microbial populations in response to in situ remediation treatments, including nutrient amendments and the removal of surface vegetation. Most probable number (MPN) esimates o...

  13. Minimal models of growth and decline of microbial populations.

    PubMed

    Juška, Alfonsas

    2011-01-21

    Dynamics of growth and decline of microbial populations were analysed and respective models were developed in this investigation. Analysis of the dynamics was based on general considerations concerning the main properties of microorganisms and their interactions with the environment which was supposed to be affected by the activity of the population. Those considerations were expressed mathematically by differential equations or systems of the equations containing minimal sets of parameters characterizing those properties. It has been found that: (1) the factors leading to the decline of the population have to be considered separately, namely, accumulation of metabolites (toxins) in the medium and the exhaustion of resources; the latter have to be separated again into renewable ('building materials') and non-renewable (sources of energy); (2) decline of the population is caused by the exhaustion of sources of energy but no decline is predicted by the model because of the exhaustion of renewable resources; (3) the model determined by the accumulation of metabolites (toxins) in the medium does not suggest the existence of a separate 'stationary phase'; (4) in the model determined by the exhaustion of energy resources the 'stationary' and 'decline' phases are quite discernible; and (5) there is no symmetry in microbial population dynamics, the decline being slower than the rise. Mathematical models are expected to be useful in getting insight into the process of control of the dynamics of microbial populations. The models are in agreement with the experimental data.

  14. Evolutionary Dynamics and Diversity in Microbial Populations

    NASA Astrophysics Data System (ADS)

    Thompson, Joel; Fisher, Daniel

    2013-03-01

    Diseases such as flu and cancer adapt at an astonishing rate. In large part, viruses and cancers are so difficult to prevent because they are continually evolving. Controlling such ``evolutionary diseases'' requires a better understanding of the underlying evolutionary dynamics. It is conventionally assumed that adaptive mutations are rare and therefore will occur and sweep through the population in succession. Recent experiments using modern sequencing technologies have illuminated the many ways in which real population sequence data does not conform to the predictions of conventional theory. We consider a very simple model of asexual evolution and perform simulations in a range of parameters thought to be relevant for microbes and cancer. Simulation results reveal complex evolutionary dynamics typified by competition between lineages with different sets of adaptive mutations. This dynamical process leads to a distribution of mutant gene frequencies different than expected under the conventional assumption that adaptive mutations are rare. Simulated gene frequencies share several conspicuous features with data collected from laboratory-evolved yeast and the worldwide population of influenza.

  15. Population Distribution, Settlement Patterns and Accessibility across Africa in 2010

    PubMed Central

    Linard, Catherine; Gilbert, Marius; Snow, Robert W.; Noor, Abdisalan M.; Tatem, Andrew J.

    2012-01-01

    The spatial distribution of populations and settlements across a country and their interconnectivity and accessibility from urban areas are important for delivering healthcare, distributing resources and economic development. However, existing spatially explicit population data across Africa are generally based on outdated, low resolution input demographic data, and provide insufficient detail to quantify rural settlement patterns and, thus, accurately measure population concentration and accessibility. Here we outline approaches to developing a new high resolution population distribution dataset for Africa and analyse rural accessibility to population centers. Contemporary population count data were combined with detailed satellite-derived settlement extents to map population distributions across Africa at a finer spatial resolution than ever before. Substantial heterogeneity in settlement patterns, population concentration and spatial accessibility to major population centres is exhibited across the continent. In Africa, 90% of the population is concentrated in less than 21% of the land surface and the average per-person travel time to settlements of more than 50,000 inhabitants is around 3.5 hours, with Central and East Africa displaying the longest average travel times. The analyses highlight large inequities in access, the isolation of many rural populations and the challenges that exist between countries and regions in providing access to services. The datasets presented are freely available as part of the AfriPop project, providing an evidence base for guiding strategic decisions. PMID:22363717

  16. Self-Driven Jamming in Growing Microbial Populations

    PubMed Central

    Delarue, Morgan; Hartung, Jörn; Schreck, Carl; Gniewek, Pawel; Hu, Lucy; Herminghaus, Stephan; Hallatschek, Oskar

    2016-01-01

    In natural settings, microbes tend to grow in dense populations [1–4] where they need to push against their surroundings to accommodate space for new cells. The associated contact forces play a critical role in a variety of population-level processes, including biofilm formation [5–7], the colonization of porous media [8, 9], and the invasion of biological tissues [10–12]. Although mechanical forces have been characterized at the single cell level [13–16], it remains elusive how collective pushing forces result from the combination of single cell forces. Here, we reveal a collective mechanism of confinement, which we call self-driven jamming, that promotes the build-up of large mechanical pressures in microbial populations. Microfluidic experiments on budding yeast populations in space-limited environments show that self-driven jamming arises from the gradual formation and sudden collapse of force chains driven by microbial proliferation, extending the framework of driven granular matter [17–20]. The resulting contact pressures can become large enough to slow down cell growth, to delay the cell cycle in the G1 phase, and to strain or even destroy the microenvironment through crack propagation. Our results suggest that self-driven jamming and build-up of large mechanical pressures is a natural tendency of microbes growing in confined spaces, contributing to microbial pathogenesis and biofouling [21–26]. PMID:27642362

  17. Self-driven jamming in growing microbial populations

    NASA Astrophysics Data System (ADS)

    Delarue, Morgan; Hartung, Jörn; Schreck, Carl; Gniewek, Pawel; Hu, Lucy; Herminghaus, Stephan; Hallatschek, Oskar

    2016-08-01

    In natural settings, microbes tend to grow in dense populations where they need to push against their surroundings to accommodate space for new cells. The associated contact forces play a critical role in a variety of population-level processes, including biofilm formation, the colonization of porous media, and the invasion of biological tissues. Although mechanical forces have been characterized at the single-cell level, it remains elusive how collective pushing forces result from the combination of single-cell forces. Here, we reveal a collective mechanism of confinement, which we call self-driven jamming, that promotes the build-up of large mechanical pressures in microbial populations. Microfluidic experiments on budding yeast populations in space-limited environments show that self-driven jamming arises from the gradual formation and sudden collapse of force chains driven by microbial proliferation, extending the framework of driven granular matter. The resulting contact pressures can become large enough to slow down cell growth, to delay the cell cycle in the G1 phase, and to strain or even destroy the micro-environment through crack propagation. Our results suggest that self-driven jamming and build-up of large mechanical pressures is a natural tendency of microbes growing in confined spaces, contributing to microbial pathogenesis and biofouling.

  18. Biogeography of Metabolically Active Microbial Populations within the Subseafloor Biosphere

    NASA Astrophysics Data System (ADS)

    Reese, B. K.; Shepard, A.; St. Peter, C.; Mills, H. J.

    2011-12-01

    Microbial life in deep marine sediments is widespread, metabolically active and diverse. Evidence of prokaryotic communities in sediments as deep as 800 m below the seafloor (mbsf) have been found. By recycling carbon and nutrients through biological and geochemical processes, the deep subsurface has the potential to remain metabolically active over geologic time scales. While a vast majority of the subsurface biosphere remains under studied, recent advances in molecular techniques and an increased focus on microbiological sampling during IODP expeditions have provided the initial steps toward better characterizations of the microbial communities. Coupling of geochemistry and RNA-based molecular analysis is essential to the description of the active microbial populations within the subsurface biosphere. Studies based on DNA may describe the taxa and metabolic pathways from the total microbial community within the sediment, whether the cells sampled were metabolically active, quiescent or dead. Due to a short lifespan within a cell, only an RNA-based analysis can be used to identify linkages between active populations and observed geochemistry. This study will coalesce and compare RNA sequence and geochemical data from Expeditions 316 (Nankai Trough), 320 (Pacific Equatorial Age Transect), 325 (Great Barrier Reef) and 329 (South Pacific Gyre) to evaluate the biogeography of microbial lineages actively altering the deep subsurface. The grouping of sediments allows for a wide range of geochemical environments to be compared, including two environments limited in organic carbon. Significant to this study is the use of similar extraction, amplification and simultaneous 454 pyrosequencing on all sediment populations allowing for robust comparisons with similar protocol strengths and biases. Initial trends support previously described reduction of diversity with increasing depth. The co-localization of active reductive and oxidative lineages suggests a potential cryptic

  19. Population Education Accessions List, September-December 1996.

    ERIC Educational Resources Information Center

    United Nations Educational, Scientific and Cultural Organization, Bangkok (Thailand). Principal Regional Office for Asia and the Pacific.

    This issue of the Population Education Accessions List is an output from United Nation's Educational Social and Cultural Organization's (UNESCO) computerized bibliographic database. It categorizes entries into three parts. Part I, Population Education, consists of titles that address various aspects of population education arranged by country in…

  20. Population-reaction model and microbial experimental ecosystems for understanding hierarchical dynamics of ecosystems.

    PubMed

    Hosoda, Kazufumi; Tsuda, Soichiro; Kadowaki, Kohmei; Nakamura, Yutaka; Nakano, Tadashi; Ishii, Kojiro

    2016-02-01

    Understanding ecosystem dynamics is crucial as contemporary human societies face ecosystem degradation. One of the challenges that needs to be recognized is the complex hierarchical dynamics. Conventional dynamic models in ecology often represent only the population level and have yet to include the dynamics of the sub-organism level, which makes an ecosystem a complex adaptive system that shows characteristic behaviors such as resilience and regime shifts. The neglect of the sub-organism level in the conventional dynamic models would be because integrating multiple hierarchical levels makes the models unnecessarily complex unless supporting experimental data are present. Now that large amounts of molecular and ecological data are increasingly accessible in microbial experimental ecosystems, it is worthwhile to tackle the questions of their complex hierarchical dynamics. Here, we propose an approach that combines microbial experimental ecosystems and a hierarchical dynamic model named population-reaction model. We present a simple microbial experimental ecosystem as an example and show how the system can be analyzed by a population-reaction model. We also show that population-reaction models can be applied to various ecological concepts, such as predator-prey interactions, climate change, evolution, and stability of diversity. Our approach will reveal a path to the general understanding of various ecosystems and organisms.

  1. Facilitation as Attenuating of Environmental Stress among Structured Microbial Populations

    PubMed Central

    Santaella, Sandra Tédde; Martins, Claudia Miranda; Martins, Rogério Parentoni

    2016-01-01

    There is currently an intense debate in microbial societies on whether evolution in complex communities is driven by competition or cooperation. Since Darwin, competition for scarce food resources has been considered the main ecological interaction shaping population dynamics and community structure both in vivo and in vitro. However, facilitation may be widespread across several animal and plant species. This could also be true in microbial strains growing under environmental stress. Pure and mixed strains of Serratia marcescens and Candida rugosa were grown in mineral culture media containing phenol. Growth rates were estimated as the angular coefficients computed from linearized growth curves. Fitness index was estimated as the quotient between growth rates computed for lineages grown in isolation and in mixed cultures. The growth rates were significantly higher in associated cultures than in pure cultures and fitness index was greater than 1 for both microbial species showing that the interaction between Serratia marcescens and Candida rugosa yielded more efficient phenol utilization by both lineages. This result corroborates the hypothesis that facilitation between microbial strains can increase their fitness and performance in environmental bioremediation. PMID:26904719

  2. [Vulnerable populations and access to care].

    PubMed

    Castello, Christine; Michard-Lenoir, Anne-Pascale; Allemand, Robert

    2012-01-01

    Precariousness is a very complex concept that brings together a diverse and fragmented population. The interest in comparing views and opinions is clear for understanding of this phenomenon. A physician in the paediatric emergency unit of a hospital and the head of a "Medecins du Monde" branch evoke the different faces of precariousness. A difficult and sometimes poignant reality, which health care providers must try to cope with.

  3. Metabolic Differences in Microbial Cell Populations Revealed by Nanophotonic Ionization

    SciTech Connect

    Walker, Bennett; Antonakos, Cory; Retterer, Scott T; Vertes, Akos

    2013-01-01

    ellular differences are linked to cell differentiation, the proliferation of cancer and to the development of drug resistance in microbial infections. Due to sensitivity limitations, however, large- scale metabolic analysis at the single cell level is only available for cells significantly larger in volume than Saccharomyces cerevisiae (~30 fL). Here we demonstrate that by a nanophotonic ionization platform and mass spectrometry, over one hundred up to 108 metabolites, or up to 18% of the known S. cerevisiae metabolome, can be identified in very small cell populations (n < 100). Under ideal conditions, r Relative quantitation of up to 4% of the metabolites is achieved at the single cell level.

  4. Multi-population model of a microbial electrolysis cell.

    PubMed

    Pinto, R P; Srinivasan, B; Escapa, A; Tartakovsky, B

    2011-06-01

    This work presents a multi-population dynamic model of a microbial electrolysis cell (MEC). The model describes the growth and metabolic activity of fermentative, electricigenic, methanogenic acetoclastic, and methanogenic hydrogenophilic microorganisms and is capable of simulating hydrogen production in a MEC fed with complex organic matter, such as wastewater. The model parameters were estimated with the experimental results obtained in continuous flow MECs fed with acetate or synthetic wastewater. Following successful model validation with an independent data set, the model was used to analyze and discuss the influence of applied voltage and organic load on hydrogen production and COD removal.

  5. Programming microbial population dynamics by engineered cell-cell communication.

    PubMed

    Song, Hao; Payne, Stephen; Tan, Cheemeng; You, Lingchong

    2011-07-01

    A major aim of synthetic biology is to program novel cellular behavior using engineered gene circuits. Early endeavors focused on building simple circuits that fulfill simple functions, such as logic gates, bistable toggle switches, and oscillators. These gene circuits have primarily focused on single-cell behaviors since they operate intracellularly. Thus, they are often susceptible to cell-cell variations due to stochastic gene expression. Cell-cell communication offers an efficient strategy to coordinate cellular behavior at the population level. To this end, we review recent advances in engineering cell-cell communication to achieve reliable population dynamics, spanning from communication within single species to multispecies, from one-way sender-receiver communication to two-way communication in synthetic microbial ecosystems. These engineered systems serve as well-defined model systems to better understand design principles of their naturally occurring counterparts and to facilitate novel biotechnology applications.

  6. Population dynamics of microbial communities in the zebrafish gut

    NASA Astrophysics Data System (ADS)

    Jemielita, Matthew; Taormina, Michael; Burns, Adam; Hampton, Jennifer; Rolig, Annah; Wiles, Travis; Guillemin, Karen; Parthasarathy, Raghuveer

    2015-03-01

    The vertebrate intestine is home to a diverse microbial community, which plays a crucial role in the development and health of its host. Little is known about the population dynamics and spatial structure of this ecosystem, including mechanisms of growth and interactions between species. We have constructed an experimental model system with which to explore these issues, using initially germ-free larval zebrafish inoculated with defined communities of fluorescently tagged bacteria. Using light sheet fluorescence microscopy combined with computational image analysis we observe and quantify the entire bacterial community of the intestine during the first 24 hours of colonization, during which time the bacterial population grows from tens to tens of thousands of bacteria. We identify both individual bacteria and clusters of bacteria, and quantify the growth rate and spatial distribution of these distinct subpopulations. We find that clusters of bacteria grow considerably faster than individuals and are located in specific regions of the intestine. Imaging colonization by two species reveals spatial segregation and competition. These data and their analysis highlight the importance of spatial organization in the establishment of gut microbial communities, and can provide inputs to physical models of real-world ecological dynamics.

  7. Microbial Population Changes During Bioremediation of an Experimental Oil Spill

    SciTech Connect

    Chang, Y.J.; Davis, G.A.; Macnaughton, S.J.; Stephen, J.R.; Venosa, A.D.; White, D.C.

    1998-08-08

    A field experiment was conducted in Delaware (USA) to evaluate three crude oil bioremediation techniques. Four treatments were studied: no oil control, oil alone, oil + nutrients, and oil + nutrients + an indigenous inoculum. The microbial populations were monitored by standard MPN techniques, PLFA profile analysis, and 16S rDNA DGGE analysis for species definition. Viable MPN estimates showed high but steadily declining microbial numbers and no significant differences among treatments during the 14-weeks. Regarding the PLFA results, the communities shifted over the 14-week period from being composed primarily of eukaryotes to Gram-negative bacteria. The Gram-negative communities shifted from the exponential to the stationary phase of growth after week 0. All Gram-negative communities showed evidence of environmental stress. The 16S rDNA DGGE profile of all plots revealed eight prominent bands at time zero. The untreated control plots revealed a simple, dynamic dominant population structure throughout the experiment. The original banding pattern disappeared rapidly in all oiled plots, indicating that the dominant species diversity changed and increased substantially over 14 weeks. The nature of this change was altered by nutrient-addition and the addition of the indigenous inoculum.

  8. Monitoring Spatial Segregation in Surface Colonizing Microbial Populations

    PubMed Central

    Hölscher, Theresa; Dragoš, Anna; Gallegos-Monterrosa, Ramses; Martin, Marivic; Mhatre, Eisha; Richter, Anne; Kovács, Ákos T.

    2016-01-01

    Microbes provide an intriguing system to study social interaction among individuals within a population. The short generation times and relatively simple genetic modification procedures of microbes facilitate the development of the sociomicrobiology field. To assess the fitness of certain microbial species, selected strains or their genetically modified derivatives within one population, can be fluorescently labelled and tracked using microscopy adapted with appropriate fluorescence filters. Expanding colonies of diverse microbial species on agar media can be used to monitor the spatial distribution of cells producing distinctive fluorescent proteins. Here, we present a detailed protocol for the use of green- and red-fluorescent protein producing bacterial strains to follow spatial arrangement during surface colonization, including flagellum-driven community movement (swarming), exopolysaccharide- and hydrophobin-dependent growth mediated spreading (sliding), and complex colony biofilm formation. Non-domesticated isolates of the Gram-positive bacterium, Bacillus subtilis can be utilized to scrutinize certain surface spreading traits and their effect on two-dimensional distribution on the agar-solidified medium. By altering the number of cells used to initiate colony biofilms, the assortment levels can be varied on a continuous scale. Time-lapse fluorescent microscopy can be used to witness the interaction between different phenotypes and genotypes at a certain assortment level and to determine the relative success of either. PMID:27842347

  9. Population Education Accessions List. January-December 1993.

    ERIC Educational Resources Information Center

    United Nations Educational, Scientific and Cultural Organization, Bangkok (Thailand). Principal Regional Office for Asia and the Pacific.

    This document consists of the two issues of the bi-annual Population Education Accessions list, an output from a computerized bibliographic database. The first issue lists the entries from January to June, and the second issue lists the entries from July to December. The issues categorize the total of 387 entries into four parts. Part I,…

  10. Eco-evolutionary feedbacks can rescue cooperation in microbial populations

    PubMed Central

    Moreno-Fenoll, Clara; Cavaliere, Matteo; Martínez-García, Esteban; Poyatos, Juan F.

    2017-01-01

    Bacterial populations whose growth depends on the cooperative production of public goods are usually threatened by the rise of cheaters that do not contribute but just consume the common resource. Minimizing cheater invasions appears then as a necessary mechanism to maintain these populations. However, that invasions result instead in the persistence of cooperation is a prospect that has yet remained largely unexplored. Here, we show that the demographic collapse induced by cheaters in the population can actually contribute to the rescue of cooperation, in a clear illustration of how ecology and evolution can influence each other. The effect is made possible by the interplay between spatial constraints and the essentiality of the shared resource. We validate this result by carefully combining theory and experiments, with the engineering of a synthetic bacterial community in which the public compound allows survival to a lethal stress. The characterization of the experimental system identifies additional factors that can matter, like the impact of the lag phase on the tolerance to stress, or the appearance of spontaneous mutants. Our work explains the unanticipated dynamics that eco-evolutionary feedbacks can generate in microbial communities, feedbacks that reveal fundamental for the adaptive change of ecosystems at all scales. PMID:28211914

  11. Characterization of Microbial Population Shifts during Sample Storage.

    PubMed

    Mills, Heath J; Reese, Brandi Kiel; Peter, Cruz St

    2012-01-01

    The objective of this study was to determine shifts in the microbial community structure and potential function based on standard Integrated Ocean Drilling Program (IODP) storage procedures for sediment cores. Standard long-term storage protocols maintain sediment temperature at 4°C for mineralogy, geochemical, and/or geotechnical analysis whereas standard microbiological sampling immediately preserves sediments at -80°C. Storage at 4°C does not take into account populations may remain active over geologic time scales at temperatures similar to storage conditions. Identification of active populations within the stored core would suggest geochemical and geophysical conditions within the core change over time. To test this potential, the metabolically active fraction of the total microbial community was characterized from IODP Expedition 325 Great Barrier Reef sediment cores prior to and following a 3-month storage period. Total RNA was extracted from complementary 2, 20, and 40 m below sea floor sediment samples, reverse transcribed to complementary DNA and then sequenced using 454 FLX sequencing technology, yielding over 14,800 sequences from the six samples. Interestingly, 97.3% of the sequences detected were associated with lineages that changed in detection frequency during the storage period including key biogeochemically relevant lineages associated with nitrogen, iron, and sulfur cycling. These lineages have the potential to permanently alter the physical and chemical characteristics of the sediment promoting misleading conclusions about the in situ biogeochemical environment. In addition, the detection of new lineages after storage increases the potential for a wider range of viable lineages within the subsurface that may be underestimated during standard community characterizations.

  12. MICROBIAL DEGRADATION OF SEVEN AMIDES BY SUSPENDED BACTERIAL POPULATIONS

    EPA Science Inventory

    Microbial transformation rate constants were determined for seven amides in natural pond water. A second-order mathematical rate expression served as the model for describing the microbial transformation. Also investigated was the relationship between the infrared spectra and the...

  13. Modeling the impact of the indigenous microbial population on the maximum population density of Salmonella on alfalfa.

    PubMed

    Rijgersberg, Hajo; Franz, Eelco; Nierop Groot, Masja; Tromp, Seth-Oscar

    2013-07-01

    Within a microbial risk assessment framework, modeling the maximum population density (MPD) of a pathogenic microorganism is important but often not considered. This paper describes a model predicting the MPD of Salmonella on alfalfa as a function of the initial contamination level, the total count of the indigenous microbial population, the maximum pathogen growth rate and the maximum population density of the indigenous microbial population. The model is parameterized by experimental data describing growth of Salmonella on sprouting alfalfa seeds at inoculum size, native microbial load and Pseudomonas fluorescens 2-79. The obtained model fits well to the experimental data, with standard errors less than ten percent of the fitted average values. The results show that the MPD of Salmonella is not only dictated by performance characteristics of Salmonella but depends on the characteristics of the indigenous microbial population like total number of cells and its growth rate. The model can improve the predictions of microbiological growth in quantitative microbial risk assessments. Using this model, the effects of preventive measures to reduce pathogenic load and a concurrent effect on the background population can be better evaluated. If competing microorganisms are more sensitive to a particular decontamination method, a pathogenic microorganism may grow faster and reach a higher level. More knowledge regarding the effect of the indigenous microbial population (size, diversity, composition) of food products on pathogen dynamics is needed in order to make adequate predictions of pathogen dynamics on various food products.

  14. Microbial Population of Feedlot Waste and Associated Sites

    PubMed Central

    Rhodes, R. A.; Hrubant, G. R.

    1972-01-01

    A quantitative determination was made every 2 months for a year of the microflora of beef cattle waste and runoff at a medium-sized midwestern feedlot. Counts were obtained for selected groups of organisms in waste taken from paved areas of pens cleaned daily and, therefore, reflect the flora of raw waste. Overall, in terms of viable count per gram dry weight, the feedlot waste contained 1010 total organisms, 109 anaerobes, 108 gram-negative bacteria, 107 coliforms, 106 sporeformers, and 105 yeasts, fungi, and streptomycetes. The specific numbers and pattern of these groups of organisms varied only slightly during the study in spite of a wide variation in weather. Data indicate that little microbial growth occurs in the waste as it exists in the feedlot. Runoff from the pens contained the same general population pattern but with greater variation attributable to volume of liquid. Comparable determinations of an associated field disposal area (before and after cropping), stockpiled waste, and elevated dirt areas in the pens indicate that fungi, and especially streptomycetes, are the aerobic organisms most associated with final stabilization of the waste. Yeasts, which are the dominant type of organism in the ensiled corn fed the cattle, do not occur in large numbers in the animal waste. Large ditches receiving runoff and subsurface water from the fields have a population similar to the runoff but with fewer coliforms. PMID:16349931

  15. Microbial Character Related Sulfur Cycle under Dynamic Environmental Factors Based on the Microbial Population Analysis in Sewerage System

    PubMed Central

    Dong, Qian; Shi, Hanchang; Liu, Yanchen

    2017-01-01

    The undesired sulfur cycle derived by microbial population can ultimately causes the serious problems of sewerage systems. However, the microbial community characters under dynamic environment factors in actual sewerage system is still not enough. This current study aimed to character the distributions and compositions of microbial communities that participate in the sulfur cycle under the dynamic environmental conditions in a local sewerage system. To accomplish this, microbial community compositions were assessed using 454 high-throughput sequencing (16S rDNA) combined with dsrB gene-based denaturing gradient gel electrophoresis. The results indicated that a higher diversity of microbial species was present at locations in sewers with high concentrations of H2S. Actinobacteria and Proteobacteria were dominant in the sewerage system, while Actinobacteria alone were dominant in regions with high concentrations of H2S. Specifically, the unique operational taxonomic units could aid to characterize the distinct microbial communities within a sewerage manhole. The proportion of sulfate-reducing bacteria, each sulfur-oxidizing bacteria (SOB) were strongly correlated with the liquid parameters (DO, ORP, COD, Sulfide, NH3-N), while the Mycobacterium and Acidophilic SOB (M&A) was strongly correlated with gaseous factors within the sewer, such as H2S, CH4, and CO. Identifying the distributions and proportions of critical microbial communities within sewerage systems could provide insights into how the microbial sulfur cycle is affected by the dynamic environmental conditions that exist in sewers and might be useful for explaining the potential sewerage problems. PMID:28261160

  16. Feedback between Population and Evolutionary Dynamics Determines the Fate of Social Microbial Populations

    PubMed Central

    Sanchez, Alvaro; Gore, Jeff

    2013-01-01

    The evolutionary spread of cheater strategies can destabilize populations engaging in social cooperative behaviors, thus demonstrating that evolutionary changes can have profound implications for population dynamics. At the same time, the relative fitness of cooperative traits often depends upon population density, thus leading to the potential for bi-directional coupling between population density and the evolution of a cooperative trait. Despite the potential importance of these eco-evolutionary feedback loops in social species, they have not yet been demonstrated experimentally and their ecological implications are poorly understood. Here, we demonstrate the presence of a strong feedback loop between population dynamics and the evolutionary dynamics of a social microbial gene, SUC2, in laboratory yeast populations whose cooperative growth is mediated by the SUC2 gene. We directly visualize eco-evolutionary trajectories of hundreds of populations over 50–100 generations, allowing us to characterize the phase space describing the interplay of evolution and ecology in this system. Small populations collapse despite continual evolution towards increased cooperative allele frequencies; large populations with a sufficient number of cooperators “spiral” to a stable state of coexistence between cooperator and cheater strategies. The presence of cheaters does not significantly affect the equilibrium population density, but it does reduce the resilience of the population as well as its ability to adapt to a rapidly deteriorating environment. Our results demonstrate the potential ecological importance of coupling between evolutionary dynamics and the population dynamics of cooperatively growing organisms, particularly in microbes. Our study suggests that this interaction may need to be considered in order to explain intraspecific variability in cooperative behaviors, and also that this feedback between evolution and ecology can critically affect the demographic fate

  17. Self-Driven Jamming of Growing Microbial Populations

    NASA Astrophysics Data System (ADS)

    Schreck, Carl; Delarue, Morgan; Gneiwek, Pawel; Hallatschek, Oskar

    When cells grow in confined spaces, they assemble into dense populations that interact both chemically and physically. Although in recent years scientists have uncovered a previously hidden layer of mechanical regulation in mammalian tissues that impacts gene expression and development, little is known about the consequences of mechanical constraints on single-celled microbes. This is largely due to a lack of appropriate culturing techniques and accurate computational models. Using physically explicit computer models that are developed alongside microfluidic experiments, we address two fundamental questions: (1) what structures self-assemble in confined geometries due to the cell growth and division process? and (2) how do those structures and associated stresses feed back on to cell physiology? We find that microbial growth in confinement can lead to jamming, heterogeneous stress fields, and intermittent flow that in turn result in spatially and temporally heterogeneous physiological responses. With computer simulations, we further explore the differences between this 'active' flow that is driven internally by cell growth and 'inactive' flow, such as shear and hopper flow, that is driven externally.

  18. Evaluating digestion efficiency in full-scale anaerobic digesters by identifying active microbial populations through the lens of microbial activity

    NASA Astrophysics Data System (ADS)

    Mei, Ran; Narihiro, Takashi; Nobu, Masaru K.; Kuroda, Kyohei; Liu, Wen-Tso

    2016-09-01

    Anaerobic digestion is a common technology to biologically stabilize wasted solids produced in municipal wastewater treatment. Its efficiency is usually evaluated by calculating the reduction in volatile solids, which assumes no biomass growth associated with digestion. To determine whether this assumption is valid and further evaluate digestion efficiency, this study sampled 35 digester sludge from different reactors at multiple time points together with the feed biomass in a full-scale water reclamation plant at Chicago, Illinois. The microbial communities were characterized using Illumina sequencing technology based on 16S rRNA and 16S rRNA gene (rDNA). 74 core microbial populations were identified and represented 58.7% of the entire digester community. Among them, active populations were first identified using the ratio of 16S rRNA and 16S rDNA (rRNA/rDNA) for individual populations, but this approach failed to generate consistent results. Subsequently, a recently proposed mass balance model was applied to calculate the specific growth rate (μ), and this approach successfully identified active microbial populations in digester (positive μ) that could play important roles than those with negative μ. It was further estimated that 82% of microbial populations in the feed sludge were digested in comparison with less than 50% calculated using current equations.

  19. Evaluating digestion efficiency in full-scale anaerobic digesters by identifying active microbial populations through the lens of microbial activity

    PubMed Central

    Mei, Ran; Narihiro, Takashi; Nobu, Masaru K.; Kuroda, Kyohei; Liu, Wen-Tso

    2016-01-01

    Anaerobic digestion is a common technology to biologically stabilize wasted solids produced in municipal wastewater treatment. Its efficiency is usually evaluated by calculating the reduction in volatile solids, which assumes no biomass growth associated with digestion. To determine whether this assumption is valid and further evaluate digestion efficiency, this study sampled 35 digester sludge from different reactors at multiple time points together with the feed biomass in a full-scale water reclamation plant at Chicago, Illinois. The microbial communities were characterized using Illumina sequencing technology based on 16S rRNA and 16S rRNA gene (rDNA). 74 core microbial populations were identified and represented 58.7% of the entire digester community. Among them, active populations were first identified using the ratio of 16S rRNA and 16S rDNA (rRNA/rDNA) for individual populations, but this approach failed to generate consistent results. Subsequently, a recently proposed mass balance model was applied to calculate the specific growth rate (μ), and this approach successfully identified active microbial populations in digester (positive μ) that could play important roles than those with negative μ. It was further estimated that 82% of microbial populations in the feed sludge were digested in comparison with less than 50% calculated using current equations. PMID:27666090

  20. Molecular Characterization of Swine Manure Lagoon Microbial and Antibiotic Resistant Populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: The differences in swine manure lagoon effluent based on differing management styles or approaches such as different stages of swine rearing determines the presence of variable antibiotic resistance determinants and functional microbial populations. These concerns determine the suitabil...

  1. Ileal and cecal microbial populations in broilers given specific essential oil blends and probiotics in two consecutive grow-outs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Digestive microbial populations (MP) are key components for sustained healthy broiler production. Specific essential oil (EO) blends and probiotics used as feed additives have shown to promote healthy digestive microbials, resulting in improved poultry production. Two consecutive experiments were ...

  2. MICROBIAL POPULATION CHANGES DURING BIOREMEDIATION OF AN EXPERIMENTAL OIL SPILL

    EPA Science Inventory

    Three crude oil bioremediation techniques were applied in a randomized block field experiment simulating a coastal oil-spill. Four treatments (no oil control, oil alone, oil + nutrients, and oil + nutrients + an indigenous inoculum) were applied. In-situ microbial community str...

  3. Ecological perspectives on synthetic biology: insights from microbial population biology

    PubMed Central

    Escalante, Ana E.; Rebolleda-Gómez, María; Benítez, Mariana; Travisano, Michael

    2015-01-01

    The metabolic capabilities of microbes are the basis for many major biotechnological advances, exploiting microbial diversity by selection or engineering of single strains. However, there are limits to the advances that can be achieved with single strains, and attention has turned toward the metabolic potential of consortia and the field of synthetic ecology. The main challenge for the synthetic ecology is that consortia are frequently unstable, largely because evolution by constituent members affects their interactions, which are the basis of collective metabolic functionality. Current practices in modeling consortia largely consider interactions as fixed circuits of chemical reactions, which greatly increases their tractability. This simplification comes at the cost of essential biological realism, stripping out the ecological context in which the metabolic actions occur and the potential for evolutionary change. In other words, evolutionary stability is not engineered into the system. This realization highlights the necessity to better identify the key components that influence the stable coexistence of microorganisms. Inclusion of ecological and evolutionary principles, in addition to biophysical variables and stoichiometric modeling of metabolism, is critical for microbial consortia design. This review aims to bring ecological and evolutionary concepts to the discussion on the stability of microbial consortia. In particular, we focus on the combined effect of spatial structure (connectivity of molecules and cells within the system) and ecological interactions (reciprocal and non-reciprocal) on the persistence of microbial consortia. We discuss exemplary cases to illustrate these ideas from published studies in evolutionary biology and biotechnology. We conclude by making clear the relevance of incorporating evolutionary and ecological principles to the design of microbial consortia, as a way of achieving evolutionarily stable and sustainable systems. PMID

  4. Ecological perspectives on synthetic biology: insights from microbial population biology.

    PubMed

    Escalante, Ana E; Rebolleda-Gómez, María; Benítez, Mariana; Travisano, Michael

    2015-01-01

    The metabolic capabilities of microbes are the basis for many major biotechnological advances, exploiting microbial diversity by selection or engineering of single strains. However, there are limits to the advances that can be achieved with single strains, and attention has turned toward the metabolic potential of consortia and the field of synthetic ecology. The main challenge for the synthetic ecology is that consortia are frequently unstable, largely because evolution by constituent members affects their interactions, which are the basis of collective metabolic functionality. Current practices in modeling consortia largely consider interactions as fixed circuits of chemical reactions, which greatly increases their tractability. This simplification comes at the cost of essential biological realism, stripping out the ecological context in which the metabolic actions occur and the potential for evolutionary change. In other words, evolutionary stability is not engineered into the system. This realization highlights the necessity to better identify the key components that influence the stable coexistence of microorganisms. Inclusion of ecological and evolutionary principles, in addition to biophysical variables and stoichiometric modeling of metabolism, is critical for microbial consortia design. This review aims to bring ecological and evolutionary concepts to the discussion on the stability of microbial consortia. In particular, we focus on the combined effect of spatial structure (connectivity of molecules and cells within the system) and ecological interactions (reciprocal and non-reciprocal) on the persistence of microbial consortia. We discuss exemplary cases to illustrate these ideas from published studies in evolutionary biology and biotechnology. We conclude by making clear the relevance of incorporating evolutionary and ecological principles to the design of microbial consortia, as a way of achieving evolutionarily stable and sustainable systems.

  5. Oxygen Effects on Thermophilic Microbial Populations in Biofilters Treating Nitric Oxide Containing Off-Gas Streams

    SciTech Connect

    Lee, Brady Douglas; Apel, William Arnold; Smith, William Aaron

    2004-04-01

    Electricity generation from coal has increased by an average of 51 billion kWh per year over the past 3 years. For this reason cost-effective strategies to control nitrogen oxides (NOx) from coal-fired power plant combustion gases must be developed. Compost biofilters operated at 55°C at an empty bed contact time (EBCT) of 13 seconds were shown to be feasible for removal of nitric oxide (NO) from synthetic flue gas. Denitrifying microbial populations in these biofilters were shown to reduce influent NO feeds by 90 to 95% at inlet NO concentrations of 500 ppmv. Oxygen was shown to have a significant effect on the NO removal efficiency demonstrated by these biofilters. Two biofilters were set up under identical conditions for the purpose of monitoring NO removal as well as changes in the microbial population in the bed medium under anaerobic and aerobic conditions. Changes in the microbial population were monitored to determine the maximum oxygen tolerance of a denitrifying biofilter as well as methods of optimizing microbial populations capable of denitrification in the presence of low oxygen concentrations. Nitric oxide removal dropped to between 10 and 20% when oxygen was present in the influent stream. The inactive compost used to pack the biofilters may have also caused the decreased NO removal efficiency compared to previous biofiltration experiments. Analysis of the bed medium microbial population using environmental scanning electron microscopy indicated significant increases in biomass populating the surface of the compost when compared to unacclimated compost.

  6. Linking temperature sensitivity of soil organic matter decomposition to its molecular structure, accessibility, and microbial physiology.

    PubMed

    Wagai, Rota; Kishimoto-Mo, Ayaka W; Yonemura, Seiichiro; Shirato, Yasuhito; Hiradate, Syuntaro; Yagasaki, Yasumi

    2013-04-01

    Temperature sensitivity of soil organic matter (SOM) decomposition may have a significant impact on global warming. Enzyme-kinetic hypothesis suggests that decomposition of low-quality substrate (recalcitrant molecular structure) requires higher activation energy and thus has greater temperature sensitivity than that of high-quality, labile substrate. Supporting evidence, however, relies largely on indirect indices of substrate quality. Furthermore, the enzyme-substrate reactions that drive decomposition may be regulated by microbial physiology and/or constrained by protective effects of soil mineral matrix. We thus tested the kinetic hypothesis by directly assessing the carbon molecular structure of low-density fraction (LF) which represents readily accessible, mineral-free SOM pool. Using five mineral soil samples of contrasting SOM concentrations, we conducted 30-days incubations (15, 25, and 35 °C) to measure microbial respiration and quantified easily soluble C as well as microbial biomass C pools before and after the incubations. Carbon structure of LFs (<1.6 and 1.6-1.8 g cm(-3) ) and bulk soil was measured by solid-state (13) C-NMR. Decomposition Q10 was significantly correlated with the abundance of aromatic plus alkyl-C relative to O-alkyl-C groups in LFs but not in bulk soil fraction or with the indirect C quality indices based on microbial respiration or biomass. The warming did not significantly change the concentration of biomass C or the three types of soluble C despite two- to three-fold increase in respiration. Thus, enhanced microbial maintenance respiration (reduced C-use efficiency) especially in the soils rich in recalcitrant LF might lead to the apparent equilibrium between SOM solubilization and microbial C uptake. Our results showed physical fractionation coupled with direct assessment of molecular structure as an effective approach and supported the enzyme-kinetic interpretation of widely observed C quality-temperature relationship for

  7. Transcriptome analysis of a microbial coculture in which the cell populations are separated by a membrane.

    PubMed

    Hosoda, Kazufumi; Ono, Naoaki; Suzuki, Shingo; Yomo, Tetsuya

    2014-01-01

    The microbial coculture of multiple cell populations is used to study community evolution and for bioengineering applications. The cells in coculture undergo dynamic changes because of cell-cell and cell-environment interactions. Transcriptome analysis allows us to study the molecular basis of these changes in cell physiology. For transcriptome analysis, it is essential that the cell populations in the coculture are harvested separately. Here, we describe a method for transcriptome analysis of a microbial coculture in which two different cell populations are separated by a porous membrane.

  8. Mechanism for microbial population collapse in a fluctuating resource environment.

    PubMed

    Turkarslan, Serdar; Raman, Arjun V; Thompson, Anne W; Arens, Christina E; Gillespie, Mark A; von Netzer, Frederick; Hillesland, Kristina L; Stolyar, Sergey; López García de Lomana, Adrian; Reiss, David J; Gorman-Lewis, Drew; Zane, Grant M; Ranish, Jeffrey A; Wall, Judy D; Stahl, David A; Baliga, Nitin S

    2017-03-20

    Managing trade-offs through gene regulation is believed to confer resilience to a microbial community in a fluctuating resource environment. To investigate this hypothesis, we imposed a fluctuating environment that required the sulfate-reducer Desulfovibrio vulgaris to undergo repeated ecologically relevant shifts between retaining metabolic independence (active capacity for sulfate respiration) and becoming metabolically specialized to a mutualistic association with the hydrogen-consuming Methanococcus maripaludis Strikingly, the microbial community became progressively less proficient at restoring the environmentally relevant physiological state after each perturbation and most cultures collapsed within 3-7 shifts. Counterintuitively, the collapse phenomenon was prevented by a single regulatory mutation. We have characterized the mechanism for collapse by conducting RNA-seq analysis, proteomics, microcalorimetry, and single-cell transcriptome analysis. We demonstrate that the collapse was caused by conditional gene regulation, which drove precipitous decline in intracellular abundance of essential transcripts and proteins, imposing greater energetic burden of regulation to restore function in a fluctuating environment.

  9. Integral structural-functional method for characterizing microbial populations

    NASA Astrophysics Data System (ADS)

    Yakushev, A. V.

    2015-04-01

    An original integral structural-functional method has been proposed for characterizing microbial communities. The novelty of the approach is the in situ study of microorganisms based on the growth kinetics of microbial associations in liquid nutrient broth media under selective conditions rather than on the level of taxa or large functional groups. The method involves the analysis of the integral growth model of a periodic culture. The kinetic parameters of such associations reflect their capacity of growing on different media, i.e., their physiological diversity, and the metabolic capacity of the microorganisms for growth on a nutrient medium. Therefore, the obtained parameters are determined by the features of the microbial ecological strategies. The inoculation of a dense medium from the original inoculate allows characterizing the taxonomic composition of the dominants in the soil community. The inoculation from the associations developed on selective media characterizes the composition of syntrophic groups, which fulfill a specific function in nature. This method is of greater information value than the classical methods of inoculation on selective media.

  10. Soil ventilation: Effects on microbial populations in gasoline-contaminated subsurface soils

    SciTech Connect

    Hickey, W.J.

    1995-07-01

    Short- and long-term effects of vapor extraction (VE) in an unsaturated subsurface soil and in situ biodegradation of gasoline were evaluated in a field study. Subsurface temperature, moisture, solid- and gas-phase contaminant levels, atmospheric gases, nutrient levels, and microbial population densities were measured during and after soil VE for 462 d. Microbial activity, based on in situ O{sub 2} consumption rates, measured 7 d after VE started averaged 3.8% O{sub 2} d{sup -1}; by Day 62 these rates dropped to 0.2% O{sub 2} d{sup -1}. Soil VE was stopped on Day 180 and about 70 d elapsed before renewed, low-level (0.05% O{sub 2} d{sup -1}) activity was detectable. Following a second round of VE, average O{sub 2} consumption rates increased to 0.11% O{sub 2} d{sup -1}. Microbial population densities did not consistently reflect activity changes measured by O{sub 2} consumption. Activity increases in the latter part of the study were not adequately accounted for by changes in subsurface moisture levels, temperature, or contaminant vapor concentrations. At the study`s completion, 400 kg of gasoline was volatilized from the soil and another 139 kg estimated to be biodegraded in situ. A two-phase process is proposed to account for the effects of VE on microbial activity. The initial phase is characterized by declining microbial activity levels in response to substrate reduction. Microbial activity slowly increases as a result of interactions between gasoline vapor concentrations and possibly changes in degradative activities of the microbial population. More work is needed to identify the gasoline constituents serving as substrates for microbial populations before and after ventilation. 31 refs., 8 figs., 5 tabs.

  11. [Formation of microbial populations on the surface of protective coatings].

    PubMed

    Kopteva, Zh P; Zanina, V V; Piliashenko-Novokhatnyĭ, A I; Kopteva, A E; Kozlova, I A

    2001-01-01

    Formation of microbial cenosis on the surface of polyethylene-, polyurethane- and oil-bitumen-based protective coatings was studied in dynamics during 1, 3, 7, 14 and 21 days. It has been shown that the biofilm was formed on the protective materials during 14 days and consisted of ammonifying, denitrifying, hydrocarbon-oxidizing and sulphate-reducing bacteria referred to Pseudomonas, Arthrobacter, Bacillus and Kesulfovibrio genera. The bacteria which form the biofilm on coatings possess high denitrifying and sulphate-reducing activities. Corrosion inhibitors-biocydes, introduced in composition of oil-bitumen coatings suppressed growth and metabolic activity of corrosion-active bacteria.

  12. The Biodiversity Changes in the Microbial Population of Soils Contaminated with Crude Oil.

    PubMed

    Abbasian, Firouz; Lockington, Robin; Megharaj, Mallavarapu; Naidu, Ravi

    2016-06-01

    Crude oil spills resulting from excavation, transportation and downstream processes can cause intensive damage to living organisms and result in changes in the microbial population of that environment. In this study, we used a pyrosequencing analysis to investigate changes in the microbial population of soils contaminated with crude oil. Crude oil contamination in soil resulted in the creation of a more homogenous population of microorganisms dominated by members of the Actinomycetales, Clostridiales and Bacillales (all belonging to Gram-positive bacteria) as well as Flavobacteriales, Pseudomonadales, Burkholderiales, Rhizobiales and Sphingomonadales (all belonging to Gram-negative bacteria). These changes in the biodiversity decreased the ratios of chemoheterotrophic bacteria at higher concentrations of crude oil contamination, with these being replaced by photoheterotrophic bacteria, mainly Rhodospirillales. Several of the dominant microbial orders in the crude oil contaminated soils are able to degrade crude oil hydrocarbons and therefore are potentially useful for remediation of crude oil in contaminated sites.

  13. Large-scale distribution of microbial and viral populations in the South Atlantic Ocean.

    PubMed

    De Corte, Daniele; Sintes, Eva; Yokokawa, Taichi; Lekunberri, Itziar; Herndl, Gerhard J

    2016-04-01

    Viruses are abundant, diverse and dynamic components of the marine environments and play a significant role in the ocean biogeochemical cycles. To assess potential variations in the relation between viruses and microbes in different geographic regions and depths, viral and microbial abundance and production were determined throughout the water column along a latitudinal transect in the South Atlantic Ocean. Path analysis was used to examine the relationships between several abiotic and biotic parameters and the different microbial and viral populations distinguished by flow cytometry. The depth-integrated contribution of microbial and viral abundance to the total microbial and viral biomass differed significantly among the different provinces. Additionally, the virus-to-microbe ratio increased with depth and decreased laterally towards the more productive regions. Our data revealed that the abundance of phytoplankton and microbes is the main controlling factor of the viral populations in the euphotic and mesopelagic layers, whereas in the bathypelagic realm, viral abundance was only weakly related to the biotic and abiotic variables. The relative contribution of the three viral populations distinguished by flow cytometry showed a clear geographical pattern throughout the water column, suggesting that these populations are composed of distinct taxa able to infect specific hosts. Overall, our data indicate the presence of distinct microbial patterns along the latitudinal transect. This variability is not limited to the euphotic layer but also detectable in the meso- and bathypelagic layers.

  14. Large‐scale distribution of microbial and viral populations in the South Atlantic Ocean

    PubMed Central

    Sintes, Eva; Yokokawa, Taichi; Lekunberri, Itziar; Herndl, Gerhard J.

    2016-01-01

    Summary Viruses are abundant, diverse and dynamic components of the marine environments and play a significant role in the ocean biogeochemical cycles. To assess potential variations in the relation between viruses and microbes in different geographic regions and depths, viral and microbial abundance and production were determined throughout the water column along a latitudinal transect in the South Atlantic Ocean. Path analysis was used to examine the relationships between several abiotic and biotic parameters and the different microbial and viral populations distinguished by flow cytometry. The depth‐integrated contribution of microbial and viral abundance to the total microbial and viral biomass differed significantly among the different provinces. Additionally, the virus‐to‐microbe ratio increased with depth and decreased laterally towards the more productive regions. Our data revealed that the abundance of phytoplankton and microbes is the main controlling factor of the viral populations in the euphotic and mesopelagic layers, whereas in the bathypelagic realm, viral abundance was only weakly related to the biotic and abiotic variables. The relative contribution of the three viral populations distinguished by flow cytometry showed a clear geographical pattern throughout the water column, suggesting that these populations are composed of distinct taxa able to infect specific hosts. Overall, our data indicate the presence of distinct microbial patterns along the latitudinal transect. This variability is not limited to the euphotic layer but also detectable in the meso‐ and bathypelagic layers. PMID:26765966

  15. Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation.

    PubMed Central

    Borneman, J; Triplett, E W

    1997-01-01

    Although the Amazon Basin is well known for its diversity of flora and fauna, this report represents the first description of the microbial diversity in Amazonian soils involving a culture-independent approach. Among the 100 sequences of genes coding for small-subunit rRNA obtained by PCR amplification with universal small-subunit rRNA primers, 98 were bacterial and 2 were archaeal. No duplicate sequences were found, and none of the sequences had been previously described. Eighteen percent of the bacterial sequences could not be classified in any known bacterial kingdom. Two sequences may represent a unique branch between the vast majority of bacteria and the deeply branching, predominantly thermophilic bacteria. Five sequences formed a clade that may represent a novel group within the class Proteobacteria. In addition, rRNA intergenic spacer analysis was used to show significant microbial population differences between a mature forest soil and an adjacent pasture soil. PMID:9212415

  16. A two-population bio-electrochemical model of a microbial fuel cell.

    PubMed

    Pinto, R P; Srinivasan, B; Manuel, M-F; Tartakovsky, B

    2010-07-01

    This work presents a two-population model describing the competition of anodophilic and methanogenic microbial populations for a common substrate in a microbial fuel cell (MFC). Fast numerical solution of the model is provided by using ordinary differential equations to describe biomass growth and retention in the anodic compartment. The model parameters are estimated and validated using experimental results obtained in four continuous-flow air-cathode MFCs operated at various external resistances and organic loads. Model analysis demonstrates the influence of operating conditions on MFC performance and suggests ways to maximize MFC power output. The model is suitable both for process optimization and on-line control applications.

  17. Suppression of Beneficial Mutations in Dynamic Microbial Populations

    NASA Astrophysics Data System (ADS)

    Bittihn, Philip; Hasty, Jeff; Tsimring, Lev S.

    2017-01-01

    Quantitative predictions for the spread of mutations in bacterial populations are essential to interpret evolution experiments and to improve the stability of synthetic gene circuits. We derive analytical expressions for the suppression factor for beneficial mutations in populations that undergo periodic dilutions, covering arbitrary population sizes, dilution factors, and growth advantages in a single stochastic model. We find that the suppression factor grows with the dilution factor and depends nontrivially on the growth advantage, resulting in the preferential elimination of mutations with certain growth advantages. We confirm our results by extensive numerical simulations.

  18. Milankovitch-scale correlations between deeply-buried microbial populations and biogenic ooze lithology

    NASA Astrophysics Data System (ADS)

    Aiello, I. W.; Bekins, B.

    2008-12-01

    Active populations of buried microbes are unevenly distributed in the sub-seafloor of the world's ocean. Globally, the rates of microbial activity in the sub-seafloor of open-ocean, oligotrophic basins are much lower than in ocean-margin eutrophic basins. Variations of cell abundances and metabolic activity are often independent from sediment depths with increased prokaryotic activity at geochemical and/or sedimentary interfaces. At the scale of lithologic units, higher microbial activity has been detected in units with abundant diatom ooze. Given these broad-scale relationships between paleoceanography and sub-seafloor microbial life it is plausible that variations in microbial populations at scales finer than lithologic units may also occur, if properties, such as organic carbon (OC), porosity, or solid-phase electron acceptors, vary within individual beds. In this study we demonstrate that microbial populations vary at the scale of individual beds in the biogenic oozes of a drill site in the eastern equatorial Pacific (Ocean Drilling Program Leg 201, Site 1226). We relate bedding-scale changes in biogenic ooze sediment composition to OC and microbial cell concentrations using high-resolution color reflectance data as proxy for lithology. Our analyses demonstrate that microbial concentrations are larger by an order of magnitude in the more organic-rich diatom oozes than in the nannofossil oozes. The variations mimic small-scale variations in diatom abundance and OC indicating that the modern distribution of microbial biomass is ultimately controlled by Milankovitch-frequency variations in past oceanographic conditions. Because OC becomes more refractory with depth, bedding-scale differences in OC and microbial concentrations are no longer apparent below 200 meters below seafloor (mbsf). The evidence presented in this study suggests that future microbiology sampling schemes that account for small- scale lithologic variations should be part of the study design

  19. Genetic Diversity Affects the Daily Transcriptional Oscillations of Marine Microbial Populations

    PubMed Central

    Shilova, Irina N.; Robidart, Julie C.; DeLong, Edward F.; Zehr, Jonathan P.

    2016-01-01

    Marine microbial communities are genetically diverse but have robust synchronized daily transcriptional patterns at the genus level that are similar across a wide variety of oceanic regions. We developed a microarray-inspired gene-centric approach to resolve transcription of closely-related but distinct strains/ecotypes in high-throughput sequence data. Applying this approach to the existing metatranscriptomics datasets collected from two different oceanic regions, we found unique and variable patterns of transcription by individual taxa within the abundant picocyanobacteria Prochlorococcus and Synechococcus, the alpha Proteobacterium Pelagibacter and the eukaryotic picophytoplankton Ostreococcus. The results demonstrate that marine microbial taxa respond differentially to variability in space and time in the ocean. These intra-genus individual transcriptional patterns underlie whole microbial community responses, and the approach developed here facilitates deeper insights into microbial population dynamics. PMID:26751368

  20. Genetic Diversity Affects the Daily Transcriptional Oscillations of Marine Microbial Populations.

    PubMed

    Shilova, Irina N; Robidart, Julie C; DeLong, Edward F; Zehr, Jonathan P

    2016-01-01

    Marine microbial communities are genetically diverse but have robust synchronized daily transcriptional patterns at the genus level that are similar across a wide variety of oceanic regions. We developed a microarray-inspired gene-centric approach to resolve transcription of closely-related but distinct strains/ecotypes in high-throughput sequence data. Applying this approach to the existing metatranscriptomics datasets collected from two different oceanic regions, we found unique and variable patterns of transcription by individual taxa within the abundant picocyanobacteria Prochlorococcus and Synechococcus, the alpha Proteobacterium Pelagibacter and the eukaryotic picophytoplankton Ostreococcus. The results demonstrate that marine microbial taxa respond differentially to variability in space and time in the ocean. These intra-genus individual transcriptional patterns underlie whole microbial community responses, and the approach developed here facilitates deeper insights into microbial population dynamics.

  1. Microbial strain-level population structure and genetic diversity from metagenomes

    PubMed Central

    Tett, Adrian

    2017-01-01

    Among the human health conditions linked to microbial communities, phenotypes are often associated with only a subset of strains within causal microbial groups. Although it has been critical for decades in microbial physiology to characterize individual strains, this has been challenging when using culture-independent high-throughput metagenomics. We introduce StrainPhlAn, a novel metagenomic strain identification approach, and apply it to characterize the genetic structure of thousands of strains from more than 125 species in more than 1500 gut metagenomes drawn from populations spanning North and South American, European, Asian, and African countries. The method relies on per-sample dominant sequence variant reconstruction within species-specific marker genes. It identified primarily subject-specific strain variants (<5% inter-subject strain sharing), and we determined that a single strain typically dominated each species and was retained over time (for >70% of species). Microbial population structure was correlated in several distinct ways with the geographic structure of the host population. In some cases, discrete subspecies (e.g., for Eubacterium rectale and Prevotella copri) or continuous microbial genetic variations (e.g., for Faecalibacterium prausnitzii) were associated with geographically distinct human populations, whereas few strains occurred in multiple unrelated cohorts. We further estimated the genetic variability of gut microbes, with Bacteroides species appearing remarkably consistent (0.45% median number of nucleotide variants between strains), whereas P. copri was among the most plastic gut colonizers. We thus characterize here the population genetics of previously inaccessible intestinal microbes, providing a comprehensive strain-level genetic overview of the gut microbial diversity. PMID:28167665

  2. Controls upon microbial accessibility to soil organic matter following woody plant encroachment into grasslands

    NASA Astrophysics Data System (ADS)

    Creamer, C. A.; Boutton, T. W.; Filley, T. R.

    2009-12-01

    Woody plant encroachment (WPE) into savannas and grasslands is a global phenomenon that alters soil organic matter (SOM) dynamics through changes in litter quality and quantity, soil structure, microbial ecology, and soil hydrology. To elucidate the controls upon microbial accessibility to SOM, bulk soils from a chronosequence of progressive WPE into native grasslands at the Texas A&M Agricultural Experimental Station La Copita Research Area were incubated for one year. The quantity and stable carbon isotope composition of respired CO2, plant biopolymer chemistry in SOM, and microbial community structure were tracked. Respiration rates declined steadily over the course of the experiment with 15-25% of the total CO2 respired released in the first month of incubation. Between 8 and 18% of the total carbon was mineralized to CO2 throughout the incubation. After day 84 a significantly (p < 0.05) greater portion of carbon was mineralized from soils of older woody clusters (34-86 years) than from soils of younger clusters (14-23 years) and the native grassland. Approximately 80% of patterns seen in cumulative CO2 loss could be explained by the proportions of macro- and micro-aggregates within each soil, suggesting soil structure is a major controlling factor of respiration rates. Despite documented carbon accrual within La Copita soils due to WPE, we observed no evidence of enhanced carbon stabilization in these respiration experiments. In fact, a greater proportion of total carbon was lost from the soil of mature woody stands than from young stands, suggesting carbon accumulation observed with WPE may be due to greater input rates or microbial dynamics not captured in the laboratory incubation. A cluster approximately 34 years in age represents a transition point in WPE where respiration dynamics become distinct between grassland and wooded elements. By day 84 of the incubation CO2 respired from all soils was depleted with respect to bulk SOM (1.5 to 5‰) and this

  3. Assessment of microbial populations dynamics in a blue cheese by culturing and denaturing gradient gel electrophoresis.

    PubMed

    Alegría, Angel; González, Renata; Díaz, Mario; Mayo, Baltasar

    2011-03-01

    The composition and development of microbial population during the manufacture and ripening of two batches of a blue-veined cheese was examined by culturing and polymerase chain reaction (PCR) denaturing gradient gel electrophoresis (DGGE) (PCR-DGGE). Nine selective and/or differential media were used to track the cultivable populations of total and indicator microbial groups. For PCR-DGGE, the V3 hyper variable region of the bacterial 16S rRNA gene and the eukaryotic D1 domain of 28S rDNA were amplified with universal primers, specific for prokaryotes and eukaryotes, respectively. Similarities and differences between the results obtained by the culturing and the molecular method were recorded for some populations. Culturing analysis allows minority microbial groups (coliforms, staphylococci) to be monitored, although in this study PCR-DGGE identified a population of Streptococcus thermophilus that went undetected by culturing. These results show that the characterization of the microbial populations interacting and evolving during the cheese-making process is improved by combining culturing and molecular methods.

  4. Controlling Salmonella infection in weanling pigs through water delivery of direct-fed microbials or organic acids; Part I. Effects on growth performance, microbial populations and immune status

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pigs (n=88) weaned at 19 ± 2 d of age were used in a 14 d study to evaluate the effects of water-delivered direct-fed microbials (DFM) or organic acids on immune status, Salmonella infection and shedding, and intestinal microbial populations following a Salmonella Typhimurium challenge. Pigs were ch...

  5. Aerobic Microbial Community of Insectary Population of Phlebotomus papatasi

    PubMed Central

    Maleki-Ravasan, Naseh; Oshaghi, Mohammad Ali; Hajikhani, Sara; Saeidi, Zahra; Akhavan, Amir Ahmad; Gerami-Shoar, Mohsen; Shirazi, Mohammad Hasan; Yakhchali, Bagher; Rassi, Yavar; Afshar, Davoud

    2014-01-01

    Background: Microbes particularly bacteria presenting in the gut of haematophagous insects may have an important role in the epidemiology of human infectious disease. Methods: The microbial flora of gut and surrounding environmental of a laboratory strain of Phlebotomus papatasi, the main vector of Zoonotic Cutaneous Leishmaniasis (ZCL) in the old world, was investigated. Biochemical reactions and 16s rDNA sequencing of the isolated bacteria against 24 sugars and amino acids were used for bacteria species identification. Common mycological media used for fungi identification as well. Results: Most isolates belonged to the Enterobacteriaceae, a large, heterogeneous group of gram-negative rods whose natural habitat is the intestinal tract of humans and animals. Enterobacteriaceae groups included Edwardsiella, Enterobacter, Escherichia, Klebsiella, Kluyvera, Leminorella, Pantoea, Proteus, Providencia, Rahnella, Serratia, Shigella, Tatumella, and Yersinia and non Enterobacteriaceae groups included Bacillus, Staphylococcus and Pseudomonas. The most prevalent isolates were Proteus mirabilis and P. vulgaris. These saprophytic and swarming motile bacteria were isolated from all immature, pupae, and mature fed or unfed male or female sand flies as well as from larval and adult food sources. Five fungi species were also isolated from sand flies, their food sources and colonization materials where Candida sp. was common in all mentioned sources. Conclusion: Midgut microbiota are increasingly seen as an important factor for modulating vector competence in insect vectors so their possible effects of the mirobiota on the biology of P. papatasi and their roles in the sandfly-Leishmania interaction are discussed. PMID:25629067

  6. A RESTful API for accessing microbial community data for MG-RAST

    SciTech Connect

    Wilke, Andreas; Bischof, Jared; Harrison, Travis; Brettin, Tom; D'Souza, Mark; Gerlach, Wolfgang; Matthews, Hunter; Paczian, Tobias; Wilkening, Jared; Glass, Elizabeth M.; Desai, Narayan; Meyer, Folker; Gardner, Paul P.

    2015-01-08

    Metagenomic sequencing has produced significant amounts of data in recent years. For example, as of summer 2013, MGRAST has been used to annotate over 110,000 data sets totaling over 43 Terabases. With metagenomic sequencing finding even wider adoption in the scientific community, the existing web-based analysis tools and infrastructure in MG-RAST provide limited capability for data retrieval and analysis, such as comparative analysis between multiple data sets. Moreover, although the system provides many analysis tools, it is not comprehensive. By opening MG-RAST up via a web services API (application programmers interface) we have greatly expanded access to MG-RAST data, as well as provided a mechanism for the use of third-party analysis tools with MG-RAST data. This RESTful API makes all data and data objects created by the MG-RAST pipeline accessible as JSON objects. As part of the DOE Systems Biology Knowledgebase project (KBase, http:// kbase.us) we have implemented a web services API for MG-RAST. This API complements the existing MG-RAST web interface and constitutes the basis of KBase’s microbial community capabilities. In addition, the API exposes a comprehensive collection of data to programmers. This API, which uses a RESTful (Representational State Transfer) implementation, is compatible with most programming environments and should be easy to use for end users and third parties. It provides comprehensive access to sequence data, quality control results, annotations, and many other data types. Where feasible, we have used standards to expose data and metadata. Code examples are provided in a number of languages both to show the versatility of the API and to provide a starting point for users. We present an API that exposes the data in MG-RAST for consumption by our users, greatly enhancing the utility of the MG-RAST service.

  7. A RESTful API for accessing microbial community data for MG-RAST

    DOE PAGES

    Wilke, Andreas; Bischof, Jared; Harrison, Travis; ...

    2015-01-08

    Metagenomic sequencing has produced significant amounts of data in recent years. For example, as of summer 2013, MGRAST has been used to annotate over 110,000 data sets totaling over 43 Terabases. With metagenomic sequencing finding even wider adoption in the scientific community, the existing web-based analysis tools and infrastructure in MG-RAST provide limited capability for data retrieval and analysis, such as comparative analysis between multiple data sets. Moreover, although the system provides many analysis tools, it is not comprehensive. By opening MG-RAST up via a web services API (application programmers interface) we have greatly expanded access to MG-RAST data, asmore » well as provided a mechanism for the use of third-party analysis tools with MG-RAST data. This RESTful API makes all data and data objects created by the MG-RAST pipeline accessible as JSON objects. As part of the DOE Systems Biology Knowledgebase project (KBase, http:// kbase.us) we have implemented a web services API for MG-RAST. This API complements the existing MG-RAST web interface and constitutes the basis of KBase’s microbial community capabilities. In addition, the API exposes a comprehensive collection of data to programmers. This API, which uses a RESTful (Representational State Transfer) implementation, is compatible with most programming environments and should be easy to use for end users and third parties. It provides comprehensive access to sequence data, quality control results, annotations, and many other data types. Where feasible, we have used standards to expose data and metadata. Code examples are provided in a number of languages both to show the versatility of the API and to provide a starting point for users. We present an API that exposes the data in MG-RAST for consumption by our users, greatly enhancing the utility of the MG-RAST service.« less

  8. Estimation of the Number of Microbial Species Comprising a Population

    DTIC Science & Technology

    2008-03-01

    Sample Sizes .................68 19. Minimum Sample Sizes Require to Equate Non-Parametric and Parametric Estimation Methods...63 PARAMETRIC ESTIMATION OF NUMBER OF SPECIES COMPRISING A POPULATION I. Introduction Background The current state of the environment...estimation of the number of species which are currently used include both parametric and non- parametric estimation techniques. There are advantages and

  9. IN SITU APPARENT CONDUCTIVITY MEASUREMENTS AND MICROBIAL POPULATION DISTRIBUTION AT A HYDROCARBON CONTAMINATED SITE

    EPA Science Inventory

    We investigated the bulk electrical conductivity and microbial population distribution in sediments at a site contaminated with light non-aqueous phase liquid (LNAPL). The bulk conductivity was measured using in situ vertical resistivity probes, while the most probable number met...

  10. Effects of dilution on dissolved oxygen depletion and microbial populations in the biochemical oxygen demand determination.

    PubMed

    Seo, Kyo Seong; Chang, Ho Nam; Park, Joong Kon; Choo, Kwang-Ho

    2007-09-01

    The biochemical oxygen demand (BOD) value is still a key parameter that can determine the level of organics, particularly the content of biodegradable organics in water. In this work, the effects of sample dilution, which should be done inevitably to get appropriate dissolved oxygen (DO) depletion, on the measurement of 5-day BOD (BOD(5)), was investigated with and without seeding using natural and synthetic water. The dilution effects were also evaluated for water samples taken in different seasons such as summer and winter because water temperature can cause a change in the types of microbial species, thus leading to different oxygen depletion profiles during BOD testing. The predation phenomenon between microbial cells was found to be dependent on the inorganic nutrients and carbon sources, showing a change in cell populations according to cell size after 5-day incubation. The dilution of water samples for BOD determination was linked to changes in the environment for microbial growth such as nutrition. The predation phenomenon between microbial cells was more important with less dilution. BOD(5) increased with the specific amount of inorganic nutrient per microbial mass when the natural water was diluted. When seeding was done for synthetic water samples, the seed volume also affected BOD due to the rate of organic uptake by microbes. BOD(5) increased with the specific bacterial population per organic source supplied at the beginning of BOD measurement. For more accurate BOD measurements, specific guidelines on dilution should be established.

  11. A new device for real time monitoring of microbial population dynamics during in situ and ex situ bioremediation

    SciTech Connect

    Woodward, R.E.; Malone, R.W.

    1995-12-31

    Monitoring of microbial population dynamics is an important operating parameter for successful bioremediation projects. The traditional method of plate counts or most probable number (MPN) requires 2 to 7 days for development and therefore provides a historical measurement of little real-time operational significance. Selected enzyme activity is directly proportional to microbial population density and is linear in the population range from 10{sub 4} to 10{sup 8} CFU/mL. This paper summarizes the use of this enzyme based, real-time measurement of microbial population dynamics for the management of four bioremediation projects: (1) differentiation of assimilation from nitrification during the metabolism of ammonia in an industrial waste stream, (2) treatability assessment and management of activated sludge processes during the treatment of a hazardous, petrochemical waste, (3) measurement of intrinsic microbial activity in soil cores at a spill site, and (4) non-invasive monitoring of microbial populations during in situ bioremediation of two aquifers.

  12. Population Education Accessions List. May-August 1997.

    ERIC Educational Resources Information Center

    United Nations Educational, Scientific and Cultural Organization, Bangkok (Thailand). Principal Regional Office for Asia and the Pacific.

    This annotated bibliography lists available resources that address many issues involved in population education. Entries are categorized into three parts. Part I, "Population Education," consists of titles on various aspects of population education arranged by country in the first section and by general materials in the second section.…

  13. Population Education Accessions List. January-April 1997.

    ERIC Educational Resources Information Center

    United Nations Educational, Scientific and Cultural Organization, Bangkok (Thailand). Principal Regional Office for Asia and the Pacific.

    This bibliography addresses the subject of population education. Entries are categorized into three parts. Part 1, "Population Education," consists of titles of books and other documents addressing various aspects of population education arranged by country in the first section and general materials in the second section. Part 2,…

  14. Composition of the phyllospheric microbial populations on vegetable plants with different glucosinolate and carotenoid compositions.

    PubMed

    Ruppel, Silke; Krumbein, Angelika; Schreiner, Monika

    2008-08-01

    The plant phyllosphere is intensely colonized by a complex and highly diverse microbial population and shows pronounced plant-species-specific differences. The mechanisms and influencing factors determining whether and in which density microorganisms colonize plant phyllosphere tissues are not yet fully understood. One of the key influencing factors is thought to be phytochemical concentration and composition. Therefore, correlations between various concentrations of individual glucosinolates and carotenoids in four different plant species-Brassica juncea, Brassica campestris, Cichorium endivia, and Spinacea oleracea-and the phyllospheric bacterial population size associated with the aerial parts of the same plants were analyzed. The concentration of various individual glucosinolates and carotenoids were measured using high-performance liquid chromatography. The phyllospheric bacterial population size including both nonculturable and culturable organisms was assessed using quantitative real-time polymerase chain reaction, and the physiological profile of the culturable microbial community was analyzed using the Biolog system. Results show significant differences between plant species in both concentration and composition of secondary metabolites, bacterial population size, and microbial community composition in three consecutively performed experiments. An interesting and underlying trend was that bacterial density was positively correlated to concentrations of beta-carotene in the plant phyllosphere of the four plant species examined. Likewise, the alkenyl glucosinolates, 2-propenyl, 3-butenyl, and 4-pentenyl, concentrations were positively correlated to the bacterial population density, whereas the aromatic glucosinolate 2-phenylethyl showed a negative correlation to the phyllospheric bacterial population size. Thus, we report for the first time the relationship between individual glucosinolate and carotenoid concentrations and the phyllospheric bacterial

  15. Effect of hybrid poplar trees on microbial populations important to hazardous waste bioremediation

    SciTech Connect

    Jordahl, J.L.; Foster, L.; Schnoor, J.L.; Alvarez, P.J.J.

    1997-06-01

    Microbial concentrations of denitrifiers, pseudomonads, and monoaromatic petroleum hydrocarbon (BTX) degraders were significantly higher (p < 0.1) in soil samples from the rhizosphere of poplar trees than in adjacent agricultural soils, and atrazine degraders were found only in one rhizosphere sample. The relative abundance of these phenotypes (as a fraction of total heterotrophs) was not significantly different between rhizosphere and surrounding soils. Therefore, the poplar rhizosphere enhanced the growth of microbial populations that participate in natural bioremediation without exerting selective pressure for them.

  16. Influence of combined pollution of antimony and arsenic on culturable soil microbial populations and enzyme activities.

    PubMed

    Wang, Qiongshan; He, Mengchang; Wang, Ying

    2011-01-01

    The effects of both combined and single pollution of antimony (Sb) and arsenic (As) in different concentrations on culturable soil microbial populations and enzyme activities were studied under laboratory conditions. Joint effects of both Sb and As were different from that of Sb or As alone. The inhibition rate of culturable soil microbial populations under Sb and As pollution followed the order: bacterial > fungi > actinomycetes. There existed antagonistic inhibiting effect on urease and acid phophatase and synergistic inhibiting effect on protease under the combined pollution of Sb (III) and As (III). Only urease appeared to be the most sensitive indicator under Sb (V) and As (V) pollution, and there existed antagonistic inhibiting effect on acid phophatase and synergistic inhibiting effect on urease and protease under Sb (V) and As (V) combined pollution at most time. In this study, we also confirmed that the trivalent states of Sb and As were more toxic to all the microbes tested and more inhibitory on microbial enzyme activities then their pentavalent counterparts. The results also suggest that not only the application rate of the two metalloids but also the chemical form of metalloids should be considered while assessing the effect of metalloid on culturable microbial populations and enzyme activities. Urease and acid phosphatase can be used as potential biomarkers to evaluate the intensity of Sb (III) and As (III) stress.

  17. Environmental Whole-Genome Amplification to Access Microbial Diversity in Contaminated Sediments

    SciTech Connect

    Abulencia, C.B.; Wyborski, D.L.; Garcia, J.; Podar, M.; Chen, W.; Chang, S.H.; Chang, H.W.; Watson, D.; Brodie,E.I.; Hazen, T.C.; Keller, M.

    2005-12-10

    Low-biomass samples from nitrate and heavy metal contaminated soils yield DNA amounts that have limited use for direct, native analysis and screening. Multiple displacement amplification (MDA) using ?29 DNA polymerase was used to amplify whole genomes from environmental, contaminated, subsurface sediments. By first amplifying the genomic DNA (gDNA), biodiversity analysis and gDNA library construction of microbes found in contaminated soils were made possible. The MDA method was validated by analyzing amplified genome coverage from approximately five Escherichia coli cells, resulting in 99.2 percent genome coverage. The method was further validated by confirming overall representative species coverage and also an amplification bias when amplifying from a mix of eight known bacterial strains. We extracted DNA from samples with extremely low cell densities from a U.S. Department of Energy contaminated site. After amplification, small subunit rRNA analysis revealed relatively even distribution of species across several major phyla. Clone libraries were constructed from the amplified gDNA, and a small subset of clones was used for shotgun sequencing. BLAST analysis of the library clone sequences showed that 64.9 percent of the sequences had significant similarities to known proteins, and ''clusters of orthologous groups'' (COG) analysis revealed that more than half of the sequences from each library contained sequence similarity to known proteins. The libraries can be readily screened for native genes or any target of interest. Whole-genome amplification of metagenomic DNA from very minute microbial sources, while introducing an amplification bias, will allow access to genomic information that was not previously accessible.

  18. Recombinant Environmental Libraries Provide Access to Microbial Diversity for Drug Discovery from Natural Products

    PubMed Central

    Courtois, Sophie; Cappellano, Carmela M.; Ball, Maria; Francou, Francois-Xavier; Normand, Philippe; Helynck, Gérard; Martinez, Asuncion; Kolvek, Steven J.; Hopke, Joern; Osburne, Marcia S.; August, Paul R.; Nalin, Renaud; Guérineau, Michel; Jeannin, Pascale; Simonet, Pascal; Pernodet, Jean-Luc

    2003-01-01

    To further explore possible avenues for accessing microbial biodiversity for drug discovery from natural products, we constructed and screened a 5,000-clone “shotgun” environmental DNA library by using an Escherichia coli-Streptomyces lividans shuttle cosmid vector and DNA inserts from microbes derived directly (without cultivation) from soil. The library was analyzed by several means to assess diversity, genetic content, and expression of heterologous genes in both expression hosts. We found that the phylogenetic content of the DNA library was extremely diverse, representing mostly microorganisms that have not been described previously. The library was screened by PCR for sequences similar to parts of type I polyketide synthase genes and tested for the expression of new molecules by screening of live colonies and cell extracts. The results revealed new polyketide synthase genes in at least eight clones. In addition, at least five additional clones were confirmed by high-pressure liquid chromatography analysis and/or biological activity to produce heterologous molecules. These data reinforce the idea that exploiting previously unknown or uncultivated microorganisms for the discovery of novel natural products has potential value and, most importantly, suggest a strategy for developing this technology into a realistic and effective drug discovery tool. PMID:12513976

  19. Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products.

    PubMed

    Courtois, Sophie; Cappellano, Carmela M; Ball, Maria; Francou, Francois-Xavier; Normand, Philippe; Helynck, Gérard; Martinez, Asuncion; Kolvek, Steven J; Hopke, Joern; Osburne, Marcia S; August, Paul R; Nalin, Renaud; Guérineau, Michel; Jeannin, Pascale; Simonet, Pascal; Pernodet, Jean-Luc

    2003-01-01

    To further explore possible avenues for accessing microbial biodiversity for drug discovery from natural products, we constructed and screened a 5,000-clone "shotgun" environmental DNA library by using an Escherichia coli-Streptomyces lividans shuttle cosmid vector and DNA inserts from microbes derived directly (without cultivation) from soil. The library was analyzed by several means to assess diversity, genetic content, and expression of heterologous genes in both expression hosts. We found that the phylogenetic content of the DNA library was extremely diverse, representing mostly microorganisms that have not been described previously. The library was screened by PCR for sequences similar to parts of type I polyketide synthase genes and tested for the expression of new molecules by screening of live colonies and cell extracts. The results revealed new polyketide synthase genes in at least eight clones. In addition, at least five additional clones were confirmed by high-pressure liquid chromatography analysis and/or biological activity to produce heterologous molecules. These data reinforce the idea that exploiting previously unknown or uncultivated microorganisms for the discovery of novel natural products has potential value and, most importantly, suggest a strategy for developing this technology into a realistic and effective drug discovery tool.

  20. Population Education Accessions List. July-December 1978.

    ERIC Educational Resources Information Center

    United Nations Educational, Scientific, and Cultural Organization, Bangkok (Thailand). Regional Office for Education in Asia and Oceania.

    Identified in this pamphlet are 317 resources about population education. Compiled by UNESCO's Population Education Clearing House in Thailand, the list contains references to journal articles, monographs, research reports, teaching guides, and curriculum materials. Most were published in Asian countries and the United States during the period…

  1. Population Education Accessions List, May-August 1999.

    ERIC Educational Resources Information Center

    United Nations Educational, Scientific and Cultural Organization, Bangkok (Thailand). Principal Regional Office for Asia and the Pacific.

    This document is comprised of output from the Regional Clearinghouse on Population Education and Communication (RCPEC) computerized bibliographic database on reproductive and sexual health and geography. Entries are categorized into four parts: (1) "Population Education"; (2) "Knowledge-base Information"; (3) "Audio-Visual and IEC Materials; and…

  2. Population Education Accessions List. January-April, 1999.

    ERIC Educational Resources Information Center

    United Nations Educational, Scientific, and Cultural Organization, Bangkok (Thailand). Regional Office for Education in Asia and the Pacific.

    This document features output from a computerized bibliographic database. The list categorizes entries into three parts. Part I, Population Education, consists of titles that address various aspects of population education arranged by country in the first section and general materials in the second. Part II, Knowledge Base Information, consists of…

  3. Midgut Microbial Community of Culex quinquefasciatus Mosquito Populations from India

    PubMed Central

    Chandel, Kshitij; Mendki, Murlidhar J.; Parikh, Rasesh Y.; Kulkarni, Girish; Tikar, Sachin N.; Sukumaran, Devanathan; Prakash, Shri; Parashar, Brahma D.; Shouche, Yogesh S.; Veer, Vijay

    2013-01-01

    The mosquito Culex quinquefasciatus is a ubiquitous species that serves as a major vector for west nile virus and lymphatic filariasis. Ingestion of bloodmeal by females triggers a series of physiological processes in the midgut and also exposes them to infection by these pathogens. The bacteria normally harbored in the midgut are known to influence physiology and can also alter the response to various pathogens. The midgut bacteria in female Cx. quinquefasciatus mosquitoes collected over a large geographical area from India was studied. Examination of 16S ribosomal DNA amplicons from culturable microflora revealed the presence of 83 bacterial species belonging to 31 bacterial genera. All of these species belong to three phyla i.e. Proteobacteria, Firmicutes and Actinobacteria. Phylum Proteobacteria was the most dominant phylum (37 species), followed by Firmicutes (33 species) and Actinobacteria (13 species). Phylum Proteobacteria, was dominated by members of γ-proteobacteria class. The genus Staphylococcus was the largest genus represented by 11 species whereas Enterobacter was the most prevalent genus and recovered from all the field stations except Leh. Highest bacterial prevalence was observed from Bhuj (22 species) followed by Nagrota (18 species), Masimpur (18 species) and Hathigarh (16 species). Whereas, least species were observed from Leh (8 species). It has been observed that individual mosquito harbor extremely diverse gut bacteria and have very small overlap bacterial taxa in their gut. This variation in midgut microbiota may be one of the factors responsible for variation in disease transmission rates or vector competence within mosquito population. The present data strongly encourage further investigations to verify the potential role of the detected bacteria in mosquito for the transmission of lymphatic filariasis and west nile virus. To the best of our knowledge this is the first study on midgut microbiota of wild Cx. quinquefasciatus from over a

  4. Monitoring the microbial populations and temperatures of fresh broccoli from harvest to retail display.

    PubMed

    Dallaire, R; LeBlanc, D I; Tranchant, C C; Vasseur, L; Delaquis, P; Beaulieu, C

    2006-05-01

    Microbial populations and the temperature of fresh broccoli were monitored at several steps of a supply chain by sampling 33 distinct lots of locally grown produce over two seasons during harvest, storage, wholesale handling, and retail display. Imported broccoli was also sampled, but only at retail display. Microbiological analyses were conducted on the florets of 201 local and 60 imported broccoli samples to determine populations of total aerobic bacteria (aerobic colony count), fecal coliforms, Escherichia coli, and Listeria monocytogenes. All the samples had mean aerobic colony counts ranging between 4 and 6 log CFU/g, but L. monocytogenes was not detected (limit of detection =100 CFU/g). Fecal coliforms and E. coli (limit of detection =20 most probable number per 100 g) were found in 22 of 126 samples of local broccoli collected at various steps of the production and distribution system during the first season. None was found in 75 samples collected in the second season. Fecal coliforms and E. coli were found in 2 of 60 imported broccoli samples. Broccoli temperatures were relatively well controlled throughout the production and distribution system. No clear change in produce microbial populations was evident between harvest and retail display, during both sampling seasons. However, a large experimental variability was found, possibly associated with the high variability of the initial levels of microbial populations on broccoli at harvest.

  5. Dynamics of indigenous microbial populations of butter head lettuce grown in mulch and on bare soil.

    PubMed

    Ponce, A G; Agüero, M V; Roura, S I; Del Valle, C E; Moreira, M R

    2008-08-01

    The native microflora of lettuce cultivated in mulch and on bare soil and its evolution during storage at optimal condition were evaluated. Inner, mid, and outer leaves of the lettuce heads were analyzed separately and the evolution of the microbial populations were fitted to Gompertz and logistic models. The cultivation method (bare soil and mulch) introduced differences in the initial counts, evolution, and tolerance to refrigeration temperatures for some of the microbial populations under study. Most microbial populations from mulch lettuce presented a decline or little growth under refrigerated storage. However, populations from bare soil lettuce presented some growth phase during storage. Lactic acid bacteria from bare soil lettuce presented significant growth after 8 d of storage while LAB from mulch grown lettuce did not. Concurrently with the LAB growth, there was a decline in the coliform counts in bare soil grown lettuce. At the end of storage, the inner and mid leaves of mulch lettuce presented lower counts of psychrotrophic bacteria, LAB, and yeast and molds.

  6. Modeling microbial populations with the original and modified versions of the continuous and discrete logistic equations.

    PubMed

    Peleg, M

    1997-08-01

    The life histories of microbial populations, under favorable and adverse conditions, exhibit a variety of growth, decay, and fluctuation patterns. They have been described by numerous mathematical models that varies considerably in structure and number of constants. The continuous logistic equation alone and combined with itself or with its mirror image, the Fermi function, can produce many of the observed growth patterns. They include those that are traditionally described by the Gompertz equation and peaked curves, with the peak being symmetric or asymmetric narrow or wide. The shape of survival and dose response curves appears to be determined by the distribution of the resistance's to the lethal agent among the individual organisms. Thus, exponential decay and Fermian or Gompertz-type curves can be considered manifestations of skewed to the right, symmetric, and skewed to the left distributions, respectively. Because of the mathematical constraints and determinism, the original discrete logistic equation can rarely be an adequate model of real microbial populations. However, by making its proportionality constant a normal-random variate it can simulate realistic histories of fluctuating microbial populations, including scenarios of aperiodic population explosions of varying intensities of the kind found in food-poisoning episodes.

  7. Long Live Rock! Exploring Active Microbial Populations in North Pond Subsurface Basalt

    NASA Astrophysics Data System (ADS)

    Mills, H. J.; Lehne, J.

    2014-12-01

    Microbial life should be considered as an active source for subsurface alterations of crustal material. Over the past several decades, microbial populations have been qualitatively and quantitatively characterized in marine sediments from the near shore to gyre centers, from the surface to two kilometers below the surface. Recent exploration of the underlying basement has revealed bacterial populations within the basalt. Initial cultivation-based and in situ analysis of subsurface basalt has produced some structural identification of populations that have the potential to alter the crust. Within this study, we have advanced this understanding by characterizing the metabolically active fraction of these populations. A 16S rRNA gene transcript approach was conducted using high throughput sequencing on RNA extracted from breccia, glass basalts and ultramafic basalts of the western flank of the Mid-Atlantic Ridge. Previous research has shown that the fluid within the basement is oxic. As expected, populations associated with aerobic metabolism were detected. In addition, iron-utilizing populations were observed to be metabolically active within the basalt samples characterized. Future characterization will reveal overlap between previous studies to determine the total versus metabolically active populations.

  8. Microbial Diversity and Population Structure of Extremely Acidic Sulfur-Oxidizing Biofilms From Sulfidic Caves

    NASA Astrophysics Data System (ADS)

    Jones, D.; Stoffer, T.; Lyon, E. H.; Macalady, J. L.

    2005-12-01

    Extremely acidic (pH 0-1) microbial biofilms called snottites form on the walls of sulfidic caves where gypsum replacement crusts isolate sulfur-oxidizing microorganisms from the buffering action of limestone host rock. We investigated the phylogeny and population structure of snottites from sulfidic caves in central Italy using full cycle rRNA methods. A small subunit rRNA bacterial clone library from a Frasassi cave complex snottite sample contained a single sequence group (>60 clones) similar to Acidithiobacillus thiooxidans. Bacterial and universal rRNA clone libraries from other Frasassi snottites were only slightly more diverse, containing a maximum of 4 bacterial species and probably 2 archaeal species. Fluorescence in situ hybridization (FISH) of snottites from Frasassi and from the much warmer Rio Garrafo cave complex revealed that all of the communities are simple (low-diversity) and dominated by Acidithiobacillus and/or Ferroplasma species, with smaller populations of an Acidimicrobium species, filamentous fungi, and protists. Our results suggest that sulfidic cave snottites will be excellent model microbial ecosystems suited for ecological and metagenomic studies aimed at elucidating geochemical and ecological controls on microbial diversity, and at mapping the spatial history of microbial evolutionary events such as adaptations, recombinations and gene transfers.

  9. Milankovitch-scale correlations between deeply buried microbial populations and biogenic ooze lithology

    USGS Publications Warehouse

    Aiello, I.W.; Bekins, B.A.

    2010-01-01

    The recent discoveries of large, active populations of microbes in the subseafloor of the world's oceans supports the impact of the deep biosphere biota on global biogeochemical cycles and raises important questions concerning the functioning of these extreme environments for life. These investigations demonstrated that subseafloor microbes are unevenly distributed and that cell abundances and metabolic activities are often independent from sediment depths, with increased prokaryotic activity at geochemical and/or sedimentary interfaces. In this study we demonstrate that microbial populations vary at the scale of individual beds in the biogenic oozes of a drill site in the eastern equatorial Pacific (Ocean Drilling Program Leg 201, Site 1226). We relate bedding-scale changes in biogenic ooze sediment composition to organic carbon (OC) and microbial cell concentrations using high-resolution color reflectance data as proxy for lithology. Our analyses demonstrate that microbial concentrations are an order of magnitude higher in the more organic-rich diatom oozes than in the nannofossil oozes. The variations mimic small-scale variations in diatom abundance and OC, indicating that the modern distribution of microbial biomass is ultimately controlled by Milankovitch-frequency variations in past oceanographic conditions. ?? 2010 Geological Society of America.

  10. Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla.

    PubMed

    Emerson, Joanne B; Thomas, Brian C; Alvarez, Walter; Banfield, Jillian F

    2016-06-01

    Research on geologic carbon sequestration raises questions about potential impacts of subsurface microbiota on carbon cycling and biogeochemistry. Subsurface, high-CO2 systems are poorly biologically characterized, partly because of difficulty accessing high-volume, uncontaminated samples. CO2 -driven Crystal Geyser (CG, Utah, USA), an established geologic carbon sequestration analogue, provides high volumes of deep (∼ 200-500 m) subsurface fluids. We explored microbial diversity and metabolic potential in this high-CO2 environment by assembly and analysis of metagenomes recovered from geyser water filtrate. The system is dominated by neutrophilic, iron-oxidizing bacteria, including 'marine' Mariprofundus (Zetaproteobacteria) and 'freshwater' Gallionellales, sulfur-oxidizing Thiomicrospira crunogena and Thiobacillus-like Hydrogenophilales. Near-complete genomes were reconstructed for these bacteria. CG is notably populated by a wide diversity of bacteria and archaea from phyla lacking isolated representatives (candidate phyla) and from as-yet undefined lineages. Many bacteria affiliate with OD1, OP3, OP9, PER, ACD58, WWE3, BD1-5, OP11, TM7 and ZB2. The recovery of nearly 100 genes encoding ribulose-1,5 bisphosphate carboxylase-oxygenase subunit proteins of the Calvin cycle and AMP salvage pathways suggests a strong biological role in high-CO2 subsurface carbon cycling. Overall, we predict microbial impacts on subsurface biogeochemistry via iron, sulfur, and complex carbon oxidation, carbon and nitrogen fixation, fermentation, hydrogen metabolism, and aerobic and anaerobic respiration.

  11. Monomethylhydrazine degradation and its effect on carbon dioxide evolution and microbial populations in soil

    SciTech Connect

    Ou, L.T.; Street, J.J.

    1988-09-01

    Monomethylhydrazine (MMH), along with hydrazine and 1,1-dimethylhydrazine are the main components of hydrazine fuels. Information on the fate of MMH in soil and its overall effect on soil microbial activity is not known, though MMH is known to be toxic to a number of soil bacteria. Despite the fact that axenic bacterial cultures are inhibited by the three hydrazines, Ou and Street reported that soil respiration, and total bacterial and fungal populations in soil, were not inhibited by hydrazine at concentrations of 100 ..mu..g/g and lower. Even at 500 ..mu..g/g, only total bacterial populations in soil were inhibited by the presence of hydrazine. They also reported that hydrazine rapidly disappeared in soil. The authors initiated this study to investigate the effect of MMH on soil microbial activity and on degradation of the chemical in soil.

  12. Controls on microbial accessibility to soil organic carbon following woody plant encroachment into grasslands

    NASA Astrophysics Data System (ADS)

    Creamer, Courtney; Boutton, Thomas; Olk, Dan; Filley, Timothy

    2010-05-01

    Woody plant encroachment (WPE) into savannas and grasslands is a global phenomenon that alters soil organic carbon (SOC) dynamics through changes in litter quality and quantity, soil structure, microbial ecology, and hydrology. To elucidate the controls on microbial accessibility to SOC, bulk soils from a chronosequence of progressive WPE into native grasslands at the Texas Agrilife La Copita Research Area were incubated for one year. The quantity and stable carbon isotope composition of respired CO2, and plant biopolymer chemistry in SOC were tracked. Respiration rates declined exponentially over the course of the experiment with 15-25% of the total CO2 respired released in the first month of incubation. Between 8 and 18% of the total SOC was mineralized to CO2 throughout the incubation. After day 84 a significantly (p<0.05) greater portion of SOC was mineralized from soils of older woody clusters (34-86 years) than from soils of younger woody clusters (14-23 years) and the native grassland. Invading woody stands of ≃≥35 years of age represent a transition point in WPE where respiration dynamics become distinct in wooded elements compared to grasslands; this distinction has been previously observed through changes in belowground SOC accrual, C input chemistry, and mycorrhizal productivity. Despite documented SOC accrual following WPE at La Copita, we observed no evidence of enhanced SOC stabilization in these respiration experiments. In fact, a greater proportion of total SOC was lost from the soil of mature woody stands than from young stands, suggesting SOC accumulation observed with WPE may be due to greater input rates or microbial dynamics not captured in the laboratory incubation. Compound-specific analyses indicated there was a significant (p<0.05) loss of C from carbohydrates, amino acids, and amino sugars during the incubation. Amino nitrogen tended to become more concentrated during the incubation, although the trend was not significant. Relatively

  13. Access to healthful foods among an urban food insecure population: perceptions versus reality.

    PubMed

    Freedman, Darcy A; Bell, Bethany A

    2009-11-01

    The influence of local food environments on the risk for obesity is important overall, but may be particularly important for food insecure populations in urban settings. Access to healthful foods is most limited among racial and ethnic minorities and low-income populations; these same populations experience the highest rates of obesity and food insecurity. Few valid and reliable measures have been developed to assess the quality of local food environments. This research addresses this gap by introducing an inventory for measuring self-reported perceptions of food access and then compares the perceptions measure to objective assessments of local food environments. Data are focused on an urban population experiencing disproportionate rates of food insecurity. The four-item perceptions of food access inventory had high internal consistency (Cronbach's alpha = 0.80). Participants' perceptions of access to healthful foods mirrored the reality of their food environment; however, perceptions of access to alcohol and tobacco were less accurate. Findings suggest that people living in low-income, urban, minority, and food insecure communities can validly assess (in)access to healthful foods. Future research is needed to further validate the perceptions of food access measure introduced and, more importantly, to develop strategies for increasing access to healthful foods in food insecure contexts.

  14. Dynamics of organic matter and microbial populations in amended soil: a multidisciplinary approach

    NASA Astrophysics Data System (ADS)

    Gigliotti, Giovanni; Pezzolla, Daniela; Zadra, Claudia; Albertini, Emidio; Marconi, Gianpiero; Turchetti, Benedetta; Buzzini, Pietro

    2013-04-01

    The application of organic amendments to soils, such as pig slurry, sewage sludge and compost is considered a tool for improving soil fertility and enhancing C stock. The addition of these different organic materials allows a good supply of nutrients for plants but also contributes to C sequestration, affects the microbial activity and the transformation of soil organic matter (SOM). Moreover, the addition of organic amendment has gained importance as a source of greenhouse gas (GHG) emissions and then as a cause of the "Global Warming". Therefore, it is important to investigate the factors controlling the SOM mineralization in order to improve soil C sequestration and decreasing at the same time the GHG emissions. The quality of organic matter added to the soil will play an important role in these dynamics, affecting the microbial activity and the changes in microbial community structure. A laboratory, multidisciplinary experiment was carried out to test the effect of the amendment by anaerobic digested livestock-derived organic materials on labile organic matter evolution and on dynamics of microbial population, this latter both in terms of consistence of microbial biomass, as well as in terms of microbial biodiversity. Different approaches were used to study the microbial community structure: chemical (CO2 fluxes, WEOC, C-biomass, PLFA), microbiological (microbial enumeration) and molecular (DNA extraction and Roche 454, Next Generation Sequencing, NGS). The application of fresh digestate, derived from the anaerobic treatment of animal wastes, affected the short-term dynamics of microbial community, as reflected by the increase of CO2 emissions immediately after the amendment compared to the control soil. This is probably due to the addition of easily available C added with the digestate, demonstrating that this organic material was only partially stabilized by the anaerobic process. In fact, the digestate contained a high amounts of available C, which led to

  15. Increasing access by priority populations to Australian sexual health clinics.

    PubMed

    Ali, Hammad; Donovan, Basil; Fairley, Christopher K; Chen, Marcus Y; O'Connor, Catherine C; Grulich, Andrew E; McNulty, Anna; Ryder, Nathan; Hellard, Margaret E; Guy, Rebecca J

    2013-10-01

    Data from a network of 35 Australian sexual health clinics, in geographically diverse locations, showed that the number and proportion of patients from priority populations (ie, young people, men who have sex with men, indigenous people, and female sex workers) increased significantly between 2004 and 2011.

  16. Population Education Accessions List, January-April 2000.

    ERIC Educational Resources Information Center

    United Nations Educational, Scientific and Cultural Organization, Bangkok (Thailand). Principal Regional Office for Asia and the Pacific.

    This document contains output from a computerized bibliographic database. This issue is divided into four parts. Part I consists of titles that address various aspects of population education and is arranged by country in the first section, and general materials in the second section. Part II presents knowledge base information and consists of…

  17. Population Education Accessions Lists, July-December 1986.

    ERIC Educational Resources Information Center

    United Nations Educational, Scientific, and Cultural Organization, Bangkok (Thailand). Regional Office for Education in Asia and the Pacific.

    Part I of this resource guide contains listings of instructional materials, computer-assisted instructions, classroom activities and teaching methods. Part II deals with the knowledge base of population education. These publications are divided into 11 topics including: (1) demography; (2) documentation; (3) education (including environmental,…

  18. Bioremediation of hydrocarbon degradation in a petroleum-contaminated soil and microbial population and activity determination.

    PubMed

    Wu, Manli; Li, Wei; Dick, Warren A; Ye, Xiqiong; Chen, Kaili; Kost, David; Chen, Liming

    2017-02-01

    Bioremediation of hydrocarbon degradation in petroleum-polluted soil is carried out by various microorganisms. However, little information is available for the relationships between hydrocarbon degradation rates in petroleum-contaminated soil and microbial population and activity in laboratory assay. In a microcosm study, degradation rate and efficiency of total petroleum hydrocarbons (TPH), alkanes, and polycyclic aromatic hydrocarbons (PAH) in a petroleum-contaminated soil were determined using an infrared photometer oil content analyzer and a gas chromatography mass spectrometry (GC-MS). Also, the populations of TPH, alkane, and PAH degraders were enumerated by a modified most probable number (MPN) procedure, and the hydrocarbon degrading activities of these degraders were determined by the Biolog (MT2) MicroPlates assay. Results showed linear correlations between the TPH and alkane degradation rates and the population and activity increases of TPH and alkane degraders, but no correlation was observed between the PAH degradation rates and the PAH population and activity increases. Petroleum hydrocarbon degrading microbial population measured by MPN was significantly correlated with metabolic activity in the Biolog assay. The results suggest that the MPN procedure and the Biolog assay are efficient methods for assessing the rates of TPH and alkane, but not PAH, bioremediation in oil-contaminated soil in laboratory.

  19. Spatial shifts in microbial population structure within poultry litter associated with physicochemical properties.

    PubMed

    Lovanh, N; Cook, K L; Rothrock, M J; Miles, D M; Sistani, K

    2007-09-01

    Microbial populations within poultry litter have been largely ignored with the exception of potential human or livestock pathogens. A better understanding of the community structure and identity of the microbial populations within poultry litter could aid in the development of management practices that would reduce populations responsible for toxic air emissions and pathogen incidence. In this study, poultry litter air and physical properties were correlated to shifts in microbial community structure as analyzed by principal component analysis (PCA) and measured by denaturing gradient gel electrophoresis (DGGE). Litter samples were taken in a 36-point grid pattern at 5 m across and 12 m down a 146 m x 12.8 m chicken house. At each sample point, physical parameters such as litter moisture, pH, air and litter temperature, and relative humidity were recorded, and samples were taken for molecular analysis. The DGGE analysis showed that the banding pattern of samples from the back and water/feeder areas of poultry house were distinct from those of samples from other areas. There were distinct clusters of banding patterns corresponding to the front, middle front, middle back, back, and waterer/feeder areas. The PCA analysis showed similar cluster patterns, but with more distinct separation of the front and midhouse samples. The PCA analysis also showed that moisture content and litter temperature (accounting for 51.5 and 31.5% of the separation of samples, respectively) play a major role in spatial diversity of microbial community in the poultry house. Based on analysis of DGGE fingerprints and cloned DGGE band sequences, there appear to be differences in the types of microorganisms over the length of the house, which correspond to differences in the physical properties of the litter.

  20. Effects of Flavonoids on Rumen Fermentation Activity, Methane Production, and Microbial Population

    PubMed Central

    Abdullah, Norhani; Oskoueian, Armin

    2013-01-01

    This research was carried out to evaluate the effects of flavone, myricetin, naringin, catechin, rutin, quercetin, and kaempferol at the concentration of 4.5% of the substrate (dry matter basis) on the rumen microbial activity in vitro. Mixture of guinea grass and concentrate (60 : 40) was used as the substrate. The results showed that all the flavonoids except naringin and quercetin significantly (P < 0.05) decreased the dry matter degradability. The gas production significantly (P < 0.05) decreased by flavone, myricetin, and kaempferol, whereas naringin, rutin, and quercetin significantly (P < 0.05) increased the gas production. The flavonoids suppressed methane production significantly (P < 0.05). The total VFA concentration significantly (P < 0.05) decreased in the presence of flavone, myricetin, and kaempferol. All flavonoids except naringin and quercetin significantly (P < 0.05) reduced the carboxymethyl cellulase, filter paperase, xylanase, and β-glucosidase activities, purine content, and the efficiency of microbial protein synthesis. Flavone, myricetin, catechin, rutin, and kaempferol significantly (P < 0.05) reduced the population of rumen microbes. Total populations of protozoa and methanogens were significantly (P < 0.05) suppressed by naringin and quercetin. The results of this research demonstrated that naringin and quercetin at the concentration of 4.5% of the substrate (dry matter basis) were potential metabolites to suppress methane production without any negative effects on rumen microbial fermentation. PMID:24175289

  1. Geochemical Attributes and Gradients Within Geothermal Systems Define the Distribution of Specific Microbial Populations

    NASA Astrophysics Data System (ADS)

    Inskeep, W. P.; Macur, R. E.; Korf, S.; Taylor, W. P.; Ackerman, G.; Kozubal, M.; Nagy, A.

    2006-12-01

    Microorganisms in natural habitats interact with mineral surfaces in many different respects. For example, microorganisms are known to enhance the dissolution rates of some minerals via the production of organic acids and other exudates, but at the same time, may mineralize solid phases as a direct or indirect result of metabolic processes. It is also well-established that many microorganisms form biofilms on mineral surfaces, and may preferentially attach to surfaces rich in necessary nutrients or in elements used for energy conservation. In part due to the complexity of natural soil, water and sediments systems, it is generally difficult to ascertain mechanisms controlling the distribution of organisms on mineral surfaces and their role in mineral precipitation-dissolution reactions. Geothermal microbial communities are often less diverse than surface soils and sediments and offer opportunities for understanding relationships among specific microbial populations and geochemical processes that define the biogeochemical cycles of individual elements. We have investigated numerous acidic and near-neutral geothermal sites in Yellowstone National Park, and have performed a number of complimentary chemical and microbiological analyses to ascertain the role of microorganisms in S, Fe, As and Sb cycling in geothermal systems. Our results demonstrate the importance of microbiota in the formation of various Fe(III) oxide phases with variable anion chemistry, and the importance of chemolithotrophic metabolisms in Fe, S and As cycling. Where possible, these metabolisms are linked to specific microbial populations identified via molecular methods, and in some cases confirmed using isolation and characterization of individual organisms.

  2. Efficacy of gaseous ozone against Salmonella and microbial population on dried oregano.

    PubMed

    Torlak, Emrah; Sert, Durmuş; Ulca, Pelin

    2013-08-01

    Interest in potential food applications of ozone has expanded in recent years in response to consumer demands for green technologies. This study was conducted to evaluate the efficacy of gaseous ozone for the microbial reduction and elimination of Salmonella on dried oregano. Ozone treatment was performed up to 120min under continuous stream of two different constant ozone concentrations (2.8 and 5.3mg/L). Significant (P<0.05) reductions of 2.7 and 1.8 log were observed in aerobic plate counts and yeast and mold counts after ozonation at 2.8mg/L for 120min, respectively. Ozonation performed at 5.3mg/L for 90min yielded a reduction of over 3.2 log in the aerobic plate counts. Initial population of a cocktail of Salmonella serotypes (S. Typhimurium, S. Newport and S. Montevideo) on inoculated oregano determined as 5.8logCFU/g decreased significantly by 2.8 and 3.7 log after ozonation at 2.8 and 5.3mg/L for 120min, respectively. Sensory evaluation results suggested that over the 2 log reduction in the microbial population can be obtained on dried oregano by gaseous ozone treatments with an acceptable taste, flavor and appearance. The results demonstrated that the gaseous ozone treatment is an effective alternative microbial reduction technique for dried oregano.

  3. Household computer and Internet access: The digital divide in a pediatric clinic population.

    PubMed

    Carroll, Aaron E; Rivara, Frederick P; Ebel, Beth; Zimmerman, Frederick J; Christakis, Dimitri A

    2005-01-01

    Past studies have noted a digital divide, or inequality in computer and Internet access related to socio-economic class. This study sought to measure how many households in a pediatric primary care outpatient clinic had household access to computers and the Internet, and whether this access differed by socio-economic status or other demographic information. We conducted a phone survey of a population-based sample of parents with children ages 0 to 11 years old. Analyses assessed predictors of having home access to a computer, the Internet, and high-speed Internet service. Overall, 88.9% of all households owned a personal computer, and 81.4% of all households had Internet access. Among households with Internet access, 48.3% had high speed Internet at home. There were significant associations between home computer ownership or Internet access and parental income or education. There was no relationship these factors and high speed Internet access. Over 60% of families with annual household income of $10,000-$25,000, and nearly 70% of families with only a high-school education had Internet access at home. While income and education remain significant predictors of household computer and internet access, many patients and families at all economic levels have access, and might benefit from health promotion interventions using these modalities.

  4. Registration of RMPAP-C4, a random-mated primitive race accession cotton germplasm population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A random mated population involving four cultivars of Upland cotton, Gossypium hirsutum L., and thirty day-neutral primitive accessions, RMPAP-C4, was developed and jointly released by USDA-ARS and the Mississippi Agricultural and Forestry Experiment Station in 2014. This population involved five c...

  5. Changes of microbial population structure related to lignin degradation during lignocellulosic waste composting.

    PubMed

    Huang, Dan-Lian; Zeng, Guang-Ming; Feng, Chong-Ling; Hu, Shuang; Lai, Cui; Zhao, Mei-Hua; Su, Feng-Feng; Tang, Lin; Liu, Hong-Liang

    2010-06-01

    Microbial populations and their relationship to bioconversion during lignocellulosic waste composting were studied by quinone profiling. Nine quinones were observed in the initial composting materials, and 15 quinones were found in compost after 50days of composting. The quinone species Q-9(H2), Q-10 and Q-10(H2) which are indicative of certain fungi appeared at the thermophilic stage but disappeared at the cooling stage. Q-10, indicative of certain fungi, and MK-7, characteristic of certain bacteria, were the predominant quinones during the thermophilic stage and were correlated with lignin degradation at the thermophilic stage. The highest lignin degradation ratio (26%) and good cellulose degradation were found at the cooling stage and were correlated with quinones Q-9, MK-7 and long-chain menaquinones attributed to mesophilic fungi, bacteria and actinomycetes, respectively. The present findings will improve the understandings of microbial dynamics and roles in composting, which could provide useful references for development of composting technology.

  6. Effect of inclusion of different levels of Leucaena silage on rumen microbial population and microbial protein synthesis in dairy steers fed on rice straw

    PubMed Central

    Nguyen, Thien Truong Giang; Wanapat, Metha; Phesatcha, Kampanat; Kang, Sungchhang

    2017-01-01

    Objective Leucaena leucocephala (Leucaena) is a perennial tropical legume that can be directly grazed or harvested and offered to ruminants as hay, silage, or fresh. However, Leucaena contain phenolic compounds, which are considered anti-nutritional factors as these may reduce intake, digestibility and thus animal performance. Therefore, the objective of this experiment was to determine effects of Leucaena silage (LS) feeding levels on rumen microbial populations, N-balance and microbial protein synthesis in dairy steers. Methods Four, rumen fistulated dairy steers with initial weight of 167±12 kg were randomly assigned to receive dietary treatments according to a 4×4 Latin square design. Treatments were as followings: T1 = untreated rice straw (RS; Control), T2 = 70% RS+30% LS, T3 = 40% RS+60% LS, and T4 = 100% LS. Dairy steers were fed rice straw and LS ad libitum and supplemented with concentrate at 0.2% of body weight/d. Results Results revealed that the rumen microbial population, especially cellulolytic, proteolytic bacteria and fungal zoospores were enhanced in steers that received 60% of LS (p<0.05), whereas the amylolytic bacteria population was not affected by treatments (p>0.05). Protozoal population was linearly decreased with increasing level of LS (p<0.05). Moreover, N-balance and microbial protein synthesis were enhanced by LS feeding (p<0.05) and were the highest in 60% LS group. Conclusion Based on this study, it could be concluded that replacement of RS with 60% LS significantly improved microbial population and microbial protein synthesis in diary steers. PMID:27165024

  7. Quantitative Modeling of Microbial Population Responses to Chronic Irradiation Combined with Other Stressors

    PubMed Central

    Shuryak, Igor; Dadachova, Ekaterina

    2016-01-01

    Microbial population responses to combined effects of chronic irradiation and other stressors (chemical contaminants, other sub-optimal conditions) are important for ecosystem functioning and bioremediation in radionuclide-contaminated areas. Quantitative mathematical modeling can improve our understanding of these phenomena. To identify general patterns of microbial responses to multiple stressors in radioactive environments, we analyzed three data sets on: (1) bacteria isolated from soil contaminated by nuclear waste at the Hanford site (USA); (2) fungi isolated from the Chernobyl nuclear-power plant (Ukraine) buildings after the accident; (3) yeast subjected to continuous γ-irradiation in the laboratory, where radiation dose rate and cell removal rate were independently varied. We applied generalized linear mixed-effects models to describe the first two data sets, whereas the third data set was amenable to mechanistic modeling using differential equations. Machine learning and information-theoretic approaches were used to select the best-supported formalism(s) among biologically-plausible alternatives. Our analysis suggests the following: (1) Both radionuclides and co-occurring chemical contaminants (e.g. NO2) are important for explaining microbial responses to radioactive contamination. (2) Radionuclides may produce non-monotonic dose responses: stimulation of microbial growth at low concentrations vs. inhibition at higher ones. (3) The extinction-defining critical radiation dose rate is dramatically lowered by additional stressors. (4) Reproduction suppression by radiation can be more important for determining the critical dose rate, than radiation-induced cell mortality. In conclusion, the modeling approaches used here on three diverse data sets provide insight into explaining and predicting multi-stressor effects on microbial communities: (1) the most severe effects (e.g. extinction) on microbial populations may occur when unfavorable environmental

  8. Mapping Microbial Populations Relative to Sites of Ongoing Serpentinization: Results from the Tablelands Ophiolite Complex, Canada

    NASA Astrophysics Data System (ADS)

    Schrenk, M. O.; Brazelton, W. J.; Woodruff, Q.; Szponar, N.; Morrill, P. L.

    2010-12-01

    assemblages consisting of diverse taxa at neutral pH background sites. Terrestrial serpentinite-hosted microbial ecosystems with their accessibility, their low phylogenetic diversity, and limited range of energetic resources provide an excellent opportunity to explore the interplay between geochemical energy and life and to elucidate the native serpentinite subsurface biosphere. From the perspective of Mars exploration, studies of serpentinite ecosystems provide the opportunity to pinpoint the organisms and physiological adaptations specifically associated with serpentinization and to directly measure their geochemical impacts. Both of these results will inform modeling and life detection efforts of the Martian subsurface environment.

  9. Accessing the population of high-redshift Gamma Ray Bursts

    NASA Astrophysics Data System (ADS)

    Ghirlanda, G.; Salvaterra, R.; Ghisellini, G.; Mereghetti, S.; Tagliaferri, G.; Campana, S.; Osborne, J. P.; O'Brien, P.; Tanvir, N.; Willingale, D.; Amati, L.; Basa, S.; Bernardini, M. G.; Burlon, D.; Covino, S.; D'Avanzo, P.; Frontera, F.; Götz, D.; Melandri, A.; Nava, L.; Piro, L.; Vergani, S. D.

    2015-04-01

    Gamma Ray Bursts (GRBs) are a powerful probe of the high-redshift Universe. We present a tool to estimate the detection rate of high-z GRBs by a generic detector with defined energy band and sensitivity. We base this on a population model that reproduces the observed properties of GRBs detected by Swift, Fermi and CGRO in the hard X-ray and γ-ray bands. We provide the expected cumulative distributions of the flux and fluence of simulated GRBs in different energy bands. We show that scintillator detectors, operating at relatively high energies (e.g. tens of keV to the MeV), can detect only the most luminous GRBs at high redshifts due to the link between the peak spectral energy and the luminosity (Epeak-Liso) of GRBs. We show that the best strategy for catching the largest number of high-z bursts is to go softer (e.g. in the soft X-ray band) but with a very high sensitivity. For instance, an imaging soft X-ray detector operating in the 0.2-5 keV energy band reaching a sensitivity, corresponding to a fluence, of ˜10-8 erg cm-2 is expected to detect ≈40 GRBs yr-1 sr-1 at z ≥ 5 (≈3 GRBs yr-1 sr-1 at z ≥ 10). Once high-z GRBs are detected the principal issue is to secure their redshift. To this aim we estimate their NIR afterglow flux at relatively early times and evaluate the effectiveness of following them up and construct usable samples of events with any forthcoming GRB mission dedicated to explore the high-z Universe.

  10. Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems

    NASA Astrophysics Data System (ADS)

    Maslov, Sergei; Sneppen, Kim

    2017-01-01

    Determinants of species diversity in microbial ecosystems remain poorly understood. Bacteriophages are believed to increase the diversity by the virtue of Kill-the-Winner infection bias preventing the fastest growing organism from taking over the community. Phage-bacterial ecosystems are traditionally described in terms of the static equilibrium state of Lotka-Volterra equations in which bacterial growth is exactly balanced by losses due to phage predation. Here we consider a more dynamic scenario in which phage infections give rise to abrupt and severe collapses of bacterial populations whenever they become sufficiently large. As a consequence, each bacterial population in our model follows cyclic dynamics of exponential growth interrupted by sudden declines. The total population of all species fluctuates around the carrying capacity of the environment, making these cycles cryptic. While a subset of the slowest growing species in our model is always driven towards extinction, in general the overall ecosystem diversity remains high. The number of surviving species is inversely proportional to the variation in their growth rates but increases with the frequency and severity of phage-induced collapses. Thus counter-intuitively we predict that microbial communities exposed to more violent perturbations should have higher diversity.

  11. Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems.

    PubMed

    Maslov, Sergei; Sneppen, Kim

    2017-01-04

    Determinants of species diversity in microbial ecosystems remain poorly understood. Bacteriophages are believed to increase the diversity by the virtue of Kill-the-Winner infection bias preventing the fastest growing organism from taking over the community. Phage-bacterial ecosystems are traditionally described in terms of the static equilibrium state of Lotka-Volterra equations in which bacterial growth is exactly balanced by losses due to phage predation. Here we consider a more dynamic scenario in which phage infections give rise to abrupt and severe collapses of bacterial populations whenever they become sufficiently large. As a consequence, each bacterial population in our model follows cyclic dynamics of exponential growth interrupted by sudden declines. The total population of all species fluctuates around the carrying capacity of the environment, making these cycles cryptic. While a subset of the slowest growing species in our model is always driven towards extinction, in general the overall ecosystem diversity remains high. The number of surviving species is inversely proportional to the variation in their growth rates but increases with the frequency and severity of phage-induced collapses. Thus counter-intuitively we predict that microbial communities exposed to more violent perturbations should have higher diversity.

  12. Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems

    PubMed Central

    Maslov, Sergei; Sneppen, Kim

    2017-01-01

    Determinants of species diversity in microbial ecosystems remain poorly understood. Bacteriophages are believed to increase the diversity by the virtue of Kill-the-Winner infection bias preventing the fastest growing organism from taking over the community. Phage-bacterial ecosystems are traditionally described in terms of the static equilibrium state of Lotka-Volterra equations in which bacterial growth is exactly balanced by losses due to phage predation. Here we consider a more dynamic scenario in which phage infections give rise to abrupt and severe collapses of bacterial populations whenever they become sufficiently large. As a consequence, each bacterial population in our model follows cyclic dynamics of exponential growth interrupted by sudden declines. The total population of all species fluctuates around the carrying capacity of the environment, making these cycles cryptic. While a subset of the slowest growing species in our model is always driven towards extinction, in general the overall ecosystem diversity remains high. The number of surviving species is inversely proportional to the variation in their growth rates but increases with the frequency and severity of phage-induced collapses. Thus counter-intuitively we predict that microbial communities exposed to more violent perturbations should have higher diversity. PMID:28051127

  13. Characterization of Microbial Population Structures in Recreational Waters and Primary Sources of Fecal Pollution with a Next-Generation Sequencing Approach

    EPA Science Inventory

    The invention of new approaches to DNA sequencing commonly referred to as next generation sequencing technologies is revolutionizing the study of microbial diversity. In this chapter, we discuss the characterization of microbial population structures in recreational waters and p...

  14. Pattern and synchrony of gene expression among sympatric marine microbial populations

    PubMed Central

    Ottesen, Elizabeth A.; Young, Curtis R.; Eppley, John M.; Ryan, John P.; Chavez, Francisco P.; Scholin, Christopher A.; DeLong, Edward F.

    2013-01-01

    Planktonic marine microbes live in dynamic habitats that demand rapid sensing and response to periodic as well as stochastic environmental change. The kinetics, regularity, and specificity of microbial responses in situ, however, are not well-described. We report here simultaneous multitaxon genome-wide transcriptome profiling in a naturally occurring picoplankton community. An in situ robotic sampler using a Lagrangian sampling strategy enabled continuous tracking and repeated sampling of coherent microbial populations over 2 d. Subsequent RNA sequencing analyses yielded genome-wide transcriptome profiles of eukaryotic (Ostreococcus) and bacterial (Synechococcus) photosynthetic picoplankton as well as proteorhodopsin-containing heterotrophs, including Pelagibacter, SAR86-cluster Gammaproteobacteria, and marine Euryarchaea. The photosynthetic picoplankton exhibited strong diel rhythms over thousands of gene transcripts that were remarkably consistent with diel cycling observed in laboratory pure cultures. In contrast, the heterotrophs did not cycle diurnally. Instead, heterotrophic picoplankton populations exhibited cross-species synchronous, tightly regulated, temporally variable patterns of gene expression for many genes, particularly those genes associated with growth and nutrient acquisition. This multitaxon, population-wide gene regulation seemed to reflect sporadic, short-term, reversible responses to high-frequency environmental variability. Although the timing of the environmental responses among different heterotrophic species seemed synchronous, the specific metabolic genes that were expressed varied from taxon to taxon. In aggregate, these results provide insights into the kinetics, diversity, and functional patterns of microbial community response to environmental change. Our results also suggest a means by which complex multispecies metabolic processes could be coordinated, facilitating the regulation of matter and energy processing in a dynamically

  15. Pattern and synchrony of gene expression among sympatric marine microbial populations.

    PubMed

    Ottesen, Elizabeth A; Young, Curtis R; Eppley, John M; Ryan, John P; Chavez, Francisco P; Scholin, Christopher A; DeLong, Edward F

    2013-02-05

    Planktonic marine microbes live in dynamic habitats that demand rapid sensing and response to periodic as well as stochastic environmental change. The kinetics, regularity, and specificity of microbial responses in situ, however, are not well-described. We report here simultaneous multitaxon genome-wide transcriptome profiling in a naturally occurring picoplankton community. An in situ robotic sampler using a Lagrangian sampling strategy enabled continuous tracking and repeated sampling of coherent microbial populations over 2 d. Subsequent RNA sequencing analyses yielded genome-wide transcriptome profiles of eukaryotic (Ostreococcus) and bacterial (Synechococcus) photosynthetic picoplankton as well as proteorhodopsin-containing heterotrophs, including Pelagibacter, SAR86-cluster Gammaproteobacteria, and marine Euryarchaea. The photosynthetic picoplankton exhibited strong diel rhythms over thousands of gene transcripts that were remarkably consistent with diel cycling observed in laboratory pure cultures. In contrast, the heterotrophs did not cycle diurnally. Instead, heterotrophic picoplankton populations exhibited cross-species synchronous, tightly regulated, temporally variable patterns of gene expression for many genes, particularly those genes associated with growth and nutrient acquisition. This multitaxon, population-wide gene regulation seemed to reflect sporadic, short-term, reversible responses to high-frequency environmental variability. Although the timing of the environmental responses among different heterotrophic species seemed synchronous, the specific metabolic genes that were expressed varied from taxon to taxon. In aggregate, these results provide insights into the kinetics, diversity, and functional patterns of microbial community response to environmental change. Our results also suggest a means by which complex multispecies metabolic processes could be coordinated, facilitating the regulation of matter and energy processing in a dynamically

  16. Ecological distribution and population physiology defined by proteomics in a natural microbial community

    USGS Publications Warehouse

    Mueller, Ryan S.; Denef, Vincent J.; Kalnejais, Linda H.; Suttle, K. Blake; Thomas, Brian C.; Wilmes, Paul; Smith, Richard L.; Nordstrom, D. Kirk; McCleskey, R. Blaine; Shah, Menesh B.; VerBekmoes, Nathan C.; Hettich, Robert L.; Banfield, Jillian F.

    2010-01-01

    An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems. We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism's metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ.

  17. Ecological distribution and population physiology defined by proteomics in a natural microbial community

    SciTech Connect

    Muller, R; Denef, Vincent; Kalnejals, Linda; Suttle, K Blake; Thomas, Brian; Wilmes, P; Smith, Richard L.; Nordstrom, D Kirk; McCleskey, R Blaine; Shah, Manesh B; Verberkmoes, Nathan C; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2010-01-01

    An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems.We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism s metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ

  18. Microbial populations related to PAH biodegradation in an aged biostimulated creosote-contaminated soil.

    PubMed

    Lladó, Salvador; Jiménez, Nuria; Viñas, Marc; Solanas, Anna Maria

    2009-09-01

    A previous bioremediation survey on a creosote-contaminated soil showed that aeration and optimal humidity promoted depletion of three-ringed polycyclic aromatic hydrocarbons (PAHs), but residual concentrations of four-ringed benzo(a)anthracene (B(a)A) and chrysene (Chry) remained. In order to explain the lack of further degradation of heavier PAHs such as four-ringed PAHs and to analyze the microbial population responsible for PAH biodegradation, a chemical and microbial molecular approach was used. Using a slurry incubation strategy, soil in liquid mineral medium with and without additional B(a)A and Chry was found to contain a powerful PAH-degrading microbial community that eliminated 89% and 53% of the added B(a)A and Chry, respectively. It is hypothesized that the lack of PAH bioavailability hampered their further biodegradation in the unspiked soil. According to the results of the culture-dependent and independent techniques Mycobacterium parmense, Pseudomonas mexicana, and Sphingobacterials group could control B(a)A and Chry degradation in combination with several microorganisms with secondary metabolic activity.

  19. Molecular Analysis of Surfactant-Driven Microbial Population Shifts in Hydrocarbon-Contaminated Soil†

    PubMed Central

    Colores, Gregory M.; Macur, Richard E.; Ward, David M.; Inskeep, William P.

    2000-01-01

    We analyzed the impact of surfactant addition on hydrocarbon mineralization kinetics and the associated population shifts of hydrocarbon-degrading microorganisms in soil. A mixture of radiolabeled hexadecane and phenanthrene was added to batch soil vessels. Witconol SN70 (a nonionic, alcohol ethoxylate) was added in concentrations that bracketed the critical micelle concentration (CMC) in soil (CMC′) (determined to be 13 mg g−1). Addition of the surfactant at a concentration below the CMC′ (2 mg g−1) did not affect the mineralization rates of either hydrocarbon. However, when surfactant was added at a concentration approaching the CMC′ (10 mg g−1), hexadecane mineralization was delayed and phenanthrene mineralization was completely inhibited. Addition of surfactant at concentrations above the CMC′ (40 mg g−1) completely inhibited mineralization of both phenanthrene and hexadecane. Denaturing gradient gel electrophoresis of 16S rRNA gene segments showed that hydrocarbon amendment stimulated Rhodococcus and Nocardia populations that were displaced by Pseudomonas and Alcaligenes populations at elevated surfactant levels. Parallel cultivation studies revealed that the Rhodococcus population can utilize hexadecane and that the Pseudomonas and Alcaligenes populations can utilize both Witconol SN70 and hexadecane for growth. The results suggest that surfactant applications necessary to achieve the CMC alter the microbial populations responsible for hydrocarbon mineralization. PMID:10877792

  20. Diets of differentially processed wheat alter ruminal fermentation parameters and microbial populations in beef cattle.

    PubMed

    Jiang, S Z; Yang, Z B; Yang, W R; Li, Z; Zhang, C Y; Liu, X M; Wan, F C

    2015-11-01

    The influences of differently processed wheat products on rumen fermentation, microbial populations, and serum biochemistry profiles in beef cattle were studied. Four ruminally cannulated Limousin × Luxi beef cattle (400 ± 10 kg) were used in the experiment with a 4 × 4 Latin square design. The experimental diets contained (on a DM basis) 60% corn silage as a forage source and 40% concentrate with 4 differently processed wheat products (extruded, pulverized, crushed, and rolled wheat). Concentrations of ruminal NH-N and microbial protein (MCP) in cattle fed crushed and rolled wheat were greater ( < 0.05) than the corresponding values in cattle fed pulverized and extruded wheat. Ruminal concentrations of total VFA and acetate and the ratio of acetate to propionate decreased ( < 0.05) with increased geometric mean particle size (geometric mean diameter) of processed wheat, except for extruded wheat; cattle fed extruded wheat had the lowest concentrations of total VFA and acetate among all treatments. The relative abundance of , , ciliated protozoa, and was lower in cattle fed the pulverized wheat diet than in the other 3 diets ( < 0.05), whereas the relative abundance of was decreased in cattle fed extruded wheat compared with cattle fed crushed and rolled wheat ( < 0.05). No treatment effect was obtained for serum enzyme activity and protein concentration ( > 0.05). Our findings suggest that the method of wheat processing could have a significant effect on ruminal fermentation parameters and microbial populations in beef cattle and that crushed and rolled processing is better in terms of ruminal NH-N and MCP content, acetate-to-propionate ratio, and relative abundance of rumen microorganisms.

  1. Pectin induces an in vitro rumen microbial population shift attributed to the pectinolytic Treponema group.

    PubMed

    Liu, Jing; Pu, Yi-Yi; Xie, Qian; Wang, Jia-Kun; Liu, Jian-Xin

    2015-01-01

    Pectin is a non-fiber carbohydrate (NFC) that exists in forages, but it is not clear how pectin exerts its effect on populations of either known microbial species or uncultured ruminal bacteria. PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and real-time PCR analysis were used in the present study to investigate the effects of pectin on microbial communities in an in vitro rumen fermentation system. The fermentations were conducted using forage (corn stover or alfalfa), an NFC source (pectin or corn starch), or their combination as the substrates. Addition of pectin increased acetate (P < 0.05), whereas inclusion of starch increased butyrate production (P < 0.05). The pectate lyase activity was higher with alfalfa than with corn straw, or with pectin than with corn starch (P < 0.05), while the amylase activity was higher in corn starch-included treatments than the others (P < 0.05). The cluster analysis of the bacterial 16S rRNA gene showed that the DGGE banding patterns differed significantly between the treatments and led to the identification of three groups that were highly associated with the NFC sources. The specific bands associated with pectin-rich treatments were identified to be dominated by members of the Treponema genus. The growth of the Treponema genus was remarkably supported by the inclusion of pectin, highlighting their specific ability to degrade pectin. The results from the present study expand our knowledge of the microbial populations associated with pectin digestion, which may not only facilitate future research on utilization of pectin in feeds, but also improve our understanding of pectin digestion with respect to the rumen micro-ecosystem.

  2. Evolutionary consequences of intra-patient phage predation on microbial populations.

    PubMed

    Seed, Kimberley D; Yen, Minmin; Shapiro, B Jesse; Hilaire, Isabelle J; Charles, Richelle C; Teng, Jessica E; Ivers, Louise C; Boncy, Jacques; Harris, Jason B; Camilli, Andrew

    2014-08-26

    The impact of phage predation on bacterial pathogens in the context of human disease is not currently appreciated. Here, we show that predatory interactions of a phage with an important environmentally transmitted pathogen, Vibrio cholerae, can modulate the evolutionary trajectory of this pathogen during the natural course of infection within individual patients. We analyzed geographically and temporally disparate cholera patient stool samples from Haiti and Bangladesh and found that phage predation can drive the genomic diversity of intra-patient V. cholerae populations. Intra-patient phage-sensitive and phage-resistant isolates were isogenic except for mutations conferring phage resistance, and moreover, phage-resistant V. cholerae populations were composed of a heterogeneous mix of many unique mutants. We also observed that phage predation can significantly alter the virulence potential of V. cholerae shed from cholera patients. We provide the first molecular evidence for predatory phage shaping microbial community structure during the natural course of infection in humans.

  3. Microbial Populations Stimulated for Hexavalent Uranium Reduction in Uranium Mine Sediment

    PubMed Central

    Suzuki, Yohey; Kelly, Shelly D.; Kemner, Kenneth M.; Banfield, Jillian F.

    2003-01-01

    Uranium-contaminated sediment and water collected from an inactive uranium mine were incubated anaerobically with organic substrates. Stimulated microbial populations removed U almost entirely from solution within 1 month. X-ray absorption near-edge structure analysis showed that U(VI) was reduced to U(IV) during the incubation. Observations by transmission electron microscopy, selected area diffraction pattern analysis, and energy-dispersive X-ray spectroscopic analysis showed two distinct types of prokaryotic cells that precipitated only a U(IV) mineral uraninite (UO2) or both uraninite and metal sulfides. Prokaryotic cells associated with uraninite and metal sulfides were inferred to be sulfate-reducing bacteria. Phylogenetic analysis of 16S ribosomal DNA obtained from the original and incubated sediments revealed that microbial populations were changed from microaerophilic Proteobacteria to anaerobic low-G+C gram-positive sporeforming bacteria by the incubation. Forty-two out of 94 clones from the incubated sediment were related to sulfate-reducing Desulfosporosinus spp., and 23 were related to fermentative Clostridium spp. The results suggest that, if in situ bioremediation were attempted in the uranium mine ponds, Desulfosporosinus spp. would be a major contributor to U(VI) and sulfate reduction and Clostridium spp. to U(VI) reduction. PMID:12620814

  4. Molecular characterization of microbial populations in groundwater sources and sand filters for drinking water production.

    PubMed

    de Vet, W W J M; Dinkla, I J T; Muyzer, G; Rietveld, L C; van Loosdrecht, M C M

    2009-01-01

    In full-scale drinking water production from groundwater, subsurface aeration is an effective means of enhancing the often troublesome process of nitrification. Until now the exact mechanism, however, has been unknown. By studying the microbial population we can improve the understanding of this process. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments of bacteria, archaea and ammonia-oxidizing bacteria was used to characterize the microbial populations in raw groundwater and trickling filters of an active nitrifying surface aerated system and an inactive non-surface aerated system. Only in the active filter were nitrifying microorganisms found above the detection limit of the method. In ammonia oxidation in this groundwater filter both bacteria and archaea played a role, while members belonging to the genus Nitrospira were the only nitrite-oxidizing species found. The subsurface aerated groundwater did not contain any of the nitrifying organisms active in the filter above the detection limit, but did contain Gallionella species that might play a major role in iron oxidation in the filter.

  5. Microbial Population Differentials between Mucosal and Submucosal Intestinal Tissues in Advanced Crohn's Disease of the Ileum.

    PubMed

    Chiodini, Rodrick J; Dowd, Scot E; Chamberlin, William M; Galandiuk, Susan; Davis, Brian; Glassing, Angela

    2015-01-01

    Since Crohn's disease is a transmural disease, we hypothesized that examination of deep submucosal tissues directly involved in the inflammatory disease process may provide unique insights into bacterial populations transgressing intestinal barriers and bacterial populations more representative of the causes and agents of the disease. We performed deep 16s microbiota sequencing on isolated ilea mucosal and submucosal tissues on 20 patients with Crohn's disease and 15 non-inflammatory bowel disease controls with a depth of coverage averaging 81,500 sequences in each of the 70 DNA samples yielding an overall resolution down to 0.0001% of the bacterial population. Of the 4,802,328 total sequences generated, 98.9% or 4,749,183 sequences aligned with the Kingdom Bacteria that clustered into 8545 unique sequences with <3% divergence or operational taxonomic units enabling the identification of 401 genera and 698 tentative bacterial species. There were significant differences in all taxonomic levels between the submucosal microbiota in Crohn's disease compared to controls, including organisms of the Order Desulfovibrionales that were present within the submucosal tissues of most Crohn's disease patients but absent in the control group. A variety of organisms of the Phylum Firmicutes were increased in the subjacent submucosa as compared to the parallel mucosal tissue including Ruminococcus spp., Oscillospira spp., Pseudobutyrivibrio spp., and Tumebacillus spp. In addition, Propionibacterium spp. and Cloacibacterium spp. were increased as well as large increases in Proteobacteria including Parasutterella spp. and Methylobacterium spp. This is the first study to examine the microbial populations within submucosal tissues of patients with Crohn's disease and to compare microbial communities found deep within the submucosal tissues with those present on mucosal surfaces. Our data demonstrate the existence of a distinct submucosal microbiome and ecosystem that is not well

  6. Microbial Population Differentials between Mucosal and Submucosal Intestinal Tissues in Advanced Crohn's Disease of the Ileum

    PubMed Central

    Chiodini, Rodrick J.; Dowd, Scot E.; Chamberlin, William M.; Galandiuk, Susan; Davis, Brian; Glassing, Angela

    2015-01-01

    Since Crohn's disease is a transmural disease, we hypothesized that examination of deep submucosal tissues directly involved in the inflammatory disease process may provide unique insights into bacterial populations transgressing intestinal barriers and bacterial populations more representative of the causes and agents of the disease. We performed deep 16s microbiota sequencing on isolated ilea mucosal and submucosal tissues on 20 patients with Crohn's disease and 15 non-inflammatory bowel disease controls with a depth of coverage averaging 81,500 sequences in each of the 70 DNA samples yielding an overall resolution down to 0.0001% of the bacterial population. Of the 4,802,328 total sequences generated, 98.9% or 4,749,183 sequences aligned with the Kingdom Bacteria that clustered into 8545 unique sequences with <3% divergence or operational taxonomic units enabling the identification of 401 genera and 698 tentative bacterial species. There were significant differences in all taxonomic levels between the submucosal microbiota in Crohn's disease compared to controls, including organisms of the Order Desulfovibrionales that were present within the submucosal tissues of most Crohn's disease patients but absent in the control group. A variety of organisms of the Phylum Firmicutes were increased in the subjacent submucosa as compared to the parallel mucosal tissue including Ruminococcus spp., Oscillospira spp., Pseudobutyrivibrio spp., and Tumebacillus spp. In addition, Propionibacterium spp. and Cloacibacterium spp. were increased as well as large increases in Proteobacteria including Parasutterella spp. and Methylobacterium spp. This is the first study to examine the microbial populations within submucosal tissues of patients with Crohn's disease and to compare microbial communities found deep within the submucosal tissues with those present on mucosal surfaces. Our data demonstrate the existence of a distinct submucosal microbiome and ecosystem that is not well

  7. Health Benefits for Vocational Rehabilitation Consumers: Comparison of Access Rates with Workers in the General Population

    ERIC Educational Resources Information Center

    Lustig, Daniel C.; Strauser, David R.

    2010-01-01

    Access to health insurance is one of the critical aspects of securing employment for people with disabilities. This study investigated whether vocational rehabilitation consumers secured employment with an employer who offered health insurance at similar rates to workers in the general population. In general, the results show that vocational…

  8. Genetic diversity and population structure of Korean and Chinese soybean [Glycine max (L.) Merr.] accessions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Korean and Chinese cultivated soybean [Glycine max (L.) Merr.] populations are major soybean gene pools. Information has been reported comparing genetic diversity between soybeans from the two countries using an unequal number of accessions and only 6 to 35 genetic markers. This study compares diffe...

  9. Gaining Access to Economically Marginalized Rural Populations: Lessons Learned from Nonprobability Sampling

    ERIC Educational Resources Information Center

    Mammen, Sheila; Sano, Yoshie

    2012-01-01

    Poverty is a significant problem in rural America. Gaining access to economically marginalized rural populations in order to recruit individuals to participate in a research study, however, is often a challenge. This article compares three different nonprobability sampling techniques that have been used to recruit rural, low-income…

  10. Permanent Genetic Access to Transiently Active Neurons via TRAP: Targeted Recombination in Active Populations

    PubMed Central

    Guenthner, Casey J.; Miyamichi, Kazunari; Yang, Helen H.; Heller, H. Craig; Luo, Liqun

    2013-01-01

    SUMMARY Targeting genetically encoded tools for neural circuit dissection to relevant cellular populations is a major challenge in neurobiology. We developed a new approach, Targeted Recombination in Active Populations (TRAP), to obtain genetic access to neurons that were activated by defined stimuli. This method utilizes mice in which the tamoxifen-dependent recombinase CreERT2 is expressed in an activity-dependent manner from the loci of the immediate early genes Arc and Fos. Active cells that express CreERT2 can undergo recombination only when tamoxifen is present, allowing genetic access to neurons that are active during a time window of less than 12 h. We show that TRAP can selectively provide access to neurons activated by specific somatosensory, visual, and auditory stimuli, and by experience in a novel environment. When combined with tools for labeling, tracing, recording, and manipulating neurons, TRAP offers a powerful new approach for understanding how the brain processes information and generates behavior. PMID:23764283

  11. Impact of nanoscale zero valent iron on geochemistry and microbial populations in trichloroethylene contaminated aquifer materials.

    PubMed

    Kirschling, Teresa L; Gregory, Kelvin B; Minkley, Edwin G; Lowry, Gregory V; Tilton, Robert D

    2010-05-01

    Nanoscale zerovalent iron (NZVI) particles are a promising technology for reducing trichloroethylene (TCE) contamination in the subsurface. Prior to injecting large quantities of nanoparticles into the groundwater it is important to understand what impact the particles will have on the geochemistry and indigenous microbial communities. Microbial populations are important not only for nutrient cycling, but also for contaminant remediation and heavy metal immobilization. Microcosms were used to determine the effects of NZVI addition on three different aquifer materials from TCE contaminated sites in Alameda Point, CA, Mancelona, MI, and Parris Island, SC. The oxidation and reduction potential of the microcosms consistently decreased by more than 400 mV when NZVI was added at 1.5 g/L concentrations. Sulfate concentrations decreased in the two coastal aquifer materials, and methane was observed in the presence of NZVI in Alameda Point microcosms, but not in the other two materials. Denaturing gradient gel electrophoresis (DGGE) showed significant shifts in Eubacterial diversity just after the Fe(0) was exhausted, and quantitative polymerase chain reaction (qPCR) analyses showed increases of the dissimilatory sulfite reductase gene (dsrA) and Archaeal 16s rRNA genes, indicating that reducing conditions and hydrogen created by NZVI stimulate both sulfate reducer and methanogen populations. Adding NZVI had no deleterious effect on total bacterial abundance in the microcosms. NZVI with a biodegradable polyaspartate coating increased bacterial populations by an order of magnitude relative to controls. The lack of broad bactericidal effect, combined with the stimulatory effect of polyaspartate coatings, has positive implications for NZVI field applications.

  12. Microbial population dynamics during fed-batch operation of commercially available garbage composters.

    PubMed

    Narihiro, T; Abe, T; Yamanaka, Y; Hiraishi, A

    2004-09-01

    Microbial populations in terms of quantity, quality, and activity were monitored during 2 months of start-up operation of commercially available composters for fed-batch treatment of household biowaste. All the reactors, operated at a waste-loading rate of 0.7 kg day(-1) (wet wt), showed a mass reduction efficiency of 88-93%. The core temperature in the reactors fluctuated between 31 degrees C and 58 degrees C due to self-heating. The pH declined during the early stage of operation and steadied at pH 7.4-9.3 during the fully acclimated stage. The moisture content was 48-63% early in the process and 30-40% at the steady state. Both direct total counts and plate counts of bacteria increased via two phases (designated phases I, II) and reached an order of magnitude of 10(11) cells g(-1) (dry wt) at the steady state. Microbial community changes during the start-up period were studied by culture-independent quinone profiling and denatured gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA. In all the reactors, ubiquinones predominated during phase I, whereas partially saturated menaquinones became predominant during phase II. This suggested that there was a drastic population shift from ubiquinone-containing Proteobacteria to Actinobacteria during the start-up period. The DGGE analysis of the bacterial community in one of the reactors also demonstrated a drastic population shift during phase I and the predominance of members of the phyla Proteobacteria and Bacteroidetes during the overall period. But this molecular analysis failed to detect actinobacterial clones from the reactor at any stage.

  13. Implications for informatics given expanding access to care for Veterans and other populations.

    PubMed

    Dixon, Brian E; Haggstrom, David A; Weiner, Michael

    2015-07-01

    Recent investigations into appointment scheduling within facilities operated by the US Department of Veterans Affairs (VA) illuminate systemic challenges in meeting its goal of providing timely access to care for all Veterans. In the wake of these investigations, new policies have been enacted to expand access to care at VA facilities as well as non-VA facilities if the VA is unable to provide access within a reasonable timeframe or a Veteran lives more than 40 miles from a VA medical facility. These policies are similar to broader health reform efforts that seek to expand access to care for other vulnerable populations. In this perspective, we discuss the informatics implications of expanded access within the VA and its wider applicability across the US health system. Health systems will require robust health information exchange, to maintain coordination while access to care is expanded. Existing informatics research can guide short-term implementation; furthermore, new research is needed to generate evidence about how best to achieve the long-term aim of expanded access to care.

  14. Effects of feed intake on composition of sheep rumen contents and their microbial population size.

    PubMed

    Rodríguez, C A; González, J; Alvir, M R; Redondo, R; Cajarville, C

    2003-01-01

    The present study was conducted to determine the effect of feed intake on the composition of the rumen contents of sheep and on their bacterial densities. Whole rumen contents were sampled after a period of continuous inter-rumen infusion of 15NH3 from four rumen-cannulated wethers successively fed on a hay-concentrate diet (2:1, w/w on a DM basis) at two rates of feed intake: 40 and 80 g DM/kg body weight0.75. Total weight and chemical composition of rumen contents, as well as the distribution by size and chemical composition of particles, were determined. The populations of bacteria associated with the liquid (liquid-associated bacteria, LAB) and solid (solid-associated bacteria, SAB) fractions of rumen digesta and the distribution of SAB according to feed particle size were also examined. The greater feed intake caused an increase in the mass of the rumen contents, while its chemical composition did not change, except for a higher content of organic matter (P=0.023). The distribution of feed particles by size was similar at both levels of intake. The concentrations of neutral- and acid-detergent fibre in feed particles decreased and those of total, dietary, and microbial N increased, both with a quadratic response (P=0.001), as particle size decreased. The proportion of LAB in the microbial biomass of rumen digesta reached only 8.0 %. This proportion and the density of LAB were unaffected by the level of feed intake, whereas an apparent reduction (10.4 %) occurred with the SAB biomass in whole rumen contents. A systematic, but not significant, reduction (mean value 11.9 %) in the level of microbial colonisation in the different particle fractions with the increase of feed intake was also observed.

  15. The Abundance and Activity of Nitrate-Reducing Microbial Populations in Estuarine Sediments

    NASA Astrophysics Data System (ADS)

    Cardarelli, E.; Francis, C. A.

    2014-12-01

    Estuaries are productive ecosystems that ameliorate nutrient and metal contaminants from surficial water supplies. At the intersection of terrestrial and aquatic environments, estuarine sediments host major microbially-mediated geochemical transformations. These include denitrification (the conversion of nitrate to nitrous oxide and/or dinitrogen) and dissimilatory nitrate reduction to ammonium (DNRA). Denitrification has historically been seen as the predominant nitrate attenuation process and functions as an effective sink for nitrate. DNRA has previously been believed to be a minor nitrate reduction process and transforms nitrate within the ecosystem to ammonium, a more biologically available N species. Recent studies have compared the two processes in coastal environments and determined fluctuating environmental conditions may suppress denitrification, supporting an increased role for DNRA in the N cycle. Nitrate availability and salinity are factors thought to influence the membership of the microbial communities present, and the nitrate reduction process that predominates. The aim of this study is to investigate how nitrate concentration and salinity alter the transcript abundances of N cycling functional gene markers for denitrification (nirK, nirS) and DNRA (nrfA) in estuarine sediments at the mouth of the hypernutrified Old Salinas River, CA. Short-term whole core incubations amended with artificial freshwater/artificial seawater (2 psu, 35 psu) and with varying NO3- concentrations (200mM, 2000mM) were conducted to assess the activity as well as the abundance of the nitrate-reducing microbial populations present. Gene expression of nirK, nirS, and nrfA at the conclusion of the incubations was quantified using reverse transcription quantitative polymerase chain reaction (RT-qPCR). High abundances of nirK, nirS, and nrfA under particular conditions coupled with the resulting geochemical data ultimately provides insight onto how the aforementioned factors

  16. Long-term effects of timber harvesting on hemicellulolytic microbial populations in coniferous forest soils

    PubMed Central

    Leung, Hilary T C; Maas, Kendra R; Wilhelm, Roland C; Mohn, William W

    2016-01-01

    Forest ecosystems need to be sustainably managed, as they are major reservoirs of biodiversity, provide important economic resources and modulate global climate. We have a poor knowledge of populations responsible for key biomass degradation processes in forest soils and the effects of forest harvesting on these populations. Here, we investigated the effects of three timber-harvesting methods, varying in the degree of organic matter removal, on putatively hemicellulolytic bacterial and fungal populations 10 or more years after harvesting and replanting. We used stable-isotope probing to identify populations that incorporated 13C from labeled hemicellulose, analyzing 13C-enriched phospholipid fatty acids, bacterial 16 S rRNA genes and fungal ITS regions. In soil microcosms, we identified 104 bacterial and 52 fungal hemicellulolytic operational taxonomic units (OTUs). Several of these OTUs are affiliated with taxa not previously reported to degrade hemicellulose, including the bacterial genera Methylibium, Pelomonas and Rhodoferax, and the fungal genera Cladosporium, Pseudeurotiaceae, Capronia, Xenopolyscytalum and Venturia. The effect of harvesting on hemicellulolytic populations was evaluated based on in situ bacterial and fungal OTUs. Harvesting treatments had significant but modest long-term effects on relative abundances of hemicellulolytic populations, which differed in strength between two ecozones and between soil layers. For soils incubated in microcosms, prior harvesting treatments did not affect the rate of incorporation of hemicellulose carbon into microbial biomass. In six ecozones across North America, distributions of the bacterial hemicellulolytic OTUs were similar, whereas distributions of fungal ones differed. Our work demonstrates that diverse taxa in soil are hemicellulolytic, many of which are differentially affected by the impact of harvesting on environmental conditions. However, the hemicellulolytic capacity of soil communities appears

  17. Acinetobacter, Aeromonas, and Trichococcus populations dominate the microbial community within urban sewer infrastructure

    PubMed Central

    VandeWalle, J. L.; Goetz, G.W.; Huse, S.M.; Morrison, H. G.; Sogin, M.L.; Hoffmann, R.G.; Yan, K.; McLellan, S.L.

    2012-01-01

    We evaluated the population structure and temporal dynamics of the dominant community members within sewage influent from two wastewater treatment plants (WWTPs) in Milwaukee, WI. We generated >1.1M bacterial pyrotag sequences from the V6 hypervariable region of 16S rRNA genes from 38 influent samples and two samples taken upstream in the sanitary sewer system. Only a small fraction of pyrotags from influent samples (~15%) matched sequences from human fecal samples. The fecal components of the sewage samples included enriched pyrotag populations from Lactococcus and Enterobacteriaceae relative to their fractional representation in human fecal samples. In contrast to the large number of distinct pyrotags that represent fecal bacteria such as Lachnospiraceae and Bacteroides, only one or two unique V6 sequences represented Acinetobacter, Trichococcus and Aeromonas, which collectively account for nearly 35% of the total sewage community. Two dominant Acinetobacter V6 pyrotags (designated Acineto tag 1 and Acineto tag 2) fluctuated inversely with a seasonal pattern over a 3-year period, suggesting two distinct Acinetobacter populations respond differently to ecological forcings in the system. A single nucleotide change in the V6 pyrotags accounted for the difference in these populations and corresponded to two phylogenically distinct clades based on full-length sequences. Analysis of wavelet functions, derived from a mathematical model of temporal fluctuations, demonstrated that other abundant sewer associated populations including Trichococcus and Aeromonas had temporal patterns similar to either Acineto tag 1 or Acineto tag 2. Populations with related temporal fluctuations were found to significantly correlate with the same WWTP variables (5-day BOD, flow, ammonia, total phosphorous, and suspended solids). These findings illustrate that small differences in V6 sequences can represent phylogenetically and ecologically distinct taxa. This work provides insight into

  18. 2009 MICROBIAL POPULATION BIOLOGY GORDON RESEARCH CONFERENCES JULY 19-24,2009

    SciTech Connect

    ANTHONY DEAN

    2009-07-24

    The 2009 Gordon Conference on Microbial Population Biology will cover a diverse range of cutting edge issues in the microbial sciences and beyond. Firmly founded in evolutionary biology and with a strongly integrative approach, past Conferences have covered a range of topics from the dynamics and genetics of adaptation to the evolution of mutation rate, community ecology, evolutionary genomics, altruism, and epidemiology. The 2009 Conference is no exception, and will include sessions on the evolution of infectious diseases, social evolution, the evolution of symbioses, experimental evolution, adaptive landscapes, community dynamics, and the evolution of protein structure and function. While genomic approaches continue to make inroads, broadening our knowledge and encompassing new questions, the conference will also emphasize the use of experimental approaches to test hypotheses decisively. As in the past, this Conference provides young scientists and graduate students opportunities to present their work in poster format and exchange ideas with leading investigators from a broad spectrum of disciplines. This meeting is never dull: some of the most significant and contentious issues in biology have been thrashed out here. The 2009 meeting will be no exception.

  19. Visualizing the population dynamics of microbial communities in the larval zebrafish gut

    NASA Astrophysics Data System (ADS)

    Parthasarathy, Raghuveer

    In each of our digestive tracts, trillions of microbes representing hundreds of different species colonize local environments, reproduce, and compete with one another. The resulting ecosystems influence many aspects their host's development and health. Little is known about how gut microbial communities vary in space and time: how they grow, fluctuate, and respond to various perturbations. To address this and investigate microbial colonization of the vertebrate gut, we apply light sheet fluorescence microscopy to a model system that combines a realistic in vivo environment with a high degree of experimental control: larval zebrafish with defined subsets of commensal bacterial species. Light sheet microscopy enables three-dimensional imaging with high resolution over the entire intestine, providing visualizations that would be difficult or impossible to achieve with other techniques. Quantitative analysis of image data enables measurement of bacterial abundances and distributions. I will describe this approach and focus especially on recent experiments in which a colonizing bacterial species is challenged by the invasion of a second species, which leads to the decline of the first group. Imaging reveals dramatic population collapses that differentially affect the two species due to their different biogeographies and morphologies. The collapses are driven by the peristaltic motion of the zebrafish intestine, indicating that the physical activity of the host environment can play a major role in mediating inter-species competition. role in mediating inter-species competition. Supported by the National Science Foundation under Grant No. 0922951 and the National Institutes of Health under Award Number 1P50GM098911.

  20. Role of Aerobic Microbial Populations in Cellulose Digestion by Desert Millipedes

    PubMed Central

    Taylor, Elsa C.

    1982-01-01

    I examined the role of aerobic microbial populations in cellulose digestion by two sympatric species of desert millipedes, Orthoporus ornatus and Comanchelus sp. High numbers of bacteria able to grow on media containing cellulose, carboxymethyl cellulose, or cellobiose as the substrate were found in the alimentary tracts of the millipedes. Enzyme assays indicated that most cellulose and hemicellulose degradation occurred in the midgut, whereas the hindgut was an important site for pectin degradation. Hemicellulase and β-glucosidase in both species and possibly Cx-cellulase and pectinase in O. ornatus were of possible microbial origin. Degradation of [14C]cellulose by millipedes whose gut floras were reduced by antibiotic treatment and starvation demonstrated a reduction in 14CO2 release and 14C assimilation and an increase in 14C excretion over values for controls. It appears that the millipede-bacterium association is mutualistic and makes available to millipedes an otherwise mostly unutilizable substrate. Such an association may be an important pathway for decomposition in desert ecosystems. Images PMID:16346074

  1. Ecological differentiation in planktonic and sediment-associated chemotrophic microbial populations in Yellowstone hot springs.

    PubMed

    Colman, Daniel R; Feyhl-Buska, Jayme; Robinson, Kirtland J; Fecteau, Kristopher M; Xu, Huifang; Shock, Everett L; Boyd, Eric S

    2016-09-01

    Chemosynthetic sediment and planktonic community composition and sizes, aqueous geochemistry and sediment mineralogy were determined in 15 non-photosynthetic hot springs in Yellowstone National Park (YNP). These data were used to evaluate the hypothesis that differences in the availability of dissolved or mineral substrates in the bulk fluids or sediments within springs coincides with ecologically differentiated microbial communities and their populations. Planktonic and sediment-associated communities exhibited differing ecological characteristics including community sizes, evenness and richness. pH and temperature influenced microbial community composition among springs, but within-spring partitioning of taxa into sediment or planktonic communities was widespread, statistically supported (P < 0.05) and could be best explained by the inferred metabolic strategies of the partitioned taxa. Microaerophilic genera of the Aquificales predominated in many of the planktonic communities. In contrast, taxa capable of mineral-based metabolism such as S(o) oxidation/reduction or Fe-oxide reduction predominated in sediment communities. These results indicate that ecological differentiation within thermal spring habitats is common across a range of spring geochemistry and is influenced by the availability of dissolved nutrients and minerals that can be used in metabolism.

  2. Access to drinking water and health of populations in Sub-Saharan Africa.

    PubMed

    Ntouda, Julien; Sikodf, Fondo; Ibrahim, Mohamadou; Abba, Ibrahim

    2013-01-01

    Water is at the center of the plant and animal life, the foundation upon which the health of human settlement and development of civilizations rely on. In tropical regions, 80% of diseases are transmitted either by germs in the water, or by vectors staying in it. In Sub-Saharan Africa, statistics show particularly high levels of unmet needs of populations in access to drinking water in a context of socioeconomic development. For this purpose, this study aims to determine the influence of access to drinking water on the health of populations in Sub-Saharan Africa. Using data from Demographic and Health Surveys (DHS) from Cameroon, Senegal and Chad, it is clear from the descriptive analysis that 60% (Cameroon), and 59% (Chad) of the cases of childhood diarrhea in these two countries are due to the consumption of dirty water. In terms of explanatory analysis, we note that when a household in Cameroon, Senegal or Chad does not have access to drinking water, children under 5 years old residing there are respectively 1.29, 1.27 and 1.03 times more likely to have diarrhea than those residing in households with easy access to drinking water. In view of these results, it is recommended to increase access to drinking water in particular by reducing disparities between the rich and poor people.

  3. Effects of Exogenous Yeast and Bacteria on the Microbial Population Dynamics and Outcomes of Olive Fermentations.

    PubMed

    Zaragoza, Jose; Bendiks, Zachary; Tyler, Charlotte; Kable, Mary E; Williams, Thomas R; Luchkovska, Yelizaveta; Chow, Elaine; Boundy-Mills, Kyria; Marco, Maria L

    2017-01-01

    In this study, we examined Sicilian-style green olive fermentations upon the addition of Saccharomyces cerevisiae UCDFST 09-448 and/or Pichia kudriazevii UCDFST09-427 or the lactic acid bacteria (LAB) Lactobacillus plantarum AJ11R and Leuconostoc pseudomesenteroides BGM3R. Olives containing S. cerevisiae UCDFST 09-448, a strain able to hydrolyze pectin, but not P. kudriazevii UCDFST 09-427, a nonpectinolytic strain, exhibited excessive tissue damage within 4 weeks. DNA sequencing of fungal internal transcribed spacer (ITS) regions and comparisons to a yeast-specific ITS sequence database remarkably showed that neither S. cerevisiae UCDFST 09-448 nor P. kudriazevii UCDFST 09-427 resulted in significant changes to yeast species diversity. Instead, Candida boidinii constituted the majority (>90%) of the total yeast present, independent of whether S. cerevisiae or P. kudriazevii was added. By comparison, Lactobacillus species were enriched in olives inoculated with potential starter LAB L. plantarum AJ11R and L. pseudomesenteroides BGM3R according to community 16S rRNA gene sequence analysis. The bacterial diversity of those olives was significantly reduced and resembled control fermentations incubated for a longer period of time. Importantly, microbial populations were highly dynamic at the strain level, as indicated by the large variations in AJ11R and BGM3R cell numbers over time and reductions in the numbers of yeast isolates expressing polygalacturonase activity. These findings show the distinct effects of exogenous spoilage and starter microbes on indigenous communities in plant-based food fermentations that result in very different impacts on product quality. IMPORTANCE Food fermentations are subject to tremendous selective pressures resulting in the growth and persistence of a limited number of bacterial and fungal taxa. Although these foods are vulnerable to spoilage by unintended contamination of certain microorganisms, or alternatively, can be

  4. Effects of Exogenous Yeast and Bacteria on the Microbial Population Dynamics and Outcomes of Olive Fermentations

    PubMed Central

    Zaragoza, Jose; Bendiks, Zachary; Tyler, Charlotte; Kable, Mary E.; Williams, Thomas R.; Luchkovska, Yelizaveta; Chow, Elaine; Boundy-Mills, Kyria

    2017-01-01

    ABSTRACT In this study, we examined Sicilian-style green olive fermentations upon the addition of Saccharomyces cerevisiae UCDFST 09-448 and/or Pichia kudriazevii UCDFST09-427 or the lactic acid bacteria (LAB) Lactobacillus plantarum AJ11R and Leuconostoc pseudomesenteroides BGM3R. Olives containing S. cerevisiae UCDFST 09-448, a strain able to hydrolyze pectin, but not P. kudriazevii UCDFST 09-427, a nonpectinolytic strain, exhibited excessive tissue damage within 4 weeks. DNA sequencing of fungal internal transcribed spacer (ITS) regions and comparisons to a yeast-specific ITS sequence database remarkably showed that neither S. cerevisiae UCDFST 09-448 nor P. kudriazevii UCDFST 09-427 resulted in significant changes to yeast species diversity. Instead, Candida boidinii constituted the majority (>90%) of the total yeast present, independent of whether S. cerevisiae or P. kudriazevii was added. By comparison, Lactobacillus species were enriched in olives inoculated with potential starter LAB L. plantarum AJ11R and L. pseudomesenteroides BGM3R according to community 16S rRNA gene sequence analysis. The bacterial diversity of those olives was significantly reduced and resembled control fermentations incubated for a longer period of time. Importantly, microbial populations were highly dynamic at the strain level, as indicated by the large variations in AJ11R and BGM3R cell numbers over time and reductions in the numbers of yeast isolates expressing polygalacturonase activity. These findings show the distinct effects of exogenous spoilage and starter microbes on indigenous communities in plant-based food fermentations that result in very different impacts on product quality. IMPORTANCE Food fermentations are subject to tremendous selective pressures resulting in the growth and persistence of a limited number of bacterial and fungal taxa. Although these foods are vulnerable to spoilage by unintended contamination of certain microorganisms, or alternatively, can

  5. Microbial population, activity, and phylogenetic diversity in the subseafloor core sediment from the Sea of Okhotsk

    NASA Astrophysics Data System (ADS)

    Inagaki, F.; Suzuki, M.; Takai, K.; Nealson, K. H.; Horikoshi, K.

    2002-12-01

    Subseafloor environments has already been recognized as the largest biosphere on the planet Earth, however, the microbial diversity and activity has been still poorly understood, even in their impacts on biogeochemical processes, tectonic settings, and paleoenvironmental events. We demonstrate here the evaluation of microbial community structure and active habitats in deeply buried cold marine sediments collected from the Sea of Okhotsk by a combined use of molecular ecological surveys and culturing assays. The piston core sediment (MD01-2412) was collected by IMAGES (International Marine Global Change Study) Project from the southeastern Okhotsk Sea, June 2001. The total recovered length was about 58m. The lithology of the core sediment was mainly constructed from pelagic clay (PC) and volcanic ash layers (Ash). We collected aseptically the most inside core parts from 16 sections at different depths for microbiological study. The direct count of DAPI-stained cells revealed that the cells in Ash samples were present 1.2 to 2.2 times higher than in PC samples. The quantitative-PCR of 16S rDNA between bacterial and archaeal rDNA suggested that the increased population density in Ash layers was caused by the bacterial components. We studied approximately 650 and 550 sequences from bacterial and archaeal rDNA clone libraries, respectively. The similarity and phylogenetic analyses revealed that the microbial community structures were apparently different between in Ash layers and PC samples. From bacterial rDNA clone libraries, the members within gamma-Proteobacteria such as genera Halomonas, Shewanella, Psychromonas and Methylosinus were predominantly detected in Ash layers whereas the Dehalococcoides group and delta-Proteobacteria were major bacterial components in PC samples. From archaeal libraries, the sequences from Ash and PC samples were affiliated into the clusters represented by the environmental sequences obtained from terrestrial and deep-sea environments

  6. The dynamical analogy between microbial growth on mixtures of substrates and population growth of competing species.

    PubMed

    Narang, A

    1998-07-05

    There is a similarity between the metabolic dynamics of a microbial species growing on a mixture of two substrates and the dynamics of growth of two competing populations. Specifically, the enzymes catalyzing the uptake and catabolism of substrates exhibit phenomena analogous to extinction and coexistence."Extinction" of the enzymes associated with one of the substrates results in sequential utilization of the substrates (diauxie) (Monod, 1942). "Coexistence" of the enzymes associated with the substrates results in simultaneous utilization of the substrates (Egli, 1995). Here, we formulate a simple model that shows the basis for this dynamical similarity: The equations describing the evolution of the enzyme levels are dynamical analogs of the Lotka-Volterra model for two competing species. The analogy suggests ways of capturing the experimentally observed preculture-dependent growth patterns, i.e., growth patterns that vary depending on the physiological state of the preculture.

  7. [Factors affecting access to health care institutions by the internally displaced population in Colombia].

    PubMed

    Mogollón-Pérez, Amparo Susana; Vázquez, María Luisa

    2008-04-01

    In Colombia, the on-going armed conflict causes displacement of thousands of persons that suffer its economic, social, and health consequences. Despite government regulatory efforts, displaced people still experience serious problems in securing access to health care. In order to analyze the institutional factors that affect access to health care by the internally displaced population, a qualitative, exploratory, and descriptive study was carried out by means of semi-structured individual interviews with a criterion sample of stakeholders (81). A narrative content analysis was performed, with mixed generation of categories and segmentation of data by themes and informants. Inadequate funding, providers' problems with reimbursement by insurers, and lack of clear definition as to coverage under the Social Security System in Health pose barriers to access to health care by the internally displaced population. Bureaucratic procedures, limited inter- and intra-sector coordination, and scarce available resources for public health service providers also affect access. Effective government action is required to ensure the right to health care for this population.

  8. Response of microbial community of tundra soil to global warming: Simulation of seasonal and long-term population dynamics

    SciTech Connect

    Panikov, N.S.

    1994-11-01

    A mathematical model has been constructed and verified to simulate dynamics of a microbial community in typical tundra. The model contains the following state variables: the population densities of three competing microbial species (exemplified by Arthrobacter, Pseudomonas, and Bacillus), indexes of their physiological state, concentration of available organic substrate, plant litter reserves, the amount of microbiovorous protozoans, and temperature. The mathematical model simulates adequately the qualitative features of microbial seasonal dynamics observed in tundra. The global warming and associated increase in primary productivity, as predicted by simulation, will relieve the pressure of L-selection and thus result in stabilization of the tundra microbial community. The model also predicts that aerobic decomposition of dead organic matter in solid will be accelerated compared to its formation. 24 refs., 7 figs., 1 tab.

  9. Range expansions transition from pulled to pushed waves with increasing cooperativity in an experimental microbial population

    NASA Astrophysics Data System (ADS)

    Gandhi, Saurabh; Yurtsev, Eugene; Korolev, Kirill; Gore, Jeff

    Range expansions are becoming more frequent due to environmental changes and rare long distance dispersal, often facilitated by anthropogenic activities. Simple models in theoretical ecology explain many emergent properties of range expansions, such as a constant expansion velocity, in terms of organism-level properties such as growth and dispersal rates. Testing these quantitative predictions in natural populations is difficult because of large environmental variability. Here, we used a controlled microbial model system to study range expansions of populations with and without intra-specific cooperativity. For non-cooperative growth, the expansion dynamics were dominated by population growth at the low-density front, which pulled the expansion forward. We found these expansions to be in close quantitative agreement with the classical theory of pulled waves by Fisher and Skellam, suitably adapted to our experimental system. However, as cooperativity increased, the expansions transitioned to being pushed, i.e. controlled by growth in the bulk as well as in the front. Although both pulled and pushed waves expand at a constant velocity and appear otherwise similar, their distinct dynamics leads to very different evolutionary consequences. Given the prevalence of cooperative growth in nature, understanding the effects of cooperativity is essential to managing invading species and understanding their evolution.

  10. Thermodynamic concepts in the study of microbial populations: age structure in Plasmodium falciparum infected red blood cells.

    PubMed

    Ferrer, Jordi; Prats, Clara; López, Daniel; Vidal-Mas, Jaume; Gargallo-Viola, Domingo; Guglietta, Antonio; Giró, Antoni

    2011-01-01

    Variability is a hallmark of microbial systems. On the one hand, microbes are subject to environmental heterogeneity and undergo changeable conditions in their immediate surroundings. On the other hand, microbial populations exhibit high cellular diversity. The relation between microbial diversity and variability of population dynamics is difficult to assess. This connection can be quantitatively studied from a perspective that combines in silico models and thermodynamic methods and interpretations. The infection process of Plasmodium falciparum parasitizing human red blood cells under laboratory cultivation conditions is used to illustrate the potential of Individual-based models in the context of predictive microbiology and parasitology. Experimental data from several in vitro cultures are compared to the outcome of an individual-based model and analysed from a thermodynamic perspective. This approach allows distinguishing between intrinsic and external constraints that give rise to the diversity in the infection forms, and it provides a criterion to quantitatively define transient and stationary regimes in the culture. Increasing the ability of models to discriminate between different states of microbial populations enhances their predictive capability which finally leads to a better the control over culture systems. The strategy here presented is of general application and it can substantially improve modelling of other types of microbial communities.

  11. Spatial analysis of cattle and shoat population in Ethiopia: growth trend, distribution and market access.

    PubMed

    Leta, Samson; Mesele, Frehiwot

    2014-01-01

    The livestock subsector has an enormous contribution to Ethiopia's national economy and livelihoods of many Ethiopians. The subsector contributes about 16.5% of the national Gross Domestic Product (GDP) and 35.6% of the agricultural GDP. It also contributes 15% of export earnings and 30% of agricultural employment. The livestock subsector currently support and sustain livelihoods for 80% of all rural population. The GDP of livestock related activities valued at 59 billion birr. Ethiopian livestock population trends, distribution and marketing vary considerably across space and time due to a variety of reasons. This study was aimed to assess cattle and shoat population growth trend, distribution and their access to market. Regression analysis was used to assess the cattle and shoat population growth trend and Geographic Information Systems (GIS) techniques were used to determine the spatial distribution of cattle and shoats, and their relative access to market. The data sets used are agricultural census (2001/02) and annual CSA agricultural sample survey (1995/96 to 2012/13). In the past eighteen years, the livestock population namely cattle, sheep and goat grew from 54.5 million to over 103.5 million with average annual increment of 3.4 million. The current average national cattle, sheep and goat population per km(2) are estimated to be 71, 33 and 29 respectively (excluding Addis Ababa, Afar and Somali regions). From the total livestock population the country owns about 46% cattle, 43% sheep and 40% goats are reared within 10 km radius from major livestock market centres and all-weather roads. On the other hand, three fourth of the country's land mass which comprises 15% of the cattle, 20% of the sheep and 21% of goat population is not accessible to market (greater than 30 km from major livestock market centres). It is found that the central highland regions account for the largest share of livestock population and also more accessible to market. Defining the

  12. Accessibility of dog populations for rabies control in Kathmandu valley, Nepal.

    PubMed Central

    Bögel, K.; Joshi, D. D.

    1990-01-01

    The accessibility of dogs in urban areas of Kathmandu valley was measured using the following approaches: determination of the proportion of dogs that bore signs of having been the objects of religious worship and other signs of household association, supplemented by information obtained by interviewing people in the neighbourhood; and the vaccination coverage attained in a rabies control campaign that was preceded by intensive activities to encourage the community to participate. An accessibility rate of 90-95% was determined using the first of these approaches, whereas 75-80% of the total dog population was reached in the vaccination campaign. PMID:2289296

  13. A microwave-powered sterilizable interface for aseptic access to bioreactors that are vulnerable to microbial contamination

    NASA Technical Reports Server (NTRS)

    Atwater, J. E.; Michalek, W. F.; Wheeler, R. R. Jr; Dahl, R.; Lunsford, T. D.; Garmon, F. C.; Sauer, R. L.

    2001-01-01

    Novel methods and apparatus that employ the rapid heating characteristics of microwave irradiation to facilitate the aseptic transfer of nutrients, products, and other materials between microbially sensitive systems and the external environment are described. The microwave-sterilizable access port (MSAP) consists of a 600-W magnetron emitting at a frequency of 2.45 GHz, a sterilization chamber with inlet and outlet flow lines, and a specimen transfer interface. Energy is routed to the sterilization chamber via a coaxial transmission line where small quantities of water couple strongly with the incident radiation to produce a superheated vapor phase. The efficiency of energy transfer is enhanced through the use of microwave susceptors within the sterilization chamber. Mating surfaces are thermally sterilized through direct contact with the hot gas. Efficacy has been demonstrated using the thermophile Bacillus stearothermophilus.

  14. A microwave-powered sterilizable interface for aseptic access to bioreactors that are vulnerable to microbial contamination.

    PubMed

    Atwater, J E; Michalek, W F; Wheeler, R R; Dahl, R; Lunsford, T D; Garmon, F C; Sauer, R L

    2001-01-01

    Novel methods and apparatus that employ the rapid heating characteristics of microwave irradiation to facilitate the aseptic transfer of nutrients, products, and other materials between microbially sensitive systems and the external environment are described. The microwave-sterilizable access port (MSAP) consists of a 600-W magnetron emitting at a frequency of 2.45 GHz, a sterilization chamber with inlet and outlet flow lines, and a specimen transfer interface. Energy is routed to the sterilization chamber via a coaxial transmission line where small quantities of water couple strongly with the incident radiation to produce a superheated vapor phase. The efficiency of energy transfer is enhanced through the use of microwave susceptors within the sterilization chamber. Mating surfaces are thermally sterilized through direct contact with the hot gas. Efficacy has been demonstrated using the thermophile Bacillus stearothermophilus.

  15. Demographic population model for American shad: will access to additional habitat upstream of dams increase population sizes?

    USGS Publications Warehouse

    Harris, Julianne E.; Hightower, Joseph E.

    2012-01-01

    American shad Alosa sapidissima are in decline in their native range, and modeling possible management scenarios could help guide their restoration. We developed a density-dependent, deterministic, stage-based matrix model to predict the population-level results of transporting American shad to suitable spawning habitat upstream of dams on the Roanoke River, North Carolina and Virginia. We used data on sonic-tagged adult American shad and oxytetracycline-marked American shad fry both above and below dams on the Roanoke River with information from other systems to estimate a starting population size and vital rates. We modeled the adult female population over 30 years under plausible scenarios of adult transport, effective fecundity (egg production), and survival of adults (i.e., to return to spawn the next year) and juveniles (from spawned egg to age 1). We also evaluated the potential effects of increased survival for adults and juveniles. The adult female population size in the Roanoke River was estimated to be 5,224. With no transport, the model predicted a slow population increase over the next 30 years. Predicted population increases were highest when survival was improved during the first year of life. Transport was predicted to benefit the population only if high rates of effective fecundity and juvenile survival could be achieved. Currently, transported adults and young are less likely to successfully out-migrate than individuals below the dams, and the estimated adult population size is much smaller than either of two assumed values of carrying capacity for the lower river; therefore, transport is not predicted to help restore the stock under present conditions. Research on survival rates, density-dependent processes, and the impacts of structures to increase out-migration success would improve evaluation of the potential benefits of access to additional spawning habitat for American shad.

  16. GC fractionation enhances microbial community diversity assessment and detection of minority populations of bacteria by denaturing gradient gel electrophoresis.

    PubMed

    Holben, William E; Feris, Kevin P; Kettunen, Anu; Apajalahti, Juha H A

    2004-04-01

    Effectively and accurately assessing total microbial community diversity is one of the primary challenges in modern microbial ecology. This is particularly true with regard to the detection and characterization of unculturable populations and those present only in low abundance. We report a novel strategy, GC fractionation combined with denaturing gradient gel electrophoresis (GC-DGGE), which combines mechanistically different community analysis approaches to enhance assessment of microbial community diversity and detection of minority populations of microbes. This approach employs GC fractionation as an initial step to reduce the complexity of the community in each fraction. This reduced complexity facilitates subsequent detection of diversity in individual fractions. DGGE analysis of individual fractions revealed bands that were undetected or only poorly represented when total bacterial community DNA was analyzed. Also, directed cloning and sequencing of individual bands from DGGE lanes corresponding to individual G+C fractions allowed detection of numerous phylotypes that were not recovered using a traditional random cloning and sequencing approach.

  17. Effect of Plants Containing Secondary Compounds with Palm Oil on Feed Intake, Digestibility, Microbial Protein Synthesis and Microbial Population in Dairy Cows

    PubMed Central

    Anantasook, N.; Wanapat, M.; Cherdthong, A.; Gunun, P.

    2013-01-01

    The objective of this study was to determine the effect of rain tree pod meal with palm oil supplementation on feed intake, digestibility, microbial protein synthesis and microbial populations in dairy cows. Four, multiparous early-lactation Holstein-Friesian crossbred (75%) lactating dairy cows with an initial body weight (BW) of 405±40 kg and 36±8 DIM were randomly assigned to receive dietary treatments according to a 4×4 Latin square design. The four dietary treatments were un-supplementation (control), supplementation with rain tree pod meal (RPM) at 60 g/kg, supplementation with palm oil (PO) at 20 g/kg, and supplementation with RPM at 60 g/kg and PO at 20 g/kg (RPO), of total dry matter intake. The cows were offered concentrates, at a ratio of concentrate to milk production of 1:2, and chopped 30 g/kg of urea treated rice straw was fed ad libitum. The RPM contained condensed tannins and crude saponins at 88 and 141 g/kg of DM, respectively. It was found that supplementation with RPM and/or PO to dairy cows diets did not show negative effects on feed intake and ruminal pH and BUN at any times of sampling (p>0.05). However, RPM supplementation resulted in lower crude protein digestibility, NH3-N concentration and number of proteolytic bacteria. It resulted in greater allantoin absorption and microbial crude protein (p<0.05). In addition, dairy cows showed a higher efficiency of microbial N supply (EMNS) in both RPM and RPO treatments. Moreover, NDF digestibility and cellulolytic bacteria numbers were highest in RPO supplementation (p<0.05) while, supplementation with RPM and/or PO decreased the protozoa population in dairy cows. Based on this study, supplementation with RPM and/or PO in diets could improve fiber digestibility, microbial protein synthesis in terms of quantity and efficiency and microbial populations in dairy cows. PMID:25049855

  18. RELATIONSHIPS BETWEEN CULTURABLE SOIL MICROBIAL POPULATIONS AND GROSS NITROGEN TRANSFORMATION PROCESSES IN A CLAY LOAM SOIL ACROSS ECOSYSTEMS

    EPA Science Inventory

    The size and quality of soil organic matter (SOM) pool can vary between ecosystems and can affect many soil properties. The objective of this study was to examine the relationship between gross N transformation rates and microbial populations and to investigate the role that SOM...

  19. A framework for guiding health literacy research in populations with universal access to healthcare.

    PubMed

    Weld, Konstantine Keian; Padden, Diane; Ramsey, Gloria; Garmon Bibb, Sandra C

    2008-01-01

    At least one third of the US population suffers from limited health literacy, which has been linked to poorer health status, higher costs, and individuals who are socioeconomically disadvantaged. However, research and the development of theoretical frameworks to study health literacy have only recently begun to occur. The purpose of this article is to describe theoretical frameworks that have either been used or may be used to guide health literacy research and to identify implications for nursing research and practice related to an adaptation of a health literacy framework developed specifically for conducting research in populations with universal access to healthcare.

  20. Effect of Portulaca oleracea extracts on growth performance and microbial populations in ceca of broilers.

    PubMed

    Zhao, X H; He, X; Yang, X F; Zhong, X H

    2013-05-01

    The aim of this study was to investigate the effects of Portulaca oleracea extracts on growth performance and microbial populations in the ceca of broilers. A total of 120 one-day-old broilers were randomly divided into 3 groups. Portulaca oleracea extracts were added to diets at 0.2 and 0.4% (wt/wt; POL-0.2, POL-0.4), respectively. The control (CON) group was administered with no P. oleracea extract supplementation. Body weight gain and feed conversion ratio were recorded every 2 wk. On d 28 and 42, the cecal contents were collected and assayed for Escherichia coli, Lactobacillus, and Bifidobacterium populations. Additionally, the pH of the ileum and cecum was measured. The results showed that both on d 28 and 42 BW gain of P. oleracea extract supplementation groups was significantly higher, whereas the feed conversion ratio was lower (P < 0.05) compared with CON. On d 28 and 42, significantly (P < 0.05) fewer E. coli were recovered from ceca of broilers provided with the POL-0.2 diet than from broilers provided with the control diet. The quantities of Lactobacillus and Bifidobacterium of POL-0.2 were significantly (P < 0.05) higher than CON. Results showed P. oleracea extracts have no distinct influence on intestinal pH. These data suggest that P. oleracea extract supplementation significantly altered the cecal bacterial community without affecting the intestinal pH.

  1. Influence of packaging conditions on natural microbial population growth of endive.

    PubMed

    Charles, Florence; Rugani, Nathalie; Gontard, Nathalie

    2005-05-01

    The influence of three packaging conditions, i.e., unmodified atmosphere packaging (UAP), passive modified atmosphere packaging (MAP), and active MAP, on the natural microbial population growth of endive was investigated at 20 degrees C. For UAP, endive was placed in macroperforated oriented polypropylene pouches that maintained gas composition close to that of air (21 kPa O2 and 0 kPa CO2) but also limited superficial product dehydration. For MAP, endive was placed in low-density polyethylene pouches that induced a 3 kPa O2 and 5 kPa CO2 equilibrium atmosphere composition. Steady state was reached after 25 h of storage with an oxygen absorbing packet (active MAP) compared with 100 h without the packet (passive MAP) and was maintained for 200 h. After 312 h of storage, both active and passive MAP reduced total aerobic mesophile, yeast, and mold population growth compared with endive in UAP. Active MAP accelerated and improved the inhibition of Pseudomonas spp. and Enterobacteriaceae, respectively, probably because of the rapid O2 depletion during the transition period. A shift in the Enterobacteriaceae subpopulation from Rhanella aquatilis to Enterobacter agglomerans was observed for both passive and active MAP.

  2. Identification of microbial populations driving biopolymer degradation in acidic peatlands by metatranscriptomic analysis.

    PubMed

    Ivanova, Anastasia A; Wegner, Carl-Eric; Kim, Yongkyu; Liesack, Werner; Dedysh, Svetlana N

    2016-10-01

    Northern peatlands play a crucial role in the global carbon balance, serving as a persistent sink for atmospheric CO2 and a global carbon store. Their most extensive type, Sphagnum-dominated acidic peatlands, is inhabited by microorganisms with poorly understood degradation capabilities. Here, we applied a combination of barcoded pyrosequencing of SSU rRNA genes and Illumina RNA-Seq of total RNA (metatranscriptomics) to identify microbial populations and enzymes involved in degrading the major components of Sphagnum-derived litter and exoskeletons of peat-inhabiting arthropods: cellulose, xylan, pectin and chitin. Biopolymer addition to peat induced a threefold to fivefold increase in bacterial cell numbers. Functional community profiles of assembled mRNA differed between experimental treatments. In particular, pectin and xylan triggered increased transcript abundance of genes involved in energy metabolism and central carbon metabolism, such as glycolysis and TCA cycle. Concurrently, the substrate-induced activity of bacteria on these two biopolymers stimulated grazing of peat-inhabiting protozoa. Alveolata (ciliates) was the most responsive protozoa group as confirmed by analysis of both SSU rRNA genes and SSU rRNA. A stimulation of alphaproteobacterial methanotrophs on pectin was consistently shown by rRNA and mRNA data. Most likely, their significant enrichment was due to the utilization of methanol released during the degradation of pectin. Analysis of SSU rRNA and total mRNA revealed a specific response of Acidobacteria and Actinobacteria to chitin and pectin, respectively. Relatives of Telmatobacter bradus were most responsive among the Acidobacteria, while the actinobacterial response was primarily affiliated with Frankiales and Propionibacteriales. The expression of a wide repertoire of carbohydrate-active enzymes (CAZymes) corresponded well to the detection of a highly diverse peat-inhabiting microbial community, which is dominated by yet uncultivated

  3. Biodegradation of DDT by stimulation of indigenous microbial populations in soil with cosubstrates.

    PubMed

    Ortíz, Irmene; Velasco, Antonio; Le Borgne, Sylvie; Revah, Sergio

    2013-04-01

    Stimulation of native microbial populations in soil by the addition of small amounts of secondary carbon sources (cosubstrates) and its effect on the degradation and theoretical mineralization of DDT [l,l,l-trichloro-2,2-bis(p-chlorophenyl)ethane] and its main metabolites, DDD and DDE, were evaluated. Microbial activity in soil polluted with DDT, DDE and DDD was increased by the presence of phenol, hexane and toluene as cosubstrates. The consumption of DDT was increased from 23 % in a control (without cosubstrate) to 67, 59 and 56 % in the presence of phenol, hexane and toluene, respectively. DDE was completely removed in all cases, and DDD removal was enhanced from 67 % in the control to ~86 % with all substrates tested, except for acetic acid and glucose substrates. In the latter cases, DDD removal was either inhibited or unchanged from the control. The optimal amount of added cosubstrate was observed to be between 0.64 and 2.6 mg C [Formula: see text]. The CO2 produced was higher than the theoretical amount for complete cosubstrate mineralization indicating possible mineralization of DDT and its metabolites. Bacterial communities were evaluated by denaturing gradient gel electrophoresis, which indicated that native soil and the untreated control presented a low bacterial diversity. The detected bacteria were related to soil microorganisms and microorganisms with known biodegradative potential. In the presence of toluene a bacterium related to Azoarcus, a genus that includes species capable of growing at the expense of aromatic compounds such as toluene and halobenzoates under denitrifying conditions, was detected.

  4. Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well.

    PubMed

    Robbins, Steven J; Evans, Paul N; Parks, Donovan H; Golding, Suzanne D; Tyson, Gene W

    2016-01-01

    Coal bed methane (CBM) is generated primarily through the microbial degradation of coal. Despite a limited understanding of the microorganisms responsible for this process, there is significant interest in developing methods to stimulate additional methane production from CBM wells. Physical techniques including hydraulic fracture stimulation are commonly applied to CBM wells, however the effects of specific additives contained in hydraulic fracture fluids on native CBM microbial communities are poorly understood. Here, metagenomic sequencing was applied to the formation waters of a hydraulically fractured and several non-fractured CBM production wells to determine the effect of this stimulation technique on the in-situ microbial community. The hydraulically fractured well was dominated by two microbial populations belonging to the class Phycisphaerae (within phylum Planctomycetes) and candidate phylum Aminicenantes. Populations from these phyla were absent or present at extremely low abundance in non-fractured CBM wells. Detailed metabolic reconstruction of near-complete genomes from these populations showed that their high relative abundance in the hydraulically fractured CBM well could be explained by the introduction of additional carbon sources, electron acceptors, and biocides contained in the hydraulic fracture fluid.

  5. Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well

    PubMed Central

    Robbins, Steven J.; Evans, Paul N.; Parks, Donovan H.; Golding, Suzanne D.; Tyson, Gene W.

    2016-01-01

    Coal bed methane (CBM) is generated primarily through the microbial degradation of coal. Despite a limited understanding of the microorganisms responsible for this process, there is significant interest in developing methods to stimulate additional methane production from CBM wells. Physical techniques including hydraulic fracture stimulation are commonly applied to CBM wells, however the effects of specific additives contained in hydraulic fracture fluids on native CBM microbial communities are poorly understood. Here, metagenomic sequencing was applied to the formation waters of a hydraulically fractured and several non-fractured CBM production wells to determine the effect of this stimulation technique on the in-situ microbial community. The hydraulically fractured well was dominated by two microbial populations belonging to the class Phycisphaerae (within phylum Planctomycetes) and candidate phylum Aminicenantes. Populations from these phyla were absent or present at extremely low abundance in non-fractured CBM wells. Detailed metabolic reconstruction of near-complete genomes from these populations showed that their high relative abundance in the hydraulically fractured CBM well could be explained by the introduction of additional carbon sources, electron acceptors, and biocides contained in the hydraulic fracture fluid. PMID:27375557

  6. Accessing the black box of microbial diversity and ecophysiology: recent advances through polyphasic experiments.

    PubMed

    Collins, Gavin; Kavanagh, Siobhán; McHugh, Sharon; Connaughton, Sean; Kearney, Aileen; Rice, Olivia; Carrigg, Cora; Scully, Colm; Bhreathnach, Niamh; Mahony, Thérèse; Madden, Pádhraig; Enright, Anne-Marie; O'flaherty, Vincent

    2006-01-01

    The microbial ecology of a range of anaerobic biological assemblages (granular sludge) from full- and laboratory-scale wastewater treatment bioreactors, and of crop-growing and peat soils, was determined using a variety of 16S rRNA gene-based techniques, including clone library, terminal restriction fragment length polymorphism (TRFLP) and denaturing gradient gel electrophoresis (DGGE) analyses. Fluorescent in situ hybridization (FISH) using 16S rRNA gene-targeted probes was employed to complete a "full-cycle rRNA approach" with selected biomass. Genetic fingerprinting (TRFLP and DGGE) was effectively used to elucidate community structure-crop relationships, and to detect and monitor trends in bioreactor sludge and specific enrichment cultures of peat soil. Greater diversity was resolved within bacterial than within archaeal communities, and unexpected reservoirs of uncultured Crenarchaeota were detected in sludge granules. Advanced radiotracer incubations and micro-beta imaging were employed in conjunction with FISH to elucidate the eco-functionalism of these organisms. Crenarchaeota clusters were identified in close associated with methanogenic Archaea and both were localised with acetate uptake in biofilm structure.

  7. Accessibility

    EPA Pesticide Factsheets

    Federal laws, including Section 508 of the Rehabilitation Act, mandate that people with disabilities have access to the same information that someone without a disability would have. 508 standards cover electronic and information technology (EIT) products.

  8. Effect of incremental doses of radiation on viability of the microbial population on synthetic operating room gowns.

    PubMed Central

    Whitby, J L; Storey, D G

    1982-01-01

    A total of 700 25-cm2 samples of surgical gown material were exposed to doses of cobalt-60 radiation of 0.0 to 0.6 Mrad in 0.1-Mrad increments. Pour plates were made, and the microbial colonies that arose were enumerated, isolated, and identified as to species. The death rate of the microbial population was calculated, and the mean D10 value of 0.269 Mrad was obtained. Analysis showed that the initial population on unirradiated material had been underestimated; when the counts obtained by homogenization of unirradiated material were substituted, a corrected mean D10 value of 0.249 Mrad was obtained. The isolates obtained were identified, and 70.7% were found to be Bacillus spp. with 12 different species identified, 16.2% were Micrococcus spp. with 6 different species identified, and 8.2% were fungi with 10 different species identified. Calculations were made for appropriate doses of radiation to sterilize gowns with this contaminating microbial population. These calculations gave an estimated dose of radiation of 1.98 to 1.81 Mrad to reduce the observed population to 0.001, a standard where 1 gown in 1,000 might contain a living organism. Comparison of the radiation resistance of this population with that of others reported in the literature showed good agreement. PMID:7073273

  9. Permanent genetic access to transiently active neurons via TRAP: targeted recombination in active populations.

    PubMed

    Guenthner, Casey J; Miyamichi, Kazunari; Yang, Helen H; Heller, H Craig; Luo, Liqun

    2013-06-05

    Targeting genetically encoded tools for neural circuit dissection to relevant cellular populations is a major challenge in neurobiology. We developed an approach, targeted recombination in active populations (TRAP), to obtain genetic access to neurons that were activated by defined stimuli. This method utilizes mice in which the tamoxifen-dependent recombinase CreER(T2) is expressed in an activity-dependent manner from the loci of the immediate early genes Arc and Fos. Active cells that express CreER(T2) can only undergo recombination when tamoxifen is present, allowing genetic access to neurons that are active during a time window of less than 12 hr. We show that TRAP can provide selective access to neurons activated by specific somatosensory, visual, and auditory stimuli and by experience in a novel environment. When combined with tools for labeling, tracing, recording, and manipulating neurons, TRAP offers a powerful approach for understanding how the brain processes information and generates behavior.

  10. Fluorescently Labeled Virus Probes Show that Natural Virus Populations Can Control the Structure of Marine Microbial Communities.

    PubMed

    Hennes, K P; Suttle, C A; Chan, A M

    1995-10-01

    Fluorescently stained viruses were used as probes to label, identify, and enumerate specific strains of bacteria and cyanobacteria in mixed microbial assemblages. Several marine virus isolates were fluorescently stained with YOYO-1 or POPO-1 (Molecular Probes, Inc.) and added to seawater samples that contained natural microbial communities. Cells to which the stained viruses adsorbed were easily distinguished from nonhost cells; typically, there was undetectable binding of stained viruses to natural microbial assemblages containing >10(sup6) bacteria ml(sup-1) but to which host cells were not added. Host cells that were added to natural seawater were quantified with 99% (plusmn) 2% (mean (plusmn) range) efficiency with fluorescently labeled virus probes (FLVPs). A marine bacterial isolate (strain PWH3a), tentatively identified as Vibrio natriegens, was introduced into natural microbial communities that were either supplemented with nutrients or untreated, and changes in the abundance of the isolate were monitored with FLVPs. Simultaneously, the concentrations of viruses that infected strain PWH3a were monitored by plaque assay. Following the addition of PWH3a, the concentration of viruses infecting this strain increased from undetectable levels (<1 ml(sup-1)) to 2.9 x 10(sup7) and 8.3 x 10(sup8) ml(sup-1) for the untreated and nutrient-enriched samples, respectively. The increase in viruses was associated with a collapse in populations of strain PWH3a from ca. 30 to 2% and 43 to 0.01% of the microbial communities in untreated and nutrient-enriched samples, respectively. These results clearly demonstrate that FLVPs can be used to identify and quantify specific groups of bacteria in mixed microbial communities. The data show as well that viruses which are present at low abundances in natural aquatic viral communities can control microbial community structure.

  11. Fluorescently Labeled Virus Probes Show that Natural Virus Populations Can Control the Structure of Marine Microbial Communities

    PubMed Central

    Hennes, K. P.; Suttle, C. A.; Chan, A. M.

    1995-01-01

    Fluorescently stained viruses were used as probes to label, identify, and enumerate specific strains of bacteria and cyanobacteria in mixed microbial assemblages. Several marine virus isolates were fluorescently stained with YOYO-1 or POPO-1 (Molecular Probes, Inc.) and added to seawater samples that contained natural microbial communities. Cells to which the stained viruses adsorbed were easily distinguished from nonhost cells; typically, there was undetectable binding of stained viruses to natural microbial assemblages containing >10(sup6) bacteria ml(sup-1) but to which host cells were not added. Host cells that were added to natural seawater were quantified with 99% (plusmn) 2% (mean (plusmn) range) efficiency with fluorescently labeled virus probes (FLVPs). A marine bacterial isolate (strain PWH3a), tentatively identified as Vibrio natriegens, was introduced into natural microbial communities that were either supplemented with nutrients or untreated, and changes in the abundance of the isolate were monitored with FLVPs. Simultaneously, the concentrations of viruses that infected strain PWH3a were monitored by plaque assay. Following the addition of PWH3a, the concentration of viruses infecting this strain increased from undetectable levels (<1 ml(sup-1)) to 2.9 x 10(sup7) and 8.3 x 10(sup8) ml(sup-1) for the untreated and nutrient-enriched samples, respectively. The increase in viruses was associated with a collapse in populations of strain PWH3a from ca. 30 to 2% and 43 to 0.01% of the microbial communities in untreated and nutrient-enriched samples, respectively. These results clearly demonstrate that FLVPs can be used to identify and quantify specific groups of bacteria in mixed microbial communities. The data show as well that viruses which are present at low abundances in natural aquatic viral communities can control microbial community structure. PMID:16535146

  12. Particulate DNA in smoker fluids: Evidence for existence of microbial populations in hot hydrothermal systems

    SciTech Connect

    Straube, W.L.; Colwell, R.R. Univ. of Maryland, Baltimore ); Deming, J.W.; Baross, J.A. ); Somerville, C.C. )

    1990-05-01

    As part of an interdisciplinary study of hydrothermal vents on the Endeavour Segment of the Juan de Fuca Ridge, we used the submersible ALVIN to collect 57 fluid samples from 17 different hot vents (smokers and flanges) and their environs for the purpose of extracting particulate DNA. Particulate material concentrated from these samples was lysed enzymatically (enz) and by a combination of enzyme and French press treatment (fp). Concentrations of partially purified DNA recovered from these lysates were determined spectrofluorometrically. Ambient seawater surrounding the vents was found to contain low DNA concentrations, 0.18 to 0.32 ng of DNA per ml, while low-temperature vent samples yielded significantly higher concentrations of 0.37 to 2.12 ng of DNA per ml. Although DNA recovery values from superheated (210 to 345{degree}C) flange samples were not significantly different from ambient seawater values, most of the superheated (174 to 357{degree}C) smoker fluid samples contained particulate DNA in concentrations too high to be attributable to entrained seawater. Detailed sampling at one smoker site demonstrated not only the existence of significant levels of particulate DNA in the superheated smoker fluids but also the presence of an elevated microbial population in the buoyant plume 20 to 100 m above the smoker. These results underscore the heterogeneity of smoker environments within a given hydrothermal vent fluid and indicate that microorganisms exist in some superheated fluids.

  13. Impacts of Co-Solvent Flushing on Microbial Populations Capable of Degrading Trichloroethylene

    PubMed Central

    Ramakrishnan, Vijayalakshmi; Ogram, Andrew V.; Lindner, Angela S.

    2005-01-01

    With increased application of co-solvent flushing technologies for removal of nonaqueous phase liquids from groundwater aquifers, concern over the effects of the solvent on native microorganisms and their ability to degrade residual contaminant has also arisen. This study assessed the impact of ethanol flushing on the numbers and activity potentials of trichloroethylene (TCE)-degrading microbial populations present in aquifer soils taken immediately after and 2 years after ethanol flushing of a former dry cleaners site. Polymerase chain reaction analysis revealed soluble methane monooxygenase genes in methanotrophic enrichments, and 16S rRNA analysis identified Methylocystis parvus with 98% similarity, further indicating the presence of a type II methanotroph. Dissimilatory sulfite reductase genes in sulfate-reducing enrichments prepared were also observed. Ethanol flushing was simulated in columns packed with uncontaminated soils from the dry cleaners site that were dosed with TCE at concentrations observed in the field; after flushing, the columns were subjected to a continuous flow of 500 pore volumes of groundwater per week. Total acridine orange direct cell counts of the flushed and nonflushed soils decreased over the 15-week testing period, but after 5 weeks, the flushed soils maintained higher cell counts than the nonflushed soils. Inhibition of methanogenesis by sulfate reduction was observed in all column soils, as was increasing removal of total methane by soils incubated under methanotrophic conditions. These results showed that impacts of ethanol were not as severe as anticipated and imply that ethanol may mitigate the toxicity of TCE to the microorganisms. PMID:15626648

  14. Effects of intermittent and continuous aeration on accelerative stabilization and microbial population dynamics in landfill bioreactors.

    PubMed

    Sang, Nguyen Nhu; Soda, Satoshi; Inoue, Daisuke; Sei, Kazunari; Ike, Michihiko

    2009-10-01

    Performance and microbial population dynamics in landfill bioreactors were investigated in laboratory experiments. Three reactors were operated without aeration (control reactor, CR), with cyclic 6-h aeration and 6-h non-aeration (intermittently aerated reactor, IAR), and with continuous aeration (continuously aerated reactor, CAR). Each reactor was loaded with high-organic solid waste. The performance of IAR was highest among the reactors up to day 90. The respective solid weight, organic matter content, and waste volume on day 90 in the CR, IAR, and CAR were 50.9, 39.1, and 47.5%; 46.5, 29.3 and 35.0%; and 69, 38, and 53% of the initial values. Organic carbon and nitrogen compounds in leachate in the IAR and the CAR showed significant decreases in comparison to those in the CR. The most probable number (MPN) values of fungal 18S rDNA in the CAR and the IAR were higher than those in the CR. Terminal restriction fragment length polymorphism analysis showed that unique and diverse eubacterial and archaeal communities were formed in the IAR. The intermittent aeration strategy was favorable for initiation of solubilization of organic matter by the aerobic fungal populations and the reduction of the acid formation phase. Then the anaerobic H(2)-producing bacteria Clostridium became dominant in the IAR. Sulfate-reducing bacteria, which cannot use acetate/sulfate but which instead use various organics/sulfate as the electron donor/acceptor were also dominant in the IAR. Consequently, Methanosarcinales, which are acetate-utilizing methanogens, became the dominant archaea in the IAR, where high methane production was observed.

  15. Unequal Accessibility of Nurseries for Sick Children in Over- and Under-Populated Areas of Japan.

    PubMed

    Ehara, Akira

    2017-01-01

    Infants and toddlers are prone to rapidly contracting illnesses, which are usually attributed to infectious diseases. Most nurseries and schools in Japan, however, refuse to accept children even with mild illnesses. For working parents, a sick child may therefore create new problems as the situation requires new day-care arrangements. To support such families, the Japanese government subsidizes construction and management of nurseries that operate especially for sick children. However, it has not been known whether most families are able to access such nurseries. To clarify the accessibility of these services, I calculated the distance to the nurseries from each of the 211,012 "blocks" (small residential areas with a median of 0.18 km(2)) in Japan and determined the proportion of children aged 0-4 years who lived within 3, 5, 10, 20 or 30 km of the nearest such nursery. Overall, 82.1% of these children lived within 10 km. However, the proportion was lower in northern parts of Japan such as Hokkaido and Tohoku, which have expansive land areas and low population and pediatric department densities. The proportion of children who lived within that same distance of the nearest nursery was also much lower in small towns and villages with 10,000 or fewer residents. Nurseries for sick children were not evenly distributed, and children and their caregivers in under-populated areas had to travel further to access these facilities. As the national government subsidizes such services, children and caregivers throughout Japan should have equal access to them.

  16. Metaproteomic and metagenomic analyses of defined oceanic microbial populations using microwave cell fixation and flow cytometric sorting.

    PubMed

    Mary, Isabelle; Oliver, Anna; Skipp, Paul; Holland, Ross; Topping, Juliette; Tarran, Glen; Scanlan, David J; O'Connor, C David; Whiteley, Andrew S; Burkill, Peter H; Zubkov, Mikhail V

    2010-10-01

    A major obstacle in the molecular investigation of natural, especially oceanic, microbial cells is their adequate preservation for further land-based molecular analyses. Here, we examined the use of microwaves for cell fixation before high-speed flow cytometric sorting to define the metaproteomes and metagenomes of key microbial populations. The microwave fixation procedure was established using cultures of Synechococcus cyanobacteria, the photosynthetic eukaryote Micromonas pusilla and the gammaproteobacterium Halomonas variabilis. Shotgun proteomic analyses showed that the profile of microwave-fixed and -unfixed Synechococcus sp. WH8102 cells was the same, and hence proteome identification of microwave-fixed sorted cells by nanoLC-MS/MS is possible. Microwave-fixed flow-sorted Synechococcus cells can also be successfully used for whole-genome amplification and fosmid library construction. We then carried out successful metaproteomic and metagenomic analyses of microwave-fixed Synechococcus cells flow sorted from concentrates of microbial cells, collected in the North Atlantic Ocean. Thus, the microwave fixation procedure developed appears to be useful for molecular studies of microbial populations in aquatic ecosystems.

  17. Identification of vaginal fluid, saliva, and feces using microbial signatures in a Han Chinese population.

    PubMed

    Zou, Kai-Nan; Ren, Li-Jie; Ping, Yuan; Ma, Ke; Li, Hui; Cao, Yu; Zhou, Huai-Gu; Wei, Yi-Liang

    2016-10-01

    In recent years, forensic scientists have focused on the discrimination of body fluids using microbial signatures. In this study, we performed PCR-based detection of microbial signatures of vaginal fluid, saliva, and feces in a Han Chinese population. We investigated the 16S rRNA genes of Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus jensenii, Lactobacillus iners, and Atopobium vaginae in vaginal fluid, the 16S rRNA and the glucosyltransferase enzyme genes of Streptococcus salivarius and Streptococcus mutans in saliva, and the 16S rRNA genes of Enterococcus species, the RNA polymerase β-subunit gene of Bacteroides uniformis and Bacteroides vulgatus, and the α-1-6 mannanase gene of Bacteroides thetaiotaomicron in feces. As a result, the detection proportions of L. crispatus, L. gasseri, L. jensenii, L. iners, and A. vaginae were 15/16, 5/16, 8/16, 14/16, and 3/16 in 16 vaginal fluid donors, respectively. L. crispatus and L. jensenii were specifically detected in vaginal fluid; L. gasseri, L. iners, and A. vaginae were also detected in non-vaginal fluid. S. salivarius and S. mutans were not specifically detected in saliva. The detection proportions of Enterococcus species, B. uniformis, B. vulgatus, and B. thetaiotaomicron in 16 feces samples were 16/16, 12/16, 15/16, and 11/16, respectively. B. uniformis and B. thetaiotaomicron were specifically detected in feces. In addition, DNA samples prepared for the identification of body fluid can also be used for individual identification by short tandem repeat typing. The mean detection sensitivities of L. crispatus and L. jensenii were 0.362 and 0.249 pg/uL, respectively. In conclusion, L. crispatus, L. jensenii, B. uniformis, and B. thetaiotaomicron can be used as effective markers for forensic identification of vaginal fluid and feces.

  18. Effects of Momordica charantia Saponins on In vitro Ruminal Fermentation and Microbial Population

    PubMed Central

    Kang, Jinhe; Zeng, Bo; Tang, Shaoxun; Wang, Min; Han, Xuefeng; Zhou, Chuanshe; Yan, Qiongxian; He, Zhixiong; Liu, Jinfu; Tan, Zhiliang

    2016-01-01

    This study was conducted to investigate the effects of Momordica charantia saponin (MCS) on ruminal fermentation of maize stover and abundance of selected microbial populations in vitro. Five levels of MCS supplements (0, 0.01, 0.06, 0.30, 0.60 mg/mL) were tested. The pH, NH3-N, and volatile fatty acid were measured at 6, 24, 48 h of in vitro mixed incubation fluids, whilst the selected microbial populations were determined at 6 and 24 h. The high dose of MCS increased the initial fractional rate of degradation at t-value = 0 (FRD0) and the fractional rate of gas production (k), but decreased the theoretical maximum of gas production (VF) and the half-life (t0.5) compared with the control. The NH3-N concentration reached the lowest concentration with 0.01 mg MCS/mL at 6 h. The MSC inclusion increased (p<0.001) the molar proportion of butyrate, isovalerate at 24 h and 48 h, and the molar proportion of acetate at 24 h, but then decreased (p<0.05) them at 48 h. The molar proportion of valerate was increased (p<0.05) at 24 h. The acetate to propionate ratio (A/P; linear, p<0.01) was increased at 24 h, but reached the least value at the level of 0.30 mg/mL MCS. The MCS inclusion decreased (p<0.05) the molar proportion of propionate at 24 h and then increased it at 48 h. The concentration of total volatile fatty acid was decreased (p<0.001) at 24 h, but reached the greatest concentration at the level of 0.01 mg/mL and the least concentration at the level of 0.60 mg/mL. The relative abundance of Ruminococcus albus was increased at 6 h and 24 h, and the relative abundance of Fibrobacter succinogenes was the lowest (p<0.05) at 0.60 mg/mL at 6 h and 24 h. The relative abundance of Butyrivibrio fibrisolvens and fungus reached the greatest value (p<0.05) at low doses of MCS inclusion and the least value (p<0.05) at 0.60 mg/mL at 24 h. The present results demonstrates that a high level of MCS quickly inhibits in vitro fermentation of maize stover, while MCS at low doses has the

  19. Deposition and postdeposition mechanisms as possible drivers of microbial population variability in glacier ice.

    PubMed

    Xiang, Shu-Rong; Shang, Tian-Cui; Chen, Yong; Yao, Tan-Dong

    2009-11-01

    Glaciers accumulate airborne microorganisms year by year and thus are good archives of microbial communities and their relationship to climatic and environmental changes. Hypotheses have focused on two possible drivers of microbial community composition in glacier systems. One is aeolian deposition, in which the microbial load by aerosol, dust, and precipitation events directly determines the amount and composition of microbial species in glacier ice. The other is postdepositional selection, in which the metabolic activity in surface snow causes microbial community shifts in glacier ice. An additional possibility is that both processes occur simultaneously. Aeolian deposition initially establishes a microbial community in the ice, whereas postdeposition selection strengthens the deposition patterns of microorganisms with the development of tolerant species in surface snow, resulting in varying structures of microbial communities with depth. In this minireview, we examine these postulations through an analysis of physical-chemical and biological parameters from the Malan and Vostok ice cores, and the Kuytun 51 Glacial surface and deep snow. We discuss these and other recent results in the context of the hypothesized mechanisms driving microbial community succession in glaciers. We explore our current gaps in knowledge and point out future directions for research on microorganisms in glacial ecosystems.

  20. Lack of access and continuity of adult health care: a national population-based survey

    PubMed Central

    Dilélio, Alitéia Santiago; Tomasi, Elaine; Thumé, Elaine; da Silveira, Denise Silva; Siqueira, Fernando Carlos Vinholes; Piccini, Roberto Xavier; Silva, Suele Manjourany; Nunes, Bruno Pereira; Facchini, Luiz Augusto

    2015-01-01

    OBJECTIVE To describe the lack of access and continuity of health care in adults. METHODS A cross-sectional population-based study was performed on a sample of 12,402 adults aged 20 to 59 years in urban areas of 100 municipalities of 23 states in the five Brazilian geopolitical regions. Barriers to the access and continuity of health care and were investigated based on receiving, needing and seeking health care (hospitalization and accident/emergency care in the last 12 months; care provided by a doctor, by other health professional or home care in the last three months). Based on the results obtained by the description of the sample, a projection is provided for adults living in Brazilian urban areas. RESULTS The highest prevalence of lack of access to health services and to provision of care by health professionals was for hospitalization (3.0%), whilst the lowest prevalence was for care provided by a doctor (1.1%). The lack of access to care provided by other health professionals was 2.0%; to accident and emergency services, 2.1%; and to home care, 2.9%. As for prevalences, the greatest absolute lack of access occurred in emergency care (more than 360,000 adults). The main reasons were structural and organizational problems, such as unavailability of hospital beds, of health professionals, of appointments for the type of care needed and charges made for care. CONCLUSIONS The universal right to health care in Brazil has not yet been achieved. These projections can help health care management in scaling the efforts needed to overcome this problem, such as expanding the infrastructure of health services and the workforce. PMID:26061454

  1. Grain-rich diets differently alter ruminal and colonic abundance of microbial populations and lipopolysaccharide in goats.

    PubMed

    Metzler-Zebeli, Barbara U; Schmitz-Esser, Stephan; Klevenhusen, Fenja; Podstatzky-Lichtenstein, Leopold; Wagner, Martin; Zebeli, Qendrim

    2013-04-01

    High grain feeding has been associated with ruminal pH depression and microbial dysbiosis in cattle. Yet, the impact of high grain feeding on the caprine rumen and hindgut microbial community and lipopolysaccharide (LPS) release is largely unknown. Therefore, the objective was to investigate the effect of increasing dietary levels of barley grain on the microbial composition and LPS concentrations in the rumen and colon of goats. Effects were compared with respect to the responses of ruminal and colonic pH and short-chain fatty acid (SCFA) generation. Growing goats (n = 5-6) were fed diets containing 0, 30, or 60% coarsely ground barley grain for 6 weeks. Ruminal ciliate protozoa were counted with Bürker counting chamber, and quantitative PCR was used to compare bacterial populations. Increasing dietary grain level linearly increased (P < 0.05) ruminal numbers of entodiniomorphids. With the 60% grain diet, there was a reduction in ruminal abundance of the genus Prevotella and Fibrobacter succinogenes, whereas the ruminal abundance of Lactobacillus spp. increased compared to the 0 and 30% grain diets (P < 0.05). In the colon, abundance of the genus Prevotella and F. succinogenes increased (P < 0.05) in goats fed the 60% grain diet compared to those fed the other diets. Colonic abundance of Clostridium cluster I was related to the presence of grain in the diet. Ruminal LPS concentration decreased (P < 0.05) in response to the 60% grain diet, whereas its colonic concentration increased in response to the same diet (P < 0.05). Present results provide first insight on the adaptive response of rumen protozoa and rumen and colonic bacterial populations to increasing dietary levels of grain in goats. Although luminal pH largely affects microbial populations, fermentable substrate flow to the caprine hindgut may have played a greater role for colonic bacterial populations in the present study.

  2. Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarrays

    NASA Technical Reports Server (NTRS)

    El Fantroussi, Said; Urakawa, Hidetoshi; Bernhard, Anne E.; Kelly, John J.; Noble, Peter A.; Smidt, H.; Yershov, G. M.; Stahl, David A.

    2003-01-01

    Oligonucleotide microarrays were used to profile directly extracted rRNA from environmental microbial populations without PCR amplification. In our initial inspection of two distinct estuarine study sites, the hybridization patterns were reproducible and varied between estuarine sediments of differing salinities. The determination of a thermal dissociation curve (i.e., melting profile) for each probe-target duplex provided information on hybridization specificity, which is essential for confirming adequate discrimination between target and nontarget sequences.

  3. Population density and total biomass of microbial communities in chestnut soils and solonetzes of the dry steppe zone in the Lower Volga region

    NASA Astrophysics Data System (ADS)

    Kashirskaya, N. N.; Khomutova, T. E.; Chernysheva, E. V.; El'tsov, M. V.; Demkin, V. A.

    2015-03-01

    The population density and total biomass of microbial communities were determined in chestnut soils and solonetzes of the dry steppe zone in the Lower Volga region with the use of the methods of sequential fractionation of the soil and direct counting. The mean weighted values of the population density of the microbial communities in the soil profiles (A1 + B1 + B2 horizons) in the studied soils varied within 3.8-8.0 × 1011 cells/g of soil. The total microbial biomass in the soils of the Privolzhskaya Upland reached 0.9-2.4 mg C/g of soil; in the soils of the Ergeni Upland, it was 20 to 75% lower. The microbial cells in the soils of the Privolzhskaya Upland were larger than those in the soils of the Ergeni Upland. Sequential fractionation of the soil prior to direct counting contributed to the more complete assessment of the population density of the microbial communities.

  4. Electricity generation from cattle dung using microbial fuel cell technology during anaerobic acidogenesis and the development of microbial populations.

    PubMed

    Zhao, Guang; Ma, Fang; Wei, Li; Chua, Hong; Chang, Chein-Chi; Zhang, Xiao-Jun

    2012-09-01

    A microbial fuel cell (MFC) was constructed to investigate the possible generation of electricity using cattle dung as a substrate. After 30 days of operation, stable electricity was generated, and the maximum volumetric power density was 0.220 W/m(3). The total chemical oxygen demand (TCOD) removal and coulombic efficiency (CE) of the MFC reached 73.9±1.8% and 2.79±0.6%, respectively, after 120 days of operation. Acetate was the main metabolite in the anolyte, and other volatile fatty acids (VFAs) (propionate and butyrate) were present in minor amounts. The PCR-DGGE analysis indicated that the following five groups of microbes were present: Proteobacteria, Bacteroides, Chloroflexi, Actinobacteria and Firmicutes. Proteobacteria and Firmicutes were the dominant phyla in the sample; specifically, 36.3% and 24.2% of the sequences obtained were Proteobacteria and Firmicutes, respectively. Clostridium sp., Pseudomonas luteola and Ochrobactrum pseudogrignonense were the most dominant groups during the electricity generation process. The diversity of archaea dramatically decreased after 20 days of operation. The detected archaea were hydrogenotrophic methanogens, and the Methanobacterium genus disappeared during the periods of stable electricity generation via acidogenesis.

  5. Spatial Heterogeneity of Gut Microbial Composition along the Gastrointestinal Tract in Natural Populations of House Mice

    PubMed Central

    Nachman, Michael W.

    2016-01-01

    There is a growing appreciation of the role of gut microbial communities in host biology. However, the nature of variation in microbial communities among different segments of the gastrointestinal (GI) tract is not well understood. Here, we describe microbial communities from ten different segments of the GI tract (mouth, esophagus, stomach, duodenum, ileum, proximal cecum, distal cecum, colon, rectum, and feces) in wild house mice using 16S rRNA gene amplicon sequencing. We also measured carbon and nitrogen stable isotopic ratios from hair samples of individual mice as a proxy for diet. We identified factors that may explain differences in microbial composition among gut segments, and we tested for differences among individual mice in the composition of the microbiota. Consistent with previous studies, the lower GI tract was characterized by a greater relative abundance of anaerobic bacteria and greater microbial diversity relative to the upper GI tract. The upper and lower GI tracts also differed in the relative abundances of predicted microbial gene functions, including those involved in metabolic pathways. However, when the upper and lower GI tracts were considered separately, gut microbial composition was associated with individual mice. Finally, microbial communities derived from fecal samples were similar to those derived from the lower GI tract of their respective hosts, supporting the utility of fecal sampling for studying the gut microbiota of mice. These results show that while there is substantial heterogeneity among segments of the GI tract, individual hosts play a significant role in structuring microbial communities within particular segments of the GI tract. PMID:27669007

  6. Combination of sodium chlorite and calcium propionate reduces enzymatic browning and microbial population of fresh-cut ‘Granny Smith’ apples

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tissue browning and microbial growth are the main concerns associated with fresh-cut apples. In this study, effects of sodium chlorite (SC) and calcium propionate (CP), individually and combined, on quality and microbial population of apple slices were investigated. ‘Granny Smith’ apple slices, dipp...

  7. Analysis of rumen microbial populations in lactating dairy cattle fed diets varying in carbohydrate profiles and Saccharomyces cerevisiae fermentation product.

    PubMed

    Mullins, C R; Mamedova, L K; Carpenter, A J; Ying, Y; Allen, M S; Yoon, I; Bradford, B J

    2013-09-01

    The rumen microbial ecosystem is a critical factor that links diets to bovine physiology and productivity; however, information about dietary effects on microbial populations has generally been limited to small numbers of samples and qualitative assessment. To assess whether consistent shifts in microbial populations occur in response to common dietary manipulations in dairy cattle, samples of rumen contents were collected from 2 studies for analysis by quantitative real-time PCR (qPCR). In one study, lactating Holstein cows (n=8) were fed diets in which a nonforage fiber source replaced an increasing proportion of forages and concentrates in a 4×4 Latin square design, and samples of ruminal digesta were collected at 9-h intervals over 3 d at the end of each period. In the second study, lactating Holstein cows (n=15) were fed diets with or without the inclusion of a Saccharomyces cerevisiae fermentation product (SCFP) in a crossover design. In this study, rumen liquid and solid samples were collected during total rumen evacuations before and after feeding in a 42-h period. In total, 146 samples of ruminal digesta were used for microbial DNA isolation and analysis by qPCR. Validated primer sets were used to quantify total bacterial and anaerobic fungal populations as well as 12 well-studied bacterial taxa. The relative abundance of the target populations was similar to those previously reported. No significant treatment effects were observed for any target population. A significant interaction of treatment and dry matter intake was observed, however, for the abundance of Eubacterium ruminantium. Increasing dry matter intake was associated with a quadratic decrease in E. ruminantium populations in control animals but with a quadratic increase in E.ruminantium populations in cows fed SCFP. Analysis of sample time effects revealed that Fibrobacter succinogenes and fungal populations were more abundant postfeeding, whereas Ruminococcus albus tended to be more abundant

  8. Dietary cellulose, fructooligosaccharides, and pectin modify fecal protein catabolites and microbial populations in adult cats.

    PubMed

    Barry, K A; Wojcicki, B J; Middelbos, I S; Vester, B M; Swanson, K S; Fahey, G C

    2010-09-01

    Twelve young adult (1.7 +/- 0.1 yr) male cats were used in a replicated 3 x 3 Latin square design to determine the effects of fiber type on nutrient digestibility, fermentative end products, and fecal microbial populations. Three diets containing 4% cellulose, fructooligosaccharides (FOS), or pectin were evaluated. Feces were scored based on the 5-point system: 1 being hard, dry pellets, and 5 being watery liquid that can be poured. No differences were observed (P > 0.100) in intake of DM, OM, CP, or acid-hydrolyzed fat; DM or OM digestibility; or fecal pH, DM%, output on an as-is or DM basis, or concentrations of histamine or phenylalanine. Crude protein and fat digestibility decreased (P = 0.079 and 0.001, respectively) in response to supplementation with pectin compared with cellulose. Both FOS and pectin supplementation resulted in increased fecal scores (P < 0.001) and concentrations of ammonia (P = 0.003) and 4-methyl phenol (P = 0.003). Fecal indole concentrations increased (P = 0.049) when cats were supplemented with FOS. Fecal acetate (P = 0.030), propionate (P = 0.035), and total short-chain fatty acid (P = 0.016) concentrations increased in pectin-supplemented cats. Fecal butyrate (P = 0.010), isobutyrate (P = 0.011), isovalerate (P = 0.012), valerate (P = 0.026), and total branched-chain fatty acids + valerate (P = 0.008) concentrations increased with supplementation of FOS and pectin. Fecal cadaverine (P < 0.001) and tryptamine (P < 0.001) concentrations increased with supplementation of FOS and pectin. Fecal tyramine concentrations decreased (P = 0.039) in FOS-supplemented cats, whereas spermidine concentrations increased (P < 0.001) in pectin-supplemented cats. Whereas fecal concentrations of putrescine (P < 0.001) and total biogenic amines (P < 0.001) increased with FOS and pectin, the concentrations of these compounds were increased (P < 0.001) in cats supplemented with pectin. Fecal Bifidobacterium spp. concentrations increased (P = 0.006) and

  9. Organizational interventions improving access to community-based primary health care for vulnerable populations: a scoping review.

    PubMed

    Khanassov, Vladimir; Pluye, Pierre; Descoteaux, Sarah; Haggerty, Jeannie L; Russell, Grant; Gunn, Jane; Levesque, Jean-Frederic

    2016-10-10

    Access to community-based primary health care (hereafter, 'primary care') is a priority in many countries. Health care systems have emphasized policies that help the community 'get the right service in the right place at the right time'. However, little is known about organizational interventions in primary care that are aimed to improve access for populations in situations of vulnerability (e.g., socioeconomically disadvantaged) and how successful they are. The purpose of this scoping review was to map the existing evidence on organizational interventions that improve access to primary care services for vulnerable populations. Scoping review followed an iterative process. Eligibility criteria: organizational interventions in Organisation for Economic Cooperation and Development (OECD) countries; aiming to improve access to primary care for vulnerable populations; all study designs; published from 2000 in English or French; reporting at least one outcome (avoidable hospitalization, emergency department admission, or unmet health care needs).

  10. Genetic diversity and population structure of Musa accessions in ex situ conservation

    PubMed Central

    2013-01-01

    Background Banana cultivars are mostly derived from hybridization between wild diploid subspecies of Musa acuminata (A genome) and M. balbisiana (B genome), and they exhibit various levels of ploidy and genomic constitution. The Embrapa ex situ Musa collection contains over 220 accessions, of which only a few have been genetically characterized. Knowledge regarding the genetic relationships and diversity between modern cultivars and wild relatives would assist in conservation and breeding strategies. Our objectives were to determine the genomic constitution based on Internal Transcribed Spacer (ITS) regions polymorphism and the ploidy of all accessions by flow cytometry and to investigate the population structure of the collection using Simple Sequence Repeat (SSR) loci as co-dominant markers based on Structure software, not previously performed in Musa. Results From the 221 accessions analyzed by flow cytometry, the correct ploidy was confirmed or established for 212 (95.9%), whereas digestion of the ITS region confirmed the genomic constitution of 209 (94.6%). Neighbor-joining clustering analysis derived from SSR binary data allowed the detection of two major groups, essentially distinguished by the presence or absence of the B genome, while subgroups were formed according to the genomic composition and commercial classification. The co-dominant nature of SSR was explored to analyze the structure of the population based on a Bayesian approach, detecting 21 subpopulations. Most of the subpopulations were in agreement with the clustering analysis. Conclusions The data generated by flow cytometry, ITS and SSR supported the hypothesis about the occurrence of homeologue recombination between A and B genomes, leading to discrepancies in the number of sets or portions from each parental genome. These phenomenons have been largely disregarded in the evolution of banana, as the “single-step domestication” hypothesis had long predominated. These findings will have an

  11. Enhanced anaerobic digestion of organic contaminants containing diverse microbial population by combined microbial electrolysis cell (MEC) and anaerobic reactor under Fe(III) reducing conditions.

    PubMed

    Zhang, Jingxin; Zhang, Yaobin; Quan, Xie; Chen, Shuo; Afzal, Shahzad

    2013-05-01

    Microbial electrolysis cell (MEC) devices are efficient for wastewater treatment, but its application was limited due to low anode oxidation rate. The objective of this study was to improve anode performance of a MEC combined anaerobic reactor (R1) for high concentration industrial wastewater treatment via dosing Fe(OH)3. For the first 53 days without power, the addition of Fe(OH)3 in R1 enhanced the degradation of reactive brilliant red X-3B dye and sucrose. Applying a voltage of 0.8 V in R1 resulted in a higher decolorization and COD removal through driving the redox reactions at electrodes under Fe(III)-reducing conditions. Real-time PCR and enzyme activity analysis showed that the abundance and azoreductase activity of bacteria were improved in R1. Pyrosequencing revealed that dominant populations in anode biofilm and R1 were more diverse and abundant than the common anaerobic reactor (R2), and there was a significant distinction among anode film, R1 and R2 in microbial community structure.

  12. Multivariate analysis of complex DNA sequence electropherograms for high-throughput quantitative analysis of mixed microbial populations.

    PubMed

    Trosvik, Pål; Skånseng, Beate; Jakobsen, Kjetill S; Stenseth, Nils C; Naes, Tormod; Rudi, Knut

    2007-08-01

    High-throughput quantification of genetically coherent units (GCUs) is essential for deciphering population dynamics and species interactions within a community of microbes. Current techniques for microbial community analyses are, however, not suitable for this kind of high-throughput application. Here, we demonstrate the use of multivariate statistical analysis of complex DNA sequence electropherograms for the effective and accurate estimation of relative genotype abundance in cell samples from mixed microbial populations. The procedure is no more labor-intensive than standard automated DNA sequencing and provides a very effective means of quantitative data acquisition from experimental microbial communities. We present results with the Campylobacter jejuni strain-specific marker gene gltA, as well as the 16S rRNA gene, which is a universal marker across bacterial assemblages. The statistical models computed for these genes are applied to genetic data from two different experimental settings, namely, a chicken infection model and a multispecies anaerobic fermentation model, demonstrating collection of time series data from model bacterial communities. The method presented here is, however, applicable to any experimental scenario where the interest is quantification of GCUs in genetically heterogeneous DNA samples.

  13. Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations.

    PubMed

    Wu, Xiaofen; Holmfeldt, Karin; Hubalek, Valerie; Lundin, Daniel; Åström, Mats; Bertilsson, Stefan; Dopson, Mark

    2016-05-01

    Microorganisms in the terrestrial deep biosphere host up to 20% of the earth's biomass and are suggested to be sustained by the gases hydrogen and carbon dioxide. A metagenome analysis of three deep subsurface water types of contrasting age (from <20 to several thousand years) and depth (171 to 448 m) revealed phylogenetically distinct microbial community subsets that either passed or were retained by a 0.22 μm filter. Such cells of <0.22 μm would have been overlooked in previous studies relying on membrane capture. Metagenomes from the three water types were used for reconstruction of 69 distinct microbial genomes, each with >86% coverage. The populations were dominated by Proteobacteria, Candidate divisions, unclassified archaea and unclassified bacteria. The estimated genome sizes of the <0.22 μm populations were generally smaller than their phylogenetically closest relatives, suggesting that small dimensions along with a reduced genome size may be adaptations to oligotrophy. Shallow 'modern marine' water showed community members with a predominantly heterotrophic lifestyle. In contrast, the deeper, 'old saline' water adhered more closely to the current paradigm of a hydrogen-driven deep biosphere. The data were finally used to create a combined metabolic model of the deep terrestrial biosphere microbial community.

  14. Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations

    PubMed Central

    Wu, Xiaofen; Holmfeldt, Karin; Hubalek, Valerie; Lundin, Daniel; Åström, Mats; Bertilsson, Stefan; Dopson, Mark

    2016-01-01

    Microorganisms in the terrestrial deep biosphere host up to 20% of the earth's biomass and are suggested to be sustained by the gases hydrogen and carbon dioxide. A metagenome analysis of three deep subsurface water types of contrasting age (from <20 to several thousand years) and depth (171 to 448 m) revealed phylogenetically distinct microbial community subsets that either passed or were retained by a 0.22 μm filter. Such cells of <0.22 μm would have been overlooked in previous studies relying on membrane capture. Metagenomes from the three water types were used for reconstruction of 69 distinct microbial genomes, each with >86% coverage. The populations were dominated by Proteobacteria, Candidate divisions, unclassified archaea and unclassified bacteria. The estimated genome sizes of the <0.22 μm populations were generally smaller than their phylogenetically closest relatives, suggesting that small dimensions along with a reduced genome size may be adaptations to oligotrophy. Shallow ‘modern marine' water showed community members with a predominantly heterotrophic lifestyle. In contrast, the deeper, ‘old saline' water adhered more closely to the current paradigm of a hydrogen-driven deep biosphere. The data were finally used to create a combined metabolic model of the deep terrestrial biosphere microbial community. PMID:26484735

  15. Supplementation of direct-fed microbials as an alternative to antibiotic on growth performance, immune response, cecal microbial population, and ileal morphology of broiler chickens.

    PubMed

    Salim, H M; Kang, H K; Akter, N; Kim, D W; Kim, J H; Kim, M J; Na, J C; Jong, H B; Choi, H C; Suh, O S; Kim, W K

    2013-08-01

    An experiment was conducted to investigate the supplementation of direct-fed microbials (DFM) as an alternative to antibiotics on growth performance, immune response, cecal microbial population, and ileal morphology of broiler chickens. A total of 800 one-day-old male broiler chicks (Ross × Ross) were randomly allotted to 4 dietary treatments with 4 replicate pens per treatment (50 birds/replicate pen). The 4 dietary treatments fed for 35 d were a corn-soybean meal basal diet (control); control plus 0.1% virginiamycin, as an antibiotic growth promoter (AGP); control plus 0.1% direct-fed microbials that contained Lactobacillus reuteri (DFM 1); and control plus 0.1% direct-fed microbials that contained a mixture of L. reuteri, Bacillus subtilis, and Saccharomyces cerevisiae (DFM 2). Results showed that dietary AGP and DFM supplementation significantly increased (P < 0.05) the BW gain of broilers during 0 to 21 d. The feed intake was reduced, whereas the feed conversion was improved significantly when birds were fed DFM 2 at 0 to 7 d of age. The white blood cell and monocyte levels were significantly higher in the DFM 2 group compared with the control. In addition, feeding DFM significantly (P < 0.05) increased the plasma immunoglobulin levels where a higher level was observed in DFM 2 compared with those of the other treatments. Neither DFM nor AGP treatments affected the cecal Lactobacillus and Salmonella content; however, cecal Escherichia coli content significantly decreased in broiler chickens fed DFM and AGP. The ileal villus height, and width and total thickness of muscularis externa were significantly increased when birds were fed DFM compared with AGP and control. These results indicate that the dietary supplementation of DFM increases the growth performance of birds at an early age, stimulates the immune response, decreases the number of E. coli, and improves the ileal morphology of broiler chickens. Thus, DFM that contained a mixture of several beneficial

  16. Microbial protein synthesis, ruminal digestion, microbial populations, and nitrogen balance in sheep fed diets varying in forage-to-concentrate ratio and type of forage.

    PubMed

    Ramos, S; Tejido, M L; Martínez, M E; Ranilla, M J; Carro, M D

    2009-09-01

    Six ruminally and duodenally cannulated sheep were used in a partially replicated 4 x 4 Latin square to evaluate the effects of 4 diets on microbial synthesis, microbial populations, and ruminal digestion. The experimental diets had forage to concentrate ratios (F:C; DM basis) of 70:30 (HF) or 30:70 (HC) with alfalfa hay (A) or grass hay (G) as forage and were designated as HFA, HCA, HFG, and HCG. The concentrate was based on barley, gluten feed, wheat middlings, soybean meal, palmkern meal, wheat, corn, and mineral-vitamin premix in the proportions of 22, 20, 20, 13, 12, 5, 5, and 3%, respectively (as-is basis). Sheep were fed the diets at a daily rate of 56 g/kg of BW(0.75) to minimize feed selection. High-concentrate diets resulted in greater (P < 0.001) total tract apparent OM digestibility compared with HF diets, but no differences were detected in NDF digestibility. Ruminal digestibility of OM, NDF, and ADF was decreased by increasing the proportion of concentrate, but no differences between forages were detected. Compared with sheep fed HF diets, sheep receiving HC diets had less ruminal pH values and acetate proportions, but greater butyrate proportions. No differences among diets were detected in numbers of cellulolytic bacteria, but protozoa numbers were less (P = 0.004) and total bacteria numbers tended (P = 0.08) to be less for HC diets. Carboxymethylcellulase, xylanase, and amylase activities were greater for HC compared with HF diets, with A diets showing greater (P = 0.008) carboxymethylcellulase activities than G diets. Retained N ranged from 28.7 to 37.9% of N intake and was not affected by F:C (P = 0.62) or the type of forage (P = 0.31). Microbial N synthesis and its efficiency was greater (P < 0.001) for HC diets compared with HF diets. The results indicate that concentrates with low cereal content can be included in the diet of sheep up to 70% of the diet without detrimental effects on ruminal activity, microbial synthesis efficiency, and N

  17. Development of a Web-Accessible Population Pharmacokinetic Service—Hemophilia (WAPPS-Hemo): Study Protocol

    PubMed Central

    Foster, Gary; Navarro-Ruan, Tamara; McEneny-King, Alanna; Edginton, Andrea N; Thabane, Lehana

    2016-01-01

    Background Individual pharmacokinetic assessment is a critical component of tailored prophylaxis for hemophilia patients. Population pharmacokinetics allows using individual sparse data, thus simplifying individual pharmacokinetic studies. Implementing population pharmacokinetics capacity for the hemophilia community is beyond individual reach and requires a system effort. Objective The Web-Accessible Population Pharmacokinetic Service—Hemophilia (WAPPS-Hemo) project aims to assemble a database of patient pharmacokinetic data for all existing factor concentrates, develop and validate population pharmacokinetics models, and integrate these models within a Web-based calculator for individualized pharmacokinetic estimation in patients at participating treatment centers. Methods Individual pharmacokinetic studies on factor VIII and IX concentrates will be sourced from pharmaceutical companies and independent investigators. All factor concentrate manufacturers, hemophilia treatment centers (HTCs), and independent investigators (identified via a systematic review of the literature) having on file pharmacokinetic data and willing to contribute full or sparse pharmacokinetic data will be eligible for participation. Multicompartmental modeling will be performed using a mixed-model approach for derivation and Bayesian forecasting for estimation of individual sparse data. NONMEM (ICON Development Solutions) will be used as modeling software. Results The WAPPS-Hemo research network has been launched and is currently joined by 30 HTCs from across the world. We have gathered dense individual pharmacokinetic data on 878 subjects, including several replicates, on 21 different molecules from 17 different sources. We have collected sparse individual pharmacokinetic data on 289 subjects from the participating centers through the testing phase of the WAPPS-Hemo Web interface. We have developed prototypal population pharmacokinetics models for 11 molecules. The WAPPS-Hemo website

  18. Microbial population dynamics in an anaerobic CSTR treating a chemical synthesis-based pharmaceutical wastewater.

    PubMed

    Oz, Nilgun Ayman; Ince, Orhan; Ince, Bahar Kasapgil; Akarsubasi, Alper Tunga; Eyice, Ozge

    2003-01-01

    Effects of a chemical synthesis based pharmaceutical wastewater on performance of an anaerobic completely stirred tank reactor (CSTR), activity of acetoclastic methanogens and microbial composition were evaluated under various influent compositions. Initially, the CSTR was fed with glucose up to an organic loading rate (OLR) of 6 kg COD/m3 x d corresponding to an F/M ratio of 0.43 with a hydraulic retention time (HRT) of 2.5 days. A COD removal efficiency of 92% and a methane yield of 0.32 m3 CH4/kg COD(removed) were achieved whilst specific methanogenic activity (SMA) was found to be 336mL CH4/gTVS x d. After the CSTR was fed with pre-aerated wastewater diluted by glucose in different dilution ratios of 10% (w/v), 30% (w/v), 70% (w/v), and 100% (w/v) pre-aerated wastewater, gradual decreases in COD removal efficiency to 71%, methane yield to 0.28 m3CH4/kg COD(removed) and SMA to 166 mL CH4/gTVS d occurred whilst volatile fatty acid concentration reached to 1474 mg/L. After the raw wastewater diluted with the pre-aerated wastewater was fed into the CSTR in increasing ratios of 10% (w/v), 30% (w/v), and 60% (w/v), there was a proportional deterioration in performance in terms of COD removal efficiency, methane yield and acetoclastic methanogenic activity. Epifluorescence microscopy of the seed sludge revealed that Methanococcus-like species, short, and medium rods were found to be equally dominant. The short and medium rod species remained equally dominant groups in the CSTR throughout the feeding regime whilst Methanococcus-like species and long rods were found to be in insignificant numbers at the end of the study. Changes in archael diversity were determined using molecular analyses such as polymerase chain reaction (PCR), and denaturent gradient gel electrophoresis (DGGE). Results showed that overall archeal diversity did not change much whereas changes in composition of eubacterial population occurred.

  19. 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.

  20. Microbial population and community dynamics on plant roots and their feedbacks on plant communities.

    PubMed

    Bever, James D; Platt, Thomas G; Morton, Elise R

    2012-01-01

    The composition of the soil microbial community can be altered dramatically due to association with individual plant species, and these effects on the microbial community can have important feedbacks on plant ecology. Negative plant-soil feedback plays primary roles in maintaining plant community diversity, whereas positive plant-soil feedback may cause community conversion. Host-specific differentiation of the microbial community results from the trade-offs associated with overcoming plant defense and the specific benefits associated with plant rewards. Accumulation of host-specific pathogens likely generates negative feedback on the plant, while changes in the density of microbial mutualists likely generate positive feedback. However, the competitive dynamics among microbes depends on the multidimensional costs of virulence and mutualism, the fine-scale spatial structure within plant roots, and active plant allocation and localized defense. Because of this, incorporating a full view of microbial dynamics is essential to explaining the dynamics of plant-soil feedbacks and therefore plant community ecology.

  1. Interactions between snow chemistry, mercury inputs and microbial population dynamics in an Arctic snowpack.

    PubMed

    Larose, Catherine; Prestat, Emmanuel; Cecillon, Sébastien; Berger, Sibel; Malandain, Cédric; Lyon, Delina; Ferrari, Christophe; Schneider, Dominique; Dommergue, Aurélien; Vogel, Timothy M

    2013-01-01

    We investigated the interactions between snowpack chemistry, mercury (Hg) contamination and microbial community structure and function in Arctic snow. Snowpack chemistry (inorganic and organic ions) including mercury (Hg) speciation was studied in samples collected during a two-month field study in a high Arctic site, Svalbard, Norway (79 °N). Shifts in microbial community structure were determined by using a 16S rRNA gene phylogenetic microarray. We linked snowpack and meltwater chemistry to changes in microbial community structure by using co-inertia analyses (CIA) and explored changes in community function due to Hg contamination by q-PCR quantification of Hg-resistance genes in metagenomic samples. Based on the CIA, chemical and microbial data were linked (p = 0.006) with bioavailable Hg (BioHg) and methylmercury (MeHg) contributing significantly to the ordination of samples. Mercury was shown to influence community function with increases in merA gene copy numbers at low BioHg levels. Our results show that snowpacks can be considered as dynamic habitats with microbial and chemical components responding rapidly to environmental changes.

  2. Poplar clones of different sizes, grown on a heavy metal polluted site, are associated with microbial populations of varying composition.

    PubMed

    Gamalero, Elisa; Cesaro, Patrizia; Cicatelli, Angela; Todeschini, Valeria; Musso, Chiara; Castiglione, Stefano; Fabiani, Arturo; Lingua, Guido

    2012-05-15

    We performed a field trial to evaluate the response of different poplar clones to heavy metals. We found that poplar plants of the same clone, propagated by cuttings, had a marked variability of survival and growth in different zones of the field that were characterized by very similar physical-chemical prosperities. Since metal uptake and its accumulation by plants can be affected by soil microorganisms, we investigated soil microbial populations that were collected in proximity to the roots of large and small poplar plants. We used microbiological and molecular tools to ascertain whether bacterial strains or species were associated with large, or small poplars, and whether these were different from those present in the bulk (without plants) soil. We found that the culturable fraction of the bacteria differed in the three cases (bulk soil, small or large poplars). While some taxa were always present, two species (Chryseobacterium soldanellicola and Variovorax paradoxus) were only found in the soil where poplars (large or small) were growing, independently from the plant size. Bacterial strains of the genus Flavobacterium were prevalent in the soil with large poplar plants. The existence of different microbial populations in the bulk and in the poplar grown soils was confirmed by the DGGE profiles of the bacterial culturable fractions. Cluster analysis of the DGGE profiles highlighted the clear separation of the culturable fraction from the whole microbial community. The isolation and identification of poplar-associated bacterial strains from the culturable fraction of the microbial community provided the basis for further studies aimed at the combined use of plants and soil microorganisms in the remediation of heavy metal polluted soils.

  3. Effect of untreated sewage effluent irrigation on heavy metal content, microbial population and enzymatic activities of soils in Aligarh.

    PubMed

    Bansal, O P; Singh, Gajraj; Katiyar, Pragati

    2014-07-01

    The study pertains to the impact of domestic and industrial sewage water irrigation on the chemical, biological and enzymatic activities in alluvial soils of Aligarh District. Results showed that soil enzymatic [dehydogenase (DHA), acid and alkaline phosphatase, urease and catalase] activities in the soils increased up to 14 days of incubation and thereafter inhibited significantly. The enzymatic activity were in the order sewage effluent > partial sewage effluent > ground water irrigated soils. Increase in soil enzymatic activities up to 2nd week of incubation was due to decomposition of organic matter. Maximum inhibition of enzymatic activities, after 14 days of incubation were found in sewage effluent irrigated soils and minimum in ground water irrigated soils. Similar trend was also seen for microbial population. Soil enzymatic activities and microbial population were significantly and positively correlated with soil organic matter. Results also indicated that the microbial population and enzymatic activities in sewage irrigated soils decreased continually with irrigation period. The average concentration of total heavy metals in sewage irrigated soils and partial sewage irrigated soils increased and was 3 and 2 times higher for Zn; 4.5 and 1.7 times higher for Cu; 3.8 and 2.4 times higher for Cr; 5.7 and 3.5 times higher for Pb; 3.5 and 2.2 times higher for Cd and 2.7 and 2.0 times higher for Ni respectively than that of ground water irrigated soils. Results also showed that though total heavy metals concentration increased with period of sewage irrigation but the concentration of diethylene triamine pentaacetic acid (DTPA) extractable heavy metals in partial sewage irrigated and sewage irrigated soils remained almost same, which might be due to deposition of heavy metals in crops grown on the soils.

  4. Analyses of microbial populations and antibiotic resistance present in stored swine manure from underground storage pits

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Antimicrobial compounds have been commonly used as feed additives for domestic animals to reduce infection and promote growth. Recent concerns have suggested such feeding practices may result in increased microbial resistance to antibiotics, which can have an impact on human health. While many inves...

  5. Cow Teat Skin, a Potential Source of Diverse Microbial Populations for Cheese Production

    PubMed Central

    Gagne, Geneviève; Bornes, Stéphanie; Monsallier, Françoise; Veisseire, Philippe; Delbès-Paus, Céline; Montel, Marie-Christine

    2012-01-01

    The diversity of the microbial community on cow teat skin was evaluated using a culture-dependent method based on the use of different dairy-specific media, followed by the identification of isolates by 16S rRNA gene sequencing. This was combined with a direct molecular approach by cloning and 16S rRNA gene sequencing. This study highlighted the large diversity of the bacterial community that may be found on teat skin, where 79.8% of clones corresponded to various unidentified species as well as 66 identified species, mainly belonging to those commonly found in raw milk (Enterococcus, Pediococcus, Enterobacter, Pantoea, Aerococcus, and Staphylococcus). Several of them, such as nonstarter lactic acid bacteria (NSLAB), Staphylococcus, and Actinobacteria, may contribute to the development of the sensory characteristics of cheese during ripening. Therefore, teat skin could be an interesting source or vector of biodiversity for milk. Variations of microbial counts and diversity between the farms studied have been observed. Moreover, Staphylococcus auricularis, Staphylococcus devriesei, Staphylococcus arlettae, Streptococcus bovis, Streptococcus equinus, Clavibacter michiganensis, Coprococcus catus, or Arthrobacter gandavensis commensal bacteria of teat skin and teat canal, as well as human skin, are not common in milk, suggesting that there is a breakdown of microbial flow from animal to milk. It would then be interesting to thoroughly study this microbial flow from teat to milk. PMID:22081572

  6. Heterotrophic and autotrophic microbial populations in cold perennial springs of the high arctic.

    PubMed

    Perreault, Nancy N; Greer, Charles W; Andersen, Dale T; Tille, Stefanie; Lacrampe-Couloume, Georges; Lollar, Barbara Sherwood; Whyte, Lyle G

    2008-11-01

    The saline springs of Gypsum Hill in the Canadian high Arctic are a rare example of cold springs originating from deep groundwater and rising to the surface through thick permafrost. The heterotrophic bacteria and autotrophic sulfur-oxidizing bacteria (up to 40% of the total microbial community) isolated from the spring waters and sediments were classified into four phyla (Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria) based on 16S rRNA gene analysis; heterotrophic isolates were primarily psychrotolerant, salt-tolerant, facultative anaerobes. Some of the isolates contained genes for thiosulfate oxidation (soxB) and anoxygenic photosynthesis (pufM), possibly enabling the strains to better compete in these sulfur-rich environments subject to long periods of illumination in the Arctic summer. Although leucine uptake by the spring water microbial community was low, CO(2) uptake was relatively high under dark incubation, reinforcing the idea that primary production by chemoautotrophs is an important process in the springs. The small amounts of hydrocarbons in gases exsolving from the springs (0.38 to 0.51% CH(4)) were compositionally and isotopically consistent with microbial methanogenesis and possible methanotrophy. Anaerobic heterotrophic sulfur oxidation and aerobic autotrophic sulfur oxidation activities were demonstrated in sediment slurries. Overall, our results describe an active microbial community capable of sustainability in an extreme environment that experiences prolonged periods of continuous light or darkness, low temperatures, and moderate salinity, where life seems to rely on chemolithoautotrophy.

  7. Microbial evaluation of activated sludge and filamentous population at eight Czech nutrient removal activated sludge plants during year 2000.

    PubMed

    Krhutková, O; Ruzicková, I; Wanner, J

    2002-01-01

    The long-term project on the survey of filamentous microorganisms, which started in 1996, was finished in 2000 by the survey of eight Czech activated sludge plants with biological nutrient removal (BNR) systems. At all plants with enhanced biological nutrient removal, specific microbial population (mostly from the point of view of filaments occurrence), operational problems (presence of biological foaming, bulking) and plant operation were observed periodically and longer than 1 year. In our paper the relationship between the composition of activated sludge (especially filaments) consortia and modification of the process with nutrient removal is discussed. At the surveyed plants Type 0092 and Microthrix parvicella were identified as dominant Eikelboom filamentous types.

  8. The Affordable Care Act's Impacts on Access to Insurance and Health Care for Low-Income Populations.

    PubMed

    Kominski, Gerald F; Nonzee, Narissa J; Sorensen, Andrea

    2017-03-20

    The Patient Protection and Affordable Care Act (ACA) expands access to health insurance in the United States, and, to date, an estimated 20 million previously uninsured individuals have gained coverage. Understanding the law's impact on coverage, access, utilization, and health outcomes, especially among low-income populations, is critical to informing ongoing debates about its effectiveness and implementation. Early findings indicate that there have been significant reductions in the rate of uninsurance among the poor and among those who live in Medicaid expansion states. In addition, the law has been associated with increased health care access, affordability, and use of preventive and outpatient services among low-income populations, though impacts on inpatient utilization and health outcomes have been less conclusive. Although these early findings are generally consistent with past coverage expansions, continued monitoring of these domains is essential to understand the long-term impact of the law for underserved populations.

  9. Flow cytometry and cell sorting of heterogeneous microbial populations: the importance of single-cell analyses.

    PubMed Central

    Davey, H M; Kell, D B

    1996-01-01

    The most fundamental questions such as whether a cell is alive, in the sense of being able to divide or to form a colony, may sometimes be very hard to answer, since even axenic microbial cultures are extremely heterogeneous. Analyses that seek to correlate such things as viability, which is a property of an individual cell, with macroscopic measurements of culture variables such as ATP content, respiratory activity, and so on, must inevitably fail. It is therefore necessary to make physiological measurements on individual cells. Flow cytometry is such a technique, which allows one to analyze cells rapidly and individually and permits the quantitative analysis of microbial heterogeneity. It therefore offers many advantages over conventional measurements for both routine and more exploratory analyses of microbial properties. While the technique has been widely applied to the study of mammalian cells, is use in microbiology has until recently been much more limited, largely because of the smaller size of microbes and the consequently smaller optical signals obtainable from them. Since these technical barriers no longer hold, flow cytometry with appropriate stains has been used for the rapid discrimination and identification of microbial cells, for the rapid assessment of viability and of the heterogeneous distributions of a wealth of other more detailed physiological properties, for the analysis of antimicrobial drug-cell interactions, and for the isolation of high-yielding strains of biotechnological interest. Flow cytometric analyses provide an abundance of multivariate data, and special methods have been devised to exploit these. Ongoing advances mean that modern flow cytometers may now be used by nonspecialists to effect a renaissance in our understanding of microbial heterogeneity. PMID:8987359

  10. Microbial populations identified by fluorescence in situ hybridization in a constructed wetland treating acid coal mine drainage

    SciTech Connect

    Nicomrat, D.; Dick, W.A.; Tuovinen, O.H.

    2006-07-15

    Microorganisms are an integral part of the biogeochemical processes in wetlands, yet microbial communities in sediments within constructed wetlands receiving acid mine drainage (AMD) are only poorly understood. The purpose of this study was to characterize the microbial diversity and abundance in a wetland receiving AMD using fluorescence in situ hybridization (FISH) analysis. Seasonal samples of oxic surface sediments, comprised of Fe(III) precipitates, were collected from two treatment cells of the constructed wetland system. The pH of the bulk samples ranged between pH 2.1 and 3.9. Viable counts of acidophilic Fe and S oxidizers and heterotrophs were determined with a most probable number (MPN) method. The MPN counts were only a fraction of the corresponding FISH counts. The sediment samples contained microorganisms in the Bacteria (including the subgroups of acidophilic Fe- and S-oxidizing bacteria and Acidiphilium spp.) and Eukarya domains. Archaea were present in the sediment surface samples at < 0.01% of the total microbial community. The most numerous bacterial species in this wetland system was Acidithiobacillus ferrooxidans, comprising up to 37% of the bacterial population. Acidithiobacillus thiooxidans was also abundant.

  11. Oil Biodegradation and Oil-Degrading Microbial Populations in Marsh Sediments Impacted by Oil from the Deepwater Horizon Well Blowout.

    PubMed

    Atlas, Ronald M; Stoeckel, Donald M; Faith, Seth A; Minard-Smith, Angela; Thorn, Jonathan R; Benotti, Mark J

    2015-07-21

    To study hydrocarbon biodegradation in marsh sediments impacted by Macondo oil from the Deepwater Horizon well blowout, we collected sediment cores 18-36 months after the accident at the marshes in Bay Jimmy (Upper Barataria Bay), Louisiana, United States. The highest concentrations of oil were found in the top 2 cm of sediment nearest the waterline at the shorelines known to have been heavily oiled. Although petroleum hydrocarbons were detectable, Macondo oil could not be identified below 8 cm in 19 of the 20 surveyed sites. At the one site where oil was detected below 8 cm, concentrations were low. Residual Macondo oil was already highly weathered at the start of the study, and the concentrations of individual saturated hydrocarbons and polycyclic aromatic hydrocarbons continued to decrease over the course of the study due to biodegradation. Desulfococcus oleovorans, Marinobacter hydrocarbonoclasticus, Mycobacterium vanbaalenii, and related mycobacteria were the most abundant oil-degrading microorganisms detected in the top 2 cm at the oiled sites. Relative populations of these taxa declined as oil concentrations declined. The diversity of the microbial community was low at heavily oiled sites compared to that of the unoiled reference sites. As oil concentrations decreased over time, microbial diversity increased and approached the diversity levels of the reference sites. These trends show that the oil continues to be biodegraded, and microbial diversity continues to increase, indicating ongoing overall ecological recovery.

  12. Development and evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in Acid Mine Drainages and bioleaching systems.

    PubMed

    Yin, Huaqun; Cao, Linhui; Qiu, Guanzhou; Wang, Dianzuo; Kellogg, Laurie; Zhou, Jizhong; Dai, Zhimin; Liu, Xueduan

    2007-07-01

    To effectively monitor microbial populations in acidic environments and bioleaching systems, a comprehensive 50-mer-based oligonucleotide microarray was developed based on most of the known genes associated with the acidophiles. This array contained 1,072 probes in which there were 571 related to 16S rRNA and 501 related to functional genes. The functional genes in the microarray were involved in carbon metabolism (158), nitrogen metabolism (72), sulfur metabolism (39), iron metabolism (68), DNA replication and repair (97), metal-resistance (27), membrane-relate gene (16), transposon (13) and IST sequence (11). Based on the results of microarray hybridizations, specificity tests with representative pure cultures indicated that the designed probes on the arrays appeared to be specific to their corresponding target genes. The detection limit was 5 ng of genomic DNA in the absence of background DNA. Strong linear relationships between the signal intensity and the target DNA were observed (r(2) approximately 0.98). Application of this type of the microarray to analyze the acidic environments and bioleaching systems demonstrated that the developed microarray appeared to be useful for profiling differences in microbial community structures of acidic environments and bioleaching systems. Our results indicate that this technology has potential as a specific, sensitive, and quantitative tool in revealing a comprehensive picture of the compositions of genes related with acidophilic microorganism and the microbial community in acidic environments and bioleaching systems, although more work is needed to improve.

  13. Access to Primary Care and Visits to Emergency Departments in England: A Cross-Sectional, Population-Based Study

    PubMed Central

    Cowling, Thomas E.; Cecil, Elizabeth V.; Soljak, Michael A.; Lee, John Tayu; Millett, Christopher; Majeed, Azeem; Wachter, Robert M.; Harris, Matthew J.

    2013-01-01

    Background The number of visits to hospital emergency departments (EDs) in England has increased by 20% since 2007-08, placing unsustainable pressure on the National Health Service (NHS). Some patients attend EDs because they are unable to access primary care services. This study examined the association between access to primary care and ED visits in England. Methods A cross-sectional, population-based analysis of patients registered with 7,856 general practices in England was conducted, for the time period April 2010 to March 2011. The outcome measure was the number of self-referred discharged ED visits by the registered population of a general practice. The predictor variables were measures of patient-reported access to general practice services; these were entered into a negative binomial regression model with variables to control for the characteristics of patient populations, supply of general practitioners and travel times to health services. Main Result and Conclusion General practices providing more timely access to primary care had fewer self-referred discharged ED visits per registered patient (for the most accessible quintile of practices, RR = 0.898; P<0.001). Policy makers should consider improving timely access to primary care when developing plans to reduce ED utilisation. PMID:23776694

  14. Among-Population Variation in Microbial Community Structure in the Floral Nectar of the Bee-Pollinated Forest Herb Pulmonaria officinalis L

    PubMed Central

    Jacquemyn, Hans; Lenaerts, Marijke; Brys, Rein; Willems, Kris; Honnay, Olivier; Lievens, Bart

    2013-01-01

    Background Microbial communities in floral nectar have been shown to be characterized by low levels of species diversity, yet little is known about among-plant population variation in microbial community composition. Methodology/Principal Findings We investigated the microbial community structure (yeasts and bacteria) in floral nectar of ten fragmented populations of the bee-pollinated forest herb Pulmonaria officinalis. We also explored possible relationships between plant population size and microbial diversity in nectar, and related microbial community composition to the distance separating plant populations. Culturable bacteria and yeasts occurring in the floral nectar of a total of 100 plant individuals were isolated and identified by partially sequencing the 16S rRNA gene and D1/D2 domains of the 26S rRNA gene, respectively. A total of 9 and 11 yeast and 28 and 39 bacterial OTUs was found, taking into account a 3% (OTU0.03) and 1% sequence dissimilarity cut-off (OTU0.01). OTU richness at the plant population level (i.e. the number of OTUs per population) was low for yeasts (mean: 1.7, range: 0–4 OTUs0.01/0.03 per population), whereas on average 6.9 (range: 2–13) OTUs0.03 and 7.9 (range 2–16) OTUs0.01 per population were found for bacteria. Both for yeasts and bacteria, OTU richness was not significantly related to plant population size. Similarity in community composition among populations was low (average Jaccard index: 0.14), and did not decline with increasing distance between populations. Conclusions/Significance We found low similarity in microbial community structure among populations, suggesting that the assembly of nectar microbiota is to a large extent context-dependent. Although the precise factors that affect variation in microbial community structure in floral nectar require further study, our results indicate that both local and regional processes may contribute to among-population variation in microbial community structure in nectar. PMID

  15. Food web structure in the recently flooded Sep Reservoir as inferred from phytoplankton population dynamics and living microbial biomass.

    PubMed

    Tadonléké, R D; Jugnia, L B; Sime-Ngando, T; Devaux, J; Romagoux, J C

    2002-01-01

    Phytoplankton dynamics, bacterial standing stocks and living microbial biomass (derived from ATP measurements, 0.7-200 mm size class) were examined in 1996 in the newly flooded (1995) Sep Reservoir ('Massif Central,' France), for evidence of the importance of the microbial food web relative to the traditional food chain. Phosphate concentrations were low, N:P ratios were high, and phosphate losses converted into carbon accounted for <50% of phytoplankton biomass and production, indicating that P was limiting phytoplankton development during the study. The observed low availability of P contrasts with the high release of "directly" assimilable P often reported in newly flooded reservoirs, suggesting that factors determining nutrient dynamics in such ecosystems are complex. The phosphate availability, but also the water column stability, seemed to be among the major factors determining phytoplankton dynamics, as (i) large-size phytoplankton species were prominent during the period of increasing water column stability, whereas small-size species dominated phytoplankton assemblages during the period of decreasing stability, and (ii) a Dinobryon divergens bloom occurred during a period when inorganic P was undetectable, coinciding with the lowest values of bacterial standing stocks. Indication of grazing limitation of bacterial populations by the mixotrophic chrysophyte D. divergens (in late spring) and by other potential grazers (mainly rotifers in summer) seemed to be confirmed by the Model II or functional slopes of the bacterial vs phytoplankton regressions, which were always <0.63. Phytoplankton biomass was not correlated with phosphorus sources and its contribution was remarkably low relative to the living microbial biomass which, in contrast, was positively correlated with total phosphorus in summer. We conclude that planktonic microheterotrophs are strongly implicated in the phosphorus dynamics in the Sep Reservoir, and thus support the idea that an important

  16. Transbrachial Access for Radiologic Manipulation of Problematic Central Venous Catheters in a Pediatric Population

    SciTech Connect

    Rao, Sandeep Hogan, Mark J.

    2010-08-15

    A transfemoral venous approach is the current standard for accessing malpositioned and fractured central venous catheters (CVCs). The purpose of this study was (1) to describe a transbrachial approach for correction and (2) to assess the success and failure of this method in a pediatric population. A 12-year retrospective review of all patients referred for correction of malpositioned, retained, and fractured CVCs was conducted. Based on the performing interventionalist's preference, transbrachial or transfemoral venous sheaths where placed under ultrasonographic guidance. Diagnostic angiographic catheters and snares were used to manipulate the catheters. Patients who underwent the transfemoral approach received postprocedural monitoring for 4 hours, whereas patients who underwent the transbrachial approach were allowed unrestricted activity immediately after hemostasis was obtained. Technical success of malpositioned lines was defined (1) by final position in the superior vena cava or at the cavoatrial junction on postprocedural imaging or (2) by successful removal of retained catheter fragments, if present. Transbrachial approach was used for access in 11 patients. Problematic lines included malpositioned (n = 10) and retained (n = 1) lines. The ipsilateral arm was used for transbrachial entry in 7 patients. Initial use of angiographic catheters was attempted in 7 cases, of which 4 were successful. All 3 unsuccessful cases had tips positioned in the contralateral brachiocephalic vein, and these were successfully repositioned using snares. A combination of snares and angiographic catheters was used in 2 cases. Snares were used for all other cases. Technical success by way of the transbrachial approach was observed in all cases. Periprocedural follow-up demonstrated no immediate complications. We conclude that the transbrachial approach is a suitable alternative to the transfemoral approach for catheter tip position correction. Tip malposition in the contralateral

  17. Non-tuberculous mycobacteria and microbial populations in drinking water distribution systems.

    PubMed

    Briancesco, Rossella; Semproni, Maurizio; Della Libera, Simonetta; Sdanganelli, Massimo; Bonadonna, Lucia

    2010-01-01

    Data on the occurrence of non-tuberculous mycobacteria (NTM), in parallel with those obtained for bacterial indicators and amoebae, are presented with the aim to collect information on the spread of NTM in drinking water distribution systems in Italy. Samples were collected from taps of hospitals and households in Central and Southern Italy. The concentration values obtained for the more traditional microbial parameters complied with the mandatory requirements for drinking water. Conversely, moderate-to-high microbial loads (till 300 CFU/L) were observed for the NTM. Positive samples were obtained from 62% of the investigated water samples. Analogous results were observed for amoebae showing a higher percentage of positive samples (76%). In terms of public health, the presence of mycobacteria in water distribution systems may represent a potential risk especially for vulnerable people such as children, the elderly or immunocompromised individuals.

  18. Involvement of microbial populations during the composting of olive mill wastewater sludge.

    PubMed

    Abid, N; Chamkha, M; Godon, J J; Sayadi, S

    2007-07-01

    Olive mill waste water sludge obtained by the electro-Fenton oxidation of olive mill waste water was composted in a bench scale reactor. The evolution of microbial species within the composter was investigated using a respirometric test and by means of both cultivation-dependent and independent approaches (Polymerase Chain Reaction-Single Strand Conformation Polymorphism, PCR SSCP). During the period of high respiration rate (7-24 days), cultivation method showed that thermophilic bacteria as well as actinomycetes dominated over eumycetes. During the composting process, the PCR-SSCP method showed a higher diversity of the bacterial community than the eukaryotic one. After 60 days of composting, the compost exhibited a microbial stability and a clear absence of phytotoxicity.

  19. Microbial populations in Antarctic permafrost: biodiversity, state, age, and implication for astrobiology.

    PubMed

    Gilichinsky, D A; Wilson, G S; Friedmann, E I; McKay, C P; Sletten, R S; Rivkina, E M; Vishnivetskaya, T A; Erokhina, L G; Ivanushkina, N E; Kochkina, G A; Shcherbakova, V A; Soina, V S; Spirina, E V; Vorobyova, E A; Fyodorov-Davydov, D G; Hallet, B; Ozerskaya, S M; Sorokovikov, V A; Laurinavichyus, K S; Shatilovich, A V; Chanton, J P; Ostroumov, V E; Tiedje, J M

    2007-04-01

    Antarctic permafrost soils have not received as much geocryological and biological study as has been devoted to the ice sheet, though the permafrost is more stable and older and inhabited by more microbes. This makes these soils potentially more informative and a more significant microbial repository than ice sheets. Due to the stability of the subsurface physicochemical regime, Antarctic permafrost is not an extreme environment but a balanced natural one. Up to 10(4) viable cells/g, whose age presumably corresponds to the longevity of the permanently frozen state of the sediments, have been isolated from Antarctic permafrost. Along with the microbes, metabolic by-products are preserved. This presumed natural cryopreservation makes it possible to observe what may be the oldest microbial communities on Earth. Here, we describe the Antarctic permafrost habitat and biodiversity and provide a model for martian ecosystems.

  20. Turnover of microbial lipids in the deep biosphere and growth of benthic archaeal populations.

    PubMed

    Xie, Sitan; Lipp, Julius S; Wegener, Gunter; Ferdelman, Timothy G; Hinrichs, Kai-Uwe

    2013-04-09

    Deep subseafloor sediments host a microbial biosphere with unknown impact on global biogeochemical cycles. This study tests previous evidence based on microbial intact polar lipids (IPLs) as proxies of live biomass, suggesting that Archaea dominate the marine sedimentary biosphere. We devised a sensitive radiotracer assay to measure the decay rate of ([(14)C]glucosyl)-diphytanylglyceroldiether (GlcDGD) as an analog of archaeal IPLs in continental margin sediments. The degradation kinetics were incorporated in model simulations that constrained the fossil fraction of subseafloor IPLs and rates of archaeal turnover. Simulating the top 1 km in a generic continental margin sediment column, we estimated degradation rate constants of GlcDGD being one to two orders of magnitude lower than those of bacterial IPLs, with half-lives of GlcDGD increasing with depth to 310 ky. Given estimated microbial community turnover times of 1.6-73 ky in sediments deeper than 1 m, 50-96% of archaeal IPLs represent fossil signals. Consequently, previous lipid-based estimates of global subseafloor biomass probably are too high, and the widely observed dominance of archaeal IPLs does not rule out a deep biosphere dominated by Bacteria. Reverse modeling of existing concentration profiles suggest that archaeal IPL synthesis rates decline from around 1,000 pg⋅mL(-1) sediment⋅y(-1) at the surface to 0.2 pg⋅mL(-1)⋅y(-1) at 1 km depth, equivalent to production of 7 × 10(5) to 140 archaeal cells⋅mL(-1) sediment⋅y(-1), respectively. These constraints on microbial growth are an important step toward understanding the relationship between the deep biosphere and the carbon cycle.

  1. Microbial population and functional dynamics associated with surface potential and carbon metabolism

    PubMed Central

    Ishii, Shun'ichi; Suzuki, Shino; Norden-Krichmar, Trina M; Phan, Tony; Wanger, Greg; Nealson, Kenneth H; Sekiguchi, Yuji; Gorby, Yuri A; Bretschger, Orianna

    2014-01-01

    Microbial extracellular electron transfer (EET) to solid surfaces is an important reaction for metal reduction occurring in various anoxic environments. However, it is challenging to accurately characterize EET-active microbial communities and each member's contribution to EET reactions because of changes in composition and concentrations of electron donors and solid-phase acceptors. Here, we used bioelectrochemical systems to systematically evaluate the synergistic effects of carbon source and surface redox potential on EET-active microbial community development, metabolic networks and overall electron transfer rates. The results indicate that faster biocatalytic rates were observed under electropositive electrode surface potential conditions, and under fatty acid-fed conditions. Temporal 16S rRNA-based microbial community analyses showed that Geobacter phylotypes were highly diverse and apparently dependent on surface potentials. The well-known electrogenic microbes affiliated with the Geobacter metallireducens clade were associated with lower surface potentials and less current generation, whereas Geobacter subsurface clades 1 and 2 were associated with higher surface potentials and greater current generation. An association was also observed between specific fermentative phylotypes and Geobacter phylotypes at specific surface potentials. When sugars were present, Tolumonas and Aeromonas phylotypes were preferentially associated with lower surface potentials, whereas Lactococcus phylotypes were found to be closely associated with Geobacter subsurface clades 1 and 2 phylotypes under higher surface potential conditions. Collectively, these results suggest that surface potentials provide a strong selective pressure, at the species and strain level, for both solid surface respirators and fermentative microbes throughout the EET-active community development. PMID:24351938

  2. Microbial populations identified by fluorescence in situ hybridization in a constructed wetland treating acid coal mine drainage.

    PubMed

    Nicomrat, Duongruitai; Dick, Warren A; Tuovinen, Olli H

    2006-01-01

    Microorganisms are an integral part of the biogeochemical processes in wetlands, yet microbial communities in sediments within constructed wetlands receiving acid mine drainage (AMD) are only poorly understood. The purpose of this study was to characterize the microbial diversity and abundance in a wetland receiving AMD using fluorescence in situ hybridization (FISH) analysis. Seasonal samples of oxic surface sediments, comprised of Fe(III) precipitates, were collected from two treatment cells of the constructed wetland system. The pH of the bulk samples ranged between pH 2.1 and 3.9. Viable counts of acidophilic Fe and S oxidizers and heterotrophs were determined with a most probable number (MPN) method. The MPN counts were only a fraction of the corresponding FISH counts. The sediment samples contained microorganisms in the Bacteria (including the subgroups of acidophilic Fe- and S-oxidizing bacteria and Acidiphilium spp.) and Eukarya domains. Archaea were present in the sediment surface samples at < 0.01% of the total microbial community. The most numerous bacterial species in this wetland system was Acidithiobacillus ferrooxidans, comprising up to 37% of the bacterial population. Acidithiobacillus thiooxidans was also abundant. Heterotrophs in the Acidiphilium genus totaled 20% of the bacterial population. Leptospirillum ferrooxidans was below the level of detection in the bacterial community. The results from the FISH technique from this field study are consistent with results from other experiments involving enumeration by most probable number, dot-blot hybridization, and denaturing gradient gel electrophoresis analyses and with the geochemistry of the site.

  3. The Influence of Age and Gender on Skin-Associated Microbial Communities in Urban and Rural Human Populations

    PubMed Central

    Ying, Shi; Zeng, Dan-Ning; Chi, Liang; Tan, Yuan; Galzote, Carlos; Cardona, Cesar; Lax, Simon; Gilbert, Jack; Quan, Zhe-Xue

    2015-01-01

    Differences in the bacterial community structure associated with 7 skin sites in 71 healthy people over five days showed significant correlations with age, gender, physical skin parameters, and whether participants lived in urban or rural locations in the same city. While body site explained the majority of the variance in bacterial community structure, the composition of the skin-associated bacterial communities were predominantly influenced by whether the participants were living in an urban or rural environment, with a significantly greater relative abundance of Trabulsiella in urban populations. Adults maintained greater overall microbial diversity than adolescents or the elderly, while the intragroup variation among the elderly and rural populations was significantly greater. Skin-associated bacterial community structure and composition could predict whether a sample came from an urban or a rural resident ~5x greater than random. PMID:26510185

  4. The Influence of Age and Gender on Skin-Associated Microbial Communities in Urban and Rural Human Populations.

    PubMed

    Ying, Shi; Zeng, Dan-Ning; Chi, Liang; Tan, Yuan; Galzote, Carlos; Cardona, Cesar; Lax, Simon; Gilbert, Jack; Quan, Zhe-Xue

    2015-01-01

    Differences in the bacterial community structure associated with 7 skin sites in 71 healthy people over five days showed significant correlations with age, gender, physical skin parameters, and whether participants lived in urban or rural locations in the same city. While body site explained the majority of the variance in bacterial community structure, the composition of the skin-associated bacterial communities were predominantly influenced by whether the participants were living in an urban or rural environment, with a significantly greater relative abundance of Trabulsiella in urban populations. Adults maintained greater overall microbial diversity than adolescents or the elderly, while the intragroup variation among the elderly and rural populations was significantly greater. Skin-associated bacterial community structure and composition could predict whether a sample came from an urban or a rural resident ~5x greater than random.

  5. The influence of age and gender on skin-associated microbial communities in urban and rural human populations

    DOE PAGES

    Ying, Shi; Zeng, Dan -Ning; Chi, Liang; ...

    2015-10-28

    Differences in the bacterial community structure associated with 7 skin sites in 71 healthy people over five days showed significant correlations with age, gender, physical skin parameters, and whether participants lived in urban or rural locations in the same city. While body site explained the majority of the variance in bacterial community structure, the composition of the skin-associated bacterial communities were predominantly influenced by whether the participants were living in an urban or rural environment, with a significantly greater relative abundance of Trabulsiella in urban populations. Adults maintained greater overall microbial diversity than adolescents or the elderly, while the intragroupmore » variation among the elderly and rural populations was significantly greater. Lastly, skin-associated bacterial community structure and composition could predict whether a sample came from an urban or a rural resident ~ 5x greater than random.« less

  6. The influence of age and gender on skin-associated microbial communities in urban and rural human populations

    SciTech Connect

    Ying, Shi; Zeng, Dan -Ning; Chi, Liang; Tan, Yuan; Galzote, Carlos; Cardona, Cesar; Lax, Simon; Gilbert, Jack; Quan, Zhe -Xue; Badger, Jonathan H.

    2015-10-28

    Differences in the bacterial community structure associated with 7 skin sites in 71 healthy people over five days showed significant correlations with age, gender, physical skin parameters, and whether participants lived in urban or rural locations in the same city. While body site explained the majority of the variance in bacterial community structure, the composition of the skin-associated bacterial communities were predominantly influenced by whether the participants were living in an urban or rural environment, with a significantly greater relative abundance of Trabulsiella in urban populations. Adults maintained greater overall microbial diversity than adolescents or the elderly, while the intragroup variation among the elderly and rural populations was significantly greater. Lastly, skin-associated bacterial community structure and composition could predict whether a sample came from an urban or a rural resident ~ 5x greater than random.

  7. Archaeal Populations in Hypersaline Sediments Underlying Orange Microbial Mats in the Napoli Mud Volcano▿†

    PubMed Central

    Lazar, Cassandre Sara; L'Haridon, Stéphane; Pignet, Patricia; Toffin, Laurent

    2011-01-01

    Microbial mats in marine cold seeps are known to be associated with ascending sulfide- and methane-rich fluids. Hence, they could be visible indicators of anaerobic oxidation of methane (AOM) and methane cycling processes in underlying sediments. The Napoli mud volcano is situated in the Olimpi Area that lies on saline deposits; from there, brine fluids migrate upward to the seafloor. Sediments associated with a brine pool and microbial orange mats of the Napoli mud volcano were recovered during the Medeco cruise. Based on analysis of RNA-derived sequences, the “active” archaeal community was composed of many uncultured lineages, such as rice cluster V or marine benthic group D. Function methyl coenzyme M reductase (mcrA) genes were affiliated with the anaerobic methanotrophic Archaea (ANME) of the ANME-1, ANME-2a, and ANME-2c groups, suggesting that AOM occurred in these sediment layers. Enrichment cultures showed the presence of viable marine methylotrophic Methanococcoides in shallow sediment layers. Thus, the archaeal community diversity seems to show that active methane cycling took place in the hypersaline microbial mat-associated sediments of the Napoli mud volcano. PMID:21335391

  8. Archaeal populations in hypersaline sediments underlying orange microbial mats in the Napoli mud volcano.

    PubMed

    Lazar, Cassandre Sara; L'haridon, Stéphane; Pignet, Patricia; Toffin, Laurent

    2011-05-01

    Microbial mats in marine cold seeps are known to be associated with ascending sulfide- and methane-rich fluids. Hence, they could be visible indicators of anaerobic oxidation of methane (AOM) and methane cycling processes in underlying sediments. The Napoli mud volcano is situated in the Olimpi Area that lies on saline deposits; from there, brine fluids migrate upward to the seafloor. Sediments associated with a brine pool and microbial orange mats of the Napoli mud volcano were recovered during the Medeco cruise. Based on analysis of RNA-derived sequences, the "active" archaeal community was composed of many uncultured lineages, such as rice cluster V or marine benthic group D. Function methyl coenzyme M reductase (mcrA) genes were affiliated with the anaerobic methanotrophic Archaea (ANME) of the ANME-1, ANME-2a, and ANME-2c groups, suggesting that AOM occurred in these sediment layers. Enrichment cultures showed the presence of viable marine methylotrophic Methanococcoides in shallow sediment layers. Thus, the archaeal community diversity seems to show that active methane cycling took place in the hypersaline microbial mat-associated sediments of the Napoli mud volcano.

  9. Access and Completion of a Web-Based Treatment in a Population-Based Sample of Tornado-Affected Adolescents

    PubMed Central

    Price, Matthew; Yuen, Erica; Davidson, Tatiana M.; Hubel, Grace; Ruggiero, Kenneth J.

    2015-01-01

    Although web-based treatments have significant potential to assess and treat difficult to reach populations, such as trauma-exposed adolescents, the extent that such treatments are accessed and used is unclear. The present study evaluated the proportion of adolescents who accessed and completed a web-based treatment for post-disaster mental health symptoms. Correlates of access and completion were examined. A sample of 2,000 adolescents living in tornado-affected communities was assessed via structured telephone interview and invited to a web-based treatment. The modular treatment addressed symptoms of PTSD, depression, and alcohol and tobacco use. Participants were randomized to experimental or control conditions after accessing the site. Overall access for the intervention was 35.8%. Module completion for those who accessed ranged from 52.8% to 85.6%. Adolescents with parents who used the Internet to obtain health-related information were more likely to access the treatment. Adolescent males were less likely to access the treatment. Future work is needed to identify strategies to further increase the reach of web-based treatments to provide clinical services in a post-disaster context. PMID:25622071

  10. Access and completion of a Web-based treatment in a population-based sample of tornado-affected adolescents.

    PubMed

    Price, Matthew; Yuen, Erica K; Davidson, Tatiana M; Hubel, Grace; Ruggiero, Kenneth J

    2015-08-01

    Although Web-based treatments have significant potential to assess and treat difficult-to-reach populations, such as trauma-exposed adolescents, the extent that such treatments are accessed and used is unclear. The present study evaluated the proportion of adolescents who accessed and completed a Web-based treatment for postdisaster mental health symptoms. Correlates of access and completion were examined. A sample of 2,000 adolescents living in tornado-affected communities was assessed via structured telephone interview and invited to a Web-based treatment. The modular treatment addressed symptoms of posttraumatic stress disorder, depression, and alcohol and tobacco use. Participants were randomized to experimental or control conditions after accessing the site. Overall access for the intervention was 35.8%. Module completion for those who accessed ranged from 52.8% to 85.6%. Adolescents with parents who used the Internet to obtain health-related information were more likely to access the treatment. Adolescent males were less likely to access the treatment. Future work is needed to identify strategies to further increase the reach of Web-based treatments to provide clinical services in a postdisaster context.

  11. Microbial population in the rumen of swamp buffalo (Bubalus bubalis) as influenced by coconut oil and mangosteen peel supplementation.

    PubMed

    Pilajun, R; Wanapat, M

    2013-06-01

    Four, rumen fistulated swamp buffalo bulls were used to study microbial populations in the rumen when supplemented with coconut oil and mangosteen peel. Animals were randomly assigned to a 4 × 4 Latin square design. Four treatments were un-supplemented (Control), supplementation with coconut oil at 50 g/kg (CO5), supplementation with mangosteen peel at 30 g/kg (MP3) and supplementation with CO5 and MP3 (COM), of total DM intake. Animals received concentrate at 10 g/kg of BW, and rice straw was given ad libitum. Abundance of total bacteria was increased by CO5 supplementation, whereas populations of protozoa and Fibrobacter succinogenes were reduced by CO5 and COM supplementation. Dietary supplementation did not affect methanogen, Ruminococcus flavefaciens or Ruminococcus albus abundances. Dietary treatments changed denaturing gradient gel electrophoresis (DGGE) band patterns of methanogens and protozoa when compared with the control group, especially when supplemented with MP3. Supplementation of COM resulted in the greatest difference in pattern of DGGE bands for total bacteria compared with the control. Coconut oil and mangosteen peel supplementation resulted in changing of rumen microbial abundances and communities; however, combination of them could be more benefit to improve rumen fermentation of swamp buffalo fed on rice straw.

  12. Enhancement of the sweep efficiency of waterflooding operations by the in-situ microbial population of petroleum reservoirs

    SciTech Connect

    Brown, L.R.; Vadie, A.A.; Stephens, J.O.; Azadpour, A.

    1995-12-31

    Live cores were obtained from five reservoirs using special precautions to prevent contamination by exogenous microorganisms and minimize exposure to oxygen. The depths from which the cores were obtained ranged from 2,705 ft to 6,568 ft. Core plugs were cut radially from live cores, encased in heat-shrink plastic tubes, placed in core holders, and fitted with inlets and outlets. Nutrient additions stimulated the in-situ microbial population to increase, dissolve stratal material, produce gases, and release oil. Reduction in flow through the core plugs was observed in some cases, while in other cases flow was increased, probably due to the dissolution of carbonates in the formation. A field demonstration of the ability of the in-situ microbial population to increase oil recovery by blocking the more permeable zones of the reservoir is currently underway. This demonstration is being conducted in the North Blowhorn Creek Unit situated in Lamar County, Alabama. Live cores were obtained from a newly drilled well in the field and tested as described above. The field project involves four test patterns each including one injector, four to five producers, and a comparable control injector with its four to five producers. Nutrient injection in the field began November 1994.

  13. Access and Attitudes to HPV Vaccination amongst Hard-To-Reach Populations in Kenya

    PubMed Central

    Watson-Jones, Deborah; Mugo, Nelly; Lees, Shelley; Mathai, Muthoni; Vusha, Sophie; Ndirangu, Gathari; Ross, David A.

    2015-01-01

    Background Sub-Saharan Africa bears the greatest burden of cervical cancer. Human papillomavirus (HPV) vaccination programmes to prevent the disease will need to reach vulnerable girls who may not be able access health and screening services in the future. We conducted formative research on facilitators and barriers to HPV vaccination and potential acceptability of a future HPV vaccination programme amongst girls living in hard-to-reach populations in Kenya. Methods Stakeholder interviews with Ministry of Health staff explored barriers to and support for the uptake of HPV vaccination. A situation assessment was conducted to assess community services in Maasai nomadic pastoralist communities in Kajiado County and in Korogocho informal settlement in Nairobi city, followed by focus group discussions (n=14) and semi-structured interviews (n=28) with health workers, parents, youth, and community and religious leaders. These covered marriage, knowledge of cervical cancer and HPV, factors that might inhibit or support HPV vaccine uptake and intention to accept HPV vaccine if a programme was in place. Results Reported challenges to an HPV vaccination programme included school absenteeism and drop-out, early age of sex and marriage, lack of parental support, population mobility and distance from services. Despite little prior knowledge of cervical cancer and HPV, communities were interested in receiving HPV vaccination. Adequate social mobilisation and school-based vaccination, supplemented by out-reach activities, were considered important facilitating factors to achieve high coverage. There was some support for a campaign approach to vaccine delivery. Conclusions Given the high level of support for a vaccine against cervical cancer and the experience of reaching pastoralist and slum-dwellers for other immunizations, implementing an HPV vaccine programme should be feasible in such hard-to-reach communities. This may require additional delivery strategies in addition to the

  14. Spatial accessibility of the population to urban health centres in Kermanshah, Islamic Republic of Iran: a geographic information systems analysis.

    PubMed

    Reshadat, S; Saedi, S; Zangeneh, A; Ghasemi, S R; Gilan, N R; Karbasi, A; Bavandpoor, E

    2015-09-08

    Geographic information systems (GIS) analysis has not been widely used in underdeveloped countries to ensure that vulnerable populations have accessibility to primary health-care services. This study applied GIS methods to analyse the spatial accessibility to urban primary-care centres of the population in Kermanshah city, Islamic Republic of Iran, by age and sex groups. In a descriptive-analytical study over 3 time periods, network analysis, mean centre and standard distance methods were applied using ArcGIS 9.3. The analysis was based on a standard radius of 750 m distance from health centres, walking speed of 1 m/s and desired access time to health centres of 12.5 mins. The proportion of the population with inadequate geographical access to health centres rose from 47.3% in 1997 to 58.4% in 2012. The mean centre and standard distance mapping showed that the spatial distribution of health centres in Kermanshah needed to be adjusted to changes in population distribution.

  15. Microbial Populations Associated with Phosphate-Mediated Vadose Zone Sequestration of Strontium and Uranium

    NASA Astrophysics Data System (ADS)

    Wu, C. H.; Chou, J.; Fujita, Y.; Bill, M.; Brodie, E. L.; Andersen, G. L.; Hazen, T. C.; Conrad, M. S.

    2007-12-01

    Significant quantities of metals and radionuclides are contained in thick unsaturated zones at several contaminated sites in the western US. In many cases, this contamination has migrated to underlying groundwater, sometimes decades after being released into the subsurface. Because of the prohibitive costs associated with physically removing the contamination, an attractive remedy to this problem is to develop methods for long-term in situ stabilization of the contamination in the vadose zone. Our research focuses on developing a method of introducing gaseous compounds to stimulate precipitation of stable phosphate mineral phases in the vadose zone to immobilize soluble contaminants thus minimizing further transport to groundwater. Preliminary studies have demonstrated that biological precipitation of phosphate minerals can be stimulated under unsaturated conditions by injection of triethyl phosphate (TEP) gas. Microorganisms hydrolyze TEP, releasing inorganic phosphate, catalyzing the precipitation of metals and radionuclide-containing phosphate minerals. Our initial results demonstrate that a mixed culture of aerobic microorganisms from vadose zone sediments, enriched with TEP, produce significantly higher concentrations of inorganic phosphate than the no TEP control. A high-density microarray (PhyloChip) capable of detecting up to 9,000 prokaryotic taxa will be used to identify the microbial community composition of the enriched culture. In addition, the metabolically active organisms will be investigated through extraction and hybridization of ribosomal RNA. Organisms capable of hydrolyzing TEP to inorganic phosphate will be further characterized to determine the requirements for aerobic microbially-mediated radionuclide immobilization. The chemical and isotopic compositions of the reactants and products will be measured to enable in situ monitoring of microbial TEP utilization. The result of these studies will be the basis for unsaturated column experiments

  16. Prediction of microbial accessibility of carbon-14-phenanthrene in soil in the presence of pyrene or benzo[a]pyrene using an aqueous cyclodextrin extraction technique.

    PubMed

    Papadopoulos, Apostolos; Reid, Brian J; Semple, Kirk T

    2007-01-01

    Traditionally, solvent extractions are routinely used in the assessment of contaminated land. However, vigorous solvent extractions only give total concentrations rather than that relating to the bioaccessible fraction. Recently, less harsh, aqueous-based extraction methods have been shown to be a better estimate of the microbial degradation of polycyclic aromatic hydrocarbons (PAHs). The aqueous-based hydroxypropyl-beta-cyclodextrin (HPCD) extraction technique was tested using 14C-PAHs in soils and compared against indigenous microbial mineralization (a measure of bioaccessibility) of 14C-phenanthrene in the presence of pyrene or benzo[a]pyrene (B[a]P) over a range of concentrations (0, 5, 10, or 50 mg kg(-1)) and aged for 0, 25, 50, and 100 d in four soils. At each time point, the total loss, extractability, and mineralization of 14C-phenanthrene was measured in each of the soils. The presence of the other PAHs had little effect on the behavior of 14C-phenanthrene in any of the soils. Comparisons between the amounts of 14C-phenanthrene extracted using HPCD and mineralized were made and showed that there was a correlation (1:1). This study demonstrates that HPCD extraction is able to predict the microbial accessibility fraction of 14C-phenanthrene in the presence of other PAHs in a range of soils, further supporting the applicability of this technique.

  17. Using populations of human and microbial genomes for organism detection in metagenomes

    DOE PAGES

    Ames, Sasha K.; Gardner, Shea N.; Marti, Jose Manuel; ...

    2015-04-29

    Identifying causative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful tool to apply when other targeted diagnostics fail. Numerous technical challenges remain, however, before SMS can move beyond the role of research tool. Accurately separating the known and unknown organism content remains difficult, particularly when SMS is applied as a last resort. The true amount of human DNA that remains in a sample after screening against the human reference genome and filtering nonbiological components left from library preparation has previously been underreported. In this study, we create the most comprehensive collection of microbial and reference-freemore » human genetic variation available in a database optimized for efficient metagenomic search by extracting sequences from GenBank and the 1000 Genomes Project. The results reveal new human sequences found in individual Human Microbiome Project (HMP) samples. Individual samples contain up to 95% human sequence, and 4% of the individual HMP samples contain 10% or more human reads. In conclusion, left unidentified, human reads can complicate and slow down further analysis and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected.« less

  18. Using populations of human and microbial genomes for organism detection in metagenomes

    SciTech Connect

    Ames, Sasha K.; Gardner, Shea N.; Marti, Jose Manuel; Slezak, Tom R.; Gokhale, Maya B.; Allen, Jonathan E.

    2015-04-29

    Identifying causative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful tool to apply when other targeted diagnostics fail. Numerous technical challenges remain, however, before SMS can move beyond the role of research tool. Accurately separating the known and unknown organism content remains difficult, particularly when SMS is applied as a last resort. The true amount of human DNA that remains in a sample after screening against the human reference genome and filtering nonbiological components left from library preparation has previously been underreported. In this study, we create the most comprehensive collection of microbial and reference-free human genetic variation available in a database optimized for efficient metagenomic search by extracting sequences from GenBank and the 1000 Genomes Project. The results reveal new human sequences found in individual Human Microbiome Project (HMP) samples. Individual samples contain up to 95% human sequence, and 4% of the individual HMP samples contain 10% or more human reads. In conclusion, left unidentified, human reads can complicate and slow down further analysis and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected.

  19. Feasibility of mini-sequencing schemes based on nucleotide polymorphisms for microbial identification and population analyses.

    PubMed

    Araujo, Ricardo; Eusebio, Nadia; Caramalho, Rita

    2015-03-01

    Practical schemes based on single nucleotide polymorphisms (SNP) have been proposed as alternatives to simplify and replace the molecular methodologies based on the extensive sequencing analysis of genes. SNaPshot mini-sequencing has been progressively experienced during the last decade and represents a fast and robust strategy to analyze critical polymorphisms. Such assays have been proposed to characterize some bacteria and microbial eukaryotes, and its feasibility was now reviewed in the present manuscript. The mini-sequencing schemes showed high discriminatory power and competence for identification of microorganisms, but some specificity errors were still found, particularly for species of the Burkholderia cepacia complex and mycobacteria. SNP assays designed for other goals, e.g., comparison of strains, detection of serotypes, virulence, epidemic, and phylogenetic-related subgroups of isolates, can be very useful by facilitating the investigation of large collections of isolates. The next-generation of SNP assays might consider the inclusion of large number of markers to fully characterize microbial taxonomy and strains; nevertheless, these new technologies are still prone to errors and can largely benefit from integration with well-established mini-sequencing assays. Newly proposed molecular tools should be systematically tested in collections of isolates with high indexes of diversity and guarantee interlaboratorial validation.

  20. Comparison of the microbial population in rabbits and guinea pigs by next generation sequencing

    PubMed Central

    Crowley, Edward J.; King, Jonathan M.; Wilkinson, Toby; Worgan, Hilary J.; Huson, Kathryn M.; Rose, Michael T.; McEwan, Neil R.

    2017-01-01

    This study aimed to determine the microbial composition of faeces from two groups of caecotrophagic animals; rabbits and guinea pigs. In addition the study aimed to determine the community present in the different organs in the rabbit. DNA was extracted from seven of the organs in wild rabbits (n = 5) and from faecal samples from domesticated rabbits (n = 6) and guinea pigs (n = 6). Partial regions of the small ribosomal sub-unit were amplified by PCR and then the sequences present in each sample were determined by next generation sequencing. Differences were detected between samples from rabbit and guinea pig faeces, suggesting that there is not a microbial community common to caecotrophagic animals. Differences were also detected in the different regions of the rabbits’ digestive tracts. As with previous work, many of the organisms detected were Firmicutes or unclassified species and there was a lack of Fibrobacteres, but for the first time we observed a high number of Bacteroidetes in rabbit samples. This work re-iterates high levels of Firmicutes and unclassified species are present in the rabbit gut, together with low number of Fibrobacteres. This suggests that in the rabbit gut, organisms other than the Fibrobacteres must be responsible for fibre digestion. However observation of high numbers of Bacteroidetes suggests that this phylum may indeed have a role to play in digestion in the rabbit gut. PMID:28182658

  1. metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences

    PubMed Central

    2013-01-01

    Environmental shotgun sequencing (ESS) has potential to give greater insight into microbial communities than targeted sequencing of 16S regions, but requires much higher sequence coverage. The advent of next-generation sequencing has made it feasible for the Human Microbiome Project and other initiatives to generate ESS data on a large scale, but computationally efficient methods for analysing such data sets are needed. Here we present metaBEETL, a fast taxonomic classifier for environmental shotgun sequences. It uses a Burrows-Wheeler Transform (BWT) index of the sequencing reads and an indexed database of microbial reference sequences. Unlike other BWT-based tools, our method has no upper limit on the number or the total size of the reference sequences in its database. By capturing sequence relationships between strains, our reference index also allows us to classify reads which are not unique to an individual strain but are nevertheless specific to some higher phylogenetic order. Tested on datasets with known taxonomic composition, metaBEETL gave results that are competitive with existing similarity-based tools: due to normalization steps which other classifiers lack, the taxonomic profile computed by metaBEETL closely matched the true environmental profile. At the same time, its moderate running time and low memory footprint allow metaBEETL to scale well to large data sets. Code to construct the BWT indexed database and for the taxonomic classification is part of the BEETL library, available as a github repository at git@github.com:BEETL/BEETL.git. PMID:23734710

  2. Impact of demographics on human gut microbial diversity in a US Midwest population

    PubMed Central

    Chen, Jun; Ryu, Euijung; Hathcock, Matthew; Ballman, Karla; Chia, Nicholas; Olson, Janet E

    2016-01-01

    The clinical utility of microbiome biomarkers depends on the reliable and reproducible nature of comparative results. Underappreciation of the variation associated with common demographic, health, and behavioral factors may confound associations of interest and generate false positives. Here, we present the Midwestern Reference Panel (MWRP), a resource for comparative gut microbiome studies conducted in the Midwestern United States. We analyzed the relationships between demographic and health behavior-related factors and the microbiota in this cohort, and estimated their effect sizes. Most variables investigated were associated with the gut microbiota. Specifically, body mass index (BMI), race, sex, and alcohol use were significantly associated with microbial β-diversity (P < 0.05, unweighted UniFrac). BMI, race and alcohol use were also significantly associated with microbial α-diversity (P < 0.05, species richness). Tobacco use showed a trend toward association with the microbiota (P < 0.1, unweighted UniFrac). The effect sizes of the associations, as quantified by adjusted R2 values based on unweighted UniFrac distances, were small (< 1% for all variables), indicating that these factors explain only a small percentage of overall microbiota variability. Nevertheless, the significant associations between these variables and the gut microbiota suggest that they could still be potential confounders in comparative studies and that controlling for these variables in study design, which is the main objective of the MWRP, is important for increasing reproducibility in comparative microbiome studies. PMID:26839739

  3. Using populations of human and microbial genomes for organism detection in metagenomes

    PubMed Central

    Ames, Sasha K.; Gardner, Shea N.; Marti, Jose Manuel; Slezak, Tom R.; Gokhale, Maya B.; Allen, Jonathan E.

    2015-01-01

    Identifying causative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful tool to apply when other targeted diagnostics fail. Numerous technical challenges remain, however, before SMS can move beyond the role of research tool. Accurately separating the known and unknown organism content remains difficult, particularly when SMS is applied as a last resort. The true amount of human DNA that remains in a sample after screening against the human reference genome and filtering nonbiological components left from library preparation has previously been underreported. In this study, we create the most comprehensive collection of microbial and reference-free human genetic variation available in a database optimized for efficient metagenomic search by extracting sequences from GenBank and the 1000 Genomes Project. The results reveal new human sequences found in individual Human Microbiome Project (HMP) samples. Individual samples contain up to 95% human sequence, and 4% of the individual HMP samples contain 10% or more human reads. Left unidentified, human reads can complicate and slow down further analysis and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected. PMID:25926546

  4. Controlling Salmonella infection in weanling pigs through water delivery of direct-fed microbials or organic acids. Part I: effects on growth performance, microbial populations, and immune status.

    PubMed

    Walsh, M C; Rostagno, M H; Gardiner, G E; Sutton, A L; Richert, B T; Radcliffe, J S

    2012-01-01

    Pigs (n = 88) weaned at 19 ± 2 d of age were used in a 14-d study to evaluate the effects of water-delivered direct-fed microbials (DFM) or organic acids on growth, immune status, Salmonella infection and shedding, and intestinal microbial populations after intranasal inoculation of Salmonella Typhimurium (10(10) cfu/pig). Pigs were challenged with Salmonella 6 d after commencement of water treatments. Treatments were 1) control diet; 2) control diet + DFM (Enterococcus faecium, Bacillus subtilis, and Bacillus licheniformis) in drinking water at 10(9) cfu/L for each strain of bacteria; 3) control diet + an organic acid-based blend (predominantly propionic, acetic, and benzoic acid) in drinking water at 2.58 mL/L; and 4) control diet + 55 mg/kg of carbadox. Serum samples were taken on d 6, 8, 10, and 14 for determination of tumor necrosis factor α (TNFα) concentrations. Fecal samples were taken on d 0, 5, 7, and 11 for determination of Salmonella shedding and enumeration of coliforms. Pigs were euthanized on d 6, 8, 10, and 14. Intestinal and cecal tissue and digesta and mesenteric lymph nodes were sampled and analyzed for Salmonella. Duodenal, jejunal, and ileal mucosal scrapings were sampled for measurement of mucosal TNFα concentrations. Water delivery of DFM prevented a decline in ADG on d 2 to 6 postchallenge compared with the negative control (P < 0.05). Coliform counts tended to be greater (P = 0.09) in the cecum of the DFM treatment group on d 2 postinfection compared with the negative control and acid treatment groups. However, Salmonella prevalence in the feces, gastrointestinal tract, or lymph nodes was not affected by water delivery of acids or DFM. Serum and mucosal TNFα concentrations were not affected by treatment throughout the study with the exception of ileal concentrations on d 4 postchallenge, which were greater in the negative control group compared with all other treatments (P < 0.05). The in-feed antibiotic was the only treatment that

  5. Progression of natural attenuation processes at a crude oil spill site: II. Controls on spatial distribution of microbial populations

    USGS Publications Warehouse

    Bekins, B.A.; Cozzarelli, I.M.; Godsy, E.M.; Warren, E.; Essaid, H.I.; Tuccillo, M.E.

    2001-01-01

    A multidisciplinary study of a crude-oil contaminated aquifer shows that the distribution of microbial physiologic types is strongly controlled by the aquifer properties and crude oil location. The microbial populations of four physiologic types were analyzed together with permeability, pore-water chemistry, nonaqueous oil content, and extractable sediment iron. Microbial data from three vertical profiles through the anaerobic portion of the contaminated aquifer clearly show areas that have progressed from iron-reduction to methanogenesis. These locations contain lower numbers of iron reducers, and increased numbers of fermenters with detectable methanogens. Methanogenic conditions exist both in the area contaminated by nonaqueous oil and also below the oil where high hydrocarbon concentrations correspond to local increases in aquifer permeability. The results indicate that high contaminant flux either from local dissolution or by advective transport plays a key role in determining which areas first become methanogenic. Other factors besides flux that are important include the sediment Fe(II) content and proximity to the water table. In locations near a seasonally oscillating water table, methanogenic conditions exist only below the lowest typical water table elevation. During 20 years since the oil spill occurred, a laterally continuous methanogenic zone has developed along a narrow horizon extending from the source area to 50-60 m downgradient. A companion paper [J. Contam. Hydrol. 53, 369-386] documents how the growth of the methanogenic zone results in expansion of the aquifer volume contaminated with the highest concentrations of benzene, toluene, ethylbenzene, and xylenes. Copyright ?? 2001 Elsevier Science B.V.

  6. Spatial distribution of microbial populations and carbon cycle in the subsurface environment of the Horonobe area, Hokkaido, Japan

    NASA Astrophysics Data System (ADS)

    Amano, Y.; Ise, K.; Terashima, M.; Sasaki, Y.; Amamiya, H.; Yoshikawa, H.

    2014-12-01

    Microorganisms are widely distributed in the subsurface environments. However, the distribution, role and rate of metabolisms, and the source of their activity are not well known. In this study, we investigated deep groundwater samples from sedimentary rocks, containing saturated methane and CO2, using boreholes at the Horonobe Underground Research Laboratory (URL), northern Hokkaido, Japan. The hydrochemical conditions of groundwaters, such as in-situ water pressure, temperature, electric conductivity, pH, redox potential, were monitored without degassing at multiple intervals along the borehole. Groundwater samples were taken periodically and chemical composition was analyzed using ICP-MS, etc. Cell counts were in the range of 103 to 105 cells ml-1. Molecular analyses revealed the spatial distribution and heterogeneity of the microbial population. Abundant methanogens were detected in the groundwater, and 80% of them were related to either Methanoregula boonei or Methanobacterium flexile that can utilize H2/CO2 by methanogenesis. Phylotypes clustered within the phylum Firmicutes, beta-Proteobacteria, delta-Proteobacteria and candidate division TM7 were dominant in the groundwater samples. Laboratory experiments using a culture technique showed that humic substances purified from the groundwater at Horonobe area appear to be degraded by microorganisms. Our results suggest that microbial spatial distributions in the subsurface environment were correlated closely with geochemical conditions, such as redox condition and carbon sources. In addition, it is inferred that humic substances are one of the important carbon sources for the subsurface microbial redox processes in the environment. This study was partly funded by the Ministry of Economy, Trade and Industry of Japan.

  7. Population, Population and Family Education, and Family Planning: A Bibliography, Supplement to Bibliography, and Accessions List, February-June 1973.

    ERIC Educational Resources Information Center

    United Nations Educational, Scientific, and Cultural Organization, Bangkok (Thailand). Regional Office for Education in Asia and Oceania.

    This is a bibliography of books, periodical articles and pamphlets on population and family education which are available in the library of the Population Education Clearing House Service of the Unesco Regional Office for Education in Asia, Bangkok. Most of the documents cited were published in the 60's and 70's with the exception of a few which…

  8. Mapping the Centimeter-Scale Spatial Variability of PAHs and Microbial Populations in the Rhizosphere of Two Plants

    PubMed Central

    Bourceret, Amélia; Leyval, Corinne; de Fouquet, Chantal; Cébron, Aurélie

    2015-01-01

    Rhizoremediation uses root development and exudation to favor microbial activity. Thus it can enhance polycyclic aromatic hydrocarbon (PAH) biodegradation in contaminated soils. Spatial heterogeneity of rhizosphere processes, mainly linked to the root development stage and to the plant species, could explain the contrasted rhizoremediation efficiency levels reported in the literature. Aim of the present study was to test if spatial variability in the whole plant rhizosphere, explored at the centimetre-scale, would influence the abundance of microorganisms (bacteria and fungi), and the abundance and activity of PAH-degrading bacteria, leading to spatial variability in PAH concentrations. Two contrasted rhizospheres were compared after 37 days of alfalfa or ryegrass growth in independent rhizotron devices. Almost all spiked PAHs were degraded, and the density of the PAH-degrading bacterial populations increased in both rhizospheres during the incubation period. Mapping of multiparametric data through geostatistical estimation (kriging) revealed that although root biomass was spatially structured, PAH distribution was not. However a greater variability of the PAH content was observed in the rhizosphere of alfalfa. Yet, in the ryegrass-planted rhizotron, the Gram-positive PAH-degraders followed a reverse depth gradient to root biomass, but were positively correlated to the soil pH and carbohydrate concentrations. The two rhizospheres structured the microbial community differently: a fungus-to-bacterium depth gradient similar to the root biomass gradient only formed in the alfalfa rhizotron. PMID:26599438

  9. Detailed Analysis of the Microbial Population in Malaysian Spontaneous Cocoa Pulp Fermentations Reveals a Core and Variable Microbiota

    PubMed Central

    Mathawan, Melissa; Wittocx, Pieter-Jan; Saels, Veerle; Struyf, Nore; Bernaert, Herwig; Vrancken, Gino; Verstrepen, Kevin J.

    2013-01-01

    The fermentation of cocoa pulp is one of the few remaining large-scale spontaneous microbial processes in today's food industry. The microbiota involved in cocoa pulp fermentations is complex and variable, which leads to inconsistent production efficiency and cocoa quality. Despite intensive research in the field, a detailed and comprehensive analysis of the microbiota is still lacking, especially for the expanding Asian production region. Here, we report a large-scale, comprehensive analysis of four spontaneous Malaysian cocoa pulp fermentations across two time points in the harvest season and two fermentation methods. Our results show that the cocoa microbiota consists of a “core” and a “variable” part. The bacterial populations show a remarkable consistency, with only two dominant species, Lactobacillus fermentum and Acetobacter pasteurianus. The fungal diversity is much larger, with four dominant species occurring in all fermentations (“core” yeasts), and a large number of yeasts that only occur in lower numbers and specific fermentations (“variable” yeasts). Despite this diversity, a clear pattern emerges, with early dominance of apiculate yeasts and late dominance of Saccharomyces cerevisiae. Our results provide new insights into the microbial diversity in Malaysian cocoa pulp fermentations and pave the way for the selection of starter cultures to increase efficiency and consistency. PMID:24358116

  10. Evaluation of the Microbial Population in the Multibiological Life Support System Experiments

    NASA Astrophysics Data System (ADS)

    Fu, Yuming; Tong, Ling; Li, Ming; Hu, Enzhu; Hu, Dawei; He, Wenting; Liu, Hong

    In order to develop and evaluate a ground-based bioregenerative life support system satisfying half of one crew member's requirement towards O2 , Multibiological Life Support System Exper-iments (MLSSE) have been conducted. The MLSSE involved humans participating in the gas exchange with the closed equipment simulating the future extraterrestrial life support systems, which included three phases. The Phase I test involved one person participating in the gas exchange with lettuce in plant chamber as the primary means of air revitalization for 3 months. The Phase II test involved one person participating in the gas exchange with lettuce in plant chamber and micoalgae in bioreactor as the means of air revitalization for 1 month. In the Phase III test, silkworm was introduced into animal chamber for 2 months based on Phase II. The microbial dynamics in the closed chambers were evaluated during the whole experiments. The surfaces, water, and air of closed equipment were sampled for microbial content during the whole experiments. In general, the numbers of microbes in the chambers slowly increased with length of occupation. Compared with Phase I, the numbers of microbes of Phase II ob-viously increased, however, the numbers of microbes of Phase III did not increase relative to Phase II. The types of microbes found on the surfaces and in the air in all the experimental phases were similar. The most common bacteria were Bacillus sp., Pseudomonas sp., as well as Sphingomonas sp., with Pencillium sp. and Cladosporium sp. the most common fungi. A few opportunistic pathogens were also determined, but neither phase had levels of microbes that would be considered an occupational health threat.

  11. A surface swab method for culturing Foley catheters assays the pericatheter (urethral) but not the urine (luminal) microbial population.

    PubMed

    Johnson, J R; Dykstra, D; Brown, J J; Kringstad, B; Pryor, J L

    1997-07-01

    Assessment of the urethral flora in patients with indwelling bladder catheters is problematic in the presence of urinary tract infection (UTI). A new surface swab method that samples the external catheter surface without interference from contaminated luminal contents is described. In vitro, recovery of adherent bacteria from the external catheter surface by the surface swab method was proportional to the bacterial density as measured by a comparison scrape method. In a prospective longitudinal assessment of three chronically catheterized subjects with polymicrobial catheter-associated UTI, a conventional roll plate catheter culture method suggested substantial overlap between the urethral and urine microbial populations, possibly a result of contamination of catheter cultures by infected urine. In contrast, the surface swab method revealed little overlap between these floras, evidence suggesting a predominantly luminal (rather than meatal) route of UTI acquisition. The new surface swab method should prove useful in future studies of the pathogenesis and prevention of catheter-associated UTI.

  12. The spatial profiles and metabolic capabilities of microbial populations impact the growth of antibiotic-resistant mutants

    PubMed Central

    Kaushik, Karishma S.; Ratnayeke, Nalin; Katira, Parag; Gordon, Vernita D.

    2015-01-01

    Antibiotic resistance adversely affects clinical and public health on a global scale. Using the opportunistic human pathogen Pseudomonas aeruginosa, we show that increasing the number density of bacteria, on agar containing aminoglycoside antibiotics, can non-monotonically impact the survival of antibiotic-resistant mutants. Notably, at high cell densities, mutant survival is inhibited. A wide range of bacterial species can inhibit antibiotic-resistant mutants. Inhibition results from the metabolic breakdown of amino acids, which results in alkaline by-products. The consequent increase in pH acts in conjunction with aminoglycosides to mediate inhibition. Our work raises the possibility that the manipulation of microbial population structure and nutrient environment in conjunction with existing antibiotics could provide therapeutic approaches to combat antibiotic resistance. PMID:25972434

  13. Microbial-mammalian co-metabolites dominate the age-associated urinary metabolic phenotype in Taiwanese and American Populations

    PubMed Central

    Swann, Jonathan R.; Spagou, Konstantina; Lewis, Matthew; Nicholson, Jeremy K.; Glei, Dana A.; Seeman, Teresa E.; Coe, Christopher L.; Goldman, Noreen; Ryff, Carol D.; Weinstein, Maxine; Holmes, Elaine

    2013-01-01

    Understanding the metabolic processes associated with aging is key to developing effective management and treatment strategies for age-related diseases. We investigated the metabolic profiles associated with age in a Taiwanese and an American population. 1H NMR spectral profiles were generated for urine specimens collected from the Taiwanese Social Environment and Biomarkers of Aging Study (SEBAS; n= 857; age 54-91 years) and the Mid-Life in the USA study (MIDUS II; n= 1148; age 35-86 years). Multivariate and univariate linear projection methods revealed some common age-related characteristics in urinary metabolite profiles in the American and Taiwanese populations, as well as some distinctive features. In both cases, two metabolites--4-cresyl sulfate (4CS) and phenylacetylglutamine (PAG)—were positively associated with age. In addition, creatine and β-hydroxy-β-methylbutyrate (HMB) were negatively correlated with age in both populations (p<4×10-6). These age-associated gradients in creatine and HMB reflect decreasing muscle mass with age. The systematic increase in PAG and 4CS was confirmed using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS). Both are products of concerted microbial-mammalian host co-metabolism and indicate an age-related association with the balance of host-microbiome metabolism. PMID:23701591

  14. Range expansions transition from pulled to pushed waves as growth becomes more cooperative in an experimental microbial population

    PubMed Central

    Yurtsev, Eugene Anatoly; Korolev, Kirill S.; Gore, Jeff

    2016-01-01

    Range expansions are becoming more frequent due to environmental changes and rare long-distance dispersal, often facilitated by anthropogenic activities. Simple models in theoretical ecology explain many emergent properties of range expansions, such as a constant expansion velocity, in terms of organism-level properties such as growth and dispersal rates. Testing these quantitative predictions in natural populations is difficult because of large environmental variability. Here, we used a controlled microbial model system to study range expansions of populations with and without intraspecific cooperativity. For noncooperative growth, the expansion dynamics were dominated by population growth at the low-density front, which pulled the expansion forward. We found these expansions to be in close quantitative agreement with the classical theory of pulled waves by Fisher [Fisher RA (1937) Ann Eugen 7(4):355–369] and Skellam [Skellam JG (1951) Biometrika 38(1-2):196–218], suitably adapted to our experimental system. However, as cooperativity increased, the expansions transitioned to being pushed, that is, controlled by growth and dispersal in the bulk as well as in the front. Given the prevalence of cooperative growth in nature, understanding the effects of cooperativity is essential to managing invading species and understanding their evolution. PMID:27185918

  15. Influence of pulsed magnetic field on soybean (Glycine max L.) seed germination, seedling growth and soil microbial population.

    PubMed

    Radhakrishnan, Ramalingam; Kumari, Bollipo Dyana Ranjitha

    2013-08-01

    The effects of pulsed magnetic field (PMF) treatment of soybean (Glycine max L. cv CO3) seeds were investigated on rate of seed germination, seedling growth, physico-chemical properties of seed leachates and soil microbial population under laboratory conditions. Seeds were exposed to PMF of 1500 nT at 0.1, 1.0 10.0 and 100.0 Hz for 5 h per day for 20 days, induced by enclosure coil systems. Non-treated seeds were considered as controls. All PMF treatments significantly increased the rate of seed germination, while 10 and 100 Hz PMFs showed the most effective response. The 1.0 and 10 Hz PMFs remarkably improved the fresh weight of shoots and roots, leaf area and plant height from seedlings from magnetically-exposed seeds compared to the control, while 10 Hz PMF increased the total soluble sugar, total protein and phenol contents. The leaf chlorophyll a, b and total chlorophyll were higher in PMF (10 and 100 Hz) pretreated plants, as compared to other treatments. In addition, activities of alpha-amylase, acid phosphatase, alkaline phosphatase, nitrate reductase, peroxidase and polyphenoloxidase were increased, while beta-amylase and protease activities were declined in PMF (10 Hz)-exposed soybean plants. Similarly, the capacity of absorbance of water by seeds and electrical conductivity of seed leachates were significantly enhanced by 10 Hz PMF exposure, whereas PMF (10 Hz) pretreated plants did not affect the microbial population in rhizosphere soil. The results suggested the potential of 10 Hz PMF treatment to enhance the germination and seedling growth of soybean.

  16. [Effects of bio-mulching on rhizosphere soil microbial population, enzyme activity and tree growth in poplar plantation].

    PubMed

    Liu, Jiu-Jun; Fang, Sheng-Zuo; Xie, Bao-Dong; Hao, Juan-Juan

    2008-06-01

    Coriaria nepalensis, Pteridium aquilinum var. latiuscukum, Imperata cylindrical var. major, and Quercus fabric were used as mulching materials to study their effects on the rhizosphere soil microbial population and enzyme activity and the tree growth in poplar plantation. The results showed that after mulching with test materials, the populations of both bacteria and fungi in rhizosphere soil were more than those of the control. Of the mulching materials, I. cylindrical and Q. fabric had the best effect, with the numbers of bacteria and fungi being 23.56 and 1.43 times higher than the control, respectively. The bacterial and fungal populations in rhizosphere soil increased with increasing mulching amount. When the mulching amount was 7.5 kg m(-2), the numbers of bacteria and fungi in rhizosphere soil were 0.5 and 5.14 times higher than the control, respectively. Under bio-mulching, the bacterial and fungal populations in rhizosphere soil had a similar annual variation trend, which was accorded with the annual fluctuation of soil temperature and got to the maximum in July and the minimum in December. The urease and phosphatase activities in rhizosphere soil also increased with increasing mulching amount. As for the effects of different mulching materials on the enzyme activities, they were in the order of C. nepalensis > P. aquilinum > I. cylindrical > Q. fabric. The annual variation of urease and phosphatase activities in rhizosphere soil was similar to that of bacterial and fungal populations, being the highest in July and the lowest in December. Bio-mulching promoted the tree height, DBH, and biomass of poplar trees significantly.

  17. Unraveling the active microbial populations involved in nitrogen utilization in a vertical subsurface flow constructed wetland treating urban wastewater.

    PubMed

    Pelissari, Catiane; Guivernau, Miriam; Viñas, Marc; de Souza, Samara Silva; García, Joan; Sezerino, Pablo Heleno; Ávila, Cristina

    2017-04-15

    The dynamics of the active microbial populations involved in nitrogen transformation in a vertical subsurface flow constructed wetland (VF) treating urban wastewater was assessed. The wetland (1.5m(2)) operated under average loads of 130gCODm(-2)d(-1) and 17gTNm(-2)d(-1) in Period I, and 80gCODm(-2)d(-1) and 19gTNm(-2)d(-1) in Period II. The hydraulic loading rate (HLR) was 375mmd(-1) and C/N ratio was 2 in both periods. Samples for microbial characterization were collected from the filter medium (top and bottom layers) of the wetland, water influent and effluent at the end of Periods I (Jun-Oct) and II (Nov-Jan). The combination of qPCR and high-throughput sequencing (NGS, MiSeq) assessment at DNA and RNA level of 16S rRNA genes and nitrogen-based functional genes (amoA and nosZ-clade I) revealed that nitrification was associated both with ammonia-oxidizing bacteria (AOB) (Nitrosospira) and ammonia-oxidizing archaea (AOA) (Nitrososphaeraceae), and nitrite-oxidizing bacteria (NOB) such as Nitrobacter. Considering the active abundance (based in amoA transcripts), the AOA population revealed to be more stable than AOB in both periods and depths of the wetland, being less affected by the organic loading rate (OLR). Although denitrifying bacteria (nosZ copies and transcripts) were actively detected in all depths, the denitrification process was low (removal of 2gTNm(-2)d(-1) for both periods) concomitant with NOx-N accumulation in the effluent. Overall, AOA, AOB and denitrifying bacteria (nosZ) were observed to be more active in bottom than in top layer at lower OLR (Period II). A proper design of OLR and HLR seems to be crucial to control the activity of microbial biofilms in VF wetlands on the basis of oxygen, organic-carbon and NOx-N forms, to improve their capacity for total nitrogen removal.

  18. Effects of supercritical fluid extraction pressure on chemical composition, microbial population, polar lipid profile, and microstructure of goat cheese.

    PubMed

    Sánchez-Macías, D; Laubscher, A; Castro, N; Argüello, A; Jiménez-Flores, R

    2013-03-01

    The consumer trend for healthier food choices and preferences for low-fat products has increased the interest in low-fat cheese and nutraceutical dairy products. However, consumer preference is still for delicious food. Low- and reduced-fat cheeses are not completely accepted because of their unappealing properties compared with full-fat cheeses. The method reported here provides another option to the conventional cheese-making process to obtain lower fat cheese. Using CO(2) as a supercritical fluid offers an alternative to reduce fat in cheese after ripening, while maintaining the initial characteristics and flavor. The aim of this experiment was to evaluate the effect of pressure (10, 20, 30, and 40 × 10(6) Pa) of supercritical CO(2) on the amount of fat extracted, microbial population, polar lipid profile, and microstructure of 2 varieties of goat cheese: Majorero, a protected denomination of origin cheese from Spain, and goat Gouda-type cheese. The amount of fat was reduced 50 to 57% and 48 to 55% for Majorero and goat Gouda-type cheeses, respectively. Higher contents (on a fat basis) of sphingomyelin and phosphatidylcholine were found in Majorero cheese compared with control and goat Gouda-type cheeses. The microbial population was reduced after supercritical fluid extraction in both cheeses, and the lethality was higher as pressure increased in Majorero cheese, most noticeably on lactococcus and lactobacillus bacteria. The Gouda-type cheese did not contain any lactobacilli. Micrographs obtained from confocal laser scanning microscopy showed a more open matrix and whey pockets in the Majorero control cheese. This could explain the ease of extracting fat and reducing the microbial counts in this cheese after treatment with supercritical CO(2). Supercritical fluid extraction with CO(2) has great potential in the dairy industry and in commercial applications. The Majorero cheese obtained after the supercritical fluid extraction treatment was an excellent

  19. Comparison of knowledge and accessibility to information sources of HIV/AIDS between blind and sighted populations in Nigeria.

    PubMed

    Otte, Willem M; van der Maas, Frank; de Boer, Anthonius

    2008-10-01

    The aim of this study was to compare the HIV/AIDS knowledge and accessibility to HIV/AIDS information between blind and sighted individuals in Nigeria. A cross-sectional survey was undertaken among rural and urban blind (57) and sighted (62) adolescents in 2006. A structured questionnaire was used to collect data about HIV/AIDS symptoms, transmission and prevention knowledge, as well as accessibility to sources of HIV/AIDS information. Binary logistic regression and chi-square statistics were applied to compare responses between the two populations. Blindness was found to be associated with diminished knowledge of HIV/AIDS transmission, prevention and symptoms. At the same time, the blind rely on different sources of HIV/AIDS information than sighted respondents. A lack of knowledge and limited accessibility to proper sources of information causes the blind disabled to be more vulnerable. It is necessary to supply them with proper information and increase their HIV/AIDS knowledge.

  20. Population structure and physiological changes within a hot spring microbial mat community following disturbance.

    PubMed

    Ferris, M J; Nold, S C; Revsbech, N P; Ward, D M

    1997-04-01

    The influence of disturbance on a hot spring cyanobacterial mat community was investigated by physically removing the top 3.0 mm, which included the entire cyanobacterial layer. Changes in 16S rRNA-defined populations were monitored by denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rRNA gene segments. Some previously absent cyanobacterial populations colonized the disturbed areas, while some populations which were present before the disturbance remained absent for up to 40 days. Changes in physiological activity were measured by oxygen microelectrode analyses and by 14CO2 incorporation into cyanobacterial molecular components. These investigations indicated substantial differences between the disturbed and undisturbed mats, including an unexplained light-induced oxygen consumption in the freshly exposed mat, increased carbon partitioning by phototrophs into growth-related macromolecules, bimodal vertical photosynthesis profiles, and delayed recovery of respiration relative to photosynthesis.

  1. Nonantibiotic interventions to control pathogens and undesired microbial activities in mixed microbial populations residing in the gut of food-producing animals and their excreted wastes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The intensification and industrialization of animal agriculture throughout the world has led to considerable increases in animal production efficiencies but has also led to concerns that microbial pathogens, antibiotic residues, and other chemical contaminants could be concentrated in the environmen...

  2. Access to health-care in Canadian immigrants: a longitudinal study of the National Population Health Survey.

    PubMed

    Setia, Maninder Singh; Quesnel-Vallee, Amelie; Abrahamowicz, Michal; Tousignant, Pierre; Lynch, John

    2011-01-01

    Immigrants often lose their health advantage as they start adapting to the ways of the new society. Having access to care when it is needed is one way that individuals can maintain their health. We assessed the healthcare access in Canadian immigrants and the socioeconomic factors associated with access over a 12-year period. We compared two measures of healthcare access (having a regular doctor and reporting an unmet healthcare need in the past 12 months) among immigrants and Canadian-born men and women, aged more than 18 years. We applied a logistic random effects model to evaluate these outcomes separately, in 3081 males and 4187 females from the National Population Health Survey (1994-2006). Adjusting for all covariates, immigrant men and women (white and non-white) had similar odds of having a regular doctor than the Canadian-born individuals (white immigrants: males OR: 1.32, 95% C.I.: 0.89-1.94, females OR: 1.14, 95% C.I.: 0.78-1.66; non-white immigrants: males OR: 1.28, 95% C.I.: 0.73-2.23, females OR: 1.23, 95% C.I.: 0.64-2.36). Interestingly, non-white immigrant women had significantly fewer unmet health needs (OR: 0.32, 95% C.I.: 0.17-0.59). Among immigrants, time since immigration was associated with having access to a regular doctor (OR per year: 1.02, 95% C.I.: 1.00-1.04). Visible minority female immigrants were least likely to report an unmet healthcare need. In general, there is little evidence that immigrants have worse access to health-care than the Canadian-born population.

  3. Effects of corn silage and grass silage in ruminant rations on diurnal changes of microbial populations in the rumen of dairy cows.

    PubMed

    Lengowski, Melanie B; Witzig, Maren; Möhring, Jens; Seyfang, Gero M; Rodehutscord, Markus

    2016-12-01

    Here, we examined diurnal changes in the ruminal microbial community and fermentation characteristics of dairy cows fed total mixed rations containing either corn silage (CS) or grass silage (GS) as forage. The rations, which consisted of 52% concentrate and 48% GS or CS, were offered for ad libitum intake over 20 days to three ruminal-fistulated lactating Jersey cows during three consecutive feeding periods. Feed intake, ruminal pH, concentrations of short chain fatty acids and ammonia in rumen liquid, as well as abundance change in the microbial populations in liquid and solid fractions, were monitored in 4-h intervals on days 18 and 20. The abundance of total bacteria and Fibrobacter succinogenes increased in solids in cows fed CS instead of GS, and that of protozoa increased in both solid and liquid fractions. Feeding GS favored numbers of F. succinogenes and Selenomonas ruminantium in the liquid fraction as well as the numbers of Ruminobacter amylophilus, Prevotella bryantii and ruminococci in both fractions. Minor effects of silage were detected on populations of methanogens. Despite quantitative changes in the composition of the microbial community, fermentation characteristics were less affected by forage source. These results suggest a functional adaptability of the ruminal microbiota to total mixed rations containing either GS or CS as the source of forage. Diurnal changes in microbial populations were primarily affected by feed intake and differed between species and fractions, with fewer temporal fluctuations evident in the solid than in the liquid fraction. Interactions between forage source and sampling time were of minor importance to most of the microbial species examined. Thus, diurnal changes of microbial populations and fermentative activity were less affected by the two silages.

  4. Changes in psychrotrophic microbial populations during milk creaming to produce Grana Trentino cheese.

    PubMed

    Franciosi, Elena; De Sabbata, Giorgia; Gardini, Fausto; Cavazza, Agostino; Poznanski, Elisa

    2011-02-01

    The aim of this study was to study the psychrotrophic microbiota developing during milk creaming of Grana Trentino cheese-making. 138 isolates from raw whole milk, cream and skim milk samples were screened by Randomly amplified polymorphic DNA PCR biotyping and representative strains of each biotype were characterised by partial 16S rRNA gene sequencing and enzymatic activity. Pseudomonadaceae were commonly isolated in cream samples while Streptococcaceae and Enterobacteriaceae in milk samples. Moraxellaceae and Flavobacteriaceae were found in both cream and milk samples. More than 80% of psychrotrophic isolates could grow at 37°C. All Flavobacteriaceae and half of Pseudomonadaceae biotypes displayed proteolytic activity on milk agar even at low temperatures such as 10°C. All Streptococcaceae and some of Enterobacteriaceae displayed acidifying activity and almost all Acinetobacter spp. (Moraxellaceae) displayed lipolytic activity towards tributyrin. Even if psychrotrophic bacteria is not the dominant microbial group in raw milk, their total number increases during creaming and becomes one of the most present group together with Lactic Acid Bacteria. Their enzymatic activities may be key players in determining milk quality for cheese making.

  5. On the use of antibiotics to reduce rhizoplane microbial populations in root physiology and ecology investigations

    NASA Technical Reports Server (NTRS)

    Smart, D. R.; Ferro, A.; Ritchie, K.; Bugbee, B. G.

    1995-01-01

    No straightforward method exists for separating the proportion of ion exchange and respiration due to rhizoplane microbial organisms from that of root ion exchange and respiration. We examined several antibiotics that might be used for the temporary elimination of rhizoplane bacteria from hydroponically grown wheat roots (Triticum aestivum cv. Veery 10). Each antibiotic was tested for herbicidal activity and plate counts were used to enumerate bacteria and evaluate antibiotic kinetics. Only lactam antibiotics (penicillins and cephalosporins) did not reduce wheat growth rates. Aminoglycosides, the pyrimidine trimethoprim, colistin and rifampicin reduced growth rates substantially. Antibiotics acted slowly, with maximum reductions in rhizoplane bacteria occurring after more than 48 h of exposure. Combinations of nonphytotoxic antibiotics reduced platable rhizoplane bacteria by as much as 98%; however, this was generally a reduction from about 10(9) to 10(6) colony forming units per gram of dry root mass, so that many viable bacteria remained on root surfaces. We present evidence which suggests that insufficient bacterial biomass exists on root surfaces of nonstressed plants grown under well-aerated conditions to quantitatively interfere with root nitrogen absorption measurements.

  6. Lagrangian coherent structures are associated with fluctuations in airborne microbial populations

    NASA Astrophysics Data System (ADS)

    Tallapragada, P.; Ross, S. D.; Schmale, D. G.

    2011-09-01

    Many microorganisms are advected in the lower atmosphere from one habitat to another with scales of motion being hundreds to thousands of kilometers. The concentration of these microbes in the lower atmosphere at a single geographic location can show rapid temporal changes. We used autonomous unmanned aerial vehicles equipped with microbe-sampling devices to collect fungi in the genus Fusarium 100 m above ground level at a single sampling location in Blacksburg, Virginia, USA. Some Fusarium species are important plant and animal pathogens, others saprophytes, and still others are producers of dangerous toxins. We correlated punctuated changes in the concentration of Fusarium to the movement of atmospheric transport barriers identified as finite-time Lyapunov exponent-based Lagrangian coherent structures (LCSs). An analysis of the finite-time Lyapunov exponent field for periods surrounding 73 individual flight collections of Fusarium showed a relationship between punctuated changes in concentrations of Fusarium and the passage times of LCSs, particularly repelling LCSs. This work has implications for understanding the atmospheric transport of invasive microbial species into previously unexposed regions and may contribute to information systems for pest management and disease control in the future.

  7. Identification of Microbial Pathogens in Periodontal disease and Diabetic patients of South Indian Population

    PubMed Central

    Chiranjeevi, Tikka; Prasad, Osuru Hari; Prasad, Uppu Venkateswara; Kumar, Avula Kishor; Chakravarthi, Veeraraghavulu Praveen; Rao, Paramala Balaji; Sarma, Potuguchi Venkata Gurunadha Krishna; Reddy, Nagi reddy Raveendra; Bhaskar, Matcha

    2014-01-01

    Periodontitis have been referred to as the sixth complication of diabetes found in high prevalence among diabetic patients than among healthy controls. The aim of the present study was to examine the periodontal disease status among collected dental plaque samples. Chromosomal DNA was isolated and amplified by universal primers. The DNA was sequenced for bacterial confirmation and phylogenetic analysis performed for the evolutionary relationship with other known pathogens. No amplification products were observed in groups labeled non periodontal and non Diabetes (NP&ND) and non Periodontal and Diabetes (NP&D). But in the case of Periodontal and non Diabetes (P&ND) groups 22 amplified products were observed. In case of Periodontal and Diabetes (P&D), 32 amplified products were positive for microbes. Among the four microbial groups, Treponemadenticola, and Tannerella forsythia were found to be prevalent in P&D. The phylogenetic analysis of 16s rRNA of Treponemadenticola showed the relationship with other Treponema oral pathogen species and with the Spirochaetazuelaera. Tannerella forsythia shows its evolutionary relationship only with four oral pathogens (Macellibacteroidesfermentans, Porphyromadaceae bacterium, Parabacteroidesmeredae and Bacillus fosythus). Prevotellaintermedia also showed its evolutionary relationship only with Prevotella Spcs while Fusobacterium revealed close evolutionary relationship only with Porpiromonasgingivalis. PMID:24966528

  8. Strong inter-population cooperation leads to partner intermixing in microbial communities

    PubMed Central

    Momeni, Babak; Brileya, Kristen A; Fields, Matthew W; Shou, Wenying

    2013-01-01

    Patterns of spatial positioning of individuals within microbial communities are often critical to community function. However, understanding patterning in natural communities is hampered by the multitude of cell–cell and cell–environment interactions as well as environmental variability. Here, through simulations and experiments on communities in defined environments, we examined how ecological interactions between two distinct partners impacted community patterning. We found that in strong cooperation with spatially localized large fitness benefits to both partners, a unique pattern is generated: partners spatially intermixed by appearing successively on top of each other, insensitive to initial conditions and interaction dynamics. Intermixing was experimentally observed in two obligatory cooperative systems: an engineered yeast community cooperating through metabolite-exchanges and a methane-producing community cooperating through redox-coupling. Even in simulated communities consisting of several species, most of the strongly-cooperating pairs appeared intermixed. Thus, when ecological interactions are the major patterning force, strong cooperation leads to partner intermixing. DOI: http://dx.doi.org/10.7554/eLife.00230.001 PMID:23359860

  9. Population dynamics of anaerobic microbial consortia in thermophilic granular sludge in response to feed composition change.

    PubMed

    Syutsubo, K; Sinthurat, N; Ohashi, A; Harada, H

    2001-01-01

    A thermophilic UASB reactor was operated at 55 degrees C for greater than 470 days in order to investigate the effects of feed composition on the changes in microbial community structure where thermophilic granular sludge was used as the inoculum source. The feed compositions were changed with cultivation days; phase 1 (1-70 days), alcohol distillery wastewater; phase 2 (71-281 days), artificial acetate wastewater; phase 3 (282-474 days), artificial sucrose wastewater. During the first one month of each phase, the methanogenic activity and cell density of methanogens quantified by fluorescence in situ hybridization (FISH) drastically changed as a result of shift in feed composition. When artificial acetate wastewater was used as feed, retained granular sludge was partially disintegrated due to a decrease in the number of symbiotic bacterial community members: acetogens (acidogens) and hydrogenotrophic methanogens. In contrast, when the feed was shifted to sucrose (phase 3), granulation of biomass was promoted by a remarkable proliferation of the symbiotic community. The presence of hydrogen-utilizing methanogens and acetogens (acidogens) are shown to be effective for the enhancement of thermophilic granulation. The cell density of methanogens determined by FISH was strongly correlated with the methane-producing potential of the retained thermophilic granular sludge.

  10. PCR-based detection of bioluminescent microbial populations in Tyrrhenian Sea

    NASA Astrophysics Data System (ADS)

    Gentile, Gabriela; De Luca, Massimo; Denaro, Renata; La Cono, Violetta; Smedile, Francesco; Scarfì, Simona; De Domenico, Emilio; De Domenico, Maria; Yakimov, Michail M.

    2009-05-01

    The present study is focused on the development of a cultivation-independent molecular approach for specific detection of bioluminescent bacteria within microbial communities by direct amplification of luxA gene from environmental DNA. A new set of primers, specifically targeting free-living bioluminescent bacteria, was designed on the base of l uxA sequences available from the public database. Meso- and bathypelagic seawater samples were collected from two stations in Tyrrhenian Sea at the depths of 500 and 2750 m. The same seawater samples also were used to isolate bioluminescent bacteria that were further subjected to luxA and 16S rRNA gene sequencing. PCR products obtained by amplification with designed primers were cloned, and the phylogenetic affiliation of 40 clones was determined. All of them were clustered into three groups, only distantly related to the Photobacterium phosphoreum and Photobacterium kishitanii clades. The half of all clones formed a tight monophyletic clade, while the rest of clones were organized in "compartment"-specific, meso- and bathypelagic ecotypes. No matches with luxA gene sequences of four bioluminescent strains, isolated from the same seawater samples, were observed. These findings indicate that the PCR-based approach developed in present manuscript, allowed us to detect the novel, "yet to be cultivated" lineages of bioluminescent bacteria, which are likely specific for distinct warm bathypelagic realms of Mediterranean Sea.

  11. Effect of dietary copper on litter microbial population and broiler performance.

    PubMed

    Johnson, E L; Nicholoson, J L; Doerr, J A

    1985-04-01

    Proprietary broiler diets, containing added copper (125 mg/kg) as sulphate, were fed to broilers in 4 trials (32 pens each) over a one year period without a change of litter. Mould counts in the litter of pens containing birds fed the standard diets decreased to 2 X 10(3) propagules per g in trial 4. Those in the pens with birds fed the diets containing supplemental copper decreased to 6 X 10(2) propagules per g. Litter bacterial counts (10(7) organisms/g) were not affected by dietary copper. Litter copper concentrations in pens where the birds were fed supplemented diets increased significantly to more than 600 mg/kg in trial 4. Dietary copper sulphate addition significantly increased broiler weight gains at 7 weeks in trials 3 and 4 (P less than 0.05) and the efficiency of food utilisation was significantly improved in trial 4. The copper content of the chicks' livers remained unchanged. It is suggested that broiler performance may be independent of dietary copper content. Litter copper concentrations and litter microbial alterations may be important factors.

  12. Anaerobic treatment performance and microbial population of thermophilic upflow anaerobic filter reactor treating awamori distillery wastewater.

    PubMed

    Tang, Yue-Qin; Fujimura, Yutaka; Shigematsu, Toru; Morimura, Shigeru; Kida, Kenji

    2007-10-01

    Distillery wastewater from awamori making was anaerobically treated for one year using thermophilic upflow anaerobic filter (UAF) reactors packed with pyridinium group-containing nonwoven fabric material. The microbial structure and spatial distribution of microorganisms on the support material were characterized using molecular biological methods. The reactor steadily achieved a high TOC loading rate of 18 g/l/d with approximately 80% TOC removal efficiency when non-diluted wastewater was fed. The maximum TOC loading rate increased to 36 g/l/d when treating thrice-diluted wastewater. However, the TOC removal efficiency and gas evolution rate decreased compared with that when non-diluted wastewater was used. Methanogens closely related to Methanosarcina thermophila and Methanoculleus bourgensis and bacteria in the phyla Firmicutes and Bacteroidetes were predominant methanogens and bacteria in the thermophilic UFA reactor, as indicated by 16S rRNA gene clone analysis. Fluorescence in situ hybridization (FISH) results showed that a large quantity of bacterial cells adhered throughout the whole support, and Methanosarcina-like methanogens existed mainly in the relative outside region while Methanoculleus cells were located in the relative inner part of the support. The support material used proved to be an excellent carrier for microorganisms, and a UAF reactor using this kind of support can be used for high-rate treatment of awamori/shochu distillery wastewater.

  13. On the use of antibiotics to reduce rhizoplane microbial populations in root physiology and ecology investigations.

    PubMed

    Smart, D R; Ferro, A; Ritchie, K; Bugbee, B G

    1995-01-01

    No straightforward method exists for separating the proportion of ion exchange and respiration due to rhizoplane microbial organisms from that of root ion exchange and respiration. We examined several antibiotics that might be used for the temporary elimination of rhizoplane bacteria from hydroponically grown wheat roots (Triticum aestivum cv. Veery 10). Each antibiotic was tested for herbicidal activity and plate counts were used to enumerate bacteria and evaluate antibiotic kinetics. Only lactam antibiotics (penicillins and cephalosporins) did not reduce wheat growth rates. Aminoglycosides, the pyrimidine trimethoprim, colistin and rifampicin reduced growth rates substantially. Antibiotics acted slowly, with maximum reductions in rhizoplane bacteria occurring after more than 48 h of exposure. Combinations of nonphytotoxic antibiotics reduced platable rhizoplane bacteria by as much as 98%; however, this was generally a reduction from about 10(9) to 10(6) colony forming units per gram of dry root mass, so that many viable bacteria remained on root surfaces. We present evidence which suggests that insufficient bacterial biomass exists on root surfaces of nonstressed plants grown under well-aerated conditions to quantitatively interfere with root nitrogen absorption measurements.

  14. A study of deep-sea natural microbial populations and barophilic pure cultures using a high-pressure chemostat.

    PubMed

    Wirsen, C O; Molyneaux, S J

    1999-12-01

    Continuous cultures in which a high-pressure chemostat was used were employed to study the growth responses of (i) deep-sea microbial populations with the naturally occurring carbon available in seawater and with limiting concentrations of supplemental organic substrates and (ii) pure cultures of copiotrophic barophilic and barotolerant deep-sea isolates in the presence of limiting carbon concentrations at various pressures, dilution rates, and temperatures. We found that the growth rates of natural populations could not be measured or were extremely low (e.g., a doubling time of 629 h), as determined from the difference between the dilution rate and the washout rate. A low concentration of supplemental carbon (0.33 mg/liter) resulted in positive growth responses in the natural population, which resulted in an increase in the number of cells and eventually a steady population of cells. We found that the growth responses to imposed growth pressure by barophilic and barotolerant pure-culture isolates that were previously isolated and characterized under high-nutrient-concentration conditions were maintained under the low-nutrient-concentration limiting conditions (0.33 to 3.33 mg of C per liter) characteristic of the deep-sea environment. Our results indicate that deep-sea microbes can respond to small changes in substrate availability. Also, barophilic microbes that are copiotrophic as determined by their isolation in the presence of high carbon concentrations and their preference for high carbon concentrations are versatile and are able to compete and grow as barophiles in the low-carbon-concentration oligotrophic deep-sea environment in which they normally exist.

  15. Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platform (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Tremblay, Julien [DOE JGI

    2016-07-12

    Julien Tremblay from DOE JGI presents "Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platorm" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  16. Fate of the microbial population and the physico-chemical parameters of "Sanganel" a typical blood sausages of the Friuli, a north-east region of Italy.

    PubMed

    Iacumin, Lucilla; Manzano, Marisa; Stella, Simone; Comi, Giuseppe

    2017-05-01

    In Friuli, a Northeastern region of Italy, a blood sausage called Sanganel is produced by farmers, butchers, shops, and factories. This sausage is made with pork meat, boiled blood, lard, spices, and salt. It is stored at 4 ± 2 °C and usually eaten fresh or boiled within 14 days of its manufacture. Little is known about its microbial populations and safety for consumption. The aim of this study is to characterise the microbial populations and the physico-chemical parameters of Sanganel to establish its quality and the safety of consuming it. The microbial population of Sanganel is typical of meat products, and psychrotrophic enterobacteria and lactic acid bacteria (LAB) grow while it is stored. Enterobacteria produce total basic volatile nitrogen (TVB-N) and biogenic amines that, despite the presence of LAB, increase the pH of the sausage to approximately 6.9. Considering the concentrations of Enterobacteriaceae and TVB-N in the sausage, a shelf-life of 14 days is suggested. However, at 30 days the sausage is safe to eat and presents normal odours and flavours. In addition, boiling the sausage for 30 min before consumption eliminates the asporogenous microbial population.

  17. Analysis of Genetic Diversity and Population Structure of Sesame Accessions from Africa and Asia as Major Centers of Its Cultivation

    PubMed Central

    Dossa, Komivi; Wei, Xin; Zhang, Yanxin; Fonceka, Daniel; Yang, Wenjuan; Diouf, Diaga; Liao, Boshou; Cissé, Ndiaga; Zhang, Xiurong

    2016-01-01

    Sesame is an important oil crop widely cultivated in Africa and Asia. Understanding the genetic diversity of accessions from these continents is critical to designing breeding methods and for additional collection of sesame germplasm. To determine the genetic diversity in relation to geographical regions, 96 sesame accessions collected from 22 countries distributed over six geographic regions in Africa and Asia were genotyped using 33 polymorphic SSR markers. Large genetic variability was found within the germplasm collection. The total number of alleles was 137, averaging 4.15 alleles per locus. The accessions from Asia displayed more diversity than those from Africa. Accessions from Southern Asia (SAs), Eastern Asia (EAs), and Western Africa (WAf) were highly diversified, while those from Western Asia (WAs), Northern Africa (NAf), and Southeastern Africa (SAf) had the lowest diversity. The analysis of molecular variance revealed that more than 44% of the genetic variance was due to diversity among geographic regions. Five subpopulations, including three in Asia and two in Africa, were cross-identified through phylogenetic, PCA, and STRUCTURE analyses. Most accessions clustered in the same population based on their geographical origins. Our results provide technical guidance for efficient management of sesame genetic resources in breeding programs and further collection of sesame germplasm from these different regions. PMID:27077887

  18. Analysis of Genetic Diversity and Population Structure of Sesame Accessions from Africa and Asia as Major Centers of Its Cultivation.

    PubMed

    Dossa, Komivi; Wei, Xin; Zhang, Yanxin; Fonceka, Daniel; Yang, Wenjuan; Diouf, Diaga; Liao, Boshou; Cissé, Ndiaga; Zhang, Xiurong

    2016-04-12

    Sesame is an important oil crop widely cultivated in Africa and Asia. Understanding the genetic diversity of accessions from these continents is critical to designing breeding methods and for additional collection of sesame germplasm. To determine the genetic diversity in relation to geographical regions, 96 sesame accessions collected from 22 countries distributed over six geographic regions in Africa and Asia were genotyped using 33 polymorphic SSR markers. Large genetic variability was found within the germplasm collection. The total number of alleles was 137, averaging 4.15 alleles per locus. The accessions from Asia displayed more diversity than those from Africa. Accessions from Southern Asia (SAs), Eastern Asia (EAs), and Western Africa (WAf) were highly diversified, while those from Western Asia (WAs), Northern Africa (NAf), and Southeastern Africa (SAf) had the lowest diversity. The analysis of molecular variance revealed that more than 44% of the genetic variance was due to diversity among geographic regions. Five subpopulations, including three in Asia and two in Africa, were cross-identified through phylogenetic, PCA, and STRUCTURE analyses. Most accessions clustered in the same population based on their geographical origins. Our results provide technical guidance for efficient management of sesame genetic resources in breeding programs and further collection of sesame germplasm from these different regions.

  19. Microbial Properties Database Editor Tutorial

    EPA Science Inventory

    A Microbial Properties Database Editor (MPDBE) has been developed to help consolidate microbial-relevant data to populate a microbial database and support a database editor by which an authorized user can modify physico-microbial properties related to microbial indicators and pat...

  20. Comparison of the gut microbial community between obese and lean peoples using 16S gene sequencing in a Japanese population.

    PubMed

    Andoh, Akira; Nishida, Atsushi; Takahashi, Kenichiro; Inatomi, Osamu; Imaeda, Hirotsugu; Bamba, Shigeki; Kito, Katsuyuki; Sugimoto, Mitsushige; Kobayashi, Toshio

    2016-07-01

    Altered gut microbial ecology contributes to the development of metabolic diseases including obesity. In this study, we performed 16S rRNA sequence analysis of the gut microbiota profiles of obese and lean Japanese populations. The V3-V4 hypervariable regions of 16S rRNA of fecal samples from 10 obese and 10 lean volunteers were sequenced using the Illumina MiSeq(TM)II system. The average body mass index of the obese and lean group were 38.1 and 16.6 kg/m(2), respectively (p<0.01). The Shannon diversity index was significantly higher in the lean group than in the obese group (p<0.01). The phyla Firmicutes and Fusobacteria were significantly more abundant in obese people than in lean people. The abundance of the phylum Bacteroidetes and the Bacteroidetes/Firmicutes ratio were not different between the obese and lean groups. The genera Alistipes, Anaerococcus, Corpococcus, Fusobacterium and Parvimonas increased significantly in obese people, and the genera Bacteroides, Desulfovibrio, Faecalibacterium, Lachnoanaerobaculum and Olsenella increased significantly in lean people. Bacteria species possessing anti-inflammatory properties, such as Faecalibacterium prausnitzii, increased significantly in lean people, but bacteria species possessing pro-inflammatory properties increased in obese people. Obesity-associated gut microbiota in the Japanese population was different from that in Western people.

  1. Comparison of the gut microbial community between obese and lean peoples using 16S gene sequencing in a Japanese population

    PubMed Central

    Andoh, Akira; Nishida, Atsushi; Takahashi, Kenichiro; Inatomi, Osamu; Imaeda, Hirotsugu; Bamba, Shigeki; Kito, Katsuyuki; Sugimoto, Mitsushige; Kobayashi, Toshio

    2016-01-01

    Altered gut microbial ecology contributes to the development of metabolic diseases including obesity. In this study, we performed 16S rRNA sequence analysis of the gut microbiota profiles of obese and lean Japanese populations. The V3–V4 hypervariable regions of 16S rRNA of fecal samples from 10 obese and 10 lean volunteers were sequenced using the Illumina MiSeqTMII system. The average body mass index of the obese and lean group were 38.1 and 16.6 kg/m2, respectively (p<0.01). The Shannon diversity index was significantly higher in the lean group than in the obese group (p<0.01). The phyla Firmicutes and Fusobacteria were significantly more abundant in obese people than in lean people. The abundance of the phylum Bacteroidetes and the Bacteroidetes/Firmicutes ratio were not different between the obese and lean groups. The genera Alistipes, Anaerococcus, Corpococcus, Fusobacterium and Parvimonas increased significantly in obese people, and the genera Bacteroides, Desulfovibrio, Faecalibacterium, Lachnoanaerobaculum and Olsenella increased significantly in lean people. Bacteria species possessing anti-inflammatory properties, such as Faecalibacterium prausnitzii, increased significantly in lean people, but bacteria species possessing pro-inflammatory properties increased in obese people. Obesity-associated gut microbiota in the Japanese population was different from that in Western people. PMID:27499582

  2. Population dynamics and current-generation mechanisms in cassette-electrode microbial fuel cells.

    PubMed

    Watanabe, Kazuya; Miyahara, Morio; Shimoyama, Takefumi; Hashimoto, Kazuhito

    2011-12-01

    Cassette-electrode microbial fuel cells (CE-MFCs) have been demonstrated useful to treat biomass wastes and recover electric energy from them. In order to reveal electricity-generation mechanisms in CE-MFCs, the present study operated a bench-scale reactor (1 l in capacity; approximately 1,000 cm(2) in anode and cathode areas) for treating a high-strength model organic wastewater (comprised of starch, peptone, and fish extract). Approximately 1 month was needed for the bench reactor to attain a stable performance, after which volumetric maximum power densities persisted between 120 and 150 mW/l throughout the experiment (for over 2 months). Temporal increases in the external resistance were found to induce subsequent increases in power outputs. After electric output became stable, electrolyte and anode were sampled from the reactor for evaluating their current-generation abilities; it was estimated that most of current (over 80%) was generated by microbes in the electrolyte. Cyclic voltammetry of an electrolyte supernatant detected several electron shuttles with different standard redox potentials at high concentrations (equivalent to or more than 100 μM 5-hydroxy-1,4-naphthoquinone). Denaturing gradient gel electrophoresis and quantitative real-time PCR of 16S ribosomal RNA gene fragments showed that bacteria related to the genus Dysgonomonas occurred abundantly in association with the increases in power outputs. These results suggest that mediated electron transfer was the main mechanism for electricity generation in CE-MFC, where high-concentration electron shuttles and Dysgonomonas bacteria played important roles.

  3. Phenol- and Toluene-Degrading Microbial Populations from an Aquifer in Which Successful Trichloroethene Cometabolism Occurred

    PubMed Central

    Fries, M. R.; Forney, L. J.; Tiedje, J. M.

    1997-01-01

    We characterized the bacterial populations that grew in a Moffett Field, Calif., aquifer following three sequential field tests of phenol- or toluene-driven cometabolism of trichloroethene (TCE). Reducing the toluene and phenol concentrations in most-probable-number (MPN) tubes from 50 to 5 ppm increased the population density measured for these degraders by 1.5 and 1 log units, respectively, suggesting that natural populations might be quite sensitive to these substrates. Phenol and toluene degraders were isolated from the terminal MPN dilution tubes; 63 genetically distinct strains were identified among the 273 phenol- and toluene-degrading isolates obtained. TCE was cometabolized by 60% of the genetically distinct strains. Most strains (57%) grew on both phenol and toluene, and 78% of these strains hybridized to the toluene ortho-monooxygenase (TOM) probe. None of the strains hybridized to probes from the four other toluene oxygenase pathways. Gram-positive strains comprised 30% of the collection; all of these grew on phenol, and 47% of them also grew on toluene, but none hybridized to the TOM probe. Among the gram-negative strains, 86% of those that grew on both toluene and phenol hybridized to the TOM probe, while only 5% of those that were TOM-positive grew on toluene alone. A larger proportion of TCE degraders was found among gram-negative than gram-positive strains and among organisms that grew on phenol than those that grew on toluene. Hybridization of strains to the TOM probe was somewhat predictive of their TCE-cometabolizing ability, especially for strains isolated on toluene, but there was also a significant number (20%) of strains that hybridized to the TOM probe but were poor TCE cooxidizers. No Moffett Field isolates were as effective as Burkholderia cepacia G4 in cooxidizing TCE. Most of the aquifer strains ranged from moderately effective to ineffective in TCE cooxidation. Such populations, however, apparently accounted for the successful phenol

  4. The impact of access to health services on prediabetes awareness: A population-based study.

    PubMed

    Campbell, Tonya J; Alberga, Amanda; Rosella, Laura C

    2016-12-01

    Research demonstrates that prediabetes awareness has important implications for participation in diabetes risk-reducing behaviors. We examined the impact of levels of access to health services on prediabetes awareness. In 2016, we conducted an analysis among U.S. adults with prediabetes using cross-sectional data from three cycles (2007-2008, 2009-2010, and 2011-2012) of the National Health and Nutrition Examination Survey. Participants aware and unaware of their prediabetes were classified as having full, partial, or no access to health services based on current health insurance coverage and having a routine place to go for health care. Multivariable logistic regression was used to estimate the association between access to health services and prediabetes awareness. Among a total sample of 2999U.S. adults with prediabetes, an estimated 92.0% were unaware of their prediabetes status. Participants that were unaware of their prediabetes tended to be younger, male, and were less likely to be obese or have a family history of diabetes. Having no access to health services significantly increased the odds of being prediabetes unaware (AOR: 2.65; 95% CI: 1.10-6.38). However, participants with insurance but no place of regular care had the greatest odds of being prediabetes unaware (AOR: 3.21; 95% CI: 1.21-8.55). These findings suggest that access to health services is a key factor for prediabetes awareness. Health policies and interventions should strive to ensure equitable access to health services in order to detect prediabetes, and promote awareness and engagement in risk-reducing behaviors to decrease the incidence of diabetes.

  5. Correlations between arsenic in Maine groundwater and microbial populations as determined by fluorescence in situ hybridization.

    PubMed

    Weldon, Jennifer M; MacRae, Jean D

    2006-04-01

    Arsenic is known to cause serious health effects when consumed in drinking water. In the state of Maine, approximately half of the population relies on private groundwater wells for their drinking water. Of those wells, as many as 13% may contain arsenic levels above the current EPA maximum contaminant level of 10 microgl(-1). Microorganisms can potentially contribute to arsenic release into groundwater through several mechanisms. Some can reduce arsenate to arsenite, which is more toxic and may be more mobile. Sulfurospirillum species NP4, which was isolated from well water, respires arsenate and could act in this way. Microorganisms can also act indirectly by reducing bedrock surface coatings, such as iron oxyhydroxides, that adsorb arsenic in the groundwater environment. The genus Geobacter contains many species that are capable of iron reduction that could play a role in the indirect release of arsenic into groundwater. Water samples from Northport, ME and the Branch Lake region of Ellsworth, ME, which both have elevated groundwater arsenic levels, have been probed using fluorescence in situ hybridization (FISH), to determine the percentage of the population that is NP4 and the percentage that are Geobacter species. Geobacter abundance correlates well with the total arsenic concentration indicating that indirect mechanisms could be important in releasing arsenic. NP4 appears to be reducing arsenate since its prevalence correlates well with arsenite, the end product of arsenate respiration.

  6. [Characterization of microbial population present in the edible seaweed, Monostroma undulatum, Wittrock].

    PubMed

    Gallardo, Adriana Alicia; Risso, Susana; Fajardo, María Angélica; Estevao Belchior, Silvia

    2004-09-01

    The microbiological quality of Monostroma undulatum, Wittrock from the Southern Argentinean coast, was studied for its application for human food. Also the diversity and function of the native bacterial population to this green seaweed was analyzed. Samples were collected in Puerto Deseado, province of Santa Cruz, Southern Argentina (47 degrees 45'L.S., 65 degrees 55'L.W). The samples were analyzed for the presence of psycotrophic heterotrophic bacteria, marine heterotrophic bacteria, low nutritional request bacteria (LNRB), marine low nutritional request bacteria (LNRB marine), Vibrio spp, total and thermotolerant colifom bacteria, anaerobic sulfite reducing bacteria, yeasts and moulds. The isolates were identified using standard techniques based on morphologic, physiologic and metabolic characteristics. Among the gram-negative bacteria isolated, the predominant genera belonged to Vibrio (20%), E. coli inactiva (18%), Flavobacterium (11%), Flexibacter (9%), Moraxella (9%), Alcaligenes/Pseudomonas group (9%), Aeromonas (2%), Acinetobacter (2%). Cotophaga (2%), Photobacterium (2%), Ps/Caulobacter/Alteromonas/Spirillum group (2), The main genus of gram-positive bacteria was Staphylococcus. Human pathogenic bacteria were not detected. Fecal contamination indicator bacteria were not isolated from fresh seaweed and seawater. These results showed an adequate microbiological quality of seaweed acceptable for human food. The bacterial population associated to Monostroma undulatum, consisted of gram-negative, marine and psycotrophic microorganisms, including vibrios and enterobacteria as their main components. Also the identified bacteria showed a great capacity to hydrolyze different substrates and so they might contribute to the balance of this marine ecosystem.

  7. Degradation of hazardous chemicals in liquid radioactive wastes from biomedical research using a mixed microbial population

    SciTech Connect

    Wolfram, J.H.; Radtke, M.; Wey, J.E.; Rogers, R.D.; Rau, E.H.

    1997-10-01

    As the costs associated with treatment of mixed wastes by conventional methods increase, new technologies will be investigated as alternatives. This study examines the potential of using a selected mixed population of microorganisms to treat hazardous chemical compounds in liquid low level radioactive wastes from biomedical research procedures. Microorganisms were isolated from various waste samples and enriched against compounds known to occur in the wastes. Individual isolates were tested for their ability to degrade methanol, ethanol, phenol, toluene, phthalates, acetonitrile, chloroform, and trichloroacetic acid. Following these tests, the organisms were combined in a media with a mixture of the different compounds. Three compounds: methanol, acetonitrile, and pseudocumene, were combined at 500 microliter/liter each. Degradation of each compound was shown to occur (75% or greater) under batch conditions with the mixed population. Actual wastes were tested by adding an aliquot to the media, determining the biomass increase, and monitoring the disappearance of the compounds. The compounds in actual waste were degraded, but at different rates than the batch cultures that did not have waste added. The potential of using bioprocessing methods for treating mixed wastes from biomedical research is discussed.

  8. Improvement in shelf life of minimally processed cilantro leaves through integration of kinetin pretreatment and packaging interventions: Studies on microbial population dynamics, biochemical characteristics and flavour retention.

    PubMed

    Ranjitha, K; Shivashankara, K S; Sudhakar Rao, D V; Oberoi, Harinder Singh; Roy, T K; Bharathamma, H

    2017-04-15

    Effect of integrating optimized combination of pretreatment with packaging on shelf life of minimally processed cilantro leaves (MPCL) was appraised through analysis of their sensory attributes, biochemical characteristics, microbial population and flavour profile during storage. Minimally pretreated cilantro leaves pretreated with 50ppm kinetin and packed in 25μ polypropylene bags showed a shelf life of 21days. Optimized combination helped in efficiently maintaining sensory parameters, flavour profile, and retention of antioxidants in MPCL until 21days. Studies conducted on the effect of optimized combination on microbial population and flavour profile revealed that among different microorganisms, pectinolysers had a significant effect on spoilage of MPCL and their population of ⩽3.59logcfu/g was found to be acceptable. Principal component analysis of headspace volatiles revealed that (E)-2-undecenal, (E)-2-hexadecenal, (E)-2-tetradecenal & (E)-2-tetradecen-1-ol in stored samples clustered with fresh samples and therefore, could be considered as freshness indicators for MPCL.

  9. Pristine soils mineralize 3-chlorobenzoate and 2,4-dichlorophenoxyacetate via different microbial populations.

    PubMed Central

    Fulthorpe, R R; Rhodes, A N; Tiedje, J M

    1996-01-01

    Biodegradation of two chlorinated aromatic compounds was found to be a common capability of the microorganisms found in the soils of undisturbed, pristine ecosystems. We used 2,4-dichlorophenoxyacetate (2,4-D) and 3-chlorobenzoate (3CBA) as enrichment substrates to compare populations of degrading bacteria from six different regions making up two ecosystems. We collected soil samples from four Mediterranean (California, central Chile, the Cape region of South Africa, and southwestern Australia) and two boreal (northern Saskatchewan and northwestern Russia) ecosystems that had no direct exposure to pesticides or to human disturbance. Between 96 and 120 samples from each of the six regions were incubated with 50 ppm of [U-14C]2,4-D or [U-14C]3CBA. Soils from all regions samples mineralized both 2,4-D and 3CBA, but 3CBA was mineralized without a lag period, while 2,4-D was generally not mineralized until the second week. 3CBA degradative capabilities were more evenly distributed spatially than those for 2,4-D. The degradative capabilities of the soils were readily transferred to fresh liquid medium. 3CBA degraders were easily isolated from most soils. We recovered 610 strains that could release carbon dioxide from ring-labeled 3CBA. Of these, 144 strains released chloride and degraded over 80% of 1 mM 3CBA in 3 weeks or less. In contrast, only five 2,4-D degraders could be isolated, although a variety of methods were used in an attempt to culture the degraders. The differences in the distribution and culturability of the bacteria responsible for 3CBA and 2,4-D degradation in these ecosystems suggest that the two substrates are degraded by different populations. We also describe a 14C-based microtiter plate method that allows efficient screening of a large number of samples for biodegradation activity. PMID:8919776

  10. 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

    Kaden, Rene; Krolla-Sidenstein, Peter

    2015-10-20

    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.

  11. Elemental composition of natural populations of key microbial groups in Atlantic waters.

    PubMed

    Grob, Carolina; Ostrowski, Martin; Holland, Ross J; Heldal, Mikal; Norland, Svein; Erichsen, Egil S; Blindauer, Claudia; Martin, Adrian P; Zubkov, Mikhail V; Scanlan, David J

    2013-11-01

    Intracellular carbon (C), nitrogen (N) and phosphorus (P) content of marine phytoplankton and bacterioplankton can vary according to cell requirements or physiological acclimation to growth under nutrient limited conditions. Although such variation in macronutrient content is well known for cultured organisms, there is a dearth of data from natural populations that reside under a range of environmental conditions. Here, we compare C, N and P content of Synechococcus, Prochlorococcus, low nucleic acid (LNA) content bacterioplankton and small plastidic protists inhabiting surface waters of the North and South subtropical gyres and the Equatorial Region of the Atlantic Ocean. While intracellular C:N ratios ranged between 3.5 and 6, i.e. below the Redfield ratio of 6.6, all the C:P and N:P ratios were up to 10 times higher than the corresponding Redfield ratio of 106 and 16, respectively, reaching and in some cases exceeding maximum values reported in the literature. Similar C:P or N:P ratios in areas with different concentrations of inorganic phosphorus suggests that this is not just a response to the prevailing environmental conditions but an indication of the extremely low P content of these oceanic microbes.

  12. Microbial infections in a declining wild turkey population in Texas (USA)

    USGS Publications Warehouse

    Rocke, T.E.; Yuill, Thomas M.

    1987-01-01

    A survey was conducted at 5 locations in Texas for avian pathogens that might adversely affect wild turkey (Meleagris gallopavo) productivity and survival. At 1 site, the Rob and Bessie Welder Wildlife Refuge (WWR), turkeys have declined precipitously in recent years. During the winters of 1983-85, 442 wild turkeys were caught with cannon and drop nets, 161 of these on WWR. Blood samples were drawn for serologic evaluation, and cloacal and tracheal swabs were collected for isolation attempts. Salmonella spp. bacteria, Newcastle disease virus (NDV), and avian influenza virus (AIV) were not detected in any samples tested. Serologic tests for antibodies to NDV and AIV also were negative. Many mycoplasma isolates were recovered from turkeys from every location. Characterization of these isolates indicated that several species were present. None were species typically associated with mycoplasmosis in domestic turkeys, such as Mycoplasma gallisepticum (MG), M. meleagridis (MM), or M. synoviae (MS), although antibodies to these pathogens were detected in turkeys at every location sampled. There was no evidence to link any of these disease causing agents to the decline observed in the population of wild turkeys on the WWR.

  13. Effects of replacing dietary starch with neutral detergent-soluble fibre on ruminal fermentation, microbial synthesis and populations of ruminal cellulolytic bacteria using the rumen simulation technique (RUSITEC).

    PubMed

    Zhao, X H; Liu, C J; Liu, Y; Li, C Y; Yao, J H

    2013-12-01

    A rumen simulation technique (RUSITEC) apparatus with eight 800 ml fermenters was used to investigate the effects of replacing dietary starch with neutral detergent-soluble fibre (NDSF) by inclusion of sugar beet pulp in diets on ruminal fermentation, microbial synthesis and populations of ruminal cellulolytic bacteria. Experimental diets contained 12.7, 16.4, 20.1 or 23.8% NDSF substituted for starch on a dry matter basis. The experiment was conducted over two independent 15-day incubation periods with the last 8 days used for data collection. There was a tendency that 16.4% NDSF in the diet increased the apparent disappearance of organic matter (OM) and neutral detergent fibre (NDF). Increasing dietary NDSF level increased carboxymethylcellulase and xylanase activity in the solid fraction and apparent disappearance of acid detergent fibre (ADF) but reduced the 16S rDNA copy numbers of Ruminococcus albus in both liquid and solid fractions and R. flavefaciens in the solid fraction. The apparent disappearance of dietary nitrogen (N) was reduced by 29.6% with increased dietary NDSF. Substituting NDSF for starch appeared to increase the ratios of acetate/propionate and methane/volatile fatty acids (VFA) (mol/mol). Replacing dietary starch with NDSF reduced the daily production of ammonia-N and increased the growth of the solid-associated microbial pellets (SAM). Total microbial N flow and efficiency of microbial synthesis (EMS), expressed as g microbial N/kg OM fermented, tended to increase with increased dietary NDSF, but the numerical increase did not continue as dietary NDSF exceeded 20.1% of diet DM. Results suggested that substituting NDSF for starch up to 16.4% of diet DM increased digestion of nutrients (except for N) and microbial synthesis, and further increases (from 16.4% to 23.8%) in dietary NDSF did not repress microbial synthesis but did significantly reduce digestion of dietary N.

  14. Impact of Fungicide Mancozeb at Different Application Rates on Soil Microbial Populations, Soil Biological Processes, and Enzyme Activities in Soil

    PubMed Central

    Mehta, Preeti; Guleria, Shiwani; Chauhan, Anjali; Shirkot, C. K.

    2014-01-01

    The use of fungicides is the continuous exercise particularly in orchard crops where fungal diseases, such as white root rot, have the potential to destroy horticultural crops rendering them unsaleable. In view of above problem, the present study examines the effect of different concentrations of mancozeb (0–2000 ppm) at different incubation periods for their harmful side effects on various microbiological processes, soil microflora, and soil enzymes in alluvial soil (pH 6.8) collected from apple orchards of Shimla in Himachal Pradesh (India). Low concentrations of mancozeb were found to be deleterious towards fungal and actinomycetes population while higher concentrations (1000 and 2000 ppm) were found to be detrimental to soil bacteria. Mancozeb impaired the process of ammonification and nitrification. Similar results were observed for nitrifying and ammonifying bacteria. Phosphorus solubilization was increased by higher concentration of mancozeb, that is, 250 ppm and above. In unamended soil, microbial biomass carbon and carbon mineralization were adversely affected by mancozeb. Soil enzymes, that is, amylase, invertase, and phosphatase showed adverse and disruptive effect when mancozeb used was above 10 ppm in unamended soil. These results conclude that, to lessen the harmful effects in soil biological processes caused by this fungicide, addition of higher amount of nitrogen based fertilizers is required. PMID:25478598

  15. Microbial populations associated with fixed- and floating-bed reactors during a two-stage anaerobic process.

    PubMed

    Sonakya, Vikas; Raizada, Neena; Hausner, Martina; Wildere, Peter A

    2007-12-01

    Microbial populations associated with methanogenic fixed- or floating-bed bioreactors used for anaerobic digestion of lignocellulosic waste were investigated. Fluorescent in situ hybridization (FISH) was used to characterize microorganisms in samples obtained from different heights in the reactors, which were operated in a semi-continuous manner (feeding and mixing once every 2 days). The FISH results showed that Methanosaeta concilii cells were most numerous at the bottom of both reactors. M. concilii cells were more abundant in the fixed-bed reactor (FXBR), which performed better than the floating-bed reactor (FLBR). Species of the Methanosarcina genera (mainly M. barkeri and M. mazei) were also observed in the FLBR but rarely in the FXBR. Methane production in each of the reactors ranged from 0.29 to 0.33 m3 CH(4)/kg COD(rem) (chemical oxygen demand removed). The removal of volatile fatty acids (VFA; 70-75 h) in the FXBR was more efficient than in the FLBR.

  16. Impact of fungicide mancozeb at different application rates on soil microbial populations, soil biological processes, and enzyme activities in soil.

    PubMed

    Walia, Abhishek; Mehta, Preeti; Guleria, Shiwani; Chauhan, Anjali; Shirkot, C K

    2014-01-01

    The use of fungicides is the continuous exercise particularly in orchard crops where fungal diseases, such as white root rot, have the potential to destroy horticultural crops rendering them unsaleable. In view of above problem, the present study examines the effect of different concentrations of mancozeb (0-2000 ppm) at different incubation periods for their harmful side effects on various microbiological processes, soil microflora, and soil enzymes in alluvial soil (pH 6.8) collected from apple orchards of Shimla in Himachal Pradesh (India). Low concentrations of mancozeb were found to be deleterious towards fungal and actinomycetes population while higher concentrations (1000 and 2000 ppm) were found to be detrimental to soil bacteria. Mancozeb impaired the process of ammonification and nitrification. Similar results were observed for nitrifying and ammonifying bacteria. Phosphorus solubilization was increased by higher concentration of mancozeb, that is, 250 ppm and above. In unamended soil, microbial biomass carbon and carbon mineralization were adversely affected by mancozeb. Soil enzymes, that is, amylase, invertase, and phosphatase showed adverse and disruptive effect when mancozeb used was above 10 ppm in unamended soil. These results conclude that, to lessen the harmful effects in soil biological processes caused by this fungicide, addition of higher amount of nitrogen based fertilizers is required.

  17. Quantitative analysis of ruminal methanogenic microbial populations in beef cattle divergent in phenotypic residual feed intake (RFI) offered contrasting diets

    PubMed Central

    2014-01-01

    Background Methane (CH4) emissions in cattle are an undesirable end product of rumen methanogenic fermentative activity as they are associated not only with negative environmental impacts but also with reduced host feed efficiency. The aim of this study was to quantify total and specific rumen microbial methanogenic populations in beef cattle divergently selected for residual feed intake (RFI) while offered (i) a low energy high forage (HF) diet followed by (ii) a high energy low forage (LF) diet. Ruminal fluid was collected from 14 high (H) and 14 low (L) RFI animals across both dietary periods. Quantitative real time PCR (qRT-PCR) analysis was conducted to quantify the abundance of total and specific rumen methanogenic microbes. Spearman correlation analysis was used to investigate the association between the relative abundance of methanogens and animal performance, rumen fermentation variables and diet digestibility. Results Abundance of methanogens, did not differ between RFI phenotypes. However, relative abundance of total and specific methanogen species was affected (P < 0.05) by diet type, with greater abundance observed while animals were offered the LF compared to the HF diet. Conclusions These findings suggest that differences in abundance of specific rumen methanogen species may not contribute to variation in CH4 emissions between efficient and inefficient animals, however dietary manipulation can influence the abundance of total and specific methanogen species. PMID:25276350

  18. Prawn Shell Chitosan Has Anti-Obesogenic Properties, Influencing Both Nutrient Digestibility and Microbial Populations in a Pig Model

    PubMed Central

    Egan, Áine M.; Sweeney, Torres; Hayes, Maria; O’Doherty, John V.

    2015-01-01

    The potential of natural products to prevent obesity have been investigated, with evidence to suggest that chitosan has anti-obesity effects. The current experiment investigated the anti-obesity potential of prawn shell derived chitosan on a range of variables relevant to obesity in a pig model. The two dietary treatment groups included in this 63 day study were: T1) basal diet and T2) basal diet plus 1000 ppm chitosan (n = 20 gilts per group (70 ± 0.90 kg). The parameter categories which were assessed included: performance, nutrient digestibility, serum leptin concentrations, nutrient transporter and digestive enzyme gene expression and gut microbial populations. Pigs offered chitosan had reduced feed intake and final body weight (P< 0.001), lower ileal digestibility of dry matter (DM), gross energy (GE) (P< 0.05) and reduced coefficient of apparent total tract digestibility (CATTD) of gross energy and nitrogen (P<0.05) when compared to the basal group. Fatty acid binding protein 2 (FABP2) gene expression was down-regulated in pigs offered chitosan (P = 0.05) relative to the basal diet. Serum leptin concentrations increased (P< 0.05) in animals offered the chitosan diet compared to pigs offered the basal diet. Fatness traits, back-fat depth (mm), fat content (kg), were significantly reduced while lean meat (%) was increased (P<0.05) in chitosan supplemented pigs. Pigs offered chitosan had decreased numbers of Firmicutes in the colon (P <0.05), and Lactobacillus spp. in both the caecum (P <0.05) and colon (P <0.001). Bifidobacteria populations were increased in the caecum of animals offered the chitosan diet (P <0.05). In conclusion, these findings suggest that prawn shell chitosan has potent anti-obesity/body weight control effects which are mediated through multiple biological systems in vivo. PMID:26636332

  19. Prawn Shell Chitosan Has Anti-Obesogenic Properties, Influencing Both Nutrient Digestibility and Microbial Populations in a Pig Model.

    PubMed

    Egan, Áine M; Sweeney, Torres; Hayes, Maria; O'Doherty, John V

    2015-01-01

    The potential of natural products to prevent obesity have been investigated, with evidence to suggest that chitosan has anti-obesity effects. The current experiment investigated the anti-obesity potential of prawn shell derived chitosan on a range of variables relevant to obesity in a pig model. The two dietary treatment groups included in this 63 day study were: T1) basal diet and T2) basal diet plus 1000 ppm chitosan (n = 20 gilts per group (70 ± 0.90 kg). The parameter categories which were assessed included: performance, nutrient digestibility, serum leptin concentrations, nutrient transporter and digestive enzyme gene expression and gut microbial populations. Pigs offered chitosan had reduced feed intake and final body weight (P< 0.001), lower ileal digestibility of dry matter (DM), gross energy (GE) (P< 0.05) and reduced coefficient of apparent total tract digestibility (CATTD) of gross energy and nitrogen (P<0.05) when compared to the basal group. Fatty acid binding protein 2 (FABP2) gene expression was down-regulated in pigs offered chitosan (P = 0.05) relative to the basal diet. Serum leptin concentrations increased (P< 0.05) in animals offered the chitosan diet compared to pigs offered the basal diet. Fatness traits, back-fat depth (mm), fat content (kg), were significantly reduced while lean meat (%) was increased (P<0.05) in chitosan supplemented pigs. Pigs offered chitosan had decreased numbers of Firmicutes in the colon (P <0.05), and Lactobacillus spp. in both the caecum (P <0.05) and colon (P <0.001). Bifidobacteria populations were increased in the caecum of animals offered the chitosan diet (P <0.05). In conclusion, these findings suggest that prawn shell chitosan has potent anti-obesity/body weight control effects which are mediated through multiple biological systems in vivo.

  20. Patterns of ecological specialization among microbial populations in the Red Sea and diverse oligotrophic marine environments

    PubMed Central

    Thompson, Luke R; Field, Chris; Romanuk, Tamara; Ngugi, David; Siam, Rania; El Dorry, Hamza; Stingl, Ulrich

    2013-01-01

    Large swaths of the nutrient-poor surface ocean are dominated numerically by cyanobacteria (Prochlorococcus), cyanobacterial viruses (cyanophage), and alphaproteobacteria (SAR11). How these groups thrive in the diverse physicochemical environments of different oceanic regions remains poorly understood. Comparative metagenomics can reveal adaptive responses linked to ecosystem-specific selective pressures. The Red Sea is well-suited for studying adaptation of pelagic-microbes, with salinities, temperatures, and light levels at the extreme end for the surface ocean, and low nutrient concentrations, yet no metagenomic studies have been done there. The Red Sea (high salinity, high light, low N and P) compares favorably with the Mediterranean Sea (high salinity, low P), Sargasso Sea (low P), and North Pacific Subtropical Gyre (high light, low N). We quantified the relative abundance of genetic functions among Prochlorococcus, cyanophage, and SAR11 from these four regions. Gene frequencies indicate selection for phosphorus acquisition (Mediterranean/Sargasso), DNA repair and high-light responses (Red Sea/Pacific Prochlorococcus), and osmolyte C1 oxidation (Red Sea/Mediterranean SAR11). The unexpected connection between salinity-dependent osmolyte production and SAR11 C1 metabolism represents a potentially major coevolutionary adaptation and biogeochemical flux. Among Prochlorococcus and cyanophage, genes enriched in specific environments had ecotype distributions similar to nonenriched genes, suggesting that inter-ecotype gene transfer is not a major source of environment-specific adaptation. Clustering of metagenomes using gene frequencies shows similarities in populations (Red Sea with Pacific, Mediterranean with Sargasso) that belie their geographic distances. Taken together, the genetic functions enriched in specific environments indicate competitive strategies for maintaining carrying capacity in the face of physical stressors and low nutrient availability. PMID

  1. Patterns of ecological specialization among microbial populations in the Red Sea and diverse oligotrophic marine environments.

    PubMed

    Thompson, Luke R; Field, Chris; Romanuk, Tamara; Ngugi, David; Siam, Rania; El Dorry, Hamza; Stingl, Ulrich

    2013-06-01

    Large swaths of the nutrient-poor surface ocean are dominated numerically by cyanobacteria (Prochlorococcus), cyanobacterial viruses (cyanophage), and alphaproteobacteria (SAR11). How these groups thrive in the diverse physicochemical environments of different oceanic regions remains poorly understood. Comparative metagenomics can reveal adaptive responses linked to ecosystem-specific selective pressures. The Red Sea is well-suited for studying adaptation of pelagic-microbes, with salinities, temperatures, and light levels at the extreme end for the surface ocean, and low nutrient concentrations, yet no metagenomic studies have been done there. The Red Sea (high salinity, high light, low N and P) compares favorably with the Mediterranean Sea (high salinity, low P), Sargasso Sea (low P), and North Pacific Subtropical Gyre (high light, low N). We quantified the relative abundance of genetic functions among Prochlorococcus, cyanophage, and SAR11 from these four regions. Gene frequencies indicate selection for phosphorus acquisition (Mediterranean/Sargasso), DNA repair and high-light responses (Red Sea/Pacific Prochlorococcus), and osmolyte C1 oxidation (Red Sea/Mediterranean SAR11). The unexpected connection between salinity-dependent osmolyte production and SAR11 C1 metabolism represents a potentially major coevolutionary adaptation and biogeochemical flux. Among Prochlorococcus and cyanophage, genes enriched in specific environments had ecotype distributions similar to nonenriched genes, suggesting that inter-ecotype gene transfer is not a major source of environment-specific adaptation. Clustering of metagenomes using gene frequencies shows similarities in populations (Red Sea with Pacific, Mediterranean with Sargasso) that belie their geographic distances. Taken together, the genetic functions enriched in specific environments indicate competitive strategies for maintaining carrying capacity in the face of physical stressors and low nutrient availability.

  2. Effect of microbial inoculants on the indigenous actinobacterial endophyte population in the roots of wheat as determined by terminal restriction fragment length polymorphism.

    PubMed

    Conn, Vanessa M; Franco, Christopher M M

    2004-11-01

    The effect of single actinobacterial endophyte seed inoculants and a mixed microbial soil inoculant on the indigenous endophytic actinobacterial population in wheat roots was investigated by using the molecular technique terminal restriction fragment length polymorphism (T-RFLP). Wheat was cultivated either from seeds coated with the spores of single pure actinobacterial endophytes of Microbispora sp. strain EN2, Streptomyces sp. strain EN27, and Nocardioides albus EN46 or from untreated seeds sown in soil with and without a commercial mixed microbial soil inoculant. The endophytic actinobacterial population within the roots of 6-week-old wheat plants was assessed by T-RFLP. Colonization of the wheat roots by the inoculated actinobacterial endophytes was detected by T-RFLP, as were 28 to 42 indigenous actinobacterial genera present in the inoculated and uninoculated plants. The presence of the commercial mixed inoculant in the soil reduced the endophytic actinobacterial diversity from 40 genera to 21 genera and reduced the detectable root colonization by approximately half. The results indicate that the addition of a nonadapted microbial inoculum to the soil disrupted the natural actinobacterial endophyte population, reducing diversity and colonization levels. This was in contrast to the addition of a single actinobacterial endophyte to the wheat plant, where the increase in colonization level could be confirmed even though the indigenous endophyte population was not adversely affected.

  3. Geobacter, Anaeromyxobacter and Anaerolineae populations are enriched on anodes of root exudate-driven microbial fuel cells in rice field soil.

    PubMed

    Cabezas, Angela; Pommerenke, Bianca; Boon, Nico; Friedrich, Michael W

    2015-06-01

    Plant-based sediment microbial fuel cells (PMFCs) couple the oxidation of root exudates in living rice plants to current production. We analysed the composition of the microbial community on anodes from PMFC with natural rice field soil as substratum for rice by analysing 16S rRNA as an indicator of microbial activity and diversity. Terminal restriction fragment length polymorphism (TRFLP) analysis indicated that the active bacterial community on anodes from PMFCs differed strongly compared with controls. Moreover, clones related to Deltaproteobacteria and Chloroflexi were highly abundant (49% and 21%, respectively) on PMFCs anodes. Geobacter (19%), Anaeromyxobacter (15%) and Anaerolineae (17%) populations were predominant on anodes with natural rice field soil and differed strongly from those previously detected with potting soil. In open circuit (OC) control PMFCs, not allowing electron transfer, Deltaproteobacteria (33%), Betaproteobacteria (20%), Chloroflexi (12%), Alphaproteobacteria (10%) and Firmicutes (10%) were detected. The presence of an electron accepting anode also had a strong influence on methanogenic archaea. Hydrogenotrophic methanogens were more active on PMFC (21%) than on OC controls (10%), whereas acetoclastic Methanosaetaceae were more active on OC controls (31%) compared with PMFCs (9%). In conclusion, electron accepting anodes and rice root exudates selected for distinct potential anode-reducing microbial populations in rice soil inoculated PMFC.

  4. Modeling of Nonlinear Dynamics and Synchronized Oscillations of Microbial Populations, Carbon and Oxygen Concentrations, Induced by Root Exudation in the Rhizosphere

    NASA Astrophysics Data System (ADS)

    Molz, F. J.; Faybishenko, B.; Jenkins, E. W.

    2012-12-01

    Mass and energy fluxes within the soil-plant-atmosphere continuum are highly coupled and inherently nonlinear. The main focus of this presentation is to demonstrate the results of numerical modeling of a system of 4 coupled, nonlinear ordinary differential equations (ODEs), which are used to describe the long-term, rhizosphere processes of soil microbial dynamics, including the competition between nitrogen-fixing bacteria and those unable to fix nitrogen, along with substrate concentration (nutrient supply) and oxygen concentration. Modeling results demonstrate the synchronized patterns of temporal oscillations of competing microbial populations, which are affected by carbon and oxygen concentrations. The temporal dynamics and amplitude of the root exudation process serve as a driving force for microbial and geochemical phenomena, and lead to the development of the Gompetzian dynamics, synchronized oscillations, and phase-space attractors of microbial populations and carbon and oxygen concentrations. The nonlinear dynamic analysis of time series concentrations from the solution of the ODEs was used to identify several types of phase-space attractors, which appear to be dependent on the parameters of the exudation function and Monod kinetic parameters. This phase space analysis was conducted by means of assessing the global and local embedding dimensions, correlation time, capacity and correlation dimensions, and Lyapunov exponents of the calculated model variables defining the phase space. Such results can be used for planning experimental and theoretical studies of biogeochemical processes in the fields of plant nutrition, phyto- and bio-remediation, and other ecological areas.

  5. HMOs and the barriers to access for the pediatric population requiring emergency medical services.

    PubMed

    Uva, J L

    1996-06-01

    The main objectives of this study are to analyze the Massachusetts Health Maintenance Organizations (HMOs) in order to determine their standard definition of an emergency, the HMOs instructions for seeking emergency care, and distribution of such instructions for the pediatric population. A 15-question survey concerning pediatric emergency care policies and procedures was asked of each of the 20 HMOs contacted. Quarterly statements of each of the 20 HMOs were obtained from the Division of Insurance as well as the HMO's written materials distributed to the enrollees as member handbooks. Ninety percent of the HMOs had a definition of emergency care for the adult population, whereas 0% had a definition of emergency care specifically for the pediatric population. One hundred percent of the HMOs had instructions for emergency care, but 0% had specific provisions for pediatric emergency care. All 20 HMOs inform their enrollees about emergency policies through a member handbook. The results of this study reveal the lack of a standard definition of an emergency for HMOs. The current definitions of "urgent," "emergency," and "life-threatening emergency" care do not reflect the pediatric population, rather, these definitions are based on the adult population. The lack of specific pediatric guidelines could compromise the health of the children in HMOs.

  6. Arabinoxylan‐oligosaccharides (AXOS) affect the protein/carbohydrate fermentation balance and microbial population dynamics of the Simulator of Human Intestinal Microbial Ecosystem

    PubMed Central

    Sanchez, J. I.; Marzorati, M.; Grootaert, C.; Baran, M.; Van Craeyveld, V.; Courtin, C. M.; Broekaert, W. F.; Delcour, J. A.; Verstraete, W.; Van de Wiele, T.

    2009-01-01

    Summary Arabinoxylan‐oligosaccharides (AXOS) are a recently newly discovered class of candidate prebiotics as – depending on their structure – they are fermented in different regions of gastrointestinal tract. This can have an impact on the protein/carbohydrate fermentation balance in the large intestine and, thus, affect the generation of potentially toxic metabolites in the colon originating from proteolytic activity. In this study, we screened different AXOS preparations for their impact on the in vitro intestinal fermentation activity and microbial community structure. Short‐term fermentation experiments with AXOS with an average degree of polymerization (avDP) of 29 allowed part of the oligosaccharides to reach the distal colon, and decreased the concentration of proteolytic markers, whereas AXOS with lower avDP were primarily fermented in the proximal colon. Additionally, prolonged supplementation of AXOS with avDP 29 to the Simulator of Human Intestinal Microbial Ecosystem (SHIME) reactor decreased levels of the toxic proteolytic markers phenol and p‐cresol in the two distal colon compartments and increased concentrations of beneficial short‐chain fatty acids (SCFA) in all colon vessels (25–48%). Denaturant gradient gel electrophoresis (DGGE) analysis indicated that AXOS supplementation only slightly modified the total microbial community, implying that the observed effects on fermentation markers are mainly caused by changes in fermentation activity. Finally, specific quantitative PCR (qPCR) analysis showed that AXOS supplementation significantly increased the amount of health‐promoting lactobacilli as well as of Bacteroides–Prevotella and Clostridium coccoides–Eubacterium rectale groups. These data allow concluding that AXOS are promising candidates to modulate the microbial metabolism in the distal colon. PMID:21261885

  7. Increasing Accessibility: Lessons Learned in Retaining Special Population Students in Canada

    ERIC Educational Resources Information Center

    Smith, Clayton; Gottheil, Susan

    2011-01-01

    In Canada, changing demographics and increased competition--as well as social values based on equity--have inspired efforts to increase the postsecondary education (PSE) participation rates of youths from under-represented/under-served groups. Despite its population having the highest level of educational attainment among those of OECD countries,…

  8. Genetic diversity, population structure, and formulation of a core collection of 1,197 Citrullus accessions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There has been continuing interests in breeding of watermelon for economic benefits, but information on the scope and utilization of genetic variations in this genus (Citrullus) is still limited. We evaluated the genetic diversity and population structure of 1,197 watermelon collections, which belon...

  9. Comparison of fermentation of diets of variable composition and microbial populations in the rumen of sheep and Rusitec fermenters. I. Digestibility, fermentation parameters, and microbial growth.

    PubMed

    Martínez, M E; Ranilla, M J; Tejido, M L; Ramos, S; Carro, M D

    2010-08-01

    Four ruminally and duodenally cannulated sheep and 8 Rusitec fermenters were used to determine the effects of forage to concentrate (F:C) ratio and type of forage in the diet on ruminal fermentation and microbial protein synthesis. The purpose of the study was to assess how closely fermenters can mimic the dietary differences found in vivo. The 4 experimental diets contained F:C ratios of 70:30 or 30:70 with either alfalfa hay or grass hay as the forage. Microbial growth was determined in both systems using (15)N as a microbial marker. Rusitec fermenters detected differences between diets similar to those observed in sheep by changing F:C ratio on pH; neutral detergent fiber digestibility; total volatile fatty acid concentrations; molar proportions of acetate, propionate, butyrate, isovalerate, and caproate; and amylase activity. In contrast, Rusitec fermenters did not reproduce the dietary differences found in sheep for NH(3)-N and lactate concentrations, dry matter (DM) digestibility, proportions of isobutyrate and valerate, carboxymethylcellulase and xylanase activities, and microbial growth and its efficiency. Regarding the effect of the type of forage in the diet, Rusitec fermenters detected differences between diets similar to those found in sheep for most determined parameters, with the exception of pH, DM digestibility, butyrate proportion, and carboxymethylcellulase activity. Minimum pH and maximal volatile fatty acid concentrations were reached at 2h and at 6 to 8h postfeeding in sheep and fermenters, respectively, indicating that feed fermentation was slower in fermenters compared with that in sheep. There were differences between systems in the magnitude of most determined parameters. In general, fermenters showed lower lactate concentrations, neutral detergent fiber digestibility, acetate:propionate ratios, and enzymatic activities. On the contrary, fermenters showed greater NH(3)-N concentrations, DM digestibility, and proportions of propionate

  10. Dietary protein concentration affects intestinal microbiota of adult cats: a study using DGGE and qPCR to evaluate differences in microbial populations in the feline gastrointestinal tract.

    PubMed

    Lubbs, D C; Vester, B M; Fastinger, N D; Swanson, K S

    2009-02-01

    The objective of this study was to identify qualitative and quantitative differences in microbial populations of adult cats fed diets containing different protein concentrations. Following a 4 week baseline period, eight healthy adult domestic short-hair queens (>1-year-old) were randomly allotted to a moderate-protein (MP; n = 4) or high-protein (HP; n = 4) diet for 8 weeks. Fresh faecal samples were collected after baseline and 8 weeks on treatment and stored at -80 degrees C. Following DNA extraction, samples were analyzed using denaturing gradient gel electrophoresis to distinguish qualitative changes between diets. Quantitative polymerase chain reaction was used to measure E. coli, Bifidobacterium, Clostridium perfringens, and Lactobacillus populations. Compared to baseline, cats fed MP had a bacterial similarity index of 66.7% as opposed to 40.6% similarity for those fed HP, exhibiting marked changes in intestinal bacteria of cats fed HP. Bifidobacterium populations were greater (p < 0.05) in cats fed MP versus HP (9.44 vs. 5.63 CFU/g). Clostridium perfringens populations were greater (p < 0.05) in cats fed HP than MP (12.39 vs. 10.83 CFU/g). In this experiment, a high-protein diet resulted in a dramatic shift in microbial populations. Decreased Bifidobacterium population in cats fed HP may justify prebiotic supplementation for such diets.

  11. Comparison of fermentation of diets of variable composition and microbial populations in the rumen of sheep and Rusitec fermenters. II. Protozoa population and diversity of bacterial communities.

    PubMed

    Martínez, M E; Ranilla, M J; Tejido, M L; Saro, C; Carro, M D

    2010-08-01

    Four ruminally and duodenally cannulated sheep and 8 Rusitec fermenters were used to determine the effects of dietary characteristics on microbial populations and bacterial diversity. The purpose of the study was to assess how closely fermenters can mimic the differences between diets found in vivo. The 4 experimental diets contained forage to concentrate (F:C) ratios of 70:30 (high forage; HF) or 30:70 (high concentrate; HC) with either alfalfa hay (A) or grass hay (G) as the forage. Total bacterial numbers were greater in the rumen of sheep fed HF diets compared with those fed HC diets, whereas the opposite was found in fermenters. The numbers of cellulolytic bacteria were not affected by F:C ratio in any fermentation system, but cellulolytic numbers were 2.7 and 1.8 times greater in sheep than in fermenters for HF and HC diets, respectively. Neither total bacterial nor cellulolytic numbers were affected by the type of forage in sheep or fermenters. Decreasing F:C ratio increased total protozoa and Entodiniae numbers in sheep by about 29 and 25%, respectively, but it had no effect in fermenters. Isotrichidae and Ophryoscolecinae numbers in sheep were not affected by changing F:C ratio, but both disappeared completely from fermenters fed HC diets. Total protozoa and Entodiniae numbers were greater in sheep fed A diets than in those fed G diets, whereas the opposite was found in fermenters. Results indicate that under the conditions of the present study, protozoa population in Rusitec fermenters was not representative of that in the rumen of sheep fed the same diets. In addition, protozoa numbers in fermenters were 121 and 226 times lower than those in the sheep rumen for HF and HC diets, respectively. The automated ribosomal intergenic spacer analysis of the 16S ribosomal DNA was used to analyze the diversity of liquid- and solid-associated bacteria in both systems. A total of 170 peaks were detected in the automated ribosomal intergenic spacer analysis

  12. Performance, meat quality, meat mineral contents and caecal microbial population responses to humic substances administered in drinking water in broilers.

    PubMed

    Ozturk, E; Coskun, I; Ocak, N; Erener, G; Dervisoglu, M; Turhan, S

    2014-01-01

    This study was conducted to examine the effect of different levels of humic substances (HS) administered in drinking water on caecal microflora and mineral composition and colour characteristics of breast and thigh meats and the growth performance, carcass and gastrointestinal tract (GIT) traits of broiler chicks. A total of 480 3-d-old broiler chickens were randomly allocated to 4 treatments with 4 cages per treatment and 30 bird (15 males and 15 females) chicks per cage. All birds were fed on commercial basal diet. The control birds (HS0) received drinking water with no additions, whereas birds in the other treatment groups received a drinking water with 7.5 (HS7.5), 15.0 (HS15.0) and 22.5 (HS22.5) g/kg HS. Mush feed were provided on an ad libitum basis. Body weight and feed intake of broilers were determined at d 0, 21, and 42, and feed conversion ratio was calculated. On d 42, 4 broilers (2 males and 2 females) from each cage were slaughtered and the breast and thigh meats were collected for mineral composition and quality measurements. Performance, carcass and GIT traits and caecal microbial population of broiler chicks at d 42 were not affected by the dietary treatments. The lightness (L*) of breast and thigh meat decreased in broilers supplemented with 15 and 22.5 g/kg HS in drinking water. Although the redness (a*) of breast meat increased, yellowness of thigh meat decreased in broilers supplemented with 15 and 22.5 g/kg HS in drinking water (P < 0.05). In conclusion, the 15 and 22.5 g/kg HS administration in drinking water can be applied for broiler chicks to maintain growth performance and improve meat quality without changing caecal microflora.

  13. [Dynamic changes of soil microbial populations and enzyme activities in super-high yielding summer maize farmland soil].

    PubMed

    Hou, Peng; Wang, Yong-jun; Wang, Kong-jun; Yang, Jin-sheng; Li, Deng-hai; Dong, Shu-ting; Liu, Jing-guo

    2008-08-01

    To reveal the characteristics of the dynamic changes of soil microbial populations and enzyme activities in super-high yielding ( > 15,000 kg x hm(-2)) summer maize farmland soil, a comparative study was conducted in the experimental fields in National Maize Engineering Research Center (Shandong). On the fields with an annual yield of >15,000 kg x hm(-2) in continuous three years, a plot with the yield of 20 322 kg x hm(-2) (HF) was chosen to make comparison with the conventional farmland (CF) whose maize yield was 8920. 1 kg x hm(-2). The numbers of bacteria, fungi, and actinomycetes as well as the activities of urease and invertase in 0-20 cm soil layer were determined. The results showed that in the growth period of maize, the numbers of bacteria, fungi, and actinomycetes in the two farmland soils increased first and declined then. At the later growth stages of maize, the numbers of soil microbes, especially those of bacteria and actinomycetes, were lower in HF than those in CF. At harvest stage, the ratio of the number of soil bacteria to fungi (B/ F) in HF was 2.03 times higher than that at sowing stage, and 3.02 times higher than that in CF. The B/F in CF had less difference at harvest and sowing stages. The soil urease activity in HF was significantly lower than that in CF at jointing stage, and the invertase activity in HF decreased rapidly after blooming stage, being significantly lower than that in CF.

  14. Effects of coconut and fish oils on ruminal methanogenesis, fermentation, and abundance and diversity of microbial populations in vitro.

    PubMed

    Patra, A K; Yu, Z

    2013-03-01

    Coconut (CO) and fish (FO) oils were previously shown to inhibit rumen methanogenesis and biohydrogenation, which mitigates methane emission and helps improve beneficial fatty acids in meat and milk. This study aimed at investigating the comparative effects of CO and FO on the methanogenesis, fermentation, and microbial abundances and diversity in vitro rumen cultures containing different doses (0, 3.1, and 6.2 mL/L) of each oil and 400mg feed substrate using rumen fluid from lactating dairy cows as inocula. Increasing doses of CO and FO quadratically decreased concentrations of methane, but hydrogen concentrations were only increased quadratically by CO. Both oils linearly decreased dry matter and neutral detergent fiber digestibility of feeds but did not affect the concentration of total volatile fatty acids. However, CO reduced acetate percentage and acetate to propionate ratio and increased the percentages of propionate and butyrate to a greater extent than FO. Ammonia concentration was greater for CO than FO. As determined by quantitative real-time PCR, FO had greater inhibition to methanogens than CO, but the opposite was true for protozoal, Ruminococcus flavefaciens, and Fibrobacter succinogenes. Ruminococcus albus was not affected by either oil. Denaturing gradient gel electrophoresis (DGGE) profiles revealed that bacterial and archaeal community composition were changed differently by oil type. Based on Pareto-Lorenz evenness curve analysis of the DGGE profiles, CO noticeably changed the functional organization of archaea compared with FO. In conclusion, although both CO and FO decreased methane concentrations to a similar extent, the mode of reduction and the effect on abundances and diversity of archaeal and bacterial populations differed between the oils. Thus, the use of combination of CO and FO at a low dose may additively lower methanogenesis in the rumen while having little adverse effect on rumen fermentation.

  15. Effects of rumen fluid collection site on microbial population structure during in vitro fermentation of the different substrates quantified by 16S rRNA hybridisation.

    PubMed

    Muetzel, S; Krishnamoorthy, U; Becker, K

    2001-01-01

    Rumen fluid samples from a cow were withdrawn manually from the feed mat (solid phase) or the liquid phase below this mat and incubated in vitro with wheat straw, sorghum hay and a concentrate mixture. From the inoculum and several samples collected during in vitro incubation RNA was extracted to assess microbial population size and structure. RNA content recovered from the solid phase rumen fluid was significantly higher than from the liquid phase. The composition of the microbial population in the solid phase material was characterised by a high proportion of Ruminococci. Neither the proportion of other cell wall degrading organisms (Fibrobacter and Chytridiomycetes) nor the Eukarya and Archaea populations differed between the two sampling sites. Gas production was higher when substrates were incubated with solid phase than with liquid phase rumen fluid regardless of sampling time. However, the higher level of gas production was not accompanied by a corresponding increase in true digestibility. The RNA probes showed that during in vitro incubation with liquid phase rumen fluid, the eukaryotic population was inactive no matter which substrate was used and the activity of methanogens (Archaea) was lower than with solid phase rumen fluid. The population pattern of the cell wall degrading organisms was influenced mainly by the substrate fermented, and to a smaller extent by the inoculum used for in vitro fermentation.

  16. Improved Yield of High Molecular Weight DNA Coincides with Increased Microbial Diversity Access from Iron Oxide Cemented Sub-Surface Clay Environments

    DOE PAGES

    Hurt, Jr., Richard A.; Robeson II, Michael S.; Shakya, Migun; ...

    2014-07-14

    Despite more than three decades of progress, efficient nucleic acid extraction from microbial communities has remained difficult, particularly from clay environments. Lysis with concentrated guanidine followed by concentrated sodium phosphate extraction supported DNA and RNA recovery from high iron, low humus content clay. Alterating the extraction pH or using other ionic solutions (Na2SO4 and NH4H2PO4) yielded no detectable nucleic acid. DNA recovered using a lysis solution with 500 mM phosphate buffer (PB) followed by a 1 M PB wash was 15.22±2.33 g DNA/g clay, with most DNA consisting of >20 Kb fragments, compared to 2.46±0.25 g DNA/g clay with themore » Powerlyzer soil DNA system (MoBio). Increasing [PB] in the lysis reagent coincided with increasing DNA fragment length. Rarefaction plots based on16S rRNA (V1/V3 region) pyrosequencing libraries from A-horizon and clay soils showed an ~80% and ~400% larger accessed diversity compared to a previous grinding protocol or the Powerlyzer soil DNA system, respectively. The observed diversity from the Firmicutes showed the strongest increase with >3-fold more bacterial species recovered using this system. Additionally, some OTU's having more than 100 sequences in these libraries were absent in samples extracted using the PowerLyzer reagents or the previous lysis method.« less

  17. Improved Yield of High Molecular Weight DNA Coincides with Increased Microbial Diversity Access from Iron Oxide Cemented Sub-Surface Clay Environments

    SciTech Connect

    Hurt, Jr., Richard A.; Robeson II, Michael S.; Shakya, Migun; Moberly, James G.; Vishnivetskaya, Tatiana; Gu, Baohua; Elias, Dwayne A.

    2014-07-14

    Despite more than three decades of progress, efficient nucleic acid extraction from microbial communities has remained difficult, particularly from clay environments. Lysis with concentrated guanidine followed by concentrated sodium phosphate extraction supported DNA and RNA recovery from high iron, low humus content clay. Alterating the extraction pH or using other ionic solutions (Na2SO4 and NH4H2PO4) yielded no detectable nucleic acid. DNA recovered using a lysis solution with 500 mM phosphate buffer (PB) followed by a 1 M PB wash was 15.22±2.33 g DNA/g clay, with most DNA consisting of >20 Kb fragments, compared to 2.46±0.25 g DNA/g clay with the Powerlyzer soil DNA system (MoBio). Increasing [PB] in the lysis reagent coincided with increasing DNA fragment length. Rarefaction plots based on16S rRNA (V1/V3 region) pyrosequencing libraries from A-horizon and clay soils showed an ~80% and ~400% larger accessed diversity compared to a previous grinding protocol or the Powerlyzer soil DNA system, respectively. The observed diversity from the Firmicutes showed the strongest increase with >3-fold more bacterial species recovered using this system. Additionally, some OTU's having more than 100 sequences in these libraries were absent in samples extracted using the PowerLyzer reagents or the previous lysis method.

  18. Immigrant mothers and access to prenatal care: evidence from a regional population study in Italy

    PubMed Central

    Chiavarini, Manuela; Lanari, Donatella; Minelli, Liliana; Pieroni, Luca

    2016-01-01

    Objectives We addressed the question of whether use of adequate prenatal care differs between foreign-born and Italian mothers and estimated the extent to which unobservable characteristics bias results. Setting This study is on primary care and especially on adequate access to prenatal healthcare services by immigrant mothers. Participants Approximately 37 000 mothers of both Italian and foreign nationality were studied. Data were obtained from the Standard Certificate of Live Birth between 2005 and 2010 in Umbria. Results Estimates from the bivariate probit model indicate that immigrant mothers are three times more likely to make fewer than four prenatal visits (OR=3.35) and 1.66 times more likely to make a late first visit (OR=1.66). The effect is found to be strongest for Asian women. Conclusions Standard probit models lead to underestimation of the probability of inadequate use of prenatal care services by immigrant women, whereas bivariate probit models, which allow us to consider immigrant status as an endogenous variable, estimated ORs to be three times larger than those obtained with univariate models. PMID:26861935

  19. Distress syndromes, illness behavior, access to care and medical utilization in a defined population.

    PubMed

    Mechanic, D; Cleary, P D; Greenley, J R

    1982-04-01

    This article examines the use of general medical services in a representative sample from a defined geographic area and in a sample of persons seeking psychiatric care from the same area. Psychiatric patients made 100 per cent more general medical care visits in the retrospective period and 83 per cent more in the prospective period than persons who did not seek mental health care. The analysis focuses on the determinants in general medical care use between those who sought mental health care and those who did not. The first hypothesis is that physical symptoms and dysfunction concomitant with psychologic disorder explain the difference. The second argues that the association is a product of help-seeking orientations and illness behavior. The third focuses on variations due to differences in access. The first two types of factors are the most important. Using sex, physical symptoms and illness behavior measures, we explain 50 per cent of the differences in retrospective utilization and 40 per cent of the differences in prospective data.

  20. People living with HIV travel farther to access healthcare: a population-based geographic analysis from rural Uganda

    PubMed Central

    Akullian, Adam N; Mukose, Aggrey; Levine, Gillian A; Babigumira, Joseph B

    2016-01-01

    Introduction The availability of specialized HIV services is limited in rural areas of sub-Saharan Africa where the need is the greatest. Where HIV services are available, people living with HIV (PLHIV) must overcome large geographic, economic and social barriers to access healthcare. The objective of this study was to understand the unique barriers PLHIV face when accessing healthcare compared with those not living with HIV in a rural area of sub-Saharan Africa with limited availability of healthcare infrastructure. Methods We conducted a population-based cross-sectional study of 447 heads of household on Bugala Island, Uganda. Multiple linear regression models were used to compare travel time, cost and distance to access healthcare, and log binomial models were used to test for associations between HIV status and access to nearby health services. Results PLHIV travelled an additional 1.9 km (95% CI (0.6, 3.2 km), p=0.004) to access healthcare compared with those not living with HIV, and they were 56% less likely to access healthcare at the nearest health facility to their residence, so long as that facility lacked antiretroviral therapy (ART) services (aRR=0.44, 95% CI (0.24 to 0.83), p=0.011). We found no evidence that PLHIV travelled further for care if the nearest facility supplies ART services (aRR=0.95, 95% CI (0.86 to 1.05), p=0.328). Among those who reported uptake of care at one of two facilities on the island that provides ART (81% of PLHIV and 68% of HIV-negative individuals), PLHIV tended to seek care at a higher tiered facility that provides ART, even when this facility was not their closest facility (30% of PLHIV travelled further than the closest ART facility compared with 16% of HIV-negative individuals), and travelled an additional 2.2 km (p=0.001) to access that facility, relative to HIV-negative individuals (aRR=1.91, 95% CI (1.00 to 3.65), p=0.05). Among PLHIV, residential distance was associated with access to facilities providing ART (RR=0

  1. From the Margins to the Spotlight: Diverse Deaf and Hard of Hearing Student Populations and Standardized Assessment Accessibility.

    PubMed

    Cawthon, Stephanie

    2015-01-01

    Designing assessments and tests is one of the more challenging aspects of creating an accessible learning environment for students who are deaf or hard of hearing (DHH), particularly for deaf students with a disability (DWD). Standardized assessments are a key mechanism by which the educational system in the United States measures student progress, teacher effectiveness, and the impact of school reform. The diversity of student characteristics within DHH and DWD populations is only now becoming visible in the research literature relating to standardized assessments and their use in large-scale accountability reforms. The purpose of this article is to explore the theoretical frameworks surrounding assessment policy and practice, current research related to standardized assessment and students who are DHH and DWD, and potential implications for practice within both the assessment and instruction contexts.

  2. Assessing the population-level impact of vouchers on access to health facility delivery for women in Kenya.

    PubMed

    Obare, Francis; Warren, Charlotte; Abuya, Timothy; Askew, Ian; Bellows, Ben

    2014-02-01

    Although available evidence indicates that vouchers improve service utilization among the target populations, we do not know whether increased utilization results from improved access (new clients who would not have used services without the voucher) or from shifting clients from non-accredited to contracted service providers. This paper examines whether the safe motherhood voucher program in Kenya is associated with improved access to health facility delivery using information on births within two years preceding the survey in voucher and comparison sites. Data were collected in 2010-2011 and in 2012 among 2933 and 3094 women aged 15-49 years reporting 962 and 1494 births within two years before the respective surveys. Analysis entails cross-tabulations and estimation of multilevel random-intercept logit models. The results show that the proportion of births occurring at home declined by more than 10 percentage points while the proportion of births delivered in health facilities increased by a similar margin over time in voucher sites. The increase in facility-based births occurred in both public and private health facilities. There was also a significant increase in the likelihood of facility-based delivery (odds ratios [OR]: 2.04; 95% confidence interval [CI]: 1.40-2.98 in the 2006 voucher arm; OR: 1.72; 95% CI: 1.22-2.43 in the 2010-2011 voucher arm) in voucher sites over time. In contrast, there were no significant changes in the likelihood of facility-based delivery in the comparison arm over time. These findings suggest that the voucher program contributed to improved access to institutional delivery by shifting births from home to health facilities. However, available evidence from qualitative data shows that some women who purchased the vouchers did not use them because of high transportation costs to accredited facilities. The implication is that substantial improvements in service uptake could be achieved if the program subsidized transportation costs as

  3. Ileal MUC2 gene expression and microbial population, but not growth performance and immune response, are influenced by in ovo injection of probiotics in broiler chickens.

    PubMed

    Majidi-Mosleh, A; Sadeghi, A A; Mousavi, S N; Chamani, M; Zarei, A

    2017-02-01

    1. The objective of present study was to evaluate the effects of intra-amniotic injection of different probiotic strains (Bacillus subtilis, Enterococcus faecium and Pediococcus acidilactici) on the intestinal MUC2 gene expression, microbial population, growth performance and immune response in broiler chicken. 2. In a completely randomised design, different probiotic strains were injected into the amniotic fluid of the 480 live embryos (d 18 of incubation), with 4 treatments and 5 replicates. Ileal MUC2 gene expression, microbial profile, growth performance and immune response were determined. 3. Injection of probiotic strains, especially B. subtilis, had significant effect on expression of the MUC2 on d 21 of incubation and d 3 post-hatch, but not on d 19 of incubation. 4. Injection of the probiotic strains decreased significantly the Escherichia coli population and increased the lactic acid bacteria population during the first week post-hatch. 5. Inoculation of probiotics had no significant effect on antibody titres against Newcastle disease virus, antibody titres against sheep red blood cell and cell-mediated immune response of chickens compared to control. 6. In ovo injection of the probiotic strains had no significant effect on growth performance of broiler chickens. 7. It was concluded that injection of probiotic bacteria especially B. subtilis into the amniotic fluid has a beneficial effect on ileal MUC2 gene expression and bacteria population during the first week post-hatch, but has no effect on growth performance and immune response in broiler chickens.

  4. "Population and poverty: major barriers to food accessibility" -- a panel discussion on civil society and people's participation.

    PubMed

    1996-01-01

    This paper summarizes conference statements on poverty and food policies that were made by parliamentary members from Malaysia, the Philippines, and India. These presentations were made after the main panel discussion on barriers to food accessibility. In Malaysia the government adopted a National Agricultural Policy in 1984. This policy encouraged increased productivity, effective use of resources, agricultural credit and incentives, and integrated pest management. Strong support was given to the food processing industry. Poverty was the main reason for food inaccessibility. Through government efforts, poverty was reduced from 16.5% in 1990 to 8.9% in 1995. The Filipino member reported that government efforts had focused on national campaigns to combat hunger and to encourage community participation. The government was forced to implement a national Plan of Action for Food Security due to increased population, environmental degradation, closing land frontiers, and the global economy. The Plan encouraged increases in productivity, price and supply stabilization, maintenance of stocks, and rice subsidies for the poor. Gender concerns were being incorporated into development programs. The Indian member linked food insecurity to world resource problems. He stated that food problems included imbalances between supply and demand, but more importantly inequalities in access to food and differences in nutritional content of food. Populations in developing countries spent a larger proportion of income on food of lesser quality and variety that contributed to nutritional deficiencies, particularly among women and children. Food insecurity was part of the cycle of poverty, hunger, low productivity, and high mortality. Poverty was the primary cause and a major consequence of hunger and chronic food insecurity. Although India increased food productivity, food insecurity remained. Multidisciplinary approaches are needed.

  5. Is the Brazilian pharmaceutical policy ensuring population access to essential medicines?

    PubMed Central

    2012-01-01

    Background To evaluate medicine prices, availability and affordability in Brazil, considering the differences across three types of medicines (originator brands, generics and similar medicines) and different types of facilities (private pharmacies, public sector pharmacies and “popular pharmacies”). Methods Data on prices and availability of 50 medicines were collected in 56 pharmacies across six cities in Southern Brazil using the World Health Organization / Health Action International methodology. Median prices obtained were divided by international reference prices to derive the median price ratio (MPR). Results In the private sector, prices were 8.6 MPR for similar medicines, 11.3 MRP for generics and 18.7 MRP for originator brands, respectively. Mean availability was 65%, 74% and 48% for originator brands, generics and similar medicines, respectively. In the public sector, mean availability of similar medicines was 2–7 times higher than that of generics. Mean overall availability in the public sector ranged from 68.8% to 81.7%. In “popular pharmacies”, mean availability was greater than 90% in all cities. Conclusions Availability of medicines in the public sector does not meet the challenge of supplying essential medicines to the entire population, as stated in the Brazilian constitution. This has unavoidable repercussions for affordability, particularly amongst the lower socio-economic strata. PMID:22436555

  6. Mapping socio-environmentally vulnerable populations access and exposure to ecosystem services at the U.S.-Mexico borderlands

    USGS Publications Warehouse

    Norman, Laura M.; Villarreal, Miguel L.; Lara-Valencia, Francisco; Yuan, Yongping; Nie, Wenming; Wilson, Sylvia; Amaya, Gladys; Sleeter, Rachel

    2012-01-01

    Socio-environmental vulnerable populations are often unrepresented in land-use planning yet have great potential for loss when exposed to changes in ecosystem services. Administrative boundaries, cultural differences, and language barriers increase the disassociation between land-use management and marginalized populations living in the U.S.–Mexico borderlands. This paper describes the development of a Modified Socio-Environmental Vulnerability Index (M-SEVI), using determinants from binational census and neighborhood data that describe levels of education, access to resources, migratory status, housing, and number of dependents, to provide a simplified snapshot of the region's populace that can be used in binational planning efforts. We apply this index at the SCW, located on the border between Arizona, USA and Sonora, Mexico. For comparison, the Soil and Water Assessment Tool is concurrently applied to assess the provision of erosion- and flood control services over a 9-year period. We describe how this coupling of data can form the base for an ecosystem services assessment across political boundaries that can be used by land-use planners. Results reveal potential disparities in environmental risks and burdens throughout the binational watershed in residential districts surrounding and between urban centers. The M-SEVI can be used as an important first step in addressing environmental justice for binational decision-making.

  7. Seasonal distributions of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis.

    PubMed Central

    Ferris, M J; Ward, D M

    1997-01-01

    Denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rRNA gene segments was used to examine the distributions of bacterial populations within a hot spring microbial mat (Octopus Spring, Yellowstone National Park). Populations at sites along the thermal gradient of the spring's effluent channel were surveyed at seasonal intervals. No shift in the thermal gradient was detected, and populations at spatially or temperature-defined sites exhibited only slight changes over the annual sampling period. A new cyanobacterial 16S rRNA sequence type was detected at temperatures from 63 to 75 degrees C. A new green nonsulfur bacterium-like sequence type was also detected at temperatures from 53 to 62 degrees C. Genetically unique though closely related cyanobacterial and green nonsulfur bacterium-like populations were successively distributed along the thermal gradient of the Octopus Spring effluent channel. At least two cyanobacterial populations were detected at each site; however, a limited ability to detect some cyanobacterial populations suggests that only dominant populations were observed. PMID:9097434

  8. Three-dimensional soil organic matter distribution, accessibility and microbial respiration in macroaggregates using osmium staining and synchrotron X-ray computed tomography

    NASA Astrophysics Data System (ADS)

    Rawlins, Barry G.; Wragg, Joanna; Reinhard, Christina; Atwood, Robert C.; Houston, Alasdair; Lark, R. Murray; Rudolph, Sebastian

    2016-12-01

    The spatial distribution and accessibility of organic matter (OM) to soil microbes in aggregates - determined by the fine-scale, 3-D distribution of OM, pores and mineral phases - may be an important control on the magnitude of soil heterotrophic respiration (SHR). Attempts to model SHR on fine scales requires data on the transition probabilities between adjacent pore space and soil OM, a measure of microbial accessibility to the latter. We used a combination of osmium staining and synchrotron X-ray computed tomography (CT) to determine the 3-D (voxel) distribution of these three phases (scale 6.6 µm) throughout nine aggregates taken from a single soil core (range of organic carbon (OC) concentrations: 4.2-7.7 %). Prior to the synchrotron analyses we had measured the magnitude of SHR for each aggregate over 24 h under controlled conditions (moisture content and temperature). We test the hypothesis that larger magnitudes of SHR will be observed in aggregates with (i) shorter length scales of OM variation (more aerobic microsites) and (ii) larger transition probabilities between OM and pore voxels. After scaling to their OC concentrations, there was a 6-fold variation in the magnitude of SHR for the nine aggregates. The distribution of pore diameters and tortuosity index values for pore branches was similar for each of the nine aggregates. The Pearson correlation between aggregate surface area (normalized by aggregate volume) and normalized headspace C gas concentration was both positive and reasonably large (r = 0.44), suggesting that the former may be a factor that influences SHR. The overall transition probabilities between OM and pore voxels were between 0.07 and 0.17, smaller than those used in previous simulation studies. We computed the length scales over which OM, pore and mineral phases vary within each aggregate using 3-D indicator variograms. The median range of models fitted to variograms of OM varied between 38 and 175 µm and was generally larger than

  9. Planetary Resources and Astroecology. Planetary Microcosm Models of Asteroid and Meteorite Interiors: Electrolyte Solutions and Microbial Growth- Implications for Space Populations and Panspermia

    NASA Astrophysics Data System (ADS)

    Mautner, Michael N.

    2002-03-01

    Planetary microcosms were constructed using extracts from meteorites that simulate solutions in the pores of carbonaceous chondrites. The microcosms were found to support the growth of complex algal and microbial populations. Such astroecology experiments demonstrate how a diverse ecosystem could exist in fluids within asteroids, and in meteorites that land on aqueous planets. The microcosm solutions were obtained by extracting nutrient electrolytes under natural conditions from powders of the Allende (CV3) and Murchison (CM2) meteorites at low (0.02 g/ml) and high (10.0 g/ml) solid/solution ratios. The latter solutions contain >3 mol/L electrolytes and about 10 g/L organics, that simulate natural fluids in asteroids during aqueous alteration and in the pores of meteorites, which can help prebiotic synthesis and the survival of early microorganisms. These solutions and wet solids were in fact found to support complex self-sustaining microbial communities with populations of 4 × 105 algae and 6 × 106 bacteria and fungi for long periods (>8 months). The results show that planetary microcosms based on meteorites can: assay the fertilities of planetary materials; identify space bioresources; target astrobiology exploration; and model past and future space-based ecosystems. The results show that bioresources in the carbonaceous asteroids can sustain a biomass of 1018 kg, comprising 1032 microorganisms and a human population of 1014. The results also suggest that protoplanetary nebulae can support and disperse microorganisms and can be therefore effective environments for natural and directed panspermia.

  10. Dissolved carbon dioxide and oxygen concentrations in purge of vacuum-packaged pork chops and the relationship to shelf life and models for estimating microbial populations.

    PubMed

    Adams, K R; Niebuhr, S E; Dickson, J S

    2015-12-01

    The objectives of this study were to determine the dissolved CO2 and O2 concentrations in the purge of vacuum-packaged pork chops over a 60 day storage period, and to elucidate the relationship of dissolved CO2 and O2 to the microbial populations and shelf life. As the populations of spoilage bacteria increased, the dissolved CO2 increased and the dissolved O2 decreased in the purge. Lactic acid bacteria dominated the spoilage microflora, followed by Enterobacteriaceae and Brochothrix thermosphacta. The surface pH decreased to 5.4 due to carbonic acid and lactic acid production before rising to 5.7 due to ammonia production. A mathematical model was developed which estimated microbial populations based on dissolved CO2 concentrations. Scanning electron microscope images were also taken of the packaging film to observe the biofilm development. The SEM images revealed a two-layer biofilm on the packaging film that was the result of the tri-phase growth environment.

  11. Diversity and evolution of the microbial populations during manufacture and ripening of Casín, a traditional Spanish, starter-free cheese made from cow's milk.

    PubMed

    Alegría, Angel; Alvarez-Martín, Pablo; Sacristán, Noelia; Fernández, Elena; Delgado, Susana; Mayo, Baltasar

    2009-11-30

    Classical culturing and denaturing gradient gel electrophoresis (DGGE) techniques have been used for studying the microbial diversity and dynamics of the traditional Spanish Casín cheese during manufacturing and ripening. As with other starter-free cheeses made from raw milk, the microbial diversity of Casín was shown to be high by both culturing and DGGE analyses. The culture technique showed that lactic acid bacteria (LAB) species constituted the majority of the microbial populations. Of the 14 bacterial species identified, Lactococcus garvieae was predominant in the three-day-old cheese sample, although it was replaced by Lactococcus lactis subsp. lactis at day 30. As expected, the DGGE profiles obtained were complex, consisting, depending on the sample, in five to ten different amplification bands. Among these, a band corresponding to Streptococcus thermophilus was observed throughout the whole manufacturing process. This species had never been identified from traditional Spanish cheeses previously. Culturing and molecular methods showed high populations of undesirable microorganisms, arguing for a required improvement in the hygiene of Casín manufacture. Random amplification of polymorphic DNA (RAPD) profiling suggested that the L. garvieae and L. lactis populations were composed of one and five strains, respectively. In addition, only a single L. lactis RAPD pattern was stably maintained from day three to day 30, indicating high succession of strains along ripening. After a thoroughly characterisation, strains of the two Lactococcus species could be used in designing specific starter cultures for Casín. Additional species (such as Lactobacillus plantarum and Corynebacterium variabile) might be included as adjunct cultures.

  12. Rapid changes in key ruminal microbial populations during the induction of and recovery from diet-induced milk fat depression in dairy cows.

    PubMed

    Rico, D E; Preston, S H; Risser, J M; Harvatine, K J

    2015-08-14

    The ruminant provides a powerful model for understanding the temporal dynamics of gastrointestinal microbial communities. Diet-induced milk fat depression (MFD) in the dairy cow is caused by rumen-derived bioactive fatty acids, and is commonly attributed to the changes in the microbial population. The aim of the present study was to determine the changes occurring in nine ruminal bacterial taxa with well-characterised functions, and abundance of total fungi, ciliate protozoa and bacteria during the induction of and recovery from MFD. Interactions between treatment and time were observed for ten of the twelve populations. The total number of both fungi and ciliate protozoa decreased rapidly (days 4 and 8, respectively) by more than 90% during the induction period and increased during the recovery period. The abundance of Streptococcus bovis (amylolytic) peaked at 350% of control levels on day 4 of induction and rapidly decreased during the recovery period. The abundance of Prevotella bryantii (amylolytic) decreased by 66% from day 8 to 20 of the induction period and increased to the control levels on day 12 of the recovery period. The abundance of Megasphaera elsdenii and Selenomonas ruminantium (lactate-utilising bacteria) increased progressively until day 12 of induction (>170%) and decreased during the recovery period. The abundance of Fibrobacter succinogenes (fibrolytic) decreased by 97% on day 4 of induction and increased progressively to an equal extent during the recovery period, although smaller changes were observed for other fibrolytic bacteria. The abundance of the Butyrivibrio fibrisolvens/Pseudobutyrivibrio group decreased progressively during the induction period and increased during the recovery period, whereas the abundance of Butyrivibrio hungatei was not affected by treatment. Responsive taxa were modified rapidly, with the majority of changes occurring within 8 d and their time course was similar to the time course of the induction of MFD

  13. Assessing the microbial quality of improved drinking water sources: results from the Dominican Republic.

    PubMed

    Baum, Rachel; Kayser, Georgia; Stauber, Christine; Sobsey, Mark

    2014-01-01

    Millennium Development Goal Target 7c (to halve between 1990 and 2015 the proportion of the global population without sustainable access to safe drinking water), was celebrated as achieved in 2012. However, new studies show that we may be prematurely celebrating. Access to safe drinking water may be overestimated if microbial water quality is considered. The objective of this study was to examine the relationship between microbial drinking water quality and drinking water source in the Puerto Plata region of the Dominican Republic. This study analyzed microbial drinking water quality data from 409 households in 33 communities. Results showed that 47% of improved drinking water sources were of high to very-high risk water quality, and therefore unsafe for drinking. This study provides evidence that the current estimate of safe water access may be overly optimistic, and microbial water quality data are needed to reliably assess the safety of drinking water.

  14. EVALUATION OF THE EFFECTIVENESS OF RIPARIAN ZONE RESTORATION IN THE SOUTHERN APPALACHIANS BY ASSESSING SOIL MICROBIAL POPULATIONS

    EPA Science Inventory

    Microbial biomass, nitrifiers and denitrifiers in surface soil (0?10 cm) were quantified in a riparian zone restoration project at Coweeta, North Carolina, USA. Four treatments are included in this study: (1) a degraded (+N) riparian zone with continued compaction, vegetation rem...

  15. Microbial populations of crude oil spill polluted soils at the Jordan-Iraq desert (the Badia region)

    PubMed Central

    Saadoun, Ismail; Mohammad, Munir J.; Hameed, Khalid M.; Shawaqfah, Mo’ayyad

    2008-01-01

    Microbial populations’ inhabitants in crude petroleum contaminated soils were analyzed in relation with the soil characteristics. A noticeable greater decline of bacterial counts and diversity but a prevalence of the genus Pseudomonas over the other identified genera in the fresh contaminated soils as compared to the old ones was observed. PMID:24031245

  16. An Evaluation of Behavioral Health Compliance and Microbial Risk Factors on Student Populations within a High-Density Campus

    ERIC Educational Resources Information Center

    Decker, Jody F.; Slawson, Robin M.

    2012-01-01

    Objective: The aim of this Canadian study was to assess student behavioral response to disease transmission risk, while identifying high microbial deposition/transmission sites. Participants: A student survey was conducted during October 2009. Methods: The methods included a survey of students to assess use of health services, vaccination…

  17. Deep Diversity: Novel Approach to Overcoming the PCR Bias Encountered During Environmental Analysis of Microbial Populations for Alpha-Diversity

    NASA Technical Reports Server (NTRS)

    Ramirez, Gustavo A; Vaishampayan, Parag A.

    2011-01-01

    Alpha-diversity studies are of crucial importance to environmental microbiologists. The polymerase chain reaction (PCR) method has been paramount for studies interrogating microbial environmental samples for taxon richness. Phylogenetic studies using this technique are based on the amplification and comparison of the 16S rRNA coding regions. PCR, due disproportionate distribution of microbial species in the environment, increasingly favors the amplification of the most predominant phylotypes with every subsequent reaction cycle. The genetic and chemical complexity of environmental samples are intrinsic factors that exacerbate an inherit bias in PCR-based quantitative and qualitative studies of microbial communities. We report that treatment of a genetically complex total genomic environmental DNA extract with Propidium Monoazide (PMA), a DNA intercalating molecule capable of forming a covalent cross-linkage to organic moieties upon light exposure, disproportionally inactivates predominant phylotypes and results in the exponential amplification of previously shadowed microbial ?-diversity quantified as a 19.5% increase in OUTs reported via phylogenetic screening using PhyloChip.

  18. [Health status and access to health services by the population of L'Aquila (Abruzzo Region, Italy) six years after the earthquake].

    PubMed

    Altobelli, Emma; Vittorini, Pierpaolo; Leuter, Cinzia; Bianchini, Valeria; Angelone, Anna Maria; Aloisio, Federica; Cofini, Vincenza; Zazzara, Francesca; Di Orio, Ferdinando

    2016-01-01

    Natural disasters, such as the earthquake that occurred in the province of L'Aquila in central Italy, in 2009, generally increase the demand for healthcare. A survey was conducted to assess perception of health status an d use of health services in a sample of L'Aquila's resident population, five years after the event, and in a comparison population consisting of a sample of the resident population of Avezzano, a town in the same region, not affected by the earthquake. No differences were found in perception of health status between the two populations. Both groups reported difficulties in accessing specialized healthcare and rehabilitation services.

  19. A nutrition strategy to reduce the burden of diet related disease: access to dietician services must complement population health approaches

    PubMed Central

    Segal, Leonie; Opie, Rachelle S.

    2015-01-01

    Poor diet quality is implicated in almost every disease and health issue. And yet, in most advanced market economies diet quality is poor, with a minority meeting guidelines for healthy eating. Poor diet is thus responsible for substantial disease burden. Societies have at their disposal a range of strategies to influence diet behaviors. These can be classified into: (i) population level socio-educational approaches to enhance diet knowledge; (ii) pricing incentives (subsidies on healthy foods, punitive taxes on unhealthy foods); (iii) regulations to modify the food environment, and (iv) the provision of clinical dietetic services. There is little evidence that societies are active in implementing the available strategies. Advertising of “junk foods” is largely unchecked, contrasting with strict controls on advertising tobacco products, which also attract punitive taxes. Access to dieticians is restricted in most countries, even in the context of universal health care. In Australia in 2011 there were just 2,969 practicing dieticians/nutritionists or 1.3 clinicians per 10,000 persons, compared with 5.8 physiotherapists per 10,000 persons, 14.8 general practitioners (family physicians) per 10,000 persons or 75 nurses per 10,000 persons. It is time to implement comprehensive national nutrition strategies capable of effecting change. Such strategies need to be multi-component, incorporating both public health approaches and expanded publicly funded dietetic services. Access to individualized dietetic services is needed by those at risk, or with current chronic conditions, given the complexity of the diet message, the need for professional support for behavior change and to reflect individual circumstances. The adoption of a comprehensive nutrition strategy offers the promise of substantial improvement in diet quality, better health and wellbeing and lower health care costs. PMID:26321951

  20. A nutrition strategy to reduce the burden of diet related disease: access to dietician services must complement population health approaches.

    PubMed

    Segal, Leonie; Opie, Rachelle S

    2015-01-01

    Poor diet quality is implicated in almost every disease and health issue. And yet, in most advanced market economies diet quality is poor, with a minority meeting guidelines for healthy eating. Poor diet is thus responsible for substantial disease burden. Societies have at their disposal a range of strategies to influence diet behaviors. These can be classified into: (i) population level socio-educational approaches to enhance diet knowledge; (ii) pricing incentives (subsidies on healthy foods, punitive taxes on unhealthy foods); (iii) regulations to modify the food environment, and (iv) the provision of clinical dietetic services. There is little evidence that societies are active in implementing the available strategies. Advertising of "junk foods" is largely unchecked, contrasting with strict controls on advertising tobacco products, which also attract punitive taxes. Access to dieticians is restricted in most countries, even in the context of universal health care. In Australia in 2011 there were just 2,969 practicing dieticians/nutritionists or 1.3 clinicians per 10,000 persons, compared with 5.8 physiotherapists per 10,000 persons, 14.8 general practitioners (family physicians) per 10,000 persons or 75 nurses per 10,000 persons. It is time to implement comprehensive national nutrition strategies capable of effecting change. Such strategies need to be multi-component, incorporating both public health approaches and expanded publicly funded dietetic services. Access to individualized dietetic services is needed by those at risk, or with current chronic conditions, given the complexity of the diet message, the need for professional support for behavior change and to reflect individual circumstances. The adoption of a comprehensive nutrition strategy offers the promise of substantial improvement in diet quality, better health and wellbeing and lower health care costs.

  1. Effect of packaging during storage time on retail display microbial population of beef strip loins from two different production systems.

    PubMed

    Luzardo, S; Woerner, D R; Geornaras, I; Hess, A M; Belk, K E

    2016-06-01

    Two studies were conducted to evaluate the influence of packaging during storage of strip loins (to simulate export shipment) from steers fattened on intensive grazing systems (Uruguay; UR) or on a high-concentrate diet (United States; US) on retail display life microbial growth. Four or 3 different packaging treatments were applied to UR and US strip loin roasts or steaks during 35 d of storage; treatments were applied 7 d following slaughter. After 35 d of storage, the samples were evaluated during simulated retail display for up to 6 d. In Exp. 1, the treatments were vacuum packaging (VP), low-oxygen modified atmosphere packaging (MAP) with N and CO (MAP/CO), low-oxygen MAP with N plus CO and CO, and VP plus an application of peroxyacetic acid (VP/PAA). In Exp. 2, block 1, the treatments were VP, MAP/CO, and VP with ethyl--lauroyl--arginate HCl incorporated into the film as an antimicrobial agent (VP/AM). In Exp. 2, block 2, the treatments were VP, MAP/CO, MAP/CO, and VP/AM. For retail display, VP treatments were sliced and repackaged in PVC overwrap, and MAP treatments were actually PVC overwrap trays that were removed from a master bag with the prescribed gas treatment. Regardless of production system and packaging treatment, mesophilic and psychrotrophic counts of 6.9 to 7.8 and 6.7 to 7.7 log10 CFU/cm, respectively, were obtained at the end of retail display, except for US samples in Exp. 2 (5.5 to 6.3 log CFU/cm). No differences ( > 0.05) were detected for spp. counts among packaging treatments in US steaks at the end of the display time in Exp.1, whereas, for UR steaks, both MAP treatments had lower ( < 0.05) spp. counts than VP treatments. spp. counts were lower ( < 0.05) in the MAP/CO treatment than in the other 3 treatments in US samples on d 6 of retail display for Exp. 2. At the end of display time and for Exp. 1, US steaks under MAP/CO had greater ( < 0.05) lactic acid bacteria (LAB) counts than samples in both VP treatments; no differences ( > 0

  2. Access to HIV community services by vulnerable populations: evidence from an enhanced HIV/AIDS surveillance system.

    PubMed

    Madden, H C E; Phillips-Howard, P A; Hargreaves, S C; Downing, J; Bellis, M A; Vivancos, R; Morley, C; Syed, Q; Cook, P A

    2011-05-01

    HIV disproportionately affects vulnerable populations such as black and minority ethnic groups, men who have sex with men (MSM) and migrants, in many countries including those in the UK. Community organisations in the UK are charitable non-governmental organisations with a proportion of the workforce who volunteer, and provide invaluable additional support for people living with HIV (PLWHIV). Information on their contribution to HIV care in vulnerable groups is relatively sparse. Data generated from an enhanced HIV surveillance system in North West England, UK, was utilised for this study. We aimed to determine the characteristics of individuals who chose to access community services in addition to clinical services (1375 out of 4195 records of PLWHIV in clinical services). Demographic information, risk factors including residency status, uniquely gathered in this region, and deprivation scores were examined. Multivariate logistic regression modelling was conducted to predict the relative effect of patient characteristics on attendance at community services. Attendance at community services was highest in those living in the most, compared with least, deprived areas (p<0.001), and was most evident in MSM and heterosexuals. Compared to white UK nationals attendance was significantly higher in non-UK nationals of uncertain residency status (Adjusted odds ratio [AOR] = 21.91, 95% confidence interval [CI] 10.48-45.83; p<0.001), refugees (AOR = 5.75, 95% CI 3.3-10.03; p<0.001), migrant workers (AOR = 5.48, 95% CI 2.22-13.51; p<0.001) and temporary visitors (AOR = 3.44, 95% CI 1.68-7.05; p<0.001). Community services, initially established predominantly to support MSM, have responded to the changing demography of HIV and reach the most vulnerable members of society. Consequent to their support of migrant populations, community services are vital for the management of HIV in black and minority groups. Paradoxically, this coincides with increasing funding pressures on these

  3. Ecology, Microbial

    SciTech Connect

    Konopka, Allan

    2009-03-19

    Microbial ecology is a relatively young discipline within the field of microbiology. Its modern history spans just the past 60 years, and the field is defined by its emphasis on understanding the interactions of microbes with their environment, rather than their behavior under artificial laboratory conditions. Because microbes are ubiquitous, microbial ecologists study a broad diversity of habitats that range from aquatic to terrestrial to plant- or animal-associated. This has made it a challenge to identify unifying principles within the field. One approach is to recognize that although the activity of microbes in nature have effects at the macroscale, they interact with their physical, chemical and biological milieu at a scale of micrometers. At this scale, several different microbial ecosystems can be defined, based upon association with particles, the presence of environmental gradients and the continuous availability of water. Principles applicable to microbial ecology reflect not only their population ecology and physiological ecology, but also their broad versatility and quantitative importance in the biosphere as biogeochemical catalysts and capacity for rapid physiological and evolutionary responses.

  4. Ecology, Microbial

    SciTech Connect

    Konopka, Allan

    2009-05-15

    Microbial ecology is a relatively young discipline within the field of microbiology. Its modern history spans just the past 60 years, and the field is defined by its emphasis on understanding the interactions of microbes with their environment, rather than their behavior under artificial laboratory conditions. Because microbes are ubiquitous, microbial ecologists study a broad diversity of habitats that range from aquatic to terrestrial to plant- or animal-associated. This has made it a challenge to identify unifying principles within the field. One approach is to recognize that although the activity of microbes in nature have effects at the macroscale, they interact with their physical, chemical and biological milieu at a scale of micrometers. At this scale, several different microbial ecosystems can be defined, based upon association with particles, the presence of environmental gradients and the continuous availability of water. Principles applicable to microbial ecology reflect not only their population ecology and physiological ecology, but also their broad versatility and quantitative importance in the biosphere as biogeochemical catalysts and capacity for rapid physiological and evolutionary responses.

  5. Milk fatty acid composition, rumen microbial population, and animal performances in response to diets rich in linoleic acid supplemented with chestnut or quebracho tannins in dairy ewes.

    PubMed

    Buccioni, A; Pauselli, M; Viti, C; Minieri, S; Pallara, G; Roscini, V; Rapaccini, S; Marinucci, M Trabalza; Lupi, P; Conte, G; Mele, M

    2015-02-01

    The aim of the study was to evaluate milk fatty acid (FA) profile, animal performance, and rumen microbial population in response to diets containing soybean oil supplemented or not with chestnut and quebracho tannins in dairy ewes. Eighteen Comisana ewes at 122±6 d in milking were allotted into 3 experimental groups. Diets were characterized by chopped grass hay administered ad libitum and by 800 g/head and day of 3 experimental concentrates containing 84.5 g of soybean oil/kg of dry matter (DM) and 52.8 g/kg of DM of bentonite (control diet), chestnut tannin extract (CHT diet), or quebracho tannin extract (QUE diet). The trial lasted 4 wk. Milk yield was recorded daily, and milk composition and blood parameters were analyzed weekly. At the end of the experiment, samples of rumen fluid were collected to analyze pH, volatile fatty acid profile, and the relative proportions of Butyrivibrio fibrisolvens and Butyrivibrio proteoclasticus in the rumen microbial population. Hepatic functionality, milk yield, and gross composition were not affected by tannin extracts, whereas milk FA composition was characterized by significant changes in the concentration of linoleic acid (CHT +2.77% and QUE +9.23%), vaccenic acid (CHT +7.07% and QUE +13.88%), rumenic acid (CHT -1.88% and QUE +24.24%), stearic acid (CHT + 8.71% and QUE -11.45%), and saturated fatty acids (CHT -0.47% and QUE -3.38%). These differences were probably due to the ability of condensed versus hydrolyzable tannins to interfere with rumen microbial metabolism, as indirectly confirmed by changes in the relative proportions of B. fibrisolvens and B. proteoclasticus populations and by changes in the molar proportions of volatile fatty acids. The effect of the CHT diet on the milk FA profile and microbial species considered in this trial was intermediate between that of QUE and the control diet, suggesting a differential effect of condensed and hydrolyzable tannins on rumen microbes. Compared with control animals

  6. Responses in digestion, rumen fermentation and microbial populations to inhibition of methane formation by a halogenated methane analogue.

    PubMed

    Mitsumori, Makoto; Shinkai, Takumi; Takenaka, Akio; Enishi, Osamu; Higuchi, Koji; Kobayashi, Yosuke; Nonaka, Itoko; Asanuma, Narito; Denman, Stuart E; McSweeney, Christopher S

    2012-08-01

    The effects of the anti-methanogenic compound, bromochloromethane (BCM), on rumen microbial fermentation and ecology were examined in vivo. Japanese goats were fed a diet of 50 % Timothy grass and 50 % concentrate and then sequentially adapted to low, mid and high doses of BCM. The goats were placed into the respiration chambers for analysis of rumen microbial function and methane and H2 production. The levels of methane production were reduced by 5, 71 and 91 %, and H2 production was estimated at 545, 2941 and 3496 mmol/head per d, in response to low, mid and high doses of BCM, respectively, with no effect on maintenance feed intake and digestibility. Real-time PCR quantification of microbial groups showed a significant decrease relative to controls in abundance of methanogens and rumen fungi, whereas there were increases in Prevotella spp. and Fibrobacter succinogenes, a decrease in Ruminococcus albus and R. flavefaciens was unchanged. The numbers of protozoa were also unaffected. Denaturing gradient gel electrophoresis and quantitative PCR analysis revealed that several Prevotella spp. were the bacteria that increased most in response to BCM treatment. It is concluded that the methane-inhibited rumen adapts to high hydrogen levels by shifting fermentation to propionate via Prevotella spp., but the majority of metabolic hydrogen is expelled as H2 gas.

  7. Data Analysis Protocol for the Development and Evaluation of Population Pharmacokinetic Models for Incorporation Into the Web-Accessible Population Pharmacokinetic Service - Hemophilia (WAPPS-Hemo)

    PubMed Central

    McEneny-King, Alanna; Foster, Gary; Edginton, Andrea N

    2016-01-01

    Background Hemophilia is an inherited bleeding disorder caused by a deficiency in a specific clotting factor. This results in spontaneous bleeding episodes and eventual arthropathy. The mainstay of hemophilia treatment is prophylactic replacement of the missing factor, but an optimal regimen remains to be determined. Rather, individualized prophylaxis has been suggested to improve both patient safety and resource utilization. However, uptake of this approach has been hampered by the demanding sampling schedules and complex calculations required to obtain individual estimates of pharmacokinetic (PK) parameters. The use of population pharmacokinetics (PopPK) can alleviate this burden by reducing the number of plasma samples required for accurate estimation, but few tools incorporating this approach are readily available to clinicians. Objective The Web-accessible Population Pharmacokinetic Service - Hemophilia (WAPPS-Hemo) project aims to bridge this gap by providing a Web-accessible service for the reliable estimation of individual PK parameters from only a few patient samples. This service is predicated on the development of validated brand-specific PopPK models. Methods We describe the data analysis plan for the development and evaluation of each PopPK model to be incorporated into the WAPPS-Hemo platform. The data sources and structure of the dataset are discussed first, followed by the procedures for handling both data below limit of quantification (BLQ) and absence of such BLQ data. Next, we outline the strategies for building the appropriate structural and covariate models, including the possible need for a process algorithm when PK behavior varies between subjects or significant covariates are not provided. Prior to use in a prospective manner, the models will undergo extensive evaluation using a variety of techniques such as diagnostic plots, bootstrap analysis and cross-validation. Finally, we describe the incorporation of a validated PopPK model into the

  8. Probiotic table olives: microbial populations adhering on olive surface in fermentation sets inoculated with the probiotic strain Lactobacillus paracasei IMPC2.1 in an industrial plant.

    PubMed

    De Bellis, Palmira; Valerio, Francesca; Sisto, Angelo; Lonigro, Stella Lisa; Lavermicocca, Paola

    2010-05-30

    This study reports the dynamics of microbial populations adhering on the surface of debittered green olives cv. Bella di Cerignola in fermentation sets inoculated with the probiotic strain Lactobacillus paracasei IMPC2.1 in different brining conditions (4% and 8% (w/v) NaCl) at room temperature and 4 degrees C. The probiotic strain successfully colonized the olive surface dominating the natural LAB population and decreasing the pH of brines to microbial populations associated with olive surface and belonging to the different groups indicated that inoculated olives held at room temperature did not host Enterobacteriaceae at the end of fermentation. Yeast populations were present in a low number (

  9. Postprandial variations in the activity of polysaccharide-degrading enzymes in microbial populations from the digesta solids and liquor fractions of rumen contents.

    PubMed

    Williams, A G; Withers, S E; Strachan, N H

    1989-01-01

    The diurnal variations in the specific activities of polysaccharide-degrading enzymes after feeding were monitored in adherent and non-adherent microbial populations separated from bovine rumen liquor and digesta solids. There were marked differences in the activity profiles of the enzymes within the subpopulations. Enzymes involved in the degradation of soluble carbohydrates were more active in the non-adherent populations, and in the liquor phase subpopulation activities increased in the 1-2 h post-feed period. The muralytic enzymes were most active in the adherent population. Specific activities increased by up to 20-fold over the 24 h period, with an initial five-fold increase occurring between 8 h and 12 h after feeding. Enzyme levels in the three non-adherent populations were similar at the end of the postprandial period. In the population recovered from the liquid associated with the digesta particles, however, the activities did not increase until the latter stages of the period, whereas in the non-adherent population from the digesta solids the activities varied little during the diurnal cycle. The numbers of micro-organisms associated with the digesta solids were similar at 2 h and 20 h after feeding; the variations in enzyme levels did not occur as a result of a population increase but were due to increased activities in an established population. The plant cell wall structural polysaccharides were degraded at different rates. There was no appreciable cellulose digestion during the first 8 h of the postprandial period and although hemicellulosic constituents were removed continuously the rate of loss of both polymers was increased in the later stages of the diurnal cycle when enzyme activities were maximal.

  10. Do Children in Rural Areas Still Have Different Access to Health Care? Results from a Statewide Survey of Oregon's Food Stamp Population

    ERIC Educational Resources Information Center

    Devoe, Jennifer E.; Krois, Lisa; Stenger, Rob

    2009-01-01

    Purpose: To determine if rural residence is independently associated with different access to health care services for children eligible for public health insurance. Methods: We conducted a mail-return survey of 10,175 families randomly selected from Oregon's food stamp population (46% rural and 54% urban). With a response rate of 31%, we used a…

  11. Socio Economic Position in TB Prevalence and Access to Services: Results from a Population Prevalence Survey and a Facility-Based Survey in Bangladesh

    PubMed Central

    Hossain, Shahed; Quaiyum, Mohammad Abdul; Zaman, Khalequ; Banu, Sayera; Husain, Mohammad Ashaque; Islam, Mohammad Akramul; Cooreman, Erwin; Borgdorff, Martien; Lönnroth, Knut; Salim, Abdul Hamid; van Leth, Frank

    2012-01-01

    Background In Bangladesh DOTS has been provided free of charge since 1993, yet information on access to TB services by different population group is not well documented. The objective of this study was to assess and compare the socio economic position (SEP) of actively detected cases from the community and the cases being routinely detected under National Tuberculosis Control Programme (NTP) in Bangladesh. Methods and Findings SEP was assessed by validated asset item for each of the 21,427 households included in the national tuberculosis prevalence survey 2007–2009. A principal component analysis generated household scores and categorized in quartiles. The distribution of 33 actively identified cases was compared with the 240 NTP cases over the identical SEP quartiles to evaluate access to TB services by different groups of the population. The population prevalence of tuberculosis was 5 times higher in the lowest quartiles of population (95.4, 95% CI: 48.0–189.7) to highest quartile population (19.5, 95% CI: 6.9–55.0). Among the 33 cases detected during survey, 25 (75.8%) were from lower two quartiles, and the rest 8 (24.3%) were from upper two quartiles. Among TB cases detected passively under NTP, more than half of them 137 (57.1%) were from uppermost two quartiles, 98 (41%) from the second quartile, and 5 (2%) in the lowest quartile of the population. This distribution is not affected when adjusted for other factors or interactions among them. Conclusions The findings indicate that despite availability free of charge, DOTS is not equally accessed by the poorer sections of the population. However, these figures should be interpreted with caution since there is a need for additional studies that assess in-depth poverty indicators and its determinants in relation to access of the TB services provided in Bangladesh. PMID:23028718

  12. Energy, ecology and the distribution of microbial life

    PubMed Central

    Macalady, Jennifer L.; Hamilton, Trinity L.; Grettenberger, Christen L.; Jones, Daniel S.; Tsao, Leah E.; Burgos, William D.

    2013-01-01

    Mechanisms that govern the coexistence of multiple biological species have been studied intensively by ecologists since the turn of the nineteenth century. Microbial ecologists in the meantime have faced many fundamental challenges, such as the lack of an ecologically coherent species definition, lack of adequate methods for evaluating population sizes and community composition in nature, and enormous taxonomic and functional diversity. The accessibility of powerful, culture-independent molecular microbiology methods offers an opportunity to close the gap between microbial science and the main stream of ecological theory, with the promise of new insights and tools needed to meet the grand challenges humans face as planetary engineers and galactic explorers. We focus specifically on resources related to energy metabolism because of their direct links to elemental cycling in the Earth's history, engineering applications and astrobiology. To what extent does the availability of energy resources structure microbial communities in nature? Our recent work on sulfur- and iron-oxidizing autotrophs suggests that apparently subtle variations in the concentration ratios of external electron donors and acceptors select for different microbial populations. We show that quantitative knowledge of microbial energy niches (population-specific patterns of energy resource use) can be used to predict variations in the abundance of specific taxa in microbial communities. Furthermore, we propose that resource ratio theory applied to micro-organisms will provide a useful framework for identifying how environmental communities are organized in space and time. PMID:23754819

  13. Microbial ecology of a crude oil contaminated aquifer

    USGS Publications Warehouse

    Bekins, B.A.; Cozzarelli, I.M.; Warren, E.; Godsy, E.M.

    2002-01-01

    Detailed microbial analyses of a glacial outwash aquifer contaminated by crude oil provide insights into the pattern of microbial succession from iron reducing to methanogenic in the anaerobic portion of the contaminant plume. We analysed sediments from this area for populations of aerobes, iron reducers, fermenters and methanogens, using the most probable number method. On the basis of the microbial data the anaerobic area can be divided into distinct physiological zones dominated by either iron-reducers or a consortium of fermenters and methanogens. Chemistry and permeability data show that methanogenic conditions develop first in areas of high hydrocarbon flux. Thus, we find methanogens both in high permeability horizons and also where separate-phase crude oil is present in either the saturated or unsaturated zone. Microbial numbers peak at the top of the separate-phase oil suggesting that growth is most rapid in locations with access to both hydrocarbons and nutrients infiltrating from the surface.

  14. Community Characterization of Microbial Populations Found at a Cold Water Sulfidic Spring in the Canadian High Arctic

    NASA Astrophysics Data System (ADS)

    Trivedi, C.; Lau, G. E.; Templeton, A. S.; Grasby, S. E.; Spear, J. R.

    2015-12-01

    The unique environment on Europa makes it an ideal target for astrobiological investigation. One such earth-based analogue to aid in this investigation is the sulfur-dominated glacial spring system found at Borup Fiord Pass (BFP), Ellesmere Island, Nunavut, Canada. In this system, subsurface microbial sulfate reduction produces hydrogen sulfide, which is transported through the glacier along spring channels [1]. As the surface oxidation of H2S occurs, resultant deposition of elemental sulfur (S0) and other minerals becomes visible (attached image). The energy released from these reactions can support potential microbial metabolisms and may be a valuable representation of microbial processes occurring on Europa. The resulting sulfur minerals provide sensitive records of dynamic atmospheric, geological, hydrological, chemical, and biological processes on planetary surfaces. Moreover, we expect that the S0-rich deposits of this glacial spring system will serve as a mineralogical record for biological activity and will provide a valuable tool for recognizing potential sulfur-based life on Europa. During a recent collaborative expedition (2014) to BFP, samples were taken from the toe of the glacier in an area called the 'Blister Crust' (attached image). At this location, glacial channels reach the surface, representing an active interface between subsurface and surface processes. Initial geochemical characterization at the site revealed high amounts of aqueous sulfide (1.8 mM) and hydrogen (29 nM), which likely serve as the electron donation potential in the system. Furthermore, preliminary 16S rRNA gene sequencing has shown a high abundance of the genus Sulfurimonas, which is a known sulfur metabolizer. Our research seeks to further characterize microbial communities found at this interface in order to elucidate information regarding in situ sulfur cycling and the potential to tie this into subsurface/surface processes on Europa. Continued work will provide guidance

  15. Confirmation of putative stormwater impact on water quality at a Florida beach by microbial source tracking methods and structure of indicator organism populations.

    PubMed

    Brownell, M J; Harwood, V J; Kurz, R C; McQuaig, S M; Lukasik, J; Scott, T M

    2007-08-01

    The effect of a stormwater conveyance system on indicator bacteria levels at a Florida beach was assessed using microbial source tracking methods, and by investigating indicator bacteria population structure in water and sediments. During a rain event, regulatory standards for both fecal coliforms and Enterococcus spp. were exceeded, contrasting with significantly lower levels under dry conditions. Indicator bacteria levels were high in sediments under all conditions. The involvement of human sewage in the contamination was investigated using polymerase chain reaction (PCR) assays for the esp gene of Enterococcus faecium and for the conserved T antigen of human polyomaviruses, all of which were negative. BOX-PCR subtyping of Escherichia coli and Enterococcus showed higher population diversity during the rain event; and higher population similarity during dry conditions, suggesting that without fresh inputs, only a subset of the population survives the selective pressure of the secondary habitat. These data indicate that high indicator bacteria levels were attributable to a stormwater system that acted as a reservoir and conduit, flushing high levels of indicator bacteria to the beach during a rain event. Such environmental reservoirs of indicator bacteria further complicate the already questionable relationship between indicator organisms and human pathogens, and call for a better understanding of the ecology, fate and persistence of indicator bacteria.

  16. Planetary resources and astroecology. Planetary microcosm models of asteroid and meteorite interiors: electrolyte solutions and microbial growth--implications for space populations and panspermia.

    PubMed

    Mautner, Michael N

    2002-01-01

    Planetary microcosms were constructed using extracts from meteorites that simulate solutions in the pores of carbonaceous chondrites. The microcosms were found to support the growth of complex algal and microbial populations. Such astroecology experiments demonstrate how a diverse ecosystem could exist in fluids within asteroids, and in meteorites that land on aqueous planets. The microcosm solutions were obtained by extracting nutrient electrolytes under natural conditions from powders of the Allende (CV3) and Murchison (CM2) meteorites at low (0.02 g/ml) and high (10.0 g/ml) solid/solution ratios. The latter solutions contain > 3 mol/L electrolytes and about 10 g/L organics, that simulate natural fluids in asteroids during aqueous alteration and in the pores of meteorites, which can help prebiotic synthesis and the survival of early microorganisms. These solutions and wet solids were in fact found to support complex self-sustaining microbial communities with populations of 4 x 10(5) algae and 6 x 10(6) bacteria and fungi for long periods (> 8 months). The results show that planetary microcosms based on meteorites can: assay the fertilities of planetary materials; identify space bioresources; target astrobiology exploration; and model past and future space-based ecosystems. The results show that bioresources in the carbonaceous asteroids can sustain a biomass of 10(18) kg, comprising 10(32) microorganisms and a human population of 10(14). The results also suggest that protoplanetary nebulae can support and disperse microorganisms and can be therefore effective environments for natural and directed panspermia.

  17. Differential Incorporation of Carbon Substrates among Microbial Populations Identified by Field-Based, DNA Stable-Isotope Probing in South China Sea

    PubMed Central

    Xie, Xiabing; Jiao, Nianzhi

    2016-01-01

    To determine the adapted microbial populations to variant dissolved organic carbon (DOC) sources in the marine environment and improve the understanding of the interaction between microorganisms and marine DOC pool, field-based incubation experiments were carried out using supplemental 13C-labeled typical substrates D-glucose and D-glucosamine (D-Glc and D-GlcN, respectively), which are two important components in marine DOC pool in the South China Sea. 13C- and 12C-DNA were then fractionated by ultracentrifugation and the microbial community was analyzed by terminal-restriction fragment length polymorphism and 454 pyrosequencing of 16S rRNA gene. 12C-DNA-based communities showed relatively high similarities with their corresponding in situ communities, and their bacterial diversities were generally higher than 13C-DNA-based counterparts. Distinct differences in community composition were found between 13C- and 12C-DNA-based communities and between two substrate-supplemented 13C-DNA-based communities; these differences distinctly varied with depth and site. In most cases, there were more genera with relative abundances of >0.1% in D-Glc-incorporating communities than in D-GlcN-incorporating communities. The Roseobacter clade was one of the prominent actively substrate-incorporating bacterial populations in all 13C-DNA-based communities. Vibrio was another prominent actively D-GlcN-incorporating bacterial population in most incubations. However notably, different OTUs dominated this clade or genus in different treatments at different depths. Altogether, these results suggested that there were taxa-specific differences in DOC assimilations and, moreover, their differences varied among the typical water masses, which could have been caused by the variant compositions of original bacterial communities from different hydrological environments. This implies that ecologically, the levels of labile or recalcitrance of DOC can be maintained only in a specific environmental

  18. Using spatial accessibility to identify polyclinic service gaps and volume of under-served population in Singapore using Geographic Information System.

    PubMed

    Wong, Lai Yin; Heng, Bee Hoon; Cheah, Jason Tiang Seng; Tan, Chee Beng

    2012-01-01

    Primary care services in Singapore are provided by 18 Government-funded polyclinics and about 1200 private General Practitioners (GPs). This study aims to examine the spatial accessibility to polyclinics and identify service gaps, and suggest optimal sites using Geographic Information System (GIS) to aid in future planning. A national database containing 3.6 million polyclinic visits in 2006 were geo-analysed using ArcView GIS. Patients' travel impedance to the nearest polyclinic was computed using DriveTime to identify areas with the lowest spatial accessibility and highest volume of under-served population. Jurong West and Sembawang were ranked as top areas with poor spatial accessibility to polyclinic services. ArcGIS was used to identify optimal sites with the minimum accumulated distance impedance to this under-served population. If new facilities were set up at these identified sites, volume of visits by Jurong West and Sembawang patients who could access the nearest polyclinics within 4 km Euclidean distance from their residence would total at 123 000 and 93 000, respectively. Future efforts in polyclinic planning should take this into consideration to maximize patients' benefits and minimize patients' travelling costs in order to achieve social equity on healthcare access.

  19. Effect of decontamination agents on the microbial population, sensorial quality, and nutrient content of grated carrots (Daucus carota L.).

    PubMed

    Vandekinderen, Isabelle; Van Camp, John; Devlieghere, Frank; Veramme, Kim; Denon, Quenten; Ragaert, Peter; De Meulenaer, Bruno

    2008-07-23

    Several decontamination agents including water, sodium hypochlorite, peroxyacetic acid, neutral electrolyzed oxidizing water, and chlorine dioxide gas were tested for their effectiveness to reduce the natural microflora on grated carrots. Microbial reductions of the total aerobic count obtained after the different treatments varied between 0.11 and 3.29 log colony-forming units (cfu)/g. Whether or not a decontamination step induced significant changes in the sensory attributes of grated carrots is highly dependent on the type and concentration of disinfectant. To maintain the nutritional value, the influence of the decontamination agents on carotenoid content, alpha-tocopherol content, total phenols, and antioxidant capacity was studied. Besides the part of the nutrients that was leached away from the cutting areas by water, the nutrient losses caused by adding sanitizers were rather limited. Compared with the untreated carrots alpha-tocopherol content was, however, significantly reduced when 250 ppm of peroxyacetic acid (-80%) or 200 ppm of sodium hypochlorite (-59%) was used. Additional losses in carotenoid content were caused by contact with chlorine dioxide gas (-9%). On the condition of an optimized decontamination process toward time and concentration, the microbial quality of fresh-cut carrots could be improved without negatively influencing their sensory quality and nutrient content.

  20. Effect of monochloramine treatment on the microbial ecology of Legionella and associated bacterial populations in a hospital hot water system.

    PubMed

    Baron, Julianne L; Harris, J Kirk; Holinger, Eric P; Duda, Scott; Stevens, Mark J; Robertson, Charles E; Ross, Kimberly A; Pace, Norman R; Stout, Janet E

    2015-05-01

    Opportunistic pathogens, including Legionella spp. and non-tuberculous mycobacteria, can thrive in building hot water systems despite municipal and traditional on-site chlorine disinfection. Monochloramine is a relatively new approach to on-site disinfection, but the microbiological impact of on-site chloramine use has not been well studied. We hypothesized that comparison of the microbial ecology associated with monochloramine treatment versus no on-site treatment would yield highly dissimilar bacterial communities. Hot water samples were collected monthly from 7 locations for three months from two buildings in a Pennsylvania hospital complex supplied with common municipal water: (1) a hospital administrative building (no on-site treatment) and (2) an adjacent acute-care hospital treated on-site with monochloramine to control Legionella spp. Water samples were subjected to DNA extraction, rRNA PCR, and 454 pyrosequencing. Stark differences in the microbiome of the chloraminated water and the control were observed. Bacteria in the treated samples were primarily Sphingomonadales and Limnohabitans, whereas Flexibacter and Planctomycetaceae predominated in untreated control samples. Serendipitously, one sampling month coincided with dysfunction of the on-site disinfection system that resulted in a Legionella bloom detected by sequencing and culture. This study also demonstrates the potential utility of high-throughput DNA sequencing to monitor microbial ecology in water systems.

  1. Temperature and solids retention time control microbial population dynamics and volatile fatty acid production in replicated anaerobic digesters

    PubMed Central

    Vanwonterghem, Inka; Jensen, Paul D.; Rabaey, Korneel; Tyson, Gene W.

    2015-01-01

    Anaerobic digestion is a widely used technology for waste stabilization and generation of biogas, and has recently emerged as a potentially important process for the production of high value volatile fatty acids (VFAs) and alcohols. Here, three reactors were seeded with inoculum from a stably performing methanogenic digester, and selective operating conditions (37°C and 55°C; 12 day and 4 day solids retention time) were applied to restrict methanogenesis while maintaining hydrolysis and fermentation. Replicated experiments performed at each set of operating conditions led to reproducible VFA production profiles which could be correlated with specific changes in microbial community composition. The mesophilic reactor at short solids retention time showed accumulation of propionate and acetate (42 ± 2% and 15 ± 6% of CODhydrolyzed, respectively), and dominance of Fibrobacter and Bacteroidales. Acetate accumulation (>50% of CODhydrolyzed) was also observed in the thermophilic reactors, which were dominated by Clostridium. Under all tested conditions, there was a shift from acetoclastic to hydrogenotrophic methanogenesis, and a reduction in methane production by >50% of CODhydrolyzed. Our results demonstrate that shortening the SRT and increasing the temperature are effective strategies for driving microbial communities towards controlled production of high levels of specific volatile fatty acids. PMID:25683239

  2. Microbial populations and hydrocarbon biodegradation potentials in fertilized shoreline sediments affected by the T/V Exxon Valdez oil spill

    SciTech Connect

    Lindstrom, J.E.; Yeager, T.R.; Braddock, J.F.; Brown, E.J. ); Prince, R.C.; Grossman, M.J. ); Clark, J.C. )

    1991-09-01

    The effort to clean up the T/V Exxon Valdez oil spill in Prince William Sound, Alaska, included the use of fertilizers to accelerate natural microbial degradation of stranded oil. A program to monitor various environmental parameter associated with this technique took place during the summer of 1990. Microbiological assays for numbers of heterotrophic and oil-degrading microbes and their hydrocarbon mineralization potentials were performed in support of this program. Fertilizer addition resulted in higher hexadecane and phenanthrene mineralization potentials on treated plots than on untreated reference plots. Microbial numbers in treated and reference surface sediments were not significantly different immediately after the first nutrient application in May 1990. However, subsurface sediments different immediately after the first nutrient application in May 1990. However, subsurface sediments from treated plots had higher numbers of hydrocarbon degraders than did reference sediments shortly after treatment. The second application of fertilizer, later in summer, resulted in surface and subsurface increases in numbers of hydrocarbon degraders with respect to reference sediments at two of three study sites. Elevated mineralization potentials, coupled with increased numbers of hydrocarbon degraders, indicated that natural hydrocarbon biodegradation was enhanced. However, these microbiological measurements alone are not sufficient to determine in situ rates of crude oil biodegradation.

  3. Microbial populations and hydrocarbon biodegradation potentials in fertilized shoreline sediments affected by the T/V Exxon Valdez oil spill.

    PubMed

    Lindstrom, J E; Prince, R C; Clark, J C; Grossman, M J; Yeager, T R; Braddock, J F; Brown, E J

    1991-09-01

    The effort of clean up the T/V Exxon Valdez oil spill in Prince William Sound, Alaska, included the use of fertilizers to accelerate natural microbial degradation of stranded oil. A program to monitor various environmental parameters associated with this technique took place during the summer of 1990. Microbiological assays for numbers of heterotrophic and oil-degrading microbes and their hydrocarbon mineralization potentials were performed in support of this program. Fertilizer addition resulted in higher hexadecane and phenanthrene mineralization potentials on treated plots than on untreated reference plots. Microbial numbers in treated and reference surface sediments were not significantly different immediately after the first nutrient application in May 1990. However, subsurface sediments from treated plots had higher numbers of hydrocarbon degraders than did reference sediments shortly after treatment. The second application of fertilizer, later in summer, resulted in surface and subsurface increases in numbers of hydrocarbon degraders with respect to reference sediments at two of the three study sites. Elevated mineralization potentials, coupled with increased numbers of hydrocarbon degraders, indicated that natural hydrocarbon biodegradation was enhanced. However, these microbiological measurements alone are not sufficient to determine in situ rates of crude oil biodegradation.

  4. Temperature and solids retention time control microbial population dynamics and volatile fatty acid production in replicated anaerobic digesters

    NASA Astrophysics Data System (ADS)

    Vanwonterghem, Inka; Jensen, Paul D.; Rabaey, Korneel; Tyson, Gene W.

    2015-02-01

    Anaerobic digestion is a widely used technology for waste stabilization and generation of biogas, and has recently emerged as a potentially important process for the production of high value volatile fatty acids (VFAs) and alcohols. Here, three reactors were seeded with inoculum from a stably performing methanogenic digester, and selective operating conditions (37°C and 55°C 12 day and 4 day solids retention time) were applied to restrict methanogenesis while maintaining hydrolysis and fermentation. Replicated experiments performed at each set of operating conditions led to reproducible VFA production profiles which could be correlated with specific changes in microbial community composition. The mesophilic reactor at short solids retention time showed accumulation of propionate and acetate (42 +/- 2% and 15 +/- 6% of CODhydrolyzed, respectively), and dominance of Fibrobacter and Bacteroidales. Acetate accumulation (>50% of CODhydrolyzed) was also observed in the thermophilic reactors, which were dominated by Clostridium. Under all tested conditions, there was a shift from acetoclastic to hydrogenotrophic methanogenesis, and a reduction in methane production by >50% of CODhydrolyzed. Our results demonstrate that shortening the SRT and increasing the temperature are effective strategies for driving microbial communities towards controlled production of high levels of specific volatile fatty acids.

  5. Comparison of indigenous and exogenous microbial populations during slurry phase biodegradation of long-term hydrocarbon-contaminated soil.

    PubMed

    Aburto-Medina, Arturo; Adetutu, Eric M; Aleer, Sam; Weber, John; Patil, Sayali S; Sheppard, Petra J; Ball, Andrew S; Juhasz, Albert L

    2012-11-01

    In this study, a number of slurry-phase strategies were trialled over a 42 day period in order to determine the efficacy of bioremediation for long-term hydrocarbon-contaminated soil (145 g kg(-1) C(10)-C(40)). The addition of activated sludge and nutrients to slurries (bioaugmentation) resulted in enhanced hydrocarbon removal (51.6 ± 8.5 %) compared to treatments receiving only nutrients (enhanced natural attenuation [ENA]; 41.3 ± 6.4 %) or no amendments (natural attenuation; no significant hydrocarbon removal, P < 0.01). This data suggests that the microbial community in the activated sludge inoculum contributed to the enhanced removal of hydrocarbons in ENA slurries. Microbial diversity in slurries was monitored using DGGE with dominant bands excised and sequenced for identification. Applying the different bioremediation strategies resulted in the formation of four distinct community clusters associated with the activated sludge (inoculum), bioaugmentation strategy at day 0, bioaugmentation strategy at weeks 2-6 and slurries with autoclaved sludge and nutrient additions (bioaugmentation negative control). While hydrocarbon-degrading bacteria genera (e.g. Aquabacterium and Haliscomenobacter) were associated with the hydrocarbon-contaminated soil, bioaugmentation of soil slurries with activated sludge resulted in the introduction of bacteria associated with hydrocarbon degradation (Burkholderiales order and Klebsiella genera) which presumably contributed to the enhanced efficacy for this slurry strategy.

  6. Dynamics and persistence of Dead Sea microbial populations as shown by high-throughput sequencing of rRNA.

    PubMed

    Rhodes, Matthew E; Oren, Aharon; House, Christopher H

    2012-04-01

    16S rRNA amplicon libraries from a haloarchaeal bloom in the hypersaline Dead Sea in 1992 were analyzed together with the 2007 residual population and simulated blooms in experimental mesocosms. Significant population shifts were observed during the bloom, and surprisingly a signature from the bloom was retained 15 years later.

  7. Effect of Saccharomyces cerevisiae on alfalfa nutrient degradation characteristics and rumen microbial populations of steers fed diets with different concentrate-to-forage ratios

    PubMed Central

    2014-01-01

    Live yeast (Saccharomyces cerevisiae) constitutes an effective additive for animal production; its probiotic effect may be related to the concentrate-to-forage ratio (CTFR). The objective of this study was to assess the effects of S. cerevisiae (SC) on fiber degradation and rumen microbial populations in steers fed diets with different levels of dietary concentrate. Ten Simmental × Local crossbred steers (450 ± 50 kg BW) were assigned to a control group or an SC group. Both groups were fed the same basal diet but the SC group received SC supplementation (8 × 109 cfu/h/d through the ruminal fistula) following a two-period crossover design. Each period consisted of four phases, each of which lasted 17 d: 10 d for dietary adaptation, 6 d for degradation study, and 1 d for rumen sample collection. From the 1st to the 4th phase, steers were fed in a stepwise fashion with increasing CTFRs, i.e., 30:70, 50:50, 70:30, and 90:10. The kinetics of dry matter and fiber degradation of alfalfa pellets were evaluated; the rumen microbial populations were detected using real-time PCR. The results revealed no significant (P > 0.05) interactions between dietary CTFR and SC for most parameters. Dietary CTFR had a significant effect (P < 0.01) on degradation characteristics of alfalfa pellets and the copies of rumen microorganism; the increasing concentrate level resulted in linear, quadratic or cubic variation trend for these parameters. SC supplementation significantly (P < 0.05) affected dry matter (DM) and neutral detergent fiber (NDF) degradation rates (cDM, cNDF) and NDF effective degradability (EDNDF). Compared with the control group, there was an increasing trend of rumen fungi and protozoa in SC group (P < 0.1); copies of total bacteria in SC group were significantly higher (P < 0.05). Additionally, percentage of Ruminobacter amylophilus was significantly lower (P < 0.05) but percentage of Selenomonas ruminantium was significantly

  8. Assessing evidence of inequalities in access to medication for diabetic populations in low- and middle-income countries: a systematic review

    PubMed Central

    Christiani, Yodi; Dhippayom, Teerapon; Chaiyakunapruk, Nathorn

    2016-01-01

    Background Inequalities in access to medications among people diagnosed with diabetes inlow- and middle-income countries (LMICs) is a public health concern since untreated diabetes can lead to severe complications and premature death. Objective To assess evidence of inequalities in access to medication for diabetes in adult populations of people with diagnosed diabetes in LMICs. Design We conducted a systematic review of the literature using the PRISMA-Equity guidelines. A search of five databases – PubMed, Cochrane, CINAHL, PsycINFO, and EMBASE – was conducted from inception to November 2015. Using deductive content analysis, information extracted from the selected articles was analysed according to the PRISMA-Equity guidelines, based on exposure variables (place of residence, race/ethnicity, occupation, gender, religion, education, socio-economic status, social capital, and others). Results Fifteen articles (seven quantitative and eight qualitative studies) are included in this review. There were inconsistent findings between studies conducted in different countries and regions although financial and geographic barriers generally contributed to inequalities in access to diabetes medications. The poor, those with relatively low education, and people living in remote areas had less access to diabetes medications. Furthermore, we found that the level of government political commitment through primary health care and in the provision of essential medicines was an important factor in promoting access to medications. Conclusions The review indicates that inequalities exist in accessing medication among diabetic populations, although this was not evident in all LMICs. Further research is needed to assess the social determinants of health and medication access for people with diabetes in LMICs. PMID:27938647

  9. Assessing evidence of inequalities in access to medication for diabetic populations in low- and middle-income countries: a systematic review.

    PubMed

    Christiani, Yodi; Dhippayom, Teerapon; Chaiyakunapruk, Nathorn

    2016-01-01

    Background Inequalities in access to medications among people diagnosed with diabetes in low- and middle-income countries (LMICs) is a public health concern since untreated diabetes can lead to severe complications and premature death. Objective To assess evidence of inequalities in access to medication for diabetes in adult populations of people with diagnosed diabetes in LMICs. Design We conducted a systematic review of the literature using the PRISMA-Equity guidelines. A search of five databases - PubMed, Cochrane, CINAHL, PsycINFO, and EMBASE - was conducted from inception to November 2015. Using deductive content analysis, information extracted from the selected articles was analysed according to the PRISMA-Equity guidelines, based on exposure variables (place of residence, race/ethnicity, occupation, gender, religion, education, socio-economic status, social capital, and others). Results Fifteen articles (seven quantitative and eight qualitative studies) are included in this review. There were inconsistent findings between studies conducted in different countries and regions although financial and geographic barriers generally contributed to inequalities in access to diabetes medications. The poor, those with relatively low education, and people living in remote areas had less access to diabetes medications. Furthermore, we found that the level of government political commitment through primary health care and in the provision of essential medicines was an important factor in promoting access to medications. Conclusions The review indicates that inequalities exist in accessing medication among diabetic populations, although this was not evident in all LMICs. Further research is needed to assess the social determinants of health and medication access for people with diabetes in LMICs.

  10. Population.

    ERIC Educational Resources Information Center

    King, Pat; Landahl, John

    This pamphlet has been prepared in response to a new problem, a rapidly increasing population, and a new need, population education. It is designed to help teachers provide their students with some basic population concepts with stress placed on the elements of decision making. In the first section of the pamphlet, some of the basic concepts of…

  11. [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.

  12. Hydrophobicity of diverse bacterial populations in activated sludge and biofilm revealed by microbial adhesion to hydrocarbons assay and high-throughput sequencing.

    PubMed

    Chao, Yuanqing; Guo, Feng; Fang, Herbert H P; Zhang, Tong

    2014-02-01

    Cell hydrophobicity is one of the key physicochemical properties of bacteria in activated sludge (AS) and biofilms can influence the efficient operation of wastewater treatment plants (WWTPs). In the present study the cell hydrophobicity of diverse bacterial populations in AS and biofilms from the Shatin and Stanley WWTPs of Hong Kong was characterized by combining the microbial adhesion to hydrocarbons (MATH) assay with the Illumina high-throughput sequencing. The results indicated that, at the phylum level, a majority of bacteria in AS and biofilms showed medium hydrophobicity. Most of the top 20 bacterial genera in the AS samples were hydrophilic. However, the top 20 genera in biofilms showed higher hydrophobicity than in the top 20 genera in AS samples, suggesting more hydrophobic bacteria existed in biofilms than in AS. Meanwhile, the hydrophobicity of two specific bacterial groups, including foaming and biosurfactant-producing bacteria, were also evaluated. The results demonstrated that, by combining the MATH assay with the Illumina sequencing approach, bacterial hydrophobicity could be evaluated with high efficiency and coverage in complex systems with high microbial diversity, e.g. AS and biofilms in WWTPs.

  13. Microbial population in the biomass adhering to supporting material in a packed-bed reactor degrading organic solid waste.

    PubMed

    Sasaki, Kengo; Haruta, Shin; Ueno, Yoshiyuki; Ishii, Masaharu; Igarashi, Yasuo

    2007-06-01

    An anaerobic packed-bed reactor using carbon fiber textiles (CFT) as the supporting material was continuously operated using an artificial garbage slurry. 16S rRNA gene analysis showed that many bacteria in the biomass adhering to CFT were closely related to those observed from other anaerobic environments, although a wide variety of unidentified bacteria were also found. Dot blot hybridization results clarified that 16S rRNA levels of methanogens in the adhering biomass were higher than those in the effluent. Based on microscopic observation, the adhering biomass consisted of microorganisms, organic material, and void areas. Bacteria and Archaea detected by fluorescence in situ hybridization were distributed from the surface to the inner regions of the adhering biomass. Methanosarcina sp. tended to be more abundant in the inner part of the adhering biomass than at the surface. This is the first report to elucidate the structure of the microbial community on CFT in a packed-bed reactor.

  14. Changes of the microbial population structure in an overloaded fed-batch biogas reactor digesting maize silage.

    PubMed

    Kampmann, Kristina; Ratering, Stefan; Geißler-Plaum, Rita; Schmidt, Michael; Zerr, Walter; Schnell, Sylvia

    2014-12-01

    Two parallel, stable operating biogas reactors were fed with increasing amounts of maize silage to monitor microbial community changes caused by overloading. Changes of microorganisms diversity revealed by SSCP (single strand conformation polymorphism) indicating an acidification before and during the pH-value decrease. The earliest indicator was the appearance of a Methanosarcina thermophila-related species. Diversity of dominant fermenting bacteria within Bacteroidetes, Firmicutes and other Bacteria decreased upon overloading. Some species became dominant directly before and during acidification and thus could be suitable as possible indicator organisms for detection of futurity acidification. Those bacteria were related to Prolixibacter bellariivorans and Streptococcus infantarius subsp. infantarius. An early detection of community shifts will allow better feeding management for optimal biogas production.

  15. Population dynamics of transgenic strain Escherichia coli Z905/pPHL7 in freshwater and saline lake water microcosms with differing microbial community structures

    NASA Astrophysics Data System (ADS)

    Popova, L. Yu.; Kargatova, T. V.; Ganusova, E. E.; Lobova, T. I.; Boyandin, A. N.; Mogilnaya, O. A.; Pechurkin, N. S.

    Populations of Escherichia coli Z905/pPHL7, a transgenic microorganism, were heterogenic in the expression of plasmid genes when adapting to the conditions of water microcosms of various mineralization levels and structure of microbial community. This TM has formed two subpopulations (ampicillin-resistant and ampicillin-sensitive) in every microcosm. Irrespective of mineralization level of a microcosm, when E. coli Z905/pPHL7 alone was introduced, the ampicillin-resistant subpopulation prevailed, while introduction of the TM together with indigenous bacteria led to the dominance of the ampicillin-sensitive subpopulation. A high level of lux gene expression maintained longer in the freshwater microcosms than in sterile saline lake water microcosms. A horizontal gene transfer has been revealed between the jointly introduced TM and Micrococcus sp. 9/pSH1 in microcosms with the Lake Shira sterile water.

  16. Population dynamics of transgenic strain Escherichia coli Z905/pPHL7 in freshwater and saline lake water microcosms with differing microbial community structures

    NASA Technical Reports Server (NTRS)

    Popova, L. Yu; Kargatova, T. V.; Ganusova, E. E.; Lobova, T. I.; Boyandin, A. N.; Mogilnaya, O. A.; Pechurkin, N. S.

    2005-01-01

    Populations of Escherichia coli Z905/pPHL7, a transgenic microorganism, were heterogenic in the expression of plasmid genes when adapting to the conditions of water microcosms of various mineralization levels and structure of microbial community. This TM has formed two subpopulations (ampicillin-resistant and ampicillin-sensitive) in every microcosm. Irrespective of mineralization level of a microcosm, when E. coli Z905/pPHL7 alone was introduced, the ampicillin-resistant subpopulation prevailed, while introduction of the TM together with indigenous bacteria led to the dominance of the ampicillin-sensitive subpopulation. A high level of lux gene expression maintained longer in the freshwater microcosms than in sterile saline lake water microcosms. A horizontal gene transfer has been revealed between the jointly introduced TM and Micrococcus sp. 9/pSH1 in microcosms with the Lake Shira sterile water. c2005 COSPAR. Published by Elsevier Ltd. All rights reserved.

  17. Distinct microbial populations are tightly linked to the profile of dissolved iron in the methanic sediments of the Helgoland mud area, North Sea.

    PubMed

    Oni, Oluwatobi; Miyatake, Tetsuro; Kasten, Sabine; Richter-Heitmann, Tim; Fischer, David; Wagenknecht, Laura; Kulkarni, Ajinkya; Blumers, Mathias; Shylin, Sergii I; Ksenofontov, Vadim; Costa, Benilde F O; Klingelhöfer, Göstar; Friedrich, Michael W

    2015-01-01

    Iron reduction in subseafloor sulfate-depleted and methane-rich marine sediments is currently a subject of interest in subsurface geomicrobiology. While iron reduction and microorganisms involved have been well studied in marine surface sediments, little is known about microorganisms responsible for iron reduction in deep methanic sediments. Here, we used quantitative PCR-based 16S rRNA gene copy numbers and pyrosequencing-based relative abundances of bacteria and archaea to investigate covariance between distinct microbial populations and specific geochemical profiles in the top 5 m of sediment cores from the Helgoland mud area, North Sea. We found that gene copy numbers of bacteria and archaea were specifically higher around the peak of dissolved iron in the methanic zone (250-350 cm). The higher copy numbers at these depths were also reflected by the relative sequence abundances of members of the candidate division JS1, methanogenic and Methanohalobium/ANME-3 related archaea. The distribution of these populations was strongly correlated to the profile of pore-water Fe(2+) while that of Desulfobacteraceae corresponded to the pore-water sulfate profile. Furthermore, specific JS1 populations also strongly co-varied with the distribution of Methanosaetaceae in the methanic zone. Our data suggest that the interplay among JS1 bacteria, methanogenic archaea and Methanohalobium/ANME-3-related archaea may be important for iron reduction and methane cycling in deep methanic sediments of the Helgoland mud area and perhaps in other methane-rich depositional environments.

  18. Distinct microbial populations are tightly linked to the profile of dissolved iron in the methanic sediments of the Helgoland mud area, North Sea

    PubMed Central

    Oni, Oluwatobi; Miyatake, Tetsuro; Kasten, Sabine; Richter-Heitmann, Tim; Fischer, David; Wagenknecht, Laura; Kulkarni, Ajinkya; Blumers, Mathias; Shylin, Sergii I.; Ksenofontov, Vadim; Costa, Benilde F. O.; Klingelhöfer, Göstar; Friedrich, Michael W.

    2015-01-01

    Iron reduction in subseafloor sulfate-depleted and methane-rich marine sediments is currently a subject of interest in subsurface geomicrobiology. While iron reduction and microorganisms involved have been well studied in marine surface sediments, little is known about microorganisms responsible for iron reduction in deep methanic sediments. Here, we used quantitative PCR-based 16S rRNA gene copy numbers and pyrosequencing-based relative abundances of bacteria and archaea to investigate covariance between distinct microbial populations and specific geochemical profiles in the top 5 m of sediment cores from the Helgoland mud area, North Sea. We found that gene copy numbers of bacteria and archaea were specifically higher around the peak of dissolved iron in the methanic zone (250–350 cm). The higher copy numbers at these depths were also reflected by the relative sequence abundances of members of the candidate division JS1, methanogenic and Methanohalobium/ANME-3 related archaea. The distribution of these populations was strongly correlated to the profile of pore-water Fe2+ while that of Desulfobacteraceae corresponded to the pore-water sulfate profile. Furthermore, specific JS1 populations also strongly co-varied with the distribution of Methanosaetaceae in the methanic zone. Our data suggest that the interplay among JS1 bacteria, methanogenic archaea and Methanohalobium/ANME-3-related archaea may be important for iron reduction and methane cycling in deep methanic sediments of the Helgoland mud area and perhaps in other methane-rich depositional environments. PMID:25983723

  19. Microbial Populations in Naked Neck Chicken Ceca Raised on Pasture Flock Fed with Commercial Yeast Cell Wall Prebiotics via an Illumina MiSeq Platform

    PubMed Central

    Park, Si Hong; Lee, Sang In; Ricke, Steven C.

    2016-01-01

    Prebiotics are non-digestible carbohydrate dietary supplements that selectively stimulate the growth of one or more beneficial bacteria in the gastrointestinal tract of the host. These bacteria can inhibit colonization of pathogenic bacteria by producing antimicrobial substances such as short chain fatty acids (SCFAs) and competing for niches with pathogens within the gut. Pasture flock chickens are generally raised outdoors with fresh grass, sunlight and air, which represents different environmental growth conditions compared to conventionally raised chickens. The purpose of this study was to evaluate the difference in microbial populations from naked neck chicken ceca fed with commercial prebiotics derived from brewer’s yeast cell wall via an Illumina MiSeq platform. A total of 147 day-of-hatch naked neck chickens were distributed into 3 groups consisted of 1) C: control (no prebiotic), 2) T1: Biolex® MB40 with 0.2%, and 3) T2: Leiber® ExCel with 0.2%, consistently supplemented prebiotics during the experimental period. At 8 weeks, a total of 15 birds from each group were randomly selected and ceca removed for DNA extraction. The Illumina Miseq platform based on V4 region of 16S rRNA gene was applied for microbiome analysis. Both treatments exhibited limited impact on the microbial populations at the phylum level, with no significant differences in the OTU number of Bacteroidetes among groups and an increase of Proteobacteria OTUs for the T1 (Biolex® MB40) group. In addition there was a significant increase of genus Faecalibacterium OTU, phylum Firmicutes. According to the development of next generation sequencing (NGS), microbiome analysis based on 16S rRNA gene proved to be informative on the prebiotic impact on poultry gut microbiota in pasture-raised naked neck birds. PMID:26992104

  20. Microbial Populations in Naked Neck Chicken Ceca Raised on Pasture Flock Fed with Commercial Yeast Cell Wall Prebiotics via an Illumina MiSeq Platform.

    PubMed

    Park, Si Hong; Lee, Sang In; Ricke, Steven C

    2016-01-01

    Prebiotics are non-digestible carbohydrate dietary supplements that selectively stimulate the growth of one or more beneficial bacteria in the gastrointestinal tract of the host. These bacteria can inhibit colonization of pathogenic bacteria by producing antimicrobial substances such as short chain fatty acids (SCFAs) and competing for niches with pathogens within the gut. Pasture flock chickens are generally raised outdoors with fresh grass, sunlight and air, which represents different environmental growth conditions compared to conventionally raised chickens. The purpose of this study was to evaluate the difference in microbial populations from naked neck chicken ceca fed with commercial prebiotics derived from brewer's yeast cell wall via an Illumina MiSeq platform. A total of 147 day-of-hatch naked neck chickens were distributed into 3 groups consisted of 1) C: control (no prebiotic), 2) T1: Biolex® MB40 with 0.2%, and 3) T2: Leiber® ExCel with 0.2%, consistently supplemented prebiotics during the experimental period. At 8 weeks, a total of 15 birds from each group were randomly selected and ceca removed for DNA extraction. The Illumina Miseq platform based on V4 region of 16S rRNA gene was applied for microbiome analysis. Both treatments exhibited limited impact on the microbial populations at the phylum level, with no significant differences in the OTU number of Bacteroidetes among groups and an increase of Proteobacteria OTUs for the T1 (Biolex® MB40) group. In addition there was a significant increase of genus Faecalibacterium OTU, phylum Firmicutes. According to the development of next generation sequencing (NGS), microbiome analysis based on 16S rRNA gene proved to be informative on the prebiotic impact on poultry gut microbiota in pasture-raised naked neck birds.

  1. Effects of various plant protein sources in high-quality feed block on feed intake, rumen fermentation, and microbial population in swamp buffalo.

    PubMed

    Foiklang, Suban; Wanapat, Metha; Toburan, Wetchasit

    2011-12-01

    This study was designed to determine effect of various plant protein sources in high-quality feed block (HQFB) on feed intake, rumen fermentation, and microbial population in swamp buffalo. Four rumen-fistulated swamp buffaloes (Bubalus bubalis) were randomly assigned according to a 4 × 4 Latin square design. Four kinds of plant protein sources (coarse rice bran (CRB), cassava hay (CH), Phaseolus calcaratus hay, and mulberry hay (MH)) were mixed in the HQFB. HQFBs were allowed to be licked at free choice, and urea-lime-treated rice straw (ULRS) were fed ad libitum. It was found that bacterial population and fungal zoospores in CH-fed group tended to be higher than those in other groups. Moreover, protozoal population in CH, P. calcaratus hay, and MH were lower than those in CRB supplemented group (P < 0.05). Cellulolytic bacterial population was highest in CH-fed group while proteolytic bacteria population was highest in P. calcaratus hay-fed group (P < 0.05). CH-fed group had higher ULRS intake than those in other groups (P < 0.05). Nutrient digestibility of CP, NDF, and ADF in CH-fed group was significantly higher than those in other groups (P < 0.05). Total VFA was highest in CH-fed group (P < 0.05). N absorption was highest in CH-fed group (P < 0.05). Based on this study, it could be concluded that cassava hay, P. calcaratus hay, and mulberry hay are potential to be used as protein sources in the HQFBs especially cassava hay.

  2. IPUMS-International High Precision Population Census Microdata Samples: Balancing the Privacy-Quality Tradeoff by Means of Restricted Access Extracts

    PubMed Central

    McCaa, Robert; Ruggles, Steven; Davern, Michael; Swenson, Tami; Palipudi, Krishna Mohan

    2016-01-01

    A breakthrough in the tradeoff between privacy and data quality has been achieved for restricted access to population census microdata samples. The IPUMS-International website, as of June 2006, offers integrated microdata for 47 censuses, totaling more than 140 million person records, with 13 countries represented. Over the next four years, the global collaboratory led by the Minnesota Population Center, with major funding by the United States National Science Foundation and the National Institutes of Health, will disseminate samples for more than 100 additional censuses. The statistical authorities of more than 50 countries have already entrusted microdata to the project under a uniform memorandum of understanding which permits researchers to obtain custom extracts without charge and to analyze the microdata using their own hardware and software. This paper describes the disclosure control methods used by the IPUMS initiative to protect privacy and to provide access to high precision census microdata samples.

  3. Direct and indirect effects of temperature on the population dynamics and ecosystem functioning of aquatic microbial ecosystems.

    PubMed

    Beveridge, Oliver S; Petchey, Owen L; Humphries, Stuart

    2010-11-01

    1. While much is known about the direct effect that temperature can have on aquatic communities, less is known about its indirect effect via the temperature dependence of viscosity and temperature-dependent trophic interactions. 2. We manipulated the temperature (5-20 °C) and the viscosity (equivalent to 5-20 °C) of water in laboratory-based bacteria-protist communities. Communities contained food chains with one, two or three trophic levels. Responses measured were population dynamics (consumer carrying capacity and growth rate, average species population density, and the coefficient of variation of population density through time) and ecosystem function (decomposition). 3. Temperature, viscosity and food chain length produced significant responses in population dynamics. Temperature-dependent viscosity had a significant effect on the carrying capacity and growth rates of consumers, as well as the average density of the top predator. Overall, indirect effects of temperature via changes in viscosity were subtle in comparison to the indirect effect of temperature via trophic interactions. 4. Our results highlight the importance of direct and indirect effects of temperature, mediated through trophic interactions and physical changes in the environment, both for population dynamics and ecosystem processes. Future mechanistic modelling of effects of environmental change on species will benefit from distinguishing the different mechanisms of the overall effect of temperature.

  4. Quantitative Analysis of Small-Subunit rRNA Genes in Mixed Microbial Populations via 5′-Nuclease Assays

    PubMed Central

    Suzuki, Marcelino T.; Taylor, Lance T.; DeLong, Edward F.

    2000-01-01

    Few techniques are currently available for quantifying specific prokaryotic taxa in environmental samples. Quantification of specific genotypes has relied mainly on oligonucleotide hybridization to extracted rRNA or intact rRNA in whole cells. However, low abundance and cellular rRNA content limit the application of these techniques in aquatic environments. In this study, we applied a newly developed quantitative PCR assay (5′-nuclease assay, also known as TaqMan) to quantify specific small-subunit (SSU) rRNA genes (rDNAs) from uncultivated planktonic prokaryotes in Monterey Bay. Primer and probe combinations for quantification of SSU rDNAs at the domain and group levels were developed and tested for specificity and quantitative reliability. We examined the spatial and temporal variations of SSU rDNAs from Synechococcus plus Prochlorococcus and marine Archaea and compared the results of the quantitative PCR assays to those obtained by alternative methods. The 5′-nuclease assays reliably quantified rDNAs over at least 4 orders of magnitude and accurately measured the proportions of genes in artificial mixtures. The spatial and temporal distributions of planktonic microbial groups measured by the 5′-nuclease assays were similar to the distributions estimated by quantitative oligonucleotide probe hybridization, whole-cell hybridization assays, and flow cytometry. PMID:11055900

  5. Effect of conventional chemical treatment on the microbial population in a biofouling layer of reverse osmosis systems.

    PubMed

    Bereschenko, L A; Prummel, H; Euverink, G J W; Stams, A J M; van Loosdrecht, M C M

    2011-01-01

    The impact of conventional chemical treatment on initiation and spatiotemporal development of biofilms on reverse osmosis (RO) membranes was investigated in situ using flow cells placed in parallel with the RO system of a full-scale water treatment plant. The flow cells got the same feed (extensively pre-treated fresh surface water) and operational conditions (temperature, pressure and membrane flux) as the full-scale installation. With regular intervals both the full-scale RO membrane modules and the flow cells were cleaned using conventional chemical treatment. For comparison some flow cells were not cleaned. Sampling was done at different time periods of flow cell operation (i.e., 1, 5, 10 and 17 days and 1, 3, 6 and 12 months). The combination of molecular (FISH, DGGE, clone libraries and sequencing) and microscopic (field emission scanning electron, epifluorescence and confocal laser scanning microscopy) techniques made it possible to thoroughly analyze the abundance, composition and 3D architecture of the emerged microbial layers. The results suggest that chemical treatment facilitates initiation and subsequent maturation of biofilm structures on the RO membrane and feed-side spacer surfaces. Biofouling control might be possible only if the cleaning procedures are adapted to effectively remove the (dead) biomass from the RO modules after chemical treatment.

  6. Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments

    PubMed Central

    Musilova, Lucie; Ridl, Jakub; Polivkova, Marketa; Macek, Tomas; Uhlik, Ondrej

    2016-01-01

    Secondary plant metabolites (SPMEs) play an important role in plant survival in the environment and serve to establish ecological relationships between plants and other organisms. Communication between plants and microorganisms via SPMEs contained in root exudates or derived from litter decomposition is an example of this phenomenon. In this review, the general aspects of rhizodeposition together with the significance of terpenes and phenolic compounds are discussed in detail. We focus specifically on the effect of SPMEs on microbial community structure and metabolic activity in environments contaminated by polychlorinated biphenyls (PCBs) and polyaromatic hydrocarbons (PAHs). Furthermore, a section is devoted to a complex effect of plants and/or their metabolites contained in litter on bioremediation of contaminated sites. New insights are introduced from a study evaluating the effects of SPMEs derived during decomposition of grapefruit peel, lemon peel, and pears on bacterial communities and their ability to degrade PCBs in a long-term contaminated soil. The presented review supports the “secondary compound hypothesis” and demonstrates the potential of SPMEs for increasing the effectiveness of bioremediation processes. PMID:27483244

  7. A short overview of the microbial population in clouds: Potential roles in atmospheric chemistry and nucleation processes

    NASA Astrophysics Data System (ADS)

    Delort, Anne-Marie; Vaïtilingom, Mickael; Amato, Pierre; Sancelme, Martine; Parazols, Marius; Mailhot, Gilles; Laj, Paolo; Deguillaume, Laurent

    2010-11-01

    Recent studies showed that living microorganisms, including bacteria, fungi and yeasts, are present in the atmospheric water phase (fog and clouds) and their role in chemical processes may have been underestimated. At the interface between atmospheric science and microbiology, information about this field of science suffers from the fact that not all recent findings are efficiently conveyed to both scientific communities. The purpose of this paper is therefore to provide a short overview of recent work linked to living organisms in the atmospheric water phase, from their activation to cloud droplets and ice crystal, to their potential impact on atmospheric chemical processes. This paper is focused on the microorganisms present in clouds and on the role they could play in atmospheric chemistry and nucleation processes. First, the life cycle of microorganisms via the atmosphere is examined, including their aerosolization from sources, their integration into clouds and their wet deposition on the ground. Second, special attention is paid to the possible impacts of microorganisms on liquid and ice nucleation processes. Third, a short description of the microorganisms that have been found in clouds and their variability in numbers and diversity is presented, emphasizing some specific characteristics that could favour their occurrence in cloud droplets. In the last section, the potential role of microbial activity as an alternative route to photochemical reaction pathways in cloud chemistry is discussed.

  8. Changes of microbial populations in a ship's ballast water and sediments on a voyage from Japan to Qatar.

    PubMed

    Mimura, Haruo; Katakura, Ryo; Ishida, Hiroshi

    2005-07-01

    Colony-forming eutrophic marine microorganisms in ballast water were counted in samples taken on board in 2002 and 2003. In the ballast water in Japan, viable cell numbers were highly variable but not by more than 10(5.1) colony-forming units (CFU)ml(-1) regardless of season. Even when ballast water was discharged offshore, values varied but not by more than 10(5.0) CFUml(-1). The effectiveness of the ballast water exchange was unconfirmed, except for the February 2003 voyage. No microbial colonies were counted in the reloaded ballast water in the high seas on that voyage, which contributed to the reduction of the total number of viable cells sampled in the discharged ballast water at the Ras Laffan port in Qatar. In sediment samples, the values of 10(5.2) - 10(6.0) CFUml(-1) were estimated for all seasons in which voyages took place. The maximum of the marine Vibrio species, 110 CFUml(-1), was observed in the ballast water sample taken in July 2003. The estimated total viable cell numbers in sediments were higher than those counted in the ballast water throughout the experiments, indicating the importance of sediment management as well as ballast water management on vessels traveling from Japan.

  9. 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,…

  10. Comparative assessment of bacterial inoculation and propionic acid treatment of aerobic stability and microbial populations of ensiled high-moisture ear corn.

    PubMed

    Sebastian, S; Phillip, L E; Fellner, V; Idziak, E S

    1996-02-01

    High-moisture ear corn (HMEC) was untreated, treated with propionic acid (PA), or inoculated with a mixture of Lactobacillus plantarum and Enterococcus faecium and allowed to ensile in laboratory silos for 0, 7, 21, 42, 138, or 202 d. The silages were evaluated for fermentation quality, microbial populations, and aerobic stability. In all treatments, silage pH declined rapidly within 7 d, but the rate of decline seemed greatest with the inoculum. The lactic acid content of inoculated HMEC was higher (P < .05) than that of control of PA-treated HMEC. Regardless of treatment, the population of lactic acid bacteria (LAB) increased (P < .1) up to 7 to 21 d of fermentation then declined; LAB counts decreased (P < .05) up to 42 d in control and PA-treated silage but continued to decline until 138 d for inoculated silage. Yeast and mold counts tended to decrease up to 42 d of ensiling then decreased (P < .05) as fermentation progressed. Between 138 and 202 d of ensiling, the control silage showed a marked increase (P < .10) in pH and yeast and mold populations, providing evidence of secondary fermentation; PA treatment and bacterial inoculation prevented secondary fermentation. Inoculation tended to reduce estimates of sample temperature for silage stored for 138 d and exposed to air, but not for the corresponding silage stored for 202 d. Treatment with PA prevented the loss (P > .05) of acetic acid and the rise (P > .05) in pH during air exposure of the 138-d silage; both control and PA-treated silage showed an increase (P < .05) in yeast and mold populations, but the increments were 38% and 23%, respectively. Compared with PA, the relative efficacy of inoculation in improving aerobic spoilage of HMEC depended on the period of silo storage and the criterion used to assess aerobic stability.

  11. Predominant Acidilobus-Like Populations from Geothermal Environments in Yellowstone National Park Exhibit Similar Metabolic Potential in Different Hypoxic Microbial Communities

    PubMed Central

    Jay, Z. J.; Rusch, D. B.; Tringe, S. G.; Bailey, C.; Jennings, R. M.

    2014-01-01

    High-temperature (>70°C) ecosystems in Yellowstone National Park (YNP) provide an unparalleled opportunity to study chemotrophic archaea and their role in microbial community structure and function under highly constrained geochemical conditions. Acidilobus spp. (order Desulfurococcales) comprise one of the dominant phylotypes in hypoxic geothermal sulfur sediment and Fe(III)-oxide environments along with members of the Thermoproteales and Sulfolobales. Consequently, the primary goals of the current study were to analyze and compare replicate de novo sequence assemblies of Acidilobus-like populations from four different mildly acidic (pH 3.3 to 6.1) high-temperature (72°C to 82°C) environments and to identify metabolic pathways and/or protein-encoding genes that provide a detailed foundation of the potential functional role of these populations in situ. De novo assemblies of the highly similar Acidilobus-like populations (>99% 16S rRNA gene identity) represent near-complete consensus genomes based on an inventory of single-copy genes, deduced metabolic potential, and assembly statistics generated across sites. Functional analysis of coding sequences and confirmation of gene transcription by Acidilobus-like populations provide evidence that they are primarily chemoorganoheterotrophs, generating acetyl coenzyme A (acetyl-CoA) via the degradation of carbohydrates, lipids, and proteins, and auxotrophic with respect to several external vitamins, cofactors, and metabolites. No obvious pathways or protein-encoding genes responsible for the dissimilatory reduction of sulfur were identified. The presence of a formate dehydrogenase (Fdh) and other protein-encoding genes involved in mixed-acid fermentation supports the hypothesis that Acidilobus spp. function as degraders of complex organic constituents in high-temperature, mildly acidic, hypoxic geothermal systems. PMID:24162572

  12. Changes of Microbial Population in the Rumen of Dairy Steers as Influenced by Plant Containing Tannins and Saponins and Roughage to Concentrate Ratio

    PubMed Central

    Anantasook, N.; Wanapat, M.; Cherdthong, A.; Gunun, P.

    2013-01-01

    The objective of this study was to investigate microbial population in the rumen of dairy steers as influenced by supplementing with dietary condensed tannins and saponins and different roughage to concentrate ratios. Four, rumen fistulated dairy steers (Bos indicus) were used in a 2×2 factorial arrangement in a 4×4 Latin square design. The main factors were two roughage to concentrate ratios (R:C, 60:40 and 40:60) and two supplementations of rain tree pod meal (RPM) (0 and 60 g/kg of total DM intake). Chopped 30 g/kg urea treated rice straw was used as a roughage source. All animals received feed according to respective R:C ratios at 25 g/kg body weight. The RPM contained crude tannins and saponins at 84 and 143 g/kg of DM, respectively. It was found that ruminal pH decreased while ruminal temperature increased by a higher concentrate ratio (R:C 40:60) (p<0.05). In contrast, total bacterial, Ruminococus albus and viable proteolytic bacteria were not affected by dietary supplementation. Numbers of fungi, cellulolytic bacteria, Fibrobactor succinogenes and Ruminococus flavefaciens were higher while amylolytic bacteria was lower when steers were fed at 400 g/kg of concentrate. The population of Fibrobactor succinogenes, was found to be higher with RPM supplementation. In addition, the use of real-time PCR technique indicated that the population of protozoa and methanogens were decreased (p<0.05) with supplementation of RPM and with an increasing concentrate ratio. Supplementation of RPM and feeding different concentrate ratios resulted in changing the rumen microbes especially, when the animals were fed at 600 g/kg of concentrate and supplemented with RPM which significantly reduced the protozoa and methanogens population. PMID:25049745

  13. Predominant Acidilobus-like populations from geothermal environments in yellowstone national park exhibit similar metabolic potential in different hypoxic microbial communities.

    PubMed

    Jay, Z J; Rusch, D B; Tringe, S G; Bailey, C; Jennings, R M; Inskeep, W P

    2014-01-01

    High-temperature (>70°C) ecosystems in Yellowstone National Park (YNP) provide an unparalleled opportunity to study chemotrophic archaea and their role in microbial community structure and function under highly constrained geochemical conditions. Acidilobus spp. (order Desulfurococcales) comprise one of the dominant phylotypes in hypoxic geothermal sulfur sediment and Fe(III)-oxide environments along with members of the Thermoproteales and Sulfolobales. Consequently, the primary goals of the current study were to analyze and compare replicate de novo sequence assemblies of Acidilobus-like populations from four different mildly acidic (pH 3.3 to 6.1) high-temperature (72°C to 82°C) environments and to identify metabolic pathways and/or protein-encoding genes that provide a detailed foundation of the potential functional role of these populations in situ. De novo assemblies of the highly similar Acidilobus-like populations (>99% 16S rRNA gene identity) represent near-complete consensus genomes based on an inventory of single-copy genes, deduced metabolic potential, and assembly statistics generated across sites. Functional analysis of coding sequences and confirmation of gene transcription by Acidilobus-like populations provide evidence that they are primarily chemoorganoheterotrophs, generating acetyl coenzyme A (acetyl-CoA) via the degradation of carbohydrates, lipids, and proteins, and auxotrophic with respect to several external vitamins, cofactors, and metabolites. No obvious pathways or protein-encoding genes responsible for the dissimilatory reduction of sulfur were identified. The presence of a formate dehydrogenase (Fdh) and other protein-encoding genes involved in mixed-acid fermentation supports the hypothesis that Acidilobus spp. function as degraders of complex organic constituents in high-temperature, mildly acidic, hypoxic geothermal systems.

  14. Faecal microbiota of forage-fed horses in New Zealand and the population dynamics of microbial communities following dietary change.

    PubMed

    Fernandes, Karlette A; Kittelmann, Sandra; Rogers, Christopher W; Gee, Erica K; Bolwell, Charlotte F; Bermingham, Emma N; Thomas, David G

    2014-01-01

    The effects of abrupt dietary transition on the faecal microbiota of forage-fed horses over a 3-week period were investigated. Yearling Thoroughbred fillies reared as a cohort were exclusively fed on either an ensiled conserved forage-grain diet ("Group A"; n = 6) or pasture ("Group B"; n = 6) for three weeks prior to the study. After the Day 0 faecal samples were collected, horses of Group A were abruptly transitioned to pasture. Both groups continued to graze similar pasture for three weeks, with faecal samples collected at 4-day intervals. DNA was isolated from the faeces and microbial 16S and 18S rRNA gene amplicons were generated and analysed by pyrosequencing. The faecal bacterial communities of both groups of horses were highly diverse (Simpson's index of diversity > 0.8), with differences between the two groups on Day 0 (P < 0.017 adjusted for multiple comparisons). There were differences between Groups A and B in the relative abundances of four genera, BF311 (family Bacteroidaceae; P = 0.003), CF231 (family Paraprevotellaceae; P = 0.004), and currently unclassified members within the order Clostridiales (P = 0.003) and within the family Lachnospiraceae (P = 0.006). The bacterial community of Group A horses became similar to Group B within four days of feeding on pasture, whereas the structure of the archaeal community remained constant pre- and post-dietary change. The community structure of the faecal microbiota (bacteria, archaea and ciliate protozoa) of pasture-fed horses was also identified. The initial differences observed appeared to be linked to recent dietary history, with the bacterial community of the forage-fed horses responding rapidly to abrupt dietary change.

  15. [Effects of returning straw to soil and different tillage methods on paddy field soil fertility and microbial population].

    PubMed

    Ren, Wan-Jun; Liu, Dai-Yin; Wu, Jin-Xiu; Wu, Ju-Xian; De, Chen-Chun; Yang, Wen-Yu

    2009-04-01

    A field experiment was conducted on a paddy field to study the effects of returning straw to soil and different tillage methods (no-tillage + returning straw, no-tillage, tillage + returning straw, and tillage) on the fertility level and microbial quantities of different soil layers. The results showed that in upper soil layer, the organic matter content in treatment 'no-tillage + returning straw' was 5.33, 2.79, and 5.37 g x kg(-1) higher than that in treatments 'no-tillage', 'tillage + returning straw', and 'tillage', respectively, and the contents of total and available N, P and K in treatment 'no-tillage + returning straw' were also the highest, followed by in treatments 'no-tillage' and 'tillage + returning straw', and in treatment 'tillage'. In deeper soil layer, all the fertility indices were higher in treatment 'tillage + returning straw'. Treatments of 'returning straw to soil' had the highest quantities of soil microbes. The quantities of bacteria, fungi, and actinomycetes in upper soil layer were the highest in treatment 'no-tillage + returning straw', and thus, the cellulose decomposition intensity in this treatment at maturity period was 26.44%, 79.01%, and 98. 15% higher than that in treatments 'tillage + returning straw', 'no-tillage', and 'tillage', respectively. In deeper soil layer, the quantities of bacteria, fungi, and actinomycetes were the highest in treatment 'tillage + returning straw'. Treatment 'no-tillage + returning straw' had the features of high fertility and abundant microbes in surface soil layer. The quantities of soil bacteria and actinomycetes and the decomposition intensity of soil cellulose were significantly positively correlated with soil fertility level.

  16. Faecal Microbiota of Forage-Fed Horses in New Zealand and the Population Dynamics of Microbial Communities following Dietary Change

    PubMed Central

    Fernandes, Karlette A.; Kittelmann, Sandra; Rogers, Christopher W.; Gee, Erica K.; Bolwell, Charlotte F.; Bermingham, Emma N.; Thomas, David G.

    2014-01-01

    The effects of abrupt dietary transition on the faecal microbiota of forage-fed horses over a 3-week period were investigated. Yearling Thoroughbred fillies reared as a cohort were exclusively fed on either an ensiled conserved forage-grain diet (“Group A”; n = 6) or pasture (“Group B”; n = 6) for three weeks prior to the study. After the Day 0 faecal samples were collected, horses of Group A were abruptly transitioned to pasture. Both groups continued to graze similar pasture for three weeks, with faecal samples collected at 4-day intervals. DNA was isolated from the faeces and microbial 16S and 18S rRNA gene amplicons were generated and analysed by pyrosequencing. The faecal bacterial communities of both groups of horses were highly diverse (Simpson’s index of diversity >0.8), with differences between the two groups on Day 0 (P<0.017 adjusted for multiple comparisons). There were differences between Groups A and B in the relative abundances of four genera, BF311 (family Bacteroidaceae; P = 0.003), CF231 (family Paraprevotellaceae; P = 0.004), and currently unclassified members within the order Clostridiales (P = 0.003) and within the family Lachnospiraceae (P = 0.006). The bacterial community of Group A horses became similar to Group B within four days of feeding on pasture, whereas the structure of the archaeal community remained constant pre- and post-dietary change. The community structure of the faecal microbiota (bacteria, archaea and ciliate protozoa) of pasture-fed horses was also identified. The initial differences observed appeared to be linked to recent dietary history, with the bacterial community of the forage-fed horses responding rapidly to abrupt dietary change. PMID:25383707

  17. Lack of correlation between Legionella colonization and microbial population quantification using heterotrophic plate count and adenosine triphosphate bioluminescence measurement.

    PubMed

    Duda, Scott; Baron, Julianne L; Wagener, Marilyn M; Vidic, Radisav D; Stout, Janet E

    2015-07-01

    This investigation compared biological quantification of potable and non-potable (cooling) water samples using pour plate heterotrophic plate count (HPC) methods and adenosine triphosphate (ATP) concentration measurement using bioluminescence. The relationship between these measurements and the presence of Legionella spp. was also examined. HPC for potable and non-potable water were cultured on R2A and PCA, respectively. Results indicated a strong correlation between HPC and ATP measurements in potable water (R = 0.90, p < 0.001). In the make-up water and two cooling towers, the correlations between ATP and HPC were much weaker but statistically significant (make-up water: R = 0.37, p = 0.005; cooling tower 1: R = 0.52, p < 0.001; cooling tower 2: R = 0.54, p < 0.001). For potable and non-potable samples, HPC exhibited higher measurement variability than ATP. However, ATP measurements showed higher microbial concentrations than HPC measurements. Following chlorination of the cooling towers, ATP measurements indicated very low bacterial concentrations (<10 colony-forming units (CFU)/mL) despite high HPC concentrations (>1000 CFU/mL) which consisted primarily of non-tuberculous mycobacteria. HPC concentrations have been suggested to be predictive of Legionella presence, although this has not been proven. Our evaluation showed that HPC or ATP demonstrated a fair predictive capacity for Legionella positivity in potable water (HPC: receiver operating characteristic (ROC) = 0.70; ATP: ROC = 0.78; p = 0.003). However, HPC or ATP correctly classified sites as positive only 64 and 62% of the time, respectively. No correlation between HPC or ATP and Legionella colonization in non-potable water samples was found (HPC: ROC = 0.28; ATP: ROC = 0.44; p = 0.193).

  18. Evaluation of microbial population and functional genes during the bioremediation of petroleum-contaminated soil as an effective monitoring approach.

    PubMed

    Shahi, Aiyoub; Aydin, Sevcan; Ince, Bahar; Ince, Orhan

    2016-03-01

    This study investigated the abundance and diversity of soil n-alkane and polycyclic aromatic hydrocarbon (PAH)-degrading bacterial communities. It also investigated the quantity of the functional genes, the occurrence of horizontal gene transfer (HGT) in the identified bacterial communities and the effect that such HGT can have on biostimulation process. Illumina sequencing was used to detect the microbial diversity of petroleum-polluted soil prior to the biostimulation process, and quantitative real-time PCR was used to determine changes in the bacterial community and functional genes (alkB, phnAc and nah) expressions throughout the biostimulation of petroleum-contaminated soil. The illumine results revealed that γ-proteobacteria, Chloroflexi, Firmicutes, and δ-proteobacteria were the most dominant bacterial phyla in the contaminated site, and that most of the strains were Gram-negative. The results of the gene expression results revealed that gram-negative bacteria and alkB are critical to successful bioremediation. Failure to maintain the stability of hydrocarbon-degrading bacteria and functional gene will reduce the extend to which alkanes and PAHs are degraded. According to the results of the study, the application of a C:N:P ratio of was 100:15:1 in the biodegradation experiment resulted in the highest rate at which petroleum hydrocarbons were biodegraded. The diversity of pollutant-degrading bacteria and the effective transfer of degrading genes among resident microorganisms are essential factors for the successful biostimulation of petroleum hydrocarbons. As such, screening these factors throughout the biostimulation process represents an effective monitoring approach by which the success of the biostimulation can be assessed.

  19. On the Discrepancy of Access to Higher Education in a Province with a Large Ethnic Minority Population

    ERIC Educational Resources Information Center

    Dong, Yunchuan; Zhang, Jianxin

    2007-01-01

    Based on a survey of students from different social strata, different family backgrounds and different levels of access to higher education in 10 higher education institutions (HEIs) in Yunnan, an ethnic minority (EM) province, this essay tries to find out the discrepancy in the enrollment opportunity of higher education for children from…

  20. Microbial diversity in the larval gut of field and laboratory populations of the sugarcane weevil Sphenophorus levis (Coleoptera, Curculionidae).

    PubMed

    Rinke, R; Costa, A S; Fonseca, F P P; Almeida, L C; Delalibera Júnior, I; Henrique-Silva, F

    2011-11-01

    The sugarcane weevil, Sphenophorus levis, is a wide-spread sugarcane pest in Brazil. Sphenophorus levis may depend on microorganisms that inhabit its intestinal tract. We examined the diversity of the gut microbiota of S. levis, which was characterized using culture-dependent and culture-independent methods. Analysis of 16S rRNA amplified directly from the gut community revealed the presence of 14 genera, one group from the Candidatus category, one uncultured group assigned to the family Flavobacteriaceae, and one uncultured group assigned to the family Enterobacteriaceae; all of them are members of the Alpha-Proteobacteria, Beta-Proteobacteria, Gamma-Proteobacteria, Firmicutes, and Bacteroidetes phyla. Microorganisms isolated through culture-dependent methods were classified according to morphological parameters and by 16S rRNA gene sequences. In addition to bacteria, four filamentous fungi were isolated. A higher bacterial diversity was observed in field populations of larvae than in laboratory populations, according to the Shannon index (Field H' = 3.36; Laboratory H' = 3.26). Five genera of bacteria and two filamentous fungi were found to have cellulolytic activity. This is the first report of S. levis gut microbiota; it may contribute to development of strategies for controlling this sugarcane pest.

  1. Microbiology of subtidal sediments: Monitoring microbial populations. Restoration project 93047-2. Exxon Valdez oil spill restoration project final report

    SciTech Connect

    Braddock, J.F.; Richter, Z.

    1994-06-01

    Following the Exxon Valdez oil spill in 1989, the authors measured numbers of hydrocarbon-degrading microorganisms and hydrocarbon mineralization potentials of microorganisms in oiled and unoiled surface sediments from the shore through 100 m depth offshore. The authors found both temporal and spatial variations in numbers and activity of hydrocarbon-degrading microorganisms with statistically significant higher values at the oiled sites than at reference sites. In the summer of 1993, the authors returned to ten study sites within Prince William Sound to monitor the changes in the numbers and activities of hydrocarbon-degrading microorganisms at these sites with time. In 1993 the numbers and activities of hydrocarbon-degrading microorganisms were generally very low at all sites although elevated populations and activities were measured in intertidal sub-surface samples at several sites (Northwest Bay, Herring Bay and Sleepy Bay) with observable sub-surface oiling.

  2. Use of chemical sanitizers to reduce microbial populations and maintain quality of whole and fresh-cut cantaloupe.

    PubMed

    Fan, Xuetong; Annous, Bassam A; Keskinen, Lindsey A; Mattheis, James P

    2009-12-01

    Whole cantaloupes either not inoculated or inoculated with Salmonella Poona were submerged in water, 180 ppm of chlorine, acidified calcium sulfate (ACS: 1.2% Safe(2)O-ACS50), 1,000 ppm of acidified sodium chlorite (ASC), 80 ppm of peroxyacetic acid (PAA), and a combination of ACS and PAA for 10 min. Although only ASC and the combination of ACS and PAA significantly reduced the aerobic plate count of samples taken from the surface of whole cantaloupe (compared with samples taken from cantaloupe submerged in water only), all treatments reduced yeast and mold counts on the whole cantaloupe. However, none of the treatments of whole cantaloupes consistently reduced yeast and mold counts for the samples of fresh-cut cantaloupes. The aerobic plate counts for fresh-cut cantaloupe were reduced by 1 to 2 log CFU/g by sanitization of whole fruit with ASC, ACS, and the combination of ACS and PAA. The low bacterial population on the fresh-cut fruit was maintained during 14 days of storage at 4 degrees C. All treatments had a limited effect on the population of Salmonella, achieving no more than a 1.5-log reduction of the pathogen inoculated on the surface of the whole cantaloupes. Salmonella was nondetectable via direct plating (with a detection limit of 0.4 log CFU/g) in fresh-cut cantaloupes prepared from whole cantaloupes treated with any of the sanitizers. However, after enrichment, Salmonella often was detectable. Color, texture, soluble solids, pH, ascorbic acid, and drip loss of cut cantaloupes were not consistently affected by any of the whole-fruit treatments. Overall, treatments of whole cantaloupe with ASC, ACS, and the combination of ACS and PAA at the concentrations tested permitted a significant reduction in Salmonella and native microflora of whole and cut fruit; however, Salmonella still could be found in cut cantaloupes from all treatments.

  3. Impact of Irradiation and Polycyclic Aromatic Hydrocarbon Spiking on Microbial Populations in Marine Sediment for Future Aging and Biodegradability Studies

    PubMed Central

    Melcher, Rebecca J.; Apitz, Sabine E.; Hemmingsen, Barbara B.

    2002-01-01

    Experiments were carried out to develop methods to generate well-characterized, polycyclic aromatic hydrocarbon (PAH)-spiked, aged but minimally altered sediments for fate, biodegradation, and bioavailability experiments. Changes in indigenous bacterial populations were monitored in mesocosms constructed of relatively clean San Diego Bay sediments, with and without exposure to gamma radiation, and then spiked with five different PAHs and hexadecane. While phenanthrene and chrysene degraders were present in the unspiked sediments and increased during handling, PAH spiking of nonirradiated sediments led to dramatic increases in their numbers. Phenotypic characterization of isolates able to grow on phenanthrene or chrysene placed them in several genera of marine bacteria: Vibrio, Marinobacter or Cycloclasticus, Pseudoalteromonas, Marinomonas, and Halomonas. This is the first time that marine PAH degraders have been identified as the latter two genera, expanding the diversity of marine bacteria with this ability. Even at the highest irradiation dose (10 megarads), heterotrophs and endospore formers reappeared within weeks. However, while bacteria from the unirradiated sediments had the capacity to both grow on and mineralize 14C-labeled phenanthrene and chrysene, irradiation prevented the reappearance of PAH degraders for up to 4 months, allowing spikes to age onto the sediments, which can be used to model biodegradation in marine sediments. PMID:12039743

  4. Characterization of microbial population of breba and main crops (Ficus carica) during cold storage: Influence of passive modified atmospheres (MAP) and antimicrobial extract application.

    PubMed

    Villalobos, María Del Carmen; Serradilla, Manuel Joaquín; Martín, Alberto; Hernández-León, Alejandro; Ruíz-Moyano, Santiago; Córdoba, María de Guía

    2017-05-01

    The purpose of this work was to study the changes of bacterial and fungal population of breba fruits such as 'Banane' and 'San Antonio' as well as 'Cuello Dama Negro', 'Cuello Dama Blanco' and 'San Antonio' fig cultivars stored in passive modified atmospheres (MAP) by the use of three different microperforated films (M10 with 16 holes; M30 with five holes and M50 with three holes). Moreover the effects of the application of aqueous soy polyphenolic antimicrobial extract (APE), alone or combined with MAP, were also studied for 'Cuello Dama Negro' and 'Cuello Dama Blanco' fig cultivars. Bacteria and fungi isolates were identified by PCR-RFLP of 16S rRNA and ITS regions, respectively, and subsequently sequence of the different patterns obtained. The results indicated that Pseudomonas gessardii, Pantoea agglomerans and Enterobacter asburiae were the main species of bacteria found in all the treatments studied. The fungal species identified were Aureobasidium pulullans, Cladosporium cladosporioides and Alternaria alternata, which were found in a lower percentage in fruit stored in MAP and fruits treated with antimicrobial extracts, as this treatments allowed to reduce the microbial growth of moulds and yeasts. Thus, the application of treatments such as M30, M50 or the combination of MAP with antimicrobial extract was highly effective to control fruit spoilage in fig and breba crops.

  5. Performance, carotenoids yield and microbial population dynamics in a photobioreactor system treating acidic wastewater: Effect of hydraulic retention time (HRT) and organic loading rate (OLR).

    PubMed

    Liu, Shuli; Zhang, Guangming; Zhang, Jie; Li, Xiangkun; Li, Jianzheng

    2016-01-01

    Effects of hydraulic retention time (HRT) and influent organic loading rate (OLR) were investigated in a photobioreactor containing PNSB (Rhodopseudomonas palustris)-chemoheterotrophic bacteria to treat volatile fatty acid wastewater. Pollutants removal, biomass production and carotenoids yield in different phases were investigated in together with functional microbial population dynamics. The results indicated that properly decreasing HRT and increasing OLR improved the nutrient removal performance as well as the biomass and carotenoids productions. 85.7% COD, 89.9% TN and 91.8% TP removals were achieved under the optimal HRT of 48h and OLR of 2.51g/L/d. Meanwhile, the highest biomass production and carotenoids yield were 2719.3mg/L and 3.91mg/g-biomass respectively. In addition, HRT and OLR have obvious impacts on PNSB and total bacteria dynamics. Statistical analyses indicated that the COD removal exhibited a positive relationship with OLR, biomass and carotenoids production. PNSB/total bacteria ratio had a positive correlation with the carotenoids yield.

  6. Biogeochemistry of Microbial Mats

    NASA Technical Reports Server (NTRS)

    DesMarais, David J.; DeVincenizi, D. (Technical Monitor)

    2002-01-01

    The hierarchical organization of microbial ecosystems determines the rates of processes that shape Earth's environment, define the stage upon which major evolutionary events occurred, and create biosignatures in sediments and atmospheres. In cyanobacterial mats, oxygenic photosynthesis provides energy, organic substrates and oxygen to the ecosystem. Incident light changes with depth in the mat, both in intensity and spectral composition, and counteracting gradients of oxygen and sulfide shape the chemical microenvironment. A combination of benefits and hazards of light, oxygen and sulfide promotes the allocation of the various essential mat processes between light and dark periods and to various depths in the mat. Microliters produce hydrogen, small organic acids, nitrogen and sulfur species. Such compounds fuel a flow of energy and electrons in these ecosystems and thus shape interactions between groups of microorganisms. Coordinated observations of population distribution, abundance, and activity for an entire community are making fundamental questions in ecology accessible. These questions address those factors that sustain the remarkable diversity of microorganisms that are now being revealed by molecular techniques. These questions also target the processes that shape the various kinds of biosignatures that we will seek, both in ancient rocks from Earth and Mars, and in atmospheres of distant planets beyond our Solar System.

  7. Effect of Dietary Supplementation of Red Ginseng By-product on Laying Performance, Blood Biochemistry, Serum Immunoglobulin and Microbial Population in Laying Hens.

    PubMed

    Kang, H K; Park, S-B; Kim, C H

    2016-10-01

    This study was carried out to investigate the effect of dietary supplementation of red ginseng by-product (RGB) on the laying performance, blood biochemistry, and microbial population in laying hens. A total of 120 Hy-Line Brown laying hens (75 weeks old) were randomly allotted to 1 of 3 dietary treatments with 4 replicates per treatment. A commercial-type basal diet was prepared, and 2 additional diets were prepared by supplementing 5.0 or 10.0 g/kg of RGB to the basal diet at the expense of corn. The diets were fed to hens on an ad libitum basis for 4 weeks. There were no differences in feed intake, egg weight, and feed conversion ratio during 4 weeks of the feeding trial. However, hen-day egg production was significantly greater (p<0.05) for the RGB treatment groups than that for the basal treatment group. There were no differences in triglyceride, aspartate aminotransferase, and alanine aminotransferase during the 4-week feeding trial. However, RGB supplementation increased (p<0.05) the serum immunoglobulin G (IgG) and IgM content compared with basal treatment group. The total cholesterol was lower (p<0.05) in the RGB treatments groups than that in the basal treatment group. The intestinal Lactobacillus population was greater (p<0.05) for the RGB treatments groups than that for the basal treatment group. However, the numbers of Salmonella and Escherichia coli were not different among dietary treatments. During the entire experiment, there was no significant difference in egg quality among all the treatments. In conclusion, in addition to improving hen-day production, there were positive effects of dietary RGB supplementation on serum immunoglobulin and cholesterol levels in laying hens.

  8. [Providing vulnerable populations in subSaharan Africa access to obstetrical care: strategy for improving prenatal services].

    PubMed

    Dugas, M

    2011-12-01

    The outlook for reaching key Millennium Development goals in Africa in 2015 is mostly positive. However, two critical indicators, i.e., maternal and neonatal mortality, show lagging progress. The purpose of this report is to underline the importance of prenatal care in efforts to reduce maternal mortality. It describes the minimum prenatal care package recommended by WHO and propses strategies for increasing access to prenatal examination. Health education, improvement of care quality and outreach services are promising avenues to increasing the use of prenatal services.

  9. Effects of essential oils on digestion, ruminal fermentation, rumen microbial populations, milk production, and milk composition in dairy cows fed alfalfa silage or corn silage.

    PubMed

    Benchaar, C; Petit, H V; Berthiaume, R; Ouellet, D R; Chiquette, J; Chouinard, P Y

    2007-02-01

    Four Holstein cows fitted with ruminal cannulas were used in a 4 x 4 Latin square design (28-d periods) with a 2 x 2 factorial arrangement of treatments to investigate the effects of addition of a specific mixture of essential oil compounds (MEO; 0 vs. 750 mg/d) and silage source [alfalfa silage (AS) vs. corn silage (CS)] on digestion, ruminal fermentation, rumen microbial populations, milk production, and milk composition. Total mixed rations containing either AS or CS as the sole forage source were balanced to be isocaloric and isonitrogenous. In general, no interactions between MEO addition and silage source were observed. Except for ruminal pH and milk lactose content, which were increased by MEO supplementation, no changes attributable to the administration of MEO were observed for feed intake, nutrient digestibility, end-products of ruminal fermentation, microbial counts, and milk performance. Dry matter intake and milk production were not affected by replacing AS with CS in the diet. However, cows fed CS-based diets produced milk with lower fat and higher protein and urea N concentrations than cows fed AS-based diets. Replacing AS with CS increased the concentration of NH(3)-N and reduced the acetate-to-propionate ratio in ruminal fluid. Total viable bacteria, cellulolytic bacteria, and protozoa were not influenced by MEO supplementation, but the total viable bacteria count was higher with CS- than with AS-based diets. The apparent digestibility of crude protein did not differ between the AS and CS treatments, but digestibilities of neutral detergent fiber and acid detergent fiber were lower when cows were fed CS-based diets than when they were fed AS-based diets. Duodenal bacterial N flow, estimated using urinary purine derivatives and the amount of N retained, increased in cows fed CS-based diets compared with those fed AS-based diets. Feeding cows AS increased the milk fat contents of cis-9, trans-11 18:2 (conjugated linoleic acid) and 18:3 (n-3 fatty

  10. Effects of diets containing different concentrations of mannanoligosaccharide or antibiotics on growth performance, intestinal development, cecal and litter microbial populations, and carcass parameters of broilers.

    PubMed

    Baurhoo, B; Ferket, P R; Zhao, X

    2009-11-01

    The effects of 2 levels of mannanoligosaccharide (MOS) in feed were compared with antibiotic growth promoters on growth performance, intestinal morphology, cecal and litter microbial populations, and carcass parameters in broilers raised in a sanitary environment. Dietary treatments included: 1) antibiotic growth promoter-free diet (control), 2) VIRG (diet 1 + 16.5 mg/kg of virginiamycin), 3) BACT (diet 1 + 55 mg/kg of bacitracin), 4) LMOS (diet 1 + 0.2% MOS), and 5) HMOS (diet 1 + 0.5% MOS). Birds were randomly assigned to 3 replicate pens/treatment (n = 55/pen). Body weight and feed intake were recorded weekly throughout 38 d. At d 14, 24, and 34, a 1-cm segment of duodenum, jejunum, and ileum was used in morphological analysis (n = 9 birds/d per treatment). At the same bird ages, cecal contents were assayed for lactobacilli, bifidobacteria, Salmonella, Campylobacter, and Escherichia coli, whereas litter was analyzed for Salmonella, Campylobacter, and E. coli. Carcass yields (breast fillet and tenders, thigh, drumstick, and wing) were determined at d 38. Body weight, feed conversion, and carcass yields did not differ among treatments. In contrast to birds fed VIRG or BACT, LMOS and HMOS consistently increased (P < 0.05) villi height and goblet cell number per villus in all intestinal segments at d 24 and 34. Bifidobacteria concentrations were higher (P < 0.05) in LMOS- and HMOS-fed birds at all time points. Birds and litter from all treatments were free of Salmonella. At d 14 and 24, cecal E. coli and Campylobacter counts were not different among treatments. In comparison to birds fed control, at d 34, BACT, LMOS, and HMOS significantly reduced (P < 0.05) cecal E. coli concentrations, whereas Campylobacter counts were reduced (P < 0.05) by VIRG, BACT, and LMOS. Litter bacterial counts were not altered by dietary treatments. In conclusion, under conditions of this study, MOS conferred intestinal health benefits to chickens by improving its morphological

  11. Culturally Diverse and Underserved Populations of Gifted Students in the United States and in Taiwan: Equitable Access to Gifted Education

    ERIC Educational Resources Information Center

    Ho, Ya-Ting

    2014-01-01

    There is a continuing increase in the African American and Hispanic student populations in public schools. The students who are invited to gifted programs are overwhelmingly White. This is the situation in schools in the United States and also in Taiwan. Misunderstanding or unawareness of culture difference among educators might contribute to…

  12. Does Universally Accessible Child Care Protect Children from Late Talking? Results from a Norwegian Population-Based Prospective Study

    ERIC Educational Resources Information Center

    Lekhal, Ratib; Zachrisson, Henrik Daae; Wang, Mari Vaage; Schjolberg, Synnve; von Soest, Tilmann

    2011-01-01

    This study examines the association between type of child care arrangement at age 1, 1.5 and 3 years and late talking (LT). The data were from 19,919 children in the population-based prospective Norwegian Mother and Child Cohort Study (MoBa) and included information about child care arrangement, LT and a variety of covariates. Attendance at…

  13. Mineralogic control on abundance and diversity of surface-adherent microbial communities

    USGS Publications Warehouse

    Mauck, Brena S.; Roberts, Jennifer A.

    2007-01-01

    In this study, we investigated the role of mineral-bound P and Fe in defining microbial abundance and diversity in a carbon-rich groundwater. Field colonization experiments of initially sterile mineral surfaces were combined with community structure characterization of the attached microbial population. Silicate minerals containing varying concentrations of P (∼1000 ppm P) and Fe (∼4 wt % Fe 2 O3), goethite (FeOOH), and apatite [Ca5(PO4)3(OH)] were incubated for 14 months in three biogeochemically distinct zones within a petroleum-contaminated aquifer. Phospholipid fatty acid analysis of incubated mineral surfaces and groundwater was used as a measure of microbial community structure and biomass. Microbial biomass on minerals exhibited distinct trends as a function of mineralogy depending on the environment of incubation. In the carbon-rich, aerobic groundwater attached biomass did not correlate to the P- or Fe- content of the mineral. In the methanogenic groundwater, however, biomass was most abundant on P-containing minerals. Similarly, in the Fe-reducing groundwater a correlation between Fe-content and biomass was observed. The community structure of the mineral-adherent microbial population was compared to the native groundwater community. These two populations were significantly different regardless of mineralogy, suggesting differentiation of the planktonic community through attachment, growth, and death of colonizing cells. Biomarkers specific for dissimilatory Fe-reducing bacteria native to the aquifer were identified only on Fe-containing minerals in the Fe-reducing groundwater. These results demonstrate that the trace nutrient content of minerals affects both the abundance and diversity of surface-adherent microbial communities. This behavior may be a means to access limiting nutrients from the mineral, creating a niche for a particular microbial population. These results suggest that heterogeneity of microbial populations and their associated

  14. Patient access to healthcare services and optimisation of self-management for ethnic minority populations living with diabetes: a systematic review.

    PubMed

    Wilson, Charlotte; Alam, Rahul; Latif, Saima; Knighting, Katherine; Williamson, Susan; Beaver, Kinta

    2012-01-01

    A higher risk of diabetes mellitus in South Asian and Black African populations combined with lower reported access and self-management-related health outcomes informed the aims of this study. Our aims were to synthesise and evaluate evidence relating to patient self-management and access to healthcare services for ethnic minority groups living with diabetes. A comprehensive search strategy was developed capturing a full range of study types from 1995-2010, including relevant hand-searched literature pre-dating 1995. Systematic database searches of MEDLINE, Cochrane, DARE, HTA and NHSEED, the British Nursing Index, CAB abstracts, EMBASE, Global Health, Health Management Information Consortium and PsychInfo were conducted, yielding 21,288 abstracts. Following search strategy refinement and the application of review eligibility criteria; 11 randomised controlled trials (RCTs), 18 qualitative studies and 18 quantitative studies were evaluated and principal results extracted. Results suggest that self-management practices are in need of targeted intervention in terms of patients' knowledge and understanding of their illness, inadequacy of information and language and communication difficulties arising from cultural differences. Access to health-care is similarly hindered by a lack of cultural sensitivity in service provision and under use of clinic-based interpreters and community-based services. Recommendations for practice and subsequent intervention primarily rest at the service level but key barriers at patient and provider levels are also identified.

  15. Changes in Access to Health Services of the Immigrant and Native-Born Population in Spain in the Context of Economic Crisis †

    PubMed Central

    Garcia-Subirats, Irene; Vargas, Ingrid; Sanz-Barbero, Belén; Malmusi, Davide; Ronda, Elena; Ballesta, Mónica; Vázquez, María Luisa

    2014-01-01

    Aim: To analyze changes in access to health care and its determinants in the immigrant and native-born populations in Spain, before and during the economic crisis. Methods: Comparative analysis of two iterations of the Spanish National Health Survey (2006 and 2012). Outcome variables were: unmet need and use of different healthcare levels; explanatory variables: need, predisposing and enabling factors. Multivariate models were performed (1) to compare outcome variables in each group between years, (2) to compare outcome variables between both groups within each year, and (3) to determine the factors associated with health service use for each group and year. Results: unmet healthcare needs decreased in 2012 compared to 2006; the use of health services remained constant, with some changes worth highlighting, such as the decline in general practitioner visits among autochthons and a narrowed gap in specialist visits between the two populations. The factors associated with health service use in 2006 remained constant in 2012. Conclusion: Access to healthcare did not worsen, possibly due to the fact that, until 2012, the national health system may have cushioned the deterioration of social determinants as a consequence of the financial crisis. Further studies are necessary to evaluate the effects of health policy responses to the crisis after 2012. PMID:25272078

  16. Population structure and genetic variability in the Murrah dairy breed of water buffalo in Brazil accessed via pedigree analysis.

    PubMed

    Malhado, Carlos Henrique Mendes; Malhado, Ana Claudia Mendes; Carneiro, Paulo Luiz Souza; Ramos, Alcides Amorim; Ambrosini, Diego Pagung; Pala, Akin

    2012-12-01

    The objective of this study was to use pedigree analysis to evaluate the population structure and genetic variability in the Murrah dairy breed of water buffalo (Bubalus bubalis) in Brazil. Pedigree analysis was performed on 5,061 animals born between 1972 and 2002. The effective number of founders (fe) was 60, representing 6.32 % of the potential number of founders. The effective number of ancestors (fa) was 36 and the genetic contribution of the 17 most influent ancestors explained 50 % of the genetic variability in the population. The ratio fe/fa (effective number of founders/effective number of ancestors), which expresses the effect of population bottlenecks, was 1.66. Completeness level for the whole pedigree was 76.8, 49.2, 27.7, and 12.8 % for, respectively, the first, second, third, and fourth known parental generations. The average inbreeding values for the whole analyzed pedigree and for inbreed animals were, respectively, 1.28 and 7.64 %. The average relatedness coefficient between individuals of the population was estimated to be 2.05 %-the highest individual coefficient was 10.31 %. The actual inbreeding and average relatedness coefficient are probably higher than estimated due to low levels of pedigree completeness. Moreover, the inbreeding coefficient increased with the addition of each generation to the pedigree, indicating that incomplete pedigrees tend to underestimate the level of inbreeding. Introduction of new sires with the lowest possible average relatedness coefficient and the use of appropriate mating strategies are recommended to keep inbreeding at acceptable levels and increase the genetic variability in this economically important species, which has relatively low numbers compared to other commercial cattle breeds. The inclusion of additional parameters, such as effective number of founders, effective number of ancestors, and fe/fa ratio, provides better resolution as compared to the inclusion of inbreeding coefficient and may help

  17. Facilitators of and barriers to accessing clinical prevention services for the South Asian population in Surrey, British Columbia: a qualitative study

    PubMed Central

    Majid, Sanaa; Douglas, Rachel; Lee, Victoria; Stacy, Elizabeth; Garg, Arun K.; Ho, Kendall

    2016-01-01

    Background: British Columbia falls short in uptake of recommended clinical prevention services, with even lower rates among immigrant populations. This study explored facilitators of and barriers to uptake of clinical prevention services among people from South Asia, who represent 31% of the population in Surrey, British Columbia. Methods: We used a qualitative descriptive approach and employed vignettes in a focus group setting to elicit perspectives of South Asian people on accessing clinical prevention services. Participants aged 40 years or more were recruited between October 2014 and February 2015 from health care and community settings such as older-adult housing, day programs and health education events. Letters of introduction to the study were provided in English or Punjabi or both to all potential participants. We conducted qualitative content analysis of the results. Results: Sixty-two South Asian adults (36 women and 26 men) aged 40-87 years participated in 1 of 8 focus groups in health care or community settings. Facilitators of and barriers to accessing clinical prevention services were noted at the patient, primary care provider and health care system levels. Facilitators at the patient level included taking ownership over one's health, health literacy and respecting the provider's advice; barriers included fear of the diagnosis, death and/or procedures, perceived low risk of disease or utility of the intervention, and side effects of procedures. Provider factors centred on a trust-based patient-provider relationship, strong communication and adequate time during visits. Health care system factors included such facilitators as processes to routinely offer prevention services as part of other health care or social services, systems that encourage prevention-oriented family practice and services at low or no cost to the patient. Interpretation: Our findings validate previously identified facilitators of and barriers to accessing preventive care for

  18. Novel microbial populations in ambient and mesophilic biogas-producing and phenol-degrading consortia unraveled by high-throughput sequencing.

    PubMed

    Ju, Feng; Zhang, Tong

    2014-08-01

    Methanogenesis from wastewater-borne organics and organic solid wastes (e.g., food residues) can be severely suppressed by the presence of toxic phenols. In this work, ambient (20 °C) and mesophilic (37 °C) methane-producing and phenol-degrading consortia were enriched and characterized using high-throughput sequencing (HTS). 454 Pyrosequencing indicated novel W22 (25.0 % of bacterial sequences) in the WWE1 and Sulfurovum-resembled species (32.0 %) in the family Campylobacterales were the most abundant in mesophilic and ambient reactors, respectively, which challenges previous knowledge that Syntrophorhabdus was the most predominant. Previous findings may underestimate bacterial diversity and low-abundance bacteria, but overestimate abundance of Syntrophorhabdus. Illumina HTS revealed that archaeal populations were doubled in ambient reactor and tripled in mesophilic reactor, respectively, compared to the ∼4.9 % (of the bacteria and archaea sequences) in the seed sludge. Moreover, unlike the dominance of Methanosarcina in seed sludge, acetotrophic Methanosaeta predominated both (71.4-76.5 % of archaeal sequences) ambient and mesophilic enrichments. Noteworthy, this study, for the first time, discovered the co-occurrence of green sulfur bacteria Chlorobia, sulfur-reducing Desulfovibrio, and Sulfurovum-resembling species under ambient condition, which could presumably establish mutualistic relationships to compete with syntrophic bacteria and methanogens, leading to the deterioration of methanogenic activity. Taken together, this HTS-based study unravels the high microbial diversity and complicated bacterial interactions within the biogas-producing and phenol-degrading bioreactors, and the identification of novel bacterial species and dominant methanogens involved in the phenol degradation provides novel insights into the operation of full-scale bioreactors for maximizing biogas generation.

  19. Effects of Adaptation of In vitro Rumen Culture to Garlic Oil, Nitrate, and Saponin and Their Combinations on Methanogenesis, Fermentation, and Abundances and Diversity of Microbial Populations

    PubMed Central

    Patra, Amlan K.; Yu, Zhongtang

    2015-01-01

    This study investigated the effects of garlic oil (0.25 g/L), nitrate (5 mM), and quillaja saponin (0.6 g/L), alone and in binary or ternary combinations, on methanogenesis, rumen fermentation, and abundances of select microbial populations using in vitro rumen cultures. Potential adaptation to these compounds was also examined by repeated transfers of the cultures on alternate days until day 18. All treatments except saponin alone significantly decreased methanogenesis. Ternary combinations of garlic oil, nitrate, and saponin additively/synergistically suppressed methane production by 65% at day 2 and by 40% at day 18. Feed digestion was not adversely affected by any of the treatments at day 2, but was decreased by the combinations (binary and ternary) of garlic oil with the other inhibitors at days 10 and 18. Saponin, alone or in combinations, and garlic oil alone lowered ammonia concentration at day 2, while nitrate increased ammonia concentration at days 10 and 18. Total volatile fatty acid concentration was decreased by garlic oil alone or garlic oil-saponin combination. Molar proportions of acetate and propionate were affected to different extents by the different treatments. The abundances of methanogens were similar among treatments at day 2; however, garlic oil and its combination with saponin and/or nitrate at day 10 and all treatments except saponin at day 18 significantly decreased the abundances of methanogens. All the inhibitors, either alone or in combinations, did not adversely affect the abundances of total bacteria or Ruminococcus flavefaciens. However, at day 18 the abundances of Fibrobacter succinogenes and Ruminococcus albus were lowered in the presence of garlic oil and saponin, respectively. The results suggest that garlic oil-nitrate-saponin combination (at the doses used in this study) can effectively decreases methanogenesis in the rumen, but its efficacy may decrease while inhibition to feed digestion can increase over time. PMID:26733975

  20. Development of a predictive model for the growth kinetics of aerobic microbial population on pomegranate marinated chicken breast fillets under isothermal and dynamic temperature conditions.

    PubMed

    Lytou, Anastasia; Panagou, Efstathios Z; Nychas, George-John E

    2016-05-01

    The aim of this study was the development of a model to describe the growth kinetics of aerobic microbial population of chicken breast fillets marinated in pomegranate juice under isothermal and dynamic temperature conditions. Moreover, the effect of pomegranate juice on the extension of the shelf life of the product was investigated. Samples (10 g) of chicken breast fillets were immersed in marinades containing pomegranate juice for 3 h at 4 °C following storage under aerobic conditions at 4, 10, and 15 °C for 10 days. Total Viable Counts (TVC), Pseudomonas spp and lactic acid bacteria (LAB) were enumerated, in parallel with sensory assessment (odor and overall appearance) of marinated and non-marinated samples. The Baranyi model was fitted to the growth data of TVC to calculate the maximum specific growth rate (μmax) that was further modeled as a function of temperature using a square root-type model. The validation of the model was conducted under dynamic temperature conditions based on two fluctuating temperature scenarios with periodic changes from 6 to 13 °C. The shelf life was determined both mathematically and with sensory assessment and its temperature dependence was modeled by an Arrhenius type equation. Results showed that the μmax of TVC of marinated samples was significantly lower compared to control samples regardless temperature, while under dynamic temperature conditions the model satisfactorily predicted the growth of TVC in both control and marinated samples. The shelf-life of marinated samples was significantly extended compared to the control (5 days extension at 4 °C). The calculated activation energies (Ea), 82 and 52 kJ/mol for control and marinated samples, respectively, indicated higher temperature dependence of the shelf life of control samples compared to marinated ones. The present results indicated that pomegranate juice could be used as an alternative ingredient in marinades to prolong the shelf life of chicken.

  1. The burden of drinking water-associated cryptosporidiosis in China: the large contribution of the immunodeficient population identified by quantitative microbial risk assessment.

    PubMed

    Xiao, Shumin; An, Wei; Chen, Zhimin; Zhang, Dongqing; Yu, Jianwei; Yang, Min

    2012-09-01

    A comprehensive quantitative microbial risk assessment (QMRA) of Cryptosporidium infection, considering pathogen removal efficiency, different exposure pathways and different susceptible subpopulations, was performed based on the result of a survey of source water from 66 waterworks in 33 major cities across China. The Cryptosporidium concentrations in source water were 0-6 oocysts/10 L, with a mean value of 0.7 oocysts/10 L. The annual diarrhea morbidity caused by Cryptosporidium in drinking water was estimated to be 2701 (95% confidence interval (CI): 138-9381) cases per 100,000 immunodeficient persons and 148 (95% CI: 1-603) cases per 100,000 immunocompetent persons, giving an overall rate of 149.0 (95% CI: 1.3-606.4) cases per 100,000 population. The cryptosporidiosis burden associated with drinking water treated with the conventional process was calculated to be 8.31 × 10(-6) (95% CI: 0.34-30.93 × 10(-6)) disability-adjusted life years (DALYs) per person per year, which was higher than the reference risk level suggested by the World Health Organization (WHO), but lower than that suggested by the United States Environmental Protection Agency (USEPA). Sixty-six percent of the total health burden due to cryptosporidiosis that occurred in the immunodeficient subpopulation, and 90% of the total DALYs was attributed to adults aged 15-59 years. The sensitivity analysis highlighted the great importance of stability of the treatment process and the importance of watershed protection. The results of this study will be useful in better evaluating and reducing the burden of Cryptosporidium infection.

  2. Application of spatial analysis technology to the planning of access to oral health care for at-risk populations in Australian capital cities.

    PubMed

    Almado, Haidar; Kruger, Estie; Tennant, Marc

    2015-01-01

    Australians are one of the healthiest populations in the world but there is strong evidence that health inequalities exist. Australia has 23.1 million people spread very unevenly over -20 million square kilometres. This study aimed to apply spatial analysis tools to measure the spatial distribution of fixed adult public dental clinics in the eight metropolitan capital cities of Australia. All population data for metropolitan areas of the eight capital cities were integrated with socioeconomic data and health-service locations, using Geographic Information Systems, and then analysed. The adult population was divided into three subgroups according to age, consisting of 15-year-olds and over (n = 7.2 million), retirees 65 years and over (n = 1.2 million), and the elderly, who were 85 years and over (n = 0.15 million). It was evident that the States fell into two groups; Tasmania, Northern Territory, Australian Capital Territory and Western Australia in one cluster, and Victoria, New South Wales, Queensland and South Australia in the other. In the first group, the average proportion of the population of low socioeconomic status living in metropolitan areas within 2.5 km of a government dental clinic is 13%, while for the other cluster, it is 42%. The clustering remains true at 5 km from the clinics. The first cluster finds that almost half (46%) of the poorest 30% of the population live within 5km of a government dental clinic. The other cluster of States finds nearly double that proportion (86%). The results from this study indicated that access distances to government dental services differ substantially in metropolitan areas of the major Australian capital cities.

  3. Understanding benefits and addressing misperceptions and barriers to intrauterine device access among populations in the United States

    PubMed Central

    Yoost, Jennie

    2014-01-01

    Three intrauterine devices (IUDs), one copper and two containing the progestin levonorgestrel, are available for use in the United States. IUDs offer higher rates of contraceptive efficacy than nonlong-acting methods, and several studies have demonstrated higher satisfaction rates and continuation rates of any birth control method. This efficacy is not affected by age or parity. The safety of IUDs is well studied, and the risks of pelvic inflammatory disease, perforation, expulsion, and ectopic pregnancy are all of very low incidence. Noncontraceptive benefits include decreased menstrual blood loss, improved dysmenorrhea, improved pelvic pain associated with endometriosis, and protection of the endometrium from hyperplasia. The use of IUDs is accepted in patients with multiple medical problems who may have contraindications to other birth control methods. Yet despite well-published data, concerns and misperceptions still persist, especially among younger populations and nulliparous women. Medical governing bodies advocate for use of IUDs in these populations, as safety and efficacy is unchanged, and IUDs have been shown to decrease unintended pregnancies. Dispersion of accurate information among patients and practitioners is needed to further increase the acceptability and use of IUDs. PMID:25050062

  4. pH and peptide supply can radically alter bacterial populations and short-chain fatty acid ratios within microbial communities from the human colon.

    PubMed

    Walker, Alan W; Duncan, Sylvia H; McWilliam Leitch, E Carol; Child, Matthew W; Flint, Harry J

    2005-07-01

    The effects of changes in the gut environment upon the human colonic microbiota are poorly understood. The response of human fecal microbial communities from two donors to alterations in pH (5.5 or 6.5) and peptides (0.6 or 0.1%) was studied here in anaerobic continuous cultures supplied with a mixed carbohydrate source. Final butyrate concentrations were markedly higher at pH 5.5 (0.6% peptide mean, 24.9 mM; 0.1% peptide mean, 13.8 mM) than at pH 6.5 (0.6% peptide mean, 5.3 mM; 0.1% peptide mean, 7.6 mM). At pH 5.5 and 0.6% peptide input, a high butyrate production coincided with decreasing acetate concentrations. The highest propionate concentrations (mean, 20.6 mM) occurred at pH 6.5 and 0.6% peptide input. In parallel, major bacterial groups were monitored by using fluorescence in situ hybridization with a panel of specific 16S rRNA probes. Bacteroides levels increased from ca. 20 to 75% of total eubacteria after a shift from pH 5.5 to 6.5, at 0.6% peptide, coinciding with high propionate formation. Conversely, populations of the butyrate-producing Roseburia group were highest (11 to 19%) at pH 5.5 but fell at pH 6.5, a finding that correlates with butyrate formation. When tested in batch culture, three Bacteroides species grew well at pH 6.7 but poorly at pH 5.5, which is consistent with the behavior observed for the mixed community. Two Roseburia isolates grew equally well at pH 6.7 and 5.5. These findings suggest that a lowering of pH resulting from substrate fermentation in the colon may boost butyrate production and populations of butyrate-producing bacteria, while at the same time curtailing the growth of Bacteroides spp.

  5. Disparities in health and access to healthcare between asylum seekers and residents in Germany: a population-based cross-sectional feasibility study

    PubMed Central

    Schneider, Christine; Joos, Stefanie; Bozorgmehr, Kayvan

    2015-01-01

    Objectives To assess disparities in health and healthcare between asylum seekers (AS) and residents in Germany as a proof of concept using European Core Health Indicators (ECHI). Design Population-based cross-sectional feasibility study. Participants All AS (aged 18 years or above) registered in three counties in Germany during a 3-month study period (N=1017). Cross-sectional data on the resident population were taken from the German Health Interview (2008–2011, N=8152), and the European Union Statistics on Income and Living Conditions (2012, N=23 065). Outcome measures Self-reported health status and healthcare access (utilisation and unmet medical need) in line with ECHI. Method Inequalities in health and access to healthcare were quantified both by crude and age-stratified/sex-stratified ORs with 95% CI using cross-tabulations. Results A total of N=156 AS (15.34%) participated in the study. Compared with residents, AS were significantly more likely to report a bad health status (OR=1.72 (1.23 to 2.41)), activity limitations (OR=1.97 (1.39 to 2.79)) or (only younger age groups) any chronic morbidity (18–24 years: OR=6.23 (2.62 to 14.57); 25–49 years: OR=2.05 (1.23 to 3.37)). AS had significantly lower odds for consulting any physician (OR=0.1 (0.07 to 0.16)) or general practitioners (OR=0.44 (0.31 to 0.62)), but higher odds for hospital admissions (OR=2.29 (1.54 to 3.34)), visits to psychotherapists (OR=4.07 (2.48 to 6.43)) and unmet needs (OR=3.74 (2.62 to 5.21)). The direction of healthcare-related associations was consistent across all strata despite variation in magnitude and statistical significance. Conclusions Quantifying disparities between AS and the resident population by means of selected ECHI proved to be feasible. The approach yielded first quantitative evidence for disparities in health and access to healthcare in the German context. Further research is needed to generate representative estimates, for example, by including AS in

  6. Understanding Women's Awareness and Access to Preconception Health Care in a Rural Population: A Cross Sectional Study.

    PubMed

    Lammers, Cristina R; Hulme, Polly A; Wey, Howard; Kerkvliet, Jennifer; Arunachalam, Shivaram P

    2016-10-18

    Despite evidence of the benefits of preconception health care (PCHC), little is known about awareness and access to PCHC for rural, reproductive-aged women. This study aimed to assess the prevalence of PCHC conversations between rural reproductive-age women and health care providers, PCHC interventions received in the past year, and ascertain predictors of PCHC conversations and interventions. Women (n = 868; 18-45 years) completed a questionnaire including reproductive history, health care services utilization, and interest in PCHC. The prevalence of health care providers' PCHC conversations was 53.9 %, and the mean number of interventions reported was 2.6 ± 2.7 (±SD). Significant predictors of PCHC conversation based on adjusted odds ratios from logistic regression were race (Native American 76 % greater than White), health care provider type (non-physician 63 % greater than physician), visits to a health care provider (3+ times 32 % greater than 1-2 times), and pregnancy planning (considering in next 1-5 years 51 % greater than no plans). Significant predictors of PCHC interventions received in the past 12 months based on adjusted risk ratios from negative binomial regression were race (Native American 22 % greater than White), PCHC conversation with a health care provider (yes 52 % lower than no), reporting PCHC as beneficial (yes 32 % greater than don't know), and visits to a health care provider in the past year (3+ times 90 % greater than 1-2 times). Increasing conversations about PCHC between health care providers and their reproductive-aged patients can improve awareness and increase their likelihood of receiving all of the recommended interventions.

  7. Teaching Microbial Growth by Simulation.

    ERIC Educational Resources Information Center

    Ruiz, A. Fernandez; And Others

    1989-01-01

    Presented is a simulation program for Apple II computer which assays the effects of a series of variables on bacterial growth and interactions between microbial populations. Results of evaluation of the program with students are summarized. (CW)

  8. Access to, and use of, water by populations living in a schistosomiasis and fascioliasis co-endemic area of northern Côte d'Ivoire.

    PubMed

    Krauth, Stefanie J; Musard, Capucine; Traoré, Seïdinan I; Zinsstag, Jakob; Achi, Louise Y; N'Goran, Eliézer K; Utzinger, Jürg

    2015-09-01

    Water is an essential element of life, but it can also be a source of disease. Apart from direct consumption of unsafe water, direct contact and indirect consumption puts people at risk of many different types of pathogens. Employing a mixed methods approach, consisting of questionnaires and direct observations, we assessed access to, and use of, different water sources by the participants of the district des Savanes in northern Côte d'Ivoire. The use of water sources was put in relation to the potential risk of acquiring schistosomiasis and fascioliasis. Overall, 489 people aged 8 to 82 years participated. While all participants had access to safe water, 63% were in direct contact with unimproved water and 31% directly consumed unsafe water. More than a third of the people who otherwise reported using only improved water for all activities came in contact with unimproved water through crossing open water when going to their workplace, school or other destinations. Self-reported blood in urine - a marker for Schistosoma haematobium with reasonable sensitivity and specificity - was reported by 6% (n=30), self-reported blood in stool - an unspecific marker for Schistosoma mansoni - was reported by 7% (n=35), while blood co-occurring in both urine and stool was reported by another 10% (n=48) of participants. Accessing unimproved water for any activity (including crossing) was associated with higher odds of reporting blood in urine and/or blood in stool (odds ratio: 1.90; 95% confidence interval: 1.07-3.36). Our results have important rami-fications for intervention programmes targeting neglected tropical diseases, and emphasize the need for a wider supply of safe water to rural populations, since the water supply at the workplace needs to be considered as well next to the water supply at home. Crossing of open water sources is an important risk factor for sustained transmission of schistosomiasis.

  9. Accessible Neurobehavioral Anger-Related Markers for Vulnerability to Post-Traumatic Stress Symptoms in a Population of Male Soldiers

    PubMed Central

    Lin, Tamar; Gilam, Gadi; Raz, Gal; Or-Borichev, Ayelet; Bar-Haim, Yair; Fruchter, Eyal; Hendler, Talma

    2017-01-01

    Identifying vulnerable individuals prone to develop post-traumatic stress symptoms (PTSS) is of paramount importance, especially in populations at high risk for stress exposure such as combat soldiers. While several neural and psychological risk factors are known, no post-traumatic stress disorder (PTSD) biomarker has yet progressed to clinical use. Here we present novel and clinically applicable anger-related neurobehavioral risk markers for military-related PTSS in a large cohort of Israeli soldiers. The psychological, electrophysiological and neural (Simultaneous recording of scalp electroencephalography [EEG] and functional magnetic resonance imaging [fMRI]) reaction to an anger-inducing film were measured prior to advanced military training and PTSS were recorded at 1-year follow-up. Limbic modulation was measured using a novel approach that monitors amygdala modulation using fMRI-inspired EEG, hereafter termed amygdala electrical fingerprint (amyg-EFP). Inter-subject correlation (ISC) analysis on fMRI data indicated that during movie viewing participants’ brain activity was synchronized in limbic regions including the amygdala. Self-reported state-anger and amyg-EFP modulation successfully predicted PTSS levels. State-anger significantly accounted for 20% of the variance in PTSS, and amyg-EFP signal modulation significantly accounted for additional 15% of the variance. Our study was limited by the moderate PTSS levels and lack of systematic baseline symptoms assessment. These results suggest that pre-stress neurobehavioral measures of anger may predict risk for later PTSS, pointing to anger-related vulnerability factors that can be measured efficiently and at a low cost before stress exposure. Possible mechanisms underlying the association between the anger response and risk for PTSS are discussed. PMID:28326027

  10. Microbial Translocation and Cardiometabolic Risk Factors in HIV Infection

    PubMed Central

    Manner, Ingjerd W.; Pedersen, Karin K.; Haissman, Judith M.; Kvale, Dag; Nielsen, Susanne D.

    2014-01-01

    Abstract The widespread access to antiretroviral treatment during the past decades has transformed HIV infection from a lethal disease to a chronic condition, in which the relative burden of non-AIDS-related chronic disorders such as cardiovascular disease, malignancy, renal, liver, and bone disease has increased. The adjusted relative risk for myocardial infarction is reported to be around 2-fold compared to that of the general population, which over time is likely to translate into increased absolute risk in an aging population. Thus, delineating potentially HIV-specific pathogenetic mechanisms is crucial in order to tailor novel strategies for prophylaxis and treatment. This review will focus on advances in the field that possibly link HIV-induced alterations of the gut mucosa and consequent microbial translocation to cardiometabolic risk factors in HIV infection. Recent work suggests that markers of microbial translocation are closely associated with several cardiovascular risk factors such as dyslipidemia, insulin resistance, hypertension, coagulation abnormalities, endothelial dysfunction, and carotid atherosclerosis. Future studies should investigate whether associations between microbial translocation and cardiovascular risk factors will translate into increased risk of acute events, and whether strategies to target gut microbiota and microbial translocation might reduce such a risk. PMID:24521167

  11. Effect of Scrophularia striata and Ferulago angulata, as alternatives to virginiamycin, on growth performance, intestinal microbial population, immune response, and blood constituents of broiler chickens.

    PubMed

    Rostami, Farhad; Ghasemi, Hossein A; Taherpour, Kamran

    2015-09-01

    An experiment was conducted to investigate the comparative effect of Scrophularia striata, Ferulago angulata, and virginiamycin (VM) on performance, intestinal microbial population, immune response, and blood constituents of broilers. A total of 300 Ross 308 male broiler chickens were randomly assigned to 5 treatments, with 5 replicates/treatment (10 chickens/pen). Birds were fed either a corn-soybean meal basal diet (control) or the basal diet supplemented with 200 mg/kg VM; 4 g/kg S. striata (SS1); 8 g/kg S. striata (SS2); 4 g/kg F. angulata (FA1); or 8 g/kg F. angulata (FA2). After 6 wk, the BW, ADG, and feed-to-gain ratio (F:G) of the VM, SS1, and FA1 groups were better (P<0.01) compared with the control group. At 42 d, cecal lactobacillus counts were higher (P=0.032) in SS2 and FA2 groups compared with the control and VM groups. In addition, broilers fed any of the diets exhibited lower coliform counts (P<0.05) in the ileum and ceca than those fed the control diet. Total and IgG antibody titers against SRBC for secondary responses, relative spleen weight, and lymphocyte counts were higher (P<0.05) in birds fed the SS2 or FA2 diet compared with the control group. Moreover, feeding the SS2 or FA2 diet decreased (P<0.05) the blood heterophil/lymphocyte ratio and plasma triglyceride level, whereas only the SS2 diet increased (P=0.037) the white blood cell counts compared with the control diet. All diets, except for the VM diet, decreased (P=0.009) the plasma cholesterol level compared to the control treatment. The plasma high-density lipoprotein cholesterol level was also increased (P=0.042) in the SS2 and FA2 groups. In conclusion, dietary S. striata or F. angulata at a level of 4 g/kg diet enhanced growth performance, which was comparable to that of VM used as an antibiotic growth promoter. Furthermore, a high dose of both herbs (8 g/kg diet) could beneficially affect the intestinal health and immune status of broilers.

  12. Predicting the distribution and ecological niche of unexploited snow crab (Chionoecetes opilio) populations in Alaskan waters: a first open-access ensemble model.

    PubMed

    Hardy, Sarah M; Lindgren, Michael; Konakanchi, Hanumantharao; Huettmann, Falk

    2011-10-01

    Populations of the snow crab (Chionoecetes opilio) are widely distributed on high-latitude continental shelves of the North Pacific and North Atlantic, and represent a valuable resource in both the United States and Canada. In US waters, snow crabs are found throughout the Arctic and sub-Arctic seas surrounding Alaska, north of the Aleutian Islands, yet commercial harvest currently focuses on the more southerly population in the Bering Sea. Population dynamics are well-monitored in exploited areas, but few data exist for populations further north where climate trends in the Arctic appear to be affecting species' distributions and community structure on multiple trophic levels. Moreover, increased shipping traffic, as well as fisheries and petroleum resource development, may add additional pressures in northern portions of the range as seasonal ice cover continues to decline. In the face of these pressures, we examined the ecological niche and population distribution of snow crabs in Alaskan waters using a GIS-based spatial modeling approach. We present the first quantitative open-access model predictions of snow-crab distribution, abundance, and biomass in the Chukchi and Beaufort Seas. Multi-variate analysis of environmental drivers of species' distribution and community structure commonly rely on multiple linear regression methods. The spatial modeling approach employed here improves upon linear regression methods in allowing for exploration of nonlinear relationships and interactions between variables. Three machine-learning algorithms were used to evaluate relationships between snow-crab distribution and environmental parameters, including TreeNet, Random Forests, and MARS. An ensemble model was then generated by combining output from these three models to generate consensus predictions for presence-absence, abundance, and biomass of snow crabs. Each algorithm identified a suite of variables most important in predicting snow-crab distribution, including

  13. A molecular survey of S. mutans and P. gingivalis oral microbial burden in human saliva using Relative Endpoint Polymerase Chain Reaction (RE-PCR) within the population of a Nevada dental school revealed disparities among minorities

    PubMed Central

    2012-01-01

    Background The University of Nevada, Las Vegas School of Dental Medicine recently opened an orthodontic treatment clinic to address the needs of the racially and ethnically diverse population of Southern Nevada, primarily focusing on the treatment and care of low-income and minority patients. Although orthodontic treatment and therapy has been shown to induce changes in the oral cavity, much of this evidence was collected from traditional White, teenage orthodontic clinic populations. The primary goal of this study was to describe the microbial burden of the cariogenic and periodontal pathogens, Streptococcus mutans and Porphyromonas gingivalis within the UNLV-SDM patient population. Methods Representative saliva samples were collected from healthy adult patients for DNA isolation. Relative endpoint polymerase chain reaction (RE-PCR) was performed to ascertain the presence and relative microbial burden of these oral pathogens. Results Nearly one quarter (13/56) or 23.3% of these patients had elevated levels of S. mutans, while (10/56) and 17.8% of these samples were found to have elevated levels of P. gingivalis, - with (90%) of P. gingivalis-positive samples from minority patients (X2 = 17.921, d.f. = 1; p < 0.0001). Conclusions These findings of elevated P. gingivalis levels, primarily among minority patients, may suggest underlying oral health practices contributing to adverse oral health conditions within this population. Oral health knowledge and practices among minority patients may be strongly influenced by other factors, including education and socioeconomic status, suggesting additional research may be needed to accurately determine the most appropriate standards for care and oral health education within this patient population. PMID:22925755

  14. Monitoring microbial metabolites using an inductively coupled resonance circuit

    PubMed Central

    Karnaushenko, Daniil; Baraban, Larysa; Ye, Dan; Uguz, Ilke; Mendes, Rafael G.; Rümmeli, Mark H.; de Visser, J. Arjan G. M.; Schmidt, Oliver G.; Cuniberti, Gianaurelio; Makarov, Denys

    2015-01-01

    We present a new approach to monitor microbial population dynamics in emulsion droplets via changes in metabolite composition, using an inductively coupled LC resonance circuit. The signal measured by such resonance detector provides information on the magnetic field interaction with the bacterial culture, which is complementary to the information accessible by other detection means, based on electric field interaction, i.e. capacitive or resistive, as well as optical techniques. Several charge-related factors, including pH and ammonia concentrations, were identified as possible contributors to the characteristic of resonance detector profile. The setup enables probing the ionic byproducts of microbial metabolic activity at later stages of cell growth, where conventional optical detection methods have no discriminating power. PMID:26264183

  15. Monitoring microbial metabolites using an inductively coupled resonance circuit

    NASA Astrophysics Data System (ADS)

    Karnaushenko, Daniil; Baraban, Larysa; Ye, Dan; Uguz, Ilke; Mendes, Rafael G.; Rümmeli, Mark H.; de Visser, J. Arjan G. M.; Schmidt, Oliver G.; Cuniberti, Gianaurelio; Makarov, Denys

    2015-08-01

    We present a new approach to monitor microbial population dynamics in emulsion droplets via changes in metabolite composition, using an inductively coupled LC resonance circuit. The signal measured by such resonance detector provides information on the magnetic field interaction with the bacterial culture, which is complementary to the information accessible by other detection means, based on electric field interaction, i.e. capacitive or resistive, as well as optical techniques. Several charge-related factors, including pH and ammonia concentrations, were identified as possible contributors to the characteristic of resonance detector profile. The setup enables probing the ionic byproducts of microbial metabolic activity at later stages of cell growth, where conventional optical detection methods have no discriminating power.

  16. Microbial community and population dynamics of single-stage autotrophic nitrogen removal for dilute wastewater at the benchmark oxygen rate supply.

    PubMed

    Huang, Yu-Tzu; Chen, Shiou-Shiou; Lee, Po-Heng; Bae, Jaeho

    2013-11-01

    Microbial communities and their kinetic performance in a single-stage autotrophic nitrogen-removal filter at an optimal oxygen supply were examined to determine the presence and activity of denitrifiers, anaerobic ammonia-oxidizing (anammox), ammonia-oxidizing, and nitrite-oxidizing bacteria. To this end, different molecular biology techniques such as real-time quantitative polymerase chain reaction (qPCR) and biomarkers such as 16S rRNA revealed a diverse microbial community along the filter. It was important to survey the specific species of anammox bacteria using a newly designed Candidatus Brocadiafulgida (BF) specific primer, as well as Candidatus Brocadia anammoxidans (BA) and Candidatus Kuenenia stuttgartiensis (KS) specific primers. An unexpected finding was that the predominant anammox species switched from KS in concentrated wastewater to BA in dilute wastewaters. The Eckenfelder model of the NH3-N transformation along the filter was Se=S0 exp(-0.192D/L(2.3217)). These results provide a foundational understanding of the microbial structure and reaction kinetics in such systems.

  17. Biogeochemical Processes in Microbial Ecosystems

    NASA Technical Reports Server (NTRS)

    DesMarais, David J.

    2001-01-01

    The hierarchical organization of microbial ecosystems determines process rates that shape Earth's environment, create the biomarker sedimentary and atmospheric signatures of life, and define the stage upon which major evolutionary events occurred. In order to understand how microorganisms have shaped the global environment of Earth and, potentially, other worlds, we must develop an experimental paradigm that links biogeochemical processes with ever-changing temporal and spatial distributions of microbial populations and their metabolic properties. Additional information is contained in the original extended abstract.

  18. GEOELECTRICAL EVIDENCE OF MICROBIAL DEGRADATION OF DIESEL CONTAMINATED SEDIMENTS

    EPA Science Inventory

    The alteration of physical properties by microbial activity in petroleum contaminated sediments was investigated using geophysical techniques in laboratory column experiments. Microbial population growth was determined by the Most Probable Number technique (MPN), community dynami...

  19. Feasibility and Acceptability of Brighter Bites: A Food Co-Op in Schools to Increase Access, Continuity and Education of Fruits and Vegetables Among Low-Income Populations.

    PubMed

    Sharma, Shreela; Helfman, Lisa; Albus, Katherine; Pomeroy, Mike; Chuang, Ru-Jye; Markham, Christine

    2015-08-01

    &V access and education in low-income populations using existing infrastructure of schools and food banks.

  20. Changes in gut microbial populations, intestinal morphology, expression of tight junction proteins, and cytokine production between two pig breeds after challenge with Escherichia coli K88: a comparative study.

    PubMed

    Gao, Y; Han, F; Huang, X; Rong, Y; Yi, H; Wang, Y

    2013-12-01

    This study hypothesized that the gut microbial populations, intestinal morphology, and cytokine production are differentially altered in 2 different pig breeds, namely, Chinese native Jinhua pigs and European Landrace pigs, after orally challenge with enterotoxigenic Escherichia coli (ETEC) K88. A total of 12 Jinhua pigs and 12 Landrace pigs were allocated to either the nonchallenged or the challenged groups (6 pigs per group). The challenged pigs were orally administered ETEC K88, and their nonchallenged counterparts were given sterile Luria-Bertani broth. Selected gut microbial populations, intestinal morphology, mRNA expression of tight junction proteins, and the levels of ileal cytokines and secretory immunoglobulin A (sIgA) production were measured in Jinhua and Landrace pigs. The results showed that the challenged Jinhua pigs exhibited a significantly (P < 0.05) lower incidence of diarrhea compared with their Landrace counterparts. The Escherichia coli (E.coli) population and the percentage of E. coli in the total bacteria population were increased in response to ETEC K88 challenge in both Jinhua and Landrace pigs. The challenged Landrace pigs shed more E. coli (P < 0.05) and had higher percentage of E. coli in the total bacteria population in the colon (P < 0.05) compared with their Jinhua counterparts. Both pig breeds tended to exhibit greater villous atrophy and crypt depth reduction in all of the intestinal segments with challenge. The expression of tight junction proteins decreased in response to ETEC K88 challenge in both pig breeds. The levels of the proinflammatory cytokines interferon (IFN)-γ, tumor necrosis factor-α, and IL-6 and the secretion of sIgA were positively altered whereas the levels of the anti-inflammatory cytokine IL-4 and transforming growth factor (TGF)-β were negatively altered by ETEC K88 challenge in both breeds. Jinhua pigs exhibited significantly higher levels of IFN-γ and TGF-β (P < 0.05) in the challenged group. Our

  1. Low socioeconomic status is associated with adverse events in children and teens on insulin pumps under a universal access program: a population-based cohort study

    PubMed Central

    Shulman, Rayzel; Stukel, Therese A; Miller, Fiona A; Newman, Alice; Daneman, Denis; Wasserman, Jonathan D; Guttmann, Astrid

    2016-01-01

    Objective To describe adverse events in pediatric insulin pump users since universal funding in Ontario and to explore the role of socioeconomic status and 24-hour support. Research design and methods Population-based cohort study of youth (<19 years) with type 1 diabetes (n=3193) under a universal access program in Ontario, Canada, from 2006 to 2013. We linked 2012 survey data from 33 pediatric diabetes centers to health administrative databases. The relationship between patient and center-level characteristics and time to first diabetic ketoacidosis (DKA) admission or death was tested using a Cox proportional hazards model and the rate of diabetes-related emergency department visits and hospitalizations with a Poisson model, both using generalized estimating equations. Results The rate of DKA was 5.28/100 person-years and mortality 0.033/100 person-years. Compared with the least deprived quintile, the risk of DKA or death for those in the most deprived quintile was significantly higher (HR 1.58, 95% CI 1.05 to 2.38) as was the rate of diabetes-related acute care use (RR 1.60, 95% CI 1.27 to 2.00). 24-hour support was not associated with these outcomes. Higher glycated hemoglobin, prior DKA, older age, and higher nursing patient load were associated with a higher risk of DKA or death. Conclusions The safety profile of pump therapy in the context of universal funding is similar to other jurisdictions and unrelated to 24-hour support. Several factors including higher deprivation were associated with an increased risk of adverse events and could be used to inform the design of interventions aimed at preventing poor outcomes in high-risk individuals. PMID:27547416

  2. Identification of microbial populations assimilating nitrogen from RDX in munitions contaminated military training range soils by high sensitivity stable isotope probing.

    PubMed

    Andeer, Peter; Stahl, David A; Lillis, Lorraine; Strand, Stuart E

    2013-09-17

    The leaching of RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) from particulates deposited in live-fire military training range soils contributes to significant pollution of groundwater. In situ microbial degradation has been proposed as a viable method for onsite containment of RDX. However, there is only a single report of RDX degradation in training range soils and the soil microbial communities involved in RDX degradation were not identified. Here we demonstrate aerobic RDX degradation in soils taken from a target area of an Eglin Air Force Base bombing range, C52N Cat's Eye, (Eglin, Florida U.S.A.). RDX-degradation activity was spatially heterogeneous (found in less than 30% of initial target area field samples) and dependent upon the addition of exogenous carbon sources to the soils. Therefore, biostimulation (with exogenous carbon sources) and bioaugmentation may be necessary to sustain timely and effective in situ microbial biodegradation of RDX. High sensitivity stable isotope probing analysis of extracted soils incubated with fully labeled (15)N-RDX revealed several organisms with (15)N-labeled DNA during RDX-degradation, including xplA-bearing organisms. Rhodococcus was the most prominent genus in the RDX-degrading soil slurries and was completely labeled with (15)N-nitrogen from the RDX. Rhodococcus and Williamsia species isolated from these soils were capable of using RDX as a sole nitrogen source and possessed the genes xplB and xplA associated with RDX-degradation, indicating these genes may be suitable genetic biomarkers for assessing RDX degradation potential in soils. Other highly labeled species were primarily Proteobacteria, including: Mesorhizobium sp., Variovorax sp., and Rhizobium sp.

  3. Increasing the Size of the Microbial Biomass Altered Bacterial Community Structure which Enhances Plant Phosphorus Uptake

    PubMed Central

    Shen, Pu; Murphy, Daniel Vaughan; George, Suman J.; Lapis-Gaza, Hazel; Xu, Minggang

    2016-01-01

    Agricultural production can be limited by low phosphorus (P) availability, with soil P being constrained by sorption and precipitation reactions making it less available for plant uptake. There are strong links between carbon (C) and nitrogen (N) availability and P cycling within soil P pools, with microorganisms being an integral component of soil P cycling mediating the availability of P to plants. Here we tested a conceptual model that proposes (i) the addition of readily-available organic substrates would increase the size of the microbial biomass thus exhausting the pool of easily-available P and (ii) this would cause the microbial biomass to access P from more recalcitrant pools. In this model it is hypothesised that the size of the microbial population is regulating access to less available P rather than the diversity of organisms contained within this biomass. To test this hypothesis we added mixtures of simple organic compounds that reflect typical root exudates at different C:N ratios to a soil microcosm experiment and assessed changes in soil P pools, microbial biomass and bacterial diversity measures. We report that low C:N ratio (C:N = 12.5:1) artificial root exudates increased the size of the microbial biomass while high C:N ratio (C:N = 50:1) artificial root exudates did not result in a similar increase in microbial biomass. Interestingly, addition of the root exudates did not alter bacterial diversity (measured via univariate diversity indices) but did alter bacterial community structure. Where C, N and P supply was sufficient to support plant growth the increase observed in microbial biomass occurred with a concurrent increase in plant yield. PMID:27893833

  4. Dynamic changes in microbial community structure and function in phenol-degrading microcosms inoculated with cells from a contaminated aquifer.

    PubMed

    Elliott, David R; Scholes, Julie D; Thornton, Steven F; Rizoulis, Athanasios; Banwart, Steven A; Rolfe, Stephen A

    2010-02-01

    Contamination of aquifers by organic pollutants threatens groundwater supplies and the environment. In situ biodegradation of organic pollutants by microbial communities is important for the remediation of contaminated sites, but our understanding of the relationship between microbial development and pollutant biodegradation is poor. A particular challenge is understanding the in situ status of microorganisms attached to solid surfaces, but not accessible via conventional sampling of groundwater. We have developed novel flow-through microcosms and examined dynamic changes in microbial community structure and function in a phenol-degrading system. Inoculation of these microcosms with a complex