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Sample records for access microbial populations

  1. Environmental whole-genome amplification to access microbial populations in contaminated sediments

    SciTech Connect

    Abulencia, Carl B; Wyborski, Denise L.; Garcia, Joseph A.; Podar, Mircea; Chen, Wenqiong; Chang, Sherman H.; Chang, Hwai W.; Watson, David B; Brodie, Eoin L.; Hazen, Terry; Keller, Martin

    2006-05-01

    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 {phi}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% 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% 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.

  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. Monitoring microbial population dynamics at low densities

    NASA Astrophysics Data System (ADS)

    Julou, Thomas; Desprat, Nicolas; Bensimon, David; Croquette, Vincent

    2012-07-01

    We propose a new and simple method for the measurement of microbial concentrations in highly diluted cultures. This method is based on an analysis of the intensity fluctuations of light scattered by microbial cells under laser illumination. Two possible measurement strategies are identified and compared using simulations and measurements of the concentration of gold nanoparticles. Based on this comparison, we show that the concentration of Escherichia coli and Saccharomyces cerevisiae cultures can be easily measured in situ across a concentration range that spans five orders of magnitude. The lowest measurable concentration is three orders of magnitude (1000×) smaller than in current optical density measurements. We show further that this method can also be used to measure the concentration of fluorescent microbial cells. In practice, this new method is well suited to monitor the dynamics of population growth at early colonization of a liquid culture medium. The dynamic data thus obtained are particularly relevant for microbial ecology studies.

  5. 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.

  6. BIOSORPTION OF HYDROPHOBIC ORGANIC POLLUTANTS BY MIXED MICROBIAL POPULATIONS

    EPA Science Inventory

    In recognition of the need to estimate biosorption for natural microbial populations, the variability of partition coefficients for two hydrophobic pollutants to natural populations from a variety of aquatic systems was investigated. Biosorption partition coefficients for pyrene ...

  7. Accessing the Soil Metagenome for Studies of Microbial Diversity▿ †

    PubMed Central

    Delmont, Tom O.; Robe, Patrick; Cecillon, Sébastien; Clark, Ian M.; Constancias, Florentin; Simonet, Pascal; Hirsch, Penny R.; Vogel, Timothy M.

    2011-01-01

    Soil microbial communities contain the highest level of prokaryotic diversity of any environment, and metagenomic approaches involving the extraction of DNA from soil can improve our access to these communities. Most analyses of soil biodiversity and function assume that the DNA extracted represents the microbial community in the soil, but subsequent interpretations are limited by the DNA recovered from the soil. Unfortunately, extraction methods do not provide a uniform and unbiased subsample of metagenomic DNA, and as a consequence, accurate species distributions cannot be determined. Moreover, any bias will propagate errors in estimations of overall microbial diversity and may exclude some microbial classes from study and exploitation. To improve metagenomic approaches, investigate DNA extraction biases, and provide tools for assessing the relative abundances of different groups, we explored the biodiversity of the accessible community DNA by fractioning the metagenomic DNA as a function of (i) vertical soil sampling, (ii) density gradients (cell separation), (iii) cell lysis stringency, and (iv) DNA fragment size distribution. Each fraction had a unique genetic diversity, with different predominant and rare species (based on ribosomal intergenic spacer analysis [RISA] fingerprinting and phylochips). All fractions contributed to the number of bacterial groups uncovered in the metagenome, thus increasing the DNA pool for further applications. Indeed, we were able to access a more genetically diverse proportion of the metagenome (a gain of more than 80% compared to the best single extraction method), limit the predominance of a few genomes, and increase the species richness per sequencing effort. This work stresses the difference between extracted DNA pools and the currently inaccessible complete soil metagenome. PMID:21183646

  8. 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)

  9. 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.

  10. 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.

  11. Experimental demonstration of an Allee effect in microbial populations.

    PubMed

    Kaul, RajReni B; Kramer, Andrew M; Dobbs, Fred C; Drake, John M

    2016-04-01

    Microbial populations can be dispersal limited. However, microorganisms that successfully disperse into physiologically ideal environments are not guaranteed to establish. This observation contradicts the Baas-Becking tenet: 'Everything is everywhere, but the environment selects'. Allee effects, which manifest in the relationship between initial population density and probability of establishment, could explain this observation. Here, we experimentally demonstrate that small populations ofVibrio fischeriare subject to an intrinsic demographic Allee effect. Populations subjected to predation by the bacterivoreCafeteria roenbergensisdisplay both intrinsic and extrinsic demographic Allee effects. The estimated critical threshold required to escape positive density-dependence is around 5, 20 or 90 cells ml(-1)under conditions of high carbon resources, low carbon resources or low carbon resources with predation, respectively. This work builds on the foundations of modern microbial ecology, demonstrating that mechanisms controlling macroorganisms apply to microorganisms, and provides a statistical method to detect Allee effects in data. PMID:27048467

  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. 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.

  14. Effect of Gamma radiation on microbial population of natural casings

    NASA Astrophysics Data System (ADS)

    Trigo, M. J.; Fraqueza, M. J.

    1998-06-01

    The high microbial load of fresh and dry natural casings increases the risk of meat product contamination with pathogenic microorganisms, agents of foodborn diseases. The aim of this work is to evaluate the killing effect of gamma radiation of the resident microbial population of pork and beef casings, to improve their hygiene and safety. Portions of fresh pork (small intestines and colon) and dry beef casings were irradiated in a Cobalt 60 source with with absorbed doses of 1,2,5 and 10 kGy. The D 10 values of total aerobic microorganisms in the pork casings were 1.65 kGy for colon and 1.54 kGy for small intestine. The D 10 value found in beef dry casings (small intestine) was 10.17 kGy. Radurization with 5 kGy was able to reduce, at least, 6 logs the coliform bacteria in pork casings. The killing effect over faecal Streptococci was 4 logs for pork fresh casings and 2 logs for beef dry casings. Gamma radiation with 5 kGy proved to be a convenient method to reduce substantially the microbial population of pork fresh casings. Otherwise, the microbial population of beef dry casings still resisted to 10 kGy.

  15. Strongly Deterministic Population Dynamics in Closed Microbial Communities

    NASA Astrophysics Data System (ADS)

    Frentz, Zak; Kuehn, Seppe; Leibler, Stanislas

    2015-10-01

    Biological systems are influenced by random processes at all scales, including molecular, demographic, and behavioral fluctuations, as well as by their interactions with a fluctuating environment. We previously established microbial closed ecosystems (CES) as model systems for studying the role of random events and the emergent statistical laws governing population dynamics. Here, we present long-term measurements of population dynamics using replicate digital holographic microscopes that maintain CES under precisely controlled external conditions while automatically measuring abundances of three microbial species via single-cell imaging. With this system, we measure spatiotemporal population dynamics in more than 60 replicate CES over periods of months. In contrast to previous studies, we observe strongly deterministic population dynamics in replicate systems. Furthermore, we show that previously discovered statistical structure in abundance fluctuations across replicate CES is driven by variation in external conditions, such as illumination. In particular, we confirm the existence of stable ecomodes governing the correlations in population abundances of three species. The observation of strongly deterministic dynamics, together with stable structure of correlations in response to external perturbations, points towards a possibility of simple macroscopic laws governing microbial systems despite numerous stochastic events present on microscopic levels.

  16. 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.

  17. CRISPR-Induced Distributed Immunity in Microbial Populations

    PubMed Central

    Young, Mark J.; Weitz, Joshua S.; Whitaker, Rachel J.

    2014-01-01

    In bacteria and archaea, viruses are the primary infectious agents, acting as virulent, often deadly pathogens. A form of adaptive immune defense known as CRISPR-Cas enables microbial cells to acquire immunity to viral pathogens by recognizing specific sequences encoded in viral genomes. The unique biology of this system results in evolutionary dynamics of host and viral diversity that cannot be fully explained by the traditional models used to describe microbe-virus coevolutionary dynamics. Here, we show how the CRISPR-mediated adaptive immune response of hosts to invading viruses facilitates the emergence of an evolutionary mode we call distributed immunity - the coexistence of multiple, equally-fit immune alleles among individuals in a microbial population. We use an eco-evolutionary modeling framework to quantify distributed immunity and demonstrate how it emerges and fluctuates in multi-strain communities of hosts and viruses as a consequence of CRISPR-induced coevolution under conditions of low viral mutation and high relative numbers of viral protospacers. We demonstrate that distributed immunity promotes sustained diversity and stability in host communities and decreased viral population density that can lead to viral extinction. We analyze sequence diversity of experimentally coevolving populations of Streptococcus thermophilus and their viruses where CRISPR-Cas is active, and find the rapid emergence of distributed immunity in the host population, demonstrating the importance of this emergent phenomenon in evolving microbial communities. PMID:25000306

  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 distribution, settlement patterns and accessibility across Africa in 2010.

    PubMed

    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

  20. Growth dynamics and the evolution of cooperation in microbial populations

    NASA Astrophysics Data System (ADS)

    Cremer, Jonas; Melbinger, Anna; Frey, Erwin

    2012-02-01

    Microbes providing public goods are widespread in nature despite running the risk of being exploited by free-riders. However, the precise ecological factors supporting cooperation are still puzzling. Following recent experiments, we consider the role of population growth and the repetitive fragmentation of populations into new colonies mimicking simple microbial life-cycles. Individual-based modeling reveals that demographic fluctuations, which lead to a large variance in the composition of colonies, promote cooperation. Biased by population dynamics these fluctuations result in two qualitatively distinct regimes of robust cooperation under repetitive fragmentation into groups. First, if the level of cooperation exceeds a threshold, cooperators will take over the whole population. Second, cooperators can also emerge from a single mutant leading to a robust coexistence between cooperators and free-riders. We find frequency and size of population bottlenecks, and growth dynamics to be the major ecological factors determining the regimes and thereby the evolutionary pathway towards cooperation.

  1. "Inosaminoacids": novel inositol-amino acid hybrid structures accessed by microbial arene oxidation.

    PubMed

    Pilgrim, Sarah; Kociok-Köhn, Gabriele; Lloyd, Matthew D; Lewis, Simon E

    2011-04-28

    Microbial 1,2-dihydroxylation of sodium benzoate permits the rapid construction of novel inositol-amino acid hybrid structures. Both β- and γ-amino acids are accessible by means of an acylnitroso Diels-Alder cycloaddition. PMID:21409268

  2. 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. PMID:26747638

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

    PubMed

    Martins, Suzana Cláudia Silveira; 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

  4. 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

  5. Single gene-based distinction of individual microbial genomes from a mixed population of microbial cells

    PubMed Central

    Tamminen, Manu V.; Virta, Marko P. J.

    2015-01-01

    Recent progress in environmental microbiology has revealed vast populations of microbes in any given habitat that cannot be detected by conventional culturing strategies. The use of sensitive genetic detection methods such as CARD-FISH and in situ PCR have been limited by the cell wall permeabilization requirement that cannot be performed similarly on all cell types without lysing some and leaving some nonpermeabilized. Furthermore, the detection of low copy targets such as genes present in single copies in the microbial genomes, has remained problematic. We describe an emulsion-based procedure to trap individual microbial cells into picoliter-volume polyacrylamide droplets that provide a rigid support for genetic material and therefore allow complete degradation of cellular material to expose the individual genomes. The polyacrylamide droplets are subsequently converted into picoliter-scale reactors for genome amplification. The amplified genomes are labeled based on the presence of a target gene and differentiated from those that do not contain the gene by flow cytometry. Using the Escherichia coli strains XL1 and MC1061, which differ with respect to the presence (XL1), or absence (MC1061) of a single copy of a tetracycline resistance gene per genome, we demonstrate that XL1 genomes present at 0.1% of MC1061 genomes can be differentiated using this method. Using a spiked sediment microbial sample, we demonstrate that the method is applicable to highly complex environmental microbial communities as a target gene-based screen for individual microbes. The method provides a novel tool for enumerating functional cell populations in complex microbial communities. We envision that the method could be optimized for fluorescence-activated cell sorting to enrich genetic material of interest from complex environmental samples. PMID:25814987

  6. The bacteriocin bactofencin A subtly modulates gut microbial populations.

    PubMed

    Guinane, Caitriona M; Lawton, Elaine M; O'Connor, Paula M; O'Sullivan, Órla; Hill, Colin; Ross, R Paul; Cotter, Paul D

    2016-08-01

    The diverse and dynamic microbiota of the gastrointestinal tract represents a vast source of bioactive substances. These include bacteriocins, which are antimicrobial peptides with the potential to modulate gut populations to impact positively on human health. Although several gut-derived bacteriocins have been isolated, there remain only a few exceptional studies in which their influence on microbial populations within the gut has been investigated. To facilitate such investigations, in vitro faecal fermentation systems can be used to simulate the anaerobic environment of the colon. In this instance, such a system was employed to explore the impact of bactofencin A, a novel broad spectrum class IId bacteriocin produced by gut isolates of Lactobacillus salivarius, on intestinal populations and overall microbial diversity. The study reveals that, although bactofencin A is a broad spectrum bacteriocin, it has a relatively subtle influence on intestinal communities, with a potentially positive impact on anaerobic populations such as Bacteroides, Clostridium and Bifidibacterium spp. The strategy taken is an important first step in investigating the merits of using bactofencin A to manipulate the gut microbiota in a beneficial way for health. PMID:27154638

  7. Linking Toluene Degradation with Specific Microbial Populations in Soil

    PubMed Central

    Hanson, Jessica R.; Macalady, Jennifer L.; Harris, David; Scow, Kate M.

    1999-01-01

    Phospholipid fatty acid (PLFA) analysis of a soil microbial community was coupled with 13C isotope tracer analysis to measure the community’s response to addition of 35 μg of [13C]toluene ml of soil solution−1. After 119 h of incubation with toluene, 96% of the incorporated 13C was detected in only 16 of the total 59 PLFAs (27%) extracted from the soil. Of the total 13C-enriched PLFAs, 85% were identical to the PLFAs contained in a toluene-metabolizing bacterium isolated from the same soil. In contrast, the majority of the soil PLFAs (91%) became labeled when the same soil was incubated with [13C]glucose. Our study showed that coupling 13C tracer analysis with PLFA analysis is an effective technique for distinguishing a specific microbial population involved in metabolism of a labeled substrate in complex environments such as soil. PMID:10583996

  8. Optimization modeling to maximize population access to comprehensive stroke centers

    PubMed Central

    Branas, Charles C.; Kasner, Scott E.; Wolff, Catherine; Williams, Justin C.; Albright, Karen C.; Carr, Brendan G.

    2015-01-01

    Objective: The location of comprehensive stroke centers (CSCs) is critical to ensuring rapid access to acute stroke therapies; we conducted a population-level virtual trial simulating change in access to CSCs using optimization modeling to selectively convert primary stroke centers (PSCs) to CSCs. Methods: Up to 20 certified PSCs per state were selected for conversion to maximize the population with 60-minute CSC access by ground and air. Access was compared across states based on region and the presence of state-level emergency medical service policies preferentially routing patients to stroke centers. Results: In 2010, there were 811 Joint Commission PSCs and 0 CSCs in the United States. Of the US population, 65.8% had 60-minute ground access to PSCs. After adding up to 20 optimally located CSCs per state, 63.1% of the US population had 60-minute ground access and 86.0% had 60-minute ground/air access to a CSC. Across states, median CSC access was 55.7% by ground (interquartile range 35.7%–71.5%) and 85.3% by ground/air (interquartile range 59.8%–92.1%). Ground access was lower in Stroke Belt states compared with non–Stroke Belt states (32.0% vs 58.6%, p = 0.02) and lower in states without emergency medical service routing policies (52.7% vs 68.3%, p = 0.04). Conclusion: Optimal system simulation can be used to develop efficient care systems that maximize accessibility. Under optimal conditions, a large proportion of the US population will be unable to access a CSC within 60 minutes. PMID:25740858

  9. 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.

  10. [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. PMID:23074804

  11. 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.

  12. 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.

  13. Characterization of Microbial Population Shifts during Sample Storage

    PubMed Central

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

    2011-01-01

    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. PMID:22363327

  14. Modeling population access to New Zealand public hospitals

    PubMed Central

    Brabyn, Lars; Skelly, Chris

    2002-01-01

    This paper demonstrates a method for estimating the geographical accessibility of public hospitals. Cost path analysis was used to determine the minimum travel time and distance to the closest hospital via a road network. This analysis was applied to 38,000 census enumeration district centroids in New Zealand allowing geographical access to be linked to local populations. Average time and distance statistics have been calculated for local populations by modeling the total travel of a population if everybody visited a hospital once. These types of statistics can be generated for different population groups and enable comparisons to be made between regions. This study has shown that the northern and southern parts of New Zealand have high average travel times to hospital services. PMID:12459048

  15. 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...

  16. Spatial Shifts in Microbial Population Structure Within Poultry Litter Associated with Physicochemical Properties

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 t...

  17. 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

  18. An in vitro comparison of microbial ingress into 8 different needleless IV access devices.

    PubMed

    Casey, Anna; Karpanen, Tarja; Nightingale, Peter; Elliott, Tom

    2015-01-01

    There are conflicting reports of the effect needleless intravenous access devices have on rates of catheter-related bloodstream infection. The aim of this study was to identify any differences between the rates of microbial ingress into 8 different devices following contamination. Each type of device was subjected to a 7-day clinical simulation that involved repeated microbial contamination of the injection site and decontamination followed by saline flushes. Significant differences in the number of microorganisms associated with each device were detected in the saline eluates. Three positive-displacement mechanical valves were associated with the ingress of significantly fewer microorganisms compared with other devices. PMID:25545971

  19. 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.

  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. Metagenomic Approach for Understanding Microbial Population from Petroleum Muck

    PubMed Central

    Joshi, M. N.; Dhebar, S. V.; Dhebar, S. V.; Bhargava, P.; Pandit, A. S.; Patel, R. P.; Saxena, A. K.

    2014-01-01

    Petroleum products play a major role in fueling the economy of the world but the pollution they create has become a critical issue. Understanding the diversity present in pipeline muck will help with the exploration of new microbial strains with better hydrocarbon degrading capacities for bioremediation of polluted sites. This study provides an analysis of petroleum muck using next generation sequencing. PMID:24874664

  3. Metagenomic approach for understanding microbial population from petroleum muck.

    PubMed

    Joshi, M N; Dhebar, S V; Dhebar, S V; Bhargava, P; Pandit, A S; Patel, R P; Saxena, A K; Bagatharia, S B

    2014-01-01

    Petroleum products play a major role in fueling the economy of the world but the pollution they create has become a critical issue. Understanding the diversity present in pipeline muck will help with the exploration of new microbial strains with better hydrocarbon degrading capacities for bioremediation of polluted sites. This study provides an analysis of petroleum muck using next generation sequencing. PMID:24874664

  4. 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...

  5. 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

  6. 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. PMID

  7. 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.

  8. 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.

  9. 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

  10. 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. PMID:26858133

  11. 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. PMID:26765966

  12. 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

  13. Molecular Characterization of Water Column Microbial Populations within the Northern Gulf of Mexico Hypoxic Zone

    NASA Astrophysics Data System (ADS)

    Mills, H. J.; Reese, B. K.; Romero, B.

    2012-12-01

    The Gulf of Mexico hypoxic zone displays spatial and temporal variability on seasonal, diurnal, and hourly timescales. The highly dynamic geochemistry can be a result of physical and chemical factors as well as pelagic microbial populations. As part of an ongoing project to determine the mechanisms controlling hypoxia and understand the biological factors within this region, shifts in the composition of the metabolically active microbial populations within the water column were characterized. Understanding these shifts provide information on microbial populations that have the potential to decrease oxygen concentrations through respiration and increase oxygen through photosynthesis. Temporal and spatial variations of metabolically active microbial populations were investigated along a well-studied 20 m isobath extending east of Terrebonne Bay to a location offshore from the Atchafalaya Bay. An RNA-based molecular characterization of the microbial population was used to determine the distribution of the metabolically active lineages. Bacterial SSU rRNA were pyrosequenced (Roche 454 FLX) providing over 700,000 sequences with an average read length of more than 400 bases. Known photosynthetic lineages varied in frequency of detection at depth and time of sampling, as was expected. Additional lineages with the capacity for suboxic metabolic processes were detected mid-water column associated with hypoxic water formation. These data suggest hypoxic conditions persist long enough in the mid-water to promote a physiological response within the microbial populations. In addition, temporal switches between photosynthesis and respiration should be considered when analyzing the extent of hypoxia. The techniques used provide a unique view of the biological mechanisms controlling hypoxia within the northern Gulf of Mexico.

  14. Strain-level microbial epidemiology and population genomics from shotgun metagenomics.

    PubMed

    Scholz, Matthias; Ward, Doyle V; Pasolli, Edoardo; Tolio, Thomas; Zolfo, Moreno; Asnicar, Francesco; Truong, Duy Tin; Tett, Adrian; Morrow, Ardythe L; Segata, Nicola

    2016-05-01

    Identifying microbial strains and characterizing their functional potential is essential for pathogen discovery, epidemiology and population genomics. We present pangenome-based phylogenomic analysis (PanPhlAn; http://segatalab.cibio.unitn.it/tools/panphlan), a tool that uses metagenomic data to achieve strain-level microbial profiling resolution. PanPhlAn recognized outbreak strains, produced the largest strain-level population genomic study of human-associated bacteria and, in combination with metatranscriptomics, profiled the transcriptional activity of strains in complex communities. PMID:26999001

  15. 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

  16. Radiation resistance of the natural microbial population in buffer materials

    SciTech Connect

    Stroes-Gascoyne, S.; Lucht, L.M.; Borsa, J.; Delaney, T.L.; Haveman, S.A.; Hamon, C.J.

    1995-12-31

    The radiation sensitivity of naturally occurring microorganisms in buffer materials was investigated as well as the sensitivity of Bacillus subtillis spores and Acinetobacter radioresistens in a buffer matrix. The D{sub 10} values obtained in these radiation experiments varied from 0.34 to 1.68 kGy and it was calculated that the surface of a nuclear fuel waste container would be sterilized in 9 to 33 d after emplacement, depending on the type of container, and the initial bioburden. This suggests that formation of biofilms and microbially influenced corrosion would not be of concern of some time after emplacement. The results also indicated that sterilization throughout a 25 cm thick buffer layer is unlikely and that repopulation of the container surface after some time is a possibility, depending on the mobility of microbes in compacted buffer material.

  17. 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...

  18. Profiling the Change in Fecal Microbial Populations of Mares and Foals Over Time

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The gastrointestinal tract of the mature horse contains a complex community of microorganisms, many of which aid in digestion. Little information is available concerning the establishment of these microbial populations in young horses. The limited research that has been conducted has utilized cultur...

  19. USE OF ARISA TO MONITOR SHIFTS IN RUMEN MICROBIAL POPULATIONS CAUSED BY CHANGES IN DIET

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective was to determine whether automated ribosomal intergenic spacer analysis (ARISA) is sensitive enough to detect shifts in rumen microbial populations caused by dietary changes. Six ruminally cannulated, non-lactating, non-pregnant Holstein cows were sampled for rumen contents in a random...

  20. 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...

  1. 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

  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. 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.

  4. 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.

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

    DOE PAGESBeta

    Wilke, Andreas; Bischof, Jared; Harrison, Travis; Brettin, Tom; D'Souza, Mark; Gerlach, Wolfgang; Matthews, Hunter; Paczian, Tobias; Wilkening, Jared; Glass, Elizabeth M.; et al

    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

  6. A RESTful API for Accessing Microbial Community Data for MG-RAST

    PubMed Central

    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

    2015-01-01

    Metagenomic sequencing has produced significant amounts of data in recent years. For example, as of summer 2013, MG-RAST 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. PMID:25569221

  7. 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.

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

    PubMed

    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

    2015-01-01

    Metagenomic sequencing has produced significant amounts of data in recent years. For example, as of summer 2013, MG-RAST 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. PMID:25569221

  9. Microbial Dioxygenase Gene Population Shifts during Polycyclic Aromatic Hydrocarbon Biodegradation

    PubMed Central

    Ní Chadhain, Sinéad M.; Norman, R. Sean; Pesce, Karen V.; Kukor, Jerome J.; Zylstra, Gerben J.

    2006-01-01

    The degradation of polycyclic aromatic hydrocarbons (PAHs) by bacteria has been widely studied. While many pure cultures have been isolated and characterized for their ability to grow on PAHs, limited information is available on the diversity of microbes involved in PAH degradation in the environment. We have designed generic PCR primers targeting the gene fragment encoding the Rieske iron sulfur center common to all PAH dioxygenase enzymes. These Rieske primers were employed to track dioxygenase gene population shifts in soil enrichment cultures following exposure to naphthalene, phenanthrene, or pyrene. PAH degradation was monitored by gas chromatograph with flame ionization detection. DNA was extracted from the enrichment cultures following PAH degradation. 16S rRNA and Rieske gene fragments were PCR amplified from DNA extracted from each enrichment culture and an unamended treatment. The PCR products were cloned and sequenced. Molecular monitoring of the enrichment cultures before and after PAH degradation using denaturing gradient gel electrophoresis and 16S rRNA gene libraries suggests that specific phylotypes of bacteria were associated with the degradation of each PAH. Sequencing of the cloned Rieske gene fragments showed that different suites of genes were present in soil microbe populations under each enrichment culture condition. Many of the Rieske gene fragment sequences fell into clades which are distinct from the reference dioxygenase gene sequences used to design the PCR primers. The ability to profile not only the bacterial community but also the dioxygenases which they encode provides a powerful tool for both assessing bioremediation potential in the environment and for the discovery of novel dioxygenase genes. PMID:16751518

  10. Patient-centred access to health care: conceptualising access at the interface of health systems and populations

    PubMed Central

    2013-01-01

    Background Access is central to the performance of health care systems around the world. However, access to health care remains a complex notion as exemplified in the variety of interpretations of the concept across authors. The aim of this paper is to suggest a conceptualisation of access to health care describing broad dimensions and determinants that integrate demand and supply-side-factors and enabling the operationalisation of access to health care all along the process of obtaining care and benefiting from the services. Methods A synthesis of the published literature on the conceptualisation of access has been performed. The most cited frameworks served as a basis to develop a revised conceptual framework. Results Here, we view access as the opportunity to identify healthcare needs, to seek healthcare services, to reach, to obtain or use health care services, and to actually have a need for services fulfilled. We conceptualise five dimensions of accessibility: 1) Approachability; 2) Acceptability; 3) Availability and accommodation; 4) Affordability; 5) Appropriateness. In this framework, five corresponding abilities of populations interact with the dimensions of accessibility to generate access. Five corollary dimensions of abilities include: 1) Ability to perceive; 2) Ability to seek; 3) Ability to reach; 4) Ability to pay; and 5) Ability to engage. Conclusions This paper explains the comprehensiveness and dynamic nature of this conceptualisation of access to care and identifies relevant determinants that can have an impact on access from a multilevel perspective where factors related to health systems, institutions, organisations and providers are considered with factors at the individual, household, community, and population levels. PMID:23496984

  11. 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, "Knowledge Base…

  12. Microbial Genomics of a Host-Associated Commensal Bacterium in Fragmented Populations of Endangered Takahe.

    PubMed

    Grange, Zoë L; Gartrell, Brett D; Biggs, Patrick J; Nelson, Nicola J; Anderson, Marti; French, Nigel P

    2016-05-01

    Isolation of wildlife into fragmented populations as a consequence of anthropogenic-mediated environmental change may alter host-pathogen relationships. Our understanding of some of the epidemiological features of infectious disease in vulnerable populations can be enhanced by the use of commensal bacteria as a proxy for invasive pathogens in natural ecosystems. The distinctive population structure of a well-described meta-population of a New Zealand endangered flightless bird, the takahe (Porphyrio hochstetteri), provided a unique opportunity to investigate the influence of host isolation on enteric microbial diversity. The genomic epidemiology of a prevalent rail-associated endemic commensal bacterium was explored using core genome and ribosomal multilocus sequence typing (rMLST) of 70 Campylobacter sp. nova 1 isolated from one third of the takahe population resident in multiple locations. While there was evidence of recombination between lineages, bacterial divergence appears to have occurred and multivariate analysis of 52 rMLST genes revealed location-associated differentiation of C. sp. nova 1 sequence types. Our results indicate that fragmentation and anthropogenic manipulation of populations can influence host-microbial relationships, with potential implications for niche adaptation and the evolution of micro-organisms in remote environments. This study provides a novel framework in which to explore the complex genomic epidemiology of micro-organisms in wildlife populations. PMID:26707136

  13. 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.

  14. Effect of oenological practices on microbial populations using culture-independent techniques.

    PubMed

    Andorrà, Imma; Landi, Sara; Mas, Albert; Guillamón, José M; Esteve-Zarzoso, Braulio

    2008-10-01

    Sulphur dioxide (SO(2)) addition and yeast inoculation are well-established practices in winemaking for restricting the growth of indigenous yeasts and bacterial populations. The effect of these oenological practices on wine microbial populations has been evaluated using culture-independent methods. These are quantitative PCR (qPCR) for the enumeration of yeasts, lactic acid bacteria (LAB) and acetic acid bacteria (AAB), and PCR-DGGE to determine the yeast and bacteria species diversity. The PCR-DGGE method detected a low yeast and bacteria species diversity. On the contrary, the specificity of the primers designed for the qPCR allowed that minor microbial groups such as Hanseniaspora were accurately quantified regardless of a large presence of other microbial groups such as Saccharomyces. From an oenological point of view, inoculation increased the proportion of Saccharomyces vs. non-Saccharomyces in a shorter time. Hanseniaspora increased during the first phase and decreased during the latter phases of the process, especially in the sulphited fermentations. Both yeast inoculation and SO(2) kept the LAB populations at very low level, while the AAB populations were hardly affected by these two practices. PMID:18721672

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Targeted Access to the Genomes of Low Abundance Organisms in Complex Microbial Communities

    SciTech Connect

    Podar, Mircea; Abulencia, Carl; Walcher, Marion; Hutchinson, Don; Zengler, Karsten; Garcia, Joseph; Holland, Trevin; Cotton, Dave; Hauser, Loren John; Keller, Martin

    2007-01-01

    Current metagenomic approaches to the study of complex microbial consortia provide a glimpse into the community metabolism, and occasionally allow genomic assemblies for the most abundant organisms. However, little information is gained for the members of the community present at low frequency, especially those representing yet uncultured taxa-which includes the bulk of the diversity present in most environments. Here we used phylogenetically directed cell separation by fluorescence in situ hybridization and flow cytometry, followed by amplification and sequencing of a fraction of the genomic DNA of several bacterial cells that belong to the TM7 phylum. Partial genomic assembly allowed, for the first time, a look into the evolution and potential metabolism of a soil representative from this group of organisms for which there are no species in stable laboratory cultures. Genomic reconstruction from targeted cells of uncultured organisms directly isolated from the environment represents a powerful approach to access any specific members of a community and an alternative way to assess the community metabolic potential.

  1. 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. PMID:25727367

  2. Management and control of microbial populations' development in LSS of missions of different durations.

    PubMed

    Somova, L A; Pechurkin, N S

    2005-01-01

    The problem of interaction between man and microorganisms in closed habitats is an inextricable part of the whole problem of co-existence between macro- and microorganisms. Concerning the support of human life in closed habitat, we can, conventionally, divide microorganisms, acting in life support system (LSS) into three groups: useful, neutral and harmful. The tasks, for human beings for optimal coexistence with microhabitants seem to be trivial: (1) to increase the activity of useful forms, (2) decrease the activity harmful forms, (3) not allow the neutral forms to become the harmful ones and even to help them to gain useful activity. The task of efficient management and control of microbial population's development in LSS highly depends on mission duration. As for short-term missions without recycling, the proper hygienic procedures are developed. For longer missions, the probability of transformation of the neutral forms into the harmful ones is becoming more dangerous. The LSS for long-term missions are to use cycling-recycling systems, including system with biological recycling. In these systems, microbial populations as regenerative link should be useful and active agents. Some problems of microbial populations control and management are discussed in the paper. PMID:16175696

  3. 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…

  4. 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…

  5. 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…

  6. 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

  7. Negative frequency-dependent interactions can underlie phenotypic heterogeneity in a clonal microbial population.

    PubMed

    Healey, David; Axelrod, Kevin; Gore, Jeff

    2016-01-01

    Genetically identical cells in microbial populations often exhibit a remarkable degree of phenotypic heterogeneity even in homogenous environments. Such heterogeneity is commonly thought to represent a bet-hedging strategy against environmental uncertainty. However, evolutionary game theory predicts that phenotypic heterogeneity may also be a response to negative frequency-dependent interactions that favor rare phenotypes over common ones. Here we provide experimental evidence for this alternative explanation in the context of the well-studied yeast GAL network. In an environment containing the two sugars glucose and galactose, the yeast GAL network displays stochastic bimodal activation. We show that in this mixed sugar environment, GAL-ON and GAL-OFF phenotypes can each invade the opposite phenotype when rare and that there exists a resulting stable mix of phenotypes. Consistent with theoretical predictions, the resulting stable mix of phenotypes is not necessarily optimal for population growth. We find that the wild-type mixed strategist GAL network can invade populations of both pure strategists while remaining uninvasible by either. Lastly, using laboratory evolution we show that this mixed resource environment can directly drive the de novo evolution of clonal phenotypic heterogeneity from a pure strategist population. Taken together, our results provide experimental evidence that negative frequency-dependent interactions can underlie the phenotypic heterogeneity found in clonal microbial populations. PMID:27487817

  8. Microbial Populations Associated with Treatment of an Industrial Dye Effluent in an Anaerobic Baffled Reactor

    PubMed Central

    Plumb, Jason J.; Bell, Joanne; Stuckey, David C.

    2001-01-01

    Fluorescent in situ hybridization (FISH) using 16S and 23S rRNA-targeted probes together with construction of an archaeal 16S ribosomal DNA (rDNA) clone library was used to characterize the microbial populations of an anaerobic baffled reactor successfully treating industrial dye waste. Wastewater produced during the manufacture of food dyes containing several different azo and other dye compounds was decolorized and degraded under sulfidogenic and methanogenic conditions. Use of molecular methods to describe microbial populations showed that a diverse group of Bacteria and Archaea was involved in this treatment process. FISH enumeration showed that members of the gamma subclass of the class Proteobacteria and bacteria in the Cytophaga-Flexibacter-Bacteroides phylum, together with sulfate-reducing bacteria, were prominent members of a mixed bacterial population. A combination of FISH probing and analysis of 98 archaeal 16S rDNA clone inserts revealed that together with the bacterial population, a methanogenic population dominated by Methanosaeta species and containing species of Methanobacterium and Methanospirillum and a relatively unstudied methanogen, Methanomethylovorans hollandica, contributed to successful anaerobic treatment of the industrial waste. We suggest that sulfate reducers, or more accurately sulfidogenic bacteria, together with M. hollandica contribute considerably to the treatment process through metabolism of dye-associated sulfonate groups and subsequent conversion of sulfur compounds to carbon dioxide and methane. PMID:11425746

  9. Improving rumen ecology and microbial population by dried rumen digesta in beef cattle.

    PubMed

    Cherdthong, Anusorn; Wanapat, Metha; Saenkamsorn, Anuthida; Supapong, Chanadol; Anantasook, Nirawan; Gunun, Pongsatorn

    2015-06-01

    Four Thai native beef cattle with initial body weight (BW) of 91.8 ± 4.75 kg were randomly assigned according to a 4 × 4 Latin square design to receive four concentrates replacement levels of soybean meal (SBM) by dried rumen digesta (DRD) at 0, 33, 67, and 100 % on dry matter (DM) basis. All cattle were fed rice straw ad libitum while additional concentrate was fed at 0.5 % BW daily. The experiment was conducted for four periods of 21 days. Rumen fluid was analyzed for predominant cellulolytic bacterial population by using real-time PCR technique. Increasing levels of DRD did not alter total feed intake, ruminal pH and temperature, and plasma urea nitrogen (P > 0.05). Protozoa and fungal population were not differed by DRD supplementation while population of bacteria at 4 h post feeding was increased when SBM was replaced with DRD at 66 and 100 % DM. Population of total bacteria and R. flavefaciens at 4 h post feeding were significantly highest with inclusion of 100 % of DRD in the ration. The experimental diets has no effect on excretion and absorption of purine derivatives (P > 0.05), while microbial crude protein and efficiency of microbial N synthesis were significantly increased with DRD inclusion in the diet and highest with 100 % DRD replacement (P > 0.05). Replacement of SBM by DRD at 100 % DM improved the rumen ecology and microbial population in beef cattle fed on rice straw. PMID:25851930

  10. 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

  11. 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.

  12. 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

  13. Microbial population dynamics in a thermophilic methane digester fed with garbage.

    PubMed

    Cheon, J; Hong, F; Hidaka, T; Koshikawa, H; Tsuno, H

    2007-01-01

    The diversity of microbial communities in three full-scale thermophilic anaerobic digesters which treated garbage, sewage sludge and livestock wastes (hereafter called TGD, TSD and TLD, respectively) was investigated using 16S rDNA clone libraries in triplicate. The population dynamics of TGD were also studied. The purposes were to show the microbial diversity in each reactor and to suggest which key microbes in a thermophilic methane digester fed with garbage, including a check of reproducibility and the suggestion of an error range in this molecular biology method. 736 clones were identified, and the maximum error was estimated to be around +/-10% for the same OTU (operational taxonomic unit) and for most detected OTUs. The most frequently detected OTU shows a close relationship to Uncultured bacterium clone MBA08, Unidentified bacterium clone TUG22 and Uncultured archaeal symbiont PA204 in TGD, TSD and TLD, respectively. The microbial population dynamics in TGD were studied over a period of 90 days, and the occupying ratios of Bacillus infernus and Methanothermobacter wolfeii were shown to change with the change in VFA concentration. From the dynamic change and characteristics of the microbes, it is concluded that Bacillus infernus and Methanothermobacter wolfeii played an important role and were recommended as key microbes in TGD. PMID:17564383

  14. [Nutrient contents and microbial populations of aeolian sandy soil in Sanjiangyuan region of Qinghai Province].

    PubMed

    Lin, Chao-feng; Chen, Zhan-quan; Xue, Quan-hong; Lai, Hang-xian; Chen, Lai-sheng; Zhang, Deng-shan

    2007-01-01

    Sanjiangyuan region (the headstream of three rivers) in Qinghai Province of China is the highest and largest inland alpine wetland in the world. The study on the nutrient contents and microbial populations of aeolian sandy soils in this region showed that soil organic matter content increased with the evolution of aeolian sand dunes from un-stabilized to stabilized state, being 5.9 and 3.8 times higher in stabilized sand dune than in mobile and semi-stabilized sand dunes, respectively. Soil nitrogen and phosphorus contents increased in line with the amount of organic matter, while potassium content and pH value varied slightly. The microbial populations changed markedly with the development of vegetation, fixing of mobile sand, and increase of soil nutrients. The quantities of soil bacteria, fungi and actinomycetes were 4.0 and 2.8 times, 19.6 and 6.3 times, and 12.4 and 2.6 times higher in stabilized and semi-stabilized sand dunes than in mobile sand dune, respectively, indicating that soil microbial bio-diversity was increased with the evolution of aeolian sand dunes from mobile to stabilized state. In addition, the quantities of soil microbes were closely correlated with the contents of soil organic matter, total nitrogen, and available nitrogen and phosphorus, but not correlated with soil total phosphorus, total and available potassium, or pH value. PMID:17396507

  15. Activity and growth of microbial populations in pressurized deep-sea sediment and animal gut samples.

    PubMed

    Tabor, P S; Deming, J W; Ohwada, K; Colwell, R R

    1982-08-01

    Benthic animals and sediment samples were collected at deep-sea stations in the northwest (3,600-m depth) and southeast (4,300- and 5200-m depths) Atlantic Ocean. Utilization rates of [14C]glutamate (0.67 to 0.74 nmol) in sediment suspensions incubated at in situ temperatures and pressures (3 to 5 degrees C and 360, 430, or 520 atmospheres) were relatively slow, ranging from 0.09 to 0.39 nmol g-1 day-1, whereas rates for pressurized samples of gut suspensions varied widely, ranging from no detectable activity to a rapid rate of 986 nmol g-1 day-1. Gut flora from a holothurian specimen and a fish demonstrated rapid, barophilic substrate utilization, based on relative rates calculated for pressurized samples and samples held at 1 atm (101.325 kPa). Substrate utilization by microbial populations in several sediment samples was not inhibited by in situ pressure. Deep-sea pressures did not restrict growth, measured as doubling time, of culturable bacteria present in a northwest Atlantic sediment sample and in a gut suspension prepared from an abyssal scavenging amphipod. From the results of this study, it was concluded that microbial populations in benthic environments can demonstrate significant metabolic activity under deep-ocean conditions of temperature and pressure. Furthermore, rates of microbial activity in the guts of benthic macrofauna are potentially more rapid than in surrounding deep-sea sediments. PMID:6127054

  16. Activity and growth of microbial populations in pressurized deep-sea sediment and animal gut samples.

    PubMed Central

    Tabor, P S; Deming, J W; Ohwada, K; Colwell, R R

    1982-01-01

    Benthic animals and sediment samples were collected at deep-sea stations in the northwest (3,600-m depth) and southeast (4,300- and 5200-m depths) Atlantic Ocean. Utilization rates of [14C]glutamate (0.67 to 0.74 nmol) in sediment suspensions incubated at in situ temperatures and pressures (3 to 5 degrees C and 360, 430, or 520 atmospheres) were relatively slow, ranging from 0.09 to 0.39 nmol g-1 day-1, whereas rates for pressurized samples of gut suspensions varied widely, ranging from no detectable activity to a rapid rate of 986 nmol g-1 day-1. Gut flora from a holothurian specimen and a fish demonstrated rapid, barophilic substrate utilization, based on relative rates calculated for pressurized samples and samples held at 1 atm (101.325 kPa). Substrate utilization by microbial populations in several sediment samples was not inhibited by in situ pressure. Deep-sea pressures did not restrict growth, measured as doubling time, of culturable bacteria present in a northwest Atlantic sediment sample and in a gut suspension prepared from an abyssal scavenging amphipod. From the results of this study, it was concluded that microbial populations in benthic environments can demonstrate significant metabolic activity under deep-ocean conditions of temperature and pressure. Furthermore, rates of microbial activity in the guts of benthic macrofauna are potentially more rapid than in surrounding deep-sea sediments. PMID:6127054

  17. Variation in microbial population during composting of agro-industrial waste.

    PubMed

    Coelho, Luísa; Reis, Mário; Dionísio, Lídia

    2013-05-01

    Two compost piles were prepared, using two ventilation systems: forced ventilation and ventilation through mechanical turning. The material to compost was a mixture of orange waste, olive pomace, and grass clippings (2:1:1 v/v). During the composting period (375 days), samples were periodically taken from both piles, and the enumeration of fungi, actinomycetes, and heterotrophic bacteria was carried out. All studied microorganisms were incubated at 25 and 55 °C after inoculation in appropriate growth media. Fungi were dominant in the early stages of both composting processes; heterotrophic bacteria proliferated mainly during the thermophilic stage, and actinomycetes were more abundant in the final stage of the composting process. Our results showed that the physical and chemical parameters: temperature, pH, moisture, and aeration influenced the variation of the microbial population along the composting process. This study demonstrated that composting of these types of wastes, despite the prolonged mesophilic stage, provided an expected microbial variation. PMID:22699450

  18. New Methods for Analysis of Spatial Distribution and Coaggregation of Microbial Populations in Complex Biofilms

    PubMed Central

    Almstrand, Robert; Daims, Holger; Persson, Frank; Sörensson, Fred

    2013-01-01

    In biofilms, microbial activities form gradients of substrates and electron acceptors, creating a complex landscape of microhabitats, often resulting in structured localization of the microbial populations present. To understand the dynamic interplay between and within these populations, quantitative measurements and statistical analysis of their localization patterns within the biofilms are necessary, and adequate automated tools for such analyses are needed. We have designed and applied new methods for fluorescence in situ hybridization (FISH) and digital image analysis of directionally dependent (anisotropic) multispecies biofilms. A sequential-FISH approach allowed multiple populations to be detected in a biofilm sample. This was combined with an automated tool for vertical-distribution analysis by generating in silico biofilm slices and the recently developed Inflate algorithm for coaggregation analysis of microbial populations in anisotropic biofilms. As a proof of principle, we show distinct stratification patterns of the ammonia oxidizers Nitrosomonas oligotropha subclusters I and II and the nitrite oxidizer Nitrospira sublineage I in three different types of wastewater biofilms, suggesting niche differentiation between the N. oligotropha subclusters, which could explain their coexistence in the same biofilms. Coaggregation analysis showed that N. oligotropha subcluster II aggregated closer to Nitrospira than did N. oligotropha subcluster I in a pilot plant nitrifying trickling filter (NTF) and a moving-bed biofilm reactor (MBBR), but not in a full-scale NTF, indicating important ecophysiological differences between these phylogenetically closely related subclusters. By using high-resolution quantitative methods applicable to any multispecies biofilm in general, the ecological interactions of these complex ecosystems can be understood in more detail. PMID:23892743

  19. 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…

  20. 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

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

    PubMed

    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

  2. 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.

  3. Effect of temperature decrease on the microbial population and process performance of a mesophilic anaerobic bioreactor.

    PubMed

    Bohn, I; Björnsson, L; Mattiasson, B

    2007-08-01

    The effect of a temperature decrease from 33 degrees C to 12 degrees C was investigated for anaerobic digestion of crop residues. A laboratory-scale reactor (R0) was inoculated with mesophilic sludge and operated as continuously stirred fed-batch system at temperatures of 12 degrees C, 18 degrees C and 33 degrees C. Changes in the microbial populations of the sludge were followed by means of fluorescence in situ hybridization analysis. Methane was produced in R0 at all temperatures. Stable long-term operation at 18 degress C was achieved yielding 151 mlCH4 gVS(added(-1) at a rate of 108 mlCH4 l(R)(-1)d(-1) once the microbial populations of the sludge had adapted to this temperature. After operation at 18 degrees C, the contents of R0 was mixed and distributed into three smaller reactors, which were operated at 18 degrees C (R18), 25 degrees C (R25) and 37 degrees C (R37), respectively. Methane production rates for R37 and R25 were 366 and 310 mlCH4 l(R)(-1)d(-1), respectively, which were higher than the 215 mlCH4 l(R)(-1)d(-1) obtained in R0 when this was operated at 33 degrees C. Hydrolysis was found to decrease when temperature was decreased and especially below 25 degrees C. At temperatures below 16 degrees C, acidogenesis and methanogenesis were the rate-limiting steps. Adaptation of the mesophilic sludge to 18 degrees C was indicated by an increase in the ratio of Bacteria to total prokaryotes (sum of Archaea and Bacteria). This was thought to be caused by enrichment of Bacteria in the sludge, which appeared to be an important adaptation mechanism. During the adaptation, the Methanomicrobiales and Methanosarcinaceae populations increased relative to the total Archaea population whereas the Methanosaeta population decreased. The population changes were reflected by reactor performance. PMID:17879853

  4. ECOLOGICALLY SIGNIFICANT EFFECTS OF #PSEUDOMONAS PUTIDA# PP0103 (PR0103), GENETICALLY ENGINEERED TO DEGRADE 2,4-DICHLOROPHENOXYACETATE, ON MICROBIAL POPULATIONS AND PROCESSES IN SOIL

    EPA Science Inventory

    Genetically engineered microorganisms (GEMS) released to the environment may perturb microbial populations and their processes in soil. hanges in microbial communities, biogeochemical processes, and the physiochemical characteristics of soil might result from the introduction of ...

  5. 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...

  6. Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition

    PubMed Central

    Saeed, Isaam; Tang, Sen-Lin; Halgamuge, Saman K.

    2012-01-01

    An approach to infer the unknown microbial population structure within a metagenome is to cluster nucleotide sequences based on common patterns in base composition, otherwise referred to as binning. When functional roles are assigned to the identified populations, a deeper understanding of microbial communities can be attained, more so than gene-centric approaches that explore overall functionality. In this study, we propose an unsupervised, model-based binning method with two clustering tiers, which uses a novel transformation of the oligonucleotide frequency-derived error gradient and GC content to generate coarse groups at the first tier of clustering; and tetranucleotide frequency to refine these groups at the secondary clustering tier. The proposed method has a demonstrated improvement over PhyloPythia, S-GSOM, TACOA and TaxSOM on all three benchmarks that were used for evaluation in this study. The proposed method is then applied to a pyrosequenced metagenomic library of mud volcano sediment sampled in southwestern Taiwan, with the inferred population structure validated against complementary sequencing of 16S ribosomal RNA marker genes. Finally, the proposed method was further validated against four publicly available metagenomes, including a highly complex Antarctic whale-fall bone sample, which was previously assumed to be too complex for binning prior to functional analysis. PMID:22180538

  7. Growth performance and intestinal microbial populations of growing pigs fed diets containing sucrose thermal oligosaccharide caramel.

    PubMed

    Orban, J I; Patterson, J A; Adeola, O; Sutton, A L; Richards, G N

    1997-01-01

    Four experiments were conducted to determine growth performance and changes in intestinal microbial populations of growing pigs fed diets containing sucrose thermal oligosaccharide caramel (STOC). Ninety-six barrows and 96 gilts were group-fed experimental nursery diets for 32 d after weaning in both Exp. 1 and 2. For each experiment, pigs were divided into four groups of 48 pigs and were fed either control, antibiotic (Apramycin sulfate, 34 mg/kg), 1% STOC, or 2% STOC diets for 32 d after weaning. Each diet was replicated six times with eight pigs per replication. Pigs were either orally gavaged (Exp 1) with water of STOC (2 g per pig) or pigs were creep-fed (Exp 2) either a control diet or a 2% STOC diet for 5 d before weaning (33 d). At the end of Exp 1 and 2, cecal material was collected for enumeration of total aerobes, total anaerobes, coliforms, lactobacilli, and bifidobacteria. Gilts (96 per experiment) used in Exp. 3 and 4 were weaned at 26 d and fed experimental nursery diets for 32 d. They were fed either a control or 1% STOC diet and were otherwise treated as previously described. There were no significant effects of STOC or antibiotic on ADG, ADFI, feed efficiency, or cecal microbial populations in pigs in this study. Feeding diets containing either antibiotic of STOC did not improve animal performance or change intestinal bacterial populations in the present study. PMID:9027562

  8. Study on Biodegradation Process of Polyethylene Glycol with Exponential Glowth of Microbial Population

    NASA Astrophysics Data System (ADS)

    Watanabe, Masaji; Kawai, Fusako

    Biodegradation of polyethylene glycol is studied mathematically. A mathematical model for depolymerization process of exogenous type is described. When a degradation rate is a product of a time factor and a molecular factor, a time dependent model can be transformed into a time independent model, and techniques developed in previous studies can be applied to the time independent model to determine the molecular factor. The time factor can be determined assuming the exponential growth of the microbial population. Those techniques are described, and numerical results are presented. A comparison between a numerical result and an experimental result shows that the mathematical method is appropriate for practical applications.

  9. Measuring spatial accessibility to healthcare for populations with multiple transportation modes.

    PubMed

    Mao, Liang; Nekorchuk, Dawn

    2013-11-01

    Few measures of healthcare accessibility have considered multiple transportation modes when people seek healthcare. Based on the framework of the 2 Step Floating Catchment Area Method (2SFCAM), we proposed an innovative method to incorporate transportation modes into the accessibility estimation. Taking Florida, USA, as a study area, we illustrated the implementation of the multi-mode 2SFCAM, and compared the accessibility estimates with those from the traditional single-mode 2SFCAM. The results suggest that the multi-modal method, by accounting for heterogeneity in populations, provides more realistic accessibility estimations, and thus offers a better guidance for policy makers to mitigate health inequity issues. PMID:24077335

  10. 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...

  11. 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

  12. 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. PMID:19153811

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

    PubMed Central

    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, Manesh B; VerBerkmoes, 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. PMID:20531404

  14. 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.

  15. Development of a microbial population within a hot-drinks vending machine and the microbial load of vended hot chocolate drink.

    PubMed

    Hall, A; Short, K; Saltmarsh, M; Fielding, L; Peters, A

    2007-09-01

    In order to understand the development of the microbial population within a hot-drinks vending machine a new machine was placed in a staff area of a university campus vending only hot chocolate. The machine was cleaned weekly using a detergent based protocol. Samples from the mixing bowl, dispense area, and drink were taken over a 19-wk period and enumerated using plate count agar. Bacillus cereus was identified using biochemical methods. Vended drinks were sampled at 0, 3, 6, and 9 min after vending; the hot chocolate powder was also sampled. Over the 1st 8 wk, a significant increase in the microbial load of the machine components was observed. By the end of the study, levels within the vended drink had also increased significantly. Inactivation of the automatic flush over a subsequent 5-wk period led to a statistically but not operationally significant increase in the microbial load of the dispense area and vended drink. The simple weekly clean had a significant impact on the microbial load of the machine components and the vended drink. This study demonstrated that a weekly, detergent-based cleaning protocol was sufficient to maintain the microbial population of the mixing bowl and dispense point in a quasi-steady state below 3.5 log CFU/cm2 ensuring that the microbial load of the vended drinks was maintained below 3.4 log CFU/mL. The microbial load of the drinks showed no significant changes over 9 min after vending, suggesting only spores are present in the final product. PMID:17995650

  16. 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

  17. Microbial populations stimulated for hexavalent uranium reduction in uranium mine sediment.

    SciTech Connect

    Suzuki, Y.; Kelly, S. D.; Kemner, K. M.; Banfield, J. F.; Environmental Research; Univ. of Wisconsin-Madison; Univ. of California-Berkeley

    2003-03-01

    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 (UO{sub 2}) 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.

  18. 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

  19. Temporal variation of microbial population in a thermophilic biofilter for SO₂ removal.

    PubMed

    Zhang, Jingying; Li, Lin; Liu, Junxin

    2016-01-01

    The performance of a biofilter relies on the activity of microorganisms during the gas contaminant treatment process. In this study, SO2 was treated using a laboratory-scale biofilter packed with polyurethane foam cubes (PUFC), on which thermophilic desulfurization bacteria were attached. The thermophilic biofilter effectively reduced SO2 within 10months of operation time, with a maximum elimination capacity of 48.29 g/m(3)/hr. Temporal shifts in the microbial population in the thermophilic biofilter were determined through polymerase chain reaction-denaturing gradient gel electrophoresis and deoxyribonucleic acid (DNA) sequence analysis. The substrate species and environmental conditions in the biofilter influenced the microbial population. Oxygen distribution in the PUFC was analyzed using a microelectrode. When the water-containing rate in PUFC was over 98%, the oxygen distribution presented aerobic-anoxic-aerobic states along the test route on the PUFC. The appearance of sulfate-reducing bacteria was caused by the anaerobic conditions and sulfate formation after 4months of operation. PMID:26899638

  20. Effects of different sources of physically effective fiber on rumen microbial populations.

    PubMed

    Shaw, C N; Kim, M; Eastridge, M L; Yu, Z

    2016-03-01

    Physically effective fiber is needed by dairy cattle to prevent ruminal acidosis. This study aimed to examine the effects of different sources of physically effective fiber on the populations of fibrolytic bacteria and methanogens. Five ruminally cannulated Holstein cows were each fed five diets differing in physically effective fiber sources over 15 weeks (21 days/period) in a Latin Square design: (1) 44.1% corn silage, (2) 34.0% corn silage plus 11.5% alfalfa hay, (3) 34.0% corn silage plus 5.1% wheat straw, (4) 36.1% corn silage plus 10.1% wheat straw, and (5) 34.0% corn silage plus 5.5% corn stover. The impact of the physically effective fiber sources on total bacteria and archaea were examined using denaturing gradient gel electrophoresis. Specific real-time PCR assays were used to quantify total bacteria, total archaea, the genus Butyrivibrio, Fibrobacter succinogenes, Ruminococcus albus, Ruminococcus flavefaciens and three uncultured rumen bacteria that were identified from adhering ruminal fractions in a previous study. No significant differences were observed among the different sources of physical effective fiber with respect to the microbial populations quantified. Any of the physically effective fiber sources may be fed to dairy cattle without negative impact on the ruminal microbial community. PMID:26365790

  1. 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

  2. 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.

  3. Microbial Biomass and Population Densities of Non-Sorted Circles in High Arctic Ecosystems

    NASA Astrophysics Data System (ADS)

    Rivera-Figueroa, F.; González, G.; Gould, W. A.; Cantrell, S.; Pérez, J.

    2006-12-01

    Non-sorted circles are small patterned-ground features that occur in arctic soils as a result of intensive frost heave action. This tundra feature has been extensively described. However, little is known about the ecological relationships between this pattern and above- and belowground organisms. In this study, we compare the biomass and populaton densities of microbes in non-sorted circles and the vegetated surrounding soils (inter-circles) in the High Arctic. We collected soil samples during the summer of 2004 and 2005 on Banks and Prince Patrick and Ellef Ringnes Islands, Canada. Soil samples (0-10 cm) were gathered from non- sorted circles and inter-circles along a topographic sequence: dry (ridge), mesic (mid slope) and wet (valley) and along three transects in zonal (mesic) sites on each island. We estimated total microbial biomass and bacterial population densities using substrate induce respiration (SIR) and the most probable number method (MPN), respectively. We also isolated soil fungi using Rose Bengal and Saboraud Dextrose culture media. We are in the process of analyzing the catena samples using a terminal restriction fragment length polymorphism (TRFLP) technique of PCR-amplified 16S rRNA. Based on the SIR trials, the average microbial biomass at the mid slope position in the Banks site (Green Cabin) was 0.49 mg C g-1 dry soil in the non- sorted circles and 0.95 mg C g-1 dry soil in the inter-circles. At Prince Patrick Island (Mould Bay) the microbial biomass was 0.54 mg C g-1 dry soil in the non-sorted circles and 0.74 mg C g-1 dry soil in the inter-circles. In Ellef Ringnes (Isachsen) the microbial biomass was 0.09 mg C g-1 dry soil in the non- sorted circles and 0.14 mg C g-1 dry soil in the inter-circles. At the mesic site at Green Cabin, bacteria vary from 2.92 x 106 cell g-1 dry soil in the non-sorted circles to 6.74 x 106 cell g-1 dry soil in the inter-circles. At Mould Bay the range was 7.67 x 105 cells g-1 dry soil in the non-sorted circles

  4. Soil Bacteria Population Dynamics Following Stimulation for Ureolytic Microbial-Induced CaCO3 Precipitation.

    PubMed

    Gat, Daniella; Ronen, Zeev; Tsesarsky, Michael

    2016-01-19

    Microbial-induced CaCO3 precipitation (MICP) via urea-hydrolysis (ureolysis) is an emerging soil improvement technique for various civil engineering and environmental applications. In-situ application of MICP in soils is performed either by augmenting the site with ureolytic bacteria or by stimulating indigenous ureolytic bacteria. Both of these approaches may lead to changes in the indigenous bacterial population composition and to the accumulation of large quantities of ammonium. In this batch study, effective ureolysis was stimulated in coastal sand from a semiarid environment, with low initial ureolytic bacteria abundance. Two different carbon sources were used: yeast-extract and molasses. No ureolysis was observed in their absence. Ureolysis was achieved using both carbon sources, with a higher rate in the yeast-extract enrichment resulting from increased bacterial growth. The changes to the indigenous bacterial population following biostimulation of ureolysis were significant: Bacilli class abundancy increased from 5% in the native sand up to 99% in the yeast-extract treatment. The sand was also enriched with ammonium-chloride, where ammonia-oxidation was observed after 27 days, but was not reflected in the bacterial population composition. These results suggest that biostimulation of ureolytic bacteria can be applied even in a semiarid and nutrient-poor environment using a simple carbon source, that is, molasses. The significant changes to bacterial population composition following ureolysis stimulation could result in a decrease in trophic activity and diversity in the treated site, thus they require further attention. PMID:26689904

  5. 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. PMID:15480624

  6. Population Accessibility to Radiotherapy Services in New South Wales Region of Australia: a methodological contribution

    NASA Astrophysics Data System (ADS)

    Shukla, Nagesh; Wickramasuriya, Rohan; Miller, Andrew; Perez, Pascal

    2015-05-01

    This paper proposes an integrated modelling process to assess the population accessibility to radiotherapy treatment services in future based on future cancer incidence and road network-based accessibility. Previous research efforts assessed travel distance/time barriers affecting access to cancer treatment services, as well as epidemiological studies that showed that cancer incidence rates vary with population demography. It is established that travel distances to treatment centres and demographic profiles of the accessible regions greatly influence the demand for cancer radiotherapy (RT) services. However, an integrated service planning approach that combines spatially-explicit cancer incidence projections, and the RT services accessibility based on patient road network have never been attempted. This research work presents this novel methodology for the accessibility assessment of RT services and demonstrates its viability by modelling New South Wales (NSW) cancer incidence rates for different age-sex groups based on observed cancer incidence trends; estimating the road network-based access to current NSW treatment centres; and, projecting the demand for RT services in New South Wales, Australia from year 2011 to 2026.

  7. Distribution of microbial populations and their relationship with environmental variables in the North Yellow Sea, China

    NASA Astrophysics Data System (ADS)

    Bai, Xiaoge; Wang, Min; Liang, Yantao; Zhang, Zhifeng; Wang, Fang; Jiang, Xuejiao

    2012-03-01

    In order to understand the large-scale spatial distribution characteristics of picoplankton, nanophytoplankton and virioplankton and their relationship with environmental variables in coastal and offshore waters, flow cytometry (FCM) was used to analyze microbial abundance of samples collected in summer from four depths at 36 stations in the North Yellow Sea (NYS). The data revealed spatial heterogeneity in microbial populations in the offshore and near-shore waters of the NYS during the summer. For the surface layer, picoeukaryotes were abundant in the near-shore waters, Synechococcus was abundant in the offshore areas, and bacterial and viral abundances were high in the near-shore waters around the Liaodong peninsula. In the near-shore waters, no significant vertical variation of picophytoplankton (0.2-2μm) abundance was found. However, the nanophytoplankton abundance was higher in the upper layers (from the surface to 10 m depth) than in the bottom layer. For the offshore waters, both pico- and nanophytoplankton (2-20μm) abundance decreased sharply with depth in the North Yellow Sea Cold Water Mass (NYSCWM). But, for the vertical distribution of virus and bacteria abundance, no significant variation was observed in both near-shore and offshore waters. Autotrophic microbes were more sensitive to environmental change than heterotrophic microbes and viruses. Viruses showed a positive correlation with bacterial abundance, suggesting that the bacteriophage might be prominent for virioplankton (about 0.45μm) in summer in the NYS and that viral abundance might play an important role in microbial loop functions.

  8. High throughput sequencing reveals distinct microbial populations within the mucosal and luminal niches in healthy individuals

    PubMed Central

    Ringel, Yehuda; Maharshak, Nitsan; Ringel-Kulka, Tamar; Wolber, Elizabeth Ashley; Sartor, R Balfour; Carroll, Ian M

    2015-01-01

    Background: The intestinal microbiota is associated with human health and diseases. The luminal microbiota (LM) and the mucosal-associated microbiota (MAM) are 2 distinct ecosystems with different metabolic and immunological functions. Aim: To characterize the intestinal LM and MAM in humans using high throughput sequencing of the 16S rRNA gene. Methods: Fresh fecal samples and distal colonic mucosal biopsies collected from 24 healthy subjects before (fecal) and during (mucosa) a flexible sigmoidoscopy of an un-prepared bowel. High throughput sequencing of the 16S rRNA gene was used to characterize bacterial communities. Sequences were processed using the QIIME pipeline. Results: LM and MAM populations were significantly different (ANOSIM: R = 0.49, P = 0.001). The LM displayed tighter clustering compared to the MAM (average weighted UniFrac distances 0.27 ± 0.05 vs. 0.43 ± 0.09, P < 0.001, respectively), and showed higher diversity (Shannon diversity index: 4.96 ± 0.37 vs 4.14 ± 0.56, respectively, P < 0.001). The dominant phyla in the LM and MAM were significantly different: Firmicutes (41.4% vs. 29.1%, FDR < 0.0001, respectively), Bacteroidetes (20.2% vs. 26.3%, FDR < 0.05, respectively), Actinobacteria (22% vs. 12.6%, FDR < 0.0001, respectively) and Proteobacteria (9.3% vs. 19.3%, FDR < 0.0001, respectively). The abundance of 56 genera differed significantly (FDR < 0.1) between the 2 niches. All of the genera in the fecal microbiota were present in the MAM while 10 genera were found to be unique to the MAM. Conclusion: The LM and MAM are distinct microbial ecosystems that differ significantly from each other in microbial diversity and composition. These two microbial niches should be investigated independently to better understand the role of the intestinal microbiota in health and disease. PMID:25915459

  9. 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

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

    PubMed

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

    2016-02-01

    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 (13)C from labeled hemicellulose, analyzing (13)C-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

  11. 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

  12. 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.

  13. 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. PMID:27306555

  14. 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.

  15. Accessibility

    MedlinePlus

    ... www.nlm.nih.gov/medlineplus/accessibility.html MedlinePlus Accessibility To use the sharing features on this page, ... Subscribe to RSS Follow us Disclaimers Copyright Privacy Accessibility Quality Guidelines Viewers & Players MedlinePlus Connect for EHRs ...

  16. Microbial population dynamics in response to bioaugmentation in a constructed wetland system under 10°C.

    PubMed

    Zhao, Xinyue; Yang, Jixian; Bai, Shunwen; Ma, Fang; Wang, Li

    2016-04-01

    Compound microbial inocula were enriched and applied to a pilot-scale constructed wetland system to investigate their bioaugmentation effect on nitrogen removal under cold temperature (10°C). The results showed a 10% higher removal efficiency of ammonia and total nitrogen compared to a control (unbioaugmented) group. The microbial community structures before and after the bioaugmentation were analyzed through high throughput sequencing using Miseq Illumina platform. A variation of species richness and community equitability was observed in both systems. It is demonstrated that, based on the response of both the performance and microbial community, bioaugmentation using compound microbial inocula can fine tune the bacterial population and enhance the nitrogen removal efficiency of a constructed wetland system. PMID:26826956

  17. 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

  18. Effect of feed starvation on side-stream anammox activity and key microbial populations.

    PubMed

    Reeve, Petra J; Mouilleron, Irina; Chuang, Hui-Ping; Thwaites, Ben; Hyde, Kylie; Dinesh, Nirmala; Krampe, Joerg; Lin, Tsair-Fuh; van den Akker, Ben

    2016-04-15

    The anaerobic ammonium oxidation (anammox) process is widely acknowledged to be susceptible to a wide range of environmental factors given the slow growth rate of the anammox bacteria. Surprisingly there is limited experimental data regarding the susceptibility of the anammox process to feed starvations which may be encountered in full-scale applications. Therefore, a study was established to investigate the impact of feed starvations on nitritation and anammox activity in a demonstration-scale sequencing batch reactor. Three starvation periods were trialled, lasting one fortnight (15 d), one month (33 d) and two months (62 d). Regardless of the duration of the starvation period, assessment of the ammonia removal performance demonstrated nitritation and anammox activity were reinstated within one day of recovery operation. Characterisation of the community structure using 16S rRNA and functional genes specific for nitrogen-related microbes showed there was no clear impact or shift in the microbial populations between starvation and recovery phases. PMID:26861222

  19. Comparative effects of Aroclor 1254 (polychlorinated biphenyls) and phenanthrene on glucose uptake by freshwater microbial populations.

    PubMed Central

    Sayler, G S; Lund, L C; Shiaris, M P; Sherrill, T W; Perkins, R E

    1979-01-01

    The effects of polychlorinated biphenyl (PCB) and phenanthrene stress on glucose uptake by natural microbial populations were examined by the heterotrophic potential technique. Temporal and spatial distributions in glucose uptake velocities were examined for natural samples as well as PCB- and phenanthrene-stressed samples. Statistical analysis indicated significant variability among the various samples. It was demonstrated that the environmental variables contributed significantly to the variability in uptake kinetics. Although general trends indicated a PCB-induced stimulation in uptake velocities, these trends were in part masked by sample variability. Data analysis indicated no statistically significant PCB or phenanthrene effect on either total glucose uptake velocities or the proportion of 14CO2 evolved, as compared to natural unstressed samples. PMID:114110

  20. Microbial population dynamics during sludge granulation in an A/O/A sequencing batch reactor.

    PubMed

    He, Qiulai; Zhou, Jun; Wang, Hongyu; Zhang, Jing; Wei, Li

    2016-08-01

    The evolution of the bacterial population during formation of denitrifying phosphorus removal granular sludge was investigated using high-throughput pyrosequencing. As a result, mature granules with a compact structure were obtained in an anaerobic/aerobic/anoxic (A/O/A) sequencing batch reactor under an organic loading rate as low as 0.3kg COD/(m(3)·d). Rod-shaped microbes were observed to cover with the outer surface of granules. Besides, reliable COD and simultaneous nitrogen and phosphorus removal efficiencies were achieved over the whole operation period. MiSeq pyrosequencing analysis illustrated that both the microbial diversity and richness increased sharply during the granulation process, whereas they stayed stable after the presence of granules. Some microorganisms seemed to contribute to the formation of granules, and some were identified as functional bacterial groups responsible for constructing the biological reactor. PMID:27115745

  1. Survey of microbial populations within Lake Michigan nearshore waters at two Chicago public beaches.

    PubMed

    Malki, Kema; Bruder, Katherine; Putonti, Catherine

    2015-12-01

    Lake Michigan is a critical resource for the residents of Chicago, providing drinking water to its 9+ million area residents. Along Chicago׳s 26 miles of public beaches the populous urban environment and this freshwater environment meet. While city-led monitoring initiatives investigate pathogenic bacteria in these nearshore waters, very little is known about other microbial species present. We collected surface water samples from two Chicago public beaches - Montrose Beach and 57th Street Beach - every ten days from June 5 through August 4, 2013 as well as once in early Fall (October 4, 2013). Sixteen bacterial communities in total were surveyed through targeted sequencing of the V4 16S rRNA gene. Taxa were identified using Mothur. Raw sequence data is available via NCBI׳s SRA database (part of BioProject PRJNA245802). OTU calls for each read are also available at our online repository: www.lakemichiganmicrobes.com/bacteria/. PMID:26958608

  2. Heterotrophic activity and biodegradation of labile and refractory compounds by groundwater and stream microbial populations.

    PubMed Central

    Ladd, T I; Ventullo, R M; Wallis, P M; Costerton, J W

    1982-01-01

    The bacteriology and heterotrophic activity of a stream and of nearby groundwater in Marmot Basin, Alberta, Canada, were studied. Acridine orange direct counts indicated that bacterial populations in the groundwater were greater than in the stream. Bacteria that were isolated from the groundwater were similar to species associated with soils. Utilization of labile dissolved organic material as measured by the heterotrophic potential technique with glutamic acid, phenylalanine, and glycolic acid as substrates was generally greater in the groundwater. In addition, specific activity indices for the populations suggested greater metabolic activity per bacterium in the groundwater. 14C-labeled lignocellulose, preferentially labeled in the lignin fraction by feeding Picea engelmannii [14C]phenylalanine, was mineralized by microorganisms in both the groundwater and the stream, but no more than 4% of the added radioactivity was lost as 14CO2 within 960 h. Up to 20% of [3'-14C]cinnamic acid was mineralized by microorganisms in both environments within 500 h. Both microbial populations appear to influence the levels of labile and recalcitrant dissolved organic material in mountain streams. PMID:7125651

  3. 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.

  4. 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...

  5. 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…

  6. 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…

  7. The Challenges and Recommendations of Accessing to Affected Population for Humanitarian Assistance: A Narrative Review

    PubMed Central

    Moslehi, Shandiz; Fatemi, Farin; Mahboubi, Mohammad; Mozafarsaadati, Hossein; Karami, Shirzad

    2015-01-01

    Objective: Access to affected people pays an important role in United Nation Organization for Coordination and Humanitarian Affairs (OCHA). The aim of this article is to identify the main obstacles of humanitarian access and the humanitarian organization responses to these obstacles and finally suggest some recommendations and strategies. Methods: In this narrative study the researchers searched in different databases. This study focused on the data from five countries in the following areas: access challenges and constraints to affected population and response strategies selected for operations in the affected countries by humanitarian organizations. Results: Three main issues were studied: security threats, bureaucratic restrictions and indirect constraint, which each of them divided to three subcategories. Finally, nine related subcategories emerged from this analysis. Conclusion: Most of these constraints relate to political issues. Changes in policy structures, negotiations and advocacy can be recommended to solve most of the problems in access issues. PMID:25948440

  8. 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

  9. Effect of plants containing secondary compounds with palm oil on feed intake, digestibility, microbial protein synthesis and microbial population in dairy cows.

    PubMed

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

    2013-06-01

    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

  10. 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...

  11. Monitoring microbial populations of sulfate-reducing bacteria using an impedimetric immunosensor based on agglutination assay.

    PubMed

    Wan, Yi; Zhang, Dun; Hou, Baorong

    2009-11-15

    An impedimetric immunosensor was fabricated for rapid and non-labeled detection of sulfate-reducing bacteria, Desulforibrio caledoiensis (SRB) by immobilizing lectin-Concanavalin A using an agglutination assay. The immobilization of lectin was conducted using amine coupling on the surface of a gold (Au) electrode assembled with 11-Mercaptoundecanoic acid. Electrochemical impedance spectroscopy (EIS) was used to verify the stepwise assembly of the sensor system. The work conditions of the impedimetric immunosensor, such as pH of the buffer solutions and the incubation time of lectin, were optimized. Faradic impedance spectra for charge transfer for the redox probe Fe(CN)(6)(3-/4-)were measured to determine SRB concentrations. The diameter of the Nyquist diagram that is equal to the charge-transfer resistance (R(ct)) increased with increasing SRB concentration. A linear relationship between R(ct) and SRB concentration was obtained in SRB concentration range of 1.8 to 1.8 x 10(7)cfu/ml. The variation of the SRB population during the growth process was also monitored using the impedimetric immunosensor. This approach has great potential for simple, low-cost, and time-saving monitoring of microbial populations. PMID:19782217

  12. Assessment of partial nitrification reactor performance through microbial population shift using quinone profile, FISH and SEM.

    PubMed

    Sinha, B; Annachhatre, A P

    2007-12-01

    In engineered systems, biological nitrogen removal through partial nitrification to nitrite is of great interest. Accordingly, effect of operating parameters such as pH, DO and temperature on the accumulation of ammonia-oxidizers was investigated. pH of 8, DO of 0.3-0.5mg/l and temperature of 35 degrees C yielded a ratio of 0.9-1.5 of NO(2)N:NH(4)N in the effluent suitable as a feed for Anammox reactor. Microbial population shift during start-up was assessed using quinone profile, SEM and FISH. UQ-8 in the biomass, which is the predominant quinone in ammonia-oxidizers, increased from 24.8% on Day 1 to 61.2% on Day 136. Fluorescence in situ hybridization analysis in the reactor showed that ammonia-oxidizing bacteria gradually outcompeted other bacteria and was the dominant population. The morphology and inner structure of the granular sludge was observed using SEM and the photographs indicated that the aerobic granular sludge showed a shift towards spherical and small rod-shaped clusters. PMID:17257833

  13. 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. PMID:15895736

  14. [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. PMID:18392351

  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. Microbial population dynamics and changes in main nutrients during the acidification process of pig manures.

    PubMed

    Zhang, Dongdong; Yuan, Xufeng; Guo, Peng; Suo, Yali; Wang, Xiaofen; Wang, Weidong; Cui, Zongjun

    2011-01-01

    This study evaluated the impact of pig manure acidification on anaerobic treatment and composition of the fecal microbial community. According to the different chemical oxygen demand (COD) in the anaerobic treatment processes, pig manure was diluted 4 times (x4), 16 times (x16), or 64 times (x64) and subjected to acidification. During the acidification process, pH, soluble chemical oxygen demand (SCOD), volatile fatty acids (VFAs), nitrogen (N), phosphorus (P) and potassium (K) were determined along with microbial population dynamics. The pH of the three dilutions first declined, and then slowly increased. The total VFAs of x4 and x16 dilutions peaked on day 15 and 20, respectively. The content of acetic acid, propanoic acid, butanoic acid and valeric acid of the x4 dilution were 23.6, 11.4, 8.8 and 0.6 g/L respectively, and that of the x16 dilution was 5.6, 2.3, 0.9 and 0.2 g/L respectively. Only acetic acid was detected in the x64 dilution, and its level peaked on day 10. The results showed that the liquid pig manure was more suitable to enter the anaerobic methanogenic bioreactors after two weeks of acidification. During the acidification process, total P concentration increased during the first ten days, then dropped sharply, and rose again to a relatively high final concentration, while total N concentration rose initially and then declined. Based on the analysis of denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone library, we concluded that the acidification process reduced the number of pathogenic bacteria species in pig manure. PMID:21520820

  17. 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.

  18. 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. PMID:11587573

  19. 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

  20. Comparisons of ruminal fermentation characteristics and microbial populations in bison and cattle.

    PubMed Central

    Towne, G; Nagaraja, T G; Cochran, R C; Harmon, D L; Owensby, C E; Kaufman, D W

    1988-01-01

    Ruminal microbial populations, fermentation characteristics, digestibility, and liquid flow rates in two ruminally cannulated bison and two ruminally cannulated Hereford steers fed a prairie hay diet were compared. No significant differences in anaerobic bacterial counts, volatile fatty acid concentrations, or ruminal pHs were evident between bison and cattle. Also, no significant differences in neutral detergent fiber digestibility, indigestible fiber retention time, or intake were detected between bison and cattle, although cattle had higher levels (P less than 0.08) of ruminal dry matter and indigestible fiber than bison. Bison had a smaller (P = .02) ruminoreticular volume, faster liquid dilution rates, and faster liquid turnover times than cattle. The average ruminal ammonia nitrogen concentration was higher (P = 0.02) in bison (1.17 mg/dl) than in cattle (0.79 mg/dl). Total ciliate protozoal counts and cell volume were greater (P = 0.07) in bison (32.8 x 10(4)/g and 407.1 x 10(-4) ml/g, respectively) than in cattle (15.7 x 10(4)/g and 162.2 x 10(-4) ml/g, respectively). Bison harbored higher (P less than 0.02) numbers of Dasytricha spp., Eudiplodinium maggii, Eudiplodinium bursa, and Epidinium spp. than cattle and possessed a type B protozoan population. The cattle possessed a mixed type A-type B population that was characterized by Ophryoscolex spp. and Polyplastron spp. in association with low concentrations of Epidinium spp. and Eudiplodinium maggii. PMID:3272131

  1. Effect of sulfate and lactate loading rates on the respiration process and microbial population changes measured by ecological indices.

    PubMed

    García-Saucedo, C; Fernández, F J; Cuervo-López, F M; Gómez, J

    2015-01-01

    In a sulfate reducing process, increasing loading rates and sulfide accumulation may induce population changes resulting in decreasing effectiveness of the process. Thus, the relationship between microbial metabolism changes and population dynamics was studied. An upflow anaerobic sludge blanket reactor was operated at different sulfate loading rates (SLR), from 290 to 981 mg SO4-S/L d at a constant carbon/sulfur ratio of 0.75. When the SLR was increased, the total organic carbon and sulfate consumption efficiencies decreased to nearly 30% and 25%, respectively. The acetate and propionate yields increased with increasing SLR and 385±7 mg sulfide-S/L d was reached. The ecological indices, determined by random amplified polymorphic DNA and denaturing gradient gel electrophoresis techniques, diversity and evenness were found to be constant, and similarity coefficient values remained higher than 76%. The results suggest that the microbial population changes were negligible compared with metabolic changes when SLR was increased. The sulfide accumulation did not modify the microbial diversity. The sequencing of 16S rRNA genes showed strains related to sulfate reducing, fermentation, and methanogenesis processes. The results indicated that the decreasing of effectiveness, under the experimental conditions tested, was dependent more on operational parameters than microbial changes. PMID:25607675

  2. 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. PMID:27375557

  3. 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

  4. Microbial Population Analysis of the Salivary Glands of Ticks; A Possible Strategy for the Surveillance of Bacterial Pathogens

    PubMed Central

    Qiu, Yongjin; Nakao, Ryo; Ohnuma, Aiko; Kawamori, Fumihiko; Sugimoto, Chihiro

    2014-01-01

    Ticks are one of the most important blood-sucking vectors for infectious microorganisms in humans and animals. When feeding they inject saliva, containing microbes, into the host to facilitate the uptake of blood. An understanding of the microbial populations within their salivary glands would provide a valuable insight when evaluating the vectorial capacity of ticks. Three tick species (Ixodes ovatus, I. persulcatus and Haemaphysalis flava) were collected in Shizuoka Prefecture of Japan between 2008 and 2011. Each tick was dissected and the salivary glands removed. Bacterial communities in each salivary gland were characterized by 16S amplicon pyrosequencing using a 454 GS-Junior Next Generation Sequencer. The Ribosomal Database Project (RDP) Classifier was used to classify sequence reads at the genus level. The composition of the microbial populations of each tick species were assessed by principal component analysis (PCA) using the Metagenomics RAST (MG-RAST) metagenomic analysis tool. Rickettsia-specific PCR was used for the characterization of rickettsial species. Almost full length of 16S rDNA was amplified in order to characterize unclassified bacterial sequences obtained in I. persulcatus female samples. The numbers of bacterial genera identified for the tick species were 71 (I. ovatus), 127 (I. persulcatus) and 59 (H. flava). Eighteen bacterial genera were commonly detected in all tick species. The predominant bacterial genus observed in all tick species was Coxiella. Spiroplasma was detected in Ixodes, and not in H. flava. PCA revealed that microbial populations in tick salivary glands were different between tick species, indicating that host specificities may play an important role in determining the microbial complement. Four female I. persulcatus samples contained a high abundance of several sequences belonging to Alphaproteobacteria symbionts. This study revealed the microbial populations within the salivary glands of three species of ticks, and the

  5. 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.

  6. Microbial population index and community structure in saline-alkaline soil using gene targeted metagenomics.

    PubMed

    Keshri, Jitendra; Mishra, Avinash; Jha, Bhavanath

    2013-03-30

    Population indices of bacteria and archaea were investigated from saline-alkaline soil and a possible microbe-environment pattern was established using gene targeted metagenomics. Clone libraries were constructed using 16S rRNA and functional gene(s) involved in carbon fixation (cbbL), nitrogen fixation (nifH), ammonia oxidation (amoA) and sulfur metabolism (apsA). Molecular phylogeny revealed the dominance of Actinobacteria, Firmicutes and Proteobacteria along with archaeal members of Halobacteraceae. The library consisted of novel bacterial (20%) and archaeal (38%) genera showing ≤95% similarity to previously retrieved sequences. Phylogenetic analysis indicated ability of inhabitant to survive in stress condition. The 16S rRNA gene libraries contained novel gene sequences and were distantly homologous with cultured bacteria. Functional gene libraries were found unique and most of the clones were distantly related to Proteobacteria, while clones of nifH gene library also showed homology with Cyanobacteria and Firmicutes. Quantitative real-time PCR exhibited that bacterial abundance was two orders of magnitude higher than archaeal. The gene(s) quantification indicated the size of the functional guilds harboring relevant key genes. The study provides insights on microbial ecology and different metabolic interactions occurring in saline-alkaline soil, possessing phylogenetically diverse groups of bacteria and archaea, which may be explored further for gene cataloging and metabolic profiling. PMID:23083746

  7. Effects of Environmental Factors on Microbial Populations in Brackish Waters off the Southern Coast of Finland

    PubMed Central

    Väätänen, Pentti

    1980-01-01

    The roles played by environmental factors in seasonal changes in microbial populations were investigated in the Tvärminne area, off the southern coast of Finland. Surface-layer samples were collected at 1- or 2-week intervals in 1976-78, and 14 microbiological and 10 environmental parameters were determined. Stepwise multiple regression analysis was used to explain seasonal variation in the microbiological parameters. Separate analyses were made of the data from the open-water and ice-cover periods. In analyses of data from both periods, the environmental factors included accounted for a significant proportion of the variation in the parameters for community respiration (90%) and bacterial spores (80%), and a smaller proportion (60 to 65%) of the variation in total counts of bacteria and plate counts of psychrophiles and yeasts. Lower values (40 to 55%) were obtained for the variation in the other microbiological parameters. The environmental factors with maximal contributions were organic matter, water temperature, chlorophyll a, and salinity, but rainfall and winds also explained part of the variation in some microbiological parameters. In the winter analysis the results differed from those obtained for the other seasons, the variation being governed by parameters indicating freshwater outflows, namely, humic matter, salinity, water temperature (positive regression coefficient), and rainfall (negative regression coefficient). PMID:16345595

  8. Fermentation and microbial population dynamics during the ensiling of native grass and subsequent exposure to air.

    PubMed

    Zhang, Qing; Wu, Baiyila; Nishino, Naoki; Wang, Xianguo; Yu, Zhu

    2016-03-01

    To study the microbial population and fermentation dynamics of large needlegrass (LN) and Chinese leymus (CL) during ensiling and subsequent exposure to air, silages were sampled and analyzed using culture-based techniques and denaturing gradient gel electrophoresis (DGGE). A total of 112 lactic acid bacteria (LAB) strains were isolated and identified using the 16S rRNA sequencing method. Lactic acid was not detected in the first 20 days in LN silage and the pH decreased to 6.13 after 45 days of ensiling. The temperature of the LN silage increased after approximately 30 h of air exposure and the CL silage showed a slight temperature variation. Enterococcus spp. were mainly present in LN silage. The proportion of Lactobacillus brevis in CL silage increased after exposure to air. LN silage with a higher proportion of Enterococcus spp. and propionic acid concentration did not show higher fermentation quality or aerobic stability than CL silage, which had a higher concentration of acetic acid, butyric acid and increased proportion of L. brevis after exposure to air. PMID:26950516

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

    SciTech Connect

    Whitby, J.L.; Storey, D.G.

    1982-03-01

    A total of 700 25-cm/sup 2/ 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 D/sub 10/ 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 D/sub 10/ value of 0.249 Mrad was obtained. The isolates obtained were identified, and 70.7% were found to be Bacillus spp. with 12 different spcies 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 standad where 1 gown in 1,000 might contain a living organism. Comparison of the radiation resistance of this popultion with that of others reported in the literature showed good agreement.

  10. 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. PMID:16702066

  11. 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. PMID:27570236

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

    PubMed

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

    2016-04-01

    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 (V F) 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

  13. 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

  14. Distribution and Composition of Microbial Populations in a Landfill Leachate Contaminated Aquifer (Grindsted, Denmark).

    PubMed

    Ludvigsen; Albrechtsen; Ringelberg; Ekelund; Christensen

    1999-04-01

    > Abstract To investigate whether landfill leachates affected the microbial biomass and/or community composition of the extant microbiota, 37 samples were collected along a 305-m transect of a shallow landfill-leachate polluted aquifer. The samples were analyzed for total numbers of bacteria by use of the acridine orange direct count method (AODC). Numbers of dominant, specific groups of bacteria and total numbers of protozoa were measured by use of the most probable number method (MPN). Viable biomass estimates were obtained from measures of ATP and ester-linked phospholipid fatty acid (PLFA) concentrations. The estimated numbers of total bacteria by direct counts were relatively constant throughout the aquifer, ranging from a low of 4.8 x 10(6) cells/g dry weight (dw) to a high of 5.3 x 10(7) cells/g dw. Viable biomass estimates based on PLFA concentrations were one to three orders of magnitude lower with the greatest concentrations (up to 4 x 10(5) cells/g dw) occurring at the border of the landfill and in samples collected from thin lenses of clay and silt with sand streaks. Cell number estimates based on ATP concentrations were also found to be lower than the direct count measurements (<2.2 x 10(6) cells/g dw), and with the greatest concentrations close to the landfill. Methanogens (Archaea) and reducers of sulfate, iron, manganese, and nitrate were all observed in the aquifer. Methanogens were found to be restricted to the most polluted and reduced part of the aquifer at a maximum cell number of 5.4 x 10(4) cells/g dw. Populations of sulfate reducers decreased with an increase in horizontal distance from the landfill ranging from a high of 9.0 x 10(3) cells/g dw to a low of 6 cells/g dw. Iron, manganese, and nitrate reducers were detected throughout the leachate plume all at maximum cell numbers of 10(6) cells/g dw. Changes in PLFA profiles indicated that a shift in microbial community composition occurred with increasing horizontal distance from the landfill

  15. 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.

  16. 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...

  17. 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. PMID:22595839

  18. Particulate DNA in Smoker Fluids: Evidence for Existence of Microbial Populations in Hot Hydrothermal Systems

    PubMed Central

    Straube, W. L.; Deming, J. W.; Somerville, C. C.; Colwell, R. R.; Baross, J. A.

    1990-01-01

    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 in titanium syringes and Go Flo Niskin bottles from 17 different hot vents (smokers and flanges) and their environs for the purpose of extracting particulate DNA. The relative purity of the vent fluids collected was determined by Mg content as an indicator of seawater entrainment. 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 by using the dye Hoechst 33258. Ambient seawater surrounding the vents was found to contain low DNA concentrations, 0.18 to 0.32 ng of DNA per ml (n = 4; meanenz = 0.23 ± 0.05; meanfp = 0.26 ± 0.05), while low-temperature vent samples yielded significantly higher concentrations of 0.37 to 2.12 ng of DNA per ml (n = 4; meanenz = 0.97 ± 0.68; meanfp = 1.05 ± 0.54). Although DNA recovery values from superheated (210 to 345°C) flange samples (meanenz = 0.14 ± 0.10; meanfp = 0.12 ± 0.14) were not significantly different from ambient seawater values, most of the superheated (174 to 357°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 field and indicate that microorganisms exist in some superheated fluids. PMID:16348193

  19. Particulate DNA in smoker fluids: evidence for existence of microbial populations in hot hydrothermal systems.

    PubMed

    Straube, W L; Deming, J W; Somerville, C C; Colwell, R R; Baross, J A

    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 in titanium syringes and Go Flo Niskin bottles from 17 different hot vents (smokers and flanges) and their environs for the purpose of extracting particulate DNA. The relative purity of the vent fluids collected was determined by Mg content as an indicator of seawater entrainment. 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 by using the dye Hoechst 33258. Ambient seawater surrounding the vents was found to contain low DNA concentrations, 0.18 to 0.32 ng of DNA per ml (n = 4; mean(enz) = 0.23 +/- 0.05; mean(fp) = 0.26 +/- 0.05), while low-temperature vent samples yielded significantly higher concentrations of 0.37 to 2.12 ng of DNA per ml (n = 4; mean(enz) = 0.97 +/- 0.68; mean(fp) = 1.05 +/- 0.54). Although DNA recovery values from superheated (210 to 345 degrees C) flange samples (mean(enz) = 0.14 +/- 0.10; mean(fp) = 0.12 +/- 0.14) were not significantly different from ambient seawater values, most of the superheated (174 to 357 degrees 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 field and indicate that microorganisms exist in some superheated fluids. PMID:16348193

  20. Reexamining microRNA Site Accessibility in Drosophila: A Population Genomics Study

    PubMed Central

    Chen, Kevin; Maaskola, Jonas; Siegal, Mark L.; Rajewsky, Nikolaus

    2009-01-01

    Kertesz et al. (Nature Genetics 2008) described PITA, a miRNA target prediction algorithm based on hybridization energy and site accessibility. In this note, we used a population genomics approach to reexamine their data and found that the PITA algorithm had lower specificity than methods based on evolutionary conservation at comparable levels of sensitivity. We also showed that deeply conserved miRNAs tend to have stronger hybridization energies to their targets than do other miRNAs. Although PITA had higher specificity in predicting targets than a naïve seed-match method, this signal was primarily due to the use of a single cutoff score for all miRNAs and to the observed correlation between conservation and hybridization energy. Overall, our results clarify the accuracy of different miRNA target prediction algorithms in Drosophila and the role of site accessibility in miRNA target prediction. PMID:19478854

  1. Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates.

    PubMed

    Sonnenburg, Erica D; Sonnenburg, Justin L

    2014-11-01

    The gut microbiota of a healthy person may not be equivalent to a healthy microbiota. It is possible that the Western microbiota is actually dysbiotic and predisposes individuals to a variety of diseases. The asymmetric plasticity between the relatively stable human genome and the more malleable gut microbiome suggests that incompatibilities between the two could rapidly arise. The Western lifestyle, which includes a diet low in microbiota-accessible carbohydrates (MACs), has selected for a microbiota with altered membership and functionality compared to those of groups living traditional lifestyles. Interactions between resident microbes and host leading to immune dysregulation may explain several diseases that share inflammation as a common basis. The low-MAC Western diet results in poor production of gut microbiota-generated short-chain fatty acids (SCFAs), which attenuate inflammation through a variety of mechanisms in mouse models. Studies focused on modern and traditional societies, combined with animal models, are needed to characterize the connection between diet, microbiota composition, and function. Differentiating between an optimal microbiota, one that increases disease risk, and one that is causative or potentiates disease will be required to further understand both the etiology and possible treatments for health problems related to microbiota dysbiosis. PMID:25156449

  2. Starving our Microbial Self: The Deleterious Consequences of a Diet Deficient in Microbiota-Accessible Carbohydrates

    PubMed Central

    Sonnenburg, Erica D.; Sonnenburg, Justin L.

    2016-01-01

    The gut microbiota of a healthy person may not be equivalent to a healthy microbiota. It is possible that the Western microbiota is actually dysbiotic and predisposes individuals to a variety of diseases. The asymmetric plasticity between the relatively stable human genome and the more malleable gut microbiome suggests that incompatibilities between the two could rapidly arise. The Western lifestyle, which includes a diet low in microbiota-accessible carbohydrates (MACs), has selected for a microbiota with altered membership and functionality compared to those of groups living traditional lifestyles. Interactions between resident microbes and host leading to immune dysregulation may explain several diseases that share inflammation as a common basis. The low-MAC Western diet results in poor production of gut microbiota-generated short-chain fatty acids (SCFAs), which attenuate inflammation through a variety of mechanisms in mouse models. Studies focused on modern and traditional societies, combined with animal models, are needed to characterize the connection between diet, microbiota composition, and function. Differentiating between an optimal microbiota, one that increases disease risk, and one that is causative or potentiates disease will be required to further understand both the etiology and possible treatments for health problems related to microbiota dysbiosis. PMID:25156449

  3. Combination of sodium chlorite and calcium propionate reduces enzymatic browning and microbial population of fresh-cut "Granny Smith" apples.

    PubMed

    Guan, Wenqiang; Fan, Xuetong

    2010-03-01

    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, dipped for 5 min in CP solutions at 0%, 0.5%, 1%, and 2% (w/v) either alone or in combination with 0.05% (w/v) SC, were stored at 3 and 10 degrees C for up to 14 d. Color, firmness, and microflora population were measured at 1, 7, and 14 d of storage. Results showed that CP alone had no significant effect on the browning of cut apples. Even though SC significantly inhibited tissue browning initially, the apple slices turned brown during storage at 10 degrees C. The combination of CP and SC was able to inhibit apple browning during storage. Samples treated with the combination of SC with CP did not show any detectable yeast and mold growth during the entire storage period at 3 degrees C. At 10 degrees C, yeast and mold count increased on apple slices during storage while CP reduced the increase. However, high concentrations of CP reduced the efficacy of SC in inactivating E. coli inoculated on apples. Overall, our results suggested that combination of SC with 0.5% and 1% CP could be used to inhibit tissue browning and maintain firmness while reducing microbial population. Practical Application: Apple slices, which contain antioxidants and other nutrient components, have emerged as popular snacks in food service establishments, school lunch programs, and for family consumption. However, the further growth of the industry is limited by product quality deterioration caused by tissue browning, short shelf-life due to microbial growth, and possible contamination with human pathogens during processing. Therefore, this study was conducted to develop treatments to reduce microbial population and tissue browning of "Granny Smith" apple slices. Results showed that an antimicrobial

  4. Chronic impact of sulfamethoxazole on acetate utilization kinetics and population dynamics of fast growing microbial culture.

    PubMed

    Kor-Bicakci, G; Pala-Ozkok, I; Rehman, A; Jonas, D; Ubay-Cokgor, E; Orhon, D

    2014-08-01

    The study evaluated the chronic impact of sulfamethoxazole on metabolic activities of fast growing microbial culture. It focused on changes induced on utilization kinetics of acetate and composition of the microbial community. The experiments involved a fill and draw reactor, fed with acetate and continuous sulfamethoxazole dosing of 50 mg/L. The evaluation relied on model evaluation of the oxygen uptake rate profiles, with parallel assessment of microbial community structure by 454-pyrosequencing. Continuous sulfamethoxazole dosing inflicted a retardation effect on acetate utilization in a way commonly interpreted as competitive inhibition, blocked substrate storage and accelerated endogenous respiration. A fraction of acetate was utilized at a much lower rate with partial biodegradation of sulfamethoxazole. Results of pyrosequencing with a replacement mechanism within a richer more diversified microbial culture, through inactivation of vulnerable fractions in favor of species resistant to antibiotic, which made them capable of surviving and competing even with a slower metabolic response. PMID:24908607

  5. EFFECT OF BIOSOLARISATION ON THE MICROBIAL POPULATIONS OF SUBSTRATES INFESTED WITH FUSARIUM OXYSPORUM BY PCR-DGGE.

    PubMed

    Pugliese, M; Ferrocino, I; Gilardi, G; Gullino, M L; Garibaldi, A

    2015-01-01

    Biosolarisation consists of combining solarisation and organic matter application for controlling soilborne pathogens. The effects of this control strategy on the microbial community is almost unknown and needs to be investigated with molecular tools. The aim of the research was to investigate how biosolarisation can affect the structure of the microbial populations evaluated by a culture independent method using DGGE of PCR-amplified 18S-ITS genes-coding fragments from DNA extracted directly from infested substrate. Substrate samples were artificially infested with Fusarium oxysporum f. sp. conglutinans (FOC) and F. oxysporum f.sp. basilici (FOB) in order to evaluate the shift in fungal population by using culture independent methods. Solarisation was carried out with transparent polyethylene film during the summer period in a greenhouse located in Northern Italy, in combination or not with Brassica carinata defatted seed meals and/or compost. Biosolarisation treatment was carried out in a growth chamber by heating the substrate for 7 and 14 days at optimal (55-52 degrees C for 6 h, 50-48 degrees C for 8 h and 47-45 degrees C for 10 h/day) and sub-optimal (50-48 degrees C for 20 h, 45-43 degrees C for 8 h and 40-38 degrees C for 10 h/day) temperatures. Plate counts and polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) analyses were performed to evaluate the effect of biosolarisation on the microbial population. The abundance of FOC and FOB was reduced as a consequence of biosolarisation, while bacterial populations were higher compared to control samples during the experiment. PCR-DGGE fingerprints of the ascomycete community obtained from DNA directly extracted from infested substrate samples showed that the use of organic amendments increased the similarity of the fungal populations. PMID:27141761

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

    PubMed

    Dilélio, Alitéia Santiago; Tomasi, Elaine; Thumé, Elaine; Silveira, Denise Silva da; 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

  7. 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

  8. 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. PMID:26484735

  9. Measuring health care access and quality to improve health in populations.

    PubMed

    Kottke, Thomas E; Isham, George J

    2010-07-01

    Poor health status, rapidly escalating health care costs, and seemingly little association between investments in health care and health outcomes have prompted a call for a "pay-for-performance" system to improve population health. We suggest that both health plans and clinical service providers measure and report the rates of 5 behaviors: 1) smoking, 2) physical activity, 3) excessive drinking, 4) nutrition, and 5) condom use by sexually active youth. Because preventive services can improve population health, we suggest that health plans and clinical service providers report delivery rates of preventive services. We also suggest that an independent organization report 8 county-level indicators of health care performance: 1) health care expenditures, 2) insurance coverage, 3) rates of unmet medical, dental, and prescription drug needs, 4) preventive services delivery rates, 5) childhood vaccination rates, 6) rates of preventable hospitalizations, 7) an index of affordability, and 8) disparities in access to health care associated with race and income. To support healthy behaviors, access to work site wellness and health promotion programs should be measured. To promote coordinated care, an indicator should be developed for whether a clinical service provider is a member of an accountable care organization. To encourage clinical service providers and health plans to address the social determinants of health, organizational participation in community-benefit initiatives that address the leading social determinants of health should be assessed. PMID:20550831

  10. Microbial Population and Community Dynamics on Plant Roots and Their Feedbacks on Plant Communities

    PubMed Central

    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. PMID:22726216

  11. 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.

  12. Interactions between Snow Chemistry, Mercury Inputs and Microbial Population Dynamics in an Arctic Snowpack

    PubMed Central

    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. PMID:24282515

  13. 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

  14. 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...

  15. Heterotrophic and Autotrophic Microbial Populations in Cold Perennial Springs of the High Arctic ▿ †

    PubMed Central

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

    2008-01-01

    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, CO2 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% CH4) 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. PMID:18805995

  16. 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

  17. 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.

  18. 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. PMID:26091189

  19. 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

  20. 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

  1. Zinc, cadmium and lead accumulation and characteristics of rhizosphere microbial population associated with hyperaccumulator Sedum alfredii Hance under natural conditions.

    PubMed

    Long, Xin-Xian; Zhang, Yu-Gang; Jun, Dai; Zhou, Qixing

    2009-04-01

    A field survey was conducted to study the characteristics of zinc, cadmium, and lead accumulation and rhizosphere microbial population associated with hyperaccumulator Sedum alfredii Hance growing natively on an old lead/zinc mining site. We found significant hyperaccumulation of zinc and cadmium in field samples of S. alfredii, with maximal shoot concentrations of 9.10-19.61 g kg(-1) zinc and 0.12-1.23 g kg(-1) cadmium, shoot/root ratios ranging from 1.75 to 3.19 (average 2.54) for zinc, 3.36 to 4.43 (average 3.85) for cadmium, shoot bioaccumulation factors of zinc and cadmium being 1.46-4.84 and 7.35-17.41, respectively. While most of lead was retained in roots, thus indicating exclusion as a tolerance strategy for lead. Compared to the non-rhizosphere soil, organic matter and total nitrogen and phosphorus content, CEC and water extractable zinc, cadmium, and lead concentration were significantly higher, but pH was smaller in rhizosphere soil. The rhizosphere soil of S. alfredii harbored a wide variety of microorganism. In general, significantly higher numbers of culturable bacteria, actinomycetes, and fungi were found in the rhizosphere compared to bulk soil, confirming the stimulatory effect of the S. alfredii rhizosphere on microbial growth and proliferation. Analyses of BIOLOG data also showed that the growth of S. alfredii resulted in observable changes in BIOLOG metabolic profiles, utilization ability of different carbon substrates of microbial communities in the rhizosphere soil were also higher than the non-rhizosphere, confirming a functional effect of the rhizosphere of S. alfredii on bacterial population. PMID:19183820

  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. PMID:16825452

  3. 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. PMID:17674648

  4. 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

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

    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 ([14C]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 pgṡmL-1 sedimentṡy-1 at the surface to 0.2 pgṡmL-1ṡy-1 at 1 km depth, equivalent to production of 7 × 105 to 140 archaeal cellsṡmL-1 sedimentṡy-1, respectively. These constraints on microbial growth are an important step toward understanding the relationship between the deep biosphere and the carbon cycle.

  6. 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

  7. Specific microbial populations thrive under fluctuating redox conditions in tropical soils

    NASA Astrophysics Data System (ADS)

    Deangelis, K. M.; Silver, W. L.; Thompson, A.; Firestone, M. K.

    2008-12-01

    The highly weathered soils of upland humid tropical forests are characterized by rapidly fluctuating redox conditions, dominated by Fe-oxide mineralogy, and have relatively low sulfate availability. To assess how fluctuating redox conditions and accompanying biogeochemistry impact microbial community structure and function, we collected soil cores from the Luquillo LTER forest in Puerto Rico and incubated them for 32 days under one of three redox regimes: static oxic, static anoxic, and 4-day fluctuating redox. Over this time course we measured CO2, CH4, and N2O production, amorphous iron and Fe(II), and microbial community structure by high density microarray (PhyloChip) analysis. Static oxic, anoxic, and fluctuating redox soils all had statistically indistinguishable respiration rates over the course of the experiment. Fluctuating redox conditions permitted simultaneous methanogenesis, N2O production, and iron reduction, all accompanied by steady CO2 production. We analyzed the standing and active microbial community using the 16S ribosomal DNA and RNA biomarkers, identifying 2489 taxa in these soils. Ordination analysis showed significant separation between the active (RNA-based) and standing (DNA-based) communities, with much more variation in the active community compared to the standing community. Fluctuating redox conditions maintained a microbial community structure similar to that of the pre-incubation samples, while static anaerobic conditions had the most profound effect on the communities. Finally, there was considerable overlap between the taxa that were the most highly correlated with production of CH4 and Fe(II). Association of groups of taxa with specific biogeochemical processes begins to identify organisms potentially responsible for field biogeochemical processing.

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

    PubMed Central

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

    2013-01-01

    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 ([14C]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 × 105 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. PMID:23530229

  9. Accessibility and utilization patterns of a mobile medical clinic among vulnerable populations.

    PubMed

    Gibson, Britton A; Ghosh, Debarchana; Morano, Jamie P; Altice, Frederick L

    2014-07-01

    We mapped mobile medical clinic (MMC) clients for spatial distribution of their self-reported locations and travel behaviors to better understand health-seeking and utilization patterns of medically vulnerable populations in Connecticut. Contrary to distance decay literature, we found that a small but significant proportion of clients was traveling substantial distances to receive repeat care at the MMC. Of 8404 total clients, 90.2% lived within 5 miles of a MMC site, yet mean utilization was highest (5.3 visits per client) among those living 11-20 miles of MMCs, primarily for those with substance use disorders. Of clients making >20 visits, 15.0% traveled >10 miles, suggesting that a significant minority of clients traveled to MMC sites because of their need-specific healthcare services, which are not only free but available at an acceptable and accommodating environment. The findings of this study contribute to the important research on healthcare utilization among vulnerable population by focusing on broader dimensions of accessibility in a setting where both mobile and fixed healthcare services coexist. PMID:24853039

  10. 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.

  11. In vitro utilization of gold and green kiwifruit oligosaccharides by human gut microbial populations.

    PubMed

    Parkar, Shanthi G; Rosendale, Doug; Paturi, Gunaranjan; Herath, Thanuja D; Stoklosinski, Halina; Phipps, Janet E; Hedderley, Duncan; Ansell, Juliet

    2012-09-01

    We examined the effects of whole kiwifruit on gut microbiota using an in vitro batch model of gastric-ileal digestion and colonic fermentation. Faecal fermentations of gold and green kiwifruit, inulin and water (control) digests were performed for up to 48 h. As compared to the control, gold and green kiwifruit increased Bifidobacterium spp. by 0.9 and 0.8 log(10) cfu/ml, respectively (P < 0.001), and the Bacteroides-Prevotella-Porphyromonas group by 0.4 and 0.5 log(10) cfu/ml, respectively. Inulin only had a bifidogenic effect (+0.4 log(10) cfu/ml). This was accompanied with increases in microbial glycosidases, especially those with substrate specificities relating to the breakdown of kiwifruit oligosaccharides, and with increased generation of short chain fatty acids. The microbial metabolic activity was sustained for up to 48 h, which we attribute to the complexity of the carbohydrate substrate provided by whole kiwifruit. Kiwifruit fermenta supernatant was also separately shown to affect the in vitro proliferation of Bifidobacterium longum, and its adhesion to Caco-2 intestinal epithelial cells. Collectively, these data suggest that whole kiwifruit may modulate human gut microbial composition and metabolism to produce metabolites conducive to increased bifidobacteria-host association. PMID:22576129

  12. 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. PMID:21335391

  13. Segregated flux balance analysis constrained by population structure/function data: the case of PHA production by mixed microbial cultures.

    PubMed

    Pardelha, F; Albuquerque, M G E; Carvalho, G; Reis, M A M; Dias, J M L; Oliveira, R

    2013-08-01

    In this study we developed a segregated flux balance analysis (FBA) method to calculate metabolic flux distributions of the individual populations present in a mixed microbial culture (MMC). Population specific flux data constraints were derived from the raw data typically obtained by the fluorescence in situ hybridization (FISH) and microautoradiography (MAR)-FISH techniques. This method was applied to study the metabolic heterogeneity of a MMC that produces polyhydroxyalkanoates (PHA) from fermented sugar cane molasses. Three populations were identified by FISH, namely Paracoccus sp., Thauera sp., and Azoarcus sp. The segregated FBA method predicts a flux distribution for each of the identified populations. The method is shown to predict with high accuracy the average PHA storage flux and the respective monomeric composition for 16 independent experiments. Moreover, flux predictions by segregated FBA were slightly better than those obtained by nonsegregated FBA, and also highly concordant with metabolic flux analysis (MFA) estimated fluxes. The segregated FBA method can be of high value to assess metabolic heterogeneity in MMC systems and to derive more efficient eco-engineering strategies. For the case of PHA-producing MMC considered in this work, it becomes apparent that the PHA average monomeric composition might be controlled not only by the volatile fatty acids (VFA) feeding profile but also by the population composition present in the MMC. PMID:23475571

  14. Intravenous access during pre-hospital emergency care of non-injured patients: a population-based outcome study

    PubMed Central

    Seymour, Christopher W.; Cooke, Colin R.; Hebert, Paul L.; Rea, Thomas D.

    2011-01-01

    Study objective Advanced, pre-hospital procedures such as intravenous access are commonly performed by emergency medical services (EMS) personnel, yet little evidence supports their use among non-injured patients. We evaluated the association between pre-hospital, intravenous access and mortality among non-injured, non-arrest patients. Methods We analyzed a population-based cohort of adult (aged ≥18 years) non-injured, non-arrest patients transported by four advanced life support agencies to one of 16 hospitals from January 1, 2002 until December 31, 2006. We linked eligible EMS records to hospital administrative data, and used multivariable logistic regression to determine the risk-adjusted association between pre-hospital, intravenous access and hospital mortality. We also tested whether this association differed by patient acuity using a previously published, out-of-hospital triage score. Results Among 56,332 eligible patients, one half (N=28,978, 50%) received pre-hospital intravenous access from EMS personnel. Overall hospital mortality in patients who did and did not receive intravenous access was 3%. However, in multivariable analyses, the placement of pre-hospital, intravenous access was associated with an overall reduction in odds of hospital mortality (OR=0.68, 95%CI: 0.56, 0.81). The beneficial association of intravenous access appeared to depend on patient acuity (p=0.13 for interaction). For example, the OR of mortality associated with intravenous access was 1.38 (95%CI: 0.28, 7.0) among those with lowest acuity (score = 0). In contrast, the OR of mortality associated with intravenous access was 0.38 (95%CI: 0.17, 0.9) among patients with highest acuity (score ≥ 6). Conclusions In this population-based cohort, pre-hospital, intravenous access was associated with a reduction in hospital mortality among non-injured, non-arrest patients with the highest acuity. PMID:21872970

  15. 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

  16. 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

  17. Effect of different preservative treatments on the microbial population of Nigerian orange juice.

    PubMed

    Sodeko, O O; Izuagbe, Y S; Ukhun, M E

    1987-01-01

    The effect of different preservative treatments on the microbial load of Nigerian orange juice was studied over a period of 1 month. Results obtained indicated that pasteurization at 60 degrees and 80 degrees C for 20 to 40 min, freezing at -5 degrees C, and addition of sodium benzoate at a concentration of 0.1 to 0.4% (w/v) could form a microbiological basis for the preservation of the juice for 1 month. Leuconostoc mesenteroides, L. paramesenteroides, Streptococcus avium, Lactobacillus plantarum, L. fermentum, L. fructivorans, Klebsiella pneumoniae and Saccharomyces cerevisiae were the micro-organisms isolated from the untreated and treated juice samples. PMID:3316936

  18. Influence of Electron Donor Type and Concentration on Microbial Population Structure During Uranium Reduction and Remobilization

    NASA Astrophysics Data System (ADS)

    Daly, R. A.; Brodie, E. L.; Kim, Y.; Wan, J.; Tokunaga, T.; Desantis, T. Z.; Andersen, G. L.; Hazen, T. C.; Firestone, M. K.

    2007-12-01

    Enhanced reductive precipitation of U(VI) through stimulation of indigenous microorganisms is an attractive, low- cost strategy for in-situ remediation of contaminated groundwaters and sediments. The rate of organic carbon (OC) supply determines not only the amount of electron donor available for bioreduction of U(VI), but also affects the resulting concentration of aqueous (bi)carbonate generated by microbial respiration. Increased (bi)carbonate concentrations drive aqueous U(VI) concentrations to higher levels and make U(IV) oxidation under reducing conditions favorable. We designed a long-term column study to investigate the effects of different OC forms and supply rates on the stability of bioreduced U and on the structure and dynamics of the microbial communities. OC was supplied as acetate or lactate at four different concentrations and columns were sampled at three time points. In the columns receiving high OC supply the time points correspond to a phases of net U-reduction, U(IV) reoxidation and U(VI) remobilization, and stable levels of U mobilization. DNA was extracted from column sediments, 16S rRNA genes were amplified and the communities analyzed using a high-density phylogenetic microarray (PhyloChip). Lactate and acetate supplied at equivalent rates had a similar impact on uranium mobility with higher OC resulting in re-oxidation of U(IV) after an initial period of U(VI) reduction. Similarly, organic carbon (OC) supply rate, not OC form, had the largest impact on microbial community structure. The diversity (richness) of bacterial and archaeal communities increased over time with those receiving lactate having higher initial richness. Known U-reducing bacteria were present in all columns and time points, however the dynamics of these organisms varied with both organic carbon supply rate and form. This data demonstrates that the initial rate of electron donor supply during heavy metal remediation strongly impacts microbial community development

  19. Population-Sequencing as a Biomarker of Burkholderia mallei and Burkholderia pseudomallei Evolution through Microbial Forensic Analysis

    PubMed Central

    Jakupciak, John P.; Wells, Jeffrey M.; Karalus, Richard J.; Pawlowski, David R.; Lin, Jeffrey S.; Feldman, Andrew B.

    2013-01-01

    Large-scale genomics projects are identifying biomarkers to detect human disease. B. pseudomallei and B. mallei are two closely related select agents that cause melioidosis and glanders. Accurate characterization of metagenomic samples is dependent on accurate measurements of genetic variation between isolates with resolution down to strain level. Often single biomarker sensitivity is augmented by use of multiple or panels of biomarkers. In parallel with single biomarker validation, advances in DNA sequencing enable analysis of entire genomes in a single run: population-sequencing. Potentially, direct sequencing could be used to analyze an entire genome to serve as the biomarker for genome identification. However, genome variation and population diversity complicate use of direct sequencing, as well as differences caused by sample preparation protocols including sequencing artifacts and mistakes. As part of a Department of Homeland Security program in bacterial forensics, we examined how to implement whole genome sequencing (WGS) analysis as a judicially defensible forensic method for attributing microbial sample relatedness; and also to determine the strengths and limitations of whole genome sequence analysis in a forensics context. Herein, we demonstrate use of sequencing to provide genetic characterization of populations: direct sequencing of populations. PMID:24455204

  20. Evaluation of microbial populations, Rhizobium Trifolii, and endomycorrhizal associations in reclamation of surface mine spoils in Texas

    SciTech Connect

    Mott, J.B.

    1984-01-01

    The deficiency of nitrogen and phosphorus in mixed overburden mine spoils has resulted in interest in strategies to minimize fertilizer application. In this study, the abundance of microbial populations, with emphasis on those involved in nitrogen cycle transformations was estimated in variously aged spoils. Two beneficial plant-microbe associations, the clover-Rhizobium trifolii symbiosis and endomycorrhizal associations, were investigated in field and laboratory studies. While most groups of microorganisms regained pre-mining levels in revegetated spoils within 1.5 years after disturbance, algal populations were still reduced ten years after mining. Populations of nitrifying bacteria and asymbiotic nitrogen-fixing bacteria were as high in all spoils as in unmined soil. Indigenous populations of ineffective R. trifolii were present in spoil banks and older revegetated spoil. A laboratory study of survival of three commercial strains of R. trifolii for subterranean clover showed lethal effects of high temperature (45/sup 0/C) especially in moist spoil, and superior survival of strain 162X95. Endomycorrhizal associations, evaluated by assessment of root infection in bermudagrass, reached pre-mining levels by three to seven years after disturbance. Growth chamber studies to investigate the effects of the two symbiotic associations on subterranean clover in mine spoil at different fertility levels indicated that dual infection with Rhizobium and VAM fungi was most beneficial for plant growth, nitrogen fixation, and nitrogen and phosphorus contents.

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

    PubMed

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

    2015-07-01

    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

  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

    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.

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

    DOE PAGESBeta

    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-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

  5. Production of bioavailable and refractory dissolved organic matter by coastal heterotrophic microbial populations

    NASA Astrophysics Data System (ADS)

    Lønborg, Christian; Álvarez-Salgado, Xosé A.; Davidson, Keith; Miller, Axel E. J.

    2009-05-01

    Production of dissolved organic matter (DOM) by heterotrophic microbial communities isolated from Loch Creran (Scotland) was studied in time course incubations in which cells were re-suspended in artificial seawater amended with variable proportions of glucose, ammonium and phosphate. The incubation experiments demonstrated that microheterotrophs released part of the substrate as new DOM, with a production efficiency of 11 ± 1% for DOC, 18 ± 2% for DON and 17 ± 2% for DOP. Estimating the impact of this production in Loch Creran, showed that from 3 ± 1% (DOC) to 72 ± 16% (DOP) of DOM could originate from the heterotrophic microbial community. The produced DOM (PDOM) was both bioavailable (BDOM) and refractory (RDOM). Bioavailability as assessed by the difference between the maximum and the end DOM concentration, was generally higher than found in natural systems, with DOP (73 ± 15%, average ± SD) more bioavailable than DON (70 ± 15%), and DON than DOC (34 ± 13%). The stoichiometry of PDOM was linked to both nutrient uptake and BDOM ratios. Absorption and fluorescence of DOM increased significantly during the incubation time, indicating that microheterotrophs were also a source of coloured DOM (CDOM) and that they produce both bioavailable protein-like and refractory humic-like fluorophores.

  6. 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

  7. 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.

  8. 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

  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. PMID:25622071

  11. Accessibility of dental services according to family income in a non-insured population.

    PubMed

    Grytten, J; Holst, D; Laake, P

    1993-12-01

    The aim of this study was to examine the effect of family income on accessibility to dental services among adults in Norway. The analysis was performed on a set of national data collected in 1989, which was representative of the non-institutionalized Norwegian population aged 20 years and above. The sample size was 1200 individuals. The data were analyzed according to a two-part model. The first part determined the probability of whether the consumer had demanded the services or not during the last year according to family income. The second part estimated how the amount of services utilized depended on family income, for those with demand. The elasticity of the odds of having demanded the services with respect to family income was 0.48. Family income had no effect on the amount of services utilized. Additional analyses also showed that there was no effect of family income on the probability of having received a filling or a crown when visiting the dentist. In Norway, almost all costs for dental services are paid by the consumer. It is not possible from the data alone to say whether subsidized dental care is an effective way of reducing the inequalities in demand. PMID:8303334

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

    PubMed

    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

  13. 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

  14. 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

  15. Brain Microbial Populations in HIV/AIDS: α-Proteobacteria Predominate Independent of Host Immune Status

    PubMed Central

    Branton, William G.; Ellestad, Kristofor K.; Maingat, Ferdinand; Wheatley, B. Matt; Rud, Erling; Warren, René L.; Holt, Robert A.; Surette, Michael G.; Power, Christopher

    2013-01-01

    The brain is assumed to be a sterile organ in the absence of disease although the impact of immune disruption is uncertain in terms of brain microbial diversity or quantity. To investigate microbial diversity and quantity in the brain, the profile of infectious agents was examined in pathologically normal and abnormal brains from persons with HIV/AIDS [HIV] (n = 12), other disease controls [ODC] (n = 14) and in cerebral surgical resections for epilepsy [SURG] (n = 6). Deep sequencing of cerebral white matter-derived RNA from the HIV (n = 4) and ODC (n = 4) patients and SURG (n = 2) groups revealed bacterially-encoded 16 s RNA sequences in all brain specimens with α-proteobacteria representing over 70% of bacterial sequences while the other 30% of bacterial classes varied widely. Bacterial rRNA was detected in white matter glial cells by in situ hybridization and peptidoglycan immunoreactivity was also localized principally in glia in human brains. Analyses of amplified bacterial 16 s rRNA sequences disclosed that Proteobacteria was the principal bacterial phylum in all human brain samples with similar bacterial rRNA quantities in HIV and ODC groups despite increased host neuroimmune responses in the HIV group. Exogenous viruses including bacteriophage and human herpes viruses-4, -5 and -6 were detected variably in autopsied brains from both clinical groups. Brains from SIV- and SHIV-infected macaques displayed a profile of bacterial phyla also dominated by Proteobacteria but bacterial sequences were not detected in experimentally FIV-infected cat or RAG1−/− mouse brains. Intracerebral implantation of human brain homogenates into RAG1−/− mice revealed a preponderance of α-proteobacteria 16 s RNA sequences in the brains of recipient mice at 7 weeks post-implantation, which was abrogated by prior heat-treatment of the brain homogenate. Thus, α-proteobacteria represented the major bacterial component of the primate brain

  16. 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

    2015-06-01

    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. PMID:26369997

  17. Quantification of microbial populations associated with the manufacture of vacuum-packaged, smoked vienna sausages.

    PubMed

    Dykes, G A; Cloete, T E; von Holy, A

    1991-08-01

    Sources of contamination of vacuum-packaged vienna sausages by spoilage microorganisms were examined in a meat-processing plant. Microbial numbers present in the environment, on working surfaces and workers' hands and aprons were quantified by plate counting on selective media. Product line samples were taken at critical control points in the manufacturing process and analysed before and after preliminary incubation of vacuum-packaged samples at 25 degrees C for 24 h. In all samples the numbers of aerobic bacteria, Enterobacteriaceae, lactic acid bacteria and yeasts were determined by standard procedures. Contamination of sausage surfaces by lactic acid bacteria occurred as a result of the manufacturing and handling processes. The environment and specifically packers' hands, as well as working surfaces contributed to microbiological contamination of various types after removal of the peel from individual sausages. The preliminary incubation procedure allowed detection of low numbers of spoilage microorganisms. PMID:1911080

  18. 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.

  19. 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

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

    PubMed

    Gandhi, Saurabh R; Yurtsev, Eugene Anatoly; Korolev, Kirill S; Gore, Jeff

    2016-06-21

    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

  1. 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

  2. [Facilitating access to care for most-at-risk populations : the Bamako night sexual health clinic experience (Mali)].

    PubMed

    Coulibaly, Alou; Dembelé Keita, Bintou; Henry, Emilie; Trenado, Emmanuel

    2014-01-01

    The estimated prevalence of HIV in Mali is 1.3 % of the general population. The epidemic is concentrated in certain groups, particularly men who have sex with men (MSM) and sex workers (SW). Access to care is limited for these populations, notably because of structural obstacles (e.g. marked social rejection ; health care services poorly adapted to the real needs of these people). Innovative strategies must be envisaged to ensure access to care services and retention in care for these populations. As part of a health promotion process, ARCAD-SIDA, a Malian NGO involved in the fight against AIDS since 1995, set up a night sexual health clinic in 2010 as part of a strategy to more adequately respond to the health needs of these populations. This clinic adapts health service timetables to match the lifestyles of the targeted populations, brings services in closer physical proximity to the places in which these populations live, proposes patient-tailored consultations, works to improve the patients' psychosocial skills, and promotes community-based peer mobilization. In an environment which is generally hostile to MSM and SW, ARCAD-SIDA also works in advocacy, targeting political decision-makers, defense forces and journalists. The NGO has also played a key role in ensuring that these populations are taken into account in the national strategy for the fight against HIV. Since opening in 2010, the clinic has helped reach a large number of MSM and SW and has improved retention in care. This innovative strategy has also enabled the NGO to improve its professional practices in terms of an individual-based approach to prevention. Interventions that are better adapted to the needs and environment of the populations for whom they are intented to have a positive effect on access to and use of healthcare services. PMID:25380379

  3. 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...

  4. A Population-based Study of Age Inequalities in Access to Palliative Care Among Cancer Patients

    PubMed Central

    Burge, Frederick I.; Lawson, Beverley J.; Johnston, Grace M.; Grunfeld, Eva

    2013-01-01

    Background Inequalities in access to palliative care programs (PCP) by age have been shown to exist in Canada and elsewhere. Few studies have been able to provide greater insight by simultaneously adjusting for multiple demographic, health service, and socio-cultural indicators. Objective To re-examine the relationship between age and registration to specialized community-based PCP programs among cancer patients and identify the multiple indicators contributing to these inequalities. Methods This retrospective, population-based study was a secondary data analysis of linked individual level information extracted from 6 administrative health databases and contextual (neighborhood level) data from provincial and census information. Subjects included all adults who died due to cancer between 1998 and 2003 living within 2 District Health Authorities in the province of Nova Scotia, Canada. The relationship between registration in a PCP and age was examined using hierarchical nonlinear regression modeling techniques. Identification of potential patient and ecologic contributing indicators was guided by Andersen’s conceptual model of health service utilization. Results Overall, 66% of 7511 subjects were registered with a PCP. Older subjects were significantly less likely than those <65 years of age to be registered with a PCP, in particular those aged 85 years and older (adjusted odds ratio: 0.4; 95% confidence interval: 0.3–0.5). Distance to the closest cancer center had a major impact on registration. Conclusions Age continues to be a significant predictor of PCP registration in Nova Scotia even after controlling for the confounding effects of many new demographic, health service, and ecologic indicators. PMID:19300309

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

    SciTech Connect

    Tremblay, Julien

    2012-06-01

    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.

  6. 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

    2013-01-25

    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.

  7. The effects of methyl bromide alternatives on soil and seedling microbial populations, weeds, and seedling morphology in Oregon and Washington forest tree nurseries

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Six fumigant treatments were evaluated at two forest tree nurseries in Oregon and one forest tree nursery in Washington for their effects on soil microbial populations, weeds, and seedling morphology during a 2-year study. Fusarium commune, F. oxysporum, Gibberella fujikuroi complex, P. irregulare,...

  8. 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...

  9. 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.

  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.