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Sample records for access microbial populations

  1. Environmental Whole-Genome Amplification To Access Microbial Populations in Contaminated Sediments

    PubMed Central

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

    2006-01-01

    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 φ29 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. PMID:16672469

  2. Microbial populations in contaminant plumes

    USGS Publications Warehouse

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

    2000-01-01

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

  3. Microbial diversity--insights from population genetics.

    PubMed

    Mes, Ted H M

    2008-01-01

    Although many environmental microbial populations are large and genetically diverse, both the level of diversity and the extent to which it is ecologically relevant remain enigmatic. Because the effective (or long-term) population size, N(e), is one of the parameters that determines population genetic diversity, tests and simulations that assume selectively neutral mutations may help to identify the processes that have shaped microbial diversity. Using ecologically important genes, tests of selective neutrality suggest that adaptive as well as non-adaptive types of selection act and that departure from neutrality may be widespread or restricted to small groups of genotypes. Population genetic simulations using population sizes between 10(3) and 10(7) suggest extremely high levels of microbial diversity in environments that sustain large populations. However, census and effective population sizes may differ considerably, and because we know nothing of the evolutionary history of environmental microbial populations, we also have no idea what N(e) of environmental populations is. On the one hand, this reflects our ignorance of the microbial world. On the other hand, the tests and simulations illustrate interactions between microbial diversity and microbial population genetics that should inform our thinking in microbial ecology. Because of the different views on microbial diversity across these disciplines, such interactions are crucial if we are to understand the role of genes in microbial communities.

  4. 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

  5. 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.

  6. Septic tank additive impacts on microbial populations.

    PubMed

    Pradhan, S; Hoover, M T; Clark, G H; Gumpertz, M; Wollum, A G; Cobb, C; Strock, J

    2008-01-01

    Environmental health specialists, other onsite wastewater professionals, scientists, and homeowners have questioned the effectiveness of septic tank additives. This paper describes an independent, third-party, field scale, research study of the effects of three liquid bacterial septic tank additives and a control (no additive) on septic tank microbial populations. Microbial populations were measured quarterly in a field study for 12 months in 48 full-size, functioning septic tanks. Bacterial populations in the 48 septic tanks were statistically analyzed with a mixed linear model. Additive effects were assessed for three septic tank maintenance levels (low, intermediate, and high). Dunnett's t-test for tank bacteria (alpha = .05) indicated that none of the treatments were significantly different, overall, from the control at the statistical level tested. In addition, the additives had no significant effects on septic tank bacterial populations at any of the septic tank maintenance levels. Additional controlled, field-based research iswarranted, however, to address additional additives and experimental conditions.

  7. 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.

  8. Undecompressed microbial populations from the deep sea.

    PubMed Central

    Jannasch, H J; Wirsen, C O; Taylor, C D

    1976-01-01

    Metabolic transformations of glutamate and Casamino Acids by natural microbial populations collected from deep waters (1,600 to 3,100 m) were studied in decompressed and undecompressed samples. Pressure-retaining sampling/incubation vessels and appropriate subsampling/incubation vessels and appropriate subsampling techniques permitted time course experiments. In all cases the metabolic activity in undecompressed samples was lower than it was when incubated at 1 atm. Surface water controls showed a reduced activity upon compression. The processes involving substrate incorporation into cell material were more pressure sensitive than was respiration. The low utilization of substrates, previously found by in situ incubations for up to 12 months, was confirmed and demonstrated to consist of an initial phase of activity, in the range of 5 to 60 times lower than the controls, followed by a stationary phase of virtually no substrate utilization. No barophilic growth response (higher rates at elevated pressure than at 1 atm) was recorded; all populations observed exhibition various degrees of barotolerance. Images PMID:791117

  9. 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

  10. Web-accessible proteome databases for microbial research.

    PubMed

    Pleissner, Klaus-Peter; Eifert, Till; Buettner, Sven; Schmidt, Frank; Boehme, Martina; Meyer, Thomas F; Kaufmann, Stefan H E; Jungblut, Peter R

    2004-05-01

    The analysis of proteomes of biological organisms represents a major challenge of the post-genome era. Classical proteomics combines two-dimensional electrophoresis (2-DE) and mass spectrometry (MS) for the identification of proteins. Novel technologies such as isotope coded affinity tag (ICAT)-liquid chromatography/mass spectrometry (LC/MS) open new insights into protein alterations. The vast amount and diverse types of proteomic data require adequate web-accessible computational and database technologies for storage, integration, dissemination, analysis and visualization. A proteome database system (http://www.mpiib-berlin.mpg.de/2D-PAGE) for microbial research has been constructed which integrates 2-DE/MS, ICAT-LC/MS and functional classification data of proteins with genomic, metabolic and other biological knowledge sources. The two-dimensional polyacrylamide gel electrophoresis database delivers experimental data on microbial proteins including mass spectra for the validation of protein identification. The ICAT-LC/MS database comprises experimental data for protein alterations of mycobacterial strains BCG vs. H37Rv. By formulating complex queries within a functional protein classification database "FUNC_CLASS" for Mycobacterium tuberculosis and Helicobacter pylori the researcher can gather precise information on genes, proteins, protein classes and metabolic pathways. The use of the R language in the database architecture allows high-level data analysis and visualization to be performed "on-the-fly". The database system is centrally administrated, and investigators without specific bioinformatic competence in database construction can submit their data. The database system also serves as a template for a prototype of a European Proteome Database of Pathogenic Bacteria. Currently, the database system includes proteome information for six strains of microorganisms.

  11. 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)

  12. 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.

  13. Evaluation of DNA extraction methods of rumen microbial populations.

    PubMed

    Villegas-Rivera, Gabriela; Vargas-Cabrera, Yevani; González-Silva, Napoleón; Aguilera-García, Florentino; Gutiérrez-Vázquez, Ernestina; Bravo-Patiño, Alejandro; Cajero-Juárez, Marcos; Baizabal-Aguirre, Víctor Manuel; Valdez-Alarcón, Juan José

    2013-02-01

    The dynamism of microbial populations in the rumen has been studied with molecular methods that analyze single nucleotide polymorphisms of ribosomal RNA gene fragments (rDNA). Therefore DNA of good quality is needed for this kind of analysis. In this work we report the evaluation of four DNA extraction protocols (mechanical lysis or chemical lysis with CTAB, ethylxanthogenate or DNAzol(®)) from ruminal fluid. The suitability of two of these protocols (mechanical lysis and DNAzol(®)) was tested on single-strand conformation polymorphism (SSCP) of rDNA of rumen microbial populations. DNAzol(®) was a simple method that rendered good integrity, yield and purity. With this method, subtle changes in protozoan populations were detected in young bulls fed with slightly different formulations of a supplement of multinutritional blocks of molasses and urea. Sequences related to Eudiplodinium maggi and a non-cultured Entodiniomorphid similar to Entodinium caudatum, were related to major fluctuating populations in an SSCP assay.

  14. 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...

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

    PubMed

    Juška, Alfonsas

    2011-01-21

    Dynamics of growth and decline of microbial populations were analysed and respective models were developed in this investigation. Analysis of the dynamics was based on general considerations concerning the main properties of microorganisms and their interactions with the environment which was supposed to be affected by the activity of the population. Those considerations were expressed mathematically by differential equations or systems of the equations containing minimal sets of parameters characterizing those properties. It has been found that: (1) the factors leading to the decline of the population have to be considered separately, namely, accumulation of metabolites (toxins) in the medium and the exhaustion of resources; the latter have to be separated again into renewable ('building materials') and non-renewable (sources of energy); (2) decline of the population is caused by the exhaustion of sources of energy but no decline is predicted by the model because of the exhaustion of renewable resources; (3) the model determined by the accumulation of metabolites (toxins) in the medium does not suggest the existence of a separate 'stationary phase'; (4) in the model determined by the exhaustion of energy resources the 'stationary' and 'decline' phases are quite discernible; and (5) there is no symmetry in microbial population dynamics, the decline being slower than the rise. Mathematical models are expected to be useful in getting insight into the process of control of the dynamics of microbial populations. The models are in agreement with the experimental data. PMID:21036180

  16. 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.

  17. 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.

  18. 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.

  19. "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.

  20. CRISPR-induced distributed immunity in microbial populations.

    PubMed

    Childs, Lauren M; England, Whitney E; 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.

  1. 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.

  2. 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

  3. 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

  4. 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

  5. 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

  6. Effect of surgical scrub on microbial population under the fingernails.

    PubMed

    Gross, A; Cutright, D E; D'Alessandro, S M

    1979-09-01

    The effectiveness of two methods of presurgical hand preparation, the 10 minute routine scrub and the 90 second Hydroscrub, in reducing microbial numbers under the fingernails was determined. Bacteriologic cultures of 162 subungual areas of nine subjects revealed prescrub microbial counts of up to 1.9 X 10(5) colony-forming units per area. After the surgical scrub, bacterial concentrations were reduced to a different degree among the persons tested. The mean values of 3.0 X 10(3) to 7.8 X 10(3) colony-forming units immediately after scrub indicated that neither of the two methods tested reduced the microbial population under the fingernails of most persons to acceptable levels. The finding of high postscrub microbial counts under the fingernails is of particular interest and significance in view of the relatively low counts on the fingertips. On the basis of the results of this study, we conclude that degerming of the areas under the fingernails by present methods is not satisfactory. The implication of these findings is discussed.

  7. 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.

  8. 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

  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. 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.

  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 access to new vaccines in European countries.

    PubMed

    Blank, Patricia R; Schwenkglenks, Matthias; Sardos, Christelle Saint; Patris, Julien; Szucs, Thomas D

    2013-06-12

    Time from registration to population access to new vaccines can take considerable time in European countries. Reasons might be found in the regulatory framework, decision-making processes or the assessment of vaccines by evaluating bodies. The aim of this study was to determine whether some decision-making processes can explain between-country differences in the time to population access to new vaccination programs. Information gathered from a survey among European National Vaccine Industry Groups was combined with information from official health authorities, vaccine manufacturers and literature published. Firstly, a retrospective survey was conducted to measure access time to new vaccines against three diseases in 17 European countries. Secondly, qualitative information on the country-specific decision-making frameworks for the introduction of new "vaccination programs" was identified in a cross-sectional survey. Spearman's rank correlation coefficients (ρ) were used for data analysis. The median access time to new vaccines was 6.4 years (95% confidence interval: 5.7-7.1 years) post marketing authorization. National assessments underlying immunization policy decisions (recommendation phase) absorbed most of the access time. Correlation analysis suggested that processes with established timelines and clarity in regard to vaccine evaluation criteria used could ameliorate the effectiveness of the decision-making process. In order to reduce the time to access for new, beneficial vaccines, the underlying vaccination recommendation, implementation and funding process needs to be understood and optimized, where necessary. PMID:23632307

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

    ERIC Educational Resources Information Center

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

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

  14. 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...

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

    PubMed

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

    2013-07-01

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

  16. 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

  17. Enumeration of microbial populations in radioactive environments by epifluorescence microscopy

    SciTech Connect

    Pansoy-Hjelvik, M.E.; Strietelmeier, B.A.; Paffett, M.T.

    1997-01-01

    Epifluorescence microscopy was utilized to enumerate halophilic bacterial populations in two studies involving inoculated, actual waste/brine mixtures and pure brine solutions. The studies include an initial set of experiments designed to elucidate potential transformations of actinide-containing wastes under salt-repository conditions, including microbially mediated changes. The first study included periodic enumeration of bacterial populations of a mixed inoculum initially added to a collection of test containers. The contents of the test containers are the different types of actual radioactive waste that could potentially be stored in nuclear waste repositories in a salt environment. The transuranic waste was generated from materials used in actinide laboratory research. The results show that cell numbers decreased with time. Sorption of the bacteria to solid surfaces in the test system is discussed as a possible mechanism for the decrease in cell numbers. The second study was designed to determine radiological and/or chemical effects of {sup 239}Pu, {sup 243}Am, {sup 237}Np, {sup 232}Th and {sup 238}U on the growth of pure and mixed anaerobic, denitrifying bacterial cultures in brine media. Pu, Am, and Np isotopes at concentrations of {le}1x10{sup -6} M , {le}5x10{sup -6} M and {le}5x10{sup -4}M respectively, and Th and U isotopes {le}4x10{sup -3}M were tested in these media. The results indicate that high concentrations of certain actinides affected both the bacterial growth rate and morphology. However, relatively minor effects from Am were observed at all tested concentrations with the pure culture.

  18. Enumeration of Microbial Populations in Radioactive Environments by Epifluorescence Microscopy

    SciTech Connect

    Pansoy-Hjelvik, M.E.A.; Strietelmeierr, B.A.; Paffett, M.T.; Kitten, S.M.; Leonard, P.A.; Dunn, M.; Gillow, J.B.; Dodge, C.J.; Villarreal, R.; Triay, I.; Francis, A.J.

    1996-12-02

    Epifluorescence microscopy was utilized to enumerate halophilic bacterial populations in two studies involving inoculated, actual radioactive waste/brine mixtures and pure brine solutions. The studies include an initial set of experiments designed to elucidate potential transformations of actinide-containing wastes under salt-repository conditions, including microbially mediated changes. The first study included periodic enumeration of bacterial populations of a mixed inoculum initially added to a collection of test containers. The contents of the test containers are the different types of actual radioactive waste that could potentially be stored in nuclear waste repositories in a salt environment. The transuranic waste was generated from materials used in actinide laboratory research. The results show that cell numbers decreased with time. Sorption of the bacteria to solid surfaces in the test system is discussed as a possible mechanism for the decrease in cell numbers. The second study was designed to determine radiological and/or chemical effects of {sup 239}Pu, {sup 243}Am, {sup 237}Np, {sup 232}Th and {sup 238}U on the growth of pure and mixed anaerobic, denitrifying bacterial cultures in brine media. Pu, Am, and Np isotopes at concentrations of <=1 x 10{sup {minus}5}M, <=5 x 10{sup {minus}6}M and <=5 x 10{sup {minus}4}M respectively, and Th and U isotopes <=4 x 10{sup {minus}3}M were tested in these media. The results indicate that high actinide concentration affected both the bacterial growth rate and morphology. However, relatively minor effects from Am were observed at all tested concentrations with the pure culture.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

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

    PubMed Central

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

    2016-01-01

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

  1. [Characteristics of soil microbial populations in depressions between karst hills under different land use patterns].

    PubMed

    Song, Min; Zou, Dong-Sheng; Du, Hu; Peng, Wan-Xia; Zeng, Fu-Ping; Tan, Qiu-Jin; Fan, Fu-Jing

    2013-09-01

    Based on the investigation and analysis of six soil microbial indices, eight soil conventional nutrient indices, six soil mineral nutrient indices, and 15 vegetation indices in the farmland, grassland, scrub, forest plantation, secondary forest, and primary forest in the depressions between karst hills, this paper analyzed the main soil microbial populations, soil microbial biomass carbon (MBC), nitrogen (MBN), and phosphorus (MBP) and their fractal characteristics, and the relationships of the soil microbes with vegetation, soil nutrients, and soil mineral components under different land use patterns. The soil microbial populations differed in their quantity and composition under different land use patterns. Primary forest and farmland had the highest quantity of soil microbial populations, while forest plantation had the lowest one. The three forests had a higher proportion of soil bacteria, the farmland, grassland, and scrub had a higher proportion of actinomycetes, and all the six land use patterns had a low proportion of soil fungi. Under the six land use patterns, the soil MBC, MBN, and MBP were all high, with the maximum in primary forest. There was a good fractal relationship between the soil MBC and microbial populations, but no fractal relationships between the soil MBN and MBP and the microbial populations. Significant relationships were observed between the soil microbes and the vegetation, soil nutrients, and soil mineral components, and the soil MBC had the closest relationships with the Shannon index of tree layer and the soil total nitrogen, Fe2O3, and CaO contents.

  2. Nutrient Limitation and Adaptation of Microbial Populations to Chemical Transformations

    PubMed Central

    Lewis, David L.; Kollig, Heinz P.; Hodson, Robert E.

    1986-01-01

    Using field-collected periphyton and bacterial isolates, we determined adaptation lag periods for microbial transformation of p-cresol. Lag periods were longer for periphyton samples collected from field sites that were low in dissolved inorganic nitrogen and phosphorus. Moreover, lag periods decreased in samples amended with N or P. Our data suggest that adaptation lag periods for microbial transformation of low concentrations of chemicals may correlate with limiting nutrient concentrations, and this correlation may provide a basis for predictive mathematical modeling of lag periods. PMID:16347021

  3. 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

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

    SciTech Connect

    Hickey, W.J.

    1995-07-01

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

  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.

  11. 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

  12. 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.

  13. 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

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

    PubMed

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  17. 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

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. 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...

  3. 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…

  4. Transport and mixing of microbial population by atmospheric coherent structures

    NASA Astrophysics Data System (ADS)

    Bozorg Magham, A.; Ross, S. D.

    2012-12-01

    Lagrangian coherent structures (LCSs) provide a new means for discussion of spatiotemporal characteristics of the passive transport and mixing of atmospheric pathogen populations, paving the way for new management strategies regarding the spread of infectious diseases affecting plants, domestic animals, and humans, including identification of probable source regions and forecasts of regions at high risk. We report on the relationship of coherent structures to the patchiness of pathogen populations, and the effects of imperfect forecast wind data on the resultant LCSs. Regarding forecasting LCSs, our main contributions are to quantify the accuracy and sensitivity of such predictions with respect to the forecasting parameters. To obtain more reliable atmospheric LCS features, we have incorporated two more concepts. First is the effect of unresolved turbulent motion; this consideration leads to the stochastic finite-time Lyapunov exponent (SFTLE) field and the resultant stochastic LCS. The second concept is ensemble FTLE/LCS forecasting using individual members of the ensemble wind field forecasts.

  5. Rapid evolution of adaptive niche construction in experimental microbial populations.

    PubMed

    Callahan, Benjamin J; Fukami, Tadashi; Fisher, Daniel S

    2014-11-01

    Many species engage in adaptive niche construction: modification of the local environment that increases the modifying organism's competitive fitness. Adaptive niche construction provides an alternative pathway to higher fitness, shaping the environment rather than conforming to it. Yet, experimental evidence for the evolutionary emergence of adaptive niche construction is lacking, leaving its role in evolution uncertain. Here we report a direct observation of the de novo evolution of adaptive niche construction in populations of the bacteria Pseudomonas fluorescens. In a laboratory experiment, we allowed several bacterial populations to adapt to a novel environment and assessed whether niche construction evolved over time. We found that adaptive niche construction emerged rapidly, within approximately 100 generations, and became ubiquitous after approximately 400 generations. The large fitness effect of this niche construction was dominated by the low fitness of evolved strains in the ancestrally modified environment: evolved niche constructors were highly dependent on their specific environmental modifications. Populations were subjected to frequent resetting of environmental conditions and severe reduction of spatial habitat structure, both of which are thought to make adaptive niche construction difficult to evolve. Our finding that adaptive niche construction nevertheless evolved repeatably suggests that it may play a more important role in evolution than generally thought.

  6. 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.

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

    PubMed

    Wang, Qiongshan; He, Mengchang; Wang, Ying

    2011-01-01

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

  8. 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…

  9. 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…

  10. 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.

  11. 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.

  12. Epidemiology. Opposite effects of anthelmintic treatment on microbial infection at individual versus population scales.

    PubMed

    Ezenwa, Vanessa O; Jolles, Anna E

    2015-01-01

    Parasitic worms modulate host immune responses in ways that affect microbial co-infections. For this reason, anthelmintic therapy may be a potent tool for indirectly controlling microbial pathogens. However, the population-level consequences of this type of intervention on co-infecting microbes are unknown. We evaluated the effects of anthelmintic treatment on bovine tuberculosis (BTB) acquisition, mortality after infection, and pathogen fitness in free-ranging African buffalo. We found that treatment had no effect on the probability of BTB infection, but buffalo survival after infection was ninefold higher among treated individuals. These contrasting effects translated into an approximately eightfold increase in the reproductive number of BTB for anthelmintic-treated compared with untreated buffalo. Our results indicate that anthelmintic treatment can enhance the spread of microbial pathogens in some real-world situations.

  13. The microbial population in the air of cultivation facility of oyster mushrooms.

    PubMed

    Chun, Se Chul; Ahn, Yu Na; Khan, Sajid Mohamad; Chung, Il Min; Won, Hyang Yoen; Jhune, Chang Sung; Park, Yool Jin

    2012-12-01

    The microbial population in the air of mushroom cultivation facility was studied to understand the population structure and size depending on the cultivation methods and regions. The air contents of ten farmers' oyster mushroom cultivation facilities in Kyunggi province were sampled. The results indicated that there was no difference in population size depending on the regions of mushroom cultivation. In addition, the population size of bacteria in the growth room was bigger than that of the cooling room and outside of the mushroom house, but the fungal population was similar in size between cultivation stages. With regard to population structure, Pseudomonas and Penicillium species were most frequently isolated from the air of oyster mushroom cultivation facility. PMID:23274995

  14. 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

  15. 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.

  16. The tragedy of the commons in microbial populations: insights from theoretical, comparative and experimental studies.

    PubMed

    MacLean, R C

    2008-03-01

    First principles of thermodynamics imply that metabolic pathways are faced with a trade-off between the rate and yield of ATP production. Simple evolutionary models argue that this trade-off generates a fundamental social conflict in microbial populations: average fitness in a population is highest if all individuals exploit common resources efficiently, but individual reproductive rate is maximized by consuming common resources at the highest possible rate, a scenario known as the tragedy of the commons. In this paper, I review studies that have addressed two key questions: What is the evidence that the rate-yield trade-off is an evolutionary constraint on metabolic pathways? And, if so, what determines evolutionary outcome of the conflicts generated by this trade-off? Comparative studies and microbial experiments provide evidence that the rate-yield trade-off is an evolutionary constraint that is driven by thermodynamic constraints that are common to all metabolic pathways and pathway-specific constraints that reflect the evolutionary history of populations. Microbial selection experiments show that the evolutionary consequences of this trade-off depend on both kin selection and biochemical constraints. In well-mixed populations with low relatedness, genotypes with rapid and efficient metabolism can coexist as a result of negative frequency-dependent selection generated by density-dependent biochemical costs of rapid metabolism. Kin selection can promote the maintenance of efficient metabolism in structured populations with high relatedness by ensuring that genotypes with efficient metabolic pathways gain an indirect fitness benefit from their competitive restraint. I conclude by suggesting avenues for future research and by discussing the broader implications of this work for microbial social evolution.

  17. The tragedy of the commons in microbial populations: insights from theoretical, comparative and experimental studies.

    PubMed

    MacLean, R C

    2008-05-01

    First principles of thermodynamics imply that metabolic pathways are faced with a trade-off between the rate and yield of ATP production. Simple evolutionary models argue that this trade-off generates a fundamental social conflict in microbial populations: average fitness in a population is highest if all individuals exploit common resources efficiently, but individual reproductive rate is maximized by consuming common resources at the highest possible rate, a scenario known as the tragedy of the commons. In this paper, I review studies that have addressed two key questions: What is the evidence that the rate-yield trade-off is an evolutionary constraint on metabolic pathways? And, if so, what determines evolutionary outcome of the conflicts generated by this trade-off? Comparative studies and microbial experiments provide evidence that the rate-yield trade-off is an evolutionary constraint that is driven by thermodynamic constraints that are common to all metabolic pathways and pathway-specific constraints that reflect the evolutionary history of populations. Microbial selection experiments show that the evolutionary consequences of this trade-off depend on both kin selection and biochemical constraints. In well-mixed populations with low relatedness, genotypes with rapid and efficient metabolism can coexist as a result of negative frequency-dependent selection generated by density-dependent biochemical costs of rapid metabolism. Kin selection can promote the maintenance of efficient metabolism in structured populations with high relatedness by ensuring that genotypes with efficient metabolic pathways gain an indirect fitness benefit from their competitive restraint. I conclude by suggesting avenues for future research and by discussing the broader implications of this work for microbial social evolution.

  18. 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.

  19. 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.

  20. Frog virus 3 prevalence in tadpole populations inhabiting cattle-access and non-access wetlands in Tennessee, USA.

    PubMed

    Gray, Matthew J; Miller, Debra L; Schmutzer, A Chandler; Baldwin, Charles A

    2007-09-14

    Ranaviruses have been associated with most of the reported larval anuran die-offs in the United States. It is hypothesized that anthropogenically induced stress may increase pathogen prevalence in amphibian populations by compromising immunity. Cattle use of wetlands may stress resident tadpole populations by reducing water quality. We isolated a Ranavirus from green frog Rana clamitans (n = 80) and American bullfrog R. catesbeiana (n = 104) tadpoles collected at 5 cattle-access and 3 non-access wetlands on the Cumberland Plateau, Tennessee, USA. Sequencing confirmed Frog virus 3 (FV3); therefore, we compared its prevalence between tadpole populations inhabiting cattle-access and non-access wetlands, and among 3 seasons (winter, summer, and autumn) in 2005. We found FV3 in both tadpole species and cattle land-use types; however, prevalence of FV3 was greater in green frog tadpoles residing in cattle-access wetlands compared to those in non-access wetlands. No difference in FV3 prevalence was detected between cattle land uses for American bullfrog tadpoles. A seasonal trend in FV3 prevalence also existed, with prevalence greater in autumn and winter than in summer for both species. In addition, we found that FV3 prevalence decreased significantly as Gosner stage increased in American bullfrog tadpoles. No trend was detected between FV3 prevalence and developmental stage for green frog tadpoles. Our results suggest that cattle use of wetlands may increase prevalence of FV3 in Rana tadpoles, although this effect may depend on species, season, and tadpole developmental stage. PMID:17972750

  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.

  2. 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

  3. 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…

  4. Management and control of microbial populations: development in LSS of missions of different durations

    NASA Astrophysics Data System (ADS)

    Somova, L. A.

    The problem of interaction between man and microorganisms in closed habitats is an inalienable 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 LSS into three groups: useful, neutral and harmful. The tasks, for human beings for optimal coexistence with micro habitants 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 biological recycling. In these systems, microbial populations should be the most useful and active agents. Some problems of microbial populations control and management are discussed in the paper.

  5. 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

  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. Soil-specific limitations for access and analysis of soil microbial communities by metagenomics.

    PubMed

    Lombard, Nathalie; Prestat, Emmanuel; van Elsas, Jan Dirk; Simonet, Pascal

    2011-10-01

    Metagenomics approaches represent an important way to acquire information on the microbial communities present in complex environments like soil. However, to what extent do these approaches provide us with a true picture of soil microbial diversity? Soil is a challenging environment to work with. Its physicochemical properties affect microbial distributions inside the soil matrix, metagenome extraction and its subsequent analyses. To better understand the bias inherent to soil metagenome 'processing', we focus on soil physicochemical properties and their effects on the perceived bacterial distribution. In the light of this information, each step of soil metagenome processing is then discussed, with an emphasis on strategies for optimal soil sampling. Then, the interaction of cells and DNA with the soil matrix and the consequences for microbial DNA extraction are examined. Soil DNA extraction methods are compared and the veracity of the microbial profiles obtained is discussed. Finally, soil metagenomic sequence analysis and exploitation methods are reviewed.

  10. Microbial Population Dynamics Associated with Crude-Oil Biodegradation in Diverse Soils

    PubMed Central

    Hamamura, Natsuko; Olson, Sarah H.; Ward, David M.; Inskeep, William P.

    2006-01-01

    Soil bacterial population dynamics were examined in several crude-oil-contaminated soils to identify those organisms associated with alkane degradation and to assess patterns in microbial response across disparate soils. Seven soil types obtained from six geographically distinct areas of the United States (Arizona, Oregon, Indiana, Virginia, Oklahoma, and Montana) were used in controlled contamination experiments containing 2% (wt/wt) crude oil spiked with [1-14C]hexadecane. Microbial populations present during hydrocarbon degradation were analyzed using both 16S rRNA gene sequence analysis and by traditional methods for cultivating hydrocarbon-oxidizing bacteria. After a 50-day incubation, all seven soils showed comparable hydrocarbon depletion, where >80% of added crude oil was depleted and approximately 40 to 70% of added [14C]hexadecane was converted to 14CO2. However, the initial rates of hydrocarbon depletion differed up to 10-fold, and preferential utilization of shorter-chain-length n-alkanes relative to longer-chain-length n-alkanes was observed in some soils. Distinct microbial populations developed, concomitant with crude-oil depletion. Phylogenetically diverse bacterial populations were selected across different soils, many of which were identical to hydrocarbon-degrading isolates obtained from the same systems (e.g., Nocardioides albus, Collimonas sp., and Rhodococcus coprophilus). In several cases, soil type was shown to be an important determinant, defining specific microorganisms responding to hydrocarbon contamination. However, similar Rhodococcus erythropolis-like populations were observed in four of the seven soils and were the most common hydrocarbon-degrading organisms identified via cultivation. PMID:16957258

  11. 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.

  12. 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.

  13. 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

  14. 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.

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

    PubMed

    Torlak, Emrah; Sert, Durmuş; Ulca, Pelin

    2013-08-01

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

  16. 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

  17. New methods for analysis of spatial distribution and coaggregation of microbial populations in complex biofilms.

    PubMed

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

    2013-10-01

    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.

  18. 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

  19. 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

  20. 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.

  1. Seasonal variations in microbial populations and environmental conditions in an extreme acid mine drainage environment.

    PubMed

    Edwards, K J; Gihring, T M; Banfield, J F

    1999-08-01

    Microbial populations, their distributions, and their aquatic environments were studied over a year (1997) at an acid mine drainage (AMD) site at Iron Mountain, Calif. Populations were quantified by fluorescence in situ hybridizations with group-specific probes. Probes were used for the domains Eucarya, Bacteria, and Archaea and the two species most widely studied and implicated for their role in AMD production, Thiobacillus ferrooxidans and Leptospirillum ferrooxidans. Results show that microbial populations, in relative proportions and absolute numbers, vary spatially and seasonally and correlate with geochemical and physical conditions (pH, temperature, conductivity, and rainfall). Bacterial populations were in the highest proportion (>95%) in January. Conversely, archaeal populations were in the highest proportion in July and September ( approximately 50%) and were virtually absent in the winter. Bacterial and archaeal populations correlated with conductivity and rainfall. High concentrations of dissolved solids, as reflected by high conductivity values (up to 125 mS/cm), occurred in the summer and correlated with high archaeal populations and proportionally lower bacterial populations. Eukaryotes were not detected in January, when total microbial cell numbers were lowest (<10(5) cells/ml), but eukaryotes increased at low-pH sites ( approximately 0.5) during the remainder of the year. This correlated with decreasing water temperatures (50 to 30 degrees C; January to November) and increasing numbers of prokaryotes (10(8) to 10(9) cells/ml). T. ferrooxidans was in highest abundance (>30%) at moderate pHs and temperatures ( approximately 2.5 and 20 degrees C) in sites that were peripheral to primary acid-generating sites and lowest (0 to 5%) at low-pH sites (pH approximately 0.5) that were in contact with the ore body. L. ferrooxidans was more widely distributed with respect to geochemical conditions (pH = 0 to 3; 20 to 50 degrees C) but was more abundant at

  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. 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

  4. 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

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

    PubMed

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

    2013-02-01

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

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

    PubMed Central

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

    2013-01-01

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

  7. 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...

  8. 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

  9. 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.

  10. Assessment of microbial populations in methyl ethyl ketone degrading biofilters by denaturing gradient gel electrophoresis.

    PubMed

    Li, C; Moe, W M

    2004-05-01

    Denaturing gradient gel electrophoresis (DGGE) analysis of polymerase chain reaction-amplified genes coding for 16S rRNA was used to assess differences in bacterial community structure as a function of spatial location along the height of two biofilters used to treat a model waste gas stream containing methyl ethyl ketone (MEK). One of the laboratory-scale biofilters was operated as a conventional continuous-flow biofilter (CFB) and the other was operated as a sequencing batch biofilter (SBB). Both biofilters, inoculated with an identical starting culture and operated over a period lasting more than 300 days, received the same influent MEK concentration and same mass of MEK on a daily basis. The systems differed, however, in terms of the fraction of time during which contaminated air was supplied and the overall operating strategy employed. DGGE analysis indicated that microbial community structures differed as a function of height in each of the biofilters. The DGGE banding patterns also differed between the two biofilters, suggesting that operating strategies imposed on the biofilters imparted a sufficiently large selective pressure to influence microbial community structures. This may explain, in part, the superior performance of the SBB over the CFB during model transient loading conditions, and it may open new possibilities for purposely manipulating the microbial populations in biofilters treating gas-phase contaminants in a manner that leads to more favorable treatment performance.

  11. 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

  12. 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.

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

    PubMed

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

    2015-11-01

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

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

    PubMed

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

    2014-08-26

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

  15. 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

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

    PubMed

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

    2009-01-01

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

  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. Division synchrony and the dynamics of microbial populations: a size-specific model.

    PubMed

    Gage, T B; Williams, F M; Horton, J B

    1984-12-01

    A discrete, environmentally coupled, size-specific model of microbial population dynamics in continuous culture is presented. It is mathematically simpler than other models based on similar assumptions and lends itself to numerical and analytic solutions. It displays several phenomena which have been reported in the experimental literature but which are not well understood; specifically, a loose relationship between biomass and numbers (i.e., a time lag between mass growth and cell division) and a critical damping of biomass while numbers continue to oscillate. In addition, the model provides several new predictions: The stable biomass distribution is independent of the environmental factors considered in the model and uniformly distributes the biomass among the size classes. The rate of approach to stability and the frequency of waves through the size distributions are a function of the flow rate and the variance in rate of growth and size at division. The model should provide a useful basis for studying the effects of size specificity on the dynamics of microbial populations cultured in chemostats.

  19. 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

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

    PubMed

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

    2015-01-01

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

  1. Population genomics and local adaptation in wild isolates of a model microbial eukaryote.

    PubMed

    Ellison, Christopher E; Hall, Charles; Kowbel, David; Welch, Juliet; Brem, Rachel B; Glass, N L; Taylor, John W

    2011-02-15

    Elucidating the connection between genotype, phenotype, and adaptation in wild populations is fundamental to the study of evolutionary biology, yet it remains an elusive goal, particularly for microscopic taxa, which comprise the majority of life. Even for microbes that can be reliably found in the wild, defining the boundaries of their populations and discovering ecologically relevant phenotypes has proved extremely difficult. Here, we have circumvented these issues in the microbial eukaryote Neurospora crassa by using a "reverse-ecology" population genomic approach that is free of a priori assumptions about candidate adaptive alleles. We performed Illumina whole-transcriptome sequencing of 48 individuals to identify single nucleotide polymorphisms. From these data, we discovered two cryptic and recently diverged populations, one in the tropical Caribbean basin and the other endemic to subtropical Louisiana. We conducted high-resolution scans for chromosomal regions of extreme divergence between these populations and found two such genomic "islands." Through growth-rate assays, we found that the subtropical Louisiana population has a higher fitness at low temperature (10 °C) and that several of the genes within these distinct regions have functions related to the response to cold temperature. These results suggest the divergence islands may be the result of local adaptation to the 9 °C difference in average yearly minimum temperature between these two populations. Remarkably, another of the genes identified using this unbiased, whole-genome approach is the well-known circadian oscillator frequency, suggesting that the 2.4°-10.6° difference in latitude between the populations may be another important environmental parameter. PMID:21282627

  2. 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…

  3. 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…

  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.

  5. 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

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

    PubMed

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

    2015-07-01

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

  7. 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.

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

    PubMed

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

    2010-05-01

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

  9. The role of microbial populations in the containment of aromatic hydrocarbons in the subsurface.

    PubMed

    Franzmann, P D; Robertson, W J; Zappia, L R; Davis, G B

    2002-01-01

    A survey of soil gases associated with gasoline stations on the Swan Coastal Plain of Western Australia has shown that 20% leak detectable amounts of petroleum. The fates of volatile hydrocarbons in the vadose zone at one contaminated site, and dissolved hydrocarbons in groundwater at another site were followed in a number of studies which are herein reviewed. Geochemical evidence from a plume of hydrocarbon-contaminated groundwater has shown that sulfate reduction rapidly developed as the terminal electron accepting process. Toluene degradation but not benzene degradation was linked to sulfate reduction. The sulfate-reducing bacteria isolated from the plume represented a new species, Desulfosporosinus meridiei. Strains of the species do not mineralise 14C-toluene in pure culture. The addition of large numbers of cells and sulfate to microcosms did stimulate toluene mineralisation but not benzene mineralisation. Attempts to follow populations of sulfate-reducing bacteria by phospholipid signatures, or Desulfosporosinus meridiei by FISH in the plume were unsuccessful, but fluorescently-labeled polyclonal antibodies were successfully used. In the vadose zone at a different site, volatile hydrocarbons were consumed in the top 0.5 m of the soil profile. The fastest measured rate of mineralisation of 14C-benzene in soils collected from the most active zone (6.5 mg kg(-1) day(-1)) could account for the majority of the flux of hydrocarbon vapourtowards the surface. The studies concluded that intrinsic remediation by subsurface microbial populations in groundwater on the Swan Coastal Plain can control transport of aromatic hydrocarbon contamination, except for the transport of benzene in groundwater. In the vadose zone, intrinsic remediation by the microbial populations in the soil profile can contain the transport of aromatic hydrocarbons, provided the physical transport of gases, in particular oxygen from the atmosphere, is not impeded by structures.

  10. 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

  11. 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

  12. 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

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

    PubMed

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

    2013-01-01

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

  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.

  15. [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

  16. 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.

  17. 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.

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

    SciTech Connect

    ANTHONY DEAN

    2009-07-24

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

  19. 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

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

    PubMed

    Leta, Samson; Mesele, Frehiwot

    2014-01-01

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

  1. 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

  2. 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/.

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

    PubMed Central

    Malki, Kema; Bruder, Katherine; Putonti, Catherine

    2015-01-01

    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

  4. Effect of moisture, organic matter, microbial population and fortification level on dissipation of pyraclostrobin in soils.

    PubMed

    Reddy, S Navakishore; Gupta, Suman; Gajbhiye, Vijay T

    2013-09-01

    The dissipation of pyraclostrobin, a strobilurin fungicide, in soil was found to be influenced by soil moisture, organic matter content and microbial population. Among the different moisture regimes, dissipation was faster under submerged condition (T1/2 10 days) followed by field capacity (T1/2 28.7 days) and in dry soil (T1/2 41.8 days). Use of sludge at 5 % level to Inceptisol favoured a faster dissipation of pyraclostrobin, whereas a slower rate of dissipation was observed in partial organic matter removed soil as compared to normal soil. Slower rate of dissipation was also observed in sterile soil (T1/2 47 days) compared to normal soil. Pyraclostrobin dissipated faster in Vertisol (T1/2 21.8 days) than in Inceptisol (T1/2 28.7 days). No significant difference in the dissipation rate was observed at 1 and 10 μg g(-1) fortification levels.

  5. 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

  6. 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

  7. 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

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

    SciTech Connect

    Panikov, N.S.

    1994-11-01

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

  9. 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.

  10. 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.

  11. Linking TFT-LCD wastewater treatment performance to microbial population abundance of Hyphomicrobium and Thiobacillus spp.

    PubMed

    Fukushima, Toshikazu; Whang, Liang-Ming; Chen, Po-Chun; Putri, Dyah Wulandari; Chang, Ming-Yu; Wu, Yi-Ju; Lee, Ya-Ching

    2013-08-01

    This study investigated the linkage between performance of two full-scale membrane bioreactor (MBR) systems treating thin-film transistor liquid crystal display (TFT-LCD) wastewater and the population dynamics of dimethylsulfoxide (DMSO)/dimethylsulfide (DMS) degrading bacteria. High DMSO degradation efficiencies were achieved in both MBRs, while the levels of nitrification inhibition due to DMS production from DMSO degradation were different in the two MBRs. The results of real-time PCR targeting on DMSO/DMS degrading populations, including Hyphomicrobium and Thiobacillus spp., indicated that a higher DMSO oxidation efficiency occurred at a higher Hyphomicrobium spp. abundance in the systems, suggesting that Hyphomicrobium spp. may be more important for complete DMSO oxidation to sulfate compared with Thiobacillus spp. Furthermore, Thiobacillus spp. was more abundant during poor nitrification, while Hyphomicrobium spp. was more abundant during good nitrification. It is suggested that microbial population of DMSO/DMS degrading bacteria is closely linking to both DMSO/DMS degradation efficiency and nitrification performance. PMID:23628318

  12. 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

  13. Contribution of wheat endogenous and wheat kernel associated microbial endoxylanases to changes in the arabinoxylan population during breadmaking.

    PubMed

    Dornez, Emmie; Cuyvers, Sven; Gebruers, Kurt; Delcour, Jan A; Courtin, Christophe M

    2008-03-26

    Wheat kernel associated endoxylanases consist of a majority of microbial endoxylanases and a minority of endogenous endoxylanases. At least part of these enzymes can be expected to end up in wheat flour upon milling. In this study, the contribution of both types of these endoxylanases to changes in the arabinoxylan (AX) population during wheat flour breadmaking was assessed. To this end, wheat flour produced from two wheat varieties with different endoxylanase activity levels, both before and after sodium hypochlorite surface treatment of the wheat kernels, was used in a straight dough breadmaking procedure. Monitoring of the AX population during the breadmaking process showed that changes in AX are to a large extent caused by endogenous endoxylanases, whereas the contribution of microbial endoxylanases to these changes was generally very low. The latter points to a limited contamination of wheat flour with microbial enzymes during milling or to an extensive inactivation of these wheat flour associated microbial endoxylanases by endoxylanase inhibitors, present in wheat flour. When all wheat kernel associated microbial endoxylanases were first washed from the kernels and then added to the bread recipe, they drastically affected the AX population, suggesting that they can have a large impact on whole meal breadmaking.

  14. MbT-Tool: An open-access tool based on Thermodynamic Electron Equivalents Model to obtain microbial-metabolic reactions to be used in biotechnological process.

    PubMed

    Araujo, Pablo Granda; Gras, Anna; Ginovart, Marta

    2016-01-01

    Modelling cellular metabolism is a strategic factor in investigating microbial behaviour and interactions, especially for bio-technological processes. A key factor for modelling microbial activity is the calculation of nutrient amounts and products generated as a result of the microbial metabolism. Representing metabolic pathways through balanced reactions is a complex and time-consuming task for biologists, ecologists, modellers and engineers. A new computational tool to represent microbial pathways through microbial metabolic reactions (MMRs) using the approach of the Thermodynamic Electron Equivalents Model has been designed and implemented in the open-access framework NetLogo. This computational tool, called MbT-Tool (Metabolism based on Thermodynamics) can write MMRs for different microbial functional groups, such as aerobic heterotrophs, nitrifiers, denitrifiers, methanogens, sulphate reducers, sulphide oxidizers and fermenters. The MbT-Tool's code contains eighteen organic and twenty inorganic reduction-half-reactions, four N-sources (NH4 (+), NO3 (-), NO2 (-), N2) to biomass synthesis and twenty-four microbial empirical formulas, one of which can be determined by the user (CnHaObNc). MbT-Tool is an open-source program capable of writing MMRs based on thermodynamic concepts, which are applicable in a wide range of academic research interested in designing, optimizing and modelling microbial activity without any extensive chemical, microbiological and programing experience. PMID:27635191

  15. MbT-Tool: An open-access tool based on Thermodynamic Electron Equivalents Model to obtain microbial-metabolic reactions to be used in biotechnological process.

    PubMed

    Araujo, Pablo Granda; Gras, Anna; Ginovart, Marta

    2016-01-01

    Modelling cellular metabolism is a strategic factor in investigating microbial behaviour and interactions, especially for bio-technological processes. A key factor for modelling microbial activity is the calculation of nutrient amounts and products generated as a result of the microbial metabolism. Representing metabolic pathways through balanced reactions is a complex and time-consuming task for biologists, ecologists, modellers and engineers. A new computational tool to represent microbial pathways through microbial metabolic reactions (MMRs) using the approach of the Thermodynamic Electron Equivalents Model has been designed and implemented in the open-access framework NetLogo. This computational tool, called MbT-Tool (Metabolism based on Thermodynamics) can write MMRs for different microbial functional groups, such as aerobic heterotrophs, nitrifiers, denitrifiers, methanogens, sulphate reducers, sulphide oxidizers and fermenters. The MbT-Tool's code contains eighteen organic and twenty inorganic reduction-half-reactions, four N-sources (NH4 (+), NO3 (-), NO2 (-), N2) to biomass synthesis and twenty-four microbial empirical formulas, one of which can be determined by the user (CnHaObNc). MbT-Tool is an open-source program capable of writing MMRs based on thermodynamic concepts, which are applicable in a wide range of academic research interested in designing, optimizing and modelling microbial activity without any extensive chemical, microbiological and programing experience.

  16. 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.

  17. Improved Access To Aging Ocean Basement Biosphere For Microbial Geochemical Studies

    NASA Astrophysics Data System (ADS)

    Cowen, J. P.; Glazer, B.; Rappe, M.; Kenig, F.; Fisher, A.; Copson, D.; Harris, D.; Jolly, J.; Nuzzio, D.

    2005-12-01

    CORK observatories affixed to Integrated Ocean Drilling Program (IODP) boreholes offer an unprecedented opportunity to study biogeochemical properties and microbial diversity in circulating fluids from sediment-buried ocean basement. Preliminary 16S rRNA gene sequence data from 65 degrees C fluids escaping from the top of the over-pressured ODP borehole 1026B, on the flanks of the Juan de Fuca Ridge indicated the presence of diverse Bacteria and Archaea, including gene clones with varying degrees of relatedness to known dissimilatory nitrate reducers (with ammonia production), thermophilic sulfate reducers, and thermophilic fermentative heterotrophs, consistent with fluid chemistry measurements. However, questions remain regarding microbial community structure, key metabolic pathways and rates, and redox chemistry of the basement fluids, along with concerns for contamination issues. We describe ongoing developments intended to address key in situ analytical and sampling challenges including: 1) The new generation CORKs' dedicated microbiological/geochemical fluid delivery system specifically designed to minimize chemical contamination and surface biofouling; and 2) Development of a seafloor instrument sled for coupling to the CORK's bio-fluid delivery system for acquisition of real-time, in situ electrochemical (voltammetry) redox chemistry data on basement fluids, in addition to in situ particle filtration of basement fluids for molecular genetics, culturing and biogeochemical studies. Results of the first deployment of this instrument sled to new CORK observatory 1301A in Cascadia Basin, on the flanks of the Juan de Fuca Ridge, will be described.

  18. Molecular characterization of microbial populations in full-scale biofilters treating iron, manganese and ammonia containing groundwater in Harbin, China.

    PubMed

    Li, Xiang-kun; Chu, Zhao-rui; Liu, Ya-jun; Zhu, Meng-ting; Yang, Liu; Zhang, Jie

    2013-11-01

    In iron and manganese-containing groundwater treatment for drinking water production, biological filter is an effective process to remove such pollutants. Until now the exact microbial mechanism of iron and manganese removal, especially coupled with other pollutants, such as ammonia, has not been clearly understood. To assess this issue, the performance of a full-scale biofilter located in Harbin, China was monitored over four months. Microbial populations in the biofilter were investigated using T-RFLP and clone library technique. Results suggested that Gallionella, Leptothrix, Nitrospira, Hyphomicrobium and Pseudomonas are dominant in the biofilter and play major roles in the removal of iron, manganese and ammonia. The spatial distribution of microbial populations along the depth of the biofilter demonstrated the stratification of the removal of iron, manganese and ammonia. Additionally, the absence of ammonia-oxidizing bacteria in the biofilter implicated that ammonia-oxidizing archaea might be responsible for the oxidation of ammonia to nitrite. PMID:23994965

  19. Molecular characterization of microbial populations in full-scale biofilters treating iron, manganese and ammonia containing groundwater in Harbin, China.

    PubMed

    Li, Xiang-kun; Chu, Zhao-rui; Liu, Ya-jun; Zhu, Meng-ting; Yang, Liu; Zhang, Jie

    2013-11-01

    In iron and manganese-containing groundwater treatment for drinking water production, biological filter is an effective process to remove such pollutants. Until now the exact microbial mechanism of iron and manganese removal, especially coupled with other pollutants, such as ammonia, has not been clearly understood. To assess this issue, the performance of a full-scale biofilter located in Harbin, China was monitored over four months. Microbial populations in the biofilter were investigated using T-RFLP and clone library technique. Results suggested that Gallionella, Leptothrix, Nitrospira, Hyphomicrobium and Pseudomonas are dominant in the biofilter and play major roles in the removal of iron, manganese and ammonia. The spatial distribution of microbial populations along the depth of the biofilter demonstrated the stratification of the removal of iron, manganese and ammonia. Additionally, the absence of ammonia-oxidizing bacteria in the biofilter implicated that ammonia-oxidizing archaea might be responsible for the oxidation of ammonia to nitrite.

  20. Detecting rare structural variation in evolving microbial populations from new sequence junctions using breseq

    PubMed Central

    Deatherage, Daniel E.; Traverse, Charles C.; Wolf, Lindsey N.; Barrick, Jeffrey E.

    2014-01-01

    New mutations leading to structural variation (SV) in genomes—in the form of mobile element insertions, large deletions, gene duplications, and other chromosomal rearrangements—can play a key role in microbial evolution. Yet, SV is considerably more difficult to predict from short-read genome resequencing data than single-nucleotide substitutions and indels (SN), so it is not yet routinely identified in studies that profile population-level genetic diversity over time in evolution experiments. We implemented an algorithm for detecting polymorphic SV as part of the breseq computational pipeline. This procedure examines split-read alignments, in which the two ends of a single sequencing read match disjoint locations in the reference genome, in order to detect structural variants and estimate their frequencies within a sample. We tested our algorithm using simulated Escherichia coli data and then applied it to 500- and 1000-generation population samples from the Lenski E. coli long-term evolution experiment (LTEE). Knowledge of genes that are targets of selection in the LTEE and mutations present in previously analyzed clonal isolates allowed us to evaluate the accuracy of our procedure. Overall, SV accounted for ~25% of the genetic diversity found in these samples. By profiling rare SV, we were able to identify many cases where alternative mutations in key genes transiently competed within a single population. We also found, unexpectedly, that mutations in two genes that rose to prominence at these early time points always went extinct in the long term. Because it is not limited by the base-calling error rate of the sequencing technology, our approach for identifying rare SV in whole-population samples may have a lower detection limit than similar predictions of SNs in these data sets. We anticipate that this functionality of breseq will be useful for providing a more complete picture of genome dynamics during evolution experiments with haploid microorganisms

  1. 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...

  2. Microbial populations of an upflow anaerobic sludge blanket reactor treating wastewater from a gelatin industry.

    PubMed

    Vieira, A M; Bergamasco, R; Gimenes, M L; Nakamura, C V; Dias Filho, B P

    2001-12-01

    The microbial populations of an upflow anaerobic sludge blanket reactor, used for treating wastewater from the gelatin industry, were studied by microbiological methods and phase-contrast and electron microscopy. Microscopy examination of the sludge showed a complex mixture of various rod-shaped and coccoid bacterial pluslong filaments and verymobile curved rods. In addition free-living anaerobic ciliates and flagellates were also observed. The trophic group population observed in decreasing order of dominance were hydrolytic and acetogenic at 10(6) and sulfate reducing and methanogenic at 10(5). The rate of methane production in anaerobic granular sludge cultivated in growth medium supplement with formate pressurized with H2:CO2 showed a significant increase in methane yield compared with theseed culture containingthe same substrate and atmosphere of N2:CO2. Similar rates of methane production were observed when the growth medium was supplemented with acetate pressurized either with H2:CO2 or N2:CO2. The number of total anaerobic bacteria at 10(7), fecal coliforms and total coliforms at 10(6), and fecal streptococci at 10(3) is based on colony counts on solid media. The four prevalent species of facultative anaerobic gram-negative bacteria that belong to the family of Enterobacteriaceae were identified as Escherichia coli, Esherichia fergusonii, Klebsiella oxytoca, and Citrobacter freundii. The species Aeromonas hydrophila, Aeromonas veronii, Acinetobacter iwoffi and Stenotrophomonas maltophila were the most frequently isolated glucose fermenting and nonfermenting gram-negative bacilli.

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

    PubMed

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

    2013-04-01

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

  4. 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

  5. Soybean oligosaccharides alter colon short-chain fatty acid production and microbial population in vitro.

    PubMed

    Zhou, X L; Kong, X F; Yang, X J; Yin, Y L

    2012-12-01

    This study was conducted to the determine fermentation characteristics of soybean oligosaccharides (SBOS) in an in vitro system. Digesta collected from the colon of Huanjiang mini-pigs was used as inoculums, and SBOS (0.2 g per 10 mL fermentation broth) was used as substrate during the in vitro fermentation. The inoculum or inoculum + glucose (0.2 g) was used as negative or positive control, respectively. The slurry was fermented in an anaerobic chamber and gas production (GP) recording was taken after 48 h of incubation by referring to the moving scale on the plunger of the glass syringes, and then GP parameters, pH value, NH(3)-N content, short chain fatty acid (SCFA) levels, and microbial community in the fermentation broth were determined. For gas production parameters, pH, and fermentation product determination after 1, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 28, 32, 36, 42, and 48 h of incubation, SBOS and glucose demonstrated similar responses compared to control including increase maximal gas production, decreased lag time, decreased pH, and accumulation of NH(3) and increased SCFA. The exception was rate of GP, which was higher (P < 0.05) for SBOS compared with glucose. Incubation with SBOS increased (P < 0.05) the microbial diversity and population of Bifidobacterium and Lactobacillus but decreased (P < 0.05) Escherichia and Streptococcus when compared with incubation with glucose. These findings suggested that the SBOS can improve the gut microbiota balance in colon and modulate its metabolism. PMID:23365277

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

    PubMed

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

    2016-10-01

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

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

    PubMed

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

    2016-10-01

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

  8. 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.

  9. 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

  10. 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

  11. 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.

  12. 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

  13. [Improve the accessibility of essential drugs for the populations of one medical region in Burkina Faso].

    PubMed

    Ridde, Valéry; Nitièma, Abdoulaye P; Dadjoari, Moussa

    2005-01-01

    Despite the formulation of the Bamako initiative in 1992 in Burkina Faso, not until 2001 and the launching of a project by a nongovernmental organization was the policy really implemented in a region of the country. One of the goals of this policy is to improve access to health care by using generic essential drugs. The objective of this article is to summarize the results of the evaluation of the project's ability to improve the population's access to drugs. The project lasted three years (2001-2003) and the interventions took place in 41 basic health centres of three districts. According to WHO, improving access to drugs requires consideration of four essential factors: rational use, affordable prices, financial viability, and effectiveness of the distribution. The average number of drugs prescribed per prescription sheet (n = 1061) was 2.4; 93% of the drugs were prescribed by their generic name (international non-proprietary names); 44% of infant diarrheas were treated with oral rehydration salt. National drug prices were respected but not the directives aiming at exempting from payment or subsidizing certain population sub-groups (children, indigents). The average annual cash flow of the basic health centres was 1.2 million F CFA and it increased by 854% compared to the beginning of the project. The cost-recovery scheme for administrative expenses was 106%. The average annual availability of the 10 essential drugs was 89%. Utilization rates increased (0.13 in 1999 to 0.21 in 2003) but not significantly differently than in other basic health centres of the area not supported by the project (p = 0.084). The project succeeded in improving access to these drugs for the overall population but not for the worst-off. The drugs are now geographically available for all and financially accessible for those who can afford to pay. The intervention strategy supported the sustainability of the project's activities but much remains to be done to provide the poorest with

  14. 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

  15. 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.

  16. [Problems of accessibility for the population of Georgian modern outpatient and inpatient care].

    PubMed

    Bolkvadze, R A; Gerzmava, O Kh

    2014-12-01

    Which began in 2013, the implementation of the priority national project - Universal health programs for population of Georgia - has important social significance, given the increased accessibility of the population in case of timely and quality medical care. Various forms of public participation in the payment of services received in varying degrees allow us to find a compromise between containment of demand and increase access to treatment. And if the insurance in its various forms, largely solves the last problem, but may create a problem of rising costs, the different types of direct payments more efficient demand, however creates a need to control access to health care for populations with a high demand for medical care. Co-payments under the defined government programs and directly to the patient, on the one hand, imply severally pay for health care and the fear of the occurrence of catastrophic costs of treatment, and on the other hand, allow you to control the rising costs of the health system. The problem of reducing the availability of medical care is overcome by introducing exemptions from co-payments for vulnerable groups, which in turn leads to a substantial increase in government spending. It must be emphasized that the tools developed and the results of the calculations can be used to compare the effects of the introduction of various schemes of co-payments and choose the most suitable scheme, in terms of the extent of the burden of private expenditure on treatment, as well as income and expenses of the health system in general. PMID:25617109

  17. 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

  18. Prokaryotic diversity and metabolically active microbial populations in sediments from an active mud volcano in the Gulf of Mexico.

    PubMed

    Martinez, Robert J; Mills, Heath J; Story, Sandra; Sobecky, Patricia A

    2006-10-01

    In this study, ribosomes and genomic DNA were extracted from three sediment depths (0-2, 6-8 and 10-12 cm) to determine the vertical changes in the microbial community composition and identify metabolically active microbial populations in sediments obtained from an active seafloor mud volcano site in the northern Gulf of Mexico. Domain-specific Bacteria and Archaea 16S polymerase chain reaction primers were used to amplify 16S rDNA gene sequences from extracted DNA. Complementary 16S ribosomal DNA (crDNA) was obtained from rRNA extracted from each sediment depth that had been subjected to reverse transcription polymerase chain reaction amplification. Twelve different 16S clone libraries, representing the three sediment depths, were constructed and a total of 154 rDNA (DNA-derived) and 142 crDNA (RNA-derived) Bacteria clones and 134 rDNA and 146 crDNA Archaea clones obtained. Analyses of the 576 clones revealed distinct differences in the composition and patterns of metabolically active microbial phylotypes relative to sediment depth. For example, epsilon-Proteobacteria rDNA clones dominated the 0-2 cm clone library whereas gamma-Proteobacteria dominated the 0-2 cm crDNA library suggesting gamma to be among the most active in situ populations detected at 0-2 cm. Some microbial lineages, although detected at a frequency as high as 9% or greater in the total DNA library (i.e. Actinobacteria, alpha-Proteobacteria), were markedly absent from the RNA-derived libraries suggesting a lack of in situ activity at any depth in the mud volcano sediments. This study is one of the first to report the composition of the microbial assemblages and physiologically active members of archaeal and bacterial populations extant in a Gulf of Mexico submarine mud volcano. PMID:16958759

  19. 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.

  20. 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

  1. 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

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

    NASA Technical Reports Server (NTRS)

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

    2003-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

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

    PubMed

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

    2012-09-01

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

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

    PubMed Central

    Nachman, Michael W.

    2016-01-01

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

  6. 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

  7. 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

  8. Effects of butachlor on microbial populations and enzyme activities in paddy soil.

    PubMed

    Min, H; Ye, Y F; Chen, Z Y; Wu, W X; Yufeng, D

    2001-09-01

    This paper reports the influences of the herbicide butachlor (n-butoxymethlchloro -2', 6'-diethylacetnilide) on microbial populations, respiration, nitrogen fixation and nitrification, and on the activities of dehydrogenase and hydrogen peroxidase in paddy soil. The results showed that the number of actinomycetes declined significantly after the application of butachlor at different concentrations ranging from 5.5 microg g(-1) to 22.0 microg g(-1) dried soil, while that of bacteria and fungi increased. Fungi were easily affected by butachlor compared to the bacteria. The growth of fungi was retarded by butachlor at higher concentrations. Butachlor however, stimulated the growth of anaerobic hydrolytic fermentative bacteria, sulfate-reducing bacteria (SRB) and denitrifying bacteria. The increased concentration of butachlor applied resulted in the higher number of SRB. Butachlor inhibited the growth of hydrogen-producing acetogenic bacteria. The effect of butachlor varied on methane-producing bacteria (MPB) at different concentrations. Butachlor at the concentration of 1.0 microg g(-1) dried soil or less than this concentration accelerated the growth of MPB, while at 22.0 microg g(-1) dried soil showed an inhibition. Butachlor enhanced the activity of dehydrogenase at increasing concentrations. The soil dehydrogenase showed the highest activity on the 16th day after application of 22.0 microg g(-1) dried soil of butachlor. The hydrogen peroxidase could be stimulated by butachlor. The soil respiration was depressed during the period from several days to more than 20 days, depending on concentrations of butachlor applied. Both the nitrogen fixation and nitrification were stimulated in the beginning but reduced greatly afterwards in paddy soil.

  9. Biodegradation of trichloroethylene and toluene by indigenous microbial populations in soil.

    PubMed

    Fan, S; Scow, K M

    1993-06-01

    The biodegradation of trichloroethylene (TCE) and toluene, incubated separately and in combination, by indigenous microbial populations was measured in three unsaturated soils incubated under aerobic conditions. Sorption and desorption of TCE (0.1 to 10 micrograms ml-1) and toluene (1.0 to 20 micrograms ml-1) were measured in two soils and followed a reversible linear isotherm. At a concentration of 1 micrograms ml-1, TCE was not degraded in the absence of toluene in any of the soils. In combination, both 1 microgram of TCE ml-1 and 20 micrograms of toluene ml-1 were degraded simultaneously after a lag period of approximately 60 to 80 h, and the period of degradation lasted from 70 to 90 h. Usually 60 to 75% of the initial 1 microgram of TCE ml-1 was degraded, whereas 100% of the toluene disappeared. A second addition of 20 micrograms of toluene ml-1 to a flask with residual TCE resulted in another 10 to 20% removal of the chemical. Initial rates of degradation of toluene and TCE were similar at 32, 25, and 18 degrees C; however, the lag period increased with decreasing temperature. There was little difference in degradation of toluene and TCE at soil moisture contents of 16, 25, and 30%, whereas there was no detectable degradation at 5 and 2.5% moisture. The addition of phenol, but not benzoate, stimulated the degradation of TCE in Rindge and Yolo silt loam soils, methanol and ethylene slightly stimulated TCE degradation in Rindge soil, glucose had no effect in either soil, and dissolved organic carbon extracted from soil strongly sorbed TCE but did not affect its rate of biodegradation. PMID:8328806

  10. 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...

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

    PubMed

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

    2013-09-01

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

  12. 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

  13. 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

  14. 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.

  15. 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

  16. 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

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

    PubMed Central

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

    2016-01-01

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

  18. 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.

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

    PubMed

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

    2009-09-01

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

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

    PubMed

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

    2003-01-01

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

  1. 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

  2. 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

  3. 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.

  4. Microbial Populations in Extreme Environments: Investigations and Characterizations of the Microbiology and Geochemistry of Galapagos Island Fumaroles

    NASA Astrophysics Data System (ADS)

    Mayhew, L. E.; Childers, S. E.; Geist, D.

    2005-12-01

    The extreme physiochemical conditions, insularity, and wide range in ages of fumaroles of the Galapagos Islands provide an excellent opportunity to explore for novel microorganisms and to study life in extreme environments. This is the first study that measures microbial diversity of Galapagos fumaroles. Forty-seven samples were collected from six distinct fumarole fields on Sierra Negra and Alcedo volcanoes. Vulcan Chico, on Sierra Negra, was activated during the last eruption in 1979. Two of the other fumarole fields on Sierra Negra are associated with a long-lived fault system on the caldera floor and are therefore likely to be significantly older. The fault-associated fumaroles have widespread alteration haloes (up to 100 m in diameter) and thick deposits of native sulfur. The most vigorous of the fumarole fields on Alcedo activated in late 1993 to early 1994. The second fumarole field on Alcedo is associated with a recently extinct geyser and the third is located on a rhyolite vent. A diversity of colors was observed in the substrates at all of the fumarole fields and some may be the result of microbial activity. Collection sites were chosen on the basis of temperature and the variations in the substrate in order to obtain samples from a variety of environments. Temperatures at sample sites range from 25.0 to 178.5° C, and pH from 0 to 6. The material collected varies between sites and includes crystalline sulfur deposits, clay, sandy and rocky soils, and microbial mats. Substrate material is characterized by powder x-ray diffractometry and scanning electron microscopy and gases collected from five of the fumarole fields are being analyzed to test for chemical controls on the microbial populations. Genomic DNA is being extracted from all of the samples. Primers for Bacteria and Archaea are used for PCR amplification of the 16S rRNA gene. To date, 22 of 37 processed samples have amplifiable DNA. Microbial diversity of samples possessing amplifiable DNA is

  5. 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

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

    PubMed

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

    2014-07-01

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

  7. Cow teat skin, a potential source of diverse microbial populations for cheese production.

    PubMed

    Verdier-Metz, Isabelle; 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.

  8. Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction.

    PubMed

    Reddy, Amitha P; Allgaier, Martin; Singer, Steven W; Hazen, Terry C; Simmons, Blake A; Hugenholtz, Philip; VanderGheynst, Jean S

    2011-09-01

    Thermophilic microbial communities that are active in a high-solids environment offer great potential for the discovery of industrially relevant enzymes that efficiently deconstruct bioenergy feedstocks. In this study, finished green waste compost was used as an inoculum source to enrich microbial communities and associated enzymes that hydrolyze cellulose and hemicellulose during thermophilic high-solids fermentation of the bioenergy feedstocks switchgrass and corn stover. Methods involving the disruption of enzyme and plant cell wall polysaccharide interactions were developed to recover xylanase and endoglucanase activity from deconstructed solids. Xylanase and endoglucanase activity increased by more than a factor of 5, upon four successive enrichments on switchgrass. Overall, the changes for switchgrass were more pronounced than for corn stover; solids reduction between the first and second enrichments increased by a factor of four for switchgrass while solids reduction remained relatively constant for corn stover. Amplicon pyrosequencing analysis of small-subunit ribosomal RNA genes recovered from enriched samples indicated rapid changes in the microbial communities between the first and second enrichment with the simplified communities achieved by the third enrichment. The results demonstrate a successful approach for enrichment of unique microbial communities and enzymes active in a thermophilic high-solids environment.

  9. 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

  10. 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

  11. 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

  12. 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.

  13. 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

  14. 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

  15. 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

  16. 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.

  17. 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

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

    PubMed

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

    2007-04-01

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

  19. 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.

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

    PubMed

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

    2013-04-01

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

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

    PubMed Central

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

    2014-01-01

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

  2. 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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

  5. Microbial characterization and population changes in nonpotable reclaimed water distribution systems.

    PubMed

    Ryu, Hodon; Alum, Absar; Abbaszadegan, Morteza

    2005-11-15

    Changes in the microbial quality of nonpotable reclaimed water distribution systems in seven metropolitan areas of the southwestern United States were investigated by performing pathogen monitoring and bacterial growth. Water samples were collected from tertiary-treated effluents at point of entry and point of use in the distribution systems. The samples were analyzed for Cryptosporidium oocysts, Giardia cysts, enteroviruses, microbial indicators, and assimilable organic carbon (AOC). Cryptosporidium and Giardia were detected in 16% (12/77) and 43% (33/77) of nonpotable reclaimed water samples, whereas no infectious Cryptosporidium parvum were detected in any of the samples. No infectious enteroviruses were detected in any sample (0/27). At point of entry total coliform and fecal coliforms ranged from 0.7 to 280 and from 0 to 1.9 colony-forming units (cfu)/100 mL, respectively. Increases in the number of coliforms were observed as water passed through the reclaimed water distribution systems. However, no such increase in the number of coliphages was found. The chlorination practices at some utilities were not sufficient to inactivate coliforms and coliphages, but supplemental ultraviolet disinfection resulted in lower numbers of these microbial indicators. AOC levels decreased by 3-fold as water passed through the distribution systems, which inversely correlated with bacterial regrowth.

  6. 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.

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

    PubMed Central

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

    2011-01-01

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

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

    PubMed

    Pilajun, R; Wanapat, M

    2013-06-01

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

  9. Factors affecting the microbial populations at full-scale enhanced biological phosphorus removal (EBPR) wastewater treatment plants in The Netherlands.

    PubMed

    López-Vázquez, Carlos M; Hooijmans, Christine M; Brdjanovic, Damir; Gijzen, Huub J; van Loosdrecht, Mark C M

    2008-05-01

    The influence of operating and environmental conditions on the microbial populations of the enhanced biological phosphorus removal (EBPR) process at seven full-scale municipal activated sludge wastewater treatment plants (WWTPs) in The Netherlands was studied. Data from the selected WWTPs concerning process configuration, operating and environmental conditions were compiled. The EBPR activity from each plant was determined by execution of anaerobic-anoxic-aerobic batch tests using fresh activated sludge. Fractions of Accumulibacter as potential phosphorus accumulating organisms (PAO), and Competibacter, Defluviicoccus-related microorganisms and Sphingomonas as potential glycogen accumulating organisms (GAO) were quantified using fluorescence in situ hybridization (FISH). The relationships among plant process configurations, operating parameters, environmental conditions, EBPR activity and microbial populations fractions were evaluated using a statistical approach. A well-defined and operated denitrification stage and a higher mixed liquor pH value in the anaerobic stage were positively correlated with the occurrence of Accumulibacter. A well-defined denitrification stage also stimulated the development of denitrifying PAO (DPAO). A positive correlation was observed between Competibacter fractions and organic matter concentrations in the influent. Nevertheless, Competibacter did not cause a major effect on the EBPR performance. The observed Competibacter fractions were not in the range that would have led to EBPR deterioration. Likely, the low average sewerage temperature (12+/-2 degrees C) limited their proliferation. Defluviicoccus-related microorganisms were seen only in negligible fractions in a few plants (<0.1% as EUB), whereas Sphingomonas were not observed.

  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. 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

  12. Responses of microbial populations in the rhizosphere to deposition of simulated acidic rain onto foliage and/or soil.

    PubMed

    Shafer, S R

    1992-01-01

    Air pollutants or some chemicals applied to plant foliage can alter the ecology of the rhizosphere. Experiments were conducted to distinguish among possible foliage-mediated versus soil- or root-mediated effects of acid deposition on microorganism in the rhizosphere. Seedlings of a sorghum x sudangrass hybrid in pots of non-sterile soil-sand mix in a greenhouse were exposed to simulated rain solution adjusted with H2SO4 + HNO3 to pH 4.9, 4.2, 3.5 or 2.8. Solutions were applied as simulated rain to foliage and soil, foliage only (soil covered by plastic, and deionized water applied directly to the soil), or soil only (solution applied directly to the soil). Solutions were applied on 16 days during a 6-week period (1.5 cm deposition in 1 h per application). Plant shoot and root dry weights and population densities of selected types of bacteria, filamentous actinomycetes and fungi in the rhizosphere were quantified after exposures were completed. Deposition of simulated acidic rain onto foliage alone had no effect on plant biomass or microbial population densities in the rhizosphere (colony-forming units per gram of rhizosphere soil). However, plant growth was stimulated and all microbial populations in the rhizosphere increased 3- to 8-fold with increased solution acidity (relative to pH 4.9 solution) when solution penetrated the soil. Statistical analyses indicated that the acid dose-population response relationships for soil-only and foliage-and-soil applications were not different. Thus, no foliage-mediated effect of simulated acidic rain on rhizosphere ecology was detected.

  13. Molecular monitoring of microbial population dynamics during operational periods of anaerobic hybrid reactor treating cassava starch wastewater.

    PubMed

    Boonapatcharoen, Nimaradee; Meepian, Kulyanee; Chaiprasert, Pawinee; Techkarnjanaruk, Somkiet

    2007-07-01

    This study characterized the microbial community and population dynamics in an anaerobic hybrid reactor (AHR) treating cassava starch wastewater. Methanogens and nonmethanogens were followed during the start-up and operation of the reactor, and linked to operational and performance data. Biomass samples taken from the sludge bed and packed bed zones of the AHR at intervals throughout the operational period were examined by 16S rRNA fluorescence in situ hybridization (FISH). The start-up seed and the reactor biomass were sampled during the feeding of the wastewater with a chemical oxygen demand (COD) value of 8 g L(-1) and a hydraulic retention time (HRT) of 8 days. These samples were characterized by the predominance of cells with long-rod morphology similar to Methanosaeta spp. Following a sharp operational change, accomplished by increasing the COD concentration of the organic influent from 8 to 10 g L(-1) and reducing the HRT from 8 to 5 days, there was a doubling of the organic loading rate, a reduction of the COD removal efficiency, as well as decreased methane content in the biogas and an accumulation of total volatile acids in the reactor. Moreover, this operational change resulted in a significant population shift from long-rod Methanosaeta-like cells to tetrad-forming Methanosarcina-like cells. The distributions of microbial populations involved in different zones of the AHR were determined. The results showed that nonmethanogens became the predominant population in both sludge and the packed bed zone. However, the percentage of methanogens in the packed bed zone was higher than that in the sludge bed zone. This higher percentage of methanogens was likely caused by the fact that the packed bed zone provided a suitable environmental condition with an appropriate nutrient availability for methanogen growth.

  14. Interprofessional collaborative model for medication therapy management (MTM) services to improve health care access and quality for underserved populations.

    PubMed

    Truong, Hoai-An; Groves, C Nicole; Congdon, Heather Brennan; Botchway, Rosemary; Dang, Diem-Thanh Tanya; Clark, Nancy Ripp; Zarfeshan, Faramarz

    2012-08-01

    As part of the Health Resources and Services Administration Patient Safety and Clinical Pharmacy Services Collaborative (PSPC), an interprofessional model with medication therapy management documentation and outcomes tracking tools (MTM-DOTT) is established to improve health care access and quality for underserved populations. Despite limitations, there have been positive outcomes and national recognitions.

  15. 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

  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

    2015-09-08

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

  17. Work-First Federal Policies: Eroding Access to Community Colleges for Latinos and Low-Income Populations

    ERIC Educational Resources Information Center

    Shaw, Kathleen M.; Goldrick-Rab, Sara

    2006-01-01

    This chapter describes how the implementation of the 1996 welfare reform and the 1998 Workforce Investment Acts affected community colleges' willingness and capacity to provide access to postsecondary education and training for Latinos and other low-income populations. (Contains 3 figures.)

  18. Natural variation of salinity response, population structure and candidate genes associated with salinity tolerance in perennial ryegrass accessions.

    PubMed

    Tang, Jinchi; Yu, Xiaoqing; Luo, Na; Xiao, Fangming; Camberato, James J; Jiang, Yiwei

    2013-11-01

    Natural variation in salinity response, effects of population structure on growth and physiological traits and gene-trait association were examined in 56 global collections of diverse perennial ryegrass (Lolium perenne L.) accessions. Three population structure groups were identified with 66 simple sequence repeat markers, which on average accounted for 9 and 11% of phenotypic variation for the control and salinity treatment at 300 mm NaCl. Group 1 (10 accessions) had greater plant height, leaf dry weight and water content, chlorophyll index, K(+) concentration and K(+) /Na(+) than group 2 (39 accessions) and group 3 (7 accessions) under salinity stress, while group 3 had higher Na(+) than groups 1 and 2. Eighty-seven single nucleotide polymorphisms were detected from four partial candidate genes encoding aquaporin and Na(+) /H(+) antiporter in both plasma and tonoplast membranes. Overall, rapid decay of linkage disequilibrium was observed within 500 bp. Significant associations were found between the putative LpTIP1 and Na(+) for the control and between the putative LpNHX1 and K(+) /Na(+) under the control and salinity treatments after controlling population structure. These results indicate that population structure influenced phenotypic traits, and allelic variation in LpNHX1 may affect salinity tolerance of perennial ryegrass.

  19. 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

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

    PubMed

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

    2014-05-01

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

  1. 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.

  2. 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.

  3. 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

  4. [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.

  5. 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.

  6. 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

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

    PubMed

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

    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 R(2) 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

  8. Distribution of phototrophic populations and primary production in a microbial mat from the Ebro Delta, Spain.

    PubMed

    Martínez-Alonso, Maira; Mir, Joan; Caumette, Pierre; Gaju, Núria; Guerrero, Ricardo; Esteve, Isabel

    2004-03-01

    Microbial mats arising in the sand flats of the Ebro Delta (Tarragona, Spain) were investigated during the summer season, when the community was highly developed. These mats are composed of three pigmented layers of phototrophic organisms, an upper brown layer mainly composed of Lyngbya aestuarii and diatoms, an intermediate green layer of the cyanobacterium Microcoleus chthonoplastes, and an underlying pink layer of a so-far unidentified purple sulfur bacterium. In the photic zone, oxygenic phototrophs constitute about 58% of total photosynthetic biomass, measured as biovolume, and anoxygenic phototrophs represent 42%. Diatoms constitute 11.8% of the oxygenic biomass, M. chthonoplastes 61.2%, and L. aestuarii and coccoid cyanobacteria 20.6 and 6.4%, respectively. In this laminated community, organic matter has an autochthonous origin, and photosynthesis is the most important source of organic carbon. Oxygen production reaches up to 27.2 mmol O(2) m(-2) h(-1), measured at 1000 microE m(-2) s(-1) light intensity, whereas oxidation of sulfide in the light has been calculated to be 18.6 mmol S m(-2) h(-1). This amount represents 26% of the total photosynthetic production in terms of photoassimilated carbon, demonstrating the important role of anoxygenic phototrophs as primary producers in the pink layer of Ebro Delta microbial mats.

  9. 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

  10. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  12. 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.

  13. 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

  14. 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

  15. High frequency ultrasound pretreatment for sludge anaerobic digestion: effect on floc structure and microbial population.

    PubMed

    Braguglia, C M; Gagliano, M C; Rossetti, S

    2012-04-01

    In this work the potential of high frequency ultrasounds as pretreatment for sludge anaerobic digestion has been assessed. Irradiation with 200kHz ultrasounds was efficient in disintegrating the floc structure increasing the available fraction of soluble organic matter (up to seven times at 25,000kJ/kgTS). Batch anaerobic digestion tests were carried out on lab-scale reactors fed either with untreated or disintegrated sludge inoculated with anaerobic sludge, at different feed/inoculum ratio (F/I=0.5 and 1). Degradation of particulate matter, biogas production and related microbial community composition (estimated by fluorescence in situ hybridization, FISH) were investigated. Sludge ultrasounds pretreatment led to an overall improvement of the digestion performances, with a maximum biogas gain of 40% at F/I=0.5. FISH showed a key-role of Methanosarcina spp. in the main reactions of biogas synthesis.

  16. Metaproteomic survey of six aquatic habitats: discovering the identities of microbial populations active in biogeochemical cycling.

    PubMed

    Hanson, Buck T; Hewson, Ian; Madsen, Eugene L

    2014-04-01

    Our goal is to strengthen the foundations of metaproteomics as a microbial community analysis tool that links the functional identity of actively expressed gene products with host phylogeny. We used shotgun metaproteomics to survey waters in six disparate aquatic habitats (Cayuga Lake, NY; Oneida Lake, NY; Gulf of Maine; Chesapeake Bay, MD; Gulf of Mexico; and the South Pacific). Peptide pools prepared from filter-gathered microbial biomass, analyzed by nano-liquid chromatography-mass spectrometry (MS/MS) generating 9,693 ± 1,073 mass spectra identified 326 ± 107 bacterial proteins per sample. Distribution of proteobacterial (Alpha and Beta) and cyanobacterial (Prochlorococcus and Synechococcus spp.) protein hosts across all six samples was consistent with the previously published biogeography for these microorganisms. Marine samples were enriched in transport proteins (TRAP-type for dicarboxylates and ATP binding cassette (ABC)-type for amino acids and carbohydrates) compared with the freshwater samples. We were able to match in situ expression of many key proteins catalyzing C-, N-, and S-cycle processes with their bacterial hosts across all six habitats. Pelagibacter was identified as the host of ABC-type sugar-, organic polyanion-, and glycine betaine-transport proteins; this extends previously published studies of Pelagibacter's in situ biogeochemical role in marine C- and N-metabolism. Proteins matched to Ruegeria confirmed these organism's role in marine waters oxidizing both carbon monoxide and sulfide. By documenting both processes expressed in situ and the identity of host cells, metaproteomics tested several existing hypotheses about ecophysiological processes and provided fodder for new ones. PMID:24425229

  17. 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.

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

    PubMed

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

    2015-06-01

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

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

    PubMed Central

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

    2015-01-01

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

  20. Influences of Dietary and Environmental Stress on Microbial Populations in the Murine Gastrointestinal Tract

    PubMed Central

    Tannock, Gerald W.; Savage, Dwayne C.

    1974-01-01

    Aerobic and anaerobic cultural techniques and histological methods were used in a study of the effects of environmental and dietary stress on the indigenous microbiota of the gastrointestinal tract of mice. Mice previously inoculated with Salmonella typhimurium were examined in a similar manner. Three strains of mice (CD-1, Ha/ICr, and C57BL) were used. Control animals previously inoculated with S. typhimurium had low population levels of Salmonella bacteria in the small and large bowel. Mice previously inoculated with Salmonella and then deprived of food, water, and bedding for 48 h harbored high population levels of these bacteria in their small and large bowels. Coliforms increased in numbers in the large bowel of stressed mice inoculated with Salmonella and in the jejunum-ileum and cecum of stressed mice not previously inoculated with Salmonella. Control mice had high population levels of lactobacilli inhabiting the keratinized squamous epithelium of the stomach. Stressed mice showed dramatic reductions in these populations of lactobacilli. Populations of fusiform-shaped bacteria associated with the mucosal epithelium of the cecum and colon in control mice were reduced in stressed mice as determined by microscope examination of histological sections. Total anaerobic counts were similar, however, in both stressed and control animals. Environmental and dietary stress markedly alter the gastrointestinal microbiota in mice. Therefore, such stressful conditions profoundly affect the factors that regulate the localization and population levels of microorganisms in the stomach and intestines. Images PMID:4593471

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

    PubMed

    Radhakrishnan, Ramalingam; Kumari, Bollipo Dyana Ranjitha

    2013-08-01

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

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

    PubMed

    Radhakrishnan, Ramalingam; Kumari, Bollipo Dyana Ranjitha

    2013-08-01

    The effects of pulsed magnetic field (PMF) treatment of soybean (Glycine max L. cv CO3) seeds were investigated on rate of seed germination, seedling growth, physico-chemical properties of seed leachates and soil microbial population under laboratory conditions. Seeds were exposed to PMF of 1500 nT at 0.1, 1.0 10.0 and 100.0 Hz for 5 h per day for 20 days, induced by enclosure coil systems. Non-treated seeds were considered as controls. All PMF treatments significantly increased the rate of seed germination, while 10 and 100 Hz PMFs showed the most effective response. The 1.0 and 10 Hz PMFs remarkably improved the fresh weight of shoots and roots, leaf area and plant height from seedlings from magnetically-exposed seeds compared to the control, while 10 Hz PMF increased the total soluble sugar, total protein and phenol contents. The leaf chlorophyll a, b and total chlorophyll were higher in PMF (10 and 100 Hz) pretreated plants, as compared to other treatments. In addition, activities of alpha-amylase, acid phosphatase, alkaline phosphatase, nitrate reductase, peroxidase and polyphenoloxidase were increased, while beta-amylase and protease activities were declined in PMF (10 Hz)-exposed soybean plants. Similarly, the capacity of absorbance of water by seeds and electrical conductivity of seed leachates were significantly enhanced by 10 Hz PMF exposure, whereas PMF (10 Hz) pretreated plants did not affect the microbial population in rhizosphere soil. The results suggested the potential of 10 Hz PMF treatment to enhance the germination and seedling growth of soybean. PMID:24772951

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

    PubMed

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

    2008-06-01

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

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

    PubMed

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

    2013-03-01

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

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

    PubMed

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

    2011-01-01

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

  7. 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...

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

    PubMed Central

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-09-01

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

  10. 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.

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

    PubMed

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

    2011-09-01

    Many microorganisms are advected in the lower atmosphere from one habitat to another with scales of motion being hundreds to thousands of kilometers. The concentration of these microbes in the lower atmosphere at a single geographic location can show rapid temporal changes. We used autonomous unmanned aerial vehicles equipped with microbe-sampling devices to collect fungi in the genus Fusarium 100 m above ground level at a single sampling location in Blacksburg, Virginia, USA. Some Fusarium species are important plant and animal pathogens, others saprophytes, and still others are producers of dangerous toxins. We correlated punctuated changes in the concentration of Fusarium to the movement of atmospheric transport barriers identified as finite-time Lyapunov exponent-based Lagrangian coherent structures (LCSs). An analysis of the finite-time Lyapunov exponent field for periods surrounding 73 individual flight collections of Fusarium showed a relationship between punctuated changes in concentrations of Fusarium and the passage times of LCSs, particularly repelling LCSs. This work has implications for understanding the atmospheric transport of invasive microbial species into previously unexposed regions and may contribute to information systems for pest management and disease control in the future. PMID:21974657

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

    PubMed

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

    2011-09-01

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

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

    PubMed Central

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

    2016-01-01

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

  14. Effects of chestnut tannins and coconut oil on growth performance, methane emission, ruminal fermentation, and microbial populations in sheep.

    PubMed

    Liu, H; Vaddella, V; Zhou, D

    2011-12-01

    This study was conducted to evaluate the effects of chestnut tannins (CT) and coconut oil (CO) on growth performance, methane (CH₄) emission, ruminal fermentation, and microbial populations in sheep. A total of 48 Rideau Arcott sheep (average body weight 31.5±1.97 kg, 16 wk old) were randomly assigned into 6 treatment groups in a 3 × 2 factorial design, with CT and CO as the main effects (8 sheep per group). The treatments were control diet (CTR), 10 or 30 g of CT/kg of diet (CT10 and CT30), 25 g of CO/kg of concentrate (CO25), and 10 or 30 g of CT/kg of diet+25 g of CO/kg of concentrate (CT10CO25 and CT30CO25). After the feeding trial (60 d), all sheep were moved to respiratory chambers to measure CH₄ emission. After CH₄ emission measurements, all sheep were slaughtered to obtain rumen fluid samples. Results showed that the addition of CT, CO, and CT+CO had no significant effects on growth performance of sheep but reduced CH₄ emission. Addition of CT reduced the NH₃-N concentration in rumen fluid in CT30. Addition of CO decreased the concentration of total volatile fatty acids in rumen fluid. No significant differences were observed in pH and molar proportion of volatile fatty acids among treatments. Addition of CT, CO, and CT+CO significantly decreased methanogen and protozoa populations. Moreover, CO decreased counts of Fibrobacter succinogenes. No significant differences were observed in populations of fungi, Ruminococcus flavefaciens, or Ruminococcus albus among treatments. In conclusion, supplementation of CT and CO seemed to be a feasible means of decreasing emissions of CH₄ from sheep by reduction of methanogen and protozoa populations with no negative effect on growth performance.

  15. Effect of common pesticides used in the Niger Delta basin of southern Nigeria on soil microbial populations.

    PubMed

    Ekundayo, E O

    2003-11-01

    The effects of eleven pesticides on the populations of bacteria, actinomycetes, fungi and protozoa was investigated by treating a garden soil with their recommended rates. The microbial populations were estimated using the standard plate-count technique. Of the 11 pesticides investigated, phenylmercuric acetate (agrosan) at 50 microg g(-1) inhibited bacterial density the most, i.e. from 4,600,000 to 220 cells g(-1). The pesticides were Pentachloronitrobenzene (PCNB), tetramethylmethylthiuram disulphide (thiram), 1-naphthylmethylcarbamate (Vetox 85), 1,2,3,4,5,6-hexachlorocyclohexane (Gammalin 20), phenylmercuric acetate (Agrosan), tetrachloroterephthalic acid (Dacthal), 4-nitrophenyl-2-nitro-4-trifluoromethylphenyl ether (Preforan), 2-ethyl-6-methyl-N-2-methoxy-1-methyl ethyl-chloroacetanide (Dual), Benlate, Brestan and Gramoxone. Pentachloronitrobenzene (PCNB) at 240,000 microg g(-1) reduced bacterial population from 4,600,000 to 2,100 cells g(-1), whereas tetramethylthiuram disulphide (thiram) at 100 microg g(-1) suppressed it by 2 log orders of magnitude. Soil application of 1-naphthylmethylcarbamate (Vetox 85) at 100 microg g(-1) and 1,2,3,4,5,6,-hexachlorocyclohexane (Gamalin 20) at 1,300 microg g(-1) repressed the bacterial numbers by 2 log orders of magnitude each. Pentachloronitrobenzene reduced the actinomycetes density from 340,000 to 320 cells g(-1) and completely eliminated all fungal and protozoan propagules from the soil. The Gammalin 20 completely wiped out all the fungi, whereas phenylmercuric acetate totally eliminated all the protozoa and reduced the fungal population from 34,000 to 60 cells g(-1). In general, protozoa and fungi were more susceptible to fungicides than bacteria and actinomycetes. Pentachloronitrobenzene, 1,2,3,4,5,6,-hexachlorocyclohexane and phenylmercuric acetate were toxic particularly to soil microorganisms, whereas the herbicides dacthal, Preforan and Dual were quite harmless in soil at application rates of 0.1, 0.06 and 0

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

    ScienceCinema

    Tremblay, Julien [DOE JGI

    2016-07-12

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

  17. 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.

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

    PubMed

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

    2016-07-01

    Altered gut microbial ecology contributes to the development of metabolic diseases including obesity. In this study, we performed 16S rRNA sequence analysis of the gut microbiota profiles of obese and lean Japanese populations. The V3-V4 hypervariable regions of 16S rRNA of fecal samples from 10 obese and 10 lean volunteers were sequenced using the Illumina MiSeq(TM)II system. The average body mass index of the obese and lean group were 38.1 and 16.6 kg/m(2), respectively (p<0.01). The Shannon diversity index was significantly higher in the lean group than in the obese group (p<0.01). The phyla Firmicutes and Fusobacteria were significantly more abundant in obese people than in lean people. The abundance of the phylum Bacteroidetes and the Bacteroidetes/Firmicutes ratio were not different between the obese and lean groups. The genera Alistipes, Anaerococcus, Corpococcus, Fusobacterium and Parvimonas increased significantly in obese people, and the genera Bacteroides, Desulfovibrio, Faecalibacterium, Lachnoanaerobaculum and Olsenella increased significantly in lean people. Bacteria species possessing anti-inflammatory properties, such as Faecalibacterium prausnitzii, increased significantly in lean people, but bacteria species possessing pro-inflammatory properties increased in obese people. Obesity-associated gut microbiota in the Japanese population was different from that in Western people. PMID:27499582

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

    PubMed Central

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

    2016-01-01

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

  20. A modeling and simulation study of the role of suspended microbial populations in nitrification in a biofilm reactor.

    PubMed

    Mašić, Alma; Eberl, Hermann J

    2014-01-01

    Many biological wastewater treatment processes are based on bacterial biofilms, i.e. layered aggregates of microbial populations deposited on surfaces. Detachment and (re-)attachment leads to an exchange of biomass between the biofilm and the surrounding aqueous phase. Traditionally, mathematical models of biofilm processes do not take the contribution of the suspended, non-attached bacteria into account, implicitly assuming that these are negligible due to the relatively small amount of suspended biomass compared to biofilm biomass. In this paper, we present a model for a nitrifying biofilm reactor that explicitly includes both types of biomass. The model is derived by coupling a reactor mass balance for suspended populations and substrates with a full one-dimensional Wanner-Gujer type biofilm model. The complexity of this model, both with respect to mathematical structure and number of parameters, prevents a rigorous analysis of its dynamics, wherefore we study the model numerically.Our investigations show that suspended biomass needs to be considered explicitly in the model if the interests of the study are the details of the nitrification process and its intermediate steps and compounds. However, suspended biomass may be neglected if the primary interests are the overall reactor performance criteria, such as removal rates. Furthermore, it can be expected that changes in the biofilm area, attachment, detachment, and dilution rates are more likely to affect the variables primarily associated with the second step of nitrification, while the variables associated with the first step tend to be more robust.

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

    PubMed

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

    2016-07-01

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

  2. Population structure of microbial communities associated with two deep, anaerobic, alkaline aquifers.

    PubMed Central

    Fry, N K; Fredrickson, J K; Fishbain, S; Wagner, M; Stahl, D A

    1997-01-01

    Microbial communities of two deep (1,270 and 316 m) alkaline (pH 9.94 and 8.05), anaerobic (Eh, -137 and -27 mV) aquifers were characterized by rRNA-based analyses. Both aquifers, the Grande Ronde (GR) and Priest rapids (PR) formations, are located within the Columbia River Basalt Group in south-central Washington, and sulfidogenesis and methanogenesis characterize the GR and PR formations, respectively. RNA was extracted from microorganisms collected from groundwater by ultrafiltration through hollow-fiber membranes and hybridized to taxon-specific oligonucleotide probes. Of the three domains, Bacteria dominated both communities, making up to 92.0 and 64.4% of the total rRNA from the GR and PR formations, respectively. Eucarya comprised 5.7 and 14.4%, and Archaea comprised 1.8% and 2.5%, respectively. The gram-positive target group was found in both aquifers, 11.7% in GR and 7.6% in PR. Two probes were used to target sulfate- and/or metal-reducing bacteria within the delta subclass of Proteobacteria. The Desulfobacter groups was present (0.3%) only in the high-sulfate groundwater (GR). However, comparable hybridization to a probe selective for the desulfovibrios and some metal-reducing bacteria was found in both aquifers, 2.5 and 2.9% from the GR and PR formations, respectively. Selective PCR amplification and sequencing of the desulfovibrio/metal-reducing group revealed a predominance of desulfovibrios in both systems (17 of 20 clones), suggesting that their environmental distribution is not restricted by sulfate availability. PMID:9097447

  3. Dominant Microbial Populations in Limestone-Corroding Stream Biofilms, Frasassi Cave System, Italy

    PubMed Central

    Macalady, Jennifer L.; Lyon, Ezra H.; Koffman, Bess; Albertson, Lindsey K.; Meyer, Katja; Galdenzi, Sandro; Mariani, Sandro

    2006-01-01

    Waters from an extensive sulfide-rich aquifer emerge in the Frasassi cave system, where they mix with oxygen-rich percolating water and cave air over a large surface area. The actively forming cave complex hosts a microbial community, including conspicuous white biofilms coating surfaces in cave streams, that is isolated from surface sources of C and N. Two distinct biofilm morphologies were observed in the streams over a 4-year period. Bacterial 16S rDNA libraries were constructed from samples of each biofilm type collected from Grotta Sulfurea in 2002. β-, γ-, δ-, and ɛ-proteobacteria in sulfur-cycling clades accounted for ≥75% of clones in both biofilms. Sulfate-reducing and sulfur-disproportionating δ-proteobacterial sequences in the clone libraries were abundant and diverse (34% of phylotypes). Biofilm samples of both types were later collected at the same location and at an additional sample site in Ramo Sulfureo and examined, using fluorescence in situ hybridization (FISH). The biomass of all six stream biofilms was dominated by filamentous γ-proteobacteria with Beggiatoa-like and/or Thiothrix-like cells containing abundant sulfur inclusions. The biomass of ɛ-proteobacteria detected using FISH was consistently small, ranging from 0 to less than 15% of the total biomass. Our results suggest that S cycling within the stream biofilms is an important feature of the cave biogeochemistry. Such cycling represents positive biological feedback to sulfuric acid speleogenesis and related processes that create subsurface porosity in carbonate rocks. PMID:16885314

  4. Subterranean microbial populations metabolize hydrogen and acetate under in situ conditions in granitic groundwater at 450 m depth in the Äspö Hard Rock Laboratory, Sweden.

    PubMed

    Pedersen, Karsten

    2012-07-01

    Pressure-resistant circulating systems were constructed to enable the investigation of attached and unattached microbial populations under in situ pressure (2.5 MPa), diversity, dissolved gas and chemistry conditions. Three parallel flow cell cabinets were configured to allow observation of the effect on microbial metabolic activity of adding 3 mM hydrogen or 2.4 mM acetate, compared with an untreated control. Hydrogen addition reduced the generation time fourfold to 2 weeks, doubled the sulphide production rate and increased acetate production by approximately 50%. The acetate addition induced acetate consumption. The studied subterranean microbial processes appeared to proceed very slowly in terms of volume and time, although the results suggest that individual cells could be very active. Lytic bacteriophages are hypothesized to have caused this contradictive observation. Phages may consequently significantly reduce the rates of subterranean microbial processes. Furthermore, the results suggest that hydrogen from corroding underground constructions could induce significant local microbial activity and that the low concentrations of hydrogen often observed in pristine subterranean environments may support slow but sustainable microbial activity in deep groundwater.

  5. Modeling and quantifying frequency-dependent fitness in microbial populations with cross-feeding interactions.

    PubMed

    Ribeck, Noah; Lenski, Richard E

    2015-05-01

    Coexistence of two or more populations by frequency-dependent selection is common in nature, and it often arises even in well-mixed experiments with microbes. If ecology is to be incorporated into models of population genetics, then it is important to represent accurately the functional form of frequency-dependent interactions. However, measuring this functional form is problematic for traditional fitness assays, which assume a constant fitness difference between competitors over the course of an assay. Here, we present a theoretical framework for measuring the functional form of frequency-dependent fitness by accounting for changes in abundance and relative fitness during a competition assay. Using two examples of ecological coexistence that arose in a long-term evolution experiment with Escherichia coli, we illustrate accurate quantification of the functional form of frequency-dependent relative fitness. Using a Monod-type model of growth dynamics, we show that two ecotypes in a typical cross-feeding interaction-such as when one bacterial population uses a byproduct generated by another-yields relative fitness that is linear with relative frequency.

  6. 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...

  7. Phenol- and toluene-degrading microbial populations from an aquifer in which successful trichloroethene cometabolism occurred.

    PubMed

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

    1997-04-01

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

  8. How Often Do They Have Sex? A Comparative Analysis of the Population Structure of Seven Eukaryotic Microbial Pathogens

    PubMed Central

    Tomasini, Nicolás; Lauthier, Juan José; Ayala, Francisco José; Tibayrenc, Michel; Diosque, Patricio

    2014-01-01

    The model of predominant clonal evolution (PCE) proposed for micropathogens does not state that genetic exchange is totally absent, but rather, that it is too rare to break the prevalent PCE pattern. However, the actual impact of this “residual” genetic exchange should be evaluated. Multilocus Sequence Typing (MLST) is an excellent tool to explore the problem. Here, we compared online available MLST datasets for seven eukaryotic microbial pathogens: Trypanosoma cruzi, the Fusarium solani complex, Aspergillus fumigatus, Blastocystis subtype 3, the Leishmania donovani complex, Candida albicans and Candida glabrata. We first analyzed phylogenetic relationships among genotypes within each dataset. Then, we examined different measures of branch support and incongruence among loci as signs of genetic structure and levels of past recombination. The analyses allow us to identify three types of genetic structure. The first was characterized by trees with well-supported branches and low levels of incongruence suggesting well-structured populations and PCE. This was the case for the T. cruzi and F. solani datasets. The second genetic structure, represented by Blastocystis spp., A. fumigatus and the L. donovani complex datasets, showed trees with weakly-supported branches but low levels of incongruence among loci, whereby genetic structuration was not clearly defined by MLST. Finally, trees showing weakly-supported branches and high levels of incongruence among loci were observed for Candida species, suggesting that genetic exchange has a higher evolutionary impact in these mainly clonal yeast species. Furthermore, simulations showed that MLST may fail to show right clustering in population datasets even in the absence of genetic exchange. In conclusion, these results make it possible to infer variable impacts of genetic exchange in populations of predominantly clonal micro-pathogens. Moreover, our results reveal different problems of MLST to determine the genetic

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

    PubMed

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

    2004-09-01

    The microbiological quality of Monostroma undulatum, Wittrock from the Southern Argentinean coast, was studied for its application for human food. Also the diversity and function of the native bacterial population to this green seaweed was analyzed. Samples were collected in Puerto Deseado, province of Santa Cruz, Southern Argentina (47 degrees 45'L.S., 65 degrees 55'L.W). The samples were analyzed for the presence of psycotrophic heterotrophic bacteria, marine heterotrophic bacteria, low nutritional request bacteria (LNRB), marine low nutritional request bacteria (LNRB marine), Vibrio spp, total and thermotolerant colifom bacteria, anaerobic sulfite reducing bacteria, yeasts and moulds. The isolates were identified using standard techniques based on morphologic, physiologic and metabolic characteristics. Among the gram-negative bacteria isolated, the predominant genera belonged to Vibrio (20%), E. coli inactiva (18%), Flavobacterium (11%), Flexibacter (9%), Moraxella (9%), Alcaligenes/Pseudomonas group (9%), Aeromonas (2%), Acinetobacter (2%). Cotophaga (2%), Photobacterium (2%), Ps/Caulobacter/Alteromonas/Spirillum group (2), The main genus of gram-positive bacteria was Staphylococcus. Human pathogenic bacteria were not detected. Fecal contamination indicator bacteria were not isolated from fresh seaweed and seawater. These results showed an adequate microbiological quality of seaweed acceptable for human food. The bacterial population associated to Monostroma undulatum, consisted of gram-negative, marine and psycotrophic microorganisms, including vibrios and enterobacteria as their main components. Also the identified bacteria showed a great capacity to hydrolyze different substrates and so they might contribute to the balance of this marine ecosystem. PMID:15807211

  10. Shedding light on microbial predator-prey population dynamics using a quantitative bioluminescence assay.

    PubMed

    Im, Hansol; Kim, Dasol; Ghim, Cheol-Min; Mitchell, Robert J

    2014-01-01

    This study assessed the dynamics of predation by Bdellovibrio bacteriovorus HD 100. Predation tests with two different bioluminescent strains of Escherichia coli, one expressing a heat-labile bacterial luciferase and the other a heat-stable form, showed near identical losses from both, indicating that protein expression and stability are not responsible for the "shutting-off" of the prey bioluminescence (BL). Furthermore, it was found that the loss in the prey BL was not proportional with the predator-to-prey ratio (PPR), with significantly greater losses seen as this value was increased. This suggests that other factors also play a role in lowering the prey BL. The loss in BL, however, was very consistent within nine independent experiments to the point that we were able to reliably estimate the predator numbers within only 1 h when present at a PPR of 6 or higher, Using a fluorescent prey, we found that premature lysis of the prey occurs at a significant level and was more prominent as the PPR ratio increased. Based upon the supernatant fluorescent signal, even a relatively low PPR of 10-20 led to approximately 5% of the prey population being prematurely lysed within 1 h, while a PPR of 90 led to nearly 15% lysis. Consequently, we developed a modified Lotka-Volterra predator-prey model that accounted for this lysis and is able to reliably estimate the prey and bdelloplast populations for a wide range of PPRs. PMID:24272279

  11. Is Accessing Dental Care Becoming More Difficult? Evidence from Canada's Middle-Income Population

    PubMed Central

    Ramraj, Chantel; Sadeghi, Laleh; Lawrence, Herenia P.; Dempster, Laura; Quiñonez, Carlos

    2013-01-01

    Objective To explore trends in access to dental care among middle-income Canadians. Methods A secondary data analysis of six Canadian surveys that collected information on dental insurance coverage, cost-barriers to dental care, and out-of-pocket expenditures for dental care was conducted for select years from 1978 to 2009. Descriptive analyses were used to outline and compare trends among middle-income Canadians with other levels of income as well as national averages. Results By 2009, middle-income Canadians had the lowest levels of dental insurance coverage (48.7%) compared to all other income groups. They reported the greatest increase in cost-barriers to dental care, from 12.6% in 1996 to 34.1% by 2009. Middle-income Canadians had the largest rise in out-of-pocket expenditures for dental care since 1978. Conclusions This study suggests that affordability issues in accessing dental care are no longer just a problem for the lowest income groups in Canada, but are now impacting middle-income earners as a consequence of their lack of, or decreased access to, comprehensive dental insurance. PMID:23437378

  12. The Effect of Access and Satisfaction on Regular Mammogram and Papanicolaou Test Screening in a Multiethnic Population

    PubMed Central

    Somkin, Carol P.; McPhee, Stephen J.; Nguyen, Tung; Stewart, Susan; Shema, Sarah J.; Nguyen, Bang; Pasick, Rena

    2006-01-01

    Background Access and satisfaction are determinants of preventive service use, but few studies have evaluated their role in breast and cervical cancer screening in multiethnic populations. Objectives We sought to investigate the relationship between race/ethnicity, access, satisfaction, and regular mammogram and Papanicolaou test receipt in 5 racial/ethnic groups. Research Design We conducted a telephone survey in 4 languages. Subjects Our subjects were black, Chinese, Filipino, Latino, or white women aged 40 to 74 residing in Alameda County, California. Measures Outcome: regular mammograms (last test within 15 months and another within 2 years prior) and Papanicolaou tests (36 months and 3 years, respectively). Independent: race/ethnicity, sociodemographic variables, access (health insurance, usual site of care, regular doctor, check-up within 12 months, knowing where to go, copayment for tests), and satisfaction (overall satisfaction scale, waiting times, test-related pain and embarrassment, test satisfaction). Results Among women who had ever had a mammogram or Papanicolaou test, 54% and 77%, respectively, received regular screening. In multivariate analyses, regular mammography was positively associated with increased age (odds ratio [OR] 1.05 per year), private insurance (OR 1.7), check-up in the past year (OR 2.3), knowing where to go for mammography (OR 3.0), and greater satisfaction with processes of care (OR 1.04 per unit), and negatively with not knowing copayment amount (OR 0.4), too many forms to fill out (OR 0.5), embarrassment at the last mammogram (OR 0.6), and Filipino race/ethnicity. Similar results were found for regular Papanicolaou tests. Conclusions Access and satisfaction are important predictors of screening but do little to explain racial/ethnic variation. Tailored interventions to improve regular mammography and Papanicolaou test screening in multiethnic populations are needed. PMID:15319618

  13. Assessing the population health impact of market interventions to improve access to antiretroviral treatment.

    PubMed

    Bärnighausen, Till; Kyle, Margaret; Salomon, Joshua A; Waning, Brenda

    2012-09-01

    Despite extraordinary global progress in increasing coverage of antiretroviral treatment (ART), the majority of people needing ART currently are not receiving treatment. Both the number of people needing ART and the average ART price per patient-year are expected to increase in coming years, which will dramatically raise funding needs for ART. Several international organizations are using interventions in ART markets to decrease ART price or to improve ART quality, delivery and innovation, with the ultimate goal of improving population health. These organizations need to select those market interventions that are most likely to substantially affect population health outcomes (ex ante assessment) and to evaluate whether implemented interventions have improved health outcomes (ex post assessment). We develop a framework to structure ex ante and ex post assessment of the population health impact of market interventions, which is transmitted through effects in markets and health systems. Ex ante assessment should include evaluation of the safety and efficacy of the ART products whose markets will be affected by the intervention; theoretical consideration of the mechanisms through which the intervention will affect population health; and predictive modelling to estimate the potential population health impact of the intervention. For ex post assessment, analysts need to consider which outcomes to estimate empirically and which to model based on empirical findings and understanding of the economic and biological mechanisms along the causal pathway from market intervention to population health. We discuss methods for ex post assessment and analyse assessment issues (unintended intervention effects, interaction effects between different interventions, and assessment impartiality and cost). We offer seven recommendations for ex ante and ex post assessment of population health impact of market interventions.

  14. Assessing the population health impact of market interventions to improve access to antiretroviral treatment

    PubMed Central

    Bärnighausen, Till; Kyle, Margaret; Salomon, Joshua A; Waning, Brenda

    2012-01-01

    Despite extraordinary global progress in increasing coverage of antiretroviral treatment (ART), the majority of people needing ART currently are not receiving treatment. Both the number of people needing ART and the average ART price per patient-year are expected to increase in coming years, which will dramatically raise funding needs for ART. Several international organizations are using interventions in ART markets to decrease ART price or to improve ART quality, delivery and innovation, with the ultimate goal of improving population health. These organizations need to select those market interventions that are most likely to substantially affect population health outcomes (ex ante assessment) and to evaluate whether implemented interventions have improved health outcomes (ex post assessment). We develop a framework to structure ex ante and ex post assessment of the population health impact of market interventions, which is transmitted through effects in markets and health systems. Ex ante assessment should include evaluation of the safety and efficacy of the ART products whose markets will be affected by the intervention; theoretical consideration of the mechanisms through which the intervention will affect population health; and predictive modelling to estimate the potential population health impact of the intervention. For ex post assessment, analysts need to consider which outcomes to estimate empirically and which to model based on empirical findings and understanding of the economic and biological mechanisms along the causal pathway from market intervention to population health. We discuss methods for ex post assessment and analyse assessment issues (unintended intervention effects, interaction effects between different interventions, and assessment impartiality and cost). We offer seven recommendations for ex ante and ex post assessment of population health impact of market interventions. PMID:21914713

  15. Microbial ecology of Bacillus thuringiensis: fecal populations recovered from wildlife in Korea.

    PubMed

    Lee, Dong-Hyun; Cha, In Hwan; Woo, Doo Sung; Ohba, Michio

    2003-07-01

    A total of 34 fecal samples, collected from 14 species of wild mammals in Korea, were examined for the occurrence of Bacillus thuringiensis. The organism was detected in 18 (53%) samples. Among the three food-habit groups, herbivorous animals yielded the highest frequency (69%) of samples positive for B. thuringiensis, followed by omnivorous animals (50%). Of the six fecal samples from carnivorous animals, only one sample contained B. thurin giensis. Among 527 isolates belonging to the Bacillus cereus - B. thuringiensis group, 43 (8%) were assigned to B. thurin giensis on the basis of the formation of parasporal inclusions. Of the 43 isolates, 13 were serologically allocated to the nine H-antigenic serotypes: H3ad (serovar sumiyoshiensis), H15 (dakota), H17/27 (tohokuensis/ mexicanensis), H19 (tochigiensis), H21 (colmeri), H29 (amagiensis), H31/49 (toguchini/muju), H42 (jinghongiensis), and H44 (higo). Other isolates were untestable or untypable by the 55 reference H antisera available. Insecticidal activity was associated with 23% of the fecal populations: three isolates killed larvae of the silkworm, Bombyx mori (Lepidoptera), and seven exhibited larvicidal activity against the mosquito, Aedes aegypti (Diptera). There was no larvicidal activity against the three lepidopterous insects: Plutella xylostella, Spodoptera exigua, and Spodoptera litura. The overall results suggest that wild animals in Korea are in contact with naturally occurring B. thuringiensis at high frequencies through the daily food intake of plants.

  16. Unravelling the interactions among microbial populations found in activated sludge during biofilm formation.

    PubMed

    Liébana, Raquel; Arregui, Lucía; Santos, Antonio; Murciano, Antonio; Marquina, Domingo; Serrano, Susana

    2016-09-01

    Microorganisms colonize surfaces and develop biofilms through interactions that are not yet thoroughly understood, with important implications for water and wastewater systems. This study investigated the interactions between N-acyl homoserine lactone (AHL)-producing bacteria, yeasts and protists, and their contribution to biofilm development. Sixty-one bacterial strains were isolated from activated sludge and screened for AHL production, with Aeromonas sp. found to be the dominant AHL producer. Shewanella xiamenensis, Aeromonas allosaccharophila, Acinetobacter junii and Pseudomonas aeruginosa recorded the highest adherence capabilities, with S. xiamenensis being the most effective in surface colonization. Additionally, highly significant interactions (i.e. synergic or antagonistic) were described for dual and multistrain mixtures of bacterial strains (P. aeruginosa, S. xiamenensis, A. junii and Pseudomonas stutzeri), as well as for strongly adherent bacteria co-cultured with yeasts. In this last case, the adhered biomass in co-cultures was lower than the monospecific biofilms of bacteria and yeast, with biofilm observations by microscopy suggesting that bacteria had an antagonist effect on the whole or part of the yeast population. Finally, protist predation by Euplotes sp. and Paramecium sp. on Aeromonas hydrophila biofilms not only failed to reduce biofilm formation, but also recorded unexpected results leading to the development of aggregates of high density and complexity. PMID:27306553

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

    USGS Publications Warehouse

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

    1987-01-01

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

  18. Efficacy of three light technologies for reducing microbial populations in liquid suspensions.

    PubMed

    Birmpa, Angeliki; Vantarakis, Apostolos; Paparrodopoulos, Spyros; Whyte, Paul; Lyng, James

    2014-01-01

    The aim of the current study was to evaluate the effectiveness of three nonthermal light technologies (NUV-Vis, continuous UV, and HILP) on their ability to inactivate Escherichia coli K12 and Listeria innocua.  E. coli K12 was selected as a representative microorganism for the enterohaemorrhagic foodborne pathogen E. coli O157:H7 and L. innocua as a surrogate microorganism for the common foodborne pathogen Listeria monocytogenes, respectively. The liquid matrix used for the disinfection experiments was a liquid matrix (MRD solution). The results of the present study show that the HILP treatment inactivated both E. coli and L. innocua more rapidly and effectively than either continuous UV-C or NUV-vis treatment. With HILP at 2.5 cm from the lamp, E. coli and L. innocua populations were reduced by 3.07 and 3.77 log10 CFU/mL, respectively, after a 5 sec treatment time, and were shown to be below the limit of detection (<0.22 log10 CFU/mL) following 30 sec exposure to HILP (106.2 J/cm(2)). These studies demonstrate the bactericidal efficacy of alternative nonthermal light technologies and their potential as decontamination strategies in the food industry.

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

    PubMed

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

    2013-11-01

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

  20. Unravelling the interactions among microbial populations found in activated sludge during biofilm formation.

    PubMed

    Liébana, Raquel; Arregui, Lucía; Santos, Antonio; Murciano, Antonio; Marquina, Domingo; Serrano, Susana

    2016-09-01

    Microorganisms colonize surfaces and develop biofilms through interactions that are not yet thoroughly understood, with important implications for water and wastewater systems. This study investigated the interactions between N-acyl homoserine lactone (AHL)-producing bacteria, yeasts and protists, and their contribution to biofilm development. Sixty-one bacterial strains were isolated from activated sludge and screened for AHL production, with Aeromonas sp. found to be the dominant AHL producer. Shewanella xiamenensis, Aeromonas allosaccharophila, Acinetobacter junii and Pseudomonas aeruginosa recorded the highest adherence capabilities, with S. xiamenensis being the most effective in surface colonization. Additionally, highly significant interactions (i.e. synergic or antagonistic) were described for dual and multistrain mixtures of bacterial strains (P. aeruginosa, S. xiamenensis, A. junii and Pseudomonas stutzeri), as well as for strongly adherent bacteria co-cultured with yeasts. In this last case, the adhered biomass in co-cultures was lower than the monospecific biofilms of bacteria and yeast, with biofilm observations by microscopy suggesting that bacteria had an antagonist effect on the whole or part of the yeast population. Finally, protist predation by Euplotes sp. and Paramecium sp. on Aeromonas hydrophila biofilms not only failed to reduce biofilm formation, but also recorded unexpected results leading to the development of aggregates of high density and complexity.

  1. Efficacy of Three Light Technologies for Reducing Microbial Populations in Liquid Suspensions

    PubMed Central

    Paparrodopoulos, Spyros; Whyte, Paul

    2014-01-01

    The aim of the current study was to evaluate the effectiveness of three nonthermal light technologies (NUV-Vis, continuous UV, and HILP) on their ability to inactivate Escherichia coli K12 and Listeria innocua.  E. coli K12 was selected as a representative microorganism for the enterohaemorrhagic foodborne pathogen E. coli O157:H7 and L. innocua as a surrogate microorganism for the common foodborne pathogen Listeria monocytogenes, respectively. The liquid matrix used for the disinfection experiments was a liquid matrix (MRD solution). The results of the present study show that the HILP treatment inactivated both E. coli and L. innocua more rapidly and effectively than either continuous UV-C or NUV-vis treatment. With HILP at 2.5 cm from the lamp, E. coli and L. innocua populations were reduced by 3.07 and 3.77 log10 CFU/mL, respectively, after a 5 sec treatment time, and were shown to be below the limit of detection (<0.22 log10 CFU/mL) following 30 sec exposure to HILP (106.2 J/cm2). These studies demonstrate the bactericidal efficacy of alternative nonthermal light technologies and their potential as decontamination strategies in the food industry. PMID:24724092

  2. How to Show the Real Microbial Biodiversity? A Comparison of Seven DNA Extraction Methods for Bacterial Population Analyses in Matrices Containing Highly Charged Natural Nanoparticles

    PubMed Central

    Kaden, Rene; Krolla-Sidenstein, Peter

    2015-01-01

    A DNA extraction that comprises the DNA of all available taxa in an ecosystem is an essential step in population analysis, especially for next generation sequencing applications. Many nanoparticles as well as naturally occurring clay minerals contain charged surfaces or edges that capture negatively charged DNA molecules after cell lysis within DNA extraction. Depending on the methodology of DNA extraction, this phenomenon causes a shift in detection of microbial taxa in ecosystems and a possible misinterpretation of microbial interactions. With the aim to describe microbial interactions and the bio-geo-chemical reactions during a clay alteration experiment, several methods for the detection of a high number of microbial taxa were examined in this study. Altogether, 13 different methods of commercially available DNA extraction kits provided by seven companies as well as the classical phenol-chloroform DNA extraction were compared. The amount and the quality of nucleic acid extracts were determined and compared to the amplifiable amount of DNA. The 16S rRNA gene fragments of several taxa were separated using denaturing gradient gel electrophoresis (DGGE) to determine the number of different species and sequenced to get the information about what kind of species the microbial population consists of. A total number of 13 species was detected in the system. Up to nine taxa could be detected with commercially available DNA extraction kits while phenol-chloroform extraction lead to three detected species. In this paper, we describe how to combine several DNA extraction methods for the investigation of microbial community structures in clay. PMID:27682112

  3. How to Show the Real Microbial Biodiversity? A Comparison of Seven DNA Extraction Methods for Bacterial Population Analyses in Matrices Containing Highly Charged Natural Nanoparticles

    PubMed Central

    Kaden, Rene; Krolla-Sidenstein, Peter

    2015-01-01

    A DNA extraction that comprises the DNA of all available taxa in an ecosystem is an essential step in population analysis, especially for next generation sequencing applications. Many nanoparticles as well as naturally occurring clay minerals contain charged surfaces or edges that capture negatively charged DNA molecules after cell lysis within DNA extraction. Depending on the methodology of DNA extraction, this phenomenon causes a shift in detection of microbial taxa in ecosystems and a possible misinterpretation of microbial interactions. With the aim to describe microbial interactions and the bio-geo-chemical reactions during a clay alteration experiment, several methods for the detection of a high number of microbial taxa were examined in this study. Altogether, 13 different methods of commercially available DNA extraction kits provided by seven companies as well as the classical phenol-chloroform DNA extraction were compared. The amount and the quality of nucleic acid extracts were determined and compared to the amplifiable amount of DNA. The 16S rRNA gene fragments of several taxa were separated using denaturing gradient gel electrophoresis (DGGE) to determine the number of different species and sequenced to get the information about what kind of species the microbial population consists of. A total number of 13 species was detected in the system. Up to nine taxa could be detected with commercially available DNA extraction kits while phenol-chloroform extraction lead to three detected species. In this paper, we describe how to combine several DNA extraction methods for the investigation of microbial community structures in clay.

  4. HMOs and the barriers to access for the pediatric population requiring emergency medical services.

    PubMed

    Uva, J L

    1996-06-01

    The main objectives of this study are to analyze the Massachusetts Health Maintenance Organizations (HMOs) in order to determine their standard definition of an emergency, the HMOs instructions for seeking emergency care, and distribution of such instructions for the pediatric population. A 15-question survey concerning pediatric emergency care policies and procedures was asked of each of the 20 HMOs contacted. Quarterly statements of each of the 20 HMOs were obtained from the Division of Insurance as well as the HMO's written materials distributed to the enrollees as member handbooks. Ninety percent of the HMOs had a definition of emergency care for the adult population, whereas 0% had a definition of emergency care specifically for the pediatric population. One hundred percent of the HMOs had instructions for emergency care, but 0% had specific provisions for pediatric emergency care. All 20 HMOs inform their enrollees about emergency policies through a member handbook. The results of this study reveal the lack of a standard definition of an emergency for HMOs. The current definitions of "urgent," "emergency," and "life-threatening emergency" care do not reflect the pediatric population, rather, these definitions are based on the adult population. The lack of specific pediatric guidelines could compromise the health of the children in HMOs.

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

    PubMed

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

    2014-01-01

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

  6. Effect of aeration on stabilization of organic solid waste and microbial population dynamics in lab-scale landfill bioreactors.

    PubMed

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

    2008-11-01

    This study investigated microbial population dynamics and performance in lab-scale conventional, anaerobic, and aerobic landfill bioreactors specialized for high-organic wastes. Each reactor (2.35 l) was loaded with 1.5 kg of organic solid waste made of sludge cake, dry dog food, and wood chips. The conventional reactor was operated without leachate recirculation and aeration, but the other reactors used leachate recirculation at 200 ml/d and without aeration (anaerobic bioreactor) or with aeration at 2 l/min (aerobic bioreactor). The respective final waste volumes on day 138 of the conventional, anaerobic, and aerobic reactors were approximately 75%, 65%, and 60% of the initial volumes. Leachate recirculation in the anaerobic bioreactor accelerated biochemical reactions and promoted methane production. However, leachate from the anaerobic bioreactor showed TOC and NH(4)(+)-N concentrations that were as high as those of the conventional reactor. Aeration lowered leachate production and methane concentration and decreased organic matter in solid waste and leachate. Furthermore, the MPN value of amoA gene reached 10(5) MPN-copies/g-dry in the aerobic bioreactor, where nitrogen was removed from organic solid waste and leachate. During the first 72 d, the aerobic bioreactor's MPN value of fungal 18S rDNA was the highest among reactors, but it decreased gradually. All reactors showed similar MPN values of eubacterial 16S rDNA, nirS, and nirK. PMID:19111637

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

    PubMed Central

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2013-12-01

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

  10. Effects of Flavonoid-rich Plant Extracts on In vitro Ruminal Methanogenesis, Microbial Populations and Fermentation Characteristics

    PubMed Central

    Kim, Eun T.; Guan, Le Luo; Lee, Shin J.; Lee, Sang M.; Lee, Sang S.; Lee, Il D.; Lee, Su K.; Lee, Sung S.

    2015-01-01

    The objective of this study was to evaluate the in vitro effects of flavonoid-rich plant extracts (PE) on ruminal fermentation characteristics and methane emission by studying their effectiveness for methanogenesis in the rumen. A fistulated Holstein cow was used as a donor of rumen fluid. The PE (Punica granatum, Betula schmidtii, Ginkgo biloba, Camellia japonica, and Cudrania tricuspidata) known to have high concentrations of flavonoid were added to an in vitro fermentation incubated with rumen fluid. Total gas production and microbial growth with all PE was higher than that of the control at 24 h incubation, while the methane emission was significantly lower (p<0.05) than that of the control. The decrease in methane accumulation relative to the control was 47.6%, 39.6%, 46.7%, 47.9%, and 48.8% for Punica, Betula, Ginkgo, Camellia, and Cudrania treatments, respectively. Ciliate populations were reduced by more than 60% in flavonoid-rich PE treatments. The Fibrobacter succinogenes diversity in all added flavonoid-rich PE was shown to increase, while the Ruminoccocus albus and R. flavefaciens populations in all PE decreased as compared with the control. In particular, the F. succinogenes community with the addition of Birch extract increased to a greater extent than that of others. In conclusion, the results of this study showed that flavonoid-rich PE decreased ruminal methane emission without adversely affecting ruminal fermentation characteristics in vitro in 24 h incubation time, suggesting that the flavonoid-rich PE have potential possibility as bio-active regulator for ruminants. PMID:25656200

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed

    Thompson, Luke R; Field, Chris; Romanuk, Tamara; Ngugi, David; Siam, Rania; El Dorry, Hamza; Stingl, Ulrich

    2013-06-01

    Large swaths of the nutrient-poor surface ocean are dominated numerically by cyanobacteria (Prochlorococcus), cyanobacterial viruses (cyanophage), and alphaproteobacteria (SAR11). How these groups thrive in the diverse physicochemical environments of different oceanic regions remains poorly understood. Comparative metagenomics can reveal adaptive responses linked to ecosystem-specific selective pressures. The Red Sea is well-suited for studying adaptation of pelagic-microbes, with salinities, temperatures, and light levels at the extreme end for the surface ocean, and low nutrient concentrations, yet no metagenomic studies have been done there. The Red Sea (high salinity, high light, low N and P) compares favorably with the Mediterranean Sea (high salinity, low P), Sargasso Sea (low P), and North Pacific Subtropical Gyre (high light, low N). We quantified the relative abundance of genetic functions among Prochlorococcus, cyanophage, and SAR11 from these four regions. Gene frequencies indicate selection for phosphorus acquisition (Mediterranean/Sargasso), DNA repair and high-light responses (Red Sea/Pacific Prochlorococcus), and osmolyte C1 oxidation (Red Sea/Mediterranean SAR11). The unexpected connection between salinity-dependent osmolyte production and SAR11 C1 metabolism represents a potentially major coevolutionary adaptation and biogeochemical flux. Among Prochlorococcus and cyanophage, genes enriched in specific environments had ecotype distributions similar to nonenriched genes, suggesting that inter-ecotype gene transfer is not a major source of environment-specific adaptation. Clustering of metagenomes using gene frequencies shows similarities in populations (Red Sea with Pacific, Mediterranean with Sargasso) that belie their geographic distances. Taken together, the genetic functions enriched in specific environments indicate competitive strategies for maintaining carrying capacity in the face of physical stressors and low nutrient availability.

  15. Consumption of lysozyme-rich milk can alter microbial fecal populations.

    PubMed

    Maga, Elizabeth A; Desai, Prerak T; Weimer, Bart C; Dao, Nguyet; Kültz, Dietmar; Murray, James D

    2012-09-01

    Human milk contains antimicrobial factors such as lysozyme and lactoferrin that are thought to contribute to the development of an intestinal microbiota beneficial to host health. However, these factors are lacking in the milk of dairy animals. Here we report the establishment of an animal model to allow the dissection of the role of milk components in gut microbiota modulation and subsequent changes in overall and intestinal health. Using milk from transgenic goats expressing human lysozyme at 68%, the level found in human milk and young pigs as feeding subjects, the fecal microbiota was analyzed over time using 16S rRNA gene sequencing and the G2 Phylochip. The two methods yielded similar results, with the G2 Phylochip giving more comprehensive information by detecting more OTUs. Total community populations remained similar within the feeding groups, and community member diversity was changed significantly upon consumption of lysozyme milk. Levels of Firmicutes (Clostridia) declined whereas those of Bacteroidetes increased over time in response to the consumption of lysozyme-rich milk. The proportions of these major phyla were significantly different (P < 0.05) from the proportions seen with control-fed animals after 14 days of feeding. Within phyla, the abundance of bacteria associated with gut health (Bifidobacteriaceae and Lactobacillaceae) increased and the abundance of those associated with disease (Mycobacteriaceae, Streptococcaceae, Campylobacterales) decreased with consumption of lysozyme milk. This study demonstrated that a single component of the diet with bioactivity changed the gut microbiome composition. Additionally, this model enabled the direct examination of the impact of lysozyme on beneficial microbe enrichment versus detrimental microbe reduction in the gut microbiome community.

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

    PubMed

    Thompson, Luke R; Field, Chris; Romanuk, Tamara; Ngugi, David; Siam, Rania; El Dorry, Hamza; Stingl, Ulrich

    2013-06-01

    Large swaths of the nutrient-poor surface ocean are dominated numerically by cyanobacteria (Prochlorococcus), cyanobacterial viruses (cyanophage), and alphaproteobacteria (SAR11). How these groups thrive in the diverse physicochemical environments of different oceanic regions remains poorly understood. Comparative metagenomics can reveal adaptive responses linked to ecosystem-specific selective pressures. The Red Sea is well-suited for studying adaptation of pelagic-microbes, with salinities, temperatures, and light levels at the extreme end for the surface ocean, and low nutrient concentrations, yet no metagenomic studies have been done there. The Red Sea (high salinity, high light, low N and P) compares favorably with the Mediterranean Sea (high salinity, low P), Sargasso Sea (low P), and North Pacific Subtropical Gyre (high light, low N). We quantified the relative abundance of genetic functions among Prochlorococcus, cyanophage, and SAR11 from these four regions. Gene frequencies indicate selection for phosphorus acquisition (Mediterranean/Sargasso), DNA repair and high-light responses (Red Sea/Pacific Prochlorococcus), and osmolyte C1 oxidation (Red Sea/Mediterranean SAR11). The unexpected connection between salinity-dependent osmolyte production and SAR11 C1 metabolism represents a potentially major coevolutionary adaptation and biogeochemical flux. Among Prochlorococcus and cyanophage, genes enriched in specific environments had ecotype distributions similar to nonenriched genes, suggesting that inter-ecotype gene transfer is not a major source of environment-specific adaptation. Clustering of metagenomes using gene frequencies shows similarities in populations (Red Sea with Pacific, Mediterranean with Sargasso) that belie their geographic distances. Taken together, the genetic functions enriched in specific environments indicate competitive strategies for maintaining carrying capacity in the face of physical stressors and low nutrient availability. PMID

  17. Combinatorial multicomponent access to natural-products-inspired peptidomimetics: discovery of selective inhibitors of microbial metallo-aminopeptidases.

    PubMed

    Méndez, Yanira; Pérez-Labrada, Karell; González-Bacerio, Jorge; Valdés, Gilberto; de los Chávez, María Á; Osuna, Joel; Charli, Jean-Louis; Pascual, Isel; Rivera, Daniel G

    2014-10-01

    The development of selective inhibitors of microbial metallo-aminopeptidases is an important goal in the pursuit of antimicrobials for therapeutic applications. Herein, we disclose a combinatorial approach relying on two Ugi reactions for the generation of peptidomimetics inspired by natural metallo-aminopeptidase inhibitors. The library was screened for inhibitory activity against the neutral metallo-aminopeptidase of Escherichia coli (ePepN) and the porcine kidney cortex metallo-aminopeptidase (pAPN), which was used as a model of the M1-aminopeptidases of mammals. Six compounds showed typical dose-response inhibition profiles toward recombinant ePepN, with two of them being very potent and highly selective for ePepN over pAPN. Another compound showed moderate ePepN inhibition but total selectivity for this bacterial enzyme over its mammalian orthologue at concentrations of physiological relevance. This strategy proved to be useful for the identification of lead compounds for further optimization and development.

  18. Effect of Microbial Inoculants on the Indigenous Actinobacterial Endophyte Population in the Roots of Wheat as Determined by Terminal Restriction Fragment Length Polymorphism

    PubMed Central

    Conn, Vanessa M.; Franco, Christopher M. M.

    2004-01-01

    The effect of single actinobacterial endophyte seed inoculants and a mixed microbial soil inoculant on the indigenous endophytic actinobacterial population in wheat roots was investigated by using the molecular technique terminal restriction fragment length polymorphism (T-RFLP). Wheat was cultivated either from seeds coated with the spores of single pure actinobacterial endophytes of Microbispora sp. strain EN2, Streptomyces sp. strain EN27, and Nocardioides albus EN46 or from untreated seeds sown in soil with and without a commercial mixed microbial soil inoculant. The endophytic actinobacterial population within the roots of 6-week-old wheat plants was assessed by T-RFLP. Colonization of the wheat roots by the inoculated actinobacterial endophytes was detected by T-RFLP, as were 28 to 42 indigenous actinobacterial genera present in the inoculated and uninoculated plants. The presence of the commercial mixed inoculant in the soil reduced the endophytic actinobacterial diversity from 40 genera to 21 genera and reduced the detectable root colonization by approximately half. The results indicate that the addition of a nonadapted microbial inoculum to the soil disrupted the natural actinobacterial endophyte population, reducing diversity and colonization levels. This was in contrast to the addition of a single actinobacterial endophyte to the wheat plant, where the increase in colonization level could be confirmed even though the indigenous endophyte population was not adversely affected. PMID:15528499

  19. The effects of the presence of Bt-transgenic oilseed rape in wild mustard populations on the rhizosphere nematode and microbial communities.

    PubMed

    Liu, Yongbo; Li, Junsheng; Stewart, C Neal; Luo, Zunlan; Xiao, Nengwen

    2015-10-15

    The adventitious presence of transgenic crops in wild plant populations is of ecological and regulatory concern. In this context, their effects on non-target, below-ground organisms are not well understood. Here, we introduced, at various frequencies, Bt-transgenic oilseed rape (OSR, Brassica napus) into wild mustard (Brassica juncea) populations in the presence and absence of the target herbivore (Plutella xylostella). The impacts on soil nematode and microbial communities were assessed in this system. There were no significant changes on the number of nematode genera and abundance in proportions of OSR with mustard. Nonetheless, the Shannon-Wiener and Pielou evenness index was lowest in plant stands containing 50% of Bt-transgenic OSR. Among treatments, there was no significant variation for culturable soil microbes. There was a positive association between foliar herbivory and the abundance of plant parasitic (PP) and cp-3 nematodes, whereas there was no association between herbivory and soil microbial populations. There was no direct effects of the presence of Bt-transgenic OSR in wild mustard populations on the rhizosphere nematode and microbial communities, whereas its indirect effects via aboveground herbivory might be important to consider for biosafety assessments. PMID:26047860

  20. Geobacter, Anaeromyxobacter and Anaerolineae populations are enriched on anodes of root exudate-driven microbial fuel cells in rice field soil.

    PubMed

    Cabezas, Angela; Pommerenke, Bianca; Boon, Nico; Friedrich, Michael W

    2015-06-01

    Plant-based sediment microbial fuel cells (PMFCs) couple the oxidation of root exudates in living rice plants to current production. We analysed the composition of the microbial community on anodes from PMFC with natural rice field soil as substratum for rice by analysing 16S rRNA as an indicator of microbial activity and diversity. Terminal restriction fragment length polymorphism (TRFLP) analysis indicated that the active bacterial community on anodes from PMFCs differed strongly compared with controls. Moreover, clones related to Deltaproteobacteria and Chloroflexi were highly abundant (49% and 21%, respectively) on PMFCs anodes. Geobacter (19%), Anaeromyxobacter (15%) and Anaerolineae (17%) populations were predominant on anodes with natural rice field soil and differed strongly from those previously detected with potting soil. In open circuit (OC) control PMFCs, not allowing electron transfer, Deltaproteobacteria (33%), Betaproteobacteria (20%), Chloroflexi (12%), Alphaproteobacteria (10%) and Firmicutes (10%) were detected. The presence of an electron accepting anode also had a strong influence on methanogenic archaea. Hydrogenotrophic methanogens were more active on PMFC (21%) than on OC controls (10%), whereas acetoclastic Methanosaetaceae were more active on OC controls (31%) compared with PMFCs (9%). In conclusion, electron accepting anodes and rice root exudates selected for distinct potential anode-reducing microbial populations in rice soil inoculated PMFC.

  1. Access and Retention of Marginalized Populations within Undergraduate Music Education Degree Programs

    ERIC Educational Resources Information Center

    Fitzpatrick, Kate R.; Henninger, Jacqueline C.; Taylor, Don M.

    2014-01-01

    The purpose of this collective instrumental case study was to examine the experiences of six undergraduate students from traditionally marginalized populations with regard to their preparation for, admission to, and retention within a music education degree program. Analyzed and reported through the lens of critical theory, data sources included…

  2. Genetic diversity, population structure, and formulation of a core collection of 1,197 Citrullus accessions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There has been continuing interests in breeding of watermelon for economic benefits, but information on the scope and utilization of genetic variations in this genus (Citrullus) is still limited. We evaluated the genetic diversity and population structure of 1,197 watermelon collections, which belon...

  3. Increasing Accessibility: Lessons Learned in Retaining Special Population Students in Canada

    ERIC Educational Resources Information Center

    Smith, Clayton; Gottheil, Susan

    2011-01-01

    In Canada, changing demographics and increased competition--as well as social values based on equity--have inspired efforts to increase the postsecondary education (PSE) participation rates of youths from under-represented/under-served groups. Despite its population having the highest level of educational attainment among those of OECD countries,…

  4. Effects of coconut and fish oils on ruminal methanogenesis, fermentation, and abundance and diversity of microbial populations in vitro.

    PubMed

    Patra, A K; Yu, Z

    2013-03-01

    Coconut (CO) and fish (FO) oils were previously shown to inhibit rumen methanogenesis and biohydrogenation, which mitigates methane emission and helps improve beneficial fatty acids in meat and milk. This study aimed at investigating the comparative effects of CO and FO on the methanogenesis, fermentation, and microbial abundances and diversity in vitro rumen cultures containing different doses (0, 3.1, and 6.2 mL/L) of each oil and 400mg feed substrate using rumen fluid from lactating dairy cows as inocula. Increasing doses of CO and FO quadratically decreased concentrations of methane, but hydrogen concentrations were only increased quadratically by CO. Both oils linearly decreased dry matter and neutral detergent fiber digestibility of feeds but did not affect the concentration of total volatile fatty acids. However, CO reduced acetate percentage and acetate to propionate ratio and increased the percentages of propionate and butyrate to a greater extent than FO. Ammonia concentration was greater for CO than FO. As determined by quantitative real-time PCR, FO had greater inhibition to methanogens than CO, but the opposite was true for protozoal, Ruminococcus flavefaciens, and Fibrobacter succinogenes. Ruminococcus albus was not affected by either oil. Denaturing gradient gel electrophoresis (DGGE) profiles revealed that bacterial and archaeal community composition were changed differently by oil type. Based on Pareto-Lorenz evenness curve analysis of the DGGE profiles, CO noticeably changed the functional organization of archaea compared with FO. In conclusion, although both CO and FO decreased methane concentrations to a similar extent, the mode of reduction and the effect on abundances and diversity of archaeal and bacterial populations differed between the oils. Thus, the use of combination of CO and FO at a low dose may additively lower methanogenesis in the rumen while having little adverse effect on rumen fermentation. PMID:23332846

  5. Microbial population dynamics in response to increasing loadings of pre-hydrolyzed pig manure in an expanded granular sludge bed.

    PubMed

    Wang, Haoyu; Tao, Yu; Gao, Dawen; Liu, Gang; Chen, Chunhong; Ren, Nanqi; van Lier, Jules B; de Kreuk, Merle

    2015-12-15

    In recent years, pig manure (PM) has been regarded as a valuable substrate for energy and resource recovery via bioprocesses such as anaerobic digestion (AD), however, the efficiency of digesting raw PM is limited by the presence of refractory compounds. In this study, we applied a series of pretreatment on raw PM, consisting of subsequent thermochemical pretreatment, enzymatic hydrolysis, tyndallization and filtration. The liquid PM hydrolysates were fed to an expanded granular sludge bed (EGSB) for the production of biogas. The general performance and population dynamics of the EGSB reactor were assessed during an extended operational period of 339 days. An efficient and stable digestion process was achieved under high organic loading rates (OLRs) up to 21 kg-COD/(m(3)·d), agreeing with a sludge loading rate of 0.75 kg-COD/(kg-VSS·d), 1600 mg-NH4(+)-N/L and 17 mg/L of free ammonia nitrogen. The tyndallization decreased the total amount of active cells from 1 × 10(8) to 1 × 10(2) CFU/ml. Hence, bio-augmentation with pigs' intestinal microbiota was absent and the community dynamics were mainly credited to the composition of the substrate (i.e. PM hydrolysates) and the environmental conditions inside the reactor. The results showed the influence of both the seed community and the imposed loading rates on the evolutionary trajectory of the EGSB microbial community. Four bacterial genera (Clostridium, Cytophaga, Bacillus and Bacteroides) and two methanogenic genera (Methanosaeta and Methanobacterium) dominated the communities. An obvious shift from aceticlastic Methanosaeta to hydrogenotrophic Methanobacterium appeared when the OLR was increased to over 10 kg-COD/(m(3)·d). PMID:26378729

  6. Performance, meat quality, meat mineral contents and caecal microbial population responses to humic substances administered in drinking water in broilers.

    PubMed

    Ozturk, E; Coskun, I; Ocak, N; Erener, G; Dervisoglu, M; Turhan, S

    2014-01-01

    This study was conducted to examine the effect of different levels of humic substances (HS) administered in drinking water on caecal microflora and mineral composition and colour characteristics of breast and thigh meats and the growth performance, carcass and gastrointestinal tract (GIT) traits of broiler chicks. A total of 480 3-d-old broiler chickens were randomly allocated to 4 treatments with 4 cages per treatment and 30 bird (15 males and 15 females) chicks per cage. All birds were fed on commercial basal diet. The control birds (HS0) received drinking water with no additions, whereas birds in the other treatment groups received a drinking water with 7.5 (HS7.5), 15.0 (HS15.0) and 22.5 (HS22.5) g/kg HS. Mush feed were provided on an ad libitum basis. Body weight and feed intake of broilers were determined at d 0, 21, and 42, and feed conversion ratio was calculated. On d 42, 4 broilers (2 males and 2 females) from each cage were slaughtered and the breast and thigh meats were collected for mineral composition and quality measurements. Performance, carcass and GIT traits and caecal microbial population of broiler chicks at d 42 were not affected by the dietary treatments. The lightness (L*) of breast and thigh meat decreased in broilers supplemented with 15 and 22.5 g/kg HS in drinking water. Although the redness (a*) of breast meat increased, yellowness of thigh meat decreased in broilers supplemented with 15 and 22.5 g/kg HS in drinking water (P < 0.05). In conclusion, the 15 and 22.5 g/kg HS administration in drinking water can be applied for broiler chicks to maintain growth performance and improve meat quality without changing caecal microflora.

  7. Immigrant mothers and access to prenatal care: evidence from a regional population study in Italy

    PubMed Central

    Chiavarini, Manuela; Lanari, Donatella; Minelli, Liliana; Pieroni, Luca

    2016-01-01

    Objectives We addressed the question of whether use of adequate prenatal care differs between foreign-born and Italian mothers and estimated the extent to which unobservable characteristics bias results. Setting This study is on primary care and especially on adequate access to prenatal healthcare services by immigrant mothers. Participants Approximately 37 000 mothers of both Italian and foreign nationality were studied. Data were obtained from the Standard Certificate of Live Birth between 2005 and 2010 in Umbria. Results Estimates from the bivariate probit model indicate that immigrant mothers are three times more likely to make fewer than four prenatal visits (OR=3.35) and 1.66 times more likely to make a late first visit (OR=1.66). The effect is found to be strongest for Asian women. Conclusions Standard probit models lead to underestimation of the probability of inadequate use of prenatal care services by immigrant women, whereas bivariate probit models, which allow us to consider immigrant status as an endogenous variable, estimated ORs to be three times larger than those obtained with univariate models. PMID:26861935

  8. Increasing Public Awareness of Direct-to-Consumer Genetic Tests: Health Care Access, Internet Use, and Population Density Correlates

    PubMed Central

    Finney Rutten, Lila J.; Gollust, Sarah E.; Naveed, Sana; Moser, Richard P.

    2012-01-01

    Uncertainty around the value of and appropriate regulatory models for direct-to-consumer (DTC) genetic testing underscores the importance of tracking public awareness of these services. We analyzed nationally representative, cross-sectional data from the Health Information National Trends Survey in 2008 (n = 7, 674) and 2011 (n = 3, 959) to assess population-level changes in awareness of DTC genetic testing in the U.S. and to explore sociodemographic, health care, Internet use, and population density correlates. Overall, awareness increased significantly from 29% in 2008 to 37% in 2011. The observed increase in awareness from 2008 to 2011 remained significant (OR = 1.39) even when adjusted for sociodemographic variables, health care access, Internet use, and population density. Independent of survey year, the odds of awareness of DTC genetic tests were significantly higher for those aged 50–64 (OR = 1.64), and 65–74 (OR = 1.60); college graduates (OR = 2.02); those with a regular source of health care (OR = 1.27); those with a prior cancer diagnosis (OR = 1.24); those who use the Internet (OR = 1.27); and those living in urban areas (OR = 1.25). Surveillance of awareness—along with empirical data on use of and response to genetic risk information—can inform public health and policy efforts to maximize benefits and minimize risks of DTC genetic testing. PMID:22899921

  9. Improved Yield of High Molecular Weight DNA Coincides with Increased Microbial Diversity Access from Iron Oxide Cemented Sub-Surface Clay Environments

    SciTech Connect

    Hurt, Jr., Richard Ashley; Moberly, James G; Shakya, Migun; Vishnivetskaya, T.; Elias, Dwayne A

    2014-01-01

    Despite more than three decades of progress, efficient nucleic acid extraction from microbial communities has remained difficult, particularly from clay environments. Lysis with concentrated guanidine followed by concentrated sodium phosphate extraction supported DNA and RNA recovery from high iron, low humus content clay. Alterating the extraction pH or using other ionic solutions (Na2SO4 and NH4H2PO4) yielded no detectable nucleic acid. DNA recovered using a lysis solution with 500 mM phosphate buffer (PB) followed by a 1 M PB wash was 15.22 2.33 g DNA/g clay, with most DNA consisting of >20 Kb fragments, compared to 2.46 0.25 g DNA/g clay with the Powerlyzer soil DNA system (MoBio). Increasing [PB] in the lysis reagent coincided with increasing DNA fragment length. Rarefaction plots based on16S rRNA (V1/V3 region) pyrosequencing libraries from A-horizon and clay soils showed an ~80% and ~400% larger accessed diversity compared to a previous grinding protocol or the Powerlyzer soil DNA system, respectively. The observed diversity from the Firmicutes showed the strongest increase with >3-fold more bacterial species recovered using this system. Additionally, some OTU s having more than 100 sequences in these libraries were absent in samples extracted using the PowerLyzer reagents or the previous lysis method.

  10. From the Margins to the Spotlight: Diverse Deaf and Hard of Hearing Student Populations and Standardized Assessment Accessibility.

    PubMed

    Cawthon, Stephanie

    2015-01-01

    Designing assessments and tests is one of the more challenging aspects of creating an accessible learning environment for students who are deaf or hard of hearing (DHH), particularly for deaf students with a disability (DWD). Standardized assessments are a key mechanism by which the educational system in the United States measures student progress, teacher effectiveness, and the impact of school reform. The diversity of student characteristics within DHH and DWD populations is only now becoming visible in the research literature relating to standardized assessments and their use in large-scale accountability reforms. The purpose of this article is to explore the theoretical frameworks surrounding assessment policy and practice, current research related to standardized assessment and students who are DHH and DWD, and potential implications for practice within both the assessment and instruction contexts. PMID:26497076

  11. From the Margins to the Spotlight: Diverse Deaf and Hard of Hearing Student Populations and Standardized Assessment Accessibility.

    PubMed

    Cawthon, Stephanie

    2015-01-01

    Designing assessments and tests is one of the more challenging aspects of creating an accessible learning environment for students who are deaf or hard of hearing (DHH), particularly for deaf students with a disability (DWD). Standardized assessments are a key mechanism by which the educational system in the United States measures student progress, teacher effectiveness, and the impact of school reform. The diversity of student characteristics within DHH and DWD populations is only now becoming visible in the research literature relating to standardized assessments and their use in large-scale accountability reforms. The purpose of this article is to explore the theoretical frameworks surrounding assessment policy and practice, current research related to standardized assessment and students who are DHH and DWD, and potential implications for practice within both the assessment and instruction contexts.

  12. Assessing the population-level impact of vouchers on access to health facility delivery for women in Kenya.

    PubMed

    Obare, Francis; Warren, Charlotte; Abuya, Timothy; Askew, Ian; Bellows, Ben

    2014-02-01

    Although available evidence indicates that vouchers improve service utilization among the target populations, we do not know whether increased utilization results from improved access (new clients who would not have used services without the voucher) or from shifting clients from non-accredited to contracted service providers. This paper examines whether the safe motherhood voucher program in Kenya is associated with improved access to health facility delivery using information on births within two years preceding the survey in voucher and comparison sites. Data were collected in 2010-2011 and in 2012 among 2933 and 3094 women aged 15-49 years reporting 962 and 1494 births within two years before the respective surveys. Analysis entails cross-tabulations and estimation of multilevel random-intercept logit models. The results show that the proportion of births occurring at home declined by more than 10 percentage points while the proportion of births delivered in health facilities increased by a similar margin over time in voucher sites. The increase in facility-based births occurred in both public and private health facilities. There was also a significant increase in the likelihood of facility-based delivery (odds ratios [OR]: 2.04; 95% confidence interval [CI]: 1.40-2.98 in the 2006 voucher arm; OR: 1.72; 95% CI: 1.22-2.43 in the 2010-2011 voucher arm) in voucher sites over time. In contrast, there were no significant changes in the likelihood of facility-based delivery in the comparison arm over time. These findings suggest that the voucher program contributed to improved access to institutional delivery by shifting births from home to health facilities. However, available evidence from qualitative data shows that some women who purchased the vouchers did not use them because of high transportation costs to accredited facilities. The implication is that substantial improvements in service uptake could be achieved if the program subsidized transportation costs as

  13. Is the Brazilian pharmaceutical policy ensuring population access to essential medicines?

    PubMed Central

    2012-01-01

    Background To evaluate medicine prices, availability and affordability in Brazil, considering the differences across three types of medicines (originator brands, generics and similar medicines) and different types of facilities (private pharmacies, public sector pharmacies and “popular pharmacies”). Methods Data on prices and availability of 50 medicines were collected in 56 pharmacies across six cities in Southern Brazil using the World Health Organization / Health Action International methodology. Median prices obtained were divided by international reference prices to derive the median price ratio (MPR). Results In the private sector, prices were 8.6 MPR for similar medicines, 11.3 MRP for generics and 18.7 MRP for originator brands, respectively. Mean availability was 65%, 74% and 48% for originator brands, generics and similar medicines, respectively. In the public sector, mean availability of similar medicines was 2–7 times higher than that of generics. Mean overall availability in the public sector ranged from 68.8% to 81.7%. In “popular pharmacies”, mean availability was greater than 90% in all cities. Conclusions Availability of medicines in the public sector does not meet the challenge of supplying essential medicines to the entire population, as stated in the Brazilian constitution. This has unavoidable repercussions for affordability, particularly amongst the lower socio-economic strata. PMID:22436555

  14. Population Of US Practicing Psychiatrists Declined, 2003-13, Which May Help Explain Poor Access To Mental Health Care.

    PubMed

    Bishop, Tara F; Seirup, Joanna K; Pincus, Harold Alan; Ross, Joseph S

    2016-07-01

    A large proportion of the US population suffers from mental illness. Limited access to psychiatrists may be a contributor to the underuse of mental health services. We studied changes in the supply of psychiatrists from 2003 to 2013, compared to changes in the supply of primary care physicians and neurologists. During this period the number of practicing psychiatrists declined from 37,968 to 37,889, which represented a 10.2 percent reduction in the median number of psychiatrists per 100,000 residents in hospital referral regions. In contrast, the numbers of primary care physicians and neurologists grew during the study period. These findings may help explain why patients report poor access to mental health care. Future research should explore the impact of the declining psychiatrist supply on patients and investigate new models of care that seek to integrate mental health and primary care or use team-based care that combines the services of psychiatrists and nonphysician providers for individuals with severe mental illnesses. PMID:27385244

  15. "Population and poverty: major barriers to food accessibility" -- a panel discussion on civil society and people's participation.

    PubMed

    1996-01-01

    This paper summarizes conference statements on poverty and food policies that were made by parliamentary members from Malaysia, the Philippines, and India. These presentations were made after the main panel discussion on barriers to food accessibility. In Malaysia the government adopted a National Agricultural Policy in 1984. This policy encouraged increased productivity, effective use of resources, agricultural credit and incentives, and integrated pest management. Strong support was given to the food processing industry. Poverty was the main reason for food inaccessibility. Through government efforts, poverty was reduced from 16.5% in 1990 to 8.9% in 1995. The Filipino member reported that government efforts had focused on national campaigns to combat hunger and to encourage community participation. The government was forced to implement a national Plan of Action for Food Security due to increased population, environmental degradation, closing land frontiers, and the global economy. The Plan encouraged increases in productivity, price and supply stabilization, maintenance of stocks, and rice subsidies for the poor. Gender concerns were being incorporated into development programs. The Indian member linked food insecurity to world resource problems. He stated that food problems included imbalances between supply and demand, but more importantly inequalities in access to food and differences in nutritional content of food. Populations in developing countries spent a larger proportion of income on food of lesser quality and variety that contributed to nutritional deficiencies, particularly among women and children. Food insecurity was part of the cycle of poverty, hunger, low productivity, and high mortality. Poverty was the primary cause and a major consequence of hunger and chronic food insecurity. Although India increased food productivity, food insecurity remained. Multidisciplinary approaches are needed. PMID:12292317

  16. "Population and poverty: major barriers to food accessibility" -- a panel discussion on civil society and people's participation.

    PubMed

    1996-01-01

    This paper summarizes conference statements on poverty and food policies that were made by parliamentary members from Malaysia, the Philippines, and India. These presentations were made after the main panel discussion on barriers to food accessibility. In Malaysia the government adopted a National Agricultural Policy in 1984. This policy encouraged increased productivity, effective use of resources, agricultural credit and incentives, and integrated pest management. Strong support was given to the food processing industry. Poverty was the main reason for food inaccessibility. Through government efforts, poverty was reduced from 16.5% in 1990 to 8.9% in 1995. The Filipino member reported that government efforts had focused on national campaigns to combat hunger and to encourage community participation. The government was forced to implement a national Plan of Action for Food Security due to increased population, environmental degradation, closing land frontiers, and the global economy. The Plan encouraged increases in productivity, price and supply stabilization, maintenance of stocks, and rice subsidies for the poor. Gender concerns were being incorporated into development programs. The Indian member linked food insecurity to world resource problems. He stated that food problems included imbalances between supply and demand, but more importantly inequalities in access to food and differences in nutritional content of food. Populations in developing countries spent a larger proportion of income on food of lesser quality and variety that contributed to nutritional deficiencies, particularly among women and children. Food insecurity was part of the cycle of poverty, hunger, low productivity, and high mortality. Poverty was the primary cause and a major consequence of hunger and chronic food insecurity. Although India increased food productivity, food insecurity remained. Multidisciplinary approaches are needed.

  17. Influence of the zinc hyperaccumulator Thlaspi caerulescens J. & C. Presl. and the nonmetal accumulator Trifolium pratense L. on soil microbial populations.

    PubMed

    Delorme, T A; Gagliardi, J V; Angle, J S; Chaney, R L

    2001-08-01

    Metal hyperaccumulator plants like Thlaspi caerulescens J. & C. Presl. are used for phytoremediation of contaminated soils. Since little is known about the rhizosphere of hyperaccumulators, the influence of T. caerulescens was compared with the effects of Trifolium pratense L. on soil microbes. High- and low-metal soils were collected near a zinc smelter in Palmerton, Penn. Soil pH was adjusted to 5.8 and 6.8 by the addition of Ca(OH)2. Liming increased bacterial populations and decreased metal toxicity to levels allowing growth of both plants. The effects of the plants on total (culturable) bacteria, total fungi, as well as cadmium- and zinc-resistant populations were assessed in nonrhizosphere and rhizosphere soil. Both plants increased microbial populations in rhizosphere soil compared with nonrhizosphere soil. Microbial populations were higher in soils planted with T. pratense, but higher ratios of metal-resistant bacteria were found in the presence of T. caerulescens. We hypothesize that T. caerutescens acidifies its rhizosphere. Soil acidification in the rhizosphere of T. caerulescens would affect metal uptake by increasing available metals around the roots and consequently, increase the selection for metal-resistant bacteria. Soil acidification may be part of the hyperaccumulation process enhancing metal uptake from soil.

  18. Mapping socio-environmentally vulnerable populations access and exposure to ecosystem services at the U.S.-Mexico borderlands

    USGS Publications Warehouse

    Norman, Laura M.; Villarreal, Miguel L.; Lara-Valencia, Francisco; Yuan, Yongping; Nie, Wenming; Wilson, Sylvia; Amaya, Gladys; Sleeter, Rachel

    2012-01-01

    Socio-environmental vulnerable populations are often unrepresented in land-use planning yet have great potential for loss when exposed to changes in ecosystem services. Administrative boundaries, cultural differences, and language barriers increase the disassociation between land-use management and marginalized populations living in the U.S.–Mexico borderlands. This paper describes the development of a Modified Socio-Environmental Vulnerability Index (M-SEVI), using determinants from binational census and neighborhood data that describe levels of education, access to resources, migratory status, housing, and number of dependents, to provide a simplified snapshot of the region's populace that can be used in binational planning efforts. We apply this index at the SCW, located on the border between Arizona, USA and Sonora, Mexico. For comparison, the Soil and Water Assessment Tool is concurrently applied to assess the provision of erosion- and flood control services over a 9-year period. We describe how this coupling of data can form the base for an ecosystem services assessment across political boundaries that can be used by land-use planners. Results reveal potential disparities in environmental risks and burdens throughout the binational watershed in residential districts surrounding and between urban centers. The M-SEVI can be used as an important first step in addressing environmental justice for binational decision-making.

  19. Functional Diversity and Electron Donor Dependence of Microbial Populations Capable of U(VI) Reduction in Radionuclide-Contaminated Subsurface Sediments▿

    PubMed Central

    Akob, Denise M.; Mills, Heath J.; Gihring, Thomas M.; Kerkhof, Lee; Stucki, Joseph W.; Anastácio, Alexandre S.; Chin, Kuk-Jeong; Küsel, Kirsten; Palumbo, Anthony V.; Watson, David B.; Kostka, Joel E.

    2008-01-01

    In order to elucidate the potential mechanisms of U(VI) reduction for the optimization of bioremediation strategies, the structure-function relationships of microbial communities were investigated in microcosms of subsurface materials cocontaminated with radionuclides and nitrate. A polyphasic approach was used to assess the functional diversity of microbial populations likely to catalyze electron flow under conditions proposed for in situ uranium bioremediation. The addition of ethanol and glucose as supplemental electron donors stimulated microbial nitrate and Fe(III) reduction as the predominant terminal electron-accepting processes (TEAPs). U(VI), Fe(III), and sulfate reduction overlapped in the glucose treatment, whereas U(VI) reduction was concurrent with sulfate reduction but preceded Fe(III) reduction in the ethanol treatments. Phyllosilicate clays were shown to be the major source of Fe(III) for microbial respiration by using variable-temperature Mössbauer spectroscopy. Nitrate- and Fe(III)-reducing bacteria (FeRB) were abundant throughout the shifts in TEAPs observed in biostimulated microcosms and were affiliated with the genera Geobacter, Tolumonas, Clostridium, Arthrobacter, Dechloromonas, and Pseudomonas. Up to two orders of magnitude higher counts of FeRB and enhanced U(VI) removal were observed in ethanol-amended treatments compared to the results in glucose-amended treatments. Quantification of citrate synthase (gltA) levels demonstrated a stimulation of Geobacteraceae activity during metal reduction in carbon-amended microcosms, with the highest expression observed in the glucose treatment. Phylogenetic analysis indicated that the active FeRB share high sequence identity with Geobacteraceae members cultivated from contaminated subsurface environments. Our results show that the functional diversity of populations capable of U(VI) reduction is dependent upon the choice of electron donor. PMID:18378664

  20. Microbial dechlorination of historically present and freshly spiked chlorinated dioxins and diversity of dioxin-dechlorinating populations.

    PubMed Central

    Barkovskii, A L; Adriaens, P

    1996-01-01

    The ability of a microbial consortium eluted from dioxin-contaminated Passaic River sediments to dechlorinate polychlorinated dibenzo-p-dioxins (PCDDs) was investigated under methanogenic conditions. Aged 2,3,7,8-tetraCDD, which had partitioned into the microbial consortium from sediments, was stoichiometrically converted to tri- and monoCDD congeners. During dechlorination, dominant microbial activity within the consortium shifted from methanogenic to nonmethanogenic activity. Freshly spiked octaCDD was converted to hepta-, hexa-, penta-, tetra-, tri-, di-, and monochlorinated isomers, but the reaction stoichiometry was not determined. No methanogenic activity was observed, and the maximum yield of protein coincided with the production of less-chlorinated DD congeners. Two distinct pathways of dechlorination were observed: the peri-dechlorination pathway of 2,3,7,8-substituted hepta- to pentaCDDs, resulting in the production of 2,3,7,8-tetraCDD, and the peri-lateral dechlorination pathway of non-2,3,7,8-substituted congeners. Direct evidence of further lateral dechlorination of 2,3,7,8-tetraCDD was obtained from the historically contaminated incubations; no isomer-specific identification of triCDDs in spiked incubations was determined. Pasteurized cells exhibited no peri-dechlorination pathway, and triCDDs were the least-chlorinated congeners produced in these treatments. These results demonstrate that (i) both freshly spiked and aged PCDDs are available to microbial reductive dechlorination, (ii) the peri and triCDD dechlorinations are attributed to activities of nonmethanogenic, non-spore-forming microbial subpopulations, and (iii) the 2,3,7,8-residue patterns in historically contaminated sediments are likely affected by microbial activity. PMID:8953727

  1. [Health status and access to health services by the population of L'Aquila (Abruzzo Region, Italy) six years after the earthquake].

    PubMed

    Altobelli, Emma; Vittorini, Pierpaolo; Leuter, Cinzia; Bianchini, Valeria; Angelone, Anna Maria; Aloisio, Federica; Cofini, Vincenza; Zazzara, Francesca; Di Orio, Ferdinando

    2016-01-01

    Natural disasters, such as the earthquake that occurred in the province of L'Aquila in central Italy, in 2009, generally increase the demand for healthcare. A survey was conducted to assess perception of health status an d use of health services in a sample of L'Aquila's resident population, five years after the event, and in a comparison population consisting of a sample of the resident population of Avezzano, a town in the same region, not affected by the earthquake. No differences were found in perception of health status between the two populations. Both groups reported difficulties in accessing specialized healthcare and rehabilitation services.

  2. [Health status and access to health services by the population of L'Aquila (Abruzzo Region, Italy) six years after the earthquake].

    PubMed

    Altobelli, Emma; Vittorini, Pierpaolo; Leuter, Cinzia; Bianchini, Valeria; Angelone, Anna Maria; Aloisio, Federica; Cofini, Vincenza; Zazzara, Francesca; Di Orio, Ferdinando

    2016-01-01

    Natural disasters, such as the earthquake that occurred in the province of L'Aquila in central Italy, in 2009, generally increase the demand for healthcare. A survey was conducted to assess perception of health status an d use of health services in a sample of L'Aquila's resident population, five years after the event, and in a comparison population consisting of a sample of the resident population of Avezzano, a town in the same region, not affected by the earthquake. No differences were found in perception of health status between the two populations. Both groups reported difficulties in accessing specialized healthcare and rehabilitation services. PMID:27077558

  3. Dissolved carbon dioxide and oxygen concentrations in purge of vacuum-packaged pork chops and the relationship to shelf life and models for estimating microbial populations.

    PubMed

    Adams, K R; Niebuhr, S E; Dickson, J S

    2015-12-01

    The objectives of this study were to determine the dissolved CO2 and O2 concentrations in the purge of vacuum-packaged pork chops over a 60 day storage period, and to elucidate the relationship of dissolved CO2 and O2 to the microbial populations and shelf life. As the populations of spoilage bacteria increased, the dissolved CO2 increased and the dissolved O2 decreased in the purge. Lactic acid bacteria dominated the spoilage microflora, followed by Enterobacteriaceae and Brochothrix thermosphacta. The surface pH decreased to 5.4 due to carbonic acid and lactic acid production before rising to 5.7 due to ammonia production. A mathematical model was developed which estimated microbial populations based on dissolved CO2 concentrations. Scanning electron microscope images were also taken of the packaging film to observe the biofilm development. The SEM images revealed a two-layer biofilm on the packaging film that was the result of the tri-phase growth environment. PMID:26143235

  4. Planetary Resources and Astroecology. Planetary Microcosm Models of Asteroid and Meteorite Interiors: Electrolyte Solutions and Microbial Growth- Implications for Space Populations and Panspermia

    NASA Astrophysics Data System (ADS)

    Mautner, Michael N.

    2002-03-01

    Planetary microcosms were constructed using extracts from meteorites that simulate solutions in the pores of carbonaceous chondrites. The microcosms were found to support the growth of complex algal and microbial populations. Such astroecology experiments demonstrate how a diverse ecosystem could exist in fluids within asteroids, and in meteorites that land on aqueous planets. The microcosm solutions were obtained by extracting nutrient electrolytes under natural conditions from powders of the Allende (CV3) and Murchison (CM2) meteorites at low (0.02 g/ml) and high (10.0 g/ml) solid/solution ratios. The latter solutions contain >3 mol/L electrolytes and about 10 g/L organics, that simulate natural fluids in asteroids during aqueous alteration and in the pores of meteorites, which can help prebiotic synthesis and the survival of early microorganisms. These solutions and wet solids were in fact found to support complex self-sustaining microbial communities with populations of 4 × 105 algae and 6 × 106 bacteria and fungi for long periods (>8 months). The results show that planetary microcosms based on meteorites can: assay the fertilities of planetary materials; identify space bioresources; target astrobiology exploration; and model past and future space-based ecosystems. The results show that bioresources in the carbonaceous asteroids can sustain a biomass of 1018 kg, comprising 1032 microorganisms and a human population of 1014. The results also suggest that protoplanetary nebulae can support and disperse microorganisms and can be therefore effective environments for natural and directed panspermia.

  5. Rapid changes in key ruminal microbial populations during the induction of and recovery from diet-induced milk fat depression in dairy cows.

    PubMed

    Rico, D E; Preston, S H; Risser, J M; Harvatine, K J

    2015-08-14

    The ruminant provides a powerful model for understanding the temporal dynamics of gastrointestinal microbial communities. Diet-induced milk fat depression (MFD) in the dairy cow is caused by rumen-derived bioactive fatty acids, and is commonly attributed to the changes in the microbial population. The aim of the present study was to determine the changes occurring in nine ruminal bacterial taxa with well-characterised functions, and abundance of total fungi, ciliate protozoa and bacteria during the induction of and recovery from MFD. Interactions between treatment and time were observed for ten of the twelve populations. The total number of both fungi and ciliate protozoa decreased rapidly (days 4 and 8, respectively) by more than 90% during the induction period and increased during the recovery period. The abundance of Streptococcus bovis (amylolytic) peaked at 350% of control levels on day 4 of induction and rapidly decreased during the recovery period. The abundance of Prevotella bryantii (amylolytic) decreased by 66% from day 8 to 20 of the induction period and increased to the control levels on day 12 of the recovery period. The abundance of Megasphaera elsdenii and Selenomonas ruminantium (lactate-utilising bacteria) increased progressively until day 12 of induction (>170%) and decreased during the recovery period. The abundance of Fibrobacter succinogenes (fibrolytic) decreased by 97% on day 4 of induction and increased progressively to an equal extent during the recovery period, although smaller changes were observed for other fibrolytic bacteria. The abundance of the Butyrivibrio fibrisolvens/Pseudobutyrivibrio group decreased progressively during the induction period and increased during the recovery period, whereas the abundance of Butyrivibrio hungatei was not affected by treatment. Responsive taxa were modified rapidly, with the majority of changes occurring within 8 d and their time course was similar to the time course of the induction of MFD

  6. Rapid changes in key ruminal microbial populations during the induction of and recovery from diet-induced milk fat depression in dairy cows.

    PubMed

    Rico, D E; Preston, S H; Risser, J M; Harvatine, K J

    2015-08-14

    The ruminant provides a powerful model for understanding the temporal dynamics of gastrointestinal microbial communities. Diet-induced milk fat depression (MFD) in the dairy cow is caused by rumen-derived bioactive fatty acids, and is commonly attributed to the changes in the microbial population. The aim of the present study was to determine the changes occurring in nine ruminal bacterial taxa with well-characterised functions, and abundance of total fungi, ciliate protozoa and bacteria during the induction of and recovery from MFD. Interactions between treatment and time were observed for ten of the twelve populations. The total number of both fungi and ciliate protozoa decreased rapidly (days 4 and 8, respectively) by more than 90% during the induction period and increased during the recovery period. The abundance of Streptococcus bovis (amylolytic) peaked at 350% of control levels on day 4 of induction and rapidly decreased during the recovery period. The abundance of Prevotella bryantii (amylolytic) decreased by 66% from day 8 to 20 of the induction period and increased to the control levels on day 12 of the recovery period. The abundance of Megasphaera elsdenii and Selenomonas ruminantium (lactate-utilising bacteria) increased progressively until day 12 of induction (>170%) and decreased during the recovery period. The abundance of Fibrobacter succinogenes (fibrolytic) decreased by 97% on day 4 of induction and increased progressively to an equal extent during the recovery period, although smaller changes were observed for other fibrolytic bacteria. The abundance of the Butyrivibrio fibrisolvens/Pseudobutyrivibrio group decreased progressively during the induction period and increased during the recovery period, whereas the abundance of Butyrivibrio hungatei was not affected by treatment. Responsive taxa were modified rapidly, with the majority of changes occurring within 8 d and their time course was similar to the time course of the induction of MFD

  7. Diversity and evolution of the microbial populations during manufacture and ripening of Casín, a traditional Spanish, starter-free cheese made from cow's milk.

    PubMed

    Alegría, Angel; Alvarez-Martín, Pablo; Sacristán, Noelia; Fernández, Elena; Delgado, Susana; Mayo, Baltasar

    2009-11-30

    Classical culturing and denaturing gradient gel electrophoresis (DGGE) techniques have been used for studying the microbial diversity and dynamics of the traditional Spanish Casín cheese during manufacturing and ripening. As with other starter-free cheeses made from raw milk, the microbial diversity of Casín was shown to be high by both culturing and DGGE analyses. The culture technique showed that lactic acid bacteria (LAB) species constituted the majority of the microbial populations. Of the 14 bacterial species identified, Lactococcus garvieae was predominant in the three-day-old cheese sample, although it was replaced by Lactococcus lactis subsp. lactis at day 30. As expected, the DGGE profiles obtained were complex, consisting, depending on the sample, in five to ten different amplification bands. Among these, a band corresponding to Streptococcus thermophilus was observed throughout the whole manufacturing process. This species had never been identified from traditional Spanish cheeses previously. Culturing and molecular methods showed high populations of undesirable microorganisms, arguing for a required improvement in the hygiene of Casín manufacture. Random amplification of polymorphic DNA (RAPD) profiling suggested that the L. garvieae and L. lactis populations were composed of one and five strains, respectively. In addition, only a single L. lactis RAPD pattern was stably maintained from day three to day 30, indicating high succession of strains along ripening. After a thoroughly characterisation, strains of the two Lactococcus species could be used in designing specific starter cultures for Casín. Additional species (such as Lactobacillus plantarum and Corynebacterium variabile) might be included as adjunct cultures.

  8. Effects of electron-beam irradiation on the shelf life, microbial populations and sensory characteristics of summer truffles (Tuber aestivum) packaged under modified atmospheres.

    PubMed

    Rivera, Carmen Susana; Blanco, Domingo; Marco, Pedro; Oria, Rosa; Venturini, María Eugenia

    2011-02-01

    The effects of two doses of electron-beam irradiation (1.5 kGy and 2.5 kGy) on the microbial populations (total mesophilic aerobes, Pseudomonas genus, Enterobacteriaceae family, molds and yeasts) and sensory characteristics of Tuber aestivum packaged under modified atmospheres were monitored immediately after treatment, and weekly during 42 days of storage at 4 °C. Treatment with 1.5 and 2.5 kGy reduced the pseudomonads populations by 4.3 and 5.5 logs, respectively. Enterobacteriaceae counts decreased by 5.4 logs with the 1.5 kGy dose and counts below the detection limit (<1.0 log cfu/g) were obtained with the 2.5 kGy dose. Lactic acid bacteria and yeasts were less affected by the ionizing radiation treatments and they became the dominant microbial populations throughout storage with microbial counts up to 7.1 log cfu/g. The carbon dioxide levels inside the packages containing irradiated truffles were lower than those of the non-irradiated ones, suggesting a decrease in the respiration rate of the treated ascocarps. The treatments with 1.5 and 2.5 kGy e-beam did not negatively affect the sensory characteristics of truffles, but a visible superficial yeast growth was detected in truffles irradiated with 1.5 kGy at the end of their shelf life (day 28). Treatment with 2.5 kGy e-beam has prolonged the shelf life to 42 days, compared with 21 days for the untreated samples.

  9. A nutrition strategy to reduce the burden of diet related disease: access to dietician services must complement population health approaches.

    PubMed

    Segal, Leonie; Opie, Rachelle S

    2015-01-01

    Poor diet quality is implicated in almost every disease and health issue. And yet, in most advanced market economies diet quality is poor, with a minority meeting guidelines for healthy eating. Poor diet is thus responsible for substantial disease burden. Societies have at their disposal a range of strategies to influence diet behaviors. These can be classified into: (i) population level socio-educational approaches to enhance diet knowledge; (ii) pricing incentives (subsidies on healthy foods, punitive taxes on unhealthy foods); (iii) regulations to modify the food environment, and (iv) the provision of clinical dietetic services. There is little evidence that societies are active in implementing the available strategies. Advertising of "junk foods" is largely unchecked, contrasting with strict controls on advertising tobacco products, which also attract punitive taxes. Access to dieticians is restricted in most countries, even in the context of universal health care. In Australia in 2011 there were just 2,969 practicing dieticians/nutritionists or 1.3 clinicians per 10,000 persons, compared with 5.8 physiotherapists per 10,000 persons, 14.8 general practitioners (family physicians) per 10,000 persons or 75 nurses per 10,000 persons. It is time to implement comprehensive national nutrition strategies capable of effecting change. Such strategies need to be multi-component, incorporating both public health approaches and expanded publicly funded dietetic services. Access to individualized dietetic services is needed by those at risk, or with current chronic conditions, given the complexity of the diet message, the need for professional support for behavior change and to reflect individual circumstances. The adoption of a comprehensive nutrition strategy offers the promise of substantial improvement in diet quality, better health and wellbeing and lower health care costs. PMID:26321951

  10. A nutrition strategy to reduce the burden of diet related disease: access to dietician services must complement population health approaches.

    PubMed

    Segal, Leonie; Opie, Rachelle S

    2015-01-01

    Poor diet quality is implicated in almost every disease and health issue. And yet, in most advanced market economies diet quality is poor, with a minority meeting guidelines for healthy eating. Poor diet is thus responsible for substantial disease burden. Societies have at their disposal a range of strategies to influence diet behaviors. These can be classified into: (i) population level socio-educational approaches to enhance diet knowledge; (ii) pricing incentives (subsidies on healthy foods, punitive taxes on unhealthy foods); (iii) regulations to modify the food environment, and (iv) the provision of clinical dietetic services. There is little evidence that societies are active in implementing the available strategies. Advertising of "junk foods" is largely unchecked, contrasting with strict controls on advertising tobacco products, which also attract punitive taxes. Access to dieticians is restricted in most countries, even in the context of universal health care. In Australia in 2011 there were just 2,969 practicing dieticians/nutritionists or 1.3 clinicians per 10,000 persons, compared with 5.8 physiotherapists per 10,000 persons, 14.8 general practitioners (family physicians) per 10,000 persons or 75 nurses per 10,000 persons. It is time to implement comprehensive national nutrition strategies capable of effecting change. Such strategies need to be multi-component, incorporating both public health approaches and expanded publicly funded dietetic services. Access to individualized dietetic services is needed by those at risk, or with current chronic conditions, given the complexity of the diet message, the need for professional support for behavior change and to reflect individual circumstances. The adoption of a comprehensive nutrition strategy offers the promise of substantial improvement in diet quality, better health and wellbeing and lower health care costs.

  11. A nutrition strategy to reduce the burden of diet related disease: access to dietician services must complement population health approaches

    PubMed Central

    Segal, Leonie; Opie, Rachelle S.

    2015-01-01

    Poor diet quality is implicated in almost every disease and health issue. And yet, in most advanced market economies diet quality is poor, with a minority meeting guidelines for healthy eating. Poor diet is thus responsible for substantial disease burden. Societies have at their disposal a range of strategies to influence diet behaviors. These can be classified into: (i) population level socio-educational approaches to enhance diet knowledge; (ii) pricing incentives (subsidies on healthy foods, punitive taxes on unhealthy foods); (iii) regulations to modify the food environment, and (iv) the provision of clinical dietetic services. There is little evidence that societies are active in implementing the available strategies. Advertising of “junk foods” is largely unchecked, contrasting with strict controls on advertising tobacco products, which also attract punitive taxes. Access to dieticians is restricted in most countries, even in the context of universal health care. In Australia in 2011 there were just 2,969 practicing dieticians/nutritionists or 1.3 clinicians per 10,000 persons, compared with 5.8 physiotherapists per 10,000 persons, 14.8 general practitioners (family physicians) per 10,000 persons or 75 nurses per 10,000 persons. It is time to implement comprehensive national nutrition strategies capable of effecting change. Such strategies need to be multi-component, incorporating both public health approaches and expanded publicly funded dietetic services. Access to individualized dietetic services is needed by those at risk, or with current chronic conditions, given the complexity of the diet message, the need for professional support for behavior change and to reflect individual circumstances. The adoption of a comprehensive nutrition strategy offers the promise of substantial improvement in diet quality, better health and wellbeing and lower health care costs. PMID:26321951

  12. EVALUATION OF THE EFFECTIVENESS OF RIPARIAN ZONE RESTORATION IN THE SOUTHERN APPALACHIANS BY ASSESSING SOIL MICROBIAL POPULATIONS

    EPA Science Inventory

    Microbial biomass, nitrifiers and denitrifiers in surface soil (0?10 cm) were quantified in a riparian zone restoration project at Coweeta, North Carolina, USA. Four treatments are included in this study: (1) a degraded (+N) riparian zone with continued compaction, vegetation rem...

  13. Deep Diversity: Novel Approach to Overcoming the PCR Bias Encountered During Environmental Analysis of Microbial Populations for Alpha-Diversity

    NASA Technical Reports Server (NTRS)

    Ramirez, Gustavo A; Vaishampayan, Parag A.

    2011-01-01

    Alpha-diversity studies are of crucial importance to environmental microbiologists. The polymerase chain reaction (PCR) method has been paramount for studies interrogating microbial environmental samples for taxon richness. Phylogenetic studies using this technique are based on the amplification and comparison of the 16S rRNA coding regions. PCR, due disproportionate distribution of microbial species in the environment, increasingly favors the amplification of the most predominant phylotypes with every subsequent reaction cycle. The genetic and chemical complexity of environmental samples are intrinsic factors that exacerbate an inherit bias in PCR-based quantitative and qualitative studies of microbial communities. We report that treatment of a genetically complex total genomic environmental DNA extract with Propidium Monoazide (PMA), a DNA intercalating molecule capable of forming a covalent cross-linkage to organic moieties upon light exposure, disproportionally inactivates predominant phylotypes and results in the exponential amplification of previously shadowed microbial ?-diversity quantified as a 19.5% increase in OUTs reported via phylogenetic screening using PhyloChip.

  14. An Evaluation of Behavioral Health Compliance and Microbial Risk Factors on Student Populations within a High-Density Campus

    ERIC Educational Resources Information Center

    Decker, Jody F.; Slawson, Robin M.

    2012-01-01

    Objective: The aim of this Canadian study was to assess student behavioral response to disease transmission risk, while identifying high microbial deposition/transmission sites. Participants: A student survey was conducted during October 2009. Methods: The methods included a survey of students to assess use of health services, vaccination…

  15. Microbial populations of crude oil spill polluted soils at the Jordan-Iraq desert (the Badia region)

    PubMed Central

    Saadoun, Ismail; Mohammad, Munir J.; Hameed, Khalid M.; Shawaqfah, Mo’ayyad

    2008-01-01

    Microbial populations’ inhabitants in crude petroleum contaminated soils were analyzed in relation with the soil characteristics. A noticeable greater decline of bacterial counts and diversity but a prevalence of the genus Pseudomonas over the other identified genera in the fresh contaminated soils as compared to the old ones was observed. PMID:24031245

  16. Assessing the microbial quality of improved drinking water sources: results from the Dominican Republic.

    PubMed

    Baum, Rachel; Kayser, Georgia; Stauber, Christine; Sobsey, Mark

    2014-01-01

    Millennium Development Goal Target 7c (to halve between 1990 and 2015 the proportion of the global population without sustainable access to safe drinking water), was celebrated as achieved in 2012. However, new studies show that we may be prematurely celebrating. Access to safe drinking water may be overestimated if microbial water quality is considered. The objective of this study was to examine the relationship between microbial drinking water quality and drinking water source in the Puerto Plata region of the Dominican Republic. This study analyzed microbial drinking water quality data from 409 households in 33 communities. Results showed that 47% of improved drinking water sources were of high to very-high risk water quality, and therefore unsafe for drinking. This study provides evidence that the current estimate of safe water access may be overly optimistic, and microbial water quality data are needed to reliably assess the safety of drinking water.

  17. Access to HIV community services by vulnerable populations: evidence from an enhanced HIV/AIDS surveillance system.

    PubMed

    Madden, H C E; Phillips-Howard, P A; Hargreaves, S C; Downing, J; Bellis, M A; Vivancos, R; Morley, C; Syed, Q; Cook, P A

    2011-05-01

    HIV disproportionately affects vulnerable populations such as black and minority ethnic groups, men who have sex with men (MSM) and migrants, in many countries including those in the UK. Community organisations in the UK are charitable non-governmental organisations with a proportion of the workforce who volunteer, and provide invaluable additional support for people living with HIV (PLWHIV). Information on their contribution to HIV care in vulnerable groups is relatively sparse. Data generated from an enhanced HIV surveillance system in North West England, UK, was utilised for this study. We aimed to determine the characteristics of individuals who chose to access community services in addition to clinical services (1375 out of 4195 records of PLWHIV in clinical services). Demographic information, risk factors including residency status, uniquely gathered in this region, and deprivation scores were examined. Multivariate logistic regression modelling was conducted to predict the relative effect of patient characteristics on attendance at community services. Attendance at community services was highest in those living in the most, compared with least, deprived areas (p<0.001), and was most evident in MSM and heterosexuals. Compared to white UK nationals attendance was significantly higher in non-UK nationals of uncertain residency status (Adjusted odds ratio [AOR] = 21.91, 95% confidence interval [CI] 10.48-45.83; p<0.001), refugees (AOR = 5.75, 95% CI 3.3-10.03; p<0.001), migrant workers (AOR = 5.48, 95% CI 2.22-13.51; p<0.001) and temporary visitors (AOR = 3.44, 95% CI 1.68-7.05; p<0.001). Community services, initially established predominantly to support MSM, have responded to the changing demography of HIV and reach the most vulnerable members of society. Consequent to their support of migrant populations, community services are vital for the management of HIV in black and minority groups. Paradoxically, this coincides with increasing funding pressures on these

  18. Effect of packaging during storage time on retail display microbial population of beef strip loins from two different production systems.

    PubMed

    Luzardo, S; Woerner, D R; Geornaras, I; Hess, A M; Belk, K E

    2016-06-01

    Two studies were conducted to evaluate the influence of packaging during storage of strip loins (to simulate export shipment) from steers fattened on intensive grazing systems (Uruguay; UR) or on a high-concentrate diet (United States; US) on retail display life microbial growth. Four or 3 different packaging treatments were applied to UR and US strip loin roasts or steaks during 35 d of storage; treatments were applied 7 d following slaughter. After 35 d of storage, the samples were evaluated during simulated retail display for up to 6 d. In Exp. 1, the treatments were vacuum packaging (VP), low-oxygen modified atmosphere packaging (MAP) with N and CO (MAP/CO), low-oxygen MAP with N plus CO and CO, and VP plus an application of peroxyacetic acid (VP/PAA). In Exp. 2, block 1, the treatments were VP, MAP/CO, and VP with ethyl--lauroyl--arginate HCl incorporated into the film as an antimicrobial agent (VP/AM). In Exp. 2, block 2, the treatments were VP, MAP/CO, MAP/CO, and VP/AM. For retail display, VP treatments were sliced and repackaged in PVC overwrap, and MAP treatments were actually PVC overwrap trays that were removed from a master bag with the prescribed gas treatment. Regardless of production system and packaging treatment, mesophilic and psychrotrophic counts of 6.9 to 7.8 and 6.7 to 7.7 log10 CFU/cm, respectively, were obtained at the end of retail display, except for US samples in Exp. 2 (5.5 to 6.3 log CFU/cm). No differences ( > 0.05) were detected for spp. counts among packaging treatments in US steaks at the end of the display time in Exp.1, whereas, for UR steaks, both MAP treatments had lower ( < 0.05) spp. counts than VP treatments. spp. counts were lower ( < 0.05) in the MAP/CO treatment than in the other 3 treatments in US samples on d 6 of retail display for Exp. 2. At the end of display time and for Exp. 1, US steaks under MAP/CO had greater ( < 0.05) lactic acid bacteria (LAB) counts than samples in both VP treatments; no differences ( > 0

  19. Milk fatty acid composition, rumen microbial population, and animal performances in response to diets rich in linoleic acid supplemented with chestnut or quebracho tannins in dairy ewes.

    PubMed

    Buccioni, A; Pauselli, M; Viti, C; Minieri, S; Pallara, G; Roscini, V; Rapaccini, S; Marinucci, M Trabalza; Lupi, P; Conte, G; Mele, M

    2015-02-01

    The aim of the study was to evaluate milk fatty acid (FA) profile, animal performance, and rumen microbial population in response to diets containing soybean oil supplemented or not with chestnut and quebracho tannins in dairy ewes. Eighteen Comisana ewes at 122±6 d in milking were allotted into 3 experimental groups. Diets were characterized by chopped grass hay administered ad libitum and by 800 g/head and day of 3 experimental concentrates containing 84.5 g of soybean oil/kg of dry matter (DM) and 52.8 g/kg of DM of bentonite (control diet), chestnut tannin extract (CHT diet), or quebracho tannin extract (QUE diet). The trial lasted 4 wk. Milk yield was recorded daily, and milk composition and blood parameters were analyzed weekly. At the end of the experiment, samples of rumen fluid were collected to analyze pH, volatile fatty acid profile, and the relative proportions of Butyrivibrio fibrisolvens and Butyrivibrio proteoclasticus in the rumen microbial population. Hepatic functionality, milk yield, and gross composition were not affected by tannin extracts, whereas milk FA composition was characterized by significant changes in the concentration of linoleic acid (CHT +2.77% and QUE +9.23%), vaccenic acid (CHT +7.07% and QUE +13.88%), rumenic acid (CHT -1.88% and QUE +24.24%), stearic acid (CHT + 8.71% and QUE -11.45%), and saturated fatty acids (CHT -0.47% and QUE -3.38%). These differences were probably due to the ability of condensed versus hydrolyzable tannins to interfere with rumen microbial metabolism, as indirectly confirmed by changes in the relative proportions of B. fibrisolvens and B. proteoclasticus populations and by changes in the molar proportions of volatile fatty acids. The effect of the CHT diet on the milk FA profile and microbial species considered in this trial was intermediate between that of QUE and the control diet, suggesting a differential effect of condensed and hydrolyzable tannins on rumen microbes. Compared with control animals

  20. Responses in digestion, rumen fermentation and microbial populations to inhibition of methane formation by a halogenated methane analogue.

    PubMed

    Mitsumori, Makoto; Shinkai, Takumi; Takenaka, Akio; Enishi, Osamu; Higuchi, Koji; Kobayashi, Yosuke; Nonaka, Itoko; Asanuma, Narito; Denman, Stuart E; McSweeney, Christopher S

    2012-08-01

    The effects of the anti-methanogenic compound, bromochloromethane (BCM), on rumen microbial fermentation and ecology were examined in vivo. Japanese goats were fed a diet of 50 % Timothy grass and 50 % concentrate and then sequentially adapted to low, mid and high doses of BCM. The goats were placed into the respiration chambers for analysis of rumen microbial function and methane and H2 production. The levels of methane production were reduced by 5, 71 and 91 %, and H2 production was estimated at 545, 2941 and 3496 mmol/head per d, in response to low, mid and high doses of BCM, respectively, with no effect on maintenance feed intake and digestibility. Real-time PCR quantification of microbial groups showed a significant decrease relative to controls in abundance of methanogens and rumen fungi, whereas there were increases in Prevotella spp. and Fibrobacter succinogenes, a decrease in Ruminococcus albus and R. flavefaciens was unchanged. The numbers of protozoa were also unaffected. Denaturing gradient gel electrophoresis and quantitative PCR analysis revealed that several Prevotella spp. were the bacteria that increased most in response to BCM treatment. It is concluded that the methane-inhibited rumen adapts to high hydrogen levels by shifting fermentation to propionate via Prevotella spp., but the majority of metabolic hydrogen is expelled as H2 gas.

  1. Dynamics of bacterial populations during bench-scale bioremediation of oily seawater and desert soil bioaugmented with coastal microbial mats.

    PubMed

    Ali, Nidaa; Dashti, Narjes; Salamah, Samar; Sorkhoh, Naser; Al-Awadhi, Husain; Radwan, Samir

    2016-03-01

    This study describes a bench-scale attempt to bioremediate Kuwaiti, oily water and soil samples through bioaugmentation with coastal microbial mats rich in hydrocarbonoclastic bacterioflora. Seawater and desert soil samples were artificially polluted with 1% weathered oil, and bioaugmented with microbial mat suspensions. Oil removal and microbial community dynamics were monitored. In batch cultures, oil removal was more effective in soil than in seawater. Hydrocarbonoclastic bacteria associated with mat samples colonized soil more readily than seawater. The predominant oil degrading bacterium in seawater batches was the autochthonous seawater species Marinobacter hydrocarbonoclasticus. The main oil degraders in the inoculated soil samples, on the other hand, were a mixture of the autochthonous mat and desert soil bacteria; Xanthobacter tagetidis, Pseudomonas geniculata, Olivibacter ginsengisoli and others. More bacterial diversity prevailed in seawater during continuous than batch bioremediation. Out of seven hydrocarbonoclastic bacterial species isolated from those cultures, only one, Mycobacterium chlorophenolicum, was of mat origin. This result too confirms that most of the autochthonous mat bacteria failed to colonize seawater. Also culture-independent analysis of seawater from continuous cultures revealed high-bacterial diversity. Many of the bacteria belonged to the Alphaproteobacteria, Flavobacteria and Gammaproteobacteria, and were hydrocarbonoclastic. Optimal biostimulation practices for continuous culture bioremediation of seawater via mat bioaugmentation were adding the highest possible oil concentration as one lot in the beginning of bioremediation, addition of vitamins, and slowing down the seawater flow rate. PMID:26751253

  2. Ecology, Microbial

    SciTech Connect

    Konopka, Allan

    2009-05-15

    Microbial ecology is a relatively young discipline within the field of microbiology. Its modern history spans just the past 60 years, and the field is defined by its emphasis on understanding the interactions of microbes with their environment, rather than their behavior under artificial laboratory conditions. Because microbes are ubiquitous, microbial ecologists study a broad diversity of habitats that range from aquatic to terrestrial to plant- or animal-associated. This has made it a challenge to identify unifying principles within the field. One approach is to recognize that although the activity of microbes in nature have effects at the macroscale, they interact with their physical, chemical and biological milieu at a scale of micrometers. At this scale, several different microbial ecosystems can be defined, based upon association with particles, the presence of environmental gradients and the continuous availability of water. Principles applicable to microbial ecology reflect not only their population ecology and physiological ecology, but also their broad versatility and quantitative importance in the biosphere as biogeochemical catalysts and capacity for rapid physiological and evolutionary responses.

  3. Ecology, Microbial

    SciTech Connect

    Konopka, Allan

    2009-03-19

    Microbial ecology is a relatively young discipline within the field of microbiology. Its modern history spans just the past 60 years, and the field is defined by its emphasis on understanding the interactions of microbes with their environment, rather than their behavior under artificial laboratory conditions. Because microbes are ubiquitous, microbial ecologists study a broad diversity of habitats that range from aquatic to terrestrial to plant- or animal-associated. This has made it a challenge to identify unifying principles within the field. One approach is to recognize that although the activity of microbes in nature have effects at the macroscale, they interact with their physical, chemical and biological milieu at a scale of micrometers. At this scale, several different microbial ecosystems can be defined, based upon association with particles, the presence of environmental gradients and the continuous availability of water. Principles applicable to microbial ecology reflect not only their population ecology and physiological ecology, but also their broad versatility and quantitative importance in the biosphere as biogeochemical catalysts and capacity for rapid physiological and evolutionary responses.

  4. 'If she is a good woman …' and 'to be a real man …': gender, risk and access to HIV services among key populations in Tajikistan.

    PubMed

    King, Elizabeth J; Maksymenko, Kateryna M; Almodovar-Diaz, Yadira; Johnson, Sarah

    2016-01-01

    The HIV epidemic continues to grow in Tajikistan, especially among people who inject drugs, sex workers, men who have sex with men and incarcerated populations. Despite their susceptibility to HIV, members of these groups do not always have access to HIV prevention, testing and treatment. The purpose of this study was to identify and understand the gender constraints in accessing HIV services for key populations in Tajikistan. Using focus-group discussions and key-informant interviews the assessment team collected information from members of key populations and those who work with them. Several themes emerged from the data, including: low levels of HIV knowledge, gender constraints to condom use and safer drug use, gender constraints limit HIV testing opportunities, gender-based violence, stigma and discrimination, and the lack of female spaces in the HIV response. The results of this study show that there are well-defined gender norms in Tajikistan, and these gender norms influence key populations' access to HIV services. Addressing these gender constraints may offer opportunities for more equitable access to HIV services in Tajikistan.

  5. Do Children in Rural Areas Still Have Different Access to Health Care? Results from a Statewide Survey of Oregon's Food Stamp Population

    ERIC Educational Resources Information Center

    Devoe, Jennifer E.; Krois, Lisa; Stenger, Rob

    2009-01-01

    Purpose: To determine if rural residence is independently associated with different access to health care services for children eligible for public health insurance. Methods: We conducted a mail-return survey of 10,175 families randomly selected from Oregon's food stamp population (46% rural and 54% urban). With a response rate of 31%, we used a…

  6. Socio Economic Position in TB Prevalence and Access to Services: Results from a Population Prevalence Survey and a Facility-Based Survey in Bangladesh

    PubMed Central

    Hossain, Shahed; Quaiyum, Mohammad Abdul; Zaman, Khalequ; Banu, Sayera; Husain, Mohammad Ashaque; Islam, Mohammad Akramul; Cooreman, Erwin; Borgdorff, Martien; Lönnroth, Knut; Salim, Abdul Hamid; van Leth, Frank

    2012-01-01

    Background In Bangladesh DOTS has been provided free of charge since 1993, yet information on access to TB services by different population group is not well documented. The objective of this study was to assess and compare the socio economic position (SEP) of actively detected cases from the community and the cases being routinely detected under National Tuberculosis Control Programme (NTP) in Bangladesh. Methods and Findings SEP was assessed by validated asset item for each of the 21,427 households included in the national tuberculosis prevalence survey 2007–2009. A principal component analysis generated household scores and categorized in quartiles. The distribution of 33 actively identified cases was compared with the 240 NTP cases over the identical SEP quartiles to evaluate access to TB services by different groups of the population. The population prevalence of tuberculosis was 5 times higher in the lowest quartiles of population (95.4, 95% CI: 48.0–189.7) to highest quartile population (19.5, 95% CI: 6.9–55.0). Among the 33 cases detected during survey, 25 (75.8%) were from lower two quartiles, and the rest 8 (24.3%) were from upper two quartiles. Among TB cases detected passively under NTP, more than half of them 137 (57.1%) were from uppermost two quartiles, 98 (41%) from the second quartile, and 5 (2%) in the lowest quartile of the population. This distribution is not affected when adjusted for other factors or interactions among them. Conclusions The findings indicate that despite availability free of charge, DOTS is not equally accessed by the poorer sections of the population. However, these figures should be interpreted with caution since there is a need for additional studies that assess in-depth poverty indicators and its determinants in relation to access of the TB services provided in Bangladesh. PMID:23028718

  7. Optimising locational access of deprived populations to farmers' markets at a national scale: one route to improved fruit and vegetable consumption?

    PubMed

    Pearson, Amber L; Wilson, Nick

    2013-01-01

    Background. Evidence suggests that improved locational access to farmers' markets increases fruit and vegetable (FV) consumption, particularly for low-income groups. Therefore, we modelled potential alternative distributions of farmers' markets in one country (New Zealand) to explore the potential impact for deprived populations and an indigenous population (Māori). Methods. Data were collected on current farmers' markets (n = 48), population distributions, area deprivation, and roads. Geographic analyses were performed to optimize market locations for the most deprived populations. Results. We found that, currently, farmers' markets provided fairly poor access for the total population: 7% within 12.5 km (15 min driving time); 5% within 5 km; and 3% within 2 km. Modelling the optimal distribution of the 48 markets substantially improved access for the most deprived groups: 9% (vs 2% currently) within 12.5 km; 5% (vs 1%) within 5 km; and 3% (vs 1%) within 2 km. Access for Māori also improved: 22% (vs 7%) within 12.5 km; 12% (vs 4%) within 5 km; and 6% (vs 2%) within 2 km. Smaller pro-equity results arose from optimising the locations of the 18 least pro-equity markets or adding 10 new markets. Conclusion. These results highlight the potential for improving farmers' market locations to increase accessibility for groups with low FV consumption. Given that such markets are easily established and relocated, local governments could consider these results to inform decisions, including subsidies for using government land and facilities. Such results can also inform central governments planning around voucher schemes for such markets and exempting them from taxes (e.g., VAT/GST).

  8. Energy, ecology and the distribution of microbial life

    PubMed Central

    Macalady, Jennifer L.; Hamilton, Trinity L.; Grettenberger, Christen L.; Jones, Daniel S.; Tsao, Leah E.; Burgos, William D.

    2013-01-01

    Mechanisms that govern the coexistence of multiple biological species have been studied intensively by ecologists since the turn of the nineteenth century. Microbial ecologists in the meantime have faced many fundamental challenges, such as the lack of an ecologically coherent species definition, lack of adequate methods for evaluating population sizes and community composition in nature, and enormous taxonomic and functional diversity. The accessibility of powerful, culture-independent molecular microbiology methods offers an opportunity to close the gap between microbial science and the main stream of ecological theory, with the promise of new insights and tools needed to meet the grand challenges humans face as planetary engineers and galactic explorers. We focus specifically on resources related to energy metabolism because of their direct links to elemental cycling in the Earth's history, engineering applications and astrobiology. To what extent does the availability of energy resources structure microbial communities in nature? Our recent work on sulfur- and iron-oxidizing autotrophs suggests that apparently subtle variations in the concentration ratios of external electron donors and acceptors select for different microbial populations. We show that quantitative knowledge of microbial energy niches (population-specific patterns of energy resource use) can be used to predict variations in the abundance of specific taxa in microbial communities. Furthermore, we propose that resource ratio theory applied to micro-organisms will provide a useful framework for identifying how environmental communities are organized in space and time. PMID:23754819

  9. Community Characterization of Microbial Populations Found at a Cold Water Sulfidic Spring in the Canadian High Arctic

    NASA Astrophysics Data System (ADS)

    Trivedi, C.; Lau, G. E.; Templeton, A. S.; Grasby, S. E.; Spear, J. R.

    2015-12-01

    The unique environment on Europa makes it an ideal target for astrobiological investigation. One such earth-based analogue to aid in this investigation is the sulfur-dominated glacial spring system found at Borup Fiord Pass (BFP), Ellesmere Island, Nunavut, Canada. In this system, subsurface microbial sulfate reduction produces hydrogen sulfide, which is transported through the glacier along spring channels [1]. As the surface oxidation of H2S occurs, resultant deposition of elemental sulfur (S0) and other minerals becomes visible (attached image). The energy released from these reactions can support potential microbial metabolisms and may be a valuable representation of microbial processes occurring on Europa. The resulting sulfur minerals provide sensitive records of dynamic atmospheric, geological, hydrological, chemical, and biological processes on planetary surfaces. Moreover, we expect that the S0-rich deposits of this glacial spring system will serve as a mineralogical record for biological activity and will provide a valuable tool for recognizing potential sulfur-based life on Europa. During a recent collaborative expedition (2014) to BFP, samples were taken from the toe of the glacier in an area called the 'Blister Crust' (attached image). At this location, glacial channels reach the surface, representing an active interface between subsurface and surface processes. Initial geochemical characterization at the site revealed high amounts of aqueous sulfide (1.8 mM) and hydrogen (29 nM), which likely serve as the electron donation potential in the system. Furthermore, preliminary 16S rRNA gene sequencing has shown a high abundance of the genus Sulfurimonas, which is a known sulfur metabolizer. Our research seeks to further characterize microbial communities found at this interface in order to elucidate information regarding in situ sulfur cycling and the potential to tie this into subsurface/surface processes on Europa. Continued work will provide guidance

  10. Differential access to digital communication technology: association with health and health survey recruitment within an African-American underserviced urban population.

    PubMed

    Schneider, John; Makelarski, Jennifer A; Van Haitsma, Martha; Lipton, Rebecca B; Abramsohn, Emily; Lauderdale, Diane S; Lindau, Stacy Tessler

    2011-06-01

    Digital communication technologies (DCT), such as cell phones and the internet, have begun to replace more traditional technologies even in technology-poor communities. We characterized access to DCT in an underserved urban population and whether access is associated with health and study participation. A general probability community sample and a purposive high-turnover housing sample were recruited and re-interviewed after 3 months. Selected characteristics were compared by sample type and retention. Associations between DCT access and self-reported health were examined using multivariable logistic regression. Of 363 eligible individuals, 184 (general community = 119; high-turnover housing = 65) completed the baseline survey. Eighty-four percent of respondents had a cell phone and 62% had ever texted. Ever use of the internet was high (69%) overall, but frequency and years of internet use were higher in the general community sample. Self-reported fair or poor health was more common for residents of cell phone-only households and those with less frequent internet use. Technology use was similar for those retained and not retained. Overall, access to DCT was high in this underserved urban population but varied by sample type. Health varied significantly by DCT use, but study retention did not. These data have implications for incorporating DCT into health-related research in urban populations.

  11. Planetary resources and astroecology. Planetary microcosm models of asteroid and meteorite interiors: electrolyte solutions and microbial growth--implications for space populations and panspermia.

    PubMed

    Mautner, Michael N

    2002-01-01

    Planetary microcosms were constructed using extracts from meteorites that simulate solutions in the pores of carbonaceous chondrites. The microcosms were found to support the growth of complex algal and microbial populations. Such astroecology experiments demonstrate how a diverse ecosystem could exist in fluids within asteroids, and in meteorites that land on aqueous planets. The microcosm solutions were obtained by extracting nutrient electrolytes under natural conditions from powders of the Allende (CV3) and Murchison (CM2) meteorites at low (0.02 g/ml) and high (10.0 g/ml) solid/solution ratios. The latter solutions contain > 3 mol/L electrolytes and about 10 g/L organics, that simulate natural fluids in asteroids during aqueous alteration and in the pores of meteorites, which can help prebiotic synthesis and the survival of early microorganisms. These solutions and wet solids were in fact found to support complex self-sustaining microbial communities with populations of 4 x 10(5) algae and 6 x 10(6) bacteria and fungi for long periods (> 8 months). The results show that planetary microcosms based on meteorites can: assay the fertilities of planetary materials; identify space bioresources; target astrobiology exploration; and model past and future space-based ecosystems. The results show that bioresources in the carbonaceous asteroids can sustain a biomass of 10(18) kg, comprising 10(32) microorganisms and a human population of 10(14). The results also suggest that protoplanetary nebulae can support and disperse microorganisms and can be therefore effective environments for natural and directed panspermia. PMID:12449855

  12. Differential Incorporation of Carbon Substrates among Microbial Populations Identified by Field-Based, DNA Stable-Isotope Probing in South China Sea

    PubMed Central

    Xie, Xiabing; Jiao, Nianzhi

    2016-01-01

    To determine the adapted microbial populations to variant dissolved organic carbon (DOC) sources in the marine environment and improve the understanding of the interaction between microorganisms and marine DOC pool, field-based incubation experiments were carried out using supplemental 13C-labeled typical substrates D-glucose and D-glucosamine (D-Glc and D-GlcN, respectively), which are two important components in marine DOC pool in the South China Sea. 13C- and 12C-DNA were then fractionated by ultracentrifugation and the microbial community was analyzed by terminal-restriction fragment length polymorphism and 454 pyrosequencing of 16S rRNA gene. 12C-DNA-based communities showed relatively high similarities with their corresponding in situ communities, and their bacterial diversities were generally higher than 13C-DNA-based counterparts. Distinct differences in community composition were found between 13C- and 12C-DNA-based communities and between two substrate-supplemented 13C-DNA-based communities; these differences distinctly varied with depth and site. In most cases, there were more genera with relative abundances of >0.1% in D-Glc-incorporating communities than in D-GlcN-incorporating communities. The Roseobacter clade was one of the prominent actively substrate-incorporating bacterial populations in all 13C-DNA-based communities. Vibrio was another prominent actively D-GlcN-incorporating bacterial population in most incubations. However notably, different OTUs dominated this clade or genus in different treatments at different depths. Altogether, these results suggested that there were taxa-specific differences in DOC assimilations and, moreover, their differences varied among the typical water masses, which could have been caused by the variant compositions of original bacterial communities from different hydrological environments. This implies that ecologically, the levels of labile or recalcitrance of DOC can be maintained only in a specific environmental

  13. Microbial populations on animal hides and beef carcasses at different stages of slaughter in plants employing multiple-sequential interventions for decontamination.

    PubMed

    Bacon, R T; Belk, K E; Sofos, J N; Clayton, R P; Reagan, J O; Smith, G C

    2000-08-01

    Multiple-sequential interventions were applied commercially to reduce beef carcass contamination in eight packing plants. The study evaluated microbial populations on animal hides and changes in carcass microbial populations at various stages in the slaughtering process. Sponge swab samples yielded mean (log CFU/100 cm2) total plate counts (TPC), total coliform counts (TCC), and Escherichia coli counts (ECC) on the exterior hide in the ranges of 8.2 to 12.5, 6.0 to 7.9, and 5.5 to 7.5, respectively, while corresponding contamination levels on carcass surfaces, after hide removal but before application of any decontamination intervention, were in the ranges of 6.1 to 9.1, 3.0 to 6.0, and 2.6 to 5.3, respectively. Following the slaughtering process and application of multiple-sequential decontamination interventions that included steam vacuuming, pre-evisceration carcass washing, pre-evisceration organic acid solution rinsing, hot water carcass washing, postevisceration final carcass washing, and postevisceration organic acid solution rinsing, mean TPC, TCC, and ECC on carcass surfaces were 3.8 to 7.1, 1.5 to 3.7, and 1.0 to 3.0, respectively, while corresponding populations following a 24 to 36 h chilling period were 2.3 to 5.3, 0.9 to 1.3, and 0.9, respectively. The results support the concept of using sequential decontamination processes in beef packing plants as a means of improving the microbiological quality of beef carcasses.

  14. Planetary resources and astroecology. Planetary microcosm models of asteroid and meteorite interiors: electrolyte solutions and microbial growth--implications for space populations and panspermia.

    PubMed

    Mautner, Michael N

    2002-01-01

    Planetary microcosms were constructed using extracts from meteorites that simulate solutions in the pores of carbonaceous chondrites. The microcosms were found to support the growth of complex algal and microbial populations. Such astroecology experiments demonstrate how a diverse ecosystem could exist in fluids within asteroids, and in meteorites that land on aqueous planets. The microcosm solutions were obtained by extracting nutrient electrolytes under natural conditions from powders of the Allende (CV3) and Murchison (CM2) meteorites at low (0.02 g/ml) and high (10.0 g/ml) solid/solution ratios. The latter solutions contain > 3 mol/L electrolytes and about 10 g/L organics, that simulate natural fluids in asteroids during aqueous alteration and in the pores of meteorites, which can help prebiotic synthesis and the survival of early microorganisms. These solutions and wet solids were in fact found to support complex self-sustaining microbial communities with populations of 4 x 10(5) algae and 6 x 10(6) bacteria and fungi for long periods (> 8 months). The results show that planetary microcosms based on meteorites can: assay the fertilities of planetary materials; identify space bioresources; target astrobiology exploration; and model past and future space-based ecosystems. The results show that bioresources in the carbonaceous asteroids can sustain a biomass of 10(18) kg, comprising 10(32) microorganisms and a human population of 10(14). The results also suggest that protoplanetary nebulae can support and disperse microorganisms and can be therefore effective environments for natural and directed panspermia.

  15. Differential Incorporation of Carbon Substrates among Microbial Populations Identified by Field-Based, DNA Stable-Isotope Probing in South China Sea.

    PubMed

    Zhang, Yao; Deng, Wenchao; Xie, Xiabing; Jiao, Nianzhi

    2016-01-01

    To determine the adapted microbial populations to variant dissolved organic carbon (DOC) sources in the marine environment and improve the understanding of the interaction between microorganisms and marine DOC pool, field-based incubation experiments were carried out using supplemental 13C-labeled typical substrates D-glucose and D-glucosamine (D-Glc and D-GlcN, respectively), which are two important components in marine DOC pool in the South China Sea. 13C- and 12C-DNA were then fractionated by ultracentrifugation and the microbial community was analyzed by terminal-restriction fragment length polymorphism and 454 pyrosequencing of 16S rRNA gene. 12C-DNA-based communities showed relatively high similarities with their corresponding in situ communities, and their bacterial diversities were generally higher than 13C-DNA-based counterparts. Distinct differences in community composition were found between 13C- and 12C-DNA-based communities and between two substrate-supplemented 13C-DNA-based communities; these differences distinctly varied with depth and site. In most cases, there were more genera with relative abundances of >0.1% in D-Glc-incorporating communities than in D-GlcN-incorporating communities. The Roseobacter clade was one of the prominent actively substrate-incorporating bacterial populations in all 13C-DNA-based communities. Vibrio was another prominent actively D-GlcN-incorporating bacterial population in most incubations. However notably, different OTUs dominated this clade or genus in different treatments at different depths. Altogether, these results suggested that there were taxa-specific differences in DOC assimilations and, moreover, their differences varied among the typical water masses, which could have been caused by the variant compositions of original bacterial communities from different hydrological environments. This implies that ecologically, the levels of labile or recalcitrance of DOC can be maintained only in a specific environmental

  16. Differential Incorporation of Carbon Substrates among Microbial Populations Identified by Field-Based, DNA Stable-Isotope Probing in South China Sea.

    PubMed

    Zhang, Yao; Deng, Wenchao; Xie, Xiabing; Jiao, Nianzhi

    2016-01-01

    To determine the adapted microbial populations to variant dissolved organic carbon (DOC) sources in the marine environment and improve the understanding of the interaction between microorganisms and marine DOC pool, field-based incubation experiments were carried out using supplemental 13C-labeled typical substrates D-glucose and D-glucosamine (D-Glc and D-GlcN, respectively), which are two important components in marine DOC pool in the South China Sea. 13C- and 12C-DNA were then fractionated by ultracentrifugation and the microbial community was analyzed by terminal-restriction fragment length polymorphism and 454 pyrosequencing of 16S rRNA gene. 12C-DNA-based communities showed relatively high similarities with their corresponding in situ communities, and their bacterial diversities were generally higher than 13C-DNA-based counterparts. Distinct differences in community composition were found between 13C- and 12C-DNA-based communities and between two substrate-supplemented 13C-DNA-based communities; these differences distinctly varied with depth and site. In most cases, there were more genera with relative abundances of >0.1% in D-Glc-incorporating communities than in D-GlcN-incorporating communities. The Roseobacter clade was one of the prominent actively substrate-incorporating bacterial populations in all 13C-DNA-based communities. Vibrio was another prominent actively D-GlcN-incorporating bacterial population in most incubations. However notably, different OTUs dominated this clade or genus in different treatments at different depths. Altogether, these results suggested that there were taxa-specific differences in DOC assimilations and, moreover, their differences varied among the typical water masses, which could have been caused by the variant compositions of original bacterial communities from different hydrological environments. This implies that ecologically, the levels of labile or recalcitrance of DOC can be maintained only in a specific environmental

  17. Temperature and solids retention time control microbial population dynamics and volatile fatty acid production in replicated anaerobic digesters.

    PubMed

    Vanwonterghem, Inka; Jensen, Paul D; Rabaey, Korneel; Tyson, Gene W

    2015-02-16

    Anaerobic digestion is a widely used technology for waste stabilization and generation of biogas, and has recently emerged as a potentially important process for the production of high value volatile fatty acids (VFAs) and alcohols. Here, three reactors were seeded with inoculum from a stably performing methanogenic digester, and selective operating conditions (37°C and 55°C; 12 day and 4 day solids retention time) were applied to restrict methanogenesis while maintaining hydrolysis and fermentation. Replicated experiments performed at each set of operating conditions led to reproducible VFA production profiles which could be correlated with specific changes in microbial community composition. The mesophilic reactor at short solids retention time showed accumulation of propionate and acetate (42 ± 2% and 15 ± 6% of CODhydrolyzed, respectively), and dominance of Fibrobacter and Bacteroidales. Acetate accumulation (>50% of CODhydrolyzed) was also observed in the thermophilic reactors, which were dominated by Clostridium. Under all tested conditions, there was a shift from acetoclastic to hydrogenotrophic methanogenesis, and a reduction in methane production by >50% of CODhydrolyzed. Our results demonstrate that shortening the SRT and increasing the temperature are effective strategies for driving microbial communities towards controlled production of high levels of specific volatile fatty acids.

  18. Effect of decontamination agents on the microbial population, sensorial quality, and nutrient content of grated carrots (Daucus carota L.).

    PubMed

    Vandekinderen, Isabelle; Van Camp, John; Devlieghere, Frank; Veramme, Kim; Denon, Quenten; Ragaert, Peter; De Meulenaer, Bruno

    2008-07-23

    Several decontamination agents including water, sodium hypochlorite, peroxyacetic acid, neutral electrolyzed oxidizing water, and chlorine dioxide gas were tested for their effectiveness to reduce the natural microflora on grated carrots. Microbial reductions of the total aerobic count obtained after the different treatments varied between 0.11 and 3.29 log colony-forming units (cfu)/g. Whether or not a decontamination step induced significant changes in the sensory attributes of grated carrots is highly dependent on the type and concentration of disinfectant. To maintain the nutritional value, the influence of the decontamination agents on carotenoid content, alpha-tocopherol content, total phenols, and antioxidant capacity was studied. Besides the part of the nutrients that was leached away from the cutting areas by water, the nutrient losses caused by adding sanitizers were rather limited. Compared with the untreated carrots alpha-tocopherol content was, however, significantly reduced when 250 ppm of peroxyacetic acid (-80%) or 200 ppm of sodium hypochlorite (-59%) was used. Additional losses in carotenoid content were caused by contact with chlorine dioxide gas (-9%). On the condition of an optimized decontamination process toward time and concentration, the microbial quality of fresh-cut carrots could be improved without negatively influencing their sensory quality and nutrient content.

  19. Temperature and solids retention time control microbial population dynamics and volatile fatty acid production in replicated anaerobic digesters

    PubMed Central

    Vanwonterghem, Inka; Jensen, Paul D.; Rabaey, Korneel; Tyson, Gene W.

    2015-01-01

    Anaerobic digestion is a widely used technology for waste stabilization and generation of biogas, and has recently emerged as a potentially important process for the production of high value volatile fatty acids (VFAs) and alcohols. Here, three reactors were seeded with inoculum from a stably performing methanogenic digester, and selective operating conditions (37°C and 55°C; 12 day and 4 day solids retention time) were applied to restrict methanogenesis while maintaining hydrolysis and fermentation. Replicated experiments performed at each set of operating conditions led to reproducible VFA production profiles which could be correlated with specific changes in microbial community composition. The mesophilic reactor at short solids retention time showed accumulation of propionate and acetate (42 ± 2% and 15 ± 6% of CODhydrolyzed, respectively), and dominance of Fibrobacter and Bacteroidales. Acetate accumulation (>50% of CODhydrolyzed) was also observed in the thermophilic reactors, which were dominated by Clostridium. Under all tested conditions, there was a shift from acetoclastic to hydrogenotrophic methanogenesis, and a reduction in methane production by >50% of CODhydrolyzed. Our results demonstrate that shortening the SRT and increasing the temperature are effective strategies for driving microbial communities towards controlled production of high levels of specific volatile fatty acids. PMID:25683239

  20. Iron Kinetics and Evolution of Microbial Populations in Low-pH, Ferrous Iron-Oxidizing Bioreactors.

    PubMed

    Jones, Rose M; Johnson, D Barrie

    2016-08-01

    Iron-rich, acidic wastewaters are commonplace pollutants associated with metal and coal mining. Continuous-flow bioreactors were commissioned and tested for their capacities to oxidize ferrous iron in synthetic and actual acid mine drainage waters using (initially) pure cultures of the recently described acidophilic, iron-oxidizing heterotrophic bacterium Acidithrix ferrooxidans grown in the presence of glucose and yeast extract. The bioreactors became rapidly colonized by this bacterium, which formed macroscopic streamer growths in the flowing waters. Over 97% of ferrous iron in pH 2.0-2.2 synthetic mine water was oxidized (at up to 225 mg L(-1) h(-1)) at dilution rates (D) of 0.6 h(-1). Rates of iron oxidation decreased with pH but were still significant, with influent liquors as low as pH 1.37. When fed with actual mine water, >90% of ferrous iron was oxidized at D values of 0.4 h(-1), and microbial communities within the bioreactors changed over time, with Atx. ferrooxidans becoming increasingly displaced by the autotrophic iron-oxidizing acidophiles Ferrovum myxofaciens, Acidithiobacillus ferrivorans, and Leptospirillum ferrooxidans (which were all indigenous to the mine water), although this did not have a negative impact on net ferrous-iron oxidation. The results confirmed the potential of using a heterotrophic acidophile to facilitate the rapid commissioning of iron-oxidizing bioreactors and illustrated how microbial communities within them can evolve without compromising the performances of the bioreactors. PMID:27377871

  1. Microbial populations and hydrocarbon biodegradation potentials in fertilized shoreline sediments affected by the T/V Exxon Valdez oil spill.

    PubMed

    Lindstrom, J E; Prince, R C; Clark, J C; Grossman, M J; Yeager, T R; Braddock, J F; Brown, E J

    1991-09-01

    The effort of clean up the T/V Exxon Valdez oil spill in Prince William Sound, Alaska, included the use of fertilizers to accelerate natural microbial degradation of stranded oil. A program to monitor various environmental parameters associated with this technique took place during the summer of 1990. Microbiological assays for numbers of heterotrophic and oil-degrading microbes and their hydrocarbon mineralization potentials were performed in support of this program. Fertilizer addition resulted in higher hexadecane and phenanthrene mineralization potentials on treated plots than on untreated reference plots. Microbial numbers in treated and reference surface sediments were not significantly different immediately after the first nutrient application in May 1990. However, subsurface sediments from treated plots had higher numbers of hydrocarbon degraders than did reference sediments shortly after treatment. The second application of fertilizer, later in summer, resulted in surface and subsurface increases in numbers of hydrocarbon degraders with respect to reference sediments at two of the three study sites. Elevated mineralization potentials, coupled with increased numbers of hydrocarbon degraders, indicated that natural hydrocarbon biodegradation was enhanced. However, these microbiological measurements alone are not sufficient to determine in situ rates of crude oil biodegradation. PMID:1662935

  2. Microbial populations and hydrocarbon biodegradation potentials in fertilized shoreline sediments affected by the T/V Exxon Valdez oil spill

    SciTech Connect

    Lindstrom, J.E.; Yeager, T.R.; Braddock, J.F.; Brown, E.J. ); Prince, R.C.; Grossman, M.J. ); Clark, J.C. )

    1991-09-01

    The effort to clean up the T/V Exxon Valdez oil spill in Prince William Sound, Alaska, included the use of fertilizers to accelerate natural microbial degradation of stranded oil. A program to monitor various environmental parameter associated with this technique took place during the summer of 1990. Microbiological assays for numbers of heterotrophic and oil-degrading microbes and their hydrocarbon mineralization potentials were performed in support of this program. Fertilizer addition resulted in higher hexadecane and phenanthrene mineralization potentials on treated plots than on untreated reference plots. Microbial numbers in treated and reference surface sediments were not significantly different immediately after the first nutrient application in May 1990. However, subsurface sediments different immediately after the first nutrient application in May 1990. However, subsurface sediments from treated plots had higher numbers of hydrocarbon degraders than did reference sediments shortly after treatment. The second application of fertilizer, later in summer, resulted in surface and subsurface increases in numbers of hydrocarbon degraders with respect to reference sediments at two of three study sites. Elevated mineralization potentials, coupled with increased numbers of hydrocarbon degraders, indicated that natural hydrocarbon biodegradation was enhanced. However, these microbiological measurements alone are not sufficient to determine in situ rates of crude oil biodegradation.

  3. Microbial populations and hydrocarbon biodegradation potentials in fertilized shoreline sediments affected by the T/V Exxon Valdez oil spill.

    PubMed

    Lindstrom, J E; Prince, R C; Clark, J C; Grossman, M J; Yeager, T R; Braddock, J F; Brown, E J

    1991-09-01

    The effort of clean up the T/V Exxon Valdez oil spill in Prince William Sound, Alaska, included the use of fertilizers to accelerate natural microbial degradation of stranded oil. A program to monitor various environmental parameters associated with this technique took place during the summer of 1990. Microbiological assays for numbers of heterotrophic and oil-degrading microbes and their hydrocarbon mineralization potentials were performed in support of this program. Fertilizer addition resulted in higher hexadecane and phenanthrene mineralization potentials on treated plots than on untreated reference plots. Microbial numbers in treated and reference surface sediments were not significantly different immediately after the first nutrient application in May 1990. However, subsurface sediments from treated plots had higher numbers of hydrocarbon degraders than did reference sediments shortly after treatment. The second application of fertilizer, later in summer, resulted in surface and subsurface increases in numbers of hydrocarbon degraders with respect to reference sediments at two of the three study sites. Elevated mineralization potentials, coupled with increased numbers of hydrocarbon degraders, indicated that natural hydrocarbon biodegradation was enhanced. However, these microbiological measurements alone are not sufficient to determine in situ rates of crude oil biodegradation.

  4. Comparison of indigenous and exogenous microbial populations during slurry phase biodegradation of long-term hydrocarbon-contaminated soil.

    PubMed

    Aburto-Medina, Arturo; Adetutu, Eric M; Aleer, Sam; Weber, John; Patil, Sayali S; Sheppard, Petra J; Ball, Andrew S; Juhasz, Albert L

    2012-11-01

    In this study, a number of slurry-phase strategies were trialled over a 42 day period in order to determine the efficacy of bioremediation for long-term hydrocarbon-contaminated soil (145 g kg(-1) C(10)-C(40)). The addition of activated sludge and nutrients to slurries (bioaugmentation) resulted in enhanced hydrocarbon removal (51.6 ± 8.5 %) compared to treatments receiving only nutrients (enhanced natural attenuation [ENA]; 41.3 ± 6.4 %) or no amendments (natural attenuation; no significant hydrocarbon removal, P < 0.01). This data suggests that the microbial community in the activated sludge inoculum contributed to the enhanced removal of hydrocarbons in ENA slurries. Microbial diversity in slurries was monitored using DGGE with dominant bands excised and sequenced for identification. Applying the different bioremediation strategies resulted in the formation of four distinct community clusters associated with the activated sludge (inoculum), bioaugmentation strategy at day 0, bioaugmentation strategy at weeks 2-6 and slurries with autoclaved sludge and nutrient additions (bioaugmentation negative control). While hydrocarbon-degrading bacteria genera (e.g. Aquabacterium and Haliscomenobacter) were associated with the hydrocarbon-contaminated soil, bioaugmentation of soil slurries with activated sludge resulted in the introduction of bacteria associated with hydrocarbon degradation (Burkholderiales order and Klebsiella genera) which presumably contributed to the enhanced efficacy for this slurry strategy.

  5. Temperature and solids retention time control microbial population dynamics and volatile fatty acid production in replicated anaerobic digesters

    NASA Astrophysics Data System (ADS)

    Vanwonterghem, Inka; Jensen, Paul D.; Rabaey, Korneel; Tyson, Gene W.

    2015-02-01

    Anaerobic digestion is a widely used technology for waste stabilization and generation of biogas, and has recently emerged as a potentially important process for the production of high value volatile fatty acids (VFAs) and alcohols. Here, three reactors were seeded with inoculum from a stably performing methanogenic digester, and selective operating conditions (37°C and 55°C 12 day and 4 day solids retention time) were applied to restrict methanogenesis while maintaining hydrolysis and fermentation. Replicated experiments performed at each set of operating conditions led to reproducible VFA production profiles which could be correlated with specific changes in microbial community composition. The mesophilic reactor at short solids retention time showed accumulation of propionate and acetate (42 +/- 2% and 15 +/- 6% of CODhydrolyzed, respectively), and dominance of Fibrobacter and Bacteroidales. Acetate accumulation (>50% of CODhydrolyzed) was also observed in the thermophilic reactors, which were dominated by Clostridium. Under all tested conditions, there was a shift from acetoclastic to hydrogenotrophic methanogenesis, and a reduction in methane production by >50% of CODhydrolyzed. Our results demonstrate that shortening the SRT and increasing the temperature are effective strategies for driving microbial communities towards controlled production of high levels of specific volatile fatty acids.

  6. [Population].

    PubMed

    1979-01-01

    Data on the population of Venezuela between 1975 and 1977 are presented in descriptive tables and graphs. Information is included on the employed population according to category, sex, and type of economic activity, and by sex, age, and area on the employment rate and the total, the economically active, and the unemployed population.

  7. Use of field-based stable isotope probing to identify adapted populations and track carbon flow through a phenol-degrading soil microbial community.

    PubMed

    DeRito, Christopher M; Pumphrey, Graham M; Madsen, Eugene L

    2005-12-01

    The goal of this field study was to provide insight into three distinct populations of microorganisms involved in in situ metabolism of phenol. Our approach measured 13CO2 respired from [13C]phenol and stable isotope probing (SIP) of soil DNA at an agricultural field site. Traditionally, SIP-based investigations have been subject to the uncertainties posed by carbon cross-feeding. By altering our field-based, substrate-dosing methodologies, experiments were designed to look beyond primary degraders to detect trophically related populations in the food chain. Using gas chromatography-mass spectrometry (GC/MS), it was shown that (13)C-labeled biomass, derived from primary phenol degraders in soil, was a suitable growth substrate for other members of the soil microbial community. Next, three dosing regimes were designed to examine active members of the microbial community involved in phenol metabolism in situ: (i) 1 dose of [13C]phenol, (ii) 11 daily doses of unlabeled phenol followed by 1 dose of [13C]phenol, and (iii) 12 daily doses of [13C]phenol. GC/MS analysis demonstrated that prior exposure to phenol boosted 13CO2 evolution by a factor of 10. Furthermore, imaging of 13C-treated soil using secondary ion mass spectrometry (SIMS) verified that individual bacteria incorporated 13C into their biomass. PCR amplification and 16S rRNA gene sequencing of 13C-labeled soil DNA from the 3 dosing regimes revealed three distinct clone libraries: (i) unenriched, primary phenol degraders were most diverse, consisting of alpha-, beta-, and gamma-proteobacteria and high-G+C-content gram-positive bacteria, (ii) enriched primary phenol degraders were dominated by members of the genera Kocuria and Staphylococcus, and (iii) trophically related (carbon cross-feeders) were dominated by members of the genus Pseudomonas. These data show that SIP has the potential to document population shifts caused by substrate preexposure and to follow the flow of carbon through terrestrial microbial

  8. Effect of Saccharomyces cerevisiae on alfalfa nutrient degradation characteristics and rumen microbial populations of steers fed diets with different concentrate-to-forage ratios

    PubMed Central

    2014-01-01

    Live yeast (Saccharomyces cerevisiae) constitutes an effective additive for animal production; its probiotic effect may be related to the concentrate-to-forage ratio (CTFR). The objective of this study was to assess the effects of S. cerevisiae (SC) on fiber degradation and rumen microbial populations in steers fed diets with different levels of dietary concentrate. Ten Simmental × Local crossbred steers (450 ± 50 kg BW) were assigned to a control group or an SC group. Both groups were fed the same basal diet but the SC group received SC supplementation (8 × 109 cfu/h/d through the ruminal fistula) following a two-period crossover design. Each period consisted of four phases, each of which lasted 17 d: 10 d for dietary adaptation, 6 d for degradation study, and 1 d for rumen sample collection. From the 1st to the 4th phase, steers were fed in a stepwise fashion with increasing CTFRs, i.e., 30:70, 50:50, 70:30, and 90:10. The kinetics of dry matter and fiber degradation of alfalfa pellets were evaluated; the rumen microbial populations were detected using real-time PCR. The results revealed no significant (P > 0.05) interactions between dietary CTFR and SC for most parameters. Dietary CTFR had a significant effect (P < 0.01) on degradation characteristics of alfalfa pellets and the copies of rumen microorganism; the increasing concentrate level resulted in linear, quadratic or cubic variation trend for these parameters. SC supplementation significantly (P < 0.05) affected dry matter (DM) and neutral detergent fiber (NDF) degradation rates (cDM, cNDF) and NDF effective degradability (EDNDF). Compared with the control group, there was an increasing trend of rumen fungi and protozoa in SC group (P < 0.1); copies of total bacteria in SC group were significantly higher (P < 0.05). Additionally, percentage of Ruminobacter amylophilus was significantly lower (P < 0.05) but percentage of Selenomonas ruminantium was significantly

  9. Effects of soaking with natural additives in combinations with vacuum or modified atmosphere packaging on microbial populations and shelf life of fresh truffles (Chinese Tuber indicum).

    PubMed

    Miao, Yuzhi; Chen, Cuiping; Ma, Qinqin; Wang, Yiding; Zhang, Xiaoyu; Guo, Fanglan; Li, Wei; Yong, Bin

    2014-10-01

    The objective of this study was to evaluate the relative effects and interactions of combined soaking treatment using citric acid (CTA) and apple polyphenol (APP) at mild heating temperatures for the inactivation of the external and internal microflora (mesophilic aerobic bacteria, mesophilic anaerobic bacteria, and fungi) in Chinese Tuber indicum, as well as to analyze the microbiological and sensory changes under modified atmosphere packaging (MAP)- and vacuum atmosphere packaging (VAC)-packed Chinese T. indicum stored at 4 °C for up to 55 d. Chinese T. indicum was soaked with CTA and APP alone or in combination for 10, 20, and 30 min at 35, 45, and 55 °C. A disinfection method using CTA and APP (3% CTA + 3% APP for 20 min at 45 °C) was obtained. Under this set of combination, the experimental values of microbial counts of mesophilic aerobic bacteria, mesophilic anaerobic bacteria, and fungi were 2.31 ± 0.4 log CFU/g, <1.0 log CFU/g, and <1.0 log CFU/g, respectively. Through the analysis of sensory qualities and microbial populations for MAP- or VAC-packed Chinese T. indicum, the shelf life of soaked truffles was prolonged to 45 or 40 d, respectively. The synergistic effect of CTA and APP may provide valuable insight into the reduction of microorganisms on fresh truffles.

  10. Virulence-associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach.

    PubMed

    Durso, Lisa M; Harhay, Gregory P; Bono, James L; Smith, Timothy P L

    2011-02-01

    The bovine fecal microbiota impacts human food safety as well as animal health. Although the bacteria of cattle feces have been well characterized using culture-based and culture-independent methods, techniques have been lacking to correlate total community composition with community function. We used high throughput sequencing of total DNA extracted from fecal material to characterize general community composition and examine the repertoire of microbial genes present in beef cattle feces, including genes associated with antibiotic resistance and bacterial virulence. Results suggest that traditional 16S sequencing using "universal" primers to generate full-length sequence may under represent Acitinobacteria and Proteobacteria. Over eight percent (8.4%) of the sequences from our beef cattle fecal pool sample could be categorized as virulence genes, including a suite of genes associated with resistance to antibiotic and toxic compounds (RATC). This is a higher proportion of virulence genes found in Sargasso sea, chicken cecum, and cow rumen samples, but comparable to the proportion found in Antarctic marine derived lake, human fecal, and farm soil samples. The quantitative nature of metagenomic data, combined with the large number of RATC classes represented in samples from widely different habitats indicates that metagenomic data can be used to track relative amounts of antibiotic resistance genes in individual animals over time. Consequently, these data can be used to generate sample-specific and temporal antibiotic resistance gene profiles to facilitate an understanding of the ecology of the microbial communities in each habitat as well as the epidemiology of antibiotic resistant gene transport between and among habitats.

  11. Virulence-associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach.

    PubMed

    Durso, Lisa M; Harhay, Gregory P; Bono, James L; Smith, Timothy P L

    2011-02-01

    The bovine fecal microbiota impacts human food safety as well as animal health. Although the bacteria of cattle feces have been well characterized using culture-based and culture-independent methods, techniques have been lacking to correlate total community composition with community function. We used high throughput sequencing of total DNA extracted from fecal material to characterize general community composition and examine the repertoire of microbial genes present in beef cattle feces, including genes associated with antibiotic resistance and bacterial virulence. Results suggest that traditional 16S sequencing using "universal" primers to generate full-length sequence may under represent Acitinobacteria and Proteobacteria. Over eight percent (8.4%) of the sequences from our beef cattle fecal pool sample could be categorized as virulence genes, including a suite of genes associated with resistance to antibiotic and toxic compounds (RATC). This is a higher proportion of virulence genes found in Sargasso sea, chicken cecum, and cow rumen samples, but comparable to the proportion found in Antarctic marine derived lake, human fecal, and farm soil samples. The quantitative nature of metagenomic data, combined with the large number of RATC classes represented in samples from widely different habitats indicates that metagenomic data can be used to track relative amounts of antibiotic resistance genes in individual animals over time. Consequently, these data can be used to generate sample-specific and temporal antibiotic resistance gene profiles to facilitate an understanding of the ecology of the microbial communities in each habitat as well as the epidemiology of antibiotic resistant gene transport between and among habitats. PMID:21167876

  12. Emergence of resistance and resistance management in field populations of tropical Culex quinquefasciatus to the microbial control agent Bacillus sphaericus.

    PubMed

    Mulla, Mir S; Thavara, Usavadee; Tawatsin, Apiwat; Chomposri, Jakkrawarn; Su, Tianyun

    2003-03-01

    In recent years, highly potent mosquitocidal strains of the microbial agent Bacillus sphaericus (Bsph) have been isolated and developed for the control of mosquito larvae around the world. Laboratory selection experiments with the most active strains and their use in large-scale operational mosquito control programs resulted in the emergence of resistance in larvae of the Culex pipiens complex. This generated great concern among vector control agencies around the world, who feared reduced efficacy of this highly active larvicidal agent. To address this issue, the current studies were started to find practical strategies for controlling resistant mosquitoes and more importantly to develop resistance management strategies that would prevent or delay development of resistance. We initiated field studies in 3 low-income communities in Nonthaburi Province, Thailand. In 1 of the communities, larvae of Culex quinquefasciatus that were highly resistant (>125,000-fold) to Bsph strain 2362 were successfully controlled with applications of Bacillus thuringiensis var. israelensis (Bti) alone or in combination with Bsph. To prevent or delay resistance to Bsph, 2 other sites were selected, 1 treated with Bsph 2362 alone and the other treated with a mixture of Bsph 2362 and Bti. Mosquitoes treated with Bsph 2362 alone showed some resistance by the 9th treatment and almost complete failure of control occurred by the 17th treatment. After 9 treatments with the mixture over a 9-month period at another site, no noticeable change in susceptibility to Bsph was detected. During this period, the site treated with Bsph alone required 19 treatments, whereas the site treated with mixtures took only 9 treatments because of slower resurgence of larvae at the site treated with the mixture than at the site treated with Bsph alone. This is the 1st field evidence for delay or prevention of resistance to microbial agents in larval Cx. quinquefasciatus by using mixtures of Bti and Bsph. Further

  13. Populations of selected microbial and fungal species growing on the surface of rape seeds following treatment with desiccants or plant growth regulators.

    PubMed

    Frac, Magdalena; Jezierska-Tys, Stefania; Tys, Jerzy

    2010-01-01

    The aim of this study was to determine the effects of desiccants and plant growth regulators on selected microbial species affecting rape seeds, with special emphasis on the growth of fungi and identification of the genus and species composition. The experimental material in the study was seeds of winter rape cv. Californium that were collected from the field during combine harvest. The chemical agents applied, both desiccants and growth regulators, generally decreased the populations of bacteria occurring on the surface of rape seeds. The responses of fungi depended upon the type of agent applied and were manifested as either stimulation or inhibition of the growth of the fungal species. The fungi isolated from the surface of rape seeds were characteristic of those found in the field environment (Cladosporium and Penicillium) and typical for those present on the surface of rape seeds (Alternaria).

  14. Population dynamics of transgenic strain Escherichia coli Z905/pPHL7 in freshwater and saline lake water microcosms with differing microbial community structures

    NASA Technical Reports Server (NTRS)

    Popova, L. Yu; Kargatova, T. V.; Ganusova, E. E.; Lobova, T. I.; Boyandin, A. N.; Mogilnaya, O. A.; Pechurkin, N. S.

    2005-01-01

    Populations of Escherichia coli Z905/pPHL7, a transgenic microorganism, were heterogenic in the expression of plasmid genes when adapting to the conditions of water microcosms of various mineralization levels and structure of microbial community. This TM has formed two subpopulations (ampicillin-resistant and ampicillin-sensitive) in every microcosm. Irrespective of mineralization level of a microcosm, when E. coli Z905/pPHL7 alone was introduced, the ampicillin-resistant subpopulation prevailed, while introduction of the TM together with indigenous bacteria led to the dominance of the ampicillin-sensitive subpopulation. A high level of lux gene expression maintained longer in the freshwater microcosms than in sterile saline lake water microcosms. A horizontal gene transfer has been revealed between the jointly introduced TM and Micrococcus sp. 9/pSH1 in microcosms with the Lake Shira sterile water. c2005 COSPAR. Published by Elsevier Ltd. All rights reserved.

  15. Ocean microbial metagenomics

    NASA Astrophysics Data System (ADS)

    Kerkhof, Lee J.; Goodman, Robert M.

    2009-09-01

    Technology for accessing the genomic DNA of microorganisms, directly from environmental samples without prior cultivation, has opened new vistas to understanding microbial diversity and functions. Especially as applied to soils and the oceans, environments on Earth where microbial diversity is vast, metagenomics and its emergent approaches have the power to transform rapidly our understanding of environmental microbiology. Here we explore select recent applications of the metagenomic suite to ocean microbiology.

  16. Distinct microbial populations are tightly linked to the profile of dissolved iron in the methanic sediments of the Helgoland mud area, North Sea

    PubMed Central

    Oni, Oluwatobi; Miyatake, Tetsuro; Kasten, Sabine; Richter-Heitmann, Tim; Fischer, David; Wagenknecht, Laura; Kulkarni, Ajinkya; Blumers, Mathias; Shylin, Sergii I.; Ksenofontov, Vadim; Costa, Benilde F. O.; Klingelhöfer, Göstar; Friedrich, Michael W.

    2015-01-01

    Iron reduction in subseafloor sulfate-depleted and methane-rich marine sediments is currently a subject of interest in subsurface geomicrobiology. While iron reduction and microorganisms involved have been well studied in marine surface sediments, little is known about microorganisms responsible for iron reduction in deep methanic sediments. Here, we used quantitative PCR-based 16S rRNA gene copy numbers and pyrosequencing-based relative abundances of bacteria and archaea to investigate covariance between distinct microbial populations and specific geochemical profiles in the top 5 m of sediment cores from the Helgoland mud area, North Sea. We found that gene copy numbers of bacteria and archaea were specifically higher around the peak of dissolved iron in the methanic zone (250–350 cm). The higher copy numbers at these depths were also reflected by the relative sequence abundances of members of the candidate division JS1, methanogenic and Methanohalobium/ANME-3 related archaea. The distribution of these populations was strongly correlated to the profile of pore-water Fe2+ while that of Desulfobacteraceae corresponded to the pore-water sulfate profile. Furthermore, specific JS1 populations also strongly co-varied with the distribution of Methanosaetaceae in the methanic zone. Our data suggest that the interplay among JS1 bacteria, methanogenic archaea and Methanohalobium/ANME-3-related archaea may be important for iron reduction and methane cycling in deep methanic sediments of the Helgoland mud area and perhaps in other methane-rich depositional environments. PMID:25983723

  17. Microbial Populations in Naked Neck Chicken Ceca Raised on Pasture Flock Fed with Commercial Yeast Cell Wall Prebiotics via an Illumina MiSeq Platform.

    PubMed

    Park, Si Hong; Lee, Sang In; Ricke, Steven C

    2016-01-01

    Prebiotics are non-digestible carbohydrate dietary supplements that selectively stimulate the growth of one or more beneficial bacteria in the gastrointestinal tract of the host. These bacteria can inhibit colonization of pathogenic bacteria by producing antimicrobial substances such as short chain fatty acids (SCFAs) and competing for niches with pathogens within the gut. Pasture flock chickens are generally raised outdoors with fresh grass, sunlight and air, which represents different environmental growth conditions compared to conventionally raised chickens. The purpose of this study was to evaluate the difference in microbial populations from naked neck chicken ceca fed with commercial prebiotics derived from brewer's yeast cell wall via an Illumina MiSeq platform. A total of 147 day-of-hatch naked neck chickens were distributed into 3 groups consisted of 1) C: control (no prebiotic), 2) T1: Biolex® MB40 with 0.2%, and 3) T2: Leiber® ExCel with 0.2%, consistently supplemented prebiotics during the experimental period. At 8 weeks, a total of 15 birds from each group were randomly selected and ceca removed for DNA extraction. The Illumina Miseq platform based on V4 region of 16S rRNA gene was applied for microbiome analysis. Both treatments exhibited limited impact on the microbial populations at the phylum level, with no significant differences in the OTU number of Bacteroidetes among groups and an increase of Proteobacteria OTUs for the T1 (Biolex® MB40) group. In addition there was a significant increase of genus Faecalibacterium OTU, phylum Firmicutes. According to the development of next generation sequencing (NGS), microbiome analysis based on 16S rRNA gene proved to be informative on the prebiotic impact on poultry gut microbiota in pasture-raised naked neck birds.

  18. The influence of mineral fertilizer combined with a nitrification inhibitor on microbial populations and activities in calcareous Uzbekistanian soil under cotton cultivation.

    PubMed

    Egamberdiyeva, D; Mamiev, M; Poberejskaya, S K

    2001-10-30

    Application of fertilizers combined with nitrification inhibitors affects soil microbial biomass and activity. The objective of this research was to determine the effects of fertilizer application combined with the nitrification inhibitor potassium oxalate (PO) on soil microbial population and activities in nitrogen-poor soil under cotton cultivation in Uzbekistan. Fertilizer treatments were N as urea, P as ammophos, and K as potassium chloride. The nitrification inhibitor PO was added to urea and ammophos at the rate of 2%. Three treatments--N200 P140 K60 (T1), N200 PO P140 K60 (T2), and N200 P140 PO K60 (T3) mg kg(-1) soil--were applied for this study. The control (C) was without fertilizer and PO. The populations of oligotrophic bacteria, ammonifying bacteria, nitrifying bacteria, denitrifying bacteria, mineral assimilating bacteria, oligonitrophilic bacteria, and bacteria group Azotobacter were determined by the most probable number method. The treatments T2 and T3 increased the number of oligonitrophilic bacteria and utilization mineral forms of nitrogen on the background of reducing number of ammonifying bacteria. T2 and T3 also decreased the number of nitrifying bacteria, denitrifying bacteria, and net nitrification. In conclusion, our experiments showed that PO combined with mineral fertilizer is one of the most promising compounds for inhibiting nitrification rate, which was reflected in the increased availability and efficiency of fertilizer nitrogen to the cotton plants. PO combined with mineral fertilizer has no negative effects on nitrogen-fixing bacteria Azotobacter and oligo-nitrophilic bacteria.

  19. Microbial Populations in Naked Neck Chicken Ceca Raised on Pasture Flock Fed with Commercial Yeast Cell Wall Prebiotics via an Illumina MiSeq Platform.

    PubMed

    Park, Si Hong; Lee, Sang In; Ricke, Steven C

    2016-01-01

    Prebiotics are non-digestible carbohydrate dietary supplements that selectively stimulate the growth of one or more beneficial bacteria in the gastrointestinal tract of the host. These bacteria can inhibit colonization of pathogenic bacteria by producing antimicrobial substances such as short chain fatty acids (SCFAs) and competing for niches with pathogens within the gut. Pasture flock chickens are generally raised outdoors with fresh grass, sunlight and air, which represents different environmental growth conditions compared to conventionally raised chickens. The purpose of this study was to evaluate the difference in microbial populations from naked neck chicken ceca fed with commercial prebiotics derived from brewer's yeast cell wall via an Illumina MiSeq platform. A total of 147 day-of-hatch naked neck chickens were distributed into 3 groups consisted of 1) C: control (no prebiotic), 2) T1: Biolex® MB40 with 0.2%, and 3) T2: Leiber® ExCel with 0.2%, consistently supplemented prebiotics during the experimental period. At 8 weeks, a total of 15 birds from each group were randomly selected and ceca removed for DNA extraction. The Illumina Miseq platform based on V4 region of 16S rRNA gene was applied for microbiome analysis. Both treatments exhibited limited impact on the microbial populations at the phylum level, with no significant differences in the OTU number of Bacteroidetes among groups and an increase of Proteobacteria OTUs for the T1 (Biolex® MB40) group. In addition there was a significant increase of genus Faecalibacterium OTU, phylum Firmicutes. According to the development of next generation sequencing (NGS), microbiome analysis based on 16S rRNA gene proved to be informative on the prebiotic impact on poultry gut microbiota in pasture-raised naked neck birds. PMID:26992104

  20. Microbial Populations in Naked Neck Chicken Ceca Raised on Pasture Flock Fed with Commercial Yeast Cell Wall Prebiotics via an Illumina MiSeq Platform

    PubMed Central

    Park, Si Hong; Lee, Sang In; Ricke, Steven C.

    2016-01-01

    Prebiotics are non-digestible carbohydrate dietary supplements that selectively stimulate the growth of one or more beneficial bacteria in the gastrointestinal tract of the host. These bacteria can inhibit colonization of pathogenic bacteria by producing antimicrobial substances such as short chain fatty acids (SCFAs) and competing for niches with pathogens within the gut. Pasture flock chickens are generally raised outdoors with fresh grass, sunlight and air, which represents different environmental growth conditions compared to conventionally raised chickens. The purpose of this study was to evaluate the difference in microbial populations from naked neck chicken ceca fed with commercial prebiotics derived from brewer’s yeast cell wall via an Illumina MiSeq platform. A total of 147 day-of-hatch naked neck chickens were distributed into 3 groups consisted of 1) C: control (no prebiotic), 2) T1: Biolex® MB40 with 0.2%, and 3) T2: Leiber® ExCel with 0.2%, consistently supplemented prebiotics during the experimental period. At 8 weeks, a total of 15 birds from each group were randomly selected and ceca removed for DNA extraction. The Illumina Miseq platform based on V4 region of 16S rRNA gene was applied for microbiome analysis. Both treatments exhibited limited impact on the microbial populations at the phylum level, with no significant differences in the OTU number of Bacteroidetes among groups and an increase of Proteobacteria OTUs for the T1 (Biolex® MB40) group. In addition there was a significant increase of genus Faecalibacterium OTU, phylum Firmicutes. According to the development of next generation sequencing (NGS), microbiome analysis based on 16S rRNA gene proved to be informative on the prebiotic impact on poultry gut microbiota in pasture-raised naked neck birds. PMID:26992104

  1. Characterization of microbial populations across geochemical and lithological boundaries in urban lake sediments under environmental change in Minneapolis-St. Paul

    NASA Astrophysics Data System (ADS)

    Gilbertson, M.; Harrison, B. K.; Flood, B. E.; Myrbo, A.; Bailey, J. V.

    2013-12-01

    The characterization of microbial communities within urban lake sediments may offer a promising method to observe changes in lake geochemistry due to human impact. By mapping the abundances and diversity of microorganisms through the uppermost meter of sediment in three distinctive Minneapolis-St. Paul lakes (Brownie Lake and Twin Lake, both meromictic, and oligomictic Lake McCarrons) using 16S rRNA characterization, our aim was to observe changes in microbial populations across steep geochemical and lithological gradients. Lake McCarrons underwent a process of eutrophication and a shift to bottom water anoxia beginning around 1910 due mostly to agricultural run-off. This shift greatly increased the preservation potential of seasonal sedimentation and finely laminated varve accumulation. The onset of meromixis in Brownie Lake in ~1915 is abrupt and has been attributed to a sudden drop in water level. Twin Lake is perennially meromictic due to the topography of the watershed. The three lakes were sampled by collecting freeze cores in July, 2012 (McCarrons, Brownie) and February, 2013 (Twin) at the deepest locations beneath anoxic to hypoxic bottom waters. The cores were then subsampled with high resolution techniques at places of interest: within individual lamina, across mass flow deposits, and near the onset of laminae preservation (beginning of oxygen-depleted bottom waters). Terminal Restriction Fragment Length Polymorphism (T-RFLP) allows for comparison of the microbial assemblages throughout the sediment columns of each lake and from lake to lake, with a focus on the horizons mentioned previously. The microbial assemblages present in specific horizons are often introduced via sedimentation and are partially derived from community composition at the time of sedimentation. T-RFLP analyses are complemented by mineralogical and lithological descriptions. The lakes have each been subject to their own set of variables and inputs. Brownie Lake contains high levels of

  2. Population.

    ERIC Educational Resources Information Center

    International Planned Parenthood Federation, London (England).

    In an effort to help meet the growing interest and concern about the problems created by the rapid growth of population, The International Planned Parenthood Federation has prepared this booklet with the aim of assisting the study of the history and future trends of population growth and its impact on individual and family welfare, national,…

  3. Effect of conventional chemical treatment on the microbial population in a biofouling layer of reverse osmosis systems.

    PubMed

    Bereschenko, L A; Prummel, H; Euverink, G J W; Stams, A J M; van Loosdrecht, M C M

    2011-01-01

    The impact of conventional chemical treatment on initiation and spatiotemporal development of biofilms on reverse osmosis (RO) membranes was investigated in situ using flow cells placed in parallel with the RO system of a full-scale water treatment plant. The flow cells got the same feed (extensively pre-treated fresh surface water) and operational conditions (temperature, pressure and membrane flux) as the full-scale installation. With regular intervals both the full-scale RO membrane modules and the flow cells were cleaned using conventional chemical treatment. For comparison some flow cells were not cleaned. Sampling was done at different time periods of flow cell operation (i.e., 1, 5, 10 and 17 days and 1, 3, 6 and 12 months). The combination of molecular (FISH, DGGE, clone libraries and sequencing) and microscopic (field emission scanning electron, epifluorescence and confocal laser scanning microscopy) techniques made it possible to thoroughly analyze the abundance, composition and 3D architecture of the emerged microbial layers. The results suggest that chemical treatment facilitates initiation and subsequent maturation of biofilm structures on the RO membrane and feed-side spacer surfaces. Biofouling control might be possible only if the cleaning procedures are adapted to effectively remove the (dead) biomass from the RO modules after chemical treatment.

  4. Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments

    PubMed Central

    Musilova, Lucie; Ridl, Jakub; Polivkova, Marketa; Macek, Tomas; Uhlik, Ondrej

    2016-01-01

    Secondary plant metabolites (SPMEs) play an important role in plant survival in the environment and serve to establish ecological relationships between plants and other organisms. Communication between plants and microorganisms via SPMEs contained in root exudates or derived from litter decomposition is an example of this phenomenon. In this review, the general aspects of rhizodeposition together with the significance of terpenes and phenolic compounds are discussed in detail. We focus specifically on the effect of SPMEs on microbial community structure and metabolic activity in environments contaminated by polychlorinated biphenyls (PCBs) and polyaromatic hydrocarbons (PAHs). Furthermore, a section is devoted to a complex effect of plants and/or their metabolites contained in litter on bioremediation of contaminated sites. New insights are introduced from a study evaluating the effects of SPMEs derived during decomposition of grapefruit peel, lemon peel, and pears on bacterial communities and their ability to degrade PCBs in a long-term contaminated soil. The presented review supports the “secondary compound hypothesis” and demonstrates the potential of SPMEs for increasing the effectiveness of bioremediation processes. PMID:27483244

  5. Microbial populations description in Deception Island (Antarctica): exploring the surface and the permafrost using an antibody microrray

    NASA Astrophysics Data System (ADS)

    Blanco, Y.; Prieto-Ballesteros, O.; Gómez, M. J.; Moreno-Paz, M.; García-Villadangos, M.; Rodríguez-Manfredi, J. A.; Cruz-Gil, P.; Sánchez-Román, M.; Rivas, L. A.; Parro, V.

    2012-09-01

    We performed assays with a Life Detector Chip (so called LDChip300) to study on site the microbial diversity on the surface and the permafrost from a Deception Island borehole. LDChip300 contains more than 300 antibodies developed against bacterial and archaeal strains, crude extracts from environmental samples, proteins, peptides and other biological polymers [1,2,3]. Superficial and core permafrost samples were analyzed by sandwich microarray immunoassays (SMI) with LDChip300 by using a cocktail of 300 different fluorescent antibodies. Pyroclasts and rocks from the surface and the top layer of the permafrost showed positive antigen-antibody reactions against Alpha-, Delta- and Gamma-proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, archaeal species and proteins and peptides involved in nitrogen fixation and methanogenic processes, iron homeostasis and ABC transporters. Immunoarray results were validated on site with an oligonucleotide microarray for prokaryotic diversity and then in the laboratory through 16S and 23S rRNA gene sequence analysis, aerobic viable counts and microscopy studies. Those results revealed Acidobacteria, Actinobacteria, Proteobacteria, Bacteroidetes and phototrophs as dominant groups in the top active layer of the Deception Island permafrost [4].

  6. Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments.

    PubMed

    Musilova, Lucie; Ridl, Jakub; Polivkova, Marketa; Macek, Tomas; Uhlik, Ondrej

    2016-01-01

    Secondary plant metabolites (SPMEs) play an important role in plant survival in the environment and serve to establish ecological relationships between plants and other organisms. Communication between plants and microorganisms via SPMEs contained in root exudates or derived from litter decomposition is an example of this phenomenon. In this review, the general aspects of rhizodeposition together with the significance of terpenes and phenolic compounds are discussed in detail. We focus specifically on the effect of SPMEs on microbial community structure and metabolic activity in environments contaminated by polychlorinated biphenyls (PCBs) and polyaromatic hydrocarbons (PAHs). Furthermore, a section is devoted to a complex effect of plants and/or their metabolites contained in litter on bioremediation of contaminated sites. New insights are introduced from a study evaluating the effects of SPMEs derived during decomposition of grapefruit peel, lemon peel, and pears on bacterial communities and their ability to degrade PCBs in a long-term contaminated soil. The presented review supports the "secondary compound hypothesis" and demonstrates the potential of SPMEs for increasing the effectiveness of bioremediation processes. PMID:27483244

  7. Predominant Acidilobus-Like Populations from Geothermal Environments in Yellowstone National Park Exhibit Similar Metabolic Potential in Different Hypoxic Microbial Communities

    PubMed Central

    Jay, Z. J.; Rusch, D. B.; Tringe, S. G.; Bailey, C.; Jennings, R. M.

    2014-01-01

    High-temperature (>70°C) ecosystems in Yellowstone National Park (YNP) provide an unparalleled opportunity to study chemotrophic archaea and their role in microbial community structure and function under highly constrained geochemical conditions. Acidilobus spp. (order Desulfurococcales) comprise one of the dominant phylotypes in hypoxic geothermal sulfur sediment and Fe(III)-oxide environments along with members of the Thermoproteales and Sulfolobales. Consequently, the primary goals of the current study were to analyze and compare replicate de novo sequence assemblies of Acidilobus-like populations from four different mildly acidic (pH 3.3 to 6.1) high-temperature (72°C to 82°C) environments and to identify metabolic pathways and/or protein-encoding genes that provide a detailed foundation of the potential functional role of these populations in situ. De novo assemblies of the highly similar Acidilobus-like populations (>99% 16S rRNA gene identity) represent near-complete consensus genomes based on an inventory of single-copy genes, deduced metabolic potential, and assembly statistics generated across sites. Functional analysis of coding sequences and confirmation of gene transcription by Acidilobus-like populations provide evidence that they are primarily chemoorganoheterotrophs, generating acetyl coenzyme A (acetyl-CoA) via the degradation of carbohydrates, lipids, and proteins, and auxotrophic with respect to several external vitamins, cofactors, and metabolites. No obvious pathways or protein-encoding genes responsible for the dissimilatory reduction of sulfur were identified. The presence of a formate dehydrogenase (Fdh) and other protein-encoding genes involved in mixed-acid fermentation supports the hypothesis that Acidilobus spp. function as degraders of complex organic constituents in high-temperature, mildly acidic, hypoxic geothermal systems. PMID:24162572

  8. Changes of Microbial Population in the Rumen of Dairy Steers as Influenced by Plant Containing Tannins and Saponins and Roughage to Concentrate Ratio

    PubMed Central

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

    2013-01-01

    The objective of this study was to investigate microbial population in the rumen of dairy steers as influenced by supplementing with dietary condensed tannins and saponins and different roughage to concentrate ratios. Four, rumen fistulated dairy steers (Bos indicus) were used in a 2×2 factorial arrangement in a 4×4 Latin square design. The main factors were two roughage to concentrate ratios (R:C, 60:40 and 40:60) and two supplementations of rain tree pod meal (RPM) (0 and 60 g/kg of total DM intake). Chopped 30 g/kg urea treated rice straw was used as a roughage source. All animals received feed according to respective R:C ratios at 25 g/kg body weight. The RPM contained crude tannins and saponins at 84 and 143 g/kg of DM, respectively. It was found that ruminal pH decreased while ruminal temperature increased by a higher concentrate ratio (R:C 40:60) (p<0.05). In contrast, total bacterial, Ruminococus albus and viable proteolytic bacteria were not affected by dietary supplementation. Numbers of fungi, cellulolytic bacteria, Fibrobactor succinogenes and Ruminococus flavefaciens were higher while amylolytic bacteria was lower when steers were fed at 400 g/kg of concentrate. The population of Fibrobactor succinogenes, was found to be higher with RPM supplementation. In addition, the use of real-time PCR technique indicated that the population of protozoa and methanogens were decreased (p<0.05) with supplementation of RPM and with an increasing concentrate ratio. Supplementation of RPM and feeding different concentrate ratios resulted in changing the rumen microbes especially, when the animals were fed at 600 g/kg of concentrate and supplemented with RPM which significantly reduced the protozoa and methanogens population. PMID:25049745

  9. Predominant Acidilobus-like populations from geothermal environments in yellowstone national park exhibit similar metabolic potential in different hypoxic microbial communities.

    PubMed

    Jay, Z J; Rusch, D B; Tringe, S G; Bailey, C; Jennings, R M; Inskeep, W P

    2014-01-01

    High-temperature (>70°C) ecosystems in Yellowstone National Park (YNP) provide an unparalleled opportunity to study chemotrophic archaea and their role in microbial community structure and function under highly constrained geochemical conditions. Acidilobus spp. (order Desulfurococcales) comprise one of the dominant phylotypes in hypoxic geothermal sulfur sediment and Fe(III)-oxide environments along with members of the Thermoproteales and Sulfolobales. Consequently, the primary goals of the current study were to analyze and compare replicate de novo sequence assemblies of Acidilobus-like populations from four different mildly acidic (pH 3.3 to 6.1) high-temperature (72°C to 82°C) environments and to identify metabolic pathways and/or protein-encoding genes that provide a detailed foundation of the potential functional role of these populations in situ. De novo assemblies of the highly similar Acidilobus-like populations (>99% 16S rRNA gene identity) represent near-complete consensus genomes based on an inventory of single-copy genes, deduced metabolic potential, and assembly statistics generated across sites. Functional analysis of coding sequences and confirmation of gene transcription by Acidilobus-like populations provide evidence that they are primarily chemoorganoheterotrophs, generating acetyl coenzyme A (acetyl-CoA) via the degradation of carbohydrates, lipids, and proteins, and auxotrophic with respect to several external vitamins, cofactors, and metabolites. No obvious pathways or protein-encoding genes responsible for the dissimilatory reduction of sulfur were identified. The presence of a formate dehydrogenase (Fdh) and other protein-encoding genes involved in mixed-acid fermentation supports the hypothesis that Acidilobus spp. function as degraders of complex organic constituents in high-temperature, mildly acidic, hypoxic geothermal systems.

  10. Evaluation of microbial population and functional genes during the bioremediation of petroleum-contaminated soil as an effective monitoring approach.

    PubMed

    Shahi, Aiyoub; Aydin, Sevcan; Ince, Bahar; Ince, Orhan

    2016-03-01

    This study investigated the abundance and diversity of soil n-alkane and polycyclic aromatic hydrocarbon (PAH)-degrading bacterial communities. It also investigated the quantity of the functional genes, the occurrence of horizontal gene transfer (HGT) in the identified bacterial communities and the effect that such HGT can have on biostimulation process. Illumina sequencing was used to detect the microbial diversity of petroleum-polluted soil prior to the biostimulation process, and quantitative real-time PCR was used to determine changes in the bacterial community and functional genes (alkB, phnAc and nah) expressions throughout the biostimulation of petroleum-contaminated soil. The illumine results revealed that γ-proteobacteria, Chloroflexi, Firmicutes, and δ-proteobacteria were the most dominant bacterial phyla in the contaminated site, and that most of the strains were Gram-negative. The results of the gene expression results revealed that gram-negative bacteria and alkB are critical to successful bioremediation. Failure to maintain the stability of hydrocarbon-degrading bacteria and functional gene will reduce the extend to which alkanes and PAHs are degraded. According to the results of the study, the application of a C:N:P ratio of was 100:15:1 in the biodegradation experiment resulted in the highest rate at which petroleum hydrocarbons were biodegraded. The diversity of pollutant-degrading bacteria and the effective transfer of degrading genes among resident microorganisms are essential factors for the successful biostimulation of petroleum hydrocarbons. As such, screening these factors throughout the biostimulation process represents an effective monitoring approach by which the success of the biostimulation can be assessed.

  11. Evaluation of microbial population and functional genes during the bioremediation of petroleum-contaminated soil as an effective monitoring approach.

    PubMed

    Shahi, Aiyoub; Aydin, Sevcan; Ince, Bahar; Ince, Orhan

    2016-03-01

    This study investigated the abundance and diversity of soil n-alkane and polycyclic aromatic hydrocarbon (PAH)-degrading bacterial communities. It also investigated the quantity of the functional genes, the occurrence of horizontal gene transfer (HGT) in the identified bacterial communities and the effect that such HGT can have on biostimulation process. Illumina sequencing was used to detect the microbial diversity of petroleum-polluted soil prior to the biostimulation process, and quantitative real-time PCR was used to determine changes in the bacterial community and functional genes (alkB, phnAc and nah) expressions throughout the biostimulation of petroleum-contaminated soil. The illumine results revealed that γ-proteobacteria, Chloroflexi, Firmicutes, and δ-proteobacteria were the most dominant bacterial phyla in the contaminated site, and that most of the strains were Gram-negative. The results of the gene expression results revealed that gram-negative bacteria and alkB are critical to successful bioremediation. Failure to maintain the stability of hydrocarbon-degrading bacteria and functional gene will reduce the extend to which alkanes and PAHs are degraded. According to the results of the study, the application of a C:N:P ratio of was 100:15:1 in the biodegradation experiment resulted in the highest rate at which petroleum hydrocarbons were biodegraded. The diversity of pollutant-degrading bacteria and the effective transfer of degrading genes among resident microorganisms are essential factors for the successful biostimulation of petroleum hydrocarbons. As such, screening these factors throughout the biostimulation process represents an effective monitoring approach by which the success of the biostimulation can be assessed. PMID:26685788

  12. Faecal Microbiota of Forage-Fed Horses in New Zealand and the Population Dynamics of Microbial Communities following Dietary Change

    PubMed Central

    Fernandes, Karlette A.; Kittelmann, Sandra; Rogers, Christopher W.; Gee, Erica K.; Bolwell, Charlotte F.; Bermingham, Emma N.; Thomas, David G.

    2014-01-01

    The effects of abrupt dietary transition on the faecal microbiota of forage-fed horses over a 3-week period were investigated. Yearling Thoroughbred fillies reared as a cohort were exclusively fed on either an ensiled conserved forage-grain diet (“Group A”; n = 6) or pasture (“Group B”; n = 6) for three weeks prior to the study. After the Day 0 faecal samples were collected, horses of Group A were abruptly transitioned to pasture. Both groups continued to graze similar pasture for three weeks, with faecal samples collected at 4-day intervals. DNA was isolated from the faeces and microbial 16S and 18S rRNA gene amplicons were generated and analysed by pyrosequencing. The faecal bacterial communities of both groups of horses were highly diverse (Simpson’s index of diversity >0.8), with differences between the two groups on Day 0 (P<0.017 adjusted for multiple comparisons). There were differences between Groups A and B in the relative abundances of four genera, BF311 (family Bacteroidaceae; P = 0.003), CF231 (family Paraprevotellaceae; P = 0.004), and currently unclassified members within the order Clostridiales (P = 0.003) and within the family Lachnospiraceae (P = 0.006). The bacterial community of Group A horses became similar to Group B within four days of feeding on pasture, whereas the structure of the archaeal community remained constant pre- and post-dietary change. The community structure of the faecal microbiota (bacteria, archaea and ciliate protozoa) of pasture-fed horses was also identified. The initial differences observed appeared to be linked to recent dietary history, with the bacterial community of the forage-fed horses responding rapidly to abrupt dietary change. PMID:25383707

  13. Microbial population in cloud water at the Puy de Dôme: Implications for the chemistry of clouds

    NASA Astrophysics Data System (ADS)

    Amato, Pierre; Ménager, Matthieu; Sancelme, Martine; Laj, Paolo; Mailhot, Gilles; Delort, Anne-Marie

    Airborne micro-organisms are ubiquitous in the atmosphere where they can remain alive and be transported over long distances, thus colonizing new environments. Despite their great importance in relation to ecological and socio-economical issues (bio-terrorism, health, etc.) very few studies have been carried out in this field. In this study, the structure of the microbial community present in atmospheric water samples from clouds at the Puy de Dôme (alt 1465 m, Massif Central, France) is described and the metabolic potential of some bacteria is investigated. The total microflora has been quantified by epifluorescence microscopy, while the cultivable aerobic micro-organisms were isolated. Bacteria were identified by 16S DNA sequencing and fungi by morphological criteria. The total bacterial count reached about 3×10 4 cells m -3 of cloud volume (1×10 5 cells mL -1 of cloud water), of which less than 1% are cultivable. Most of the isolated micro-organisms, including 12 fungal and 17 bacterial strains, are described here for the first time in atmospheric water. Many bacterial strains seem to be adapted to the extreme conditions found in cloud water (pH, T°, UV radiations, etc.). Comparison of the two samples (March 2003) shows that pH can be a major factor controlling the structure of this community: an acidic pH (Sample 1: pH=4, 9) favours the presence of fungi and spore-forming bacteria, while a more neutral pH (Sample 2: pH=5, 8) favours greater biodiversity. We have also shown, using in situ 1H NMR, that most of the isolated bacteria are able to degrade various organic substrates such as formate, acetate, lactate, methanol and formaldehyde which represent the major organic compounds present in cloud water. In addition, the detection of intermediates indicated preferential metabolic routes for some of the strains.

  14. Lack of correlation between Legionella colonization and microbial population quantification using heterotrophic plate count and adenosine triphosphate bioluminescence measurement.

    PubMed

    Duda, Scott; Baron, Julianne L; Wagener, Marilyn M; Vidic, Radisav D; Stout, Janet E

    2015-07-01

    This investigation compared biological quantification of potable and non-potable (cooling) water samples using pour plate heterotrophic plate count (HPC) methods and adenosine triphosphate (ATP) concentration measurement using bioluminescence. The relationship between these measurements and the presence of Legionella spp. was also examined. HPC for potable and non-potable water were cultured on R2A and PCA, respectively. Results indicated a strong correlation between HPC and ATP measurements in potable water (R = 0.90, p < 0.001). In the make-up water and two cooling towers, the correlations between ATP and HPC were much weaker but statistically significant (make-up water: R = 0.37, p = 0.005; cooling tower 1: R = 0.52, p < 0.001; cooling tower 2: R = 0.54, p < 0.001). For potable and non-potable samples, HPC exhibited higher measurement variability than ATP. However, ATP measurements showed higher microbial concentrations than HPC measurements. Following chlorination of the cooling towers, ATP measurements indicated very low bacterial concentrations (<10 colony-forming units (CFU)/mL) despite high HPC concentrations (>1000 CFU/mL) which consisted primarily of non-tuberculous mycobacteria. HPC concentrations have been suggested to be predictive of Legionella presence, although this has not been proven. Our evaluation showed that HPC or ATP demonstrated a fair predictive capacity for Legionella positivity in potable water (HPC: receiver operating characteristic (ROC) = 0.70; ATP: ROC = 0.78; p = 0.003). However, HPC or ATP correctly classified sites as positive only 64 and 62% of the time, respectively. No correlation between HPC or ATP and Legionella colonization in non-potable water samples was found (HPC: ROC = 0.28; ATP: ROC = 0.44; p = 0.193).

  15. Lack of correlation between Legionella colonization and microbial population quantification using heterotrophic plate count and adenosine triphosphate bioluminescence measurement.

    PubMed

    Duda, Scott; Baron, Julianne L; Wagener, Marilyn M; Vidic, Radisav D; Stout, Janet E

    2015-07-01

    This investigation compared biological quantification of potable and non-potable (cooling) water samples using pour plate heterotrophic plate count (HPC) methods and adenosine triphosphate (ATP) concentration measurement using bioluminescence. The relationship between these measurements and the presence of Legionella spp. was also examined. HPC for potable and non-potable water were cultured on R2A and PCA, respectively. Results indicated a strong correlation between HPC and ATP measurements in potable water (R = 0.90, p < 0.001). In the make-up water and two cooling towers, the correlations between ATP and HPC were much weaker but statistically significant (make-up water: R = 0.37, p = 0.005; cooling tower 1: R = 0.52, p < 0.001; cooling tower 2: R = 0.54, p < 0.001). For potable and non-potable samples, HPC exhibited higher measurement variability than ATP. However, ATP measurements showed higher microbial concentrations than HPC measurements. Following chlorination of the cooling towers, ATP measurements indicated very low bacterial concentrations (<10 colony-forming units (CFU)/mL) despite high HPC concentrations (>1000 CFU/mL) which consisted primarily of non-tuberculous mycobacteria. HPC concentrations have been suggested to be predictive of Legionella presence, although this has not been proven. Our evaluation showed that HPC or ATP demonstrated a fair predictive capacity for Legionella positivity in potable water (HPC: receiver operating characteristic (ROC) = 0.70; ATP: ROC = 0.78; p = 0.003). However, HPC or ATP correctly classified sites as positive only 64 and 62% of the time, respectively. No correlation between HPC or ATP and Legionella colonization in non-potable water samples was found (HPC: ROC = 0.28; ATP: ROC = 0.44; p = 0.193). PMID:26038316

  16. Microbial Diversity in the Midguts of Field and Lab-Reared Populations of the European Corn Borer Ostrinia nubilalis

    PubMed Central

    Belda, Eugeni; Pedrola, Laia; Peretó, Juli; Martínez-Blanch, Juan F.; Montagud, Arnau; Navarro, Emilio; Urchueguía, Javier; Ramón, Daniel; Moya, Andrés; Porcar, Manuel

    2011-01-01

    Background Insects are associated with microorganisms that contribute to the digestion and processing of nutrients. The European Corn Borer (ECB) is a moth present world-wide, causing severe economical damage as a pest on corn and other crops. In the present work, we give a detailed view of the complexity of the microorganisms forming the ECB midgut microbiota with the objective of comparing the biodiversity of the midgut-associated microbiota and explore their potential as a source of genes and enzymes with biotechnological applications. Methodological/Principal Findings A high-throughput sequencing approach has been used to identify bacterial species, genes and metabolic pathways, particularly those involved in plant-matter degradation, in two different ECB populations (field-collected vs. lab-reared population with artificial diet). Analysis of the resulting sequences revealed the massive presence of Staphylococcus warneri and Weissella paramesenteroides in the lab-reared sample. This enabled us to reconstruct both genomes almost completely. Despite the apparently low diversity, 208 different genera were detected in the sample, although most of them at very low frequency. By contrast, the natural population exhibited an even higher taxonomic diversity along with a wider array of cellulolytic enzyme families. However, in spite of the differences in relative abundance of major taxonomic groups, not only did both metagenomes share a similar functional profile but also a similar distribution of non-redundant genes in different functional categories. Conclusions/Significance Our results reveal a highly diverse pool of bacterial species in both O. nubilalis populations, with major differences: The lab-reared sample is rich in gram-positive species (two of which have almost fully sequenced genomes) while the field sample harbors mainly gram-negative species and has a larger set of cellulolytic enzymes. We have found a clear relationship between the diet and the midgut

  17. Evaluation of soybean germplasm accessions for resistance to Phakopsora pachyrhizi populations in the southeastern United States, 2009-2012

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soybean [Glycine max (L.) Merr.] germplasm accessions from the USDA Soybean Germplasm Collection were screened for resistance to soybean rust (Phakopsora pachyrhizi) at up to five locations in the southeastern United States in 2009, 2011 and 2012. In 2009, plant introductions (PIs) from maturity gro...

  18. Using Geographical Information Systems to Identify Populations in Need of Improved Accessibility to Antivenom Treatment for Snakebite Envenoming in Costa Rica

    PubMed Central

    Hansson, Erik; Sasa, Mahmood; Mattisson, Kristoffer; Robles, Arodys; Gutiérrez, José María

    2013-01-01

    Introduction Snakebite accidents are an important health problem in rural areas of tropical countries worldwide, including Costa Rica, where most bites are caused by the pit-viper Bothrops asper. The treatment of these potentially fatal accidents is based on the timely administration of specific antivenom. In many regions of the world, insufficient health care systems and lack of antivenom in remote and poor areas where snakebites are common, means that efficient treatment is unavailable for many snakebite victims, leading to unnecessary mortality and morbidity. In this study, geographical information systems (GIS) were used to identify populations in Costa Rica with a need of improved access to antivenom treatment: those living in areas with a high risk of snakebites and long time to reach antivenom treatment. Method/Principal Findings Populations living in areas with high risk of snakebites were identified using two approaches: one based on the district-level reported incidence, and another based on mapping environmental factors favoring B. asper presence. Time to reach treatment using ambulance was estimated using cost surface analysis, thereby enabling adjustment of transportation speed by road availability and quality, topography and land use. By mapping populations in high risk of snakebites and the estimated time to treatment, populations with need of improved treatment access were identified. Conclusion/Significance This study demonstrates the usefulness of GIS for improving treatment of snakebites. By mapping reported incidence, risk factors, location of existing treatment resources, and the time estimated to reach these for at-risk populations, rational allocation of treatment resources is facilitated. PMID:23383352

  19. Microbiology of subtidal sediments: Monitoring microbial populations. Restoration project 93047-2. Exxon Valdez oil spill restoration project final report

    SciTech Connect

    Braddock, J.F.; Richter, Z.

    1994-06-01

    Following the Exxon Valdez oil spill in 1989, the authors measured numbers of hydrocarbon-degrading microorganisms and hydrocarbon mineralization potentials of microorganisms in oiled and unoiled surface sediments from the shore through 100 m depth offshore. The authors found both temporal and spatial variations in numbers and activity of hydrocarbon-degrading microorganisms with statistically significant higher values at the oiled sites than at reference sites. In the summer of 1993, the authors returned to ten study sites within Prince William Sound to monitor the changes in the numbers and activities of hydrocarbon-degrading microorganisms at these sites with time. In 1993 the numbers and activities of hydrocarbon-degrading microorganisms were generally very low at all sites although elevated populations and activities were measured in intertidal sub-surface samples at several sites (Northwest Bay, Herring Bay and Sleepy Bay) with observable sub-surface oiling.

  20. Towards achieving Abuja targets: identifying and addressing barriers to access and use of insecticides treated nets among the poorest populations in Kenya

    PubMed Central

    2010-01-01

    Background Ensuring that the poor and vulnerable population benefit from malaria control interventions remains a challenge for malaria endemic countries. Until recently, ownership and use of insecticides treated nets (ITNs) in most countries was low and inequitable, although coverage has increased in countries where free ITN distribution is integrated into mass vaccination campaigns. In Kenya, free ITNs were distributed to children aged below five years in 2006 through two mass campaigns. High and equitable coverage were reported after the campaigns in some districts, although national level coverage remained low, suggesting that understanding barriers to access remains important. This study was conducted to explore barriers to ownership and use of ITNs among the poorest populations before and after the mass campaigns, to identify strategies for improving coverage, and to make recommendations on how increased coverage levels can be sustained. Methods The study was conducted in the poorest areas of four malaria endemic districts in Kenya. Multiple data collection methods were applied including: cross-sectional surveys (n = 708 households), 24 focus group discussions and semi-structured interviews with 70 ITN suppliers. Results Affordability was reported as a major barrier to access but non-financial barriers were also shown to be important determinants. On the demand side key barriers to access included: mismatch between the types of ITNs supplied through interventions and community preferences; perceptions and beliefs on illness causes; physical location of suppliers and; distrust in free delivery and in the distribution agencies. Key barriers on the supply side included: distance from manufacturers; limited acceptability of ITNs provided through interventions; crowding out of the commercial sector and the price. Infrastructure, information and communication played a central role in promoting or hindering access. Conclusions Significant resources have been directed

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

    PubMed

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

    2015-05-01

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

  2. Impact of Irradiation and Polycyclic Aromatic Hydrocarbon Spiking on Microbial Populations in Marine Sediment for Future Aging and Biodegradability Studies

    PubMed Central

    Melcher, Rebecca J.; Apitz, Sabine E.; Hemmingsen, Barbara B.

    2002-01-01

    Experiments were carried out to develop methods to generate well-characterized, polycyclic aromatic hydrocarbon (PAH)-spiked, aged but minimally altered sediments for fate, biodegradation, and bioavailability experiments. Changes in indigenous bacterial populations were monitored in mesocosms constructed of relatively clean San Diego Bay sediments, with and without exposure to gamma radiation, and then spiked with five different PAHs and hexadecane. While phenanthrene and chrysene degraders were present in the unspiked sediments and increased during handling, PAH spiking of nonirradiated sediments led to dramatic increases in their numbers. Phenotypic characterization of isolates able to grow on phenanthrene or chrysene placed them in several genera of marine bacteria: Vibrio, Marinobacter or Cycloclasticus, Pseudoalteromonas, Marinomonas, and Halomonas. This is the first time that marine PAH degraders have been identified as the latter two genera, expanding the diversity of marine bacteria with this ability. Even at the highest irradiation dose (10 megarads), heterotrophs and endospore formers reappeared within weeks. However, while bacteria from the unirradiated sediments had the capacity to both grow on and mineralize 14C-labeled phenanthrene and chrysene, irradiation prevented the reappearance of PAH degraders for up to 4 months, allowing spikes to age onto the sediments, which can be used to model biodegradation in marine sediments. PMID:12039743

  3. Bias Caused by Using Different Isolation Media for Assessing the Genetic Diversity of a Natural Microbial Population.

    PubMed

    Tabacchioni; Chiarini; Bevivino; Cantale; Dalmastri

    2000-08-01

    The influence of isolation medium on the biodiversity of Burkholderia cepacia strains recovered from the rhizosphere of Zea mays was evaluated by comparing the genetic diversity of isolates obtained by plating serial dilutions of root macerates on the two selective media TB-T and PCAT. From each medium, 50 randomly chosen colonies were isolated. On the basis of the restriction patterns of DNA coding for 16S rRNA (16S rDNA) amplified by means of PCR (ARDRA), all strains isolated from TB-T medium were assigned to the B. cepacia species, whereas among PCAT isolates only 74% were assigned to the B. cepacia species. Genetic diversity among the PCAT and TB-T isolates was evaluated by the random amplified polymorphic DNA (RAPD) technique. The analysis of molecular variance (AMOVA) method was applied to determine the variance component for RAPD patterns. Most of the genetic diversity (90.59%) was found within the two groups of isolates, but an appreciable amount (9.41%) still separated the two groups (P < 0.001). Mean genetic distances among PCAT isolates (10.39) and TB-T isolates (9.36) were significantly different (P < 0.0001). The results indicate that the two different isolation media select for B. cepacia populations with a different degree of genetic diversity. Moreover, a higher degree of genetic diversity was observed among strains isolated from PCAT medium than among those isolated from TB-T medium. PMID:11080375

  4. Evaluation of microbial population dynamics in the co-composting of cow manure and rice straw using high throughput sequencing analysis.

    PubMed

    Ren, Guangming; Xu, Xiuhong; Qu, Juanjuan; Zhu, Liping; Wang, Tingting

    2016-06-01

    Microbial population dynamics in co-composting of cow manure and rice straw were evaluated using 16S high throughput sequencing technology. Physicochemical factors, including temperature, pH, nitrogen contents, the ratio of carbon and nitrogen, and germination index, were also determined in this study. 16S high throughput sequencing results showed that bacterial community structure and composition significantly varied in each phase of composting. The major phyla included Bacteroidetes, Proteobacteria, Firmicutes, Actinobacteria and Planctomycetes, respectively. Bacteroidetes and Proteobacteria were the most abundant phyla in all phases, and Actinobacteria was just dominant in the mesophilic phase, while Firmicutes and Planctomycetes were ubiquitous. At the genus level, Simiduia, Flavobacterium, unclassified Chitinophagaceae and Flexibacter notably changed in each phase of composting. Bacterial community diversity in the mesophilic phase was higher than that in others based on the Shannon-Wiener index and Simpson diversity index. The ratio of carbon and nitrogen and germination index indicated that the co-composting of cow manure and rice straw reached maturation. The result of nitrogen contents showed that nitrogen loss mainly occurred in the thermophilic phase. In addition, the differences in the distributions of key OTUs between in the late thermophilic phase and the cooling and maturation phase were unobvious compared with other phase's base on the principal component analysis. Redundancy analysis revealed that the changes of nitrogen played a predominant role in the distributions of OTUs during the composting process. PMID:27116967

  5. Effect of Dietary Supplementation of Red Ginseng By-product on Laying Performance, Blood Biochemistry, Serum Immunoglobulin and Microbial Population in Laying Hens.

    PubMed

    Kang, H K; Park, S-B; Kim, C H

    2016-10-01

    This study was carried out to investigate the effect of dietary supplementation of red ginseng by-product (RGB) on the laying performance, blood biochemistry, and microbial population in laying hens. A total of 120 Hy-Line Brown laying hens (75 weeks old) were randomly allotted to 1 of 3 dietary treatments with 4 replicates per treatment. A commercial-type basal diet was prepared, and 2 additional diets were prepared by supplementing 5.0 or 10.0 g/kg of RGB to the basal diet at the expense of corn. The diets were fed to hens on an ad libitum basis for 4 weeks. There were no differences in feed intake, egg weight, and feed conversion ratio during 4 weeks of the feeding trial. However, hen-day egg production was significantly greater (p<0.05) for the RGB treatment groups than that for the basal treatment group. There were no differences in triglyceride, aspartate aminotransferase, and alanine aminotransferase during the 4-week feeding trial. However, RGB supplementation increased (p<0.05) the serum immunoglobulin G (IgG) and IgM content compared with basal treatment group. The total cholesterol was lower (p<0.05) in the RGB treatments groups than that in the basal treatment group. The intestinal Lactobacillus population was greater (p<0.05) for the RGB treatments groups than that for the basal treatment group. However, the numbers of Salmonella and Escherichia coli were not different among dietary treatments. During the entire experiment, there was no significant difference in egg quality among all the treatments. In conclusion, in addition to improving hen-day production, there were positive effects of dietary RGB supplementation on serum immunoglobulin and cholesterol levels in laying hens. PMID:26954140

  6. Effect of Dietary Supplementation of Red Ginseng By-product on Laying Performance, Blood Biochemistry, Serum Immunoglobulin and Microbial Population in Laying Hens.

    PubMed

    Kang, H K; Park, S-B; Kim, C H

    2016-10-01

    This study was carried out to investigate the effect of dietary supplementation of red ginseng by-product (RGB) on the laying performance, blood biochemistry, and microbial population in laying hens. A total of 120 Hy-Line Brown laying hens (75 weeks old) were randomly allotted to 1 of 3 dietary treatments with 4 replicates per treatment. A commercial-type basal diet was prepared, and 2 additional diets were prepared by supplementing 5.0 or 10.0 g/kg of RGB to the basal diet at the expense of corn. The diets were fed to hens on an ad libitum basis for 4 weeks. There were no differences in feed intake, egg weight, and feed conversion ratio during 4 weeks of the feeding trial. However, hen-day egg production was significantly greater (p<0.05) for the RGB treatment groups than that for the basal treatment group. There were no differences in triglyceride, aspartate aminotransferase, and alanine aminotransferase during the 4-week feeding trial. However, RGB supplementation increased (p<0.05) the serum immunoglobulin G (IgG) and IgM content compared with basal treatment group. The total cholesterol was lower (p<0.05) in the RGB treatments groups than that in the basal treatment group. The intestinal Lactobacillus population was greater (p<0.05) for the RGB treatments groups than that for the basal treatment group. However, the numbers of Salmonella and Escherichia coli were not different among dietary treatments. During the entire experiment, there was no significant difference in egg quality among all the treatments. In conclusion, in addition to improving hen-day production, there were positive effects of dietary RGB supplementation on serum immunoglobulin and cholesterol levels in laying hens.

  7. Effect of Dietary Supplementation of Red Ginseng By-product on Laying Performance, Blood Biochemistry, Serum Immunoglobulin and Microbial Population in Laying Hens

    PubMed Central

    Kang, H. K.; Park, S.-B.; Kim, C. H.

    2016-01-01

    This study was carried out to investigate the effect of dietary supplementation of red ginseng by-product (RGB) on the laying performance, blood biochemistry, and microbial population in laying hens. A total of 120 Hy-Line Brown laying hens (75 weeks old) were randomly allotted to 1 of 3 dietary treatments with 4 replicates per treatment. A commercial-type basal diet was prepared, and 2 additional diets were prepared by supplementing 5.0 or 10.0 g/kg of RGB to the basal diet at the expense of corn. The diets were fed to hens on an ad libitum basis for 4 weeks. There were no differences in feed intake, egg weight, and feed conversion ratio during 4 weeks of the feeding trial. However, hen-day egg production was significantly greater (p<0.05) for the RGB treatment groups than that for the basal treatment group. There were no differences in triglyceride, aspartate aminotransferase, and alanine aminotransferase during the 4-week feeding trial. However, RGB supplementation increased (p<0.05) the serum immunoglobulin G (IgG) and IgM content compared with basal treatment group. The total cholesterol was lower (p<0.05) in the RGB treatments groups than that in the basal treatment group. The intestinal Lactobacillus population was greater (p<0.05) for the RGB treatments groups than that for the basal treatment group. However, the numbers of Salmonella and Escherichia coli were not different among dietary treatments. During the entire experiment, there was no significant difference in egg quality among all the treatments. In conclusion, in addition to improving hen-day production, there were positive effects of dietary RGB supplementation on serum immunoglobulin and cholesterol levels in laying hens. PMID:26954140

  8. Improving Access to Primary Care for a Growing Latino Population: The Role of Safety Net Providers in the Rural Midwest

    ERIC Educational Resources Information Center

    Blewett, Lynn A.; Casey, Michelle; Call, Kathleen Thiede

    2004-01-01

    Many rural Midwestern communities are experiencing rapid growth in Latino populations with low rates of health insurance coverage, limited financial resources, language and cultural differences, and special health care needs. We report on 2-day site visits conducted in 2001 and 2002 in 3 communities (Marshalltown, Iowa; Great Bend, Kansas; and…

  9. Culturally Diverse and Underserved Populations of Gifted Students in the United States and in Taiwan: Equitable Access to Gifted Education

    ERIC Educational Resources Information Center

    Ho, Ya-Ting

    2014-01-01

    There is a continuing increase in the African American and Hispanic student populations in public schools. The students who are invited to gifted programs are overwhelmingly White. This is the situation in schools in the United States and also in Taiwan. Misunderstanding or unawareness of culture difference among educators might contribute to…

  10. Does Universally Accessible Child Care Protect Children from Late Talking? Results from a Norwegian Population-Based Prospective Study

    ERIC Educational Resources Information Center

    Lekhal, Ratib; Zachrisson, Henrik Daae; Wang, Mari Vaage; Schjolberg, Synnve; von Soest, Tilmann

    2011-01-01

    This study examines the association between type of child care arrangement at age 1, 1.5 and 3 years and late talking (LT). The data were from 19,919 children in the population-based prospective Norwegian Mother and Child Cohort Study (MoBa) and included information about child care arrangement, LT and a variety of covariates. Attendance at…

  11. Biogeochemistry of Microbial Mats

    NASA Technical Reports Server (NTRS)

    DesMarais, David J.; DeVincenizi, D. (Technical Monitor)

    2002-01-01

    The hierarchical organization of microbial ecosystems determines the rates of processes that shape Earth's environment, define the stage upon which major evolutionary events occurred, and create biosignatures in sediments and atmospheres. In cyanobacterial mats, oxygenic photosynthesis provides energy, organic substrates and oxygen to the ecosystem. Incident light changes with depth in the mat, both in intensity and spectral composition, and counteracting gradients of oxygen and sulfide shape the chemical microenvironment. A combination of benefits and hazards of light, oxygen and sulfide promotes the allocation of the various essential mat processes between light and dark periods and to various depths in the mat. Microliters produce hydrogen, small organic acids, nitrogen and sulfur species. Such compounds fuel a flow of energy and electrons in these ecosystems and thus shape interactions between groups of microorganisms. Coordinated observations of population distribution, abundance, and activity for an entire community are making fundamental questions in ecology accessible. These questions address those factors that sustain the remarkable diversity of microorganisms that are now being revealed by molecular techniques. These questions also target the processes that shape the various kinds of biosignatures that we will seek, both in ancient rocks from Earth and Mars, and in atmospheres of distant planets beyond our Solar System.

  12. Changes in Access to Health Services of the Immigrant and Native-Born Population in Spain in the Context of Economic Crisis †

    PubMed Central

    Garcia-Subirats, Irene; Vargas, Ingrid; Sanz-Barbero, Belén; Malmusi, Davide; Ronda, Elena; Ballesta, Mónica; Vázquez, María Luisa

    2014-01-01

    Aim: To analyze changes in access to health care and its determinants in the immigrant and native-born populations in Spain, before and during the economic crisis. Methods: Comparative analysis of two iterations of the Spanish National Health Survey (2006 and 2012). Outcome variables were: unmet need and use of different healthcare levels; explanatory variables: need, predisposing and enabling factors. Multivariate models were performed (1) to compare outcome variables in each group between years, (2) to compare outcome variables between both groups within each year, and (3) to determine the factors associated with health service use for each group and year. Results: unmet healthcare needs decreased in 2012 compared to 2006; the use of health services remained constant, with some changes worth highlighting, such as the decline in general practitioner visits among autochthons and a narrowed gap in specialist visits between the two populations. The factors associated with health service use in 2006 remained constant in 2012. Conclusion: Access to healthcare did not worsen, possibly due to the fact that, until 2012, the national health system may have cushioned the deterioration of social determinants as a consequence of the financial crisis. Further studies are necessary to evaluate the effects of health policy responses to the crisis after 2012. PMID:25272078

  13. Population structure and genetic variability in the Murrah dairy breed of water buffalo in Brazil accessed via pedigree analysis.

    PubMed

    Malhado, Carlos Henrique Mendes; Malhado, Ana Claudia Mendes; Carneiro, Paulo Luiz Souza; Ramos, Alcides Amorim; Ambrosini, Diego Pagung; Pala, Akin

    2012-12-01

    The objective of this study was to use pedigree analysis to evaluate the population structure and genetic variability in the Murrah dairy breed of water buffalo (Bubalus bubalis) in Brazil. Pedigree analysis was performed on 5,061 animals born between 1972 and 2002. The effective number of founders (fe) was 60, representing 6.32 % of the potential number of founders. The effective number of ancestors (fa) was 36 and the genetic contribution of the 17 most influent ancestors explained 50 % of the genetic variability in the population. The ratio fe/fa (effective number of founders/effective number of ancestors), which expresses the effect of population bottlenecks, was 1.66. Completeness level for the whole pedigree was 76.8, 49.2, 27.7, and 12.8 % for, respectively, the first, second, third, and fourth known parental generations. The average inbreeding values for the whole analyzed pedigree and for inbreed animals were, respectively, 1.28 and 7.64 %. The average relatedness coefficient between individuals of the population was estimated to be 2.05 %-the highest individual coefficient was 10.31 %. The actual inbreeding and average relatedness coefficient are probably higher than estimated due to low levels of pedigree completeness. Moreover, the inbreeding coefficient increased with the addition of each generation to the pedigree, indicating that incomplete pedigrees tend to underestimate the level of inbreeding. Introduction of new sires with the lowest possible average relatedness coefficient and the use of appropriate mating strategies are recommended to keep inbreeding at acceptable levels and increase the genetic variability in this economically important species, which has relatively low numbers compared to other commercial cattle breeds. The inclusion of additional parameters, such as effective number of founders, effective number of ancestors, and fe/fa ratio, provides better resolution as compared to the inclusion of inbreeding coefficient and may help

  14. Widening access to medical education for under-represented socioeconomic groups: population based cross sectional analysis of UK data, 2002-6

    PubMed Central

    Mathers, Jonathan; Sitch, Alice; Marsh, Jennifer L

    2011-01-01

    Objective To determine whether new programmes developed to widen access to medicine in the United Kingdom have produced more diverse student populations. Design Population based cross sectional analysis. Setting 31 UK universities that offer medical degrees. Participants 34 407 UK medical students admitted to university in 2002-6. Main outcome measures Age, sex, socioeconomic status, and ethnicity of students admitted to traditional courses and newer courses (graduate entry courses (GEC) and foundation) designed to widen access and increase diversity. Results The demographics of students admitted to foundation courses were markedly different from traditional, graduate entry, and pre-medical courses. They were less likely to be white and to define their background as higher managerial and professional. Students on the graduate entry programme were older than students on traditional courses (25.5 v 19.2 years) and more likely to be white (odds ratio 3.74, 95% confidence interval 3.27 to 4.28; P<0.001) than those on traditional courses, but there was no difference in the ratio of men. Students on traditional courses at newer schools were significantly older by an average of 2.53 (2.41 to 2.65; P<0.001) years, more likely to be white (1.55, 1.41 to 1.71; P<0.001), and significantly less likely to have higher managerial and professional backgrounds than those at established schools (0.67, 0.61 to 0.73; P<0.001). There were marked differences in demographics across individual established schools offering both graduate entry and traditional courses. Conclusions The graduate entry programmes do not seem to have led to significant changes to the socioeconomic profile of the UK medical student population. Foundation programmes have increased the proportion of students from under-represented groups but numbers entering these courses are small. PMID:21343208

  15. Understanding benefits and addressing misperceptions and barriers to intrauterine device access among populations in the United States.

    PubMed

    Yoost, Jennie

    2014-01-01

    Three intrauterine devices (IUDs), one copper and two containing the progestin levonorgestrel, are available for use in the United States. IUDs offer higher rates of contraceptive efficacy than nonlong-acting methods, and several studies have demonstrated higher satisfaction rates and continuation rates of any birth control method. This efficacy is not affected by age or parity. The safety of IUDs is well studied, and the risks of pelvic inflammatory disease, perforation, expulsion, and ectopic pregnancy are all of very low incidence. Noncontraceptive benefits include decreased menstrual blood loss, improved dysmenorrhea, improved pelvic pain associated with endometriosis, and protection of the endometrium from hyperplasia. The use of IUDs is accepted in patients with multiple medical problems who may have contraindications to other birth control methods. Yet despite well-published data, concerns and misperceptions still persist, especially among younger populations and nulliparous women. Medical governing bodies advocate for use of IUDs in these populations, as safety and efficacy is unchanged, and IUDs have been shown to decrease unintended pregnancies. Dispersion of accurate information among patients and practitioners is needed to further increase the acceptability and use of IUDs.

  16. Effects of Adaptation of In vitro Rumen Culture to Garlic Oil, Nitrate, and Saponin and Their Combinations on Methanogenesis, Fermentation, and Abundances and Diversity of Microbial Populations

    PubMed Central

    Patra, Amlan K.; Yu, Zhongtang

    2015-01-01

    This study investigated the effects of garlic oil (0.25 g/L), nitrate (5 mM), and quillaja saponin (0.6 g/L), alone and in binary or ternary combinations, on methanogenesis, rumen fermentation, and abundances of select microbial populations using in vitro rumen cultures. Potential adaptation to these compounds was also examined by repeated transfers of the cultures on alternate days until day 18. All treatments except saponin alone significantly decreased methanogenesis. Ternary combinations of garlic oil, nitrate, and saponin additively/synergistically suppressed methane production by 65% at day 2 and by 40% at day 18. Feed digestion was not adversely affected by any of the treatments at day 2, but was decreased by the combinations (binary and ternary) of garlic oil with the other inhibitors at days 10 and 18. Saponin, alone or in combinations, and garlic oil alone lowered ammonia concentration at day 2, while nitrate increased ammonia concentration at days 10 and 18. Total volatile fatty acid concentration was decreased by garlic oil alone or garlic oil-saponin combination. Molar proportions of acetate and propionate were affected to different extents by the different treatments. The abundances of methanogens were similar among treatments at day 2; however, garlic oil and its combination with saponin and/or nitrate at day 10 and all treatments except saponin at day 18 significantly decreased the abundances of methanogens. All the inhibitors, either alone or in combinations, did not adversely affect the abundances of total bacteria or Ruminococcus flavefaciens. However, at day 18 the abundances of Fibrobacter succinogenes and Ruminococcus albus were lowered in the presence of garlic oil and saponin, respectively. The results suggest that garlic oil-nitrate-saponin combination (at the doses used in this study) can effectively decreases methanogenesis in the rumen, but its efficacy may decrease while inhibition to feed digestion can increase over time. PMID:26733975

  17. Development of a predictive model for the growth kinetics of aerobic microbial population on pomegranate marinated chicken breast fillets under isothermal and dynamic temperature conditions.

    PubMed

    Lytou, Anastasia; Panagou, Efstathios Z; Nychas, George-John E

    2016-05-01

    The aim of this study was the development of a model to describe the growth kinetics of aerobic microbial population of chicken breast fillets marinated in pomegranate juice under isothermal and dynamic temperature conditions. Moreover, the effect of pomegranate juice on the extension of the shelf life of the product was investigated. Samples (10 g) of chicken breast fillets were immersed in marinades containing pomegranate juice for 3 h at 4 °C following storage under aerobic conditions at 4, 10, and 15 °C for 10 days. Total Viable Counts (TVC), Pseudomonas spp and lactic acid bacteria (LAB) were enumerated, in parallel with sensory assessment (odor and overall appearance) of marinated and non-marinated samples. The Baranyi model was fitted to the growth data of TVC to calculate the maximum specific growth rate (μmax) that was further modeled as a function of temperature using a square root-type model. The validation of the model was conducted under dynamic temperature conditions based on two fluctuating temperature scenarios with periodic changes from 6 to 13 °C. The shelf life was determined both mathematically and with sensory assessment and its temperature dependence was modeled by an Arrhenius type equation. Results showed that the μmax of TVC of marinated samples was significantly lower compared to control samples regardless temperature, while under dynamic temperature conditions the model satisfactorily predicted the growth of TVC in both control and marinated samples. The shelf-life of marinated samples was significantly extended compared to the control (5 days extension at 4 °C). The calculated activation energies (Ea), 82 and 52 kJ/mol for control and marinated samples, respectively, indicated higher temperature dependence of the shelf life of control samples compared to marinated ones. The present results indicated that pomegranate juice could be used as an alternative ingredient in marinades to prolong the shelf life of chicken.

  18. The burden of drinking water-associated cryptosporidiosis in China: the large contribution of the immunodeficient population identified by quantitative microbial risk assessment.

    PubMed

    Xiao, Shumin; An, Wei; Chen, Zhimin; Zhang, Dongqing; Yu, Jianwei; Yang, Min

    2012-09-01

    A comprehensive quantitative microbial risk assessment (QMRA) of Cryptosporidium infection, considering pathogen removal efficiency, different exposure pathways and different susceptible subpopulations, was performed based on the result of a survey of source water from 66 waterworks in 33 major cities across China. The Cryptosporidium concentrations in source water were 0-6 oocysts/10 L, with a mean value of 0.7 oocysts/10 L. The annual diarrhea morbidity caused by Cryptosporidium in drinking water was estimated to be 2701 (95% confidence interval (CI): 138-9381) cases per 100,000 immunodeficient persons and 148 (95% CI: 1-603) cases per 100,000 immunocompetent persons, giving an overall rate of 149.0 (95% CI: 1.3-606.4) cases per 100,000 population. The cryptosporidiosis burden associated with drinking water treated with the conventional process was calculated to be 8.31 × 10(-6) (95% CI: 0.34-30.93 × 10(-6)) disability-adjusted life years (DALYs) per person per year, which was higher than the reference risk level suggested by the World Health Organization (WHO), but lower than that suggested by the United States Environmental Protection Agency (USEPA). Sixty-six percent of the total health burden due to cryptosporidiosis that occurred in the immunodeficient subpopulation, and 90% of the total DALYs was attributed to adults aged 15-59 years. The sensitivity analysis highlighted the great importance of stability of the treatment process and the importance of watershed protection. The results of this study will be useful in better evaluating and reducing the burden of Cryptosporidium infection.

  19. Disparities in health and access to healthcare between asylum seekers and residents in Germany: a population-based cross-sectional feasibility study

    PubMed Central

    Schneider, Christine; Joos, Stefanie; Bozorgmehr, Kayvan

    2015-01-01

    Objectives To assess disparities in health and healthcare between asylum seekers (AS) and residents in Germany as a proof of concept using European Core Health Indicators (ECHI). Design Population-based cross-sectional feasibility study. Participants All AS (aged 18 years or above) registered in three counties in Germany during a 3-month study period (N=1017). Cross-sectional data on the resident population were taken from the German Health Interview (2008–2011, N=8152), and the European Union Statistics on Income and Living Conditions (2012, N=23 065). Outcome measures Self-reported health status and healthcare access (utilisation and unmet medical need) in line with ECHI. Method Inequalities in health and access to healthcare were quantified both by crude and age-stratified/sex-stratified ORs with 95% CI using cross-tabulations. Results A total of N=156 AS (15.34%) participated in the study. Compared with residents, AS were significantly more likely to report a bad health status (OR=1.72 (1.23 to 2.41)), activity limitations (OR=1.97 (1.39 to 2.79)) or (only younger age groups) any chronic morbidity (18–24 years: OR=6.23 (2.62 to 14.57); 25–49 years: OR=2.05 (1.23 to 3.37)). AS had significantly lower odds for consulting any physician (OR=0.1 (0.07 to 0.16)) or general practitioners (OR=0.44 (0.31 to 0.62)), but higher odds for hospital admissions (OR=2.29 (1.54 to 3.34)), visits to psychotherapists (OR=4.07 (2.48 to 6.43)) and unmet needs (OR=3.74 (2.62 to 5.21)). The direction of healthcare-related associations was consistent across all strata despite variation in magnitude and statistical significance. Conclusions Quantifying disparities between AS and the resident population by means of selected ECHI proved to be feasible. The approach yielded first quantitative evidence for disparities in health and access to healthcare in the German context. Further research is needed to generate representative estimates, for example, by including AS in

  20. Challenges in access to health services and its impact on quality of life: a randomised population-based survey within Turkish speaking immigrants in London

    PubMed Central

    2012-01-01

    Background and aim There are a significant number of Turkish speaking immigrants living in London. Their special health issues including women's health, mental health, and alcohol and smoking habits has been assessed. The aim of this study was to explore the ongoing challenges in access to health care services and its impact on Quality of Life of immigrants. Material and methods This cross-sectional population-based study was conducted between March and August 2010 with Turkish immigrants (n = 416) living in London. Of these, 308 (74%) were Turkish and 108 (26%) were Turkish Cypriots. All healthy or unhealthy adults of 17-65 years of age were enrolled. A structured questionnaire with 44 items in five subcategories and 26-items WHOQOL BREF were used. Results Mean duration of stay for Turkish Cypriots (26.9 ± 13.9 years) was significantly longer than Turkish immigrants (13.3 ± 7.5) (p < 0.001). Turkish immigrants (n = 108, 36.5%) need interpretation more often when using health services than Turkish Cypriots (n = 16, 15%) (p < 0.001). Multivariate analyses suggested significant effects of older age, non-homeownership, low socioeconomic class, poor access to health services, being ill, poor community integration and being obese on physical well-being and also significant effects of low income and poor community integration on perceived overall Quality of Life (WHOQOL) of the participants. Conclusions The results of this study demonstrate how the health and well-being of members of the Turkish speaking community living in London are affected by social aspects of their lives. Providing culturally competent care and interpretation services and advocacy may improve the accessibility of the health care. PMID:22280521

  1. Birth data accessibility via primary care health records to classify health status in a multi-ethnic population of children: an observational study

    PubMed Central

    Bonner, Rachel; Bountziouka, Vassiliki; Stocks, Janet; Harding, Seeromanie; Wade, Angela; Griffiths, Chris; Sears, David; Fothergill, Helen; Slevin, Hannah; Lum, Sooky

    2015-01-01

    Background: Access to reliable birth data (birthweight (BW) and gestational age (GA)) is essential for the identification of individuals who are at subsequent health risk. Aims: This study aimed to explore the feasibility of retrospectively collecting birth data for schoolchildren from parental questionnaires (PQ) and general practitioners (GPs) in primary care clinics, in inner city neighbourhoods with high density of ethnic minority and disadvantaged populations. Methods: Attempts were made to obtain birth data from parents and GPs for 2,171 London primary schoolchildren (34% White, 29% Black African origin, 25% South Asians, 12% Other) as part of a larger study of respiratory health. Results: Information on BW and/or GA were obtained from parents for 2,052 (95%) children. Almost all parents (2,045) gave consent to access their children’s health records held by GPs. On the basis of parental information, GPs of 1,785 children were successfully contacted, and GPs of 1,202 children responded. Birth data were retrieved for only 482 children (22% of 2,052). Missing birth data from GPs were associated with non-white ethnicity, non-UK born, English not the dominant language at home or socioeconomic disadvantage. Paired data were available in 376 children for BW and in 407 children for GA. No significant difference in BW or GA was observed between PQ and GP data, with <5% difference between sources regardless of normal or low birth weight, or term or preterm status. Conclusions: Parental recall of birth data for primary schoolchildren yields high quality and rapid return of data, and it should be considered as a viable alternative in which there is limited access to birth records. It provides the potential to include children with an increased risk of health problems within epidemiological studies. PMID:25612149

  2. Access to, and use of, water by populations living in a schistosomiasis and fascioliasis co-endemic area of northern Côte d'Ivoire.

    PubMed

    Krauth, Stefanie J; Musard, Capucine; Traoré, Seïdinan I; Zinsstag, Jakob; Achi, Louise Y; N'Goran, Eliézer K; Utzinger, Jürg

    2015-09-01

    Water is an essential element of life, but it can also be a source of disease. Apart from direct consumption of unsafe water, direct contact and indirect consumption puts people at risk of many different types of pathogens. Employing a mixed methods approach, consisting of questionnaires and direct observations, we assessed access to, and use of, different water sources by the participants of the district des Savanes in northern Côte d'Ivoire. The use of water sources was put in relation to the potential risk of acquiring schistosomiasis and fascioliasis. Overall, 489 people aged 8 to 82 years participated. While all participants had access to safe water, 63% were in direct contact with unimproved water and 31% directly consumed unsafe water. More than a third of the people who otherwise reported using only improved water for all activities came in contact with unimproved water through crossing open water when going to their workplace, school or other destinations. Self-reported blood in urine - a marker for Schistosoma haematobium with reasonable sensitivity and specificity - was reported by 6% (n=30), self-reported blood in stool - an unspecific marker for Schistosoma mansoni - was reported by 7% (n=35), while blood co-occurring in both urine and stool was reported by another 10% (n=48) of participants. Accessing unimproved water for any activity (including crossing) was associated with higher odds of reporting blood in urine and/or blood in stool (odds ratio: 1.90; 95% confidence interval: 1.07-3.36). Our results have important rami-fications for intervention programmes targeting neglected tropical diseases, and emphasize the need for a wider supply of safe water to rural populations, since the water supply at the workplace needs to be considered as well next to the water supply at home. Crossing of open water sources is an important risk factor for sustained transmission of schistosomiasis.

  3. Absence of socioeconomic inequalities in access to good-quality breast cancer treatment within a population-wide screening programme in Turin (Italy).

    PubMed

    Zengarini, Nicolás; Ponti, Antonio; Tomatis, Mariano; Casella, Denise; Giordano, Livia; Mano, Maria P; Segnan, Nereo; Whitehead, Margaret; Costa, Giuseppe; Spadea, Teresa

    2016-11-01

    Several studies suggest that population-based breast cancer screening programmes might help reduce social inequalities in breast cancer survival both by increasing early diagnosis and by improving access to effective treatments. To start disentangling the two effects, we evaluated social inequalities in quality of treatment of screen-detected breast cancer in the city of Turin (Italy). Combining data from the Audit System on Quality of Breast Cancer Treatment and the Turin Longitudinal Study, we analysed 2700 cases in the screening target age class 50-69 diagnosed in the period 1995-2008. We selected 10 indicators of the pathway of care, relative to timeliness and appropriateness of diagnosis and treatment, and three indicators of socioeconomic position: education, occupational status and housing characteristics. For each indicator of care, relative risks of failure were estimated by robust Poisson regression models, controlling for calendar period of diagnosis, size of tumour and activity volume of the surgery units. The principal predictor of failure of the good care indicators was the calendar period of diagnosis, with a general improvement with time in the quality of diagnosis and treatment, followed by size of the tumour and volume of activity. Socioeconomic indicators show only a marginal independent effect on timeliness indicators. The observed associations of quality indicators with socioeconomic characteristics are lower than expected, suggesting a possible role of the screening programme in reducing disparities in the access to good-quality treatments thanks to its capability to enter screen-detected women into a protected pathway of care.

  4. Teaching Microbial Growth by Simulation.

    ERIC Educational Resources Information Center

    Ruiz, A. Fernandez; And Others

    1989-01-01

    Presented is a simulation program for Apple II computer which assays the effects of a series of variables on bacterial growth and interactions between microbial populations. Results of evaluation of the program with students are summarized. (CW)

  5. Measuring microbial metabolism in atypical environments: Bentonite in used nuclear fuel storage.

    PubMed

    Stone, Wendy; Kroukamp, Otini; Moes, Ana; McKelvie, Jennifer; Korber, Darren R; Wolfaardt, Gideon M

    2016-01-01

    Genomics enjoys overwhelming popularity in the study of microbial ecology. However, extreme or atypical environments often limit the use of such well-established tools and consequently demand a novel approach. The bentonite clay matrix proposed for use in Deep Geological Repositories for the long-term storage of used nuclear fuel is one such challenging microbial habitat. Simple, accessible tools were developed for the study of microbial ecology and metabolic processes that occur within this habitat, since the understanding of the microbiota-niche interaction is fundamental to describing microbial impacts on engineered systems such as compacted bentonite barriers. Even when genomic tools are useful for the study of community composition, techniques to describe such microbial impacts and niche interactions should complement these. Tools optimised for assessing localised microbial activity within bentonite included: (a) the qualitative use of the resazurin-resorufin indicator system for redox localisation, (b) the use of a CaCl2 buffer for the localisation of pH, and (c) fluorometry for the localisation of precipitated sulphide. The use of the Carbon Dioxide Evolution Monitoring System was also validated for measuring microbial activity in desiccated and saturated bentonite. Finally, the buffering of highly-basic bentonite at neutral pH improved the success of isolation of microbial populations, but not DNA, from the bentonite matrix. Thus, accessible techniques were optimised for exploring microbial metabolism in the atypical environments of clay matrices and desiccated conditions. These tools have application to the applied field of used nuclear fuel management, as well as for examining the fundamental biogeochemical cycles active in sedimentary and deep geological environments.

  6. Improved yield of high molecular weight DNA coincides with increased microbial diversity access from iron oxide cemented sub-surface clay environments.

    PubMed

    Hurt, Richard A; Robeson, Michael S; Shakya, Migun; Moberly, James G; Vishnivetskaya, Tatiana A; Gu, Baohua; Elias, Dwayne A

    2014-01-01

    Despite over three decades of progress, extraction of high molecular weight (HMW) DNA from high clay soils or iron oxide cemented clay has remained challenging. HMW DNA is desirable for next generation sequencing as it yields the most comprehensive coverage. Several DNA extraction procedures were compared from samples that exhibit strong nucleic acid adsorption. pH manipulation or use of alternative ion solutions offered no improvement in nucleic acid recovery. Lysis by liquid N2 grinding in concentrated guanidine followed by concentrated sodium phosphate extraction supported HMW DNA recovery from clays high in iron oxides. DNA recovered using 1 M sodium phosphate buffer (PB) as a competitive desorptive wash was 15.22±2.33 µg DNA/g clay, with most DNA consisting of >20 Kb fragments, compared to 2.46±0.25 µg DNA/g clay with the Powerlyzer system (MoBio). Increasing PB concentration in the lysis reagent coincided with increasing DNA fragment length during initial extraction. Rarefaction plots of 16S rRNA (V1-V3 region) pyrosequencing from A-horizon and clay soils showed an ∼80% and ∼400% larger accessed diversity compared to the Powerlyzer soil DNA system, respectively. The observed diversity from the Firmicutes showed the strongest increase with >3-fold more operational taxonomic units (OTU) recovered.

  7. Effect of Scrophularia striata and Ferulago angulata, as alternatives to virginiamycin, on growth performance, intestinal microbial population, immune response, and blood constituents of broiler chickens.

    PubMed

    Rostami, Farhad; Ghasemi, Hossein A; Taherpour, Kamran

    2015-09-01

    An experiment was conducted to investigate the comparative effect of Scrophularia striata, Ferulago angulata, and virginiamycin (VM) on performance, intestinal microbial population, immune response, and blood constituents of broilers. A total of 300 Ross 308 male broiler chickens were randomly assigned to 5 treatments, with 5 replicates/treatment (10 chickens/pen). Birds were fed either a corn-soybean meal basal diet (control) or the basal diet supplemented with 200 mg/kg VM; 4 g/kg S. striata (SS1); 8 g/kg S. striata (SS2); 4 g/kg F. angulata (FA1); or 8 g/kg F. angulata (FA2). After 6 wk, the BW, ADG, and feed-to-gain ratio (F:G) of the VM, SS1, and FA1 groups were better (P<0.01) compared with the control group. At 42 d, cecal lactobacillus counts were higher (P=0.032) in SS2 and FA2 groups compared with the control and VM groups. In addition, broilers fed any of the diets exhibited lower coliform counts (P<0.05) in the ileum and ceca than those fed the control diet. Total and IgG antibody titers against SRBC for secondary responses, relative spleen weight, and lymphocyte counts were higher (P<0.05) in birds fed the SS2 or FA2 diet compared with the control group. Moreover, feeding the SS2 or FA2 diet decreased (P<0.05) the blood heterophil/lymphocyte ratio and plasma triglyceride level, whereas only the SS2 diet increased (P=0.037) the white blood cell counts compared with the control diet. All diets, except for the VM diet, decreased (P=0.009) the plasma cholesterol level compared to the control treatment. The plasma high-density lipoprotein cholesterol level was also increased (P=0.042) in the SS2 and FA2 groups. In conclusion, dietary S. striata or F. angulata at a level of 4 g/kg diet enhanced growth performance, which was comparable to that of VM used as an antibiotic growth promoter. Furthermore, a high dose of both herbs (8 g/kg diet) could beneficially affect the intestinal health and immune status of broilers. PMID:26217029

  8. Effect of Scrophularia striata and Ferulago angulata, as alternatives to virginiamycin, on growth performance, intestinal microbial population, immune response, and blood constituents of broiler chickens.

    PubMed

    Rostami, Farhad; Ghasemi, Hossein A; Taherpour, Kamran

    2015-09-01

    An experiment was conducted to investigate the comparative effect of Scrophularia striata, Ferulago angulata, and virginiamycin (VM) on performance, intestinal microbial population, immune response, and blood constituents of broilers. A total of 300 Ross 308 male broiler chickens were randomly assigned to 5 treatments, with 5 replicates/treatment (10 chickens/pen). Birds were fed either a corn-soybean meal basal diet (control) or the basal diet supplemented with 200 mg/kg VM; 4 g/kg S. striata (SS1); 8 g/kg S. striata (SS2); 4 g/kg F. angulata (FA1); or 8 g/kg F. angulata (FA2). After 6 wk, the BW, ADG, and feed-to-gain ratio (F:G) of the VM, SS1, and FA1 groups were better (P<0.01) compared with the control group. At 42 d, cecal lactobacillus counts were higher (P=0.032) in SS2 and FA2 groups compared with the control and VM groups. In addition, broilers fed any of the diets exhibited lower coliform counts (P<0.05) in the ileum and ceca than those fed the control diet. Total and IgG antibody titers against SRBC for secondary responses, relative spleen weight, and lymphocyte counts were higher (P<0.05) in birds fed the SS2 or FA2 diet compared with the control group. Moreover, feeding the SS2 or FA2 diet decreased (P<0.05) the blood heterophil/lymphocyte ratio and plasma triglyceride level, whereas only the SS2 diet increased (P=0.037) the white blood cell counts compared with the control diet. All diets, except for the VM diet, decreased (P=0.009) the plasma cholesterol level compared to the control treatment. The plasma high-density lipoprotein cholesterol level was also increased (P=0.042) in the SS2 and FA2 groups. In conclusion, dietary S. striata or F. angulata at a level of 4 g/kg diet enhanced growth performance, which was comparable to that of VM used as an antibiotic growth promoter. Furthermore, a high dose of both herbs (8 g/kg diet) could beneficially affect the intestinal health and immune status of broilers.

  9. Predicting the distribution and ecological niche of unexploited snow crab (Chionoecetes opilio) populations in Alaskan waters: a first open-access ensemble model.

    PubMed

    Hardy, Sarah M; Lindgren, Michael; Konakanchi, Hanumantharao; Huettmann, Falk

    2011-10-01

    Populations of the snow crab (Chionoecetes opilio) are widely distributed on high-latitude continental shelves of the North Pacific and North Atlantic, and represent a valuable resource in both the United States and Canada. In US waters, snow crabs are found throughout the Arctic and sub-Arctic seas surrounding Alaska, north of the Aleutian Islands, yet commercial harvest currently focuses on the more southerly population in the Bering Sea. Population dynamics are well-monitored in exploited areas, but few data exist for populations further north where climate trends in the Arctic appear to be affecting species' distributions and community structure on multiple trophic levels. Moreover, increased shipping traffic, as well as fisheries and petroleum resource development, may add additional pressures in northern portions of the range as seasonal ice cover continues to decline. In the face of these pressures, we examined the ecological niche and population distribution of snow crabs in Alaskan waters using a GIS-based spatial modeling approach. We present the first quantitative open-access model predictions of snow-crab distribution, abundance, and biomass in the Chukchi and Beaufort Seas. Multi-variate analysis of environmental drivers of species' distribution and community structure commonly rely on multiple linear regression methods. The spatial modeling approach employed here improves upon linear regression methods in allowing for exploration of nonlinear relationships and interactions between variables. Three machine-learning algorithms were used to evaluate relationships between snow-crab distribution and environmental parameters, including TreeNet, Random Forests, and MARS. An ensemble model was then generated by combining output from these three models to generate consensus predictions for presence-absence, abundance, and biomass of snow crabs. Each algorithm identified a suite of variables most important in predicting snow-crab distribution, including

  10. Predicting the distribution and ecological niche of unexploited snow crab (Chionoecetes opilio) populations in Alaskan waters: a first open-access ensemble model.

    PubMed

    Hardy, Sarah M; Lindgren, Michael; Konakanchi, Hanumantharao; Huettmann, Falk

    2011-10-01

    Populations of the snow crab (Chionoecetes opilio) are widely distributed on high-latitude continental shelves of the North Pacific and North Atlantic, and represent a valuable resource in both the United States and Canada. In US waters, snow crabs are found throughout the Arctic and sub-Arctic seas surrounding Alaska, north of the Aleutian Islands, yet commercial harvest currently focuses on the more southerly population in the Bering Sea. Population dynamics are well-monitored in exploited areas, but few data exist for populations further north where climate trends in the Arctic appear to be affecting species' distributions and community structure on multiple trophic levels. Moreover, increased shipping traffic, as well as fisheries and petroleum resource development, may add additional pressures in northern portions of the range as seasonal ice cover continues to decline. In the face of these pressures, we examined the ecological niche and population distribution of snow crabs in Alaskan waters using a GIS-based spatial modeling approach. We present the first quantitative open-access model predictions of snow-crab distribution, abundance, and biomass in the Chukchi and Beaufort Seas. Multi-variate analysis of environmental drivers of species' distribution and community structure commonly rely on multiple linear regression methods. The spatial modeling approach employed here improves upon linear regression methods in allowing for exploration of nonlinear relationships and interactions between variables. Three machine-learning algorithms were used to evaluate relationships between snow-crab distribution and environmental parameters, including TreeNet, Random Forests, and MARS. An ensemble model was then generated by combining output from these three models to generate consensus predictions for presence-absence, abundance, and biomass of snow crabs. Each algorithm identified a suite of variables most important in predicting snow-crab distribution, including

  11. Modeling microbial communities: current, developing, and future technologies for predicting microbial community interaction.

    PubMed

    Larsen, Peter; Hamada, Yuki; Gilbert, Jack

    2012-07-31

    Never has there been a greater opportunity for investigating microbial communities. Not only are the profound effects of microbial ecology on every aspect of Earth's geochemical cycles beginning to be understood, but also the analytical and computational tools for investigating microbial Earth are undergoing a rapid revolution. This environmental microbial interactome, the system of interactions between the microbiome and the environment, has shaped the planet's past and will undoubtedly continue to do so in the future. We review recent approaches for modeling microbial community structures and the interactions of microbial populations with their environments. Different modeling approaches consider the environmental microbial interactome from different aspects, and each provides insights to different facets of microbial ecology. We discuss the challenges and opportunities for the future of microbial modeling and describe recent advances in microbial community modeling that are extending current descriptive technologies into a predictive science.

  12. Modeling microbial communities: current, developing, and future technologies for predicting microbial community interaction.

    PubMed

    Larsen, Peter; Hamada, Yuki; Gilbert, Jack

    2012-07-31

    Never has there been a greater opportunity for investigating microbial communities. Not only are the profound effects of microbial ecology on every aspect of Earth's geochemical cycles beginning to be understood, but also the analytical and computational tools for investigating microbial Earth are undergoing a rapid revolution. This environmental microbial interactome, the system of interactions between the microbiome and the environment, has shaped the planet's past and will undoubtedly continue to do so in the future. We review recent approaches for modeling microbial community structures and the interactions of microbial populations with their environments. Different modeling approaches consider the environmental microbial interactome from different aspects, and each provides insights to different facets of microbial ecology. We discuss the challenges and opportunities for the future of microbial modeling and describe recent advances in microbial community modeling that are extending current descriptive technologies into a predictive science. PMID:22465599

  13. Importance of positioning for microbial evolution.