Plutonium Oxidation State Distribution under Aerobic and Anaerobic Subsurface Conditions for Metal-Reducing Bacteria

NASA Astrophysics Data System (ADS)

Reed, D. T.; Swanson, J.; Khaing, H.; Deo, R.; Rittmann, B.

2009-12-01

The fate and potential mobility of plutonium in the subsurface is receiving increased attention as the DOE looks to cleanup the many legacy nuclear waste sites and associated subsurface contamination. Plutonium is the near-surface contaminant of concern at several DOE sites and continues to be the contaminant of concern for the permanent disposal of nuclear waste. The mobility of plutonium is highly dependent on its redox distribution at its contamination source and along its potential migration pathways. This redox distribution is often controlled, especially in the near-surface where organic/inorganic contaminants often coexist, by the direct and indirect effects of microbial activity. The redox distribution of plutonium in the presence of facultative metal reducing bacteria (specifically Shewanella and Geobacter species) was established in a concurrent experimental and modeling study under aerobic and anaerobic conditions. Pu(VI), although relatively soluble under oxidizing conditions at near-neutral pH, does not persist under a wide range of the oxic and anoxic conditions investigated in microbiologically active systems. Pu(V) complexes, which exhibit high chemical toxicity towards microorganisms, are relatively stable under oxic conditions but are reduced by metal reducing bacteria under anaerobic conditions. These facultative metal-reducing bacteria led to the rapid reduction of higher valent plutonium to form Pu(III/IV) species depending on nature of the starting plutonium species and chelating agents present in solution. Redox cycling of these lower oxidation states is likely a critical step in the formation of pseudo colloids that may lead to long-range subsurface transport. The CCBATCH biogeochemical model is used to explain the redox mechanisms and final speciation of the plutonium oxidation state distributions observed. These results for microbiologically active systems are interpreted in the context of their importance in defining the overall migration of plutonium in the subsurface.

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 phénomènes hydrogéologiques et microbiologiques des environnements souterrains. Ces contraintes pratiques sont dues à des contradictions entre les échelles d'étude de l'hydrogéologie et de la microbiologie et à des limitations pratiques sur la capacitéà définir avec précision les populations microbiennes dans les échantillons. Cependant, des progrès dans l'application de méthodes d'échantillonnage à l'échelle locale et des approches pluridisciplinaires des études de terrain ont commencéà améliorer de façon significative notre compréhension des interactions hydrogéologiques et microbiologiques. De plus, les analyses moléculaires et sur les cultures des populations microbiennes présentes dans les panaches de pollution souterraine ont mis en évidence une adaptation significative de ces populations aux conditions environnementales du panache. Les résultats d'études récentes laissent penser que la variabilité des conditions géochimiques et hydrologiques souterraines influence significativement la structure des communautés microbiennes souterraines. Des recherches combinées sur les conditions de terrain et sur la structure des communautés microbiennes apportent les informations nécessaires à la compréhension des interactions entre les populations microbiennes souterraines, la géochimie du panache et la biodégradation du polluant. Para que la biodegradación de los contaminantes en el subsuelo sea eficiente se requiere: (1) una población microbiana con capacidad de degradación y (2) unas condiciones hidrológicas y geoquímicas favorables. Las restricciones de tipo práctico en los diseños y la interpretación de experimentos, tanto hidrogeológicos como microbiológicos, han dado lugar a un conocimiento limitado de la interrelación entre estas dos ciencias por lo que respecta al subsuelo. Estas restricciones incluyen: (1) inconsistencias entre las escalas de investigación en ambas ciencias (hidrogeología y microbiología) y (2) limitaciones prácticas para definir poblaciones microbianas en las muestras. Sin embargo, los avances en la aplicación de métodos de muestreo a pequeña escala y las investigaciones de campo con equipos interdisciplinares están mejorando significativamente el conocimiento de las interacciones entre hidrogeología y microbiología. Del mismo modo, los análisis moleculares y de cultivos sobre poblaciones microbianas en penachos contaminados han mostrado la adaptación de los microbios a las condiciones naturales. Estudios recientes sugieren que la variabilidad en las condiciones geoquímicas e hidrogeológicas del subsuelo afecta enormemente la estructura de la comunidad microbiana. Las investigaciones que combinan las condiciones del medio con la estructura de la comunidad microbiana proporcionarán el conocimiento necesario para entender las complejas relaciones entre las poblaciones microbianas subsuperficiales, la geoquímica de los penachos de contaminación y la biodegradación de los contaminantes.

Subsurface Environment Sampler for Improved In Situ Characterization of Subsurface Microbial Communities

NASA Astrophysics Data System (ADS)

Barnhart, E. P.; Ruppert, L. F.; Orem, W. H.; McIntosh, J. C.; Cunningham, A. B.; Fields, M. W.; Hiebert, R.; Hyatt, R.

2016-12-01

There is an increasing threat that deep aquifers, an important drinking water resource, may be contaminated by the extraction and transport of fossil fuels. This threat increases the need for improved groundwater monitoring and the ability to predict the extent to which microbial activity may remediate such contamination. The characterization of subsurface microbial communities could provide an ideal biomonitoring tool for the assessment of subsurface contamination due to prokaryotes environmental ubiquity, rapidity of response to environmental perturbation and the important role they play in hydrocarbon degradation and bioremediation. New DNA sequencing technologies provide the opportunity to cost-effectively identify the vast subsurface microbial ecosystem, but use of this new technology is restricted due to issues with sampling. Prior subsurface microbiology studies have relied on core samples that are expensive to obtain hard to collect aseptically and/or ground water samples that do not reflect in situ microbial densities or activities. The development of down-well incubation of sterile sediment with a Diffusive Microbial Sampler (DMS) has emerged as an alternative method to sample subsurface microbial communities that minimizes cost and contamination issues associated with traditional methods. We have designed a Subsurface Environment Sampler with a DMS module that could enable the anaerobic transport of the in situ microbial community from the field for laboratory bioremediation studies. This sampler could provide an inexpensive and standard method for subsurface microbial sampling which would make this tool useful for Federal, State, private and local agencies interested in monitoring contamination or the effectiveness of bioremediation activities in subsurface aquifers.

Natural attenuation of chlorinated-hydrocarbon contamination at Fort Wainwright, Alaska; a hydrogeochemical and microbiological investigation workplan

USGS Publications Warehouse

McCarthy, Kathleen A.; Lilly, Michael R.; Braddock, Joan F.; Hinzman, Larry D.

1998-01-01

Natural attenuation processes include biological degradation, by which microorganisms break down contaminants into simpler product compounds; adsorption of contaminants to soil particles, which decreases the mass of contaminants dissolved in ground water; and dispersion, which decreases dissolved contaminant concentrations through dilution. The primary objectives of this study are to (1) assess the degree to which such natural processes are attenuating chlorinated-hydrocarbon contamination in ground water, and (2) evaluate the effects of ground-water/surface-water interactions on natural-attenuation processes in the area of the former East and West Quartermasters Fueling Systems for Fort Wainwright, Alaska. The study will include investigations of the hydrologic, geochemical, and microbiological processes occurring at this site that influence the transport and fate of chlorinated hydrocarbons in ground water. To accomplish these objectives, a data-collection program has been initiated that includes measurements of water-table elevations and the stage of the Chena River; measurements of vertical temperature profiles within the subsurface; characterization of moisture distribution and movement in the unsaturated zone; collection of ground-water samples for determination of both organic and inorganic chemical constituents; and collection of ground-water samples for enumeration of microorganisms and determination of their potential to mineralize contaminants. We will use results from the data-collection program described above to refine our conceptual model of hydrology and contaminant attenuation at this site. Measurements of water-table elevations and river stage will help us to understand the magnitude and direction of ground-water flow and how changes in the stage of the Chena River affect ground-water flow. Because ambient ground water and surface water typically have different temperature characteristics, temperature monitoring will likely provide further insight into ground-water/surface-water interactions in the subsurface. Characterization of the unsaturated zone will improve our understanding of interactions among ground water, the unsaturated zone, and the atmosphere. The interactions likely of importance to this study include the migration of water, dissolved contaminants, nutrients, and gases (oxygen, carbon dioxide, and methane) between the saturated and unsaturated zones. We will use the results of ground-water chemical analyses to determine the spatial and temporal distribution of (1) chlorinated-hydrocarbon contaminants and their degradation products, (2) oxidation-reduction indicators, (3) nutrients, and (4) major ground-water ions. These water-quality data will provide insight into ground-water flow directions, interactions between ground water and surface water, attenuation of contaminant concentrations caused by dispersion, and intrinsic microbiological processes. Microbiological analyses will indicate whether microorganisms at the site are capable of degrading the contaminants of interest, and will allow us to estimate their potential to attenuate existing contamination. Physical and chemical data interpreted as part of the analysis of ground water and surface water mixing will improve our understanding of the relationship between water quality and contaminant source mixing.

Microbiology of Ultrabasic Groundwaters of the Coast Range Ophiolite, California

NASA Astrophysics Data System (ADS)

Schrenk, M. O.; Brazelton, W. J.; Twing, K. I.; Kubo, M.; Cardace, D.; Hoehler, T. M.; McCollom, T. M.

2013-12-01

Upon exposure to water, ultramafic rocks characteristic of the Earth's mantle undergo a process known as serpentinization. These water-rock reactions lead to highly reducing conditions and some of the highest pH values reported in nature. In contrast to alkaline soda lakes, actively serpentinizing environments exposed on land are commonly associated with low salinity freshwaters, imparting unique challenges upon their resident microbial communities. These environments are especially prevalent along continental margins, and cover extensive portions of the west coast of North America. Most studies of serpentinizing environments have focused upon springs that emanate from fractures in the subsurface. Here, we present microbiological data from a series of groundwater wells associated with active serpentinization in the California Coast Range, an ophiolite complex near Lower Lake, California. Waters from ultrabasic wells had lower microbial cell concentrations and diversity than were found in moderate pH wells in the same area. Bacteria consistently made up a higher proportion of the microbial communities compared to Archaea as determined by qPCR. High pH wells were dominated by taxa within the Betaproteobacteria and Clostridia, whereas moderate pH wells predominantly contained common soil taxa related to Gammaproteobacteria and Bacilli. Multivariate statistical analyses incorporating key environmental parameters supported these observations and also highlighted correlations between the high-pH taxa and the abundance of hydrogen and methane gas. Similarly, colony forming units of alkaliphilic microorganisms were consistently 1-2 orders of magnitude higher in the ultrabasic wells and were taxonomically distinct from the moderate pH groundwaters. Together, these results show that distinct populations inhabit subsurface environments associated with active serpentinization, consistent with previous observations, and suggest that Betaproteobacteria and Clostridia probably play significant roles in the microbiology of these ecosystems. The low diversity microbial communities of serpentinizing subsurface habitats are likely sustained by the high hydrogen and methane fluxes that emanate from such systems and further investigations will directly test their roles in mediating biogeochemical cycles in these environments.

Influences of Coupled Hydrologic and Microbial Processes on River Corridor Biogeochemistry and Ecology

NASA Astrophysics Data System (ADS)

Scheibe, T. D.; Song, H. S.; Stegen, J.; Graham, E.; Bao, J.; Goldman, A.; Zhou, T.; Crump, A.; Hou, Z.; Hammond, G. E.; Chen, X.; Huang, M.; Zhang, X.; Nelson, W. C.; Garayburu-Caruso, V. A.

2017-12-01

The exchange of water between rivers and surrounding subsurface environments (hydrologic exchange flows or HEFs) is a vital aspect of river ecology and watershed function. HEFs play a key role in water quality, nutrient cycling, and ecosystem health, and they modulate water temperatures and enhance exchange of terrestrial and aquatic nutrients, which lead to elevated biogeochemical activity. However, these coupled hydrologic and microbiological processes are not well understood, particularly in the context of large managed river systems with highly variable discharge, and are poorly represented in system-scale quantitative models. Using the 75 km Hanford Reach of the Columbia River as the research domain, we apply high-resolution flow simulations supported by field observations to understand how variable river discharge interacts with hydromorphic and hydrogeologic structures to generate HEFs and distributions of subsurface residence times. We combine this understanding of hydrologic processes with microbiological activity measurements and reactive transport models to elucidate the holistic impacts of variable discharge on river corridor (surface and subsurface) ecosystems. In particular, our project seeks to develop and test new conceptual and numerical models that explicitly incorporate i) the character (chemical speciation and thermodynamics) of natural organic matter as it varies along flow paths and through mixing of groundwater and surface water, and ii) the history-dependent response of microbial communities to varying time scales of inundation associated with fluctuations in river discharge. The results of these high-resolution mechanistic models are guiding formulation and parameterization of reduced-order models applicable at reach to watershed scales. New understanding of coupled hydrology and microbiology in the river corridor will play a key role in reduction of uncertainties associated with major Earth system biogeochemical fluxes, improving predictions of environmental and human impacts on water quality and riverine ecosystems, and supporting environmentally responsible management of linked energy-water systems.

Microbiological Transformations of Radionuclides in the Subsurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marshall, Matthew J.; Beliaev, Alex S.; Fredrickson, Jim K.

2010-01-04

Microorganisms are ubiquitous in subsurface environments although their populations sizes and metabolic activities can vary considerably depending on energy and nutrient inputs. As a result of their metabolic activities and the chemical properties of their cell surfaces and the exopolymers they produce, microorganisms can directly or indirectly facilitate the biotransformation of radionuclides, thus altering their solubility and overall fate and transport in the environment. Although biosorption to cell surfaces and exopolymers can be an important factor modifying the solubility of some radionuclides under specific conditions, oxidation state is often considered the single most important factor controlling their speciation and, therefore,more » environmental behavior.« less

Evaluation of positron emission tomography as a method to visualize subsurface microbial processes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kinsella K.; Schlyer D.; Kinsella, K.

2012-01-18

Positron emission tomography (PET) provides spatiotemporal monitoring in a nondestructive manner and has higher sensitivity and resolution relative to other tomographic methods. Therefore, this technology was evaluated for its application to monitor in situ subsurface bacterial activity. To date, however, it has not been used to monitor or image soil microbial processes. In this study, PET imaging was applied as a 'proof-of-principle' method to assess the feasibility of visualizing a radiotracer labeled subsurface bacterial strain (Rahnella sp. Y9602), previously isolated from uranium contaminated soils and shown to promote uranium phosphate precipitation. Soil columns packed with acid-purified simulated mineral soils weremore » seeded with 2-deoxy-2-[{sup 18}F]fluoro-d-glucose ({sup 18}FDG) labeled Rahnella sp. Y9602. The applicability of [{sup 18}F]fluoride ion as a tracer for measuring hydraulic conductivity and {sup 18}FDG as a tracer to identify subsurface metabolically active bacteria was successful in our soil column studies. Our findings indicate that positron-emitting isotopes can be utilized for studies aimed at elucidating subsurface microbiology and geochemical processes important in contaminant remediation.« less

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir.

PubMed

Freedman, Adam J E; Tan, BoonFei; Thompson, Janelle R

2017-06-01

Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected supercritical (sc) CO 2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO 2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO 2 , harbor a 'deep carbonated biosphere' with carbon cycling potential. We sampled subsurface fluids from scCO 2 -water separators at a natural scCO 2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four members of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO 2 and N 2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. The existence of a microbial ecosystem associated with the McElmo Dome scCO 2 reservoir indicates that potential impacts of the deep biosphere on CO 2 fate and transport should be taken into consideration as a component of GCS planning and modelling. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Effects of vegetations and temperature on nutrient removal and microbiology in horizontal subsurface low constructed wetland for treatment of domestic sewage

USDA-ARS?s Scientific Manuscript database

The direct discharge of untreated domestic wastewater represents a major source of nutrients entering into aquatic environments, which may cause serious ecological problems, e.g., eutrophication. In this regard, low-cost and easily managed technologies such as constructed wetlands (CWs) provide a go...

Post-test evaluation of the geology, geochemistry, microbiology, and hydrology of the in situ air stripping demonstration site at the Savannah River Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eddy Dilek, C.A.; Looney, B.B.; Hazen, T.C.

A full-scale demonstration of the use of horizontal wells for in situ air stripping for environment restoration was completed as part of the Savannah River Integrated Demonstration Program. The demonstration of in situ air stripping was the first in a series of demonstrations of innovative remediation technologies for the cleanup of sites contaminated with volatile organic contaminants. The in situ air stripping system consisted of two directionally drilled wells that delivered gases to and extract contamination from the subsurface. The demonstration was designed to remediate soils and sediments in the unsaturated and saturated zones as well as groundwater contaminated withmore » volatile organic compounds. The demonstration successfully removed significant quantities of solvent from the subsurface. The field site and horizontal wells were subsequently used for an in situ bioremediation demonstration during which methane was added to the injected air. The field conditions documented herein represent the baseline status of the site for evaluating the in situ bioremediation as well as the post-test conditions for the in situ air stripping demonstration. Characterization activities focused on documenting the nature and distribution of contamination in the subsurface. The post-test characterization activities discussed herein include results from the analysis of sediment samples, three-dimensional images of the pretest and post-test data, contaminant inventories estimated from pretest and post-test models, a detailed lithologic cross sections of the site, results of aquifer testing, and measurements of geotechnical parameters of undisturbed core sediments.« less

Radiochemically-supported microbial communities. A potential mechanism for biocolloid production of importance to actinide transport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moser, Duane P.; Hamilton-Brehm, Scott D.; Fisher, Jenny C.

The work described here revealed the presence of diverse microbial communities located across 19 subsurface sites at the NNSS/NTTR and nearby locations. Overall, the diversity of microorganisms was high for subsurface habitats and variable between sites. As of this writing, preparations are being made to combine the Illumina sequences and 16S rRNA clone libraries with other non-NNSS/NTTR well sites of Southern Nevada Regional Flow System for a publication manuscript describing our very broad landscape scale survey of subsurface microbial diversity. Isolates DRI-13 and DRI-14 remain to be fully characterized and named in accordance with the conventions established by Bergey's Manualmore » of Systematic Bacteriology. In preparation to be published, these microorganisms will be submitted to the American Type Culture Collection (ATCC) and the Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ).It is anticipated that the data resulting from this study in combination with other data sets that will allow us to produce a number of publications that will be impactful to the subsurface microbiology community.« less

Exploring the Deep Biosphere in Ophiolite-hosted Systems: What Can Metabolic Processes in Surface Seeps Tell Us About Subsurface Ecosystems in Serpentinizing Fluids?

NASA Astrophysics Data System (ADS)

Meyer-Dombard, D. R.; Cardace, D.; Woycheese, K. M.; Vallalar, B.; Casar, C.; Simon, A.; Arcilla, C. A.

2016-12-01

Serpentinization in the subsurface produces highly reduced, high pH fluids that provide microbial habitats. It is assumed that these deep subsurface fluids contain copious H2 and CH4 gas, little/no inorganic carbon, and limited electron acceptors. As serpentinized fluids reach the oxygenated surface environment, microbial biomes shift and organisms capable of metabolizing O2 thrive (Woycheese et al., 2015). However, the relationship of microbial communities found in surface expressions of serpentinizing fluids to the subsurface biosphere is still a target of exploration. Our work in the Zambales ophiolite (Philippines) defines surface microbial habitats with geochemistry, targeted culturing efforts, and community analysis (Cardace et al., 2015; Woycheese et al., 2015). Springs range from pH 9-11.5, and contain 0.06-2 ppm DO, 0-3.7 ppm sulfide, 30-800 ppm silica. Gases include H2 and CH4 > 10uM, CO2 > 1 mM, and trace amounts of CO. These surface data allow prediction of the subsurface metabolic landscape. For example, Cardace et al., (2015) predicted that metabolism of iron is important in both biospheres. Growth media were designed to target iron reduction yielding heterotrophic and autotrophic iron reducers at high pH. Reduced iron minerals were produced in several cultures (Casar et al., sub.), and isolation efforts are underway. Shotgun metagenomic analysis shows the metabolic capacity for methanogenesis, suggesting microbial origins for some CH4 present. The enzymes methyl coenzyme M reductase, and formylmethanofuran dehydrogenase were detected, and relative abundance increased near the near-anoxic spring source. The metagenomes indicate carbon cycling at these sites is reliant on methanogenesis, acetogenesis, sulfate reduction, and H2 and CH4 oxidation. In this tropical climate, cellulose is also a likely carbon source; cellulose degrading isolates have been obtained. These results indicate a metabolically flexible community at the surface where serpentinizing fluids are expressed. The next step is to understand what these surface systems might tell us about the subsurface biosphere. References: Cardace et al., 2015 Frontiers in Extreme Microbiology 6: doi: 10.3389/fmicb.2015.00010 Woycheese et al., 2015 Frontiers in Extreme Microbiology 6: doi: 10.3389/fmicb.2015.00044

42 CFR 493.909 - Microbiology.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 42 Public Health 5 2014-10-01 2014-10-01 false Microbiology. 493.909 Section 493.909 Public Health... Proficiency Testing Programs by Specialty and Subspecialty § 493.909 Microbiology. The subspecialties under the specialty of microbiology for which a program may offer proficiency testing are bacteriology...

42 CFR 493.909 - Microbiology.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 42 Public Health 5 2013-10-01 2013-10-01 false Microbiology. 493.909 Section 493.909 Public Health... Proficiency Testing Programs by Specialty and Subspecialty § 493.909 Microbiology. The subspecialties under the specialty of microbiology for which a program may offer proficiency testing are bacteriology...

42 CFR 493.909 - Microbiology.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 42 Public Health 5 2010-10-01 2010-10-01 false Microbiology. 493.909 Section 493.909 Public Health... Proficiency Testing Programs by Specialty and Subspecialty § 493.909 Microbiology. The subspecialties under the specialty of microbiology for which a program may offer proficiency testing are bacteriology...

42 CFR 493.909 - Microbiology.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 42 Public Health 5 2012-10-01 2012-10-01 false Microbiology. 493.909 Section 493.909 Public Health... Proficiency Testing Programs by Specialty and Subspecialty § 493.909 Microbiology. The subspecialties under the specialty of microbiology for which a program may offer proficiency testing are bacteriology...

42 CFR 493.909 - Microbiology.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 42 Public Health 5 2011-10-01 2011-10-01 false Microbiology. 493.909 Section 493.909 Public Health... Proficiency Testing Programs by Specialty and Subspecialty § 493.909 Microbiology. The subspecialties under the specialty of microbiology for which a program may offer proficiency testing are bacteriology...

The Serpentinite Subsurface Microbiome

NASA Astrophysics Data System (ADS)

Schrenk, M. O.; Nelson, B. Y.; Brazelton, W. J.

2011-12-01

Microbial habitats hosted in ultramafic rocks constitute substantial, globally-distributed portions of the subsurface biosphere, occurring both on the continents and beneath the seafloor. The aqueous alteration of ultramafics, in a process known as serpentinization, creates energy rich, high pH conditions, with low concentrations of inorganic carbon which place fundamental constraints upon microbial metabolism and physiology. Despite their importance, very few studies have attempted to directly access and quantify microbial activities and distributions in the serpentinite subsurface microbiome. We have initiated microbiological studies of subsurface seeps and rocks at three separate continental sites of serpentinization in Newfoundland, Italy, and California and compared these results to previous analyses of the Lost City field, near the Mid-Atlantic Ridge. In all cases, microbial cell densities in seep fluids are extremely low, ranging from approximately 100,000 to less than 1,000 cells per milliliter. Culture-independent analyses of 16S rRNA genes revealed low-diversity microbial communities related to Gram-positive Firmicutes and hydrogen-oxidizing bacteria. Interestingly, unlike Lost City, there has been little evidence for significant archaeal populations in the continental subsurface to date. Culturing studies at the sites yielded numerous alkaliphilic isolates on nutrient-rich agar and putative iron-reducing bacteria in anaerobic incubations, many of which are related to known alkaliphilic and subsurface isolates. Finally, metagenomic data reinforce the culturing results, indicating the presence of genes associated with organotrophy, hydrogen oxidation, and iron reduction in seep fluid samples. Our data provide insight into the lifestyles of serpentinite subsurface microbial populations and targets for future quantitative exploration using both biochemical and geochemical approaches.

Biogenic Carbon on Mars: A Subsurface Chauvinistic Viewpoint

NASA Astrophysics Data System (ADS)

Onstott, T. C.; Lau, C. Y. M.; Magnabosco, C.; Harris, R.; Chen, Y.; Slater, G.; Sherwood Lollar, B.; Kieft, T. L.; van Heerden, E.; Borgonie, G.; Dong, H.

2015-12-01

A review of 150 publications on the subsurface microbiology of the continental subsurface provides ~1,400 measurements of cellular abundances down to 4,800 meter depth. These data suggest that the continental subsurface biomass is comprised of ~1016-17 grams of carbon, which is higher than the most recent estimates of ~1015 grams of carbon (1 Gt) for the marine deep biosphere. If life developed early in Martian history and Mars sustained an active hydrological cycle during its first 500 million years, then is it possible that Mars could have developed a subsurface biomass of comparable size to that of Earth? Such a biomass would comprise a much larger fraction of the total known Martian carbon budget than does the subsurface biomass on Earth. More importantly could a remnant of this subsurface biosphere survive to the present day? To determine how sustainable subsurface life could be in isolation from the surface we have been studying subsurface fracture fluids from the Precambrian Shields in South Africa and Canada. In these environments the energetically efficient and deeply rooted acetyl-CoA pathway for carbon fixation plays a central role for chemolithoautotrophic primary producers that form the base of the biomass pyramid. These primary producers appear to be sustained indefinitely by H2 generated through serpentinization and radiolytic reactions. Carbon isotope data suggest that in some subsurface locations a much larger population of secondary consumers are sustained by the primary production of biogenic CH4 from a much smaller population of methanogens. These inverted biomass and energy pyramids sustained by the cycling of CH4 could have been and could still be active on Mars. The C and H isotopic signatures of Martian CH4 remain key tools in identifying potential signatures of an extant Martian biosphere. Based upon our results to date cavity ring-down spectroscopic technologies provide an option for making these measurements on future rover missions.

Diagnosis of In Situ Metabolic State and Rates of Microbial Metabolism During In Situ Uranium Bioremediation with Molecular Techniques

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lovley, Derek R.

2012-11-28

The goal of these projects was to develop molecule tools to tract the metabolic activity and physiological status of microorganisms during in situ uranium bioremediation. Such information is important in able to design improved bioremediation strategies. As summarized below, the research was highly successful with new strategies developed for estimating in situ rates of metabolism and diagnosing the physiological status of the predominant subsurface microorganisms. This is a first not only for groundwater bioremediation studies, but also for subsurface microbiology in general. The tools and approaches developed in these studies should be applicable to the study of microbial communities inmore » a diversity of soils and sediments.« less

Under the sea: microbial life in volcanic oceanic crust.

PubMed

Edwards, Katrina J; Wheat, C Geoffrey; Sylvan, Jason B

2011-09-06

Exploration of the microbiology in igneous, 'hard rock' oceanic crust represents a major scientific frontier. The igneous crust harbours the largest aquifer system on Earth, most of which is hydrologically active, resulting in a substantial exchange of fluids, chemicals and microorganisms between oceanic basins and crustal reservoirs. Study of the deep-subsurface biosphere in the igneous crust is technically challenging. However, technologies have improved over the past decade, providing exciting new opportunities for the study of deep-seated marine life, including in situ and cross-disciplinary experimentation in microbiology, geochemistry and hydrogeology. In this Progress article, we describe the recent advances, available technology and remaining challenges in the study of the marine intraterrestrial microbial life that is harboured in igneous oceanic crust.

Arsenic, microbes and contaminated aquifers

USGS Publications Warehouse

Oremland, Ronald S.; Stolz, John F.

2005-01-01

The health of tens of millions of people world-wide is at risk from drinking arsenic-contaminated well water. In most cases this arsenic occurs naturally within the sub-surface aquifers, rather than being derived from identifiable point sources of pollution. The mobilization of arsenic into the aqueous phase is the first crucial step in a process that eventually leads to human arsenicosis. Increasing evidence suggests that this is a microbiological phenomenon.

Vadose zone microbiology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kieft, Thomas L.; Brockman, Fred J.

2001-01-17

The vadose zone is defined as the portion of the terrestrial subsurface that extends from the land surface downward to the water table. As such, it comprises the surface soil (the rooting zone), the underlying subsoil, and the capillary fringe that directly overlies the water table. The unsaturated zone between the rooting zone and the capillary fringe is termed the "intermediate zone" (Chapelle, 1993). The vadose zone has also been defined as the unsaturated zone, since the sediment pores and/or rock fractures are generally not completely water filled, but instead contain both water and air. The latter characteristic results inmore » the term "zone of aeration" to describe the vadose zone. The terms "vadose zone," "unsaturated zone", and "zone of aeration" are nearly synonymous, except that the vadose zone may contain regions of perched water that are actually saturated. The term "subsoil" has also been used for studies of shallow areas of the subsurface immediately below the rooting zone. This review focuses almost exclusively on the unsaturated region beneath the soil layer since there is already an extensive body of literature on surface soil microbial communities and process, e.g., Paul and Clark (1989), Metting (1993), Richter and Markowitz, (1995), and Sylvia et al. (1998); whereas the deeper strata of the unsaturated zone have only recently come under scrutiny for their microbiological properties.« less

Influence of microorganisms on the oxidation state distribution of multivalent actinides under anoxic conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reed, Donald Timothy; Borkowski, Marian; Lucchini, Jean - Francois

2010-12-10

The fate and potential mobility of multivalent actinides in the subsurface is receiving increased attention as the DOE looks to cleanup the many legacy nuclear waste sites and associated subsurface contamination. Plutonium, uranium and neptunium are the near-surface multivalent contaminants of concern and are also key contaminants for the deep geologic disposal of nuclear waste. Their mobility is highly dependent on their redox distribution at their contamination source as well as along their potential migration pathways. This redox distribution is often controlled, especially in the near-surface where organic/inorganic contaminants often coexist, by the direct and indirect effects of microbial activity.more » Under anoxic conditions, indirect and direct bioreduction mechanisms exist that promote the prevalence of lower-valent species for multivalent actinides. Oxidation-state-specific biosorption is also an important consideration for long-term migration and can influence oxidation state distribution. Results of ongoing studies to explore and establish the oxidation-state specific interactions of soil bacteria (metal reducers and sulfate reducers) as well as halo-tolerant bacteria and Archaea for uranium, neptunium and plutonium will be presented. Enzymatic reduction is a key process in the bioreduction of plutonium and uranium, but co-enzymatic processes predominate in neptunium systems. Strong sorptive interactions can occur for most actinide oxidation states but are likely a factor in the stabilization of lower-valent species when more than one oxidation state can persist under anaerobic microbiologically-active conditions. These results for microbiologically active systems are interpreted in the context of their overall importance in defining the potential migration of multivalent actinides in the subsurface.« less

Massive Microbiological Groundwater Contamination Associated with a Waterborne Outbreak in Lake Erie, South Bass Island, Ohio

PubMed Central

Fong, Theng-Theng; Mansfield, Linda S.; Wilson, David L.; Schwab, David J.; Molloy, Stephanie L.; Rose, Joan B.

2007-01-01

Background A groundwater-associated outbreak affected approximately 1,450 residents and visitors of South Bass Island, Ohio, between July and September 2004. Objectives To examine the microbiological quality of groundwater wells located on South Bass Island, we sampled 16 wells that provide potable water to public water systems 15–21 September 2004. Methods We tested groundwater wells for fecal indicators, enteric viruses and bacteria, and protozoa (Cryptosporidium and Giardia). The hydrodynamics of Lake Erie were examined to explore the possible surface water–groundwater interactions. Results All wells were positive for both total coliform and Escherichia coli. Seven wells tested positive for enterococci and Arcobacter (an emerging bacterial pathogen), and F+-specific coliphage was present in four wells. Three wells were positive for all three bacterial indicators, coliphages, and Arcobacter; adenovirus DNA was recovered from two of these wells. We found a cluster of the most contaminated wells at the southeast side of the island. Conclusions Massive groundwater contamination on the island was likely caused by transport of microbiological contaminants from wastewater treatment facilities and septic tanks to the lake and the subsurface, after extreme precipitation events in May–July 2004. This likely raised the water table, saturated the subsurface, and along with very strong Lake Erie currents on 24 July, forced a surge in water levels and rapid surface water–groundwater interchange throughout the island. Landsat images showed massive influx of organic material and turbidity surrounding the island before the peak of the outbreak. These combinations of factors and information can be used to examine vulnerabilities in other coastal systems. Both wastewater and drinking water issues are now being addressed by the Ohio Environmental Protection Agency and the Ohio Department of Health. PMID:17589591

[Current panorama of the teaching of microbiology and parasitology in Spain].

PubMed

Cantón, Rafael; Sánchez-Romero, María Isabel; Gómez-Mampaso, Enrique

2010-10-01

The training program of residents in microbiology and parasitology in Spain includes clinical skills, ranging from the diagnostic approach to the patient and adequate sample collection for diagnosis of infectious diseases to antimicrobial therapy and infection control measures. Training also includes new challenges in clinical microbiology that ensure residents' participation in infection control programs of health-care associated infections, training in the resolution of public health problems, and application of new molecular microbiology methods. Specialization in clinical microbiology may be undertaken by graduates in Medicine, Biology, Biochemistry and Chemistry. The training is performed in accredited microbiology laboratories at different hospitals (n = 61) across the country through 4-year residency programs. In the last few years, there has been a major imbalance between the number of intended residents (0.17 per 100,000 inhabitants) and those graduating as specialists in clinical microbiology (0.13 per 100,000 inhabitants), with wide variations across the country. The current tendency in Europe is to strengthen the role of clinical microbiologists as key figures in the diagnosis of infectious diseases and in public health microbiology. Training programs have been hampered by the practice of sending samples for microbiological tests to external, centralized multipurpose laboratories with few clinical microbiologists and without a core curriculum. Essential elements in the training of specialists in clinical microbiology are a close relationship between the laboratory and the clinical center and collaboration with other specialists. Copyright © 2010 Elsevier España S.L. All rights reserved.

Chemical and microbiological water quality of subsurface agricultural drains during a field trial of liquid dairy manure effluent application rate and varying tillage practices, Upper Tiffin Watershed, southeastern Michigan

USGS Publications Warehouse

Haack, Sheridan Kidd; Duris, Joseph W.

2008-01-01

A field trial was done in the Upper Tiffin River Watershed, in southeastern Michigan, to determine the influence of liquid dairy manure effluent (LDME) management practices on the quality of agricultural subsurface-drain water. Samples from subsurface drains were analyzed for nutrients, fecal-coliform and Escherichia coli (E. coli) bacteria, antibiotics, chemicals typically detected in wastewater, and the occurrence of genes indicating the presence of shiga-toxin-producing E. coli, or of bovine-specific Bacteroidetes bacteria. Samples were collected from November 2, 2006, to March 20, 2007, from eight subsurface drains under field plots that received no LDME and no tillage (controls) or received 4,000 or 8,000 gallons per acre (gal/acre) of LDME and either no tillage or two different types of tillage. The two types of tillage tested were (1) ground-driven, rotary, subsurface cultivation and (2) rolling-tine aeration. Samples were collected before LDME application and at 4 hours, and 1, 2, 6, 7, and 14 days post-application. Nutrient concentrations were high in subsurface-drain water throughout the field-trial period and could not be attributed to the field-trial LDME application. Of the 59 drain-water samples, including those collected before LDME application and control samples for each date, 56 had concentrations greater than the U.S. Environmental Protection Agency (USEPA), Ecoregion VI recommended surface-water criterion for total phosphorus, and all samples had concentrations greater than the recommended total nitrogen criterion. Nitrate + nitrite nitrogen concentration exceeded 20 milligrams per liter for every sample and contributed most to the total nitrogen concentrations. Substantial increases in drain-water concentrations of organic and ammonia nitrogen and total phosphorus were found for all treatments, including controls, at 14 days post-application after 0.84 inch of rainfall over 2 days. E. coli concentrations exceeded the USEPA recreational-water-quality single-sample criterion of 235 colony forming units per 100 milliliters in only 3 of 56 samples. Of these three samples, two were collected within 1 day post-LDME application from the treatment receiving 8,000 gal/acre LDME with no tillage (NT8000). The third sample was from the rolling-tine aerator treatment with 4,000 gal/acre LDME application rate after the first significant rainfall. Two wastewater chemicals and two bacterial genes (eaeA and stx1) detected in the LDME, but absent in field blank or pre-application samples, were detected in the 4-hour or 1-day postapplication NT8000 samples. No LDME-associated chemicals were detected in later samples from the NT8000 treatment, and none were detected in samples from other treatments after the first significant rainfall. Results of this field trial were somewhat equivocal with respect to the influence of LDME concentration and tillage practices on subsurface-drain water quality, both immediately after LDME application and in the longer term, after significant rainfall. Interpretation of study findings is limited by the fact that treatments were not replicated, and flow rate or discharge from the subsurface drains was not measured. Nevertheless, study results provide useful information about nutrient and bacteria concentrations in subsurface drains during the non-growing season. In addition, study results demonstrate some potential for the use of chemical and microbiological indicators of LDME transport to subsurface drains.

Recovery Act: Understanding the Impact of CO 2 Injection on the Subsurface Microbial Community in an Illinois Basin CCS Reservoir: Integrated Student Training in Geoscience and Geomicrobiology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fouke, Bruce

An integrated research and teaching program was developed to provide cross--disciplinary training opportunities in the emerging field of carbon capture and storage (CCS) for geobiology students attending the University of Illinois Urbana-­Champaign (UIUC). Students from across the UIUC campus participated, including those from the departments of Geology, Microbiology, Biochemistry, Civil and Environmental Engineering, Animal Sciences and the Institute for Genomic Biology. The project took advantage of the unique opportunity provided by the drilling and sampling of the large-­scale Phase III CCS demonstration Illinois Basin - Decatur Project (IBDP) in the central Illinois Basin at nearby Decatur, Illinois. The IBPD ismore » under the direction of the Illinois State Geological Survey (ISGS, located on the UIUC campus) and the Midwest Geological Sequestration Consortium (MGSC). The research component of this project focused on the subsurface sampling and identification of microbes inhabiting the subsurface Cambrian-­age Mt. Simon Sandstone. In addition to formation water collected from the injection and monitoring wells, sidewall rock cores were collected and analyzed to characterize the cements and diagenetic features of the host Mt. Simon Sandstone. This established a dynamic geobiological framework, as well as a comparative baseline, for future studies of how CO 2 injection might affect the deep microbial biosphere at other CCS sites. Three manuscripts have been prepared as a result of these activities, which are now being finalized for submission to top-­tier international peer-­reviewed research journals. The training component of this project was structured to ensure that a broad group of UIUC students, faculty and staff gained insight into CCS issues. An essential part of this training was that the UIUC faculty mentored and involved undergraduate and graduate students, as well as postdocs and research scientists, at all stages of the project in order to develop CCS-­focused classroom and field courses, as well as seminars. This program provided an excellent opportunity for participants to develop the background necessary to establish longer-­term research in CCS-­related geology and microbial ecology. Further, the program provided an ongoing dynamic platform to foster long-term collaboration with the regional ISGS and MGSC sequestration partnership, while offering hands-­on, applied learning experiences.« less

75 FR 4094 - National Institute of Allergy And Infectious Diseases; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-26

...). Contact Person: Edward W. Schroder, PhD, Chief, Microbiology Review Branch, Scientific Review Program...). Contact Person: Edward W. Schroder, PhD, Chief, Microbiology Review Branch, Scientific Review Program....855, Allergy, Immunology, and Transplantation Research; 93.856, Microbiology and Infectious Diseases...

Observation to Theory in Deep Subsurface Microbiology Research: Can We Piece It Together?

NASA Astrophysics Data System (ADS)

Colwell, F. S.; Thurber, A. R.

2016-12-01

Three decades of observations of microbes in deep environments have led to startling discoveries of life in the subsurface. Now, a few theoretical frameworks exist that help to define Stygian life. Temperature, redox gradients, productivity (e.g., in the overlying ocean), and microbial power requirements are thought to determine the distribution of microbes in the subsurface. Still, we struggle to comprehend the spatial and temporal spectra of Earth processes that define how deep microbe communities survive. Stommel diagrams, originally used to guide oceanographic sampling, may be useful in depicting the subsurface where microbial communities are impacted by co-occurring spatial and temporal phenomena that range across exponential scales. Spatially, the geological settings that influence the activity and distribution of microbes range from individual molecules or minerals all the way up to the planetary-scale where geological formations, occupying up to 105 km3, dictate the bio- and functional geography of microbial communities. Temporally, life in the subsurface may respond in time units familiar to humans (e.g., seconds to days) or to events that unfold over hundred millennial time periods. While surface community dynamics are underpinned by solar and lunar cycles, these cycles only fractionally dictate survival underground where phenomena like tectonic activity, isostatic rebound, and radioactive decay are plausible drivers of microbial life. Geological or planetary processes that occur on thousand or million year cycles could be uniquely important to microbial viability in the subsurface. Such an approach aims at a holistic comprehension of the interaction of Earth system dynamics with microbial ecology.

Identification and Removal of Contaminant Sequences From Ribosomal Gene Databases: Lessons From the Census of Deep Life

PubMed Central

Sheik, Cody S.; Reese, Brandi Kiel; Twing, Katrina I.; Sylvan, Jason B.; Grim, Sharon L.; Schrenk, Matthew O.; Sogin, Mitchell L.; Colwell, Frederick S.

2018-01-01

Earth’s subsurface environment is one of the largest, yet least studied, biomes on Earth, and many questions remain regarding what microorganisms are indigenous to the subsurface. Through the activity of the Census of Deep Life (CoDL) and the Deep Carbon Observatory, an open access 16S ribosomal RNA gene sequence database from diverse subsurface environments has been compiled. However, due to low quantities of biomass in the deep subsurface, the potential for incorporation of contaminants from reagents used during sample collection, processing, and/or sequencing is high. Thus, to understand the ecology of subsurface microorganisms (i.e., the distribution, richness, or survival), it is necessary to minimize, identify, and remove contaminant sequences that will skew the relative abundances of all taxa in the sample. In this meta-analysis, we identify putative contaminants associated with the CoDL dataset, recommend best practices for removing contaminants from samples, and propose a series of best practices for subsurface microbiology sampling. The most abundant putative contaminant genera observed, independent of evenness across samples, were Propionibacterium, Aquabacterium, Ralstonia, and Acinetobacter. While the top five most frequently observed genera were Pseudomonas, Propionibacterium, Acinetobacter, Ralstonia, and Sphingomonas. The majority of the most frequently observed genera (high evenness) were associated with reagent or potential human contamination. Additionally, in DNA extraction blanks, we observed potential archaeal contaminants, including methanogens, which have not been discussed in previous contamination studies. Such contaminants would directly affect the interpretation of subsurface molecular studies, as methanogenesis is an important subsurface biogeochemical process. Utilizing previously identified contaminant genera, we found that ∼27% of the total dataset were identified as contaminant sequences that likely originate from DNA extraction and DNA cleanup methods. Thus, controls must be taken at every step of the collection and processing procedure when working with low biomass environments such as, but not limited to, portions of Earth’s deep subsurface. Taken together, we stress that the CoDL dataset is an incredible resource for the broader research community interested in subsurface life, and steps to remove contamination derived sequences must be taken prior to using this dataset. PMID:29780369

Identification and Removal of Contaminant Sequences From Ribosomal Gene Databases: Lessons From the Census of Deep Life.

PubMed

Sheik, Cody S; Reese, Brandi Kiel; Twing, Katrina I; Sylvan, Jason B; Grim, Sharon L; Schrenk, Matthew O; Sogin, Mitchell L; Colwell, Frederick S

2018-01-01

Earth's subsurface environment is one of the largest, yet least studied, biomes on Earth, and many questions remain regarding what microorganisms are indigenous to the subsurface. Through the activity of the Census of Deep Life (CoDL) and the Deep Carbon Observatory, an open access 16S ribosomal RNA gene sequence database from diverse subsurface environments has been compiled. However, due to low quantities of biomass in the deep subsurface, the potential for incorporation of contaminants from reagents used during sample collection, processing, and/or sequencing is high. Thus, to understand the ecology of subsurface microorganisms (i.e., the distribution, richness, or survival), it is necessary to minimize, identify, and remove contaminant sequences that will skew the relative abundances of all taxa in the sample. In this meta-analysis, we identify putative contaminants associated with the CoDL dataset, recommend best practices for removing contaminants from samples, and propose a series of best practices for subsurface microbiology sampling. The most abundant putative contaminant genera observed, independent of evenness across samples, were Propionibacterium , Aquabacterium , Ralstonia , and Acinetobacter . While the top five most frequently observed genera were Pseudomonas , Propionibacterium , Acinetobacter , Ralstonia , and Sphingomonas . The majority of the most frequently observed genera (high evenness) were associated with reagent or potential human contamination. Additionally, in DNA extraction blanks, we observed potential archaeal contaminants, including methanogens, which have not been discussed in previous contamination studies. Such contaminants would directly affect the interpretation of subsurface molecular studies, as methanogenesis is an important subsurface biogeochemical process. Utilizing previously identified contaminant genera, we found that ∼27% of the total dataset were identified as contaminant sequences that likely originate from DNA extraction and DNA cleanup methods. Thus, controls must be taken at every step of the collection and processing procedure when working with low biomass environments such as, but not limited to, portions of Earth's deep subsurface. Taken together, we stress that the CoDL dataset is an incredible resource for the broader research community interested in subsurface life, and steps to remove contamination derived sequences must be taken prior to using this dataset.

Scenario simulation based assessment of subsurface energy storage

NASA Astrophysics Data System (ADS)

Beyer, C.; Bauer, S.; Dahmke, A.

2014-12-01

Energy production from renewable sources such as solar or wind power is characterized by temporally varying power supply. The politically intended transition towards renewable energies in Germany („Energiewende") hence requires the installation of energy storage technologies to compensate for the fluctuating production. In this context, subsurface energy storage represents a viable option due to large potential storage capacities and the wide prevalence of suited geological formations. Technologies for subsurface energy storage comprise cavern or deep porous media storage of synthetic hydrogen or methane from electrolysis and methanization, or compressed air, as well as heat storage in shallow or moderately deep porous formations. Pressure build-up, fluid displacement or temperature changes induced by such operations may affect local and regional groundwater flow, geomechanical behavior, groundwater geochemistry and microbiology. Moreover, subsurface energy storage may interact and possibly be in conflict with other "uses" like drinking water abstraction or ecological goods and functions. An utilization of the subsurface for energy storage therefore requires an adequate system and process understanding for the evaluation and assessment of possible impacts of specific storage operations on other types of subsurface use, the affected environment and protected entities. This contribution presents the framework of the ANGUS+ project, in which tools and methods are developed for these types of assessments. Synthetic but still realistic scenarios of geological energy storage are derived and parameterized for representative North German storage sites by data acquisition and evaluation, and experimental work. Coupled numerical hydraulic, thermal, mechanical and reactive transport (THMC) simulation tools are developed and applied to simulate the energy storage and subsurface usage scenarios, which are analyzed for an assessment and generalization of the imposed THMC-processes, mutual effects and influences on protected entities. The scenario analyses allow the deduction of monitoring concepts as well as a first methodology for large scale spatial planning of the geological subsurface. This concept is illustrated for different storage options and their impacts in space and time.

Field and Lab-Based Microbiological Investigations of the Marcellus Shale

NASA Astrophysics Data System (ADS)

Wishart, J. R.; Neumann, K.; Edenborn, H. M.; Hakala, A.; Yang, J.; Torres, M. E.; Colwell, F. S.

2013-12-01

The recent exploration of shales for natural gas resources has provided the opportunity to study their subsurface geochemistry and microbiology. Evidence indicates that shale environments are marked by extreme conditions such as high temperature and pressure, low porosity, permeability and connectivity, and the presence of heavy metals and radionuclides. It has been postulated that many of these shales are naturally sterile due to the high pressure and temperature conditions under which they were formed. However, it has been shown in the Antrim and New Albany shales that microbial communities do exist in these environments. Here we review geochemical and microbiological evidence for the possible habitation of the Marcellus shale by microorganisms and compare these conditions to other shales in the U.S. Furthermore, we describe the development of sampling and analysis techniques used to evaluate microbial communities present in the Marcellus shale and associated hydraulic fracturing fluid. Sampling techniques thus far have consisted of collecting flowback fluids from wells and water impoundments and collecting core material from previous drilling expeditions. Furthermore, DNA extraction was performed on Marcellus shale sub-core with a MoBio PowerSoil kit to determine its efficiency. Assessment of the Marcellus shale indicates that it has low porosity and permeability that are not conducive to dense microbial populations; however, moderate temperatures and a natural fracture network may support a microbial community especially in zones where the Marcellus intersects more porous geologic formations. Also, hydraulic fracturing extends this fracture network providing more environments where microbial communities can exist. Previous research which collected flowback fluids has revealed a diverse microbial community that may be derived from hydrofrac fluid production or from the subsurface. DNA extraction from 10 g samples of Marcellus shale sub-core were unsuccessful even when samples were spiked with 8x108 cells/g of shale. This indicated that constituents of shale such as high levels of carbonates, humic acids and metals likely inhibited components of the PowerSoil kit. Future research is focused on refining sample collection and analyses to gain a full understanding of the microbiology of the Marcellus shale and associated flowback fluids. This includes the development of an in situ osmosampler, which will collect temporally relevant fluid and colonized substrate samples. The design of the osmosampler for hydraulic fracturing wells is being adapted from those used to sample marine environments. Furthermore, incubation experiments are underway to study interactions between microbial communities associated with hydraulic fracturing fluid and Marcellus shale samples. In conclusion, evidence suggests that the Marcellus shale is a possible component of the subsurface biosphere. Future studies will be valuable in determining the microbial community structure and function in relation to the geochemistry of the Marcellus shale and its future development as a natural gas resource.

Biofilm development in a hotspot of mixing between shallow and deep groundwater in a fractured aquifer: field evidence from joint flow, chemical and microbiological characterization

NASA Astrophysics Data System (ADS)

Bochet, Olivier; Le Borgne, Tanguy; Pédrot, Mathieu; Labasque, Thierry; Lavenant, Nicolas; Petton, Christophe; Dufresne, Alexis; Ben Maamar, Sarah; Chatton, Eliot; De la Bernardie, Jérôme; Aquilina, Luc

2015-04-01

Biofilm development in a hotspot of mixing between shallow and deep groundwater in a fractured aquifer: field evidence from joint flow, chemical and microbiological characterization Olivier Bochet1, Tanguy Le Borgne1, Mathieu Pédrot1, Thierry Labasque1, Nicolas Lavenant1, Christophe Petton1, Alexis Dufresne2,Sarah Ben Maamar1-2, Eliot Chatton1, Jérôme de la Bernardie1, Luc Aquilina1 1: Géosciences Rennes, CNRS UMR 6118, Université de Rennes 1, Campus de Beaulieu bât 14B, Rennes, France 2: Ecobio, CNRS UMR 6553, Université de Rennes 1, Campus de Beaulieu, bât 14, Rennes, France Biofilms play a major role in controlling the fluxes and reactivity of chemical species transported in hydrological systems. Their development can have either positive impacts on groundwater quality (e.g. attenuation of contaminants under natural or stimulated conditions), or possible negative effects on subsurface operations (e.g. bio-clogging of geothermal dipoles or artificial recharge systems). Micro-organisms require both electron donors and electron acceptors for cellular growth, proliferation and maintenance of their metabolic functions. The mechanisms controlling these reactions derive from the interactions occurring at the micro-scale that depend on mineral compositions, the biota of subsurface environment, but also fluid mixing, which determines the local concentrations of nutriments, electron donors and electron acceptors. Hence, mixing zones between oxygen and nutriment rich shallow groundwater and mineralized deep groundwater are often considered as potential hotspots of microbial activity, although relatively few field data document flow distributions, transport properties, chemical gradients and micro-organisms distributions across these mixing interfaces. Here we investigate the origin of a localized biofilm development observed in the fractured granite aquifer at the Ploemeur observatory (H+ network hplus.ore.fr).This biofilm composed of ferro-oxidizing bacteria is observed in an 130m deep artesian well. Borehole video logs show an important colonization of the well by the biofilm in the shallower part (0 to 60m), while it is inexistent in the deeper part (60 to 130m). As flow is localized in a few deep and shallow fractures, we presume that the spatial distribution of biofilm is controlled by mixing between shallow and deep groundwater. To verify this hypothesis we conducted a field campaign with joint characterization of the flow and chemical composition of water flowing from the different fractures, as well as the microbiological composition of the biofilm at different depth, using pyrosequencing techniques. We will discuss in this presentation the results of this interdisciplinary dataset and their implications for the occurrence of hotspots of microbiological activity in the subsurface.

Microbial Life of North Pacific Oceanic Crust

NASA Astrophysics Data System (ADS)

Schumann, G.; Koos, R.; Manz, W.; Reitner, J.

2003-12-01

Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed reactions that influence the geophysical properties of these environments. Drilling into 45-Ma oceanic basaltic crust in a deepwater environment during ODP Leg 200 provided a promising opportunity to explore the abundance, diversity and activity of micro-organisms. The combined use of culture-independent molecular phylogenetic analyses and enrichment culture techniques is an advantageous approach in investigating subsurface microbial ecosystems. Enrichment culture methods allow the evaluation of potential activities and functions. Microbiological investigations revealed few aerobic cultivable, in part hitherto unknown, micro-organisms in deep submarine sediments and basaltic lava flows. 16S rDNA sequencing of isolates from sediment revealed the next relatives to be members of the genera Halomonas, Pseudomonas, and Lactobacillus. Within the Pseudomonadaceae the closest relative is Acinetobacter sp., which was isolated from a deep subsurface environment. The next phylogenetical relatives within the Halomonadaceae are bacteria typically isolated from Soda lakes, which are considered as model of early life conditions. Interestingly, not only sediment bacteria could be obtained in pure culture. Aerobic strains could also be successfully isolated from the massive tholeiitic basalt layer at a depth of 76.16 mbsf (46 m below the sediment/basement contact). These particular isolates are gram-positive with low G+C content of DNA, phylogenetically affiliated to the phylum Firmicutes. The closest neighbors are e.g. a marine Bacillus isolated from the Gulf of Mexico and a low G+C gram-positive bacterium, which belongs to the microbial flora in the deepest sea mud of the Mariana Trench, isolated from a depth of 10,897 m. Based on the similarity values, the isolates represent hitherto undescribed species of the deep biosphere. Molecular microbial diversity is currently determined by cloning und comparative 16S rRNA gene analyses. The first results will also be presented. In summary, the low number of isolates, cultivated under aerobic conditions, is in good agreement with the common opinion that most of the bacteria within the deep biosphere are anaerobic. Thus, studies of microbial community structure in solid geological materials are feasible and constitute further evidence that continuing microbiological activity in the challenging exploration of the deep sub-seafloor biosphere environment is absolutely promising.

Geomicrobiology and Metagenomics of Terrestrial Deep Subsurface Microbiomes.

PubMed

Itävaara, M; Salavirta, H; Marjamaa, K; Ruskeeniemi, T

2016-01-01

Fractures in the deep subsurface of Earth's crust are inhabited by diverse microbial communities that participate in biogeochemical cycles of the Earth. Life on Earth, which arose c. 3.5-4.0 billion years ago, reaches down at least 5 km in the crust. Deep mines, caves, and boreholes have provided scientists with opportunities to sample deep subsurface microbiomes and to obtain information on the species diversity and functions. A wide variety of bacteria, archaea, eukaryotes, and viruses are now known to reside in the crust, but their functions are still largely unknown. The crust at different depths has varying geological composition and hosts endemic microbiomes accordingly. The diversity is driven by geological formations and gases evolving from deeper depths. Cooperation among different species is still mostly unexplored, but viruses are known to restrict density of bacterial and archaeal populations. Due to the complex growth requirements of the deep subsurface microbiomes, the new knowledge about their diversity and functions is mostly obtained by molecular methods, eg, meta'omics'. Geomicrobiology is a multidisciplinary research area combining disciplines from geology, mineralogy, geochemistry, and microbiology. Geomicrobiology is concerned with the interaction of microorganisms and geological processes. At the surface of mineralogical or rock surfaces, geomicrobial processes occur mainly under aerobic conditions. In the deep subsurface, however, the environmental conditions are reducing and anaerobic. The present chapter describes the world of microbiomes in deep terrestrial geological environments as well as metagenomic and metatranscriptomic methods suitable for studies of these enigmatic communities. Copyright © 2016 Elsevier Inc. All rights reserved.

An Option in Applied Microbiology.

ERIC Educational Resources Information Center

Lee, William E., III

1988-01-01

Describes a program option for undergraduate chemical engineering students interested in biotechnology. Discusses how this program is deployed at the University of Southern Florida. Lists courses which apply to this program. Discusses the goals of teaching applied microbiology to engineering majors. (CW)

Analysis of Tank 38H (HTF-38-15-47, 49) and Tank 43H (HTF-43-15-51, 53) surface and subsurface supernatant samples in support of enrichment and corrosion control programs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oji, L. N.

This report provides the results of analyses on Tanks 38H and 43H surface and subsurface supernatant liquid samples in support of the Enrichment Control Program (ECP) and the Corrosion Control Program (CCP).

[Analysis of the results of the SEIMC External Quality Control Program. Year 2011].

PubMed

Ruiz de Gopegui Bordes, Enrique; Guna Serrano, M del Remedio; Orta Mira, Nieves; Ovies, María Rosario; Poveda, Marta; Gimeno Cardona, Concepción

2013-02-01

The External Quality Control Program of the Spanish Society of Infectious Diseases and Clinical Microbiology (Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica [SEIMC]) includes controls for bacteriology, serology, mycology, parasitology, mycobacteria, virology, and molecular microbiology. This article presents the most relevant conclusions and lessons from the 2011 controls. Overall, the results obtained in 2011 confirm the excellent skill and good technical standards found in previous years. Nevertheless, erroneous results can be obtained in any laboratory and in clinically relevant determinations. The results of this program highlight the need to implement both internal and external controls, such as those offered by the SEIMC program, in order to ensure maximal quality of microbiological tests. Copyright © 2013 Elsevier España, S.L. All rights reserved.

Linking deposit morphology and clogging in subsurface remediation: Final Technical Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mays, David C.

2013-12-11

Groundwater is a crucial resource for water supply, especially in arid and semiarid areas of the United States west of the 100th meridian. Accordingly, remediation of contaminated groundwater is an important application of science and technology, particularly for the U.S. Department of Energy (DOE), which oversees a number of groundwater remediation sites from Cold War era mining. Groundwater remediation is complex, because it depends on identifying, locating, and treating contaminants in the subsurface, where remediation reactions depend on interacting geological, hydrological, geochemical, and microbiological factors. Within this context, permeability is a fundamental concept, because it controls the rates and pathwaysmore » of groundwater flow. Colloid science is intimately related to permeability, because when colloids are present (particles with equivalent diameters between 1 nanometer and 10 micrometers), changes in hydrological or geochemical conditions can trigger a detrimental reduction in permeability called clogging. Accordingly, clogging is a major concern in groundwater remediation. Several lines of evidence suggest that clogging by colloids depends on (1) colloid deposition, and (2) deposit morphology, that is, the structure of colloid deposits, which can be quantified as a fractal dimension. This report describes research, performed under a 2-year, exploratory grant from the DOE’s Subsurface Biogeochemical Research (SBR) program. This research employed a novel laboratory technique to simultaneously measure flow, colloid deposition, deposit morphology, and permeability in a flow cell, and also collected field samples from wells at the DOE’s Old Rifle remediation site. Field results indicate that suspended solids at the Old Rifle site have fractal structures. Laboratory results indicate that clogging is associated with colloid deposits with smaller fractal dimensions, in accordance with previous studies on initially clean granular media. Preliminary modeling has identified the deposit radius of gyration as a candidate variable to account for clogging as a function of (1) colloid accumulation and (2) deposit morphology.« less

Deep subsurface life in Bengal Fan sediments (IODP Exp. 354)

NASA Astrophysics Data System (ADS)

Adhikari, R. R.; Heuer, V. B.; Elvert, M.; Kallmeyer, J.; Kitte, J. A.; Wörmer, L.; Hinrichs, K. U.

2017-12-01

We collected Bengal Fan sediment samples along a 8°N transect during International Ocean Discovery Program Expedition 354 (February - March 2015, Singapore - Colombo, Sri Lanka) to study subseafloor life in this, as yet unstudied, area. Among other biogeochemical parameters, we quantified microbial biomass by analyzing prokaryotic cells using epifluorescence microscopy after detaching cells from the sediment, and bacterial endospores by analyzing the diagnostic biomarker dipicolinic acid (DPA) by detection of fluorescence of the terbium-DPA complex. To gain understanding of total microbial activity, we quantified hydrogen utilization potential of hydrogenase enzymes, which are ubiquitous in subsurface microorganisms, by using a tritium assay. We measured highest cell concentrations of ca. 108 cells g-1 in shallow sediments close to the seafloor. These concentrations are one to two orders of magnitude lower than in most marine continental margin settings [1]. Similar to the global trend [1], cell concentrations decreased with depth according to a power-law function. Endospore concentrations scattered between ca. 105 and 107 cells g-1 sediment at all sites and depths. We could not observe a clear relationship of endospore concentration and sediment depth; instead, it appears to be linked to lithology and total organic carbon content. Bulk Hydrogenase enzyme activity ranged from nmolar to μmolar range of H2 g-1d-1. Similar to previous observations [2], per-cell hydrogen utilization depends on vertical biogeochemical zones, which could be due to the differences in hydrogen utilization requirements/efficiency of the respective metabolic processes such as sulfate reduction, methanogenesis, fermentation etc. Bengal fan is highly dynamic due to channel and levee systems and the sediments are dominated by turbidites, thick sand layers and hemipelagic deposits, which may control biogeochemical zonation. Based on our microbial biomass and activity data, we suggest that the nature, quality and origin of sedimentary material influence the deep subsurface life. [1] Kallmeyer et al., (2012) PNAS 109(40), 16213-16216 [2] Adhikari et al., (2016) Frontiers in Microbiology 7:8

[Analysis of the results of the 2010 External Quality Control Program of the Spanish Society of Infectious Diseases and Clinical Microbiology].

PubMed

Ruiz de Gopegui Bordes, Enrique; Serrano, M del Remedio Guna; Orta Mira, Nieves; Ovies, María Rosario; Poveda, Marta; Cardona, Concepción Gimeno

2011-12-01

The External Quality Control Program of the Spanish Society of Infectious Diseases and Clinical Microbiology includes controls for bacteriology, serology, mycology, parasitology, mycobacteria, virology and molecular microbiology. This article presents the most important conclusions and lessons of the 2010 controls. As a whole, the results obtained in 2010 confirm the excellent skill and good technical standards found in previous years. However, erroneous results can be obtained in any laboratory and in clinically relevant determinations. The results of this program highlight the need to implement both internal and external controls to ensure maximal quality of microbiological tests(1). Copyright © 2011 Elsevier España S.L. All rights reserved.

In-situ Subsurface Soil Analyzer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ulmer, Chris

The Department of Energy’s (DOE’s) Terrestrial Ecosystem Science (TES) program is seeking improved sensor systems for monitoring hydro-biogeochemical processes in complex subsurface environments. The TES program is specifically interested in acquiring chemical and structural information regarding the type and nature of the hydration and redox states of subsurface chemical species. The technology should be able to perform on-site and real-time measurements to provide information not available using current sample acquisition and preservation processes. To address the needs of the DOE and the terrestrial science community, Physical Optics Corporation (POC) worked on the development of a new In-Situ Subsurface Soil Analyzermore » (ISSA) based on magnetic resonance technologies. Benchtop testing was performed to assess the feasibility of continuous wave electron pair resonance (CW-EPR) detection of chemical species in subsurface soil systems.« less

77 FR 298 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-04

....gov . Name of Committee: Microbiology, Infectious Diseases and AIDS Initial Review Group; Microbiology... Assistance Program Nos. 93.855, Allergy, Immunology, and Transplantation Research; 93.856, Microbiology and...

Microbiological monitoring for the US Geological Survey National Water-Quality Assessment Program

USGS Publications Warehouse

Francy, Donna S.; Myers, Donna N.; Helsel, Dennis R.

2000-01-01

Data to characterize the microbiological quality of the Nation?s fresh, marine, and estuarine waters are usually collected for local purposes, most often to judge compliance with standards for protection of public health in swimmable or drinkable waters. Methods and procedures vary with the objectives and practices of the parties collecting data and are continuously being developed or modified. Therefore, it is difficult to provide a nationally consistent picture of the microbial quality of the Nation?s waters. Study objectives and guidelines for a national microbiological monitoring program are outlined in this report, using the framework of the U.S. Geological Survey (USGS) National Water-Quality Assessment (NAWQA) program. A national program is designed to provide long-term data on the presence of microbiological pathogens and indicators in ground water and surface water to support effective water policy and management. Three major groups of waterborne pathogens affect the public health acceptability of waters in the United States?bacteria, protozoa, and viruses. Microbiological monitoring in NAWQA would be designed to assess the occurrence, distribution, and trends of pathogenic organisms and indicators in surface waters and ground waters; relate the patterns discerned to factors that help explain them; and improve our understanding of the processes that control microbiological water quality.

Microbial Stimulation and Succession following a Test Well Injection Simulating CO₂ Leakage into a Shallow Newark Basin Aquifer

PubMed Central

O’Mullan, Gregory; Dueker, M. Elias; Clauson, Kale; Yang, Qiang; Umemoto, Kelsey; Zakharova, Natalia; Matter, Juerg; Stute, Martin; Takahashi, Taro; Goldberg, David

2015-01-01

In addition to efforts aimed at reducing anthropogenic production of greenhouse gases, geological storage of CO2 is being explored as a strategy to reduce atmospheric greenhouse gas emission and mitigate climate change. Previous studies of the deep subsurface in North America have not fully considered the potential negative effects of CO2 leakage into shallow drinking water aquifers, especially from a microbiological perspective. A test well in the Newark Rift Basin was utilized in two field experiments to investigate patterns of microbial succession following injection of CO2-saturated water into an isolated aquifer interval, simulating a CO2 leakage scenario. A decrease in pH following injection of CO2 saturated aquifer water was accompanied by mobilization of trace elements (e.g. Fe and Mn), and increased bacterial cell concentrations in the recovered water. 16S ribosomal RNA gene sequence libraries from samples collected before and after the test well injection were compared to link variability in geochemistry to changes in aquifer microbiology. Significant changes in microbial composition, compared to background conditions, were found following the test well injections, including a decrease in Proteobacteria, and an increased presence of Firmicutes, Verrucomicrobia and microbial taxa often noted to be associated with iron and sulfate reduction. The concurrence of increased microbial cell concentrations and rapid microbial community succession indicate significant changes in aquifer microbial communities immediately following the experimental CO2 leakage event. Samples collected one year post-injection were similar in cell number to the original background condition and community composition, although not identical, began to revert toward the pre-injection condition, indicating microbial resilience following a leakage disturbance. This study provides a first glimpse into the in situ successional response of microbial communities to CO2 leakage after subsurface injection in the Newark Basin and the potential microbiological impact of CO2 leakage on drinking water resources. PMID:25635675

Biofilm development in a hotspot of mixing between shallow and deep groundwater in a fractured aquifer: field evidence from joint flow, chemical and microbiological measurements

NASA Astrophysics Data System (ADS)

Bochet, O.; Dufresne, A.; Pédrot, M.; Chatton, E.; Labasque, T.; Ben Maamar, S.; Burté, L.; de la Bernardie, J.; Guihéneuf, N.; Lavenant, N.; Petton, C.; Bour, O.; Aquilina, L.; Le Borgne, T.

2015-12-01

Biofilms play a major role in controlling the fluxes and reactivity of chemical species transported in hydro-logical systems. Micro-organisms require both electron donors and electron acceptors for cellular growth, proliferation and maintenance of their metabolic functions. The mechanisms controlling these reactions derive from the interactions occurring at the micro-scale that depend on mineral compositions, the biota of subsurface environment, but also fluid mixing, which determines the local concentrations of nutriments, electron donors and electron acceptors. Hence, mixing zones between oxygen and nutriment rich shallow groundwater and mineralized deep groundwater are often considered as potential hotspots of microbial activity, although relatively few field data document flow distributions, transport properties, chemical gradients and micro-organisms distributions across these mixing interfaces. Here we investigate the origin of a localized biofilm development observed in the fractured granite aquifer at the Ploemeur observatory (H+ network hplus.ore.fr).This biofilm composed of ferro-oxidizing bacteria is observed in an 130m deep artesian well. Borehole video logs show an important colonization of the well by the biofilm in the shallower part (0 to 60m), while it is inexistent in the deeper part (60 to 130m). As flow is localized in a few deep and shallow fractures, we presume that the spatial distribution of biofilm is controlled by mixing between shallow and deep groundwater. To verify this hypothesis we conducted a field campaign with joint characterization of the flow and chemical composition of water flowing from the different fractures, as well as the microbiological composition of the biofilm at different depth, using pyrosequencing techniques. We will discuss in this presentation the results of this interdisciplinary dataset and their implications for the occurrence of hotspots of microbiological activity in the subsurface.

Opportunities and challenges in studies of deep life (Invited)

NASA Astrophysics Data System (ADS)

Edwards, K. J.

2010-12-01

Over the past two decades, there has been an increasing awareness within the geological, microbiological, and oceanographic communities of the potentially vast microbial biosphere that is harbored beneath the surface of the Earth. With this awareness has come a mounting effort to study this potential biome - to better quantify biomass abundance, activity, and biogeochemical activity. In the Earth system, the largest deep subsurface biome is also the least accessible - the deep ocean subsurface biosphere. The oceanic deep biosphere also has greatest potential for influencing global scale biogeochemical processes -the carbon and energy cycles for example, and other elemental cycles. To address these topics and mount interdisciplinary efforts to study the deep subsurface marine biosphere, we have recently formed a center in support integrative, collaborative investigations. The national science foundation Center for Dark Biosphere Investigations (C-DEBI), has been initiated for the explicit purpose of resolving the extent, function, dynamics and implications of the subseafloor biosphere. This talk will discuss C-DEBI science, with focus on some of the opportunities and challenges in the study of deep life in the ocean, and the role that C-DEBI will play in meeting them

Super-long Anabiosis of Ancient Microorganisms in Ice and Terrestrial Models for Development of Methods to Search for Life on Mars, Europa and other Planetary Bodies

NASA Technical Reports Server (NTRS)

Abyzov, S. S.; Duxbury, N. S.; Bobin, N. E.; Fukuchi, M.; Hoover, R. B.; Kanda, H.; Mitskevich, I. N.; Mulyukin, A. L.; Naganuma, T.; Poglazova, M. N.;

Monitoring of Gasoline-ethanol Degradation In Undisturbed Soil

NASA Astrophysics Data System (ADS)

Österreicher-Cunha, P.; Nunes, C. M. F.; Vargas, E. A.; Guimarães, J. R. D.; Costa, A.

Environmental contamination problems are greatly emphasised nowadays because of the direct threat they represent for human health. Traditional remediation methods fre- quently present low efficiency and high costs; therefore, biological treatment is being considered as an accessible and efficient alternative for soil and water remediation. Bioventing, commonly used to remediate petroleum hydrocarbon spills, stimulates the degradation capacity of indigenous microorganisms by providing better subsur- face oxygenation. In Brazil, gasoline and ethanol are mixed (78:22 v/v); some authors indicate that despite gasoline high degradability, its degradation in subsurface is hin- dered by the presence of much more rapidly degrading ethanol. Contaminant distribu- tion and degradation in the subsurface can be monitored by several physical, chemical and microbiological methodologies. This study aims to evaluate and follow the degra- dation of a gasoline-ethanol mixture in a residual undisturbed tropical soil from Rio de Janeiro. Bioventing was used to enhance microbial degradation. Shifts in bacte- rial culturable populations due to contamination and treatment effects were followed by conventional microbiology methods. Ground Penetrating Radar (GPR) measure- ments, which consist of the emission of electro-magnetic waves into the soil, yield a visualisation of contaminant degradation because of changes in soil conductivity due to microbial action on the pollutants. Chemical analyses will measure contaminant residue in soil. Our results disclosed contamination impact as well as bioventing stim- ulation on soil culturable heterotrophic bacterial populations. This multidisciplinary approach allows for a wider evaluation of processes occurring in soil.

Introduction to Biological Research: A Laboratory Course in Microbiology

ERIC Educational Resources Information Center

Dudley, Aimee M.; Cardozo, David Lopes

2006-01-01

In this paper, the authors describe their development of an introductory laboratory course in microbiology that is geared towards students in grades 8-10. The course was developed as part of the Mentoring for Science Program at Harvard Medical School, an outreach program created by the Minority Faculty Development Program, directed towards…

Antimicrobial Stewardship: How the Microbiology Laboratory Can Right the Ship.

PubMed

Morency-Potvin, Philippe; Schwartz, David N; Weinstein, Robert A

2017-01-01

Antimicrobial stewardship is a bundle of integrated interventions employed to optimize the use of antimicrobials in health care settings. While infectious-disease-trained physicians, with clinical pharmacists, are considered the main leaders of antimicrobial stewardship programs, clinical microbiologists can play a key role in these programs. This review is intended to provide a comprehensive discussion of the different components of antimicrobial stewardship in which microbiology laboratories and clinical microbiologists can make significant contributions, including cumulative antimicrobial susceptibility reports, enhanced culture and susceptibility reports, guidance in the preanalytic phase, rapid diagnostic test availability, provider education, and alert and surveillance systems. In reviewing this material, we emphasize how the rapid, and especially the recent, evolution of clinical microbiology has reinforced the importance of clinical microbiologists' collaboration with antimicrobial stewardship programs. Copyright © 2016 American Society for Microbiology.

Polymer-Enhanced Subsurface Delivery and Distribution of Permanganate

DTIC Science & Technology

2013-02-01

Subsurface Delivery and Distribution of Permanganate February 2013 Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for...SUBTITLE Polymer-Enhanced Subsurface Delivery and Distribution of Permanganate 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6...SAMPLING RESULTS ........................................................................................ 28 5.6.1 Permanganate Distribution and Sweep

A New Sensitive GC-MS-based Method for Analysis of Dipicolinic Acid and Quantifying Bacterial Endospores in Deep Marine Subsurface Sediment

NASA Astrophysics Data System (ADS)

Fang, J.

2015-12-01

Marine sediments cover more than two-thirds of the Earth's surface and represent a major part of the deep biosphere. Microbial cells and microbial activity appear to be widespread in these sediments. Recently, we reported the isolation of gram-positive anaerobic spore-forming piezophilic bacteria and detection of bacterial endospores in marine subsurface sediment from the Shimokita coalbed, Japan. However, the modern molecular microbiological methods (e.g., DNA-based microbial detection techniques) cannot detect bacterial endospore, because endospores are impermeable and are not stained by fluorescence DNA dyes or by ribosomal RNA staining techniques such as catalysed reporter deposition fluorescence in situ hybridization. Thus, the total microbial cell abundance in the deep biosphere may has been globally underestimated. This emphasizes the need for a new cultivation independent approach for the quantification of bacterial endospores in the deep subsurface. Dipicolinic acid (DPA, pyridine-2,6-dicarboxylic acid) is a universal and specific component of bacterial endospores, representing 5-15wt% of the dry spore, and therefore is a useful indicator and quantifier of bacterial endospores and permits to estimate total spore numbers in the subsurface biosphere. We developed a sensitive analytical method to quantify DPA content in environmental samples using gas chromatography-mass spectrometry. The method is sensitive and more convenient in use than other traditional methods. We applied this method to analyzing sediment samples from the South China Sea (obtained from IODP Exp. 349) to determine the abundance of spore-forming bacteria in the deep marine subsurface sediment. Our results suggest that gram-positive, endospore-forming bacteria may be the "unseen majority" in the deep biosphere.

Microbial communities at the borehole observatory on the Costa Rica Rift flank (Ocean Drilling Program Hole 896A).

PubMed

Nigro, Lisa M; Harris, Kate; Orcutt, Beth N; Hyde, Andrew; Clayton-Luce, Samuel; Becker, Keir; Teske, Andreas

2012-01-01

The microbiology of subsurface, hydrothermally influenced basaltic crust flanking mid-ocean ridges has remained understudied, due to the difficulty in accessing the subsurface environment. The instrumented boreholes resulting from scientific ocean drilling offer access to samples of the formation fluids circulating through oceanic crust. We analyzed the phylogenetic diversity of bacterial communities of fluid and microbial mat samples collected in situ from the observatory at Ocean Drilling Program Hole 896A, drilled into ~6.5 million-year-old basaltic crust on the flank of the Costa Rica Rift in the equatorial Pacific Ocean. Bacterial 16S rRNA gene sequences recovered from borehole fluid and from a microbial mat coating the outer surface of the fluid port revealed both unique and shared phylotypes. The dominant bacterial clones from both samples were related to the autotrophic, sulfur-oxidizing genus Thiomicrospira. Both samples yielded diverse gamma- and alphaproteobacterial phylotypes, as well as members of the Bacteroidetes, Planctomycetes, and Verrucomicrobia. Analysis of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) genes (cbbL and cbbM) from the sampling port mat and from the borehole fluid demonstrated autotrophic carbon assimilation potential for in situ microbial communities; most cbbL genes were related to those of the sulfur-oxidizing genera Thioalkalivibrio and Thiomicrospira, and cbbM genes were affiliated with uncultured phylotypes from hydrothermal vent plumes and marine sediments. Several 16S rRNA gene phylotypes from the 896A observatory grouped with phylotypes recovered from seawater-exposed basalts and sulfide deposits at inactive hydrothermal vents, but there is little overlap with hydrothermally influenced basaltic boreholes 1026B and U1301A on the Juan de Fuca Ridge flank, suggesting that site-specific characteristics of Hole 896A (i.e., seawater mixing into borehole fluids) affect the microbial community composition.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balkwill, D.L.; Reeves, R.H.

The present document is an interim technical report in which we describe the research which has been completed during the seven-month period since the start of the grant. Progress is summarized in two main areas. The first is microbiological characterization of subsurface materials from the Hanford reservation and the Idaho National Engineering Laboratory, and the second is phylogenetic characterization of these microorganisms. The major tools used for phylogenetic characterization are RFLP analysis of PCR derived material and 16S rRNA sequencing. A description of manuscripts ready for publication is also provided. 4 refs. (MHB)

Thermal Impact of Medium Deep Borehole Thermal Energy Storage on the Shallow Subsurface

NASA Astrophysics Data System (ADS)

Welsch, Bastian; Schulte, Daniel O.; Rühaak, Wolfram; Bär, Kristian; Sass, Ingo

2017-04-01

Borehole heat exchanger arrays are a well-suited and already widely applied method for exploiting the shallow subsurface as seasonal heat storage. However, in most of the populated regions the shallow subsurface also comprises an important aquifer system used for drinking water production. Thus, the operation of shallow geothermal heat storage systems leads to a significant increase in groundwater temperatures in the proximity of the borehole heat exchanger array. The magnitude of the impact on groundwater quality and microbiology associated with this temperature rise is controversially discussed. Nevertheless, the protection of shallow groundwater resources has priority. Accordingly, water authorities often follow restrictive permission policies for building such storage systems. An alternative approach to avoid this issue is the application of medium deep borehole heat exchanger arrays instead of shallow ones. The thermal impact on shallow aquifers can be significantly reduced as heat is stored at larger depth. Moreover, it can be further diminished by the installation of a thermally insulating materials in the upper section of the borehole heat exchangers. Based on a numerical simulation study, the advantageous effects of medium deep borehole thermal energy storage are demonstrated and quantified. A finite element software is used to model the heat transport in the subsurface in 3D, while the heat transport in the borehole heat exchangers is solved analytically in 1D. For this purpose, an extended analytical solution is implemented, which also allows for the consideration of a thermally insulating borehole section.

Competency assessment of microbiology medical laboratory technologists in Ontario, Canada.

PubMed

Desjardins, Marc; Fleming, Christine Ann

2014-08-01

Accreditation in Ontario, Canada, requires that licensed clinical laboratories participate in external quality assessment (also known as proficiency testing) and perform competency evaluation of their staff. To assess the extent of ongoing competency assessment practices, the Quality Management Program--Laboratory Services (QMP-LS) Microbiology Committee surveyed all 112 licensed Ontario microbiology laboratories. The questionnaire consisted of a total of 21 questions that included yes/no, multiple-choice, and short-answer formats. Participants were asked to provide information about existing programs, the frequency of testing, what areas are evaluated, and how results are communicated to the staff. Of the 111 responding laboratories, 6 indicated they did not have a formal evaluation program since they perform only limited bacteriology testing. Of the remaining 105 respondents, 87% perform evaluations at least annually or every 2 years, and 61% include any test or task performed, whereas 16% and 10% focus only on problem areas and high-volume complex tasks, respectively. The most common methods of evaluation were review of external quality assessment (EQA) challenges, direct observation, and worksheet review. With the exception of one participant, all communicate results to staff, and most take remedial action to correct the deficiencies. Although most accredited laboratories have a program to assess the ongoing competency of their staff, the methods used are not standardized or consistently applied, indicating that there is room for improvement. The survey successfully highlighted potential areas for improvement and allowed the QMP-LS Microbiology Committee to provide guidance to Ontario laboratories for establishing or improving existing microbiology-specific competency assessment programs. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Program and Abstracts of the National Meeting of the Society for Leukocyte Biology (25th) Held in Washington, DC on October 27-30, 1988. Journal of Leukocyte Biology. Volume 44, Number 4

DTIC Science & Technology

1988-10-01

C.P. Schaffner. Waksman Institute of Microbiology @ Rutgers-The State University, New Brunswick, NJ 08855-0759. 242 1988 Annual Meeting Program...Eierman, C. Johnson and S. Haskill. Depts. of Microbiology and Immunology, Ub/Gyn, and Lineberger Cancer Research Center, Univ. of North Carolina...ING. Mary Haak-Frendscho, Charles J. Czuprynski and Donna M. Paulnock. Depts. Medical Microbiology and Pathobiology Sciences, University Wisconsin

Advancing Knowledge on Fugitive Natural Gas from Energy Resource Development at a Controlled Release Field Observatory

NASA Astrophysics Data System (ADS)

Cahill, A. G.; Chao, J.; Forde, O.; Prystupa, E.; Mayer, K. U.; Black, T. A.; Tannant, D. D.; Crowe, S.; Hallam, S.; Mayer, B.; Lauer, R. M.; van Geloven, C.; Welch, L. A.; Salas, C.; Levson, V.; Risk, D. A.; Beckie, R. D.

2017-12-01

Fugitive gas, comprised primarily of methane, can be unintentionally released from upstream oil and gas development either at surface from leaky infrastructure or in the subsurface through failure of energy well bore integrity. For the latter, defective cement seals around energy well casings may permit buoyant flow of natural gas from the deeper subsurface towards shallow aquifers, the ground surface and potentially into the atmosphere. Concerns associated with fugitive gas release at surface and in the subsurface include contributions to greenhouse gas emissions, subsurface migration leading to accumulation in nearby infrastructure and impacts to groundwater quality. Current knowledge of the extent of fugitive gas leakage including how to best detect and monitor over time, and particularly its migration and fate in the subsurface, is incomplete. We have established an experimental field observatory for evaluating fugitive gas leakage in an area of historic and ongoing hydrocarbon resource development within the Montney Resource Play of the Western Canadian Sedimentary Basin, British Columbia, Canada. Natural gas will be intentionally released at surface and up to 25 m below surface at various rates and durations. Resulting migration patterns and impacts will be evaluated through examination of the geology, hydrogeology, hydro-geochemistry, isotope geochemistry, hydro-geophysics, vadose zone and soil gas processes, microbiology, and atmospheric conditions. The use of unmanned aerial vehicles and remote sensors for monitoring and detection of methane will also be assessed for suitability as environmental monitoring tools. Here we outline the experimental design and describe initial research conducted to develop a detailed site conceptual model of the field observatory. Subsequently, results attained from pilot surface and sub-surface controlled natural gas releases conducted in late summer 2017 will be presented as well as results of numerical modelling conducted to plan methane release experiments in 2018 and onwards. This research will create knowledge which informs strategies to detect and monitor fugitive gas fluxes at the surface and in groundwater; as well as guide associated regulatory and technical policies.

Programmed Lab Experiments for Biochemical Investigation of Quorum-Sensing Signal Molecules in Rhizospheric Soil Bacteria

ERIC Educational Resources Information Center

Nievas, Fiorela L.; Bogino, Pablo C.; Giordano, Walter

2016-01-01

Biochemistry courses in the Department of Molecular Biology at the National University of Río Cuarto, Argentina, are designed for undergraduate students in biology, microbiology, chemistry, agronomy, and veterinary medicine. Microbiology students typically have previous coursework in general, analytical, and organic chemistry. Programmed sequences…

75 FR 3472 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-21

... clearly unwarranted invasion of personal privacy. Name of Committee: Microbiology, Infectious Diseases and AIDS Initial Review Group; Microbiology and Infectious Diseases B Subcommittee. Date: February 11-12... Assistance Program Nos. 93.855, Allergy, Immunology, and Transplantation Research; 93.856, Microbiology and...

75 FR 26760 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-12

... clearly unwarranted invasion of personal privacy. Name of Committee: Microbiology, Infectious Diseases and AIDS Initial Review Group; Microbiology and Infectious Diseases Research Committee. Date: June 17, 2010... Assistance Program Nos. 93.855, Allergy, Immunology, and Transplantation Research; 93.856, Microbiology and...

Bacterial community structure and dissolved organic matter in repeatedly flooded subsurface karst water pools.

PubMed

Shabarova, Tanja; Villiger, Jörg; Morenkov, Oleg; Niggemann, Jutta; Dittmar, Thorsten; Pernthaler, Jakob

2014-07-01

Bacterial diversity, community assembly, and the composition of the dissolved organic matter (DOM) were studied in three temporary subsurface karst pools with different flooding regimes. We tested the hypothesis that microorganisms introduced to the pools during floods faced environmental filtering toward a 'typical' karst water community, and we investigated whether DOM composition was related to floodings and the residence time of water in stagnant pools. As predicted, longer water residence consistently led to a decline of bacterial diversity. The microbial assemblages in the influx water harbored more 'exotic' lineages with large distances to known genotypes, yet these initial communities already appeared to be shaped by selective processes. β-Proteobacterial operational taxonomic units (OTUs) closely related to microbes from subsurface or surface aquatic environments were mainly responsible for the clustering of samples according to water residence time in the pools. By contrast, several Cytophagaceae and Flavobacteriaceae OTUs were related to different floodings, which were also the main determinants of DOM composition. A subset of compounds distinguishable by molecular mass and O/C content were characteristic for individual floods. Moreover, there was a transformation of DOM in stagnant pools toward smaller and more aromatic compounds, potentially also reflecting microbial utilization. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Planetary science and exploration in the deep subsurface: results from the MINAR Program, Boulby Mine, UK

NASA Astrophysics Data System (ADS)

Payler, Samuel J.; Biddle, Jennifer F.; Coates, Andrew J.; Cousins, Claire R.; Cross, Rachel E.; Cullen, David C.; Downs, Michael T.; Direito, Susana O. L.; Edwards, Thomas; Gray, Amber L.; Genis, Jac; Gunn, Matthew; Hansford, Graeme M.; Harkness, Patrick; Holt, John; Josset, Jean-Luc; Li, Xuan; Lees, David S.; Lim, Darlene S. S.; McHugh, Melissa; McLuckie, David; Meehan, Emma; Paling, Sean M.; Souchon, Audrey; Yeoman, Louise; Cockell, Charles S.

2017-04-01

The subsurface exploration of other planetary bodies can be used to unravel their geological history and assess their habitability. On Mars in particular, present-day habitable conditions may be restricted to the subsurface. Using a deep subsurface mine, we carried out a program of extraterrestrial analog research - MINe Analog Research (MINAR). MINAR aims to carry out the scientific study of the deep subsurface and test instrumentation designed for planetary surface exploration by investigating deep subsurface geology, whilst establishing the potential this technology has to be transferred into the mining industry. An integrated multi-instrument suite was used to investigate samples of representative evaporite minerals from a subsurface Permian evaporite sequence, in particular to assess mineral and elemental variations which provide small-scale regions of enhanced habitability. The instruments used were the Panoramic Camera emulator, Close-Up Imager, Raman spectrometer, Small Planetary Linear Impulse Tool, Ultrasonic drill and handheld X-ray diffraction (XRD). We present science results from the analog research and show that these instruments can be used to investigate in situ the geological context and mineralogical variations of a deep subsurface environment, and thus habitability, from millimetre to metre scales. We also show that these instruments are complementary. For example, the identification of primary evaporite minerals such as NaCl and KCl, which are difficult to detect by portable Raman spectrometers, can be accomplished with XRD. By contrast, Raman is highly effective at locating and detecting mineral inclusions in primary evaporite minerals. MINAR demonstrates the effective use of a deep subsurface environment for planetary instrument development, understanding the habitability of extreme deep subsurface environments on Earth and other planetary bodies, and advancing the use of space technology in economic mining.

Analysis of tank 4 (FTF-4-15-22, 23) surface and subsurface supernatant samples in support of enrichment control, corrosion control and evaporator feed qualification programs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oji, L. N.

This report provides the results of analyses on Savannah River Site Tank 4 surface and subsurface supernatant liquid samples in support of the Enrichment Control Program (ECP), the Corrosion Control Program (CCP) and the Evaporator Feed Qualification (EFQ) Program. The purpose of the ECP sample taken from Tank 4 in August 2015 was to determine if the supernatant liquid would be “acceptable feed” to the 2H and 3H evaporator systems.

Microbiological, Geochemical and Hydrologic Processes Controlling Uranium Mobility: An Integrated Field-Scale Subsurface Research Challenge Site at Rifle, Colorado, Quality Assurance Project Plan

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fix, N. J.

The U.S. Department of Energy (DOE) is cleaning up and/or monitoring large, dilute plumes contaminated by metals, such as uranium and chromium, whose mobility and solubility change with redox status. Field-scale experiments with acetate as the electron donor have stimulated metal-reducing bacteria to effectively remove uranium [U(VI)] from groundwater at the Uranium Mill Tailings Site in Rifle, Colorado. The Pacific Northwest National Laboratory and a multidisciplinary team of national laboratory and academic collaborators has embarked on a research proposed for the Rifle site, the object of which is to gain a comprehensive and mechanistic understanding of the microbial factors andmore » associated geochemistry controlling uranium mobility so that DOE can confidently remediate uranium plumes as well as support stewardship of uranium-contaminated sites. This Quality Assurance Project Plan provides the quality assurance requirements and processes that will be followed by the Rifle Integrated Field-Scale Subsurface Research Challenge Project.« less

Utilization of fluorescent microspheres and a green fluorescent protein-marked strain for assessment of microbiological contamination of permafrost and ground ice core samples from the Canadian High Arctic.

PubMed

Juck, D F; Whissell, G; Steven, B; Pollard, W; McKay, C P; Greer, C W; Whyte, L G

2005-02-01

Fluorescent microspheres were applied in a novel fashion during subsurface drilling of permafrost and ground ice in the Canadian High Arctic to monitor the exogenous microbiological contamination of core samples obtained during the drilling process. Prior to each drill run, a concentrated fluorescent microsphere (0.5-microm diameter) solution was applied to the interior surfaces of the drill bit, core catcher, and core tube and allowed to dry. Macroscopic examination in the field demonstrated reliable transfer of the microspheres to core samples, while detailed microscopic examination revealed penetration levels of less than 1 cm from the core exterior. To monitor for microbial contamination during downstream processing of the permafrost and ground ice cores, a Pseudomonas strain expressing the green fluorescent protein (GFP) was painted on the core exterior prior to processing. Contamination of the processed core interiors with the GFP-expressing strain was not detected by culturing the samples or by PCR to detect the gfp marker gene. These methodologies were quick, were easy to apply, and should help to monitor the exogenous microbiological contamination of pristine permafrost and ground ice samples for downstream culture-dependent and culture-independent microbial analyses.

Ridge-flank crustal microbiology investigated with long-term borehole observatories

NASA Astrophysics Data System (ADS)

Orcutt, B. N.; Bach, W.; Becker, K.; Edwards, K. J.; Fisher, A. T.; Haddad, A.; Hulme, S.; Teske, A.; Toner, B.; Wheat, C. G.

2011-12-01

The ridge flank environment represents an important habitat for microbial life on Earth, considering its size and chemical disequilibria between circulating fluids and rocks. However, the potential for this habitat to harbor life, and the characteristics that such life might have, are poorly known at present. Furthermore, the interactions of microbial communities across deep sediment-basement interfaces are not well-characterized. Subseafloor borehole observatories provide a novel platform for sampling and monitoring the microbiology of the crustal ridge flank environment. We present current results from a series of subsurface microbial colonization experiments using borehole observatories on the eastern flank of the Juan de Fuca Ridge, as well as analysis of samples collected on a transect away from a seawater-recharging seamount on this ridge flank. These results are compared to the microbiology of observatories installed in the Costa Rica Rift flank with similar fluid composition and temperatures (i.e. anoxic and warm). We will also discuss on-going experiments on the western-flank of the Mid-Atlantic Ridge, where formation fluids in basement are oxic and cool. Results from these experiments represent some of the extremes in crustal fluid conditions, paving the way for additional studies that are needed to address the importance of this biome as a carbon reservoir and a mechanism for crustal alteration.

Utilization of Fluorescent Microspheres and a Green Fluorescent Protein-Marked Strain for Assessment of Microbiological Contamination of Permafrost and Ground Ice Core Samples from the Canadian High Arctic

PubMed Central

Juck, D. F.; Whissell, G.; Steven, B.; Pollard, W.; McKay, C. P.; Greer, C. W.; Whyte, L. G.

2005-01-01

Fluorescent microspheres were applied in a novel fashion during subsurface drilling of permafrost and ground ice in the Canadian High Arctic to monitor the exogenous microbiological contamination of core samples obtained during the drilling process. Prior to each drill run, a concentrated fluorescent microsphere (0.5-μm diameter) solution was applied to the interior surfaces of the drill bit, core catcher, and core tube and allowed to dry. Macroscopic examination in the field demonstrated reliable transfer of the microspheres to core samples, while detailed microscopic examination revealed penetration levels of less than 1 cm from the core exterior. To monitor for microbial contamination during downstream processing of the permafrost and ground ice cores, a Pseudomonas strain expressing the green fluorescent protein (GFP) was painted on the core exterior prior to processing. Contamination of the processed core interiors with the GFP-expressing strain was not detected by culturing the samples or by PCR to detect the gfp marker gene. These methodologies were quick, were easy to apply, and should help to monitor the exogenous microbiological contamination of pristine permafrost and ground ice samples for downstream culture-dependent and culture-independent microbial analyses. PMID:15691963

Department of Defense In-House RDT&E Activities

DTIC Science & Technology

1983-10-30

CONDUCT.RESEARCH IN MICROBIOLOGY , CHEM- ISTRY, BIOCHEMISTRY, IMMUNOLOGY, RADIATION EFFECTS, PHlA1fACOLOGY, PHYSI- OLOf;Y, HISTOLOGY & PATHOLOGY AS THEY...IMPORTANT PROGRAMS BURN INFECTION, TREATMENT & PREVENTION. METABOLISM & NUTRITIONAL EFFECTS OF BURN INJURY IN SOLDIERS. INFECTION & MICROBIOLOGIC ...RESEARCH CAPABILITIES IN THE FIELDS OF PATHOLOGY, MICROBIOLOGY , EXPERIMENTAL SURGERY, & BIOCHEMISTRY. MAINTAINS AN ANIMAL COLONY, ELECTRONIC SHOP

Tetracycline Resistance in the Subsurface of a Poultry Farm: Influence of Poultry Wastes

NASA Astrophysics Data System (ADS)

You, Y.; Ball, W. P.; Ward, M. J.; Hilpert, M.

2007-12-01

Concentrated animal feeding operations (CAFOs) are considered to be important man-made reservoir of antibiotic resistant bacteria. Using the electromagnetic induction (EMI) method of geophysical characterization, we measured the apparent subsurface electrical conductivity (ECa) at a CAFO site in order to assess the movement of pollutants associated with animal waste. The map of ECa and other available data suggest that (1) soil surrounding a poultry litter storage shed is contaminated by poultry waste, (2) a contamination plume in the subsurface emanates from that shed, and (3) the development of that plume is due to groundwater flow. We focused on understanding the spread of tetracycline resistance (Tc\\tiny R), because tetracycline is one of the most frequently used antibiotics in food animal production and therefore probably used at our field site. Microbiological experiments show the presence of Tc\\tiny R bacteria in the subsurface and indicate higher concentrations in the top soil than in the aquifer. Environmental DNA was extracted to identify CAFO- associated Tc\\tiny R genes and to explore a link between the presence of Tc\\tiny R and CAFO practices. A "shot-gun" cloning approach is under development to target the most prevalent Tc\\tiny R gene. This gene will be monitored in future experiments, in which we will study the transmission of Tc\\tiny R to naive E.~coli under selective pressure of Tc. Experimental results will be used to develop a mathematical/numerical model in order to describe the transmission process and to subsequently make estimates regarding the large-scale spread of antibiotic resistance.

Development and Antarctic Testing of a Maneuverable Probe for Clean In-Situ Analysis and Sampling of Subsurface Ice and Subglacial Aquatic Ecosystems

NASA Astrophysics Data System (ADS)

Francke, G.; Dachwald, B.; Kowalski, J.; Digel, I.; Tulaczyk, S. M.; Mikucki, J.; Feldmann, M.; Espe, C.; Schöngarth, S.; Hiecker, S.; Blandfort, D.; Schüller, K.; Plescher, E.

2016-12-01

There is significant interest in sampling subglacial environments for geochemical and microbiological studies, but those environments are difficult to access. Such environments exist not only on Earth but are also expected beneath the icy crusts of some outer solar system bodies, like the Jovian moon Europa and the Saturnian moon Enceladus. Existing ice drilling technologies make it cumbersome to maintain microbiologically clean access for sample acquisition and environmental stewardship of potentially fragile subglacial aquatic ecosystems. The "IceMole" is a maneuverable subsurface ice probe for clean in-situ analysis and sampling of glacial ice and subglacial materials. The design is based on combining melting and mechanical propulsion, using an ice screw at the tip of the melting head to maintain firm contact between the melting head and the ice. It can change melting direction by differential heating of the melting head and optional side wall heaters. The first two prototypes were successfully tested between 2010 and 2012 on glaciers in Switzerland and Iceland, where they demonstrated downward, horizontal and upward melting, as well as curve driving and dirt layer penetration. Hence, the IceMole allows maneuvers which may be necessary for obstacle avoidance or target selection. Maneuverability, however, necessitates a sophisticated on-board navigation system capable of autonomous operations. Therefore, between 2012 and 2014, a more advanced probe was developed as part of the "Enceladus Explorer" (EnEx) project. The EnEx-IceMole offers systems for relative positioning based on in-ice attitude determination, acoustic positioning, ultrasonic obstacle and target detection, which is all integrated through a high-level sensor fusion. In December 2014, it was used for clean access into a unique subglacial aquatic environment at Blood Falls, Antarctica, where a subglacial brine sample was successfully obtained after about 17 meters of oblique melting. Particular attention was paid to clean protocols for the sampling of subglacial materials for geochemical and microbiological analysis. Much more development has to be done in many areas, however, until the probe can be used for extraterrestrial applications.

Merging genomes with geochemistry in hydrothermal ecosystems.

PubMed

Reysenbach, Anna-Louise; Shock, Everett

2002-05-10

Thermophilic microbial inhabitants of active seafloor and continental hot springs populate the deepest branches of the universal phylogenetic tree, making hydrothermal ecosystems the most ancient continuously inhabited ecosystems on Earth. Geochemical consequences of hot water-rock interactions render these environments habitable and supply a diverse array of energy sources. Clues to the strategies for how life thrives in these dynamic ecosystems are beginning to be elucidated through a confluence of biogeochemistry, microbiology, ecology, molecular biology, and genomics. These efforts have the potential to reveal how ecosystems originate, the extent of the subsurface biosphere, and the driving forces of evolution.

[Analysis of the results of the SEIMC External Quality Control Program. Year 2012].

PubMed

de Gopegui Bordes, Enrique Ruiz; Guna Serrano, M del Remedio; Orta Mira, Nieves; Ovies, María Rosario; Poveda, Marta; Gimeno Cardona, Concepción

2014-02-01

The External Quality Control Program of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC) include controls for bacteriology, serology, mycology, parasitology, mycobacteria, virology and molecular microbiology. This article presents the most relevant conclusions and lessons from the 2012 controls. As a whole, the results obtained in 2012 confirm the excellent skill and good technical standards found in previous editions. However, erroneous results can be obtained in any laboratory and in clinically relevant determinations. Once again, the results of this program highlighted the need to implement both internal and external controls in order to assure the maximal quality of the microbiological tests. Copyright © 2014 Elsevier España, S.L. All rights reserved.

[Analysis of the results of the SEIMC External Quality Control Program. Year 2014].

PubMed

Gopegui Bordes, Enrique Ruiz de; Guna Serrano, M Del Remedio; Orta Mira, Nieves; Medina González, Rafael; Rosario Ovies, María; Poveda, Marta; Gimeno Cardona, Concepción

2016-07-01

The External Quality Control Program of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC) include controls for bacteriology, serology, mycology, parasitology, mycobacteria, virology and molecular microbiology. This article presents the most relevant conclusions and lessons from the 2014 controls. As a whole, the results obtained in 2014 confirm the excellent skill and good technical standards found in previous editions. However, erroneous results can be obtained in any laboratory and in clinically relevant determinations. Once again, the results of the SEIMC program highlighted the need to implement both internal and external controls in order to assure the maximal quality of the microbiological tests. Copyright © 2016 Elsevier España, S.L.U. All rights reserved.

Investigating the Hydro-geochemical Impact of Fugitive Methane on Groundwater: The Borden Aquifer Controlled Release Study

NASA Astrophysics Data System (ADS)

Cahill, A. G.; Parker, B. L.; Cherry, J. A.; Mayer, K. U.; Mayer, B.; Ryan, C.

2014-12-01

Shale gas development by hydraulic fracturing is believed by many to have the potential to transform the world's energy economy. The propensity of this technique to cause significant environmental impact is strongly contested and lacks evidence. Fugitive methane (CH4), potentially mobilized during well drilling, the complex extraction process and/or leaking well seals over time is arguably the greatest concern. Advanced understanding of CH4 mobility and fate in the subsurface is needed in order to assess risks, design suitable monitoring systems and gain public trust. Currently knowledge on subsurface CH4 mobilization and migration at scales relevant to shale gas development is lacking. Consequently a shallow aquifer controlled CH4 release experiment is being conducted at the Borden aquifer research facility (an unconfined, unconsolidated silicate sand aquifer) in Ontario, Canada. During the experiment, 100 m3 of gas phase CH4 was injected into the saturated zone over approximately 60 days through 2 inclined sparging wells (4.5 and 9 m depth) at rates relevant to natural gas well casing vent flows. The gas mobility and fate is being comprehensively monitored temporally and spatially in both the saturated and unsaturated zones considering; aqueous chemistry (including stable isotopes), soil gas characterization, surface efflux, geophysics (GPR and ERT), real time sensors (total dissolved gas pressure, soil moisture content, CH4 and CO2), mineralogical and microbiological characterization before, during and after injection. An overview of this unique study will be given including experimental design, monitoring system configuration and preliminary results. This multidisciplinary study will provide important insights regarding the mechanisms and rates for shallow CH4 migration, attenuation and water quality impacts that will inform baseline groundwater monitoring programs and retrospective forensic studies.

Investigating the Hydro-geochemical Impact of Fugitive Methane on Groundwater: The Borden Aquifer Controlled Release Study

NASA Astrophysics Data System (ADS)

Cahill, A. G.; Parker, B. L.; Cherry, J. A.; Mayer, K. U.; Mayer, B.; Ryan, C.

2015-12-01

Shale gas development by hydraulic fracturing is believed by many to have the potential to transform the world's energy economy. The propensity of this technique to cause significant environmental impact is strongly contested and lacks evidence. Fugitive methane (CH4), potentially mobilized during well drilling, the complex extraction process and/or leaking well seals over time is arguably the greatest concern. Advanced understanding of CH4 mobility and fate in the subsurface is needed in order to assess risks, design suitable monitoring systems and gain public trust. Currently knowledge on subsurface CH4 mobilization and migration at scales relevant to shale gas development is lacking. Consequently a shallow aquifer controlled CH4 release experiment is being conducted at the Borden aquifer research facility (an unconfined, unconsolidated silicate sand aquifer) in Ontario, Canada. During the experiment, 100 m3 of gas phase CH4 was injected into the saturated zone over approximately 60 days through 2 inclined sparging wells (4.5 and 9 m depth) at rates relevant to natural gas well casing vent flows. The gas mobility and fate is being comprehensively monitored temporally and spatially in both the saturated and unsaturated zones considering; aqueous chemistry (including stable isotopes), soil gas characterization, surface efflux, geophysics (GPR and ERT), real time sensors (total dissolved gas pressure, soil moisture content, CH4 and CO2), mineralogical and microbiological characterization before, during and after injection. An overview of this unique study will be given including experimental design, monitoring system configuration and preliminary results. This multidisciplinary study will provide important insights regarding the mechanisms and rates for shallow CH4 migration, attenuation and water quality impacts that will inform baseline groundwater monitoring programs and retrospective forensic studies.

Microbiological investigations

NASA Technical Reports Server (NTRS)

Ferguson, J. K.; Taylor, G. R.; Mieszkuc, B. J.

1975-01-01

The crew microbiology program was conducted to evaluate lunar contamination, to detect potentially pathogenic microoganisms, to identify medically important microorganisms recovered from ill crewmen, to aid in diagnosis and treatment, and to collect microbiological data that would aid in elucidating the response of the crew microbial autoflora to the space flight environment and in evaluating the resultant effect on the crewmember. Microbiological sampling of selected sites in the command module was initiated in support of the quarantine program. During lunar quarantine missions, microbial screening was accomplished for all support personnel to be isolated with the returning crewman. Virology support for the Apollo project consisted of characterization of the viral and mycoplasma flora of the crewmembers and performance of viral serology for crewmembers, crew contacts, and key mission personnel. Procedures and results are discussed in detail.

[Analysis and prospect of projects funded in discipline of microbiology (NSFC) from 2006 to 2010].

PubMed

Liao, Hai; Wen, Mingzhang; Yang, Haihua

2011-01-01

The overview of projects funded by general programs,key programs and national science fund for distinguished young scholars in discipline of microbiology, National Natural Science Foundation of China (NSFC) from 2006 to 2010 was recommended. Some important characters such as the distribution of projects in different subjects, organizations, regions and research fields were analyzed. Some important research fields which should be supported in "The Twelfth Five-Year Plan" was also put forward. The goal of the paper is to provide information of funding in NSFC for researchers in the field of microbiology.

Historic Shipwrecks as Ecosystem Monitoring Platforms in the Wake of Deepwater Horizon? Results of the Gulf of Mexico Shipwreck Corrosion, Hydrocarbon Exposure, Microbiology, and Archaeology (GOM-SCHEMA) Project

NASA Astrophysics Data System (ADS)

Damour, M.; Hamdan, L. J.; Salerno, J. L.; McGown, C.; Blackwell, C. A.; Church, R.; Warren, D.; Horrell, C.; Jordan, B.; Moore, J.

2016-02-01

Historic shipwrecks and other archaeological sites are protected by a well-established body of historic preservation laws intended to preserve these sensitive, non-renewable resources. While the cultural, historical, and archaeological value of historic shipwrecks is unequivocal, their function and value as ecosystem monitoring platforms following a major environmental disaster is becoming apparent. Shipwrecks have been found in previous studies to serve as artificial reefs and hotspots of biodiversity, essentially providing the basis for an intact ecosystem. This is especially true in the deepwater marine environment where natural hard-bottom is sparse. Micro- and macro-infaunal diversity on shipwrecks and their sensitivity to environmental change demonstrates the suitability of these platforms for monitoring ecosystem impact and recovery. After the 2010 Deepwater Horizon oil spill, the Bureau of Ocean Energy Management (BOEM) and partners initiated a multidisciplinary study to examine spill effects on shipwrecks and their associated microbial communities. To assess these impacts and to perform comparative analyses, the team collected microbiological, geochemical, and archaeological data at wooden- and metal-hulled shipwrecks within and outside of the subsurface spill-impacted area. Microbial community biodiversity informs us of micro-scale changes while 3D laser and sonar data reveal macro-scale changes. A multidisciplinary approach informs us of the roles microorganisms have in shipwreck degradation and corrosion as well as their response to ecosystem impacts. Results of the study identified multiple lines of evidence that sites were impacted by exposure to spill-related contaminants. Future multidisciplinary studies at these sites, as part of a long-term monitoring program, should inform on ecosystem recovery.

Analysis of Tank 38H (HTF-38-15-119, 127) Surface, Subsurface and Tank 43H (HTF-43-15-116, 117 and 118) Surface, Feed Pump Suction and Jet Suction Subsurface Supernatant Samples in Support of Enrichment, Corrosion Control and Salt Batch Planning Programs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oji, L.

Compositional feed limits have been established to ensure that a nuclear criticality event for the 2H and 3H Evaporators is not possible. The Enrichment Control Program (ECP) requires feed sampling to determine the equivalent enriched uranium content prior to transfer of waste other than recycle transfers (requires sampling to determine the equivalent enriched uranium at two locations in Tanks 38H and 43H every 26 weeks) The Corrosion Control Program (CCP) establishes concentration and temperature limits for key constituents and periodic sampling and analysis to confirm that waste supernate is within these limits. This report provides the results of analyses onmore » Tanks 38H and 43H surface and subsurface supernatant liquid samples in support of the ECP, the CCP, and the Salt Batch 10 Planning Program.« less

The intersection of antimicrobial stewardship and microbiology: educating the next generation of health care professionals.

PubMed

O'Donnell, Lauren A; Guarascio, Anthony J

2017-01-01

With the alarming rise of antibiotic resistance, clinical professionals are called upon to manage antibiotic therapies using the most relevant and recent clinical and laboratory data. To this end, antimicrobial stewardship (AMS) programs aim to reduce unnecessary or suboptimal use of antibiotics while maximizing outcomes for the patient. For AMS programs to succeed, the active participation of clinical professionals at all levels of patient care is required. Although programs exist to train established clinicians in AMS, there is a paucity of literature on how and when to integrate AMS concepts and skills in pre-clinical and clinical coursework. Here, we discuss the crucial microbiology concepts and proficiencies that are necessary for building and supporting an AMS program. We provide recommendations for key points to include in clinical curricula in order to develop the necessary microbiology interpretation skills to participate in AMS. The influence of AMS programs on local organism susceptibility patterns is emphasized. The importance of antibiograms, rapid diagnostic testing and the practical interpretations of microbiology laboratory reporting are discussed in regard to prioritization in clinical curricula. We also review the current literature on instructional strategies for introducing AMS into clinical programs, and propose concepts that should be included in didactic coursework in order to provide a foundation for AMS education. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Arsenic Detoxification by Geobacter Species.

PubMed

Dang, Yan; Walker, David J F; Vautour, Kaitlin E; Dixon, Steven; Holmes, Dawn E

2017-02-15

Insight into the mechanisms for arsenic detoxification by Geobacter species is expected to improve the understanding of global cycling of arsenic in iron-rich subsurface sedimentary environments. Analysis of 14 different Geobacter genomes showed that all of these species have genes coding for an arsenic detoxification system (ars operon), and several have genes required for arsenic respiration (arr operon) and methylation (arsM). Genes encoding four arsenic repressor-like proteins were detected in the genome of G. sulfurreducens; however, only one (ArsR1) regulated transcription of the ars operon. Elimination of arsR1 from the G. sulfurreducens chromosome resulted in enhanced transcription of genes coding for the arsenic efflux pump (Acr3) and arsenate reductase (ArsC). When the gene coding for Acr3 was deleted, cells were not able to grow in the presence of either the oxidized or reduced form of arsenic, while arsC deletion mutants could grow in the presence of arsenite but not arsenate. These studies shed light on how Geobacter influences arsenic mobility in anoxic sediments and may help us develop methods to remediate arsenic contamination in the subsurface. This study examines arsenic transformation mechanisms utilized by Geobacter, a genus of iron-reducing bacteria that are predominant in many anoxic iron-rich subsurface environments. Geobacter species play a major role in microbially mediated arsenic release from metal hydroxides in the subsurface. This release raises arsenic concentrations in drinking water to levels that are high enough to cause major health problems. Therefore, information obtained from studies of Geobacter should shed light on arsenic cycling in iron-rich subsurface sedimentary environments, which may help reduce arsenic-associated illnesses. These studies should also help in the development of biosensors that can be used to detect arsenic contaminants in anoxic subsurface environments. We examined 14 different Geobacter genomes and found that all of these species possess genes coding for an arsenic detoxification system (ars operon), and some also have genes required for arsenic respiration (arr operon) and arsenic methylation (arsM). Copyright © 2017 American Society for Microbiology.

Effects of Hydraulic Frac Fluids on Subsurface Microbial Communities in Gas Shales

NASA Astrophysics Data System (ADS)

Jiménez, Núria; Krüger, Martin

2014-05-01

Shale gas is being considered as a complementary energy resource to coal or other fossil fuels. The exploitation of unconventional gas reservoirs requires the use of advanced drilling techniques and hydraulic stimulation (fracking). During fracking operations, large amounts of fluids (fresh water, proppants and chemical additives) are injected at high pressures into the formations, to produce fractures and fissures, and thus to release gas from the source rock into the wellbore. The injected fluids partly remain in the formation, while about 20 to 40% of the originally injected fluid flows back to the surface, together with formation waters, sometimes containing dissolved hydrocarbons, high salt concentrations, etc. The overall production operation will likely affect and be affected by subsurface microbial communities associated to the shale formations. On the one hand microbial activity (like growth, biofilm formation) can cause unwanted processes like corrosion, clogging, etc. On the other hand, the introduction of frac fluids could either enhance microbial growth or cause toxicity to the shale-associated microbial communities. To investigate the potential impacts of changing environmental reservoir conditions, like temperature, salinity, oxgen content and pH, as well as the introduction of frac or geogenic chemicals on subsurface microbial communities, laboratory experiments under in situ conditions (i.e. high temperatures and pressures) are being conducted. Enrichment cultures with samples from several subsurface environments (e.g. shale and coal deposits, gas reservoirs, geothermal fluids) have been set up using a variety of carbon sources, including hydrocarbons and typical frac chemicals. Classical microbiological and molecular analysis are used to determine changes in the microbial abundance, community structure and function after the exposure to different single frac chemicals, "artificial" frac fluids or production waters. On the other hand, potential transformation reactions of frac or geogenic chemicals by subsurface microbiota and their lifetime are investigated. In our "fracking simulation" experiments, an increasing number of hydrocarbon-degrading or halophilic microorganisms is to be expected after exposure of subsurface communities to artificial production waters. Whereas the introduction of freshwater and of easily biodegradable substrates might favor the proliferation of fast-growing generalistic heterotrophs in shale-associated communities. Nevertheless toxicity of some of the frac components cannot be excluded.

Microbiological and Geochemical Survey of CO2-Dominated Mofette and Mineral Waters of the Cheb Basin, Czech Republic.

PubMed

Krauze, Patryk; Kämpf, Horst; Horn, Fabian; Liu, Qi; Voropaev, Andrey; Wagner, Dirk; Alawi, Mashal

2017-01-01

The Cheb Basin (NW Bohemia, Czech Republic) is a shallow, neogene intracontinental basin. It is a non-volcanic region which features frequent earthquake swarms and large-scale diffuse degassing of mantle-derived CO 2 at the surface that occurs in the form of CO 2 -rich mineral springs and wet and dry mofettes. So far, the influence of CO 2 degassing onto the microbial communities has been studied for soil environments, but not for aquatic systems. We hypothesized, that deep-trenching CO 2 conduits interconnect the subsurface with the surface. This admixture of deep thermal fluids should be reflected in geochemical parameters and in the microbial community compositions. In the present study four mineral water springs and two wet mofettes were investigated through an interdisciplinary survey. The waters were acidic and differed in terms of organic carbon and anion/cation concentrations. Element geochemical and isotope analyses of fluid components were used to verify the origin of the fluids. Prokaryotic communities were characterized through quantitative PCR and Illumina 16S rRNA gene sequencing. Putative chemolithotrophic, anaerobic and microaerophilic organisms connected to sulfur (e.g., Sulfuricurvum, Sulfurimonas ) and iron (e.g., Gallionella, Sideroxydans ) cycling shaped the core community. Additionally, CO 2 -influenced waters form an ecosystem containing many taxa that are usually found in marine or terrestrial subsurface ecosystems. Multivariate statistics highlighted the influence of environmental parameters such as pH, Fe 2+ concentration and conductivity on species distribution. The hydrochemical and microbiological survey introduces a new perspective on mofettes. Our results support that mofettes are either analogs or rather windows into the deep biosphere and furthermore enable access to deeply buried paleo-sediments.

Microbiological and Geochemical Survey of CO2-Dominated Mofette and Mineral Waters of the Cheb Basin, Czech Republic

PubMed Central

Krauze, Patryk; Kämpf, Horst; Horn, Fabian; Liu, Qi; Voropaev, Andrey; Wagner, Dirk; Alawi, Mashal

2017-01-01

The Cheb Basin (NW Bohemia, Czech Republic) is a shallow, neogene intracontinental basin. It is a non-volcanic region which features frequent earthquake swarms and large-scale diffuse degassing of mantle-derived CO2 at the surface that occurs in the form of CO2-rich mineral springs and wet and dry mofettes. So far, the influence of CO2 degassing onto the microbial communities has been studied for soil environments, but not for aquatic systems. We hypothesized, that deep-trenching CO2 conduits interconnect the subsurface with the surface. This admixture of deep thermal fluids should be reflected in geochemical parameters and in the microbial community compositions. In the present study four mineral water springs and two wet mofettes were investigated through an interdisciplinary survey. The waters were acidic and differed in terms of organic carbon and anion/cation concentrations. Element geochemical and isotope analyses of fluid components were used to verify the origin of the fluids. Prokaryotic communities were characterized through quantitative PCR and Illumina 16S rRNA gene sequencing. Putative chemolithotrophic, anaerobic and microaerophilic organisms connected to sulfur (e.g., Sulfuricurvum, Sulfurimonas) and iron (e.g., Gallionella, Sideroxydans) cycling shaped the core community. Additionally, CO2-influenced waters form an ecosystem containing many taxa that are usually found in marine or terrestrial subsurface ecosystems. Multivariate statistics highlighted the influence of environmental parameters such as pH, Fe2+ concentration and conductivity on species distribution. The hydrochemical and microbiological survey introduces a new perspective on mofettes. Our results support that mofettes are either analogs or rather windows into the deep biosphere and furthermore enable access to deeply buried paleo-sediments. PMID:29321765

Antimicrobial Stewardship: How the Microbiology Laboratory Can Right the Ship

PubMed Central

Schwartz, David N.; Weinstein, Robert A.

2016-01-01

SUMMARY Antimicrobial stewardship is a bundle of integrated interventions employed to optimize the use of antimicrobials in health care settings. While infectious-disease-trained physicians, with clinical pharmacists, are considered the main leaders of antimicrobial stewardship programs, clinical microbiologists can play a key role in these programs. This review is intended to provide a comprehensive discussion of the different components of antimicrobial stewardship in which microbiology laboratories and clinical microbiologists can make significant contributions, including cumulative antimicrobial susceptibility reports, enhanced culture and susceptibility reports, guidance in the preanalytic phase, rapid diagnostic test availability, provider education, and alert and surveillance systems. In reviewing this material, we emphasize how the rapid, and especially the recent, evolution of clinical microbiology has reinforced the importance of clinical microbiologists' collaboration with antimicrobial stewardship programs. PMID:27974411

Microbial life associated with low-temperature alteration of ultramafic rocks in the Leka ophiolite complex.

PubMed

Daae, F L; Økland, I; Dahle, H; Jørgensen, S L; Thorseth, I H; Pedersen, R B

2013-07-01

Water-rock interactions in ultramafic lithosphere generate reduced chemical species such as hydrogen that can fuel subsurface microbial communities. Sampling of this environment is expensive and technically demanding. However, highly accessible, uplifted oceanic lithospheres emplaced onto continental margins (ophiolites) are potential model systems for studies of the subsurface biosphere in ultramafic rocks. Here, we describe a microbiological investigation of partially serpentinized dunite from the Leka ophiolite (Norway). We analysed samples of mineral coatings on subsurface fracture surfaces from different depths (10-160 cm) and groundwater from a 50-m-deep borehole that penetrates several major fracture zones in the rock. The samples are suggested to represent subsurface habitats ranging from highly anaerobic to aerobic conditions. Water from a surface pond was analysed for comparison. To explore the microbial diversity and to make assessments about potential metabolisms, the samples were analysed by microscopy, construction of small subunit ribosomal RNA gene clone libraries, culturing and quantitative-PCR. Different microbial communities were observed in the groundwater, the fracture-coating material and the surface water, indicating that distinct microbial ecosystems exist in the rock. Close relatives of hydrogen-oxidizing Hydrogenophaga dominated (30% of the bacterial clones) in the oxic groundwater, indicating that microbial communities in ultramafic rocks at Leka could partially be driven by H2 produced by low-temperature water-rock reactions. Heterotrophic organisms, including close relatives of hydrocarbon degraders possibly feeding on products from Fischer-Tropsch-type reactions, dominated in the fracture-coating material. Putative hydrogen-, ammonia-, manganese- and iron-oxidizers were also detected in fracture coatings and the groundwater. The microbial communities reflect the existence of different subsurface redox conditions generated by differences in fracture size and distribution, and mixing of fluids. The particularly dense microbial communities in the shallow fracture coatings seem to be fuelled by both photosynthesis and oxidation of reduced chemical species produced by water-rock reactions. © 2013 John Wiley & Sons Ltd.

Microbiology

ERIC Educational Resources Information Center

Spooner, D.

1973-01-01

Describes various types of training programs carried out in the study of microbiology. Indicates that the need for new energy sources and the expansion of medical schools and food industry may lead to an increasing demand for qualified microbiologists. (CC)

76 FR 35224 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-16

... clearly unwarranted invasion of personal privacy. Name of Committee: Microbiology, Infectious Diseases and... Assistance Program Nos. 93.855, Allergy, Immunology, and Transplantation Research; 93.856, Microbiology and...

76 FR 10383 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-24

... clearly unwarranted invasion of personal privacy. Name of Committee: Microbiology, Infectious Diseases and... Program Nos. 93.855, Allergy, Immunology, and Transplantation Research; 93.856, Microbiology and...

77 FR 36563 - National Institute of Allergy And Infectious Diseases; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-19

... clearly unwarranted invasion of personal privacy. Name of Committee: Microbiology, Infectious Diseases and... Assistance Program Nos. 93.855, Allergy, Immunology, and Transplantation Research; 93.856, Microbiology and...

Metabolic stratification driven by surface and subsurface interactions in a terrestrial mud volcano.

PubMed

Cheng, Ting-Wen; Chang, Yung-Hsin; Tang, Sen-Lin; Tseng, Ching-Hung; Chiang, Pei-Wen; Chang, Kai-Ti; Sun, Chih-Hsien; Chen, Yue-Gau; Kuo, Hung-Chi; Wang, Chun-Ho; Chu, Pao-Hsuan; Song, Sheng-Rong; Wang, Pei-Ling; Lin, Li-Hung

2012-12-01

Terrestrial mud volcanism represents the prominent surface geological feature, where fluids and hydrocarbons are discharged along deeply rooted structures in tectonically active regimes. Terrestrial mud volcanoes (MVs) directly emit the major gas phase, methane, into the atmosphere, making them important sources of greenhouse gases over geological time. Quantification of methane emission would require detailed insights into the capacity and efficiency of microbial metabolisms either consuming or producing methane in the subsurface, and establishment of the linkage between these methane-related metabolisms and other microbial or abiotic processes. Here we conducted geochemical, microbiological and genetic analyses of sediments, gases, and pore and surface fluids to characterize fluid processes, community assemblages, functions and activities in a methane-emitting MV of southwestern Taiwan. Multiple lines of evidence suggest that aerobic/anaerobic methane oxidation, sulfate reduction and methanogenesis are active and compartmentalized into discrete, stratified niches, resembling those in marine settings. Surface evaporation and oxidation of sulfide minerals are required to account for the enhanced levels of sulfate that fuels subsurface sulfate reduction and anaerobic methanotrophy. Methane flux generated by in situ methanogenesis appears to alter the isotopic compositions and abundances of thermogenic methane migrating from deep sources, and to exceed the capacity of microbial consumption. This metabolic stratification is sustained by chemical disequilibria induced by the mixing between upward, anoxic, methane-rich fluids and downward, oxic, sulfate-rich fluids.

An electrical resistivity-based method for investigation of subsurface structure

NASA Astrophysics Data System (ADS)

Alves Meira Neto, A.; Litwin, D.; Troch, P. A. A.; Ferre, T. P. A.

2017-12-01

Resolving the spatial distribution of soil porosity within the subsurface is of great importance for understanding flow and transport within heterogeneous media. Additionally, porosity patterns can be associated with the availability of water and carbon dioxide that will drive geochemical reactions and constrain microbiological growth. The use of controlled experimentation has the potential to circumvent problems related to the external and internal variability of natural systems, while also allowing a higher degree of observability. In this study, we suggest an ERT-based method of retrieving porosity fields based on the application of Archie's law associated with an experimental procedure that can be used in laboratory-scale studies. We used a 2 cubic meter soil lysimeter, equipped with 238 electrodes distributed along its walls for testing the method. The lysimeter serves as a scaled-down version of the highly monitored artificial hillslopes at the Landscape Evolution Observatory (LEO) located at Biosphere 2 - University of Arizona. The capability of the ERT system in deriving spatially distributed patterns of porosity with respect to its several sources of uncertainty was numerically evaluated. The results will be used to produce an optimal experimental design and for assessing the reliability of experimental results. This novel approach has the potential to further resolve subsurface heterogeneity within the LEO project, and highlight the use of ERT-derived results for hydro-bio-geochemical studies.

Metabolic stratification driven by surface and subsurface interactions in a terrestrial mud volcano

PubMed Central

Cheng, Ting-Wen; Chang, Yung-Hsin; Tang, Sen-Lin; Tseng, Ching-Hung; Chiang, Pei-Wen; Chang, Kai-Ti; Sun, Chih-Hsien; Chen, Yue-Gau; Kuo, Hung-Chi; Wang, Chun-Ho; Chu, Pao-Hsuan; Song, Sheng-Rong; Wang, Pei-Ling; Lin, Li-Hung

2012-01-01

Terrestrial mud volcanism represents the prominent surface geological feature, where fluids and hydrocarbons are discharged along deeply rooted structures in tectonically active regimes. Terrestrial mud volcanoes (MVs) directly emit the major gas phase, methane, into the atmosphere, making them important sources of greenhouse gases over geological time. Quantification of methane emission would require detailed insights into the capacity and efficiency of microbial metabolisms either consuming or producing methane in the subsurface, and establishment of the linkage between these methane-related metabolisms and other microbial or abiotic processes. Here we conducted geochemical, microbiological and genetic analyses of sediments, gases, and pore and surface fluids to characterize fluid processes, community assemblages, functions and activities in a methane-emitting MV of southwestern Taiwan. Multiple lines of evidence suggest that aerobic/anaerobic methane oxidation, sulfate reduction and methanogenesis are active and compartmentalized into discrete, stratified niches, resembling those in marine settings. Surface evaporation and oxidation of sulfide minerals are required to account for the enhanced levels of sulfate that fuels subsurface sulfate reduction and anaerobic methanotrophy. Methane flux generated by in situ methanogenesis appears to alter the isotopic compositions and abundances of thermogenic methane migrating from deep sources, and to exceed the capacity of microbial consumption. This metabolic stratification is sustained by chemical disequilibria induced by the mixing between upward, anoxic, methane-rich fluids and downward, oxic, sulfate-rich fluids. PMID:22739492

[Role of the independent microbiology laboratory in supporting infection control programs in small to mid-sized hospitals].

PubMed

Yanagisawa, Hideji

2009-05-01

With the revision of the Medical Service Law in 2006 by the Japanese Ministry of Health, Labour and Welfare (MHLW), all healthcare institutions are now required to implement a healthcare risk management program including infection control program. At a national level, an infection control surveillance program (JANIS) was implemented in July 2007. Regular weekly, monthly, and yearly infection control surveillance reports from independent microbiology laboratories can make significant contributions to infection control programs in small to mid-sized hospitals; furthermore, such programs are consistent with the framework of the MHLW's objective of strengthening risk management in healthcare institutions. Against the backdrop of current efforts to improve risk management, independent laboratories can make a significant contribution. Independent laboratories must play a role beyond merely receiving and processing specimens for microbiological examination. In addition to generating results for patients, hospital epidemiological data that contribute to local infection control programs must be a value-added component of the service. A major obstacle for independent laboratories to make a significant contribution to risk management is the current reimbursement system, which makes it economically impossible for independent laboratories to support infection control programs in healthcare institutions.

Microbiology in Introductory Biology.

ERIC Educational Resources Information Center

Callery, Michael L.; And Others

1980-01-01

Describes a microbiology unit developed for an introductory college biology course in which the identity of an unknown bacterium is determined. Also described is an interactive taxonomy computer program which aids in the identity of the unknown organism. (CS)

Microbiological surveillance of food handling at NASA-MSFC

NASA Technical Reports Server (NTRS)

Beyerle, F. J.

1973-01-01

A microbiological surveillance program of cafeterias and snack bars was conducted to supplement the inspections by NASA Medical Center personnel and to gather information for cafeteria management to pinpoint areas of possible contamination. The work conducted under the program from its inception in January, 1972, to its termination on September 15, 1972 is summarized. Ten food handling facilities were included in the surveillance at NASA-MSFC.

Development of an interdisciplinary pre-matriculation program designed to promote medical students’ self efficacy

PubMed Central

Kosobuski, Anna Wirta; Whitney, Abigail; Skildum, Andrew; Prunuske, Amy

2017-01-01

ABSTRACT Background and objectives: A four-week interdisciplinary pre-matriculation program for Native American and rural medical students was created and its impact on students’ transition to medical school was assessed. The program extends the goals of many pre-matriculation programs by aiming to increase not only students’ understanding of basic science knowledge, but also to build student self-efficacy through practice with medical school curricular elements while developing their academic support networks. Design: A mixed method evaluation was used to determine whether the goals of the program were achieved (n = 22). Student knowledge gains and retention of the microbiology content were assessed using a microbiology concept inventory. Students participated in focus groups to identify the benefits of participating in the program as well as the key components of the program that benefitted the students. Results: Program participants showed retention of microbiology content and increased confidence about the overall medical school experience after participating in the summer program. Conclusions: By nurturing self-efficacy, participation in a pre-matriculation program supported medical students from Native American and rural backgrounds during their transition to medical school. Abbreviations: CAIMH: Center of American Indian and Minority Health; MCAT: Medical College Admission Test; PBL: Problem based learning; UM MSD: University of Minnesota Medical School Duluth PMID:28178916

Computer Modeling of Microbiological Experiments in the Teaching Laboratory: Animation Techniques.

ERIC Educational Resources Information Center

Tritz, Gerald J.

1987-01-01

Discusses the use of computer assisted instruction in the medical education program of the Kirksville College of Osteopathic Medicine (Missouri). Describes the animation techniques used in a series of simulations for microbiology. (TW)

Food Protection Has Many Facets

ERIC Educational Resources Information Center

Walker, Bailus, Jr.; And Others

1972-01-01

Developments in food protection are described for microbiological contaminants, delicatessen foods, seafoods, mycotoxins, food additives, and regulatory surveillance. Proposed and advocated is a cooperative, basic data, monitoring program focusing on microbiological, chemical, nutritional, toxicological, and related food quality indices. (BL)

Polymer-Enhanced Subsurface Delivery and Distribution of Permanganate

DTIC Science & Technology

2013-02-01

C-0006 Polymer-Enhanced Subsurface Delivery and Distribution of Permanganate 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S...this project was to demonstrate and validate the use of a water-soluble polymer with permanganate for in situ chemical oxidation (ISCO) of organic

Characterization of the geology, geochemistry, hydrology and microbiology of the in-situ air stripping demonstration site at the Savannah River Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eddy, C.A.; Looney, B.B.; Dougherty, J.M.

1991-05-01

The Savannah River Site is the location of an Integrated Demonstration Project designed to evaluate innovative remediation technologies for environmental restoration at sites contaminated with volatile organic contaminants. This demonstration utilizes directionally drilled horizontal wells to deliver gases and extract contaminants from the subsurface. Phase I of the Integrated Demonstration focused on the application and development of in-situ air stripping technologies to remediate soils and sediments above and below the water table as well as groundwater contaminated with volatile organic contaminants. The objective of this report is to provide baseline information on the geology, geochemistry, hydrology, and microbiology of themore » demonstration site prior to the test. The distribution of contaminants in soils and sediments in the saturated zone and groundwater is emphasized. These data will be combined with data collected after the demonstration in order to evaluate the effectiveness of in-situ air stripping. New technologies for environmental characterization that were evaluated include depth discrete groundwater sampling (HydroPunch) and three-dimensional modeling of contaminant data.« less

Competency Assessment of Microbiology Medical Laboratory Technologists in Ontario, Canada

PubMed Central

Fleming, Christine Ann

2014-01-01

Accreditation in Ontario, Canada, requires that licensed clinical laboratories participate in external quality assessment (also known as proficiency testing) and perform competency evaluation of their staff. To assess the extent of ongoing competency assessment practices, the Quality Management Program—Laboratory Services (QMP-LS) Microbiology Committee surveyed all 112 licensed Ontario microbiology laboratories. The questionnaire consisted of a total of 21 questions that included yes/no, multiple-choice, and short-answer formats. Participants were asked to provide information about existing programs, the frequency of testing, what areas are evaluated, and how results are communicated to the staff. Of the 111 responding laboratories, 6 indicated they did not have a formal evaluation program since they perform only limited bacteriology testing. Of the remaining 105 respondents, 87% perform evaluations at least annually or every 2 years, and 61% include any test or task performed, whereas 16% and 10% focus only on problem areas and high-volume complex tasks, respectively. The most common methods of evaluation were review of external quality assessment (EQA) challenges, direct observation, and worksheet review. With the exception of one participant, all communicate results to staff, and most take remedial action to correct the deficiencies. Although most accredited laboratories have a program to assess the ongoing competency of their staff, the methods used are not standardized or consistently applied, indicating that there is room for improvement. The survey successfully highlighted potential areas for improvement and allowed the QMP-LS Microbiology Committee to provide guidance to Ontario laboratories for establishing or improving existing microbiology-specific competency assessment programs. PMID:24899030

SUBSURFACE CHARACTERIZATION AND MONITORING TECHNIQUES: A DESK REFERENCE GUIDE - VOLUME I: SOLIDS AND GROUND WATER - APPENDICES A AND B

EPA Science Inventory

Many EPA programs, including those under the Resource Conservation and Recovery Act (RCRA) and the Comprehensive Response, Compensation, and Liability Act (CERCLA), require subsurface characterization and monitoring to detect ground-water contamination and provide data to devel...

[Analysis of the results of the SEIMC External Quality Control Program. Year 2013].

PubMed

de Gopegui Bordes, Enrique Ruiz; Orta Mira, Nieves; Del Remedio Guna Serrano, M; Medina González, Rafael; Rosario Ovies, María; Poveda, Marta; Gimeno Cardona, Concepción

2015-07-01

The External Quality Control Program of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC) include controls for bacteriology, serology, mycology, parasitology, mycobacteria, virology, molecular microbiology and HIV-1, HCV and HBV viral loads. This manuscript presents the analysis of results obtained of the participants from the 2013 SEIMC External Quality Control Programme, except viral loads controls, that they are summarized in a manuscript abroad. As a whole, the results obtained in 2013 confirm the excellent skill and good technical standards found in previous editions. However, erroneous results can be obtained in any laboratory and in clinically relevant determinations. Once again, the results of this program highlighted the need to implement both internal and external controls in order to assure the maximal quality of the microbiological tests. Copyright © 2015 Elsevier España, S.L.U. All rights reserved.

A Search for Life in the Subsurface At Rio Tinto Spain, An Analog To Searching For Life On Mars.

NASA Astrophysics Data System (ADS)

Stoker, C. R.

2003-12-01

Most familiar life forms on Earth live in the surface biosphere where liquid water, sunlight, and the essential chemical elements for life are abundant. However, such environments are not found on Mars or anywhere else in the solar system. On Mars, the surface environmental conditions of pressure and temperature prevent formation of liquid water. Furthermore, conditions at the Martian surface are unfavorable to life due to intense ultraviolet radiation and strong oxidizing compounds that destroy organic compounds. However, subsurface liquid water on Mars has been predicted on theoretical grounds. The recent discovery of near surface ground ice by the Mars Odyssey mission, and the abundant evidence for recent Gully features observed by the Mars Global Surveyor mission strengthen the case for subsurface liquid water on Mars. Thus, the strategy for searching for life on Mars points to drilling to the depth of liquid water, bringing samples to the surface and analyzing them with instrumentation to detect in situ organisms and biomarker compounds. The MARTE (Mars Astrobiology Research and Technology Experiment) project is a field experiment focused on searching for a hypothesized subsurface anaerobic chemoautotrophic biosphere in the region of the Rio Tinto, a river in southwestern Spain while also demonstrating technology relevant to searching for a subsurface biosphere on Mars. The Tinto river is located in the Iberian Pyrite belt, one of the largest deposits of sulfide minerals in the world. The surface (river) system is an acidic extreme environment produced and maintained by microbes that metabolize sulfide minerals and produce sulfuric acid as a byproduct. Evidence suggests that the river is a surface manifestation of an underground biochemical reactor. Organisms found in the river are capable of chemoautotrophic metabolism using sulfide and ferric iron mineral substrates, suggesting these organisms could thrive in groundwater which is the source of the Rio Tinto. The MARTE project will simulate the search for subsurface life on Mars using a drilling system developed for future Mars flight to accomplish subsurface access. Augmenting the drill are robotic systems for extracting the cores from the drill head and performing analysis using a suite of instruments to understand the composition, mineralogy, presence of organics, and to search for life signatures in subsurface samples. A robotic bore-hole inspection system will characterize borehole properties in situ. A Mars drilling mission simulation including remote operation of the drilling, sample handling, and instruments and interpretation of results by a remote science team will be performed. This simulated mission will be augmented by manual methods of drilling, sample handling, and sample analysis to fully document the subsurface, prevent surface microbial contamination, identify subsurface biota, and compare what can be learned with robotically-operated instruments. The first drilling campaign in the MARTE project takes place in September 2003 and is focused on characterizing the microbiology of the subsurface at Rio Tinto using conventional drilling, sample handling and laboratory analysis techniques. Lessons learned from this "ground truth" drilling campaign will guide the development of robotic systems and instruments needed for searching for life underground on Mars.

Analysis of Tank 13H (HTF-13-14-156, 157) Surface and Subsurface Supernatant Samples in Support of Enrichment Control, Corrosion Control and Sodium Aluminosilicate Formation Potential Programs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oji, L. N.

2015-02-18

The 2H Evaporator system includes mainly Tank 43H (feed tank) and Tank 38H (drop tank) with Tank 22H acting as the DWPF recycle receipt tank. The Tank 13H is being characterized to ensure that it can be transferred to the 2H evaporator. This report provides the results of analyses on Tanks 13H surface and subsurface supernatant liquid samples to ensure compliance with the Enrichment Control Program (ECP), the Corrosion Control Program and Sodium Aluminosilicate Formation Potential in the Evaporator. The U-235 mass divided by the total uranium averaged 0.00799 (0.799 % uranium enrichment) for both the surface and subsurface Tankmore » 13H samples. This enrichment is slightly above the enrichment for Tanks 38H and 43H, where the enrichment normally ranges from 0.59 to 0.7 wt%. The U-235 concentration in Tank 13H samples ranged from 2.01E-02 to 2.63E-02 mg/L, while the U-238 concentration in Tank 13H ranged from 2.47E+00 to 3.21E+00 mg/L. Thus, the U-235/total uranium ratio is in line with the prior 2H-evaporator ECP samples. Measured sodium and silicon concentrations averaged, respectively, 2.46 M and 1.42E-04 M (3.98 mg/L) in the Tank 13H subsurface sample. The measured aluminum concentration in Tanks 13H subsurface samples averaged 2.01E-01 M.« less

Evaluation of an online program to teach microbiology to internal medicine residents.

PubMed

Guarner, Jeannette; Burd, Eileen M; Kraft, Colleen S; Armstrong, Wendy S; Lenorr, Kenya; Spicer, Jennifer O; Martin, Donna; del Rio, Carlos

2015-01-01

Microbiology rounds are an integral part of infectious disease consultation service. During microbiology rounds, we highlight microbiology principles using vignettes. We created case-based, interactive, microbiology online modules similar to the vignettes presented during microbiology rounds. Since internal medicine residents rotating on our infectious disease elective have limited time to participate in rounds and learn microbiology, our objective was to evaluate the use of the microbiology online modules by internal medicine residents. We asked residents to complete 10 of 25 online modules during their infectious disease elective. We evaluated which modules they chose and the change in their knowledge level. Forty-six internal medicine residents completed assessments given before and after accessing the modules with an average of 11/20 (range, 6 to 19) and 16/20 (range, 9 to 20) correct questions, respectively (average improvement, 5 questions; P = 0.0001). The modules accessed by more than 30 residents included those related to Clostridium difficile, anaerobes, Candida spp., Streptococcus pneumoniae, influenza, Mycobacterium tuberculosis, and Neisseria meningitidis. We demonstrated improved microbiology knowledge after completion of the online modules. This improvement may not be solely attributed to completing the online modules, as fellows and faculty may have provided additional microbiology education during the rotation. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Impact disruption and recovery of the deep subsurface biosphere

USGS Publications Warehouse

Cockell, Charles S.; Voytek, Mary A.; Gronstal, Aaron L.; Finster, Kai; Kirshtein, Julie D.; Howard, Kieren; Reitner, Joachim; Gohn, Gregory S.; Sanford, Ward E.; Horton, J. Wright; Kallmeyer, Jens; Kelly, Laura; Powars, David S.

2012-01-01

Although a large fraction of the world's biomass resides in the subsurface, there has been no study of the effects of catastrophic disturbance on the deep biosphere and the rate of its subsequent recovery. We carried out an investigation of the microbiology of a 1.76 km drill core obtained from the ~35 million-year-old Chesapeake Bay impact structure, USA, with robust contamination control. Microbial enumerations displayed a logarithmic downward decline, but the different gradient, when compared to previously studied sites, and the scatter of the data are consistent with a microbiota influenced by the geological disturbances caused by the impact. Microbial abundance is low in buried crater-fill, ocean-resurge, and avalanche deposits despite the presence of redox couples for growth. Coupled with the low hydraulic conductivity, the data suggest the microbial community has not yet recovered from the impact ~35 million years ago. Microbial enumerations, molecular analysis of microbial enrichment cultures, and geochemical analysis showed recolonization of a deep region of impact-fractured rock that was heated to above the upper temperature limit for life at the time of impact. These results show how, by fracturing subsurface rocks, impacts can extend the depth of the biosphere. This phenomenon would have provided deep refugia for life on the more heavily bombarded early Earth, and it shows that the deeply fractured regions of impact craters are promising targets to study the past and present habitability of Mars.

Impact disruption and recovery of the deep subsurface biosphere.

PubMed

Cockell, Charles S; Voytek, Mary A; Gronstal, Aaron L; Finster, Kai; Kirshtein, Julie D; Howard, Kieren; Reitner, Joachim; Gohn, Gregory S; Sanford, Ward E; Horton, J Wright; Kallmeyer, Jens; Kelly, Laura; Powars, David S

2012-03-01

Although a large fraction of the world's biomass resides in the subsurface, there has been no study of the effects of catastrophic disturbance on the deep biosphere and the rate of its subsequent recovery. We carried out an investigation of the microbiology of a 1.76 km drill core obtained from the ∼35 million-year-old Chesapeake Bay impact structure, USA, with robust contamination control. Microbial enumerations displayed a logarithmic downward decline, but the different gradient, when compared to previously studied sites, and the scatter of the data are consistent with a microbiota influenced by the geological disturbances caused by the impact. Microbial abundance is low in buried crater-fill, ocean-resurge, and avalanche deposits despite the presence of redox couples for growth. Coupled with the low hydraulic conductivity, the data suggest the microbial community has not yet recovered from the impact ∼35 million years ago. Microbial enumerations, molecular analysis of microbial enrichment cultures, and geochemical analysis showed recolonization of a deep region of impact-fractured rock that was heated to above the upper temperature limit for life at the time of impact. These results show how, by fracturing subsurface rocks, impacts can extend the depth of the biosphere. This phenomenon would have provided deep refugia for life on the more heavily bombarded early Earth, and it shows that the deeply fractured regions of impact craters are promising targets to study the past and present habitability of Mars.

The Impact of Apollo-Era Microbiology on Human Space Flight

NASA Technical Reports Server (NTRS)

Elliott, T. F; Castro, V. A.; Bruce, R. J.; Pierson, D. L.

2014-01-01

The microbiota of crewmembers and the spacecraft environment contributes significant risk to crew health during space flight missions. NASA reduces microbial risk with various mitigation methods that originated during the Apollo Program and continued to evolve through subsequent programs: Skylab, Shuttle, and International Space Station (ISS). A quarantine of the crew and lunar surface samples, within the Lunar Receiving Laboratory following return from the Moon, was used to prevent contamination with unknown extraterrestrial organisms. The quarantine durations for the crew and lunar samples were 21 days and 50 days, respectively. A series of infections among Apollo crewmembers resulted in a quarantine before launch to limit exposure to infectious organisms. This Health Stabilization Program isolated the crew for 21 days before flight and was effective in reducing crew illness. After the program developed water recovery hardware for Apollo spacecraft, the 1967 National Academy of Science Space Science Board recommended the monitoring of potable water. NASA implemented acceptability limits of 10 colony forming units (CFU) per mL and the absence of viable E. coli, anaerobes, yeasts, and molds in three separate 150 mL aliquots. Microbiological investigations of the crew and spacecraft environment were conducted during the Apollo program, including the Apollo-Soyuz Test Project and Skylab. Subsequent space programs implemented microbial screening of the crew for pathogens and acceptability limits on spacecraft surfaces and air. Microbiology risk mitigation methods have evolved since the Apollo program. NASA cancelled the quarantine of the crew after return from the lunar surface, reduced the duration of the Health Stabilization Program; and implemented acceptability limits for spacecraft surfaces and air. While microbial risks were not a main focus of the early Mercury and Gemini programs, the extended duration of Apollo flights resulted in the increased scrutiny of impact of the space flight environment on crew health. The lessons learned during that era of space flight continue to impact microbiology risk mitigation in space programs today.

SUBSURFACE CHARACTERIZATION AND MONITORING TECHNIQUES: A DESK REFERENCE GUIDE - VOLUME II: THE VADOSE ZONE, FIELD SCREENING AND ANALYTICAL METHODS - APPENDICES C AND D

EPA Science Inventory

Many EPA programs, including those under the Resource Conservation and Recovery Act (RCRA) and the Comprehensive Response, Compensation, and Liability Act (CERCLA), require subsurface characterization and monitoring to detect ground-water contamination and provide data to deve...

ENVIRONMENTAL MONITORING FOR PUBLIC ACCESS AND COMMUNITY TRACKING (EMPACT) PROGRAM MICROBIOLOGICAL MONITORING OF RECREATIONAL WATER

EPA Science Inventory

Current Environmental Protection Agency (EPA) recommended microbiological monitoring practices for bathing beach water quality were suggested in 1968, as a part of the fecal coliform guideline developed by the Federal Water Pollution Control Administration. The guideline stated ...

AN OVERVIEW OF PATHOGEN RESEARCH IN THE MICROBIOLOGICAL AND CHEMICAL EXPOSURE ASSESSMENT RESEARCH DIVISION

EPA Science Inventory

The Microbiological and Chemical Exposure Assessment Research Division of the EPA Office of Research and Development's National Exposure Research Laboratory has a robust in-house research program aimed at developing better occurrence and exposure methods for waterborne pathogens....

Lattice Boltzmann-Based Approaches for Pore-Scale Reactive Transport

DOE PAGES

Yoon, Hongkyu; Kang, Qinjun; Valocchi, Albert J.

2015-07-29

Here an important geoscience and environmental applications such as geologic carbon storage, environmental remediation, and unconventional oil and gas recovery are best understood in the context of reactive flow and multicomponent transport in the subsurface environment. The coupling of chemical and microbiological reactions with hydrological and mechanical processes can lead to complex behaviors across an enormous range of spatial and temporal scales. These coupled responses are also strongly influenced by the heterogeneity and anisotropy of the geologic formations. Reactive transport processes can change the pore morphology at the pore scale, thereby leading to nonlinear interactions with advective and diffusive transport,more » which can strongly influence larger-scale properties such as permeability and dispersion.« less

Relating sub-surface ice features to physiological stress in a climate sensitive mammal, the American pika (Ochotona princeps).

PubMed

Wilkening, Jennifer L; Ray, Chris; Varner, Johanna

2015-01-01

The American pika (Ochotona princeps) is considered a sentinel species for detecting ecological effects of climate change. Pikas are declining within a large portion of their range, and ongoing research suggests loss of sub-surface ice as a mechanism. However, no studies have demonstrated physiological responses of pikas to sub-surface ice features. Here we present the first analysis of physiological stress in pikas living in and adjacent to habitats underlain by ice. Fresh fecal samples were collected non-invasively from two adjacent sites in the Rocky Mountains (one with sub-surface ice and one without) and analyzed for glucocorticoid metabolites (GCM). We also measured sub-surface microclimates in each habitat. Results indicate lower GCM concentration in sites with sub-surface ice, suggesting that pikas are less stressed in favorable microclimates resulting from sub-surface ice features. GCM response was well predicted by habitat characteristics associated with sub-surface ice features, such as lower mean summer temperatures. These results suggest that pikas inhabiting areas without sub-surface ice features are experiencing higher levels of physiological stress and may be more susceptible to changing climates. Although post-deposition environmental effects can confound analyses based on fecal GCM, we found no evidence for such effects in this study. Sub-surface ice features are key to water cycling and storage and will likely represent an increasingly important component of water resources in a warming climate. Fecal samples collected from additional watersheds as part of current pika monitoring programs could be used to further characterize relationships between pika stress and sub-surface ice features.

Evaluation of an Online Program To Teach Microbiology to Internal Medicine Residents

PubMed Central

Burd, Eileen M.; Kraft, Colleen S.; Armstrong, Wendy S.; Lenorr, Kenya; Spicer, Jennifer O.; Martin, Donna; del Rio, Carlos

2014-01-01

Microbiology rounds are an integral part of infectious disease consultation service. During microbiology rounds, we highlight microbiology principles using vignettes. We created case-based, interactive, microbiology online modules similar to the vignettes presented during microbiology rounds. Since internal medicine residents rotating on our infectious disease elective have limited time to participate in rounds and learn microbiology, our objective was to evaluate the use of the microbiology online modules by internal medicine residents. We asked residents to complete 10 of 25 online modules during their infectious disease elective. We evaluated which modules they chose and the change in their knowledge level. Forty-six internal medicine residents completed assessments given before and after accessing the modules with an average of 11/20 (range, 6 to 19) and 16/20 (range, 9 to 20) correct questions, respectively (average improvement, 5 questions; P = 0.0001). The modules accessed by more than 30 residents included those related to Clostridium difficile, anaerobes, Candida spp., Streptococcus pneumoniae, influenza, Mycobacterium tuberculosis, and Neisseria meningitidis. We demonstrated improved microbiology knowledge after completion of the online modules. This improvement may not be solely attributed to completing the online modules, as fellows and faculty may have provided additional microbiology education during the rotation. PMID:25392364

Modeling Subsurface Behavior at the System Level: Considerations and a Path Forward

NASA Astrophysics Data System (ADS)

Geesey, G.

2005-12-01

The subsurface is an obscure but essential resource to life on Earth. It is an important region for carbon production and sequestration, a source and reservoir for energy, minerals and metals and potable water. There is a growing need to better understand subsurface possesses that control the exploitation and security of these resources. Our best models often fail to predict these processes at the field scale because of limited understanding of 1) the processes and the controlling parameters, 2) how processes are coupled at the field scale 3) geological heterogeneities that control hydrological, geochemical and microbiological processes at the field scale and 4) lack of data sets to calibrate and validate numerical models. There is a need for experimental data obtained at scales larger than those obtained at the laboratory bench that take into account the influence of hydrodynamics, geochemical reactions including complexation and chelation/adsorption/precipitation/ion exchange/oxidation-reduction/colloid formation and dissolution, and reactions of microbial origin. Furthermore, the coupling of each of these processes and reactions needs to be evaluated experimentally at a scale that produces data that can be used to calibrate numerical models so that they accurately describe field scale system behavior. Establishing the relevant experimental scale for collection of data from coupled processes remains a challenge and will likely be process-dependent and involve iterations of experimentation and data collection at different intermediate scales until the models calibrated with the appropriate date sets achieve an acceptable level of performance. Assuming that the geophysicists will soon develop technologies to define geological heterogeneities over a wide range of scales in the subsurface, geochemists need to continue to develop techniques to remotely measure abiotic reactions, while geomicrobiologists need to continue their development of complementary technologies to remotely measure microbial community parameters that define their key functions at a scale that accurately reflects their role in large scale subsurface system behavior. The practical questions that geomicrobiologist must answer in the short term are: 1) What is known about the activities of the dominant microbial populations or those of their closest relatives? 2) Which of these activities is likely to dominate under in situ conditions? In the process of answering these questions, researchers will obtain answers to questions of a more fundamental nature such as 1) How deep does "active" life extend below the surface of the seafloor and terrestrial subsurface? 2) How are electrons exchanged between microbial cells and solid phase minerals? 3) What is the metabolic state and mechanism of survival of "inactive" life forms in the subsurface? 4) What can genomes of life forms trapped in geological material tell us about evolution of life that current methods cannot? The subsurface environment represents a challenging environment to understand and model. As the need to understand subsurface processes increases and the technologies to characterize them become available, modeling subsurface behavior will approach the level of sophistication of models used today to predict behavior of other large scale systems such as the oceans.

Predicting Sensitivity of Breast Tumors to Src-Targeted Therapies through Assessment of Cas/Src/BCAR3 Activity

DTIC Science & Technology

2016-10-01

Amy H. Bouton, Ph.D. Associate Dean of Graduate and Medical ScienXst Programs Professor of Microbiology , Immunology, and Cancer Biology Box...We found that all of the BCAR3 in invasive breast cancer cells is present in a complex with Cas and 1Department of Microbiology , Immunology and Cancer...Harrisonburg, VA, USA. Correspondence: Dr AH Bouton, Department of Microbiology , Immunology and Cancer Biology, University of Virginia School of Medicine, Box

[Microbiology laboratory as a base of information sending].

PubMed

Komori, Toshiaki; Fujita, Naohisa; Hirose, Yuri; Kimura, Takeshi; Kyotani, Noriko; Kurahashi, Satoko; Yamada, Yukiji; Ushiyama, Masaji; Yasumoto, Towa; Yuasa, Soh-ichi

2007-10-01

The goal of our microbiology laboratory is to provide an accurate microbiological result and a useful information for every healthcare workers (HCWs). For this purpose, we were trying to do several activities, such as improving the work-flow of microbiology testings, starting 365-day-open microbiology tests, providing some training courses of microbiology and sending many useful informations about infectious diseases and infection control. Before these activities, we needed another 5 microbiology technicians beside 3 technicians and had started the program to educate them. We have successfully finished it and enabled all plans begin in April, 2005. Since then we are open for 365 days and also sending HCWs many newsletters for performing effective microbiological testings via the intra-network system and having lectures for both doctors and nurses, especially for new resident doctors at the orientation. We had also the training course for certified infection control nurses and accepted two technicians from Africa, who came to study a basic microbiology via JICA. These activities have enabled every technician not only to report and analyze microbiological test result effectively but also to improve writing and presentation skills. Through these activities all technicians have realized that accurate and rapid information from a microbiology laboratory is a key to treat patients with infectious diseases and improve their prognosis. It is suggested that skill-up of technicians lead to report an accurate result in microbiology and at the same time improve the attitude for their job.

Use of Computer-Assisted Instruction to Review Microbiology and Antimicrobial Agents.

ERIC Educational Resources Information Center

Carver, Peggy L.; And Others

1991-01-01

A study assessed the effectiveness of a microcomputer-assisted instructional program using graphics, color, and text in simulations to enhance pharmacy students' knowledge of microbiology and antimicrobial agents. Results indicated high short- and long-term retention of information presented and higher levels of knowledge and comprehension among…

Geochemical and microbiological characteristics during in situ chemical oxidation and in situ bioremediation at a diesel contaminated site.

PubMed

Sutton, Nora B; Kalisz, Mariusz; Krupanek, Janusz; Marek, Jan; Grotenhuis, Tim; Smidt, Hauke; de Weert, Jasperien; Rijnaarts, Huub H M; van Gaans, Pauline; Keijzer, Thomas

2014-02-18

While in situ chemical oxidation with persulfate has seen wide commercial application, investigations into the impacts on groundwater characteristics, microbial communities and soil structure are limited. To better understand the interactions of persulfate with the subsurface and to determine the compatibility with further bioremediation, a pilot scale treatment at a diesel-contaminated location was performed consisting of two persulfate injection events followed by a single nutrient amendment. Groundwater parameters measured throughout the 225 day experiment showed a significant decrease in pH and an increase in dissolved diesel and organic carbon within the treatment area. Molecular analysis of the microbial community size (16S rRNA gene) and alkane degradation capacity (alkB gene) by qPCR indicated a significant, yet temporary impact; while gene copy numbers initially decreased 1-2 orders of magnitude, they returned to baseline levels within 3 months of the first injection for both targets. Analysis of soil samples with sequential extraction showed irreversible oxidation of metal sulfides, thereby changing subsurface mineralogy and potentially mobilizing Fe, Cu, Pb, and Zn. Together, these results give insight into persulfate application in terms of risks and effective coupling with bioremediation.

Microbiological, Geochemical and Hydrologic Processes Controlling Uranium Mobility: An Integrated Field Scale Subsurface Research Challenge Site at Rifle, Colorado, February 2011 to January 2012

DOE Office of Scientific and Technical Information (OSTI.GOV)

Long, Philip E.; Banfield, Jill; Chandler, Darrell P.

The Rifle IFRC continued to make excellent progress during the last 12 months. As noted above, a key field experiment (Best Western) was performed during 2011 as a logical follow-on to the Super 8 field experiment preformed in 2010. In the Super 8 experiment, we successfully combined desorption and bioreduction and deployed a number of novel tracer techniques to enhance our ability to interpret the biogeochemistry of the experiment. In the Best Western experiment, we used the same experimental plot (Plot C) as was used for Super 8. The overarching objective of the Best Western field experiment was to comparedmore » the impacts of abiotic vs. biotic increases in alkalinity and to assess the mass of the sorbed pool of U(VI) at Rifle at the field scale. Both of these objectives were met. Preliminary analysis of the data indicate that the underlying biogeochemical data sets were obtained that will support a mechanistic understanding of the underlying processes, including remarkable insight into previously unrecognized microbial processes taking place during acetate amendment of the subsurface for a second time.« less

Respiratory interactions of soil bacteria with (semi)conductive iron-oxide minerals.

PubMed

Kato, Souichiro; Nakamura, Ryuhei; Kai, Fumiyoshi; Watanabe, Kazuya; Hashimoto, Kazuhito

2010-12-01

Pure-culture studies have shown that dissimilatory metal-reducing bacteria are able to utilize iron-oxide nanoparticles as electron conduits for reducing distant terminal acceptors; however, the ecological relevance of such energy metabolism is poorly understood. Here, soil microbial communities were grown in electrochemical cells with acetate as the electron donor and electrodes (poised at 0.2 V versus Ag/AgCl) as the electron acceptors in the presence and absence of iron-oxide nanoparticles, and respiratory current generation and community structures were analysed. Irrespective of the iron-oxide species (hematite, magnetite or ferrihydrite), the supplementation with iron-oxide minerals resulted in large increases (over 30-fold) in current, while only a moderate increase (∼10-fold) was observed in the presence of soluble ferric/ferrous irons. During the current generation, insulative ferrihydrite was transformed into semiconductive goethite. Clone-library analyses of 16S rRNA gene fragments PCR-amplified from the soil microbial communities revealed that iron-oxide supplementation facilitated the occurrence of Geobacter species affiliated with subsurface clades 1 and 2. We suggest that subsurface-clade Geobacter species preferentially thrive in soil by utilizing (semi)conductive iron oxides for their respiration. © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.

Anaerobic consortia of fungi and sulfate reducing bacteria in deep granite fractures.

PubMed

Drake, Henrik; Ivarsson, Magnus; Bengtson, Stefan; Heim, Christine; Siljeström, Sandra; Whitehouse, Martin J; Broman, Curt; Belivanova, Veneta; Åström, Mats E

2017-07-04

The deep biosphere is one of the least understood ecosystems on Earth. Although most microbiological studies in this system have focused on prokaryotes and neglected microeukaryotes, recent discoveries have revealed existence of fossil and active fungi in marine sediments and sub-seafloor basalts, with proposed importance for the subsurface energy cycle. However, studies of fungi in deep continental crystalline rocks are surprisingly few. Consequently, the characteristics and processes of fungi and fungus-prokaryote interactions in this vast environment remain enigmatic. Here we report the first findings of partly organically preserved and partly mineralized fungi at great depth in fractured crystalline rock (-740 m). Based on environmental parameters and mineralogy the fungi are interpreted as anaerobic. Synchrotron-based techniques and stable isotope microanalysis confirm a coupling between the fungi and sulfate reducing bacteria. The cryptoendolithic fungi have significantly weathered neighboring zeolite crystals and thus have implications for storage of toxic wastes using zeolite barriers.Deep subsurface microorganisms play an important role in nutrient cycling, yet little is known about deep continental fungal communities. Here, the authors show organically preserved and partly mineralized fungi at 740 m depth, and find evidence of an anaerobic fungi and sulfate reducing bacteria consortium.

Life Beneath Glacial Ice - Earth(!) Mars(?) Europa(?)

NASA Technical Reports Server (NTRS)

Allen, Carlton C.; Grasby, Stephen E.; Longazo, Teresa G.; Lisle, John T.; Beauchamp, Benoit

2002-01-01

We are investigating a set of cold springs that deposit sulfur and carbonate minerals on the surface of a Canadian arctic glacier. The spring waters and mineral deposits contain microorganisms, as well as clear evidence that biological processes mediate subglacial chemistry, mineralogy, and isotope fractionation . The formation of native sulphur and associated deposits are related to bacterially mediated reduction and oxidation of sulphur below the glacier. A non-volcanic, topography driven geothermal system, harboring a microbiological community, operates in an extremely cold environment and discharges through solid ice. Microbial life can thus exist in isolated geothermal refuges despite long-term subfreezing surface conditions. Earth history includes several periods of essentially total glaciation. lee in the near subsurface of Mars may have discharged liquid water in the recent past Cracks in the ice crust of Europa have apparently allowed the release of water to the surface. Chemolithotrophic bacteria, such as those in the Canadian springs, could have survived beneath the ice of "Snowball Earth", and life forms with similar characteristics might exist beneath the ice of Mars or Europa. Discharges of water from such refuges may have brought to the surface living microbes, as well as longlasting chemical, mineralogical, and isotopic indications of subsurface life.

The Oman Drilling Project

NASA Astrophysics Data System (ADS)

Matter, J.; Kelemen, P. B.; Teagle, D. A. H.

2014-12-01

With seed funds from the Sloan Foundation, the International Continental Drilling Program (ICDP) approved a proposal by 39 international proponents for scientific drilling in the Oman ophiolite. Via observations on core, geophysical logging, fluid sampling, hydrological measurements, and microbiological sampling in a series of boreholes, we will address long-standing, unresolved questions regarding melt and solid transport in the mantle beneath oceanic spreading ridges, igneous accretion of oceanic crust, mass transfer between the oceans and the crust via hydrothermal alteration, and recycling of volatile components in subduction zones. We will undertake frontier exploration of subsurface weathering processes in mantle peridotite, including natural mechanisms of carbon dioxide uptake from surface waters and the atmosphere, and the nature of the subsurface biosphere. Societally relevant aspects include involvement and training of university students, including numerous students from Sultan Qaboos University in Oman. Studies of natural mineral carbonation will contribute to design of engineered systems for geological carbon dioxide capture and storage. Studies of alteration will contribute to fundamental understanding of the mechanisms of reaction-driven cracking, which could enhance geothermal power generation and extraction of unconventional hydrocarbon resources. We hope to begin drilling in late 2015. Meanwhile, we are seeking an additional $2M to match the combined Sloan and ICDP funding from national and international funding agencies. Matching funds are needed for operational costs of drilling, geophysical logging, downhole fluid sampling, and core description. Information on becoming part of the named investigator pool is in Appendix 14 (page 70) of the ICDP proposal, available at https://www.ldeo.columbia.edu/gpg/projects/icdp-workshop-oman-drilling-project. This formal process should begin at about the time of the 2014 Fall AGU Meeting. Meanwhile, potential investigators who can help raise matching funds, e.g. for core description as part of petrological or structural studies or for drill site operations, are encouraged to contact the authors of this abstract.

Mars Analog Research and Technology Experiment (MARTE): A Simulated Mars Drilling Mission to Search for Subsurface Life at the Rio Tinto, Spain

NASA Technical Reports Server (NTRS)

Stoker, Carol; Lemke, Larry; Mandell, Humboldt; McKay, David; George, Jeffrey; Gomez-Alvera, Javier; Amils, Ricardo; Stevens, Todd; Miller, David

2003-01-01

The MARTE (Mars Astrobiology Research and Technology Experiment) project was selected by the new NASA ASTEP program, which supports field experiments having an equal emphasis on Astrobiology science and technology development relevant to future Astrobiology missions. MARTE will search for a hypothesized subsurface anaerobic chemoautotrophic biosphere in the region of the Tinto River in southwestern Spain while also demonstrating technology needed to search for a subsurface biosphere on Mars. The experiment is informed by the strategy for searching for life on Mars.

Relating Sub-Surface Ice Features to Physiological Stress in a Climate Sensitive Mammal, the American Pika (Ochotona princeps)

PubMed Central

Wilkening, Jennifer L.; Ray, Chris; Varner, Johanna

2015-01-01

The American pika (Ochotona princeps) is considered a sentinel species for detecting ecological effects of climate change. Pikas are declining within a large portion of their range, and ongoing research suggests loss of sub-surface ice as a mechanism. However, no studies have demonstrated physiological responses of pikas to sub-surface ice features. Here we present the first analysis of physiological stress in pikas living in and adjacent to habitats underlain by ice. Fresh fecal samples were collected non-invasively from two adjacent sites in the Rocky Mountains (one with sub-surface ice and one without) and analyzed for glucocorticoid metabolites (GCM). We also measured sub-surface microclimates in each habitat. Results indicate lower GCM concentration in sites with sub-surface ice, suggesting that pikas are less stressed in favorable microclimates resulting from sub-surface ice features. GCM response was well predicted by habitat characteristics associated with sub-surface ice features, such as lower mean summer temperatures. These results suggest that pikas inhabiting areas without sub-surface ice features are experiencing higher levels of physiological stress and may be more susceptible to changing climates. Although post-deposition environmental effects can confound analyses based on fecal GCM, we found no evidence for such effects in this study. Sub-surface ice features are key to water cycling and storage and will likely represent an increasingly important component of water resources in a warming climate. Fecal samples collected from additional watersheds as part of current pika monitoring programs could be used to further characterize relationships between pika stress and sub-surface ice features. PMID:25803587

COST EFFECTIVE AND HIGH RESOLUTION SUBSURFACE CHARACTERIZATION USING HYDRAULIC TOMOGRAPHY

DTIC Science & Technology

2017-08-01

FINAL REPORT Cost -Effective and High-Resolution Subsurface Characterization Using Hydraulic Tomography ESTCP Project ER-201212 AUGUST...This document has been cleared for public release Page Intentionally Left Blank This report was prepared under contract to the Department of...Defense Environmental Security Technology Certification Program (ESTCP). The publication of this report does not indicate endorsement by the Department

Prevention and Control of Antimicrobial Resistant Healthcare-Associated Infections: The Microbiology Laboratory Rocks!

PubMed

Simões, Alexandra S; Couto, Isabel; Toscano, Cristina; Gonçalves, Elsa; Póvoa, Pedro; Viveiros, Miguel; Lapão, Luís V

2016-01-01

In Europe, each year, more than four milion patients acquire a healthcare-associated infection (HAI) and almost 40 thousand die as a direct consequence of it. Regardless of many stategies to prevent and control HAIs, they remain an important cause of morbidity and mortality worldwide with a significant economic impact: a recent estimate places it at the ten billion dollars/year. The control of HAIs requires a prompt and efficient identification of the etiological agent and a rapid communication with the clinician. The Microbiology Laboratory has a significant role in the prevention and control of these infections and is a key element of any Infection Control Program. The work of the Microbiology Laboratory covers microbial isolation and identification, determination of antimicrobial susceptibility patterns, epidemiological surveillance and outbreak detection, education, and report of quality assured results. In this paper we address the role and importance of the Microbiology Laboratory in the prevention and control of HAI and in Antibiotic Stewardship Programs and how it can be leveraged when combined with the use of information systems. Additionally, we critically review some challenges that the Microbiology Laboratory has to deal with, including the selection of analytic methods and the proper use of communication channels with other healthcare services.

Legacy of contaminant N sources to the NO3- signature in rivers: a combined isotopic (δ15N-NO3-, δ18O-NO3-, δ11B) and microbiological investigation

NASA Astrophysics Data System (ADS)

Briand, Cyrielle; Sebilo, Mathieu; Louvat, Pascale; Chesnot, Thierry; Vaury, Véronique; Schneider, Maude; Plagnes, Valérie

2017-02-01

Nitrate content of surface waters results from complex mixing of multiple sources, whose signatures can be modified through N reactions occurring within the different compartments of the whole catchment. Despite this complexity, the determination of nitrate origin is the first and crucial step for water resource preservation. Here, for the first time, we combined at the catchment scale stable isotopic tracers (δ15N and δ18O of nitrate and δ11B) and fecal indicators to trace nitrate sources and pathways to the stream. We tested this approach on two rivers in an agricultural region of SW France. Boron isotopic ratios evidenced inflow from anthropogenic waters, microbiological markers revealed organic contaminations from both human and animal wastes. Nitrate δ15N and δ18O traced inputs from the surface leaching during high flow events and from the subsurface drainage in base flow regime. They also showed that denitrification occurred within the soils before reaching the rivers. Furthermore, this study highlighted the determinant role of the soil compartment in nitrate formation and recycling with important spatial heterogeneity and temporal variability.

Microbial Diversity in Natural Asphalts of the Rancho La Brea Tar Pits▿

PubMed Central

Kim, Jong-Shik; Crowley, David E.

2007-01-01

Bacteria commonly inhabit subsurface oil reservoirs, but almost nothing is known yet about microorganisms that live in naturally occurring terrestrial oil seeps and natural asphalts that are comprised of highly recalcitrant petroleum hydrocarbons. Here we report the first survey of microbial diversity in ca. 28,000-year-old samples of natural asphalts from the Rancho La Brea Tar Pits in Los Angeles, CA. Microbiological studies included analyses of 16S rRNA gene sequences and DNA encoding aromatic ring-hydroxylating dioxygenases from two tar pits differing in chemical composition. Our results revealed a wide range of phylogenetic groups within the Archaea and Bacteria domains, in which individual taxonomic clusters were comprised of sets of closely related species within novel genera and families. Fluorescent staining of asphalt-soil particles using phylogenetic probes for Archaea, Bacteria, and Pseudomonas showed coexistence of mixed microbial communities at high cell densities. Genes encoding dioxygenases included three novel clusters of enzymes. The discovery of life in the tar pits provides an avenue for further studies of the evolution of enzymes and catabolic pathways for bacteria that have been exposed to complex hydrocarbons for millennia. These bacteria also should have application for industrial microbiology and bioremediation. PMID:17416692

42 CFR 121.9 - Designated transplant program requirements.

Code of Federal Regulations, 2012 CFR

2012-10-01

... RESOURCES DEVELOPMENT ORGAN PROCUREMENT AND TRANSPLANTATION NETWORK § 121.9 Designated transplant program...) Has immediate access to microbiology, clinical chemistry, histocompatibility testing, radiology, and...

42 CFR 121.9 - Designated transplant program requirements.

Code of Federal Regulations, 2014 CFR

2014-10-01

... RESOURCES DEVELOPMENT ORGAN PROCUREMENT AND TRANSPLANTATION NETWORK § 121.9 Designated transplant program...) Has immediate access to microbiology, clinical chemistry, histocompatibility testing, radiology, and...

42 CFR 121.9 - Designated transplant program requirements.

Code of Federal Regulations, 2013 CFR

2013-10-01

... RESOURCES DEVELOPMENT ORGAN PROCUREMENT AND TRANSPLANTATION NETWORK § 121.9 Designated transplant program...) Has immediate access to microbiology, clinical chemistry, histocompatibility testing, radiology, and...

Thaumarchaeal ammonium oxidation and evidence for a nitrogen cycle in a subsurface radioactive thermal spring in the Austrian Central Alps.

PubMed

Gerbl, Friedrich W; Weidler, Gerhard W; Wanek, Wolfgang; Erhardt, Angelika; Stan-Lotter, Helga

2014-01-01

Previous studies had suggested the presence of ammonium oxidizing Thaumarchaeota as well as nitrite oxidizing Bacteria in the subsurface spring called Franz Josef Quelle (FJQ), a slightly radioactive thermal mineral spring with a temperature of 43.6-47°C near the alpine village of Bad Gastein, Austria. The microbiological consortium of the FJQ was investigated for its utilization of nitrogen compounds and the putative presence of a subsurface nitrogen cycle. Microcosm experiments made with samples from the spring water, containing planktonic microorganisms, or from biofilms, were used in this study. Three slightly different media, enriched with vitamins and trace elements, and two incubation temperatures (30 and 40°C, respectively) were employed. Under aerobic conditions, high rates of conversion of ammonium to nitrite, as well as nitrite to nitrate were measured. Under oxygen-limited conditions nitrate was converted to gaseous compounds. Stable isotope probing with (15)NH4Cl or ((15)NH4)2SO4as sole energy sources revealed incorporation of (15)N into community DNA. Genomic DNA as well as RNA were extracted from all microcosms. The following genes or fragments of genes were successfully amplified, cloned and sequenced by standard PCR from DNA extracts: Ammonia monooxygenase subunit A (amoA), nitrite oxidoreductase subunits A and B (nxrA and nxrB), nitrate reductase (narG), nitrite reductase (nirS), nitric oxide reductases (cnorB and qnorB), nitrous oxide reductase (nosZ). Reverse transcription of extracted total RNA and real-time PCR suggested the expression of each of those genes. Nitrogen fixation (as probed with nifH and nifD) was not detected. However, a geological origin of NH(+) 4 in the water of the FJQ cannot be excluded, considering the silicate, granite and gneiss containing environment. The data suggested the operation of a nitrogen cycle in the subsurface environment of the FJQ.

Thaumarchaeal ammonium oxidation and evidence for a nitrogen cycle in a subsurface radioactive thermal spring in the Austrian Central Alps

PubMed Central

Gerbl, Friedrich W.; Weidler, Gerhard W.; Wanek, Wolfgang; Erhardt, Angelika; Stan-Lotter, Helga

2014-01-01

Previous studies had suggested the presence of ammonium oxidizing Thaumarchaeota as well as nitrite oxidizing Bacteria in the subsurface spring called Franz Josef Quelle (FJQ), a slightly radioactive thermal mineral spring with a temperature of 43.6–47°C near the alpine village of Bad Gastein, Austria. The microbiological consortium of the FJQ was investigated for its utilization of nitrogen compounds and the putative presence of a subsurface nitrogen cycle. Microcosm experiments made with samples from the spring water, containing planktonic microorganisms, or from biofilms, were used in this study. Three slightly different media, enriched with vitamins and trace elements, and two incubation temperatures (30 and 40°C, respectively) were employed. Under aerobic conditions, high rates of conversion of ammonium to nitrite, as well as nitrite to nitrate were measured. Under oxygen-limited conditions nitrate was converted to gaseous compounds. Stable isotope probing with 15NH4Cl or (15NH4)2SO4as sole energy sources revealed incorporation of 15N into community DNA. Genomic DNA as well as RNA were extracted from all microcosms. The following genes or fragments of genes were successfully amplified, cloned and sequenced by standard PCR from DNA extracts: Ammonia monooxygenase subunit A (amoA), nitrite oxidoreductase subunits A and B (nxrA and nxrB), nitrate reductase (narG), nitrite reductase (nirS), nitric oxide reductases (cnorB and qnorB), nitrous oxide reductase (nosZ). Reverse transcription of extracted total RNA and real-time PCR suggested the expression of each of those genes. Nitrogen fixation (as probed with nifH and nifD) was not detected. However, a geological origin of NH+4 in the water of the FJQ cannot be excluded, considering the silicate, granite and gneiss containing environment. The data suggested the operation of a nitrogen cycle in the subsurface environment of the FJQ. PMID:24904540

Microbiological Methodology in Astrobiology

NASA Technical Reports Server (NTRS)

Abyzov, S. S.; Gerasimenko, L. M.; Hoover, R. B.; Mitskevich, I. N.; Mulyukin, A. L.; Poglazova, M. N.; Rozanov, A. Y.

2005-01-01

Searching for life in astromaterials to be delivered from the future missions to extraterrestrial bodies is undoubtedly related to studies of the properties and signatures of living microbial cells and microfossils on Earth. As model terrestrial analogs of Martian polar subsurface layers are often regarded the Antarctic glacier and Earth permafrost habitats where alive microbial cells preserved viability for millennia years due to entering the anabiotic state. For the future findings of viable microorganisms in samples from extraterrestrial objects, it is important to use a combined methodology that includes classical microbiological methods, plating onto nutrient media, direct epifluorescence and electron microscopy examinations, detection of the elemental composition of cells, radiolabeling techniques, PCR and FISH methods. Of great importance is to ensure authenticity of microorganisms (if any in studied samples) and to standardize the protocols used to minimize a risk of external contamination. Although the convincing evidence of extraterrestrial microbial life will may come from the discovery of living cells in astromaterials, biomorphs and microfossils must also be regarded as a target in search of life evidence bearing in mind a scenario that alive microorganisms had not be preserved and underwent mineralization. Under the laboratory conditions, processes that accompanied fossilization of cyanobacteria were reconstructed, and artificially produced cyanobacterial stromatolites resembles by their morphological properties those found in natural Earth habitats. Regarding the vital importance of distinguishing between biogenic and abiogenic signatures and between living and fossil microorganisms in analyzed samples, it is worthwhile to use some previously developed approaches based on electron microscopy examinations and analysis of elemental composition of biomorphs in situ and comparison with the analogous data obtained for laboratory microbial cultures and fossilized microorganisms. This communication will be focused on the analysis of our experience in working with ancient microorganisms and fossils and discussion of some issues that are crucial for development of the program for future finding of extraterrestrial life and its evidence.

Image-based overlay measurement using subsurface ultrasonic resonance force microscopy

NASA Astrophysics Data System (ADS)

Tamer, M. S.; van der Lans, M. J.; Sadeghian, H.

2018-03-01

Image Based Overlay (IBO) measurement is one of the most common techniques used in Integrated Circuit (IC) manufacturing to extract the overlay error values. The overlay error is measured using dedicated overlay targets which are optimized to increase the accuracy and the resolution, but these features are much larger than the IC feature size. IBO measurements are realized on the dedicated targets instead of product features, because the current overlay metrology solutions, mainly based on optics, cannot provide sufficient resolution on product features. However, considering the fact that the overlay error tolerance is approaching 2 nm, the overlay error measurement on product features becomes a need for the industry. For sub-nanometer resolution metrology, Scanning Probe Microscopy (SPM) is widely used, though at the cost of very low throughput. The semiconductor industry is interested in non-destructive imaging of buried structures under one or more layers for the application of overlay and wafer alignment, specifically through optically opaque media. Recently an SPM technique has been developed for imaging subsurface features which can be potentially considered as a solution for overlay metrology. In this paper we present the use of Subsurface Ultrasonic Resonance Force Microscopy (SSURFM) used for IBO measurement. We used SSURFM for imaging the most commonly used overlay targets on a silicon substrate and photoresist. As a proof of concept we have imaged surface and subsurface structures simultaneously. The surface and subsurface features of the overlay targets are fabricated with programmed overlay errors of +/-40 nm, +/-20 nm, and 0 nm. The top layer thickness changes between 30 nm and 80 nm. Using SSURFM the surface and subsurface features were successfully imaged and the overlay errors were extracted, via a rudimentary image processing algorithm. The measurement results are in agreement with the nominal values of the programmed overlay errors.

Programmed Lab Experiments for Biochemical Investigation of Quorum-Sensing Signal Molecules in Rhizospheric Soil Bacteria.

PubMed

Nievas, Fiorela L; Bogino, Pablo C; Giordano, Walter

2016-05-06

Biochemistry courses in the Department of Molecular Biology at the National University of Río Cuarto, Argentina, are designed for undergraduate students in biology, microbiology, chemistry, agronomy, and veterinary medicine. Microbiology students typically have previous coursework in general, analytical, and organic chemistry. Programmed sequences of lab experiments allow these students to investigate biochemical problems whose solution is feasible within the context of their knowledge and experience. We previously designed and reported a programmed lab experiment that familiarizes microbiology students with techniques for detection and characterization of quorum-sensing (QS) and quorum-quenching (QQ) signal molecules. Here, we describe a sequence of experiments designed to expand the understanding and capabilities of biochemistry students using techniques for extraction and identification of QS and QQ signal molecules from peanut rhizospheric soil bacteria, including culturing and manipulation of bacteria under sterile conditions. The program provides students with an opportunity to perform useful assays, draw conclusions from their results, and discuss possible extensions of the study. © 2016 by The International Union of Biochemistry and Molecular Biology, 44:256-262, 2016. © 2016 The International Union of Biochemistry and Molecular Biology.

BRNBOX v.1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aldridge, David F.

Program BRNBOX conducts a systematic search through a pre-defined 3D volume of candidate sub-surface Born scattering points in order to identify the particular point that minimizes the misfit between predicted (i.e., calculated) and observed electromagnetic (EM) data. This global minimum misfit point is interpreted as the location where electrically conductive proppant is injected into a sub-surface petroleum reservoir in a hydraulic fracturing experiment.

Complete Subsurface Elemental Composition Measurements With PING

NASA Technical Reports Server (NTRS)

Parsons, A. M.

2012-01-01

The Probing In situ with Neutrons and Gamma rays (PING) instrument will measure the complete bulk elemental composition of the subsurface of Mars as well as any other solid planetary body. PING can thus be a highly effective tool for both detailed local geochemistry science investigations and precision measurements of Mars subsurface reSOurces in preparation for future human exploration. As such, PING is thus fully capable of meeting a majority of both ncar and far term elements in Challenge #1 presented for this conference. Measuring the ncar subsurface composition of Mars will enable many of the MEPAG science goals and will be key to filling an important Strategic Knowledge Gap with regard to In situ Resources Utilization (ISRU) needs for human exploration. [1, 2] PING will thus fill an important niche in the Mars Exploration Program.

DUSEL and the future of deep terrestrial microbiology (Invited)

NASA Astrophysics Data System (ADS)

Onstott, T. C.; Peters, C. A.; Murdoch, L. C.; Elsworth, D.; Sonnenthal, E. L.; Kieft, T.; Boutt, D. F.; Germanovich, L.; Glaser, S. D.; Wang, H. F.; Roggenthen, B.; Lesko, K.; Cushman, P.; Stetler, L. D.; Bang, S.; Anderson, C.

2009-12-01

DUSEL will take advantage of the existing subsurface architecture of the deepest mine in the U.S. to provide a platform for launching new exploration into the deep terrestrial biosphere. Multi-year experiments are currently being designed to delineate the relationships between microbial diversity and activity and hydraulic connectivity, temperature, pressure, strain rate and multiphase fluids. Unlike the physics experiments, which will be located close to the center of the mine, most of these experiments will be located at the periphery in existing tunnels at 100 to 2400 m depth in order to access fluid fill fractures with boreholes. Hydrological models suggest that DUSEL could sample ~100 km3 volume for microbial biogeographic and transport studies. The high-capacity underground water filtration plant used to generate ultrapure water for neutrino detectors will readily supply water for microbiology coring projects reducing microbial contamination. This will be essential for the drilling platform located at 2400 m depth that will drill down to 7+ km and 120oC in search of the upper temperature limit for life. Another advantage of underground coring is that the drilling fluid pressure will be much less than that of the fracture water, which means that when the coring bit intersects a water-filled fracture, the fracture water will flow into the core barrel reducing the contamination of fracture surfaces in the cores. The ultra-low radiation background counting facility to be located at 1475 m depth will potentially enable 106 times improvement in the detection limit for subsurface microbial respiration rates using radioactive tracers. The Coupled Thermal-Hydrological-Mechanical-Chemical-Biological, block-heating experiment will examine how the microbial communities within fractures respond to the increased thermal and fluid flux. The Fracture Processes Facility is not only designed to determine what controls rock strength, but could also determine to what extent subsurface chemoautotrophic activity is regulated by tectonic episodicity. The DUSEL CO2 Facility will investigate how microbial activity is impacted by CO2 injection and whether microbial activity has a significant impact upon long-term sequestration of CO2. These three experiments represent a subset of the integrated suite of experiments planned for the first 5 years, but many more microbial experiments can be accommodated within DUSEL. With its unique experimental assets, km-scale spatial access and multi-decade observational lifetime, DUSEL will usher in the next generation of exploration into the deep terrestrial biosphere and not only reveal the answers to many of its well-hidden secrets, but perhaps to the origin of life itself.

Robert Earle Buchanan: an unappreciated scientist.

PubMed Central

Singleton, R.

1999-01-01

Robert Earle Buchanan (1883-1973), 19th President of the Society of American Bacteriologists (later American Society for Microbiology), was one of the more important 20th century microbiologists. He was a dominant force in creating the field of bacterial systematics and made significant contributions to microbial physiology. He also numbered a number of influential textbooks. A reasonable conclusion is that Buchanan was a major cultivator of modern microbiology. To justify that assertion, I have four major objectives in this essay: i) a brief biographical review of Buchanan's early life; ii) a brief review of his scientific contributions, many of which go beyond his recognized contributions to bacterial systematics; iii) Buchanan was an important academic administrator who created the microbiology program and fostered a strong graduate education program at Iowa State, iv)finally, I close the essay with a focus on Buchanan's "moral character." Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:11049164

Fueling the Bio-economy: European Culture Collections and Microbiology Education and Training.

PubMed

Antunes, André; Stackebrandt, Erko; Lima, Nelson

2016-02-01

A survey of European Microbial Biological Resource Centers and their users provided an overview on microbiology education and training. The results identified future increases in demand despite several shortcomings and gaps in the current offer. Urgent adjustments are needed to match users' needs, integrate innovative programs, and adopt new technologies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Clinical Investigation Program Annual Progress Report

DTIC Science & Technology

1989-09-30

initiatives for the study of relatedness of bacterial and HLA antigens as they influence autoimmune diseases. Microbiology Service - FY 89 An in-house...1030 87/103 0 Identification of Those at Risk for Osteoporotic Hip Fractures, by an Noninvasive Measurement (P) (PR)... 105 87/104 0 SWOG 8600 - A...233 82/302 0 The Evaluation of Recently Introduced, Commercially Available Clinical Microbiology Products for Possible

In situ hydrogen consumption kinetics as an indicator of subsurface microbial activity

USGS Publications Warehouse

Harris, S.H.; Smith, R.L.; Suflita, J.M.

2007-01-01

There are few methods available for broadly assessing microbial community metabolism directly within a groundwater environment. In this study, hydrogen consumption rates were estimated from in situ injection/withdrawal tests conducted in two geochemically varying, contaminated aquifers as an approach towards developing such a method. The hydrogen consumption first-order rates varied from 0.002 nM h-1 for an uncontaminated, aerobic site to 2.5 nM h-1 for a contaminated site where sulfate reduction was a predominant process. The method could accommodate the over three orders of magnitude range in rates that existed between subsurface sites. In a denitrifying zone, the hydrogen consumption rate (0.02 nM h-1) was immediately abolished in the presence of air or an antibiotic mixture, suggesting that such measurements may also be sensitive to the effects of environmental perturbations on field microbial activities. Comparable laboratory determinations with sediment slurries exhibited hydrogen consumption kinetics that differed substantially from the field estimates. Because anaerobic degradation of organic matter relies on the rapid consumption of hydrogen and subsequent maintenance at low levels, such in situ measures of hydrogen turnover can serve as a key indicator of the functioning of microbial food webs and may be more reliable than laboratory determinations. ?? 2007 Federation of European Microbiological Societies.

Quantification of hydrophobic interaction affinity of colloids

NASA Astrophysics Data System (ADS)

Saini, G.; Nasholm, N.; Wood, B. D.

2009-12-01

Colloids play an important role in a wide variety of disciplines, including water and wastewater treatment, subsurface transport of metals and organic contaminants, migration of fines in oil reservoirs, biocolloid (virus and bacteria) transport in subsurface, and are integral to laboratory transport studies. Although the role of hydrophobicity in adhesion and transport of colloids, particularly bacteria, is well known; there is scarcity of literature regarding hydrophobicity measurement of non-bacterial colloids and other micron-sized particles. Here we detail an experimental approach based on differential partitioning of colloids between two liquid phases (hydrocarbon and buffer) as a measure of the hydrophobic interaction affinity of colloids. This assay, known as Microbial adhesion to hydrocarbons or MATH, is frequently used in microbiology and bacteriology for quantifying the hydrophobicity of microbes. Monodispersed colloids and particles, with sizes ranging from 1 micron to 33 micron, were used for the experiments. A range of hydrophobicity values were observed for different particles. The hydrophobicity results are also verified against water contact angle measurements of these particles. This liquid-liquid partitioning assay is quick, easy-to-perform and requires minimal instrumentation. Estimation of the hydrophobic interaction affinity of colloids would lead to a better understanding of their adhesion to different surfaces and subsequent transport in porous media.

Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes.

PubMed

Graham, Emily B; Crump, Alex R; Resch, Charles T; Fansler, Sarah; Arntzen, Evan; Kennedy, David W; Fredrickson, Jim K; Stegen, James C

2017-04-01

Subsurface groundwater-surface water mixing zones (hyporheic zones) have enhanced biogeochemical activity, but assembly processes governing subsurface microbiomes remain a critical uncertainty in understanding hyporheic biogeochemistry. To address this obstacle, we investigated (a) biogeographical patterns in attached and waterborne microbiomes across three hydrologically-connected, physicochemically-distinct zones (inland hyporheic, nearshore hyporheic and river); (b) assembly processes that generated these patterns; (c) groups of organisms that corresponded to deterministic changes in the environment; and (d) correlations between these groups and hyporheic metabolism. All microbiomes remained dissimilar through time, but consistent presence of similar taxa suggested dispersal and/or common selective pressures among zones. Further, we demonstrated a pronounced impact of deterministic assembly in all microbiomes as well as seasonal shifts from heterotrophic to autotrophic microorganisms associated with increases in groundwater discharge. The abundance of one statistical cluster of organisms increased with active biomass and respiration, revealing organisms that may strongly influence hyporheic biogeochemistry. Based on our results, we propose a conceptualization of hyporheic zone metabolism in which increased organic carbon concentrations during surface water intrusion support heterotrophy, which succumbs to autotrophy under groundwater discharge. These results provide new opportunities to enhance microbially-explicit ecosystem models describing hyporheic zone biogeochemistry and its influence over riverine ecosystem function. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Intraterrestrial life in igneous ocean crust: advances, technologies, and the future (Invited)

NASA Astrophysics Data System (ADS)

Edwards, K. J.; Wheat, C. G.

2010-12-01

The “next frontier” of scientific investigation in the deep sub-seafloor microbial biosphere lies in a realm that has been a completely unexplored until just the past decade: the igneous oceanic crust. Problems that have hampered exploration of the “hard rock” marine deep biosphere have revolved around sample access (hard rock drilling is technologically complex), contamination (a major hurdle), momentum (why take on this challenge when the relatively “easier” marine muds also have been a frontier) and suspicion that microbes in more readily accessed using (simpler) non-drilling technologies - like vents - are truly are endemic of subsurface clades/activities. Since the late 1990’s, however, technologies and resultant studies on microbes in the igneous ocean crust deep biosphere have risen sharply, and offer a new and distinct view on this biome. Moreover, microbiologists are now taking leading roles in technological developments that are critically required to address this biosphere - interfacing and collaborating closely with engineers, genomic biologists, geologists, seismologists, and geochemists to accomplish logistically complex and long-term studies that bring observatory research to this deep realm. The future of this field for the least decade is rich - opportunities abound for microbiologists to play new roles in how we study microbiology in the deep subsurface in an oceanographic and Earth system science perspective.

Thermodynamic and Kinetic Response of Microbial Reactions to High CO2.

PubMed

Jin, Qusheng; Kirk, Matthew F

2016-01-01

Geological carbon sequestration captures CO 2 from industrial sources and stores the CO 2 in subsurface reservoirs, a viable strategy for mitigating global climate change. In assessing the environmental impact of the strategy, a key question is how microbial reactions respond to the elevated CO 2 concentration. This study uses biogeochemical modeling to explore the influence of CO 2 on the thermodynamics and kinetics of common microbial reactions in subsurface environments, including syntrophic oxidation, iron reduction, sulfate reduction, and methanogenesis. The results show that increasing CO 2 levels decreases groundwater pH and modulates chemical speciation of weak acids in groundwater, which in turn affect microbial reactions in different ways and to different extents. Specifically, a thermodynamic analysis shows that increasing CO 2 partial pressure lowers the energy available from syntrophic oxidation and acetoclastic methanogenesis, but raises the available energy of microbial iron reduction, hydrogenotrophic sulfate reduction and methanogenesis. Kinetic modeling suggests that high CO 2 has the potential of inhibiting microbial sulfate reduction while promoting iron reduction. These results are consistent with the observations of previous laboratory and field studies, and highlight the complexity in microbiological responses to elevated CO 2 abundance, and the potential power of biogeochemical modeling in evaluating and quantifying these responses.

Thermodynamic and Kinetic Response of Microbial Reactions to High CO2

PubMed Central

Jin, Qusheng; Kirk, Matthew F.

2016-01-01

Geological carbon sequestration captures CO2 from industrial sources and stores the CO2 in subsurface reservoirs, a viable strategy for mitigating global climate change. In assessing the environmental impact of the strategy, a key question is how microbial reactions respond to the elevated CO2 concentration. This study uses biogeochemical modeling to explore the influence of CO2 on the thermodynamics and kinetics of common microbial reactions in subsurface environments, including syntrophic oxidation, iron reduction, sulfate reduction, and methanogenesis. The results show that increasing CO2 levels decreases groundwater pH and modulates chemical speciation of weak acids in groundwater, which in turn affect microbial reactions in different ways and to different extents. Specifically, a thermodynamic analysis shows that increasing CO2 partial pressure lowers the energy available from syntrophic oxidation and acetoclastic methanogenesis, but raises the available energy of microbial iron reduction, hydrogenotrophic sulfate reduction and methanogenesis. Kinetic modeling suggests that high CO2 has the potential of inhibiting microbial sulfate reduction while promoting iron reduction. These results are consistent with the observations of previous laboratory and field studies, and highlight the complexity in microbiological responses to elevated CO2 abundance, and the potential power of biogeochemical modeling in evaluating and quantifying these responses. PMID:27909425

Viral activities and life cycles in deep subseafloor sediments.

PubMed

Engelhardt, Tim; Orsi, William D; Jørgensen, Bo Barker

2015-12-01

Viruses are highly abundant in marine subsurface sediments and can even exceed the number of prokaryotes. However, their activity and quantitative impact on microbial populations are still poorly understood. Here, we use gene expression data from published continental margin subseafloor metatranscriptomes to qualitatively assess viral diversity and activity in sediments up to 159 metres below seafloor (mbsf). Mining of the metatranscriptomic data revealed 4651 representative viral homologues (RVHs), representing 2.2% of all metatranscriptome sequence reads, which have close translated homology (average 77%, range 60-97% amino acid identity) to viral proteins. Archaea-infecting RVHs are exclusively detected in the upper 30 mbsf, whereas RVHs for filamentous inoviruses predominate in the deepest sediment layers. RVHs indicative of lysogenic phage-host interactions and lytic activity, notably cell lysis, are detected at all analysed depths and suggest a dynamic virus-host association in the marine deep biosphere studied here. Ongoing lytic viral activity is further indicated by the expression of clustered, regularly interspaced, short palindromic repeat-associated cascade genes involved in cellular defence against viral attacks. The data indicate the activity of viruses in subsurface sediment of the Peruvian margin and suggest that viruses indeed cause cell mortality and may play an important role in the turnover of subseafloor microbial biomass. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Subsurface microbial diversity in deep-granitic-fracture water in Colorado

USGS Publications Warehouse

Sahl, J.W.; Schmidt, R.; Swanner, E.D.; Mandernack, K.W.; Templeton, A.S.; Kieft, Thomas L.; Smith, R.L.; Sanford, W.E.; Callaghan, R.L.; Mitton, J.B.; Spear, J.R.

2008-01-01

A microbial community analysis using 16S rRNA gene sequencing was performed on borehole water and a granite rock core from Henderson Mine, a >1,000-meter-deep molybdenum mine near Empire, CO. Chemical analysis of borehole water at two separate depths (1,044 m and 1,004 m below the mine entrance) suggests that a sharp chemical gradient exists, likely from the mixing of two distinct subsurface fluids, one metal rich and one relatively dilute; this has created unique niches for microorganisms. The microbial community analyzed from filtered, oxic borehole water indicated an abundance of sequences from iron-oxidizing bacteria (Gallionella spp.) and was compared to the community from the same borehole after 2 weeks of being plugged with an expandable packer. Statistical analyses with UniFrac revealed a significant shift in community structure following the addition of the packer. Phospholipid fatty acid (PLFA) analysis suggested that Nitrosomonadales dominated the oxic borehole, while PLFAs indicative of anaerobic bacteria were most abundant in the samples from the plugged borehole. Microbial sequences were represented primarily by Firmicutes, Proteobacteria, and a lineage of sequences which did not group with any identified bacterial division; phylogenetic analyses confirmed the presence of a novel candidate division. This "Henderson candidate division" dominated the clone libraries from the dilute anoxic fluids. Sequences obtained from the granitic rock core (1,740 m below the surface) were represented by the divisions Proteobacteria (primarily the family Ralstoniaceae) and Firmicutes. Sequences grouping within Ralstoniaceae were also found in the clone libraries from metal-rich fluids yet were absent in more dilute fluids. Lineage-specific comparisons, combined with phylogenetic statistical analyses, show that geochemical variance has an important effect on microbial community structure in deep, subsurface systems. Copyright ?? 2008, American Society for Microbiology. All Rights Reserved.

Exploring Genomic Diversity Using Metagenomics of Deep-Sea Subsurface Microbes from the Louisville Seamount and the South Pacific Gyre

NASA Astrophysics Data System (ADS)

Tully, B. J.; Sylvan, J. B.; Heidelberg, J. F.; Huber, J. A.

2014-12-01

There are many limitations involved with sampling microbial diversity from deep-sea subsurface environments, ranging from physical sample collection, low microbial biomass, culturing at in situ conditions, and inefficient nucleic acid extractions. As such, we are continually modifying our methods to obtain better results and expanding what we know about microbes in these environments. Here we present analysis of metagenomes sequences from samples collected from 120 m within the Louisville Seamount and from the top 5-10cm of the sediment in the center of the south Pacific gyre (SPG). Both systems are low biomass with ~102 and ~104 cells per cm3 for Louisville Seamount samples analyzed and the SPG sediment, respectively. The Louisville Seamount represents the first in situ subseafloor basalt and the SPG sediments represent the first in situ low biomass sediment microbial metagenomes. Both of these environments, subseafloor basalt and sediments underlying oligotrophic ocean gyres, represent large provinces of the seafloor environment that remain understudied. Despite the low biomass and DNA generated from these samples, we have generated 16 near complete genomes (5 from Louisville and 11 from the SPG) from the two metagenomic datasets. These genomes are estimated to be between 51-100% complete and span a range of phylogenetic groups, including the Proteobacteria, Actinobacteria, Firmicutes, Chloroflexi, and unclassified bacterial groups. With these genomes, we have assessed potential functional capabilities of these organisms and performed a comparative analysis between the environmental genomes and previously sequenced relatives to determine possible adaptations that may elucidate survival mechanisms for these low energy environments. These methods illustrate a baseline analysis that can be applied to future metagenomic deep-sea subsurface datasets and will help to further our understanding of microbiology within these environments.

STATE WATER RESOURCES RESEARCH INSTITUTE PROGRAM: GROUND WATER RESEARCH.

USGS Publications Warehouse

Burton, James S.; ,

1985-01-01

This paper updates a review of the accomplishments of the State Water Resources Research Program in ground water contamination research. The aim is to assess the progress made towards understanding the mechanisms of ground water contamination and based on this understanding, to suggest procedures for the prevention and control of ground water contamination. The following research areas are covered: (1) mechanisms of organic contaminant transport in the subsurface environment; (2) bacterial and viral contamination of ground water from landfills and septic tank systems; (3) fate and persistence of pesticides in the subsurface; (4) leachability and transport of ground water pollutants from coal production and utilization; and (5) pollution of ground water from mineral mining activities.

Modeling the GPR response of leaking, buried pipes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Powers, M.H.; Olhoeft, G.R.

1996-11-01

Using a 2.5D, dispersive, full waveform GPR modeling program that generates complete GPR response profiles in minutes on a Pentium PC, the effects of leaking versus non-leaking buried pipes are examined. The program accounts for the dispersive, lossy nature of subsurface materials to GPR wave propagation, and accepts complex functions of dielectric permittivity and magnetic permeability versus frequency through Cole-Cole parameters fit to laboratory data. Steel and plastic pipes containing a DNAPL chlorinated solvent, an LNAPL hydrocarbon, and natural gas are modeled in a surrounding medium of wet, moist, and dry sand. Leaking fluids are found to be more detectablemore » when the sand around the pipes is fully water saturated. The short runtimes of the modeling program and its execution on a PC make it a useful tool for exploring various subsurface models.« less

Geochemical features of the ore-bearing medium in uranium deposits in the Khiagda ore field

NASA Astrophysics Data System (ADS)

Kochkin, B. T.; Solodov, I. N.; Ganina, N. I.; Rekun, M. L.; Tarasov, N. N.; Shugina, G. A.; Shulik, L. S.

2017-09-01

The Neogene uranium deposits of the Khiagda ore field (KOF) belong to the paleovalley variety of the hydrogene type and differ from other deposits of this genetic type in the geological and geochemical localization conditions. The contemporary hydrogeochemical setting and microbiological composition of ore-bearing medium are discussed. The redox potential of the medium (Eh is as low as-400 mV) is much lower than those established at other hydrogenic deposits, both ancient Late Mesozoic and young Late Alpine, studied with the same methods in Russia, Uzbekistan, and southern Kazakhstan. The pH of subsurface water (6.86-8.13) differs in significant fluctuations both between neighboring deposits and within individual ore lodes. Hydrogen-forming and denitrifying bacteria are predominant in microbiological populations, whereas sulfate-reducing bacteria are low-active. The consideration of these factors allowed us to describe the mechanism of uranium ore conservation as resulting from the development of the cryolithic zone, which isolates ore lodes from the effect of the external medium. Carbonated water supplied from the basement along fault zones also participates in the formation of the present-day hydrogeochemical setting. Based on the features of the ore-bearing medium, we propose a method of borehole in situ acid leaching to increase the efficiency of mining in the Khiagda ore field.

Legacy of contaminant N sources to the NO3− signature in rivers: a combined isotopic (δ15N-NO3−, δ18O-NO3−, δ11B) and microbiological investigation

PubMed Central

Briand, Cyrielle; Sebilo, Mathieu; Louvat, Pascale; Chesnot, Thierry; Vaury, Véronique; Schneider, Maude; Plagnes, Valérie

2017-01-01

Nitrate content of surface waters results from complex mixing of multiple sources, whose signatures can be modified through N reactions occurring within the different compartments of the whole catchment. Despite this complexity, the determination of nitrate origin is the first and crucial step for water resource preservation. Here, for the first time, we combined at the catchment scale stable isotopic tracers (δ15N and δ18O of nitrate and δ11B) and fecal indicators to trace nitrate sources and pathways to the stream. We tested this approach on two rivers in an agricultural region of SW France. Boron isotopic ratios evidenced inflow from anthropogenic waters, microbiological markers revealed organic contaminations from both human and animal wastes. Nitrate δ15N and δ18O traced inputs from the surface leaching during high flow events and from the subsurface drainage in base flow regime. They also showed that denitrification occurred within the soils before reaching the rivers. Furthermore, this study highlighted the determinant role of the soil compartment in nitrate formation and recycling with important spatial heterogeneity and temporal variability. PMID:28150819

Where the Wild Microbes Are: Education and Outreach on Sub-Seafloor Microbes

NASA Astrophysics Data System (ADS)

Cooper, S. K.; Kurtz, K.; Orcutt, B.; Strong, L.; Collins, J.; Feagan, A.

2014-12-01

Sub-seafloor microbiology has the power to spark the imaginations of children, students and the general public with its mysterious nature, cutting-edge research, and connections to the search for extraterrestrial life. These factors have been utilized to create a number of educational and outreach products to bring subsurface microbes to non-scientist audiences in creative and innovative ways. The Adopt a Microbe curriculum for middle school students provides hands-on activities and investigations for students to learn about microbes and the on-going research about them, and provides opportunities to connect with active expeditions. A new series of videos engages non-scientists with stories about research expeditions and the scientists themselves. A poster and associated activities explore the nature of science using a microbiologist and her research as examples. A new e-book for young children will engage them with age-appropriate text and illustrations. These projects are multidisciplinary, involve science and engineering practices, are available to all audiences and provide examples of high level and meaningful partnerships between scientists and educators and the kinds of products that can result. Subseafloor microbiology projects such as these, aimed at K-12 students and the general public, have the potential to entice the interest of the next generation of microbe scientists and increase general awareness of this important science.

The life sulfuric: microbial ecology of sulfur cycling in marine sediments.

PubMed

Wasmund, Kenneth; Mußmann, Marc; Loy, Alexander

2017-08-01

Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes. Sulfur-transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate-rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep-subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

The microbial community structure in petroleum-contaminated sediments corresponds to geophysical signatures

USGS Publications Warehouse

Allen, J.P.; Atekwana, E.A.; Duris, J.W.; Werkema, D.D.; Rossbach, S.

2007-01-01

The interdependence between geoelectrical signatures at underground petroleum plumes and the structures of subsurface microbial communities was investigated. For sediments contaminated with light non-aqueousphase liquids, anomalous high conductivity values have been observed. Vertical changes in the geoelectrical properties of the sediments were concomitant with significant changes in the microbial community structures as determined by the construction and evaluation of 16S rRNA gene libraries. DNA sequencing of clones from four 16S rRNA gene libraries from different depths of a contaminated field site and two libraries from an uncontaminated background site revealed spatial heterogeneity in the microbial community structures. Correspondence analysis showed that the presence of distinct microbial populations, including the various hydrocarbon-degrading, syntrophic, sulfate-reducing, and dissimilatory-iron-reducing populations, was a contributing factor to the elevated geoelectrical measurements. Thus, through their growth and metabolic activities, microbial populations that have adapted to the use of petroleum as a carbon source can strongly influence their geophysical surroundings. Since changes in the geophysical properties of contaminated sediments parallel changes in the microbial community compositions, it is suggested that geoelectrical measurements can be a cost-efficient tool to guide microbiological sampling for microbial ecology studies during the monitoring of natural or engineered bioremediation processes. Copyright ?? 2007, American Society for Microbiology. All Rights Reserved.

Who's Who in Biology.

ERIC Educational Resources Information Center

Norman, Colin

1983-01-01

Provides top-rated programs (by university) in biochemistry, botany, cellular/molecular biology, microbiology, physiology, and zoology. Overall scores included with each program were obtained from 1,848 biologists who were asked to rate programs in terms of faculty quality and their effectiveness in educating graduate students. (Author/JN)

[Establishment of a microbiology laboratory open 365 days a year and its impact].

PubMed

Komori, Toshiaki; Fujita, Naohisa; Hirose, Yuri; Kimura, Takeshi; Kyotani, Noriko; Kurahashi, Satoko; Yamada, Yukiji; Ushiyama, Masaji; Yasumoto, Towa; Yuasa, Soh-Ichi

2009-12-01

The microbiology laboratory of our university hospital aims to provide accurate and rapid microbiological results and useful information for healthcare workers involved in both the treatment of infectious diseases and infection control. For this purpose, we have been running a microbiology laboratory open 365 days a year since 2005. Before starting this laboratory, we formulated both a precise procedural manual and educational program to increase the number of microbiological technologists from 4 to 8 persons and improve their skills. Moreover, we reviewed the reporting system. As a result, we could report positive blood cultures up to 1.4 days earlier than previously possible, and significantly improved the prognosis of MRSA bacteremia patients by the early treatment of anti-MRSA antimicrobials within 48 hours after positive blood culture. In addition, the rate of MRSA/Staphylococcus aureus decreased to 35.8%. It is essential for the treatment of infectious diseases and infection control to accept only appropriate specimens and report the results rapidly and accurately.

Manual Laboratorio de Microbiologia. Documento de trabajo Programa de Educacion en Ocupaciones de Salud (Microbiology Laboratory Manual. Curriculum Document. Program of Education in Health Occupations).

ERIC Educational Resources Information Center

Puerto Rico State Dept. of Education, Hato Rey. Area for Vocational and Technical Education.

This laboratory manual on microbiology begins with an introduction relating the study of microorganisms to health occupations education and stressing the importance of teaching critical thinking. The introduction is followed by general instructions for the use of the manual and an illustration of hand washing procedures. The 13 laboratory…

A Cultured Learning Environment: Implementing a Problem- and Service-Based Microbiology Capstone Course to Assess Process- and Skill-Based Learning Objectives

ERIC Educational Resources Information Center

Watson, Rachel M.; Willford, John D.; Pfeifer, Mariel A.

2018-01-01

In this study, a problem-based capstone course was designed to assess the University of Wyoming Microbiology Program's skill-based and process-based student learning objectives. Students partnered with a local farm, a community garden, and a free downtown clinic in order to conceptualize, propose, perform, and present studies addressing problems…

The Microbiology of Subsurface, Salt-Based Nuclear Waste Repositories: Using Microbial Ecology, Bioenergetics, and Projected Conditions to Help Predict Microbial Effects on Repository Performance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swanson, Juliet S.; Cherkouk, Andrea; Arnold, Thuro

This report summarizes the potential role of microorganisms in salt-based nuclear waste repositories using available information on the microbial ecology of hypersaline environments, the bioenergetics of survival under high ionic strength conditions, and “repository microbiology” related studies. In areas where microbial activity is in question, there may be a need to shift the research focus toward feasibility studies rather than studies that generate actual input for performance assessments. In areas where activity is not necessary to affect performance (e.g., biocolloid transport), repository-relevant data should be generated. Both approaches will lend a realistic perspective to a safety case/performance scenario that willmore » most likely underscore the conservative value of that case.« less

Can Sanitary Inspection Surveys Predict Risk of Microbiological Contamination of Groundwater Sources? Evidence from Shallow Tubewells in Rural Bangladesh

PubMed Central

Ercumen, Ayse; Naser, Abu Mohd; Arnold, Benjamin F.; Unicomb, Leanne; Colford, John M.; Luby, Stephen P.

2017-01-01

Accurately assessing the microbiological safety of water sources is essential to reduce waterborne fecal exposures and track progress toward global targets of safe water access. Sanitary inspections are a recommended tool to assess water safety. We collected 1,684 water samples from 902 shallow tubewells in rural Bangladesh and conducted sanitary surveys to assess whether sanitary risk scores could predict water quality, as measured by Escherichia coli. We detected E. coli in 41% of tubewells, mostly at low concentrations. Based on sanitary scores, 31% of wells were low risk, 45% medium risk, and 25% high or very high risk. Older wells had higher risk scores. Escherichia coli levels were higher in wells where the platform was cracked or broken (Δlog10 = 0.09, 0.00–0.18) or undercut by erosion (Δlog10 = 0.13, 0.01–0.24). However, the positive predictive value of these risk factors for E. coli presence was low (< 50%). Latrine presence within 10 m was not associated with water quality during the wet season but was associated with less frequent E. coli detection during the dry season (relative risk = 0.72, 0.59–0.88). Sanitary scores were not associated with E. coli presence or concentration. These findings indicate that observed characteristics of a tubewell, as measured by sanitary inspections in their current form, do not sufficiently characterize microbiological water quality, as measured by E. coli. Assessments of local groundwater and geological conditions and improved water quality indicators may reveal more clear relationships. Our findings also suggest that the dominant contamination route for shallow groundwater sources is short-circuiting at the wellhead rather than subsurface transport. PMID:28115666

Can Sanitary Inspection Surveys Predict Risk of Microbiological Contamination of Groundwater Sources? Evidence from Shallow Tubewells in Rural Bangladesh.

PubMed

Ercumen, Ayse; Naser, Abu Mohd; Arnold, Benjamin F; Unicomb, Leanne; Colford, John M; Luby, Stephen P

2017-03-01

AbstractAccurately assessing the microbiological safety of water sources is essential to reduce waterborne fecal exposures and track progress toward global targets of safe water access. Sanitary inspections are a recommended tool to assess water safety. We collected 1,684 water samples from 902 shallow tubewells in rural Bangladesh and conducted sanitary surveys to assess whether sanitary risk scores could predict water quality, as measured by Escherichia coli . We detected E. coli in 41% of tubewells, mostly at low concentrations. Based on sanitary scores, 31% of wells were low risk, 45% medium risk, and 25% high or very high risk. Older wells had higher risk scores. Escherichia coli levels were higher in wells where the platform was cracked or broken (Δlog 10 = 0.09, 0.00-0.18) or undercut by erosion (Δlog 10 = 0.13, 0.01-0.24). However, the positive predictive value of these risk factors for E. coli presence was low (< 50%). Latrine presence within 10 m was not associated with water quality during the wet season but was associated with less frequent E. coli detection during the dry season (relative risk = 0.72, 0.59-0.88). Sanitary scores were not associated with E. coli presence or concentration. These findings indicate that observed characteristics of a tubewell, as measured by sanitary inspections in their current form, do not sufficiently characterize microbiological water quality, as measured by E. coli . Assessments of local groundwater and geological conditions and improved water quality indicators may reveal more clear relationships. Our findings also suggest that the dominant contamination route for shallow groundwater sources is short-circuiting at the wellhead rather than subsurface transport.

ANALYTICAL METHODS DEVELOPMENT FOR DIETARY SAMPLES

EPA Science Inventory

The Microbiological and Chemical Exposure Assessment Research Division's (MCEARD) dietary exposure research program is conducted to complement the NERL aggregate and cumulative exposure program. Its purpose is to reduce the level of uncertainty in exposure assessment by improvin...

Pacific Northwest Laboratory annual report for 1992 to the DOE Office of Energy Research

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grove, L.K.

1993-03-01

The 1992 Annual Report from Pacific Northwest Laboratory (PNL) to the US Department of Energy (DOE) describes research in environment and health conducted during fiscal year 1992. This report consists of four volumes oriented to particular segments of the PNL program, describing research performed for the DOE Office of Health and Environmental Research in the Office of Energy Research. The parts of the 1992 Annual Report are: Biomedical Sciences; Environmental Sciences; Atmospheric Sciences; and Physical Sciences. This Report is Part II: Environmental Sciences. Included in this report are developments in Subsurface Science, Terrestrial Science, Laboratory-Directed Research and Development, Interactions withmore » Educational Institutions, Technology Transfer, Publications, and Presentations. The research is directed toward developing a fundamental understanding of subsurface and terrestrial systems as a basis for both managing these critical resources and addressing environmental problems such as environmental restoration and global change. The Technology Transfer section of this report describes a number of examples in which fundamental research is laying the groundwork for the technology needed to resolve important environmental problems. The Interactions with Educational Institutions section of the report illustrates the results of a long-term, proactive program to make PNL facilities available for university and preuniversity education and to involve educational institutions in research programs. The areas under investigation include the effect of geochemical and physical phenomena on the diversity and function of microorganisms in deep subsurface environments, ways to address subsurface heterogeneity, and ways to determine the key biochemical and physiological pathways (and DNA markers) that control nutrient, water, and energy dynamics in arid ecosystems and the response of these systems to disturbance and climatic change.« less

Pacific Northwest Laboratory annual report for 1992 to the DOE Office of Energy Research. Part 2, Environmental sciences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grove, L.K.; Wildung, R.E.

1993-03-01

The 1992 Annual Report from Pacific Northwest Laboratory (PNL) to the US Department of Energy (DOE) describes research in environment and health conducted during fiscal year 1992. This report consists of four volumes oriented to particular segments of the PNL program, describing research performed for the DOE Office of Health and Environmental Research in the Office of Energy Research. The parts of the 1992 Annual Report are: Biomedical Sciences; Environmental Sciences; Atmospheric Sciences; and Physical Sciences. This Report is Part 2: Environmental Sciences. Included in this report are developments in Subsurface Science, Terrestrial Science, Laboratory-Directed Research and Development, Interactions withmore » Educational Institutions, Technology Transfer, Publications, and Presentations. The research is directed toward developing a fundamental understanding of subsurface and terrestrial systems as a basis for both managing these critical resources and addressing environmental problems such as environmental restoration and global change. The Technology Transfer section of this report describes a number of examples in which fundamental research is laying the groundwork for the technology needed to resolve important environmental problems. The Interactions with Educational Institutions section of the report illustrates the results of a long-term, proactive program to make PNL facilities available for university and preuniversity education and to involve educational institutions in research programs. The areas under investigation include the effect of geochemical and physical phenomena on the diversity and function of microorganisms in deep subsurface environments, ways to address subsurface heterogeneity, and ways to determine the key biochemical and physiological pathways (and DNA markers) that control nutrient, water, and energy dynamics in arid ecosystems and the response of these systems to disturbance and climatic change.« less

National collaborative shellfish pollution-indicator study: Site selection. Phase 2. Rept. for 1988-89

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leonard, D.L.; Slaughter, E.A.; Corning, B.C.

1990-07-01

Each year, about 16 million areas of estuarine waters are classified for the harvest of molluscan shellfish as open or limited to harvest according to microbiological 'indicator' standards and pollution survey guidelines established by the National Shellfish Sanitation Program. The program was developed in the 1920s in response to typhoid fever outbreaks associated with shellfish consumption. Current microbiological indicator standards in shellfish and shellfish-growing waters are extrpolated from standards set in the 1920s. Results from studies in the last decade have indicated that these microbiological indicator standards and thus classification of shellfish-growing waters may no longer be valid. The Nationalmore » Collaborative Shellfish Pollution Indicator Study is proposed as a four-year study to evaluate the current relationships between indicators of human enteric pathogens and the incidence of shellfish-borne diseases. Tasks forces were established to address specific issues, including site selection, shoreline surveys, and laboratory methodologies.« less

ANME-2D Archaea Catalyze Methane Oxidation in Deep Subsurface Sediments Independent of Nitrate Reduction

NASA Astrophysics Data System (ADS)

Hernsdorf, A. W.; Amano, Y.; Suzuki, Y.; Ise, K.; Thomas, B. C.; Banfield, J. F.

2015-12-01

Terrestrial sediments are an important global reservoir for methane. Microorganisms in the deep subsurface play a critical role in the methane cycle, yet much remains to be learned about their diversity and metabolisms. To provide more comprehensive insight into the microbiology of the methane cycle in the deep subsurface, we conducted a genome-resolved study of samples collected from the Horonobe Underground Research Laboratory (HURL), Japan. Groundwater samples were obtained from three boreholes from a depth range of between 140 m and 250 m in two consecutive years. Groundwater was filtered and metagenomic DNA extracted and sequenced, and the sequence data assembled. Based on the sequences of phylogenetically informative genes on the assembled fragments, we detected a high degree of overlap in community composition across a vertical transect within one borehole at the two sampling times. However, there was comparatively little similarity observed among communities across boreholes. Spatial and temporal abundance patterns were used in combination with tetranucleotide signatures of assembled genome fragments to bin the data and reconstruct over 200 unique draft genomes, of which 137 are considered to be of high quality (>90% complete). The deepest samples from one borehole were highly dominated by an archaeon identified as ANME-2D; this organism was also present at lower abundance in all other samples from that borehole. Also abundant in these microbial communities were novel members of the Gammaproteobacteria, Saccharibacteria (TM7) and Tenericute phyla. Notably, a ~2 Mbp draft genome for the ANME-2D archaeon was reconstructed. As expected, the genome encodes all of the genes predicted to be involved in the reverse methanogenesis pathway. In contrast with the previously reported ANME2-D genome, the HURL ANME-2D genome lacks the capacity to reduce nitrate. However, we identified many multiheme cytochromes with closest similarity to those of the known Fe-reducing/oxidizing archaeon Ferroglobus placidus. Thus, we suggest that ANME2-D may couple methane oxidation to reduction of ferric iron minerals in the sediment and may be generally important as a link between the iron and methane cycles in deep subsurface environments. Such information has important implications for modeling the global carbon cycle.

Cultivating the Deep Subsurface Microbiome

NASA Astrophysics Data System (ADS)

Casar, C. P.; Osburn, M. R.; Flynn, T. M.; Masterson, A.; Kruger, B.

2017-12-01

Subterranean ecosystems are poorly understood because many microbes detected in metagenomic surveys are only distantly related to characterized isolates. Cultivating microorganisms from the deep subsurface is challenging due to its inaccessibility and potential for contamination. The Deep Mine Microbial Observatory (DeMMO) in Lead, SD however, offers access to deep microbial life via pristine fracture fluids in bedrock to a depth of 1478 m. The metabolic landscape of DeMMO was previously characterized via thermodynamic modeling coupled with genomic data, illustrating the potential for microbial inhabitants of DeMMO to utilize mineral substrates as energy sources. Here, we employ field and lab based cultivation approaches with pure minerals to link phylogeny to metabolism at DeMMO. Fracture fluids were directed through reactors filled with Fe3O4, Fe2O3, FeS2, MnO2, and FeCO3 at two sites (610 m and 1478 m) for 2 months prior to harvesting for subsequent analyses. We examined mineralogical, geochemical, and microbiological composition of the reactors via DNA sequencing, microscopy, lipid biomarker characterization, and bulk C and N isotope ratios to determine the influence of mineralogy on biofilm community development. Pre-characterized mineral chips were imaged via SEM to assay microbial growth; preliminary results suggest MnO2, Fe3O4, and Fe2O3 were most conducive to colonization. Solid materials from reactors were used as inoculum for batch cultivation experiments. Media designed to mimic fracture fluid chemistry was supplemented with mineral substrates targeting metal reducers. DNA sequences and microscopy of iron oxide-rich biofilms and fracture fluids suggest iron oxidation is a major energy source at redox transition zones where anaerobic fluids meet more oxidizing conditions. We utilized these biofilms and fluids as inoculum in gradient cultivation experiments targeting microaerophilic iron oxidizers. Cultivation of microbes endemic to DeMMO, a system locally dominated by unclassified and candidate phyla, has the potential to yield novel subsurface organisms with unique physiologies. We intend to further utilize subsurface isolates to probe the effects of geochemical perturbations on biosignatures in future studies, thus broadening our understanding of subterranean ecosystems.

New Developments in Mitigation of Microbiologically Influenced Corrosion

DTIC Science & Technology

2007-07-12

either bacterium. Higher R1, values for surfaces colonized by S . marcescens compared to those colonized by Pseudomonas sp. were attributed to higher...numbers of S . marcescens cells attached to the metal surface. Impedance spectra (see Figure 1) after immersion in sterile and inoculated VNSS demonstrated...NUMBER New Developments in Mitigation of Microbiologically Influenced Corrosion. 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 0601153N 6. AUTHOR( S ) 5d

The Natural Classroom: A Directory of Field Courses, Programs, and Expeditions in the Natural Sciences.

ERIC Educational Resources Information Center

Edelman, Jack R.

The purpose of this book is to increase awareness of the numerous seminars, short courses, field courses, workshops, and programs for teachers, students, naturalists, and independent scholars. These programs emphasize the natural sciences including general biology, botany, zoology, ecology, marine biology, ichthyology, microbiology, natural…

Microbial community stratification controlled by the subseafloor fluid flow and geothermal gradient at the Iheya North hydrothermal field in the Mid-Okinawa Trough (Integrated Ocean Drilling Program Expedition 331).

PubMed

Yanagawa, Katsunori; Breuker, Anja; Schippers, Axel; Nishizawa, Manabu; Ijiri, Akira; Hirai, Miho; Takaki, Yoshihiro; Sunamura, Michinari; Urabe, Tetsuro; Nunoura, Takuro; Takai, Ken

2014-10-01

The impacts of lithologic structure and geothermal gradient on subseafloor microbial communities were investigated at a marginal site of the Iheya North hydrothermal field in the Mid-Okinawa Trough. Subsurface marine sediments composed of hemipelagic muds and volcaniclastic deposits were recovered through a depth of 151 m below the seafloor at site C0017 during Integrated Ocean Drilling Program Expedition 331. Microbial communities inferred from 16S rRNA gene clone sequencing in low-temperature hemipelagic sediments were mainly composed of members of the Chloroflexi and deep-sea archaeal group. In contrast, 16S rRNA gene sequences of marine group I Thaumarchaeota dominated the microbial phylotype communities in the coarse-grained pumiceous gravels interbedded between the hemipelagic sediments. Based on the physical properties of sediments such as temperature and permeability, the porewater chemistry, and the microbial phylotype compositions, the shift in the physical properties of the sediments is suggested to induce a potential subseafloor recharging flow of oxygenated seawater in the permeable zone, leading to the generation of variable chemical environments and microbial communities in the subseafloor habitats. In addition, the deepest section of sediments under high-temperature conditions (∼90°C) harbored the sequences of an uncultivated archaeal lineage of hot water crenarchaeotic group IV that may be associated with the high-temperature hydrothermal fluid flow. These results indicate that the subseafloor microbial community compositions and functions at the marginal site of the hydrothermal field are highly affected by the complex fluid flow structure, such as recharging seawater and underlying hydrothermal fluids, coupled with the lithologic transition of sediments. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Environmental Assessment for Selection and Operation of the Proposed Field Research Centers for the Natural and Accelerated Bioremediation Research (NABIR) Program

DOE Office of Scientific and Technical Information (OSTI.GOV)

N /A

2000-04-18

The US Department of Energy (DOE) Office of Biological and Environmental Research (OBER), within the Office of Science (SC), proposes to add a Field Research Center (FRC) component to the existing Natural and Accelerated Bioremediation Research (NABIR) Program. The NABIR Program is a ten-year fundamental research program designed to increase the understanding of fundamental biogeochemical processes that would allow the use of bioremediation approaches for cleaning up DOE's contaminated legacy waste sites. An FRC would be integrated with the existing and future laboratory and field research and would provide a means of examining the fundamental biogeochemical processes that influence bioremediationmore » under controlled small-scale field conditions. The NABIR Program would continue to perform fundamental research that might lead to promising bioremediation technologies that could be demonstrated by other means in the future. For over 50 years, DOE and its predecessor agencies have been responsible for the research, design, and production of nuclear weapons, as well as other energy-related research and development efforts. DOE's weapons production and research activities generated hazardous, mixed, and radioactive waste products. Past disposal practices have led to the contamination of soils, sediments, and groundwater with complex and exotic mixtures of compounds. This contamination and its associated costs and risks represents a major concern to DOE and the public. The high costs, long duration, and technical challenges associated with remediating the subsurface contamination at DOE sites present a significant need for fundamental research in the biological, chemical, and physical sciences that will contribute to new and cost-effective solutions. One possible low-cost approach for remediating the subsurface contamination of DOE sites is through the use of a technology known as bioremediation. Bioremediation has been defined as the use of microorganisms to biodegrade or biotransform hazardous organic contaminants to environmentally safe levels in soils, subsurface materials, water, sludges, and residues.. While bioremediation technology is promising, DOE managers and non-DOE scientists have recognized that the fundamental scientific information needed to develop effective bioremediation technologies for cleanup of the legacy waste sites is lacking in many cases. DOE believes that field-based research is needed to realize the full potential of bioremediation. The Department of Energy faces a unique set of challenges associated with cleaning up waste at its former weapons production and research sites. These sites contain complex mixtures of contaminants in the subsurface, including radioactive compounds. In many cases, the fundamental field-based scientific information needed to develop safe and effective remediation and cleanup technologies is lacking. DOE needs fundamental research on the use of microorganisms and their products to assist DOE in the decontamination and cleanup of its legacy waste sites. The existing NABIR program to-date has focused on fundamental scientific research in the laboratory. Because subsurface hydrologic and geologic conditions at contaminated DOE sites cannot easily be duplicated in a laboratory, however, the DOE needs a field component to permit existing and future laboratory research results to be field-tested on a small scale in a controlled outdoor setting. Such field-testing needs to be conducted under actual legacy waste field conditions representative of those that DOE is most in need of remediating. Ideally, these field conditions should be as representative as practicable of the types of subsurface contamination conditions that resulted from legacy wastes from the nuclear weapons program activities. They should also be representative of the types of hydrologic and geologic conditions that exist across the DOE complex.« less

Relevance of deep-subsurface microbiology for underground gas storage and geothermal energy production.

PubMed

Gniese, Claudia; Bombach, Petra; Rakoczy, Jana; Hoth, Nils; Schlömann, Michael; Richnow, Hans-Hermann; Krüger, Martin

2014-01-01

This chapter gives the reader an introduction into the microbiology of deep geological systems with a special focus on potential geobiotechnological applications and respective risk assessments. It has been known for decades that microbial activity is responsible for the degradation or conversion of hydrocarbons in oil, gas, and coal reservoirs. These processes occur in the absence of oxygen, a typical characteristic of such deep ecosystems. The understanding of the responsible microbial processes and their environmental regulation is not only of great scientific interest. It also has substantial economic and social relevance, inasmuch as these processes directly or indirectly affect the quantity and quality of the stored oil or gas. As outlined in the following chapter, in addition to the conventional hydrocarbons, new interest in such deep subsurface systems is rising for different technological developments. These are introduced together with related geomicrobiological topics. The capture and long-termed storage of large amounts of carbon dioxide, carbon capture and storage (CCS), for example, in depleted oil and gas reservoirs, is considered to be an important options to mitigate greenhouse gas emissions and global warming. On the other hand, the increasing contribution of energy from natural and renewable sources, such as wind, solar, geothermal energy, or biogas production leads to an increasing interest in underground storage of renewable energies. Energy carriers, that is, biogas, methane, or hydrogen, are often produced in a nonconstant manner and renewable energy may be produced at some distance from the place where it is needed. Therefore, storing the energy after its conversion to methane or hydrogen in porous reservoirs or salt caverns is extensively discussed. All these developments create new research fields and challenges for microbiologists and geobiotechnologists. As a basis for respective future work, we introduce the three major topics, that is, CCS, underground storage of gases from renewable energy production, and the production of geothermal energy, and summarize the current stat of knowledge about related geomicrobiological and geobiotechnological aspects in this chapter. Finally, recommendations are made for future research.

American Society for Microbiology resources in support of an evidence-based approach to teaching microbiology.

PubMed

Merkel, Susan M

2016-08-01

Numerous national reports have addressed the need for changing how science courses in higher education are taught, so that students develop a deeper understanding of critical concepts and the analytical and cognitive skills needed to address future challenges. This review presents some evidence-based approaches to curriculum development and teaching. Results from discipline-based education research indicate that it is critically important for educators to formulate learning goals, provide frequent and authentic assessments and actively engage students in their learning. Professional societies can play a role in helping to put these changes into practice. To this end, the American Society for Microbiology has developed a number of educational programs and resources, which are described here to encourage the implementation of student-centered learning in microbiology education. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Preflight and postflight microbiological results from 25 space shuttle crews

NASA Technical Reports Server (NTRS)

Pierson, Duane L.; Bassinger, Virginia J.; Molina, Thomas C.; Gunter, Emelie G.; Groves, Theron O.; Cioletti, Louis J.; Mishra, S. K.

1993-01-01

Clinical-microbiological investigations are an important aspect of the crew health stabilization program. To ensure that space crews have neither active nor latent infections, clinical specimens, including throat and nasal swabs and urine samples, are collected at 10 days (L-10) and 2days (L-2) before launch, and immediately after landing (L+0). All samples are examined for the presence of bacteria and fungi. In addition, fecal samples are collected at L-10 and examined for bacteria, fungi and parasites. This paper describes clinical-microbiological findings from 144 astronauts participating in 25 Space Shuttle missions spanning Space Transportation System (STS)-26 to STS-50. The spectrum of microbiological findings from the specimens included 25 bacterial and 11 fungal species. Among the bacteria isolated most frequently were Staphylococcus aureus, Enterobacter aerogenes, Enterococcus faecalis, Escherichia coli, Proteus mirabilis and Streptococcus agalactiae. Candida albicans was the most frequently isolated fungal pathogen.

Enhancing active learning in microbiology through case based learning: experiences from an Indian medical school.

PubMed

Ciraj, A M; Vinod, P; Ramnarayan, K

2010-01-01

Case-based learning (CBL) is an interactive student-centered exploration of real life situations. This paper describes the use of CBL as an educational strategy for promoting active learning in microbiology. CBL was introduced in the microbiology curriculum for the second year medical students after an orientation program for faculty and students. After intervention, the average student scores in CBL topics were compared with scores obtained in lecture topics. An attempt was also made to find the effect of CBL on the academic performance. Student and faculty perception on CBL were also recorded. In a cross sectional survey conducted to assess the effectiveness of CBL, students responded that, apart from helping them acquire substantive knowledge in microbiology, CBL sessions enhanced their analytic, collaborative, and communication skills. The block examination scores in CBL topics were significantly higher than those obtained for lecture topics. Faculty rated the process to be highly effective in stimulating student interest and long term retention of microbiology knowledge. The student scores were significantly higher in the group that used CBL, compared to the group that had not used CBL as a learning strategy. Our experience indicated that CBL sessions enhanced active learning in microbiology. More frequent use of CBL sessions would not only help the student gain requisite knowledge in microbiology but also enhance their analytic and communication skills.

Microbial life in cold, hydrologically active oceanic crustal fluids

NASA Astrophysics Data System (ADS)

Meyer, J. L.; Jaekel, U.; Girguis, P. R.; Glazer, B. T.; Huber, J. A.

2012-12-01

It is estimated that at least half of Earth's microbial biomass is found in the deep subsurface, yet very little is known about the diversity and functional roles of these microbial communities due to the limited accessibility of subseafloor samples. Ocean crustal fluids, which may have a profound impact on global nutrient cycles given the large volumes of water moving through the crustal aquifer, are particularly difficult to sample. Access to uncontaminated ocean crustal fluids is possible with CORK (Circulation Obviation Retrofit Kit) observatories, installed through the Integrated Ocean Drilling Program (IODP). Here we present the first microbiological characterization of the formation fluids from cold, oxygenated igneous crust at North Pond on the western flank of the Mid Atlantic Ridge. Fluids were collected from two CORKs installed at IODP boreholes 1382A and 1383C and include fluids from three different depth horizons within oceanic crust. Collection of borehole fluids was monitored in situ using an oxygen optode and solid-state voltammetric electrodes. In addition, discrete samples were analyzed on deck using a comparable lab-based system as well as a membrane-inlet mass spectrometer to quantify all dissolved volatiles up to 200 daltons. The instruments were operated in parallel and both in situ and shipboard geochemical measurements point to a highly oxidized fluid, revealing an apparent slight depletion of oxygen in subsurface fluids (~215μM) relative to bottom seawater (~245μM). We were unable to detect reduced hydrocarbons, e.g. methane. Cell counts indicated the presence of roughly 2 x 10^4 cells per ml in all fluid samples, and DNA was extracted and amplified for the identification of both bacterial and archaeal community members. The utilization of ammonia, nitrate, dissolved inorganic carbon, and acetate was measured using stable isotopes, and oxygen consumption was monitored to provide an estimate of the rate of respiration per cell per day. These results provide the first dataset describing the diversity of microbes present in cold, oxygenated ocean crustal fluids and the biogeochemical processes they mediate in the subseafloor.

Teaming Up with Scientists.

ERIC Educational Resources Information Center

Moreno, Nancy P.; Chang, Kimberly A.; Tharp, Barbara Z.; Denk, James P.; Roberts, J. Kyle; Cutler, Paula H.; Rahmati, Sonia

2001-01-01

Introduces the Science Education Leadership Fellows (SELF) program which is an innovative cooperation program between teachers and scientists. Engages teachers in subject areas such as microbiology, molecular biology, immunology, and other professional development activities. Presents an activity in which students observe bacteria cultures and…

Microbiological sampling of spacecraft cabling, antennas, solar panels and thermal blankets

NASA Technical Reports Server (NTRS)

Koukol, R. C.

1973-01-01

Sampling procedures and techniques described resulted from various flight project microbiological monitoring programs of unmanned planetary spacecraft. Concurrent with development of these procedures, compatibility evaluations were effected with the cognizant spacecraft subsystem engineers to assure that degradation factors would not be induced during the monitoring program. Of significance were those areas of the spacecraft configuration for which special handling precautions and/or nonstandard sample gathering techniques were evolved. These spacecraft component areas were: cabling, high gain antenna, solar panels, and thermal blankets. The compilation of these techniques provides a historical reference for both the qualification and quantification of sampling parameters as applied to the Mariner Spacecraft of the late 1960's and early 1970's.

Characterizing the subsurface geology in and around the U.S. Army Camp Stanley Storage Activity, south-central Texas

USGS Publications Warehouse

Blome, Charles D.; Clark, Allan K.

2018-02-15

Several U.S. Geological Survey projects, supported by the National Cooperative Geologic Mapping Program, have used multi-disciplinary approaches over a 14-year period to reveal the surface and subsurface geologic frameworks of the Edwards and Trinity aquifers of central Texas and the Arbuckle-Simpson aquifer of south-central Oklahoma. Some of the project achievements include advancements in hydrostratigraphic mapping, three-dimensional subsurface framework modeling, and airborne geophysical surveys as well as new methodologies that link geologic and groundwater flow models. One area where some of these milestones were achieved was in and around the U.S. Army Camp Stanley Storage Activity, located in north­western Bexar County, Texas, about 19 miles north­west of downtown San Antonio.

Field Simulation of a Drilling Mission to Mars to Search for Subsurface Life

NASA Technical Reports Server (NTRS)

Stoker, C. R.; Lemke, L. G.; Cannon, H.; Glass, B.; Dunagan, S.; Zavaleta, J.; Miller, D.; Gomez-Elvira, J.

2005-01-01

The discovery of near surface ground ice by the Mars Odyssey mission and the abundant evidence for recent Gulley features observed by the Mars Global Surveyor mission support longstanding theoretical arguments for subsurface liquid water on Mars. Thus, implementing the Mars program goal to search for life points to drilling on Mars to reach liquid water, collecting samples and analyzing them with instrumentation to detect in situ organisms and biomarker compounds. Searching for life in the subsurface of Mars will require drilling, sample extraction and handling, and new technologies to find and identify biomarker compounds and search for living organisms. In spite of its obvious advantages, robotic drilling for Mars exploration is in its technological infancy and has yet to be demonstrated in even a terrestrial field environment.

Center for Subsurface Sensing & Imaging Systems (CenSSIS)

Science.gov Websites

Contact Us Home Wavelets ALERT Center PROTECT Program Gordon Engineering Leadership Program Center Members Simon Pitts awarded 2015 Gordon Prize ALERT Center Director, Michael B. Silevitch and Gordon Engineering Leadership Director, Simon Pitts have been awarded the 2015 Bernard M. Gordon Prize for Engineering Education

Processes affecting transport of uranium in a suboxic aquifer

USGS Publications Warehouse

Davis, J.A.; Curtis, G.P.; Wilkins, M.J.; Kohler, M.; Fox, P.; Naftz, D.L.; Lloyd, J.R.

2006-01-01

At the Naturita site in Colorado, USA, groundwaters were sampled and analyzed for chemical composition and by culture and culture-independent microbiological techniques. In addition, sediments were extracted with a dilute sodium carbonate solution to determine quantities of labile uranium within the sediments. Samples from the upgradient portion of the contaminated aquifer, where very little dissolved Fe(II) is found in the groundwater, have uranium content that is controlled by U(VI) adsorption and few metal-reducing bacteria are observed. In the extreme downgradient portion of the aquifer, where dissolved Fe(II) is observed, uranium content of the sediments includes significant quantities of reduced U(IV) and diverse populations of Fe(III)-reducing bacteria were present in the subsurface with the potential of reducing U(VI) to U(IV). ?? 2006 Elsevier Ltd. All rights reserved.

Influence of design, physico-chemical and environmental parameters on pharmaceuticals and fragrances removal by constructed wetlands.

PubMed

Hijosa-Valsero, M; Matamoros, V; Sidrach-Cardona, R; Pedescoll, A; Martín-Villacorta, J; García, J; Bayona, J M; Bécares, E

2011-01-01

The ability of several mesocosm-scale and full-scale constructed wetlands (CWs) to remove pharmaceuticals and personal care products (PPCPs) from urban wastewater was assessed. The results of three previous works were considered as a whole to find common patterns in PPCP removal. The experiment took place outdoors under winter and summer conditions. The mesocosm-scale CWs differed in some design parameters, namely the presence of plants, the vegetal species chosen (Typha angustifolia versus Phragmites australis), the flow configuration (surface flow versus subsurface flow), the primary treatment (sedimentation tank versus HUSB), the feeding regime (batch flow versus continuous saturation) and the presence of gravel bed. The full-scale CWs consisted of a combination of various subsystems (ponds, surface flow CWs and subsurface flow CWs). The studied PPCPs were ketoprofen, naproxen, ibuprofen, diclofenac, salicylic acid, carbamazepine, caffeine, methyl dihydrojasmonate, galaxolide and tonalide. The performance of the evaluated treatment systems was compound dependent and varied as a function of the CW-configuration. In addition, PPCP removal efficiencies were lower during winter. The presence of plants favoured naproxen, ibuprofen, diclofenac, salicylic acid, caffeine, methyl dihydrojasmonate, galaxolide and tonalide removal. Significant positive correlations were observed between the removal of most PPCPs and temperature or redox potential. Accordingly, microbiological pathways appear to be the most likely degradation route for the target PPCPs in the CWs studied.

Evidence for marine origin and microbial-viral habitability of sub-zero hypersaline aqueous inclusions within permafrost near Barrow, Alaska.

PubMed

Colangelo-Lillis, J; Eicken, H; Carpenter, S D; Deming, J W

2016-05-01

Cryopegs are sub-surface hypersaline brines at sub-zero temperatures within permafrost; their global extent and distribution are unknown. The permafrost barrier to surface and groundwater advection maintains these brines as semi-isolated systems over geological time. A cryopeg 7 m below ground near Barrow, Alaska, was sampled for geochemical and microbiological analysis. Sub-surface brines (in situtemperature of -6 °C, salinity of 115 ppt), and an associated sediment-infused ice wedge (melt salinity of 0.04 ppt) were sampled using sterile technique. Major ionic concentrations in the brine corresponded more closely to other (Siberian) cryopegs than to Standard seawater or the ice wedge. Ionic ratios and stable isotope analysis of water conformed to a marine or brackish origin with subsequent Rayleigh fractionation. The brine contained ∼1000× more bacteria than surrounding ice, relatively high viral numbers suggestive of infection and reproduction, and an unusually high ratio of particulate to dissolved extracellular polysaccharide substances. A viral metagenome indicated a high frequency of temperate viruses and limited viral diversity compared to surface environments, with closest similarity to low water activity environments. Interpretations of the results underscore the isolation of these underexplored microbial ecosystems from past and present oceans. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Variability of subseafloor viral abundance at the geographically and geologically distinct continental margins.

PubMed

Yanagawa, Katsunori; Morono, Yuki; Yoshida-Takashima, Yukari; Eitoku, Masamitsu; Sunamura, Michinari; Inagaki, Fumio; Imachi, Hiroyuki; Takai, Ken; Nunoura, Takuro

2014-04-01

We studied the relationship between viral particle and microbial cell abundances in marine subsurface sediments from three geographically distinct locations in the continental margins (offshore of the Shimokita Peninsula of Japan, the Cascadia Margin off Oregon, and the Gulf of Mexico) and found depth variations in viral abundances among these sites. Viruses in sediments obtained offshore of the Shimokita and in the Cascadia Margin generally decreased with increasing depth, whereas those in sediments from the Gulf of Mexico were relatively constant throughout the investigated depths. In addition, the abundance ratios of viruses to microbial cells notably varied among the sites, ranging between 10(-3) and 10(1) . The subseafloor viral abundance offshore of the Shimokita showed a positive relationship with the microbial cell abundance and the sediment porosity. In contrast, no statistically significant relationship was observed in the Cascadia Margin and the Gulf of Mexico sites, presumably due to the long-term preservation of viruses from enzymatic degradation within the low-porosity sediments. Our observations indicate that viral abundance in the marine subsurface sedimentary environment is regulated not only by in situ production but also by the balance of preservation and decay, which is associated with the regional sedimentation processes in the geological settings. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Transforming a sequence of microbiology courses using student profile data.

PubMed

Buxeda, R J; Moore, D A

2000-05-01

A study was performed in the General Microbiology and Industrial Microbiology courses to increase research awareness at an early stage of the educational process and to establish collaboration between students in an Industrial Microbiology program and industry. In both courses, the professor helped students determine their learning styles and then used these data to design activities in order to accomplish the above objectives. In both the treatment and the control sections, students learned about strategies to optimize learning based on their learning styles. A cooperative learning format was introduced to promote active learning and team-building skills. The diverse learning styles data profile was used by students during cooperative learning activities for effective team integration. In the General Microbiology course, a mentor-mentee structure was introduced to expose students to research in microbiology by visiting research facilities on campus. This structure was an addition to the regular curriculum, which meets American Society for Microbiology curriculum recommendations. The results suggest an increase in interest in research by students. In the Industrial Microbiology course, a strategy was introduced to establish collaboration with industry in which students visit the workplace and identify microbial processes, microbiologist roles, and skills needed by microbiologists. Evaluation of these topics using pre- and posttest data indicates a significant increase in acquired knowledge relevant to daily workplace environments with the reformed course. In both courses, students gain information early in their academic experience to help them consider participation in research experiences while providing them with real-world experience toward the end of their academic careers, when they see the need for it.

[Microbiological assessment of the Gouda-type cheese-making process in a Venezuelan industry].

PubMed

Dáivila, Jacqueline; Reyes, Genara; Corzo, Otoniel

2006-03-01

The adoption of the Hazard Analysis and Critical Control Point (HACCP) system is necessary to assure the safety of the product in the cheese-making industry. The compliment of pre-requisite programs as Good Manufacture Practices (GMPs) and Sanitation Standard Operating Procedures (SSOPs) are required before the implementation of the HACCP plan. GMPs are the standards related to equipments, tools, personnel, etc. SSOPs are the procedures related to hygiene and sanitation of the plant and workers. The aim of this study was to assess the compliment of the pre-requisite programs and the microbiological conditions of the Gouda type cheese-making process in a Venezuelan processing plant before designing a HACCP plan. Samples were: (a) raw milk, pasteurized milk, curd and ripened cheese, (b) water, (c) environment of the production areas and ripening premises, (d) equipments before and after sanitation, (e) food handlers. Microbiological analyses were done according to COVENIN standards. This study showed that even though pasteurization process was effective to kill pathogen bacteria of the raw milk and the water was safe, however there are deficient manufacture practices in the hygiene as well as in sanitation of the plant and food handlers. Prerequisite programs (GMP-SSOP) of this industry need to be well established, controlled and evaluated.

Chemical and microbiological experimentation for development of environmental control and life support systems

NASA Technical Reports Server (NTRS)

Whitman, G. A.; Wilson, M. E.; Cole, H. E.; Traweek, M.

1992-01-01

Microbiological techniques are under study with a view to the identification of viable microorganisms in liquid cultures, improve the identification of stressed organisms, and determine the biocidal activity of iodine and other chemicals on isolates from recycled water. A quality-assurance program has been implemented to validate data employed in making decisions concerning engineering and human health and safety. Analytical laboratory refinements will strongly aid the development of environmental control and life-support systems.

[Implementation of quality standard UNE-EN ISO/IEC 17043 in the External Quality Control Program of the Spanish Society of Infectious Diseases and Clinical Microbiology].

PubMed

Poveda Gabaldón, Marta; Ovies, María Rosario; Orta Mira, Nieves; Serrano, M del Remedio Guna; Avila, Javier; Giménez, Alicia; Cardona, Concepción Gimeno

2011-12-01

The quality standard "UNE-EN-ISO 17043: 2010. Conformity assessment. General requirements for proficiency testing" applies to centers that organize intercomparisons in all areas. In the case of clinical microbiology laboratories, these intercomparisons must meet the management and technical standards required to achieve maximum quality in the performance of microbiological analysis and the preparation of test items (sample, product, data or other information used in the proficiency test) to enable them to be accredited. Once accredited, these laboratories can operate as a tool for quality control laboratories and competency assessment. In Spain, accreditation is granted by the Spanish Accreditation Body [Entidad Nacional de Acreditación (ENAC)]. The objective of this review is to explain how to apply the requirements of the standard to laboratories providing intercomparisons in the field of clinical microbiology (the organization responsible for all the tasks related to the development and operation of a proficiency testing program). This requires defining the scope and specifying the technical requirements (personnel management, control of equipment, facilities and environment, the design of the proficiency testing and data analysis for performance evaluation, communication with participants and confidentiality) and management requirements (document control, purchasing control, monitoring of complaints / claims, non-compliance, internal audits and management reviews). Copyright © 2011 Elsevier España S.L. All rights reserved.

Subsurface microbiology and biogeochemistry of a deep, cold-water carbonate mound from the Porcupine Seabight (IODP Expedition 307)

PubMed Central

Webster, Gordon; Blazejak, Anna; Cragg, Barry A; Schippers, Axel; Sass, Henrik; Rinna, Joachim; Tang, Xiaohong; Mathes, Falko; Ferdelman, Timothy G; Fry, John C; Weightman, Andrew J; Parkes, R John

2009-01-01

The Porcupine Seabight Challenger Mound is the first carbonate mound to be drilled (∼270 m) and analyzed in detail microbiologically and biogeochemically. Two mound sites and a non-mound Reference site were analyzed with a range of molecular techniques [catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH), quantitative PCR (16S rRNA and functional genes, dsrA and mcrA), and 16S rRNA gene PCR-DGGE] to assess prokaryotic diversity, and this was compared with the distribution of total and culturable cell counts, radiotracer activity measurements and geochemistry. There was a significant and active prokaryotic community both within and beneath the carbonate mound. Although total cell numbers at certain depths were lower than the global average for other subseafloor sediments and prokaryotic activities were relatively low (iron and sulfate reduction, acetate oxidation, methanogenesis) they were significantly enhanced compared with the Reference site. In addition, there was some stimulation of prokaryotic activity in the deepest sediments (Miocene, > 10 Ma) including potential for anaerobic oxidation of methane activity below the mound base. Both Bacteria and Archaea were present, with neither dominant, and these were related to sequences commonly found in other subseafloor sediments. With an estimate of some 1600 mounds in the Porcupine Basin alone, carbonate mounds may represent a significant prokaryotic subseafloor habitat. PMID:18826439

Snowmelt induced hydrologic perturbations drive dynamic microbiological and geochemical behaviors across a shallow riparian aquifer

NASA Astrophysics Data System (ADS)

Danczak, Robert; Yabusaki, Steven; Williams, Kenneth; Fang, Yilin; Hobson, Chad; Wilkins, Michael

2016-05-01

Shallow riparian aquifers represent hotspots of biogeochemical activity in the arid western US. While these environments provide extensive ecosystem services, little is known of how natural environmental perturbations influence subsurface microbial communities and associated biogeochemical processes. Over a six-month period we tracked the annual snowmelt-driven incursion of groundwater into the vadose zone of an aquifer adjacent to the Colorado River, leading to increased dissolved oxygen (DO) concentrations in the normally suboxic saturated zone. Strong biogeochemical heterogeneity was measured across the site, with abiotic reactions between DO and sulfide minerals driving rapid DO consumption and mobilization of redox active species in reduced aquifer regions. Conversely, extensive DO increases were detected in less reduced sediments. 16S rRNA gene surveys tracked microbial community composition within the aquifer, revealing strong correlations between increases in putative oxygen-utilizing chemolithoautotrophs and heterotrophs and rising DO concentrations. The gradual return to suboxic aquifer conditions favored increasing abundances of 16S rRNA sequences matching members of the Microgenomates (OP11) and Parcubacteria (OD1) that have been strongly implicated in fermentative processes. Microbial community stability measurements indicated that deeper aquifer locations were relatively less affected by geochemical perturbations, while communities in shallower locations exhibited the greatest change. Reactive transport modeling of the geochemical and microbiological results supported field observations, suggesting that a predictive framework can be applied to develop a greater understanding of such environments.

Executive summary: Pre-exposure prophylaxis for prevention of HIV infection in adults in Spain: July 2016.

PubMed

Moreno, Santiago; Antela, Antonio; García, Felipe; Del Amo, Julia; Boix, Vicente; Coll, Pep; Fortuny, Claudia; Sirvent, Juan L Gómez; Gutiérrez, Félix; Iribarren, José A; Llibre, Josep M; Quirós, Juan C López Bernaldo de; Losa, Juan Emilio; Lozano, Ana; Meulbroek, Michael; Olalla, Julián; Pujol, Ferran; Pulido, Federico; Crespo Casal, Manuel; García, Juan González; Aldeguer, José López; Molina, Jose A Pérez; Podzamczer Palter, Daniel; Román, Antonio Rivero

Administration of antiretroviral drugs to individuals exposed to, but not infected by, HIV has been shown to reduce the risk of transmission. The efficacy of pre-exposure prophylaxis (PrEP) makes it obligatory to include it in an integral program of prevention of HIV transmission, together with other measures, such as use of the condom, training, counseling, and appropriate treatment of infected individuals. In this document, the AIDS Study Group (GeSIDA) of the Spanish Society of Infectious Diseases and Clinical Microbiology (Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica [SEIMC]) provides its views on this important subject. The available evidence on the usefulness of PrEP in the prevention of transmission of HIV is presented, and the components that should make up a PrEP program and whose development and implementation are feasible in Spain are set out. Copyright © 2017 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

A Mobile Acoustic Subsurface Sensing (MASS) System for Rapid Roadway Assessment

PubMed Central

Lu, Yifeng; Zhang, Yi; Cao, Yinghong; McDaniel, J. Gregory; Wang, Ming L.

2013-01-01

Surface waves are commonly used for vibration-based nondestructive testing for infrastructure. Spectral Analysis of Surface Waves (SASW) has been used to detect subsurface properties for geologic inspections. Recently, efforts were made to scale down these subsurface detection approaches to see how they perform on small-scale structures such as concrete slabs and pavements. Additional efforts have been made to replace the traditional surface-mounted transducers with non-contact acoustic transducers. Though some success has been achieved, most of these new approaches are inefficient because they require point-to-point measurements or off-line signal analysis. This article introduces a Mobile Acoustic Subsurface Sensing system as MASS, which is an improved surface wave based implementation for measuring the subsurface profile of roadways. The compact MASS system is a 3-wheeled cart outfitted with an electromagnetic impact source, distance register, non-contact acoustic sensors and data acquisition/processing equipment. The key advantage of the MASS system is the capability to collect measurements continuously at walking speed in an automatic way. The fast scan and real-time analysis advantages are based upon the non-contact acoustic sensing and fast air-coupled surface wave analysis program. This integration of hardware and software makes the MASS system an efficient mobile prototype for the field test. PMID:23698266

Key subsurface data help to refine Trinity aquifer hydrostratigraphic units, south-central Texas

USGS Publications Warehouse

Blome, Charles D.; Clark, Allan K.

2014-01-01

The geologic framework and hydrologic characteristics of aquifers are important components for studying the nation’s subsurface heterogeneity and predicting its hydraulic budgets. Detailed study of an aquifer’s subsurface hydrostratigraphy is needed to understand both its geologic and hydrologic frameworks. Surface hydrostratigraphic mapping can also help characterize the spatial distribution and hydraulic connectivity of an aquifer’s permeable zones. Advances in three-dimensional (3-D) mapping and modeling have also enabled geoscientists to visualize the spatial relations between the saturated and unsaturated lithologies. This detailed study of two borehole cores, collected in 2001 on the Camp Stanley Storage Activity (CSSA) area, provided the foundation for revising a number of hydrostratigraphic units representing the middle zone of the Trinity aquifer. The CSSA area is a restricted military facility that encompasses approximately 4,000 acres and is located in Boerne, Texas, northwest of the city of San Antonio. Studying both the surface and subsurface geology of the CSSA area are integral parts of a U.S. Geological Survey project funded through the National Cooperative Geologic Mapping Program. This modification of hydrostratigraphic units is being applied to all subsurface data used to construct a proposed 3-D EarthVision model of the CSSA area and areas to the south and west.

[Design of a Hazard Analysis and Critical Control Points (HACCP) plan to assure the safety of a bologna product produced by a meat processing plant].

PubMed

Bou Rached, Lizet; Ascanio, Norelis; Hernández, Pilar

2004-03-01

The Hazard Analysis and Critical Control Point (HACCP) is a systematic integral program used to identify and estimate the hazards (microbiological, chemical and physical) and the risks generated during the primary production, processing, storage, distribution, expense and consumption of foods. To establish a program of HACCP has advantages, being some of them: to emphasize more in the prevention than in the detection, to diminish the costs, to minimize the risk of manufacturing faulty products, to allow bigger trust to the management, to strengthen the national and international competitiveness, among others. The present work is a proposal based on the design of an HACCP program to guarantee the safety of the Bologna Special Type elaborated by a meat products industry, through the determination of hazards (microbiological, chemical or physical), the identification of critical control points (CCP), the establishment of critical limits, plan corrective actions and the establishment of documentation and verification procedures. The used methodology was based in the application of the seven basic principles settled down by the Codex Alimentarius, obtaining the design of this program. In view of the fact that recently the meat products are linked with pathogens like E. coli O157:H7 and Listeria monocytogenes, these were contemplated as microbiological hazard for the establishment of the HACCP plan whose application will guarantee the obtaining of a safe product.

Detection of microbes in the subsurface

NASA Technical Reports Server (NTRS)

White, David C.; Tunlid, Anders

1989-01-01

The search for evidence of microbial life in the deep subsurface of Earth has implications for the Mars Rover Sampling Return Missions program. If suitably protected environments can be found on Mars then the instrumentation to detect biomarkers could be used to examine the molecular details. Finding a lipid in Martian soil would represent possibly the simplest test for extant or extinct life. A device that could do a rapid extraction possibly using the supercritical fluid technology under development now with a detection of the carbon content would clearly indicate a sample to be returned.

Microbiological testing of Skylab foods.

NASA Technical Reports Server (NTRS)

Heidelbaugh, N. D.; Mcqueen, J. L.; Rowley, D. B.; Powers , E. M.; Bourland, C. T.

1973-01-01

Review of some of the unique food microbiology problems and problem-generating circumstances the Skylab manned space flight program involves. The situations these problems arise from include: extended storage times, variations in storage temperatures, no opportunity to resupply or change foods after launch of the Skylab Workshop, first use of frozen foods in space, first use of a food-warming device in weightlessness, relatively small size of production lots requiring statistically valid sampling plans, and use of food as an accurately controlled part in a set of sophisticated life science experiments. Consideration of all of these situations produced the need for definite microbiological tests and test limits. These tests are described along with the rationale for their selection. Reported test results show good compliance with the test limits.

The Microbiological@mind project: a public engagement initiative of Turin University bringing microbiology and health education into primary schools.

PubMed

Scalas, Daniela; Roana, Janira; Mandras, Narcisa; Cuccu, Sonia; Banche, Giuliana; Marra, Elisa Simona; Collino, Nicoletta; Piersigilli, Giorgia; Allizond, Valeria; Tullio, Vivian; Cuffini, Anna Maria

2017-10-01

Despite ongoing global efforts, antimicrobial resistance continues to threaten the treatment of an ever-increasing range of bacterial infections. There is substantial evidence that public education programs that foster microbial literacy amongst young school audiences may improve correct knowledge of specific health issues, such as prevention of microbial infections and responsible use of antibiotics. The aim of the Microbiological@mind project was to engage primary school students with the subject of microbiology, to promote both scientific interest and awareness towards correct behaviors that may ensure a safer lifestyle. Interactive workshops based on a full ''hands-on'' approach were carried out by an expert team from the University of Turin to over 1200 children aged 9-11 years at primary schools in Turin. A questionnaire (pre- and post-activity test) on the main topic (i.e. antibiotics) was used to assess project effectiveness. The workshops provided a useful means to strengthen the understanding of basic microbiology concepts amongst students. Students' baseline knowledge of antibiotics was quite low, as low percentages of correct answers on antibiotic action and use (5.0% and 12.1%, respectively) were found in the pre-activity tests. A significant increase (P <0.0001) in correct knowledge was observed in the post-activity tests, after implementation of the teaching activity. Our findings support the idea that microbial literacy in early childhood through hands-on educational programs is of great importance to foster children's interest in science learning, and to provide young people with information about general and specific health-related issues, such as prudent antibiotic use, for a more responsible citizenship. Copyright © 2017 Elsevier B.V. and International Society of Chemotherapy. All rights reserved.

Subsurface Microsensors for Assisted Recertification of TPS (SmarTPS)

NASA Technical Reports Server (NTRS)

Pallix, Joan B.; Milos, Frank S.; Huestis, Dave; Arnold, James O. (Technical Monitor)

1999-01-01

Commercialization of a competitive reusable launch vehicle (RLV) is a primary goal for both NASA and the U.S. aerospace industry. To expedite achievement of this goal, the Bantam-X Technology Program is funding development of innovative technologies to lower costs for access to space. Ground operations is one area where significant cost reduction is required. For the Shuttle fleet, ground operations account for over 80% of the life cycle costs, and TPS recertification accounts for 27% of the operation costs ($4.5M per flight). Bantam Task TPS-7, Subsurface Microsensors for Assisted Recertification of TPS (SmarTPS), is a joint effort between NASA centers and industry partners to develop rapid remote detection and scanning technology for inspection of TPS and detection of subsurface defects. This short paper will provide a general overview of the SmarTPS concept.

Subsurface injection of liquid waste in Florida, United States of America

USGS Publications Warehouse

Vecchioli, John

1981-01-01

In 1979, liquid waste was injected into the subsurface of Florida by 10 injection systems at an aggregate average rate of 165,000 m3/d. All the systems inject into carbonate rocks that contain salty water. Extensive precautions are taken in the construction of the injection wells and in the monitoring of their operation to provide assurance that overlying and laterally contiguous freshwater resources do not become contaminated with either the injected waste or the saltwater displaced by the waste. Several concerns relating to the effectiveness of the confining bed above the injection zone for containing the injected wastes have arisen over the years. These concerns accentuate the value of a well-planned and implemented monitoring program from which one can evaluate the potential impact of waste injection on the subsurface environment.

Compilation of Annual Reports of the Navy ELF (Extremely Low Frequency) Communications System Ecological Monitoring Program. Volume 1. Tabs A-E.

DTIC Science & Technology

1984-07-01

mhhhhmhhmmm EEmhohEEmhmhEE EohhEohEEEEohI 1111 11111_L25 1.18 6 MICROCOPY RESOLUTION TESI CHART 95. Pedon Classification: Typic Dystrochrept, sandy, mixed...prepared by team researchers in the MTU Forestry Department and delivered to the Environmental Microbiology lab in the Department of Biological Sciences...unsuccessful. Using methods given in a presentation at the 1982 American Society for Microbiology Annual Meetings, virtually no bacteria of any type were

Clinical and Microbiological Characteristics of Invasive Group A Streptococcal Infections Before and After Implementation of a Universal Varicella Vaccine Program.

PubMed

Frère, Julie; Bidet, Philippe; Tapiéro, Bruce; Rallu, Fabien; Minodier, Philippe; Bonacorsi, Stephane; Bingen, Edouard; Ovetchkine, Philippe

2016-01-01

Since the introduction of the varicella vaccine to the routine immunization schedule, we have observed a 70% reduction in the rate of varicella-associated invasive group A streptococcal infections (IGASI). In the mean time, the clinical presentation of IGASI and microbiological characteristics of GAS strains have changed significantly. © The Author 2015. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

Deepwater Program: Exploration and Research of Northern Gulf of Mexico Deepwater Natural and Artificial Hard Bottom Habitats with Emphasis on Coral Communities: Reefs, Rigs and Wrecks

DTIC Science & Technology

2009-01-01

Dr. Sheli Smith (PAST Foundation) - eighteenth and nineteenth century marine architecture, Dr. Christina A. Kellogg, USGS, microbiology In...of Mexico. Investigations at the wooden wrecks detailed them with video and still imagery and placed long and short-term microbiological experiments...Study MMS 2008-018. Church, Robert and Lynn Samuel. 2004. Archaeological, Engineering and Hazard Study for a Proposed 16-inch Oil Export Pipeline

CORRELATOR 5.2 - A program for interactive lithostratigraphic correlation of wireline logs

USGS Publications Warehouse

Olea, R.A.

2004-01-01

The limited radius of investigation of petrophysical measurements made in boreholes and the relatively large distances between wells result in an incomplete sensing of the subsurface through well logging. CORRELATOR is a program for estimating geological properties between logged boreholes. An initial and fundamental step is the lithostratigraphic correlation of logs in different wells. The method employed by the program closely emulates the process of visual inspection used by experienced subsurface geologists in manual correlation. Mathematically, the determination of lithostratigraphical equivalence is based on the simultaneous assessment of similarity in shale content, similarity in the patterns of vertical variation in a petrophysical property that is measured with high vertical resolution, and spatial consistency of stratigraphic relationships as determined by an expert system. Multiple additional options for processing log readings allow maximization in the extraction of information from pairs of logs per well and great flexibility in the final display of results in the form of cross sections and dip diagrams. ?? 2004 Elsevier Ltd. All rights reserved.

7 CFR 91.2 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Agriculture. Analyses. Microbiological, chemical, or physical tests performed on a commodity. Applicant. Any person or organization requesting services provided by the Science and Technology (S&T) programs. Legal...

7 CFR 91.2 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Agriculture. Analyses. Microbiological, chemical, or physical tests performed on a commodity. Applicant. Any person or organization requesting services provided by the Science and Technology (S&T) programs. Legal...

7 CFR 91.2 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Agriculture. Analyses. Microbiological, chemical, or physical tests performed on a commodity. Applicant. Any person or organization requesting services provided by the Science and Technology (S&T) programs. Legal...

7 CFR 91.2 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Agriculture. Analyses. Microbiological, chemical, or physical tests performed on a commodity. Applicant. Any person or organization requesting services provided by the Science and Technology (S&T) programs. Legal...

Accelerating Subsurface Transport Simulation on Heterogeneous Clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Villa, Oreste; Gawande, Nitin A.; Tumeo, Antonino

Reactive transport numerical models simulate chemical and microbiological reactions that occur along a flowpath. These models have to compute reactions for a large number of locations. They solve the set of ordinary differential equations (ODEs) that describes the reaction for each location through the Newton-Raphson technique. This technique involves computing a Jacobian matrix and a residual vector for each set of equation, and then solving iteratively the linearized system by performing Gaussian Elimination and LU decomposition until convergence. STOMP, a well known subsurface flow simulation tool, employs matrices with sizes in the order of 100x100 elements and, for numerical accuracy,more » LU factorization with full pivoting instead of the faster partial pivoting. Modern high performance computing systems are heterogeneous machines whose nodes integrate both CPUs and GPUs, exposing unprecedented amounts of parallelism. To exploit all their computational power, applications must use both the types of processing elements. For the case of subsurface flow simulation, this mainly requires implementing efficient batched LU-based solvers and identifying efficient solutions for enabling load balancing among the different processors of the system. In this paper we discuss two approaches that allows scaling STOMP's performance on heterogeneous clusters. We initially identify the challenges in implementing batched LU-based solvers for small matrices on GPUs, and propose an implementation that fulfills STOMP's requirements. We compare this implementation to other existing solutions. Then, we combine the batched GPU solver with an OpenMP-based CPU solver, and present an adaptive load balancer that dynamically distributes the linear systems to solve between the two components inside a node. We show how these approaches, integrated into the full application, provide speed ups from 6 to 7 times on large problems, executed on up to 16 nodes of a cluster with two AMD Opteron 6272 and a Tesla M2090 per node.« less

Biological CO2 conversion to acetate in subsurface coal-sand formation using a high-pressure reactor system.

PubMed

Ohtomo, Yoko; Ijiri, Akira; Ikegawa, Yojiro; Tsutsumi, Masazumi; Imachi, Hiroyuki; Uramoto, Go-Ichiro; Hoshino, Tatsuhiko; Morono, Yuki; Sakai, Sanae; Saito, Yumi; Tanikawa, Wataru; Hirose, Takehiro; Inagaki, Fumio

2013-01-01

Geological CO2 sequestration in unmineable subsurface oil/gas fields and coal formations has been proposed as a means of reducing anthropogenic greenhouse gasses in the atmosphere. However, the feasibility of injecting CO2 into subsurface depends upon a variety of geological and economic conditions, and the ecological consequences are largely unpredictable. In this study, we developed a new flow-through-type reactor system to examine potential geophysical, geochemical and microbiological impacts associated with CO2 injection by simulating in-situ pressure (0-100 MPa) and temperature (0-70°C) conditions. Using the reactor system, anaerobic artificial fluid and CO2 (flow rate: 0.002 and 0.00001 ml/min, respectively) were continuously supplemented into a column comprised of bituminous coal and sand under a pore pressure of 40 MPa (confined pressure: 41 MPa) at 40°C for 56 days. 16S rRNA gene analysis of the bacterial components showed distinct spatial separation of the predominant taxa in the coal and sand over the course of the experiment. Cultivation experiments using sub-sampled fluids revealed that some microbes survived, or were metabolically active, under CO2-rich conditions. However, no methanogens were activated during the experiment, even though hydrogenotrophic and methylotrophic methanogens were obtained from conventional batch-type cultivation at 20°C. During the reactor experiment, the acetate and methanol concentration in the fluids increased while the δ(13)Cacetate, H2 and CO2 concentrations decreased, indicating the occurrence of homo-acetogenesis. 16S rRNA genes of homo-acetogenic spore-forming bacteria related to the genus Sporomusa were consistently detected from the sandstone after the reactor experiment. Our results suggest that the injection of CO2 into a natural coal-sand formation preferentially stimulates homo-acetogenesis rather than methanogenesis, and that this process is accompanied by biogenic CO2 conversion to acetate.

Biological CO2 conversion to acetate in subsurface coal-sand formation using a high-pressure reactor system

PubMed Central

Ohtomo, Yoko; Ijiri, Akira; Ikegawa, Yojiro; Tsutsumi, Masazumi; Imachi, Hiroyuki; Uramoto, Go-Ichiro; Hoshino, Tatsuhiko; Morono, Yuki; Sakai, Sanae; Saito, Yumi; Tanikawa, Wataru; Hirose, Takehiro; Inagaki, Fumio

2013-01-01

Geological CO2 sequestration in unmineable subsurface oil/gas fields and coal formations has been proposed as a means of reducing anthropogenic greenhouse gasses in the atmosphere. However, the feasibility of injecting CO2 into subsurface depends upon a variety of geological and economic conditions, and the ecological consequences are largely unpredictable. In this study, we developed a new flow-through-type reactor system to examine potential geophysical, geochemical and microbiological impacts associated with CO2 injection by simulating in-situ pressure (0–100 MPa) and temperature (0–70°C) conditions. Using the reactor system, anaerobic artificial fluid and CO2 (flow rate: 0.002 and 0.00001 ml/min, respectively) were continuously supplemented into a column comprised of bituminous coal and sand under a pore pressure of 40 MPa (confined pressure: 41 MPa) at 40°C for 56 days. 16S rRNA gene analysis of the bacterial components showed distinct spatial separation of the predominant taxa in the coal and sand over the course of the experiment. Cultivation experiments using sub-sampled fluids revealed that some microbes survived, or were metabolically active, under CO2-rich conditions. However, no methanogens were activated during the experiment, even though hydrogenotrophic and methylotrophic methanogens were obtained from conventional batch-type cultivation at 20°C. During the reactor experiment, the acetate and methanol concentration in the fluids increased while the δ13Cacetate, H2 and CO2 concentrations decreased, indicating the occurrence of homo-acetogenesis. 16S rRNA genes of homo-acetogenic spore-forming bacteria related to the genus Sporomusa were consistently detected from the sandstone after the reactor experiment. Our results suggest that the injection of CO2 into a natural coal-sand formation preferentially stimulates homo-acetogenesis rather than methanogenesis, and that this process is accompanied by biogenic CO2 conversion to acetate. PMID:24348470

Survival of Escherichia coli in common garden mulches spiked with synthetic greywater.

PubMed

Boyte, S; Quaife, S; Horswell, J; Siggins, A

2017-05-01

Reuse of domestic wastewater is increasingly practiced as a means to address global demands on fresh water. Greywater is primarily reused via subsurface irrigation of gardens, where the soil environment is seen to be an integral part of the treatment process. The fate of biological contaminants (i.e. pathogens) in the soil is reasonably well understood, but their persistence and survival in soil cover layers is largely unexplored. This study investigated the ability of Escherichia coli to survive in common soil cover layers. Three garden mulches were investigated: pea straw mulch, a bark-based mulch and a coconut husk mulch. Each mulch was treated with an E. coli solution, a synthetic greywater with E. coli, or a freshwater control. Escherichia coli was applied at 1 × 10 4  most probable number (MPN) per g dry weight mulch. Subsamples were temporally analysed for E. coli. The bark and coconut husk mulches showed a steady decline in E. coli numbers, while E. coli increased in the pea straw mulch for the duration of the 50 days experiment, peaking at 1·8 × 10 8  MPN per g dry weight mulch. This study highlighted the importance of selection of a suitable material for covering areas that are subsurface irrigated with greywater. Potential for microbial contamination is one of the limiting factors for domestic greywater reuse. Although subsurface irrigation is considered to be one of the lowest risk applications, there is still a possibility of microbes reaching the soil surface if the environmental conditions are not favourable or if soil movement inadvertently exposes the irrigation line. In these circumstances, the soil cover layer may be contaminated by greywater microbes. This study assesses the survival rates of the pathogen indicator organism Escherichia coli in three soil cover materials commonly used worldwide and makes clear recommendations to facilitate the safe reuse of domestic greywater. © 2017 The Society for Applied Microbiology.

MULTI-MEDIA MICROBIOLOGICAL RISK ASSESSMENT METHODOLOGY FOR MUNICIPAL WASTEWATER SLUDGES

EPA Science Inventory

In order to reduce the risk of municipal sludge to acceptable levels, the U.S. EPA has undertaken a regulatory program based on risk assessment and risk management. The key to such a program is the development of a methodology which allows the regulatory agency to quantify the re...

Life in the Ice

NASA Technical Reports Server (NTRS)

Allen, C. C.; Wainwright, N. R.; Grasby, S. E.; Harvey, R. P.

2003-01-01

The current Martian surface environment is extremely hostile to any known form of life. The combination of subfreezing temperature, low atmospheric pressure and high ultraviolet flux, combined with desiccated and possibly oxidizing soil, could destroy even the hardiest microorganisms. The Viking biology experiments are generally interpreted to indicate that the surface of Mars is currently devoid of life and organic molecules at the part-per-billion level. Speculation on the possibility of extant or preserved microbial life on Mars thus centers on refuges in some manner protected from the current surface environment, either in space or time. Terrestrial analogs include hydrothermal systems, lakes, caves and subsurface aquifers as well as more clement conditions in the distant past. We are examining the evidence for microbiology in Earth's glaciated polar regions as analogs to the polar caps of Mars. This research concerns the detection of microorganisms or their preserved remains at the surface and within polar glacial ice.

The ASM Curriculum Guidelines for Undergraduate Microbiology: A Case Study of the Advocacy Role of Societies in Reform Efforts

PubMed Central

Horak, Rachel E. A.; Merkel, Susan; Chang, Amy

2015-01-01

A number of national reports, including Vision and Change in Undergraduate Biology Education: A Call to Action, have called for drastic changes in how undergraduate biology is taught. To that end, the American Society for Microbiology (ASM) has developed new Curriculum Guidelines for undergraduate microbiology that outline a comprehensive curriculum for any undergraduate introductory microbiology course or program of study. Designed to foster enduring understanding of core microbiology concepts, the Guidelines work synergistically with backwards course design to focus teaching on student-centered goals and priorities. In order to qualitatively assess how the ASM Curriculum Guidelines are used by educators and learn more about the needs of microbiology educators, the ASM Education Board distributed two surveys to the ASM education community. In this report, we discuss the results of these surveys (353 responses). We found that the ASM Curriculum Guidelines are being implemented in many different types of courses at all undergraduate levels. Educators indicated that the ASM Curriculum Guidelines were very helpful when planning courses and assessments. We discuss some specific ways in which the ASM Curriculum Guidelines have been used in undergraduate classrooms. The survey identified some barriers that microbiology educators faced when trying to adopt the ASM Curriculum Guidelines, including lack of time, lack of financial resources, and lack of supporting resources. Given the self-reported challenges to implementing the ASM Curriculum Guidelines in undergraduate classrooms, we identify here some activities related to the ASM Curriculum Guidelines that the ASM Education Board has initiated to assist educators in the implementation process. PMID:25949769

The ASM Curriculum Guidelines for Undergraduate Microbiology: A Case Study of the Advocacy Role of Societies in Reform Efforts.

PubMed

Horak, Rachel E A; Merkel, Susan; Chang, Amy

2015-05-01

A number of national reports, including Vision and Change in Undergraduate Biology Education: A Call to Action, have called for drastic changes in how undergraduate biology is taught. To that end, the American Society for Microbiology (ASM) has developed new Curriculum Guidelines for undergraduate microbiology that outline a comprehensive curriculum for any undergraduate introductory microbiology course or program of study. Designed to foster enduring understanding of core microbiology concepts, the Guidelines work synergistically with backwards course design to focus teaching on student-centered goals and priorities. In order to qualitatively assess how the ASM Curriculum Guidelines are used by educators and learn more about the needs of microbiology educators, the ASM Education Board distributed two surveys to the ASM education community. In this report, we discuss the results of these surveys (353 responses). We found that the ASM Curriculum Guidelines are being implemented in many different types of courses at all undergraduate levels. Educators indicated that the ASM Curriculum Guidelines were very helpful when planning courses and assessments. We discuss some specific ways in which the ASM Curriculum Guidelines have been used in undergraduate classrooms. The survey identified some barriers that microbiology educators faced when trying to adopt the ASM Curriculum Guidelines, including lack of time, lack of financial resources, and lack of supporting resources. Given the self-reported challenges to implementing the ASM Curriculum Guidelines in undergraduate classrooms, we identify here some activities related to the ASM Curriculum Guidelines that the ASM Education Board has initiated to assist educators in the implementation process.

The Design and Implementation of Instruments for Low-Frequency Electromagnetic Sounding of the Martian Subsurface

NASA Technical Reports Server (NTRS)

Delory, G. T.; Grimm, R. E.

2003-01-01

Low-frequency electromagnetic soundings of the subsurface can identify liquid water at depths ranging from hundreds of meters to approx. 10 km in an environment such as Mars. Among the tools necessary to perform these soundings are low-frequency electric and magnetic field sensors capable of being deployed from a lander or rover such that horizontal and vertical components of the fields can be measured free of structural or electrical interference. Under a NASA Planetary Instrument Definition and Development Program (PIDDP), we are currently engaged in the prototype stages of low frequency sensor implementations that will enable this technique to be performed autonomously within the constraints of a lander platform. Once developed, this technique will represent both a complementary and alternative method to orbital radar sounding investigations, as the latter may not be able to identify subsurface water without significant ambiguities. Low frequency EM methods can play a crucial role as a ground truth measurement, performing deep soundings at sites identified as high priority areas by orbital radars. Alternatively, the penetration depth and conductivity discrimination of low-frequency methods may enable detection of subsurface water in areas that render radar methods ineffective. In either case, the sensitivity and depth of penetration inherent in low frequency EM exploration makes this tool a compelling candidate method to identify subsurface liquid water from a landed platform on Mars or other targets of interest.

The Mojave Subsurface Bio-Geochemistry Explorer (MOSBE)

NASA Technical Reports Server (NTRS)

Guerrero, J.; Beegle, L.; Abbey, W.; Bhartia, R.; Kounaves, S.; Russell, M.; Towles, D.

2012-01-01

The MOSBE Team has developed a terrestrial field campaign to explore two subsurface biological habitats under the Mojave Desert. This field campaign will not only help us understand terrestrial desert biology, but also will develop methodologies and strategies for potential future Mars missions that would seek to explore the Martian subsurface. We have proposed to the ASTEP program to integrate a suite of field demonstrated instruments with a 20 m subsurface drill as a coherent unit, the Mojave Subsurface Bio-geochemistry Explorer. The ATK Space Modular Planetary Drill System (MPDS) requires no drilling fluid, which allows aseptic sampling, can penetrate lithic ground up to 20 meters of depth, and utilizes less than 100 Watts throughout the entire depth. The drill has been developed and demonstrated in field testing to a depth of 10 meters in Arizona, December 2002. In addition to caching a continuous core throughout the drilling depth, it also generates and caches cuttings and fines that are strata-graphically correlated with the core. As a core segment is brought to the surface, it will be analyzed for texture and structure by a color microscopic imager and for relevant chemistry and mineralogy with a UV fluorescence/Raman spectrometer. Organic and soluble ionic species will be identified through two instruments -- a microcapillary electrophoresis, and an ion trap mass spectrometer that have been developed under PIDDP, ASTID and MIDP funding.

A Combined Study of Photospheric Magnetic and Current Helicities and Subsurface Kinetic Helicities of Solar Active Regions during 2006-2012

NASA Astrophysics Data System (ADS)

Seligman, Darryl; Petrie, G.; Komm, R.

2014-01-01

We compare the average photospheric current helicity H_c, photospheric twist parameter α (a well-known proxy for the full relative magnetic helicity), and subsurface kinetic helicity K_h for 128 active regions observed between 2006-2012. We use 1436 Hinode photospheric vector magnetograms and subsurface fluid velocity data from GONG Dopplergrams. We find a significant hemispheric bias in all three parameters. The K_h parameter is preferentially positive/negative in the southern/northern hemisphere. The H_c and α parameters have the same bias for strong fields |{B}|>1000 G). We examine the temporal variability of each parameter for each active region and identify a significant subset of regions whose three helicity parameters all exhibit clear increasing or decreasing trends. The temporal profiles of these regions have the same bias: positive/negative helicity in the northern/southern hemisphere. The results are consistent with Longcope et al.'s Σ-effect. This work is carried out through the National Solar Observatory Research Experiences for Undergraduate (REU) site program, which is co-funded by the Department of Defense in partnership with the NSF REU Program. The National Solar Observatory is operated by the Association of Universities for Research in Astronomy, Inc. (AURA) under cooperative agreement with the National Science Foundation.

Vertical stratification of subsurface microbial community composition across geological formations at the Hanford Site.

PubMed

Lin, Xueju; Kennedy, David; Fredrickson, Jim; Bjornstad, Bruce; Konopka, Allan

2012-02-01

Microbial diversity in subsurface sediments at the Hanford Site 300 Area near Richland, Washington state (USA) was investigated by analysing 21 samples recovered from depths of 9-52 m. Approximately 8000 near full-length 16S rRNA gene sequences were analysed across geological strata that include a natural redox transition zone. These strata included the oxic coarse-grained Hanford formation, fine-grained oxic and anoxic Ringold Formation sediments, and the weathered basalt group. We detected 1233 and 120 unique bacterial and archaeal OTUs (operational taxonomic units at the 97% identity level) respectively. Microbial community structure and richness varied substantially across the different geological strata. Bacterial OTU richness (Chao1 estimator) was highest (> 700) in the upper Hanford formation, and declined to about 120 at the bottom of the Hanford formation. Just above the Ringold oxic-anoxic interface, richness was about 325 and declined to less than 50 in the deeper reduced zones. The deeper Ringold strata were characterized by a preponderance (c. 90%) of Proteobacteria. The bacterial community in the oxic sediments contained not only members of nine well-recognized phyla but also an unusually high proportion of three candidate divisions (GAL15, NC10 and SPAM). Additionally, 13 novel phylogenetic orders were identified within the Deltaproteobacteria, a clade rich in microbes that carry out redox transformations of metals that are important contaminants on the Hanford Site. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

77 FR 13133 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-05

... Infectious Diseases Special Emphasis Panel Integrated Preclinical/Clinical Program for HIV Topical..., and Transplantation Research; 93.856, Microbiology and Infectious Diseases Research, National...

78 FR 40756 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-08

... Infectious Diseases Special Emphasis Panel; Integrated Preclinical/Clinical AIDS Vaccine Development Program..., and Transplantation Research; 93.856, Microbiology and Infectious Diseases Research, National...

Micro-Eukaryote Diversity in Freshwater Ponds That Harbor the Amphibian Pathogen "Batrachochytrium Dendrobatidis" ("Bd")

ERIC Educational Resources Information Center

Lauer, Antje; McConnel, Lonnie; Singh, Navdeep

2012-01-01

We designed a microbiology project that fully engaged undergraduate biology students, high school students, and their teachers in a summer research program as part of the Research Education Vitalizing Science University Program conducted at California State University Bakersfield. Modern molecular biological methods and microscopy were used to…

Symposium: The Role of Biological Sciences in the Optometric Curriculum.

ERIC Educational Resources Information Center

And Others; Rapp, Jerry

1980-01-01

Papers from a symposium probing some of the curricular elements of the program in biological sciences at a school or college of optometry are provided. The overall program sequence in the biological sciences, microbiology, pharmacology, and the curriculum in the biological sciences from a clinical perspective are discussed. (Author/MLW)

77 FR 70724 - Eligibility of the Republic of Korea To Export Poultry Products to the United States

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-27

...) official controls over condemned product; (8) a Hazard Analysis and Critical Control Point (HACCP) system...) Hazard Analysis and Critical Control Point (HACCP) Systems, (5) Chemical Residue Testing Programs, and (6) Microbiological Testing Programs. FSIS evaluates the information submitted to verify that the critical points in...

Needs, opportunities and strategies for a long-term oceanic sciences satellite program

NASA Technical Reports Server (NTRS)

Ruttenberg, S. (Editor)

1981-01-01

Several areas of the National Oceanic Satellite System are addressed including Satellite-borne communication systems, subsurface remote sensing, data coordination, color scanners, formatting important historical data sets, and sea surface temperature observations.

IN SITU ENHANCED SOURCE REMOVAL

EPA Science Inventory

This html report describes and compares the performance of in situ technologies designed to accelerate the removal of organic contaminants from unconsolidated soils and aquifers. The research was conducted through the Enhanced Source Removal (ESR) Program within the Subsurface Pr...

Deep and Ultra-deep Underground Observatory for In Situ Stress, Fluids, and Life

NASA Astrophysics Data System (ADS)

Boutt, D. F.; Wang, H.; Kieft, T. L.

2008-12-01

The question 'How deeply does life extend into the Earth?' forms a single, compelling vision for multidisciplinary science opportunities associated with physical and biological processes occurring naturally or in response to construction in the deep and ultra-deep subsurface environment of the Deep Underground Science and Engineering Laboratory (DUSEL) in the former Homestake mine. The scientific opportunity is to understand the interaction between the physical environment and microbial life, specifically, the coupling among (1) stress state and deformation; (2) flow and transport and origin of fluids; and (3) energy and nutrient sources for microbial life; and (4) microbial identity, diversity and activities. DUSEL-Homestake offers the environment in which these questions can be addressed unencumbered by competing human activities. Associated with the interaction among these variables are a number of questions that will be addressed at variety of depths and scales in the facility: What factors control the distribution of life as a function of depth and temperature? What patterns in microbial diversity, microbial activity and nutrients are found along this gradient? How do state variables (stress, strain, temperature, and pore pressure) and constitutive properties (permeability, porosity, modulus, etc.) vary with scale (space, depth, time) in a large 4D heterogeneous system: core - borehole - drift - whole mine - regional? How are fluid flow and stress coupled in a low-permeability, crystalline environment dominated by preferential flow paths? How does this interaction influence the distribution of fluids, solutes, gases, colloids, and biological resources (e.g. energy and nutritive substrates) in the deep continental subsurface? What is the interaction between geomechanics/geohydrology and microbiology (microbial abundance, diversity, distribution, and activities)? Can relationships elucidated within the mechanically and hydrologically altered subsurface habitat of the Homestake DUSEL be extrapolated to the pristine subsurface biosphere? In the absence of extensive intrusive investigations (drifts, mines, etc), can we characterize hydrogeologic and geomechanical processes in the subsurface? To what depth can we effectively characterize such processes, and what is the confidence in our interpretations? In addition to addressing these question in the 10-km3 of mine volume, the Homestake facility offers the deepest drilling platform in North America. The extant depth of 8000 feet can be doubled by drilling. An array of three or more 8,200 ft. boreholes, wire-line drilled from the 8,000 ft. level at Homestake will probe to at least 16,200 ft. below land surface, a depth at this location approaching the expected lower biosphere limit (e.g. the 120°C isotherm). Cores will be collected aseptically and then fracture patterns (e.g., orientation, aperture, etc.) will be determined and fracture fluids will be intensively sampled over time. Cores and fracture fluids will be analyzed for indigenous microbial communities, including their genetic elements, metabolic processes, and biosignatures.

Snowmelt Induced Hydrologic Perturbations Drive Dynamic Microbiological and Geochemical Behaviors across a Shallow Riparian Aquifer

DOE PAGES

Danczak, Robert E.; Yabusaki, Steven B.; Williams, Kenneth H.; ...

2016-05-11

Shallow riparian aquifers represent hotspots of biogeochemical activity in the arid western US. While these environments provide extensive ecosystem services, little is known of how natural environmental perturbations influence subsurface microbial communities and associated biogeochemical processes. Over a 6-month period we tracked the annual snowmelt-driven incursion of groundwater into the vadose zone of an aquifer adjacent to the Colorado River, leading to increased dissolved oxygen (DO) concentrations in the normally suboxic saturated zone. Strong biogeochemical heterogeneity was measured across the site, with abiotic reactions between DO and sulfide minerals driving rapid DO consumption and mobilization of redox active species inmore » reduced aquifer regions. Conversely, extensive DO increases were detected in less reduced sediments. 16S rRNA gene surveys tracked microbial community composition within the aquifer, revealing strong correlations between increases in putative oxygen-utilizing chemolithoautotrophs and heterotrophs and rising DO concentrations. The gradual return to suboxic aquifer conditions favored increasing abundances of 16S rRNA sequences matching members of the Microgenomates (OP11) and Parcubacteria (OD1) that have been strongly implicated in fermentative processes. Microbial community stability measurements indicated that deeper aquifer locations were relatively less affected by geochemical perturbations, while communities in shallower locations exhibited the greatest change. Thus, reactive transport modeling of the geochemical and microbiological results supported field observations, suggesting that a predictive framework can be applied to develop a greater understanding of such environments.« less

Snowmelt Induced Hydrologic Perturbations Drive Dynamic Microbiological and Geochemical Behaviors across a Shallow Riparian Aquifer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Danczak, Robert E.; Yabusaki, Steven B.; Williams, Kenneth H.

Shallow riparian aquifers represent hotspots of biogeochemical activity in the arid western US. While these environments provide extensive ecosystem services, little is known of how natural environmental perturbations influence subsurface microbial communities and associated biogeochemical processes. Over a 6-month period we tracked the annual snowmelt-driven incursion of groundwater into the vadose zone of an aquifer adjacent to the Colorado River, leading to increased dissolved oxygen (DO) concentrations in the normally suboxic saturated zone. Strong biogeochemical heterogeneity was measured across the site, with abiotic reactions between DO and sulfide minerals driving rapid DO consumption and mobilization of redox active species inmore » reduced aquifer regions. Conversely, extensive DO increases were detected in less reduced sediments. 16S rRNA gene surveys tracked microbial community composition within the aquifer, revealing strong correlations between increases in putative oxygen-utilizing chemolithoautotrophs and heterotrophs and rising DO concentrations. The gradual return to suboxic aquifer conditions favored increasing abundances of 16S rRNA sequences matching members of the Microgenomates (OP11) and Parcubacteria (OD1) that have been strongly implicated in fermentative processes. Microbial community stability measurements indicated that deeper aquifer locations were relatively less affected by geochemical perturbations, while communities in shallower locations exhibited the greatest change. Thus, reactive transport modeling of the geochemical and microbiological results supported field observations, suggesting that a predictive framework can be applied to develop a greater understanding of such environments.« less

Communication Ambassadors—an Australian Social Media Initiative to Develop Communication Skills in Early Career Scientists

PubMed Central

Wang, Jack T. H.; Power, Cheryl J.; Kahler, Charlene M.; Lyras, Dena; Young, Paul R.; Iredell, Jonathan; Robins-Browne, Roy

2018-01-01

Science communication is a skill set to be developed through ongoing interactions with different stakeholders across a variety of platforms. Opportunities to engage the general public are typically reserved for senior scientists, but the use of social media in science communication allows all scientists to instantaneously disseminate their findings and interact with online users. The Communication Ambassador program is a social media initiative launched by the Australian Society for Microbiology to expand the online presence and science communication portfolios of early-career scientists. Through their participation in the program, a rotating roster of Australian microbiologists have broadened the online reach of the Society’s social media channels as well as their own professional networks by attending and live-tweeting microbiology events throughout the year. We present the Communication Ambassador program as a case study of coordinated social media activity in science communication to the general public, and describe the potential for its applications in science education and training. PMID:29904520

Communication Ambassadors-an Australian Social Media Initiative to Develop Communication Skills in Early Career Scientists.

PubMed

Wang, Jack T H; Power, Cheryl J; Kahler, Charlene M; Lyras, Dena; Young, Paul R; Iredell, Jonathan; Robins-Browne, Roy

2018-01-01

Science communication is a skill set to be developed through ongoing interactions with different stakeholders across a variety of platforms. Opportunities to engage the general public are typically reserved for senior scientists, but the use of social media in science communication allows all scientists to instantaneously disseminate their findings and interact with online users. The Communication Ambassador program is a social media initiative launched by the Australian Society for Microbiology to expand the online presence and science communication portfolios of early-career scientists. Through their participation in the program, a rotating roster of Australian microbiologists have broadened the online reach of the Society's social media channels as well as their own professional networks by attending and live-tweeting microbiology events throughout the year. We present the Communication Ambassador program as a case study of coordinated social media activity in science communication to the general public, and describe the potential for its applications in science education and training.

[Validation and verfication of microbiology methods].

PubMed

Camaró-Sala, María Luisa; Martínez-García, Rosana; Olmos-Martínez, Piedad; Catalá-Cuenca, Vicente; Ocete-Mochón, María Dolores; Gimeno-Cardona, Concepción

2015-01-01

Clinical microbiologists should ensure, to the maximum level allowed by the scientific and technical development, the reliability of the results. This implies that, in addition to meeting the technical criteria to ensure their validity, they must be performed with a number of conditions that allows comparable results to be obtained, regardless of the laboratory that performs the test. In this sense, the use of recognized and accepted reference methodsis the most effective tool for these guarantees. The activities related to verification and validation of analytical methods has become very important, as there is continuous development, as well as updating techniques and increasingly complex analytical equipment, and an interest of professionals to ensure quality processes and results. The definitions of validation and verification are described, along with the different types of validation/verification, and the types of methods, and the level of validation necessary depending on the degree of standardization. The situations in which validation/verification is mandatory and/or recommended is discussed, including those particularly related to validation in Microbiology. It stresses the importance of promoting the use of reference strains as controls in Microbiology and the use of standard controls, as well as the importance of participation in External Quality Assessment programs to demonstrate technical competence. The emphasis is on how to calculate some of the parameters required for validation/verification, such as the accuracy and precision. The development of these concepts can be found in the microbiological process SEIMC number 48: «Validation and verification of microbiological methods» www.seimc.org/protocols/microbiology. Copyright © 2013 Elsevier España, S.L.U. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

[Role of medium-sized independent laboratories in control of healthcare-associated infection].

PubMed

Anzai, Eiko; Fukui, Toru

2009-05-01

In 2006, the Ministry of Health and Welfare revised the regulations regarding the Medical Service Law. The amendments stipulate that all healthcare institutions are required to implement infection control programs. However, small hospitals and clinics have no clinical microbiology laboratories, whereas medium-sized hospitals have few medical technologists and the outsourcing of microbiology tests to independent laboratories is common. The decreasing number of laboratories and recent outsourcing tendency reflect the increasing commercialization, and, with it, the escalating number of commercially operating chains. Each independent laboratory is responsible for supporting activities related to the surveillance, control, and prevention of healthcare-associated infections in the associated small and medium-sized hospitals. The people responsible for infection control in these hospitals usually do not have a background in microbiology. The evaluation of communication between independent laboratory staff and hospital personnel, and rapid turnaround time of microbiology laboratory test reports are important elements ensuring the quality of independent laboratory work. With the pressures of financial constraints in the Japanese medical insurance system, the development of a cost-effective and practical protocol for quality assurance is a real dilemma.

76 FR 56207 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-12

... clearly unwarranted invasion of personal privacy. Name of Committee: Allergy, Immunology, and... Program Nos. 93.855, Allergy, Immunology, and Transplantation Research; 93.856, Microbiology and...

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

NASA Astrophysics Data System (ADS)

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

2011-12-01

The marine subsurface environment contains abundant and active microorganisms. These microbial populations are considered integral players in the marine subsurface biogeochemical system with significance in global geochemical cycles and reservoirs. However, variations in microbial community structure, activity and function associated with the wide-ranging sedimentary and geochemical environments found globally have not been fully resolved. Integrated Ocean Drilling Program Expedition 320 recovered sediments from site U1332. Two sampling depths were selected for analysis that spanned differing lithological units in the sediment core. Sediments were composed of mostly clay with zeolite minerals at 8 meters below sea floor (mbsf). At 27 mbsf, sediments were composed of alternating clayey radiolarian ooze and nannofossil ooze. The concentration of SO42- had little variability throughout the core and the concentration of Fe2+ remained close to, or below, detection limits (0.4 μM). Total organic carbon content ranged from a low of 0.03 wt% to a high of 0.07 wt% between 6 and 30 mbsf providing an opportunity to evaluate marine subsurface microbial communities under extreme electron donor limiting conditions. The metabolically active fraction of the bacterial population was isolated by the extraction and amplification of 16S ribosomal RNA. Pyrosequencing of 16S rRNA transcripts and subsequent bioinformatic analyses provided a robust data set (15,931 total classified sequences) to characterize the community at a high resolution. As observed in other subsurface environments, the overall diversity of active bacterial populations decreased with depth. The population shifted from a diverse but evenly distributed community at approximately 8 mbsf to a Firmicutes dominated population at 27 mbsf (80% of sequences). A total of 95% of the sequences at 27 mbsf were grouped into three genera: Lactobacillus (phylum Firmicutes) at 80% of the total sequences, Marinobacter (phylum Proteobacteria) at 8%, and Formosa (phylum Bacteroidetes) at 7%. These lineages support a paradigm suggesting the importance of fermentation in the subsurface. However, this study extends the predicted range for fermentation below the shallow subsurface and into organic carbon limited marine sediments. Other previously characterized subsurface active populations from environments with higher organic carbon concentrations do not show similar levels of reduced diversity or predominance of fermentative populations. This study further emphasizes the spatial variability of microbial populations in the deep subsurface and highlights the need for continued exploration.

Assessing and reducing hydrogeologic model uncertainty

USDA-ARS?s Scientific Manuscript database

NRC is sponsoring research that couples model abstraction techniques with model uncertainty assessment methods. Insights and information from this program will be useful in decision making by NRC staff, licensees and stakeholders in their assessment of subsurface radionuclide transport. All analytic...

78 FR 71628 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-29

... Diseases Special Emphasis Panel Immunology Quality Assessment (IQA) Program. Date: December 19, 2013. Time....855, Allergy, Immunology, and Transplantation Research; 93.856, Microbiology and Infectious Diseases...

78 FR 38065 - Center for Scientific Review; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-25

... Review Special Emphasis Panel; Fellowships: Infectious Diseases and Microbiology. Date: July 18-19, 2013... Domestic Assistance Program Nos. 93.306, Comparative Medicine; 93.333, Clinical Research, 93.306, 93.333...

77 FR 29678 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-18

... Infectious Diseases Special Emphasis Panel; ``Integrated Preclinical/Clinical Program for HIV Topical..., Microbiology and Infectious Diseases Research, National Institutes of Health, HHS) Dated: May 11, 2012...

Actinobacterial diversity across a marine transgression in the deep subsurface off Shimokita Peninsula, Japan

NASA Astrophysics Data System (ADS)

Harrison, B. K.; Bailey, J. V.

2013-12-01

Sediment horizons represent a significant - but not permanent - barrier to microbial transport. Cells commonly attach to mineral surfaces in unconsolidated sediments. However, by taxis, growth, or passive migration under advecting fluids, some portion of the microbial community may transgress sedimentary boundaries. Few studies have attempted to constrain such transport of community signatures in the marine subsurface and its potential impact on biogeography. Integrated Ocean Drilling Program (IODP) Expedition 337 off the Shimokita Peninsula recovered sediments over a greater than 1km interval representing a gradual decrease of terrestrial influence, from tidal to continental shelf depositional settings. This sequence represents a key opportunity to link subsurface microbial communities to lithological variability and investigate the permanence of community signatures characteristic of distinct depositional regimes. The phylogenetic connectivity between marine and terrestrially-influenced deposits may demonstrate to what degree sediments offer a substantial barrier to cell transport in the subsurface. Previous work has demonstrated that the Actinobacterial phylum is broadly distributed in marine sediments (Maldonado et al., 2005), present and active in the deep subsurface (Orsi et al., 2013), and that marine and terrestrial lineages may potentially be distinguished by 16S rRNA gene sequencing (e.g. Prieto-Davó et al., 2013). We report on Actinobacteria-specific 16S rRNA gene diversity recovered between 1370 and 2642 mbsf with high-throughput sequencing using the Illumina MiSeq platform, as well as selective assembly and analysis of environmental clone libraries.

Microbiological monitoring of marine recreational waters in southern California.

PubMed

Schiff, K C; Weisberg, S B; Dorsey, J H

2001-01-01

An inventory was conducted to assess the number, type, spatial distribution, and costs of microbiological monitoring programs in southern California marine waters from Point Conception to the US/Mexico International Border. The location of each sampling site was determined using global positioning system (GPS), and estimates of geographic coverage were determined using geographic information system (GIS) techniques. Twenty-one programs conducted 87,007 tests annually at 576 sites in the study area. The largest number of sites was sampled in Orange County, whereas the largest number of analyses was performed in Los Angeles County because monitoring programs in this area focused on daily monitoring. Fifteen of the 21 programs were managed by National Pollutant Discharge Elimination System (NPDES) permitted sewage effluent dischargers who sampled both offshore and shoreline waters and typically tested for three indicator bacteria (total coliform, fecal coliform, and enterococcus). Their combined efforts comprised 82% of all of the microbiological indicator analyses conducted on an annual basis. Five of the remaining monitoring organizations were public health agencies, which typically focus their efforts on testing only total coliforms. Laboratory methodology also varied considerably, with NPDES permittees predominantly utilizing membrane filtration while public health agencies generally used multiple tube fermentation or premanufactured test kits. Nearly three quarters of all the effort expended in southern California occurred along the shoreline as opposed to offshore locations. Two thirds of this shoreline effort was focused on high-use sandy beaches and in proximity to perennial fresh-water outlets (storm drains and creeks). Most sampling occurred at a set of fixed sites that were revisited frequently, but only represented about 7% of the total shoreline. We estimated that roughly $3 million is spent annually on monitoring bathing water quality in southern California, exceeding that spent in any other part of the country.

Mars Analog Rio Tinto Experiment (MARTE): An Experimental Demonstration of Key Technologies for Searching for Life on Mars

NASA Technical Reports Server (NTRS)

Stoker, Carol

2004-01-01

The discovery of near surface ground ice by the Mars Odyssey mission and the abundant evidence for recent Gulley features observed by the Mars Global Surveyor mission support longstanding theoretical arguments for subsurface liquid water on Mars. Thus, implementing the Mars program goal to search for life points to drilling on Mars to reach liquid water, collecting samples and analyzing them with instrumentation to detect in situ organisms and biomarker compounds. Searching for life in the subsurface of Mars will require drilling, sample extraction and handling, and new technologies to find and identify biomarker compounds and search for living organisms.

Microbial diversity within basement fluids of the sediment-buried Juan de Fuca Ridge flank

PubMed Central

Jungbluth, Sean P; Grote, Jana; Lin, Huei-Ting; Cowen, James P; Rappé, Michael S

2013-01-01

Despite its immense size, logistical and methodological constraints have largely limited microbiological investigations of the subseafloor basement biosphere. In this study, a unique sampling system was used to collect fluids from the subseafloor basaltic crust via a Circulation Obviation Retrofit Kit (CORK) observatory at Integrated Ocean Drilling Program borehole 1301A, located at a depth of 2667 m in the Pacific Ocean on the eastern flank of the Juan de Fuca Ridge. Here, a fluid delivery line directly accesses a 3.5 million years old basalt-hosted basement aquifer, overlaid by 262 m of sediment, which serves as a barrier to direct exchange with bottom seawater. At an average of 1.2 × 104 cells ml−1, microorganisms in borehole fluids were nearly an order of magnitude less abundant than in surrounding bottom seawater. Ribosomal RNA genes were characterized from basement fluids, providing the first snapshots of microbial community structure using a high-integrity fluid delivery line. Interestingly, microbial communities retrieved from different CORKs (1026B and 1301A) nearly a decade apart shared major community members, consistent with hydrogeological connectivity. However, over three sampling years, the dominant gene clone lineage changed from relatives of Candidatus Desulforudis audaxviator within the bacterial phylum Firmicutes in 2008 to the Miscellaneous Crenarchaeotic Group in 2009 and a lineage within the JTB35 group of Gammaproteobacteria in 2010, and statistically significant variation in microbial community structure was observed. The enumeration of different phylogenetic groups of cells within borehole 1301A fluids supported our observation that the deep subsurface microbial community was temporally dynamic. PMID:22791235

Implementation of gINT software at the Virginia Department of Transportation.

DOT National Transportation Integrated Search

2008-01-01

A set of software tools was developed to enable staff of the Virginia Department of Transportation (VDOT) and consultants to streamline processing of subsurface exploration data. Built around the gINT program (geotechnical database and graphics packa...

78 FR 78984 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-27

... Infectious Diseases Special Emphasis Panel; NIAID Clinical Trial Planning Grant (R34) and Clinical Trial... Assistance Program Nos. 93.855, Allergy, Immunology, and Transplantation Research; 93.856, Microbiology and...

77 FR 48165 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-13

... Emphasis Panel; Clinical Trials in Organ Transplantation in Children. Date: September 10-11, 2012. Time: 8... Program Nos. 93.855, Allergy, Immunology, and Transplantation Research; 93.856, Microbiology and...

78 FR 24761 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-26

... Infectious Diseases Special Emphasis Panel; ``Clinical Trials Units for NIAID Network'' (Meeting 2). Date... Assistance Program Nos. 93.855, Allergy, Immunology, and Transplantation Research; 93.856, Microbiology and...

Design and implementation of an external quality assessment program for HIV viral load measurements using dried blood spots.

PubMed

Prach, Lisa M; Puren, Adrian; Lippman, Sheri A; Carmona, Sergio; Stephenson, Sophie; Cutler, Ewalde; Barnhart, Scott; Liegler, Teri

2015-03-01

An external quality assurance program was developed for HIV-1 RNA viral load measurements taken from dried blood spots using a reference panel and field-collected specimens. The program demonstrated that accurate and reproducible quantitation can be obtained from field-collected specimens. Residual proviral DNA may confound interpretation in virologically suppressed subjects. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

[A historical view of the specialty of clinical microbiology].

PubMed

Pérez, Evelio Perea; Álvarez, Rogelio Martín

2010-10-01

Clinical microbiology today is a well established specialty in Spain whose development has necessarily been linked to improvements in the diagnosis, treatment and prevention of infectious diseases. Over time, clinical, teaching, and research structures have been organized around these diseases. In addition, a scientific society for specialists in infectious diseases (Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica) has been set up, which in turn, publishes the journal ENFERMEDADES INFECCIOSAS Y MICROBIOLOGÍA CLÍNICA, and organizes congresses, meetings, working groups and a quality control program, etc. Clinical microbiologists will continue to be needed to meet future challenges (identification of new pathogenic microorganisms, methodological changes, diagnostic quality and speed, nosocomial infections, the development of antimicrobial resistance, etc.), which constitute a well-defined area of knowledge specific to our specialty. Copyright © 2010 Elsevier España S.L. All rights reserved.

Cleaning and disinfection programs against Campylobacter jejuni for broiler chickens: productive performance, microbiological assessment and characterization1

PubMed Central

Deliberali Lelis, Karoline; Granghelli, Carlos Alexandre; Carão de Pinho, Agatha Cristina; Ribeiro Almeida Queiroz, Sabrina; Fernandes, Andrezza Maria; Moro de Souza, Ricardo Luiz; Gaglianone Moro, Maria Estela; de Andrade Bordin, Roberto; de Albuquerque, Ricardo

2017-01-01

Abstract Detailed cleaning and disinfection programs aims to reduce infection pressure from microorganisms from one flock to the next. However, studies evaluating the benefits to poultry performance, the sanitary status of the facilities, and the sanitary quality of the meat are rarely found. Thus, this study was designed to evaluate 2 cleaning and disinfecting programs regarding their influence on productive performance, elimination of Campylobacter, and characterization of Campylobacter jejuni strains when applied to broiler chickens’ facilities. Two subsequent flocks with 960 birds each were distributed into 32 pens containing 30 birds each. In the first, the whole flock was inoculated with a known strain of Campylobacter jejuni in order to contaminate the environment. In the second flock, performance and microbiological evaluations were done, characterizing an observational study between 2 cleaning and disinfection programs, regular and proposed. The regular program consisted of sweeping facilities, washing equipment and environment with water and neutral detergent. The proposed cleaning program consisted of dry and wet cleaning, application of 2 detergents (one acid and one basic) and 2 disinfectants (250 g/L glutaraldehyde and 185 g/L formaldehyde at 0.5% and 210 g/L para-chloro-meta-cresol at 4%). Total microorganism count in the environment and Campylobacter spp. identification were done for the microbiological assessment of the environment and carcasses. The positive samples were submitted to molecular identification of Campylobacter spp. and posterior genetic sequencing of the species identified as Campylobacter jejuni. The birds housed in the facilities and submitted to the proposed treatment had better performance when compared to the ones in the regular treatment, most likely because there was a smaller total microorganism count on the floor, walls, feeders and drinkers. The proposed program also resulted in a reduction of Campylobacter spp. on floors, drinkers and birds. Moreover, it was possible to identify 6 different Campylobacter jejuni strains in the facilities. The proposed treatment resulted in a positive influence on the birds’ performance and reduction of environment contamination for broiler chickens. PMID:28854757

Cleaning and disinfection programs against Campylobacter jejuni for broiler chickens: productive performance, microbiological assessment and characterization.

PubMed

Castro Burbarelli, Maria Fernanda de; do Valle Polycarpo, Gustavo; Deliberali Lelis, Karoline; Granghelli, Carlos Alexandre; Carão de Pinho, Agatha Cristina; Ribeiro Almeida Queiroz, Sabrina; Fernandes, Andrezza Maria; Moro de Souza, Ricardo Luiz; Gaglianone Moro, Maria Estela; de Andrade Bordin, Roberto; de Albuquerque, Ricardo

2017-09-01

Detailed cleaning and disinfection programs aims to reduce infection pressure from microorganisms from one flock to the next. However, studies evaluating the benefits to poultry performance, the sanitary status of the facilities, and the sanitary quality of the meat are rarely found. Thus, this study was designed to evaluate 2 cleaning and disinfecting programs regarding their influence on productive performance, elimination of Campylobacter, and characterization of Campylobacter jejuni strains when applied to broiler chickens' facilities. Two subsequent flocks with 960 birds each were distributed into 32 pens containing 30 birds each. In the first, the whole flock was inoculated with a known strain of Campylobacter jejuni in order to contaminate the environment. In the second flock, performance and microbiological evaluations were done, characterizing an observational study between 2 cleaning and disinfection programs, regular and proposed. The regular program consisted of sweeping facilities, washing equipment and environment with water and neutral detergent. The proposed cleaning program consisted of dry and wet cleaning, application of 2 detergents (one acid and one basic) and 2 disinfectants (250 g/L glutaraldehyde and 185 g/L formaldehyde at 0.5% and 210 g/L para-chloro-meta-cresol at 4%). Total microorganism count in the environment and Campylobacter spp. identification were done for the microbiological assessment of the environment and carcasses. The positive samples were submitted to molecular identification of Campylobacter spp. and posterior genetic sequencing of the species identified as Campylobacter jejuni. The birds housed in the facilities and submitted to the proposed treatment had better performance when compared to the ones in the regular treatment, most likely because there was a smaller total microorganism count on the floor, walls, feeders and drinkers. The proposed program also resulted in a reduction of Campylobacter spp. on floors, drinkers and birds. Moreover, it was possible to identify 6 different Campylobacter jejuni strains in the facilities. The proposed treatment resulted in a positive influence on the birds' performance and reduction of environment contamination for broiler chickens. © The Author 2017. Published by Oxford University Press on behalf of Poultry Science Association.

Estimating geological CO2 storage security to deliver on climate mitigation.

PubMed

Alcalde, Juan; Flude, Stephanie; Wilkinson, Mark; Johnson, Gareth; Edlmann, Katriona; Bond, Clare E; Scott, Vivian; Gilfillan, Stuart M V; Ogaya, Xènia; Haszeldine, R Stuart

2018-06-12

Carbon capture and storage (CCS) can help nations meet their Paris CO 2 reduction commitments cost-effectively. However, lack of confidence in geologic CO 2 storage security remains a barrier to CCS implementation. Here we present a numerical program that calculates CO 2 storage security and leakage to the atmosphere over 10,000 years. This combines quantitative estimates of geological subsurface CO 2 retention, and of surface CO 2 leakage. We calculate that realistically well-regulated storage in regions with moderate well densities has a 50% probability that leakage remains below 0.0008% per year, with over 98% of the injected CO 2 retained in the subsurface over 10,000 years. An unrealistic scenario, where CO 2 storage is inadequately regulated, estimates that more than 78% will be retained over 10,000 years. Our modelling results suggest that geological storage of CO 2 can be a secure climate change mitigation option, but we note that long-term behaviour of CO 2 in the subsurface remains a key uncertainty.

Properties of Subsurface Soil Cores from Four Geologic Provinces Surrounding Mars Desert Research Station, Utah: Characterizing Analog Martian Soil in a Human Exploration Scenario

NASA Technical Reports Server (NTRS)

Stoker, C. R.; Clarke, J. D. A.; Direito, S.; Foing, B.

2011-01-01

The DOMEX program is a NASA-MMAMA funded project featuring simulations of human crews on Mars focused on science activities that involve collecting samples from the subsurface using both manual and robotic equipment methods and analyzing them in the field and post mission. A crew simulating a human mission to Mars performed activities focused on subsurface science for 2 weeks in November 2009 at Mars Desert Research Station near Hanksville, Utah --an important chemical and morphological Mars analog site. Activities performed included 1) survey of the area to identify geologic provinces, 2) obtaining soil and rock samples from each province and characterizing their mineralogy, chemistry, and biology; 3) site selection and reconnaissance for a future drilling mission; 4) deployment and testing of Mars Underground Mole, a percussive robotic soil sampling device; and 5) recording and analyzing how crew time was used to accomplish these tasks. This paper summarizes results from analysis of soil cores

[The interplay of diagnostic and antimicrobial stewardship for the management of septic patients: the Tuscan model.

PubMed

Forni, Silvia; Toccafondi, Giulio; Viaggi, Bruno; Grazzini, Maddalena; D'Arienzo, Sara; Gemmi, Fabrizio; Vannucci, Andrea; Tulli, Giorgio

2018-02-01

Antimicrobial resistance is a global threat caused by the rapid spread of multiresistant microorganisms. Antimicrobial stewardship (AS) is a coordinated intervention designed to improve the appropriate use of antimicrobials by promoting the selection of the optimal drug regimen, dose, duration of therapy and route of administration. AS programs have proved effective in reducing antimicrobial resistance, inappropriate antimicrobial use and in improving patient outcomes. Recently developed rapid diagnostic technologies in microbiology (RDTM) allows a faster and etiological diagnosis of infection and a reduction in the use of unnecessary empirical therapies. This may result in important advancement in time-critical care pathways for septic patients. Nevertheless, RDTM are costly and if not rationally positioned may consume resources and hinder the efficacy of AS programs. In this regard, Tuscany Region is engaged in designing, through a systemic approach, an effective high-quality clinical microbiological service grid. In order to develop a sustainable and equitable model for integrating diagnostic and antimicrobial stewardship we conducted a survey in the regional network of 14 microbiological laboratories. The results shows that in order to develop a sustainable service we need to improve the communication at the interface between laboratories and care unit, harmonize the time windows for processing samples and to devise a robust score for stratifying patient with suspected sepsis.

Evaluation of Pharmacist Impact on Culture Review Process for Patients Discharged From the Emergency Department.

PubMed

Santiago, Ruben D; Bazan, Jose A; Brown, Nicole V; Adkins, Eric J; Shirk, Mary Beth

2016-10-01

Background: Accurate and timely review of microbiological test results is a core component of antimicrobial stewardship. There is documented success of these programs in the inpatient setting; however, emergency department (ED) patients are typically not included in these initiatives. Objectives: To assess the impact of an emergency medicine pharmacist (EMP)-facilitated review process of positive microbiological test results from patients discharged from the ED as measured by time to positive result review and number of indicated interventions completed. Methods: This was a retrospective study that compared EMP-facilitated to ED charge nurse (CN)-facilitated physician review of randomly selected positive microbiological test results. Groups were compared concurrently within the time frame of July 1, 2012 through December 31, 2012. Results: One hundred seventy-eight positive microbiological test results were included (EMP, n = 91; CN, n = 87). The median (IQR) time to initial review was 3 (1.0-6.3) hours for the EMP and 2 (0.3-5.5) hours for the CN group ( p = .35). Four percent (1/25) of indicated interventions were not completed in the EMP group versus 47% (14/30) in the CN group ( p = .0004). Conclusion: An EMP was significantly less likely to miss an intervention when indicated with no difference in time to review of positive microbiological results. These findings support the role of the EMP in antimicrobial stewardship in the ED.

Broadening Participation of Women and Underrepresented Minorities in STEM through a Hybrid Online Transfer Program

ERIC Educational Resources Information Center

Drew, Jennifer C.; Galindo-Gonzalez, Sebastian; Ardissone, Alexandria N.; Triplett, Eric W.

2016-01-01

The Microbiology and Cell Science (MCS) Department at the University of Florida (UF) developed a new model of a 2 + 2 program that uses a hybrid online approach to bring its science, technology, engineering, and mathematics (STEM) curriculum to students. In this paradigm, 2-year graduates transfer as online students into the Distance Education in…

Characterization of microbial communities in subsurface nuclear blast cavities of the Nevada Test Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moser, Duane P; Czerwinski, Ken; Russell, Charles E

2010-07-13

This US Department of Energy (DOE) Environmental Remediation Sciences Project (ERSP) was designed to test fundamental hypotheses concerning the existence and nature of indigenous microbial populations of Nevada Test Site subsurface nuclear test/detonation cavities. Now called Subsurface Biogeochemical Research (SBR), this program's Exploratory Research (ER) element, which funded this research, is designed to support high risk, high potential reward projects. Here, five cavities (GASCON, CHANCELLOR, NASH, ALEMAN, and ALMENDRO) and one tunnel (U12N) were sampled using bailers or pumps. Molecular and cultivation-based techniques revealed bacterial signatures at five sites (CHANCELLOR may be lifeless). SSU rRNA gene libraries contained diverse andmore » divergent microbial sequences affiliated with known metal- and sulfur-cycling microorganisms, organic compound degraders, microorganisms from deep mines, and bacteria involved in selenate reduction and arsenite oxidation. Close relatives of Desulforudis audaxviator, a microorganism thought to subsist in the terrestrial deep subsurface on H2 and SO42- produced by radiochemical reactions, was detected in the tunnel waters. NTS-specific media formulations were used to culture and quantify nitrate-, sulfate-, iron-reducing, fermentative, and methanogenic microorganisms. Given that redox manipulations mediated by microorganisms can impact the mobility of DOE contaminants, our results should have implications for management strategies at this and other DOE sites.« less

Analysis of Tank 38H (HTF-38-16-80, 81) and Tank 43H (HTF-43-16-82, 83) Samples for Support of the Enrichment Control and Corrosion Control Programs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hay, M.

2016-10-24

SRNL analyzed samples from Tank 38H and Tank 43H to support ECP and CCP. The total uranium in the Tank 38H surface sample was 57.6 mg/L, while the sub-surface sample was 106 mg/L. The Tank 43H samples ranged from 50.0 to 51.9 mg/L total uranium. The U-235 percentage was consistent for all four samples at 0.62%. The total uranium and percent U-235 results appear consistent with recent Tank 38H and Tank 43H uranium measurements. The Tank 38H plutonium results show a large difference between the surface and sub-surface sample concentrations and somewhat higher concentrations than previous samples. The Pu-238 concentrationmore » is more than forty times higher in the Tank 38H sub-surface sample than the surface sample. The surface and sub-surface Tank 43H samples contain similar plutonium concentrations and are within the range of values measured on previous samples. The four samples analyzed show silicon concentrations somewhat higher than the previous sample with values ranging from 104 to 213 mg/L.« less

NIGHTHAWK - A Program for Modeling Saturated Batch and Column Experiments Incorporating Equilibrium and Kinetic Biogeochemistry

EPA Science Inventory

NIGHTHAWK simulates the fate and transport of biogeochemically reactive contaminants in the saturated subsurface. Version 1.2 supports batch and one- dimensional advective-dispersive-reactive transport involving a number of biogeochemical processes, including: microbially-mediate...

Evaluation of Subsurface Engineered Barriers at Waste Sites Volumes 1 and 2

EPA Pesticide Factsheets

This report provides the U.S. Environmental Protection Agency’s (EPA) waste programs with a national retrospective analysis of barrier field performance, as well as information that useful in developing guidance on the use and evaluation of barrier systems

18 CFR 4.41 - Contents of application.

Code of Federal Regulations, 2012 CFR

2012-04-01

... regarding the acceptability of the recommendations; (ii) The results of surveys, inventories, and subsurface... educational facilities and programs; (iv) On-site manpower requirements and payroll during and after project... incremental local government revenues that would result from the construction of the proposed project...

18 CFR 4.41 - Contents of application.

Code of Federal Regulations, 2011 CFR

2011-04-01

... regarding the acceptability of the recommendations; (ii) The results of surveys, inventories, and subsurface... educational facilities and programs; (iv) On-site manpower requirements and payroll during and after project... incremental local government revenues that would result from the construction of the proposed project...

18 CFR 4.41 - Contents of application.

Code of Federal Regulations, 2013 CFR

2013-04-01

... regarding the acceptability of the recommendations; (ii) The results of surveys, inventories, and subsurface... educational facilities and programs; (iv) On-site manpower requirements and payroll during and after project... incremental local government revenues that would result from the construction of the proposed project...

18 CFR 4.41 - Contents of application.

Code of Federal Regulations, 2010 CFR

2010-04-01

... regarding the acceptability of the recommendations; (ii) The results of surveys, inventories, and subsurface... educational facilities and programs; (iv) On-site manpower requirements and payroll during and after project... incremental local government revenues that would result from the construction of the proposed project...

18 CFR 4.41 - Contents of application.

Code of Federal Regulations, 2014 CFR

2014-04-01

... regarding the acceptability of the recommendations; (ii) The results of surveys, inventories, and subsurface... educational facilities and programs; (iv) On-site manpower requirements and payroll during and after project... incremental local government revenues that would result from the construction of the proposed project...

ISCO'S LONG-TERM IMPACT ON AQUIFER CONDITIONS AND MICROBIAL ACTIVITY

EPA Science Inventory

Potential for lasting negative environmental effects has clouded remediation programs using permanganate and other oxidants. A major concern about using In-Situ Chemical Oxidation (ISCO) for remediation of CVOCs is that application of strong oxidants to subsurface systems may pe...

OPTIMIZATION OF IN-SITU THERMAL REMEDIATION: THE LORING AFB STEAM INJECTION PROJECT EXAMPLE

EPA Science Inventory

Environmental remediation programs require that adequate planning be done before field work for characterization or remediation is undertaken. However, the heterogeneous nature of the subsurface can often thwart our best planning efforts. More recently, dynamic work plans which...

Understanding and preventing tick bites | NIH MedlinePlus the Magazine

MedlinePlus

... Disease Research Program Officer in NIAID's Division of Microbiology and Infectious Diseases, said it is important to ... the importance of a sensitive and specific diagnostic test for Lyme disease, particularly to detect it early. ...

76 FR 8753 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-15

...; ``Integrated Preclinical/Clinical AIDS Vaccine Development Program.'' Date: March 9, 2011. Time: 8:30 a.m. to 5... Transplantation Research; 93.856, Microbiology and Infectious Diseases Research, National Institutes of Health...

EPA METHOD STUDY 8, TOTAL MERCURY IN WATER

EPA Science Inventory

The Environmental Monitoring and Support Laboratory-Cincinnati of EPA conducts EPA's quality assurance program for the water laboratories and assists EPA laboratories in the choice of methods for physical, chemical, biological and microbiological analyses. The responsibility for ...

7 CFR 91.4 - Kinds of services.

Code of Federal Regulations, 2014 CFR

2014-01-01

... in performing commodity testing services. (c) Quality assurance reviews. The Science and Technology..., Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE (CONTINUED) COMMODITY LABORATORY TESTING PROGRAMS.... Analytical laboratory testing services under the regulations in this subchapter consist of microbiological...

7 CFR 91.4 - Kinds of services.

Code of Federal Regulations, 2011 CFR

2011-01-01

... in performing commodity testing services. (c) Quality assurance reviews. The Science and Technology..., Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE (CONTINUED) COMMODITY LABORATORY TESTING PROGRAMS.... Analytical laboratory testing services under the regulations in this subchapter consist of microbiological...

7 CFR 91.4 - Kinds of services.

Code of Federal Regulations, 2012 CFR

2012-01-01

... in performing commodity testing services. (c) Quality assurance reviews. The Science and Technology..., Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE (CONTINUED) COMMODITY LABORATORY TESTING PROGRAMS.... Analytical laboratory testing services under the regulations in this subchapter consist of microbiological...

7 CFR 91.4 - Kinds of services.

Code of Federal Regulations, 2013 CFR

2013-01-01

... in performing commodity testing services. (c) Quality assurance reviews. The Science and Technology..., Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE (CONTINUED) COMMODITY LABORATORY TESTING PROGRAMS.... Analytical laboratory testing services under the regulations in this subchapter consist of microbiological...

115-year-old society knows how to reach young scientists: ASM Young Ambassador Program.

PubMed

Karczewska-Golec, Joanna

2015-12-25

With around 40,000 members in more than 150 countries, American Society for Microbiology (ASM) faces the challenge of meeting very diverse needs of its increasingly international members base. The newly launched ASM Young Ambassador Program seeks to aid the Society in this effort. Equipped with ASM conceptual support and financing, Young Ambassadors (YAs) design and pursue country-tailored approaches to strengthen the Society's ties with local microbiological communities. In a trans-national setting, the active presence of YAs at important scientific events, such as 16th European Congress on Biotechnology, forges new interactions between ASM and sister societies. The paper presents an overview of the Young Ambassadors-driven initiatives at both global and country levels, and explores the topic of how early-career scientists can contribute to science diplomacy and international relations. Copyright © 2014 Elsevier B.V. All rights reserved.

2D Time-lapse Resistivity Monitoring of an Organic Produced Gas Plume in a Landfill using ERT.

NASA Astrophysics Data System (ADS)

Amaral, N. D.; Mendonça, C. A.; Doherty, R.

2014-12-01

This project has the objective to study a landfill located on the margins of Tietê River, in São Paulo, Brazil, using the electroresistivity tomography method (ERT). Due to huge organic matter concentrations in the São Paulo Basin quaternary sediments, there is subsurface depth related biogas accumulation (CH4 and CO2), induced by anaerobic degradation of the organic matter. 2D resistivity sections were obtained from a test area since March 2012, a total of 7 databases, being the last one dated from October 2013. The studied line has the length of 56m, the electrode interval is of 2m. In addition, there are two boreholes along the line (one with 3 electrodes and the other one with 2) in order to improve data quality and precision. The boreholes also have a multi-level sampling system that indicates the fluid (gas or water) presence in relation to depth. With our results it was possible to map the gas plume position and its area of extension in the sections as it is a positive resistivity anomaly, with the gas level having approximately 5m depth. With the time-lapse analysis (Matlab script) between the obtained 2D resistivity sections from the site, it was possible to map how the biogas volume and position change in the landfill in relation to time. Our preliminary results show a preferential gas pathway through the subsurface studied area. A consistent relation between the gas depth and obtained microbiological data from archea and bacteria population was also observed.

Geochemical and microbiological responses to oxidant introduction into reduced subsurface sediment from the Hanford 300 Area, Washington.

PubMed

Percak-Dennett, Elizabeth M; Roden, Eric E

2014-08-19

Pliocene-aged reduced lacustrine sediment from below a subsurface redox transition zone at the 300 Area of the Hanford site (southeastern Washington) was used in a study of the geochemical response to introduction of oxygen or nitrate in the presence or absence of microbial activity. The sediments contained large quantities of reduced Fe in the form of Fe(II)-bearing phyllosilicates, together with smaller quantities of siderite and pyrite. A loss of ca. 50% of 0.5 M HCl-extractable Fe(II) [5-10 mmol Fe(II) L(-1)] and detectable generation of sulfate (ca. 0.2 mM, equivalent to 10% of the reduced inorganic sulfur pool) occurred in sterile aerobic reactors. In contrast, no systematic loss of Fe(II) or production of sulfate was observed in any of the other oxidant-amended sediment suspensions. Detectable Fe(II) accumulation and sulfate consumption occurred in non-sterile oxidant-free reactors. Together, these results indicate the potential for heterotrophic carbon metabolism in the reduced sediments, consistent with the proliferation of known heterotrophic taxa (e.g., Pseudomonadaceae, Burkholderiaceae, and Clostridiaceae) inferred from 16S rRNA gene pyrosequencing. Microbial carbon oxidation by heterotrophic communities is likely to play an important role in maintaining the redox boundary in situ, i.e., by modulating the impact of downward oxidant transport on Fe/S redox speciation. Diffusion-reaction simulations of oxygen and nitrate consumption coupled to solid-phase organic carbon oxidation indicate that heterotrophic consumption of oxidants could maintain the redox boundary at its current position over millennial time scales.

Transport and removal of viruses in saturated sand columns under oxic and anoxic conditions--Potential implications for groundwater protection.

PubMed

Frohnert, Anne; Apelt, Susann; Klitzke, Sondra; Chorus, Ingrid; Szewzyk, Regine; Selinka, Hans-Christoph

2014-11-01

To protect groundwater as a drinking water resource from microbiological contamination, protection zones are installed. While travelling through these zones, concentrations of potential pathogens should decline to levels that pose no risks to human health. Removal of viruses during subsurface passage is influenced by physicochemical conditions, such as oxygen concentration, which also affects virus survival. The aim of our study was to evaluate the effect of redox conditions on the removal of viruses during sand filtration. Experiments in glass columns filled with medium-grained sand were conducted to investigate virus removal in the presence and absence of dissolved oxygen. Bacteriophages MS2 and PhiX174, as surrogates for human enteric viruses were spiked in pulsed or in continuous mode and pumped through the columns at a filter velocity of about 1m/d. Virus breakthrough curves were analyzed by calculating total viral elimination and fitted using one-dimensional transport models (CXTFIT and HYDRUS-1D). While short-term experiments with pulsed virus application showed only small differences with regard to virus removal under oxic and anoxic conditions, a long-term experiment with continuous dosing revealed a clearly lower elimination of viruses under anoxic conditions. These findings suggest that less inactivation and less adsorption of viruses in anoxic environments affect their removal. Therefore, in risk assessment studies aimed to secure drinking water resources from viral contamination and optimization of protection zones, the oxic and anoxic conditions in the subsurface should also be considered. Copyright © 2014 Elsevier GmbH. All rights reserved.

Optimal conditions for chlorothalonil and dissolved organic carbon in horizontal subsurface flow constructed wetlands.

PubMed

Rìos-Montes, Karina A; Casas-Zapata, Juan C; Briones-Gallardo, Roberto; Peñuela, Gustavo

2017-04-03

The most efficient system of horizontal subsurface flow constructed wetlands (HSSFCW) for removing dissolved organic carbon (DOC) in the presence of chlorothalonil pesticide (CLT) present in synthetic domestic wastewater was determined using the macrophyte Phragmites australis. Two concentrations of CLT (85 and 385 μg L -1 ) and one concentration of glucose (20 mg L -1 ) were evaluated in four pilot scale horizontal surface flow constructed wetlands coupled with two sizes of silica gravel, igneous gravel, fine chalky gravel (3.18-6.35 mm), coarse gravel (12.70-25.40 mm) and two water surface heights (20 and 40 cm). For a month, wetlands were acclimated with domestic wastewater. Some groups of bacteria were also identified in the biofilm attached to the gravel. In each treatment periodic samplings were conducted in the influent and effluent. Chlorothalonil was quantified by gas chromatography (GC-ECD m), DOC by an organic carbon analyzer and bacterial groups using conventional microbiology in accordance with Standard Methods. The largest removals of DOC (85.82%-85.31%) were found when using fine gravel (3.18-6.35 mm) and the lower layer of water (20 cm). The bacterial groups quantified in the biofilm were total heterotrophic, revivable heterotrophic, Pseudomonas and total coliforms. The results of this study indicate that fine grain gravel (3.18-6.35 mm) and both water levels (20 to 40 cm) can be used in the removal of organic matter and for the treatment of agricultural effluents contaminated with organo-chloride pesticides like CLT in HSSFCW.

Anaerobic biodegradation of partially hydrolyzed polyacrylamide in long-term methanogenic enrichment cultures from production water of oil reservoirs.

PubMed

Hu, Hao; Liu, Jin-Feng; Li, Cai-Yun; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong

2018-06-01

The increasing usage of partially hydrolyzed polyacrylamide (HPAM) in oilfields as a flooding agent to enhance oil recovery at so large quantities is an ecological hazard to the subsurface ecosystem due to persistence and inertness. Biodegradation of HPAM is a potentially promising strategy for dealing with this problem among many other methods available. To understand the responsible microorganisms and mechanism of HPAM biodegradation under anaerobic conditions, an enrichment culture from production waters of oil reservoirs were established with HPAM as the sole source of carbon and nitrogen incubated for over 328 days, and analyzed using both molecular microbiology and chemical characterization methods. Gel permeation chromatography, High-pressure liquid chromatography and Fourier-transformed infrared spectroscopy results indicated that, after 328 days of anaerobic incubation, some of the amide groups on HPAM were removed and released as ammonia/ammonium and carboxylic groups, while the carbon backbone of HPAM was converted to smaller polymeric fragments, including oligomers and various fatty acids. Based on these results, the biochemical process of anaerobic biodegradation of HPAM was proposed. The phylogenetic analysis of 16S rRNA gene sequences retrieved from the enrichments showed that Proteobacteria and Planctomycetes were the dominant bacteria in the culture with HPAM as the source of carbon and nitrogen, respectively. For archaea, Methanofollis was more abundant in the anaerobic enrichment. These results are helpful for understanding the process of HPAM biodegradation and provide significant insights to the fate of HPAM in subsurface environment and for possible bioremediation.

Subsurface geomicrobiology in a Mars terrestrial analogue, Río Tinto (SW, Spain)

NASA Astrophysics Data System (ADS)

Amils, R.; Fernández-Remolar, D.; Gómez, F.; González-Toril, E.; Rodríguez, N.; Prieto-Ballesteros, O.; Sanz, J. L.; Díaz, E.; Stoker, C.

2008-09-01

Since its discovery, only few years ago, subsurface geomicrobiology is a matter of growing interest [1]. From a fundamental point of view, it seeks to determine whether life can be sustained in the absence of radiation. From an astrobiological point of view, it is an interesting model for life in other planetary bodies, e.g., Mars, as well as early life on Earth. Río Tinto is an unusual extreme acidic environment due to its size (around 100 km), constant acidic pH (mean pH 2.3), high concentrations of heavy metals and high level of microbial diversity [2]. Río Tinto rises in the core of the Iberian Pyritic Belt, one of the biggest sulfidic ore deposits in the world [3]. Today it is well stablished that the extreme characteristics of Río Tinto are not due to acid mine drainage from mining activity, as has been suggested in the past. To explore the hypothesis that a continuous underground reactor of chemolithotrophic microorganisms thriving in the rich sulfidic minerals of the Iberian Pyritic Belt is responsible for the extreme conditions found in the system, a drilling project has been developed to detect evidence of subsurface microbial activity and potential resources to support these microbial communities in situ (MARTE project) [4]. Here we report a search for subsurface life in volcanically hosted massive sulfidic deposits from the Iberian Pyritic Belt. Aseptic core samples were obtained within and down-gradient from the massive sulfide deposits and formation water was sampled within the resulting bore holes. Microbial activity was detected in un-contaminated samples by culture-dependent and culture-independent methods. Aerobic iron- and sulfide- oxidizing bacteria, and anaerobic denitrifying thiosulfate-oxidizing bacteria, sulfate reducing bacteria and methanogenic archaea have been identified. Potential energy fluxes detected in the system include oxidation of reduced iron and sulfur, or hydrogen gas coupled to nitrite, sulfate, ferric iron, inorganic carbon or transient oxygen. These results suggest that multiple energy sources are available from sulfide-mineral weathering to support microbial metabolism, even in the absence of atmospheric oxygen. [1] Stevens, T.O and McKinley, J.P. (1995) Scienc,, 270, 450-454. [2] Amis, R. et al. (2007) Planet Space Sci, 55, 370- 381. [3] Fernández-Remolar, D. et al. (2005) Earth Planet Sci Lett, 240, 149-167. [4] Amils, R. et al. (2008) Microbiology of Extreme Soils, 205-223.

Subsurface Exploration Methods for Soft Ground Rapid Transit Tunnels : Volume 1. Sections 1-6 and references.

DOT National Transportation Integrated Search

1976-04-01

The objectives of the Urban Mass Transportation Administration (UMTA) Tunneling Program are to lower subway construction costs and reduce construction hazards and damage to the environment. Some measure of each of these objectives for bored tunnels a...

10 CFR 60.141 - Confirmation of geotechnical and design parameters.

Code of Federal Regulations, 2012 CFR

2012-01-01

... reported to the Commission. (e) In situ monitoring of the thermomechanical response of the underground... IN GEOLOGIC REPOSITORIES Performance Confirmation Program § 60.141 Confirmation of geotechnical and... needed in design to accommodate actual field conditions encountered. (b) Subsurface conditions shall be...

10 CFR 60.141 - Confirmation of geotechnical and design parameters.

Code of Federal Regulations, 2014 CFR

2014-01-01

... reported to the Commission. (e) In situ monitoring of the thermomechanical response of the underground... IN GEOLOGIC REPOSITORIES Performance Confirmation Program § 60.141 Confirmation of geotechnical and... needed in design to accommodate actual field conditions encountered. (b) Subsurface conditions shall be...

10 CFR 60.141 - Confirmation of geotechnical and design parameters.

Code of Federal Regulations, 2013 CFR

2013-01-01

... reported to the Commission. (e) In situ monitoring of the thermomechanical response of the underground... IN GEOLOGIC REPOSITORIES Performance Confirmation Program § 60.141 Confirmation of geotechnical and... needed in design to accommodate actual field conditions encountered. (b) Subsurface conditions shall be...

Monitoring of subsurface injection of wastes, Florida

USGS Publications Warehouse

Vecchioli, John

1979-01-01

Injection of waste liquids into Florida's subsurface is physically feasible in many places but should be accompanied by monitoring of the waste-receiving aquifer system in addition to the injection facility. Monitoring of the interaction of factors including hydrogeologic conditions, well construction, waste volumes and characteristics, and potable-water sources is desirable to assure that fresh-water resources are not being adversely affected. An effective aquifer-system monitoring program includes on-site wells located close to an injection well and open to the next-higher permeable stratum, satellite wells located hundreds to several thousands of feet from an injection well and open to the receiving aquifer, and regional wells located miles from individual injection wells and open to the receiving aquifer. An extensive aquifer-system monitoring program associated with two waste-injection facilities near Pensacola, Florida, has provided data which have aided hydrologists to understand the aquifer system's response to the injection and, accordingly, to evaluate the potential for affecting the area's fresh-water resources.

78 FR 9931 - Center for Scientific Review; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-12

...: Topics in Microbiology. Date: February 18, 2013. Time: 11:00 a.m. to 12:00 p.m. Agenda: To review and... Federal Domestic Assistance Program Nos. 93.306, Comparative Medicine; 93.333, Clinical Research, 93.306...

Controlling Subsurface Fractures and Fluid Flow: A Basic Research Agenda

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pyrak-Nolte, Laura J; DePaolo, Donald J.; Pietraß, Tanja

2015-05-22

From beneath the surface of the earth, we currently obtain about 80-percent of the energy our nation consumes each year. In the future we have the potential to generate billions of watts of electrical power from clean, green, geothermal energy sources. Our planet’s subsurface can also serve as a reservoir for storing energy produced from intermittent sources such as wind and solar, and it could provide safe, long-term storage of excess carbon dioxide, energy waste products and other hazardous materials. However, it is impossible to underestimate the complexities of the subsurface world. These complexities challenge our ability to acquire themore » scientific knowledge needed for the efficient and safe exploitation of its resources. To more effectively harness subsurface resources while mitigating the impacts of developing and using these resources, the U.S. Department of Energy established SubTER – the Subsurface Technology and Engineering RD&D Crosscut team. This DOE multi-office team engaged scientists and engineers from the national laboratories to assess and make recommendations for improving energy-related subsurface engineering. The SubTER team produced a plan with the overall objective of “adaptive control of subsurface fractures and fluid flow.”This plan revolved around four core technological pillars—Intelligent Wellbore Systems that sustain the integrity of the wellbore environment; Subsurface Stress and Induced Seismicity programs that guide and optimize sustainable energy strategies while reducing the risks associated with subsurface injections; Permeability Manipulation studies that improve methods of enhancing, impeding and eliminating fluid flow; and New Subsurface Signals that transform our ability to see into and characterize subsurface systems. The SubTER team developed an extensive R&D plan for advancing technologies within these four core pillars and also identified several areas where new technologies would require additional basic research. In response, the Office of Science, through its Office of Basic Energy Science (BES), convened a roundtable consisting of 15 national lab, university and industry geoscience experts to brainstorm basic research areas that underpin the SubTER goals but are currently underrepresented in the BES research portfolio. Held in Germantown, Maryland on May 22, 2015, the round-table participants developed a basic research agenda that is detailed in this report. Highlights include the following: -A grand challenge calling for advanced imaging of stress and geological processes to help understand how stresses and chemical substances are distributed in the subsurface—knowledge that is critical to all aspects of subsurface engineering; -A priority research direction aimed at achieving control of fluid flow through fractured media; -A priority research direction aimed at better understanding how mechanical and geochemical perturbations to subsurface rock systems are coupled through fluid and mineral interactions; -A priority research direction aimed at studying the structure, permeability, reactivity and other properties of nanoporous rocks, like shale, which have become critical energy materials and exhibit important hallmarks of mesoscale materials; -A cross-cutting theme that would accelerate development of advanced computational methods to describe heterogeneous time-dependent geologic systems that could, among other potential benefits, provide new and vastly improved models of hydraulic fracturing and its environmental impacts; -A cross-cutting theme that would lead to the creation of “geo-architected materials” with controlled repeatable heterogeneity and structure that can be tested under a variety of thermal, hydraulic, chemical and mechanical conditions relevant to subsurface systems; -A cross-cutting theme calling for new laboratory studies on both natural and geo-architected subsurface materials that deploy advanced high-resolution 3D imaging and chemical analysis methods to determine the ;rates and mechanisms of fluid-rock processes, and to test predictive models of such phenomena. Many of the key energy challenges of the future demand a greater understanding of the subsurface world in all of its complexity. This greater under- standing will improve the ability to control and manipulate the subsurface world in ways that will benefit both the economy and the environment. This report provides specific basic research pathways to address some of the most fundamental issues of energy-related subsurface engineering.« less

Exuberant mucometra associated with atresia of the cervix in a queen.

PubMed

Batista-Arteaga, M; Santana, M; Espinosa-de-los-Monteros, A; Déniz, S; Alamo, D; Herráez, P

2012-10-01

This short communication reports the clinical, ultrasonographic and histopathological findings in a cat with atresia of the uterine cervix and mucometra. After 6 months of continuous oestrous behaviour, a remarkable abdominal enlargement was observed in a 14-year-old queen. A presumptive diagnosis of mucometra was concluded after the ultrasound evaluation and based on clinical signs and blood analyses. Ovariohysterectomy revealed a notable symmetrical distension (4-5 cm in diameter) of both uterine horns that were filled with fluid (690 ml); microbiological analyses confirmed the aseptic nature of the uterine fluid. Ovarian follicular cysts and cystic subsurface epithelial structures, >1.5 cm in diameter, were present in both ovaries and no corpora lutea were observed. Gross and microscopic evaluation of the uterus confirmed the development of cystic endometrial hyperplasia and the absence of an internal cervical os. The endometrial hyperplasia and mucometra could have developed as a consequence of repeated oestrogenic stimulation. © 2011 Blackwell Verlag GmbH.

Connectivity between surface and deep waters determines prokaryotic diversity in the North Atlantic Deep Water.

PubMed

Frank, Alexander H; Garcia, Juan A L; Herndl, Gerhard J; Reinthaler, Thomas

2016-06-01

To decipher the influence of depth stratification and surface provincialism on the dark ocean prokaryotic community composition, we sampled the major deep-water masses in the eastern North Atlantic covering three biogeographic provinces. Their diversity was evaluated using ordination and canonical analysis of 454 pyrotag sequences. Variance partitioning suggested that 16% of the variation in the bacterial community composition was based on depth stratification while 9% of the variation was due to geographic location. General linear mixed effect models showed that the community of the subsurface waters was connected to the dark ocean prokaryotic communities in different biogeographic provinces. Cluster analysis indicated that some prokaryotic taxa are specific to distinct regions in bathypelagic water masses. Taken together, our data suggest that the dark ocean prokaryotic community composition of the eastern North Atlantic is primed by the formation and the horizontal transport of water masses. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Use of PRD1 bacteriophage in groundwater viral transport, inactivation, and attachment studies

USGS Publications Warehouse

Harvey, R.W.; Ryan, J.N.

2004-01-01

PRD1, an icosahedra-shaped, 62 nm (diameter), double-stranded DNA bacteriophage with an internal membrane, has emerged as an important model virus for studying the manner in which microorganisms are transported through a variety of groundwater environments. The popularity of this phage for use in transport studies involving geologic media is due, in part, to its relative stability over a range of temperatures and low degree of attachment in aquifer sediments. Laboratory and field investigations employing PRD1 are leading to a better understanding of viral attachment and transport behaviors in saturated geologic media and to improved methods for describing mathematically subsurface microbial transport at environmentally significant field scales. Radioisotopic labeling of PRD1 is facilitating additional information about the nature of viral interactions with solid surfaces in geologic media, the importance of iron oxide surfaces, and allowing differentiation between inactivation and attachment in field-scale tracer tests. ?? 2004 Published by Elsevier B.V. on behalf of the Federation of European Microbiological Societies.

Removal and factors influencing removal of sulfonamides and trimethoprim from domestic sewage in constructed wetlands.

PubMed

Dan A; Yang, Yang; Dai, Yu-Nv; Chen, Chun-Xing; Wang, Su-Yu; Tao, Ran

2013-10-01

Twelve pilot-scale constructed wetlands with different configurations were set up in the field to evaluate the removal and factors that influence removal of sulfonamides (sulfadiazine, sulfapyridine, sulfacetamide, sulfamethazine and sulfamethoxazole) and trimethoprim from domestic sewage. The treatments included four flow types, three substrates, two plants and three hydraulic loading rates across two seasons (summer and winter). Most target antibiotics were efficiently removed by specific constructed wetlands; in particular, all types of constructed wetlands performed well for the degradation of sulfapyridine. Flow types were the most important influencing factor in this study, and the best removal of sulfonamides was achieved in vertical subsurface-flow constructed wetlands; however, the opposite phenomenon was found with trimethoprim. Significant relationships were observed between antibiotic degradation and higher temperature and redox potential, which indicated that microbiological pathways were the most probable degradation route for sulfonamides and trimethoprim in constructed wetlands. Copyright © 2013 Elsevier Ltd. All rights reserved.

Identification of subsurface microorganisms at Yucca Mountain. Quarterly report, July 1, 1995--September 30, 1995

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stetzenbach, L.D.

1995-12-01

More than 1100 bacterial isolates were obtained over a two year period from 31 springs in a region along the southern boarder of California and Nevada. Water samples were collected from 17 springs in Ash Meadows National Wildlife Refuge and 14 springs in Death Valley National Park. Bacteria isolated from these samples were subjected to extraction and gas chromatography to determine the cellular fatty acid profile of each isolate. Fatty acid methyl esters (FAME) extracted from cell membranes were separated and classified using the Hewlett Packard by gas chromatography. The FAME profiles of each isolate were then subjected to clustermore » analysis by the unweighted pair-group method using arithmetic averages. During this quarter the relatedness of FAME patterns of bacterial isolates were examined at the genus level by counting the number of clusters produced in a MIDI dendrogram at a Euclidian distance of 25. This information was then used to determine microbiological relationships among springs.« less

Assessment of groundwater pathways and contaminant transport in Florida and Georgia using multiple chemical and microbiological indicators

USGS Publications Warehouse

Mahon, Gary L.

2011-01-01

The hydrogeology of Florida, especially in the northern part of the state, and southwestern Georgia is characterized by a predominance of limestone aquifers overlain by varying amounts of sands, silts, and clays. This karstic system of aquifers and their associated springs is particularly vulnerable to contamination from various anthropogenic activities at the land surface. Numerous sinkholes, disappearing streams, and conduit systems or dissolution pathways, often associated with large spring systems, allow rapid movement of contaminants from the land surface to the groundwater system with little or no attenuation or degradation. The fate of contaminants in the groundwater system is not fully understood, but traveltimes from sources are greatly reduced when conduits are intercepted by pumping wells and springs. Contaminant introduction to groundwater systems in Florida and Georgia is not limited to seepage from land surface, but can be associated with passive (drainage wells) and forced subsurface injection (aquifer storage and recovery, waste-water disposal).

Mars Sulfur: A Review of Landed Mission Data (Invited)

NASA Astrophysics Data System (ADS)

Sutter, B.; Ming, D. W.; Niles, P. B.

2013-12-01

Sulfur (S) has been detected (1.0 - 36 wt. % SO3) in martian surface materials at the Viking, Pathfinder, Mars Exploration Rovers (MER), Phoenix, and Mars Science Laboratory (MSL) landing sites. The accumulation of S at these landing sites is attributed to the hyperarid martian climate that inhibits dissolution and leaching of surface S into the subsurface. The S cycle involving sources, sinks, and the processes involved in redistributing S after initial deposition are not well constrained. This work reviews the state of knowledge of S as derived from landed missions. Results suggest that aqueous processes have been involved in the S cycling suggesting that conditions may have been favorable microbiology. Chemical data and the apparent oxidizing condition of the soil suggest that the Viking and Pathfinder soils consist of Mg-sulfate and possible Fe-sulfate. Sulfur-rich soils (up to 36 wt. % SO3) in Gusev crater examined by MER Spirit consist of mixed Fe3+)-, Mg- , and Ca-sulfates. Meridiani Plenum explored by MER Opportunity is dominated by outcrops of mixed Fe-, Mg- and Ca-sulfate while rocks stratigraphically below this at Endeavor Crater contain veins composed of calcium sulfate. Soil solutions evaluated at the Phoenix Landing site were consistent with the presence of Mg-sulfate, while the thermal and evolved gas data collected from this site suggested that Ca-sulfate could also be present. X-ray diffraction analysis of the Rocknest sand shadow in Gale Crater detected anhydrite (CaSO4)(~1 wt.%) The source of S on the martian surface may be derived from S-bearing volcanic aerosols and/or from subsurface hydrothermal fluids that have interacted with sulfide minerals in the crust. For example, volcanic derived S aerosols in water or ice have been proposed to alter basaltic material where acidic fluids evaporated or ice sublimed leaving behind the large-scale Meridiani sulfate outcrops. On the other hand, local small-scale hydrothermal processes may be responsible for locally concentrated S in the Paso Robles soils in the Columbia Hills encountered by Spirit. Subsequent to deposition, redistribution of S by aqueous or eolian processes is possible. Physical erosion of S deposits detected elsewhere on Mars followed by eolian redistribution of S bearing dust could contribute to soil S. Downward water flow has been proposed to have leached sulfates in select Gusev soils and may be involved in sulfate redistribution in the Meridiani deposits. Sources of downward water flow could be caused by percolating snow melt that occurs during periods of high obliquity. Subsequent to deposition, groundwater interactions are also proposed as a mechanism for the redistributed the Meridiani sulfates. The evaluation of martian of the S cycle should shed light on the past martian climate and indicate the types of aqueous geochemical conditions that were encountered by potential microbiology. Aqueous processes involved the S cycle appear to span a wide pH range from acidic (Fe-sulfates) to more neutral (Fe-sulfate limiting). This range of pH suggests that martian microbiology, if ever present, was diverse and consisted of species that thrived in low pH solutions (e.g., acidophilles) along with species that thrived in more neutral pH solutions.

The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats.

PubMed

Dick, Gregory J; Anantharaman, Karthik; Baker, Brett J; Li, Meng; Reed, Daniel C; Sheik, Cody S

2013-01-01

Hydrothermal plumes are an important yet understudied component of deep-sea vent microbial ecosystems. The significance of plume microbial processes can be appreciated from three perspectives: (1) mediation of plume biogeochemistry, (2) dispersal of seafloor hydrothermal vent microbes between vents sites, (3) as natural laboratories for understanding the ecology, physiology, and function of microbial groups that are distributed throughout the pelagic deep sea. Plume microbiology has been largely neglected in recent years, especially relative to the extensive research conducted on seafloor and subseafloor systems. Rapidly advancing technologies for investigating microbial communities provide new motivation and opportunities to characterize this important microbial habitat. Here we briefly highlight microbial contributions to plume and broader ocean (bio)geochemistry and review recent work to illustrate the ecological and biogeographic linkages between plumes, seafloor vent habitats, and other marine habitats such as oxygen minimum zones (OMZs), cold seeps, and oil spills. 16S rRNA gene surveys and metagenomic/-transcriptomic data from plumes point to dominant microbial populations, genes, and functions that are also operative in OMZs (SUP05, ammonia-oxidizing Archaea, and SAR324 Deltaproteobacteria) and hydrocarbon-rich environments (methanotrophs). Plume microbial communities are distinct from those on the seafloor or in the subsurface but contain some signatures of these habitats, consistent with the notion that plumes are potential vectors for dispersal of microorganisms between seafloor vent sites. Finally, we put forward three pressing questions for the future of deep-sea hydrothermal plume research and consider interactions between vents and oceans on global scales.

The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats

PubMed Central

Dick, Gregory J.; Anantharaman, Karthik; Baker, Brett J.; Li, Meng; Reed, Daniel C.; Sheik, Cody S.

2013-01-01

Hydrothermal plumes are an important yet understudied component of deep-sea vent microbial ecosystems. The significance of plume microbial processes can be appreciated from three perspectives: (1) mediation of plume biogeochemistry, (2) dispersal of seafloor hydrothermal vent microbes between vents sites, (3) as natural laboratories for understanding the ecology, physiology, and function of microbial groups that are distributed throughout the pelagic deep sea. Plume microbiology has been largely neglected in recent years, especially relative to the extensive research conducted on seafloor and subseafloor systems. Rapidly advancing technologies for investigating microbial communities provide new motivation and opportunities to characterize this important microbial habitat. Here we briefly highlight microbial contributions to plume and broader ocean (bio)geochemistry and review recent work to illustrate the ecological and biogeographic linkages between plumes, seafloor vent habitats, and other marine habitats such as oxygen minimum zones (OMZs), cold seeps, and oil spills. 16S rRNA gene surveys and metagenomic/-transcriptomic data from plumes point to dominant microbial populations, genes, and functions that are also operative in OMZs (SUP05, ammonia-oxidizing Archaea, and SAR324 Deltaproteobacteria) and hydrocarbon-rich environments (methanotrophs). Plume microbial communities are distinct from those on the seafloor or in the subsurface but contain some signatures of these habitats, consistent with the notion that plumes are potential vectors for dispersal of microorganisms between seafloor vent sites. Finally, we put forward three pressing questions for the future of deep-sea hydrothermal plume research and consider interactions between vents and oceans on global scales. PMID:23720658

Identification of subsurface microorganisms at Yucca Mountain; Third quarterly report, January 1, 1994--March 31, 1994

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stetzenbach, L.D.

1994-05-01

Bacteria isolated from ground water samples taken from 31 springs during 1993 were collected and processed according to procedures described in earlier reports. These procedures required aseptic collection of surface water samples in sterile screw-capped containers, transportation to the HRC microbiology laboratory, and culture by spread plating onto R2A medium. The isolates were further processed for identification using a gas chromatographic analysis of fatty acid methyl esters (FAME) extracted from cell membranes. This work generated a presumptive identification of 113 bacterial species distributed among 45 genera using a database obtained from Microbial ID, Inc., Newark, Delaware (MIDI). A preliminary examinationmore » of the FAME data was accomplished using cluster analysis and principal component analysis software obtained from MIDI. Typically, bacterial strains that cluster at less than 10 Euclidian distance units have fatty acid patterns consistent among members of the same species. Thus an organism obtained from one source can be recognized if it is isolated again from the same or any other source. This makes it possible to track the distribution of organisms and monitor environmental conditions or fluid transport mechanisms. Microorganisms are seldom found as monocultures in natural environments. They are more likely to be closely associated with other genera with complementary metabolic requirements. An understanding of the indigenous microorganism population is useful in understanding subtle changes in the environment. However, classification of environmental organisms using traditional methods is not ideal because differentiation of species with small variations or genera with very similar taxonomic characteristics is beyond the capabilities of traditional microbiological methods.« less

Comparative Single-Cell Genomics of Chloroflexi from the Okinawa Trough Deep-Subsurface Biosphere.

PubMed

Fullerton, Heather; Moyer, Craig L

2016-05-15

Chloroflexi small-subunit (SSU) rRNA gene sequences are frequently recovered from subseafloor environments, but the metabolic potential of the phylum is poorly understood. The phylum Chloroflexi is represented by isolates with diverse metabolic strategies, including anoxic phototrophy, fermentation, and reductive dehalogenation; therefore, function cannot be attributed to these organisms based solely on phylogeny. Single-cell genomics can provide metabolic insights into uncultured organisms, like the deep-subsurface Chloroflexi Nine SSU rRNA gene sequences were identified from single-cell sorts of whole-round core material collected from the Okinawa Trough at Iheya North hydrothermal field as part of Integrated Ocean Drilling Program (IODP) expedition 331 (Deep Hot Biosphere). Previous studies of subsurface Chloroflexi single amplified genomes (SAGs) suggested heterotrophic or lithotrophic metabolisms and provided no evidence for growth by reductive dehalogenation. Our nine Chloroflexi SAGs (seven of which are from the order Anaerolineales) indicate that, in addition to genes for the Wood-Ljungdahl pathway, exogenous carbon sources can be actively transported into cells. At least one subunit for pyruvate ferredoxin oxidoreductase was found in four of the Chloroflexi SAGs. This protein can provide a link between the Wood-Ljungdahl pathway and other carbon anabolic pathways. Finally, one of the seven Anaerolineales SAGs contains a distinct reductive dehalogenase homologous (rdhA) gene. Through the use of single amplified genomes (SAGs), we have extended the metabolic potential of an understudied group of subsurface microbes, the Chloroflexi These microbes are frequently detected in the subsurface biosphere, though their metabolic capabilities have remained elusive. In contrast to previously examined Chloroflexi SAGs, our genomes (several are from the order Anaerolineales) were recovered from a hydrothermally driven system and therefore provide a unique window into the metabolic potential of this type of habitat. In addition, a reductive dehalogenase gene (rdhA) has been directly linked to marine subsurface Chloroflexi, suggesting that reductive dehalogenation is not limited to the class Dehalococcoidia This discovery expands the nutrient-cycling and metabolic potential present within the deep subsurface and provides functional gene information relating to this enigmatic group. Copyright © 2016 Fullerton and Moyer.

Demonstration of innovative monitoring technologies at the Savannah River Integrated Demonstration Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rossabi, J.; Jenkins, R.A.; Wise, M.B.

1993-12-31

The Department of Energy`s Office of Technology Development initiated an Integrated Demonstration Program at the Savannah River Site in 1989. The objective of this program is to develop, demonstrate, and evaluate innovative technologies that can improve present-day environmental restoration methods. The Integrated Demonstration Program at SRS is entitled ``Cleanup of Organics in Soils and Groundwater at Non-Arid Sites.`` New technologies in the areas of drilling, characterization, monitoring, and remediation are being demonstrated and evaluated for their technical performance and cost effectiveness in comparison with baseline technologies. Present site characterization and monitoring methods are costly, time-consuming, overly invasive, and often imprecise.more » Better technologies are required to accurately describe the subsurface geophysical and geochemical features of a site and the nature and extent of contamination. More efficient, nonintrusive characterization and monitoring techniques are necessary for understanding and predicting subsurface transport. More reliable procedures are also needed for interpreting monitoring and characterization data. Site characterization and monitoring are key elements in preventing, identifying, and restoring contaminated sites. The remediation of a site cannot be determined without characterization data, and monitoring may be required for 30 years after site closure.« less

The UK Centre for Astrobiology: A Virtual Astrobiology Centre. Accomplishments and Lessons Learned, 2011-2016.

PubMed

Cockell, Charles S; Biller, Beth; Bryce, Casey; Cousins, Claire; Direito, Susana; Forgan, Duncan; Fox-Powell, Mark; Harrison, Jesse; Landenmark, Hanna; Nixon, Sophie; Payler, Samuel J; Rice, Ken; Samuels, Toby; Schwendner, Petra; Stevens, Adam; Nicholson, Natasha; Wadsworth, Jennifer

2018-02-01

The UK Centre for Astrobiology (UKCA) was set up in 2011 as a virtual center to contribute to astrobiology research, education, and outreach. After 5 years, we describe this center and its work in each of these areas. Its research has focused on studying life in extreme environments, the limits of life on Earth, and implications for habitability elsewhere. Among its research infrastructure projects, UKCA has assembled an underground astrobiology laboratory that has hosted a deep subsurface planetary analog program, and it has developed new flow-through systems to study extraterrestrial aqueous environments. UKCA has used this research backdrop to develop education programs in astrobiology, including a massive open online course in astrobiology that has attracted over 120,000 students, a teacher training program, and an initiative to take astrobiology into prisons. In this paper, we review these activities and others with a particular focus on providing lessons to others who may consider setting up an astrobiology center, institute, or science facility. We discuss experience in integrating astrobiology research into teaching and education activities. Key Words: Astrobiology-Centre-Education-Subsurface-Analog research. Astrobiology 18, 224-243.

HBCU Summer Undergraduate Training Program in Prostate Cancer Research

DTIC Science & Technology

2011-08-01

in Prostate Cancer Research INTRODUCTION: The goal of this award was to provide prostate cancer (CaP) research summer internships to the...Selection Process: USU/CPDR summer internship program announcements for 2008, 2009 and 2010 were made by Dr. Deepak Kumar (Partnering PI) at the...Department of Anatomy, Physiology and Genetics and Department of Microbiology and Immunology actively participated in training of UDC students under the

A diagnosis of the microbiological quality of dehydrated bee-pollen produced in Brazil.

PubMed

De-Melo, A A M; Estevinho, M L M F; Almeida-Muradian, L B

2015-11-01

Bee-pollen is an apicultural product with potential for medical and nutritional applications; therefore, its microbiology quality should be monitored. In this context, the objective of this study was to diagnose the microbiological quality of 45 dehydrated bee-pollen samples collected from November 2011 to December 2013 in nine Brazilian States. All the samples were negative for sulphite-reducing Clostridium spores, Salmonella, coagulase-positive Staphylococcus and Escherichia coli, which are micro-organisms of public health concern. Total aerobic mesophilic micro-organism counts ranged from <10 to 1·10 × 10(4) CFU g(-1) , with psychrotroph counts ranging from <10 to 1·12 × 10(3) CFU g(-1) and total coliforms from <10 to 2·80 × 10(3) CFU g(-1) , while the values for yeasts and moulds were between <10 to 7·67 × 10(3) CFU g(-1) . According to the literature, the microbiota observed in this study were typical; however, it is important to consider that these micro-organisms may cause spoilage and diminish shelf life, reason by which quality control programs should be implemented. Contamination of bee-pollen can occur during production, collection and processing, but there are few studies of the microbiological quality of this product. Brazil is an important producer of dehydrated bee-pollen, therefore, a diagnosis of the microbiological status is important to ensure the safety of many consumers. Salmonella sp., genus Clostridium, coagulase-positive Staphylococcus, Escherichia coli and even some yeast species are micro-organisms of public health concern and their presence must be monitored. Furthermore, the determination of spoilage micro-organisms indicates whether the production and the processing practices carried out by beekeepers and warehouses were adequate. © 2015 The Society for Applied Microbiology.

Assessing the Public Health Impact and Effectiveness of Interventions To Prevent Salmonella Contamination of Sprouts.

PubMed

Ding, Hongliu; Fu, Tong-Jen

2016-01-01

Sprouts have been a recurring public health challenge due to microbiological contamination, and Salmonella has been the major cause of sprout-associated outbreaks. Although seed treatment and microbiological testing have been applied as risk reduction measures during sprout production, the extent to which their effectiveness in reducing the public health risks associated with sprouts has not been well investigated. We conducted a quantitative risk assessment to measure the risk posed by Salmonella contamination in sprouts and to determine whether and how mitigation strategies can achieve a satisfactory risk reduction based on the assumption that the risk reduction achieved by a microbiological sampling and testing program at a given sensitivity is equivalent to that achieved by direct inactivation of pathogens. Our results indicated that if the sprouts were produced without any risk interventions, the health impact caused by sprouts contaminated with Salmonella would be very high, with a median annual estimated loss of disability-adjusted life years (DALYs) of 691,412. Seed treatment (with 20,000 ppm of calcium hypochlorite) or microbiological sampling and testing of spent irrigation water (SIW) alone could reduce the median annual impact to 734 or 4,856 DALYs, respectively. Combining seed treatment with testing of the SIW would further decrease the risk to 58 DALYs. This number could be dramatically lowered to 3.99 DALYs if sprouts were produced under conditions that included treating seeds with 20,000 ppm of calcium hypochlorite plus microbiological testing of seeds, SIW, and finished products. Our analysis shows that the public health impact due to Salmonella contamination in sprouts could be controlled if seeds are treated to reduce pathogens and microbiological sampling and testing is implemented. Future advances in intervention strategies would be important to improve sprout safety further.

Numerical simulation of seasonal heat storage in a contaminated shallow aquifer - Temperature influence on flow, transport and reaction processes

NASA Astrophysics Data System (ADS)

Popp, Steffi; Beyer, Christof; Dahmke, Andreas; Bauer, Sebastian

2015-04-01

The energy market in Germany currently faces a rapid transition from nuclear power and fossil fuels towards an increased production of energy from renewable resources like wind or solar power. In this context, seasonal heat storage in the shallow subsurface is becoming more and more important, particularly in urban regions with high population densities and thus high energy and heat demand. Besides the effects of increased or decreased groundwater and sediment temperatures on local and large-scale groundwater flow, transport, geochemistry and microbiology, an influence on subsurface contaminations, which may be present in the urban surbsurface, can be expected. Currently, concerns about negative impacts of temperature changes on groundwater quality are the main barrier for the approval of heat storage at or close to contaminated sites. The possible impacts of heat storage on subsurface contamination, however, have not been investigated in detail yet. Therefore, this work investigates the effects of a shallow seasonal heat storage on subsurface groundwater flow, transport and reaction processes in the presence of an organic contamination using numerical scenario simulations. A shallow groundwater aquifer is assumed, which consists of Pleistoscene sandy sediments typical for Northern Germany. The seasonal heat storage in these scenarios is performed through arrays of borehole heat exchangers (BHE), where different setups with 6 and 72 BHE, and temperatures during storage between 2°C and 70°C are analyzed. The developing heat plume in the aquifer interacts with a residual phase of a trichloroethene (TCE) contamination. The plume of dissolved TCE emitted from this source zone is degraded by reductive dechlorination through microbes present in the aquifer, which degrade TCE under anaerobic redox conditions to the degradation products dichloroethene, vinyl chloride and ethene. The temperature dependence of the microbial degradation activity of each degradation step is taken into account for the numerical simulations. Hence, the simulations are performed with the code OpenGeoSys, which is especially suited for simulating coupled thermal, hydraulic and geochemical processes. The scenario simulations show an increase in the source zone emission of TCE at higher temperatures, which is primarily due to the focusing of the groundwater flow in the area of higher temperatures within the source zone and to a lesser part to an increase in TCE solubility. On the other hand, a widening of the contaminant plume and enlargement of the area for TCE biodegradation is induced, which leads to an increase in biodegradation of the chlorinated hydrocarbons. In combination almost no change in the overall ratio of degraded to emitted TCE is found, which shows that the seasonal heat storage is not negatively influencing the present TCE contamination under these assumptions. The results of this work serve to support the risk assessment for the interaction between heat storage and contaminations in the shallow subsurface and show positive interactions as well as possible conflicts.

[The influence of "hygienic minimum" course on quality of catering establishments].

PubMed

Venus, Miroslav; Petrovcić, Darija

2010-01-01

The aim of this article was to define the quality of catering establishments in Virovitica Podravina county before and after the course of "hygienic minimum". Research was realized through interview and assessment of microbiological swabs of the same catering establishments before and after the course of "hygienic minimum". All procedures were performed according to Regulations on standard specification in microbiological cleanness and methods of its determining. Twenty-five catering establishments from a group of restaurants and bars were analyzed. In all of them we found improvement in the most of examined parameters. So, implementation of the course through the existing program has proven to be justified.

THE RAPID OPTICAL TOOL (TM) LASER-INDUCED FLUORESCENCE SYSTEM FOR SCREENING OF PETROLEUM HYDROCARBONS IN SUBSURFACE SOILS

EPA Science Inventory

The Consortium for Site Characterization Technology (CSCT) has established a formal program to accelerate acceptance and application of innovative monitoring and site characterization technologies that improve the way the nation manages its environmental problems. In 1995 the CS...

Organic Carbon as Inhibitor to SVOC and Metal Migration in Stormwater Drywells Discharging to the Subsurface-SLIDES

EPA Science Inventory

The Safe Drinking Water Act (SDWA) authorizes the Underground Injection Control (UIC) program to protect underground drinking water (USDW) sources from contamination caused by underground injection wells, including regulation of stormwater drainage drywells for parking lot and ro...

Emerging Contaminant Sources Fate in Recharged Treated Wasterwater, Lake Havasu City, Arizona

EPA Science Inventory

In 2008 the City of Lake Havasu, Arizona, began a subsurface, effluent injection program to store treated wastewater effluent, which will eventually be seasonally recovered to balance the demand for irrigation during the summer months. As a proactive measure, the City decided to ...

Impact on the deep biosphere of CO2 geological sequestration in (ultra)mafic rocks and retroactive consequences on its fate

NASA Astrophysics Data System (ADS)

Ménez, Bénédicte; Gérard, Emmanuelle; Rommevaux-Jestin, Céline; Dupraz, Sébastien; Guyot, François; Arnar Alfreősson, Helgi; Reynir Gíslason, Sigurőur; Sigurőardóttir, Hólmfríiur

2010-05-01

Due to their reactivity and high potential of carbonation, mafic and ultramafic rocks constitute targets of great interest to safely and permanently sequestrate anthropogenic CO2 and thus, limit the potential major environmental consequences of its increasing atmospheric level. In addition, subsurface (ultra)mafic environments are recognized to harbor diverse and active microbial populations that may be stimulated or decimated following CO2 injection (± impurities) and subsequent acidification. However, the nature and amplitude of the involved biogeochemical pathways are still unknown. To avoid unforeseen consequences at all time scales (e.g. reservoir souring and clogging, bioproduction of H2S and CH4), the impact of CO2 injection on deep biota with unknown ecology, and their retroactive effects on the capacity and long-term stability of CO2 storage sites, have to be determined. We present here combined field and experimental investigations focused on the Icelandic pilot site, implemented in the Hengill area (SW Iceland) at the Hellisheidi geothermal power plant (thanks to the CarbFix program, a consortium between the University of Iceland, Reykjavik Energy, the French CNRS of Toulouse and Columbia University in N.Y., U.S.A. and to the companion French ANR-CO2FIX project). This field scale injection of CO2 charged water is here designed to study the feasibility of storing permanently CO2 in basaltic rocks and to optimize industrial methods. Prior to the injection, the microbiological initial state was characterized through regular sampling at various seasons (i.e., October '08, July '09, February '10). DNA was extracted and amplified from the deep and shallow observatory wells, after filtration of 20 to 30 liters of groundwater collected in the depth interval 400-980 m using a specifically developed sampling protocol aiming at reducing contamination risks. An inventory of living indigenous bacteria and archaea was then done using molecular methods based on the amplification of small subunit ribosomal RNA genes (SSU rDNAs). The stratigraphic levels targeted to store the injected CO2 as aqueous phase harbor numerous new species close to cultivable species belonging to the genus Thermus or Proteobacteria species known to be linked in particular with the hydrogen and iron cycles. After injection, the evolution of these microbial communities will be monitored using the Denaturing Gradient Gel Electrophoresis technique. Beyond the ecological impact of storing high levels of CO2 in deep environments, particularly important is the ability of intraterrestrial microbes to potentially interact with the injected fluids. For example, carbonation has been shown to be strongly influenced by microbiological activities that can locally modify pH and induce nucleation of solid carbonates. To improve the understanding of these processes and to better constrain the influence of deep biota on the evolving chemical and petrophysical properties of the reservoir, an experimental and numerical modeling is carried out in parallel, using model strains representative of the subsurface (including acetogens, sulphate and iron reducing bacteria), as single-species or consortia. A set of batch experiments in presence of crushed olivine or basalts was especially designed to evaluate how microbial activity could overcome the slow kinetics of mineral-fluid reactions and reduce the energy needed to hasten the carbonation process.

Resource conservation program in terms of Vostokgazprom environmental policy

NASA Astrophysics Data System (ADS)

Tsibulnikova, M. R.; Nadyumov, S. V.; Adam, A. M.; Korotchenko, T. V.

2016-09-01

The article examines a number of key areas of environmental policy of Vostokgazprom. The Associated Petroleum Gas program is an important step within the resource conservation and environmental protection framework. In addition, the company undertakes the extensive work on emergency response programs, and carries out continuous protection of the subsurface and control over environmental safety in all production sites. Vostokgazprom continuously modernizes the basic industrial facilities and invests money in new projects. The study analyzes the steps being taken by the company within the energy saving policy that leads to significant costs cut.

76 FR 27069 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-10

..., Immunology and Transplantation (R24).'' Date: May 31, 2011. Time: 2 p.m. to 4 p.m. Agenda: To review and... Assistance Program Nos. 93.855, Allergy, Immunology, and Transplantation Research; 93.856, Microbiology and...

77 FR 61009 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-05

..., Immunology & Transplantation. Date: October 25, 2012. Time: 1:00 p.m. to 5:00 p.m. Agenda: To review and... Assistance Program Nos. 93.855, Allergy, Immunology, and Transplantation Research; 93.856, Microbiology and...

Student Admission Criteria as Predictors of Research Potential.

ERIC Educational Resources Information Center

Cotton, Gary L.; And Others

1986-01-01

A study at one university found that traditional admission criteria for a graduate microbiology program, undergraduate grade point average, and Graduate Record Examination scores, were not good predictors of student potential as a researcher, as measured by faculty ratings. (MSE)

BACLAB: A Computer Simulation of a Medical Bacteriology Laboratory--An Aid for Teaching Tertiary Level Microbiology.

ERIC Educational Resources Information Center

Lewington, J.; And Others

1985-01-01

Describes a computer simulation program which helps students learn the main biochemical tests and profiles for identifying medically important bacteria. Also discusses the advantages and applications of this type of approach. (ML)

Microbiology of Shell Egg Production in the United States

USDA-ARS?s Scientific Manuscript database

A significant proportion of human illnesses caused by Salmonella are linked to the consumption of contaminated eggs. Substantial government and industry resources have been committed to comprehensive Salmonella testing and risk reduction programs for commercial egg-laying flocks. The implementation ...

77 FR 15783 - Center for Scientific Review; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-16

...: Infectious Diseases and Microbiology. Date: March 22-23, 2012. Time: 9 a.m. to 5 p.m. Agenda: To review and... Domestic Assistance Program Nos. 93.306, Comparative Medicine; 93.333, Clinical Research, 93.306, 93.333...

78 FR 21616 - Center for Scientific Review; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-11

..., oral microbiology and oral pathology. Date: May 1, 2013. Time: 1:00 p.m. to 4:30 p.m. Agenda: To review... Domestic Assistance Program Nos. 93.306, Comparative Medicine; 93.333, Clinical Research, 93.306, 93.333...

7 CFR 91.5 - Where services are offered.

Code of Federal Regulations, 2010 CFR

2010-01-01

...) Science and Technology Programs National Science Laboratory. A variety of proximate, chemical, microbiological and biomolecular tests and laboratory analyses performed on fruits and vegetables, poultry, meat and meat products, fiber products and processed foods are performed at the Science and Technology...

Mapping Site Remediation with Electrical Resistivity Tomography Explored via Coupled-Model Simulations

NASA Astrophysics Data System (ADS)

Power, C.; Gerhard, J. I.; Tsourlos, P.; Giannopoulos, A.

2011-12-01

Remediation programs for sites contaminated with dense non-aqueous phase liquids (DNAPLs) would benefit from an ability to non-intrusively map the evolving volume and extent of the DNAPL source zone. Electrical resistivity tomography (ERT) is a well-established geophysical tool, widely used outside the remediation industry, that has significant potential for mapping DNAPL source zones. However, that potential has not been realized due to challenges in data interpretation from contaminated sites - in either a qualitative or quantitative way. The objective of this study is to evaluate the potential of ERT to map realistic, evolving DNAPL source zones within complex subsurface environments during remedial efforts. For this purpose, a novel coupled model was developed that integrates a multiphase flow model (DNAPL3D-MT), which generates realistic DNAPL release scenarios, with 3DINV, an ERT model which calculates the corresponding resistivity response. This presentation will describe the developed model coupling methodology, which integrates published petrophysical relationships to generate an electrical resistivity field that accounts for both the spatial heterogeneity of subsurface soils and the evolving spatial distribution of fluids (including permeability, porosity, clay content and air/water/DNAPL saturation). It will also present an example in which the coupled model was employed to explore the ability of ERT to track the remediation of a DNAPL source zone. A field-scale, three-dimensional release of chlorinated solvent DNAPL into heterogeneous clayey sand was simulated, including the subsurface migration and subsequent removal of the DNAPL source zone via dissolution in groundwater. Periodic surveys of this site via ERT applied at the surface were then simulated and inversion programs were used to calculate the subsurface distribution of electrical properties. This presentation will summarize this approach and its potential as a research tool exploring the range of site conditions under which ERT may prove useful in aiding DNAPL site remediation. Moreover, it is expected to provide a cost-effective avenue to test optimum ERT data acquisition, inversion and interpretative tools at contaminated sites.

U-tube based near-surface environmental monitoring in the Shenhua carbon dioxide capture and storage (CCS) project.

PubMed

Li, Qi; Song, Ranran; Shi, Hui; Ma, Jianli; Liu, Xuehao; Li, Xiaochun

2018-04-01

The CO 2 injected into deep formations during implementation of carbon dioxide (CO 2 ) capture and storage (CCS) technology may leak and migrate into shallow aquifers or ground surfaces through a variety of pathways over a long period. The leaked CO 2 can threaten shallow environments as well as human health. Therefore, almost all monitoring programs for CCS projects around the world contain near-surface monitoring. This paper presents a U-tube based near-surface monitoring technology focusing on its first application in the Shenhua CCS demonstration project, located in the Ordos Basin, Inner Mongolia, China. First, background information on the site monitoring program of the Shenhua CCS demonstration project was provided. Then, the principle of fluid sampling and the monitoring methods were summarized for the U-tube sampler system, and the monitoring data were analyzed in detail. The U-tube based monitoring results showed that the U-tube sampler system is accurate, flexible, and representative of the subsurface fluid sampling process. The monitoring indicators for the subsurface water and soil gas at the Shenhua CCS site indicate good stratification characteristics. The concentration level of each monitoring indicator decreases with increasing depth. Finally, the significance of this near-surface environmental monitoring technology for CO 2 leakage assessments was preliminarily confirmed at the Shenhua CCS site. The application potential of the U-tube based monitoring technology was also demonstrated during the subsurface environmental monitoring of other CCS projects.

From Nanowires to Biofilms: An Exploration of Novel Mechanisms of Uranium Transformation Mediated by Geobacter Bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

REGUERA, GEMMA

2014-01-16

One promising strategy for the in situ bioremediation of radioactive groundwater contaminants that has been identified by the SBR Program is to stimulate the activity of dissimilatory metal-reducing microorganisms to reductively precipitate uranium and other soluble toxic metals. The reduction of U(VI) and other soluble contaminants by Geobacteraceae is directly dependent on the reduction of Fe(III) oxides, their natural electron acceptor, a process that requires the expression of Geobacter’s conductive pili (pilus nanowires). Expression of conductive pili by Geobacter cells leads to biofilm development on surfaces and to the formation of suspended biogranules, which may be physiological closer to biofilmsmore » than to planktonic cells. Biofilm development is often assumed in the subsurface, particularly at the matrix-well screen interface, but evidence of biofilms in the bulk aquifer matrix is scarce. Our preliminary results suggest, however, that biofilms develop in the subsurface and contribute to uranium transformations via sorption and reductive mechanisms. In this project we elucidated the mechanism(s) for uranium immobilization mediated by Geobacter biofilms and identified molecular markers to investigate if biofilm development is happening in the contaminated subsurface. The results provided novel insights needed in order to understand the metabolic potential and physiology of microorganisms with a known role in contaminant transformation in situ, thus having a significant positive impact in the SBR Program and providing novel concept to monitor, model, and predict biological behavior during in situ treatments.« less

Effects on crops of irrigation with treated municipal wastewaters.

PubMed

Fasciolo, G E; Meca, M I; Gabriel, E; Morábito, J

2002-01-01

The fertilizing potential of treated municipal wastewater (oxidation ditch) and crop sanitary acceptability for direct human consumption were evaluated in Mendoza, Argentina. Two experiments were performed on a pilot plot planted with garlic (1998) and onions (1999) using furrow irrigation with three types of water in 10 random blocks: treated effluent (2.5 x 10(3) MPN Escherichia coli/100 ml, 3 helminth eggs/l, and Salmonella (positive); and well water (free of microorganisms), with and without fertilizer. Two responses were evaluated: (1) crop yield, and (2) crop microbiological quality for human consumption at different times after harvest. Crop yields were compared using Variance analysis. Crops' sanitary acceptability was assessed using a two-class sampling program for Salmonella (n=10; c=0), and a three-class program for E. coli (n=5, c=2, M=10(3) and m=10 MPN/g) as proposed by the International Commission on Microbiological Specifications for Foods (ICMSF) for fresh vegetables. Wastewater irrigation acted as well water with fertilizer, increasing garlic and onion yields by 10% and 15%, respectively, compared to irrigation with well water with no fertilizer. Wastewater-irrigated garlic reached sanitary acceptability 90 days after harvest, once attached roots and soil were removed. Onions, which were cleaned immediately after harvest, met this qualification earlier than garlic (55 days). Neither the wastewater-irrigated crops nor the control crops were microbiologically acceptable for consumption raw at harvest.

Microbiological and Biogeochemical Investigations of the Accreted Ice Above Subglacial Lake Vostok, Antarctica

NASA Astrophysics Data System (ADS)

Christner, B. C.; Foreman, C. F.; Arnold, B. R.; Welch, K. A.; Lyons, W. B.; Priscu, J. C.

2004-12-01

Subglacial Lake Vostok is located ~4 km beneath the surface of the East Antarctic ice sheet and has been isolated from the atmosphere for at least 15 million years. The lake has a surface area near 14,000 km2 and a depth exceeding 1000 m. While the nature of the environment within Subglacial Lake Vostok remains uncertain, if a sustained microbial ecosystem is present, life in this subsurface environment operates under arguably the most extreme conditions in the biosphere (i.e., high pressure, constant cold, high oxygen concentrations, and no light). The lake represents an analogue for ecosystems that may exist in Europa's ice-covered ocean and also provides an Earthly-based model for the evaluation of technology to search for life in icy extraterrestrial subsurface environments. Concerns for environmental protection have prevented direct sampling of the lake water thus far, as a prudent sampling plan that will not contaminate this pristine environment has yet to be developed and tested. However, an ice core has been retrieved at Vostok Station in which the bottom ~85 meters consists of lake water that has accreted to the bottom of the ice sheet, providing frozen samples of water from the lakes' surface. The ice from 3539 to 3609 mbs (accretion ice I) contains visible inclusions due to accretion in the shallow embayment or western grounding line, whereas ice from 3610-3623 mbs (accretion ice II) is very clean, forming above the deep eastern basin of the main lake. Using a multifaceted protocol to monitor cellular and molecular decontamination of ice cores, we show that the microbiology and geochemistry (i.e., dissolve organic carbon, nutrients, and ions) of accretion ice is very different from the overlying glacial ice. The numbers of cells are 2- to 7-fold higher in accretion ice I than in the overlying glacial ice, and decrease with increasing depth in accretion ice II. Cell viability in accretion ice samples has been confirmed by the measurable respiration of 14C-glucose at 10oC and recovery of bacterial isolates by enrichment culturing. Direct amplification and phylogenetic analysis of 16S rDNA sequences related to β -, γ -, and δ -proteobacterial species from samples originating from the open lake basin (i.e., accretion ice II) suggest dissimilatory metal oxidation/reduction and methylotrophic metabolic lifestyles may exist. Together, these data imply a priori that Subglacial Lake Vostok is a viable ecosystem.

Investigating the Influence of Remedial Capping on the Hydrological, Geochemical, and Microbial Processes that Control Subsurface Contaminant Migration at WAG 5 on the Oak Ridge Reservation: Implications toward Long-Term Stewardship

NASA Astrophysics Data System (ADS)

Jardine, P. M.; Mehlhorn, T. L.

2006-05-01

The following research investigated the effectiveness of an aggressive, large scale remedial action that is occurring to subsurface waste trenches containing radioactive and organic waste at the Oak Ridge National Laboratory. The site is being remediated as one of the top cleanup prioritization for the Oak Ridge Accelerated Remediation endeavor. Site landlords, Bechtel Jacobs Co., LLC (BJC) are installing a minimal RCRA cap with the primary objective of controlling the infiltration of storm water into the hundreds of unconfined waste trenches containing radioactive and organic waste. The site now offers a unique scientific opportunity to track the kinetic evolution of post-cap processes influencing contaminant migration and immobilization, because we have many years of pre-cap coupled processes information and knowledge. Since the cap is certain to disrupt the near steady-state contaminant discharge profiles that have existed for many years from the site, we have been quantifying the influence of post-cap hydrological, geochemical, and microbial processes on contaminant discharge as a function of scale and time in an effort to assess local-scale cap influences versus regional scale groundwater flow influences on contaminant discharge. We have been allowed to maintain numerous groundwater monitoring wells at a field site and these have a rich historical data set with regard to hydrology, geochemistry, microbiology, and contaminant flux. Our objectives are to investigate cap induced changes in (1) groundwater and surface hydrology and contaminant flux, (2) geochemistry and contaminant speciation, and (3) microbial community structure and organic contaminant degradation and inorganic contaminant immobilization. Our approach monitors coupled processes during base-flow and during storm events in both the groundwater and surface water discharge from the site and the surrounding watershed. Pre- and post-cap data will than be modeled with a multiprocess, multicomponent, transport model which is linked to pre- and post-cap surface water hydrograph analysis from the site and the surrounding watershed. Our goal is to provide an improved fundamental understanding of the long-term fate and transport of contaminants and an improved ability to predict system response to remedial actions. The experimental and numerical results from this investigation will provide knowledge and information in previously unexplored areas of cap performance with regard to coupled hydrology, geochemistry, microbiology, and contaminant flux in humid regimes. The products will support DOE's mission of long-term stewardship of contaminated environments and be transferable to other site where similar remediation exists or is planned.

Three-dimensional vapor intrusion modeling approach that combines wind and stack effects on indoor, atmospheric, and subsurface domains.

PubMed

Shirazi, Elham; Pennell, Kelly G

2017-12-13

Vapor intrusion (IV) exposure risks are difficult to characterize due to the role of atmospheric, building and subsurface processes. This study presents a three-dimensional VI model that extends the common subsurface fate and transport equations to incorporate wind and stack effects on indoor air pressure, building air exchange rate (AER) and indoor contaminant concentration to improve VI exposure risk estimates. The model incorporates three modeling programs: (1) COMSOL Multiphysics to model subsurface fate and transport processes, (2) CFD0 to model atmospheric air flow around the building, and (3) CONTAM to model indoor air quality. The combined VI model predicts AER values, zonal indoor air pressures and zonal indoor air contaminant concentrations as a function of wind speed, wind direction and outdoor and indoor temperature. Steady state modeling results for a single-story building with a basement demonstrate that wind speed, wind direction and opening locations in a building play important roles in changing the AER, indoor air pressure, and indoor air contaminant concentration. Calculated indoor air pressures ranged from approximately -10 Pa to +4 Pa depending on weather conditions and building characteristics. AER values, mass entry rates and indoor air concentrations vary depending on weather conditions and building characteristics. The presented modeling approach can be used to investigate the relationship between building features, AER, building pressures, soil gas concentrations, indoor air concentrations and VI exposure risks.

An estimation of the electrical characteristics of planetary shallow subsurfaces with TAPIR antennas

NASA Astrophysics Data System (ADS)

Le Gall, A.; Reineix, A.; Ciarletti, V.; Berthelier, J. J.; Ney, R.; Dolon, F.; Corbel, C.

2006-06-01

In the frame of the NETLANDER program, we have developed the Terrestrial And Planetary Investigation by Radar (TAPIR) imaging ground-penetrating radar to explore the Martian subsurface at kilometric depths and search for potential water reservoirs. This instrument which is to operate from a fixed lander is based on a new concept which allows one to image the various underground reflectors by determining the direction of propagation of the reflected waves. The electrical parameters of the shallow subsurface (permittivity and conductivity) need to be known to correctly determine the propagation vector. In addition, these electrical parameters can bring valuable information on the nature of the materials close to the surface. The electric antennas of the radar are 35 m long resistively loaded monopoles that are laid on the ground. Their impedance, measured during a dedicated mode of operation of the radar, depends on the electrical parameters of soil and is used to infer the permittivity and conductivity of the upper layer of the subsurface. This paper presents an experimental and theoretical study of the antenna impedance and shows that the frequency profile of the antenna complex impedance can be used to retrieve the geoelectrical characteristics of the soil. Comparisons between a numerical modeling and in situ measurements have been successfully carried over various soils, showing a very good agreement.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hoak, T.E.; Klawitter, A.L.

Fractured production trends in Piceance Basin Cretaceous-age Mesaverde Group gas reservoirs are controlled by subsurface structures. Because many of the subsurface structures are controlled by basement fault trends, a new interpretation of basement structure was performed using an integrated interpretation of Landsat Thematic Mapper (TM), side-looking airborne radar (SLAR), high altitude, false color aerial photography, gas and water production data, high-resolution aeromagnetic data, subsurface geologic information, and surficial fracture maps. This new interpretation demonstrates the importance of basement structures on the nucleation and development of overlying structures and associated natural fractures in the hydrocarbon-bearing section. Grand Valley, Parachute, Rulison, Plateau,more » Shire Gulch, White River Dome, Divide Creek and Wolf Creek fields all produce gas from fractured tight gas sand and coal reservoirs within the Mesaverde Group. Tectonic fracturing involving basement structures is responsible for development of permeability allowing economic production from the reservoirs. In this context, the significance of detecting natural fractures using the intergrated fracture detection technique is critical to developing tight gas resources. Integration of data from widely-available, relatively inexpensive sources such as high-resolution aeromagnetics, remote sensing imagery analysis and regional geologic syntheses provide diagnostic data sets to incorporate into an overall methodology for targeting fractured reservoirs. The ultimate application of this methodology is the development and calibration of a potent exploration tool to predict subsurface fractured reservoirs, and target areas for exploration drilling, and infill and step-out development programs.« less

Sub-slab vs. Near-slab Soil Vapor Profiles at a Chlorinated Solvent Site (1)

EPA Science Inventory

A critical issue in assessing the vapor intrusion pathway is the distribution and migration of VOCs from the subsurface source to the near surface environment. Of particular importance is the influence of a slab. Therefore, EPA/ORD is funding a research program with the primary...

Installation Restoration Program Records Search for Dobbins Air Force Base, Georgia

DTIC Science & Technology

1982-04-01

migation Death to irond water ____________ lift ogaeiitation 1 . Subsurface flow_____I a _____________ Direct aess W 4round water______ j Submrs(10 x actr...potential pathways, surface water migation , flooding, and ground-water * migration. Select the highest rating, and proceed to C. f 1. Surface water migration

Qtracer Program for Tracer-Breakthrough Curve Analysis for Karst and Fractured-Rock Aquifers (2000)

EPA Science Inventory

Tracer tests are generally regarded as being the most reliable and efficient means of gathering subsurface hydraulic information. This is true for all types of aquifers, but especially so for karst and fractured-rock aquifers. Qualitative tracing tests have been conventionally em...

The effects of supplemental online learning aids on student performance and student engagement in Medical Microbiology

NASA Astrophysics Data System (ADS)

Murray, Kimberly

The purpose of this study was to determine the effects of online learning aids on student performance and engagement. The thirty-five participants of the current study were students enrolled in two sections of a junior level Medical Microbiology laboratory. The experimental section was required to spend ten minutes each week on an online learning aid. The online program, StudyMate(TM), was used to present text and images in the form of flash cards, multiple choice questions, matching, and crossword puzzles. Both groups completed the Index of Learning Style survey, an initial engagement survey at the start of the course, and a final engagement survey at the end of the course. Statistical analysis showed no significant differences between the groups at the start of the course or after the course was completed for learning style, science grade point average, overall grade point average, initial engagement or final engagement. A moderate correlation was found between microbiology course and laboratory grades and a reflective learning style.

RELATIONSHIP OF MICROBIAL INDICATORS TO HEALTH EFFECTS AT MARINE BATHING BEACHES

EPA Science Inventory

Finds are described from the second year of an epidemiological-microbiological study conducted at New York City beaches as part of the U.S. Environmental Protection Agency program to develop health effects-recreational water quality criteria. Symptomatology rates among swimmers (...

75 FR 11897 - Center for Scientific Review; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-12

... Microbiology. Date: March 25-26, 2010. Time: 8:30 a.m. to 5 p.m. Agenda: To review and evaluate grant... Assistance Program Nos. 93.306, Comparative Medicine; 93.333, Clinical Research, 93.306, 93.333, 93.337, 93...

7 CFR 91.5 - Where services are offered.

Code of Federal Regulations, 2011 CFR

2011-01-01

...) Science and Technology Programs National Science Laboratory. A variety of proximate for composition, chemical, physical, microbiological and biomolecular (DNA-based) tests and laboratory analyses performed on..., honey, meat and meat products, fiber products and processed foods are performed at the Science and...

7 CFR 91.5 - Where services are offered.

Code of Federal Regulations, 2013 CFR

2013-01-01

...) Science and Technology Programs National Science Laboratory. A variety of proximate for composition, chemical, physical, microbiological and biomolecular (DNA-based) tests and laboratory analyses performed on..., honey, meat and meat products, fiber products and processed foods are performed at the Science and...

7 CFR 91.5 - Where services are offered.

Code of Federal Regulations, 2014 CFR

2014-01-01

...) Science and Technology Programs National Science Laboratory. A variety of proximate for composition, chemical, physical, microbiological and biomolecular (DNA-based) tests and laboratory analyses performed on..., honey, meat and meat products, fiber products and processed foods are performed at the Science and...

7 CFR 91.5 - Where services are offered.

Code of Federal Regulations, 2012 CFR

2012-01-01

...) Science and Technology Programs National Science Laboratory. A variety of proximate for composition, chemical, physical, microbiological and biomolecular (DNA-based) tests and laboratory analyses performed on..., honey, meat and meat products, fiber products and processed foods are performed at the Science and...

NERL MICROBIAL PROGRAM WITH EMPHASIS ON PROTOZOAN METHODS

EPA Science Inventory

The National Exposure Research Laboratory's facility in Cincinnati is engated in a variety of microbiological research projects that include studies on bacteria, viruses, fungi and protozoa. One of these was a protzoology project to determine the best way to evaluate methods rep...

Workshop to develop deep-life continental scientific drilling projects

DOE PAGES

Kieft, T. L.; Onstott, T. C.; Ahonen, L.; ...

2015-05-29

The International Continental Scientific Drilling Program (ICDP) has long espoused studies of deep subsurface life, and has targeted fundamental questions regarding subsurface life, including the following: "(1) What is the extent and diversity of deep microbial life and what are the factors limiting it? (2) What are the types of metabolism/carbon/energy sources and the rates of subsurface activity? (3) How is deep microbial life adapted to subsurface conditions? (4) How do subsurface microbial communities affect energy resources? And (5) how does the deep biosphere interact with the geosphere and atmosphere?" (Horsfield et al., 2014) Many ICDP-sponsored drilling projects have includedmore » a deep-life component; however, to date, not one project has been driven by deep-life goals, in part because geomicrobiologists have been slow to initiate deep biosphere-driven ICDP projects. Therefore, the Deep Carbon Observatory (DCO) recently partnered with the ICDP to sponsor a workshop with the specific aim of gathering potential proponents for deep-life-driven ICDP projects and ideas for candidate drilling sites. Twenty-two participants from nine countries proposed projects and sites that included compressional and extensional tectonic environments, evaporites, hydrocarbon-rich shales, flood basalts, Precambrian shield rocks, subglacial and subpermafrost environments, active volcano–tectonic systems, megafan deltas, and serpentinizing ultramafic environments. The criteria and requirements for successful ICDP applications were presented. Deep-life-specific technical requirements were discussed and it was concluded that, while these procedures require adequate planning, they are entirely compatible with the sampling needs of other disciplines. As a result of this workshop, one drilling workshop proposal on the Basin and Range Physiographic Province (BRPP) has been submitted to the ICDP, and several other drilling project proponents plan to submit proposals for ICDP-sponsored drilling workshops in 2016.« less

Color images of Kansas subsurface geology from well logs

USGS Publications Warehouse

Collins, D.R.; Doveton, J.H.

1986-01-01

Modern wireline log combinations give highly diagnostic information that goes beyond the basic shale content, pore volume, and fluid saturation of older logs. Pattern recognition of geology from logs is made conventionally through either the examination of log overlays or log crossplots. Both methods can be combined through the use of color as a medium of information by setting the three color primaries of blue, green, and red light as axes of three dimensional color space. Multiple log readings of zones are rendered as composite color mixtures which, when plotted sequentially with depth, show lithological successions in a striking manner. The method is extremely simple to program and display on a color monitor. Illustrative examples are described from the Kansas subsurface. ?? 1986.

Profilometry and subsurface imaging in point of care diagnosis in ocular disease and lymphedema after breast cancer treatment

NASA Astrophysics Data System (ADS)

Sayegh, Samir I.; Taghian, Alphonse

2013-03-01

Breast cancer-related lymphedema (BCRL) can be irreversible with profound negative impact on patients' quality of life. Programs that provide screening and active surveillance for BCRL are essential to determine whether early detection and intervention influences the course of lymphedema development. Established methods of quantitatively assessing lymphedema at early stages include "volume" methods such as perometry and bioimpedance spectroscopy. Here we demonstrate 1) Use of topographical techniques analogous to those used in corneal topography 2) Development of point-of-care lymphedema detection and characterization based on off-the-shelf hardward 3) The role of subsurface imaging 4) Multimodal diagnostics and integration yielding higher sensitivity/ specificity.

Microbiological water methods: quality control measures for Federal Clean Water Act and Safe Drinking Water Act regulatory compliance.

PubMed

Root, Patsy; Hunt, Margo; Fjeld, Karla; Kundrat, Laurie

2014-01-01

Quality assurance (QA) and quality control (QC) data are required in order to have confidence in the results from analytical tests and the equipment used to produce those results. Some AOAC water methods include specific QA/QC procedures, frequencies, and acceptance criteria, but these are considered to be the minimum controls needed to perform a microbiological method successfully. Some regulatory programs, such as those at Code of Federal Regulations (CFR), Title 40, Part 136.7 for chemistry methods, require additional QA/QC measures beyond those listed in the method, which can also apply to microbiological methods. Essential QA/QC measures include sterility checks, reagent specificity and sensitivity checks, assessment of each analyst's capabilities, analysis of blind check samples, and evaluation of the presence of laboratory contamination and instrument calibration and checks. The details of these procedures, their performance frequency, and expected results are set out in this report as they apply to microbiological methods. The specific regulatory requirements of CFR Title 40 Part 136.7 for the Clean Water Act, the laboratory certification requirements of CFR Title 40 Part 141 for the Safe Drinking Water Act, and the International Organization for Standardization 17025 accreditation requirements under The NELAC Institute are also discussed.

DISTRIBUTION SYSTEM EVALUATIONS OF THE CONTAMINANT CANDIDATE LIST

EPA Science Inventory

The Safe Drinking Water Act (SDWA), as amended in 1996, requires EPA to establish a list of unregulated microbiological and chemical contaminants to aid in priority setting for the Agency's drinking water program. The list is referred to as the Contaminant Candidate List (CCL). A...

BACTERIAL PATHOGENIC RESEARCH IN RESPONSE TO CONTAMINANT CANDIDATE LIST NEEDS

EPA Science Inventory

The Safe Drinking Water Act, as amended in 1996, requires EPA to establish a Contaminant Candidate List (CCL) of unregulated microbiological and chemical contaminants to aid in priority setting for the Agency's drinking water program. At predetermined intervals the Agency must s...

Predictive microbiology for food packaging applications

USDA-ARS?s Scientific Manuscript database

Mathematical modeling has been applied to describe the microbial growth and inactivation in foods for decades and is also known as ‘Predictive microbiology’. When models are developed and validated, their applications may save cost and time. The Pathogen Modeling Program (PMP), a collection of mode...

[Analysis of the results of the 2010 External Quality Control Program of the Spanish Society of Infectious Diseases and Clinical Microbiology for HIV-1, HCV, and HBV viral loads].

PubMed

Orta Mira, Nieves; Serrano, María del Remedio Guna; Martínez, José-Carlos Latorre; Ovies, María Rosario; Poveda, Marta; de Gopegui, Enrique Ruiz; Cardona, Concepción Gimeno

2011-12-01

Human immunodeficiency virus type 1 (HIV-1) and hepatitis B (HBV) and C virus (HCV) viral load determinations are among the most important markers for the follow-up of patients infected with these viruses. External quality control tools are crucial to ensure the accuracy of the results obtained by microbiology laboratories. This article summarized the results obtained in the 2010 External Quality Control Program of the Spanish Society of Infectious Diseases and Clinical Microbiology for HIV-1, HCV, and HBV viral loads and HCV genotyping. In the HIV-1 program, a total of five standards were sent. One standard consisted of seronegative human plasma, while the remaining four contained plasma from three different viremic patients, in the range of 3-5 log(10) copies/mL; two of these standards were identical, with the aim of determining repeatability. A significant proportion of the laboratories (22.6% on average) obtained values out of the accepted range (mean ± 0.2 log(10)copies/mL), depending on the standard and on the method used for quantification. Repeatability was very good, with up to 95% of laboratories reporting results within the limits (Δ<0.5 log(10)copies/mL). The HBV and HCV program consisted of two standards with different viral load contents. Most of the participants, 86.1% in the case of HCV and 87.1% in HBV, obtained all the results within the accepted range (mean ± 1.96 SD log(10)UI/mL). Post-analytical errors due to mistranscription of the results were detected in these controls. Data from this analysis reinforce the utility of proficiency programs to ensure the quality of the results obtained by a particular laboratory, as well as the importance of the post-analytical phase in overall quality. Due to interlaboratory variability, use of the same method and the same laboratory for patient follow-up is advisable. Copyright © 2011 Elsevier España S.L. All rights reserved.

Rates of microbial metabolism in deep coastal plain aquifers

USGS Publications Warehouse

Chapelle, F.H.; Lovley, D.R.

1990-01-01

Rates of microbial metabolism in deep anaerobic aquifers of the Atlantic coastal plain of South Carolina were investigated by both microbiological and geochemical techniques. Rates of [2-14C]acetate and [U-14C]glucose oxidation as well as geochemical evidence indicated that metabolic rates were faster in the sandy sediments composing the aquifers than in the clayey sediments of the confining layers. In the sandy aquifer sediments, estimates of the rates of CO2 production (millimoles of CO2 per liter per year) based on the oxidation of [2-14C]acetate were 9.4 x 10-3 to 2.4 x 10-1 for the Black Creek aquifer, 1.1 x 10-2 for the Middendorf aquifer, and <7 x 10-5 for the Cape Fear aquifer. These estimates were at least 2 orders of magnitude lower than previously published estimates that were based on the accumulation of CO2 in laboratory incubations of similar deep subsurface sediments. In contrast, geochemical modeling of groundwater chemistry changes along aquifer flowpaths gave rate estimates that ranged from 10-4 to 10-6 mmol of CO2 per liter per year. The age of these sediments (ca. 80 million years) and their organic carbon content suggest that average rates of CO2 production could have been no more than 10-4 mmol per liter per year. Thus, laboratory incubations may greatly overestimate the in situ rates of microbial metabolism in deep subsurface environments. This has important implications for the use of laboratory incubations in attempts to estimate biorestoration capacities of deep aquifers. The rate estimates from geochemical modeling indicate that deep aquifers are among the most oligotrophic aquatic environments in which there is ongoing microbial metabolism.

Field-scale investigations on the biodegradation of chlorinated aromatic compounds and HCH in the subsurface environment

NASA Astrophysics Data System (ADS)

Feidieker, Doris; Kämpfer, Peter; Dott, Wolfgang

1995-08-01

The biological in situ remediation of a former pesticide production site, highly contaminated with chlorobenzenes, chlorophenols and hexachlorocyclohexanes, was studied for a period of one year. Field experiments testing the remediation technology were carried out in the subsurface to a depth of 5.5 m. Detailed monitoring of several chemical and microbiological parameters was made in order to evaluate the remediation success. The initial pollution of this site ranged from 0.03-0.30 g EOX (extractable halogenated organic compounds)/kg soil in the saturated layer to 1-20 g kg -1 EOX in the unsaturated layer, whereas the impounded water was polluted with 8-13 mg L -1 AOX (adsorbable halogenated organic compounds). No significant decrease of the pollutants in the subsoil was observed, although oxygen and nutrients were supplied in sufficient concentrations. In contrast, several of the chlorinated organic compounds were eliminated from the water treatment plant, either by physical or biological processes. Based on measurements of AOX in different parts of the plant, 26% of the pollutants was found adsorbed on the activated carbon and 3% was found in the sludge of the filter back-wash. Dependent on these measurements, elimination of ˜ 70% of the pollutants was attributed to microbial degradation. The latter fact is supported by oxygen consumption data, by increase in the microbial counts and by changes in the distribution of the pollutants in the plant effluent. Among the chlorobenzenes, 1,2,4-trichlorobenzene, and among the hexachlorocyclohexanes, a-hexachlorocyclohexane were eliminated preferentially. The results suggest that an in situ remediation of a site polluted with chlorinated organic compounds cannot be recommended; however, an on site circulation water treatment is possible by a combination of physical and biological processes.

Applying Reactive Barrier Technology to Enhance Microbially-mediated Denitrification during Managed Aquifer Recharge

NASA Astrophysics Data System (ADS)

Beganskas, S.; Weir, W. B.; Harmon, R. E.; Gorski, G.; Fisher, A. T.; Saltikov, C.; Young, K. S.; Runneals, D.; Teo, E. K.; Stoneburner, B.; Hernandez, J.

2015-12-01

We are running field experiments to observe and quantify microbially-mediated water quality improvement via denitrification during infiltration in the shallow subsurface. Nitrate is a pervasive groundwater contaminant, and nitrate removal through denitrification can occur during infiltration in natural and anthropogenic systems, including during managed aquifer recharge (MAR). The rate of denitrification can vary depending on factors such as infiltration rate; previous work suggests that denitrification rates can increase monotonically with infiltration rates until reaching a critical threshold. We are performing controlled field tests of variables that affect denitrification rate, including sampling to link water chemistry changes to microbial ecology and activity. This study explores how microbial activity and denitrification rates respond to different infiltration rates and the presence or absence of a reactive material (wood chips, a carbon source). We are conducting four two-week-long tests, each under different conditions. For each test, we measure bulk infiltration rate (the sum of lateral and vertical infiltration), vertical infiltration rate using heat as a tracer, and water level. We collect surface and subsurface water samples daily, and we collect soil samples at the start and end of each test. For each water sample, we are measuring NO3-, NO2-, NH3, DOC, and N and O isotopes in nitrate. Soil samples will be tested for grain size, total C/N, and the presence of microbiological genes associated with denitrification. These results will expand our knowledge of the conditions under which denitrification occurs by implicating specific microorganisms and physical infiltration parameters. Our design has the potential for additional experimentation with variables that impact water chemistry during infiltration. This study has broad applications for designing MAR systems that effectively improve water supply and water quality.

Microfluidic Experiments Studying Pore Scale Interactions of Microbes and Geochemistry

NASA Astrophysics Data System (ADS)

Chen, M.; Kocar, B. D.

2016-12-01

Understanding how physical phenomena, chemical reactions, and microbial behavior interact at the pore-scale is crucial to understanding larger scale trends in groundwater chemistry. Recent studies illustrate the utility of microfluidic devices for illuminating pore-scale physical-biogeochemical processes and their control(s) on the cycling of iron, uranium, and other important elements 1-3. These experimental systems are ideal for examining geochemical reactions mediated by microbes, which include processes governed by complex biological phenomenon (e.g. biofilm formation, etc.)4. We present results of microfluidic experiments using a model metal reducing bacteria and varying pore geometries, exploring the limitations of the microorganisms' ability to access tight pore spaces, and examining coupled biogeochemical-physical controls on the cycling of redox sensitive metals. Experimental results will provide an enhanced understanding of coupled physical-biogeochemical processes transpiring at the pore-scale, and will constrain and compliment continuum models used to predict and describe the subsurface cycling of redox-sensitive elements5. 1. Vrionis, H. A. et al. Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site. Appl. Environ. Microbiol. 71, 6308-6318 (2005). 2. Pearce, C. I. et al. Pore-scale characterization of biogeochemical controls on iron and uranium speciation under flow conditions. Environ. Sci. Technol. 46, 7992-8000 (2012). 3. Zhang, C., Liu, C. & Shi, Z. Micromodel investigation of transport effect on the kinetics of reductive dissolution of hematite. Environ. Sci. Technol. 47, 4131-4139 (2013). 4. Ginn, T. R. et al. Processes in microbial transport in the natural subsurface. Adv. Water Resour. 25, 1017-1042 (2002). 5. Scheibe, T. D. et al. Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation. Microb. Biotechnol. 2, 274-286 (2009).

Biodegradability of pentachlorophenol in the environment: A literature review

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakles, D.

1993-04-01

Pentachlorophenol has been widely used as a wood preserving agent for over 50 years to treat millions of electrical utility poles and crossarms. Treatment of poles with pentachlorophenol has in some cases resulted in contamination of soils, groundwater, and surface water. Environmental releases are a concern because of the potential toxicity of pentachlorophenol and its stringent regulation. Microbiological degradation of pentachlorophenol in environmental media has been demonstrated in numerous cases. The potential for pentachlorophenol to be biologically degraded is of interest to the electrical utility industry for two reasons. First, it is a factor in understanding the probable fate ofmore » pentachlorophenol where it has been released into the environment, and second, its biodegradability can potentially result in effective and economical treatment strategies for soils, water, and subsurface environments. The objective of this literature review is to collect a baseline of information on the biodegradability of pentachlorophenol in soils, surface water, and groundwater for the electric utility industry. The focus of the electric utility industry's interest in the environmental management and control of pentachlorophenol is primarily in the management of environmental media, particularly soils, that may have become incidentally contaminated with pentachlorophenol in association with the treatment, storage, or use of utility poles and crossarms. The review of the literature has found that [open quotes]unassisted[close quotes] biodegradation of pentachlorophenol in aquatic, soil, and subsurface environments may occur, presumably if there is an acclimated microbial population of sufficient density. Aerobic conditions appear to be most conducive to biodegradation in these cases. Several studies have shown that with an acclimated, mixed culture and conventional wastewater treatment approaches, pentachlorophenol can be effectively treated in water.« less

Biodegradability of pentachlorophenol in the environment: A literature review. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakles, D.

1993-04-01

Pentachlorophenol has been widely used as a wood preserving agent for over 50 years to treat millions of electrical utility poles and crossarms. Treatment of poles with pentachlorophenol has in some cases resulted in contamination of soils, groundwater, and surface water. Environmental releases are a concern because of the potential toxicity of pentachlorophenol and its stringent regulation. Microbiological degradation of pentachlorophenol in environmental media has been demonstrated in numerous cases. The potential for pentachlorophenol to be biologically degraded is of interest to the electrical utility industry for two reasons. First, it is a factor in understanding the probable fate ofmore » pentachlorophenol where it has been released into the environment, and second, its biodegradability can potentially result in effective and economical treatment strategies for soils, water, and subsurface environments. The objective of this literature review is to collect a baseline of information on the biodegradability of pentachlorophenol in soils, surface water, and groundwater for the electric utility industry. The focus of the electric utility industry`s interest in the environmental management and control of pentachlorophenol is primarily in the management of environmental media, particularly soils, that may have become incidentally contaminated with pentachlorophenol in association with the treatment, storage, or use of utility poles and crossarms. The review of the literature has found that {open_quotes}unassisted{close_quotes} biodegradation of pentachlorophenol in aquatic, soil, and subsurface environments may occur, presumably if there is an acclimated microbial population of sufficient density. Aerobic conditions appear to be most conducive to biodegradation in these cases. Several studies have shown that with an acclimated, mixed culture and conventional wastewater treatment approaches, pentachlorophenol can be effectively treated in water.« less

Antimicrobial Stewardship Program Implementation of a Quality Improvement Intervention Using Real-Time Feedback and an Electronic Order Set for the Management of Staphylococcus aureus Bacteremia.

PubMed

Rosa, Rossana; Zavala, Bruno; Cain, Natalie; Anjan, Shweta; Aragon, Laura; Abbo, Lilian M

2018-03-01

Antimicrobial stewardship programs can optimize the management of Staphylococcus aureus bacteremia by integrating information technology and microbiology laboratory resources. This study describes our experience implementing an intervention consisting of real-time feedback and the use of an electronic order set for the management of S. aureus bacteremia. Infect Control Hosp Epidemiol 2018;39:346-349.

Depletion of Alveolar Macrophages Does Not Prevent Hantavirus Disease Pathogenesis in Golden Syrian Hamsters

DTIC Science & Technology

2016-05-20

ANDV strain Chile -9717869 (27) was propagated in Vero E6 cells 122 (Vero C1008, ATCC CRL 1586). Preparation of twice-plaque-purified ANDV stock has...Research and Material Command, Military 537 Infectious Disease Research Program , Program Area T. Research reported in this publication 538 was also...prior to kidney, involvement, and diagnosed by viral 684 inclusions in lung macrophages. European journal of clinical microbiology & infectious

Elements of Success in Chicago Botanic Garden's Science Career Continuum.

PubMed

Johnson, Katherine A

2016-03-01

The Science Career Continuum at the Chicago Botanic Garden is a model program for successfully encouraging youth from diverse backgrounds into STEM careers. This program has shown that when students are given an opportunity to participate in real scientific research under the mentorship of a caring professional over multiple years, they are more likely to go to college and pursue STEM careers than their peers. Journal of Microbiology & Biology Education.

Elements of Success in Chicago Botanic Garden’s Science Career Continuum

PubMed Central

Johnson, Katherine A.

2016-01-01

The Science Career Continuum at the Chicago Botanic Garden is a model program for successfully encouraging youth from diverse backgrounds into STEM careers. This program has shown that when students are given an opportunity to participate in real scientific research under the mentorship of a caring professional over multiple years, they are more likely to go to college and pursue STEM careers than their peers. Journal of Microbiology & Biology Education PMID:27047595

USGS Toxic Substances Hydrology Program, 2010

USGS Publications Warehouse

Buxton, Herbert T.

2010-01-01

The U.S. Geological Survey (USGS) Toxic Substances Hydrology Program adapts research priorities to address the most important contamination issues facing the Nation and to identify new threats to environmental health. The Program investigates two major types of contamination problems: * Subsurface Point-Source Contamination, and * Watershed and Regional Contamination. Research objectives include developing remediation methods that use natural processes, characterizing and remediating contaminant plumes in fractured-rock aquifers, identifying new environmental contaminants, characterizing new and understudied pesticides in common pesticide-use settings, explaining mercury methylation and bioaccumulation, and developing approaches for remediating watersheds affected by active and historic mining.

Publications of the environmental health program: 1980-1990

NASA Technical Reports Server (NTRS)

Wallace-Robinson, Janice; Hess, Elizabeth; Dickson, Katherine J.

1992-01-01

A 10-year cumulative bibliography of publications resulting from research supported by the Environmental Health Program of the Life Sciences Division of NASA is given. The goals of this program are to utilize ground based studies to understand the effects of the spacecraft and EVA environments on humans and other organisms; to specify, measure, and control these environments; and to develop countermeasures, where necessary, to optimize crew health, safety, and productivity. The primary subjects encompassed are barophysiology, toxicology, and microbiology. Principal Investigators whose research tasks resulted in publication are identified.

The Qtracer2 Program for Tracer-Breakthrough Curve Analysis for Tracer Tests in Karstic Aquifers and Other Hydrologic Systems (2002)

EPA Science Inventory

Tracer testing is generally regarded as the most reliable and efficient method of gathering surface and subsurface hydraulic information. This is especially true for karstic and fractured-rock aquifers. Qualitative tracing tests have been conventionally employed in most karst s...

Internal hydrological mechanism of permeable pavement and interaction with subsurface water - slides

EPA Science Inventory

A permeable pavement site located at the Seitz Elementary School on Fort Riley, Kansas was selected for this study. An 80-space parking lot was built behind the school as part of an EPA ORD collaboration with the U.S. Army under the Net Zero program. The parking lot design includ...

Strategic Planning for Exploration of the Martian Subsurface

NASA Technical Reports Server (NTRS)

Beaty, D. W.; Briggs, G.; Clifford, S. M.

2000-01-01

Exploration of the upper 2-5 km of the martian crust (i.e. the portion that we can realistically envision physically accessing) is a tantalizing prospect. This may provide our best opportunity to advance the three current objectives of the Mars exploration program: Life, Climate, and Resources, with a common theme of water.

Miniature robotic sample analysis lab for planetary in situ mineralogy and microbiology

NASA Astrophysics Data System (ADS)

Kruzelecky, Roman; Wong, Brian; Haddad, Emile; Jamroz, Wes; Cloutis, Edward; Strong, Kimberly; Ghafoor, Nadeem; Jessen, Sean

The current Martian surface conditions are relatively inhospitable, with average diurnal temperature ranges from 170 K to 268 K, a low air pressure of about 7 to 10 mbar consisting mainly of CO2 and negligible ozone to moderate the UV portion of the incident solar radiation. The intense UV effectively sterilizes the surface, and in combination with the low air pressure, makes any unbound surface liquid water unstable. However, there is mounting evidence to support the notion that the near subsurface of Mars may differ dramatically from the uppermost surface. The Inukshuk landed Mars mission, as initially developed under a pre-Phase A study for the Canadian Space Agency, focuses on the search for hydrated mineralogy and subsurface water sites that can provide evidence of past or present life. The mission will be achieved using a miniature suite of complementary spectral instruments operating in collaboration with a robotic tethered mole drill system for the systematic in situ subsurface exploration of the planetary mineralogy, water content and microbiology. The Inukshuk mission will, for the first time, study variations in the Mars subsurface characteristics and composition in detail at different locations. These will be correlated with the current planetary boundary layer conditions using an elevating Skycam platform and surface stand-off measurement capabilities. The subsurface analysis will be provided using a miniature bore-hole probe integrated within the mole driller and interfaced to the rover-based instrument suite using an IR fiber-optic link. This will allow subsurface mapping of the stratigraphy and composition in steps of a few mm to depths beyond 1 m. During the drilling, the bore-hole probe will be shielded using a wiper/shutter system. The in situ bore-hole analysis has an advantage for detecting biomarkers for astrobiology on Mars in that the alteration of the sample by surface radiation can be minimized. The bore-hole sample analysis will employ the data synergy provided by infrared (IR) reflection between 900 and 4300 nm at about 4 nm resolution, visible micro-imaging, and complementary IR Raman spectroscopy from about 400 to 4000 cm-1 . IR spectroscopy provides direct information on the presence of H2 O or OH, either as free H2 O or bonded within hydrated minerals. The IR Raman provides for direct C-C biological detection and supplementary measurement of IR inactive modes. The boresight microimaging provides information on the sample grain structure to assist the spectral data analysis. The combined data synergy can, for the first time, directly and unambiguously detect H2 O and determine its state (ice/liquid/structural), distinguish key mineral species (including those associated with favourable habitats for microbial activity) and determine their hydration states, as well as detect and differentiate various C-H and C-C molecular structures for astrobiological investigations. The mission features a small He-inflatable Skycam aerostat tethered to the rover. It will provide stereographic 2-D VIS surface maps of the rover and its geolocation from a 10-15 m altitude to improve the rover autonomy and maneuverability around obstacles. The Skycam aerostat will also provide boundary layer investigations of Mars weather and residual atmospheric processes with high 0.015 nm spectral resolution for CO2 and CH4 using tunable fiber-optic sources to study the C isotopic ratios. Mission cost effectiveness is achieved through a synergistic instrument suite based on advanced but mature patented MPBC miniaturization technologies that enable high IR spectral measurement performance with minimal mass and power, and an innovative MDA tethered mole drill design. The estimated Inukshuk net payload mass including instrument suite, robotic tethered mole drill with insitu bore-hole probe and Skycam aerostat is under 12 kg. The core IR spectral processor is based on MPBC's patented IOSPEC technology for miniature guided-wave spectrometers. The integration of the spectrometer optics using a low-loss IR waveguide structure provides robust optical alignment and facilitates optimization of the output focal plane and detector array coupling with minimal mechanical components. A precision master grating, micromachined in thin silicon, provides atomically smooth grating elements that enable a background signal scattering below 0.05%. Smart active optical signal processing and dark signal compensation have been developed for IR arrays that can provide over 60 dB of dynamic signal range to enable trace detection. A test bread-board has been prepared and the basic measurement performance verified using a variety of minerals known to exist on Mars. The following paper will discuss the breadboarding of the core spectral instrumentation towards the potential Inukshuk Mars mission science requirements. Acknowledgements: The authors greatfully acknowledge the suggestions of Marcus Dejmek and Eric Vachon from CSA, as well as the financial support of the Canadian Space Agency.

76 FR 30373 - National Institute of Allergy and Infectious Diseases; Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-25

... Allergy and Infectious Diseases; Meeting Notice of Closed Meeting Pursuant to section 10(d) of the Federal... Infectious Diseases Special Emphasis Panel; NIAID Investigator Initiated Program Project Applications (P01... Research; 93.856, Microbiology and Infectious Diseases Research, National Institutes of Health, HHS) Dated...

REMOVING ORGANIC CONTAMINANTS OF REGULATORY INTEREST WITH MEMBRANE PROCESSES: USEPA'S SCREENING STUDIES

EPA Science Inventory

The 1996 amendments to the Safe Drinking Water Act require the US Environmental Protection Agency (USEPA) to establish a list of unregulated microbiological and chemical contaminants to aid in priority-setting for the Agency's drinking water program. This list, known as the Cont...

Microbiological Consequences of Different Housing Systems for Laying Hens: Field and Experimental Infection Studies

USDA-ARS?s Scientific Manuscript database

A significant proportion of human illnesses caused by Salmonella are linked to the consumption of contaminated eggs. In response, substantial government and private industry resources are committed to comprehensive Salmonella testing and risk reduction programs for commercial egg-laying flocks. Envi...

Multimedia Programs in Microbiology.

ERIC Educational Resources Information Center

Kirschbrown, Lita, Ed.

This is a catalog of films, filmstrips, slides, video tapes, and audio cassettes. Most of the materials listed are for college or adult levels. The entries contain the following information: title, format, date released, distributor, running time, costs, author, consultants, and producer. Some of the entries bear recommendations or reviews. The…

Methods of Data Collection, Sample Processing, and Data Analysis for Edge-of-Field, Streamgaging, Subsurface-Tile, and Meteorological Stations at Discovery Farms and Pioneer Farm in Wisconsin, 2001-7

USGS Publications Warehouse

Stuntebeck, Todd D.; Komiskey, Matthew J.; Owens, David W.; Hall, David W.

2008-01-01

The University of Wisconsin (UW)-Madison Discovery Farms (Discovery Farms) and UW-Platteville Pioneer Farm (Pioneer Farm) programs were created in 2000 to help Wisconsin farmers meet environmental and economic challenges. As a partner with each program, and in cooperation with the Wisconsin Department of Natural Resources and the Sand County Foundation, the U.S. Geological Survey (USGS) Wisconsin Water Science Center (WWSC) installed, maintained, and operated equipment to collect water-quantity and water-quality data from 25 edge-offield, 6 streamgaging, and 5 subsurface-tile stations at 7 Discovery Farms and Pioneer Farm. The farms are located in the southern half of Wisconsin and represent a variety of landscape settings and crop- and animal-production enterprises common to Wisconsin agriculture. Meteorological stations were established at most farms to measure precipitation, wind speed and direction, air and soil temperature (in profile), relative humidity, solar radiation, and soil moisture (in profile). Data collection began in September 2001 and is continuing through the present (2008). This report describes methods used by USGS WWSC personnel to collect, process, and analyze water-quantity, water-quality, and meteorological data for edge-of-field, streamgaging, subsurface-tile, and meteorological stations at Discovery Farms and Pioneer Farm from September 2001 through October 2007. Information presented includes equipment used; event-monitoring and samplecollection procedures; station maintenance; sample handling and processing procedures; water-quantity, waterquality, and precipitation data analyses; and procedures for determining estimated constituent concentrations for unsampled runoff events.

Constructive Activation of Reservoir-Resident Microbes for Enhanced Oil Recovery

NASA Astrophysics Data System (ADS)

DeBruyn, R. P.

2017-12-01

Microbial communities living in subsurface oil reservoirs biodegrade oil, producing methane. If this process could create methane within the waterflooded pore spaces of an oilfield, the methane would be expected to remain and occupy pore space, decreasing water relative permeability, diverting water flow, and increasing oil recovery by expanding the swept zone of the waterflood. This approach was tested in an oilfield in northern Montana. Preliminary assessments were made of geochemical conditions and microbiological habitations. Then, a formulation of microbial activators, with composition tailored for the reservoir's conditions, was metered at low rates into the existing injection water system for one year. In the field, the responses observed included improved oil production performance; a slight increase in injection pressure; and increased time needed for tracers to move between injection and producing wells. We interpret these results to confirm that successful stimulation of the microbial community caused more methane to be created within the swept zone of the waterflooded reservoir. When the methane exsolved as water flowed between high-pressure injection and low-pressure production wells, the bubbles occupied pore space, reducing water saturation and relative permeability, and re-directing some water flow to "slower" unswept rock with lower permeability and higher oil saturation. In total, the waterflood's swept zone had been expanded to include previously-unflooded rock. This technology was applied in this field after screening based on careful anaerobic sampling, advanced microbiological analysis, and the ongoing success of its waterflood. No reservoir or geological or geophysical simulation models were employed, and physical modifications to field facilities were minor. This technology of utilizing existing microbial populations for enhanced oil recovery can therefore be considered for deployment into waterfloods where small scale, advanced maturity, or insufficiency of data make other technologies too expensive.

Microbial stowaways: Addressing oil spill impacts and the artificial reef effect on deep-sea microbiomes

NASA Astrophysics Data System (ADS)

Hamdan, L. J.; Salerno, J. L.; Blackwell, C. A.; Little, B.; McGown, C.; Fitzgerald, L. A.; Damour, M.

2016-02-01

Shipwrecks enhance macro-biological diversity in the deep ocean, but, to date, studies have not explored the reef effect on deep-sea microbiological diversity. This is an important concept to address in a restoration framework, as microbial biogeochemical function impacts recruitment and adhesion of higher trophic levels on artificial reefs. In addition, microbial biofilms influence the preservation of shipwrecks through biologically mediated corrosion. Oil and gas-related activities have potential to disrupt the base of the reef trophic web; therefore, bacterial diversity and gene function at six shipwrecks (3 steel-hulled; 3 wood-hulled) in the northern Gulf of Mexico was investigated as part of the GOM-SCHEMA (Shipwreck Corrosion, Hydrocarbon Exposure, Microbiology, and Archaeology) project. Sites were selected based on proximity to the Deepwater Horizon spill's subsurface plume, depth, hull type, and existing archaeological data. Classification of taxa in sediments adjacent to and at distance from wrecks, in water, and on experimental steel coupons was used to evaluate how the presence of shipwrecks and spill contaminants in the deep biosphere influenced diversity. At all sites, and in all sample types, Proteobacteria were most abundant. Biodiversity was highest in surface sediments and in coupon biofilms adjacent to two steel-hulled wrecks in the study (Halo and Anona) and decreased with sediment depth and distance from the wrecks. Sequences associated with the iron oxidizing Mariprofundus genus were elevated at steel-hulled sites, indicating wreck-specific environmental selection. Despite evidence of the reef effect on microbiomes, bacterial composition was structured primarily by proximity to the spill and secondarily by hull material at all sites. This study provides the first evidence of an artificial reef effect on deep-sea microbial communities and suggests that biodiversity and function of primary colonizers of shipwrecks may be impacted by the spill.

Nature's Helpers: Using Microorganisms to Remove Trichloroethene (TCE) from Groundwater

NASA Astrophysics Data System (ADS)

Delgado, A. G.; Krajmlanik-Brown, R.; Fajardo-Williams, D.; Halloum, I.

2015-12-01

Organic chlorinated solvents, such as perchloroethene (PCE) and trichloroethene (TCE), are toxic pollutants threatening ground water quality worldwide and present at many superfund sites. Bioremediation using microorganisms is a promising, green, efficient, and sustainable approach to remove PCE and TCE contamination from soil and groundwater. Under anaerobic conditions, specialized microorganisms (dechlorinators) can reduce these chlorinated ethenes to ethene, an innocuous product, and gain energy for growth by a process known as reductive dechlorination. Dechlorinators are most often present in the environment and in dechlorinating cultures alongside other microbes such as fermenters, methanogens, and acetogens. Fermenters, methanogens, and acetogens syntrophically provide essential nutrients and growth factors to dechlorinators, most specifically to the only members able to reduce TCE all the way to ethene: Dehalococcoides; unfortunately, they also compete with dechlorinators for electron donors. My laboratory devises reductive chlorination platforms to study competition and syntrophy among Dehalococcoides, and other microbes to optimize remediation reactions and transport in the subsurface. We look at competing processes present as part of the natural soil chemistry and microbiology and address these challenges through a combination of enrichment techniques, molecular microbial ecology (deep sequencing), water chemistry, and electron balances. We have applied knowledge gathered in my laboratory to: 1) enrich microbial dechlorinating cultures capable of some of the fastest rates of TCE to ethene dechlorination ever reported, and 2) successfully design and operate three different continuous dechlorinating reactor types. We attribute our successful reactor operations to our multidisciplinary approach which links microbiology and engineering. Our reactors produce robust dechlorinating cultures used for in-situ bioaugmentation of PCE and TCE at contaminated sites. The results gathered to date provide a fundamental understanding of the role of homoacetogens and methanogens in electron and carbon flow in dechlorinating consortia.

Biogeochemical Modeling of In Situ U(VI) Reduction and Immobilization with Emulsified Vegetable Oil as the Electron Donor at a Field Site in Oak Ridge, Tennessee

NASA Astrophysics Data System (ADS)

Tang, G.; Parker, J.; Wu, W.; Schadt, C. W.; Watson, D. B.; Brooks, S. C.; Orifrc Team

2011-12-01

A comprehensive biogeochemical model was developed to quantitatively describe the coupled hydrologic, geochemical and microbiological processes that occurred following injection of emulsified vegetable oil (EVO) as the electron donor to immobilize U(VI) at the Oak Ridge Integrated Field Research Challenge site (ORIFRC) in Tennessee. The model couples the degradation of EVO, production and oxidation of long-chain fatty acids (LCFA), glycerol, hydrogen and acetate, reduction of nitrate, manganese, ferrous iron, sulfate and uranium, and methanoganesis with growth of multiple microbial groups. The model describes the evolution of geochemistry and microbial populations not only in the aqueous phase as typically observed, but also in the mineral phase and therefore enables us to evaluate the applicability of rates from the literature for field scale assessment, estimate the retention and degradation rates of EVO and LCFA, and assess the influence of the coupled processes on fate and transport of U(VI). Our results suggested that syntrophic bacteria or metal reducers might catalyze LCFA oxidation in the downstream locations when sulfate was consumed, and competition between methanogens and others for electron donors and slow growth of methanogen might contribute to the sustained reducing condition. Among the large amount of hydrologic, geochemical and microbiological parameter values, the initial biomass, and the interactions (e.g., inhibition) of the microbial functional groups, and the rate and extent of Mn and Fe oxide reduction appear as the major sources of uncertainty. Our model provides a platform to conduct numerical experiments to study these interactions, and could be useful for further iterative experimental and modeling investigations into the bioreductive immobiliztion of radionuclide and metal contaminants in the subsurface.

16S rRNA Gene Survey of Microbial Communities in Winogradsky Columns

PubMed Central

Rundell, Ethan A.; Banta, Lois M.; Ward, Doyle V.; Watts, Corey D.; Birren, Bruce; Esteban, David J.

2014-01-01

A Winogradsky column is a clear glass or plastic column filled with enriched sediment. Over time, microbial communities in the sediment grow in a stratified ecosystem with an oxic top layer and anoxic sub-surface layers. Winogradsky columns have been used extensively to demonstrate microbial nutrient cycling and metabolic diversity in undergraduate microbiology labs. In this study, we used high-throughput 16s rRNA gene sequencing to investigate the microbial diversity of Winogradsky columns. Specifically, we tested the impact of sediment source, supplemental cellulose source, and depth within the column, on microbial community structure. We found that the Winogradsky columns were highly diverse communities but are dominated by three phyla: Proteobacteria, Bacteroidetes, and Firmicutes. The community is structured by a founding population dependent on the source of sediment used to prepare the columns and is differentiated by depth within the column. Numerous biomarkers were identified distinguishing sample depth, including Cyanobacteria, Alphaproteobacteria, and Betaproteobacteria as biomarkers of the soil-water interface, and Clostridia as a biomarker of the deepest depth. Supplemental cellulose source impacted community structure but less strongly than depth and sediment source. In columns dominated by Firmicutes, the family Peptococcaceae was the most abundant sulfate reducer, while in columns abundant in Proteobacteria, several Deltaproteobacteria families, including Desulfobacteraceae, were found, showing that different taxonomic groups carry out sulfur cycling in different columns. This study brings this historical method for enrichment culture of chemolithotrophs and other soil bacteria into the modern era of microbiology and demonstrates the potential of the Winogradsky column as a model system for investigating the effect of environmental variables on soil microbial communities. PMID:25101630

Snowmelt Induced Hydrologic Perturbations Drive Dynamic Microbiological and Geochemical Behaviors across a Shallow Riparian Aquifer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Danczak, Robert E.; Yabusaki, Steven B.; Williams, Kenneth H.

Shallow riparian aquifers represent hotspots of biogeochemical activity in the arid western US. While these environments provide extensive ecosystem services, little is known of how natural environmental perturbations influence subsurface microbial communities and associated biogeochemical processes. Over a six-month period we tracked the annual snowmelt-driven incursion of groundwater into the vadose zone of an aquifer adjacent to the Colorado River, leading to increased dissolved oxygen (DO) concentrations in the normally suboxic saturated zone. Strong biogeochemical heterogeneity was measured across the site, with abiotic reactions between DO and sulfide minerals driving rapid DO consumption and mobilization of redox active species inmore » reduced aquifer regions. Conversely, extensive DO increases were detected in less reduced sediments. 16S rRNA gene surveys tracked microbial community composition within the aquifer, revealing strong correlations between increases in putative oxygen-utilizing chemolithoautotrophs and heterotrophs and rising DO concentrations. The gradual return to suboxic aquifer conditions favored increasing abundances of 16S rRNA sequences matching members of the Microgenomates (OP11) and Parcubacteria (OD1) that have been strongly implicated in fermentative processes. Microbial community stability measurements indicated that deeper aquifer locations were relatively less affected by geochemical perturbations, while communities in shallower locations exhibited the greatest change. Reactive transport modeling of the geochemical and microbiological results supported field observations, suggesting that a predictive framework can be applied to develop a greater understanding of such environments. Frontiers in Earth Science Journal Impact & Description - ResearchGate - Impact Rankings ( 2015 and 2016 ). Available from: https://www.researchgate.net/journal/2296-6463_Frontiers_in_Earth_Science [accessed Jul 25, 2016].« less

Numerical modeling of gas mixing and bio-chemical transformations during underground hydrogen storage within the project H2STORE

NASA Astrophysics Data System (ADS)

Hagemann, B.; Feldmann, F.; Panfilov, M.; Ganzer, L.

2015-12-01

The change from fossil to renewable energy sources is demanding an increasing amount of storage capacities for electrical energy. A promising technological solution is the storage of hydrogen in the subsurface. Hydrogen can be produced by electrolysis using excessive electrical energy and subsequently converted back into electricity by fuel cells or engine generators. The development of this technology starts with adding small amounts of hydrogen to the high pressure natural gas grid and continues with the creation of pure underground hydrogen storages. The feasibility of hydrogen storage in depleted gas reservoirs is investigated in the lighthouse project H2STORE financed by the German Ministry for Education and Research. The joint research project has project members from the University of Jena, the Clausthal University of Technology, the GFZ Potsdam and the French National Center for Scientic Research in Nancy. The six sub projects are based on laboratory experiments, numerical simulations and analytical work which cover the investigation of mineralogical, geochemical, physio-chemical, sedimentological, microbiological and gas mixing processes in reservoir and cap rocks. The focus in this presentation is on the numerical modeling of underground hydrogen storage. A mathematical model was developed which describes the involved coupled hydrodynamic and microbiological effects. Thereby, the bio-chemical reaction rates depend on the kinetics of microbial growth which is induced by the injection of hydrogen. The model has been numerically implemented on the basis of the open source code DuMuX. A field case study based on a real German gas reservoir was performed to investigate the mixing of hydrogen with residual gases and to discover the consequences of bio-chemical reactions.

Development of Enabling Scientific Tools to Characterize the Geologic Subsurface at Hanford

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kenna, Timothy C.; Herron, Michael M.

2014-07-08

This final report to the Department of Energy provides a summary of activities conducted under our exploratory grant, funded through U.S. DOE Subsurface Biogeochemical Research Program in the category of enabling scientific tools, which covers the period from July 15, 2010 to July 14, 2013. The main goal of this exploratory project is to determine the parameters necessary to translate existing borehole log data into reservoir properties following scientifically sound petrophysical relationships. For this study, we focused on samples and Ge-based spectral gamma logging system (SGLS) data collected from wells located in the Hanford 300 Area. The main activities consistedmore » of 1) the analysis of available core samples for a variety of mineralogical, chemical and physical; 2) evaluation of selected spectral gamma logs, environmental corrections, and calibration; 3) development of algorithms and a proposed workflow that permits translation of log responses into useful reservoir properties such as lithology, matrix density, porosity, and permeability. These techniques have been successfully employed in the petroleum industry; however, the approach is relatively new when applied to subsurface remediation. This exploratory project has been successful in meeting its stated objectives. We have demonstrated that our approach can lead to an improved interpretation of existing well log data. The algorithms we developed can utilize available log data, in particular gamma, and spectral gamma logs, and continued optimization will improve their application to ERSP goals of understanding subsurface properties.« less

Analysis of Tank 38H (HTF-38-17-52, -53) and Tank 43H (HTF-43-17-54, -55) Samples for Support of the Enrichment Control and Corrosion Control Programs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hay, M.; Coleman, C.; Diprete, D.

SRNL analyzed samples from Tank 38H and Tank 43H to support ECP and CCP. The total uranium in the Tank 38H surface sample was 41.3 mg/L while the sub-surface sample was 43.5 mg/L. The Tank 43H samples contained total uranium concentrations of 28.5 mg/L in the surface sample and 28.1 mg/L in the sub-surface sample. The U-235 percentage ranged from 0.62% to 0.63% for the Tank 38H samples and Tank 43H samples. The total uranium and percent U-235 results in the table appear slightly lower than recent Tank 38H and Tank 43H uranium measurements. The plutonium results in the tablemore » show a large difference between the surface and sub-surface sample concentrations for Tank 38H. The Tank 43H plutonium results closely match the range of values measured on previous samples. The Cs-137 results for the Tank 38H surface and sub-surface samples show similar concentrations slightly higher than the concentrations measured in recent samples. The Cs-137 results for the two Tank 43H samples also show similar concentrations within the range of values measured on previous samples. The four samples show silicon concentrations somewhat lower than the previous samples with values ranging from 124 to 168 mg/L.« less

Constraints on the depth and geometry of the magma chamber of the Olympus Mons Volcano, Mars

NASA Technical Reports Server (NTRS)

Zuber, Maria T.; Mouginis-Mark, Peter J.

1990-01-01

The summit caldera of the Olympus Mons volcano exhibits one of the clearest examples of tectonic processes associated with shield volcanism on Mars. The radial distance from the center of the transition from concentric ridges to concentric graben within the oldest crater provides a constraint on the geometry and depth of the subsurface magmatic reservoir at the time of subsidence. Here, researchers use this constraint to investigate the size, shape, and depth of the reservoir. Their approach consists of calculating radial surface stresses corresponding to the range of subsurface pressure distributions representing an evacuating magma chamber. They then compare stress patterns to the observed radial positions of concentric ridges and graben. The problem is solved by employing the finite element approach using the program TECTON.

Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data--The Influence of Different Parameters in a Routine Clinical Microbiology Laboratory.

PubMed

Kohlmann, Rebekka; Gatermann, Sören G

2016-01-01

Many clinical microbiology laboratories report on cumulative antimicrobial susceptibility testing (cAST) data on a regular basis. Criteria for generation of cAST reports, however, are often obscure and inconsistent. Whereas the CLSI has published a guideline for analysis and presentation of cAST data, national guidelines directed at clinical microbiology laboratories are not available in Europe. Thus, we sought to describe the influence of different parameters in the process of cAST data analysis in the setting of a German routine clinical microbiology laboratory during 2 consecutive years. We developed various program scripts to assess the consequences ensuing from different algorithms for calculation of cumulative antibiograms from the data collected in our clinical microbiology laboratory in 2013 and 2014. One of the most pronounced effects was caused by exclusion of screening cultures for multi-drug resistant organisms which decreased the MRSA rate in some cases to one third. Dependent on the handling of duplicate isolates, i.e. isolates of the same species recovered from successive cultures on the same patient during the time period analyzed, we recorded differences in resistance rates of up to 5 percentage points for S. aureus, E. coli and K. pneumoniae and up to 10 percentage points for P. aeruginosa. Stratification by site of care and specimen type, testing of antimicrobials selectively on resistant isolates, change of interpretation rules and analysis at genus level instead of species level resulted in further changes of calculated antimicrobial resistance rates. The choice of parameters for cAST data analysis may have a substantial influence on calculated antimicrobial resistance rates. Consequently, comparability of cAST reports from different clinical microbiology laboratories may be limited. We suggest that laboratories communicate the strategy used for cAST data analysis as long as national guidelines for standardized cAST data analysis and reporting do not exist in Europe.

76 FR 80955 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-27

... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Institute of Allergy and Infectious Diseases; Notice of Closed Meeting Pursuant to section 10(d) of the Federal... Program Nos. 93.855, Allergy, Immunology, and Transplantation Research; 93.856, Microbiology and...

78 FR 13360 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meeting

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2013-02-27

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2013-03-29

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2013-04-19

... Allergy and Infectious Diseases; Notice of Closed Meeting Pursuant to section 10(d) of the Federal... clearly unwarranted invasion of personal privacy. Name of Committee: National Institute of Allergy and... Assistance Program Nos. 93.855, Allergy, Immunology, and Transplantation Research; 93.856, Microbiology and...

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2012-04-11

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Marine Caulobacters. Isolation, Characterization and Assessing the Potential for Genetic Experimentation.

DTIC Science & Technology

1987-01-01

grants from the Washington SeaGrant Program, the Office of Naval Research (N00014-81-C-0570) and the California Toxic Substances Research and Teaching ...negative bacteria. Biotechnology _, 269-275. 45.ZoBell, C.E. (1946) Marine microbiology: a monograph on hydrobacteriology. Chronica Botanica Co., Waltham

78 FR 18355 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meeting

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2013-03-26

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REMOVAL OF ORGANIC CCL CONTAMINANTS FROM DRINKING WATERS BY GAC, AIR STRIPPING, AND MEMBRANE PROCESSES

EPA Science Inventory

The 1996 amendments to the Safe Drinking Water Act (SWDA) require the US Environmental Protection Agency (USEPA) to establish a list of unregulated microbiological and chemical contaminants to aid in priority-setting for the Agency's drinking water program. This list, known as t...

THE GOOD, THE BAD AND THE UGLY - DETERMINATION OF BACTERIAL VIRULENCE USING ANIMAL MODELS AND MICROARRAY TECHNOLOGY

EPA Science Inventory

In its Computational Toxicology Program, EPA/ORD proposes to integrate genomics and computational methods to provide a mechanistic basis for the prediction of toxicity of chemicals and the pathogenicity of microorganisms. The goal of microbiological water testing is to be able to...

40 CFR 141.63 - Maximum contaminant levels (MCLs) for microbiological contaminants.

Code of Federal Regulations, 2012 CFR

2012-07-01

... water pressure in all parts of the distribution system; (4) Filtration and/or disinfection of surface water, as described in subpart H, or disinfection of ground water using strong oxidants such as chlorine... (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS National Primary Drinking...

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2013-05-10

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Check Sample Abstracts.

PubMed

Alter, David; Grenache, David G; Bosler, David S; Karcher, Raymond E; Nichols, James; Rajadhyaksha, Aparna; Camelo-Piragua, Sandra; Rauch, Carol; Huddleston, Brent J; Frank, Elizabeth L; Sluss, Patrick M; Lewandrowski, Kent; Eichhorn, John H; Hall, Janet E; Rahman, Saud S; McPherson, Richard A; Kiechle, Frederick L; Hammett-Stabler, Catherine; Pierce, Kristin A; Kloehn, Erica A; Thomas, Patricia A; Walts, Ann E; Madan, Rashna; Schlesinger, Kathie; Nawgiri, Ranjana; Bhutani, Manoop; Kanber, Yonca; Abati, Andrea; Atkins, Kristen A; Farrar, Robert; Gopez, Evelyn Valencerina; Jhala, Darshana; Griffin, Sonya; Jhala, Khushboo; Jhala, Nirag; Bentz, Joel S; Emerson, Lyska; Chadwick, Barbara E; Barroeta, Julieta E; Baloch, Zubair W; Collins, Brian T; Middleton, Owen L; Davis, Gregory G; Haden-Pinneri, Kathryn; Chu, Albert Y; Keylock, Joren B; Ramoso, Robert; Thoene, Cynthia A; Stewart, Donna; Pierce, Arand; Barry, Michelle; Aljinovic, Nika; Gardner, David L; Barry, Michelle; Shields, Lisa B E; Arnold, Jack; Stewart, Donna; Martin, Erica L; Rakow, Rex J; Paddock, Christopher; Zaki, Sherif R; Prahlow, Joseph A; Stewart, Donna; Shields, Lisa B E; Rolf, Cristin M; Falzon, Andrew L; Hudacki, Rachel; Mazzella, Fermina M; Bethel, Melissa; Zarrin-Khameh, Neda; Gresik, M Vicky; Gill, Ryan; Karlon, William; Etzell, Joan; Deftos, Michael; Karlon, William J; Etzell, Joan E; Wang, Endi; Lu, Chuanyi M; Manion, Elizabeth; Rosenthal, Nancy; Wang, Endi; Lu, Chuanyi M; Tang, Patrick; Petric, Martin; Schade, Andrew E; Hall, Geraldine S; Oethinger, Margret; Hall, Geraldine; Picton, Avis R; Hoang, Linda; Imperial, Miguel Ranoa; Kibsey, Pamela; Waites, Ken; Duffy, Lynn; Hall, Geraldine S; Salangsang, Jo-Anne M; Bravo, Lulette Tricia C; Oethinger, Margaret D; Veras, Emanuela; Silva, Elvia; Vicens, Jimena; Silva, Elvio; Keylock, Joren; Hempel, James; Rushing, Elizabeth; Posligua, Lorena E; Deavers, Michael T; Nash, Jason W; Basturk, Olca; Perle, Mary Ann; Greco, Alba; Lee, Peng; Maru, Dipen; Weydert, Jamie Allen; Stevens, Todd M; Brownlee, Noel A; Kemper, April E; Williams, H James; Oliverio, Brock J; Al-Agha, Osama M; Eskue, Kyle L; Newlands, Shawn D; Eltorky, Mahmoud A; Puri, Puja K; Royer, Michael C; Rush, Walter L; Tavora, Fabio; Galvin, Jeffrey R; Franks, Teri J; Carter, James Elliot; Kahn, Andrea Graciela; Lozada Muñoz, Luis R; Houghton, Dan; Land, Kevin J; Nester, Theresa; Gildea, Jacob; Lefkowitz, Jerry; Lacount, Rachel A; Thompson, Hannis W; Refaai, Majed A; Quillen, Karen; Lopez, Ana Ortega; Goldfinger, Dennis; Muram, Talia; Thompson, Hannis

2009-02-01

The following abstracts are compiled from Check Sample exercises published in 2008. These peer-reviewed case studies assist laboratory professionals with continuing medical education and are developed in the areas of clinical chemistry, cytopathology, forensic pathology, hematology, microbiology, surgical pathology, and transfusion medicine. Abstracts for all exercises published in the program will appear annually in AJCP.

Assessment of a Bioinformatics across Life Science Curricula Initiative

ERIC Educational Resources Information Center

Howard, David R.; Miskowski, Jennifer A.; Grunwald, Sandra K.; Abler, Michael L.

2007-01-01

At the University of Wisconsin-La Crosse, we have undertaken a program to integrate the study of bioinformatics across the undergraduate life science curricula. Our efforts have included incorporating bioinformatics exercises into courses in the biology, microbiology, and chemistry departments, as well as coordinating the efforts of faculty within…

Applications of Surface Penetrating Radar for Mars Exploration

NASA Astrophysics Data System (ADS)

Li, H.; Li, C.; Ran, S.; Feng, J.; Zuo, W.

2015-12-01

Surface Penetrating Radar (SPR) is a geophysical method that uses electromagnetic field probe the interior structure and lithological variations of a lossy dielectric materials, it performs quite well in dry, icy and shallow-soil environments. The first radar sounding of the subsurface of planet was carried out by Apollo Lunar Sounder Experiment (ALSE) of the Apollo 17 in 1972. ALSE provided very precise information about the moon's topography and revealed structures beneath the surface in both Mare Crisium and Mare Serenitatis. Russian Mars'92 was the first Mars exploration mission that tried to use SPR to explore martian surface, subsurface and ionosphere. Although Mars'96 launch failed in 1996, Russia(Mars'98, cancelled in 1998; Phobos-Grunt, launch failed in 2011), ESA(Mars Express, succeeded in 2003; Netlander, cancelled in 2003; ExoMars 2018) and NASA(MRO, succeeded in 2005; MARS 2020) have been making great effects to send SPR to Mars, trying to search for the existence of groundwater and life in the past 20 years. So far, no Ground Penetrating Radar(GPR) has yet provided in situ observations on the surface of Mars. In December 2013, China's CE-3 lunar rover (Yuto) equipped with a GPR made the first direct measurement of the structure and depth of the lunar soil, and investigation of the lunar crust structure along the rover path. China's Mars Exploration Program also plans to carry the orbiting radar sounder and rover GPR to characterize the nature of subsurface water or ices and the layered structure of shallow subsurface of Mars. SPR can provide diversity of applications for Mars exploration , that are: to map the distribution of solid and liquid water in the upper portions of the Mars' crust; to characterize the subsurface geologic environment; to investigate the planet's subsurface to better understand the evolution and habitability of Mars; to perform the martain ionosphere sounding. Based on SPR's history and achievements, combined with the development of radar technology, SPR's technological trends applied in moon and deep space exploration are summarized in the following: Technological convergence in SPR and SAR(Synthetic Aperture Radar); Muliti-frequency and Multi-polarization; Bistatic or multistatic SPRs for geophysical network; Tomography.

United States Air Force Summer Faculty Research Program (1986). Program Technical Report. Volume 3

DTIC Science & Technology

1986-12-01

Engineering University of New Mexico Assigned: WL Albuquerque, NM 87131 (505) 271-6296 Dr. Roy M. Ventullo Degree: Ph.D., Microbiology, 1978 Associate...from Holloman Air Force Base, New Mexico . The figure includes the altitude and azimuth of each satellite. (Courtesy of Rockwell Collins) IV AFGL...energy systems over the past six years. I served as Manager of Solar Electric Projects at the New Mexico Solar Energy Institute prior to my recent move

Catalysis and biocatalysis program

NASA Technical Reports Server (NTRS)

1991-01-01

The annual report presents the fiscal year (FY) 1990 research activities and accomplishments for the Catalysis and Biocatalysis Program of the Advanced Industrial Concepts Division (AICD), Office of Industrial Technologies of the Department of Energy (DOE). The mission of the AICD is to create a balanced program of high risk, long term, directed interdisciplinary research and development that will improve energy efficiency and enhance fuel flexibility in the industrial sector. The Catalysis and Biocatalysis Program's technical activities were organized into five work elements: the Molecular Modeling and Catalysis by Design element; the Applied Microbiology and Genetics element; the Bioprocess Engineering element; the Separations and Novel Chemical Processes element; and the Process Design and Analysis element.

Transmission mode acoustic time-reversal imaging for nondestructive evaluation

NASA Astrophysics Data System (ADS)

Lehman, Sean K.; Devaney, Anthony J.

2002-11-01

In previous ASA meetings and JASA papers, the extended and formalized theory of transmission mode time reversal in which the transceivers are noncoincident was presented. When combined with the subspace concepts of a generalized MUltiple SIgnal Classification (MUSIC) algorithm, this theory is used to form super-resolution images of scatterers buried in a medium. These techniques are now applied to ultrasonic nondestructive evaluation (NDE) of parts, and shallow subsurface seismic imaging. Results are presented of NDE experiments on metal and epoxy blocks using data collected from an adaptive ultrasonic array, that is, a ''time-reversal machine,'' at Lawrence Livermore National Laboratory. Also presented are the results of seismo-acoustic subsurface probing of buried hazardous waste pits at the Idaho National Engineering and Environmental Laboratory. [Work performed under the auspices of the U.S. Department of Energy by University of California Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48.] [Work supported in part by CenSSIS, the Center for Subsurface Sensing and Imaging Systems, under the Engineering Research Centers Program of the NSF (award number EEC-9986821) as well as from Air Force Contracts No. F41624-99-D6002 and No. F49620-99-C0013.

ALMA Thermal Mapping of Ceres – Search for Subsurface Water Ice

NASA Astrophysics Data System (ADS)

Moullet, Arielle; Li, Jian-Yang; Titus, Timothy N.; Sykes, Mark V.; Hsieh, Henry H.

2018-06-01

Spectroscopic observations of the surface of Ceres by Dawn have demonstrated that hydrated minerals are ubiquitous, but only few smaller sites are enriched with water ice. This is somewhat surprising as Ceres is believed to host a large amount a water in its interior.The possibility of inhomogeneous subsurface water distribution can be investigated by tracing thermal inertia distribution. To that effect, we mapped the temperature of Ceres using 1.3mm maps of the whole surface obtained with the Atacama Large Millimeter Array (ALMA) over three different epochs during one Ceres’ year. Assessing the thermal conditions at the depths probed by sub millimeter observations (a few cm below the surface, within the annual thermal skin depth) is critical to constrain the effective thermal inertia, and hence the status of subsurface water ice. We will present preliminary results in terms of temperature features and the corresponding thermal inertia derived based on comparisons from the KRC thermal model which has been extensively used for Mars. Initial analysis is consistent with the presence of near-surface high thermal inertia layer, presumably water ice, in the north polar region.This work is supported by the NASA Solar System Observations Program NNX15AE02G.

New views of the Gulf Stream

NASA Astrophysics Data System (ADS)

Todd, R. E.

2016-02-01

The Gulf Stream plays a major role in the climate system and is a significant forcing agent for the coastal circulation along the US East Coast, yet routine subsurface measurements of Gulf Stream structure are only collected in the Florida Straits and between New Jersey and Bermuda. A recent pilot program demonstrated the feasibility of using underwater gliders to repeatedly survey across the Gulf Stream and to provide subsurface Gulf Stream observations to the community in realtime. Spray gliders were deployed on three-month missions from Miami, Florida to the New England shelf south of Cape Cod, during which they zigzagged back and forth across the Gulf Stream. Three such deployments have been completed so far with a total of more than 20 cross-Gulf Stream transects occupied. These new observations detail the subsurface structure and variability of the Gulf Stream upstream and downstream of its separation from the continental margin, reveal large-amplitude internal waves within the boundary current, and capture numerous eddies along the flanks of the Gulf Stream. Future routine glider deployments in the Gulf Stream promise to provide critical observations for examining inherent Gulf Stream variability, investigating western boundary current influences on coastal circulation, and constraining numerical simulations.

Large scale and long term application of bioslurping: the case of a Greek petroleum refinery site.

PubMed

Gidarakos, E; Aivalioti, M

2007-11-19

This paper presents the course and the remediation results of a 4-year application of bioslurping technology on the subsurface of a Greek petroleum refinery, which is still under full operation and has important and complicated subsurface contamination problems, mainly due to the presence of light non-aqueous phase liquids (LNAPL). About 55 wells are connected to the central bioslurping unit, while a mobile bioslurping unit is also used whenever and wherever is necessary. Moreover, there are about 120 additional wells for the monitoring of the subsurface of the facilities that cover a total area of 1,000,000 m(2). An integrated monitoring program has also been developed and applied on the site, including frequent LNAPL layer depth and thickness measurements, conduction of bail-down and recovery tests, sampling and chemical analysis of the free oil phase, etc., so as to evaluate the remediation technique's efficiency and ensure a prompt tracing of any new potential leak. Despite the occurrence of new leaks within the last 4 years and the observed entrapment of LNAPL in the vadoze zone, bioslurping has managed to greatly restrict the original plume within certain and relatively small parts of the refinery facilities.

Microbiology of Fresh Produce: Route of Contamination, Detection Methods, and Remedy.

PubMed

Rajwar, Asmita; Srivastava, Pragati; Sahgal, Manvika

2016-10-25

Fresh fruits and vegetables are an important part of a healthful diet. They provide vitamins, minerals and fiber to help keep our body healthy. Occasionally, fresh fruits and vegetables can become contaminated with harmful bacteria or viruses, which are also known as pathogens. The major family of pathogen associated with food are members of Enterobacteriaceae which commonly form a part of microbiological criteria and their presence is traditionally related to hygiene and safety of foods. Organic fertilizers, irrigation water quality and soil are major source of contamination. For removal of pathogens, various decontamination procedures are also followed to reduce microbial load on the fruits. These are chemical preservatives and irradiation. Microbiological study of fresh produce can be done by various phenotypic, biochemical and molecular techniques so that pathogen can properly be identified. The World Health Organization (WHO) developed global risk communication message and training materials to assist countries in strengthening their food educating programs. There is a need for improved surveillance systems on food-borne pathogens, on food products and on outbreaks so that comparable data are available from a wider range of countries.

Occurrence and distribution of microbiological indicators in groundwater and stream water

USGS Publications Warehouse

Francy, D.S.; Helsel, D.R.; Nally, R.A.

2000-01-01

A total of 136 stream water and 143 groundwater samples collected in five important hydrologic systems of the United States were analyzed for microbiological indicators to test monitoring concepts in a nationally consistent program. Total coliforms were found in 99%, Escherichia coli in 97%, and Clostridium perfringens in 73% of stream water samples analyzed for each bacterium. Total coliforms were found in 20%, E. coli in less than 1%, and C. perfringens in none of the groundwater samples analyzed for each bacterium. Although coliphage analyses were performed on many of the samples, contamination in the laboratory and problems discerning discrete plaques precluded quantification. Land use was found to have the most significant effect on concentrations of bacterial indicators in stream water. Presence of septic systems on the property near the sampling site and well depth were found to be related to detection of coliforms in groundwater, although these relationships were not statistically significant. A greater diversity of sites, more detailed information about some factors, and a larger dataset may provide further insight to factors that affect microbiological indicators.

Groundwater Resources Assessment under the Pressures of Humanity and Climate Changes

Treesearch

Bret Bruce; Diana Allen; Henrique Chaves; Gordon Grant; Gualbert Oude Essink; Henk Kooi; Ian White; Jason Gurdak; Jay Famiglietti; Jose Luis Martin-Bordes; Kevin Hiscock; Matthew Rodell; Neno Kukuric; Peter B. McMahon; Richard Taylor; Timothy Green; Yoseph Yechieli

2008-01-01

Given the vision and mission statements for GRAPHIC above, this document provides an updated framework for the GRAPHIC program. The approach to addressing global issues under the GRAPHIC umbrella involves case studies designed to cover a broad range of the identified Subjects, Methods, and Regions. Interdependencies of factors and processes affecting subsurface water...

Methane-producing microbial community in a coal bed of the Illinois Basin

USGS Publications Warehouse

Strapoc, D.; Picardal, F.W.; Turich, C.; Schaperdoth, I.; Macalady, J.L.; Lipp, J.S.; Lin, Y.-S.; Ertefai, T.F.; Schubotz, F.; Hinrichs, K.-U.; Mastalerz, Maria; Schimmelmann, A.

2008-01-01

A series of molecular and geochemical studies were performed to study microbial, coal bed methane formation in the eastern Illinois Basin. Results suggest that organic matter is biodegraded to simple molecules, such as H 2 and CO2, which fuel methanogenesis and the generation of large coal bed methane reserves. Small-subunit rRNA analysis of both the in situ microbial community and highly purified, methanogenic enrichments indicated that Methanocorpusculum is the dominant genus. Additionally, we characterized this methanogenic microorganism using scanning electron microscopy and distribution of intact polar cell membrane lipids. Phylogenetic studies of coal water samples helped us develop a model of methanogenic biodegradation of macromolecular coal and coal-derived oil by a complex microbial community. Based on enrichments, phylogenetic analyses, and calculated free energies at in situ subsurface conditions for relevant metabolisms (H2-utilizing methanogenesis, acetoclastic methanogenesis, and homoacetogenesis), H 2-utilizing methanogenesis appears to be the dominant terminal process of biodegradation of coal organic matter at this location. Copyright ?? 2008, American Society for Microbiology. All Rights Reserved.

A comparative in situ decomposition study using still born piglets and leaf litter from a deciduous forest.

PubMed

Olakanye, Ayodeji O; Nelson, Andrew; Ralebitso-Senior, T Komang

2017-07-01

A cadaver and dead plant organic matter, or litter, are rich energy sources that undergo a complex decomposition process, which impact the surrounding environmental microbiota. Advances in molecular microbiology techniques, with study of the 16S RNA genes, in particular, have highlighted the application of forensic ecogenomics in addressing key knowledge gaps. To investigate subsurface microbiome shifts as a novel tool to establish "postmortem microbial clock" and augment postmortem interval (PMI) and time-since-burial estimations, an in situ study with triplicate underground burials of piglets as human taphonomic proxies and Quercus robur leaf litter was monitored for 270 days. Changes in microbial community structure and composition were related directly to changes in seasonal temperature, with microbial shifts more pronounced during the summer. For example, Methylococcaceae could be used as seasonal bacterial indicators, from winter to summer, in establishing postmortem microbial clock for this site. Furthermore, Methylophilaceae (Methylophilales order) and Anaerolineaceae would differentiate for the piglet and leaf litter soils, respectively, 180 days after internment. Copyright © 2017 Elsevier B.V. All rights reserved.

Quality in the molecular microbiology laboratory.

PubMed

Wallace, Paul S; MacKay, William G

2013-01-01

In the clinical microbiology laboratory advances in nucleic acid detection, quantification, and sequence analysis have led to considerable improvements in the diagnosis, management, and monitoring of infectious diseases. Molecular diagnostic methods are routinely used to make clinical decisions based on when and how to treat a patient as well as monitor the effectiveness of a therapeutic regime and identify any potential drug resistant strains that may impact on the long term patient treatment program. Therefore, confidence in the reliability of the result provided by the laboratory service to the clinician is essential for patient treatment. Hence, suitable quality assurance and quality control measures are important to ensure that the laboratory methods and service meet the necessary regulatory requirements both at the national and international level. In essence, the modern clinical microbiology laboratory ensures the appropriateness of its services through a quality management system that monitors all aspects of the laboratory service pre- and post-analytical-from patient sample receipt to reporting of results, from checking and upholding staff competency within the laboratory to identifying areas for quality improvements within the service offered. For most European based clinical microbiology laboratories this means following the common International Standard Organization (ISO9001) framework and ISO15189 which sets out the quality management requirements for the medical laboratory (BS EN ISO 15189 (2003) Medical laboratories-particular requirements for quality and competence. British Standards Institute, Bristol, UK). In the United States clinical laboratories performing human diagnostic tests are regulated by the Centers for Medicare and Medicaid Services (CMS) following the requirements within the Clinical Laboratory Improvement Amendments document 1988 (CLIA-88). This chapter focuses on the key quality assurance and quality control requirements within the modern microbiology laboratory providing molecular diagnostics.

Vertical distribution of the subsurface microorganisms in Sagara oil reservoir

NASA Astrophysics Data System (ADS)

Nunoura, T.; Oida, H.; Masui, N.; Ingaki, F.; Takai, K.; Nealson, K. H.; Horikoshi, K.

2002-12-01

The recent microbiological studies reported that active microbial habitat for methanogen, sulfate reducers (Archaeoglobus, d-Proteobacteria, gram positives), fermenters (Thermococcus, Thermotogales, gram positives etc.) and other heterotrophs (g-Proteobacteria etc.) are in subsurface petroleum oil reservoirs. However, microbial distribution at vertical distances in depth has not been demonstrated since the samples in previous studies are only to use oil and the formation water. Here, we show the vertical profile of microbial community structure in Japanese terrestrial oil reservoir by a combination of molecular ecological analyses and culture dependent studies. The sequential WRC (Whole Round Core) samples (200 mbsf) were recovered from a drilling project for Sagara oil reservoir, Shizuoka Prefecture, Japan, conducted in Jar. -Mar. 2002. The lithology of the core samples was composed of siltstone, sandstone, or partially oil containing sand. The major oil components were gasoline, kerosene and light oil, that is a unique feature observed in the Sagara oil reservoir. The direct count of DAPI-stained cells suggested that the biomass was relatively constant, 1.0x104cells/g through the core of the non-oil layers, whereas the oil-bearing layers had quite higher population density at a range of 1.0x105 ? 3.7x107cells/g. The vertical profile of microbial community structures was analyzed by the sequence similarity analysis, phylogenetic analysis and T-RFLP fingerprinting of PCR-amplified 16S rDNA. From bacterial rDNA clone libraries, most of the examined rDNA were similar with the sequence of genera Pseudomanas, Stenotrophomonas and Sphingomonas within g-Proteobacteria. Especially, Pseudomonas stutzeri was predominantly present in all oil-bearing layers. From archaeal rDNA clone libraries, all rDNA clone sequences were phylogenetically associated with uncultured soil group in Crenarchaeota. We detected none of the sequences of sulfate reducers, sulfur dependent fermenters and methanogens that have been previously detected as dominant microbial components in other oil reservoir environments. The absence of methanogen was consistent with the results from the stable isotopic analysis that major hydrocarbon components including methane in Sagara oil reservoir are thermogenic origin. In this presentation, we will also show the activity of the subsurface microbial components by the cultivation assays and discuss about the relationship between the microbial community structure and the formation process of petroleum in Sagara oil reservoir.

Long Term Geoelectrical Monitoring of Deep-water Horizon Oil Spill in the Gulf Coast

NASA Astrophysics Data System (ADS)

Heenan, J. W.; Ntarlagiannis, D.; Slater, L. D.; Atekwana, E. A.; Ross, C.; Nolan, J. T.; Atekwana, E. A.

2011-12-01

In the aftermath of the catastrophic Deep-water Horizon (DWH) spill in the Gulf Coast, opportunities exist to study the evolution of fresh crude oil contamination in beach sediments and marshes. Grand Terre 1 Island, off the coast of Grand Isle in southern Louisiana, is an uninhabited barrier island, heavily impacted by the DWH spill, and ideal for undisturbed long term monitoring of crude oil degradation processes. A 10 channel Syscal-Pro resistivity / IP instrument (IRIS Instruments, France) is the heart of the fully autonomous geoelectrical monitoring system; the system, which is housed in a weatherproof container, relies solely on solar power, is controlled by an energy efficient PC and can be accessed remotely via web tools. The monitoring scheme involves collecting bi-daily resistivity measurements from surface and shallow boreholes, ranging from January 2011 to the present; environmental parameters, such as T, are continuously recorded at several depths. During regular field trips we perform larger scale geophysical surveys, and geochemical measurements (pH, DO, T, fluid C) to support the continuous geophysical monitoring. The contaminated layer on site is a visually distinctive layer of crude oil, isolated by cleaner sands above and below which is identified by a clear and obvious resistive anomaly in preliminary surveys. Early results show a decrease in average of the resistance values of each dataset over time. Further processing of the data yields a linearly shaped resistive anomaly, which coincides with the location of the oil layer. The changes in subsurface resistivity appear to be focused within this anomaly. Time filtering of the data by the time that they were collected, morning or evening, reveals a diurnal variation. While both time frames follow the same overall trend, the measurements in the morning are slightly more resistive than those in the evening. This indicates that there are environmental factors, such as temperature, that need to be accounted for when analyzing the data for evidence of biological processes. These preliminary findings indicate changes in the subsurface properties of the contaminated area and suggest that geoelectrical methods are sensitive to contamination evolution processes. Such geophysical data, constrained by geochemical and microbiological information, have the potential to be used as a long term monitoring tool for biological and geochemical processes in the subsurface.

Evaluation of nutrient removal efficiency and microbial enzyme activity in a baffled subsurface-flow constructed wetland system

Treesearch

Lihua Cui; Ying Ouyang; Wenjie Gu; Weozhi Yang; Qiaoling Xu

2013-01-01

In this study, the enzyme activities and their relationships to domestic wastewater purification are investigated in four different types of subsurface-flow constructed wetlands (CWs), namely the traditional horizontal subsurface-flow, horizontal baffled subsurface-flow, vertical baffled subsurface-flow, and composite baffled subsurface-flow CWs. Results showed that...

The NASA planetary biology internship experience

NASA Technical Reports Server (NTRS)

Hinkle, G.; Margulis, L.

1991-01-01

By providing students from around the world with the opportunity to work with established scientists in the fields of biogeochemistry, remote sensing, and origins of life, among others, the NASA Planetary Biology Internship (PBI) Program has successfully launched many scientific careers. Each year approximately ten interns participate in research related to planetary biology at NASA Centers, NASA-sponsored research in university laboratories, and private institutions. The PBI program also sponsors three students every year in both the Microbiology and Marine Ecology summer courses at the Marine Biological Laboratory. Other information about the PBI Program is presented including application procedure.

Innovations in Undergraduate Science Education: Going Viral.

PubMed

Hatfull, Graham F

2015-08-01

Bacteriophage discovery and genomics provides a powerful and effective platform for integrating missions in research and education. Implementation of the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program facilitates a broad impact by including a diverse array of schools, faculty, and students. The program generates new insights into the diversity and evolution of the bacteriophage population and presents a model for introducing first-year undergraduate students to discovery-based research experiences. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

A Retrospective Examination of Two Professional Society–Sponsored Fellowships for Predoctoral Microbiology Students

PubMed Central

Chang, Amy L.

2016-01-01

At the American Society for Microbiology (ASM), fellowships are a key means of providing immersive research opportunities for the student sector. To assess the impact of ASM student activities and inform their planning, the Society commissioned a study of two long-standing initiatives in 2015, namely the ASM Undergraduate Research Fellowship (URF), established in 1993, and the ASM Robert D. Watkins Graduate Research Fellowship (Watkins) Program, established in 1980. A mixed-methods approach was used to collect data about the participants’ fellowship experience, track educational and employment status, and determine program impacts from 325 individuals (223 URF and 73 Watkins fellows). Challenges presented by the study include the fact that inherent in fellowships is the provision of financial support that affords participants opportunities that might otherwise be unavailable to them. As a result, participant feelings of indebtedness to the Society may have introduced biased study responses. In addition, some respondents were asked to reflect on experiences from 20 to 30 years ago—a lapse in time that may have challenged their memories. Based on measures such as enrollment in or completion of advanced degree programs, employment in science, and publication and presentation history, project participants show evidence of accomplishment. Participants also reported gains in affective behaviors such as confidence and belonging. PMID:27158299

A Comparative Analysis of Public and Private Sector Graduate Programs in Public Policy

DTIC Science & Technology

1989-12-01

Wilson Approved by: 7" ’it: (’’ Nancq CXRobert Tesis Advisor ’R.ichard . ister, ecofd Reader David R. i * ’ rmanDepartment of Administra e enceqes ii...1864 - Medical Construction Liaison -18U _Piochi istry 1811 Toxicology -1815 Microbiology Iblb Lpidemiology -1817 Imunology 1819 Parasitology "�

REMOVAL OF ORGANIC CCL CONTAMINANTS FROM DRINKING WATERS BY ENHANCED COAGULATION, POWDERED ACTIVATED CARBON, CHEMICAL SOFTENING, AND OXIDATION

EPA Science Inventory

The 1996 amendments to the Safe Drinking Water Act (SWDA) require the US Environmental Protection Agency (USEPA) to establish a list of unregulated microbiological and chemical contaminants to aid in priority-setting for the Agency's drinking water program. This list, known as t...

9 CFR 381.94 - Contamination with Microorganisms; process control verification criteria and testing; pathogen...

Code of Federal Regulations, 2010 CFR

2010-01-01

...) Analysis of samples. Laboratories may use any quantitative method for analysis of E. coli that is approved... FSIS in its nationwide microbiological baseline data collection programs and surveys. (Copies of... Surveys used in determining the prevalence of Salmonella on raw products are available in the FSIS Docket...

9 CFR 381.94 - Contamination with Microorganisms; process control verification criteria and testing; pathogen...

Code of Federal Regulations, 2011 CFR

2011-01-01

...) Analysis of samples. Laboratories may use any quantitative method for analysis of E. coli that is approved... FSIS in its nationwide microbiological baseline data collection programs and surveys. (Copies of... Surveys used in determining the prevalence of Salmonella on raw products are available in the FSIS Docket...

9 CFR 381.94 - Contamination with Microorganisms; process control verification criteria and testing; pathogen...

Code of Federal Regulations, 2014 CFR

2014-01-01

...) Analysis of samples. Laboratories may use any quantitative method for analysis of E. coli that is approved... FSIS in its nationwide microbiological baseline data collection programs and surveys. (Copies of... Surveys used in determining the prevalence of Salmonella on raw products are available in the FSIS Docket...

9 CFR 381.94 - Contamination with Microorganisms; process control verification criteria and testing; pathogen...

Code of Federal Regulations, 2012 CFR

2012-01-01

...) Analysis of samples. Laboratories may use any quantitative method for analysis of E. coli that is approved... FSIS in its nationwide microbiological baseline data collection programs and surveys. (Copies of... Surveys used in determining the prevalence of Salmonella on raw products are available in the FSIS Docket...

9 CFR 381.94 - Contamination with Microorganisms; process control verification criteria and testing; pathogen...

Code of Federal Regulations, 2013 CFR

2013-01-01

...) Analysis of samples. Laboratories may use any quantitative method for analysis of E. coli that is approved... FSIS in its nationwide microbiological baseline data collection programs and surveys. (Copies of... Surveys used in determining the prevalence of Salmonella on raw products are available in the FSIS Docket...

NON-NEOPLASTIC LESIONS: USE OF DATA FROM PRE- OR NON-NEOPLASTIC LESIONS THAT MAY INDICATE POTENTIAL FOR CARCINOGENESIS

EPA Science Inventory

The Toxicology and Microbiology Division of the US EPA, Health Effects Research Laboratory has initiated a research program to develop a matrix of short-term tests to distinguish carcinogens from non-carcinogens among genotoxic substances and to develop methods for predicting rel...

THE COMMUNITY RESOURCES POOL SEMINAR DESCRIPTIONS.

ERIC Educational Resources Information Center

SATURDAY MORNING SEMINARS FOR ELEMENTARY AND SECONDARY SCHOOL STUDENTS WERE CONDUCTED WITH PROFESSIONAL RESOURCE PERSONS AS TEACHERS. THE PROGRAM WAS VOLUNTARY. THREE 9-WEEK SEMINARS WERE CONDUCTED IN THE FALL. SUBJECTS STUDIED WERE MICROBIOLOGY AND ZOOLOGY (6TH GRADE), COMPUTER MATH (7TH AND 8TH GRADE), AND CHEMISTRY (GRADES 9-12). DURING THE…

40 CFR 141.63 - Maximum contaminant levels (MCLs) for microbiological contaminants.

Code of Federal Regulations, 2013 CFR

2013-07-01

... parts of the distribution system; (4) Filtration and/or disinfection of surface water, as described in subparts H, P, T, and W of this part, or disinfection of ground water, as described in subpart S of this... (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS National Primary Drinking...

40 CFR 141.63 - Maximum contaminant levels (MCLs) for microbiological contaminants.

Code of Federal Regulations, 2014 CFR

2014-07-01

... parts of the distribution system; (4) Filtration and/or disinfection of surface water, as described in subparts H, P, T, and W of this part, or disinfection of ground water, as described in subpart S of this... (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS National Primary Drinking...

Potential of Probing the Lunar Regolith using Rover-Mounted Ground Penetrating Radar: Moses Lake Dune Field Analog Study

NASA Technical Reports Server (NTRS)

Horz, F.; Heggy, E.; Fong, T.; Kring, D.; Deans, M.; Anglade, A.; Mahiouz, K.; Bualat, M.; Lee, P.; Bluethmann, W.

2009-01-01

Probing radars have been widely recognized by the science community to be an efficient tool to explore lunar subsurface providing a unique capability to address several scientific and operational issues. A wideband (200 to 1200 MHz) Ground Penetrating Radar (GPR) mounted on a surface rover can provide high vertical resolution and probing depth from few tens of centimeters to few tens of meters depending on the sounding frequency and the ground conductivity. This in term can provide a better understand regolith thickness, elemental iron concentration (including ilmenite), volatile presence, structural anomalies and fracturing. All those objectives are of important significance for understanding the local geology and potential sustainable resources for future landing sites in particular exploring the thickness, structural heterogeneity and potential volatiles presence in the lunar regolith. While the operation and data collection of GPR is a straightforward case for most terrestrial surveys, it is a challenging task for remote planetary study especially on robotic platforms due to the complexity of remote operation in rough terrains and the data collection constrains imposed by the mechanical motion of the rover and limitation in data transfer. Nevertheless, Rover mounted GPR can be of great support to perform systematic subsurface surveys for a given landing site as it can provide scientific and operational support in exploring subsurface resources and sample collections which can increase the efficiency of the EVA activities for potential human crews as part of the NASA Constellation Program. In this study we attempt to explore the operational challenges and their impact on the EVA scientific return for operating a rover mounted GPR in support of potential human activity on the moon. In this first field study, we mainly focused on the ability of GPR to support subsurface sample collection and explore shallow subsurface volatiles.

Detailed 3D Geophysical Model of the Shallow Subsurface (Zancara River Basin, Iberian Peninsula)

NASA Astrophysics Data System (ADS)

Carbonell, R.; Marzán, I.; Martí, D.; Lobo, A.; Jean, K.; Alvarez-Marrón, J.

2016-12-01

Detailed knowledge of the structure and lithologies of the shallow subsurface is required when designing and building singular geological storage facilities this is the case of the study area in Villar de Cañas (Cuenca, Central Spain). In which an extensive multidisciplinary data acquisition program has been carried out. This include studies on: geology, hydrology, geochemistry, geophysics, borehole logging, etc. Because of this data infrastructure, it can be considered a subsurface imaging laboratory to test and validate indirect underground characterization approaches. The field area is located in a Miocene syncline within the Záncara River Basin (Cuenca, Spain). The sedimentary sequence consists in a transition from shales to massive gypsums, and underlying gravels. The stratigraphic succession features a complex internal structure, diffused lithological boundaries and relatively large variability of properties within the same lithology, these makes direct geological interpretation very difficult and requires of the integration of all the measured physical properties. The ERT survey, the seismic tomography data and the logs have been used jointly to build a 3-D multi-parameter model of the subsurface in a surface of 500x500 m. The Vp model (a 10x20x5 m grid) is able to map the high velocities of the massive gypsum, however it was neither able to map the details of the shale-gypsm transition (low velocity contrast) nor to differentiate the outcropping altered gypsum from the weathered shales. The integration of the electrical resistivity and the log data by means of a supervised statistical tools (Linear Discriminant Analysis, LDA) resulted in a new 3D multiparametric subsurface model. This new model integrates the different data sets resolving the uncertainties characteristic of the models obtained independently by the different techniques separately. Furthermore, this test seismic dataset has been used to test FWI approaches in order to study their capacities. (Research supports: CGL2014-56548-P, 2009-SGR-1595, CGL2013-47412-C2-1-P).

Bioterrorism and the Role of the Clinical Microbiology Laboratory

PubMed Central

2015-01-01

SUMMARY Regular review of the management of bioterrorism is essential for maintaining readiness for these sporadically occurring events. This review provides an overview of the history of biological disasters and bioterrorism. I also discuss the recent recategorization of tier 1 agents by the U.S. Department of Health and Human Services, the Laboratory Response Network (LRN), and specific training and readiness processes and programs, such as the College of American Pathologists (CAP) Laboratory Preparedness Exercise (LPX). LPX examined the management of cultivable bacterial vaccine and attenuated strains of tier 1 agents or close mimics. In the LPX program, participating laboratories showed improvement in the level of diagnosis required and referral of isolates to an appropriate reference laboratory. Agents which proved difficult to manage in sentinel laboratories included the more fastidious Gram-negative organisms, especially Francisella tularensis and Burkholderia spp. The recent Ebola hemorrhagic fever epidemic provided a check on LRN safety processes. Specific guidelines and recommendations for laboratory safety and risk assessment in the clinical microbiology are explored so that sentinel laboratories can better prepare for the next biological disaster. PMID:26656673

Fluid Management Plan for Corrective Action Unit 447: Project Shoal Area, Subsurface, Nevada, Rev. No.: 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Findlay, Rick

The U.S. Department of Energy (DOE), National Nuclear Security Administration Nevada Site Office (NNSA/NSO) initiated the Offsites Project to characterize the risk posed to human health and the environment as a result of testing at formerly used nuclear sites in Alaska, Colorado, Mississippi, Nevada, and New Mexico. The scope of this Fluid Management Plan (FMP) is to support the subsurface investigation at the Project Shoal Area (PSA) Corrective Action Unit (CAU) 447, Shoal - Subsurface, Nevada, in accordance with the ''Federal Facility Agreement and Consent Order'' (FFACO) (1996). Corrective Action Unit 447 is located in the Sand Spring Range, southmore » of Highway 50, about 39 miles southeast of Fallon, Nevada. (Figure 1-1). This FMP will be used at the PSA in lieu of an individual discharge permit for each well or a general water pollution control permit for management of all fluids produced during the drilling, construction, development, testing, experimentation, and/or sampling of wells conducted by the Offsites Project. The FMP provides guidance for the management of fluids generated during investigation activities and provides the standards by which fluids may be discharged on site. Although the Nevada Division of Environmental Protection (NDEP), Bureau of Federal Facilities (BoFF) is not a signatory to this FMP, it is involved in the negotiation of the contents of this plan and approves the conditions contained within. The major elements of this FMP include: (1) establishment of a well-site operations strategy; (2) site design/layout; (3) monitoring of contamination indicators (monitoring program); (4) sump characterization (sump sampling program); (5) fluid management decision criteria and fluid disposition; and (6) reporting requirements.« less

Fluid Management Plan for Corrective Action Unit 447: Project Shoal Area, Subsurface, Nevada, Rev. No.: 1 with ROTC 1 and Errata Sheet

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tim Echelard

The U.S. Department of Energy (DOE), National Nuclear Security Administration Nevada Site Office (NNSA/NSO) initiated the Offsites Project to characterize the risk posed to human health and the environment as a result of testing at formerly used nuclear sites in Alaska, Colorado, Mississippi, Nevada, and New Mexico. The scope of this Fluid Management Plan (FMP) is to support the subsurface investigation at the Project Shoal Area (PSA) Corrective Action Unit (CAU) 447, Shoal-Subsurface, Nevada, in accordance with the ''Federal Facility Agreement and Consent Order'' (FFACO) (1996). Corrective Action Unit 447 is located in the Sand Spring Range, south of Highwaymore » 50, about 39 miles southeast of Fallon, Nevada. (Figure 1-1). This FMP will be used at the PSA in lieu of an individual discharge permit for each well or a general water pollution control permit for management of all fluids produced during the drilling, construction, development, testing, experimentation, and/or sampling of wells conducted by the Offsites Project. The FMP provides guidance for the management of fluids generated during investigation activities and provides the standards by which fluids may be discharged on site. Although the Nevada Division of Environmental Protection (NDEP), Bureau of Federal Facilities (BoFF) is not a signatory to this FMP, it is involved in the negotiation of the contents of this plan and approves the conditions contained within. The major elements of this FMP include: (1) establishment of a well-site operations strategy; (2) site design/layout; (3) monitoring of contamination indicators (monitoring program); (4) sump characterization (sump sampling program); (5) fluid management decision criteria and fluid disposition; and (6) reporting requirements.« less

Microbiological-enhanced mixing across scales during in-situ bioreduction of metals and radionuclides at Department of Energy Sites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valocchi, Albert; Werth, Charles; Liu, Wen-Tso

Bioreduction is being actively investigated as an effective strategy for subsurface remediation and long-term management of DOE sites contaminated by metals and radionuclides (i.e. U(VI)). These strategies require manipulation of the subsurface, usually through injection of chemicals (e.g., electron donor) which mix at varying scales with the contaminant to stimulate metal reducing bacteria. There is evidence from DOE field experiments suggesting that mixing limitations of substrates at all scales may affect biological growth and activity for U(VI) reduction. Although current conceptual models hold that biomass growth and reduction activity is limited by physical mixing processes, a growing body of literaturemore » suggests that reaction could be enhanced by cell-to-cell interaction occurring over length scales extending tens to thousands of microns. Our project investigated two potential mechanisms of enhanced electron transfer. The first is the formation of single- or multiple-species biofilms that transport electrons via direct electrical connection such as conductive pili (i.e. ‘nanowires’) through biofilms to where the electron acceptor is available. The second is through diffusion of electron carriers from syntrophic bacteria to dissimilatory metal reducing bacteria (DMRB). The specific objectives of this work are (i) to quantify the extent and rate that electrons are transported between microorganisms in physical mixing zones between an electron donor and electron acceptor (e.g. U(IV)), (ii) to quantify the extent that biomass growth and reaction are enhanced by interspecies electron transport, and (iii) to integrate mixing across scales (e.g., microscopic scale of electron transfer and macroscopic scale of diffusion) in an integrated numerical model to quantify these mechanisms on overall U(VI) reduction rates. We tested these hypotheses with five tasks that integrate microbiological experiments, unique micro-fluidics experiments, flow cell experiments, and multi-scale numerical models. Continuous fed-batch reactors were used to derive kinetic parameters for DMRB, and to develop an enrichment culture for elucidation of syntrophic relationships in a complex microbial community. Pore and continuum scale experiments using microfluidic and bench top flow cells were used to evaluate the impact of cell-to-cell and microbial interactions on reaction enhancement in mixing-limited bioactive zones, and the mechanisms of this interaction. Some of the microfluidic experiments were used to develop and test models that considers direct cell-to-cell interactions during metal reduction. Pore scale models were incorporated into a multi-scale hybrid modeling framework that combines pore scale modeling at the reaction interface with continuum scale modeling. New computational frameworks for combining continuum and pore-scale models were also developed« less

An open, object-based modeling approach for simulating subsurface heterogeneity

NASA Astrophysics Data System (ADS)

Bennett, J.; Ross, M.; Haslauer, C. P.; Cirpka, O. A.

2017-12-01

Characterization of subsurface heterogeneity with respect to hydraulic and geochemical properties is critical in hydrogeology as their spatial distribution controls groundwater flow and solute transport. Many approaches of characterizing subsurface heterogeneity do not account for well-established geological concepts about the deposition of the aquifer materials; those that do (i.e. process-based methods) often require forcing parameters that are difficult to derive from site observations. We have developed a new method for simulating subsurface heterogeneity that honors concepts of sequence stratigraphy, resolves fine-scale heterogeneity and anisotropy of distributed parameters, and resembles observed sedimentary deposits. The method implements a multi-scale hierarchical facies modeling framework based on architectural element analysis, with larger features composed of smaller sub-units. The Hydrogeological Virtual Reality simulator (HYVR) simulates distributed parameter models using an object-based approach. Input parameters are derived from observations of stratigraphic morphology in sequence type-sections. Simulation outputs can be used for generic simulations of groundwater flow and solute transport, and for the generation of three-dimensional training images needed in applications of multiple-point geostatistics. The HYVR algorithm is flexible and easy to customize. The algorithm was written in the open-source programming language Python, and is intended to form a code base for hydrogeological researchers, as well as a platform that can be further developed to suit investigators' individual needs. This presentation will encompass the conceptual background and computational methods of the HYVR algorithm, the derivation of input parameters from site characterization, and the results of groundwater flow and solute transport simulations in different depositional settings.

Subsurface Conditions Controlling Uranium Incorporation in Iron Oxides: A Redox Stable Sink

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fendorf, Scott

2016-04-05

Toxic metals and radionuclides throughout the U.S. Department of Energy Complex pose a serious threat to ecosystems and to human health. Of particular concern is the redox-sensitive radionuclide uranium, which is classified as a priority pollutant in soils and groundwaters at most DOE sites owing to its large inventory, its health risks, and its mobility with respect to primary waste sources. The goal of this research was to contribute to the long-term mission of the Subsurface Biogeochemistry Program by determining reactions of uranium with iron (hydr)oxides that lead to long-term stabilization of this pervasive contaminant. The research objectives of thismore » project were thus to (1) identify the (bio)geochemical conditions, including those of the solid-phase, promoting uranium incorporation in Fe (hydr)oxides, (2) determine the magnitude of uranium incorporation under a variety of relevant subsurface conditions in order to quantify the importance of this pathway when in competition with reduction or adsorption; (3) identify the mechanism(s) of U(VI/V) incorporation in Fe (hydr)oxides; and (4) determine the stability of these phases under different biogeochemical (inclusive of redox) conditions. Our research demonstrates that redox transformations are capable of achieving U incorporation into goethite at ambient temperatures, and that this transformation occurs within days at U and Fe(II) concentrations that are common in subsurface geochemical environments with natural ferrihydrites—inclusive of those with natural impurities. Increasing Fe(II) or U concentration, or initial pH, made U(VI) reduction to U(IV) a more competitive sequestration pathway in this system, presumably by increasing the relative rate of U reduction. Uranium concentrations commonly found in contaminated subsurface environments are often on the order of 1-10 μM, and groundwater Fe(II) concentrations can reach exceed 1 mM in reduced zones of the subsurface. The redox-driven U(V) incorporation mechanism may help to explain U retention in some geologic materials, improving our understanding of U-based geochronology and the redox status of ancient geochemical environments. Additionally, U(VI) may be incorporated within silicate minerals though encapsulation of U-bearing iron oxides, leading to a redox stable solid. Our research detailing previously unrecognized mechanism of U incorporation within sediment minerals may even lead to new approaches for in situ contamination remediation techniques, and will help refine models of U fate and transport in reduced subsurface zones.« less

Structural analyses of a rigid pavement overlaying a sub-surface void

NASA Astrophysics Data System (ADS)

Adam, Fatih Alperen

Pavement failures are very hazardous for public safety and serviceability. These failures in pavements are mainly caused by subsurface voids, cracks, and undulation at the slab-base interface. On the other hand, current structural analysis procedures for rigid pavement assume that the slab-base interface is perfectly planar and no imperfections exist in the sub-surface soil. This assumption would be violated if severe erosion were to occur due to inadequate drainage, thermal movements, and/or mechanical loading. Until now, the effect of erosion was only considered in the faulting performance model, but not with regards to transverse cracking at the mid-slab edge. In this research, the bottom up fatigue cracking potential, caused by the combined effects of wheel loading and a localized imperfection in the form of a void below the mid-slab edge, is studied. A robust stress and surface deflection analysis was also conducted to evaluate the influence of a sub-surface void on layer moduli back-calculation. Rehabilitative measures were considered, which included a study on overlay and fill remediation. A series regression of equations was proposed that provides a relationship between void size, layer moduli stiffness, and the overlay thickness required to reduce the stress to its original pre-void level. The effect of the void on 3D pavement crack propagation was also studied under a single axle load. The amplifications to the stress intensity was shown to be high but could be mitigated substantially if stiff material is used to fill the void and impede crack growth. The pavement system was modeled using the commercial finite element modeling program Abaqus RTM. More than 10,000 runs were executed to do the following analysis: stress analysis of subsurface voids, E-moduli back-calculation of base layer, pavement damage calculations of Beaumont, TX, overlay thickness estimations, and mode I crack analysis. The results indicate that the stress and stress intensity are, on average, amplified considerably: 80% and 150%, respectively, by the presence of the void and more severe in a bonded pavement system compared to an un-bonded system. The sub-surface void also significantly affects the layer moduli back-calculation. The equivalent moduli of the layers are reduced considerably when a sub-surface void is present. However, the results indicate the back-calculated moduli derived using surface deflection, and longitudinal stress basins did not yield equivalent layer moduli under mechanical loading; the back-calculated deflection-based moduli were larger than the stress-based moduli, leading to stress calculations that were lower than those found in the real system.

Team-Based Learning in a Pipeline Course in Medical Microbiology for Under-Represented Student Populations in Medicine Improves Learning of Microbiology Concepts.

PubMed

Behling, K C; Murphy, M M; Mitchell-Williams, J; Rogers-McQuade, H; Lopez, O J

2016-12-01

As part of an undergraduate pipeline program at our institution for students from underrepresented minorities in medicine backgrounds, we created an intensive four-week medical microbiology course. Team-based learning (TBL) was implemented in this course to enhance student learning of course content. Three different student cohorts participated in the study, and there were no significant differences in their prior academic achievement based on their undergraduate grade point average (GPA) and pre-course examination scores. Teaching techniques included engaged lectures using an audience response system, TBL, and guided self-directed learning. We hypothesized that more active learning exercises, irrespective of the amount of lecture time, would help students master course content. In year 2 as compared with year 1, TBL exercises were decreased from six to three with a concomitant increase in lecture time, while in year 3, TBL exercises were increased from three to six while maintaining the same amount of lecture time as in year 2. As we hypothesized, there was significant ( p < 0.01) improvement in performance on the post-course examination in years 1 and 3 compared with year 2, when only three TBL exercises were used. In contrast to the students' perceptions that more lecture time enhances learning of course content, our findings suggest that active learning strategies, such as TBL, are more effective than engaged lectures in improving student understanding of course content, as measured by post-course examination performance. Introduction of TBL in pipeline program courses may help achieve better student learning outcomes.

Clean Sampling of an Englacial Conduit at Blood Falls, Antarctica - Some Experimental and Numerical Results

NASA Astrophysics Data System (ADS)

Kowalski, Julia; Francke, Gero; Feldmann, Marco; Espe, Clemens; Heinen, Dirk; Digel, Ilya; Clemens, Joachim; Schüller, Kai; Mikucki, Jill; Tulaczyk, Slawek M.; Pettit, Erin; Berry Lyons, W.; Dachwald, Bernd

2017-04-01

There is significant interest in sampling subglacial environments for geochemical and microbiological studies, yet those environments are typically difficult to access. Existing ice-drilling technologies make it cumbersome to maintain microbiologically clean access for sample acquisition and environmental stewardship of potentially fragile subglacial aquatic ecosystems. With the "IceMole", a minimally invasive, maneuverable subsurface ice probe, we have developed a clean glacial exploration technology for in-situ analysis and sampling of glacial ice and sub- and englacial materials. Its design is based on combining melting and mechanical stabilization, using an ice screw at the tip of the melting head to maintain firm contact between the melting head and the ice. The IceMole can change its melting direction by differential heating of the melting head and optional side wall heaters. Downward, horizontal and upward melting, as well as curve driving and penetration of particulate-ladden layers has already been demonstrated in several field tests. This maneuverability of the IceMole also necessitates a sophisticated on-board navigation system, capable of autonomous operations. Therefore, between 2012 and 2014, a more advanced probe was developed as part of the "Enceladus Explorer" (EnEx) project. The EnEx-IceMole offers systems for accurate positioning, based on in-ice attitude determination, acoustic positioning, ultrasonic obstacle and target detection, which is all integrated through a high-level sensor fusion algorithm. In December 2014, the EnEx-IceMole was used for clean access into a unique subglacial aquatic environment at Blood Falls, Antarctica, where an englacial brine sample was successfully obtained after about 17 meters of oblique melting. Particular attention was paid to clean protocols for sampling for geochemical and microbiological analysis. In this contribution, we will describe the general technological approach of the IceMole and report on the results of its deployment at Blood Falls. In contrast to conventional melting-probe applications, which can only melt vertically, the IceMole realized an oblique melting path to penetrate the englacial conduit. Experimental and numerical results on melting at oblique angles are rare. Besides reporting on the IceMole technology and the field deployment itself, we will compare and discuss the observed melting behavior with re-analysis results in the context of a recently developed numerical model. Finally, we will present our first steps in utilizing the model to infer on the ambient cryo-environment.

Microbiological Lessons Learned from the Space Shuttle

NASA Technical Reports Server (NTRS)

Pierson, Duane L.; Ott, C. Mark; Bruce, Rebekah; Castro, Victoria A.; Mehta, Satish K.

2011-01-01

After 30 years of being the centerpiece of NASA s human spacecraft, the Space Shuttle will retire. This highly successful program provided many valuable lessons for the International Space Station (ISS) and future spacecraft. Major microbiological risks to crewmembers include food, water, air, surfaces, payloads, animals, other crewmembers, and ground support personnel. Adverse effects of microorganisms are varied and can jeopardize crew health and safety, spacecraft systems, and mission objectives. Engineering practices and operational procedures can minimize the negative effects of microorganisms. To minimize problems associated with microorganisms, appropriate steps must begin in the design phase of new spacecraft or space habitats. Spacecraft design must include requirements to control accumulation of water including humidity, leaks, and condensate on surfaces. Materials used in habitable volumes must not contribute to microbial growth. Use of appropriate materials and the implementation of robust housekeeping that utilizes periodic cleaning and disinfection will prevent high levels of microbial growth on surfaces. Air filtration can ensure low levels of bioaerosols and particulates in the breathing air. The use of physical and chemical steps to disinfect drinking water coupled with filtration can provide safe drinking water. Thorough preflight examination of flight crews, consumables, and the environment can greatly reduce pathogens in spacecraft. The advances in knowledge of living and working onboard the Space Shuttle formed the foundation for environmental microbiology requirements and operations for the International Space Station (ISS) and future spacecraft. Research conducted during the Space Shuttle Program resulted in an improved understanding of the effects of spaceflight on human physiology, microbial properties, and specifically the host-microbe interactions. Host-microbe interactions are substantially affected by spaceflight. Astronaut immune functions were found to be altered. Selected microorganisms were found to become more virulent during spaceflight. The increased knowledge gained on the Space Shuttle resulted in further studies of the host-microbe interactions on the ISS to determine if countermeasures were necessary. Lessons learned from the Space Shuttle Program were integrated into the ISS resulting in the safest space habitat to date.

MX Siting Investigation Water Resources Program.

DTIC Science & Technology

1980-10-31

bedrock units are highly dependent upon the degree of secondary permeability ( fractures and solution open- ings). Although the first unit is believed to...the Fortification Range. Carbonate rocks, largely limestone and dolomite , are exposed in the Bristol and Highland I ranges. Deposits composing the...infiltration of precipitation, surface runoff, and subsurface underflow from fractured or solutioned volcanic and/or carbonate bedrock. Recharge by di- Irect

Pioneer Mars surface penetrator mission. Mission analysis and orbiter design

NASA Technical Reports Server (NTRS)

1974-01-01

The Mars Surface Penetrator mission was designed to provide a capability for multiple and diverse subsurface science measurements at a low cost. Equipment required to adapt the Pioneer Venus spacecraft for the Mars mission is described showing minor modifications to hardware. Analysis and design topics which are similar and/or identical to the Pioneer Venus program are briefly discussed.

Development of an Extra-vehicular (EVA) Infrared (IR) Camera Inspection System

NASA Technical Reports Server (NTRS)

Gazarik, Michael; Johnson, Dave; Kist, Ed; Novak, Frank; Antill, Charles; Haakenson, David; Howell, Patricia; Pandolf, John; Jenkins, Rusty; Yates, Rusty

2006-01-01

Designed to fulfill a critical inspection need for the Space Shuttle Program, the EVA IR Camera System can detect crack and subsurface defects in the Reinforced Carbon-Carbon (RCC) sections of the Space Shuttle s Thermal Protection System (TPS). The EVA IR Camera performs this detection by taking advantage of the natural thermal gradients induced in the RCC by solar flux and thermal emission from the Earth. This instrument is a compact, low-mass, low-power solution (1.2cm3, 1.5kg, 5.0W) for TPS inspection that exceeds existing requirements for feature detection. Taking advantage of ground-based IR thermography techniques, the EVA IR Camera System provides the Space Shuttle program with a solution that can be accommodated by the existing inspection system. The EVA IR Camera System augments the visible and laser inspection systems and finds cracks and subsurface damage that is not measurable by the other sensors, and thus fills a critical gap in the Space Shuttle s inspection needs. This paper discusses the on-orbit RCC inspection measurement concept and requirements, and then presents a detailed description of the EVA IR Camera System design.

Subsurface Structure Determination of Geotermal Area in Siogung-ogung Samosir District by Using Magnetic Method

NASA Astrophysics Data System (ADS)

Tampubolon, Togi; Hutahaean, Juniar; Siregar, Suryani N. J.

2018-03-01

Underwater research often uses geomagnets. It is one of the geophysical methods for measuring magnetic field variations. This research was done to identify how the subsurface rock structure is and determine kinds of rock based on its susceptibility value in Siogung-ogung geothermal area, Pangururan, Samosir District. The tool measurement of total magnetic field called Proton Precission Magnetometer, positioning using Global Position System, and north axis determination using geological compass. Data collection was done randomly with total 51 measuring points obtained. Data analysis started with International geomagnetics Reference Field correction to obtain the total magnetic field anomaly. Then, the data analysis of total magnetic anomaly was done by using surfer program 12. To get a magnetic anomaly cross section used Magdc For Windows program. Magnetic measurement results indicated that the variation of magnetic field strength in each point with the lowest magnetic intensity value of 41785.67 nano tesla. The highest magnetic intensity value is 43140, 33. From the results of qualitative interpretation, the magnetic anomaly value is at -200.92 to 1154.45 whereas the quantitative interpretive results of model show the existence of degradation and andesitic rocks, with the value of susceptibility

[Development of a predictive program for microbial growth under various temperature conditions].

PubMed

Fujikawa, Hiroshi; Yano, Kazuyoshi; Morozumi, Satoshi; Kimura, Bon; Fujii, Tateo

2006-12-01

A predictive program for microbial growth under various temperature conditions was developed with a mathematical model. The model was a new logistic model recently developed by us. The program predicts Escherichia coli growth in broth, Staphylococcus aureus growth and its enterotoxin production in milk, and Vibrio parahaemolyticus growth in broth at various temperature patterns. The program, which was built with Microsoft Excel (Visual Basic Application), is user-friendly; users can easily input the temperature history of a test food and obtain the prediction instantly on the computer screen. The predicted growth and toxin production can be important indices to determine whether a food is microbiologically safe or not. This program should be a useful tool to confirm the microbial safety of commercial foods.

MEP (Mars Environment Package): toward a package for studying environmental conditions at the surface of Mars from future lander/rover missions.

PubMed

Chassefière, E; Bertaux, J-L; Berthelier, J-J; Cabane, M; Ciarletti, V; Durry, G; Forget, F; Hamelin, M; Leblanc, F; Menvielle, M; Gerasimov, M; Korablev, O; Linkin, S; Managadze, G; Jambon, A; Manhès, G; Lognonné, Ph; Agrinier, P; Cartigny, P; Giardini, D; Pike, T; Kofman, W; Herique, A; Coll, P; Person, A; Costard, F; Sarda, Ph; Paillou, Ph; Chaussidon, M; Marty, B; Robert, F; Maurice, S; Blanc, M; d'Uston, C; Sabroux, J-Ch; Pineau, J-F; Rochette, P

2004-01-01

In view to prepare Mars human exploration, it is necessary to promote and lead, at the international level, a highly interdisciplinary program, involving specialists of geochemistry, geophysics, atmospheric science, space weather, and biology. The goal of this program will be to elaborate concepts of individual instruments, then of integrated instrumental packages, able to collect exhaustive data sets of environmental parameters from future landers and rovers of Mars, and to favour the conditions of their implementation. Such a program is one of the most urgent need for preparing human exploration, in order to develop mitigation strategies aimed at ensuring the safety of human explorers, and minimizing risk for surface operations. A few main areas of investigation may be listed: particle and radiation environment, chemical composition of atmosphere, meteorology, chemical composition of dust, surface and subsurface material, water in the subsurface, physical properties of the soil, search for an hypothesized microbial activity, characterization of radio-electric properties of the Martian ionosphere. Scientists at the origin of the present paper, already involved at a high degree of responsibility in several Mars missions, and actively preparing in situ instrumentation for future landed platforms (Netlander--now cancelled, MSL-09), express their readiness to participate in both ESA/AURORA and NASA programs of Mars human exploration. They think that the formation of a Mars Environment working group at ESA, in the course of the AURORA definition phase, could act positively in favour of the program, by increasing its scientific cross-section and making it still more focused on human exploration. c2004 Published by Elsevier Ltd on behalf of COSPAR.

Increasing diversity in the geosciences through the AfricaArray geophysics field course

NASA Astrophysics Data System (ADS)

Vallejo, G.; Emry, E.; Galindo, B. L.; Carranza, V.; Gomez, C. D.; Ortiz, K.; Castro, J. G.; Guandique, J.; Falzone, C.; Webb, S. J.; Manzi, M.; Mngadi, S. B.; Stephens, K.; Chinamora, B.; Whitehead, R.; de Villiers, D. P.; Tshitlho, K.; Delhaye, R. P.; Smith, J. A.; Nyblade, A.

2014-12-01

For the past nine years, the AfricaArray diversity program, sponsored by industry, the National Science Foundation, and several partnering universities have supported outstanding U.S. STEM underrepresented minority undergraduates to gain field experience in near-surface geophysical techniques during an 8-week summer program at Penn State University and the University of Witwatersrand (Wits). The AfricaArray geophysics field school, which is run by Wits, has been teaching field-based geophysics to African students for over a decade. In the first 2-3 weeks of the program, the U.S. students are given basic instruction in near-surface geophysics, South African geology, and South African history and culture. The students then join the Wits AfricaArray geophysics field school - working alongside Wits students and students from several other African universities to map the shallow subsurface in prospective areas of South Africa for platinum mining. In addition to the primary goals of collecting and interpreting gravity, magnetic, resistivity, seismic refraction, seismic reflection, and EM data, students spend time mapping geologic units and gathering information on the physical properties of the rocks in the region (i.e. seismic velocity, density, and magnetic susceptibility). Subsurface targets include mafic dikes, faults, the water table, and overburden thickness. Upon returning to the U.S., students spend 2-3 weeks finalizing their project reports and presentations. The program has been effective at not only providing students with fundamental skills in applied geophysics, but also in fostering multicultural relationships, preparing students for graduate work in the geosciences, and attracting STEM students into the geosciences. Student presenters will discuss their experiences gained through the field school and give their impressions about how the program works towards the goal of increasing diversity in the geosciences in the U.S.

The subsurface record for the Anthropocene based on the global analysis of deep wells

NASA Astrophysics Data System (ADS)

Rose, K.

2016-12-01

While challenges persist in the characterization of Earth's subsurface, over two centuries of exploration resulting in more than six million deep wellbores, offer insights into these systems. Characteristics of the subsurface vary and can be analyzed on a variety of spatial scales using geospatial tools and methods. Characterization and prediction of subsurface properties, such as depth, thickness, porosity, permeability, pressure and temperature, are important for models and interpretations of the subsurface. Subsurface studies contribute to insights and understanding of natural system but also enable predictions and assessments of subsurface resources and support environmental and geohazard assessments. As the geo-data science landscape shifts, becoming more open, there are increasing opportunities to fill knowledge gaps, mine large, interrelated datasets, and develop innovative methods to improve our understanding of the subsurface and the impacts of its exploration. In this study, a global dataset of more than 6,000,000 deep subsurface wells has been assembled using ArcGIS and Access, which reflects to a first order, the cumulative representation of over two centuries of drilling. Wellbore data, in general represent the only portal for direct measurement and characterization of deep subsurface properties. As human engineering of the subsurface evolves from a focus on hydrocarbon resource development to include subsurface waste product disposal (e.g. CO2, industrial waste, etc) and production of other deep subsurface resources, such as heat and water resources, there is the increasing need to improve characterization techniques and understand local and global ramifications of anthropogenic interaction with the subsurface. Data and geospatial analyses are reviewed to constrain the extent to which human interactions, not just with Earth's surface systems, atmospheric and geologic, but subsurface systems will result in an enduring signature of human influences on the planet. Specifically, the extent and enduring signature of subsurface interactions with the planet, utilizing the four-dimensional, spatial and temporal, record for known deep wellbores is utilized.

Control of microbial contamination.

NASA Technical Reports Server (NTRS)

Mcdade, J. J.

1971-01-01

Two specific applications are discussed of microbial contamination control in planetary quarantine. Under the first concept, using the clean room to control environmental microorganisms, the objective is to reduce the microbial species and keep the numbers of microorganisms within an enclosure at a low level. The clean room concept is aimed at obtaining a product that has a controlled and reduced level of microbial contamination. Under the second concept, using the microbiological barrier to control microbial contamination of a specific product, the barrier techniques are designed to prevent the entry of any microorganisms into a sterile work area. Thus the assembly of space flight hardware within the confines of a microbiological barrier is aimed at obtaining a sterile product. In theory and practice, both approaches are shown to be applicable to the planetary quarantine program.

Heat Melt Compaction as an Effective Treatment for Eliminating Microorganisms from Solid Waste

NASA Technical Reports Server (NTRS)

Hummerick, Mary P.; Strayer, Richard F.; McCoy, Lashelle E.; Richards, Jeffrey T.; Ruby, Anna Maria; Wheeler, Ray; Fisher, John

2013-01-01

One of the technologies being tested at NASA Ames Research Center (ARC) for the Advance Exploration Systems program and as part of the logistics and repurposing project is heat melt compaction (HMC) of solid waste. Reduces volume, removes water and renders a biologically stable and safe product. The HMC compacts and reduces the trash volume as much as 90o/o greater than the current manual compaction used by the crew.The project has three primary goals or tasks. 1. Microbiological analysis of HMC hardware surfaces before and after operation. 2. Microbiological and physical characterizations of heat melt tiles made from trash at different processing times and temperatures. 3. Long term storage and stability of HMC trash tiles or "Do the bugs grow back?"

Assessing student understanding of host pathogen interactions using a concept inventory.

PubMed

Marbach-Ad, Gili; Briken, Volker; El-Sayed, Najib M; Frauwirth, Kenneth; Fredericksen, Brenda; Hutcheson, Steven; Gao, Lian-Yong; Joseph, Sam; Lee, Vincent T; McIver, Kevin S; Mosser, David; Quimby, B Booth; Shields, Patricia; Song, Wenxia; Stein, Daniel C; Yuan, Robert T; Smith, Ann C

2009-01-01

As a group of faculty with expertise and research programs in the area of host-pathogen interactions (HPI), we are concentrating on students' learning of HPI concepts. As such we developed a concept inventory to measure level of understanding relative to HPI after the completion of a set of microbiology courses (presently eight courses). Concept inventories have been useful tools for assessing student learning, and our interest was to develop such a tool to measure student learning progression in our microbiology courses. Our teaching goal was to create bridges between our courses which would eliminate excessive overlap in our offerings and support a model where concepts and ideas introduced in one course would become the foundation for concept development in successive courses. We developed our HPI concept inventory in several phases. The final product was an 18-question, multiple-choice concept inventory. In fall 2006 and spring 2007 we administered the 18-question concept inventory in six of our courses. We collected pre- and postcourse surveys from 477 students. We found that students taking pretests in the advanced courses retained the level of understanding gained in the general microbiology prerequisite course. Also, in two of our courses there was significant improvement on the scores from pretest to posttest. As we move forward, we will concentrate on exploring the range of HPI concepts addressed in each course and determine and/or create effective methods for meaningful student learning of HPI aspects of microbiology.

The Lebanese Society for Infectious Diseases and Clinical Microbiology (LSIDCM) guidelines for adult community-acquired pneumonia (Cap) in Lebanon.

PubMed

Moghnieh, Rima; Yared Sakr, Nadine; Kanj, Souha S; Musharrafieh, Umayya; Husni, Rula; Jradeh, Mona; Al-Awar, Ghassan; Matar, Madona; Jureij, Wafa; Antoine, Saad; Azar, Eid; Abi Hanna, Pierre; Minari, Afaf; Hammoud, Jamale; Kfoury, Joumana; Mahfouz, Tahsin; Abou Chakra, Diaa; Zaatari, Mohamad; Tabbarah, Zuhayr A

2014-01-01

Adult community-acquired pneumonia (CAP) is a common cause of morbidity and mortality which is managed by different disciplines in a heterogeneous fashion. Development of consensus guidelines to standardize these wide variations in care has become a prime objective. The Lebanese Society of Infectious Diseases and Clinical Microbiology (LSIDCM) convened to set Lebanese national guidelines for the management of CAP since it is a major and a prevalent disease affecting the Lebanese population. These guidelines, besides being helpful in direct clinical practice, play a major role in establishing stewardship programs in hospitals in an effort to contain antimicrobial resistance on the national level. These guidelines are intended for primary care practitioners and emergency medicine physicians. They constitute an appropriate starting point for specialists' consultation being based on the available local epidemiological and resistance data. This document includes the following: 1/ Rationale and scope of the guidelines; 2/ Microbiology of CAP based on Lebanese data; 3/ Clinical presentation and diagnostic workup of CAP; 4/ Management and prevention strategies based on the IDSA/ATS Consensus Guidelines, 2007, and the ESCMID Guidelines, 2011, and tailored to the microbiological data in Lebanon; 5/ Comparison to regional guidelines. The recommendations made in this document were graded based on the strength of the evidence as in the 2007 IDSA/ATS Consensus Guidelines. Hopefully, these guidelines will be an important step towards standardization of CAP care in Lebanon and set the agenda for further research in this area.

Detailed Geophysical Fault Characterization in Yucca Flat, Nevada Test Site, Nevada

USGS Publications Warehouse

Asch, Theodore H.; Sweetkind, Donald S.; Burton, Bethany L.; Wallin, Erin L.

2009-01-01

Yucca Flat is a topographic and structural basin in the northeastern part of the Nevada Test Site (NTS) in Nye County, Nevada. Between the years 1951 and 1992, 659 underground nuclear tests took place in Yucca Flat; most were conducted in large, vertical excavations that penetrated alluvium and the underlying Cenozoic volcanic rocks. Radioactive and other potential chemical contaminants at the NTS are the subject of a long-term program of investigation and remediation by the U.S. Department of Energy (DOE), National Nuclear Security Administration, Nevada Site Office, under its Environmental Restoration Program. As part of the program, the DOE seeks to assess the extent of contamination and to evaluate the potential risks to humans and the environment from byproducts of weapons testing. To accomplish this objective, the DOE Environmental Restoration Program is constructing and calibrating a ground-water flow model to predict hydrologic flow in Yucca Flat as part of an effort to quantify the subsurface hydrology of the Nevada Test Site. A necessary part of calibrating and evaluating a model of the flow system is an understanding of the location and characteristics of faults that may influence ground-water flow. In addition, knowledge of fault-zone architecture and physical properties is a fundamental component of the containment of the contamination from underground nuclear tests, should such testing ever resume at the Nevada Test Site. The goal of the present investigation is to develop a detailed understanding of the geometry and physical properties of fault zones in Yucca Flat. This study was designed to investigate faults in greater detail and to characterize fault geometry, the presence of fault splays, and the fault-zone width. Integrated geological and geophysical studies have been designed and implemented to work toward this goal. This report describes the geophysical surveys conducted near two drill holes in Yucca Flat, the data analyses performed, and the integrated interpretations developed from the suite of geophysical methodologies utilized in this investigation. Data collection for this activity started in the spring of 2005 and continued into 2006. A suite of electrical geophysical surveys were run in combination with ground magnetic surveys; these surveys resulted in high-resolution subsurface data that portray subsurface fault geometry at the two sites and have identified structures not readily apparent from surface geologic mapping, potential field geophysical data, or surface effects fracture maps.

Careers in Microbiology...Horizons Unlimited

ERIC Educational Resources Information Center

Goldschmidt Millicent C.; Whitt, Dixie

1978-01-01

A broad range of present microbiological work is discussed in order to indicate the many possible careers now open in microbiology. Some areas are immunology, environmental microbiology, agricultural, industrial, and food microbiology, and space microbiology. An employment outlook is also given. (MDR)

Advances Afoot in Microbiology.

PubMed

Patel, Robin; Karon, Brad S

2017-07-01

In 2016, the American Academy of Microbiology convened a colloquium to examine point-of-care (POC) microbiology testing and to evaluate its effects on clinical microbiology. Colloquium participants included representatives from clinical microbiology laboratories, industry, and the government, who together made recommendations regarding the implementation, oversight, and evaluation of POC microbiology testing. The colloquium report is timely and well written (V. Dolen et al., Changing Diagnostic Paradigms for Microbiology , 2017, https://www.asm.org/index.php/colloquium-reports/item/6421-changing-diagnostic-paradigms-for-microbiology?utm_source=Commentary&utm_medium=referral&utm_campaign=diagnostics). Emerging POC microbiology tests, especially nucleic acid amplification tests, have the potential to advance medical care. Copyright © 2017 American Society for Microbiology.

Integration of Computers into the Medical School Curriculum: An Example from a Microbiology Course.

ERIC Educational Resources Information Center

Platt, Mark W.; And Others

1994-01-01

While the use of computers has become widespread in recent years, a unified, integrated approach to their use in the medical school curriculum has not yet emerged. Describes a program at the University of New Mexico that will phase-in computerization of its curriculum beginning in the fall of 1993. (LZ)

Installation Restoration Program. Phase 1. Records Search for the 167th Tactical Airlift Group, Shepherd Field Air National Guard Base, Martinsburg, West Virginia. Revised.

DTIC Science & Technology

1986-03-01

Evaluation of Past Operations ] at Listed Sites Contamination Delee StesPotential for I De’ere tesI Migrationl S Potential for IOther N Environmental... Microbiology , New Orleans. Louisiana. March 1983. Effect of particles on degradation of bromobenzene in a simulated groundwater environment

CpG Oligodeoxyribonucleotides Protect Mice from Burkholderia Pseudomallei but not Francisella Tularensis Schu S4 Aerosols

DTIC Science & Technology

2010-01-01

of Defense, project number ZZ0001_06_RD_B. This project was supported in part by appointments to the Internship /Research Participation Program for...Francisella novicida) associated with human disease. Journal of clinical microbiology 1989, 27(7):1601-1608. doi:10.1186/1476-8518-8-2 Cite this article

Europe Report, Science and Technology.

DTIC Science & Technology

1986-06-06

the question, of course , whether the combined treatment will cause chromosome damage. In the case of chromosomes from in vitro cultivated human ...latest acquisition, this division collaborates to major engine programs, in particular with Snecma ( Atar , CFM 56) and Turbomeca (ARTM 405). 9294 CSO...microbiology, enzymology, molecular and cell biology , organic chemistry, etc. Several large public research organizations are involved: CNRS [National

Altaf Mohammed, PhD | Division of Cancer Prevention

Cancer.gov

Dr. Altaf Mohammed serves as a Program Director and COR for the Chemopreventive Agent Development Research Group (CADRG), Division of Cancer Prevention (DCP), National Cancer Institute (NCI). Dr. Mohammed obtained his Ph.D. in Microbiology from India before moving to the Department of Medicine at University of Oklahoma Health Sciences Center (OUHSC) in Oklahoma City for a

Program for Educational Mobility for Health Manpower (The Basic Sciences), June 12-August 25, 1970. Preliminary Report.

ERIC Educational Resources Information Center

Coordinating Council for Education in the Health Sciences for San Diego and Imperial Counties, CA.

Community college administrators and faculty in the areas of anatomy, physiology, chemistry, physics, and microbiology attended an 11-day workshop to redefine, modify, and develop science concepts for a core curriculum in the allied health field. To achieve workshop objectives, the committee heard presentations by consultants, visited clinical…

Animal Science Technology. An Experimental Developmental Program. Volume II, Curriculum Course Outlines.

ERIC Educational Resources Information Center

Brant, Herman G.

This volume, the second of a two part evaluation report, is devoted exclusively to the presentation of detailed course outlines representing an Animal Science Technology curriculum. Arranged in 6 terms of study (2 academic years), outlines are included on such topics as: (1) Introductory Animal Science, (2) General Microbiology, (3) Zoonoses, (4)…

75 FR 63433 - National Advisory Committee on Microbiological Criteria for Foods; Re-Establishment

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-15

... discrimination in all its programs and activities on the basis of race, color, national origin, gender, religion... at 202-720-2600 (voice and TTY). To file a written complaint of discrimination, write USDA, Office of.... Consequently, in an effort to ensure that the public and in particular minorities, women, and persons with...

Nitrogen Stimulates the Growth of Subsurface Basalt-associated Microorganisms at the Western Flank of the Mid-Atlantic Ridge

PubMed Central

Zhang, Xinxu; Fang, Jing; Bach, Wolfgang; Edwards, Katrina J.; Orcutt, Beth N.; Wang, Fengping

2016-01-01

Oceanic crust constitutes the largest aquifer system on Earth, and microbial activity in this environment has been inferred from various geochemical analyses. However, empirical documentation of microbial activity from subsurface basalts is still lacking, particularly in the cool (<25°C) regions of the crust, where are assumed to harbor active iron-oxidizing microbial communities. To test this hypothesis, we report the enrichment and isolation of crust-associated microorganisms from North Pond, a site of relatively young and cold basaltic basement on the western flank of the Mid-Atlantic Ridge that was sampled during Expedition 336 of the Integrated Ocean Drilling Program. Enrichment experiments with different carbon (bicarbonate, acetate, methane) and nitrogen (nitrate and ammonium) sources revealed significant cell growth (one magnitude higher cell abundance), higher intracellular DNA content, and increased Fe3+/ΣFe ratios only when nitrogen substrates were added. Furthermore, a Marinobacter strain with neutrophilic iron-oxidizing capabilities was isolated from the basalt. This work reveals that basalt-associated microorganisms at North Pond had the potential for activity and that microbial growth could be stimulated by in vitro nitrogen addition. Furthermore, iron oxidation is supported as an important process for microbial communities in subsurface basalts from young and cool ridge flank basement. PMID:27199959

Installation restoration research program: Assessment of geophysical methods for subsurface geologic mapping, cluster 13, Edgewood Area, Aberdeen Proving Ground, Maryland. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Butler, D.K.; Sharp, M.K.; Sjostrom, K.J.

1996-10-01

Seismic refraction, electrical resistivity, and transient electromagnetic surveys were conducted at a portion of Cluster 13, Edgewood Area of Aberdeen Proving Ground, Maryland. Seismic refraction cross sections map the topsoil layer and the water table (saturated zone). The water table elevations from the seismic surveys correlate closely with water table elevations in nearby monitoring wells. Electrical resistivity cross sections reveal a very complicated distribution of sandy and clayey facies in the upper 10 - 15 m of the subsurface. A continuous surficial (topsoil) layer correlates with the surficial layer of the seismic section and nearby boring logs. The complexity andmore » details of the electrical resistivity cross section correlate well with boring and geophysical logs from nearby wells. The transient electromagnetic surveys map the Pleistocene-Cretaceous boundary, the saprolite, and the top of the Precambrian crystalline rocks. Conducting the transient electromagnetic surveys on a grid pattern allows the construction of a three-dimensional representation of subsurface geology (as represented by variations of electrical resistivity). Thickness and depth of the saprolitic layer and depth to top of the Precambrian rocks are consistent with generalized geologic cross sections for the Edgewood Area and depths projected from reported depths at the Aberdeen Proving Ground NW boundary using regional dips.« less

Development of a 1 x N Fiber Optic Sensor Array for Carbon Sequestration Site Monitoring

DOE Office of Scientific and Technical Information (OSTI.GOV)

Repasky, Kevin

2014-02-01

A fiber sensor array for sub-surface CO 2 concentrations measurements was developed for monitoring geologic carbon sequestration sites. The fiber sensor array uses a single temperature tunable distributed feedback (DFB) laser operating with a nominal wavelength of 2.004 μm. Light from this DFB laser is direct to one of the 4 probes via an in-line 1 x 4 fiber optic switch. Each of the 4 probes are buried and allow the sub-surface CO 2 to enter the probe through Millipore filters that allow the soil gas to enter the probe but keeps out the soil and water. Light from themore » DFB laser interacts with the CO 2 before it is directed back through the in-line fiber optic switch. The DFB laser is tuned across two CO 2 absorption features where a transmission measurement is made allowing the CO 2 concentration to be retrieved. The fiber optic switch then directs the light to the next probe where this process is repeated allowing sub-surface CO 2 concentration measurements at each of the probes to be made as a function of time. The fiber sensor array was deployed for fifty-eight days beginning June 19, 2012 at the Zero Emission Research Technology (ZERT) field site where sub-surface CO 2 concentrations were monitored. Background measurements indicate the fiber sensor array can monitor background levels as low as 1,000 parts per million (ppm). A thirty four day sub-surface release of 0.15 tones CO 2/day began on July 10, 2012. The elevated subsurface CO 2 concentration was easily detected by each of the four probes with values ranging to over 60,000 ppm, a factor of greater than 6 higher than background measurements. The fiber sensor array was also deploy at the Big Sky Carbon Sequestration Partnership (BSCSP) site in north-central Montana between July 9th and August 7th, 2013 where background measurements were made in a remote sequestration site with minimal infrastructure. The project provided opportunities for two graduate students to participate in research directly related to geologic carbon sequestration. Furthermore, commercialization of the technology developed is being pursued with five different companies via the Department of energy SBIR/STTR program« less

Small County: Development of a Virtual Environment for Instruction in Geological Characterization of Petroleum Reservoirs

NASA Astrophysics Data System (ADS)

Banz, B.; Bohling, G.; Doveton, J.

2008-12-01

Traditional programs of geological education continue to be focused primarily on the evaluation of surface or near-surface geology accessed at outcrops and shallow boreholes. However, most students who graduate to careers in geology work almost entirely on subsurface problems, interpreting drilling records and petrophysical logs from exploration and production wells. Thus, college graduates commonly find themselves ill-prepared when they enter the petroleum industry and require specialized training in drilling and petrophysical log interpretation. To aid in this training process, we are developing an environment for interactive instruction in the geological aspects of petroleum reservoir characterization employing a virtual subsurface closely reflecting the geology of the US mid-continent, in the fictional setting of Small County, Kansas. Stochastic simulation techniques are used to generate the subsurface characteristics, including the overall geological structure, distributions of facies, porosity, and fluid saturations, and petrophysical logs. The student then explores this subsurface by siting exploratory wells and examining drilling and petrophysical log records obtained from those wells. We are developing the application using the Eclipse Rich Client Platform, which allows for the rapid development of a platform-agnostic application while providing an immersive graphical interface. The application provides an array of views to enable relevant data display and student interaction. One such view is an interactive map of the county allowing the student to view the locations of existing well bores and select pertinent data overlays such as a contour map of the elevation of an interesting interval. Additionally, from this view a student may choose the site of a new well. Another view emulates a drilling log, complete with drilling rate plot and iconic representation of examined drill cuttings. From here, students are directed to stipulate subsurface lithology and interval tops as they progress through the drilling operation. Once the interpretation process is complete, the student is guided through an exercise emulating a drill stem test and then is prompted to decide on perforation intervals. The application provides a graphical framework by which the student is guided through well site selection, drilling data interpretation, and well completion or dry-hole abandonment, creating a tight feedback loop by which the student gains an over-arching view of drilling logistics and the subsurface data evaluation process.

Sociodemographic, Sexual Behavior, and Microbiological Profiles of Men Attending Public Health Laboratories for Testing for Sexually Transmitted Diseases.

PubMed

Sviben, Mario; Ljubin-Sternak, Sunčanica; Meštrović, Tomislav; Vraneš, Jasmina

2017-07-01

In order to identify the groups at risk of sexually transmitted diseases (STDs), we assessed the sociodemographic profiles of men testing for STD, their sexual habits, and the results of microbiological analysis. During a three-year period, a total of 700 men older than 18 years of age completed the questionnaire regarding sociodemographic and sexual behavior. Urethral swabs were taken for microbiological analysis. Thirty-three percent of respondents reported not using condoms. Those that do not use condoms were predominantly less educated, unmarried but in steady relationships, employed, with children, and smokers. Alcohol or drug usage before sexual intercourse was disclosed by 21.4% of respondents, and 10.3% respondents reported sexual intercourses with commercial sex workers. Finally, 24.0% respondents reported sexual relations abroad. In 28.1% of subjects, one or more pathogens were observed in urethral swabs. The most commonly diagnosed microorganism was Ureaplasma urealyticum, followed by Chlamydia trachomatis, Mycoplasma hominis, Trichomonas vaginalis, and Neisseria gonorrhoeae. This study identified several factors that may contribute to the general risk of STD transmission, which will serve to better understand the transmission dynamics and implementation of adequate prevention programs.

Teaching microbiology to undergraduate students in the humanities and the social sciences.

PubMed

Oren, Aharon

2015-10-01

This paper summarizes my experiences teaching a 28-hour course on the bacterial world for undergraduate students in the humanities and the social sciences at the Hebrew University of Jerusalem. This course was offered in the framework of a program in which students must obtain credit points for courses offered by other faculties to broaden their education. Most students had little biology in high school and had never been exposed to the basics of chemistry. Using a historical approach, highlighting the work of pioneers such as van Leeuwenhoek, Koch, Fleming, Pasteur, Winogradsky and Woese, I covered a broad area of general, medical, environmental and evolutionary microbiology. The lectures included basic concepts of organic and inorganic chemistry necessary to understand the principles of fermentations and chemoautotrophy, and basic molecular biology to explain biotechnology using transgenic microorganisms and molecular phylogeny. Teaching the basics of microbiology to intelligent students lacking any background in the natural sciences was a rewarding experience. Some students complained that, in spite of my efforts, basic concepts of chemistry remained beyond their understanding. But overall the students' evaluation showed that the course had achieved its goal. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Electronic tools for infectious diseases and microbiology

PubMed Central

Burdette, Steven D

2007-01-01

Electronic tools for infectious diseases and medical microbiology have the ability to change the way the diagnosis and treatment of infectious diseases are approached. Medical information today has the ability to be dynamic, keeping up with the latest research or clinical issues, instead of being static and years behind, as many textbooks are. The ability to rapidly disseminate information around the world opens up the possibility of communicating with people thousands of miles away to quickly and efficiently learn about emerging infections. Electronic tools have expanded beyond the desktop computer and the Internet, and now include personal digital assistants and other portable devices such as cellular phones. These pocket-sized devices have the ability to provide access to clinical information at the point of care. New electronic tools include e-mail listservs, electronic drug databases and search engines that allow focused clinical questions. The goal of the present article is to provide an overview of how electronic tools can impact infectious diseases and microbiology, while providing links and resources to allow users to maximize their efficiency in accessing this information. Links to the mentioned Web sites and programs are provided along with other useful electronic tools. PMID:18978984

Life Support Systems Microbial Challenges

NASA Technical Reports Server (NTRS)

Roman, Monsi C.

2010-01-01

Many microbiological studies were performed during the development of the Space Station Water Recovery and Management System from1990-2009. Studies include assessments of: (1) bulk phase (planktonic) microbial population (2) biofilms, (3) microbially influenced corrosion (4) biofouling treatments. This slide presentation summarizes the studies performed to assess the bulk phase microbial community during the Space Station Water Recovery Tests (WRT) from 1990 to 1998. This report provides an overview of some of the microbiological analyses performed during the Space Station WRT program. These tests not only integrated several technologies with the goal of producing water that met NASA s potable water specifications, but also integrated humans, and therefore human flora into the protocols. At the time these tests were performed, not much was known (or published) about the microbial composition of these types of wastewater. It is important to note that design changes to the WRS have been implemented over the years and results discussed in this report might be directly related to test configurations that were not chosen for the final flight configuration. Results microbiological analyses performed Conclusion from the during the WRT showed that it was possible to recycle water from different sources, including urine, and produce water that can exceed the quality of municipally produced water.